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Sample records for dna double-strand break

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  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. 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

  7. 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.

  8. 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.

  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. 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?

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  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. 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.

  20. 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.

  1. Solid phase sequencing of double-stranded nucleic acids

    DOE Patents [OSTI]

    Fu, Dong-Jing (Waltham, MA); Cantor, Charles R. (Boston, MA); Koster, Hubert (Concord, MA); Smith, Cassandra L. (Boston, MA)

    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.

  2. Screening Tool for Providers of Double-Stranded DNA - Energy...

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

    PDF Document Publication 11-G00227ID2510 (2).pdf (829 KB) Technology Marketing SummaryThe ... method composed of a system and software.BenefitsHelps safeguard the advancing ...

  3. 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.

  4. 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...

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  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. 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.

  19. 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.

  20. 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 approach.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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.

  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. 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.

  9. 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.

  10. 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.

  11. WHERE MULTIFUNCTIONAL DNA REPAIR PROTEINS MEET: MAPPING THE INTERACTION DOMAINS BETWEEN XPG AND WRN

    SciTech Connect (OSTI)

    Rangaraj, K.; Cooper, P.K.; Trego, K.S.

    2009-01-01

    The rapid recognition and repair of DNA damage is essential for the maintenance of genomic integrity and cellular survival. Multiple complex and interconnected DNA damage responses exist within cells to preserve the human genome, and these repair pathways are carried out by a specifi c interplay of protein-protein interactions. Thus a failure in the coordination of these processes, perhaps brought about by a breakdown in any one multifunctional repair protein, can lead to genomic instability, developmental and immunological abnormalities, cancer and premature aging. This study demonstrates a novel interaction between two such repair proteins, Xeroderma pigmentosum group G protein (XPG) and Werner syndrome helicase (WRN), that are both highly pleiotropic and associated with inherited genetic disorders when mutated. XPG is a structure-specifi c endonuclease required for the repair of UV-damaged DNA by nucleotide excision repair (NER), and mutations in XPG result in the diseases Xeroderma pigmentosum (XP) and Cockayne syndrome (CS). A loss of XPG incision activity results in XP, whereas a loss of non-enzymatic function(s) of XPG causes CS. WRN is a multifunctional protein involved in double-strand break repair (DSBR), and consists of 3’–5’ DNA-dependent helicase, 3’–5’ exonuclease, and single-strand DNA annealing activities. Nonfunctional WRN protein leads to Werner syndrome, a premature aging disorder with increased cancer incidence. Far Western analysis was used to map the interacting domains between XPG and WRN by denaturing gel electrophoresis, which separated purifi ed full length and recombinant XPG and WRN deletion constructs, based primarily upon the length of each polypeptide. Specifi c interacting domains were visualized when probed with the secondary protein of interest which was then detected by traditional Western analysis using the antibody of the secondary protein. The interaction between XPG and WRN was mapped to the C-terminal region of XPG as well as the C-terminal region of WRN. The physical interaction between XPG and WRN links NER, (made evident by the disease XP) with DSBR, which imparts additional knowledge of the overlapping nature of these two proteins and the previously distinct DNA repair pathways they are associated with. Since genomic integrity is constantly threatened by both endogenous and exogenous (internal and external) damage, understanding the roles of these proteins in coordinating DNA repair processes with replication will signifi cantly further understanding how defects instigate physiological consequences in response to various DNA damaging sources. This ultimately contributes to our understanding of cancer and premature aging.

  12. 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

  13. 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.

  14. Pair breaking versus symmetry breaking: Origin of the Raman modes...

    Office of Scientific and Technical Information (OSTI)

    Pair breaking versus symmetry breaking: Origin of the Raman modes in superconducting cuprates Citation Details In-Document Search Title: Pair breaking versus symmetry breaking:...

  15. 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

  16. 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 application papers of sequencing up to this level were also published in the mid 1990's. A major interest of the sequencing community has always been read length. The longer the sequence read per run the more efficient the process as well as the ability to read repeat sequences. We therefore devoted a great deal of time to studying the factors influencing read length in capillary electrophoresis, including polymer type and molecule weight, capillary column temperature, applied electric field, etc. In our initial optimization, we were able to demonstrate, for the first time, the sequencing of over 1000 bases with 90% accuracy. The run required 80 minutes for separation. Sequencing of 1000 bases per column was next demonstrated on a multiple capillary instrument. Our studies revealed that linear polyacrylamide produced the longest read lengths because the hydrophilic single strand DNA had minimal interaction with the very hydrophilic linear polyacrylamide. Any interaction of the DNA with the polymer would lead to broader peaks and lower read length. Another important parameter was the molecular weight of the linear chains. High molecular weight (> 1 MDA) was important to allow the long single strand DNA to reptate through the entangled polymer matrix. In an important paper, we showed an inverse emulsion method to prepare reproducibility linear polyacrylamide polymer with an average MWT of 9MDa. This approach was used in the polymer for sequencing the human genome. Another critical factor in the successful use of capillary electrophoresis for sequencing was the sample preparation method. In the Sanger sequencing reaction, high concentration of salts and dideoxynucleotide remained. Since the sample was introduced to the capillary column by electrokinetic injection, these salt ions would be favorably injected into the column over the sequencing fragments, thus reducing the signal for longer fragments and hence reading read length. In two papers, we examined the role of individual components from the sequencing reaction and then developed a protocol to reduce the deleterio

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Probing strong electroweak symmetry breaking dynamics through...

    Office of Scientific and Technical Information (OSTI)

    Probing strong electroweak symmetry breaking dynamics through quantum interferometry at ... Title: Probing strong electroweak symmetry breaking dynamics through quantum ...

  2. 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.

  3. DNB CP - Steamline Break Analysis

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

    5-000 DNB Challenge Problem Progress - Steamline Break Analysis Industry Council Meeting April 12, 2016 2 CASL-U-2016-1085-000 Outline * DNB CP to Meet Industry's Needs * PWR Steamline Break (SLB) Analysis Overview * Ongoing FY16 Activities on SLB Analysis 3 CASL-U-2016-1085-000 Departure from Nucleate Boiling (DNB) * DNB also referred to as Critical Heat Flux (CHF) - Local clad surface dryout causes dramatic reduction in heat transfer during transients - One of safety and regulatory acceptance

  4. Breaking the Biological Barriers to Cellulosic Ethanol, June...

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

    Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 Breaking the Biological Barriers to Cellulosic...

  5. Total-derivative supersymmetry breaking

    SciTech Connect (OSTI)

    Haba, Naoyuki; Uekusa, Nobuhiro

    2010-05-15

    On an interval compactification in supersymmetric theory, boundary conditions for bulk fields must be treated carefully. If they are taken arbitrarily following the requirement that a theory is supersymmetric, the conditions could give redundant constraints on the theory. We construct a supersymmetric action integral on an interval by introducing brane interactions with which total-derivative terms under the supersymmetry transformation become zero due to a cancellation. The variational principle leads equations of motion and also boundary conditions for bulk fields, which determine boundary values of bulk fields. By estimating mass spectrum, spontaneous supersymmetry breaking in this simple setup can be realized in a new framework. This supersymmetry breaking does not induce a massless R axion, which is favorable for phenomenology. It is worth noting that fermions in hyper-multiplet, gauge bosons, and the fifth-dimensional component of gauge bosons can have zero-modes (while the other components are all massive as Kaluza-Klein modes), which fits the gauge-Higgs unification scenarios.

  6. Vanadium catalysts break down biomass for fuels

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

    Vanadium catalysts break down biomass for fuels Vanadium catalysts break down biomass into useful components Breaking down biomass could help in converting biomass to fuels. March 26, 2012 Biomass Due to diminishing petroleum reserves, non-food biomass (lignocellulose) is an attractive alternative as a feedstock for the production of renewable chemicals and fuels. Get Expertise Researcher Susan Hanson Inorganic Isotope & Actinide Chem Email Researcher Ruilian Wu Bioenergy & Environmental

  7. NREL: Technology Transfer - Popular Mechanics: Scientists Break...

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

    Popular Mechanics: Scientists Break This Virtual Power Grid to Save the Real One July 27, 2015 Popular Mechanics describes how NREL's Energy Systems Integration Facility (ESIF)...

  8. 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.

  9. 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.

  10. A Fullerene that Breaks the Rules

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

    A Fullerene that Breaks the Rules A Fullerene that Breaks the Rules Print Tuesday, 28 April 2015 00:00 In the 30 years since the discovery of the classic fullerene "buckyball" of 60 carbon atoms, scientists have found many variations on the fullerene theme: carbon nanotubes (elongated buckyballs), endohedral fullerenes (buckyballs with molecules inside), and even carbon "peapods" (nanotubes with buckyballs inside). Within this great diversity, however, certain rules emerged.

  11. Breaking Down Stovepipes | Department of Energy

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

    Breaking Down Stovepipes Breaking Down Stovepipes Coordination with other DOE-wide teams and groups An assigned liaison to DOE's NEPA [National Environmental Policy Act] Six Sigma Team Coordination with the Facilities and Infrastructure Steering Committee: Ten-Year Site Plan requirements, streamlining processes for transferring facilities, work for others Communication across sites, programs, and communities to share lessons learned Kansas City Office coordinating with Oak Ridge and the Office

  12. Bending-induced Symmetry Breaking of Lithiation in Germanium...

    Office of Scientific and Technical Information (OSTI)

    Bending-induced Symmetry Breaking of Lithiation in Germanium Nanowires Citation Details In-Document Search Title: Bending-induced Symmetry Breaking of Lithiation in Germanium ...

  13. Symmetry breaking in the formation of magnetic vortex states...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Symmetry breaking in the formation of magnetic vortex states in a permalloy nanodisk Citation Details In-Document Search Title: Symmetry breaking in the formation ...

  14. Breaking Ground on Computational Research and Theory Facility

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

    Berkeley Lab Breaks Ground on New Computational Research Facility Breaking Ground on Computational Research and Theory Facility CRT to Foster Scientific Collaboration in...

  15. Chiral symmetry and chiral-symmetry breaking

    SciTech Connect (OSTI)

    Peskin, M.E.

    1982-12-01

    These lectures concern the dynamics of fermions in strong interaction with gauge fields. Systems of fermions coupled by gauge forces have a very rich structure of global symmetries, which are called chiral symmetries. These lectures will focus on the realization of chiral symmetries and the causes and consequences of thier spontaneous breaking. A brief introduction to the basic formalism and concepts of chiral symmetry breaking is given, then some explicit calculations of chiral symmetry breaking in gauge theories are given, treating first parity-invariant and then chiral models. These calculations are meant to be illustrative rather than accurate; they make use of unjustified mathematical approximations which serve to make the physics more clear. Some formal constraints on chiral symmetry breaking are discussed which illuminate and extend the results of our more explicit analysis. Finally, a brief review of the phenomenological theory of chiral symmetry breaking is presented, and some applications of this theory to problems in weak-interaction physics are discussed. (WHK)

  16. Workshop on electroweak symmetry breaking: proceedings

    SciTech Connect (OSTI)

    Hinchliffe, I.

    1984-10-01

    A theoretical workshop on electroweak symmetry breaking at the Superconducting Supercollider was held at Lawrence Berkeley Laboratory, June 4-22, 1984. The purpose of the workshop was to focus theoretical attention on the ways in which experimentation at the SSC could reveal manifestations of the phenomenon responsible for electroweak symmetry breaking. This issue represents, at present, the most compelling scientific argument for the need to explore the energy region to be made accessible by the SSC, and a major aim of the workshop was to involve a broad cross section of particle theorists in the ongoing process of sharpening the requirements for both accelerator and detector design that will ensure detection and identification of meaningful signals, whatever form the electroweak symmetry breaking phenomenon should actually take. Separate entries were prepared for the data base for the papers presented.

  17. Textural break foundation wall construction modules

    DOE Patents [OSTI]

    Phillips, Steven J.

    1990-01-01

    Below-grade, textural-break foundation wall structures are provided for inhibiting diffusion and advection of liquids and gases into and out from a surrounding hydrogeologic environment. The foundation wall structure includes a foundation wall having an interior and exterior surface and a porous medium disposed around a portion of the exterior surface. The structure further includes a modular barrier disposed around a portion of the porous medium. The modular barrier is substantially removable from the hydrogeologic environment.

  18. A Fullerene that Breaks the Rules

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

    A Fullerene that Breaks the Rules Print In the 30 years since the discovery of the classic fullerene "buckyball" of 60 carbon atoms, scientists have found many variations on the fullerene theme: carbon nanotubes (elongated buckyballs), endohedral fullerenes (buckyballs with molecules inside), and even carbon "peapods" (nanotubes with buckyballs inside). Within this great diversity, however, certain rules emerged. One such rule governed the number and placement of the

  19. A Fullerene that Breaks the Rules

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

    A Fullerene that Breaks the Rules Print In the 30 years since the discovery of the classic fullerene "buckyball" of 60 carbon atoms, scientists have found many variations on the fullerene theme: carbon nanotubes (elongated buckyballs), endohedral fullerenes (buckyballs with molecules inside), and even carbon "peapods" (nanotubes with buckyballs inside). Within this great diversity, however, certain rules emerged. One such rule governed the number and placement of the

  20. new chemistry to break down cell walls

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

    new chemistry to break down cell walls - Sandia Energy Energy Search Icon Sandia Home Locations Contact Us Employee Locator Energy & Climate Secure & Sustainable Energy Future Stationary Power Energy Conversion Efficiency Solar Energy Wind Energy Water Power Supercritical CO2 Geothermal Natural Gas Safety, Security & Resilience of the Energy Infrastructure Energy Storage Nuclear Power & Engineering Grid Modernization Battery Testing Nuclear Fuel Cycle Defense Waste Management

  1. A Fullerene that Breaks the Rules

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

    A Fullerene that Breaks the Rules Print In the 30 years since the discovery of the classic fullerene "buckyball" of 60 carbon atoms, scientists have found many variations on the fullerene theme: carbon nanotubes (elongated buckyballs), endohedral fullerenes (buckyballs with molecules inside), and even carbon "peapods" (nanotubes with buckyballs inside). Within this great diversity, however, certain rules emerged. One such rule governed the number and placement of the

  2. A Fullerene that Breaks the Rules

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

    A Fullerene that Breaks the Rules Print In the 30 years since the discovery of the classic fullerene "buckyball" of 60 carbon atoms, scientists have found many variations on the fullerene theme: carbon nanotubes (elongated buckyballs), endohedral fullerenes (buckyballs with molecules inside), and even carbon "peapods" (nanotubes with buckyballs inside). Within this great diversity, however, certain rules emerged. One such rule governed the number and placement of the

  3. Electroweak Symmetry Breaking in Historical Perspective

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

    Quigg, Chris

    2015-10-01

    The discovery of the Higgs boson is a major milestone in our progress toward understanding the natural world. A particular aim of my review is to show how diverse ideas came together in the conception of electroweak symmetry breaking that led up to the discovery. Furthermore, I survey what we know now that we did not know before, what properties of the Higgs boson remain to be established, and what new questions we may now hope to address.

  4. Breaking a Pocket of Resistance in the Fight Against Cancer

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

    Breaking a Pocket of Resistance in the Fight Against Cancer Breaking a Pocket of Resistance in the Fight Against Cancer Print Thursday, 12 December 2013 11:55 ras protein The new...

  5. A mutational signature in gastric cancer suggests therapeutic strategies

    SciTech Connect (OSTI)

    Alexandrov, Ludmil B.; Nik-Zainal, Serena; Siu, Hoi Cheong; Leung, Suet Yi; Stratton, Michael R.

    2015-10-29

    Targeting defects in the DNA repair machinery of neoplastic cells, for example, those due to inactivating BRCA1 and/or BRCA2 mutations, has been used for developing new therapies in certain types of breast, ovarian and pancreatic cancers. Recently, a mutational signature was associated with failure of double-strand DNA break repair by homologous recombination based on its high mutational burden in samples harbouring BRCA1 or BRCA2 mutations. In pancreatic cancer, all responders to platinum therapy exhibit this mutational signature including a sample that lacked any defects in BRCA1 or BRCA2. Here, we examine 10,250 cancer genomes across 36 types of cancer and demonstrate that, in addition to breast, ovarian and pancreatic cancers, gastric cancer is another cancer type that exhibits this mutational signature. Furthermore, our results suggest that 7–12% of gastric cancers have defective double-strand DNA break repair by homologous recombination and may benefit from either platinum therapy or PARP inhibitors.

  6. A mutational signature in gastric cancer suggests therapeutic strategies

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

    Alexandrov, Ludmil B.; Nik-Zainal, Serena; Siu, Hoi Cheong; Leung, Suet Yi; Stratton, Michael R.

    2015-10-29

    Targeting defects in the DNA repair machinery of neoplastic cells, for example, those due to inactivating BRCA1 and/or BRCA2 mutations, has been used for developing new therapies in certain types of breast, ovarian and pancreatic cancers. Recently, a mutational signature was associated with failure of double-strand DNA break repair by homologous recombination based on its high mutational burden in samples harbouring BRCA1 or BRCA2 mutations. In pancreatic cancer, all responders to platinum therapy exhibit this mutational signature including a sample that lacked any defects in BRCA1 or BRCA2. Here, we examine 10,250 cancer genomes across 36 types of cancer andmore » demonstrate that, in addition to breast, ovarian and pancreatic cancers, gastric cancer is another cancer type that exhibits this mutational signature. Furthermore, our results suggest that 7–12% of gastric cancers have defective double-strand DNA break repair by homologous recombination and may benefit from either platinum therapy or PARP inhibitors.« less

  7. Flavor symmetry breaking and vacuum alignment on orbifolds (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Flavor symmetry breaking and vacuum alignment on orbifolds Citation Details In-Document Search Title: Flavor symmetry breaking and vacuum alignment on orbifolds Flavor symmetry has been widely studied for figuring out the masses and mixing angles of standard model fermions. In this paper we present a framework for handling flavor symmetry breaking where the symmetry breaking is triggered by boundary conditions of scalar fields in extra-dimensional space. The

  8. Gravity dual of metastable dynamical supersymmetry breaking (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Gravity dual of metastable dynamical supersymmetry breaking Citation Details In-Document Search Title: Gravity dual of metastable dynamical supersymmetry breaking Metastable, supersymmetry-breaking configurations can be created in flux geometries by placing antibranes in warped throats. Via gauge/gravity duality, such configurations should have an interpretation as supersymmetry-breaking states in the dual field theory. In this paper, we perturbatively determine

  9. Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 |

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

    Department of Energy Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 PDF icon b2blowres63006.pdf More Documents & Publications Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 Review of Recent Pilot Scale Cellulosic Ethanol Demonstration Biochemical Conversion: Using Hydrolysis, Fermentation, and Catalysis to Make Fuels and

  10. Breaking Barriers in Polymer Additive Manufacturing

    SciTech Connect (OSTI)

    Love, Lonnie J; Duty, Chad E; Post, Brian K; Lind, Randall F; Lloyd, Peter D; Kunc, Vlastimil; Peter, William H; Blue, Craig A

    2015-01-01

    Additive Manufacturing (AM) enables the creation of complex structures directly from a computer-aided design (CAD). There are limitations that prevent the technology from realizing its full potential. AM has been criticized for being slow and expensive with limited build size. Oak Ridge National Laboratory (ORNL) has developed a large scale AM system that improves upon each of these areas by more than an order of magnitude. The Big Area Additive Manufacturing (BAAM) system directly converts low cost pellets into a large, three-dimensional part at a rate exceeding 25 kg/h. By breaking these traditional barriers, it is possible for polymer AM to penetrate new manufacturing markets.

  11. Chip breaking system for automated machine tool

    DOE Patents [OSTI]

    Arehart, Theodore A.; Carey, Donald O.

    1987-01-01

    The invention is a rotary selectively directional valve assembly for use in an automated turret lathe for directing a stream of high pressure liquid machining coolant to the interface of a machine tool and workpiece for breaking up ribbon-shaped chips during the formation thereof so as to inhibit scratching or other marring of the machined surfaces by these ribbon-shaped chips. The valve assembly is provided by a manifold arrangement having a plurality of circumferentially spaced apart ports each coupled to a machine tool. The manifold is rotatable with the turret when the turret is positioned for alignment of a machine tool in a machining relationship with the workpiece. The manifold is connected to a non-rotational header having a single passageway therethrough which conveys the high pressure coolant to only the port in the manifold which is in registry with the tool disposed in a working relationship with the workpiece. To position the machine tools the turret is rotated and one of the tools is placed in a material-removing relationship of the workpiece. The passageway in the header and one of the ports in the manifold arrangement are then automatically aligned to supply the machining coolant to the machine tool workpiece interface for breaking up of the chips as well as cooling the tool and workpiece during the machining operation.

  12. Breaking Ground in Miami-Dade

    Broader source: Energy.gov [DOE]

    Officials from Miami-Dade County and the U.S. Department of Energy were on hand Wednesday, October 13th to formally break ground on an innovative project that will help improve the energy efficiency of one of the county’s major water treatment facilities.   The project will upgrade and expand the existing power generation system at the water plant which generates electricity from digester gas produced at the plant.  Landfill gas, which is produced from the Solid Waste Department’s South Dade Landfill, will be collected and piped across a canal to the water plant where it will be mixed with digester gases.  By combining landfill and digester gases, the county will increase the amount of self-generated electricity, and reduce the county's consumption of electricity generated from fossil fuels.  

  13. Supersymmetry Breaking, Gauge Mediation, and the LHC

    SciTech Connect (OSTI)

    Shih, David

    2015-04-14

    Gauge mediated SUSY breaking (GMSB) is a promising class of supersymmetric models that automatically satisfies the precision constraints. Prior work of Meade, Seiberg and Shih in 2008 established the full, model-independent parameter space of GMSB, which they called "General Gauge Mediation" (GGM). During the first half of 2010-2015, Shih and his collaborators thoroughly explored the parameter space of GGM and established many well-motivated benchmark models for use by the experimentalists at the LHC. Through their work, the current constraints on GGM from LEP, the Tevatron and the LHC were fully elucidated, together with the possible collider signatures of GMSB at the LHC. This ensured that the full discovery potential for GGM could be completely realized at the LHC.

  14. Metastable supersymmetry breaking vacua from conformal dynamics (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Metastable supersymmetry breaking vacua from conformal dynamics Citation Details In-Document Search Title: Metastable supersymmetry breaking vacua from conformal dynamics We study the scenario that conformal dynamics leads to metastable supersymmetry breaking vacua. At a high energy scale, the superpotential is not R-symmetric and has a supersymmetric minimum. However, conformal dynamics suppresses several operators along renormalization group flow toward the

  15. Metastable supersymmetry breaking vacua from conformal dynamics (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Metastable supersymmetry breaking vacua from conformal dynamics Citation Details In-Document Search Title: Metastable supersymmetry breaking vacua from conformal dynamics We study the scenario that conformal dynamics leads to metastable supersymmetry breaking vacua. At a high energy scale, the superpotential is not R-symmetric, and has a supersymmetric minimum. However, conformal dynamics suppresses several operators along renormalization group flow toward the

  16. Moduli stabilization, F-term uplifting, and soft supersymmetry breaking

    Office of Scientific and Technical Information (OSTI)

    terms (Journal Article) | SciTech Connect Moduli stabilization, F-term uplifting, and soft supersymmetry breaking terms Citation Details In-Document Search Title: Moduli stabilization, F-term uplifting, and soft supersymmetry breaking terms We study moduli stabilization with F-term uplifting. As a source of uplifting F-term, we consider spontaneous supersymmetry breaking models, e.g. the Polonyi model and the Intriligator-Seiberg-Shih model. We analyze potential minima by requiring almost

  17. Modulated Tool-Path (MTP) Chip Breaking System - Energy Innovation...

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

    Industrial Technologies Industrial Technologies Find More Like This Return to Search Modulated Tool-Path (MTP) Chip Breaking System Y-12 National Security Complex Contact Y12 About...

  18. Symmetry Breaking of H2 Dissociation by a Single Photon

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

    breaking the molecular symmetry. A Molecular Paradox Symmetries in nature, such as the human body's bilateral symmetry and the snowflake's six-fold rotational symmetry, abound but...

  19. Pantex breaks ground on renewable energy project | National Nuclear...

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

    breaks ground on renewable energy project | National Nuclear Security Administration Facebook Twitter Youtube Flickr RSS People Mission Managing the Stockpile Preventing...

  20. ESnet's Science DMZ Breaks Down Barriers, Speeds up Science

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

    ESnet's Science DMZ Breaks Down Barriers, Speeds up Science News & Publications ESnet News Media & Press Publications and Presentations Galleries ESnet Awards and Honors Contact Us...

  1. A Gravity Dual of Metastable Dynamical Supersymmetry Breaking...

    Office of Scientific and Technical Information (OSTI)

    Subject: 72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS; DUALITY; EXPECTATION VALUE; RENORMALIZATION; SUPERGRAVITY; SUPERSYMMETRY; SYMMETRY BREAKING; SU GROUPS Theory-HEP,HEPTH...

  2. LANL breaks ground on key sediment control project

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

    Sediment control project LANL breaks ground on key sediment control project Called "grade-control" structures, the approximately 2 million features are up to eight feet high and...

  3. Novel Thermal Break with Simplified Manufacturing for R7 Commercial...

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

    Contacts DOE Technology Manager: Karma Sawyer Lead Performer: Sneh Kumar, Alcoa Related Publications PDF icon 2016 BTO Peer Review Presentation-Novel Thermal Break with Simplified ...

  4. 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.

  5. Modulated Tool Path Chip Breaking Operation | Y-12 National Security

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

    Complex Modulated Tool Path Chip ... Modulated Tool Path Chip Breaking Operation The mp4 video format is not supported by this browser. Download video Captions: On Time: 2:09 min. The developers of the MTP chip-breaking system, an R&D 100 award winning technology, share some of the system's benefits and uses

  6. The hidden X-ray breaks in afterglow light curves

    SciTech Connect (OSTI)

    Curran, P. A.; Wijers, R. A. M. J.; Horst, A. J. van der; Starling, R. L. C.

    2008-05-22

    Gamma-Ray Burst (GRB) afterglow observations in the Swift era have a perceived lack of achromatic jet breaks compared to the BeppoSAX, or pre-Swift era. Specifically, relatively few breaks, consistent with jet breaks, are observed in the X-ray light curves of these bursts. If these breaks are truly missing, it has serious consequences for the interpretation of GRB jet collimation and energy requirements, and the use of GRBs as standard candles.Here we address the issue of X-ray breaks which are possibly 'hidden' and hence the light curves are misinterpreted as being single power-laws. We show how a number of precedents, including GRB 990510 and GRB 060206, exist for such hidden breaks and how, even with the well sampled light curves of the Swift era, these breaks may be left misidentified. We do so by synthesising X-ray light curves and finding general trends via Monte Carlo analysis. Furthermore, in light of these simulations, we discuss how to best identify achromatic breaks in afterglow light curves via multi-wavelength analysis.

  7. 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.

  8. 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.

  9. Natural little hierarchy for SUSY from radiative breaking of...

    Office of Scientific and Technical Information (OSTI)

    Title: Natural little hierarchy for SUSY from radiative breaking of the Peccei-Quinn symmetry Authors: Bae, Kyu Jung ; Baer, Howard ; Serce, Hasan Publication Date: 2015-01-06 OSTI ...

  10. Symmetry-Breaking Orbital Anisotropy Observed for Detwinned Ba...

    Office of Scientific and Technical Information (OSTI)

    Symmetry-Breaking Orbital Anisotropy Observed for Detwinned Ba(Fe (1-X) Co (X) ) (2) As (2) Above the Spin Density Wave Transition Citation Details In-Document Search Title: ...

