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1

Quantitative, non-invasive imaging of radiation-induced DNA double strand breaks in vivo  

NLE Websites -- All DOE Office Websites (Extended Search)

Quantitative, non-invasive imaging of radiation-induced DNA double strand breaks in vivo Quantitative, non-invasive imaging of radiation-induced DNA double strand breaks in vivo Wenrong Li 1, , Fang Li 1 , Qian Huang 1 , Jingping Shen 1 , Frank Wolf 1 , Yujun He 1 , Xinjian Liu 1 , Y. Angela Hu 1 , Joel. S. Bedford 5 , and Chuan-Yuan Li 1,2,* Departments of 1 Radiation Oncology, 2 Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA; 3 Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA DNA double strand breaks are a major form of DNA damage and a key mechanism through which radiotherapy and some chemotherapeutic agents kill cancer cells. Despite its importance, measuring DNA double strand breaks is still a tedious task that is normally carried out by gel electrophoresis or immunofluorescence staining. Here we report a novel approach to image and

2

ASSESSMENT OF INDIVIDUAL VARIATION IN DNA DOUBLE-STRAND BREAK REPAIR CAPACITY IN HUMAN DIPLOID FIBROBLASTS  

NLE Websites -- All DOE Office Websites (Extended Search)

ASSESSMENT OF INDIVIDUAL VARIATION IN DNA DOUBLE-STRAND ASSESSMENT OF INDIVIDUAL VARIATION IN DNA DOUBLE-STRAND BREAK REPAIR CAPACITY IN HUMAN DIPLOID FIBROBLASTS Paul F. Wilson, John M. Hinz, Peter B. Nham, Salustra S. Urbin, Cynthia B. Thomas, Irene M. Jones, and Larry H. Thompson Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA The induction of bi-stranded clustered DNA damage (BCD), which includes direct DNA double-strand breaks (DSBs), is a hallmark of ionizing radiation (IR) exposure. Incorrectly repaired DSBs can cause chromosomal rearrangements and an increased risk of genomic instability and cancer. Because there is polymorphic variation in DNA repair genes and much of this variation is predicted to have a functional impact, healthy people likely vary in their capacity to repair DSBs and other BCD. This project

3

The Role of DNA double-strand break repair in cellular response to low  

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DNA double-strand break repair in cellular response to low DNA double-strand break repair in cellular response to low dose radiation exposure. David J. Chen Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas TX 75390 It has been assumed that molecular pathways that involved in the biological response for low dose of radiation should be similar to those for high dose radiation in general. The low dose-rate effect and DNA double-strand break repair are inextricably linked in mammalian cells. It has been reported that mammalian mutant cells deficient in nonhomologous end join (NHEJ) pathway have little or no cellular recovery when expose to low-dose-rate radiation. Recently, it has also been reported that cells deficient in

4

A Key Step in Repairing DNA Double-Strand Breaks | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (Extended Search)

X-ray Rainbow X-ray Rainbow An Insulating Breakthrough Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed A Key Step in Repairing DNA Double-Strand Breaks JANUARY 10, 2007 Bookmark and Share The atomic structure of the protein 53BP1 identified by Mayo researchers. (Courtesy: Mayo Clinic) A team of Mayo Clinic researchers has uncovered a key step in the molecular pathway of repairing DNA double-strand breaks. The studies were carried out using the 19-ID beamline (SBC-CAT) at the Advanced Photon Source (APS, Argonne) and the X12-C beamline at the National Synchrotron Light Source (NSLS, Brookhaven National Laboratory). Both the APS and the NSLS are funded by the U.S. Department of Energy's Office of Basic Energy

5

Gene Expression Pathways Activated and Repair of DNA of Double Strand  

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Pathways Activated and Repair of DNA of Double Strand Pathways Activated and Repair of DNA of Double Strand Breaks (DSBs) Following Low Dose Ionizing Radiation in Human Bronchial Epithelial Cells (HBECs) With and Without Defined Premalignant Oncogenic Changes John Minna University of Texas Southwestern Medical Center at Dallas Abstract We want to determine the effect of low dose ionizing radiation on the molecular progression of lung epithelial cells towards lung cancer. Our endpoints are focused on specific molecular and cellular changes known to be associated with lung cancer development and quantitating those changes as a function of low dose ionizing radiation. We use immortalized human bronchial epithelial cells (HBECs) developed from >40 individuals (including those from current, former, and never smokers, males, females,

6

Co-localisation of ?-H2AX and 53BP1 to sites of DNA double strand...  

NLE Websites -- All DOE Office Websites (Extended Search)

-H2AX and 53BP1 to sites of DNA double strand breaks following low- and high-LET irradiation of mammalian cells Jennifer Anderson, Jane Harper, 1 Frank Cucinotta, 2 Janice...

7

Mechanistic studies of bleomycin-mediated double-stranded DNA cleavage and structural studies of DNA containing normal and 4'-oxidized abasic sites  

E-Print Network (OSTI)

In order to examine the role of partial intercalation in double-stranded (ds) DNA cleavage mediated by a single bleomycin (BLM), a bulky group ([-cyclodextrin) was chemically attached to the polyamine tail of BLM A5 to ...

Chen, Jingyang, Ph. D. Massachusetts Institute of Technology

2006-01-01T23:59:59.000Z

8

Sulforaphane induces DNA double strand breaks predominantly repaired by homologous recombination pathway in human cancer cells  

Science Conference Proceedings (OSTI)

Cytotoxicity and DNA double strand breaks (DSBs) were studied in HeLa cells treated with sulforaphane (SFN), a well-known chemo-preventive agent. Cell survival was impaired by SFN in a concentration and treatment time-dependent manner. Both constant field gel electrophoresis (CFGE) and {gamma}-H2AX assay unambiguously indicated formation of DSBs by SFN, reflecting the cell survival data. These DSBs were predominantly processed by homologous recombination repair (HRR), judging from the SFN concentration-dependent manner of Rad51 foci formation. On the other hand, the phosphorylation of DNA-PKcs, a key non-homologous end joining (NHEJ) protein, was not observed by SFN treatment, suggesting that NHEJ may not be involved in DSBs induced by this chemical. G2/M arrest by SFN, a typical response for cells exposed to ionizing radiation was also observed. Our new data indicate the clear induction of DSBs by SFN and a useful anti-tumor aspect of SFN through the induction of DNA DSBs.

Sekine-Suzuki, Emiko [Heavy-Ion Radiobiology Research Group, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan); Graduate School of Advanced Integration Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522 (Japan); Yu, Dong [Heavy-Ion Radiobiology Research Group, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan); Kubota, Nobuo [Department of Radiological Sciences, Ibaraki Prefectural University of Health Sciences, 4669-2 Ami, Ami-machi, Inashiki-gun, Ibaraki 300-0394 (Japan); Okayasu, Ryuichi [Heavy-Ion Radiobiology Research Group, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan); Anzai, Kazunori [Heavy-Ion Radiobiology Research Group, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan); Graduate School of Advanced Integration Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522 (Japan)], E-mail: anzai@nirs.go.jp

2008-12-12T23:59:59.000Z

9

Accumulation of DNA Double-Strand Breaks in Normal Tissues After Fractionated Irradiation  

SciTech Connect

Purpose: There is increasing evidence that genetic factors regulating the recognition and/or repair of DNA double-strand breaks (DSBs) are responsible for differences in radiosensitivity among patients. Genetically defined DSB repair capacities are supposed to determine patients' individual susceptibility to develop adverse normal tissue reactions after radiotherapy. In a preclinical murine model, we analyzed the impact of different DSB repair capacities on the cumulative DNA damage in normal tissues during the course of fractionated irradiation. Material and Methods: Different strains of mice with defined genetic backgrounds (SCID{sup -/-} homozygous, ATM{sup -/-} homozygous, ATM{sup +/-}heterozygous, and ATM{sup +/+}wild-type mice) were subjected to single (2 Gy) or fractionated irradiation (5 x 2 Gy). By enumerating gammaH2AX foci, the formation and rejoining of DSBs were analyzed in organs representative of both early-responding (small intestine) and late-responding tissues (lung, kidney, and heart). Results: In repair-deficient SCID{sup -/-} and ATM{sup -/-}homozygous mice, large proportions of radiation-induced DSBs remained unrepaired after each fraction, leading to the pronounced accumulation of residual DNA damage after fractionated irradiation, similarly visible in early- and late-responding tissues. The slight DSB repair impairment of ATM{sup +/-}heterozygous mice was not detectable after single-dose irradiation but resulted in a significant increase in unrepaired DSBs during the fractionated irradiation scheme. Conclusions: Radiation-induced DSBs accumulate similarly in acute- and late-responding tissues during fractionated irradiation, whereas the whole extent of residual DNA damage depends decisively on the underlying genetically defined DSB repair capacity. Moreover, our data indicate that even minor impairments in DSB repair lead to exceeding DNA damage accumulation during fractionated irradiation and thus may have a significant impact on normal tissue responses in clinical radiotherapy.

Ruebe, Claudia E., E-mail: claudia.ruebe@uks.e [Department of Radiation Oncology, Saarland University, Homburg/Saar (Germany); Fricke, Andreas; Wendorf, Juliane; Stuetzel, Annika; Kuehne, Martin [Department of Radiation Oncology, Saarland University, Homburg/Saar (Germany); Ong, Mei Fang [Institute of Medical Biometrics, Epidemiology and Medical Informatics, Saarland University, Homburg/Saar (Germany); Lipp, Peter [Institute for Molecular Cell Biology, Saarland University, Homburg/Saar (Germany); Ruebe, Christian [Department of Radiation Oncology, Saarland University, Homburg/Saar (Germany)

2010-03-15T23:59:59.000Z

10

Dyes designed for high sensitivity detection of double-stranded DNA  

DOE Patents (OSTI)

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.

Glazer, Alexander N. (Orinda, CA); Benson, Scott C. (Oakland, CA)

1998-01-01T23:59:59.000Z

11

Dyes designed for high sensitivity detection of double-stranded DNA  

DOE Patents (OSTI)

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.

Glazer, Alexander N. (Orinda, CA); Benson, Scott C. (Albany, CA)

1994-01-01T23:59:59.000Z

12

Dyes designed for high sensitivity detection of double-stranded DNA  

DOE Patents (OSTI)

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.

Glazer, Alexander N. (Orinda, CA); Benson, Scott C. (Oakland, CA)

2000-01-01T23:59:59.000Z

13

Dyes designed for high sensitivity detection of double-stranded DNA  

DOE Patents (OSTI)

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.

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

1998-07-21T23:59:59.000Z

14

Effects of garlic on cellular doubling time and DNA strand breaks caused by UV light and BPL, enhanced with catechol and TPA  

Science Conference Proceedings (OSTI)

3T3 cell cultures were exposed to UV light and Beta-Propiolactone. Neoplastic cell transformation (TF) was demonstrated after concurrent addition of catechol, or repeated addition of TPA. Addition of garlic to all fluences/concentrations of the carcinogen/cocarcinogen/promoter groups reduced the number of transformed foci/dish by at least 40%. Since the cell cycle is prolonged following exposure to carcinogens, it is likely the cell requires a longer time to repair this damage. The doubling time (DT) was extended from 12 to 36 hrs. when cells were exposed to BPL and from 12 o 28 hrs. when cells were exposed to 3.0J/M2/sec. If an anticarcinogenic compound is also added, it is reasonable to assume that the cell cycle may be further elongated. The cell cycle, denoted by DT was lengthened from 12 to 47 hrs and from 12 to 86 hrs for BPL and UVC, respectively. The extensions occurred in a dope dependent manner. The concentrations of the cocarcinogen and promoter remained constant throughout the experiment. When strand breaks were determined at the same dose sequences, by alkaline elution, more repair was seen with garlic where the lowest and middle doses of BPL were used and almost no decrease in % DNA eluted was seen with UVC exposed cells. With catechol, there was a two-fold decrease in % DNA eluted at the lowest and middle fluences. When TPA was added, all three fluences of UVC showed more than a threefold decrease in % DNA eluted. BPS with both TPA and catechol, again showed a reduction in strand breaks only low and middle doses. Both a direct-acting alkylating agent, BPL, and a physical carcinogen, UVC, were homogeneously affected, in terms of doubling time, but not when strand break repair was examined. A separate mechanism may be responsible for repair, and the mechanism associated with combinations of physical carcinogen enhancing agents combined with some non-carcinogens may be more profoundly affected by some natural products.

Baturay, N.Z.; Gayle, F.; Liu, S.; Kreidinger, C.

1995-11-01T23:59:59.000Z

15

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

SciTech Connect

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.

Ibanez, Irene L. [Comision Nacional de Energia Atomica, San Martin (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires (Argentina); Bracalente, Candelaria [Comision Nacional de Energia Atomica, San Martin (Argentina); Molinari, Beatriz L. [Comision Nacional de Energia Atomica, San Martin (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires (Argentina); Palmieri, Monica A. [Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (Argentina); Policastro, Lucia [Comision Nacional de Energia Atomica, San Martin (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires (Argentina); Kreiner, Andres J. [Comision Nacional de Energia Atomica, San Martin (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires (Argentina); Escuela de Ciencia y Tecnologia, Universidad Nacional de San Martin (Argentina); Burlon, Alejandro A. [Comision Nacional de Energia Atomica, San Martin (Argentina); Escuela de Ciencia y Tecnologia, Universidad Nacional de San Martin (Argentina); Valda, Alejandro [Escuela de Ciencia y Tecnologia, Universidad Nacional de San Martin (Argentina); Navalesi, Daniela [Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (Argentina); Davidson, Jorge; Davidson, Miguel [Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires (Argentina); Vazquez, Monica; Ozafran, Mabel [Comision Nacional de Energia Atomica, San Martin (Argentina); Duran, Hebe [Comision Nacional de Energia Atomica, San Martin (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires (Argentina); Escuela de Ciencia y Tecnologia, Universidad Nacional de San Martin (Argentina)], E-mail: hduran@cnea.gov.ar

2009-07-15T23:59:59.000Z

16

Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation  

SciTech Connect

The understanding of interactions between double stranded (ds) DNA and charged nanoparticles will have a broad bearing on many important applications from drug delivery [ 1 4 ] to DNAtemplated metallization. [ 5 , 6 ] Cationic nanoparticles (NPs) can bind to DNA, a negatively charged molecule, through a combination of electrostatic attraction, groove binding, and intercalation. Such binding events induce changes in the conformation of a DNA strand. In nature, DNA wraps around a cylindrical protein assembly (diameter and height of 6 nm) [ 7 ] with an 220 positive charge, [ 8 ] creating the complex known as chromatin. Wrapping and bending of DNA has also been achieved in the laboratory through the binding of highly charged species such as molecular assemblies, [ 9 , 10 ] cationic dendrimers, [ 11 , 12 ] and nanoparticles. [ 13 15 ] The charge of a nanoparticle plays a crucial role in its ability to induce DNA structural changes. If a nanoparticle has a highly positive surface charge density, the DNA is likely to wrap and bend upon binding to the nanoparticle [ 13 ] (as in the case of chromatin). On the other hand, if a nanoparticle is weakly charged it will not induce dsDNA compaction. [ 9 , 10 , 15 ] Consequently, there is a transition zone from extended to compact DNA conformations which depends on the chemical nature of the nanoparticle and occurs for polycations with charges between 5 and 10. [ 9 ] While the interactions between highly charged NPs and DNA have been extensively studied, the processes that occur within the transition zone are less explored.

Railsback, Justin [North Carolina State University; Singh, Abhishek [North Carolina State University; Pearce, Ryan [North Carolina State University; McKnight, Timothy E [ORNL; Collazo, Ramon [North Carolina State University; Sitar, Zlatko [ORNL; Yingling, Yaroslava [North Carolina State University; Melechko, Anatoli Vasilievich [ORNL

2012-01-01T23:59:59.000Z

17

DNA Double-Strand Break Analysis by {gamma}-H2AX Foci: A Useful Method for Determining the Overreactors to Radiation-Induced Acute Reactions Among Head-and-Neck Cancer Patients  

SciTech Connect

Purpose: Interindividual variability in normal tissue toxicity during radiation therapy is a limiting factor for successful treatment. Predicting the risk of developing acute reactions before initiation of radiation therapy may have the benefit of opting for altered radiation therapy regimens to achieve minimal adverse effects with improved tumor cure. Methods and Materials: DNA double-strand break (DSB) induction and its repair kinetics in lymphocytes of head-and-neck cancer patients undergoing chemoradiation therapy was analyzed by counting {gamma}-H2AX foci, neutral comet assay, and a modified version of neutral filter elution assay. Acute normal tissue reactions were assessed by Radiation Therapy Oncology Group criteria. Results: The correlation between residual DSBs and the severity of acute reactions demonstrated that residual {gamma}-H2AX foci in head-and-neck cancer patients increased with the severity of oral mucositis and skin reaction. Conclusions: Our results suggest that {gamma}-H2AX analysis may have predictive implications for identifying the overreactors to mucositis and skin reactions among head-and-neck cancer patients prior to initiation of radiation therapy.

Goutham, Hassan Venkatesh; Mumbrekar, Kamalesh Dattaram [Division of Radiobiology and Toxicology, Manipal Life Sciences Centre, Manipal University, Manipal, Karnataka (India)] [Division of Radiobiology and Toxicology, Manipal Life Sciences Centre, Manipal University, Manipal, Karnataka (India); Vadhiraja, Bejadi Manjunath [Manipal Hospital, Bangalore, Karnataka (India)] [Manipal Hospital, Bangalore, Karnataka (India); Fernandes, Donald Jerard; Sharan, Krishna [Department of Radiotherapy and Oncology, Shiridi Sai Baba Cancer Hospital and Research Centre, Kasturba Hospital, Manipal, Karnataka (India)] [Department of Radiotherapy and Oncology, Shiridi Sai Baba Cancer Hospital and Research Centre, Kasturba Hospital, Manipal, Karnataka (India); Kanive Parashiva, Guruprasad; Kapaettu, Satyamoorthy [Division of Biotechnology, Manipal Life Sciences Centre, Manipal University, Manipal, Karnataka (India)] [Division of Biotechnology, Manipal Life Sciences Centre, Manipal University, Manipal, Karnataka (India); Bola Sadashiva, Satish Rao, E-mail: satishraomlsc@gmail.com [Division of Radiobiology and Toxicology, Manipal Life Sciences Centre, Manipal University, Manipal, Karnataka (India)

2012-12-01T23:59:59.000Z

18

Solid phase sequencing of double-stranded nucleic acids  

DOE Patents (OSTI)

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.

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

2002-01-01T23:59:59.000Z

19

The T4 Phage SF1B Helicase Dda Is Structurally Optimized to Perform DNA Strand Separation  

Science Conference Proceedings (OSTI)

Helicases move on DNA via an ATP binding and hydrolysis mechanism coordinated by well-characterized helicase motifs. However, the translocation along single-stranded DNA (ssDNA) and the strand separation of double-stranded (dsDNA) may be loosely or tightly coupled. Dda is a phage T4 SF1B helicase with sequence homology to the Pif1 family of helicases that tightly couples translocation to strand separation. The crystal structure of the Dda-ssDNA binary complex reveals a domain referred to as the pin that was previously thought to remain static during strand separation. The pin contains a conserved phenylalanine that mediates a transient base-stacking interaction that is absolutely required for separation of dsDNA. The pin is secured at its tip by protein-protein interactions through an extended SH3 domain thereby creating a rigid strut. The conserved interface between the pin and the SH3 domain provides the mechanism for tight coupling of translocation to strand separation.

He, Xiaoping; Byrd, Alicia K.; Yun, Mi-Kyung; Pemble IV, Charles W.; Harrison, David; Yeruva, Laxmi; Dahl, Christopher; Kreuzer, Kenneth N.; Raney, Kevin D.; White, Stephen W. (Duke); (SJCH); (Arkansas)

2012-10-16T23:59:59.000Z

20

Why DNA is a double helix  

NLE Websites -- All DOE Office Websites (Extended Search)

Guest14 Location: NA Country: NA Date: NA Question: Why is DNA in a double-helix shape? Replies: The why questions are always the worst. Why is anything the way it is? The...

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Velocity and processivity of helicase unwinding of double-stranded nucleic acids  

E-Print Network (OSTI)

Helicases are molecular motors which unwind double-stranded nucleic acids (dsNA) in cells. Many helicases move with directional bias on single-stranded (ss) nucleic acids, and couple their directional translocation to strand separation. A model of the coupling between translocation and unwinding uses an interaction potential to represent passive and active helicase mechanisms. A passive helicase must wait for thermal fluctuations to open dsNA base pairs before it can advance and inhibit NA closing. An active helicase directly destabilizes dsNA base pairs, accelerating the opening rate. Here we extend this model to include helicase unbinding from the nucleic-acid strand. The helicase processivity depends on the form of the interaction potential. A passive helicase has a mean attachment time which does not change between ss translocation and ds unwinding, while an active helicase in general shows a decrease in attachment time during unwinding relative to ss translocation. In addition, we describe how helicase u...

Betterton, M D; Julicher, Frank

2005-01-01T23:59:59.000Z

22

Velocity and processivity of helicase unwinding of double-stranded nucleic acids  

E-Print Network (OSTI)

Helicases are molecular motors which unwind double-stranded nucleic acids (dsNA) in cells. Many helicases move with directional bias on single-stranded (ss) nucleic acids, and couple their directional translocation to strand separation. A model of the coupling between translocation and unwinding uses an interaction potential to represent passive and active helicase mechanisms. A passive helicase must wait for thermal fluctuations to open dsNA base pairs before it can advance and inhibit NA closing. An active helicase directly destabilizes dsNA base pairs, accelerating the opening rate. Here we extend this model to include helicase unbinding from the nucleic-acid strand. The helicase processivity depends on the form of the interaction potential. A passive helicase has a mean attachment time which does not change between ss translocation and ds unwinding, while an active helicase in general shows a decrease in attachment time during unwinding relative to ss translocation. In addition, we describe how helicase unwinding velocity and processivity vary if the base-pair binding free energy is changed.

M. D. Betterton; Frank Julicher

2005-09-15T23:59:59.000Z

23

Jefferson Lab Science Series - DNA: The Strand That Connects Us All  

NLE Websites -- All DOE Office Websites (Extended Search)

The Mysterious Universe The Mysterious Universe Previous Video (The Mysterious Universe) Science Series Video Archive Next Video (The Science of Chocolate) The Science of Chocolate DNA: The Strand That Connects Us All Dr. Matt Kaplan - University of Arizona Genetics Core March 29, 2011 Learn how the methods and discoveries of human population genetics are applied for personal genealogical reconstruction and anthropological testing. We will start with a short general review of human genetics and the biology behind this form of DNA testing. We will look at how DNA testing is performed and how samples are processed in our laboratory. We will also examine examples of personal genealogical results from Family Tree DNA and personal anthropological results from the Genographic Project. Finally, I will describe the newest project in our laboratory, the DNA

24

Intermediate States of Ribonuclease III in Complex with Double-Stranded RNA  

SciTech Connect

Bacterial ribonuclease III (RNase III) can affect RNA structure and gene expression in either of two ways: as a processing enzyme that cleaves double-stranded (ds) RNA, or as a binding protein that binds but does not cleave dsRNA. We previously proposed a model of the catalytic complex of RNase III with dsRNA based on three crystal structures, including the endonuclease domain of RNase III with and without bound metal ions and a dsRNA binding protein complexed with dsRNA. We also reported a noncatalytic assembly observed in the crystal structure of an RNase III mutant, which binds but does not cleave dsRNA, complexed with dsRNA. We hypothesize that the RNase III {center_dot} dsRNA complex can exist in two functional forms, a catalytic complex and a noncatalytic assembly, and that in between the two forms there may be intermediate states. Here, we present four crystal structures of RNase III complexed with dsRNA, representing possible intermediates.

Gan, Jianhua; Tropea, Joseph E.; Austin, Brian P.; Court, Donald L.; Waugh, David S.; Ji, Xinhua (NIH)

2010-07-19T23:59:59.000Z

25

Unfolding mechanism and the free energy landscape of a single stranded DNA i-motif  

E-Print Network (OSTI)

We present Molecular Dynamics simulations of a single stranded unprotonated DNA i-motif in explicit solvent. Our results indicate that the native structure in non-acidic solution at 300 K is unstable and completely vanishes on a time scale up to 10 ns. Two unfolding mechanisms with decreasing connectivity between the initially interacting nucleobases can be identified where one pathway is characterized as entropically more favorable. The entropic preference can be mainly explained by strong water ordering effects due to hydrogen bonds for several occurring structures along the pathways. Finally we are able to indicate via free energy calculations the most stable configurations belonging to distinct hairpin structures in good agreement to experimental results.

Smiatek, Jens; Liu, Dongsheng; Heuer, Andreas

2011-01-01T23:59:59.000Z

26

Inhibition of Plasmodium falciparum proliferation in vitro by double-stranded RNA directed against malaria histone deacetylase  

SciTech Connect

Acetylation and deacetylation of histones play important roles in transcription regulation, cell cycle progression and development events. The steady state status of histone acetylation is controlled by a dynamic equilibrium between competing histone acetylase and deacetylase (HDAC). We have used long PfHDAC-1 double-stranded (ds)RNA to interfere with its cognate mRNA expression and determined the effect on malaria parasite growth and development. Chloroquine- and pyrimethamine-resistant Plasmodium falciparum K1 strain was exposed to 1-25 {mu}g of dsRNA/ml of culture for 48 h and growth was determined by [{sup 3}H]-hypoxanthine incorporation and microscopic examination. Parasite culture treated with 10 {mu}g/ml pfHDAC-1 dsRNA exhibited 47% growth inhibition when compared with either untreated control or culture treated with an unrelated dsRNA. PfHDAC-1 dsRNA specifically blocked maturation of trophozoite to schizont stages and decreased PfHDAC-1 transcript 44% in treated trophozoites. These results indicate the potential of HDAC-1 as a target for development of novel antimalarials.

Sriwilaijaroen, N. [Faculty of Medicine, Thammasat University (Rangsit Campus), Pathumthani 12120 (Thailand); Boonma, S. [Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400 (Thailand); Attasart, P. [Institute of Molecular Biology and Genetics, Mahidol University, Salaya, Nakornpathom 73170 (Thailand); Pothikasikorn, J. [Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400 (Thailand); Panyim, S. [Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400 (Thailand); Institute of Molecular Biology and Genetics, Mahidol University, Salaya, Nakornpathom 73170 (Thailand); Noonpakdee, W. [Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400 (Thailand)], E-mail: scwnp@mahidol.ac.th

2009-04-03T23:59:59.000Z

27

DNA purification by triplex-affinity capture and affinity capture electrophoresis  

DOE Patents (OSTI)

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.

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

1996-01-09T23:59:59.000Z

28

Mitigating security issues in the evolving DNA synthesis industry  

E-Print Network (OSTI)

DNA synthesis technologies are advancing at exponential rates, with production of ever longer, more complex, and less expensive sequences of double stranded DNA. This has fostered development of industrial scale design, ...

Turlington, Ralph Donald, III

2013-01-01T23:59:59.000Z

29

First-In-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G  

Science Conference Proceedings (OSTI)

APOBEC3G is a single-stranded DNA cytosine deaminase that comprises part of the innate immune response to viruses and transposons. Although APOBEC3G is the prototype for understanding the larger mammalian polynucleotide deaminase family, no specific chemical inhibitors exist to modulate its activity. High-throughput screening identified 34 compounds that inhibit APOBEC3G catalytic activity. Twenty of 34 small molecules contained catechol moieties, which are known to be sulfhydryl reactive following oxidation to the orthoquinone. Located proximal to the active site, C321 was identified as the binding site for the inhibitors by a combination of mutational screening, structural analysis, and mass spectrometry. Bulkier substitutions C321-to-L, F, Y, or W mimicked chemical inhibition. A strong specificity for APOBEC3G was evident, as most compounds failed to inhibit the related APOBEC3A enzyme or the unrelated enzymes E. coli uracil DNA glycosylase, HIV-1 RNase H, or HIV-1 integrase. Partial, but not complete, sensitivity could be conferred to APOBEC3A by introducing the entire C321 loop from APOBEC3G. Thus, a structural model is presented in which the mechanism of inhibition is both specific and competitive, by binding a pocket adjacent to the APOBEC3G active site, reacting with C321, and blocking access to substrate DNA cytosines.

Li, Ming; Shandilya, Shivender M.D.; Carpenter, Michael A.; Rathore, Anurag; Brown, William L.; Perkins, Angela L.; Harki, Daniel A.; Solberg, Jonathan; Hook, Derek J.; Pandey, Krishan K.; Parniak, Michael A.; Johnson, Jeffrey R.; Krogan, Nevan J.; Somasundaran, Mohan; Ali, Akbar; Schiffer, Celia A.; Harris, Reuben S. (Pitt); (UMASS, MED); (SLUHSC); (UCSF); (UMM)

2012-04-04T23:59:59.000Z

30

ZIP4H (TEX11) Deficiency in the Mouse Impairs Meiotic Double Strand Break Repair and the Regulation of Crossing Over  

E-Print Network (OSTI)

We have recently shown that hypomorphic Mre11 complex mouse mutants exhibit defects in the repair of meiotic double strand breaks (DSBs). This is associated with perturbation of synaptonemal complex morphogenesis, repair and regulation of crossover formation. To further assess the Mre11 complex’s role in meiotic progression, we identified testis-specific NBS1interacting proteins via two-hybrid screening in yeast. In this screen, Zip4h (Tex11), a male germ cell specific X-linked gene was isolated. Based on sequence and predicted structural similarity to the S. cerevisiae and A. thaliana Zip4 orthologs, ZIP4H appears to be the mammalian ortholog. In S. cerevisiae and A. thaliana, Zip4 is a meiosis-specific protein that regulates the level of meiotic crossovers, thus influencing homologous chromosome segregation in these organisms. As is true for hypomorphic Nbs1 (Nbs1 DB/DB) mice, Zip4h 2/Y mutant mice were fertile. Analysis of spermatocytes revealed a delay in meiotic double strand break repair and decreased crossover formation as inferred from DMC1 and MLH1 staining patterns, respectively. Achiasmate chromosomes at the first meiotic division were also observed in Zip4h 2/Y mutants, consistent with the observed reduction in MLH1 focus formation. These results indicate that meiotic functions of Zip4 family members are conserved and support the view that the Mre11 complex and ZIP4H interact functionally during the execution of the

Carrie A. Adelman; John H. J. Petrini

2008-01-01T23:59:59.000Z

31

On the possibility of electronic DNA nanobiochips  

E-Print Network (OSTI)

We have considered as a theoretical possibility for the development of a nanobiochip the operation principle of which is based on measuring conductance in single-stranded and double-stranded DNA. Calculations have demonstrated that in the majority of cases the conductance of double-stranded nucleotides considerably exceeds that of single-stranded ones. The results obtained are in agreement with recent experiments on measuring the oligonucleotide conductance. It has been shown that an electronic biochip containing 11 nucleotide pairs will recognize approximately 97% sequences. It has also been demonstrated that the percentage of identifiable sequences will grow with the sequence length.

Lakhno, V D; 10.1021/ct6003438

2013-01-01T23:59:59.000Z

32

DNA repair is the target of novel antibiotics  

E-Print Network (OSTI)

Lloyd, (2006) Rep and PriA helicase activities prevent RecAR. G. Lloyd, (2004) RecG helicase promotes DNA double-strandM. A. Petit, (2005) UvrD helicase, unlike Rep helicase,

Gunderson, Carl Wayne

2007-01-01T23:59:59.000Z

33

A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication  

Science Conference Proceedings (OSTI)

During pre-replication complex (pre-RC) formation, origin recognition complex (ORC), Cdc6, and Cdt1 cooperatively load the 6-subunit mini chromosome maintenance (MCM2-7) complex onto DNA. Loading of MCM2-7 is a prerequisite for DNA licensing that restricts DNA replication to once per cell cycle. During S phase MCM2-7 functions as part of the replicative helicase but within the pre-RC MCM2-7 is inactive. The organization of replicative DNA helicases before and after loading onto DNA has been studied in bacteria and viruses but not eukaryotes and is of major importance for understanding the MCM2-7 loading mechanism and replisome assembly. Lack of an efficient reconstituted pre-RC system has hindered the detailed mechanistic and structural analysis of MCM2-7 loading for a long time. We have reconstituted Saccharomyces cerevisiae pre-RC formation with purified proteins and showed efficient loading of MCM2-7 onto origin DNA in vitro. MCM2-7 loading was found to be dependent on the presence of all pre-RC proteins, origin DNA, and ATP hydrolysis. The quaternary structure of MCM2-7 changes during pre-RC formation: MCM2-7 before loading is a single hexamer in solution but is transformed into a double-hexamer during pre-RC formation. Using electron microscopy (EM), we observed that loaded MCM2-7 encircles DNA. The loaded MCM2-7 complex can slide on DNA, and sliding is not directional. Our results provide key insights into mechanisms of pre-RC formation and have important implications for understanding the role of the MCM2-7 in establishment of bidirectional replication forks.

Evrin, C.; Li, H.; Clarke, P.; Zech, J.; Lurz, R.; Sun, J.; Uhle, S.; Stillman, B.; Speck, C.

2009-12-01T23:59:59.000Z

34

Forster Resonance Energy Transfer and Laser Fluorescent Analysis of Defects in DNA Double Helix  

E-Print Network (OSTI)

Real time laser induced fluorescence spectroscopy usage for microanalysis of DNA double helix defects is shown. The method is based on Forster resonance energy transfer (FRET) in intercalator-donor pair (acridine orange as a donor and ethidium bromide as an acceptor). Transition metal ions such as Cu(II), Cu(I), Ag(I), silver nanoparticles (AgNPs), photo- and thermo effects were used to cause double helix defects in DNA. FRET radii were experimentally estimated in background electrolyte solution (0.01 M NaNO3) and proved to be 3.9 +- 0.3 nm and the data are in satisfactory agreement with the theoretically calculated value Ro = 3.5 +- 0.3 nm. Concentration of DNA sites, exposed to Cu(II), Cu(I), Ag(I) ions, AgNPs impact as well as laser irradiation ({\\lambda} = 457 nm) and temperature, which are applicable for intercalation, were estimated in relative units. FRET method allows to estimate the concentration of double helix areas with high quality stability applicable for intercalation in DNA after it was subjec...

Bregadze, Vasil G; Giorgadze, Tamar G; Jaliashvili, Zaza V; Chkhaberidze, Jemal G; Monaselidze, Jamlet R; Khuskivadze, Temur B

2013-01-01T23:59:59.000Z

35

DNA Duplication Revealed in New Beginnings | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

DNA Duplication Revealed in New Beginnings 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 protein (not shown) is the enzyme that unwinds the double stranded DNA so each strand can be replicated. | Illustration courtesy of Brookhaven Lab. The DNA replication origin recognition complex (ORC) is a six-protein machine with a slightly twisted half-ring structure (yellow). ORC is

36

Single-Strand Conformational Polymorphism Analysis  

Science Conference Proceedings (OSTI)

base change in the sequence can cause single-stranded DNA to migrate ... human genome is thus increasingly important in elucidating the pathogenesis.

37

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

E-Print Network (OSTI)

tightly regulated for doxycycline-inducible shRNA expressioninduced by adding 1 µg/ml doxycycline to the growth mediumfor 16 h (without doxycycline) or 18 h (with doxycycline).

Zafar, Faria

2010-01-01T23:59:59.000Z

38

DNA  

NLE Websites -- All DOE Office Websites (Extended Search)

directed directed assembly of nanoparticle linear structure for nanophotonics Baoquan Ding, a͒ Stefano Cabrini, b͒ Ronald N. Zuckermann, and Jeffrey Bokor Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California 94720 ͑Received 17 June 2008; accepted 22 December 2008; published 2 February 2009͒ Assemblies of metal nanospheres have shown interesting properties for nanophotonics. Here the authors describe a method to use robust DNA multicrossover molecules to organize Au nanoparticles with different sizes to form well controlled linear chain structures with desired distance below 10 nm between the particles. Au particles with only one piece of DNA attached are purified individually. Three different sizes DNA-Au conjugates then hybridize with five other DNA strands to form the stiff triple crossover ͑TX͒ motif. The linkage position

39

The effects of bio-fluid on the internal motion of DNA  

E-Print Network (OSTI)

The internal motions of DNA immersed in bio-fluid are investigated. The interactions between the fragments of DNA and the surrounding bio-fluid are modeled using the gauge fluid lagrangian. In the model, the bio-fluid is coupled to the standard gauge invariant bosonic lagrangian describing the DNA. It is shown that at non-relativistic limit various equation of motions, from the well-known Sine-Gordon equation to the simultaneous nonlinear equations, can be constructed within a single framework. The effects of bio-fluid are investigated for two cases : single and double stranded DNA. It is argued that the small and large amplitudes of a single stranded DNA motion immersed in bio-fluid can be explained in a natural way within the model as a solitonic wave regardless with the fluid velocity. In contrary the double stranded DNA behaves as regular or damped harmonic oscillator and is highly depending on the fluid velocity.

Sulaiman, A; 10.1166/jctn.2011.1669

2011-01-01T23:59:59.000Z

40

Rapid purification of circular DNA by triplex-mediated affinity capture  

DOE Patents (OSTI)

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.

Ji, Huamin (4817 Sheboygan Ave., Madison, WI 53705); Smith, Lloyd M. (1115 Amherst Dr., Madison, WI 53705)

1997-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

Rapid purification of circular DNA by triplex-mediated affinity capture  

DOE Patents (OSTI)

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.

Ji, H.; Smith, L.M.

1997-01-07T23:59:59.000Z

42

Live Cell Imaging and in situ analysis of cellular responses to DNA doublestrand  

NLE Websites -- All DOE Office Websites (Extended Search)

Live Cell Imaging and in situ analysis of cellular responses to DNA double- Live Cell Imaging and in situ analysis of cellular responses to DNA double- strand breaks in mammalian cells. David J. Chen Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas TX 75390 The integrity of the human genome is constantly threatened by internal as well as external factors with the propensity to cause DNA damage. Of the various types of DNA damage that can occur within the mammalian cell nucleus, the DNA double strand break (DSB) is perhaps the most dangerous. Estimates put the number of endogenous DSBs anywhere between 10-100 per nucleus per day. A direct link between DSBs and cancer has been surmised by researchers based upon the fact that many cancer-predisposition

43

Derivatized versions of ligase enzymes for constructing DNA sequences  

DOE Patents (OSTI)

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.

Mariella, Jr., Raymond P. (Danville, CA); Christian, Allen T. (Tracy, CA); Tucker, James D. (Novi, MN); Dzenitis, John M. (Livermore, CA); Papavasiliou, Alexandros P. (Oakland, CA)

2006-08-15T23:59:59.000Z

44

Manipulating a single adsorbed DNA for a critical endpoint  

E-Print Network (OSTI)

We show the existence of a critical endpoint in the phase diagram of unzipping of an adsorbed double-stranded (ds) polymer like DNA. The competition of base pairing, adsorption and stretching by an external force leads to the critical end point. From exact results, the location of the critical end point is determined and its classical nature established.

Rajeev Kapri; Somendra M. Bhattacharjee

2008-03-24T23:59:59.000Z

45

Probe and method for DNA detection  

SciTech Connect

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

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

2013-07-02T23:59:59.000Z

46

Unzipping DNA by force: thermodynamics and finite size behaviour  

E-Print Network (OSTI)

We discuss the thermodynamic behaviour near the force induced unzipping transition of a double stranded DNA in two different ensembles. The Y-fork is identified as the coexisting phases in the fixed distance ensemble. From finite size scaling of thermodynamic quantities like the extensibility, the length of the unzipped segment of a Y-fork, the phase diagram can be recovered. We suggest that such procedures could be used to obtain the thermodynamic phase diagram from experiments on finite length DNA.

Rajeev Kapri; Somendra M. Bhattacharjee

2005-11-22T23:59:59.000Z

47

Electrophoretic detection and separation of mutant DNA using replaceable polymer matrices  

DOE Patents (OSTI)

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.

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

1997-05-27T23:59:59.000Z

48

Helicase on DNA: A Phase coexistence based mechanism  

E-Print Network (OSTI)

We propose a phase coexistence based mechanism for activity of helicases, ubiquitous enzymes that unwind double stranded DNA. The helicase-DNA complex constitutes a fixed-stretch ensemble that entails a coexistence of domains of zipped and unzipped phases of DNA, separated by a domain wall. The motor action of the helicase leads to a change in the position of the fixed constraint thereby shifting the domain wall on dsDNA. We associate this off-equilibrium domain wall motion with the unzipping activity of helicase. We show that this proposal gives a clear and consistent explanation of the main observed features of helicases.

Somendra M. Bhattacharjee; Flavio Seno

2002-05-13T23:59:59.000Z

49

A model for DNA helicase mechanism based on a flashing ratchet  

E-Print Network (OSTI)

Helicases are molecular motors that consume energy supplied by chemical reactions to unwind double-stranded nucleic acids (like DNA and RNA) and to translocate along one of the single-strands. Motivated by the recent claims, based on experimental observations on the helicase NS3 of hepatitis C virus (HCV), that monomeric helicases are governed by a Brownian ratchet mechanism, here we develope a quantitative model. Our Brownian ratchet model, which is a somewhat new reformulation of the Betterton-J\\"ulicher theory of helicases, is generic two-state model and is applicable to all helicases which follow the Brownian ratchet mechanism. We illustrate the predictive power of the model by calculating some experimentally testable motor properties of a few monomeric helicases. Speficically, we predict the speed of unwinding of the double-stranded DNA and fluctuations around the average drift of the helicase. Our predictions are in excellent quantitative agreement with the corresponding experimental data.

Garai, Ashok; Chowdhury, Debashish

2007-01-01T23:59:59.000Z

50

Low-cost, Rapid DNA Sequencing Technique  

Sequencing DNA is crucial for future breakthroughs in biological and biomedical research. Until now, ... The nucleic acid strand transport

51

Mutations Altering the Interplay between GkDnaC Helicase and DNA Reveal an Insight into Helicase Unwinding  

E-Print Network (OSTI)

Replicative helicases are essential molecular machines that utilize energy derived from NTP hydrolysis to move along nucleic acids and to unwind double-stranded DNA (dsDNA). Our earlier crystal structure of the hexameric helicase from Geobacillus kaustophilus HTA426 (GkDnaC) in complex with single-stranded DNA (ssDNA) suggested several key residues responsible for DNA binding that likely play a role in DNA translocation during the unwinding process. Here, we demonstrated that the unwinding activities of mutants with substitutions at these key residues in GkDnaC are 2–4-fold higher than that of wildtype protein. We also observed the faster unwinding velocities in these mutants using single-molecule experiments. A partial loss in the interaction of helicase with ssDNA leads to an enhancement in helicase efficiency, while their ATPase activities remain unchanged. In strong contrast, adding accessory proteins (DnaG or DnaI) to GkDnaC helicase alters the ATPase, unwinding efficiency and the unwinding velocity of the helicase. It suggests that the unwinding velocity of helicase

Yu-hua Lo; Shih-wei Liu; Yuh-ju Sun; Hung-wen Lizz; Chwan-deng Hsiao

2011-01-01T23:59:59.000Z

52

Helicase activity on DNA as a propagating front  

E-Print Network (OSTI)

We develop a propagating front analysis, in terms of a local probability of zipping, for the helicase activity of opening up a double stranded DNA (dsDNA). In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front separates the zipped and unzipped phases of a dsDNA and a drive acts locally around the front. Bounds from variational analysis and numerical estimates for the speed of a helicase are obtained. Different types of helicase behaviours can be distinguished by the nature of the drive.

