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Sample records for dna double-strand breaks

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

    SciTech Connect (OSTI)

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

    1995-12-01

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

  6. 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.

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

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

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

  8. 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.

  9. 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

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

    SciTech Connect (OSTI)

    Simchi, Hamidreza; Esmaeilzadeh, Mahdi Mazidabadi, Hossein

    2014-05-28

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

  11. 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.

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

    SciTech Connect (OSTI)

    Simchi, Hamidreza; Esmaeilzadeh, Mahdi Mazidabadi, Hossein

    2014-02-07

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

  13. 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.

  14. 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.

  15. 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

  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, 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.

  18. 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.

  19. 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.

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

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

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

    2016-02-04

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

  1. 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.

  2. 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.

  3. 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.

  4. Solid phase sequencing of double-stranded nucleic acids

    DOE Patents [OSTI]

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

    2002-01-01

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

  5. 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.

  6. 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...

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

    SciTech Connect (OSTI)

    Ganesan, Shanthi Keating, Aileen F.

    2015-02-01

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

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

    SciTech Connect (OSTI)

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

    2015-02-06

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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

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

    SciTech Connect (OSTI)

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

    1991-01-01

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

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

    SciTech Connect (OSTI)

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

    2010-10-11

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

  16. 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.

  17. 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

  18. 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.

  19. 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

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

    SciTech Connect (OSTI)

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

    2014-10-03

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

  1. 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.

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

    SciTech Connect (OSTI)

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

    2013-05-03

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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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.

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

    SciTech Connect (OSTI)

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

    2007-02-15

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

  13. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

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

  14. 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

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

    SciTech Connect (OSTI)

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

    2012-11-01

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

  16. 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.

  17. 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.

  18. BREAKING BOND

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

    BREAKING BOND the Can chemistry help unbind us from fossil fuels? 1663 July 2016 21 When ... Their goal: to use chemistry to construct gasoline-like hydrocarbons from plant sugars. ...

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

    DOE Patents [OSTI]

    Soares, Marcelo Bento; Bonaldo, Maria de Fatima

    1998-01-01

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

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

    DOE Patents [OSTI]

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

    1998-12-08

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

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

    SciTech Connect (OSTI)

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

    2013-02-01

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

  2. 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

  3. 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.

  4. 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:...

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. Breaking the Bond

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

    Breaking the Bond 1663 Los Alamos science and technology magazine Latest Issue:July 2016 past issues All Issues » submit Breaking the Bond Can chemistry help unbind us from fossil fuels? July 21, 2016 info graphic gas pump Accelerating toward a more sustainable future: gas pumps may someday soon contain bio-gasoline made from plants. We are condensing millions of years of fossilization into a few chemical reactions. Fossil fuels are a finite resource. Unfortunately, the existing global

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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 ...

  15. Give Young Scientists a Break

    SciTech Connect (OSTI)

    Wiley, H. S.

    2009-11-01

    There has been much concern about the impact of tight funding on the careers of young scientists. When only a small percentage of grants are approved, even the smallest problem or error with an application can push it out of the funding range. Unfortunately, the relative lack of grant writing skills by new investigators often has this effect. To avoid a situation where only experienced investigators with polished writing skills are funded, the National Institutes of Health has instituted a more generous ranking scale for new investigators. Not surprisingly, some senior investigators have protested, calling it reverse discrimination. I say that their anger is misplaced. New investigators do deserve a break.

  16. 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.

  17. 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)...

  18. 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 ... Stationary Power Energy Conversion Efficiency Solar Energy Wind Energy Water Power ...

  19. Vanadium catalysts break down biomass for fuels

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

    break down biomass into useful components Due to diminishing petroleum reserves, non-food biomass (lignocellulose) is an attractive alternative as a feedstock for the...

  20. 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.

  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 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.

  2. 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 ...

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

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

    Thermal Break with Simplified Manufacturing for R7 Commercial Windows Novel Thermal Break with Simplified Manufacturing for R7 Commercial Windows Lead Performer: Alcoa - ...

