National Library of Energy BETA

Sample records for dna double strand

  1. Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA glycosylase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Schormann, Norbert; Banerjee, Surajit; Ricciardi, Robert; Chattopadhyay, Debasish

    2015-06-02

    Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. Results: This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This alsomore » represents the first structure of a uracil DNA glycosylase in complex with an undamaged DNA. In the asymmetric unit two D4 subunits bind simultaneously to complementary strands of the DNA double helix. Each D4 subunit interacts mainly with the central region of one strand. DNA binds to the opposite side of the A20-binding surface on D4. In comparison of the present structure with the structure of uracil-containing DNA-bound human uracil-DNA glycosylase suggests that for DNA binding and uracil removal D4 employs a unique set of residues and motifs that are highly conserved within the poxvirus family but different in other organisms. Conclusion: The first structure of D4 bound to a truly non-specific undamaged double-stranded DNA suggests that initial binding of DNA may involve multiple non-specific interactions between the protein and the phosphate backbone.« less

  2. Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA glycosylase

    SciTech Connect (OSTI)

    Schormann, Norbert; Banerjee, Surajit; Ricciardi, Robert; Chattopadhyay, Debasish

    2015-06-02

    Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. Results: This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This also represents the first structure of a uracil DNA glycosylase in complex with an undamaged DNA. In the asymmetric unit two D4 subunits bind simultaneously to complementary strands of the DNA double helix. Each D4 subunit interacts mainly with the central region of one strand. DNA binds to the opposite side of the A20-binding surface on D4. In comparison of the present structure with the structure of uracil-containing DNA-bound human uracil-DNA glycosylase suggests that for DNA binding and uracil removal D4 employs a unique set of residues and motifs that are highly conserved within the poxvirus family but different in other organisms. Conclusion: The first structure of D4 bound to a truly non-specific undamaged double-stranded DNA suggests that initial binding of DNA may involve multiple non-specific interactions between the protein and the phosphate backbone.

  3. Method of preparing and applying single stranded DNA probes to double stranded target DNAs in situ

    DOE Patents [OSTI]

    Gray, Joe W.; Pinkel, Daniel

    1991-01-01

    A method is provided for producing single stranded non-self-complementary nucleic acid probes, and for treating target DNA for use therewith. Probe is constructed by treating DNA with a restriction enzyme and an exonuclease to form template/primers for a DNA polymerase. The digested strand is resynthesized in the presence of labeled nucleoside triphosphate precursor. Labeled single stranded fragments are separated from the resynthesized fragments to form the probe. Target DNA is treated with the same restriction enzyme used to construct the probe, and is treated with an exonuclease before application of the probe. The method significantly increases the efficiency and specificity of hybridization mixtures by increasing effective probe concentration by eliminating self-hybridization between both probe and target DNAs, and by reducing the amount of target DNA available for mismatched hybridizations.

  4. Method of preparing and applying single stranded DNA probes to double stranded target DNAs in situ

    DOE Patents [OSTI]

    Gray, J.W.; Pinkel, D.

    1991-07-02

    A method is provided for producing single stranded non-self-complementary nucleic acid probes, and for treating target DNA for use therewith. The probe is constructed by treating DNA with a restriction enzyme and an exonuclease to form template/primers for a DNA polymerase. The digested strand is resynthesized in the presence of labeled nucleoside triphosphate precursor. Labeled single stranded fragments are separated from the resynthesized fragments to form the probe. Target DNA is treated with the same restriction enzyme used to construct the probe, and is treated with an exonuclease before application of the probe. The method significantly increases the efficiency and specificity of hybridization mixtures by increasing effective probe concentration by eliminating self-hybridization between both probe and target DNAs, and by reducing the amount of target DNA available for mismatched hybridizations. No Drawings

  5. Spin transport and spin polarization properties in double-stranded DNA

    SciTech Connect (OSTI)

    Simchi, Hamidreza; Esmaeilzadeh, Mahdi Mazidabadi, Hossein

    2013-11-21

    We study the spin-dependent electron transport through a double-stranded DNA (dsDNA) using the Bogoliubov-de Gennes equations and non-equilibrium Green's function method. We calculate the spin-dependent electron conductance and spin-polarization for different lengths, helix angles, twist angles of dsDNA, the environment-induced dephasing factors, and hopping integral. It is shown that the conductance decreases by increasing the length and dephasing factor. Also, we show that the spin-polarization depends on the helical symmetry and the length of DNA. It is shown that the double-stranded DNA can act as a perfect spin filter. Finally, we show that the sign of spin polarization can be inverted from +1 (−1) to −1 (+1) for some values of hopping integral.

  6. Screening Tool for Providers of Double-Stranded DNA - Energy Innovation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Portal Startup America Startup America Industrial Technologies Industrial Technologies Energy Analysis Energy Analysis Biomass and Biofuels Biomass and Biofuels Find More Like This Return to Search Screening Tool for Providers of Double-Stranded DNA Oak Ridge National Laboratory Contact ORNL About This Technology Publications: PDF Document Publication 11-G00227_ID2510 (2).pdf (829 KB) Technology Marketing SummaryThe invention screens purchase orders submitted to DNA synthesis

  7. Zinc chromate induces chromosome instability and DNA double strand breaks in human lung cells

    SciTech Connect (OSTI)

    Xie Hong; Holmes, Amie L.; Young, Jamie L.; Qin Qin; Joyce, Kellie; Pelsue, Stephen C.; Peng Cheng; Wise, Sandra S.; Jeevarajan, Antony S.; Wallace, William T.; Hammond, Dianne; Wise, John Pierce E-mail: John.Wise@usm.maine.edu

    2009-02-01

    Hexavalent chromium Cr(VI) is a respiratory toxicant and carcinogen, with solubility playing an important role in its carcinogenic potential. Zinc chromate, a water insoluble or 'particulate' Cr(VI) compound, has been shown to be carcinogenic in epidemiology studies and to induce tumors in experimental animals, but its genotoxicity is poorly understood. Our study shows that zinc chromate induced concentration-dependent increases in cytotoxicity, chromosome damage and DNA double strand breaks in human lung cells. In response to zinc chromate-induced breaks, MRE11 expression was increased and ATM and ATR were phosphorylated, indicating that the DNA double strand break repair system was initiated in the cells. In addition, our data show that zinc chromate-induced double strand breaks were only observed in the G2/M phase population, with no significant amount of double strand breaks observed in G1 and S phase cells. These data will aid in understanding the mechanisms of zinc chromate toxicity and carcinogenesis.

  8. Double stranded nucleic acid biochips

    DOE Patents [OSTI]

    Chernov, Boris; Golova, Julia

    2006-05-23

    This invention describes a new method of constructing double-stranded DNA (dsDNA) microarrays based on the use of pre-synthesized or natural DNA duplexes without a stem-loop structure. The complementary oligonucleotide chains are bonded together by a novel connector that includes a linker for immobilization on a matrix. A non-enzymatic method for synthesizing double-stranded nucleic acids with this novel connector enables the construction of inexpensive and robust dsDNA/dsRNA microarrays. DNA-DNA and DNA-protein interactions are investigated using the microarrays.

  9. Double-stranded DNA organization in bacteriophage heads: An alternative toroid-based model

    SciTech Connect (OSTI)

    Hud, N.V.

    1995-10-01

    Studies of the organization of double-stranded DNA within bacteriophage heads during the past four decades have produced a wealth of data. However, despite the presentation of numerous models, the true organization of DNA within phage heads remains unresolved. The observations of toroidal DNA structures in electron micrographs of phage lysates have long been cited as support for the organization of DNA in a spool-like fashion. This particular model, like all other models, has not been found to be consistent with all available data. Recently, the authors proposed that DNA within toroidal condensates produced in vitro is organized in a manner significantly different from that suggested by the spool model. This new toroid model has allowed the development of an alternative model for DNA organization within bacteriophage heads that is consistent with a wide range of biophysical data. Here the authors propose that bacteriophage DNA is packaged in a toroid that is folded into a highly compact structure.

  10. The effect of a magnetic field on the spin-selective transport in double-stranded DNA

    SciTech Connect (OSTI)

    Simchi, Hamidreza; Esmaeilzadeh, Mahdi Mazidabadi, Hossein

    2014-05-28

    Spin-polarization in double-stranded DNA is studied in the presence of a magnetic field applied along its helix axis using the non-equilibrium Green's function method. The spin-polarization could be tuned by changing the magnetic field. In some special cases, the double-stranded DNA behaved as a perfect spin-filter. Furthermore, the dependency of the spin-polarization on the spin-orbit strength and dephasing strength is studied.

  11. Proximity-induced superconductivity effect in a double-stranded DNA

    SciTech Connect (OSTI)

    Simchi, Hamidreza; Esmaeilzadeh, Mahdi Mazidabadi, Hossein

    2014-02-07

    We study the proximity-induced superconductivity effect in a double-stranded DNA by solving the Bogoliubov-de Gennes equations and taking into account the effect of thermal fluctuations of the twist angle between neighboring base pairs. We show that the electron conductance is spin-dependent and the conductance of spin up (down) increases (decreases) due to the spin-orbit coupling (SOC). It is found that, for T < 100 K, the band gap energy is temperature-independent and it decreases due to the SOC. In addition, by solving the Bogoliubov-de Gennes equations and local gap parameter equation self-consistently, we find the critical temperature at which transition to superconductivity can take place.

  12. Probability of double-strand breaks in genome-sized DNA by {gamma}-ray decreases markedly as the DNA concentration increases

    SciTech Connect (OSTI)

    Shimobayashi, Shunsuke F.; Iwaki, Takafumi; Mori, Toshiaki; Yoshikawa, Kenichi

    2013-05-07

    By use of the single-molecule observation, we count the number of DNA double-strand breaks caused by {gamma}-ray irradiation with genome-sized DNA molecules (166 kbp). We find that P{sub 1}, the number of double-strand breaks (DSBs) per base pair per unit Gy, is nearly inversely proportional to the DNA concentration above a certain threshold DNA concentration. The inverse relationship implies that the total number of DSBs remains essentially constant. We give a theoretical interpretation of our experimental results in terms of attack of reactive species upon DNA molecules, indicating the significance of the characteristics of genome-sized giant DNA as semiflexible polymers for the efficiency of DSBs.

  13. Dyes designed for high sensitivity detection of double-stranded DNA

    DOE Patents [OSTI]

    Glazer, Alexander N.; Benson, Scott C.

    1998-01-01

    Novel fluorescent dyes are provided, characterized by having a fluorophore joined to a cationic chain. The dyes are found to provide for high enhancement upon binding to nucleic acid and have strong binding affinities to the nucleic acid, as compared to the fluorophore without the polycationic chain. The dyes find use in detection of dsDNA in gel electrophoresis and solution at substantially higher sensitivities using substantially less dye.

  14. Dyes designed for high sensitivity detection of double-stranded DNA

    DOE Patents [OSTI]

    Glazer, A.N.; Benson, S.C.

    1998-07-21

    Novel fluorescent dyes are provided, characterized by having a fluorophore joined to a cationic chain. The dyes are found to provide for high enhancement upon binding to nucleic acid and have strong binding affinities to the nucleic acid, as compared to the fluorophore without the polycationic chain. The dyes find use in detection of dsDNA in gel electrophoresis and solution at substantially higher sensitivities using substantially less dye. 10 figs.

  15. Dyes designed for high sensitivity detection of double-stranded DNA

    DOE Patents [OSTI]

    Glazer, Alexander N.; Benson, Scott C.

    2000-01-01

    Novel fluorescent dyes are provided, characterized by having a fluorophore joined to a cationic chain. The dyes are found to provide for high enhancement upon binding to nucleic acid and have strong binding affinities to the nucleic acid, as compared to the fluorophore without the polycationic chain. The dyes find use in detection of dsDNA in gel electrophoresis and solution at substantially higher sensitivities using substantially less dye.

  16. Dyes designed for high sensitivity detection of double-stranded DNA

    DOE Patents [OSTI]

    Glazer, Alexander N.; Benson, Scott C.

    1994-01-01

    Novel fluorescent dyes are provided, characterized by having a fluorophore joined to a polycationic chain of at least two positive charges. The dyes are found to provide for high enhancement upon binding to nucleic acid and have strong binding affinities to the nucleic acid, as compared to the fluorophore without the polycationic chain. The dyes find use in detection of dsDNA in gel electrophoresis and solution at substantially higher sensitivities using substantially less dye.

  17. Homologous recombination contributes to the repair of DNA double-strand breaks induced by high-energy iron ions

    SciTech Connect (OSTI)

    Zafar, Faria; Seidler, Sara B.; Kronenberg, Amy; Schild, David; Wiese, Claudia

    2010-06-29

    To test the contribution of homologous recombinational repair (HRR) in repairing DNA damaged sites induced by high-energy iron ions, we used: (1) HRR-deficient rodent cells carrying a deletion in the RAD51D gene and (2) syngeneic human cells impaired for HRR by RAD51D or RAD51 knockdown using RNA interference. We show that in response to iron ions, HRR contributes to cell survival in rodent cells, and that HRR-deficiency abrogates RAD51 foci formation. Complementation of the HRR defect by human RAD51D rescues both enhanced cytotoxicity and RAD51 foci formation. For human cells irradiated with iron ions, cell survival is decreased, and, in p53 mutant cells, the levels of mutagenesis are increased when HRR is impaired. Human cells synchronized in S phase exhibit more pronounced resistance to iron ions as compared with cells in G1 phase, and this increase in radioresistance is diminished by RAD51 knockdown. These results implicate a role for RAD51-mediated DNA repair (i.e. HRR) in removing a fraction of clustered lesions induced by charged particle irradiation. Our results are the first to directly show the requirement for an intact HRR pathway in human cells in ensuring DNA repair and cell survival in response to high-energy high LET radiation.

  18. Induction and Rejoining of DNA Double Strand Breaks Assessed by H2AX Phosphorylation in Melanoma Cells Irradiated with Proton and Lithium Beams

    SciTech Connect (OSTI)

    Ibanez, Irene L.; Bracalente, Candelaria; Molinari, Beatriz L.; Palmieri, Monica A.; Policastro, Lucia; Kreiner, Andres J.; Burlon, Alejandro A.; Valda, Alejandro; Navalesi, Daniela; Davidson, Jorge; Davidson, Miguel; Vazquez, Monica; Ozafran, Mabel; Duran, Hebe

    2009-07-15

    Purpose: The aim of this study was to evaluate the induction and rejoining of DNA double strand breaks (DSBs) in melanoma cells exposed to low and high linear energy transfer (LET) radiation. Methods and Materials: DSBs and survival were determined as a function of dose in melanoma cells (B16-F0) irradiated with monoenergetic proton and lithium beams and with a gamma source. Survival curves were obtained by clonogenic assay and fitted to the linear-quadratic model. DSBs were evaluated by the detection of phosphorylated histone H2AX ({gamma}H2AX) foci at 30 min and 6 h post-irradiation. Results: Survival curves showed the increasing effectiveness of radiation as a function of LET. {gamma}H2AX labeling showed an increase in the number of foci vs. dose for all the radiations evaluated. A decrease in the number of foci was found at 6 h post-irradiation for low LET radiation, revealing the repair capacity of DSBs. An increase in the size of {gamma}H2AX foci in cells irradiated with lithium beams was found, as compared with gamma and proton irradiations, which could be attributed to the clusters of DSBs induced by high LET radiation. Foci size increased at 6 h post-irradiation for lithium and proton irradiations in relation with persistent DSBs, showing a correlation with surviving fraction. Conclusions: Our results showed the response of B16-F0 cells to charged particle beams evaluated by the detection of {gamma}H2AX foci. We conclude that {gamma}H2AX foci size is an accurate parameter to correlate the rejoining of DSBs induced by different LET radiations and radiosensitivity.

  19. Defects in the kinetics of the repair of DNA double-strand breaks and inhibition of DNA synthesis in the ataxia telangiectasia AT5Bl-VA cell line: Comparison to a corrected hybrid, atxbc

    SciTech Connect (OSTI)

    Kysela, B.P.; Lohrer, H.; Arrand, J.E.

    1995-12-01

    The nature of the primary biochemical defect in the human radiosensitive and cancer-prone syndrome, ataxia telangiectasia (AT), has remained obscure despite many efforts to elucidate it. In this study, AT complementation group D cells and a nearly isogenic corrected AT-hamster hybrid derivative have been analyzed for induction and repair of initial double-strand breaks (DSBs) after exposure to ionizing radiation, using a sensitive field-inversion electrophoresis technique. Results suggesting that initial levels of damage are the same in these two cell types, but indicating differences in the fast component of DNA repair, have been compared and correlated with those resulting from a study of the radioresistant DNA synthesis defect and its correction in the same cell lines. These measurements show that the radioresistant phenotype of the substantially corrected AT-hamster hybrid correlates with its higher level of fast-component DSB repair and higher level of inhibition of DNA synthesis, but that the initial damage induction does not contribute to the phenotype. We propose that the AT gene product(s) is likely to act early in a signaling pathway which controls both DNA repair and progression of cells through the phases of the cell cycle in response to ionizing radiation. 36 refs., 3 figs., 2 tabs.

  20. MicroRNAs form triplexes with double stranded DNA at sequence-specific binding sites; a eukaryotic mechanism via which microRNAs could directly alter gene expression

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Paugh, Steven W.; Coss, David R.; Bao, Ju; Laudermilk, Lucas T.; Grace, Christy R.; Ferreira, Antonio M.; Waddell, M. Brett; Ridout, Granger; Naeve, Deanna; Leuze, Michael Rex; et al

    2016-02-04

    MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA). Recent studies indicate that microRNAs may also play a role in up-regulating mRNA transcription levels, although a definitive mechanism has not been established. Double-helical DNA is capable of forming triple-helical structures through Hoogsteen and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence that microRNAs form triple-helical structures with duplex DNA, and identify microRNA sequences that favor triplex formation. We developed an algorithm (Trident) to search genome-wide for potential triplex-forming sites and show thatmore » several mammalian and non-mammalian genomes are enriched for strong microRNA triplex binding sites. We show that those genes containing sequences favoring microRNA triplex formation are markedly enriched (3.3 fold, p<2.2 x 10-16) for genes whose expression is positively correlated with expression of microRNAs targeting triplex binding sequences. As a result, this work has thus revealed a new mechanism by which microRNAs can interact with gene promoter regions to modify gene transcription.« less

  1. Nonenzymatic Role for WRN in Preserving Nascent DNA Strands after Replication Stress

    SciTech Connect (OSTI)

    Su, Fengtao; Mukherjee, Shibani; Yang, Yanyong; Mori, Eiichiro; Bhattacharya, Souparno; Kobayashi, Junya; Yannone, Steven  M.; Chen, David  J.; Asaithamby, Aroumougame

    2014-11-20

    WRN, the protein defective in Werner syndrome (WS), is a multifunctional nuclease involved in DNA damage repair, replication, and genome stability maintenance. It was assumed that the nuclease activities of WRN were critical for these functions. Here, we report a nonenzymatic role for WRN in preserving nascent DNA strands following replication stress. We found that lack of WRN led to shortening of nascent DNA strands after replication stress. Furthermore, we discovered that the exonuclease activity of MRE11 was responsible for the shortening of newly replicated DNA in the absence of WRN. Mechanistically, the N-terminal FHA domain of NBS1 recruits WRN to replication-associated DNA double-stranded breaks to stabilize Rad51 and to limit the nuclease activity of its C-terminal binding partner MRE11. Thus, this previously unrecognized nonenzymatic function of WRN in the stabilization of nascent DNA strands sheds light on the molecular reason for the origin of genome instability in WS individuals.

  2. Solid phase sequencing of double-stranded nucleic acids

    DOE Patents [OSTI]

    Fu, Dong-Jing; Cantor, Charles R.; Koster, Hubert; Smith, Cassandra L.

    2002-01-01

    This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.

  3. Unidirectional Scaffold-Strand Arrangement in DNA Origami

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Unidirectional Scaffold-Strand Arrangement in DNA Origami Authors: Han, D., Jiang, S., Samanta, A., Liu, Y., and Yan, H. Title: Unidirectional Scaffold-Strand Arrangement in DNA Origami Source: Angewandte Chemie International Edition Year: 2013 Volume: 52 Pages: 9031-9034 ABSTRACT: Date of online publication: Sun, 2013-07-14 Link online: http://onlinelibrary.wiley.com/doi/10.1002/anie.201302177/suppinfo

  4. An intercalation-locked parallel-stranded DNA tetraplex

    SciTech Connect (OSTI)

    Tripathi, S.; Zhang, D.; Paukstelis, P. J.

    2015-01-27

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A base pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.

  5. An intercalation-locked parallel-stranded DNA tetraplex

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Tripathi, S.; Zhang, D.; Paukstelis, P. J.

    2015-01-27

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A base pairs betweenmore » adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

  6. Nonenzymatic Role for WRN in Preserving Nascent DNA Strands after Replication Stress

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Su, Fengtao; Mukherjee, Shibani; Yang, Yanyong; Mori, Eiichiro; Bhattacharya, Souparno; Kobayashi, Junya; Yannone, Steven  M.; Chen, David  J.; Asaithamby, Aroumougame

    2014-11-20

    WRN, the protein defective in Werner syndrome (WS), is a multifunctional nuclease involved in DNA damage repair, replication, and genome stability maintenance. It was assumed that the nuclease activities of WRN were critical for these functions. Here, we report a nonenzymatic role for WRN in preserving nascent DNA strands following replication stress. We found that lack of WRN led to shortening of nascent DNA strands after replication stress. Furthermore, we discovered that the exonuclease activity of MRE11 was responsible for the shortening of newly replicated DNA in the absence of WRN. Mechanistically, the N-terminal FHA domain of NBS1 recruits WRNmore » to replication-associated DNA double-stranded breaks to stabilize Rad51 and to limit the nuclease activity of its C-terminal binding partner MRE11. Thus, this previously unrecognized nonenzymatic function of WRN in the stabilization of nascent DNA strands sheds light on the molecular reason for the origin of genome instability in WS individuals.« less

  7. Synthesis of DNA

    DOE Patents [OSTI]

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  8. Method for producing labeled single-stranded nucleic acid probes

    DOE Patents [OSTI]

    Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

    1999-10-19

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  9. Method for nucleic acid hybridization using single-stranded DNA binding protein

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1996-01-01

    Method of nucleic acid hybridization for detecting the presence of a specific nucleic acid sequence in a population of different nucleic acid sequences using a nucleic acid probe. The nucleic acid probe hybridizes with the specific nucleic acid sequence but not with other nucleic acid sequences in the population. The method includes contacting a sample (potentially including the nucleic acid sequence) with the nucleic acid probe under hybridizing conditions in the presence of a single-stranded DNA binding protein provided in an amount which stimulates renaturation of a dilute solution (i.e., one in which the t.sub.1/2 of renaturation is longer than 3 weeks) of single-stranded DNA greater than 500 fold (i.e., to a t.sub.1/2 less than 60 min, preferably less than 5 min, and most preferably about 1 min.) in the absence of nucleotide triphosphates.

  10. Double-stranded RNA transcribed from vector-based oligodeoxynucleotide acts as transcription factor decoy

    SciTech Connect (OSTI)

    Xiao, Xiao; Gang, Yi; Wang, Honghong; Wang, Jiayin; Zhao, Lina; Xu, Li; Liu, Zhiguo

    2015-02-06

    Highlights: • A shRNA vector based transcription factor decoy, VB-ODN, was designed. • VB-ODN for NF-κB inhibited cell viability in HEK293 cells. • VB-ODN inhibited expression of downstream genes of target transcription factors. • VB-ODN may enhance nuclear entry ratio for its feasibility of virus production. - Abstract: In this study, we designed a short hairpin RNA vector-based oligodeoxynucleotide (VB-ODN) carrying transcription factor (TF) consensus sequence which could function as a decoy to block TF activity. Specifically, VB-ODN for Nuclear factor-κB (NF-κB) could inhibit cell viability and decrease downstream gene expression in HEK293 cells without affecting expression of NF-κB itself. The specific binding between VB-ODN produced double-stranded RNA and NF-κB was evidenced by electrophoretic mobility shift assay. Moreover, similar VB-ODNs designed for three other TFs also inhibit their downstream gene expression but not that of themselves. Our study provides a new design of decoy for blocking TF activity.

  11. Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens

    SciTech Connect (OSTI)

    Elfenbein, Johanna R.; Knodler, Leigh A.; Nakayasu, Ernesto S.; Ansong, Charles; Brewer, Heather M.; Bogomolnaya, Lydia; Adams, L. Garry; McClelland, Michael; Adkins, Joshua N.; Andrews-Polymenis, Helene L.; Fang, Ferric C.

    2015-09-14

    Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking its retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate, but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules.

  12. Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Elfenbein, Johanna R.; Knodler, Leigh A.; Nakayasu, Ernesto S.; Ansong, Charles; Brewer, Heather M.; Bogomolnaya, Lydia; Adams, L. Garry; McClelland, Michael; Adkins, Joshua N.; Andrews-Polymenis, Helene L.; et al

    2015-09-14

    Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking itsmore » retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate, but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules.« less

  13. Activation of double-stranded RNA-dependent protein kinase inhibits proliferation of pancreatic ?-cells

    SciTech Connect (OSTI)

    Chen, Shan-Shan [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China) [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China); Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing (China); Jiang, Teng [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China)] [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China); Wang, Yi; Gu, Li-Ze [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China) [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China); Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing (China); Wu, Hui-Wen [Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing (China)] [Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing (China); Tan, Lan [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China)] [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China); Guo, Jun, E-mail: Guoj@njmu.edu.cn [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China) [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China); Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing (China)

    2014-01-17

    Highlights: PKR can be activated by glucolipitoxicity and pro-inflammatory cytokines in ?-cells. Activated PKR inhibited ?-cell proliferation by arresting cell cycle at G1 phase. Activated PKR fully abrogated the pro-proliferative effects of IGF-I on ?-cells. -- Abstract: Double-stranded RNA-dependent protein kinase (PKR) is revealed to participate in the development of insulin resistance in peripheral tissues in type 2 diabetes (T2DM). Meanwhile, PKR is also characterized as a critical regulator of cell proliferation. To date, no study has focused on the impact of PKR on the proliferation of pancreatic ?-cells. Here, we adopted insulinoma cell lines and mice islet ?-cells to investigate: (1) the effects of glucolipotoxicity and pro-inflammatory cytokines on PKR activation; (2) the effects of PKR on proliferation of pancreatic ?-cells and its underlying mechanisms; (3) the actions of PKR on pro-proliferative effects of IGF-I and its underlying pathway. Our results provided the first evidence that PKR can be activated by glucolipitoxicity and pro-inflammatory cytokines in pancreatic ?-cells, and activated PKR significantly inhibited cell proliferation by arresting cell cycle at G1 phase. Reductions in cyclin D1 and D2 as well as increases in p27 and p53 were associated with the anti-proliferative effects of PKR, and proteasome-dependent degradation took part in the reduction of cyclin D1 and D2. Besides, PKR activation abrogated the pro-proliferative effects of IGF-I by activating JNK and disrupting IRS1/PI3K/Akt signaling pathway. These findings indicate that the anti-proliferative actions of PKR on pancreatic ?-cells may contribute to the pathogenesis of T2DM.

  14. Method for assaying clustered DNA damages

    DOE Patents [OSTI]

    Sutherland, Betsy M.

    2004-09-07

    Disclosed is a method for detecting and quantifying clustered damages in DNA. In this method, a first aliquot of the DNA to be tested for clustered damages with one or more lesion-specific cleaving reagents under conditions appropriate for cleavage of the DNA to produce single-strand nicks in the DNA at sites of damage lesions. The number average molecular length (Ln) of double stranded DNA is then quantitatively determined for the treated DNA. The number average molecular length (Ln) of double stranded DNA is also quantitatively determined for a second, untreated aliquot of the DNA. The frequency of clustered damages (.PHI..sub.c) in the DNA is then calculated.

  15. Synthesis of DNA (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Synthesis of DNA Citation Details In-Document Search Title: Synthesis of DNA A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined...

  16. Mutations Abrogating VP35 Interaction with Double-Stranded RNA Render Ebola Virus Avirulent in Guinea Pigs

    SciTech Connect (OSTI)

    Prins, Kathleen C.; Delpeut, Sebastien; Leung, Daisy W.; Reynard, Olivier; Volchkova, Valentina A.; Reid, St. Patrick; Ramanan, Parameshwaran; Cárdenas, Washington B.; Amarasinghe, Gaya K.; Volchkov, Viktor E.; Basler, Christopher F.

    2010-10-11

    Ebola virus (EBOV) protein VP35 is a double-stranded RNA (dsRNA) binding inhibitor of host interferon (IFN)-{alpha}/{beta} responses that also functions as a viral polymerase cofactor. Recent structural studies identified key features, including a central basic patch, required for VP35 dsRNA binding activity. To address the functional significance of these VP35 structural features for EBOV replication and pathogenesis, two point mutations, K319A/R322A, that abrogate VP35 dsRNA binding activity and severely impair its suppression of IFN-{alpha}/{beta} production were identified. Solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography reveal minimal structural perturbations in the K319A/R322A VP35 double mutant and suggest that loss of basic charge leads to altered function. Recombinant EBOVs encoding the mutant VP35 exhibit, relative to wild-type VP35 viruses, minimal growth attenuation in IFN-defective Vero cells but severe impairment in IFN-competent cells. In guinea pigs, the VP35 mutant virus revealed a complete loss of virulence. Strikingly, the VP35 mutant virus effectively immunized animals against subsequent wild-type EBOV challenge. These in vivo studies, using recombinant EBOV viruses, combined with the accompanying biochemical and structural analyses directly correlate VP35 dsRNA binding and IFN inhibition functions with viral pathogenesis. Moreover, these studies provide a framework for the development of antivirals targeting this critical EBOV virulence factor.

  17. DNA purification by triplex-affinity capture and affinity capture electrophoresis

    DOE Patents [OSTI]

    Cantor, Charles R.; Ito, Takashi; Smith, Cassandra L.

    1996-01-01

    The invention provides a method for purifying or isolating double stranded DNA intact using triple helix formation. The method includes the steps of complexing an oligonucleotide and double stranded DNA to generate a triple helix and immobilization of the triple helix on a solid phase by means of a molecular recognition system such as avidin/biotin. The purified DNA is then recovered intact by treating the solid phase with a reagent that breaks the bonds between the oligonucleotide and the intact double stranded DNA while not affecting the Watson-Crick base pairs of the double helix. The present invention also provides a method for purifying or isolating double stranded DNA intact by complexing the double stranded DNA with a specific binding partner and recovering the complex during electrophoresis by immobilizing it on a solid phase trap imbedded in an electrophoretic gel.

  18. DNA purification by triplex-affinity capture and affinity capture electrophoresis

    DOE Patents [OSTI]

    Cantor, C.R.; Ito, Takashi; Smith, C.L.

    1996-01-09

    The invention provides a method for purifying or isolating double stranded DNA intact using triple helix formation. The method includes the steps of complexing an oligonucleotide and double stranded DNA to generate a triple helix and immobilization of the triple helix on a solid phase by means of a molecular recognition system such as avidin/biotin. The purified DNA is then recovered intact by treating the solid phase with a reagent that breaks the bonds between the oligonucleotide and the intact double stranded DNA while not affecting the Watson-Crick base pairs of the double helix. The present invention also provides a method for purifying or isolating double stranded DNA intact by complexing the double stranded DNA with a specific binding partner and recovering the complex during electrophoresis by immobilizing it on a solid phase trap imbedded in an electrophoretic gel. 6 figs.

  19. Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

    DOE Patents [OSTI]

    Soares, Marcelo Bento; Bonaldo, Maria de Fatima

    1998-01-01

    This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods.

  20. Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

    DOE Patents [OSTI]

    Soares, M.B.; Fatima Bonaldo, M. de

    1998-12-08

    This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods. 25 figs.

  1. Transient oxidative stress and inflammation after intraperitoneal administration of multiwalled carbon nanotubes functionalized with single strand DNA in rats

    SciTech Connect (OSTI)

    Clichici, Simona; Biris, Alexandru Radu; Tabaran, Flaviu; Filip, Adriana

    2012-03-15

    Multi-walled carbon nanotubes (MWCNTs) are widely used for nanotechnology. Their impact on living organisms is, however, not entirely clarified. Oxidative stress and inflammation seem to be the key mechanisms involved in MWCNTs' cytotoxicity. Until present, pulmonary and skin models were the main tested experimental designs to assess carbon nanotubes' toxicity. The systemic administration of MWCNTs is essential, with respect for future medical applications. Our research is performed on Wistar rats and is focused on the dynamics of oxidative stress parameters in blood and liver and pro-inflammatory cytokines in liver, after single dose (270 mg l{sup −1}) ip administration of MWCNTs (exterior diameter 15–25 nm, interior diameter 10–15 nm, surface 88 m{sup 2} g{sup −1}) functionalized with single strand DNA (ss-DNA). The presence of MWCNTs in blood was assessed by Raman spectroscopy, while in liver histological examination and confocal microscopy were used. It was found that ss-DNA-MWCNTs induce oxidative stress in plasma and liver, with the return of the tested parameters to normal values, 6 h after ip injection of nanotubes, with the exception of reduced glutathione in plasma. The inflammatory cytokines (TNF-α, IL-1β) had a similar pattern of evolution. We also assessed the level of ERK1/2 and the phosphorylation of p65 subunit of NF-kB in liver that had a transient increase and returned to normal at the end of the tested period. Our results demonstrate that ss-DNA-MWCNTs produce oxidative stress and inflammation, but with a transient pattern. Given the fact that antioxidants modify the profile not only for oxidative stress, but also of inflammation, the dynamics of these alterations may be of practical importance for future protective strategies. -- Highlights: ► ss-DNA-MWCNTs ip administration induce oxidative stress in plasma and liver. ► ss-DNA-MWCNTs ip administration determine liver inflammation. ► ERK1/2 and p65 phosphorylated NF-KB increase

  2. Chemical repair of base lesions, AP-sites, and strand breaks on plasmid DNA in dilute aqueous solution by ascorbic acid

    SciTech Connect (OSTI)

    Hata, Kuniki; Advanced Science Research Center, Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-mura, Naka-gun, Ibaraki 319-1195 ; Urushibara, Ayumi; Yamashita, Shinichi; Shikazono, Naoya; Yokoya, Akinari; Katsumura, Yosuke; Nuclear Professional School, School of Engineering, The University of Tokyo, 2-22 Shirakatashirane, Tokai-mura, Naka-gun, Ibaraki 319-1188

    2013-05-03

    Highlights: We report a novel mechanism of radiation protection of DNA by chemical activity of ascorbic acid. The chemical repair of DNA damage was revealed using biochemical assay and chemical kinetics analysis. We found that ascorbic acid significantly repairs precursors of nucleobase lesions and abasic sites. However, ascorbic acid seldom repairs precursors of DNA-strand breaks. -- Abstract: We quantified the damage yields produced in plasmid DNA by ?-irradiation in the presence of low concentrations (10100 ?M) of ascorbic acid, which is a major antioxidant in living systems, to clarify whether it chemically repairs radiation damage in DNA. The yield of DNA single strand breaks induced by irradiation was analyzed with agarose gel electrophoresis as conformational changes in closed circular plasmids. Base lesions and abasic sites were also observed as additional conformational changes by treating irradiated samples with glycosylase proteins. By comparing the suppression efficiencies to the induction of each DNA lesion, in addition to scavenging of the OH radicals derived from water radiolysis, it was found that ascorbic acid promotes the chemical repair of precursors of AP-sites and base lesions more effectively than those of single strand breaks. We estimated the efficiency of the chemical repair of each lesion using a kinetic model. Approximately 5060% of base lesions and AP-sites were repaired by 10 ?M ascorbic acid, although strand breaks were largely unrepaired by ascorbic acid at low concentrations. The methods in this study will provide a route to understanding the mechanistic aspects of antioxidant activity in living systems.

  3. Flow cytomeric measurement of DNA and incorporated nucleoside analogs

    DOE Patents [OSTI]

    Dolbeare, Frank A.; Gray, Joe W.

    1989-01-01

    A method is provided for simultaneously measuring total cellular DNA and incorporated nucleoside analog. The method entails altering the cellular DNA of cells grown in the presence of a nucleoside analog so that single stranded and double stranded portions are present. Separate stains are used against the two portions. An immunochemical stain is used against the single stranded portion to provide a measure of incorporated nucleoside analog, and a double strand DNA-specific stain is used against the double stranded portion to simultaneously provide a measure of total cellular DNA. The method permits rapid flow cytometric analysis of cell populations, rapid identification of cycling and noncycling subpopulations, and determination of the efficacy of S phase cytotoxic anticancer agents.

  4. Segregation of DNA polynucleotide strands into sister chromatids and the use of endoreduplicated cells to track sister chromatid exchanges induced by crosslinks, alkylations, or x-ray damage

    SciTech Connect (OSTI)

    Wolff, S.; Afzal, V.

    1996-06-11

    The method of Matsumoto and Ohta to induce large numbers of endoreduplicated Chinese hamster ovary cells has now been coupled with the fluorescence-plus-Giemsa method of Perry and Wolff to produce harlequin endoreduplicated chromosomes that after the third round of DNA replication are composed of a chromosome with a light chromatid and a dark chromatid in close apposition to its sister chromosome containing two light chromatids. Unless the pattern is disrupted by sister chromatid exchange (SCE), the dark chromatid is always in the center, so that the order of the chromatids is light-dark light-light. The advent of this method, which permits the observation of SCEs in endoreduplicated cells, makes it possible to determine with great ease in which cell cycle an SCE occurred. This now allows us to approach several vexing questions about the induction of SCEs (genetic damage and its repair) after exposure to various types of mutagenic carcinogens. The present experiments have allowed observation of how many cell cycles various types of lesions that are induced in DNA by a crosslinking agent, an alkylating agent, or ionizing radiation, and that are responsible for the induction of SCEs, persist before being repaired and thus lose their ability to inflict genetic damage. Other experiments with various types of mutagenic carcinogens and various types of cell lines that have defects in different DNA repair processes, such as mismatch repair, excision repair, crosslink repair, and DNA-strand-break repair, can now be carried out to determine the role of these types of repair in removing specific types of lesions. 22 refs., 3 figs., 1 tab.

  5. Dna Sequencing

    DOE Patents [OSTI]

    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.

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

    DOE Patents [OSTI]

    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.

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

    DOE Patents [OSTI]

    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.

  8. Protective effects of pulmonary epithelial lining fluid on oxidative stress and DNA single-strand breaks caused by ultrafine carbon black, ferrous sulphate and organic extract of diesel exhaust particles

    SciTech Connect (OSTI)

    Chuang, Hsiao-Chi; Cheng, Yi-Ling; Lei, Yu-Chen; Chang, Hui-Hsien; Cheng, Tsun-Jen

    2013-02-01

    Pulmonary epithelial lining fluid (ELF) is the first substance to make contact with inhaled particulate matter (PM) and interacts chemically with PM components. The objective of this study was to determine the role of ELF in oxidative stress, DNA damage and the production of proinflammatory cytokines following physicochemical exposure to PM. Ultrafine carbon black (ufCB, 15 nm; a model carbonaceous core), ferrous sulphate (FeSO{sub 4}; a model transition metal) and a diesel exhaust particle (DEP) extract (a model organic compound) were used to examine the acellular oxidative potential of synthetic ELF and non-ELF systems. We compared the effects of exposure to ufCB, FeSO{sub 4} and DEP extract on human alveolar epithelial Type II (A549) cells to determine the levels of oxidative stress, DNA single-strand breaks and interleukin-8 (IL-8) production in ELF and non-ELF systems. The effects of ufCB and FeSO{sub 4} on the acellular oxidative potential, cellular oxidative stress and DNA single-strand breakage were mitigated significantly by the addition of ELF, whereas there was no decrease following treatment with the DEP extract. There was no significant effect on IL-8 production following exposure to samples that were suspended in ELF/non-ELF systems. The results of the present study indicate that ELF plays an important role in the initial defence against PM in the pulmonary environment. Experimental components, such as ufCB and FeSO{sub 4}, induced the production of oxidative stress and led to DNA single-strand breaks, which were moderately prevented by the addition of ELF. These findings suggest that ELF plays a protective role against PM-driven oxidative stress and DNA damage. -- Highlights: ► To determine the role of ELF in ROS, DNA damage and IL-8 after exposure to PM. ► ufCB, FeSO{sub 4} and DEP extract were used to examine the protective effects of ELF. ► PM-driven oxidative stress and DNA single-strand breakage were mitigated by ELF. ► The findings

  9. Derivatized versions of ligase enzymes for constructing DNA sequences

    DOE Patents [OSTI]

    Mariella, Jr., Raymond P.; Christian, Allen T.; Tucker, James D.; Dzenitis, John M.; Papavasiliou, Alexandros P.

    2006-08-15

    A method of making very long, double-stranded synthetic poly-nucleotides. A multiplicity of short oligonucleotides is provided. The short oligonucleotides are sequentially hybridized to each other. Enzymatic ligation of the oligonucleotides provides a contiguous piece of PCR-ready DNA of predetermined sequence.

