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Sample records for extrachromosomal circular dna

  1. Extrachromosomal circular DNA is common in yeast

    PubMed Central

    Møller, Henrik D.; Parsons, Lance; Jørgensen, Tue S.; Botstein, David; Regenberg, Birgitte

    2015-01-01

    Examples of extrachromosomal circular DNAs (eccDNAs) are found in many organisms, but their impact on genetic variation at the genome scale has not been investigated. We mapped 1,756 eccDNAs in the Saccharomyces cerevisiae genome using Circle-Seq, a highly sensitive eccDNA purification method. Yeast eccDNAs ranged from an arbitrary lower limit of 1 kb up to 38 kb and covered 23% of the genome, representing thousands of genes. EccDNA arose both from genomic regions with repetitive sequences ≥15 bases long and from regions with short or no repetitive sequences. Some eccDNAs were identified in several yeast populations. These eccDNAs contained ribosomal genes, transposon remnants, and tandemly repeated genes (HXT6/7, ENA1/2/5, and CUP1-1/-2) that were generally enriched on eccDNAs. EccDNAs seemed to be replicated and 80% contained consensus sequences for autonomous replication origins that could explain their maintenance. Our data suggest that eccDNAs are common in S. cerevisiae, where they might contribute substantially to genetic variation and evolution. PMID:26038577

  2. Amplification of a Zygosaccharomyces bailii DNA Segment in Wine Yeast Genomes by Extrachromosomal Circular DNA Formation

    PubMed Central

    Galeote, Virginie; Bigey, Frédéric; Beyne, Emmanuelle; Novo, Maite; Legras, Jean-Luc; Casaregola, Serge; Dequin, Sylvie

    2011-01-01

    We recently described the presence of large chromosomal segments resulting from independent horizontal gene transfer (HGT) events in the genome of Saccharomyces cerevisiae strains, mostly of wine origin. We report here evidence for the amplification of one of these segments, a 17 kb DNA segment from Zygosaccharomyces bailii, in the genome of S. cerevisiae strains. The copy number, organization and location of this region differ considerably between strains, indicating that the insertions are independent and that they are post-HGT events. We identified eight different forms in 28 S. cerevisiae strains, mostly of wine origin, with up to four different copies in a single strain. The organization of these forms and the identification of an autonomously replicating sequence functional in S. cerevisiae, strongly suggest that an extrachromosomal circular DNA (eccDNA) molecule serves as an intermediate in the amplification of the Z. bailii region in yeast genomes. We found little or no sequence similarity at the breakpoint regions, suggesting that the insertions may be mediated by nonhomologous recombination. The diversity between these regions in S. cerevisiae represents roughly one third the divergence among the genomes of wine strains, which confirms the recent origin of this event, posterior to the start of wine strain expansion. This is the first report of a circle-based mechanism for the expansion of a DNA segment, mediated by nonhomologous recombination, in natural yeast populations. PMID:21423766

  3. Rapid Evolution of Recombinant Saccharomyces cerevisiae for Xylose Fermentation through Formation of Extra-chromosomal Circular DNA

    PubMed Central

    Demeke, Mekonnen M.; Foulquié-Moreno, María R.; Dumortier, Françoise; Thevelein, Johan M.

    2015-01-01

    Circular DNA elements are involved in genome plasticity, particularly of tandem repeats. However, amplifications of DNA segments in Saccharomyces cerevisiae reported so far involve pre-existing repetitive sequences such as ribosomal DNA, Ty elements and Long Terminal Repeats (LTRs). Here, we report the generation of an eccDNA, (extrachromosomal circular DNA element) in a region without any repetitive sequences during an adaptive evolution experiment. We performed whole genome sequence comparison between an efficient D-xylose fermenting yeast strain developed by metabolic and evolutionary engineering, and its parent industrial strain. We found that the heterologous gene XylA that had been inserted close to an ARS sequence in the parent strain has been amplified about 9 fold in both alleles of the chromosomal locus of the evolved strain compared to its parent. Analysis of the amplification process during the adaptive evolution revealed formation of a XylA-carrying eccDNA, pXI2-6, followed by chromosomal integration in tandem arrays over the course of the evolutionary adaptation. Formation of the eccDNA occurred in the absence of any repetitive DNA elements, probably using a micro-homology sequence of 8 nucleotides flanking the amplified sequence. We isolated the pXI2-6 eccDNA from an intermediate strain of the evolutionary adaptation process, sequenced it completely and showed that it confers high xylose fermentation capacity when it is transferred to a new strain. In this way, we have provided clear evidence that gene amplification can occur through generation of eccDNA without the presence of flanking repetitive sequences and can serve as a rapid means of adaptation to selection pressure. PMID:25738959

  4. Identification of extrachromosomal circular DNA in hop via rolling circle amplification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During a survey looking for viruses affecting hop plants in the Willamette Valley of Oregon, a circular DNA molecule was identified via rolling circle amplification (RCA) and later characterized. The 5.7 kb long molecule only matched in a minor cover to a microsatellite region in the Humulus lupulus...

  5. Formation of extrachromosomal circles from telomeric DNA in Xenopus laevis.

    PubMed

    Cohen, Sarit; Méchali, Marcel

    2002-12-01

    Instability and plasticity of telomeric DNA, which includes extrachromosomal DNA, are usually correlated with the absence of telomerase and with abnormal growth of mammalian cells. Here, we show the formation of extrachromosomal circular DNA of telomeric repeats (tel-eccDNA) during the development of Xenopus laevis. Tel-eccDNA is double-stranded relaxed circles composed of the vertebrate consensus telomeric repeats [TTAGGG](n). Its size varies from <2 to >20 kb and it comprises up to 10% of the total cellular telomere content of the early embryo (pre-MBT stage). The amount of tel-eccDNA is reduced in later developmental stages and in adult tissues. Using a cell-free system derived from Xenopus egg extracts, we show that tel-eccDNA can be formed de novo from the telomere chromosomal tracts of sperm nuclei and naked DNA in a replication-independent manner. These results reveal an unusual plasticity of telomeric DNA during normal development of Xenopus. PMID:12446568

  6. Visualization and quantitative analysis of extrachromosomal telomere-repeat DNA in individual human cells by Halo-FISH

    PubMed Central

    Komosa, Martin; Root, Heather; Meyn, M. Stephen

    2015-01-01

    Current methods for characterizing extrachromosomal nuclear DNA in mammalian cells do not permit single-cell analysis, are often semi-quantitative and frequently biased toward the detection of circular species. To overcome these limitations, we developed Halo-FISH to visualize and quantitatively analyze extrachromosomal DNA in single cells. We demonstrate Halo-FISH by using it to analyze extrachromosomal telomere-repeat (ECTR) in human cells that use the Alternative Lengthening of Telomeres (ALT) pathway(s) to maintain telomere lengths. We find that GM847 and VA13 ALT cells average ∼80 detectable G/C-strand ECTR DNA molecules/nucleus, while U2OS ALT cells average ∼18 molecules/nucleus. In comparison, human primary and telomerase-positive cells contain <5 ECTR DNA molecules/nucleus. ECTR DNA in ALT cells exhibit striking cell-to-cell variations in number (<20 to >300), range widely in length (<1 to >200 kb) and are composed of primarily G- or C-strand telomere-repeat DNA. Halo-FISH enables, for the first time, the simultaneous analysis of ECTR DNA and chromosomal telomeres in a single cell. We find that ECTR DNA comprises ∼15% of telomere-repeat DNA in GM847 and VA13 cells, but <4% in U2OS cells. In addition to its use in ALT cell analysis, Halo-FISH can facilitate the study of a wide variety of extrachromosomal DNA in mammalian cells. PMID:25662602

  7. Visualization and quantitative analysis of extrachromosomal telomere-repeat DNA in individual human cells by Halo-FISH.

    PubMed

    Komosa, Martin; Root, Heather; Meyn, M Stephen

    2015-02-27

    Current methods for characterizing extrachromosomal nuclear DNA in mammalian cells do not permit single-cell analysis, are often semi-quantitative and frequently biased toward the detection of circular species. To overcome these limitations, we developed Halo-FISH to visualize and quantitatively analyze extrachromosomal DNA in single cells. We demonstrate Halo-FISH by using it to analyze extrachromosomal telomere-repeat (ECTR) in human cells that use the Alternative Lengthening of Telomeres (ALT) pathway(s) to maintain telomere lengths. We find that GM847 and VA13 ALT cells average ∼80 detectable G/C-strand ECTR DNA molecules/nucleus, while U2OS ALT cells average ∼18 molecules/nucleus. In comparison, human primary and telomerase-positive cells contain <5 ECTR DNA molecules/nucleus. ECTR DNA in ALT cells exhibit striking cell-to-cell variations in number (<20 to >300), range widely in length (<1 to >200 kb) and are composed of primarily G- or C-strand telomere-repeat DNA. Halo-FISH enables, for the first time, the simultaneous analysis of ECTR DNA and chromosomal telomeres in a single cell. We find that ECTR DNA comprises ∼15% of telomere-repeat DNA in GM847 and VA13 cells, but <4% in U2OS cells. In addition to its use in ALT cell analysis, Halo-FISH can facilitate the study of a wide variety of extrachromosomal DNA in mammalian cells. PMID:25662602

  8. Extrachromosomal DNA and cell differentiation in cultured pea roots (Pisum sativum)

    SciTech Connect

    Van't Hof, J.

    1986-01-01

    Histological, cytological and molecular analyses of DNA replication and differentiation and meristematic precursors of vascular parenchyma in cultured pea roots show that the initial steps in the transition from a dividing to a differentiated cell involve retardation of DNA replication in late S phase and production of extrachromosomal molecules by excision from late replicating chromosomal DNA. Portions of the extrachromosomal DNA are displaced by a strand displacement mechanism thereby producing free single-stranded molecules. That extrachromosomal molecules have rDNA reflects the fact that in pea roots replication of the ribosomal genes is maximal during late S phase (unpublished results). It is likely, therefore, that the excised late replicating DNA contains some rDNA sequences. 30 refs., 3 figs.

  9. Extrachromosomal DNA of pea (Pisum sativum) root-tip cells replicates by strand displacement

    SciTech Connect

    Krimer, D.B.; Van't Hof, J.

    1983-04-01

    In cultured pea roots there is extrachromosomal DNA associated with cells that differentiate from the G/sub 2/ phase of the cell cycle that is absent from those that differentiate from the G/sub 1/ phase. The authors examined this extrachromosomal DNA by electron microscopy and found that it consisted of three types: (i) double-stranded linear molecules with single-stranded branches (74%), (ii) double-stranded molecules without branches (26%), and (iii) free single-stranded molecules. The double-stranded molecules with or without branches were similar in length, having a modal length of 10-15 ..mu..m. The free single-stranded molecules were shorter and had a mean length of 3.8 ..mu..m. The length of the branches attached to the duplex molecules was only slightly less than that of the free form. The duplex molecules with branches were interpreted as configurations reflecting an ongoing strand-displacement process that results in free single-stranded molecules. Finally, measurements on duplex molecules with multiple branches suggested that the extrachromosomal DNA may exist in the form of tandemly repeated sequences. 8 references, 8 figures.

  10. Tandem Repeats in Extrachromosomal Ribosomal DNA of Dictyostelium Discoideum, Resulting from Chromosomal Mutations

    PubMed Central

    Cole, R. A.; Williams, K. L.

    1992-01-01

    Extrachromosomal ribosomal DNA in the simple eukaryote Dictyostelium discoideum is readily separated from chromosomal DNA by orthogonal field electrophoresis (OFAGE), forming a prominent band in the 110-kb region of the gel. Here we show that mutations in at least two chromosomal genes give rise to a ladder of rDNA bands increasing in size up to about 300 kb. One of these mutations, the rrcA350 allele, which is recessive to wild type and maps to the centromere-proximal region of linkage group II, has an unstable phenotype; spontaneous revertants, which no longer exhibit the rDNA ladder, have been recovered. Another mutation rrc-351, provisionally mapped to linkage group IV, is dominant to wild type. The rDNA ladder is caused by concatamerization of a 34-kb fragment in the nontranscribed central spacer region of the 88-kb linear rDNA palindrome. Restriction enzyme analysis has revealed that each concatamer is generated by crossovers between two rDNA molecules. PMID:1582557

  11. Resistance of Spiroplasma citri Lines to the Virus SVTS2 Is Associated with Integration of Viral DNA Sequences into Host Chromosomal and Extrachromosomal DNA

    PubMed Central

    Sha, Y.; Melcher, U.; Davis, R. E.; Fletcher, J.

    1995-01-01

    Spiroplasmavirus SVTS2, isolated from Spiroplasma melliferum TS2, produces plaques when inoculated onto lawns of Spiroplasma citri M200H, a derivative of the type strain Maroc R8A2. S. citri strains MR2 and MR3, originally selected as colonies growing within plaques on a lawn of M200H inoculated with SVTS2, were resistant to SVTS2. Genomic DNA fingerprints and electrophoretic protein profiles of M200H, MR2, and MR3 were similar, but three proteins present in M200H were missing or significantly reduced in both resistant lines. None of these three polypeptides reacted with antiserum against S. citri membrane proteins, indicating that they probably are not surface-located virus receptors. Electroporation with SVTS2 DNA produced 1.5 x 10(sup5) transfectants per (mu)g of DNA in M200H but none in MR2 or MR3, suggesting that resistance may result from inhibition of viral replication. The digestion patterns of the extrachromosomal double-stranded (ds) DNA of these lines were similar. Three TaqI fragments of MR2 extrachromosomal DNA that were not present in M200H extrachromosomal DNA hybridized strongly to an SVTS2 probe, and two of these fragments plus an additional one hybridized with the MR3 extrachromosomal DNA, indicating that a fragment of SVTS2 DNA was present in the extrachromosomal ds DNA of MR2 and MR3 but not of M200H. When the restricted genomes of all three lines were probed with SVTS2 DNA, strong hybridization to two EcoRI fragments of chromosomal MR2 and MR3 DNA but not M200H DNA indicated that SVTS2 DNA had integrated into the genomes of MR2 and MR3 but not of M200H. When MR3 extrachromosomal ds DNA containing a 2.1-kb SVTS2 DNA fragment was transfected into M200H, the transformed spiroplasmas were resistant to SVTS2. These results suggest that SVTS2 DNA fragments, possibly integrated into the chromosomal or extrachromosomal DNA of a previously susceptible spiroplasma, may function as viral incompatibility elements, providing resistance to superinfection by

  12. Condensation of circular DNA

    NASA Astrophysics Data System (ADS)

    Starostin, E. L.

    2013-04-01

    A simple model of a circularly closed double-stranded DNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and torsional elastic components and the effective self-attraction energy. The model includes a relative orientation or sequence dependence of the effective attraction forces between different pieces of the polymer chain. Two series of conformations are analysed: a multicovered circle (a toroid) and a multifold two-headed racquet. The results are presented as a diagram of state. It is suggested that the stability of particular conformations may be controlled by proper adjustment of the primary structure. Application of the model to other semi-flexible polymers is considered.

  13. Argonaute Proteins Affect siRNA Levels and Accumulation of a Novel Extrachromosomal DNA from the Dictyostelium Retrotransposon DIRS-1*

    PubMed Central

    Boesler, Benjamin; Meier, Doreen; Förstner, Konrad U.; Friedrich, Michael; Hammann, Christian; Sharma, Cynthia M.; Nellen, Wolfgang

    2014-01-01

    The retrotransposon DIRS-1 is the most abundant retroelement in Dictyostelium discoideum and constitutes the pericentromeric heterochromatin of the six chromosomes in D. discoideum. The vast majority of cellular siRNAs is derived from DIRS-1, suggesting that the element is controlled by RNAi-related mechanisms. We investigated the role of two of the five Argonaute proteins of D. discoideum, AgnA and AgnB, in DIRS-1 silencing. Deletion of agnA resulted in the accumulation of DIRS-1 transcripts, the expression of DIRS-1-encoded proteins, and the loss of most DIRS-1-derived secondary siRNAs. Simultaneously, extrachromosomal single-stranded DIRS-1 DNA accumulated in the cytoplasm of agnA− strains. These DNA molecules appear to be products of reverse transcription and thus could represent intermediate structures before transposition. We further show that transitivity of endogenous siRNAs is impaired in agnA− strains. The deletion of agnB alone had no strong effect on DIRS-1 transposon regulation. However, in agnA−/agnB− double mutant strains strongly reduced accumulation of extrachromosomal DNA compared with the single agnA− strains was observed. PMID:25352599

  14. Detection of circular and linear herpesvirus DNA molecules in mammalian cells by gel electrophoresis.

    PubMed Central

    Gardella, T; Medveczky, P; Sairenji, T; Mulder, C

    1984-01-01

    A simple gel technique is described for the detection of large, covalently closed, circular DNA molecules in eucaryotic cells. The procedure is based on the electrophoretic technique of Eckhardt (T. Eckhardt, Plasmid 1:584-588, 1978) for detecting bacterial plasmids and has been modified for the detection of circular and linear extrachromosomal herpesvirus genomes in mammalian cells. Gentle lysis of suspended cells in the well of an agarose gel followed by high-voltage electrophoresis allows separation of extrachromosomal DNA from the bulk of cellular DNA. Circular viral DNA from cells which carry the genomes of Epstein-Barr virus, Herpesvirus saimiri, and Herpesvirus ateles can be detected in these gels as sharp bands which comigrate with bacterial plasmid DNA of 208 kilobases. Epstein-Barr virus producer cell lines also show a sharp band of linear 160-kilobase DNA. The kinetics of the appearance of this linear band after induction of viral replication after temperature shift parallels the known kinetics of Epstein-Barr virus production in these cell lines. Hybridization of DNA after transfer to filters shows that the circular and linear DNA bands are virus specific and that as little as 0.25 Epstein-Barr virus genome per cell can be detected. The technique is simple, rapid, and sensitive and requires relatively low amounts of cells (0.5 X 10(6) to 2.5 X 10(6)). Images PMID:6321792

  15. Extrachromosomal homologous DNA recombination in plant cells is fast and is not affected by CpG methylation.

    PubMed Central

    Puchta, H; Kocher, S; Hohn, B

    1992-01-01

    Using a sensitive transient assay, we investigated extrachromosomal homologous DNA recombination (ECR) in plant cells. As the plant genome is highly C methylated, we addressed the question of whether CpG methylation has an influence on DNA recombination efficiencies. Whereas the expression level of the fully CpG-methylated DNA molecules was reduced drastically, we found no significant changes in ECR efficiencies between two partly CpG-methylated plasmids or between one fully CpG-methylated and one nonmethylated plasmid. Using a modified polymerase chain reaction analysis, we were able to detect recombination between two fully CpG-methylated plasmids. Furthermore, we characterized the kinetics of the ECR reaction. Cotransfection of plasmids carrying truncated copies of the beta-glucuronidase (GUS) gene resulted in enzyme activity with a delay of only half an hour compared with that of the plasmid carrying the functional marker gene. This indicates that the ECR reaction itself requires no more than 30 min. By polymerase chain reaction, we were able to detect the recombined GUS gene as early as 2 h after transfection. This result and the time course of the transient GUS activity indicate that ECR occurs mainly early after transfection. The biological significance of this finding is discussed, and properties of ECR and intrachromosomal recombination are compared. Images PMID:1630452

  16. Extrachromosomal genetic elements in Micrococcus.

    PubMed

    Dib, Julián Rafael; Liebl, Wolfgang; Wagenknecht, Martin; Farías, María Eugenia; Meinhardt, Friedhelm

    2013-01-01

    Micrococci are Gram-positive G + C-rich, nonmotile, nonspore-forming actinomycetous bacteria. Micrococcus comprises ten members, with Micrococcus luteus being the type species. Representatives of the genus play important roles in the biodegradation of xenobiotics, bioremediation processes, production of biotechnologically important enzymes or bioactive compounds, as test strains in biological assays for lysozyme and antibiotics, and as infective agents in immunocompromised humans. The first description of plasmids dates back approximately 28 years, when several extrachromosomal elements ranging in size from 1.5 to 30.2 kb were found in Micrococcus luteus. Up to the present, a number of circular plasmids conferring antibiotic resistance, the ability to degrade aromatic compounds, and osmotolerance are known, as well as cryptic elements with unidentified functions. Here, we review the Micrococcus extrachromosomal traits reported thus far including phages and the only quite recently described large linear extrachromosomal genetic elements, termed linear plasmids, which range in size from 75 kb (pJD12) to 110 kb (pLMA1) and which confer putative advantageous capabilities, such as antibiotic or heavy metal resistances (inferred from sequence analyses and curing experiments). The role of the extrachromosomal elements for the frequently proven ecological and biotechnological versatility of the genus will be addressed as well as their potential for the development and use as genetic tools. PMID:23138713

  17. Induction of circles of heterogeneous sizes in carcinogen-treated cells: two-dimensional gel analysis of circular DNA molecules.

    PubMed Central

    Cohen, S; Lavi, S

    1996-01-01

    Extrachromosomal circular DNA molecules are associated with genomic instability, and circles containing inverted repeats were suggested to be the early amplification products. Here we present for the first time the use of neutral-neutral two-dimensional (2D) gel electrophoresis as a technique for the identification, isolation, and characterization of heterogeneous populations of circular molecules. Using this technique, we demonstrated that in N-methyl-N'-nitro-N-nitrosoguanidine-treated simian virus 40-transformed Chinese hamster cells (CO60 cells), the viral sequences are amplified as circular molecules of various sizes. The supercoiled circular fraction was isolated and was shown to contain molecules with inverted repeats. 2D gel analysis of extrachromosomal DNA from CHO cells revealed circular molecules containing highly repetitive DNA which are similar in size to the simian virus 40-amplified molecules. Moreover, enhancement of the amount of circular DNA was observed upon N-methyl-N'-nitro-N-nitrosoguanidine treatment of CHO cells. The implications of these findings regarding the processes of gene amplification and genomic instability and the possible use of the 2D gel technique to study these phenomena are discussed. PMID:8628266

  18. Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella

    PubMed Central

    Papenfort, Kai; Espinosa, Elena; Casadesús, Josep; Vogel, Jörg

    2015-01-01

    Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution but constitutes a complex process that requires synchronization with the physiological state of the host bacteria. Although several host transcription factors are known to regulate plasmid-borne transfer genes, RNA-based regulatory circuits for host–plasmid communication remain unknown. We describe a posttranscriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two separate seed-pairing domains to activate the mRNAs of both the sigma-factor σS and the RicI protein, a previously uncharacterized membrane protein here shown to inhibit conjugation. Transcription of ricI requires σS and, together, RprA and σS orchestrate a coherent feedforward loop with AND-gate logic to tightly control the activation of RicI synthesis. RicI interacts with the conjugation apparatus protein TraV and limits plasmid transfer under membrane-damaging conditions. To our knowledge, this study reports the first small RNA-controlled feedforward loop relying on posttranscriptional activation of two independent targets and an unexpected role of the conserved RprA small RNA in controlling extrachromosomal DNA transfer. PMID:26307765

  19. Circular DNA Molecules in the Genus Drosophila

    PubMed Central

    Travaglini, E. C.; Schultz, J.

    1972-01-01

    The satellite DNA's from the embryos of five species of Drosophila (D. melanogaster, D. simulans, D. nasuta, D. virilis and D. hydei) have been analyzed for the presence of closed circular duplex DNA molecules, as determined by CsCl-EBr gradients. Circular DNA molecules were found in every species but D. melanogaster. Analyses of cell fractions from adult Drosophila and organ fractions from Drosophila larvae show that fractions containing mitochondria are highly enriched in these molecules. PMID:4643820

  20. A novel cell-free system reveals a mechanism of circular DNA formation from tandem repeats.

    PubMed

    Cohen, S; Mechali, M

    2001-06-15

    One characteristic of genomic plasticity is the presence of extrachromosomal circular DNA (eccDNA). High levels of eccDNA are associated with genomic instability, exposure to carcinogens and aging. We have recently reported developmentally regulated formation of eccDNA that occurs preferentially in pre-blastula Xenopus laevis embryos. Multimers of tandemly repeated sequences were over-represented in the circle population while dispersed sequences were not detected, indicating that circles were not formed at random from any chromosomal sequence. Here we present detailed mechanistic studies of eccDNA formation in a cell-free system derived from Xenopus egg extracts. We show that naked chromosomal DNA from sperm or somatic tissues serves as a substrate for direct tandem repeat circle formation. Moreover, a recombinant bacterial tandem repeat can generate eccDNA in the extract through a de novo mechanism which is independent of DNA replication. These data suggest that the presence of a high level of any direct tandem repeat can confer on DNA the ability to be converted into circular multimers in the early embryo irrespective of its sequence and that homologous recombination is involved in this process. PMID:11410662

  1. Extra-chromosomal DNA maintenance in Bacillus subtilis, dependence on flagellation factor FliF and moonlighting mediator EdmS.

    PubMed

    Hakumai, Yuichi; Shimomoto, Kouko; Ashiuchi, Makoto

    2015-05-15

    Extra-chromosomal DNA maintenance (EDM) as an important process in the propagation and genetic engineering of microbes. Bacillus subtilis EdmS (formerly PgsE), a protein comprising 55 amino acids, is a mediator of the EDM process. In this study, the effect of mutation of global regulators on B. subtilis EDM was examined. Mutation of the swrA gene abolished EdmS-mediated EDM. It is known that swrA predominantly regulates expression of the fla/che operon in B. subtilis. We therefore performed EDM analysis using fla/che-deletion mutants and identified an EDM-mediated EDM cooperator in the flgB-fliL region. Further genetic investigation identified the flagellation factor FliF is a crucial EDM cooperator. To our knowledge, this is the first observation of the moonlighting function of FliF in DNA maintenance. PMID:25843804

  2. Beyond the chromosome: the prevalence of unique extra-chromosomal bacteriophages with integrated virulence genes in pathogenic Staphylococcus aureus.

    PubMed

    Utter, Bryan; Deutsch, Douglas R; Schuch, Raymond; Winer, Benjamin Y; Verratti, Kathleen; Bishop-Lilly, Kim; Sozhamannan, Shanmuga; Fischetti, Vincent A

    2014-01-01

    In Staphylococcus aureus, the disease impact of chromosomally integrated prophages on virulence is well described. However, the existence of extra-chromosomal prophages, both plasmidial and episomal, remains obscure. Despite the recent explosion in bacterial and bacteriophage genomic sequencing, studies have failed to specifically focus on extra-chromosomal elements. We selectively enriched and sequenced extra-chromosomal DNA from S. aureus isolates using Roche-454 technology and uncovered evidence for the widespread distribution of multiple extra-chromosomal prophages (ExPΦs) throughout both antibiotic-sensitive and -resistant strains. We completely sequenced one such element comprised of a 43.8 kbp, circular ExPΦ (designated ФBU01) from a vancomycin-intermediate S. aureus (VISA) strain. Assembly and annotation of ФBU01 revealed a number of putative virulence determinants encoded within a bacteriophage immune evasion cluster (IEC). Our identification of several potential ExPΦs and mobile genetic elements (MGEs) also revealed numerous putative virulence factors and antibiotic resistance genes. We describe here a previously unidentified level of genetic diversity of stealth extra-chromosomal elements in S. aureus, including phages with a larger presence outside the chromosome that likely play a prominent role in pathogenesis and strain diversity driven by horizontal gene transfer (HGT). PMID:24963913

  3. Archaeal Extrachromosomal Genetic Elements

    PubMed Central

    Wang, Haina; Peng, Nan; Shah, Shiraz A.

    2015-01-01

    SUMMARY Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes, such as spindles, rods, filaments, spheres, head-tails, bottles, and droplets, and some of these new viruses have been classified into one order, 10 families, and 16 genera. Investigation of model archaeal viruses has yielded important insights into mechanisms underlining various steps in the viral life cycle, including infection, DNA replication and transcription, and virion egression. Many of these mechanisms are unprecedented for any known bacterial or eukaryal viruses. Studies of plasmids isolated from different archaeal hosts have also revealed a striking diversity in gene content and innovation in replication strategies. Highly divergent replication proteins are identified in both viral and plasmid genomes. Genomic studies of archaeal ECEs have revealed a modular sequence structure in which modules of DNA sequence are exchangeable within, as well as among, plasmid families and probably also between viruses and plasmids. In particular, it has been suggested that ECE-host interactions have shaped the coevolution of ECEs and their archaeal hosts. Furthermore, archaeal hosts have developed defense systems, including the innate restriction-modification (R-M) system and the adaptive CRISPR (clustered regularly interspaced short palindromic repeats) system, to restrict invasive plasmids and viruses. Together, these interactions permit a delicate balance between ECEs and their hosts, which is vitally important for maintaining an innovative gene reservoir carried by ECEs. In conclusion, while research on archaeal ECEs has just started to unravel the molecular biology of these genetic entities and their interactions with archaeal hosts, it is expected to accelerate in the next decade. PMID

  4. Topologically non-linked circular duplex DNA.

    PubMed

    Biegeleisen, Ken

    2002-05-01

    The discovery of circular DNA, over 30 years ago, introduced an element of uneasiness in what had been, up to that point, the almost picture-perfect story of the elucidation of the molecular biology of heredity. If DNA indeed has the Watson-Crick right-handed helical secondary structure, then in circular DNA, thousands, or perhaps even millions of twists must be removed in each generation, and re-wound in the next generation. Although enzyme systems adequate for this task have long since been found and characterized, there have nevertheless arisen a number of proposals for alternative DNA structures in which the strands are topologically non-linked, so that they might separate during replication without having to be unwound. These structures have generally been put forth as theory only, and have been largely unaccompanied by experimental evidence to support their applicability to native DNA from living systems. Recently, however, a report has emerged suggesting that it might be possible to separate, intact, the individual single-stranded circular half-chromosomes which constitute the double-stranded circular chromosomes of certain plasmids. This would not be possible unless the chromosomes had one of the alternative, topologically non-linked structures. It is widely believed that after a half-century of worldwide DNA research, any significant change to the Watson-Crick structure is unlikely to stand up to scrutiny. Nevertheless, the present author has found that in many instances in which the behavior of circular duplex DNA is considered to be explicable only in terms of the topologically linked helical model, it is also possible to explain that same behavior in terms of a topologically non-linked model. It is necessary, in these instances, to make certain logical assumptions which cannot be conclusively proven at the present time. The author herein offers an example of one such instance, namely an examination of the behavior of circular duplex DNA in an alkaline

  5. Entropic penalties in circular DNA assembly

    NASA Astrophysics Data System (ADS)

    Zoli, Marco

    2014-11-01

    The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to the classical action are evaluated separately by simulating a broad ensemble of twisted conformations. We obtain, for two short sequences, a free energy landscape with multiple wells corresponding to the most convenient values of helical repeat. Our results point to a intrinsic flexibility of the circular structures in which the base pair fluctuations move the system from one well to the next thus causing the local unwinding of the helix. The latter is more pronounced in the shorter sequence whose cyclization causes a higher bending stress. The entropic reductions associated to the formation of the ordered helicoidal structure are estimated.

  6. Entropic penalties in circular DNA assembly.

    PubMed

    Zoli, Marco

    2014-11-01

    The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to the classical action are evaluated separately by simulating a broad ensemble of twisted conformations. We obtain, for two short sequences, a free energy landscape with multiple wells corresponding to the most convenient values of helical repeat. Our results point to a intrinsic flexibility of the circular structures in which the base pair fluctuations move the system from one well to the next thus causing the local unwinding of the helix. The latter is more pronounced in the shorter sequence whose cyclization causes a higher bending stress. The entropic reductions associated to the formation of the ordered helicoidal structure are estimated. PMID:25381507

  7. Entropic penalties in circular DNA assembly

    SciTech Connect

    Zoli, Marco

    2014-11-07

    The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to the classical action are evaluated separately by simulating a broad ensemble of twisted conformations. We obtain, for two short sequences, a free energy landscape with multiple wells corresponding to the most convenient values of helical repeat. Our results point to a intrinsic flexibility of the circular structures in which the base pair fluctuations move the system from one well to the next thus causing the local unwinding of the helix. The latter is more pronounced in the shorter sequence whose cyclization causes a higher bending stress. The entropic reductions associated to the formation of the ordered helicoidal structure are estimated.

  8. Construction of DNA Hemicatenanes from Two Small Circular DNA Molecules

    PubMed Central

    Gaillard, Claire; Strauss, François

    2015-01-01

    DNA hemicatenanes, one of the simplest possible junctions between two double stranded DNA molecules, have frequently been mentioned in the literature for their possible function in DNA replication, recombination, repair, and organization in chromosomes. They have been little studied experimentally, however, due to the lack of an appropriate method for their preparation. Here we have designed a method to build hemicatenanes from two small circular DNA molecules. The method involves, first, the assembly of two linear single strands and their circularization to form a catenane of two single stranded circles, and, second, the addition and base-pairing of the two single stranded circles complementary to the first ones, followed by their annealing using DNA topoisomerase I. The product was purified by gel electrophoresis and characterized. The arrangement of strands was as expected for a hemicatenane and clearly distinct from a full catenane. In addition, each circle was unwound by an average of half a double helical turn, also in excellent agreement with the structure of a hemicatenane. It was also observed that hemicatenanes are quickly destabilized by a single cut on either of the two strands passing inside the junction, strongly suggesting that DNA strands are able to slide easily inside the hemicatenane. This method should make it possible to study the biochemical properties of hemicatenanes and to test some of the hypotheses that have been proposed about their function, including a possible role for this structure in the organization of complex genomes in loops and chromosomal domains. PMID:25799010

  9. Z-DNA: vacuum ultraviolet circular dichroism

    SciTech Connect

    Sutherland, J.C.; Griffin, K.P.; Keck, P.C.; Takacs, P.Z.

    1981-08-01

    In concentrated salt or ethanolic solutions, the self-complementary copolymer poly(dG-dC)-poly(dG-dC) forms a left-handed double-helical structure that has been termed Z-DNA. The first evidence for this structure came from changes observed in the circular dichroism (CD) spectrum between 230 and 300 nm for low- and high-salt solutions. In 3 M NaCl, the CD spectrum is approximately inverted compared to the B-form spectrum observed in low salt solution. We measured the vacuum ultraviolet CD spectrum of poly(dG-dC)-poly(dG-dC) down to 180 nm under conditions in which the 230- to 300-nm spectrum is inverted. Below 200 nm, where the B form exhibits the large positive peak at 187 nm that is characteristic of right-handed double-helical DNAs, the Z form exhibits a large negative peak at 194 nm and a positive band below 186 nm. Therefore, the Z-form vacuum ultraviolet CD spectrum resembles an inverted and red-shifted B-form spectrum. The magnitudes of the differences observed between the B and Z forms in the CD spectrum below 200 nm are about 10 times greater than those observed between 230 and 300 nm. The vacuum ultraviolet CD spectrum of poly(dG-dC)-poly(dG-dC) is 3 M C/sub 2/O/sub 4/ also is inverted compared to the B-form spectrum; however, between 230 and 300 nm, it is nonconservative with a negative maximum at 290 nm and a weak positive CD signal above 300 nm, presumably reflecting differential light scattering and indicating the existence of molecular aggregates. Our results suggest that the vacuum ultraviolet CD spectrum is sensitive to the handedness of doublehelical DNA structures.

  10. Z-DNA Vacuum ultraviolet circular dichroism

    SciTech Connect

    Sutherland, J.C.; Griffin, K.P.; Keck, P.C.; Takacs, P.Z.

    1981-08-01

    In concentrated salt or ethanolic solutions, the self-complementary copolymer poly(dG-dC).poly(dG-dC) forms a left-handed double-helical structure that has been termed ZDNA. The first evidence for this structure came from changes observed in the circular dichroism (CD) spectrum between 230 and 300 nm for low- and high-salt solutions (Pohl, F.M. and Jovin, T.M. (1972) J. Mol. Biol. 67, 675-696). In 3 M NaCl, the CD spectrum is approximately inverted compared to the B-form spectrum observed in low-salt solution. We measured the vacuum ultraviolet CD spectrum of poly(dG-dC).poly(dG-dC) down to 180 nm under conditions in which the 230 to 300 nm spectrum is inverted. Below 200 nm, where the B form exhibits the large positive peak at 187 nm that is characteristic of right-handed double-helical DNAs, the Z form exhibits a large negative peak at 194 nm and a positive band below 186 nm. Therefore, the Z-form vacuum ultraviolet CD spectrum resembles an inverted and red-shifted B-form spectrum. The magnitudes of the differences observed between the Band Z forms in the CD spectrum below 200 nm are about 10 times greater than those observed between 230 and 300 nm. The vacuum ultraviolet CD spectrum of poly(dG-dC).poly(dG-dC) in 3 M Cs/sub 2/SO/sub 4/ also is inverted compared to the B-form spectrum; however, between 230 and 300 nm, it is nonconservative with a negative maximum at 290 nm and a weak positive CD signal above 300 nm, presumably reflecting differential light scattering and indicating the existence of molecular aggregates. Our results suggest that the vacuum ultraviolet CD spectrum is sensitive to the handedness of double-helical DNA structures.

  11. Purification of circular DNA using benzoylated naphthoylated DEAE-cellulose.

    PubMed

    Gamper, H; Lehman, N; Piette, J; Hearst, J E

    1985-04-01

    Un-nicked circular DNA can be separated from protein, RNA, and other DNA in a simple three-step protocol consisting of exonuclease III digestion, extraction with benzoylated naphthoylated DEAE-cellulose (BND cellulose) in 1 M NaCl, and alcohol precipitation of the remaining supercoiled DNA. Exonuclease III treatment introduces single-stranded regions into contaminating linear and nicked circular DNA. This DNA, together with most RNA and protein, is adsorbed onto BND cellulose leaving form I DNA in solution. The protocol can be used to purify analytical as well as preparative amounts of supercoiled DNA. This procedure is a substitute for cesium chloride-ethidium bromide gradient ultracentrifugation and gives a comparable yield of pure form I DNA. Other classes of DNA can be isolated by changing the pretreatment step. Selective digestion of linear DNA with lambda exonuclease permits the isolation of both nicked circular and supercoiled DNA while brief heat-induced or alkali-induced denaturation leads to the recovery of rapidly reannealing DNA. In large-scale purifications, the basic protocol is usually preceded by one or more BND cellulose extractions in 1 M NaCl to remove contaminants absorbing UV or inhibiting exonuclease III. PMID:3996184

  12. Identification of a novel circular DNA virus in pig feces

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Metagenomic analysis of fecal samples collected from a swine with diarrhea detected sequences encoding a replicase (Rep) protein typically found in small circular Rep-encoding ssDNA (CRESS-DNA) viruses. The complete 3,062 nucleotide genome was generated and found to encode two bi-directionally trans...

  13. CSA: An efficient algorithm to improve circular DNA multiple alignment

    PubMed Central

    Fernandes, Francisco; Pereira, Luísa; Freitas, Ana T

    2009-01-01

    Background The comparison of homologous sequences from different species is an essential approach to reconstruct the evolutionary history of species and of the genes they harbour in their genomes. Several complete mitochondrial and nuclear genomes are now available, increasing the importance of using multiple sequence alignment algorithms in comparative genomics. MtDNA has long been used in phylogenetic analysis and errors in the alignments can lead to errors in the interpretation of evolutionary information. Although a large number of multiple sequence alignment algorithms have been proposed to date, they all deal with linear DNA and cannot handle directly circular DNA. Researchers interested in aligning circular DNA sequences must first rotate them to the "right" place using an essentially manual process, before they can use multiple sequence alignment tools. Results In this paper we propose an efficient algorithm that identifies the most interesting region to cut circular genomes in order to improve phylogenetic analysis when using standard multiple sequence alignment algorithms. This algorithm identifies the largest chain of non-repeated longest subsequences common to a set of circular mitochondrial DNA sequences. All the sequences are then rotated and made linear for multiple alignment purposes. To evaluate the effectiveness of this new tool, three different sets of mitochondrial DNA sequences were considered. Other tests considering randomly rotated sequences were also performed. The software package Arlequin was used to evaluate the standard genetic measures of the alignments obtained with and without the use of the CSA algorithm with two well known multiple alignment algorithms, the CLUSTALW and the MAVID tools, and also the visualization tool SinicView. Conclusion The results show that a circularization and rotation pre-processing step significantly improves the efficiency of public available multiple sequence alignment algorithms when used in the

  14. Analysis of extrachromosomal Ac/Ds transposable elements.

    PubMed Central

    Gorbunova, V; Levy, A A

    2000-01-01

    The mechanism of transposition of the maize Ac/Ds elements is not well understood. The true transposition intermediates are not known and it has not been possible to distinguish between excision models involving 8-bp staggered cuts or 1-bp staggered cuts followed by hairpin formation. In this work, we have analyzed extrachromosomal excision products to gain insight into the excision mechanism. Plasmid rescue was used to demonstrate that Ds excision is associated with the formation of circular molecules. In addition, we present evidence for the formation of linear extrachromosomal species during Ds excision. Sequences found at the termini of circular and linear elements showed a broad range of nucleotide additions or deletions, suggesting that these species are not true intermediates. Additional nucleotides adjacent to the termini in extrachromosomal elements were compared to the sequence of the original donor site. This analysis showed that: (1) the first nucleotide adjacent to the transposon end was significantly more similar to the first nucleotide flanking the element in the donor site than to a random sequence and (2) the second and farther nucleotides did not resemble the donor site. The implications of these findings for excision models are discussed. PMID:10790408

  15. Isolation of Circular DNA from a Mitochondrial Fraction from Yeast

    PubMed Central

    Clark-Walker, G. D.

    1972-01-01

    Breakage and fractionation of respiratory competent yeast in the presence of ethidium bromide, and subsequent centrifugation of a detergent lysate of the mitochondrial fraction by the dye-buoyant-density technique, results in the isolation of closed-circular DNA. After removal of bound dye, this DNA has two components when analyzed by equilibrium buoyant density in the analytical ultracentrifuge. A minor component has a buoyant density of 1.684 g/cm3, which is characteristic of mitochondrial DNA, but the major component has a buoyant density of 1.701 g/cm3. This species of DNA is also present in yeast that have been mutagenized to respiratory deficiency in the presence of the highest concentration of ethidium bromide compatible with cell growth. The closed-circular DNA of buoyant density 1.701 g/cm3, and free of linear DNA, is associated with the sole particulate band obtained on sucrose gradient centrifugation of a mitochondrial preparation from respiratory-deficient cells. Two particulate bands are obtained on sucrose gradient centrifugation of a mitochondrial preparation from respiratory-competent cells, the upper band containing DNA of buoyant density 1.701 g/cm3 and the lower band DNA of buoyant density 1.684 g/cm3. The suggestion is advanced, in view of the reputed sedimentation behaviour of yeast peroxisomes, that the closed-circular DNA of buoyant density 1.701 g/cm3 may be located in peroxisomes. Images PMID:4551142

  16. Efficient gene transfer in C.elegans: extrachromosomal maintenance and integration of transforming sequences.

    PubMed Central

    Mello, C C; Kramer, J M; Stinchcomb, D; Ambros, V

    1991-01-01

    We describe a dominant behavioral marker, rol-6(su-1006), and an efficient microinjection procedure which facilitate the recovery of Caenorhabditis elegans transformants. We use these tools to study the mechanism of C.elegans DNA transformation. By injecting mixtures of genetically marked DNA molecules, we show that large extrachromosomal arrays assemble directly from the injected molecules and that homologous recombination drives array assembly. Appropriately placed double-strand breaks stimulated homologous recombination during array formation. Our data indicate that the size of the assembled transgenic structures determines whether or not they will be maintained extrachromosomally or lost. We show that low copy number extrachromosomal transformation can be achieved by adjusting the relative concentration of DNA molecules in the injection mixture. Integration of the injected DNA, though relatively rare, was reproducibly achieved when single-stranded oligonucleotide was co-injected with the double-stranded DNA. Images PMID:1935914

  17. Chiral plasmonic DNA nanostructures with switchable circular dichroism

    NASA Astrophysics Data System (ADS)

    Schreiber, Robert; Luong, Ngoc; Fan, Zhiyuan; Kuzyk, Anton; Nickels, Philipp C.; Zhang, Tao; Smith, David M.; Yurke, Bernard; Kuang, Wan; Govorov, Alexander O.; Liedl, Tim

    2013-12-01

    Circular dichroism spectra of naturally occurring molecules and also of synthetic chiral arrangements of plasmonic particles often exhibit characteristic bisignate shapes. Such spectra consist of peaks next to dips (or vice versa) and result from the superposition of signals originating from many individual chiral objects oriented randomly in solution. Here we show that by first aligning and then toggling the orientation of DNA-origami-scaffolded nanoparticle helices attached to a substrate, we are able to reversibly switch the optical response between two distinct circular dichroism spectra corresponding to either perpendicular or parallel helix orientation with respect to the light beam. The observed directional circular dichroism of our switchable plasmonic material is in good agreement with predictions based on dipole approximation theory. Such dynamic metamaterials introduce functionality into soft matter-based optical devices and may enable novel data storage schemes or signal modulators.

  18. Sound Packing DNA: packing open circular DNA with low-intensity ultrasound

    NASA Astrophysics Data System (ADS)

    Park, Donghee; Jung, Bong-Kwang; Park, Hyunjin; Lee, Hyungbeen; Lee, Gyudo; Park, Jingam; Shin, Unchul; Won, Jong Ho; Jo, Yong Jun; Chang, Jin Woo; Lee, Sangwoo; Yoon, Daesung; Seo, Jongbum; Kim, Chul-Woo

    2015-04-01

    Supercoiling DNA (folding DNA into a more compact molecule) from open circular forms requires significant bending energy. The double helix is coiled into a higher order helix form; thus it occupies a smaller footprint. Compact packing of DNA is essential to improve the efficiency of gene delivery, which has broad implications in biology and pharmaceutical research. Here we show that low-intensity pulsed ultrasound can pack open circular DNA into supercoil form. Plasmid DNA subjected to 5.4 mW/cm2 intensity ultrasound showed significant (p-values <0.001) supercoiling compared to DNA without exposure to ultrasound. Radiation force induced from ultrasound and dragging force from the fluid are believed to be the main factors that cause supercoiling. This study provides the first evidence to show that low-intensity ultrasound can directly alter DNA topology. We anticipate our results to be a starting point for improved non-viral gene delivery.

  19. Sound Packing DNA: packing open circular DNA with low-intensity ultrasound

    PubMed Central

    Park, DongHee; Jung, Bong-Kwang; Park, Hyunjin; Lee, Hyungbeen; Lee, Gyudo; Park, Jingam; Shin, Unchul; Won, Jong Ho; Jo, Yong Jun; Chang, Jin Woo; Lee, Sangwoo; Yoon, Daesung; Seo, Jongbum; Kim, Chul-Woo

    2015-01-01

    Supercoiling DNA (folding DNA into a more compact molecule) from open circular forms requires significant bending energy. The double helix is coiled into a higher order helix form; thus it occupies a smaller footprint. Compact packing of DNA is essential to improve the efficiency of gene delivery, which has broad implications in biology and pharmaceutical research. Here we show that low-intensity pulsed ultrasound can pack open circular DNA into supercoil form. Plasmid DNA subjected to 5.4 mW/cm2 intensity ultrasound showed significant (p-values <0.001) supercoiling compared to DNA without exposure to ultrasound. Radiation force induced from ultrasound and dragging force from the fluid are believed to be the main factors that cause supercoiling. This study provides the first evidence to show that low-intensity ultrasound can directly alter DNA topology. We anticipate our results to be a starting point for improved non-viral gene delivery. PMID:25892035

  20. Uncovering novel mobile genetic elements and their dynamics through an extra-chromosomal sequencing approach.

    PubMed

    Deutsch, Douglas R; Utter, Bryan; Fischetti, Vincent A

    2016-01-01

    Staphylococcus aureus is a major clinically important pathogen with well-studied phage contributions to its virulence potential. In this commentary, we describe our method to enrich and sequence stealth extra-chromosomal DNA elements in the bacterial cell, allowing the identification of novel extra-chromosomal prophages in S. aureus clinical strains. Extra-chromosomal sequencing is a useful and broadly applicable tool to study bacterial genomics, giving a temporal glance at the extra-chromosomal compartment of the cell and allowing researchers to uncover lower-copy plasmidial elements (e.g., prophages) as well as gain a greater understanding of mobile genetic elements that shuffle on and off the chromosome. Here, we describe how episomal and plasmidial DNA elements can have profound downstream effects on the host cell and surrounding bacterial population, and discuss specific examples of their importance in Gram-positive bacteria. We also offer potential avenues of future research where extra-chromosomal sequencing may play a key role in our understanding of the complete virulence potential of infectious bacteria. PMID:27581613

  1. Circular Herpesvirus sylvilagus DNA in spleen cells of experimentally infected cottontail rabbits.

    PubMed

    Medveczky, P; Kramp, W J; Sullivan, J L

    1984-11-01

    Cottontail rabbits (Sylvilagus floridanus) were infected with Herpesvirus sylvilagus, and spleen cells were analyzed for the presence of virus-specific, covalently closed circular, and linear DNA molecules by a simple electrophoretic technique, followed by transfer to nitrocellulose filters and hybridization with cloned viral DNA (Gardella et al., J. Virol. 50:248-254, 1984). Approximately 0.2 copies per cell of circular DNA and 0.2 copies per cell of linear DNA were detected by hybridization with a cloned viral DNA fragment. The size of the viral DNA was estimated at ca. 158 kilobase pairs. Restriction endonuclease patterns suggested structural similarities to cottontail herpesvirus DNA. PMID:6092696

  2. Programmed pH-Driven Reversible Association and Dissociation of Interconnected Circular DNA Dimer Nanostructures.

    PubMed

    Hu, Yuwei; Ren, Jiangtao; Lu, Chun-Hua; Willner, Itamar

    2016-07-13

    The switchable pH-driven reversible assembly and dissociation of interlocked circular DNA dimers is presented. The circular DNA dimers are interconnected by pH-responsive nucleic acid bridges. In one configuration, the two-ring nanostructure is separated at pH = 5.0 to individual rings by reconfiguring the interlocking bridges into C-G·C(+) triplex units, and the two-ring assembly is reformed at pH = 7.0. In the second configuration, the dimer of circular DNAs is bridged at pH = 7.0 by the T-A·T triplex bridging units that are separated at pH = 10.0, leading to the dissociation of the dimer to single circular DNA nanostructures. The two circular DNA units are also interconnected by two pH-responsive locks. The pH-programmed opening of the locks at pH = 5.0 or pH = 10.0 yields two isomeric dimer structures composed of two circular DNAs. The switchable reconfigured states of the circular DNA nanostructures are followed by time-dependent fluorescence changes of fluorophore/quencher labeled systems and by complementary gel electrophoresis experiments. The dimer circular DNA structures are further implemented as scaffolds for the assembly of Au nanoparticle dimers exhibiting controlled spatial separation. PMID:27225955

  3. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    SciTech Connect

    Greulich-Bode, Karin; Wang, Mei; Rhein, Andreas; Weier, Jingly; Weier, Heinz-Ulli

    2008-12-16

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-?B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  4. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    SciTech Connect

    Greulich-Bode, Karin M.; Wang, Mei; Rhein, Andreas P.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-12-04

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-{kappa}B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  5. [Electron microscopic research on the extrachromosomal genetic elements of Escherichia coli].

    PubMed

    Kiseleva, E V; Vorob'eva, N V; Romashchenko, A G; Serdiukova, N A; Khristoliubova, N B

    1986-08-01

    The structural organization of extrachromosomal genetic elements were studied in a subfraction obtained after centrifugation of the lysate of E. coli spheroplasts. With this method of isolation, the tertiary structure of the extrachromosomal genetic elements was preserved. The majority of DNA macromolecules were released in the form of single and connected rosettes. Typical rosettes composed of radial loops of DNA clustered around the central dense core (the diameter is about 60 nm). The mean length of the rosette loops was 1.06 +/- 0.4 micron. Both relaxed folded and supercoiled folded forms of DNA were observed on the preparation. Sometimes the rosettes were connected with large aggregates of DNA (possibly the material of bacterial chromosomes) and had the appearance of thick fibers with numerous lateral loops. Linear, cyclic and various replicative forms of DNA have also been observed. It is assumed that rosettes of the extrachromosomal elements of E. coli reflect one of the levels of organization of prokaryotic genetic material. PMID:3535183

  6. Characterization of the Host Factors Required for Hepadnavirus Covalently Closed Circular (ccc) DNA Formation

    PubMed Central

    Zhou, Tianlun; Block, Timothy M.; Guo, Ju-Tao

    2012-01-01

    Synthesis of the covalently closed circular (ccc) DNA is a critical, but not well-understood step in the life cycle of hepadnaviruses. Our previous studies favor a model that removal of genome-linked viral DNA polymerase occurs in the cytoplasm and the resulting deproteinized relaxed circular DNA (DP-rcDNA) is subsequently transported into the nucleus and converted into cccDNA. In support of this model, our current study showed that deproteinization of viral double-stranded linear (dsl) DNA also took place in the cytoplasm. Furthermore, we demonstrated that Ku80, a component of non-homologous end joining DNA repair pathway, was essential for synthesis of cccDNA from dslDNA, but not rcDNA. In an attempt to identify additional host factors regulating cccDNA biosynthesis, we found that the DP-rcDNA was produced in all tested cell lines that supported DHBV DNA replication, but cccDNA was only synthesized in the cell lines that accumulated high levels of DP-rcDNA, except for NCI-H322M and MDBK cells, which failed to synthesize cccDNA despite of the existence of nuclear DP-rcDNA. The results thus imply that while removal of the genome-linked viral DNA polymerase is most likely catalyzed by viral or ubiquitous host function(s), nuclear factors required for the conversion of DP-rcDNA into cccDNA and/or its maintenance are deficient in the above two cell lines, which could be useful tools for identification of the elusive host factors essential for cccDNA biosynthesis or maintenance. PMID:22912842

  7. Identification of novel Bromus- and Trifolium-associated circular DNA viruses.

    PubMed

    Kraberger, Simona; Farkas, Kata; Bernardo, Pauline; Booker, Cameron; Argüello-Astorga, Gerardo R; Mesléard, François; Martin, Darren P; Roumagnac, Philippe; Varsani, Arvind

    2015-05-01

    The genomes of a large number of highly diverse novel circular DNA viruses from a wide range of sources have been characterised in recent years, including circular single-stranded DNA (ssDNA) viruses that share similarities with plant-infecting ssDNA viruses of the family Geminiviridae. Here, we describe six novel circular DNA viral genomes that encode replication-associated (Rep) proteins that are most closely related to those of either geminiviruses or gemycircularviruses (a new group of ssDNA viruses that are closely related to geminiviruses). Four possible viral genomes were recovered from Bromus hordeaceus sampled in New Zealand, and two were recovered from B. hordeaceus and Trifolium resupinatum sampled in France. Two of the viral genomes from New Zealand (one from the North Island and one from the South Island each) share >99 % sequence identity, and two genomes recovered from B. hordeaceus and T. resupinatum sampled in France share 74 % identity. All of the viral genomes that were recovered were found to have a major open reading frame on both their complementary and virion-sense strands, one of which likely encodes a Rep and the other a capsid protein. Although future infectivity studies are needed to identify the host range of these viruses, this is the first report of circular DNA viruses associated with grasses in New Zealand. PMID:25701210

  8. Estimation of circular DNA size using gamma-irradiation and pulsed-field gel electrophoresis

    SciTech Connect

    Beverley, S.M. )

    1989-02-15

    A method is described for estimating the size of large circular DNAs found within complex chromosomal DNA preparations. DNAs are treated with low levels of gamma-irradiation, sufficient to introduce a single double-stranded break per circle, and the resulting linear DNA is sized by pulsed-field electrophoresis and blot hybridization. The method is fast, reproducible, and very conveniently applied to the agarose-enclosed chromosomal DNA preparations commonly used in pulsed field electrophoresis.

  9. Epigenetic Repeat-Induced Gene Silencing in the Chromosomal and Extrachromosomal Contexts in Human Cells.

    PubMed

    Mitsuda, Sho-Hei; Shimizu, Noriaki

    2016-01-01

    A plasmid bearing both a replication initiation region and a matrix attachment region is spontaneously amplified in transfected mammalian cells and generates plasmid repeats in the extrachromosomal double minutes (DMs) or the chromosomal homogeneously staining region (HSR). Generally, the repeat sequences are subject to repeat-induced gene silencing, the mechanism of which remains to be elucidated. Previous research showed that gene expression from the same plasmid repeat was higher from repeats located at DMs than at the HSR, which may reflect the extrachromosomal environment of the DMs. In the current study, plasmid repeats in both DMs and HSR were associated with repressive histone modifications (H3K9me3, H3K9me2), and the levels of repressive chromatin markers were higher in HSR than in DMs. Inactive chromatin is known to spread to neighboring regions in chromosome arm. Here, we found that such spreading also occurs in extrachromosomal DMs. Higher levels of active histone modifications (H3K9Ac, H3K4me3, and H3K79me2) were detected at plasmid repeats in DMs than in HSR. The level of DNA CpG methylation was generally low in both DMs and HSR; however, there were some hypermethylated copies within the population of repeated sequences, and the frequency of such copies was higher in DMs than in HSR. Together, these data suggest a "DNA methylation-core and chromatin-spread" model for repeat-induced gene silencing. The unique histone modifications at the extrachromosomal context are discussed with regard to the model. PMID:27525955

  10. Epigenetic Repeat-Induced Gene Silencing in the Chromosomal and Extrachromosomal Contexts in Human Cells

    PubMed Central

    Mitsuda, Sho-hei; Shimizu, Noriaki

    2016-01-01

    A plasmid bearing both a replication initiation region and a matrix attachment region is spontaneously amplified in transfected mammalian cells and generates plasmid repeats in the extrachromosomal double minutes (DMs) or the chromosomal homogeneously staining region (HSR). Generally, the repeat sequences are subject to repeat-induced gene silencing, the mechanism of which remains to be elucidated. Previous research showed that gene expression from the same plasmid repeat was higher from repeats located at DMs than at the HSR, which may reflect the extrachromosomal environment of the DMs. In the current study, plasmid repeats in both DMs and HSR were associated with repressive histone modifications (H3K9me3, H3K9me2), and the levels of repressive chromatin markers were higher in HSR than in DMs. Inactive chromatin is known to spread to neighboring regions in chromosome arm. Here, we found that such spreading also occurs in extrachromosomal DMs. Higher levels of active histone modifications (H3K9Ac, H3K4me3, and H3K79me2) were detected at plasmid repeats in DMs than in HSR. The level of DNA CpG methylation was generally low in both DMs and HSR; however, there were some hypermethylated copies within the population of repeated sequences, and the frequency of such copies was higher in DMs than in HSR. Together, these data suggest a “DNA methylation-core and chromatin-spread” model for repeat-induced gene silencing. The unique histone modifications at the extrachromosomal context are discussed with regard to the model. PMID:27525955

  11. Rapid purification of circular DNA by triplex-mediated affinity capture

    DOEpatents

    Ji, H.; Smith, L.M.

    1997-01-07

    A single-step capture of a target supercoiled double-stranded DNA molecule is accomplished by forming a local triple-helix among two strands of the supercoiled circular DNA and an oligonucleotide probe. The oligonucleotide is bound to an immobilizing support which facilitates the immobilization and purification of target DNA molecules. Non-target DNA molecules and other contaminating cellular material are easily removed by washing. The triple-helical structure is destabilized by raising the pH, leaving purified target DNA in the supernatant and reusable affinity capture oligonucleotide secured to the immobilizing support. 3 figs.

  12. Rapid purification of circular DNA by triplex-mediated affinity capture

    DOEpatents

    Ji, Huamin; Smith, Lloyd M.

    1997-01-01

    A single-step capture of a target supercoiled double-stranded DNA molecule is accomplished by forming a local triple-helix among two strands of the supercoiled circular DNA and an oligonucleotide probe. The oligonucleotide is bound to an immobilizing support which facilitates the immobilization and purification of target DNA molecules. Non-target DNA molecules and other contaminating cellular material are easily removed by washing. The triple-helical structure is destabilized by raising the pH, leaving purified target DNA in the supernatant and reusable affinity capture oligonucleotide secured to the immobilizing support.