  4. Break-out Discussion i: Modeling Consumer Behavior Residential...

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

    Break-out Discussion i: Modeling Consumer Behavior Residential Scale Break-out Discussion i: Modeling Consumer Behavior Residential Scale This presentaion summarizes the ...

  5. Dna Sequencing

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  6. 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)

  7. 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.

  8. 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

  9. 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

  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 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

  11. 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

  12. 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.

  13. 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.

  14. Cloud Properties Working Group Break Out Session

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

    Break Out Session ARM Science Team Meeting Louisville, KY 30 March 2009 The Chair's Objectives for CPWG *Maintain continuity of "base" instruments - We're building a climatology! *Advocate for sufficient programmatic support to make our measurements useful. *Better retrieval vetting framework - moving towards Cloud Properties Best Estimate *Build a stronger connection with the modeling community - Producing the products they want. CPWG Breakout Agenda 30 March 2009, 3-5 pm *3:00-3:15

  15. 5-MW Dynamometer Ground Breaking | Department of Energy

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

    5-MW Dynamometer Ground Breaking 5-MW Dynamometer Ground Breaking December 19, 2011 - 3:04pm Addthis This is an excerpt from the Fourth Quarter 2011 edition of the Wind Program R&D ...

  16. 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...

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

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

    PDF Document Publication R&D 100 award (Chip Breaking)(final).pdf (8,767 KB) Technology Marketing Summary The MTP chip breaking system is a cost-saving solution for machining ...

  18. Ground Breaking of Blythe Solar Power Project | Department of...

    Energy Savers [EERE]

    Breaking of Blythe Solar Power Project Ground Breaking of Blythe Solar Power Project June 20, 2011 - 2:16pm Addthis Secretary Chu Secretary Chu Former Secretary of Energy What will ...

  19. 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 b2blowres63006.pdf (8.11 MB) 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

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.  

  5. 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.

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. Breaking of Symmetry in Graphene Growth on Metal Substrates ...

    Office of Scientific and Technical Information (OSTI)

    Breaking of Symmetry in Graphene Growth on Metal Substrates Not Available Temp HTML Storage 2: Artyukhov, Vasilii I.; Hao, Yufeng; Ruoff, Rodney S.; Yakobson, Boris I. Temp Plain ...

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

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

    ... including optical, X ray, elec- tron, and atomic force; and archives for molecular dynamic simulations of the molecular machinery that breaks down plant cell-wall components. ...

  12. NREL: Solar Research - New Partnerships Help Utilities Break...

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

    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 ...

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

    Office of Scientific and Technical Information (OSTI)

    widely studied for figuring out the masses and mixing angles of standard model fermions. ... MIXING; POTENTIALS; SCALAR FIELDS; STANDARD MODEL; SYMMETRY; SYMMETRY BREAKING; ...

  14. 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...

  15. 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

  16. 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.

  17. 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.

  18. 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.

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

    Office of Scientific and Technical Information (OSTI)

    US0801780 DOE Contract Number: AC02-76SF00515 Resource ... Language: English Subject: 72 PHYSICS OF ELEMENTARY ... BREAKING; SU GROUPS Theory-HEP,HEPTH Word Cloud More ...

  20. 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: ...

  1. How Things Break (And Why Scientists Want to Know) | Argonne...

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

    This article was published in the spring 2016 issue of Argonne Now, the laboratory science magazine. Click for the rest of the issue. How Things Break (And Why Scientists Want to ...

  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 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

  3. Regional Test Centers Breaking Down Barriers to Solar Energy Deployment |

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

    Department of Energy Regional Test Centers Breaking Down Barriers to Solar Energy Deployment Regional Test Centers Breaking Down Barriers to Solar Energy Deployment September 3, 2014 - 6:16pm Addthis EERE Assistant Secretary Dr. David Danielson stands with Senator Bernie Sanders of Vermont at the state's new regional solar test center. | Photo credit Kevin Fitzmaurice, Energy Department. EERE Assistant Secretary Dr. David Danielson stands with Senator Bernie Sanders of Vermont at the state's

