National Library of Energy BETA

Sample records for dna damage response

  1. Cellular responses to environmental DNA damage

    SciTech Connect (OSTI)

    Not Available

    1994-08-01

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

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

    SciTech Connect (OSTI)

    Roper, Katherine; Coverley, Dawn

    2012-03-10

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

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

    SciTech Connect (OSTI)

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

    2012-11-01

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

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

    SciTech Connect (OSTI)

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

    2014-09-12

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

  5. Persistent activation of DNA damage signaling in response to complex mixtures of PAHs in air particulate matter

    SciTech Connect (OSTI)

    Jarvis, Ian W.H.; Bergvall, Christoffer; Bottai, Matteo; Westerholm, Roger; Stenius, Ulla; Dreij, Kristian

    2013-02-01

    Complex mixtures of polycyclic aromatic hydrocarbons (PAHs) are present in air particulate matter (PM) and have been associated with many adverse human health effects including cancer and respiratory disease. However, due to their complexity, the risk of exposure to mixtures is difficult to estimate. In the present study the effects of binary mixtures of benzo[a]pyrene (BP) and dibenzo[a,l]pyrene (DBP) and complex mixtures of PAHs in urban air PM extracts on DNA damage signaling was investigated. Applying a statistical model to the data we observed a more than additive response for binary mixtures of BP and DBP on activation of DNA damage signaling. Persistent activation of checkpoint kinase 1 (Chk1) was observed at significantly lower BP equivalent concentrations in air PM extracts than BP alone. Activation of DNA damage signaling was also more persistent in air PM fractions containing PAHs with more than four aromatic rings suggesting larger PAHs contribute a greater risk to human health. Altogether our data suggests that human health risk assessment based on additivity such as toxicity equivalency factor scales may significantly underestimate the risk of exposure to complex mixtures of PAHs. The data confirms our previous findings with PAH-contaminated soil (Niziolek-Kierecka et al., 2012) and suggests a possible role for Chk1 Ser317 phosphorylation as a biological marker for future analyses of complex mixtures of PAHs. -- Highlights: ? Benzo[a]pyrene (BP), dibenzo[a,l]pyrene (DBP) and air PM PAH extracts were compared. ? Binary mixture of BP and DBP induced a more than additive DNA damage response. ? Air PM PAH extracts were more potent than toxicity equivalency factor estimates. ? Larger PAHs (> 4 rings) contribute more to the genotoxicity of PAHs in air PM. ? Chk1 is a sensitive marker for persistent activation of DNA damage signaling from PAH mixtures.

  6. TH-C-18A-09: Exam and Patient Parameters Affecting the DNA Damage Response Following CT Studies

    SciTech Connect (OSTI)

    Elgart, S; Adibi, A; Bostani, M; Ruehm, S; Enzmann, D; McNitt-Gray, M; Iwamoto, K

    2014-06-15

    Purpose: To identify exam and patient parameters affecting the biological response to CT studies using in vivo and ex vivo blood samples. Methods: Blood samples were collected under IRB approval from 16 patients undergoing clinically-indicated CT exams. Blood was procured prior to, immediately after and 30minutes following irradiation. A sample of preexam blood was placed on the patient within the exam region for ex vivo analysis. Whole blood samples were fixed immediately following collection and stained for ?H2AX to assess DNA damage response (DDR). Median fluorescence of treated samples was compared to non-irradiated control samples for each patient. Patients were characterized by observed biological kinetic response: (a) fast phosphorylation increased by 2minutes and fell by 30minutes, (b) slow phosphorylation continued to increase to 30minutes and (c) none little change was observed or irradiated samples fell below controls. Total dose values were normalized to exam time for an averaged dose-rate in dose/sec for each exam. Relationships between patient biological responses and patient and exam parameters were investigated. Results: A clearer dose response at 30minutes is observed for young patients (<61yoa; R2>0.5) compared to old patients (>61yoa; R{sup 2}<0.11). Fast responding patients were significantly younger than slow responding patients (p<0.05). Unlike in vivo samples, age did not significantly affect the patient response ex vivo. Additionally, fast responding patients received exams with significantly smaller dose-rate than slow responding patients (p<0.05). Conclusion: Age is a significant factor in the biological response suggesting that DDR may be more rapid in a younger population and slower as the population ages. Lack of an agerelated response ex vivo suggests a systemic response to radiation not present when irradiated outside the body. Dose-rate affects the biological response suggesting that patient response may be related to scan timing and dose delivery within an exam protocol. All authors receive(d) funding from a Master Research Agreement from Siemens Healthcare with UCLA Radiological Sciences.

  7. Method for assaying clustered DNA damages

    DOE Patents [OSTI]

    Sutherland, Betsy M.

    2004-09-07

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

  8. Chk2 regulates transcription-independent p53-mediated apoptosis in response to DNA damage

    SciTech Connect (OSTI)

    Chen Chen [Department of Geriatric Research, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, Obu, Aichi 474-8522 (Japan); Shimizu, Shigeomi [Department of Post-Genomics Diseases, Osaka University Medical School, Suita, Osaka 565-0871 (Japan); Tsujimoto, Yoshihide [Department of Post-Genomics Diseases, Osaka University Medical School, Suita, Osaka 565-0871 (Japan); Motoyama, Noboru [Department of Geriatric Research, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, Obu, Aichi 474-8522 (Japan)]. E-mail: motoyama@nils.go.jp

    2005-07-29

    The tumor suppressor protein p53 plays a central role in the induction of apoptosis in response to genotoxic stress. The protein kinase Chk2 is an important regulator of p53 function in mammalian cells exposed to ionizing radiation (IR). Cells derived from Chk2-deficient mice are resistant to the induction of apoptosis by IR, and this resistance has been thought to be a result of the defective transcriptional activation of p53 target genes. It was recently shown, however, that p53 itself and histone H1.2 translocate to mitochondria and thereby induces apoptosis in a transcription-independent manner in response to IR. We have now examined whether Chk2 also regulates the transcription-independent induction of apoptosis by p53 and histone H1.2. The reduced ability of IR to induce p53 stabilization in Chk2-deficient thymocytes was associated with a marked impairment of p53 and histone H1 translocation to mitochondria. These results suggest that Chk2 regulates the transcription-independent mechanism of p53-mediated apoptosis by inducing stabilization of p53 in response to IR.

  9. Systems Biology Model of Interactions Between Tissue Growth Factors and DNA Damage Pathways: Low Dose Response and Cross-Talk in TGFbeta and ATM Signaling

    SciTech Connect (OSTI)

    O'Neill, Peter; Anderson, Jennifer

    2014-10-02

    The etiology of radiation carcinogenesis has been described in terms of aberrant changes that span several levels of biological organization. Growth factors regulate many important cellular and tissue functions including apoptosis, differentiation and proliferation. A variety of genetic and epigenetic changes of growth factors have been shown to contribute to cancer initiation and progression. It is known that cellular and tissue damage to ionizing radiation is in part initiated by the production of reactive oxygen species, which can activate cytokine signaling, and the DNA damage response pathways, most notably the ATM signaling pathway. Recently the transforming growth factor ? (TGF?) pathway has been shown to regulate or directly interact with the ATM pathway in the response to radiation. The relevance of this interaction with the ATM pathway is not known although p53 becomes phosphorylated and DNA damage responses are involved. However, growth factor interactions with DNA damage responses have not been elucidated particularly at low doses and further characterization of their relationship to cancer processes is warranted. Our goal will be to use a systems biology approach to mathematically and experimentally describe the low dose responses and cross-talk between the ATM and TGF? pathways initiated by low and high LET radiation. We will characterize ATM and TGF? signaling in epithelial and fibroblast cells using 2D models and ultimately extending to 3D organotypic cell culture models to begin to elucidate possible differences that may occur for different cell types and/or inter-cellular communication. We will investigate the roles of the Smad and Activating transcription factor 2 (ATF2) proteins as the potential major contributors to cross- talk between the TGF? and ATM pathways, and links to cell cycle control and/or the DNA damage response, and potential differences in their responses at low and high doses. We have developed various experimental approaches to apply to these problems using confocal microscopy and flow cytometry to detail changes at low dose/dose-rate in order to understand individual cell responses, and will establish our mathematical models based on the experimental findings resulting from changes in DNA repair, apoptosis and proliferation.

  10. Arsenic transformation predisposes human skin keratinocytes to UV-induced DNA damage yet enhances their survival apparently by diminishing oxidant response

    SciTech Connect (OSTI)

    Sun Yang; Kojima, Chikara; Chignell, Colin; Mason, Ronald; Waalkes, Michael P.

    2011-09-15

    Inorganic arsenic and UV, both human skin carcinogens, may act together as skin co-carcinogens. We find human skin keratinocytes (HaCaT cells) are malignantly transformed by low-level arsenite (100 nM, 30 weeks; termed As-TM cells) and with transformation concurrently undergo full adaptation to arsenic toxicity involving reduced apoptosis and oxidative stress response to high arsenite concentrations. Oxidative DNA damage (ODD) is a possible mechanism in arsenic carcinogenesis and a hallmark of UV-induced skin cancer. In the current work, inorganic arsenite exposure (100 nM) did not induce ODD during the 30 weeks required for malignant transformation. Although acute UV-treatment (UVA, 25 J/cm{sup 2}) increased ODD in passage-matched control cells, once transformed by arsenic to As-TM cells, acute UV actually further increased ODD (> 50%). Despite enhanced ODD, As-TM cells were resistant to UV-induced apoptosis. The response of apoptotic factors and oxidative stress genes was strongly mitigated in As-TM cells after UV exposure including increased Bcl2/Bax ratio and reduced Caspase-3, Nrf2, and Keap1 expression. Several Nrf2-related genes (HO-1, GCLs, SOD) showed diminished responses in As-TM cells after UV exposure consistent with reduced oxidant stress response. UV-exposed As-TM cells showed increased expression of cyclin D1 (proliferation gene) and decreased p16 (tumor suppressor). UV exposure enhanced the malignant phenotype of As-TM cells. Thus, the co-carcinogenicity between UV and arsenic in skin cancer might involve adaptation to chronic arsenic exposure generally mitigating the oxidative stress response, allowing apoptotic by-pass after UV and enhanced cell survival even in the face of increased UV-induced oxidative stress and increased ODD. - Highlights: > Arsenic transformation adapted to UV-induced apoptosis. > Arsenic transformation diminished oxidant response. > Arsenic transformation enhanced UV-induced DNA damage.

  11. Characterizing the DNA damage response by cell tracking algorithms and cell features classification using high-content time-lapse analysis

    SciTech Connect (OSTI)

    Georgescu, Walter; Osseiran, Alma; Rojec, Maria; Liu, Yueyong; Bombrun, Maxime; Tang, Jonathan; Costes, Sylvain V.; Huen, Michael Shing-Yan

    2015-06-24

    Traditionally, the kinetics of DNA repair have been estimated using immunocytochemistry by labeling proteins involved in the DNA damage response (DDR) with fluorescent markers in a fixed cell assay. However, detailed knowledge of DDR dynamics across multiple cell generations cannot be obtained using a limited number of fixed cell time-points. Here we report on the dynamics of 53BP1 radiation induced foci (RIF) across multiple cell generations using live cell imaging of non-malignant human mammary epithelial cells (MCF10A) expressing histone H2B-GFP and the DNA repair protein 53BP1-mCherry. Using automatic extraction of RIF imaging features and linear programming techniques, we were able to characterize detailed RIF kinetics for 24 hours before and 24 hours after exposure to low and high doses of ionizing radiation. High-content-analysis at the single cell level over hundreds of cells allows us to quantify precisely the dose dependence of 53BP1 protein production, RIF nuclear localization and RIF movement after exposure to X-ray. Using elastic registration techniques based on the nuclear pattern of individual cells, we could describe the motion of individual RIF precisely within the nucleus. We show that DNA repair occurs in a limited number of large domains, within which multiple small RIFs form, merge and/or resolve with random motion following normal diffusion law. Large foci formation is shown to be mainly happening through the merging of smaller RIF rather than through growth of an individual focus. We estimate repair domain sizes of 7.5 to 11 m2 with a maximum number of ~15 domains per MCF10A cell. This work also highlights DDR which are specific to doses larger than 1 Gy such as rapid 53BP1 protein increase in the nucleus and foci diffusion rates that are significantly faster than for spontaneous foci movement. We hypothesize that RIF merging reflects a "stressed" DNA repair process that has been taken outside physiological conditions when too many DSB occur at once. High doses of ionizing radiation lead to RIF merging into repair domains which in turn increases DSB proximity and misrepair. Such finding may therefore be critical to explain the supralinear dose dependence for chromosomal rearrangement and cell death measured after exposure to ionizing radiation.

  12. Characterizing the DNA damage response by cell tracking algorithms and cell features classification using high-content time-lapse analysis

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

    Georgescu, Walter; Osseiran, Alma; Rojec, Maria; Liu, Yueyong; Bombrun, Maxime; Tang, Jonathan; Costes, Sylvain V.; Huen, Michael Shing-Yan

    2015-06-24

    Traditionally, the kinetics of DNA repair have been estimated using immunocytochemistry by labeling proteins involved in the DNA damage response (DDR) with fluorescent markers in a fixed cell assay. However, detailed knowledge of DDR dynamics across multiple cell generations cannot be obtained using a limited number of fixed cell time-points. Here we report on the dynamics of 53BP1 radiation induced foci (RIF) across multiple cell generations using live cell imaging of non-malignant human mammary epithelial cells (MCF10A) expressing histone H2B-GFP and the DNA repair protein 53BP1-mCherry. Using automatic extraction of RIF imaging features and linear programming techniques, we were ablemore » to characterize detailed RIF kinetics for 24 hours before and 24 hours after exposure to low and high doses of ionizing radiation. High-content-analysis at the single cell level over hundreds of cells allows us to quantify precisely the dose dependence of 53BP1 protein production, RIF nuclear localization and RIF movement after exposure to X-ray. Using elastic registration techniques based on the nuclear pattern of individual cells, we could describe the motion of individual RIF precisely within the nucleus. We show that DNA repair occurs in a limited number of large domains, within which multiple small RIFs form, merge and/or resolve with random motion following normal diffusion law. Large foci formation is shown to be mainly happening through the merging of smaller RIF rather than through growth of an individual focus. We estimate repair domain sizes of 7.5 to 11 µm2 with a maximum number of ~15 domains per MCF10A cell. This work also highlights DDR which are specific to doses larger than 1 Gy such as rapid 53BP1 protein increase in the nucleus and foci diffusion rates that are significantly faster than for spontaneous foci movement. We hypothesize that RIF merging reflects a "stressed" DNA repair process that has been taken outside physiological conditions when too many DSB occur at once. High doses of ionizing radiation lead to RIF merging into repair domains which in turn increases DSB proximity and misrepair. Furthermore, such finding may therefore be critical to explain the supralinear dose dependence for chromosomal rearrangement and cell death measured after exposure to ionizing radiation.« less

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

    SciTech Connect (OSTI)

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

    2008-02-21

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

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

    SciTech Connect (OSTI)

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

    2007-12-01

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

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

    DOE Patents [OSTI]

    McCutchen-Maloney, Sandra L. (Pleasanton, CA)

    2002-01-01

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

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

    SciTech Connect (OSTI)

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

    2015-02-22

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

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

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

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

    2015-02-22

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

  18. Structure and Activation Mechanism of the CHK2 DNA Damage Checkpoint...

    Office of Scientific and Technical Information (OSTI)

    Structure and Activation Mechanism of the CHK2 DNA Damage Checkpoint Kinase Citation Details In-Document Search Title: Structure and Activation Mechanism of the CHK2 DNA Damage ...

  19. Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2...

    Office of Scientific and Technical Information (OSTI)

    Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2 Complex Citation Details In-Document Search Title: Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2 ...

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

    SciTech Connect (OSTI)

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

    2008-01-18

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

  1. Inhibition of HAS2 induction enhances the radiosensitivity of cancer cells via persistent DNA damage

    SciTech Connect (OSTI)

    Shen, Yan Nan; Shin, Hyun-Jin; Joo, Hyun-Yoo; Park, Eun-Ran; Kim, Su-Hyeon; Hwang, Sang-Gu; Park, Sang Jun; Kim, Chun-Ho; Lee, Kee-Ho

    2014-01-17

    Highlights: •HAS2 may be a promising target for the radiosensitization of human cancer. •HAS2 is elevated (up to ∼10-fold) in irradiated radioresistant and -sensitive cancer cells. •HAS2 knockdown sensitizes cancer cells to radiation. •HAS2 knockdown potentiates irradiation-induced DNA damage and apoptotic death. •Thus, the irradiation-induced up-regulation of HAS2 contributes to the radioresistance of cancer cells. -- Abstract: Hyaluronan synthase 2 (HAS2), a synthetic enzyme for hyaluronan, regulates various aspects of cancer progression, including migration, invasion and angiogenesis. However, the possible association of HAS2 with the response of cancer cells to anticancer radiotherapy, has not yet been elucidated. Here, we show that HAS2 knockdown potentiates irradiation-induced DNA damage and apoptosis in cancer cells. Upon exposure to radiation, all of the tested human cancer cell lines exhibited marked (up to 10-fold) up-regulation of HAS2 within 24 h. Inhibition of HAS2 induction significantly reduced the survival of irradiated radioresistant and -sensitive cells. Interestingly, HAS2 depletion rendered the cells to sustain irradiation-induced DNA damage, thereby leading to an increase of apoptotic death. These findings indicate that HAS2 knockdown sensitizes cancer cells to radiation via persistent DNA damage, further suggesting that the irradiation-induced up-regulation of HAS2 contributes to the radioresistance of cancer cells. Thus, HAS2 could potentially be targeted for therapeutic interventions aimed at radiosensitizing cancer cells.

  2. Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2 Complex

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2 Complex Citation Details In-Document Search Title: Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2 Complex Ultraviolet (UV) light-induced pyrimidine photodimers are repaired by the nucleotide excision repair pathway. Photolesions have biophysical parameters closely resembling undamaged DNA, impeding discovery through damage surveillance proteins. The DDB1DDB2 complex serves in

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

    DOE Patents [OSTI]

    McCutchen-Maloney, Sandra L. (Pleasanton, CA)

    2002-01-01

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

  4. IN VITRO MUTAGENIC AND DNA AND CHROMOSOMAL DAMAGE ACTIVITY BY SURFACTANT

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

    DISPERSION OR SOLVENT EXTRACT OF A REFERENCE DIESEL EXHAUST PARTICULATE MATERIAL | Department of Energy IN VITRO MUTAGENIC AND DNA AND CHROMOSOMAL DAMAGE ACTIVITY BY SURFACTANT DISPERSION OR SOLVENT EXTRACT OF A REFERENCE DIESEL EXHAUST PARTICULATE MATERIAL IN VITRO MUTAGENIC AND DNA AND CHROMOSOMAL DAMAGE ACTIVITY BY SURFACTANT DISPERSION OR SOLVENT EXTRACT OF A REFERENCE DIESEL EXHAUST PARTICULATE MATERIAL Presentation given at DEER 2006, August 20-24, 2006, Detroit, Michigan. Sponsored by

  5. Structure and Activation Mechanism of the CHK2 DNA Damage Checkpoint Kinase

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Structure and Activation Mechanism of the CHK2 DNA Damage Checkpoint Kinase Citation Details In-Document Search Title: Structure and Activation Mechanism of the CHK2 DNA Damage Checkpoint Kinase Authors: Cai, Zhenjian ; Chehab, Nabil H. ; Pavletich, Nikola P. ; MSKCC) [1] + Show Author Affiliations ( Publication Date: 2010-01-28 OSTI Identifier: 1006023 Resource Type: Journal Article Resource Relation: Journal Name: Mol. Cell; Journal Volume: 35; Journal

  6. Sulforaphane prevents pulmonary damage in response to inhaled arsenic by activating the Nrf2-defense response

    SciTech Connect (OSTI)

    Zheng, Yi; Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, AZ 85721 ; Tao, Shasha; Lian, Fangru; Chau, Binh T.; Chen, Jie; Sun, Guifan; Fang, Deyu; Lantz, R. Clark; Arizona Cancer Center, University of Arizona, 1515 North Campbell Avenue, Tucson, AZ 85724 ; Zhang, Donna D.

    2012-12-15

    Exposure to arsenic is associated with an increased risk of lung disease. Novel strategies are needed to reduce the adverse health effects associated with arsenic exposure in the lung. Nrf2, a transcription factor that mediates an adaptive cellular defense response, is effective in detoxifying environmental insults and prevents a broad spectrum of diseases induced by environmental exposure to harmful substances. In this report, we tested whether Nrf2 activation protects mice from arsenic-induced toxicity. We used an in vivo arsenic inhalation model that is highly relevant to low environmental human exposure to arsenic-containing dusts. Two-week exposure to arsenic-containing dust resulted in pathological alterations, oxidative DNA damage, and mild apoptotic cell death in the lung; all of which were blocked by sulforaphane (SF) in an Nrf2-dependent manner. Mechanistically, SF-mediated activation of Nrf2 alleviated inflammatory responses by modulating cytokine production. This study provides strong evidence that dietary intervention targeting Nrf2 activation is a feasible approach to reduce adverse health effects associated with arsenic exposure. -- Highlights: ? Exposed to arsenic particles and/or SF have elevated Nrf2 and its target genes. ? Sulforaphane prevents pathological alterations, oxidative damage and cell death. ? Sulforaphane alleviates infiltration of inflammatory cells into the lungs. ? Sulforaphane suppresses arsenic-induced proinflammatory cytokine production.

  7. Cytochrome P450 2A13 enhances the sensitivity of human bronchial epithelial cells to aflatoxin B1-induced DNA damage

    SciTech Connect (OSTI)

    Yang, Xuejiao; Zhang, Zhan; Wang, Xichen; Wang, Yun; Zhang, Xiaoming; Lu, Huiyuan; Wang, Shou-Lin

    2013-07-15

    Cytochrome P450 2A13 (CYP2A13) mainly expresses in human respiratory system and mediates the metabolic activation of aflatoxin B1 (AFB1). Our previous study suggested that CYP2A13 could increase the cytotoxic and apoptotic effects of AFB1 in immortalized human bronchial epithelial cells (BEAS-2B). However, the role of CYP2A13 in AFB1-induced DNA damage is unclear. Using BEAS-2B cells that stably express CYP2A13 (B-2A13), CYP1A2 (B-1A2), and CYP2A6 (B-2A6), we compared their effects in AFB1-induced DNA adducts, DNA damage, and cell cycle changes. BEAS-2B cells that were transfected with vector (B-vector) were used as a control. The results showed that AFB1 (580 nM) dose- and time-dependently induced DNA damage in B-2A13 cells. AFB1 at 10 and 80 nM significantly augmented this effect in B-2A13 and B-1A2 cells, respectively. B-2A6 cells showed no obvious DNA damage, similar to B-vector cells and the vehicle control. Similarly, compared with B-vector, B-1A2 or B-2A6 cells, B-2A13 cells showed more sensitivity in AFB1-induced ?H2AX expression, DNA adduct 8-hydroxy-deoxyguanosine formation, and S-phase cell-cycle arrest. Furthermore, AFB1 activated the proteins related to DNA damage responses, such as ATM, ATR, Chk2, p53, BRCA1, and H2AX, rather than the proteins related to DNA repair. These effects could be almost completely inhibited by 100 ?M nicotine (a substrate of CYP2A13) or 1 ?M 8-methoxypsoralen (8-MOP; an inhibitor of CYP enzyme). Collectively, these findings suggest that CYP2A13 plays an important role in low-concentration AFB1-induced DNA damage, possibly linking environmental airborne AFB1 to genetic injury in human respiratory system. - Highlights: CYP2A13 plays a critical role in low concentration of AFB1-induced DNA damage. B-2A13 cells were more sensitive to AFB1 than B-1A2 cells and B-2A6 cells. AFB1 dose- and time-dependently induced DNA damage in B-2A13 cells AFB1-induced DNA adducts and damage can be inhibited by nicotine and 8-MOP.

  8. Cytogenetic status and oxidative DNA-damage induced by atorvastatin in human peripheral blood lymphocytes: Standard and Fpg-modified comet assay

    SciTech Connect (OSTI)

    Gajski, Goran Garaj-Vrhovac, Vera; Orescanin, Visnja

    2008-08-15

    To investigate the genotoxic potential of atorvastatin on human lymphocytes in vitro standard comet assay was used in the evaluation of basal DNA damage and to investigate possible oxidative DNA damage produced by reactive oxygen species (ROS) Fpg-modified version of comet assay was also conducted. In addition to these techniques the new criteria for scoring micronucleus test were applied for more complete detection of baseline damage in binuclear lymphocytes exposed to atorvastatin 80 mg/day in different time periods by virtue of measuring the frequency of micronuclei, nucleoplasmic bridges and nuclear buds. All parameters obtained with the standard comet assay and Fpg-modified comet assay were significantly higher in the treated than in control lymphocytes. The Fpg-modified comet assay showed a significantly greater tail length, tail intensity, and tail moment in all treated lymphocytes than did the standard comet assay, which suggests that oxidative stress is likely to be responsible for DNA damage. DNA damage detected by the standard comet assay indicates that some other mechanism is also involved. In addition to the comet assay, a total number of micronuclei, nucleoplasmic bridges and nuclear buds were significantly higher in the exposed than in controlled lymphocytes. Regression analyses showed a positive correlation between the results obtained by the comet (Fpg-modified and standard) and micronucleus assay. Overall, the study demonstrated that atorvastatin in its highest dose is capable of producing damage on the level of DNA molecule and cell.

  9. Nitrative DNA damage induced by multi-walled carbon nanotube via endocytosis in human lung epithelial cells

    SciTech Connect (OSTI)

    Guo, Feiye; Ma, Ning; Horibe, Yoshiteru; Kawanishi, Shosuke; Murata, Mariko; Hiraku, Yusuke

    2012-04-15

    Carbon nanotube (CNT) has a promising usage in the field of material science for industrial purposes because of its unique physicochemical property. However, intraperitoneal administration of CNT was reported to cause mesothelioma in experimental animals. Chronic inflammation may contribute to carcinogenesis induced by fibrous materials. 8-Nitroguanine is a mutagenic DNA lesion formed during inflammation and may play a role in CNT-induced carcinogenesis. In this study, we examined 8-nitroguanine formation in A549 human lung alveolar epithelial cells treated with multi-walled CNT (MWCNT) by fluorescent immunocytochemistry. Both MWCNTs with diameter of 2030 nm (CNT20) and 4070 nm (CNT40) significantly induced 8-nitroguanine formation at 5 and 10 ?g/ml (p < 0.05), which persisted for 24 h, although there was no significant difference in DNA-damaging abilities of these MWCNTs. MWCNTs significantly induced the expression of inducible nitric oxide synthase (iNOS) for 24 h (p < 0.05). MWCNTs also significantly increased the level of nitrite, a hydrolysis product of oxidized NO, in the culture supernatant at 4 and 8 h (p < 0.05). MWCNT-induced 8-nitroguanine formation and iNOS expression were largely suppressed by inhibitors of iNOS (1400 W), nuclear factor-?B (Bay11-7082), actin polymerization (cytochalasin D), caveolae-mediated endocytosis (methyl-?-cyclodextrin, MBCD) and clathrin-mediated endocytosis (monodansylcadaverine, MDC). Electron microscopy revealed that MWCNT was mainly located in vesicular structures in the cytoplasm, and its cellular internalization was reduced by MBCD and MDC. These results suggest that MWCNT is internalized into cells via clathrin- and caveolae-mediated endocytosis, leading to inflammatory reactions including iNOS expression and resulting nitrative DNA damage, which may contribute to carcinogenesis. Highlights: ?Multi-walled carbon nanotube (MWCNT) caused DNA damage in A549 cells. ?MWCNT formed 8-nitroguanine, a DNA lesion associated with inflammatory response. ?MWCNT was internalized into cells via caveolin- and clathrin-mediated endocytosis. ?8-Nitroguanine formation and iNOS expression involved these types of endocytosis. ?Internalized MWCNT plays a key role in inflammatory response and DNA damage.

  10. Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 Diabetes

    SciTech Connect (OSTI)

    Bhatt, Shweta; Gupta, Manoj; Khamaisi, Mogher; Martinez, Rachael; Gritsenko, Marina A.; Wagner, Bridget; Guye, Patrick; Busskamp, Volker; Shirakawa, Jun; Wu, Gongxiong; Liew, Chong Wee; Clauss, Therese RW; Valdez, Ivan; EL Ouaaman, Abdelfattah; Dirice, Ercument; Takatani, Tomozumi; Keenan, Hillary; Smith, Richard D.; Church, George; Weiss, Ron; Wagers, Amy J.; Qian, Weijun; King, George L.; Kulkami, Rohit N.

    2015-08-04

    Themechanisms underlying the development of complications in type 1 diabetes (T1D) are poorly understood. Disease modeling of induced pluripotent stem cells (iPSCs) from patients with longstanding T1D(disease durationR50 years) with severe (Medalist +C) or absent to mild complications (Medalist *C) revealed impaired growth, reprogramming, and differentiation in Medalist +C. Genomics and proteomics analyses suggested differential regulation of DNA damage checkpoint proteins favoring protection from cellular apoptosis in Medalist *C. In silico analyses showed altered expression patterns of DNA damage checkpoint factors among the Medalist groups to be targets of miR200, whose expression was significantly elevated in Medalist +C serum. Notably, neurons differentiated from Medalist +C iPSCs exhibited enhanced susceptibility to genotoxic stress that worsened upon miR200 overexpression. Furthermore, knockdown of miR200 in Medalist +C fibroblasts and iPSCs rescued checkpoint protein expression and reduced DNA damage.WeproposemiR200-regulated DNA damage checkpoint pathway as a potential therapeutic target for treating complications of diabetes.

  11. Genome-Wide Identification and 3D Modeling of Proteins involved in DNA Damage Recognition and Repair (Final Report)

    SciTech Connect (OSTI)

    Ruben A. Abagyan, PhD

    2004-04-15

    OAK-B135 DNA Damage Recognition and Repair (DDR and R) proteins play a critical role in cellular responses to low-dose radiation and are associated with cancer. the authors have performed a systematic, genome-wide computational analysis of genomic data for human genes involved in the DDR and R process. The significant achievements of this project include: (1) Construction of the computational pipeline for searching DDR and R genes, building and validation of 3D models of proteins involved in DDR and R; (2) Functional and structural annotation of the 3D models and generation of comprehensive lists of suggested knock-out mutations; (3) Important improvement of macromolecular docking technology and its application to predict the DNA-Protein complex conformation; (4) Development of a new algorithm for improved analysis of high-density oligonucleotide arrays for gene expression profiling; (5) Construction and maintenance of the DNA Damage Recognition and Repair Database; and (6) Producing 14 research papers (10 published and 4 in preparation).

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

    SciTech Connect (OSTI)

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

    2013-02-01

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

  13. Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

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

    Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun; Park, Beomseok; Shim, Yoonjung; Kim, Youngchang; Liu, Lili; Van Houten, Bennett; He, Chuan; Ansari, Anjum; et al

    2015-01-06

    The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformations similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivitymore » arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump pertubation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.« less

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

    SciTech Connect (OSTI)

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

    2014-09-22

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

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

    SciTech Connect (OSTI)

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

    2013-05-14

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

  16. DNA damage in internal organs after cutaneous exposure to sulphur mustard

    SciTech Connect (OSTI)

    Batal, Mohamed; Boudry, Isabelle; Mouret, Stéphane; Cléry-Barraud, Cécile; Wartelle, Julien; Bérard, Izabel

    2014-07-01

    Sulphur mustard (SM) is a chemical warfare agent that attacks mainly skin, eye and lungs. Due to its lipophilic properties, SM is also able to diffuse through the skin and reach internal organs. DNA represents one of the most critical molecular targets of this powerful alkylating agent which modifies DNA structure by forming monoadducts and biadducts. These DNA lesions are involved in the acute toxicity of SM as well as its long-term carcinogenicity. In the present work we studied the formation and persistence of guanine and adenine monoadducts and guanine biadducts in the DNA of brain, lungs, kidneys, spleen, and liver of SKH-1 mice cutaneously exposed to 2, 6 and 60 mg/kg of SM. SM-DNA adducts were detected in all studied organs, except in liver at the two lowest doses. Brain and lungs were the organs with the highest level of SM-DNA adducts, followed by kidney, spleen and liver. Monitoring the level of adducts for three weeks after cutaneous exposure showed that the lifetime of adducts were not the same in all organs, lungs being the organ with the longest persistence. Diffusion from skin to internal organs was much more efficient at the highest compared to the lowest dose investigated as the result of the loss of the skin barrier function. These data provide novel information on the distribution of SM in tissues following cutaneous exposures and indicate that brain is an important target. - Highlights: • Sulphur mustard reaches internal organs after skin exposure • Adducts are detected in the DNA of internal organs • Brain is the organ with the highest level of DNA damage • The barrier function of skin is lost at high dose of sulphur mustard • DNA adducts persist in organs for 2 or 3 weeks.