  13. PicoGreen Assay of Circular DNA for Radiation Biodosimetry

    PubMed Central

    Zhang, Steven B.; Yang, Shanmin; Vidyasagar, Sadasivan; Zhang, Mei; Casey-Sawicki, Katherine; Liu, Chaomei; Yin, Liangjie; Zhang, Lei; Cao, Yongbing; Tian, Yeping; Swarts, Steven; Fenton, Bruce M.; Keng, Peter; Zhang, Lurong; Okunieff, Paul

    2015-01-01

    We developed a simple, rapid and quantitative assay using the fluorescent probe PicoGreen to measure the concentration of ionizing radiation-induced double-stranded DNA (dsDNA) in mouse plasma, and we correlated this concentration with the radiation dose. With 70 μl of blood obtained by fingerstick, this 30 min assay reduces protein interference without extending sample processing time. Plasma from nonirradiated mice (BALB/c and NIH Swiss) was pooled, diluted and spiked with dsDNA to establish sensitivity and reproducibility of the assay to quantify plasma dsDNA. The assay was then used to directly quantify dsDNA in plasma at 0–48 h after mice received 0–10 Gy total-body irradiation (TBI). There are three optimal conditions for this assay: 1:10 dilution of plasma in water; 1:200 dilution of PicoGreen reagent in water; and calibration of radiation-induced dsDNA concentration through a standard addition method using serial spiking of samples with genomic dsDNA. Using the internal standard calibration curve of the spiked samples method, the signal developed within 5 min, exhibiting a linear signal (r2 0.997). The radiation-induced elevation of plasma DNA in mice started at 1–3 h, peaked at 9 h and gradually returned to baseline at 24 h after TBI (6 Gy). DNA levels in plasma collected from mice 9 h after 0–10 Gy TBI correlated strongly with dose (r2 0.991 and 0.947 for BALB/c and NIH Swiss, respectively). Using the PicoGreen assay, we observed a radiation dose-dependent response in extracellular plasma DNA 9 h after irradiation with an assay time ≤30 min. PMID:25574588

  14. Evaluation of circular DNA substrates for whole genome amplification prior to forensic analysis.

    PubMed

    Tate, Courtney M; Nuñez, Ada N; Goldstein, Cori A; Gomes, Iva; Robertson, James M; Kavlick, Mark F; Budowle, Bruce

    2012-03-01

    Forensic biological evidence often contains low quantities of DNA or substantially degraded DNA which makes samples refractory to genotype analysis. One approach that shows promise to overcome the limited quantity of DNA is whole genome amplification (WGA). One WGA technique, termed rolling circle amplification (RCA), involves the amplification of circular DNA fragments and this study evaluates a single-stranded (ss) DNA ligase enzyme for generating circular DNA templates for RCA WGA. Fast, efficient ligation of several sizes of ssDNA templates was achieved. The enzyme also ligated double-stranded (ds) DNA templates, a novel activity not previously reported. Adapter sequences containing optimal terminal nucleotide ends for increased ligation efficiency were designed and ligation of adapters to template DNA was optimized. Increased amplification of DNA templates was observed following WGA; however, no amplification advantage for ssDNA ligase treatment of templates was evident compared to linear templates. A multi-step process to utilize ssDNA ligase prior to WGA was developed and short tandem repeat (STR) analysis of simulated low template (LT) and fragmented DNA was evaluated. The process resulted in the loss of template DNA and failed STR analysis whereas input of linear genomic DNA template directly into WGA prior to STR analysis improved STR genotyping results compared to non-WGA treated samples. Inclusion of an extreme thermostable single-stranded DNA binding protein (SSB) during WGA also increased DNA yields. While STR artifacts such as peak imbalance, drop-in, and dropout persisted, WGA shows potential for successful genetic profiling of LT and fragmented DNA samples. Further research and development is warranted prior to use of WGA in forensic casework. PMID:21570374

  15. Discovery of a novel circular DNA virus in the Forbes sea star, Asterias forbesi.

    PubMed

    Fahsbender, Elizabeth; Hewson, Ian; Rosario, Karyna; Tuttle, Allison D; Varsani, Arvind; Breitbart, Mya

    2015-09-01

    A single-stranded DNA (ssDNA) virus, Asterias forbesi-associated circular virus (AfaCV), was discovered in a Forbes sea star displaying symptoms of sea star wasting disease (SSWD). The AfaCV genome organization is typical of circular Rep-encoding ssDNA (CRESS-DNA) viruses and is similar to that of members of the family Circoviridae. PCR-based surveys indicate that AfaCV is not clearly associated with SSWD, whereas the sea star-associated densovirus (SSaDV), recently implicated in SSWD in the Pacific, was prevalent in symptomatic specimens. AfaCV represents the first CRESS-DNA virus detected in echinoderms, adding to the growing diversity of these viruses recently recovered from invertebrates. PMID:26112764

  16. New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and Metagenomics

    PubMed Central

    Hansen, Thomas Arn; Fridholm, Helena; Frøslev, Tobias Guldberg; Kjartansdóttir, Kristín Rós; Willerslev, Eske; Nielsen, Lars Peter; Hansen, Anders Johannes

    2015-01-01

    Rattus norvegicus (R. norvegicus) are ubiquitous and their presence has several effects on the human populations in our urban areas on a global scale. Both historically and presently, this close interaction has facilitated the dissemination of many pathogens to humans, making screening for potentially zoonotic and emerging viruses in rats highly relevant. We have investigated faecal samples from R. norvegicus collected from urban areas using a protocol based on metagenomic enrichment of circular DNA genomes and subsequent sequencing. We found a new type of papillomavirus, with a L1 region 82% identical to that of the known R. norvegicus Papillomavirus 2. Additionally, we found 20 different circular replication associated protein (Rep)-encoding single stranded DNA (CRESS-DNA) virus-like genomes, one of which has homology to the replication-associated gene of Beak and feather disease virus. Papillomaviruses are a group of viruses known for their carcinogenic potential, and although they are known to infect several different vertebrates, they are mainly studied and characterised in humans. CRESS-DNA viruses are found in many different environments and tissue types. Both papillomaviruses and CRESS-DNA viruses are known to have pathogenic potential and screening for novel and known viruses in R. norvegicus could help identify viruses with pathogenic potential. PMID:26559957

  17. Induction of differentiation in HL60 cells by the reduction of extrachromosomally amplified c-myc.

    PubMed Central

    Eckhardt, S G; Dai, A; Davidson, K K; Forseth, B J; Wahl, G M; Von Hoff, D D

    1994-01-01

    Oncogene amplification in tumor cells results in the overexpression of proteins that confer a growth advantage in vitro and in vivo. Amplified oncogenes can reside intrachromosomally, within homogeneously staining regions (HSRs), or extrachromosomally, within double minute chromosomes (DMs). Since previous studies have shown that low concentrations of hydroxyurea (HU) can eliminate DMs, we studied the use of HU as a gene-targeting agent in tumor cells containing extrachromosomally amplified oncogenes. In a neuroendocrine cell line (COLO 320), we have shown that HU can eliminate amplified copies of c-myc located on DMs, leading to a reduction in tumorigenicity in vitro and in vivo. To determine whether the observed reduction in tumorigenicity was due to differentiation, we next investigated whether HU could induce differentiation in HL60 cells containing extrachromosomally amplified c-myc. We compared the effects of HU, as well as two other known differentiating agents (dimethyl sulfoxide and retinoic acid), on c-myc gene copy number, c-myc expression, and differentiation in HL60 cells containing amplified c-myc genes either on DMs or HSRs. We discovered that HU and dimethyl sulfoxide reduced both c-myc gene copy number and expression and induced differentiation in cells containing c-myc amplified on DMs. These agents failed to have similar effects on HL60 cells with amplified c-myc in HSRs. By contrast, retinoic acid induced differentiation independent of the localization of amplified c-myc. These data illustrate the utility of targeting extrachromosomal DNA to modulate tumor phenotype and reveal that both HU and dimethyl sulfoxide induce differentiation in HL60 cells through DM elimination. Images PMID:8022834

  18. [Circular dichroism of DNA liquid-crystalline dispersion particles].

    PubMed

    Semenov, S V; Yevdokimov, Yu M

    2015-01-01

    The optical activity of DNA liquid-crystalline dispersions is being investigated based on a theory for absorption of electromagnetic waves by large molecular aggregates. The impact on the dispersions-optical properties, exerted by the interaction between the complexes of nucleic acid molecules and nanoparticles, is being considered. PMID:26016021

  19. Amplified DNAs in laboratory stocks of Leishmania tarentolae: extrachromosomal circles structurally and functionally similar to the inverted-H-region amplification of methotrexate-resistant Leishmania major

    SciTech Connect

    Petrillo-Peixoto, M.L.; Beverley, S.M. )

    1988-12-01

    We describe the structure of amplified DNA that was discovered in two laboratory stocks of the protozoan parasite Leishmania tarentolae. Restriction mapping and molecular cloning revealed that a region of 42 kilobases was amplified 8- to 30-fold in these lines. Southern blot analyses of digested DNAs or chromosomes separated by pulsed-field electrophoresis showed that the amplified DNA corresponded to the H region, a locus defined originally by its amplification in methotrexate-resistant Leishmania major. Similarities between the amplified DNA of the two species included (i) extensive cross-hybridization; (ii) approximate conservation of sequence order; (iii) extrachromosomal localization; (iv) an overall inverted, head-to-head configuration as a circular 140-kilobase tetrameric molecule; (v) two regions of DNA sequence rearrangement, each of which was closely associated with the two centers of the inverted repeats; (vi) association with methotrexate resistance; and (vii) phenotypically conservative amplification, in which the wild-type chromosomal arrangement was retained without apparent modification. Our data showed that amplified DNA mediating drug resistance arose in unselected L. tarentolae, although the pressures leading to apparently spontaneous amplification and maintenance of the H region are not known. The simple structure and limited extent of DNA amplified in these and other Leishmania lines suggests that the study of gene amplification in Leishmania spp. offers an attractive model system for the study of amplification in cultured mammalian cells and tumors. We also introduced a method for measuring the size of large circular DNAs, using gamma-irradiation to introduce limited double-strand breaks followed by sizing of the linear DNAs by pulsed-field electrophoresis.

  20. Convergent DNA synthesis: a non-enzymatic dimerization approach to circular oligodeoxynucleotides.

    PubMed Central

    Rubin, E; Rumney, S; Wang, S; Kool, E T

    1995-01-01

    We report a novel convergent approach to the construction of circular DNA oligonucleotides from two smaller linear precursors. Circular DNAs 34-74 nucleotides (nt) in size are constructed non-enzymatically in a single step from two half-length oligomers. A DNA template is used to assemble the constituent parts into a triple helical complex which brings the four reactive ends together for chemical ligation with BrCN/imidazole/Ni2+. A homodimerization reaction strategy is successfully used on a small scale to construct circles 42, 58 and 74 nt in size. In addition, a heterodimerization strategy is successfully used in two cases to construct circular 34mers from different 16mer and 18mer precursors. Measurement of preparative yields for one biologically active 34mer circle shows that the dimerization strategy gives a yield higher than that from conventional cyclization and nearly as high as that for a normally synthesized linear DNA, establishing that there is not necessarily a yield penalty for circle construction. Six additional preparative circle constructions, giving conversions of approximately 33-85% from precursors to circular product, are also described. Convergent strategies allow the construction of medium and large size DNA molecules in higher yields than can be achieved by standard linear synthesis alone. Images PMID:7567468

  1. The circular dichroism and X-ray diffraction of DNA condensed from ethanolic solutions.

    PubMed Central

    Gray, D M; Edmondson, S P; Lang, D; Vaughan, M

    1979-01-01

    It is known that DNA in aqueous-ethanol solutions undergoes a B to A conformational change between 60% and 80% (w/w) ethanol. We have found that precipitates formed by adding salt to DNA in 60% and 80% ethanolic solutions can be very different. DNA precipitated from 60% ethanol forms a fine condensate that only slowly settles out of suspension and shows a characteristic differential scattering of circularly polarized light at long wavelengths. DNA precipitated from 80% ethanol forms a flocculent aggregate that exhibits the CD spectral features of the A conformation. Data from circular dichroism spectra of natural and synthetic nucleic acids and from X-ray diffraction patterns of the precipitates show that DNA molecules precipitated from 60% and 80% ethanol are, respectively, in the B and A conformation. Therefore, the different secondary conformations of DNA in ethanolic solutions are maintained during precipitation under these conditions. These results are of general importance for the preparation and study of condensed forms of DNA, since a relatively small change in the extent of dehydration can change the secondary conformation of DNA and markedly affect the character of a subsequent precipitate. Images PMID:572544

  2. Circular dichroic properties and average dimensions of DNA-containing reverse micellar aggregates.

    PubMed

    Pietrini, Adriana V; Luisi, Pier Luigi

    2002-05-01

    With the aim of investigating the compartmentation of nucleic acids and surfactant aggregates, we have studied the circular dichroic properties of DNA solubilized in reverse micelles. DNA incorporated in AOT/isooctane reverse micelles (AOT=bis-2-ethyl-hexyl sodium sulfosuccinate) assumes an anomalous circular dichroism (CD) spectrum with the characteristic features of a psi spectrum. Older literature observations could therefore be confirmed that attribute these spectral changes to the fact that the reverse micelles induce the formation of a condensed form of DNA. A dynamic light scattering (DLS) characterization of the DNA-containing micellar solutions was carried out, and three populations of aggregates in a polar solvent are observed, with an average radius centered at 5, 100 and 1000 nm, respectively, all three containing DNA. Several forms of DNA, including a plasmid, have been investigated. The formation of 1 microm-large aggregates depends on the DNA concentration and such aggregates disappear in the course of a few hours. Conversely, the 100 nm aggregates are stable for at least 1 day and contain DNA in a normal spectral state at low concentration and in a condensed form-it is the characteristic psi spectrum-in a higher concentration range. The solubilization of DNA in reverse micelles brings about unexpected larger structures in hydrocarbon solution, and whereas the very large component can be with all likelihood be attributed to clusters of smaller reverse micelles, the components at 100 nm radius appear to be a quite stable and characteristic feature of DNA-containing reverse micelles. PMID:11988222

  3. Identification of a Novel Circular DNA Virus in New Zealand Fur Seal (Arctocephalus forsteri) Fecal Matter

    PubMed Central

    Sikorski, Alyssa; Dayaram, Anisha

    2013-01-01

    Fur seal feces-associated circular DNA virus (FSfaCV) is a novel virus isolated from the fecal matter of New Zealand fur seals. FSfaCV has two main open reading frames in its 2,925-nucleotide (nt) genome. The replication-associated protein (Rep) of FSfaCV has similarity to Rep-like sequences in the Giardia intestinalis genome. PMID:23929471

  4. Identification of a Novel Circular DNA Virus in New Zealand Fur Seal (Arctocephalus forsteri) Fecal Matter.

    PubMed

    Sikorski, Alyssa; Dayaram, Anisha; Varsani, Arvind

    2013-01-01

    Fur seal feces-associated circular DNA virus (FSfaCV) is a novel virus isolated from the fecal matter of New Zealand fur seals. FSfaCV has two main open reading frames in its 2,925-nucleotide (nt) genome. The replication-associated protein (Rep) of FSfaCV has similarity to Rep-like sequences in the Giardia intestinalis genome. PMID:23929471

  5. Hexamminecobalt(III)-induced condensation of calf thymus DNA: circular dichroism and hydration measurements

    PubMed Central

    Kankia, Besik I.; Buckin, Vitaly; Bloomfield, Victor A.

    2001-01-01

    The interaction of hexamminecobalt(III), Co(NH3)63+, with 160 and 3000–8000 bp length calf thymus DNA has been investigated by circular dichroism, acoustic and densimetric techniques. The acoustic titration curves of 160 bp DNA revealed three stages of interaction: (i) Co(NH3)63+ binding up to the molar ratio [Co(NH3)63+]/[P] = 0.25, prior to DNA condensation; (ii) a condensation process between [Co(NH3)63+]/[P] = 0.25 and 0.30; and (iii) precipitation after [Co(NH3)63+]/[P] = 0.3. In the case of 3000–8000 bp DNA only two processes were observed: (i) binding up to [Co(NH3)63+]/[P] = 0.3; and (ii) precipitation after this point. In agreement with earlier observations, long DNA aggregates without changes in its B-form circular dichroism spectrum, while short DNA demonstrates a positive B→Ψ transition after [Co(NH3)63+]/[P] = 0.25. From ultrasonic and densimetric measurements the effects of Co(NH3)63+ binding on volume and compressibility have been obtained. The binding of Co(NH3)63+ to both short and long DNA is characterized by similar changes in volume and compressibility calculated per mole Co(NH3)63+: ΔV = 9 cm3 mol–1 and Δκ = 33 × 10–4 cm3 mol–1 bar–1. The positive sign of the parameters indicates dehydration, i.e. water release from Co(NH3)63+ and the atomic groups of DNA. This extent of water displacement would be consistent with the formation of two direct, hydrogen bonded contacts between the cation and the phosphates of DNA. PMID:11433025

  6. Novel, reversible, benzo[a]pyrene metabolite binding sites in closed-circular, single-stranded DNA

    SciTech Connect

    Price, H.L.

    1991-01-01

    The formation of reversible hydrocarbon epoxide-DNA complexes and the simultaneous increase in the reactivity of these bound epoxides is a general phenomenon. The relationship between physical binding, catalysis of epoxide reactions, and the formation of covalent adducts is not clearly understood at present. In these investigations it was found that linear, double-stranded DNA and supercoiled plasmid DNA both bind and enhance the reactivity of epoxide metabolites of benzo[a]pyrene to similar extents. The results of experiments carried out with closed-circular, single-stranded DNA however, indicate that this DNA possesses a unique binding site not present in either linear, double-stranded DNA or supercoiled DNA. Results of kinetic studies revealed that closed-circular, single-stranded DNA was less efficient at catalyzing epoxide reactions that double-stranded DNA. The results of these kinetic studies are explained in terms of a model which takes into account the polyelectrolyte nature of DNA.

  7. Long Terminal Repeat Circular DNA as Markers of Active Viral Replication of Human T Lymphotropic Virus-1 in Vivo

    PubMed Central

    Fox, James M; Hilburn, Silva; Demontis, Maria-Antonietta; Brighty, David W; Rios Grassi, Maria Fernanda; Galvão-Castro, Bernardo; Taylor, Graham P; Martin, Fabiola

    2016-01-01

    Clonal expansion of human T-lymphotropic virus type-1 (HTLV-1) infected cells in vivo is well documented. Unlike human immunodeficiency virus type 1 (HIV-1), HTLV-1 plasma RNA is sparse. The contribution of the “mitotic” spread of HTLV-1 compared with infectious spread of the virus to HTLV-1 viral burden in established infection is uncertain. Since extrachromosomal long terminal repeat (LTR) DNA circles are indicators of viral replication in HIV-1 carriers with undetectable plasma HIV RNA, we hypothesised that HTLV-1 LTR circles could indicate reverse transcriptase (RT) usage and infectious activity. 1LTR and 2LTR DNA circles were measured in HTLV-1 cell lines and peripheral blood mononuclear cells (PBMC) of asymptomatic carriers (ACs) and patients with HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) or adult T cell leukaemia/lymphoma (ATLL). 1LTR DNA circles were detected in 14/20 patients at a mean of 1.38/100 PBMC but did not differentiate disease status nor correlate with HTLV-1 DNA copies. 2LTR DNA circles were detected in 30/31 patients and at higher concentrations in patients with HTLV-1-associated diseases, independent of HTLV-1 DNA load. In an incident case the 2LTR DNA circle concentration increased 2.1 fold at the onset of HAM/TSP compared to baseline. Detectable and fluctuating levels of HTLV-1 DNA circles in patients indicate viral RT usage and virus replication. Our results indicate HTLV-1 viral replication capacity is maintained in chronic infection and may be associated with disease onset. PMID:26985903

  8. Long Terminal Repeat Circular DNA as Markers of Active Viral Replication of Human T Lymphotropic Virus-1 in Vivo.

    PubMed

    Fox, James M; Hilburn, Silva; Demontis, Maria-Antonietta; Brighty, David W; Rios Grassi, Maria Fernanda; Galvão-Castro, Bernardo; Taylor, Graham P; Martin, Fabiola

    2016-03-01

    Clonal expansion of human T-lymphotropic virus type-1 (HTLV-1) infected cells in vivo is well documented. Unlike human immunodeficiency virus type 1 (HIV-1), HTLV-1 plasma RNA is sparse. The contribution of the "mitotic" spread of HTLV-1 compared with infectious spread of the virus to HTLV-1 viral burden in established infection is uncertain. Since extrachromosomal long terminal repeat (LTR) DNA circles are indicators of viral replication in HIV-1 carriers with undetectable plasma HIV RNA, we hypothesised that HTLV-1 LTR circles could indicate reverse transcriptase (RT) usage and infectious activity. 1LTR and 2LTR DNA circles were measured in HTLV-1 cell lines and peripheral blood mononuclear cells (PBMC) of asymptomatic carriers (ACs) and patients with HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) or adult T cell leukaemia/lymphoma (ATLL). 1LTR DNA circles were detected in 14/20 patients at a mean of 1.38/100 PBMC but did not differentiate disease status nor correlate with HTLV-1 DNA copies. 2LTR DNA circles were detected in 30/31 patients and at higher concentrations in patients with HTLV-1-associated diseases, independent of HTLV-1 DNA load. In an incident case the 2LTR DNA circle concentration increased 2.1 fold at the onset of HAM/TSP compared to baseline. Detectable and fluctuating levels of HTLV-1 DNA circles in patients indicate viral RT usage and virus replication. Our results indicate HTLV-1 viral replication capacity is maintained in chronic infection and may be associated with disease onset. PMID:26985903

  9. Duck hepatitis B virus covalently closed circular DNA appears to survive hepatocyte mitosis in the growing liver

    SciTech Connect

    Reaiche-Miller, Georget Y.; Thorpe, Michael; Low, Huey Chi; Qiao, Qiao; Scougall, Catherine A.; Mason, William S.; Litwin, Samuel; Jilbert, Allison R.

    2013-11-15

    Nucleos(t)ide analogues that inhibit hepatitis B virus (HBV) DNA replication are typically used as monotherapy for chronically infected patients. Treatment with a nucleos(t)ide analogue eliminates most HBV DNA replication intermediates and produces a gradual decline in levels of covalently closed circular DNA (cccDNA), the template for viral RNA synthesis. It remains uncertain if levels of cccDNA decline primarily through hepatocyte death, or if loss also occurs during hepatocyte mitosis. To determine if cccDNA survives mitosis, growing ducklings infected with duck hepatitis B virus (DHBV) were treated with the nucleoside analogue, Entecavir. Viremia was suppressed at least 10{sup 5}-fold, during a period when average liver mass increased 23-fold. Analysis of the data suggested that if cccDNA synthesis was completely inhibited, at least 49% of cccDNA survived hepatocyte mitosis. However, there was a large duck-to-duck variation in cccDNA levels, suggesting that low level cccDNA synthesis may contribute to this apparent survival through mitosis. - Highlights: • The hepatitis B virus nuclear template is covalently closed circular DNA (cccDNA). • cccDNA was studied during liver growth in duck hepatitis B virus infected ducks. • Virus DNA replication and new cccDNA synthesis were inhibited with Entecavir. • At least 49% of cccDNA appeared to survive hepatocyte mitosis. • Low level virus DNA synthesis may contribute to survival of cccDNA through mitosis.

  10. A novel transcriptional element in circular DNA monomers of the duck hepatitis B virus.

    PubMed

    Beckel-Mitchener, A; Summers, J

    1997-10-01

    We report the presence of two elements, pet and net, that are required for proper transcription of the duck hepatitis B virus (DHBV). These regions were previously identified by using plasmid clones of the virus in transient expression assays (M. Huang and J. Summers, J. Virol. 68:1564-1572, 1994). In this study, we further analyzed these regions by using in vitro-synthesized circular DHBV DNA monomers to mimic the authentic transcriptional template. We observed that pet was required for pregenome transcription from circular viral monomers, and in the absence of pet-dependent transcription, expression of the viral envelope genes was increased. We found that deletion of net in circularized DNA monomers led to the production of abnormally long transcripts due to a failure to form 3' ends during transcription. In addition, we report the presence of a net-like region in the mammalian hepadnavirus woodchuck hepatitis virus. These results are consistent with a model that net is a region involved in transcription termination and that in DHBV, pet is required for transcription complexes to read through this region during the first pass through net. PMID:9311882

  11. Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures.

    PubMed

    Gattuso, Hugo; Spinello, Angelo; Terenzi, Alessio; Assfeld, Xavier; Barone, Giampaolo; Monari, Antonio

    2016-03-31

    We report on the comparison between the computational and experimental determination of electronic circular dichroism spectra of different guanine quadruplexes obtained from human telomeric sequences. In particular the difference between parallel, antiparallel, and hybrid structures is evidenced, as well as the induction of transitions between the polymorphs depending on the solution environment. Extensive molecular dynamics simulations (MD) are used to probe the conformational space of the different quadruplexes, and subsequently state-of-the-art hybrid quantum mechanics/molecular mechanics (QM/MM) techniques coupled with excitonic semiempirical Hamiltonian are used to simulate the macromolecular induced circular dichroism. The coupling of spectroscopy and molecular simulation allows an efficient one-to-one mapping between structures and optical properties, offering a way to disentangle the rich, yet complicated, quantity of information embedded in circular dichroism spectra. We show that our methodology is robust and efficient and allows us to take into account subtle conformational changes. As such, it could be used as an efficient tool to investigate structural modification upon DNA/drug interactions. PMID:26943487

  12. Genomic characterization of novel circular ssDNA viruses from insectivorous bats in Southern Brazil.

    PubMed

    Lima, Francisco Esmaile de Sales; Cibulski, Samuel Paulo; Dos Santos, Helton Fernandes; Teixeira, Thais Fumaco; Varela, Ana Paula Muterle; Roehe, Paulo Michel; Delwart, Eric; Franco, Ana Cláudia

    2015-01-01

    Circoviruses are highly prevalent porcine and avian pathogens. In recent years, novel circular ssDNA genomes have recently been detected in a variety of fecal and environmental samples using deep sequencing approaches. In this study the identification of genomes of novel circoviruses and cycloviruses in feces of insectivorous bats is reported. Pan-reactive primers were used targeting the conserved rep region of circoviruses and cycloviruses to screen DNA bat fecal samples. Using this approach, partial rep sequences were detected which formed five phylogenetic groups distributed among the Circovirus and the recently proposed Cyclovirus genera of the Circoviridae. Further analysis using inverse PCR and Sanger sequencing led to the characterization of four new putative members of the family Circoviridae with genome size ranging from 1,608 to 1,790 nt, two inversely arranged ORFs, and canonical nonamer sequences atop a stem loop. PMID:25688970

  13. Genomic Characterization of Novel Circular ssDNA Viruses from Insectivorous Bats in Southern Brazil

    PubMed Central

    Lima, Francisco Esmaile de Sales; Cibulski, Samuel Paulo; dos Santos, Helton Fernandes; Teixeira, Thais Fumaco; Varela, Ana Paula Muterle; Roehe, Paulo Michel; Delwart, Eric; Franco, Ana Cláudia

    2015-01-01

    Circoviruses are highly prevalent porcine and avian pathogens. In recent years, novel circular ssDNA genomes have recently been detected in a variety of fecal and environmental samples using deep sequencing approaches. In this study the identification of genomes of novel circoviruses and cycloviruses in feces of insectivorous bats is reported. Pan-reactive primers were used targeting the conserved rep region of circoviruses and cycloviruses to screen DNA bat fecal samples. Using this approach, partial rep sequences were detected which formed five phylogenetic groups distributed among the Circovirus and the recently proposed Cyclovirus genera of the Circoviridae. Further analysis using inverse PCR and Sanger sequencing led to the characterization of four new putative members of the family Circoviridae with genome size ranging from 1,608 to 1,790 nt, two inversely arranged ORFs, and canonical nonamer sequences atop a stem loop. PMID:25688970

  14. Genetic diversity of novel circular ssDNA viruses in bats in China.

    PubMed

    Ge, Xingyi; Li, Jialu; Peng, Cheng; Wu, Lijun; Yang, Xinglou; Wu, Yongquan; Zhang, Yunzhi; Shi, Zhengli

    2011-11-01

    Novel circular ssDNA genomes have recently been detected in animals and in the environment using metagenomic and high-throughput sequencing approaches. In this study, five full-length circular ssDNA genomes were recovered from bat faecal samples using inverse PCR with sequences designed based on circovirus-related sequences obtained from Solexa sequencing data derived from a random amplification method. These five sequences shared a similar genomic organization to circovirus or the recently proposed cyclovirus of the family Circoviridae. The newly obtained circovirus/cyclovirus-like genomes ranged from 1741 to 2177 bp, and each consisted of two major ORFs, ORF1 and ORF2, encoding putative replicase (Rep) and capsid (Cap) proteins, respectively. The potential stem-loop region was predicted in all five genomes, and three of them had the typical conserved nonanucleotide motif of cycloviruses. A set of primers targeting the conserved Rep region was designed and used to detect the prevalence of circovirus/cyclovirus sequences in individual bats. Among 199 samples tested, 47 were positive (23.6%) for the circovirus genome and two (1.0%) were positive for the cyclovirus genome. In total, 48 partial Rep sequences plus the five full-length genomes were obtained in this study. Detailed analysis indicated that these sequences are distantly related to known circovirus/cyclovirus genomes and may represent 22 novel species that belong to the family Circoviridae. PMID:21795473

  15. Isolation of an IgH gene circular DNA clone from human bone marrow.

    PubMed Central

    Abe, M; Shiku, H

    1989-01-01

    Circular DNA was obtained from human bone marrow. Then a phage library was prepared and screened by use of two probes of the IgH gene; 5'-DHQ52, containing the 5' flanking region of DHQ52, and JH4.3, containing the sequence from JH3 to the 3' flanking region of JH6. One clone, HBMC-1, that was DHQ52+JH4.3- was obtained. HBMC-1 had the germline IgH region upstream of JH1 and the 3' flanking region of DXP1. A recombination signal sequence flanking the 5' side of the JH1 segment was attached to the recombination signal sequence flanking the 3' side of DXP1 forming a head-to-head structure of two 7mers with 10 nucleotides in-between. HBMC-1 is thus considered to be a circular DNA deleted as a consequence of DXP1-JH1 joining of the IgH gene. Images PMID:2492093

  16. Portable and sensitive quantitative detection of DNA based on personal glucose meters and isothermal circular strand-displacement polymerization reaction.

    PubMed

    Xu, Xue-tao; Liang, Kai-yi; Zeng, Jia-ying

    2015-02-15

    A portable and sensitive quantitative DNA detection method based on personal glucose meters and isothermal circular strand-displacement polymerization reaction was developed. The target DNA triggered target recycling process, which opened capture DNA. The released target then found another capture DNA to trigger another polymerization cycle, which was repeated for many rounds, resulting in the multiplication of the DNA-invertase conjugation on the surface of Streptavidin-MNBs. The DNA-invertase was used to catalyze the hydrolysis of sucrose into glucose for PGM readout. There was a liner relationship between the signal of PGM and the concentration of target DNA in the range of 5.0 to 1000 fM, which is lower than some DNA detection method. In addition, the method exhibited excellent sequence selectivity and there was almost no effect of biological complex to the detection performance, which suggested our method can be successfully applied to DNA detection in real biological samples. PMID:25441417

  17. Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types

    PubMed Central

    Swanson, Maud M.; Cock, Peter J. A.; Dawson, Lorna; Freitag, Thomas E.; Singh, Brajesh K.; Torrance, Lesley; Mushegian, Arcady R.

    2015-01-01

    The potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the family Microviridae (icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis of Microviridae major coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamily Gokushovirinae, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar family Circoviridae in BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in the Circoviridae showed that they are a novel clade of Circoviridae-related CRESS-DNA viruses distinct from known Circoviridae genera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors. PMID:25841004

  18. Distinct circular single-stranded DNA viruses exist in different soil types.

    PubMed

    Reavy, Brian; Swanson, Maud M; Cock, Peter J A; Dawson, Lorna; Freitag, Thomas E; Singh, Brajesh K; Torrance, Lesley; Mushegian, Arcady R; Taliansky, Michael

    2015-06-15

    The potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the family Microviridae (icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis of Microviridae major coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamily Gokushovirinae, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar family Circoviridae in BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in the Circoviridae showed that they are a novel clade of Circoviridae-related CRESS-DNA viruses distinct from known Circoviridae genera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors. PMID:25841004

  19. Identification of Disubstituted Sulfonamide Compounds as Specific Inhibitors of Hepatitis B Virus Covalently Closed Circular DNA Formation

    PubMed Central

    Cai, Dawei; Mills, Courtney; Yu, Wenquan; Yan, Ran; Aldrich, Carol E.; Saputelli, Jeffry R.; Mason, William S.; Xu, Xiaodong; Guo, Ju-Tao; Block, Timothy M.

    2012-01-01

    Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) plays a central role in viral infection and persistence and is the basis for viral rebound after the cessation of therapy, as well as the elusiveness of a cure even after extended treatment. Therefore, there is an urgent need for the development of novel therapeutic agents that directly target cccDNA formation and maintenance. By employing an innovative cell-based cccDNA assay in which secreted HBV e antigen is a cccDNA-dependent surrogate, we screened an in-house small-molecule library consisting of 85,000 drug-like compounds. Two structurally related disubstituted sulfonamides (DSS), termed CCC-0975 and CCC-0346, emerged and were confirmed as inhibitors of cccDNA production, with low micromolar 50% effective concentrations (EC50s) in cell culture. Further mechanistic studies demonstrated that DSS compound treatment neither directly inhibited HBV DNA replication in cell culture nor reduced viral polymerase activity in the in vitro endogenous polymerase assay but synchronously reduced the levels of HBV cccDNA and its putative precursor, deproteinized relaxed circular DNA (DP-rcDNA). However, DSS compounds did not promote the intracellular decay of HBV DP-rcDNA and cccDNA, suggesting that the compounds interfere primarily with rcDNA conversion into cccDNA. In addition, we demonstrated that CCC-0975 was able to reduce cccDNA biosynthesis in duck HBV-infected primary duck hepatocytes. This is the first attempt, to our knowledge, to identify small molecules that target cccDNA formation, and DSS compounds thus potentially serve as proof-of-concept drug candidates for development into therapeutics to eliminate cccDNA from chronic HBV infection. PMID:22644022

  20. Suppression of rolling circle amplification by nucleotide analogs in circular template for three DNA polymerases.

    PubMed

    Tang, Suming; Wei, Hua; Hu, Tianyu; Jiang, Jiquan; Chang, Jinglin; Guan, Yifu; Zhao, Guojie

    2016-08-01

    Among wide applications of nucleotide analogs, their roles in enzyme catalytic reactions are significant in both fundamental and medical researches. By introducing analogs into circular templates, we succeeded in determining effects of four analogs on RCA efficiency for three different DNA polymerases. Results showed an obvious suppression effect for 2'-OMeRNA modification, which might be due to the size of the C2'-modified moieties. 2'-F RNA, LNA and PS had little interference, suggesting good analog candidates for application in RCA. Different polymerases and nucleobases made a little difference according to analogs we used. These results are useful for understanding polymerase catalytic mechanism and analogs applications in RCA reaction. PMID:27151504

  1. Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli.

    PubMed

    Jackson, D A; Symons, R H; Berg, P

    1972-10-01

    We have developed methods for covalently joining duplex DNA molecules to one another and have used these techniques to construct circular dimers of SV40 DNA and to insert a DNA segment containing lambda phage genes and the galactose operon of E. coli into SV40 DNA. The method involves: (a) converting circular SV40 DNA to a linear form, (b) adding single-stranded homodeoxypolymeric extensions of defined composition and length to the 3' ends of one of the DNA strands with the enzyme terminal deoxynucleotidyl transferase (c) adding complementary homodeoxypolymeric extensions to the other DNA strand, (d) annealing the two DNA molecules to form a circular duplex structure, and (e) filling the gaps and sealing nicks in this structure with E. coli DNA polymerase and DNA ligase to form a covalently closed-circular DNA molecule. PMID:4342968

  2. Biochemical Method for Inserting New Genetic Information into DNA of Simian Virus 40: Circular SV40 DNA Molecules Containing Lambda Phage Genes and the Galactose Operon of Escherichia coli

    PubMed Central

    Jackson, David A.; Symons, Robert H.; Berg, Paul

    1972-01-01

    We have developed methods for covalently joining duplex DNA molecules to one another and have used these techniques to construct circular dimers of SV40 DNA and to insert a DNA segment containing lambda phage genes and the galactose operon of E. coli into SV40 DNA. The method involves: (a) converting circular SV40 DNA to a linear form, (b) adding single-stranded homodeoxypolymeric extensions of defined composition and length to the 3′ ends of one of the DNA strands with the enzyme terminal deoxynucleotidyl transferase (c) adding complementary homodeoxypolymeric extensions to the other DNA strand, (d) annealing the two DNA molecules to form a circular duplex structure, and (e) filling the gaps and sealing nicks in this structure with E. coli DNA polymerase and DNA ligase to form a covalently closed-circular DNA molecule. PMID:4342968

  3. Nonselective Persistence of a Rickettsia conorii Extrachromosomal Plasmid during Mammalian Infection.

    PubMed

    Riley, Sean P; Fish, Abigail I; Garza, Daniel A; Banajee, Kaikhushroo H; Harris, Emma K; del Piero, Fabio; Martinez, Juan J

    2016-03-01

    Scientific analysis of the genus Rickettsia is undergoing a rapid period of change with the emergence of viable genetic tools. The development of these tools for the mutagenesis of pathogenic bacteria will permit forward genetic analysis of Rickettsia pathogenesis. Despite these advances, uncertainty still remains regarding the use of plasmids to study these bacteria in in vivo mammalian models of infection, namely, the potential for virulence changes associated with the presence of extrachromosomal DNA and nonselective persistence of plasmids in mammalian models of infection. Here, we describe the transformation of Rickettsia conorii Malish 7 with the plasmid pRam18dRGA[AmTrCh]. Transformed R. conorii stably maintains this plasmid in infected cell cultures, expresses the encoded fluorescent proteins, and exhibits growth kinetics in cell culture similar to those of nontransformed R. conorii. Using a well-established murine model of fatal Mediterranean spotted fever, we demonstrate that R. conorii(pRam18dRGA[AmTrCh]) elicits the same fatal outcomes in animals as its untransformed counterpart and, importantly, maintains the plasmid throughout infection in the absence of selective antibiotic pressure. Interestingly, plasmid-transformed R. conorii was readily observed both in endothelial cells and within circulating leukocytes. Together, our data demonstrate that the presence of an extrachromosomal DNA element in a pathogenic rickettsial species does not affect either in vitro proliferation or in vivo infectivity in models of disease and that plasmids such as pRam18dRGA[AmTrCh] are valuable tools for the further genetic manipulation of pathogenic rickettsiae. PMID:26755154

  4. Isolation of bacterial plasmid-related replication-associated circular DNA from a serum sample of a multiple sclerosis patient.

    PubMed

    Gunst, Karin; Zur Hausen, Harald; de Villiers, Ethel-Michele

    2014-01-01

    Psychrobacter species are considered to be opportunistic human pathogens. We report here the isolation of a circular DNA molecule, MSSI1.162, from a serum sample taken from a multiple sclerosis patient during relapse. This isolate is distantly related to known Psychrobacter species and their plasmids. PMID:25169857

  5. Isolation of Bacterial Plasmid-Related Replication-Associated Circular DNA from a Serum Sample of a Multiple Sclerosis Patient

    PubMed Central

    Gunst, Karin; zur Hausen, Harald

    2014-01-01

    Psychrobacter species are considered to be opportunistic human pathogens. We report here the isolation of a circular DNA molecule, MSSI1.162, from a serum sample taken from a multiple sclerosis patient during relapse. This isolate is distantly related to known Psychrobacter species and their plasmids. PMID:25169857

  6. Radiation damage to a DNA-binding protein. Combined circular dichroism and molecular dynamics simulation analysis.

    PubMed

    Mazier, S; Villette, S; Goffinont, S; Renouard, S; Maurizot, J C; Genest, D; Spotheim-Maurizot, M

    2008-11-01

    The E. coli lactose operon, the paradigm of gene expression regulation systems, is the best model for studying the effect of radiation on such systems. The operon function requires the binding of a protein, the repressor, to a specific DNA sequence, the operator. We have previously shown that upon irradiation the repressor loses its operator binding ability. The main radiation-induced lesions of the headpiece have been identified by mass spectrometry. All tyrosine residues are oxidized into 3,4-dihydroxyphenylalanine (DOPA). In the present study we report a detailed characterization of the headpiece radiation-induced modification. An original approach combining circular dichroism measurements and the analysis of molecular dynamics simulation of headpieces bearing DOPA-s instead of tyrosines has been applied. The CD measurements reveal an irreversible modification of the headpiece structure and stability. The molecular dynamics simulation shows a loss of stability shown by an increase in internal dynamics and allows the estimation of the modifications due to tyrosine oxidation for each structural element of the protein. The changes in headpiece structure and stability can explain at least in part the radiation-induced loss of binding ability of the repressor to the operator. This conclusion should hold for all proteins containing radiosensitive amino acids in their DNA-binding site. PMID:18959464

  7. Yeast RNA polymerase II transcription of circular DNA at different degrees of supercoiling.

    PubMed Central

    Pedone, F; Filetici, P; Ballario, P

    1982-01-01

    Purified yeast RNA polymerase II was tested for transcriptional activity as a function of the degree of circular DNA supercoiling. Chimaeric plasmids P30 and P31 both containing inserts from the yeast transposable element TY1 cloned in pBR322 and the vector pBR322 were used as templates. For pBR322 the transcriptional activity increases about 4 fold from the fully relaxed covalently closed circles to the native supercoiled forms, further supercoiling having no effect on transcription. P30 shows a 5 fold increase of transcriptional activity reaching a plateau at the native supercoiled conformation. However, at an intermediate degree of supercoiling (sigma = 0.024), transcription decreases to a value close to zero. P31 too exhibits a conformation (sigma = 0.014) in which there is a drop of transcriptional activity. Furthermore, a 10 fold increase of transcription is obtained at the higher values of superhelix density. Both kinetic and autoradiographic experiments confirm the existence of DNA conformations that can inhibit "in vitro" transcription. Images PMID:6292834

  8. The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin.

    PubMed

    Phan, Tung Gia; da Costa, Antonio Charlys; Del Valle Mendoza, Juana; Bucardo-Rivera, Filemon; Nordgren, Johan; O'Ryan, Miguel; Deng, Xutao; Delwart, Eric

    2016-04-01

    Viral metagenomics of feces collected from 58 Peruvian children with unexplained diarrhea revealed several small circular ssDNA genomes. Two genomes related to sequences previously reported in feces from chimpanzees and other mammals and recently named smacoviruses were characterized and then detected by PCR in 1.7 % (1/58) and 19 % (11/58) of diarrheal samples, respectively. Another three genomes from a distinct small circular ssDNA viral group provisionally called pecoviruses encoded Cap and Rep proteins with <35 % identity to those in related genomes reported in human, seal, porcine and dromedary feces. Pecovirus DNA was detected in 15.5 % (9/58), 5.9 % (3/51) and 3 % (3/100) of fecal samples from unexplained diarrhea in Peru, Nicaragua and Chile, respectively. Feces containing these ssDNA genomes also contained known human enteric viral pathogens. The cellular origins of these circular ssDNA viruses, whether human cells, ingested plants, animals or fungal foods, or residents of the gut microbiome, are currently unknown. PMID:26780893

  9. Epstein-Barr-based episomal chromosomes shuttle 100 kb of self-replicating circular human DNA in mouse cells

    SciTech Connect

    Kelleher, Z.T.; Fu, H.; Livanos, E.; Wendelburg, B.; Gulino, S.; Vos, J.M.

    1998-08-01

    The authors describe the microcell fusion transfer of 100--200 kb self-replicating circular human minichromosomes from human into mouse cells. This experimental approach is illustrated through the shuttling of the latent 170 kb double-stranded DNA genome from the human herpesvirus, Epstein-Barr virus, into nonpermissive rodent cells. Using this interspecies transfer strategy, circular episomes carrying 95--105 kb of human DNA were successfully established at low copy number in mouse A9 cells. Selected episomes were stably maintained for 6 months, and unselected episomes were characterized by a 95% episomal retention per cell division. The establishment of a mouse artificial episomal chromosome system should facilitate evolutionary and therapeutic studies of large human DNA in rodent genetic backgrounds.

  10. PENICILLINASE PLASMID DNA FROM Staphylococcus aureus*

    PubMed Central

    Rush, Mark G.; Gordon, C. N.; Novick, Richard P.; Warner, Robert C.

    1969-01-01

    A penicillinase plasmid from Staphylococcus aureus and three of its derivatives, all previously identified as extrachromosomal genetic elements, have been isolated in high yield as circular duplex DNA molecules. The wild-type plasmid was found by contour-length measurements of electron micrographs to have a molecular weight of 18.6 × 106 daltons. Two plasmids with deletions encompassing six and eight of the eleven known plasmid cistrons had molecular weights of 16.4 × 106 and 15.3 × 106 daltons, respectively. This information was used to establish approximate physical distances for the genetic map. A high-frequency transducing element also derived from the plasmid had a molecular weight of approximately 24 × 106 daltons. Although each plasmid preparation appeared homogeneous by ultracentrifugal analysis, electron micrographs always revealed the presence of a low percentage of complex oligomeric forms, particularly circular and catenated dimers. Images PMID:5260933

  11. Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand.

    PubMed

    Steel, Olivia; Kraberger, Simona; Sikorski, Alyssa; Young, Laura M; Catchpole, Ryan J; Stevens, Aaron J; Ladley, Jenny J; Coray, Dorien S; Stainton, Daisy; Dayaram, Anisha; Julian, Laurel; van Bysterveldt, Katherine; Varsani, Arvind

    2016-09-01

    In recent years, innovations in molecular techniques and sequencing technologies have resulted in a rapid expansion in the number of known viral sequences, in particular those with circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA genomes. CRESS DNA viruses are present in the virome of many ecosystems and are known to infect a wide range of organisms. A large number of the recently identified CRESS DNA viruses cannot be classified into any known viral families, indicating that the current view of CRESS DNA viral sequence space is greatly underestimated. Animal faecal matter has proven to be a particularly useful source for sampling CRESS DNA viruses in an ecosystem, as it is cost-effective and non-invasive. In this study a viral metagenomic approach was used to explore the diversity of CRESS DNA viruses present in the faeces of domesticated and wild animals in New Zealand. Thirty-eight complete CRESS DNA viral genomes and two circular molecules (that may be defective molecules or single components of multicomponent genomes) were identified from forty-nine individual animal faecal samples. Based on shared genome organisations and sequence similarities, eighteen of the isolates were classified as gemycircularviruses and twelve isolates were classified as smacoviruses. The remaining eight isolates lack significant sequence similarity with any members of known CRESS DNA virus groups. This research adds significantly to our knowledge of CRESS DNA viral diversity in New Zealand, emphasising the prevalence of CRESS DNA viruses in nature, and reinforcing the suggestion that a large proportion of CRESS DNA viruses are yet to be identified. PMID:27211884

  12. Conformational state of DNA in chromatin subunits. Circular dichroism, melting, and ethidium bromide binding analysis.

    PubMed Central

    Lawrence, J J; Chan, D C; Piette, L H

    1976-01-01

    This study compares some physical properties of DNA in native chromatin and mono-, di-, trinucleosomes obtained after mild micrococcal nuclease digestion. Melting curves and derivatives are shown to be very similar from one sample to another although a shift from 79 to 82 degrees C is observed between the mainly monophasic peak of multimers and chromatin. Careful analysis of the positive band of the circular dichroism spectra shows the appearance of a shoulder at 275nm, the intensity of which increases from the mono- to the di- and trinucleosome. This shoulder is maximum for native chromatin. At the same time binding isotherms of ethidium - bromide are characterized by two highly fluorescent binding sites for all the samples but the product KN of the apparent binding constant of the higher affinity binding sites by the apparent number of those sites increases from the mono- to the di- and trinucleosome. There again the valus is maximum for native chromatin. Such results strongly suggest that the native state of chromatin requires something more than the indefinite repeat of an elementary subunit. Images PMID:1005108

  13. Mercury-induced DNA polymorphism: Probing the conformation of Hg(II)-DNA via Staphylococcal nuclease digestion and circular dichroism measurements

    SciTech Connect

    Gruenwedel, D.W.; Cruikshank, M.K. )

    1990-02-27

    Exposing native calf thymus DNA to increasing concentrations of Hg(ClO{sub 4}){sub 2} not only produces dramatic changes in its circular dichroism (CD) but results also in the decrease, and ultimate cessation, of endonucleolytic DNA cleavage by staphylococcal nuclease. DNA cleavage proceeds at or near the rates exhibited by untreated DNA. At Hg(II) levels of 0.08 < r < 0.5, the rate of DNA hydrolysis decreases monotonically with increasing Hg(II) concentrations, and at r > 0.4, DNA cleavage ceases. Both the CD changes and the changes in the rate of DNA digestion are totally reversible upon the removal of Hg(II). For comparison purposes, native calf thymus DNA was also treated with methylmercury (CH{sub 3}Hg(II)), an agent known to disrupt the secondary structure of DNA. The treatment yielded single-stranded methylmercurated DNA with preserved right-handed helix screwness. The authors interpret the Hg(II)-induced alterations in the CD of native calf thymus DNA, and the hydrolysis rate changes observed with staphylococcal nuclease, to indicate that Hg(II) either produces in DNA reversible B {leftrightarrow} Z transitions, passing transiently through C-like conformations, or generates non-B-conformational structures of presumably left-handed geometry.

  14. Cleavage of supercoiled circular double-stranded DNA induced by a eukaryotic cambialistic superoxide dismutase from Cinnamomum camphora.

    PubMed

    Wang, Bao-Zhong; Wei, Xu-Bin; Liu, Wang-Yi

    2004-09-01

    A eukaryotic cambialistic superoxide dismutase (SOD) has been purified to homogeneity from mature seeds of the disease- and insect-resistant camphor tree (Cinnamomum camphora). Besides the known role of this SOD in protecting cells against oxidative stress, it can induce the cleavage of supercoiled double-stranded DNA into nicked and linear DNA. It can not cleave linear DNA or RNA, demonstrating there is no DNase or RNase in the purified cambialistic SOD. Furthermore, the SOD can linearize circular pGEM-4Z DNA that is relaxed by topoisomerase I. This result indicates that the DNA-cleaving activity requires substrates being topologically constrained. The supercoiled DNA-cleaving activity of the cambialistic SOD can be inhibited by either SOD inhibitor (azide) or catalase and hydroxyl radical scavengers (ethanol and mannitol). The chelator of iron, diethylenetriaminepentaacetic acid (DTPA), also inhibits the supercoiled DNA-cleaving activity. These results show that the dismutation activity is crucial for the supercoiled DNA cleavage. The modification of tryptophan residue of the cambialistic SOD with N-bromosuccinimide (NBS) shows that these two activities are structurally correlative. The reaction mechanism is proposed that the hydroxyl radical formed in a transition-metal-catalyzing Fenton-type reaction contributes to the DNA-cleaving activity. In addition, the cleavage sites in supercoiled pGEM-4Z DNA are random. PMID:15346198

  15. Development of an extrachromosomal cloning vector system for use in Borrelia burgdorferi.

    PubMed

    Sartakova, M; Dobrikova, E; Cabello, F C

    2000-04-25

    Molecular genetic analysis of Borrelia burgdorferi, the cause of Lyme disease, has been hampered by the absence of any means of efficient generation, identification, and complementation of chromosomal and plasmid null gene mutants. The similarity of borrelial G + C content to that of Gram-positive organisms suggested that a wide-host-range plasmid active in Gram-positive bacteria might also be recognized by borrelial DNA replication machinery. One such plasmid, pGK12, is able to propagate in both Gram-positive and Gram-negative bacteria and carries erythromycin and chloramphenicol resistance markers. pGK12 propagated extrachromosomally in B. burgdorferi B31 after electroporation but conferred only erythromycin resistance. pGK12 was used to express enhanced green fluorescent protein in B31 under the control of the flaB promoter. Escherichia coli transformed with pGK12 DNA extracted from B31 expressing only erythromycin resistance developed both erythromycin and chloramphenicol resistance, and plasmid DNA isolated from these transformed E. coli had a restriction pattern similar to the original pGK12. Our data indicate that the replicons of pGK12 can provide the basis to continue developing efficient genetic systems for B. burgdorferi together with the erythromycin resistance and reporter egfp genes. PMID:10781091

  16. A divergent clade of circular single-stranded DNA viruses from pig feces

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using metagenomics and molecular cloning methods, we characterized five novel small circular viral genomes from pig feces distantly related to chimpanzee and porcine stool-associated circular viruses, (ChiSCV and PoSCV1). Phylogenetic analysis placed these viruses into a new, highly divergent, clade...

  17. MuA-mediated in vitro cloning of circular DNA: transpositional autointegration and the effect of MuB.

    PubMed

    Pulkkinen, Elsi; Haapa-Paananen, Saija; Savilahti, Harri

    2016-06-01

    Transposons provide useful tools for genetics and genomics studies, as they can be modified easily for a variety of purposes. In this study, a strategy to clone circular DNA was developed on the basis of an efficient Mu in vitro transposition reaction catalyzed by MuA transposase. The transposon used contains a selectable marker as well as an origin of replication, and in vitro integration of the transposon into circular DNA generates a plasmid that can replicate in E. coli. We show that the substrate stoichiometry plays an important role in the profile of intermolecular versus intramolecular transposition reaction products. Increasing the relative amount of target DNA reduced the frequency of intramolecular products that are non-productive with regard to the developed cloning application. Such autointegration was also reduced in the reactions containing phage Mu-encoded MuB, indicating that this protein can be used for cloning in combination with MuA, and it is particularly useful with a limited amount of target DNA. The developed strategy can now be utilized to clone DNA circles regardless of their origin as long as their size is not prohibitive for transformation. PMID:26847688

  18. Isothermal circular-strand-displacement polymerization of DNA and microRNA in digital microfluidic devices.

    PubMed

    Giuffrida, Maria Chiara; Zanoli, Laura Maria; D'Agata, Roberta; Finotti, Alessia; Gambari, Roberto; Spoto, Giuseppe

    2015-02-01

    Nucleic-acid amplification is a crucial step in nucleic-acid-sequence-detection assays. The use of digital microfluidic devices to miniaturize amplification techniques reduces the required sample volume and the analysis time and offers new possibilities for process automation and integration in a single device. The recently introduced droplet polymerase-chain-reaction (PCR) amplification methods require repeated cycles of two or three temperature-dependent steps during the amplification of the nucleic-acid target sequence. In contrast, low-temperature isothermal-amplification methods have no need for thermal cycling, thus requiring simplified microfluidic-device features. Here, the combined use of digital microfluidics and molecular-beacon (MB)-assisted isothermal circular-strand-displacement polymerization (ICSDP) to detect microRNA-210 sequences is described. MicroRNA-210 has been described as the most consistently and predominantly upregulated hypoxia-inducible factor. The nmol L(-1)-pmol L(-1) detection capabilities of the method were first tested by targeting single-stranded DNA sequences from the genetically modified Roundup Ready soybean. The ability of the droplet-ICSDP method to discriminate between full-matched, single-mismatched, and unrelated sequences was also investigated. The detection of a range of nmol L(-1)-pmol L(-1) microRNA-210 solutions compartmentalized in nanoliter-sized droplets was performed, establishing the ability of the method to detect as little as 10(-18) mol of microRNA target sequences compartmentalized in 20 nL droplets. The suitability of the method for biological samples was tested by detecting microRNA-210 from transfected K562 cells. PMID:25579461

  19. Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma

    PubMed Central

    Vogt, Nicolas; Gibaud, Anne; Lemoine, Frédéric; de la Grange, Pierre; Debatisse, Michelle; Malfoy, Bernard

    2014-01-01

    The mechanisms of gene amplification in tumour cells are poorly understood and the relationship between extrachromosomal DNA molecules, named double minutes (dmins), and intrachromosomal homogeneously staining regions (hsr) is not documented at nucleotide resolution. Using fluorescent in situ hybridization and whole genome sequencing, we studied a xenografted human oligodendroglioma where the co-amplification of the EGFR and MYC loci was present in the form of dmins at early passages and of an hsr at later passages. The amplified regions underwent multiple rearrangements and deletions during the formation of the dmins and their transformation into hsr. In both forms of amplification, non-homologous end-joining and microhomology-mediated end-joining rather than replication repair mechanisms prevailed in fusions. Small fragments, some of a few tens of base pairs, were associated in contigs. They came from clusters of breakpoints localized hundreds of kilobases apart in the amplified regions. The characteristics of some pairs of junctions suggest that at least some fragments were not fused randomly but could result from the concomitant repair of neighbouring breakpoints during the interaction of remote DNA sequences. This characterization at nucleotide resolution of the transition between extra- and intrachromosome amplifications highlights a hitherto uncharacterized organization of the amplified regions suggesting the involvement of new mechanisms in their formation. PMID:25378339

  20. DNA Electronic Circular Dichroism on the Inter-Base Pair Scale: An Experimental-Theoretical Case Study of the AT Homo-Oligonucleotide.

    PubMed

    Di Meo, Florent; Pedersen, Morten N; Rubio-Magnieto, Jenifer; Surin, Mathieu; Linares, Mathieu; Norman, Patrick

    2015-02-01

    A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment. PMID:26261947

  1. Actinophage R4 integrase-based site-specific chromosomal integration of non-replicative closed circular DNA.

    PubMed

    Miura, Takamasa; Nishizawa, Akito; Nishizawa, Tomoyasu; Asayama, Munehiko; Shirai, Makoto

    2016-06-01

    The actinophage R4 integrase (Sre)-based molecular genetic engineering system was developed for the chromosomal integration of multiple genes in Escherichia coli. A cloned DNA fragment containing two attP sites, green fluorescent protein (gfp) as a first transgene, and an antibiotic resistance gene as a selection marker was self-ligated to generate non-replicative closed circular DNA (nrccDNA) for integration. nrccDNA was introduced into attB-inserted E. coli cells harboring the plasmid expressing Sre by electroporation. The expressed Sre catalyzed site-specific integration between one of the two attP sites on nrccDNA and the attB site on the E. coli chromosome. The integration frequency was affected by the chromosomal location of the target site. A second nrccDNA containing two attB sites, lacZα encoding the alpha fragment of β-galactosidase as a transgene, and another antibiotic resistance gene was integrated into the residual attP site on the gfp-integrated E. coli chromosome via one of the two attB sites according to reiterating site-specific recombination. The integrants clearly exhibited β-galactosidase activity and green fluorescence, suggesting the simultaneous expression of multiple recombinant proteins in E. coli. The results of the present study showed that a step-by-step integration procedure using nrccDNA achieved the chromosomal integration of multiple genes. PMID:26870903

  2. Co-existence of circular and multiple linear amplicons in methotrexate-resistant Leishmania.

    PubMed Central

    Olmo, A; Arrebola, R; Bernier, V; González-Pacanowska, D; Ruiz-Pérez, L M

    1995-01-01

    Circular and linear amplicons were analyzed in detail in Leishmania tropica cells resistant to methotrexate (MTX). Both types of elements presented sequences related to the H locus and coexisted in resistant cells. The linear amplicons appeared first during the selection process (at 10 microM MTX) and varied with regard to size and structure in cells exposed to increasing concentrations of drug. The circular element was evident at higher concentrations (50 microMs) but was the major amplified DNA in cells resistant to 1000 microM MTX while the level of amplification of the linear elements remained low. The extrachromosomal DNAs were unstable in the absence of drug and their disappearance coincided with an increase in sensitivity to MTX. Mapping of the minichromosomes and the circular element showed that they were all constituted by inverted duplications. The circular amplicon contained an inverted repeat derived from the H locus that encompassed the pteridine reductase gene (PTR1) responsible for MTX resistance. The amplified segment in the linear amplicons was longer and included the pgpB and pgpC genes that encode P-glycoproteins of unknown function previously characterized in different Leishmania species. Images PMID:7659507

  3. TTV, a new human virus with single stranded circular DNA genome.

    PubMed

    Hino, Shigeo

    2002-01-01

    TT virus (TTV) was found in 1997 from a hepatitis patient without virus markers. However, the real impact of TTV on liver diseases remains uncertain to date. Due to the lack of suitable cell systems to support the growth of TTV, the biology of TTV is still obscure. This review tries to summarise the current status of TTV on aspects other than the taxonomic diversity of TTV. TTV was the first human virus with a single stranded circular DNA genome. TTV was considered to be a member of Circoviridae, but others suggested it conformed to a new family. TTV is distinct from ambisense viruses in the genus Circovirus, since the former genome is negative stranded. The genome structure of TTV is more related to chicken anaemia virus in the genus Gyrovirus, however, the sequence similarity is minimal except for a short stretch at 3816-3851 of TA278. Currently the working group is proposing the full name for TTV as TorqueTenoVirus and the TTV-like mini virus as TorqueTenoMiniVirus (TTMV) in a new genus Anellovirus (ring). TTVs are prevalent in non-human primates and human TTV can cross-infect chimpanzees. Furthermore, TTV sequences have been detected in chickens, pigs, cows and sheep. TTV can be transmitted by mother-to-child infection. However, within a year after birth, the prevalence reaches the same level for children born to both TTV-positive and TTV-negative mothers even without breast-feeding. The non-coding region surrounding a short 113 nt GC-rich stretch and occupying approximately one-third of the genome is considered to contain the putative replication origin. Three mRNAs are expressed by TTV, 3.0 and 1.2 and 1.0 kb species. A protein translated from the 3.0 kb mRNA is considered to be the major capsid protein as well as replicase. The nature of the proteins translated by the other two mRNAs are still putative. PMID:11987140

  4. Chromosomally and Extrachromosomally Mediated High-Level Gentamicin Resistance in Streptococcus agalactiae.

    PubMed

    Sendi, Parham; Furitsch, Martina; Mauerer, Stefanie; Florindo, Carlos; Kahl, Barbara C; Shabayek, Sarah; Berner, Reinhard; Spellerberg, Barbara

    2016-03-01

    Streptococcus agalactiae (group B Streptococcus [GBS]) is a leading cause of sepsis in neonates. The rate of invasive GBS disease in nonpregnant adults also continues to climb. Aminoglycosides alone have little or no effect on GBS, but synergistic killing with penicillin has been shown in vitro. High-level gentamicin resistance (HLGR) in GBS isolates, however, leads to the loss of a synergistic effect. We therefore performed a multicenter study to determine the frequency of HLGR GBS isolates and to elucidate the molecular mechanisms leading to gentamicin resistance. From eight centers in four countries, 1,128 invasive and colonizing GBS isolates were pooled and investigated for the presence of HLGR. We identified two strains that displayed HLGR (BSU1203 and BSU452), both of which carried the aacA-aphD gene, typically conferring HLGR. However, only one strain (BSU1203) also carried the previously described chromosomal gentamicin resistance transposon designated Tn3706. For the other strain (BSU452), plasmid purification and subsequent DNA sequencing resulted in the detection of plasmid pIP501 carrying a remnant of a Tn3 family transposon. Its ability to confer HLGR was proven by transfer into an Enterococcus faecalis isolate. Conversely, loss of HLGR was documented after curing both GBS BSU452 and the transformed E. faecalis strain from the plasmid. This is the first report showing plasmid-mediated HLGR in GBS. Thus, in our clinical GBS isolates, HLGR is mediated both chromosomally and extrachromosomally. PMID:26729498

  5. Identification of several clades of novel single-stranded circular DNA viruses with conserved stem-loop structures in pig feces

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Metagenomic analysis of fecal samples collected from swine with diarrhea detected sequences encoding a replication initiator protein (Rep) typically found in small circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses. Complete nucleotide sequences of ten novel genomes were cloned and determ...