  4. 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

  5. Break-out Discussion i: Modeling Consumer Behavior Residential Scale |

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

    Department of Energy Break-out Discussion i: Modeling Consumer Behavior Residential Scale Break-out Discussion i: Modeling Consumer Behavior Residential Scale This presentaion summarizes the information discussed during the breakout session on modeling consumer behavior during the DOE Ad Lucem Workshop on Feb. 17, 2012. adlucem2012_behavior_breakout.pdf (589.64 KB) More Documents & Publications Ad Lucem: Modeling of Market Transformation Pathways Workshop Agenda Modeling Solar Energy

  6. 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

  7. 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

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

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

  9. The Honorable Deborah L. Wince-Smith Discusses Breaking the Glass...

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

    The Honorable Deborah L. Wince-Smith Discusses Breaking the Glass Ceiling in Manufacturing The Honorable Deborah L. Wince-Smith Discusses Breaking the Glass Ceiling in ...

  10. 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.

  11. 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.

  12. 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.

  13. SB Electronics Breaks Ground on New Factory | Department of Energy

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

    SB Electronics Breaks Ground on New Factory SB Electronics Breaks Ground on New Factory April 29, 2010 - 5:22pm Addthis U.S. Rep. Peter Welch (from left), Vermont Lt. Gov. Brian Dubie, SBE board member Win Hunter, SBE board chair Stan Fishkin, Assi U.S. Rep. Peter Welch (from left), Vermont Lt. Gov. Brian Dubie, SBE board member Win Hunter, SBE board chair Stan Fishkin, Assi Paul Lester Paul Lester Digital Content Specialist, Office of Public Affairs A Vermont company broke ground on a new

  14. Margins in high temperature leak-before-break assessments

    SciTech Connect (OSTI)

    Budden, P.J.; Hooton, D.G.

    1997-04-01

    Developments in the defect assessment procedure R6 to include high-temperature mechanisms in Leak-before-Break arguments are described. In particular, the effect of creep on the time available to detect a leak and on the crack opening area, and hence leak rate, is discussed. The competing influence of these two effects is emphasized by an example. The application to Leak-before-Break of the time-dependent failure assessment diagram approach for high temperature defect assessment is then outlined. The approach is shown to be of use in assessing the erosion of margins by creep.

  15. 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)

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Traveling solitons in Lorentz and CPT breaking systems

    SciTech Connect (OSTI)

    Souza Dutra, A. de; Correa, R. A. C.

    2011-05-15

    In this work we present a class of traveling solitons in Lorentz and CPT breaking systems. In the case of Lorentz violating scenarios, as far as we know, only static solitonic configurations were analyzed up to now in the literature. Here it is shown that it is possible to construct some traveling solitons which cannot be mapped into static configurations by means of Lorentz boosts due to explicit breaking. In fact, the traveling solutions cannot be reached from the static ones by using something similar to a Lorentz boost in those cases. Furthermore, in the model studied, a complete set of exact solutions is obtained. The solutions present a critical behavior controlled by the choice of an arbitrary integration constant.

  4. 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.

  5. 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.

  6. New Partnerships Help Utilities Break Down Solar Barriers | Energy Systems

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

    Integration | NREL 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),

  7. 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

  8. 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

  9. 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

  10. Break-out Discussion i: Modeling Consumer Behavior Residential Scale

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

    Break-out Discussion I: Modeling Consumer Behavior Residential Scale  Are we asking the right questions?  What is a question we could ask about modeling consumer behavior that might lead to deeper insights into how to spur innovation? Why Are We Here? 2 Opower: visual comparison 3 opower 4 EERE Home Energy Score 5 * Similar comparison model * Adds climate context * Simple, visual  Data: - How much - What type  Data: - What is actionable today? - What is bodacious, over-the-top

  11. Symmetry-breaking instability of quadratic soliton bound states

    SciTech Connect (OSTI)

    Delque, Michaeel; Fanjoux, Gil; Maillotte, Herve; Kockaert, Pascal; Sylvestre, Thibaut; Haelterman, Marc

    2011-01-15

    We study both numerically and experimentally two-dimensional soliton bound states in quadratic media and demonstrate their symmetry-breaking instability. The experiment is performed in a potassium titanyl phosphate crystal in a type-II configuration. The bound state is generated by the copropagation of the antisymmetric fundamental beam locked in phase with the symmetrical second harmonic one. Experimental results are in good agreement with numerical simulations of the nonlinear wave equations.