  11. Low-energy supersymmetry breaking without the gravitino problem (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Low-energy supersymmetry breaking without the gravitino problem Citation Details In-Document Search This content will become publicly available on July 8, 2016 Title: Low-energy supersymmetry breaking without the gravitino problem Authors: Hook, Anson ; Murayama, Hitoshi Publication Date: 2015-07-09 OSTI Identifier: 1198646 Grant/Contract Number: SC0009988; AC03-76SF00098 Type: Publisher's Accepted Manuscript Journal Name: Physical Review D Additional Journal

  12. Natural little hierarchy for SUSY from radiative breaking of the

    Office of Scientific and Technical Information (OSTI)

    Peccei-Quinn symmetry (Journal Article) | SciTech Connect little hierarchy for SUSY from radiative breaking of the Peccei-Quinn symmetry Citation Details In-Document Search Title: Natural little hierarchy for SUSY from radiative breaking of the Peccei-Quinn symmetry Authors: Bae, Kyu Jung ; Baer, Howard ; Serce, Hasan Publication Date: 2015-01-06 OSTI Identifier: 1180704 Type: Publisher's Accepted Manuscript Journal Name: Physical Review D Additional Journal Information: Journal Volume: 91;

  13. EERE Success Story-Indiana Manufacturing Institute Breaks Ground at

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

    Purdue University in support of Composites Manufacturing Research | Department of Energy Indiana Manufacturing Institute Breaks Ground at Purdue University in support of Composites Manufacturing Research EERE Success Story-Indiana Manufacturing Institute Breaks Ground at Purdue University in support of Composites Manufacturing Research July 14, 2015 - 1:16pm Addthis Left: Gary Bertoline, Dean of Purdue Polytechnic Institute; Kelly Visconti, Technology Manager for the U.S. Department of

  14. Symmetry Breaking of H2 Dissociation by a Single Photon

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

    Symmetry Breaking of H2 Dissociation by a Single Photon Symmetry Breaking of H2 Dissociation by a Single Photon Print Wednesday, 25 July 2007 00:00 A single hydrogen (or deuterium) molecule consists of only two protons (deuterons) and two electrons and is perfectly symmetric. Linearly polarized photons are similarly symmetric. So one might think that the angular distribution of photoelectrons resulting from photoionization of the molecule by the photon accompanied by dissociation into a hydrogen

  15. Probing strong electroweak symmetry breaking dynamics through quantum

    Office of Scientific and Technical Information (OSTI)

    interferometry at the LHC (Journal Article) | SciTech Connect Probing strong electroweak symmetry breaking dynamics through quantum interferometry at the LHC Citation Details In-Document Search This content will become publicly available on December 6, 2016 Title: Probing strong electroweak symmetry breaking dynamics through quantum interferometry at the LHC Authors: Murayama, Hitoshi ; Rentala, Vikram ; Shu, Jing Publication Date: 2015-12-07 OSTI Identifier: 1228286 Grant/Contract Number:

  16. Effective field theory for spacetime symmetry breaking (Journal Article) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect SciTech Connect Search Results Journal Article: Effective field theory for spacetime symmetry breaking Citation Details In-Document Search This content will become publicly available on August 17, 2016 Title: Effective field theory for spacetime symmetry breaking Authors: Hidaka, Yoshimasa ; Noumi, Toshifumi ; Shiu, Gary Publication Date: 2015-08-18 OSTI Identifier: 1212121 Grant/Contract Number: HKUST4/CRF/13G; FG-02-95ER40896; 604213; 16304414 Type: Publisher's Accepted

  17. Deputy Secretary Poneman Attends Ground Breaking at Tennessee Advanced

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

    Vehicle Battery Plant | Department of Energy Attends Ground Breaking at Tennessee Advanced Vehicle Battery Plant Deputy Secretary Poneman Attends Ground Breaking at Tennessee Advanced Vehicle Battery Plant May 26, 2010 - 12:00am Addthis Smyrna, TN - Today, U.S. Deputy Secretary of Energy Daniel Poneman participated in the groundbreaking ceremony for Nissan North America's advanced battery manufacturing facility in Smyrna, Tennessee. This past January the Department closed a $1.4 billion loan

  18. Breaking Barriers in Polymer Additive Manufacturing (Conference) | SciTech

    Office of Scientific and Technical Information (OSTI)

    Connect Conference: Breaking Barriers in Polymer Additive Manufacturing Citation Details In-Document Search Title: Breaking Barriers in Polymer Additive Manufacturing Additive Manufacturing (AM) enables the creation of complex structures directly from a computer-aided design (CAD). There are limitations that prevent the technology from realizing its full potential. AM has been criticized for being slow and expensive with limited build size. Oak Ridge National Laboratory (ORNL) has developed

  19. Breaking Ground on Computational Research and Theory Facility

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

    Berkeley Lab Breaks Ground on New Computational Research Facility Breaking Ground on Computational Research and Theory Facility CRT to Foster Scientific Collaboration in Energy-Efficient Setting February 1, 2012 Jon Bashor, Jbashor@lbl.gov, +1 510-486-5849 Department of Energy Secretary Steven Chu, along with Lawrence Berkeley National Laboratory (Berkeley Lab) and University of California leaders, broke ground on the Lab's Computational Research and Theory (CRT) facility, Wednesday, Feb. 1. The

  20. Energy Department Training Breaks New Ground | Department of Energy

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

    Training Breaks New Ground Energy Department Training Breaks New Ground December 3, 2013 - 1:00pm Addthis The Federal Energy Management Program is now an authorized provider of continuing education units from the International Association for Continuing Education and Training. Watch the video above to learn more. Timothy Unruh Timothy Unruh FEMP Director High quality education for federal government employees helps streamline operations, improve services, and ensure that taxpayer dollars are

  1. Symmetry breaking indication for supergravity inflation in light of the

    Office of Scientific and Technical Information (OSTI)

    Planck 2015 (Journal Article) | SciTech Connect Symmetry breaking indication for supergravity inflation in light of the Planck 2015 Citation Details In-Document Search Title: Symmetry breaking indication for supergravity inflation in light of the Planck 2015 Supergravity (SUGRA) theories with exact global U(1) symmetry or shift symmetry in Kähler potential provide natural frameworks for inflation. However, quadratic inflation is disfavoured by the new results on primordial tensor

  2. 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.

  3. Strong Electroweak Symmetry Breaking and Spin-0 Resonances

    SciTech Connect (OSTI)

    Evans, Jared; Luty, Markus A.

    2009-09-04

    We argue that theories of the strong electroweak symmetry breaking sector necessarily contain new spin 0 states at the TeV scale in the tt and tb/bt channels, even if the third generation quarks are not composite at the TeV scale. These states couple sufficiently strongly to third generation quarks to have significant production at LHC via gg->phi{sup 0} or gb->tphi{sup -}. The existence of narrow resonances in QCD suggests that the strong electroweak breaking sector contains narrow resonances that decay to tt or tb/bt, with potentially significant branching fractions to 3 or more longitudinal W and Z bosons. These may give new 'smoking gun' signals of strong electroweak symmetry breaking.

  4. Application of break preclusion concept in German nuclear power plants

    SciTech Connect (OSTI)

    Roos, E.; Maier, V.; Nagel, G.

    1997-04-01

    The break preclusion concept is based on {open_quotes}KTA rules{close_quotes}, {open_quotes}RSK guidelines{close_quotes} and {open_quotes}Rahmenspeziflkation Basissicherheit{close_quotes}. These fundamental rules containing for example requirements on material, design, calculation, manufacturing and testing procedures are explained and the technical realisation is shown by means of examples. The proof of the quality of these piping systems can be executed by means of fracture mechanics calculations by showing that in every case the leakage monitoring system already detect cracks which are clearly smaller than the critical crack. Thus the leak before break behavior and the break preclusion concept is implicitly affirmed. In order to further diminish conservativities in the fracture mechanics procedures, specific research projects are executed which are explained in this contribution.

  5. Jefferson Lab Breaks Ground On $310 Million Project | Jefferson Lab

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

    Breaks Ground On $310 Million Project Jefferson Lab Breaks Ground On $310 Million Project groundbreaking Newport News Mayor Joe Frank addresses the crowd at the groundbreaking ceremony for the Jefferson Lab 12 GeV Upgrade. Also on the stage are (front row, l-r) U.S. Rep. Rob Wittman of Virginia's 1st District; U.S. Rep. Bobby Scott of Virginia's 3rd District; Gene Henry, Associate Director of the DOE's Office of Science for Nuclear Physics; Jefferson Lab Director Hugh Montgomery; (back row, l-r)

  6. 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.

  7. How does a thermal binary crystal break under shear?

    SciTech Connect (OSTI)

    Horn, Tobias Löwen, Hartmut

    2014-12-14

    When exposed to strong shearing, the particles in a crystal will rearrange and ultimately, the crystal will break by forming large nonaffine defects. Even for the initial stage of this process, only little effort has been devoted to the understanding of the breaking process on the scale of the individual particle size for thermalized mixed crystals. Here, we explore the shear-induced breaking for an equimolar two-dimensional binary model crystal with a high interaction asymmetry between the two different species such that the initial crystal has an intersecting square sublattice of the two constituents. Using Brownian dynamics computer simulations, we show that the combination of shear and thermal fluctuations leads to a characteristic hierarchical breaking scenario where initially, the more strongly coupled particles are thermally distorted, paving the way for the weakly coupled particles to escape from their cage. This in turn leads to mobile defects which may finally merge, proliferating a cascade of defects, which triggers the final breakage of the crystal. This scenario is in marked contrast to the breakage of one-component crystals close to melting. Moreover, we explore the orientational dependence of the initial shear direction relative to the crystal orientation and compare this to the usual melting scenario without shear. Our results are verifiable in real-space experiments of superparamagnetic colloidal mixtures at a pending air-water interface in an external magnetic field where the shear can be induced by an external laser field.

  8. Towards breaking temperature equilibrium in multi-component Eulerian schemes

    SciTech Connect (OSTI)

    Grove, John W; Masser, Thomas

    2009-01-01

    We investigate the effects ofthermal equilibrium on hydrodynamic flows and describe models for breaking the assumption ofa single temperature for a mixture of components in a cell. A computational study comparing pressure-temperature equilibrium simulations of two dimensional implosions with explicit front tracking is described as well as implementation and J-D calculations for non-equilibrium temperature methods.

  9. EECBG Success Story: Breaking Ground in Miami-Dade

    Broader source: Energy.gov [DOE]

    Officials from Miami-Dade County and the U.S. Department of Energy were on hand Wednesday, October 13th to formally break ground on an innovative project that will help improve the energy efficiency of one of the county’s major water treatment facilities. Learn more.

  10. Inhibition of Hsp27 Radiosensitizes Head-and-Neck Cancer by Modulating Deoxyribonucleic Acid Repair

    SciTech Connect (OSTI)

    Guttmann, David M.; Hart, Lori; Du, Kevin; Seletsky, Andrew; Koumenis, Constantinos

    2013-09-01

    Purpose: To present a novel method of tumor radiosensitization through Hsp27 knockdown using locked nucleic acid (LNA) and to investigate the role of Hsp27 in DNA double strand break (DSB) repair. Methods and Materials: Clonogenic survival assays, immunoblotting, the proximity ligation assay, and ?H2AX foci analysis were conducted in SQ20B and FaDu human head-and-neck cancer cell lines treated with Hsp27 LNA and Hsp27 short hairpin RNA (shRNA). Additionally, nude mice with FaDu flank tumors were treated with fractionated radiation therapy after pretreatment with Hsp27 LNA and monitored for tumor growth. Results: Hsp27 LNA and Hsp27 shRNA radiosensitized head-and-neck cancer cell lines in an Hsp27-dependent manner. Ataxia-Telangectasia Mutated-mediated DNA repair signaling was impaired in irradiated cells with Hsp27 knockdown. ATM kinase inhibition abrogated the radiosensitizing effect of Hsp27. Furthermore, Hsp27 LNA and shRNA both attenuated DNA repair kinetics after radiation, and Hsp27 was found to colocalize with ATM in both untreated and irradiated cells. Last, combined radiation and Hsp27 LNA treatment in tumor xenografts in nude mice suppressed tumor growth compared with either treatment alone. Conclusions: These results support a radiosensitizing property of Hsp27 LNA in vitro and in vivo, implicate Hsp27 in double strand break repair, and suggest that Hsp27 LNA might eventually serve as an effective clinical agent in the radiotherapy of head-and-neck cancer.

  11. Gedanken Worlds without Higgs: QCD-Induced Electroweak Symmetry Breaking

    SciTech Connect (OSTI)

    Quigg, Chris; Shrock, Robert; /YITP, Stony Brook

    2009-01-01

    To illuminate how electroweak symmetry breaking shapes the physical world, we investigate toy models in which no Higgs fields or other constructs are introduced to induce spontaneous symmetry breaking. Two models incorporate the standard SU(3){sub c} {circle_times} SU(2){sub L} {circle_times} U(1){sub Y} gauge symmetry and fermion content similar to that of the standard model. The first class--like the standard electroweak theory--contains no bare mass terms, so the spontaneous breaking of chiral symmetry within quantum chromodynamics is the only source of electroweak symmetry breaking. The second class adds bare fermion masses sufficiently small that QCD remains the dominant source of electroweak symmetry breaking and the model can serve as a well-behaved low-energy effective field theory to energies somewhat above the hadronic scale. A third class of models is based on the left-right-symmetric SU(3){sub c} {circle_times} SU(2){sub L} {circle_times} SU(2){sub R} {circle_times} U(1)B?L gauge group. In a fourth class of models, built on SU(4){sub PS} {circle_times} SU(2){sub L} {circle_times} SU(2){sub R} gauge symmetry, lepton number is treated as a fourth color. Many interesting characteristics of the models stem from the fact that the effective strength of the weak interactions is much closer to that of the residual strong interactions than in the real world. The Higgs-free models not only provide informative contrasts to the real world, but also lead us to consider intriguing issues in the application of field theory to the real world.

  12. 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.

  13. 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.

  14. Site directed recombination

    DOE Patents [OSTI]

    Jurka, Jerzy W.

    1997-01-01

    Enhanced homologous recombination is obtained by employing a consensus sequence which has been found to be associated with integration of repeat sequences, such as Alu and ID. The consensus sequence or sequence having a single transition mutation determines one site of a double break which allows for high efficiency of integration at the site. By introducing single or double stranded DNA having the consensus sequence flanking region joined to a sequence of interest, one can reproducibly direct integration of the sequence of interest at one or a limited number of sites. In this way, specific sites can be identified and homologous recombination achieved at the site by employing a second flanking sequence associated with a sequence proximal to the 3'-nick.

  15. Breaking discrete symmetries in the effective field theory of inflation

    SciTech Connect (OSTI)

    Cannone, Dario; Gong, Jinn-Ouk; Tasinato, Gianmassimo

    2015-08-03

    We study the phenomenon of discrete symmetry breaking during the inflationary epoch, using a model-independent approach based on the effective field theory of inflation. We work in a context where both time reparameterization symmetry and spatial diffeomorphism invariance can be broken during inflation. We determine the leading derivative operators in the quadratic action for fluctuations that break parity and time-reversal. Within suitable approximations, we study their consequences for the dynamics of linearized fluctuations. Both in the scalar and tensor sectors, we show that such operators can lead to new direction-dependent phases for the modes involved. They do not affect the power spectra, but can have consequences for higher correlation functions. Moreover, a small quadrupole contribution to the sound speed can be generated.

  16. Single-Sector Supersymmetry Breaking, Chirality, and Unification

    SciTech Connect (OSTI)

    Behbahani, Siavosh R.; Craig, Nathaniel; Torroba, Gonzalo; /SLAC /Stanford U., Phys. Dept.

    2011-08-12

    Calculable single-sector models provide an elegant framework for generating the flavor textures via compositeness, breaking supersymmetry, and explaining the electroweak scale. Such models may be realized naturally in supersymmetric QCD with additional gauge singlets (SSQCD), though it remains challenging to construct models without a surfeit of light exotic states where the Standard Model index emerges naturally. We classify possible single-sector models based on Sp confining SSQCD according to their Standard Model index and number of composite messengers. This leads to simple, calculable models that spontaneously break supersymmetry, reproduce the fermion flavor hierarchy, and explain the Standard Model index dynamically with little or no additional matter. At low energies these theories realize a 'more minimal' soft spectrum with direct mediation and a gravitino LSP.

  17. 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.

  18. NREL: Solar Research - New Partnerships Help Utilities Break Down Solar

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

    Barriers New Partnerships Help Utilities Break Down Solar Barriers May 11, 2016 The Solar Technical Assistance Team (STAT) Network launched its first program of technical assistance to electric utilities and announced three new efforts to provide direct support to utility partners. The activities range from providing interconnection training to conducting detailed techno-economic modeling to leveraging community solar finance tools. The National Renewable Energy Laboratory (NREL), a member

  19. Transgenic Lignin Easier to Break Down for Biofuel - Energy Innovation

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

    Portal Transgenic Lignin Easier to Break Down for Biofuel Great Lakes Bioenergy Research Center Contact GLBRC About This Technology Technology Marketing Summary Lignocellulosic biomass is a very desirable feedstock for biofuel production. If the fermentation process could be optimized, conversion of this biomass could yield 25 to 50 billion gallons of ethanol or other biofuels per year. Yet lignocellulose is composed of tough lignin, cellulose and hemicelluloses that resist breakdown. This

  20. Symmetry Breaking of H2 Dissociation by a Single Photon

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

    Symmetry Breaking of H2 Dissociation by a Single Photon Print A single hydrogen (or deuterium) molecule consists of only two protons (deuterons) and two electrons and is perfectly symmetric. Linearly polarized photons are similarly symmetric. So one might think that the angular distribution of photoelectrons resulting from photoionization of the molecule by the photon accompanied by dissociation into a hydrogen atom and a hydrogen ion would itself be symmetric. However, an international team of

  1. Symmetry Breaking of H2 Dissociation by a Single Photon

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

    Symmetry Breaking of H2 Dissociation by a Single Photon Print A single hydrogen (or deuterium) molecule consists of only two protons (deuterons) and two electrons and is perfectly symmetric. Linearly polarized photons are similarly symmetric. So one might think that the angular distribution of photoelectrons resulting from photoionization of the molecule by the photon accompanied by dissociation into a hydrogen atom and a hydrogen ion would itself be symmetric. However, an international team of

  2. Symmetry Breaking of H2 Dissociation by a Single Photon

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

    Symmetry Breaking of H2 Dissociation by a Single Photon Print A single hydrogen (or deuterium) molecule consists of only two protons (deuterons) and two electrons and is perfectly symmetric. Linearly polarized photons are similarly symmetric. So one might think that the angular distribution of photoelectrons resulting from photoionization of the molecule by the photon accompanied by dissociation into a hydrogen atom and a hydrogen ion would itself be symmetric. However, an international team of

  3. Sandia California breaks ground on new building | National Nuclear Security

    National Nuclear Security Administration (NNSA)

    Administration Home / Blog Sandia California breaks ground on new building Monday, August 3, 2015 - 11:11am A groundbreaking ceremony was recently held in Livermore, Calif., for a building that will enable consolidation of "front door" activities for Sandia National Laboratories California. NNSA Blog Building 926 will house the site's human resources department and will be home of the training center for students and new hires. The new 20,000 square foot facility, funded by

  4. LANL breaks ground on key sediment control project

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

    Sediment control project LANL breaks ground on key sediment control project Called "grade-control" structures, the approximately $2 million features are up to eight feet high and made of rocks packed tightly into wire enclosures. November 5, 2009 Los Alamos National Laboratory sits on top of a once-remote mesa in northern New Mexico with the Jemez mountains as a backdrop to research and innovation covering multi-disciplines from bioscience, sustainable energy sources, to plasma physics

  5. NNSA, Pantex Break Ground on High Explosives Pressing Facility | National

    National Nuclear Security Administration (NNSA)

    Nuclear Security Administration NNSA, Pantex Break Ground on High Explosives Pressing Facility August 30, 2011 AMARILLO, Texas - Officials from National Nuclear Security Administration (NNSA) and Pantex today joined local dignitaries to mark the beginning of construction on the new High Explosives Pressing Facility (HEPF) at the Pantex Plant in Amarillo, Texas. The new $65 million facility will replace buildings constructed during World War II. "The future of Pantex continues to take

  6. Symmetry Breaking of H2 Dissociation by a Single Photon

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

    Symmetry Breaking of H2 Dissociation by a Single Photon Print A single hydrogen (or deuterium) molecule consists of only two protons (deuterons) and two electrons and is perfectly symmetric. Linearly polarized photons are similarly symmetric. So one might think that the angular distribution of photoelectrons resulting from photoionization of the molecule by the photon accompanied by dissociation into a hydrogen atom and a hydrogen ion would itself be symmetric. However, an international team of

  7. U.S. Department of Energy Breaks Ground on State-of-the-Art Wind...

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

    U.S. Department of Energy Breaks Ground on State-of-the-Art Wind Turbine Test Facility U.S. Department of Energy Breaks Ground on State-of-the-Art Wind Turbine Test Facility ...

  8. Bubbles Help Break Energy Storage Record for Lithium Air-Batteries

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

    Bubbles Help Break Energy Storage Record for Lithium Air-Batteries Bubbles Help Break Energy Storage Record for Lithium Air-Batteries Foam-base graphene keeps oxygen flowing in ...

  9. Detection of a Spectral Break in the Extra Hard Component of...

    Office of Scientific and Technical Information (OSTI)

    Detection of a Spectral Break in the Extra Hard Component of GRB 090926A Citation Details In-Document Search Title: Detection of a Spectral Break in the Extra Hard Component of GRB ...

  10. Three-dimensional Invasion of Human Glioblastoma Cells Remains Unchanged by X-ray and Carbon Ion Irradiation In Vitro

    SciTech Connect (OSTI)

    Eke, Iris; Storch, Katja; Kaestner, Ina; Vehlow, Anne; Faethe, Christina; Mueller-Klieser, Wolfgang; Taucher-Scholz, Gisela; Temme, Achim; Schackert, Gabriele; Department of Radiation Oncology, Medical Faculty Carl Gustav Carus, Dresden University of Technology, Dresden

    2012-11-15

    Purpose: Cell invasion represents one of the major determinants that treatment has failed for patients suffering from glioblastoma. Contrary findings have been reported for cell migration upon exposure to ionizing radiation. Here, the migration and invasion capability of glioblastoma cells on and in collagen type I were evaluated upon irradiation with X-rays or carbon ions. Methods and Materials: Migration on and invasion in collagen type I were evaluated in four established human glioblastoma cell lines exposed to either X-rays or carbon ions. Furthermore, clonogenic radiation survival, proliferation (5-bromo-2-deoxyuridine positivity), DNA double-strand breaks ({gamma}H2AX/53BP1-positive foci), and expression of invasion-relevant proteins (eg, {beta}1 integrin, FAK, MMP2, and MMP9) were explored. Migration and invasion assays for primary glioblastoma cells also were carried out with X-ray irradiation. Results: Neither X-ray nor carbon ion irradiation affected glioblastoma cell migration and invasion, a finding similarly observed in primary glioblastoma cells. Intriguingly, irradiated cells migrated unhampered, despite DNA double-strand breaks and reduced proliferation. Clonogenic radiation survival was increased when cells had contact with extracellular matrix. Specific inhibition of the {beta}1 integrin or proliferation-associated signaling molecules revealed a critical function of JNK, PI3K, and p38 MAPK in glioblastoma cell invasion. Conclusions: These findings indicate that X-rays and carbon ion irradiation effectively reduce proliferation and clonogenic survival without modifying the migration and invasion ability of glioblastoma cells in a collagen type I environment. Addition of targeted agents against members of the MAPK and PI3K signaling axis to conventional chemoradiation therapy seems potentially useful to optimize glioblastoma therapy.

  11. 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.

  12. 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.

  13. 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.

  14. 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...

  15. Controlling DNA Methylation

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

    ... Induced DNA bending. Primary Citation Sawaya, M. R. Zhu, Z., Mersha, F., Chan, S-h., ... restriction-modification system control element C.BclI and mapping of its binding site. ...

  16. 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.

  17. Leak before break application in French PWR plants under operation

    SciTech Connect (OSTI)

    Faidy, C.

    1997-04-01

    Practical applications of the leak-before break concept are presently limited in French Pressurized Water Reactors (PWR) compared to Fast Breeder Reactors. Neithertheless, different fracture mechanic demonstrations have been done on different primary, auxiliary and secondary PWR piping systems based on similar requirements that the American NUREG 1061 specifications. The consequences of the success in different demonstrations are still in discussion to be included in the global safety assessment of the plants, such as the consequences on in-service inspections, leak detection systems, support optimization,.... A large research and development program, realized in different co-operative agreements, completes the general approach.

  18. 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.

  19. Flavour symmetry breaking in the kaon parton distribution amplitude

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

    none,

    2014-11-01

    We compute the kaon's valence-quark (twist-two parton) distribution amplitude (PDA) by projecting its Poincar-covariant BetheSalpeter wave-function onto the light-front. At a scale ? = 2 GeV, the PDA is a broad, concave and asymmetric function, whose peak is shifted 1216% away from its position in QCD's conformal limit. These features are a clear expression of SU(3)-flavour-symmetry breaking. They show that the heavier quark in the kaon carries more of the bound-state's momentum than the lighter quark and also that emergent phenomena in QCD modulate the magnitude of flavour-symmetry breaking: it is markedly smaller than one might expect based on themoredifference between light-quark current masses. Our results add to a body of evidence which indicates that at any energy scale accessible with existing or foreseeable facilities, a reliable guide to the interpretation of experiment requires the use of such nonperturbatively broadened PDAs in leading-order, leading-twist formulae for hard exclusive processes instead of the asymptotic PDA associated with QCD's conformal limit. We illustrate this via the ratio of kaon and pion electromagnetic form factors: using our nonperturbative PDAs in the appropriate formulae, FK/F?=1.23 at spacelike-Q2=17 GeV2, which compares satisfactorily with the value of 0.92(5) inferred in e+e- annihilation at s=17 GeV2.less

  20. Spontaneous supersymmetry breaking in two dimensional lattice super QCD

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

    Catterall, Simon; Veernala, Aarti

    2015-10-02

    We report on a non-perturbative study of two dimensional N=(2,2) super QCD. Our lattice formulation retains a single exact supersymmetry at non-zero lattice spacing, and contains Nf fermions in the fundamental representation of a U(Nc) gauge group. The lattice action we employ contains an additional Fayet-Iliopoulos term which is also invariant under the exact lattice supersymmetry. This work constitutes the first numerical study of this theory which serves as a toy model for understanding some of the issues that are expected to arise in four dimensional super QCD. As a result, we present evidence that the exact supersymmetry breaks spontaneouslymore » when Nf < Nc in agreement with theoretical expectations.« less

  1. Spontaneous supersymmetry breaking in two dimensional lattice super QCD

    SciTech Connect (OSTI)

    Catterall, Simon; Veernala, Aarti

    2015-10-02

    We report on a non-perturbative study of two dimensional N=(2,2) super QCD. Our lattice formulation retains a single exact supersymmetry at non-zero lattice spacing, and contains Nf fermions in the fundamental representation of a U(Nc) gauge group. The lattice action we employ contains an additional Fayet-Iliopoulos term which is also invariant under the exact lattice supersymmetry. This work constitutes the first numerical study of this theory which serves as a toy model for understanding some of the issues that are expected to arise in four dimensional super QCD. As a result, we present evidence that the exact supersymmetry breaks spontaneously when Nf < Nc in agreement with theoretical expectations.

  2. ON THE EVOLUTION OF THE SPECTRAL BREAK IN THE AFTERGLOW OF GAMMA-RAY BURSTS

    SciTech Connect (OSTI)

    Dado, Shlomo; Dar, Arnon [Physics Department, Technion, Haifa 32000 (Israel)

    2012-02-20

    The temporal evolution of the spectral break in the time-resolved spectral energy density of the broadband afterglow of gamma-ray bursts (GRBs) 091127 and 080319B was shown recently to be inconsistent with that expected for the cooling break in the standard fireball model of GRBs. Here we show that it is, however, in good agreement with the predicted temporal evolution of the smooth injection break/bend in the cannonball model of GRBs.

  3. 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.

  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. Tips for Running an Air Conditioner Without Breaking the Bank | Department

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

    of Energy Tips for Running an Air Conditioner Without Breaking the Bank Tips for Running an Air Conditioner Without Breaking the Bank July 22, 2014 - 3:15pm Addthis Cooling your home doesn't have to break the bank, with these tips you can save money and stay comfortable.| Photo courtesy of ©iStockphoto.com/galinast Cooling your home doesn't have to break the bank, with these tips you can save money and stay comfortable.| Photo courtesy of ©iStockphoto.com/galinast Elizabeth Spencer

  6. Break-Even Cost for Residential Solar Water Heating in the United...

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

    Break-even Cost for Residential Solar Water Heating in the United States: Key Drivers and Sensitivities Hannah Cassard, Paul Denholm, and Sean Ong Technical Report NREL...

  7. 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.

  8. 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.

  9. Break-Even Cost for Residential Photovoltaics in the United States: Key Drivers and Sensitivities

    SciTech Connect (OSTI)

    Denholm, P.; Margolis, R. M.; Ong, S.; Roberts, B.

    2009-12-01

    Grid parity--or break-even cost--for photovoltaic (PV) technology is defined as the point where the cost of PV-generated electricity equals the cost of electricity purchased from the grid. Break-even cost is expressed in $/W of an installed system. Achieving break-even cost is a function of many variables. Consequently, break-even costs vary by location and time for a country, such as the United States, with a diverse set of resources, electricity prices, and other variables. In this report, we analyze PV break-even costs for U.S. residential customers. We evaluate some key drivers of grid parity both regionally and over time. We also examine the impact of moving from flat to time-of-use (TOU) rates, and we evaluate individual components of the break-even cost, including effect of rate structure and various incentives. Finally, we examine how PV markets might evolve on a regional basis considering the sensitivity of the break-even cost to four major drivers: technical performance, financing parameters, electricity prices and rates, and policies. We find that local incentives rather than ?technical? parameters are in general the key drivers of the break-even cost of PV. Additionally, this analysis provides insight about the potential viability of PV markets.

  10. 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.

  11. 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.

  12. 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.

  13. Treatment methods for breaking certain oil and water emulsions

    DOE Patents [OSTI]

    Sealock, Jr., L. John; Baker, Eddie G.; Elliott, Douglas C.

    1992-01-01

    Disclosed are treatment methods for breaking emulsions of petroleum oil and salt water, fatty oil and water, and those resulting from liquefication of organic material. The emulsions are broken by heating to a predetermined temperature at or above about 200.degree. C. and pressurizing to a predetermined pressure above the vapor pressure of water at the predetermined temperature to produce a heated and pressurized fluid. The heated and pressurized fluid is contained in a single vessel at the predetermined temperature and pressure for a predetermined period of time to effectively separate the emulsion into substantially distinct first and second phases, the first phase comprising primarily the petroleum oil, the second phase comprising primarily the water. The first and second phases are separately withdrawn from the vessel at a withdraw temperature between about 200.degree. C. and 374.degree. C. and a withdraw pressure above the vapor pressure of water at the withdraw temperature. Where solids are present in the certain emulsions, the above described treatment may also effectively separate the certain emulsion into a substantially distinct third phase comprising primarily the solids.