  10. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA Duplication Revealed in New Beginnings DNA Duplication Revealed in New Beginnings April 3, 2012 - 9:36am Addthis The DNA replication origin recognition complex (ORC) is a six-protein machine with a slightly twisted half-ring structure (yellow). ORC is proposed to wrap around and bend approximately 70 base pairs of double stranded DNA (red and blue). When a replication initiator Cdc6 (green) joins ORC, the partial ring is now complete and ready to load another protein onto the DNA. This last

  11. DNA Duplication Revealed in New Beginnings | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    DNA Duplication Revealed in New Beginnings DNA Duplication Revealed in New Beginnings April 3, 2012 - 9:36am Addthis The DNA replication origin recognition complex (ORC) is a six-protein machine with a slightly twisted half-ring structure (yellow). ORC is proposed to wrap around and bend approximately 70 base pairs of double stranded DNA (red and blue). When a replication initiator Cdc6 (green) joins ORC, the partial ring is now complete and ready to load another protein onto the DNA. This last

  12. Photochemistry of psoralen-DNA adducts, biological effects of psoralen-DNA adducts, applications of psoralen-DNA photochemistry

    SciTech Connect (OSTI)

    Shi, Yun-bo

    1988-03-01

    This thesis consists of three main parts and totally eight chapters. In Part I, The author will present studies on the photochemistry of psoralen-DNA adducts, specifically, the wavelength dependencies for the photoreversals of thymidine-HMT (4'-hydroxymethyl-4, 5', 8-trimenthylpsoralen) monoadducts and diadduct and the same adducts incorporated in DNA helices and the wavelength dependecies for the photocrossslinking of thymidine-HMT monoadducts in double-stranded helices. In Part II, The author will report some biological effects of psoralen-DNA adducts, i.e., the effects on double-stranded DNA stability, DNA structure, and transcription by E. coli and T7 RNA polymerases. Finally, The author will focus on the applications of psoralen-DNA photochemistry to investigation of protein-DNA interaction during transcription, which includes the interaction of E. coli and T7 RNA polymerases with DNA in elongation complexes arrested at specific psoralen-DNA adduct sites as revealed by DNase I footprinting experiments. 123 refs., 52 figs., 12 tabs.

  13. Probe and method for DNA detection

    DOE Patents [OSTI]

    Yeh, Hsin-Chih; Werner, James Henry; Sharma, Jaswinder Kumar; Martinez, Jennifer Suzanne

    2013-07-02

    A hybridization probe containing two linear strands of DNA lights up upon hybridization to a target DNA using silver nanoclusters that have been templated onto one of the DNA strands. Hybridization induces proximity between the nanoclusters on one strand and an overhang on the other strand, which results in enhanced fluorescence emission from the nanoclusters.

  14. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing ...

  15. Electrophoretic detection and separation of mutant DNA using replaceable polymer matrices

    DOE Patents [OSTI]

    Karger, Barry L.; Thilly, William G.; Foret, Frantisek; Khrapko, Konstaintin; Koehavong, Phouthone; Cohen, Aharon S.; Giese, Roger W.

    1997-01-01

    The disclosure relates to a method for resolving double-stranded DNA species differing by at least one base pair. Each of the species is characterized by an iso-melting domain with a unique melting temperature contiguous with a melting domain of higher thermal stability.

  16. Electrophoretic detection and separation of mutant DNA using replaceable polymer matrices

    DOE Patents [OSTI]

    Karger, B.L.; Thilly, W.G.; Foret, F.; Khrapko, K.; Koehavong, P.; Cohen, A.S.; Giese, R.W.

    1997-05-27

    The disclosure relates to a method for resolving double-stranded DNA species differing by at least one base pair. Each of the species is characterized by an iso-melting domain with a unique melting temperature contiguous with a melting domain of higher thermal stability. 18 figs.

  17. DUPLEX: A molecular mechanics program in torsion angle space for computing structures of DNA and RNA

    SciTech Connect (OSTI)

    Hingerty, B.E.

    1992-07-01

    DUPLEX produces energy minimized structures of DNA and RNA of any base sequence for single and double strands. The smallest subunits are deoxydinucleoside monophosphates, and up to 12 residues, single or double stranded can be treated. In addition, it can incorporate NMR derived interproton distances an constraints in the minimizations. Both upper and lower bounds for these distances can be specified. The program has been designed to run on a UNICOS Cray supercomputer, but should run, albeit slowly, on a laboratory computer such as a VAX or a workstation.

  18. Phosphoramide mustard exposure induces DNA adduct formation and the DNA damage repair response in rat ovarian granulosa cells

    SciTech Connect (OSTI)

    Ganesan, Shanthi Keating, Aileen F.

    2015-02-01

    Phosphoramide mustard (PM), the ovotoxic metabolite of the anti-cancer agent cyclophosphamide (CPA), destroys rapidly dividing cells by forming NOR-G-OH, NOR-G and G-NOR-G adducts with DNA, potentially leading to DNA damage. A previous study demonstrated that PM induces ovarian DNA damage in rat ovaries. To investigate whether PM induces DNA adduct formation, DNA damage and induction of the DNA repair response, rat spontaneously immortalized granulosa cells (SIGCs) were treated with vehicle control (1% DMSO) or PM (3 or 6 μM) for 24 or 48 h. Cell viability was reduced (P < 0.05) after 48 h of exposure to 3 or 6 μM PM. The NOR-G-OH DNA adduct was detected after 24 h of 6 μM PM exposure, while the more cytotoxic G-NOR-G DNA adduct was formed after 48 h by exposure to both PM concentrations. Phosphorylated H2AX (γH2AX), a marker of DNA double stranded break occurrence, was also increased by PM exposure, coincident with DNA adduct formation. Additionally, induction of genes (Atm, Parp1, Prkdc, Xrcc6, and Brca1) and proteins (ATM, γH2AX, PARP-1, PRKDC, XRCC6, and BRCA1) involved in DNA repair were observed in both a time- and dose-dependent manner. These data support that PM induces DNA adduct formation in ovarian granulosa cells, induces DNA damage and elicits the ovarian DNA repair response. - Highlights: • PM forms ovarian DNA adducts. • DNA damage marker γH2AX increased by PM exposure. • PM induces ovarian DNA double strand break repair.

  19. An improved DNA force field for ssDNA interactions with gold nanoparticles

    SciTech Connect (OSTI)

    Jiang, Xiankai; Huai, Ping; Fan, Chunhai; Song, Bo E-mail: bosong@sinap.ac.cn; Gao, Jun; Huynh, Tien; Zhou, Ruhong E-mail: bosong@sinap.ac.cn

    2014-06-21

    The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones protecting hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the protection by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

  20. Patterning nanocrystals using DNA

    SciTech Connect (OSTI)

    Williams, Shara Carol

    2003-09-01

    One of the goals of nanotechnology is to enable programmed self-assembly of patterns made of various materials with nanometer-sized control. This dissertation describes the results of experiments templating arrangements of gold and semiconductor nanocrystals using 2'-deoxyribonucleic acid (DNA). Previously, simple DNA-templated linear arrangements of two and three nanocrystals structures have been made.[1] Here, we have sought to assemble larger and more complex nanostructures. Gold-DNA conjugates with 50 to 100 bases self-assembled into planned arrangements using strands of DNA containing complementary base sequences. We used two methods to increase the complexity of the arrangements: using branched synthetic doublers within the DNA covalent backbone to create discrete nanocrystal groupings, and incorporating the nanocrystals into a previously developed DNA lattice structure [2][3] that self-assembles from tiles made of DNA double-crossover molecules to create ordered nanoparticle arrays. In the first project, the introduction of a covalently-branched synthetic doubler reagent into the backbone of DNA strands created a branched DNA ''trimer.'' This DNA trimer templated various structures that contained groupings of three and four gold nanoparticles, giving promising, but inconclusive transmission electron microscopy (TEM) results. Due to the presence of a variety of possible structures in the reaction mixtures, and due to the difficulty of isolating the desired structures, the TEM and gel electrophoresis results for larger structures having four particles, and for structures containing both 5 and 10 nm gold nanoparticles were inconclusive. Better results may come from using optical detection methods, or from improved sample preparation. In the second project, we worked toward making two-dimensional ordered arrays of nanocrystals. We replicated and improved upon previous results for making DNA lattices, increasing the size of the lattices to a length greater than

  1. Plasma induced DNA damage: Comparison with the effects of ionizing radiation

    SciTech Connect (OSTI)

    Lazovi?, S.; Maleti?, D.; Pua?, N.; Malovi?, G.; Petrovi?, Z. Lj.; Leskovac, A.; Filipovi?, J.; Joksi?, G.

    2014-09-22

    We use human primary fibroblasts for comparing plasma and gamma rays induced DNA damage. In both cases, DNA strand breaks occur, but of fundamentally different nature. Unlike gamma exposure, contact with plasma predominantly leads to single strand breaks and base-damages, while double strand breaks are mainly consequence of the cell repair mechanisms. Different cell signaling mechanisms are detected confirming this (ataxia telangiectasia mutated - ATM and ataxia telangiectasia and Rad3 related - ATR, respectively). The effective plasma doses can be tuned to match the typical therapeutic doses of 2?Gy. Tailoring the effective dose through plasma power and duration of the treatment enables safety precautions mainly by inducing apoptosis and consequently reduced frequency of micronuclei.

  2. DNA Sequencing Using capillary Electrophoresis

    SciTech Connect (OSTI)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  3. DNA damage in cells exhibiting radiation-induced genomic instability

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Keszenman, Deborah J.; Kolodiuk, Lucia; Baulch, Janet E.

    2015-02-22

    Cells exhibiting radiation induced genomic instability exhibit varied spectra of genetic and chromosomal aberrations. Even so, oxidative stress remains a common theme in the initiation and/or perpetuation of this phenomenon. Isolated oxidatively modified bases, abasic sites, DNA single strand breaks and clustered DNA damage are induced in normal mammalian cultured cells and tissues due to endogenous reactive oxygen species generated during normal cellular metabolism in an aerobic environment. While sparse DNA damage may be easily repaired, clustered DNA damage may lead to persistent cytotoxic or mutagenic events that can lead to genomic instability. In this study, we tested the hypothesismore » that DNA damage signatures characterised by altered levels of endogenous, potentially mutagenic, types of DNA damage and chromosomal breakage are related to radiation-induced genomic instability and persistent oxidative stress phenotypes observed in the chromosomally unstable progeny of irradiated cells. The measurement of oxypurine, oxypyrimidine and abasic site endogenous DNA damage showed differences in non-double-strand breaks (DSB) clusters among the three of the four unstable clones evaluated as compared to genomically stable clones and the parental cell line. These three unstable clones also had increased levels of DSB clusters. The results of this study demonstrate that each unstable cell line has a unique spectrum of persistent damage and lead us to speculate that alterations in DNA damage signaling and repair may be related to the perpetuation of genomic instability.« less

  4. DNA damage in cells exhibiting radiation-induced genomic instability

    SciTech Connect (OSTI)

    Keszenman, Deborah J.; Kolodiuk, Lucia; Baulch, Janet E.

    2015-02-22

    Cells exhibiting radiation induced genomic instability exhibit varied spectra of genetic and chromosomal aberrations. Even so, oxidative stress remains a common theme in the initiation and/or perpetuation of this phenomenon. Isolated oxidatively modified bases, abasic sites, DNA single strand breaks and clustered DNA damage are induced in normal mammalian cultured cells and tissues due to endogenous reactive oxygen species generated during normal cellular metabolism in an aerobic environment. While sparse DNA damage may be easily repaired, clustered DNA damage may lead to persistent cytotoxic or mutagenic events that can lead to genomic instability. In this study, we tested the hypothesis that DNA damage signatures characterised by altered levels of endogenous, potentially mutagenic, types of DNA damage and chromosomal breakage are related to radiation-induced genomic instability and persistent oxidative stress phenotypes observed in the chromosomally unstable progeny of irradiated cells. The measurement of oxypurine, oxypyrimidine and abasic site endogenous DNA damage showed differences in non-double-strand breaks (DSB) clusters among the three of the four unstable clones evaluated as compared to genomically stable clones and the parental cell line. These three unstable clones also had increased levels of DSB clusters. The results of this study demonstrate that each unstable cell line has a unique spectrum of persistent damage and lead us to speculate that alterations in DNA damage signaling and repair may be related to the perpetuation of genomic instability.

  5. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1997-06-10

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3{prime} noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. 4 figs.

  6. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B.; Efstratiadis, Argiris

    1997-01-01

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library.

  7. DNA

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    drives achievement in protein structure research September 15, 2014 Computational analysis key to structural understanding of molecular machine that targets viral DNA LOS ALAMOS, N.M., Sept. 15, 2014-When this week's print issue of the journal Science comes out, a collective cheer will go up from New Mexico, Montana and even the Netherlands, thanks to the type of collaborative effort that is more and more the norm in these connected times. Yes, the research was brilliant, and if we're lucky, it

  8. DNA polymorphism identity determination using flow cytometry

    DOE Patents [OSTI]

    Nolan, John P.; White, P. Scott; Cai, Hong

    2001-01-01

    DNA polymorphism identity determination using flow cytometry. Primers designed to be immobilized on microspheres are allowed to anneal to the DNA strand under investigation, and are extended by either DNA polymerase using fluorescent dideoxynucleotides or ligated by DNA ligase to fluorescent reporter oligonucleotides. The fluorescence of either the dideoxynucleotide or the reporter oligonucleotide attached to the immobilized primer is measured by flow cytometry, thereby identifying the nucleotide polymorphism on the DNA strand.

  9. Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair

    SciTech Connect (OSTI)

    Du, Fengxia; Zhang, Minjie; Li, Xiaohua; Yang, Caiyun; Meng, Hao; Wang, Dong; Chang, Shuang; Xu, Ye; Price, Brendan; Sun, Yingli

    2014-10-03

    Highlights: • ATM phosphorylates the opposite strand of the dimer in response to DNA damage. • The PETPVFRLT box of ATM plays a key role in its dimer dissociation in DNA repair. • The dephosphorylation of ATM is critical for dimer re-formation after DNA repair. - Abstract: The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair.

  10. Binary electrokinetic separation of target DNA from background DNA primers.

    SciTech Connect (OSTI)

    James, Conrad D.; Derzon, Mark Steven

    2005-10-01

    This report contains the summary of LDRD project 91312, titled ''Binary Electrokinetic Separation of Target DNA from Background DNA Primers''. This work is the first product of a collaboration with Columbia University and the Northeast BioDefense Center of Excellence. In conjunction with Ian Lipkin's lab, we are developing a technique to reduce false positive events, due to the detection of unhybridized reporter molecules, in a sensitive and multiplexed detection scheme for nucleic acids developed by the Lipkin lab. This is the most significant problem in the operation of their capability. As they are developing the tools for rapidly detecting the entire panel of hemorrhagic fevers this technology will immediately serve an important national need. The goal of this work was to attempt to separate nucleic acid from a preprocessed sample. We demonstrated the preconcentration of kilobase-pair length double-stranded DNA targets, and observed little preconcentration of 60 base-pair length single-stranded DNA probes. These objectives were accomplished in microdevice formats that are compatible with larger detection systems for sample pre-processing. Combined with Columbia's expertise, this technology would enable a unique, fast, and potentially compact method for detecting/identifying genetically-modified organisms and multiplexed rapid nucleic acid identification. Another competing approach is the DARPA funded IRIS Pharmaceutical TIGER platform which requires many hours for operation, and an 800k$ piece of equipment that fills a room. The Columbia/SNL system could provide a result in 30 minutes, at the cost of a few thousand dollars for the platform, and would be the size of a shoebox or smaller.

  11. Double hull grounding experiments

    SciTech Connect (OSTI)

    Rodd, J.L.; Sikora, J.P.

    1995-12-31

    In the last few years the public and governments of many nations have become increasingly aware of the need for improving oil tanker safety. The requirements for double hull tankers are an attempt to address this need through legislation. Even though a number of investigations on the mechanics of collisions have been done in the past, until recently very little research supported the development of structural improvements to reduce oil tanker damage during grounding and stranding accidents. An aggressive evaluation of double hull tanker crashworthiness in stranding and grounding accidents is underway at CD/NSWC (formerly the David Taylor Research Center). The ability to predict damage from grounding accidents accurately is not currently available. The objective of this paper is to present qualitatively the structural failure mechanisms associated with stranding and grounding events for candidate double hull tanker structures and to present some simple methods for comparing damage scenarios. A comparison of the structural performance of key features in several very different designs will provide useful information toward this understanding.

  12. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    SciTech Connect (OSTI)

    Snodin, Benedict E. K. Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; ulc, Petr; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.

    2015-06-21

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  13. Applications of Strand-Specific in situ Hybridization

    SciTech Connect (OSTI)

    Goodwin, E.H.; Meyne, J.; Bailey, S.M.; Quigley, D.; Smith, L.; Tennyson, R.

    1997-01-01

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Fluorescence in situ hybridization (FISH) is used to determine the location of specific DNA sequences on chromosomes. It is an effective tool in genomic mapping and is finding increasing use in medical diagnosis. A ''strand-specific'' version of FISH has been developed in the Life Sciences Division of LANL. The new procedure, named CO-FISH, reveals not only location but also the 5'-to-3'direction of a target sequence, such as the sense strand of a gene. This project was designed to investigate applications of the new technique. Strand-specific FISH was found to be useful and informative for genomic mapping of repetitive DNA sequences. The method provide a valuable new tool for investigating the mechanisms of aneuploidy inducing agents and the cytogenetic phenomena called lateral asymmetry. Finally, using strand-specific FISH, the authors were able to detect certain types of chromosome aberrations (isochromosomes, inversions and Robertsonian translocations) that can be difficult to observe with standard techniques.

  14. Using DNA to Build Nanomaterials

    DOE R&D Accomplishments [OSTI]

    Walsh, Karen McNulty

    2011-05-09

    Scientists use complementary strands of synthetic DNA to build functional materials from the bottom up. Future applications include biosensors, optical nano-devices, and new kinds of solar cells.

  15. Radiation-Induced Upregulation of Gene Expression From Adenoviral Vectors Mediated by DNA Damage Repair and Regulation

    SciTech Connect (OSTI)

    Nokisalmi, Petri; Rajecki, Maria; Pesonen, Sari; Escutenaire, Sophie; Soliymani, Rabah; Tenhunen, Mikko; Ahtiainen, Laura; Hemminki, Akseli

    2012-05-01

    Purpose: In the present study, we evaluated the combination of replication-deficient adenoviruses and radiotherapy in vitro. The purpose of the present study was to analyze the mechanism of radiation-mediated upregulation of adenoviral transgene expression. Methods and Materials: Adenoviral transgene expression (luciferase or green fluorescent protein) was studied with and without radiation in three cell lines: breast cancer M4A4-LM3, prostate cancer PC-3MM2, and lung cancer LNM35/enhanced green fluorescent protein. The effect of the radiation dose, modification of the viral capsid, and five different transgene promoters were studied. The cellular responses were studied using mass spectrometry and immunofluorescence analysis. Double strand break repair was modulated by inhibitors of heat shock protein 90, topoisomerase-I, and DNA protein kinase, and transgene expression was measured. Results: We found that a wide range of radiation doses increased adenoviral transgene expression regardless of the cell line, transgene, promoter, or viral capsid modification. Treatment with adenovirus, radiation, and double strand break repair inhibitors resulted in persistence of double strand breaks and subsequent increases in adenovirus transgene expression. Conclusions: Radiation-induced enhancement of adenoviral transgene expression is linked to DNA damage recognition and repair. Radiation induces a global cellular response that results in increased production of RNA and proteins, including adenoviral transgene products. This study provides a mechanistic rationale for combining radiation with adenoviral gene delivery.

  16. Determining orientation and direction of DNA sequences

    DOE Patents [OSTI]

    Goodwin, Edwin H.; Meyne, Julianne

    2000-01-01

    Determining orientation and direction of DNA sequences. A method by which fluorescence in situ hybridization can be made strand specific is described. Cell cultures are grown in a medium containing a halogenated nucleotide. The analog is partially incorporated in one DNA strand of each chromatid. This substitution takes place in opposite strands of the two sister chromatids. After staining with the fluorescent DNA-binding dye Hoechst 33258, cells are exposed to long-wavelength ultraviolet light which results in numerous strand nicks. These nicks enable the substituted strand to be denatured and solubilized by heat, treatment with high or low pH aqueous solutions, or by immersing the strands in 2.times.SSC (0.3M NaCl+0.03M sodium citrate), to name three procedures. It is unnecessary to enzymatically digest the strands using Exo III or another exonuclease in order to excise and solubilize nucleotides starting at the sites of the nicks. The denaturing/solubilizing process removes most of the substituted strand while leaving the prereplication strand largely intact. Hybridization of a single-stranded probe of a tandem repeat arranged in a head-to-tail orientation will result in hybridization only to the chromatid with the complementary strand present.

  17. Melatonin Protects Human Cells from Clustered DNA Damages, Killing and Acquisition of Soft Agar Growth Induced by X-rays or 970 MeV/n Fe ions

    SciTech Connect (OSTI)

    Das, B.; Sutherland, B.; Bennett, P. V.; Cutter, N. C.; Sutherland, J. C.

    2011-06-01

    We tested the ability of melatonin (N-acetyl-5 methoxytryptamine), a highly effective radical scavenger and human hormone, to protect DNA in solution and in human cells against induction of complex DNA clusters and biological damage induced by low or high linear energy transfer radiation (100 kVp X-rays, 970 MeV/nucleon Fe ions). Plasmid DNA in solution was treated with increasing concentrations of melatonin (0.0-3.5 mM) and were irradiated with X-rays. Human cells (28SC monocytes) were also irradiated with X-rays and Fe ions with and without 2 mM melatonin. Agarose plugs containing genomic DNA were subjected to Contour Clamped Homogeneous Electrophoretic Field (CHEF) followed by imaging and clustered DNA damages were measured by using Number Average length analysis. Transformation experiments on human primary fibroblast cells using soft agar colony assay were carried out which were irradiated with Fe ions with or without 2 mM melatonin. In plasmid DNA in solution, melatonin reduced the induction of single- and double-strand breaks. Pretreatment of human 28SC cells for 24 h before irradiation with 2 mM melatonin reduced the level of X-ray induced double-strand breaks by {approx}50%, of abasic clustered damages about 40%, and of Fe ion-induced double-strand breaks (41% reduction) and abasic clusters (34% reduction). It decreased transformation to soft agar growth of human primary cells by a factor of 10, but reduced killing by Fe ions only by 20-40%. Melatonin's effective reduction of radiation-induced critical DNA damages, cell killing, and striking decrease of transformation suggest that it is an excellent candidate as a countermeasure against radiation exposure, including radiation exposure to astronaut crews in space travel.

  18. Effects of solar ultraviolet photons on mammalian cell DNA. [UVA (320-400 nm):a2

    SciTech Connect (OSTI)

    Peak, M.J.; Peak, J.G.

    1991-01-01

    This document presents information on the possible mechanisms of carcinogenesis caused by UVA (ultraviolet radiation in the 320--400 nm region). Most studies showing the carcinogenic effects of ultraviolet light have concentrated on UVB (280--320 nm). UVA had been considered harmless even though it penetrates biological tissues better than UVB. Recently, it has become apparent that UVA is also capable of causing damage to cellular DNA. This was unexpected because the DNA UV absorption spectrum indicates a negligible probability that photons of wavelengths longer than 320 nm will be directly absorbed. The most common defects induced in DNA by UVB are pyrimidine photoproducts, such as thymidine dimers. UVA photons produce defects resembling those caused by ionizing radiations: single- and double-strand breaks, and DNA-protein crosslinks. This paper also discusses the role of DNA repair mechanisms in UVA-induced defects and the molecular mechanisms of UVA damage induction. 38 refs. (MHB)

  19. DNA Sequencing apparatus

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1992-01-01

    An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

  20. Procedure for normalization of cDNA libraries

    DOE Patents [OSTI]

    Bonaldo, Maria DeFatima; Soares, Marcelo Bento

    1997-01-01

    This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library.

  1. Procedure for normalization of cDNA libraries

    DOE Patents [OSTI]

    Bonaldo, M.D.; Soares, M.B.

    1997-12-30

    This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library. 1 fig.

  2. Neutrino Physics AAPT Strand Day

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Physics AAPT Strand Day NSTA Regional, 2005 Jocelyn Monroe, Columbia University 1. What Is a Neutrino Anyway? 2. The Question Of Neutrino Mass 3. Searching For Neutrino Oscillations 4. Where Are We Now? ν Neutrinos, they are very small. They have no charge and have no mass And do not interact at all. The earth is just a silly ball To them, through which they simply pass... ...And pierce the lover and his lass From underneath the bed- you call It wonderful; I call it crass. J from ``Cosmic

  3. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1996-01-09

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form. The method comprises: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3` noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. 4 figs.

  4. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B.; Efstratiadis, Argiris

    1996-01-01

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library.

  5. Probing the Conformational Distributions of Sub-Persistence Length DNA

    SciTech Connect (OSTI)

    Mastroianni, Alexander; Sivak, David; Geissler, Phillip; Alivisatos, Paul

    2009-06-08

    We have measured the bending elasticity of short double-stranded DNA (dsDNA) chains through small-angle X-ray scattering from solutions of dsDNA-linked dimers of gold nanoparticles. This method, which does not require exertion of external forces or binding to a substrate, reports on the equilibrium distribution of bending fluctuations, not just an average value (as in ensemble FRET) or an extreme value (as in cyclization), and in principle provides a more robust data set for assessing the suitability of theoretical models. Our experimental results for dsDNA comprising 42-94 basepairs (bp) are consistent with a simple worm-like chain model of dsDNA elasticity, whose behavior we have determined from Monte Carlo simulations that explicitly represent nanoparticles and their alkane tethers. A persistence length of 50 nm (150 bp) gave a favorable comparison, consistent with the results of single-molecule force-extension experiments on much longer dsDNA chains, but in contrast to recent suggestions of enhanced flexibility at these length scales.

  6. After Cajun, what next for stranded costs?

    SciTech Connect (OSTI)

    Pembroke, J.D.

    1994-10-01

    Members of FERC have said that the Cajun decision does not pose a serious problem to its proposed rulemaking on stranded costs. But the D.C. Circuit`s Cajun decision, criticizing the concept of recovery for stranded investment in broad terms, promises to make that task difficult, if not impossible. The United States Court of Appeals for the District of Columbia Circuit, in its July 12, 1994 opinion in Cajun Electric Power Cooperative, Inc. v. Federal Energy Regulatory Commission, subjected the Entergy Corporations`s transmission tariff`s stranded investment provision to broad and, perhaps, fatal criticism. The Cajun opinion, premised on basic concepts of antitrust law, was issued at a time of substantial industry discussion on the concept of stranded investment and should greatly impact the decisions of both federal and state regulators on stranded investment.

  7. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA

  8. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA

  9. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA

  10. Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

    SciTech Connect (OSTI)

    Suh, Myungkoo

    1995-12-06

    Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7{beta}, 8{alpha}-dihydoxy-9{alpha}, l0{alpha}-epoxy-7,8,9, 10-tetrahydrobenzo[{alpha}]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, ({minus})-trans-, (+)-cis- and ({minus})-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( {approximately} 25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant {pi}-{pi} stacking interactions between the pyrenyl residues and the bases. Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G{sub 2} or G{sub 3} (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N{sup 2}-dG in DNA isolated from the skin of mice treated topically with benzo[{alpha}]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N{sup 2}-dG.

  11. DNA attachment to support structures

    DOE Patents [OSTI]

    Balhorn, Rodney L.; Barry, Christopher H.

    2002-01-01

    Microscopic beads or other structures are attached to nucleic acids (DNA) using a terminal transferase. The transferase adds labeled dideoxy nucleotide bases to the ends of linear strands of DNA. The labels, such as the antigens digoxigenin and biotin, bind to the antibody compounds or other appropriate complementary ligands, which are bound to the microscopic beads or other support structures. The method does not require the synthesis of a synthetic oligonucleotide probe. The method can be used to tag or label DNA even when the DNA has an unknown sequence, has blunt ends, or is a very large fragment (e.g., >500 kilobase pairs).

  12. Method for rapid base sequencing in DNA and RNA with two base labeling

    DOE Patents [OSTI]

    Jett, James H.; Keller, Richard A.; Martin, John C.; Posner, Richard G.; Marrone, Babetta L.; Hammond, Mark L.; Simpson, Daniel J.

    1995-01-01

    Method for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand.

  13. Method for rapid base sequencing in DNA and RNA with two base labeling

    DOE Patents [OSTI]

    Jett, J.H.; Keller, R.A.; Martin, J.C.; Posner, R.G.; Marrone, B.L.; Hammond, M.L.; Simpson, D.J.

    1995-04-11

    A method is described for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand. 4 figures.

  14. Reconstitution of the cellular response to DNA damage in vitro using damage-activated extracts from mammalian cells

    SciTech Connect (OSTI)

    Roper, Katherine; Coverley, Dawn

    2012-03-10

    In proliferating mammalian cells, DNA damage is detected by sensors that elicit a cellular response which arrests the cell cycle and repairs the damage. As part of the DNA damage response, DNA replication is inhibited and, within seconds, histone H2AX is phosphorylated. Here we describe a cell-free system that reconstitutes the cellular response to DNA double strand breaks using damage-activated cell extracts and naieve nuclei. Using this system the effect of damage signalling on nuclei that do not contain DNA lesions can be studied, thereby uncoupling signalling and repair. Soluble extracts from G1/S phase cells that were treated with etoposide before isolation, or pre-incubated with nuclei from etoposide-treated cells during an in vitro activation reaction, restrain both initiation and elongation of DNA replication in naieve nuclei. At the same time, H2AX is phosphorylated in naieve nuclei in a manner that is dependent upon the phosphatidylinositol 3-kinase-like protein kinases. Notably, phosphorylated H2AX is not focal in naieve nuclei, but is evident throughout the nucleus suggesting that in the absence of DNA lesions the signal is not amplified such that discrete foci can be detected. This system offers a novel screening approach for inhibitors of DNA damage response kinases, which we demonstrate using the inhibitors wortmannin and LY294002. -- Highlights: Black-Right-Pointing-Pointer A cell free system that reconstitutes the response to DNA damage in the absence of DNA lesions. Black-Right-Pointing-Pointer Damage-activated extracts impose the cellular response to DNA damage on naieve nuclei. Black-Right-Pointing-Pointer PIKK-dependent response impacts positively and negatively on two separate fluorescent outputs. Black-Right-Pointing-Pointer Can be used to screen for inhibitors that impact on the response to damage but not on DNA repair. Black-Right-Pointing-Pointer LY294002 and wortmannin demonstrate the system's potential as a pathway focused screening

  15. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1998-11-03

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3` noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries. 19 figs.

  16. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B.; Efstratiadis, Argiris

    1998-01-01

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries.

  17. Ligation of single-stranded oligodeoxyribonucleotides by T4 RNA ligase

    SciTech Connect (OSTI)

    Tessier, D.C.; Brousseau, R.; Vernet, T.

    1986-10-01

    Despite its unique ability to ligate single-stranded DNA molecules, T4 RNA ligase has so far seen little use in molecular biology due to long reaction times, modest yields, and apparent inability to promote ligations of long oligodeoxyribonucleotides. The authors describe here a set of reaction conditions which dramatically shorten the reaction time and give reproducible 40 to 60% ligation of DNA fragments of up to 40 bases in length. These improvements open promising new fields of application to T4 RNA ligase.

  18. Method and apparatus for testing a forward-moving strand

    DOE Patents [OSTI]

    Ducommun, Joel; Vulliens, Philippe

    1980-01-01

    In a method for testing a continuously forward-moving strand a light beam which passes along a plane that extends approximately perpendicularly to the longitudinal axis of the strand is introduced into the strand. The brightness value is measured on a place of the strand exterior which is distal from the light incidence place by means of at least one photoelectronic element disposed directly on the strand exterior and the measured result is evaluated in a gating circuit which is electrically connected to the photoelectronic element.

  19. Radiosensitivity profiles from a panel of ovarian cancer cell lines exhibiting genetic alterations in p53 and disparate DNA-dependent protein kinase activities

    SciTech Connect (OSTI)

    Langland, Gregory T.; Yannone, Steven M.; Langland, Rachel A.; Nakao, Aki; Guan, Yinghui; Long, Sydney B.T.; Vonguyen, Lien; Chen, David J.; Gray, Joe W; Chen, Fanqing

    2009-09-07

    The variability of radiation responses in ovarian tumors and tumor-derived cell lines is poorly understood. Since both DNA repair capacity and p53 status can significantly alter radiation sensitivity, we evaluated these factors along with radiation sensitivity in a panel of sporadic human ovarian carcinoma cell lines. We observed a gradation of radiation sensitivity among these sixteen lines, with a five-fold difference in the LD50 between the most radiosensitive and the most radioresistant cells. The DNA-dependent protein kinase (DNA-PK) is essential for the repair of radiation induced DNA double-strand breaks in human somatic cells. Therefore, we measured gene copy number, expression levels, protein abundance, genomic copy and kinase activity for DNA-PK in all of our cell lines. While there were detectable differences in DNA-PK between the cell lines, there was no clear correlation with any of these differences and radiation sensitivity. In contrast, p53 function as determined by two independent methods, correlated well with radiation sensitivity, indicating p53 mutant ovarian cancer cells are typically radioresistant relative to p53 wild-type lines. These data suggest that the activity of regulatory molecules such as p53 may be better indicators of radiation sensitivity than DNA repair enzymes such as DNAPK in ovarian cancer.

  20. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    When DNA Needs to Stand Up and Be Counted When DNA Needs to Stand Up and Be Counted Print Wednesday, 31 May 2006 00:00 DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for

  1. Microfluidic DNA sample preparation method and device

    DOE Patents [OSTI]

    Krulevitch, Peter A.; Miles, Robin R.; Wang, Xiao-Bo; Mariella, Raymond P.; Gascoyne, Peter R. C.; Balch, Joseph W.

    2002-01-01

    Manipulation of DNA molecules in solution has become an essential aspect of genetic analyses used for biomedical assays, the identification of hazardous bacterial agents, and in decoding the human genome. Currently, most of the steps involved in preparing a DNA sample for analysis are performed manually and are time, labor, and equipment intensive. These steps include extraction of the DNA from spores or cells, separation of the DNA from other particles and molecules in the solution (e.g. dust, smoke, cell/spore debris, and proteins), and separation of the DNA itself into strands of specific lengths. Dielectrophoresis (DEP), a phenomenon whereby polarizable particles move in response to a gradient in electric field, can be used to manipulate and separate DNA in an automated fashion, considerably reducing the time and expense involved in DNA analyses, as well as allowing for the miniaturization of DNA analysis instruments. These applications include direct transport of DNA, trapping of DNA to allow for its separation from other particles or molecules in the solution, and the separation of DNA into strands of varying lengths.

  2. Assembling semiconductor nanocomposites using DNA replication technologies.

    SciTech Connect (OSTI)

    Heimer, Brandon W.; Crown, Kevin K.; Bachand, George David

    2005-11-01

    Deoxyribonucleic acid (DNA) molecules represent Nature's genetic database, encoding the information necessary for all cellular processes. From a materials engineering perspective, DNA represents a nanoscale scaffold with highly refined structure, stability across a wide range of environmental conditions, and the ability to interact with a range of biomolecules. The ability to mass-manufacture functionalized DNA strands with Angstrom-level resolution through DNA replication technology, however, has not been explored. The long-term goal of the work presented in this report is focused on exploiting DNA and in vitro DNA replication processes to mass-manufacture nanocomposite materials. The specific objectives of this project were to: (1) develop methods for replicating DNA strands that incorporate nucleotides with ''chemical handles'', and (2) demonstrate attachment of nanocrystal quantum dots (nQDs) to functionalized DNA strands. Polymerase chain reaction (PCR) and primer extension methodologies were used to successfully synthesize amine-, thiol-, and biotin-functionalized DNA molecules. Significant variability in the efficiency of modified nucleotide incorporation was observed, and attributed to the intrinsic properties of the modified nucleotides. Noncovalent attachment of streptavidin-coated nQDs to biotin-modified DNA synthesized using the primer extension method was observed by epifluorescence microscopy. Data regarding covalent attachment of nQDs to amine- and thiol-functionalized DNA was generally inconclusive; alternative characterization tools are necessary to fully evaluate these attachment methods. Full realization of this technology may facilitate new approaches to manufacturing materials at the nanoscale. In addition, composite nQD-DNA materials may serve as novel recognition elements in sensor devices, or be used as diagnostic tools for forensic analyses. This report summarizes the results obtained over the course of this 1-year project.

  3. Methods to estimate stranded commitments for a restructuring US electricity industry

    SciTech Connect (OSTI)

    Hirst, E.; Hadley, S.; Baxter, L.

    1996-01-01

    Estimates of stranded commitments for US investor-owned electric utilities range widely, from as little as $20 billion to as much as $500 billion (more than double the shareholder equity in US utilities). These potential losses are a consequence of the above-market book values for some utility-owned power plants, long-term power-purchase contracts, deferred income taxes, regulatory assets, and public-policy programs. Because of the wide range of estimates and the potentially large dollar amounts involved, state and federal regulators need a clear understanding of the methods used to calculate these estimates. In addition, they may want simple methods that they can use to check the reasonableness of the estimates that utilities and other parties present in regulatory proceedings. This report explains various top-down and bottom-up methods to calculate stranded commitments. The purpose of this analysis is to help regulators and others understand the implications of different analytical approaches to estimating stranded-commitment amounts. Top-down methods, because they use the utility as the unit of analysis, are simple to apply and to understand. However, their aggregate nature makes it difficult to determine what specific assets and liabilities affect their estimates. Bottom-up methods use the individual asset (e.g., power plant) or liability (e.g., power-purchase contract, fuel-supply contract, and deferred income taxes) as the unit of analysis. These methods have substantial data and computational requirements.

  4. Chemosensitivity of primary human fibroblasts with defective unhooking of DNA interstrand cross-links

    SciTech Connect (OSTI)

    Clingen, Peter H. . E-mail: p.clingen@ucl.ac.uk; Arlett, Colin F.; Hartley, John A.; Parris, Christopher N.

    2007-02-15

    Xeroderma pigmentosum (XP) is characterised by defects in nucleotide excision repair, ultraviolet (UV) radiation sensitivity and increased skin carcinoma. Compared to other complementation groups, XP-F patients show relatively mild cutaneous symptoms. DNA interstrand cross-linking agents are a highly cytotoxic class of DNA damage induced by common cancer chemotherapeutics such as cisplatin and nitrogen mustards. Although the XPF-ERCC1 structure-specific endonuclease is required for the repair of ICLs cellular sensitivity of primary human XP-F cells has not been established. In clonogenic survival assays, primary fibroblasts from XP-F patients were moderately sensitive to both UVC and HN2 compared to normal cells (2- to 3-fold and 3- to 5-fold, respectively). XP-A fibroblasts were considerably more sensitive to UVC (10- to 12-fold) but not sensitive to HN2. The sensitivity of XP-F fibroblasts to HN2 correlated with the defective incision or 'unhooking' step of ICL repair. Using the comet assay, XP-F cells exhibited only 20% residual unhooking activity over 24 h. Over the same time, normal and XP-A cells unhooked greater than 95% and 62% of ICLs, respectively. After HN2 treatment, ICL-associated DNA double-strand breaks (DSBs) are detected by pulse field gel electrophoresis in dividing cells. Induction and repair of DNA DSBs was normal in XP-F fibroblasts. These findings demonstrate that in primary human fibroblasts, XPF is required for the unhooking of ICLs and not for the induction or repair of ICL-associated DNA DSBs induced by HN2. In terms of cancer chemotherapy, people with mild DNA repair defects affecting ICL repair may be more prevalent in the general population than expected. Since cellular sensitivity of primary human fibroblasts usually reflects clinical sensitivity such patients with cancer would be at risk of increased toxicity.

  5. Structure of DNA-Bound FEN1 Reveals Mechanism of Action

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to the template's nucleotides. But before polymerase builds the duplicate strand, an RNA primer must bind to the template acting as a short length of "pseudo-DNA" to whose...

  6. Jefferson Lab Hosts Upcoming Science Lectures on DNA and Chocolate |

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Jefferson Lab Upcoming Science Lectures on DNA and Chocolate Jefferson Lab Hosts Upcoming Science Lectures on DNA and Chocolate NEWPORT NEWS, Va., Feb. 24, 2011 - Jefferson Lab will host a public lecture on March 29 titled DNA: The Strand That Connects Us All presented by Matt Kaplan from the Human Origins Genotyping Laboratory, Phoenix, Ariz. Kaplan will discuss how the methods and discoveries of human population genetics studies are applied for personal genealogical reconstruction and

  7. Background meeting and technology demonstration: Chromium electroplating of superconductor strand

    SciTech Connect (OSTI)

    1995-05-01

    A meeting concerned with electroplating copper onto superconducting wires was held. Topics of discussion were concerned with the market, strand cleanliness, and an improved rinsing system for the process.

  8. Gel Electrophoresis of Gold-DNA Nanoconjugates

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Pellegrino, T.; Sperling, R. A.; Alivisatos, A. P.; Parak, W. J.