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

    National Nuclear Security Administration (NNSA)

    Administration | (NNSA) 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 institutional investments,

  13. Women in STEM careers: Breaking down barriers | Argonne National Laboratory

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

    This article was published in the spring 2016 issue of Argonne Now, the laboratory science magazine. Click for the rest of the issue. Women in STEM careers: Breaking down barriers By Diana Anderson * March 7, 2016 Tweet EmailPrint This article was originally published in the spring 2016 issue of Argonne Now, the laboratory's science magazine. Growing national attention is focused on increasing the number of women in Science, Technology, Engineering, and Mathematics (STEM) careers. Even as

  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 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

  15. 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

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

    Office of Scientific and Technical Information (OSTI)

    Soft supersymmetry breaking terms from Dsub 4xZsub 2 lepton flavor symmetry Citation Details In-Document Search Title: Soft supersymmetry breaking terms from Dsub 4xZsub 2 ...

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

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

    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 October 1, 2012 - 12:08pm ...

  18. 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.

  19. 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.

  20. Controlling DNA Methylation

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

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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Quantitive DNA Fiber Mapping

    SciTech Connect (OSTI)

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

    2008-01-28

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

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

    DOE Patents [OSTI]

    McCutchen-Maloney, Sandra L.

    2002-01-01

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

  7. DNA-PK assay

    DOE Patents [OSTI]

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12

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

  8. 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

  9. Intrinsic transverse momentum and dynamical chiral symmetry breaking

    SciTech Connect (OSTI)

    Christian Weiss, Peter Schweitzer, Mark Strikman

    2013-01-01

    We study the effect of QCD vacuum structure on the intrinsic transverse momentum distribution of partons in the nucleon at a low scale. The dynamical breaking of chiral symmetry is caused by non-perturbative interactions at distances of the order rho ~ 0.2 - 0.3 fm, much smaller than the typical nucleon size R ~ 1 fm, resulting in a two-scale picture of nucleon structure. Using an effective dynamical model based on chiral constituent quark degrees of freedom and the 1/N_c expansion (chiral quark-soliton model), we calculate the transverse momentum distribution of quarks and antiquarks at a low scale. The distribution of valence quarks is localized at p_T ~ 1/R. The distribution of flavor-singlet unpolarized sea quarks exhibits a power-like tail extending up to the chiral-symmetry-breaking scale 1/{rho}. A similar tail is present in the flavor-nonsinglet polarized sea. These features are model-independent and represent the imprint of the QCD vacuum on the nucleon's partonic structure. At the level of the nucleon's light-cone wave function, we show that sea quarks partly exist in correlated pairs of transverse size {rho} << R, analogous to short-range NN correlations in nuclei. We discuss the implications of our findings for the transverse momentum distributions in hard scattering processes (semi-inclusive DIS, Drell-Yan pair production) and possible experimental tests of the non-perturbative parton correlations induced by QCD vacuum structure.

  10. 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.

  11. DNA | Open Energy Information

    Open Energy Info (EERE)

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

  12. Patterning nanocrystals using DNA

    SciTech Connect (OSTI)

    Williams, Shara Carol

    2003-09-01

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

  13. 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.

  14. CSNI specialist meeting on leak-before-break in nuclear reactor piping: proceedings

    SciTech Connect (OSTI)

    Not Available

    1984-08-01

    On September 1 and 2, 1983, the CSNI subcommittee on primary system integrity held a special meeting in Monterey, California, on the subject of leak-before-break in nuclear reactor piping systems. The purpose of the meeting was to provide an international forum for the exchange of ideas, positions, and research results; to identify areas requiring additional research and development; and to determine the general attitude toward acceptance of the leak-before-break concept. The importance of the leak-before-break issue was evidenced by excellent attendance at the meeting and through active participation by the meeting attendees. Approximately 125 people representing fifteen different nations attended the meeting. The meeting was divided into four technical sessions addressing the following areas: Application of Piping Fracture Mechanics to Leak-Before Break, Leak Rate and Leak Detection, Leak-Before-Break Studies, Methods and Results, Current and Proposed Positions on Leak-Before-Break.