  17. Investigations of DNA damage induction and repair resulting from cellular exposure to high dose-rate pulsed proton beams

    SciTech Connect (OSTI)

    Renis, M.; Malfa, G.; Tomasello, B.; Borghesi, M.; Schettino, G.; Favetta, M.; Romano, F.; Cirrone, G. A. P.; Manti, L.

    2013-07-26

    Studies regarding the radiobiological effects of low dose radiation, microbeam irradiation services have been developed in the world and today laser acceleration of protons and heavy ions may be used in radiation therapy. The application of different facilities is essential for studying bystander effects and relating signalling phenomena in different cells or tissues. In particular the use of ion beams results advantageous in cancer radiotherapy compared to more commonly used X-rays, since the ability of ions in delivering lethal amount of doses into the target tumour avoiding or limiting damage to the contiguous healthy tissues. At the INFN-LNS in Catania, a multidisciplinary radiobiology group is strategically structured aimed to develop radiobiological research, finalised to therapeutic applications, compatible with the use of high dose laser-driven ion beams. The characteristic non-continuous dose rates with several orders of magnitude of laser-driven ion beams makes this facility very interesting in the cellular systems' response to ultra-high dose rates with non-conventional pulse time intervals cellular studies. Our group have projected to examine the effect of high dose laser-driven ion beams on two cellular types: foetal fibroblasts (normal control cells) and DU145 (prostate cancer cells), studying the modulation of some different bio-molecular parameters, in particular cell proliferation and viability, DNA damage, redox cellular status, morphological alterations of both the cytoskeleton components and some cell organelles and the possible presence of apoptotic or necrotic cell death. Our group performed preliminary experiments with high energy (60 MeV), dose rate of 10 Gy/min, doses of 1, 2, 3 Gy and LET 1 keV/?m on human foetal fibroblasts (control cells). We observed that cell viability was not influenced by the characteristics of the beam, the irradiation conditions or the analysis time. Conversely, DNA damage was present at time 0, immediately following irradiation in a dose-dependent manner. The analysis of repair capability showed that the cells irradiated with 1 and 2 Gy almost completely recovered from the damage, but not, however, 3 Gy treated cells in which DNA damage was not recovered. In addition, the results indicate the importance of the use of an appropriate control in radiobiological in vitro analysis.

  18. Genome-Wide Identification and 3D Modeling of Proteins involved in DNA Damage Recognition and Repair (Final Report)

    SciTech Connect (OSTI)

    Abagyan, Ruben; An, Jianghong

    2005-08-12

    DNA Damage Recognition and Repair (DDR&R) proteins play a critical role in cellular responses to low-dose radiation and are associated with cancer. We have performed a systematic, genome-wide computational analysis of genomic data for human genes involved in the DDR&R process. The significant achievements of this project include: 1) Construction of the computational pipeline for searching DDR&R genes, building and validation of 3D models of proteins involved in DDR&R; 2) Functional and structural annotation of the 3D models and generation of comprehensive lists of suggested knock-out mutations; and the development of a method to predict the effects of mutations. Large scale testing of technology to identify novel small binding pockets in protein structures leading to new DDRR inhibitor strategies 3) Improvements of macromolecular docking technology (see the CAPRI 1-3 and 4-5 results) 4) Development of a new algorithm for improved analysis of high-density oligonucleotide arrays for gene expression profiling; 5) Construction and maintenance of the DNA Damage Recognition and Repair Database; 6) Producing 15 research papers (12 published and 3 in preparation).

  19. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    of genomic integrity and responses to DNA damage relevant to pathogens and cancer development. DNA Repair Switch A process similar in spirit to that of a railroad...

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

    SciTech Connect (OSTI)

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

    2012-05-01

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

  1. DNA repair efficiency in germ cells and early mouse embryos and consequences for radiation-induced transgenerational genomic damage

    SciTech Connect (OSTI)

    Marchetti, Francesco; Wyrobek, Andrew J.

    2009-01-18

    Exposure to ionizing radiation and other environmental agents can affect the genomic integrity of germ cells and induce adverse health effects in the progeny. Efficient DNA repair during gametogenesis and the early embryonic cycles after fertilization is critical for preventing transmission of DNA damage to the progeny and relies on maternal factors stored in the egg before fertilization. The ability of the maternal repair machinery to repair DNA damage in both parental genomes in the fertilizing egg is especially crucial for the fertilizing male genome that has not experienced a DNA repair-competent cellular environment for several weeks prior to fertilization. During the DNA repair-deficient period of spermatogenesis, DNA lesions may accumulate in sperm and be carried into the egg where, if not properly repaired, could result in the formation of heritable chromosomal aberrations or mutations and associated birth defects. Studies with female mice deficient in specific DNA repair genes have shown that: (i) cell cycle checkpoints are activated in the fertilized egg by DNA damage carried by the sperm; and (ii) the maternal genotype plays a major role in determining the efficiency of repairing genomic lesions in the fertilizing sperm and directly affect the risk for abnormal reproductive outcomes. There is also growing evidence that implicates DNA damage carried by the fertilizing gamete as a mediator of postfertilization processes that contribute to genomic instability in subsequent generations. Transgenerational genomic instability most likely involves epigenetic mechanisms or error-prone DNA repair processes in the early embryo. Maternal and embryonic DNA repair processes during the early phases of mammalian embryonic development can have far reaching consequences for the genomic integrity and health of subsequent generations.

  2. Silencing of poly(ADP-ribose) glycohydrolase sensitizes lung cancer cells to radiation through the abrogation of DNA damage checkpoint

    SciTech Connect (OSTI)

    Nakadate, Yusuke; Department of Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585 ; Kodera, Yasuo; Kitamura, Yuka; Tachibana, Taro; Tamura, Tomohide; Koizumi, Fumiaki

    2013-11-29

    Highlights: Radiosensitization by PARG silencing was observed in multiple lung cancer cells. PAR accumulation was enhanced by PARG silencing after DNA damage. Radiation-induced G2/M arrest and checkpoint activation were impaired by PARG siRNA. -- Abstract: Poly(ADP-ribose) glycohydrolase (PARG) is a major enzyme that plays a role in the degradation of poly(ADP-ribose) (PAR). PARG deficiency reportedly sensitizes cells to the effects of radiation. In lung cancer, however, it has not been fully elucidated. Here, we investigated whether PARG siRNA contributes to an increased radiosensitivity using 8 lung cancer cell lines. Among them, the silencing of PARG induced a radiosensitizing effect in 5 cell lines. Radiation-induced G2/M arrest was largely suppressed by PARG siRNA in PC-14 and A427 cells, which exhibited significantly enhanced radiosensitivity in response to PARG knockdown. On the other hand, a similar effect was not observed in H520 cells, which did not exhibit a radiosensitizing effect. Consistent with a cell cycle analysis, radiation-induced checkpoint signals were not well activated in the PC-14 and A427 cells when treated with PARG siRNA. These results suggest that the increased sensitivity to radiation induced by PARG knockdown occurs through the abrogation of radiation-induced G2/M arrest and checkpoint activation in lung cancer cells. Our findings indicate that PARG could be a potential target for lung cancer treatments when used in combination with radiotherapy.

  3. Accident response group (ARG) containers for recovery of damaged warheads

    SciTech Connect (OSTI)

    York, A.R. II; Hoffman, J.P.

    1993-09-01

    This report provides an overview of the containers that are currently stored at Pantex and available for use in response to an accident or for use in any other application where a sealed containment vessel and accident resistant overpack may be needed.

  4. Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2...

    Office of Scientific and Technical Information (OSTI)

    DETECTION; DNA; EXCISION REPAIR; IN VIVO; LIGASES; NUCLEOTIDES; PROTEINS; PYRIMIDINES; TARGETS Word Cloud More Like This Full Text Journal Articles DOI: 10.1016j.cell.2008.10.045

  5. Response and representation of ductile damage under varying shock loading conditions in tantalum

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

    Bronkhorst, C. A.; Gray, III, G. T.; Addessio, F. L.; Livescu, V.; Bourne, N. K.; MacDonald, S. A.; Withers, P. J.

    2016-02-25

    The response of polycrystalline metals, which possess adequate mechanisms for plastic deformation under extreme loading conditions, is often accompanied by the formation of pores within the structure of the material. This large deformation process is broadly identified as progressive with nucleation, growth, coalescence, and failure the physical path taken over very short periods of time. These are well known to be complex processes strongly influenced by microstructure, loading path, and the loading profile, which remains a significant challenge to represent and predict numerically. In the current study, the influence of loading path on the damage evolution in high-purity tantalum ismore » presented. Tantalum samples were shock loaded to three different peak shock stresses using both symmetric impact, and two different composite flyer plate configurations such that upon unloading the three samples displayed nearly identical “pull-back” signals as measured via rear-surface velocimetry. While the “pull-back” signals observed were found to be similar in magnitude, the sample loaded to the highest peak stress nucleated a connected field of ductile fracture which resulted in complete separation, while the two lower peak stresses resulted in incipient damage. The damage evolution in the “soft” recovered tantalum samples was quantified using optical metallography, electron-back-scatter diffraction, and tomography. These experiments are examined numerically through the use of a model for shock-induced porosity evolution during damage. The model is shown to describe the response of the tantalum reasonably well under strongly loaded conditions but less well in the nucleation dominated regime. As a result, numerical results are also presented as a function of computational mesh density and discussed in the context of improved representation of the influence of material structure upon macro-scale models of ductile damage.« less

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

    SciTech Connect (OSTI)

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

    2011-06-01

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

  7. Modeling of Damage, Permeability Changes and Pressure Responses during Excavation of the TSX Tunnel in Granitic Rock at URL, Canada

    SciTech Connect (OSTI)

    Rutqvist, Jonny; Borgesson, Lennart; Chijimatsu, Masakazu; Hernelind, Jan; Jing, Lanru; Kobayashi, Akira; Nguyen, Son

    2008-08-01

    This paper presents numerical modeling of excavation-induced damage, permeability changes, and fluid-pressure responses during excavation of the TSX tunnel at the underground research laboratory (URL) in Canada. Four different numerical models were applied, using a wide range of approaches to model damage and permeability changes in the excavation disturbed zone (EDZ) around the tunnel. Using in situ calibration of model parameters the modeling could reproduce observed spatial distribution of damage and permeability changes around the tunnel, as a combination of disturbance induced by stress redistribution around the tunnel and by the drill-and-blast operation. The modeling showed that stress-induced permeability increase above the tunnel is a result of micro and macrofracturing under high deviatoric (shear) stress, whereas permeability increases alongside the tunnel as a result of opening of existing microfractures under decreased mean stress. The remaining observed fracturing and permeability changes around the periphery of the tunnel were attributed to damage from the drill-and-blast operation. Moreover, a reasonably good agreement was achieved between simulated and observed excavation-induced pressure responses around the TSX tunnel for 1 year following its excavation. The simulations showed that these pressure responses are caused by poroelastic effects as a result of increasing or decreasing mean stress, with corresponding contraction or expansion of the pore volume. The simulation results for pressure evolution were consistent with previous studies, indicating that the observed pressure responses could be captured in a Biot model using a relatively low Biot-Willis coefficient, {alpha} {approx} 0.2, a porosity of n {approx} 0.007, and a relatively low permeability of k {approx} 2 x 10{sup -22} m{sup 2}, which is consistent with the very tight, unfractured granite at the site.

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

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

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

    2014-01-01

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

  9. DNA

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

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

  10. Chemopreventive activity of compounds extracted from Casearia sylvestris (Salicaceae) Sw against DNA damage induced by particulate matter emitted by sugarcane burning near Araraquara, Brazil

    SciTech Connect (OSTI)

    Prieto, A.M.; Santos, A.G.; Csipak, A.R.; Caliri, C.M.; Silva, I.C.; Arbex, M.A.; Silva, F.S.; Marchi, M.R.R.

    2012-12-15

    Ethanolic extract of Casearia sylvestris is thought to be antimutagenic. In this study, we attempted to determine whether this extract and casearin X (a clerodane diterpene from C. sylvestris) are protective against the harmful effects of airborne pollutants from sugarcane burning. To that end, we used the Tradescantia micronucleus test in meiotic pollen cells of Tradescantia pallida, the micronucleus test in mouse bone marrow cells, and the comet assay in mouse blood cells. The mutagenic compound was total suspended particulate (TSP) from air. For the Tradescantia micronucleus test, T. pallida cuttings were treated with the extract at 0.13, 0.25, or 0.50 mg/ml. Subsequently, TSP was added at 0.3 mg/ml, and tetrads from the inflorescences were examined for micronuclei. For the micronucleus test in mouse bone marrow cells and the comet assay in mouse blood cells, Balb/c mice were treated for 15 days with the extract3.9, 7.5, or 15.0 mg/kg body weight (BW)or with casearin X0.3, 0.25, or 1.2 mg/kg BWafter which they received TSP (3.75 mg/kg BW). In T. pallida and mouse bone marrow cells, the extract was antimutagenic at all concentrations tested. In mouse blood cells, the extract was antigenotoxic at all concentrations, whereas casearin X was not antimutagenic but was antigenotoxic at all concentrations. We conclude that C. sylvestris ethanolic extract and casearin X protect DNA from damage induced by airborne pollutants from sugarcane burning. -- Highlights: ? We assessed DNA protection of C. sylvestris ethanolic extract. ? We assessed DNA protection of casearin X. ? We used Tradescantia pallida micronucleus test as screening. ? We used comet assay and micronucleus test in mice. ? The compounds protected DNA against sugar cane burning pollutants.

  11. Oxidative DNA damage and repair in children exposed to low levels of arsenic in utero and during early childhood: Application of salivary and urinary biomarkers

    SciTech Connect (OSTI)

    Hinhumpatch, Pantip; Navasumrit, Panida; Chaisatra, Krittinee; Promvijit, Jeerawan; Mahidol, Chulabhorn; Ruchirawat, Mathuros

    2013-12-15

    The present study aimed to assess arsenic exposure and its effect on oxidative DNA damage and repair in young children exposed in utero and continued to live in arsenic-contaminated areas. To address the need for biological specimens that can be acquired with minimal discomfort to children, we used non-invasive urinary and salivary-based assays for assessing arsenic exposure and early biological effects that have potentially serious health implications. Levels of arsenic in nails showed the greatest magnitude of difference between exposed and control groups, followed by arsenic concentrations in saliva and urine. Arsenic levels in saliva showed significant positive correlations with other biomarkers of arsenic exposure, including arsenic accumulation in nails (r = 0.56, P < 0.001) and arsenic concentration in urine (r = 0.50, P < 0.05). Exposed children had a significant reduction in arsenic methylation capacity indicated by decreased primary methylation index and secondary methylation index in both urine and saliva samples. Levels of salivary 8-OHdG in exposed children were significantly higher (? 4-fold, P < 0.01), whereas levels of urinary 8-OHdG excretion and salivary hOGG1 expression were significantly lower in exposed children (? 3-fold, P < 0.05), suggesting a defect in hOGG1 that resulted in ineffective cleavage of 8-OHdG. Multiple regression analysis results showed that levels of inorganic arsenic (iAs) in saliva and urine had a significant positive association with salivary 8-OHdG and a significant negative association with salivary hOGG1 expression. - Highlights: The effects of arsenic exposure in utero and through early childhood were studied. Arsenic-exposed children had a reduction in arsenic methylation capacity. Exposed children had more DNA damage, observed as elevated salivary 8-OHdG. Lower salivary hOGG1 in exposed children indicated impairment of 8-OHdG repair. Salivary and urinary 8-OHdG levels were discordant.

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

    SciTech Connect (OSTI)

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

    2014-01-01

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

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

    SciTech Connect (OSTI)

    Quirk, W.A.

    1993-04-01

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

  14. A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin

    SciTech Connect (OSTI)

    Davlieva, Milya; Shi, Yiwen; Leonard, Paul G.; Johnson, Troy A.; Zianni, Michael R.; Arias, Cesar A.; Ladbury, John E.; Shamoo, Yousif

    2015-04-19

    LiaR is a ‘master regulator’ of the cell envelope stress response in enterococci and many other Gram-positive organisms. Mutations to liaR can lead to antibiotic resistance to a variety of antibiotics including the cyclic lipopeptide daptomycin. LiaR is phosphorylated in response to membrane stress to regulate downstream target operons. Using DNA footprinting of the regions upstream of the liaXYZ and liaFSR operons we show that LiaR binds an extended stretch of DNA that extends beyond the proposed canonical consensus sequence suggesting a more complex level of regulatory control of target operons. We go on to determine the biochemical and structural basis for increased resistance to daptomycin by the adaptive mutation to LiaR (D191N) first identified from the pathogen Enterococcus faecalis S613. LiaRD191N increases oligomerization of LiaR to form a constitutively activated tetramer that has high affinity for DNA even in the absence of phosphorylation leading to increased resistance. The crystal structures of the LiaR DNA binding domain complexed to the putative consensus sequence as well as an adjoining secondary sequence show that upon binding, LiaR induces DNA bending that is consistent with increased recruitment of RNA polymerase to the transcription start site and upregulation of target operons.

  15. A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin

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

    Davlieva, Milya; Shi, Yiwen; Leonard, Paul G.; Johnson, Troy A.; Zianni, Michael R.; Arias, Cesar A.; Ladbury, John E.; Shamoo, Yousif

    2015-04-19

    LiaR is a ‘master regulator’ of the cell envelope stress response in enterococci and many other Gram-positive organisms. Mutations to liaR can lead to antibiotic resistance to a variety of antibiotics including the cyclic lipopeptide daptomycin. LiaR is phosphorylated in response to membrane stress to regulate downstream target operons. Using DNA footprinting of the regions upstream of the liaXYZ and liaFSR operons we show that LiaR binds an extended stretch of DNA that extends beyond the proposed canonical consensus sequence suggesting a more complex level of regulatory control of target operons. We go on to determine the biochemical and structuralmore » basis for increased resistance to daptomycin by the adaptive mutation to LiaR (D191N) first identified from the pathogen Enterococcus faecalis S613. LiaRD191N increases oligomerization of LiaR to form a constitutively activated tetramer that has high affinity for DNA even in the absence of phosphorylation leading to increased resistance. The crystal structures of the LiaR DNA binding domain complexed to the putative consensus sequence as well as an adjoining secondary sequence show that upon binding, LiaR induces DNA bending that is consistent with increased recruitment of RNA polymerase to the transcription start site and upregulation of target operons.« less

  16. Activation of eNOS in endothelial cells exposed to ionizing radiation involves components of the DNA damage response pathway

    SciTech Connect (OSTI)

    Nagane, Masaki; Yasui, Hironobu; Sakai, Yuri; Yamamori, Tohru; Niwa, Koichi; Hattori, Yuichi; Kondo, Takashi; Inanami, Osamu

    2015-01-02

    Highlights: eNOS activity is increased in BAECs exposed to X-rays. ATM is involved in this increased eNOS activity. HSP90 modulates the radiation-induced activation of ATM and eNOS. - Abstract: In this study, the involvement of ataxia telangiectasia mutated (ATM) kinase and heat shock protein 90 (HSP90) in endothelial nitric oxide synthase (eNOS) activation was investigated in X-irradiated bovine aortic endothelial cells. The activity of nitric oxide synthase (NOS) and the phosphorylation of serine 1179 of eNOS (eNOS-Ser1179) were significantly increased in irradiated cells. The radiation-induced increases in NOS activity and eNOS-Ser1179 phosphorylation levels were significantly reduced by treatment with either an ATM inhibitor (Ku-60019) or an HSP90 inhibitor (geldanamycin). Geldanamycin was furthermore found to suppress the radiation-induced phosphorylation of ATM-Ser1181. Our results indicate that the radiation-induced eNOS activation in bovine aortic endothelial cells is regulated by ATM and HSP90.

  17. Analysis of Flow Cytometry DNA Damage Response Protein Activation Kinetics Following X-rays and High Energy Iron Nuclei Exposure

    SciTech Connect (OSTI)

    Universities Space Research Association; Chappell, Lori J.; Whalen, Mary K.; Gurai, Sheena; Ponomarev, Artem; Cucinotta, Francis A.; Pluth, Janice M.

    2010-12-15

    We developed a mathematical method to analyze flow cytometry data to describe the kinetics of {gamma}H2AX and pATF2 phosphorylations ensuing various qualities of low dose radiation in normal human fibroblast cells. Previously reported flow cytometry kinetic results for these DSB repair phospho-proteins revealed that distributions of intensity were highly skewed, severely limiting the detection of differences in the very low dose range. Distributional analysis reveals significant differences between control and low dose samples when distributions are compared using the Kolmogorov-Smirnov test. Radiation quality differences are found in the distribution shapes and when a nonlinear model is used to relate dose and time to the decay of the mean ratio of phosphoprotein intensities of irradiated samples to controls. We analyzed cell cycle phase and radiation quality dependent characteristic repair times and residual phospho-protein levels with these methods. Characteristic repair times for {gamma}H2AX were higher following Fe nuclei as compared to X-rays in G1 cells (4.5 {+-} 0.46 h vs 3.26 {+-} 0.76 h, respectively), and in S/G2 cells (5.51 {+-} 2.94 h vs 2.87 {+-} 0.45 h, respectively). The RBE in G1 cells for Fe nuclei relative to X-rays for {gamma}H2AX was 2.05 {+-} 0.61 and 5.02 {+-} 3.47, at 2 h and 24-h postirradiation, respectively. For pATF2, a saturation effect is observed with reduced expression at high doses, especially for Fe nuclei, with much slower characteristic repair times (>7 h) compared to X-rays. RBEs for pATF2 were 0.66 {+-} 0.13 and 1.66 {+-} 0.46 at 2 h and 24 h, respectively. Significant differences in {gamma}H2AX and pATF2 levels comparing irradiated samples to control were noted even at the lowest dose analyzed (0.05 Gy) using these methods of analysis. These results reveal that mathematical models can be applied to flow cytometry data to uncover important and subtle differences following exposure to various qualities of low dose radiation.

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

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

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

    2014-04-01

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

  19. DNA ELECTROPHORESIS AT SURFACES

    SciTech Connect (OSTI)

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01

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

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

    SciTech Connect (OSTI)

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

    2014-11-20

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

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

    SciTech Connect (OSTI)

    Peng, Jamy C.

    2007-05-05

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

  2. Sulforaphane, a cancer chemopreventive agent, induces pathways associated with membrane biosynthesis in response to tissue damage by aflatoxin B{sub 1}

    SciTech Connect (OSTI)

    Techapiesancharoenkij, Nirachara; Fiala, Jeannette L.A.; Navasumrit, Panida; Croy, Robert G.; Wogan, Gerald N.; Groopman, John D.; Ruchirawat, Mathuros; Essigmann, John M.

    2015-01-01

    Aflatoxin B{sub 1} (AFB{sub 1}) is one of the major risk factors for liver cancer globally. A recent study showed that sulforaphane (SF), a potent inducer of phase II enzymes that occurs naturally in widely consumed vegetables, effectively induces hepatic glutathione S-transferases (GSTs) and reduces levels of hepatic AFB{sub 1}-DNA adducts in AFB{sub 1}-exposed Sprague Dawley rats. The present study characterized the effects of SF pre-treatment on global gene expression in the livers of similarly treated male rats. Combined treatment with AFB{sub 1} and SF caused reprogramming of a network of genes involved in signal transduction and transcription. Changes in gene regulation were observable 4 h after AFB{sub 1} administration in SF-pretreated animals and may reflect regeneration of cells in the wake of AFB{sub 1}-induced hepatotoxicity. At 24 h after AFB{sub 1} administration, significant induction of genes that play roles in cellular lipid metabolism and acetyl-CoA biosynthesis was detected in SF-pretreated AFB{sub 1}-dosed rats. Induction of this group of genes may indicate a metabolic shift toward glycolysis and fatty acid synthesis to generate and maintain pools of intermediate molecules required for tissue repair, cell growth and compensatory hepatic cell proliferation. Collectively, gene expression data from this study provide insights into molecular mechanisms underlying the protective effects of SF against AFB{sub 1} hepatotoxicity and hepatocarcinogenicity, in addition to the chemopreventive activity of this compound as a GST inducer. - Highlights: • This study revealed sulforaphane (SF)-deregulated gene sets in aflatoxin B{sub 1} (AFB{sub 1})-treated rat livers. • SF redirects biochemical networks toward lipid biosynthesis in AFB{sub 1}-dosed rats. • SF enhanced gene sets that would be expected to favor cell repair and regeneration.

  3. Response Response

    National Nuclear Security Administration (NNSA)

    Attachment 7 Response Response Response Response Response Response Response Response Response Response Response Response Percent of Mentors that are People with Disabilities 9.00% Total number of Mentors (The count used to calculate the Mentor percentages) 252 Demographic Information Percent of Mentors Two or More Races Not reported Percent of White Mentors 63.00% Percent of Female Mentors 39.00% Percent of Male Mentors 61.00% Percent of Veteran Mentors 21.00% Percent of Asian American Mentors

  4. Response

    Energy Savers [EERE]

    Response SEAB Recommendations Related to the Evaluation of New Funding Constructs for Energy R&D in the Department of Energy Introduction Over the past seven years, the Department of Energy (DOE) has introduced several new energy research and development (R&D) management and funding mechanisms, designed to complement each other, with the goal of maximizing the Nation's ability to achieve energy breakthroughs as quickly as possible. * Energy Frontier Research Centers (EFRCs) focus on

  5. Dna Sequencing

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

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

  6. Convention on Supplementary Compensation for Nuclear Damage Contingent...

    Office of Environmental Management (EM)

    Section 934 Convention on Supplementary Compensation for Nuclear Damage Contingent Cost Allocation, Section 934 LES comments in response to Notice of Inquiry on Convention on...

  7. BuD, a helixloophelix DNA-binding domain for genome modification

    SciTech Connect (OSTI)

    Stella, Stefano; Molina, Rafael; Lpez-Mndez, Blanca; Juillerat, Alexandre; Bertonati, Claudia; Daboussi, Fayza; Campos-Olivas, Ramon; Duchateau, Phillippe; Montoya, Guillermo

    2014-07-01

    Crystal structures of BurrH and the BurrHDNA complex are reported. DNA editing offers new possibilities in synthetic biology and biomedicine for modulation or modification of cellular functions to organisms. However, inaccuracy in this process may lead to genome damage. To address this important problem, a strategy allowing specific gene modification has been achieved through the addition, removal or exchange of DNA sequences using customized proteins and the endogenous DNA-repair machinery. Therefore, the engineering of specific proteinDNA interactions in protein scaffolds is key to providing toolkits for precise genome modification or regulation of gene expression. In a search for putative DNA-binding domains, BurrH, a protein that recognizes a 19 bp DNA target, was identified. Here, its apo and DNA-bound crystal structures are reported, revealing a central region containing 19 repeats of a helixloophelix modular domain (BurrH domain; BuD), which identifies the DNA target by a single residue-to-nucleotide code, thus facilitating its redesign for gene targeting. New DNA-binding specificities have been engineered in this template, showing that BuD-derived nucleases (BuDNs) induce high levels of gene targeting in a locus of the human haemoglobin ? (HBB) gene close to mutations responsible for sickle-cell anaemia. Hence, the unique combination of high efficiency and specificity of the BuD arrays can push forward diverse genome-modification approaches for cell or organism redesign, opening new avenues for gene editing.

  8. G2 Checkpoint Responses in Arabidopsis

    SciTech Connect (OSTI)

    Britt, Anne

    2013-03-18

    This project focused on the mechanism and biological significance of the G2 arrest response to replication stress in plants. We employed both forward and reverse genetic approaches to identify genes required for this response. A total of 3 different postdocs, 5 undergraduates, and 2 graduate students participated in the project. We identified several genes required for damage response in plants, including homologs of genes previously identified in animals (ATM and ATR), novel, a plant-specific genes (SOG1) and a gene known in animals but previously thought to be missing from the Arabidopsis genome (ATRIP). We characterized the transcriptome of gamma-irradiated plants, and found that plants, unlike animals, express a robust transcriptional response to damage, involving genes that regulate the cell cycle and DNA metabolism. This response requires both ATM and the transcription factor SOG1. We found that both ATM and ATR play a role in meiosis in plants. We also found that plants have a cell-type-specific programmed cell death response to ionizing radiation and UV light, and that this response requires ATR, ATM, and SOG1. These results were published in a series of 5 papers.

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

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

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

    2014-11-20

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

  10. Oxidative phosphorylation-dependent regulation of cancer cell apoptosis in response to anticancer agents

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

    Yadav, N.; Kumar, S.; Marlowe, T.; Chaudhary, A. K.; Kumar, R.; Wang, J.; O'Malley, J.; Boland, P. M.; Jayanthi, S.; Kumar, T. K. S.; et al

    2015-11-05

    Cancer cells tend to develop resistance to various types of anticancer agents, whether they adopt similar or distinct mechanisms to evade cell death in response to a broad spectrum of cancer therapeutics is not fully defined. Current study concludes that DNA-damaging agents (etoposide and doxorubicin), ER stressor (thapsigargin), and histone deacetylase inhibitor (apicidin) target oxidative phosphorylation (OXPHOS) for apoptosis induction, whereas other anticancer agents including staurosporine, taxol, and sorafenib induce apoptosis in an OXPHOS-independent manner. DNA-damaging agents promoted mitochondrial biogenesis accompanied by increased accumulation of cellular and mitochondrial ROS, mitochondrial protein-folding machinery, and mitochondrial unfolded protein response. Induction of mitochondrialmore » biogenesis occurred in a caspase activation-independent mechanism but was reduced by autophagy inhibition and p53-deficiency. Abrogation of complex-I blocked DNA-damage-induced caspase activation and apoptosis, whereas inhibition of complex-II or a combined deficiency of OXPHOS complexes I, III, IV, and V due to impaired mitochondrial protein synthesis did not modulate caspase activity. Mechanistic analysis revealed that inhibition of caspase activation in response to anticancer agents associates with decreased release of mitochondrial cytochrome c in complex-I-deficient cells compared with wild type (WT) cells. Gross OXPHOS deficiencies promoted increased release of apoptosis-inducing factor from mitochondria compared with WT or complex-I-deficient cells, suggesting that cells harboring defective OXPHOS trigger caspase-dependent as well as caspase-independent apoptosis in response to anticancer agents. Interestingly, DNA-damaging agent doxorubicin showed strong binding to mitochondria, which was disrupted by complex-I-deficiency but not by complex-II-deficiency. Thapsigargin-induced caspase activation was reduced upon abrogation of complex-I or gross OXPHOS deficiency whereas a reverse trend was observed with apicidin. Together, these finding provide a new strategy for differential mitochondrial targeting in cancer therapy.« less

  11. Convention on Supplementary Compensation for Nuclear Damage Contingent Cost

    Office of Environmental Management (EM)

    Allocation, Section 934 | Department of Energy Allocation, Section 934 Convention on Supplementary Compensation for Nuclear Damage Contingent Cost Allocation, Section 934 LES comments in response to Notice of Inquiry on Convention on Supplementary Compensation for Nuclear Damage Contingent Cost Allocation, Section 934 PDF icon Convention on Supplementary Compensation for Nuclear Damage Contingent Cost Allocation, Section 934 More Documents & Publications Public comment re Convention on

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

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

    Engine Vehicle Exhaust Particulate and Semi-Volatile Organic Compound Materials In Vitro Genotoxicity of Particulate and Semi-Volatile Organic Compound Exhaust Materails from a ...

  13. Structural damage detection using the holder exponent.

    SciTech Connect (OSTI)

    Farrar, C. R.; Do, N. B.; Green, S. R.; Schwartz, T. A.

    2002-01-01

    This paper implements a damage detection strategy that identifies damage sensitive features associated with nonlinearities. Some rion-linezlrities result from discontinuities introduced into the data by certain types of darnage. These discontinuities may also result from noise in the measured dynamic response data or can be caused by random excitation of the system. The Holder Exponent, which is a measure of the degree to which a signal is differentiable, is used to detect the discontinuities. By studying the Holder bponent as a function af time, a statistical model is developed that classifies changes in the Holder Exponent that are associated with clamage-induced discontinuities. The results show that for certain cases, the Holder Exponent is an effective technique to detect damage.

  14. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

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

  15. BPA-2011-00384-FOIA Response

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

    damaged due to gunfire, on or around January 2010, in the Tiger Mountain Summit area of King County Washington. Response: BPA has provided a responsive document with the...

  16. Uncertainty of silicon 1-MeV damage function

    SciTech Connect (OSTI)

    Danjaji, M.B.; Griffin, P.J.