Somendra M. Bhattacharjee

2003-07-16T23:59:59.000Z

53

Low Dose Radiation Research Program: Assessing Biological Function of DNA  

NLE Websites -- All DOE Office Websites (Extended Search)

Assessing Biological Function of DNA Damage Response Genes Assessing Biological Function of DNA Damage Response Genes Larry H. Thompson Lawrence Livermore National Laboratory Why This Project To understand the relative importance of individual DNA repair and DNA-damage response pathways to the recovery of mammalian cells after exposure to low doses of ionizing radiation (IR). This understanding may lead to better ways of setting limits on human exposure to IR. In spite of the discovery of many mammalian DNA repair genes, our current knowledge of how many of these genes contribute to cellular recovery from IR exposure is quite limited. Project Goals Measure cellular responses at doses in the 5-100 cGy range, which generally cause changes too small to detect in normal, repair-proficient cells Focus on DNA double-strand breaks (DSBs) and DNA oxidative base

54

Persistent DNA damage foci, cellular senescence and low dose radiation  

NLE Websites -- All DOE Office Websites (Extended Search)

Persistent DNA damage foci, cellular senescence and low dose radiation Persistent DNA damage foci, cellular senescence and low dose radiation Denise Munoz 1 , Albert Davalos 1 , Francis Rodier 1 , Misako Kawahara 1 , Judith Campisi 1,2 and Steven Yannone 1,3 1 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 84-171, Berkeley CA 94720; 2 Buck Institute for Age Research, 8001 Redwood Boulevard, Novato CA 94945; 3 Corresponding author Ionizing radiation (IR) induced DNA double-strand breaks (DSBs) are cytologically detectable as large nuclear foci that contain phosphorylated histone H2AX (γH2AX), the adaptor protein 53BP1, and several other proteins that participate in the sensing and processing of DNA damage (DNA damage foci). In normal human cells, moderately high IR (0.5-1 Gy) doses cause the rapid appearance of these foci (acute DNA damage foci), which gradually disappear

55

When DNA Needs to Stand Up and Be Counted  

NLE Websites -- All DOE Office Websites (Extended Search)

When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA...

56

DNA Sequencing Using capillary Electrophoresis  

Science Conference Proceedings (OSTI)

The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other application papers of sequencing up to this level were also published in the mid 1990's. A major interest of the sequencing community has always been read length. The longer the sequence read per run the more efficient the process as well as the ability to read repeat sequences. We therefore devoted a great deal of time to studying the factors influencing read length in capillary electrophoresis, including polymer type and molecule weight, capillary column temperature, applied electric field, etc. In our initial optimization, we were able to demonstrate, for the first time, the sequencing of over 1000 bases with 90% accuracy. The run required 80 minutes for separation. Sequencing of 1000 bases per column was next demonstrated on a multiple capillary instrument. Our studies revealed that linear polyacrylamide produced the longest read lengths because the hydrophilic single strand DNA had minimal interaction with the very hydrophilic linear polyacrylamide. Any interaction of the DNA with the polymer would lead to broader peaks and lower read length. Another important parameter was the molecular weight of the linear chains. High molecular weight (> 1 MDA) was important to allow the long single strand DNA to reptate through the entangled polymer matrix. In an important paper, we showed an inverse emulsion method to prepare reproducibility linear polyacrylamide polymer with an average MWT of 9MDa. This approach was used in the polymer for sequencing the human genome. Another critical factor in the successful use of capillary electrophoresis for sequencing was the sample preparation method. In the Sanger sequencing reaction, high concentration of salts and dideoxynucleotide remained. Since the sample was introduced to the capillary column by electrokinetic injection, these salt ions would be favorably injected into the column over the sequencing fragments, thus reducing the signal for longer fragments and hence reading read length. In two papers, we examined the role of individual components from the sequencing reaction and then developed a protocol to reduce the deleterio

Dr. Barry Karger

2011-05-09T23:59:59.000Z

57

Single-nucleotide polymorphisms in base excision repair, nucleotide excision repair, and double strand break genes as markers for response to radiotherapy in patients with Stage I to II head-and-neck cancer  

SciTech Connect

Purpose: Polymorphisms in DNA repair genes can influence response to radiotherapy. We analyzed single-nucleotide polymorphisms (SNP) in nine DNA repair genes in 108 patients with head-and-neck cancer (HNSCC) who had received radiotherapy only. Methods and Materials: From May 1993 to December 2004, patients with Stage I and II histopathologically confirmed HNSCC underwent radiotherapy. DNA was obtained from paraffin-embedded tissue, and SNP analysis was performed using a real-time polymerase chain reaction allelic discrimination TaqMan assay with minor modifications. Results: Patients were 101 men (93.5%) and 7 (6.5%) women, with a median age of 64 years (range, 40 to 89 years). Of the patients, 76 (70.4%) patients were Stage I and 32 (29.6%) were Stage II. The XPF/ERCC1 SNP at codon 259 and XPG/ERCC5 at codon 46 emerged as significant predictors of progression (p 0.00005 and 0.049, respectively) and survival (p = 0.0089 and 0.0066, respectively). Similarly, when variant alleles of XPF/ERCC1, XPG/ERCC5 and XPA were examined in combination, a greater number of variant alleles was associated with shorter time to progression (p = 0.0003) and survival (p 0.0002). Conclusions: Genetic polymorphisms in XPF/ERCC1, XPG/ERCC5, and XPA may significantly influence response to radiotherapy; large studies are warranted to confirm their role in HNSCC.

Carles, Joan [Department of Medical Oncology, Hospital del Mar, University Autonoma of Barcelona, Barcelona (Spain)]. E-mail: jcarles@imas.imim.es; Monzo, Mariano [Department of Human Anatomy, Faculty of Medicine, University of Barcelona, Barcelona (Spain); Amat, Marta [Department of Otolaryngology, Hospital del Mar, University Autonoma of Barcelona, Barcelona (Spain); Jansa, Sonia [Department of Human Anatomy, Faculty of Medicine, University of Barcelona, Barcelona (Spain); Artells, Rosa [Department of Human Anatomy, Faculty of Medicine, University of Barcelona, Barcelona (Spain); Navarro, Alfons [Department of Human Anatomy, Faculty of Medicine, University of Barcelona, Barcelona (Spain); Foro, Palmira [Department of Radiation Oncology, Hospital del Mar, University Autonoma of Barcelona, Barcelona (Spain); Alameda, Francesc [Department of Pathology, Hospital del Mar, University Autonoma of Barcelona, Barcelona (Spain); Gayete, Angel [Department of Radiology, Hospital del Mar, University Autonoma of Barcelona, Barcelona (Spain); Gel, Bernat [Department of Human Anatomy, Faculty of Medicine, University of Barcelona, Barcelona (Spain); Miguel, Maribel [Department of Human Anatomy, Faculty of Medicine, University of Barcelona, Barcelona (Spain); Albanell, Joan [Department of Medical Oncology, Hospital del Mar, University Autonoma of Barcelona, Barcelona (Spain); Fabregat, Xavier [Department of Medical Oncology, Hospital del Mar, University Autonoma of Barcelona, Barcelona (Spain)

2006-11-15T23:59:59.000Z

58

The Boltzmann factor, DNA melting, and Brownian ratchets: Topics in an introductory physics sequence for biology and premedical students  

E-Print Network (OSTI)

Three, interrelated biologically-relevant examples of biased random walks are presented: (1) A model for DNA melting, modelled as DNA unzipping, which provides a way to illustrate the role of the Boltzmann factor in a venue well-known to biology and pre-medical students; (2) the activity of helicase motor proteins in unzipping double-stranded DNA, for example, at the replication fork, which is an example of a Brownian ratchet; (3) force generation by actin polymerization, which is another Brownian ratchet, and for which the force and actin-concentration dependence of the velocity of actin polymerization is determined.

Mochrie, S G J

2011-01-01T23:59:59.000Z

59

The Initiation of Bacterial DNA Replication  

NLE Websites -- All DOE Office Websites (Extended Search)

The Initiation of Bacterial DNA The Initiation of Bacterial DNA Replication The Initiation of Bacterial DNA Replication Print Wednesday, 31 January 2007 00:00 For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates that this AAA+ superhelix will wrap coils of the DNA around its exterior, causing the DNA double helix to deform as a first step in the separation and unwinding of its strands. Eukaryotic and archaeal initiators also have the structural elements that promote open-helix formation, indicating that a spiral, open-ring AAA+ assembly is a conserved element from a common evolutionary ancestor of Archaea, Bacteria, and Eukarya.

60

The Initiation of Bacterial DNA Replication  

NLE Websites -- All DOE Office Websites (Extended Search)

The Initiation of Bacterial DNA Replication Print The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates that this AAA+ superhelix will wrap coils of the DNA around its exterior, causing the DNA double helix to deform as a first step in the separation and unwinding of its strands. Eukaryotic and archaeal initiators also have the structural elements that promote open-helix formation, indicating that a spiral, open-ring AAA+ assembly is a conserved element from a common evolutionary ancestor of Archaea, Bacteria, and Eukarya.

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


61

The Initiation of Bacterial DNA Replication  

NLE Websites -- All DOE Office Websites (Extended Search)

The Initiation of Bacterial DNA Replication Print The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates that this AAA+ superhelix will wrap coils of the DNA around its exterior, causing the DNA double helix to deform as a first step in the separation and unwinding of its strands. Eukaryotic and archaeal initiators also have the structural elements that promote open-helix formation, indicating that a spiral, open-ring AAA+ assembly is a conserved element from a common evolutionary ancestor of Archaea, Bacteria, and Eukarya.

62

Binary electrokinetic separation of target DNA from background DNA primers.  

Science Conference Proceedings (OSTI)

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.

James, Conrad D.; Derzon, Mark Steven

2005-10-01T23:59:59.000Z

63

Rotations of the 2B Sub-domain of E. coli UvrD Helicase/Translocase Coupled to Nucleotide and DNA Binding  

Science Conference Proceedings (OSTI)

Escherichia coli UvrD is a superfamily 1 DNA helicase and single-stranded DNA (ssDNA) translocase that functions in DNA repair and plasmid replication and as an anti-recombinase by removing RecA protein from ssDNA. UvrD couples ATP binding and hydrolysis to unwind double-stranded DNA and translocate along ssDNA with 3'-to-5' directionality. Although a UvrD monomer is able to translocate along ssDNA rapidly and processively, DNA helicase activity in vitro requires a minimum of a UvrD dimer. Previous crystal structures of UvrD bound to a ssDNA/duplex DNA junction show that its 2B sub-domain exists in a 'closed' state and interacts with the duplex DNA. Here, we report a crystal structure of an apo form of UvrD in which the 2B sub-domain is in an 'open' state that differs by an {approx} 160{sup o} rotation of the 2B sub-domain. To study the rotational conformational states of the 2B sub-domain in various ligation states, we constructed a series of double-cysteine UvrD mutants and labeled them with fluorophores such that rotation of the 2B sub-domain results in changes in fluorescence resonance energy transfer. These studies show that the open and closed forms can interconvert in solution, with low salt favoring the closed conformation and high salt favoring the open conformation in the absence of DNA. Binding of UvrD to DNA and ATP binding and hydrolysis also affect the rotational conformational state of the 2B sub-domain, suggesting that 2B sub-domain rotation is coupled to the function of this nucleic acid motor enzyme.

Jia, Haifeng; Korolev, Sergey; Niedziela-Majka, Anita; Maluf, Nasib K.; Gauss, George H.; Myong, Sua; Ha, Taekjip; Waksman, Gabriel; Lohman, Timothy M. (UIUC); (St. Louis-MED); (WU-MED); (UCL)

2011-11-02T23:59:59.000Z

64

Low Dose Radiation Induced DNA Damage Signaling and Repair Responses in  

NLE Websites -- All DOE Office Websites (Extended Search)

Induced DNA Damage Signaling and Repair Responses in Induced DNA Damage Signaling and Repair Responses in Human 3-Dimensional Skin Model System Yanrong Su, Jarah Meador and Adayabalam S. Balajee Center for Radiological Research, College of Physicians and Surgeons, Columbia University, 630 West, 168th Street, New York, NY 10032. Exposure to ionizing radiation (IR) inflicts a wide variety of lesions in the genomic DNA. Among them, DNA double strand break (DSB) is considered to be the critical lesion for most of the deleterious radiation effects including carcinogenesis. Much of our knowledge on induction and repair kinetics of DSB has come from studies in two dimensional cell culture systems. However, the damage signaling and repair responses to DSB in tissue microenvironment are largely unknown. Knowledge of tissue responses to

65

Suberoylanilide Hydroxyamic Acid Modification of Chromatin Architecture Affects DNA Break Formation and Repair  

Science Conference Proceedings (OSTI)

Purpose: Chromatin-modifying compounds that inhibit the activity of histone deacetylases have shown potency as radiosensitizers, but the action of these drugs at a molecular level is not clear. Here we investigated the effect of suberoylanilide hydroxyamic acid (SAHA) on DNA breaks and their repair and induction of rearrangements. Methods and Materials: The effect of SAHA on both clonogenic survival and repair was assessed using cell lines SCC-25, MCF7, and TK6. In order to study unique DNA double-strand breaks, anti-CD95 antibody was employed to introduce a DNA double-strand break at a known location within the 11q23 region. The effects of SAHA on DNA cleavage and rearrangements were analyzed by ligation-mediated PCR and inverse PCR, respectively. Results: SAHA acts as radiosensitizer at 1 {mu}M, with dose enhancement factors (DEFs) at 10% survival of: SCC-25 - 1.24 +- 0.05; MCF7 - 1.16 +- 0.09 and TK6 - 1.17 +- 0.05, and it reduced the capacity of SCC-25 cells to repair radiation induced lesions. Additionally, SAHA treatment diffused site-specific fragmentation over at least 1 kbp in TK6 cells. Chromosomal rearrangements produced in TK6 cells exposed to SAHA showed a reduction in microhomology at the breakpoint between 11q23 and partner chromosomes. Conclusions: SAHA shows efficacy as a radiosensitizer at clinically obtainable levels. In its presence, targeted DNA strand breaks occur over an expanded region, indicating increased chromatin access. The rejoining of such breaks is degraded by SAHA when measured as rearrangements at the molecular level and rejoining that contributes to cell survival.

Singh, Sheetal; Le Hongan; Shih, S.-J.; Ho, Bay [Department of Radiation Oncology, University of California at Davis, 4501 X St., Sacramento, California 95817 (United States); Vaughan, Andrew T., E-mail: andrew.vaughan@ucdmc.ucdavis.ed [Department of Radiation Oncology, University of California at Davis, 4501 X St., Sacramento, California 95817 (United States); Department of Veterans Affairs, Mather, California 95655 (United States)

2010-02-01T23:59:59.000Z

66

ExpandplusCrystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA  

Science Conference Proceedings (OSTI)

Poly(ADP-ribose) polymerase-1 (PARP-1) has two homologous zinc finger domains, Zn1 and Zn2, that bind to a variety of DNA structures to stimulate poly(ADP-ribose) synthesis activity and to mediate PARP-1 interaction with chromatin. The structural basis for interaction with DNA is unknown, which limits our understanding of PARP-1 regulation and involvement in DNA repair and transcription. Here, we have determined crystal structures for the individual Zn1 and Zn2 domains in complex with a DNA double strand break, providing the first views of PARP-1 zinc fingers bound to DNA. The Zn1-DNA and Zn2-DNA structures establish a novel, bipartite mode of sequence-independent DNA interaction that engages a continuous region of the phosphodiester backbone and the hydrophobic faces of exposed nucleotide bases. Biochemical and cell biological analysis indicate that the Zn1 and Zn2 domains perform distinct functions. The Zn2 domain exhibits high binding affinity to DNA compared with the Zn1 domain. However, the Zn1 domain is essential for DNA-dependent PARP-1 activity in vitro and in vivo, whereas the Zn2 domain is not strictly required. Structural differences between the Zn1-DNA and Zn2-DNA complexes, combined with mutational and structural analysis, indicate that a specialized region of the Zn1 domain is re-configured through the hydrophobic interaction with exposed nucleotide bases to initiate PARP-1 activation.

M Langelier; J Planck; S Roy; J Pascal

2011-12-31T23:59:59.000Z

67

DNA damage produced by exposure of supercoiled plasmid DNA to high- and low-LET ionizing radiation: Effects of hydroxyl radical quenchers. DNA breakage, neutrons, OH radicals  

SciTech Connect

A supercoiled plasmid of 7300 base pairs was isolated and exposed in an aqueous environment to {sup 60}Co {gamma} rays and JANUS 0.85 MeV fission-spectrum neutrons. Dose responses for the production of single-strand breaks (SSBs), double-strand breaks (DSBs) and alkali-labile sites (ALSs) were compared with computations made from the conversion of the supercoil to its relaxed and linear forms. The relative biological effectiveness (RBE) for production of SSBs and DSBs was similar to that previously measured in the cellular environment. The RBE for destruction of genetic transforming activity of M13 viral DNA followed that for DNA damage. This is in contrast to the situation for biological effects such as lethality, mutagenesis, and cellular transformation measured in mammalian cells, where the RBE values are reversed. The role of hydroxyl (OH) radical in DNA damage induction by neutrons was investigated by exposure of plasmid in the presence of known quenchers of this species. Of four quenchers tested, all were able to reduce the yields of both SSBs and DSBs. These findings are consistent with a model for SSB and DSB induction by high linear energy transfer that involves OH radical mediation.

Peak, J.G.; Ito, T.; Peak, M.J. [Argonne National Lab., IL (United States); Robb, F.T. [Univ. of Maryland, Baltimore, MD (United States). Center for Marine Biotechnology

1994-08-01T23:59:59.000Z

68

Structural Analysis of Rtt106p Reveals a DNA Binding Role Required for Heterochromatin Silencing  

Science Conference Proceedings (OSTI)

Rtt106p is a Saccharomyces cerevisiae histone chaperone with roles in heterochromatin silencing and nucleosome assembly. The molecular mechanism by which Rtt106p engages in chromatin dynamics remains unclear. Here, we report the 2.5 {angstrom} crystal structure of the core domain of Rtt106p, which adopts an unusual 'double pleckstrin homology' domain architecture that represents a novel structural mode for histone chaperones. A histone H3-H4-binding region and a novel double-stranded DNA-binding region have been identified. Mutagenesis studies reveal that the histone and DNA binding activities of Rtt106p are involved in Sir protein-mediated heterochromatin formation. Our results uncover the structural basis of the diverse functions of Rtt106p and provide new insights into its cellular roles.

Liu, Y.; Huang, H; Zhou, B; Wang, S; Hu, Y; Li, X; Liu, J; Niu, L; Wu, J; et. al.

2010-01-01T23:59:59.000Z

69

Procedure for normalization of cDNA libraries  

DOE Patents (OSTI)

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

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

1997-12-30T23:59:59.000Z

70

Structure of the guide-strand-containing argonaute silencing complex  

SciTech Connect

The slicer activity of the RNA-induced silencing complex is associated with argonaute, the RNase H-like PIWI domain of which catalyses guide-strand-mediated sequence-specific cleavage of target messenger RNA. Here we report on the crystal structure of Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-base DNA guide strand, thereby identifying the nucleic-acid-binding channel positioned between the PAZ- and PIWI-containing lobes, as well as the pivot-like conformational changes associated with complex formation. The bound guide strand is anchored at both of its ends, with the solvent-exposed Watson-Crick edges of stacked bases 2 to 6 positioned for nucleation with the mRNA target, whereas two critically positioned arginines lock bases 10 and 11 at the cleavage site into an unanticipated orthogonal alignment. Biochemical studies indicate that key amino acid residues at the active site and those lining the 5'-phosphate-binding pocket made up of the Mid domain are critical for cleavage activity, whereas alterations of residues lining the 2-nucleotide 3'-end-binding pocket made up of the PAZ domain show little effect.

Wang, Yanli; Sheng, Gang; Juranek, Stefan; Tuschl, Thomas; Patel, Dinshaw J. (MSKCC); (HHMI)

2009-01-15T23:59:59.000Z

71

Method for construction of normalized cDNA libraries  

DOE Patents (OSTI)

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

Soares, M.B.; Efstratiadis, A.

1996-01-09T23:59:59.000Z

72

Genome scanning : an AFM-based DNA sequencing technique  

E-Print Network (OSTI)

Genome Scanning is a powerful new technique for DNA sequencing. The method presented in this thesis uses an atomic force microscope with a functionalized cantilever tip to sequence single stranded DNA immobilized to a mica ...

Elmouelhi, Ahmed (Ahmed M.), 1979-

2003-01-01T23:59:59.000Z

73

Armchair Science: DNA Strands That Select Nanotubes Are ...  

Science Conference Proceedings (OSTI)

... are needed to make “quantum wires” for low-loss, long distance electricity transmission and wiring. ... like rolling up a piece of chicken wire. ...

2012-10-18T23:59:59.000Z

74

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

Science Conference Proceedings (OSTI)

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.

Suh, Myungkoo

1995-12-06T23:59:59.000Z

75

KUB5/HERA: a dual acting protein that suppresses genomic instability and promotes DNA repair after low dose IR exposure  

NLE Websites -- All DOE Office Websites (Extended Search)

KUB5/HERA: a dual acting protein that suppresses genomic instability and KUB5/HERA: a dual acting protein that suppresses genomic instability and promotes DNA repair after low dose IR exposure Julio C. Morales 1 , Amy Rommel 1 , Konstantin Leskov 2 , Walter M. Hittelman 3 , David A. Boothman 1# 1 Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. 2 Department of Radiation Oncology, Case Western Reserve University, Cleveland, OH 44106, USA. 3 Department of Experimental Therapeutics, M.D. Anderson Cancer Center, Houston, TX 77030, USA. # To whom correspondence should be addressed. E-mail: David.Boothman@utsouthwestern.edu Eukaryotic cells can respond to DNA double strand breaks created by low doses of IR by activating homologous recombination (HR) or non-homologous end- joining (NHEJ) pathways to repair DNA. A yeast two-hybrid screen using Ku70 as

76

1999 Gordon Research Conference on Mammalian DNA Repair. Final Progress Report  

SciTech Connect

This Conference will examine DNA repair as the key component in genomic surveillance that is so crucial to the overall integrity and function of mammalian cells. Recent discoveries have catapulted the field of DNA repair into a pivotal position for fundamental investigations into oncology, aging, environmental health, and developmental biology. We hope to highlight the most promising and exciting avenues of research in robust discussions at this conference. This Mammalian DNA Repair Gordon Conference differs from the past conferences in this series, in which the programs were broader in scope, with respect to topics and biological systems covered. A conference sponsored by the Genetics Society in April 1998 emphasized recombinational mechanisms for double-strand break repair and the role of mismatch repair deficiency in colorectal cancer. These topics will therefore receive somewhat less emphasis in the upcoming Conference. In view of the recent mechanistic advances in mammalian DNA repair, an upcoming comprehensive DNA repair meeting next autumn at Hilton Head; and the limited enrollment for Gordon Conferences we have decided to focus session-by-session on particular areas of controversy and/or new developments specifically in mammalian systems. Thus, the principal presentations will draw upon results from other cellular systems only to the extent that they impact our understanding of mammalian DNA repair.

1999-02-12T23:59:59.000Z

77

Mechanism of DNA Translocation in a Replicative Hexameric Helicase  

Science Conference Proceedings (OSTI)

The E1 protein of papillomavirus is a hexameric ring helicase belonging to the AAA + family. The mechanism that couples the ATP cycle to DNA translocation has been unclear. Here we present the crystal structure of the E1 hexamer with single-stranded DNA discretely bound within the hexamer channel and nucleotides at the subunit interfaces. This structure demonstrates that only one strand of DNA passes through the hexamer channel and that the DNA-binding hairpins of each subunit form a spiral 'staircase' that sequentially tracks the oligonucleotide backbone. Consecutively grouped ATP, ADP and apo configurations correlate with the height of the hairpin, suggesting a straightforward DNA translocation mechanism. Each subunit sequentially progresses through ATP, ADP and apo states while the associated DNA-binding hairpin travels from the top staircase position to the bottom, escorting one nucleotide of single-stranded DNA through the channel. These events permute sequentially around the ring from one subunit to the next.

Enemark,E.; Joshua-Tor, L.

2006-01-01T23:59:59.000Z

78

DNA hybridization kinetics: zippering, internal displacement and sequence dependence  

E-Print Network (OSTI)

While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on binding rates. Here we use a coarse-grained model to explore the hybridization kinetics of DNA oligomers, finding that strand association proceeds through a complex set of intermediate states. Successful binding events start with the formation of a few metastable base-pairing interactions, followed by zippering of the remaining bonds. However, despite reasonably strong interstrand interactions, initial contacts frequently fail to lead to zippering because the typical configurations in which they form differ from typical states of similar enthalpy in the double-stranded equilibrium ensemble. Therefore, if the association process is analyzed on the base-pair (secondary structure) level, it shows non-Markovian behavior. Initial contacts must be stabilized by two or three base pairs before full zippering is likely, resulting in negative effective activation enthalpies. Non-Arrhenius behavior is observed as the number of base pairs in the effective transition state increases with temperature. In addition, we find that alternative pathways involving misbonds can increase association rates. For repetitive sequences, misaligned duplexes frequently rearrange to form fully paired duplexes by two distinct processes which we label `pseudoknot' and `inchworm' internal displacement. We show how the above processes can explain why experimentally observed association rates of GC-rich oligomers are higher than rates of AT-rich equivalents. More generally, we argue that association rates can be modulated by sequence choice.

Thomas E. Ouldridge; Petr Šulc; Flavio Romano; Jonathan P. K. Doye; Ard A. Louis

2013-03-14T23:59:59.000Z

79

Electronic transport and localization in short and long DNA  

E-Print Network (OSTI)

The question of whether DNA conducts electric charges is intriguing to physicists and biologists alike. The suggestion that electron transfer/transport in DNA might be biologically important has triggered a series of experimental and theoretical investigations. Here, we review recent theoretical progress by concentrating on quantum-chemical, molecular dynamics-based approaches to short DNA strands and physics-motivated tight-binding transport studies of long or even complete DNA sequences. In both cases, we observe small, but significant differences between specific DNA sequences such as periodic repetitions and aperiodic sequences of AT bases, lambda-DNA, centromeric DNA, promoter sequences as well as random-ATGC DNA.

H. Wang; R. Marsh; J. P. Lewis; R. A. Roemer

2005-11-04T23:59:59.000Z

80

Generalized Poland-Scheraga model for DNA hybridization  

E-Print Network (OSTI)

The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the binding (or hybridization) of two complementary strands of DNA of equal length, with the restriction that only bases with the same index along the strands are allowed to bind. In this paper, we extend this model by relaxing these constraints: We propose a generalization of the PS model which allows for the binding of two strands of unequal lengths $N_{1}$ and $N_{2}$ with unrelated sequences. We study in particular (i) the effect of mismatches on the hybridization of complementary strands (ii) the hybridization of non complementary strands (as resulting from point mutations) of unequal lengths $N_{1}$ and $N_{2}$. The use of a Fixman-Freire scheme scales down the computational complexity of our algorithm from $O(N_{1}^{2}N_{2}^{2})$ to $O(N_{1}N_{2})$.The simulation of complementary strands of a few kbps yields results almost identical to the PS model. For short strands of equal or unequal lengths, the binding displays a strong sensitivity to mutations. This model may be relevant to the experimental protocol in DNA microarrays, and more generally to the molecular recognition of DNA fragments. It also provides a physical implementation of sequence alignments.

Thomas Garel; Henri Orland

2004-02-18T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

Monetizing stranded gas : economic valuation of GTL and LNG projects.  

E-Print Network (OSTI)

??Globally, there are significant quantities of natural gas reserves that lie economically or physically stranded from markets. Options to monetize such reserves include Gas to… (more)

Black, Brodie Gene, 1986-

2010-01-01T23:59:59.000Z

82

Cold atmospheric pressure plasma jets: Interaction with plasmid DNA and tailored electron heating using dual-frequency excitation  

SciTech Connect

Recent progress in plasma science and technology has enabled the development of a new generation of stable cold non-equilibrium plasmas operating at ambient atmospheric pressure. This opens horizons for new plasma technologies, in particular in the emerging field of plasma medicine. These non-equilibrium plasmas are very efficient sources for energy transport through reactive neutral particles (radicals and metastables), charged particles (ions and electrons), UV radiation, and electro-magnetic fields. The effect of a cold radio frequency-driven atmospheric pressure plasma jet on plasmid DNA has been investigated. The formation of double strand breaks correlates well with the atomic oxygen density. Taken with other measurements, this indicates that neutral components in the jet are effective in inducing double strand breaks. Plasma manipulation techniques for controlled energy delivery are highly desirable. Numerical simulations are employed for detailed investigations of the electron dynamics, which determines the generation of reactive species. New concepts based on nonlinear power dissipation promise superior strategies to control energy transport for tailored technological exploitations.

Niemi, K.; O'Neill, C.; Cox, L. J.; Waskoenig, J.; Hyland, W. B.; McMahon, S. J.; Reuter, S.; Currell, F. J.; Graham, W. G.; O'Connell, D.; Gans, T. [Centre for Plasma Physics, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland (United Kingdom)

2012-05-25T23:59:59.000Z

83

Etoposide Metabolites Enhance DNA Topoisomerase II Cleavage near Leukemia-Associated MLL Translocation Breakpoints †  

E-Print Network (OSTI)

ABSTRACT: Chromosomal breakage resulting from stabilization of DNA topoisomerase II covalent complexes by epipodophyllotoxins may play a role in the genesis of leukemia-associated MLL gene translocations. We investigated whether etoposide catechol and quinone metabolites can damage the MLL breakpoint cluster region in a DNA topoisomerase II-dependent manner like the parent drug and the nature of the damage. Cleavage of two DNA substrates containing the normal homologues of five MLL intron 6 translocation breakpoints was examined in vitro upon incubation with human DNA topoisomerase IIR, ATP, and either etoposide, etoposide catechol, or etoposide quinone. Many of the same cleavage sites were induced by etoposide and by its metabolites, but several unique sites were induced by the metabolites. There was a preference for G(-1) among the unique sites, which differs from the parent drug. Cleavage at most sites was greater and more heat-stable in the presence of the metabolites compared to etoposide. The MLL translocation breakpoints contained within the substrates were near strong and/or stable cleavage sites. The metabolites induced more cleavage than etoposide at the same sites within a 40 bp double-stranded oligonucleotide containing two of the translocation breakpoints, confirming the results

Brian D. Lovett; Dirk Strumberg; Ian A. Blair; Shaokun Pang; O Donald; A. Burden; Maureen D. Megonigal; Timothy R. Rebbeck; Neil Osheroff; Yves G. Pommier; Carolyn A. Felix

2000-01-01T23:59:59.000Z

84

Holliday Triangle Hunter (HolT Hunter): Efficient Software for Identifying Low Strain DNA Triangular Configurations  

SciTech Connect

Synthetic DNA nanostructures are typically held together primarily by Holliday junctions. One of the most basic types of structures possible to assemble with only DNA and Holliday junctions is the triangle. To date, however, only equilateral triangles have been assembled in this manner - primarily because it is difficult to figure out what configurations of Holliday triangles have low strain. Early attempts at identifying such configurations relied upon calculations that followed the strained helical paths of DNA. Those methods, however, were computationally expensive, and failed to find many of the possible solutions. I have developed a new approach to identifying Holliday triangles that is computationally faster, and finds well over 95% of the possible solutions. The new approach is based on splitting the problem into two parts. The first part involves figuring out all the different ways that three featureless rods of the appropriate length and diameter can weave over and under one another to form a triangle. The second part of the computation entails seeing whether double helical DNA backbones can fit into the shape dictated by the rods in such a manner that the strands can cross over from one domain to the other at the appropriate spots. Structures with low strain (that is, good fit between the rods and the helices) on all three edges are recorded as promising for assembly.

Sherman, W.B.

2012-04-16T23:59:59.000Z

85

Microfluidic DNA sample preparation method and device  

DOE Patents (OSTI)

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

Krulevitch, Peter A. (Pleasanton, CA); Miles, Robin R. (Danville, CA); Wang, Xiao-Bo (San Diego, CA); Mariella, Raymond P. (Danville, CA); Gascoyne, Peter R. C. (Bellaire, TX); Balch, Joseph W. (Livermore, CA)

2002-01-01T23:59:59.000Z

86

Slow closure of denaturation bubbles in DNA: twist matters  

E-Print Network (OSTI)

The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a non-zero torsional modulus in the duplex state, $\\kappa_\\phi=$200 to 300 kT. For DNAs of lengths N=40 to 100 base-pairs (bps) with a large initial bubble in their middle, long closure times of 0.1 to 100 microseconds are found. The bubble starts winding from both ends until it reaches a 10 bp metastable state. The final closure is limited by three competing mechanisms depending on $\\kappa_\\phi$ and N: arms diffusion until their alignment, bubble diffusion along the DNA until one end is reached, or local Kramers process (crossing over a torsional energy barrier). For clamped ends or long DNAs, the closure occurs via this latter temperature activated mechanism, yielding for the first time a good quantitative agreement with experiments.

Anil Kumar Dasanna; Nicolas Destainville; John Palmeri; Manoel Manghi

2013-02-07T23:59:59.000Z

87

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

Science Conference Proceedings (OSTI)

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

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

2009-01-01T23:59:59.000Z

88

Double Crystal Analyzer System  

Science Conference Proceedings (OSTI)

... 2002 Page 2. Bloomberg Center for Physics & Astronomy • Johns Hopkins University • Baltimore • Maryland MACS Double ...

2002-02-25T23:59:59.000Z

89

Characterizing marine mammal stranding events along the Texas coast  

E-Print Network (OSTI)

The Texas Marine Mammal Stranding Network (TMMSN) is a valuable data resource for the marine mammal community. Limitations of funding and personnel severely impact the ability of the Network to maintain impeccable databases. This research constructed an application to address database complications and focused on investigating the species identification, temporal and spatial trends for stranding events along the Texas coast. From 1980 to 2004, Tursiops truncatus accounted for approximately 80% of all stranding events. The remainder was 20 additional whale and dolphin species known to reside in the Gulf of Mexico. Tursiops truncatus strand along the entire coastline and are the only species stranding in the bays. All other species stranding are most dense along the southern coastline. The temporal scales of events revealed no linear patterns from 1980 to 2004. A unique cyclic fluctuation occurred from 1992 to 1998, including the highest yearly counts and one isolated mortality event in Port Aransas. Attempts to forecast stranding events beyond 2004 were inconclusive due to multiple factors influencing a stranding event. A bimodal seasonal trend was evident, with events peaking in the spring and fall months. Density distributions by decade isolated three frequent stranding areas: Sabine-Galveston-Brazoria counties, Galveston Shipping Channel, and Corpus Christi Shipping Channel. The final aspect analyzed spatial elaboration of events by creating six location values to describe the Texas coastline. Each event was assigned from the geographical location and the orientation of an event along the coastline. Analysis revealed the segregation of Tursiops truncatus in the bays and confirmed earlier results of density distributions. Examining the locations by time revealed a specific incident connected to a mortality event in 1992, accounting for 59% of the stranding events. Location categories were compared to the TMMSN stranding regions and the regions experienced different location frequencies. This study demonstrated how to construct a stronger database and the necessity for database accuracy. Study conclusions demonstrated the need to better isolate and research factors responsible for event distributions in time and space along the Texas coast to forecast the magnitude and location of stranding events to better aid the TMMSN response efforts.

Mullins, Ruth Louise

2008-08-01T23:59:59.000Z

90

DOE Hydrogen Analysis Repository: Stranded Biogas Decision Tool for Fuel  

NLE Websites -- All DOE Office Websites (Extended Search)

Stranded Biogas Decision Tool for Fuel Cell Co-Production Stranded Biogas Decision Tool for Fuel Cell Co-Production Project Summary Full Title: Stranded Biogas Decision Tool for Fuel Cell Co-Production Project ID: 257 Principal Investigator: Michael Ulsh Brief Description: This project will explore the feasibility and utility of using stranded biogas resources in fuel cell co-production networks as well as lay the basis for development of analysis and decision-making tools for potential biogas sources and energy end-users to evaluate the economic feasibility of deploying these systems. Performer Principal Investigator: Michael Ulsh Organization: National Renewable Energy Laboratory (NREL) Address: 1617 Cole Blvd. Golden, CO 80401 Telephone: 303-275-3842 Email: michael.ulsh@nrel.gov Website: http://www.nrel.gov

91

mitochondrial DNA  

Science Conference Proceedings (OSTI)

... are formed by a process similar to binary fission. ... H-strand codes for 28 gene products while the ... to transcribe 8 tRNAs and the ND6 protein product. ...

2006-10-25T23:59:59.000Z

92

When DNA Needs to Stand Up and Be Counted  

NLE Websites -- All DOE Office Websites (Extended Search)

When DNA Needs to Stand Up and Be Counted Print When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA chips are parallel, accurate, fast, and small. These advantages, however, can only be realized if the fragile biomolecules survive the attachment process intact. Furthermore, biomolecules must be properly oriented to perform their biological function. In other words, the DNA literally must stand up to be counted. Understanding both the attachment and orientation of DNA on gold surfaces was the goal of recent experiments performed at ALS Beamline 8.0.1 by an international collaboration of scientists.

93

When DNA Needs to Stand Up and Be Counted  

NLE Websites -- All DOE Office Websites (Extended Search)

When DNA Needs to Stand Up and Be Counted Print When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA chips are parallel, accurate, fast, and small. These advantages, however, can only be realized if the fragile biomolecules survive the attachment process intact. Furthermore, biomolecules must be properly oriented to perform their biological function. In other words, the DNA literally must stand up to be counted. Understanding both the attachment and orientation of DNA on gold surfaces was the goal of recent experiments performed at ALS Beamline 8.0.1 by an international collaboration of scientists.

94

c) UNBUNDLING.- Any stranded cost recovery charge authorized by the  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

c) UNBUNDLING.- Any stranded cost recovery charge authorized by the c) UNBUNDLING.- Any stranded cost recovery charge authorized by the Commission to be assessed by the Tennessee Valley Authority shall be unbundled from the otherwise applicable rates and charges to such customer and separately stated on the bill of such customer. The Tennessee Valley Authority shall not recover wholesale stranded costs from any customer through any other rate, charge, or mechanism. (d) REPORT.-Beginning in fiscal year 2001, as part of the annual management report submitted by the Tennessee Valley Authority to Congress, the Tennessee Valley Authority shall also specifically report: (1) the status of the Tennessee Valley Authority's long-range financial plans and the progress toward its goal of competitively priced electric power, and a general discussion of the Tennessee

95

DNA Record  

Science Conference Proceedings (OSTI)

... 4. Field 18.004: Source agency/SRC 5. Field 18.005: DNA Record Header Information (DRI) ... Field 18.005: DNA Record Header Information (DRI) ...

2010-08-03T23:59:59.000Z

96

Method for fabricating multi-strand superconducting cable  

DOE Patents (OSTI)

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

Borden, A.R.

1985-04-01T23:59:59.000Z

97

Apparatus and method for fabricating multi-strand superconducting cable  

DOE Patents (OSTI)

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

Borden, Albert R. (El Cerrito, CA)

1986-01-01T23:59:59.000Z

98

Industry participation workshop: Chromium electroplating of superconductor strand. Proceedings  

Science Conference Proceedings (OSTI)

The primary objective of the workshop was to inform US plating vendors about the opportunity to participate in the effort on Cr plating of large quantities of superconducting wires required for the ITER and the TPX projects and DOE`s interest in developing several reliable and high quality suppliers of Chromium plating services for the superconducting strand industry. The objective was also to inform plating vendors about the Cr plating technology developed in LLNL and invite interested plating vendors to get the technology. Finally the workshop was intended to inform the plating vendors about the plan to get verification of capability of two to four vendors for Cr plating of superconducting strands.

NONE

1994-12-13T23:59:59.000Z

99

Crystal Structure of the Chromodomain Helicase DNA-binding Protein 1 (Chd1) DNA-binding Domain in Complex with DNA  

Science Conference Proceedings (OSTI)

Chromatin remodelers are ATP-dependent machines that dynamically alter the chromatin packaging of eukaryotic genomes by assembling, sliding, and displacing nucleosomes. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. The structure of the Chd1 DNA-binding domain was recently shown to consist of a SANT and SLIDE domain, analogous to the DNA-binding domain of the ISWI family, yet the details of how Chd1 recognized DNA were not known. Here we present the crystal structure of the Saccharomyces cerevisiae Chd1 DNA-binding domain in complex with a DNA duplex. The bound DNA duplex is straight, consistent with the preference exhibited by the Chd1 DNA-binding domain for extranucleosomal DNA. Comparison of this structure with the recently solved ISW1a DNA-binding domain bound to DNA reveals that DNA lays across each protein at a distinct angle, yet contacts similar surfaces on the SANT and SLIDE domains. In contrast to the minor groove binding seen for Isw1 and predicted for Chd1, the SLIDE domain of the Chd1 DNA-binding domain contacts the DNA major groove. The majority of direct contacts with the phosphate backbone occur only on one DNA strand, suggesting that Chd1 may not strongly discriminate between major and minor grooves.

Sharma A.; Heroux A.; Jenkins K. R.; Bowman G. D.

2011-12-09T23:59:59.000Z

100

Storing data encoded DNA in living organisms  

DOE Patents (OSTI)

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

Wong; Pak C. (Richland, WA), Wong; Kwong K. (Sugar Land, TX), Foote; Harlan P. (Richland, WA)

2006-06-06T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


101

DNA Extraction  

NLE Websites -- All DOE Office Websites (Extended Search)

DNA Extraction DNA Extraction Being able to extract deoxyribonucleic acid (DNA) is important for a number of reasons. By studying DNA, scientists can identify genetic disorders or diseases, and they can also possibly find cures for them by manipulating or experimenting with this DNA. At the Laboratory, researchers have studied DNA to detect biothreat agents in environmental and forensic samples. Scientists also are studying how human DNA may be destroyed by certain types of electromagnetic waves at certain frequencies. Classroom Activity: This activity is about the extraction of DNA from strawberries. Strawberries are a great fruit to use for this lesson because each student can work on his or her own. Strawberries are recommended because they yield more DNA than any other fruit. Strawberries are octoploid, which means that they have eight copies of each

102

Double Degenerate Binary Systems  

Science Conference Proceedings (OSTI)

In this study, angular momentum loss via gravitational radiation in double degenerate binary (DDB)systems (NS + NS, NS + WD, WD + WD, and AM CVn) is studied. Energy loss by gravitational waves has been estimated for each type of systems.

Yakut, K. [University of Ege, Department of Astronomy and Space Sciences, 35100-Izmir (Turkey)

2011-09-21T23:59:59.000Z

103

Physical Interactions between Mcm10, DNA, and DNA Polymerase [alpha  

SciTech Connect

Mcm10 is an essential eukaryotic protein required for the initiation and elongation phases of chromosomal replication. Specifically, Mcm10 is required for the association of several replication proteins, including DNA polymerase {alpha} (pol {alpha}), with chromatin. We showed previously that the internal (ID) and C-terminal (CTD) domains of Mcm10 physically interact with both single-stranded (ss) DNA and the catalytic p180 subunit of pol {alpha}. However, the mechanism by which Mcm10 interacts with pol {alpha} on and off DNA is unclear. As a first step toward understanding the structural details for these critical intermolecular interactions, x-ray crystallography and NMR spectroscopy were used to map the binary interfaces between Mcm10-ID, ssDNA, and p180. The crystal structure of an Mcm10-ID {center_dot} ssDNA complex confirmed and extended our previous evidence that ssDNA binds within the oligonucleotide/oligosaccharide binding-fold cleft of Mcm10-ID. We show using NMR chemical shift perturbation and fluorescence spectroscopy that p180 also binds to the OB-fold and that ssDNA and p180 compete for binding to this motif. In addition, we map a minimal Mcm10 binding site on p180 to a small region within the p180 N-terminal domain (residues 286-310). These findings, together with data for DNA and p180 binding to an Mcm10 construct that contains both the ID and CTD, provide the first mechanistic insight into how Mcm10 might use a handoff mechanism to load and stabilize pol {alpha} within the replication fork.