  6. Experimental Analysis of a Paternally Inherited Extrachromosomal Factor

    PubMed Central

    Werren, John H.; van den Assem, Johannes

    1986-01-01

    Virtually all known cases of extrachromosomal inheritance involve cytoplasmic inheritance through the maternal line. Recently, a paternally transmitted factor that causes the production of all-male families has been discovered in a parasitic wasp. The wasp has haplodiploid sex determination: male offspring are haploid and usually develop from unfertilized eggs, whereas females are diploid and usually develop from fertilized eggs. It has been postulated that this paternal sex-ratio factor (psr) is either (1) an infectious agent (a venereal disease) that is transmitted to the female reproductive tract during copulation with an infected male and, subsequently, causes all-male families or (2) a male cytoplasmic factor that is transmitted by sperm to eggs upon egg fertilization and, somehow, causes loss of the paternal set of chromosomes.—Experimental evidence is presented which shows that the factor requires egg fertilization for transmission to the next generation; therefore, it is likely to be a cytoplasmic factor. Significant potential intragenomic conflict results from the presence of this factor and two other sex-ratio distorters in this wasp species. PMID:17246344

  7. Soma to germline inheritance of extrachromosomal genetic information via a LINE-1 reverse transcriptase-based mechanism.

    PubMed

    Spadafora, Corrado

    2016-08-01

    Mature spermatozoa are permeable to foreign DNA and RNA molecules. Here I propose a model, whereby extrachromosomal genetic information, mostly encoded in the form of RNA in somatic cells, can cross the Weismann barrier and reach epididymal spermatozoa. LINE-1 retrotransposon-derived reverse transcriptase (RT) can play key roles in the process by expanding the RNA-encoded information. Retrotransposon-encoded RT is stored in mature gametes, is highly expressed in early embryos and undifferentiated cells, and becomes downregulated in differentiated cells. In turn, RT plays a role in developmental control, as its inhibition arrests developmental progression of early embryos with globally altered transcriptomic profiles. Thus, sperm cells act as recipients, and transgenerational vectors of somatically derived genetic information which they pass to the next generation with the potential to modify the fate of the developing embryos. PMID:27315018

  8. Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage.

    PubMed

    Phan, Tung Gia; Mori, Daisuke; Deng, Xutao; Rajindrajith, Shaman; Ranawaka, Udaya; Fan Ng, Terry Fei; Bucardo-Rivera, Filemon; Orlandi, Patricia; Ahmed, Kamruddin; Delwart, Eric

    2015-08-01

    Viruses with small circular ssDNA genomes encoding a replication initiator protein can infect a wide range of eukaryotic organisms ranging from mammals to fungi. The genomes of two such viruses, a cyclovirus (CyCV-SL) and gemycircularvirus (GemyCV-SL) were detected by deep sequencing of the cerebrospinal fluids of Sri Lankan patients with unexplained encephalitis. One and three out of 201 CSF samples (1.5%) from unexplained encephalitis patients tested by PCR were CyCV-SL and GemyCV-SL DNA positive respectively. Nucleotide similarity searches of pre-existing metagenomics datasets revealed closely related genomes in feces from unexplained cases of diarrhea from Nicaragua and Brazil and in untreated sewage from Nepal. Whether the tropism of the cyclovirus and gemycircularvirus reported here include humans or other cellular sources in or on the human body remains to be determined. PMID:25839169

  9. Differential replication of circular DNA molecules co-injected into early Xenopus laevis embryos.

    PubMed Central

    Marini, N J; Hiriyanna, K T; Benbow, R M

    1989-01-01

    Replication of co-injected supercoiled DNA molecules in fertilized Xenopus eggs was monitored through the blastula stage of development. The extent of replication, as measured by 32P-dTMP incorporation into form I DNA, was directly proportional to the number of molecules, rather than the size, of the plasmid injected. Although only a small fraction of molecules of either template was replicated, incorporation was predominantly into full length daughter molecules. Over at least a 20-fold concentration range of microinjected DNA, injection of equal masses of DNA resulted in greater incorporation into the smaller form I DNA present in molar excess. The extent of incorporation into supercoiled DNA for a particular plasmid was apparently independent of the concentration of a second, co-injected plasmid. The relative extents of replication of co-injected supercoiled templates could be altered simply by changing the molar ratios of the templates. Images PMID:2762153

  10. In-Phase Assembly of Slim DNA Lattices with Small Circular DNA Motifs via Short Connections of 11 and 16 Base Pairs.

    PubMed

    Wang, Meng; Guo, Xin; Jiang, Chuan; Wang, Xuemei; Xiao, Shou-Jun

    2016-06-16

    Two kinds of stable motif were constructed: SAE (semi-crossover, antiparallel, even half-turns) tile from one small circular DNA molecule (42 or 64 nt) and two linear oligonucleotides; and DAE (double-crossover, antiparallel, even half-turns) tile from one small circular DNA molecule (42 or 64 nt) and four linear oligonucleotides. With the SAE tiles, in-phase assembly of SAE-E (SAE tiles with even half-turns as connections (-E)) with the shortest -E of 11 base pairs (bp) generated homogeneous nanotubes with an average length of over 14 μm and a diameter of 16-20 nm; with the DAE tiles, in-phase assembly of DAE-O (DAE tiles with odd half-turns as connections (-O)) with the shortest -O of 16 bp produced slim monolayer nanoyarns (25-30 nm wide), nanoscarfs (100-300 nm wide), and nanoribbons (∼100 nm wide). Interestingly, a phenomenon we term "knitting nanoyarns" into nanoscarfs was observed. Finally a curvature mechanism according to the ring rotation directions is suggested to explain the formation of nanotubes, wavy nanoyarns, nanoscarfs, and nanoribbons. PMID:27187004

  11. A set of mini-Mu transposons for versatile cloning of circular DNA and novel dual-transposon strategy for increased efficiency.

    PubMed

    Pulkkinen, Elsi; Haapa-Paananen, Saija; Turakainen, Hilkka; Savilahti, Harri

    2016-07-01

    Mu transposition-based cloning of DNA circles employs in vitro transposition reaction to deliver both the plasmid origin of replication and a selectable marker into the target DNA of interest. We report here the construction of a platform for the purpose that contains ten mini-Mu transposons with five different replication origins, enabling a variety of research approaches for the discovery and study of circular DNA. We also demonstrate that the simultaneous use of two transposons, one with the origin of replication and the other with selectable marker, is beneficial as it improves the cloning efficiency by reducing the fraction of autointegration-derived plasmid clones. The constructed transposons now provide a set of new tools for the studies on DNA circles and widen the applicability of Mu transposition based approaches to clone circular DNA from various sources. PMID:27387339

  12. Isolation of Protein-Associated Circular DNA from Healthy Cattle Serum

    PubMed Central

    Funk, Mathis; Gunst, Karin; Lucansky, Vincent; Müller, Hermann; zur Hausen, Harald

    2014-01-01

    Three replication-competent single-stranded DNA molecules sharing nucleotide similarity to transmissible spongiform encephalopathy (TSE)-associated isolate Sphinx 2.36 were isolated from healthy bovine serum. PMID:25169856

  13. Isolation of protein-associated circular DNA from healthy cattle serum.

    PubMed

    Funk, Mathis; Gunst, Karin; Lucansky, Vincent; Müller, Hermann; Zur Hausen, Harald; de Villiers, Ethel-Michele

    2014-01-01

    Three replication-competent single-stranded DNA molecules sharing nucleotide similarity to transmissible spongiform encephalopathy (TSE)-associated isolate Sphinx 2.36 were isolated from healthy bovine serum. PMID:25169856

  14. Acinetobacter phage genome is similar to Sphinx 2.36, the circular DNA copurified with TSE infected particles.

    PubMed

    Longkumer, Toshisangba; Kamireddy, Swetha; Muthyala, Venkateswar Reddy; Akbarpasha, Shaikh; Pitchika, Gopi Krishna; Kodetham, Gopinath; Ayaluru, Murali; Siddavattam, Dayananda

    2013-01-01

    While analyzing plasmids of Acinetobacter sp. DS002 we have detected a circular DNA molecule pTS236, which upon further investigation is identified as the genome of a phage. The phage genome has shown sequence similarity to the recently discovered Sphinx 2.36 DNA sequence co-purified with the Transmissible Spongiform Encephalopathy (TSE) particles isolated from infected brain samples collected from diverse geographical regions. As in Sphinx 2.36, the phage genome also codes for three proteins. One of them codes for RepA and is shown to be involved in replication of pTS236 through rolling circle (RC) mode. The other two translationally coupled ORFs, orf106 and orf96, code for coat proteins of the phage. Although an orf96 homologue was not previously reported in Sphinx 2.36, a closer examination of DNA sequence of Sphinx 2.36 revealed its presence downstream of orf106 homologue. TEM images and infection assays revealed existence of phage AbDs1 in Acinetobacter sp. DS002. PMID:23867905

  15. Acinetobacter phage genome is similar to Sphinx 2.36, the circular DNA copurified with TSE infected particles

    PubMed Central

    Longkumer, Toshisangba; Kamireddy, Swetha; Muthyala, Venkateswar Reddy; Akbarpasha, Shaikh; Pitchika, Gopi Krishna; Kodetham, Gopinath; Ayaluru, Murali; Siddavattam, Dayananda

    2013-01-01

    While analyzing plasmids of Acinetobacter sp. DS002 we have detected a circular DNA molecule pTS236, which upon further investigation is identified as the genome of a phage. The phage genome has shown sequence similarity to the recently discovered Sphinx 2.36 DNA sequence co-purified with the Transmissible Spongiform Encephalopathy (TSE) particles isolated from infected brain samples collected from diverse geographical regions. As in Sphinx 2.36, the phage genome also codes for three proteins. One of them codes for RepA and is shown to be involved in replication of pTS236 through rolling circle (RC) mode. The other two translationally coupled ORFs, orf106 and orf96, code for coat proteins of the phage. Although an orf96 homologue was not previously reported in Sphinx 2.36, a closer examination of DNA sequence of Sphinx 2.36 revealed its presence downstream of orf106 homologue. TEM images and infection assays revealed existence of phage AbDs1 in Acinetobacter sp. DS002. PMID:23867905

  16. Circularly permuted viral pRNA active and specific in the packaging of bacteriophage phi 29 DNA.

    PubMed

    Zhang, C; Trottier, M; Guo, P

    1995-03-10

    A viral-encoded 120-base pRNA has been shown to have an essential role in the packaging of bacteriophage phi 29 DNA. The finding that both the 5'- and 3'-termini of the pRNA are proximate and crucial for biological function (C. Zhang, C. Lee, and P. Guo, 1994, Virology, 201, 77-85) prompted investigation of the activity of circularly permuted pRNAs (cpRNA) and of the expandability and essentiality of bases extending from the termini. A 117-base pRNA with a deletion of three bases downstream of the proximal terminus was active in DNA packaging. Concatemeric DNAs containing two tandem pRNA genes separated by a short or a long loop sequence were constructed. The cpRNAs from these DNA templates were transcribed in vitro and shown to be active in phi 29 DNA packaging, with activity comparable to the parental (noncircularly permuted) pRNA, indicating that neither of the loops tested affected the activity and folding of the cpRNA. As few as four bases were sufficient to serve as a loop for the terminal 180 degree turn, and a loop as long as 27 bases did not affect the cpRNA structure and function. Eight cpRNAs were constructed to assess the effect of openings within the wild-type pRNA structure. Opening of the bulge at residue 38 did not affect cpRNA activity, but opening the bulge at residue 55 greatly reduced it. Although the sequence of the 5',3'-terminal loop was not important for the folding and activity of the cpRNA, the activities of cpRNAs with openings at individual bulges or hairpins were different, indicating that each region plays a different role in pRNA folding and function. Our results indicate that it is possible to generate active circularly permuted pRNA by assigning internal sites of the pRNA as new 3'- and 5'-termini. The creation of new variable ends makes the labeling of internal bases of the pRNA molecule possible and will facilitate the analysis of pRNA secondary and tertiary structure. PMID:7533964

  17. Single primer-mediated circular polymerase chain reaction for hairpin DNA cloning and plasmid editing.

    PubMed

    Huang, Jiansheng; Khan, Inamullah; Liu, Rui; Yang, Yan; Zhu, Naishuo

    2016-05-01

    We developed and validated a universal polymerase chain reaction (PCR) method, single primer circular (SPC)-PCR, using single primer to simultaneously insert and amplify a short hairpin sequence into a vector with a high success rate. In this method, the hairpin structure is divided into two parts and fused into a vector by PCR. Then, a single primer is used to cyclize the chimera into a mature short hairpin RNA (shRNA) expression vector. It is not biased by loop length or palindromic structures. Six hairpin DNAs with short 4-nucleotide loops were successfully cloned. Moreover, SPC-PCR was also applied to plasmid editing within 3 h with a success rate higher than 95%. PMID:26792375

  18. Discovery, Prevalence, and Persistence of Novel Circular Single-Stranded DNA Viruses in the Ctenophores Mnemiopsis leidyi and Beroe ovata.

    PubMed

    Breitbart, Mya; Benner, Bayleigh E; Jernigan, Parker E; Rosario, Karyna; Birsa, Laura M; Harbeitner, Rachel C; Fulford, Sidney; Graham, Carina; Walters, Anna; Goldsmith, Dawn B; Berger, Stella A; Nejstgaard, Jens C

    2015-01-01

    Gelatinous zooplankton, such as ctenophores and jellyfish, are important components of marine and brackish ecosystems and play critical roles in aquatic biogeochemistry. As voracious predators of plankton, ctenophores have key positions in aquatic food webs and are often successful invaders when introduced to new areas. Gelatinous zooplankton have strong impacts on ecosystem services, particularly in coastal environments. However, little is known about the factors responsible for regulating population dynamics of gelatinous organisms, including biological interactions that may contribute to bloom demise. Ctenophores are known to contain specific bacterial communities and a variety of invertebrate parasites and symbionts; however, no previous studies have examined the presence of viruses in these organisms. Building upon recent studies demonstrating a diversity of single-stranded DNA viruses that encode a replication initiator protein (Rep) in aquatic invertebrates, this study explored the presence of circular, Rep-encoding single-stranded DNA (CRESS-DNA) viruses in the ctenophores Mnemiopsis leidyi and Beroe ovata collected from the Skidaway River Estuary and Savannah River in Georgia, USA. Using rolling circle amplification followed by restriction enzyme digestion, this study provides the first evidence of viruses in ctenophores. Investigation of four CRESS-DNA viruses over an 8-month period using PCR demonstrated temporal trends in viral prevalence and indicated that some of the viruses may persist in ctenophore populations throughout the year. Although future work needs to examine the ecological roles of these ctenophore-associated viruses, this study indicates that viral infection may play a role in population dynamics of gelatinous zooplankton. PMID:26733971

  19. Discovery, Prevalence, and Persistence of Novel Circular Single-Stranded DNA Viruses in the Ctenophores Mnemiopsis leidyi and Beroe ovata

    PubMed Central

    Breitbart, Mya; Benner, Bayleigh E.; Jernigan, Parker E.; Rosario, Karyna; Birsa, Laura M.; Harbeitner, Rachel C.; Fulford, Sidney; Graham, Carina; Walters, Anna; Goldsmith, Dawn B.; Berger, Stella A.; Nejstgaard, Jens C.

    2015-01-01

    Gelatinous zooplankton, such as ctenophores and jellyfish, are important components of marine and brackish ecosystems and play critical roles in aquatic biogeochemistry. As voracious predators of plankton, ctenophores have key positions in aquatic food webs and are often successful invaders when introduced to new areas. Gelatinous zooplankton have strong impacts on ecosystem services, particularly in coastal environments. However, little is known about the factors responsible for regulating population dynamics of gelatinous organisms, including biological interactions that may contribute to bloom demise. Ctenophores are known to contain specific bacterial communities and a variety of invertebrate parasites and symbionts; however, no previous studies have examined the presence of viruses in these organisms. Building upon recent studies demonstrating a diversity of single-stranded DNA viruses that encode a replication initiator protein (Rep) in aquatic invertebrates, this study explored the presence of circular, Rep-encoding single-stranded DNA (CRESS-DNA) viruses in the ctenophores Mnemiopsis leidyi and Beroe ovata collected from the Skidaway River Estuary and Savannah River in Georgia, USA. Using rolling circle amplification followed by restriction enzyme digestion, this study provides the first evidence of viruses in ctenophores. Investigation of four CRESS-DNA viruses over an 8-month period using PCR demonstrated temporal trends in viral prevalence and indicated that some of the viruses may persist in ctenophore populations throughout the year. Although future work needs to examine the ecological roles of these ctenophore-associated viruses, this study indicates that viral infection may play a role in population dynamics of gelatinous zooplankton. PMID:26733971

  20. Formation of AAV Single Stranded DNA Genome from a Circular Plasmid in Saccharomyces cerevisiae

    PubMed Central

    Cervelli, Tiziana; Backovic, Ana; Galli, Alvaro

    2011-01-01

    Adeno-associated virus (AAV)-based vectors are promising tools for targeted transfer in gene therapy studies. Many efforts have been accomplished to improve production and purification methods. We thought to develop a simple eukaryotic system allowing AAV replication which could provide an excellent opportunity for studying AAV biology and, more importantly, for AAV vector production. It has been shown that yeast Saccharomyces cerevisiae is able to replicate and form the capsid of many viruses. We investigated the ability of the yeast Saccharomyces cerevisiae to carry out the replication of a recombinant AAV (rAAV). When a plasmid containing a rAAV genome in which the cap gene was replaced with the S. cerevisiae URA3 gene, was co-transformed in yeast with a plasmid expressing Rep68, a significant number of URA3+ clones were scored (more than 30-fold over controls). Molecular analysis of low molecular weight DNA by Southern blotting revealed that single stranded DNA is formed and that the plasmid is entirely replicated. The ssDNA contains the ITRs, URA3 gene and also vector sequences suggesting the presence of two distinct molecules. Its formation was dependent on Rep68 expression and ITR. These data indicate that DNA is not obtained by the canonical AAV replication pathway. PMID:21853137

  1. Formation of AAV single stranded DNA genome from a circular plasmid in Saccharomyces cerevisiae.

    PubMed

    Cervelli, Tiziana; Backovic, Ana; Galli, Alvaro

    2011-01-01

    Adeno-associated virus (AAV)-based vectors are promising tools for targeted transfer in gene therapy studies. Many efforts have been accomplished to improve production and purification methods. We thought to develop a simple eukaryotic system allowing AAV replication which could provide an excellent opportunity for studying AAV biology and, more importantly, for AAV vector production. It has been shown that yeast Saccharomyces cerevisiae is able to replicate and form the capsid of many viruses. We investigated the ability of the yeast Saccharomyces cerevisiae to carry out the replication of a recombinant AAV (rAAV). When a plasmid containing a rAAV genome in which the cap gene was replaced with the S. cerevisiae URA3 gene, was co-transformed in yeast with a plasmid expressing Rep68, a significant number of URA3(+) clones were scored (more than 30-fold over controls). Molecular analysis of low molecular weight DNA by Southern blotting revealed that single stranded DNA is formed and that the plasmid is entirely replicated. The ssDNA contains the ITRs, URA3 gene and also vector sequences suggesting the presence of two distinct molecules. Its formation was dependent on Rep68 expression and ITR. These data indicate that DNA is not obtained by the canonical AAV replication pathway. PMID:21853137

  2. Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes.

    PubMed

    Delwart, Eric; Li, Linlin

    2012-03-01

    The genomes of numerous circoviruses and distantly related circular ssDNA viruses encoding a rolling circle replication initiator protein (Rep) have been characterized from the tissues of mammals, fish, insects, plants (geminivirus and nanovirus), in human and animal feces, in an algae cell, and in diverse environmental samples. We review the genome organization, phylogenetic relationships and initial prevalence studies of cycloviruses, a proposed new genus in the Circoviridae family. Viral fossil rep sequences were also recently identified integrated on the chromosomes of mammals, frogs, lancelets, crustaceans, mites, gastropods, roundworms, placozoans, hydrozoans, protozoans, land plants, fungi, algae, and phytoplasma bacterias and their plasmids, reflecting the very wide past host range of rep bearing viruses. An ancient origin for viruses with Rep-encoding small circular ssDNA genomes, predating the diversification of eukaryotes, is discussed. The cellular hosts and pathogenicity of many recently described rep-containing circular ssDNA genomes remain to be determined. Future studies of the virome of single cell and multi-cellular eukaryotes are likely to further extend the known diversity and host-range of small rep-containing circular ssDNA viral genomes. PMID:22155583

  3. Novel Replication-Competent Circular DNA Molecules from Healthy Cattle Serum and Milk and Multiple Sclerosis-Affected Human Brain Tissue

    PubMed Central

    Whitley, Corinna; Gunst, Karin; Müller, Hermann; Funk, Mathis; zur Hausen, Harald

    2014-01-01

    Epidemiological data point to the involvement of a cow milk factor in the etiology of multiple sclerosis (MS). Eleven circular DNA molecules closely related to transmissible spongiform encephalopathy (TSE)-associated isolate Sphinx 1.76 were isolated from healthy cattle serum, cow milk, and serum and brain tissue from MS patients. PMID:25169859

  4. Novel replication-competent circular DNA molecules from healthy cattle serum and milk and multiple sclerosis-affected human brain tissue.

    PubMed

    Whitley, Corinna; Gunst, Karin; Müller, Hermann; Funk, Mathis; Zur Hausen, Harald; de Villiers, Ethel-Michele

    2014-01-01

    Epidemiological data point to the involvement of a cow milk factor in the etiology of multiple sclerosis (MS). Eleven circular DNA molecules closely related to transmissible spongiform encephalopathy (TSE)-associated isolate Sphinx 1.76 were isolated from healthy cattle serum, cow milk, and serum and brain tissue from MS patients. PMID:25169859

  5. Elimination of extrachromosomally amplified MYC genes from human tumor cells reduces their tumorigenicity.

    PubMed Central

    Von Hoff, D D; McGill, J R; Forseth, B J; Davidson, K K; Bradley, T P; Van Devanter, D R; Wahl, G M

    1992-01-01

    Oncogene amplification has been observed in a broad spectrum of human tumors and has been associated with a poor prognosis for patients with several different types of malignancies. Importantly, at biopsy, the amplified genes localize to acentric extrachromosomal elements such as double-minute chromosomes (DMs) in the vast majority of cases. We show here that treatment of several human tumor cell lines with low concentrations of hydroxyurea accelerates the loss of their extrachromosomally amplified oncogenes. The decreases in MYC copy number in a human tumor cell line correlated with a dramatic reduction in cloning efficiency in soft agar and tumorigenicity in nude mice. No effect on gene copy number or tumorigenicity was observed for a closely related cell line containing the same number of chromosomally amplified MYC genes. One step involved in the accelerated loss of extrachromosomal elements is shown to involve their preferential entrapment of DMs within micronuclei. The data suggest that agents that accelerate the loss of extrachromosomally amplified genes could provide valuable tools for moderating the growth of a large number of human neoplasms. Images PMID:1518843

  6. Detection of Short-Range DNA Interactions in Mammalian Cells Using High-Resolution Circular Chromosome Conformation Capture Coupled to Deep Sequencing.

    PubMed

    Millau, Jean-François; Gaudreau, Luc

    2015-01-01

    DNA interactions shape the genome to physically and functionally connect regulatory elements to their target genes. Studying these interactions is crucial to understanding the molecular mechanisms that regulate gene expression. In this chapter, we present a protocol for high-resolution circular chromosome conformation capture coupled to deep sequencing. This methodology allows to investigate short-range DNA interactions (<100 kbp) and to obtain high-resolution DNA interaction maps of loci. It is a powerful tool to explore how regulatory elements and genes are connected together. PMID:26404155

  7. Diverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica).

    PubMed

    Zawar-Reza, Peyman; Argüello-Astorga, Gerardo R; Kraberger, Simona; Julian, Laurel; Stainton, Daisy; Broady, Paul A; Varsani, Arvind

    2014-08-01

    Antarctica has some of the harshest environmental conditions for existence of life on Earth. In this pilot study we recovered eight diverse circular single-stranded DNA (ssDNA) viral genome sequences (1904-3120 nts) from benthic mats dominated by filamentous cyanobacteria in a freshwater pond on the McMurdo Ice Shelf sampled in 1988. All genomes contain two to three major open reading frames (ORFs) that are uni- or bi-directionally transcribed and all have an ORF encoding a replication-associated protein (Rep). In one genome, the second ORF has similarity to a capsid protein (CP) of Nepavirus which is most closely related to geminiviruses. Additionally, all genomes have two intergenic regions that contain putative stem loop structures, six genomes have NANTATTAC as the nonanucleotide motif, while one has CCTTATTAC, and another has a non-canonical stem loop. In the large intergenic region, we identified iterative sequences flanking the putative stem-loop elements which are a hallmark of most circular ssDNA viruses encoding rolling circle replication (RCR) initiators of the HUH endonuclease superfamily. The Reps encoded by ssDNA viral genomes recovered in this study shared <38% pairwise identity to all other Reps of known ssDNA viruses. A previous study on Lake Limnopolar (Livingston Island, South Shetland Islands), using next-generation sequencing identified circular ssDNA viruses and their putative Reps share <35% pairwise identity to those from the viral genomes removed in this study. It is evident from our pilot study that the global diversity of ssDNA viruses is grossly underestimated and there is limited knowledge on ssDNA viruses in Antarctica. PMID:24859088

  8. Discovery of a novel mastrevirus and alphasatellite-like circular DNA in dragonflies (Epiprocta) from Puerto Rico.

    PubMed

    Rosario, Karyna; Padilla-Rodriguez, Marco; Kraberger, Simona; Stainton, Daisy; Martin, Darren P; Breitbart, Mya; Varsani, Arvind

    2013-01-01

    Geminiviruses have emerged as serious agricultural pathogens. Despite all the species that have been already catalogued, new molecular techniques continue to expand the diversity and geographical ranges of these single-stranded DNA viruses and their associated satellite molecules. Since all geminiviruses are insect-transmitted, examination of insect vector populations through vector-enabled metagenomics (VEM) has been recently used to investigate the diversity of geminiviruses transmitted by a specific vector in a given region. Here we used a more comprehensive adaptation of the VEM approach by surveying small circular DNA viruses found within top insect predators, specifically dragonflies (Epiprocta). This 'predator-enabled' approach is not limited to viral groups transmitted by specific vectors since dragonflies can accumulate the wide range of viruses transmitted by their diverse insect prey. Analysis of six dragonflies collected from an agricultural field in Puerto Rico culminated in the discovery of the first mastrevirus (Dragonfly-associated mastrevirus; DfasMV) and alphasatellite molecule (Dragonfly-associated alphasatellite; Dfas-alphasatellite) from the Caribbean. Since DfasMV and Dfas-alphasatellite are divergent from the limited number of sequences that have been reported from the Americas, this study unequivocally demonstrates that there have been at least two independent past introductions of both mastreviruses and alphasatellites to the New World. Overall, the use of predacious insects as sampling tools can profoundly alter our views of natural plant virus diversity and biogeography by allowing the discovery of novel geminiviruses and associated satellite molecules without a priori knowledge of the types of viruses or insect vectors in a given area. PMID:23116593

  9. Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins

    PubMed Central

    Rosario, Karyna; Schenck, Ryan O.; Harbeitner, Rachel C.; Lawler, Stephanie N.; Breitbart, Mya

    2015-01-01

    Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses were originally thought to only infect plants and vertebrates, recent studies have identified these viruses in a number of invertebrates. To further explore CRESS-DNA viruses in the marine environment, this study surveyed CRESS-DNA viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA viruses that included approximately one third of the marine invertebrate associated viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap) encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs), which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these viruses. PMID:26217327

  10. I. RNA A-to-Z transitions and DNA B-to-Z transitions. II. Circular intensity differential scattering of cholesteric liquid crystals

    SciTech Connect

    Hall, K.B.

    1984-12-01

    The thesis is composed of two parts: Part I describes the conformational transitions of DNA and RNA from right-handed helices to left-handed helices. These transitions, referred to as B-to-Z for DNA and A-to-Z for RNA, are effected by specific solvents and temperatures. Various spectroscopic methods show the details of the transition, with near ultraviolet circular dichroism (CD) indicating the differences in the transition moments between the DNA and RNA, and nuclear magnetic resonance (NMR) and vacuum ultraviolet CD indicating that the structures are very similar. Thermodynamic parameters for the DNA polymer transition are calculated, indicating that the transition is not isoenthalpic as previously postulated. A tetramer of RNA, rCGCG, is used for obtaining thermodynamic data on the RNA A-to-Z transition. This short sequence also appears to adopt a left-handed structure, but thermodynamic data indicates that the A-form is more favorable. Part II describes the circular differential scattering (CIDS) of cholesteric liquid crystals. These compounds have a natural helical order, with enormous scattering power. The scattering patterns obtained from the liquid crystals are influenced by the helical parameters such as pitch and handedness, as predicted by the theory. It is hoped that these model compounds will provide information for the interpretation of the CIDS spectra obtained for biological samples, such as gels of DNA or oriented viruses.

  11. Ultrasensitive electrochemical biosensor for specific detection of DNA based on molecular beacon mediated circular strand displacement polymerization and hyperbranched rolling circle amplification.

    PubMed

    Li, Xiaolu; Guo, Jing; Zhai, Qian; Xia, Jing; Yi, Gang

    2016-08-31

    Using a cascade signal amplification strategy, an ultrasensitive electrochemical biosensor for specific detection of DNA based on molecular beacon (MB) mediated circular strand displacement polymerization (CSDP) and hyperbranched rolling circle amplification (HRCA) was proposed. The hybridization of MB probe to target DNA resulted in a conformational change of the MB and triggered the CSDP in the presence of bio-primer and Klenow fragment (KF exo(-)), leading to multiple biotin-tagged DNA duplex. Furthermore, the HRCA was implemented to product amounts of double-stranded DNA (ds-DNA) fragments using phi29 DNA polymerase via biotin-streptavidin interaction. After the product of HRCA binded numerous biotinylated detection probes, an ultrasensitive electrochemical readout by further employing the streptavidin-alkaline phosphatase. The proposed biosensor exhibited excellent detection sensitivity and specificity with a log-linear response to target DNA from 0.01 fM to 10 pM as low as 8.9 aM. The proposed method allowed DNA detection with simplicity, rapidness, low cost and high specificity, which might have the potential for application in clinical molecular diagnostics and environmental monitoring. PMID:27506343

  12. DNA replication origins in archaea

    PubMed Central

    Wu, Zhenfang; Liu, Jingfang; Yang, Haibo; Xiang, Hua

    2014-01-01

    DNA replication initiation, which starts at specific chromosomal site (known as replication origins), is the key regulatory stage of chromosome replication. Archaea, the third domain of life, use a single or multiple origin(s) to initiate replication of their circular chromosomes. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several conserved repeats (origin recognition box, ORB) that are located adjacent to a replication initiator gene. Both the ORB sequence and the adjacent initiator gene are considerably diverse among different replication origins, while in silico and genetic analyses have indicated the specificity between the initiator genes and their cognate origins. These replicator–initiator pairings are reminiscent of the oriC-dnaA system in bacteria, and a model for the negative regulation of origin activity by a downstream cluster of ORB elements has been recently proposed in haloarchaea. Moreover, comparative genomic analyses have revealed that the mosaics of replicator-initiator pairings in archaeal chromosomes originated from the integration of extrachromosomal elements. This review summarizes the research progress in understanding of archaeal replication origins with particular focus on the utilization, control and evolution of multiple replication origins in haloarchaea. PMID:24808892

  13. Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes

    PubMed Central

    Delwart, Eric; Li, Linlin

    2011-01-01

    The genomes of numerous circoviruses and distantly related circular DNA viruses encoding a rolling circle replication initiator protein (Rep) have been characterized from the tissues of mammals, fish, insects, and plants (geminivirus and nanovirus), human and animal feces, in an algae cell, and in diverse environmental samples. We review the genome organization, phylogenetic relationships and initial prevalence studies of cycloviruses, a proposed new genus in the Circoviridae family. Viral fossil rep sequences were also identified integrated on the chromosomes of mammals, frogs, lancelets, crustaceans, mites, gastropods, roundworms, placozoans, hydrozoans, protozoans, land plants, fungi, algae, and phytoplasma bacterias and their plasmids, reflecting their past host range. An ancient origin for viruses with rep-encoding single stranded small circular genomes, predating the diversification of eukaryotes, is discussed. The cellular hosts and pathogenicity of many recently described rep-containing circular genomes remain to be determined. Future studies of the virome of single cell and multi-cellular eukaryotes are likely to further extend the known diversity and host-range of small rep-containing circular viral genomes. PMID:22155583

  14. Chromosomal and extrachromosomal deoxyribonucleic acid from four bacterial endosymbionts derived from stock 51 of Paramecium tetraurelia.

    PubMed Central

    Dilts, J A

    1977-01-01

    Four variant lines of stock 51 kappa (Paramecium tetraurelia) were screened for the presence of covalently closed circular (CCC) deoxyribonucleic acid (DNA). Stock 51m43 kappa, a nonkiller resistant to 51 killing, contained four classes of CCC DNA: 2.9 X 10(7), 9.7 X 10(7), and 11.8 X 10(7) daltons. The buoyant densities of 51m43 kappa chromosomal and CCC DNA were 1.700 and 1.698 g/cm3, respectively. Stock 51m43 pi, a sensitive nonkiller, contained two CCC species: 0.3 X 10(7) and 4.4 X 10(7) daltons. The buoyant densities of both the chromosomal and CCC DNA were 1.694 to 1.695 g/cm3. Three sizes of CCC DNA were found in 51m1 pi: 0.3 X 10(7), 2.3 X 10(7), and 4.5 X 10(7) daltons. The buoyant densities of both the chromosoaml DNA and the CC DNA were 1.694 to 1.695 g/cm3. It is not known whether 51m1 kappa, a sensitive spinner killer, contains CCC DNA. The buoyant density of its chromosomal DNA was 1.703 g/cm3. Of the four variant lines, only 51m43 kappa appears to be a mutant of 51 kappa. The chromosomal and CCC DNAs of 51m43 kappa have the same buoyant densities as those of 51 kappa; in addition 51m43 kappa contain a CCC molecule the same size as that found in 51 kappa (2.8 x 10(7) daltons). The three other lines are probably bacterial species that are distinct from 51 kappa and which, at one time, were co-inhabitants with 51 kappa in stock 51 paramecia. PMID:838691

  15. Circular Coinduction

    NASA Technical Reports Server (NTRS)

    Rosu, Grigore; Goguen, Joseph; Norvig, Peter (Technical Monitor)

    2001-01-01

    Circular coinduction is a technique for behavioral reasoning that extends cobasis coinduction to specifications with circularities. Because behavioral satisfaction is not recursively enumerable, no algorithm can work for every behavioral statement. However. algorithms using circular coinduction can prove every practical behavioral result that we know. This paper proves the correctness of circular coinduction and some consequences.

  16. Association of Hepatitis B Virus Covalently Closed Circular DNA and Human APOBEC3B in Hepatitis B Virus-Related Hepatocellular Carcinoma.

    PubMed

    Luo, Xuan; Huang, Yao; Chen, Yanmeng; Tu, Zeng; Hu, Jieli; Tavis, John E; Huang, Ailong; Hu, Yuan

    2016-01-01

    Chronic Hepatitis B Virus (HBV) infections can progresses to liver cirrhosis and hepatocellular carcinoma (HCC). The HBV covalently-closed circular DNA cccDNA is a key to HBV persistence, and its degradation can be induced by the cellular deaminase APOBEC3. This study aimed to measure the distribution of intrahepatic cccDNA levels and evaluate the association between levels of cccDNA and APOBEC3 in HCC patients. Among 49 HCC patients, 35 matched cancerous and contiguous noncancerous liver tissues had detectable cccDNA, and the median intrahepatic cccDNA in the cancerous tissues (CT) was significantly lower than in the contiguous noncancerous tissues (CNCT) (p = 0.0033). RCA (rolling circle amplification), followed by 3D-PCR identified positive amplification in 27 matched HCC patients. Sequence analysis indicated G to A mutations accumulated to higher levels in CT samples compared to CNCT samples, and the dinucleotide context showed preferred editing in the GpA context. Among 7 APOBEC3 genes, APOBEC3B was the only one up-regulated in cancerous tissues both at the transcriptional and protein levels (p < 0.05). This implies APOBEC3B may contribute to cccDNA editing and subsequent degradation in cancerous tissues. PMID:27310677

  17. Association of Hepatitis B Virus Covalently Closed Circular DNA and Human APOBEC3B in Hepatitis B Virus-Related Hepatocellular Carcinoma

    PubMed Central

    Chen, Yanmeng; Tu, Zeng; Hu, Jieli; Tavis, John E.; Huang, Ailong; Hu, Yuan

    2016-01-01

    Chronic Hepatitis B Virus (HBV) infections can progresses to liver cirrhosis and hepatocellular carcinoma (HCC). The HBV covalently-closed circular DNA cccDNA is a key to HBV persistence, and its degradation can be induced by the cellular deaminase APOBEC3. This study aimed to measure the distribution of intrahepatic cccDNA levels and evaluate the association between levels of cccDNA and APOBEC3 in HCC patients. Among 49 HCC patients, 35 matched cancerous and contiguous noncancerous liver tissues had detectable cccDNA, and the median intrahepatic cccDNA in the cancerous tissues (CT) was significantly lower than in the contiguous noncancerous tissues (CNCT) (p = 0.0033). RCA (rolling circle amplification), followed by 3D-PCR identified positive amplification in 27 matched HCC patients. Sequence analysis indicated G to A mutations accumulated to higher levels in CT samples compared to CNCT samples, and the dinucleotide context showed preferred editing in the GpA context. Among 7 APOBEC3 genes, APOBEC3B was the only one up-regulated in cancerous tissues both at the transcriptional and protein levels (p < 0.05). This implies APOBEC3B may contribute to cccDNA editing and subsequent degradation in cancerous tissues. PMID:27310677

  18. Detection of Hepatitis B Virus Covalently Closed Circular DNA in the Plasma of Iranian HBeAg-Negative Patients With Chronic Hepatitis B

    PubMed Central

    Tajik, Zahra; Keyvani, Hossein; Bokharaei-Salim, Farah; Zolfaghari, Mohammad Reza; Fakhim, Shahin; Keshvari, Maryam; Alavian, Seyed Moayed

    2015-01-01

    Background: Covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV) is a marker of HBV replication in the liver of patients infected with HBV. Objectives: This study aimed to investigate the association between the presence of cccDNA in the plasma samples of Iranian treatment-naive patients with chronic hepatitis B infection and HBV viral load and HBsAg levels. Patients and Methods: From April 2012 to May 2015, 106 treatment-naive patients with chronic hepatitis B infection were enrolled in this cross-sectional study. The HBsAg titer was measured by the Roche HBsAg II assay on the Cobas e411 system, and HBV DNA quantitation was performed using the COBAS TaqMan 48 kit. Real-time polymerase chain reaction was performed for the detection of HBV cccDNA. Results: The mean (SD) age of the patients was 41.1 ± 12.4 years (range, 20 - 62 years). From a total of 106 study participants, 67 (63.2%) were males. The HBV cccDNA was detected in plasma specimens in 19 (17.9%) out of the total 106 patients, and a significant relationship was found between the presence of cccDNA in plasma sample of males (23.9%) and females (7.7%) (P = 0.039). Also, a significant correlation was found between the presence of cccDNA in plasma sample of the patients and HBV viral load level (P < 0.0001) and HBsAg titer (P = 0.0043). Conclusions: This study showed that cccDNA can be detected in the plasma specimen of 17.9% of Iranian treatment-naive patients with chronic hepatitis B infection. Therefore, designing prospective studies focusing on the detection of cccDNA in these patients would provide more information. PMID:26504471

  19. One-step cloning and chromosomal integration of DNA.

    PubMed

    St-Pierre, François; Cui, Lun; Priest, David G; Endy, Drew; Dodd, Ian B; Shearwin, Keith E

    2013-09-20

    We describe "clonetegration", a method for integrating DNA into prokaryotic chromosomes that approaches the simplicity of cloning DNA within extrachromosomal vectors. Compared to existing techniques, clonetegration drastically decreases the time and effort needed for integration of single or multiple DNA fragments. Additionally, clonetegration facilitates cloning and expression of genetic elements that are impossible to propagate within typical multicopy plasmids. PMID:24050148

  20. Sub-femtomolar electrochemical detection of DNA using surface circular strand-replacement polymerization and gold nanoparticle catalyzed silver deposition for signal amplification.

    PubMed

    Gao, Fenglei; Zhu, Zhu; Lei, Jianping; Geng, Yao; Ju, Huangxian

    2013-01-15

    A highly sensitive method was developed for detection of target DNA. This method combined circular strand-displacement polymerization (CSRP) with silver enhancement to achieve dual signal amplification. After molecular beacon (MB) hybridized with target DNA, the reporter gold nanoparticle (Au NPs) was attached to an electrode surface by hybridization between Au NP labeled primer and stem part of the MB to initiate a polymerization of DNA strand, which led to the release of target and another polymerization cycle. Thus the CSRP produced the multiplication of target-related reporter Au NPs on the surface. The Au NPs then catalyzed silver deposition for subsequent stripping analysis of silver. The dual signal amplification offered a dramatic enhancement of the stripping response. This signal could discriminate perfect matched target DNA from 1-base mismatch DNA. The dynamic range of the sequence-specific DNA detection was from 10(-16) to 10(-12)mol L(-1) with a detection limit down to sub-femtomolar level. This proposed method exhibited an efficient amplification performance, and would open new opportunities for sensitive detection of other biorecognition events. PMID:22883748

  1. Metagenomic identification of a nodavirus and a circular ssDNA virus in semi-purified viral nucleic acids from the hepatopancreas of healthy Farfantepenaeus duorarum shrimp.

    PubMed

    Ng, Terry Fei; Alavandi, Shankar; Varsani, Arvind; Burghart, Scott; Breitbart, Mya

    2013-09-01

    Fisheries and aquaculture are impacted sporadically by newly emerged viral diseases. In most cases, searches for a causative pathogen only occur after a serious disease has emerged. As random shotgun sequencing (metagenomics) offers opportunities to identify novel viruses preemptively, the method was tested on nucleic acids extracted from the hepatopancreas of 12 healthy northern pink shrimp Farfantepenaeus duorarum captured from the Gulf of Mexico. Among the sequences, a nodavirus (Farfantepenaeus duorarum nodavirus, FdNV) and a virus with similarities to circoviruses and cycloviruses that possess circular single-stranded DNA (ssDNA) genomes, were identified. The FdNV genome sequence was most closely related phylogenetically to nodaviruses causing white tail disease in Macrobrachium rosenbergii and muscle necrosis disease in Litopenaeus vannamei. While the circular ssDNA virus represents the third to be detected in association with a marine invertebrate, transmission trials are needed to confirm its infectivity for F. duorarum. This study highlights the potential for using metagenomic approaches in fisheries and aquaculture industries to identify new potential pathogens in asymptomatic marine invertebrates, uncharacterized pathogens causing a new disease, or multiple pathogens associated with disease syndromes. PMID:23999707

  2. Analysis of the VPE sequences in the Caenorhabditis elegans vit-2 promoter with extrachromosomal tandem array-containing transgenic strains.

    PubMed Central

    MacMorris, M; Spieth, J; Madej, C; Lea, K; Blumenthal, T

    1994-01-01

    The Caenorhabditis elegans vit genes, encoding vitellogenins, are abundantly expressed in the adult hermaphrodite intestine. Two repeated elements, vit promoter element 1 (VPE1 [TGTCAAT]) and VPE2 (CTGATAA), have been identified in the 5' flanking DNA of each of the vit genes of C. elegans and Caenorhabditis briggsae. These elements have previously been shown to be needed for correctly regulated expression of a vit-2/vit-6 fusion gene in low-copy-number, integrated transgenes. Here we extend the analysis of the function of VPE1 and VPE2 by using transgenic lines carrying large, extrachromosomal arrays of the test genes. The results validate the use of such arrays for transgenic analysis of gene regulation in C. elegans, by confirming previous findings showing that the VPE1 at -45 and both VPE2s are sites of activation. Additional experiments now indicate that when the -45 VPE1 is inverted or replaced by a VPE2, nearly total loss of promoter function results, suggesting that the highly conserved -45 VPE1 plays a unique role in vit-2 promoter function. In contrast, single mutations eliminating the three upstream VPE1s are without effect. However, in combination in double and triple mutants, these upstream VPE1 mutations cause drastic reductions in expression levels. The -150 VPE2 can be replaced by a XhoI site (CTCGAG), and the -90 VPE2 can be eliminated, as long as the overlapping VPE1 is left intact, but when these two replacements are combined, activity is lost. Thus, the promoter must have at least one VPE2 and it must have at least two VPE1s, one at -45 and one additional upstream element. Images PMID:8264616

  3. Kaposi's sarcoma-associated herpesvirus LANA recruits the DNA polymerase clamp loader to mediate efficient replication and virus persistence

    PubMed Central

    Sun, Qiming; Tsurimoto, Toshiki; Juillard, Franceline; Li, Lin; Li, Shijun; De León Vázquez, Erika; Chen, She; Kaye, Kenneth

    2014-01-01

    Kaposi's sarcoma-associated herpesvirus (KSHV) latently infects tumor cells and persists as a multiple-copy, extrachromosomal, circular episome. To persist, the viral genome must replicate with each cell cycle. The KSHV latency-associated nuclear antigen (LANA) mediates viral DNA replication and persistence, but little is known regarding the underlying mechanisms. We find that LANA recruits replication factor C (RFC), the DNA polymerase clamp [proliferating cell nuclear antigen (PCNA)] loader, to drive DNA replication efficiently. Mutated LANA lacking RFC interaction was deficient for LANA-mediated DNA replication and episome persistence. RFC depletion had a negative impact on LANA’s ability to replicate and maintain viral DNA in cells containing artificial KSHV episomes or in infected cells, leading to loss of virus. LANA substantially increased PCNA loading onto DNA in vitro and recruited RFC and PCNA to KSHV DNA in cells. These findings suggest that PCNA loading is a rate-limiting step in DNA replication that is incompatible with viral survival. LANA enhancement of PCNA loading permits efficient virus replication and persistence, revealing a previously unidentified mechanism for KSHV latency. PMID:25071216

  4. Single molecule analysis of DNA wrapping and looping by a circular 14mer wheel of the bacteriophage 186 CI repressor.

    PubMed

    Wang, Haowei; Dodd, Ian B; Dunlap, David D; Shearwin, Keith E; Finzi, Laura

    2013-06-01

    The lytic-lysogenic decision in bacteriophage 186 is governed by the 186 CI repressor protein in a unique way. The 186 CI is proposed to form a wheel-like oligomer that can mediate either wrapped or looped nucleoprotein complexes to provide the cooperative and competitive interactions needed for regulation. Although consistent with structural, biochemical and gene expression data, many aspects of this model are based on inference. Here, we use atomic force microscopy (AFM) to reveal the various predicted wrapped and looped species, and new ones, for CI regulation of lytic and lysogenic transcription. Automated AFM analysis showed CI particles of the predicted dimensions on the DNA, with CI multimerization favoured by DNA binding. Measurement of the length of the wrapped DNA segments indicated that CI may move on the DNA, wrapping or releasing DNA on either side of the wheel. Tethered particle motion experiments were consistent with wrapping and looping of DNA by CI in solution, where in contrast to λ repressor, the looped species were exceptionally stable. The CI regulatory system provides an intriguing comparison with that of nucleosomes, which share the ability to wrap and release similar sized segments of DNA. PMID:23620280

  5. Temperate membrane-containing halophilic archaeal virus SNJ1 has a circular dsDNA genome identical to that of plasmid pHH205.

    PubMed

    Zhang, Ziqian; Liu, Ying; Wang, Shuai; Yang, Di; Cheng, Yichen; Hu, Jiani; Chen, Jin; Mei, Yunjun; Shen, Ping; Bamford, Dennis H; Chen, Xiangdong

    2012-12-20

    A temperate haloarchaeal virus, SNJ1, was induced from the lysogenic host, Natrinema sp. J7-1, with mitomycin C, and the virus produced plaques on lawns of Natrinema sp. J7-2. Optimization of the induction conditions allowed us to increase the titer from ~10(4) PFU/ml to ~10(11) PFU/ml. Single-step growth curves exhibited a burst size of ~100 PFU/cell. The genome of SNJ1 was observed to be a circular, double-stranded DNA (dsDNA) molecule (16,341 bp). Surprisingly, the sequence of SNJ1 was identical to that of a previously described plasmid, pHH205, indicating that this plasmid is the provirus of SNJ1. Several structural protein-encoding genes were identified in the viral genome. In addition, the comparison of putative packaging ATPase sequences from bacterial, archaeal and eukaryotic viruses, as well as the presence of lipid constituents from the host phospholipid pool, strongly suggest that SNJ1 belongs to the PRD1-type lineage of dsDNA viruses, which have an internal membrane. PMID:22784791

  6. Extrachromosomal recombination substrates recapitulate beyond 12/23 restricted VDJ recombination in nonlymphoid cells.

    PubMed

    Jung, David; Bassing, Craig H; Fugmann, Sebastian D; Cheng, Hwei-Ling; Schatz, David G; Alt, Frederick W

    2003-01-01

    V(D)J recombination occurs efficiently only between gene segments flanked by recombination signals (RSs) containing 12 and 23 base pair spacers (the 12/23 rule). A further limitation "beyond the 12/23 rule" (B12/23) exists at the TCRbeta locus and ensures Dbeta usage. Herein, we show that extrachromosomal V(D)J recombination substrates recapitulate B12/23 restriction in nonlymphoid cells. We further demonstrate that the Vbeta coding flank, the 12-RS heptamer/nonamer, and the 23-RS spacer each can significantly influence B12/23 restriction. Finally, purified core RAG1 and RAG2 proteins (together with HMG2) also reproduce B12/23 restriction in a cell-free system. Our findings indicate that B12/23 restriction of V(D)J recombination is cemented at the level of interactions between the RAG proteins and TCRbeta RS sequences. PMID:12530976

  7. Oxidative stress and starvation in Dinoroseobacter shibae: the role of extrachromosomal elements

    PubMed Central

    Soora, Maya; Tomasch, Jürgen; Wang, Hui; Michael, Victoria; Petersen, Jörn; Engelen, Bert; Wagner-Döbler, Irene; Cypionka, Heribert

    2015-01-01

    Aerobic anoxygenic phototrophic bacteria (AAP) are abundant in the photic zone of the marine environment. Dinoroseobacter shibae, a representative of the Roseobacter group, converts light into additional energy that enhances its survival especially under starvation. However, light exposure results in the production of cytotoxic reactive oxygen species in AAPs. Here we investigated the response of D. shibae to starvation and oxidative stress, focusing on the role of extrachromosomal elements (ECRs). D. shibae possessing five ECRs (three plasmids and two chromids) was starved for 4 weeks either in the dark or under light/dark cycles and the survival was monitored. Transcriptomics showed that on the chromosome genes with a role in oxidative stress response and photosynthesis were differentially expressed during the light period. Most extrachromosomal genes in contrast showed a general loss of transcriptional activity, especially in dark-starved cells. The observed decrease of gene expression was not due to plasmid loss, as all five ECRs were maintained in the cells. Interestingly, the genes on the 72-kb chromid were the least downregulated, and one region with genes of the oxygen stress response and a light-dependent protochlorophyllide reductase of cyanobacterial origin was strongly activated under the light/dark cycle. A Δ72-kb curing mutant lost the ability to survive under starvation in a light/dark cycle demonstrating the essential role of this chromid for adaptation to starvation and oxidative stress. Our data moreover suggest that the other four ECRs of D. shibae have no vital function under the investigated conditions and therefore were transcriptionally silenced. PMID:25859246

  8. Characterization of Rhizobium grahamii extrachromosomal replicons and their transfer among rhizobia

    PubMed Central

    2014-01-01

    Background Rhizobium grahamii belongs to a new phylogenetic group of rhizobia together with Rhizobium mesoamericanum and other species. R. grahamii has a broad-host-range that includes Leucaena leucocephala and Phaseolus vulgaris, although it is a poor competitor for P. vulgaris nodulation in the presence of Rhizobium etli or Rhizobium phaseoli strains. This work analyzed the genome sequence and transfer properties of R. grahamii plasmids. Results Genome sequence was obtained from R. grahamii CCGE502 type strain isolated from Dalea leporina in Mexico. The CCGE502 genome comprises one chromosome and two extrachromosomal replicons (ERs), pRgrCCGE502a and pRgrCCGE502b. Additionally, a plasmid integrated in the CCGE502 chromosome was found. The genomic comparison of ERs from this group showed that gene content is more variable than average nucleotide identity (ANI). Well conserved nod and nif genes were found in R. grahamii and R. mesoamericanum with some differences. R. phaseoli Ch24-10 genes expressed in bacterial cells in roots were found to be conserved in pRgrCCGE502b. Regarding conjugative transfer we were unable to transfer the R. grahamii CCGE502 symbiotic plasmid and its megaplasmid to other rhizobial hosts but we could transfer the symbiotic plasmid to Agrobacterium tumefaciens with transfer dependent on homoserine lactones. Conclusion Variable degrees of nucleotide identity and gene content conservation were found among the different R. grahamii CCGE502 replicons in comparison to R. mesoamericanum genomes. The extrachromosomal replicons from R. grahamii were more similar to those found in phylogenetically related Rhizobium species. However, limited similarities of R. grahamii CCGE502 symbiotic plasmid and megaplasmid were observed in other more distant Rhizobium species. The set of conserved genes in R. grahamii comprises some of those that are highly expressed in R. phaseoli on plant roots, suggesting that they play an important role in root colonization

  9. Characterization of a conserved extrachromosomal element isolated from the avian malarial parasite Plasmodium gallinaceum.

    PubMed Central

    Joseph, J T; Aldritt, S M; Unnasch, T; Puijalon, O; Wirth, D F

    1989-01-01

    We have identified a conserved, repeated, and highly transcribed DNA element from the avian malarial parasite Plasmodium gallinaceum. The element produced multiple transcripts in both zygotes and asexual blood stages of this parasite. It was found to be highly conserved in all of five malarial species tested and hybridized at reduced stringency to other members of the phylum Apicomplexa, including the genera Babesia, Eimeria, Toxoplasma, and Theileria. The copy number of the element was about 15, and it had a circularly permuted restriction map with a repeat unit length of about 6.2 kilobases. It could be separated from the main genomic DNA by using sucrose gradients and agarose gels, and it migrated separately from the recognized Plasmodium chromosomes on pulse-field gels. In the accompanying paper (S. M. Aldritt, J. T. Joseph, and D. F. Wirth, Mol. Cell. Biol. 9:3614-3620, 1989), evidence is presented that element contains the mitochondrial genes for the protein cytochrome b and a fragment of the large rRNA. We postulate that this element is an episome in the mitochondria of the obligate parasites belonging to the phylum Apicomplexa. Images PMID:2779561

  10. Detection of DNA damage induced in vivo by a cross-linking agent with a circular channel crucible oscillating viscometer.

    PubMed

    Balbi, C; Abelmoschi, M L; Roner, R; Giaretti, W; Parodi, S; Santi, L

    1985-11-01

    DNA damage induced in vivo by the cross-linking agent mitomycin C (MMC) was investigated with a new oscillating crucible viscometer. Viscosity was measured by lysing rat liver nuclei in an alkaline lysing solution (pH 12.5; 25 degrees C). In control samples the viscosity increased very slowly with time, reaching a plateau only after 10-12 h. The process was accelerated and the maximum viscosity was decreased by alkaline single-stranded breaks arising from methylation and subsequent depurination of DNA in vitro with dimethylsulphate (DMS). MMC, when given alone, had no evident effect on the time needed for reaching plateau viscosity but it induced a small increase in maximum viscosity. When MMC was given in association with DMS, the time of disentanglement remained unchanged (accelerated) but maximum viscosity was increased in a dose dependent way. We conclude that these data clearly confirm that the slow steady increase of the viscosity of control DNA with time reflects mainly the process of unwinding of the two strands. The speed of this process seems to depend only from the number of unwinding points in DNA (breaks). PMID:3935335

  11. Circular motion

    NASA Astrophysics Data System (ADS)

    Newton, Isaac; Henry, Richard Conn

    2000-07-01

    An extraordinarily simple and transparent derivation of the formula for the acceleration that occurs in uniform circular motion is presented, and is advocated for use in high school and college freshman physics textbooks.

  12. Alternative model for chromatin organization of the Saccharomyces cerevisiae chromosomal DNA plasmid TRP1 RI circle (YARp1).