    1997-02-01

    The electronics radiation hardness-testing community uses the ASTM E722-93 Standard Practice to define the energy dependence of the nonionizing neutron damage to silicon semiconductors. This neutron displacement damage response function is defined to be equal to the silicon displacement kerma as calculated from the ORNL Si cross-section evaluation. Experimental work has shown that observed damage ratios at various test facilities agree with the defined response function to within 5%. Here, a covariance matrix for the silicon 1-MeV neutron displacement damage function is developed. This uncertainty data will support the electronic radiation hardness-testing community and will permit silicon displacement damage sensors to be used in least squares spectrum adjustment codes.

  17. 8-Oxoguanine DNA glycosylase 1 (ogg1) maintains the function of cardiac progenitor cells during heart formation in zebrafish

    SciTech Connect (OSTI)

    Yan, Lifeng; Zhou, Yong; Yu, Shanhe; Ji, Guixiang; Liu, Wei; Gu, Aihua

    2013-11-15

    Genomic damage may devastate the potential of progenitor cells and consequently impair early organogenesis. We found that ogg1, a key enzyme initiating the base-excision repair, was enriched in the embryonic heart in zebrafish. So far, little is known about DNA repair in cardiogenesis. Here, we addressed the critical role of ogg1 in cardiogenesis for the first time. ogg1 mainly expressed in the anterior lateral plate mesoderm (ALPM), the primary heart tube, and subsequently the embryonic myocardium by in situ hybridisation. Loss of ogg1 resulted in severe cardiac morphogenesis and functional abnormalities, including the short heart length, arrhythmia, decreased cardiomyocytes and nkx2.5{sup +} cardiac progenitor cells. Moreover, the increased apoptosis and repressed proliferation of progenitor cells caused by ogg1 deficiency might contribute to the heart phenotype. The microarray analysis showed that the expression of genes involved in embryonic heart tube morphogenesis and heart structure were significantly changed due to the lack of ogg1. Among those, foxh1 is an important partner of ogg1 in the cardiac development in response to DNA damage. Our work demonstrates the requirement of ogg1 in cardiac progenitors and heart development in zebrafish. These findings may be helpful for understanding the aetiology of congenital cardiac deficits. - Highlights: A key DNA repair enzyme ogg1 is expressed in the embryonic heart in zebrafish. We found that ogg1 is essential for normal cardiac morphogenesis in zebrafish. The production of embryonic cardiomyocytes requires appropriate ogg1 expression. Ogg1 critically regulated proliferation of cardiac progenitor cells in zebrafish. foxh1 is a partner of ogg1 in the cardiac development in response to DNA damage.

  18. Microfluidic DNA sample preparation method and device

    DOE Patents [OSTI]

    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)

    2002-01-01

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

  19. DNA polymerase with modified processivity

    DOE Patents [OSTI]

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

    1999-01-01

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

  20. Radiation Damage/Materials Modification

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

    Radiation Damage/Materials Modification High-energy ion irradiation is an important tool for studying radiation damage effects Materials in a nuclear reactor are exposed to extreme temperature and radiation conditions that degrade their physical properties to the point of failure. For example, alpha-decay in nuclear fuels results in dislocation damage to and accumulation of helium and fission gasses in the material. Similarly, neutrons interacting with non-nuclear components can displace atoms

  1. Synthesis of DNA

    DOE Patents [OSTI]

    Mariella, Jr., Raymond P. (Danville, CA)

    2008-11-18

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

  2. Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic

    Office of Scientific and Technical Information (OSTI)

    Thermophile Alvinella pompejana (Journal Article) | DOE PAGES Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana Title: Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana Human DNA polymerase η (HsPol η ) plays an important role in translesion synthesis (TLS), which allows for replication past DNA damage such as UV-induced cis-syn cyclobutane pyrimidine dimers (CPDs). Here, we

  3. DNA encoding a DNA repair protein

    DOE Patents [OSTI]

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

    2006-08-15

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

  4. Shock Initiation of Damaged Explosives

    SciTech Connect (OSTI)

    Chidester, S K; Vandersall, K S; Tarver, C M

    2009-10-22

    Explosive and propellant charges are subjected to various mechanical and thermal insults that can increase their sensitivity over the course of their lifetimes. To quantify this effect, shock initiation experiments were performed on mechanically and thermally damaged LX-04 (85% HMX, 15% Viton by weight) and PBX 9502 (95% TATB, 5% Kel-F by weight) to obtain in-situ manganin pressure gauge data and run distances to detonation at various shock pressures. We report the behavior of the HMX-based explosive LX-04 that was damaged mechanically by applying a compressive load of 600 psi for 20,000 cycles, thus creating many small narrow cracks, or by cutting wedge shaped parts that were then loosely reassembled, thus creating a few large cracks. The thermally damaged LX-04 charges were heated to 190 C for long enough for the beta to delta solid - solid phase transition to occur, and then cooled to ambient temperature. Mechanically damaged LX-04 exhibited only slightly increased shock sensitivity, while thermally damaged LX-04 was much more shock sensitive. Similarly, the insensitive explosive PBX 9502 was mechanically damaged using the same two techniques. Since PBX 9502 does not undergo a solid - solid phase transition but does undergo irreversible or 'rachet' growth when thermally cycled, thermal damage to PBX 9502 was induced by this procedure. As for LX-04, the thermally damaged PBX 9502 demonstrated a greater shock sensitivity than mechanically damaged PBX 9502. The Ignition and Growth reactive flow model calculated the increased sensitivities by igniting more damaged LX-04 and PBX 9502 near the shock front based on the measured densities (porosities) of the damaged charges.

  5. DNA repair of a single UV photoproduct in a designed nucleosome

    SciTech Connect (OSTI)

    Kosmoskil, Joseph V.; Ackerman, Eric J. ); Smerdon, Michael J.

    2001-08-28

    Eukaryotic DNA repair enzymes must interact with the architectural hierarchy of chromatin. The challenge of finding damaged DNA complexed with histone proteins in nucleosomes is complicated by the need to maintain local chromatin structures involved in regulating other DNA processing events. The heterogeneity of lesions induced by DNA-damaging agents has led us to design homogeneously damaged substrates to directly compare repair of naked DNA with that of nucleosomes. Here we report that nucleotide excision repair in Xenopus nuclear extracts can effectively repair a single UV radiation photoproduct located 5 bases from the dyad center of a positioned nucleosome, although the nucleosome is repaired at about half the rate at which the naked DNA fragment is. Extract repair within the nucleosome is > 50-fold more rapid than either enzymatic photoreversal or endonuclease cleavage of the lesion in vitro. Furthermore, nucleosome formation occurs (after repair) only on damaged naked DNA ( 165-bp fragments) during a 1-h incubation in these extracts, even in the presence of a large excess of undamaged DNA. This is an example of selective nucleosome assembly by Xenopus nuclear extracts on a short linear DNA fragment containing a DNA lesion.

  6. Quantitative DNA fiber mapping

    DOE Patents [OSTI]

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

    1998-01-01

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

  7. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

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

  8. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

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

  9. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

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

  10. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

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

  11. Acoustic emission sensor radiation damage threshold experiment

    SciTech Connect (OSTI)

    Beeson, K.M.; Pepper, C.E.

    1994-09-01

    Determination of the threshold for damage to acoustic emission sensors exposed to radiation is important in their application to leak detection in radioactive waste transport and storage. Proper response to system leaks is necessary to ensure the safe operation of these systems. A radiation impaired sensor could provide ``false negative or false positive`` indication of acoustic signals from leaks within the system. Research was carried out in the Radiochemical Technology Division at Oak Ridge National Laboratory to determine the beta/gamma radiation damage threshold for acoustic emission sensor systems. The individual system consisted of an acoustic sensor mounted with a two part epoxy onto a stainless steel waveguide. The systems were placed in an irradiation fixture and exposed to a Cobalt-60 source. After each irradiation, the sensors were recalibrated by Physical Acoustics Corporation. The results were compared to the initial calibrations performed prior to irradiation and a control group, not exposed to radiation, was used to validate the results. This experiment determines the radiation damage threshold of each acoustic sensor system and verifies its life expectancy, usefulness and reliability for many applications in radioactive environments.

  12. Sensitivity of silicon 1-MeV damage function to cross-section evaluation

    SciTech Connect (OSTI)

    Griffin, P.J.; Danjaji, M.B.

    1995-12-31

    The electronics radiation hardness-testing community uses the American Society for Testing and Materials (ASTM) E722-93 Standard Practice to define the energy dependence of the nonionizing neutron damage to silicon semiconductors. This neutron displacement damage response function is defined to be equal to the silicon displacement kerma. An Oak Ridge National Laboratory (ORNL) {sup 28}Si cross-section evaluation and the NJOY code are used to define the standard response function to be used in reporting 1-MeV (silicon) neutron damage and in determining neutron damage equivalence between test facilities. This paper provides information for the precision and bias section of the E722 standard.

  13. Boulder damage symposium annual thin film laser damage competition

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

    Stolz, Christopher J.

    2012-11-28

    Optical instruments and laser systems are often fluence-limited by multilayer thin films deposited on the optical surfaces. When comparing publications within the laser damage literature, there can be confusing and conflicting laser damage results. This is due to differences in testing protocols between research groups studying very different applications. In this series of competitions, samples from multiple vendors are compared under identical testing parameters and a single testing service. Unlike a typical study where a hypothesis is tested within a well-controlled experiment with isolated variables, this competition isolates the laser damage testing variables so that trends can be observed betweenmore » different deposition processes, coating materials, cleaning techniques, and multiple coating suppliers. The resulting series of damage competitions has also been designed to observe general trends of damage morphologies and mechanisms over a wide range of coating types (high reflector and antireflector), wavelengths (193 to 1064 nm), and pulse lengths (180 fs to 13 ns). A double blind test assured sample and submitter anonymity were used in each of the competitions so only a summary of the deposition process, coating materials, layer count and spectral results are presented. Laser resistance was strongly affected by substrate cleaning, coating deposition method, and coating material selection whereas layer count and spectral properties had minimal impact.« less

  14. DNA tagged microparticles

    DOE Patents [OSTI]

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

    2015-05-05

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

  15. DNA Sequencing apparatus

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1992-01-01

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

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

    SciTech Connect (OSTI)

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

    2010-06-29

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

  17. Controlling DNA Methylation

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

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

  18. Method for producing damage resistant optics

    DOE Patents [OSTI]

    Hackel, Lloyd A. (Livermore, CA); Burnham, Alan K. (Livermore, CA); Penetrante, Bernardino M. (San Ramon, CA); Brusasco, Raymond M. (Livermore, CA); Wegner, Paul J. (Livermore, CA); Hrubesh, Lawrence W. (Pleasanton, CA); Kozlowski, Mark R. (Windsor, CA); Feit, Michael D. (Livermore, CA)

    2003-01-01

    The present invention provides a system that mitigates the growth of surface damage in an optic. Damage to the optic is minimally initiated. In an embodiment of the invention, damage sites in the optic are initiated, located, and then treated to stop the growth of the damage sites. The step of initiating damage sites in the optic includes a scan of the optic using a laser to initiate defects. The exact positions of the initiated sites are identified. A mitigation process is performed that locally or globally removes the cause of subsequent growth of the damaged sites.

  19. Dynamically Driven Phase Transformations in Damaged Composite Materials

    SciTech Connect (OSTI)

    Plohr, JeeYeon N.; Clements, Brad E.; Addessio, Frank L

    2006-07-28

    A model developed for composite materials undergoing dynamicaly driven phase transitions in its constituents has been extended to allow for complex material micro-structure and evolution of damage. In this work, damage is described by interfacial debonding and micro-crack growth. We have applied the analysis to silicon carbide-titanium (SiC-Ti) unidirectional metal matrix composites. In these composites, Ti can undergo a low pressure and temperature solid-solid phase transition. With these extensions we have carried out simulations to study the complex interplay between loading rates, micro-structure, damage, and the thermo-mechanical response of the system as it undergoes a solid-solid phase transitions.

  20. Application of Nonlinear Elastic Resonance Spectroscopy For Damage Detection In Concrete: An Interesting Story

    SciTech Connect (OSTI)

    Byers, Loren W.; Ten Cate, James A.; Johnson, Paul A.

    2012-06-28

    Nonlinear resonance ultrasound spectroscopy experiments conducted on concrete cores, one chemically and mechanically damaged by alkali-silica reactivity, and one undamaged, show that this material displays highly nonlinear wave behavior, similar to many other damaged materials. They find that the damaged sample responds more nonlinearly, manifested by a larger resonant peak and modulus shift as a function of strain amplitude. The nonlinear response indicates that there is a hysteretic influence in the stress-strain equation of state. Further, as in some other materials, slow dynamics are present. The nonlinear response they observe in concrete is an extremely sensitive indicator of damage. Ultimately, nonlinear wave methods applied to concrete may be used to guide mixing, curing, or other production techniques, in order to develop materials with particular desired qualities such as enhanced strength or chemical resistance, and to be used for damage inspection.

  1. DNA-PK assay

    DOE Patents [OSTI]

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12

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

  2. Cellular response to low dose radiation: Role of phosphatidylinositol-3 kinase like kinases

    SciTech Connect (OSTI)

    Balajee, A.S.; Meador, J.A.; Su, Y.

    2011-03-24

    It is increasingly realized that human exposure either to an acute low dose or multiple chronic low doses of low LET radiation has the potential to cause different types of cancer. Therefore, the central theme of research for DOE and NASA is focused on understanding the molecular mechanisms and pathways responsible for the cellular response to low dose radiation which would not only improve the accuracy of estimating health risks but also help in the development of predictive assays for low dose radiation risks associated with tissue degeneration and cancer. The working hypothesis for this proposal is that the cellular mechanisms in terms of DNA damage signaling, repair and cell cycle checkpoint regulation are different for low and high doses of low LET radiation and that the mode of action of phosphatidylinositol-3 kinase like kinases (PIKK: ATM, ATR and DNA-PK) determines the dose dependent cellular responses. The hypothesis will be tested at two levels: (I) Evaluation of the role of ATM, ATR and DNA-PK in cellular response to low and high doses of low LET radiation in simple in vitro human cell systems and (II) Determination of radiation responses in complex cell microenvironments such as human EpiDerm tissue constructs. Cellular responses to low and high doses of low LET radiation will be assessed from the view points of DNA damage signaling, DNA double strand break repair and cell cycle checkpoint regulation by analyzing the activities (i.e. post-translational modifications and kinetics of protein-protein interactions) of the key target proteins for PI-3 kinase like kinases both at the intra-cellular and molecular levels. The proteins chosen for this proposal are placed under three categories: (I) sensors/initiators include ATM ser1981, ATR, 53BP1, gamma-H2AX, MDC1, MRE11, Rad50 and Nbs1; (II) signal transducers include Chk1, Chk2, FANCD2 and SMC1; and (III) effectors include p53, CDC25A and CDC25C. The primary goal of this proposal is to elucidate the differences in cellular defense mechanisms between low and high doses of low LET radiation and to define the radiation doses where the cellular DNA damage signaling and repair mechanisms tend to shift. This information is critically important to address and advance some of the low dose research program objectives of DOE. The results of this proposed study will lead to a better understanding of the mechanisms for the cellular responses to low and high doses of low LET radiation. Further, systematic analysis of the role of PIKK signaling pathways as a function of radiation dose in tissue microenvironment will provide useful mechanistic information for improving the accuracy of radiation risk assessment for low doses. Knowledge of radiation responses in tissue microenvironment is important for the accurate prediction of ionizing radiation risks associated with cancer and tissue degeneration in humans.

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

    SciTech Connect (OSTI)

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

    2009-02-01

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

  4. Multiplex analysis of DNA

    DOE Patents [OSTI]

    Church, George M.; Kieffer-Higgins, Stephen

    1992-01-01

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

  5. DNA | Open Energy Information

    Open Energy Info (EERE)

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

  6. Correlating cookoff violence with pre-ignition damage.

    SciTech Connect (OSTI)

    Wente, William Baker; Hobbs, Michael L.; Kaneshige, Michael Jiro

    2010-03-01

    Predicting the response of energetic materials during accidents, such as fire, is important for high consequence safety analysis. We hypothesize that responses of ener-getic materials before and after ignition depend on factors that cause thermal and chemi-cal damage. We have previously correlated violence from PETN to the extent of decom-position at ignition, determined as the time when the maximum Damkoehler number ex-ceeds a threshold value. We seek to understand if our method of violence correlation ap-plies universally to other explosive starting with RDX.

  7. Impurity-doped optical shock, detonation and damage location sensor

    DOE Patents [OSTI]

    Weiss, J.D.

    1995-02-07

    A shock, detonation, and damage location sensor providing continuous fiber-optic means of measuring shock speed and damage location, and could be designed through proper cabling to have virtually any desired crush pressure. The sensor has one or a plurality of parallel multimode optical fibers, or a singlemode fiber core, surrounded by an elongated cladding, doped along their entire length with impurities to fluoresce in response to light at a different wavelength entering one end of the fiber(s). The length of a fiber would be continuously shorted as it is progressively destroyed by a shock wave traveling parallel to its axis. The resulting backscattered and shifted light would eventually enter a detector and be converted into a proportional electrical signals which would be evaluated to determine shock velocity and damage location. The corresponding reduction in output, because of the shortening of the optical fibers, is used as it is received to determine the velocity and position of the shock front as a function of time. As a damage location sensor the sensor fiber cracks along with the structure to which it is mounted. The size of the resulting drop in detector output is indicative of the location of the crack. 8 figs.

  8. Impurity-doped optical shock, detonation and damage location sensor

    DOE Patents [OSTI]

    Weiss, Jonathan D. (Albuquerque, NM)

    1995-01-01

    A shock, detonation, and damage location sensor providing continuous fiber-optic means of measuring shock speed and damage location, and could be designed through proper cabling to have virtually any desired crush pressure. The sensor has one or a plurality of parallel multimode optical fibers, or a singlemode fiber core, surrounded by an elongated cladding, doped along their entire length with impurities to fluoresce in response to light at a different wavelength entering one end of the fiber(s). The length of a fiber would be continuously shorted as it is progressively destroyed by a shock wave traveling parallel to its axis. The resulting backscattered and shifted light would eventually enter a detector and be converted into a proportional electrical signals which would be evaluated to determine shock velocity and damage location. The corresponding reduction in output, because of the shortening of the optical fibers, is used as it is received to determine the velocity and position of the shock front as a function of time. As a damage location sensor the sensor fiber cracks along with the structure to which it is mounted. The size of the resulting drop in detector output is indicative of the location of the crack.

  9. Rapid Damage eXplorer (RDX): A Probabilistic Framework for Learning Changes From Bitemporal Images

    SciTech Connect (OSTI)

    Vatsavai, Raju

    2012-01-01

    Recent decade has witnessed major changes on the Earth, for example, deforestation, varying cropping and human settlement patterns, and crippling damages due to disasters. Accurate damage assessment caused by major natural and anthropogenic disasters is becoming critical due to increases in human and economic loss. This increase in loss of life and severe damages can be attributed to the growing population, as well as human migration to the disaster prone regions of the world. Rapid assessment of these changes and dissemination of accurate information is critical for creating an effective emergency response. Change detection using high-resolution satellite images is a primary tool in assessing damages, monitoring biomass and critical infrastructures, and identifying new settlements. In this demo, we present a novel supervised probabilistic framework for identifying changes using very high-resolution multispectral, and bitemporal remote sensing images. Our demo shows that the rapid damage explorer (RDX) system is resilient to registration errors and differing sensor characteristics.

  10. Quantifying uncertainty in material damage from vibrational data

    SciTech Connect (OSTI)

    Butler, T.; Huhtala, A.; Juntunen, M.

    2015-02-15

    The response of a vibrating beam to a force depends on many physical parameters including those determined by material properties. Damage caused by fatigue or cracks results in local reductions in stiffness parameters and may drastically alter the response of the beam. Data obtained from the vibrating beam are often subject to uncertainties and/or errors typically modeled using probability densities. The goal of this paper is to estimate and quantify the uncertainty in damage modeled as a local reduction in stiffness using uncertain data. We present various frameworks and methods for solving this parameter determination problem. We also describe a mathematical analysis to determine and compute useful output data for each method. We apply the various methods in a specified sequence that allows us to interface the various inputs and outputs of these methods in order to enhance the inferences drawn from the numerical results obtained from each method. Numerical results are presented using both simulated and experimentally obtained data from physically damaged beams.

  11. 2010 MICROBIAL STRESS RESPONSE GORDON RESEARCH CONFERENCE, JULY 18-23, 2010

    SciTech Connect (OSTI)

    Sarah Ades

    2011-07-23

    The 2010 Gordon Research Conference on Microbial Stress Responses provides an open and exciting forum for the exchange of scientific discoveries on the remarkable mechanisms used by microbes to survive in nearly every niche on the planet. Understanding these stress responses is critical for our ability to control microbial survival, whether in the context of biotechnology, ecology, or pathogenesis. From its inception in 1994, this conference has traditionally employed a very broad definition of stress in microbial systems. Sessions will cover the major steps of stress responses from signal sensing to transcriptional regulation to the effectors that mediate responses. A wide range of stresses will be represented. Some examples include (but are not limited to) oxidative stress, protein quality control, antibiotic-induced stress and survival, envelope stress, DNA damage, and nutritional stress. The 2010 meeting will also focus on the role of stress responses in microbial communities, applied and environmental microbiology, and microbial development. This conference brings together researchers from both the biological and physical sciences investigating stress responses in medically- and environmentally relevant microbes, as well as model organisms, using cutting-edge techniques. Computational, systems-level, and biophysical approaches to exploring stress responsive circuits will be integrated throughout the sessions alongside the more traditional molecular, physiological, and genetic approaches. The broad range of excellent speakers and topics, together with the intimate and pleasant setting at Mount Holyoke College, provide a fertile ground for the exchange of new ideas and approaches.

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

    DOE Patents [OSTI]

    Tabor, S.; Richardson, C.

    1997-03-25

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

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

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles

    1997-01-01

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

  14. Structure of an aprataxin?DNA complex with insights into AOA1 neurodegenerative disease

    SciTech Connect (OSTI)

    Tumbale, Percy; Appel, C. Denise; Kraehenbuehl, Rolf; Robertson, Patrick D.; Williams, Jessica S.; Krahn, Joe; Ahel, Ivan; Williams, R. Scott (NIEHS); (Manchester)

    2012-09-17

    DNA ligases finalize DNA replication and repair through DNA nick-sealing reactions that can abort to generate cytotoxic 5'-adenylation DNA damage. Aprataxin (Aptx) catalyzes direct reversal of 5'-adenylate adducts to protect genome integrity. Here the structure of a Schizosaccharomyces pombe Aptx-DNA-AMP-Zn{sup 2+} complex reveals active site and DNA interaction clefts formed by fusing a histidine triad (HIT) nucleotide hydrolase with a DNA minor groove-binding C{sub 2}HE zinc finger (Znf). An Aptx helical 'wedge' interrogates the base stack for sensing DNA ends or DNA nicks. The HIT-Znf, the wedge and an '[F/Y]PK' pivot motif cooperate to distort terminal DNA base-pairing and direct 5'-adenylate into the active site pocket. Structural and mutational data support a wedge-pivot-cut HIT-Znf catalytic mechanism for 5'-adenylate adduct recognition and removal and suggest that mutations affecting protein folding, the active site pocket and the pivot motif underlie Aptx dysfunction in the neurodegenerative disorder ataxia with oculomotor apraxia 1 (AOA1).

  15. Structural damage identification in wind turbine blades using piezoelectric active sensing with ultrasonic validation

    SciTech Connect (OSTI)

    Claytor, Thomas N; Ammerman, Curtt N; Park, Gyu Hae; Farinholt, Kevin M; Farrar, Charles R; Atterbury, Marie K

    2010-01-01

    This paper gives a brief overview of a new project at LANL in structural damage identification for wind turbines. This project makes use of modeling capabilities and sensing technology to understand realistic blade loading on large turbine blades, with the goal of developing the technology needed to automatically detect early damage. Several structural health monitoring (SHM) techniques using piezoelectric active materials are being investigated for the development of wireless, low power sensors that interrogate sections of the wind turbine blade using Lamb wave propagation data, frequency response functions (FRFs), and time-series analysis methods. The modeling and sensor research will be compared with extensive experimental testing, including wind tunnel experiments, load and fatigue tests, and ultrasonic scans - on small- to mid-scale turbine blades. Furthermore, this study will investigate the effect of local damage on the global response of the blade by monitoring low-frequency response changes.

  16. Testing model for predicting spillway cavitation damage

    SciTech Connect (OSTI)

    Lee, W.; Hoopes, J.A.

    1995-12-31

    Using fuzzy mathematics a comprehensive model has been developed to predict the time, location and level (intensity) of spillway cavitation damage. Five damage levels and four factors affecting damage are used. Membership functions express the degree that each factor effects damage, and weights express the relative importance of each factor. The model has been calibrated and tested with operating data and experience from the Glen Canyon Dam left tunnel spillway, which had major cavitation damage in 1983. An error analysis for the Glen Canyon Dam left tunnel spillway gave the best ranges for model weights. Prediction of damage at other spillways (4 tunnels, 3 chutes) with functions and parameters as for the Glen Canyon Dam left tunnel spillway gave reasonable predictions of damage intensity and location and poor estimates of occurrence time in the tunnels. Chute predictions were in poor agreement with observations, indicating need for different parameter values. Finally, two membership functions with constant or time varying parameters are compared with observed results from the Glen Canyon Dam left tunnel spillway.

  17. Underground infrastructure damage for a Chicago scenario

    SciTech Connect (OSTI)

    Dey, Thomas N; Bos, Rabdall J

    2011-01-25

    Estimating effects due to an urban IND (improvised nuclear device) on underground structures and underground utilities is a challenging task. Nuclear effects tests performed at the Nevada Test Site (NTS) during the era of nuclear weapons testing provides much information on how underground military structures respond. Transferring this knowledge to answer questions about the urban civilian environment is needed to help plan responses to IND scenarios. Explosions just above the ground surface can only couple a small fraction of the blast energy into an underground shock. The various forms of nuclear radiation have limited penetration into the ground. While the shock transmitted into the ground carries only a small fraction of the blast energy, peak stresses are generally higher and peak ground displacement is lower than in the air blast. While underground military structures are often designed to resist stresses substantially higher than due to the overlying rocks and soils (overburden), civilian structures such as subways and tunnels would generally only need to resist overburden conditions with a suitable safety factor. Just as we expect the buildings themselves to channel and shield air blast above ground, basements and other underground openings as well as changes of geology will channel and shield the underground shock wave. While a weaker shock is expected in an urban environment, small displacements on very close-by faults, and more likely, soils being displaced past building foundations where utility lines enter could readily damaged or disable these services. Immediately near an explosion, the blast can 'liquefy' a saturated soil creating a quicksand-like condition for a period of time. We extrapolate the nuclear effects experience to a Chicago-based scenario. We consider the TARP (Tunnel and Reservoir Project) and subway system and the underground lifeline (electric, gas, water, etc) system and provide guidance for planning this scenario.

  18. War damages and reconstruction of Peruca dam

    SciTech Connect (OSTI)

    Nonveiller, E.; Rupcic, J.; Sever, Z.

    1999-04-01

    The paper describes the heavy damages caused by blasting in the Peruca rockfill dam in Croatia in January 1993. Complete collapse of the dam by overtopping was prevented through quick action of the dam owner by dumping clayey gravel on the lowest sections of the dam crest and opening the bottom outlet of the reservoir, thus efficiently lowering the water level. After the damages were sufficiently established and alternatives for restoration of the dam were evaluated, it was decided to construct a diaphragm wall through the damaged core in the central dam part as the impermeable dam element and to rebuild the central clay core at the dam abutments. Reconstruction works are described.

  19. Mono-2-ethylhexyl phthalate induces oxidative stress responses in human placental cells in vitro

    SciTech Connect (OSTI)

    Tetz, Lauren M.; Cheng, Adrienne A.; Korte, Cassandra S.; Giese, Roger W.; Wang, Poguang; Harris, Craig; Meeker, John D.; Loch-Caruso, Rita

    2013-04-01

    Di-2-ethylhexyl phthalate (DEHP) is an environmental contaminant commonly used as a plasticizer in polyvinyl chloride products. Exposure to DEHP has been linked to adverse pregnancy outcomes in humans including preterm birth, low birth-weight, and pregnancy loss. Although oxidative stress is linked to the pathology of adverse pregnancy outcomes, effects of DEHP metabolites, including the active metabolite, mono-2-ethylhexyl phthalate (MEHP), on oxidative stress responses in placental cells have not been previously evaluated. The objective of the current study is to identify MEHP-stimulated oxidative stress responses in human placental cells. We treated a human placental cell line, HTR-8/SVneo, with MEHP and then measured reactive oxygen species (ROS) generation using the dichlorofluorescein assay, oxidized thymine with mass-spectrometry, redox-sensitive gene expression with qRT-PCR, and apoptosis using a luminescence assay for caspase 3/7 activity. Treatment of HTR-8 cells with 180 ?M MEHP increased ROS generation, oxidative DNA damage, and caspase 3/7 activity, and resulted in differential expression of redox-sensitive genes. Notably, 90 and 180 ?M MEHP significantly induced mRNA expression of prostaglandin-endoperoxide synthase 2 (PTGS2), an enzyme important for synthesis of prostaglandins implicated in initiation of labor. The results from the present study are the first to demonstrate that MEHP stimulates oxidative stress responses in placental cells. Furthermore, the MEHP concentrations used were within an order of magnitude of the highest concentrations measured previously in human umbilical cord or maternal serum. The findings from the current study warrant future mechanistic studies of oxidative stress, apoptosis, and prostaglandins as molecular mediators of DEHP/MEHP-associated adverse pregnancy outcomes. - Highlights: ? MEHP increased reactive oxygen species, oxidative DNA damage, and caspase activity. ? MEHP induced expression of PTGS2, a gene important in pregnancy and parturition ? MEHP treatment resulted in differential expression of GLRX2, TXNRD1, and DHCR24.

  20. [Localized fracture damage effects in toughened ceramics]. Final report

    SciTech Connect (OSTI)

    1997-12-31

    The primary research goal was to investigate localized fracture damage due to single point cutting of ceramic materials and then to compare this to multipoint cutting during precision grinding of the same materials. Two test systems were designed and constructed for the single-point cutting tests. The first system used a PZT actuator for closed-loop load control. An acoustic emission data acquisition system was used for crack initiation detection. The second test system employed a high-precision diamond-turning machine for closed-loop position (cutting depth) control. A high stiffness load cell and data acquisition system were used for crack initiation detection. Microcutting tests were carried out on silicon, borosilicate glass and CVD silicon carbide. The crack initiation thresholds and the fracture damage distribution were determined as a function of the loading conditions using a Vickers diamond as the cutting tool. The grinding tests were done using a plunge-grinding technique with metal-bonded diamond wheels. Optical microscopy, surface roughness and specific cutting energy were measured in order to characterize the fracture damage as a function of the grinding infeed rate. Simulation models were developed in order to estimate the average grain-depth of cut in grinding so that the response could be compared to the single-point microcutting tests.

  1. Fleet DNA (Presentation)

    SciTech Connect (OSTI)

    Walkokwicz, K.; Duran, A.

    2014-06-01

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

  2. Identification of Human Repetitive DNA Elements

    Energy Science and Technology Software Center (OSTI)

    1995-11-01

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

  3. Hardware Controller DNA Synthesizer

    Energy Science and Technology Software Center (OSTI)

    1995-07-27

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

  4. Laser Damage Precursors in Fused Silica

    SciTech Connect (OSTI)

    Miller, P; Suratwala, T; Bude, J; Laurence, T A; Shen, N; Steele, W A; Feit, M; Menapace, J; Wong, L

    2009-11-11

    There is a longstanding, and largely unexplained, correlation between the laser damage susceptibility of optical components and both the surface quality of the optics, and the presence of near surface fractures in an optic. In the present work, a combination of acid leaching, acid etching, and confocal time resolved photoluminescence (CTP) microscopy has been used to study laser damage initiation at indentation sites. The combination of localized polishing and variations in indentation loads allows one to isolate and characterize the laser damage susceptibility of densified, plastically flowed and fractured fused silica. The present results suggest that: (1) laser damage initiation and growth are strongly correlated with fracture surfaces, while densified and plastically flowed material is relatively benign, and (2) fracture events result in the formation of an electronically defective rich surface layer which promotes energy transfer from the optical beam to the glass matrix.

  5. Thin Film Femtosecond Laser Damage Competition

    SciTech Connect (OSTI)

    Stolz, C J; Ristau, D; Turowski, M; Blaschke, H

    2009-11-14

    In order to determine the current status of thin film laser resistance within the private, academic, and government sectors, a damage competition was started at the 2008 Boulder Damage Symposium. This damage competition allows a direct comparison of the current state of the art of high laser resistance coatings since they are tested using the same damage test setup and the same protocol. In 2009 a high reflector coating was selected at a wavelength of 786 nm at normal incidence at a pulse length of 180 femtoseconds. A double blind test assured sample and submitter anonymity so only a summary of the results are presented here. In addition to the laser resistance results, details of deposition processes, coating materials and layer count, and spectral results will also be shared.