  14. Particle-Hole Symmetry Breaking in the Pseudogap State of Bi2201

    SciTech Connect (OSTI)

    Hashimoto, M.; He, R.-H.; Tanaka, K.; Testaud, J.P.; Meevasana1, W.; Moore, R.G.; Lu, D.H.; Yao, H.; Yoshida, Y.; Eisaki, H.; Devereaux, T.P.; Hussain, Z.; Shen, Z.-X.; /SIMES, Stanford /Stanford U., Geballe Lab.

    2011-08-19

    In conventional superconductors, a gap exists in the energy absorption spectrum only below the transition temperature (T{sub c}), corresponding to the energy price to pay for breaking a Cooper pair of electrons. In high-T{sub c} cuprate superconductors above T{sub c}, an energy gap called the pseudogap exists, and is controversially attributed either to pre-formed superconducting pairs, which would exhibit particle-hole symmetry, or to competing phases which would typically break it. Scanning tunnelling microscopy (STM) studies suggest that the pseudogap stems from lattice translational symmetry breaking and is associated with a different characteristic spectrum for adding or removing electrons (particle-hole asymmetry). However, no signature of either spatial or energy symmetry breaking of the pseudogap has previously been observed by angle-resolved photoemission spectroscopy (ARPES). Here we report ARPES data from Bi2201 which reveals both particle-hole symmetry breaking and dramatic spectral broadening indicative of spatial symmetry breaking without long range order, upon crossing through T* into the pseudogap state. This symmetry breaking is found in the dominant region of the momentum space for the pseudogap, around the so-called anti-node near the Brillouin zone boundary. Our finding supports the STM conclusion that the pseudogap state is a broken-symmetry state that is distinct from homogeneous superconductivity.

  15. Española entrepreneur breaks ground; expansion will create 50 new jobs

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

    Española entrepreneur breaks ground; expansion will create 50 new jobs Community Connections: Your link to news and opportunities from Los Alamos National Laboratory Latest Issue:May 2016 all issues All Issues » submit Española entrepreneur breaks ground; expansion will create 50 new jobs Governor Susana Martinez initiated new site on June 17 August 1, 2014 Breaking ground at PMI's new site. Española Mayor Alice Lucero, New Mexico Economic Development Dept. Cabinet Secretary Jon Barela, New

  16. Soft supersymmetry breaking terms from D{sub 4}xZ{sub 2} lepton flavor

    Office of Scientific and Technical Information (OSTI)

    symmetry (Journal Article) | SciTech Connect Soft supersymmetry breaking terms from D{sub 4}xZ{sub 2} lepton flavor symmetry Citation Details In-Document Search Title: Soft supersymmetry breaking terms from D{sub 4}xZ{sub 2} lepton flavor symmetry We study the supersymmetric model with D{sub 4}xZ{sub 2} lepton flavor symmetry. We evaluate soft supersymmetry breaking terms, i.e., soft slepton masses and A-terms, which are predicted in the D{sub 4} flavor model. We consider constraints due to

  17. Dynamics of Peccei-Quinn breaking field after inflation and axion isocurvature perturbations

    SciTech Connect (OSTI)

    Harigaya, Keisuke; Ibe, Masahiro; Kawasaki, Masahiro; Yanagida, Tsutomu T.

    2015-11-04

    The Peccei-Quinn mechanism suffers from the problem of the isocurvature perturbations. The isocurvature perturbations are suppressed if the Peccei-Quinn breaking scale is large during inflation. The oscillation of the Peccei-Quinn breaking field after inflation, however, leads to the formation of domain walls due to the parametric resonance effect. In this paper, we discuss the evolution of the Peccei-Quinn breaking field after inflation in detail, and propose a model where the parametric resonance is ineffective and hence domain walls are not formed. We also discuss consistency of our model with supersymmetric theory.

  18. 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...

  19. 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).

  20. 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.

  1. Fermi-LAT Detection of a Break in the Gamma-Ray Spectrum of the...

    Office of Scientific and Technical Information (OSTI)

    in the Gamma-Ray Spectrum of the Supernova Remnant Cassiopeia A Citation Details In-Document Search Title: Fermi-LAT Detection of a Break in the Gamma-Ray Spectrum of the Supernova ...

  2. San Carlos Apache Tribe Set to Break Ground on New Solar Project...

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

    This spring, the San Carlos Apache Tribe is planning to break ground on a new tribally financed and owned 1.1-megawatt (MW) solar photovoltaic (PV) array. The PV system will ...

  3. Dynamics of Peccei-Quinn breaking field after inflation and axion...

    Office of Scientific and Technical Information (OSTI)

    In this paper, we discuss the evolution of the Peccei-Quinn breaking field after inflation in detail, and propose a model where the parametric resonance is ineffective and hence ...

  4. U.S. gasoline prices decreases for 16th week in a row; breaking...

    U.S. Energy Information Administration (EIA) Indexed Site

    18, 2015 U.S. gasoline prices decreases for 16th week in a row; breaking previous record ... Pump prices were highest in the West Coast states at 2.38 a gallon, down 10.8 cents from a ...

  5. U.S. gasoline prices decreases for 16th week in a row; breaking...

    Annual Energy Outlook [U.S. Energy Information Administration (EIA)]

    for regular gasoline fell 7.3 cents from a week ago to 2.07 a gallon on Monday. This marks a record of 16 consecutive weeks of price drops and breaks the previous record set at...

  6. Pairing state with a time-reversal symmetry breaking in FeAs...

    Office of Scientific and Technical Information (OSTI)

    Technical Report: Pairing state with a time-reversal symmetry breaking in FeAs-based superconductors Citation Details In-Document Search Title: Pairing state with a time-reversal ...

  7. Better batteries to break dependence on fossil fuels > EMC2 News...

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

    Better batteries to break dependence on fossil fuels April 28th, 2015 By Linda B. ... said Abrua, which means better and more affordable designs for fuel cells and batteries. ...

  8. Detection of a Spectral Break in the Extra Hard Component of...

    Office of Scientific and Technical Information (OSTI)

    the Extra Hard Component of GRB 090926A Citation Details In-Document Search Title: Detection of a Spectral Break in the Extra Hard Component of GRB 090926A You are accessing a ...

  9. Breaking Up (Hydrogen) No Longer As Hard To Do | Department of Energy

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

    Breaking Up (Hydrogen) No Longer As Hard To Do Breaking Up (Hydrogen) No Longer As Hard To Do December 29, 2011 - 1:12pm Addthis Researchers at Argonne National Lab have recently developed a process to improve the efficiency of producing hydrogen to run cars such as this prototype, which was developed at the Oakridge National Lab. | Photo courtesy of Oak Ridge National Laboratory. Researchers at Argonne National Lab have recently developed a process to improve the efficiency of producing

  10. Breaking Ground and Driving Discovery | U.S. DOE Office of Science (SC)

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

    Breaking Ground and Driving Discovery News News Home Featured Articles 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 Science Headlines Science Highlights Presentations & Testimony News Archives Communications and Public Affairs Contact Information Office of Science U.S. Department of Energy 1000 Independence Ave., SW Washington, DC 20585 P: (202) 586-5430 12.16.11 Breaking Ground and Driving Discovery Director Brinkman welcomes the Illinois Accelerator Research Center. Print

  11. Breaking Up - And Making Up - Are Hard To Do | U.S. DOE Office of

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

    Breaking Up (Hydrogen) No Longer As Hard To Do Breaking Up (Hydrogen) No Longer As Hard To Do December 29, 2011 - 1:12pm Addthis Researchers at Argonne National Lab have recently developed a process to improve the efficiency of producing hydrogen to run cars such as this prototype, which was developed at the Oakridge National Lab. | Photo courtesy of Oak Ridge National Laboratory. Researchers at Argonne National Lab have recently developed a process to improve the efficiency of producing

  12. Bubbles Help Break Energy Storage Record for Lithium Air-Batteries

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

    Bubbles Help Break Energy Storage Record for Lithium Air-Batteries Bubbles Help Break Energy Storage Record for Lithium Air-Batteries Foam-base graphene keeps oxygen flowing in batteries that holds promise for electric vehicles January 25, 2012 Linda Vu, lvu@lbl.gov, +1 510 495 2402 Using a new approach, the team built a graphene membrane for use in lithium-air batteries, which could, one day, replace conventional batteries in electric vehicles. Resembling coral, this porous graphene material

  13. Pairing state with a time-reversal symmetry breaking in FeAs-based

    Office of Scientific and Technical Information (OSTI)

    superconductors (Technical Report) | SciTech Connect Technical Report: Pairing state with a time-reversal symmetry breaking in FeAs-based superconductors Citation Details In-Document Search Title: Pairing state with a time-reversal symmetry breaking in FeAs-based superconductors We investigate the competition between the extended s{+-} wave and dx2-y2 -wave pairing order parameters in the iron-based superconductors. Because of the frustrating pairing interactions among the electron and the

  14. More than $3 million raised during record-breaking Employee Giving Campaign

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

    Record-breaking employee giving campaign Community Connections: Your link to news and opportunities from Los Alamos National Laboratory Latest Issue:May 2016 all issues All Issues » submit More than $3 million raised during record-breaking Employee Giving Campaign Contributions will benefit regional nonprofits December 1, 2014 Mobile medical and dental clinic owned by Tierra Amarillas' La Clinica del Pueblo de Rio Arriba. The purchase of the vehicle was made possible by donations through United

  15. Novel Thermal Break with Simplified Manufacturing for R7 Commercial Windows

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

    | Department of Energy Novel Thermal Break with Simplified Manufacturing for R7 Commercial Windows Novel Thermal Break with Simplified Manufacturing for R7 Commercial Windows Lead Performer: Alcoa - Pittsburgh, PA DOE Funding: $1,123,838 Cost Share: $280,960 Project Term: October 2014 - September 2016 Funding Opportunity: Building Energy Efficiency Frontiers and Incubator Technologies (BENEFIT) - 2014 (DE-FOA-0001027) Project Objective Alcoa proposes to develop a novel sandwich-type foam

  16. 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 ...

  17. 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 ...

  18. 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...

  19. 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...

  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. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Symmetry breaking indication for supergravity inflation in light of the Planck 2015

    SciTech Connect (OSTI)

    Li, Tianjun; Li, Zhijin; Nanopoulos, Dimitri V.

    2015-09-01

    Supergravity (SUGRA) theories with exact global U(1) symmetry or shift symmetry in Kähler potential provide natural frameworks for inflation. However, quadratic inflation is disfavoured by the new results on primordial tensor fluctuations from the Planck Collaboration. To be consistent with the new Planck data, we point out that the explicit symmetry breaking is needed, and study these two SUGRA inflation in detail. For SUGRA inflation with global U(1) symmetry, the symmetry breaking term leads to a trigonometric modulation on inflaton potential. Coefficient of the U(1) symmetry breaking term is of order 10{sup −2}, which is sufficient large to improve the inflationary predictions while its higher order corrections are negligible. Such models predict sizeable tensor fluctuations and highly agree with the Planck results. In particular, the model with a linear U(1) symmetry breaking term predicts the tensor-to-scalar ratio around r∼0.01 and running spectral index α{sub s}∼−0.004, which comfortably fit with the Planck observations. For SUGRA inflation with breaking shift symmetry, the inflaton potential is modulated by an exponential factor. The modulated linear and quadratic models are consistent with the Planck observations. In both types of models the tensor-to-scalar ratio can be of order 10{sup −2}, which will be tested by the near future observations.

  6. The evolution of the break preclusion concept for nuclear power plants in Germany

    SciTech Connect (OSTI)

    Schulz, H.

    1997-04-01

    In the updating of the Guidelines for PWR`s of the {open_quotes}Reaktor-Sicherheitskommission{close_quotes} (RSK) in 1981 the requirements on the design have been changed with respect to the postulated leaks and breaks in the primary pressure boundary. The major change was a revision in the requirements for pipe whip protection. As a logical consequence of the {open_quotes}concept of basic safety{close_quotes} a guillotine type break or any other break type resulting in a large opening is not postulated any longer for the calculation of reaction and jet forces. As an upper limit for a leak an area of 0, 1 A (A = open cross section of the pipe) is postulated. This decision was based on a general assessment of the present PWR system design in Germany. Since then a number of piping systems have been requalified in the older nuclear power plants to comply with the break preclusion concept. Also a number of extensions of the concept have been developed to cover also leak-assumptions for branch pipes. Furthermore due considerations have been given to other aspects which could contribute to a leak development in the primary circuit, like vessel penetrations, manhole covers, flanges, etc. Now the break preclusion concept originally applied to the main piping has been developed into an integrated concept for the whole pressure boundary within the containment and will be applied also in the periodic safety review of present nuclear power plants.

  7. Homologous recombination and non-homologous end-joining repair pathways in bovine embryos with different developmental competence

    SciTech Connect (OSTI)

    Henrique Barreta, Marcos; Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS ; Garziera Gasperin, Bernardo; Braga Rissi, Vitor; Cesaro, Matheus Pedrotti de; Ferreira, Rogerio; Oliveira, Joao Francisco de; Goncalves, Paulo Bayard Dias; Bordignon, Vilceu

    2012-10-01

    This study investigated the expression of genes controlling homologous recombination (HR), and non-homologous end-joining (NHEJ) DNA-repair pathways in bovine embryos of different developmental potential. It also evaluated whether bovine embryos can respond to DNA double-strand breaks (DSBs) induced with ultraviolet irradiation by regulating expression of genes involved in HR and NHEJ repair pathways. Embryos with high, intermediate or low developmental competence were selected based on the cleavage time after in vitro insemination and were removed from in vitro culture before (36 h), during (72 h) and after (96 h) the expected period of embryonic genome activation. All studied genes were expressed before, during and after the genome activation period regardless the developmental competence of the embryos. Higher mRNA expression of 53BP1 and RAD52 was found before genome activation in embryos with low developmental competence. Expression of 53BP1, RAD51 and KU70 was downregulated at 72 h and upregulated at 168 h post-insemination in response to DSBs induced by ultraviolet irradiation. In conclusion, important genes controlling HR and NHEJ DNA-repair pathways are expressed in bovine embryos, however genes participating in these pathways are only regulated after the period of embryo genome activation in response to ultraviolet-induced DSBs.

  8. The influence of pairing correlations on the isospin symmetry breaking corrections of superallowed Fermi beta decays

    SciTech Connect (OSTI)

    Cal Latin-Small-Letter-Dotless-I k, A. E.; Gerceklioglu, M.; Selam, C.

    2013-05-15

    Within the framework of quasi-particle random phase approximation, the isospin breaking correction of superallowed 0{sup +} {yields} 0{sup +} beta decay and unitarity of Cabibbo-Kobayashi-Maskawa mixing matrix have been investigated. The broken isotopic symmetry of nuclear part of Hamiltonian has been restored by Pyatov's method. The isospin symmetry breaking correction with pairing correlations has been compared with the previous results without pairing. The effect of pairing interactions has been examined for nine superallowed Fermi beta decays; their parent nuclei are {sup 26}Al, {sup 34}Cl, {sup 38}K, {sup 42}Sc, {sup 46}V, {sup 50}Mn, {sup 54}Co, {sup 62}Ga, {sup 74}Rb.

  9. Fermi-LAT Detection of a Break in the Gamma-Ray Spectrum of the Supernova

    Office of Scientific and Technical Information (OSTI)

    Remnant Cassiopeia A (Journal Article) | SciTech Connect Fermi-LAT Detection of a Break in the Gamma-Ray Spectrum of the Supernova Remnant Cassiopeia A Citation Details In-Document Search Title: Fermi-LAT Detection of a Break in the Gamma-Ray Spectrum of the Supernova Remnant Cassiopeia A Authors: Yuan, Y. ; Funk, S. ; Johannesson, G. ; Lande, J. ; Tibaldo, L. ; Uchiyama, Y. ; /Stanford U., HEPL /KIPAC, Menlo Park /SLAC /Iceland U. ; , Publication Date: 2013-11-07 OSTI Identifier: 1104713

  10. Wave breaking phenomenon of lower-hybrid oscillations induced by a background inhomogeneous magnetic field

    SciTech Connect (OSTI)

    Maity, Chandan; Chakrabarti, Nikhil [Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064 (India); Sengupta, Sudip [Institute for Plasma Research, Bhat, Gandhinagar 382428 (India)

    2012-10-15

    In a fluid description, we study space-time evolution of lower hybrid modes in a cold quasi-neutral homogeneous plasma in presence of a background inhomogeneous magnetic field. Within a linear analysis, a dispersion relation with inhomogeneous magnetic field shows 'phase mixing' of such oscillations. A manifestation of 'phase mixing' is shown in 'mode coupling.' By using Lagrangian variables, an exact solution is presented in parametric form of this nonlinear time dependent problem. It is demonstrated that initially excited lower hybrid modes always break via phase mixing phenomenon in presence of an inhomogeneous magnetic field. Breaking of such oscillations is revealed by the appearance of spikes in the plasma density profile.

  11. From Decay to Complete Breaking: Pulling the Strings in SU(2) Yang-Mills Theory

    SciTech Connect (OSTI)

    Pepe, M.; Wiese, U.-J.

    2009-05-15

    We study (2Q+1) strings connecting two static charges Q in (2+1)D SU(2) Yang-Mills theory. While the fundamental (2) string between two charges Q=(1/2) is unbreakable, the adjoint (3) string connecting two charges Q=1 can break. When a (4) string is stretched beyond a critical length, it decays into a (2) string by gluon pair creation. When a (5) string is stretched, it first decays into a (3) string, which eventually breaks completely. The energy of the screened charges at the ends of a string is well described by a phenomenological constituent gluon model.

  12. The concepts of leak before break and absolute reliability of NPP equipment and piping

    SciTech Connect (OSTI)

    Getman, A.F.; Komarov, O.V.; Sokov, L.M.

    1997-04-01

    This paper describes the absolute reliability (AR) concept for ensuring safe operation of nuclear plant equipment and piping. The AR of a pipeline or component is defined as the level of reliability when the probability of an instantaneous double-ended break is near zero. AR analysis has been applied to Russian RBMK and VVER type reactors. It is proposed that analyses required for application of the leak before break concept should be included in AR implementation. The basic principles, methods, and approaches that provide the basis for implementing the AR concept are described.

  13. Media Advisory Jefferson Lab Breaks Ground Sept. 1 for $73 Million

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

    Technology & Engineering Facility | Jefferson Lab Jefferson Lab Breaks Ground Sept. 1 for $73 Million Technology &amp; Engineering Facility Media Advisory Jefferson Lab Breaks Ground Sept. 1 for $73 Million Technology & Engineering Facility Date: Wednesday, Sept. 1, 2010 Time: 9 - 10 a.m. News media representatives are asked to arrive no later than 8:45 a.m. to allow time to get in place for the event. Place: Jefferson Lab, 12000 Jefferson Avenue, Newport News, VA 23606 Event:

  14. Symmetry-Breaking Orbital Anisotropy Observed for Detwinned Ba(Fe (1-X) Co

    Office of Scientific and Technical Information (OSTI)

    (X) ) (2) As (2) Above the Spin Density Wave Transition (Journal Article) | SciTech Connect Symmetry-Breaking Orbital Anisotropy Observed for Detwinned Ba(Fe (1-X) Co (X) ) (2) As (2) Above the Spin Density Wave Transition Citation Details In-Document Search Title: Symmetry-Breaking Orbital Anisotropy Observed for Detwinned Ba(Fe (1-X) Co (X) ) (2) As (2) Above the Spin Density Wave Transition Authors: Yi, M. ; Lu, D. ; Chu, J.-H. ; Analytis, J.G. ; Sorini, A.P. ; Kemper, A.F. ; Mortiz, B. ;

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. WHERE DOES FLUID-LIKE TURBULENCE BREAK DOWN IN THE SOLAR WIND?

    SciTech Connect (OSTI)

    Perri, S.; Carbone, V.; Veltri, P.

    2010-12-10

    Power spectra of the magnetic field in solar wind display a Kolmogorov law f {sup -5/3} at intermediate range of frequencies f, say within the inertial range. Two spectral breaks are also observed: one separating the inertial range from an f {sup -1} spectrum at lower frequencies, and another one between the inertial range and an f {sup -7/3} spectrum at higher frequencies. The breaking of fluid-like turbulence at high frequencies has been attributed to either the occurrence of kinetic Alfven wave fluctuations above the ion-cyclotron frequency or to whistler turbulence above the frequency corresponding to the proton gyroradius. Using solar wind data, we show that the observed high-frequency spectral break seems to be independent of the distance from the Sun, and then of both the ion-cyclotron frequency and the proton gyroradius. We suppose that the observed high-frequency break could be either caused by a combination of different physical processes or associated with a remnant signature of coronal turbulence.

  2. Long distance high power optical laser fiber break detection and continuity monitoring systems and methods

    DOE Patents [OSTI]

    Rinzler, Charles C.; Gray, William C.; Faircloth, Brian O.; Zediker, Mark S.

    2016-02-23

    A monitoring and detection system for use on high power laser systems, long distance high power laser systems and tools for performing high power laser operations. In particular, the monitoring and detection systems provide break detection and continuity protection for performing high power laser operations on, and in, remote and difficult to access locations.

  3. Coherent States and Spontaneous Symmetry Breaking in Light Front Scalar Field Theory

    SciTech Connect (OSTI)

    Vary, J.P.; Chakrabarti, D.; Harindranath, A.; Lloyd, R.; Martinovic, L.; Spence, J.R.; /Iowa State U.

    2005-12-14

    Recently developed nuclear many-body techniques provide novel results when applied to constituent quark models and to light-front scalar field theory. We show how spontaneous symmetry breaking arises and is consistent with a coherent state ansatz in a variational treatment. The kink and the kink-antikink topological features are identified and the onset of symmetry restoration is demonstrated.

  4. Downregulation of SWI/SNF chromatin remodeling factor subunits modulates cisplatin cytotoxicity

    SciTech Connect (OSTI)

    Kothandapani, Anbarasi; Gopalakrishnan, Kathirvel; Kahali, Bhaskar; Reisman, David; Patrick, Steve M.

    2012-10-01

    Chromatin remodeling complex SWI/SNF plays important roles in many cellular processes including transcription, proliferation, differentiation and DNA repair. In this report, we investigated the role of SWI/SNF catalytic subunits Brg1 and Brm in the cellular response to cisplatin in lung cancer and head/neck cancer cells. Stable knockdown of Brg1 and Brm enhanced cellular sensitivity to cisplatin. Repair kinetics of cisplatin DNA adducts revealed that downregulation of Brg1 and Brm impeded the repair of both intrastrand adducts and interstrand crosslinks (ICLs). Cisplatin ICL-induced DNA double strand break repair was also decreased in Brg1 and Brm depleted cells. Altered checkpoint activation with enhanced apoptosis as well as impaired chromatin relaxation was observed in Brg1 and Brm deficient cells. Downregulation of Brg1 and Brm did not affect the recruitment of DNA damage recognition factor XPC to cisplatin DNA lesions, but affected ERCC1 recruitment, which is involved in the later stages of DNA repair. Based on these results, we propose that SWI/SNF chromatin remodeling complex modulates cisplatin cytotoxicity by facilitating efficient repair of the cisplatin DNA lesions. -- Highlights: Black-Right-Pointing-Pointer Stable knockdown of Brg1 and Brm enhances cellular sensitivity to cisplatin. Black-Right-Pointing-Pointer Downregulation of Brg1 and Brm impedes the repair of cisplatin intrastrand adducts and interstrand crosslinks. Black-Right-Pointing-Pointer Brg1 and Brm deficiency results in impaired chromatin relaxation, altered checkpoint activation as well as enhanced apoptosis. Black-Right-Pointing-Pointer Downregulation of Brg1 and Brm affects recruitment of ERCC1, but not XPC to cisplatin DNA lesions.

  5. 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).

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

    Office of Scientific and Technical Information (OSTI)

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

  7. Mobilization of Viable Tumor Cells Into the Circulation During Radiation Therapy

    SciTech Connect (OSTI)

    Martin, Olga A.; Anderson, Robin L.; Russell, Prudence A.; Ashley Cox, R.; Ivashkevich, Alesia; Swierczak, Agnieszka; Doherty, Judy P.; Jacobs, Daphne H.M.; Smith, Jai; Siva, Shankar; Daly, Patricia E.; Ball, David L.; and others

    2014-02-01

    Purpose: To determine whether radiation therapy (RT) could mobilize viable tumor cells into the circulation of non-small cell lung cancer (NSCLC) patients. Methods and Materials: We enumerated circulating tumor cells (CTCs) by fluorescence microscopy of blood samples immunostained with conventional CTC markers. We measured their DNA damage levels using ?-H2AX, a biomarker for radiation-induced DNA double-strand breaks, either by fluorescence-activated cell sorting or by immunofluorescence microscopy. Results: Twenty-seven RT-treated NSCLC patients had blood samples analyzed by 1 or more methods. We identified increased CTC numbers after commencement of RT in 7 of 9 patients treated with palliative RT, and in 4 of 8 patients treated with curative-intent RT. Circulating tumor cells were also identified, singly and in clumps in large numbers, during RT by cytopathologic examination (in all 5 cases studied). Elevated ?-H2AX signal in post-RT blood samples signified the presence of CTCs derived from irradiated tumors. Blood taken after the commencement of RT contained tumor cells that proliferated extensively in vitro (in all 6 cases studied). Circulating tumor cells formed ?-H2AX foci in response to ex vivo irradiation, providing further evidence of their viability. Conclusions: Our findings provide a rationale for the development of strategies to reduce the concentration of viable CTCs by modulating RT fractionation or by coadministering systemic therapies.

  8. 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:...

  9. Co-targeting Deoxyribonucleic AcidDependent Protein Kinase and Poly(Adenosine Diphosphate-Ribose) Polymerase-1 Promotes Accelerated Senescence of Irradiated Cancer Cells

    SciTech Connect (OSTI)

    Azad, Arun; Bukczynska, Patricia; Jackson, Susan; Haput, Ygal; Cullinane, Carleen; McArthur, Grant A.; Solomon, Benjamin

    2014-02-01

    Purpose: To examine the effects of combined blockade of DNA-dependent protein kinase (DNA-PK) and poly(adenosine diphosphate-ribose) polymerase-1 (PARP-1) on accelerated senescence in irradiated H460 and A549 non-small cell lung cancer cells. Methods and Materials: The effects of KU5788 and AG014699 (inhibitors of DNA-PK and PARP-1, respectively) on clonogenic survival, DNA double-strand breaks (DSBs), apoptosis, mitotic catastrophe, and accelerated senescence in irradiated cells were examined in vitro. For in vivo experiments, H460 xenografts established in athymic nude mice were treated with BEZ235 (a DNA-PK, ATM, and phosphatidylinositol 3-kinase/mammalian target of rapamycin inhibitor) and AG014699 to determine effects on proliferation, DNA DSBs, and accelerated senescence after radiation. Results: Compared with either inhibitor alone, combination treatment with KU57788 and AG014699 reduced postradiation clonogenic survival and significantly increased persistence of Gamma-H2AX (?H2AX) foci in irradiated H460 and A549 cells. Notably, these effects coincided with the induction of accelerated senescence in irradiated cells as reflected by positive ?-galactosidase staining, G2-M cell-cycle arrest, enlarged and flattened cellular morphology, increased p21 expression, and senescence-associated cytokine secretion. In irradiated H460 xenografts, concurrent therapy with BEZ235 and AG014699 resulted in sustained Gamma-H2AX (?H2AX) staining and prominent ?-galactosidase activity. Conclusion: Combined DNA-PK and PARP-1 blockade increased tumor cell radiosensitivity and enhanced the prosenescent properties of ionizing radiation in vitro and in vivo. These data provide a rationale for further preclinical and clinical testing of this therapeutic combination.

  10. 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.

  11. 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 Chemical Biology Year: 2010 Volume: 14 Pages: 608-615 ABSTRACT: Researchers have been using DNA for the rational design and construction of nanoscale objects for nearly 30 years. Recently, [`]scaffolded DNA origami' has emerged as one of the most promising assembly techniques in DNA nanotechnology with a broad range of

  12. 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.

  13. 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.

  14. Breaking of relativistically intense longitudinal space charge waves: A description using Dawson sheet model

    SciTech Connect (OSTI)

    Sengupta, Sudip, E-mail: sudip@ipr.res.in [Institute for Plasma Research, Bhat , Gandhinagar - 382428 (India)

    2014-02-11

    Spatio-temporal evolution of relativistically intense longitudinal space charge waves in a cold homogeneous plasma is studied analytically as well as numerically, as an initial value problem, using Dawson sheet model. It is found that, except for very special initial conditions which generates the well known longitudinal Akhiezer-Polovin mode, for all other initial conditions, the waves break through a novel mechanism called phase mixing at an amplitude well below the Akhiezer-Polovin limit. An immediate consequence of this is, that Akhiezer-Polovin waves break when subjected to arbitrarily small longitudinal perturbations. We demonstrate this by performing extensive numerical simulations. This result may be of direct relevance to ultrashort, ultraintense laser/beam pulse-plasma interaction experiments where relativistically intense waves are routinely excited.