Warren, Eric M.; Huang, Hao; Fanning, Ellen; Chazin, Walter J.; Eichman, Brandt F.; (Vanderbilt)

2009-10-21T23:59:59.000Z

104

On the relationship between strand spaces and multi-agent systems  

Science Conference Proceedings (OSTI)

Strand spaces are a popular framework for the analysis of security protocols. Strand spaces have some similarities to a formalism used successfully to model protocols for distributed systems, namely multi-agent systems. We explore the exact ... Keywords: Agents, expressiveness, multi-agent systems, security protocols, strand spaces

Joseph Y. Halpern; Riccardo Pucella

2003-02-01T23:59:59.000Z

105

Price caps for standard offer service: A hidden stranded cost  

Science Conference Proceedings (OSTI)

Some utility commissions or legislatures, concerned about mis-estimating the market line when calculating stranded costs, are choosing to require a price-capped standard offer service (SOS) to be offered by utilities in the competitive marketplace. This grants to customers the flexibility to switch from a fixed-price alternative with the utility to (or even to and from) a non-utility power supplier. Given the enormous uncertainty in future power market prices, this flexibility, which is being bestowed free-of-charge to customers, may prove to be of considerable value. Valuation of this SOS flexibility using call option techniques shows that this can be a non-trivial fraction of total stranded costs. The costs of price-capped SOS can be ameliorated through the structure of the price cap. This article describes the option-based techniques for valuing SOS and some approaches to limiting its cost to utilities.

Graves, F.; Liu, P. [Brattle Group, Cambridge, MA (United States)]|[Brattle Group, Washington, DC (United States)]|[Brattle Group, London (United Kingdom)

1998-12-01T23:59:59.000Z

106

DNA Biometrics  

Science Conference Proceedings (OSTI)

... presentation at Advances in Forensic DNA Analysis workshop held at the American Academy of Forensic Sciences meeting (Seattle, WA), February ...

2013-03-15T23:59:59.000Z

107

Forensic DNA:  

Science Conference Proceedings (OSTI)

... January 17, 2008 Press Release From Mayor Bloomberg's STATE OF THE CITY ADDRESS Efforts towards Portable/Mobile DNA Devices ...

2008-09-29T23:59:59.000Z

108

Hepatitis C virus NS3/4A protein interacts with ATM, impairs DNA repair and enhances sensitivity to ionizing radiation  

Science Conference Proceedings (OSTI)

Hepatitis C virus (HCV) infection is frequently associated with the development of hepatocellular carcinomas and non-Hodgkin's B-cell lymphomas. Nonstructural protein 3 (NS3) of HCV possesses serine protease, nucleoside triphosphatase, and helicase activities, while NS4A functions as a cofactor for the NS3 serine protease. Here, we show that HCV NS3/4A interacts with the ATM (ataxia-telangiectasia mutated), a cellular protein essential for cellular response to irradiation. The expression of NS3/4A caused cytoplasmic translocation of either endogenous or exogenous ATM and delayed dephosphorylation of the phosphorylated ATM and {gamma}-H2AX following ionizing irradiation. As a result, the irradiation-induced {gamma}-H2AX foci persisted longer in the NS3/4A-expressing cells. Furthermore, these cells showed increased comet tail moment in single-cell electrophoresis assay, indicating increased double-strand DNA breaks. The cells harboring an HCV replicon also exhibited cytoplasmic localization of ATM and increased sensitivity to irradiation. These results demonstrate that NS3/4A impairs the efficiency of DNA repair by interacting with ATM and renders the cells more sensitive to DNA damage. This effect may contribute to HCV oncogenesis.

Lai, Chao-Kuen; Jeng, King-Song [Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan (China); Machida, Keigo [Department of Molecular Microbiology and Immunology, University of Southern California, Keck School of Medicine, 2001 Zonal Avenue, Los Angeles, CA 90033 (United States); Cheng, Yi-Sheng [Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan (China); Lai, Michael M.C. [Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan (China); Department of Molecular Microbiology and Immunology, University of Southern California, Keck School of Medicine, 2001 Zonal Avenue, Los Angeles, CA 90033 (United States)], E-mail: michlai@gate.sinica.edu.tw

2008-01-20T23:59:59.000Z

109

DNA sequencing with pyrophosphatase  

DOE Patents (OSTI)

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

Tabor, S.; Richardson, C.C.

1996-03-12T23:59:59.000Z

110

Histone H2AX participates the DNA damage-induced ATM activation through interaction with NBS1  

SciTech Connect

Phosphorylated histone H2AX ({gamma}-H2AX) functions in the recruitment of DNA damage response proteins to DNA double-strand breaks (DSBs) and facilitates DSB repair. ATM also co-localizes with {gamma}-H2AX at DSB sites following its auto-phosphorylation. However, it is unclear whether {gamma}-H2AX has a role in activation of ATM-dependent cell cycle checkpoints. Here, we show that ATM as well as NBS1 is recruited to damaged-chromatin in a {gamma}-H2AX-dependent manner. Foci formation of phosphorylated ATM and ATM-dependent phosphorylation is repressed in H2AX-knockdown cells. Furthermore, anti-{gamma}-H2AX antibody co-immunoprecipitates an ATM-like protein kinase activity in vitro and recombinant H2AX increases in vitro kinase activity of ATM from un-irradiated cells. Moreover, H2AX-deficient cells exhibited a defect in ATM-dependent cell cycle checkpoints. Taken together, {gamma}-H2AX has important role for effective DSB-dependent activation of ATM-related damage responses via NBS1.

Kobayashi, Junya [Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto 606-8501 (Japan)], E-mail: jkobayashi@house.rbc.kyoto-u.ac.jp; Tauchi, Hiroshi [Department of Environmental Sciences, Ibaraki University, Ibaraki 310-8512 (Japan); Chen, Benjamin; Bruma, Sandeep [Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas, Southwestern Medical Center at Dallas, Dallas, TX 75390-9187 (United States); Tashiro, Satoshi [Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553 (Japan); Matsuura, Shinya [Department of Radiation Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553 (Japan); Tanimoto, Keiji [Department of Oral and Maxillofacial Radiology, Graduate School of Biomedical Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8553 (Japan); Chen, David J. [Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas, Southwestern Medical Center at Dallas, Dallas, TX 75390-9187 (United States); Komatsu, Kenshi [Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto 606-8501 (Japan)], E-mail: komatsu@house.rbc.kyoto-u.ac.jp

2009-03-20T23:59:59.000Z

111

A matterless double slit  

E-Print Network (OSTI)

Double-slits provide incoming photons with a choice. Those that survive the passage have chosen from two possible paths which interfere to distribute them in a wave-like manner. Such wave-particle duality continues to be challenged and investigated in a broad range of disciplines with electrons, neutrons, helium atoms, C60 fullerenes, Bose-Einstein condensates and biological molecules. All variants have hitherto involved material constituents. We present a matterless double-slit scenario in which photons generated from virtual electron-positron pair annihilation in head-on collisions of a probe laser field with two ultra-intense laser beams form a double-slit interference pattern. Such electromagnetic fields are predicted to induce material-like behaviour in the vacuum, supporting elastic scattering between photons. Our double-slit scenario presents on the one hand a realisable method to observe photon-photon scattering, and demonstrates on the other, the possibility of both controlling light with light and non-locally investigating features of the quantum vacuum's structure.

B. King; A. Di Piazza; C. H. Keitel

2013-01-29T23:59:59.000Z

112

DOUBLE MAJORS Imaging Science + ...  

E-Print Network (OSTI)

DOUBLE MAJORS Imaging Science + ... Applied Mathematics Biomedical Sciences Computer Science Undergraduate Research Internships and Cooperative Education (Co-op) (optional) Study Abroad WHY IMAGING SCIENCE Science: BS, MS, PhD Color Science: MS, PhD BS + MS/PhD Combos HUMAN VISION BIO- MEDICAL ASTRO- PHYSICS

Zanibbi, Richard

113

Double-digit growth  

SciTech Connect

The global need for additional generating capacity continues to grow at double digit rates in some cases. Opportunities for partnerships and joint ventures vary considerably by country and region. A closer look is taken at five countries where the playing fields are increasingly tipping to favor outside partners in power development projects -- India, Indonesia, Malaysia, Thailand, and Mexico.

Cartselos, T.; Meade, W.; Hernandez, L.

1993-09-01T23:59:59.000Z

114

Will stranded cost recovery distort Pennsylvania`s electricity market?  

Science Conference Proceedings (OSTI)

It is ironic indeed that the forecasting errors of Keystone State utilities that have led to today`s claims of stranded costs are now to be remediated in new legislation which, unaccountably, utterly fails to take account of the same problem: utility forecasting errors. On December 3, 1996, the Governor of Pennsylvania signed into law the Electricity Generation Customer Choice and Competition Act (66 Pa. C.S. 2801 et seq.). The Act set in motion an ambitious timetable for restructuring Pennsylvania`s electric utility industry to substantially deregulate its generation component. Customer choice of electricity supplier is to be phased in over a two year period beginning January 1, 1999. As indicated by the appearance of the word {open_quotes}competition{close_quotes} in the official title of the Act, the resulting institutional transformation is expected to foster free market competition in the generation and retail sale of electricity. However, there is already dispute among the Act`s commentators and critics, who are legion, as to whether its strategy for achieving this commendable objective will produce significant cost savings to consumers any time soon. One need look no further than the Act`s transition cost recovery provisions to find cause for skepticism. Section 2808 of the Act empowers the Pennsylvania Public Utility Commission to impose, for a period of up to nine years from January 1, 1997 (or longer at the Commission`s discretion), a {open_quotes}competitive transition charge{close_quotes} (CTC) upon {open_quotes}every customer accessing the transmission or distribution network.{close_quotes} The CTC is intended to afford Pennsylvania`s regulated electric utilities the opportunity to recover those of their {open_quotes}transition or stranded costs{close_quotes} (collectively {open_quotes}stranded costs{close_quotes}) approved by the Commission.

Caplan, R.L. [Caplan & Luber, Philadelphia, PA (United States)

1997-10-01T23:59:59.000Z

115

Modeling Solid Propellant Strand Burner Experiments with Catalytic Additives  

E-Print Network (OSTI)

This dissertation studies how nanoadditives influence burning rates through the development and use of a model to conduct parametric studies on nanoadditive interaction and to formulate theories. Decades of research have yet to determine the specific mechanisms for additive influence and the theories remain diverse and fragmented. It has been theorized that additives catalyze the combustion and thermal decomposition of AP, influence the condensed phases, and enhance the pyrolysis and regression of the binder. The main focus of the thesis was to approximate the enhanced boratory using spray-dried, spray-dried/heat-treated, and premixed TiO2 nanoadditives with ammonium perchlorate (AP) / hydroxyl-terminated polybutadiene (HTPB) composite propellants. The model is based on the classic Beckstead-Derr-Price (BDP) and Cohen-Strand models and contains a component that determines the pressure changes within the strand burner during a test. The model accurately predicts measured burning rates for baseline propellants without additives over a range of 500 - 3000 psi within 10%. The strand burner component of the model predicts the experimental pressure trace accurately. Further, the strand burner component determines an average burning rate over time and predicts a transient burning rate if provided a pressure trace. A parametric study with the model parameters determined that the nanoadditives appear to be increasing the AP condensed phase reaction rate. This conclusion was drawn because only changes in AP condensed-phase reaction rate would adequately and realistically replicate burning rate enhancements seen in laboratory experiments. Parametric studies with binder kinetics, binder regression rate, AP surface kinetics, and primary flame kinetics produced burning rate behavior that did not match that seen in experiments with the additives. The model was further used to develop a theory for how the nanoadditive affects the AP condensed phase, and a new parameter, (Omega)c, that influences the AP condensed phase reaction rate was created that replicates spray-dried, spray-dried/heat-treated, and premixed TiO2 nanoadditive experimental burning rates. Finally, the model was used to develop a first approximation of predicting anomalous burning rate trends such as a negative pressure dependence and extinguishment. A new term, Mc, that modifies the ratio of binder mass flux to oxidizer mass flux is used in tandem with (Omega)c to develop a negative burning rate trend that is close to the experimental result.

Frazier, Corey

2011-12-01T23:59:59.000Z

116

A Newly Discovered DNA Repair Mechanism | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (Extended Search)

scanning for these lesions. When they encounter one, they break the base pair bond and flip the deformed base out of the DNA double helix. The enzyme contains a specially shaped...

117

Workshop on effects of chromium coating on Nb{sub 3}Sn superconductor strand: Proceedings  

Science Conference Proceedings (OSTI)

This report discusses the following topics: Chromium coating on superconductor strand -- an overview; technology of chromium plating; comparison of wires plated by different platers; search for chromium in copper; strand manufactures` presentations; chromium plating at the Lawrence Livermore National Laboratory; a first look at a chromium plating process development project tailored for T.P.X. and I.T.E.R. strand; and influence of chromium diffusion and related phenomena on the reference ratios of bare and chromium plated Nb{sub 3}Sn strand.

Not Available

1994-04-12T23:59:59.000Z

118

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads  

E-Print Network (OSTI)

transcriptome assembly pipeline from stranded RNA-Seq readsRnnotator assembly pipeline. Figure 2. Read dereplicationan automated software pipeline that generates transcript

Martin, Jeffrey

2011-01-01T23:59:59.000Z

119

(RTD) of Fluid Flows in a Four Strand Delta-shaped Tundish  

Science Conference Proceedings (OSTI)

Abstract Scope, In this one third scale water model study of a four strand billet casting operation, residence time distribution (RTD) curves under steady state ...

120

Study on Fluid Flow in a Twelve-strand Tundish under the Operation ...  

Science Conference Proceedings (OSTI)

Analysis of Residence Time Distribution (RTD) of Fluid Flows in a Four Strand Delta-shaped Tundish Operating Under Isothermal and Non-isothermal ...

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

Low Dose Radiation Research Program: Quantification of Repair...  

NLE Websites -- All DOE Office Websites (Extended Search)

Quantification of Repair of Low-Dose-Induced DNA Double-Strand Breaks in Diploid Human Cells David Schild Lawrence Berkeley National Laboratory Berkeley, California Why this...

122

When DNA Needs to Stand Up and Be Counted  

NLE Websites -- All DOE Office Websites (Extended Search)

When DNA Needs to Stand Up and When DNA Needs to Stand Up and Be Counted When DNA Needs to Stand Up and Be Counted Print Wednesday, 31 May 2006 00:00 DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA chips are parallel, accurate, fast, and small. These advantages, however, can only be realized if the fragile biomolecules survive the attachment process intact. Furthermore, biomolecules must be properly oriented to perform their biological function. In other words, the DNA literally must stand up to be counted. Understanding both the attachment and orientation of DNA on gold surfaces was the goal of recent experiments performed at ALS Beamline 8.0.1 by an international collaboration of scientists.

123

Generalized Poland-Scheraga model for supercoiled DNA  

E-Print Network (OSTI)

The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the thermally induced binding of two complementary strands of DNA. In this paper, we show how to modify the PS model when a torque is applied to the extremities of DNA: We propose a simple model for the energy of twisted DNA and compute the entropy of a loop, subject to angular constraints (supercoiling). The denaturation curves are shifted towards lower or higher temperatures depending on the sign of the torque, and the UV absorption peaks are softened. The properties of supercoiled DNA can be deduced through the use of a numerical Legendre transform. In the homogeneous case, we find that for weak supercoiling, the phenomenological quadratic law relating the torsional energy to the number of unpaired bases is recovered.

Thomas Garel; Henri Orland; Edouard Yeramian

2004-07-28T23:59:59.000Z

124

Supplementary Materials: A Partition Function Algorithm for Interacting Nucleic Acid Strands  

E-Print Network (OSTI)

Hamidreza Chitsaz 1, Raheleh Salari1, S. Cenk Sahinalp 1, and Rolf Backofen 2, 1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada 2 Bioinformatics, Institute of Computer Science, Albert nucleic acid strands by R and S. Strand R is indexed from 1 to LR, and S is indexed from 1 to LS both in 5

Will, Sebastian

125

Double domino driver  

DOE Patents (OSTI)

The double domino driver is fully differential and is optimized for low switching noise and power. The noise behavior and power dissipation is improved by limiting the signal swing. The domino driver consists of a combination of mini drivers, each of which is switched on in two steps. In the first step a voltage equal to a fraction of the supply voltage propagates through the chain of mini drivers and turn them partially on. In the second step the voltage is increased to its maximum value and is made to propagate through the chain, turning the mini drivers completely on. The rise and fall time of the output signal can be increased by adding mini drivers. For a 5 volt supply voltage with 5 mini drivers the switching noise in decreased to levels less than 100 micro volts. The power dissipation with this driver is least as compared to ECL and other logic systems. The double domino driver is useful in communication and VLSI systems.

Vanstraelen, G.F.

1992-01-01T23:59:59.000Z

126

A New DNA Binding Protein Highly Conserved in Diverse Crenarchaeal Viruses  

DOE Green Energy (OSTI)

Sulfolobus turreted icosahedral virus (STIV) infects Sulfolobus species found in the hot springs of Yellowstone National Park. Its 37 open reading frames (ORFs) generally lack sequence similarity to other genes. One exception, however, is ORF B116. While its function is unknown, orthologs are found in three additional crenarchaeal viral families. Due to the central importance of this protein family to crenarchaeal viruses, we have undertaken structural and biochemical studies of B116. The structure reveals a previously unobserved fold consisting of a five-stranded beta-sheet flanked on one side by three alpha helices. Two subunits come together to form a homodimer with a 10-stranded mixed beta-sheet, where the topology of the central strands resembles an unclosed beta-barrel. Highly conserved loops rise above the surface of the saddle-shaped protein and suggest an interaction with the major groove of DNA. The predicted B116-DNA interaction is confirmed by electrophoretic mobility shift assays.

Larson, E.T.; Eilers, B.J.; Reiter, D.; Ortmann, A.C.; Young, M.J.; Lawrence, C.M.; /Montana State U. /Tubingen U.

2007-07-09T23:59:59.000Z

127

Hydrodynamic Simulation of a nano-flare heated multi-strand solar atmospheric loop  

E-Print Network (OSTI)

There is a growing body of evidence that the plasma loops seen with current instrumentation (SOHO, TRACE and Hinode) may consist of many sub-resolution elements or strands. Thus, the overall plasma evolution we observe in these features could be the cumulative result of numerous individual strands undergoing sporadic heating. This paper presents a short (10^9 cm ~ 10 Mm) ``global loop'' as 125 individual strands where each strand is modelled independently by a one-dimensional hydrodynamic simulation. The energy release mechanism across the strands consists of localised, discrete heating events (nano-flares). The strands are ``coupled'' together through the frequency distribution of the total energy input to the loop which follows a power law distribution with index alpha. The location and lifetime of each energy event occurring is random. Although a typical strand can go through a series of well-defined heating/cooling cycles, when the strands are combined, the overall quasi-static emission measure weighted thermal profile for the global loop reproduces a hot apex/cool base structure. Localised cool plasma blobs are seen to travel along individual strands which could cause the loop to `disappear' from coronal emission and appear in transition or chromospheric ones. As alpha increases (from 0 to 2.29 to 3.29), more weight is given to the smallest heating episodes. Consequently, the overall global loop apex temperature increases while the variation of the temperature around that value decreases. Any further increase in alpha saturates the loop apex temperature variations at the current simulation resolution. The effect of increasing the number of strands and the loop length as well as the implications of these results upon possible future observing campaigns for TRACE and Hinode are discussed.

Aveek Sarkar; Robert W Walsh

2008-04-18T23:59:59.000Z

128

DNA Activity  

NLE Websites -- All DOE Office Websites (Extended Search)

DNA Activity DNA Activity Name: Sara Location: N/A Country: N/A Date: N/A Question: Is DNA an anion or a cation? I thought since it was negatively charged it was an anion but mt teacher in class today said it was a cation because negatively charged molecules logically migrate to the positively charged plate of the cathode, ie molecules that migrate towards a cathode are cations. Where is the error in my logic or there error in my logic? Replies: DNA is negatively charged due to the phosphate ions present in the ribose-phosphate backbone. It moves towards the positive pole during electrophoresis. The definition kation/anion is confusing because: 1. a cation moves to the cathode 2. the cathode is negative, thus 3. a cation is positive DNA is an anion. The confusion is that a cathode is negative, but a cation is positively charged. For that reason these terms are not generally used in this context.

129

Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation  

SciTech Connect

DNMT1, the major maintenance DNA methyltransferase in animals, helps to regulate gene expression, genome imprinting, and X-chromosome inactivation. We report on the crystal structure of a productive covalent mouse DNMT1(731-1602)-DNA complex containing a central hemimethylated CpG site. The methyl group of methylcytosine is positioned within a shallow hydrophobic concave surface, whereas the cytosine on the target strand is looped out and covalently anchored within the catalytic pocket. The DNA is distorted at the hemimethylated CpG step, with side chains from catalytic and recognition loops inserting through both grooves to fill an intercalation-type cavity associated with a dual base flip-out on partner strands. Structural and biochemical data establish how a combination of active and autoinhibitory mechanisms ensures the high fidelity of DNMT1-mediated maintenance DNA methylation.

Song, Jikui; Teplova, Marianna; Ishibe-Murakami, Satoko; Patel, Dinshaw J. (MSKCC)

2012-03-26T23:59:59.000Z

130

Programmable Immobilized PCR in Nanoscale: Bridging Nanoelectrodes with Single dsDNA Molecules  

E-Print Network (OSTI)

We present a method for controlled connection of gold electrodes with single dsDNA molecules (locally on a chip) by utilizing PCR. Single-stranded thiol-modified oligonucleotides are directed and immobilized to nanoscale electrodes by means of dielectrophoretic trapping, and extended in a PCR procedure finally forming a complete dsDNA bridging the gap between the electrodes. The technique opens up opportunities for detection and sensing applications, and for molecular electronics.

Linko, Veikko; Shen, Boxuan; Niskanen, Einari; Hytönen, Vesa P; Toppari, J Jussi

2011-01-01T23:59:59.000Z

131

Radiation induced strand breakage analyzed by tunel technique  

E-Print Network (OSTI)

The objective of this research is to fully characterize the effectiveness and limits of using the terminal deoxynucleotidyl transferase mediated biotin-dUTP nick end labeling (TUNEL) technique for analysis of radiation induced strand breakage. If the TUNEL technique is found valuable, it could be applied to develop a biodosimetry protocol, primarily useful for individuals exposed in radiological accidents. Several techniques currently in use include fluorescent in-situ hybridization, the comet assay and the dicentric assay, yet each has drawbacks such as limited sensitivity or considerable preparation time. Recently, the TUNEL assay has been used in studies by Harvey and Ford (1997) to investigate chromatid breaks due to restriction enzymes. This research uses similar protocols to examine breaks due to radiation. Chinese hamster ovary (CHO) cells were cultured and exposed to X rays, receiving a dose ranging from 0 to 2 Gy. Slides were created using a standard metaphase chromosome preparation technique, followed by the TUNEL reaction to highlight chromosome breaks. The results were used to build a dose response curve. Although the expected increase in TUNEL positives per metaphase cell with increased x-ray dose was seen, large errors were associated with the results rendering TUNEL assay less than ideal for biodosimetry purposes. Additionally, TUNEL is not very effective at high doses because each TUNEL positive becomes indistinguishable from neighboring positives due to the high number of positives on each chromosome.

Reynolds, Marissa Dawn

2003-01-01T23:59:59.000Z

132

The human actin-related protein hArp5: Nucleo-cytoplasmic shuttling and involvement in DNA repair  

Science Conference Proceedings (OSTI)

Certain actin-related proteins (Arps) of budding yeast are localized in the nucleus, and have essential roles as stoichiometric components of histone acetyltransferase (HAT) and chromatin remodeling complexes. On the other hand, identification of vertebrate nuclear Arps and their functional analyses are just beginning. We show that human Arp5 (hArp5) proteins are localized in the nucleus, and that arp5{delta} yeast cells are partially complemented by hArp5. Thus, hArp5 is a novel member of the nuclear Arps of vertebrates, which possess evolutionarily conserved functions from yeast to humans. We show here that hArp5 shuttles between the nucleus and the cytoplasm. Furthermore, after the induction of DNA double strand breaks (DSB), cell growth and the accumulation of phosphorylated histone H2AX ({gamma}-H2AX) are impaired by hArp5 depletion. Association of hArp5 with the hIno80 chromatin remodeling enzyme and decrease of chromatin-bound hIno80 by hArp5-depletion indicate that hArp5 may have a role in the recruitment of the hINO80 complex to chromatin. Overexpression of hArp5 and hIno80 enhanced {gamma}-H2AX accumulation. These observations suggest that hArp5 is involved in the process of DSB repair through the regulation of the chromatin remodelling machinery.

Kitayama, Kumiko; Kamo, Mariko [Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Tsutsumidori-Amamiyamachi 1-1, Aoba-ku, Sendai 981-8555 (Japan); Oma, Yukako [Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Tsutsumidori-Amamiyamachi 1-1, Aoba-ku, Sendai 981-8555 (Japan); Department of Molecular and Cellular Genetics, UMR7156 CNRS-ULP, University of Strasbourg, 67084 Strasbourg cedex (France); Matsuda, Ryo [Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Tsutsumidori-Amamiyamachi 1-1, Aoba-ku, Sendai 981-8555 (Japan); Uchida, Takafumi [Enzymology, Graduate School of Agricultural, Tohoku University, Tsutsumidori-Amamiyamachi 1-1, Aoba-ku, Sendai 981-8555 (Japan); Ikura, Tsuyoshi [Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryoumachi 2 2-1, Aoba-ku, Sendai 980-8575 (Japan); Tashiro, Satoshi [Department of Cellular Biology, Hiroshima University, Hiroshima 734-8553 (Japan); Ohyama, Takashi [Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480 (Japan); Winsor, Barbara [Department of Molecular and Cellular Genetics, UMR7156 CNRS-ULP, University of Strasbourg, 67084 Strasbourg cedex (France); Harata, Masahiko [Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Tsutsumidori-Amamiyamachi 1-1, Aoba-ku, Sendai 981-8555 (Japan)], E-mail: mharata@biochem.tohoku.ac.jp

2009-01-15T23:59:59.000Z

133

Sequencing Intractable DNA to Close Microbial Genomes  

Science Conference Proceedings (OSTI)

Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

2012-01-01T23:59:59.000Z

134

Fast DNA Sequencing via Transverse Electronic Transport  

E-Print Network (OSTI)

A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of single-stranded DNA while it translocates through a nanopore. Our estimates, based on the statistics of these distributions, reveal that sequencing of an entire human genome could be done with very high accuracy in a matter of hours without parallelization, e.g., orders of magnitude faster than present techniques. The practical implementation of our approach would represent a substantial advancement in our ability to study, predict and cure diseases from the perspective of the genetic makeup of each individual.

Johan Lagerqvist; Michael Zwolak; Massimiliano Di Ventra

2006-01-18T23:59:59.000Z

135

ITER Model Coil Tests Overview: Nb3Sn Strand Properties in Cable-in-Conduit-Conductors  

SciTech Connect

During the ITER Model Coil Program two large coils and three Insert coils were built and tested. The test campaigns provided very valuable data on the Conductor in Conduit Cable (CICC) properties. The tests showed that the Nb3Sn strands in CICC behave differently than so-called witness strands, which underwent the same heat treatment. The paper describes Volt-temperature characteristics (VTC) and Volt-Ampere characteristics (VAC) measured in the tests, presents comparisons with the witness strands, and interprets the test results.

Martovetsky, N N

2003-04-14T23:59:59.000Z

136

Double acting bit holder  

DOE Patents (OSTI)

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

Morrell, Roger J. (Blommington, MN); Larson, David A. (Minneapolis, MN); Ruzzi, Peter L. (Eagan, MN)

1994-01-01T23:59:59.000Z

137

The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target  

SciTech Connect

DNA recognition by TAL effectors is mediated by tandem repeats, each 33 to 35 residues in length, that specify nucleotides via unique repeat-variable diresidues (RVDs). The crystal structure of PthXo1 bound to its DNA target was determined by high-throughput computational structure prediction and validated by heavy-atom derivatization. Each repeat forms a left-handed, two-helix bundle that presents an RVD-containing loop to the DNA. The repeats self-associate to form a right-handed superhelix wrapped around the DNA major groove. The first RVD residue forms a stabilizing contact with the protein backbone, while the second makes a base-specific contact to the DNA sense strand. Two degenerate amino-terminal repeats also interact with the DNA. Containing several RVDs and noncanonical associations, the structure illustrates the basis of TAL effector-DNA recognition.

Mak, Amanda Nga-Sze; Bradley, Philip; Cernadas, Raul A.; Bogdanove, Adam J.; Stoddard, Barry L. (FHCRC); (Iowa State)

2012-02-10T23:59:59.000Z

138

Effect of Twist Pitch in the Strands on the Saturation and Losses in the Nb3Sn Strands for the ITER TF CICC  

SciTech Connect

ITER TF coils will see a significant longitudinal magnetic field in the event of the plasma disruption. This abrupt change of magnetic fields results in the appearance of an additional electrical field in the strands. The mechanism of this electrical field is the induced currents that expel the flux from the strands. This effect was known since the late 1970's [1-3] and most of the details necessary for the analyses given in this report are presented in [4]. Let's assume for simplicity a zero transport current in the strand. When a longitudinal pulsed field is applied, the outer filaments will carry an induced current repelling the change of flux. The current density of this current is 'critical' in the simplification of Bean's critical state model, where superconducting transition is represented as j=j{sub c} at any non-zero electrical field and zero where the electrical field has not penetrated. In reality, since the current density is roughly logarithmic with the electrical field, E=E{sub c}*exp[(j-j{sub c})/jo], Bean's model is just a simplification, and current density is slightly nonuniform in the outer filament and more so for the interior strands. The inner portion of the filaments will carry a current of the opposite sign. Even in the Bean's model it is not uniform, but the assumption that it is uniform and less than critical simplifies mathematics significantly and does not deviate far from the real current density distribution. In certain circumstances, the average electrical field in the strands will be high enough to exceed the take-off electrical field averaged across the cross section. In this case, the multifilamentary strand will become unstable and will experience transition to the normal state. With zero transport current, it will eventually recover, of course. This phenomenon is analogous to the flux jump. If the strand carries a transport current, the situation becomes more complicated. If it goes unstable and the transport current is higher than the cryostability limit (by Stekly), or if there are enough losses to bring the temperature above the current sharing temperature taking into account limited heat capacity of the CICC, the strand will not recover, and the CICC will go normal. Conservatively, we will consider that if we find an instantaneous unstable situation, it is not acceptable. In presence of a transport current, the situation is sensitive to the direction of the strand twist, direction of the pulsed field and direction of the transport current. Recently, ITER decided to increase the twist pitch of the TF strands from 15 mm to 30 mm to improve the stability of the strands against the longitudinal field. In this report we will quantify the effects of this proposed change and perform a trade off study. The issue is that by increasing the twist pitch of the strands we not only increase the coupling losses in the transverse magnetic field, as expected in classical multifilamentary composite superconductors, but also increase the hysteresis losses in the strands with internal tin. In classical multifilamentary superconductors, twist pitch change should not cause an increase of the hysteresis losses in the transverse field. However the high Nb3Sn content internal tin strands develop transverse links, which couple the filaments into clusters. These links turn out to contribute a significant fraction to hysteresis losses [5]. If we project the results of [5] onto the ITER proposal to increase the twist pitch from 15 to 30 mm, we should expect the hysteresis losses to increase by a factor of two, which will likely disqualify strands with 30 mm twist pitch. This very strand twisted to 15 mm twist pitch would likely pass the ITER criteria. So, increasing the twist pitch has a very negative consequence and we need to make sure that it is absolutely necessary. Recently, A. Vostner (private communication) reported preliminary results on the losses in candidate TF strands. In agreement with what was reported in [5]; he found that TF strands with 15 mm twist pitch have hysteresis losses about half of wh

Martovetsky, N N

2007-12-06T23:59:59.000Z

139

SoundStrand : a tangible interface for composing music with limited degrees of freedom  

E-Print Network (OSTI)

This thesis presents SoundStrand, a novel tangible interface for composing music. A new paradigm is also presented - one that allows for music composition with limited degrees of freedom, and therefore is well suited for ...

Shahar, Eyal

2012-01-01T23:59:59.000Z

140

Increase Jc by Improving the Array of Nb3Sn strands for Fusion Application  

SciTech Connect

During Phase I, our efforts were focusing on improving the array of subelement in the tube type strands by hardening the Sn core and the subelement matrix to effectively increase the Jc of the strands. Below is a summary of the results. 1) We were unsuccessful in improving the array using a Cu-Sn matrix approach. 2) We slightly improved the array using Sn with 1.5at%Ti doped core, and a 217-subelement restacked strand was made and drawn down without any breakage. 3) We greatly improved the array using the Glidcop Al-15 to replace the pure Cu sheath in the subelement, and a 217-subelement restacked strand was made and drawn down. Both strands have very good drawability and the array showed good improvement. 4) We also improved the array using improved wire drawing techniques using Hyper Tech�¢����s new caterpillar wire drawing machines to enable straight wire drawing for the entire wire drawing process. 5) The 919-subelement restack strand shows its non-Cu Jc over 2100 A/mm2 at 12 T/4.2 K and AC loss of 508 mJ/cm3.

Dr. Xuan Peng

2012-12-17T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


141

Reduce Nb3Sn Strand Deformation when Fabricating High Jc Rutherford Cables  

SciTech Connect

During Phase I, our efforts were to reduce subelements deformation when fabricating Nb3Sn Rutherford cables. Our first focus is on 217-sublement tube type strand. We successfully made a few billets in ���¾�¢��� OD tube with different Cu spacing between subelements, and supplied the strands to Fermi Lab for cabling. Through the rolling test characterization, these types of strands did not have enough bonding between subelements to withstand the deformation. We saw copper cracking between subelements in the deformed strands. We scaled up the billet from ���¾�¢��� OD to 1.5�¢��� OD, and made two billets. This greatly improves the bonding. There is no copper cracking in the deformed strands when we scaled up the diameter of the billets. Fermi Lab successfully made cables using one of this improved strands. In their cables, no Cu cracking and no filament bridging occurred. We also successfully made a couple of billets with hex OD and round ID subelements for 61-subelement restack. Due to the lack of bonding, we could not judge its cabling property properly. But we know through this experiment, we could keep the Nb round, once we select the proper Cu spacing.

Dr. Xuan Peng

2012-12-17T23:59:59.000Z

142

Alloy by Double Mechanical Milling  

Science Conference Proceedings (OSTI)

The results show that the morphology of double mechanical milling powder is regular and the TiAl phase and Ti3Al phase were observed in the powders.

143

Double-super-connected digraphs  

Science Conference Proceedings (OSTI)

A strongly connected digraph D is said to be super-connected if every minimum vertex-cut is the out-neighbor or in-neighbor set of a vertex. A strongly connected digraph D is said to be double-super-connected if every minimum vertex-cut is both the out-neighbor ... Keywords: Cartesian product, Double-super-connected, Lexicographic product, Line digraphs, Super-connected

Juan Liu; Jixiang Meng; Zhao Zhang

2010-05-01T23:59:59.000Z

144

Physical approaches to DNA sequencing and detection  

E-Print Network (OSTI)

With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the cost-effective and rapid interrogation of individual genomes. This capability is likely to be provided by a physical approach to probing DNA at the single nucleotide level. This is in sharp contrast to current techniques and instruments which probe, through chemical elongation, electrophoresis, and optical detection, length differences and terminating bases of strands of DNA. In this Colloquium we review several physical approaches to DNA detection that have the potential to deliver fast and low-cost sequencing. Center-fold to these approaches is the concept of nanochannels or nanopores which allow for the spatial confinement of DNA molecules. In addition to their possible impact in medicine and biology, the methods offer ideal test beds to study open scientific issues and challenges in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale. We emphasize the physics behind these methods and ideas, critically describe their advantages and drawbacks, and discuss future research opportunities in this field.

Michael Zwolak; Massimiliano Di Ventra

2007-08-20T23:59:59.000Z

145

Intermittency as a universal characteristic of the complete chromosome DNA sequences of eukaryotes: From protozoa to human genomes  

E-Print Network (OSTI)

Large-scale dynamical properties of complete chromosome DNA sequences of eukaryotes are considered. By the proposed deterministic models with intermittency and symbolic dynamics we describe a wide spectrum of large-scale patterns inherent in these sequences, such as segmental duplications, tandem repeats, and other complex sequence structures. It is shown that the recently discovered gene number balance on the strands is not of random nature, and a complete chromosome DNA sequence exhibits the properties of deterministic chaos.

Sergei Rybalko; Sergei Larionov; Maria Poptsova; Alexander Loskutov

2011-04-18T23:59:59.000Z

146

Hexameric ring structure of the N-terminal domain of Mycobacterium tuberculosis DnaB helicase  

Science Conference Proceedings (OSTI)

Hexameric DnaB helicase unwinds the DNA double helix during replication of genetic material in bacteria. DnaB is an essential bacterial protein; therefore, it is an important potential target for antibacterial drug discovery. We report a crystal structure of the N-terminal region of DnaB from the pathogen Mycobacterium tuberculosis (MtDnaBn), determined at 2.0 {angstrom} resolution. This structure provides atomic resolution details of formation of the hexameric ring of DnaB by two distinct interfaces. An extensive hydrophobic interface stabilizes a dimer of MtDnaBn by forming a four-helix bundle. The other, less extensive, interface is formed between the dimers, connecting three of them into a hexameric ring. On the basis of crystal packing interactions between MtDnaBn rings, we suggest a model of a helicase-primase complex that explains previously observed effects of DnaB mutations on DNA priming.

Biswas, Tapan; Tsodikov, Oleg V. (Michigan)

2009-01-15T23:59:59.000Z

147

Speeding up a single-molecule DNA motor with a simple catalyst  

E-Print Network (OSTI)

We demonstrate a catalytic control method for speeding up the single-molecule DNA motor introduced by Li and Tan [Nano Lett. {\\bf 2}, 315 (2002)]. A key rate-limiting barrier in the reaction part of the cycle is the tendency for the second fuel strand $B$ to fold into the chair-like configuration of the original motor strand $M$. This seriously impedes the restoration reaction. We have designed a catalytic strand to inhibit the folding of $B$. Introduction of the catalyst speeds up the restoration reaction by roughly a factor of 2. The catalyst shows robust behavior for more than one cycle. The experimental data can be understood with a model with intermediate products. This technique provides dynamic control of the restoration rate of the motor without affecting the straightening rate.

Yufang Wang; Y. Zhang; N. P. Ong

2004-12-10T23:59:59.000Z

148

Comparison and Analysis of Twist Pitch Length Test Methods for ITER Nb3Sn and NbTi Strands  

E-Print Network (OSTI)

A twisted multifilamentary structure is needed for Nb3Sn and NbTi strands to be used in the International Thermonuclear Experimental Reactor (ITER) magnets. As important parameters for the superconducting strands design and production, the twist pitch length and direction of strands must meet the requirements according to ITER Procurement Arrangement (PA) and this must be verified. The technical requirements are 15mm+/-2mm for twist pitch length and right hand twist for direction. The strand twist pitch and the twist direction can be measured on straight sections of strand, which is recognized by the repetition of filament bundles or by the angle of the filaments. Several test methods and results are described and compared in this paper. The accuracy, uncertainty and feasibility of different methods are analyzed and recommended measurement methods are proposed for ITER strands verification.

Fang Liu; Feng Long; Chao Chen; Bo Liu; Yu Wu; Huajun Liu

2013-05-08T23:59:59.000Z

149

Specificity, flexibility and valence of DNA bonds guide emulsion architecture  

E-Print Network (OSTI)

The specificity and thermal reversibility of DNA interactions have enabled the self-assembly of crystal structures, self-replicating materials and colloidal molecules. Grafting DNA onto liquid interfaces of emulsions leads to exciting new architectural possibilities due to the mobility of the DNA ligands and the patches they form between bound droplets. Here we show that the size and number of these adhesion patches (valency) can be controlled. Valence 2 leads to flexible polymers of emulsion droplets, while valence above 4 leads to rigid droplet networks. A simple thermodynamic model quantitatively describes the increase in the patch size with droplet radii, DNA concentration and the stiffness of the tether to the sticky-end. The patches are formed between droplets with complementary DNA strands or alternatively with complementary colloidal nanoparticles to mediate DNA binding between droplets. This emulsion system opens the route to directed self-assembly of more complex structures through distinct DNA bonds with varying strengths and controlled valence and flexibility.

Lang Feng; Lea-Laetitia Pontani; Remi Dreyfus; Paul Chaikin; Jasna Brujic

2013-02-28T23:59:59.000Z

150

The DNA project - CECM  

E-Print Network (OSTI)

Software-package files: dna6.zip (for Maple 6), dna7.zip (for Maple 7). Contents: DNA routines, Release 1.04 ( last updated Nov/06/2001 ). Changes over ...

151

The hidden strand of mathematical proficiency : defining and assessing for productive disposition in elementary school teachers' mathematical content knowledge  

E-Print Network (OSTI)

and one's own efficacy? (NRC, 2001, p. 116). In this xviithe National Research Council [NRC] released its consensusand doer of mathematics? (NRC, 2001, p. 131). This strand is

Siegfried, John (Zig) Michael; Siegfried, John (Zig) Michael

2012-01-01T23:59:59.000Z

152

Decimal System and Double Digits  

NLE Websites -- All DOE Office Websites (Extended Search)

Decimal System and Double Digits Decimal System and Double Digits Name: Ken Status: other Grade: other Country: Canada Date: April 2011 Question: If the origin of the decimal system reflects counting on ten fingers and if zero came into use after the decimal system had been established why did we not create a single symbol for our tenth digit rather than use the double digit 10? If T were to represent the tenth number this would have created a counting system where the number series 1,2...9,T is followed by the same series having a 1 to the left then followed by the same series having a 2 to the left, etc. The T would be the last number in a series of ten single digits rather than be the first number in a series of double digits. The symbol zero would be used only between negative one and positive one because it represents the existence of nothing and, therefore, would have no other function.

153

Using DNA to Build Nanomaterials | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Using DNA to Build Nanomaterials Using DNA to Build Nanomaterials Stories of Discovery & Innovation Using DNA to Build Nanomaterials Enlarge Photo Photo courtesy of Brookhaven National Laboratory Oleg Gang, left, and Mircea Cotlet at Brookhaven's Center for Functional Nanomaterials. Enlarge Photo 05.09.11 Using DNA to Build Nanomaterials 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. One central idea in the field of nanoscience is that if you can build things from the bottom up, atom-by-atom or molecule-by-molecule, you can rationally design materials to achieve desired functions. Taking a cue from how nature does this-using genetic code to instruct the

154

Clinical DNA Online  

Science Conference Proceedings (OSTI)

Welcome to the NIST Clinical DNA Information Resource. ... Future materials have progress updates. General Information. ...

2013-04-26T23:59:59.000Z

155

Quantitative DNA fiber mapping  

DOE Patents (OSTI)

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.