  6. Controlled ion implant damage profile for etching

    DOE Patents [OSTI]

    Arnold, Jr., George W. (Tijeras, NM); Ashby, Carol I. H. (Edgewood, NM); Brannon, Paul J. (Albuquerque, NM)

    1990-01-01

    A process for etching a material such as LiNbO.sub.3 by implanting ions having a plurality of different kinetic energies in an area to be etched, and then contacting the ion implanted area with an etchant. The various energies of the ions are selected to produce implant damage substantially uniformly throughout the entire depth of the zone to be etched, thus tailoring the vertical profile of the damaged zone.

  7. Quantitative damage evaluation of localized deep pitting

    SciTech Connect (OSTI)

    Al Beed, A.A.; Al Garni, M.A.

    2000-04-01

    Localized deep pitting is considered difficult to precisely measure and evaluate using simple techniques and daily-use analysis approaches. A case study was made of carbon steel heat exchangers in a typical fresh cooling water environment that experienced severe pitting. To effectively and precisely evaluate the encountered pitting damage, a simple measurement and analyses approach was devised. In this article, the pitting measurement technique and the damage evaluation approach are presented and discussed in detail.

  8. Seismic damage estimation for buried pipelines - challenges after three decades of progress

    SciTech Connect (OSTI)

    Pineda-porras, Omar Andrey; Najafi, Mohammand

    2009-01-01

    This paper analyzes the evolution over the past three decades of seismic damage estimation for buried pipelines and identifies some challenges for future research studies on the subject. The first section of this paper presents a chronological description of the evolution since the mid-1970s of pipeline fragility relations - the most common tool for pipeline damage estimation - and follows with a careful analysis of the use of several ground motion parameters as pipeline damage indicators. In the second section of the paper, four gaps on the subject are identified and proposed as challenges for future research studies. The main conclusion of this work is that enhanced fragility relations must be developed for improving pipeline damage estimation, which must consider relevant parameters that could influence the seismic response of pipelines.

  9. Performance of Damaged Soil-Concrete Wraparound Dam Sections...

    Office of Scientific and Technical Information (OSTI)

    of Damaged Soil-Concrete Wraparound Dam Sections under Dynamic Loading Predicting seismic or shock loading damage of the soil-concrete interface where an embankment wraparound...

  10. Unified Creep Plasticity Damage (UCPD) Model for Rigid Polyurethane Foams.

    SciTech Connect (OSTI)

    Neilsen, Michael K.; Lu, Wei-Yang; Scherzinger, William M.; Hinnerichs, Terry D.; Lo, Chi S.

    2015-06-01

    Numerous experiments were performed to characterize the mechanical response of several different rigid polyurethane foams (FR3712, PMDI10, PMDI20, and TufFoam35) to large deformation. In these experiments, the effects of load path, loading rate, and temperature were investigated. Results from these experiments indicated that rigid polyurethane foams exhibit significant volumetric and deviatoric plasticity when they are compressed. Rigid polyurethane foams were also found to be very strain-rate and temperature dependent. These foams are also rather brittle and crack when loaded to small strains in tension or to larger strains in compression. Thus, a new Unified Creep Plasticity Damage (UCPD) model was developed and implemented into SIERRA with the name Foam Damage to describe the mechanical response of these foams to large deformation at a variety of temperatures and strain rates. This report includes a description of recent experiments and experimental findings. Next, development of a UCPD model for rigid, polyurethane foams is described. Selection of material parameters for a variety of rigid polyurethane foams is then discussed and finite element simulations with the new UCPD model are compared with experimental results to show behavior that can be captured with this model.

  11. Final Report [The c-Abl signaling network in the radioadaptive response

    SciTech Connect (OSTI)

    Chi-Min, Yuan

    2014-01-28

    The radioadaptive response, or radiation hormesis, i.e. a low dose of radiation can protect cells and organisms from the effects of a subsequent higher dose, is a widely recognized phenomenon. Mechanisms underlying such radiation hormesis, however, remain largely unclear. Preliminary studies indicate an important role of c-Abl signaling in mediating the radioadaptive response. We propose to investigate how c-Abl regulates the crosstalk between p53 and NF?B in response to low doses irradiation. We found in our recent study that low dose IR induces a reciprocal p53 suppression and NF?B activation, which induces HIF-a and subsequently a metabolic reprogramming resulting in a transition from oxidative phosphorylation to glycolysis. Of importance is that this glycolytic switch is essential for the radioadaptive response. This low-dose radiationinduced HIF1? activation was in sharp contrast with the high-dose IR-induced p53 activation and HIF1? inhibition. HIF1? and p53 seem to play distinct roles in mediating the radiation dose-dependent metabolic response. The induction of HIF1?-mediated glycolysis is restricted to a low dose range of radiation, which may have important implications in assessing the level of radiation exposure and its potential health risk. Our results support a dose-dependent metabolic response to IR. When IR doses are below the threshold of causing detectable DNA damage (<0.2Gy) and thus little p53 activation, HIF1? is induced resulting in induction of glycolysis and increased radiation resistance. When the radiation dose reaches levels eliciting DNA damage, p53 is activated and diminishes the activity of HIF1? and glycolysis, leading to the induction of cell death. Our work challenges the LNT model of radiation exposure risk and provides a metabolic mechanism of radioadaptive response. The study supports a need for determining the p53 and HIF1? activity as a potential reliable biological readout of radiation exposure in humans. The exquisite sensitivity of cellular metabolism to low doses of radiation could also serve as a valuable biomarker for estimating the health effects of low-level radiation exposure.

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

    Office of Scientific and Technical Information (OSTI)

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

  13. DNA attachment to support structures

    DOE Patents [OSTI]

    Balhorn, Rodney L. (Livermore, CA); Barry, Christopher H. (Fresno, CA)

    2002-01-01

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

  14. Thermal Damage Characterization of Energetic Materials

    SciTech Connect (OSTI)

    Hsu, P C; DeHaven, M R; Springer, H K; Maienschein, J L

    2009-08-14

    We conducted thermal damage experiments at 180?C on PBXN-9 and characterized its material properties. Volume expansion at high temperatures was very significant which led to a reduction in material density. 2.6% of weight loss was observed, which was higher than other HMX-based formulations. Porosity of PBXN-9 increased to 16% after thermal exposure. Small-scale safety tests (impact, friction, and spark) showed no significant sensitization when the damaged samples were tested at room temperature. Gas permeation measurements showed that gas permeability in damaged materials was several orders of magnitude higher than that in pristine materials. In-situ measurements of gas permeability and density were proved to be possible at higher temperatures.

  15. Method to reduce damage to backing plate

    DOE Patents [OSTI]

    Perry, Michael D.; Banks, Paul S.; Stuart, Brent C.

    2001-01-01

    The present invention is a method for penetrating a workpiece using an ultra-short pulse laser beam without causing damage to subsequent surfaces facing the laser. Several embodiments are shown which place holes in fuel injectors without damaging the back surface of the sack in which the fuel is ejected. In one embodiment, pulses from an ultra short pulse laser remove about 10 nm to 1000 nm of material per pulse. In one embodiment, a plasma source is attached to the fuel injector and initiated by common methods such as microwave energy. In another embodiment of the invention, the sack void is filled with a solid. In one other embodiment, a high viscosity liquid is placed within the sack. In general, high-viscosity liquids preferably used in this invention should have a high damage threshold and have a diffusing property.

  16. Frequency Response Tool

    Energy Science and Technology Software Center (OSTI)

    2014-03-13

    According to the North American Electric Reliability Corporation (NERC) definition: “Frequency response is a measure of an Interconnection’s ability to stabilize frequency immediately following the sudden loss of generation or load, and is a critical component of the reliable operation of the Bulk-Power System, particularly during disturbances and recoveries. Failure to maintain frequency can disrupt the operation of equipment and initiate disconnection of power plant equipment to prevent it from being damaged, which could leadmore » to wide-spread blackouts.” Frequency Response Tool automates the power system frequency response analysis process. The tool performs initial estimation of the system frequency parameters (initial frequency, minimum frequency, settling point). User can visually inspect and adjust these parameters. The tool also calculates the frequency response performance metrics of the system, archives the historic events and baselines the system performance. Frequency response performance characteristics of the system are calculated using phasor measurement unit (PMU) information. Methodology of the frequency response performance assessment implemented in the tool complies with the NERC Frequency response standard.« less

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

    SciTech Connect (OSTI)

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

    2007-10-15

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

  18. Undulator Radiation Damage Experience at LCLS

    SciTech Connect (OSTI)

    Nuhn, H. D.; Field, C.; Mao, S.; Levashov, Y.; Santana, M.; Welch, J. N.; Wolf, Z.

    2015-01-06

    The SLAC National Accelerator Laboratory has been running the Linac Coherent Light Source (LCLS), the first x-ray Free Electron Laser since 2009. Undulator magnet damage from radiation, produced by the electron beam traveling through the 133-m long straight vacuum tube, has been and is a concern. A damage measurement experiment has been performed in 2007 in order to obtain dose versus damage calibrations. Radiation reduction and detection devices have been integrated into the LCLS undulator system. The accumulated radiation dose rate was continuously monitored and recorded. In addition, undulator segments have been routinely removed from the beamline to be checked for magnetic (50 ppm, rms) and mechanic (about 0.25 m, rms) changes. A reduction in strength of the undulator segments is being observed, at a level, which is now clearly above the noise. Recently, potential sources for the observed integrated radiation levels have been investigated. The paper discusses the results of these investigation as well as comparison between observed damage and measured dose accumulations and discusses, briefly, strategies for the new LCLS-II upgrade, which will be operating at more than 300 times larger beam rate.

  19. How do energetic ions damage metallic surfaces?

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

    Osetskiy, Yury N.; Calder, Andrew F.; Stoller, Roger E.

    2015-02-20

    Surface modification under bombardment by energetic ions observed under different conditions in structural and functional materials and can be either unavoidable effect of the conditions or targeted modification to enhance materials properties. Understanding basic mechanisms is necessary for predicting properties changes. The mechanisms activated during ion irradiation are of atomic scale and atomic scale modeling is the most suitable tool to study these processes. In this paper we present results of an extensive simulation program aimed at developing an understanding of primary surface damage in iron by energetic particles. We simulated 25 keV self-ion bombardment of Fe thin films withmore(100) and (110) surfaces at room temperature. A large number of simulations, ~400, were carried out allow a statistically significant treatment of the results. The particular mechanism of surface damage depends on how the destructive supersonic shock wave generated by the displacement cascade interacts with the free surface. Three basic scenarios were observed, with the limiting cases being damage created far below the surface with little or no impact on the surface itself, and extensive direct surface damage on the timescale of a few picoseconds. In some instances, formation of large vacancy loops beneath the free surface was observed, which may explain some earlier experimental observations.less

  20. Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase

    SciTech Connect (OSTI)

    Adhikary, Suraj; Eichman, Brandt F.

    2014-10-02

    DNA glycosylases specialized for the repair of alkylation damage must identify, with fine specificity, a diverse array of subtle modifications within DNA. The current mechanism involves damage sensing through interrogation of the DNA duplex, followed by more specific recognition of the target base inside the active site pocket. To better understand the physical basis for alkylpurine detection, we determined the crystal structure of Schizosaccharomyces pombe Mag1 (spMag1) in complex with DNA and performed a mutational analysis of spMag1 and the close homologue from Saccharomyces cerevisiae (scMag). Despite strong homology, spMag1 and scMag differ in substrate specificity and cellular alkylation sensitivity, although the enzymological basis for their functional differences is unknown. We show that Mag preference for 1,N{sup 6}-ethenoadenine ({var_epsilon}A) is influenced by a minor groove-interrogating residue more than the composition of the nucleobase-binding pocket. Exchanging this residue between Mag proteins swapped their {var_epsilon}A activities, providing evidence that residues outside the extrahelical base-binding pocket have a role in identification of a particular modification in addition to sensing damage.

  1. Forensic DNA data banking by state crime labortaories

    SciTech Connect (OSTI)

    McEwen, J.E.

    1995-06-01

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

  2. Severe fuel-damage scoping test performance. [PWR

    SciTech Connect (OSTI)

    Gruen, G.E.; Buescher, B.J.

    1983-01-01

    As a result of the Three Mile Island Unit-2 (TMI-2) accident, the Nuclear Regulatory Commission has initiated a severe fuel damage test program to evaluate fuel rod and core response during severe accidents similar to TMI-2. The first test of Phase I of this series has been successfully completed in the Power Burst Facility at the Idaho National Engineering Laboratory. Following the first test, calculations were performed using the TRAC-BD1 computer code with actual experimental boundary conditions. This paper discusses the test conduct and performance and presents the calculated and measured test bundle results. The test resulted in a slow heatup to 2000 K over about 4 h, with an accelerated reaction of the zirconium cladding at temperatures above 1600 K in the lower part or the bundle and 2000 K in the upper portion of the bundle.

  3. The Initiation of Bacterial DNA Replication

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

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

  4. The Initiation of Bacterial DNA Replication

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

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

  5. Challenges and opportunities for structural DNA nanotechnology

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

    Challenges and opportunities for structural DNA nanotechnology Authors: Pinheiro, A. V., Han, D., Shih, W. M., and Yan, H. Title: Challenges and opportunities for structural DNA...

  6. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, S.K.

    1998-03-24

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

  7. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, Stefan K.

    1998-01-01

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

  8. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B. (New York, NY); Efstratiadis, Argiris (Englewood, NJ)

    1997-01-01

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

  9. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1997-06-10

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

  10. Radiation damage in cubic-stabilized zirconia

    SciTech Connect (OSTI)

    Costantini, Jean-Marc; Beuneu, Francois; Weber, William J

    2013-01-01

    Cubic yttria-stabilized zirconia (YSZ) can be used for nuclear applications as an inert matrix for actinide immobilization or transmutation. Indeed, the large amount of native oxygen vacancies leads to a high radiation tolerance of this material owing to defect recombination occurring in the atomic displacements cascades induced by fast neutron irradiation or ion implantations, as showed by Molecular dynamics (MD) simulations. Amorphization cannot be obtained in YSZ either by nuclear-collision or electronic-excitation damage, just like in urania. A kind of polygonization structure with slightly disoriented crystalline domains is obtained in both cases. In the first steps of damage, specific isolated point defects (like F+-type color centers) and point-defect clusters are produced by nuclear collisions with charged particles or neutrons. Further increase of damage leads to dislocation-loop formation, then to collapse of the dislocation network into a polygonization structure. For swift heavy ion irradiations, a similar polygonization structure is obtained above a threshold stopping power value of about 20-30 keV nm-1.

  11. Alkylation damage repair in mammalian genomes

    SciTech Connect (OSTI)

    Mitra, S.; Roy, R.; Kim, N.K. |; Tano, K. |; Ibeanu, G.C. |; Dunn, W.C.; Natarajan, A.T.; Hartenstein, B.; Kaina, B.

    1992-11-01

    The repair of O{sup 6} -alkylguanine in DNA involves only O{sup 6} -methyltransferase (MGMT) while the repair of N-alkylpurines requires multiple proteins including N-methylpurine-DNA glycosylase (MPG). While the biochemical properties human and mouse MGMTs are very similar, the mouse MPG removes 7-methylguanine more efficiently than the human protein. An increased level of MGMT, without a change in the level of MPG associated with gene amplification, was observed in a mouse cell line resistant to 2-chloroethyl-N-nitrosourea. In contrast, no correlation was observed between MPG level and resistance to methyl methanesulfonate in Chinese hamster ovary (CHO) cells. This result suggests a protein other than MPG limits the repair rate of N-alkylpurine in CHO cells.

  12. Alkylation damage repair in mammalian genomes

    SciTech Connect (OSTI)

    Mitra, S.; Roy, R.; Kim, N.K. . Sealy Center for Molecular Science Oak Ridge National Lab., TN ); Tano, K. Oak Ridge National Lab., TN ); Ibeanu, G.C. Oak Ridge National Lab., TN ); Dunn, W.C. (

    1992-01-01

    The repair of O{sup 6} -alkylguanine in DNA involves only O{sup 6} -methyltransferase (MGMT) while the repair of N-alkylpurines requires multiple proteins including N-methylpurine-DNA glycosylase (MPG). While the biochemical properties human and mouse MGMTs are very similar, the mouse MPG removes 7-methylguanine more efficiently than the human protein. An increased level of MGMT, without a change in the level of MPG associated with gene amplification, was observed in a mouse cell line resistant to 2-chloroethyl-N-nitrosourea. In contrast, no correlation was observed between MPG level and resistance to methyl methanesulfonate in Chinese hamster ovary (CHO) cells. This result suggests a protein other than MPG limits the repair rate of N-alkylpurine in CHO cells.

  13. Using DNA to Build Nanomaterials

    DOE R&D Accomplishments [OSTI]

    Walsh, Karen McNulty

    2011-05-09

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

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

    SciTech Connect (OSTI)

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

    2013-12-01

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

  15. Probing Radiation Damage in Plutonium Alloys with Multiple Measurement

    Office of Scientific and Technical Information (OSTI)

    Techniques (Conference) | SciTech Connect Conference: Probing Radiation Damage in Plutonium Alloys with Multiple Measurement Techniques Citation Details In-Document Search Title: Probing Radiation Damage in Plutonium Alloys with Multiple Measurement Techniques A material subjected to radiation damage will usually experience changes in its physical properties. Measuring these changes in the physical properties provides a basis to study radiation damage in a material which is important for a

  16. DNA analysis conference in Santa Fe

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

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

  17. DNA polymorphism identity determination using flow cytometry

    DOE Patents [OSTI]

    Nolan, John P. (Santa Fe, NM); White, P. Scott (Los Alamos, NM); Cai, Hong (Los Alamos, NM)

    2001-01-01

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

  18. Natural Resource Damage Assessment Cooperation and Integration

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2012-06-19

    The Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), 42 U.S.C. 9601, et seq., Executive Order 12580, and CERCLA's implementing regulations in the National Contingency Plan (NCP), 40 CFR Part 300, give the DOE three roles at DOE facilities undergoing environmental cleanup: lead response agency, natural resource trustee, and the party responsible for releases and threatened releases of hazardous substances. Does not cancel other directives.

  19. Minimizing radiation damage in nonlinear optical crystals

    DOE Patents [OSTI]

    Cooke, D.W.; Bennett, B.L.; Cockroft, N.J.

    1998-09-08

    Methods are disclosed for minimizing laser induced damage to nonlinear crystals, such as KTP crystals, involving various means for electrically grounding the crystals in order to diffuse electrical discharges within the crystals caused by the incident laser beam. In certain embodiments, electrically conductive material is deposited onto or into surfaces of the nonlinear crystals and the electrically conductive surfaces are connected to an electrical ground. To minimize electrical discharges on crystal surfaces that are not covered by the grounded electrically conductive material, a vacuum may be created around the nonlinear crystal. 5 figs.

  20. Minimizing radiation damage in nonlinear optical crystals

    DOE Patents [OSTI]

    Cooke, D. Wayne (Santa Fe, NM); Bennett, Bryan L. (Los Alamos, NM); Cockroft, Nigel J. (Santa Fe, NM)

    1998-01-01

    Methods are disclosed for minimizing laser induced damage to nonlinear crystals, such as KTP crystals, involving various means for electrically grounding the crystals in order to diffuse electrical discharges within the crystals caused by the incident laser beam. In certain embodiments, electrically conductive material is deposited onto or into surfaces of the nonlinear crystals and the electrically conductive surfaces are connected to an electrical ground. To minimize electrical discharges on crystal surfaces that are not covered by the grounded electrically conductive material, a vacuum may be created around the nonlinear crystal.

  1. Surface state reconstruction in ion-damaged SmB?

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

    Wakeham, N.; Wang, Y. Q.; Fisk, Z.; Ronning, F.; Thompson, J. D.

    2015-02-01

    We have used ion-irradiation to damage the (001) surfaces of SmB? single crystals to varying depths, and have measured the resistivity as a function of temperature for each depth of damage. We observe a reduction in the residual resistivity with increasing depth of damage. Our data are consistent with a model in which the surface state is not destroyed by the ion-irradiation, but instead the damaged layer is poorly conducting and the initial surface state is reconstructed below the damage. This behavior is consistent with a surface state that is topologically protected.

  2. Damage of MEMS thermal actuators heated by laser irradiation.

    SciTech Connect (OSTI)

    Walraven, Jeremy Allen; Klody, Kelly Anne; Sackos, John T.; Phinney, Leslie Mary

    2005-01-01

    Optical actuation of microelectromechanical systems (MEMS) is advantageous for applications for which electrical isolation is desired. Thirty-two polycrystalline silicon opto-thermal actuators, optically-powered MEMS thermal actuators, were designed, fabricated, and tested. The design of the opto-thermal actuators consists of a target for laser illumination suspended between angled legs that expand when heated, providing the displacement and force output. While the amount of displacement observed for the opto-thermal actuators was fairly uniform for the actuators, the amount of damage resulting from the laser heating ranged from essentially no damage to significant amounts of damage on the target. The likelihood of damage depended on the target design with two of the four target designs being more susceptible to damage. Failure analysis of damaged targets revealed the extent and depth of the damage.

  3. Damage of MEMS thermal actuators heated by laser irradiation.

    SciTech Connect (OSTI)

    Walraven, Jeremy Allen; Klody, Kelly Anne; Sackos, John T.; Phinney, Leslie Mary

    2004-11-01

    Optical actuation of microelectromechanical systems (MEMS) is advantageous for applications for which electrical isolation is desired. Thirty-two polycrystalline silicon opto-thermal actuators, optically-powered MEMS thermal actuators, were designed, fabricated, and tested. The design of the opto-thermal actuators consists of a target for laser illumination suspended between angled legs that expand when heated, providing the displacement and force output. While the amount of displacement observed for the opto-thermal actuators was fairly uniform for the actuators, the amount of damage resulting from the laser heating ranged from essentially no damage to significant amounts of damage on the target. The likelihood of damage depended on the target design with two of the four target designs being more susceptible to damage. Failure analysis of damaged targets revealed the extent and depth of the damage.

  4. Apparatus for improved DNA sequencing

    DOE Patents [OSTI]

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

    1996-05-07

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

  5. Apparatus for improved DNA sequencing

    DOE Patents [OSTI]

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

    1996-01-01

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

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

    SciTech Connect (OSTI)

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

    2013-11-15

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

  7. Extraction of PCR-amplifiable genomic DNA from Bacillus anthracisspores

    SciTech Connect (OSTI)

    Torok, Tamas

    2003-05-19

    Bacterial endospore disruption and nucleic acid extractionresulting in DNA of PCR-amplifiable quality and quantity are not trivial.Responding to the needs of the Hazardous Materials Response Unit (HMRU),Laboratory Division, Federal Bureau of Investigation, protocols weredeveloped to close these gaps. Effectiveness and reproducibility of thetechniques were validated with laboratory grown pure spores of Bacillusanthracis and its close phylogenetic neighbors, and with spiked soils anddamaged samples.

  8. Chromosome specific repetitive DNA sequences

    DOE Patents [OSTI]

    Moyzis, Robert K. (Los Alamos, NM); Meyne, Julianne (Los Alamos, NM)

    1991-01-01

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

  9. Interconnecting gold islands with DNA origami

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

    Interconnecting gold islands with DNA origami Authors: Ding, B., Wu, H., Xu, W., Zhao, Z., Liu, Y., Yu, H., and Yan, H. Title: Interconnecting gold islands with DNA origami Source:...

  10. A DNA tweezer-actuated enzyme nanoreactor

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

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

  11. Identification of Intrinsic Order and Disorder in the DNA Repair Protein XPA

    SciTech Connect (OSTI)

    Iakoucheva, Lilia M.; Kimzey, Amy L.; Masselon, Christophe D.; Bruce, James E.; Garner, Ethan C.; Brown, Celeste J.; Dunker, A. K.; Smith, Richard D.; Ackerman, Eric J.

    2001-03-01

    The damage recognition protein XPA is required to recognize a wide variety of bulky lesions during nucleotide excision repair (NER). Independent NMR solution structures of a human XPA protein (hXPA) fragment comprising approximately one-third of the full-length protein, the minimal DNA-binding domain (MBD), revealed that ~30% of the molecule was structurally disordered. To better characterize structural features of XPA, we performed time-resolved trypsin proteolysis on active, full-length recombinant Xenopus XPA protein (xXPA). The resulting proteolytic fragments were analyzed by electrospray ionization interface coupled to a Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometry, SDS-polyacrylamide gel electrophoresis (PAGE), and selected N-terminal sequence determinations. The mass spectrum of the full-length xXPA was consistent with the predicted sequence, 30922.02 vs. 30922.45 Da; respectively. Moreover, the mass spectrometric data allowed the assignment of multiple xXPA fragments not resolvable by SDS PAGE. Full-length xXPA exhibited aberrant mobility on SDS-PAGE with an apparent MW of ~40 kDa. To test predictions that a Glu-rich region (E70-E76) or other local regions of high charge were responsible for this ~40% aberrant SDS-PAGE mobility, the MW's of partial proteolytic fragments from ~5 to 25 kDa precisely determined by ESI-FTICR MS were correlated with their gel positions. Surprisingly, all tested partial tryptic fragments within this size-range exhibited 10-42% divergence between calculated MW and that estimated by SDS-PAGE, thus indicating the origin of anomalous migration of XPA is not localized. The computer program Predictor of Natural Disordered Regions (PONDR) correctly identified several regions of xXPA either sensitive or resistant to partial proteolysis, thereby indicating that disorder in XPA shares sequence features with other well-characterized intrinsically unstructured proteins.

  12. Features of primary damage by high energy displacement cascades in

    Office of Scientific and Technical Information (OSTI)

    concentrated Ni-based alloys (Journal Article) | DOE PAGES Features of primary damage by high energy displacement cascades in concentrated Ni-based alloys This content will become publicly available on February 25, 2017 « Prev Next » Title: Features of primary damage by high energy displacement cascades in concentrated Ni-based alloys Alloying of Ni with Fe or Co reduces primary damage production under ion irradiation. Similar results have been obtained from classical molecular dynamics

  13. Los Alamos offers new insights into radiation damage evolution

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

    New insights into radiation damage evolution Los Alamos offers new insights into radiation damage evolution Two reports are helping crack the code of how certain materials respond in the highly-damaging radiation environments within a nuclear reactor. March 16, 2015 Researchers at Los Alamos are studying complex materials issues, in this case the defects deep inside certain types of cubic metals. This image shows a reaction between two "stacking fault tetrahedra," a perfect SFT

  14. Transparency and damage tolerance of patternable omniphobic lubricated

    Office of Scientific and Technical Information (OSTI)

    surfaces based on inverse colloidal monolayers (Journal Article) | DOE PAGES Transparency and damage tolerance of patternable omniphobic lubricated surfaces based on inverse colloidal monolayers « Prev Next » Title: Transparency and damage tolerance of patternable omniphobic lubricated surfaces based on inverse colloidal monolayers A transparent coating that repels a wide variety of liquids, prevents staining, is capable of self-repair and is robust towards mechanical damage can have a

  15. Amplification of chromosomal DNA in situ

    DOE Patents [OSTI]

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

    2002-01-01

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

  16. DNA Origami: A History and Current Perspective

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

    Origami: A History and Current Perspective Authors: Nangreave, J., Han, D., Liu, Y., and Yan, H. Title: DNA Origami: A History and Current Perspective Source: Current Opinion in Chemical Biology Year: 2010 Volume: 14 Pages: 608-615 ABSTRACT: Researchers have been using DNA for the rational design and construction of nanoscale objects for nearly 30 years. Recently, [`]scaffolded DNA origami' has emerged as one of the most promising assembly techniques in DNA nanotechnology with a broad range of

  17. Probing Radiation Damage in Plutonium Alloys with Multiple Measurement...

    Office of Scientific and Technical Information (OSTI)

    Conference: Probing Radiation Damage in Plutonium Alloys with Multiple Measurement ... as well as external parameters such as the temperature and starting material composition. ...

  18. Performance of Damaged Soil-Concrete Wraparound Dam Sections...

    Office of Scientific and Technical Information (OSTI)

    National Technical Information Service, Springfield, VA at www.ntis.gov. Predicting seismic or shock loading damage of the soil-concrete interface where an embankment wraparound...

  19. Antibody specific for a DNA repair protein

    DOE Patents [OSTI]

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

    2006-07-11

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

  20. Probe and method for DNA detection

    DOE Patents [OSTI]

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

    2013-07-02

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

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

    Open Energy Info (EERE)

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

  2. Fleet DNA Project (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2012-10-01

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

  3. Particle sizer and DNA sequencer

    DOE Patents [OSTI]

    Olivares, Jose A.; Stark, Peter C.

    2005-09-13

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

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

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

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

    2015-06-02

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

  5. The Initiation of Bacterial DNA Replication

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

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

  6. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

    Sessler, Andrew M. (Oakland, CA); Dawson, John (Pacific Palisades, CA)

    1993-01-01

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

  7. Channel plate for DNA sequencing

    DOE Patents [OSTI]

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

    1998-01-13

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

  8. Channel plate for DNA sequencing

    DOE Patents [OSTI]

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

    1998-01-01

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

  9. Corporate Responsibility

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

    Our Workplace » Corporate Responsibility Corporate Responsibility Explore the multiple dimensions of a career at Los Alamos Lab: work with the best minds on the planet in an inclusive environment that is rich in intellectual vitality and opportunities for growth. Contact LANS, LLC Office (505) 606-0105 The nation turns to us for solutions to the most complex national security technical challenges of our times, whether a threat may be nuclear, biological, or chemical. At the heart of the Lab is

  10. Micro-mechanical modeling of perforating shock damage

    SciTech Connect (OSTI)

    Swift, R.P.; Krogh, K.E.; Behrmann, L.A.; Halleck, P.M.

    1997-11-17

    Shaped charge jet induced formation damage from perforation treatments hinders productivity. Manifestation of this damage is in the form of grain fragmentation resulting in fines that plug up pore throats along with the breakdown of inter-grain cementation. The authors use the Smooth Particle Hydrodynamic (SPH) computational method as a way to explicitly model, on a grain pore scale, the dynamic interactions of grains and grain/pores to calculate the damage resulting from perforation type stress wave loading. The SPH method is a continuum Lagrangian, meshless approach that features particles. Clusters of particles are used for each grain to provide representation of a grain pore structure that is similar to x-ray synchrotron microtomography images. Numerous damage models are available to portray fracture and fragmentation. In this paper the authors present the results of well defined impact loading on a grain pore structure that illustrate how the heterogeneity affects stress wave behavior and damage evolution. The SPH approach easily accommodates the coupling of multi-materials. Calculations for multi-material conditions with the pore space treated as a void, fluid filled, and/or clay filled show diverse effects on the stress wave propagation behavior and damage. SPH comparisons made with observed damage from recovered impacted sandstone samples in gas gun experiments show qualitatively the influence of stress intensity. The modeling approach presented here offers a unique way in concert with experiments to define a better understanding of formation damage resulting from perforation completion treatments.

  11. Soft x-ray free-electron laser induced damage to inorganic scintillators

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

    Burian, Tomáš; Hájková, Věra; Chalupský, Jaromír; Vyšín, Luděk; Boháček, Pavel; Přeček, Martin; Wild, Jan; Özkan, Cigdem; Coppola, Nicola; Farahani, Shafagh Dastjani; et al

    2015-01-07

    An irreversible response of inorganic scintillators to intense soft x-ray laser radiation was investigated at the FLASH (Free-electron LASer in Hamburg) facility. Three ionic crystals, namely, Ce:YAG (cerium-doped yttrium aluminum garnet), PbWO4 (lead tungstate), and ZnO (zinc oxide), were exposed to single 4.6 nm ultra-short laser pulses of variable pulse energy (up to 12 μJ) under normal incidence conditions with tight focus. Damaged areas produced with various levels of pulse fluences, were analyzed on the surface of irradiated samples using differential interference contrast (DIC) and atomic force microscopy (AFM). The effective beam area of 22.2 ± 2.2 μm2 was determinedmore » by means of the ablation imprints method with the use of poly(methyl methacrylate) - PMMA. Applied to the three inorganic materials, this procedure gave almost the same values of an effective area. The single-shot damage threshold fluence was determined for each of these inorganic materials. The Ce:YAG sample seems to be the most radiation resistant under the given irradiation conditions, its damage threshold was determined to be as high as 660.8 ± 71.2 mJ/cm2. Contrary to that, the PbWO4 sample exhibited the lowest radiation resistance with a threshold fluence of 62.6 ± 11.9 mJ/cm2. The threshold for ZnO was found to be 167.8 ± 30.8 mJ/cm2. Both interaction and material characteristics responsible for the damage threshold difference are discussed in the article.« less

  12. Analysis of 1w Bulk Laser Damage in KDP

    SciTech Connect (OSTI)

    Cross, D A; Carr, C W

    2011-04-11

    The influence of laser parameters on laser-induced damage in the bulk of KDP is difficult to determine because the damage manifests as discrete sites a few microns in diameter distributed throughout a relatively large volume of material. Here, they present a method to directly measure the size and location of many thousands of such sites and correlate them to the laser conditions which produced them. This technique is used to characterize the effects of pulse duration on damage initiated by 1053 nm light in the bulk of KDP crystals. They find that the density of damage sites produced by 1053 nm light is less sensitive to pulse duration than was previously reported for 526 nm and 351 nm light. In addition, the effect of pulse duration on the size of the damage sites produced appears insensitive to wavelength.