  15. The response of plasma density to breaking inertial gravity wave in the lower regions of ionosphere

    SciTech Connect (OSTI)

    Tang, Wenbo Mahalov, Alex

    2014-04-15

    We present a three-dimensional numerical study for the E and lower F region ionosphere coupled with the neutral atmosphere dynamics. This model is developed based on a previous ionospheric model that examines the transport patterns of plasma density given a prescribed neutral atmospheric flow. Inclusion of neutral dynamics in the model allows us to examine the charge-neutral interactions over the full evolution cycle of an inertial gravity wave when the background flow spins up from rest, saturates and eventually breaks. Using Lagrangian analyses, we show the mixing patterns of the ionospheric responses and the formation of ionospheric layers. The corresponding plasma density in this flow develops complex wave structures and small-scale patches during the gravity wave breaking event.

  16. RADIAL DEPENDENCE OF THE FREQUENCY BREAK BETWEEN FLUID AND KINETIC SCALES IN THE SOLAR WIND FLUCTUATIONS

    SciTech Connect (OSTI)

    Bruno, R.; Trenchi, L.

    2014-06-01

    We investigate the radial dependence of the spectral break separating the inertial from the dissipation range in power density spectra of interplanetary magnetic field fluctuations, between 0.42 and 5.3 AU, during radial alignments between MESSENGER and WIND for the inner heliosphere and between WIND and ULYSSES for the outer heliosphere. We found that the spectral break moves to higher and higher frequencies as the heliocentric distance decreases. The radial dependence of the corresponding wavenumber is of the kind κ {sub b} ∼ R {sup –1.08}, in good agreement with that of the wavenumber derived from the linear resonance condition for proton cyclotron damping. These results support conclusions from previous studies which suggest that a cyclotron-resonant dissipation mechanism must participate in the spectral cascade together with other possible kinetic noncyclotron-resonant mechanisms.

  17. Vacuum Bellows, Vacuum Piping, Cryogenic Break, and Copper Joint Failure Rate Estimates for ITER Design Use

    SciTech Connect (OSTI)

    L. C. Cadwallader

    2010-06-01

    The ITER international project design teams are working to produce an engineering design in preparation for construction of the International Thermonuclear Experimental Reactor (ITER) tokamak. During the course of this work, questions have arisen in regard to safety barriers and equipment reliability as important facets of system design. The vacuum system designers have asked several questions about the reliability of vacuum bellows and vacuum piping. The vessel design team has asked about the reliability of electrical breaks and copper-copper joints used in cryogenic piping. Research into operating experiences of similar equipment has been performed to determine representative failure rates for these components. The following chapters give the research results and the findings for vacuum system bellows, power plant stainless steel piping (amended to represent vacuum system piping), cryogenic system electrical insulating breaks, and copper joints.

  18. Breaking Down the Mechanisms of Biomass Deconstruction | U.S. DOE Office of

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

    Science (SC) Breaking Down the Mechanisms of Biomass Deconstruction Biological and Environmental Research (BER) BER Home About Research Facilities Science Highlights Searchable Archive of BER Highlights External link Benefits of BER Funding Opportunities Biological & Environmental Research Advisory Committee (BERAC) Community Resources Contact Information Biological and Environmental Research U.S. Department of Energy SC-23/Germantown Building 1000 Independence Ave., SW Washington, DC

  19. Cynthia Phillips, ground-breaking expert in plasma waves &amp; Princeton

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

    graduate school lecturer, dies after long illness | Princeton Plasma Physics Lab Cynthia Phillips, ground-breaking expert in plasma waves & Princeton graduate school lecturer, dies after long illness By Jeanne Jackson DeVoe September 4, 2015 Tweet Widget Google Plus One Share on Facebook Cynthia Philips (Photo by Elle Starkman ) Cynthia Philips Cynthia K. Phillips, a physicist at PPPL for 32 years and a former lecturer in Princeton's graduate program in plasma physics, died on Sept. 1

  20. Largest Federally Owned Wind Farm Breaks Ground at U.S. Weapons Facility |

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

    Y-12 National Security Complex Largest Federally Owned ... Largest Federally Owned Wind Farm Breaks Ground at U.S. Weapons Facility Posted: August 13, 2013 - 12:01pm WASHINGTON - Building on President Obama's Climate Action Plan, which calls for steady, responsible steps to reduce carbon pollution, the Energy Department today broke ground on the nation's largest federally owned wind project at the Pantex Plant in Amarillo, Texas. Once completed, this five-turbine 11.5 megawatt project will

  1. 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 ...

  2. 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...

  3. Simulation of a main steam line break with steam generator tube rupture using trace

    SciTech Connect (OSTI)

    Gallardo, S.; Querol, A.; Verdu, G.

    2012-07-01

    A simulation of the OECD/NEA ROSA-2 Project Test 5 was made with the thermal-hydraulic code TRACE5. Test 5 performed in the Large Scale Test Facility (LSTF) reproduced a Main Steam Line Break (MSLB) with a Steam Generator Tube Rupture (SGTR) in a Pressurized Water Reactor (PWR). The result of these simultaneous breaks is a depressurization in the secondary and primary system in loop B because both systems are connected through the SGTR. Good approximation was obtained between TRACE5 results and experimental data. TRACE5 reproduces qualitatively the phenomena that occur in this transient: primary pressure falls after the break, stagnation of the pressure after the opening of the relief valve of the intact steam generator, the pressure falls after the two openings of the PORV and the recovery of the liquid level in the pressurizer after each closure of the PORV. Furthermore, a sensitivity analysis has been performed to know the effect of varying the High Pressure Injection (HPI) flow rate in both loops on the system pressures evolution. (authors)

  4. 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.

  5. 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.

  6. Human Genome Research: Decoding DNA

    Office of Scientific and Technical Information (OSTI)

    Decoding DNA Resources with Additional Information Charles DeLisi As head of DOE's Office of Health and Environmental Research, Charles DeLisi played a pivotal role in proposing and initiating the Human Genome Program in 1986. The U.S. Department of Energy (DOE) has historically been active in supporting human genome research. On September 10, 2003, Secretary of Energy Spencer Abraham presented the Secretary's Gold Award to Aristides Patrinos and Francis Collins for their leadership of the

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. DNA

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

    Yes, the research was brilliant, and if we're lucky, it will produce innovations in biology, medicine, biotechnology and agriculture. It could save lives, and it happened because ...

  13. Introduction of Break-Out Session 2 of the 2011 International PV Module Quality Assurance Forum(Presentation)

    SciTech Connect (OSTI)

    Wohlgemuth, J.; Kurtz, S.; Sample, T.; Yamamichi, M.

    2011-07-01

    This presentation outlines the goals and specific tasks of break-out session 2 of the 2011 International PV Module Quality Assurance Forum, along with a review of accelerated stress tests used for photovoltaics (PV).

  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. Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures Citation Details In-Document Search Title: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures The RecA family of ATPases mediates homologous recombination, a reaction essential for maintaining genomic integrity and for generating genetic diversity. RecA, ATP and single-stranded DNA (ssDNA) form a helical

  16. 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.

  17. Break-Even Cost for Residential Solar Water Heating in the United States: Key Drivers and Sensitivities

    SciTech Connect (OSTI)

    Cassard, H.; Denholm, P.; Ong, S.

    2011-02-01

    This paper examines the break-even cost for residential rooftop solar water heating (SWH) technology, defined as the point where the cost of the energy saved with a SWH system equals the cost of a conventional heating fuel purchased from the grid (either electricity or natural gas). We examine the break-even cost for the largest 1,000 electric and natural gas utilities serving residential customers in the United States as of 2008. Currently, the break-even cost of SWH in the United States varies by more than a factor of five for both electricity and natural gas, despite a much smaller variation in the amount of energy saved by the systems (a factor of approximately one and a half). The break-even price for natural gas is lower than that for electricity due to a lower fuel cost. We also consider the relationship between SWH price and solar fraction and examine the key drivers behind break-even costs. Overall, the key drivers of the break-even cost of SWH are a combination of fuel price, local incentives, and technical factors including the solar resource location, system size, and hot water draw.

  18. 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.

  19. Sphericity and symmetry breaking in the formation of Frank–Kasper phases from one component materials

    SciTech Connect (OSTI)

    Lee, Sangwoo; Leighton, Chris; Bates, Frank S.

    2014-11-05

    Frank–Kasper phases are tetrahedrally packed structures occurring in numerous materials, from elements to intermetallics to self-assembled soft materials. They exhibit complex manifolds of Wigner–Seitz cells with many-faceted polyhedra, forming an important bridge between the simple close-packed periodic and quasiperiodic crystals. The recent discovery of the Frank–Kasper σ-phase in diblock and tetrablock polymers stimulated the experiments reported here on a poly(isoprene-b-lactide) diblock copolymer melt. Thus, analysis of small-angle X-ray scattering and mechanical spectroscopy exposes an undiscovered competition between the tendency to form self-assembled particles with spherical symmetry, and the necessity to fill space at uniform density within the framework imposed by the lattice. We thus deduce surprising analogies between the symmetry breaking at the body-centered cubic phase to σ-phase transition in diblock copolymers, mediated by exchange of mass, and the symmetry breaking in certain metals and alloys (such as the elements Mn and U), mediated by exchange of charge. Similar connections are made between the role of sphericity in real space for polymer systems, and the role of sphericity in reciprocal space for metallic systems such as intermetallic compounds and alloys. These findings establish new links between disparate materials classes, provide opportunities to improve the understanding of complex crystallization by building on synergies between hard and soft matter, and, perhaps most significantly, challenge the view that the symmetry breaking required to form reduced symmetry structures (possibly even quasiperiodic crystals) requires particles with multiple predetermined shapes and/or sizes.

  20. Sphericity and symmetry breaking in the formation of Frank–Kasper phases from one component materials

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

    Lee, Sangwoo; Leighton, Chris; Bates, Frank S.

    2014-11-05

    Frank–Kasper phases are tetrahedrally packed structures occurring in numerous materials, from elements to intermetallics to self-assembled soft materials. They exhibit complex manifolds of Wigner–Seitz cells with many-faceted polyhedra, forming an important bridge between the simple close-packed periodic and quasiperiodic crystals. The recent discovery of the Frank–Kasper σ-phase in diblock and tetrablock polymers stimulated the experiments reported here on a poly(isoprene-b-lactide) diblock copolymer melt. Thus, analysis of small-angle X-ray scattering and mechanical spectroscopy exposes an undiscovered competition between the tendency to form self-assembled particles with spherical symmetry, and the necessity to fill space at uniform density within the framework imposed bymore » the lattice. We thus deduce surprising analogies between the symmetry breaking at the body-centered cubic phase to σ-phase transition in diblock copolymers, mediated by exchange of mass, and the symmetry breaking in certain metals and alloys (such as the elements Mn and U), mediated by exchange of charge. Similar connections are made between the role of sphericity in real space for polymer systems, and the role of sphericity in reciprocal space for metallic systems such as intermetallic compounds and alloys. These findings establish new links between disparate materials classes, provide opportunities to improve the understanding of complex crystallization by building on synergies between hard and soft matter, and, perhaps most significantly, challenge the view that the symmetry breaking required to form reduced symmetry structures (possibly even quasiperiodic crystals) requires particles with multiple predetermined shapes and/or sizes.« less

  1. Large Break LOCA Accident Management Strategies for Accidents With Large Containment Leaks

    SciTech Connect (OSTI)

    Sdouz, Gert

    2006-07-01

    The goal of this work is the investigation of the influence of different accident management strategies on the thermal-hydraulics in the containment during a Large Break Loss of Coolant Accident with a large containment leak from the beginning of the accident. The increasing relevance of terrorism suggests a closer look at this kind of severe accidents. Normally the course of severe accidents and their associated phenomena are investigated with the assumption of an intact containment from the beginning of the accident. This intact containment has the ability to retain a large part of the radioactive inventory. In these cases there is only a release via a very small leakage due to the un-tightness of the containment up to cavity bottom melt through. This paper represents the last part of a comprehensive study on the influence of accident management strategies on the source term of VVER-1000 reactors. Basically two different accident sequences were investigated: the 'Station Blackout'- sequence and the 'Large Break LOCA'. In a first step the source term calculations were performed assuming an intact containment from the beginning of the accident and no accident management action. In a further step the influence of different accident management strategies was studied. The last part of the project was a repetition of the calculations with the assumption of a damaged containment from the beginning of the accident. This paper concentrates on the last step in the case of a Large Break LOCA. To be able to compare the results with calculations performed years ago the calculations were performed using the Source Term Code Package (STCP), hydrogen explosions are not considered. In this study four different scenarios have been investigated. The main parameter was the switch on time of the spray systems. One of the results is the influence of different accident management strategies on the source term. In the comparison with the sequence with intact containment it was demonstrated that the accident management measures have quite lower consequences. In addition it was shown that in the case of a 'Large Break LOCA'-sequence the intact containment retains the nuclides up to a factor of 20 000. This is much more than in the case of a 'Station Blackout'-sequence. Within the frame of the study 17 source terms have been generated to evaluate in detail accident management strategies for VVER-1000 reactors. (authors)0.

  2. Technology Solutions Case Study: Capillary Break Beneath a Slab: Polyethylene Sheeting over Aggregate, Southwestern Pennsylvania

    SciTech Connect (OSTI)

    2014-07-01

    In this project, Building America team IBACOS worked with a builder of single- and multifamily homes in southwestern Pennsylvania (climate zone 5) to understand its methods of successfully using polyethylene sheeting over aggregate as a capillary break beneath the slab in new construction. This builder’s homes vary in terms of whether they have crawlspaces or basements. However, in both cases, the strategy protects the home from water intrusion via capillary action (e.g., water wicking into cracks and spaces in the slab), thereby helping to preserve the durability of the home.

  3. TACIS 91: Application of leak-before-break concept in VVER 440-230

    SciTech Connect (OSTI)

    Bartholome, G.; Faidy, C.; Franco, C.

    1997-04-01

    The applicability of the leak-before-break (LBB) concept for primary piping in the first generation of WWER type plants in Russia is investigated. The procedures for LBB behavior used in France and Germany are applied, and the evaluation is discussed within the framework of the European Technical Assistance for the Community of Independent States (TACIS) project. Emphasis is placed on experimental validation of national and international engineering practice for evaluating and optimizing existing installations. Design criteria of WWER plants are compared to western standard design.

  4. Performance improvements of symmetry-breaking reflector structures in nonimaging devices

    DOE Patents [OSTI]

    Winston, Roland

    2004-01-13

    A structure and method for providing a broken symmetry reflector structure for a solar concentrator device. The component of the optical direction vector along the symmetry axis is conserved for all rays propagated through a translationally symmetric optical device. This quantity, referred to as the translational skew invariant, is conserved in rotationally symmetric optical systems. Performance limits for translationally symmetric nonimaging optical devices are derived from the distributions of the translational skew invariant for the optical source and for the target to which flux is to be transferred. A numerically optimized non-tracking solar concentrator utilizing symmetry-breaking reflector structures can overcome the performance limits associated with translational symmetry.

  5. Charge independence, charge symmetry breaking in the S-wave nucleon-nucleon interaction, and renormalization

    SciTech Connect (OSTI)

    Alvaro Calle Cordon,Manuel Pavon Valderrama,Enrique Ruiz Arriola

    2012-02-01

    We study the interplay between charge symmetry breaking and renormalization in the NN system for S-waves. We find a set of universality relations which disentangle explicitly the known long distance dynamics from low energy parameters and extend them to the Coulomb case. We analyze within such an approach the One-Boson-Exchange potential and the theoretical conditions which allow to relate the proton-neutron, proton-proton and neutron-neutron scattering observables without the introduction of extra new parameters and providing good phenomenological success.

  6. A probabilistic method for leak-before-break analysis of CANDU reactor pressure tubes

    SciTech Connect (OSTI)

    Puls, M.P.; Wilkins, B.J.S.; Rigby, G.L.

    1997-04-01

    A probabilistic code for the prediction of the cumulative probability of pressure tube ruptures in CANDU type reactors is described. Ruptures are assumed to result from the axial growth by delayed hydride cracking. The BLOOM code models the major phenomena that affect crack length and critical crack length during the reactor sequence of events following the first indications of leakage. BLOOM can be used to develop unit-specific estimates of the actual probability of pressure rupture in operating CANDU reactors and supplement the existing leak before break analysis.

  7. 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.

  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. 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

  11. 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

  12. 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

  13. 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

  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 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

  15. 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.

  16. 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

  17. Garcinol, a Histone Acetyltransferase Inhibitor, Radiosensitizes Cancer Cells by Inhibiting Non-Homologous End Joining

    SciTech Connect (OSTI)

    Oike, Takahiro; Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo; Department of Radiation Oncology, Gunma University Graduate School of Medicine, Maebashi, Gunma ; Ogiwara, Hideaki; Torikai, Kohta; Nakano, Takashi; Yokota, Jun; Kohno, Takashi

    2012-11-01

    Purpose: Non-homologous end joining (NHEJ), a major pathway used to repair DNA double-strand breaks (DSBs) generated by ionizing radiation (IR), requires chromatin remodeling at DSB sites through the acetylation of histones by histone acetyltransferases (HATs). However, the effect of compounds with HAT inhibitory activities on the DNA damage response (DDR), including the NHEJ and cell cycle checkpoint, as well as on the radiosensitivity of cancer cells, remains largely unclear. Here, we investigated whether garcinol, a HAT inhibitor found in the rinds of Garcinia indica fruit (called mangosteens), has effects on DDR, and whether it can be used for radiosensitization. Methods and Materials: The following assays were used to examine the effect of garcinol on the inhibition of DSB repair, including the following: a conventional neutral comet assay; a cell-based assay recently developed by us, in which NHEJ repair of DSBs on chromosomal DNA was evaluated; the micrococcal nuclease sensitivity assay; and immunoblotting for autophosphorylation of DNA-dependent protein kinase catalytic subunit (DNA-PKcs). We assessed the effect of garcinol on the cell cycle checkpoint after IR treatment by analyzing the phosphorylation levels of checkpoint kinases CHK1 and CHK2 and histone H3, and by cell cycle profile analysis using flow cytometry. The radiosensitizing effect of garcinol was assessed by a clonogenic survival assay, whereas its effects on apoptosis and senescence were examined by annexin V and senescence-associated {beta}-galactosidase (SA-{beta}-Gal) staining, respectively. Results: We found that garcinol inhibits DSB repair, including NHEJ, without affecting cell cycle checkpoint. Garcinol radiosensitized A549 lung and HeLa cervical carcinoma cells with dose enhancement ratios (at 10% surviving fraction) of 1.6 and 1.5, respectively. Cellular senescence induced by IR was enhanced by garcinol. Conclusion: These results suggest that garcinol is a radiosensitizer that inhibits NHEJ and facilitates senescence without impairing activation of the cell cycle checkpoint.

  18. Mode of ATM-dependent suppression of chromosome translocation

    SciTech Connect (OSTI)

    Yamauchi, Motohiro; Suzuki, Keiji; Oka, Yasuyoshi; Suzuki, Masatoshi; Kondo, Hisayoshi; Yamashita, Shunichi

    2011-12-09

    Highlights: Black-Right-Pointing-Pointer We addressed how ATM suppresses frequency of chromosome translocation. Black-Right-Pointing-Pointer We found ATM/p53-dependent G1 checkpoint suppresses translocation frequency. Black-Right-Pointing-Pointer We found ATM and DNA-PKcs function in a common pathway to suppress translocation. -- Abstract: It is well documented that deficiency in ataxia telangiectasia mutated (ATM) protein leads to elevated frequency of chromosome translocation, however, it remains poorly understood how ATM suppresses translocation frequency. In the present study, we addressed the mechanism of ATM-dependent suppression of translocation frequency. To know frequency of translocation events in a whole genome at once, we performed centromere/telomere FISH and scored dicentric chromosomes, because dicentric and translocation occur with equal frequency and by identical mechanism. By centromere/telomere FISH analysis, we confirmed that chemical inhibition or RNAi-mediated knockdown of ATM causes 2 to 2.5-fold increase in dicentric frequency at first mitosis after 2 Gy of gamma-irradiation in G0/G1. The FISH analysis revealed that ATM/p53-dependent G1 checkpoint suppresses dicentric frequency, since RNAi-mediated knockdown of p53 elevated dicentric frequency by 1.5-fold. We found ATM also suppresses dicentric occurrence independently of its checkpoint role, as ATM inhibitor showed additional effect on dicentric frequency in the context of p53 depletion and Chk1/2 inactivation. Epistasis analysis using chemical inhibitors revealed that ATM kinase functions in the same pathway that requires kinase activity of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to suppress dicentric frequency. From the results in the present study, we conclude that ATM minimizes translocation frequency through its commitment to G1 checkpoint and DNA double-strand break repair pathway that requires kinase activity of DNA-PKcs.

  19. 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...

  20. the Adaptive Response, Genetic Haplo-Insufficiency and Genomic Instability

    SciTech Connect (OSTI)

    Geard, Charles R.

    2014-12-12

    The linear no-threshold (LNT) hypothesis is the driving force in the establishment of radiation protection standards. However, the scientific basis for linearity has been brought into question, particularly due to the concerns about induced radiation resistance as it pertains to oxidative stress. Specifically, we investigated the observation that tumor hypoxia is associated with malignant progression, increased metastases, chemo- and radioresistance and poor prognosis. Experiments were conducted with non-malignant 3T3/NIH cells and normal human lung fibroblasts (NHLF) that were subjected to ?-irradiation under the levels of oxygen resembling those in growing tumors, and related our data to the concentrations of dissolved oxygen (DO), which is a better indicator of the amounts of residual oxygen inside the cells cultured in the hypoxic or anoxic atmosphere. We found that at DO levels about 0.5 mg/L cells subjected to both short-term (17 hours) and prolonged (48-72 hours) hypoxia continued to proliferate, and that apoptotic events were decreased at the early hours of hypoxic treatment. We showed that the short-term hypoxia up-regulated p53-binding protein 1 (53BP1) and resulted in facilitated 53BP1 nuclear foci formation and disappearance, thus indicating the higher efficiency of DNA double strand breaks repair processes. The latter was confirmed by the lower micronuclei incidence in irradiated hypoxic cells.

  1. Subcellular Spatial Correlation of Particle Traversal and Biological Response in Clinical Ion Beams

    SciTech Connect (OSTI)

    Niklas, Martin; Abdollahi, Amir; Akselrod, Mark S.; Debus, Jrgen; Jkel, Oliver; and others

    2013-12-01

    Purpose: To report on the spatial correlation of physical track information (fluorescent nuclear track detectors, FNTDs) and cellular DNA damage response by using a novel hybrid detector (Cell-Fit-HD). Methods and Materials: The FNTDs were coated with a monolayer of human non-small cell lung carcinoma (A549) cells and irradiated with carbon ions (270.55 MeV u{sup ?1}, rising flank of the Bragg peak). Phosphorylated histone variant H2AX accumulating at the irradiation-induced double-strand break site was labeled (RIF). The position and direction of ion tracks in the FNTD were registered with the location of the RIF sequence as an ion track surrogate in the cell layer. Results: All RIF sequences could be related to their corresponding ion tracks, with mean deviations of 1.09 ?m and ?1.72 ?m in position and of 2.38 in slope. The mean perpendicular between ion track and RIF sequence was 1.58 ?m. The mean spacing of neighboring RIFs exhibited a regular rather than random spacing. Conclusions: Cell-Fit-HD allows for unambiguous spatial correlation studies of cell damage with respect to the intracellular ion traversal under therapeutic beam conditions.

  2. A LYMAN BREAK GALAXY IN THE EPOCH OF REIONIZATION FROM HUBBLE SPACE TELESCOPE GRISM SPECTROSCOPY

    SciTech Connect (OSTI)

    Rhoads, James E.; Malhotra, Sangeeta; Cohen, Seth; Zheng Zhenya; Stern, Daniel; Dickinson, Mark; Pirzkal, Norbert; Grogin, Norman; Koekemoer, Anton; Peth, Michael A.; Spinrad, Hyron; Reddy, Naveen; Hathi, Nimish; Budavari, Tamas; Ferreras, Ignacio; Gardner, Jonathan P.; Gronwall, Caryl; Haiman, Zoltan; Kuemmel, Martin; Meurer, Gerhardt; and others

    2013-08-10

    We present observations of a luminous galaxy at z = 6.573-the end of the reionization epoch-which has been spectroscopically confirmed twice. The first spectroscopic confirmation comes from slitless Hubble Space Telescope Advanced Camera for Surveys grism spectra from the PEARS survey (Probing Evolution And Reionization Spectroscopically), which show a dramatic continuum break in the spectrum at rest frame 1216 A. The second confirmation is done with Keck + DEIMOS. The continuum is not clearly detected with ground-based spectra, but high wavelength resolution enables the Ly{alpha} emission line profile to be determined. We compare the line profile to composite line profiles at z = 4.5. The Ly{alpha} line profile shows no signature of a damping wing attenuation, confirming that the intergalactic gas is ionized at z = 6.57. Spectra of Lyman breaks at yet higher redshifts will be possible using comparably deep observations with IR-sensitive grisms, even at redshifts where Ly{alpha} is too attenuated by the neutral intergalactic medium to be detectable using traditional spectroscopy from the ground.

  3. WIMP and SIMP dark matter from the spontaneous breaking of a global group

    SciTech Connect (OSTI)

    Bernal, Nicolás; Garcia-Cely, Camilo; Rosenfeld, Rogério

    2015-04-09

    We propose and study a scalar extension of the Standard Model which respects a ℤ{sub 3} symmetry remnant of the spontaneous breaking of a global U(1){sub DM} symmetry. Consequently, this model has a natural dark matter candidate and a Goldstone boson in the physical spectrum. In addition, the Higgs boson properties are changed with respect to the Standard Model due to the mixing with a new particle. We explore regions in the parameter space taking into account bounds from the measured Higgs properties, dark matter direct detection as well as measurements of the effective number of neutrino species before recombination. The dark matter relic density is determined by three classes of processes: the usual self-annihilation, semi-annihilation and purely dark matter 3→2 processes. The latter has been subject of recent interest leading to the so-called ‘Strongly Interacting Massive Particle’ (SIMP) scenario. We show under which conditions our model can lead to a concrete realization of such scenario and study the possibility that the dark matter self-interactions could address the small scale structure problems. In particular, we find that in order for the SIMP scenario to work, the dark matter mass must be in the range 7−115 MeV, with the global symmetry energy breaking scale in the TeV range.

  4. Transition pathways in a many-body system: Application to hydrogen-bond breaking in water

    SciTech Connect (OSTI)

    Csajka, F.S.; Chandler, D.

    1998-07-01

    We apply a stochastic method introduced by Dellago {ital et al.} [J. Chem. Phys. {bold 108}, 1964 (1998)] to sample transition paths in high-dimensional systems. The method connects two endpoint regions (for example a reactant and a product region) by a set of space-time paths. This approach is an importance sampling for rare events that does not require prior knowledge of the location of dynamical bottlenecks. Transition paths are generated with a weight corresponding to a chain of Metropolis Monte Carlo steps. We derive Monte Carlo algorithms and apply the technique to the dynamics of hydrogen-bond breaking in liquid water. We obtain averages in a transition path ensemble for the structure and energy along the trajectory. While characterized by a rate constant, hydrogen-bond breaking in water occurs frequently enough to be studied by standard methods. The process therefore provides a useful test of path sampling methods. The comparison between path sampling and standard Monte Carlo demonstrate the feasibility of transition path sampling for a many-body system with a rough potential energy surface. {copyright} {ital 1998 American Institute of Physics.}

  5. Leak before break evaluation for main steam piping system made of SA106 Gr.C

    SciTech Connect (OSTI)

    Yang, Kyoung Mo; Jee, Kye Kwang; Pyo, Chang Ryul; Ra, In Sik

    1997-04-01

    The basis of the leak before break (LBB) concept is to demonstrate that piping will leak significantly before a double ended guillotine break (DEGB) occurs. This is demonstrated by quantifying and evaluating the leak process and prescribing safe shutdown of the plant on the basis of the monitored leak rate. The application of LBB for power plant design has reduced plant cost while improving plant integrity. Several evaluations employing LBB analysis on system piping based on DEGB design have been completed. However, the application of LBB on main steam (MS) piping, which is LBB applicable piping, has not been performed due to several uncertainties associated with occurrence of steam hammer and dynamic strain aging (DSA). The objective of this paper is to demonstrate the applicability of the LBB design concept to main steam lines manufactured with SA106 Gr.C carbon steel. Based on the material properties, including fracture toughness and tensile properties obtained from the comprehensive material tests for base and weld metals, a parametric study was performed as described in this paper. The PICEP code was used to determine leak size crack (LSC) and the FLET code was used to perform the stability assessment of MS piping. The effects of material properties obtained from tests were evaluated to determine the LBB applicability for the MS piping. It can be shown from this parametric study that the MS piping has a high possibility of design using LBB analysis.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  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. 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.

  14. 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.

  15. 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...

  16. On the breaking of a plasma wave in a thermal plasma. I. The structure of the density singularity

    SciTech Connect (OSTI)

    Bulanov, Sergei V.; Esirkepov, Timur Zh.; Kando, Masaki; Koga, James K.; Pirozhkov, Alexander S.; Nakamura, Tatsufumi; Bulanov, Stepan S.; Schroeder, Carl B.; Esarey, Eric; Califano, Francesco; Pegoraro, Francesco

    2012-11-15

    The structure of the singularity that is formed in a relativistically large amplitude plasma wave close to the wave breaking limit is found by using a simple waterbag electron distribution function. The electron density distribution in the breaking wave has a typical 'peakon' form. The maximum value of the electric field in a thermal breaking plasma is obtained and compared to the cold plasma limit. The results of computer simulations for different initial electron distribution functions are in agreement with the theoretical conclusions. The after-wavebreak regime is then examined, and a semi-analytical model of the density evolution is constructed. Finally the results of two dimensional particle in cell simulations for different initial electron distribution functions are compared, and the role of thermal effects in enhancing particle injection is noted.