    PubMed Central

    Long, C M; Brajkovich, C M; Scott, J F

    1985-01-01

    TRP1 RI circle (now designated YARp1, yeast acentric ring plasmid 1) is a 1,453-base-pair artificial plasmid composed exclusively of Saccharomyces cerevisiae chromosomal DNA. It contains both the TRP1 gene and ARS1 (a DNA sequence that permits extrachromosomal maintenance of recombinant plasmids). This high-copy-number, relatively stable plasmid was shown to be organized into nucleosomes comparable to typical yeast chromatin, containing a possible maximum of nine nucleosomes per circle. Therefore, YARp1 can be used to examine the structure of chromatin of both a chromosomally derived replicator and a functional gene. By mapping regions of micrococcal nuclease cleavage in chromatin versus purified DNA, we located the positions of protected regions on the circle with reference to six unique restriction sites. Measurements made on patterns of early digestion products indicated that a region of approximately 300 base pairs in the vicinity of ARS1 was strongly resistant to micrococcal nuclease. The remainder of the plasmid appeared to be associated with five positioned nucleosomes and two nonnucleosomal, partially protected regions on the bulk of the molecules. After similar extents of digestion, naked DNA did not exhibit an equivalent pattern, although some hypersensitive cleavage sites matched sites found in the chromatin. These results are consistent with the interpretation that the protected domains are aligned with respect to a specific site or sites on the small circular chromatin. Images PMID:3018502

  13. Switch telomerase to ALT mechanism by inducing telomeric DNA damages and dysfunction of ATRX and DAXX.

    PubMed

    Hu, Yang; Shi, Guang; Zhang, Laichen; Li, Feng; Jiang, Yuanling; Jiang, Shuai; Ma, Wenbin; Zhao, Yong; Songyang, Zhou; Huang, Junjiu

    2016-01-01

    Activation of telomerase or alternative lengthening of telomeres (ALT) is necessary for tumours to escape from dysfunctional telomere-mediated senescence. Anti-telomerase drugs might be effective in suppressing tumour growth in approximately 85-90% of telomerase-positive cancer cells. However, there are still chances for these cells to bypass drug treatment after switching to the ALT mechanism to maintain their telomere integrity. But the mechanism underlying this switch is unknown. In this study, we used telomerase-positive cancer cells (HTC75) to discover the mechanism of the telomerase-ALT switch by inducing telomere-specific DNA damage, alpha-thalassemia X-linked syndrome protein (ATRX) knockdown and deletion of death associated protein (DAXX). Surprisingly, two important ALT hallmarks in the ALT-like HTC75 cells were observed after treatments: ALT-associated promyelocytic leukaemia bodies (APBs) and extrachromosomal circular DNA of telomeric repeats. Moreover, knocking out hTERT by utilizing the CRISPR/Cas9 technique led to telomere elongation in a telomerase-independent manner in ALT-like HTC75 cells. In summary, this is the first report to show that inducing telomeric DNA damage, disrupting the ATRX/DAXX complex and inhibiting telomerase activity in telomerase-positive cancer cells lead to the ALT switch. PMID:27578458

  14. Switch telomerase to ALT mechanism by inducing telomeric DNA damages and dysfunction of ATRX and DAXX

    PubMed Central

    Hu, Yang; Shi, Guang; Zhang, Laichen; Li, Feng; Jiang, Yuanling; Jiang, Shuai; Ma, Wenbin; Zhao, Yong; Songyang, Zhou; Huang, Junjiu

    2016-01-01

    Activation of telomerase or alternative lengthening of telomeres (ALT) is necessary for tumours to escape from dysfunctional telomere-mediated senescence. Anti-telomerase drugs might be effective in suppressing tumour growth in approximately 85–90% of telomerase-positive cancer cells. However, there are still chances for these cells to bypass drug treatment after switching to the ALT mechanism to maintain their telomere integrity. But the mechanism underlying this switch is unknown. In this study, we used telomerase-positive cancer cells (HTC75) to discover the mechanism of the telomerase-ALT switch by inducing telomere-specific DNA damage, alpha-thalassemia X-linked syndrome protein (ATRX) knockdown and deletion of death associated protein (DAXX). Surprisingly, two important ALT hallmarks in the ALT-like HTC75 cells were observed after treatments: ALT-associated promyelocytic leukaemia bodies (APBs) and extrachromosomal circular DNA of telomeric repeats. Moreover, knocking out hTERT by utilizing the CRISPR/Cas9 technique led to telomere elongation in a telomerase-independent manner in ALT-like HTC75 cells. In summary, this is the first report to show that inducing telomeric DNA damage, disrupting the ATRX/DAXX complex and inhibiting telomerase activity in telomerase-positive cancer cells lead to the ALT switch. PMID:27578458

  15. Regulation and targeting of recombination in extrachromosomal substrates carrying immunoglobulin switch region sequences.

    PubMed Central

    Leung, H; Maizels, N

    1994-01-01

    We have used extrachromosomal substrates carrying immunoglobulin heavy-chain S mu and S gamma 3 switch region sequences to study activation and targeting of recombination by a transcriptional enhancer element. Substrates are transiently introduced into activated primary murine B cells, in which recombination involving S-region sequences deletes a conditionally lethal marker, and recombination is measured by transformation of Escherichia coli in the second step of the assay. Previously we found that as many as 25% of replicated substrates recombined during 40-h transfection of lipopolysaccharide (LPS)-stimulated primary cells and that efficient recombination was dependent on the presence of S-region sequences as well as a transcriptional activator region in the constructs (H. Leung and N. Maizels, Proc. Natl. Acad. Sci. USA 89:4154-4158, 1992). Here we show that recombination of the switch substrates is threefold more efficient in LPS-cultured primary B cells than in the T-cell line EL4; the activities responsible for switch substrate recombination thus appear to be more abundant or more active in cells which can carry out chromosomal switch recombination. We test the role of the transcriptional activator region and show that the immunoglobulin heavy-chain intron enhancer (E mu) alone stimulates recombination as well as E mu combined with a heavy-chain promoter and that mutations that diminish enhancer-dependent transcription 500-fold diminish recombinational activation less than 2-fold. These observations suggest that the enhancer stimulates recombination by a mechanism that does not depend on transcript production or that is insensitive to the level of transcript production over a very broad range. Furthermore, we find that E mu stimulates recombination when located either upstream or downstream of S mu but that the position of the recombinational activator does affect the targeting of recombination junctions, suggesting that the relatively imprecise targeting of

  16. Son-Killer: A Third Extrachromosomal Factor Affecting the Sex Ratio in the Parasitoid Wasp, NASONIA (=MORMONIELLA) VITRIPENNIS

    PubMed Central

    Skinner, Samuel Way

    1985-01-01

    An extrachromosomal factor, termed son-killer (sk), affects the sex ratio in a parasitoid wasp, Nasonia (=Mormoniella ) vitripennis. The factor is maternally transmitted and alters the secondary sex ratio of an infected female through mortality of approximately 80% of the male embryos. No effect on the primary (zygotic) sex ratio is observed. Ninety-five percent of the daughters of an infected female inherit son-killer. The factor can also be transmitted contagiously when the progeny of infected and uninfected females develop simultaneously on a single host. In newly infected strains, the sex ratio effects are equivalent to those in the original. PMID:3988039

  17. Cervical keratinocytes containing stably replicating extrachromosomal HPV-16 are refractory to transformation by oncogenic H-Ras

    PubMed Central

    Berger, Kristi L.; Barriga, Felicia; Lace, Michael J.; Turek, Lubomir P.; Zamba, Gideon J.; Domann, Frederick E.; Lee, John H.; Klingelhutz, Aloysius J.

    2007-01-01

    Ras expression in human epithelial cells with integrated HPV genomes has been shown to cause tumorigenic transformation. The effects of Ras in cells representing early stage HPV-associated disease (i.e., when HPV is extrachromosomal and the oncogenes are under control of native promoters) have not been examined. Here, we used human cervical keratinocyte cell lines containing stably replicating extrachromosomal HPV-16 and present the novel finding that these cells resist transformation by oncogenic H-Ras. Ras expression consistently diminished anchorageindependent growth (AI), reduced E6 and E7 expression, and caused p53 induction in these cells. Conversely, AI was enhanced or maintained in Ras-transduced cervical cells that were immortalized with a 16E6/E7 retrovirus, and minimal effects on E6 and E7 expression were observed. Ras expression with either episomal HPV-16 or LXSN-E6/E7 was insufficient for tumorigenic growth suggesting that other events are needed for tumorigenic transformation. In conclusion, our results indicate that Ras-mediated transformation depends on the context of HPV oncogene expression and that this is an important point to address when developing HPV tumor models. PMID:16945398

  18. Genome defense against exogenous nucleic acids in eukaryotes by non-coding DNA occurs through CRISPR-like mechanisms in the cytosol and the bodyguard protection in the nucleus.

    PubMed

    Qiu, Guo-Hua

    2016-01-01

    In this review, the protective function of the abundant non-coding DNA in the eukaryotic genome is discussed from the perspective of genome defense against exogenous nucleic acids. Peripheral non-coding DNA has been proposed to act as a bodyguard that protects the genome and the central protein-coding sequences from ionizing radiation-induced DNA damage. In the proposed mechanism of protection, the radicals generated by water radiolysis in the cytosol and IR energy are absorbed, blocked and/or reduced by peripheral heterochromatin; then, the DNA damage sites in the heterochromatin are removed and expelled from the nucleus to the cytoplasm through nuclear pore complexes, most likely through the formation of extrachromosomal circular DNA. To strengthen this hypothesis, this review summarizes the experimental evidence supporting the protective function of non-coding DNA against exogenous nucleic acids. Based on these data, I hypothesize herein about the presence of an additional line of defense formed by small RNAs in the cytosol in addition to their bodyguard protection mechanism in the nucleus. Therefore, exogenous nucleic acids may be initially inactivated in the cytosol by small RNAs generated from non-coding DNA via mechanisms similar to the prokaryotic CRISPR-Cas system. Exogenous nucleic acids may enter the nucleus, where some are absorbed and/or blocked by heterochromatin and others integrate into chromosomes. The integrated fragments and the sites of DNA damage are removed by repetitive non-coding DNA elements in the heterochromatin and excluded from the nucleus. Therefore, the normal eukaryotic genome and the central protein-coding sequences are triply protected by non-coding DNA against invasion by exogenous nucleic acids. This review provides evidence supporting the protective role of non-coding DNA in genome defense. PMID:27036064

  19. Complete Genome Sequence of a Cylindrospermopsin-Producing Cyanobacterium, Cylindrospermopsis raciborskii CS505, Containing a Circular Chromosome and a Single Extrachromosomal Element.

    PubMed

    Fuentes-Valdés, Juan J; Plominsky, Alvaro M; Allen, Eric E; Tamames, Javier; Vásquez, Mónica

    2016-01-01

    Cylindrospermopsis raciborskii is a freshwater cyanobacterium producing bloom events and toxicity in drinking water source reservoirs. We present the first genome sequence for C. raciborskii CS505 (Australia), containing one 4.1-Mbp chromosome and one 110-Kbp plasmid having G+C contents of 40.3% (3933 genes) and 39.3% (111 genes), respectively. PMID:27563040

  20. Complete Genome Sequence of a Cylindrospermopsin-Producing Cyanobacterium, Cylindrospermopsis raciborskii CS505, Containing a Circular Chromosome and a Single Extrachromosomal Element

    PubMed Central

    Fuentes-Valdés, Juan J.; Plominsky, Alvaro M.; Allen, Eric E.; Tamames, Javier

    2016-01-01

    Cylindrospermopsis raciborskii is a freshwater cyanobacterium producing bloom events and toxicity in drinking water source reservoirs. We present the first genome sequence for C. raciborskii CS505 (Australia), containing one 4.1-Mbp chromosome and one 110-Kbp plasmid having G+C contents of 40.3% (3933 genes) and 39.3% (111 genes), respectively. PMID:27563040

  1. Characterization of Circular RNAs.

    PubMed

    Zhang, Yang; Yang, Li; Chen, Ling-Ling

    2016-01-01

    Accumulated lines of evidence reveal that a large number of circular RNAs are produced in transcriptomes from fruit fly to mouse and human. Unlike linear RNAs shaped with 5' cap and 3' tail, circular RNAs are characterized by covalently closed loop structures without open terminals, thus requiring specific treatments for their identification and validation. Here, we describe a detailed pipeline for the characterization of circular RNAs. It has been successfully applied to the study of circular intronic RNAs derived from intron lariats (ciRNAs) and circular RNAs produced from back spliced exons (circRNAs) in human. PMID:26721494

  2. Molecular recognition principles and stationary-phase characteristics of topoisomer-selective chemoaffinity materials for chromatographic separation of circular plasmid DNA topoisomers.

    PubMed

    Mahut, Marek; Lindner, Wolfgang; Lämmerhofer, Michael

    2012-01-18

    We recently discovered the molecular recognition capability of a quinine carbamate ligand attached to silica as a powerful chemoaffinity material for the chromatographic separation of circular plasmid topoisomers of different linking numbers. In this paper we develop structure-selectivity relationship studies to figure out the essential structural features for topoisomer recognition. By varying different moieties of the original cinchonan-derived selector, it was shown that intercalation by the quinoline moiety of the ligand as assumed initially as the working hypothesis is not an essential feature for topoisomer recognition during chromatography. We found that the key elements for topoisomer selectivity are the presence of a rigid weak anion-exchange site and a H-donor site separated from each other in a defined distance by a 4-atom spacer. Additionally, incorporation of the weak anion-exchange site into a cyclic ring structure provides greater rigidity of the ligand molecule and turned out to be advantageous, if not mandatory, for (close to) baseline separation. PMID:22191385

  3. DNA.

    ERIC Educational Resources Information Center

    Felsenfeld, Gary

    1985-01-01

    Structural form, bonding scheme, and chromatin structure of and gene-modification experiments with deoxyribonucleic acid (DNA) are described. Indicates that DNA's double helix is variable and also flexible as it interacts with regulatory and other molecules to transfer hereditary messages. (DH)

  4. Toroidal circular dichroism

    NASA Astrophysics Data System (ADS)

    Raybould, T. A.; Fedotov, V. A.; Papasimakis, N.; Kuprov, I.; Youngs, I. J.; Chen, W. T.; Tsai, D. P.; Zheludev, N. I.

    2016-07-01

    We demonstrate that the induced toroidal dipole, represented by currents flowing on the surface of a torus, makes a distinct and indispensable contribution to circular dichroism. We show that toroidal circular dichroism supplements the well-known mechanism involving electric dipole and magnetic dipole transitions. We illustrate this with rigorous analysis of the experimentally measured polarization-sensitive transmission spectra of an artificial metamaterial, constructed from elements of toroidal symmetry. We argue that toroidal circular dichroism will be found in large biomolecules with elements of toroidal symmetry and should be taken into account in the interpretation of circular dichroism spectra of organics.

  5. 2. Northwest circular bastion, seen from edge of southwest circular ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. Northwest circular bastion, seen from edge of southwest circular bastion wall. Metal roof beams extend up to form peak. World War II gun installation at right. - Fort Hamilton, Northwest Circular Bastion, Rose Island, Newport, Newport County, RI

  6. DNA

    ERIC Educational Resources Information Center

    Stent, Gunther S.

    1970-01-01

    This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)

  7. A mechanism of gene amplification driven by small DNA fragments.

    PubMed

    Mukherjee, Kuntal; Storici, Francesca

    2012-01-01

    DNA amplification is a molecular process that increases the copy number of a chromosomal tract and often causes elevated expression of the amplified gene(s). Although gene amplification is frequently observed in cancer and other degenerative disorders, the molecular mechanisms involved in the process of DNA copy number increase remain largely unknown. We hypothesized that small DNA fragments could be the trigger of DNA amplification events. Following our findings that small fragments of DNA in the form of DNA oligonucleotides can be highly recombinogenic, we have developed a system in the yeast Saccharomyces cerevisiae to capture events of chromosomal DNA amplification initiated by small DNA fragments. Here we demonstrate that small DNAs can amplify a chromosomal region, generating either tandem duplications or acentric extrachromosomal DNA circles. Small fragment-driven DNA amplification (SFDA) occurs with a frequency that increases with the length of homology between the small DNAs and the target chromosomal regions. SFDA events are triggered even by small single-stranded molecules with as little as 20-nt homology with the genomic target. A double-strand break (DSB) external to the chromosomal amplicon region stimulates the amplification event up to a factor of 20 and favors formation of extrachromosomal circles. SFDA is dependent on Rad52 and Rad59, partially dependent on Rad1, Rad10, and Pol32, and independent of Rad51, suggesting a single-strand annealing mechanism. Our results reveal a novel molecular model for gene amplification, in which small DNA fragments drive DNA amplification and define the boundaries of the amplicon region. As DNA fragments are frequently found both inside cells and in the extracellular environment, such as the serum of patients with cancer or other degenerative disorders, we propose that SFDA may be a common mechanism for DNA amplification in cancer cells, as well as a more general cause of DNA copy number variation in nature. PMID

  8. Squaring a Circular Segment

    ERIC Educational Resources Information Center

    Gordon, Russell

    2008-01-01

    Consider a circular segment (the smaller portion of a circle cut off by one of its chords) with chord length c and height h (the greatest distance from a point on the arc of the circle to the chord). Is there a simple formula involving c and h that can be used to closely approximate the area of this circular segment? Ancient Chinese and Egyptian…

  9. Tunable circular patch antennas

    NASA Astrophysics Data System (ADS)

    Lan, G.-L.; Sengupta, D. L.

    1985-10-01

    A method to control the resonant or operating frequencies of circular patch antennas has been investigated experimentally and theoretically. It consists of the placement of passive metallic or tuning posts at approximate locations within the input region of the antenna. Comparison of measured and analytical results seems to establish the validity of a theoretical model proposed to determine the input performance of such circular patch antennas.

  10. Circular free-electron laser

    DOEpatents

    Brau, Charles A.; Kurnit, Norman A.; Cooper, Richard K.

    1984-01-01

    A high efficiency, free electron laser utilizing a circular relativistic electron beam accelerator and a circular whispering mode optical waveguide for guiding optical energy in a circular path in the circular relativistic electron beam accelerator such that the circular relativistic electron beam and the optical energy are spatially contiguous in a resonant condition for free electron laser operation. Both a betatron and synchrotron are disclosed for use in the present invention. A free electron laser wiggler is disposed around the circular relativistic electron beam accelerator for generating a periodic magnetic field to transform energy from the circular relativistic electron beam to optical energy.

  11. Compact waveguide circular polarizer

    DOEpatents

    Tantawi, Sami G.

    2016-08-16

    A multi-port waveguide is provided having a rectangular waveguide that includes a Y-shape structure with first top arm having a first rectangular waveguide port, a second top arm with second rectangular waveguide port, and a base arm with a third rectangular waveguide port for supporting a TE.sub.10 mode and a TE.sub.20 mode, where the end of the third rectangular waveguide port includes rounded edges that are parallel to a z-axis of the waveguide, a circular waveguide having a circular waveguide port for supporting a left hand and a right hand circular polarization TE.sub.11 mode and is coupled to a base arm broad wall, and a matching feature disposed on the base arm broad wall opposite of the circular waveguide for terminating the third rectangular waveguide port, where the first rectangular waveguide port, the second rectangular waveguide port and the circular waveguide port are capable of supporting 4-modes of operation.

  12. Wiimote Experiments: Circular Motion

    ERIC Educational Resources Information Center

    Kouh, Minjoon; Holz, Danielle; Kawam, Alae; Lamont, Mary

    2013-01-01

    The advent of new sensor technologies can provide new ways of exploring fundamental physics. In this paper, we show how a Wiimote, which is a handheld remote controller for the Nintendo Wii video game system with an accelerometer, can be used to study the dynamics of circular motion with a very simple setup such as an old record player or a…

  13. Copyright Basics. Circular 1.

    ERIC Educational Resources Information Center

    Library of Congress, Washington, DC. Copyright Office.

    This circular answers some of the questions that are frequently asked about copyright, a form of protection provided by the laws of the United States to authors of "original works of authorship" including library, dramatic musical, artistic, and certain other intellectual works. The Copyright Act of 1976 (title 17 of the United States Code), which…

  14. Wiimote Experiments: Circular Motion

    NASA Astrophysics Data System (ADS)

    Kouh, Minjoon; Holz, Danielle; Kawam, Alae; Lamont, Mary

    2013-03-01

    The advent of new sensor technologies can provide new ways of exploring fundamental physics. In this paper, we show how a Wiimote, which is a handheld remote controller for the Nintendo Wii video game system with an accelerometer, can be used to study the dynamics of circular motion with a very simple setup such as an old record player or a bicycle wheel.

  15. Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences

    PubMed Central

    Yoo, Wonseok; Lim, Dongbin

    2016-01-01

    A retron is a bacterial retroelement that encodes an RNA gene and a reverse transcriptase (RT). The former, once transcribed, works as a template primer for reverse transcription by the latter. The resulting DNA is covalently linked to the upstream part of the RNA; this chimera is called multicopy single-stranded DNA (msDNA), which is extrachromosomal DNA found in many bacterial species. Based on the conserved features in the eight known msDNA sequences, we developed a detection method and applied it to scan National Center for Biotechnology Information (NCBI) RefSeq bacterial genome sequences. Among 16,844 bacterial sequences possessing a retron-type RT domain, we identified 48 unique types of msDNA. Currently, the biological role of msDNA is not well understood. Our work will be a useful tool in studying the distribution, evolution, and physiological role of msDNA. PMID:27103888

  16. Circular inferences in schizophrenia.

    PubMed

    Jardri, Renaud; Denève, Sophie

    2013-11-01

    A considerable number of recent experimental and computational studies suggest that subtle impairments of excitatory to inhibitory balance or regulation are involved in many neurological and psychiatric conditions. The current paper aims to relate, specifically and quantitatively, excitatory to inhibitory imbalance with psychotic symptoms in schizophrenia. Considering that the brain constructs hierarchical causal models of the external world, we show that the failure to maintain the excitatory to inhibitory balance results in hallucinations as well as in the formation and subsequent consolidation of delusional beliefs. Indeed, the consequence of excitatory to inhibitory imbalance in a hierarchical neural network is equated to a pathological form of causal inference called 'circular belief propagation'. In circular belief propagation, bottom-up sensory information and top-down predictions are reverberated, i.e. prior beliefs are misinterpreted as sensory observations and vice versa. As a result, these predictions are counted multiple times. Circular inference explains the emergence of erroneous percepts, the patient's overconfidence when facing probabilistic choices, the learning of 'unshakable' causal relationships between unrelated events and a paradoxical immunity to perceptual illusions, which are all known to be associated with schizophrenia. PMID:24065721

  17. Switchable circular beam deflectors

    NASA Astrophysics Data System (ADS)

    Shang, Xiaobing; Joshi, Pankaj; Tan, Jin-Yi; De Smet, Jelle; Cuypers, Dieter; Baghdasaryan, Tigran; Vervaeke, Michael; Thienpont, Hugo; De Smet, Herbert

    2016-04-01

    In this work, we report two types of electrically tunable photonic devices with circularly symmetric polarization independent beam steering performance (beam condensing resp. beam broadening). The devices consist of circular micro grating structures combined with nematic liquid crystal (LC) layers with anti-parallel alignment. A single beam deflector converts a polarized and monochromatic green laser beam (λ =543.5 nm) into a diffraction pattern, with the peak intensity appearing at the third order when 0~{{V}\\text{pp}} is applied and at the zeroth order (no deflection) for voltages above 30~{{V}\\text{pp}} . Depending on the shape of the grating structure (non-inverted or inverted), the deflection is inwards or outwards. Both grating types can be made starting from the same diamond-tooled master mold. A polarized white light beam is symmetrically condensed resp. broadened over 2° in the off state and is passed through unchanged in the on state. By stacking two such devices with mutually orthogonal LC alignment layers, polarization independent switchable circular beam deflectors are realized with a high transmittance (>80%), and with the same beam steering performance as the polarization dependent single devices.

  18. Sources of varieties and quality of circular Fructus Ligustri Lucidi.

    PubMed

    Li, Yan-Peng; Wang, Si-Jia; Zang, Yi-Mei; Hu, Zhong-Sheng; Liu, Chun-Sheng

    2016-03-01

    This study aimed to trace sources and quantitatively analyze the specnuezhenide content of circular Fructus Ligustri Lucidi for clinical use. Different specifications of Fructus Ligustri Lucidi were identified using DNA barcoding technology and the specnuezhenide content was analyzed by High Performance Liquid Chromatography (HPLC). The ITS sequence of circular Fructus Ligustri Lucidi was identical to that of standard privet, which was determined through botanical identification. ITS sequence similarity between circular Fructus Ligustri Lucidi and Fructus Ligustri Lucidi which was registered in NCBI ranged from 99.5% to 100%. The sequences of circular and other Fructus Ligustri Lucidi were clustered in a Neighbor-Joining tree with bootstrap value of 95, and these sequences could be distinguished from adulterants. Conforming to pharmacopoeia standard, the average specnuezhenide content of circular Fructus Ligustri Lucidi was higher than that of chicken waist Fructus Ligustri Lucidi. Circular Fructus Ligustri Lucidi derived from Ligustrum lucidum Ait. and the specnuezhenide content was higher in circular Fructus Ligustri Lucidi than that in chicken waist Fructus Ligustri Lucidi. PMID:27025372

  19. The Influence of Copy-Number of Targeted Extrachromosomal Genetic Elements on the Outcome of CRISPR-Cas Defense

    PubMed Central

    Severinov, Konstantin; Ispolatov, Iaroslav; Semenova, Ekaterina

    2016-01-01

    Prokaryotic type I CRISPR-Cas systems respond to the presence of mobile genetic elements such as plasmids and phages in two different ways. CRISPR interference efficiently destroys foreign DNA harboring protospacers fully matching CRISPR RNA spacers. In contrast, even a single mismatch between a spacer and a protospacer can render CRISPR interference ineffective but causes primed adaptation—efficient and specific acquisition of additional spacers from foreign DNA into the CRISPR array of the host. It has been proposed that the interference and primed adaptation pathways are mediated by structurally different complexes formed by the effector Cascade complex on matching and mismatched protospacers. Here, we present experimental evidence and present a simple mathematical model that shows that when plasmid copy number maintenance/phage genome replication is taken into account, the two apparently different outcomes of the CRISPR-Cas response can be accounted for by just one kind of effector complex on both targets. The results underscore the importance of consideration of targeted genome biology when considering consequences of CRISPR-Cas systems action.

  20. Circular RNA oligonucleotides. Synthesis, nucleic acid binding properties, and a comparison with circular DNAs.

    PubMed Central

    Wang, S; Kool, E T

    1994-01-01

    We report the synthesis and nucleic acid binding properties of two cyclic RNA oligonucleotides designed to bind single-stranded nucleic acids by pyr.pur.pyr-type triple helix formation. The circular RNAs are 34 nucleotides in size and were cyclized using a template-directed nonenzymatic ligation. To ensure isomeric 3'-5' purity in the ligation reaction, one nucleotide at the ligation site is a 2'-deoxyribose. One circle (1) is complementary to the sequence 5'-A12, and the second (2) is complementary to 5'-AAGAAAGAAAAG. Results of thermal denaturation experiments and mixing studies show that both circles bind complementary single-stranded DNA or RNA substrates by triple helix formation, in which two domains in a pyrimidine-rich circle sandwich a central purine-rich substrate. The affinities of these circles with their purine complements are much higher than the affinities of either the linear precursors or simple Watson-Crick DNA complements. For example, circle 1 binds rA12 (pH 7.0, 10 mM MgCl2, 100 mM NaCl) with a Tm of 48 degrees C and a Kd (37 degrees C) of 4.1 x 10(-9) M, while the linear precursor of the circle binds with a Tm of 34 degrees C and a Kd of 1.2 x 10(-6) M. The complexes of circle 2 are pH-dependent, as expected for triple helical complexes involving C(+)G.C triads, and mixing plots for both circles reveal one-to-one stoichiometry of binding either to RNA or DNA substrates. Comparison of circular RNAs with previously synthesized circular DNA oligonucleotides of the same sequence reveals similar behavior in the binding of DNA, but strikingly different behavior in the binding of RNA. The cyclic DNAs show high DNA-binding selectivity, giving relatively weaker duplex-type binding with complementary RNAs. The relative order of thermodynamic stability for the four types of triplex studied here is found to be DDD >> RRR > RDR >> DRD. The results are discussed in the context of recent reports of strong triplex dependence on RNA versus DNA backbones

  1. Circular RNA oligonucleotides. Synthesis, nucleic acid binding properties, and a comparison with circular DNAs.

    PubMed

    Wang, S; Kool, E T

    1994-06-25

    We report the synthesis and nucleic acid binding properties of two cyclic RNA oligonucleotides designed to bind single-stranded nucleic acids by pyr.pur.pyr-type triple helix formation. The circular RNAs are 34 nucleotides in size and were cyclized using a template-directed nonenzymatic ligation. To ensure isomeric 3'-5' purity in the ligation reaction, one nucleotide at the ligation site is a 2'-deoxyribose. One circle (1) is complementary to the sequence 5'-A12, and the second (2) is complementary to 5'-AAGAAAGAAAAG. Results of thermal denaturation experiments and mixing studies show that both circles bind complementary single-stranded DNA or RNA substrates by triple helix formation, in which two domains in a pyrimidine-rich circle sandwich a central purine-rich substrate. The affinities of these circles with their purine complements are much higher than the affinities of either the linear precursors or simple Watson-Crick DNA complements. For example, circle 1 binds rA12 (pH 7.0, 10 mM MgCl2, 100 mM NaCl) with a Tm of 48 degrees C and a Kd (37 degrees C) of 4.1 x 10(-9) M, while the linear precursor of the circle binds with a Tm of 34 degrees C and a Kd of 1.2 x 10(-6) M. The complexes of circle 2 are pH-dependent, as expected for triple helical complexes involving C(+)G.C triads, and mixing plots for both circles reveal one-to-one stoichiometry of binding either to RNA or DNA substrates. Comparison of circular RNAs with previously synthesized circular DNA oligonucleotides of the same sequence reveals similar behavior in the binding of DNA, but strikingly different behavior in the binding of RNA. The cyclic DNAs show high DNA-binding selectivity, giving relatively weaker duplex-type binding with complementary RNAs. The relative order of thermodynamic stability for the four types of triplex studied here is found to be DDD > RRR > RDR > DRD. The results are discussed in the context of recent reports of strong triplex dependence on RNA versus DNA backbones. Triplex

  2. DNA Knots: Theory and Experiments

    NASA Astrophysics Data System (ADS)

    Sumners, D. W.

    Cellular DNA is a long, thread-like molecule with remarkably complex topology. Enzymes that manipulate the geometry and topology of cellular DNA perform many vital cellular processes (including segregation of daughter chromosomes, gene regulation, DNA repair, and generation of antibody diversity). Some enzymes pass DNA through itself via enzyme-bridged transient breaks in the DNA; other enzymes break the DNA apart and reconnect it to different ends. In the topological approach to enzymology, circular DNA is incubated with an enzyme, producing an enzyme signature in the form of DNA knots and links. By observing the changes in DNA geometry (supercoiling) and topology (knotting and linking) due to enzyme action, the enzyme binding and mechanism can often be characterized. This paper will discuss some personal research history, and the tangle model for the analysis of site-specific recombination experiments on circular DNA.

  3. CIRCULAR CAVITY SLOT ANTENNA

    DOEpatents

    Kerley, P.L.

    1959-01-01

    A small-size antenna having a doughnut-shaped field pattern and which can act both as an antenna and a resonant circuit is described. The antenna is of the slotted type and comprises a resonant cavity with a center hole. A circular slot is provided in one wall of the cavity concentric with the hole and a radio frequency source is connected across the slot. The pattern and loading of the antenna are adjusted by varying the position and shape of a center element slidably disposed within the hole and projecting from the slotted side of the resonant cavity. The disclosed structure may also be used to propagate the oscillator signal down a transniission line by replacing the center element with one leg of the transmission line in a spaced relation from the walls of the cavity.

  4. Children's Sensitivity to Circular Explanations

    ERIC Educational Resources Information Center

    Baum, Laura A.; Danovitch, Judith H.; Keil, Frank C.

    2008-01-01

    The ability to evaluate the quality of explanations is an essential part of children's intellectual growth. Explanations can be faulty in structural ways such as when they are circular. A circular explanation reiterates the question as if it were an explanation rather than providing any new information. Two experiments (N=77) examined children's…

  5. Design of a titering assay for lentiviral vectors utilizing direct extraction of DNA from transduced cells in microtiter plates

    PubMed Central

    Murphy, Michele E; Vin, Chintan D; Slough, Megan M; Gombotz, Wayne R; Kelley-Clarke, Brenna

    2016-01-01

    Using lentiviral vector products in clinical applications requires an accurate method for measuring transduction titer. For vectors lacking a marker gene, quantitative polymerase chain reaction is used to evaluate the number of vector DNA copies in transduced target cells, from which a transduction titer is calculated. Immune Design previously described an integration-deficient lentiviral vector pseudotyped with a modified Sindbis virus envelope for use in cancer immunotherapy (VP02, of the ZVex platform). Standard protocols for titering integration-competent lentiviral vectors employ commercial spin columns to purify vector DNA from transduced cells, but such columns are not optimized for isolation of extrachromosomal (nonintegrated) DNA. Here, we describe a 96-well transduction titer assay in which DNA extraction is performed in situ in the transduction plate, yielding quantitative recovery of extrachromosomal DNA. Vector titers measured by this method were higher than when commercial spin columns were used for DNA isolation. Evaluation of the method’s specificity, linear range, and precision demonstrate that it is suitable for use as a lot release assay to support clinical trials with VP02. Finally, the method is compatible with titering both integrating and nonintegrating lentiviral vectors, suggesting that it may be used to evaluate the transduction titer for any lentiviral vector. PMID:26942209

  6. Circular chemiresistors for microchemical sensors

    DOEpatents

    Ho, Clifford K.

    2007-03-13

    A circular chemiresistor for use in microchemical sensors. A pair of electrodes is fabricated on an electrically insulating substrate. The pattern of electrodes is arranged in a circle-filling geometry, such as a concentric, dual-track spiral design, or a circular interdigitated design. A drop of a chemically sensitive polymer (i.e., chemiresistive ink) is deposited on the insulating substrate on the electrodes, which spreads out into a thin, circular disk contacting the pair of electrodes. This circularly-shaped electrode geometry maximizes the contact area between the pair of electrodes and the polymer deposit, which provides a lower and more stable baseline resistance than with linear-trace designs. The circularly-shaped electrode pattern also serves to minimize batch-to-batch variations in the baseline resistance due to non-uniform distributions of conductive particles in the chemiresistive polymer film.

  7. Nuclear spin circular dichroism

    SciTech Connect

    Vaara, Juha; Rizzo, Antonio; Kauczor, Joanna; Norman, Patrick; Coriani, Sonia

    2014-04-07

    Recent years have witnessed a growing interest in magneto-optic spectroscopy techniques that use nuclear magnetization as the source of the magnetic field. Here we present a formulation of magnetic circular dichroism (CD) due to magnetically polarized nuclei, nuclear spin-induced CD (NSCD), in molecules. The NSCD ellipticity and nuclear spin-induced optical rotation (NSOR) angle correspond to the real and imaginary parts, respectively, of (complex) quadratic response functions involving the dynamic second-order interaction of the electron system with the linearly polarized light beam, as well as the static magnetic hyperfine interaction. Using the complex polarization propagator framework, NSCD and NSOR signals are obtained at frequencies in the vicinity of optical excitations. Hartree-Fock and density-functional theory calculations on relatively small model systems, ethene, benzene, and 1,4-benzoquinone, demonstrate the feasibility of the method for obtaining relatively strong nuclear spin-induced ellipticity and optical rotation signals. Comparison of the proton and carbon-13 signals of ethanol reveals that these resonant phenomena facilitate chemical resolution between non-equivalent nuclei in magneto-optic spectra.

  8. Circular Scan Streak Tube Development

    NASA Technical Reports Server (NTRS)

    Nevin, S.

    1980-01-01

    A streak tube having circular scan was designed, built and tested. Continuous circular scan, easily derived from out of phase sine waves applied to the conventional deflection plates, permits the timing of pulses traveling long baselines. At the tube's output a circular array of 720 elements is scanned to provide 30 to 40 picosecond resolution. Initial difficulties with electron bombarded silicon arrays were circumvented by using microchannel plates within the streak tube to provide the needed electronic amplification and digital sensitivity and coupling the 720 element arrays to the electron beam by means of a phosphor on a fiber optics. Two ceramic body tubes with S-20 photocathodes were tested and delivered.

  9. Localization of a bidirectional DNA replication origin in the native locus and in episomally amplified murine adenosine deaminase loci.

    PubMed Central

    Carroll, S M; DeRose, M L; Kolman, J L; Nonet, G H; Kelly, R E; Wahl, G M

    1993-01-01

    Gene amplification is frequently mediated by the initial production of acentric, autonomously replicating extrachromosomal elements. The 4,000 extrachromosomal copies of the mouse adenosine deaminase (ADA) amplicon in B-1/50 cells initiate their replication remarkably synchronously in early S phase and at approximately the same time as the single-copy chromosomal locus from which they were derived. The abundance of ADA sequences and favorable replication timing characteristics in this system led us to determine whether DNA replication initiates in ADA episomes within a preferred region and whether this region is the same as that used at the corresponding chromosomal locus prior to amplification. This study reports the detection and localization of a discrete set of DNA fragments in the ADA amplicon which label soon after release of synchronized B-1/50 cells into S phase. A switch in template strand complementarity of Okazaki fragments, indicative of the initiation of bidirectional DNA replication, was found to lie within the same region. This putative replication origin is located approximately 28.5 kbp upstream of the 5' end of the ADA gene. The same region initiated DNA replication in the single-copy ADA locus of the parental cells. These analyses provide the first evidence that the replication of episomal intermediates involved in gene amplification initiates within a preferred region and that the same region is used to initiate DNA synthesis within the native locus. Images PMID:8474455

  10. Beam Rounders for Circular Colliders

    SciTech Connect

    A. Burov; S. Nagaitsev; Ya. Derbenev

    2001-07-01

    By means of linear optics, an arbitrary uncoupled beam can be locally transformed into a round (rotation-invariant) state and then back. This provides an efficient way to round beams in the interaction region of circular colliders.

  11. Circularly-Polarized Microstrip Antenna

    NASA Technical Reports Server (NTRS)

    Stanton, P. H.

    1985-01-01

    Microstrip construction compact for mobile applications. Circularly polarized microstrip antenna made of concentric cylindrical layers of conductive and dielectric materials. Coaxial cable feedlines connected to horizontal and vertical subelements from inside. Vertical subelement acts as ground for horizontal subelement.

  12. Circularization time of binary galaxies

    NASA Astrophysics Data System (ADS)

    Junqueira, S.; de Freitas Pacheco, J. A.

    1994-11-01

    We report the results of numerical experiments performed to study the orbital circularization time of binary galaxies. We find that the time scale is quite long (larger than the Hubble time), confirming earlier calculations. The results depend on the initial conditions. From our simulations we obtained a fitting formula for the circularization time as a function of the initial orbital parameters like the pericentric distance, mass ratio, and eccentricity.

  13. Circular polarization interferometry: circularly polarized modes of cholesteric liquid crystals.

    PubMed

    Sanchez-Castillo, A; Eslami, S; Giesselmann, F; Fischer, P

    2014-12-15

    We describe a novel polarization interferometer which permits the determination of the refractive indices for circularly-polarized light. It is based on a Jamin-Lebedeff interferometer, modified with waveplates, and permits us to experimentally determine the refractive indices nL and nR of the respectively left- and right-circularly polarized modes in a cholesteric liquid crystal. Whereas optical rotation measurements only determine the circular birefringence, i.e. the difference (nL - nR), the interferometer also permits the determination of their absolute values. We report refractive indices of a cholesteric liquid crystal in the region of selective (Bragg) reflection as a function of temperature. PMID:25607071

  14. Tiny telomere DNA

    PubMed Central

    Ren, Jinsong; Qu, Xiaogang; Trent, John O.; Chaires, Jonathan B.

    2002-01-01

    We describe the design, synthesis and biophysical characterization of a novel DNA construct in which a folded quadruplex structure is joined to a standard double helix. Circular dichroism, gel electrophoresis, three-dimensional UV melting and differential scanning calorimetry were all used to characterize the structure. Rigorous molecular dynamics simulations were used to build a plausible atomic-level structural model of the DNA construct. This novel DNA construct provides a model for the duplex–quadruplex junction region at the end of chromosomal DNA and offers a system for the study of structure-selective ligand binding. PMID:12034817

  15. Generalized bi-circular projections

    NASA Astrophysics Data System (ADS)

    Lin, Pei-Kee

    2008-04-01

    Recall that a projection P on a complex Banach space X is a generalized bi-circular projection if P+[lambda](I-P) is a (surjective) isometry for some [lambda] such that [lambda]=1 and [lambda][not equal to]1. It is easy to see that every hermitian projection is generalized bi-circular. A generalized bi-circular projection is said to be nontrivial if it is not hermitian. Botelho and Jamison showed that a projection P on C([0,1]) is a nontrivial generalized bi-circular projection if and only if P-(I-P) is a surjective isometry. In this article, we prove that if P is a projection such that P+[lambda](I-P) is a (surjective) isometry for some [lambda], then either P is hermitian or [lambda] is an nth unit root of unity. We also show that for any nth unit root [lambda] of unity, there are a complex Banach space X and a nontrivial generalized bi-circular projection P on X such that P+[lambda](I-P) is an isometry.

  16. Circular codes, symmetries and transformations.

    PubMed

    Fimmel, Elena; Giannerini, Simone; Gonzalez, Diego Luis; Strüngmann, Lutz

    2015-06-01

    Circular codes, putative remnants of primeval comma-free codes, have gained considerable attention in the last years. In fact they represent a second kind of genetic code potentially involved in detecting and maintaining the normal reading frame in protein coding sequences. The discovering of an universal code across species suggested many theoretical and experimental questions. However, there is a key aspect that relates circular codes to symmetries and transformations that remains to a large extent unexplored. In this article we aim at addressing the issue by studying the symmetries and transformations that connect different circular codes. The main result is that the class of 216 C3 maximal self-complementary codes can be partitioned into 27 equivalence classes defined by a particular set of transformations. We show that such transformations can be put in a group theoretic framework with an intuitive geometric interpretation. More general mathematical results about symmetry transformations which are valid for any kind of circular codes are also presented. Our results pave the way to the study of the biological consequences of the mathematical structure behind circular codes and contribute to shed light on the evolutionary steps that led to the observed symmetries of present codes. PMID:25008961

  17. Circular birefringence of banded spherulites.

    PubMed

    Cui, Xiaoyan; Shtukenberg, Alexander G; Freudenthal, John; Nichols, Shane; Kahr, Bart

    2014-04-01

    Crystal optical properties of banded spherulites of 21 different compounds--molecular crystals, polymers, and minerals--with helically twisted fibers were analyzed with Mueller matrix polarimetry. The well-established radial oscillations in linear birefringence of many polycrystalline ensembles is accompanied by oscillations in circular birefringence that cannot be explained by the natural optical activity of corresponding compounds, some of which are centrosymmetric in the crystalline state. The circular birefringence is shown to be a consequence of misoriented, overlapping anisotropic lamellae, a kind of optical activity associated with the mesoscale stereochemistry of the refracting components. Lamellae splay as a consequence of space constraints related to simultaneous twisting of anisometric lamellae. This mechanism is supported by quantitative simulations of circular birefringence arising from crystallite twisting and splaying under confinement. PMID:24625095

  18. Stable expression and replication of hepatitis B virus genome in an integrated state in a human hepatoma cell line transfected with the cloned viral DNA

    SciTech Connect

    Tsurimoto, T.; Fujiyama, A.; Matsubara, K.

    1987-01-01

    A human hepatocellular carcinoma cell line (Huh6-c15) was transfected with a recombinant DNA molecule that consists of tandemly arranged hepatitis B virus (HBV) genome and a neomycin-resistant gene. One clone resistant to G-418 produces and releases surface antigen and e antigen into medium at a high level and accumulates core particles intracellularly. This clone has a chromosomally integrated set of the original recombinant DNA and produces a 3.5-kilobase transcript corresponding to the pregenome RNA as well as HBV DNAs in an extrachromosomal form. Most of these DNAs were in single-stranded or partially double-stranded form and were packaged in the intracellular core particles. In the medium, particles were detected that contained HBV DNA and were morphologically indistinguishable from Dane particles. These results demonstrate that the HBV genome in an integrated state acted as a template for viral gene expression and replication. The cells were maintained for more than 6 months without losing the ability to produce the extrachromosomal HBV DNA and Dane-like particles. Thus, the cells can be used as a model system for analyses of gene expression and DNA replication of HBV in human hepatocytes.

  19. Podokinetic circular vection: characteristics and interaction with optokinetic circular vection.

    PubMed

    Becker, W; Kliegl, K; Kassubek, J; Jürgens, R

    2016-07-01

    Stabilising horizontal body orientation in space without sight on a rotating platform by holding to a stationary structure and circular 'treadmill' stepping in the opposite direction can elicit an illusion of self-turning in space (Bles and Kapteyn in Agressologie 18:325-328, 1977). Because this illusion is analogous to the well-known illusion of optokinetic circular vection (oCV), we call it 'podokinetic circular vection' (pCV) here. Previous studies using eccentric stepping on a path tangential to the rotation found that pCV was always contraversive relative to platform rotation. In contrast, when our subjects stepped at the centre of rotation about their vertical axis, we observed an inverted, ipsiversive pCV as a reproducible trait in many of our subjects. This ipCV occurred at the same latency as the pCV of subjects reporting the actually expected contraversive direction, but had lower gain. In contrast to pCV, the nystagmus accompanying circular treadmill stepping had the same direction in all individuals (slow phase in the direction of platform motion). The direction of an individual's pCV predicted the characteristics of the CV resulting from combined opto- and podokinetic stimulation (circular treadmill stepping while viewing a pattern rotating together with the platform): in individuals with contraversive pCV, latency shortened and both gain and felt naturalness increased in comparison with pure oCV, whereas the opposite (longer latency, reduced gain and naturalness) occurred in individuals with ipCV. Taken together, the reproducibility of ipCV, the constant direction of nystagmus and the fact that pCV direction predicts the outcome of combined stimulation suggest that ipCV is an individual trait of many subjects during compensatory stepping at the centre of rotation. A hypothetical model is presented of how ipCV possibly could arise. PMID:26965438

  20. Maximal dinucleotide and trinucleotide circular codes.

    PubMed

    Michel, Christian J; Pellegrini, Marco; Pirillo, Giuseppe

    2016-01-21

    We determine here the number and the list of maximal dinucleotide and trinucleotide circular codes. We prove that there is no maximal dinucleotide circular code having strictly less than 6 elements (maximum size of dinucleotide circular codes). On the other hand, a computer calculus shows that there are maximal trinucleotide circular codes with less than 20 elements (maximum size of trinucleotide circular codes). More precisely, there are maximal trinucleotide circular codes with 14, 15, 16, 17, 18 and 19 elements and no maximal trinucleotide circular code having less than 14 elements. We give the same information for the maximal self-complementary dinucleotide and trinucleotide circular codes. The amino acid distribution of maximal trinucleotide circular codes is also determined. PMID:26382231

  1. Nanocrystal-based electrochemiluminescence sensor for cell detection with Au nanoparticles and isothermal circular double-assisted signal amplification.

    PubMed

    Dai, Pan-Pan; Li, Jin-Yi; Yu, Tao; Xu, Jing-Juan; Chen, Hong-Yuan

    2015-08-15

    Here we have developed a sensitive cancer cell amplified detection method which combined Au NPs enhanced electrochemiluminescence (ECL) of CdS nanocrystals (NCs) film, with isothermal circular amplification reaction of polymerase. In DNA circular amplification detection system, hairpin DNA beacon/Au NPs composite modified CdS NCs film was used as an ECL emitter. Messenger DNA is hybridized with the aptamer modified on magnetic beads (MBs) to form MB-Au bioconjugates. In the presence of HL-60 cell, the aptamer would conjugate with the glycoprotein at cell surface and messenger DNA sequence would be released. The released messenger DNA sequence was then introduced into the cycle amplification system to trigger circular polymerizations. This assay allows us to determine the released messenger DNA equivalent to 10 cells and exhibits a significant specificity for HL-60 cells. PMID:25966387

  2. Comparison of the Single Molecule Dynamics of Linear and Circular DNAs in Planar Extensional Flows

    NASA Astrophysics Data System (ADS)

    Li, Yanfei; Hsiao, Kai-Wen; Brockman, Christopher; Yates, Daniel; McKenna, Gregory; Schroeder, Charles; San Francisco, Michael; Kornfield, Julie; Anderson, Rae

    2015-03-01

    Chain topology has a profound impact on the flow behaviors of single macromolecules. The absence of free ends separates circular polymers from other chain architectures, i.e., linear, star, and branched. In the present work, we study the single chain dynamics of large circular and linear DNA molecules by comparing the relaxation dynamics, steady state coil-stretch transition, and transient molecular individualism behaviors for the two types of macromolecules. To this end, large circular DNA molecules were biologically synthesized and studied in a microfluidic device that has a cross-slot geometry to develop a stagnation point extensional flow. Although the relaxation time of rings scales in the same way as for the linear analog, the circular polymers show quantitatively different behaviors in the steady state extension and qualitatively different behaviors during a transient stretch. The existence of some commonality between these two topologies is proposed. Texas Tech University John R. Bradford Endowment.

  3. Circular RNA expands its territory.

    PubMed

    Bao, Chunyang; Lyu, Dongbin; Huang, Shenglin

    2016-03-01

    Circular RNAs (circRNAs) represent a novel class of widespread non-coding RNAs in eukaryotes. They are unusually stable RNA molecules with cell type-specific expression patterns, and are predominantly present in the cytoplasm. We recently demonstrated the existence of abundant circRNAs in exosomes and suggest a potential application of exosomal circRNAs for cancer detection. PMID:27308606

  4. Isolation of a complete circular virus genome sequence from an Alaskan black-capped chickadee (Poecile atricapillus) gastrointestinal tract sample.

    USGS Publications Warehouse

    Hanna, Zachary R.; Runckel, Charles; Fuchs, Jerome; DeRisi, Joseph L.; Mindell, David P.; Van Hemert, Caroline R.; Handel, Colleen M.; Dumbacher, John P.

    2015-01-01

    We report here the genome sequence of a circular virus isolated from samples of an Alaskan black-capped chickadee (Poecile atricapillus) gastrointestinal tract. The genome is 2,152 bp in length and is most similar (30 to 44.5% amino acid identity) to the genome sequences of other single-stranded DNA (ssDNA) circular viruses belonging to the gemycircularvirus group.

  5. 17 CFR 230.253 - Offering circular.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... in boldfaced type at least as large as that used generally in the body of such offering circular: THE... COMPLETENESS OF ANY OFFERING CIRCULAR OR OTHER SELLING LITERATURE. THESE SECURITIES ARE OFFERED PURSUANT TO...

  6. Local chromatin structure of heterochromatin regulates repeatedDNA stability, nucleolus structure, and genome integrity

    SciTech Connect

    Peng, Jamy C.

    2007-05-05

    Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in

  7. CpG methylation patterns of human mitochondrial DNA

    PubMed Central

    Liu, Baojing; Du, Qingqing; Chen, Lu; Fu, Guangping; Li, Shujin; Fu, Lihong; Zhang, Xiaojing; Ma, Chunling; Bin, Cong

    2016-01-01

    The epigenetic modification of mitochondrial DNA (mtDNA) is still in controversy. To clarify this point, we applied the gold standard method for DNA methylation, bisulfite pyrosequencing, to examine human mtDNA methylation status. Before bisulfite conversion, BamHI was used to digest DNA to open the loop of mtDNA. The results demonstrated that the linear mtDNA had significantly higher bisulfite conversion efficiency compared with circular mtDNA. Furthermore, the methylation values obtained from linear mtDNA were significantly lower than that of circular mtDNA, which was verified by SEQUENOM MassARRAY. The above impacts of circular structure were also observed in lung DNA samples but not in saliva DNA samples. Mitochondrial genome methylation of blood samples and saliva samples from 14 unrelated individuals was detected. The detected regions covered 83 CpG sites across mtDNA including D-loop, 12 S rRNA, 16 S rRNA, ND1, COXI, ND3, ND4, ND5, CYTB. We found that the average methylation levels of nine regions were all less than 2% for both sample types. In conclusion, our findings firstly show that the circular structure of mtDNA affects bisulfite conversion efficiency, which leads to overestimation of mtDNA methylation values. CpG methylation in human mtDNA is a very rare event at most DNA regions. PMID:26996456

  8. CpG methylation patterns of human mitochondrial DNA.

    PubMed

    Liu, Baojing; Du, Qingqing; Chen, Lu; Fu, Guangping; Li, Shujin; Fu, Lihong; Zhang, Xiaojing; Ma, Chunling; Bin, Cong

    2016-01-01

    The epigenetic modification of mitochondrial DNA (mtDNA) is still in controversy. To clarify this point, we applied the gold standard method for DNA methylation, bisulfite pyrosequencing, to examine human mtDNA methylation status. Before bisulfite conversion, BamHI was used to digest DNA to open the loop of mtDNA. The results demonstrated that the linear mtDNA had significantly higher bisulfite conversion efficiency compared with circular mtDNA. Furthermore, the methylation values obtained from linear mtDNA were significantly lower than that of circular mtDNA, which was verified by SEQUENOM MassARRAY. The above impacts of circular structure were also observed in lung DNA samples but not in saliva DNA samples. Mitochondrial genome methylation of blood samples and saliva samples from 14 unrelated individuals was detected. The detected regions covered 83 CpG sites across mtDNA including D-loop, 12 S rRNA, 16 S rRNA, ND1, COXI, ND3, ND4, ND5, CYTB. We found that the average methylation levels of nine regions were all less than 2% for both sample types. In conclusion, our findings firstly show that the circular structure of mtDNA affects bisulfite conversion efficiency, which leads to overestimation of mtDNA methylation values. CpG methylation in human mtDNA is a very rare event at most DNA regions. PMID:26996456

  9. Circular on planned parenthood, 1987.

    PubMed

    1987-01-01

    In 1987 fourteen units of the Government of Henan issued a Circular stating that: "Planned parenthood must be publicized deep into the grass roots and among the people, and importance must be attached to results." The Circular stresses: "In the propaganda drive, it is necessary to successfully grasp three key links: 1. It is necessary to disseminate intensively the important directive on population problems that is contained in the report of the 13th CPC National Congress and the seriousness of the population situation of our country and province so that the cadres and the masses can understand the relationship between population control and the achievement of the strategic target of the three big steps, understand the reason for carrying out planned parenthood, understand that the one-child policy is still advocated, and conscientiously carry out planned parenthood. 2. It is essential to succeed in propagating knowledge of contraception, sterilization, childbirth, and child care and in conducting ideological education for those who undergo operations and for their family members. 3. It is imperative to visit those who have undergone operations and to help them solve practically their difficulties in making a living." The Circular concludes by demanding that under the unified leadership of party committees and governments at all levels, the propaganda drive be carried out by relying on the efforts of all of society. In conjunction with their own work, departments, including the propaganda, education, public health, and cultural departments, must carry out propaganda and education for planned parenthood. PMID:12346601

  10. The circular internal hydraulic jump

    NASA Astrophysics Data System (ADS)

    Thorpe, S. A.; Kavcic, I.

    Circular hydraulic jumps are familiar in single layers. Here we report the discovery of similar jumps in two-layer flows. A thin jet of fluid impinging vertically onto a rigid horizontal plane surface submerged in a deep layer of less-dense miscible fluid spreads radially, and a near-circular internal jump forms within a few centimetres from the point of impact with the plane surface. A jump is similarly formed as a jet of relatively less-dense fluid rises to the surface of a deep layer of fluid, but it appears less stable or permanent in form. Several experiments are made to examine the case of a downward jet onto a horizontal plate, the base of a square or circular container. The inlet Reynolds numbers, Re, of the jet range from 112 to 1790. Initially jumps have an undular, laminar form with typically 2-4 stationary waves on the interface between the dense and less-dense layers but, as the depth of the dense layer beyond the jump increases, the transitions become more abrupt and turbulent, resulting in mixing between the two layers. During the transition to a turbulent regime, single and sometimes moving multiple cusps are observed around the periphery of jumps. A semi-empirical model is devised that relates the parameters of the laboratory experiment, i.e. flow rate, inlet nozzle radius, kinematic viscosity and reduced gravity, to the layer depth beyond the jump and the radius at which an undular jump occurs. The experiments imply that surface tension is not an essential ingredient in the formation of circular hydraulic jumps and demonstrate that stationary jumps can exist in stratified shear flows which can be represented as two discrete layers. No stationary circular undular jumps are found, however, in the case of a downward jet of dense fluid when the overlying, less-dense, fluid is stratified, but a stationary turbulent transition is observed. This has implications for the existence of stationary jumps in continuously stratified geophysical flows: results

  11. Exon circularization requires canonical splice signals.

    PubMed

    Starke, Stefan; Jost, Isabelle; Rossbach, Oliver; Schneider, Tim; Schreiner, Silke; Hung, Lee-Hsueh; Bindereif, Albrecht

    2015-01-01

    Circular RNAs (circRNAs), an abundant class of noncoding RNAs in higher eukaryotes, are generated from pre-mRNAs by circularization of adjacent exons. Using a set of 15 circRNAs, we demonstrated their cell-type-specific expression and circular versus linear processing in mammalian cells. Northern blot analysis combined with RNase H cleavage conclusively proved a circular configuration for two examples, LPAR1 and HIPK3. To address the circularization mechanism, we analyzed the sequence requirements using minigenes derived from natural circRNAs. Both canonical splice sites are required for circularization, although they vary in flexibility and potential use of cryptic sites. Surprisingly, we found that no specific circRNA exon sequence is necessary and that potential flanking intron structures can modulate circularization efficiency. In combination with splice inhibitor assays, our results argue that the canonical spliceosomal machinery functions in circRNA biogenesis, constituting an alternative splicing mode. PMID:25543144

  12. Conformation-selective methylation of geminivirus DNA.

    PubMed

    Paprotka, T; Deuschle, K; Metzler, V; Jeske, H

    2011-11-01

    Geminiviruses with small circular single-stranded DNA genomes replicate in plant cell nuclei by using various double-stranded DNA (dsDNA) intermediates: distinct open circular and covalently closed circular as well as heterogeneous linear DNA. Their DNA may be methylated partially at cytosine residues, as detected previously by bisulfite sequencing and subsequent PCR. In order to determine the methylation patterns of the circular molecules, the DNAs of tomato yellow leaf curl Sardinia virus (TYLCSV) and Abutilon mosaic virus were investigated utilizing bisulfite treatment followed by rolling circle amplification. Shotgun sequencing of the products yielded a randomly distributed 50% rate of C maintenance after the bisulfite reaction for both viruses. However, controls with unmethylated single-stranded bacteriophage DNA resulted in the same level of C maintenance. Only one short DNA stretch within the C2/C3 promoter of TYLCSV showed hyperprotection of C, with the protection rate exceeding the threshold of the mean value plus 1 standard deviation. Similarly, the use of methylation-sensitive restriction enzymes suggested that geminiviruses escape silencing by methylation very efficiently, by either a rolling circle or recombination-dependent replication mode. In contrast, attempts to detect methylated bases positively by using methylcytosine-specific antibodies detected methylated DNA only in heterogeneous linear dsDNA, and methylation-dependent restriction enzymes revealed that the viral heterogeneous linear dsDNA was methylated preferentially. PMID:21835804

  13. Flexural Vibrations of Circular Beams

    NASA Astrophysics Data System (ADS)

    Silverman, I. K.

    1998-03-01

    For circular cylindrical beams, the Timoshenko theory, which includes shear and rotary effects, can be applied by introducing a constantK‧=0·9. The study presented here takes into account the actual configuration and thus makes it an integral part of the analysis. A variational approach previously used [7] is followed. A simplification of the three-dimensional problem is obtained using the inverse method due to St. Venant. A biquadratic equation yields numerical results for the natural frequencies of the first three modes for the following cases: simply supported, fixed-fixed, free-free and fixed-free.

  14. Conversion of a linear to a circular plasmid in the relapsing fever agent Borrelia hermsii.

    PubMed Central

    Ferdows, M S; Serwer, P; Griess, G A; Norris, S J; Barbour, A G

    1996-01-01

    Spirochetes of the genus Borrelia have genomes composed of both linear and circular replicons. We characterized the genomic organization of B. burgdorferi, B. hermsii, B. turicatae, and B. anserina with pulsed-field gel electrophoresis. All four species contained a linear chromosome approximately 1 Mb in size and multiple linear plasmids in the 16- to 200-kb size range. Plasmids 180 and 170 kb in size, present in the relapsing fever agents B. hermsii and B. turicatae but not in the other two species, behaved as linear duplex DNA molecules under different electrophoretic conditions. A variant of strain HSI of B. hermsii had a 180-kb circular instead of linear plasmid. There were no detectable differences in the growth rates or in the expression of cellular proteins between cells bearing linear forms and those bearing circular forms of the plasmid. The conversion to a circular conformation of monomeric length was demonstrated by the introduction of strand breaks with irradiation, restriction endonuclease analysis, and direct observation of the DNA molecules by fluorescent microscopy. Consideration of different models for the replication of linear DNA suggests that circular intermediates may be involved in the replication of linear replicons in Borrelia spp. PMID:8550515

  15. Physics at Future Circular Colliders

    NASA Astrophysics Data System (ADS)

    Kotwal, Ashutosh

    2016-03-01

    The Large Hadron Collider has been a grand success with the discovery of the Higgs boson, with bright prospects for additional discoveries since the recent increase in collider energy and the anticipated large datasets. Big open questions such as the nature of dark matter, the origin of the matter-antimatter asymmetry in the Universe, and the theoretical puzzle of the finely-tuned parameters in the Higgs sector, demand new physics principles that extend the established Standard Model paradigm. Future circular colliders in a substantially larger tunnel can house both a high luminosity electron-positron collider for precision measurements of Higgs and electroweak parameters, as well as a very high energy proton-proton collider which can directly manifest particles associated with these new physics principles. We discuss the physics goals of these future circular colliders, and the prospects for elucidating fundamental new laws of nature that will significantly extend our understanding of the Universe. Detailed studies of the discovery potential in specific benchmark models will be presented, with implications for detector design.