    2007-01-01

    Gold-DNA conjugates were investigated in detail by a comprehensive gel electrophoresis study based on 1200 gels. A controlled number of single-stranded DNA of different length was attached specifically via thiol-Au bonds to phosphine-stabilized colloidal gold nanoparticles. Alternatively, the surface of the gold particles was saturated with single stranded DNA of different length either specifically via thiol-Au bonds or by nonspecific adsorption. From the experimentally determined electrophoretic mobilities, estimates for the effective diameters of the gold-DNA conjugates were derived by applying two different data treatment approaches. The first method is based on making a calibration curve for the relation between effectivemore » diameters and mobilities with gold nanoparticles of known diameter. The second method is based on Ferguson analysis which uses gold nanoparticles of known diameter as reference database. Our study shows that effective diameters derived from gel electrophoresis measurements are affected with a high error bar as the determined values strongly depend on the method of evaluation, though relative changes in size upon binding of molecules can be detected with high precision. Furthermore, in this study, the specific attachment of DNA via gold-thiol bonds to Au nanoparticles is compared to nonspecific adsorption of DNA. Also, the maximum number of DNA molecules that can be bound per particle was determined.« less

  9. A double-double/double-single computation package

    Energy Science and Technology Software Center (OSTI)

    2004-12-01

    The DDFUNIDSFUN software permits a new or existing Fortran-90 program to utilize double-double precision (approx. 31 digits) or double-single precision (approx. 14 digits) arithmetic. Double-double precision is required by a rapidly expandirtg body of scientific computations in physics and mathematics, for which the conventional 64-bit IEEE computer arithmetic (about 16 decimal digit accuracy) is not sufficient. Double-single precision permits users of systems that do not have hardware 64-bit IEEE arithmetic (such as some game systems)more » to perform arithmetic at a precision nearly as high as that of systems that do. Both packages run significantly faster Than using multiple precision or arbitrary precision software for this purpose. The package includes an extensive set of low-level routines to perform high-precision arithmetic, including routines to calculate various algebraic and transcendental functions, such as square roots, sin, ccc, exp, log and others. In addition, the package includes high-level translation facilities, so that Fortran programs can utilize these facilities by making only a few changes to conventional Fortran programs. In most cases, the only changes that are required are to change the type statements of variables that one wishes to be treated as multiple precision, plus a few other minor changes. The DDFUN package is similar in functionality to the double-double part of the GD package, which was previously written at LBNL. However, the DDFUN package is written exclusively in Fortran-90, thus avoidIng difficulties that some users experience when using GD, which includes both Fortran-90 and C++ code.« less

  10. Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA

    SciTech Connect (OSTI)

    Horton, John R.; Borgaro, Janine G.; Griggs, Rose M.; Quimby, Aine; Guan, Shengxi; Zhang, Xing; Wilson, Geoffrey G.; Zheng, Yu; Zhu, Zhenyu; Cheng, Xiaodong

    2014-07-03

    AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases, cleaves DNA containing 5-hydroxymethylctosine (5hmC) and glucosylated 5hmC (g5hmC), but not DNA containing unmodified cytosine. AbaSI has been used as a tool for mapping the genomic locations of 5hmC, an important epigenetic modification in the DNA of higher organisms. Here we report the crystal structures of AbaSI in the presence and absence of DNA. These structures provide considerable, although incomplete, insight into how this enzyme acts. AbaSI appears to be mainly a homodimer in solution, but interacts with DNA in our structures as a homotetramer. Each AbaSI subunit comprises an N-terminal, Vsr-like, cleavage domain containing a single catalytic site, and a C-terminal, SRA-like, 5hmC-binding domain. Two N-terminal helices mediate most of the homodimer interface. Dimerization brings together the two catalytic sites required for double-strand cleavage, and separates the 5hmC binding-domains by ~ 70 Å, consistent with the known activity of AbaSI which cleaves DNA optimally between symmetrically modified cytosines ~ 22 bp apart. The eukaryotic SET and RING-associated (SRA) domains bind to DNA containing 5-methylcytosine (5mC) in the hemi-methylated CpG sequence. They make contacts in both the major and minor DNA grooves, and flip the modified cytosine out of the helix into a conserved binding pocket. In contrast, the SRA-like domain of AbaSI, which has no sequence specificity, contacts only the minor DNA groove, and in our current structures the 5hmC remains intra-helical. A conserved, binding pocket is nevertheless present in this domain, suitable for accommodating 5hmC and g5hmC. We consider it likely, therefore, that base-flipping is part of the recognition and cleavage mechanism of AbaSI, but that our structures represent an earlier, pre-flipped stage, prior to actual recognition.

  11. Chromosome doubling method

    DOE Patents [OSTI]

    Kato, Akio

    2006-11-14

    The invention provides methods for chromosome doubling in plants. The technique overcomes the low yields of doubled progeny associated with the use of prior techniques for doubling chromosomes in plants such as grasses. The technique can be used in large scale applications and has been demonstrated to be highly effective in maize. Following treatment in accordance with the invention, plants remain amenable to self fertilization, thereby allowing the efficient isolation of doubled progeny plants.

  12. Storing data encoded DNA in living organisms

    DOE Patents [OSTI]

    Wong; Pak C. , Wong; Kwong K. , Foote; Harlan P.

    2006-06-06

    Current technologies allow the generation of artificial DNA molecules and/or the ability to alter the DNA sequences of existing DNA molecules. With a careful coding scheme and arrangement, it is possible to encode important information as an artificial DNA strand and store it in a living host safely and permanently. This inventive technology can be used to identify origins and protect R&D investments. It can also be used in environmental research to track generations of organisms and observe the ecological impact of pollutants. Today, there are microorganisms that can survive under extreme conditions. As well, it is advantageous to consider multicellular organisms as hosts for stored information. These living organisms can provide as memory housing and protection for stored data or information. The present invention provides well for data storage in a living organism wherein at least one DNA sequence is encoded to represent data and incorporated into a living organism.

  13. Method for detecting point mutations in DNA utilizing fluorescence energy transfer

    DOE Patents [OSTI]

    Parkhurst, Lawrence J.; Parkhurst, Kay M.; Middendorf, Lyle

    2001-01-01

    A method for detecting point mutations in DNA using a fluorescently labeled oligomeric probe and Forster resonance energy transfer (FRET) is disclosed. The selected probe is initially labeled at each end with a fluorescence dye, which act together as a donor/acceptor pair for FRET. The fluorescence emission from the dyes changes dramatically from the duplex stage, wherein the probe is hybridized to the complementary strand of DNA, to the single strand stage, when the probe is melted to become detached from the DNA. The change in fluorescence is caused by the dyes coming into closer proximity after melting occurs and the probe becomes detached from the DNA strand. The change in fluorescence emission as a function of temperature is used to calculate the melting temperature of the complex or T.sub.m. In the case where there is a base mismatch between the probe and the DNA strand, indicating a point mutation, the T.sub.m has been found to be significantly lower than the T.sub.m for a perfectly match probelstand duplex. The present invention allows for the detection of the existence and magnitude of T.sub.m, which allows for the quick and accurate detection of a point mutation in the DNA strand and, in some applications, the determination of the approximate location of the mutation within the sequence.

  14. Factors that affect electric-utility stranded commitments

    SciTech Connect (OSTI)

    Hirst, E.; Hadley, S.; Baxter, L.

    1996-07-01

    Estimates of stranded commitments for U.S. investor-owned utilities range widely, with many falling in the range of $100 to $200 billion. These potential losses exist because some utility-owned power plants, long-term power-purchase contracts and fuel-supply contracts, regulatory assets, and expenses for public-policy programs have book values that exceed their expected market values under full competition. This report quantifies the sensitivity of stranded- commitment estimates to the various factors that lead to these above- market-value estimates. The purpose of these sensitivity analyses is to improve understanding on the part of state and federal regulators, utilities, customers, and other electric-industry participants about the relative importance of the factors that affect stranded- commitment amounts.

  15. Nucleolar exit of RNF8 and BRCA1 in response to DNA damage

    SciTech Connect (OSTI)

    Guerra-Rebollo, Marta; Mateo, Francesca; Franke, Kristin; Huen, Michael S.Y.; Lopitz-Otsoa, Fernando; Rodriguez, Manuel S.; Plans, Vanessa; Thomson, Timothy M.

    2012-11-01

    The induction of DNA double-strand breaks (DSBs) elicits a plethora of responses that redirect many cellular functions to the vital task of repairing the injury, collectively known as the DNA damage response (DDR). We have found that, in the absence of DNA damage, the DSB repair factors RNF8 and BRCA1 are associated with the nucleolus. Shortly after exposure of cells to {gamma}-radiation, RNF8 and BRCA1 translocated from the nucleolus to damage foci, a traffic that was reverted several hours after the damage. RNF8 interacted through its FHA domain with the ribosomal protein RPSA, and knockdown of RPSA caused a depletion of nucleolar RNF8 and BRCA1, suggesting that the interaction of RNF8 with RPSA is critical for the nucleolar localization of these DDR factors. Knockdown of RPSA or RNF8 impaired bulk protein translation, as did {gamma}-irradiation, the latter being partially countered by overexpression of exogenous RNF8. Our results suggest that RNF8 and BRCA1 are anchored to the nucleolus through reversible interactions with RPSA and that, in addition to its known functions in DDR, RNF8 may play a role in protein synthesis, possibly linking the nucleolar exit of this factor to the attenuation of protein synthesis in response to DNA damage. -- Highlights: Black-Right-Pointing-Pointer RNF8 and BRCA1 are associated with the nucleolus of undamaged cells. Black-Right-Pointing-Pointer Upon {gamma}-radiation, RNF8 and BRCA1 are translocated from the nucleolus to damage foci. Black-Right-Pointing-Pointer The ribosomal protein RPSA anchors RNF8 to the nucleolus. Black-Right-Pointing-Pointer RNF8 may play previously unsuspected roles in protein synthesis.

  16. Method for fabricating multi-strand superconducting cable

    DOE Patents [OSTI]

    Borden, A.R.

    1985-04-01

    Multi-strand superconducting cables adapted to be used, for example, to wind a magnet are fabricated by directing wire strands inwardly from spools disposed on the perimeter of a rotating disk and wrapping them diagonally around a tapered mandrel with a flattened cross-sectional shape with a core having a wedge-shaped channel. As the cable is pulled axially, flexibly coupled wedge-shaped pieces are continuously passed through the channel in the mandrel and inserted into the cable as an internal support therefor.

  17. Double Flash | Open Energy Information

    Open Energy Info (EERE)

    Double Flash Jump to: navigation, search Retrieved from "http:en.openei.orgwindex.php?titleDoubleFlash&oldid599606...

  18. Methods for sequencing GC-rich and CCT repeat DNA templates

    DOE Patents [OSTI]

    Robinson, Donna L.

    2007-02-20

    The present invention is directed to a PCR-based method of cycle sequencing DNA and other polynucleotide sequences having high CG content and regions of high GC content, and includes for example DNA strands with a high Cytosine and/or Guanosine content and repeated motifs such as CCT repeats.

  19. Induction and Persistence of Large ?H2AX Foci by High Linear Energy Transfer Radiation in DNA-Dependent protein kinaseDeficient Cells

    SciTech Connect (OSTI)

    Bracalente, Candelaria; Ibaez, Irene L.; Molinari, Beatriz; Palmieri, Mnica; Kreiner, Andrs; Valda, Alejandro; and others

    2013-11-15

    Purpose: To evaluate the cell response to DNA double-strand breaks induced by low and high linear energy transfer (LET) radiations when the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs), an essential protein of the nonhomologous end-joining repair pathway, lacks kinase activity. Methods and Materials: CHO10B2, a Chinese hamster ovary cell line, and its derived radiosensitive mutant cell line, irs-20, lacking DNA-PKcs activity, were evaluated after 0 to 3 Gy of ?-rays, plateau and Bragg peak protons, and lithium beams by clonogenic assay, and as a measurement of double-strand breaks, phosphorylated H2AX (?H2AX) foci number and size were quantified by immunocytofluorescence. Results: Irs-20 exhibited greater radiosensitivity and a higher amount of ?H2AX foci than CHO10B2 at 6 hours after irradiation for all types of radiations. Remarkably, CHO10B2 and irs-20 maintained their difference in radiosensitivity after high-LET radiation. Six hours after low-LET radiations, irs-20 did not reach basal levels of ?H2AX at high doses, whereas CHO10B2 recovered basal levels for all doses. After high-LET radiation, only CHO10B2 exhibited a reduction in ?H2AX foci, but it never reached basal levels. Persistent foci in irs-20 confirmed a repair deficiency. Interestingly, after 30 minutes of high-LET radiation both cell lines exhibited large foci (size >0.9 ?m{sup 2}) related to the damage nature, whereas at 6 hours irs-20 showed a higher amount of large foci than CHO10B2, with a 7-fold increase at 3 Gy, that could also be associated to radiosensitivity. Conclusions: We demonstrated, for the first time, an association between deficient DNA-PKcs activity and not only high levels of H2AX phosphorylation but also persistence and size increase of ?H2AX foci after high-LET irradiation.

  20. DNA sequencing with pyrophosphatase

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1996-03-12

    A kit or solution for use in extension of an oligonucleotide primer having a first single-stranded region on a template molecule having a second single-stranded region homologous to the first single-stranded region, comprising a first agent able to cause extension of the first single-stranded region of the primer on the second single-stranded region of the template in a reaction mixture, and a second agent able to reduce the amount of pyrophosphate in the reaction mixture below the amount produced during the extension in the absence of the second agent.

  1. DNA sequencing with pyrophosphatase

    DOE Patents [OSTI]

    Tabor, S.; Richardson, C.C.

    1996-03-12

    A kit or solution is disclosed for use in extension of an oligonucleotide primer having a first single-stranded region on a template molecule and having a second single-stranded region homologous to the first single-stranded region. The first agent is able to cause extension of the first single-stranded region of the primer on the second single-stranded region of the template in a reaction mixture. The second agent is able to reduce the amount of pyrophosphate in the reaction mixture below the amount produced during the extension in the absence of the second agent.

  2. Improvements in strand feeding and its effect of sintering performance

    SciTech Connect (OSTI)

    Beer, H.; Kersting, K.; Werner, P.

    1995-12-01

    Sintering may be considered a rather simple, counter current gas-solid process. A bed of granular solids is moved horizontally on a strand of pallets and suction is applied beneath the grate. Shortly after the sinter mix is fed onto the strand the incorporated solid fuel is ignited in the surface layer and the hot gases are drawn into the bed. The temperature of the top layer is raised high enough to burn the fuel particles while air is sucked down through it. Passing the upper, already sintered part of the bed the air is first preheated then sustains the combustion reaction. The hot, still oxygen-rich combustion gases leave the sintering zone and transfer its heat to the charge below. While the solids are preheated, carbonates, combined water, and moisture are driven off, rapidly cooling the gas. Thus, a flame front propagates through the traveling bed, generating at peak temperatures enough heat to agglomerate the bed of quasi-particles into a sinter cake. The strand speed is adjusted so that the burning through of the combustion zone coincides with the end of the suction area. To ensure stable operation this cross stream reactor has to be kept in a steady state.

  3. Unveiling Stability Criteria of DNA-Carbon Nanotubes Constructs by Scanning Tunneling Microscopy and Computational Modeling

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kilina, Svetlana; Yarotski, Dzmitry A.; Talin, A. Alec; Tretiak, Sergei; Taylor, Antoinette J.; Balatsky, Alexander V.

    2011-01-01

    We present a combined approach that relies on computational simulations and scanning tunneling microscopy (STM) measurements to reveal morphological properties and stability criteria of carbon nanotube-DNA (CNT-DNA) constructs. Application of STM allows direct observation of very stable CNT-DNA hybrid structures with the well-defined DNA wrapping angle of 63.4 ° and a coiling period of 3.3 nm. Using force field simulations, we determine how the DNA-CNT binding energy depends on the sequence and binding geometry of a single strand DNA. This dependence allows us to quantitatively characterize the stability of a hybrid structure with an optimal π-stacking between DNA nucleotides andmore » the tube surface and better interpret STM data. Our simulations clearly demonstrate the existence of a very stable DNA binding geometry for (6,5) CNT as evidenced by the presence of a well-defined minimum in the binding energy as a function of an angle between DNA strand and the nanotube chiral vector. This novel approach demonstrates the feasibility of CNT-DNA geometry studies with subnanometer resolution and paves the way towards complete characterization of the structural and electronic properties of drug-delivering systems based on DNA-CNT hybrids as a function of DNA sequence and a nanotube chirality.« less

  4. Reduced repair capacity of a DNA clustered damage site comprised of 8-oxo-7,8-dihydro-2'-deoxyguanosine and 2-deoxyribonolactone results in an increased mutagenic potential of these lesions

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Cunniffe, Siobhan; O’Neill, Peter; Greenberg, Marc M.; Lomax, Martine E.

    2014-04-01

    A signature of ionizing radiation is the induction of DNA clustered damaged sites. Non-double strand break (DSB) clustered damage has been shown to compromise the base excision repair pathway, extending the lifetimes of the lesions within the cluster, compared to isolated lesions. This increases the likelihood the lesions persist to replication and thus increasing the mutagenic potential of the lesions within the cluster. Lesions formed by ionizing radiation include 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) and 2-deoxyribonolactone (dL). dL poses an additional challenge to the cell as it is not repaired by the short-patch base excision repair pathway. Here we show recalcitrant dL repairmore » is reflected in mutations observed when DNA containing it and a proximal 8-oxodGuo is replicated in Escherichia coli. 8-oxodGuo in close proximity to dL on the opposing DNA strand results in an enhanced frequency of mutation of the lesions within the cluster and a 20 base sequence flanking the clustered damage site in an E. coli based plasmid assay. In vitro repair of a dL lesion is reduced when compared to the repair of an abasic (AP) site and a tetrahydrofuran (THF), and this is due mainly to a reduction in the activity of polymerase β, leading to retarded FEN1 and ligase 1 activities. This study has given insights in to the biological effects of clusters containing dL.« less

  5. MCM ring hexamerization is a prerequisite for DNA-binding

    SciTech Connect (OSTI)

    Froelich, Clifford A.; Nourse, Amanda; Enemark, Eric J.

    2015-09-13

    The hexameric Minichromosome Maintenance (MCM) protein complex forms a ring that unwinds DNA at the replication fork in eukaryotes and archaea. Our recent crystal structure of an archaeal MCM N-terminal domain bound to single-stranded DNA (ssDNA) revealed ssDNA associating across tight subunit interfaces but not at the loose interfaces, indicating that DNA-binding is governed not only by the DNA-binding residues of the subunits (MCM ssDNA-binding motif, MSSB) but also by the relative orientation of the subunits. We now extend these findings to show that DNA-binding by the MCM N-terminal domain of the archaeal organism Pyrococcus furiosus occurs specifically in the hexameric oligomeric form. We show that mutants defective for hexamerization are defective in binding ssDNA despite retaining all the residues observed to interact with ssDNA in the crystal structure. One mutation that exhibits severely defective hexamerization and ssDNA-binding is at a conserved phenylalanine that aligns with the mouse Mcm4(Chaos3) mutation associated with chromosomal instability, cancer, and decreased intersubunit association.

  6. MCM ring hexamerization is a prerequisite for DNA-binding

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Froelich, Clifford A.; Nourse, Amanda; Enemark, Eric J.

    2015-09-13

    The hexameric Minichromosome Maintenance (MCM) protein complex forms a ring that unwinds DNA at the replication fork in eukaryotes and archaea. Our recent crystal structure of an archaeal MCM N-terminal domain bound to single-stranded DNA (ssDNA) revealed ssDNA associating across tight subunit interfaces but not at the loose interfaces, indicating that DNA-binding is governed not only by the DNA-binding residues of the subunits (MCM ssDNA-binding motif, MSSB) but also by the relative orientation of the subunits. We now extend these findings to show that DNA-binding by the MCM N-terminal domain of the archaeal organism Pyrococcus furiosus occurs specifically in themore » hexameric oligomeric form. We show that mutants defective for hexamerization are defective in binding ssDNA despite retaining all the residues observed to interact with ssDNA in the crystal structure. One mutation that exhibits severely defective hexamerization and ssDNA-binding is at a conserved phenylalanine that aligns with the mouse Mcm4(Chaos3) mutation associated with chromosomal instability, cancer, and decreased intersubunit association.« less

  7. Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Muraguchi, Hajime; Umezawa, Kiwamu; Niikura, Mai; Yoshida, Makoto; Kozaki, Toshinori; Ishii, Kazuo; Sakai, Kiyota; Shimizu, Motoyuki; Nakahori, Kiyoshi; Sakamoto, Yuichi; et al

    2015-10-28

    We report that the basidiomycete fungus Coprinopsis cinerea is an important model system for multicellular development. Fruiting bodies of C. cinerea are typical mushrooms, which can be produced synchronously on defined media in the laboratory. To investigate the transcriptome in detail during fruiting body development, high-throughput sequencing (RNA-seq) was performed using cDNA libraries strand-specifically constructed from 13 points (stages/tissues) with two biological replicates. The reads were aligned to 14,245 predicted transcripts, and counted for forward and reverse transcripts. Differentially expressed genes (DEGs) between two adjacent points and between vegetative mycelium and each point were detected by Tag Count Comparison (TCC).more » To validate RNA-seq data, expression levels of selected genes were compared using RPKM values in RNA-seq data and qRT-PCR data, and DEGs detected in microarray data were examined in MA plots of RNA-seq data by TCC. We discuss events deduced from GO analysis of DEGs. In addition, we uncovered both transcription factor candidates and antisense transcripts that are likely to be involved in developmental regulation for fruiting.« less

  8. Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea

    SciTech Connect (OSTI)

    Muraguchi, Hajime; Umezawa, Kiwamu; Niikura, Mai; Yoshida, Makoto; Kozaki, Toshinori; Ishii, Kazuo; Sakai, Kiyota; Shimizu, Motoyuki; Nakahori, Kiyoshi; Sakamoto, Yuichi; Choi, Cindy; Ngan, Chew Yee; Lindquist, Eika; Lipzen, Anna; Tritt, Andrew; Haridas, Sajeet; Barry, Kerrie; Grigoriev, Igor V.; Pukkila, Patricia J.

    2015-10-28

    We report that the basidiomycete fungus Coprinopsis cinerea is an important model system for multicellular development. Fruiting bodies of C. cinerea are typical mushrooms, which can be produced synchronously on defined media in the laboratory. To investigate the transcriptome in detail during fruiting body development, high-throughput sequencing (RNA-seq) was performed using cDNA libraries strand-specifically constructed from 13 points (stages/tissues) with two biological replicates. The reads were aligned to 14,245 predicted transcripts, and counted for forward and reverse transcripts. Differentially expressed genes (DEGs) between two adjacent points and between vegetative mycelium and each point were detected by Tag Count Comparison (TCC). To validate RNA-seq data, expression levels of selected genes were compared using RPKM values in RNA-seq data and qRT-PCR data, and DEGs detected in microarray data were examined in MA plots of RNA-seq data by TCC. We discuss events deduced from GO analysis of DEGs. In addition, we uncovered both transcription factor candidates and antisense transcripts that are likely to be involved in developmental regulation for fruiting.

  9. Double resonator cantilever accelerometer

    DOE Patents [OSTI]

    Koehler, D.R.

    1982-09-23

    A digital quartz accelerometer includes a pair of spaced double-ended tuning forks fastened at one end to a base and at the other end through a spacer mass. Transverse movement of the resonator members stresses one and compresses the other, providing a differential frequency output which is indicative of acceleration.

  10. Double resonator cantilever accelerometer

    DOE Patents [OSTI]

    Koehler, Dale R.

    1984-01-01

    A digital quartz accelerometer includes a pair of spaced double-ended tuning forks fastened at one end to a base and at the other end through a spacer mass. Transverse movement of the resonator members stresses one and compresses the other, providing a differential frequency output which is indicative of acceleration.

  11. Venezuela to double Supermetanol

    SciTech Connect (OSTI)

    1997-04-23

    Pequiven, the petrochemical arm of Venezuelan state oil company PDVSA, is conducting feasibility studies to double the size of its 750,000-m.t./year Supermetanol methanol joint venture with Ecofuel at Jose. The twin unit would be onstream by the end of the decade and would increase Pequiven`s capacity to 2.3 million m.t./year.

  12. DNA Origami with Complex Curvatures in Three-Dimensional Space

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA Origami with Complex Curvatures in Three-Dimensional Space Authors: Han, D., Pal, S., Nangreave, J., Deng, Z., Liu, Y., and Yan, H. Title: DNA Origami with Complex Curvatures in Three-Dimensional Space Source: Science Year: 2011 Volume: 332 Pages: 342-346 ABSTRACT: We present a strategy to design and construct self-assembling DNA nanostructures that define intricate curved surfaces in three-dimensional (3D) space using the DNA origami folding technique. Double-helical DNA is bent to follow

  13. The influence of TRP53 in the dose response of radiation-induced apoptosis, DNA repair and genomic stability in murine haematopoietic cells

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Lemon, Jennifer A.; Taylor, Kristina; Verdecchia, Kyle; Phan, Nghi; Boreham, Douglas R.

    2014-01-01

    Apoptotic and DNA damage endpoints are frequently used as surrogate markers of cancer risk, and have been well-studied in the Trp53+/- mouse model. We report the effect of differing Trp53 gene status on the dose response of ionizing radiation exposures (0.01-2 Gy), with the unique perspective of determining if effects of gene status remain at extended time points. Here we report no difference in the dose response for radiation-induced DNA double-strand breaks in bone marrow and genomic instability (MN-RET levels) in peripheral blood, between wild-type (Trp53+/+) and heterozygous (Trp53+/-) mice. The dose response for Trp53+/+ mice showed higher initial levelsmore » of radiation-induced lymphocyte apoptosis relative to Trp53+/- between 0 and 1 Gy. Although this trend was observed up to 12 hours post-irradiation, both genotypes ultimately reached the same level of apoptosis at 14 hours, suggesting the importance of late-onset p53-independent apoptotic responses in this mouse model. Expected radiation-induced G1 cell cycle delay was observed in Trp53+/+ but not Trp53+/-. Although p53 has an important role in cancer risk, we have shown its influence on radiation dose response can be temporally variable. This research highlights the importance of caution when using haematopoietic endpoints as surrogates to extrapolate radiation-induced cancer risk estimation.« less

  14. Analysis of Strand-Specific RNA-Seq Data Using Machine Learning...

    Office of Scientific and Technical Information (OSTI)

    Analysis of Strand-Specific RNA-Seq Data Using Machine Learning Reveals the Structures of Transcription Units in Clostridium thermocellum Citation Details In-Document Search Title: ...

  15. Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta, and IV reveal direct DNA sensing ability and differential physiological functions in DNA repair

    SciTech Connect (OSTI)

    Chen, Xi; Ballin, Jeff D.; Della-Maria, Julie; Tsai, Miaw-Sheue; White, Elizabeth J.; Tomkinson, Alan E.; Wilson, Gerald M.

    2009-05-11

    The three human LIG genes encode polypeptides that catalyze phosphodiester bond formation during DNA replication, recombination and repair. While numerous studies have identified protein partners of the human DNA ligases (hLigs), there has been little characterization of the catalytic properties of these enzymes. In this study, we developed and optimized a fluorescence-based DNA ligation assay to characterize the activities of purified hLigs. Although hLigI joins DNA nicks, it has no detectable activity on linear duplex DNA substrates with short, cohesive single-strand ends. By contrast, hLigIII{beta} and the hLigIII{alpha}/XRCC1 and hLigIV/XRCC4 complexes are active on both nicked and linear duplex DNA substrates. Surprisingly, hLigIV/XRCC4, which is a key component of the major non-homologous end joining (NHEJ) pathway, is significantly less active than hLigIII on a linear duplex DNA substrate. Notably, hLigIV/XRCC4 molecules only catalyze a single ligation event in the absence or presence of ATP. The failure to catalyze subsequent ligation events reflects a defect in the enzyme-adenylation step of the next ligation reaction and suggests that, unless there is an in vivo mechanism to reactivate DNA ligase IV/XRCC4 following phosphodiester bond formation, the cellular NHEJ capacity will be determined by the number of adenylated DNA ligaseIV/XRCC4 molecules.

  16. Selective transformations between nanoparticle superlattices via the reprogramming of DNA-mediated interactions

    SciTech Connect (OSTI)

    Zhang, Yugang; Pal, Suchetan; Srinivasan, Babji; Vo, Thi; Kumar, Sanat; Gang, Oleg

    2015-05-25

    The rapid development of self-assembly approaches has enabled the creation of materials with desired organization of nanoscale components. However, achieving dynamic control, wherein the system can be transformed on demand into multiple entirely different states, is typically absent in atomic and molecular systems and has remained elusive in designed nanoparticle systems. Here, we demonstrate with in situ small-angle x-ray scattering that, by using DNA strands as inputs, the structure of a three-dimensional lattice of DNA-coated nanoparticles can be switched from an initial 'mother' phase into one of multiple 'daughter' phases. The introduction of different types of re-programming DNA strands modifies the DNA shells of the nanoparticles within the superlattice, thereby shifting interparticle interactions to drive the transformation into a particular daughter phase. We mapped quantitatively with free-energy calculations the selective re-programming of interactions onto the observed daughter phases.

  17. Selective transformations between nanoparticle superlattices via the reprogramming of DNA-mediated interactions

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Zhang, Yugang; Pal, Suchetan; Srinivasan, Babji; Vo, Thi; Kumar, Sanat; Gang, Oleg

    2015-05-25

    The rapid development of self-assembly approaches has enabled the creation of materials with desired organization of nanoscale components. However, achieving dynamic control, wherein the system can be transformed on demand into multiple entirely different states, is typically absent in atomic and molecular systems and has remained elusive in designed nanoparticle systems. Here, we demonstrate with in situ small-angle x-ray scattering that, by using DNA strands as inputs, the structure of a three-dimensional lattice of DNA-coated nanoparticles can be switched from an initial 'mother' phase into one of multiple 'daughter' phases. The introduction of different types of re-programming DNA strands modifiesmore » the DNA shells of the nanoparticles within the superlattice, thereby shifting interparticle interactions to drive the transformation into a particular daughter phase. We mapped quantitatively with free-energy calculations the selective re-programming of interactions onto the observed daughter phases.« less

  18. A new structural framework for integrating replication protein A into DNA processing machinery

    SciTech Connect (OSTI)

    Brosey, Chris; Yan, Chunli; Tsutakawa, Susan; Heller, William; Rambo, Robert; Tainer, John; Ivanov, Ivaylo; Chazin, Walter

    2013-01-17

    By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA's DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA's DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamic on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways.

  19. Double Beta Decay Experiments

    SciTech Connect (OSTI)

    Nanal, Vandana [Dept. of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Mumbai 400 005 (India)

    2011-11-23

    At present, neutrinoless double beta decay is perhaps the only experiment that can tell us whether the neutrino is a Dirac or a Majorana particle. Given the significance of the 0{nu}{beta}{beta}, there is a widespread interest for these rare event studies employing a variety of novel techniques. This paper describes the current status of DBD experiments. The Indian effort for an underground NDBD experiment at the upcoming INO laboratory is also presented.

  20. Structural basis for DNA binding by replication initiator Mcm10

    SciTech Connect (OSTI)

    Warren, Eric M.; Vaithiyalingam, Sivaraja; Haworth, Justin; Greer, Briana; Bielinsky, Anja-Katrin; Chazin, Walter J.; Eichman, Brandt F.

    2009-06-30

    Mcm10 is an essential eukaryotic DNA replication protein required for assembly and progression of the replication fork. The highly conserved internal domain (Mcm10-ID) has been shown to physically interact with single-stranded (ss) DNA, DNA polymerase alpha, and proliferating cell nuclear antigen (PCNA). The crystal structure of Xenopus laevis Mcm10-ID presented here reveals a DNA binding architecture composed of an oligonucleotide/oligosaccharide-fold followed in tandem by a variant and highly basic zinc finger. NMR chemical shift perturbation and mutational studies of DNA binding activity in vitro reveal how Mcm10 uses this unique surface to engage ssDNA. Corresponding mutations in Saccharomyces cerevisiae result in increased sensitivity to replication stress, demonstrating the functional importance of DNA binding by this region of Mcm10 to replication. In addition, mapping Mcm10 mutations known to disrupt PCNA, polymerase alpha, and DNA interactions onto the crystal structure provides insight into how Mcm10 might coordinate protein and DNA binding within the replisome.

  1. Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

    SciTech Connect (OSTI)

    Majoros, M.; Sumption, M. D.; Collings, E. W.; Long, N. J.

    2015-04-08

    A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software. Current sharing onset was observed at about 1.02 of strand Ic. At a strand current of 1.3Ic about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s-1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3Ic) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.

  2. Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

    SciTech Connect (OSTI)

    sumption, Mike; Majoros, Milan; Collings, E. W.; Van der Laan, D. C.

    2014-11-07

    A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of IV curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software. Current sharing onset was observed at about 1.02 of strand Ic. At a strand current of 1.3Ic about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s-1, and our inter-strand resistance of 0.77 m?, (enabling a current sharing of 5% at 1.3Ic ) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 1001000 times smaller (close to those of NbTi and Nb3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.

  3. Characteristics of Cu stabilized Nb3Al strands with low Cu ratio

    SciTech Connect (OSTI)

    Kikuchi, A.; Yamada, R.; Barzi, E.; Kobayashi, M.; Lamm, M.; Nakagawa, K.; Sasaki, K.; Takeuchi, T.; Turrioni, D.; Zlobin, A.V.; /NIMC, Tsukuba /Fermilab /Hitachi, Tsuchiura Works /KEK, Tsukuba

    2008-12-01

    Characteristics of recently developed F4-Nb{sub 3}Al strand with low Cu ratio are described. The overall J{sub c} of the Nb{sub 3}Al strand could be easily increased by decreasing of the Cu ratio. Although the quench of a pulse-like voltage generation is usually observed in superconducting unstable conductor, the F4 strand with a low Cu ratio of 0.61 exhibited an ordinary critical transition of gradual voltage generation. The F4 strand does not have magnetic instabilities at 4.2 K because of the tantalum interfilament matrix. The overall J{sub c} of the F4 strand achieved was 80-85% of the RRP strand. In the large mechanical stress above 100 MPa, the overall J{sub c} of the F4 strand might be comparable to that of high J{sub c} RRP-Nb{sub 3}Sn strands. The Rutherford cable with a high packing factor of 86.5% has been fabricated using F4 strands. The small racetrack magnet, SR07, was also fabricated by a 14 m F4 cable. The quench current, I{sub q}, of SR07 were obtained 22.4 kA at 4.5 K and 25.2 kA at 2.2 K. The tantalum matrix Nb{sub 3}Al strands are promising for the application of super-cooled high-field magnets as well as 4.2 K operation magnets.

  4. Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Majoros, M.; Sumption, M. D.; Collings, E. W.; Long, N. J.

    2015-04-08

    A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software.more » Current sharing onset was observed at about 1.02 of strand Ic. At a strand current of 1.3Ic about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s-1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3Ic) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.« less

  5. Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    sumption, Mike; Majoros, Milan; Collings, E. W.; Van der Laan, D. C.

    2014-11-07

    A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software.more » Current sharing onset was observed at about 1.02 of strand Ic. At a strand current of 1.3Ic about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s-1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3Ic ) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.« less

  6. Electrostatic supersolitons and double layers at the acoustic speed

    SciTech Connect (OSTI)

    Verheest, Frank; Hellberg, Manfred A.

    2015-01-15

    Supersolitons are characterized by subsidiary extrema on the sides of a typical bipolar electric field signature or by association with a root beyond double layers in the fully nonlinear Sagdeev pseudopotential description. It has been proven that supersolitons may exist in several plasmas having at least three constituent species, but they cannot be found in weakly nonlinear theory. Another recent aspect of pseudopotential theory is that in certain plasma models and parameter regimes solitons and/or double layers can exist at the acoustic speed, having no reductive perturbation counterparts. Importantly, they signal coexistence between solitons having positive and negative polarity, in that one solution can be realized at a time, depending on infinitesimal perturbations from the equilibrium state. Weaving the two strands together, we demonstrate here that one can even find supersolitons and double layers at the acoustic speed, as illustrated using the model of cold positive and negative ions, in the presence of nonthermal electrons following a Cairns distribution. This model has been discussed before, but the existence and properties of supersolitons at the acoustic speed were not established at the time of publication.

  7. Materials, Strands, and Cables for Superconducting Accelerator Magnets. Final Report

    SciTech Connect (OSTI)

    Sumption, Mike D.; Collings, Edward W.

    2014-09-19

    This report focuses on Materials, Strands and Cables for High Energy Physics Particle accelerators. In the materials area, work has included studies of basic reactions, diffusion, transformations, and phase assemblage of Nb3Sn. These materials science aspects have been married to results, in the form of flux pinning, Bc2, Birr, and transport Jc, with an emphasis on obtaining the needed Jc for HEP needs. Attention has also been paid to the “intermediate-temperature superconductor”, magnesium diboride emphasis being placed on (i) irreversibility field enhancement, (ii) critical current density and flux pinning, and (iii) connectivity. We also report on studies of Bi-2212. The second area of the program has been in the area of “Strands” in which, aside from the materials aspect of the conductor, its physical properties and their influence on performance have been studied. Much of this work has been in the area of magnetization estimation and flux jump calculation and control. One of the areas of this work was strand instabilities in high-performance Nb3Sn conductors due to combined fields and currents. Additionally, we investigated quench and thermal propagation in YBCO coated conductors at low temperatures and high fields. The last section, “Cables”, focussed on interstrand contact resistance, ICR, it origins, control, and implications. Following on from earlier work in NbTi, the present work in Nb3Sn has aimed to make ICR intermediate between the two extremes of too little contact (no current sharing) and too much (large and unacceptable magnetization and associated beam de-focussing). Interstrand contact and current sharing measurements are being made on YBCO based Roebel cables using transport current methods. Finally, quench was investigated for YBCO cables and the magnets wound from them, presently with a focus on 50 T solenoids for muon collider applications.

  8. Allostery through protein-induced DNA bubbles

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Traverso, Joseph J.; Manoranjan, Valipuram S.; Bishop, A. R.; Rasmussen, Kim Ø.; Voulgarakis, Nikolaos K.

    2015-03-12

    Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resultingmore » melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.« less

  9. The role of structural parameters in DNA cyclization

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Alexandrov, Ludmil B.; Bishop, Alan R.; Rasmussen, Kim O.; Alexandrov, Boian S.

    2016-02-04

    The intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its propensity for cyclization, quantified by the Jacobson-Stockmayer J factor. In this paper, we use a well-established coarse-grained three-dimensional model of DNA and seven distinct sets of experimentally and computationally derived conformational parameters of the double helix to evaluate the role of structural parameters in calculating DNA cyclization.

  10. Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Sun, Jingchuan; Li, Huilin; Fernandez-Cid, Alejandra; Riera, Alberto; Tognetti, Sivia; Yuan, Zuanning; Stillman, Bruce; Speck, Christian

    2014-10-15

    Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2–7 (minichromosome maintenance proteins 2–7) double hexamer. During S phase, each Mcm2–7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC–Cdc6 function to recruit a single Cdt1–Mcm2–7 heptamer to replication origins prior to Cdt1 release and ORC–Cdc6–Mcm2–7 complex formation, but how the second Mcm2–7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC–Cdc6–Mcm2–7 complex andmore » an ORC–Cdc6–Mcm2–7–Mcm2–7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2–7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2–7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability.« less

  11. Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function

    SciTech Connect (OSTI)

    Sun, Jingchuan; Li, Huilin; Fernandez-Cid, Alejandra; Riera, Alberto; Tognetti, Sivia; Yuan, Zuanning; Stillman, Bruce; Speck, Christian

    2014-10-15

    Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2–7 (minichromosome maintenance proteins 2–7) double hexamer. During S phase, each Mcm2–7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC–Cdc6 function to recruit a single Cdt1–Mcm2–7 heptamer to replication origins prior to Cdt1 release and ORC–Cdc6–Mcm2–7 complex formation, but how the second Mcm2–7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC–Cdc6–Mcm2–7 complex and an ORC–Cdc6–Mcm2–7–Mcm2–7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2–7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2–7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability.

  12. Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function

    SciTech Connect (OSTI)

    Sun, Jingchuan [Brookhaven National Laboratory (BNL), Upton, NY (United States); Li, Huilin [Brookhaven National Laboratory (BNL), Upton, NY (United States); Stony Brook Univ., Stony Brook, NY (United States); Fernandez-Cid, Alejandra [Imperial College Faculty of Medicine, London (United Kingdom). DNA Replication Group; Riera, Alberto [Imperial College Faculty of Medicine, London (United Kingdom). MRC Clinical Sciences Centre; Tognetti, Sivia [Imperial College Faculty of Medicine, London (United Kingdom). MRC Clinical Sciences Centre; Yuan, Zuanning [Stony Brook Univ., Stony Brook, NY (United States); Stillman, Bruce [Cold Spring Harbor Lab., NY (United States); Speck, Christian [Imperial College Faculty of Medicine, London (United Kingdom). DNA Replication Group

    2014-10-15

    Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm27 (minichromosome maintenance proteins 27) double hexamer. During S phase, each Mcm27 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORCCdc6 function to recruit a single Cdt1Mcm27 heptamer to replication origins prior to Cdt1 release and ORCCdc6Mcm27 complex formation, but how the second Mcm27 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORCCdc6Mcm27 complex and an ORCCdc6Mcm27Mcm27 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm27 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm27 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability.

  13. DNA polymerase with modified processivity

    DOE Patents [OSTI]

    Bedford, Ella; Tabor, Stanley; Richardson, Charles C.

    1999-01-01

    Chimeric DNA polymerase having a DNA polymerase domain and processivity factor binding domain not naturally associated with DNA polymerase domain.

  14. DNA encoding a DNA repair protein

    DOE Patents [OSTI]

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-08-15

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  15. Magnetization anomaly of Nb3Al strands and instability of Nb3Al Rutherford cables

    SciTech Connect (OSTI)

    Yamada, Ryuji; Kikuchi, Akihiro; Wake, Masayoshi; /KEK, Tsukuba

    2006-08-01

    Using a Cu stabilized Nb{sub 3}Al strand with Nb matrix, a 30 meter long Nb{sub 3}Al Rutherford cable was made by a collaboration of Fermilab and NIMS. Recently the strand and cable were tested. In both cases instability was observed at around 1.5 Tesla. The magnetization of this Nb{sub 3}Al strand was measured first using a balanced coil magnetometer at 4.2 K. Strands showed an anomalously large magnetization behavior around at 1.6 T, which is much higher than the usual B{sub c2} {approx} 0.5 Tesla (4.2 K) of Nb matrix. This result is compared with the magnetization data of short strand samples using a SQUID magnetometer, in which a flux-jump signal was observed at 0.5 Tesla, but not at higher field. As a possible explanation for this magnetization anomaly, the interfilament coupling through the thin Nb films in the strands is suggested. The instability problem observed in low field tests of the Nb{sub 3}Al Rutherford cables is attributed to this effect.

  16. Double acting bit holder

    DOE Patents [OSTI]

    Morrell, Roger J.; Larson, David A.; Ruzzi, Peter L.

    1994-01-01

    A double acting bit holder that permits bits held in it to be resharpened during cutting action to increase energy efficiency by reducing the amount of small chips produced. The holder consist of: a stationary base portion capable of being fixed to a cutter head of an excavation machine and having an integral extension therefrom with a bore hole therethrough to accommodate a pin shaft; a movable portion coextensive with the base having a pin shaft integrally extending therefrom that is insertable in the bore hole of the base member to permit the moveable portion to rotate about the axis of the pin shaft; a recess in the movable portion of the holder to accommodate a shank of a bit; and a biased spring disposed in adjoining openings in the base and moveable portions of the holder to permit the moveable portion to pivot around the pin shaft during cutting action of a bit fixed in a turret to allow front, mid and back positions of the bit during cutting to lessen creation of small chip amounts and resharpen the bit during excavation use.