  17. SPIN-PRECESSION: BREAKING THE BLACK HOLE-NEUTRON STAR DEGENERACY

    SciTech Connect (OSTI)

    Chatziioannou, Katerina; Cornish, Neil; Klein, Antoine; Yunes, Nicols

    2015-01-01

    Mergers of compact stellar remnants are prime targets for the LIGO/Virgo gravitational wave detectors. The gravitational wave signals from these merger events can be used to study the mass and spin distribution of stellar remnants, and provide information about black hole horizons and the material properties of neutron stars. However, it has been suggested that degeneracies in the way that the star's mass and spin are imprinted in the waveforms may make it impossible to distinguish between black holes and neutron stars. Here we show that the precession of the orbital plane due to spin-orbit coupling breaks the mass-spin degeneracy, and allows us to distinguish between standard neutron stars and alternative possibilities, such as black holes or exotic neutron stars with large masses and spins.

  18. Spatio-temporal evolution and breaking of double layers: A description using Lagrangian hydrodynamics

    SciTech Connect (OSTI)

    Kaw, Predhiman; Sengupta, Sudip; Singh Verma, Prabal [Institute for Plasma Research, Bhat, Gandhinagar 382 428 (India)

    2012-10-15

    The nonlinear development and collapse (breaking) of double layers in the long scale length limit is well described by equations for the cold ion fluid with quasineutrality. It is shown that electron dynamics is responsible for giving an 'equation of state' with negative ratio of specific heats to this fluid. Introducing a transformation for the density variable, the governing equation for the transformed quantity in terms of Lagrange variables turns out exactly to be a linear partial differential equation. This equation has been analyzed in various limits of interest. Nonlinear development of double layers with a sinusoidal initial disturbance and collapse of double layers with an initial perturbation in the form of a density void are analytically investigated.

  19. Specialist meeting on leak before break in reactor piping and vessels

    SciTech Connect (OSTI)

    Bartholome, G.; Bazant, E.; Wellein, R.

    1997-04-01

    A series of research projects sponsored by the Federal Minister for Education, Science, Research and Technology, Bonn are summarized and compared to utility, manufacturer, and vendor tests. The purpose of the evaluation was to experimentally verify Leak-before-Break behavior, confirm the postulation of fracture preclusion for piping (straight pipe, bends and branches), and quantify the safety margin against massive failure. The results are applicable to safety assessment of ferritic and austenitic piping in primary and secondary nuclear power plant circuits. Moreover, because of the wide range of the test parameters, they are also important for the design and assessment of piping in other technical plant. The test results provide justification for ruling out catastrophic fractures, even on pipes of dimensions corresponding to those of a main coolant pipe of a pressurized water reactor plant on the basis of a mechanical deterministic safety analysis in correspondence with the Basis Safety Concept (Principle of Fracture Exclusion).

  20. Time-reversal symmetry breaking and the field theory of quantum chaos

    SciTech Connect (OSTI)

    Simons, B.D. [Cavendish Laboratory, Madingley Road, Cambridge, CB3 0HE (United Kingdom)] [Cavendish Laboratory, Madingley Road, Cambridge, CB3 0HE (United Kingdom); Agam, O. [NEC Research Institute, 4 Independence Way, Princeton, New Jersey 08540 (United States)] [NEC Research Institute, 4 Independence Way, Princeton, New Jersey 08540 (United States); Andreev, A.V. [Institute for Theoretical Physics, University of California, Santa Barbara, California 93106 (United States)] [Institute for Theoretical Physics, University of California, Santa Barbara, California 93106 (United States)

    1997-04-01

    Recent studies have shown that the quantum statistical properties of systems which are chaotic in their classical limit can be expressed in terms of an effective field theory. Within this description, spectral properties are determined by low energy relaxation modes of the classical evolution operator. It is in the interaction of these modes that quantum interference effects are encoded. In this paper we review this general approach and discuss how the theory is modified to account for time-reversal symmetry breaking. To keep our discussion general, we will also briefly describe how the theory is modified by the presence of an additional discrete symmetry such as inversion. Throughout, parallels are drawn between quantum chaotic systems and the properties of weakly disordered conductors. {copyright} {ital 1997 American Institute of Physics.}

  1. Fuel-rod response during the large-break LOCA Test LOC-6. [PWR

    SciTech Connect (OSTI)

    Vinjamuri, K.; Cook, B.A.; Hobbins, R.R.

    1981-01-01

    The large break Loss of Coolant Accident (LOCA) Test LOC-6 was conducted in the Power Burst Facility (PBF) at the Idaho National Engineering Laboratory by EG and G Idaho, Inc. The objectives of the PBF LOCA tests are to obtain in-pile cladding ballooning data under blowdown and reflood conditions and assess how well out-of-pile ballooning data represent in-pile fuel rod behavior. The primary objective of the LOC-6 test was to determine the effects of internal rod pressures and prior irradiation on the deformation behavior of fuel rods that reached cladding temperatures high in the alpha phase of zircaloy. Test LOC-6 was conducted with four rods of PWR 15 x 15 design with the exception of fuel stack length (89 cm) and enrichment (12.5 W% /sup 235/U). Each rod was surrounded by an individual flow shroud.

  2. Practical applications of the R6 leak-before-break procedure

    SciTech Connect (OSTI)

    Bouchard, P.J.

    1997-04-01

    A forthcoming revision to the R6 Leak-before-Break Assessment Procedure is briefly described. Practical application of the LbB concepts to safety-critical nuclear plant is illustrated by examples covering both low temperature and high temperature (>450{degrees}C) operating regimes. The examples highlight a number of issues which can make the development of a satisfactory LbB case problematic: for example, coping with highly loaded components, methodology assumptions and the definition of margins, the effect of crack closure owing to weld residual stresses, complex thermal stress fields or primary bending fields, the treatment of locally high stresses at crack intersections with free surfaces, the choice of local limit load solution when predicting ligament breakthrough, and the scope of calculations required to support even a simplified LbB case for high temperature steam pipe-work systems.

  3. Isospin-symmetry-breaking effects in A∼70 nuclei within beyond-mean-field approach

    SciTech Connect (OSTI)

    Petrovici, A.; Andrei, O.

    2015-02-24

    Particular isospin-symmetry-breaking probes including Coulomb energy differences (CED), mirror energy differences (MED), and triplet energy differences (TED) manifest anomalies in the A∼70 isovector triplets of nuclei. The structure of proton-rich nuclei in the A∼70 mass region suggests shape coexistence and competition between pairing correlations in different channels. Recent results concerning the interplay between isospin-mixing and shape-coexistence effects on exotic phenomena in A∼70 nuclei obtained within the beyond-mean-field complex Excited Vampir variational model with symmetry projection before variation using a realistic effective interaction in a relatively large model space are presented. Excited Vampir predictions concerning the Gamow-Teller β decay to the odd-odd N=Z {sup 66}As and {sup 70}Br nuclei correlated with the pair structure analysis in the T=1 and T=0 channel of the involved wave functions are discussed.

  4. Break-up of Pt catalyst surfaces by high CO coverage

    SciTech Connect (OSTI)

    Tao, Feng; Dag, Sefa; Wang, Lin-Wang; Liu, Zhi; Butcher, Derek; Bluhm, Henrik; Salmeron, Miquel; Somorjai, Gabor

    2009-09-16

    Stepped Platinum surfaces were found to undergo extensive and reversible restructuring when exposed to CO at pressures above 0.1 Torr. This radically new and previously unknown restructuring phenomenon, has important implications for Pt based catalytic reactions. Novel Scanning Tunneling Microscopy and Photoelectron Spectroscopy techniques operating under gaseous environments near ambient pressure and temperature revealed that as the CO surface coverage approaches 100percent, the originally flat terraces of stepped Pt crystals break up into nanometer size clusters. At room temperature the crystal surface reverts to its initial flat morphology after pumping away the gas phase CO. Density Functional Theory energy calculations provide a rationale for the observations whereby the creation of increased concentrations of low coordination Pt sites at the edges of the formed nanoclusters relieves the strong CO-CO repulsion in the highly compressed adsorbate film.

  5. 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

  6. The behavior of ANGRA 2 nuclear power plant core for a small break LOCA simulated with RELAP5 code

    SciTech Connect (OSTI)

    Sabundjian, Gaiane; Andrade, Delvonei A.; Belchior, Antonio Jr.; Silva Rocha, Marcelo da; Conti, Thadeu N.; Torres, Walmir M.; Macedo, Luiz A.; Umbehaun, Pedro E.; Mesquita, Roberto N.; Masotti, Paulo H. F.; Souza Lima, Ana Cecilia de

    2013-05-06

    This work discusses the behavior of Angra 2 nuclear power plant core, for a postulate Loss of Coolant Accident (LOCA) in the primary circuit for Small Break Loss Of Coolant Accident (SBLOCA). A pipe break of the hot leg Emergency Core Cooling System (ECCS) was simulated with RELAP 5 code. The considered rupture area is 380 cm{sup 2}, which represents 100% of the ECCS pipe flow area. Results showed that the cooling is enough to guarantee the integrity of the reactor core.

  7. 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...

  8. 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...

  9. 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...

  10. 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, ...

  11. IN VITRO MUTAGENIC AND DNA AND CHROMOSOMAL DAMAGE ACTIVITY BY...

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

    IN VITRO MUTAGENIC AND DNA AND CHROMOSOMAL DAMAGE ACTIVITY BY SURFACTANT DISPERSION OR SOLVENT EXTRACT OF A REFERENCE DIESEL EXHAUST PARTICULATE MATERIAL IN VITRO MUTAGENIC AND DNA ...

  12. 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.

  13. 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.

  14. 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.

  15. 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...

  16. 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.

  17. 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

  18. SREL Reprint #3317

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

    7 First case of ranavirus and associated morbidity and mortality in an eastern mud turtle Kinosternon subrubrum in South Carolina Megan E. Winzeler, Matthew T. Hamilton, Tracey D. Tuberville, and Stacey L. Lance Savannah River Ecology Lab, University of Georgia, Drawer E, Aiken, SC 29802, USA Abstract: Ranaviruses are double-stranded DNA viruses that infect amphibians, fish, and reptiles, causing global epidemics in some amphibian populations. It is important to identify new species that may be

  19. 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 nanoreactor Source: Nature Communications Year: 2013 Volume: 4 Pages: article 2127 ABSTRACT: Date of online publication: Wed, 2013-07-03 Link online: http://dx.doi.org/10.1038/ncomms3127

  20. 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.

  1. 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.

  2. On the non-existence of a sharp cooling break in gamma-ray burst afterglow spectra

    SciTech Connect (OSTI)

    Uhm, Z. Lucas; Zhang, Bing, E-mail: uhm@physics.unlv.edu, E-mail: zhang@physics.unlv.edu [Kavli Institute for Astronomy and Astrophysics, Peking University, Beijing 100871 (China)

    2014-01-01

    Although the widely used analytical afterglow model of gamma-ray bursts (GRBs) predicts a sharp cooling break ? {sub c} in its afterglow spectrum, the GRB observations so far rarely show clear evidence for a cooling break in their spectra or a corresponding temporal break in their light curves. Employing a Lagrangian description of the blast wave, we conduct a sophisticated calculation of the afterglow emission. We precisely follow the cooling history of non-thermal electrons accelerated into each Lagrangian shell. We show that a detailed calculation of afterglow spectra does not in fact give rise to a sharp cooling break at ? {sub c}. Instead, it displays a very mild and smooth transition, which occurs gradually over a few orders of magnitude in energy or frequency. The main source of this slow transition is that different mini shells have different evolutionary histories of the comoving magnetic field strength B, so that deriving the current value of ? {sub c} of each mini shell requires an integration of its cooling rate over the time elapsed since its creation. We present the time evolution of optical and X-ray spectral indices to demonstrate the slow transition of spectral regimes and discuss the implications of our result in interpreting GRB afterglow data.

  3. 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.

  4. Mechanism of homologous recombination from the RecA-ssDNA/dsDNA...

    Office of Scientific and Technical Information (OSTI)

    Subject: 60 APPLIED LIFE SCIENCES; ATP-ASE; ATP; CRYSTAL STRUCTURE; DNA; ESCHERICHIA COLI; FILAMENTS; GENETICS; HYDROLYSIS; INTERFACES; LYSINE; RECOMBINATION; RESIDUES; SAMPLING ...

  5. A lead-before-break strategy for primary heat transport piping of 500 MWe Indian PHWR

    SciTech Connect (OSTI)

    Chattopadhyay, J.; Dutta, B.K.; Kushwaha, H.S.

    1997-04-01

    Leak-Before-Break (LBB) is being used to design the primary heat transport piping system of 500 MWe Indian Pressurized Heavy Water Reactors (IPHWR). The work is categorized in three directions to demonstrate three levels of safety against sudden catastrophic break. Level 1 is inherent in the design procedure of piping system as per ASME Sec.III with a well defined factor of safety. Level 2 consists of fatigue crack growth study of a postulated part-through flaw at the inside surface of pipes. Level 3 is stability analysis of a postulated leakage size flaw under the maximum credible loading condition. Developmental work related to demonstration of level 2 and level 3 confidence is described in this paper. In a case study on fatigue crack growth on PHT straight pipes for level 2, negligible crack growth is predicted for the life of the reactor. For level 3 analysis, the R6 method has been adopted. A database to evaluate SIF of elbows with throughwall flaws under combined internal pressure and bending moment has been generated to provide one of the inputs for R6 method. The methodology of safety assessment of elbow using R6 method has been demonstrated for a typical pump discharge elbow. In this analysis, limit load of the cracked elbow has been determined by carrying out elasto-plastic finite element analysis. The limit load results compared well with those given by Miller. However, it requires further study to give a general form of limit load solution. On the experimental front, a set of small diameter pipe fracture experiments have been carried out at room temperature and 300{degrees}C. Two important observations of the experiments are - appreciable drop in maximum load at 300{degrees}C in case of SS pipes and out-of-plane crack growth in case of CS pipes. Experimental load deflection curves are finally compared with five J-estimation schemes predictions. A material database of PHT piping materials is also being generated for use in LBB analysis.

  6. 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

  7. PT-symmetric sinusoidal optical lattices at the symmetry-breaking threshold

    SciTech Connect (OSTI)

    Graefe, Eva-Maria [Mathematics Department, Imperial College, London SW7 2BZ (United Kingdom); Jones, H. F. [Physics Department, Imperial College, London SW7 2BZ (United Kingdom)

    2011-07-15

    The PT-symmetric potential V{sub 0}[cos(2{pi}x/a)+i{lambda}sin(2{pi}x/a)] has a completely real spectrum for {lambda}{<=}1 and begins to develop complex eigenvalues for {lambda}>1. At the symmetry-breaking threshold {lambda}=1 some of the eigenvectors become degenerate, giving rise to a Jordan-block structure for each degenerate eigenvector. In general this is expected to result in a secular growth in the amplitude of the wave. However, it has been shown in a recent paper by Longhi, by numerical simulation and by the use of perturbation theory, that for a broad initial wave packet this growth is suppressed, and instead a saturation leading to a constant maximum amplitude is observed. We revisit this problem by explicitly constructing the Bloch wave functions and the associated Jordan functions and using the method of stationary states to find the dependence on the longitudinal distance z for a variety of different initial wave packets. This allows us to show in detail how the saturation of the linear growth arises from the close connection between the contributions of the Jordan functions and those of the neighboring Bloch waves.

  8. Modulated Tool-Path Chip Breaking For Depleted Uranium Machining Operations

    SciTech Connect (OSTI)

    Barkman, W. E.; Babelay Jr., E. F.; Smith, K. S.; Assaid T. S.; McFarland, J. T.; Tursky, D. A.

    2010-04-15

    Turning operations involving depleted uranium frequently generate long, stringy chips that present a hazard to both the machinist and the machine tool. While a variety of chip-breaking techniques are available, they generally depend on a mechanism that increases the bending of the chip or the introduction of a one dimensional vibration that produces an interrupted cutting pattern. Unfortunately, neither of these approaches is particularly effective when making a 'light depth-of-cut' on a contoured workpiece. The historical solution to this problem has been for the machinist to use long-handled tweezers to 'pull the chip' and try to keep it submerged in the chip pan; however, this approach is not practical for all machining operations. This paper discusses a research project involving the Y-12 National Security Complex and the University of North Carolina at Charlotte in which unique, oscillatory part programs are used to continuously create an interrupted cut that generates pre-defined, user-selectable chip lengths.

  9. Next Generation of Renewable Electricity Policy: How Rapid Change is Breaking Down Conventional Policy Categories

    SciTech Connect (OSTI)

    Couture, T. D.; Jacobs, D.; Rickerson, W.; Healey, V.

    2015-02-01

    A number of policies have been used historically in order to stimulate the growth of the renewable electricity sector. This paper examines four of these policy instruments: competitive tendering, sometimes called renewable electricity auctions, feed-in tariffs, net metering and net billing, and tradable renewable energy certificates. In recent years, however, a number of changes to both market circumstances and to policy priorities have resulted in numerous policy innovations, including the emergence of policy hybrids. With no common language for these evolving policy mechanisms, policymakers have generally continued to use the same traditional policy labels, occasionally generating confusion as many of these new policies no longer look, or act, like their traditional predecessors. In reviewing these changes, this paper makes two separate but related claims: first, policy labels themselves are breaking down and evolving. As a result, policy comparisons that rely on the conventional labels may no longer be appropriate, or advisable. Second, as policymakers continue to adapt, we are in effect witnessing the emergence of the next generation of renewable electricity policies, a change that could have significant impacts on investment, as well as on market growth in both developed and developing countries.

  10. LATE-TIME OBSERVATIONS OF GRB 080319B: JET BREAK, HOST GALAXY, AND ACCOMPANYING SUPERNOVA

    SciTech Connect (OSTI)

    Tanvir, N. R.; O'Brien, P. T.; Wiersema, K.; Starling, R. L. C.; Rol, E.; Levan, A. J.; Svensson, K.; Fruchter, A. S.; Granot, J.; Jakobsson, P.; Fynbo, J.; Hjorth, J.; Curran, P. A.; Burrows, D. N.; Genet, F.

    2010-12-10

    The Swift-discovered GRB 080319B was by far the most distant source ever observed at naked-eye brightness, reaching a peak apparent magnitude of 5.3 at a redshift of z = 0.937. We present our late-time optical (Hubble Space Telescope, Gemini, and Very Large Telescope) and X-ray (Chandra) observations, which confirm that an achromatic break occurred in the power-law afterglow light curve at {approx}11 days post-burst. This most likely indicates that the gamma-ray burst (GRB) outflow was collimated, which for a uniform jet would imply a total energy in the jet E{sub jet} {approx}> 10{sup 52} erg. Our observations also show a late-time excess of red light, which is well explained if the GRB was accompanied by a supernova (SN), similar to those seen in some other long-duration GRBs. The latest observations are dominated by light from the host and show that the GRB took place in a faint dwarf galaxy (r(AB) {approx} 27.0, rest frame M{sub B} {approx} -17.2). This galaxy is small even by the standards of other GRB hosts, which is suggestive of a low-metallicity environment. Intriguingly, the properties of this extreme event-a small host and bright SN-are entirely typical of the very low luminosity bursts such as GRB 980425 and GRB 060218.

  11. Inducing chaos by breaking axial symmetry in a black hole magnetosphere

    SciTech Connect (OSTI)

    Kopáček, O.; Karas, V.

    2014-06-01

    While the motion of particles near a rotating, electrically neutral (Kerr), and charged (Kerr-Newman) black hole is always strictly regular, a perturbation in the gravitational or the electromagnetic field generally leads to chaos. The transition from regular to chaotic dynamics is relatively gradual if the system preserves axial symmetry, whereas non-axisymmetry induces chaos more efficiently. Here we study the development of chaos in an oblique (electro-vacuum) magnetosphere of a magnetized black hole. Besides the strong gravity of the massive source represented by the Kerr metric, we consider the presence of a weak, ordered, large-scale magnetic field. An axially symmetric model consisting of a rotating black hole embedded in an aligned magnetic field is generalized by allowing an oblique direction of the field having a general inclination with respect to the rotation axis of the system. The inclination of the field acts as an additional perturbation to the motion of charged particles as it breaks the axial symmetry of the system and cancels the related integral of motion. The axial component of angular momentum is no longer conserved and the resulting system thus has three degrees of freedom. Our primary concern within this contribution is to find out how sensitive the system of bound particles is to the inclination of the field. We employ the method of the maximal Lyapunov exponent to distinguish between regular and chaotic orbits and to quantify their chaoticity. We find that even a small misalignment induces chaotic motion.

  12. Method for in vitro recombination

    DOE Patents [OSTI]

    Gibson, Daniel Glenn; Smith, Hamilton O

    2013-05-07

    The present invention relates to an in vitro method, using isolated protein reagents, for joining two double-stranded (ds) DNA molecules of interest, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule share a region of sequence identity. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest.

  13. 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.

  14. Statistical recoupling: A new way to break the link between electric-utility sales and revenues

    SciTech Connect (OSTI)

    Hirst, E.

    1993-09-01

    In 1991, US electric utilities spent almost $1.8 billion on demand-side management (DSM) programs. These programs cut peak demands 5% and reduced electricity sales 1% that year. Utility projections suggest that these reductions will increase to 9% and 3%, respectively, by the year 2001. However, utility DSM efforts vary enormously across the country, concentrated in a few states along the east and west coasts and the upper midwest. To some extent, this concentration is a function of regulatory reforms that remove disincentives to utility shareholders for investments in DSM programs. A key component of these reforms is recovery of the net lost revenues caused by utility DSM programs. These lost revenues occur between rate cases when a utility encourages its customers to improve energy efficiency and cut demand. The reduction in sales means that the utility has less revenue to cover its fixed costs. This report describes a new method, statistical recoupling (SR), that addresses this net-lost-revenue problem. Like other decoupling approaches, SR breaks the link between electric-utility revenues and sales. Unlike other approaches, SR minimizes changes from traditional regulation. In particular, the risks of revenue swings associated with year-to-year changes in weather and the economy remain with the utility under SR. Statistical recoupling uses statistical models, based on historical data, that explain retail electricity sales as functions of the number of utility customers, winter and summer weather, the condition of the local economy, electricity price, and perhaps a few other key variables. These models, along with the actual values of the explanatory variables, are then used to estimate ``allowed`` electricity sales and revenues in future years.

  15. Additional requirements for leak-before-break application to primary coolant piping in Belgium

    SciTech Connect (OSTI)

    Roussel, G.

    1997-04-01

    Leak-Before-Break (LBB) technology has not been applied in the first design of the seven Pressurized Water Reactors the Belgian utility is currently operating. The design basis of these plants required to consider the dynamic effects associated with the ruptures to be postulated in the high energy piping. The application of the LBB technology to the existing plants has been recently approved by the Belgian Safety Authorities but with a limitation to the primary coolant loop. LBB analysis has been initiated for the Doel 3 and Tihange 2 plants to allow the withdrawal of some of the reactor coolant pump snubbers at both plants and not reinstall some of the restraints after steam generator replacement at Doel 3. LBB analysis was also found beneficial to demonstrate the acceptability of the primary components and piping to the new conditions resulting from power uprating and stretch-out operation. LBB analysis has been subsequently performed on the primary coolant loop of the Tihange I plant and is currently being performed for the Doel 4 plant. Application of the LBB to the primary coolant loop is based in Belgium on the U.S. Nuclear Regulatory Commission requirements. However the Belgian Safety Authorities required some additional analyses and put some restrictions on the benefits of the LBB analysis to maintain the global safety of the plant at a sufficient level. This paper develops the main steps of the safety evaluation performed by the Belgian Safety Authorities for accepting the application of the LBB technology to existing plants and summarizes the requirements asked for in addition to the U.S. Nuclear Regulatory Commission rules.

  16. 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

  17. Spontaneous breaking of scale invariance in a D = 3 U(N ) model with Chern-Simons gauge fields

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

    Bardeen, William A.; Moshe, Moshe

    2014-06-18

    We study spontaneous breaking of scale invariance in the large N limit of three dimensional U(N )κ Chern-Simons theories coupled to a scalar field in the fundamental representation. When a λ6 ( ؆ · Ø)3 self interaction term is added to the action we find a massive phase at a certain critical value for a combination of the λ(6) and ’t Hooft’s λ = N/κ couplings. This model attracted recent attention since at finite κ it contains a singlet sector which is conjectured to be dual to Vasiliev’s higher spin gravity on AdS4. Our paper concentrates on the massive phasemore » of the 3d boundary theory. We discuss the advantage of introducing masses in the boundary theory through spontaneous breaking of scale invariance.« less

  18. Impact of the control rod consumption on the reactivity control of a SFR break-even core

    SciTech Connect (OSTI)

    Blanchet, D.; Fontaine, B.

    2012-07-01

    Current design studies on Sodium Fast Reactor (SFR) differ from those performed in the past by the fact that design criteria are now those of the Generation IV reactors. In order to improve their safety, reactors with break-even cores are preferred because they minimize the needs in terms of reactivity control and limit the consequences of control rod withdrawal. Furthermore, as the reactivity control needs are low, break-even core enables the use of absorbing materials with reduced efficiency (natural boron, hafnium...). Nevertheless, the use of control rods with few absorbing materials may present the disadvantage of a non-negligible ({approx}10%) loss of efficiency due to their consumption under irradiation. This paper presents a methodology to calculate accurately and analyze this consumption. (authors)

  19. GAMMA-RAY BURST AFTERGLOW LIGHT CURVES FROM A LORENTZ-BOOSTED SIMULATION FRAME AND THE SHAPE OF THE JET BREAK

    SciTech Connect (OSTI)

    Van Eerten, Hendrik; MacFadyen, Andrew

    2013-04-20

    The early stages of decelerating gamma-ray burst (GRB) afterglow jets have been notoriously difficult to resolve numerically using two-dimensional hydrodynamical simulations even at very high resolution, due to the extreme thinness of the blast wave and high outflow Lorentz factors. However, these resolution issues can be avoided by performing the simulations in a boosted frame, which makes it possible to calculate afterglow light curves from numerically computed flows in sufficient detail to accurately quantify the shape of the jet break and the post-break steepening of the light curve. Here, we study afterglow jet breaks for jets with opening angles of 0.05, 0.1, and 0.2 radians decelerating in a surrounding medium of constant density, observed at various angles ranging from on-axis to the edge of the jet. A single set of scale-invariant functions describing the time evolution of afterglow synchrotron spectral break frequencies and peak flux, depending only on jet opening angle and observer angle, are all that is needed to reconstruct light curves for arbitrary explosion energy, circumburst density and synchrotron particle distribution power law slope p. These functions are presented in the paper. Their time evolutions change directly following the jet break, although an earlier reported temporary post-break steepening of the cooling break is found to have been resolution-induced. We compare synthetic light curves to fit functions using sharp power law breaks as well as smooth power law transitions. We confirm our earlier finding that the measured jet break time is very sensitive to the angle of the observer and can be postponed significantly. We find that the difference in temporal indices across the jet break is larger than theoretically anticipated and is about -(0.5 + 0.5p) below the cooling break and about -(0.25 + 0.5p) above the cooling break, both leading to post-break slopes of roughly about 0.25 - 1.3p, although different observer angles, jet opening angles and heuristic descriptions of the break introduce a wide range of temporal indices. Nevertheless, the post-break slope from our constant density interstellar medium simulations is sufficiently steep to be hard to reconcile with post-break slopes measured for the Swift sample, suggesting that Swift GRBs mostly do not explode in a homogeneous medium or that the jet breaks are hidden from view by additional physics such as prolonged energy injection or viewing angle effects. A comparison between different smooth power law fit functions shows that although smooth power law transitions of the type introduced by Harrison et al. often provide better fits, smooth power law transitions of the type introduced by Beuermann et al. or even sharp power law fits are easier to interpret in terms of the underlying model. Light curves and spectral break and peak flux evolution functions will be made publicly available online at http://cosmo.nyu.edu/afterglowlibrary.

  20. The {open_quotes}leak-before-break{close_quotes} applicability in decision support system {open_quotes}strength{close_quotes}

    SciTech Connect (OSTI)

    Torop, V.M.; Orynyak, I.V.; Kutovoy, O.L.

    1997-04-01

    A software decision support system, STRENGTH, for application of leak before break analysis, is described. The background methodology and sample application are outlined. The program allows multioptional computation of loading parameters for different types of defects, and variable properties for metals and welded joints. Structural strength is assessed, and service life predictions are made. The program is used to analyze specific defects identified by nondestructive testing.

  1. 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.

  2. Assessment of RELAP/MOD3 using BETHSY 6.2TC 6-inch cold leg side break comparative test

    SciTech Connect (OSTI)

    Chung, Young-Jong; Jeong, Jae-Jun; Chang, Won-Pyo; Kim, Dong-Su

    1996-10-01

    This report presents the results of the RELAP5/MOD3 Version 7j assessment on BETHSY 6.2TC. BETHSY 6.2TC test corresponding to a six inch cold leg break LOCA of the Pressurizer Water Reactor(PWR). The primary objective of the test was to provide reference data of two facilities of different scales (BETHSY and LSTF facility). On the other hand, the present calculation aims at analysis of RELAP5/N4OD3 capability on the small break LOCA simulation, The results of calculation have shown that the RELAP5/MOD3 reasonably predicts occurrences as well as trends of the major phenomena such as primary pressure, timing of loop seal clearing, liquid hold up, etc. However, some disagreements also have been found in the predictions of loop seal clearing, collapsed core water level after loop seal clearing, and accumulator injection behaviors. For better understanding of discrepancies in same predictions, several sensitivity calculations have been performed as well. These include the changes of two-phase discharge coefficient at the break junction and some corrections of the interphase drag term. As result, change of a single parameter has not improved the overall predictions and it has been found that the interphase drag model has still large uncertainties.