Gray, Joe W. (San Francisco, CA); Weier, Heinz-Ulrich G. (Oakland, CA)

1998-01-01T23:59:59.000Z

156

Procedure to construct a multi-scale coarse-grained model of DNA-coated colloids from experimental data  

E-Print Network (OSTI)

We present a quantitative, multi-scale coarse-grained model of DNA coated colloids. The parameters of this model are transferable and are solely based on experimental data. As a test case, we focus on nano-sized colloids carrying single-stranded DNA strands of length comparable to the colloids' size. We show that in this regime, the common theoretical approach of assuming pairwise additivity of the colloidal pair interactions leads to quantitatively and sometimes even qualitatively wrong predictions of the phase behaviour of DNA-grafted colloids. Comparing to experimental data, we find that our coarse-grained model correctly predicts the equilibrium structure and melting temperature of the formed solids. Due to limited experimental information on the persistence length of single-stranded DNA, some quantitative discrepancies are found in the prediction of spatial quantities. With the availability of better experimental data, the present approach provides a path for the rational design of DNA-functionalised building blocks that can self-assemble in complex, three-dimensional structures.

Bianca M. Mladek; Julia Fornleitner; Francisco J. Martinez-Veracoechea; Alexandre Dawid; Daan Frenkel

2013-05-03T23:59:59.000Z

157

Hierarchy in a double braneworld  

Science Conference Proceedings (OSTI)

We show that the hierarchy between the Planck and the weak scales can follow from the tendency of gravitons and fermions to localize at different edges of a thick double wall embedded in an AdS{sub 5} spacetime without reflection symmetry. This double wall is a stable BPS thick-wall solution with two subwalls located at its edges; fermions are coupled to the scalar field through Yukawa interactions, but the lack of reflection symmetry forces them to be localized in one of the subwalls. We show that the graviton zero-mode wave function is suppressed in the fermion edge by an exponential function of the distance between the subwalls, and that the massive modes decouple so that Newtonian gravity is recuperated.

Guerrero, Rommel; Rodriguez, R. Omar [Unidad de Investigacion en Ciencias Matematicas, Universidad Centroccidental Lisandro Alvarado, 400 Barquisimeto (Venezuela); Melfo, Alejandra; Pantoja, Nelson [Centro de Fisica Fundamental, Universidad de Los Andes, Merida (Venezuela)

2006-10-15T23:59:59.000Z

158

Prostate brachytherapy postimplant dosimetry: Seed orientation and the impact of dosimetric anisotropy in stranded implants  

SciTech Connect

Purpose: In postimplant dosimetry for prostate brachytherapy, dose is commonly calculated using the TG-43 1D formalism, because seed orientations are difficult to determine from CT images, the current standard for the procedure. However, the orientation of stranded seeds soon after implantation is predictable, as these seeds tend to maintain their relative spacing, and orient themselves along the implant trajectory. The aim of this study was to develop a method for determining seed orientations from reconstructed strand trajectories, and to use this information to investigate the dosimetric impact of applying the TG-43 2D formalism to clinical postimplant analysis. Methods: Using in-house software, the preplan to postimplant seed correspondence was determined for a cohort of 30 patients during routine day-0 CT-based postimplant dosimetry. All patients were implanted with stranded-seed trains. Spline curves were fit to each set of seeds composing a strand, with the requirement that the distance along the spline between seeds be equal to the seed spacing within the strand. The orientations of the seeds were estimated by the tangents to the spline at each seed centroid. Dose distributions were then determined using the 1D and 2D TG-43 formalisms. These were compared using the TG-137 recommended dose metrics for the prostate, prostatic urethra, and rectum. Results: Seven hundred and sixty one strands were analyzed in total. Defining the z-axis to be cranial-positive and the x-axis to be left-lateral positive in the CT coordinate system, the average seed had an inclination of 21 deg. {+-} 10 deg. and an azimuth of -81 deg. {+-} 57 deg. These values correspond to the average strand rising anteriorly from apex to base, approximately parallel to the midsagittal plane. Clinically minor but statistically significant differences in dose metrics were noted. Compared to the 2D calculation, the 1D calculation underestimated prostate V100 by 1.1% and D90 by 2.3 Gy, while overestimating V150 and V200 by 1.6% and 1.3%, respectively. Urethral and rectal dose quantifiers tended to be underestimated by the 1D calculation. The most pronounced differences were in the urethral D30 and rectal D2cc, which rose by 3.8 and 1.9 Gy, respectively, using the 2D calculation. The total volume of the 100% isodose region as a percentage of the prostate volume was found to increase by 0.4%. Conclusions: Stranded seeds in the supine patient are not oriented in a uniformly random manner, nor are they aligned along the axis of the CT scanner. Instead, this study identified a consistent anterior pitch that is likely attributable to differences in patient pose between implant and CT imaging. The angle of the ultrasound probe with respect to the patient during implant may have also been a contributing factor. The dose metrics derived using the 1D formalism were found to be within 2%, on average, of those derived using the 2D formalism. For greater accuracy, 2D dosimetry can be pursued using the strand-fitting method described in this work. If a 1D representation is used, integrating over the empirically determined seed orientation density reported here may be more appropriate than assuming that seed inclinations are distributed uniformly.

Chng, Nicholas; Spadinger, Ingrid; Rasoda, Rosey; Morris, W. James; Salcudean, Septimiu [Department of Medical Physics, British Columbia Cancer Agency, Vancouver Cancer Centre, 600 West 10th, Vancouver, British Columbia V5Z 4E6 (Canada); Department of Electrical and Computer Engineering, University of British Columbia, 5500-2332 Main Mall, Vancouver, British Columbia V6T 1Z4 (Canada); Department of Radiation Oncology, British Columbia Cancer Agency, Vancouver Cancer Centre, 600 West 10th, Vancouver, British Columbia V5Z 4E6 (Canada); Department of Electrical and Computer Engineering, University of British Columbia, 5500-2332 Main Mall, Vancouver, British Columbia V6T 1Z4 (Canada)

2012-02-15T23:59:59.000Z

159

Reactivity studies of antitumor active dirhodium compounds with DNA oligonucleotides  

E-Print Network (OSTI)

The study of the mechanism of action of an antitumor active drug is essential for improving the efficacy and reducing the side effects of the drug as well as for developing better alternatives. In this vein, reactions of dirhodium compounds with DNA oligonucleotides were investigated by the techniques of mass spectrometry, HPLC, and NMR spectroscopic analytical methods. The relative reactivities of three dirhodium compounds, namely Rh2(O2CCH3)4, Rh2(O2CCF3)4, and [Rh2(O2CCH3)2(CH3CN)6](BF4)2, with DNA oligonucleotides were studied and compared to the clinically used anticancer drugs cisplatin and carboplatin using both MALDI and ESI mass spectrometric methods. The compound Rh2(O2CCF3)4 exhibits the highest reactivity among the dirhodium compounds, which is comparable to cisplatin, followed by [Rh2(O2CCH3)2(CH3CN)6](BF4)2, and finally Rh2(O2CCH3)4 which is the least reactive. Various dirhodium-oligonucleotide adducts were detected with both MALDI and ESI methods, which involve substitution of different numbers of the original ligands of the given dirhodium compound. ESI MS was found to be a sufficiently soft ionization method for detecting intact metal adducts, and CID MS-MS was useful for detecting weakly bound species such as axial adducts [M+Rh2(O2CCH3)4] and for comparing the relative bond strength between ligands in the metal adduct. A combination of anion exchange HPLC purification and enzymatic digestion studies of the adducts of Rh2(O2CCH3)4 with the 5'-CCTTCAACTCTC oligonucleotide revealed that Rh2(O2CCH3)4 binds to the center or to the ends of the oligonucleotide sequence by displacement of one or two acetate groups. Kinetic products of the type [M+Rh2(O2CCH3)3] obtained from the reaction of Rh2(O2CCH3)4 with 5'-CTCTCAACTTCC were separated by employing both reverse phase and anion exchange HPLC methods. The adduct that involves binding of the dirhodium unit to the exocyclic N4 atom of C5 and the N7 of A6 was found to be most stable whereas other adducts involving binding of C3 or C12 residues are clearly less stable. Reaction of cis-[Rh2(DAP)(O2CCH3)3(CH3OH)](O2CCH3) (DAP = 1,12- diazaperylene) with 5'-CTCTCAACTTCC produced a major adduct in which DAP group intercalates between 6A and 7A in the double stranded adduct with the rhodium atom that is not coordinated to the DAP group forming a covalent bond to the N7 atom of 6A which lends stability to the adduct.

Kang, Mijeong

2005-12-01T23:59:59.000Z

160

How scientists use DNA  

NLE Websites -- All DOE Office Websites (Extended Search)

How scientists use DNA Name: Peter and Edmund Age: NA Location: NA Country: NA Date: NA Question: Dear Scientists, We would like to know some ways that scientists use DNA. For...

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

DNA and Biometrics  

Science Conference Proceedings (OSTI)

... January 17, 2008 Press Release From Mayor Bloomberg's STATE OF THE CITY ADDRESS Efforts towards Portable/Mobile DNA Devices ...

2008-06-25T23:59:59.000Z

162

Estimating potential stranded commitments for U.S. investor-owned electric utilities  

SciTech Connect

New technologies, low natural gas prices, and federal and state utility regions are restructuring the electricity industry. Yesterday`s vertically integrated utility with a retail monopoly franchise may be a very different organization in a few years. Conferences, regulatory-commission hearings, and other industry fora are dominated by debates over the extent and form of utility deintegration, wholesale competition, and retail wheeling. A key obstacle to restructuring the electricity industry is stranded commitments. Past investments, power-purchase contracts, and public-policy-driven programs that made sense in an era of cost-of-service regulation may not be cost-effective in a competitive power market. Regulators, utilities, and other parties face tough decisions concerning the mitigation and allocation of these stranded commitments. The authors developed and applied a simple method to calculate the amount of stranded commitments facing US investor-owned electric utilities. The results obtained with this method depend strongly on a few key assumptions: (1) the fraction of utility sales that is at risk with respect to competition, (2) the market price of electric generation, and (3) the number of years during which the utility would lose money because of differences between its embedded cost of production and the market price.

Baxter, L.; Hirst, E.

1995-01-01T23:59:59.000Z

163

Increasing the Jc of Tube-Type Nb3Sn Strands  

Science Conference Proceedings (OSTI)

In this Phase I, we successfully made strands with better Cu/Sn ratio to reduce the coarse Nb3Sn grain region, thereby providing the potential of increasing the non-Cu Jc in the Phase II and scaling up to 2�¢��� billets with 331 subelements. In order to improve the strand�¢����s high field properties, we successfully doped low amount of Ti in the subelements and made a 217-subelement wire which has been drawn down to 0.7 mm without any breakage. This strand gave subelement size of 35 ���µm. We will scale up the Ti-doped billet to 271-subelement in 1.5�¢��� billet in this proposed Phase II. The hexagonal shaped subelements with round Nb-Sn have been developed for a 61-subelement restack. Thus the results indicated that for 217-subelement restack in a 2�¢��� billet we have the potential to draw down this type of construction without problems while maintaining a good array to react more Nb to get higher non-Cu Jc in the Phase II.

Dr. Xuan Peng

2012-12-17T23:59:59.000Z

164

Sound strand design : designing mechanical joints to facilitate user interaction within a physical representation of digital music  

E-Print Network (OSTI)

This project involved the mechanical design of a modular musical instrument, named the "Sound Strand." Intended to be attached end-to-end one onto another in order to produce a string of music, each module was constructed ...

Shen, Yan, S.B. Massachusetts Institute of Technology

2011-01-01T23:59:59.000Z

165

A Double Smoothing Technique for Constrained Convex ...  

E-Print Network (OSTI)

In this paper, we propose an efficient approach for solving a class of convex opti- ... accelerate our scheme, we introduce a novel double smoothing technique ...

166

Micromegas readouts for double beta decay searches  

E-Print Network (OSTI)

Double beta $\\beta\\beta$ decay experiments are one of the most active research topics in Neutrino Physics. The measurement of the neutrinoless mode $0\

Cebrián, S; Ferrer-Ribas, E; Galán, J; García, J A; Giomataris, I; Gómez, H; Herrera, D C; Iguaz, F J; Irastorza, I G; Luzón, G; Rodríguez, A; Seguí, L; Tomás, A

2010-01-01T23:59:59.000Z

167

Micromegas readouts for double beta decay searches  

E-Print Network (OSTI)

Double beta $\\beta\\beta$ decay experiments are one of the most active research topics in Neutrino Physics. The measurement of the neutrinoless mode $0\

S. Cebrián; T. Dafni; E. Ferrer-Ribas; J. Galán; J. A. García; I. Giomataris; H. Gómez; D. C. Herrera; F. J. Iguaz; I. G. Irastorza; G. Luzón; A. Rodríguez; L. Seguí; A. Tomás

2010-09-09T23:59:59.000Z

168

Double perovskite catalysts for oxidative coupling  

DOE Patents (OSTI)

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

Campbell, K.D.

1991-01-01T23:59:59.000Z

169

Double Patenting--One Patent per Invention  

Science Conference Proceedings (OSTI)

Double Patenting—One Patent per Invention. Arnold B. Silverman. Patent claims recite the scope of protection provided by a patent. The Patent Statute ...

170

Kernridge project does double duty  

SciTech Connect

The huge volume of steam that Kernridge Oil Co. generates to increase production of heavy crude oil from California's South Belridge field may do double duty. The company, a subsidiary of Shell Oil Co., is in the planning stages with a cogeneration project that would produce enough electricity to meet the electric needs of a community of more than 200,000 people. Meanwhile, Kernridge continues to exceed projections used in the acquisition assessment for the former Belridge Oil Co. properties which the Kernridge parent, Shell, bought in December 1979. The company formed Kernridge early in 1980 to operate the former Belridge properties. Since taking over, Kernridge has pursued development aggressively and has increased production to 65,000 bopd from the previous owner's 42,000 bopd.

Not Available

1981-10-01T23:59:59.000Z

171

Large scale DNA microsequencing device  

DOE Patents (OSTI)

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

Foote, R.S.

1997-08-26T23:59:59.000Z

172

Endogenous DNA Damage and Risk of Testicular Germ Cell Tumors  

SciTech Connect

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.

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

2008-01-18T23:59:59.000Z

173

Localization of CHl1-related helicase genes to human chromosome regions 12p11 and 12p13: Similarity between parts of these genes and conserved human telomeric-associated DNA  

Science Conference Proceedings (OSTI)

The helicase enzymes are essential components of a number of multi-protein complexes, including those that regulate transcription, splicing, translation, and DNA repair. These enzymes assist in the unwinding of double-stranded DNA and RNA as an essential part of their function. The yeast Chl1 gene encodes a putative helicase that appears to be essential for normal chromosome transmission. Human cDNAs related to this yeast gene, hCHLR1 and hCHLR2, were recently isolated and shown to encode products that localize to the nucleus. Two corresponding genes have now been partially characterized and localized to human chromosome regions 12p11 and 12p13, indicating that this gene is contained with a duplicated region localized to 12p. In addition, a comparison of the hCHLR gene sequences with available databases indicates that a large portion of these genes, including exons encoding two functional domains of the carboxyl-terminal region of these proteins, has been duplicated as part of a larger human teleomeric repeat sequence found on many human chromosomes. Our results suggest that duplication of a relatively large region of chromosome 12p containing this putative helicase gene has resulted in the creation of numerous pseudogenes as part of a subtelomeric repeat. The presence of these helicase pseudogenes, as well as pseudogenes for other genes such as the interleukin-9 receptor, within many subtelomeric regions support the possibility that the spread of this region is subject to exchange between different chromosomes and may have implications for elucidation of the mechanism of intra- and interchromosomal duplication events. 21 refs., 4 figs.

Amann, J.; Kidd, V.J.; Lahti, J.M.; Valentine, M. [St. Jude Children`s Research Hospital, Memphis, TN (United States)

1996-03-01T23:59:59.000Z

174

Improved double planar probe data analysis technique  

Science Conference Proceedings (OSTI)

Plasma electron number density and ion number density in a dc multidipole weakly collisional Ar plasma are measured with a single planar Langmuir probe and a double planar probe, respectively. A factor of two discrepancy between the two density measurements is resolved by applying Sheridan's empirical formula [T. E. Sheridan, Phys. Plasmas 7, 3084 (2000)] for sheath expansion to the double probe data.

Ghim, Young-chul; Hershkowitz, Noah [Department of Engineering Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States)

2009-03-15T23:59:59.000Z

175

Double bevel construction of a diamond anvil  

DOE Patents (OSTI)

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

Moss, W.C.

1988-10-11T23:59:59.000Z

176

Reliability Estimation for Double Containment Piping  

Science Conference Proceedings (OSTI)

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

L. Cadwallader; T. Pinna

2012-08-01T23:59:59.000Z

177

Patterning nanocrystals using DNA  

E-Print Network (OSTI)

nanocrystals. Angewandte Chemie-International Edition, [2]linked by DNA. Angewandte Chemie-International Edition, 39(with proteins. Angewandte Chemie-International Edition, 40(

Williams, Shara Carol

2003-01-01T23:59:59.000Z

178

Controlling DNA Methylation  

NLE Websites -- All DOE Office Websites (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 genes and repressing others. Gene regulation is an important event in the developmental biology and the biology of various diseases, but a more complex process. 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 genes and repressing others. Gene regulation is an important event in the developmental biology and the biology of various diseases, but a more complex process. In the bacteria there are distinct enzymes while one is capable of cleaving DNA, the other protects DNA by modification. The complementary function provided by the set of enzymes offers a defense mechanism against the phage infection and DNA invasion. The incoming DNA is cleaved sequence specifically by the class of enzymes called restriction endonuclease (REase). The host DNA is protected by the sequence specific action of matching set of enzymes called the DNA methyltransferase (MTase). The control of the relative activities of the REase and MTase is critical because a reduced ratio of MTase/REase activity would lead to cell death via autorestriction. However too high a ratio would fail to provide protection against invading viral DNA. In addition a separate group of proteins capable of controlling R-M proteins have been identified in various restriction-modification (R-M) systems which are called C proteins (Roberts et al., 2003).

179

DNA's Role with Proteins  

NLE Websites -- All DOE Office Websites (Extended Search)

DNA's Role with Proteins DNA's Role with Proteins Name: Hans Location: N/A Country: N/A Date: N/A Question: Is it sure that the most important information of living cells is stored in the DNA? DNA seems to be nothing more than an inventory of useful proteins and a tool to create those proteins. Could it be that more important operational know how of how these proteins interact to build a living organism is actually located in the rest of the cell? So that the rest of the cell is the most important inheritance, whereas DNA merely takes care of the genetic variation? Replies: DNA is the entire library of protein information for an organism. All seven types of protein. It is true that in developmental stages of an organism that the presence and absences of certain proteins and other chemicals generated by proteins will influence what the DNA in a "particular" cell will express. Hence, you can start out with one cell and end up with a complex organism. You may have heard some of this information with the cloning activities that have been going on lately. All the inheritance comes from the DNA, but what parts of the DNA expression may be dictated by the cells special characteristics developed upon specializing. In that way the liver cells will only do "liver" things and the kidney cells will only do "kidney" things, BUT they use the same DNA information to operate, just a different portion of the same DNA that pertains to their particular "job". If you can convince a cell that it does not have a special job anymore, then you can develop the entire organism from this cell with the right signals; this is what cloning techniques have done!

180

DNA | Open Energy Information  

Open Energy Info (EERE)

DNA DNA Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home NEPA Casual Use Determination of NEPA Adequacy Categorical Exclusion Environmental Assessment Environmental Impact Statements Print PDF NEPA-Related Analysis: Determination of NEPA Adequacy (DNA) General Document Collections (28) Documents Regulatory Roadmap NEPA-Related Analysis: Determination of NEPA Adequacy and Land Use Plan Conformance (DNA) placeholder. This query has been included to allow you to use the black arrows in the table header cells to sort the table data. Document # Serial Number Applicant Lead Agency District Office Field Office Development Phase(s) Techniques DOI-BLM-NM-L000-2012-0020-DNA Lightning Dock Geothermal Inc BLM BLM Las Cruces District Office BLM Geothermal/Exploration

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


181

Low energy electron stimulated desorption from DNA films dosed with oxygen  

SciTech Connect

Desorption of anions stimulated by 1-18 eV electron impact on self-assembled monolayer (SAM) films of single DNA strands is measured as a function of film temperature (50-250 K). The SAMs, composed of 10 nucleotides, are dosed with O{sub 2}. The OH{sup -} desorption yields increase markedly with exposure to O{sub 2} at 50 K and are further enhanced upon heating. In contrast, the desorption yields of O{sup -}, attributable to dissociative electron attachment to trapped O{sub 2} molecules decrease with heating. Irradiation of the DNA films prior to the deposition of O{sub 2} shows that this surprising increase in OH{sup -} desorption, at elevated temperatures, arises from the reaction of O{sub 2} with damaged DNA sites. These results thus appear to be a manifestation of the so-called 'oxygen fixation' effect, well known in radiobiology.

Mirsaleh-Kohan, Nasrin; Bass, Andrew D.; Cloutier, Pierre; Massey, Sylvain; Sanche, Leon [Groupe en sciences des radiations, Faculte de medecine et des sciences de la sante, Universite de Sherbrooke, Sherbrooke, Quebec J1H 5N4 (Canada)

2012-06-21T23:59:59.000Z

182

Repair of UV damaged DNA, genes and proteins of yeast and human  

Science Conference Proceedings (OSTI)

Our objectives are to determine the molecular mechanism of the incision step of excision repair of ultraviolet (UV) light damaged DNA in eukaryotic organisms, using the yeast Saccharomyces cerevisiae as a model system, as well as studying the human homologs of yeast excision repair and postreplication repair proteins. In addition to its single-stranded DNA-dependent A TPase and DNA helicase activities, we have found that RAD3 protein also possesses DNA-RNA helicase activity, and that like RAD3, the Schizosaccharomyces pombe RAD3 homolog, rhp3{sup +}, is an essential gene. We have overexpressed the human RAD3 homolog, ERCC2, in yeast to facilitate its purification. The RAD10 protein was purified to homogeneity and shown to bind DNA. ERCC3y, the yeast homolog of the human ERCC-3/XP-B gene, has been sequenced and shown to be essential for viability. The Drosophila and human homologs of RAD6, required for postreplication repair and UV induced mutagenesis, were shown to complement the rad6 {Delta} mutation of yeast. Since defective DNA repair and enhanced neoplasia characterize several human genetic diseases, and repair proteins are highly conserved between yeast and man, a thorough understanding of the molecular mechanisms of DNA repir in yeast should provide a better understanding of the causes of carcinogenesis.

Prakash, L.

1991-04-01T23:59:59.000Z

183

Baculovirus proteins IE-1, LEF-3, and P143 interact with DNA in vivo: a formaldehyde cross-linking study  

Science Conference Proceedings (OSTI)

IE-1, LEF-3, and P143 are three of six proteins encoded by Autographa californica nucleopolyhedrovirus (AcMNPV) essential for baculovirus DNA replication in transient replication assays. IE-1 is the major baculovirus immediate early transcription regulator. LEF-3 is a single-stranded DNA binding protein (SSB) and P143 is a DNA helicase protein. To investigate their interactions in vivo, we treated AcMNPV-infected Spodoptera frugiperda cells with formaldehyde and separated soluble proteins from chromatin by cell fractionation and cesium chloride equilibrium centrifugation. Up to 70% of the total LEF-3 appeared in the fraction of soluble, probably nucleoplasmic proteins, while almost all P143 and IE-1 were associated with viral chromatin in the nucleus. This suggests that LEF-3 is produced in quantities that are higher than needed for the coverage of single stranded regions that arise during viral DNA replication and is consistent with the hypothesis that LEF-3 has other functions such as the localization of P143 to the nucleus. Using a chromatin immunoprecipitation procedure, we present the first direct evidence of LEF-3, P143, and IE-1 proteins binding to closely linked sites on viral chromatin in vivo, suggesting that they may form replication complexes on viral DNA in infected cells.

Ito, Emma [Department of Microbiology and Immunology, Queen's University, Kingston, Ontario, K7L 3N6 (Canada); Sahri, Daniela [Department of Microbiology and Immunology, Queen's University, Kingston, Ontario, K7L 3N6 (Canada); Knippers, Rolf [Department of Biology, Universitaet Konstanz, D-78464 Constance (Germany); Carstens, Eric B. [Department of Microbiology and Immunology, Queen's University, Kingston, Ontario, K7L 3N6 (Canada)]. E-mail: carstens@post.queensu.ca

2004-11-24T23:59:59.000Z

184

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

SciTech Connect

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

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

2010-01-01T23:59:59.000Z

185

T-686: IBM Tivoli Integrated Portal Java Double Literal Denial...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

686: IBM Tivoli Integrated Portal Java Double Literal Denial of Service Vulnerability T-686: IBM Tivoli Integrated Portal Java Double Literal Denial of Service Vulnerability August...

186

Double layer capacitors : automotive applications and modeling  

E-Print Network (OSTI)

This thesis documents the work on the modeling of double layer capacitors (DLCs) and the validation of the modeling procedure. Several experiments were conducted to subject the device under test to a variety of ...

New, David Allen, 1976-

2004-01-01T23:59:59.000Z

187

D-branes and doubled geometry  

E-Print Network (OSTI)

We define the open string version of the nonlinear sigma model on doubled geometry introduced by Hull and Reid-Edwards, and derive its boundary conditions. These conditions include the restriction of D-branes to maximally isotropic submanifolds as well as a compatibility condition with the Lie algebra structure on the doubled space. We demonstrate a systematic method to derive and classify D-branes from the boundary conditions, in terms of embeddings both in the doubled geometry and in the physical target space. We apply it to the doubled three-torus with constant H-flux and find D0-, D1-, and D2-branes, which we verify transform consistently under T-dualities mapping the system to f-, Q- and R-flux backgrounds.

Cecilia Albertsson; Tetsuji Kimura; Ronald A. Reid-Edwards

2008-06-11T23:59:59.000Z

188

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system  

E-Print Network (OSTI)

The ability to artificially control transcription is essential both to the study of gene function and to the construction of synthetic gene networks with desired properties. Cas9 is an RNA-guided double-stranded DNA nuclease ...

Zhang, Feng

189

Identification of Rad52 complexes reveals a functional link between...  

NLE Websites -- All DOE Office Websites (Extended Search)

Genetics and Microbiology, MSC08-4660, University of New Mexico School of Medicine, Albuquerque, NM 87131 Rad52 plays important roles in repairing DNA double-strand breaks in...

190

Genes and structural proteins of the phage SYN5 of the marine cyanobacteria, Synechococcus  

E-Print Network (OSTI)

Bacteriophage have been proposed to be the most abundant organisms on the planet, at an estimated 10³¹ particles globally (Hendrix et al., 1999). The majority of bacteriophage isolates (96%) are double-stranded DNA tailed ...

Pope, Welkin Hazel

2005-01-01T23:59:59.000Z

191

The impact of age, exposure and genetics on homologous recombination at the engineered repeat sequence in mice  

E-Print Network (OSTI)

Mitotic homologous recombination is a critical pathway for the repair of DNA double-strand breaks and broken replication forks. Although homologous recombination is generally error-free, recombination between misaligned ...

Wiktor-Brown, Dominika M

2007-01-01T23:59:59.000Z

192

Development and characterization of an in vitro culture system as a physiological model for chronic Hepatitis B infection  

E-Print Network (OSTI)

Human Hepatitis B virus (HBV) is the prototype member of the family Hepadnaviridae that consists of enveloped, partially double stranded DNA viruses that specifically target hepatocytes for viral replication. Although a ...

Sams, Alexandria V. (Alexandria Victoria)

2007-01-01T23:59:59.000Z

193

The crystal structure of Neisseria gonorrhoeae PriB reveals mechanistic differences among bacterial DNA replication restart pathways  

Science Conference Proceedings (OSTI)

Reactivation of repaired DNA replication forks is essential for complete duplication of bacterial genomes. However, not all bacteria encode homologs of the well-studied Escherichia coli DNA replication restart primosome proteins, suggesting that there might be distinct mechanistic differences among DNA replication restart pathways in diverse bacteria. Since reactivation of repaired DNA replication forks requires coordinated DNA and protein binding by DNA replication restart primosome proteins, we determined the crystal structure of Neisseria gonorrhoeae PriB at 2.7 {angstrom} resolution and investigated its ability to physically interact with DNA and PriA helicase. Comparison of the crystal structures of PriB from N. gonorrhoeae and E. coli reveals a well-conserved homodimeric structure consisting of two oligosaccharide/oligonucleotide-binding (OB) folds. In spite of their overall structural similarity, there is significant species variation in the type and distribution of surface amino acid residues. This correlates with striking differences in the affinity with which each PriB homolog binds single-stranded DNA and PriA helicase. These results provide evidence that mechanisms of DNA replication restart are not identical across diverse species and that these pathways have likely become specialized to meet the needs of individual organisms.

Dong, Jinlan; George, Nicholas P.; Duckett, Katrina L.; DeBeer, Madeleine A.P.; Lopper, Matthew E. (UDRI); (UW-MED)

2010-05-25T23:59:59.000Z

194

Quantitive DNA Fiber Mapping  

SciTech Connect

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.

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

2008-01-28T23:59:59.000Z

195

Specific DNA cleavage mediated by [SalenMn(III)][sup +  

Science Conference Proceedings (OSTI)

The combination of [SalenMn(III)][sup +] and a terminal oxidant affords efficient and specific cleavage of right-handed double-helical DNA in regions rich in A:T base pairs. Metal complexes of the tetradentate chelating ligands Salen (Salen = N,N[prime]-ethylenebis(salicylideneaminato)) have been part of the inorganic chemistry literature for several decades. The cationic manganese(III) complex [SalenMn(III)][sup +] (1) is an efficient catalyst for the epoxidation of olefins with terminal oxidants such as iodosylbenzene. 1 also catalyzes oxidative C-H bond activation. The flat, crescent shape of 1, its aromatic and cationic nature, and its ability to catalyze hydrocarbon oxidation are features shared in whole or in part by metal complexes which bind to DNA and cleave it via oxidative processes. These similarities prompted the authors to evaluate the DNA-cleaving properties of 1, and they now report that 1 mediates specific cleavage of right-handed double-helical DNA in a reaction requiring a terminal oxidant. 20 refs., 3 figs., 1 tab.

Gravert, D.J.; Griffin, J.H. (Stanford Univ., CA (United States))

1993-02-12T23:59:59.000Z

196

Double Bottom Line Project Report:Assessing Social Impact In Double Bottom Line Ventures  

E-Print Network (OSTI)

of Key Characteristics Glossary Method Summaries Theories ofin double bottom line ventures methods catalog glossary ofterms glossary of terms This glossary defines the variables

Rosenzweig, William

2004-01-01T23:59:59.000Z

197

Durability of a continuous strand mat polymeric composite for automotive structural applications  

DOE Green Energy (OSTI)

A key unanswered question that must be addressed before polymeric composites will be widely used in automotive structural components is their durability. Major durability issues are the effects of cyclic loadings, creep, automotive environments, and low-energy impacts on dimensional stability, strength, and stiffness. The U.S. Department of Energy is sponsoring a project at Oak Ridge National Laboratory to address these issues and to develop, in cooperation with the Automotive Composites Consortium, experimentally based, durability driven, design guidelines. The initial reference material is an isocyanurate reinforced with a continuous strand, swirl glass mat. This paper describes the basic deformation and failure behavior of the reference material, and it presents test results illustrating the property degradations caused by loading, time, and environmental effects. The importance of characterizing and understanding damage and how it leads to failure is also discussed. The results presented are from the initial phases of an ongoing project. The ongoing effort and plans are briefly described.

Corum, J.M.; McCoy, H.E. Jr.; Ruggles, M.B.; Simpson, W.A. Jr.

1995-12-31T23:59:59.000Z

198

Roles of the Tetrahymena thermophila type I element binding factor, TIF1, in DNA replication and genome stability  

E-Print Network (OSTI)

The Tetrahymena thermophila rDNA minichromosome has been used as a model system for studying DNA replication. Previous studies have identified cis-acting replication determinants within the rDNA origin and promoter region including the type I element that is essential for replication initiation, fork progression and promoter activation. TIF1 is a non-ORC single strand-binding protein that binds the type I element in vivo. TIF1 binds opposing strands at the origin and promoter regions indicating that it may play a role in selectively marking these regions. In this dissertation, I use gene disruption to elucidate the role of TIF1 in replication. This work reveals that TIF1 represses rDNA origin firing, and is required for proper macronuclear S phase progression and division. Replication at the rDNA origin initiates precociously despite the observation that TIF1 mutants exhibit an elongated macronuclear S phase and a diminished rate of DNA replication. The amitotic macronucleus also displays delayed and abnormal division even though cells exit S phase with a wild-type macronuclear DNA content. Nuclear defects are also evident in the diploid micronucleus as TIF1 mutants contain fewer micronuclear chromosomes and are unable to pass genetic information to progeny. This defect is progressive as clonal mutant lines exhibit micronuclear instability during subsequent vegetative cell cycling. This work reveals that these macro- and micronuclear phenotypes may be the result of DNA damage as TIF1 mutants are hypersensitive to DNA damaging agents. This suggests that TIF1 mutants may have defects in the DNA damage response pathway. TIF1-deficient cells also incur DNA damage with no exogenous damaging agents. I propose that micro- and macronuclear defects witnessed in TIF1 mutant cells result from cells exiting S phase with compromised chromosomes due to the accumulation of DNA damage. Furthermore, TIF1 appears to play a role in the prevention, recognition or repair of DNA damage in addition to regulating rDNA replication and cell cycle progression and division. Additionally, TIF1 plays an essential role in the faithful propagation of both the macro- and micronuclear genomes.

Morrison, Tara Laine

2005-08-01T23:59:59.000Z

199

Development of an Automated Microfluidic System for DNA Collection, Amplification, and Detection of Pathogens  

Science Conference Proceedings (OSTI)

This project was focused on developing and testing automated routines for a microfluidic Pathogen Detection System. The basic pathogen detection routine has three primary components; cell concentration, DNA amplification, and detection. In cell concentration, magnetic beads are held in a flow cell by an electromagnet. Sample liquid is passed through the flow cell and bacterial cells attach to the beads. These beads are then released into a small volume of fluid and delivered to the peltier device for cell lysis and DNA amplification. The cells are lysed during initial heating in the peltier device, and the released DNA is amplified using polymerase chain reaction (PCR) or strand displacement amplification (SDA). Once amplified, the DNA is then delivered to a laser induced fluorescence detection unit in which the sample is detected. These three components create a flexible platform that can be used for pathogen detection in liquid and sediment samples. Future developments of the system will include on-line DNA detection during DNA amplification and improved capture and release methods for the magnetic beads during cell concentration.

Hagan, Bethany S.; Bruckner-Lea, Cynthia J.

2002-12-01T23:59:59.000Z

200

Involvement of DNA polymerase beta in repairing oxidative damages induced by antitumor drug adriamycin  

SciTech Connect

Adriamycin (ADM) is a widely used antineoplastic drug. However, the increasing cellular resistance has become a serious limitation to ADM clinical application. The most important mechanism related to ADM-induced cell death is oxidative DNA damage mediated by reactive oxygen species (ROS). Base excision repair (BER) is a major pathway in the repair of DNA single strand break (SSB) and oxidized base. In this study, we firstly applied the murine embryo fibroblasts wild-type (pol {beta} +/+) and homozygous pol {beta} null cell (pol {beta} -/-) as a model to investigate ADM DNA-damaging effects and the molecular basis underlying these effects. Here, cellular sensitivity to ADM was examined using colorimetric assay and colony forming assay. ADM-induced cellular ROS level and the alteration of superoxide dismutase (SOD) activity were measured by commercial kits. Further, DNA strand break, chromosomal damage and gene mutation were assessed by comet assay, micronucleus test and hprt gene mutation assay, respectively. The results showed that pol {beta} -/- cells were more sensitive to ADM compared with pol {beta} +/+ cells and more severe SSB and chromosomal damage as well as higher hprt gene mutation frequency were observed in pol {beta} -/- cells. ROS level in pol {beta} -/- cells increased along with decreased activity of SOD. These results demonstrated that pol {beta} deficiency could enable ROS accumulation with SOD activity decrease, further elevate oxidative DNA damage, and subsequently result in SSB, chromosome cleavage as well as gene mutation, which may be partly responsible for the cytotoxicity of ADM and the hypersensitivity of pol {beta} -/- cells to ADM. These findings suggested that pol {beta} is vital for repairing oxidative damage induced by ADM.

Liu Shukun; Wu Mei [Department of Environmental Health, Sichuan University, West China School of Public Health, Chengdu (China); Zhang Zunzhen, E-mail: zhangzunzhen@163.co [Department of Environmental Health, Sichuan University, West China School of Public Health, Chengdu (China)

2010-08-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
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201

The double-arm barn door tracker  

NLE Websites -- All DOE Office Websites (Extended Search)

How to build a double-arm barn door tracker How to build a double-arm barn door tracker | Jefferson Lab Home Page | Science Education Home Page | Construction Notes/Photos Page | Sources: Sky & Telescope April 1989 (p436 - p441) [very good] Sky & Telescope February 1988 (p213 - p214) Original concept by Dave Trott A single-arm barn door tracker, driven by a straight screw, accumulates tangent error as time passes. Most of this error can be eliminated by adding a second hinged arm to the standard arrangement. There are four types of double-arm trackers, each with a different geometry. A comparison of accumulated error (in arc seconds) and construction parameters is given below: Error Chart [Apparently Type 1 is very bad and not worth constructing?? The two Type 4 drives vary in beta. This results in shifting the region of maximum error

202

The double-beta decay: Theoretical challenges  

Science Conference Proceedings (OSTI)

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

Horoi, Mihai [Department of Physics, Central Michigan University, Mount Pleasant, Michigan, 48859 (United States)

2012-11-20T23:59:59.000Z

203

Scintillating bolometers for Double Beta Decay search  

E-Print Network (OSTI)

In the field of Double Beta Decay (DBD) searches, the use of high resolution detectors in which background can be actively discriminated is very appealing. Scintillating bolometers containing a Double Beta Decay emitter can largely fulfill this very interesting possibility. In this paper we present the latest results obtained with CdWO4 and CaMoO4 crystals. Moreover we report, for the first time, a very interesting feature of CaMoO4 bolometers: the possibility to discriminate beta-gamma events from those induced by alpha particles thanks to different thermal pulse shape.

Gironi, Luca

2009-01-01T23:59:59.000Z

204

Scintillating bolometers for Double Beta Decay search  

E-Print Network (OSTI)

In the field of Double Beta Decay (DBD) searches, the use of high resolution detectors in which background can be actively discriminated is very appealing. Scintillating bolometers containing a Double Beta Decay emitter can largely fulfill this very interesting possibility. In this paper we present the latest results obtained with CdWO4 and CaMoO4 crystals. Moreover we report, for the first time, a very interesting feature of CaMoO4 bolometers: the possibility to discriminate beta-gamma events from those induced by alpha particles thanks to different thermal pulse shape.

Luca Gironi

2009-11-05T23:59:59.000Z

205

A Study of Stranding of Juvenile Salmon by Ship Wakes Along the Lower Columbia River Using a Before-and-After Design: Before-Phase Results  

SciTech Connect

Ship wakes produced by deep-draft vessels transiting the lower Columbia River have been observed to cause stranding of juvenile salmon. Proposed deepening of the Columbia River navigation channel has raised concerns about the potential impact of the deepening project on juvenile salmon stranding. The Portland District of the U.S. Army Corps of Engineers requested that the Pacific Northwest National Laboratory design and conduct a study to assess stranding impacts that may be associated with channel deepening. The basic study design was a multivariate analysis of covariance of field observations and measurements under a statistical design for a before and after impact comparison. We have summarized field activities and statistical analyses for the ?before? component of the study here. Stranding occurred at all three sampling sites and during all three sampling seasons (Summer 2004, Winter 2005, and Spring 2005), for a total of 46 stranding events during 126 observed vessel passages. The highest occurrence of stranding occurred at Barlow Point, WA, where 53% of the observed events resulted in stranding. Other sites included Sauvie Island, OR (37%) and County Line Park, WA (15%). To develop an appropriate impact assessment model that accounted for relevant covariates, regression analyses were conducted to determine the relationships between stranding probability and other factors. Nineteen independent variables were considered as potential factors affecting the incidence of juvenile salmon stranding, including tidal stage, tidal height, river flow, current velocity, ship type, ship direction, ship condition (loaded/unloaded), ship speed, ship size, and a proxy variable for ship kinetic energy. In addition to the ambient and ship characteristics listed above, site, season, and fish density were also considered. Although no single factor appears as the primary factor for stranding, statistical analyses of the covariates resulted in the following equations: (1) Stranding Probability {approx} Location + Kinetic Energy Proxy + Tidal Height + Salmonid Density + Kinetic energy proxy ? Tidal Height + Tidal Height x Salmonid Density. (2) Stranding Probability {approx} Location + Total Wave Distance + Salmonid Density Index. (3) Log(Total Wave Height) {approx} Ship Block + Tidal Height + Location + Ship Speed. (4) Log(Total Wave Excursion Across the Beach) {approx} Location + Kinetic Energy Proxy + Tidal Height The above equations form the basis for a conceptual model of the factors leading to salmon stranding. The equations also form the basis for an approach for assessing impacts of dredging under the before/after study design.

Pearson, Walter H.; Skalski, J R.; Sobocinski, Kathryn L.; Miller, Martin C.; Johnson, Gary E.; Williams, Greg D.; Southard, John A.; Buchanan, Rebecca A.

2006-02-01T23:59:59.000Z

206

A Microscopic Double-Slit Experiment  

NLE Websites -- All DOE Office Websites (Extended Search)

A Microscopic Double-Slit A Microscopic Double-Slit Experiment A Microscopic Double-Slit Experiment Print Wednesday, 29 February 2012 00:00 Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in establishing the validity of wave-particle duality, a puzzling concept that has ultimately become central to the interpretation of complementarity in quantum mechnanics. In a new twist on this classic experiment, the double slit (with light waves) has been replaced by a diatomic molecule (with electron waves). At ALS Beamline 10.0.1, researchers have shown that diatomic molecules can serve as two-center emitters of electron waves and that traces of electron-wave interference can be directly observed in precise measurements of vibrationally resolved photoionization spectra.

207

The Dynamics of Double Monsoon Onsets  

Science Conference Proceedings (OSTI)

Double monsoon onset develops when the strong convection in the Bay of Bengal is accompanied by the monsoonlike circulation and appears in the Indian Ocean in early May, which is about 3 weeks earlier than the climatological date of the onset (1 ...

Maria K. Flatau; Piotr J. Flatau; Daniel Rudnick

2001-11-01T23:59:59.000Z

208

Double?Quantum Light Scattering by Molecules  

Science Conference Proceedings (OSTI)

Double?quantum light scattering by a system of molecules is discussed in this paper. Expressions have been obtained for the scattered light intensity considering both the coherent and incoherent contributions. In that coherent contributions are also considered in this treatment

R. Bersohn; Yoh?Han Pao; H. L. Frisch

1966-01-01T23:59:59.000Z

209

DNA polymerase having modified nucleotide binding site for DNA sequencing  

DOE Patents (OSTI)

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.

Tabor, S.; Richardson, C.

1997-03-25T23:59:59.000Z

210

Nucleotide cleaving agents and method  

DOE Patents (OSTI)

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.