  17. Quantitative DNA fiber mapping

    DOE Patents [OSTI]

    Gray, Joe W.; Weier, Heinz-Ulrich G.

    1998-01-01

    The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

  18. Manganese oxide helices, rings, strands, and films, and methods for their preparation

    DOE Patents [OSTI]

    Suib, Steven L.; Giraldo, Oscar; Marquez, Manuel; Brock, Stephanie

    2003-01-07

    Methods for the preparation of mixed-valence manganese oxide compositions with quaternary ammonium ions are described. The compositions self-assemble into helices, rings, and strands without any imposed concentration gradient. These helices, rings, and strands, as well as films having the same composition, undergo rapid ion exchange to replace the quaternary ammonium ions with various metal ions. And the metal-ion-containing manganese oxide compositions so formed can be heat treated to form semi-conducting materials with high surface areas.

  19. The influence of TRP53 in the dose response of radiation-induced apoptosis, DNA repair and genomic stability in murine haematopoietic cells

    SciTech Connect (OSTI)

    Lemon, Jennifer A.; Taylor, Kristina; Verdecchia, Kyle; Phan, Nghi; Boreham, Douglas R.

    2014-01-01

    Apoptotic and DNA damage endpoints are frequently used as surrogate markers of cancer risk, and have been well-studied in the Trp53+/- mouse model. We report the effect of differing Trp53 gene status on the dose response of ionizing radiation exposures (0.01-2 Gy), with the unique perspective of determining if effects of gene status remain at extended time points. Here we report no difference in the dose response for radiation-induced DNA double-strand breaks in bone marrow and genomic instability (MN-RET levels) in peripheral blood, between wild-type (Trp53+/+) and heterozygous (Trp53+/-) mice. The dose response for Trp53+/+ mice showed higher initial levels of radiation-induced lymphocyte apoptosis relative to Trp53+/- between 0 and 1 Gy. Although this trend was observed up to 12 hours post-irradiation, both genotypes ultimately reached the same level of apoptosis at 14 hours, suggesting the importance of late-onset p53-independent apoptotic responses in this mouse model. Expected radiation-induced G1 cell cycle delay was observed in Trp53+/+ but not Trp53+/-. Although p53 has an important role in cancer risk, we have shown its influence on radiation dose response can be temporally variable. This research highlights the importance of caution when using haematopoietic endpoints as surrogates to extrapolate radiation-induced cancer risk estimation.

  20. Method for introducing unidirectional nested deletions

    DOE Patents [OSTI]

    Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

    1999-07-27

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  1. Method for introducing unidirectional nested deletions

    DOE Patents [OSTI]

    Dunn, J.J.; Quesada, M.A.; Randesi, M.

    1999-07-27

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector. The cloning vector has an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe. 1 fig.

  2. Double field theory inspired cosmology

    SciTech Connect (OSTI)

    Wu, Houwen; Yang, Haitang E-mail: hyanga@scu.edu.cn

    2014-07-01

    Double field theory proposes a generalized spacetime action possessing manifest T-duality on the level of component fields. We calculate the cosmological solutions of double field theory with vanishing Kalb-Ramond field. It turns out that double field theory provides a more consistent way to construct cosmological solutions than the standard string cosmology. We construct solutions for vanishing and non-vanishing symmetry preserving dilaton potentials. The solutions assemble the pre- and post-big bang evolutions in one single line element. Our results show a smooth evolution from an anisotropic early stage to an isotropic phase without any special initial conditions in contrast to previous models. In addition, we demonstrate that the contraction of the dual space automatically leads to both an inflation phase and a decelerated expansion of the ordinary space during different evolution stages.

  3. DNA tagged microparticles

    DOE Patents [OSTI]

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  4. Attosecond Double-Slit Experiment

    SciTech Connect (OSTI)

    Lindner, F.; Schaetzel, M.G.; Baltuska, A.; Goulielmakis, E.; Walther, H.; Krausz, F.; Milosevic, D.B.; Bauer, D.; Becker, W.; Paulus, G.G.

    2005-07-22

    A new scheme for a double-slit experiment in the time domain is presented. Phase-stabilized few-cycle laser pulses open one to two windows (slits) of attosecond duration for photoionization. Fringes in the angle-resolved energy spectrum of varying visibility depending on the degree of which-way information are measured. A situation in which one and the same electron encounters a single and a double slit at the same time is observed. The investigation of the fringes makes possible interferometry on the attosecond time scale. From the number of visible fringes, for example, one derives that the slits are extended over about 500 as.

  5. Nb3Sn RRP® strand and Rutherford cable development for a 15 T dipole demonstrator

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Barzi, E.; Andreev, N.; Li, P.; Lombardo, V.; Turrioni, D.; Zlobin, A. V.

    2016-03-16

    Keystoned Rutherford cables made of 28 strands and with a stainless steel core were developed and manufactured using 1 mm Nb3Sn composite wires produced by Oxford Superconducting Technology with 127 and 169 restacks using the Restacked-Rod-Process®. Furthermore, the performance and properties of these cables were studied to evaluate possible candidates for 15 T accelerator magnets.

  6. The double well mass filter

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Gueroult, Renaud; Rax, Jean -Marcel; Fisch, Nathaniel J.

    2014-02-03

    Various mass filter concepts based on rotating plasmas have been suggested with the specific purpose of nuclear waste remediation. We report on a new rotating mass filter combining radial separation with axial extraction. Lastly, the radial separation of the masses is the result of a “double-well” in effective radial potential in rotating plasma with a sheared rotation profile.

  7. Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full cyclic testing in SULTAN: II. Significant reduction of strand movement and strand damage in short twist pitch CICCs

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Sanabria, Charlos; Lee, Peter J.; Starch, William; Devred, Arnaud; Larbalestier, David C.

    2015-10-14

    Prototype cable in conduit conductors (CICCs) destined for use in the Toroidal Field (TF) and Central Solenoid (CS) coils of the ITER experimental fusion reactor underwent severe cyclic loading in the SULTAN facility. Their autopsies revealed significant and permanent transverse strand migration due to the large Lorentz forces of the SULTAN test. The movement resulted in a 3 7% void fraction increase on the Low Pressure (LP) side of the longer twist pitch CICCs. However, short twist pitch conductors exhibited less than 1% void fraction increase in the LP side, as well as a complete absence of the Nb3Sn filamentmore » fractures observed in the longer twist pitch conductors. We report here a detailed strand to cable analysis of short and longer “baseline” twist pitch CICCs. It was found that the use of Internal Tin strands in the longer “baseline” twist pitch CICCs can be beneficial possibly because of their superior stiffness—which better resist strand movement—while the use of Bronze Process strands showed more movement and poorer cyclic test performance. This was not the case for the short twist pitch CICC. Such conductor design seems to work well with both strand types. But it was found that despite the absence of filament fractures, the short twist pitch CICC made from the Internal Tin strands studied here developed severe strand distortion during cabling which resulted in diffusion barrier breaks and Sn contamination of the Cu stabilizer during the heat treatment. Furthermore, the short twist pitch CICC made from Bronze Process strands preserved diffusion barrier integrity.« less

  8. Endogenous DNA Damage and Risk of Testicular Germ Cell Tumors

    SciTech Connect (OSTI)

    Cook, M B; Sigurdson, A J; Jones, I M; Thomas, C B; Graubard, B I; Korde, L; Greene, M H; McGlynn, K A

    2008-01-18

    Testicular germ cell tumors (TGCT) are comprised of two histologic groups, seminomas and nonseminomas. We postulated that the possible divergent pathogeneses of these histologies may be partially explained by variable endogenous DNA damage. To assess our hypothesis, we conducted a case-case analysis of seminomas and nonseminomas using the alkaline comet assay to quantify single-strand DNA breaks and alkali-labile sites. The Familial Testicular Cancer study and the U.S. Radiologic Technologists cohort provided 112 TGCT cases (51 seminomas & 61 nonseminomas). A lymphoblastoid cell line was cultured for each patient and the alkaline comet assay was used to determine four parameters: tail DNA, tail length, comet distributed moment (CDM) and Olive tail moment (OTM). Odds ratios (OR) and 95% confidence intervals (95%CI) were estimated using logistic regression. Values for tail length, tail DNA, CDM and OTM were modeled as categorical variables using the 50th and 75th percentiles of the seminoma group. Tail DNA was significantly associated with nonseminoma compared to seminoma (OR{sub 50th percentile} = 3.31, 95%CI: 1.00, 10.98; OR{sub 75th percentile} = 3.71, 95%CI: 1.04, 13.20; p for trend=0.039). OTM exhibited similar, albeit statistically non-significant, risk estimates (OR{sub 50th percentile} = 2.27, 95%CI: 0.75, 6.87; OR{sub 75th percentile} = 2.40, 95%CI: 0.75, 7.71; p for trend=0.12) whereas tail length and CDM showed no association. In conclusion, the results for tail DNA and OTM indicate that endogenous DNA damage levels are higher in patients who develop nonseminoma compared with seminoma. This may partly explain the more aggressive biology and younger age-of-onset of this histologic subgroup compared with the relatively less aggressive, later-onset seminoma.

  9. Minimal Doubling and Point Splitting

    SciTech Connect (OSTI)

    Creutz, M.

    2010-06-14

    Minimally-doubled chiral fermions have the unusual property of a single local field creating two fermionic species. Spreading the field over hypercubes allows construction of combinations that isolate specific modes. Combining these fields into bilinears produces meson fields of specific quantum numbers. Minimally-doubled fermion actions present the possibility of fast simulations while maintaining one exact chiral symmetry. They do, however, introduce some peculiar aspects. An explicit breaking of hyper-cubic symmetry allows additional counter-terms to appear in the renormalization. While a single field creates two different species, spreading this field over nearby sites allows isolation of specific states and the construction of physical meson operators. Finally, lattice artifacts break isospin and give two of the three pseudoscalar mesons an additional contribution to their mass. Depending on the sign of this mass splitting, one can either have a traditional Goldstone pseudoscalar meson or a parity breaking Aoki-like phase.

  10. Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches

    DOE Patents [OSTI]

    McCutchen-Maloney, Sandra L.

    2002-01-01

    DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.

  11. Large scale DNA microsequencing device

    DOE Patents [OSTI]

    Foote, R.S.

    1999-08-31

    A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means. 11 figs.

  12. Large scale DNA microsequencing device

    DOE Patents [OSTI]

    Foote, R.S.

    1997-08-26

    A microminiature sequencing apparatus and method provide a means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus cosists of a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means. 17 figs.

  13. Large scale DNA microsequencing device

    DOE Patents [OSTI]

    Foote, Robert S.

    1999-01-01

    A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means.

  14. Large scale DNA microsequencing device

    DOE Patents [OSTI]

    Foote, Robert S.

    1997-01-01

    A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means.

  15. Green Future Double Barrel House

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    University Green Future Double Barrel House DOE Race to Zero Student Competition 2016 Sean Benson Team Leader - Net Zero Energy Design I & II Bachelor of Science in Architecture, Dec 2016 Alexis Borman Net Zero Energy Design II Bachelor of Science in Architecture, May 2016 Christopher Brown AIA COTE, Net Zero Energy Design I & II Bachelor of Science in Architecture, May 2016 Devonta Magee Net Zero Energy Design II Bachelor of Science in Architecture, Aug 2016 Yasmine Parker Net Zero

  16. Pair extended coupled cluster doubles

    SciTech Connect (OSTI)

    Henderson, Thomas M.; Scuseria, Gustavo E.; Bulik, Ireneusz W.

    2015-06-07

    The accurate and efficient description of strongly correlated systems remains an important challenge for computational methods. Doubly occupied configuration interaction (DOCI), in which all electrons are paired and no correlations which break these pairs are permitted, can in many cases provide an accurate account of strong correlations, albeit at combinatorial computational cost. Recently, there has been significant interest in a method we refer to as pair coupled cluster doubles (pCCD), a variant of coupled cluster doubles in which the electrons are paired. This is simply because pCCD provides energies nearly identical to those of DOCI, but at mean-field computational cost (disregarding the cost of the two-electron integral transformation). Here, we introduce the more complete pair extended coupled cluster doubles (pECCD) approach which, like pCCD, has mean-field cost and reproduces DOCI energetically. We show that unlike pCCD, pECCD also reproduces the DOCI wave function with high accuracy. Moreover, pECCD yields sensible albeit inexact results even for attractive interactions where pCCD breaks down.

  17. Doubling Geothermal Generation Capacity by 2020: A Strategic...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Doubling Geothermal Generation Capacity by 2020: A Strategic Analysis Doubling Geothermal Generation Capacity by 2020: A Strategic Analysis PDF icon NREL Doubling Geothermal ...

  18. DNA ELECTROPHORESIS AT SURFACES

    SciTech Connect (OSTI)

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01

    During this year we performed two major projects: I. We developed a detailed theoretical model which complements our experiments on surface DNA electrophoresis. We found that it was possible to enhance the separation of DNA chains by imposing a chemical nanoscale pattern on the surface. This approach utilized the surface interaction effect of the DNA chains with the substrate and is a refinement to our previous method in which DNA chains were separated on homogeneous flat surfaces. By introducing the nano-patterns on the surface, the conformational changes of DNA chains of different lengths can be amplified, which results in the different friction strengths with the substrate surface. Our results also show that, when compared to the DNA electrophoresis performed on homogeneous flat surfaces, nanopatterned surfaces offer a larger window in choosing different surface interactions to achieve separation. II. In collaboration with a large international manufacturer of skin care products we also embarked on a project involving photo toxicity of titanium dioxide nanoparticles, which are a key ingredient in sunscreen and cosmetic lotions. The results clearly implicated the nanoparticles in catalyzing damage to chromosomal DNA. We then used this knowledge to develop a polymer/anti-oxidant coating which prevented the photocatalytic reaction on DNA while still retaining the UV absorptive properties of the nanoparticles. The standard gel electrophoresis was not sufficient in determining the extent of the DNA damage. The conclusions of this study were based predominantly on analysis obtained with the surface electrophoresis method.

  19. Controlling DNA Methylation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Controlling DNA Methylation Though life on earth is composed of a diverse range of organisms, some with many different types of tissues and cells, all these are encoded by a molecule we call DNA. The information required to build a protein is stored in DNA within the cells. Not all the message in the DNA is used in each cell and not all the message is used all the time. During cell differentiation, the cells become dedicated for their specific function which involves selectively activating some

  20. Evaluation of Juvenile Fall Chinook Stranding on the Hanford Reach, 1997-1999 Interim Report.

    SciTech Connect (OSTI)

    Wagner, Paul; Nugent, John; Price, William

    1999-02-15

    Pilot work conducted in 1997 to aid the development of the study for the 1998 Evaluation of Juvenile Fall Chinook Stranding on The Hanford Reach. The objectives of the 1997 work were to: (1) identify juvenile chinook production and rearing areas..., (2) identify sampling sites and develop the statistical parameters necessary to complete the study, (3) develop a study plan..., (4) conduct field sampling activities...

  1. DNA-cell conjugates

    DOE Patents [OSTI]

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2016-05-03

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  2. Booster double harmonic setup notes

    SciTech Connect (OSTI)

    Gardner, C. J.

    2015-02-17

    The motivation behind implementing a booster double harmonic include the reduced transverse space charge force from a reduced peak beam current and reduced momentum spread of the beam, both of which can be achieved from flattening the RF bucket. RF capture and acceleration of polarized protons (PP) is first set up in the single harmonic mode with RF harmonic h=1. Once capture and acceleration have been set up in the single harmonic mode, the second harmonic system is brought on and programmed to operate in concert with the single harmonic system.

  3. Comparison of two freshwater turtle species as monitors of radionuclide and chemical contamination: DNA damage and residue analysis

    SciTech Connect (OSTI)

    Meyers-Schoene, L. ); Shugart, L.R.; Beauchamp, J.J.; Walton, B.T. )

    1993-08-01

    Two species of turtles that occupy different ecological niches were compared for their usefulness as monitors of freshwater ecosystems where both low-level radioactive and nonradioactive contaminants are present. The pond slider (Trachemys scripta) and common snapping turtle (Chelydra serpentina) were analyzed for the presence of [sup 90]Sr, [sup 137]Cs, [sup 60]Co, and Hg, radionuclides and chemicals known to be present at the contaminated site, and single-strand breaks in liver DNA. The integrity of the DNA was examined by the alkaline unwinding assay, a technique that detects strand breaks as a biological marker of possible exposure to genotoxic agents. This measure of DNA damage was significantly increased in both species of turtles at the contaminated site compared with turtles of the same species at a reference site, and shows that contaminant-exposed populations were under more severe genotoxic stress than those at the reference site. The level of strand breaks observed at the contaminated site was high and in the range reported for other aquatic species exposed to deleterious concentrations of genotoxic agents such as chemicals and ionizing radiation. Statistically significantly higher concentrations of radionuclides and Hg were detected in the turtles from the contaminated area. Mercury concentrations were significantly higher in the more carnivorous snapping turtle compared with the slider; however, both species were effective monitors of the contaminants.

  4. Double distributions and evolution equations

    SciTech Connect (OSTI)

    A.V. Radyushkin

    1998-05-01

    Applications of perturbative QCD to deeply virtual Compton scattering and hard exclusive meson electroproduction processes require a generalization of usual parton distributions for the case when long-distance information is accumulated in nonforward matrix elements < p{prime} {vert_bar}O(0,z){vert_bar}p > of quark and gluon light-cone operators. In their previous papers the authors used two types of nonperturbative functions parameterizing such matrix elements: double distributions F(x,y;t) and nonforward distribution functions F{sub {zeta}}(X;t). Here they discuss in more detail the double distributions (DD's) and evolution equations which they satisfy. They propose simple models for F(x,y;t=0) DD's with correct spectral and symmetry properties which also satisfy the reduction relations connecting them to the usual parton densities f(x). In this way, they obtain self-consistent models for the {zeta}-dependence of nonforward distributions. They show that, for small {zeta}, one can easily obtain nonforward distributions (in the X > {zeta} region) from the parton densities: F{sub {zeta}} (X;t=0) {approx} f(X{minus}{zeta}/2).

  5. Quantitive DNA Fiber Mapping

    SciTech Connect (OSTI)

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  6. Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches

    DOE Patents [OSTI]

    McCutchen-Maloney, Sandra L.

    2002-01-01

    Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.

  7. DNA-PK assay

    DOE Patents [OSTI]

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12

    The present invention provides a method for detecting DNA-activated protein kinase (DNA-PK) activity in a biological sample. The method includes contacting a biological sample with a detectably-labeled phosphate donor and a synthetic peptide substrate defined by the following features to provide specific recognition and phosphorylation by DNA-PK: (1) a phosphate-accepting amino acid pair which may include serine-glutamine (Ser-Gln) (SQ), threonine-glutamine (Thr-Gln) (TQ), glutamine-serine (Gln-Ser) (QS), or glutamine-threonine (Gln-Thr) (QT); (2) enhancer amino acids which may include glutamic acid or glutamine immediately adjacent at the amino- or carboxyl- side of the amino acid pair and forming an amino acid pair-enhancer unit; (3) a first spacer sequence at the amino terminus of the amino acid pair-enhancer unit; (4) a second spacer sequence at the carboxyl terminus of the amino acid pair-enhancer unit, which spacer sequences may include any combination of amino acids that does not provide a phosphorylation site consensus sequence motif; and, (5) a tag moiety, which may be an amino acid sequence or another chemical entity that permits separating the synthetic peptide from the phosphate donor. A compostion and a kit for the detection of DNA-PK activity are also provided. Methods for detecting DNA, protein phosphatases and substances that alter the activity of DNA-PK are also provided. The present invention also provides a method of monitoring protein kinase and DNA-PK activity in living cells. -A composition and a kit for monitoring protein kinase activity in vitro and a composition and a kit for monitoring DNA-PK activities in living cells are also provided. A method for identifying agents that alter protein kinase activity in vitro and a method for identifying agents that alter DNA-PK activity in living cells are also provided.

  8. The Chromodomains of the Chd1 Chromatin Remodeler Regulate DNA Access to the ATPase Motor

    SciTech Connect (OSTI)

    Hauk, G.; McKnight, J; Nodelman, I; Bowman, G

    2010-01-01

    Chromatin remodelers are ATP-driven machines that assemble, slide, and remove nucleosomes from DNA, but how the ATPase motors of remodelers are regulated is poorly understood. Here we show that the double chromodomain unit of the Chd1 remodeler blocks DNA binding and activation of the ATPase motor in the absence of nucleosome substrates. The Chd1 crystal structure reveals that an acidic helix joining the chromodomains can pack against a DNA-binding surface of the ATPase motor. Disruption of the chromodomain-ATPase interface prevents discrimination between nucleosomes and naked DNA and reduces the reliance on the histone H4 tail for nucleosome sliding. We propose that the chromodomains allow Chd1 to distinguish between nucleosomes and naked DNA by physically gating access to the ATPase motor, and we hypothesize that related ATPase motors may employ a similar strategy to discriminate among DNA-containing substrates.

  9. Cadmium sulfate and CdTe-quantum dots alter DNA repair in zebrafish (Danio rerio) liver cells

    SciTech Connect (OSTI)

    Tang, Song; Cai, Qingsong; Chibli, Hicham; Allagadda, Vinay; Nadeau, Jay L.; Mayer, Gregory D.

    2013-10-15

    Increasing use of quantum dots (QDs) makes it necessary to evaluate their toxicological impacts on aquatic organisms, since their contamination of surface water is inevitable. This study compares the genotoxic effects of ionic Cd versus CdTe nanocrystals in zebrafish hepatocytes. After 24 h of CdSO{sub 4} or CdTe QD exposure, zebrafish liver (ZFL) cells showed a decreased number of viable cells, an accumulation of Cd, an increased formation of reactive oxygen species (ROS), and an induction of DNA strand breaks. Measured levels of stress defense and DNA repair genes were elevated in both cases. However, removal of bulky DNA adducts by nucleotide excision repair (NER) was inhibited with CdSO{sub 4} but not with CdTe QDs. The adverse effects caused by acute exposure of CdTe QDs might be mediated through differing mechanisms than those resulting from ionic cadmium toxicity, and studying the effects of metallic components may be not enough to explain QD toxicities in aquatic organisms. - Highlights: Both CdSO{sub 4} and CdTe QDs lead to cell death and Cd accumulation. Both CdSO{sub 4} and CdTe QDs induce cellular ROS generation and DNA strand breaks. Both CdSO{sub 4} and CdTe QDs induce the expressions of stress defense and DNA repair genes. NER repair capacity was inhibited with CdSO{sub 4} but not with CdTe QDs.

  10. Double perovskite catalysts for oxidative coupling

    DOE Patents [OSTI]

    Campbell, Kenneth D.

    1991-01-01

    Alkali metal doped double perovskites containing manganese and at least one of cobalt, iron and nickel are useful in the oxidative coupling of alkane to higher hydrocarbons.

  11. DNA | Open Energy Information

    Open Energy Info (EERE)

    Lead Agency District Office Development Phase(s) Techniques DNA-NV-030-09-03 Dusty Miller LLC BLM BLM Carson City District Office BLM Stillwater Field Office BLM...

  12. Multiplex analysis of DNA

    DOE Patents [OSTI]

    Church, George M.; Kieffer-Higgins, Stephen

    1992-01-01

    This invention features vectors and a method for sequencing DNA. The method includes the steps of: a) ligating the DNA into a vector comprising a tag sequence, the tag sequence includes at least 15 bases, wherein the tag sequence will not hybridize to the DNA under stringent hybridization conditions and is unique in the vector, to form a hybrid vector, b) treating the hybrid vector in a plurality of vessels to produce fragments comprising the tag sequence, wherein the fragments differ in length and terminate at a fixed known base or bases, wherein the fixed known base or bases differs in each vessel, c) separating the fragments from each vessel according to their size, d) hybridizing the fragments with an oligonucleotide able to hybridize specifically with the tag sequence, and e) detecting the pattern of hybridization of the tag sequence, wherein the pattern reflects the nucleotide sequence of the DNA.

  13. Double bevel construction of a diamond anvil

    DOE Patents [OSTI]

    Moss, William C.

    1988-01-01

    A double or multiple bevel culet geometry is used on a diamond anvil in a high pressure cell apparatus to provide increased sample pressure and stability for a given force applied to the diamond tables. Double or multiple bevel culet geometries can also be used for sapphire or other hard crystal anvils. Pressures up to and above 5 Megabars can be reached.

  14. Double bevel construction of a diamond anvil

    DOE Patents [OSTI]

    Moss, W.C.

    1988-10-11

    A double or multiple bevel culet geometry is used on a diamond anvil in a high pressure cell apparatus to provide increased sample pressure and stability for a given force applied to the diamond tables. Double or multiple bevel culet geometries can also be used for sapphire or other hard crystal anvils. Pressures up to and above 5 Megabars can be reached. 8 figs.

  15. Final Report: MATERIALS, STRANDS, AND CABLES FOR SUPERCONDUCTING ACCELERATOR MAGNETS [Grant Number DE-SC0010312

    SciTech Connect (OSTI)

    Sumption, Mike; Collings, E.

    2014-10-29

    Our program consisted of the two components: Strand Research and Cable Research, with a focus on Nb3Sn, Bi2212, and YBCO for accelerator magnet applications. We demonstrated a method to refine the grains in Nb3Sn by a factor of two, reaching 45 nm grain sizes, and layer Jcs of 6 kA/mm2 at 12 T. W also measured conductor magnetization for field quality. This has been done both with Nb3Sn conductor, as well as Bi:2212 strand. Work in support of quench studies of YBCO coils was also performed. Cable loss studies in Nb3Sn focused on connecting and comparing persistent magnetization and coupling magnetization for considering their relative impact on HEP machines. In the area of HTS cables, we have investigated both the quench in multistrand YBCO CORC cables, as well as the magnetization of these cables for use in high field magnets. In addition, we examined the magnetic and thermal properties of large (50 T) solenoids.

  16. Reliability Estimation for Double Containment Piping

    SciTech Connect (OSTI)

    L. Cadwallader; T. Pinna

    2012-08-01

    Double walled or double containment piping is considered for use in the ITER international project and other next-generation fusion device designs to provide an extra barrier for tritium gas and other radioactive materials. The extra barrier improves confinement of these materials and enhances safety of the facility. This paper describes some of the design challenges in designing double containment piping systems. There is also a brief review of a few operating experiences of double walled piping used with hazardous chemicals in different industries. This paper recommends approaches for the reliability analyst to use to quantify leakage from a double containment piping system in conceptual and more advanced designs. The paper also cites quantitative data that can be used to support such reliability analyses.

  17. Instability limits for spontaneous double layer formation

    SciTech Connect (OSTI)

    Carr, J. Jr.; Department of Physics, Texas Lutheran University, Seguin, Texas 78155 ; Galante, M. E.; McCarren, D.; Scime, E. E.; Sears, S.; VanDervort, R. W.; Magee, R. M.; TriAlpha Energy, Inc., Foothill Ranch, California 92610 ; Reynolds, E.

    2013-11-15

    We present time-resolved measurements that demonstrate that large amplitude electrostatic instabilities appear in pulsed, expanding helicon plasmas at the same time as particularly strong double layers appear in the expansion region. A significant cross-correlation between the electrostatic fluctuations and fluctuations in the number of ions accelerated by the double layer electric field is observed. No correlation is observed between the electrostatic fluctuations and ions that have not passed through the double layer. These measurements confirm that the simultaneous appearance of the electrostatic fluctuations and the double layer is not simple coincidence. In fact, the accelerated ion population is responsible for the growth of the instability. The double layer strength, and therefore, the velocity of the accelerated ions, is limited by the appearance of the electrostatic instability.

  18. Structural basis for suppression of hypernegative DNA supercoiling by E. coli topoisomerase I

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Tan, Kemin; Zhou, Qingxuan; Cheng, Bokun; Zhang, Zhongtao; Joachimiak, Andrzej; Tse-Dinh, Yuk -Ching

    2015-10-20

    Escherichia coli topoisomerase I has an essential function in preventing hypernegative supercoiling of DNA. A full length structure of E. coli topoisomerase I reported here shows how the C-terminal domains bind single-stranded DNA (ssDNA) to recognize the accumulation of negative supercoils in duplex DNA. These C-terminal domains of E. coli topoisomerase I are known to interact with RNA polymerase, and two flexible linkers within the C-terminal domains may assist in the movement of the ssDNA for the rapid removal of transcription driven negative supercoils. The structure has also unveiled for the first time how the 4-Cys zinc ribbon domain andmore » zinc ribbon-like domain bind ssDNA with primarily π -stacking interactions. Finally, this novel structure, in combination with new biochemical data, provides important insights into the mechanism of genome regulation by type IA topoisomerases that is essential for life, as well as the structures of homologous type IA TOP3α and TOP3β from higher eukaryotes that also have multiple 4-Cys zinc ribbon domains required for their physiological functions.« less

  19. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... laser-accelerated protons on human lung cancer cells.more In-vitro A549 cells are ... of DNA double-strand breaks in human cancer cells Yogo, A. ; Nishikino, M. ; Mori, M. ...

  20. Double-disc gate valve

    DOE Patents [OSTI]

    Wheatley, Seth J.

    1979-01-01

    This invention relates to an improvement in a conventional double-disc gate valve having a vertically movable gate assembly including a wedge, spreaders slidably engaged therewtih, a valve disc carried by the spreaders. When the gate assembly is lowered to a selected point in the valve casing, the valve discs are moved transversely outward to close inlet and outlet ports in the casing. The valve includes hold-down means for guiding the disc-and-spreader assemblies as they are moved transversely outward and inward. If such valves are operated at relatively high differential pressures, they sometimes jam during opening. Such jamming has been a problem for many years in gate valves used in gaseous diffusion plants for the separtion of uranium isotopes. The invention is based on the finding that the above-mentioned jamming results when the outlet disc tilts about its horizontal axis in a certain way during opening of the valve. In accordance with the invention, tilting of the outlet disc is maintained at a tolerable value by providing the disc with a rigid downwardly extending member and by providing the casing with a stop for limiting inward arcuate movement of the member to a preselected value during opening of the valve.

  1. Two-subunit DNA escort mechanism and inactive subunit bypass in an ultra-fast ring ATPase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Liu, Ninning; Chistol, Gheorghe; Bustamante, Carlos

    2015-10-09

    SpoIIIE is a homo-hexameric dsDNA translocase responsible for completing chromosome segregation in Bacillus subtilis . Here, we use a single-molecule approach to monitor SpoIIIE translocation when challenged with neutral-backbone DNA and non-hydrolyzable ATP analogs. We show that SpoIIIE makes multiple essential contacts with phosphates on the 5'→3' strand in the direction of translocation. Using DNA constructs with two neutral-backbone segments separated by a single charged base pair, we deduce that SpoIIIE’s step size is 2 bp. Finally, experiments with non-hydrolyzable ATP analogs suggest that SpoIIIE can operate with non-consecutive inactive subunits. We propose a two-subunit escort translocation mechanism thatmore » is strict enough to enable SpoIIIE to track one DNA strand, yet sufficiently compliant to permit the motor to bypass inactive subunits without arrest. We speculate that such a flexible mechanism arose for motors that, like SpoIIIE, constitute functional bottlenecks where the inactivation of even a single motor can be lethal for the cell.« less

  2. Double-reed exhaust valve engine

    DOE Patents [OSTI]

    Bennett, Charles L.

    2015-06-30

    An engine based on a reciprocating piston engine that extracts work from pressurized working fluid. The engine includes a double reed outlet valve for controlling the flow of low-pressure working fluid out of the engine. The double reed provides a stronger force resisting closure of the outlet valve than the force tending to open the outlet valve. The double reed valve enables engine operation at relatively higher torque and lower efficiency at low speed, with lower torque, but higher efficiency at high speed.

  3. Development of double-decker pulse radiolysis

    SciTech Connect (OSTI)

    Kan, K.; Kondoh, T.; Yang, J.; Ogata, A.; Norizawa, K.; Yoshida, Y.

    2012-07-15

    Double-decker pulse radiolysis (DDPR), which utilizes double-decker electron beams, was investigated to develop a new pulse radiolysis with a high time resolution. The double-decker electron beams were generated by injecting two UV pulses into a photocathode radio-frequency gun. In the pulse radiolysis, one electron beam was used as a pump beam, and the other was converted to a probe pulse. Finally, as its first application, the DDPR was successfully used for observing solvated electrons in water, with a 10%-90% rise time of 8.6 ps.

  4. DNA polymerase having modified nucleotide binding site for DNA sequencing

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles

    1997-01-01

    Modified gene encoding a modified DNA polymerase wherein the modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase.

  5. DNA polymerase having modified nucleotide binding site for DNA sequencing

    DOE Patents [OSTI]

    Tabor, S.; Richardson, C.

    1997-03-25

    A modified gene encoding a modified DNA polymerase is disclosed. The modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase. 6 figs.

  6. DNA tagged microparticles

    DOE Patents [OSTI]

    Farquar, George R.; Leif, Roald N.; Wheeler, Elizabeth

    2016-03-22

    In one embodiment, a product includes a plurality of particles, each particle including: a carrier that includes a non-toxic material; and at least one DNA barcode coupled to the carrier, where the particles each have a diameter in a range from about 1 nanometer to about 100 microns.

  7. Crystal Structure of a Super Leucine Zipper an Extended Two-Stranded Super Long Coiled Coil

    SciTech Connect (OSTI)

    J Diao

    2011-12-31

    Coiled coil is a ubiquitous structural motif in proteins, with two to seven alpha helices coiled together like the strands of a rope, and coiled coil folding and assembly is not completely understood. A GCN4 leucine zipper mutant with four mutations of K3A, D7A, Y17W, and H18N has been designed, and the crystal structure has been determined at 1.6 {angstrom} resolution. The peptide monomer shows a helix trunk with short curved N- and C-termini. In the crystal, two monomers cross in 35{sup o} and form an X-shaped dimer, and each X-shaped dimer is welded into the next one through sticky hydrophobic ends, thus forming an extended two-stranded, parallel, super long coiled coil rather than a discrete, two-helix coiled coil of the wild-type GCN4 leucine zipper. Leucine residues appear at every seventh position in the super long coiled coil, suggesting that it is an extended super leucine zipper. Compared to the wild-type leucine zipper, the N-terminus of the mutant has a dramatic conformational change and the C-terminus has one more residue Glu 32 determined. The mutant X-shaped dimer has a large crossing angle of 35{sup o} instead of 18{sup o} in the wild-type dimer. The results show a novel assembly mode and oligomeric state of coiled coil, and demonstrate that mutations may affect folding and assembly of the overall coiled coil. Analysis of the formation mechanism of the super long coiled coil may help understand and design self-assembling protein fibers.

  8. Water-lithium bromide double-effect absorption cooling analysis...

    Office of Scientific and Technical Information (OSTI)

    Water-lithium bromide double-effect absorption cooling analysis Citation Details In-Document Search Title: Water-lithium bromide double-effect absorption cooling analysis You ...

  9. SciTech Connect: "neutrinoless double beta decay"

    Office of Scientific and Technical Information (OSTI)

    neutrinoless double beta decay" Find + Advanced Search Term Search Semantic Search Advanced Search All Fields: "neutrinoless double beta decay" Semantic Semantic Term Title:...

  10. Double Shock Experiments and Reactive Flow Modeling of High Pressure...

    Office of Scientific and Technical Information (OSTI)

    Double Shock Experiments and Reactive Flow Modeling of High Pressure LX-17 Detonation Reaction Product States Citation Details In-Document Search Title: Double Shock Experiments ...

  11. Double bevel construction of a diamond anvil

    DOE Patents [OSTI]

    Moss, W.C.

    1987-02-06

    Use of double or multiple bevel culet geometry on a diamond anvil to provide increased sample pressure and stability for a given force applied to the diamond tables. 7 figs.

  12. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in...

  13. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits...

  14. Double logarithmic asymptotic behavior in quantum chromodynamics

    SciTech Connect (OSTI)

    Kirschner, R.

    1981-08-01

    The double logarithmic contributions to the quark-(anti)quark scattering and annihilation amplitudes are summed to all orders in quantum chromodynamics. The results are a generalization of the calculations of Gorshkov et al. in the case of quantum electrodynamics.

  15. Wavelength-doubling optical parametric oscillator

    DOE Patents [OSTI]

    Armstrong, Darrell J.; Smith, Arlee V.

    2007-07-24

    A wavelength-doubling optical parametric oscillator (OPO) comprising a type II nonlinear optical medium for generating a pair of degenerate waves at twice a pump wavelength and a plurality of mirrors for rotating the polarization of one wave by 90 degrees to produce a wavelength-doubled beam with an increased output energy by coupling both of the degenerate waves out of the OPO cavity through the same output coupler following polarization rotation of one of the degenerate waves.

  16. Double shell tank waste analysis plan

    SciTech Connect (OSTI)

    Mulkey, C.H.; Jones, J.M.

    1994-12-15

    Waste analysis plan for the double shell tanks. SD-WM-EV-053 is Superseding SD-WM-EV-057.This document provides the plan for obtaining information needed for the safe waste handling and storage of waste in the Double Shell Tank Systems. In Particular it addresses analysis necessary to manage waste according to Washington Administrative Code 173-303 and Title 40, parts 264 and 265 of the Code of Federal Regulations.

  17. Fleet DNA (Presentation)

    SciTech Connect (OSTI)

    Walkokwicz, K.; Duran, A.

    2014-06-01

    The Fleet DNA project objectives include capturing and quantifying drive cycle and technology variation for the multitude of medium- and heavy-duty vocations; providing a common data storage warehouse for medium- and heavy-duty vehicle fleet data across DOE activities and laboratories; and integrating existing DOE tools, models, and analyses to provide data-driven decision making capabilities. Fleet DNA advantages include: for Government - providing in-use data for standard drive cycle development, R&D, tech targets, and rule making; for OEMs - real-world usage datasets provide concrete examples of customer use profiles; for fleets - vocational datasets help illustrate how to maximize return on technology investments; for Funding Agencies - ways are revealed to optimize the impact of financial incentive offers; and for researchers -a data source is provided for modeling and simulation.

  18. Hardware Controller DNA Synthesizer

    Energy Science and Technology Software Center (OSTI)

    1995-07-27

    The program controls the operation of various hardware components of an automatic 12-channel parrallel oligosynthesizer. This involves accepting information regarding the DNA sequence to be generated and converting this into a series of instructions to I/O ports to actuate the appropriate hardware components. The design and function of the software is specific to a particular hardware platform and has no utility for controlling other configurations.

  19. Identification of Human Repetitive DNA Elements

    Energy Science and Technology Software Center (OSTI)

    1995-11-01

    PYTHIA identifies the subfamily membership of Alu sequences, occurrences of repetitive human DNA elements, and simple DNA sequences.

  20. Nucleotide cleaving agents and method

    DOE Patents [OSTI]

    Que, Jr., Lawrence; Hanson, Richard S.; Schnaith, Leah M. T.

    2000-01-01

    The present invention provides a unique series of nucleotide cleaving agents and a method for cleaving a nucleotide sequence, whether single-stranded or double-stranded DNA or RNA, using and a cationic metal complex having at least one polydentate ligand to cleave the nucleotide sequence phosphate backbone to yield a hydroxyl end and a phosphate end.

  1. Laminar burn rates of gun propellants measured in the high-pressure strand burner

    SciTech Connect (OSTI)

    Reaugh, J. E., LLNL

    1997-10-01

    The pressure dependence of the laminar burn rate of gun propellants plays a role in the design and behavior of high-performance guns. We have begun a program to investigate the effects of processing variables on the laminar burn rates, using our high-pressure strand burner to measure these rates at pressures exceeding 700 MPa. We have burned JA2 and M43 propellant samples, provided by Dr. Arpad Juhasz, ARL, from propellant lots previously used in round-robin tests. Our results at room temperature are in accord with other measurements. In addition, we present results measured for propellant that has been preheated to 50 C before burning. We used our thermochemical equilibrium code, CHEETAH, to help interpret the simultaneous pressure and temperature measurements taken during the testing, and show examples of its use. It has been modified to provide performance measures and equations of state for the products that are familiar to the gun-propellant community users of BLAKE.

  2. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A Microscopic Double-Slit Experiment A Microscopic Double-Slit Experiment Print Wednesday, 29 February 2012 00:00 Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using

  3. Searches for Neutrino-less Double

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Searches for Neutrino-less Double Beta-Decay: a Decade of Discovery Ahead at the ton-scale? David Nygren University of Texas at Arlington September 2, 2015 4:00 p.m. Double beta-decay with the emission of neutrinos is an allowed second-order process and has been observed in several candidate nuclei such as 76Ge, 82Se, and 136Xe. A neutrino-less decay mode is theoretically possible as well, with profound implications such as non-conservation of lepton number. The neutrino-less decay can only

  4. The double-beta decay: Theoretical challenges

    SciTech Connect (OSTI)

    Horoi, Mihai

    2012-11-20

    Neutrinoless double beta decay is a unique process that could reveal physics beyond the Standard Model of particle physics namely, if observed, it would prove that neutrinos are Majorana particles. In addition, it could provide information regarding the neutrino masses and their hierarchy, provided that reliable nuclear matrix elements can be obtained. The two neutrino double beta decay is an associate process that is allowed by the Standard Model, and it was observed for about ten nuclei. The present contribution gives a brief review of the theoretical challenges associated with these two process, emphasizing the reliable calculation of the associated nuclear matrix elements.

  5. On the neutrinoless double ?{sup +}/EC decays

    SciTech Connect (OSTI)

    Suhonen, Jouni

    2013-12-30

    The neutrinoless double positron-emission/electron-capture (0??{sup +}/EC) decays are studied for the magnitudes of the involved nuclear matrix elements (NMEs). Decays to the ground state, 0{sub gs}{sup +}, and excited 0{sup +} states are discussed. The participant many-body wave functions are evaluated in the framework of the quasiparticle random-phase approximation (QRPA). Effective, G-matrix-derived nuclear forces are used in realistic single-particle model spaces. The channels ?{sup +}?{sup +}, ?{sup +}EC, and the resonant neutrinoless double electron capture (R0?ECEC) are discussed.