  13. Mesoscale polycrystal calculations of damage in spallation in metals

    SciTech Connect (OSTI)

    Tonks, Davis L [Los Alamos National Laboratory; Bingert, John F [Los Alamos National Laboratory; Livescu, Veronica [Los Alamos National Laboratory; Luo, Shengnian [Los Alamos National Laboratory; Bronkhorst, C A [Los Alamos National Laboratory

    2010-01-01

    The goal of this project is to produce a damage model for spallation in metals informed by the polycrystalline grain structure at the mesoscale. Earlier damage models addressed the continuwn macroscale in which these effects were averaged out. In this work we focus on cross sections from recovered samples examined with EBSD (electron backscattered diffraction), which reveal crystal grain orientations and voids. We seek to understand the loading histories of specific sample regions by meshing up the crystal grain structure of these regions and simulating the stress, strain, and damage histories in our hydro code, FLAG. The stresses and strain histories are the fundamental drivers of damage and must be calculated. The calculated final damage structures are compared with those from the recovered samples to validate the simulations.

  14. Radiation Damage In Reactor Cavity Concrete

    SciTech Connect (OSTI)

    Field, Kevin G; Le Pape, Yann; Naus, Dan J; Remec, Igor; Busby, Jeremy T; Rosseel, Thomas M; Wall, Dr. James Joseph

    2015-01-01

    License renewal up to 60 years and the possibility of subsequent license renewal to 80 years has established a renewed focus on long-term aging of nuclear generating stations materials, and recently, on concrete. Large irreplaceable sections of most nuclear generating stations include concrete. The Expanded Materials Degradation Analysis (EMDA), jointly performed by the Department of Energy, the Nuclear Regulatory Commission and Industry, identified the urgent need to develop a consistent knowledge base on irradiation effects in concrete. Much of the historical mechanical performance data of irradiated concrete does not accurately reflect typical radiation conditions in NPPs or conditions out to 60 or 80 years of radiation exposure. To address these potential gaps in the knowledge base, The Electric Power Research Institute and Oak Ridge National Laboratory are working to disposition radiation damage as a degradation mechanism. This paper outlines the research program within this pathway including: (i) defining the upper bound of the neutron and gamma dose levels expected in the biological shield concrete for extended operation (80 years of operation and beyond), (ii) determining the effects of neutron and gamma irradiation as well as extended time at temperature on concrete, (iii) evaluating opportunities to irradiate prototypical concrete under accelerated neutron and gamma dose levels to establish a conservative bound and share data obtained from different flux, temperature, and fluence levels, (iv) evaluating opportunities to harvest and test irradiated concrete from international NPPs, (v) developing cooperative test programs to improve confidence in the results from the various concretes and research reactors, (vi) furthering the understanding of the effects of radiation on concrete (see companion paper) and (vii) establishing an international collaborative research and information exchange effort to leverage capabilities and knowledge.

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

    SciTech Connect (OSTI)

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

    2015-09-14

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

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

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

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

    2015-09-14

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

  17. DNA

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

    C. Terwilliger, Randy J. Read, Blake Wiedenheft. Crystal structure of the CRISPR RNA- guided surveillance complex from Escherichia coli. Science, 2014 DOI: 10.1126 science.1256328...

  18. 7th International Workshop on Microbeam Probes of Cellular Radiation Response

    SciTech Connect (OSTI)

    Brenner, David J.

    2009-07-21

    The extended abstracts that follow present a summary of the Proceedings of the 7th International Workshop: Microbeam Probes of Cellular Radiation Response, held at Columbia University’s Kellogg Center in New York City on March 15–17, 2006. These International Workshops on Microbeam Probes of Cellular Radiation Response have been held regularly since 1993 (1–5). Since the first workshop, there has been a rapid growth (see Fig. 1) in the number of centers developing microbeams for radiobiological research, and worldwide there are currently about 30 microbeams in operation or under development. Single-cell/single-particle microbeam systems can deliver beams of different ionizing radiations with a spatial resolution of a few micrometers down to a few tenths of a micrometer. Microbeams can be used to addressquestions relating to the effects of low doses of radiation (a single radiation track traversing a cell or group of cells), to probe subcellular targets (e.g. nucleus or cytoplasm), and to address questions regarding the propagation of information about DNA damage (for example, the radiation-induced bystander effect). Much of the recent research using microbeams has been to study low-dose effects and ‘‘non-targeted’’ responses such as bystander effects, genomic instability and adaptive responses. This Workshop provided a forum to assess the current state of microbeam technology and current biological applications and to discuss future directions for development, both technological and biological. Over 100 participants reviewed the current state of microbeam research worldwide and reported on new technological developments in the fields of both physics and biology.

  19. DNA Sequencing Using capillary Electrophoresis

    SciTech Connect (OSTI)

    Dr. Barry Karger

    2011-05-09

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

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

    A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples Authors: Zhao, Z., Yan, H., and Liu, Y. Title: A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples Source: Angewandte Chemie International Edition Year: 2010 Volume: 49 Pages: 1414-1417 ABSTRACT: A new strategy is presented to scale up DNA origami using multi-helical DNA tiles as folding staples. Atomic force microscopy images (see picture) demonstrate the two-dimensional structures formed by using this strategy.

  2. Enhancing the DNA Patent Database

    SciTech Connect (OSTI)

    Walters, LeRoy B.

    2008-02-18

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

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

    SciTech Connect (OSTI)

    Shi, Yun-bo

    1988-03-01

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

  4. DNA-guided nanoparticle assemblies

    DOE Patents [OSTI]

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

    2013-07-16

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

  5. Scientists Assess Damage Caused by Earthquake near Amchitka | Department of

    Energy Savers [EERE]

    Energy Scientists Assess Damage Caused by Earthquake near Amchitka Scientists Assess Damage Caused by Earthquake near Amchitka October 14, 2014 - 10:43am Addthis What does this project do? Goal 1. Protect human health and the environment. Contractor scientists for the U.S. Department of Energy Office of Legacy Management (LM) traveled to the Amchitka, Alaska, Site in late August to assess the damage caused by a recent earthquake. The 7.9 magnitude event occurred approximately 20 miles north

  6. Variable Voltage Substation Electric Fire and Emergency Response |

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

    Department of Energy Variable Voltage Substation Electric Fire and Emergency Response Variable Voltage Substation Electric Fire and Emergency Response Question from Participant: My question is from an emergency response perspective. It was stated that it took ~ ½ for electricians to de-energize the electrical components before firefighters were allowed in to fight the fire. This delay causes more damage to equipment and potential propagation of the fire. Is there not a "master"

  7. When DNA Needs to Stand Up and Be Counted

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

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

  8. When DNA Needs to Stand Up and Be Counted

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

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

  9. When DNA Needs to Stand Up and Be Counted

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

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

  10. Assembling semiconductor nanocomposites using DNA replication technologies.

    SciTech Connect (OSTI)

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

    2005-11-01

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

  11. Microstructure in the extreme environment: understanding and predicting dynamic damage processes

    SciTech Connect (OSTI)

    Dennis-koller, Darcie L [Los Alamos National Laboratory; Cerreta, Ellen K [Los Alamos National Laboratory; Bronkhorst, Curt A [Los Alamos National Laboratory; Escobedo-diaz, Juan P [Los Alamos National Laboratory

    2010-12-21

    The future of materials science: strategic application for functionally controlled materials properties is emphasized by the need to control material performance in extreme environments. To this end, this study examines the separate effects of kinetics (in the form of dynamic loading rate and shock wave shape) from that of length-scale effects (in the form of microstructural defect distributions). Recently available mesoscale modeling techniques are being used to capture a physical link between kinetic and length-scale influences on dynamic loading. This work contributes innovative new tools in the form of shock-wave shaping techniques in dynamic experimentation, materials characterization, lending insight into 3D damage field analysis at micron resolution, and the physics necessary to provide predictive capabilities for dynamic damage evolution. Experimental results tailored for the discreet understanding of length-scale and kinetic effects during dynamic loading are obtained to provide the basis for the development of process-aware material performance models. The understanding of length-scale and kinetic effects in extreme environments of dynamic loading advances the understanding of current emerging issues relevant to phenomena such as inclusion related failure in metals, grain size dependence on ejecta, and benefits of interfaces in mitigating defect development specifically driven by the need to tailor material response. Finally, the coupling of experimental techniques with theory and simulation is aimed at advancing process-aware damage modeling as well as transitioning materials science from observation to property control.

  12. Precursors to potential severe core damage accidents: 1997 -- A status report. Volume 26

    SciTech Connect (OSTI)

    Belles, R.J.; Cletcher, J.W.; Copinger, D.A.; Muhlheim, M.D.; Dolan, B.W.; Minarick, J.W.

    1998-11-01

    This report describes the five operational events in 1997 that affected five commercial light-water reactors (LWRs) and that are considered to be precursors to potential severe core damage accidents. All these events had conditional probabilities of subsequent severe core damage greater than or equal to 1.0 {times} 10{sup {minus}6}. These events were identified by first computer-screening the 1997 licensee event reports from commercial LWRs to identify those events that could be precursors. Candidate precursors were selected and evaluated in a process similar to that used in previous assessments. Selected events underwent engineering evaluation that identified, analyzed, and documented the precursors. Other events designated by the Nuclear Regulatory Commission (NRC) also underwent a similar evaluation. Finally, documented precursors were submitted for review by licensees and NRC headquarters to ensure that the plant design and its response to the precursor were correctly characterized. This study is a continuation of earlier work, which evaluated 1969--1996 events. The report discusses the general rationale for this study, the selection and documentation of events as precursors, and the estimation of conditional probabilities of subsequent severe core damage for the events.

  13. Precursors to potential severe core damage accidents: 1995 A status report

    SciTech Connect (OSTI)

    Belles, R.J.; Cletcher, J.W.; Copinger, D.A. and others

    1997-04-01

    Ten operational events that affected 10 commercial light-water reactors during 1995 and that are considered to be precursors to potential severe core damage are described. All these events had conditional probabilities of subsequent severe core damage greater than or equal to 1.0 x 10{sup {minus}6}. These events were identified by first computer-screening the 1995 licensee event reports from commercial light-water reactors to identify those events that could potentially be precursors. Candidate precursors were selected and evaluated in a process similar to that used in previous assessments. Selected events underwent engineering evaluation that identified, analyzed, and documented the precursors. Other events designated by the Nuclear Regulatory Commission (NRC) also underwent a similar evaluation. Finally, documented precursors were submitted for review by licensees and NRC headquarters and regional offices to ensure the plant design and its response to the precursor were correctly characterized. This study is a continuation of earlier work, which evaluated 1969-1981 and 1984-1994 events. The report discusses the general rationale for this study, the selection and documentation of events as precursors, and the estimation of conditional probabilities of subsequent severe core damage for the events.

  14. Precursors to potential severe core damage accidents: 1994, a status report. Volume 22: Appendix I

    SciTech Connect (OSTI)

    Belles, R.J.; Cletcher, J.W.; Copinger, D.A.; Vanden Heuvel, L.N.; Dolan, B.W.; Minarick, J.W.

    1995-12-01

    Nine operational events that affected eleven commercial light-water reactors (LWRs) during 1994 and that are considered to be precursors to potential severe core damage are described. All these events had conditional probabilities of subsequent severe core damage greater than or equal to 1.0 {times} 10{sup {minus}6}. These events were identified by computer-screening the 1994 licensee event reports from commercial LWRs to identify those that could be potential precursors. Candidate precursors were then selected and evaluated in a process similar to that used in previous assessments. Selected events underwent engineering evaluation that identified, analyzed, and documented the precursors. Other events designated by the Nuclear Regulatory Commission (NRC) also underwent a similar evaluation. Finally, documented precursors were submitted for review by licensees and NRC headquarters and regional offices to ensure that the plant design and its response to the precursor were correctly characterized. This study is a continuation of earlier work, which evaluated 1969--1981 and 1984--1993 events. The report discusses the general rationale for this study, the selection and documentation of events as precursors, and the estimation of conditional probabilities of subsequent severe core damage for events. This document is bound in two volumes: Vol. 21 contains the main report and Appendices A--H; Vol. 22 contains Appendix 1.

  15. The Initiation of Bacterial DNA Replication

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

    The Initiation of Bacterial DNA Replication 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

  16. The Initiation of Bacterial DNA Replication

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

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

  17. The Initiation of Bacterial DNA Replication

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

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

  18. DNA sequencing using fluorescence background electroblotting membrane

    DOE Patents [OSTI]

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

    1992-01-01

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

  19. DNA sequencing using fluorescence background electroblotting membrane

    DOE Patents [OSTI]

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

    1992-05-12

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

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

    SciTech Connect (OSTI)

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

    2013-05-03

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

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

    Office of Scientific and Technical Information (OSTI)

    The DNA is underwound and stretched globally, but locally it adopts a B-DNA-like conformation that restricts the homology search to Watson-Crick-type base pairing. The ...

  2. A Tow-Level Progressive Damage for Simulating Carbon-Fiber Textile Composites: Interim Report

    SciTech Connect (OSTI)

    Zywicz, E.

    2000-07-01

    A numerical approach to model the elasto-plastic and tensile damage response of tri-axially braided carbon-fiber polymeric-matrix composites is developed. It is micromechanically based and consists of a simplified unit cell geometry, a plane-stress tow-level constitutive relationship, a one-dimensional undulation constitutive law, and a non-traditional shell element integration rule. The braided composite lamina is idealized as periodic in the plane, and a simplified three-layer representative volume (RV) is assembled from axial and braider tows and pure resin regions. The constituents in each layer are homogenized with an iso-strain assumption in the fiber-direction and an iso-stress condition in the other directions. In the upper and lower layers, the fiber-direction strain is additively decomposed into an undulation and a tow portion. A finite-deformation tow model predicts the plane-stress tow response and is coupled to the undulation constitutive relationship. The overall braid model is implemented in DYNA3D and works with traditional shell elements. The finite-deformation tow constitutive relationship is derived from the fiber elasticity and the isotropic elasto-plastic power-law hardening matrix response using a thermodynamic framework and simple homogenization assumptions. The model replicates tensile damage evolution, in a smeared sense, parallel and perpendicular to the fiber axis and is regularized to yield mesh independent results. The tow-level model demonstrates reasonable agreement, prior to damage, with detailed three-dimensional FE (finite element) elasto-plastic simulations of aligned, periodically arranged, uni-directional composites. The 3-layer braid model response is compared with predictions obtained from detailed micromechanical simulations of the braid's unit cell in uni-axial extension, shear, and flexure for three braid angles. The elastic properties show good agreement as does the non-linear response for loadings dominated by the axial tows. In loadings dominated by the braider tow response, the absence of a non-linear undulation model deteriorates the agreement. Nonetheless, the present approach is applicable to a broad range of tri-axially braided composites as well as for unidirectional composites, but presently lacks any compressive failure mechanisms and an adequate non-linear undulation model.

  3. Response Elements

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2007-07-11

    The Guide provides acceptable methods for meeting the requirement of DOE O 151.1C for response elements that respond or contribute to response as needed in an emergency. Supersedes DOE G 151.1-1, Volume 3-1, DOE G 151.1-1, Volume 3-2, DOE G 151.1-1, Volume 3-3, DOE G 151.1-1, Volume 3-4, DOE G 151.1-1, Volume 4-1, DOE G 151.1-1, Volume 4-2, DOE G 151.1-1, Volume 4-3, DOE G 151.1-1, Volume 4-4, DOE G 151.1-1, Volume 4-5, and DOE G 151.1-1, Volume 4-6.

  4. Departmental Response:

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

    3 Departmental Response: Assessment of the Report of the SEAB Task Force on Nuclear Nonproliferation Introduction Despite many successful U.S. efforts in nuclear nonproliferation, daunting challenges remain. Some nations are pursuing nuclear weapons and others are expanding their nuclear arsenals; some stockpiles of nuclear weapons and nuclear-weapons-usable materials remain dangerously insecure; and rapidly changing technologies and greater availability of dual-use knowledge are increasing the

  5. Demand Response

    Office of Environmental Management (EM)

    Demand Response Assessment for Eastern Interconnection Youngsun Baek, Stanton W. Hadley, Rocio Martinez, Gbadebo Oladosu, Alexander M. Smith, Fran Li, Paul Leiby and Russell Lee Prepared for FY12 DOE-CERTS Transmission Reliability R&D Internal Program Review September 20, 2012 2 Managed by UT-Battelle for the U.S. Department of Energy DOE National Laboratory Studies Funded to Support FOA 63 * DOE set aside $20 million from transmission funding for national laboratory studies. * DOE

  6. Investigation of Microscale Damage Evolution in High Strength...

    Office of Scientific and Technical Information (OSTI)

    Damage Evolution in High Strength A1 Alloy. Authors: Jin, Huiqing ; Lu, Wei-Yang ; Mota, Alejandro ; Foulk, James W., III ; johnson, george Publication Date: 2012-09-01 OSTI...

  7. Investigation of Microscale Damage Evolution in High-Strength...

    Office of Scientific and Technical Information (OSTI)

    Damage Evolution in High-Strength Al Alloy. Authors: Jin, Huiqing ; Lu, Wei-Yang ; Mota, Alejandro ; Foulk, James W., III Publication Date: 2012-10-01 OSTI Identifier: 1072668...

  8. Minimizing damage to a propped fracture by controlled flowback procedures

    SciTech Connect (OSTI)

    Robinson, B.M.; Holditch, S.A.; Whitehead, W.S.

    1988-06-01

    Severe fracture-conductivity damage can result from proppant crushing and/or proppant flowback into the wellbore. Such damage is often concentrated near the wellbore and can directly affect postfracture performance. Most of the time severe fracture-conductivity damage can be minimized by choosing the correct type of proppant for a particular well. In many cases, however, this is not enough. To minimize excessive crushing or to prevent proppant flowback, it is also necessary to control carefully the flowback of the well after the treatment. Specific procedures can be followed to minimize severe fracture-conductivity damage. These procedures involve controlling the rates at which load fluids are recovered and maximizing backpressure against the formation. These procedures require much more time and effort than is normally spent on postfracture cleanup; however, the efforts could result in better performance.

  9. NMSLO Water Lease Damage Bond | Open Energy Information

    Open Energy Info (EERE)

    Water Lease Damage BondLegal Published NA Year Signed or Took Effect 2012 Legal Citation Not provided DOI Not Provided Check for DOI availability: http:crossref.org Online...

  10. Neutron and gamma irradiation damage to organic materials.

    SciTech Connect (OSTI)

    White, Gregory Von, II; Bernstein, Robert

    2012-04-01

    This document discusses open literature reports which investigate the damage effects of neutron and gamma irradiation on polymers and/or epoxies - damage refers to reduced physical chemical, and electrical properties. Based on the literature, correlations are made for an SNL developed epoxy (Epon 828-1031/DDS) with an expected total fast-neutron fluence of {approx}10{sup 12} n/cm{sup 2} and a {gamma} dosage of {approx}500 Gy received over {approx}30 years at < 200 C. In short, there are no gamma and neutron irradiation concerns for Epon 828-1031/DDS. To enhance the fidelity of our hypotheses, in regards to radiation damage, we propose future work consisting of simultaneous thermal/irradiation (neutron and gamma) experiments that will help elucidate any damage concerns at these specified environmental conditions.

  11. Grain orientation dependence of lattice strains and intergranular damage

    Office of Scientific and Technical Information (OSTI)

    rates in polycrystals under cyclic loading (Journal Article) | SciTech Connect Grain orientation dependence of lattice strains and intergranular damage rates in polycrystals under cyclic loading Citation Details In-Document Search Title: Grain orientation dependence of lattice strains and intergranular damage rates in polycrystals under cyclic loading Authors: Zheng, Lili [1] ; Gao, Yanfei [2] ; Wang, Yandong [3] ; Stoica, Alexandru Dan [4] ; An, Ke [4] ; Wang, Xun-Li [4] + Show Author

  12. PV Module Intraconnect Thermomechanical Durability Damage Prediction Model

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

    | Department of Energy Module Intraconnect Thermomechanical Durability Damage Prediction Model PV Module Intraconnect Thermomechanical Durability Damage Prediction Model Presented at the PV Module Reliability Workshop, February 26 - 27 2013, Golden, Colorado PDF icon pvmrw13_ps2_dow_gaston.pdf More Documents & Publications 2014 Propulsion Materials R&D Annual Report Electro-thermal-mechanical Simulation and Reliability for Plug-in Vehicle Converters and Inverters Center for

  13. EM, Tribal, and State Officials Receive Training on Restoring Damaged

    Energy Savers [EERE]

    Natural Resources | Department of Energy EM, Tribal, and State Officials Receive Training on Restoring Damaged Natural Resources EM, Tribal, and State Officials Receive Training on Restoring Damaged Natural Resources December 29, 2015 - 12:45pm Addthis Willie Preacher was a member of the Shoshone-Bannock Tribes of Fort Hall, Idaho. Willie Preacher was a member of the Shoshone-Bannock Tribes of Fort Hall, Idaho. NEW ORLEANS - Senior EM, Tribal, and state officials gathered for a training on

  14. Damaged Surface Hydrodynamics (DSH) Flash Report (Technical Report) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Technical Report: Damaged Surface Hydrodynamics (DSH) Flash Report Citation Details In-Document Search Title: Damaged Surface Hydrodynamics (DSH) Flash Report Abstract Not Provided. Authors: Rousculp, Christopher L. [1] ; Oro, David Michael [1] ; Morris, Christopher [1] ; Saunders, Alexander [1] ; Reass, William [1] ; Griego, Jeffrey Randall [1] ; Turchi, Peter John [1] ; Reinovsky, Robert Emil [1] + Show Author Affiliations Los Alamos National Lab. (LANL), Los Alamos, NM

  15. Los Alamos National Laboratory describes storm damage to environmental

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

    monitoring stations, canyons Los Alamos National Laboratory describes storm damage Los Alamos National Laboratory describes storm damage to environmental monitoring stations, canyons Stations supporting Santa Fe water utility returned to service September 18, 2013 Los Alamos National Laboratory sits on top of a once-remote mesa in northern New Mexico with the Jemez mountains as a backdrop to research and innovation covering multi-disciplines from bioscience, sustainable energy sources, to

  16. Transparency and damage tolerance of patternable omniphobic lubricated

    Office of Scientific and Technical Information (OSTI)

    surfaces based on inverse colloidal monolayers (Journal Article) | DOE PAGES Transparency and damage tolerance of patternable omniphobic lubricated surfaces based on inverse colloidal monolayers « Prev Next » Title: Transparency and damage tolerance of patternable omniphobic lubricated surfaces based on inverse colloidal monolayers × You are accessing a document from the Department of Energy's (DOE) Public Access Gateway for Energy & Science (PAGES). This site is a product of DOE's

  17. Contract Awarded for Los Alamos National Laboratory Natural Resource Damage

    Office of Environmental Management (EM)

    Assessment | Department of Energy Los Alamos National Laboratory Natural Resource Damage Assessment Contract Awarded for Los Alamos National Laboratory Natural Resource Damage Assessment September 24, 2015 - 3:00pm Addthis Media Contact Lynette Chafin, 513-246-0461, Lynette.Chafin@emcbc.doe.gov Cincinnati - The Department of Energy (DOE) today announced the award an Indefinite Delivery/Indefinite Quantity (IDIQ) contract to Industrial Economics, Incorporated, located in Cambridge, MA.

  18. Observed damage during Argon gas cluster depth profiles of compound semiconductors

    SciTech Connect (OSTI)

    Barlow, Anders J. Portoles, Jose F.; Cumpson, Peter J.

    2014-08-07

    Argon Gas Cluster Ion Beam (GCIB) sources have become very popular in XPS and SIMS in recent years, due to the minimal chemical damage they introduce in the depth-profiling of polymer and other organic materials. These GCIB sources are therefore particularly useful for depth-profiling polymer and organic materials, but also (though more slowly) the surfaces of inorganic materials such as semiconductors, due to the lower roughness expected in cluster ion sputtering compared to that introduced by monatomic ions. We have examined experimentally a set of five compound semiconductors, cadmium telluride (CdTe), gallium arsenide (GaAs), gallium phosphide (GaP), indium arsenide (InAs), and zinc selenide (ZnSe) and a high-? dielectric material, hafnium oxide (HfO), in their response to argon cluster profiling. An experimentally determined HfO etch rate of 0.025?nm/min (3.95??10{sup ?2}?amu/atom in ion) for 6?keV Ar gas clusters is used in the depth scale conversion for the profiles of the semiconductor materials. The assumption has been that, since the damage introduced into polymer materials is low, even though sputter yields are high, then there is little likelihood of damaging inorganic materials at all with cluster ions. This seems true in most cases; however, in this work, we report for the first time that this damage can in fact be very significant in the case of InAs, causing the formation of metallic indium that is readily visible even to the naked eye.

  19. Commercial & Industrial Demand Response

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

    & Events Skip navigation links Smart Grid Demand Response Agricultural Residential Demand Response Commercial & Industrial Demand Response Cross-sector Demand Response...

  20. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

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

    1994-10-18

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

  1. Allostery through protein-induced DNA bubbles

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

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

    2015-03-12

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

  2. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

    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)

    1994-01-01

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

  3. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

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

    2011-07-05

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

  4. Storing data encoded DNA in living organisms

    DOE Patents [OSTI]

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

    2006-06-06

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

  5. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

    Sessler, A.M.; Dawson, J.

    1993-12-14

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

  6. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

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

    2006-08-01

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

  7. Structural Health Monitoring for Impact Damage in Composite Structures.

    SciTech Connect (OSTI)

    Roach, Dennis P.; Raymond Bond; Doug Adams

    2014-08-01

    Composite structures are increasing in prevalence throughout the aerospace, wind, defense, and transportation industries, but the many advantages of these materials come with unique challenges, particularly in inspecting and repairing these structures. Because composites of- ten undergo sub-surface damage mechanisms which compromise the structure without a clear visual indication, inspection of these components is critical to safely deploying composite re- placements to traditionally metallic structures. Impact damage to composites presents one of the most signi fi cant challenges because the area which is vulnerable to impact damage is generally large and sometimes very dif fi cult to access. This work seeks to further evolve iden- ti fi cation technology by developing a system which can detect the impact load location and magnitude in real time, while giving an assessment of the con fi dence in that estimate. Fur- thermore, we identify ways by which impact damage could be more effectively identi fi ed by leveraging impact load identi fi cation information to better characterize damage. The impact load identi fi cation algorithm was applied to a commercial scale wind turbine blade, and results show the capability to detect impact magnitude and location using a single accelerometer, re- gardless of sensor location. A technique for better evaluating the uncertainty of the impact estimates was developed by quantifying how well the impact force estimate meets the assump- tions underlying the force estimation technique. This uncertainty quanti fi cation technique was found to reduce the 95% con fi dence interval by more than a factor of two for impact force estimates showing the least uncertainty, and widening the 95% con fi dence interval by a fac- tor of two for the most uncertain force estimates, avoiding the possibility of understating the uncertainty associated with these estimates. Linear vibration based damage detection tech- niques were investigated in the context of structural stiffness reductions and impact damage. A method by which the sensitivity to damage could be increased for simple structures was presented, and the challenges of applying that technique to a more complex structure were identi fi ed. The structural dynamic changes in a weak adhesive bond were investigated, and the results showed promise for identifying weak bonds that show little or no static reduction in stiffness. To address these challenges in identifying highly localized impact damage, the possi- bility of detecting damage through nonlinear dynamic characteristics was also identi fi ed, with a proposed technique which would leverage impact location estimates to enable the detection of impact damage. This nonlinear damage identi fi cation concept was evaluated on a composite panel with a substructure disbond, and the results showed that the nonlinear dynamics at the damage site could be observed without a baseline healthy reference. By further developing impact load identi fi cation technology and combining load and damage estimation techniques into an integrated solution, the challenges associated with impact detection in composite struc- tures can be effectively solved, thereby reducing costs, improving safety, and enhancing the operational readiness and availability of high value assets.

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

    SciTech Connect (OSTI)

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

    2010-06-21

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

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

    SciTech Connect (OSTI)

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

    2008-10-31

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

  10. Property:NEPA DNA Worksheet | Open Energy Information

    Open Energy Info (EERE)

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

  11. Synthesis of DNA (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

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

  12. Mechanical Response of Thermoelectric Materials

    SciTech Connect (OSTI)

    Wereszczak, Andrew A.; Case, Eldon D.

    2015-05-01

    A sufficient mechanical response of thermoelectric materials (TEMats) to structural loadings is a prerequisite to the exploitation of any candidate TEMat's thermoelectric efficiency. If a TEMat is mechanically damaged or cracks from service-induced stresses, then its thermal and electrical functions can be compromised or even cease. Semiconductor TEMats tend to be quite brittle and have a high coefficient of thermal expansion; therefore, they can be quite susceptible to mechanical failure when subjected to operational thermal gradients. Because of this, sufficient mechanical response (vis-a-vis, mechanical properties) of any candidate TEMat must be achieved and sustained in the context of the service-induced stress state to which it is subjected. This report provides an overview of the mechanical responses of state-of-the-art TEMats; discusses the relevant properties that are associated with those responses and their measurement; and describes important, nonequilibrium phenomena that further complicate their use in thermoelectric devices. For reference purposes, the report also includes several appendixes that list published data on elastic properties and strengths of a variety of TEMats.

  13. Assessment of substrate-stabilizing factors for DnaK on the folding of aggregation-prone proteins

    SciTech Connect (OSTI)

    Ryu, Kisun; Kim, Chul Woo; Kim, Byung Hee [Department of Biotechnology, College of Engineering, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Han, Kyoung Sim [Protheon Incorporated, Yonsei Engineering Research Center B120E, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Kim, Kyun-Hwan [Department of Pharmacology, School of Medicine, and Center for Diagnostic Medicine, Institute of Biomedical Science and Technology, Konkuk University, Seoul 143-701 (Korea, Republic of); Choi, Seong Il [Department of Biotechnology, College of Engineering, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Institute of Life Science and Biotechnology, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of)], E-mail: seongilchoi@daum.net; Seong, Baik L. [Department of Biotechnology, College of Engineering, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Protheon Incorporated, Yonsei Engineering Research Center B120E, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Institute of Life Science and Biotechnology, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of)], E-mail: blseong@yonsei.ac.kr

    2008-08-15

    Hydrophobic interactions between molecular chaperones and their nonnative substrates have been believed to be mainly responsible for both substrate recognition and stabilization against aggregation. However, the hydrophobic contact area between DnaK and its substrate proteins is very limited and other factors of DnaK for the substrate stabilization could not be excluded. Here, we covalently fused DnaK to the N-termini of aggregation-prone proteins in vivo. In the context of a fusion protein, DnaK has the ability to efficiently solubilize its linked proteins. The point mutation of the residue of DnaK critical for the substrate recognition and the deletion of the C-terminal substrate-binding domain did not have significant effect on the solubilizing ability of DnaK. The results imply that other factors of DnaK, distinct from the hydrophobic shielding of folding intermediates, also contributes to stabilization of its noncovalently bound substrates against aggregation. Elucidation of the nature of these factors would further enhance our understanding of the substrate stabilization of DnaK for expedited protein folding.

  14. Gel Electrophoresis of Gold-DNA Nanoconjugates

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

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

    2007-01-01

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

  15. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked...

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

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

    Technology Marketing SummaryThe invention screens purchase orders submitted to DNA synthesis companies.DescriptionOrders are screened to find indicators that the ordered DNA...

  17. Unidirectional Scaffold-Strand Arrangement in DNA Origami

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

    Unidirectional Scaffold-Strand Arrangement in DNA Origami Authors: Han, D., Jiang, S., Samanta, A., Liu, Y., and Yan, H. Title: Unidirectional Scaffold-Strand Arrangement in DNA...

  18. 6.7 Engineered Enzyme Accelerates DNA Sequencing

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

    and Richardson, C. C. (1995) "A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and...

  19. When DNA Needs to Stand Up and Be Counted

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

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

  20. Method of quantitating dsDNA

    DOE Patents [OSTI]

    Stark, Peter C.; Kuske, Cheryl R.; Mullen, Kenneth I.

    2002-01-01

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

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

    SciTech Connect (OSTI)

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

    2014-06-21

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

  2. Analysis of bending properties for damaged laminated pipes

    SciTech Connect (OSTI)

    Yokoyama, A.; Nishiwaki, T.; Nakai, A.; Hamada, H.