  15. 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

  16. 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.

  17. 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: September 1, 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

  18. 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.

  19. 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...

  20. 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.

  1. 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.

  2. 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.

  3. Navy Breaks World Record With Futuristic Free-Electron Laser (FOX News.com)

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

    | Jefferson Lab Navy Breaks World Record With Futuristic Free-Electron Laser (FOX News.com) External Link: http://www.foxnews.com/scitech/2011/02/18/navy-breaks-world-record-futuristic-la... By jlab_admin on Sun, 2011-02-20

  4. Isospin-breaking two-nucleon force with explicit {delta} excitations

    SciTech Connect (OSTI)

    Epelbaum, E.; Meissner, Ulf-G.; Krebs, H.

    2008-03-15

    We study the leading isospin-breaking contributions to the two-nucleon two-pion exchange potential due to explicit {delta} degrees of freedom in chiral effective field theory. In particular, we find important contributions due to the delta mass splittings to the charge symmetry breaking potential that act opposite to the effects induced by the nucleon mass splitting.

  5. 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.

  6. DNA tagged microparticles

    DOE Patents [OSTI]

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

    2016-03-22

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

  7. Can quantum coherent solar cells break detailed balance?

    SciTech Connect (OSTI)

    Kirk, Alexander P.

    2015-07-21

    Carefully engineered coherent quantum states have been proposed as a design attribute that is hypothesized to enable solar photovoltaic cells to break the detailed balance (or radiative) limit of power conversion efficiency by possibly causing radiative recombination to be suppressed. However, in full compliance with the principles of statistical mechanics and the laws of thermodynamics, specially prepared coherent quantum states do not allow a solar photovoltaic cell—a quantum threshold energy conversion device—to exceed the detailed balance limit of power conversion efficiency. At the condition given by steady-state open circuit operation with zero nonradiative recombination, the photon absorption rate (or carrier photogeneration rate) must balance the photon emission rate (or carrier radiative recombination rate) thus ensuring that detailed balance prevails. Quantum state transitions, entropy-generating hot carrier relaxation, and photon absorption and emission rate balancing are employed holistically and self-consistently along with calculations of current density, voltage, and power conversion efficiency to explain why detailed balance may not be violated in solar photovoltaic cells.

  8. Sea quark transverse momentum distributions and dynamical chiral symmetry breaking

    SciTech Connect (OSTI)

    Schweitzer, Peter; Strikman, Mark; Weiss, Christian

    2014-01-01

    Recent theoretical studies have provided new insight into the intrinsic transverse momentum distributions of valence and sea quarks in the nucleon at a low scale. The valence quark transverse momentum distributions (q - qbar) are governed by the nucleon's inverse hadronic size R{sup -1} ~ 0.2 GeV and drop steeply at large p{sub T}. The sea quark distributions (qbar) are in large part generated by non-perturbative chiral-symmetry breaking interactions and extend up to the scale rho{sup -1} ~ 0.6 GeV. These findings have many implications for modeling the initial conditions of perturbative QCD evolution of TMD distributions (starting scale, shape of p{sub T}. distributions, coordinate-space correlation functions). The qualitative difference between valence and sea quark intrinsic p{sub T}. distributions could be observed experimentally, by comparing the transverse momentum distributions of selected hadrons in semi-inclusive deep-inelastic scattering, or those of dileptons produced in pp and pbar-p scattering.

  9. 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.

  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. 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.

  12. 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.

  13. 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.

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

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

    Test Facility | 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 October 1, 2012 - 12:08pm Addthis This is an excerpt from the Third Quarter 2012 edition of the Wind Program R&D Newsletter. The U.S. Department of Energy (DOE) joined with Texas Tech University (TTU) and Sandia National Laboratories (SNL) in July 2012 to break ground on a new state-of-the-art wind turbine

  15. 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.