  3. 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.

  4. 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...

  5. 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 recovery pathway plays a role in overriding tumor barrier in tumorigenesis. • Recovery protein dysregulation and human cancer development is correlated.

  6. STEAM LINE BREAK AND STATION BLACKOUT TRANSIENTS FOR PROLIFERATION RESISTANT HEXAGONAL TIGHT LATTICE BWR.

    SciTech Connect (OSTI)

    ROHATGI,U.S.; JO,J.; CHUNG,B.D.; TAKAHASHI,H.

    2002-06-09

    Safety analyses of a proliferation resistant, economically competitive, high conversion, boiling water reactor (HCBWR) fueled with fissile plutonium and fertile thorium oxide fuel elements, and with passive safety systems are presented here. The HCBWR developed here is characterized by a very tight lattice with a relatively small water volume fraction in the core which therefore operates with a fast reactor neutron spectrum, and a considerably improved neutron economy compared to the current generation of Light Water Reactors. The tight lattice core has a very narrow flow channels with a hydraulic diameter less than half of the regular BWR core and, thus, presents a special challenge to core cooling, because of reduced water inventory and high friction in the core. The primary safety concern when reducing the moderator to fuel ratio and when using a tightly packed lattice arrangement is to maintain adequate cooling of the core during both normal operation and accident scenarios. In the preliminary HCBWR design, the core has been placed in a vessel with a large chimney section, and the vessel is connected with Isolation Condenser System (ICs). The vessel is placed in containment with Gravity Driven Cooling System (GDCS) and Passive Containment Cooling System (PCCS) in a configuration similar to General Electric's Simplified Boiling Water Reactor (SBWR). The safety systems are similar to SBWR; ICs and PCCS are scaled with power. An internal recirculation pump was placed in the downcomer to augment the buoyancy head provided by the chimney, since the buoyancy provided by the chimney alone could not generate sufficient recirculation in the vessel as the tight lattice configuration resulted in much larger friction in the core than the SBWR. The constitutive relationships for RELAP5 were assessed for narrow channels, and as a result the heat transfer package was modified. The modified RELAP5 was used to simulate and analyze two of the most limiting events for a tight pitch lattice core: the Station Blackout and the Main Steam Line Break events. The results of the analyses indicate that the HCBWR system will be safely brought to the shutdown condition for these transients.

  7. Steam Line Break and Station Blackout Transients for Proliferation Resistant Hexagonal Tight Lattice BWR

    SciTech Connect (OSTI)

    Upendra Rohatgi; Jae Jo; Bub Dong Chung; Hiroshi Takahashi [Brookhaven National Laboratory, Energy Sciences and Technology Department, Upton, New York 11973 (United States); Downar, T.J. [Purdue University, School of Nuclear Engineering, West Lafayette, IN 47906-1290 (United States)

    2002-07-01

    Safety analyses of a proliferation resistant, economically competitive, high conversion, boiling water reactor (HCBWR) fueled with fissile plutonium and fertile thorium oxide fuel elements, and with passive safety systems are presented here. The HCBWR developed here is characterized by a very tight lattice with a relatively small water volume fraction in the core which therefore operates with a fast reactor neutron spectrum, and a considerably improved neutron economy compared to the current generation of Light Water Reactors. A tight lattice BWR core has very narrow flow channels with a hydraulic diameter less than half of the regular BWR core. The tight lattice core presented a special challenge to core cooling, because of reduced water inventory and high friction in the core. The primary safety concern when reducing the moderator to fuel ratio and when using a tightly packed lattice arrangement is to maintain adequate cooling of the core during both normal operation and accident scenarios. In the preliminary HCBWR design, the core has been placed in a vessel with a large chimney section, and the vessel is connected with an Isolation Cooling System (ICS). The vessel is placed in a containment with a Gravity Driven Cooling System (GDCS) and a Passive Containment Cooling System (PCCS) in a configuration similar to General Electric's (GE) Simplified Boiling Water Reactor (SBWR). The safety systems are similar to the SBWR; the ICS and PCCS are scaled with power. An internal recirculation pump was placed in the downcomer to augment the buoyancy head provided by the chimney. The buoyancy provided by the chimney alone could not generate sufficient recirculation in the vessel since the tight lattice configuration resulted in much larger friction in the core than the SBWR. A modified RELAP5 Code was used to simulate and analyze two of the most limiting events for a tight pitch lattice core: the Station Blackout and the Main Steam Line Break events. The constitutive relationships for RELAP5 were compared with the correlations and the data available for narrow channels, and the heat transfer package was modified for narrow channel application. The results of the analyses indicate that the HCBWR system will be safely shutdown for these transients. (authors)

  8. 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)

  9. 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.

  10. Encapsulation of Gold Nanoparticles in a DNA Origami Cage

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

    Encapsulation of Gold Nanoparticles in a DNA Origami Cage Authors: Zhao, Z., Jacovetty, E. L., Liu, Y., and Yan, H. Title: Encapsulation of Gold Nanoparticles in a DNA Origami Cage...

  11. AZD5438, an Inhibitor of Cdk1, 2, and 9, Enhances the Radiosensitivity of Non-Small Cell Lung Carcinoma Cells

    SciTech Connect (OSTI)

    Raghavan, Pavithra; Tumati, Vasu; Yu Lan; Chan, Norman; Tomimatsu, Nozomi; Burma, Sandeep; Simmons Comprehensive Cancer Center, Dallas, Texas ; Bristow, Robert G.; Saha, Debabrata; Simmons Comprehensive Cancer Center, Dallas, Texas

    2012-11-15

    Purpose: Radiation therapy (RT) is one of the primary modalities for treatment of non-small cell lung cancer (NSCLC). However, due to the intrinsic radiation resistance of these tumors, many patients experience RT failure, which leads to considerable tumor progression including regional lymph node and distant metastasis. This preclinical study evaluated the efficacy of a new-generation cyclin-dependent kinase (Cdk) inhibitor, AZD5438, as a radiosensitizer in several NSCLC models that are specifically resistant to conventional fractionated RT. Methods and Materials: The combined effect of ionizing radiation and AZD5438, a highly specific inhibitor of Cdk1, 2, and 9, was determined in vitro by surviving fraction, cell cycle distribution, apoptosis, DNA double-strand break (DSB) repair, and homologous recombination (HR) assays in 3 NSCLC cell lines (A549, H1299, and H460). For in vivo studies, human xenograft animal models in athymic nude mice were used. Results: Treatment of NSCLC cells with AZD5438 significantly augmented cellular radiosensitivity (dose enhancement ratio rangeing from 1.4 to 1.75). The degree of radiosensitization by AZD5438 was greater in radioresistant cell lines (A549 and H1299). Radiosensitivity was enhanced specifically through inhibition of Cdk1, prolonged G{sub 2}-M arrest, inhibition of HR, delayed DNA DSB repair, and increased apoptosis. Combined treatment with AZD5438 and irradiation also enhanced tumor growth delay, with an enhancement factor ranging from 1.2-1.7. Conclusions: This study supports the evaluation of newer generation Cdk inhibitors, such as AZD5438, as potent radiosensitizers in NSCLC models, especially in tumors that demonstrate variable intrinsic radiation responses.

  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. 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

  15. 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

  16. 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

  17. 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

  18. Foreign DNA Capture during CRISPR-CAS Adaptive Immunity

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

    Foreign DNA Capture during CRISPR-CAS Adaptive Immunity Foreign DNA Capture during CRISPR-CAS Adaptive Immunity Print Thursday, 21 January 2016 16:45 While we humans view bacteria as the enemy, bacteria have enemies too, for example, viruses. To protect themselves, bacteria have developed an adaptive-type immune system that revolves around a unit of DNA known as CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats. A CRISPR unit of DNA is made up of

  19. DNA origami with Complex Curvatures in 3D

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

    with Complex Curvatures in 3D 15 Apr 2011 Center researchers have developed a new DNA origami design strategy for engineering complex, arbitrarily shaped 3D DNA nanostructures that have substantial intrinsic curvatures. This strategy has been presented in a paper by Professors Hao Yan, Yan Liu and coworkers that was featured on the cover of Science for April 15, 2011. Use of DNA as a structural material is in the basis of the DNA nanotechnology searching for ways to assemble nanoscale structures

  20. 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)

  1. 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.

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. Assessment of a large break loss of coolant accident scenario requiring operator action to initiate safety injection

    SciTech Connect (OSTI)

    Grendys, R.C.; Nissley, M.E.; Baker, D.C.

    1996-11-01

    As part of the licensing basis for a nuclear power plant, the acceptability of the Emergency Core Cooling Systems (ECCS) following a postulated Loss-of-Coolant Accident (LOCA) as described in the Code of Federal Regulations (CFR), Title 10, Chapter 1, Part 50.46, must be verified. The LOCA analysis is performed with an acceptable ECCS Evaluation Model and results must show compliance with the 10 CFR 50.46 acceptance criteria. Westinghouse Electric Corporation performs Large and Small Break LOCA and LOCA-related analyses to support the licensing basis of various nuclear power plants and also performs evaluations against the licensing basis analyses as required. Occasionally, the need arises for the holder of an operating license of a nuclear power plant to submit a Licensee Event Report (LER) to the US Nuclear Regulatory Commission (USNRC) for any event of the type described in the Code of Federal Regulations, Title 10, Chapter 1, Part 50.73. To support the LER, a Justification for Past Operation (JPO) may be performed to assess the safety consequences and implications of the event based on previous operating conditions. This paper describes the work performed for the Large Break LOCA to assess the impact of an event discovered by Florida Power and Light and reported in LER-94-005-02. For this event, it was determined that under certain circumstances, operator action would have been required to initiate safety injection (SI), thus challenging the acceptability of the ECCS. This event was specifically addressed for the Large Break LOCA by using an advanced thermal hydraulic analysis methodology with realistic input assumptions.

  13. An investigation of penetrant techniques for detection of machining-induced surface-breaking cracks on monolithic ceramics

    SciTech Connect (OSTI)

    Forster, G.A.; Ellingson, W.A.

    1996-02-01

    The purpose of this effort was to evaluate penetrant methods for their ability to detect surface-breaking cracks in monolithic ceramic materials with an emphasis on detection of cracks generated by machining. There are two basic penetrant types, visible and fluorescent. The visible penetrant method is usually augmented by powder developers and cracks detected can be seen in visible light. Cracks detected by fluorescent penetrant are visible only under ultraviolet light used with or without a developer. The developer is basically a powder that wicks up penetrant from a crack to make it more observable. Although fluorescent penetrants were recommended in the literature survey conducted early in this effort, visible penetrants and two non-standard techniques, a capillary gaseous diffusion method under development at the institute of Chemical Physics in Moscow, and the {open_quotes}statiflux{close_quotes} method which involves use of electrically charged particles, were also investigated. SiAlON ring specimens (1 in. diameter, 3/4 in. wide) which had been subjected to different thermal-shock cycles were used for these tests. The capillary gaseous diffusion method is based on ammonia; the detector is a specially impregnated paper much like litmus paper. As expected, visible dye penetrants offered no detection sensitivity for tight, surface-breaking cracks in ceramics. Although the non-standard statiflux method showed promise on high-crack-density specimens, it was ineffective on limited-crack-density specimens. The fluorescent penetrant method was superior for surface-breaking crack detection, but successful application of this procedure depends greatly on the skill of the user. Two presently available high-sensitivity fluorescent penetrants were then evaluated for detection of microcracks on Si{sub 3}N{sub 4} and SiC from different suppliers. Although 50X optical magnification may be sufficient for many applications, 200X magnification provides excellent delectability.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. Nonlinear delayed symmetry breaking in a solid excited by hard x-ray free electron laser pulses

    SciTech Connect (OSTI)

    Ferrer, A.; Johnson, J. A. Mariager, S. O.; Grbel, S.; Staub, U.; Huber, T.; Trant, M.; Johnson, S. L.; Zhu, D.; Chollet, M.; Robinson, J.; Lemke, H. T.; Ingold, G.; Beaud, P.; Milne, C.

    2015-04-13

    We have studied the ultrafast changes of electronic states in bulk ZnO upon intense hard x-ray excitation from a free electron laser. By monitoring the transient anisotropy induced in an optical probe beam, we observe a delayed breaking of the initial c-plane symmetry of the crystal that lasts for several picoseconds. Interaction with the intense x-ray pulses modifies the electronic state filling in a manner inconsistent with a simple increase in electronic temperature. These results may indicate a way to use intense ultrashort x-ray pulses to investigate high-energy carrier dynamics and to control certain properties of solid-state materials.

  2. Application of the leak-before-break concept to the primary circuit piping of the Leningrad NPP

    SciTech Connect (OSTI)

    Eperin, A.P.; Zakharzhevsky, Yu.O.; Arzhaev, A.I.

    1997-04-01

    A two-year Finnish-Russian cooperation program has been initiated in 1995 to demonstrate the applicability of the leak-before-break concept (LBB) to the primary circuit piping of the Leningrad NPP. The program includes J-R curve testing of authentic pipe materials at full operating temperature, screening and computational LBB analyses complying with the USNRC Standard Review Plan 3.6.3, and exchange of LBB-related information with emphasis on NDE. Domestic computer codes are mainly used, and all tests and analyses are independently carried out by each party. The results are believed to apply generally to RBMK type plants of the first generation.

  3. Three-body break-up in deuteron-deuteron scattering at 65 MeV/nucleon

    SciTech Connect (OSTI)

    Ramazani-Moghaddam-Arani, A.; Amir-Ahmadi, H. R.; Biegun, A.; Joulaeizadeh, L.; Kalantar-Nayestanaki, N.; Mardanpour, H.; Messchendorp, J. G.; Moeini, H.; Shende, S. V.; Bacher, A. D.; Bailey, C. D.; Stephenson, E. J.; Eslami-Kalantari, M.; Gasparic, I.; Kistryn, St.; Sworst, R.; Kozela, A.; Micherdzinska, A. M.; Stephan, E.

    2011-02-15

    In an experiment with a 65 MeV/nucleon polarized deuteron beam on a liquid-deuterium target at Kernfysisch Versneller Instituut, several multibody final states in deuteron-deuteron scattering were identified. For these measurements, a unique and advanced detection system, called the Big Instrument for Nuclear-polarization Analysis, was utilized. We demonstrate the feasibility of measuring vector and tensor polarization observables of the deuteron break-up reaction leading to a three-body final state. The polarization observables were determined with high precision in a nearly background-free experiment. The analysis procedure and some results are presented.

  4. 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

  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. 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.

  7. Building a market for small wind: The break-even turnkey cost of residential wind systems in the United States

    SciTech Connect (OSTI)

    Edwards, Jennifer L.; Wiser, Ryan; Bolinger, Mark; Forsyth, Trudy

    2004-03-01

    Although small wind turbine technology and economics have improved in recent years, the small wind market in the United States continues to be driven in large part by state incentives, such as cash rebates, favorable loan programs, and tax credits. This paper examines the state-by-state economic attractiveness of small residential wind systems. Economic attractiveness is evaluated primarily using the break-even turnkey cost (BTC) of a residential wind system as the figure of merit. The BTC is defined here as the aggregate installed cost of a small wind system that could be supported such that the system owner would break even (and receive a specified return on investment) over the life of the turbine, taking into account current available incentives, the wind resource, and the retail electricity rate offset by on-site generation. Based on the analysis presented in this paper, we conclude that: (1) the economics of residential, grid-connected small wind systems is highly variable by state and wind resource class, (2) significant cost reductions will be necessary to stimulate widespread market acceptance absent significant changes in the level of policy support, and (3) a number of policies could help stimulate the market, but state cash incentives currently have the most significant impact, and will be a critical element of continued growth in this market.

  8. Experiment data report for LOFT large-break loss-of-coolant experiment L2-5. [PWR

    SciTech Connect (OSTI)

    Bayless, P.D.; Divine, J.M.

    1982-08-01

    Selected pertinent and uninterpreted data from the third nuclear large break loss-of-coolant experiment (Experiment L2-5) conducted in the Loss-of-Fluid Test (LOFT) facility are presented. The LOFT facility is a 50-MW(t) pressurized water reactor (PWR) system with instruments that measure and provide data on the system thermal-hydraulic and nuclear conditions. The operation of the LOFT system is typical of large (approx. 1000 MW(e)) commercial PWR operations. Experiment L2-5 simulated a double-ended offset shear of a cold leg in the primary coolant system. The primary coolant pumps were tripped within 1 s after the break initiation, simulating a loss of site power. Consistent with the loss of power, the starting of the high- and low-pressure injection systems was delayed. The peak fuel rod cladding temperature achieved was 1078 +- 13 K. The emergency core cooling system re-covered the core and quenched the cladding. No evidence of core damage was detected.

  9. Coal-water slurry sprays from an electronically controlled accumulator fuel injection system: Break-up distances and times

    SciTech Connect (OSTI)

    Caton, J.A.; Payne, S.E.; Terracina, D.P.; Kihm, K.D.

    1993-12-31

    Experiments have been completed to characterize coal-water slurry sprays from an electronically-controlled accumulator fuel injection system of a diesel engine. The sprays were injected into a pressurized chamber equipped with windows. High speed movies, fuel pressures and needle lifts were obtained as a function of time, orifice diameter, coal loading, gas density in the chamber, and accumulator fuel pressure. For the base conditions (50% (by man) coal loading, 0.4 mm diameter nozzle hole, coal-water slurry pressure of 82 MPa (12,000 psi), and a chamber density of 25 kg/m{sup 3}), the break-up time was 0.30 ms. An empirical correlation for spray tip penetration, break-up time and initial jet velocity was developed. For the conditions of this study, the spray tip penetration and initial jet velocity were 15% greater for coal-water slurry than for diesel fuel or water. Results of this study and the correlation are specific to the tested coal-water slurry and are not general for other coal-water slurry fuels.

  10. DNA repair decline during mouse spermiogenesis results in the accumulation of heritable DNA damage

    SciTech Connect (OSTI)

    Marchetti, Francesco; Marchetti, Francesco; Wryobek, Andrew J

    2008-02-21

    The post-meiotic phase of mouse spermatogenesis (spermiogenesis) is very sensitive to the genomic effects of environmental mutagens because as male germ cells form mature sperm they progressively lose the ability to repair DNA damage. We hypothesized that repeated exposures to mutagens during this repair-deficient phase result in the accumulation of heritable genomic damage in mouse sperm that leads to chromosomal aberrations in zygotes after fertilization. We used a combination of single or fractionated exposures to diepoxybutane (DEB), a component of tobacco smoke, to investigate how differential DNA repair efficiencies during the three weeks of spermiogenesis affected the accumulation of DEB-induced heritable damage in early spermatids (21-15 days before fertilization, dbf), late spermatids (14-8 dbf) and sperm (7- 1 dbf). Analysis of chromosomalaberrations in zygotic metaphases using PAINT/DAPI showed that late spermatids and sperm are unable to repair DEB-induced DNA damage as demonstrated by significant increases (P<0.001) in the frequencies of zygotes with chromosomal aberrations. Comparisons between single and fractionated exposures suggested that the DNA repair-deficient window during late spermiogenesis may be less than two weeks in the mouse and that during this repair-deficient window there is accumulation of DNA damage in sperm. Finally, the dose-response study in sperm indicated a linear response for both single and repeated exposures. These findings show that the differential DNA repair capacity of post-meioitic male germ cells has a major impact on the risk of paternally transmitted heritable damage and suggest that chronic exposures that may occur in the weeks prior to fertilization because of occupational or lifestyle factors (i.e, smoking) can lead to an accumulation of genetic damage in sperm and result in heritable chromosomal aberrations of paternal origin.

  11. DNA Repair Decline During Mouse Spermiogenesis Results in the Accumulation of Heritable DNA Damage

    SciTech Connect (OSTI)

    Marchetti, Francesco; Marchetti, Francesco; Wyrobek, Andrew J.

    2007-12-01

    The post-meiotic phase of mouse spermatogenesis (spermiogenesis) is very sensitive to the genomic effects of environmental mutagens because as male germ cells form mature sperm they progressively lose the ability to repair DNA damage. We hypothesized that repeated exposures to mutagens during this repair-deficient phase result in the accumulation of heritable genomic damage in mouse sperm that leads to chromosomal aberrations in zygotes after fertilization. We used a combination of single or fractionated exposures to diepoxybutane (DEB), a component of tobacco smoke, to investigate how differential DNA repair efficiencies during the three weeks of spermiogenesis affected the accumulation of DEB-induced heritable damage in early spermatids (21-15 days before fertilization, dbf), late spermatids (14-8 dbf) and sperm (7-1 dbf). Analysis of chromosomal aberrations in zygotic metaphases using PAINT/DAPI showed that late spermatids and sperm are unable to repair DEB-induced DNA damage as demonstrated by significant increases (P<0.001) in the frequencies of zygotes with chromosomal aberrations. Comparisons between single and fractionated exposures suggested that the DNA repair-deficient window during late spermiogenesis may be less than two weeks in the mouse and that during this repair-deficient window there is accumulation of DNA damage in sperm. Finally, the dose-response study in sperm indicated a linear response for both single and repeated exposures. These findings show that the differential DNA repair capacity of post-meioitic male germ cells has a major impact on the risk of paternally transmitted heritable damage and suggest that chronic exposures that may occur in the weeks prior to fertilization because of occupational or lifestyle factors (i.e, smoking) can lead to an accumulation of genetic damage in sperm and result in heritable chromosomal aberrations of paternal origin.

  12. DNA sequence and spatial expression pattern of a drought- and ABA-induced gene in tomato

    SciTech Connect (OSTI)

    Plant, A.L.; Cohen, A.; Moses, M.S.; Bray, E.A. )

    1991-05-01

    The genomic and cDNA sequence for the previously characterized drought- and ABA-induced gene pLE16 are presented. The single open reading frame contained within the gene has the capacity to encode a polypeptide of 12.7 kD with a predicted pI of 8.73. The amino-terminus is highly hydrophobic and is characteristic of signal sequences which target polypeptides for export from the cytoplasm. There is considerable homology (51.3% identity) between the amino-terminus of pLE16 and the amino-terminal domains of a group of proteins that comprise the phospholipid transfer proteins. Although this homology breaks down at the carboxy-terminal half of pLE16, the homology that exists suggests that pLE16 may be associated with membranes and may therefore play a role in maintaining membrane integrity during drought-stress. pLE16 is expressed in drought-stressed leaf, petiole and stem tissue and to a much lower extent in the seeds and pericarp of mature green tomato fruit. No expression was detected in the seeds or pericarp of red fruit or drought-stressed roots. Expression of pLE16 is induced in leaf tissue by a variety of other environmental stresses including PEG-mediated water deficit, salt, cold stress and heat stress. These stresses did not however induce expression of pLE16 in the roots. Examination of the 5{prime} flanking DNA sequences for this gene did not reveal the presence of the consensus ABA responsive element (ABRE), implicated in ABA induction of gene expression and so far common to the 5{prime} flanking DNA sequences of many genes that are ABA responsive. The expression of pLE16 in response to drought-stress and other environmental stresses in vegetative tissue, together with the lack of a consensus ABRE, suggests that the regulation of this gene by ABA may differ from those that are seed-specific.

  13. 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 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 enzymes. Combined with electron microscopy, the results point the way to the

  14. 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 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 enzymes. Combined with electron microscopy, the results point the way to the

  15. 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 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 enzymes. Combined with electron microscopy, the results point the way to the

  16. DNA Persistence in Sink Drain Environment

    SciTech Connect (OSTI)

    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.

  17. 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 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 enzymes. Combined with electron microscopy, the results point the way to the

  18. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, Frank A.; Gray, Joe W.

    1988-01-01

    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 or Hoechst 33258 is used as the probe for the measurement of total DNA content and a monoclonal antibody reactive with a DNA precursor such as halodeoxy-uridine (HdU), more specifically bromodeoxyuridine (BrdU) is used as a probe for the measurement of HdU or BrdU uptake by the cells as a measure of DNA synthesis.

  19. Photocatalytic probing of DNA sequence by using TiO{sub 2}/dopamine-DNA triads.

    SciTech Connect (OSTI)

    Liu, J.; de la Garza, L.; Zhang, L.; Dimitrijevic, N. M.; Zuo, X.; Tiede, D. M.; Rajh, T.

    2007-10-15

    A method to control charge transfer reaction in DNA using hybrid nanometer-sized TiO{sub 2} nanoparticles was developed. In this system extended charge separation reflects the sequence of DNA and was measured using metallic silver deposition or by photocurrent response. Light-induced extended charge separation in these systems was found to be dependent on the DNA-bridge length and sequence. The yield of photocatalytic deposition of silver was studied in systems having GG accepting sites imbedded in AT runs at varying distances from the TiO{sub 2} nanoparticle surface. Weak distance dependence of charge separation indicative of a hole hopping through mediating adenine (A) sites was found. The quantum yield of silver deposition in the system having a GG accepting site placed 8.5 {angstrom} from the nanoparticle surface was found to be {Phi} = 0.70 (70%) and {Phi} = 0.56 (56%) for (A){sub n} and (AT){sub n/2} bridge, respectively. Hole injection to GG trapping sites as far as 70 {angstrom} from a nanoparticle surface in the absence of G hopping sites was measured. Introduction of G hopping sites increased the efficiency of hole injection. The efficiency of photocatalytic deposition of metallic silver was found to be sensitive to the presence of a single nucleobase mismatch in the DNA sequence.

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

    SciTech Connect (OSTI)

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

    2008-12-04

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

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

    SciTech Connect (OSTI)

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

    2008-12-16

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

  2. NREL: Transportation Research - Fleet DNA: Commercial Fleet Vehicle

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

    Operating Data Fleet DNA: Commercial Fleet Vehicle Operating Data Contribute Data Learn how to contribute to Fleet DNA anonymously to help other fleets analyze and improve their drive cycle metrics. The Fleet DNA clearinghouse of commercial fleet vehicle operating data helps vehicle manufacturers and developers optimize vehicle designs and helps fleet managers choose advanced technologies for their fleets. This online tool provides data summaries and visualizations similar to real-world

  3. 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 Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Wednesday, 26 January 2011 00:00 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

  4. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

    DNA-Binding Mechanism in Prokaryotic Partition Complex Formation DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print Wednesday, 29 March 2006 00:00 The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of

  5. Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine

    Office of Scientific and Technical Information (OSTI)

    lipoplexes. Mechanism of the gel-liquid crystalline lipid phase transition (Journal Article) | SciTech Connect Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine lipoplexes. Mechanism of the gel-liquid crystalline lipid phase transition Citation Details In-Document Search Title: Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine lipoplexes. Mechanism of the gel-liquid crystalline lipid phase transition DNA arranges into rectangular columnar superlattices between

  6. DNA release from lipoplexes by anionic lipids: correlation with lipid

    Office of Scientific and Technical Information (OSTI)

    mesomorphism, interfacial curvature, and membrane fusion (Journal Article) | SciTech Connect DNA release from lipoplexes by anionic lipids: correlation with lipid mesomorphism, interfacial curvature, and membrane fusion Citation Details In-Document Search Title: DNA release from lipoplexes by anionic lipids: correlation with lipid mesomorphism, interfacial curvature, and membrane fusion DNA release from lipoplexes is an essential step during lipofection and is probably a result of charge

  7. Charge Transport within a Three-Dimensional DNA Nanostructure Framework

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

    Charge Transport within a Three-Dimensional DNA Nanostructure Framework Authors: Lu, N., Pei, H., Ge, Z., Simmons, C.R., Yan, H., and Fan, C. Title: Charge Transport within a Three-Dimensional DNA Nanostructure Framework Source: Journal of the American Chemical Society Year: 2012 Volume: 134 Pages: 13148-13151 ABSTRACT: Three-dimensional (3D) DNA nanostructures have shown great promise for various applications including molecular sensing and therapeutics. Here we report kinetic studies of

  8. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Wednesday, 28 October 2009 00:00 Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has

  9. Transposon-containing DNA cloning vector and uses thereof

    DOE Patents [OSTI]

    Berg, C.M.; Berg, D.E.; Wang, G.

    1997-07-08

    The present invention discloses a rapid method of restriction mapping, sequencing or localizing genetic features in a segment of deoxyribonucleic acid (DNA) that is up to 42 kb in size. The method in part comprises cloning of the DNA segment in a specialized cloning vector and then isolating nested deletions in either direction in vivo by intramolecular transposition into the cloned DNA. A plasmid has been prepared and disclosed. 4 figs.

  10. Transposon-containing DNA cloning vector and uses thereof

    DOE Patents [OSTI]

    Berg, Claire M.; Berg, Douglas E.; Wang, Gan

    1997-01-01

    The present invention discloses a rapid method of restriction mapping, sequencing or localizing genetic features in a segment of deoxyribonucleic acid (DNA) that is up to 42 kb in size. The method in part comprises cloning of the DNA segment in a specialized cloning vector and then isolating nested deletions in either direction in vivo by intramolecular transposition into the cloned DNA. A plasmid has been prepared and disclosed.