Que, Jr., Lawrence (Roseville, MN); Hanson, Richard S. (Falcon Heights, MN); Schnaith, Leah M. T. (Redwing, MN)

2000-01-01T23:59:59.000Z

211

Generating DNA code word for DNA computing with realtime PCR  

Science Conference Proceedings (OSTI)

A number of DNA computing models to solve mathematical graph problem such as the Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP), and the Shortest Path Problem (SPP) have been proposed and demonstrated. Normally, the DNA sequences used ... Keywords: DNA computing, TaqMan probes, real-time PCR

Muhammad Faiz Mohamed Saaid; Zuwairie Ibrahim; Nor Haniza Sarmin

2008-03-01T23:59:59.000Z

212

Low energy electron induced damage to plasmid DNA pQE30  

SciTech Connect

Low energy electrons (LEEs) are produced in copious amounts by the primary radiation used in radiation therapy. The damage caused to the DNA by these secondary electrons in the energy range 5-22 eV has been studied to understand their possible role in radiation induced damage. Electrons are irradiated on dried films of plasmid DNA (pQE30) and analysed using agarose gel electrophoresis. Single strand breaks (SSBs) induced by LEE to supercoiled plasmid DNA show resonance structures at 7, 12, and 15 eV for low doses and 6, 10, and {approx}18 eV at saturation doses. The present measurements have an overall agreement with the literature that LEEs resonantly induce SSBs in DNA. Resonant peaks in the SSBs induced by LEEs at 7, 12, and 15 eV with the lowest employed dose in the current study are somewhat different from those reported earlier by two groups. The observed differences are perhaps related to the irradiation dose, conditions and the nature of DNA employed, which is further elaborated.

Kumar, S. V. K.; Pota, Tasneem; Peri, Dinakar; Dongre, Anushka D.; Rao, Basuthkar J. [Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005 (India)

2012-07-28T23:59:59.000Z

213

Natural DNA sequencing by synthesis  

E-Print Network (OSTI)

high throughput genome sequencing by natural DNA synthesis.E.E. , et al. , Genome sequencing by natural DNA synthesis.p. 1304-51. Human Genome Sequencing, C.I. , Finishing the

Roller, Eric E.

2011-01-01T23:59:59.000Z

214

DNA Profiling Standard Reference Materials  

Science Conference Proceedings (OSTI)

... agreement with the NIST Office of Law Enforcement Standards. ... Related Programs and Projects: SRM 2372 - Human DNA Quantitation Standard. ...

2013-03-15T23:59:59.000Z

215

Searching for DNA Lesions: Structural Evidence for Lower- and Higher-Affinity DNA Binding Conformations of Human Alkyladenine DNA Glycosylase  

E-Print Network (OSTI)

To efficiently repair DNA, human alkyladenine DNA glycosylase (AAG) must search the million-fold excess of unmodified DNA bases to find a handful of DNA lesions. Such a search can be facilitated by the ability of glycosylases, ...

Drennan, Catherine L.

216

An analysis of tissues for total PCB and planar PCB concentrations in marine mammals stranded along the Gulf of Mexico  

E-Print Network (OSTI)

New methods developed in this study based upon extracting blubber by the maceration of the tissue in methylene chloride and subjecting the resulting extract to gel-permeation chromatography, provided a quick, reliable alternative to classical extraction and separation methods used for analysis of organochlorine residues in marine mammal tissues. Due to the lipophilic nature of PCBS, tissues high in lipid content, such as blubber and melon, give the best estimation of total body burden for the contaminants analyzed. Toxic Equivalents (TEQS) and baseline concentrations of total and planar PCBs in Atlantic bottlenose dolphins (Tursiops truncatus) which stranded along the Gulf of Mexico were determined in this study. The data suggests that concentrations of total PCBs and planar PCBs are not correlated, hence samples must be analyzed for both compounds in comprehensive studies. In the present study, PCB levels were statistically similar in 3 marine mammal species investigated (T. truncates, Stenella sp. , and Peponocephala electra). There appeared to be little correlation between PCB concentrations and stranding condition, stranding location or stranding year; however, a strong correlation was observed between the levels of PCBS, and the maturity and gender of the specimens analyzed. Male bottlenose dolphins accumulate PCBs throughout their lives as they mature, while females dolphins, once sexually mature, offload much of their body burdens of PCBs to their calves both transplacentally and through lactation. This trend would suggest that PCBs can be used as a chemical tracer in evaluating some biological and reproductive parameters of this species. Finally, preferential distribution of PCBs in different body blubber areas of T. truncatus was not observed in this study. This observation is possibly due to the homogeneous distribution of lipids in the thin blubber layer of these animals.

Davis, Joseph W.

1993-01-01T23:59:59.000Z

217

Carports with Solar Panels do Double Duty for Navy | Department...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Carports with Solar Panels do Double Duty for Navy Carports with Solar Panels do Double Duty for Navy May 14, 2010 - 12:22pm Addthis Joshua DeLung What does this project do? In...

218

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

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

6: Double Tracks Test Site, Nye County, Nevada EA-1136: Double Tracks Test Site, Nye County, Nevada SUMMARY This EA evaluates the environmental impacts of the proposal for the U.S....

219

The Small Quantum Group as a Quantum Double  

E-Print Network (OSTI)

We prove that the quantum double of the quasi-Hopf algebra View the MathML source of We prove that the quantum double of the quasi-Hopf algebra Aq(g)

Etingof, Pavel I.

220

Double layer capacitance of carbon foam electrodes  

DOE Green Energy (OSTI)

We have evaluated a wide variety of microcellular carbon foams prepared by the controlled pyrolysis and carbonization of several polymers including: polyacrylonitrile (PAN), polymethacrylonitrile (PMAN), resorcinol/formaldehyde (RF), divinylbenzene/methacrylonitrile (DVB), phenolics (furfuryl/alcohol), and cellulose polymers such as Rayon. The porosity may be established by several processes including: Gelation (1-5), phase separation (1-3,5-8), emulsion (1,9,10), aerogel/xerogel formation (1,11,12,13), replication (14) and activation. In this report we present the complex impedance analysis and double layer charging characteristics of electrodes prepared from one of these materials for double layer capacitor applications, namely activated cellulose derived microcellular carbon foam.

Delnick, F.M.; Ingersoll, D. [Sandia National Labs., Albuquerque, NM (United States); Firsich, D. [EG& G Mound Lab., Miamisburg, OH (United States)

1993-11-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


221

(DDBS) System Doubles Pot Suction, Reduces Roof Emission  

Science Conference Proceedings (OSTI)

... Suction (DDBS) System Doubles Pot Suction, Reduces Roof Emission .... Phase Change Materials in Thermal Energy Storage for Concentrating Solar Power ...

222

Search for ? + / EC double beta decay of 120 Te  

Science Conference Proceedings (OSTI)

We present a search for ? + / EC double beta decay of 120 Te performed with the CUORICINO experiment

C. Tomei; The CUORICINO Collaboration

2011-01-01T23:59:59.000Z

223

System Specification for the Double Shell Tank (DST) System  

Science Conference Proceedings (OSTI)

This document establishes the functional, performance, design, development, interface and test requirements for the Double-Shell Tank System.

GRENARD, C.E.

2000-04-21T23:59:59.000Z

224

Tank characterization for Double-Shell Tank 241-AP-102  

SciTech Connect

This document provides the characterization information and interprets the data for Double-Shell Tank AP-102.

DeLorenzo, D.S.; DiCenso, A.T.; Amato, L.C.; Weyns-Rollosson, M.I.; Smith, D.J. [Los Alamos Technical Associates, Inc., Kennewick, WA (United States); Simpson, B.C.; Welsh, T.L. [Westinghouse Hanford Co., Richland, WA (United States)

1994-08-01T23:59:59.000Z

225

Double-clad nuclear fuel safety rod  

DOE Patents (OSTI)

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

McCarthy, William H. (Los Altos, CA); Atcheson, Donald B. (Cupertino, CA); Vaidyanathan, Swaminathan (San Jose, CA)

1984-01-01T23:59:59.000Z

226

A Microscopic Double-Slit Experiment  

NLE Websites -- All DOE Office Websites (Extended Search)

A Microscopic Double-Slit Experiment Print A Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in establishing the validity of wave-particle duality, a puzzling concept that has ultimately become central to the interpretation of complementarity in quantum mechnanics. In a new twist on this classic experiment, the double slit (with light waves) has been replaced by a diatomic molecule (with electron waves). At ALS Beamline 10.0.1, researchers have shown that diatomic molecules can serve as two-center emitters of electron waves and that traces of electron-wave interference can be directly observed in precise measurements of vibrationally resolved photoionization spectra.

227

A Microscopic Double-Slit Experiment  

NLE Websites -- All DOE Office Websites (Extended Search)

A Microscopic Double-Slit Experiment Print A Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in establishing the validity of wave-particle duality, a puzzling concept that has ultimately become central to the interpretation of complementarity in quantum mechnanics. In a new twist on this classic experiment, the double slit (with light waves) has been replaced by a diatomic molecule (with electron waves). At ALS Beamline 10.0.1, researchers have shown that diatomic molecules can serve as two-center emitters of electron waves and that traces of electron-wave interference can be directly observed in precise measurements of vibrationally resolved photoionization spectra.

228

A background free double beta decay experiment  

E-Print Network (OSTI)

We present a new detection scheme for rejecting backgrounds in neutrino less double beta decay experiments. It relies on the detection of Cherenkov light emitted by electrons in the MeV region. The momentum threshold is tuned to reach a good discrimination between background and good events. We consider many detector concepts and a range of target materials. The most promising is a high-pressure 136Xe emitter for which the required energy threshold is easily adjusted. Combination of this concept and a high pressure Time Projection Chamber could provide an optimal solution. A simple and low cost effective solution is to use the Spherical Proportional Counter that provides two delayed signals from ionization and Cherenkov light. In solid-state double beta decay emitters, because of their higher density, the considered process is out of energy range. An alternative solution could be the development of double decay emitters with lower density by using for instance the aerogel technique. It is surprising that a technology used for particle identification in high-energy physics becomes a powerful tool for rejecting backgrounds in such low-energy experiments.

Ioannis Giomataris

2010-12-20T23:59:59.000Z

229

DNA waves and water  

E-Print Network (OSTI)

Some bacterial and viral DNA sequences have been found to induce low frequency electromagnetic waves in high aqueous dilutions. This phenomenon appears to be triggered by the ambient electromagnetic background of very low frequency. We discuss this phenomenon in the framework of quantum field theory. A scheme able to account for the observations is proposed. The reported phenomenon could allow to develop highly sensitive detection systems for chronic bacterial and viral infections.

L. Montagnier; J. Aissa; E. Del Giudice; C. Lavallee; A. Tedeschi; G. Vitiello

2010-12-23T23:59:59.000Z

230

Radiation and viral DNA  

NLE Websites -- All DOE Office Websites (Extended Search)

Radiation and viral DNA Radiation and viral DNA Name: Loretta L Lamb Age: N/A Location: N/A Country: N/A Date: N/A Question: Can viral DNA be changed through exposure to radiation? If so, what type of radiation will do this? Can these irradiated viruses cause changes in the genome of any human cells they may infect? Can these (or any) viruses actually cause cancer, or do they merely act as triggering devices for cancer? Replies: In theory, any nucleic acid (viral or otherwise) can be changed by exposure to many kinds of radiation. Depending on the type of virus, these may then change the human cells that they infect. Although there are many different things that are being implicated in causing cancers, it looks like a fairly common model involves the sequential "knockout" of several human genes. Viruses may be one cause of such gene changes, radiation and other environmental causes may also contribute. Some of these changes may be inherited through families, so it becomes more likely that the environmental factors may happen to "hit" the right places in cells to cause cancers in these families. If you ask something more specific, perhaps I can focus my response a bit more

231

Automating DNA processing  

E-Print Network (OSTI)

Technology is currently available to identify the genetic codes responsible for physical traits and genetic diseases in both plants and animals. Regardless of whether the final goal is medical diagnosis or breeder selection, extensive time and resources must be spent in laboratory research to determine the genetic structure of the relevant organisms. DNA processing is riddled with time intensive laboratory techniques that must be improved or replaced if genotyping large numbers of samples is to be accomplished. This thesis identifies and explains modules in DNA processing and how they can be improved by automation. modules associated with genome mapping are the focus of most of the discussion. A functional biochemistry background is provided so that researchers in automation can be efficiently assimilated to future biochen-fistry/automation projects. The needs of biochemistry researchers at Texas A&M University are specifically addressed. Herein, DNA processing has been defined as a series of discrete sub-processes or process modules in order to aid scheduling of future automation projects. Target process modules (sub-processes with a high probability of automation success) have been identified. In addition, possible automation solutions have been proposed for each target module along with a characterization of fundamental design parameters. Concluding this text is a discussion of procedures in genome mapping that have not been sufficiently automated. The initial focus of this thesis is on short term solutions. However, attention is given to more conceptual solutions accompanied by the biochemistry background necessary to begin developing them. Though systems are proposed to improve the efficiency of many processes, no implementation has been attempted. Design specifications are based on observation of current laboratory techniques and the variance that is typically allowed in relevant process parameters in TAMU laboratories.

Wienen, Michael Jan

1994-01-01T23:59:59.000Z

232

Properties of DnaB helicase in [lambda] DNA replication  

Science Conference Proceedings (OSTI)

A tailed nicked-circle DNA substrate was used to measure the rapid replication fork (RF) movement catalyzed by E. Coli DnaB helicase and DNA polymerase III holoenzyme (pol III HE) (DnaB-RFs) (30 DnaB hexamers/substrate). The DnaB RFs can efficiently utilize the DNA substrate (60% in 5 min at 30C), and the forks move at a rapid rate (550-780 bp/sec at 30C). The DnaB-RFs have an average maximal processivity of 40,000 nt, and addition of either SSB or primase increase the processivity (150,000 nt + SSB, 70,000-140,000 nt + primase). However, SSB and primase do not affect the rate of fork movement or the amount of substrate utilized in the assay. The [lambda] SS proteins are effective at transferring DnaB onto the DNA substrate (8 DnaB hexamers/substrate). The [lambda] SS proteins do not change the rate of RF movement or the amount of substrate utilized. However, the amount of synthesis measured in the assay is [approximately]2-fold higher in the presence of the [lambda] SS proteins. Therefore, the [lambda] SS proteins increase the processivity of DnaB at the RF (100,000 nt). The [lambda] SS proteins do not appear to play a role in elongation because the processivity of the RF in the presence of SSB and primase is equivalent to the processivity of the [lambda] SS-RFs. [lambda] P protein blocks DnaB helicase activity if added to the RF assay prior to initiation or during elongation. DnaB helicase is more resistant to P inhibition, if the helicase is allowed to bind to the substrate prior to addition of [lambda] P or if primase and rNTPs are included in the assay. These results suggest that the conformation of the RF complex (DNA or nucleoprotein structure) blocks the attack of P on DnaB helicase. The heat shock proteins may play an auxiliary role in mediating the effects of [lambda] P if the concentration of P protein in the cells are high.

Stephens, K.M.

1991-01-01T23:59:59.000Z

233

Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex  

SciTech Connect

Here we report on a 3.0 {angstrom} crystal structure of a ternary complex of wild-type Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-nucleotide guide DNA and a 20-nucleotide target RNA containing cleavage-preventing mismatches at the 10-11 step. The seed segment (positions 2 to 8) adopts an A-helical-like Watson-Crick paired duplex, with both ends of the guide strand anchored in the complex. An arginine, inserted between guide-strand bases 10 and 11 in the binary complex, locking it in an inactive conformation, is released on ternary complex formation. The nucleic-acid-binding channel between the PAZ- and PIWI-containing lobes of argonaute widens on formation of a more open ternary complex. The relationship of structure to function was established by determining cleavage activity of ternary complexes containing position-dependent base mismatch, bulge and 2'-O-methyl modifications. Consistent with the geometry of the ternary complex, bulges residing in the seed segments of the target, but not the guide strand, were better accommodated and their complexes were catalytically active.

Wang, Yanli; Juranek, Stefan; Li, Haitao; Sheng, Gang; Tuschl, Thomas; Patel, Dinshaw J. (MSKCC); (HHMI)

2009-01-08T23:59:59.000Z

234

Optical double-slit particle measuring system  

DOE Patents (OSTI)

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

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

1982-03-25T23:59:59.000Z

235

Massive Type II in Double Field Theory  

E-Print Network (OSTI)

We provide an extension of the recently constructed double field theory formulation of the low-energy limits of type II strings, in which the RR fields can depend simultaneously on the 10-dimensional space-time coordinates and linearly on the dual winding coordinates. For the special case that only the RR one-form of type IIA carries such a dependence, we obtain the massive deformation of type IIA supergravity due to Romans. For T-dual configurations we obtain a `massive' but non-covariant formulation of type IIB, in which the 10-dimensional diffeomorphism symmetry is deformed by the mass parameter.

Olaf Hohm; Seung Ki Kwak

2011-08-24T23:59:59.000Z

236

Double Photoionization of excited Lithium and Beryllium  

SciTech Connect

We present total, energy-sharing and triple differential cross sections for one-photon, double ionization of lithium and beryllium starting from aligned, excited P states. We employ a recently developed hybrid atomic orbital/ numerical grid method based on the finite-element discrete-variable representation and exterior complex scaling. Comparisons with calculated results for the ground-state atoms, as well as analogous results for ground-state and excited helium, serve to highlight important selection rules and show some interesting effects that relate to differences between inter- and intra-shell electron correlation.

Yip, Frank L.; McCurdy, C. William; Rescigno, Thomas N.

2010-05-20T23:59:59.000Z

237

Double Photoionization of Aligned Molecular Hydrogen  

SciTech Connect

We present converged, completely ab initio calculations ofthe triple differential cross sections for double photoionization ofaligned H2 molecules for a photon energy of 75.0 eV. The method ofexterior complex scaling, implemented with both the discrete variablerepresentation and B-splines, is used to solve the Schroedinger equationfor a correlated continuum wave function corresponding to a single photonhaving been absorbed by a correlated initial state. Results for a fixedinternuclear distance are compared with recent experiments and show thatintegration over experimental angular and energy resolutions is necessaryto produce good qualitative agreement, but does not eliminate somediscrepancies. Limitations of current experimental resolution are shownto sometimes obscure interesting details of the crosssection.

Vanroose, Wim; Horner, Daniel A.; Martin, Fernando; Rescigno,Thomas N.; McCurdy, C. William

2006-07-21T23:59:59.000Z

238

Double acting stirling engine phase control  

DOE Patents (OSTI)

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

Berchowitz, David M. (Scotia, NY)

1983-01-01T23:59:59.000Z

239

Neutrinoless double beta decay and neutrino masses  

SciTech Connect

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

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

2012-07-27T23:59:59.000Z

240

Characterization of a baculovirus lacking the DBP (DNA-binding protein) gene  

Science Conference Proceedings (OSTI)

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) encodes two proteins that possess properties typical of single-stranded DNA-binding proteins (SSBs), late expression factor-3 (LEF-3), and a protein referred to as DNA-binding protein (DBP). Whereas LEF-3 is a multi-functional protein essential for viral DNA replication, transporting helicase into the nucleus, and forms a stable complex with the baculovirus alkaline nuclease, the role for DBP in baculovirus replication remains unclear. Therefore, to better understand the functional role of DBP in viral replication, a DBP knockout virus was generated from an AcMNPV bacmid and analyzed. The results of a growth curve analysis indicated that the dbp knockout construct was unable to produce budded virus indicating that dbp is essential. The lack of DBP does not cause a general shutdown of the expression of viral genes, as was revealed by accumulation of early (LEF-3), late (VP39), and very late (P10) proteins in cells transfected with the dbp knockout construct. To investigate the role of DBP in DNA replication, a real-time PCR-based assay was employed and showed that, although viral DNA synthesis occurred in cells transfected with the dbp knockout, the levels were less than that of the control virus suggesting that DBP is required for normal levels of DNA synthesis or for stability of nascent viral DNA. In addition, analysis of the viral DNA replicated by the dbp knockout by using field inversion gel electrophoresis failed to detect the presence of genome-length DNA. Furthermore, analysis of DBP from infected cells indicated that similar to LEF-3, DBP was tightly bound to viral chromatin. Assessment of the cellular localization of DBP relative to replicated viral DNA by immunoelectron microscopy indicated that, at 24 h post-infection, DBP co-localized with nascent DNA at distinct electron-dense regions within the nucleus. Finally, immunoelectron microscopic analysis of cells transfected with the dbp knockout revealed that DBP is required for the production of normal-appearing nucleocapsids and for the generation of the virogenic stroma.

Vanarsdall, Adam L. [Department of Microbiology, Nash Hall Room 220, Oregon State University, Corvallis, OR 97331-3804 (United States); Mikhailov, Victor S. [Department of Microbiology, Nash Hall Room 220, Oregon State University, Corvallis, OR 97331-3804 (United States); N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 117808 (Russian Federation); Rohrmann, George F. [Department of Microbiology, Nash Hall Room 220, Oregon State University, Corvallis, OR 97331-3804 (United States)]. E-mail: rohrmanng@orst.edu

2007-08-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


241

Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs  

DOE Green Energy (OSTI)

There are no known RNA viruses that infect Archaea. Filling this gap in our knowledge of viruses will enhance our understanding of the relationships between RNA viruses from the three domains of cellular life and, in particular, could shed light on the origin of the enormous diversity of RNA viruses infecting eukaryotes. We describe here the identification of novel RNA viral genome segments from high-temperature acidic hot springs in Yellowstone National Park in the United States. These hot springs harbor low-complexity cellular communities dominated by several species of hyperthermophilic Archaea. A viral metagenomics approach was taken to assemble segments of these RNA virus genomes from viral populations isolated directly from hot spring samples. Analysis of these RNA metagenomes demonstrated unique gene content that is not generally related to known RNA viruses of Bacteria and Eukarya. However, genes for RNA-dependent RNA polymerase (RdRp), a hallmark of positive-strand RNA viruses, were identified in two contigs. One of these contigs is approximately 5,600 nucleotides in length and encodes a polyprotein that also contains a region homologous to the capsid protein of nodaviruses, tetraviruses, and birnaviruses. Phylogenetic analyses of the RdRps encoded in these contigs indicate that the putative archaeal viruses form a unique group that is distinct from the RdRps of RNA viruses of Eukarya and Bacteria. Collectively, our findings suggest the existence of novel positive-strand RNA viruses that probably replicate in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses that infect eukaryotes and even more distant from known bacterial RNA viruses. These positive-strand RNA viruses might be direct ancestors of RNA viruses of eukaryotes.

Benjamin Bolduc; Daniel P. Shaughnessy; Yuri I. Wolf; Eugene V. Koonin; Francisco F. Roberto; Mark Young

2012-05-01T23:59:59.000Z

242

DNA-based asymmetric catalysis.  

E-Print Network (OSTI)

??The goal of the research described in this thesis was to develop the general concept and methodology of DNA-based asymmetric catalysis, with the aim of… (more)

Boersma, Arnold Jacob

2009-01-01T23:59:59.000Z

243

The Double Chooz reactor neutrino experiment  

E-Print Network (OSTI)

The Double Chooz reactor neutrino experiment will be the next detector to search for a non vanishing theta13 mixing angle with unprecedented sensitivity, which might open the way to unveiling CP violation in the leptonic sector. The measurement of this angle will be based in a precise comparison of the antineutrino spectrum at two identical detectors located at different distances from the Chooz nuclear reactor cores in France. Double Chooz is particularly attractive because of its capability to measure sin2(2theta13) to 3 sigmas if sin2(2theta13) > 0.05 or to exclude sin2(2theta13) down to 0.03 at 90% C.L. for Dm2 = 2.5 x 10-3 eV2 in three years of data taking with both detectors. The construction of the far detector starts in 2008 and the first neutrino results are expected in 2009. The current status of the experiment, its physics potential and design and expected performance of the detector are reviewed.

I. Gil-Botella

2007-10-23T23:59:59.000Z

244

Creep and creep-rupture behavior of a continuous strand, swirl mat reinforced polymer composite in automotive environments  

DOE Green Energy (OSTI)

Creep and creep-rupture behavior of an isocyanurate based polyurethane matrix with a continuous strand, swirl mat E-glass reinforcement was investigated for automotive applications. The material under stress was exposed to various automobile service environments. Results show that environment has substantial effects on its creep and creep-rupture properties. Proposed design guide lines and stress reduction factors were developed for various automotive environments. These composites are considered candidate structural materials for light weight and fuel efficient automobiles of the future.

Ren, W.; Brinkman, C.R. [Oak Ridge National Lab., TN (United States). Metals and Ceramics Div.

1998-12-31T23:59:59.000Z

245

Glass Does a Double-Take | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (Extended Search)

Highlights rss feed Glass Does a Double-Take APRIL 4, 2008 Bookmark and Share Predicted phase diagram as a function of reduced temperature () and volume fraction (). Inset...

246

Duality Invariance: From M-theory to Double Field Theory  

E-Print Network (OSTI)

We show how the duality invariant approach to M-theory formulated by Berman and Perry relates to the double field theory proposed by Hull and Zwiebach. In doing so we provide suggestions as to how Ramond fields can be incorporated into the double field theory. We find that the standard dimensional reduction procedure has a duality invariant (doubled) analogue in which the gauge fields of the doubled Kaluza-Klein ansatz encode the Ramond potentials. We identify the internal gauge index of these gauge fields with a spinorial index of O(d,d).

Daniel C. Thompson

2011-06-20T23:59:59.000Z

247

Design and Synthesis of Double Perovskite Substrate Materials  

Science Conference Proceedings (OSTI)

Presentation Title, A Firm Foundation for Sr2FeMoO6: Design and Synthesis of Double Perovskite Substrate Materials. Author(s), Alexanne Holcombe, Patricia ...

248

Exclusive Double Charmonium Production from $?$ Decay  

E-Print Network (OSTI)

The exclusive decay of $\\Upsilon$ to a vector plus pseudoscalar charmonium is studied in perturbative QCD. The corresponding branching ratios are predicted to be of order $10^{-6}$ for first three $\\Upsilon$ resonances, and we expect these decay modes should be discovered in the prospective high-luminosity $e^+e^-$ facilities such as super $B$ experiment. As a manifestation of the short-distance loop contribution, the relative phases among strong, electromagnetic and radiative decay amplitudes can be deduced. It is particularly interesting to find that the relative phase between strong and electromagnetic amplitudes is nearly orthogonal. The resonance-continuum interference effect for double charmonium production near various $\\Upsilon$ resonances in $e^+e^-$ annihilation is addressed.

Yu Jia

2007-06-25T23:59:59.000Z

249

Double-shell tank waste pretreatment  

SciTech Connect

Double-shell tanks contain most of the transuranic/high-level chemical processing waste generated at the Hanford Site in recent years. A small mass fraction of this waste is responsible for its characterization as transuranic/high-level waste. Pretreatment will partition the waste into a small fraction containing most of the transuranic/high-level components and a large fraction that is a low-level waste. The operations for achieving this objective include dissolution of water-soluble salts, dissolution of precipitated metal oxides in acid, clarification of the resulting dissolver liquors, transuranium element removal by solvent extraction and cesium removal by ion exchange. The primary benefit of pretreatment is a reduction in the overall cost of waste disposal.

Orme, R.M.; Appel, J.N.

1990-01-01T23:59:59.000Z

250

Double Shell Tank (DST) Utilities Specification  

SciTech Connect

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

SUSIENE, W.T.

2000-04-27T23:59:59.000Z

251

A Crystallographic Study of the Role of Sequence Context in Thymine Glycol Bypass by a Replicative DNA Polymerase Serendipitously Sheds Light on the Exonuclease Complex  

Science Conference Proceedings (OSTI)

Thymine glycol (Tg) is the most common oxidation product of thymine and is known to be a strong block to replicative DNA polymerases. A previously solved structure of the bacteriophage RB69 DNA polymerase (RB69 gp43) in complex with Tg in the sequence context 5'-G-Tg-G shed light on how Tg blocks primer elongation: The protruding methyl group of the oxidized thymine displaces the adjacent 5'-G, which can no longer serve as a template for primer elongation [Aller, P., Rould, M. A., Hogg, M, Wallace, S. S. and Doublie S. (2007). A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol. Proc. Natl. Acad. Sci. USA, 104, 814-818.]. Several studies showed that in the sequence context 5'-C-Tg-purine, Tg is more likely to be bypassed by Klenow fragment, an A-family DNA polymerase. We set out to investigate the role of sequence context in Tg bypass in a B-family polymerase and to solve the crystal structures of the bacteriophage RB69 DNA polymerase in complex with Tg-containing DNA in the three remaining sequence contexts: 5'-A-Tg-G, 5'-T-Tg-G, and 5'-C-Tg-G. A combination of several factors - including the associated exonuclease activity, the nature of the 3' and 5' bases surrounding Tg, and the cis-trans interconversion of Tg - influences Tg bypass. We also visualized for the first time the structure of a well-ordered exonuclease complex, allowing us to identify and confirm the role of key residues (Phe123, Met256, and Tyr257) in strand separation and in the stabilization of the primer strand in the exonuclease site.

Aller, Pierre; Duclos, Stéphanie; Wallace, Susan S.; Doublié, Sylvie (Vermont)

2012-06-27T23:59:59.000Z

252

Sequence independent amplification of DNA  

DOE Patents (OSTI)

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.

Bohlander, S.K.

1998-03-24T23:59:59.000Z

253

Sequence independent amplification of DNA  

DOE Patents (OSTI)

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.

Bohlander, Stefan K. (Chicago, IL)

1998-01-01T23:59:59.000Z

254

Spin polarization in ordered and disordered double-perovskites  

Science Conference Proceedings (OSTI)

Recently, the double perovskites family A2MM'O6 (A being a divalent or trivalent cation and M, M' two transition metals) has attracted considerable interest with the view of using these materials in spin electronics. This has ... Keywords: Double perovskites, Magnetoresistance, Metal-insulator transition

B. Aguilar; O. Navarro; M. Avignon

2008-03-01T23:59:59.000Z

255

Method for double-sided processing of thin film transistors  

DOE Patents (OSTI)

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

Yuan, Hao-Chih (Madison, WI); Wang, Guogong (Madison, WI); Eriksson, Mark A. (Madison, WI); Evans, Paul G. (Madison, WI); Lagally, Max G. (Madison, WI); Ma, Zhenqiang (Middleton, WI)

2008-04-08T23:59:59.000Z

256

Double chromodomains cooperate to recognize the methylated histone H3 tail  

Science Conference Proceedings (OSTI)

Chromodomains are modules implicated in the recognition of lysine-methylated histone tails and nucleic acids. CHD (for chromo-ATPase/helicase-DNA-binding) proteins regulate ATP-dependent nucleosome assembly and mobilization through their conserved double chromodomains and SWI2/SNF2 helicase/ATPase domain. The Drosophila CHD1 localizes to the interbands and puffs of the polytene chromosomes, which are classic sites of transcriptional activity. Other CHD isoforms (CHD3/4 or Mi-2) are important for nucleosome remodelling in histone deacetylase complexes. Deletion of chromodomains impairs nucleosome binding and remodelling by CHD proteins. Here we describe the structure of the tandem arrangement of the human CHD1 chromodomains, and its interactions with histone tails. Unlike HP1 and Polycomb proteins that use single chromodomains to bind to their respective methylated histone H3 tails, the two chromodomains of CHD1 cooperate to interact with one methylated H3 tail. We show that the human CHD1 double chromodomains target the lysine 4-methylated histone H3 tail (H3K4me), a hallmark of active chromatin. Methylammonium recognition involves two aromatic residues, not the three-residue aromatic cage used by chromodomains of HP1 and Polycomb proteins. Furthermore, unique inserts within chromodomain 1 of CHD1 block the expected site of H3 tail binding seen in HP1 and Polycomb, instead directing H3 binding to a groove at the inter-chromodomain junction.

Flanagan, John F.; Mi, Li-Zhi; Chruszcz, Maksymilian; Cymborowski, Marcin; Clines, Katrina L.; Kim, Youngchang; Minor, Wladek; Rastinejad, Fraydoon; Khorasanizadeh, Sepideh (ANL/SBC); (UV)

2010-07-19T23:59:59.000Z

257

Double-duct liquid metal magnetohydrodynamic engine  

DOE Patents (OSTI)

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

Haaland, Carsten M. (Oak Ridge, TN)

1995-01-01T23:59:59.000Z

258

Double-duct liquid metal magnetohydrodynamic engine  

DOE Patents (OSTI)

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

Haaland, Carsten M. (Oak Ridge, TN)

1997-01-01T23:59:59.000Z

259

Discovery of Peculiar Double-Mode Pulsations and Period Doubling in KEPLER RRc Variables  

E-Print Network (OSTI)

We analyzed the Long Cadence photometry of 4 first overtone RR Lyr-type stars (RRc stars) observed by the KEPLER telescope. All studied variables are multiperiodic. The strongest secondary peak appears for f_2/f_1 = 1.58-1.63, or P_2/P_1 = 0.61-0.63. In each star we detect at least one subharmonic of f_2, either at ~1/2 f_2 or at ~3/2 f_2. The presence of subharmonics is a characteristic signature of a period doubling.

Moskalik, P; Kolenberg, K; Nemec, J; Kunder, A; Chadid, M; Kopacki, G; Szabó, R; members, KEPLER WG#13

2012-01-01T23:59:59.000Z

260

Double Chooz: Searching for theta13 with reactor neutrinos  

E-Print Network (OSTI)

The Double Chooz experiment is meant to search for the neutrino mixing angle theta13 taking advantage of the neutrinos generated at the nuclear power plant of Chooz. Double Chooz relies on neutrino flux measurements at two different locations, the so-called far and near detectors, although the first phase runs only with the far detector. The commissioning of the far detector started in January 2011 and first results improving the current limit on theta13 are expected by the summer 2011. The status of the Double Chooz experiment is presented.

Novella, P

2011-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

Double Chooz: Searching for theta13 with reactor neutrinos  

E-Print Network (OSTI)

The Double Chooz experiment is meant to search for the neutrino mixing angle theta13 taking advantage of the neutrinos generated at the nuclear power plant of Chooz. Double Chooz relies on neutrino flux measurements at two different locations, the so-called far and near detectors, although the first phase runs only with the far detector. The commissioning of the far detector started in January 2011 and first results improving the current limit on theta13 are expected by the summer 2011. The status of the Double Chooz experiment is presented.

P. Novella; for the Double Chooz collaboration

2011-05-30T23:59:59.000Z

262

Cellular responses to environmental DNA damage  

Science Conference Proceedings (OSTI)

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.

Not Available

1994-08-01T23:59:59.000Z

263

Instability and Diapycnal Momentum Transport in a Double-Diffusive, Stratified Shear Layer  

Science Conference Proceedings (OSTI)

The linear stability of a double-diffusively stratified, inflectional shear flow is investigated. Double-diffusive stratification has little effect on shear instability except when the density ratio R? is close to unity. Double-diffusive ...

William D. Smyth; Satoshi Kimura

2007-06-01T23:59:59.000Z

264

A Novel Fold in the Tral Relaxase-Helicase C-Terminal Domain Is Essential for Conjugative DNA Transfer  

Science Conference Proceedings (OSTI)

TraI relaxase-helicase is the central catalytic component of the multiprotein relaxosome complex responsible for conjugative DNA transfer (CDT) between bacterial cells. CDT is a primary mechanism for the lateral propagation of microbial genetic material, including the spread of antibiotic resistance genes. The 2.4-{angstrom} resolution crystal structure of the C-terminal domain of the multifunctional Escherichia coli F (fertility) plasmid TraI protein is presented, and specific structural regions essential for CDT are identified. The crystal structure reveals a novel fold composed of a 28-residue N-terminal {alpha}-domain connected by a proline-rich loop to a compact {alpha}/{beta}-domain. Both the globular nature of the {alpha}/{beta}-domain and the presence as well as rigidity of the proline-rich loop are required for DNA transfer and single-stranded DNA binding. Taken together, these data establish the specific structural features of this noncatalytic domain that are essential to DNA conjugation.

Guogas, Laura M.; Kennedy, Sarah A.; Lee, Jin-Hyup; Redinbo, Matthew R.; (UNC)

2009-06-04T23:59:59.000Z

265

Low Dose Radiation Research Program: Quantification of Repair of  

NLE Websites -- All DOE Office Websites (Extended Search)

Quantification of Repair of Low-Dose-Induced DNA Double-Strand Quantification of Repair of Low-Dose-Induced DNA Double-Strand Breaks in Diploid Human Cells Authors: David Schild,1 and Larry H. Thompson,2 Institutions: 1Life Sciences Division, Lawrence Berkeley National Laboratory; and 2BBR Program, Lawrence Livermore National Laboratory Double-strand breaks (DSBs) are the biochemical lesions of primary concern in radiation related health effects. Compelling evidence from rodent and chicken model systems indicates that homologous recombinational repair (HRR) plays an essential role for cell viability in the repair of spontaneous DSBs arising during DNA replication and an important role in the repair of IR-induced DSBs. IR-induced DSBs are also repaired by error-prone nonhomologous end joining (NHEJ). Using hTERT-immortalized

266

DUF6 Project Doubles Production in 2013 | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

DUF6 Project Doubles Production in 2013 DUF6 Project Doubles Production in 2013 DUF6 Project Doubles Production in 2013 November 26, 2013 - 12:00pm Addthis LEXINGTON, Ky. - The conversion plants at EM's Paducah and Portsmouth sites surpassed a fiscal year 2013 goal by converting 13,679 metric tons of depleted uranium hexafluoride (DUF6), more than doubling production a year earlier. EM's Portsmouth Paducah Project Office (PPPO) and contractor Babcock & Wilcox Conversion Services LLC (BWCS) began operations in 2011 to convert the nation's 800,000-metric-ton inventory of DUF6 to more benign forms for sale, ultimate disposal or long-term storage. "Since 2011, we have been ramping up production to determine and achieve the safe, sustainable operating rate of the plants," said George E.

267

DUF6 Project Doubles Production in 2013 | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

DUF6 Project Doubles Production in 2013 DUF6 Project Doubles Production in 2013 DUF6 Project Doubles Production in 2013 November 26, 2013 - 12:00pm Addthis LEXINGTON, Ky. - The conversion plants at EM's Paducah and Portsmouth sites surpassed a fiscal year 2013 goal by converting 13,679 metric tons of depleted uranium hexafluoride (DUF6), more than doubling production a year earlier. EM's Portsmouth Paducah Project Office (PPPO) and contractor Babcock & Wilcox Conversion Services LLC (BWCS) began operations in 2011 to convert the nation's 800,000-metric-ton inventory of DUF6 to more benign forms for sale, ultimate disposal or long-term storage. "Since 2011, we have been ramping up production to determine and achieve the safe, sustainable operating rate of the plants," said George E.

268

Non-Double-Couple Microearthquakes At Long Valley Caldera, California,  

Open Energy Info (EERE)

Non-Double-Couple Microearthquakes At Long Valley Caldera, California, Non-Double-Couple Microearthquakes At Long Valley Caldera, California, Provide Evidence For Hydraulic Fracturing Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Journal Article: Non-Double-Couple Microearthquakes At Long Valley Caldera, California, Provide Evidence For Hydraulic Fracturing Details Activities (1) Areas (1) Regions (0) Abstract: Most of 26 small (0.4<~M<~3.1) microearthquakes at Long Valley caldera in mid-1997, analyzed using data from a dense temporary network of 69 digital three-component seismometers, have significantly non-double-couple focal mechanisms, inconsistent with simple shear faulting. We determined their mechanisms by inverting P- and S-wave polarities and amplitude ratios using linear-programming methods, and

269

Lee-Wave Resonances over Double Bell-Shaped Obstacles  

Science Conference Proceedings (OSTI)

Lee-wave resonance over double bell-shaped obstacles is investigated through a series of idealized high-resolution numerical simulations with the nonhydrostatic Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS) model using a free-slip ...

Vanda Grubiši?; Ivana Stiperski

2009-05-01T23:59:59.000Z

270

POWER MODULE PACKAGING WITH DOUBLE SIDED PLANAR INTERCONNECTION ...  

A double sided cooled power module package having a single phase leg topology includes two IGBT and two diode semiconductor dies. Each IGBT die is spaced apart from a ...

271

Does rotation influence double-diffusive fluxes in polar oceans?  

Science Conference Proceedings (OSTI)

The diffusive (or semi-convection) regime of double-diffusive convection (DDC) is wide-spread in the polar oceans, generating “staircases” consisting of high-gradient interfaces of temperature and salinity separated by convectively mixed layers. ...

J. R. Carpenter; M.-L. Timmermans

272

Simultaneous Spin-Charge Relaxation in Double Quantum Dots  

E-Print Network (OSTI)

We investigate phonon-induced spin and charge relaxation mediated by spin-orbit and hyperfine interactions for a single electron confined within a double quantum dot. A simple toy model incorporating both direct decay to the ground state of the double dot and indirect decay via an intermediate excited state yields an electron spin relaxation rate that varies non-monotonically with the detuning between the dots. We confirm this model with experiments performed on a GaAs double dot, demonstrating that the relaxation rate exhibits the expected detuning dependence and can be electrically tuned over several orders of magnitude. Our analysis suggests that spin-orbit mediated relaxation via phonons serves as the dominant mechanism through which the double-dot electron spin-flip rate varies with detuning.

V. Srinivasa; K. C. Nowack; M. Shafiei; L. M. K. Vandersypen; J. M. Taylor

2013-03-07T23:59:59.000Z

273

Kinetic Alfven double layer formed by electron viscosity  

SciTech Connect

The effect of the electron viscosity on the kinetic Alfven solitary wave is investigated. It is found that small electron viscosity changes the electron motion along the magnetic field producing a boundary layer, and thus that in a low beta electron-ion plasma({beta} Much-Less-Than m{sub e}/m{sub i}), an obliquely propagating kinetic solitary Alfven wave can become a double layer. This double layer can exist in the sub-Alfvenic and super-Alfvenic regimes. The length scale of density drop for this double layer is on the order of that of the conventional kinetic solitary Alfven wave, and thus this double layer can accelerate electrons on a very short length scale.

Woo, M. H.; Ryu, C.-M. [Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Korea, Republic of); Choi, C. R. [Department of Physics, Korea Advanced Institute of Science and Technology, Taejon 305-701 (Korea, Republic of)

2012-07-15T23:59:59.000Z

274

Double Shell Tank (DST) Monitor and Control Subsystem Specification  

Science Conference Proceedings (OSTI)

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

BAFUS, R.R.

2000-11-03T23:59:59.000Z

275

Double Shell Tank (DST) Process Waste Sampling Subsystem Specification  

SciTech Connect

This specification establishes the performance requirements and provides references to the requisite codes and standards to be applied to the Double-Shell Tank (DST) Process Waste Sampling Subsystem which supports the first phase of Waste Feed Delivery.

RASMUSSEN, J.H.

2000-05-03T23:59:59.000Z

276

Double Beta Decay: Historical Review of 75 Years of Research  

E-Print Network (OSTI)

Main achievements during 75 years of research on double beta decay have been reviewed. The existing experimental data have been presented and the capabilities of the next-generation detectors have been demonstrated.

A. S. Barabash

2011-04-14T23:59:59.000Z

277

Spontaneous formation of double bars in dark matter dominated galaxies  

E-Print Network (OSTI)

Although nearly one-third of barred galaxies host an inner, secondary bar, the formation and evolution of double barred galaxies remain unclear. We show here an example model of a galaxy, dominated by a live dark matter halo, in which double bars form naturally, without requiring gas, and we follow its evolution for a Hubble time. The inner bar in our model galaxy rotates almost as slowly as the outer bar, and it can reach up to half of its length. The route to the formation of a double bar may be different from that of a single strong bar. Massive dark matter halo or dynamically hot stellar disc may play an important role in the formation of double bars and their subsequent evolution.

Saha, Kanak

2013-01-01T23:59:59.000Z

278

Finescale Instabilities of the Double-Diffusive Shear Flow  

Science Conference Proceedings (OSTI)

This study examines dynamics of finescale instabilities in thermohaline–shear flows. It is shown that the presence of the background diapycnal temperature and salinity fluxes due to double diffusion has a destabilizing effect on the basic ...

Timour Radko; Melvin E. Stern

2011-03-01T23:59:59.000Z

279

The Southeast Pacific Warm Band and Double ITCZ  

Science Conference Proceedings (OSTI)

The east Pacific double intertropical convergence zone (ITCZ) in austral fall is investigated with particular focus on the growing processes of its Southern Hemisphere branch. Satellite measurements from the Tropical Rainfall Measuring Mission (...