  16. Photo of the Week: Record-Breaking Solar Cells | Department of Energy

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

    Record-Breaking Solar Cells Photo of the Week: Record-Breaking Solar Cells December 7, 2012 - 2:27pm Addthis Solar Junction, in partnership with NREL, has developed solar cells that reach a record-breaking 44 percent efficiency -- meaning that more than 40 percent of the sunlight the solar cells are exposed to is converted into electrical energy. In this photo, an operator inspects a photolithography tool used to manufacture these solar cells. | Photo by Daniel Derkacs/SolarJunction. Solar

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

    Energy Savers [EERE]

    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 ...

  18. Introduction of Break-Out Session at the International PV Module Quality Assurance Forum (Presentation)

    SciTech Connect (OSTI)

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

    2011-07-01

    This presentation outlines review requirements for quality assurance (QA) rating systems, logical design of QA systems, and specific tasks for break-out session 1 of the 2011 International PV Module Quality Assurance Forum.

  19. 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 ...

  20. 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 ...

  1. 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 ...

  2. Energy Department Announces $12 Million to Accelerate Record-Breaking Solar

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

    Cell Efficiency | Department of Energy 2 Million to Accelerate Record-Breaking Solar Cell Efficiency Energy Department Announces $12 Million to Accelerate Record-Breaking Solar Cell Efficiency January 25, 2013 - 3:41pm Addthis As part of the Energy Department's SunShot Initiative, the Department today announced $12 million to develop innovative, ultra-efficient solar devices that will close the gap with the theoretical efficiency limit, or the highest potential percentage of sunlight

  3. 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: September 1, 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

  4. 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

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

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

    | Department of Energy Thermal Break with Simplified Manufacturing for R7 Commercial Windows Novel Thermal Break with Simplified Manufacturing for R7 Commercial Windows Image courtesy of Alcoa and BTO Peer Review. Image courtesy of Alcoa and BTO Peer Review. 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

  6. Metallic glass could make your next cell phone harder to break

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

    Metallic glass could make your next cell phone harder to break Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit Metallic glass could make your next cell phone harder to break Lab researcher works to rearrange the atoms in metals June 20, 2014 New insights to changing the atomic structure of metals New insights to changing the atomic structure of metals Contact Linda Anderman Email Metal and glass objects are all

  7. Helping STEM Education Take Root: Breaking Ground on a Field Station in

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

    Indian Country | Department of Energy Helping STEM Education Take Root: Breaking Ground on a Field Station in Indian Country Helping STEM Education Take Root: Breaking Ground on a Field Station in Indian Country November 7, 2012 - 10:50am Addthis (From Left) Stuart Harris, Confederated Tribes of the Umatilla Indian Reservation, Director of the Department of Science and Engineering, Dave Huizenga, Senior Advisor for the Office of Environmental Management, and Tracey LeBeau, Director of the

  8. Record-breaking year for patents | Y-12 National Security Complex

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

    Record-breaking year for ... Record-breaking year for patents Posted: February 11, 2013 - 2:57pm | Y-12 Report | Volume 9, Issue 2 | 2013 Fiscal 2012 was a fruitful year for innovative research and development at the Y-12 National Security Complex. Site inventors were issued an unprecedented 11 patents. Technologies and processes from many of Y-12's latest patents, like those from previous years, can extend beyond the Nuclear Security Enterprise into diverse areas of private industry. One

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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...

  14. 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).

  15. Human Genome Research: Decoding DNA

    Office of Scientific and Technical Information (OSTI)

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

  16. Human Genome Research: Decoding DNA

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

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

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

    SciTech Connect (OSTI)

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

    1993-08-01

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

  18. 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 ...

  19. 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.

  20. 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.

  1. 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.

  2. The Initiation of Bacterial DNA Replication

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

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

  3. The Initiation of Bacterial DNA Replication

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

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

  4. 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 ...

  5. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1997-06-10

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

  6. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B.; Efstratiadis, Argiris

    1997-01-01

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

  7. 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.

  8. 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.

  9. 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.