  6. BLOCKING OSCILLATOR DOUBLE PULSE GENERATOR CIRCUIT

    DOE Patents [OSTI]

    Haase, J.A.

    1961-01-24

    A double-pulse generator, particuiarly a double-pulse generator comprising a blocking oscillator utilizing a feedback circuit to provide means for producing a second pulse within the recovery time of the blocking oscillator, is described. The invention utilized a passive network which permits adjustment of the spacing between the original pulses derived from the blocking oscillator and further utilizes the original pulses to trigger a circuit from which other pulses are initiated. These other pulses are delayed and then applied to the input of the blocking oscillator, with the result that the output from the oscillator circuit contains twice the number of pulses originally initiated by the blocking oscillator itself.

  7. Sequential addition of short DNA oligos in DNA-polymerase-based...

    Office of Scientific and Technical Information (OSTI)

    and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of...

  8. Human Genome Research: Decoding DNA

    Office of Scientific and Technical Information (OSTI)

    ... Speeding Up the Process of Gene Discovery Engineered Enzyme Accelerates DNA Sequencing Putting a Virus to Practical Use DOE Joint Genome Institute The Human Genome Project: ...

  9. Human Genome Research: Decoding DNA

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Human Genome Research: Decoding DNA Resources with Additional Information Charles DeLisi ... role in proposing and initiating the Human Genome Program in 1986. The U.S. ...

  10. A novel sandwich hybridization method for selecting cDNAs from large genomic regions: Identification of cDNAs from the cloned genomic DNA spanning the XLRP locus

    SciTech Connect (OSTI)

    Yan, D.; McHenry, C.; Fujita, R.

    1994-09-01

    We have developed an efficient hybridization-based cDNA-selection method. A sandwich of three species - single-stranded cDNA, tagged RNA derived from genomic DNA, and biotinylated RNA complementary to the tag - allows specific retention of hybrids on an avidin-matrix. Previously, using model experiments, we demonstrated highly specific and efficient selection of a retinal gene, NRL, from complex mixtures of cDNA clones, using a sub-library from a 5 kb NRL genomic clone. We have now applied this selection strategy to isolate cDNAs from human adult retina and fetal eye libraries, with the {open_quotes}genomic RNA{close_quotes} derived from two YAC clones (OTC-C and 55B) spanning the region of X-linked retinitis pigmentosa (XLRP) locus RP3 at Xp21.1. Effectiveness of the selection-method was monitored by enrichment of TCTEX-1L gene that maps within the 55B YAC. Of the 15 selected cDNA clones that hybridized to the 55B YAC DNA, five appear to the map to specific cosmid clones derived from the 55B YAC. Inserts in these selected cDNA clones range from 0.5 to 2.3 kb in size. Additional clones are now being isolated and characterized. This procedure should be independent of the size or complexity of genomic DNA being used for selection, allow for the isolation of full-length cDNAs, and may have wider application.

  11. Double layer capacitor prospects look good

    SciTech Connect (OSTI)

    1995-07-01

    The Fourth International Seminar in Double Layer Capacitors and similar energy devices has been sponsored again by Dr. S.P. Wolsky and Dr. Nikola Marincic. The seminar was held in December 1994, at Deerfield Beach, FL. This report provides a brief description of information on supercapacitors.

  12. The Promiscuity of [beta]-Strand Pairing Allows for Rational Design of [beta]-Sheet Face Inversion

    SciTech Connect (OSTI)

    Makabe, Koki; Koide, Shohei

    2009-06-17

    Recent studies suggest the dominant role of main-chain H-bond formation in specifying {beta}-sheet topology. Its essentially sequence-independent nature implies a large degree of freedom in designing {beta}-sheet-based nanomaterials. Here we show rational design of {beta}-sheet face inversions by incremental deletions of {beta}-strands from the single-layer {beta}-sheet of Borrelia outer surface protein A. We show that a {beta}-sheet structure can be maintained when a large number of native contacts are removed and that one can design large-scale conformational transitions of a {beta}-sheet such as face inversion by exploiting the promiscuity of strand-strand interactions. High-resolution X-ray crystal structures confirmed the success of the design and supported the importance of main-chain H-bonds in determining {beta}-sheet topology. This work suggests a simple but effective strategy for designing and controlling nanomaterials based on {beta}-rich peptide self-assemblies.

  13. Solid-state NMR analysis of the {beta}-strand orientation of the protofibrils of amyloid {beta}-protein

    SciTech Connect (OSTI)

    Doi, Takashi; Masuda, Yuichi; Irie, Kazuhiro; Akagi, Ken-ichi; Monobe, Youko; Imazawa, Takayoshi; Takegoshi, K.

    2012-11-30

    Highlights: Black-Right-Pointing-Pointer The supramolecular structure of A{beta}42 protofibrils was analyzed by solid-state NMR. Black-Right-Pointing-Pointer The Ala-21 residue in the A{beta}42 protofibrils is included in a slightly disordered {beta}-strand. Black-Right-Pointing-Pointer The A{beta}42 protofibrils do not form intermolecular in-register parallel {beta}-sheets. -- Abstract: Alzheimer's disease (AD) is caused by abnormal deposition (fibrillation) of a 42-residue amyloid {beta}-protein (A{beta}42) in the brain. During the process of fibrillation, the A{beta}42 takes the form of protofibrils with strong neurotoxicity, and is thus believed to play a crucial role in the pathogenesis of AD. To elucidate the supramolecular structure of the A{beta}42 protofibrils, the intermolecular proximity of the Ala-21 residues in the A{beta}42 protofibrils was analyzed by {sup 13}C-{sup 13}C rotational resonance experiments in the solid state. Unlike the A{beta}42 fibrils, an intermolecular {sup 13}C-{sup 13}C correlation was not found in the A{beta}42 protofibrils. This result suggests that the {beta}-strands of the A{beta}42 protofibrils are not in an in-register parallel orientation. A{beta}42 monomers would assemble to form protofibrils with the {beta}-strand conformation, then transform into fibrils by forming intermolecular parallel {beta}-sheets.

  14. Double, Double Toil and Trouble: Tungsten Burns and Helium Bubbles | U.S.

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DOE Office of Science (SC) Double, Double Toil and Trouble: Tungsten Burns and Helium Bubbles Advanced Scientific Computing Research (ASCR) ASCR Home About Research Facilities Science Highlights Benefits of ASCR Funding Opportunities Advanced Scientific Computing Advisory Committee (ASCAC) Community Resources Contact Information Advanced Scientific Computing Research U.S. Department of Energy SC-21/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-7486 F: (301)

  15. Titanium subhydride potassium perchlorate (TiH1.65/KClO4) burn rates from hybrid closed bomb-strand burner experiments.

    SciTech Connect (OSTI)

    Cooper, Marcia A.; Oliver, Michael S.

    2012-08-01

    A hybrid closed bomb-strand burner is used to measure the burning behavior of the titanium subhydride potassium perchlorate pyrotechnic with an equivalent hydrogen concentration of 1.65. This experimental facility allows for simultaneous measurement of the closed bomb pressure rise and pyrotechnic burn rate as detected by electrical break wires over a range of pressures. Strands were formed by pressing the pyrotechnic powders to bulk densities between 60% and 90% theoretical maximum density. The burn rate dependance on initial density and vessel pressure are measured. At all initial strand densities, the burn is observed to transition from conductive to convective burning within the strand. The measured vessel pressure history is further analyzed following the closed bomb analysis methods developed for solid propellants.

  16. WATER-LITHIUM BROMIDE DOUBLE-EFFECT ABSORPTION COOLING ANALYSIS

    Office of Scientific and Technical Information (OSTI)

    WATER-LITHIUM BROMIDE DOUBLE-EFFECT ABSORPTION COOLING ANALYSIS Gary C . V l i e t , ... i e n t simulation of the double-effect, water-1 ithium bromide absorption cooling ...

  17. Double photoionization of helium with synchrotron x-rays: Proceedings

    SciTech Connect (OSTI)

    Not Available

    1994-01-01

    This report contains papers on the following topics: Overview and comparison of photoionization with charged particle impact; The ratio of double to single ionization of helium: the relationship of photon and bare charged particle impact ionization; Double photoionization of helium at high energies; Compton scattering of photons from electrons bound in light elements; Electron ionization and the Compton effect in double ionization of helium; Elimination of two atomic electrons by a single energy photon; Double photoionization of helium at intermediate energies; Double Photoionization: Gauge Dependence, Coulomb Explosion; Single and Double Ionization by high energy photon impact; The effect of Compton Scattering on the double to single ionization ratio in helium; and Double ionization of He by photoionization and Compton scattering. These papers have been cataloged separately for the database.

  18. Sensitivity of CUORE to Neutrinoless Double-Beta Decay (Journal...

    Office of Scientific and Technical Information (OSTI)

    Sensitivity of CUORE to Neutrinoless Double-Beta Decay Citation Details In-Document Search Title: Sensitivity of CUORE to Neutrinoless Double-Beta Decay In this paper, we study the...

  19. Sensitivity of CUORE to Neutrinoless Double-Beta Decay (Journal...

    Office of Scientific and Technical Information (OSTI)

    Sensitivity of CUORE to Neutrinoless Double-Beta Decay Citation Details In-Document Search Title: Sensitivity of CUORE to Neutrinoless Double-Beta Decay You are accessing a...

  20. HANFORD DOUBLE SHELL TANK THERMAL AND SEISMIC PROJECT SEISMIC...

    Office of Scientific and Technical Information (OSTI)

    Title: HANFORD DOUBLE SHELL TANK THERMAL AND SEISMIC PROJECT SEISMIC ANALYSIS OF HANFORD DOUBLE SHELL TANKS M&D Professional Services, Inc. (M&D) is under subcontract to Pacific ...

  1. Hanford Begins New Campaign to Remove Excess Water from Double...

    Office of Environmental Management (EM)

    Begins New Campaign to Remove Excess Water from Double-Shell Tanks Hanford Begins New Campaign to Remove Excess Water from Double-Shell Tanks September 30, 2014 - 12:00pm Addthis ...

  2. HANFORD DOUBLE SHELL TANK THERMAL AND SEISMIC PROJECT SENSITIVITY...

    Office of Scientific and Technical Information (OSTI)

    Title: HANFORD DOUBLE SHELL TANK THERMAL AND SEISMIC PROJECT SENSITIVITY OF DOUBLE SHELL ... the definition of the design ground motion or in the properties of the tank-waste system. ...

  3. National CHP Roadmap: Doubling Combined Heat and Power Capacity...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    CHP Roadmap: Doubling Combined Heat and Power Capacity in the United States by 2010, March 2001 National CHP Roadmap: Doubling Combined Heat and Power Capacity in the United States ...

  4. Competing Pathways for Nucleation of the Double Perovskite Structure...

    Office of Scientific and Technical Information (OSTI)

    Double Perovskite Structure in the Epitaxial Synthesis of La 2 MnNiO 6 Citation Details In-Document Search Title: Competing Pathways for Nucleation of the Double Perovskite ...

  5. Protection of cisplatin-induced spermatotoxicity, DNA damage and chromatin abnormality by selenium nano-particles

    SciTech Connect (OSTI)

    Rezvanfar, Mohammad Amin; Rezvanfar, Mohammad Ali; Shahverdi, Ahmad Reza; Ahmadi, Abbas; Baeeri, Maryam; Mohammadirad, Azadeh; Abdollahi, Mohammad

    2013-02-01

    Cisplatin (CIS), an anticancer alkylating agent, induces DNA adducts and effectively cross links the DNA strands and so affects spermatozoa as a male reproductive toxicant. The present study investigated the cellular/biochemical mechanisms underlying possible protective effect of selenium nano-particles (Nano-Se) as an established strong antioxidant with more bioavailability and less toxicity, on reproductive toxicity of CIS by assessment of sperm characteristics, sperm DNA integrity, chromatin quality and spermatogenic disorders. To determine the role of oxidative stress (OS) in the pathogenesis of CIS gonadotoxicity, the level of lipid peroxidation (LPO), antioxidant enzymes including superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) and peroxynitrite (ONOO) as a marker of nitrosative stress (NS) and testosterone (T) concentration as a biomarker of testicular function were measured in the blood and testes. Thirty-two male Wistar rats were equally divided into four groups. A single IP dose of CIS (7 mg/kg) and protective dose of Nano-Se (2 mg/kg/day) were administered alone or in combination. The CIS-exposed rats showed a significant increase in testicular and serum LPO and ONOO level, along with a significant decrease in enzymatic antioxidants levels, diminished serum T concentration and abnormal histologic findings with impaired sperm quality associated with increased DNA damage and decreased chromatin quality. Coadministration of Nano-Se significantly improved the serum T, sperm quality, and spermatogenesis and reduced CIS-induced free radical toxic stress and spermatic DNA damage. In conclusion, the current study demonstrated that Nano-Se may be useful to prevent CIS-induced gonadotoxicity through its antioxidant potential. Highlights: ? Cisplatin (CIS) affects spermatozoa as a male reproductive toxicant. ? Effect of Nano-Se on CIS-induced spermatotoxicity was investigated. ? CIS-exposure induces oxidative sperm DNA damage and

  6. Monitoring of Double Stud Wall Moisture Conditions in the Northeast

    SciTech Connect (OSTI)

    Ueno, K.

    2015-03-01

    Double-stud walls insulated with cellulose or low-density spray foam can have R-values of 40 or higher. However, double stud walls have a higher risk of interior-sourced condensation moisture damage, when compared with high-R approaches using exterior insulating sheathing.; Moisture conditions in double stud walls were monitored in Zone 5A (Massachusetts); three double stud assemblies were compared.

  7. Machine learning bandgaps of double perovskites

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Pilania, G.; Mannodi-Kanakkithodi, A.; Uberuaga, B. P.; Ramprasad, R.; Gubernatis, J. E.; Lookman, T.

    2016-01-19

    The ability to make rapid and accurate predictions on bandgaps of double perovskites is of much practical interest for a range of applications. While quantum mechanical computations for high-fidelity bandgaps are enormously computation-time intensive and thus impractical in high throughput studies, informatics-based statistical learning approaches can be a promising alternative. Here we demonstrate a systematic feature-engineering approach and a robust learning framework for efficient and accurate predictions of electronic bandgaps of double perovskites. After evaluating a set of more than 1.2 million features, we identify lowest occupied Kohn-Sham levels and elemental electronegativities of the constituent atomic species as the mostmore » crucial and relevant predictors. As a result, the developed models are validated and tested using the best practices of data science and further analyzed to rationalize their prediction performance.« less

  8. double-action | netl.doe.gov

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Reversible Ionic Liquids as Double-Action Solvents for Efficient CO2 Capture Project No.: DE-NT0005287 In this project, the Georgia Tech Research Corporation is using totally novel chemistryto engender the dramatic changes needed for widespread implementation of CO2 capture in a both environmentally benign and economical process. Current methods of CO2 post-combustion recovery from coal-fired power plants focus on such techniques as absorption in aqueous ethanolamine scrubbers - and this is now

  9. Double-clad nuclear fuel safety rod

    DOE Patents [OSTI]

    McCarthy, William H.; Atcheson, Donald B.; Vaidyanathan, Swaminathan

    1984-01-01

    A device for shutting down a nuclear reactor during an undercooling or overpower event, whether or not the reactor's scram system operates properly. This is accomplished by double-clad fuel safety rods positioned at various locations throughout the reactor core, wherein melting of a secondary internal cladding of the rod allows the fuel column therein to shift from the reactor core to place the reactor in a subcritical condition.

  10. Double Coil Condenser Apparatus - Energy Innovation Portal

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Energy Dosimetry Records System PIA, bechtel Jacobs Company, LLC Dosimetry Records System PIA, bechtel Jacobs Company, LLC Dosimetry Records System PIA, bechtel Jacobs Company, LLC Dosimetry Records System PIA, bechtel Jacobs Company, LLC (196.75 KB) More Documents & Publications Electronic Document Management System PIA, BechtelJacobs Company, LLC Pension Estimate System PIA, Bechtel Jacobs Company, LLC Medgate, PIA, Bechtel Jacobs Company, LLC

    Double Coil Condenser Apparatus A glass

  11. Double-Difference Tomography for Sequestration MVA

    SciTech Connect (OSTI)

    Westman, Erik

    2008-12-31

    Analysis of synthetic data was performed to determine the most cost-effective tomographic monitoring system for a geologic carbon sequestration injection site. Double-difference tomographic inversion was performed on 125 synthetic data sets: five stages of CO2 plume growth, five seismic event regions, and five geophone arrays. Each resulting velocity model was compared quantitatively to its respective synthetic velocity model to determine an accuracy value. The results were examined to determine a relationship between cost and accuracy in monitoring, verification, and accounting applications using double-difference tomography. The geophone arrays with widely-varying geophone locations, both laterally and vertically, performed best. Additionally, double difference seismic tomography was performed using travel time data from a carbon sequestration site at the Aneth oil field in southeast Utah as part of a Department of Energy initiative on monitoring, verification, and accounting (MVA) of sequestered CO2. A total of 1,211 seismic events were recorded from a borehole array consisting of 22 geophones. Artificial velocity models were created to determine the ease with which different CO2 plume locations and sizes can be detected. Most likely because of the poor geophone arrangement, a low velocity zone in the Desert Creek reservoir can only be detected when regions of test site containing the highest ray path coverage are considered. MVA accuracy and precision may be improved through the use of a receiver array that provides more comprehensive ray path coverage.

  12. Doubling Geothermal Generation Capacity by 2020: A Strategic Analysis |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy Doubling Geothermal Generation Capacity by 2020: A Strategic Analysis Doubling Geothermal Generation Capacity by 2020: A Strategic Analysis NREL Doubling Geothermal Capacity.pdf (890.69 KB) More Documents & Publications Geothermal Exploration Policy Mechanisms Offshore Wind Jobs and Economic Development Impacts in the United States: Four Regional Scenarios track 1: systems analysis | geothermal 2015 peer review

  13. DNA Sequence Determinants Controlling Affinity, Stability and...

    Office of Scientific and Technical Information (OSTI)

    the Nucleoid Protein Fis Citation Details In-Document Search Title: DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid ...

  14. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known...

  15. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication The Initiation of Bacterial DNA Replication Print Wednesday, 31 January 2007 00:00 For the first time, scientists have determined the...

  16. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, S.K.

    1998-03-24

    The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example, the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei. 25 figs.

  17. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, Stefan K.

    1998-01-01

    The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei.

  18. Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.

    SciTech Connect (OSTI)

    Avvakumov, George V.; Walker, John R.; Xue, Sheng; Li, Yanjun; Duan, Shili; Bronner, Christian; Arrowsmith, Cheryl H.; Dhe-Paganon, Sirano

    2008-11-17

    Epigenetic inheritance in mammals is characterized by high-fidelity replication of CpG methylation patterns during development. UHRF1 (also known as ICBP90 in humans and Np95 in mouse) is an E3 ligase important for the maintenance of global and local DNA methylation in vivo. The preferential affinity of UHRF1 for hemi-methylated DNA over symmetrically methylated DNA by means of its SET and RING-associated (SRA) domain and its association with the maintenance DNA methyltransferase 1 (DNMT1) suggests a role in replication of the epigenetic code. Here we report the 1.7 {angstrom} crystal structure of the apo SRA domain of human UHRF1 and a 2.2 {angstrom} structure of its complex with hemi-methylated DNA, revealing a previously unknown reading mechanism for methylated CpG sites (mCpG). The SRA-DNA complex has several notable structural features including a binding pocket that accommodates the 5-methylcytosine that is flipped out of the duplex DNA. Two specialized loops reach through the resulting gap in the DNA from both the major and the minor grooves to read the other three bases of the CpG duplex. The major groove loop confers both specificity for the CpG dinucleotide and discrimination against methylation of deoxycytidine of the complementary strand. The structure, along with mutagenesis data, suggests how UHRF1 acts as a key factor for DNMT1 maintenance methylation through recognition of a fundamental unit of epigenetic inheritance, mCpG.

  19. Studies of $${\\rm Nb}_{3}{\\rm Sn}$$ Strands Based on the Restacked-Rod Process for High Field Accelerator Magnets

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Barzi, E.; Bossert, M.; Gallo, G.; Lombardo, V.; Turrioni, D.; Yamada, R.; Zlobin, A. V.

    2011-12-21

    A major thrust in Fermilab's accelerator magnet R&D program is the development of Nb3Sn wires which meet target requirements for high field magnets, such as high critical current density, low effective filament size, and the capability to withstand the cabling process. The performance of a number of strands with 150/169 restack design produced by Oxford Superconducting Technology was studied for round and deformed wires. To optimize the maximum plastic strain, finite element modeling was also used as an aid in the design. Results of mechanical, transport and metallographic analyses are presented for round and deformed wires.

  20. Evaluation of Juvenile Fall Chinook Salmon Stranding on the Hanford Reach in the Columbia River, 1998 Interim Report.

    SciTech Connect (OSTI)

    Nugent, John; Newsome, Todd; Nugent, Michael

    2001-07-27

    The Washington Department of Fish and Wildlife (WDFW) has been contracted through the Bonneville Power Administration (BPA) and the Grant County Public Utility District (GCPUD) to perform an evaluation of juvenile fall chinook salmon (Oncorhynchus tshawytscha) stranding on the Hanford Reach. The evaluation, in the second year of a multi-year study, has been developed to assess the impacts of water fluctuations from Priest Rapids Dam on rearing juvenile fall chinook salmon, other fish species, and benthic macroinvertebrates of the Hanford Reach. This document provides the results of the 1998 field season.

  1. Evaluation of Juvenile Fall Chinook Salmon Stranding on the Hanford Reach of the Columbia River, 1999 Annual Report.

    SciTech Connect (OSTI)

    Nugent, John

    2002-01-24

    The Washington Department of Fish and Wildlife (WDFW) has been contracted through the Bonneville Power Administration (BPA) and the Grant County Public Utility District (GCPUD) to perform an evaluation of juvenile fall chinook salmon (Oncorhynchus tshawytscha) stranding on the Hanford Reach. The evaluation, in the third year of a multi-year study, has been developed to assess the impacts of water fluctuations from Priest Rapids Dam on rearing juvenile fall chinook salmon, other fishes, and benthic macroinvertebrates of the Hanford Reach. This document provides the results of the 1999 field season.

  2. Evaluation of Juvenile Fall Chinook Salmon Stranding on the Hanford Reach of the Columbia River, 2000 Annual Report.

    SciTech Connect (OSTI)

    Nugent, John; Nugent, Michael; Brock, Wendy

    2002-05-29

    The Washington Department of Fish and Wildlife (WDFW) has been contracted through the Bonneville Power Administration (BPA) and the Grant County Public Utility District (GCPUD) to perform an evaluation of juvenile fall chinook salmon (Oncorhynchus tshawytscha) stranding on the Hanford Reach. The evaluation, in the fourth year of a multi-year study, has been developed to assess the impacts of water fluctuations from Priest Rapids Dam on rearing juvenile fall chinook salmon, other fishes, and benthic macroinvertebrates of the Hanford Reach. This document provides the results of the 2000 field season.

  3. Evaluation of Juvenile Fall Chinook Salmon Stranding on the Hanford Reach of the Columbia River, 2001 Annual Report.

    SciTech Connect (OSTI)

    Nugent, John; Nugent, Michael; Brock, Wendy

    2002-05-29

    The Washington Department of Fish and Wildlife (WDFW) has been contracted through the Bonneville Power Administration (BPA) and the Grant County Public Utility District (GCPUD) to perform an evaluation of juvenile fall chinook salmon (Oncorhynchus tshawytscha) stranding on the Hanford Reach of the Columbia River. The evaluation, in the fifth year of a multi-year study, has been developed to assess the impacts of water fluctuations from Priest Rapids Dam on rearing juvenile fall chinook salmon, other fishes, and benthic macroinvertebrates of the Hanford Reach. This document provides the results of the 2001 field season.

  4. X-ray characterization of mesophases of human telomeric G-quadruplexes and other DNA analogues

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Yasar, Selcuk; Schimelman, Jacob B.; Aksoyoglu, M. Alphan; Steinmetz, Nicole F.; French, Roger H.; Parsegian, V. Adrian; Podgornik, Rudolf

    2016-06-02

    We report that observed in the folds of guanine-rich oligonucleotides, non-canonical G-quadruplex structures are based on G-quartets formed by hydrogen bonding and cation-coordination of guanosines. In dilute 5'-guanosine monophosphate (GMP) solutions, G-quartets form by the self-assembly of four GMP nucleotides. We use x-ray diffraction to characterize the columnar liquid-crystalline mesophases in concentrated solutions of various model G-quadruplexes. We then probe the transitions between mesophases by varying the PEG solution osmotic pressure, thus mimicking in vivo molecular crowding conditions. Using the GMP-quadruplex, built by the stacking of G-quartets with no covalent linking between them, as the baseline, we report the liquid-crystallinemore » phase behaviors of two other related G-quadruplexes: (i) the intramolecular parallel-stranded G-quadruplex formed by the 22-mer four-repeat human telomeric sequence AG3 (TTAG3)3 and (ii) the intermolecular parallel-stranded G-quadruplex formed by the TG(4)T oligonucleotides. Finally, we compare the mesophases of the G-quadruplexes, under PEG-induced crowding conditions, with the corresponding mesophases of the canonical duplex and triplex DNA analogues.« less

  5. Low-cost, Rapid DNA Sequencing Technique - Energy Innovation...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Biomass and Biofuels Biomass and Biofuels Advanced Materials Advanced Materials Find More ... The nucleic acid strand transport mechanism located on the dielectric surface of the ...

  6. Optical double-slit particle measuring system

    DOE Patents [OSTI]

    Tichenor, D.A.; Wang, J.C.F.; Hencken, K.R.

    1982-03-25

    A method for in situ measurement of particle size is described. The size information is obtained by scanning an image of the particle across a double-slit mask and observing the transmitted light. This method is useful when the particle size of primary interest is 3..mu..m and larger. The technique is well suited to applications in which the particles are non-spherical and have unknown refractive index. It is particularly well suited to high temperature environments in which the particle incandescence provides the light source.

  7. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in

  8. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in

  9. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in

  10. Neutrinoless double beta decay and neutrino masses

    SciTech Connect (OSTI)

    Duerr, Michael [Max-Planck-Institut fuer Kernphysik, Saupfercheckweg 1, 69117 Heidelberg (Germany)

    2012-07-27

    Neutrinoless double beta decay (0{nu}{beta}{beta}) is a promising test for lepton number violating physics beyond the standard model (SM) of particle physics. There is a deep connection between this decay and the phenomenon of neutrino masses. In particular, we will discuss the relation between 0{nu}{beta}{beta} and Majorana neutrino masses provided by the so-called Schechter-Valle theorem in a quantitative way. Furthermore, we will present an experimental cross check to discriminate 0{nu}{beta}{beta} from unknown nuclear background using only one isotope, i.e., within one experiment.

  11. Double acting stirling engine phase control

    DOE Patents [OSTI]

    Berchowitz, David M.

    1983-01-01

    A mechanical device for effecting a phase change between the expansion and compression volumes of a double-acting Stirling engine uses helical elements which produce opposite rotation of a pair of crankpins when a control rod is moved, so the phase between two pairs of pistons is changed by +.psi. and the phase between the other two pairs of pistons is changed by -.psi.. The phase can change beyond .psi.=90.degree. at which regenerative braking and then reversal of engine rotation occurs.

  12. The double contact nature of TT Herculis

    SciTech Connect (OSTI)

    Terrell, Dirk; Nelson, Robert H. E-mail: bob.nelson@shaw.ca

    2014-03-01

    We present new radial velocities and photometry of the short-period Algol TT Herculis. Previous attempts to model the light curves of the system have met with limited success, primarily because of the lack of a reliable mass ratio. Our spectroscopic observations are the first to result in radial velocities for the secondary star, and thus provide a spectroscopic mass ratio. Simultaneous analysis of the radial velocities and new photometry shows that the system is a double contact binary, with a rapidly rotating primary that fills its limiting lobe.

  13. Optical double-slit particle measuring system

    DOE Patents [OSTI]

    Hencken, Kenneth R.; Tichenor, Daniel A.; Wang, James C. F.

    1984-01-01

    A method for in situ measurement of particle size is described. The size information is obtained by scanning an image of the particle across a double-slit mask and observing the transmitted light. This method is useful when the particle size of primary interest is 3 .mu.m and larger. The technique is well suited to applications in which the particles are non-spherical and have unknown refractive index. It is particularly well suited to high temperature environments in which the particle incandescence provides the light source.

  14. Quantitative Analysis of Clustered DNA Damages Induced by Silicon Beams of Different Kinetic Energy

    SciTech Connect (OSTI)

    Keszenman D. J.; Keszenman, D.J.; Bennett, P.V.; Sutherland, B.M.; Wilson, P.F.

    2013-05-14

    Humans may b exposed to highly energetic charged particle radiation as a result of medical treatments, occupational activitie or accidental events. In recent years, our increasing presence and burgeoning interest in space exploration beyond low Earth orbit has led to a large increase in the research of the biological effects ofcharged particle radiation typical of that encountered in the space radiation environment. The study of the effects of these types of radiation qualities in terms ofDNA damage induction and repair is fundamental to understand mechanisms both underlying their greater biological effectiveness as we)) as the short and long term risks of health effects such as carcinogenesis, degen rative diseases and premature aging. Charged particle radiation induces a variety of DNA alterations, notably bistranded clustered damages, defined as two or more closely-opposed strand break , oxidized bases or abasic sites within a few helical turns. The induction of such highly complex DNA damage enhances the probability of incorrect or incomplete repair and thus constitutes greater potential for genomic instability, cell death and transformation.

  15. A novel low energy electron microscope for DNA sequencing and surface analysis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mankos, M.; Shadman, K.; Persson, H. H. J.; N’Diaye, A. T.; Schmid, A. K.; Davis, R. W.

    2014-01-31

    Monochromatic, aberration-corrected, dual-beam low energy electron microscopy (MAD-LEEM) is a novel technique that is directed towards imaging nanostructures and surfaces with sub-nanometer resolution. The technique combines a monochromator, a mirror aberration corrector, an energy filter, and dual beam illumination in a single instrument. The monochromator reduces the energy spread of the illuminating electron beam, which significantly improves spectroscopic and spatial resolution. Simulation results predict that the novel aberration corrector design will eliminate the second rank chromatic and third and fifth order spherical aberrations, thereby improving the resolution into the sub-nanometer regime at landing energies as low as one hundred electron-Volts.more » The energy filter produces a beam that can extract detailed information about the chemical composition and local electronic states of non-periodic objects such as nanoparticles, interfaces, defects, and macromolecules. The dual flood illumination eliminates charging effects that are generated when a conventional LEEM is used to image insulating specimens. A potential application for MAD-LEEM is in DNA sequencing, which requires high resolution to distinguish the individual bases and high speed to reduce the cost. The MAD-LEEM approach images the DNA with low electron impact energies, which provides nucleobase contrast mechanisms without organometallic labels. Furthermore, the micron-size field of view when combined with imaging on the fly provides long read lengths, thereby reducing the demand on assembling the sequence. Finally, experimental results from bulk specimens with immobilized single-base oligonucleotides demonstrate that base specific contrast is available with reflected, photo-emitted, and Auger electrons. Image contrast simulations of model rectangular features mimicking the individual nucleotides in a DNA strand have been developed to translate measurements of contrast on bulk DNA to the

  16. Structure of the MecI repressor from Staphylococcus aureus in complex with the cognate DNA operator of mec

    SciTech Connect (OSTI)

    Safo, Martin K.; Ko, Tzu-Ping; Musayev, Faik N.; Zhao, Qixun; Archer, Gordon L.

    2006-04-01

    The up-and-down binding of dimeric MecI to mecA dyad DNA may account for the cooperative effect of the repressor. The dimeric repressor MecI regulates the mecA gene that encodes the penicillin-binding protein PBP-2a in methicillin-resistant Staphylococcus aureus (MRSA). MecI is similar to BlaI, the repressor for the blaZ gene of β-lactamase. MecI and BlaI can bind to both operator DNA sequences. The crystal structure of MecI in complex with the 32 base-pair cognate DNA of mec was determined to 3.8 Å resolution. MecI is a homodimer and each monomer consists of a compact N-terminal winged-helix domain, which binds to DNA, and a loosely packed C-terminal helical domain, which intertwines with its counter-monomer. The crystal contains horizontal layers of virtual DNA double helices extending in three directions, which are separated by perpendicular DNA segments. Each DNA segment is bound to two MecI dimers. Similar to the BlaI–mec complex, but unlike the MecI–bla complex, the MecI repressors bind to both sides of the mec DNA dyad that contains four conserved sequences of TACA/TGTA. The results confirm the up-and-down binding to the mec operator, which may account for cooperative effect of the repressor.

  17. Cellular responses to environmental DNA damage

    SciTech Connect (OSTI)

    Not Available

    1994-08-01

    This volume contains the proceedings of the conference entitled Cellular Responses to Environmental DNA Damage held in Banff,Alberta December 1--6, 1991. The conference addresses various aspects of DNA repair in sessions titled DNA repair; Basic Mechanisms; Lesions; Systems; Inducible Responses; Mutagenesis; Human Population Response Heterogeneity; Intragenomic DNA Repair Heterogeneity; DNA Repair Gene Cloning; Aging; Human Genetic Disease; and Carcinogenesis. Individual papers are represented as abstracts of about one page in length.

  18. Interconnecting gold islands with DNA origami

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Interconnecting gold islands with DNA origami Authors: Ding, B., Wu, H., Xu, W., Zhao, Z., Liu, Y., Yu, H., and Yan, H. Title: Interconnecting gold islands with DNA origami Source: Nano Lett. Year: 2010 Volume: 10 Pages: 5065-5069 ABSTRACT: Scaffolded DNA origami has recently emerged as a versatile, programmable method to fold DNA into arbitrarily shaped nanostructures that are spatially addressable, with sub-10-nm resolution. Toward functional DNA nanotechnology, one of the key challenges is to

  19. DNA analysis conference in Santa Fe

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA analysis conference in Santa Fe DNA analysis conference in Santa Fe Los Alamos National Laboratory is hosting a DNA sequence analysis and bioinformatics event, the 10th annual Sequencing, Finishing and Analysis in the Future (SFAF) workshop. May 27, 2015 DNA extracted from a soil sample is stored in a small vial of clear liquid. In general, living cells function by using the sequences of bases in their DNA as a blueprint for assembling proteins. A particularly important type of protein is

  20. Solution structure of CEH-37 homeodomain of the nematode Caenorhabditis elegans

    SciTech Connect (OSTI)

    Moon, Sunjin; Lee, Yong Woo; Kim, Woo Taek; Lee, Weontae

    2014-01-10

    Highlights: •We have determined solution structures of CEH-37 homedomain. •CEH-37 HD has a compact α-helical structure with HTH DNA binding motif. •Solution structure of CEH-37 HD shares its molecular topology with that of the homeodomain proteins. •Residues in the N-terminal region and HTH motif are important in binding to Caenorhabditis elegans telomeric DNA. •CEH-37 could play an important role in telomere function via DNA binding. -- Abstract: The nematode Caenorhabditis elegans protein CEH-37 belongs to the paired OTD/OTX family of homeobox-containing homeodomain proteins. CEH-37 shares sequence similarity with homeodomain proteins, although it specifically binds to double-stranded C. elegans telomeric DNA, which is unusual to homeodomain proteins. Here, we report the solution structure of CEH-37 homeodomain and molecular interaction with double-stranded C. elegans telomeric DNA using nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that CEH-37 homeodomain is composed of a flexible N-terminal region and three α-helices with a helix-turn-helix (HTH) DNA binding motif. Data from size-exclusion chromatography and fluorescence spectroscopy reveal that CEH-37 homeodomain interacts strongly with double-stranded C. elegans telomeric DNA. NMR titration experiments identified residues responsible for specific binding to nematode double-stranded telomeric DNA. These results suggest that C. elegans homeodomain protein, CEH-37 could play an important role in telomere function via DNA binding.

  1. Double Retort System for Materials Compatibility Testing

    SciTech Connect (OSTI)

    V. Munne; EV Carelli

    2006-02-23

    With Naval Reactors (NR) approval of the Naval Reactors Prime Contractor Team (NRPCT) recommendation to develop a gas cooled reactor directly coupled to a Brayton power conversion system as the Space Nuclear Power Plant (SNPP) for Project Prometheus (References a and b) there was a need to investigate compatibility between the various materials to be used throughout the SNPP. Of particular interest was the transport of interstitial impurities from the nickel-base superalloys, which were leading candidates for most of the piping and turbine components to the refractory metal alloys planned for use in the reactor core. This kind of contamination has the potential to affect the lifetime of the core materials. This letter provides technical information regarding the assembly and operation of a double retort materials compatibility testing system and initial experimental results. The use of a double retort system to test materials compatibility through the transfer of impurities from a source to a sink material is described here. The system has independent temperature control for both materials and is far less complex than closed loops. The system is described in detail and the results of three experiments are presented.

  2. Stacking interactions and DNA intercalation

    SciTech Connect (OSTI)

    Li, Dr. Shen; Cooper, Valentino R; Thonhauser, Prof. Timo; Lundqvist, Prof. Bengt I.; Langreth, David C.

    2009-01-01

    The relationship between stacking interactions and the intercalation of proflavine and ellipticine within DNA is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair base-pair interactions and that of the stacked intercalator base pair system. Most notable result is the paucity of torque which so distinctively defines the Twist of DNA. Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar-phosphate backbone, was sufficient for explaining the experimentally observed proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair intercalator interactions can provide valuable information for future nonempirical studies of DNA intercalation dynamics.

  3. Apparatus for improved DNA sequencing

    DOE Patents [OSTI]

    Douthart, Richard J.; Crowell, Shannon L.

    1996-01-01

    This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection.

  4. Apparatus for improved DNA sequencing

    DOE Patents [OSTI]

    Douthart, R.J.; Crowell, S.L.

    1996-05-07

    This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection. 18 figs.

  5. Neutrinoless double beta decay search with the NEMO 3 experiment

    SciTech Connect (OSTI)

    Nasteva, Irina [Particle Physics Group, School of Physics and Astronomy, University of Manchester, Manchester, M13 9PL (United Kingdom)

    2008-11-23

    The NEMO 3 experiment searches for neutrinoless double beta decay and makes precision measurements of two-neutrino double beta decay in seven isotopes. The latest two-neutrino half-life results are presented, together with the limits on neutrinoless half-lives and the corresponding effective Majorana neutrino masses. Also given are the limits obtained on neutrinoless double beta decay mediated by R{sub p}-violating SUSY, right-hand currents and different Majoron emission modes.

  6. High School Academic Competition - Double Elimination | U.S....

    Office of Science (SC) Website

    NSB Home About High School Middle School Attending National Event Volunteers 2015 ... School Double Elimination Top Teams for 2015 News Media WDTS Home Contact Information ...

  7. Middle School Academic Competition - Double Elimination | U.S...

    Office of Science (SC) Website

    NSB Home About High School Middle School Attending National Event Volunteers 2015 ... School Double Elimination Top Teams for 2015 News Media WDTS Home Contact Information ...

  8. Radiochemical tracers as a mix diagnostic for the ignition double...

    Office of Scientific and Technical Information (OSTI)

    for the ignition double-shell capsule One of the most important challenges confronting laser-driven capsule implosion experiments will be a quantitative evaluation of the...

  9. Simulations of Cyclic Voltammetry for Electric Double Layers...

    Office of Scientific and Technical Information (OSTI)

    Simulations of Cyclic Voltammetry for Electric Double Layers in Asymmetric Electrolytes: A Generalized Modified PoissonNernstPlanck Model Citation Details In-Document Search...

  10. Status Update of the Majorana Demonstrator Neutrinoless Double...

    Office of Scientific and Technical Information (OSTI)

    Neutrinoless double beta decay searches play a major role in determining neutrino properties, in particular the Majorana or Dirac nature of the neutrino and the absolute scale of ...

  11. Neutron Interactions in the CUORE Neutrinoless Double Beta Decay...

    Office of Scientific and Technical Information (OSTI)

    Interactions in the CUORE Neutrinoless Double Beta Decay Experiment Dolinski, M J 72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS; 73 NUCLEAR PHYSICS AND RADIATION PHYSICS;...

  12. What can we learn from neutrinoless double beta decay experiments...

    Office of Scientific and Technical Information (OSTI)

    What can we learn from neutrinoless double beta decay experiments? Citation Details ... Country of Publication: United States Language: English Subject: 72 nucleus, semileptonic ...

  13. High speed double quantum 1H MAS NMR spectroscopy investigations...

    Office of Scientific and Technical Information (OSTI)

    of water dynamics in materials. Citation Details In-Document Search Title: High speed double quantum 1H MAS NMR spectroscopy investigations of water dynamics in ...

  14. Transport in interacting 1D double quantum wires

    Office of Scientific and Technical Information (OSTI)

    Transport in interacting 1D double-- quantum wires Michael Lilly Center for Integrated Nanotechnologies Sandia National Laboratories Collaborators Dominique Laroche, Guillaume ...

  15. Exploring the Neutrinoless Double Beta Decay in the Inverted...

    Office of Scientific and Technical Information (OSTI)

    Neutrinoless double beta decay (0) is one of the most sensitive probes for physics beyond the Standard Model, providing unique information on the nature of neutrinos. In this ...

  16. HANFORD DOUBLE SHELL TANK THERMAL AND SEISMIC PROJECT BUCKLING...

    Office of Scientific and Technical Information (OSTI)

    Title: HANFORD DOUBLE SHELL TANK THERMAL AND SEISMIC PROJECT BUCKLING EVALUATION METHODS ... The analysis must account for the variation in design details and operating conditions ...

  17. Double Shell Tank (DST) Utilities Specification

    SciTech Connect (OSTI)

    SUSIENE, W.T.