  16. Method of oriented circular dichroism.

    PubMed Central

    Wu, Y; Huang, H W; Olah, G A

    1990-01-01

    We present a new method for determining the orientation of alpha-helical sections of proteins or peptides in membrane. To apply this method, membranes containing proteins must be prepared in a multilayer array. Circular dichroism (CD) spectra of the multilayer sample are then measured at the normal as well as oblique incident angles with respect to the bilayer planes; we call such spectra oriented circular dichroism (OCD). The procedure of OCD measurement, particularly the ways to avoid the spectral artifacts due to the effects of dielectric interfaces, linear dichroism and birefringence, and the method of data analysis are described in detail. To illustrate the method, we analyze the OCD of alamethicin in diphytanoylphosphatidylcholine multilayers. We conclude unambiguously that the helical section of alamethicin is parallel to the membrane normal when the sample is in the full-hydration state, but the helical section rotates to the plane of membrane when the sample is in a low-hydration state. We also obtained the parallel and perpendicular CD spectra of alpha-helix, and found them to be in agreement with previous theoretical calculations based on the exciton theory. These spectra are useful for analyzing protein orientations in future experiments. Images FIGURE 5 PMID:2344464

  17. Amplification of target-specific, ligation-dependent circular probe.

    PubMed

    Zhang, D Y; Brandwein, M; Hsuih, T C; Li, H

    1998-05-12

    We describe a novel polymerase chain reaction (PCR)-based gene amplification method utilizing a circularizable oligodeoxyribonucleotide probe (C-probe). The C-probe contains two target complementary regions located at each terminus and an interposed generic PCR primer binding region. The hybridization of C-probe to a target brings two termini in direct apposition as the complementary regions of C-probe wind around the target to form a double helix. Subsequent ligation of the two termini results in a covalently linked C-probe that becomes 'locked on to' the target. The circular nature of the C-probe allows for the generation of a multimeric single-stranded DNA (ssDNA) via extension of the antisense primer by Taq DNA polymerase along the C-probe and displacement of downstream strand, analogous to 'rolling circle' replication of bacteriophage in vivo. This multimeric ssDNA then serves as a template for multiple sense primers to hybridize, extend, and displace downstream DNA, generating a large ramified (branching) DNA complex. Subsequent thermocycling denatures the dsDNA and initiates the next round of primer extension and ramification. This model results in significantly improved amplification kinetics (super-exponential) as compared to conventional PCR. Our results show that the C-probe was 1000 times more sensitive than the corresponding linear hemiprobes for detecting Epstein-Barr virus early RNA. The C-probe not only increases the power of amplification but also offers a means for decontaminating carryover amplicons. As the ligated C-probes possess no free termini, they are resistant to exonuclease digestion, whereas contaminated linear amplicons are susceptible to digestion. Treatment of the ligation reaction mixture with exonuclease prior to amplification eliminated the amplicon contaminant, which could also have been co-amplified with the same PCR primers; only the ligated C-probes were amplified. The combined advantages of the C-probe and thermocycling have a

  18. Circular permutant GFP insertion folding reporters

    SciTech Connect

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2013-04-16

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  19. Circular permutant GFP insertion folding reporters

    DOEpatents

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2008-06-24

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  20. Circular permutant GFP insertion folding reporters

    DOEpatents

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2011-06-14

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  1. Circular permutant GFP insertion folding reporters

    DOEpatents

    Waldo, Geoffrey S; Cabantous, Stephanie

    2013-02-12

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  2. Bijective transformation circular codes and nucleotide exchanging RNA transcription.

    PubMed

    Michel, Christian J; Seligmann, Hervé

    2014-04-01

    The C(3) self-complementary circular code X identified in genes of prokaryotes and eukaryotes is a set of 20 trinucleotides enabling reading frame retrieval and maintenance, i.e. a framing code (Arquès and Michel, 1996; Michel, 2012, 2013). Some mitochondrial RNAs correspond to DNA sequences when RNA transcription systematically exchanges between nucleotides (Seligmann, 2013a,b). We study here the 23 bijective transformation codes ΠX of X which may code nucleotide exchanging RNA transcription as suggested by this mitochondrial observation. The 23 bijective transformation codes ΠX are C(3) trinucleotide circular codes, seven of them are also self-complementary. Furthermore, several correlations are observed between the Reading Frame Retrieval (RFR) probability of bijective transformation codes ΠX and the different biological properties of ΠX related to their numbers of RNAs in GenBank's EST database, their polymerization rate, their number of amino acids and the chirality of amino acids they code. Results suggest that the circular code X with the functions of reading frame retrieval and maintenance in regular RNA transcription, may also have, through its bijective transformation codes ΠX, the same functions in nucleotide exchanging RNA transcription. Associations with properties such as amino acid chirality suggest that the RFR of X and its bijective transformations molded the origins of the genetic code's machinery. PMID:24565870

  3. Electrodynamics of circular dichroism and its application in the construction of a circular polaroid

    NASA Astrophysics Data System (ADS)

    Volobuev, A. N.

    2016-03-01

    Electrodynamic principles of circular dichroism are developed using a concept of conducting circular structures in matter. A simplified representation of material equations for an optically active medium is obtained in the absence of a transition to the complex domain. A dependence of the absorption coefficient of a circular polarization as a component of the linearly polarized radiation on material parameters is found. Such parameters are analyzed to reveal a possibility of construction of a circular polaroid.

  4. A Random Walk on a Circular Path

    ERIC Educational Resources Information Center

    Ching, W.-K.; Lee, M. S.

    2005-01-01

    This short note introduces an interesting random walk on a circular path with cards of numbers. By using high school probability theory, it is proved that under some assumptions on the number of cards, the probability that a walker will return to a fixed position will tend to one as the length of the circular path tends to infinity.

  5. Microstrip Antenna Generates Circularly Polarized Beam

    NASA Technical Reports Server (NTRS)

    Huang, J.

    1986-01-01

    Circular microstrip antenna excited with higher order transverse magnetic (TM) modes generates circularly polarized, conical radiation patterns. Found both theoretically and experimentally that peak direction of radiation pattern is varied within wide angular range by combination of mode selection and loading substrate with materials of different dielectric constants.

  6. DNA Technology in the Classroom.

    ERIC Educational Resources Information Center

    Williamson, John H.; Campbell, A. Malcolm

    1997-01-01

    Presents a protocol that gives students hands-on experience in generating a meaningful physical map of a circular molecule of DNA. Topics include agarose gel electrophoresis, logic of restriction maps, extracting data from an agarose gel, managing data from gels, experimental protocol, loading gels, electrophoresis, photographing gels, collecting…

  7. Circular RNAs: diversity of form and function.

    PubMed

    Lasda, Erika; Parker, Roy

    2014-12-01

    It is now clear that there is a diversity of circular RNAs in biological systems. Circular RNAs can be produced by the direct ligation of 5' and 3' ends of linear RNAs, as intermediates in RNA processing reactions, or by "backsplicing," wherein a downstream 5' splice site (splice donor) is joined to an upstream 3' splice site (splice acceptor). Circular RNAs have unique properties including the potential for rolling circle amplification of RNA, the ability to rearrange the order of genomic information, protection from exonucleases, and constraints on RNA folding. Circular RNAs can function as templates for viroid and viral replication, as intermediates in RNA processing reactions, as regulators of transcription in cis, as snoRNAs, and as miRNA sponges. Herein, we review the breadth of circular RNAs, their biogenesis and metabolism, and their known and anticipated functions. PMID:25404635

  8. Gauge-Invariant Formulation of Circular Dichroism.

    PubMed

    Raimbault, Nathaniel; de Boeij, Paul L; Romaniello, Pina; Berger, J A

    2016-07-12

    Standard formulations of magnetic response properties, such as circular dichroism spectra, are plagued by gauge dependencies, which can lead to unphysical results. In this work, we present a general gauge-invariant and numerically efficient approach for the calculation of circular dichroism spectra from the current density. First we show that in this formulation the optical rotation tensor, the response function from which circular dichroism spectra can be obtained, is independent of the origin of the coordinate system. We then demonstrate that its trace is independent of the gauge origin of the vector potential. We also show how gauge invariance can be retained in practical calculations with finite basis sets. As an example, we explain how our method can be applied to time-dependent current-density-functional theory. Finally, we report gauge-invariant circular dichroism spectra obtained using the adiabatic local-density approximation. The circular dichroism spectra we thus obtain are in good agreement with experiment. PMID:27295541

  9. Circular RNAs in Eukaryotic Cells

    PubMed Central

    Chen, Liang; Huang, Chuan; Wang, Xiaolin; Shan, Ge

    2015-01-01

    Circular RNAs (circRNAs) are now recognized as large species of transcripts in eukaryotic cells. From model organisms such as C. elegans, Drosophila, mice to human beings, thousands of circRNAs formed from back-splicing of exons have been identified. The known complexity of transcriptome has been greatly expanded upon the discovery of these RNAs. Studies about the biogenesis and physiological functions have yielded substantial knowledge for the circRNAs, and they are now more likely to be viewed as regulatory elements coded by the genome rather than unavoidable noise of gene expression. Certain human diseases may also relate to circRNAs. These circRNAs show diversifications in features such as sequence composition and cellular localization, and thus we propose that they may be divided into subtypes such as cytoplasmic circRNAs, nuclear circRNAs, and exon-intron circRNAs (EIciRNAs). Here we summarize and discuss knowns and unknowns for these RNAs, and we need to keep in mind that the whole field is still at the beginning of exciting explorations. PMID:27047251

  10. Circular on family planning, 1988.

    PubMed

    1988-01-01

    This Hubei, China, Circular, issued near the end of 1988, provides the following: "The population growth situation in our country is grim. Since 1986, the natural population growth rate has risen continuously. To draw the prompt attention of the whole party and the entire people to the issue of our population, all localities must seriously unfold the activities of publicizing family planning (FP) this winter and next spring, in coordination with education in current affairs. It is necessary to publicize FP in an all-around way and with accuracy, and the activities of publicizing must be carried out effectively in a solid and deep-going way. In the rural areas, stress must be placed on areas where FP work is not carried out well and where there is a prevailing tendency toward early marriage, early child-bearing, and extra-budgetary births. In cities, publicity and education must be conducted especially among the transient population, individual households, and jobless households. During the period of publicity, large-scale street-corner publicity activities must be carried out in cities and towns so as to create strong public opinion and to combine the endeavor to publicize current affairs and policies with the effort to popularize knowledge about contraception and birth-control, to execute measures of contraception and birth control, and to establish FP associations in the countryside." PMID:12289626

  11. Circular protecting female students, 1988.

    PubMed

    1988-01-01

    In 1988 the Ministry of Education of Benin issued a Circular designed to protect female students from sexual advances from male students and teachers. Teachers who are suspected of having sexual relations with a student are to receive a note in their file or can be suspended for a month. Teachers who have raped a student or are responsible for a student's pregnancy are to be suspended for three months if the student was not in their class, and six months if she was. Teachers who have incited their sexual partner to have an abortion are subject to demotion. Teachers who are repeat offenders or whose actions have led to an abortion resulting in death are to be fired. Students who have made a female student pregnant are to be suspended from school until delivery of the child and then are to be enrolled in a different school. The directors of schools are asked to put an end to the provocative clothes, make-up, and hairstyles of female students. PMID:12289212

  12. Rapid Detection and Identification of a Pathogen's DNA Using Phi29 DNA Polymerase

    SciTech Connect

    Xu, Y.; Dunn, J.; Gao, S.; Bruno, J. F.; Luft, B. J.

    2008-10-31

    Zoonotic pathogens including those transmitted by insect vectors are some of the most deadly of all infectious diseases known to mankind. A number of these agents have been further weaponized and are widely recognized as being potentially significant biothreat agents. We describe a novel method based on multiply-primed rolling circle in vitro amplification for profiling genomic DNAs to permit rapid, cultivation-free differential detection and identification of circular plasmids in infectious agents. Using Phi29 DNA polymerase and a two-step priming reaction we could reproducibly detect and characterize by DNA sequencing circular DNA from Borrelia burgdorferi B31 in DNA samples containing as little as 25 pg of Borrelia DNA amongst a vast excess of human DNA. This simple technology can ultimately be adapted as a sensitive method to detect specific DNA from both known and unknown pathogens in a wide variety of complex environments.

  13. Generation of circular polarization of the CMB

    NASA Astrophysics Data System (ADS)

    Zarei, M.; Bavarsad, E.; Haghighat, M.; Mohammadi, R.; Motie, I.; Rezaei, Z.

    2010-04-01

    According to the standard cosmology, near the last scattering surface, the photons scattered via Compton scattering are just linearly polarized and then the primordial circular polarization of the cosmic microwave background (CMB) photons is zero. In this work we show that CMB polarization acquires a small degree of circular polarization when a background magnetic field is considered or the quantum electrodynamic sector of standard model is extended by Lorentz-noninvariant operators as well as noncommutativity. The existence of circular polarization for the CMB radiation may be verified during future observation programs, and it represents a possible new channel for investigating new physics effects.

  14. Entanglement of quantum circular states of light

    NASA Astrophysics Data System (ADS)

    Horoshko, D. B.; De Bièvre, S.; Kolobov, M. I.; Patera, G.

    2016-06-01

    We present a general approach to calculating the entanglement of formation for superpositions of two-mode coherent states, placed equidistantly on a circle in phase space. We show that in the particular case of rotationally invariant circular states the Schmidt decomposition of two modes, and therefore the value of their entanglement, are given by analytical expressions. We analyze the dependence of the entanglement on the radius of the circle and number of components in the superposition. We also show that the set of rotationally invariant circular states creates an orthonormal basis in the state space of the harmonic oscillator, and this basis is advantageous for representation of other circular states of light.

  15. Circular Polarization in PKS 1519-273

    NASA Astrophysics Data System (ADS)

    Bennett, W.; Macquart, J. P.; Johnston, H.; Jauncey, D.

    2005-12-01

    The intra-day variable BL Lac PKS 1519-273 exhibits variations at centimeter wavelengths in total intensity, linear polarization, and circular polarization. Their variability is caused by scintillation due to the interstellar medium. PKS 1519-273 displays 4% circular polarization at 4.8 GHz and the variability has persisted as long as the source has been observed. We present observations of this source over several years, showing that the circularly polarized emission is highly variable on micro-arcsecond scales. We determine properties of the structure of the emission by examining the light curves and associated scintillation theory.

  16. Production of Double-stranded DNA Ministrings

    PubMed Central

    Wong, Shirley; Lam, Peggy; Nafissi, Nafiseh; Denniss, Steven; Slavcev, Roderick

    2016-01-01

    We constructed linear covalently closed (LCC) DNA minivectors as a non-viral gene-delivery vector alternative produced via a simple platform in vivo. DNA ministrings possess a heightened safety profile and also efficiently deliver DNA cargo to targeted cells. Conventional DNA vectors carry undesirable prokaryotic sequences, including antibiotic resistance genes, CpG motifs, and bacterial origins of replication, which may lead to the stimulation of host immunological responses. The bioavailability of conventional DNA vectors is also compromised due to their larger molecular size. Their circular nature may also impart chromosomal integration, leading to insertional mutagenesis. Bacterial sequences are excised from DNA minivectors, leaving only the gene of interest (GOI) and necessary eukaryotic expression elements. Our LCC DNA minivectors, or DNA ministrings, are devoid of immunogenic bacterial sequences; therefore improving their bioavailability and GOI expression. In the event of vector integration into the chromosome, the LCC DNA ministring will lethally disrupt the host chromosome, thereby removing the potentially dangerous mutant from the proliferating cell population. Consequently, DNA ministrings offer the benefits of 'minicircle' DNA while eliminating the potential for undesirable vector integration events. In comparison to conventional plasmids and their isogenic circular covalently closed (CCC) counterparts, DNA ministrings demonstrate superior bioavailability, transfection efficiency, and cytoplasmic kinetics - they thus require lower amounts of cationic surfactants for effective transfection of target cells. We have constructed a one-step inducible in vivo system for the production of DNA ministrings in Escherichia coli that is simple to use, rapid, and scalable. PMID:26967586

  17. Production of Double-stranded DNA Ministrings.

    PubMed

    Wong, Shirley; Lam, Peggy; Nafissi, Nafiseh; Denniss, Steven; Slavcev, Roderick

    2016-01-01

    We constructed linear covalently closed (LCC) DNA minivectors as a non-viral gene-delivery vector alternative produced via a simple platform in vivo. DNA ministrings possess a heightened safety profile and also efficiently deliver DNA cargo to targeted cells. Conventional DNA vectors carry undesirable prokaryotic sequences, including antibiotic resistance genes, CpG motifs, and bacterial origins of replication, which may lead to the stimulation of host immunological responses. The bioavailability of conventional DNA vectors is also compromised due to their larger molecular size. Their circular nature may also impart chromosomal integration, leading to insertional mutagenesis. Bacterial sequences are excised from DNA minivectors, leaving only the gene of interest (GOI) and necessary eukaryotic expression elements. Our LCC DNA minivectors, or DNA ministrings, are devoid of immunogenic bacterial sequences; therefore improving their bioavailability and GOI expression. In the event of vector integration into the chromosome, the LCC DNA ministring will lethally disrupt the host chromosome, thereby removing the potentially dangerous mutant from the proliferating cell population. Consequently, DNA ministrings offer the benefits of 'minicircle' DNA while eliminating the potential for undesirable vector integration events. In comparison to conventional plasmids and their isogenic circular covalently closed (CCC) counterparts, DNA ministrings demonstrate superior bioavailability, transfection efficiency, and cytoplasmic kinetics - they thus require lower amounts of cationic surfactants for effective transfection of target cells. We have constructed a one-step inducible in vivo system for the production of DNA ministrings in Escherichia coli that is simple to use, rapid, and scalable. PMID:26967586

  18. SMARCAL1 maintains telomere integrity during DNA replication.

    PubMed

    Poole, Lisa A; Zhao, Runxiang; Glick, Gloria G; Lovejoy, Courtney A; Eischen, Christine M; Cortez, David

    2015-12-01

    The SMARCAL1 (SWI/SNF related, matrix-associated, actin-dependent, regulator of chromatin, subfamily A-like 1) DNA translocase is one of several related enzymes, including ZRANB3 (zinc finger, RAN-binding domain containing 3) and HLTF (helicase-like transcription factor), that are recruited to stalled replication forks to promote repair and restart replication. These enzymes can perform similar biochemical reactions such as fork reversal; however, genetic studies indicate they must have unique cellular activities. Here, we present data showing that SMARCAL1 has an important function at telomeres, which present an endogenous source of replication stress. SMARCAL1-deficient cells accumulate telomere-associated DNA damage and have greatly elevated levels of extrachromosomal telomere DNA (C-circles). Although these telomere phenotypes are often found in tumor cells using the alternative lengthening of telomeres (ALT) pathway for telomere elongation, SMARCAL1 deficiency does not yield other ALT phenotypes such as elevated telomere recombination. The activity of SMARCAL1 at telomeres can be separated from its genome-maintenance activity in bulk chromosomal replication because it does not require interaction with replication protein A. Finally, this telomere-maintenance function is not shared by ZRANB3 or HLTF. Our results provide the first identification, to our knowledge, of an endogenous source of replication stress that requires SMARCAL1 for resolution and define differences between members of this class of replication fork-repair enzymes. PMID:26578802

  19. Recombination-Dependent Oligomerization of Human Papillomavirus Genomes upon Transient DNA Replication

    PubMed Central

    Orav, Marit; Henno, Liisi; Isok-Paas, Helen; Geimanen, Jelizaveta; Ustav, Mart

    2013-01-01

    We describe the extensive and progressive oligomerization of human papillomavirus (HPV) genomes after transfection into the U2OS cell line. The HPV genomic oligomers are extrachromosomal concatemeric molecules containing the viral genome in a head-to-tail orientation. The process of oligomerization does not depend on the topology of the input DNA, and it does not require any other viral factors besides replication proteins E1 and E2. We provide evidence that oligomerization of the HPV18 and HPV11 genomes involves homologous recombination. We also demonstrate oligomerization of the HPV18 and HPV11 genomes in SiHa, HeLa, and C-33 A cell lines and provide examples of oligomeric HPV genomes in clinical samples obtained from HPV-infected patients. PMID:23986589

  20. How Can Plant DNA Viruses Evade siRNA-Directed DNA Methylation and Silencing?

    PubMed Central

    Pooggin, Mikhail M.

    2013-01-01

    Plants infected with DNA viruses produce massive quantities of virus-derived, 24-nucleotide short interfering RNAs (siRNAs), which can potentially direct viral DNA methylation and transcriptional silencing. However, growing evidence indicates that the circular double-stranded DNA accumulating in the nucleus for Pol II-mediated transcription of viral genes is not methylated. Hence, DNA viruses most likely evade or suppress RNA-directed DNA methylation. This review describes the specialized mechanisms of replication and silencing evasion evolved by geminiviruses and pararetoviruses, which rescue viral DNA from repressive methylation and interfere with transcriptional and post-transcriptional silencing of viral genes. PMID:23887650

  1. Dual frequency launcher for circularly polarized antenna

    NASA Astrophysics Data System (ADS)

    Chen, Ming H.

    1989-10-01

    A dual frequency antenna feed is formed from a central, circular waveguide connected to the flat boundry of circular, disk-shaped resonant cavity. A second circular waveguide is connected one end of a disk-shaped resonant cavity. Energy of one frequency enters and exits the cavity along the common axis of the waveguides. Energy of the second frequency is introduced to the same resonant cavity by way of a plurality of bandpass filters, also connected to the cavity. This energy enters by way of slots in the cylindrical walls of the cavity. The central circular waveguide is propagating at one frequency but cut off at the second frequency. These bandpass filters are at this pass band for the second frequency, but at the rejection band for the first frequency. Therefore, the isolation between these two input ports are obtained.

  2. Low energy aspects of circular accelerators

    SciTech Connect

    Holmes, S.D.

    1990-12-01

    Performance in circular accelerators can be limited by some of the same sorts of phenomena described by Miller and Wangler in their lectures on low energy behavior in linear accelerators. In general the strength of the perturbation required to degrade performance is reduced in circular accelerators due to the repetitive nature of the orbits. For example, we shall see that space-charge can severely limit performance in circular accelerators even when operating far from the space-charge dominated regime'' as defined in linear accelerators. We will be discussing two particular aspects of low energy operation in circular accelerators -- space-charge and transition. Low energy'' is defined within the context of these phenomena. We shall see that the phenomena are really only relevant in hadron accelerators.

  3. G-quadruplex-interacting compounds alter latent DNA replication and episomal persistence of KSHV

    PubMed Central

    Madireddy, Advaitha; Purushothaman, Pravinkumar; Loosbroock, Christopher P.; Robertson, Erle S.; Schildkraut, Carl L.; Verma, Subhash C.

    2016-01-01

    Kaposi's sarcoma associated herpesvirus (KSHV) establishes life-long latent infection by persisting as an extra-chromosomal episome in the infected cells and by maintaining its genome in dividing cells. KSHV achieves this by tethering its epigenome to the host chromosome by latency associated nuclear antigen (LANA), which binds in the terminal repeat (TR) region of the viral genome. Sequence analysis of the TR, a GC-rich DNA element, identified several potential Quadruplex G-Rich Sequences (QGRS). Since quadruplexes have the tendency to obstruct DNA replication, we used G-quadruplex stabilizing compounds to examine their effect on latent DNA replication and the persistence of viral episomes. Our results showed that these G-quadruplex stabilizing compounds led to the activation of dormant origins of DNA replication, with preferential bi-directional pausing of replications forks moving out of the TR region, implicating the role of the G-rich TR in the perturbation of episomal DNA replication. Over time, treatment with PhenDC3 showed a loss of viral episomes in the infected cells. Overall, these data show that G-quadruplex stabilizing compounds retard the progression of replication forks leading to a reduction in DNA replication and episomal maintenance. These results suggest a potential role for G-quadruplex stabilizers in the treatment of KSHV-associated diseases. PMID:26837574

  4. [The effect of DNA supercoiling DNA on nucleosome structure].

    PubMed

    Sivolob, A V; Khrapunov, S N

    1991-01-01

    The circular DNA which contains nucleosomes and additional supercoils has been considered theoretically. The different possible effect of increased negative supercoiling on the nucleosome structure have been studied. According to the model proposed all supercoils in the nucleosome-containing circular DNA are realized as torsional deformations of the double helix. The free energy of both supercoiling (torsional deformations) and nucleosome stabilization have been taken into consideration to obtain the equation for free energy of nucleosome-containing circular DNA. The analysis of this equation and the experimental data by Garner et al. (II Psoc. Natl. Acad. Sci. USA. 1987. P. 2620-2623) about the maximum amount of supercoiling obtained by DNA-topoisomerase II treatment of nucleosome-containing pBR322 plasmid has been performed. It has been shown that two possibilities are consistent with both the equation and experimental data. These are: (1) the increased supercoiling induces the torsional strains not only in linker regions but also in nucleosome DNA and thus supercoiling causes an instability on nucleosome structure; (2) increased supercoiling induces a structural change of nucleosome which is accompanied by nucleosome DNA unwinding and its transition into form with approximately 11 base pairs per turn of double helix. It has been evaluated that in the first case the average torsional rigidity of nucleosome DNA should be approximately 2.5 times as much and in the second case--much more than the rigidity of naked DNA. Both types of nucleosome structural changes may cause its transition to a potentially active state for transcription. It is suggested that increased supercoiling can be a switch mechanism of chromatin activation. PMID:1654518

  5. CIRCULAR RIBBON FLARES AND HOMOLOGOUS JETS

    SciTech Connect

    Wang Haimin; Liu Chang

    2012-12-01

    Solar flare emissions in the chromosphere often appear as elongated ribbons on both sides of the magnetic polarity inversion line (PIL), which has been regarded as evidence of a typical configuration of magnetic reconnection. However, flares having a circular ribbon have rarely been reported, although it is expected in the fan-spine magnetic topology involving reconnection at a three-dimensional (3D) coronal null point. We present five circular ribbon flares with associated surges, using high-resolution and high-cadence H{alpha} blue wing observations obtained from the recently digitized films of Big Bear Solar Observatory. In all the events, a central parasitic magnetic field is encompassed by the opposite polarity, forming a circular PIL traced by filament material. Consequently, a flare kernel at the center is surrounded by a circular flare ribbon. The four homologous jet-related flares on 1991 March 17 and 18 are of particular interest, as (1) the circular ribbons brighten sequentially, with cospatial surges, rather than simultaneously, (2) the central flare kernels show an intriguing 'round-trip' motion and become elongated, and (3) remote brightenings occur at a region with the same magnetic polarity as the central parasitic field and are co-temporal with a separate phase of flare emissions. In another flare on 1991 February 25, the circular flare emission and surge activity occur successively, and the event could be associated with magnetic flux cancellation across the circular PIL. We discuss the implications of these observations combining circular flare ribbons, homologous jets, and remote brightenings for understanding the dynamics of 3D magnetic restructuring.

  6. Single particle dynamics in circular accelerators

    SciTech Connect

    Ruth, R.D.

    1986-10-01

    The purpose of this paper is to introduce the reader to the theory associated with the transverse dynamics of single particle, in circular accelerators. The discussion begins with a review of Hamiltonian dynamics and canonical transformations. The case of a single particle in a circular accelerator is considered with a discussion of non-linear terms and chromaticity. The canonical perturbation theory is presented and nonlinear resonances are considered. Finally, the concept of renormalization and residue criterion are examined. (FI)

  7. Circular polarization of sunlight reflected by clouds.

    NASA Technical Reports Server (NTRS)

    Hansen, J. E.

    1971-01-01

    Measurements of circular polarization of visible light from planets have recently been reported. It is pointed out that the values measured for the circular polarization for Jupiter and Venus are of the magnitude expected for sunlight reflected by a cloudy planetary atmosphere. The variations of the sense of the polarization with phase angle and with location on the planetary disk are also consistent with expectations for reflection by clouds.

  8. Spectroscopic Evaluation of DNA-Borate Interactions.

    PubMed

    Ozdemir, Ayse; Sarioglu, Omer Faruk; Tekinay, Turgay

    2015-12-01

    We describe the binding characteristics of two natural borates (colemanite and ulexite) to calf thymus DNA by UV-vis absorbance spectroscopy, circular dichroism (CD) spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, and a competitive DNA binding assay. Our results suggest that colemanite and ulexite interact with calf thymus DNA under a non-intercalative mode of binding and do not alter the secondary structure of the DNA helix. The FT-IR spectroscopy results indicate that the two borates might interact with DNA through sugar-phosphate backbone binding. PMID:25994227

  9. Circular Data Images for Directional Data

    NASA Technical Reports Server (NTRS)

    Morpet, William J.

    2004-01-01

    Directional data includes vectors, points on a unit sphere, axis orientation, angular direction, and circular or periodic data. The theoretical statistics for circular data (random points on a unit circle) or spherical data (random points on a unit sphere) are a recent development. An overview of existing graphical methods for the display of directional data is given. Cross-over occurs when periodic data are measured on a scale for the measurement of linear variables. For example, if angle is represented by a linear color gradient changing uniformly from dark blue at -180 degrees to bright red at +180 degrees, the color image will be discontinuous at +180 degrees and -180 degrees, which are the same location. The resultant color would depend on the direction of approach to the cross-over point. A new graphical method for imaging directional data is described, which affords high resolution without color discontinuity from "cross-over". It is called the circular data image. The circular data image uses a circular color scale in which colors repeat periodically. Some examples of the circular data image include direction of earth winds on a global scale, rocket motor internal flow, earth global magnetic field direction, and rocket motor nozzle vector direction vs. time.

  10. Efficient Sleeping Beauty DNA Transposition From DNA Minicircles

    PubMed Central

    Sharma, Nynne; Cai, Yujia; Bak, Rasmus O; Jakobsen, Martin R; Schrøder, Lisbeth Dahl; Mikkelsen, Jacob Giehm

    2013-01-01

    DNA transposon-based vectors have emerged as new potential delivery tools in therapeutic gene transfer. Such vectors are now showing promise in hematopoietic stem cells and primary human T cells, and clinical trials with transposon-engineered cells are on the way. However, the use of plasmid DNA as a carrier of the vector raises safety concerns due to the undesirable administration of bacterial sequences. To optimize vectors based on the Sleeping Beauty (SB) DNA transposon for clinical use, we examine here SB transposition from DNA minicircles (MCs) devoid of the bacterial plasmid backbone. Potent DNA transposition, directed by the hyperactive SB100X transposase, is demonstrated from MC donors, and the stable transfection rate is significantly enhanced by expressing the SB100X transposase from MCs. The stable transfection rate is inversely related to the size of circular donor, suggesting that a MC-based SB transposition system benefits primarily from an increased cellular uptake and/or enhanced expression which can be observed with DNA MCs. DNA transposon and transposase MCs are easily produced, are favorable in size, do not carry irrelevant DNA, and are robust substrates for DNA transposition. In accordance, DNA MCs should become a standard source of DNA transposons not only in therapeutic settings but also in the daily use of the SB system. PMID:23443502

  11. Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem.

    PubMed

    Dayaram, Anisha; Galatowitsch, Mark L; Argüello-Astorga, Gerardo R; van Bysterveldt, Katherine; Kraberger, Simona; Stainton, Daisy; Harding, Jon S; Roumagnac, Philippe; Martin, Darren P; Lefeuvre, Pierre; Varsani, Arvind

    2016-04-01

    Over the last five years next-generation sequencing has become a cost effective and efficient method for identifying known and unknown microorganisms. Access to this technique has dramatically changed the field of virology, enabling a wide range of environmental viral metagenome studies to be undertaken of organisms and environmental samples from polar to tropical regions. These studies have led to the discovery of hundreds of highly divergent single stranded DNA (ssDNA) virus-like sequences encoding replication-associated proteins. Yet, few studies have explored how viruses might be shared in an ecosystem through feeding relationships. Here we identify 169 circular molecules (160 CRESS DNA molecules, nine circular molecules) recovered from a New Zealand freshwater lake, that we have tentatively classified into 51 putatively novel species and five previously described species (DflaCV-3, -5, -6, -8, -10). The CRESS DNA viruses identified in this study were recovered from molluscs (Echyridella menzeisii, Musculium novaezelandiae, Potamopyrgus antipodarum and Physella acuta) and insect larvae (Procordulia grayi, Xanthocnemis zealandica, and Chironomus zealandicus) collected from Lake Sarah, as well as from the lake water and benthic sediments. Extensive diversity was observed across most CRESS DNA molecules recovered. The putative capsid protein of one viral species was found to be most similar to those of members of the Tombusviridae family, thus expanding the number of known RNA-DNA hybrid viruses in nature. We noted a strong association between the CRESS DNA viruses and circular molecules identified in the water and browser organisms (C. zealandicus, P. antipodarum and P. acuta), and between water sediments and undefended prey species (C. zealandicus). However, we were unable to find any significant correlation of viral assemblages to the potential feeding relationships of the host aquatic invertebrates. PMID:26873065

  12. 5 CFR 1310.3 - Availability of circulars.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 3 2013-01-01 2013-01-01 false Availability of circulars. 1310.3 Section 1310.3 Administrative Personnel OFFICE OF MANAGEMENT AND BUDGET OMB DIRECTIVES OMB CIRCULARS § 1310.3 Availability of circulars. Copies of individual circulars are available at OMB's Internet home page; you...

  13. 5 CFR 1310.5 - List of current circulars.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 3 2012-01-01 2012-01-01 false List of current circulars. 1310.5 Section 1310.5 Administrative Personnel OFFICE OF MANAGEMENT AND BUDGET OMB DIRECTIVES OMB CIRCULARS § 1310.5 List of current circulars. The following list includes all circulars in effect as of December 1,...

  14. 5 CFR 1310.5 - List of current circulars.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 3 2014-01-01 2014-01-01 false List of current circulars. 1310.5 Section 1310.5 Administrative Personnel OFFICE OF MANAGEMENT AND BUDGET OMB DIRECTIVES OMB CIRCULARS § 1310.5 List of current circulars. The following list includes all circulars in effect as of December 1,...

  15. 5 CFR 1310.5 - List of current circulars.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 3 2013-01-01 2013-01-01 false List of current circulars. 1310.5 Section 1310.5 Administrative Personnel OFFICE OF MANAGEMENT AND BUDGET OMB DIRECTIVES OMB CIRCULARS § 1310.5 List of current circulars. The following list includes all circulars in effect as of December 1,...

  16. 5 CFR 1310.5 - List of current circulars.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 3 2010-01-01 2010-01-01 false List of current circulars. 1310.5 Section 1310.5 Administrative Personnel OFFICE OF MANAGEMENT AND BUDGET OMB DIRECTIVES OMB CIRCULARS § 1310.5 List of current circulars. The following list includes all circulars in effect as of December 1,...

  17. 5 CFR 1310.5 - List of current circulars.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 3 2011-01-01 2011-01-01 false List of current circulars. 1310.5 Section 1310.5 Administrative Personnel OFFICE OF MANAGEMENT AND BUDGET OMB DIRECTIVES OMB CIRCULARS § 1310.5 List of current circulars. The following list includes all circulars in effect as of December 1,...

  18. 39 CFR 233.2 - Circulars and rewards.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 39 Postal Service 1 2010-07-01 2010-07-01 false Circulars and rewards. 233.2 Section 233.2 Postal Service UNITED STATES POSTAL SERVICE ORGANIZATION AND ADMINISTRATION INSPECTION SERVICE AUTHORITY § 233.2 Circulars and rewards. (a) Wanted circulars. The Inspection Service issues wanted circulars to assist...

  19. 5 CFR 1310.3 - Availability of circulars.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 3 2010-01-01 2010-01-01 false Availability of circulars. 1310.3 Section 1310.3 Administrative Personnel OFFICE OF MANAGEMENT AND BUDGET OMB DIRECTIVES OMB CIRCULARS § 1310.3 Availability of circulars. Copies of individual circulars are available at OMB's Internet home page; you...

  20. 39 CFR 233.2 - Circulars and rewards.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 39 Postal Service 1 2011-07-01 2011-07-01 false Circulars and rewards. 233.2 Section 233.2 Postal Service UNITED STATES POSTAL SERVICE ORGANIZATION AND ADMINISTRATION INSPECTION SERVICE AUTHORITY § 233.2 Circulars and rewards. (a) Wanted circulars. The Inspection Service issues wanted circulars to assist in locating and arresting fugitive...

  1. 12 CFR 563g.8 - Use of the offering circular.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Use of the offering circular. 563g.8 Section... § 563g.8 Use of the offering circular. (a) An offering circular or amendment declared effective by the... therein is as of a date not more than 16 months prior to such use. (b) An offering circular filed...

  2. 24 CFR 574.605 - Applicability of OMB circulars.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Federal Requirements § 574.605 Applicability of OMB circulars. The policies, guidelines, and requirements of 24 CFR part 85 (codified pursuant to OMB Circular No. A-102) and OMB Circular No. A-87 apply with... 24 Housing and Urban Development 3 2011-04-01 2010-04-01 true Applicability of OMB circulars....

  3. 24 CFR 574.605 - Applicability of OMB circulars.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... Federal Requirements § 574.605 Applicability of OMB circulars. The policies, guidelines, and requirements of 24 CFR part 85 (codified pursuant to OMB Circular No. A-102) and OMB Circular No. A-87 apply with... 24 Housing and Urban Development 3 2010-04-01 2010-04-01 false Applicability of OMB circulars....

  4. 5 CFR 1310.3 - Availability of circulars.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 3 2011-01-01 2011-01-01 false Availability of circulars. 1310.3 Section 1310.3 Administrative Personnel OFFICE OF MANAGEMENT AND BUDGET OMB DIRECTIVES OMB CIRCULARS § 1310.3 Availability of circulars. Copies of individual circulars are available at OMB's Internet home page; you...

  5. 49 CFR 1544.305 - Security Directives and Information Circulars.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 9 2011-10-01 2011-10-01 false Security Directives and Information Circulars... and Information Circulars. (a) TSA may issue an Information Circular to notify aircraft operators of... operator that receives a Security Directive or Information Circular and each person who...

  6. 12 CFR 563g.8 - Use of the offering circular.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Use of the offering circular. 563g.8 Section... § 563g.8 Use of the offering circular. (a) An offering circular or amendment declared effective by the... therein is as of a date not more than 16 months prior to such use. (b) An offering circular filed...

  7. Conformation-Selective Methylation of Geminivirus DNA

    PubMed Central

    Paprotka, T.; Deuschle, K.; Metzler, V.; Jeske, H.

    2011-01-01

    Geminiviruses with small circular single-stranded DNA genomes replicate in plant cell nuclei by using various double-stranded DNA (dsDNA) intermediates: distinct open circular and covalently closed circular as well as heterogeneous linear DNA. Their DNA may be methylated partially at cytosine residues, as detected previously by bisulfite sequencing and subsequent PCR. In order to determine the methylation patterns of the circular molecules, the DNAs of tomato yellow leaf curl Sardinia virus (TYLCSV) and Abutilon mosaic virus were investigated utilizing bisulfite treatment followed by rolling circle amplification. Shotgun sequencing of the products yielded a randomly distributed 50% rate of C maintenance after the bisulfite reaction for both viruses. However, controls with unmethylated single-stranded bacteriophage DNA resulted in the same level of C maintenance. Only one short DNA stretch within the C2/C3 promoter of TYLCSV showed hyperprotection of C, with the protection rate exceeding the threshold of the mean value plus 1 standard deviation. Similarly, the use of methylation-sensitive restriction enzymes suggested that geminiviruses escape silencing by methylation very efficiently, by either a rolling circle or recombination-dependent replication mode. In contrast, attempts to detect methylated bases positively by using methylcytosine-specific antibodies detected methylated DNA only in heterogeneous linear dsDNA, and methylation-dependent restriction enzymes revealed that the viral heterogeneous linear dsDNA was methylated preferentially. PMID:21835804

  8. Identification of intron/exon boundaries in genomic DNA by inverse PCR.

    PubMed

    Albertsen, H; Thliveris, A

    2001-05-01

    This unit describes identifying intron/exon boundaries in genomic DNA by comparing nucleotide sequences of genomic DNA to cDNA. Cloned genomic DNA is prepared for inverse polymerase chain reaction (PCR) by digesting the DNA with a restriction enzyme and circularizing the restriction fragments by ligation. Diverging primer pairs for each exon are designed on the basis of the cDNA sequence. The circularized restriction fragments are amplified using these diverging primers, the PCR product is sequenced, and the sequence is compared to the cDNA sequence to determine the location of the intron/exon boundaries. The lower complexity of cloned DNA (e.g., YAC, P1, or cosmid DNA) facilitates preparation of good template. This unit describes identifying intron/exon boundaries in genomic DNA by comparing nucleotide sequences of genomic DNA to cDNA. PMID:18428300

  9. Bright circularly polarized soft X-ray high harmonics for X-ray magnetic circular dichroism

    PubMed Central

    Fan, Tingting; Grychtol, Patrik; Knut, Ronny; Hernández-García, Carlos; Hickstein, Daniel D.; Zusin, Dmitriy; Gentry, Christian; Dollar, Franklin J.; Mancuso, Christopher A.; Hogle, Craig W.; Kfir, Ofer; Legut, Dominik; Carva, Karel; Ellis, Jennifer L.; Dorney, Kevin M.; Chen, Cong; Shpyrko, Oleg G.; Fullerton, Eric E.; Cohen, Oren; Oppeneer, Peter M.; Milošević, Dejan B.; Becker, Andreas; Jaroń-Becker, Agnieszka A.; Popmintchev, Tenio; Murnane, Margaret M.; Kapteyn, Henry C.

    2015-01-01

    We demonstrate, to our knowledge, the first bright circularly polarized high-harmonic beams in the soft X-ray region of the electromagnetic spectrum, and use them to implement X-ray magnetic circular dichroism measurements in a tabletop-scale setup. Using counterrotating circularly polarized laser fields at 1.3 and 0.79 µm, we generate circularly polarized harmonics with photon energies exceeding 160 eV. The harmonic spectra emerge as a sequence of closely spaced pairs of left and right circularly polarized peaks, with energies determined by conservation of energy and spin angular momentum. We explain the single-atom and macroscopic physics by identifying the dominant electron quantum trajectories and optimal phase-matching conditions. The first advanced phase-matched propagation simulations for circularly polarized harmonics reveal the influence of the finite phase-matching temporal window on the spectrum, as well as the unique polarization-shaped attosecond pulse train. Finally, we use, to our knowledge, the first tabletop X-ray magnetic circular dichroism measurements at the N4,5 absorption edges of Gd to validate the high degree of circularity, brightness, and stability of this light source. These results demonstrate the feasibility of manipulating the polarization, spectrum, and temporal shape of high harmonics in the soft X-ray region by manipulating the driving laser waveform. PMID:26534992

  10. Bright circularly polarized soft X-ray high harmonics for X-ray magnetic circular dichroism.

    PubMed

    Fan, Tingting; Grychtol, Patrik; Knut, Ronny; Hernández-García, Carlos; Hickstein, Daniel D; Zusin, Dmitriy; Gentry, Christian; Dollar, Franklin J; Mancuso, Christopher A; Hogle, Craig W; Kfir, Ofer; Legut, Dominik; Carva, Karel; Ellis, Jennifer L; Dorney, Kevin M; Chen, Cong; Shpyrko, Oleg G; Fullerton, Eric E; Cohen, Oren; Oppeneer, Peter M; Milošević, Dejan B; Becker, Andreas; Jaroń-Becker, Agnieszka A; Popmintchev, Tenio; Murnane, Margaret M; Kapteyn, Henry C

    2015-11-17

    We demonstrate, to our knowledge, the first bright circularly polarized high-harmonic beams in the soft X-ray region of the electromagnetic spectrum, and use them to implement X-ray magnetic circular dichroism measurements in a tabletop-scale setup. Using counterrotating circularly polarized laser fields at 1.3 and 0.79 µm, we generate circularly polarized harmonics with photon energies exceeding 160 eV. The harmonic spectra emerge as a sequence of closely spaced pairs of left and right circularly polarized peaks, with energies determined by conservation of energy and spin angular momentum. We explain the single-atom and macroscopic physics by identifying the dominant electron quantum trajectories and optimal phase-matching conditions. The first advanced phase-matched propagation simulations for circularly polarized harmonics reveal the influence of the finite phase-matching temporal window on the spectrum, as well as the unique polarization-shaped attosecond pulse train. Finally, we use, to our knowledge, the first tabletop X-ray magnetic circular dichroism measurements at the N4,5 absorption edges of Gd to validate the high degree of circularity, brightness, and stability of this light source. These results demonstrate the feasibility of manipulating the polarization, spectrum, and temporal shape of high harmonics in the soft X-ray region by manipulating the driving laser waveform. PMID:26534992

  11. 76 FR 62148 - Title VI; Proposed Circular, Environmental Justice; Proposed Circular

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-06

    ... Circular'' (76 FR 60593) and ``Environmental Justice; Proposed Circular'' (76 FR 60590). Corrections The... program questions, Amber Ontiveros, Office of Civil Rights, Federal Transit Administration, 1200 New Jersey Ave., SE., Washington, DC 20590, phone: (202) 366-4018, fax: (202) 366-3809, or e-mail,...

  12. Trichosanthin, a potent HIV-1 inhibitor, can cleave supercoiled DNA in vitro.

    PubMed Central

    Li, M X; Yeung, H W; Pan, L P; Chan, S I

    1991-01-01

    Trichosanthin, an abortifacient, immunosuppressive and anti-tumor protein purified from the traditional Chinese herb medicine Tian Hua Fen, is a potent inhibitor against HIV-1 replication. Under normal enzymatic digestion conditions, trichosanthin cleaves the supercoiled double-stranded DNA to produce nicked circular and linear DNA. Trichosanthin has no effect on linear double-stranded DNA. Neither does it convert relaxed circular duplex DNA into a supercoiled form in the presence of ATP. Thus trichosanthin is not a DNA gyrase. However, trichosanthin can cleave the relaxed circular DNA into a linear form, indicating that both the circular as well as the supercoiled forms are essential for trichosanthin recognition. In addition, trichosanthin contains one calcium metal ion per protein molecule, which presumably is related to its endonucleolytic activity. Images PMID:1659689

  13. Search by proteins for their DNA target site: 1. The effect of DNA conformation on protein sliding

    PubMed Central

    Bhattacherjee, Arnab; Levy, Yaakov

    2014-01-01

    The recognition of DNA-binding proteins (DBPs) to their specific site often precedes by a search technique in which proteins slide, hop along the DNA contour or perform inter-segment transfer and 3D diffusion to dissociate and re-associate to distant DNA sites. In this study, we demonstrated that the strength and nature of the non-specific electrostatic interactions, which govern the search dynamics of DBPs, are strongly correlated with the conformation of the DNA. We tuned two structural parameters, namely curvature and the extent of helical twisting in circular DNA. These two factors are mutually independent of each other and can modulate the electrostatic potential through changing the geometry of the circular DNA conformation. The search dynamics for DBPs on circular DNA is therefore markedly different compared with linear B-DNA. Our results suggest that, for a given DBP, the rotation-coupled sliding dynamics is precluded in highly curved DNA (as well as for over-twisted DNA) because of the large electrostatic energy barrier between the inside and outside of the DNA molecule. Under such circumstances, proteins prefer to hop in order to explore interior DNA sites. The change in the balance between sliding and hopping propensities as a function of DNA curvature or twisting may result in different search efficiency and speed. PMID:25324308

  14. Repetitive elements regulate circular RNA biogenesis

    PubMed Central

    Wilusz, Jeremy E

    2015-01-01

    It was long assumed that eukaryotic precursor mRNAs (pre-mRNAs) are almost always spliced to generate a linear mRNA that is subsequently translated to produce a protein. However, it is now clear that thousands of protein-coding genes can be non-canonically spliced to produce circular noncoding RNAs, some of which are expressed at much higher levels than their associated linear mRNAs. How then does the splicing machinery decide whether to generate a linear mRNA or a circular RNA? Recent work has revealed that intronic repetitive elements, including sequences derived from transposons, are critical regulators of this decision. In most cases, circular RNA biogenesis appears to be initiated when complementary sequences from 2 different introns base pair to one another. This brings the splice sites from the intervening exon(s) into close proximity and facilitates the backsplicing event that generates the circular RNA. As many pre-mRNAs contain multiple intronic repeats, distinct circular transcripts can be produced depending on which repeats base pair to one another. Intronic repeats are thus critical regulatory sequences that control the functional output of their host genes, and potentially cause the functions of protein-coding genes to be highly divergent across species. PMID:26442181

  15. Circular and Elliptic Submerged Impinging Water Jets

    NASA Astrophysics Data System (ADS)

    Claudey, Eric; Benedicto, Olivier; Ravier, Emmanuel; Gutmark, Ephraim

    1999-11-01

    Experiments and CFD have been performed to study circular and elliptic jets in a submerged water jet facility. The tests included discharge coefficient measurement to evaluate pressure losses encountered in noncircular nozzles compared to circular ones. Three-dimensional pressure mappings on the impingement surface and PIV measurement of the jet mean and turbulent velocity have been performed at different compound impingement angles relative to the impingement surface and at different stand-off distances. The objective was to investigate the effect of the non-circular geometry on the flow field and on the impact region. The tests were performed in a close loop system in which the water was pumped through the nozzles into a clear Plexiglas tank. The Reynolds numbers were typically in the range of 250000. Discharge coefficients of the elliptic nozzle was somewhat lower than that of the circular jet but spreading rate and turbulence level were higher. Pressure mapping showed that the nozzle exit geometry had an effect on the pressure distribution in the impact region and that high-pressure zones were generated at specific impact points. PIV measurements showed that for a same total exit area, the elliptic jets affected a surface area that is 8the equivalent circular. The turbulence level in the elliptic jet tripled due to the nozzle design. Results of the CFD model were in good agreement with the experimental data.

  16. Environmental issues elimination through circular economy

    NASA Astrophysics Data System (ADS)

    Špirková, M.; Pokorná, E.; Šujanová, J.; Samáková, J.

    2016-04-01

    Environmental efforts of European Union are currently going towards circular economy. Tools like Extended Producer Responsibility and Eco-design were established. The circular economy deals with resources availability issue on one hand and waste management on the other hand. There are few pioneering companies all over the world with some kind of circular economy practice. Generally the concept is not very wide-spread. The paper aims to evaluate possibility of transition towards circular economy in Slovak industrial companies. They need to have an active approach to material treatment of their products after usage stage. Innovation is another important pre-condition for the transition. Main problem of current cradle to grave system is landfilling of valuable materials after one cycle of usage. Their potential value for next manufacturing cycles is lost. Companies may do not see connection between waste management and material resource prices and volatility of supplies. Municipalities are responsible for municipal waste collection and treatment in Slovakia. The circular economy operates by cradle to cradle principle. Company manages material flow until the material comes back to the beginning of manufacturing process by itself or by another partners. Stable material supplies with quite low costs are provided this way. It is necessary to deal with environmental problems in phase of product design. Questionnaire survey results show on one hand low involvement of industrial companies in waste management area, however on the other hand they are open to environmental innovations in future.

  17. A broadband, circular-polarization selective surface

    NASA Astrophysics Data System (ADS)

    Momeni Hasan Abadi, Seyed Mohamad Amin; Behdad, Nader

    2016-06-01

    We introduce a new technique for designing wideband circular-polarization selective surfaces (CPSSs) based on anisotropic miniaturized element frequency selective surfaces. The proposed structure is a combination of two linear-to-circular polarization converters sandwiching a linear polarizer. This CPSS consists of a number of metallic layers separated from each other by thin dielectric substrates. The metallic layers are in the form of two-dimensional arrays of subwavelength capacitive patches and inductive wire grids with asymmetric dimensions and a wire grid polarizer with sub-wavelength period. The proposed device is designed to offer a wideband circular-polarization selection capability allowing waves with left-hand circular polarization to pass through while rejecting those having right-hand circular polarization. A synthesis procedure is developed that can be used to design the proposed CPSS based on its desired band of operation. Using this procedure, a prototype of the proposed CPSS operating in the 12-18 GHz is designed. Full-wave electromagnetic simulations are used to predict the response of this structure. These simulation results confirm the validity of the proposed design concept and synthesis procedure and show that proposed CPSS operates within a fractional bandwidth of 40% with a co-polarization transmission discrimination of more than 15 dB. Furthermore, the proposed design is shown to be capable of providing an extremely wide field of view of ±60°.

  18. Nanofocusing in circular sector-like nanoantennas.

    PubMed

    Zenin, Vladimir A; Pors, Anders; Han, Zhanghua; Eriksen, René L; Volkov, Valentyn S; Bozhevolnyi, Sergey I

    2014-05-01

    Gold circular sector-like nanoantennas (with a radius of 500 nm and a taper angle of 60°, 90°, and 120°) on glass are investigated in a near-infrared wavelength range (900 - 2100 nm). Amplitude- and phase-resolved near-field images of circular sector-like antenna modes at telecom wavelength feature a concentric circular line of phase contrast, demonstrating resonant excitation of a standing wave of counter-propagating surface plasmons, travelling between a tip and opposite circular edge of the antenna. Transmission spectra obtained in the range 900 - 2100 nm are in good agreement with numerical simulations, revealing the main feature of this antenna configuration, viz., the resonance wavelength, in contrast to triangular antennas, does not depend on the taper angle and is determined only by the sector radius. This feature together with a robust and easily predictable frequency response makes circular sector-like nanoantennas very promising for implementing bowtie antennas and attractive for many applications. PMID:24921736

  19. Optics modules for circular accelerator design

    SciTech Connect

    Brown, K.L.; Servranckx, R.V.

    1986-05-01

    The first-order differential equations of motion for a single particle in a closed circular machine are solved, introducing the concepts of phase shift, beta functions, and the Courant-Snyder invariant. The transfer matrix between two points in the machine is derived as a function of the phase shift and the parameters contained in the Courant-Snyder invariant. Typical optical modules used in circular machine designs are introduced and related to their characteristic transfer matrix elements, the phase shift through them, and the Courant-Snyder-Twiss parameters. The systematics of some elementary phase ellipse matching problems between optical modules are discussed. Second-order optical modules are discussed, including how they are used to provide the momentum bandwidth needed for the design of a typical circular machine. (LEW)

  20. Circularly symmetric light scattering from nanoplasmonic spirals.

    PubMed

    Trevino, Jacob; Cao, Hui; Dal Negro, Luca

    2011-05-11

    In this paper, we combine experimental dark-field imaging, scattering, and fluorescence spectroscopy with rigorous electrodynamics calculations in order to investigate light scattering from planar arrays of Au nanoparticles arranged in aperiodic spirals with diffuse, circularly symmetric Fourier space. In particular, by studying the three main types of Vogel's spirals fabricated by electron-beam lithography on quartz substrates, we demonstrate polarization-insensitive planar light diffraction in the visible spectral range. Moreover, by combining dark-field imaging with analytical multiparticle calculations in the framework of the generalized Mie theory, we show that plasmonic spirals support distinctive structural resonances with circular symmetry carrying orbital angular momentum. The engineering of light scattering phenomena in deterministic structures with circular Fourier space provides a novel strategy for the realization of optical devices that fully leverage on enhanced, polarization-insensitive light-matter coupling over planar surfaces, such as thin-film plasmonic solar cells, plasmonic polarization devices, and optical biosensors. PMID:21466155

  1. Reconnaissance with slant plane circular SAR imaging.

    PubMed

    Soumekh, M

    1996-01-01

    This paper presents a method for imaging from the slant plane data collected by a synthetic aperture radar (SAR) over the full rotation or a partial segment of a circular flight path. A Fourier analysis for the Green's function of the imaging system is provided. This analysis is the basis of an inversion for slant plane circular SAR data. The reconstruction algorithm and resolution for this SAR system are outlined. It is shown that the slant plane circular SAR, unlike the slant plane linear SAR, has the capability to extract three-dimensional imaging information of a target scene. The merits of the algorithm are demonstrated via a simulated target whose ultra wideband foliage penetrating (FOPEN) or ground penetrating (GPEN) ultrahigh frequency (UHF) radar signature varies with the radar's aspect angle. PMID:18285213

  2. Circular Proteins from Plants and Fungi*

    PubMed Central

    Göransson, Ulf; Burman, Robert; Gunasekera, Sunithi; Strömstedt, Adam A.; Rosengren, K. Johan

    2012-01-01

    Circular proteins, defined as head-to-tail cyclized polypeptides originating from ribosomal synthesis, represent a novel class of natural products attracting increasing interest. From a scientific point of view, these compounds raise questions of where and why they occur in nature and how they are formed. From a rational point of view, these proteins and their structural concept may be exploited for crop protection and novel pharmaceuticals. Here, we review the current knowledge of three protein families: cyclotides and circular sunflower trypsin inhibitors from the kingdom of plants and the Amanita toxins from fungi. A particular emphasis is placed on their biological origin, structure, and activity. In addition, the opportunity for discovery of novel circular proteins and recent insights into their mechanism of action are discussed. PMID:22700984

  3. Charged Particle Optics in Circular Higgs Factory

    SciTech Connect

    Cai, Yunhai

    2015-02-26

    Similar to a super B-factory, a circular Higgs factory will require strong focusing systems near the interaction points and a low-emittance lattice in arcs to achieve a factory luminosity. At electron beam energy of 120 GeV, beamstrahlung effects during the collision pose an additional challenge to the collider design. In particular, a large momentum acceptance at 2 percent level is necessary to retain an adequate beam lifetime. This turns out to be the most challenging aspect in the design of circular Higgs factory. In this paper, an example will be provided to illustrate the beam dynamics in circular Higgs factory, emphasizing on the chromatic optics. Basic optical modules and advanced analysis will be presented. Most important, we will show that 2% momentum aperture is achievable

  4. Time-resolved circularly polarized protein phosphorescence.

    PubMed Central

    Schauerte, J A; Steel, D G; Gafni, A

    1992-01-01

    The existence of circular polarization in room-temperature protein phosphorescence is demonstrated, and time-resolved circularly polarized phosphorescence (TR-CPP) is used to characterize unique tryptophan environments in multitryptophan proteins. Circularly polarized luminescence studies provide information regarding the excited state chirality of a lumiphore which can be used to extract sensitive structural information. It is shown by time resolving the circular polarization that it is possible to correlate the excited state chirality with unique decay components in a multiexponential phosphorescence decay profile. The present study presents a concurrent analysis of room-temperature time-resolved phosphorescence and TR-CPP of bacterial glucose-6-phosphate dehydrogenase as well as those of horse liver alcohol dehydrogenase. Only one of the two tryptophan residues per subunit of dimeric alcohol dehydrogenase is believed to phosphorescence, while the dimeric glucose-6-phosphate dehydrogenase has eight tryptophan residues per subunit and shows a corresponding complexity in its phosphorescence decay profile. The anisotropy factor [g(em) = delta I/(Itotal/2); delta I = Ileft circular-Iright circular] for alcohol dehydrogenase is time independent, suggesting a unique excited state chirality. The phosphorescence decay of glucose-6-phosphate dehydrogenase can be well fitted with four exponential terms of 4, 23, 76, and 142 msec, and the TR-CPP of this enzyme shows a strong time dependence that can be resolved into four individual time-independent anisotropy factors of -4.0, -2.1, +6.5, and +6.9 (x10(-3)), each respectively associated with one of the four lifetime components. These results demonstrate how the use of TR-CPP can facilitate the study of proteins with multiple lumiphores. PMID:1438204

  5. Scalar wave diffraction from a circular aperture

    SciTech Connect

    Cerjan, C.

    1995-01-25

    The scalar wave theory is used to evaluate the expected diffraction patterns from a circular aperture. The standard far-field Kirchhoff approximation is compared to the exact result expressed in terms of oblate spheroidal harmonics. Deviations from an expanding spherical wave are calculated for circular aperture radius and the incident beam wavelength using suggested values for a recently proposed point diffractin interferometer. The Kirchhoff approximation is increasingly reliable in the far-field limit as the aperture radius is increased, although significant errors in amplitude and phase persist.

  6. Computing Scattering Matrices For Circular Waveguides

    NASA Technical Reports Server (NTRS)

    Hoppe, Daniel J.

    1990-01-01

    Scattering Matrix Program for Circular Waveguide Junctions computes scattering matrix for series of circular waveguide sections. Sections must have same axis, but radius and length of each section completely arbitrary. Devices analyzed include simple waveguide step discontinuity like that used in a dual-mode horn, stepped matching section, or corrugated waveguide section with constant or varying slot depth. Certain types of corrugated horns also analyzed with program. Mathematical model used in program accurately predicts reflection and transmission characteristics of such devices, taking into account excitation of modes of higher order as well as multiple reflections and energy stored at each discontinuity. Written in FORTRAN 77.

  7. Rotatable non-circular forebody flow controller

    NASA Technical Reports Server (NTRS)

    Moskovitz, Cary A. (Inventor)

    1991-01-01

    The invention is a rotatable, non-circular forebody flow controller. The apparatus comprises a small geometric device located at a nose of a forebody of an aircraft and a non-circular cross-sectional area that extends toward the apex of the aircraft. The device is symmetrical about a reference plane and preferably attaches to an axle which in turn attaches to a rotating motor. The motor rotates the device about an axis of rotation. Preferably, a control unit connected to an aircraft flight control computer signals to the rotating motor the proper rotational positioning of the geometric device.