  10. Soft A4→Z3 symmetry breaking and cobimaximal neutrino mixing

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

    Ma, Ernest

    2016-03-28

    In this study, I propose a model of radiative charged-lepton and neutrino masses with A4 symmetry. The soft breaking of A4 to Z3 lepton triality is accomplished by dimension-three terms. The breaking of Z3 by dimension-two terms allows cobimaximal neutrino mixing (θ13 ≠ 0, θ23 = π/4, δcp=π/2) to be realized with only very small finite calculable deviations from the residual Z3 lepton triality. This construction solves a long-standing technical problem inherent in renormalizable A4 models since their inception.

  11. 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:

  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. 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.

  14. 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.

  15. Using DNA to Build Nanomaterials

    DOE R&D Accomplishments [OSTI]

    Walsh, Karen McNulty

    2011-05-09

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

  16. BRCA1 Mutation: A Predictive Marker for Radiation Therapy?

    SciTech Connect (OSTI)

    Kan, Charlene; Zhang, Junran

    2015-10-01

    DNA repair, in particular, DNA double-strand break (DSB) repair, is essential for the survival of both normal and cancer cells. An elaborate repair mechanism has been developed in cells to efficiently repair the damaged DNA. The pathways predominately involved in DSB repair are homologous recombination and classic nonhomologous end-joining, although the alternative NHEJ pathway, a third DSB repair pathway, could also be important in certain contexts. The protein of BRCA1 encoded by the tumor suppressor gene BRCA1 regulates all DSB repair pathways. Given that DSBs represent the most biologically significant lesions induced by ionizing radiation and that impaired DSB repair leads to radiation sensitivity, it has been expected that cancer patients with BRCA1 mutations should benefit from radiation therapy. However, the clinical data have been conflicting and inconclusive. We provide an overview about the current status of the data regarding BRCA1 deficiency and radiation therapy sensitivity in both experimental models and clinical investigations. In addition, we discuss a strategy to potentiate the effects of radiation therapy by poly(ADP-ribose) polymerase inhibitors, the pharmacologic drugs being investigated as monotherapy for the treatment of patients with BRCA1/2 mutations.

  17. 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.

  18. 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.

  19. Entropic information for travelling solitons in Lorentz and CPT breaking systems

    SciTech Connect (OSTI)

    Correa, R.A.C.; Rocha, Roldão da; Souza Dutra, A. de

    2015-08-15

    In this work we group four research topics apparently disconnected, namely solitons, Lorentz symmetry breaking, supersymmetry, and entropy. Following a recent work (Gleiser and Stamatopoulos, 2012), we show that it is possible to construct in the context of travelling wave solutions a configurational entropy measure in functional space, from the field configurations. Thus, we investigate the existence and properties of travelling solitons in Lorentz and CPT breaking scenarios for a class of models with two interacting scalar fields. Here, we obtain a complete set of exact solutions for the model studied which display both double and single-kink configurations. In fact, such models are very important in applications that include Bloch branes, Skyrmions, Yang–Mills, Q-balls, oscillons and various superstring-motivated theories. We find that the so-called Configurational Entropy (CE) for travelling solitons shows that the best value of parameter responsible to break the Lorentz symmetry is one where the energy density is distributed equally around the origin. In this way, the information-theoretical measure of travelling solitons in Lorentz symmetry violation scenarios opens a new window to probe situations where the parameters responsible for breaking the symmetries are arbitrary. In this case, the CE selects the best value of the parameter in the model.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Interconnecting gold islands with DNA origami

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

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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. BREAKING BOND

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

    BOE Reserve Class No 2001 reserves 0.1 - 10 MBOE 10.1 - 100 MBOE 100.1 - 1,000 MBOE 1,000.1 - 10,000 MBOE 10,000.1 - 100,000 MBOE > 100,000 MBOE Basin Outline ID The mapped oil and gas field boundary outlines were created by the Reserves and Production Division, Office of Oil and Gas, Energy Information Administration pursuant to studies required by Section 604 of the Energy Policy and Conservation Act Amendments of 2000 (P.L. 106-469). The boundaries are not informed by subsurface structural