    2000-04-27

    This specification establishes the performance requirements and provides the references to the requisite codes and standards to he applied during the design of the Double-Shell Tank (DST) Utilities Subsystems that support the first phase of waste feed delivery (WFD). The DST Utilities Subsystems provide electrical power, raw/potable water, and service/instrument air to the equipment and structures used to transfer low-activity waste (LAW) and high-level waste (HLW) to designated DST staging tanks. The DST Utilities Subsystems also support the equipment and structures used to deliver blended LAW and HLW feed from these staging tanks to the River Protection Project (RPP) Privatization Contractor facility where the waste will be immobilized. This specification is intended to be the basis for new projects/installations. This specification is not intended to retroactively affect previously established project design criteria without specific direction by the program.

  18. Double-rotor rotary engine and turbine

    SciTech Connect (OSTI)

    Lin, A.S.

    1990-04-03

    This patent describes a double-rotor engine. It comprises: a base; a housing rotatably mounted to the base and forming a radial cylinder; an output shaft rotatably mounted concentric with the housing and having an arm rigidly extending therefrom within the housing; a piston slidingly engaging the cylinder and forming a combustion chamber with the cylinder; means for admitting a fuel-air mixture into the cylinder; means for releasing combustion products from the cylinder following operation of the expanding means; turbine means operatively connected between the base and the housing, the turbine means providing a torque reaction against the housing in response to flow of the combustion products from the releasing means; and stop means on the shaft for limiting the relative movement between the shaft and the housing.

  19. Correlations and the neutrinoless double beta decay

    SciTech Connect (OSTI)

    Menendez, J.; Poves, A. [Departamento de Fisica Teorica, and IFT, UAM-CSIC, Universidad Autonoma de Madrid, 28049-Madrid (Spain); Caurier, E.; Nowacki, F. [IPHC, IN2P3-CNRS/Universite Louis Pasteur, 67037-Strasbourg (France)

    2009-11-09

    We explore the influence of the deformation on the nuclear matrix elements of the neutrinoless double beta decay (NME), concluding that the difference in deformation -or more generally on the amount of quadrupole correlations- between parent and grand daughter nuclei quenchs strongly the decay. We discuss how varies the nuclear matrix element of {sup 76}Ge decay when the wave functions of the two nuclei involved in the transition are constrained to reproduce the experimental occupancies. In the Interacting Shell Model description the value of the NME is enhanced about 15% compared to previous calculations, whereas in the QRPA the NME's are reduced by 20%-30%, thus, the discrepancies between both approaches diminish.

  20. Chromosome specific repetitive DNA sequences

    DOE Patents [OSTI]

    Moyzis, Robert K.; Meyne, Julianne

    1991-01-01

    A method is provided for determining specific nucleotide sequences useful in forming a probe which can identify specific chromosomes, preferably through in situ hybridization within the cell itself. In one embodiment, chromosome preferential nucleotide sequences are first determined from a library of recombinant DNA clones having families of repetitive sequences. Library clones are identified with a low homology with a sequence of repetitive DNA families to which the first clones respectively belong and variant sequences are then identified by selecting clones having a pattern of hybridization with genomic DNA dissimilar to the hybridization pattern shown by the respective families. In another embodiment, variant sequences are selected from a sequence of a known repetitive DNA family. The selected variant sequence is classified as chromosome specific, chromosome preferential, or chromosome nonspecific. Sequences which are classified as chromosome preferential are further sequenced and regions are identified having a low homology with other regions of the chromosome preferential sequence or with known sequences of other family me This invention is the result of a contract with the Department of Energy (Contract No. W-7405-ENG-36).

  1. Structural Origins of DNA Target Selection and Nucleobase Extrusion...

    Office of Scientific and Technical Information (OSTI)

    of DNA Target Selection and Nucleobase Extrusion by a DNA Cytosine Methyltransferase Citation Details In-Document Search Title: Structural Origins of DNA Target Selection ...

  2. Method for priming and DNA sequencing (Patent Application) |...

    Office of Scientific and Technical Information (OSTI)

    Subject: 55 BIOLOGY AND MEDICINE, BASIC STUDIES; DNA SEQUENCING; DNA SEQUENCERS; EXPERIMENTAL DATA; OLIGONUCLEOTIDES; DNA; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE Word Cloud More ...

  3. Structure of the Mecl Repressor from Staphylococcus aureus in Complex with the Cognate DNA Operator of mec

    SciTech Connect (OSTI)

    Safo,M.; Ko, T.; Musayev, F.; Zhao, Q.; Wang, A.; Archer, G.

    2006-01-01

    The dimeric repressor MecI regulates the mecA gene that encodes the penicillin-binding protein PBP-2a in methicillin-resistant Staphylococcus aureus (MRSA). MecI is similar to BlaI, the repressor for the blaZ gene of {beta}-lactamase. MecI and BlaI can bind to both operator DNA sequences. The crystal structure of MecI in complex with the 32 base-pair cognate DNA of mec was determined to 3.8 Angstroms resolution. MecI is a homodimer and each monomer consists of a compact N-terminal winged-helix domain, which binds to DNA, and a loosely packed C-terminal helical domain, which intertwines with its counter-monomer. The crystal contains horizontal layers of virtual DNA double helices extending in three directions, which are separated by perpendicular DNA segments. Each DNA segment is bound to two MecI dimers. Similar to the BlaI-mec complex, but unlike the MecI-bla complex, the MecI repressors bind to both sides of the mec DNA dyad that contains four conserved sequences of TACA/TGTA. The results confirm the up-and-down binding to the mec operator, which may account for cooperative effect of the repressor.

  4. A revolutionary design of double hull oil tanker

    SciTech Connect (OSTI)

    Akiba, Takehiko; Kitano, Kimio; Sumikama, Yutaka; Tsukuda, Hiroyuki; Toyofuku, Masatsugu; Shibasaki, Kohta; Hah, J.; Furukawa, Koichi

    1995-12-31

    For many years, oil tankers had been designed and constructed based on the single hull concept. However, new regulations which require ``Double Hulls`` in new oil tankers was enacted by the International Maritime Organization (IMO) in 1993. Conventional double hull tankers are designed to have the double hull spaces at the sides and bottoms which are normally used as ballast water tanks in order to reduce oil leakage in case of collision or grounding. Some critics, however, have pointed out various problems with the conventional double hull VLCC, such as difficulties in inspection and coating maintenance of the double hull spaces, higher hull girder still water bending moment, etc. In order to eliminate these potential problems, the authors have proposed a new design concept for double hull tankers. In this concept, the double hull spaces are designed as dry void spaces and the ballast water tanks are arranged in the same style as the single hull design. This paper presents a more detailed study and evaluation of this new concept, concerning the hull structural design, oil outflow probability and economic evaluation in comparison with conventional double hull tanker designs. The authors also show the advantages of this new concept which are beneficial to owners and operators.

  5. Method for double-sided processing of thin film transistors

    DOE Patents [OSTI]

    Yuan, Hao-Chih; Wang, Guogong; Eriksson, Mark A.; Evans, Paul G.; Lagally, Max G.; Ma, Zhenqiang

    2008-04-08

    This invention provides methods for fabricating thin film electronic devices with both front- and backside processing capabilities. Using these methods, high temperature processing steps may be carried out during both frontside and backside processing. The methods are well-suited for fabricating back-gate and double-gate field effect transistors, double-sided bipolar transistors and 3D integrated circuits.

  6. A DNA tweezer-actuated enzyme nanoreactor

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A DNA tweezer-actuated enzyme nanoreactor Authors: Liu, M., Fu, J., Hejesen, C., Yang, Y., Woodbury, N.W., Gothelf, K., Liu, Y., and Yan, H. Title: A DNA tweezer-actuated enzyme...

  7. Amplification of chromosomal DNA in situ

    DOE Patents [OSTI]

    Christian, Allen T.; Coleman, Matthew A.; Tucker, James D.

    2002-01-01

    Amplification of chromosomal DNA in situ to increase the amount of DNA associated with a chromosome or chromosome region is described. The amplification of chromosomal DNA in situ provides for the synthesis of Fluorescence in situ Hybridization (FISH) painting probes from single dissected chromosome fragments, the production of cDNA libraries from low copy mRNAs and improved in Comparative Genomic Hybridization (CGH) procedures.

  8. Structure of Rhodococcus equi virulence-associated protein B (VapB) reveals an eight-stranded antiparallel ?-barrel consisting of two Greek-key motifs

    SciTech Connect (OSTI)

    Geerds, Christina; Wohlmann, Jens; Haas, Albert; Niemann, Hartmut H.

    2014-06-18

    The structure of VapB, a member of the Vap protein family that is involved in virulence of the bacterial pathogen R. equi, was determined by SAD phasing and reveals an eight-stranded antiparallel ?-barrel similar to avidin, suggestive of a binding function. Made up of two Greek-key motifs, the topology of VapB is unusual or even unique. Members of the virulence-associated protein (Vap) family from the pathogen Rhodococcus equi regulate virulence in an unknown manner. They do not share recognizable sequence homology with any protein of known structure. VapB and VapA are normally associated with isolates from pigs and horses, respectively. To contribute to a molecular understanding of Vap function, the crystal structure of a protease-resistant VapB fragment was determined at 1.4 resolution. The structure was solved by SAD phasing employing the anomalous signal of one endogenous S atom and two bound Co ions with low occupancy. VapB is an eight-stranded antiparallel ?-barrel with a single helix. Structural similarity to avidins suggests a potential binding function. Unlike other eight- or ten-stranded ?-barrels found in avidins, bacterial outer membrane proteins, fatty-acid-binding proteins and lysozyme inhibitors, Vaps do not have a next-neighbour arrangement but consist of two Greek-key motifs with strand order 41238567, suggesting an unusual or even unique topology.

  9. Antibody specific for a DNA repair protein

    DOE Patents [OSTI]

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-07-11

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  10. Coronal electron confinement by double layers

    SciTech Connect (OSTI)

    Li, T. C.; Drake, J. F.; Swisdak, M.

    2013-12-01

    In observations of flare-heated electrons in the solar corona, a longstanding problem is the unexplained prolonged lifetime of the electrons compared to their transit time across the source. This suggests confinement. Recent particle-in-cell (PIC) simulations, which explored the transport of pre-accelerated hot electrons through ambient cold plasma, showed that the formation of a highly localized electrostatic potential drop, in the form of a double layer (DL), significantly inhibited the transport of hot electrons. The effectiveness of confinement by a DL is linked to the strength of the DL as defined by its potential drop. In this work, we investigate the scaling of the DL strength with the hot electron temperature by PIC simulations and find a linear scaling. We demonstrate that the strength is limited by the formation of parallel shocks. Based on this, we analytically determine the maximum DL strength, and also find a linear scaling with the hot electron temperature. The DL strength obtained from the analytic calculation is comparable to that from the simulations. At the maximum strength, the DL is capable of confining a significant fraction of hot electrons in the source.

  11. Variable thickness double-refracting plate

    DOE Patents [OSTI]

    Hadeishi, Tetsuo

    1976-01-01

    This invention provides an A.C., cyclic, current-controlled, phase retardation plate that uses a magnetic clamp to produce stress birefringence. It was developed for an Isotope-Zeeman Atomic Absorption Spectrometer that uses polarization modulation to effect automatic background correction in atomic absorption trace-element measurements. To this end, the phase retardation plate of the invention is a variable thickness, photoelastic, double-refracting plate that is alternately stressed and released by the magnetic clamp selectively to modulate specific components selected from the group consisting of circularly and plane polarized Zeeman components that are produced in a dc magnetic field so that they correspond respectively to Zeeman reference and transmission-probe absorption components. The polarization modulation changes the phase of these polarized Zeeman components, designated as .sigma. reference and .pi. absorption components, so that every half cycle the components change from a transmission mode to a mode in which the .pi. component is blocked and the .sigma. components are transmitted. Thus, the Zeeman absorption component, which corresponds in amplitude to the amount of the trace element to be measured in a sample, is alternately transmitted and blocked by a linear polarizer, while the circularly polarized reference components are continuously transmitted thereby. The result is a sinusoidally varying output light amplitude whose average corresponds to the amount of the trace element present in the sample.

  12. Pionic contribution to neutrinoless double beta decay

    SciTech Connect (OSTI)

    Vergados, J. D. [Physics Department, University of Ioannina, Ioannina, GR 451 10 (Greece); Theory Division, CERN, Geneva (Switzerland); Faessler, Amand [Institute fuer Theoretische Physik, Universitaet Tuebingen (Germany); Toki, H. [RCNP, Osaka University, Osaka, 567-0047 (Japan)

    2010-02-01

    It is well known that neutrinoless double decay is going to play a crucial role in settling the neutrino properties, which cannot be extracted from the neutrino oscillation data. It is, in particular, expected to settle the absolute scale of neutrino mass and determine whether the neutrinos are Majorana particles, i.e. they coincide with their own antiparticles. In order to extract the average neutrino mass from the data, one must be able to estimate the contribution of all possible high mass intermediate particles. The latter, which occur in practically all extensions of the standard model, can, in principle, be differentiated from the usual mass term, if data from various targets are available. One, however, must first be able to reliably calculate the corresponding nuclear matrix elements. Such calculations are extremely difficult since the effective transition operators are very short ranged. For such operators processes like pionic contributions, which are usually negligible, turn out to be dominant. We study such an effect in a nonrelativistic quark model for the pion and the nucleon.

  13. Double-duct liquid metal magnetohydrodynamic engine

    DOE Patents [OSTI]

    Haaland, Carsten M.

    1997-01-01

    An internal combustion, liquid metal (LM) magnetohydrodynamic (MHD) engine and an alternating current (AC) magnetohydrodynamic generator, are used in combination to provide useful AC electric energy output. The engine design has four pistons and a double duct configuration, with each duct containing sodium potassium liquid metal confined between free pistons located at either end of the duct. The liquid metal is forced to flow back and forth in the duct by the movement of the pistons, which are alternatively driven by an internal combustion process. In the MHD generator, the two LM-MHD ducts pass in close proximity through a Hartmann duct with output transformer. AC power is produced by operating the engine with the liquid metal in the two generator ducts always flowing in counter directions. The amount of liquid metal maintained in the ducts may be varied. This provides a variable stroke length for the pistons. The engine/generator provides variable AC power at variable frequencies that correspond to the power demands of the vehicular propulsion. Also the engine should maintain nearly constant efficiency throughout the range of power usage. Automobiles and trucks could be powered by the invention, with no transmission or power converter devices being required.

  14. Double-duct liquid metal magnetohydrodynamic engine

    DOE Patents [OSTI]

    Haaland, Carsten M.

    1995-01-01

    An internal combustion, liquid metal (LM) magnetohydrodynamic (MHD) engine and an alternating current (AC) magnetohydrodynamic generator, are used in combination to provide useful AC electric energy output. The engine design has-four pistons and a double duct configuration, with each duct containing sodium potassium liquid metal confined between free pistons located at either end of the duct. The liquid metal is forced to flow back and forth in the duct by the movement of the pistons, which are alternatively driven by an internal combustion process. In the MHD generator, the two LM-MHD ducts pass in close proximity through a Hartmann duct with output transformer. AC power is produced by operating the engine with the liquid metal in the two generator ducts always flowing in counter directions. The amount of liquid metal maintained in the ducts may be varied. This provides a variable stroke length for the pistons. The engine/generator provides variable AC power at variable frequencies that correspond to the power demands of the vehicular propulsion. Also the engine should maintain nearly constant efficiency throughout the range of power usage. Automobiles and trucks could be powered by the invention, with no transmission or power converter devices being required.

  15. Phylogenetic Analysis of Shewanella Strains by DNA Relatedness...

    Office of Scientific and Technical Information (OSTI)

    These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods ...

  16. NV-020-08-DNA-52 | Open Energy Information

    Open Energy Info (EERE)

    DNA-52 Jump to: navigation, search NEPA Document Collection for: NV-020-08-DNA-52 DNA for GeothermalExploration, DNA for Thermal Gradient Hole at Gavvs Valley for Geothermal...

  17. Fleet DNA Project (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2012-10-01

    The Fleet DNA Project - designed by the U.S. Department of Energy's National Renewable Energy Laboratory (NREL) in partnership with Oak Ridge National Laboratory - aims to accelerate the evolution of advanced vehicle development and support the strategic deployment of market-ready technologies that reduce costs, fuel consumption, and emissions. At the heart of the Fleet DNA Project is a clearinghouse of medium- and heavy-duty commercial fleet transportation data for optimizing the design of advanced vehicle technologies or for selecting a given technology to invest in. An easy-to-access online database will help vehicle manufacturers and fleets understand the broad operational range for many of today's commercial vehicle vocations.

  18. Particle sizer and DNA sequencer

    DOE Patents [OSTI]

    Olivares, Jose A.; Stark, Peter C.

    2005-09-13

    An electrophoretic device separates and detects particles such as DNA fragments, proteins, and the like. The device has a capillary which is coated with a coating with a low refractive index such as Teflon.RTM. AF. A sample of particles is fluorescently labeled and injected into the capillary. The capillary is filled with an electrolyte buffer solution. An electrical field is applied across the capillary causing the particles to migrate from a first end of the capillary to a second end of the capillary. A detector light beam is then scanned along the length of the capillary to detect the location of the separated particles. The device is amenable to a high throughput system by providing additional capillaries. The device can also be used to determine the actual size of the particles and for DNA sequencing.

  19. Channel plate for DNA sequencing

    DOE Patents [OSTI]

    Douthart, Richard J.; Crowell, Shannon L.

    1998-01-01

    This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface.

  20. Channel plate for DNA sequencing

    DOE Patents [OSTI]

    Douthart, R.J.; Crowell, S.L.

    1998-01-13

    This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface. 15 figs.

  1. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication The Initiation of Bacterial DNA Replication Print Wednesday, 31 January 2007 00:00 For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA

  2. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

    Sessler, Andrew M.; Dawson, John

    1993-01-01

    The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source.

  3. Fabrication and Measurements of 500 MHz Double Spoke Cavity

    SciTech Connect (OSTI)

    Park, HyeKyoung; Hopper, Christopher S.; Delayen, Jean R.

    2014-12-01

    A 500 MHz β0=1 double spoke cavity has been designed and optimized for a high velocity application such as a compact electron accelerator at the Center for Accelerator Science at Old Dominion University [1] and the fabrication was recently completed at Jefferson Lab. The geometry specific to the double spoke cavity required a variety of tooling and fixtures. Also a number of asymmetric weld joints were expected to make it difficult to maintain minimal geometric deviation from the design. This paper will report the fabrication procedure, resulting tolerance from the design, initial test results and the lessons learned from the first β0=1 double spoke cavity fabrication.

  4. DNA

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    LOS ALAMOS, N.M., Sept. 15, 2014-When this week's print issue of the journal Science comes out, a collective cheer will go up from New Mexico, Montana and even the Netherlands, ...

  5. Mechanisms of radiation-induced gene responses

    SciTech Connect (OSTI)

    Woloschak, G.E.; Paunesku, T.

    1996-10-01

    In the process of identifying genes differentially expressed in cells exposed ultraviolet radiation, we have identified a transcript having a 26-bp region that is highly conserved in a variety of species including Bacillus circulans, yeast, pumpkin, Drosophila, mouse, and man. When the 5` region (flanking region or UTR) of a gene, the sequence is predominantly in +/+ orientation with respect to the coding DNA strand; while in the coding region and the 3` region (UTR), the sequence is most frequently in the +/-orientation with respect to the coding DNA strand. In two genes, the element is split into two parts; however, in most cases, it is found only once but with a minimum of 11 consecutive nucleotides precisely depicting the original sequence. The element is found in a large number of different genes with diverse functions (from human ras p21 to B. circulans chitonase). Gel shift assays demonstrated the presence of a protein in HeLa cell extracts that binds to the sense and antisense single-stranded consensus oligomers, as well as to the double- stranded oligonucleotide. When double-stranded oligomer was used, the size shift demonstrated as additional protein-oligomer complex larger than the one bound to either sense or antisense single-stranded consensus oligomers alone. It is speculated either that this element binds to protein(s) important in maintaining DNA is a single-stranded orientation for transcription or, alternatively that this element is important in the transcription-coupled DNA repair process.

  6. Trench logs from a strand of the Rock Valley Fault System, Nevada Test Site, Nye County, Nevada

    SciTech Connect (OSTI)

    Yount, J.C.; Shroba, R.R.; McMasters, C.R.; Huckins, H.E.; Rodriguez, E.A.

    1987-12-31

    The Rock Valley fault system trends northeasterly through the southeast corner of the Nevada Test Site. The system records left-lateral offset of Paleozoic and Tertiary rocks, although total offset amounts to only a few kilometers. Distinct scarps in alluvial deposits of Quaternary age and a concentration of seismicity, particularly at its north end, suggest that the Rock Valley fault system may be active. Two trenches were excavated by backhoe in 1978 across a 0.5-m-high scarp produced by a strand of the Rock Valley fault system. A detailed logging of the two Rock Valley fault trenches was undertaken during the spring of 1984. This report presents: (1) logs of both walls of the two trenches, (2) a general description of the lithologic units and the soils formed in these units that are exposed in and near the fault trenches, (3) observations of the clast fabric of unfaulted and faulted deposits exposed in the trench walls, and (4) a map of the surficial deposits in the vicinity of the trenches.

  7. Performance of a double pass solar air collector

    SciTech Connect (OSTI)

    Ramani, B.M.; Gupta, Akhilesh; Kumar, Ravi

    2010-11-15

    Double pass counter flow solar air collector with porous material in the second air passage is one of the important and attractive design improvement that has been proposed to improve the thermal performance. This paper presents theoretical and experimental analysis of double pass solar air collector with and without porous material. A mathematical model has been developed based on volumetric heat transfer coefficient. Effects of various parameters on the thermal performance and pressure drop characteristics have been discussed. Comparison of results reveals that the thermal efficiency of double pass solar air collector with porous absorbing material is 20-25% and 30-35% higher than that of double pass solar air collector without porous absorbing material and single pass collector respectively. (author)

  8. EA-1136: Double Tracks Test Site, Nye County, Nevada

    Broader source: Energy.gov [DOE]

    This EA evaluates the environmental impacts of the proposal for the U.S. Department of Energy Nevada Operations Office to conduct environmental restoration operations at the Double Tracks test site...

  9. Evaluation of Double-moment Microphysical Parameterization with...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    model?" Because of the lack of data with detailed MCS cloud components, a detailed evaluation of double-moment schemes has not yet been undertaken. During April and May of 2011,...

  10. Double Well Mass Filter | Princeton Plasma Physics Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Double Well Mass Filter The disclosure described a new plasma configuration for separating elements by their mass, which would have applications in nuclear waste remediation and nuclear fuel reproccessing. No.: M-870 Inventor(s): Nathaniel J Fisch

  11. OSTIblog Articles in the neutrinos Neutrinoless Double Beta Decay...

    Office of Scientific and Technical Information (OSTI)

    Neutrinoless Double Beta Decay Topic Mining for Gold, Neutrinos and the Neutrinoless ... The site of the former Homestake Mine was once one of the largest and deepest gold mines ...

  12. Double Shell Tank (DST) Monitor and Control Subsystem Specification

    SciTech Connect (OSTI)

    BAFUS, R.R.

    2000-11-03

    This specification revises the performance requirements and provides references to the requisite codes and standards to be applied during design of the Double-Shell Tank (DST) Monitor and Control Subsystem that supports the first phase of Waste Feed Delivery.

  13. DOUBLE STARS IN THE USNO CCD ASTROGRAPHIC CATALOG

    SciTech Connect (OSTI)

    Hartkopf, William I.; Mason, Brian D.; Finch, Charlie T.; Zacharias, Norbert; Wycoff, Gary L.; Hsu, Danley E-mail: bdm@usno.navy.mil E-mail: nz@usno.navy.mil

    2013-10-01

    The newly completed Fourth USNO CCD Astrographic Catalog (UCAC4) has proven to be a rich source of double star astrometry and photometry. Following initial comparisons of UCAC4 results against those obtained by speckle interferometry, the UCAC4 catalog was matched against known double stars in the Washington Double Star Catalog in order to provide additional differential astrometry and photometry for these pairs. Matches to 58,131 pairs yielded 61,895 astrometric and 68,935 photometric measurements. Finally, a search for possible new common proper motion (CPM) pairs was made using new UCAC4 proper motion data; this resulted in 4755 new potential CPM doubles (and an additional 27,718 astrometric and photometric measures from UCAC and other sources)

  14. Energy levels of double triangular graphene quantum dots

    SciTech Connect (OSTI)

    Liang, F. X.; Jiang, Z. T. Zhang, H. Y.; Li, S.; Lv, Z. T.

    2014-09-28

    We investigate theoretically the energy levels of the coupled double triangular graphene quantum dots (GQDs) based on the tight-binding Hamiltonian model. The double GQDs including the ZZ-type, ZA-type, and AA-type GQDs with the two GQDs having the zigzag or armchair boundaries can be coupled together via different interdot connections, such as the direct coupling, the chains of benzene rings, and those of carbon atoms. It is shown that the energy spectrum of the coupled double GQDs is the amalgamation of those spectra of the corresponding two isolated GQDs with the modification triggered by the interdot connections. The interdot connection is inclined to lift up the degeneracies of the energy levels in different degree, and as the connection changes from the direct coupling to the long chains, the removal of energy degeneracies is suppressed in ZZ-type and AA-type double GQDs, which indicates that the two coupled GQDs are inclined to become decoupled. Then we consider the influences on the spectra of the coupled double GQDs induced by the electric fields applied on the GQDs or the connection, which manifests as the global spectrum redistribution or the local energy level shift. Finally, we study the symmetrical and asymmetrical energy spectra of the double GQDs caused by the substrates supporting the two GQDs, clearly demonstrating how the substrates affect the double GQDs' spectrum. This research elucidates the energy spectra of the coupled double GQDs, as well as the mechanics of manipulating them by the electric field and the substrates, which would be a significant reference for designing GQD-based devices.

  15. No-neutrino double beta decay: more than one neutrino

    SciTech Connect (OSTI)

    Rosen, S.P.

    1983-01-01

    Interference effects between light and heavy Majorana neutrinos in the amplitude for no-neutrino double beta decay are discussed. The effects include an upper bound on the heavy neutrino mass, and an A dependence for the effective mass extracted from double beta decay. Thus the search for the no-neutrino decay mode should be pursued in several nuclei, and particularly in Ca/sup 48/, where the effective mass may be quite large.

  16. Effect of nuclear deformation on double beta decay

    SciTech Connect (OSTI)

    Rodin, Vadim [Institute fuer Theoretische Physik der Universitaet Tuebingen, D-72076 Tuebingen (Germany)

    2009-11-09

    The existing ways of accounting for deformation in recent calculations of neutrinoless double beta decay matrix elements are discussed. From an analysis of relevant experimental data it is argued that only {sup 150}Nd reveals convincing evidences of strong static deformation, which should eventually be taken into account in QRPA calculations. A proposal which allows in principle to measure the neutrino less double beta decay Fermi matrix element is briefly described.

  17. Double Higgs boson production in the models with isotriplets

    SciTech Connect (OSTI)

    Godunov, S. I. Vysotsky, M. I. Zhemchugov, E. V.

    2015-12-15

    The enhancement of double Higgs boson production in the extensions of the Standard Model with extra isotriplets is studied. It is found that in see-saw type II model decays of new heavy Higgs can contribute to the double Higgs production cross section as much as Standard Model channels. In Georgi–Machacek model the cross section can be much larger since the custodial symmetry is preserved and the strongest limitation on triplet parameters is removed.

  18. Enhancing the DNA Patent Database

    SciTech Connect (OSTI)

    Walters, LeRoy B.

    2008-02-18

    Final Report on Award No. DE-FG0201ER63171 Principal Investigator: LeRoy B. Walters February 18, 2008 This project successfully completed its goal of surveying and reporting on the DNA patenting and licensing policies at 30 major U.S. academic institutions. The report of survey results was published in the January 2006 issue of Nature Biotechnology under the title The Licensing of DNA Patents by US Academic Institutions: An Empirical Survey. Lori Pressman was the lead author on this feature article. A PDF reprint of the article will be submitted to our Program Officer under separate cover. The project team has continued to update the DNA Patent Database on a weekly basis since the conclusion of the project. The database can be accessed at dnapatents.georgetown.edu. This database provides a valuable research tool for academic researchers, policymakers, and citizens. A report entitled Reaping the Benefits of Genomic and Proteomic Research: Intellectual Property Rights, Innovation, and Public Health was published in 2006 by the Committee on Intellectual Property Rights in Genomic and Protein Research and Innovation, Board on Science, Technology, and Economic Policy at the National Academies. The report was edited by Stephen A. Merrill and Anne-Marie Mazza. This report employed and then adapted the methodology developed by our research project and quoted our findings at several points. (The full report can be viewed online at the following URL: http://www.nap.edu/openbook.php?record_id=11487&page=R1). My colleagues and I are grateful for the research support of the ELSI program at the U.S. Department of Energy.

  19. DNA-guided nanoparticle assemblies

    DOE Patents [OSTI]

    Gang, Oleg; Nykypanchuk, Dmytro; Maye, Mathew; van der Lelie, Daniel

    2013-07-16

    In some embodiments, DNA-capped nanoparticles are used to define a degree of crystalline order in assemblies thereof. In some embodiments, thermodynamically reversible and stable body-centered cubic (bcc) structures, with particles occupying <.about.10% of the unit cell, are formed. Designs and pathways amenable to the crystallization of particle assemblies are identified. In some embodiments, a plasmonic crystal is provided. In some aspects, a method for controlling the properties of particle assemblages is provided. In some embodiments a catalyst is formed from nanoparticles linked by nucleic acid sequences and forming an open crystal structure with catalytically active agents attached to the crystal on its surface or in interstices.

  20. Modulation of DNA repair capacity and mRNA expression levels of XRCC1, hOGG1 and XPC genes in styrene-exposed workers

    SciTech Connect (OSTI)

    Hanova, Monika; Stetina, Rudolf; Vodickova, Ludmila; Vaclavikova, Radka; Hlavac, Pavel; Smerhovsky, Zdenek; Naccarati, Alessio; Polakova, Veronika; Soucek, Pavel; Kuricova, Miroslava; Manini, Paola; Kumar, Rajiv; Hemminki, Kari; Vodicka, Pavel

    2010-11-01

    Decreased levels of single-strand breaks in DNA (SSBs), reflecting DNA damage, have previously been observed with increased styrene exposure in contrast to a dose-dependent increase in the base-excision repair capacity. To clarify further the above aspects, we have investigated the associations between SSBs, micronuclei, DNA repair capacity and mRNA expression in XRCC1, hOGG1 and XPC genes on 71 styrene-exposed and 51 control individuals. Styrene concentrations at workplace and in blood characterized occupational exposure. The workers were divided into low (below 50 mg/m{sup 3}) and high (above 50 mg/m{sup 3}) styrene exposure groups. DNA damage and DNA repair capacity were analyzed in peripheral blood lymphocytes by Comet assay. The mRNA expression levels were determined by qPCR. A significant negative correlation was observed between SSBs and styrene concentration at workplace (R = - 0.38, p = 0.001); SSBs were also significantly higher in men (p = 0.001). The capacity to repair irradiation-induced DNA damage was the highest in the low exposure group (1.34 {+-} 1.00 SSB/10{sup 9} Da), followed by high exposure group (0.72 {+-} 0.81 SSB/10{sup 9} Da) and controls (0.65 {+-} 0.82 SSB/10{sup 9} Da). The mRNA expression levels of XRCC1, hOGG1 and XPC negatively correlated with styrene concentrations in blood and at workplace (p < 0.001) and positively with SSBs (p < 0.001). Micronuclei were not affected by styrene exposure, but were higher in older persons and in women (p < 0.001). In this study, we did not confirm previous findings on an increased DNA repair response to styrene-induced genotoxicity. However, negative correlations of SSBs and mRNA expression levels of XRCC1, hOGG1 and XPC with styrene exposure warrant further highly-targeted study.

  1. DNA Origami: A History and Current Perspective

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Origami: A History and Current Perspective Authors: Nangreave, J., Han, D., Liu, Y., and Yan, H. Title: DNA Origami: A History and Current Perspective Source: Current Opinion in ...

  2. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates

  3. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates

  4. DNA sequencing using fluorescence background electroblotting membrane

    DOE Patents [OSTI]

    Caldwell, K.D.; Chu, T.J.; Pitt, W.G.

    1992-05-12

    A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through amino groups contained on the surface. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to the target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membranes may be reprobed numerous times. No Drawings

  5. DNA sequencing using fluorescence background electroblotting membrane

    DOE Patents [OSTI]

    Caldwell, Karin D.; Chu, Tun-Jen; Pitt, William G.

    1992-01-01

    A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through said smino groups contained on the surface thereof. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to said target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membrances may be reprobed numerous times.

  6. Challenges and opportunities for structural DNA nanotechnology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    In particular, we highlight the potential use of DNA nanostructures in molecular and cellular biophysics, as biomimetic systems, in energy transfer and photonics, and in ...

  7. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates

  8. A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Chemie International Edition Year: 2010 Volume: 49 Pages: 1414-1417 ABSTRACT: A new strategy is presented to scale up DNA origami using multi-helical DNA tiles as folding...

  9. Man-made marine debris and sea turtle strandings on beaches of the upper Texas and southwestern Louisiana coasts, June 1987 through September 1989. Technical memo

    SciTech Connect (OSTI)

    Duronslet, M.J.; Revera, D.B.; Stanley, K.M.

    1991-02-01

    The upper Texas and southwestern Louisiana coastlines were divided into six sampling zones to survey the amounts, types and rates of accumulation of man-made marine debris, the number of sea turtle strandings, the incidence of sea turtle entanglements in marine debris and the incidence of ingestion of such debris by sea turtles. From June 1987 through September 1989, 473 sample plots were examined for marine debris. Significant differences were detected in mean number of debris items per 100 sq m of beach sampled by year, zone and month. Significant differences in mean weight of debris items per 100 sq m of beach sampled were detected by month and zone. Both number and weights (per 100 sq m) of debris were lowest in the winter months. Number per 100 sq m was greatest in August while weight per 100 sq m peaked in May. Tar balls and plastic items were the most frequently encountered marine debris items. Wooden items had the highest average weights while tar balls and polystyrene foam were the lightest items collected. A total of 171 sea turtles stranded on the surveyed beaches during the study. Of 26 gastrointestinal tracts examined, 16 had ingested some form of man-made debris. Six turtles were entangled in man-made debris and 9 were live stranded.

  10. Double wall vacuum tubing and method of manufacture

    DOE Patents [OSTI]

    Stahl, Charles R.; Gibson, Michael A.; Knudsen, Christian W.

    1989-01-01

    An evacuated double wall tubing is shown together with a method for the manufacture of such tubing which includes providing a first pipe of predetermined larger diameter and a second pipe having an O.D. substantially smaller than the I.D. of the first pipe. An evacuation opening is then in the first pipe. The second pipe is inserted inside the first pipe with an annular space therebetween. The pipes are welded together at one end. A stretching tool is secured to the other end of the second pipe after welding. The second pipe is then prestressed mechanically with the stretching tool an amount sufficient to prevent substantial buckling of the second pipe under normal operating conditions of the double wall pipe. The other ends of the first pipe and the prestressed second pipe are welded together, preferably by explosion welding, without the introduction of mechanical spacers between the pipes. The annulus between the pipes is evacuated through the evacuation opening, and the evacuation opening is finally sealed. The first pipe is preferably of steel and the second pipe is preferably of titanium. The pipes may be of a size and wall thickness sufficient for the double wall pipe to be structurally load bearing or may be of a size and wall thickness insufficient for the double wall pipe to be structurally load bearing, and the double wall pipe positioned with a sliding fit inside a third pipe of a load-bearing size.

  11. Sizing of DNA fragments by flow cytometry

    SciTech Connect (OSTI)

    Johnson, M.E.; Goodwin, P.M.; Ambrose, W.P.; Martin, J.C.; Marrone, B.L.; Jett, J.H.; Keller, R.A.

    1993-02-01

    Individual, stained DNA fragments were sized using a modified flow cytometer with high sensitivity fluorescence detection. The fluorescent intercalating dye ethidium homodimer was used to stain stoichiometrically lambda phage DNA and a Kpn I digest of lambda DNA. Stained, individual fragments of DNA were passed through a low average power, focused, mode-locked laser beam, and the fluorescence from each fragment was collected and quantified. Time-gated detection was used to discriminate against Raman scattering from the water solvent. The fluorescence burst from each fragment was related directly to its length, thus providing a means to size small quantities of kilobase lengths of DNA quickly. Improvements of several orders of magnitude in analysis time and sample size over current gel electrophoresis techniques were realized. Fragments of 17.1,29.9, and 48.5 thousand base pairs were well resolved, and were sized in 164 seconds. Less than one pg of DNA was required for analysis. We have demonstrated sizing of individual, stained DNA fragments with resolution approaching that of gel electrophoresis for moderately large fragments, but with significant reductions in the analysis time and the amount of sample required. Furthermore, system response is linear with DNA fragment length, in contrast to the logarithmic response in gel electrophoresis. There exists the potential to perform this sizing using relatively simple instrumentation, i.e. a continuous wave laser of low power and current mode detection.

  12. Sizing of DNA fragments by flow cytometry

    SciTech Connect (OSTI)

    Johnson, M.E.; Goodwin, P.M.; Ambrose, W.P.; Martin, J.C.; Marrone, B.L.; Jett, J.H.; Keller, R.A.

    1993-01-01

    Individual, stained DNA fragments were sized using a modified flow cytometer with high sensitivity fluorescence detection. The fluorescent intercalating dye ethidium homodimer was used to stain stoichiometrically lambda phage DNA and a Kpn I digest of lambda DNA. Stained, individual fragments of DNA were passed through a low average power, focused, mode-locked laser beam, and the fluorescence from each fragment was collected and quantified. Time-gated detection was used to discriminate against Raman scattering from the water solvent. The fluorescence burst from each fragment was related directly to its length, thus providing a means to size small quantities of kilobase lengths of DNA quickly. Improvements of several orders of magnitude in analysis time and sample size over current gel electrophoresis techniques were realized. Fragments of 17.1,29.9, and 48.5 thousand base pairs were well resolved, and were sized in 164 seconds. Less than one pg of DNA was required for analysis. We have demonstrated sizing of individual, stained DNA fragments with resolution approaching that of gel electrophoresis for moderately large fragments, but with significant reductions in the analysis time and the amount of sample required. Furthermore, system response is linear with DNA fragment length, in contrast to the logarithmic response in gel electrophoresis. There exists the potential to perform this sizing using relatively simple instrumentation, i.e. a continuous wave laser of low power and current mode detection.

  13. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

    Rambosek, J.; Piddington, C.S.; Kovacevich, B.R.; Young, K.D.; Denome, S.A.

    1994-10-18

    This invention relates to a recombinant DNA molecule containing a gene or genes which encode a biocatalyst capable of desulfurizing a fossil fuel which contains organic sulfur molecules. For example, the present invention encompasses a recombinant DNA molecule containing a gene or genes of a strain of Rhodococcus rhodochrous. 13 figs.

  14. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

    Rambosek, John; Piddington, Chris S.; Kovacevich, Brian R.; Young, Kevin D.; Denome, Sylvia A.

    1994-01-01

    This invention relates to a recombinant DNA molecule containing a gene or genes which encode a biocatalyst capable of desulfurizing a fossil fuel which contains organic sulfur molecules. For example, the present invention encompasses a recombinant DNA molecule containing a gene or genes of a strain of Rhodococcus rhodochrous.

  15. HANFORD DOUBLE SHELL TANK (DST) THERMAL & SEISMIC PROJECT SEISMIC ANALYSIS OF HANFORD DOUBLE SHELL TANKS

    SciTech Connect (OSTI)

    MACKEY, T.C.

    2006-03-17

    M&D Professional Services, Inc. (M&D) is under subcontract to Pacific Northwest National Laboratory (PNNL) to perform seismic analysis of the Hanford Site double-shell tanks (DSTs) in support of a project entitled ''Double-Shell Tank (DSV Integrity Project--DST Thermal and Seismic Analyses)''. The overall scope of the project is to complete an up-to-date comprehensive analysis of record of the DST system at Hanford in support of Tri-Party Agreement Milestone M-48-14, The work described herein was performed in support of the seismic analysis of the DSTs. The thermal and operating loads analysis of the DSTs is documented in Rinker et al. (2004). The work statement provided to M&D (PNNL 2003) required that the seismic analysis of the DSTs assess the impacts of potentially non-conservative assumptions in previous analyses and account for the additional soil mass due to the as-found soil density increase, the effects of material degradation, additional thermal profiles applied to the full structure including the soil-structure response with the footings, the non-rigid (low frequency) response of the tank roof, the asymmetric seismic-induced soil loading, the structural discontinuity between the concrete tank wall and the support footing and the sloshing of the tank waste. The seismic analysis considers the interaction of the tank with the surrounding soil and the effects of the primary tank contents. The DSTs and the surrounding soil are modeled as a system of finite elements. The depth and width of the soil incorporated into the analysis model are sufficient to obtain appropriately accurate analytical results. The analyses required to support the work statement differ from previous analysis of the DSTs in that the soil-structure interaction (SSI) model includes several (nonlinear) contact surfaces in the tank structure, and the contained waste must be modeled explicitly in order to capture the fluid-structure interaction behavior between the primary tank and contained

  16. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

    Nasarabadi, Shanavaz; Langlois, Richard G.; Venkateswaran, Kodumudi S.

    2006-08-01

    Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM, on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA, on the 5' end.

  17. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

    Sessler, A.M.; Dawson, J.

    1993-12-14

    The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source. 6 figures.

  18. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

    Nasarabadi,Shanavaz; Langlois, Richard G.; Venkateswaran, Kodumudi S.

    2011-07-05

    Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM.TM. on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA.TM., on the 5' end.