  8. Beam scanning reflectarray antenna with circular polarization

    NASA Technical Reports Server (NTRS)

    Huang, John (Inventor); Pogorzelski, Ronald J. (Inventor)

    2000-01-01

    A novel means of scanning a circularly polarized reflectarray antenna. The reflectarray is an array of metallic elements arranged on a surface designed to compensate for the various path lengths of the optical rays from an illuminating feed to the reflecting surface and then to the antenna aperture. With appropriate design, the phase in the aperture can be made to vary linearly in any desired direction and also to produce a radiated beam normal to the constant phase surface. In the case of circular polarization, this path length compensation can be accomplished by rotation of the individual elements.

  9. Circularly Polarized Luminescence from Simple Organic Molecules.

    PubMed

    Sánchez-Carnerero, Esther M; Agarrabeitia, Antonia R; Moreno, Florencio; Maroto, Beatriz L; Muller, Gilles; Ortiz, María J; de la Moya, Santiago

    2015-09-21

    This article aims to show the identity of "circularly polarized luminescent active simple organic molecules" as a new concept in organic chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and non-aggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented. PMID:26136234

  10. Circular Helix-Like Curve: An Effective Tool of Biological Sequence Analysis and Comparison.

    PubMed

    Li, Yushuang; Xiao, Wenli

    2016-01-01

    This paper constructed a novel injection from a DNA sequence to a 3D graph, named circular helix-like curve (CHC). The presented graphical representation is available for visualizing characterizations of a single DNA sequence and identifying similarities and differences among several DNAs. A 12-dimensional vector extracted from CHC, as a numerical characterization of CHC, was applied to analyze phylogenetic relationships of 11 species, 74 ribosomal RNAs, 48 Hepatitis E viruses, and 18 eutherian mammals, respectively. Successful experiments illustrated that CHC is an effective tool of biological sequence analysis and comparison. PMID:27403205

  11. Circular Helix-Like Curve: An Effective Tool of Biological Sequence Analysis and Comparison

    PubMed Central

    Li, Yushuang

    2016-01-01

    This paper constructed a novel injection from a DNA sequence to a 3D graph, named circular helix-like curve (CHC). The presented graphical representation is available for visualizing characterizations of a single DNA sequence and identifying similarities and differences among several DNAs. A 12-dimensional vector extracted from CHC, as a numerical characterization of CHC, was applied to analyze phylogenetic relationships of 11 species, 74 ribosomal RNAs, 48 Hepatitis E viruses, and 18 eutherian mammals, respectively. Successful experiments illustrated that CHC is an effective tool of biological sequence analysis and comparison. PMID:27403205

  12. 21 CFR 606.122 - Instruction circular.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... shall contain: (1) Instructions to administer a suitable plasma volume expander if Red Blood Cells are...: (1) The approximate volume of plasma from which a sample unit of Platelets is prepared. (2... container. (m) For Plasma, the instruction circular shall contain: (1) A warning against further...

  13. 17 CFR 230.253 - Offering circular.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 17 Commodity and Securities Exchanges 2 2013-04-01 2013-04-01 false Offering circular. 230.253 Section 230.253 Commodity and Securities Exchanges SECURITIES AND EXCHANGE COMMISSION GENERAL RULES AND REGULATIONS, SECURITIES ACT OF 1933 Regulation A-Conditional Small Issues Exemption § 230.253...

  14. 17 CFR 230.253 - Offering circular.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 17 Commodity and Securities Exchanges 2 2010-04-01 2010-04-01 false Offering circular. 230.253 Section 230.253 Commodity and Securities Exchanges SECURITIES AND EXCHANGE COMMISSION GENERAL RULES AND REGULATIONS, SECURITIES ACT OF 1933 Regulation A-Conditional Small Issues Exemption § 230.253...

  15. 17 CFR 230.253 - Offering circular.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 17 Commodity and Securities Exchanges 2 2012-04-01 2012-04-01 false Offering circular. 230.253 Section 230.253 Commodity and Securities Exchanges SECURITIES AND EXCHANGE COMMISSION GENERAL RULES AND REGULATIONS, SECURITIES ACT OF 1933 Regulation A-Conditional Small Issues Exemption § 230.253...

  16. 17 CFR 230.253 - Offering circular.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 17 Commodity and Securities Exchanges 2 2011-04-01 2011-04-01 false Offering circular. 230.253 Section 230.253 Commodity and Securities Exchanges SECURITIES AND EXCHANGE COMMISSION GENERAL RULES AND REGULATIONS, SECURITIES ACT OF 1933 Regulation A-Conditional Small Issues Exemption § 230.253...

  17. Using Pesticides Safely. Special Circular 296.

    ERIC Educational Resources Information Center

    Hock, W. K.

    The use of pesticides is necessary to aid in the production of food, feed and fiber, and is equally important in the control of home garden and household pests, but correct use is critical in preventing injury to persons, animals, and plants. This circular contains information on State of Pennsylvania and federal pesticide laws; different types of…

  18. Compliance Supplement. OMB Circular A-133.

    ERIC Educational Resources Information Center

    Office of Management and Budget, Washington, DC.

    This document is a supplement to Circular A-133 (1990) from the Office of Management and Budget (OMB), which extended the government's "single audit process" for agencies that administer federal financial assistance programs to higher education institutions and non-profit organizations. This supplement is based on the 1996 Amendments (the Single…

  19. Home Sewage Disposal. Special Circular 212.

    ERIC Educational Resources Information Center

    Wooding, N. Henry

    This circular provides current information for homeowners who must repair or replace existing on-lot sewage disposal systems. Site requirements, characteristics and preparation are outlined for a variety of alternatives such as elevated sand mounds, sand-lined beds and trenches, and oversized absorption area. Diagrams indicating construction…

  20. 78 FR 14620 - Joint Development: Proposed Circular

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-06

    ... published guidance on the eligibility of joint development activities for FTA funding. 72 FR 5788 (Feb. 7... review DOT's complete Privacy Act Statement published in the Federal Register on April 11, 2000 (65 FR... Federal Transit Administration Joint Development: Proposed Circular AGENCY: Federal Transit...

  1. Cold Rydberg atoms in circular states

    NASA Astrophysics Data System (ADS)

    Anderson, David; Schwarzkopf, Andrew; Raithel, Georg

    2012-06-01

    Circular-state Rydberg atoms are interesting in that they exhibit a unique combination of extraordinary properties; long lifetimes (˜n^5), large magnetic moments (l=|m|=n-1) and no first order Stark shift. Circular states have found applications in cavity quantum electrodynamics and precision measurements [1,2], among other studies. In this work we present the production of circular states in an atom trapping apparatus using an adiabatic state-switching method (the crossed-field method [3]). To date, we have observed lifetimes of adiabatically prepared states of several milliseconds. Their relatively large ionization electric fields have been verified by time-of-flight signatures of ion trajectories. We intend to explore the magnetic trapping of circular state Rydberg atoms, as well as their production and interaction properties in ultra-cold and degenerate samples.[4pt] [1] P. Bertet et al., Phys. Rev. Lett., 88, 14 (2002)[0pt] [2] M. Brune et al., Phys. Rev. Lett., 72, 21 (1994)[0pt] [3] D. Delande and J.C. Gay, Europhys. Lett., 5, 303-308 (1988).

  2. Magnifying Devices: A Resource Guide. Reference Circular.

    ERIC Educational Resources Information Center

    Strauss, Carol, Comp.

    The devices listed in this reference circular are designed to assist people who have visual impairments by magnifying objects and print or graphic materials. Before buying a magnification device, one should consult a low-vision specialist to determine the level of usable vision, the power of magnification needed for a particular eye condition and…

  3. Articulated Multimedia Physics, Lesson 10, Circular Motion.

    ERIC Educational Resources Information Center

    New York Inst. of Tech., Old Westbury.

    As the tenth lesson of the Articulated Multimedia Physics Course, instructional materials relating to circular motion are presented in this study guide. The topics are concerned with instantaneous velocity, centripetal force, centrifugal force, and satellite paths. The content is arranged in scrambled form, and the use of matrix transparencies is…

  4. Non-Circular Wheels: Reuleaux and Squares

    ERIC Educational Resources Information Center

    Mills, Allan

    2011-01-01

    Circular wheels are so familiar on vehicles of all types that it is seldom realized that alternatives do exist. This short non-mathematical article describes Reuleaux and square wheels that, rolling along appropriate tracks, can maintain a moving platform at a constant height. Easily made working models lend themselves to demonstrations at science…

  5. Circular Vibration Planing of Inconel 718

    NASA Astrophysics Data System (ADS)

    Hettiarachchi, Nandita Kalyanakumara; Moriwaki, Toshimichi; Shibasaka, Toshiro; Nakamoto, Keiichi

    Circular vibration milling (CVM) is achieved by vibrating a milling cutter about the machine tool spindle axis in a circular path, in addition to its rotary motion. CVM has been proven capable of producing better surface finishes on difficult to cut materials. However, the CVM process is far slower than conventional milling process. In circular vibration planing (CVP) process, the cutting tool is clamped without rotation and fed at a speed comparable to the feed speed of conventional milling. By superimposing circular vibration motion, necessary cutting speed could be achieved keeping the feed speed at realistic values. Inconel 718 was machined by CVP and conventional milling at a similar feed rate. It was observed that CVP could reduce tool wear and hence produce better surface finishes than conventional milling. A geometric simulation showed a major difference between uncut chip shapes of the two processes. The difference of uncut chip shapes suggests that in CVP process, less rubbing occurs between tool flank face and work before the tool penetrates in to the work to form a chip. The reduced rubbing of the flank face is proposed as the reson for reduced tool wear in CVP when compared with conventional milling.

  6. Circular tapered tape fabrication: Final report

    SciTech Connect

    Stockdale, D.A.

    1988-04-01

    A new approach to producing tapered tapes has been developed involving generating a tapered tape in a circular configuration on a lathe rather than a mill. This approach is more cost-effective and the redesigned slot configuration induced less stress on the tapes during installation and removal.

  7. Helically corrugated circular waveguides as antenna feeders

    NASA Astrophysics Data System (ADS)

    Jecko, F.; Papiernik, A.

    1983-07-01

    Rotation of the plane of polarization of the TE(11)-mode is predicted and observed in a helically corrugated circular waveguide. Rotation is suppressed by a longitudinal deformation produced on the corrugation. This modified structure can be used as an antenna feeder with low losses.

  8. Combustor with non-circular head end

    SciTech Connect

    Kim, Won -Wook; McMahan, Kevin Weston

    2015-09-29

    The present application provides a combustor for use with a gas turbine engine. The combustor may include a head end with a non-circular configuration, a number of fuel nozzles positioned about the head end, and a transition piece extending downstream of the head end.

  9. 77 FR 52116 - Title VI; Final Circular

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-28

    ... September 29, 2011, Federal Register notice (76 FR 60593), and provides information regarding implementation... Address Environmental Justice in Minority Populations and Low-Income Populations,'' 77 FR 27534, May 10...-0055) (77 FR 42077, July 17, 2012). The EJ Circular is available on FTA's Web site here:...

  10. Cleaving DNA with DNA

    NASA Astrophysics Data System (ADS)

    Carmi, Nir; Balkhi, Shameelah R.; Breaker, Ronald R.

    1998-03-01

    A DNA structure is described that can cleave single-stranded DNA oligonucleotides in the presence of ionic copper. This ``deoxyribozyme'' can self-cleave or can operate as a bimolecular complex that simultaneously makes use of duplex and triplex interactions to bind and cleave separate DNA substrates. Bimolecular deoxyribozyme-mediated strand scission proceeds with a kobs of 0.2 min-1, whereas the corresponding uncatalyzed reaction could not be detected. The duplex and triplex recognition domains can be altered, making possible the targeted cleavage of single-stranded DNAs with different nucleotide sequences. Several small synthetic DNAs were made to function as simple ``restriction enzymes'' for the site-specific cleavage of single-stranded DNA.

  11. Segregation of relaxed replicated dimers when DNA ligase and DNA polymerase I are limited during oriC-specific DNA replication.

    PubMed Central

    Munson, B R; Maier, P G; Greene, R S

    1989-01-01

    An in vitro Escherichia coli oriC-specific DNA replication system was used to investigate the DNA replication pathways of oriC plasmids. When this system was perturbed by the DNA ligase inhibitor nicotinamide mononucleotide (NMN), alterations occurred in the initiation of DNA synthesis and processing of intermediates and DNA products. Addition of high concentrations of NMN soon after initiation resulted in the accumulation of open circular dimers (OC-OC). These dimers were decatenated to open circular monomers (form II or OC), which were then processed to closed circular supercoiled monomers (form I or CC) products. After a delay, limited ligation of the interlinked dimers (OC-OC to CC-OC and CC-CC) also occurred. Similar results were obtained with replication protein extracts from polA mutants. The presence of NMN before any initiation events took place prolonged the existence of nicked template DNA and promoted, without a lag period, limited incorporation into form II molecules. This DNA synthesis was nonspecific with respect to oriC, as judged by DnaA protein dependence, and presumably occurred at nicks in the template DNA. These results are consistent with oriC-specific initiation requiring closed supercoiled molecules dependent on DNA ligase activity. The results also show that decatenation of dimers occurs readily on nicked dimer and represents an efficient pathway for processing replication intermediates in vitro. Images PMID:2544556

  12. DNA Cages with Icosahedral Symmetry in Bionanotechnology

    NASA Astrophysics Data System (ADS)

    Jonoska, Nataša; Taormina, Anne; Twarock, Reidun

    Blueprints for polyhedral cages with icosahedral symmetry made of circular DNA molecules are provided. The basic rule is that every edge of the cage is met twice in opposite directions by the DNA strand(s), and vertex junctions are realized by a set of admissible junction types. As nanocontainers for cargo storage and delivery, the icosidodecahedral cages are of special interest because they have the largest volume per surface ratio of all cages discussed here.

  13. ESI-MS Investigation of an Equilibrium between a Bimolecular Quadruplex DNA and a Duplex DNA/RNA Hybrid

    NASA Astrophysics Data System (ADS)

    Birrento, Monica L.; Bryan, Tracy M.; Samosorn, Siritron; Beck, Jennifer L.

    2015-07-01

    Electrospray ionization mass spectrometry (ESI-MS) conditions were optimized for simultaneous observation of a bimolecular qDNA and a Watson-Crick base-paired duplex DNA/RNA hybrid. The DNA sequence used was telomeric DNA, and the RNA contained the template for telomerase-mediated telomeric DNA synthesis. Addition of RNA to the quadruplex DNA (qDNA) resulted in formation of the duplex DNA/RNA hybrid. Melting profiles obtained using circular dichroism spectroscopy confirmed that the DNA/RNA hybrid exhibited greater thermal stability than the bimolecular qDNA in solution. Binding of a 13-substituted berberine ( 1) derivative to the bimolecular qDNA stabilized its structure as evidenced by an increase in its stability in the mass spectrometer, and an increase in its circular dichroism (CD) melting temperature of 10°C. The DNA/RNA hybrid did not bind the ligand extensively and its thermal stability was unchanged in the presence of ( 1). The qDNA-ligand complex resisted unfolding in the presence of excess RNA, limiting the formation of the DNA/RNA hybrid. Previously, it has been proposed that DNA secondary structures, such as qDNA, may be involved in the telomerase mechanism. DNA/RNA hybrid structures occur at the active site of telomerase. The results presented in the current work show that if telomeric DNA was folded into a qDNA structure, it is possible for a DNA/RNA hybrid to form as is required during template alignment. The discrimination of ligand ( 1) for binding to the bimolecular qDNA over the DNA/RNA hybrid positions it as a useful compound for probing the role(s), if any, of antiparallel qDNA in the telomerase mechanism.

  14. Porcine circovirus: transcription and rolling-circle DNA replication

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This review summarizes the molecular studies pertaining to porcine circovirus (PCV) transcription and DNA replication. The genome of PCV is circular, single-stranded DNA and contains 1759-1768 nucleotides. Both the genome-strand (packaged in the virus particle) and the complementary-strand (synthesi...

  15. A simple circular-polarized antenna: Circular waveguide horn coated with lossy magnetic material

    NASA Technical Reports Server (NTRS)

    Lee, C. S.; Lee, S. W.; Justice, D. W.

    1986-01-01

    A circular waveguide horn coated with a lossy material in its interior wall can be used as an alternative to a corrugated waveguide for radiating a circularly polarized (CP) field. To achieve good CP radiation, the diameter of the structure must be larger than the free-space wavelength, and the coating material must be sufficiently lossy and magnetic. This device is cheaper and lighter in weight than the corrugated one.

  16. A simple circular-polarized antenna: Circular waveguide horn coated with lossy magnetic material

    NASA Astrophysics Data System (ADS)

    Lee, Choon S.; Justice, D. W.; Lee, Shung-Wu

    1988-02-01

    It is shown that a circular waveguide horn coated with a lossy material in its interior wall can be used as an alternative to a corrugated waveguide for radiating a circularly polarized (CP) field. To achieve good CP radiation, the diameter of the structure must be larger than the free-space wavelength, and the coating material must be sufficiently lossy and magnetic. The device is cheaper and lighter in weight than the corrugated one.

  17. A simple circular-polarized antenna: Circular waveguide horn coated with lossy magnetic material

    NASA Astrophysics Data System (ADS)

    Lee, C. S.; Lee, S. W.; Justice, D. W.

    1986-08-01

    A circular waveguide horn coated with a lossy material in its interior wall can be used as an alternative to a corrugated waveguide for radiating a circularly polarized (CP) field. To achieve good CP radiation, the diameter of the structure must be larger than the free-space wavelength, and the coating material must be sufficiently lossy and magnetic. This device is cheaper and lighter in weight than the corrugated one.

  18. A simple circular-polarized antenna: Circular waveguide horn coated with lossy magnetic material

    NASA Technical Reports Server (NTRS)

    Lee, Choon S.; Justice, D. W.; Lee, Shung-Wu

    1988-01-01

    It is shown that a circular waveguide horn coated with a lossy material in its interior wall can be used as an alternative to a corrugated waveguide for radiating a circularly polarized (CP) field. To achieve good CP radiation, the diameter of the structure must be larger than the free-space wavelength, and the coating material must be sufficiently lossy and magnetic. The device is cheaper and lighter in weight than the corrugated one.

  19. Function of DNA polymerase I in RNA-primed synthesis of bacteriophage M-13 duplex DNA.

    PubMed Central

    Schneck, P K; Staudenbauer, W L; Hofschneider, P H

    1976-01-01

    Cell-free extracts from Escherichia coli contain a DNA polymerase activity resistant to SH-blocking agents, which is capable of synthesizing complementary strand DNA on a circular M-13 DNA template by extension of RNA primers. This activity is considered to be identical with DNA polymerase I (or some altered form of this enzyme) since it is missing in extracts from po1A- cells. DNA synthesis in the presence of SH-blocking agents occurs at a reduced rate as compared to untreated controls and leads to the formation of DNA chains of defined size (0.4-0.5 genome's length). It is concluded that efficient M-13 duplex DNA synthesis requires the cooperation of both DNA polymerase I and III. PMID:1272793

  20. DNA repair

    SciTech Connect

    Friedberg, E.C.; Hanawalt, P.C. )

    1988-01-01

    Topics covered in this book included: Eukaryote model systems for DNA repair study; Sensitive detection of DNA lesions and their repair; and Defined DNA sequence probes for analysis of mutagenesis and repair.

  1. 15 CFR 14.6 - Availability of OMB circulars.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Availability of OMB circulars. 14.6 Section 14.6 Commerce and Foreign Trade Office of the Secretary of Commerce UNIFORM ADMINISTRATIVE... COMMERCIAL ORGANIZATIONS General § 14.6 Availability of OMB circulars. OMB circulars cited in this part...

  2. 49 CFR 1548.19 - Security Directives and Information Circulars.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 9 2011-10-01 2011-10-01 false Security Directives and Information Circulars... CARRIER SECURITY § 1548.19 Security Directives and Information Circulars. (a) TSA may issue an Information Circular to notify indirect air carriers of security concerns. (b) When TSA determines that...

  3. 49 CFR 1549.109 - Security Directives and Information Circulars.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 9 2011-10-01 2011-10-01 false Security Directives and Information Circulars... SCREENING PROGRAM Operations § 1549.109 Security Directives and Information Circulars. (a) TSA may issue an Information Circular to notify certified cargo screening facilities of security concerns. (b) When...

  4. 17 CFR 230.255 - Preliminary Offering Circulars.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 17 Commodity and Securities Exchanges 2 2010-04-01 2010-04-01 false Preliminary Offering Circulars... Preliminary Offering Circulars. (a) Prior to qualification of the required offering statement, but after its... front cover page of the material bears the caption “Preliminary Offering Circular,” the date of...

  5. 17 CFR 230.255 - Preliminary Offering Circulars.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 17 Commodity and Securities Exchanges 2 2011-04-01 2011-04-01 false Preliminary Offering Circulars... Preliminary Offering Circulars. (a) Prior to qualification of the required offering statement, but after its... front cover page of the material bears the caption “Preliminary Offering Circular,” the date of...

  6. 15 CFR 14.6 - Availability of OMB circulars.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 15 Commerce and Foreign Trade 1 2011-01-01 2011-01-01 false Availability of OMB circulars. 14.6 Section 14.6 Commerce and Foreign Trade Office of the Secretary of Commerce UNIFORM ADMINISTRATIVE... COMMERCIAL ORGANIZATIONS General § 14.6 Availability of OMB circulars. OMB circulars cited in this part...

  7. 49 CFR 1548.19 - Security Directives and Information Circulars.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 9 2010-10-01 2010-10-01 false Security Directives and Information Circulars... CARRIER SECURITY § 1548.19 Security Directives and Information Circulars. (a) TSA may issue an Information Circular to notify indirect air carriers of security concerns. (b) When TSA determines that...

  8. 49 CFR 1549.109 - Security Directives and Information Circulars.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 9 2010-10-01 2010-10-01 false Security Directives and Information Circulars... SCREENING PROGRAM Operations § 1549.109 Security Directives and Information Circulars. (a) TSA may issue an Information Circular to notify certified cargo screening facilities of security concerns. (b) When...

  9. 49 CFR 1544.305 - Security Directives and Information Circulars.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... and Information Circulars. (a) TSA may issue an Information Circular to notify aircraft operators of... with an operational need-to-know. (2) Refuse to release the Security Directive or Information Circular, and information contained in either document, to persons other than those with an operational...

  10. Circular polarization sensitive absorbers based on graphene

    PubMed Central

    Yang, Kunpeng; Wang, Min; Pu, Mingbo; Wu, Xiaoyu; Gao, Hui; Hu, Chenggang; Luo, Xiangang

    2016-01-01

    It is well known that the polarization of a linearly polarized (LP) light would rotate after passing through a single layer graphene under the bias of a perpendicular magnetostatic field. Here we show that a corresponding phase shift could be expected for circularly polarized (CP) light, which can be engineered to design the circular polarization sensitive devices. We theoretically validate that an ultrathin graphene-based absorber with the thickness about λ/76 can be obtained, which shows efficient absorption >90% within incident angles of ±80°. The angle-independent phase shift produced by the graphene is responsible for the nearly omnidirectional absorber. Furthermore, a broadband absorber in frequencies ranging from 2.343 to 5.885 THz with absorption over 90% is designed by engineering the dispersion of graphene. PMID:27034257

  11. Circular RNAs: Novel Regulators of Neuronal Development.

    PubMed

    van Rossum, Daniëlle; Verheijen, Bert M; Pasterkamp, R Jeroen

    2016-01-01

    Circular RNAs (circRNAs) are highly stable, circularized long non-coding RNAs. circRNAs are conserved across species and appear to be specifically enriched in the nervous system. Recent studies show that many circRNAs are expressed in a tissue- and developmental-stage-specific manner, reveal a striking regulation of circRNAs during neuronal development, and detect their presence at synaptic sites. The exact functions of circRNAs remain poorly understood, but evidence from analysis of some circRNA molecules suggests that they could substantially contribute to the regulation of gene expression, particularly in architecturally complex and polarized cells such as neurons. Emerging evidence also indicates that circRNAs are involved in the development and progression of various neurological disorders. In this review, we summarize the molecular characteristics of circRNAs and discuss their proposed functions and mechanism-of-action in developing neurons. PMID:27616979

  12. Circular, confined distribution for charged particle beams

    DOEpatents

    Garnett, Robert W.; Dobelbower, M. Christian

    1995-01-01

    A charged particle beam line is formed with magnetic optics that manipulate the charged particle beam to form the beam having a generally rectangular configuration to a circular beam cross-section having a uniform particle distribution at a predetermined location. First magnetic optics form a charged particle beam to a generally uniform particle distribution over a square planar area at a known first location. Second magnetic optics receive the charged particle beam with the generally square configuration and affect the charged particle beam to output the charged particle beam with a phase-space distribution effective to fold corner portions of the beam toward the core region of the beam. The beam forms a circular configuration having a generally uniform spatial particle distribution over a target area at a predetermined second location.

  13. Circular, confined distribution for charged particle beams

    DOEpatents

    Garnett, R.W.; Dobelbower, M.C.

    1995-11-21

    A charged particle beam line is formed with magnetic optics that manipulate the charged particle beam to form the beam having a generally rectangular configuration to a circular beam cross-section having a uniform particle distribution at a predetermined location. First magnetic optics form a charged particle beam to a generally uniform particle distribution over a square planar area at a known first location. Second magnetic optics receive the charged particle beam with the generally square configuration and affect the charged particle beam to output the charged particle beam with a phase-space distribution effective to fold corner portions of the beam toward the core region of the beam. The beam forms a circular configuration having a generally uniform spatial particle distribution over a target area at a predetermined second location. 26 figs.

  14. Circular polarization sensitive absorbers based on graphene

    NASA Astrophysics Data System (ADS)

    Yang, Kunpeng; Wang, Min; Pu, Mingbo; Wu, Xiaoyu; Gao, Hui; Hu, Chenggang; Luo, Xiangang

    2016-04-01

    It is well known that the polarization of a linearly polarized (LP) light would rotate after passing through a single layer graphene under the bias of a perpendicular magnetostatic field. Here we show that a corresponding phase shift could be expected for circularly polarized (CP) light, which can be engineered to design the circular polarization sensitive devices. We theoretically validate that an ultrathin graphene-based absorber with the thickness about λ/76 can be obtained, which shows efficient absorption >90% within incident angles of ±80°. The angle-independent phase shift produced by the graphene is responsible for the nearly omnidirectional absorber. Furthermore, a broadband absorber in frequencies ranging from 2.343 to 5.885 THz with absorption over 90% is designed by engineering the dispersion of graphene.

  15. Electron capture from circular Rydberg atoms

    SciTech Connect

    Hansen, S.B.; Ehrenreich, T.; Horsdal-Pedersen, E. ); MacAdam, K.B. ); Dube, L.J. )

    1993-09-06

    Capture cross sections for circular Rydberg states have been measured as a function of the angle, [ital cphi], between ion velocity and angular momentum of the circular orbital. The system studied is 2.5 keV [sup 23]Na[sup +] on Li(1[ital s][sup 2],[ital nlm]) with [ital n]=25, [ital l]=[ital n][minus]1, and [ital m]=+[ital l], where [ital m] is defined relative to a weak, external magnetic field. A strong dependence on [ital cphi] is found. It is expected that studies such as the present will lead to an improved understanding of the three-body problem in the region of sufficiently large quantum numbers and impact velocities for classical physics to be accurate.

  16. Circular RNAs: Novel Regulators of Neuronal Development

    PubMed Central

    van Rossum, Daniëlle; Verheijen, Bert M.; Pasterkamp, R. Jeroen

    2016-01-01

    Circular RNAs (circRNAs) are highly stable, circularized long non-coding RNAs. circRNAs are conserved across species and appear to be specifically enriched in the nervous system. Recent studies show that many circRNAs are expressed in a tissue- and developmental-stage-specific manner, reveal a striking regulation of circRNAs during neuronal development, and detect their presence at synaptic sites. The exact functions of circRNAs remain poorly understood, but evidence from analysis of some circRNA molecules suggests that they could substantially contribute to the regulation of gene expression, particularly in architecturally complex and polarized cells such as neurons. Emerging evidence also indicates that circRNAs are involved in the development and progression of various neurological disorders. In this review, we summarize the molecular characteristics of circRNAs and discuss their proposed functions and mechanism-of-action in developing neurons. PMID:27616979

  17. Circular machine design techniques and tools

    SciTech Connect

    Servranckx, R.V.; Brown, K.L.

    1986-04-01

    Some of the basic optics principles involved in the design of circular accelerators such as Alternating Gradient Synchrotrons, Storage and Collision Rings, and Pulse Stretcher Rings are outlined. Typical problems facing a designer are defined, and the main references and computational tools are reviewed that are presently available. Two particular classes of problems that occur typically in accelerator design are listed - global value problems, which affect the control of parameters which are characteristic of the complete closed circular machine, and local value problems. Basic mathematical formulae are given that are considered useful for a first draft of a design. The basic optics building blocks that can be used to formulate an initial machine design are introduced, giving only the elementary properties and transfer matrices only in one transverse plane. Solutions are presented for some first-order and second-order design problems. (LEW)

  18. Impedance properties of circular microstrip antenna

    NASA Technical Reports Server (NTRS)

    Deshpande, M. D.; Bailey, M. C.

    1983-01-01

    A moment method solution to the input impedance of a circular microstrip antenna excited by either a microstrip feed or a coaxial probe is presented. Using the exact dyadic Green's function and the Fourier transform the problem is formulated in terms of Richmond's reaction integral equation from which the unknown patch current can be solved for. The patch current is expanded in terms of regular surface patch modes and an attachment mode (for probe excited case) which insures continuity of the current at probe/patch junction, proper polarization and p-dependance of patch current in the vicinity of the probe. The input impedance of a circular microstrip antenna is computed and compared with earlier results. Effect of attachment mode on the input impedance is also discussed.

  19. Shock structure in non-circular jets

    NASA Technical Reports Server (NTRS)

    Morris, Philip J.; Bhat, Thonse R. S.

    1989-01-01

    The shock-cell structure of supersonic jets with non-circular exit geometry is modeled using a linearized analysis. The model takes into account the finite thickness of the jet shear layer using realistic velocity and density profiles. The effects of the shear layer turbulence are included by incorporating eddy-viscosity terms. A finite-difference numerical method is used to solve the steady linearized equations of motion. A body-fitted coordinate system is used to describe the shear layer. The variation of the pressure fluctuation with downstream distance is given for circular jets and for an elliptic jet of aspect ratio 2.0. Comparisons with experimental data are made. Difficulties with the numerical technique are also discussed.

  20. Roles of Circular RNAs in Neurologic Disease

    PubMed Central

    Shao, Yiye; Chen, Yinghui

    2016-01-01

    Circular RNAs (circRNAs) are a novel type of endogenous noncoding RNA receiving increasing attention. They have been shown to act as a natural microRNA sponges that repress the activity of corresponding miRNAs by binding with them, thus regulating target genes. Numerous studies have shown that miRNAs are involved in the pathogenesis of neurological diseases. Therefore, circRNAs may act as important regulatory factors in the occurrence and development processes of neurological disease. PMID:27147959

  1. A fractal circular polarized RFID tag antenna

    NASA Astrophysics Data System (ADS)

    Chaouki, Guesmi; Ferchichi, Abdelhak; Gharsallah, Ali

    2013-09-01

    In this paper, we present a novel fractal antenna for radiofrequency identification (RFID) tags. The proposed antenna has a resonant frequency equal to 2.45GHz and circular polarization. The fractal technique was very useful to obtain a miniaturization of antenna size by more than 30%. The gain and directivity of the antenna are acceptable for the desired RFID application. All the results are obtained using CST Microwave simulation tool.

  2. Circular analysis in complex stochastic systems

    NASA Astrophysics Data System (ADS)

    Valleriani, Angelo

    2015-12-01

    Ruling out observations can lead to wrong models. This danger occurs unwillingly when one selects observations, experiments, simulations or time-series based on their outcome. In stochastic processes, conditioning on the future outcome biases all local transition probabilities and makes them consistent with the selected outcome. This circular self-consistency leads to models that are inconsistent with physical reality. It is also the reason why models built solely on macroscopic observations are prone to this fallacy.

  3. Calculating the CEP (Circular Error Probable)

    NASA Technical Reports Server (NTRS)

    1987-01-01

    This report compares the probability contained in the Circular Error Probable associated with an Elliptical Error Probable to that of the EEP at a given confidence level. The levels examined are 50 percent and 95 percent. The CEP is found to be both more conservative and less conservative than the associated EEP, depending on the eccentricity of the ellipse. The formulas used are derived in the appendix.

  4. Circular analysis in complex stochastic systems

    PubMed Central

    Valleriani, Angelo

    2015-01-01

    Ruling out observations can lead to wrong models. This danger occurs unwillingly when one selects observations, experiments, simulations or time-series based on their outcome. In stochastic processes, conditioning on the future outcome biases all local transition probabilities and makes them consistent with the selected outcome. This circular self-consistency leads to models that are inconsistent with physical reality. It is also the reason why models built solely on macroscopic observations are prone to this fallacy. PMID:26656656

  5. Circular zig-zag scan video format

    DOEpatents

    Peterson, C. Glen; Simmons, Charles M.

    1992-01-01

    A circular, ziz-zag scan for use with vidicon tubes. A sine wave is generated, rectified and its fourth root extracted. The fourth root, and its inverse, are used to generate horizontal ramp and sync signals. The fourth root is also used to generate a vertical sync signal, and the vertical sync signal, along with the horizontal sync signal, are used to generate the vertical ramp signal. Cathode blanking and preamplifier clamp signals are also obtained from the vertical sync signal.

  6. Circular Intensity Differential Scattering of chiral molecules

    SciTech Connect

    Bustamante, C.J.

    1980-12-01

    In this thesis a theory of the Circular Intensity Differential Scattering (CIDS) of chiral molecules as modelled by a helix oriented with respect to the direction of incidence of light is presented. It is shown that a necessary condition for the existence of CIDS is the presence of an asymmetric polarizability in the scatterer. The polarizability of the scatterer is assumed generally complex, so that both refractive and absorptive phenomena are taken into account.

  7. Accelerator considerations of large circular colliders

    NASA Astrophysics Data System (ADS)

    Chao, Alex

    2016-07-01

    As we consider the tremendous physics reaches of the big future circular electron-positron and proton-proton colliders, it might be advisable to keep a close track of what accelerator challenges they face. Good progresses are being made, and yet it is reported here that substantial investments in funding, manpower, as well as a long sustained time to the R&D efforts will be required in preparation to realize these dream colliders.

  8. Circular dichroism of planar chiral magnetic metamaterials.

    PubMed

    Decker, M; Klein, M W; Wegener, M; Linden, S

    2007-04-01

    We propose, fabricate, and study a double-layer chiral planar metamaterial that exhibits pronounced circular dichroism at near-infrared wavelengths. The antisymmetric oscillation modes of the two coupled layers allow local magnetic-dipole moments and enhanced polarization effects compared with similar single-layer systems where only electric-dipole moments occur. Experiment and rigorous theoretical calculations are in good agreement. PMID:17339960

  9. Pulsed Accretion onto Eccentric and Circular Binaries

    NASA Astrophysics Data System (ADS)

    Muñoz, Diego J.; Lai, Dong

    2016-08-01

    We present numerical simulations of circumbinary accretion onto eccentric and circular binaries using the moving-mesh code AREPO. This is the first set of simulations to tackle the problem of binary accretion using a finite-volume scheme on a freely moving mesh, which allows for accurate measurements of accretion onto individual stars for arbitrary binary eccentricity. While accretion onto a circular binary shows bursts with period of ∼ 5 times the binary period P b, accretion onto an eccentric binary is predominantly modulated at the period ∼ 1{P}{{b}}. For an equal-mass circular binary, the accretion rates onto individual stars are quite similar to each other, following the same variable pattern in time. By contrast, for eccentric binaries, one of the stars can accrete at a rate 10–20 times larger than its companion. This “symmetry breaking” between the stars, however, alternates over timescales of order 200P b and can be attributed to a slowly precessing, eccentric circumbinary disk. Over longer timescales, the net accretion rates onto individual stars are the same, reaching a quasi-steady state with the circumbinary disk. These results have important implications for the accretion behavior of binary T Tauri stars and supermassive binary black holes.

  10. Online inspection of circular fluorescent lamp

    NASA Astrophysics Data System (ADS)

    Ang, Beng-Hoe

    1998-10-01

    One step in the manufacture of circular fluorescent lamps is the mercury (Hg) injection process in which a small amount of mercury approximately 20 mg is injected into the fluorescent tube. An on-line detection of mercury is required to ensure that the amount of mercury residual inside the tube is within the acceptable tolerance. This critical operation is to reduce manufacturing overhead by controlling cost and reducing waste of materials. In view of this, an attempt has been made to design and develop an on- line mercury detection system with important benefits to the manufacturers, such as increased throughput, accuracy, reliability and consistency. This paper presents the configuration and development works of the on-line circular fluorescent lamp inspection system developed by Industrial Project Group--Machine Vision Center of Nanyang Polytechnic. The inspection system performs on-line detection of mercury particles (Hg) inside the circular fluorescent lamp. Taking the orientation and translation offsets of the lamp into consideration, it detects the presence/absence as well as the size of the injected mercury. The system has been successfully operating 15 hours per day and inspecting more than 22 thousands lamps in the production plant.

  11. Continuous-wave circular polarization terahertz imaging

    NASA Astrophysics Data System (ADS)

    Martin, Jillian P.; Joseph, Cecil S.; Giles, Robert H.

    2016-07-01

    Biomedical applications of terahertz (THz) radiation are appealing because THz radiation is nonionizing and has the demonstrated ability to detect intrinsic contrasts between cancerous and normal tissue. A linear polarization-sensitive detection technique for tumor margin delineation has already been demonstrated; however, utilization of a circular polarization-sensitive detection technique has yet to be explored at THz frequencies. A reflective, continuous-wave THz imaging system capable of illuminating a target sample at 584 GHz with either linearly or circularly polarized radiation, and capable of collecting both cross- and copolarized signals remitted from the target, is implemented. To demonstrate the system's utility, a fresh ex vivo human skin tissue specimen containing nonmelanoma skin cancer was imaged. Both polarization-sensitive detection techniques showed contrast between tumor and normal skin tissue, although some differences in images were observed between the two techniques. Our results indicate that further investigation is required to explain the contrast mechanism, as well as to quantify the specificity and sensitivity of the circular polarization-sensitive detection technique.

  12. Pulsed Accretion onto Eccentric and Circular Binaries

    NASA Astrophysics Data System (ADS)

    Muñoz, Diego J.; Lai, Dong

    2016-08-01

    We present numerical simulations of circumbinary accretion onto eccentric and circular binaries using the moving-mesh code AREPO. This is the first set of simulations to tackle the problem of binary accretion using a finite-volume scheme on a freely moving mesh, which allows for accurate measurements of accretion onto individual stars for arbitrary binary eccentricity. While accretion onto a circular binary shows bursts with period of ˜ 5 times the binary period P b, accretion onto an eccentric binary is predominantly modulated at the period ˜ 1{P}{{b}}. For an equal-mass circular binary, the accretion rates onto individual stars are quite similar to each other, following the same variable pattern in time. By contrast, for eccentric binaries, one of the stars can accrete at a rate 10–20 times larger than its companion. This “symmetry breaking” between the stars, however, alternates over timescales of order 200P b and can be attributed to a slowly precessing, eccentric circumbinary disk. Over longer timescales, the net accretion rates onto individual stars are the same, reaching a quasi-steady state with the circumbinary disk. These results have important implications for the accretion behavior of binary T Tauri stars and supermassive binary black holes.

  13. Microwave-Field Driven Acoustic Modes in Selected DNA Molecules

    NASA Astrophysics Data System (ADS)

    Edwards, Glenn Steven

    The direct coupling of a microwave field to selected DNA molecules is demonstrated using standard dielectrometry. The absorption is resonant with a typical lifetime of 300 picoseconds. Such a long lifetime is unexpected for DNA in aqueous solution at room temperature and has interesting implications for microscopic considerations in future models of solvent damping. Resonant absorption at fundamental and harmonic frequencies for both supercoiled circular and linear DNA agrees with an acoustic mode model. Our associated acoustic velocities for linear DNA are very close to the acoustic velocity of the longitudinal acoustic mode independently observed on DNA fibers using Brillouin Spectroscopy. The difference in acoustic velocities for supercoiled circular and linear DNA is discussed in terms of a conformation dependent model. *This research has been funded by the Office of Naval Research, the Center for Devices and Radiological Health, and the National Science Foundation.

  14. Navigation and vessel inspection circular No. 0-97. Index of Navigation and Vessel Inspection Circulars (NVICS). Final report

    SciTech Connect

    1996-11-21

    This Circular provides the current listing of Navigation and Vessel Inspection Circulars (NVICS). NVICs are issued by Coast Guard Headquarters in the form of duplicated circulars. Their purpose is to inform the public of Coast Guard guidance, requirements or information regarding marine safety activities.

  15. Circular RNAs as Promising Biomarkers: A Mini-Review

    PubMed Central

    Abu, Nadiah; Jamal, Rahman

    2016-01-01

    The interest in circular RNAs has resurfaced in the past few years. What was considered as “junk” for nearly two decades is now one of the most interesting molecules. Circular RNAs are non-coding RNAs that are formed by back-splicing events and have covalently closed loops with no poly-adenylated tails. The regulation of circular RNAs is distinctive and they are selectively abundant in different types of tissues. Based on the current knowledge of circular RNAs, these molecules have the potential to be the “next big thing” especially as biomarkers for different diseases. This mini-review attempts to concisely look at the biology of circular RNAs, the putative functional activities, the prevalence of circular RNAs, and the possible role of circular RNA as biomarkers for diagnosis or measuring drug response. PMID:27588005

  16. Circular RNAs as Promising Biomarkers: A Mini-Review.

    PubMed

    Abu, Nadiah; Jamal, Rahman

    2016-01-01

    The interest in circular RNAs has resurfaced in the past few years. What was considered as "junk" for nearly two decades is now one of the most interesting molecules. Circular RNAs are non-coding RNAs that are formed by back-splicing events and have covalently closed loops with no poly-adenylated tails. The regulation of circular RNAs is distinctive and they are selectively abundant in different types of tissues. Based on the current knowledge of circular RNAs, these molecules have the potential to be the "next big thing" especially as biomarkers for different diseases. This mini-review attempts to concisely look at the biology of circular RNAs, the putative functional activities, the prevalence of circular RNAs, and the possible role of circular RNA as biomarkers for diagnosis or measuring drug response. PMID:27588005

  17. A chiroptical photoswitchable DNA complex.

    PubMed

    Mammana, Angela; Carroll, Gregory T; Areephong, Jetsuda; Feringa, Ben L

    2011-10-13

    The interesting structural, electronic, and optical properties of DNA provide fascinating opportunities for developing nanoscale smart materials by integrating DNA with opto-electronic components. In this article we demonstrate the electrostatic binding of an amine-terminated dithienylethene (DET) molecular switch to double-stranded synthetic polynucleotides. The DET switch can undergo photochemical ring-closure and opening reactions. Circular dichroism (CD) and UV-vis spectroscopy show that both the open, 1o, and the closed, 1c, forms of the switch bind to DNA. Upon addition of DNA to a solution of 1o or 1c, the UV-vis spectrum displays a hypochromic effect, indicative of an interaction between the switch and the DNA. The chirality of the DNA double-helix is transmitted to the switching unit which displays a well-defined CD signal upon supramolecular complexation to the DNA. Additionally, the CD signal of the DNA attenuates, demonstrating that both components of the complex mutually influence each other's structure; the DNA induces chirality in the switch, and the switch modifies the structure of the DNA. Modulation of the chiroptical properties of the complex is achieved by photochemically switching the DET between its ring open and closed isomers. A pH dependence study of the binding shows that when the pH is increased the switches lose their binding ability, indicating that electrostatic interactions between protonated amines and the negatively charged phosphate backbone are the dominant driving force for binding to the DNA. A comparison of poly(deoxyguanylic-deoxycytidylic) acid [poly(dGdC)(2)] polynucleotides with poly(deoxyadenylic-deoxythymidylic) acid [poly(dAdT)(2)] shows distinct differences in the CD spectra of the complexes. PMID:21879715

  18. Enzymatic Polymerization on DNA Modified Gold Nanowire for Label-Free Detection of Pathogen DNA

    PubMed Central

    Jeong, Jaepil; Kim, Hyejin; Lee, Jong Bum

    2015-01-01

    This paper presents a label-free biosensor for the detection of single-stranded pathogen DNA through the target-enhanced gelation between gold nanowires (AuNW) and the primer DNAs branched on AuNW. The target DNA enables circularization of the linear DNA template, and the primer DNA is elongated continuously via rolling circle amplification. As a result, in the presence of the target DNA, a macroscopic hydrogel was fabricated by the entanglement of the elongated DNA with AuNWs as a scaffold fiber for effective gelation. In contrast, very small separate particles were generated in the absence of the target DNA. This label-free biosensor might be a promising tool for the detection of pathogen DNAs without any devices for further analysis. Moreover, the biosensor based on the weaving of AuNW and DNAs suggests a novel direction for the applications of AuNWs in biological engineering. PMID:26084045

  19. Adenovirus Type 2-Simian Virus 40 Hybrid Population: Evidence for a Hybrid Deoxyribonucleic Acid Molecule and the Absence of Adenovirus-Encapsidated Circular Simian Virus 40 Deoxyribonucleic Acid

    PubMed Central

    Crumpacker, Clyde S.; Levin, Myron J.; Wiese, William H.; Lewis, Andrew M.; Rowe, Wallace P.

    1970-01-01

    The deoxyribonucleic acid (DNA) from the adenovirus-encapsidated particles of the adenovirus type 2 (Ad2)-simian virus 40 (SV40) hybrid population plaque variant (Ad2++ HEY), known to yield SV40 virus with high efficiency, was studied by equilibrium density centrifugation followed by ribonucleic acid-DNA hybridization employing virus-specific complementary ribonucleic acids synthesized in vitro. These techniques establish linkage between the Ad2 and SV40 components in the adenovirus-encapsidated particles of this population. The linkage is alkali-resistant and presumably covalent; thus, the Ad2 DNA and SV40 DNA are present in a hybrid molecule. Velocity centrifugation studies in alkaline sucrose gradients eliminated the possibility that supercoiled circular SV40 DNA is present in the adenovirus capsids. The DNA obtained from the adenovirus-encapsidated particles of the Ad2++ HEY population appears to consist of nonhybrid Ad2 DNA and Ad2-SV40 hybrid DNA molecules. PMID:4322081

  20. Computational simulations of hydrogen circular migration in protonated acetylene induced by circularly polarized light.

    PubMed

    Shi, Xuetao; Li, Wen; Schlegel, H Bernhard

    2016-08-28

    The hydrogens in protonated acetylene are very mobile and can easily migrate around the C2 core by moving between classical and non-classical structures of the cation. The lowest energy structure is the T-shaped, non-classical cation with a hydrogen bridging the two carbons. Conversion to the classical H2CCH(+) ion requires only 4 kcal/mol. The effect of circularly polarized light on the migration of hydrogens in oriented C2H3 (+) has been simulated by Born-Oppenheimer molecular dynamics. Classical trajectory calculations were carried out with the M062X/6-311+G(3df,2pd) level of theory using linearly and circularly polarized 32 cycle 7 μm cosine squared pulses with peak intensity of 5.6 × 10(13) W/cm(2) and 3.15 × 10(13) W/cm(2), respectively. These linearly and circularly polarized pulses transfer similar amounts of energy and total angular momentum to C2H3 (+). The average angular momentum vectors of the three hydrogens show opposite directions of rotation for right and left circularly polarized light, but no directional preference for linearly polarized light. This difference results in an appreciable amount of angular displacement of the three hydrogens relative to the C2 core for circularly polarized light, but only an insignificant amount for linearly polarized light. Over the course of the simulation with circularly polarized light, this corresponds to a propeller-like motion of the three hydrogens around the C2 core of protonated acetylene. PMID:27586924

  1. Recombination between linear double-stranded DNA substrates in vivo

    PubMed Central

    Narayanan, Kumaran; Sim, Edmund Ui-Hang; Ravin, Nikolai V.; Lee, Choon-Weng

    2009-01-01

    Recombineering technology in E. coli enables targeting of linear donor DNA to circular recipient DNA using short shared homology sequences. In this work, we demonstrate that recombineering is also able to support recombination between a pair of linear DNA substrates (linear/linear recombineering) in vivo in E. coli. Linear DNA up to 100 kb is accurately modified and remains intact without undergoing rearrangements after recombination. This system will be valuable for direct in vivo manipulation of large linear DNA including the N15 and PY54 prophages and linear animal viruses, and for assembly of linear constructs as artificial chromosome vectors. PMID:19454252

  2. [Haikou issues circular on planned parenthood].

    PubMed

    1981-02-01

    The Organization Department of the Haikou Municipal CCP Committee, the municipal grain, finance, commerce, education bureau, personnel, public security, labor, civil affairs, public health, and housing bureaus, supply and marketing cooperative, and planned parenthood office recently issued a joint circular on implementing the provincial planned parenthood regulations. The circular demanded that the marriage registration and census system be seriously implemented. When people are registering for marriage, we must teach them to have only 1 child. We must give priority in housing and employment to an only child and his parents. When commercial, supply, and marketing departments are distributing coupons for fuel, and nonstaple food, they should supply a double amount to the only child. We must carry out serious health care for an only child and give them regular physical check-ups. When they are ill, hospitals should give them priority in registration, treatment, reservation of beds and medicines. The circular reiterated: We must seriously implement the stipulations on rewards and punishments contained in the provincial planned parenthood regulations. Cadres, staff, or workers who apply to have only 1 child must be given lump sums in addition to enjoying the relevant rewards stipulated by the regulations. Cadres, staff, workers, inhabitants, and commune workers who depend on state grain who violate the regulations must be punished according to the regulation. As for those who have 3 or more than 3 children, a 2nd child without planning, or an illegitimate child, the child's grain ration will be sold at negotiated price up to the age of 14. The grain department will distribute to them a supply ticket for negotiated price grain to buy grain in assigned grain shops. PMID:12338059

  3. Multipole Analysis of Circular Cylindircal Magnetic Systems

    SciTech Connect

    J Selvaggi

    2006-01-09

    This thesis deals with an alternate method for computing the external magnetic field from a circular cylindrical magnetic source. The primary objective is to characterize the magnetic source in terms of its equivalent multipole distribution. This multipole distribution must be valid at points close to the cylindrical source and a spherical multipole expansion is ill-equipped to handle this problem; therefore a new method must be introduced. This method, based upon the free-space Green's function in cylindrical coordinates, is developed as an alternative to the more familiar spherical harmonic expansion. A family of special functions, called the toroidal functions or Q-functions, are found to exhibit the necessary properties for analyzing circular cylindrical geometries. In particular, the toroidal function of zeroth order, which comes from the integral formulation of the free-space Green's function in cylindrical coordinates, is employed to handle magnetic sources which exhibit circular cylindrical symmetry. The toroidal functions, also called Q-functions, are the weighting coefficients in a ''Fourier series-like'' expansion which represents the free-space Green's function. It is also called a toroidal expansion. This expansion can be directly employed in electrostatic, magnetostatic, and electrodynamic problems which exhibit cylindrical symmetry. Also, it is shown that they can be used as an alternative to the Elliptic integral formulation. In fact, anywhere that an Elliptic integral appears, one can replace it with its corresponding Q-function representation. A number of problems, using the toroidal expansion formulation, are analyzed and compared to existing known methods in order to validate the results. Also, the equivalent multipole distribution is found for most of the solved problems along with its corresponding physical interpretation. The main application is to characterize the external magnetic field due to a six-pole permanent magnet motor in terms of

  4. Contribution of light scattering to the circular dichroism of deoxyribonucleic acid films, deoxyribonucleic acid-polylysine complexes, and deoxyribonucleic acid particles in ethanolic buffers

    SciTech Connect

    Maestre, M.F.; Reich, C.

    1980-01-01

    The contribution of scattering to the circular dichroism (CD) of DNA films with twisted structures, DNA-polylysine complexes, and condensed DNA aggregates in ethanolic buffers of defined salt concentrations has been studied by the use of novel measuring techniques. These techniques include fluorscat cuvettes, fluorescence-detected circular dichroism (FDCD) methods, backscattering capturing devices, and beam-mounted goniometer detectors. The result of the experimental measurement is that DNA films can be made which have very large ellipticities or CD at sharp specific wavelengths. The sign of these ellipticities is related to the handedness of the twists, with a right-handed twist producing large positive rotations and a left-handed one producing negative rotations. The film shows nodal angles at which the interaction with light is minimal. The scattering patterns of both films, DNA-polylysine particles and DNA-EtOH condensates, show that the main interaction is light scattering produced by a resonance phenomenon similar to that produced in cholestric liquid crystals and twisted-nematic liquid crystals. It is proposed that the so-called psi-type CD spectrum is a manifestation of a side-by-side packing of DNA molecules with a long-range twisting order whose helical parameters match the helical parameter of circularly polarized light at specific resonance or critical wavelengths. Application of the Bragg law for cholesteric liquid crystals gives the periodicity of the long-range ordered structures. 9 figures.

  5. [Anesthetic maintenance during circular face lifting].

    PubMed

    Parshin, V I; Pastukhova, N K

    2010-01-01

    The paper deals with the specific features of anesthetic maintenance (ketamine, diprivan, dormicum, perfalgan, promedol) during circular face lifting without artificial ventilation. All intravenous anesthesia procedures have yielded good results. Narcotic analgesics may be removed from the anesthetic maintenance scheme, ruling out the necessity of their licensing, storing, and recording. The use of perfalgan causes no hallucinogenic reactions and offers the optimum level of anesthesia. During face lifting, 2.3 +/- 0.6-hour anesthesia with spontaneous breathing is possible, safe, and warranted. PMID:20524331

  6. Circular orbits on a warped spandex fabric

    NASA Astrophysics Data System (ADS)

    Middleton, Chad A.; Langston, Michael

    2014-04-01

    We present a theoretical and experimental analysis of circular-like orbits made by a marble rolling on a warped spandex fabric. We show that the mass of the fabric interior to the orbital path influences the motion of the marble in a nontrivial way and can even dominate the orbital characteristics. We also compare a Kepler-like expression for such orbits to similar expressions for orbits about a spherically symmetric massive object in the presence of a constant vacuum energy, as described by general relativity.

  7. Vortex motion behind a circular cylinder

    NASA Technical Reports Server (NTRS)

    Foeppl, L.

    1983-01-01

    Vortex motion behind a circular cylinder moving through water is discussed. It is shown that a pair of vortices form behind a moving cylinder and that their centers will move along a predictable curve. This curve represents an equilibrium condition which, however, is subject to perturbation. The stability of the vortex pair is investigated. Movement of the vortex pair away from the cylinder is calculated as an explanation of the resistance of the cylinder. Finally, the principles elaborated are applied to the flow around a flat plate.

  8. Optofluidic circular grating distributed feedback dye laser

    NASA Astrophysics Data System (ADS)

    Chen, Yan; Li, Zhenyu; Henry, M. David; Scherer, Axel

    2009-07-01

    We demonstrate an optically pumped surface emitting optofluidic dye laser using a second-order circular grating distributed feedback resonator. We present a composite bilayer soft lithography technique specifically developed for the fabrication of our dye laser and investigate a hybrid polymer material system [poly(dimethylsiloxane)/perfluoropolyether] to construct high-resolution Bragg gratings. Our lasers emit single frequency light at low lasing thresholds of 6 μJ/mm2. These optofluidic dye lasers can serve as low-cost and compact coherent light sources that are fully integrated within microfluidic analysis chips and provide an efficient approach to construct compact spectroscopy systems.

  9. Circular zig-zag scan video format

    DOEpatents

    Peterson, C.G.; Simmons, C.M.

    1992-06-09

    A circular, ziz-zag scan for use with vidicon tubes is disclosed. A sine wave is generated, rectified and its fourth root extracted. The fourth root, and its inverse, are used to generate horizontal ramp and sync signals. The fourth root is also used to generate a vertical sync signal, and the vertical sync signal, along with the horizontal sync signal, are used to generate the vertical ramp signal. Cathode blanking and preamplifier clamp signals are also obtained from the vertical sync signal. 10 figs.

  10. Build a circularly polarized waveguide slot antenna

    NASA Astrophysics Data System (ADS)

    Kisliuk, M.; Axelrod, A.

    1987-06-01

    The development and design of a circularly polarized waveguide slot antenna are described. Consideration is given to the resonance frequency, radiation efficiencies, excitement, and resonant conductance of the transverse and longitudinal slots. The transverse and longitudinal slots in a rectangular guide are analyzed. The voltage distribution across the slot is calculated from the solution of a standard transmission line equation; and using the Poynting theorem the fields scattered by the slot in an arbitrary frequency range are determined. The proposed antenna is examined using an equivalent circuit; a diagram of the circuit is given. The radiation, slot, and antenna efficiencies are measured.

  11. Acceleration of polarized protons in circular accelerators

    SciTech Connect

    Courant, E.D.; Ruth, R.D.

    1980-09-12

    The theory of depolarization in circular accelerators is presented. The spin equation is first expressed in terms of the particle orbit and then converted to the equivalent spinor equation. The spinor equation is then solved for three different situations: (1) a beam on a flat top near a resonance, (2) uniform acceleration through an isolated resonance, and (3) a model of a fast resonance jump. Finally, the depolarization coefficient, epsilon, is calculated in terms of properties of the particle orbit and the results are applied to a calculation of depolarization in the AGS.

  12. DNA Compaction by Yeast Mitochondrial Protein ABF2p

    SciTech Connect

    Friddle, R W; Klare, J E; Noy, A; Corzett, M; Balhorn, R; Baskin, R J; Martin, S S; Baldwin, E P

    2003-05-09

    We used high resolution Atomic Force Microscopy (AFM) to image compaction of linear and circular DNA by the yeast mitochondrial protein ABF2p , which plays a major role in maintaining mitochondrial DNA. AFM images show that protein binding induces drastic bends in the DNA backbone for both linear and circular DNA. At high concentration of ABF2p DNA collapses into a tight globular structure. We quantified the compaction of linear DNA by measuring the end-to-end distance of the DNA molecule at increasing concentrations of ABF2p. We also derived a polymer statistical mechanics model that gives quantitative description of compaction observed in our experiments. This model shows that a number of sharp bends in the DNA backbone is often sufficient to cause DNA compaction. Comparison of our model with the experimental data showed excellent quantitative correlation and allowed us to determine binding characteristics for ABF2. Our studies indicate that ABF2 compacts DNA through a novel mechanism that involves bending of DNA backbone. We discuss the implications of such a mechanism for mitochondrial DNA maintenance.

  13. DNA maintenance in plastids and mitochondria of plants

    PubMed Central

    Oldenburg, Delene J.; Bendich, Arnold J.

    2015-01-01

    The DNA molecules in plastids and mitochondria of plants have been studied for over 40 years. Here, we review the data on the circular or linear form, replication, repair, and persistence of the organellar DNA (orgDNA) in plants. The bacterial origin of orgDNA appears to have profoundly influenced ideas about the properties of chromosomal DNA molecules in these organelles to the point of dismissing data inconsistent with ideas from the 1970s. When found at all, circular genome-sized molecules comprise a few percent of orgDNA. In cells active in orgDNA replication, most orgDNA is found as linear and branched-linear forms larger than the size of the genome, likely a consequence of a virus-like DNA replication mechanism. In contrast to the stable chromosomal DNA molecules in bacteria and the plant nucleus, the molecular integrity of orgDNA declines during leaf development at a rate that varies among plant species. This decline is attributed to degradation of damaged-but-not-repaired molecules, with a proposed repair cost-saving benefit most evident in grasses. All orgDNA maintenance activities are proposed to occur on the nucleoid tethered to organellar membranes by developmentally-regulated proteins. PMID:26579143

  14. Simple Broadband Circular Polarizer in Oversized Waveguide

    NASA Astrophysics Data System (ADS)

    Stange, Torsten

    2016-02-01

    In this paper, a possibility is shown to realize a simple waveguide polarizer producing nearly the same circular polarization over a broad frequency range up to an octave. It is based upon the combination of two smoothly squeezed oversized waveguides with different diameters. The principle is similar to an achromatic lens in optics, where two counteracting lenses with differently sloped wavelength dependencies of the refractive index are combined to compensate the dispersion in the desired wavelength range. Consequently, two different wavelengths of light are brought into focus at the same plane. A waveguide for the transmission of microwaves has a similar frequency dependence of the refractive index resulting in a frequency-dependent phase shift between two propagating waves polarized along the symmetry axes of a waveguide with an elliptical cross section. For this reason, an incident wave with a linear polarization between the axes of symmetry can be only converted into a circularly polarized wave over a limited frequency range. However, the diameter and the shape along two counteracting squeezed waveguides can be adjusted in such a way that the frequency dependence of the resultant phase shift is finally canceled out.