Hirohiko Masunaga; Tristan S. L’Ecuyer

2010-03-01T23:59:59.000Z

280

Regulation of DNA damage tolerance : studies of the translesion synthesis DNA ploymerase eta in Saccharomyces cerevisiae  

E-Print Network (OSTI)

All organisms must control the effects of DNA damage to protect the integrity of their genomes. In addition to DNA repair, this requires DNA damage tolerance pathways, which allow the continuation of essential processes ...

Woodruff, Rachel Van Etten

2008-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

Characterization of nanoparticle-DNA conjugate and control of DNA conformation on particle surface  

E-Print Network (OSTI)

Nano-science has exploited the hybridization and de-hybridization phenomena of DNA which are one of its fundamental functions. In particular, conjugates of gold nanoparticles and DNA (Au NP-DNA) have been extensively ...

Park, Sunho, 1976-

2009-01-01T23:59:59.000Z

282

Functional Analysis for Double Shell Tank (DST) Subsystems  

Science Conference Proceedings (OSTI)

This functional analysis identifies the hierarchy and describes the subsystem functions that support the Double-Shell Tank (DST) System described in HNF-SD-WM-TRD-007, System Specification for the Double-Shell Tank System. Because of the uncertainty associated with the need for upgrades of the existing catch tanks supporting the Waste Feed Delivery (WFD) mission, catch tank functions are not addressed in this document. The functions identified herein are applicable to the Phase 1 WFD mission only.

SMITH, D.F.

2000-08-22T23:59:59.000Z

283

Cross sections for short pulse single and double ionization ofhelium  

SciTech Connect

In a previous publication, procedures were proposed for unambiguously extracting amplitudes for single and double ionization from a time-dependent wavepacket by effectively propagating for an infinite time following a radiation pulse. Here we demonstrate the accuracy and utility of those methods for describing two-photon single and one-photon double ionization of helium. In particular it is shown how narrow features corresponding to autoionizing states are easily resolved with these methods.

Palacios, Alicia; Rescigno, Thomas N.; McCurdy, C. William

2007-11-27T23:59:59.000Z

284

A van der Waals density functional mapping of attraction in DNA dimers  

E-Print Network (OSTI)

The dispersion interaction between a pair of parallel DNA double-helix structures is investigated by means of the van der Waals density functional (vdW-DF) method. Each double-helix structure consists of an infinite repetition of one B-DNA coil with 10 base pairs. This parameter-free density functional theory (DFT) study illustrates the initial step in a proposed vdW-DF computational strategy for large biomolecular problems. The strategy is to first perform a survey of interaction geometries, based on the evaluation of the van der Waals (vdW) attraction, and then limit the evaluation of the remaining DFT parts (specifically the expensive study of the kinetic-energy repulsion) to the thus identified interesting geometries. Possibilities for accelerating this second step is detailed in a separate study. For the B-DNA dimer, the variation in van der Waals attraction is explored at relatively short distances (although beyond the region of density overlap) for a 360 degrees rotation. This study highlights the role...

Londero, Elisa; Schroder, Elsebeth

2013-01-01T23:59:59.000Z

285

Mechanisms of radiation-induced gene responses  

Science Conference Proceedings (OSTI)

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

Woloschak, G.E.; Paunesku, T.

1996-10-01T23:59:59.000Z

286

Energy Blog | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

4, 2012 4, 2012 The National Renewable Energy Lab's (NREL) utility rate database is a great resource for developers entering the Apps for Energy competition. | Map courtesy of NREL. Developer Resources for Apps for Energy Are you interested in participating in the Apps for Energy competition? Be sure to check out this list of resources that can help developers create energy apps. April 3, 2012 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 protein (not shown) is the enzyme that unwinds the double stranded DNA so each strand can be replicated. | Illustration courtesy of Brookhaven Lab.

287

Energy Blog | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

April 4, 2012 April 4, 2012 The National Renewable Energy Lab's (NREL) utility rate database is a great resource for developers entering the Apps for Energy competition. | Map courtesy of NREL. Developer Resources for Apps for Energy Are you interested in participating in the Apps for Energy competition? Be sure to check out this list of resources that can help developers create energy apps. April 3, 2012 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 protein (not shown) is the enzyme that unwinds the double stranded DNA so each strand can be replicated. | Illustration courtesy of Brookhaven Lab.

288

Preparation Of Dna-Containing Extract For Pcr Amplification  

NLE Websites -- All DOE Office Websites (Extended Search)

Preparation Of Dna-Containing Extract For Pcr Amplification Preparation Of Dna-Containing Extract For Pcr Amplification The method may provide a DNA-containing extract sufficiently...

289

Silencing and recombination in yeast ribosomal DNA  

E-Print Network (OSTI)

A bioinformatic and laboratory investigation into S. cerevisiae's system for the maintenance and homogenization of rDNA. Eliminating mutations and heterogeneity in rDNA repeats is necessary evolutionarily, but harmful to ...

O'Kelly, Michael J. T

2008-01-01T23:59:59.000Z

290

Amplification of chromosomal DNA in situ  

DOE Patents (OSTI)

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

Christian, Allen T. (Tracy, CA); Coleman, Matthew A. (Livermore, CA); Tucker, James D. (Livermore, CA)

2002-01-01T23:59:59.000Z

291

Topics and Techniques in Forensic DNA Analysis  

Science Conference Proceedings (OSTI)

... Topics and Techniques for Forensic DNA Analysis NYC OCME Dept of Forensic Biology ... NIST Human Identity Project Leader (1999-present) ...

2012-04-17T23:59:59.000Z

292

Quantum Dot Fluorescence Lifetime Engineering with DNA ...  

Science Conference Proceedings (OSTI)

Quantum Dot Fluorescence Lifetime Engineering with DNA Origami ... such as metal nanoparticles and semiconductor quantum dots – is challenging ...

293

Double pulse laser induced breakdown spectroscopy; experimental study of  

NLE Websites -- All DOE Office Websites (Extended Search)

Double pulse laser induced breakdown spectroscopy; experimental study of Double pulse laser induced breakdown spectroscopy; experimental study of lead emission intensity dependence on the wavelengths and sample matrix Title Double pulse laser induced breakdown spectroscopy; experimental study of lead emission intensity dependence on the wavelengths and sample matrix Publication Type Journal Article Year of Publication 2009 Authors Piscitelli, Vincent, Mauro A. Martinez, Alberto J. Fernandez, Jhanis J. Gonzalez, Xianglei Mao, and Richard E. Russo Journal Spectrochimica Acta Part B Volume 64 Issue 2 Pagination 147-154 Date Published 02/2009 Keywords Double pulse LIBS, laser induced breakdown spectroscopy, lead Abstract Lead (Pb) emission intensity (atomic line 405.78 nm) dependence on the sample matrix (metal alloy) was studied by means of collinear double pulse (DP)-laser induced breakdown spectroscopy (LIBS). The measurement of the emission intensity produced by three different wavelength combinations (i.e. I:532 nm-II:1064 nm, I:532 nm-II:532 nm, and I:532 nm-II:355 nm) from three series of standard reference materials showed that the lead atomic line 405.78 nm emission intensity was dependent on the sample matrix for all the combination of wavelengths, however reduced dependency was found for the wavelength combination I:532 nm-II:355 nm.

294

Time-resolved double-slit experiment with entangled photons  

E-Print Network (OSTI)

The double-slit experiment strikingly demonstrates the wave-particle duality of quantum objects. In this famous experiment, particles pass one-by-one through a pair of slits and are detected on a distant screen. A distinct wave-like pattern emerges after many discrete particle impacts as if each particle is passing through both slits and interfering with itself. While the direct event-by-event buildup of this interference pattern has been observed for massive particles such as electrons, neutrons, atoms and molecules, it has not yet been measured for massless particles like photons. Here we present a temporally- and spatially-resolved measurement of the double-slit interference pattern using single photons. We send single photons through a birefringent double-slit apparatus and use a linear array of single-photon detectors to observe the developing interference pattern. The analysis of the buildup allows us to compare quantum mechanics and the corpuscular model, which aims to explain the mystery of single-particle interference. Finally, we send one photon from an entangled pair through our double-slit setup and show the dependence of the resulting interference pattern on the twin photon's measured state. Our results provide new insight into the dynamics of the buildup process in the double-slit experiment, and can be used as a valuable resource in quantum information applications.

Piotr Kolenderski; Carmelo Scarcella; Kelsey D. Johnsen; Deny R. Hamel; Catherine Holloway; Lynden K. Shalm; Simone Tisa; Alberto Tosi; Kevin J. Resch; Thomas Jennewein

2013-04-17T23:59:59.000Z

295

Can Finite Size Effects in the Poland-Scheraga Model Explain Simulations of a Simple Model for DNA Denaturation ?  

E-Print Network (OSTI)

We compare results of previous simulations of a simple model of DNA denaturation to the predictions of the Poland-Scheraga model. Concentrating on the critical region of the latter model we calculate both thermodynamic quantities and the distribution functions measured in the simulations. We find that the Poland-Scheraga model yields an excellent fit to the data, provided (i) we include a (singular) factor weighting the open ends of the doubly stranded chain, and (ii) we keep the leading corrections to the finite size scaling limit. The exponent c_1, which governs the end-weighting factor, is fairly well determined: 0.1 <~ c_1 <~ 0.15. The exponent c, which governs the length distribution of large loops, is determined only poorly. The data are compatible with values of c in at least the range 1.9 <~ c <~ 2.2. From the data it therefore cannot be decided whether the denaturation transition asymptotically is of first or of second order. We suggest that simulations of doubly stranded chains closed at both ends might allow for a more precise determination of c.

Lothar Schäfer

2005-02-28T23:59:59.000Z

296

Data hiding methods based upon DNA sequences  

Science Conference Proceedings (OSTI)

In this paper, three data hiding methods are proposed, based upon properties of DNA sequences. It is highlighted that DNA sequences possess some interesting properties which can be utilized to hide data. These three methods are: the Insertion Method, ... Keywords: Complementary pair, DNA, Data hiding, Data recovery

H. J. Shiu; K. L. Ng; J. F. Fang; R. C. T. Lee; C. H. Huang

2010-06-01T23:59:59.000Z

297

Magnetic tweezers to study DNA motors  

E-Print Network (OSTI)

Magnetic tweezers to study DNA motors Maria Mañosas Ritort lab UB Barcelona Croquette-Bensimon lab ENS France #12;· Introduction to MT (magnetic tweezers) · Applications: 1. Tracking DNA motors: (i) Helicases (ii) Annealing motor 2. Studying a multiprotein system: DNA replication Outline #12;· Atomic force

Ritort, Felix

298

Dose-response analysis of infants prenatally exposed to methyl mercury: An application of a single compartment model to single-strand hair analysis  

Science Conference Proceedings (OSTI)

A new method of estimating fetal exposure is used in a dose-response analysis of data from the 1971 outbreak of methyl mercury poisoning in rural Iraq. An X-ray fluorescence instrument for the measurement of single strands of human hair was employed to obtain longitudinal profiles recapitulating fetal exposure. Logit and hockey-stick models as well as nonparametric smoothing are used to describe data on delayed development and central nervous system abnormality.

Cox, C.; Clarkson, T.W.; Marsh, D.O.; Amin-Zaki, L.; Tikriti, S.; Myers, G.G. (Univ. of Rochester School of Medicine, New York, NY (USA))

1989-08-01T23:59:59.000Z

299

HANFORD DOUBLE SHELL TANK THERMAL AND SEISMIC PROJECT SEISMIC ANALYSIS OF HANFORD DOUBLE SHELL TANKS  

Science Conference Proceedings (OSTI)

M&D Professional Services, Inc. (M&D) is under subcontract to Pacific Northwest National Laboratories (PNNL) to perform seismic analysis of the Hanford Site Double-Shell Tanks (DSTs) in support of a project entitled Double-Shell Tank (DST) Integrity Project - DST Thermal and Seismic Analyses. The original scope of the project was to complete an up-to-date comprehensive analysis of record of the DST System at Hanford in support of Tri-Party Agreement Milestone M-48-14. The work described herein was performed in support of the seismic analysis of the DSTs. The thermal and operating loads analysis of the DSTs is documented in Rinker et al. (2004). Although Milestone M-48-14 has been met, Revision I is being issued to address external review comments with emphasis on changes in the modeling of anchor bolts connecting the concrete dome and the steel primary tank. The work statement provided to M&D (PNNL 2003) required that a nonlinear soil structure interaction (SSI) analysis be performed on the DSTs. The analysis is required to include the effects of sliding interfaces and fluid sloshing (fluid-structure interaction). SSI analysis has traditionally been treated by frequency domain computer codes such as SHAKE (Schnabel, et al. 1972) and SASSI (Lysmer et al. 1999a). Such frequency domain programs are limited to the analysis of linear systems. Because of the contact surfaces, the response of the DSTs to a seismic event is inherently nonlinear and consequently outside the range of applicability of the linear frequency domain programs. That is, the nonlinear response of the DSTs to seismic excitation requires the use of a time domain code. The capabilities and limitations of the commercial time domain codes ANSYS{reg_sign} and MSC Dytran{reg_sign} for performing seismic SSI analysis of the DSTs and the methodology required to perform the detailed seismic analysis of the DSTs has been addressed in Rinker et al (2006a). On the basis of the results reported in Rinker et al. (2006a), it is concluded that time-domain SSI analysis using ANSYS{reg_sign} is justified for predicting the global response of the DSTs. The most significant difference between the current revision (Revision 1) of this report and the original issue (Revision 0) is the treatment of the anchor bolts that tie the steel dome of the primary tank to the concrete tank dome.

MACKEY TC; RINKER MW; CARPENTER BG; HENDRIX C; ABATT FG

2009-01-15T23:59:59.000Z

300

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

Science Conference Proceedings (OSTI)

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

MACKEY, T.C.

2006-03-17T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


301

NREL: News Feature - Nation Could Double Energy Productivity  

NLE Websites -- All DOE Office Websites (Extended Search)

Nation Could Double Energy Productivity Nation Could Double Energy Productivity February 7, 2013 Photo of NREL Director Dan Arvizu speaking at NREL. Enlarge image NREL Director Dan Arvizu and a blue-ribbon panel of 20 energy experts said that the United States can double its energy productivity by 2030 - and do so in ways that bolster the nation's economy. In this photo, Arvizu speaks to commercial building stakeholders at NREL. Credit: Dennis Schroeder Researchers at the U.S. Department of Energy's (DOE) National Renewable Energy Laboratory (NREL) have long understood that using energy more efficiently can be just as beneficial as finding new ways to produce energy more efficiently. On Feb. 7, NREL Director Dan Arvizu and a blue-ribbon panel of 20 energy experts drove that message home, declaring that the United States can

302

Neutrino-less Double Beta Decay and Particle Physics  

E-Print Network (OSTI)

We review the particle physics aspects of neutrino-less double beta decay. This process can be mediated by light massive Majorana neutrinos (standard interpretation) or by something else (non-standard interpretations). The physics potential of both interpretations is summarized and the consequences of future measurements or improved limits on the half-life of neutrino-less double beta decay are discussed. We try to cover all proposed alternative realizations of the decay, including light sterile neutrinos, supersymmetric or left-right symmetric theories, Majorons, and other exotic possibilities. Ways to distinguish the mechanisms from one another are discussed. Experimental and nuclear physics aspects are also briefly touched, alternative processes to double beta decay are discussed, and an extensive list of references is provided.

Werner Rodejohann

2011-06-07T23:59:59.000Z

303

Evaluation of the uranium double spike technique for environmental monitoring  

Science Conference Proceedings (OSTI)

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

Hemberger, P.H.; Rokop, D.J.; Efurd, D.W.; Roensch, F.R. [Los Alamos National Lab., NM (United States); Smith, D.H.; Turner, M.L.; Barshick, C.M.; Bayne, C.K. [Oak Ridge National Lab., TN (United States)

1998-01-01T23:59:59.000Z

304

Searching for Double Beta Decay with the Enriched Xenon Observatory  

Science Conference Proceedings (OSTI)

The Enriched Xenon Observatory (EXO) Collaboration is building a series of experiments to search for the neutrinoless double beta decay of {sup 136}Xe. The first experiment, known as EXO-200, will utilize 200 kg of xenon enriched to 80% in the isotope of interest, making it the largest double beta decay experiment to date by one order of magnitude. This experiment is rapidly being constructed, and will begin data taking in 2007. The EXO collaboration is also developing a technique to identify on an event-by-event basis the daughter barium ion of the double beta decay. If successful, this method would eliminate all conventional radioactive backgrounds to the decay, resulting in an ideal experiment. We summarize here the current status of EXO-200 construction and the barium tag R&D program.

Hall, C.; /SLAC

2007-03-16T23:59:59.000Z

305

Double Chooz: Optimizing CHOOZ for a possible theta 13 measurement  

E-Print Network (OSTI)

The proposed Double Chooz theta 13 experiment is described. Double Chooz will be an optimized reactor disappearance experiment similar to the original CHOOZ. The optimization includes an increase in the signal to noise by increasing the target volume to twice the original CHOOZ, reducing singles background with a non-scintillating oil buffer region around the target and carefully controlling systematic uncertainties by measuring the electron antineutrino flux of the source with a near detector. The Double Chooz far detector will be situated in the same cavern as CHOOZ but will detect ~50000 electron antineutrinos in three years of operation. We estimate a systematic uncertainty of 0.6%, and a reduction of the upper limit on theta 13 to 5 degrees.

Dazeley, S A

2006-01-01T23:59:59.000Z

306

Double Chooz: Optimizing CHOOZ for a possible theta 13 measurement  

E-Print Network (OSTI)

The proposed Double Chooz theta 13 experiment is described. Double Chooz will be an optimized reactor disappearance experiment similar to the original CHOOZ. The optimization includes an increase in the signal to noise by increasing the target volume to twice the original CHOOZ, reducing singles background with a non-scintillating oil buffer region around the target and carefully controlling systematic uncertainties by measuring the electron antineutrino flux of the source with a near detector. The Double Chooz far detector will be situated in the same cavern as CHOOZ but will detect ~50000 electron antineutrinos in three years of operation. We estimate a systematic uncertainty of 0.6%, and a reduction of the upper limit on theta 13 to 5 degrees.

S. A. Dazeley; for the Double Chooz Collaboration

2005-10-21T23:59:59.000Z

307

The Spacetime of Double Field Theory: Review, Remarks, and Outlook  

E-Print Network (OSTI)

We review double field theory (DFT) with emphasis on the doubled spacetime and its generalized coordinate transformations, which unify diffeomorphisms and b-field gauge transformations. We illustrate how the composition of generalized coordinate transformations fails to associate. Moreover, in dimensional reduction, the O(d,d) T-duality transformations of fields can be obtained as generalized diffeomorphisms. Restricted to a half-dimensional subspace, DFT includes `generalized geometry', but is more general in that local patches of the doubled space may be glued together with generalized coordinate transformations. Indeed, we show that for certain T-fold backgrounds with non-geometric fluxes, there are generalized coordinate transformations that induce, as gauge symmetries of DFT, the requisite O(d,d;Z) monodromy transformations. Finally we review recent results on the \\alpha' extension of DFT which, reduced to the half-dimensional subspace, yields intriguing modifications of the basic structures of generalized geometry.

Olaf Hohm; Dieter Lust; Barton Zwiebach

2013-09-11T23:59:59.000Z

308

SDSS galaxies with double-peaked emission lines: double starbursts or AGNs?  

E-Print Network (OSTI)

With the aim of investigating galaxies with two strong simultaneous starbursts, we have extracted a sample of galaxies with double-peaked emission lines in their global spectra from the SDSS spectral database. We then fitted the emission lines Halpha, Hbeta, [OIII]5007, [NII]6584, [SII]6717 and [SII]6731 of 129 spectra by two Gaussians to separate the radiation of the two (blue and red) components. A more or less reliable decomposition of the all those emission lines have been found for 55 spectra. Using a standard BPT classification diagram, we have been able to divide the galaxies from our sample into two subsamples: Sample A consisting of 18 galaxies where both components belong to the photoionised class of objects, and Sample B containing 37 galaxies which show non-thermal ionisation (AGNs). We have examined the properties of the blue and red components, and found that the differences between radial velocities of components lie within 200 - 400 km/s for galaxies of both subsamples. The equivalent number o...

Pilyugin, L S; Cedres, B; Cepa, J; Bongiovanni, A; Mattsson, L; Vilchez, J M

2011-01-01T23:59:59.000Z

309

Human Genome Research: Decoding DNA  

NLE Websites -- All DOE Office Websites (Extended Search)

Human Genome Research: Decoding DNA Human Genome Research: Decoding DNA Resources with Additional Information Charles DeLisi As head of DOE's Office of Health and Environmental Research, Charles DeLisi played a pivotal role in proposing and initiating the Human Genome Program in 1986. The U.S. Department of Energy (DOE) has historically been active in supporting human genome research. On September 10, 2003, Secretary of Energy Spencer Abraham presented the Secretary's Gold Award to Aristides Patrinos and Francis Collins for their leadership of the government's Human Genome Project. At DOE's Office of Science, Dr. Patrinos is the Associate Director for Biological and Environmental Research. He has been a researcher at the department's Oak Ridge National Laboratory and Brookhaven National Laboratory.

310

Fleet DNA Project (Fact Sheet)  

SciTech Connect

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

Not Available

2012-10-01T23:59:59.000Z

311

Channel plate for DNA sequencing  

DOE Patents (OSTI)

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

Douthart, Richard J. (Richland, WA); Crowell, Shannon L. (Eltopia, WA)

1998-01-01T23:59:59.000Z

312

Channel plate for DNA sequencing  

DOE Patents (OSTI)

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

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

1998-01-13T23:59:59.000Z

313

Double-well magnetic trap for Bose-Einstein condensates  

E-Print Network (OSTI)

We present a magnetic trapping scheme for neutral atoms based on a hybrid of Ioffe-Pritchard and Time-averaged Orbiting Potential traps. The resulting double-well magnetic potential has readily controllable barrier height and well separation. This offers a new tool for studying the behavior of Bose condensates in double-well potentials, including atom interferometry and Josephson tunneling. We formulate a description for the potential of this magnetic trap and discuss practical issues such as loading with atoms, evaporative cooling and manipulating the potential.

N. R. Thomas; C. J. Foot; A. C. Wilson

2001-08-10T23:59:59.000Z

314

Benzene-derived N2-(4-hydroxyphenyl)-deoxyguanosine adduct: UvrABC incision and its conformation in DNA  

DOE Green Energy (OSTI)

Benzene, a ubiquitous human carcinogen, forms DNA adducts through its metabolites such as p-benzoquinone (p-BQ) and hydroquinone (HQ). N(2)-(4-Hydroxyphenyl)-2'-deoxyguanosine (N(2)-4-HOPh-dG) is the principal adduct identified in vivo by (32)P-postlabeling in cells or animals treated with p-BQ or HQ. To study its effect on repair specificity and replication fidelity, we recently synthesized defined oligonucleotides containing a site-specific adduct using phosphoramidite chemistry. We here report the repair of this adduct by Escherichia coli UvrABC complex, which performs the initial damage recognition and incision steps in the nucleotide excision repair (NER) pathway. We first showed that the p-BQ-treated plasmid was efficiently cleaved by the complex, indicating the formation of DNA lesions that are substrates for NER. Using a 40-mer substrate, we found that UvrABC incises the DNA strand containing N(2)-4-HOPh-dG in a dose- and time-dependent manner. The specificity of such repair was also compared with that of DNA glycosylases and damage-specific endonucleases of E. coli, both of which were found to have no detectable activity toward N(2)-4-HOPh-dG. To understand why this adduct is specifically recognized and processed by UvrABC, molecular modeling studies were performed. Analysis of molecular dynamics trajectories showed that stable G:C-like hydrogen bonding patterns of all three Watson-Crick hydrogen bonds are present within the N(2)-4-HOPh-G:C base pair, with the hydroxyphenyl ring at an almost planar position. In addition, N(2)-4-HOPh-dG has a tendency to form more stable stacking interactions than a normal G in B-type DNA. These conformational properties may be critical in differential recognition of this adduct by specific repair enzymes.

Hang, Bo; Rodriguez, Ben; Yang, Yanu; Guliaev, Anton B.; Chenna, Ahmed

2010-06-14T23:59:59.000Z

315

Flow dynamics in a double-skin façade  

Science Conference Proceedings (OSTI)

A dynamical study of the flow in an asymmetrically heated vertical plane channel was carried out experimentally and numerically. The experiments are carried out in water for modified Rayleigh numbers (Ra*) in a range corresponding to the boundary layer ... Keywords: double skin, laminar flow, natural convection, numerical simulation, recirculation zone, vertical channel, visualization technique, wall flux

Dan Ospir; Cristian Chereches; Catalin Popa; Stéphane Fohanno; Catalin Popovici

2010-04-01T23:59:59.000Z

316

Regime Transitions in a Stochastically Forced Double-Gyre Model  

Science Conference Proceedings (OSTI)

A reduced-gravity double-gyre ocean model is used to study the influence of an additive stochastic wind stress component on the regime behavior of the wind-driven circulation. The variance of the stochastic component (spatially coherent white ...

Philip Sura; Klaus Fraedrich; Frank Lunkeit

2001-02-01T23:59:59.000Z

317

Double-shell tank waste retrieval survey package  

SciTech Connect

Westinghouse Hanford Company is seeking industry solutions to underground double-shell tank waste retrieval at the Hanford Site located in southeastern Washington. This is not a request for proposals; it is a request for information to facilitate continued discussion. Westinghouse Hanford Company will not reimburse any costs incurred for providing the information requested.

Berglin, E.J.

1995-12-01T23:59:59.000Z

318

Mixer pump test plan for double shell tank AZ-101  

Science Conference Proceedings (OSTI)

Mixer pump systems have been chosen as the method for retrieval of tank wastes contained in double shell tanks at Hanford. This document describes the plan for testing and demonstrating the ability of two 300 hp mixer pumps to mobilize waste in tank AZ-101. The mixer pumps, equipment and instrumentation to monitor the test were installed by Project W-151.

STAEHR, T.W.

1999-05-12T23:59:59.000Z

319

Geometrical tunability of plasmon excitations of double concentric metallic nanotubes  

SciTech Connect

The plasmon frequencies of a general double concentric metallic nanotube (NT) are obtained by using the plasmon hybridization method. Theoretical calculations indicate that there are four distinct plasmon modes for the system. It is shown that these two alternating layers of dielectric and metal have a greater geometrical tunability than the single metallic nanotubes of similar dimensions.

Moradi, Afshin [Department of Nano Science, Kermanshah University of Technology, Kermanshah 67178-63766 (Iran, Islamic Republic of) and Department of Nano Science, Institute for Studies in Theoretical Physics and Mathematics (IPM), Tehran 19395-5531 (Iran, Islamic Republic of)

2012-06-15T23:59:59.000Z

320

AAAS Office of Opportunities in Science The Double Bind  

E-Print Network (OSTI)

of scientists regardless of race, ethnicity or gender. Conserving of their time and energies, they tackled. Science careers in the context of gender and race or ethnic bias have been a major part of our lives of biases related to both their race or ethnicity and gender, constituting a double bind. Programs

Ortiz, Christine

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


321

EA-1905: Double Eagle Water System, Carlsbad, New Mexico  

Energy.gov (U.S. Department of Energy (DOE))

This EA, prepared by the U.S. Department of the Interior’s Bureau of Land Management Carlsbad Field Office and adopted by DOE, evaluates the expansion and upgrade of the City of Carlsbad’s Double Eagle Water System.

322

On the Flexible Connection of Rigid Double-Rail Track  

Science Conference Proceedings (OSTI)

To facilitate the loading and discharging of rolling stocks for train ferries, a new type of flexible double-rail track was recently invented. The geometric relationship of bending parameters of the flexible track is studied theoretically. The formulation ... Keywords: Flexible connection, Rail transport, Railway, Intermodal transport, Train ferry

Xie Xinlian; Li Meng; Liu Shiyong; Wang Shaocheng

2009-10-01T23:59:59.000Z

323

New Reactor Neutrino Experiments besides Double-CHOOZ  

E-Print Network (OSTI)

Several new reactor neutrino experiments are being considered to measure the parameter theta-13. The current plans for Angra, Braidwood, Daya Bay, KASKA and KR2DET are reviewed. A case is made that, together with Double-CHOOZ, a future world program should include at least three such experiments.

Maury Goodman

2005-01-21T23:59:59.000Z

324

New Reactor Neutrino Experiments besides Double-CHOOZ  

E-Print Network (OSTI)

Several new reactor neutrino experiments are being considered to measure the parameter ?13. The current plans for Angra, Braidwood, Daya Bay, KASKA and KR2DET are reviewed. A case is made that, together with Double-CHOOZ, a future world program should include at least three such experiments. 1. Introduction and Remarks

M. Goodman A

2005-01-01T23:59:59.000Z

325

Heat exchanger with leak detecting double wall tubes  

DOE Patents (OSTI)

A straight shell and tube heat exchanger utilizing double wall tubes and three tubesheets to ensure separation of the primary and secondary fluid and reliable leak detection of a leak in either the primary or the secondary fluids to further ensure that there is no mixing of the two fluids.

Bieberbach, George (Tampa, FL); Bongaards, Donald J. (Seminole, FL); Lohmeier, Alfred (Tampa, FL); Duke, James M. (St. Petersburg, all of, FL)

1981-01-01T23:59:59.000Z

326

First experiment with the double solenoid RIBRAS system  

Science Conference Proceedings (OSTI)

A description of the double solenoid system (RIBRAS) operating since 2004 in one of the beam lines of the Pelletron Laboratory of the Institute of Physics of the University of Sao Paulo is presented. The recent installation of the secondary scattering chamber after the second solenoid is reported and the first experiment in RIBRAS using both solenoids is described.

Lichtenthaeler, R.; Condori, R. Pampa; Lepine-Szily, A.; Pires, K. C. C.; Morais, M. C.; Leistenschneider, E.; Scarduelli, V. B.; Gasques, L. R. [Instituto de Fisica da USP, Sao Paulo, Brazil, C.P. 66318, 05314-970 (Brazil); Faria, P. N. de; Mendes, D. R. Jr. [Instituto de Fisica, Universidade Federal Fluminense, Niteroi, RJ, 24210-340 (Brazil); Shorto, J. M. B. [Instituto de Pesquisas Energeticas e Nucleares, IPEN/CNEN, Av. Lineu Prestes, 2242, 05508-000, Sao Paulo, SP (Brazil); Assuncao, M. [Departamento de Ciencias Exatas e da Terra, Universidade Federal de Sao Paulo, Campus Diadema, Sao Paulo (Brazil)

2013-05-06T23:59:59.000Z

327

Dual-cone double-helical downhole logging device  

DOE Patents (OSTI)

A broadband downhole logging device includes a double-helix coil wrapped over a dielectric support and surrounded by a dielectric shield. The device may also include a second coil longitudinally aligned with a first coil and enclosed within the same shield for measuring magnetic permeability of downhole formations and six additional coils for accurately determining downhole parameters.

Yu, Jiunn S. (Albuquerque, NM)

1984-01-01T23:59:59.000Z

328

Double-Sided Cooling Design for Novel Planar Module  

Science Conference Proceedings (OSTI)

A novel packaging structure for medium power modules featuring power semiconductor switches sandwiched between two symmetric substrates that fulfill electrical conduction and insulation functions is presented. Large bonding areas between dies and substrates allow this packaging technology to offer significant improvements in electrical, thermal performance. Double-sided cooling system was dedicatedly analyzed and designed for different applications.

Ning, Puqi [ORNL; Liang, Zhenxian [ORNL; Marlino, Laura D [ORNL; Wang, Fei [ORNL

2013-01-01T23:59:59.000Z

329

Organic thin film transistors with double insulator layers  

Science Conference Proceedings (OSTI)

We have investigated a double-layer structured gate dielectric for the organic thin films transistor (OTFT) with the purpose of improving the performance of the SiO"2 gate insulator. A 50nm PMMA layer was coated on top of the SiO"2 gate insulator as ... Keywords: Mobility, On/off ratio, Organic thin film transistor, PMMA

X. Liu; Y. Bai; L. Chen; F. X. Wei; X. B. Zhang; X. Y. Jiang; Zh. L. Zhang

2007-08-01T23:59:59.000Z

330

Industrial mixing techniques for Hanford double-shell tanks  

Science Conference Proceedings (OSTI)

Jet mixer pumps are currently the baseline technology for sludge mobilization and mixing in one-million gallon double-shell tanks at the Hanford and Savannah River Sites. Improvements to the baseline jet mixer pump technology are sought because jet mixer pumps have moving parts that may fail or require maintenance. Moreover, jet mixers are relatively expensive, they heat the waste, and, in some cases, may not mobilize enough of the sludge. This report documents a thorough literature search for commercially available applicable mixing technologies that could be used for double-shell tank sludge mobilization and mixing. Textbooks, research articles, conference proceedings, mixing experts, and the Thomas Register were consulted to identify applicable technologies. While there are many commercial methods that could be used to mobilize sludge or mix the contents of a one-million gallon tank, few will work given the geometrical constraints (e.g., the mixer must fit through a 1.07-m-diameter riser) or the tank waste properties (e.g., the sludge has such a high yield stress that it generally does not flow under its own weight). Pulsed fluid jets and submersible Flygt mixers have already been identified at Hanford and Savannah River Sites for double-shell tank mixing applications. While these mixing technologies may not be applicable for double-shell tanks that have a thick sludge layer at the bottom (since too many of these mixers would need to be installed to mobilize most of the sludge), they may have applications in tanks that do not have a settled solids layer. Retrieval projects at Hanford and other U.S. Department of Energy sites are currently evaluating the effectiveness of these mixing techniques for tank waste applications. The literature search did not reveal any previously unknown technologies that should be considered for sludge mobilization and mixing in one-million gallon double-shell tanks.

Daymo, E.A.

1997-09-01T23:59:59.000Z

331

Enhancing the DNA Patent Database  

Science Conference Proceedings (OSTI)

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

Walters, LeRoy B.

2008-02-18T23:59:59.000Z

332

DNA-guided nanoparticle assemblies  

DOE Patents (OSTI)

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

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

2013-07-16T23:59:59.000Z

333

Immunoglobulin motif DNA recognition and  

E-Print Network (OSTI)

binding domains of NF-kB, NFAT1, p53 and the STAT proteins. NMR spectroscopy of a 43.6 kD RD­b­DNA ternary for NF-kB3-4, the nuclear factor of acti- vated T-cells NFAT1 (refs 5,6), STAT1 (ref. 7) and STAT3b8 72 and Ser 73. In con- trast, the N-terminus of NF-kB3-4 and NFAT1 (refs 5, 6) loops around

Sali, Andrej

334

Isolation and characterization of Solenopsis invicta virus 3, a new positive-strand RNA virus infecting the red imported fire ant, Solenopsis invicta  

Science Conference Proceedings (OSTI)

We report the discovery of a new virus from the red imported fire ant, Solenopsis invicta. Solenopsis invicta virus 3 (SINV-3) represents the third virus discovered from this ant species using the metagenomics approach. The single (positive)-strand RNA, monopartite, bicistronic genome of SINV-3 was sequenced in entirety (GenBank accession number (FJ528584)), comprised of 10,386 nucleotides, and polyadenylated at the 3' terminus. This genome size was confirmed by Northern analysis. The genome revealed 2 large open reading frames (ORFs) in the sense orientation with an untranslated region (UTR) at each end and between the two ORFs. The 5' proximal ORF (ORF 1) encoded a predicted protein of 299.1 kDa (2580 amino acids). The 3' proximal ORF (ORF 2) encoded a predicted protein of 73.2 kDa (651 amino acids). RNA-dependent RNA polymerase (RdRp), helicase, and protease domains were recognized in ORF 1. SDS-PAGE separation of purified SINV-3 particles yielded 2 bands (ostensibly capsid proteins) with a combined molecular mass of 77.3 kDa which was similar to the mass predicted by ORF 2 (73.2 kDa). Phylogenetic analysis of the conserved amino acid sequences containing domains I to VIII of the RdRp from dicistroviruses, iflaviruses, plant small RNA viruses, picornaviruses, and 4 unassigned positive-strand RNA viruses revealed a trichotomous phenogram with SINV-3 and Kelp fly virus comprising a unique cluster. Electron microscopic examination of negatively stained samples of SINV-3 revealed isometric particles with apparent projections and a diameter of 27.3 +- 1.3 nm. SINV-3 was successfully transmitted to uninfected workers by feeding. The minus (replicative) strand of SINV-3 was detected in worker ants indicating replication of the virus. The possibility of using SINV-3 as a microbial control agent for fire ants is discussed.

Valles, Steven M., E-mail: Steven.Valles@ars.usda.go [Center for Medical, Agricultural and Veterinary Entomology, USDA-ARS, 1600 SW 23rd Drive, Gainesville, FL 32608 (United States); Hashimoto, Yoshifumi [Boyce Thompson Institute for Plant Research at Cornell University, Tower Road, Ithaca, NY 14853 (United States)

2009-06-05T23:59:59.000Z

335

DNA sequencing using fluorescence background electroblotting membrane  

DOE Patents (OSTI)

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

Caldwell, Karin D. (Salt Lake City, UT); Chu, Tun-Jen (Salt Lake City, UT); Pitt, William G. (Orem, UT)

1992-01-01T23:59:59.000Z

336

DNA sequencing using fluorescence background electroblotting membrane  

DOE Patents (OSTI)

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

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

1992-05-12T23:59:59.000Z

337

Precision Biochemistry Tracks DNA Damage in Fish  

Science Conference Proceedings (OSTI)

... Like coal-mine canaries, fish DNA can serve as a measure of the biological impact of water and sediment pollution—or pollution clean-up. ...

2012-10-17T23:59:59.000Z

338

Topics in Forensic DNA Analysis & Interpretation  

Science Conference Proceedings (OSTI)

... Experience • University of Virginia/FBI Laboratory (1992-1995) – Work ... Most forensic DNA laboratories follow PCR ... for the polymer) • If a lab is not ...

2011-03-24T23:59:59.000Z

339

Available Technologies: Highly Selective, Highly Efficient DNA ...  

... applications where extraction of minute amounts of DNA plays a critical role, such as in basic and applied molecular biology research, bioforensics, ...

340

Overview of DNA Programs at NIST  

Science Conference Proceedings (OSTI)

... during the PCR amplification process – This is highly affected by DNA quantity and quality ... PCR inhibitors present in the sample may reduce PCR ...

2013-04-10T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

DNA Directed Assembly Probe for Detecting DNA-Protein Interaction in Microarray Format  

E-Print Network (OSTI)

Quantifying DNA-protein interaction using DNA microarrays are gaining increasing attention due to their ability to profile specificity of interactions in a high-throughput manner. This paper describes a new approach that ...

Ng, Jin Kiat

342

A Simulation of the Separate Climate Effects of Middle-Atmospheric and Tropospheric CO2 Doubling  

Science Conference Proceedings (OSTI)

The separate climate effects of middle-atmospheric and tropospheric CO2 doubling have been simulated and analyzed with the ECHAM middle-atmosphere climate model. To this end, the CO2 concentration has been separately doubled in the middle-...

M. Sigmond; P. C. Siegmund; E. Manzini; H. Kelder

2004-06-01T23:59:59.000Z

343

Climate Change and the Middle Atmosphere. Part I: The Doubled CO2 Climate  

Science Conference Proceedings (OSTI)

The impact of doubled atmospheric CO2 on the climate of the middle atmosphere is investigated using the GISS global climate/middle atmosphere model. In the standard experiment, the CO2 concentration is doubled both in the stratosphere and ...

D. Rind; R. Suozzo; N. K. Balachandran; M. J. Prather

1990-02-01T23:59:59.000Z

344

New Double-Mode and Other RR Lyrae Stars from WASP Data  

E-Print Network (OSTI)

42 RRab, 46 RRc and 7 previously unidentified double-mode RR Lyrae stars were found in the publicly available data of the WASP archive. The Galactic double-mode RR Lyrae stars appear to show a bimodal period distribution.

Wils, Patrick

2010-01-01T23:59:59.000Z

345

Response of the Middle Atmosphere to CO2 Doubling: Results from the Canadian Middle Atmosphere Model  

Science Conference Proceedings (OSTI)

The Canadian Middle Atmosphere Model (CMAM) has been used to examine the middle atmosphere response to CO2 doubling. The radiative-photochemical response induced by doubling CO2 alone and the response produced by changes in prescribed SSTs are ...

V. I. Fomichev; A. I. Jonsson; J. de Grandpré; S. R. Beagley; C. McLandress; K. Semeniuk; T. G. Shepherd

2007-04-01T23:59:59.000Z

346

The H2 Double-Slit Experiment: Where Quantum and Classical Physics...  

NLE Websites -- All DOE Office Websites (Extended Search)

The H2 Double-Slit Experiment: Where Quantum and Classical Physics Meet Print For the first time, an international research team carried out a double-slit experiment in H2, the...

347

Speeding Up the Computation of WRF Double Moment 6-Class Microphysics Scheme with GPU  

Science Conference Proceedings (OSTI)

Weather Research and Forecasting (WRF) Double Moment 6-class (WDM6) microphysics scheme implements a double moment bulk microphysical parameterization of clouds and precipitation and is applicable in mesoscale and general circulation models. WDM6 ...