  19. Enzymatic Ligation Creates Discrete Multi-Nanoparticle Building Blocks for Self-Assembly

    SciTech Connect (OSTI)

    Claridge, Shelley A.; Mastroianni, Alexander J.; Au, Yeung B.; Liang, Huiyang W.; Micheel, Christine M.; Frechet, Jean M.J.; Alivisatos, A. Paul

    2008-05-27

    Enzymatic ligation of discrete nanoparticle?DNA conjugates creates nanoparticle dimer and trimer structures in which the nanoparticles are linked by single-stranded DNA, rather than double-stranded DNA as in previous experiments. Ligation is verified by agarose gel and small-angle X-ray scattering. This capability is utilized in two ways: first to create a new class of multiparticle building blocks for nanoscale self-assembly; second to develop a system which can amplify a population of discrete nanoparticle assemblies.

  20. Evaluation of the uranium double spike technique for environmental monitoring

    SciTech Connect (OSTI)

    Hemberger, P.H.; Rokop, D.J.; Efurd, D.W.; Roensch, F.R.; Smith, D.H.; Turner, M.L.; Barshick, C.M.; Bayne, C.K.

    1998-01-01

    Use of a uranium double spike in analysis of environmental samples showed that a {sup 235}U enrichment of 1% ({sup 235}U/{sup 238}U = 0.00732) can be distinguished from natural ({sup 235}U/{sup 238}U = 0.00725). Experiments performed jointly at Los Alamos National Laboratory (LANL) and Oak Ridge National Laboratory (ORNL) used a carefully calibrated double spike of {sup 233}U and {sup 236}U to obtain much better precision than is possible using conventional analytical techniques. A variety of different sampling media (vegetation and swipes) showed that, provided sufficient care is exercised in choice of sample type, relative standard deviations of less than {+-} 0.5% can be routinely obtained. This ability, unavailable without use of the double spike, has enormous potential significance in the detection of undeclared nuclear facilities.

  1. Spin projection with double hybrid density functional theory

    SciTech Connect (OSTI)

    Thompson, Lee M.; Hratchian, Hrant P.

    2014-07-21

    A spin projected double-hybrid density functional theory is presented that accounts for different scaling of opposite and same spin terms in the second order correction. This method is applied to three dissociation reactions which in the unprojected formalism exhibit significant spin contamination with higher spin states. This gives rise to a distorted potential surface and can lead to poor geometries and energies. The projected method presented is shown to improve the description of the potential over unprojected double hybrid density functional theory. Comparison is made with the reference states of the two double hybrid functionals considered here (B2PLYP and mPW2PLYP) in which the projected potential surface is degraded by an imbalance in the description of dynamic and static correlation.

  2. A prototype silicon double quantum dot with dispersive microwave readout

    SciTech Connect (OSTI)

    Schmidt, A. R. Henry, E.; Namaan, O.; Siddiqi, I.; Lo, C. C.; Wang, Y.-T.; Bokor, J.; Yablonovitch, E.; Li, H.; Greenman, L.; Whaley, K. B.; Schenkel, T.

    2014-07-28

    We present a unique design and fabrication process for a lateral, gate-confined double quantum dot in an accumulation mode metal-oxide-semiconductor (MOS) structure coupled to an integrated microwave resonator. All electrostatic gates for the double quantum dot are contained in a single metal layer, and use of the MOS structure allows for control of the location of the two-dimensional electron gas via the location of the accumulation gates. Numerical simulations of the electrostatic confinement potential are performed along with an estimate of the coupling of the double quantum dot to the microwave resonator. Prototype devices are fabricated and characterized by transport measurements of electron confinement and reflectometry measurements of the microwave resonator.

  3. Design considerations for corrosion control of double-hull tankers

    SciTech Connect (OSTI)

    Pendexter, L.A. ); Diettrich, D. )

    1993-09-01

    The double-hull design for large vessels engaged in the transportation of oil at sea is not a new concept. The requirement for the future exclusive use of a double-hull configuration for all oil-carrying tank vessels trading in U.S. territorial waters is a result of the Oil Pollution Act of 1990. By design, the structural area of the double-hull tanker exposed to ballast water will be considerably increased compared to the single-hull tanker. The choice of protective coatings and their application methods are of vital importance of the integrity of the structure. Of equal importance will be provision for thorough inspection and a well-planned maintenance program throughout the vessel's service life. To assist in meeting these demands, certain physical features can be incorporated during construction to provide access to all parts of the hull structure.

  4. Mechanical seal having a double-tier mating ring

    DOE Patents [OSTI]

    Khonsari, Michael M.; Somanchi, Anoop K.

    2005-09-13

    An apparatus and method to enhance the overall performance of mechanical seals in one of the following ways: by reducing seal face wear, by reducing the contact surface temperature, or by increasing the life span of mechanical seals. The apparatus is a mechanical seal (e.g., single mechanical seals, double mechanical seals, tandem mechanical seals, bellows, pusher mechanical seals, and all types of rotating and reciprocating machines) comprising a rotating ring and a double-tier mating ring. In a preferred embodiment, the double-tier mating ring comprises a first and a second stationary ring that together form an agitation-inducing, guided flow channel to allow for the removal of heat generated at the seal face of the mating ring by channeling a coolant entering the mating ring to a position adjacent to and in close proximity with the interior surface area of the seal face of the mating ring.

  5. The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

    SciTech Connect (OSTI)

    Stella, Stefano; Cascio, Duilio; Johnson, Reid C.

    2010-06-21

    The bacterial nucleoid-associated protein Fis regulates diverse reactions by bending DNA and through DNA-dependent interactions with other control proteins and enzymes. In addition to dynamic nonspecific binding to DNA, Fis forms stable complexes with DNA segments that share little sequence conservation. Here we report the first crystal structures of Fis bound to high- and low-affinity 27-base-pair DNA sites. These 11 structures reveal that Fis selects targets primarily through indirect recognition mechanisms involving the shape of the minor groove and sequence-dependent induced fits over adjacent major groove interfaces. The DNA shows an overall curvature of {approx}65{sup o}, and the unprecedented close spacing between helix-turn-helix motifs present in the apodimer is accommodated by severe compression of the central minor groove. In silico DNA structure models show that only the roll, twist, and slide parameters are sufficient to reproduce the changes in minor groove widths and recreate the curved Fis-bound DNA structure. Models based on naked DNA structures suggest that Fis initially selects DNA targets with intrinsically narrow minor grooves using the separation between helix-turn-helix motifs in the Fis dimer as a ruler. Then Fis further compresses the minor groove and bends the DNA to generate the bound structure.

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

    SciTech Connect (OSTI)

    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.

  7. Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4

    SciTech Connect (OSTI)

    Wong, Jimson H.Y.; Brown, Jessica A.; Suo, Zucai; Blum, Paul; Nohmi, Takehiko; Ling, Hong

    2010-08-23

    Y-family DNA polymerases bypass Pt-GG, the cisplatin-DNA double-base lesion, contributing to the cisplatin resistance in tumour cells. To reveal the mechanism, we determined three structures of the Y-family DNA polymerase, Dpo4, in complex with Pt-GG DNA. The crystallographic snapshots show three stages of lesion bypass: the nucleotide insertions opposite the 3{prime}G (first insertion) and 5{prime}G (second insertion) of Pt-GG, and the primer extension beyond the lesion site. We observed a dynamic process, in which the lesion was converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4. The DNA translocation-coupled conformational change may account for additional inhibition on the second insertion reaction. The structures illustrate that Pt-GG disturbs the replicating base pair in the active site, which reduces the catalytic efficiency and fidelity. The in vivo relevance of Dpo4-mediated Pt-GG bypass was addressed by a dpo-4 knockout strain of Sulfolobus solfataricus, which exhibits enhanced sensitivity to cisplatin and proteomic alterations consistent with genomic stress.

  8. Implementation of Double-Waist Chicane Optics in SPEAR3

    SciTech Connect (OSTI)

    Corbett, J.; Cornacchia, M.; Dao, T.; Dell'Orco, D.; Rafael, F.; Harrington, D.; Hettel, R.; Huang, X.; Nosochkov, Y.; Rabedeau, T.; Rarback, H.; Ringwall, A.; Safranek, J.; Scott, B.; Sebek, J.; Tanabe, J.; Terebilo, A.; Wermelskirchen, C.; Widmeyer, M.; Yoon, Moohyun; /POSTECH

    2006-08-16

    The SPEAR3 accelerator upgrade opened up two 7.6m racetrack straights in the magnet lattice. In one of these straights, we recently added a magnetic chicane to separate two insertion device (ID) beam lines by 10mrad. A quadrupole triplet in the center creates a ''double focus'' optics with {beta}y = 1.6m at the middle of each ID, hence the term ''double-waist chicane''. The new optics also reduced {beta}y in the four matching straights adjacent to the racetrack straights to 2.5m. In this paper, we outline design features of the optics and physical implementation of the lattice.

  9. Double-{beta} decay Q value of {sup 150}Nd

    SciTech Connect (OSTI)

    Kolhinen, V. S.; Eronen, T.; Gorelov, D.; Hakala, J.; Jokinen, A.; Kankainen, A.; Moore, I. D.; Rissanen, J.; Saastamoinen, A.; Suhonen, J.; Aeystoe, J. [Department of Physics, P. O. Box 35 (YFL), FI-40014 University of Jyvaeskylae (Finland)

    2010-08-15

    The double-{beta} decay Q value of {sup 150}Nd was determined by using the JYFLTRAP Penning trap mass spectrometer. The measured mass difference between {sup 150}Nd and {sup 150}Sm is 3371.38(20) keV. This new value deviates by 3.7 keV from the previously adopted value of 3367.7(22) keV and is a factor of 10 more precise. Accurate knowledge of this Q value is important because {sup 150}Nd is a primary candidate to be used in the search for neutrinoless double-{beta} decay modes in several experiments.

  10. Consistency test of neutrinoless double beta decay with one isotope

    SciTech Connect (OSTI)

    Duerr, Michael; Lindner, Manfred [Max-Planck-Institut fuer Kernphysik, Postfach 10 39 80, 69029 Heidelberg (Germany); Zuber, Kai [Technical University Dresden, Institut fuer Kern- und Teilchenphysik, 01069 Dresden (Germany)

    2011-11-01

    We discuss a consistency test which makes it possible to discriminate unknown nuclear background lines from neutrinoless double beta decay with only one isotope. By considering both the transition to the ground state and to the first excited 0{sup +} state, a sufficiently large detector can reveal if neutrinoless double beta decay or some other nuclear physics process is at work. Such a detector could therefore simultaneously provide a consistency test for a certain range of Majorana masses and be sensitive to lower values of the effective Majorana mass .

  11. Double layer -- a particle accelerator in the magnetosphere

    SciTech Connect (OSTI)

    Fu, Xiangrong

    2015-07-16

    Slides present the material under the following topics: Introduction (What is a double layer (DL)? Why is it important? Key unsolved problems); Theory -- time-independent solutions of 1D Vlasov--Poisson system; Particle-in-cell simulations (Current-driven DLs); and Electron acceleration by DL (Betatron acceleration). Key problems include the generation mechanism, stability, and electron acceleration. In summary, recent observations by Van Allen Probes show large number of DLs in the outer radiation belt, associated with enhanced flux of relativistic electrons. Simulations show that ion acoustic double layers can be generated by field-aligned currents. Thermal electrons can gain energy via betatron acceleration in a dipole magnetic field.

  12. Property:NEPA DNA Worksheet | Open Energy Information

    Open Energy Info (EERE)

    DNA Worksheet Jump to: navigation, search Property Name NEPA DNA Worksheet Property Type Page Description DNA Worksheet files for NEPA Docs. This is a property of type Page. It...

  13. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    scientists. Schematic of DNA structures in various conformations on a gold surface. Differences in overall structure and orientation are emphasized by color-coding of DNA...

  14. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Understanding both the attachment and orientation of DNA on gold surfaces was the goal of ... Schematic of DNA structures in various conformations on a gold surface. Differences in ...

  15. Microfluidics: Kinetics of Hybridized DNA With Fluid Flow Variations...

    Office of Scientific and Technical Information (OSTI)

    Microfluidics: Kinetics of Hybridized DNA With Fluid Flow Variations. Citation Details In-Document Search Title: Microfluidics: Kinetics of Hybridized DNA With Fluid Flow ...

  16. 6.7 Engineered Enzyme Accelerates DNA Sequencing

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and Richardson, C. C. (1995) "A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and...

  17. DNA-mediated engineering of multicomponent enzyme crystals (Journal...

    Office of Scientific and Technical Information (OSTI)

    DNA-mediated engineering of multicomponent enzyme crystals Citation Details In-Document Search Title: DNA-mediated engineering of multicomponent enzyme crystals Authors: Brodin, ...

  18. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked...

  19. Method of quantitating dsDNA

    DOE Patents [OSTI]

    Stark, Peter C.; Kuske, Cheryl R.; Mullen, Kenneth I.

    2002-01-01

    A method for quantitating dsDNA in an aqueous sample solution containing an unknown amount of dsDNA. A first aqueous test solution containing a known amount of a fluorescent dye-dsDNA complex and at least one fluorescence-attenutating contaminant is prepared. The fluorescence intensity of the test solution is measured. The first test solution is diluted by a known amount to provide a second test solution having a known concentration of dsDNA. The fluorescence intensity of the second test solution is measured. Additional diluted test solutions are similarly prepared until a sufficiently dilute test solution having a known amount of dsDNA is prepared that has a fluorescence intensity that is not attenuated upon further dilution. The value of the maximum absorbance of this solution between 200-900 nanometers (nm), referred to herein as the threshold absorbance, is measured. A sample solution having an unknown amount of dsDNA and an absorbance identical to that of the sufficiently dilute test solution at the same chosen wavelength is prepared. Dye is then added to the sample solution to form the fluorescent dye-dsDNA-complex, after which the fluorescence intensity of the sample solution is measured and the quantity of dsDNA in the sample solution is determined. Once the threshold absorbance of a sample solution obtained from a particular environment has been determined, any similarly prepared sample solution taken from a similar environment and having the same value for the threshold absorbance can be quantified for dsDNA by adding a large excess of dye to the sample solution and measuring its fluorescence intensity.

  20. First experiment with the double solenoid RIBRAS system

    SciTech Connect (OSTI)

    Lichtenthaeler, R.; Condori, R. Pampa; Lepine-Szily, A.; Pires, K. C. C.; Morais, M. C.; Leistenschneider, E.; Scarduelli, V. B.; Gasques, L. R.; Faria, P. N. de; Mendes, D. R. Jr.; Shorto, J. M. B.

    2013-05-06

    A description of the double solenoid system (RIBRAS) operating since 2004 in one of the beam lines of the Pelletron Laboratory of the Institute of Physics of the University of Sao Paulo is presented. The recent installation of the secondary scattering chamber after the second solenoid is reported and the first experiment in RIBRAS using both solenoids is described.

  1. Heat exchanger with leak detecting double wall tubes

    DOE Patents [OSTI]

    Bieberbach, George; Bongaards, Donald J.; Lohmeier, Alfred; Duke, James M.

    1981-01-01

    A straight shell and tube heat exchanger utilizing double wall tubes and three tubesheets to ensure separation of the primary and secondary fluid and reliable leak detection of a leak in either the primary or the secondary fluids to further ensure that there is no mixing of the two fluids.

  2. Period-doubling reconstructions of semiconductor partial dislocations

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Park, Ji -Sang; Huang, Bing; Wei, Su -Huai; Kang, Joongoo; McMahon, William E.

    2015-09-18

    Atomic-scale understanding and control of dislocation cores is of great technological importance, because they act as recombination centers for charge carriers in optoelectronic devices. Using hybrid density-functional calculations, we present period-doubling reconstructions of a 90° partial dislocation in GaAs, for which the periodicity of like-atom dimers along the dislocation line varies from one to two, to four dimers. The electronic properties of a dislocation change drastically with each period doubling. The dimers in the single-period dislocation are able to interact, to form a dispersive one-dimensional band with deep-gap states. However, the inter-dimer interaction for the double-period dislocation becomes significantly reduced;more » hence, it is free of mid-gap states. The Ga core undergoes a further period-doubling transition to a quadruple-period reconstruction induced by the formation of small hole polarons. Lastly, the competition between these dislocation phases suggests a new passivation strategy via population manipulation of the detrimental single-period phase.« less

  3. Inner-shell and double ionization potentials of aminophenol isomers.

    SciTech Connect (OSTI)

    Kryzhevoi, N. V.; Santra, R.; Cederbaum, L. S.

    2011-01-01

    A comprehensive study of single and double core ionization potentials of the aminophenol molecule is reported. The role of relaxation, correlation, relativistic, and basis set effects in these potentials is clarified. Special attention is paid to the isomer dependence of the single and double core ionization potentials. Some of them are also compared with the respective values of the phenol and aniline molecules. It is shown that the core level single ionization potentials of the para-, meta-, and ortho-aminophenol molecules differ only slightly from each other, rendering these structural isomers challenging to distinguish for conventional x-ray photoelectron spectroscopy. In contrast, the energy needed to remove two core electrons from different atoms depends noticeably on the mutual arrangement and even on the relative orientations of the hydroxyl and amine groups. Together with the electrostatic repulsion between the two core holes, relaxation effects accompanying double core ionization play a crucial role here. The pronounced sensitivity of the double ionization potentials, therefore, enables a spectroscopic characterization of the electronic structure of aminophenol isomers by means of x-ray two-photon photoelectron spectroscopy.

  4. The Majorana Double Beta Decay Experiment: Present Status

    SciTech Connect (OSTI)

    Aguayo, Estanislao; Avignone, Frank T.; Back, Henning O.; Barabash, Alexander S.; Beene, Jim; Bergevin, M.; Bertrand, F.; Boswell, M.; Brudanin, V.; Busch, Matthew; Chan, Yuen-Dat; Christofferson, C. D.; Collar, J. I.; Combs, Dustin C.; Cooper, R. J.; Detwiler, Jason A.; Doe, Peter J.; Efremenko, Yuri; Egorov, Viatcheslav; Ejiri, H.; Elliott, S. R.; Esterline, James H.; Fast, James E.; Fields, N.; Finnerty, P.; Fraenkle, Florian; Gehman, Victor M.; Giovanetti, G. K.; Green, M. P.; Guiseppe, V. E.; Gusey, K.; Hallin, A. L.; Hazama, R.; Henning, Reyco; Hime, Andrew; Hoppe, Eric W.; Horton, Mark; Howard, Stanley; Howe, M. A.; Johnson, R. A.; Keeter, K.; Keller, C.; Kidd, M. F.; Knecht, A.; Kochetov, Oleg; Konovalov, S.; Kouzes, Richard T.; Laferriere, Brian D.; LaRoque, B. H.; Leon, Jonathan D.; Leviner, L.; Loach, J. C.; MacMullin, S.; Marino, Michael G.; Martin, R. D.; Mei, Dong-Ming; Merriman, Jason H.; Miller, M. L.; Mizouni, Leila; Nomachi, Masaharu; Orrell, John L.; Overman, Nicole R.; Phillips II, D. G.; Poon, Alan; Perumpilly, Gopakumar; Prior, Gersende; Radford, D. C.; Rielage, Keith; Robertson, R. G. H.; Ronquest, M. C.; Schubert, Alexis G.; Shima, T.; Shirchenko, M.; Snavely, Kyle J.; Steele, David; Strain, J.; Thomas, K.; Timkin, V.; Tornow, W.; Vanyushin, I.; Varner, R. L.; Vetter, Kai; Vorren, Kris R.; Wilkerson, J. F.; Yakushev, E.; Young, A.; Yu, Chang-Hong; Yumatov, Vladimir; Zhang, C.

    2013-06-01

    The Majorana collaboration is actively pursuing research and development aimed at a tonne-scale 76Ge neutrinoless double-beta decay experiment, an R&D effort that will field approximately 40 kg of germanium detectors with mixed enrichment levels. This article provides a status update on the construction of the Demonstrator

  5. EA-1905: Double Eagle Water System, Carlsbad, New Mexico

    Broader source: Energy.gov [DOE]

    This EA, prepared by the U.S. Department of the Interior’s Bureau of Land Management Carlsbad Field Office and adopted by DOE, evaluates the expansion and upgrade of the City of Carlsbad’s Double Eagle Water System.

  6. Period-doubling reconstructions of semiconductor partial dislocations

    SciTech Connect (OSTI)

    Park, Ji -Sang; Huang, Bing; Wei, Su -Huai; Kang, Joongoo; McMahon, William E.

    2015-09-18

    Atomic-scale understanding and control of dislocation cores is of great technological importance, because they act as recombination centers for charge carriers in optoelectronic devices. Using hybrid density-functional calculations, we present period-doubling reconstructions of a 90° partial dislocation in GaAs, for which the periodicity of like-atom dimers along the dislocation line varies from one to two, to four dimers. The electronic properties of a dislocation change drastically with each period doubling. The dimers in the single-period dislocation are able to interact, to form a dispersive one-dimensional band with deep-gap states. However, the inter-dimer interaction for the double-period dislocation becomes significantly reduced; hence, it is free of mid-gap states. The Ga core undergoes a further period-doubling transition to a quadruple-period reconstruction induced by the formation of small hole polarons. Lastly, the competition between these dislocation phases suggests a new passivation strategy via population manipulation of the detrimental single-period phase.

  7. Mixer pump test plan for double shell tank AZ-101

    SciTech Connect (OSTI)

    STAEHR, T.W.

    1999-05-12

    Mixer pump systems have been chosen as the method for retrieval of tank wastes contained in double shell tanks at Hanford. This document describes the plan for testing and demonstrating the ability of two 300 hp mixer pumps to mobilize waste in tank AZ-101. The mixer pumps, equipment and instrumentation to monitor the test were installed by Project W-151.

  8. Scaling factor inconsistencies in neutrinoless double beta decay

    SciTech Connect (OSTI)

    Cowell, S. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

    2006-02-15

    The modern theory of neutrinoless double beta decay includes a scaling factor that has often been treated inconsistently in the literature. The nuclear contribution to the decay half-life can be suppressed by 15%-20% when scaling factors are mismatched. Correspondingly, is overestimated.

  9. Majorana neutrino masses and the neutrinoless double-beta decay

    SciTech Connect (OSTI)

    Faessler, A. [University of Tuebingen, Institute of Theoretical Physics (Germany)], E-mail: amand.faessler@uni-tuebingen.de

    2006-12-15

    Neutrinoless double-beta decay is forbidden in the Standard Model of electroweak and strong interaction but allowed in most Grand Unified Theories (GUTs). Only if the neutrino is a Majorana particle (identical with its antiparticle) and if it has a mass is neutrinoless double-beta decay allowed. Apart from one claim that the neutrinoless double-beta decay in {sup 76}Ge is measured, one has only upper limits for this transition probability. But even the upper limits allow one to give upper limits for the electron Majorana neutrino mass and upper limits for parameters of GUTs and the minimal R-parity-violating supersymmetric model. One further can give lower limits for the vector boson mediating mainly the right-handed weak interaction and the heavy mainly right-handed Majorana neutrino in left-right symmetric GUTs. For that, one has to assume that the specific mechanism is the leading one for neutrinoless double-beta decay and one has to be able to calculate reliably the corresponding nuclear matrix elements. In the present work, one discusses the accuracy of the present status of calculating of the nuclear matrix elements and the corresponding limits of GUTs and supersymmetric parameters.

  10. Neutrinoless Double Beta Decay and {nu}-Mass Determination

    SciTech Connect (OSTI)

    Pedretti, M. [Universita dell Insubria, Via Vallegio 11, 22100 Como (Italy)

    2005-10-12

    The search for Neutrinoless Double Beta Decay could improve our knowledge on neutrino properties. After a brief discussion on the implications of the observation of this rare process, I will introduce the experimental approaches and review the prospects of the search for this nuclear transition.

  11. Neutrinoless double-{beta} decay: Status and future

    SciTech Connect (OSTI)

    Bilenky, S. M. [Joint Institute for Nuclear Research (Russian Federation)], E-mail: bilenky@he.sissa.it

    2006-12-15

    A brief summary of the status of neutrino masses, mixing, and oscillations is presented. Neutrinoless double {beta} decay is considered. Predictions for the effective Majorana mass are reviewed. A possible test of the calculations of nuclear matrix elements of the 0{nu}{beta}{beta} decay is proposed.

  12. New Advances in Neutrinoless Double Beta Decay Matrix Elements

    SciTech Connect (OSTI)

    Munoz, Jose Barea [Instituto de Estructura de la Materia, C.S.I.C. Unidad Asociada al Departamento de Fisica Atomica, Molecular y Nuclear, Facultad de Fisica, Universidad de Sevilla, Apartado 1065, 41080 Sevilla (Spain)

    2010-08-04

    We present the matrix elements necessary to evaluate the half-life of some neutrinoless double beta decay candidates in the framework of the microscopic interacting boson model (IBM). We compare our results with those from other models and extract some simple features of the calculations.

  13. Neutrinoless double beta decay in the microscopic interacting boson model

    SciTech Connect (OSTI)

    Iachello, F. [Center for Theoretical Physics, Sloane Physics Laboratory Yale University New Haven, CT 06520-8120 (United States)

    2009-11-09

    The results of a calculation of the nuclear matrix elements for neutrinoless double beta decay in the closure approximation in several nuclei within the framework of the microscopic interacting boson model (IBM-2) are presented and compared with those calculated in the shell model (SM) and quasiparticle random phase approximation (QRPA)

  14. Conditions for detecting CP violation via neutrinoless double beta decay

    SciTech Connect (OSTI)

    Joniec, A.; Zralek, M. [Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice (Poland)

    2006-02-01

    Neutrinoless double beta decay data, together with information on the absolute neutrino masses obtained from the future KATRIN experiment and/or astrophysical measurements, provide a chance to find CP violation in the lepton sector with Majorana neutrinos. We derive and discuss necessary conditions which make discovery of such CP violation possible for the future neutrino oscillation and mass measurements data.

  15. Pd/Ni-WO3 anodic double layer gasochromic device

    DOE Patents [OSTI]

    Lee, Se-Hee; Tracy, C. Edwin; Pitts, J. Roland; Liu, Ping

    2004-04-20

    An anodic double layer gasochromic sensor structure for optical detection of hydrogen in improved response time and with improved optical absorption real time constants, comprising: a glass substrate; a tungsten-doped nickel oxide layer coated on the glass substrate; and a palladium layer coated on the tungsten-doped nickel oxide layer.

  16. The Los Alamos National Laboratory precision double crystal spectrometer

    SciTech Connect (OSTI)

    Morgan, D.V.; Stevens, C.J.; Liefield, R.J.

    1994-03-01

    This report discusses the following topics on the LANL precision double crystal X-ray spectrometer: Motivation for construction of the instrument; a brief history of the instrument; mechanical systems; motion control systems; computer control system; vacuum system; alignment program; scan programs; observations of the copper K{alpha} lines; and characteristics and specifications.

  17. Double Shell Tank AY-102 Radioactive Waste Leak Investigation

    SciTech Connect (OSTI)

    Washenfelder, Dennis J.

    2014-04-10

    PowerPoint. The objectives of this presentation are to: Describe Effort to Determine Whether Tank AY-102 Leaked; Review Probable Causes of the Tank AY-102 Leak; and, Discuss Influence of Leak on Hanfords Double-Shell Tank Integrity Program.

  18. Bound states in a hyperbolic asymmetric double-well

    SciTech Connect (OSTI)

    Hartmann, R. R.

    2014-01-15

    We report a new class of hyperbolic asymmetric double-well whose bound state wavefunctions can be expressed in terms of confluent Heun functions. An analytic procedure is used to obtain the energy eigenvalues and the criterion for the potential to support bound states is discussed.

  19. Dual-cone double-helical downhole logging device

    DOE Patents [OSTI]

    Yu, Jiunn S.

    1984-01-01

    A broadband downhole logging device includes a double-helix coil wrapped over a dielectric support and surrounded by a dielectric shield. The device may also include a second coil longitudinally aligned with a first coil and enclosed within the same shield for measuring magnetic permeability of downhole formations and six additional coils for accurately determining downhole parameters.

  20. Computer code for double beta decay QRPA based calculations

    SciTech Connect (OSTI)

    Barbero, C. A.; Mariano, A.; Krmpoti?, F.; Samana, A. R.; Ferreira, V. dos Santos; Bertulani, C. A.

    2014-11-11

    The computer code developed by our group some years ago for the evaluation of nuclear matrix elements, within the QRPA and PQRPA nuclear structure models, involved in neutrino-nucleus reactions, muon capture and ?{sup } processes, is extended to include also the nuclear double beta decay.

  1. DNA fragment sizing and sorting by laser-induced fluorescence

    DOE Patents [OSTI]

    Hammond, Mark L.; Jett, James H.; Keller, Richard A.; Marrone, Babetta L.; Martin, John C.

    1996-01-01

    A method is provided for sizing DNA fragments using high speed detection systems, such as flow cytometry to determine unique characteristics of DNA pieces from a sample. In one characterization the DNA piece is fragmented at preselected sites to produce a plurality of DNA fragments. The DNA piece or the resulting DNA fragments are treated with a dye effective to stain stoichiometrically the DNA piece or the DNA fragments. The fluorescence from the dye in the stained fragments is then examined to generate an output functionally related to the number of nucleotides in each one of the DNA fragments. In one embodiment, the intensity of the fluorescence emissions from each fragment is linearly related to the fragment length. The distribution of DNA fragment sizes forms a characterization of the DNA piece for use in forensic and research applications.

  2. Scar-less multi-part DNA assembly design automation

    DOE Patents [OSTI]

    Hillson, Nathan J.

    2016-06-07

    The present invention provides a method of a method of designing an implementation of a DNA assembly. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding flanking homology sequences to each of the DNA oligos. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding optimized overhang sequences to each of the DNA oligos.

  3. Industrial mixing techniques for Hanford double-shell tanks

    SciTech Connect (OSTI)

    Daymo, E.A.

    1997-09-01

    Jet mixer pumps are currently the baseline technology for sludge mobilization and mixing in one-million gallon double-shell tanks at the Hanford and Savannah River Sites. Improvements to the baseline jet mixer pump technology are sought because jet mixer pumps have moving parts that may fail or require maintenance. Moreover, jet mixers are relatively expensive, they heat the waste, and, in some cases, may not mobilize enough of the sludge. This report documents a thorough literature search for commercially available applicable mixing technologies that could be used for double-shell tank sludge mobilization and mixing. Textbooks, research articles, conference proceedings, mixing experts, and the Thomas Register were consulted to identify applicable technologies. While there are many commercial methods that could be used to mobilize sludge or mix the contents of a one-million gallon tank, few will work given the geometrical constraints (e.g., the mixer must fit through a 1.07-m-diameter riser) or the tank waste properties (e.g., the sludge has such a high yield stress that it generally does not flow under its own weight). Pulsed fluid jets and submersible Flygt mixers have already been identified at Hanford and Savannah River Sites for double-shell tank mixing applications. While these mixing technologies may not be applicable for double-shell tanks that have a thick sludge layer at the bottom (since too many of these mixers would need to be installed to mobilize most of the sludge), they may have applications in tanks that do not have a settled solids layer. Retrieval projects at Hanford and other U.S. Department of Energy sites are currently evaluating the effectiveness of these mixing techniques for tank waste applications. The literature search did not reveal any previously unknown technologies that should be considered for sludge mobilization and mixing in one-million gallon double-shell tanks.

  4. Studies of Nb3Sn Strands Based on the Restacked-Rod Process for High-Field Accelerator Magnets Nb3Sn

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Barzi, E; Bossert, M; Gallo, G; Lombardo, V; Turrioni, D; Yamada, R; Zlobin, A V

    2012-06-01

    A major thrust in Fermilab's accelerator magnet R&D program is the development of Nb3Sn wires which meet target requirements for high field magnets, such as high critical current density, low effective filament size, and the capability to withstand the cabling process. The performance of a number of strands with 150/169 restack design produced by Oxford Superconducting Technology was studied for round and deformed wires. To optimize the maximum plastic strain, finite element modeling was also used as an aid in the design. Results of mechanical, transport and metallographic analyses are presented for round and deformed wires.

  5. Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

    DOE Patents [OSTI]

    Gardner, Shea N; Mariella, Jr., Raymond P; Christian, Allen T; Young, Jennifer A; Clague, David S

    2013-06-25

    A method of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths.

  6. Extracting biological knowledge from DNA sequences

    SciTech Connect (OSTI)

    De La Vega, F.M.; Thieffry, D.; Collado-Vides, J.

    1996-12-31

    This session describes the elucidation of information from dna sequences and what challenges computational biologists face in their task of summarizing and deciphering the human genome. Techniques discussed include methods from statistics, information theory, artificial intelligence and linguistics. 1 ref.

  7. DNA Assembly Line for Nano-Construction

    ScienceCinema (OSTI)

    Oleg Gang

    2010-01-08

    Building on the idea of using DNA to link up nanoparticles scientists at Brookhaven National Lab have designed a molecular assembly line for high-precision nano-construction. Nanofabrication is essential for exploiting the unique properties of nanoparticl

  8. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9...

  9. Multiple tag labeling method for DNA sequencing

    DOE Patents [OSTI]

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  10. Multiple tag labeling method for DNA sequencing

    DOE Patents [OSTI]

    Mathies, Richard A.; Huang, Xiaohua C.; Quesada, Mark A.

    1995-01-01

    A DNA sequencing method described which uses single lane or channel electrophoresis. Sequencing fragments are separated in said lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radio-isotope labels.

  11. Oligonucleotide and Long Polymeric DNA Encoding

    SciTech Connect (OSTI)

    Miller, E; Mariella Jr., R P; Christian, A T; Gardner, S N; Williams, J M

    2003-11-24

    This report summarizes the work done at Lawrence Livermore National Laboratory for the Oligonucleotide and Long Polymeric DNA Encoding project, part of the Microelectronic Bioprocesses Program at DARPA. The goal of the project was to develop a process by which long (circa 10,000 base-pair) synthetic DNA molecules could be synthesized in a timely and economic manner. During construction of the long molecule, errors in DNA sequence occur during hybridization and/or the subsequent enzymatic process. The work done on this project has resulted in a novel synthesis scheme that we call the parallel pyramid synthesis protocol, the development of a suit of computational tools to minimize and quantify errors in the synthesized DNA sequence, and experimental proof of this technique. The modeling consists of three interrelated modules: the bioinformatics code which determines the specifics of parallel pyramid synthesis for a given chain of long DNA, the thermodynamics code which tracks the products of DNA hybridization and polymerase extension during the later steps in the process, and the kinetics model which examines the temporal and spatial processes during one thermocycle. Most importantly, we conducted the first successful syntheses of a gene using small starting oligomers (tetramers). The synthesized sequence, 813 base pairs long, contained a 725 base pair gene, modified green fluorescent protein (mGFP), which has been shown to be a functional gene by cloning into cells and observing its green fluorescent product.

  12. Mechanism of homologous recombination from the RecA-ssDNA/dsDNA...

    Office of Scientific and Technical Information (OSTI)

    Sponsoring Org: USDOE Country of Publication: United States Language: ENGLISH Subject: 60 APPLIED LIFE SCIENCES; ATP-ASE; ATP; CRYSTAL STRUCTURE; DNA; ESCHERICHIA COLI; FILAMENTS; ...

  13. Double Beta Decay in Xenon-136: Measuring the Neutrino-Emitting...

    Office of Scientific and Technical Information (OSTI)

    Double Beta Decay in Xenon-136: Measuring the Neutrino-Emitting Mode and Searching for Majoron-Emitting Modes Citation Details In-Document Search Title: Double Beta Decay in...

  14. The H2 Double-Slit Experiment: Where Quantum and Classical Physics...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The H2 Double-Slit Experiment: Where Quantum and Classical Physics Meet Print For the first time, an international research team carried out a double-slit experiment in H2, the...

  15. The 'X-Prize' Approach: Double-blind Assessment of Ductile Tearing...

    Office of Scientific and Technical Information (OSTI)

    Conference: The 'X-Prize' Approach: Double-blind Assessment of Ductile Tearing Prediction Methods. Citation Details In-Document Search Title: The 'X-Prize' Approach: Double-blind ...

  16. The 'X-Prize' approach : double-blind evaluation of ductile tearing...

    Office of Scientific and Technical Information (OSTI)

    The 'X-Prize' approach : double-blind evaluation of ductile tearing prediction methods. Citation Details In-Document Search Title: The 'X-Prize' approach : double-blind evaluation ...

  17. Effects of a tilted magnetic field in a Dirac double layer (Journal...

    Office of Scientific and Technical Information (OSTI)

    Effects of a tilted magnetic field in a Dirac double layer Citation Details In-Document Search Title: Effects of a tilted magnetic field in a Dirac double layer Authors: ...

  18. Search for Neutrinoless Double-Beta Decay in 136Xe with EXO-200...

    Office of Scientific and Technical Information (OSTI)

    Neutrinoless Double-Beta Decay in 136Xe with EXO-200 Citation Details In-Document Search Title: Search for Neutrinoless Double-Beta Decay in 136Xe with EXO-200 Authors: Auger, M. ;...

  19. The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome

    SciTech Connect (OSTI)

    Trego, Kelly S.; Chernikova, Sophia B.; Davalos, Albert R.; Perry, J. Jefferson P.; Finger, L. David; Ng, Cliff; Tsai, Miaw-Sheue; Yannone, Steven M.; Tainer, John A.; Campisi, Judith; Cooper, Priscilla K.

    2011-04-20

    XPG is a structure-specific endonuclease required for nucleotide excision repair (NER). XPG incision defects result in the cancer-prone syndrome xeroderma pigmentosum, whereas truncating mutations of XPG cause the severe postnatal progeroid developmental disorder Cockayne syndrome. We show that XPG interacts directly with WRN protein, which is defective in the premature aging disorder Werner syndrome, and that the two proteins undergo similar sub-nuclear redistribution in S-phase and co-localize in nuclear foci. The co-localization was observed in mid- to late-S-phase, when WRN moves from nucleoli to nuclear foci that have been shown to contain protein markers of both stalled replication forks and telomeric proteins. We mapped the interaction between XPG and WRN to the C-terminal domains of each and show that interaction with the C-terminal domain of XPG strongly stimulates WRN helicase activity. WRN also possesses a competing DNA single-strand annealing activity that, combined with unwinding, has been shown to coordinate regression of model replication forks to form Holliday junction/chicken foot intermediate structures. We tested whether XPG stimulated WRN annealing activity and found that XPG itself has intrinsic strand annealing activity that requires the unstructured R- and C-terminal domains, but not the conserved catalytic core or endonuclease activity. Annealing by XPG is cooperative, rather than additive, with WRN annealing. Taken together, our results suggest a novel function for XPG in S-phase that is at least in part carried out coordinately with WRN, and which may contribute to the severity of the phenotypes that occur upon loss of XPG.

  20. Investigation of structure and properties of the Nb rods manufactured by different deformation and heat treatment regimes in mass production conditions for the Nb{sub 3}Sn strands

    SciTech Connect (OSTI)

    Abdyukhanov, I. M.; Vorobieva, A. E.; Alekseev, M. V.; Mareev, K. A.; Dergunova, E. A.; Peredkova, T. N. [JSC Bochvar High-Technology Research Institute of Inorganic Materials, 5a Rogova St., Moscow, 123060 (Russian Federation); Shikov, A. K. [NRC Kurchatov Institute, 1 Akademika Kurchatova Sq., Moscow, 123182 (Russian Federation); Utkin, K. V.; Vorobieva, A. V.; Kharkovsky, D. N. [JSC Chepetsky Mechanical Plant, 7 Belova St., Glazov, 427620 (Russian Federation)

    2014-01-27

    From 2009 the mass production of the Nb{sub 3}Sn strands for ITER with the yield of several tens of tons per year operates at JSC Chepetsky Mechanical Plant (Glazov, Russia). In order to enhance the stability of output characteristics of the produced Nb{sub 3}Sn strands, to increase the Nb filaments dimensional homogeneity the manufacture regimes improvement of the used semiproducts such as Nb rods intended for the superconducting filaments formation in the finished strands has been carried out. In the work the investigations of the Nb rheological behavior, the influence of heat treatment in the wide temperature range from 700 to 1300 C on the predeformed Nb rods structure and mechanical properties have been performed. Different production routes of the Nb rods, including such operations like forging, extrusion and drawing combined with the recrystallization annealings, were used. Composite Nb{sub 3}Sn strands have been produced and their electrophysical properties have been tested. For the first time influence of the niobium rods manufacture regimes on the current carrying capacity of the industrial Nb{sub 3}Sn strands has been investigated.

  1. The Search for Neutrinoless Double Beta Decay with 130Te with CUORE-0

    SciTech Connect (OSTI)

    Jonathan Loren Ouellet

    2015-06-02

    This thesis describes the design, operation and results of an experimental search for neutrinoless double beta decay (0$\

  2. What can we learn from neutrinoless double beta decay experiments? (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect What can we learn from neutrinoless double beta decay experiments? Citation Details In-Document Search Title: What can we learn from neutrinoless double beta decay experiments? We assess how well next generation neutrinoless double beta decay and normal neutrino beta decay experiments can answer four fundamental questions. 1) If neutrinoless double beta decay searches do not detect a signal, and if the spectrum is known to be inverted hierarchy, can we conclude

  3. Monitoring of Double-Stud Wall Moisture Conditions in the Northeast

    SciTech Connect (OSTI)

    Ueno, K.

    2015-03-01

    Double-stud walls insulated with cellulose or low-density spray foam can have R-values of 40 or higher. However, double-stud walls have a higher risk of interior-sourced condensation moisture damage when compared with high-R approaches using exterior insulating sheathing. Moisture conditions in double-stud walls were monitored in Zone 5A (Massachusetts); three double-stud assemblies were compared.

  4. Origin of superstructures in (double) perovskite thin films

    SciTech Connect (OSTI)

    Shabadi, V. Major, M.; Komissinskiy, P.; Vafaee, M.; Radetinac, A.; Baghaie Yazdi, M.; Donner, W.; Alff, L.