  15. High Performance Circularly Polarized Microstrip Antenna

    NASA Technical Reports Server (NTRS)

    Bondyopadhyay, Probir K. (Inventor)

    1997-01-01

    A microstrip antenna for radiating circularly polarized electromagnetic waves comprising a cluster array of at least four microstrip radiator elements, each of which is provided with dual orthogonal coplanar feeds in phase quadrature relation achieved by connection to an asymmetric T-junction power divider impedance notched at resonance. The dual fed circularly polarized reference element is positioned with its axis at a 45 deg angle with respect to the unit cell axis. The other three dual fed elements in the unit cell are positioned and fed with a coplanar feed structure with sequential rotation and phasing to enhance the axial ratio and impedance matching performance over a wide bandwidth. The centers of the radiator elements are disposed at the corners of a square with each side of a length d in the range of 0.7 to 0.9 times the free space wavelength of the antenna radiation and the radiator elements reside in a square unit cell area of sides equal to 2d and thereby permit the array to be used as a phased array antenna for electronic scanning and is realizable in a high temperature superconducting thin film material for high efficiency.

  16. Distorted DNA structures induced by HMGB2 possess a high affinity for HMGB2.

    PubMed

    Nakamura, Yasuyuki; Shimizu, Mitsuhiro; Yoshida, Michiteru

    2002-01-01

    HMGB2 (HMG2) protein binds with DNA duplex in a sequence-nonspecific manner, then bends and unwinds the DNA. In DNA cyclization analyses for the bending activity of HMGB2, two unidentified bands, denoted alpha and beta, were observed in addition to monomer circular DNA (1C) on the gel. Re-electrophoresis and proteinase K digestion revealed that alpha and beta are complexes of circularized probe DNA (seeming 1C) with HMGB2 (K(d) approximately 10(-10) M). The DNA components of alpha and beta (alpha- and beta-DNA) showed higher affinities to HMGB2 than did the linear probe DNA (K(d) approximately 10(-7) M). The DNAs have distorted structures containing partial single-stranded regions. Nicked circular molecules presumably due to severe DNA distortion by HMGB2 were observed in alpha- and beta-DNA, in addition to closed circular double-stranded molecules. The alpha and beta bands were not formed in the presence of sole DNA binding regions which are necessary for DNA bending, indicating that the acidic C-tail in the HMGB2 molecule is necessary for inducing the peculiar distorted structures of higher affinity to HMGB2. HMGB2 binds with linker DNA and/or the entry and exit of nucleosomes fixed at both ends likewise mini-circles similar to alpha-DNA and beta-DNA. Thus, the distorted structures present in alpha-DNA and beta-DNA should be important in considering the functional mechanisms in which HMGB2 participates. PMID:11754747

  17. The effects of 4-MEI on cell proliferation, DNA breaking and DNA fragmentation.

    PubMed

    Tazehkand, M Norizadeh; Moridikia, A; Hajipour, O; Valipour, E; Timocin, T; Topaktas, M; Yilmaz, M B

    2016-01-01

    4-Methylimidazole (4-MEI) is a color widely found in cola drinks, roasted foods, grilled meats, coffee and other foods. This study was aimed to investigate the 4-MEI effects on the cell proliferation, purified circular DNA and DNA from cells of rats treated with the 4-MEI.In this study, mouse 3T3-L1 cell line was treated with 4-MEI at concentrations of 300, 450, 600 and 750 µg/mL for 24 hours and 48 hours periods, after that cytotoxic effect of the 4-MEI was studied by MTT test. Also, the effect of 4-MEI on purified circular DNA (pET22b) was investigated by treating of the DNA with 4-MEI concentrations of 300, 450, 600 and 750 µg/ml. DNA was extracted from liver cells of rats that have been treated with 4-MEI doses of 25 and 50 mg/kg for 10 week and it was subjected to agarose gel electrophoreses analyses.4-MEI significantly inhibited cell proliferation of 3T3-L1 cell line at highest concentration for 24 h and at all concentration for 48 h treatment time. DNA fragmentation assay showed that 4-MEI at 50 mg/kg concentration clearly produced characteristic DNA smear and no DNA laddering (200bp) was observed when mouse was exposed to 4-MEI. The results obtained from plasmid DNA damaging assay showed that 4-MEI has noeffect on the DNA, because the electrophoretic pattern of DNA treated with 4-MEI showed three bands on agarose gel electrophoresis as it was for untreated control. 4-MEI showed cytotoxic effect on 3T3-L1 cells but no effect on plasmid DNA breaking. According to DNA fragmentation assay 4-MEI has necrosis effects on mouse liver cells (Tab. 1, Fig. 4, Ref. 27). PMID:27546537

  18. Mitochondrial DNA.

    ERIC Educational Resources Information Center

    Wright, Russell G.; Bottino, Paul J.

    1986-01-01

    Provides background information for teachers on mitochondrial DNA, pointing out that it may have once been a free-living organism. Includes a ready-to-duplicate exercise titled "Using Microchondrial DNA to Measure Evolutionary Distance." (JN)

  19. Determination of the cationic amphiphilic drug-DNA binding mode and DNA-assisted fluorescence resonance energy transfer amplification

    NASA Astrophysics Data System (ADS)

    Yaseen, Zahid; Banday, Abdul Rouf; Hussain, Mohammed Aamir; Tabish, Mohammad; Kabir-ud-Din

    2014-03-01

    Understanding the mechanism of drug-DNA binding is crucial for predicting the potential genotoxicity of drugs. Agarose gel electrophoresis, absorption, steady state fluorescence, and circular dichroism have been used in exploring the interaction of cationic amphiphilic drugs (CADs) such as amitriptyline hydrochloride (AMT), imipramine hydrochloride (IMP), and promethazine hydrochloride (PMT) with calf thymus or pUC19 DNA. Agarose gel electrophoresis assay, along with absorption and steady state fluorescence studies, reveal interaction between the CADs and DNA. A comparative study of the drugs with respect to the effect of urea, iodide induced quenching, and ethidium bromide (EB) exclusion assay reflects binding of CADs to the DNA primarily in an intercalative fashion. Circular dichroism data also support the intercalative mode of binding. Besides quenching, there is fluorescence exchange energy transfer (FRET) in between CADs and EB using DNA as a template.

  20. A luminescent beta-cyclodextrin-based Ru(phen)3 complex as DNA compactor, enzyme inhibitor, and translocation tracer.

    PubMed

    Liu, Yu; Chen, Yong; Duan, Zhong-Yu; Feng, Xi-Zeng; Hou, Sen; Wang, Chen; Wang, Rui

    2007-11-01

    A beta-cyclodextrin-based Ru(phen)(3) complex (1) has been synthesized and exhibits good luminescent behavior. Atomic force microscopic and scanning electron microscopic studies show that 1 can induce the aggregation of originally circular DNA to toroidal or spherical shapes. The morphology of these DNA aggregates changes following a pathway of naked circular DNA --> toroid with gaps --> solid toroid --> spherical aggregate, depending on the different 1/DNA (w/w) ratios, and their average diameters vary from the nanometer to micrometer scale. Owing to its capability of inducing the aggregation of DNA, 1 can be used as an inhibitor for DNA topoisomerase and DNA cleavage enzymes. Further studies by means of fluorescence microscopy indicate that 1 can also efficiently trace the translocation of DNA into 293T cells (the human embryonic kidney cell line). These observations consequently establish 1 as not only a potential DNA carrier but also a fluorescent DNA probe. PMID:19206682

  1. DNA Banking

    SciTech Connect

    Reilly, P.R. )

    1992-11-01

    The author is involved in the ethical, legal, and social issues of banking of DNA and data from DNA analysis. In his attempt to determine the extent of DNA banking in the U.S., the author surveyed some commercial companies performing DNA banking services. This article summarizes the results of that survey, with special emphasis on the procedures the companies use to protect the privacy of individuals. 4 refs.

  2. Multispectroscopic studies of the interaction of calf thymus DNA with the anti-viral drug, valacyclovir

    NASA Astrophysics Data System (ADS)

    Shahabadi, Nahid; Fatahi, Navid; Mahdavi, Maryam; Nejad, Zahra Kiani; Pourfoulad, Mehdi

    2011-12-01

    The present study investigated the binding interaction between an antiviral drug, valacyclovir and calf thymus DNA (CT-DNA) using emission, absorption, circular dichroism, viscosity and DNA melting studies. In fluorimetric studies, thermodynamic enhancement constant ( KD) and bimolecular enhancement constant ( KB) were calculated at different temperatures and demonstrated that fluorescence enhancement is not initiated by a dynamic process, but instead by a static process that involves complex DNA formation in the ground state. Further, the enthalpy and entropy of the reaction between the drug and CT-DNA showed that the reaction is exothermic and enthalpy-favored. In addition, detectable changes in the circular dichroism spectrum of CT-DNA in the presence of valacyclovir indicated conformational changes in the DNA double helix following interaction with the drug. All these results prove that this antiviral drug interacts with CT-DNA via an intercalative mode of binding.

  3. Molecular Mechanisms of DNA Polymerase Clamp Loaders

    NASA Astrophysics Data System (ADS)

    Kelch, Brian; Makino, Debora; Simonetta, Kyle; O'Donnell, Mike; Kuriyan, John

    Clamp loaders are ATP-driven multiprotein machines that couple ATP hydrolysis to the opening and closing of a circular protein ring around DNA. This ring-shaped clamp slides along DNA, and interacts with numerous proteins involved in DNA replication, DNA repair and cell cycle control. Recently determined structures of clamp loader complexes from prokaryotic and eukaryotic DNA polymerases have revealed exciting new details of how these complex AAA+ machines perform this essential clamp loading function. This review serves as background to John Kuriyan's lecture at the 2010 Erice School, and is not meant as a comprehensive review of the contributions of the many scientists who have advanced this field. These lecture notes are derived from recent reviews and research papers from our groups.

  4. Characterization of a linear DNA plasmid from the filamentous fungal plant pathogen Glomerella musae [Anamorph: Colletotrichum musae (Berk. and Curt.) arx.

    USGS Publications Warehouse

    Freeman, S.; Redman, R.S.; Grantham, G.; Rodriguez, R.J.

    1997-01-01

    A 7.4-kilobase (kb) DNA plasmid was isolated from Glomerella musae isolate 927 and designated pGML1. Exonuclease treatments indicated that pGML1 was a linear plasmid with blocked 5' termini. Cell-fractionation experiments combined with sequence-specific PCR amplification revealed that pGML1 resided in mitochondria. The pGML1 plasmid hybridized to cesium chloride-fractionated nuclear DNA but not to A + T-rich mitochondrial DNA. An internal 7.0-kb section of pGML1 was cloned and did not hybridize with either nuclear or mitochondrial DNA from G. musae. Sequence analysis revealed identical terminal inverted repeats (TIR) of 520 bp at the ends of the cloned 7.0-kb section of pGML1. The occurrence of pGML1 did not correspond with the pathogenicity of G. musae on banana fruit. Four additional isolates of G. musae possessed extrachromosomal DNA fragments similar in size and sequence to pGML1.

  5. Global Phylogenomic Analysis Disentangles the Complex Evolutionary History of DNA Replication in Archaea

    PubMed Central

    Raymann, Kasie; Forterre, Patrick; Brochier-Armanet, Céline; Gribaldo, Simonetta

    2014-01-01

    The archaeal machinery responsible for DNA replication is largely homologous to that of eukaryotes and is clearly distinct from its bacterial counterpart. Moreover, it shows high diversity in the various archaeal lineages, including different sets of components, heterogeneous taxonomic distribution, and a large number of additional copies that are sometimes highly divergent. This has made the evolutionary history of this cellular system particularly challenging to dissect. Here, we have carried out an exhaustive identification of homologs of all major replication components in over 140 complete archaeal genomes. Phylogenomic analysis allowed assigning them to either a conserved and probably essential core of replication components that were mainly vertically inherited, or to a variable and highly divergent shell of extra copies that have likely arisen from integrative elements. This suggests that replication proteins are frequently exchanged between extrachromosomal elements and cellular genomes. Our study allowed clarifying the history that shaped this key cellular process (ancestral components, horizontal gene transfers, and gene losses), providing important evolutionary and functional information. Finally, our precise identification of core components permitted to show that the phylogenetic signal carried by DNA replication is highly consistent with that harbored by two other key informational machineries (translation and transcription), strengthening the existence of a robust organismal tree for the Archaea. PMID:24398374

  6. Role of LrpC from Bacillus subtilis in DNA transactions during DNA repair and recombination

    PubMed Central

    López-Torrejón, Gema; Martínez-Jiménez, María I.; Ayora, Silvia

    2006-01-01

    Bacillus subtilis LrpC is a sequence-independent DNA-binding and DNA-bending protein, which binds both single-stranded (ss) and double-stranded (ds) DNA and facilitates the formation of higher order protein–DNA complexes in vitro. LrpC binds at different sites within the same DNA molecule promoting intramolecular ligation. When bound to separate molecules, it promotes intermolecular ligation, and joint molecule formation between a circular ssDNA and a homologous ssDNA-tailed linear dsDNA. LrpC binding showed a higher affinity for 4-way (Holliday) junctions in their open conformation, when compared with curved dsDNA. Consistent with these biochemical activities, an lrpC null mutant strain rendered cells sensitive to DNA damaging agents such as methyl methanesulfonate and 4-nitroquinoline-1-oxide, and showed a segregation defect. These findings collectively suggest that LrpC may be involved in DNA transactions during DNA repair and recombination. PMID:16407330

  7. Dna Sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  8. 3D measurement using circular gratings

    NASA Astrophysics Data System (ADS)

    Harding, Kevin

    2013-09-01

    3D measurement using methods of structured light are well known in the industry. Most such systems use some variation of straight lines, either as simple lines or with some form of encoding. This geometry assumes the lines will be projected from one side and viewed from another to generate the profile information. But what about applications where a wide triangulation angle may not be practical, particularly at longer standoff distances. This paper explores the use of circular grating patterns projected from a center point to achieve 3D information. Originally suggested by John Caulfield around 1990, the method had some interesting potential, particularly if combined with alternate means of measurement from traditional triangulation including depth from focus methods. The possible advantages of a central reference point in the projected pattern may offer some different capabilities not as easily attained with a linear grating pattern. This paper will explore the pros and cons of the method and present some examples of possible applications.

  9. A 90° fair circular waveguide bend.

    PubMed

    Yu, Xin-hua; Deng, Ji-liang; Cao, Wei-ping; Li, Si-min; Gao, Xi; Jiang, Yan-nan

    2015-01-01

    We propose a synthesis method to design a 90° bent fair circular waveguide TE01 mode transition based on the non-uniform rational B-spline technique. The transition by this method has advantages of small geometry, high transmission with wide band and high profile fairness. An example of design of such a transition is presented. The simulation shows that the transition exhibits a transmission as high as 99.3% at the central frequency 35 GHz and has a bandwidth of 16.7% when keeping the transmission over 95%. Furthermore, the profile is extremely fair, which meets the requirements to decrease the geometry errors between actual device and its design, to reduce the machining difficulty in the machining process. The hot test data indicate that good transmission of the TE01 mode is obtained. PMID:25638106

  10. Torsion Tests of Stiffened Circular Cylinders

    NASA Technical Reports Server (NTRS)

    Moore, R L; Wescoat, C

    1944-01-01

    The design of curved sheet panels to resist shear involves a consideration of several factors: the buckling resistance of the sheet, the stress at which buckling becomes permanent, and the strength which may be developed beyond the buckling limit by tension-field action. Although some experimental as well as theoretical work has been done on the buckling and tension-field phases of this problem, neither of these types of action appears to be very well understood. The problem is of sufficient importance from the standpoint of aircraft design, it is believed, to warrant further experimental investigation. This report presents the results of the first series of torsion tests of stiffened circular cylinders to be completed in connection with this study at Aluminum Research Laboratories. (author)

  11. Electronic circular dichroism behavior of chiral Phthiobuzone

    PubMed Central

    Li, Li; Wang, Lin; Si, Yikang

    2014-01-01

    Phthiobuzone is a bis(thiosemicarbazone) derivative with a single chiral center which has been used as a racemate in the clinical treatment of herpes and trachoma diseases. In this study, its two enantiomers were prepared from chiral amino acids and their absolute configurations were investigated by electronic circular dichroism (ECD) combined with modern quantum-chemical calculations using time-dependent density functional theory. It was found that solvation changed both the conformational distribution and the ECD spectrum of each conformer. The theoretical ECD spectra of the two enantiomers were in good agreement with the experimentally determined spectra of the corresponding isomers in dimethyl sulfoxide. The ECD behavior of the bis(thiosemicarbazone) chromophore in a chiral environment is also discussed. Our results indicate that ECD spectroscopy may be a useful tool for the stereochemical evaluation of chiral drugs. PMID:26579380

  12. Magnetic circular dichroism in EELS (abstract)

    SciTech Connect

    Harp, G.R.; Farrow, R.F.; Marks, R.F.

    1996-04-01

    We evaluate the possibility of using dichroic electron energy loss spectroscopy (DEELS) as an alternative to x-ray magnetic circular dichroism (XMCD). It is well known that electron energy loss spectroscopy and x-ray absorption spectroscopy are highly analogous, providing similar information. A simple semiclassical model suggests that DEELS might have a magnetic sensitivity similar to that of XMCD. This sensitivity will be reduced, however, by multiple scattering of the probe electron before and after the energy loss event. Thus it is difficult to predict the magnitude of the DEELS effect. Experiments were performed at the {ital L}-edge of polycrystalline Fe, Co, and Ni thin film samples with uniaxial in-plane magnetic anisotropy, prepared {ital in} {ital situ} with a magnetic bias field. Even in those most favorable cases, the DEELS effect is seen to be at least 10 times smaller than similar effects in XMCD. {copyright} {ital 1996 American Institute of Physics.}

  13. Rotation sensing with a circular atomic waveguide

    NASA Astrophysics Data System (ADS)

    Zhao, Lian-jie; Yan, Xiao-jun; Zhang, Guo-wan; Zhang, An-ning

    2016-01-01

    The hollow metallic optical fibers not only retain the advantage of flexibility but possess a greater intensity gradient for atomic waveguide. Therefore, based on the vector model of Maxwell's equations, we exactly calculated the intensity distribution of the TE01 mode in a typical metallic fiber, and analyzed the optical potential for 85Rb atom. Most of all, based on a circular atomic waveguide, we creatively proposed a novel measurement scheme for rotation sensing, explained the specific measurement principle, and built a mathematical model for this novel scheme. By measuring the number of atoms in the final states, we could get the rotation rate for this typical rotation system. This novel rotation sensor not only possessed a higher measurement precision, but realized the continuity measurement. It will be widely used in navigation, geophysics and general relativity.

  14. Circular dichroism study of the hemocyanin thermostability

    NASA Astrophysics Data System (ADS)

    Nikolova Georgieva, Dessislava; Stoeva, Stanka; Abid Ali, Syed; Abbasi, Atiya; Genov, Nicolay; Voelter, Wolfgang

    1998-05-01

    Circular dichroism spectroscopy is used to investigate the thermostability of six arthropod hemocyanins (Hcs), representatives of the subphyla Crustacea (infraorder Brachyura) and Chelicerate (infraorders Xiphosura and Arachnida), and three molluscan Hcs from gastropod organisms. Melting points ( Tm) are determined from the temperature dependence of ellipticity of dioxygen-binding proteins from Maia squinado, Callinectes sapidus, Carcinus maenas, Limulus polyphemus, Buthus sindicus, Androctonus australis, Megathura crenulata, Haliotis tuberculata, and Rapana thomasiana. Both, arthropod and molluscan Hcs, are thermostable proteins with melting temperatures in the region 68-91°C. Binuclear dioxygen-binding sites contribute significantly to the thermostability and increase the Tm values of the apo-forms by 3-16°C. An elevated thermostability is observed in the case of the Limulus polyphemus Hc. One of the reasons is the high degree of hemocyanin oligomerization.

  15. Magnetic circular dichroism of peralkylated tetrasilane conformers

    PubMed Central

    Fogarty, Heather A.; Imhof, Roman; Michl, Josef

    2004-01-01

    Magnetic circular dichroism (MCD) of five peralkylated tetrasilanes (1–5) conformationally constrained to angles ranging from nearly 0° to 180° and of the open chain tetrasilane Si4Me10 (6) shows a clear conformational dependence and permits the detection of previously hidden transitions. In the tetrasilane CH2Si4Me8 (1), with the smallest dihedral angle, comparison of MCD with absorption spectra reveals four low-energy electronic transitions. In the tetrasilanes 2–4, three distinct transitions are apparent. In tetrasilanes 5 and 6, MCD reveals the very weak transition that has been predicted to be buried under the first intense peak and to which the anomalous thermochromism of 6 and other short-chain oligosilanes has been attributed. PMID:15249672

  16. Omnidirectional, circularly polarized, cylindrical microstrip antenna

    NASA Technical Reports Server (NTRS)

    Stanton, Philip H. (Inventor)

    1985-01-01

    A microstrip cylindrical antenna comprised of two concentric subelements on a ground cylinder, a vertically polarized (E-field parallel to the axis of the antenna cylinder) subelement on the inside and a horizontally polarized (E-field perpendicular to the axis) subelement on the outside. The vertical subelement is a wraparound microstrip radiator. A Y-shaped microstrip patch configuration is used for the horizontally polarized radiator that is wrapped 1.5 times to provide radiating edges on opposite sides of the cylindrical antenna for improved azimuthal pattern uniformity. When these subelements are so fed that their far fields are equal in amplitude and phased 90.degree. from each other, a circularly polarized EM wave results. By stacking a plurality of like antenna elements on the ground cylinder, a linear phased array antenna is provided that can be beam steered to the desired elevation angle.

  17. Rectenna composed of a circular microstrip antenna

    SciTech Connect

    Itoh, K.; Ohgane, T.; Ogawa, Y.

    1986-01-01

    One of the big problems in the SPS system is reradiation of the harmonic waves generated by the rectifying diode. The authors proposed the use of a circular microstrip antenna (CMSA), since the CMSA has no higher resonance-harmonic of integer multiple of the dominant resonance frequency. However, characteristics of a large rectenna array of CMSA's have not been clarified. This paper is concerned with the absorption efficiency of the rectenna composed of the CMSA. The efficiency is estimated explicitly using an infinite array model. The results show that the absorption efficiency of the infinite rectenna array composed of the CMSA is 100%. Also, this paper considers the effect of the losses of the composed of the CMSA is 100%. Also, this paper considers the effect of the losses of the CMSA. 4 references, 4 figures.

  18. Higher order diffractions from a circular disk

    NASA Technical Reports Server (NTRS)

    Marsland, Diane P.; Balanis, Constantine A.; Brumley, Stephen A.

    1987-01-01

    The backscattering from a circular disk is analyzed using the geometrical theory of diffraction. First-, second-, and third-order diffractions are included in the hard polarization analysis, while first-, second-, and third-order slope diffractions are included for soft polarization. Improvements in the prediction of the monostatic radar cross section over previous works are noted. For hard polarization, an excellent agreement is exhibited between experimental and theoretical results, while a very good agreement is noted for soft polarization. To further improve the soft polarization results for wide angles, a model for the creeping wave or circulating current on the edge of the disk is obtained and used to find an additional component of the backscattered field. The addition of this component significantly improves the results for wide angles, leading to excellent agreement for soft polarization also. An axial-caustic correction method using equivalent currents is also included in the analysis.

  19. Circular dichroism spectroscopy of membrane proteins.

    PubMed

    Miles, A J; Wallace, B A

    2016-09-21

    Circular dichroism (CD) spectroscopy is a well-established technique for studying the secondary structures, dynamics, folding pathways, and interactions of soluble proteins, and is complementary to the high resolution but generally static structures produced by X-ray crystallography, NMR spectroscopy, and cryo electron microscopy. CD spectroscopy has special relevance for the study of membrane proteins, which are difficult to crystallise and largely ignored in structural genomics projects. However, the requirement for membrane proteins to be embedded in amphipathic environments such as membranes, lipid vesicles, detergent micelles, bicelles, oriented bilayers, or nanodiscs, in order for them to be soluble or dispersed in solution whilst maintaining their structure and function, necessitates the use of different experimental and analytical approaches than those employed for soluble proteins. This review discusses specialised methods for collecting and analysing membrane protein CD data, highlighting where protocols for soluble and membrane proteins diverge. PMID:27347568

  20. Magnetic resonance of slotted circular cylinder resonators

    NASA Astrophysics Data System (ADS)

    Du, Junjie; Liu, Shiyang; Lin, Zhifang; Chui, S. T.

    2008-07-01

    By a rigorous full-wave approach, a systemic study is made on the magnetic resonance of slotted circular cylinder resonators (SCCRs) made of a perfect conductor for the lossless case. This is a two-dimensional analog of the split-ring resonator and may serve as an alternative type of essential constituent of electromagnetic metamaterials. It is found that the resonance frequency can be modulated by changing the geometrical parameters and the dielectrics filling in the cavity and the slot. An approximate empirical expression is presented for magnetic resonance frequency of SCCRs from the viewpoint of an L-C circuit system. Finally, it is demonstrated that the SCCR structure can be miniaturized to less than 1/150 resonant wavelength in size with the dielectrics available currently.

  1. Cycloviruses, gemycircularviruses and other novel replication-associated protein encoding circular viruses in Pacific flying fox (Pteropus tonganus) faeces.

    PubMed

    Male, Maketalena F; Kraberger, Simona; Stainton, Daisy; Kami, Viliami; Varsani, Arvind

    2016-04-01

    Viral metagenomic studies have demonstrated that animal faeces can be a good sampling source for exploring viral diversity associated with the host and its environment. As part of an continuing effort to identify novel circular replication-associated protein encoding single-stranded (CRESS) DNA viruses circulating in the Tongan archipelago, coupled with the fact that bats are a reservoir species of a large number of viruses, we used a metagenomic approach to investigate the CRESS DNA virus diversity in Pacific flying fox (Pteropus tonganus) faeces. Faecal matter from four roosting sites located in Ha'avakatolo, Kolovai, Ha'ateiho and Lapaha on Tongatapu Island was collected in April 2014 and January 2015. From these samples we identified five novel cycloviruses representing three putative species, 25 gemycircularviruses representing at least 14 putative species, 17 other CRESS DNA viruses (15 putative species), two circular DNA molecules and a putative novel multi-component virus for which we have identified three cognate molecules. This study demonstrates that there exists a large diversity of CRESS DNA viruses in Pacific flying fox faeces. PMID:26873064

  2. Infection by choleraphage phi 138: bacteriophage DNA and replicative intermediates.

    PubMed Central

    Chowdhury, R; Das, J

    1986-01-01

    Choleraphage phi 138 contains a linear, double-stranded, circularly permuted DNA molecule of 30 X 10(6) daltons or 45 kilobase pairs. Upon infection, the host DNA is degraded, and synthesis of phage-specific DNA is detectable 20 min after infection. The phage utilizes primarily the host DNA degradation products for its own DNA synthesis. A physical map of phi 138 DNA was constructed with the restriction endonucleases Bg/II, HindIII, and PstI. A concatemeric replicative DNA intermediate equivalent to eight mature genome lengths was identified. The concatemer was shown to be the precursor for the synthesis of mature bacteriophage DNA which is subsequently packaged by a headful mechanism. Images PMID:3951021

  3. Anharmonic stacking in supercoiled DNA

    NASA Astrophysics Data System (ADS)

    Zoli, Marco

    2012-05-01

    Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking anharmonicity stabilizes the double helix against thermal disruption of the hydrogen bonds. Twisting is essential in the model to capture the importance of nonlinear effects on the thermodynamical properties. In a ladder model with zero twist, anharmonic stacking scarcely affects the thermodynamics. Moderately untwisted helices, with respect to the equilibrium conformation, show an energetic advantage against the overtwisted ones. Accordingly moderately untwisted helices better sustain local fluctuational openings and make more unlikely the thermally driven complete strand separation.

  4. The circular velocity function of group galaxies

    SciTech Connect

    Abramson, Louis E.; Williams, Rik J.; Benson, Andrew J.; Kollmeier, Juna A.; Mulchaey, John S.

    2014-09-20

    A robust prediction of ΛCDM cosmology is the halo circular velocity function (CVF), a dynamical cousin of the halo mass function. The correspondence between theoretical and observed CVFs is uncertain, however: cluster galaxies are reported to exhibit a power-law CVF consistent with N-body simulations, but that of the field is distinctly Schechter-like, flattened compared to ΛCDM expectations at circular velocities v {sub c} ≲ 200 km s{sup –1}. Groups offer a powerful probe of the role environment plays in this discrepancy as they bridge the field and clusters. Here, we construct the CVF for a large, mass- and multiplicity-complete sample of group galaxies from the Sloan Digital Sky Survey. Using independent photometric v {sub c} estimators, we find no transition from field to ΛCDM-shaped CVF above v {sub c} = 50 km s{sup –1} as a function of group halo mass. All groups with 12.4 ≲ log M {sub halo}/M {sub ☉} ≲ 15.1 (Local Group analogs to rich clusters) display similar Schechter-like CVFs marginally suppressed at low v {sub c} compared to that of the field. Conversely, some agreement with N-body results emerges for samples saturated with late-type galaxies, with isolated late-types displaying a CVF similar in shape to ΛCDM predictions. We conclude that the flattening of the low-v {sub c} slope in groups is due to their depressed late-type fractions—environment affecting the CVF only to the extent that it correlates with this quantity—and that previous cluster analyses may suffer from interloper contamination. These results serve as useful benchmarks for cosmological simulations of galaxy formation.

  5. PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata

    PubMed Central

    Whitmore, Lee; Woollett, Benjamin; Miles, Andrew John; Klose, D. P.; Janes, Robert W.; Wallace, B. A.

    2011-01-01

    The Protein Circular Dichroism Data Bank (PCDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data and their associated experimental metadata. All entries undergo validation and curation procedures to ensure completeness, consistency and quality of the data included. A web-based interface enables users to browse and query sample types, sample conditions, experimental parameters and provides spectra in both graphical display format and as downloadable text files. The entries are linked, when appropriate, to primary sequence (UniProt) and structural (PDB) databases, as well as to secondary databases such as the Enzyme Commission functional classification database and the CATH fold classification database, as well as to literature citations. The PCDDB is available at: http://pcddb.cryst.bbk.ac.uk. PMID:21071417

  6. Interaction effect of number of circular holes in a circular plate

    SciTech Connect

    Ukadgaonker, V.G.; Agnahotri, N.A.

    1996-12-01

    The problem of circular tubesheet with uniform tension at its circular boundary and nine holes in the circular pitch pattern at its center is solved using complex stress functions. The Schwarz Alternating Technique is used to find the interaction effect of the holes on each other and then the superposition method is used to obtain desired geometry of the nine holes. This superposition gives the stress free boundary at the central hole exactly satisfied. When these results are compared with those obtained by Ukadgaonker and Kale by Finite Element Method it is found that the theoretical solutions give higher stress concentration than FEM by about 20% for a large outer radius. When the outer radius is reduced the stress concentration factor increases considerably and the difference in the analytical and the FEM solution also increases to a large extent. The analytical solution found in the present paper is verified with the FEM and Photoelasticity solution obtained by Ukadgaonker and Kale (1996) earlier. This problem is further generalized for a rhombic pitch pattern, which can be reduced to particular cases such as square pitch pattern, triangular pitch pattern, diagonal pitch pattern by changing the angle of the rhombus. The stress concentration factor around the central hole varies very little for various ligament efficiencies which is given in percentage.

  7. Circularization pathway of a bacterial group II intron.

    PubMed

    Monat, Caroline; Cousineau, Benoit

    2016-02-29

    Group II introns are large RNA enzymes that can excise as lariats, circles or in a linear form through branching, circularization or hydrolysis, respectively. Branching is by far the main and most studied splicing pathway while circularization was mostly overlooked. We previously showed that removal of the branch point A residue from Ll.LtrB, the group II intron from Lactococcus lactis, exclusively leads to circularization. However, the majority of the released intron circles harbored an additional C residue of unknown origin at the splice junction. Here, we exploited the Ll.LtrB-ΔA mutant to study the circularization pathway of bacterial group II introns in vivo. We demonstrated that the non-encoded C residue, present at the intron circle splice junction, corresponds to the first nt of exon 2. Intron circularization intermediates, harboring the first 2 or 3 nts of exon 2, were found to accumulate showing that branch point removal leads to 3' splice site misrecognition. Traces of properly ligated exons were also detected functionally confirming that a small proportion of Ll.LtrB-ΔA circularizes accurately. Overall, our data provide the first detailed molecular analysis of the group II intron circularization pathway and suggests that circularization is a conserved splicing pathway in bacteria. PMID:26673697

  8. Scattering-Matrix Program For Circular Waveguide Components

    NASA Technical Reports Server (NTRS)

    Hoppe, Daniel J.

    1993-01-01

    Scattering Matrix Program for Circular Waveguide Junctions, CWGSCAT, computes scattering matrices of series of circular waveguide sections. Sections must have same axis, but radius and length of each section completely arbitrary. Step discontinuities, corrugated sections, and horns analyzed. Written in FORTRAN.

  9. Flow-induced vibration of circular cylindrical structures

    SciTech Connect

    Chen, S.S.

    1985-06-01

    This report summarizes the flow-induced vibration of circular cylinders in quiescent fluid, axial flow, and crossflow, and applications of the analytical methods and experimental data in design evaluation of various system components consisting of circular cylinders. 219 figs., 30 tabs. (JDB)

  10. 40 CFR 30.6 - Availability of OMB circulars.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Availability of OMB circulars. 30.6 Section 30.6 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY GRANTS AND OTHER FEDERAL ASSISTANCE..., HOSPITALS, AND OTHER NON-PROFIT ORGANIZATIONS General § 30.6 Availability of OMB circulars. OMB...

  11. 40 CFR 30.6 - Availability of OMB circulars.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 1 2011-07-01 2011-07-01 false Availability of OMB circulars. 30.6 Section 30.6 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY GRANTS AND OTHER FEDERAL ASSISTANCE..., HOSPITALS, AND OTHER NON-PROFIT ORGANIZATIONS General § 30.6 Availability of OMB circulars. OMB...

  12. 31 CFR 330.10 - Modifications of other circulars.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... supplementing: Department of the Treasury Circulars Nos. 530, 653, and 750 (31 CFR parts 315, 316, and 321..., and 2-98 (31 CFR parts 351, 352, 353, 342, 359, and 360 respectively), and any revisions thereof or... 31 Money and Finance: Treasury 2 2010-07-01 2010-07-01 false Modifications of other circulars....

  13. 31 CFR 330.10 - Modifications of other circulars.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... supplementing: Department of the Treasury Circulars Nos. 530, 653, and 750 (31 CFR parts 315, 316, and 321..., and 2-98 (31 CFR parts 351, 352, 353, 342, 359, and 360 respectively), and any revisions thereof or... 31 Money and Finance:Treasury 2 2011-07-01 2011-07-01 false Modifications of other circulars....

  14. 77 FR 7656 - Advisory Circular: Public Aircraft Operations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-13

    ... the Federal Register published on April 11, 2000 (65 FR 19477-19478), as well as at http://DocketsInfo... Aircraft Operations) (76 FR 16349). This advisory circular provides additional information on the.... SUMMARY: This notice announces the availability of a proposed revision to Advisory Circular...

  15. Characterisation of DNA forms associated with cassava latent virus infection.

    PubMed Central

    Stanley, J; Townsend, R

    1985-01-01

    In addition to the major encapsidated DNA species found in preparations of cassava latent virus (genomic DNAs 1 and 2) there are minor DNA populations of twice (dimeric) and approximately half genome length. Both minor species resemble the genomic DNAs in that they are composed of predominantly circular single-stranded DNA. All of these size groups have a corresponding covalently-closed circular double-stranded DNA form in infected tissue. Infectivity studies using cloned DNAs 1 and 2 show that dimeric DNA routinely appears, suggesting it to be an intermediate in the DNA replicative cycle that can be encapsidated at low efficiency. In contrast, half unit length DNA has not yet been detected after multiple passaging of virus derived from the cloned DNA inoculum. Half unit length DNAs appear to be derived exclusively from DNA 2 and consist of a population of molecules exhibiting a relatively specific deletion. As they have an inhibitory effect on virus multiplication, their encapsidated forms are analogous to defective interfering particles associated with other eukaryotic DNA containing viruses. Small primer molecules associated with the genomic single-stranded DNAs, as reported for another geminivirus, have not been detected in CLV. Images PMID:4000956

  16. Outlier detection in a new half-circular distribution

    NASA Astrophysics Data System (ADS)

    Rambli, Adzhar; Mohamed, Ibrahim Bin; Shimizu, Kunio; Khalidin, Nurliza

    2015-10-01

    In this paper, we use a discordancy test based on spacing theory to detect outlier in a half-circular data. Up to now, numerous discordancy tests have been proposed to detect outlier in circular distributions which are defined in [0,2π). However, some circular data lie within just half of this range. Therefore, first we introduce a new half-circular distribution developed using the inverse stereographic projection technique on a gamma distributed variable. Then, we develop a new discordancy test to detect single or multiple outliers in the half-circular data based on the spacing theory. We show the practical value of the test by applying it to an eye data set obtained from a glaucoma clinic at the University of Malaya Medical Centre, Malaysia.

  17. Performance degradation in fast frequency-scanned circular arrays

    NASA Astrophysics Data System (ADS)

    Arora, R. K.; Patel, M. R.

    1983-05-01

    The effects of high-speed scanning in frequency-scanned circular arrays are investigated. It is found that at high scanning rates the performance deteriorates with both a loss of main beam amplitude and an increase in side-lobe level. The performance of a circular array is similar to that of a linear array, although the deterioration observed in the case of a circular array is less than that observed in the case of a linear array having a length equal to the diameter of the circular array. However, in contrast with the case of a linear array, the circular array does not exhibit any significant changes in the 3 dB bandwidth, nor does it show a frequency spread associated with a fast scanning linear array. Examples from both radar and sonar are examined.

  18. Detection of circular polarization in light scattered from photosynthetic microbes

    PubMed Central

    Sparks, William B.; Hough, James; Germer, Thomas A.; Chen, Feng; DasSarma, Shiladitya; DasSarma, Priya; Robb, Frank T.; Manset, Nadine; Kolokolova, Ludmilla; Reid, Neill; Macchetto, F. Duccio; Martin, William

    2009-01-01

    The identification of a universal biosignature that could be sensed remotely is critical to the prospects for success in the search for life elsewhere in the universe. A candidate universal biosignature is homochirality, which is likely to be a generic property of all biochemical life. Because of the optical activity of chiral molecules, it has been hypothesized that this unique characteristic may provide a suitable remote sensing probe using circular polarization spectroscopy. Here, we report the detection of circular polarization in light scattered by photosynthetic microbes. We show that the circular polarization appears to arise from circular dichroism of the strong electronic transitions of photosynthetic absorption bands. We conclude that circular polarization spectroscopy could provide a powerful remote sensing technique for generic life searches. PMID:19416893

  19. Circular polarization of sunlight reflected by planetary atmospheres

    NASA Technical Reports Server (NTRS)

    Kawata, Y.

    1978-01-01

    Multiple scattering calculations are performed in order to investigate the nature of the circular polarization of sunlight reflected by planetary atmospheres. Contour diagrams as a function of size parameter and phase angle are made for the integrated light from a spherical but locally plane-parallel atmosphere of spherical particles. To investigate the origin of the circular polarization, results are also computed for second-order scattering and for a simpler semiquantitative model of scattering by two particles. Observations of the circular polarization of the planets are presently too meager for accurate deduction of cloud particle properties. However, certain very broad constraints can be placed on the properties of the dominant cloud particles on Jupiter and Saturn. The cloud particle size and refractive index deduced for the Jupiter clouds by Loskutov, Morozhenko, and Yanovitskii from analyses of the linear polarization are not consistent with the circular polarization. The few available circular polarization observations of Venus are also examined.

  20. Choke position effects in double-choked circular waveguide antennas

    NASA Astrophysics Data System (ADS)

    Miyata, K.; Suzuki, M.

    1984-06-01

    A number of studies have been conducted regarding choke-loaded circular waveguide antennas. Aoki et al. (1970) have obtained improved results with respect to the beam circularity and the wide-angle radiation properties. Cowan (1973) suggested the employment of suitable compact, double choked feeds for frequency-reuse application. Further improvements can apparently be obtained by loading double chokes on a circular waveguide. The present investigation is concerned with the variation of the radiated fields for various choke positions in double-choked circular waveguide antennas. In the case of double-choked small circular waveguide antennas, it is found that the choke position has a pronounced effect on the radiation properties. Particularly sensitive to the choke position is the cross-polar level.

  1. Replication of single-stranded DNA templates by primase-polymerase complexes of the yeast, Saccharomyces cerevisiae.

    PubMed Central

    Biswas, E E; Biswas, S B

    1988-01-01

    A partially purified primase-polymerase complex from the yeast, Saccharomyces cerevisiae, was capable of replicating a single stranded circular phage DNA into a replicative form with high efficiency. The primase-polymerase complex exhibited primase activity and polymerase activity on singly primed circular ssDNA as well as on gapped DNA. In addition, it was able to replicate an unprimed, single-stranded, circular phage DNA through a coupled primase-polymerase action. On Biogel A-O.5m filtration the primase-polymerase activities appeared in the void volume, demonstrating a mass of greater than 500 kilodaltons. Primase and various primase-polymerase complexes synthesized unique primers on single stranded DNA templates and the size distribution of primers was dependent on the structure of the DNA and the nature of the primase-polymerase assembly. Images PMID:3041377

  2. Pax-3-DNA interaction: flexibility in the DNA binding and induction of DNA conformational changes by paired domains.

    PubMed Central

    Chalepakis, G; Wijnholds, J; Gruss, P

    1994-01-01

    The mouse Pax-3 gene encodes a protein that is a member of the Pax family of DNA binding proteins. Pax-3 contains two DNA binding domains: a paired domain (PD) and a paired type homeodomain (HD). Both domains are separated by 53 amino acids and interact synergistically with a sequence harboring an ATTA motif (binding to the HD) and a GTTCC site (binding to the PD) separated by 5 base pairs. Here we show that the interaction of Pax-3 with these two binding sites is independent of their angular orientation. In addition, the protein spacer region between the HD and the PD can be shortened without changing the spatial flexibility of the two DNA binding domains which interact with DNA. Furthermore, by using circular permutation analysis we determined that binding of Pax-3 to a DNA fragment containing a specific binding site causes conformational changes in the DNA, as indicated by the different mobilities of the Pax-3-DNA complexes. The ability to change the conformation of the DNA was found to be an intrinsic property of the Pax-3 PD and of all Pax proteins that we tested so far. These in vitro studies suggest that interaction of Pax proteins with their specific sequences in vivo may result in an altered DNA conformation. Images PMID:8065927

  3. DNA Immunization

    PubMed Central

    Wang, Shixia; Lu, Shan

    2013-01-01

    DNA immunization was discovered in early 1990s and its use has been expanded from vaccine studies to a broader range of biomedical research, such as the generation of high quality polyclonal and monoclonal antibodies as research reagents. In this unit, three common DNA immunization methods are described: needle injection, electroporation and gene gun. In addition, several common considerations related to DNA immunization are discussed. PMID:24510291

  4. No evidence for behavioral responses to circularly polarized light in four scarab beetle species with circularly polarizing exocuticle.

    PubMed

    Blahó, Miklós; Egri, Adám; Hegedüs, Ramón; Jósvai, Júlia; Tóth, Miklós; Kertész, Krisztián; Biró, László Péter; Kriska, György; Horváth, Gábor

    2012-02-28

    The strongest known circular polarization of biotic origin is the left-circularly polarized (LCP) light reflected from the metallic shiny exocuticle of certain beetles of the family Scarabaeidae. This phenomenon has been discovered by Michelson in 1911. Although since 1955 it has been known that the human eye perceives a visual illusion when stimulated by circularly polarized (CP) light, it was discovered only recently that a stomatopod shrimp is able to perceive circular polarization. It is pertinent to suppose that scarab beetles reflecting LCP light in an optical environment (vegetation) being deficient in CP signals may also perceive circular polarization and use it to find each other (mate/conspecifics) as until now it has been believed. We tested this hypothesis in six choice experiments with several hundred individuals of four scarab species: Anomala dubia, Anomala vitis (Coleoptera, Scarabaeidae, Rutelinae), and Cetonia aurata, Potosia cuprea (Coleoptera, Scarabaeidae, Cetoniinae), all possessing left-circularly polarizing exocuticle. From the results of our experiments we conclude that the studied four scarab species are not attracted to CP light when feeding or looking for mate or conspecifics. We demonstrated that the light reflected by host plants of the investigated scarabs is circularly unpolarized. Our results finally solve a puzzle raised over one hundred years ago, when Michaelson discovered that scarab beetles reflect circularly polarized light. PMID:22155007

  5. Three-dimensional computation for flow-induced vibrations of an upstream circular cylinder in two tandem circular cylinders

    NASA Astrophysics Data System (ADS)

    Kondo, Norio

    2014-07-01

    It is well known from a lot of experimental data that fluid forces acting on two tandem circular cylinders are quite different from those acting on a single circular cylinder. Therefore, we first present numerical results for fluid forces acting on two tandem circular cylinders, which are mounted at various spacings in a smooth flow, and second we present numerical results for flow-induced vibrations of the upstream circular cylinder in the tandem arrangement. The two circular cylinders are arranged at close spacing in a flow field. The upstream circular cylinder is elastically placed by damper-spring systems and moves in both the in-line and cross-flow directions. In such models, each circular cylinder is assumed as a rigid body. On the other hand, we do not introduce a turbulent model such as the Large Eddy Simulation (LES) or Reynolds Averaged Navier-Stokes (RANS) models into the numerical scheme to compute the fluid flow. Our numerical procedure to capture the flow-induced vibration phenomena of the upstream circular cylinder is treated as a fluid-structure interaction problem in which the ideas of weak coupling is taken into consideration.

  6. Metallization of DNA and DNA Origami Using a Palladium Seeding Method

    NASA Astrophysics Data System (ADS)

    Geng, Yanli

    In this dissertation, I developed a Pd seeding method in association with electroless plating, to successfully metallize both lambda DNA and DNA origami templates on different surfaces. On mica surfaces, this method offered a fast, simple process, and the ability to obtain a relatively high yield of metallized DNA nanostructures. When using lambda DNA as the templates, I studied the effect of Pd(II) activation time on the seed height and density, and an optimal activation time between 10 and 30 min was obtained. Based on the Pd seeds formed on DNA, as well as a Pd electroless plating solution, continuous Pd nanowires that had an average diameter of ˜28 nm were formed with good selectivity on lambda DNA. The selected Pd activation time was also applied to metallize "T"-shape DNA origami, and Au coated branched nanostructures with a length between 200-250 nm, and wire diameters of ˜40 nm were also fabricated. In addition, I found that the addition of Mg2+ ion into the reducing agent and electroless plating solution could benefit the surface retention of Pd seeded DNA and Au plated DNA structures. This work indicated that DNA molecules were promising templates to fabricate metal nanostructures; moreover, the formation of Au metallized branched nanostructures showed progress towards nanodevice fabrication using DNA origami. Silicon surfaces were also used as the substrates for DNA metallization. More complex circular circuit DNA origami templates were used. To obtain high enough seed density, multiple Pd seeding steps were applied which showed good selectivity and the seeded DNA origami remained on the surface after seeding steps. I used distribution analysis of seed height to study the effect of seeding steps on both average height and the uniformity of the Pd seeds. Four-repeated palladium seedings were confirmed to be optimal by the AFM images, seed height distribution analysis, and Au electroless plating results. Both Au and Cu metallized circular circuit design

  7. Herpesvirus saimiri DNA in a lymphoid cell line established by in vitro transformation.

    PubMed Central

    Schirm, S; Müller, I; Desrosiers, R C; Fleckenstein, B

    1984-01-01

    A lymphoid T-cell line (H1591) was established by infecting peripheral blood mononuclear cells from a cotton top marmoset with Herpesvirus saimiri OMI. Analysis of these in vitro-immortalized cells revealed nonintegrated, covalently closed circular viral DNA molecules in high multiplicities with substantial rearrangements and large deletions in their L-DNA (unique) regions. One subline, designated H1591 Er, contained circular viral DNA with one stretch of H-DNA (repetitive) and one of L-DNA; the L-DNA segment consisted of a linear fusion of a 53.2-kilobase-pair piece of L-DNA (left half of L-DNA) with a 15.2-kilobase-pair L-DNA fragment from the right end of the L-DNA region. The other subline, H1591 S, contained two short regions of L-DNA, each derived from the extreme ends of virion L-DNA. Both L-DNA regions of H1591 S cells contained inverted repetitions (15.0 +/- 0.2 and 9.1 +/- 4.7 kilobase pairs). The extensive deletions of L-DNA sequences in cell line H1591 indicate that at least 73% of the genetic information in H. saimiri is not required to maintain the persistence of viral DNA and the state of transformation in lymphoid T-cells. Images PMID:6321774

  8. The histone H3K9 methylation and RNAi pathways regulate normalnucleolar and repeated DNA organization by inhibiting formation ofextrachromosomal DNAs

    SciTech Connect

    Peng, Jamy C.; Karpen, Gary H.

    2006-06-15

    In order to identify regulators of nuclear organization, Drosophila mutants in the Su(var)3-9 histone H3K9 methyltransferase, RNAi pathway components, and other regulators of heterochromatin-mediated gene silencing were examined for altered nucleoli and positioning of repeated DNAs. Animals lacking components of the H3K9 methylation and RNAi pathways contained disorganized nucleoli, ribosomal DNA (rDNA) and satellite DNAs. The levels of H3K9 dimethylation (H3K9me2) in chromatin associated with repeated DNAs decreased dramatically in Su(var)3-9 and dcr-2 (dicer-2) mutant tissues compared to wild type. We also observed a substantial increase in extrachromosomal repeated DNAs in mutant tissues. The disorganized nucleolus phenotype depends on the presence of Ligase 4 (Lig4), and ecc DNA formation is not induced by removal of cohesin. We conclude that H3K9 methylation of rDNA and satellites, maintained by Su(var)3-9, HP1, and the RNAi pathway, is necessary for the structural stability of repeated DNAs, which is mediated through suppression of non-homologous end joining (NHEJ). These results suggest a mechanism for how local chromatin structure can regulate genome stability, and the organization of chromosomal elements and nuclear organelles.

  9. DNA condensates organized by the capsid protein VP15 in White Spot Syndrome Virus

    SciTech Connect

    Liu Yingjie; Wu Jinlu; Chen Hu; Hew, Choy Leong; Yan Jie

    2010-12-20

    The White Spot Syndrome Virus (WSSV) has a large circular double-stranded DNA genome of around 300 kb and it replicates in the nucleus of the host cells. The machinery of how the viral DNA is packaged has been remained unclear. VP15, a highly basic protein, is one of the major capsid proteins found in the virus. Previously, it was shown to be a DNA binding protein and was hypothesized to participate in the viral DNA packaging process. Using Atomic Force Microscopy imaging, we show that the viral DNA is associated with a (or more) capsid proteins. The organized viral DNA qualitatively resembles the conformations of VP15 induced DNA condensates in vitro. Furthermore, single-DNA manipulation experiments revealed that VP15 is able to condense single DNA against forces of a few pico Newtons. Our results suggest that VP15 may aid in the viral DNA packaging process by directly condensing DNA.

  10. Circular Conditional Autoregressive Modeling of Vector Fields.

    PubMed

    Modlin, Danny; Fuentes, Montse; Reich, Brian

    2012-02-01

    As hurricanes approach landfall, there are several hazards for which coastal populations must be prepared. Damaging winds, torrential rains, and tornadoes play havoc with both the coast and inland areas; but, the biggest seaside menace to life and property is the storm surge. Wind fields are used as the primary forcing for the numerical forecasts of the coastal ocean response to hurricane force winds, such as the height of the storm surge and the degree of coastal flooding. Unfortunately, developments in deterministic modeling of these forcings have been hindered by computational expenses. In this paper, we present a multivariate spatial model for vector fields, that we apply to hurricane winds. We parameterize the wind vector at each site in polar coordinates and specify a circular conditional autoregressive (CCAR) model for the vector direction, and a spatial CAR model for speed. We apply our framework for vector fields to hurricane surface wind fields for Hurricane Floyd of 1999 and compare our CCAR model to prior methods that decompose wind speed and direction into its N-S and W-E cardinal components. PMID:24353452

  11. Wave interaction with dual circular porous plates

    NASA Astrophysics Data System (ADS)

    Mondal, Arpita; Gayen, R.

    2015-12-01

    In this paper we investigated the reflection and the transmission of a system of two symmetric circular-arc-shaped thin porous plates submerged in deep water within the context of linear theory. The hypersingular integral equation technique has been used to analyze the problem mathematically. The integral equations are formulated by applying Green's integral theorem to the fundamental potential function and the scattered potential function into a suitable fluid region, and then using the boundary condition on the porous plate surface. These are solved approximately using an expansion-cum-collocation method using the behaviour of the potential functions at the tips of the plates. This method ultimately produces a very good numerical approximation for the reflection and the transmission coefficients and hydrodynamic force components. The numerical results are depicted graphically against the wave number for a variety of layouts of the arc. Some results are compared with known results for similar configurations of dual rigid plate systems available in the literature with good agreement.

  12. THE ORBIT OF CHARON IS CIRCULAR

    SciTech Connect

    Buie, Marc W.; Tholen, David J.; Grundy, William M. E-mail: tholen@ifa.hawaii.edu

    2012-07-15

    We present a detailed analysis of the orbit of Charon where we show its orbit to be circular. This analysis explores the effects of surface albedo variations on the astrometry and the resulting errors in the orbital elements. We present two new epochs of data from the Hubble Space Telescope taken in 2008 and 2010 and combine that with a re-analysis of previously published data from 1992 and 2002. Our adopted two-body Keplerian orbital elements for Charon are P = 6.3872273 {+-} 0.0000003 days, a = 19573 {+-} 2 km, e = 0., i = 96.218 {+-} 0.008 deg, L = 4.50177 {+-} 0.00018 rad, and {Omega} = 3.89249 {+-} 0.00012 rad for an epoch of JDT = 2452600.5 in the J2000 reference frame. The 1{sigma} upper limit to the eccentricity is 7.5 Multiplication-Sign 10{sup -5}. The predicted uncertainty in the position of Charon relative to Pluto at the time of the New Horizons encounter based on this orbit is 8 km.

  13. Cellular pattern formation in circular domains.

    PubMed

    Palacios, Antonio; Gunaratne, Gemunu H.; Gorman, Michael; Robbins, Kay A.

    1997-09-01

    An analysis of stationary and nonstationary cellular patterns observed in premixed flames on a circular, porous plug burner is presented. A phenomenological model is introduced, that exhibits patterns similar to the experimental states. The primary modes of the model are combinations of Fourier-Bessel functions, whose radial parts have neighboring zeros. This observation explains several features of patterns, such as the existence of concentric rings of cells and the weak coupling between rings. Properties of rotating rings of cells, including the existence of modulated rotations and heteroclinic cycles can be deduced using mode coupling. For nonstationary patterns, the modal decomposition of experimental data can be carried out using the Karhunen-Loeve (KL) analysis. Experimental states are used to demonstrate the possibility of using KL analysis to differentiate between uniform and nonuniform rotations. The methodology can be extended to study more complicated nonstationary patterns. In particular, it is shown how the complexity of "hopping states" can be unraveled through the analysis. (c) 1997 American Institute of Physics. PMID:12779674

  14. Superfluid Turbulence in a Nonuniform Circular Channel

    NASA Astrophysics Data System (ADS)

    Murphy, Paul Joseph

    The excess dissipation due to the presence of quantized vorticity in flowing helium has been studied extensively. The success of the microscopic theory proposed by Schwarz in describing many properties of this dissipation led to a belief that the major aspects of the problem had been understood at the microscopic level. The experiment of Kafkalidis and Tough demonstrated that a weak one dimensional nonuniformity in the flow field led to a dramatic departure between the observed behavior and the predictions of the Schwarz theory using the local uniformity approximation (LUA). The research presented in this thesis was undertaken to measure the dissipative states for thermal counterflow with a weak two dimensional nonuniformity. The experiment of Kafkalidis and Tough used a flow channel with a high aspect ratio. Such channels are known to exhibit only one state of superfluid turbulence. In this research the channel is circular in cross section and shows two distinct turbulent states (T-I and T-II). This experiment demonstrates that there is no difference in the excess dissipation for flows that are either converging or diverging. The T-I state is described by the same parameters as the T-I state in uniform channels. The turbulence exhibits front behavior at the transition between states. These conclusions are consistent with the LUA. The T-II state is at variance with the LUA, but is consistant with the results found in the Kafkalidis and Tough experiment.

  15. Magnetoresistance of single Permalloy circular rings

    NASA Astrophysics Data System (ADS)

    Vavassori, P.; Busato, A.; Chiapatti, A.; di Bona, A.; Valeri, S.; Metlushko, V.; Ilic, B.

    2007-09-01

    We have measured magnetoresistance in single, 1 μm external diameter, Permalloy (Ni 80Fe 20) circular rings with varied inner hole diameter of 150, 300, and 600 nm and film thickness of 25 nm. The Permalloy ring structures and the 10-nm-thick, 250-nm-wide Au nanocontacts were fabricated on a SiO 2/Si substrate using e-beam lithography. Using a four contact geometry we studied the dependence of the magnetoresistance on the direction of the applied field. The experimental data are explained by considering only the conventional anisotropic magnetoresistance effect. Numerical simulations of the current distribution within the samples combined with micromagnetic simulations of the field dependent magnetization profile, yield good agreement with the experimental data. Upon increasing the inner hole diameter (viz. decreasing the ring width) the magnetoresistance measurements show a transition of the reversal process from the "vortex nucleation-displacement-annihilation" sequence to the "onion state-reversed onion state" sequence, typical of narrow nanorings.

  16. Drops with non-circular footprints

    NASA Astrophysics Data System (ADS)

    Ravazzoli, Pablo D.; González, Alejandro G.; Diez, Javier A.

    2016-04-01

    In this paper we study the morphology of drops formed on partially wetting substrates, whose footprint is not circular. These drops are consequence of the breakup processes occurring in thin films when anisotropic contact line motions take place. The anisotropy is basically due to the hysteresis of the contact angle since there is a wetting process in some parts of the contact line, while a dewetting occurs in other parts. Here, we obtain a characteristic drop shape from the rupture of a long liquid filament sitting on a solid substrate. We analyze its shape and contact angles by means of goniometric and refractive techniques. We also find a non-trivial steady state solution for the drop shape within the long wave approximation (lubrication theory), and we compare most of its features with experimental data. This solution is presented both in Cartesian and polar coordinates, whose constants must be determined by a certain group of measured parameters. Besides, we obtain the dynamics of the drop generation from numerical simulations of the full Navier-Stokes equation, where we emulate the hysteretic effects with an appropriate spatial distribution of the static contact angle over the substrate.

  17. Doppler global velocimetry data in circular jets

    NASA Astrophysics Data System (ADS)

    Kuhlman, John; Burton, Lucinda; Scarberry, Tom

    2002-07-01

    A two-component Doppler global velocimeter (DGV) system has been improved through the use of vapour-limited iodine cells that have temperature-independent responses, along with nonpolarizing beam splitters and lower f-number lenses. Two-component DGV velocity measurements have been obtained for a 1 inch diameter uniform circular jet flow at a nominal exit velocity of 60 m s-1, as well as for an annular jet and a swirling jet. These data generally agree with earlier point Doppler velocimeter and hot wire anemometer results to within about 2-4 m s-1, and display a total variability from a smooth curve of ±2-3 m s-1. This level of accuracy has been obtained for a system that uses a cw argon ion laser and eight-bit CCD cameras and digitizers. Exceptions to this level of accuracy are noted in regions of significant secondary scattering, due to scattered laser light that is reflected off the lip of the jet nozzle, as well as in regions of low smoke seeding levels, resulting in low signal-to-noise ratios. A significant amount of the variability of the data from a smooth curve is due to the flat field correction.

  18. Radially uniform circular sweep of ion beam

    SciTech Connect

    Akhmetov, T.D.; Davydenko, V.I.; Ivanov, A.A.; Kobets, V.V.; Medvedko, A.S.; Skorobogatov, D.N.; Tiunov, M.A.

    2006-03-15

    A spiral sweep of the ion beam was suggested to provide sufficiently uniform irradiation of a circular target. It is shown that if the beam radius is small enough, the radius of the beam center should increase as a square root of time to provide uniform radial irradiation of the target. In the complex for Boron Neutron Capture Therapy developed at the Budker Institute of Nuclear Physics, the proton beam sweep will be performed by a sweeper with uniform magnetic field with strength up to 500 G and axial length {approx}20 cm, rotating at 100-2000 Hz, and scanning over the radius at a 1-10 Hz frequency. The sweeper field is produced by four longitudinal flat current windings placed near the inner walls of a box-shaped yoke with the inner opening of a square cross section. A similar sweeping technique can be used in a 200 keV oxygen implanter, which is also under development at the Budker Institute.