J. Mielikainen; B. Huang; H.-L. A. Huang; M. D. Goldberg; A. Mehta

348

NERSC's Franklin Supercomputer Upgraded to Double Its Scientific Capability  

NLE Websites -- All DOE Office Websites (Extended Search)

NERSC's Franklin NERSC's Franklin Supercomputer Upgraded to Double Its Scientific Capability NERSC's Franklin Supercomputer Upgraded to Double Its Scientific Capability July 20, 2009 OCEAN EDDIES: This image comes from a computer simulation modeling eddies in the ocean. An interesting feature is the abundance of eddies away from the equator, which is shown in the center of the image at y=0. This research collaboration led by Paola Cessi of the Scripps Institute of Oceanography performed over 15,000 years worth of deep ocean circulation simulations with 1.6 million processor core hours on the upgraded Franklin system. The Department of Energy's (DOE) National Energy Research Scientific Computing (NERSC) Center has officially accepted a series of upgrades to its Cray XT4 supercomputer, providing the facility's 3,000 users with twice

349

WATER-LITHIUM BROMIDE DOUBLE-EFFECT ABSORPTION COOLING ANALYSIS  

Office of Scientific and Technical Information (OSTI)

WATER-LITHIUM BROMIDE DOUBLE-EFFECT WATER-LITHIUM BROMIDE DOUBLE-EFFECT ABSORPTION COOLING ANALYSIS Gary C . V l i e t , Michael B . Lawson, and Rudolf0 A . Lithgow Center f o r Energy Studies The University of Texas a t Austin December 1980 Final Report f o r Contract: DE AC03-79SF10540 (Mu1 tiple-Effect Absorption Cycle Solar Cooling) with the U.S. Department of Energy DISCLAIMER This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency Thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately

350

Double Oak, Texas: Energy Resources | Open Energy Information  

Open Energy Info (EERE)

Double Oak, Texas: Energy Resources Double Oak, Texas: Energy Resources Jump to: navigation, search Equivalent URI DBpedia Coordinates 33.065122°, -97.1105669° Loading map... {"minzoom":false,"mappingservice":"googlemaps3","type":"ROADMAP","zoom":14,"types":["ROADMAP","SATELLITE","HYBRID","TERRAIN"],"geoservice":"google","maxzoom":false,"width":"600px","height":"350px","centre":false,"title":"","label":"","icon":"","visitedicon":"","lines":[],"polygons":[],"circles":[],"rectangles":[],"copycoords":false,"static":false,"wmsoverlay":"","layers":[],"controls":["pan","zoom","type","scale","streetview"],"zoomstyle":"DEFAULT","typestyle":"DEFAULT","autoinfowindows":false,"kml":[],"gkml":[],"fusiontables":[],"resizable":false,"tilt":0,"kmlrezoom":false,"poi":true,"imageoverlays":[],"markercluster":false,"searchmarkers":"","locations":[{"text":"","title":"","link":null,"lat":33.065122,"lon":-97.1105669,"alt":0,"address":"","icon":"","group":"","inlineLabel":"","visitedicon":""}]}

351

Modeling of Sulfate Double-salts in Nuclear Wastes  

Science Conference Proceedings (OSTI)

Due to limited tank space at Hanford and Savannah River, the liquid nuclear wastes or supernatants have been concentrated in evaporators to remove excess water prior to the hot solutions being transferred to underground storage tanks. As the waste solutions cooled, the salts in the waste exceeded the associated solubility limits and precipitated in the form of saltcakes. The initial step in the remediation of these saltcakes is a rehydration process called saltcake dissolution. At Hanford, dissolution experiments have been conducted on small saltcake samples from five tanks. Modeling of these experimental results, using the Environmental Simulation Program (ESP), are being performed at the Diagnostic Instrumentation and Analysis Laboratory (DIAL) at Mississippi State University. The River Protection Project (RPP) at Hanford will use these experimental and theoretical results to determine the amount of water that will be needed for its dissolution and retrieval operations. A comprehensive effort by the RPP and the Tank Focus Area continues to validate and improve the ESP and its databases for this application. The initial effort focused on the sodium, fluoride, and phosphate system due to its role in the formation of pipeline plugs. In FY 1999, an evaluation of the ESP predictions for sodium fluoride, trisodium phosphate dodecahydrate, and natrophosphate clearly indicated that improvements to the Public database of the ESP were needed. One of the improvements identified was double salts. The inability of any equilibrium thermodynamic model to properly account for double salts in the system can result in errors in the predicted solid-liquid equilibria (SLE) of species in the system. The ESP code is evaluated by comparison with experimental data where possible. However, data does not cover the range of component concentrations and temperatures found in many tank wastes. Therefore, comparison of ESP with another code is desirable, and may illuminate problems with both. For this purpose, the SOLGASMIX code was used in conjunction with a small private database developed at ORNL. This code calculates thermodynamic equilibria through minimization of Gibbs Energy, and utilizes the Pitzer model for activity coefficients. The sodium nitrate-sulfate double salt and the sodium fluoride-sulfate double salt were selected for the FY 2000 validation study of ESP. Even though ESP does not include the sulfate-nitrate double salt, this study found that this omission does not appear to be a major consequence. In this case, the solubility predictions with and without the sulfate-nitrate double salt are comparable. In contrast, even though the sulfate-fluoride double salt is included within the ESP databank, comparison to previous experimental results indicates that ESP underestimates solubility. Thus, the prediction for the sulfate-fluoride system needs to be improved. A main consequence of the inability to accurately predict the SLE of double salts is its impact on the predicted ionic strength of the solution. The ionic strength has been observed to be an important factor in the formation of pipeline plugs. To improve the ESP prediction, solubility tests on the sulfate-fluoride system are underway at DIAL, and these experimental results will be incorporated into the Public database by OLI System, Inc. Preliminary ESP simulations also indicated difficulties with the SLE prediction for anhydrous sodium sulfate. The Public database for the ESP does not include fundamental parameters for this solid in mixed solutions below 32.4 C. The limitation, in the range of anhydrous sodium sulfate, leads to convergence problems in ESP and to inaccurate predictions of solubility near the invariant point when sodium sulfate decahydrate and other salts, such as sodium nitrate, were present. These difficulties were partially corrected through the use of an additional database. In conclusion, these results indicate the need for experimental data at temperatures above 25 C and in solutions containing both nitrate and hydroxide. Furthermore, the validation and do

Toghiani, B.

2000-10-30T23:59:59.000Z

352

Hanford double shell tank corrosion monitoring instrument tree prototype  

Science Conference Proceedings (OSTI)

High-level nuclear wastes at the Hanford site are stored underground in carbon steel double-shell and single-shell tanks (DSTs and SSTs). The installation of a prototype corrosion monitoring instrument tree into DST 241-A-101 was completed in December 1995. The instrument tree has the ability to detect and discriminate between uniform corrosion, pitting, and stress corrosion cracking (SCC) through the use of electrochemical noise measurements and a unique stressed element, three-electrode probe. The tree itself is constructed of AISI 304L stainless steel (UNS S30403), with probes in the vapor space, vapor/liquid interface and liquid. Successful development of these trees will allow their application to single shell tanks and the transfer of technology to other US Department of Energy (DOE) sites. Keywords: Hanford, radioactive waste, high-level waste tanks, electrochemical noise, probes, double-shell tanks, single-shell tanks, corrosion.

Nelson, J.L.; Edgemon, G.L.; Ohl, P.C.

1995-11-01T23:59:59.000Z

353

Double Shell Tank (DST) Transfer Piping Subsystem Specification  

Science Conference Proceedings (OSTI)

This specification establishes the performance requirements and provides references to the requisite codes and standards to be applied during design of the Double-Shell Tank (DST) Transfer Piping Subsystem that supports the first phase of Waste Feed Delivery. This specification establishes the performance requirements and provides references to the requisite codes and standards to be applied during design of the Double-Shell Tank (DST) Transfer Piping Subsystem that supports the first phase of waste feed delivery. This subsystem transfers waste between transfer-associated structures (pits) and to the River Protection Project (RPP) Privatization Contractor Facility where it will be processed into an immobilized waste form. This specification is intended to be the basis for new projects/installations (W-521, etc.). This specification is not intended to retroactively affect previously established project design criteria without specific direction by the program.

GRAVES, C.E.

2000-03-22T23:59:59.000Z

354

Dynamic electric fields and double layers in laser-produced plasmas  

SciTech Connect

This paper traces the historical development of electric double layers. Properties of laser produced plasmas are discussed.

Soreq, S.E. (Nuclear Research Center, Plasma Physics Dept., Yavne (IL)); Hora, H. (New South Wales Univ., Kensington (Australia). Dept. of Theoretical Physics)

1989-12-01T23:59:59.000Z

355

Nonperturbative theory of double photoionization of the hydrogen molecule  

DOE Green Energy (OSTI)

We present completely ab initio nonperturbative calculations of the integral and single differential cross sections for double photoionization of H2 for photon energies from 53.9 to 75.7 eV. The method of exterior complex scaling, implemented with B-splines, is used to solve the Schrodinger equation for a correlated continuum wave function corresponding to a single photon having been absorbed by a correlated initial state. The results are in good agreement with experimental integral cross sections.

Vanroose, W.; Martin, F.; Rescigno, T.N.; McCurdy, C.W.

2004-10-01T23:59:59.000Z

356

241-AN Double Shell Tanks (DST) Integrity Assessment Report  

Science Conference Proceedings (OSTI)

This report presents the results of the integrity assessment of the 241-AN double-shell tank farm facility located in the 200 East Area of the Hanford Site. The assessment included the design evaluation and integrity examinations of the tanks and concluded that the facility is adequately designed, is compatible with the waste, and is fit for use. Recommendations including subsequent examinations, are made to ensure the continued safe operation of the tanks.

JENSEN, C.E.

1999-09-21T23:59:59.000Z

357

Double-clad nuclear-fuel safety rod  

DOE Patents (OSTI)

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

McCarthy, W.H.; Atcheson, D.B.

1981-12-30T23:59:59.000Z

358

Interval Translation Maps of three intervals reduce to Double Rotations  

E-Print Network (OSTI)

We show that any interval translation map (ITM) of three intervals can be reduced either to a rotation or a double rotation. As a consequence, the subset of ITMs of finite type in the space of all ITMs of three intervals is open, dense, and full Lebesgue measure. The set of ITMs of infinite type is a Cantor set of zero measure and of Hausdorff dimension less than full.

Volk, Denis

2012-01-01T23:59:59.000Z

359

241-AY Double Shell Tanks (DST) Integrity Assessment Report  

Science Conference Proceedings (OSTI)

This report presents the results of the integrity assessment of the 241-AY double-shell tank farm facility located in the 200 East Area of the Hanford Site. The assessment included the design evaluation and integrity examinations of the tanks and concluded that the facility is adequately designed, is compatible with the waste, and is fit for use. Recommendations including subsequent examinations. are made to ensure the continued safe operation of the tanks.

JENSEN, C.E.

1999-09-21T23:59:59.000Z

360

Period doubling route to chaos in Taylor-Green dynamo  

E-Print Network (OSTI)

We perform spectral simulations of dynamo for magnetic Prandtl number of one with Taylor-Green forcing. We observe dynamo transition through a supercritical pitchfork bifurcation. Beyond the transition, the numerical simulations reveal complex dynamo states with windows of constant, periodic, quasiperiodic, and chaotic magnetic field configurations. For some forcing amplitudes, multiple attractors were obtained for different initial conditions. We show that one of the chaotic windows follows the period-doubling route to chaos.

R. Yadav; M. Chandra; M. K. Verma; S. Paul; P. Wahi

2010-05-09T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


361

The double pulsar -- A new testbed for relativistic gravity  

E-Print Network (OSTI)

The first ever double pulsar, discovered by our team a few months ago, consists of two pulsars, one with period of 22 ms and the other with a period of 2.7 s. This binary system with a period of only 2.4-hr provides a truly unique laboratory for relativistic gravitational physics. In this contribution we summarize the published results and look at the prospects of future observations.

M. Kramer; A. G. Lyne; M. Burgay; A. Possenti; R. N. Manchester; F. Camilo; M. A. McLaughlin; D. R. Lorimer; N. D'Amico; B. C. Joshi; J. Reynolds; P. C. C. Freire

2004-05-10T23:59:59.000Z

362

Double Shell Tank (DST) Process Waste Sampling Subsystem Definition Report  

Science Conference Proceedings (OSTI)

This report defines the Double-Shell Tank (DST) Process Waste Sampling Subsystem (PWSS). This subsystem definition report fully describes and identifies the system boundaries of the PWSS. This definition provides a basis for developing functional, performance, and test requirements (i.e., subsystem specification), as necessary, for the PWSS. The resultant PWSS specification will include the sampling requirements to support the transfer of waste from the DSTs to the Privatization Contractor during Phase 1 of Waste Feed Delivery.

RASMUSSEN, J.H.

2000-04-25T23:59:59.000Z

363

An infant with double trisomy (48,XXX,+18)  

Science Conference Proceedings (OSTI)

The authors report on an infant with double trisomy 48,XXX,+18. She presented with manifestation of trisomy 18: prominent occiput, microphthalmia, small mouth, micrognathia, malformed ears, congenital heart defect, overlapping fingers, talipes equinovarus, and rockerbottom feet. An extra palmar crease was present only on the right hand. This patient was alive at 12 months. The clinical manifestations are compared with those of 10 previously reported cases. 13 refs., 3 figs., 1 tab.

Jaruratanasirikul, S.; Jinorose, U. [Prince of Songkla Univ. (Thailand)

1994-01-15T23:59:59.000Z

364

Retrieval technology development for Hanford double-shell tanks  

SciTech Connect

This paper describes the combined analytical, computational, and experimental program developed for identifying operating strategies for mobilization and retrieval of radioactive waste stored in double-shell tanks at Hanford. Sludge mobilization, slurry uniformity, and slurry retrieval investigations will produce guidelines for mixer pump and retrieval pump operation based on the physical properties of the waste and the geometric properties of the system (number of operating pumps and pump design and placement).

Bamberger, J.A.; Wise, B.M.; Miller, W.C.

1992-05-01T23:59:59.000Z

365

Manipulating Synchronous Optical Signals with a Double $?$ Atomic Ensemble  

E-Print Network (OSTI)

We analyze a double $\\Lambda $ atomic configuration interacting with two signal beams and two control beams. Because of the quantum interference between the two $\\Lambda $ channels, the four fields are phase-matched in electromagnetically induced transparency. Our numerical simulation shows that this system is able to manipulate synchronous optical signals, such as generation of optical twin signals, data correction, signal transfer and amplification in the atomic storage.

Zhuan Li; De-Zhong Cao; Kaige Wang

2004-10-06T23:59:59.000Z

366

Double Hot Springs Geothermal Area | Open Energy Information  

Open Energy Info (EERE)

Double Hot Springs Geothermal Area Double Hot Springs Geothermal Area Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Geothermal Resource Area: Double Hot Springs Geothermal Area Contents 1 Area Overview 2 History and Infrastructure 3 Regulatory and Environmental Issues 4 Exploration History 5 Well Field Description 6 Geology of the Area 7 Geofluid Geochemistry 8 NEPA-Related Analyses (0) 9 Exploration Activities (0) 10 References Loading map... {"minzoom":false,"mappingservice":"googlemaps3","type":"TERRAIN","zoom":6,"types":["ROADMAP","SATELLITE","HYBRID","TERRAIN"],"geoservice":"google","maxzoom":false,"width":"500px","height":"300px","centre":false,"title":"","label":"","icon":"","visitedicon":"","lines":[],"polygons":[],"circles":[],"rectangles":[],"copycoords":false,"static":false,"wmsoverlay":"","layers":[],"controls":["pan","zoom","type","scale","streetview"],"zoomstyle":"DEFAULT","typestyle":"DEFAULT","autoinfowindows":false,"kml":[],"gkml":[],"fusiontables":[],"resizable":false,"tilt":0,"kmlrezoom":false,"poi":true,"imageoverlays":[],"markercluster":false,"searchmarkers":"","locations":[{"text":"","title":"","link":null,"lat":41.048,"lon":-119.0283,"alt":0,"address":"","icon":"","group":"","inlineLabel":"","visitedicon":""}]}

367

Sensitivity of CUORE to Neutrinoless Double-Beta Decay  

SciTech Connect

In this paper, we study the sensitivity of CUORE, a bolometric double-beta decay experiment under construction at the Laboratori Nazionali del Gran Sasso in Italy. Two approaches to the computation of experimental sensitivity are discussed and compared, and the formulas and parameters used in the sensitivity estimates are provided. Assuming a background rate of 10{sup -2} cts/(keV kg y), we find that, after 5 years of live time, CUORE will have a 1#27;{sigma} sensitivity to the neutrinoless double-beta decay half-life of {caret T{sup 0{nu}}{sub 1/2}}(1{sigma}#27;) = 1.6x#2;10{sup 26} y and thus a potential to probe the effective Majorana neutrino mass down to 41-95 meV; the sensitivity at 1.64{sigma}#27;, which corresponds to 90% C.L., will be {caret T{sup 0{nu}}{sub 1/2}(1.64{sigma}#27;}) = 9.5x10{sup 25} y. This range is compared with the claim of observation of neutrinoless double-beta decay in {sup 76}Ge and the preferred range in the neutrino mass parameter space from oscillation results.

CUORE; Alessandria, F.; Andreotti, E.; Ardito, R.; Arnaboldi, C.; Avignone III, F. T.; Balata, M.; Bandac, I.; Banks, T. I.; Bari, G.; Beeman, J.; Bellini, F.; Bersani, A.; Biassoni, M.; Bloxham, T.; Brofferio, C.; Bryant, A.; Bucci, C.; Cai, X. Z.; Canonica, L.; Capelli, S.; Carbone, L.; Cardani, L.; Carrettoni, M.; Casali, N.; Chott, N.; Clemenza, M.; Cosmelli, C.; Cremonesi, O.; Creswick, R. J.; Dafinei, I.; Dally, A.; Biasi, A. De; Decowski, M. P.; Deninno, M. M.; Waard, A. de; Domizio, S. Di; Ejzak, L.; Faccini, R.; Fang, D. Q.; Farach, H. A.; Ferri, E.; Ferroni, F.; Fiorini, E.; Foggetta, L.; Franceschi, M. A.; Freedman, S. J.; Frossati, G.; Fujikawa, B. K.; Giachero, A.; Gironi, L.; Giuliani, A.; Gorla, P.; Gotti, C.; Guardincerri, E.; Gutierrez, T. D.; Haller, E. E.; Han, K.; Heeger, K. M.; Huang, H. Z.; Ichimura, K.; Kadel, R.; Kazkaz, K.; Keppel, G.; Kogler, L.; Kolomensky, Yu. G.; Kraft, S.; Lenz, D.; Li, Y. L.; Liu, X.; Longo, E.; Ma, Y. G.; Maiano, C.; Maier, G.; Maino, M.; Mancini, C.; Martinez, C.; Martinez, M.; Maruyama, R. H.; Moggi, N.; Morganti, S.; Napolitano, T.; Newman, S.; Nisi, S.; Nones, C.; Norman, E. B.; Nucciotti, A.; Orio, F.; Orlandi, D.; Ouellet, J. L.; Pallavicini, M.; Palmieri, V.; Pattavina, L.; Pavan, M.; Pedretti, M.; Pessina, G.; Pirro, S.; Previtali, E.; Rampazzo, V.; Rimondi, F.; Rosenfeld, C.; Rusconi, C.; Salvioni, C.; Sangiorgio, S.; Schaeffer, D.; Scielzo, N. D.; Sisti, M.; Smith, A. R.; Stivanello, F.; Taffarello, L.; Terenziani, G.; Tian, W. D.; Tomei, C.; Trentalange, S.; Ventura, G.; Vignati, M.; Wang, B. S.; Wang, H. W.; Whitten Jr., C. A.; Wise, T.; Woodcraft, A.; Xu, N.; Zanotti, L.; Zarra, C.; Zhu, B. X.; Zucchelli, S.

2011-11-23T23:59:59.000Z

368

The Free Energy of an Electrical Double Layer DEREK Y. C. CHAN AND D. JOHN MITCHELL  

E-Print Network (OSTI)

The Free Energy of an Electrical Double Layer DEREK Y. C. CHAN AND D. JOHN MITCHELL Department for the potential determining ions. The interaction free energy due to the overlap of two double layers has a simple The concept of the free energy of an elec- trical double layer is of considerable impor- tance in colloid

Chan, Derek Y C

369

Electrical characteristics of double stacked Ppy-PVA supercapacitor for powering biomedical MEMS devices  

Science Conference Proceedings (OSTI)

This paper discusses planar and double stacked supercapacitors with interwoven electrodes. Here, we study surface charge densities and capacitance performances of planar and sandwiched double stacked interdigital electrodes MEMS supercapacitors, and ... Keywords: BioMEMS, Double stacked supercapacitor, Polypyrrole (Ppy), Polyvinyl alcohol (PVA)

Hafzaliza Erny Zainal Abidin, Azrul Azlan Hamzah, Burhanuddin Yeop Majlis, Jumril Yunas, Norihan Abdul Hamid, Ummikalsom Abidin

2013-11-01T23:59:59.000Z

370

Reducing transistor count in clocked standard cells with ambipolar double-gate FETs  

Science Conference Proceedings (OSTI)

This paper presents a set of circuit design approaches to achieve clocked standard logic cell functions with ambipolar double-gate devices such as the Double Gate Carbon Nanotube FET (DG-CNTFET). The cells presented in this work use the infield controllability ... Keywords: CNTFETs, advanced technologies, ambipolar double-gate devices, dynamic logic, standard cells

K. Jabeur; D. Navarro; I. O'Connor; P. E. Gaillardon; M. H. Ben Jamaa; F. Clermidy

2010-06-01T23:59:59.000Z

371

Recombinant DNA encoding a desulfurization biocatalyst  

DOE Patents (OSTI)

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

Rambosek, John (Seattle, WA); Piddington, Chris S. (Seattle, WA); Kovacevich, Brian R. (Seattle, WA); Young, Kevin D. (Grand Forks, ND); Denome, Sylvia A. (Thompson, ND)

1994-01-01T23:59:59.000Z

372

Recombinant DNA encoding a desulfurization biocatalyst  

DOE Patents (OSTI)

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

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

1994-10-18T23:59:59.000Z

373

Allosteric Modulation of DNA by Small Molecules  

NLE Websites -- All DOE Office Websites (Extended Search)

Allosteric Modulation of DNA by Small Allosteric Modulation of DNA by Small Molecules Signals originating at the cell surface are conveyed by a complex system of interconnected signaling pathways to the nucleus. They converge at transcription factors, which in turn regulate the transcription of sets of genes that result in the gene expression. Many human diseases are caused by dysregulated gene expression and the oversupply of transcription factors may be required for the growth and metastatic behavior of human cancers. Cell permeable small molecules that can be programmed to disrupt transcription factor-DNA interfaces could silence aberrant gene expression pathways. Pyrrole-imidazole polyamides are DNA minor groove binding small molecules that are programmable for a large repertoire of DNA motifs.

374

Method for sequencing DNA base pairs  

DOE Patents (OSTI)

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

Sessler, A.M.; Dawson, J.

1993-12-14T23:59:59.000Z

375

Improved method for sequencing DNA base pairs  

DOE Patents (OSTI)

The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source. 1 ref.

Sessler, A.M.; Dawson, J.

1990-12-31T23:59:59.000Z

376

Improved method for sequencing DNA base pairs  

DOE Patents (OSTI)

The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source. 1 ref.

Sessler, A.M.; Dawson, J.

1990-01-01T23:59:59.000Z

377

Flow cytometric detection method for DNA samples  

Science Conference Proceedings (OSTI)

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

Nasarabadi,Shanavaz (Livermore, CA); Langlois, Richard G. (Livermore, CA); Venkateswaran, Kodumudi S. (Round Rock, TX)

2011-07-05T23:59:59.000Z

378

Flow cytometric detection method for DNA samples  

DOE Patents (OSTI)

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

Nasarabadi, Shanavaz (Livermore, CA); Langlois, Richard G. (Livermore, CA); Venkateswaran, Kodumudi S. (Livermore, CA)

2006-08-01T23:59:59.000Z

379

Flow cytometric detection method for DNA samples  

DOE Patents (OSTI)

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

Nasarabadi,Shanavaz (Livermore, CA); Langlois, Richard G. (Livermore, CA); Venkateswaran, Kodumudi S. (Round Rock, TX)

2011-07-05T23:59:59.000Z

380

The DNA sequence and biology of human chromosome 19  

SciTech Connect

Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G1C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9 percent of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25 percent of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, a nd segments of coding and non-coding conservation with the distant fish species Takifugu.

Grimwood, Jane; Gordon, Laurie A.; Olsen, Anne; Terry, Astrid; Schmutz, Jeremy; Lamerdin, Jane; Hellsten, Uffe; Goodstein, David; Couronne, Olivier; Tran-Gyamfi, Mary; Aerts, Andrea; Altherr, Michael; Ashworth, Linda; Bajorek, Eva; Black, Stacey; Branscomb, Elbert; Caenepeel, Sean; Carrano, Anthony; Caoile, Chenier; Chan, Yee Man; Christensen, Mari; Cleland, Catherine A.; Copeland, Alex; Dalin, Eileen; Dehal, Paramvir; Denys, Mirian; Detter, John C.; Escobar, Julio; Flowers, Dave; Fotopulos, Dea; Garcia, Carmen; Georgescu, Anca M.; Glavina, Tijana; Gomez, Maria; Gonzales, Eldelyn; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Ho, Issac; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Larionov, Vladimer; Leem, Sun-Hee; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Malfatti, Stephanie; Martinez, Diego; McCready, Paula; Medina, Catherine; Morgan, Jenna; Nelson, Kathryn; Nolan, Matt; Ovcharenko, Ivan; Pitluck, Sam; Pollard, Martin; Popkie, Anthony P.; Predki, Paul; Quan, Glenda; Ramirez, Lucia; Rash, Sam; Retterer, James; Rodriguez, Alex; Rogers, Stephanine; Salamov, Asaf; Salazar, Angelica; She, Xinwei; Smith, Doug; Slezak, Tom; Solovyev, Victor; Thayer, Nina; Tice, Hope; Tsai, Ming; Ustaszewska, Anna; Vo, Nu; Wagner, Mark; Wheeler, Jeremy; Wu, Kevin; Xie, Gary; Yang, Joan; Dubchak, Inna; Furey, Terrence S.; DeJong, Pieter; Dickson, Mark; Gordon, David; Eichler, Evan E.; Pennacchio, Len A.; Richardson, Paul; Stubbs, Lisa; Rokhsar, Daniel S.; Myers, Richard M.; Rubin, Edward M.; Lucas, Susan M.

2003-09-15T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


381

In silico analysis of mycobacteriophage Che12 genome: Characterization of genes required to lysogenise Mycobacterium tuberculosis  

Science Conference Proceedings (OSTI)

Che12 is a temperate Chennai phage infecting Mycobacterium tuberculosis. The nucleotide sequence of the 52,047bp linear double stranded DNA genome has a GC content of 62.9% with 70 putative ORFs identified. Functions are assigned to 24 genes based on ... Keywords: Bioinformatics, Mycobacterium tuberculosis, Temperate mycobacteriophage

N. S. Gomathi; H. Sameer; Vanaja Kumar; S. Balaji; V.N. Azger Dustackeer; P. R. Narayanan

2007-04-01T23:59:59.000Z

382

Property:NEPA DNA Worksheet | Open Energy Information  

Open Energy Info (EERE)

DNA Worksheet DNA Worksheet Jump to: navigation, search Property Name NEPA DNA Worksheet Property Type Page Description DNA Worksheet files for NEPA Docs. This is a property of type Page. It links to pages that use the form NEPA_Doc. Pages using the property "NEPA DNA Worksheet" Showing 19 pages using this property. D DOI-BLM-NV-C010-2011-0517-DNA + DOI-BLM-NV-C010-2011-0517-DNA.pdf + DOI-BLM-NV-C010-2012--044-DNA + DOI-BLM-NV-C010-2012-0044-DNA.pdf + DOI-BLM-NV-C010-2012-0005-DNA + DOI-BLM-NV-C010-2012-0005-DNA.pdf + DOI-BLM-NV-C010-2012-0016-DNA + DOI-BLM-NV-C010-2012-0016-DNA.pdf + DOI-BLM-NV-C010-2012-0019-DNA + DOI-BLM-NV-C010-2012-0019-DNA.pdf + DOI-BLM-NV-C010-2012-0020-DNA + DOI-BLM-NV-C010-2012-0020-DNA.pdf + DOI-BLM-NV-C010-2012-0028-DNA + DOI-BLM-NV-C010-2012-0028-DNA.pdf +

383

Helicase properties of the Escherichia coli UvrAb protein complex  

Science Conference Proceedings (OSTI)

The Escherichia coli UvrA protein has an associated ATPase activity with a turnover number affected by the presence of UvrB protein as well as by DNA. Specifically, the structure of DNA significantly influences the turnover rate of the UvrAB ATPase activity. Double-stranded DNA maximally activates the turnover rate 10-fold whereas single-stranded DNA maximally activates the turnover rate 20-fold, suggesting that the mode of interaction of UvrAB protein with different DNAs is distinctive. We have previously shown that the UvrAB protein complex, driven by the binding energy of ATP, can locally unwind supercoiled DNA. The nature of the DNA unwinding activity and single-stranded DNA activation of ATPase activity suggest potential helicase activity. In the presence of a number of helicase substrates, the UvrAB complex, indeed, manifests a strand-displacement activity-unwinding short duplexes and D-loop DNA, thereby generating component DNA structures. The energy for the activity is derived from ATP or dATP hydrolysis. Unlike the E. coli DnaB, the UvrAB helicase is sensitive to UV-induced photoproducts.

Oh, E.Y.; Grossman, L.

1987-06-01T23:59:59.000Z

384

When DNA Needs to Stand Up and Be Counted  

NLE Websites -- All DOE Office Websites (Extended Search)

When DNA Needs to Stand Up and Be Counted When DNA Needs to Stand Up and Be Counted Print Wednesday, 31 May 2006 00:00 DNA microarrays are small metal, glass, or silicon chips...

385

Nickel (II) Ions Interaction with Polynucleotides and DNA of Different GC Composition  

E-Print Network (OSTI)

The goal of the work was to study the role of GC alternative dimmers in the binding of DNA with Ni (II) ions. The method of ultraviolet difference spectroscopy has been applied to investigate Ni (II) ions interactions with DNA extracted from Clostridium perfringens, Mice liver (C3HA line), Calf thymus, Salmon sperm, Herring sperm, E.coli, Micrococcus luteus and polynucleotides Poly (dA-dT)xPoly (dA-dT), Poly (dG)x Poly (dC), Poly (dG-dC)xPoly (dG-dC). It is shown that Ni (II) ions at outer-spherical binding with DNA double helix from the side of the major groove choose more stable dimmers 3^'-C-G-5^' . . 5^'-G-C-3^' and get bound with N7 atoms of both guanines in dimmer forming G-G interstrand crosslink. It directly correlates to the process of forming point defects of Watson-Crick wrong pair type (creation of rare keto-enolic and amino-imino tautomeric forms) and depurinization.

Bregadze, Vasil G; Melikishvili, Sophie Z; Melikishvili, Zaza G

2009-01-01T23:59:59.000Z

386

NREL: Fleet Test and Evaluation - Fleet DNA: Vehicle Drive Cycle...  

NLE Websites -- All DOE Office Websites (Extended Search)

Fleet DNA Project graphic depicting a trail of data emerging from trucks. Fleet DNA helps vehicle manufacturers and fleet managers understand the broad operational range for many...

387

Low-cost, Rapid DNA Sequencing Technique - Energy Innovation Portal  

Description Sequencing DNA is crucial for future breakthroughs in biological and biomedical research. ... DNA sequencing for medical applications has been restricted ...

388

Computational Challenges in Simulating Large DNA over Long Times  

Science Conference Proceedings (OSTI)

Simulating DNA’s dynamics requires a sophisticated array of algorithms appropriate for DNA’s impressive spectrum of spatial and temporal levels. The authors describe computational challenges

Tamar Schlick; Daniel A. Beard; Jing Huang; Daniel A. Strahs; Xiaoliang Qian

2000-01-01T23:59:59.000Z

389

Method of quantitating dsDNA  

DOE Patents (OSTI)

A method for quantitating dsDNA in an aqueous sample solution containing an unknown amount of dsDNA. A first aqueous test solution containing a known amount of a fluorescent dye-dsDNA complex and at least one fluorescence-attenutating contaminant is prepared. The fluorescence intensity of the test solution is measured. The first test solution is diluted by a known amount to provide a second test solution having a known concentration of dsDNA. The fluorescence intensity of the second test solution is measured. Additional diluted test solutions are similarly prepared until a sufficiently dilute test solution having a known amount of dsDNA is prepared that has a fluorescence intensity that is not attenuated upon further dilution. The value of the maximum absorbance of this solution between 200-900 nanometers (nm), referred to herein as the threshold absorbance, is measured. A sample solution having an unknown amount of dsDNA and an absorbance identical to that of the sufficiently dilute test solution at the same chosen wavelength is prepared. Dye is then added to the sample solution to form the fluorescent dye-dsDNA-complex, after which the fluorescence intensity of the sample solution is measured and the quantity of dsDNA in the sample solution is determined. Once the threshold absorbance of a sample solution obtained from a particular environment has been determined, any similarly prepared sample solution taken from a similar environment and having the same value for the threshold absorbance can be quantified for dsDNA by adding a large excess of dye to the sample solution and measuring its fluorescence intensity.

Stark, Peter C. (Los Alamos, NM); Kuske, Cheryl R. (Los Alamos, NM); Mullen, Kenneth I. (Los Alamos, NM)

2002-01-01T23:59:59.000Z

390

A blue sky catastrophe in double-diffusive convection  

E-Print Network (OSTI)

A global bifurcation of the blue sky catastrophe type has been found in a small Prandtl number binary mixture contained in a laterally heated cavity. The system has been studied numerically applying the tools of bifurcation theory. The catastrophe corresponds to the destruction of an orbit which, for a large range of Rayleigh numbers, is the only stable solution. This orbit is born in a global saddle-loop bifurcation and becomes chaotic in a period doubling cascade just before its disappearance at the blue sky catastrophe.

Esteban Meca; Isabel Mercader; Oriol Batiste; Laureano Ramirez-Piscina

2004-05-27T23:59:59.000Z

391

Container lid gasket protective strip for double door transfer system  

DOE Patents (OSTI)

An apparatus and a process for forming a protective barrier seal along a "ring of concern" of a transfer container used with double door systems is provided. A protective substrate is supplied between a "ring of concern" and a safety cover in which an adhesive layer of the substrate engages the "ring of concern". A compressive foam strip along an opposite side of the substrate engages a safety cover such that a compressive force is maintained between the "ring of concern" and the adhesive layer of the substrate.

Allen, Jr., Burgess M

2013-02-19T23:59:59.000Z

392

Full Counting Statistics of Photons Emitted by Double Quantum Dot  

E-Print Network (OSTI)

We analyze the full counting statistics of photons emitted by a double quantum dot (DQD) to a high-quality microwave transmission line due to the dipole coupling. We show that at the resonant condition between the energy splitting of the DQD and the photon energy in the transmission line, photon statistics exhibits both a sub-Poissonian distribution and antibunching. In the ideal case, when the system decoherence stems only from photodetection, the photon noise is reduced below one-half of the noise for the Poisson distribution. The photon distribution remains sub-Poissonian even at moderate decoherence in the DQD.

Canran Xu; Maxim G. Vavilov

2013-03-27T23:59:59.000Z

393

Double Diffusive Natural Convection in a Nuclear Waste Repository  

Science Conference Proceedings (OSTI)

In this study, we conduct a two-dimensional numerical analysis of double diffusive natural convection in an emplacement drift for a nuclear waste repository. In-drift heat and moisture transport is driven by combined thermal- and compositional-induced buoyancy forces. Numerical results demonstrate buoyancy-driven convective flow patterns and configurations during both repository heat-up and cool-down phases. It is also shown that boundary conditions, particularly on the drip-shield surface, have strong impacts on the in-drift convective flow and transport.

Y. Hao; J. Nitao; T.A. Buscheck; Y. Sun

2006-03-28T23:59:59.000Z

394

Goos-Hanchen like Shifts in Graphene Double Barriers  

E-Print Network (OSTI)

We study the Goos-Hanchen like shifts for Dirac fermions in graphene scattered by double barrier structures. After obtaining the solution for the energy spectrum, we use the boundary conditions to explicitly determine the Goos-Hanchen like shifts and the associated transmission probability. We analyze these two quantities at resonances by studying their {main} characteristics as a function of the energy and electrostatic potential parameters. To check the validity of our computations we recover previous results obtained for a single barrier under appropriate limits.

Ahmed Jellal; Ilham Redouani; Youness Zahidi; Hocine Bahlouli

2013-06-24T23:59:59.000Z

395

Efficient double beta decay nuclear matrix elements computations  

SciTech Connect

We have developed a shell model code for the accurate computation of the two-body matrix elements of the transition operators involved in the neutrinoless double beta decay. This code features coupled cluster method short-range correlations with Jastrow-like functions, finite nucleon size effect and higher order nucleon current corrections. We present the results obtained for {sup 48}Ca and {sup 82}Se, then we compare them with other results in the literature. In the case of {sup 48}Ca, we also study the contributions of the included effects and find good agreement with other published results.

Neacsu, Andrei [Horia Hulubei Foundation (FHH) 407 Atomistilor, Horia Hulubei National Institute for Physics and Nuclear Engineering (IFIN-HH) 30 Reactorului, Magurele-Bucharest 077125 (Romania)

2012-11-20T23:59:59.000Z

396

Parity Doubling and the S Parameter Below the Conformal Window  

E-Print Network (OSTI)

We describe a lattice simulation of the masses and decay constants of the lowest-lying vector and axial resonances, and the electroweak S parameter, in an SU(3) gauge theory with $N_f = 2$ and 6 fermions in the fundamental representation. The spectrum becomes more parity doubled and the S parameter per electroweak doublet decreases when $N_f$ is increased from 2 to 6, motivating study of these trends as $N_f$ is increased further, toward the critical value for transition from confinement to infrared conformality.

Thomas Appelquist; Ron Babich; Richard C. Brower; Michael Cheng; Michael A. Clark; Saul D. Cohen; George T. Fleming; Joe Kiskis; Meifeng Lin; Ethan T. Neil; James C. Osborn; Claudio Rebbi; David Schaich; Pavlos Vranas

2010-09-29T23:59:59.000Z

397

Resonance enhancement of nonsequential double ionization by a magnetic field  

Science Conference Proceedings (OSTI)

We investigate nonsequential double ionization (NSDI) of helium by using an additional magnetic field parallel to the polarization of the laser pulse. By exploring the ability of a magnetic field for focusing the selected trajectories that contribute to the NSDI, we have found that the yield of NSDI, as a function of the magnetic-field strength, shows different behavior for different laser intensities. As a result, an additional magnetic field provides a way to identify that the NSDI mechanism of laser-assisted collision ionization begins to play an important role as the laser intensity increases.

Li Hongyun [Department of Physics, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Peking University, Beijing 100871 (China); Laboratory of Optical Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Chen Jing; Liu Jie [Center for Nonlinear Studies, Institute of Applied Physics and Computational Mathematics, Beijing 100088 (China); Jiang Hongbing; Gong Qihuang [Department of Physics, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Peking University, Beijing 100871 (China); Fu Panming; Wang Bingbing [Laboratory of Optical Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Yan Zongchao [Department of Physics, University of New Brunswick, Fredericton, New Brunswick, E3B 5A3 (Canada)

2011-01-15T23:59:59.000Z

398

Structural basis for DNA bending  

Science Conference Proceedings (OSTI)

The authors report proton NMR studies on DNA oligonucleotides that contain A tracts of lengths known to produce various degrees of bending. Spectra of duplexes in the series 5{prime}-(GGCA{sub n}CGG){center dot}(CCGT{sub n}GCC) (n = 3,4,5,7,9) reveal substantial structural changes within the A{sub n}{center dot}T{sub n} tract as its length is increased. Chemical-shift comparisons show that A tracts with fewer than about seven members do not contain regions of uniform structure. Throughout the series, there is a striking monotonic relationship between the location of an A{center dot}T pair in the A tract and the relative position of its ThyH3 resonance. The direction of this chemical-shift dispersion is opposite to that expected from consideration of ring-current effects alone. This model features a substantial negative base-pair tilt, which has been suggested previously as the source of A-tract bending. In contrast, the nuclear Overhauser effect distances are inconsistent with at least one known crystallographic A-tract structure which lacks appreciable base-pair tilt.

Nadeau, J.G.; Crothers, D.M. (Yale Univ., New Haven, CT (USA))

1989-04-01T23:59:59.000Z

399

Torque determination on DNA with magnetic tweezers  

E-Print Network (OSTI)

We deduced the torque applied on a single stretched and twisted DNA by integrating with respect to force the change in the molecule's extension as it is coiled. While consistent with previous direct measurements of the torque at high forces (F>1 pN) this method, which is simple and does not require a sophisticated set-up, allows for lower force estimates. We used this approach to deduce the effective torsional modulus of DNA, which decreases with force and to estimate the buckling torque of DNA as a function of force in various salt conditions.

Francesco Mosconi; Jean-François Allemand; David Bensimon; Vincent Croquette

2008-09-03T23:59:59.000Z

400

The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome  

Science Conference Proceedings (OSTI)

XPG is a structure-specific endonuclease required for nucleotide excision repair (NER). XPG incision defects result in the cancer-prone syndrome xeroderma pigmentosum, whereas truncating mutations of XPG cause the severe postnatal progeroid developmental disorder Cockayne syndrome. We show that XPG interacts directly with WRN protein, which is defective in the premature aging disorder Werner syndrome, and that the two proteins undergo similar sub-nuclear redistribution in S-phase and co-localize in nuclear foci. The co-localization was observed in mid- to late-S-phase, when WRN moves from nucleoli to nuclear foci that have been shown to contain protein markers of both stalled replication forks and telomeric proteins. We mapped the interaction between XPG and WRN to the C-terminal domains of each and show that interaction with the C-terminal domain of XPG strongly stimulates WRN helicase activity. WRN also possesses a competing DNA single-strand annealing activity that, combined with unwinding, has been shown to coordinate regression of model replication forks to form Holliday junction/chicken foot intermediate structures. We tested whether XPG stimulated WRN annealing activity and found that XPG itself has intrinsic strand annealing activity that requires the unstructured R- and C-terminal domains, but not the conserved catalytic core or endonuclease activity. Annealing by XPG is cooperative, rather than additive, with WRN annealing. Taken together, our results suggest a novel function for XPG in S-phase that is at least in part carried out coordinately with WRN, and which may contribute to the severity of the phenotypes that occur upon loss of XPG.

Trego, Kelly S.; Chernikova, Sophia B.; Davalos, Albert R.; Perry, J. Jefferson P.; Finger, L. David; Ng, Cliff; Tsai, Miaw-Sheue; Yannone, Steven M.; Tainer, John A.; Campisi, Judith; Cooper, Priscilla K.

2011-04-20T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


401

DOUBLE-LINED SPECTROSCOPIC BINARY STARS IN THE RAVE SURVEY  

Science Conference Proceedings (OSTI)

We devise a new method for the detection of double-lined binary stars in a sample of the Radial Velocity Experiment (RAVE) survey spectra. The method is both tested against extensive simulations based on synthetic spectra and compared to direct visual inspection of all RAVE spectra. It is based on the properties and shape of the cross-correlation function, and is able to recover {approx}80% of all binaries with an orbital period of order 1 day. Systems with periods up to 1 yr are still within the detection reach. We have applied the method to 25,850 spectra of the RAVE second data release and found 123 double-lined binary candidates, only eight of which are already marked as binaries in the SIMBAD database. Among the candidates, there are seven that show spectral features consistent with the RS CVn type (solar type with active chromosphere) and seven that might be of W UMa type (over-contact binaries). One star, HD 101167, seems to be a triple system composed of three nearly identical G-type dwarfs. The tested classification method could also be applicable to the data of the upcoming Gaia mission.

Matijevic, G.; Zwitter, T. [Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana (Slovenia); Munari, U.; Siviero, A. [INAF Osservatorio Astronomico di Padova, Asiago (Italy); Bienayme, O.; Siebert, A. [Observatorie de Strasbourg, Strasbourg (France); Binney, J. [Rudolf Pierls Center for Theoretical Physics, University of Oxford, Oxford (United Kingdom); Bland-Hawthorn, J. [Sydney Institute for Astronomy, School of Physics, University of Sydney, Sydney (Australia); Boeche, C.; Steinmetz, M. [Astrophysikalisches Institut Potsdam, Potsdam (Germany); Campbell, R. [Western Kentucky University, Bowling Green, KY (United States); Freeman, K. C. [RSAA, Australian National University, Camberra (Australia); Gibson, B. [University of Central Lancashire, Preston (United Kingdom); Gilmore, G. [Institute of Astronomy, Cambridge (United Kingdom); Grebel, E. K. [Astronomisches Rechen-Institut, Zentrum fuer Astronomie der Universitaet Heidelberg, Heidelberg (Germany); Helmi, A. [Kapteyn Astronomical Institute, University of Groningen, Groningen (Netherlands); Navarro, J. F. [University of Victoria, Victoria (Canada); Parker, Q. A. [Macquarie University, Sydney (Australia); Seabroke, G. M. [e2v Centre for Electronic Imaging, Planetary and Space Sciences Research Institute, Open University, Walton Hall, Milton Keynes (United Kingdom); Watson, F. G., E-mail: gal.matijevic@fmf.uni-lj.s [Anglo-Australian Observatory, Sydney (Australia)

2010-07-15T23:59:59.000Z

402

SUPPRESSION OF ENERGETIC ELECTRON TRANSPORT IN FLARES BY DOUBLE LAYERS  

SciTech Connect

During flares and coronal mass ejections, energetic electrons from coronal sources typically have very long lifetimes compared to the transit times across the systems, suggesting confinement in the source region. Particle-in-cell simulations are carried out to explore the mechanisms of energetic electron transport from the corona to the chromosphere and possible confinement. We set up an initial system of pre-accelerated hot electrons in contact with ambient cold electrons along the local magnetic field and let it evolve over time. Suppression of transport by a nonlinear, highly localized electrostatic electric field (in the form of a double layer) is observed after a short phase of free-streaming by hot electrons. The double layer (DL) emerges at the contact of the two electron populations. It is driven by an ion-electron streaming instability due to the drift of the back-streaming return current electrons interacting with the ions. The DL grows over time and supports a significant drop in temperature and hence reduces heat flux between the two regions that is sustained for the duration of the simulation. This study shows that transport suppression begins when the energetic electrons start to propagate away from a coronal acceleration site. It also implies confinement of energetic electrons with kinetic energies less than the electrostatic energy of the DL for the DL lifetime, which is much longer than the electron transit time through the source region.