  11. DNA Gridiron Nanostructures Based on Four-Arm Junctions

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

    DNA Gridiron Nanostructures Based on Four-Arm Junctions Authors: Han, D., Pal, S., Yang, Y., Jiang, S., Nangreave, J., Liu, Y., and Yan, H. Title: DNA Gridiron Nanostructures Based on Four-Arm Junctions Source: Science Year: 2013 Volume: 339 Pages: 1412-1415 ABSTRACT: Engineering wireframe architectures and scaffolds of increasing complexity is one of the important challenges in nanotechnology. We present a design strategy to create gridiron-like DNA structures. A series of four-arm junctions

  12. DNA-Based Optomechanical Molecular Motor

    SciTech Connect (OSTI)

    McCullagh, Martin; Franco, Ignacio; Ratner, Mark A.; Schatz, George C.

    2011-03-16

    An azobenzene-capped DNA hairpin coupled to an AFM is presented as an optically triggered single-molecule motor. The photoinduced trans to cis isomerization of azobenzene affects both the overall length of the molecule and the ability of the DNA bases to hybridize. Using a combination of molecular dynamics simulations and free energy calculations the unfolding of both isomers along the O5'-O3' extension coordinate is monitored. The potentials of mean force (PMFs) along this coordinate indicate that there are two major differences induced by photoisomerization. The first is that the interbase hydrogen bond and stacking interactions are stable for a greater range of extensions in the trans system than in the cis system. The second difference is due to a decreased chain length of the cis isomer with respect to the trans isomer. These differences are exploited to extract work in optomechanical cycles. The disruption of the hairpin structure gives a maximum of 3.4 kcal mol-1 of extractable work per cycle with an estimated maximum efficiency of 2.4%. Structure-function insights into the operation of this motor are provided, and the effect of the cantilever stiffness on the extractable work is characterized.

  13. Structure and mechanism of human DNA polymerase [eta] (Journal...

    Office of Scientific and Technical Information (OSTI)

    DNA polymerase eta Citation Details In-Document ... Here we report high-resolution crystal structures of human ... OSTI Identifier: 1002510 Resource Type: Journal Article ...

  14. 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.

  15. Jefferson Lab Hosts Upcoming Science Lectures on DNA and Chocolate...

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

    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...

  16. Nanoscale topographical replication of graphene architecture by artificial DNA nanostructures

    SciTech Connect (OSTI)

    Moon, Y.; Seo, S.; Park, J.; Park, T.; Ahn, J. R., E-mail: jrahn@skku.edu [Department of Physics, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Shin, J.; Dugasani, S. R. [Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Woo, S. H. [College of Pharmacy, Chungnam National University, Daejeon 305-764 (Korea, Republic of); Park, S. H., E-mail: sunghapark@skku.edu [Department of Physics, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 440-746 (Korea, Republic of)

    2014-06-09

    Despite many studies on how geometry can be used to control the electronic properties of graphene, certain limitations to fabrication of designed graphene nanostructures exist. Here, we demonstrate controlled topographical replication of graphene by artificial deoxyribonucleic acid (DNA) nanostructures. Owing to the high degree of geometrical freedom of DNA nanostructures, we controlled the nanoscale topography of graphene. The topography of graphene replicated from DNA nanostructures showed enhanced thermal stability and revealed an interesting negative temperature coefficient of sheet resistivity when underlying DNA nanostructures were denatured at high temperatures.

  17. DNA-NV-030-09-03 | Open Energy Information

    Open Energy Info (EERE)

    Info Energy Sector Geothermal energy Environmental Analysis Type DNA Applicant Dusty Miller LLC Geothermal Area Gabbs Valley Geothermal Area Project Location Nevada Project Phase...

  18. When DNA Needs to Stand Up and Be Counted

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

    biomolecules must be properly oriented to perform their biological function. In other words, the DNA literally must stand up to be counted. Understanding both the attachment...

  19. Ionic switch controls the DNA state in phage λ

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

    Li, Dong; Liu, Ting; Zuo, Xiaobing; Li, Tao; Qiu, Xiangyun; Evilevitch, Alex

    2015-06-19

    We have recently found that DNA packaged in phage λ undergoes a disordering transition triggered by temperature, which results in increased genome mobility. This solid-to-fluid like DNA transition markedly increases the number of infectious λ particles facilitating infection. However, the structural transition strongly depends on temperature and ionic conditions in the surrounding medium. Using titration microcalorimetry combined with solution X-ray scattering, we mapped both energetic and structural changes associated with transition of the encapsidated λ-DNA. Packaged DNA needs to reach a critical stress level in order for transition to occur. We varied the stress on DNA in the capsid bymore » changing the temperature, packaged DNA length and ionic conditions. We found striking evidence that the intracapsid DNA transition is ‘switched on’ at the ionic conditions mimicking those in vivo and also at the physiologic temperature of infection at 37°C. This ion regulated on-off switch of packaged DNA mobility in turn affects viral replication. The results suggest a remarkable adaptation of phage λ to the environment of its host bacteria in the human gut. The metastable DNA state in the capsid provides a new paradigm for the physical evolution of viruses.« less

  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. Ionic switch controls the DNA state in phage λ

    SciTech Connect (OSTI)

    Li, Dong; Liu, Ting; Zuo, Xiaobing; Li, Tao; Qiu, Xiangyun; Evilevitch, Alex

    2015-06-19

    We have recently found that DNA packaged in phage λ undergoes a disordering transition triggered by temperature, which results in increased genome mobility. This solid-to-fluid like DNA transition markedly increases the number of infectious λ particles facilitating infection. However, the structural transition strongly depends on temperature and ionic conditions in the surrounding medium. Using titration microcalorimetry combined with solution X-ray scattering, we mapped both energetic and structural changes associated with transition of the encapsidated λ-DNA. Packaged DNA needs to reach a critical stress level in order for transition to occur. We varied the stress on DNA in the capsid by changing the temperature, packaged DNA length and ionic conditions. We found striking evidence that the intracapsid DNA transition is ‘switched on’ at the ionic conditions mimicking those in vivo and also at the physiologic temperature of infection at 37°C. This ion regulated on-off switch of packaged DNA mobility in turn affects viral replication. The results suggest a remarkable adaptation of phage λ to the environment of its host bacteria in the human gut. The metastable DNA state in the capsid provides a new paradigm for the physical evolution of viruses.

  2. Three-Dimensional Modeling and Simulation of DNA Hybridization...

    Office of Scientific and Technical Information (OSTI)

    Three-Dimensional Modeling and Simulation of DNA Hybridization Kinetics and Mass Transport ... Kinetics and Mass Transport as Functions of Temperature in a Microfluidic Channel. ...

  3. Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine...

    Office of Scientific and Technical Information (OSTI)

    Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine lipoplexes. Mechanism of the gel-liquid crystalline lipid phase transition Citation Details In-Document Search ...

  4. Molecular Sunscreen: How DNA Protects Itself from UV Light |...

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

    Molecular Sunscreen: How DNA Protects Itself from UV Light Basic Energy Sciences (BES) BES Home ... and Biosciences Division of the Office of Basic Energy Sciences, Office of ...

  5. Fleet DNA Project - Data Dictionary for Public Download Files

    SciTech Connect (OSTI)

    Duran, A.; Burton, E.; Kelly, K.; Walkowicz, K.

    2014-09-01

    Reference document for the Fleet DNA results data shared on the NREL public website. The document includes variable definitions and descriptions to assist users in understanding data.

  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. Analysis of a double-ended cold-leg break simulation: THTF Test 3. 05. 5B. [PWR

    SciTech Connect (OSTI)

    Craddick, W.G.; Pevey, R.E.

    1982-09-01

    On July 3, 1980, an experiment was performed in the Oak Ridge National Laboratory Thermal-Hydraulic Test Facility that simulated a double-ended cold-leg break pressurized-water reactor (PWR) accident. Analysis of the experiment revealed that nuclear fuel rods exposed to the same hydrodynamic environment as that which existed in the experiment would have departed from nucleate boiling both earlier and later than the fuel rod simulator (FRS), depending on the size of the gap between the nuclear fuel pellets and cladding and on the initial power of the nuclear fuel rod. Comparison of the results of the current experiment, which used an FRS bundle with geometry similar to 17 x 17 PWR fuel assemblies, to the results of earlier experiments, which used an FRS bundle with geometry similar to 15 x 15 PWR fuel assemblies, revealed no differences that can be attributed to the difference in geometries.

  8. Belgian experience in applying the {open_quotes}leak-before-break{close_quotes} concept to the primary loop piping

    SciTech Connect (OSTI)

    Gerard, R.; Malekian, C.; Meessen, O.

    1997-04-01

    The Leak Before Break (LBB) concept allows to eliminate from the design basis the double-ended guillotine break of the primary loop piping, provided it can be demonstrated by a fracture mechanics analysis that a through-wall flaw, of a size giving rise to a leakage still well detectable by the plant leak detection systems, remains stable even under accident conditions (including the Safe Shutdown Earthquake (SSE)). This concept was successfully applied to the primary loop piping of several Belgian Pressurized Water Reactor (PWR) units, operated by the Utility Electrabel. One of the main benefits is to permit justification of supports in the primary loop and justification of the integrity of the reactor pressure vessel and internals in case of a Loss Of Coolant Accident (LOCA) in stretch-out conditions. For two of the Belgian PWR units, the LBB approach also made it possible to reduce the number of large hydraulic snubbers installed on the primary coolant pumps. Last but not least, the LBB concept also facilitates the steam generator replacement operations, by eliminating the need for some pipe whip restraints located close to the steam generator. In addition to the U.S. regulatory requirements, the Belgian safety authorities impose additional requirements which are described in details in a separate paper. An novel aspect of the studies performed in Belgium is the way in which residual loads in the primary loop are taken into account. Such loads may result from displacements imposed to close the primary loop in a steam generator replacement operation, especially when it is performed using the {open_quote}two cuts{close_quotes} technique. The influence of such residual loads on the LBB margins is discussed in details and typical results are presented.

  9. Comparative mapping of DNA markers from the familial Alzheimer disease and Down syndrome regions of human chromosome 21 to mouse chromosomes 16 and 17

    SciTech Connect (OSTI)

    Cheng, S.V.; Nadeau, J.H.; Tanzi, R.E.; Watkins, P.C.; Jagadesh, J.; Taylor, B.A.; Haines, J.L.; Sacchi, N.; Gusella, J.F. )

    1988-08-01

    Mouse trisomy 16 has been proposed as an animal model of Down syndrome (DS), since this chromosome contains homologues of several loci from the q22 band of human chromosome 21. The recent mapping of the defect causing familial Alzheimer disease (FAD) and the locus encoding the Alzheimer amyloid {beta} precursor protein (APP) to human chromosome 21 has prompted a more detailed examination of the extent of conservation of this linkage group between the two species. Using anonymous DNA probes and cloned genes from human chromosome 21 in a combination of recombinant inbred and interspecific mouse backcross analyses, the authors have established that the linkage group shared by mouse chromosome 16 includes not only the critical DS region of human chromosome 21 but also the APP gene and FAD-linked markers. Extending from the anonymous DNA locus D21S52 to ETS2, the linkage map of six loci spans 39% recombination in man but only 6.4% recombination in the mouse. A break in synteny occurs distal to ETS2, with the homologue of the human marker D21S56 mapping to mouse chromosome 17. Conservation of the linkage relationships of markers in the FAD region suggests that the murine homologue of the FAD locus probably maps to chromosome 16 and that detailed comparison of the corresponding region in both species could facilitate identification of the primary defect in this disorder. The break in synteny between the terminal portion of human chromosome 21 and mouse chromosome 16 indicates, however, that mouse trisomy 16 may not represent a complete model of DS.

  10. Automated DNA Base Pair Calling Algorithm

    Energy Science and Technology Software Center (OSTI)

    1999-07-07

    The procedure solves the problem of calling the DNA base pair sequence from two channel electropherogram separations in an automated fashion. The core of the program involves a peak picking algorithm based upon first, second, and third derivative spectra for each electropherogram channel, signal levels as a function of time, peak spacing, base pair signal to noise sequence patterns, frequency vs ratio of the two channel histograms, and confidence levels generated during the run. Themore » ratios of the two channels at peak centers can be used to accurately and reproducibly determine the base pair sequence. A further enhancement is a novel Gaussian deconvolution used to determine the peak heights used in generating the ratio.« less

  11. Hybridization and Selective Release of DNA Microarrays

    SciTech Connect (OSTI)

    Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J; Benett, W; Mukerjee, E; Dzenitis, J; Wheeler, E K

    2011-11-29

    DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy to single spots to release hybridized DNA. This work leverages LLNL expertise in optics, microfluids, and bioinformatics.

  12. Energy and Technology Review: Unlocking the mysteries of DNA repair

    SciTech Connect (OSTI)

    Quirk, W.A.

    1993-04-01

    DNA, the genetic blueprint, has the remarkable property of encoding its own repair following diverse types of structural damage induced by external agents or normal metabolism. We are studying the interplay of DNA damaging agents, repair genes, and their protein products to decipher the complex biochemical pathways that mediate such repair. Our research focuses on repair processes that correct DNA damage produced by chemical mutagens and radiation, both ionizing and ultraviolet. The most important type of DNA repair in human cells is called excision repair. This multistep process removes damaged or inappropriate pieces of DNA -- often as a string of 29 nucleotides containing the damage -- and replaces them with intact ones. We have isolated, cloned, and mapped several human repair genes associated with the nucleotide excision repair pathway and involved in the repair of DNA damage after exposure to ultraviolet light or mutagens in cooked food. We have shown that a defect in one of these repair genes, ERCC2, is responsible for the repair deficiency in one of the groups of patients with the recessive genetic disorder xeroderma pigmentosum (XP group D). We are exploring ways to purify sufficient quantities (milligrams) of the protein products of these and other repair genes so that we can understand their functions. Our long-term goals are to link defective repair proteins to human DNA repair disorders that predispose to cancer, and to produce DNA-repair-deficient mice that can serve as models for the human disorders.

  13. cDNA encoding a polypeptide including a hevein sequence

    DOE Patents [OSTI]

    Raikhel, N.V.; Broekaert, W.F.; Namhai Chua; Kush, A.

    1993-02-16

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids.

  14. Sensitivity to methylmercury toxicity is enhanced in oxoguanine glycosylase 1 knockout murine embryonic fibroblasts and is dependent on cellular proliferation capacity

    SciTech Connect (OSTI)

    Ondovcik, Stephanie L.; Tamblyn, Laura; McPherson, John Peter; Wells, Peter G.

    2013-07-01

    Methylmercury (MeHg) is a persistent environmental contaminant with potent neurotoxic action for which the underlying molecular mechanisms remain to be conclusively delineated. Our objectives herein were twofold: first, to corroborate our previous findings of an increased sensitivity of spontaneously-immortalized oxoguanine glycosylase 1-null (Ogg1{sup ?/?}) murine embryonic fibroblasts (MEFs) to MeHg through generation of Simian virus 40 (SV40) large T antigen-immortalized wild-type and Ogg1{sup ?/?} MEFs; and second, to determine whether MeHg toxicity is proliferation-dependent. As with the spontaneously-immortalized cells used previously, the SV40 large T antigen-immortalized cells exhibited similar tendencies to undergo MeHg-initiated cell cycle arrest, with increased sensitivity in the Ogg1{sup ?/?} MEFs as measured by clonogenic survival and DNA damage. Compared to exponentially growing cells, those seeded at a higher density exhibited compromised proliferation, which proved protective against MeHg-mediated cell cycle arrest and induction of DNA double strand breaks (DSBs), measured by phosphorylation of the core histone H2A variant (H2AX) on serine 139 (?H2AX), and by its functional confirmation by micronucleus assessment. This enhanced sensitivity of Ogg1{sup ?/?} MEFs to MeHg toxicity using discrete SV40 immortalization corroborates our previous studies, and suggests a novel role for OGG1 in minimizing MeHg-initiated DNA lesions that trigger replication-associated DSBs. Furthermore, proliferative capacity may determine MeHg toxicity in vivo and in utero. Accordingly, variations in cellular proliferative capacity and interindividual variability in repair activity may modulate the risk of toxicological consequences following MeHg exposure. - Highlights: SV40 large T antigen-immortalized Ogg1{sup ?/?} cells are more sensitive to MeHg. Sensitivity to MeHg is dependent on cellular proliferation capacity. OGG1 maintains genomic integrity following MeHg-initiated DNA damage. OGG1 may limit MeHg-initiated DNA lesions that trigger replication-associated DSBs. Variations in proliferation and repair activity may modulate toxicological risk.

  15. Inhibition of B-NHEJ in Plateau-Phase Cells Is Not a Direct Consequence of Suppressed Growth Factor Signaling

    SciTech Connect (OSTI)

    Singh, Satyendra K.; Bednar, Theresa; Zhang Lihua; Wu, Wenqi; Mladenov, Emil; Iliakis, George

    2012-10-01

    Purpose: It has long been known that the proliferation status of a cell is a determinant of radiation response, and the available evidence implicates repair of DNA double-strand breaks (DSBs) in the underlying mechanism. Recent results have shown that a novel, highly error-prone pathway of nonhomologous end joining (NHEJ) operating as backup (B-NHEJ) processes DSBs in irradiated cells when the canonical, DNA-PK (DNA-dependent protein kinase)-dependent pathway of NHEJ (D-NHEJ) is compromised. Notably, B-NHEJ shows marked reduction in efficiency when D-NHEJ-deficient cells cease to grow and enter a plateau phase. This phenomenon is widespread and observed in cells of different species with defects in core components of D-NHEJ, with the notable exception of DNA-PKcs (DNA-dependent protein kinase, catalytic subunit). Using new, standardized serum-deprivation protocols, we re-examine the growth requirements of B-NHEJ and test the role of epidermal growth factor receptor (EGFR) signaling in its regulation. Methods and Materials: DSB repair was measured by pulsed-field gel electrophoresis in cells maintained under different conditions of growth. Results: Serum deprivation in D-NHEJ-deficient cells causes a rapid reduction in B-NHEJ similar to that measured in normally growing cells that enter the plateau phase of growth. Upon serum deprivation, reduction in B-NHEJ activity is evident at 4 h and reaches a plateau reflecting maximum inhibition at 12-16 h. The inhibition is reversible, and B-NHEJ quickly recovers to the levels of actively growing cells upon supply of serum to serum-deprived cells. Chemical inhibition of EGFR in proliferating cells inhibits only marginally B-NHEJ and addition of EGFR in serum-deprived cells increases only a marginally B-NHEJ. Conclusions: The results document a rapid and fully reversible adaptation of B-NHEJ to growth activity and point to factors beyond EGFR in its regulation. They show notable differences in the regulation of error-prone DSB repair pathways between proliferating and non proliferating cells that may present new treatment design opportunities in radiation therapy.

  16. The mystery of spectral breaks: Lyman continuum absorption by photon-photon pair production in the Fermi GeV spectra of bright blazars

    SciTech Connect (OSTI)

    Stern, Boris E. [Institute for Nuclear Research, Russian Academy of Sciences, Prospekt 60-letiya Oktyabrya 7a, Moscow 117312 (Russian Federation); Poutanen, Juri, E-mail: stern.boris@gmail.com, E-mail: juri.poutanen@utu.fi [Tuorla Observatory, University of Turku, Vislntie 20, FI-21500 Piikki (Finland)

    2014-10-10

    We re-analyze Fermi/LAT ?-ray spectra of bright blazars using the new Pass 7 version of the detector response files and detect breaks at ?5 GeV in the rest-frame spectra of 3C 454.3 and possibly also 4C +21.35, associated with the photon-photon pair production absorption by the He II Lyman continuum (LyC). We also detect significant breaks at ?20 GeV associated with hydrogen LyC in both the individual spectra and the stacked redshift-corrected spectrum of several bright blazars. The detected breaks in the stacked spectra univocally prove that they are associated with atomic ultraviolet emission features of the quasar broad-line region (BLR). The dominance of the absorption by the hydrogen Ly complex over He II, a small detected optical depth, and break energy consistent with head-on collisions with LyC photons imply that the ?-ray emission site is located within the BLR, but most of the BLR emission comes from a flat disk-like structure producing little opacity. Alternatively, the LyC emission region size might be larger than the BLR size measured from reverberation mapping, and/or the ?-ray emitting region is extended. These solutions would resolve the long-standing issue of how the multi-hundred GeV photons can escape from the emission zone without being absorbed by softer photons.

  17. Pressure effects on magnetic pair-breaking in Mn- and Eu-substituted BaFe{sub 2}As{sub 2}

    SciTech Connect (OSTI)

    Rosa, P. F. S.; Garitezi, T. M.; Adriano, C.; Urbano, R. R.; Pagliuso, P. G.; Grant, T.; Fisk, Z.; Fernandes, R. M.

    2014-05-07

    We report a combined study of hydrostatic pressure (P ? 25 kbar) and chemical substitution on the magnetic pair-breaking effect in Eu- and Mn-substituted BaFe{sub 2}As{sub 2} single crystals. At ambient pressure, both substitutions suppress the superconducting (SC) transition temperature (T{sub c}) of BaFe{sub 2x}Co{sub x}As{sub 2} samples slightly under the optimally doped region, indicating the presence of a pair-breaking effect. At low pressures, an increase of T{sub c} is observed for all studied compounds followed by an expected decrease at higher pressures. However, in the Eu dilute system, T{sub c} further increases at higher pressure along with a narrowing of the SC transition, suggesting that a pair-breaking mechanism reminiscent of the Eu Kondo single impurity regime is being suppressed by pressure. Furthermore, Electron Spin Resonance (ESR) measurements indicate the presence of Mn{sup 2+} and Eu{sup 2+} local moments and the microscopic parameters extracted from the ESR analysis reveal that the AbrikosovGor'kov expression for magnetic pair-breaking in a conventional sign-preserving superconducting state cannot describe the observed reduction of T{sub c}.

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

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

    Structure of DNA-Bound FEN1 Reveals Mechanism of Action Structure of DNA-Bound FEN1 Reveals Mechanism of Action Print Tuesday, 24 January 2012 11:30 DNA replication is a critical...

  19. Structures of Clamp-Loader Complexes Are Key to DNA Replication

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

    Structures of Clamp-Loader Complexes Are Key to DNA Replication Structures of Clamp-Loader Complexes Are Key to DNA Replication Print Wednesday, 30 May 2012 00:00 DNA Replication:...

  20. DOI-BLM-NV-W030-2012-0011-DNA | Open Energy Information

    Open Energy Info (EERE)

    Notes GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. Documents DNA Worksheet: DNA R&C Doc FINAL DOI-BLM-NV-W030-2012-0011-DNA.pdf...

  1. DOI-BLM-NV-C010-2013-0007-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. 942013: DNA file uploaded Documents DNA Worksheet: DOI-BLM-NV-C010-2013-0007-DNA....

  2. DOI-BLM-NV-C010-2012-0020-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. 8292013: DNA uploaded Documents DNA Worksheet: DOI-BLM-NV-C010-2012-0020-DNA.pdf...

  3. 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

  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. DOI-BLM-NV-C010-2012-0073-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. 8292013- uploaded DNA and corrected lease number, incorrect on DNA form should be...

  6. Sensitive method for measurement of telomeric DNA content in human tissues

    DOE Patents [OSTI]

    Bryant, Jennifer E.; Hutchings, Kent G.; Moyzis, Robert K.; Griffith, Jeffrey K.

    1999-02-16

    A sensitive method for measurement of telomeric DNA content in human tissue, based upon the ratio of telomeric to centromeric DNA present in the tissue.

  7. A fair compromise to break the climate impasse. A major economies forum approach to emissions reductions budgeting

    SciTech Connect (OSTI)

    Grasso, Marco; J. Roberts, Timmons

    2013-04-15

    Key messages of the study are: Given the stalemate in U.N. climate negotiations, the best arena to strike a workable deal is among the members the Major Economies Forum on Energy and Climate (MEF); The 13 MEF members—including the EU-27 (but not double-counting the four EU countries that are also individual members of the MEF)—account for 81.3 percent of all global emissions; This proposal devises a fair compromise to break the impasse to develop a science-based approach for fairly sharing the carbon budget in order to have a 75 percent chance of avoiding dangerous climate change; To increase the likelihood of a future climate agreement, carbon accounting must shift from production-based inventories to consumption-based ones; The shares of a carbon budget to stay below 2 deg C through 2050 are calculated by cumulative emissions since 1990, i.e. according to a short-horizon polluter pays principle, and national capability (income), and allocated to MEF members through emission rights. This proposed fair compromise addresses key concerns of major emitters; According to this accounting, no countries have negative carbon budgets, there is substantial time for greening major developing economies, and some developed countries need to institute very rapid reductions in emissions; and, To provide a 'green ladder' to developing countries and to ensure a fair global deal, it will be crucial to agree how to extend sufficient and predictable financial support and the rapid transfer of technology.

  8. Dynamical instability of white dwarfs and breaking of spherical symmetry under the presence of extreme magnetic fields

    SciTech Connect (OSTI)

    Coelho, J. G.; Cceres, D. L.; Rueda, J. A.; Ruffini, R. [Dipartimento di Fisica and ICRA, Sapienza Universit di Roma, P.le Aldo Moro 5, I-00185 Rome (Italy); Marinho, R. M.; Malheiro, M. [Departamento de Fsica, Instituto Tecnolgico de Aeronutica, ITA, So Jos dos Campos, 12228-900 SP (Brazil); Negreiros, R., E-mail: jaziel.coelho@icranet.org, E-mail: jorge.rueda@icra.it, E-mail: m.malheiro@ita.br [Instituto de Fsica, Universidade Federal Fluminense, UFF, Niteri, 24210-346 RJ (Brazil)

    2014-10-10

    Massive, highly magnetized white dwarfs with fields up to 10{sup 9} G have been observed and theoretically used for the description of a variety of astrophysical phenomena. Ultramagnetized white dwarfs with uniform interior fields up to 10{sup 18} G have been recently purported to obey a new maximum mass limit, M {sub max} ? 2.58 M {sub ?}, which largely overcomes the traditional Chandrasekhar value, M {sub Ch} ? 1.44 M {sub ?}. Such a larger limit would make these astrophysical objects viable candidates for the explanation of the superluminous population of Type Ia supernovae. We show that several macro and micro physical aspects such as gravitational, dynamical stability, breaking of spherical symmetry, general relativity, inverse ? decay, and pycnonuclear fusion reactions are of most relevance for the self-consistent description of the structure and assessment of stability of these objects. It is shown in this work that the first family of magnetized white dwarfs indeed satisfy all the criteria of stability, while the ultramagnetized white dwarfs are very unlikely to exist in nature since they violate minimal requests of stability. Therefore, the canonical Chandrasekhar mass limit of white dwarfs still has to be applied.

  9. TRAC-PF1/MOD1 independent assessment: Semiscale Mod-2A intermediate break test S-IB-3

    SciTech Connect (OSTI)

    Kmetyk, L N

    1986-02-01

    The TRAC-PF1/MOD1 independent assessment project at Sandia National Laboratories is part of an overall effort funded by the NRC to determine the ability of various system codes to predict the detailed thermal/hydraulic response of light water reactors during accident and off-normal conditions. The TRAC code is being assessed at SNLA against test data from various integral and separate effects test facilities. As part of this assessment matrix, an intermediate break test (S-IB-3), performed at the Semiscale Mod-2A facility, has been analyzed. Using an input model with a 3-D VESSEL component, the vessel and downcomer inventories during 3-IB-3 were generally well predicted, but the core heatup was underpredicted compared to data. An equivalent calculation with an all 1-D input model ran about twice as fast as our basecase analysis using a 3-D VESSEL in the input model, but the results of the two calculations diverged significantly for many parameters of interest, with the 3-D VESSEL model results in better agreement with data. 22 refs., 100 figs.

  10. Identification of limiting case between DBA and SBDBA (CL break area sensitivity): A new model for the boron injection system

    SciTech Connect (OSTI)

    Gonzalez Gonzalez, R.; Petruzzi, A.; D'Auria, F.; Mazzantini, O.

    2012-07-01

    Atucha-2 is a Siemens-designed PHWR reactor under construction in the Republic of Argentina. Its geometrical complexity and (e.g., oblique Control Rods, Positive Void coefficient) required a developed and validated complex three dimensional (3D) neutron kinetics (NK) coupled thermal hydraulic (TH) model. Reactor shut-down is obtained by oblique CRs and, during accidental conditions, by an emergency shut-down system (JDJ) injecting a highly concentrated boron solution (boron clouds) in the moderator tank, the boron clouds reconstruction is obtained using a CFD (CFX) code calculation. A complete LBLOCA calculation implies the application of the RELAP5-3D{sup C} system code. Within the framework of the third Agreement 'NA-SA - Univ. of Pisa' a new RELAP5-3D control system for the boron injection system was developed and implemented in the validated coupled RELAP5-3D/NESTLE model of the Atucha 2 NPP. The aim of this activity is to find out the limiting case (maximum break area size) for the Peak Cladding Temperature for LOCAs under fixed boundary conditions. (authors)

  11. 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.

  12. 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.

  13. Method for rapid base sequencing in DNA and RNA

    DOE Patents [OSTI]

    Jett, James H.; Keller, Richard A.; Martin, John C.; Moyzis, Robert K.; Ratliff, Robert L.; Shera, E. Brooks; Stewart, Carleton C.

    1990-01-01

    A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed.