    1996-12-01

    Various composite cylinders, such as braided cylinders, could be fabricated with a high volume fabrication method, using thermoplastic composites and so on. If so, usage of composite cylinder would be extended. In this paper, a new analytical model named Quasi-Three-Dimensional model was proposed and applied to a two-layered composite cylinder. Under various service environments, a damaged cylinder with interlaminar fracture often appeared. The calculated elastic modulus was decreased with an increase of the damaged area. From deformation states and stress distribution of interlaminae, some coupling effects were recognized, even if the analytical cylinder without any damage never showed any coupling effects. This result showed the usefulness of the Quasi-Three-Dimensional model.

  3. High-energy radiation damage in zirconia: Modeling results

    SciTech Connect (OSTI)

    Zarkadoula, E.; Devanathan, R.; Weber, W. J.; Seaton, M. A.; Todorov, I. T.; Nordlund, K.; Dove, M. T.; Trachenko, K.

    2014-02-28

    Zirconia is viewed as a material of exceptional resistance to amorphization by radiation damage, and consequently proposed as a candidate to immobilize nuclear waste and serve as an inert nuclear fuel matrix. Here, we perform molecular dynamics simulations of radiation damage in zirconia in the range of 0.10.5?MeV energies with account of electronic energy losses. We find that the lack of amorphizability co-exists with a large number of point defects and their clusters. These, importantly, are largely isolated from each other and therefore represent a dilute damage that does not result in the loss of long-range structural coherence and amorphization. We document the nature of these defects in detail, including their sizes, distribution, and morphology, and discuss practical implications of using zirconia in intense radiation environments.

  4. High-energy radiation damage in zirconia: modeling results

    SciTech Connect (OSTI)

    Zarkadoula, Eva; Devanathan, Ram; Weber, William J.; Seaton, Michael; Todorov, Ilian; Nordlund, Kai; Dove, Martin T.; Trachenko, Kostya

    2014-02-28

    Zirconia has been viewed as a material of exceptional resistance to amorphization by radiation damage, and was consequently proposed as a candidate to immobilize nuclear waste and serve as a nuclear fuel matrix. Here, we perform molecular dynamics simulations of radiation damage in zirconia in the range of 0.1-0.5 MeV energies with the account of electronic energy losses. We find that the lack of amorphizability co-exists with a large number of point defects and their clusters. These, importantly, are largely disjoint from each other and therefore represent a dilute damage that does not result in the loss of long-range structural coherence and amorphization. We document the nature of these defects in detail, including their sizes, distribution and morphology, and discuss practical implications of using zirconia in intense radiation environments.

  5. High-energy radiation damage in zirconia: modeling results

    SciTech Connect (OSTI)

    Zarkadoula, Evangelia; Devanathan, Ram; Weber, William J; Seaton, M; Todorov, I T; Nordlund, Kai; Dove, Martin T; Trachenko, Kostya

    2014-01-01

    Zirconia is viewed as a material of exceptional resistance to amorphization by radiation damage, and consequently proposed as a candidate to immobilize nuclear waste and serve as an inert nuclear fuel matrix. Here, we perform molecular dynamics simulations of radiation damage in zirconia in the range of 0.1-0.5 MeV energies with account of electronic energy losses. We nd that the lack of amorphizability co-exists with a large number of point defects and their clusters. These, importantly, are largely isolated from each other and therefore represent a dilute damage that does not result in the loss of long-range structural coherence and amorphization. We document the nature of these defects in detail, including their sizes, distribution and morphology, and discuss practical implications of using zirconia in intense radiation environments.

  6. Thermal annealing of laser damage precursors on fused silica surfaces

    SciTech Connect (OSTI)

    Shen, N; Miller, P E; Bude, J D; Laurence, T A; Suratwala, T I; Steele, W A; Feit, M D; Wang, L L

    2012-03-19

    Previous studies have identified two significant precursors of laser damage on fused silica surfaces at fluenes below {approx} 35 J/cm{sup 2}, photoactive impurities in the polishing layer and surface fractures. In the present work, isothermal heating is studied as a means of remediating the highly absorptive, defect structure associated with surface fractures. A series of Vickers indentations were applied to silica surfaces at loads between 0.5N and 10N creating fracture networks between {approx} 10{micro}m and {approx} 50{micro}m in diameter. The indentations were characterized prior to and following thermal annealing under various times and temperature conditions using confocal time-resolved photo-luminescence (CTP) imaging, and R/1 optical damage testing with 3ns, 355nm laser pulses. Significant improvements in the damage thresholds, together with corresponding reductions in CTP intensity, were observed at temperatures well below the glass transition temperature (T{sub g}). For example, the damage threshold on 05.N indentations which typically initiates at fluences <8 J/cm{sup 2} could be improved >35 J/cm{sup 2} through the use of a {approx} 750 C thermal treatment. Larger fracture networks required longer or higher temperature treatment to achieve similar results. At an annealing temperature > 1100 C, optical microscopy indicates morphological changes in some of the fracture structure of indentations, although remnants of the original fracture and significant deformation was still observed after thermal annealing. This study demonstrates the potential of using isothermal annealing as a means of improving the laser damage resistance of fused silica optical components. Similarly, it provides a means of further understanding the physics associated with optical damage and related mitigation processes.

  7. Assessing Vulnerabilities, Risks, and Consequences of Damage to Critical Infrastructure

    SciTech Connect (OSTI)

    Suski, N; Wuest, C

    2011-02-04

    Since the publication of 'Critical Foundations: Protecting America's Infrastructure,' there has been a keen understanding of the complexity, interdependencies, and shared responsibility required to protect the nation's most critical assets that are essential to our way of life. The original 5 sectors defined in 1997 have grown to 18 Critical Infrastructures and Key Resources (CIKR), which are discussed in the 2009 National Infrastructure Protection Plan (NIPP) and its supporting sector-specific plans. The NIPP provides the structure for a national program dedicated to enhanced protection and resiliency of the nation's infrastructure. Lawrence Livermore National Laboratory (LLNL) provides in-depth, multi-disciplinary assessments of threat, vulnerability, and consequence across all 18 sectors at scales ranging from specific facilities to infrastructures spanning multi-state regions, such as the Oil and Natural Gas (ONG) sector. Like many of the CIKR sectors, the ONG sector is comprised of production, processing, distribution, and storage of highly valuable and potentially dangerous commodities. Furthermore, there are significant interdependencies with other sectors, including transportation, communication, finance, and government. Understanding the potentially devastating consequences and collateral damage resulting from a terrorist attack or natural event is an important element of LLNL's infrastructure security programs. Our work began in the energy sector in the late 1990s and quickly expanded other critical infrastructure sectors. We have performed over 600 physical assessments with a particular emphasis on those sectors that utilize, store, or ship potentially hazardous materials and for whom cyber security is important. The success of our approach is based on building awareness of vulnerabilities and risks and working directly with industry partners to collectively advance infrastructure protection. This approach consists of three phases: The Pre-Assessment Phase brings together infrastructure owners and operators to identify critical assets and help the team create a structured information request. During this phase, we gain information about the critical assets from those who are most familiar with operations and interdependencies, making the time we spend on the ground conducting the assessment much more productive and enabling the team to make actionable recommendations. The Assessment Phase analyzes 10 areas: Threat environment, cyber architecture, cyber penetration, physical security, physical penetration, operations security, policies and procedures, interdependencies, consequence analysis, and risk characterization. Each of these individual tasks uses direct and indirect data collection, site inspections, and structured and facilitated workshops to gather data. Because of the importance of understanding the cyber threat, LLNL has built both fixed and mobile cyber penetration, wireless penetration and supporting tools that can be tailored to fit customer needs. The Post-Assessment Phase brings vulnerability and risk assessments to the customer in a format that facilitates implementation of mitigation options. Often the assessment findings and recommendations are briefed and discussed with several levels of management and, if appropriate, across jurisdictional boundaries. The end result is enhanced awareness and informed protective measures. Over the last 15 years, we have continued to refine our methodology and capture lessons learned and best practices. The resulting risk and decision framework thus takes into consideration real-world constraints, including regulatory, operational, and economic realities. In addition to 'on the ground' assessments focused on mitigating vulnerabilities, we have integrated our computational and atmospheric dispersion capability with easy-to-use geo-referenced visualization tools to support emergency planning and response operations. LLNL is home to the National Atmospheric Release Advisory Center (NARAC) and the Interagency Modeling and Atmospheric Assessment Center (IMAAC). NA

  8. Predicting threshold and location of laser damage on optical surfaces

    DOE Patents [OSTI]

    Siekhaus, W.

    1985-02-04

    Disclosed is an apparatus useful in the prediction of the damage threshold of various optical devices, the location of weak spots on such devices and the location, identification, and elimination of optical surface impurities. The apparatus comprises a focused and pulsed laser, a photo electric detector/imaging means, and a timer. The weak spots emit photoelectrons when subjected to laser intensities that are less than the intensity actually required to produce the damage. The weak spots may be eliminated by sustained exposure to the laser beam.

  9. High-Temperature Oxide Regrowth on Mechanically-Damaged Surfaces

    SciTech Connect (OSTI)

    Blau, Peter Julian; Lowe, Tracie M

    2008-01-01

    Here we report the effects of mechanical damage from a sharp stylus on the regrowth of oxide layers on a Ni-based superalloy known as Pyromet 80A . It was found that the oxide that reformed on the damaged portion of a pre-oxidized surface differed from that which formed on undamaged areas after the equal exposures to elevated temperature in air. These findings have broad implications for modeling the processes of material degradation in applications such as exhaust valves in internal combustion engines because they imply that static oxidation data for candidate materials may not adequately reflect their reaction to operating environments that involve both mechanical contact and oxidation.

  10. DNA fragment sizing and sorting by laser-induced fluorescence

    DOE Patents [OSTI]

    Hammond, Mark L.; Jett, James H.; Keller, Richard A.; Marrone, Babetta L.; Martin, John C.

    1996-01-01

    A method is provided for sizing DNA fragments using high speed detection systems, such as flow cytometry to determine unique characteristics of DNA pieces from a sample. In one characterization the DNA piece is fragmented at preselected sites to produce a plurality of DNA fragments. The DNA piece or the resulting DNA fragments are treated with a dye effective to stain stoichiometrically the DNA piece or the DNA fragments. The fluorescence from the dye in the stained fragments is then examined to generate an output functionally related to the number of nucleotides in each one of the DNA fragments. In one embodiment, the intensity of the fluorescence emissions from each fragment is linearly related to the fragment length. The distribution of DNA fragment sizes forms a characterization of the DNA piece for use in forensic and research applications.

  11. SuppCompensationNuclearDamage_ExtensionComments.PDF | Department of Energy

    Energy Savers [EERE]

    SuppCompensationNuclearDamage_ExtensionComments.PDF SuppCompensationNuclearDamage_ExtensionComments.PDF PDF icon SuppCompensationNuclearDamage_ExtensionComments.PDF More Documents & Publications CSC_Extension.PDF Convention on Supplementary Compensation for Nuclear Damage Contingent Cost Allocation Notice of extension of public comment period for reply comments.

  12. Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

    DOE Patents [OSTI]

    Gardner, Shea N; Mariella, Jr., Raymond P; Christian, Allen T; Young, Jennifer A; Clague, David S

    2013-06-25

    A method of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths.

  13. DNA Assembly Line for Nano-Construction

    ScienceCinema (OSTI)

    Oleg Gang

    2010-01-08

    Building on the idea of using DNA to link up nanoparticles scientists at Brookhaven National Lab have designed a molecular assembly line for high-precision nano-construction. Nanofabrication is essential for exploiting the unique properties of nanoparticl

  14. Intriguing DNA Editor Has a Structural Trigger

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

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9...

  15. Extracting biological knowledge from DNA sequences

    SciTech Connect (OSTI)

    De La Vega, F.M.; Thieffry, D.; Collado-Vides, J.

    1996-12-31

    This session describes the elucidation of information from dna sequences and what challenges computational biologists face in their task of summarizing and deciphering the human genome. Techniques discussed include methods from statistics, information theory, artificial intelligence and linguistics. 1 ref.

  16. Multiple tag labeling method for DNA sequencing

    DOE Patents [OSTI]

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

    1995-01-01

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

  17. Multiple tag labeling method for DNA sequencing

    DOE Patents [OSTI]

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  18. Oligonucleotide and Long Polymeric DNA Encoding

    SciTech Connect (OSTI)

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

    2003-11-24

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

  19. DOE and State Sign Natural Resources Damages Settlement Agreement

    Broader source: Energy.gov [DOE]

    Officials from TDEC and DOE signed a Natural Resources Damages settlement agreement. The signed document designates DOE’s plans to compensate the state for ecological and human use impacts associated with contaminant releases from facilities at the Oak Ridge Reservation.

  20. Temporary patching of damaged UF{sub 6} cylinders

    SciTech Connect (OSTI)

    Cardenas, A.L.

    1991-12-31

    Patching techniques based on application of epoxy resins have been developed for temporarily repairing UF{sub 6} cylinders which have sustained relatively minor damage and must be safely emptied. The method is considerably faster and simpler than metallurgical weld repairs. Laboratory tests, detailed operational procedures, and case histories of experience at the Portsmouth Gaseous Diffusion Plant are described.

  1. Japanese Ratify Convention on Supplementary Compensation for Nuclear Damage (CSC)

    Broader source: Energy.gov [DOE]

    "The Japanese ratification of the Convention on Supplementary Compensation for Nuclear Damage (CSC) marks an important milestone towards creating a global nuclear liability regime that will assure prompt and meaningful compensation in the event of a nuclear accident and will facilitate international cooperation on nuclear projects such as ongoing clean-up work at the Fukushima site."

  2. Methods for globally treating silica optics to reduce optical damage

    DOE Patents [OSTI]

    Miller, Philip Edward; Suratwala, Tayyab Ishaq; Bude, Jeffrey Devin; Shen, Nan; Steele, William Augustus; Laurence, Ted Alfred; Feit, Michael Dennis; Wong, Lana Louie

    2012-11-20

    A method for preventing damage caused by high intensity light sources to optical components includes annealing the optical component for a predetermined period. Another method includes etching the optical component in an etchant including fluoride and bi-fluoride ions. The method also includes ultrasonically agitating the etching solution during the process followed by rinsing of the optical component in a rinse bath.

  3. Propagation of Reactions in Thermally-damaged PBX-9501

    SciTech Connect (OSTI)

    Tringe, J W; Glascoe, E A; Kercher, J R; Willey, T M; Springer, H K; Greenwood, D W; Molitoris, J D; Smilowitz, L; Henson, B F; Maienschein, J L

    2010-03-05

    A thermally-initiated explosion in PBX-9501 (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) is observed in situ by flash x-ray imaging, and modeled with the LLNL multi-physics arbitrary-Lagrangian-Eulerian code ALE3D. The containment vessel deformation provides a useful estimate of the reaction pressure at the time of the explosion, which we calculate to be in the range 0.8-1.4 GPa. Closely-coupled ALE3D simulations of these experiments, utilizing the multi-phase convective burn model, provide detailed predictions of the reacted mass fraction and deflagration front acceleration. During the preinitiation heating phase of these experiments, the solid HMX portion of the PBX-9501 undergoes a {beta}-phase to {delta}-phase transition which damages the explosive and induces porosity. The multi-phase convective burn model results demonstrate that damaged particle size and pressure are critical for predicting reaction speed and violence. In the model, energetic parameters are taken from LLNL's thermochemical-kinetics code Cheetah and burn rate parameters from Son et al. (2000). Model predictions of an accelerating deflagration front are in qualitative agreement with the experimental images assuming a mode particle diameter in the range 300-400 {micro}m. There is uncertainty in the initial porosity caused by thermal damage of PBX-9501 and, thus, the effective surface area for burning. To better understand these structures, we employ x-ray computed tomography (XRCT) to examine the microstructure of PBX-9501 before and after thermal damage. Although lack of contrast between grains and binder prevents the determination of full grain size distribution in this material, there are many domains visible in thermally damaged PBX-9501 with diameters in the 300-400 {micro}m range.

  4. DNA Extraction by Isotachophoresis in a Microfluidic Channel

    SciTech Connect (OSTI)

    Stephenson, S J

    2011-08-10

    Biological assays have many applications. For example, forensics personnel and medical professionals use these tests to diagnose diseases and track their progression or identify pathogens and the host response to them. One limitation of these tests, however, is that most of them target only one piece of the sample - such as bacterial DNA - and other components (e.g. host genomic DNA) get in the way, even though they may be useful for different tests. To address this problem, it would be useful to extract several different substances from a complex biological sample - such as blood - in an inexpensive and efficient manner. This summer, I worked with Maxim Shusteff at Lawrence Livermore National Lab on the Rapid Automated Sample Prep project. The goal of the project is to solve the aforementioned problem by creating a system that uses a series of different extraction methods to extract cells, bacteria, and DNA from a complex biological sample. Biological assays can then be run on purified output samples. In this device, an operator could input a complex sample such as blood or saliva, and would receive separate outputs of cells, bacteria, viruses, and DNA. I had the opportunity to work this summer with isotachophoresis (ITP), a technique that can be used to extract nucleic acids from a sample. This technique is intended to be the last stage of the purification device. Isotachophoresis separates particles based on different electrophoretic mobilities. This technique is convenient for out application because free solution DNA mobility is approximately equal for DNA longer than 300 base pairs in length. The sample of interest - in our case DNA - is fed into the chip with streams of leading electrolyte (LE) and trailing electrolyte (TE). When an electric field is applied, the species migrate based on their electrophoretic mobilities. Because the ions in the leading electrolyte have a high electrophoretic mobility, they race ahead of the slower sample and trailing electrolyte ions. Conversely, the trailing electrolyte ions have a slow electrophoretic mobility, so they lag behind the sample, thus trapping the species of interest between the LE and TE streams. In a typical isotachophoresis configuration, the electric field is applied in a direction parallel to the direction of flow. The species then form bands that stretch across the width of the channel. A major limitation of that approach is that only a finite amount of sample can be processed at once, and the sample must be processed in batches. For our purposes, a form of free-flow isotachophoresis is more convenient, where the DNA forms a band parallel to the edges of the channel. To achieve this, in our chip, the electric field is applied transversely. This creates a force perpendicular to the direction of flow, which causes the different ions to migrate across the flow direction. Because the mobility of the DNA is between the mobility of the leading and the trailing electrolyte, the DNA is focused in a tight band near the center of the channel. The stream of DNA can then be directed to a different output to produce a highly concentrated outlet stream without batch processing. One hurdle that must be overcome for successful ITP is isolating the electrochemical reactions that result from the application of high voltage for the actual process of isotachophoresis. The electrochemical reactions that occur around metal electrodes produce bubbles and pH changes that are detrimental to successful ITP. The design of the chips we use incorporates polyacrylamide gels to serve as electrodes along the central channel. For our design, the metal electrodes are located away from the chip, and high conductivity buffer streams carry the potential to the chip, functioning as a 'liquid electrode.' The stream then runs alongside a gel barrier. The gel electrode permits ion transfer while simultaneously isolating the separation chamber from any contaminants in the outer, 'liquid electrode' streams. The difference in potential from one side of the chip to the other creates an electric field. This field traverses the inner, separation channel, containing the leading electrolyte, the trailing electrolyte, and the sample of interest (DNA). To increase the ease of use of the chips, a newer chip design has been fabricated. This design has wire electrodes integrated on the chip, rather than elsewhere. To keep the pH changes and bubbling isolated from the separation channel, the chip contains deeper wells near the electrodes so that the flowing buffer can wash away any gases that form around the electrode. This design is significantly more compact because it eliminates the cumbersome electrode boxes. Eliminating the electrode boxes also decreases the required voltage, making the experiments safer. This happens because when the 'liquid electrode' streams travel through small diameter tubing, they lose much of their voltage due to the electrical resistance of the fluid in the tubing.

  5. When DNA Needs to Stand Up and Be Counted

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

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

  6. Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic ThermophileAlvinella pompejana

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

    Kashiwagi, Sayo; Kuraoka, Isao; Fujiwara, Yoshie; Hitomi, Kenichi; Cheng, Quen J.; Fuss, Jill O.; Shin, David S.; Masutani, Chikahide; Tainer, John A.; Hanaoka, Fumio; et al

    2010-01-01

    Human DNA polymerase?(HsPol?) plays an important role in translesion synthesis (TLS), which allows for replication past DNA damage such as UV-inducedcis-syncyclobutane pyrimidine dimers (CPDs). Here, we characterized ApPol?from the thermophilic wormAlvinella pompejana, which inhabits deep-sea hydrothermal vent chimneys. ApPol?shares sequence homology with HsPol?and contains domains for binding ubiquitin and proliferating cell nuclear antigen. Sun-induced UV does not penetrateAlvinella'senvironment; however, this novel DNA polymerase catalyzed efficient and accurate TLS past CPD, as well as 7,8-dihydro-8-oxoguanine and isomers of thymine glycol induced by reactive oxygen species. In addition, we found that ApPol?is more thermostable than HsPol?, as expected from its habitat temperature.moreMoreover, the activity of this enzyme was retained in the presence of a higher concentration of organic solvents. Therefore, ApPol?provides a robust, human-like Pol?that is more active after exposure to high temperatures and organic solvents.less

  7. The discrepancies in multistep damage evolution of yttria-stabilized zirconia irradiated with different ions

    SciTech Connect (OSTI)

    Yang, Tengfei; Taylor, Caitlin A.; Kong, Shuyan; Wang, Chenxu; Zhang, Yanwen; Huang, Xuejun; Xue, Jianming; Yan, Sha; Wang, Yugang

    2013-01-01

    This paper reports a comprehensive investigation of structural damage in yttria-stabilized zirconia irradiated with different ions over a wide fluence range. A similar multistep damage accumulation exists for the irradiations of different ions, but the critical doses for occurrence of second damage step, characterized by a faster increase in damage fraction, and the maximum elastic strain at the first damage step are varied and depend on ion mass. For irradiations of heavier ions, the second damage step occurs at a higher dose with a lower critical elastic strain. Furthermore, larger extended defects were observed in the irradiations of heavy ions at the second damage step. Associated with other experiment results and multistep damage accumulation model, the distinct discrepancies in the damage buildup under irradiations of different ions were interpreted by the effects of electronic excitation, energy of primary knock-on atom and chemistry contributions of deposited ions.

  8. A thermodynamically consistent, damage-dependent, interface debonding model for composites

    SciTech Connect (OSTI)

    Johnson, J.N.; Clements, B.E.; Addessio, F.L.; Williams, T.O.

    1998-12-31

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The ability to design composite materials and analyze processing procedures relies on the availability of constitutive models that describe their dynamic response accurately. The strength, damage evolution, and failure of interfaces within composites often dominate their macroscopic performance but are not well characterized. The design of such composites for particular applications requires adequate knowledge of interfacial characteristics. Given the large number of potential loading scenarios that an engineering composite can be subjected to, it is obviously beneficial to have reliable and accurate theoretical methods for their quantitative treatment in numerical calculation. This project addresses the fundamental aspects of interfacial debonding in composites, and examines the basic behavior in practical situations.

  9. Optical selection and collection of DNA fragments

    DOE Patents [OSTI]

    Roslaniec, Mary C. (Los Alamos, NM); Martin, John C. (Los Alamos, NM); Jett, James H. (Los Alamos, NM); Cram, L. Scott (Los Alamos, NM)

    1998-01-01

    Optical selection and collection of DNA fragments. The present invention includes the optical selection and collection of large (>.mu.g) quantities of clonable, chromosome-specific DNA from a sample of chromosomes. Chromosome selection is based on selective, irreversible photoinactivation of unwanted chromosomal DNA. Although more general procedures may be envisioned, the invention is demonstrated by processing chromosomes in a conventional flow cytometry apparatus, but where no droplets are generated. All chromosomes in the sample are first stained with at least one fluorescent analytic dye and bonded to a photochemically active species which can render chromosomal DNA unclonable if activated. After passing through analyzing light beam(s), unwanted chromosomes are irradiated using light which is absorbed by the photochemically active species, thereby causing photoinactivation. As desired chromosomes pass this photoinactivation point, the inactivating light source is deflected by an optical modulator; hence, desired chromosomes are not photoinactivated and remain clonable. The selection and photoinactivation processes take place on a microsecond timescale. By eliminating droplet formation, chromosome selection rates 50 times greater than those possible with conventional chromosome sorters may be obtained. Thus, usable quantities of clonable DNA from any source thereof may be collected.

  10. Sandia/Stanford Unified Creep Plasticity Damage Model for ANSYS

    Energy Science and Technology Software Center (OSTI)

    2006-09-03

    A unified creep plasticity (UCP) model was developed, based upon the time-dependent and time-independent deformation properties of the 95.5Sn-3.9Ag-0.6Cu (wt.%) soldier that were measured at Sandia. Then, a damage parameter, D, was added to the equation to develop the unified creep plasticity damage (UCPD) model. The parameter, D, was parameterized, using data obtained at Sandia from isothermal fatigue experiments on a double-lap shear test. The softwae was validated against a BGA solder joint exposed tomore » thermal cycling. The UCPD model was put into the ANSYS finite element as a subroutine. So, the softwae is the subroutine for ANSYS 8.1.« less

  11. Evaluation of ATWS core damage frequency for a BWR/4

    SciTech Connect (OSTI)

    Shiu, K.; Ilberg, D.; Hanan, N.

    1985-01-01

    This paper reports a study performed to evaluate the core damage frequency contribution from Anticipated Transient Without Scram (ATWS) in a BWR/4 plant. Discussions on improvements in the design and operation of BWR plants to reduce the likelihood of occurrence and core damage frequency of ATWS have continued for years. In November 1981, subsequent to the issuance of three alternate proposed ATWS rules, the Nuclear Regulatory Commission invited comments on these rules. In June 1984, a final rule on the reduction of risk from ATWS events was issued. In the study, it is assumed that the BWR/4 reactor is of an earlier vintage. However, only two of the modifications have been implemented in accordance with the final rule: a diverse scram system and automatic recirculation pump trip. It is further assumed that the setpoint for Main Steam Isolation Valves (MSIVs) closure is at reactor pressure vessel (RPV) water level 1 and that the BWR emergency procedure guidelines are implemented.

  12. Damage-tolerant nanotwinned metals with nanovoids under radiation environments

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

    Chen, Y.; Yu, K. Y.; Liu, Y.; Shao, S.; Wang, H.; Kirk, M. A.; Wang, J.; Zhang, X.

    2015-04-24

    Material performance in extreme radiation environments is central to the design of future nuclear reactors. Radiation induces significant damage in the form of dislocation loops and voids in irradiated materials, and continuous radiation often leads to void growth and subsequent void swelling in metals with low stacking fault energy. Here we show that by using in situ heavy ion irradiation in a transmission electron microscope, pre-introduced nanovoids in nanotwinned Cu efficiently absorb radiation-induced defects accompanied by gradual elimination of nanovoids, enhancing radiation tolerance of Cu. In situ studies and atomistic simulations reveal that such remarkable self-healing capability stems from highmore » density of coherent and incoherent twin boundaries that rapidly capture and transport point defects and dislocation loops to nanovoids, which act as storage bins for interstitial loops. This study describes a counterintuitive yet significant concept: deliberate introduction of nanovoids in conjunction with nanotwins enables unprecedented damage tolerance in metallic materials.« less

  13. Cryogenic and Fire Damage Analysis on Liquefied Natural Gas Ships

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

    and Fire Damage Analysis on Liquefied Natural Gas Ships - Sandia Energy Energy Search Icon Sandia Home Locations Contact Us Employee Locator Energy & Climate Secure & Sustainable Energy Future Stationary Power Energy Conversion Efficiency Solar Energy Wind Energy Water Power Supercritical CO2 Geothermal Natural Gas Safety, Security & Resilience of the Energy Infrastructure Energy Storage Nuclear Power & Engineering Grid Modernization Battery Testing Nuclear Fuel Cycle Defense

  14. Natural resource damages: A legal, economic and policy overview

    SciTech Connect (OSTI)

    Connaughton, J.L.

    1995-12-31

    Natural resource damages liability is a major development in environmental law. Government authorities are increasingly seeking damage claims for injury to natural resources, invoking the natural resource damages (NRD) provisions of the federal Superfund statute and the Oil Pollution Act. The number of Claims asserted is increasing, and the amounts sought range to hundreds of millions of dollars, with some claims exceeding $1 billion. Some assert that the federal NRD program is an awakening sleeping giant that could threaten to rival the Superfund cleanup program in cost and the potential for imposing far-reaching liabilities on a wide range of businesses as well as the federal government. Lawyers, economists, and other experts on NRD have become fully engaged in comprehensive analyses of the legal, economic and policy issues presented by NRD claims, including a full review of the NRD litigating record. Many critics find that existing NRD law and practice is flawed; produces excessive liability claims, skewed incentives and economic waste; and urgently needs reform. Changes have been recommended to improve the law and refocus the NRD program on achieving cost-effective restoration of injured natural resources. These analytical endeavors are especially timely because Congress is currently considering significant changes in NRD law. This overview will provide a brief background summary of the NRD program and highlight some of the central legal and scientific issues facing government policy makers and litigants in NRD cases.

  15. Intriguing DNA Editor Has a Structural Trigger

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

    Intriguing DNA Editor Has a Structural Trigger Intriguing DNA Editor Has a Structural Trigger Print Wednesday, 30 July 2014 00:00 A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9

  16. Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

    DOE Patents [OSTI]

    Gardner, Shea N. (San Leandro, CA); Mariella, Jr., Raymond P. (Danville, CA); Christian, Allen T. (Tracy, CA); Young, Jennifer A. (Berkeley, CA); Clague, David S. (Livermore, CA)

    2011-01-18

    A method of fabricating a DNA molecule of user-defined sequence. The method comprises the steps of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an even or odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths. In one embodiment starting sequence fragments are of different lengths, n, n+1, n+2, etc.

  17. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, Frank A. (Livermore, CA); Gray, Joe W. (Livermore, CA)

    1986-01-01

    A method for the simultaneous flow cytometric measurement of the total DNA content and the level of DNA synthesis in normal and malignant cells is disclosed. The sensitivity of the method allows a study of cell cycle traverse rates for large scale cell populations as well as single cell measurements. A DNA stain such as propidium iodide is used as the probe for the measurement of total DNA content and a monoclonal antibody reactive with a DNA precursor such as bromodeoxyuridine (BrdU) is used as a probe for the measurement of BrdU uptake by the cells as a measure of DNA synthesis.

  18. Aligned composite structures for mitigation of impact damage and resistance to wear in dynamic environments

    DOE Patents [OSTI]

    Mulligan, Anthony C.; Rigali, Mark J.; Sutaria, Manish P.; Popovich, Dragan; Halloran, Joseph P.; Fulcher, Michael L.; Cook, Randy C.

    2005-12-13

    Fibrous monolith composites having architectures that provide increased flaw insensitivity, improved hardness, wear resistance and damage tolerance and methods of manufacture thereof are provided for use in dynamic environments to mitigate impact damage and increase wear resistance.

  19. Aligned composite structures for mitigation of impact damage and resistance to wear in dynamic environments

    DOE Patents [OSTI]

    Rigali, Mark J.; Sutaria, Manish P.; Mulligan, Anthony C.; Popovich, Dragan

    2004-03-23

    Fibrous monolith composites having architectures that provide increased flaw insensitivity, improved hardness, wear resistance and damage tolerance and methods of manufacture thereof are provided for use in dynamic environments to mitigate impact damage and increase wear resistance.

  20. Aligned composite structures for mitigation of impact damage and resistance to wear in dynamic environments

    DOE Patents [OSTI]

    Mulligan, Anthony C. (Tucson, AZ); Rigali, Mark J. (Tucson, AZ); Sutaria, Manish P. (Malden, MA); Popovich, Dragan (Redmond, WA); Halloran, Joseph P. (Tucson, AZ); Fulcher, Michael L. (Tucson, AZ); Cook, Randy C. (Tucson, AZ)

    2009-04-14

    Fibrous monolith composites having architectures that provide increased flaw insensitivity, improved hardness, wear resistance and damage tolerance and methods of manufacture thereof are provided for use in dynamic environments to mitigate impact damage and increase wear resistance.

  1. Martin Marietta Energy Systems, Inc. comprehensive earthquake management plan: Engineering survey building damage assessment training manual

    SciTech Connect (OSTI)

    Not Available

    1990-01-01

    The training objectives are: differentiate between the various levels of damage caused to buildings and structures by an earthquake and classify them as to their safety of occupancy, extent of damage, and resources needed for recovery/repair.