    2014-09-21

    We have investigated the origin of superstructure peaks as observed by X-ray diffraction of multiferroic Bi(Fe{sub 0.5}Cr{sub 0.5})O{sub 3} thin films grown by pulsed laser deposition on single crystal SrTiO{sub 3} substrates. The photon energy dependence of the contrast between the atomic scattering factors of Fe and Cr is used to rule out a chemically ordered double perovskite Bi{sub 2}FeCrO{sub 6} (BFCO). Structural calculations suggest that the experimentally observed superstructure occurs due to unequal cation displacements along the pseudo-cubic [111] direction that mimic the unit cell of the chemically ordered compound. This result helps to clarify discrepancies in the correlations of structural and magnetic order reported for Bi{sub 2}FeCrO{sub 6}. The observation of a superstructure in itself is not a sufficient proof of chemical order in double perovskites.

  5. Double beta decay, Majorana neutrinos, and neutrino mass

    SciTech Connect (OSTI)

    Avignone, Frank T. III; Elliott, Steven R.; Engel, Jonathan [Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208 (United States); Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27599-3255 (United States)

    2008-04-15

    The theoretical and experimental issues relevant to neutrinoless double beta decay are reviewed. The impact that a direct observation of this exotic process would have on elementary particle physics, nuclear physics, astrophysics, and cosmology is profound. Now that neutrinos are known to have mass and experiments are becoming more sensitive, even the nonobservation of neutrinoless double beta decay will be useful. If the process is actually observed, we will immediately learn much about the neutrino. The status and discovery potential of proposed experiments are reviewed in this context, with significant emphasis on proposals favored by recent panel reviews. The importance of and challenges in the calculation of nuclear matrix elements that govern the decay are considered in detail. The increasing sensitivity of experiments and improvements in nuclear theory make the future exciting for this field at the interface of nuclear and particle physics.

  6. Complementarity of Neutrinoless Double Beta Decay and Cosmology

    SciTech Connect (OSTI)

    Dodelson, Scott; Lykken, Joseph

    2014-03-20

    Neutrinoless double beta decay experiments constrain one combination of neutrino parameters, while cosmic surveys constrain another. This complementarity opens up an exciting range of possibilities. If neutrinos are Majorana particles, and the neutrino masses follow an inverted hierarchy, then the upcoming sets of both experiments will detect signals. The combined constraints will pin down not only the neutrino masses but also constrain one of the Majorana phases. If the hierarchy is normal, then a beta decay detection with the upcoming generation of experiments is unlikely, but cosmic surveys could constrain the sum of the masses to be relatively heavy, thereby producing a lower bound for the neutrinoless double beta decay rate, and therefore an argument for a next generation beta decay experiment. In this case as well, a combination of the phases will be constrained.

  7. Neutrinoless double {beta}-decay and neutrino mass hierarchies

    SciTech Connect (OSTI)

    Bilenky, S. M. [Scuola Internazionale Superiore di Studi Avanzati, I-34014 Trieste (Italy); Faessler, Amand; Gutsche, Thomas; Simkovic, Fedor [Institute fuer Theoretische Physik der Universitaet Tuebingen, D-72076 Tuebingen (Germany)

    2005-09-01

    In the framework of the seesaw mechanism the normal hierarchy is favorable for the neutrino mass spectrum. For this spectrum we present a detailed calculation of the half-lives of neutrinoless double {beta}-decay for several nuclei of experimental interest. The half-lives are evaluated by considering the most comprehensive nuclear matrix elements, which were obtained within the renormalized quasiparticle random phase approximation by the Bratislava-Caltech-Tuebingen group. The dependence of the half-lives on sin{sup 2}{theta}{sub 13} and the lightest neutrino mass is studied. We present also the results of the calculations of the half-lives of neutrinoless double {beta}-decay in the case of the inverted hierarchy of neutrino masses.

  8. Results of the double beta decay experiment NEMO-3

    SciTech Connect (OSTI)

    Tretyak, V. I. [Joint Institute for Nuclear Research, 6 Joliot Curie, Dubna (Russian Federation); Collaboration: NEMO-3 Collaboration

    2013-12-30

    The double beta decay experiment NEMO-3 has taken data from February 2003 to January 2011. The two-neutrino decay half lives were measured for seven different isotopes ({sup 100}Mo, {sup 82}Se, {sup 116}Cd, {sup 150}Nd, {sup 96}Zr, {sup 48}Ca and {sup 130}Te). No evidence for neutrinoless double beta decay is observed. The 0??? half-life limits are found to be T{sub 1/2}{sup 0?}({sup 100}Mo)>1.010{sup 24}yr(90%C.L.) and T{sub 1/2}{sup 0?}({sup 82}Se)>3.210{sup 23}yr(90%C.L.)

  9. Extra dimensions and neutrinoless double beta decay experiments

    SciTech Connect (OSTI)

    Gozdz, Marek; Kaminski, Wieslaw A.; Faessler, Amand [Theoretical Physics Department, Maria Curie-Sklodowska University, Lublin (Poland); Institute fuer Theoretische Physik, Universitaet Tuebingen, Auf der Morgenstelle 14, D-72076 Tuebingen (Germany)

    2005-05-01

    The neutrinoless double beta decay is one of the few phenomena, belonging to the nonstandard physics, which is extensively being sought for in experiments. In the present paper the link between the half-life of the neutrinoless double beta decay and theories with large extra dimensions is explored. The use of the sensitivities of currently planned 0{nu}2{beta} experiments: DAMA, CANDLES, COBRA, DCBA, CAMEO, GENIUS, GEM, MAJORANA, MOON, CUORE, EXO, and XMASS, gives the possibility for a nondirect 'experimental' verification of various extra dimensional scenarios. We discuss also the results of the Heidelberg-Moscow Collaboration. The calculations are based on the Majorana neutrino mass generation mechanism in the Arkani-Hamed-Dimopoulos-Dvali model.

  10. Electrical-assisted double side incremental forming and processes thereof

    DOE Patents [OSTI]

    Roth, John; Cao, Jian

    2014-06-03

    A process for forming a sheet metal component using an electric current passing through the component is provided. The process can include providing a double side incremental forming machine, the machine operable to perform a plurality of double side incremental deformations on the sheet metal component and also apply an electric direct current to the sheet metal component during at least part of the forming. The direct current can be applied before or after the forming has started and/or be terminated before or after the forming has stopped. The direct current can be applied to any portion of the sheet metal. The electrical assistance can reduce the magnitude of force required to produce a given amount of deformation, increase the amount of deformation exhibited before failure and/or reduce any springback typically exhibited by the sheet metal component.

  11. 241-AY Double Shell Tanks (DST) Integrity Assessment Report

    SciTech Connect (OSTI)

    JENSEN, C.E.

    1999-09-21

    This report presents the results of the integrity assessment of the 241-AY double-shell tank farm facility located in the 200 East Area of the Hanford Site. The assessment included the design evaluation and integrity examinations of the tanks and concluded that the facility is adequately designed, is compatible with the waste, and is fit for use. Recommendations including subsequent examinations. are made to ensure the continued safe operation of the tanks.

  12. 241-SY Double Shell Tanks (DST) Integrity Assessment Report

    SciTech Connect (OSTI)

    JENSEN, C.E.

    1999-09-21

    This report presents the results of the integrity assessment of the 241-SY double-shell tank farm facility located in the 200 West Area of the Hanford Site. The assessment included the design evaluation and integrity examinations of the tanks and concluded that the facility is adequately designed, is compatible with the waste, and is fit for use. Recommendations including subsequent examinations, are made to ensure the continued safe operation of the tanks.

  13. Tritium emissions from 200 East Area Double-Shell Tanks

    SciTech Connect (OSTI)

    Bachand, D.D.

    1994-11-28

    This document evaluates the need for tritium sampling of the emissions from the 200 East Area Double Shell Tanks based on the requirements of {open_quotes}National Emission Standards for Hazardous Air Pollutants{close_quotes} (NESHAP). The NESHAP requirements are specified in 40 Code of Federal Regulation (CFR), Part 61, Subpart H; {open_quotes}National Emission Standards for Emissions of Radionuclides Other than Radon from Department of Energy Facilities{close_quotes}.

  14. Double-clad nuclear-fuel safety rod

    DOE Patents [OSTI]

    McCarthy, W.H.; Atcheson, D.B.

    1981-12-30

    A device for shutting down a nuclear reactor during an undercooling or overpower event, whether or not the reactor's scram system operates properly. This is accomplished by double-clad fuel safety rods positioned at various locations throughout the reactor core, wherein melting of a secondary internal cladding of the rod allows the fuel column therein to shift from the reactor core to place the reactor in a subcritical condition.

  15. 241-AN Double Shell Tanks (DST) Integrity Assessment Report

    SciTech Connect (OSTI)

    JENSEN, C.E.

    1999-09-21

    This report presents the results of the integrity assessment of the 241-AN double-shell tank farm facility located in the 200 East Area of the Hanford Site. The assessment included the design evaluation and integrity examinations of the tanks and concluded that the facility is adequately designed, is compatible with the waste, and is fit for use. Recommendations including subsequent examinations, are made to ensure the continued safe operation of the tanks.

  16. Solid Double-Layered Hydroxide Catalysts for Lignin Decomposition - Energy

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Innovation Portal Biomass and Biofuels Biomass and Biofuels Find More Like This Return to Search Solid Double-Layered Hydroxide Catalysts for Lignin Decomposition National Renewable Energy Laboratory Contact NREL About This Technology Technology Marketing Summary Biomass-based fuel and chemical production has shown significant promise. However, costs and utilization rates of biomass have still been a challenge for large scale commercialization. Through appropriate decomposition and

  17. Double deflection system for an electron beam device

    DOE Patents [OSTI]

    Parker, Norman W.; Golladay, Steven D.; Crewe, Albert V.

    1978-01-01

    A double deflection scanning system for electron beam instruments is provided embodying a means of correcting isotropic coma, and anisotropic coma aberrations induced by the magnetic lens of such an instrument. The scanning system deflects the beam prior to entry into the magnetic lens from the normal on-axis intersection of the beam with the lens according to predetermined formulas and thereby reduces the aberrations.

  18. Double sided circuit board and a method for its manufacture

    DOE Patents [OSTI]

    Lindenmeyer, C.W.

    1988-04-14

    Conductance between the sides of a large double sided printed circuit board is provided using a method which eliminates the need for chemical immersion or photographic exposure of the entire large board. A plurality of through-holes are drilled or punched in a substratum according to the desired pattern, conductive laminae are made to adhere to both sides of the substratum covering the holes and the laminae are pressed together and permanently joined within the holes, providing conductive paths. 4 figs.

  19. Double sided circuit board and a method for its manufacture

    DOE Patents [OSTI]

    Lindenmeyer, Carl W.

    1989-01-01

    Conductance between the sides of a large double sided printed circuit board is provided using a method which eliminates the need for chemical immersion or photographic exposure of the entire large board. A plurality of through-holes are drilled or punched in a substratum according to the desired pattern, conductive laminae are made to adhere to both sides of the substratum covering the holes and the laminae are pressed together and permanently joined within the holes, providing conductive paths.

  20. Exact nonlinear excitations in double-degenerate plasmas

    SciTech Connect (OSTI)

    Akbari-Moghanjoughi, M.

    2012-06-15

    In this work, we use the conventional hydrodynamics formalism and incorporate the Chew-Goldberger-Low double-adiabatic theory to evaluate the nonlinear electrostatic ion excitations in double-degenerate (electron spin-orbit degenerate) magnetized quantum plasmas. Based on the Sagdeev pseudopotential method, an exact general pseudopotential is calculated which leads to the allowed Mach-number range criteria for such localized density structures in an anisotropic magnetized plasma. We employ the criteria on the Mach-number range for diverse magnetized quantum plasma with different equations of state. It is remarked that various plasma fractional parameters such as the system dimensionality, ion-temperature, relativistic-degeneracy, Zeeman-energy, and plasma composition are involved in the stability of an obliquely propagating nonlinear ion-acoustic wave in a double-degenerate quantum plasma. Current study is most appropriate for nonlinear wave analysis in dense astrophysical magnetized plasma environments such as white-dwarfs and neutron-star crusts where the strong magnetic fields can be present.

  1. DNA Persistence in Sink Drain Environment

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Winder, Eric M.; Bonheyo, George T.

    2015-07-31

    Biofilms are organized structures composed mainly of cells and extracellular polymeric substances produced by the constituent microorganisms. Ubiquitous in nature, biofilms have an innate ability to capture and retain passing material and may therefore act as natural collectors of contaminants or signatures of upstream activities. To determine the persistence and detectability of DNA passing through a sink drain environment, Bacillus anthracis strain Ames35 was cultured (6.35 x 107 CFU/mL), sterilized, and disposed of by addition to a sink drain apparatus with an established biofilm. The sink drain apparatus was sampled before and for several days after the addition of themore » sterilized B. anthracis culture to detect the presence of B. anthracis DNA. Multiple PCR primer pairs were used to screen for chromosomal and plasmid DNA with primers targeting shorter sequences showing greater amplification efficiency and success. PCR amplification and detection of target sequences indicate persistence of chromosomal DNA and plasmid DNA in the biofilm for 5 or more and 14 or more days, respectively.« less

  2. Optical selection and collection of DNA fragments

    DOE Patents [OSTI]

    Roslaniec, Mary C.; Martin, John C.; Jett, James H.; Cram, L. Scott

    1998-01-01

    Optical selection and collection of DNA fragments. The present invention includes the optical selection and collection of large (>.mu.g) quantities of clonable, chromosome-specific DNA from a sample of chromosomes. Chromosome selection is based on selective, irreversible photoinactivation of unwanted chromosomal DNA. Although more general procedures may be envisioned, the invention is demonstrated by processing chromosomes in a conventional flow cytometry apparatus, but where no droplets are generated. All chromosomes in the sample are first stained with at least one fluorescent analytic dye and bonded to a photochemically active species which can render chromosomal DNA unclonable if activated. After passing through analyzing light beam(s), unwanted chromosomes are irradiated using light which is absorbed by the photochemically active species, thereby causing photoinactivation. As desired chromosomes pass this photoinactivation point, the inactivating light source is deflected by an optical modulator; hence, desired chromosomes are not photoinactivated and remain clonable. The selection and photoinactivation processes take place on a microsecond timescale. By eliminating droplet formation, chromosome selection rates 50 times greater than those possible with conventional chromosome sorters may be obtained. Thus, usable quantities of clonable DNA from any source thereof may be collected.

  3. DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Hancock, Stephen P.; Stella, Stefano; Cascio, Duilio; Johnson, Reid C.; Leng, Fenfei

    2016-03-09

    The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequencesmore » in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.« less

  4. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Intriguing DNA Editor Has a Structural Trigger Print Wednesday, 30 July 2014 00:00 A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9

  5. Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

    DOE Patents [OSTI]

    Gardner, Shea N.; Mariella, Jr., Raymond P.; Christian, Allen T.; Young, Jennifer A.; Clague, David S.

    2011-01-18

    A method of fabricating a DNA molecule of user-defined sequence. The method comprises the steps of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an even or odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths. In one embodiment starting sequence fragments are of different lengths, n, n+1, n+2, etc.

  6. Method for promoting specific alignment of short oligonucleotides on nucleic acids

    DOE Patents [OSTI]

    Studier, F. William; Kieleczawa, Jan; Dunn, John J.

    1996-01-01

    Disclosed is a method for promoting specific alignment of short oligonucleotides on a nucleic acid polymer. The nucleic acid polymer is incubated in a solution containing a single-stranded DNA-binding protein and a plurality of oligonucleotides which are perfectly complementary to distinct but adjacent regions of a predetermined contiguous nucleotide sequence in the nucleic acid polymer. The plurality of oligonucleotides anneal to the nucleic acid polymer to form a contiguous region of double stranded nucleic acid. Specific application of the methods disclosed include priming DNA synthesis and template-directed ligation.

  7. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, Frank A.; Gray, Joe W.

    1986-01-01

    A method for the simultaneous flow cytometric measurement of the total DNA content and the level of DNA synthesis in normal and malignant cells is disclosed. The sensitivity of the method allows a study of cell cycle traverse rates for large scale cell populations as well as single cell measurements. A DNA stain such as propidium iodide is used as the probe for the measurement of total DNA content and a monoclonal antibody reactive with a DNA precursor such as bromodeoxyuridine (BrdU) is used as a probe for the measurement of BrdU uptake by the cells as a measure of DNA synthesis.

  8. Parity Doubling and the S Parameter Below the Conformal Window

    SciTech Connect (OSTI)

    Appelquist, T; Babich, R; Brower, R C; Cheng, M; Clark, M A; Cohen, S D; Fleming, G T; Kiskis, J; Lin, M F; Neil, E T; Osborn, J C; Rebbi, C; Schaich, D; Vranas, P M

    2011-10-21

    We describe a lattice simulation of the masses and decay constants of the lowest-lying vector and axial resonances, and the electroweak S parameter, in an SU(3) gauge theory with N{sub f} = 2 and 6 fermions in the fundamental representation. The spectrum becomes more parity doubled and the S parameter per electroweak doublet decreases when N{sub f} is increased from 2 to 6, motivating study of these trends as N{sub f} is increased further, toward the critical value for transition from confinement to infrared conformality.

  9. Physics constraints on double-pulse LIA engineering

    SciTech Connect (OSTI)

    Ekdahl, Carl August Jr.

    2015-05-20

    The options for advanced-radiography double-pulse linear induction accelerators (LIA) under consideration naturally fall into three categories that differ by the number of cells required. Since the two major physics issues, beam breakup (BBU) and corkscrew, are also dependent on the number of cells, it may be useful for the decision process to review the engineering consequences of beam physics constraints for each class. The LIAs can be categorized three different ways, and this report compares the different categories based upon the physics of their beams.

  10. Computational modeling of electrophotonics nanomaterials: Tunneling in double quantum dots

    SciTech Connect (OSTI)

    Vlahovic, Branislav Filikhin, Igor

    2014-10-06

    Single electron localization and tunneling in double quantum dots (DQD) and rings (DQR) and in particular the localized-delocalized states and their spectral distributions are considered in dependence on the geometry of the DQDs (DQRs). The effect of violation of symmetry of DQDs geometry on the tunneling is studied in details. The cases of regular and chaotic geometries are considered. It will be shown that a small violation of symmetry drastically affects localization of electron and that anti-crossing of the levels is the mechanism of tunneling between the localized and delocalized states in DQRs.

  11. Npn double heterostructure bipolar transistor with ingaasn base region

    DOE Patents [OSTI]

    Chang, Ping-Chih; Baca, Albert G.; Li, Nein-Yi; Hou, Hong Q.; Ashby, Carol I. H.

    2004-07-20

    An NPN double heterostructure bipolar transistor (DHBT) is disclosed with a base region comprising a layer of p-type-doped indium gallium arsenide nitride (InGaAsN) sandwiched between n-type-doped collector and emitter regions. The use of InGaAsN for the base region lowers the transistor turn-on voltage, V.sub.on, thereby reducing power dissipation within the device. The NPN transistor, which has applications for forming low-power electronic circuitry, is formed on a gallium arsenide (GaAs) substrate and can be fabricated at commercial GaAs foundries. Methods for fabricating the NPN transistor are also disclosed.

  12. Efficient double beta decay nuclear matrix elements computations

    SciTech Connect (OSTI)

    Neacsu, Andrei [Horia Hulubei Foundation (FHH) 407 Atomistilor, Horia Hulubei National Institute for Physics and Nuclear Engineering (IFIN-HH) 30 Reactorului, Magurele-Bucharest 077125 (Romania)

    2012-11-20

    We have developed a shell model code for the accurate computation of the two-body matrix elements of the transition operators involved in the neutrinoless double beta decay. This code features coupled cluster method short-range correlations with Jastrow-like functions, finite nucleon size effect and higher order nucleon current corrections. We present the results obtained for {sup 48}Ca and {sup 82}Se, then we compare them with other results in the literature. In the case of {sup 48}Ca, we also study the contributions of the included effects and find good agreement with other published results.

  13. The nuclear matrix elements for neutrinoless double beta decay

    SciTech Connect (OSTI)

    Simkovic, Fedor [Department of Nuclear Physics and Biophysics, Comenius University, Mlynska dolina, SK-84248 Bratislava (Slovakia)

    2007-10-12

    The status of calculation of the neutrinoless double beta decay (0{nu}{beta}{beta}-decay) nuclear matrix elements (NME's) is reviewed. The spread of published values of NME's is discussed. The main attention is paid to the recent progress achieved in the evaluation of the 0{nu}{beta}{beta}-decay NME's in the framework of the quasiparticle random phase approximation (QRPA). The obtained results are compared with those of the nuclear shell model. The problem of reliable determination of the 0{nu}{beta}{beta}-decay NME's is addressed. The uncertainty in NME's are analyzed and further progress in calculation of the 0{nu}{beta}{beta}-decay NME's is outlined.

  14. The GERDA Neutrinoless Double Beta-Decay Experiment

    SciTech Connect (OSTI)

    Majorovits, Bela A. [Max Planck Institut fuer Physik, Foehringer Ring 6, 80805 Munich (Germany)

    2007-10-12

    Neutrinoless double beta (0{nu}{beta}{beta})-decay is the key process to gain understanding of the nature of neutrinos. The GErmanium Detector Array (GERDA) is designed to search for 0{nu}{beta}{beta}-decay of the isotope {sup 76}Ge. Germanium crystals enriched in {sup 76}Ge, acting as source and detector simultaneously, will be submerged directly into an ultra pure cooling medium that also serves as a radiation shield. This concept will allow for a reduction of the background by up to two orders of magnitudes with respect to earlier experiments.

  15. Neutrinoless double beta decay and nuclear matrix elements

    SciTech Connect (OSTI)

    Simkovic, Fedor [BLTP, JINR Dubna, 141980 Dubna, Moscow region (Russian Federation); Comenius University, Mlynska dolina, Bratislava (Slovakia)

    2011-11-23

    The fundamental importance of searching for neutrinoless double-beta decay (0{nu}{beta}{beta}-decay) is widely recognized. Observation of the decay would tell us that the total lepton number is not conserved and that, consequently, neutrinos are massive Majorana fermions. The 0{nu}{beta}{beta}-decay is discussed in context of neutrino oscillation data. The perspectives of the experimental 0{nu}{beta}{beta}-decay searches are analyzed. The importance of reliable determination of the 0{nu}{beta}{beta}-decay nuclear matrix elements is pointed out.

  16. High-performance double-filter soft x-ray

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    performance double-filter soft x-ray diagnostic for measurement of electron temperature structure and dynamics M. B. McGarry, P. Franz, D. J. Den Hartog, J. A. Goetz, M. A. Thomas et al. Citation: Rev. Sci. Instrum. 83, 10E129 (2012); doi: 10.1063/1.4740274 View online: http://dx.doi.org/10.1063/1.4740274 View Table of Contents: http://rsi.aip.org/resource/1/RSINAK/v83/i10 Published by the American Institute of Physics. Additional information on Rev. Sci. Instrum. Journal Homepage:

  17. Container lid gasket protective strip for double door transfer system

    DOE Patents [OSTI]

    Allen, Jr., Burgess M

    2013-02-19

    An apparatus and a process for forming a protective barrier seal along a "ring of concern" of a transfer container used with double door systems is provided. A protective substrate is supplied between a "ring of concern" and a safety cover in which an adhesive layer of the substrate engages the "ring of concern". A compressive foam strip along an opposite side of the substrate engages a safety cover such that a compressive force is maintained between the "ring of concern" and the adhesive layer of the substrate.

  18. Suspending DNA origami between four gold nanodots

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Morales, Piero; Wang, Liqian; Krissanaprasit, Abhichart; Dalmastri, Claudia; Caruso, Mario N.; De Stefano, Mattia; Mosiello, Lucia; Rapone, Bruno; Rinaldi, Antonio; Vespucci, Stefano; et al

    2015-01-01

    Here, connecting DNA nanostructures to metallic nanostructures at specific positions is a relatively rarely addressed issue in nanotechnology.[1-5] It is of high importance for application of the origami structures as breadboards for molecular electronics and nanosensing arrays since the metallic nanostructures may potentially serve as electrodes.

  19. Chromosome-specific DNA Repeat Probes

    SciTech Connect (OSTI)

    Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.

    2006-03-16

    In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

  20. Structures of Clamp-Loader Complexes Are Key to DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    are also crucial components of various other cellular pathways, such as DNA repair, cell cycle control, and chromatin structure. Sliding DNA clamps are loaded onto DNA by...

  1. DNA damage checkpoint recovery and cancer development

    SciTech Connect (OSTI)

    Wang, Haiyong; Zhang, Xiaoshan; Teng, Lisong; Legerski, Randy J.

    2015-06-10

    Cell cycle checkpoints were initially presumed to function as a regulator of cell cycle machinery in response to different genotoxic stresses, and later found to play an important role in the process of tumorigenesis by acting as a guard against DNA over-replication. As a counterpart of checkpoint activation, the checkpoint recovery machinery is working in opposition, aiming to reverse the checkpoint activation and resume the normal cell cycle. The DNA damage response (DDR) and oncogene induced senescence (OIS) are frequently found in precancerous lesions, and believed to constitute a barrier to tumorigenesis, however, the DDR and OIS have been observed to be diminished in advanced cancers of most tissue origins. These findings suggest that when progressing from pre-neoplastic lesions to cancer, DNA damage checkpoint barriers are overridden. How the DDR checkpoint is bypassed in this process remains largely unknown. Activated cytokine and growth factor-signaling pathways were very recently shown to suppress the DDR and to promote uncontrolled cell proliferation in the context of oncovirus infection. In recent decades, data from cell line and tumor models showed that a group of checkpoint recovery proteins function in promoting tumor progression; data from patient samples also showed overexpression of checkpoint recovery proteins in human cancer tissues and a correlation with patients' poor prognosis. In this review, the known cell cycle checkpoint recovery proteins and their roles in DNA damage checkpoint recovery are reviewed, as well as their implications in cancer development. This review also provides insight into the mechanism by which the DDR suppresses oncogene-driven tumorigenesis and tumor progression. - Highlights: • DNA damage checkpoint works as a barrier to cancer initiation. • DDR machinary response to genotoxic and oncogenic stress in similar way. • Checkpoint recovery pathways provide active signaling in cell cycle control. • Checkpoint

  2. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, Natasha V.

    2000-10-03

    Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties.

  3. DNA release from lipoplexes by anionic lipids: correlation with...

    Office of Scientific and Technical Information (OSTI)

    The separation of DNA from lipid measured this way was considerably slower and less ... This result was confirmed by centrifugal separation of released DNA and lipid. X-ray ...

  4. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, F.A.; Gray, J.W.

    1983-10-18

    A method for the simultaneous flow cylometric measurement of total cellular DNA content and of the uptake of DNA precursors as a measure of DNA synthesis during various phases of the cell cycle in normal and malignant cells in vitro and in vivo is described. The method comprises reacting cells with labelled halodeoxyuridine (HdU), partially denaturing cellular DNA, adding to the reaction medium monoclonal antibodies (mabs) reactive with HdU, reacting the bound mabs with a second labelled antibody, incubating the mixture with a DNA stain, and measuring simultaneously the intensity of the DNA stain as a measure of the total cellular DNA and the HdU incorporated as a measure of DNA synthesis. (ACR)

  5. Improved analysis techniques for cylindrical and spherical double probes

    SciTech Connect (OSTI)

    Beal, Brian; Brown, Daniel; Bromaghim, Daron; Johnson, Lee; Blakely, Joseph

    2012-07-15

    A versatile double Langmuir probe technique has been developed by incorporating analytical fits to Laframboise's numerical results for ion current collection by biased electrodes of various sizes relative to the local electron Debye length. Application of these fits to the double probe circuit has produced a set of coupled equations that express the potential of each electrode relative to the plasma potential as well as the resulting probe current as a function of applied probe voltage. These equations can be readily solved via standard numerical techniques in order to determine electron temperature and plasma density from probe current and voltage measurements. Because this method self-consistently accounts for the effects of sheath expansion, it can be readily applied to plasmas with a wide range of densities and low ion temperature (T{sub i}/T{sub e} Much-Less-Than 1) without requiring probe dimensions to be asymptotically large or small with respect to the electron Debye length. The presented approach has been successfully applied to experimental measurements obtained in the plume of a low-power Hall thruster, which produced a quasineutral, flowing xenon plasma during operation at 200 W on xenon. The measured plasma densities and electron temperatures were in the range of 1 Multiplication-Sign 10{sup 12}-1 Multiplication-Sign 10{sup 17} m{sup -3} and 0.5-5.0 eV, respectively. The estimated measurement uncertainty is +6%/-34% in density and +/-30% in electron temperature.

  6. DOUBLE TRACKS Test Site interim corrective action plan

    SciTech Connect (OSTI)

    1996-06-01

    The DOUBLE TRACKS site is located on Range 71 north of the Nellis Air Force Range, northwest of the Nevada Test Site (NTS). DOUBLE TRACKS was the first of four experiments that constituted Operation ROLLER COASTER. On May 15, 1963, weapons-grade plutonium and depleted uranium were dispersed using 54 kilograms of trinitrotoluene (TNT) explosive. The explosion occurred in the open, 0.3 m above the steel plate. No fission yield was detected from the test, and the total amount of plutonium deposited on the ground surface was estimated to be between 980 and 1,600 grams. The test device was composed primarily of uranium-238 and plutonium-239. The mass ratio of uranium to plutonium was 4.35. The objective of the corrective action is to reduce the potential risk to human health and the environment and to demonstrate technically viable and cost-effective excavation, transportation, and disposal. To achieve these objectives, Bechtel Nevada (BN) will remove soil with a total transuranic activity greater then 200 pCI/g, containerize the soil in ``supersacks,`` transport the filled ``supersacks`` to the NTS, and dispose of them in the Area 3 Radioactive Waste Management Site. During this interim corrective action, BN will also conduct a limited demonstration of an alternative method for excavation of radioactive near-surface soil contamination.

  7. Neutrinoless double beta decay and future neutrino oscillation precision experiments

    SciTech Connect (OSTI)

    Choubey, Sandhya [Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Rodejohann, Werner [Physik-Department, Technische Universitaet Muenchen, James-Franck-Strasse, D-85748 Garching (Germany)

    2005-08-01

    We discuss to what extent future precision measurements of neutrino mixing observables will influence the information we can draw from a measurement of (or an improved limit on) neutrinoless double beta decay. Whereas the {delta}m{sup 2} corresponding to solar and atmospheric neutrino oscillations are expected to be known with good precision, the parameter {theta}{sub 12} will govern a large part of the uncertainty. We focus, in particular, on the possibility of distinguishing the neutrino mass hierarchies and on setting a limit on the neutrino mass. We give the largest allowed values of the neutrino masses which allow to distinguish the normal from the inverted hierarchy. All aspects are discussed as a function of the uncertainty stemming from the involved nuclear matrix elements. The implications of a vanishing, or extremely small, effective mass are also investigated. By giving a large list of possible neutrino mass matrices and their predictions for the observables, we finally explore how a measurement of (or an improved limit on) neutrinoless double beta decay can help to identify the neutrino mass matrix if more precise values of the relevant parameters are known.

  8. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  9. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  10. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  11. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  12. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  13. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  14. Recent advances in yeast molecular biology: recombinant DNA. [Lead abstract

    SciTech Connect (OSTI)

    Not Available

    1982-09-01

    Separate abstracts were prepared for the 25 papers presented at a workshop focusing on chromosomal structure, gene regulation, recombination, DNA repair, and cell type control, that have been obtained by experimental approaches incorporating the new technologies of yeast DNA transformation, molecular cloning, and DNA sequence analysis. (KRM)

  15. Methods to alter levels of a DNA repair protein

    DOE Patents [OSTI]

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-10-17

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  16. DOI-BLM-NM-L000-2012-0200-DNA | Open Energy Information

    Open Energy Info (EERE)

    00-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NM-L000-2012-0200-DNA DNA at Lightning Dock Geothermal Area for GeothermalWell Field, DNA for Injection...

  17. DOI-BLM-NV-C010-2012--044-DNA | Open Energy Information

    Open Energy Info (EERE)

    DOI-BLM-NV-C010-2012--044-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2012--044-DNA DNA for GeothermalPower Plant, DNA for Ormatt Nevada Sundry...

  18. DOI-BLM-NV-C010-2013-0037-DNA | Open Energy Information

    Open Energy Info (EERE)

    37-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2013-0037-DNA DNA at Gabbs Valley Geothermal Area for GeothermalWell Field, DNA for Wild Rose Unit...

  19. DOI-BLM-NV-C010-2010-0006-DNA | Open Energy Information

    Open Energy Info (EERE)

    DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2010-0006-DNA DNA at Gabbs Valley Geothermal Area for GeothermalExploration, DNA for Thermal Gradient...

  20. DOI-BLM-NM-L000-2012-0111-DNA | Open Energy Information

    Open Energy Info (EERE)

    111-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NM-L000-2012-0111-DNA DNA at Lightning Dock Geothermal Area for GeothermalExploration, DNA for Three...

  1. DOI-BLM-NV-C010-2012-0005-DNA | Open Energy Information

    Open Energy Info (EERE)

    05-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2012-0005-DNA DNA at McCoy Geothermal Area for GeothermalWell Field DNA for Observation Wells 62-8...

  2. DOI-BLM-NV-C010-2011-0517-DNA | Open Energy Information

    Open Energy Info (EERE)

    7-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2011-0517-DNA DNA at Dead Horse Wells Geothermal Area for GeothermalExploration DNA at Dead Horse...

  3. DOI-BLM-NM-L000-2012-0042-DNA | Open Energy Information

    Open Energy Info (EERE)

    2-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NM-L000-2012-0042-DNA DNA at Lightning Dock Geothermal Area for GeothermalExploration DNA for Well 55-7 at...

  4. DOI-BLM-NV-B020-2008-0071-DNA | Open Energy Information

    Open Energy Info (EERE)

    0071-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-B020-2008-0071-DNA DNA at Reese River Geothermal Area for GeothermalExploration DNA at Reese River...

  5. DOI-BLM-NV-C010-2013-0026-DNA | Open Energy Information

    Open Energy Info (EERE)

    6-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2013-0026-DNA DNA at Dixie Valley Geothermal Area for GeothermalWell Field, DNA for Production...

  6. High School Academic Competition - Double Elimination | U.S. DOE Office of

    Office of Science (SC) Website

    Science (SC) Double Elimination National Science Bowl® (NSB) NSB Home About Regional Competitions National Finals Attending the National Finals 2016 Competition Results Middle School Round Robin Middle School Double Elimination Middle School Electric Car High School Round Robin High School Double Elimination Top Teams for 2016 Volunteers Key Dates Frequently Asked Questions News Media Contact Us WDTS Home Contact Information National Science Bowl® U.S. Department of Energy SC-27/ Forrestal

  7. Middle School Academic Competition - Double Elimination | U.S. DOE Office

    Office of Science (SC) Website

    of Science (SC) Academic Competition - Double Elimination National Science Bowl® (NSB) NSB Home About Regional Competitions National Finals Attending the National Finals 2016 Competition Results Middle School Round Robin Middle School Double Elimination Middle School Electric Car High School Round Robin High School Double Elimination Top Teams for 2016 Volunteers Key Dates Frequently Asked Questions News Media Contact Us WDTS Home Contact Information National Science Bowl® U.S. Department

  8. Double beta decay versus cosmology: Majorana CP phases and nuclear matrix elements

    SciTech Connect (OSTI)

    Deppisch, Frank; Paes, Heinrich [Institut fuer Theoretische Physik und Astrophysik, Universitaet Wuerzburg, D-97074 Wuerzburg (Germany); Suhonen, Jouni [Department of Physics, University of Jyvaeskylae, P.O.B. 35, FIN-40014, Jyvaeskylae (Finland)

    2005-08-01

    We discuss the relation between the absolute neutrino mass scale, the effective mass measured in neutrinoless double beta decay, and the Majorana CP phases. Emphasis is placed on estimating the upper bound on the nuclear matrix element entering calculations of the double beta decay half-life. Combining the claimed evidence for neutrinoless double beta decay with the neutrino mass bound from cosmology, one of the Majorana CP phases can be constrained.

  9. Shell model nuclear matrix elements for competing mechanisms contributing to double beta decay

    SciTech Connect (OSTI)

    Horoi, Mihai

    2013-12-30

    Recent progress in the shell model approach to the nuclear matrix elements for the double beta decay process are presented. This includes nuclear matrix elements for competing mechanisms to neutrionless double beta decay, a comparison between closure and non-closure approximation for {sup 48}Ca, and an updated shell model analysis of nuclear matrix elements for the double beta decay of {sup 136}Xe.

  10. Allosteric Modulation of DNA by Small Molecules

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Allosteric Modulation of DNA by Small Molecules Signals originating at the cell surface are conveyed by a complex system of interconnected signaling pathways to the nucleus. They converge at transcription factors, which in turn regulate the transcription of sets of genes that result in the gene expression. Many human diseases are caused by dysregulated gene expression and the oversupply of transcription factors may be required for the growth and metastatic behavior of human cancers. Cell

  11. DNA-Guided Crystallization of Colloidal Nanoparticles

    SciTech Connect (OSTI)

    Nykypanchuk,D.; Maye, M.; van der Lelie, D.; Gang, O.

    2008-01-01

    Many nanometre-sized building blocks will readily assemble into macroscopic structures. If the process is accompanied by effective control over the interactions between the blocks and all entropic effects, then the resultant structures will be ordered with a precision hard to achieve with other fabrication methods. But it remains challenging to use self-assembly to design systems comprised of different types of building blocks--to realize novel magnetic, plasmonic and photonic metamaterials for example. A conceptually simple idea for overcoming this problem is the use of 'encodable' interactions between building blocks; this can in principle be straightforwardly implemented using biomolecules6, 7, 8, 9, 10. Strategies that use DNA programmability to control the placement of nanoparticles in one and two dimensions have indeed been demonstrated. However, our theoretical understanding of how to extend this approach to three dimensions is limited14, 15, and most experiments have yielded amorphous aggregates and only occasionally crystallites of close-packed micrometre-sized particles. Here, we report the formation of three-dimensional crystalline assemblies of gold nanoparticles mediated by interactions between complementary DNA molecules attached to the nanoparticles' surface. We find that the nanoparticle crystals form reversibly during heating and cooling cycles. Moreover, the body-centred-cubic lattice structure is temperature-tuneable and structurally open, with particles occupying only {approx}4% of the unit cell volume. We expect that our DNA-mediated crystallization approach, and the insight into DNA design requirements it has provided, will facilitate both the creation of new classes of ordered multicomponent metamaterials and the exploration of the phase behaviour of hybrid systems with addressable interactions.

  12. Preparation of DNA-containing extract for PCR amplification

    DOE Patents [OSTI]

    Dunbar, John M.; Kuske, Cheryl R.

    2006-07-11

    Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 510 minutes.

  13. Stepped electrophoresis for movement and concentration of DNA

    DOE Patents [OSTI]

    Miles, Robin R.; Wang, Amy Wei-Yun; Mariella, Jr., Raymond P.

    2005-03-15

    A fluidic channel patterned with a series of thin-film electrodes makes it possible to move and concentrate DNA in a fluid passing through the fluidic channel. The DNA has an inherent negative charge and by applying a voltage between adjacent electrodes the DNA is caused to move. By using a series of electrodes, when one electrode voltage or charge is made negative with respect to adjacent electrodes, the DNA is repelled away from this electrode and attached to a positive charged electrode of the series. By sequentially making the next electrode of the series negative, the DNA can be moved to and concentrated over the remaining positive electrodes.

  14. Preparation of DNA-containing extract for PCR amplification

    DOE Patents [OSTI]

    Dunbar, John M.; Kuske, Cheryl R.

    2006-07-11

    Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 5–10 minutes.

  15. Structural and mechanistic insights into Mcm2-7 double-hexamer...

    Office of Scientific and Technical Information (OSTI)

    and mechanistic insights into Mcm2-7 double-hexamer assembly and function Sun, Jingchuan Brookhaven National Laboratory (BNL), Upton, NY (United States); Li, Huilin Brookhaven...

  16. Large Hadron Collider Probe of Supersymmetric Neutrinoless Double-Beta-Decay Mechanism

    SciTech Connect (OSTI)

    Allanach, B. C.; Kom, C. H.; Paes, H. [DAMTP, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA (United Kingdom); Cavendish Laboratory, J. J. Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Fakultaet fuer Physik, Technische Universitaet Dortmund, D-44221, Dortmund (Germany)

    2009-08-28

    In the minimal supersymmetric extension to the standard model, a nonzero lepton number violating coupling {lambda}{sub 111}{sup '} predicts both neutrinoless double-beta-decay and resonant single slepton production at the LHC. We show that, in this case, if neutrinoless double beta decay is discovered in the next generation of experiments, there exist good prospects to observe single slepton production at the LHC. Neutrinoless double beta decay could otherwise result from a different source (such as a nonzero Majorana neutrino mass). Resonant single slepton production at the LHC can therefore discriminate between the {lambda}{sub 111}{sup '} neutrinoless double-beta-decay mechanism and others.

  17. Double Power Output for GaAs Solar Cells Embedded in Luminescent...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Double power output of bifacial thin-film GaAs microscale solar cells is achieved by embedding in luminescent waveguides (LSCs) with light- trapping backside reflectors (BSRs). ...

  18. Phase one contamination migration testing of the double-lid bagless posting system

    SciTech Connect (OSTI)

    Smith, J.A.

    1994-09-01

    This document describes leak rate tests on a double lid radioactive waste storage container, developed during the Microwave Solidification Project at Rocky Flats Plant.

  19. Searching for Neutrinoless Double-Beta Decay of 130 Te with CUORE...

    Office of Scientific and Technical Information (OSTI)

    Neutrinoless double-beta (0 ) decay is a hypothesized lepton-number-violating process that offers the only known means of asserting the possible Majorana nature of ...

  20. Double Beta Decay in Xenon-136: Measuring the Neutrino-Emitting...

    Office of Scientific and Technical Information (OSTI)

    Title: Double Beta Decay in Xenon-136: Measuring the Neutrino-Emitting Mode and Searching for Majoron-Emitting Modes Authors: Herrin, Steven ; Stanford U., Phys. Dept. SLAC ...