  14. Method for rapid base sequencing in DNA and RNA

    DOE Patents [OSTI]

    Jett, J.H.; Keller, R.A.; Martin, J.C.; Moyzis, R.K.; Ratliff, R.L.; Shera, E.B.; Stewart, C.C.

    1987-10-07

    A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed. 2 figs.

  15. Method for rapid base sequencing in DNA and RNA

    DOE Patents [OSTI]

    Jett, J.H.; Keller, R.A.; Martin, J.C.; Moyzis, R.K.; Ratliff, R.L.; Shera, E.B.; Stewart, C.C.

    1990-10-09

    A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed. 2 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. Polymorphism of DNA-anionic Liposome Complexes Reveals Hierarchy...

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

    ... bound electrostatically to lipids and DNA, thus gaining translational entropy in the bulk. ... dehydration of the lipid headgroups, while others such as Mg2+ have a much smaller effect. ...

  18. 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.

  19. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    ... It turns out that ATL bridges two DNA repair pathways (base repair and nucleotide excision ... By mapping conservation of amino acid sequences between their ATL and sequences in other ...

  20. Visually Relating Gene Expression and in vivo DNA Binding Data

    SciTech Connect (OSTI)

    Huang, Min-Yu; Mackey, Lester; Ker?; nen, Soile V. E.; Weber, Gunther H.; Jordan, Michael I.; Knowles, David W.; Biggin, Mark D.; Hamann, Bernd

    2011-09-20

    Gene expression and in vivo DNA binding data provide important information for understanding gene regulatory networks: in vivo DNA binding data indicate genomic regions where transcription factors are bound, and expression data show the output resulting from this binding. Thus, there must be functional relationships between these two types of data. While visualization and data analysis tools exist for each data type alone, there is a lack of tools that can easily explore the relationship between them. We propose an approach that uses the average expression driven by multiple of ciscontrol regions to visually relate gene expression and in vivo DNA binding data. We demonstrate the utility of this tool with examples from the network controlling early Drosophila development. The results obtained support the idea that the level of occupancy of a transcription factor on DNA strongly determines the degree to which the factor regulates a target gene, and in some cases also controls whether the regulation is positive or negative.

  1. Vehicle Technologies Office Merit Review 2014: Fleet DNA

    Broader source: Energy.gov [DOE]

    Presentation given by National Renewable Energy Laboratory at 2014 DOE Hydrogen and Fuel Cells Program and Vehicle Technologies Office Annual Merit Review and Peer Evaluation Meeting about fleet DNA.

  2. Unveiling Stability Criteria of DNA-Carbon Nanotubes Constructs...

    Office of Scientific and Technical Information (OSTI)

    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...

  3. When DNA Needs to Stand Up and Be Counted

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

    stand up to be counted. Understanding both the attachment and orientation of DNA on gold surfaces was the goal of recent experiments performed at ALS Beamline 8.0.1 by an...

  4. 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

  5. Roger D. Kornberg Polymerase, DNA, RNA, and Transcription

    Office of Scientific and Technical Information (OSTI)

    Roger D. Kornberg Polymerase, DNA, RNA, and Transcription Resources with Additional Information Roger D. Kornberg Credit: Linda A. Cicero/ Stanford News Service Roger D. Kornberg was awarded the 2006 Nobel Prize in Chemistry "for his studies of the molecular basis of eukaryotic transcription". He determined 'how DNA's genetic blueprint is read and used to direct the process for protein manufacture. Kornberg carried out a significant part of the research leading to this prize at the

  6. Microfluidics: Kinetics of Hybridized DNA With Fluid Flow Variations.

    Office of Scientific and Technical Information (OSTI)

    (Conference) | SciTech Connect Microfluidics: Kinetics of Hybridized DNA With Fluid Flow Variations. Citation Details In-Document Search Title: Microfluidics: Kinetics of Hybridized DNA With Fluid Flow Variations. Abstract not provided. Authors: Sparks, Elizabeth Schares ; Manginell, Ronald Paul Publication Date: 2011-10-01 OSTI Identifier: 1106575 Report Number(s): SAND2011-7607C 464923 DOE Contract Number: AC04-94AL85000 Resource Type: Conference Resource Relation: Conference: MSEC 105

  7. Modulating the Bond Strength of DNA-Nanoparticle Superlattices (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Modulating the Bond Strength of DNA-Nanoparticle Superlattices Citation Details In-Document Search Title: Modulating the Bond Strength of DNA-Nanoparticle Superlattices Authors: Seo, Soyoung E. ; Wang, Mary X. ; Shade, Chad M. ; Rouge, Jessica L. ; Brown, Keith A. ; Mirkin, Chad A. [1] + Show Author Affiliations NWU Publication Date: 2016-03-24 OSTI Identifier: 1240175 Resource Type: Journal Article Resource Relation: Journal Name: ACS Nano; Journal Volume: 10;

  8. Forensic DNA data banking by state crime labortaories

    SciTech Connect (OSTI)

    McEwen, J.E.

    1995-06-01

    This article reports the results of a survey of the responsible crime laboratories in the first 19 states with legislation establishing forensic DNA data banks. The survey inquired into the labs` policies and procedures regarding the collection, storage, and analysis of samples; the retention of samples and data; search protocols; access to samples and data by third parties; and related matters. The research suggests that (1) the number of samples collected from convicted offenders for DNA data banking has far surpassed the number that have been analyzed; (2) data banks have already been used in a small but growing number of cases, to locate suspects and to identify associations between unresolved cases; (3) crime labs currently plan to retain indefinitely the samples collected for their data banks; and (4) the nature and extent of security safeguards that crime labs have implemented for their data banks vary among states. The recently enacted DNA Identification Act (1994) will provide $40 million in federal matching grants to states for DNA analysis activities, so long as states comply with specified quality-assurance standards, submit to external proficiency testing, and limit access to DNA information. Although these additional funds should help to ease some sample backlogs, it remains unclear how labs will allocate the funds, as between analyzing samples for their data banks and testing evidence samples in cases without suspects. The DNA Identification Act provides penalties for the disclosure or obtaining of DNA data held by data banks that participate in CODIS, the FBI`s evolving national network of DNA data banks, but individual crime labs must also develop stringent internal safeguards to prevent breaches of data-bank security. 9 refs., 3 tabs.

  9. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, Natasha V.

    1994-01-04

    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. GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon.

  10. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps

  11. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps

  12. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps

  13. Size selective absorption of DNA tetrahedra in ATO nanomaterials

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

    Size selective absorption of DNA tetrahedra in ATO nanomaterials 22 Jun 2011 A group of Center for Bio-inspired Solar Fuel Production researchers collaborating on Subtask 2 (Water oxidation catalyst) and Subtask 5 (Functional nanostructured transparent electrode materials) have found that transparent and conducting antimony tin oxide with controlled pore size incorporates DNA nanocages with high affinity and without damage. Results of the study have been published in the June 2011 issue of ACS

  14. DNA repair photomachine: Dynamics and mechanism | Stanford Synchrotron

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

    Radiation Lightsource DNA repair photomachine: Dynamics and mechanism Wednesday, March 30, 2016 - 3:00pm SLAC, Redtail Hawk Conference Room 108A Speaker: Dongping Zhong, The Ohio State University Program Description UV radiation can damage DNA and such lesion may eventually lead to skin cancer. Photolyase, a photo-repair machine in nature, can revert such damage with high efficiency. Here, by integrating femtosecond spectroscopy and molecular biology, we have completely mapped out the entire

  15. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

    DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of prokaryotic partition is the Escherichia coli P1 plasmid par system, which consists of a centromere

  16. DNA-Directed Artificial Light-Harvesting Antenna

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

    DNA-Directed Artificial Light-Harvesting Antenna Authors: Dutta, P. K., Varghese, R., Nangreave, J., Lin, S., Yan, H., and Liu, Y. Title: DNA-Directed Artificial Light-Harvesting Antenna Source: Journal of the American Chemical Society Year: 2011 Volume: 133 Pages: 11985-11993 ABSTRACT: Designing and constructing multichromophoric, artificial light-harvesting antennas with controlled interchromophore distances, orientations, and defined donor?acceptor ratios to facilitate efficient

  17. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, N.V.

    1994-01-04

    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. GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon. .

  18. WRNIP1 functions upstream of DNA polymerase ? in the UV-induced DNA damage response

    SciTech Connect (OSTI)

    Yoshimura, Akari; Kobayashi, Yume; Tada, Shusuke; Seki, Masayuki; Enomoto, Takemi

    2014-09-12

    Highlights: The UV sensitivity of POLH{sup ?/?} cells was suppressed by disruption of WRNIP1. In WRNIP1{sup ?/?/?}/POLH{sup ?/?} cells, mutation frequencies and SCE after irradiation reduced. WRNIP1 defect recovered rate of fork progression after irradiation in POLH{sup ?/?} cells. WRNIP1 functions upstream of Pol? in the translesion DNA synthesis pathway. - Abstract: WRNIP1 (WRN-interacting protein 1) was first identified as a factor that interacts with WRN, the protein that is defective in Werner syndrome (WS). WRNIP1 associates with DNA polymerase ? (Pol?), but the biological significance of this interaction remains unknown. In this study, we analyzed the functional interaction between WRNIP1 and Pol? by generating knockouts of both genes in DT40 chicken cells. Disruption of WRNIP1 in Pol?-disrupted (POLH{sup ?/?}) cells suppressed the phenotypes associated with the loss of Pol?: sensitivity to ultraviolet light (UV), delayed repair of cyclobutane pyrimidine dimers (CPD), elevated frequency of mutation, elevated levels of UV-induced sister chromatid exchange (SCE), and reduced rate of fork progression after UV irradiation. These results suggest that WRNIP1 functions upstream of Pol? in the response to UV irradiation.

  19. Breaking Barriers Wildlife Refreshment

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

    Barriers Wildlife Refreshment Walker becomes first black battalion commander. NSTec Aviation Safety Officer, RSL team honored by DOE. NNSS helping wildlife with new watering holes. See pages 8. See page 4. NSTec and UNLV Bring Technology Community Together at PDV Workshop In June 2014, National Security Technologies (NSTec) and University Nevada, Las Vegas (UNLV) co- hosted a Photon Doppler Velocimetry (PDV) Workshop at the UNLV Science and Engineering Building (SEB). More than 125 attendees

  20. DIFFUSE FAR-UV LINE EMISSION FROM THE LOW-REDSHIFT LYMAN BREAK GALAXY ANALOG KISSR242

    SciTech Connect (OSTI)

    France, Kevin; Nell, Nicholas; Green, James C. [Center for Astrophysics and Space Astronomy, 389 UCB, University of Colorado, Boulder, CO 80309 (United States); Leitherer, Claus, E-mail: kevin.france@colorado.ed [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States)

    2010-10-10

    We present new ultraviolet (UV) observations of the luminous compact blue galaxy KISSR242, obtained with the Hubble Space Telescope-Cosmic Origins Spectrograph (HST-COS). We identify multiple resolved sub-arcsecond near-UV sources within the COS aperture. The far-UV spectroscopic data show strong outflow absorption lines, consistent with feedback processes related to an episode of massive star formation. O I, C II, and Si II-Si IV are observed with a mean outflow velocity (v {sub out}) = -60 km s{sup -1}. We also detect faint fine-structure emission lines of singly ionized silicon for the first time in a low-redshift starburst galaxy. These emissions have been seen previously in deep Lyman break galaxy surveys at z {approx} 3. The Si II* lines are at the galaxy rest velocity, and they exhibit a quantitatively different line profile from the absorption features. These lines have a width of {approx}75 km s{sup -1}, too broad for point-like emission sources such as the H II regions surrounding individual star clusters. The size of the Si II* emitting region is estimated to be {approx}250 pc. We discuss the possibility of this emission arising in overlapping super star cluster H II regions, but find this explanation to be unlikely in light of existing far-UV observations of local star-forming galaxies. We suggest that the observed Si II* emission originates in a diffuse warm halo populated by interstellar gas driven out by intense star formation and/or accreted during a recent interaction that may be fueling the present starburst episode in KISSR242.

  1. A LOW ESCAPE FRACTION OF IONIZING PHOTONS OF L > L* LYMAN BREAK GALAXIES AT z = 3.3

    SciTech Connect (OSTI)

    Boutsia, K.; Grazian, A.; Giallongo, E.; Fontana, A.; Pentericci, L.; Castellano, M.; Fiore, F.; Gallozzi, S.; Testa, V.; Paris, D.; Santini, P.; Zamorani, G.; Mignoli, M.; Vanzella, E.; Lilly, S. J.

    2011-07-20

    We present an upper limit for the relative escape fraction (f{sup rel}{sub esc}) of ionizing radiation at z {approx} 3.3 using a sample of 11 Lyman break galaxies (LBGs) with deep imaging in the U band obtained with the Large Binocular Camera, mounted on the prime focus of the Large Binocular Telescope. We selected 11 LBGs with secure redshifts in the range 3.27 < z < 3.35, from three independent fields. We stacked the images of our sources in the R and U bands, which correspond to an effective rest-frame wavelength of 1500 A and 900 A, respectively, obtaining a limit in the U band image of {>=}30.7 mag (AB) at 1{sigma}. We derive a 1{sigma} upper limit of f{sup rel}{sub esc} {approx} 5%, which is one of the lowest values found in the literature so far at z {approx} 3.3. Assuming that the upper limit for the escape fraction that we derived from our sample holds for all galaxies at this redshift, the hydrogen ionization rate that we obtain ({Gamma}{sub -12} < 0.3 s{sup -1}) is not enough to keep the intergalactic medium ionized and a substantial contribution to the UV background by faint active galactic nuclei is required. Since our sample is clearly still limited in size, larger z {approx} 3 LBG samples at similar or even greater depths are necessary to confirm these results on a more firm statistical basis.

  2. 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.

  3. Structural Origins of DNA Target Selection and Nucleobase Extrusion by a

    Office of Scientific and Technical Information (OSTI)

    DNA Cytosine Methyltransferase (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Structural Origins of DNA Target Selection and Nucleobase Extrusion by a DNA Cytosine Methyltransferase Citation Details In-Document Search Title: Structural Origins of DNA Target Selection and Nucleobase Extrusion by a DNA Cytosine Methyltransferase Authors: Didovyk, Andriy ; Verdine, Gregory L. [1] ; DFCI) [2] + Show Author Affiliations (Harvard) ( Publication Date: 2013-03-04

  4. 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.

  5. Steam Line Break and Station Blackout Transients for Proliferation-Resistant Hexagonal Tight Lattice Boiling Water Reactor

    SciTech Connect (OSTI)

    Rohatgi, Upendra S. [Brookhaven National Laboratory (United States); Jo, Jae H. [Brookhaven National Laboratory (United States); Chung, Bub Dong [Brookhaven National Laboratory (United States); Takahashi, Hiroshi [Brookhaven National Laboratory (United States); Downar, Thomas J. [Purdue University (United States)

    2004-01-15

    Safety analyses of a proliferation-resistant, economically competitive, high-conversion boiling water reactor (HCBWR) fueled with fissile plutonium and fertile thorium oxide fuel elements, and with passive safety systems, are presented here. The HCBWR developed here is characterized by a very tight lattice with a relatively small water volume fraction in the core that therefore operates with a fast reactor neutron spectrum and a considerably improved neutron economy compared to the current generation of light water reactors. The tight lattice core has a very narrow flow channel with a hydraulic diameter less than half of the regular boiling water reactor (BWR) core and, thus, presents a special challenge to core cooling because of reduced water inventory and high friction in the core. The primary safety concern when reducing the moderator-to-fuel ratio and when using a tightly packed lattice arrangement is to maintain adequate cooling of the core during both normal operation and accident scenarios.In the preliminary HCBWR design, the core is placed in a vessel with a large chimney section, and the vessel is connected to the isolation condenser system (ICS). The vessel is placed in containment with the gravity driven cooling system (GDCS) and passive containment cooling system (PCCS) in a configuration similar to General Electric's simplified BWR (SBWR). The safety systems are similar to those of the SBWR; the ICS and PCCS are scaled with power. An internal recirculation pump is placed in the downcomer to augment the buoyancy head provided by the chimney since the buoyancy provided by the chimney alone could not generate sufficient recirculation in the vessel as the tight lattice configuration results in much larger friction in the core than with the SBWR.The constitutive relationships for RELAP5 are assessed for narrow channels, and as a result the heat transfer package is modified. The modified RELAP5 is used to simulate and analyze two of the most limiting events for a tight pitch lattice core: the station blackout and the main-steam-line-break events. The results of the analyses indicate that the HCBWR system will be safely brought to the shutdown condition for these transients.

  6. Process of labeling specific chromosomes using recombinant repetitive DNA

    DOE Patents [OSTI]

    Moyzis, R.K.; Meyne, J.

    1988-02-12

    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 members and consensus sequences of the repetitive DNA families for the chromosome preferential sequences. The selected low homology regions are then hybridized with chromosomes to determine those low homology regions hybridized with a specific chromosome under normal stringency conditions.

  7. New Catalytic DNA Biosensors for Radionuclides and Metal ion

    SciTech Connect (OSTI)

    Yi Lu

    2008-03-01

    We aim to develop new DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides, such as uranium, technetium, and plutonium, and metal contaminants, such as lead, chromium, and mercury. The sensors will be highly sensitive and selective. They will be applied to on-site, real-time assessment of concentration, speciation, and stability of the individual contaminants before and during bioremediation, and for long-term monitoring of DOE contaminated sites. To achieve this goal, we have employed a combinatorial method called in vitro selection to search from a large DNA library (~ 1015 different molecules) for catalytic DNA molecules that are highly specific for radionuclides or other metal ions through intricate 3-dimensional interactions as in metalloproteins. Comprehensive biochemical and biophysical studies have been performed on the selected DNA molecules. The findings from these studies have helped to elucidate fundamental principles for designing effective sensors for radionuclides and metal ions. Based on the study, the DNA have been converted to fluorescent or colorimetric sensors by attaching to it fluorescent donor/acceptor pairs or gold nanoparticles, with 11 part-per-trillion detection limit (for uranium) and over million fold selectivity (over other radionuclides and metal ions tested). Practical application of the biosensors for samples from the Environmental Remediation Sciences Program (ERSP) Field Research Center (FRC) at Oak Ridge has also been demonstrated.

  8. Genetic Factors Affecting Susceptibility to Low Dose & Low Dose-Rate Radiation

    SciTech Connect (OSTI)

    Bedford, Joel

    2014-04-18

    Our laboratory has, among other things, developed and used the gamma H2AX focus assay and other chromosomal and cell killing assays to show that differences in this DNA double strand break (dsb) related response can be clearly and distinctly demonstrated for cells which are mildly hyper-radiosensitive such as those associated with A-T heterozygosity. We have found this level of mild hypersensitivity for cells from some 20 to 30 % of apparently normal individuals and from apparently normal parents of Retinoblastoma patients. We found significant differences in gene expression in somatic cells from unaffected parents of Rb patients as compared with normal controls, suggesting that these parents may harbor some as yet unidentified genetic abnormality. In other experiments we sought to determine the extent of differences in normal human cellular reaponses to radiation depending on their irradiation in 2D monolayer vs 3D organized acinar growth conditions. We exmined cell reproductive death, chromosomal aberration induction, and the levels of ?-H2AX foci in cells after single acute gamma-ray doses and immediately after 20 hours of irradiation at a dose rate of 0.0017 Gy/min. We found no significant differences in the dose-responses of these cells under the 2D or 3D growth conditions. While this does not mean such differences cannot occur in other situations, it does mean that they do not generally or necessarily occur. In another series of studies in collaboration with Dr Chuan Li, with supprt from this current grant. We reported a role for apoptotic cell death in promoting wound healing and tissue regeneration in mice. Apoptotic cells released growth signals that stimulated the proliferation of progenitor or stem cells. In yet another collaboration with Dr, B. Chen with funds from this grant, the relative radiosensitivity to cell killing as well as chromosomal instability of 13 DNA-PKcs site-directed mutant cell lines (defective at phosphorylation sites or kinase activity) were examined after exposure of synchronized G1 cells to 137Cs c rays. DNA-PKcs mutant cells defective in phosphorylation at multiple sites withinthe T2609 cluster or within the PI3K domain displayed extreme radiosensitivity. Cells defective at the S2056 cluster or T2609 single site alone were only mildly radiosensitive, but cells defective at even one site in both the S2056 and T2609 clusters were maximally radiosensitive. Thus a synergism between the capacity for phosphorylation at the S2056 and T2609 clusterswas found to be critical for induction of radiosensitivity.

  9. 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.

  10. 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.

  11. Biochemists solve the structure of cell's DNA gatekeeper | Argonne National

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

    Laboratory Biochemists solve the structure of cell's DNA gatekeeper April 15, 2016 Tweet EmailPrint This release about a discovery partially based on research at the GM/CA-CAT beamline at the Advanced Photon Source at Argonne was originally published by Caltech. Caltech scientists have produced the most detailed map yet of the massive protein machine that controls access to the DNA-containing heart of the cell. In a new study, a team led by André Hoelz, an assistant professor of

  12. cDNA encoding a polypeptide including a hevein sequence

    DOE Patents [OSTI]

    Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

    1993-02-16

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a pu GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon.

  13. Size-Selective Incorporation of DNA Nanocages into Nanoporous

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

    Antimony-Doped Tin Oxide Materials Size-Selective Incorporation of DNA Nanocages into Nanoporous Antimony-Doped Tin Oxide Materials Authors: Simmons, C. R., Schmitt, D., Wei, X., Han, D., Volosin, A. M., Ladd, D. M., Seo, D.-K., Liu, Y., and Yan, H. Title: Size-Selective Incorporation of DNA Nanocages into Nanoporous Antimony-Doped Tin Oxide Materials Source: ACS Nano Year: 2011 Volume: 5 Pages: 6060-6068 ABSTRACT: A conductive nanoporous antimony-doped tin oxide (ATO) powder has been

  14. Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis

    DOE Patents [OSTI]

    Vandersall, Jennifer A.; Gardner, Shea N.; Clague, David S.

    2010-05-04

    A computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method and system include modules that address the bioinformatics, kinetics, and thermodynamics of DNA amplification and synthesis. Specifically, the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, are addressed, which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature and concentration of species.

  15. Determination of the bias in LOFT fuel peak cladding temperature data from the blowdown phase of large-break LOCA experiments

    SciTech Connect (OSTI)

    Berta, V.T.; Hanson, R.G.; Johnsen, G.W.; Schultz, R.R.

    1993-05-01

    Data from the Loss-of-Fluid Test (LOFT) Program help quantify the margin of safety inherent in pressurized water reactors during postulated loss-of-coolant accidents (LOCAs). As early as 1979, questions arose concerning the accuracy of LOFT fuel rod cladding temperature data during several large-break LOCA experiments. This report analyzes how well externally-mounted fuel rod cladding thermocouples in LOFT accurately reflected actual cladding surface temperature during large-break LOCA experiments. In particular, the validity of the apparent core-wide fuel rod cladding quench exhibited during blowdown in LOFT Experiments L2-2 and L2-3 is studied. Also addressed is the question of whether the externally-mounted thermocouples might have influenced cladding temperature. The analysis makes use of data and information from several sources, including later, similar LOFT Experiments in which fuel centerline temperature measurements were made, experiments in other facilities, and results from a detailed FRAP-T6 model of the LOFT fuel rod. The analysis shows that there can be a significant difference (referred to as bias) between the surface-mounted thermocouple reading and the actual cladding temperature, and that the magnitude of this bias depends on the rate of heat transfer between the fuel rod cladding and coolant. The results of the analysis demonstrate clearly that a core-wide cladding quench did occur in Experiments L2-2 and L2-3. Further, it is shown that, in terms of peak cladding temperature recording during LOFT large-break LOCA experiments, the mean bias is 11.4 {plus_minus} 16.2K (20.5 {plus_minus} 29.2{degrees} F). The best-estimate value of peak cladding temperature for LOFT LP-02-6 is 1,104.8 K. The best-estimate peak cladding temperature for LOFT LP-LB-1 is 1284.0 K.

  16. Structural basis for inhibition of DNA replication by aphidicolin

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

    Baranovskiy, A. G.; Babayeva, N. D.; Suwa, Y.; Gu, J.; Pavlov, Y. I.; Tahirov, T. H.

    2014-11-27

    Natural tetracyclic diterpenoid aphidicolin is a potent and specific inhibitor of B-family DNA polymerases, haltering replication and possessing a strong antimitotic activity in human cancer cell lines. Clinical trials revealed limitations of aphidicolin as an antitumor drug because of its low solubility and fast clearance from human plasma. The absence of structural information hampered the improvement of aphidicolin-like inhibitors: more than 50 modifications have been generated so far, but all have lost the inhibitory and antitumor properties. Here we report the crystal structure of the catalytic core of human DNA polymerase α (Pol α) in the ternary complex with anmore » RNA-primed DNA template and aphidicolin. The inhibitor blocks binding of dCTP by docking at the Pol α active site and by rotating the template guanine. The structure provides a plausible mechanism for the selectivity of aphidicolin incorporation opposite template guanine and explains why previous modifications of aphidicolin failed to improve its affinity for Pol α. With new structural information, aphidicolin becomes an attractive lead compound for the design of novel derivatives with enhanced inhibitory properties for B-family DNA polymerases.« less

  17. An overview of DNA fingerprinting with sup 32 P nucleotides

    SciTech Connect (OSTI)

    Pappas, G.G.

    1992-01-01

    The DNA probes radiolabeled with {sup 32}P, a primary tool employed by researchers in the life sciences for > 20 yr, are used by private companies, state-run laboratories, and the FBI to generate autoradiographs displaying the unique banding patterns that constitute the DNA fingerprint. The ability to identify an individual or animal from a biological sample has profound implications. Unidentified bodies, unrecognizable remains, and missing children can be tested and the DNA fingerprint compared to those of family members for positive identification. Paternity can be established before a child's birth. Immigration disputes can easily be resolved. Other uses include pedigree determination and testing for cell-line cross-contamination. Using a DNA fingerprint to determine the guilt or innocence of an individual allegedly involved in a violent crime is very controversial and has great legal and moral implications for society. Forensic laboratories have been challenged to ensure a level of quality control and quality assurance consistent with the weight given to these tests when used as evidence in a court of law.

  18. Structural basis for inhibition of DNA replication by aphidicolin

    SciTech Connect (OSTI)

    Baranovskiy, A. G.; Babayeva, N. D.; Suwa, Y.; Gu, J.; Pavlov, Y. I.; Tahirov, T. H.

    2014-11-27

    Natural tetracyclic diterpenoid aphidicolin is a potent and specific inhibitor of B-family DNA polymerases, haltering replication and possessing a strong antimitotic activity in human cancer cell lines. Clinical trials revealed limitations of aphidicolin as an antitumor drug because of its low solubility and fast clearance from human plasma. The absence of structural information hampered the improvement of aphidicolin-like inhibitors: more than 50 modifications have been generated so far, but all have lost the inhibitory and antitumor properties. Here we report the crystal structure of the catalytic core of human DNA polymerase α (Pol α) in the ternary complex with an RNA-primed DNA template and aphidicolin. The inhibitor blocks binding of dCTP by docking at the Pol α active site and by rotating the template guanine. The structure provides a plausible mechanism for the selectivity of aphidicolin incorporation opposite template guanine and explains why previous modifications of aphidicolin failed to improve its affinity for Pol α. With new structural information, aphidicolin becomes an attractive lead compound for the design of novel derivatives with enhanced inhibitory properties for B-family DNA polymerases.

  19. New Catalytic DNA Biosensors for Radionuclides and Metal ions

    SciTech Connect (OSTI)

    Lu, Yi

    2003-06-01

    The goals of the project are to develop new catalytic DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides and metal ions, and apply the sensors for on-site, real-time assessment of concentration, speciation and stability of the individual contaminants during and after bioremediation. A negative selection strategy was tested and validated. In vitro selection was shown to yield highly active and specific transition metal ion-dependent catalytic DNA/RNA. A fluorescence resonance energy transfer (FRET) study of in vitro selected DNA demonstrated that the trifluorophore labeled system is a simple and powerful tool in studying complex biomolecules structure and dynamics, and is capable of revealing new sophisticated structural changes. New fluorophore/quenchers in a single fluorosensor yielded improved signal to noise ratio in detection, identification and quantification of metal contaminants. Catalytic DNA fluorescent and colorimetric sensors were shown useful in sensing lead in lake water and in leaded paint. Project results were described in two papers and two patents, and won an international prize.

  20. New Catalytic DNA Biosensors for Radionuclides and Metal ions

    SciTech Connect (OSTI)

    Lu, Yi

    2002-06-01

    The goals of the project are to develop new catalytic DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides and metal ions, and apply the sensors for on-site, real-time assessment of concentration, speciation and stability of the individual contaminants during and after bioremediation. A negative selection strategy was tested and validated. In vitro selection was shown to yield highly active and specific transition metal ion-dependent catalytic DNA/RNA. A fluorescence resonance energy transfer (FRET) study of in vitro selected DNA demonstrated that the trifluorophore labeled system is a simple and powerful tool in studying complex biomolecules structure and dynamics, and is capable of revealing new sophisticated structural changes. New fluorophore/quenchers in a single fluorosensor yielded improved signal to noise ratio in detection, identification and quantification of metal contaminants. Catalytic DNA fluorescent and colorimetric sensors were shown useful in sensing lead in lake water and in leaded paint. Project results were described in two papers and two patents, and won an international prize.