  2. Precursors to potential severe core damage accidents: 1994, a status report. Volume 21: Main report and appendices A--H

    SciTech Connect (OSTI)

    Belles, R.J.; Cletcher, J.W.; Copinger, D.A.; Vanden Heuvel, L.N.; Dolan, B.W.; Minarick, J.W. |

    1995-12-01

    Nine operational events that affected eleven commercial light-water reactors (LWRs) during 1994 and that are considered to be precursors to potential severe core damage are described. All these events had conditional probabilities of subsequent severe core damage greater than or equal to 1.0 {times} 10{sup {minus}6}. These events were identified by computer-screening the 1994 licensee event reports from commercial LWRs to identify those that could be potential precursors. Candidate precursors were then selected and evaluated in a process similar to that used in previous assessments. Selected events underwent engineering evaluation that identified, analyzed, and documented the precursors. Other events designated by the Nuclear Regulatory Commission (NRC) also underwent a similar evaluation. Finally, documented precursors were submitted for review by licensees and NRC headquarters and regional offices to ensure that the plant design and its response to the precursor were correctly characterized. This study is a continuation of earlier work, which evaluated 1969--1981 and 1984--1993 events. The report discusses the general rationale for this study, the selection and documentation of events as precursors, and the estimation of conditional probabilities of subsequent severe core damage for events. This document is bound in two volumes: Vol. 21 contains the main report and Appendices A--H; Vol. 22 contains Appendix 1.

  3. A 3D Orthotropic Strain-Rate Dependent Elastic Damage Material Model.

    SciTech Connect (OSTI)

    English, Shawn Allen

    2014-09-01

    A three dimensional orthotropic elastic constitutive model with continuum damage and cohesive based fracture is implemented for a general polymer matrix composite lamina. The formulation assumes the possibility of distributed (continuum) damage followed b y localized damage. The current damage activation functions are simply partially interactive quadratic strain criteria . However, the code structure allows for changes in the functions without extraordinary effort. The material model formulation, implementation, characterization and use cases are presented.

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

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

    are also crucial components of various other cellular pathways, such as DNA repair, cell cycle control, and chromatin structure. Sliding DNA clamps are loaded onto DNA by...

  5. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, Natasha V.

    2000-10-03

    Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties.

  6. Synthesis of DNA (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Synthesis of DNA Citation Details In-Document Search Title: Synthesis of DNA You are accessing a document from the Department of Energy's (DOE) SciTech Connect. This site is a...

  7. Encapsulation of Gold Nanoparticles in a DNA Origami Cage

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

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

  8. DNA Gridiron Nanostructures Based on Four-Arm Junctions

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

    DNA Gridiron Nanostructures Based on Four-Arm Junctions Authors: Han, D., Pal, S., Yang, Y., Jiang, S., Nangreave, J., Liu, Y., and Yan, H. Title: DNA Gridiron Nanostructures Based...

  9. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, F.A.; Gray, J.W.

    1983-10-18

    A method for the simultaneous flow cylometric measurement of total cellular DNA content and of the uptake of DNA precursors as a measure of DNA synthesis during various phases of the cell cycle in normal and malignant cells in vitro and in vivo is described. The method comprises reacting cells with labelled halodeoxyuridine (HdU), partially denaturing cellular DNA, adding to the reaction medium monoclonal antibodies (mabs) reactive with HdU, reacting the bound mabs with a second labelled antibody, incubating the mixture with a DNA stain, and measuring simultaneously the intensity of the DNA stain as a measure of the total cellular DNA and the HdU incorporated as a measure of DNA synthesis. (ACR)

  10. Blade reliability collaborative : collection of defect, damage and repair data.

    SciTech Connect (OSTI)

    Ashwill, Thomas D.; Ogilvie, Alistair B.; Paquette, Joshua A.

    2013-04-01

    The Blade Reliability Collaborative (BRC) was started by the Wind Energy Technologies Department of Sandia National Laboratories and DOE in 2010 with the goal of gaining insight into planned and unplanned O&M issues associated with wind turbine blades. A significant part of BRC is the Blade Defect, Damage and Repair Survey task, which will gather data from blade manufacturers, service companies, operators and prior studies to determine details about the largest sources of blade unreliability. This report summarizes the initial findings from this work.

  11. Simulation of neutron radiation damage in silicon semiconductor devices.

    SciTech Connect (OSTI)

    Shadid, John Nicolas; Hoekstra, Robert John; Hennigan, Gary Lee; Castro, Joseph Pete Jr.; Fixel, Deborah A.

    2007-10-01

    A code, Charon, is described which simulates the effects that neutron damage has on silicon semiconductor devices. The code uses a stabilized, finite-element discretization of the semiconductor drift-diffusion equations. The mathematical model used to simulate semiconductor devices in both normal and radiation environments will be described. Modeling of defect complexes is accomplished by adding an additional drift-diffusion equation for each of the defect species. Additionally, details are given describing how Charon can efficiently solve very large problems using modern parallel computers. Comparison between Charon and experiment will be given, as well as comparison with results from commercially-available TCAD codes.

  12. Analysis of damage and failure in metal matrix composites

    SciTech Connect (OSTI)

    Brust, F.W.; Majumdar, B.S.; Newaz, G.M.

    1995-12-31

    This paper presents the results of the analysis of the constitutive response of a model Metal Matrix Composite (MMC) system. The model is described first, followed by some direct comparison of predicted response to corresponding experimental data. An important result discussed here is that when model verification is made, it is important to compare load direction response to the experimental data, but also, comparisons to the out of load direction response must be made, or the model may not be performing as desired. Some discussion of failure predictions using simple models is also made here.

  13. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  14. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  15. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  16. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  17. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  18. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  19. Foreign DNA Capture during CRISPR-CAS Adaptive Immunity

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

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

  20. DNA origami with Complex Curvatures in 3D

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

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

  1. Methods to alter levels of a DNA repair protein

    DOE Patents [OSTI]

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

    2006-10-17

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

  2. Recent advances in yeast molecular biology: recombinant DNA. [Lead abstract

    SciTech Connect (OSTI)

    Not Available

    1982-09-01

    Separate abstracts were prepared for the 25 papers presented at a workshop focusing on chromosomal structure, gene regulation, recombination, DNA repair, and cell type control, that have been obtained by experimental approaches incorporating the new technologies of yeast DNA transformation, molecular cloning, and DNA sequence analysis. (KRM)

  3. Surface state reconstruction in ion-damaged SmB6

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

    Wakeham, N.; Wang, Y. Q.; Fisk, Z.; Ronning, F.; Thompson, J. D.

    2015-02-12

    We have used ion-irradiation to damage the (001) surfaces of SmB₆ single crystals to varying depths, and have measured the resistivity as a function of temperature for each depth of damage. We observe a reduction in the residual resistivity with increasing depth of damage. Our data are consistent with a model in which the surface state is not destroyed by the ion-irradiation, however instead the damaged layer is poorly conducting and the initial surface state is reconstructed below the damage. This behavior is consistent with a surface state that is topologically protected.

  4. Damage-tolerant nanotwinned metals with nanovoids under radiation environments

    SciTech Connect (OSTI)

    Chen, Y.; Yu, K. Y.; Liu, Y.; Shao, S.; Wang, H.; Kirk, M. A.; Wang, J.; Zhang, X.

    2015-04-24

    Material performance in extreme radiation environments is central to the design of future nuclear reactors. Radiation induces significant damage in the form of dislocation loops and voids in irradiated materials, and continuous radiation often leads to void growth and subsequent void swelling in metals with low stacking fault energy. Here we show that by using in situ heavy ion irradiation in a transmission electron microscope, pre-introduced nanovoids in nanotwinned Cu efficiently absorb radiation-induced defects accompanied by gradual elimination of nanovoids, enhancing radiation tolerance of Cu. In situ studies and atomistic simulations reveal that such remarkable self-healing capability stems from high density of coherent and incoherent twin boundaries that rapidly capture and transport point defects and dislocation loops to nanovoids, which act as storage bins for interstitial loops. This study describes a counterintuitive yet significant concept: deliberate introduction of nanovoids in conjunction with nanotwins enables unprecedented damage tolerance in metallic materials.

  5. DDT of hot, thermally damaged PBX 9501 in heavy confinement

    SciTech Connect (OSTI)

    Parker, Gary R [Los Alamos National Laboratory; Dickerson, Peter M [Los Alamos National Laboratory; Asay, Blaine W [Los Alamos National Laboratory; Mc Afee, John M [Los Alamos National Laboratory

    2010-01-01

    The research presented examines DDT of cylinders of PBX 9501 damaged above 180 C in heavy confinement for 0-3 hours and end-ignited or ramped until self-ignition (cookoff) occurred. Progression of luminous reaction was observed by streak photography through a glass-filled slit running the length of the cylinder. Post-mortem analysis of the steel DDT tubes was also done for correlation with the optical records. Results indicate that repeatable, Type I DDT was observed to occur in hot, thermally damaged PBX 9501 with low levels of porosity. It was demonstrated that multiple parameters affect DDT behavior, most likely in a coupled fashion. These parameters are porosity, ignition temperature and thermal soak duration. Conditions leading up to cookoff were shown to sensitize the HE to DDT by increasing likelihood and decreasing run length. Over the range of porosities (0-37%) and ignition temperatures (180-235 C), run lengths and detonation velocities varied, respectively, from approximately 22-109 mm and 6.0-8.3 mm {micro}s{sup -1}. This work fills a valuable and realistic space in the understanding of high explosive violent reaction, including DDT, in abnormal thermal environments.

  6. Emulation of reactor irradiation damage using ion beams

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

    Was, G. S.; Jiao, Z.; Getto, E.; Sun, K.; Monterrosa, A. M.; Maloy, S. A.; Anderoglu, O.; Sencer, B. H.; Hackett, M.

    2014-06-14

    The continued operation of existing light water nuclear reactors and the development of advanced nuclear reactor depend heavily on understanding how damage by radiation to levels degrades materials that serve as the structural components in reactor cores. The first high dose ion irradiation experiments on a ferritic-martensitic steel showing that ion irradiation closely emulates the full radiation damage microstructure created in-reactor are described. Ferritic-martensitic alloy HT9 (heat 84425) in the form of a hexagonal fuel bundle duct (ACO-3) accumulated 155 dpa at an average temperature of 443°C in the Fast Flux Test Facility (FFTF). Using invariance theory as a guide,more » irradiation of the same heat was conducted using self-ions (Fe++) at 5 MeV at a temperature of 460°C and to a dose of 188 displacements per atom. The void swelling was nearly identical between the two irradiation and the size and density of precipitates and loops following ion irradiation are within a factor of two of those for neutron irradiation. The level of agreement across all of the principal microstructure changes between ion and reactor irradiation establishes the capability of tailoring ion irradiation to emulate the reactor-irradiated microstructure.« less

  7. Emulation of reactor irradiation damage using ion beams

    SciTech Connect (OSTI)

    Was, G. S.; Jiao, Z.; Getto, E.; Sun, K.; Monterrosa, A. M.; Maloy, S. A.; Anderoglu, O.; Sencer, B. H.; Hackett, M.

    2014-06-14

    The continued operation of existing light water nuclear reactors and the development of advanced nuclear reactor depend heavily on understanding how damage by radiation to levels degrades materials that serve as the structural components in reactor cores. The first high dose ion irradiation experiments on a ferritic-martensitic steel showing that ion irradiation closely emulates the full radiation damage microstructure created in-reactor are described. Ferritic-martensitic alloy HT9 (heat 84425) in the form of a hexagonal fuel bundle duct (ACO-3) accumulated 155 dpa at an average temperature of 443C in the Fast Flux Test Facility (FFTF). Using invariance theory as a guide, irradiation of the same heat was conducted using self-ions (Fe++) at 5 MeV at a temperature of 460C and to a dose of 188 displacements per atom. The void swelling was nearly identical between the two irradiation and the size and density of precipitates and loops following ion irradiation are within a factor of two of those for neutron irradiation. The level of agreement across all of the principal microstructure changes between ion and reactor irradiation establishes the capability of tailoring ion irradiation to emulate the reactor-irradiated microstructure.

  8. Emulation of reactor irradiation damage using ion beams

    SciTech Connect (OSTI)

    G. S. Was; Z. Jiao; E. Beckett; A. M. Monterrosa; O. Anderoglu; B. H. Sencer; M. Hackett

    2014-10-01

    The continued operation of existing light water nuclear reactors and the development of advanced nuclear reactor depend heavily on understanding how damage by radiation to levels degrades materials that serve as the structural components in reactor cores. The first high dose ion irradiation experiments on a ferritic-martensitic steel showing that ion irradiation closely emulates the full radiation damage microstructure created in-reactor are described. Ferritic-martensitic alloy HT9 (heat 84425) in the form of a hexagonal fuel bundle duct (ACO-3) accumulated 155 dpa at an average temperature of 443C in the Fast Flux Test Facility (FFTF). Using invariance theory as a guide, irradiation of the same heat was conducted using self-ions (Fe++) at 5 MeV at a temperature of 460C and to a dose of 188 displacements per atom. The void swelling was nearly identical between the two irradiations and the size and density of precipitates and loops following ion irradiation are within a factor of two of those for neutron irradiation. The level of agreement across all of the principal microstructure changes between ion and reactor irradiations establishes the capability of tailoring ion irradiations to emulate the reactor-irradiated microstructure.

  9. Modeling the mechanical response of PBX 9501

    SciTech Connect (OSTI)

    Ragaswamy, Partha; Lewis, Matthew W; Liu, Cheng; Thompson, Darla G

    2010-01-01

    An engineering overview of the mechanical response of Plastic-Bonded eXplosives (PBXs), specifically PBX 9501, will be provided with emphasis on observed mechanisms associated with different types of mechanical testing. Mechanical tests in the form of uniaxial tension, compression, cyclic loading, creep (compression and tension), and Hopkinson bar show strain rate and temperature dependence. A range of mechanical behavior is observed which includes small strain recoverable response in the form of viscoelasticity; change in stiffness and softening beyond peak strength due to damage in the form microcracks, debonding, void formation and the growth of existing voids; inelastic response in the form of irrecoverable strain as shown in cyclic tests, and viscoelastic creep combined with plastic response as demonstrated in creep and recovery tests. The main focus of this paper is to elucidate the challenges and issues involved in modeling the mechanical behavior of PBXs for simulating thermo-mechanical responses in engineering components. Examples of validation of a constitutive material model based on a few of the observed mechanisms will be demonstrated against three point bending, split Hopkinson pressure bar and Brazilian disk geometry.

  10. DOI-BLM-NM-L000-2012-0200-DNA | Open Energy Information

    Open Energy Info (EERE)

    00-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NM-L000-2012-0200-DNA DNA at Lightning Dock Geothermal Area for GeothermalWell Field, DNA for Injection...

  11. DOI-BLM-NV-C010-2012--044-DNA | Open Energy Information

    Open Energy Info (EERE)

    DOI-BLM-NV-C010-2012--044-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2012--044-DNA DNA for GeothermalPower Plant, DNA for Ormatt Nevada Sundry...

  12. DOI-BLM-NV-C010-2013-0037-DNA | Open Energy Information

    Open Energy Info (EERE)

    37-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2013-0037-DNA DNA at Gabbs Valley Geothermal Area for GeothermalWell Field, DNA for Wild Rose Unit...

  13. DOI-BLM-NV-C010-2010-0006-DNA | Open Energy Information

    Open Energy Info (EERE)

    DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2010-0006-DNA DNA at Gabbs Valley Geothermal Area for GeothermalExploration, DNA for Thermal Gradient...

  14. DOI-BLM-NM-L000-2012-0111-DNA | Open Energy Information

    Open Energy Info (EERE)

    111-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NM-L000-2012-0111-DNA DNA at Lightning Dock Geothermal Area for GeothermalExploration, DNA for Three...

  15. DOI-BLM-NV-C010-2012-0005-DNA | Open Energy Information

    Open Energy Info (EERE)

    05-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2012-0005-DNA DNA at McCoy Geothermal Area for GeothermalWell Field DNA for Observation Wells 62-8...

  16. DOI-BLM-NV-C010-2011-0517-DNA | Open Energy Information

    Open Energy Info (EERE)

    7-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2011-0517-DNA DNA at Dead Horse Wells Geothermal Area for GeothermalExploration DNA at Dead Horse...

  17. DOI-BLM-NM-L000-2012-0042-DNA | Open Energy Information

    Open Energy Info (EERE)

    2-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NM-L000-2012-0042-DNA DNA at Lightning Dock Geothermal Area for GeothermalExploration DNA for Well 55-7 at...

  18. DOI-BLM-NV-B020-2008-0071-DNA | Open Energy Information

    Open Energy Info (EERE)

    0071-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-B020-2008-0071-DNA DNA at Reese River Geothermal Area for GeothermalExploration DNA at Reese River...

  19. DOI-BLM-NV-C010-2013-0026-DNA | Open Energy Information

    Open Energy Info (EERE)

    6-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2013-0026-DNA DNA at Dixie Valley Geothermal Area for GeothermalWell Field, DNA for Production...

  20. Preparation of DNA-containing extract for PCR amplification

    DOE Patents [OSTI]

    Dunbar, John M.; Kuske, Cheryl R.

    2006-07-11

    Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 510 minutes.

  1. A Golden Ruler Used to Measure DNA Structure in Solution

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

    8 A Golden Ruler Used to Measure DNA Structure in Solution The first crystal structures of DNA double helices appeared in 1979 and directly confirmed the atomic model of Watson-Crick from 25 years earlier. Since then, DNA has been modeled as a relatively rigid polymer. An isotropic elastic rod model of the polymer has proven to be exceptionally good at integrating classical biochemical measurements on DNA with recent single-molecule results for DNA on length scales of 100 nm or longer.

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

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

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

  3. Stepped electrophoresis for movement and concentration of DNA

    DOE Patents [OSTI]

    Miles, Robin R.; Wang, Amy Wei-Yun; Mariella, Jr., Raymond P.

    2005-03-15

    A fluidic channel patterned with a series of thin-film electrodes makes it possible to move and concentrate DNA in a fluid passing through the fluidic channel. The DNA has an inherent negative charge and by applying a voltage between adjacent electrodes the DNA is caused to move. By using a series of electrodes, when one electrode voltage or charge is made negative with respect to adjacent electrodes, the DNA is repelled away from this electrode and attached to a positive charged electrode of the series. By sequentially making the next electrode of the series negative, the DNA can be moved to and concentrated over the remaining positive electrodes.

  4. DNA-Guided Crystallization of Colloidal Nanoparticles

    SciTech Connect (OSTI)

    Nykypanchuk,D.; Maye, M.; van der Lelie, D.; Gang, O.

    2008-01-01

    Many nanometre-sized building blocks will readily assemble into macroscopic structures. If the process is accompanied by effective control over the interactions between the blocks and all entropic effects, then the resultant structures will be ordered with a precision hard to achieve with other fabrication methods. But it remains challenging to use self-assembly to design systems comprised of different types of building blocks--to realize novel magnetic, plasmonic and photonic metamaterials for example. A conceptually simple idea for overcoming this problem is the use of 'encodable' interactions between building blocks; this can in principle be straightforwardly implemented using biomolecules6, 7, 8, 9, 10. Strategies that use DNA programmability to control the placement of nanoparticles in one and two dimensions have indeed been demonstrated. However, our theoretical understanding of how to extend this approach to three dimensions is limited14, 15, and most experiments have yielded amorphous aggregates and only occasionally crystallites of close-packed micrometre-sized particles. Here, we report the formation of three-dimensional crystalline assemblies of gold nanoparticles mediated by interactions between complementary DNA molecules attached to the nanoparticles' surface. We find that the nanoparticle crystals form reversibly during heating and cooling cycles. Moreover, the body-centred-cubic lattice structure is temperature-tuneable and structurally open, with particles occupying only {approx}4% of the unit cell volume. We expect that our DNA-mediated crystallization approach, and the insight into DNA design requirements it has provided, will facilitate both the creation of new classes of ordered multicomponent metamaterials and the exploration of the phase behaviour of hybrid systems with addressable interactions.

  5. Allosteric Modulation of DNA by Small Molecules

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

    Allosteric Modulation of DNA by Small Molecules Signals originating at the cell surface are conveyed by a complex system of interconnected signaling pathways to the nucleus. They converge at transcription factors, which in turn regulate the transcription of sets of genes that result in the gene expression. Many human diseases are caused by dysregulated gene expression and the oversupply of transcription factors may be required for the growth and metastatic behavior of human cancers. Cell

  6. Determining orientation and direction of DNA sequences

    DOE Patents [OSTI]

    Goodwin, Edwin H. (Los Alamos, NM); Meyne, Julianne (Los Alamos, NM)

    2000-01-01

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

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

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

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

    2015-09-13

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

  8. Cross-sector Demand Response

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

    & Events Skip navigation links Smart Grid Demand Response Agricultural Residential Demand Response Commercial & Industrial Demand Response Cross-sector Demand Response...

  9. Monitoring genetic damage to ecosystems from hazardous waste

    SciTech Connect (OSTI)

    Anderson, S.L.

    1992-03-01

    Applications of ecological toxicity testing to hazardous waste management have increased dramatically over the last few years, resulting in a greater awareness of the need for improved biomonitoring techniques. Our laboratory is developing advanced techniques to assess the genotoxic effects of environmental contamination on ecosystems. We have developed a novel mutagenesis assay using the nematode Caenorhabditis elegans, which is potentially applicable for multimedia studies in soil, sediment, and water. In addition, we are conducting validation studies of a previously developed anaphase aberration test that utilizes sea urchin embryos. Other related efforts include field validation studies of the new tests, evaluation of their potential ecological relevance, and analysis of their sensitivity relative to that of existing toxicity tests that assess only lethal effects, rather than genetic damage.

  10. LNG cascading damage study. Volume I, fracture testing report.

    SciTech Connect (OSTI)

    Petti, Jason P.; Kalan, Robert J.

    2011-12-01

    As part of the liquefied natural gas (LNG) Cascading Damage Study, a series of structural tests were conducted to investigate the thermal induced fracture of steel plate structures. The thermal stresses were achieved by applying liquid nitrogen (LN{sub 2}) onto sections of each steel plate. In addition to inducing large thermal stresses, the lowering of the steel temperature simultaneously reduced the fracture toughness. Liquid nitrogen was used as a surrogate for LNG due to safety concerns and since the temperature of LN{sub 2} is similar (-190 C) to LNG (-161 C). The use of LN{sub 2} ensured that the tests could achieve cryogenic temperatures in the range an actual vessel would encounter during a LNG spill. There were four phases to this test series. Phase I was the initial exploratory stage, which was used to develop the testing process. In the Phase II series of tests, larger plates were used and tested until fracture. The plate sizes ranged from 4 ft square pieces to 6 ft square sections with thicknesses from 1/4 inches to 3/4 inches. This phase investigated the cooling rates on larger plates and the effect of different notch geometries (stress concentrations used to initiate brittle fracture). Phase II was divided into two sections, Phase II-A and Phase II-B. Phase II-A used standard A36 steel, while Phase II-B used marine grade steels. In Phase III, the test structures were significantly larger, in the range of 12 ft by 12 ft by 3 ft high. These structures were designed with more complex geometries to include features similar to those on LNG vessels. The final test phase, Phase IV, investigated differences in the heat transfer (cooling rates) between LNG and LN{sub 2}. All of the tests conducted in this study are used in subsequent parts of the LNG Cascading Damage Study, specifically the computational analyses.

  11. Recent Advances in Understanding Radiation Damage in Reactor Cavity Concrete

    SciTech Connect (OSTI)

    Rosseel, Thomas M; Field, Kevin G; Le Pape, Yann; Remec, Igor; Giorla, Alain B; Wall, Dr. James Joseph

    2015-01-01

    License renewal up to 60 years and the possibility of subsequent license renewal to 80 years has resulted in a renewed focus on long-term aging of materials at nuclear power plants (NPPs) including concrete. Large irreplaceable sections of most nuclear generating stations include concrete. The Expanded Materials Degradation Analysis, jointly performed by the Department of Energy, the Nuclear Regulatory Commission and Nuclear Industry, identified the urgent need to develop a consistent knowledge base on irradiation effects in concrete (Graves et al., (2014)). Much of the historical mechanical performance data of irradiated concrete (Hilsdorf et al., (1978)) does not accurately reflect typical radiation conditions in NPPs or conditions out to 60 or 80 years of radiation exposure (Kontani et al., (2011)). To address these potential gaps in the knowledge base, the Electric Power Research Institute and Oak Ridge National Laboratory, are working to better understand radiation damage as a degradation mechanism. This paper outlines recent progress toward: 1) assessing the radiation environment in concrete biological shields and defining the upper bound of the neutron and gamma dose levels expected in the biological shield for extended operation, and estimating adsorbed dose, 2) evaluating opportunities to harvest and test irradiated concrete from international NPPs, 3) evaluating opportunities to irradiate prototypical concrete and its components under accelerated neutron and gamma dose levels to establish conservative bounds and inform damage models, 4) developing improved models to enhance the understanding of the effects of radiation on concrete and 5) establishing an international collaborative research and information exchange effort to leverage capabilities and knowledge including developing cooperative test programs to improve confidence in data obtained from various concretes and from accelerated irradiation experiments.

  12. Fracture Induced Sub-Band Absorption as a Precursor to Optical Damage on Fused Silica Surfaces

    SciTech Connect (OSTI)

    Miller, P E; Bude, J D; Suratwala, T I; Shen, N; Laurence, T A; Steele, W A; Menapace, J; Feit, M D; Wong, L L

    2010-03-05

    The optical damage threshold of indentation induced flaws on fused silica surfaces was explored. Mechanical flaws were characterized by laser damaged testing, SEM, optical, and photoluminescence microscopy. Localized polishing, chemical etching, and the control of indentation morphology were used to isolate the structural features which limit optical damage. A thin defect layer on fracture surfaces, including those smaller than the wavelength of visible light, was found to be the dominant source of laser damage initiation during illumination with 355nm, 3ns laser pulses. Little evidence was found that either displaced or densified material or fluence intensification plays a significant role in optical damage at fluences >35J/cm{sup 2}. Elimination of the defect layer was shown to increase the overall damage performance of fused silica optics.

  13. Critique of the carbonate mass loss model for paint damage functions

    SciTech Connect (OSTI)

    Livingston, R.A.

    1987-06-01

    One of the key questions concerning the assessment of acid deposition damage is its effect on painted surfaces. In order to determine this it is necessary to have a paint damage function that expresses the quantity of physical damage associated with a given level of acid deposition. This problem is now a major focus of EPA's current research; however, results are not yet available. Consequently, the NAPAP paint damage function was derived from data collected in several studies that substantially predated the acid rain research program. Although this damage function may appear plausible at first glance, it has been criticized, in part because paint damage constitutes such an important part of the total, but mainly because it is based largely on a conceptual model involving erosion due to dissolution loss of carbonate extenders in the paint formulation.

  14. TECHNICAL STANDARDS PROGRAM RESPONSIBILITIES

    Broader source: Energy.gov [DOE]

    PurposeThis procedure describes the responsibilities of persons who are charged with implementing the DOE Technical Standards Program.

  15. Repair of radiation-induced heat-labile sites is independent of DNA-PKcs, XRCC1 or PARP

    SciTech Connect (OSTI)

    Stenerlw, Bo; Karlsson, Karin H.; Radulescu, Irina; Rydberg, Bjorn; Stenerlow, Bo

    2008-04-29

    Ionizing radiation induces a variety of different DNA lesions: in addition to the most critical DNA damage, the DSB, numerous base alterations, SSBs and other modifications of the DNA double-helix are formed. When several non-DSB lesions are clustered within a short distance along DNA, or close to a DSB, they may interfere with the repair of DSBs and affect the measurement of DSB induction and repair. We have previously shown that a substantial fraction of DSBs measured by pulsed-field gel electrophoresis (PFGE) are in fact due to heat-labile sites (HLS) within clustered lesions, thus reflecting an artifact of preparation of genomic DNA at elevated temperature. To further characterize the influence of HLS on DSB induction and repair, four human cell lines (GM5758, GM7166, M059K, U-1810) with apparently normal DSB rejoining were tested for bi-phasic rejoining after gamma irradiation. When heat-released DSBs were excluded from the measurements the fraction of fast rejoining decreased to less than 50% of the total. However, neither the half-times of the fast (t{sub 1/2} = 7-8 min) or slow (t{sub 1/2} = 2.5 h) DSB rejoining were changed significantly. At t=0 the heat-released DSBs accounted for almost 40% of the DSBs, corresponding to 10 extra DSB/cell/Gy in the initial DSB yield. These heat-released DSBs were repaired within 60-90 min in all tested cells, including M059K cells treated with wortmannin or DNA-PKcs defect M059J cells. Furthermore, cells lacking XRCC1 or Poly(ADP-ribose) polymerase-1 (PARP-1) rejoined both total DSBs and heat-released DSBs similar to normal cells. In summary, the presence of heat-labile sites have a substantial impact on DSB induction yields and DSB rejoining rates measured by pulsed-field gel electrophoresis, and HLS repair is independent of DNA-PKcs, XRCC1 and PARP.

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

    SciTech Connect (OSTI)

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

    2009-09-07

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

  17. Defect and damage evolution quantification in dynamically-deformed metals using orientation-imaging microscopy

    SciTech Connect (OSTI)

    Gray, George T., III; Livescu, Veronica; Cerreta, Ellen K

    2010-03-18

    Orientation-imaging microscopy offers unique capabilities to quantify the defects and damage evolution occurring in metals following dynamic and shock loading. Examples of the quantification of the types of deformation twins activated, volume fraction of twinning, and damage evolution as a function of shock loading in Ta are presented. Electron back-scatter diffraction (EBSD) examination of the damage evolution in sweeping-detonation-wave shock loading to study spallation in Cu is also presented.

  18. The 2007 Eastern US Spring Freeze: Increased Cold Damage in a Warming World

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect The 2007 Eastern US Spring Freeze: Increased Cold Damage in a Warming World Citation Details In-Document Search Title: The 2007 Eastern US Spring Freeze: Increased Cold Damage in a Warming World Plant ecologists have long been concerned with a seemingly paradoxical scenario in the relationship between plant growth and climate change: warming may actually increase the risk of plant frost damage. The underlying hypothesis is that mild winters and warm, early

  19. WILD PIGS: BIOLOGY, DAMAGE, CONTROL TECHINQUES AND MANAGEMENT

    SciTech Connect (OSTI)

    Mayer, John; Brisbin, I. Lehr

    2009-12-31

    The existence of problems with wild pigs (Sus scrofa) is nothing new to the Western Hemisphere. Damage by these introduced animals was reported as far back as 1505 by the early Spanish colonies in the Caribbean, where wild pigs were killing the colonists cattle. Droves of these animals also ravaged cultivated crops of maize and sugarcane on islands in the West Indies during this same time period. These wild pigs reportedly were very aggressive and often attacked Spanish soldiers hunting rebellious Indians or escaped slaves on these islands, especially when these animals were cornered. The documentation of such impacts by introduced populations of this species in the United States has subsequently increased in recent years, and continued up through the present (Towne and Wentworth. 1950, Wood and Barrett 1979, Mayer and Brisbin 1991, Dickson et al. 2001). In spite of a fairly constant history in this country since the early 1900s, wild pigs have had a dramatic recent increase in both distribution and numbers in the United States. Between 1989 and 2009, the number of states reporting the presence of introduced wild pigs went from 19 up to as many as 44. This increase, in part natural, but largely manmade, has caused an increased workload and cost for land and resource managers in areas where these new populations are found. This is the direct result of the damage that these introduced animals do. The cost of both these impacts and control efforts has been estimated to exceed a billion dollars annually (Pimentel 2007). The complexity of this problem has been further complicated by the widespread appeal and economic potential of these animals as a big game species (Tisdell 1982, Degner 1989). Wild pigs are a controversial problem that is not going away and will likely only get worse with time. Not only do they cause damage, but wild pigs are also survivors. They reproduce at a rate faster than any other mammal of comparable size, native or introduced; they can eat just about anything; and, they can live just about anywhere. On top of that, wild pigs are both very difficult to control and, with the possible exception of island ecosystems, almost impossible to eradicate (Dickson et al. 2001, Sweeney et al. 2003). The solution to the wild pig problem has not been readily apparent. The ultimate answer as to how to control these animals has not been found to date. In many ways, wild pigs are America's most successful large invasive species. All of which means that wild pigs are a veritable nightmare for land and resource managers trying to keep the numbers of these animals and the damage that they do under control. Since the more that one knows about an invasive species, the easier it is to deal with and hopefully control. For wild pigs then, it is better to 'know thy enemy' than to not, especially if one expects to be able to successfully control them. In an effort to better 'know thy enemy,' a two-day symposium was held in Augusta, Georgia, on April 21-22, 2004. This symposium was organized and sponsored by U.S.D.A. Forest Service-Savannah River (USFS-SR), U. S. Department of Energy-Savannah River Operations Office (DOE-SR), the Westinghouse Savannah River Company (WSRC), the South Carolina Chapter of the Soil & Water Conservation Society, and the Savannah River Ecology Laboratory (SREL). The goal of this symposium was to assemble researchers and land managers to first address various aspects of the biology and damage of wild pigs, and then review the control techniques and management of this invasive species. The result would then be a collected synopsis of what is known about wild pigs in the United States. Although the focus of the symposium was primarily directed toward federal agencies, presenters also included professionals from academic institutions, and private-sector control contractors and land managers. Most of the organizations associated with implementing this symposium were affiliated with the Savannah River Site (SRS), a 803 km{sup 2} federal nuclear facility, located in western South Carolina along the Savannah River. The SRS was a very appropriate facility to host this symposium. The SRS has been dealing with its wild pig problem since the early 1950s. A lot has been learned about these animals at the site over the ensuing decades. Between the USFS-SR, DOE-SR, SREL, and the site's management and operations contractor, which is currently Savannah River Nuclear Solutions, SRS organizations have conducted a wealth of research on this wild pig population, spanning a broad spectrum of topics and disciplines. In fact, the SRS wild pig population is among the most studied, and possibly is the best studied population of this invasive species found in the United States today. Unfortunately, with all of that work, the ultimate answer to controlling wild pigs and their impacts still has not been found. This volume represents the collected synopsis that was the goal of the aforementioned symposium.