  19. Circularly Polarized Light and Growth of Plants

    NASA Astrophysics Data System (ADS)

    Shibayev, Pavel; Pergolizzi, Robert

    2011-03-01

    The influence of linearly polarized light on the direction of plants growth has been recently demonstrated. The state of circularly polarized (CP) light can also change when it is reflected from the surface of leaves and stems. However, the role of light handedness in the development of plants and CP light interaction with the complexes of chlorophyll molecules have still not been studied enough. In this work, the role of left CP light in the accelerated growth of lentil and pea plants is revealed and studied. The mechanism of such an enhancement is discussed in terms of the model considering transmission, absorption, and scattering of CP light on micro and macro levels of leaf organization. Theoretical modeling of light interaction with the interior of the leaf was conducted for a number of recently proposed models of organization of chlorophyll molecules and chloroplasts. All the calculations were performed by employing a 4x4 matrix method in solving Maxwell equations. It is shown that left-handed chiral organization of chlorophyll molecules can greatly enhance the absorption of light and therefore lead to the enhanced growth of the whole plant under CP light.

  20. Circular dichroism of bradykinin and related peptides

    PubMed Central

    Brady, A. H.; Ryan, J. W.; Stewart, J. M.

    1971-01-01

    1. The circular dichroism of bradykinin and a number of its analogues and homologues was measured over the spectral range 200–300nm. All of the biologically active peptides showed maxima at 220nm and minima at 235nm. The spectra were independent of solvent and temperature. The vibronic transitions of phenylalanyl residues in the 250–280nm range showed no evidence of intra- or inter-molecular interactions. We take this as evidence that bradykinin and its biologically active analogues and homologues exist in solution as disordered chains. 2. None of the analogues with spectra unlike bradykinin possessed biological activity. However, peptides such as retro-bradykinin, des-6-serine-bradykinin, des-1-arginine-bradykinin and des-9-arginine-bradykinin produced spectra like that of bradykinin but were devoid of biological activity. Although we could not identify spectral features that were clearly correlated with biological activity, it appears unlikely that highly ordered peptides of the same amino acid composition as bradykinin would possess bradykinin-like effects. PMID:5117026

  1. A Novel Circular TE01-Mode Bend

    SciTech Connect

    Tantawi, S

    2004-04-19

    Future Linear Colliders and Accelerators require rf systems and components that are capable of handling hundreds of megawatts power levels at x-band frequencies and higher. Standard rf components that have been in use for a long time such as waveguide bends, directional couplers and hybrids, can not be used because of peak field considerations. Indeed, one has to reinvent most of these components taking into account the constraints imposed by ultra-high-power operation. Here, we present a new design for circular waveguides bends propagating the low-loss TE{sub 01} mode. The bend has smooth walls and low field levels. We present a simple synthesis process for designing such device. The general philosophy of this technique can be applied to other components as well. We describe the detailed design of the bend and compare our design with finite element simulations and experimental data. The bend has very low ohmic losses, and the TE{sub 01} mode is transmitted with virtually perfect mode purity.

  2. LED downlights with non-circular spots

    NASA Astrophysics Data System (ADS)

    Parkyn, William A.; Pelka, David G.

    2005-09-01

    The ubiquitous downlight inhabits our ceilings by the millions. Hot, inefficient, and electrically wasteful, it is next in line for replacement by the latest high-brightness, high-efficacy white LEDs. The conventional downlight configuration of a large incandescent spotlight in a low-cost, ceiling-recessed metal can, represents the culmination of old technology, fated never to improve significantly. Incandescent downlights add greatly both to direct and indirect electrical consumption, with the lamps requiring relatively frequent replacement. The small size of LED emitters means small optical elements can produce much higher-quality beams than incandescent spotlight-lamps can produce. Herein we introduce compact high-luminosity LED downlights with lenses that deliver uniform illumination to delimited targets such as tables. One version utilizes circular lenses and micro-diffuser films to deliver square outputs. The other uses lenses cut to the target shape. In particular, one of these lenses is the first to offer a semicircular spot suitable for gambling tables.

  3. A novel broadband circularly polarised monopole antenna

    NASA Astrophysics Data System (ADS)

    Kang, Ding; Cheng, Gao; Tongbin, Yu; Dexin, Qu

    2015-11-01

    A novel broadband circularly polarised (CP) monopole antenna is designed and implemented in this article. The antenna consists of a radiating patch that is composed of an annular-ring linked by a square ring over the corner and a modified ground plane. The broadband property is achieved based on a novel monopole structure that is connected by two perturbed loops, so the CP wave is generated due to the perturbation. Besides, by cutting a rectangular slit and embedding a vertical stub on the ground plane, the impedance and axial-ratio (AR) bandwidths can be greatly enhanced. The measured results reveal that the proposed monopole antenna has an impedance bandwidth of 4.575 GHz from 2.3 to 6.85 GHz, reaching the particularly broad bandwidth of 99.5%. Furthermore, a wide 3-dB AR bandwidth of 34.6% (1.53 GHz, 3.65-5.18 GHz) centred at 4.42 GHz is achieved. The radiation characteristics of the designed antenna are also presented.

  4. Diabatic flow boiling in circular transparent microchannels

    NASA Astrophysics Data System (ADS)

    Silvério, V.; Moreira, A. L. N.

    2012-11-01

    The horizontally assembled circular microchannel (Dh= 543μm, LHT = 60mm) made of transparent borosilicate glass is kept under constant wall heat flux conditions by means of a transparent metallic thin film deposit at the channel external wall as in Silvério and Moreira [1]. Heat transfer and pressure drop measurements are achieved by measuring the temperature and pressure at the channel inlet and outlet. Temperature is also measured along the channel outer wall. Experiments are carried with two different fluids, ethanol and methanol. Inlet liquid subcooling is of 297K, mass fluxes, G, up to 689kg.m-2.s-1 and imposed heat fluxes, q"s, up to 12.5W.cm-2 at ΔTsub from 0.8 to 50K. Synchronized high-speed visualization and microscope optics are used to determine dominant two-phase flow patterns and characterize hydrodynamic instabilities. Vapor qualities, χ, of -0.1 (indicating a subcooled liquid state) to 0.5 are under investigation. Semi-periodic variation of the flow patterns is noticeable for different flow conditions.

  5. Dynamic polarizability tensor for circular cylinders

    NASA Astrophysics Data System (ADS)

    Strickland, Diana; Ayón, Arturo; Alù, Andrea

    2015-02-01

    Based on Mie scattering theory, we derive the complete dynamic polarizability tensor for circular, azimuthally symmetric cylinders excited by an arbitrary field distribution, and provide compact expressions for all of its elements. Our results comprise fully dynamic cylinder polarizabilities, improving existing approximate models that use averaged electric or magnetic current lines to describe the scattering response of moderately thin cylinders. We show that the derived polarizability tensor satisfies reciprocity and passivity relations, and analyze its response under different conditions, varying the excitation angle, material properties, and cylinder radius. Interestingly, magnetoelectric effects are shown to arise at oblique incidence, even in the case of centrosymmetric achiral thin cylinders, associated with a weak form of spatial dispersion. This finding is particularly relevant for the proper modeling of individual cylinders and arrays of them, as in the case of metamaterials. We expect this work to find applications in antenna and metamaterial design, and to improve the physical understanding of the wave interaction and spatial dispersion in artificial materials composed of elongated inclusions such as wire media.

  6. Circular Signs of the Rock Abrasion Tool

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This image was taken by Mars Exploration Rover Opportunity's front hazard-avoidance camera, providing a circular sign of the success of the rover's first grinding of a rock. The round, shallow hole seen in this image is on a rock dubbed 'McKittrick,' located in the 'El Capitan' area of the larger outcrop near Opportunity's landing site.

    Opportunity used its rock abrasion tool to grind off a patch of rock 45.5 millimeters (1.8 inches) in diameter during the 30th martian day, or sol, of its mission (Feb. 23, 2004). The grinding exposed fresh rock for close inspection by the rover's microscopic imager and two spectrometers located on its robotic arm. The Honeybee Robotics team, which designed and operates the rock abrasion tool, determined the depth of the cut at 'McKittrick' to be 4.4 millimeters (0.17 inches) deep.

    On sol 34 (Feb. 27, 2004), the rover is scheduled to grind into its second target on the 'El Capitan' area, a rock dubbed 'Guadalupe' in the upper middle part of this image. The rock abrasion tools on both Mars Exploration Rovers were supplied by Honeybee Robotics, New York, N.Y.

  7. Circular Conditional Autoregressive Modeling of Vector Fields*

    PubMed Central

    Modlin, Danny; Fuentes, Montse; Reich, Brian

    2013-01-01

    As hurricanes approach landfall, there are several hazards for which coastal populations must be prepared. Damaging winds, torrential rains, and tornadoes play havoc with both the coast and inland areas; but, the biggest seaside menace to life and property is the storm surge. Wind fields are used as the primary forcing for the numerical forecasts of the coastal ocean response to hurricane force winds, such as the height of the storm surge and the degree of coastal flooding. Unfortunately, developments in deterministic modeling of these forcings have been hindered by computational expenses. In this paper, we present a multivariate spatial model for vector fields, that we apply to hurricane winds. We parameterize the wind vector at each site in polar coordinates and specify a circular conditional autoregressive (CCAR) model for the vector direction, and a spatial CAR model for speed. We apply our framework for vector fields to hurricane surface wind fields for Hurricane Floyd of 1999 and compare our CCAR model to prior methods that decompose wind speed and direction into its N-S and W-E cardinal components. PMID:24353452

  8. Large Circular Basin - 1300-km diameter

    NASA Technical Reports Server (NTRS)

    1974-01-01

    Close-up view of one-half of a 1300-km diameter circular basin the largest observed on Mercury. The other half is hidden beyond the terminator to the left. Hills and valleys extend in a radial fashion outward from the main ring. Interior of the large basin is completely flooded by plains materials; adjacent lowlands are also partially flooded and superimposed on the plains are bowl shaped craters. Wrinkle ridges are abundant on the plains materials. The area shown is 1008 miles (1600 km) from the top to the bottom of the picture. Sun's illumination is from the right. Blurred linear lines extending across the picture near bottom are missing data lines that have been filled in by the computer. Mariner 10 encountered Mercury on Friday, March 29th, 1974, passing the planet on the darkside 431 miles (690-km) from the surface.

    The Mariner 10 mission, managed by the Jet Propulsion Laboratory for NASA's Office of Space Science, explored Venus in February 1974 on the way to three encounters with Mercury-in March and September 1974 and in March 1975. The spacecraft took more than 7,000 photos of Mercury, Venus, the Earth and the Moon.

    NOTE: This image was scanned from physical media.

  9. Circular photogalvanic effect in silicon nanowires

    NASA Astrophysics Data System (ADS)

    Dhara, Sajal; Mele, E. J.; Agarwal, Ritesh

    Circular photogalvanic effect (CPGE), the generation of a photocurrent whose magnitude and polarity depends on chirality of optical excitation, is demonstrated in the visible optical range in silicon nanowires, a bulk non-gyrotropic material with weak spin-orbit coupling. CPGE, which is absent in bulk Si is found to arise from interband transitions only at the metal-semiconductor contacts to Si nanowires where inversion symmetry is broken by a Schottky electric field. Furthermore, by applying a bias voltage that modulates this field, the sign and magnitude of the CPGE can be controlled. From excitation energy dependent measurements and symmetry considerations, it is argued that the [10] surface states due to Si chains that are not aligned with the nanowire growth direction and the Schottky field produce an artificial gyrotropic optical medium that supports CPGE. This work reveals the role of the surface states in the generation of chirality-dependent photocurrents in silicon with a purely orbital-based mechanism, and also opens up new possibilities of engineering new functionalities in Si that can be integrated with conventional electronics.

  10. Sequence-Specific DNA Binding by a Short Peptide Dimer

    NASA Astrophysics Data System (ADS)

    Talanian, Robert V.; McKnight, C. James; Kim, Peter S.

    1990-08-01

    A recently described class of DNA binding proteins is characterized by the "bZIP" motif, which consists of a basic region that contacts DNA and an adjacent "leucine zipper" that mediates protein dimerization. A peptide model for the basic region of the yeast transcriptional activator GCN4 has been developed in which the leucine zipper has been replaced by a disulfide bond. The 34-residue peptide dimer, but not the reduced monomer, binds DNA with nanomolar affinity at 4^circC. DNA binding is sequence-specific as judged by deoxyribonuclease I footprinting. Circular dichroism spectroscopy suggests that the peptide adopts a helical structure when bound to DNA. These results demonstrate directly that the GCN4 basic region is sufficient for sequence-specific DNA binding and suggest that a major function of the GCN4 leucine zipper is simply to mediate protein dimerization. Our approach provides a strategy for the design of short sequence-specific DNA binding peptides.

  11. POU proteins bend DNA via the POU-specific domain.

    PubMed Central

    Verrijzer, C P; van Oosterhout, J A; van Weperen, W W; van der Vliet, P C

    1991-01-01

    POU proteins constitute a family of ubiquitous as well as cell type-specific transcription factors that share the conserved POU DNA binding domain. This domain consists of two distinct subdomains, a POU-specific domain and a POU homeodomain, that are both required for high affinity sequence-specific DNA binding. In a circular permutation assay, several POU proteins, including Oct-1, Oct-2A, Oct-6 and Pit-1, demonstrated a position dependent mobility of the protein-DNA complexes, suggesting induction of DNA bending. This was confirmed by detection of relative bend direction, using pre-bent DNA, and by enhanced ligase mediated cyclization. Bending was caused by interaction with the POU domain. By contrast, binding of the POU homeodomain did not distort the DNA structure, indicating that the POU-specific domain confers DNA bending. Images PMID:1915275

  12. Raman spectroscopic study of plasma-treated salmon DNA

    SciTech Connect

    Lee, Geon Joon; Kim, Yong Hee; Choi, Eun Ha; Kwon, Young-Wan

    2013-01-14

    In this research, we studied the effect of plasma treatment on the optical/structural properties of the deoxyribonucleic acid (DNA) extracted from salmon sperm. DNA-cetyltrimethylammonium (CTMA) films were obtained by complexation of DNA with CTMA. Circular dichroism (CD) and Raman spectra indicated that DNA retained its double helical structure in the solid film. The Raman spectra exhibited several vibration modes corresponding to the nuclear bases and the deoxyribose-phosphate backbones of the DNA, as well as the alkylchains of CTMA. Dielectric-barrier-discharge (DBD) plasma treatment induced structural modification and damage to the DNA, as observed by changes in the ultraviolet-visible absorption, CD, and Raman spectra. The optical emission spectra of the DBD plasma confirmed that DNA modification was induced by plasma ions such as reactive oxygen species and reactive nitrogen species.

  13. Viroid-induced DNA methylation in plants.

    PubMed

    Dalakouras, Athanasios; Dadami, Elena; Wassenegger, Michael

    2013-12-01

    In eukaryotes, DNA methylation refers to the addition of a methyl group to the fifth atom in the six-atom ring of cytosine residues. At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). RdDM was first discovered in viroid-infected plants. Viroids are pathogenic circular, non-coding, single-stranded RNA molecules. Members of the Pospiviroidae family replicate in the nucleus through double-stranded RNA intermediates, attracting the host RNA silencing machinery. The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. Here, we provide an overview of the cumulative data on the field of viroid-induced RdDM and discuss three possible scenarios concerning the mechanistic details of its establishment. PMID:25436756

  14. Double circular erosion patterns on dielectric target in magnetron sputtering.

    PubMed

    Suzaki, Yoshifumi; Miyagawa, Hayato; Ejima, Seiki

    2009-10-01

    In rf magnetron sputtering, a circular erosion pattern forms on the surface of a circular metal conductor target with permanent magnets on its back. In this case, the theory behind the erosion pattern has been established. However, in the case of a dielectric target, a double circular erosion pattern is formed. So far, this pattern has been phenomenologically recognized by experimenters; however, it has not yet been investigated. In this study, we performed a magnetron sputtering experiment with a SiO2 dielectric target, and confirmed the formation of a double circular erosion pattern. The dimensions of the double circular erosion pattern varied depending on the insulation resistance or the thickness of the SiO2 target. Furthermore, we found that the dimensions of a double circular erosion pattern changed by making a gap between the SiO2 target and guard ring. Based on the experimental results, we have proposed a qualitative model to explain the formation mechanism of double circular erosion patterns. PMID:19895082

  15. Curved-Line Cutting Using a Flexible Circular Saw

    NASA Astrophysics Data System (ADS)

    Yamada, Yohei; Osumi, Nobuyuki; Takasugi, Akio; Sasahara, Hiroyuki

    We propose a flexible circular saw for high-speed cutting of curved lines in carbon fiber-reinforced plastic (CFRP). A conventional circular saw is appropriate for straight line cutting, but it cannot be applied to curved line cutting because of the interference between the saw body and the machined surface. To eliminate this problem, the flexible circular saw is deflected into a bowl shape by circular forced displacement, and the cross-section of the saw becomes a circular arc. A curved line can be cut by the bowl-like-deflection. The deflection shape is very important to realize the curved-line cutting without interference. We investigated the deflection of the flexible circular saw by a finite element method (FEM) analysis. Suitable slit shapes for the saw body are also proposed, based on the FEM results regarding stress in the saw body, the minimum radius of curvature, and the effects of cutting force and centrifugal force and eigenvalue. We also conducted a curved-line cutting test on a CFRP plate, and we found that the flexible circular saw can cut curved lines with high accuracy and high speed without interference between the saw body and the machined surface.

  16. DNA ALTERATIONS

    EPA Science Inventory

    The exposure of an organism to genotoxic chemicals may induce a cascade of genetic events. nitially, structural alterations to DNA are formed. ext, the DNA damage is processed and subsequently expressed in mutant gene products. inally, diseases result from the genetic damage. he ...

  17. Circular RNAs are abundant, conserved, and associated with ALU repeats

    PubMed Central

    Jeck, William R.; Sorrentino, Jessica A.; Wang, Kai; Slevin, Michael K.; Burd, Christin E.; Liu, Jinze; Marzluff, William F.; Sharpless, Norman E.

    2013-01-01

    Circular RNAs composed of exonic sequence have been described in a small number of genes. Thought to result from splicing errors, circular RNA species possess no known function. To delineate the universe of endogenous circular RNAs, we performed high-throughput sequencing (RNA-seq) of libraries prepared from ribosome-depleted RNA with or without digestion with the RNA exonuclease, RNase R. We identified >25,000 distinct RNA species in human fibroblasts that contained non-colinear exons (a “backsplice”) and were reproducibly enriched by exonuclease degradation of linear RNA. These RNAs were validated as circular RNA (ecircRNA), rather than linear RNA, and were more stable than associated linear mRNAs in vivo. In some cases, the abundance of circular molecules exceeded that of associated linear mRNA by >10-fold. By conservative estimate, we identified ecircRNAs from 14.4% of actively transcribed genes in human fibroblasts. Application of this method to murine testis RNA identified 69 ecircRNAs in precisely orthologous locations to human circular RNAs. Of note, paralogous kinases HIPK2 and HIPK3 produce abundant ecircRNA from their second exon in both humans and mice. Though HIPK3 circular RNAs contain an AUG translation start, it and other ecircRNAs were not bound to ribosomes. Circular RNAs could be degraded by siRNAs and, therefore, may act as competing endogenous RNAs. Bioinformatic analysis revealed shared features of circularized exons, including long bordering introns that contained complementary ALU repeats. These data show that ecircRNAs are abundant, stable, conserved and nonrandom products of RNA splicing that could be involved in control of gene expression. PMID:23249747

  18. Anisotropic elliptical dichroism and influence of imperfection of circular polarization upon anisotropic circular dichroism

    SciTech Connect

    Wakabayashi, Masamitsu; Yokojima, Satoshi; Fukaminato, Tuyoshi; Ohtani, Hiroyuki; Nakamura, Shinichiro

    2015-04-21

    In spite of the importance of anisotropic circular dichroism, in practice, it is difficult to get rid of the artifacts that arise from the imperfection of the circular polarization. Undesirable linear dichroism, interference of two orthogonal polarization states, and linear birefringence prevent us from making accurate measurements. We propose a theoretical method for evaluating the contributions of the first two, which are thought to be the main artifacts when specimens are not thick enough. Using the time-dependent perturbation theory and taking into account the direction of light propagation toward an orientationally fixed molecule, we formulated the transition probability of systems perturbed by arbitrarily polarized light and the absorption difference associated with two kinds of polarized light. We also formulated, as an extension of the dissymmetry factor of circular dichroism, a newly defined dissymmetry factor associated with two arbitrary polarization states. Furthermore, we considered a mixed-state of photon ensemble in which polarization states distribute at a certain width around a certain average. Although the purity of polarization and ellipticity does not correspond immediately, by considering the mixed state it is possible to treat them consistently. We used quantum statistical mechanics to describe the absorption difference for two kinds of photon ensembles and applied the consequent formula to examine the reported experimental results of single-molecule chiroptical responses under discussion in the recent past. The artifacts are theoretically suggested to be sensitive to the incident direction of elliptically polarized light and to the oriented systems, the ellipticity, and the orientation of ellipse. The mixed state has little, if any, effect when the polarization state distribution is narrow.

  19. Anisotropic elliptical dichroism and influence of imperfection of circular polarization upon anisotropic circular dichroism

    NASA Astrophysics Data System (ADS)

    Wakabayashi, Masamitsu; Yokojima, Satoshi; Fukaminato, Tuyoshi; Ohtani, Hiroyuki; Nakamura, Shinichiro

    2015-04-01

    In spite of the importance of anisotropic circular dichroism, in practice, it is difficult to get rid of the artifacts that arise from the imperfection of the circular polarization. Undesirable linear dichroism, interference of two orthogonal polarization states, and linear birefringence prevent us from making accurate measurements. We propose a theoretical method for evaluating the contributions of the first two, which are thought to be the main artifacts when specimens are not thick enough. Using the time-dependent perturbation theory and taking into account the direction of light propagation toward an orientationally fixed molecule, we formulated the transition probability of systems perturbed by arbitrarily polarized light and the absorption difference associated with two kinds of polarized light. We also formulated, as an extension of the dissymmetry factor of circular dichroism, a newly defined dissymmetry factor associated with two arbitrary polarization states. Furthermore, we considered a mixed-state of photon ensemble in which polarization states distribute at a certain width around a certain average. Although the purity of polarization and ellipticity does not correspond immediately, by considering the mixed state it is possible to treat them consistently. We used quantum statistical mechanics to describe the absorption difference for two kinds of photon ensembles and applied the consequent formula to examine the reported experimental results of single-molecule chiroptical responses under discussion in the recent past. The artifacts are theoretically suggested to be sensitive to the incident direction of elliptically polarized light and to the oriented systems, the ellipticity, and the orientation of ellipse. The mixed state has little, if any, effect when the polarization state distribution is narrow.

  20. Plastic welding techniques based on torsional and circular motion.

    PubMed

    Kising, J

    2001-05-01

    The torsion ultrasonic welding process and the frequency decoupled circular friction process at low frequencies deliver low particle production. In addition, the even, circular movement of the circular welding process over the whole seam area and the freely selectable frequency open up applications in the medical field that cannot be achieved, or can only be achieved with difficulty, by traditional welding processes. The processes are fast and can be process controlled to a fine degree with a facility to be integrated into automation lines. PMID:11521653

  1. Circularly polarized light emission from semiconductor planar chiral nanostructures.

    PubMed

    Konishi, Kuniaki; Nomura, Masahiro; Kumagai, Naoto; Iwamoto, Satoshi; Arakawa, Yasuhiko; Kuwata-Gonokami, Makoto

    2011-02-01

    We demonstrate circularly polarized light emission from InAs quantum dots embedded in the waveguide region of a GaAs-based chiral nanostructure. The observed phenomenon originates due to a strong imbalance between left- and right-circularly polarized components of the vacuum field and results in a degree of polarization as high as 26% at room temperature. A strong circular anisotropy of the vacuum field modes inside the chiral nanostructure is visualized using numerical simulation. The results of the simulation agree well with experimental results. PMID:21405435

  2. Absorbed Power Minimization in Cellular Users with Circular Antenna Arrays

    NASA Astrophysics Data System (ADS)

    Christofilakis, Vasilis; Votis, Constantinos; Tatsis, Giorgos; Raptis, Vasilis; Kostarakis, Panos

    2010-01-01

    Nowadays electromagnetic pollution of non ionizing radiation generated by cellular phones concerns millions of people. In this paper the use of circular antenna array as a means of minimizing the absorbed power by cellular phone users is introduced. In particular, the different characteristics of radiation patterns produced by a helical conventional antenna used in mobile phones operating at 900 MHz and those produced by a circular antenna array, hypothetically used in the same mobile phones, are in detail examined. Furthermore, the percentage of decrement of the power absorbed in the head as a function of direction of arrival is estimated for the circular antenna array.

  3. Conceptual design of X band waveguide dual circular polarizer

    NASA Astrophysics Data System (ADS)

    Xu, Chen; Tantawi, Sami; Wang, Juwen

    2016-06-01

    A new design of dual circular polarizer is presented in this paper. This innovative design converts radiofrequency (rf) energy from TE10 mode in a rectangular waveguide to two polarized TE11 modes in a circular waveguide. A reflection less than -20 db is achieved and breakdown field is less than 42 MV /m at input of 1 MW. Meanwhile, this polarizer has a megahertz bandwidth, and the thermal stability is also discussed. This device can be used for broadcasting and receiving the circular polarized signals.

  4. Interaction of cis-diamminedichloroplatinum(II) with PM-2 DNA.

    PubMed

    Mong, S; Huang, C H; Prestayko, A W; Crooke, S T

    1980-09-01

    The interaction of cis-diamminedichloroplatinum(II) (CDDP) with PM-2 DNA was studied using two techniques: (a) agarose gel electrophoresis of PM-2 DNA conformation isomers after CDDP binding; and (b) viscometric measurement of different forms of CDDP-bound PM-2 DNA. In both systems, the results indicated that the DNA isomers interacted differently with CDDP. CDDP induced a decrease of viscosity upon interacting with single-strand broken relaxed circular (Form II) and double-strand broken linear (Form III) PM-2 DNA's. These observations are consistent with a "DNA shortening effect" proposed by Cohen et al. [Science (Wash. D. C.), 203: 1014-1016, 1979] and Macquet et al. [Biochimie (Paris), 60: 901-914, 1978] When covalently closed circular (Form I) PM-2 DNA was used, increasing concentrations of CDDP induced an initial slight increase and then decrease of electrophoretic mobility to the degree that it comigrated with CDDP-bound Form II DNA. Further addition of CDDP restored the electrophoretic mobility of Form I DNA. Corresponding changes in the viscosity of CDDP-bound Form I DNA showed an initial decrease, then an increase, and a final prolonged decrease of viscosity. These effects are similar but not identical to those induced by either DNA intercalators (e.g., ethidium bromide) or certain DNA denaturating agents (e.g., formaldehyde, ultraviolet light, alkali trichloroacetate, methylmercuric hydroxide, and carbodiimide). Thus, CDP may induce a DNA superhelix-unwinding process followed either by rewinding or a denaturation process or both. Quantitative analysis of the agarose gel electrophoretic pattern plus sucrose density gradient centrifugation studies also indicated that there was little DNA strand breakage induced by CDDP treatment. PMID:7191776

  5. Molecular beacon mediated circular strand displacement strategy for constructing a ratiometric electrochemical deoxyribonucleic acid sensor.

    PubMed

    Gao, Fenglei; Du, Lili; Zhang, Yu; Tang, Daoquan; Du, Yan

    2015-07-01

    A novel ratiometric electrochemical sensor for sensitive and selective determination of deoxyribonucleic acid (DNA) had been developed based on signal-on and signal-off strategy. The target DNA hybridized with the loop portion of ferrocene (Fc) labeled hairpin probe immobilized on the gold electrode (GE), the Fc away from the surface of GE and the methylene blue (MB) was attached to an electrode surface by hybridization between hairpin probe and MB labeled primer. Such conformational changes resulted in the oxidation peak current of Fc decreased and that of MB increased, and the changes of dual signals are linear with the concentration of DNA. Furthermore, with the help of strand-displacement polymerization, polymerase catalyzed the extension of the primer and the sequential displacement of the target DNA, which led to the release of target and another polymerization cycle. Thus the circular strand displacement produced the multiplication of the MB confined near the GE surface and Fc got away from the GE surface. Therefore, the recognition of target DNA resulted in both the "signal-off" of Fc and the "signal-on" of MB for dual-signal electrochemical ratiometric readout. The dual signal strategy offered a dramatic enhancement of the stripping response. The dynamic range of the target DNA detection was from 10(-13) to 10(-8) mol L(-1) with a detection limit down to 28 fM level. Compared with the single signaling electrochemical sensor, the dual-signaling electrochemical sensing strategy developed in this paper was more selective. It would have important applications in the sensitive and selective electrochemical determination of other small molecules and proteins. PMID:26088778

  6. 77 FR 75780 - Federal Acquisition Regulation; Federal Acquisition Circular 2005-64; Small Entity Compliance Guide

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-21

    ... Acquisition Regulation; Federal Acquisition Circular 2005-64; Small Entity Compliance Guide AGENCIES... the rule appearing in Federal Acquisition Circular (FAC) 2005-64, which amends the Federal...

  7. Individual muscle contributions to circular turning mechanics.

    PubMed

    Ventura, Jessica D; Klute, Glenn K; Neptune, Richard R

    2015-04-13

    Turning is an activity of daily living that involves both the acceleration of the body center-of-mass (COM) towards the center of curvature and rotation of the pelvis towards the new heading. The purpose of this study was to understand which muscles contribute to turning using experimentation, musculoskeletal modeling and simulation. Ten healthy adults consented to walk around a 1-m radius circular path at their self-selected walking speed and then along a straight line at the same speed. Forward dynamics simulations of the individual subjects during the turning and straight-line walking tasks were generated to identify the contributions of individual muscle groups to the body mediolateral and anterior-posterior COM acceleration impulse and to the pelvis angular acceleration impulse. The stance leg gluteus medius and ankle plantarflexor muscles and the swing leg adductor muscles were the primary contributors to redirect the body's COM relative to straight-line walking. In some cases, contributions to mediolateral COM acceleration were modulated through changes in leg orientation rather than through changes in muscle force. While modulation of the muscle contributions generally occurred in both the inner and outer legs, greater changes were observed during inner single-leg support than during outer single-leg support. Total pelvis angular acceleration was minimal during the single-support phase, but the swing leg muscles contributed significantly to balancing the internal and external rotation of the pelvis. The understanding of which muscles contribute to turning the body during walking may help guide the development of more effective locomotor therapies for those with movement impairments. PMID:25700608

  8. Status of the Future Circular Collider Study

    NASA Astrophysics Data System (ADS)

    Benedikt, Michael

    2016-03-01

    Following the 2013 update of the European Strategy for Particle Physics, the international Future Circular Collider (FCC) Study has been launched by CERN as host institute, to design an energy frontier hadron collider (FCC-hh) in a new 80-100 km tunnel with a centre-of-mass energy of about 100 TeV, an order of magnitude beyond the LHC's, as a long-term goal. The FCC study also includes the design of a 90-350 GeV high-luminosity lepton collider (FCC-ee) installed in the same tunnel, serving as Higgs, top and Z factory, as a potential intermediate step, as well as an electron-proton collider option (FCC-he). The physics cases for such machines will be assessed and concepts for experiments will be developed in time for the next update of the European Strategy for Particle Physics by the end of 2018. The presentation will summarize the status of machine designs and parameters and discuss the essential technical components to be developed in the frame of the FCC study. Key elements are superconducting accelerator-dipole magnets with a field of 16 T for the hadron collider and high-power, high-efficiency RF systems for the lepton collider. In addition the unprecedented beam power presents special challenges for the hadron collider for all aspects of beam handling and machine protection. First conclusions of geological investigations and implementation studies will be presented. The status of the FCC collaboration and the further planning for the study will be outlined.

  9. Circular RNAs and systemic lupus erythematosus.

    PubMed

    Li, Lian-Ju; Huang, Qing; Pan, Hai-Feng; Ye, Dong-Qing

    2016-08-15

    Circular RNAs (circRNAs) are a large class of noncoding RNAs that form covalently closed RNA circles. The discovery of circRNAs discloses a new layer of gene regulation occurred post-transcriptionally. Identification of endogenous circRNAs benefits from the advance in high-throughput RNA sequencing and remains challenging. Many studies probing into the mechanisms of circRNAs formation occurred cotranscriptionally or posttranscriptionally emerge and conclude that canonical splicing mechanism, sequence properties, and certain regulatory factors are at play in the process. Although our knowledge on functions of circRNAs is rather limited, a few circRNAs are shown to sponge miRNA and regulate gene transcription. The clearest case is one circRNA CDR1as that serves as sponge of miR-7. Researches on circRNAs in human diseases such as cancers highlight the function and physical relevance of circRNAs. Given the implication of miRNAs in the initiation and progression of systemic lupus erythematosus (SLE) and the roles of circRNAs in sponging miRNA and gene regulation, it is appealing to speculate that circRNAs may associate with SLE and may be potential therapeutic targets for treatment of SLE. Future studies should attach more importance to the relationship between circRNAs and SLE. This review will concern identification, biogenesis, and function of circRNAs, introduce reports exploring the association of circRNAs with human diseases, and conjecture the potential roles of circRNAs in SLE. PMID:27450756

  10. Failure of Non-Circular Composite Cylinders

    NASA Technical Reports Server (NTRS)

    Hyer, M. W.

    2004-01-01

    In this study, a progressive failure analysis is used to investigate leakage in internally pressurized non-circular composite cylinders. This type of approach accounts for the localized loss of stiffness when material failure occurs at some location in a structure by degrading the local material elastic properties by a certain factor. The manner in which this degradation of material properties takes place depends on the failure modes, which are determined by the application of a failure criterion. The finite-element code STAGS, which has the capability to perform progressive failure analysis using different degradation schemes and failure criteria, is utilized to analyze laboratory scale, graphite-epoxy, elliptical cylinders with quasi-isotropic, circumferentially-stiff, and axially-stiff material orthotropies. The results are divided into two parts. The first part shows that leakage, which is assumed to develop if there is material failure in every layer at some axial and circumferential location within the cylinder, does not occur without failure of fibers. Moreover before fibers begin to fail, only matrix tensile failures, or matrix cracking, takes place, and at least one layer in all three cylinders studied remain uncracked, preventing the formation of a leakage path. That determination is corroborated by the use of different degradation schemes and various failure criteria. Among the degradation schemes investigated are the degradation of different engineering properties, the use of various degradation factors, the recursive or non-recursive degradation of the engineering properties, and the degradation of material properties using different computational approaches. The failure criteria used in the analysis include the noninteractive maximum stress criterion and the interactive Hashin and Tsai-Wu criteria. The second part of the results shows that leakage occurs due to a combination of matrix tensile and compressive, fiber tensile and compressive, and inplane

  11. The Circular Hydraulic Jump in Microgravity

    NASA Technical Reports Server (NTRS)

    Avedisian, C. Thomas

    1996-01-01

    This report summarizes the key experimental results and observations that were obtained under NASA grant NAG 3-1627 from the Fluid Physics Program. The Principle Investigator was Thomas Avedisian. In addition a half-time post-doctoral associate, Ziqun Zhao, was funded for half year. The project monitor was David Chao of the NASA-Lewis Research Center in Cleveland, Ohio. The grant period was originally for one year at $34K and a no-cost extension was applied for and granted for an additional year. The research consisted of an experimental study of the circular hydraulic jump (CHJ) in microgravity using water as the working fluid. The evolution of the CHJ radius was measured during a sudden transition from normal to microgravity in a drop tower. The downstream height of the CHJ was controlled by submerging the target plate in a tank filled with water to the desired depth, and the measurements are compared with an existing theory for the location of the CHJ. Results show that the CHJ diameter is larger in microgravity than normal gravity. The adjustment of the CHJ diameter to a sudden change in gravity occurs over a period of about 200ms for the conditions of the present study, and remains constant thereafter for most of the flow conditions examined. For flow conditions that a CHJ was not first established at normal gravity but which later appeared during the transition tb microgravity, the CHJ diameter was not constant during the period of microgravity but continually changed. Good agreement between measured and predicted CHJ radii is found for normal gravity CHJ radii, but comparatively poorer agreement is observed for the CHJ radii measurements in microgravity.

  12. Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose

    PubMed Central

    Takahashi, Hirokazu; Yamazaki, Hiroyuki; Akanuma, Satoshi; Kanahara, Hiroko; Saito, Toshiyuki; Chimuro, Tomoyuki; Kobayashi, Takayoshi; Ohtani, Toshio; Yamamoto, Kimiko; Sugiyama, Shigeru; Kobori, Toshiro

    2014-01-01

    We previously reported that multiply-primed rolling circle amplification (MRPCA) using modified random RNA primers can amplify tiny amounts of circular DNA without producing any byproducts. However, contaminating DNA in recombinant Phi29 DNA polymerase adversely affects the outcome of MPRCA, especially for negative controls such as non-template controls. The amplified DNA in negative control casts doubt on the result of DNA amplification. Since Phi29 DNA polymerase has high affinity for both single-strand and double-stranded DNA, some amount of host DNA will always remain in the recombinant polymerase. Here we describe a procedure for preparing Phi29 DNA polymerase which is essentially free of amplifiable DNA. This procedure is realized by a combination of host DNA removal using appropriate salt concentrations, inactivation of amplifiable DNA using ethidium monoazide, and irradiation with visible light from a light-emitting diode lamp. Any remaining DNA, which likely exists as oligonucleotides captured by the Phi29 DNA polymerase, is degraded by the 3′-5′ exonuclease activity of the polymerase itself in the presence of trehalose, used as an anti-aggregation reagent. Phi29 DNA polymerase purified by this procedure has little amplifiable DNA, resulting in reproducible amplification of at least ten copies of plasmid DNA without any byproducts and reducing reaction volume. This procedure could aid the amplification of tiny amounts DNA, thereby providing clear evidence of contamination from laboratory environments, tools and reagents. PMID:24505243

  13. [DNA computing].

    PubMed

    Błasiak, Janusz; Krasiński, Tadeusz; Popławski, Tomasz; Sakowski, Sebastian

    2011-01-01

    Biocomputers can be an alternative for traditional "silicon-based" computers, which continuous development may be limited due to further miniaturization (imposed by the Heisenberg Uncertainty Principle) and increasing the amount of information between the central processing unit and the main memory (von Neuman bottleneck). The idea of DNA computing came true for the first time in 1994, when Adleman solved the Hamiltonian Path Problem using short DNA oligomers and DNA ligase. In the early 2000s a series of biocomputer models was presented with a seminal work of Shapiro and his colleguas who presented molecular 2 state finite automaton, in which the restriction enzyme, FokI, constituted hardware and short DNA oligomers were software as well as input/output signals. DNA molecules provided also energy for this machine. DNA computing can be exploited in many applications, from study on the gene expression pattern to diagnosis and therapy of cancer. The idea of DNA computing is still in progress in research both in vitro and in vivo and at least promising results of these research allow to have a hope for a breakthrough in the computer science. PMID:21735816

  14. Circular dichroism and magnetic circular dichroism of iron-sulfur proteins.

    PubMed

    Stephens, P J; Thomson, A J; Dunn, J B; Keiderling, T A; Rawlings, J; Rao, K K; Hall, D O

    1978-10-31

    Circular dichroism (CD) and magnetic circular dichroism (MCD) spectra are reported for the 2-Fe ferredoxins from Pseudomonas putida and Spirulina maxima, Chromatium HIPIP, the 4-Fe ferredoxin from Bacillus stearothermophilus, and the 8-Fe ferredoxin from Clostridium pasteurianum. The spectral range spans the near-infrared, visible, and near ultraviolet. In all cases except oxidized 2-Fe ferredoxins, electronic absorption is observed continuously from less than 5000 cm-1 to above 30,000 cm-1. The CD spectra of the two 2-Fe ferredoxins are similar. In contrast, the CD of the 4-Fe and 8-Fe proteins, for a given 4-Fe cluster oxidation level, varies considerable with protein. MCD is less sensitive to protein environment than is CD. In the 2-Fe proteins, MCD at 5 T is appreciably smaller than the CD; in the 4-Fe and 8-Fe proteins, MCD and CD are comparable in magnitude. Both CD and MCD are more highly structured than the corresponding absorption spectra. The CD and MCD spectra reported provide a broader base than heretofore available for the characterization of iron-sulfur proteins containing 2-Fe and 4-Fe clusters and for the evaluation of electronic structural models for these clusters. PMID:728385

  15. Comparing modal noise and FRD of circular and non-circular cross-section fibres

    NASA Astrophysics Data System (ADS)

    Sablowski, D. P.; Plüschke, D.; Weber, M.; Strassmeier, K. G.; Järvinen, A.

    2016-03-01

    Modal noise is a common source of noise introduced to the measurements by optical fibres and is particularly important for fibre-fed spectroscopic instruments, especially for high-resolution measurements. This noise source can limit the signal-to-noise ratio and jeopardize photon-noise limited data. The subject of the present work is to compare measurements of modal noise and focal-ratio degradation (FRD) for several commonly used fibres. We study the influence of a simple mechanical scrambling method (excenter) on both FRD and modal noise. Measurements are performed with circular and octagonal fibres from Polymicro Technology (FBP-Series) with diameters of 100, 200, and 300 μm and for square and rectangular fibres from CeramOptec, among others. FRD measurements for the same sample of fibres are performed as a function of wavelength. Furthermore, we replaced the circular fibre of the STELLA-échelle-spectrograph (SES) in Tenerife with an octagonal and found a SNR increase by a factor of 1.6 at 678 nm. It is shown in the laboratory that an excenter with a large amplitude and low frequency will not influence the FRD but will reduce modal noise rather effectively by up to 180%.

  16. A mobile group I intron from Physarum polycephalum can insert itself and induce point mutations in the nuclear ribosomal DNA of saccharomyces cerevisiae.

    PubMed Central

    Muscarella, D E; Vogt, V M

    1993-01-01

    Pp LSU3 is a mobile group I intron in the extrachromosomal nuclear ribosomal DNA (rDNA) of Physarum polycephalum. As found for other mobile introns, Pp LSU3 encodes a site-specific endonuclease, I-Ppo, which mediates "homing" to unoccupied target sites in Physarum rDNA. The recognition sequence for this enzyme is conserved in all eucaryotic nuclear rDNAs. We have introduced this intron into a heterologous species, Saccharomyces cerevisiae, in which nuclear group I introns have not been detected. The expression of Pp LSU3, under control of the inducible GAL10 promoter, was found to be lethal as a consequence of double-strand breaks in the rDNA. However, surviving colonies that are resistant to the lethal effects of I-Ppo because of alterations in the rDNA at the cleavage site were recovered readily. These survivors are of two classes. The first comprises cells that acquired one of three types of point mutations. The second comprises cells in which Pp LSU3 became inserted into the rDNA. In both cases, each resistant survivor appears to carry the same alterations in all approximately 150 rDNA repeats. When it is embedded in yeast rDNA, Pp LSU3 leads to the synthesis of I-Ppo and appears to be mobile in appropriate genetic crosses. The existence of yeast cells carrying a mobile intron should allow dissection of the steps that allow expression of the highly unusual I-Ppo gene. Images PMID:8380887

  17. The DNA of ciliated protozoa.

    PubMed Central

    Prescott, D M

    1994-01-01

    Ciliates contain two types of nuclei: a micronucleus and a macronucleus. The micronucleus serves as the germ line nucleus but does not express its genes. The macronucleus provides the nuclear RNA for vegetative growth. Mating cells exchange haploid micronuclei, and a new macronucleus develops from a new diploid micronucleus. The old macronucleus is destroyed. This conversion consists of amplification, elimination, fragmentation, and splicing of DNA sequences on a massive scale. Fragmentation produces subchromosomal molecules in Tetrahymena and Paramecium cells and much smaller, gene-sized molecules in hypotrichous ciliates to which telomere sequences are added. These molecules are then amplified, some to higher copy numbers than others. rDNA is differentially amplified to thousands of copies per macronucleus. Eliminated sequences include transposonlike elements and sequences called internal eliminated sequences that interrupt gene coding regions in the micronuclear genome. Some, perhaps all, of these are excised as circular molecules and destroyed. In at least some hypotrichs, segments of some micronuclear genes are scrambled in a nonfunctional order and are recorded during macronuclear development. Vegetatively growing ciliates appear to possess a mechanism for adjusting copy numbers of individual genes, which corrects gene imbalances resulting from random distribution of DNA molecules during amitosis of the macronucleus. Other distinctive features of ciliate DNA include an altered use of the conventional stop codons. Images PMID:8078435

  18. SIMULTANEOUS MEASUREMENT OF CIRCULAR DICHROISM AND FLUORESCENCE POLARIZATION ANISOTROPY.

    SciTech Connect

    SUTHERLAND,J.C.

    2002-01-19

    Circular dichroism and fluorescence polarization anisotropy are important tools for characterizing biomolecular systems. Both are used extensively in kinetic experiments involving stopped- or continuous flow systems as well as titrations and steady-state spectroscopy. This paper presents the theory for determining circular dichroism and fluorescence polarization anisotropy simultaneously, thus insuring the two parameters are recorded under exactly the same conditions and at exactly the same time in kinetic experiments. The approach to measuring circular dichroism is that used in almost all conventional dichrographs. Two arrangements for measuring fluorescence polarization anisotropy are described. One uses a single fluorescence detector and signal processing with a lock-in amplifier that is similar to the measurement of circular dichroism. The second approach uses classic ''T'' format detection optics, and thus can be used with conventional photon-counting detection electronics. Simple extensions permit the simultaneous measurement of the absorption and excitation intensity corrected fluorescence intensity.

  19. 35. Basement, passage beneath main entrance porch, showing circular skylight ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    35. Basement, passage beneath main entrance porch, showing circular skylight opening, view to northwest - Portsmouth Naval Hospital, Hospital Building, Rixey Place, bounded by Williamson Drive, Holcomb Road, & The Circle, Portsmouth, Portsmouth, VA

  20. 11. VIEW OF CIRCULAR CAR SHOP OVER TOPS OF BOX ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    11. VIEW OF CIRCULAR CAR SHOP OVER TOPS OF BOX CARS LOOKING NORTHEAST. - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  1. 13. PHOTOCOPY OF ILLUSTRATED CIRCULAR OF 'ROOTS NEW IRON POSITIVE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    13. PHOTOCOPY OF ILLUSTRATED CIRCULAR OF 'ROOTS NEW IRON POSITIVE BLAST BLOWER,' CA. JAN. 1880, FROM FILES OF ROOTS-CONNERSVILLE BLOWER CO., CONNERSVILLE, IND. - P. H. & F. M. Roots Company, Eastern Avenue, Connersville, Fayette County, IN

  2. Procedure for Detecting Outliers in a Circular Regression Model

    PubMed Central

    Rambli, Adzhar; Abuzaid, Ali H. M.; Mohamed, Ibrahim Bin; Hussin, Abdul Ghapor

    2016-01-01

    A number of circular regression models have been proposed in the literature. In recent years, there is a strong interest shown on the subject of outlier detection in circular regression. An outlier detection procedure can be developed by defining a new statistic in terms of the circular residuals. In this paper, we propose a new measure which transforms the circular residuals into linear measures using a trigonometric function. We then employ the row deletion approach to identify observations that affect the measure the most, a candidate of outlier. The corresponding cut-off points and the performance of the detection procedure when applied on Down and Mardia’s model are studied via simulations. For illustration, we apply the procedure on circadian data. PMID:27064566

  3. High circular polarization in electroluminescence from MoSe2

    NASA Astrophysics Data System (ADS)

    Onga, Masaru; Zhang, Yijin; Suzuki, Ryuji; Iwasa, Yoshihiro

    2016-02-01

    The coupling between the valley degree of freedom and the optical helicity is one of the unique phenomena in transition metal dichalcogenides. The significant valley polarization evaluated from circularly polarized photoluminescence (PL) has been reported in many transition metal dichalcogenides, except in MoSe2. This compound is an anomalous material showing ultra-fast relaxation of the valley polarized states, which causes negligible polarization in the PL. Meanwhile, circularly polarized electroluminescence (EL) has been recently reported in a WSe2 light-emitting transistor, providing another method for using the valley degree of freedom. Here, we report the EL properties of MoSe2, demonstrating electrical switching of the optical helicity. Importantly, we observed high circular polarization reaching 66%. The results imply that the dominant mechanism of circularly polarized EL is robust against intervalley scattering, in marked contrast to the PL.

  4. Circularly polarized waves in a plasma with vacuum polarization effects

    SciTech Connect

    Lundin, J.; Stenflo, L.; Brodin, G.; Marklund, M.; Shukla, P. K.

    2007-06-15

    The theory for large amplitude circularly polarized waves propagating along an external magnetic field is extended in order to also include vacuum polarization effects. A general dispersion relation, which unites previous results, is derived.

  5. The nature of circular maria based on gravity studies.

    NASA Technical Reports Server (NTRS)

    Phillips, R. J.; Conel, J. E.; Sjogren, W. L.

    1973-01-01

    Current thinking on the evolution of major lunar morphological features, i.e., large lunar circular basins, and on the nature and origin of surface structures observed in the fill deposits is summarized. The great lunar circular basins must result from high-velocity impact of large bodies with the moon. A hydrostatic mechanism is outlined, and a working hypothesis is presented for the evolution of lunar circular basins subsequent to their origin by impact. In the main appeal is made to Doppler gravity data to support the hypothesis, although photographic and altimetric information is also used. It is considered that all large ringed circular basins follow a common evolutionary path of superisostatic volcanic flooding followed by partial and variable isostatic adjustment. The difference between basins is the amount of flooding, which in turn may be related to the center of figure-center of mass offset of the moon.

  6. 77. East facade of circular forebay showing overflow well. Photo ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    77. East facade of circular forebay showing overflow well. Photo by Jet Lowe, HAER, 1989. - Puget Sound Power & Light Company, White River Hydroelectric Project, 600 North River Avenue, Dieringer, Pierce County, WA

  7. 78. Interior of circular forebay showing valves for operating sluice ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    78. Interior of circular forebay showing valves for operating sluice gates, looking south. Photo by Jet Lowe, HAER, 1989. - Puget Sound Power & Light Company, White River Hydroelectric Project, 600 North River Avenue, Dieringer, Pierce County, WA

  8. Electrically pumped semiconductor laser with monolithic control of circular polarization

    PubMed Central

    Rauter, Patrick; Lin, Jiao; Genevet, Patrice; Khanna, Suraj P.; Lachab, Mohammad; Giles Davies, A.; Linfield, Edmund H.; Capasso, Federico

    2014-01-01

    We demonstrate surface emission of terahertz (THz) frequency radiation from a monolithic quantum cascade laser with built-in control over the degree of circular polarization by “fishbone” gratings composed of orthogonally oriented aperture antennas. Different grating concepts for circularly polarized emission are introduced along with the presentation of simulations and experimental results. Fifth-order gratings achieve a degree of circular polarization of up to 86% within a 12°-wide core region of their emission lobes in the far field. For devices based on an alternative transverse grating design, degrees of circular polarization as high as 98% are demonstrated for selected far-field regions of the outcoupled THz radiation and within a collection half-angle of about 6°. Potential and limitations of integrated antenna gratings for polarization-controlled emission are discussed. PMID:25512515

  9. Livestock Waste Management in a Quality Environment. Circular 1074.

    ERIC Educational Resources Information Center

    Jedele, D. G., Ed.

    This circular provides information to assist in assessing the pollution potential of livestock operations. It discusses a systematic approach to resolving problems through feedlot runoff control, liquid manure handling, hauling and lagooning, and ditching. (CS)

  10. Numerical simulation for flow around two circular cylinders in tandem

    NASA Astrophysics Data System (ADS)

    Kondo, Norio; Matsukuma, Daisuke

    2005-05-01

    We use a third-order upwind finite element scheme in order to perform numerical stabilization of solutions of the Navier Stokes equations and present numerical results of flow around two circular cylinders in tandem arrangement by two- and three-dimensional computations. The two circular cylinders are arranged with some spacings between the cylinders. It is well known from experimental data that the flow around two circular cylinders denotes very complicated phenomena with the variation of spacing between two cylinders. In addition, the time-averaged drag coefficients of two circular cylinders suddenly change at a certain spacing between the cylinders. We, therefore, make an investigation of such phenomena at the Reynolds number of 1000 by the use of a numerical approach, and the obtained numerical results are also qualitatively compared with experimental data.

  11. Recent progress in circular high-power overmoded waveguide

    NASA Astrophysics Data System (ADS)

    Huting, William A.; Warren, Jeffery W.; Krill, Jerry A.

    1991-03-01

    To support future combat system requirements, the use of circular TE(01) mode 'overmoded' waveguide technology has been investigated. A circular TE(01) mode overmoded waveguide of a sheathed-helix design has been optimized for application to microwave bands subject to high-power and low-attenuation objectives and to bend and cross-sectional size constraints. New circular TE(01) mode components, such as the multiple-port rectangular TE(10) to circular TE(01) mode waveguide transition, the mode-transitioning elbow, and a mode filter, provide further design flexibility for high-power waveguide systems. An application of the technology under consideration to a combat system element has been successfully demonstrated in the Cooperative Engagement Capability developed under APL technical direction.

  12. Circular stair from Parking Overlook to Clay Tennis Courts, Riverside ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Circular stair from Parking Overlook to Clay Tennis Courts, Riverside Park at 96th Street, looking southwest. - Henry Hudson Parkway, Extending 11.2 miles from West 72nd Street to Bronx-Westchester border, New York County, NY

  13. 12. DETAIL VIEW OF CIRCULAR BRONZE ROLLER GATE POSITION GAUGE, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    12. DETAIL VIEW OF CIRCULAR BRONZE ROLLER GATE POSITION GAUGE, ROLLER GATE PIER HOUSE, TYPE 2A, DAM - Mississippi River 9-Foot Channel Project, Lock & Dam No. 11, Upper Mississippi River, Dubuque, Dubuque County, IA

  14. Electrically pumped semiconductor laser with monolithic control of circular polarization.

    PubMed

    Rauter, Patrick; Lin, Jiao; Genevet, Patrice; Khanna, Suraj P; Lachab, Mohammad; Giles Davies, A; Linfield, Edmund H; Capasso, Federico

    2014-12-30

    We demonstrate surface emission of terahertz (THz) frequency radiation from a monolithic quantum cascade laser with built-in control over the degree of circular polarization by "fishbone" gratings composed of orthogonally oriented aperture antennas. Different grating concepts for circularly polarized emission are introduced along with the presentation of simulations and experimental results. Fifth-order gratings achieve a degree of circular polarization of up to 86% within a 12°-wide core region of their emission lobes in the far field. For devices based on an alternative transverse grating design, degrees of circular polarization as high as 98% are demonstrated for selected far-field regions of the outcoupled THz radiation and within a collection half-angle of about 6°. Potential and limitations of integrated antenna gratings for polarization-controlled emission are discussed. PMID:25512515

  15. Supersonic flow around circular cones at angles of attack

    NASA Technical Reports Server (NTRS)

    Ferri, Antonio

    1951-01-01

    The properties of conical flow without axial symmetry are analyzed. The flow around cones of circular cross section at small angles of attack is determined by correctly considering the effect of the entropy gradients in the flow.

  16. Research on object detection based on circular polarization property

    NASA Astrophysics Data System (ADS)

    Wu, Yun-zhi; Zeng, Xian-fang; Yin, Cheng-liang; Luo, Xiao-lin

    2013-09-01

    It is an important subject in information scout, battlefield surveillance and automatic target recognition to detect interesting objects from complicated background. Compared with intensity detection, polarization detection has its advantage in identifying some camouflage targets. Usually, in the studies of target polarization detection, circular polarization property is usually neglected because of its small value. But in particular conditions, the circular polarization property of target will be used to accomplish object detection with their obviously different value. In this study, a single reflectance model of Mueller matrix is established, and based on Fresnel's law, circular polarization property of object is analyzed which is obvious while linear polarization property is obscure in particular condition. It is available to use the circular polarization component to detect target.

  17. IFI16 Preferentially Binds to DNA with Quadruplex Structure and Enhances DNA Quadruplex Formation.

    PubMed

    Hároníková, Lucia; Coufal, Jan; Kejnovská, Iva; Jagelská, Eva B; Fojta, Miroslav; Dvořáková, Petra; Muller, Petr; Vojtesek, Borivoj; Brázda, Václav

    2016-01-01

    Interferon-inducible protein 16 (IFI16) is a member of the HIN-200 protein family, containing two HIN domains and one PYRIN domain. IFI16 acts as a sensor of viral and bacterial DNA and is important for innate immune responses. IFI16 binds DNA and binding has been described to be DNA length-dependent, but a preference for supercoiled DNA has also been demonstrated. Here we report a specific preference of IFI16 for binding to quadruplex DNA compared to other DNA structures. IFI16 binds to quadruplex DNA with significantly higher affinity than to the same sequence in double stranded DNA. By circular dichroism (CD) spectroscopy we also demonstrated the ability of IFI16 to stabilize quadruplex structures with quadruplex-forming oligonucleotides derived from human telomere (HTEL) sequences and the MYC promotor. A novel H/D exchange mass spectrometry approach was developed to assess protein interactions with quadruplex DNA. Quadruplex DNA changed the IFI16 deuteration profile in parts of the PYRIN domain (aa 0-80) and in structurally identical parts of both HIN domains (aa 271-302 and aa 586-617) compared to single stranded or double stranded DNAs, supporting the preferential affinity of IFI16 for structured DNA. Our results reveal the importance of quadruplex DNA structure in IFI16 binding and improve our understanding of how IFI16 senses DNA. IFI16 selectivity for quadruplex structure provides a mechanistic framework for IFI16 in immunity and cellular processes including DNA damage responses and cell proliferation. PMID:27280708

  18. IFI16 Preferentially Binds to DNA with Quadruplex Structure and Enhances DNA Quadruplex Formation

    PubMed Central

    Hároníková, Lucia; Coufal, Jan; Kejnovská, Iva; Jagelská, Eva B.; Fojta, Miroslav; Dvořáková, Petra; Muller, Petr; Vojtesek, Borivoj; Brázda, Václav

    2016-01-01

    Interferon-inducible protein 16 (IFI16) is a member of the HIN-200 protein family, containing two HIN domains and one PYRIN domain. IFI16 acts as a sensor of viral and bacterial DNA and is important for innate immune responses. IFI16 binds DNA and binding has been described to be DNA length-dependent, but a preference for supercoiled DNA has also been demonstrated. Here we report a specific preference of IFI16 for binding to quadruplex DNA compared to other DNA structures. IFI16 binds to quadruplex DNA with significantly higher affinity than to the same sequence in double stranded DNA. By circular dichroism (CD) spectroscopy we also demonstrated the ability of IFI16 to stabilize quadruplex structures with quadruplex-forming oligonucleotides derived from human telomere (HTEL) sequences and the MYC promotor. A novel H/D exchange mass spectrometry approach was developed to assess protein interactions with quadruplex DNA. Quadruplex DNA changed the IFI16 deuteration profile in parts of the PYRIN domain (aa 0–80) and in structurally identical parts of both HIN domains (aa 271–302 and aa 586–617) compared to single stranded or double stranded DNAs, supporting the preferential affinity of IFI16 for structured DNA. Our results reveal the importance of quadruplex DNA structure in IFI16 binding and improve our understanding of how IFI16 senses DNA. IFI16 selectivity for quadruplex structure provides a mechanistic framework for IFI16 in immunity and cellular processes including DNA damage responses and cell proliferation. PMID:27280708

  19. Electronic and vibrational circular dichroism spectra of (R)-(-)-apomorphine

    NASA Astrophysics Data System (ADS)

    Abbate, Sergio; Longhi, Giovanna; Lebon, France; Tommasini, Matteo

    2012-09-01

    Apomorphine is a chiral drug molecule; notwithstanding its extraordinary importance, little attention has been paid to the characterization of its chiroptical properties. Here we report on its electronic circular dichroism (ECD) spectra, recorded in methanol and water, and vibrational circular dichroism (VCD) in methanol and dimethyl sulfoxide (DMSO) solutions. Density functional theory (DFT) calculations have allowed us to interpret the spectra and to evaluate the role of possible conformations, charge-states and interactions with counter ions.

  20. Aharonov-Bohm effect induced by circularly polarized light

    NASA Astrophysics Data System (ADS)

    Sigurdsson, H.; Kibis, O. V.; Shelykh, I. A.

    2015-11-01

    We demonstrated theoretically that the strong electron interaction with circularly polarized photons in ring-like nanostructures changes the phase of electron wave. This optically-induced effect is caused by the breaking of time-reversal symmetry and is similar to the Aharonov-Bohm effect. As a consequence of this phenomenon, the conductance of mesoscopic rings irradiated by a circularly polarized electromagnetic wave behaves as an oscillating function of the intensity and frequency of the wave.