Li, T. C.; Drake, J. F.; Swisdak, M. [Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, MD 20742 (United States)

2012-09-20T23:59:59.000Z

403

Double Shell Tank (DST) Monitor and Control Subsystem Specification  

Science Conference Proceedings (OSTI)

This specification establishes the performance requirements and provides references to the requisite codes and standards to be applied during design of the Double-Shell Tank (DST) Monitor and Control Subsystem that supports the first phase of Waste Feed Delivery. This subsystem specification establishes the interface and performance requirements and provides references to the requisite codes and standards to be applied during the design of the Double-Shell Tank (DST) Monitor and Control Subsystem. The DST Monitor and Control Subsystem consists of the new and existing equipment that will be used to provide tank farm operators with integrated local monitoring and control of the DST systems to support Waste Feed Delivery (WFD). New equipment will provide automatic control and safety interlocks where required and provide operators with visibility into the status of DST subsystem operations (e.g., DST mixer pump operation and DST waste transfers) and the ability to manually control specified DST functions as necessary. This specification is intended to be the basis for new project/installations (W-521, etc.). This specification is not intended to retroactively affect previously established project design criteria without specific direction by the program.

BAFUS, R.R.

2000-04-27T23:59:59.000Z

404

Double Shell Tank (DST) Transfer Valving Subsystem Specification  

Science Conference Proceedings (OSTI)

This specification establishes the performance requirements and provides references to the requisite codes and standards to be applied during design of the Double-Shell Tank (DST) Transfer Valving Subsystem that supports the first phase of Waste Feed Delivery. This specification establishes the performance requirements and provides references to the requisite codes and standards to be applied during design of the Double-Shell Tank (DST) Transfer Valving Subsystem that supports the first phase of Waste Feed Delivery (WFD). The DST Transfer Valving Subsystem routes waste and other media (e.g., diluent, flush water, filtered raw water) among DSTs and from the low-activity waste (LAW) and high-level waste (HLW) feed staging tanks to the River Protection Project (RPP) Privatization Contractor facility, where it will be processed into an immobilized waste form. This specification is intended to be the basis for new projects/installations (W-521, etc.). This specification is not intended to retroactively affect previously established project design criteria without specific direction by the program.

GRAVES, C.E.

2000-03-22T23:59:59.000Z

405

Biodiesel synthesis using calcined layered double hydroxide catalysts  

SciTech Connect

The catalytic properties of calcined Li-Al, Mg-Al and Mg-Fe layered double hydroxides (LDHs) were examined in two transesterification reactions, namely, the reaction of glyceryl tributyrate with methanol, and the reaction of soybean oil with methanol. While the Li-Al catalysts showed high activity in these reactions at the reflux temperature of methanol, the Mg-Fe and Mg-Al catalysts exhibited much lower methyl ester yields. CO2 TPD measurements revealed the presence of sites of weak, medium and strong basicity on both Mg-Al and Li-Al catalysts, the latter showing higher concentrations of medium and strong base sites; by implication, these are the main sites active in transesterification catalyzed by calcined Li-Al LDHs. Maximum activity was observed for the Li-Al catalysts when a calcination temperature of 450-500 aC was applied, corresponding to decomposition of the layered double hydroxide to the mixed oxide without formation of crystalline lithium aluminate phases.

Schumaker, J. Link [University of Kentucky; Crofcheck, Czarena [University of Kentucky; TAckett, S. Adam [University of Kentucky; Santillan-Jimenez, Eduardo [University of Kentucky; Morgan, Tonya [University of Kentucky; Ji, Yaying [University of Kentucky; Crocker, Mark [University of Kentucky; Toops, Todd J [ORNL

2008-01-01T23:59:59.000Z

406

Hazard assessments of double-shell flammable gas tanks  

DOE Green Energy (OSTI)

This report is the fourth in a series of hazard assessments performed on the double-shell flammable gas watch list tanks. This report focuses on hazards associated with the double-shell watch list tanks (101-AW, 103-AN, 104-AN, and 105-AN). While a similar assessment has already been performed for tank 103-SY, it is also included here to incorporate a more representative slurry gas mixture and provide a consistent basis for comparing results for all the flammable gas tanks. This report is intended to provide an in-depth assessment by considering the details of the gas release event and slurry gas mixing as the gas is released from the waste. The consequences of postulated gas ignition are evaluated using a plume burn model and updated ignition frequency predictions. Tank pressurization which results from a gas burn, along with the structural response, is also considered. The report is intended to support the safety basis for work activities in flammable gas tanks by showing margins to safety limits that are available in the design and procedures.

Fox, G.L.; Stepnewski, D.D.

1994-09-28T23:59:59.000Z

407

Effects of a static electric field on nonsequential double ionization  

SciTech Connect

Using a three-dimensional semiclassical method, we perform a systematic analysis of the effects of an additional static electric field on nonsequential double ionization (NSDI) of a helium atom in an intense, linearly polarized laser field. It is found that the static electric field influences not only the ionization rate, but also the kinetic energy of the ionized electron returning to the parent ion, in such a way that, if the rate is increased, then the kinetic energy of the first returning electron is decreased, and vice versa. These two effects compete in NSDI. Since the effect of the static electric field on the ionization of the first electron plays a more crucial role in the competition, the symmetric double-peak structure of the He{sup 2+} momentum distribution parallel to the polarization of the laser field is destroyed. Furthermore, the contribution of the trajectories with multiple recollisions to the NSDI is also changed dramatically by the static electric field. As the static electric field increases, the trajectories with two recollisions, which start at the time when the laser and the static electric field are in the same direction, become increasingly important for the NSDI.

Li Hongyun [Laboratory of Optical Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080 (China); Department of Physics, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Peking University, Beijing 100871 (China); Wang Bingbing; Li Xiaofeng; Fu Panming [Laboratory of Optical Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080 (China); Chen Jing; Liu Jie [Center for Nonlinear Studies, Institute of Applied Physics and Computational Mathematics, Beijing 100088 (China); Jiang Hongbing; Gong Qihuang [Department of Physics, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Peking University, Beijing 100871 (China); Yan Zongchao [Department of Physics, University of New Brunswick, P.O. Box 4400, Fredericton, New Brunswick, E3B 5A3 (Canada); Research Academy of Science and Technology, Harbin Institute of Technology, Harbin 150001 (China)

2007-09-15T23:59:59.000Z

408

Double-core excitations in formamide can be probed by X-ray double-quantum-coherence spectroscopy  

Science Conference Proceedings (OSTI)

The attosecond, time-resolved X-ray double-quantum-coherence four-wave mixing signals of formamide at the nitrogen and oxygen K-edges are simulated using restricted excitation window time-dependent density functional theory and the excited core hole approximation. These signals, induced by core exciton coupling, are particularly sensitive to the level of treatment of electron correlation, thus providing direct experimental signatures of electron and core-hole many-body effects and a test of electronic structure theories.

Zhang Yu; Healion, Daniel; Biggs, Jason D.; Mukamel, Shaul [Department of Chemistry, University of California, 450 Rowland Hall, Irvine, California 92697 (United States)

2013-04-14T23:59:59.000Z

409

Deoxyribose oxidation chemistry and endogenous DNA adducts  

E-Print Network (OSTI)

Endogenous and exogenous oxidants react with cellular macromolecules to generate a variety of electrophiles that react with DNA produce cytotoxic and mutagenic adducts. One source of such electrophiles is deoxyribose in ...

Zhou, Xinfeng

2006-01-01T23:59:59.000Z

410

Linear Thermodynamics of Rodlike DNA Filtration  

E-Print Network (OSTI)

Linear thermodynamics transportation theory is employed to study filtration of rodlike DNA molecules. Using the repeated nanoarray consisting of alternate deep and shallow regions, it is demonstrated that the complex ...

Li, Zirui

411

Multiple tag labeling method for DNA sequencing  

DOE Patents (OSTI)

A DNA sequencing method described which uses single lane or channel electrophoresis. Sequencing fragments are separated in said lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radio-isotope labels.

Mathies, Richard A. (Contra Costa County, CA); Huang, Xiaohua C. (Mt. View, CA); Quesada, Mark A. (San Francisco, CA)

1995-01-01T23:59:59.000Z

412

Oligonucleotide and Long Polymeric DNA Encoding  

Science Conference Proceedings (OSTI)

This report summarizes the work done at Lawrence Livermore National Laboratory for the Oligonucleotide and Long Polymeric DNA Encoding project, part of the Microelectronic Bioprocesses Program at DARPA. The goal of the project was to develop a process by which long (circa 10,000 base-pair) synthetic DNA molecules could be synthesized in a timely and economic manner. During construction of the long molecule, errors in DNA sequence occur during hybridization and/or the subsequent enzymatic process. The work done on this project has resulted in a novel synthesis scheme that we call the parallel pyramid synthesis protocol, the development of a suit of computational tools to minimize and quantify errors in the synthesized DNA sequence, and experimental proof of this technique. The modeling consists of three interrelated modules: the bioinformatics code which determines the specifics of parallel pyramid synthesis for a given chain of long DNA, the thermodynamics code which tracks the products of DNA hybridization and polymerase extension during the later steps in the process, and the kinetics model which examines the temporal and spatial processes during one thermocycle. Most importantly, we conducted the first successful syntheses of a gene using small starting oligomers (tetramers). The synthesized sequence, 813 base pairs long, contained a 725 base pair gene, modified green fluorescent protein (mGFP), which has been shown to be a functional gene by cloning into cells and observing its green fluorescent product.

Miller, E; Mariella Jr., R P; Christian, A T; Gardner, S N; Williams, J M

2003-11-24T23:59:59.000Z

413

Everything a Trial Judge Needs to Know about DNA (in a ...  

Science Conference Proceedings (OSTI)

... evidence • Paternity testing -- identifying father • Missing persons investigations • Military DNA “dog tag” • Convicted felon DNA databases ...

2013-06-25T23:59:59.000Z

414

Folding of a DNA Hairpin Loop Structure in Explicit Solvent Using Replica-Exchange Molecular Dynamics Simulations.  

DOE Green Energy (OSTI)

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Hairpin loop structures are common motifs in folded nucleic acids. The 59-GCGCAGC sequence in DNA forms a characteristic and stable trinucleotide hairpin loop flanked by a two basepair stem helix. To better understand the structure formation of this hairpin loop motif in atomic detail, we employed replica-exchange molecular dynamics (RexMD) simulations starting from a single-stranded DNA conformation. In two independent 36 ns RexMD simulations, conformations in very close agreement with the experimental hairpin structure were sampled as dominant conformations (lowest free energy state) during the final phase of the RexMDs (;35% at the lowest temperature replica). Simultaneous compaction and accumulation of folded structures were observed. Comparison of the GCA trinucleotides from early stages of the simulations with the folded topology indicated a variety of central loop conformations, but arrangements close to experiment that are sampled before the fully folded structure also appeared. Most of these intermediates included a stacking of the C2 and G3 bases, which was further stabilized by hydrogen bonding to the A5 base and a strongly bound water molecule bridging the C2 and A5 in the DNA minor groove. The simulations suggest a folding mechanism where these intermediates can rapidly proceed toward the fully folded hairpin and emphasize the importance of loop and stem nucleotide interactions for hairpin folding. In one simulation, a loop motif with G3 in syn conformation (dihedral flip at N-glycosidic bond) accumulated, resulting in a misfolded hairpin. Such conformations may correspond to long-lived trapped states that have been postulated to account for the folding kinetics of nucleic acid hairpins that are slower than expected for a semiflexible polymer of the same size.

Kannan, Srinivasaraghavan; Zacharias, Martin W.

2007-11-01T23:59:59.000Z

415

Classical two-split interference effects in double photoionization of molecular hydrogen at high energies  

DOE Green Energy (OSTI)

The authors report a thorough theoretical study of one photon double ionization of H{sub 2}. They suggest that interference effects reported in one photon ionization will be reproducible in the case of double ionization when one of the photons carriers most of the available energy and the other electron is not observed. These calculations reproduce recent double photoionization experiments of H{sub 2}.

Horner, Daniel A [Los Alamos National Laboratory; Miyabe, S [LBNL; Rescigno, T N [LBNL; Mccurdy, C W [LBNL; Morales, F [MADRID, SPAIN; Martin, F [MADRID, SPAIN

2009-01-01T23:59:59.000Z

416

A Quantitative Tool for Producing DNA-Based Diagnostic Arrays  

SciTech Connect

The purpose of this project was to develop a precise, quantitative method to analyze oligodeoxynucleotides (ODNs) on an array to enable a systematic approach to quality control issues affecting DNA microarrays. Two types of ODN's were tested; ODN's formed by photolithography and ODN's printed onto microarrays. Initial work in Phase I, performed in conjunction with Affymetrix, Inc. who has a patent on a photolithographic in situ technique for creating DNA arrays, was very promising but did seem to indicate that the atomization process was not complete. Soon after Phase II work was under way, Affymetrix had further developed fluorescent methods and indicated they were no longer interested in our resonance ionization technique. This was communicated to the program manager and it was decided that the project would continue and be focused on printed ODNs. The method being tested is called SIRIS, Sputter-Initiated Resonance Ionization Spectroscopy. SIRIS has been shown to be a highly sensitive, selective, and quantitative tool for atomic species. This project was aimed at determining if an ODN could be labeled in such a way that SIRIS could be used to measure the label and thus provide quantitative measurements of the ODN on an array. One of the largest problems in this study has been developing a method that allows us to know the amount of an ODN on a surface independent of the SIRIS measurement. Even though we could accurately determine the amount of ODN deposited on a surface, the amount that actually attached to the surface is very difficult to measure (hence the need for a quantitative tool). A double-labeling procedure was developed in which 33P and Pt were both used to label ODNs. The radioactive 33P could be measured by a proportional counter that maps the counts in one dimension. This gave a good measurement of the amount of ODN remaining on a surface after immobilization and washing. A second label, Pt, was attached to guanine nucleotides in the ODN. Studies were conducted using this technique and comparing the results of the radioactive label vs SIRIS measurements of Pt as a function of ODN length and distance of the Pt label from the attachment end. The SIRIS signal was not proportional to the amount of oligo attached to the surface as determined by the decay of the 33P label. We intentionally tested conditions under which one might expect the atomization efficiency to change and we believe this is the problem. Different lengths of oligos, and different placement of the label in the oligo affected the final signal. This obviously makes use of SIRIS as a quantitative tool for oligonucleotides problematic except under highly controlled situations.

Tom J. Whitaker

2008-07-11T23:59:59.000Z

417

A New Design for Double Edge Triggered Flip-flops  

E-Print Network (OSTI)

The logic construction of a double-edge-triggered (DET) flip-flop, which can receive input signal at two levels of the clock, is analyzed and a new circuit design of CMOS DET flip-flop is proposed. Simulation using SPICE and a 1 micron technology shows that this DET flip-flop has ideal logic functionality, a simpler structure, lower delay time and higher maximum data rate compared to other existing CMOS DET flipflops. By simulating and comparing the proposed DET flip-flop with the traditional single-edge-triggered (SET) flip-flop, it is shown that the proposed DET flip-flop reduces power dissipation by half while keeping the same date rate.

Massoud Pedram; Qing Wu; Xunwei Wu

1998-01-01T23:59:59.000Z

418

Double-ended ceramic helical-rotor expander  

DOE Patents (OSTI)

A ceramic helical rotor expander using a double-ended or tandem herringbone type rotor arrangement with bearing and seal assemblies remote from the hot gas inlets and especially capable of operating at an inlet temperature of above 1100.degree. C. The rotors are solid or hollow and bonded to hollow metal shafts, and mounted in a composite or simple prismatic casing. The rotors, casing and shafts are constructed from low expansivity materials. In the preferred embodiment the rotors are constructed of silicon nitride and the shafts constructed of an molybdenum alloy, with the metal shafts being supported in bearings and secured to synchronizing gears. The rotors and casing may be provided with coolant channels therein, and are constructed to eliminate the problem of end leakages at inlet temperature and pressure, and the need for high temperature bearings and seals.

Mohr, Peter B. (Livermore, CA); Myers, Wendell B. (Livermore, CA)

1995-01-01T23:59:59.000Z

419

Minimally doubled fermions at one-loop level  

E-Print Network (OSTI)

Single fermionic degrees of freedom together with standard chiral symmetry at finite lattice spacing, correct continuum limit and local interactions only are precluded by the Nielsen-Ninomiya no-go theorem. The class of minimally doubled fermion actions exhibits exactly two chiral modes. Recent interest in these actions has been sparked by the investigation of fermionic actions defined on "hyperdiamond" lattices. Due to the necessity of breaking hypercubic symmetry explicitly, radiative corrections generate operator mixings with relevant and marginal operators that should vanish in continuum QCD. These cannot be avoided and must be taken into account in particular by a peculiar wave-function renormalisation and additive momentum renormalisation. Renormalisation properties at one-loop level of the self-energy, local bilinears and conserved vector and axial-vector currents are presented for Borici-Creutz and Karsten-Wilczek actions. Distinct differences and similarities between both actions are elucidated.

Capitani, Stefano; Wittig, Hartmut

2009-01-01T23:59:59.000Z

420

Full Counting Statistics of Photons Emitted by Double Quantum Dot  

E-Print Network (OSTI)

We analyze the full counting statistics of photons emitted by a double quantum dot (DQD) coupled to a high-quality microwave resonator by electric dipole interaction. We show that at the resonant condition between the energy splitting of the DQD and the photon energy in the resonator, photon statistics exhibits both a sub-Poissonian distribution and antibunching. In the ideal case, when the system decoherence stems only from photodetection, the photon noise is reduced below one-half of the noise for the Poisson distribution and is consistent with current noise. The photon distribution remains sub-Poissonian even at moderate decoherence in the DQD. We demonstrate that Josephson junction based photomultipliers can be used to experimentally assess statistics of emitted photons.

Canran Xu; Maxim G. Vavilov

2013-03-27T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


421

Reactor electron antineutrino disappearance in the Double Chooz experiment  

E-Print Network (OSTI)

The Double Chooz experiment has observed 8,249 candidate electron antineutrino events in 227.93 live days with 33.71 GW-ton-years (reactor power x detector mass x livetime) exposure using a 10.3 cubic meter fiducial volume detector located at 1050 m from the reactor cores of the Chooz nuclear power plant in France. The expectation in case of theta13 = 0 is 8,937 events. The deficit is interpreted as evidence of electron antineutrino disappearance. From a rate plus spectral shape analysis we find sin^2 2{\\theta}13 = 0.109 \\pm 0.030(stat) \\pm 0.025(syst). The data exclude the no-oscillation hypothesis at 99.9% CL (3.1{\\sigma}).

Abe, Y; Anjos, J C dos; Barriere, J C; Bergevin, M; Bernstein, A; Bezerra, T J C; Bezrukhov, L; Blucher, E; Bowden, N S; Buck, C; Busenitz, J; Cabrera, A; Caden, E; Camilleri, L; Carr, R; Cerrada, M; Chang, P -J; Chimenti, P; Classen, T; Collin, A P; Conover, E; Conrad, J M; Crespo-Anadón, J I; Crum, K; Cucoanes, A; D'Agostino, M V; Damon, E; Dawson, J V; Dazeley, S; Dietrich, D; Djurcic, Z; Dracos, M; Durand, V; Ebert, J; Efremenko, Y; Elnimr, M; Etenko, A; Fallot, M; Fechner, M; von Feilitzsch, F; Felde, J; Franco, D; Franke, A J; Franke, M; Furuta, H; Gama, R; Gil-Botella, I; Giot, L; Goger-Neff, M; Gonzalez, L F G; Goodman, M C; Goon, J TM; Greiner, D; Haag, N; Hagner, C; Hara, T; Hartmann, F X; Haser, J; Hatzikoutelis, A; Hayakawa, T; Hofmann, M; Horton-Smith, G A; Hourlier, A; Ishitsuka, M; Jochum, J; Jollet, C; Jones, C L; Kaether, F; Kalousis, L N; Kamyshkov, Y; Kaplan, D M; Kawasaki, T; Keefer, G; Kemp, E; de Kerret, H; Kibe, Y; Konno, T; Kryn, D; Kuze, M; Lachenmaier, T; Lane, C E; Langbrandtner, C; Lasserre, T; Letourneau, A; Lhuillier, D; Lima, H P; Lindner, M; López-Castanõ, J M; LoSecco, J M; Lubsandorzhiev, B K; Lucht, S; McKee, D; Maeda, J; Maesano, C N; Mariani, C; Maricic, J; Martino, J; Matsubara, T; Mention, G; Meregaglia, A; Miletic, T; Milincic, R; Miyata, H; Mueller, Th A; Nagasaka, Y; Nakajima, K; Novella, P; Obolensky, M; Oberauer, L; Onillon, A; Osborn, A; Ostrovskiy, I; Palomares, C; Pepe, I M; Perasso, S; Perrin, P; Pfahler, P; Porta, A; Potzel, W; Reichenbacher, J; Reinhold, B; Remoto, A; Rohling, M; Roncin, R; Roth, S; Sakamoto, Y; Santorelli, R; Sato, F; Schonert, S; Schoppmann, S; Schwetz, T; Shaevitz, M H; Shimojima, S; Shrestha, D; Sida, J-L; Sinev, V; Skorokhvatov, M; Smith, E; Spitz, J; Stahl, A; Stancu, I; Stokes, L F F; Strait, M; Stuken, A; Suekane, F; Sukhotin, S; Sumiyoshi, T; Sun, Y; Svoboda, R; Terao, K; Tonazzo, A; Toups, M; Thi, H H Trinh; Valdiviesso, G; Veyssiere, C; Wagner, S; Watanabe, H; White, B; Wiebusch, C; Winslow, L; Worcester, M; Wurm, M; Yermia, F; Zimmer, V

2012-01-01T23:59:59.000Z

422

Reactor electron antineutrino disappearance in the Double Chooz experiment  

E-Print Network (OSTI)

The Double Chooz experiment has observed 8,249 candidate electron antineutrino events in 227.93 live days with 33.71 GW-ton-years (reactor power x detector mass x livetime) exposure using a 10.3 cubic meter fiducial volume detector located at 1050 m from the reactor cores of the Chooz nuclear power plant in France. The expectation in case of theta13 = 0 is 8,937 events. The deficit is interpreted as evidence of electron antineutrino disappearance. From a rate plus spectral shape analysis we find sin^2 2{\\theta}13 = 0.109 \\pm 0.030(stat) \\pm 0.025(syst). The data exclude the no-oscillation hypothesis at 99.8% CL (2.9{\\sigma}).

Y. Abe; C. Aberle; J. C. dos Anjos; J. C. Barriere; M. Bergevin; A. Bernstein; T. J. C. Bezerra; L. Bezrukhov; E. Blucher; N. S. Bowden; C. Buck; J. Busenitz; A. Cabrera; E. Caden; L. Camilleri; R. Carr; M. Cerrada; P. -J. Chang; P. Chimenti; T. Classen; A. P. Collin; E. Conover; J. M. Conrad; J. I. Crespo-Anadón; K. Crum; A. Cucoanes; M. V. D'Agostino; E. Damon; J. V. Dawson; S. Dazeley; D. Dietrich; Z. Djurcic; M. Dracos; V. Durand; J. Ebert; Y. Efremenko; M. Elnimr; A. Etenko; M. Fallot; M. Fechner; F. von Feilitzsch; J. Felde; D. Franco; A. J. Franke; M. Franke; H. Furuta; R. Gama; I. Gil-Botella; L. Giot; M. Goger-Neff; L. F. G. Gonzalez; M. C. Goodman; J. TM. Goon; D. Greiner; N. Haag; C. Hagner; T. Hara; F. X. Hartmann; J. Haser; A. Hatzikoutelis; T. Hayakawa; M. Hofmann; G. A. Horton-Smith; A. Hourlier; M. Ishitsuka; J. Jochum; C. Jollet; C. L. Jones; F. Kaether; L. N. Kalousis; Y. Kamyshkov; D. M. Kaplan; T. Kawasaki; G. Keefer; E. Kemp; H. de Kerret; Y. Kibe; T. Konno; D. Kryn; M. Kuze; T. Lachenmaier; C. E. Lane; C. Langbrandtner; T. Lasserre; A. Letourneau; D. Lhuillier; H. P. Lima Jr; M. Lindner; J. M. López-Castanõ; J. M. LoSecco; B. K. Lubsandorzhiev; S. Lucht; D. McKee; J. Maeda; C. N. Maesano; C. Mariani; J. Maricic; J. Martino; T. Matsubara; G. Mention; A. Meregaglia; T. Miletic; R. Milincic; H. Miyata; Th. A. Mueller; Y. Nagasaka; K. Nakajima; P. Novella; M. Obolensky; L. Oberauer; A. Onillon; A. Osborn; I. Ostrovskiy; C. Palomares; I. M. Pepe; S. Perasso; P. Perrin; P. Pfahler; A. Porta; W. Potzel; J. Reichenbacher; B. Reinhold; A. Remoto; M. Rohling; R. Roncin; S. Roth; Y. Sakamoto; R. Santorelli; F. Sato; S. Schonert; S. Schoppmann; T. Schwetz; M. H. Shaevitz; S. Shimojima; D. Shrestha; J. -L. Sida; V. Sinev; M. Skorokhvatov; E. Smith; J. Spitz; A. Stahl; I. Stancu; L. F. F. Stokes; M. Strait; A. Stuken; F. Suekane; S. Sukhotin; T. Sumiyoshi; Y. Sun; R. Svoboda; K. Terao; A. Tonazzo; M. Toups; H. H. Trinh Thi; G. Valdiviesso; C. Veyssiere; S. Wagner; H. Watanabe; B. White; C. Wiebusch; L. Winslow; M. Worcester; M. Wurm; F. Yermia; V. Zimmer

2012-07-27T23:59:59.000Z

423

Double-ended ceramic helical-rotor expander  

DOE Patents (OSTI)

A ceramic helical rotor expander is disclosed using a double-ended or tandem herringbone type rotor arrangement with bearing and seal assemblies remote from the hot gas inlets and especially capable of operating at an inlet temperature of above 1,100 C. The rotors are solid or hollow and bonded to hollow metal shafts, and mounted in a composite or simple prismatic casing. The rotors, casing and shafts are constructed from low expansivity materials. In the preferred embodiment the rotors are constructed of silicon nitride and the shafts constructed of an molybdenum alloy, with the metal shafts being supported in bearings and secured to synchronizing gears. The rotors and casing may be provided with coolant channels therein, and are constructed to eliminate the problem of end leakages at inlet temperature and pressure, and the need for high temperature bearings and seals. 3 figs.

Mohr, P.B.; Myers, W.B.

1995-02-28T23:59:59.000Z

424

Study of a double bubbler for material balance in liquids  

Science Conference Proceedings (OSTI)

The objective of this project was to determine the potential of a double bubbler to measure density and fluid level of the molten salt contained in an electrorefiner. Such in-situ real-time measurements can provide key information for material balances in the pyroprocessing of the nuclear spent fuel. This theoretical study showed this technique has a lot of promise. Four different experiments were designed and performed. The first three experiments studied the influence of a variety of factors such as depth difference between the two tubes, gas flow rate, the radius of the tubes and determining the best operating conditions. The last experiment purpose was to determine the precision and accuracy of the apparatus during specific conditions. The elected operating conditions for the characterization of the system were a difference of depth of 25 cm and a flow rate of 55 ml/min in each tube. The measured densities were between 1,000 g/l and 1,400g/l and the level between 34cm and 40 cm. The depth difference between the tubes is critical, the larger, the better. The experiments showed that the flow rate should be the same in each tube. The concordances with theoretical predictions were very good. The density precision was very satisfying (spread<0.1%) and the accuracy was about 1%. For the level determination, the precision was also very satisfying (spread<0.1%), but the accuracy was about 3%. However, those two biases could be corrected with calibration curves. In addition to the aqueous systems studied in the present work, future work will focus on examining the behavior of the double bubbler instrumentation in molten salt systems. The two main challenges which were identified in this work are the effect of the temperature and the variation of the superficial tension.

Hugues Lambert

2013-09-01T23:59:59.000Z

425

Neural Network Input Representations that Produce Accurate Consensus Sequences from DNA Fragment Assemblies  

E-Print Network (OSTI)

Motivation: Given inputs extracted from an aligned column of DNA bases and the underlying Perkin Elmer Applied Biosystems (ABI) fluorescent traces, our goal is to train a neural network to correctly determine the consensus base for the column. Choosing an appropriate network input representation is critical to success in this task. We empirically compare five representations; one uses only base calls and the others include trace information. Results: We attained the most accurate results from networks that incorporate trace information into their input representations. Based on estimates derived from using 10-fold cross-validation, the best network topology produces consensus accuracies ranging from 99.26% to over 99.98% for coverages from two to six aligned sequences. With a coverage of six, it makes only three errors in 20,000 consensus calls. In contrast, the network that only uses base calls in its input representation has over double that error rate -- eight errors in 20,000 cons...

C.F. Allex; J.W. Shavlik; F.R. Blattner

1999-01-01T23:59:59.000Z

426

Classifying aging genes into DNA repair or non-DNA repair-related categories  

Science Conference Proceedings (OSTI)

The elderly population in almost every country is growing faster than ever before. However, our knowledge about the aging process is still limited despite decades of studies on this topic. In this report, we focus on the gradual accumulation of DNA damage ... Keywords: DNA-repair, aging, classification, feature selection, random forest

Yaping Fang, Xinkun Wang, Elias K. Michaelis, Jianwen Fang

2013-07-01T23:59:59.000Z

427

High-throughput screening assay of hepatitis C virus helicase inhibitors using fluorescence-quenching phenomenon  

Science Conference Proceedings (OSTI)

We have developed a novel high-throughput screening assay of hepatitis C virus (HCV) nonstructural protein 3 (NS3) helicase inhibitors using the fluorescence-quenching phenomenon via photoinduced electron transfer between fluorescent dyes and guanine bases. We prepared double-stranded DNA (dsDNA) with a 5'-fluorescent-dye (BODIPY FL)-labeled strand hybridized with a complementary strand, the 3'-end of which has guanine bases. When dsDNA is unwound by helicase, the dye emits fluorescence owing to its release from the guanine bases. Our results demonstrate that this assay is suitable for quantitative assay of HCV NS3 helicase activity and useful for high-throughput screening for inhibitors. Furthermore, we applied this assay to the screening for NS3 helicase inhibitors from cell extracts of microorganisms, and found several cell extracts containing potential inhibitors.

Tani, Hidenori [Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480 (Japan); Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 (Japan); Akimitsu, Nobuyoshi [Radioisotope Center, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Fujita, Osamu; Matsuda, Yasuyoshi [Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 (Japan); Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480 (Japan); Miyata, Ryo [Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 (Japan); Tsuneda, Satoshi [Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480 (Japan); Igarashi, Masayuki [Microbial Chemistry Research Center, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021 (Japan); Sekiguchi, Yuji [Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 (Japan); Noda, Naohiro [Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 (Japan); Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480 (Japan)], E-mail: noda-naohiro@aist.go.jp

2009-02-20T23:59:59.000Z

428

Complexation of DNA with Cationic Surfactant  

E-Print Network (OSTI)

Transfection of an anionic polynucleotide through a negatively charged membrane is an important problem in genetic engineering. The direct association of cationic surfactant to DNA decreases the effective negative charge of the nucleic acid, allowing the DNA-surfactant complex to approach a negatively charged membrane. The paper develops a theory for solutions composed of polyelectrolyte, salt, and ionic surfactant. The theoretical predictions are compared with the experimental measurements. PACS.05.70.Ce- Thermodynamic functions and equations of state PACS.61.20.Qg- Structure of associated liquids: electrolytes, molten salts, etc. PACS.61.25.Hq- Macromolecular and polymer solutions; polymer melts; swelling Corresponding author;

Paulo S. Kuhn; Marcia C. Barbosa; Yan Levin

1999-01-01T23:59:59.000Z

429

Physica E 40 (2008) 15601562 Shubnikov de Haas oscillations in double wells with opposite signs  

E-Print Network (OSTI)

Physica E 40 (2008) 1560­1562 Shubnikov de Haas oscillations in double wells with opposite signs on the measurements of the Shubnikov de Haas oscillations (SdH) in symmetrically doped AlxGa1�xAs double wells with different Al compositions in wells, which lead to the opposite signs of the electronic g-factor in each

Gusev, Guennady

430

Overlapping double etch technique for evaluation of metallic alloys to stress corrosion cracking  

DOE Patents (OSTI)

A double overlapping etch zone technique for evaluation of the resistance of metallic alloys to stress corrosion cracking. The technique involves evaluating the metallic alloy along the line of demarcation between an overlapping double etch zone and single etch zone formed on the metallic alloy surface.

Steeves, Arthur F. (Schenectady, NY); Stewart, James C. (Loudonville, NY)

1981-01-01T23:59:59.000Z

431

Overlapping double etch technique for evaluation of metallic alloys to stress corrosion cracking  

DOE Patents (OSTI)

A double overlapping etch zone technique for evaluation of the resistance of metallic alloys to stress corrosion cracking is described. The technique involves evaluating the metallic alloy along the line of demarcation between an overlapping double etch zone and single etch zone formed on the metallic alloy surface.

Not Available

1980-05-28T23:59:59.000Z

432

Influence of Doubled CO2 on Ozone via Changes in the Brewer–Dobson Circulation  

Science Conference Proceedings (OSTI)

In this short note, the effect of enhanced circulation due to doubling CO2 on ozone is investigated. The difference of Brewer–Dobson circulation (BDC) between the doubled CO2 and control run from an idealized atmospheric general circulation model ...

Xun Jiang; Scott J. Eichelberger; Dennis L. Hartmann; Runlie Shia; Yuk L. Yung

2007-07-01T23:59:59.000Z

433

HANFORD DOUBLE SHELL TANK (DST) THERMAL & SEISMIC PROJECT SUMMARY OF COMBINED THERMAL & OPERATING LOADS  

Science Conference Proceedings (OSTI)

This report summarizes the results of the Double-Shell Tank Thermal and Operating Loads Analysis (TOLA) combined with the Seismic Analysis. This combined analysis provides a thorough, defensible, and documented analysis that will become a part of the overall analysis of record for the Hanford double-shell tanks (DSTs).

MACKEY, T.C.

2006-03-17T23:59:59.000Z

434

Final Report for Organic Partitioning Resulting from Operation of an INTEC Double-needle Sampler  

SciTech Connect

The double needle sampler testing is a continuation of previous test series that investigated the fate of organic species in the Process Equipment Waste Evaporator (PEWE) system at the Idaho Nuclear Technology and Engineering Center (INTEC). This test series was designed to investigate the effects of operation of the double needle sampling systems on volatile organic constituents in an acidic feed matrix.

Michael B. Heiser

2003-09-01T23:59:59.000Z

435

Uniform convergence of Cesàro means of negative order of double Walsh--Fourier series  

Science Conference Proceedings (OSTI)

In this paper we prove that if f ? Cw([0, 1]2) and the function f is bounded partial p- variation for some p ? [1, + ?) then the double Walsh-Fourier series of the function f ... Keywords: Cesàro means, double Walsh-Fourier series, uniform summability

Ushangi Goginava

2003-09-01T23:59:59.000Z

436

Chaotic Behaviors in the Response of a Quasigeostrophic Oceanic Double Gyre to Seasonal External Forcing  

Science Conference Proceedings (OSTI)

In an oceanic double-gyre system, nonlinear oscillations of the ocean under seasonally changing external forcing are investigated using a 1.5-layer quasigeostrophic model and a simple model related to energy balance of the oceanic double gyre. In ...

Shinya Shimokawa; Tomonori Matsuura

2010-07-01T23:59:59.000Z

437

Liquid Polymorphism and Double Criticality in a Lattice Gas Vera B. Henriques,1,  

E-Print Network (OSTI)

Liquid Polymorphism and Double Criticality in a Lattice Gas Model Vera B. Henriques,1, Nara diagrams of a simple model for an associating liquid proposed previously. Our two-dimensional lattice model decreases, a smooth disappearance of the double criticality occurs. Possible connections to liquid-liquid

Barbosa, Marcia C. B.

438

DoubleDip: leveraging thermoelectric harvesting for low power monitoring of sporadic water use  

Science Conference Proceedings (OSTI)

We present DoubleDip, a low power monitoring system for enabling non-intrusive water flow detection. DoubleDip taps into minute thermal gradients in pipes for both replenishing energy reserves and performing low power wakeup. One of the remaining issues ... Keywords: energy harvesting, low power, sustainability, thermoelectric, water monitoring

Paul Martin; Zainul Charbiwala; Mani Srivastava

2012-11-01T23:59:59.000Z

439

Transient States of the Multiscalar Controlled Double Fed Induction Generator in the Wind Farm  

Science Conference Proceedings (OSTI)

This article presents a detailed model and analysis of wind turbine based on double fed induction generator (DFIG) including cable line to the point of common coupling (PCC). The vector control system is based on the multiscalar model of the machine. ... Keywords: Double Fed Induction Generator, Multiscalar Control, Reactive Power Compensation, Wind Farm Modelling

Piotr Kolodziejek

2011-12-01T23:59:59.000Z

440

Collector efficiency of the double-pass solar air collectors with fins  

Science Conference Proceedings (OSTI)

The experimental study on a forced-convective double-pass solar air collector with fins in the second channel has been conducted. The experiments were conducted by changing the parameters that influence the thermal efficiency of the collector. The efficiency ... Keywords: collector efficiency, double-pass solar air collector, fins absorbers

A. Fudholi; M. H. Ruslan; M. Y. Othman; M. Yahya; Supranto Supranto; A. Zaharim; K. Sopian

2010-10-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna double strand" from the National Library of EnergyBeta (NLEBeta).
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441

Angular momentum transfer between a circularly polarized photon and an electron spin in double quantum dots  

SciTech Connect

We propose an experimental scheme of photon-spin quantum interface using a semiconductor double quantum dot. A polarized electron spin is excited by a circularly polarized photon. We detect the spin state applying Pauli spin blockade which is often employed to detect orientation of a single electron spin in double quantum dots.

Asayama, T. [Department of Applied Physics and QPEC, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo (Japan); Solid State Memories Development Dept, Sony Corporation, Atsugi, Kanagawa (Japan); Fujita, T.; Kiyama, H.; Oiwa, A. [Department of Applied Physics and QPEC, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo (Japan); Tarucha, S. [Department of Applied Physics and QPEC, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo (Japan); Institute for Nano Quantum Electronics, University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo (Japan)

2011-12-23T23:59:59.000Z

442

The synchronous force control of a double-axial pneumatic actuating system  

Science Conference Proceedings (OSTI)

This paper presents the design of the synchronous force controller of a double-axial pneumatic actuating system. This system is ideally decomposed into two independent subsystems, and the coupling effect is considered as the noise effect. So, each ... Keywords: STC, double-axial pneumatic system, synchronous force control

Ying-Tsai Wang; Ming-Kun Chang

1999-07-01T23:59:59.000Z

443

Study of Shifting without Driving Force Interrupt for Double Electric Motor HEV  

Science Conference Proceedings (OSTI)

For traditional gearbox, the engine power is cut off while shifting, which will interrupt the power of power-train, make velocity down, affect the acceleration of up gear and lower the vehicle dynamic. A double electric motor hybrid electric vehicle ... Keywords: Double Electric Motor HEV, Shifting Without Driving Force Interrupt (SWDFI), Integrated Power-train

Wang Jiaxue; Wang Qingnian; Wang Weihua; Zeng Xiaohua; Li Chuan

2009-10-01T23:59:59.000Z

444

Experimental and theoretical thermal performance of double pass solar air heater with porous media  

Science Conference Proceedings (OSTI)

A theoretical model has been developed to predict the thermal performance of double pass solar air heater with porous media. It is composed of five-coupled unsteady nonlinear partial differential equations which are solved by using numerical scheme. ... Keywords: double pass solar collector, iteration, numerical, porous media, solar radiation

M. Yahya; K. Sopian; M. Y. Theeran; M. Y. Othman; M. A. Alghoul; M. Hafidz; A. Zaharim

2008-11-01T23:59:59.000Z

445

THE LONG-TERM EVOLUTION OF DOUBLE WHITE DWARF MERGERS  

SciTech Connect

In this paper, we present a model for the long-term evolution of the merger of two unequal mass C/O white dwarfs (WDs). After the dynamical phase of the merger, magnetic stresses rapidly redistribute angular momentum, leading to nearly solid-body rotation on a viscous timescale of 10{sup -4}-1 yr, long before significant cooling can occur. Due to heating during the dynamical and viscous phases, the less massive WD is transformed into a hot, slowly rotating, and radially extended envelope supported by thermal pressure. Following the viscous phase of evolution, the maximum temperature near the envelope base may already be high enough to begin off-center convective carbon burning. If not, Kelvin-Helmholtz contraction of the inner region of the envelope on a thermal timescale of 10{sup 3}-10{sup 4} yr compresses the base of the envelope, again yielding off-center burning. As a result, the long-term evolution of the merger remnant is similar to that seen in previous calculations: the burning shell diffuses inward over {approx}10{sup 4} yr, eventually yielding a high-mass O/Ne WD or a collapse to a neutron star, rather than a Type Ia supernova. During the cooling and shell-burning phases, the merger remnant radiates near the Eddington limit. Given the double WD merger rate of a few per 1000 yr, a few dozen of these {approx}10{sup 38} erg s{sup -1} sources should exist in a Milky Way type galaxy. While the end result is similar to that of previous studies, the physical picture and the dynamical state of the matter in our model differ from previous work. Furthermore, substantial remaining uncertainties related to the convective structure near the photosphere and mass loss during the thermal evolution may significantly affect our conclusions. Thus, future work within the context of the physical model presented here is required to better address the eventual fate of double WD mergers, including those for which one or both of the components is a He WD.

Shen, Ken J.; Kasen, Daniel [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Bildsten, Lars [Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106 (United States); Quataert, Eliot, E-mail: kenshen@astro.berkeley.edu [Department of Astronomy and Theoretical Astrophysics Center, University of California, Berkeley, CA 94720 (United States)

2012-03-20T23:59:59.000Z

446

T-682:Double free vulnerability in MapServer | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

2:Double free vulnerability in MapServer 2:Double free vulnerability in MapServer T-682:Double free vulnerability in MapServer August 2, 2011 - 4:08pm Addthis PROBLEM: Double free vulnerability in MapServer PLATFORM: All versions may be susceptible to SQL injection under certain circumstances ABSTRACT: MapServer developers have discovered flaws in the OGC filter support in MapServer. Specific code is used in support of WFS, WMS-SLD and SOS specifications. All versions may be susceptible to SQL injection under certain circumstances. The extent of the vulnerability depends on the MapServer version, relational database and mapfile configuration being used. All users are strongly encouraged to upgrade to these latest releases. reference LINKS: Double-free in msAddImageSymbol() when filename is a http resource