  20. Intriguing DNA Editor Has a Structural Trigger

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

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9 enzymes. Combined with electron microscopy, the results point the way to the

  1. Intriguing DNA Editor Has a Structural Trigger

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

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9 enzymes. Combined with electron microscopy, the results point the way to the

  2. Intriguing DNA Editor Has a Structural Trigger

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

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9 enzymes. Combined with electron microscopy, the results point the way to the

  3. Intriguing DNA Editor Has a Structural Trigger

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

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9 enzymes. Combined with electron microscopy, the results point the way to the

  4. Damaged Material, Heal Thyself | U.S. DOE Office of Science ...

    Office of Science (SC) Website

    Contact Information Basic Energy Sciences U.S. Department of Energy SC-22Germantown ... Damaged Material, Heal Thyself Internal storage compartments release droplets of "healing" ...

  5. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, Frank A. (Livermore, CA); Gray, Joe W. (Livermore, CA)

    1988-01-01

    A method for the simultaneous flow cytometric measurement of the total DNA content and the level of DNA synthesis in normal and malignant cells is disclosed. The sensitivity of the method allows a study of cell cycle traverse rates for large scale cell populations as well as single cell measurements. A DNA stain such as propidium iodide or Hoechst 33258 is used as the probe for the measurement of total DNA content and a monoclonal antibody reactive with a DNA precursor such as halodeoxy-uridine (HdU), more specifically bromodeoxyuridine (BrdU) is used as a probe for the measurement of HdU or BrdU uptake by the cells as a measure of DNA synthesis.

  6. Emergency Response Synchronization Matrix

    Energy Science and Technology Software Center (OSTI)

    1999-06-01

    An emergency response to a disaster is complex, requiring the rapid integration, coordination, and synchronization of multiple levels of governmental and non-governmental organizations from numerous jurisdictions into a unified community response. For example, a community’s response actions to a fixed site hazardous materials incident could occur in an area extending from an on-site storage location to points 25 or more miles away. Response actions are directed and controlled by local governments and agencies situated withinmore » the response area, as well as by state and federal operaticns centers quite removed from the area of impact. Time is critical and the protective action decision-making process is greatly compressed. The response community must carefully plan and coordinate response operations in order to have confidence that they will be effectively implemented when faced with the potentially catastrophic nature of such releases. A graphical depiction of the entire response process via an emergency response synchronization matrix is an effective tool in optimizing the planning, exercising, and implementation of emergency plans. This system—based approach to emergency planning depicts how a community organizes its response tasks across space and time in relation to hazard actions. It provides the opportunity to make real—time adjustments as necessary for maximizing the often limited resources in protecting area residents. A response must involve the entire community and must not be limited by individual jurisdictions and organizations acting on their own without coordination, integration, and synchronization.« less

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

    SciTech Connect (OSTI)

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

    2008-12-04

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

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

    SciTech Connect (OSTI)

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

    2008-12-16

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

  9. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Wednesday, 26 January 2011 00:00 Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked

  10. Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

  12. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

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

  13. Transposon-containing DNA cloning vector and uses thereof

    DOE Patents [OSTI]

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

    1997-07-08

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

  14. Transposon-containing DNA cloning vector and uses thereof

    DOE Patents [OSTI]

    Berg, Claire M. (W. Willington, CT); Berg, Douglas E. (St. Louis, MO); Wang, Gan (Storrs, CT)

    1997-01-01

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

  15. Influence of sweeping detonation-wave loading on damage evolution during spallation loading of tantalum in both a planar and curved geometry

    SciTech Connect (OSTI)

    Gray, George Thompson III; Hull, Lawrence Mark; Livescu, Veronica; Faulkner, James; Briggs, Matthew E.; Meyer, Ross Keith; Andrews, Heather Lynn; Hare, Steven John; Jakulewicz, Micah Shawn; Shinas, Michael A.

    2015-03-30

    Widespread research over the past five decades has provided a wealth of experimental data and insight concerning the shock hardening, damage evolution, and the spallation response of materials subjected to square-topped shock-wave loading profiles. However, fewer quantitative studies have been conducted on the effect of direct, in-contact, high explosive (HE)-driven Taylor wave (unsupported shocks) loading on the shock hardening, damage evolution, or spallation response of materials. Systematic studies quantifying the effect of sweeping-detonation wave loading are yet sparser. In this study, the damage evolution and spallation response of Ta is shown to be critically dependent on the peak shock stress, the geometry of the sample (flat or curved plate geometry), and the shock obliquity during sweeping-detonation-wave shock loading. Sweepingwave loading in the flat-plate geometry is observed to: a) yield a lower spall strength than previously documented for 1-D supported-shock-wave loading, b) exhibit increased shock hardening as a function of increasing obliquity, and c) lead to an increased incidence of deformation twin formation with increasing shock obliquity. Sweeping-wave loading of a 10 cm radius curved Ta plate is observed to: a) lead to an increase in the shear stress as a function of increasing obliquity, b) display a more developed level of damage evolution, extensive voids and coalescence, and lower spall strength with obliquity in the curved plate than seen in the flat-plate sweeping-detonation wave loading for an equivalent HE loading, and c) no increased propensity for deformation twin formation with increasing obliquity as seen in the flat-plate geometry. The overall observations comparing and contrasting the flat versus curved sweeping-wave spall experiments with 1D loaded spallation behavior suggests a coupled influence of obliquity and geometry on dynamic shock-induced damage evolution and spall strength. Coupled experimental and modeling research to quantify the combined effects of sweeping-wave loading with increasingly complex sample geometries on the shockwave response of materials is clearly crucial to providing the basis for developing and thereafter validation of predictive modeling capability.

  16. DNA-Based Optomechanical Molecular Motor

    SciTech Connect (OSTI)

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

    2011-03-16

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

    SciTech Connect (OSTI)

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

    2014-06-09

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

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

    Open Energy Info (EERE)

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

  20. When DNA Needs to Stand Up and Be Counted

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

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

  1. Ionic switch controls the DNA state in phage λ

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

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

    2015-06-19

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

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

    Office of Scientific and Technical Information (OSTI)

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

  3. Evolutionary theory, web-search technology combine for DNA analysis

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

    Sequedex: bioinformatics breakthrough Evolutionary theory, web-search technology combine ... Evolutionary theory, web-search technology combine for DNA analysis Bioinformatics ...

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

    SciTech Connect (OSTI)

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

    2014-09-01

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

  5. DNA release from lipoplexes by anionic lipids: correlation with...

    Office of Scientific and Technical Information (OSTI)

    Research Org: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL ... Subject: 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; CAPACITY; DNA; ENERGY ...

  6. Low Dose Radiation-Induced Genome and Epigenome Instability Symposium and Epigenetic Mechanisms, DNA Repair, and Chromatin Symposium at the EMS 2008 Annual Meeting - October 2008

    SciTech Connect (OSTI)

    Morgan, William F.; Kovalchuk, Olga; Dolinoy, Dana C.; Dubrova, Yuri E.; Coleman, Matthew A.; Schr, Primo; Pogribny, Igor; Hendzel, Michael

    2010-02-19

    The Low Dose Radiation Symposium thoughtfully addressed ionizing radiation non-mutational but transmissable alterations in surviving cells. Deregulation of epigenetic processes has been strongly implicated in carcinogenesis, and there is increasing realization that a significant fraction of non-targeted and adaptive mechanisms in response to ionizing radiation are likely to be epigenetic in nature. Much remains to be learned about how chromatin and epigenetic regulators affect responses to low doses of radiation, and how low dose radiation impacts other epigenetic processes. The Epigenetic Mechanisms Symposium focused on on epigenetic mechanisms and their interplay with DNA repair and chromatin changes. Addressing the fact that the most well understood mediators of epigenetic regulation are histone modifications and DNA methylation. Low levels of radiation can lead to changes in the methylation status of certain gene promoters and the expression of DNA methyltransferases, However, epigenetic regulation can also involve changes in higher order chromosome structure.

  7. Hydration of DNA by tritiated water and isotope distribution: a study by /sup 1/H, /sup 2/H, and /sup 3/H NMR spectroscopy

    SciTech Connect (OSTI)

    Mathur-De Vre, R.; Grimee-Declerck, R.; Lejeune, P.; Bertinchamps, A.J.

    1982-06-01

    The hydration layer of DNA (0.75%) in tritiated water represents 3.5% of solvent /sup 3/HHO. The combined effects of temperature (-6 to -40/sup 0/C) and H/sub 2/O//sup 2/H/sub 2/O solvent composition on the spin-lattice relaxation times of water protons and deuterons suggest selective distribution of isotopes in the hydration layer. The ''hydration isotope'' effect and the localization of tritiated water molecules in the hydration layer of DNA have important implications in describing the radiobiological effects of tritiated water because the initial molecular damage caused by /sup 3/HHO (internal radiation source) localizes close to /sup 3/H due to the short range and low energy of /sup 3/H ..beta.. rays.

  8. CRA Comments & Responses

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

    (51105) 11 Response to CRA Comments (92005) Enclosure 1 - Computer Code VerificationTesting (92005) Inventory and Performance Assessment Reports DOE - Performance...

  9. NNMCAB Responses from DOE

    Broader source: Energy.gov [DOE]

    Provides a listing of responses from the U.S. Department of Energy (DOE) to the recommendations provided from the Northern New Mexico Citizens’ Advisory Board (NNMCAB).

  10. Climate Change Response

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

    the Interior Climate Change Response "From the Everglades to the Great Lakes to Alaska and everywhere in between, climate change is a leading threat to natural and cultural ...

  11. GADRAS Detector Response Function.

    SciTech Connect (OSTI)

    Mitchell, Dean J.; Harding, Lee; Thoreson, Gregory G; Horne, Steven M.

    2014-11-01

    The Gamma Detector Response and Analysis Software (GADRAS) applies a Detector Response Function (DRF) to compute the output of gamma-ray and neutron detectors when they are exposed to radiation sources. The DRF is fundamental to the ability to perform forward calculations (i.e., computation of the response of a detector to a known source), as well as the ability to analyze spectra to deduce the types and quantities of radioactive material to which the detectors are exposed. This document describes how gamma-ray spectra are computed and the significance of response function parameters that define characteristics of particular detectors.

  12. Automated DNA Base Pair Calling Algorithm

    Energy Science and Technology Software Center (OSTI)

    1999-07-07

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

  13. Hybridization and Selective Release of DNA Microarrays

    SciTech Connect (OSTI)

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

    2011-11-29

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

  14. cDNA encoding a polypeptide including a hevein sequence

    DOE Patents [OSTI]

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

    1993-02-16

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

  15. Eastern Frequency Response Study

    SciTech Connect (OSTI)

    Miller, N.W.; Shao, M.; Pajic, S.; D'Aquila, R.

    2013-05-01

    This study was specifically designed to investigate the frequency response of the Eastern Interconnection that results from large loss-of-generation events of the type targeted by the North American Electric Reliability Corp. Standard BAL-003 Frequency Response and Frequency Bias Setting (NERC 2012a), under possible future system conditions with high levels of wind generation.

  16. Sensor response rate accelerator

    DOE Patents [OSTI]

    Vogt, Michael C. (Westmont, IL)

    2002-01-01

    An apparatus and method for sensor signal prediction and for improving sensor signal response time, is disclosed. An adaptive filter or an artificial neural network is utilized to provide predictive sensor signal output and is further used to reduce sensor response time delay.

  17. Low dose radiation hypersensitivity and clustered DNA damages in human fibroblasts exposed to low dose and dose rate protons or 137CS y-rays

    SciTech Connect (OSTI)

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

    2013-05-14

    Effective radioprotection for human space travelers hinges upon understanding the individual properties of charged particles. A significant fraction of particle radiation astronauts will encounter in space exploratory missions will come from high energy protons in galactic cosmic radiation (GCR) and/or possible exposures to lower energy proton flux from solar particle events (SPEs). These potential exposures present major concerns for NASA and others, in planning and executing long term space exploratory missions. We recently reported cell survival and transformation (acquisition of anchorage-independent growth in soft agar) frequencies in apparently normal NFF-28 primary human fibroblasts exposed to 0-30 cGy of 50MeV, 100MeV (SPE-like), or 1000 MeV (GCR-like) monoenergetic protons. These were modeled after 1989 SPE energies at an SPE-like low dose-rate (LDR) of 1.65 cGy/min or high dose rate (HDR) of 33.3 cGy/min delivered at the NASA Space Radiation Laboratory (NSRL) at BNL.

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

    Open Energy Info (EERE)

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

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

    Open Energy Info (EERE)

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

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

    Open Energy Info (EERE)

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

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

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

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

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

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

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

  3. DAMAGE MODELING OF INJECTION-MOLDED SHORT- AND LONG-FIBER THERMOPLASTICS

    SciTech Connect (OSTI)

    Nguyen, Ba Nghiep; Kunc, Vlastimil; Bapanapalli, Satish K.; Phelps, Jay; Tucker III, Charles L.

    2009-10-30

    This article applies the recent anisotropic rotary diffusion reduced strain closure (ARD-RSC) model for predicting fiber orientation and a new damage model for injection-molded long-fiber thermoplastics (LFTs) to analyze progressive damage leading to total failure of injection-molded long-glass-fiber/polypropylene (PP) specimens. The ARD-RSC model was implemented in a research version of the Autodesk Moldflow Plastics Insight (MPI) processing code, and it has been used to simulate injection-molding of a long-glass-fiber/PP plaque. The damage model combines micromechanical modeling with a continuum damage mechanics description to predict the nonlinear behavior due to plasticity coupled with damage in LFTs. This model has been implemented in the ABAQUS finite element code via user-subroutines and has been used in the damage analyses of tensile specimens removed from the injection-molded long-glass-fiber/PP plaques. Experimental characterization and mechanical testing were performed to provide input data to support and validate both process modeling and damage analyses. The predictions are in agreement with the experimental results.

  4. Frequency Response Analysis Tool

    SciTech Connect (OSTI)

    Etingov, Pavel V.; Kosterev, Dmitry; Dai, T.

    2014-12-31

    Frequency response has received a lot of attention in recent years at the national level, which culminated in the development and approval of North American Electricity Reliability Corporation (NERC) BAL-003-1 Frequency Response and Frequency Bias Setting Reliability Standard. This report is prepared to describe the details of the work conducted by Pacific Northwest National Laboratory (PNNL) in collaboration with the Bonneville Power Administration and Western Electricity Coordinating Council (WECC) Joint Synchronized Information Subcommittee (JSIS) to develop a frequency response analysis tool (FRAT). The document provides the details on the methodology and main features of the FRAT. The tool manages the database of under-frequency events and calculates the frequency response baseline. Frequency response calculations are consistent with frequency response measure (FRM) in NERC BAL-003-1 for an interconnection and balancing authority. The FRAT can use both phasor measurement unit (PMU) data, where available, and supervisory control and data acquisition (SCADA) data. The tool is also capable of automatically generating NERC Frequency Response Survey (FRS) forms required by BAL-003-1 Standard.

  5. Mechanical failure characterization of optical components caused by laser induced damage initiated at contaminants

    SciTech Connect (OSTI)

    Faux, D. R., LLNL

    1997-12-01

    The goal of this research is to quantify by numerical techniques the effects of surface and subsurface absorbing defects on damage initiation and growth in high power laser optical components. The defects include laser absorbing spots (e.g., surface particulate contamination) and surface damage regions (e.g., micro-cracks and voids) which are present due to environmental exposure and fabrication processes. This report focuses on three sources of contamination that can cause damage to optical components: (1) Front surface particle contamination, (2) Back surface particle contamination, and (3) Subsurface particle contamination. The DYNA2D (non-linear structural mechanics) code was used to model the growth of damage in the glass substrate. The damage in the nominally transparent glass substrate as a result of front surface particle contamination was found to be dependent on the magnitude of the resultant pressure pulse applied to the particle and the initial area of contact between the particle and glass substrate. The pressures generated from a back surface particle being blown off the surface provided sufficient loading to severely damage (crack) the glass substrate. A subsurface Ceria dioxide particle showed a strong surface interaction that influenced the formation and direction of the damage (cracking) that ultimately resulted in the blow-out of the damaged material leaving a relatively clean crater in the glass. Crater shape and size was determined. Since fused silica is the most transparent, and therefore laser damage resistant, of the optical materials, it is used for the most at-risk optical elements. The present studies are for a fused silica substrate. Some oxides such as Ceria are transparent in the infrared and visible, but absorbing in the UV part of the spectrum. Because ICF lasers like NIF use frequency tripling, effects of such oxides must be included.

  6. Automated laser-based barely visible impact damage detection in honeycomb sandwich composite structures

    SciTech Connect (OSTI)

    Girolamo, D. Yuan, F. G.; Girolamo, L.

    2015-03-31

    Nondestructive evaluation (NDE) for detection and quantification of damage in composite materials is fundamental in the assessment of the overall structural integrity of modern aerospace systems. Conventional NDE systems have been extensively used to detect the location and size of damages by propagating ultrasonic waves normal to the surface. However they usually require physical contact with the structure and are time consuming and labor intensive. An automated, contactless laser ultrasonic imaging system for barely visible impact damage (BVID) detection in advanced composite structures has been developed to overcome these limitations. Lamb waves are generated by a Q-switched Nd:YAG laser, raster scanned by a set of galvano-mirrors over the damaged area. The out-of-plane vibrations are measured through a laser Doppler Vibrometer (LDV) that is stationary at a point on the corner of the grid. The ultrasonic wave field of the scanned area is reconstructed in polar coordinates and analyzed for high resolution characterization of impact damage in the composite honeycomb panel. Two methodologies are used for ultrasonic wave-field analysis: scattered wave field analysis (SWA) and standing wave energy analysis (SWEA) in the frequency domain. The SWA is employed for processing the wave field and estimate spatially dependent wavenumber values, related to discontinuities in the structural domain. The SWEA algorithm extracts standing waves trapped within damaged areas and, by studying the spectrum of the standing wave field, returns high fidelity damage imaging. While the SWA can be used to locate the impact damage in the honeycomb panel, the SWEA produces damage images in good agreement with X-ray computed tomographic (X-ray CT) scans. The results obtained prove that the laser-based nondestructive system is an effective alternative to overcome limitations of conventional NDI technologies.

  7. Recovery From Radiation-induced Bone Marrow Damage by HSP25 Through Tie2 Signaling

    SciTech Connect (OSTI)

    Lee, Hae-June; Kwon, Hee-Chung; Chung, Hee-Yong; Lee, Yoon-Jin; Lee, Yun-Sil

    2012-09-01

    Purpose: Whole-body radiation therapy can cause severe injury to the hematopoietic system, and therefore it is necessary to identify a novel strategy for overcoming this injury. Methods and Materials: Mice were irradiated with 4.5 Gy after heat shock protein 25 (HSP25) gene transfer using an adenoviral vector. Then, peripheral blood cell counts, histopathological analysis, and Western blotting on bone marrow (BM) cells were performed. The interaction of HSP25 with Tie2 was investigated with mouse OP9 and human BM-derived mesenchymal stem cells to determine the mechanism of HSP25 in the hematopoietic system. Results: HSP25 transfer increased BM regeneration and reduced apoptosis following whole-body exposure to ionizing radiation (IR). The decrease in Tie2 protein expression that followed irradiation of the BM was blocked by HSP25 transfer, and Tie2-positive cells were more abundant among the BM cells of HSP25-transferred mice, even after IR exposure. Following systemic RNA interference of Tie2 before IR, HSP25-mediated radioprotective effects were partially blocked in both mice and cell line systems. Stability of Tie2 was increased by HSP25, a response mediated by the interaction of HSP25 with Tie2. IR-induced tyrosine phosphorylation of Tie2 was augmented by HSP25 overexpression; downstream events in the Tie2 signaling pathway, including phosphorylation of AKT and EKR1/2, were also activated. Conclusions: HSP25 protects against radiation-induced BM damage by interacting with and stabilizing Tie2. This may be a novel strategy for HSP25-mediated radioprotection in BM.

  8. Demand Response Analysis Tool

    SciTech Connect (OSTI)

    2012-03-01

    Demand Response Analysis Tool is a software developed at the Lawrence Berkeley National Laboratory. It is initially funded by Southern California Edison. Our goal in developing this tool is to provide an online, useable, with standardized methods, an analysis tool to evaluate demand and demand response performance of commercial and industrial facilities. The tool provides load variability and weather sensitivity analysis capabilities as well as development of various types of baselines. It can be used by researchers, real estate management firms, utilities, or any individuals who are interested in analyzing their demand and demand response capabilities.

  9. Demand Response Analysis Tool

    Energy Science and Technology Software Center (OSTI)

    2012-03-01

    Demand Response Analysis Tool is a software developed at the Lawrence Berkeley National Laboratory. It is initially funded by Southern California Edison. Our goal in developing this tool is to provide an online, useable, with standardized methods, an analysis tool to evaluate demand and demand response performance of commercial and industrial facilities. The tool provides load variability and weather sensitivity analysis capabilities as well as development of various types of baselines. It can be usedmore » by researchers, real estate management firms, utilities, or any individuals who are interested in analyzing their demand and demand response capabilities.« less

  10. Depth Profiling of SiC Lattice Damage Using Micro-Raman Spectroscopy

    Office of Scientific and Technical Information (OSTI)

    (Conference) | SciTech Connect Depth Profiling of SiC Lattice Damage Using Micro-Raman Spectroscopy Citation Details In-Document Search Title: Depth Profiling of SiC Lattice Damage Using Micro-Raman Spectroscopy Depth profiling for the amount of lattice damage using a Confocal Micro-Raman (CMR) spectrometer is demonstrated in this paper. Samples of n-type silicon carbide were implanted with 2 MeV He and O ions at both room temperature and 500 C, and fluences between 10{sup 15} and 10{sup 17}

  11. Los Alamos structure-damage software wins R&D 100 Award

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

    Structure-damage software wins R&D 100 Award Los Alamos structure-damage software wins R&D 100 Award A software package called SHMTools, which can detect damage in a variety of structures and was developed at Los Alamos National Laboratory, won an R&D 100 Award. December 6, 2015 Los Alamos National Laboratory sits on top of a once-remote mesa in northern New Mexico with the Jemez mountains as a backdrop to research and innovation covering multi-disciplines from bioscience,

  12. Damage thresholds of thin film materials and high reflectors at 248 nm

    SciTech Connect (OSTI)

    Rainer, F.; Lowdermilk, W.H.; Milam, D.; Carniglia, C.K.; Hart, T.T.; Lichtenstein, T.L.

    1982-01-01

    Twenty-ns, 248-nm KrF laser pulses were used to measure laser damage thresholds for halfwave-thick layers of 15 oxide and fluoride coating materials, and for high reflectance coatings made with 13 combinations of these materials. The damage thresholds of the reflectors and single-layer films were compared to measurements of several properties of the halfwave-thick films to determine whether measurements of these properties of single-layer films to determine whether measurements of these properties of single-layer films were useful for identifying materials for fabrication of damage resistant coatings.

  13. An intercalation-locked parallel-stranded DNA tetraplex

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

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

    2015-01-27

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

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

    DOE Patents [OSTI]

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

    1999-02-16

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

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

    Open Energy Info (EERE)

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

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

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

    Liu, Ninning; Chistol, Gheorghe; Bustamante, Carlos

    2015-10-09

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

  17. Technical Work Plan For: Calculation of Waste Packave and Drip Shield Response to Vibratory Ground Motion and Revision of the Seismic Consequence Abstraction

    SciTech Connect (OSTI)

    M. Gross

    2006-12-08

    The overall objective of the work scope covered by this technical work plan (TWP) is to develop new damage abstractions for the seismic scenario class in total system performance assessment (TSPA). The new abstractions will be based on a new set of waste package and drip shield damage calculations in response to vibratory ground motion and fault displacement. The new damage calculations, which are collectively referred to as damage models in this TWP, are required to represent recent changes in waste form packaging and in the regulatory time frame. The new damage models also respond to comments from the Independent Validation Review Team (IVRT) postvalidation review of the draft TSPA model regarding performance of the drip shield and to an Additional Information Need (AIN) from the U.S. Nuclear Regulatory Commission (NRC).

  18. COMMENTS AND RESPONSES

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

    ... The FFTF is a 400-megawatt sodium-cooled nuclear reactor ... of the national Liquid Metal Fast Breeder Reactor program. ... DOE Response: The FFTF and all reactors are required to be ...

  19. Your Records Management Responsibilities

    Broader source: Energy.gov [DOE]

    As a DOE federal or contractor employee, you will create or receive official records, and you are responsible for managing those records as part of accomplishing the Department's mission and...

  20. Demand Response- Policy

    Broader source: Energy.gov [DOE]

    Demand response is an electricity tariff or program established to motivate changes in electric use by end-use customers, designed to induce lower electricity use typically at times of high market prices or when grid reliability is jeopardized.

  1. Questions and Responses

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

    Government Response: The Government has determined that CMMI-SVC is a relatively new methodology and is in agreement that there is a considerable overlap of process areas shared...

  2. Demand Response Dispatch Tool

    SciTech Connect (OSTI)

    2012-08-31

    The Demand Response (DR) Dispatch Tool uses price profiles to dispatch demand response resources and create load modifying profiles. These annual profiles are used as inputs to production cost models and regional planning tools (e.g., PROMOD). The tool has been effectively implemented in transmission planning studies conducted by the Western Electricity Coordinating Council via its Transmission Expansion Planning and Policy Committee. The DR Dispatch Tool can properly model the dispatch of DR resources for both reliability and economic conditions.

  3. CRA Comments & Responses

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

    CRA Comments & Responses Home CRA - 2004 Final Recertification Decision CRA Comments & Responses CCA - 1996 CRA CARDs & TSDs CCA CARDs & TSDs Regulatory Tools Completeness Determination-Related Correspondence All EPA & DOE correspondence related to the determination of completeness and the CRA are provided below. Letter Transmitting EPA's CRA Completeness Determination (9/29/05) Notification of Completeness Determination EPA Letter # Subject 1 CRA Comments (5/20/04)

  4. Your Records Management Responsibilities

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

    Your Records Management Responsibilities Table of Contents INTRODUCTION RECORDS MANAGEMENT IN THE FEDERAL GOVERNMENT RECORDS MANAGEMENT IN THE DEPARTMENT OF ENERGY IMPORTANCE OF RECORDS MANAGEMENT YOUR RECORDS MANAGEMENT RESPONSIBILITIES RECORDS MANAGEMENT LIFE CYCLE ELECTRONIC RECORDS & RECORDKEEPING LAW, REGULATION, AND POLICY ASSISTANCE RECORDS MANAGEMENT TERMS 2 INTRODUCTION If you are a government employee or contractor working for a federal agency, records management is part of your

  5. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1996-01-09

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

  6. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B. (New York, NY); Efstratiadis, Argiris (Englewood, NJ)

    1996-01-01

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

  7. A creep-damage model for mesoscale simulations of concrete expansion-degradation phenomena

    SciTech Connect (OSTI)

    Giorla, Alain B; Le Pape, Yann

    2015-01-01

    Long-term performance of aging concrete in nuclear power plants (NPPs) requires a careful examination of the physical phenomena taking place in the material. Concrete under high neutron irradiation is subjected to large irreversible deformations as well as mechanical damage, caused by a swelling of the aggregates. However, these results, generally obtained in accelerated conditions in test reactors, cannot be directly applied to NPP irradiated structures, i.e., the biological shield, operating conditions due to difference in time scale and environmental conditions (temperature, humidity). Mesoscale numerical simulations are performed to separate the underlying mechanisms and their interactions. The cement paste creep-damage model accounts for the effect of the loading rate on the apparent damage properties of the material and uses an event-based approach to capture the competition between creep and damage. The model is applied to the simulation of irradiation experiments from the literature and shows a good agreement with the experimental data.

  8. Reduction of damage initiation density in fused silica optics via UV laser conditioning

    DOE Patents [OSTI]

    Peterson, John E.; Maricle, Stephen M.; Brusasco, Raymond M.; Penetrante, Bernardino M.

    2004-03-16

    The present invention provides a method for reducing the density of sites on the surface of fused silica optics that are prone to the initiation of laser-induced damage, resulting in optics which have far fewer catastrophic defects and are better capable of resisting optical deterioration upon exposure for a long period of time to a high-power laser beam having a wavelength of about 360 nm or less. The initiation of laser-induced damage is reduced by conditioning the optic at low fluences below levels that normally lead to catastrophic growth of damage. When the optic is then irradiated at its high fluence design limit, the concentration of catastrophic damage sites that form on the surface of the optic is greatly reduced.

  9. 01-07-2000 - Undergroud Cables Damaged during Excavation Work | The Ames

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

    Laboratory 0 - Undergroud Cables Damaged during Excavation Work Document Number: NA Effective Date: 01/2000 File (public): PDF icon 01-07-2000_blue_alert(2)

  10. United States and France Sign Joint Statement on Civil Liability for Nuclear Damage

    Broader source: Energy.gov [DOE]

    The United States and France today issued the Joint Statement on Civil Liability for Nuclear Damage that sets forth the common views of the United States and France on civil nuclear liability

  11. On the Effect of Ramp Rate in Damage Accumulation of the CPV Die-Attach: Preprint

    SciTech Connect (OSTI)

    Bosco, N. S.; Silverman, T. J.; Kurtz, S. R.

    2012-06-01

    It is commonly understood that thermal cycling at high temperature ramp rates may activate unrepresentative failure mechanisms. Increasing the temperature ramp rate of thermal cycling, however, could dramatically reduce the test time required to achieve an equivalent amount of thermal fatigue damage, thereby reducing overall test time. Therefore, the effect of temperature ramp rate on physical damage in the CPV die-attach is investigated. Finite Element Model (FEM) simulations of thermal fatigue and thermal cycling experiments are made to determine if the amount of damage calculated results in a corresponding amount of physical damage measured to the die-attach for a variety of fast temperature ramp rates. Preliminary experimental results are in good agreement with simulations and reinforce the potential of increasing temperature ramp rates. Characterization of the microstructure and resulting fatigue crack in the die-attach suggest a similar failure mechanism across all ramp rates tested.

  12. Precursors to potential severe core damage accidents. A status report, 1982--1983

    SciTech Connect (OSTI)

    Forester, J.A.; Mitchell, D.B.; Whitehead, D.W.

    1997-04-01

    This study is a continuation of earlier work that evaluated 1969-1981 and 1984-1994 events affecting commercial light-water reactors. One-hundred nine operational events that affected 51 reactors during 1982 and 1983 and that are considered to be precursors to potential severe core damage are described. All these events had conditional probabilities of subsequent severe core damage greater than or equal to 1.0 x 10{sup {minus}6}. These events were identified by first computer screening the 1982-83 licensee event reports from commercial light-water reactors to select events that could be precursors to core damage. Candidates underwent engineering evaluation that identified, analyzed, and documented the precursors. This report discusses the general rationale for the study, the selection and documentation of events as precursors, and the estimation of conditional probabilities of subsequent severe core damage for the events.

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

    SciTech Connect (OSTI)

    Suh, Myungkoo

    1995-12-06

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

  14. ASPECT Emergency Response Chemical and Radiological Mapping

    ScienceCinema (OSTI)

    LANL

    2009-09-01

    A unique airborne emergency response tool, ASPECT is a Los Alamos/U.S. Environmental Protection Agency project that can put chemical and radiological mapping tools in the air over an accident scene. The name ASPECT is an acronym for Airborne Spectral Photometric Environmental Collection Technology. Update, Sept. 19, 2008: Flying over storm-damaged refineries and chemical factories, a twin-engine plane carrying the ASPECT (Airborne Spectral Photometric Environmental Collection Technology) system has been on duty throughout the recent hurricanes that have swept the Florida and Gulf Coast areas. ASPECT is a project of the U.S. U.S. Environmental Protection Agencys National Decontamination Team. Los Alamos National Laboratory leads a science and technology program supporting the EPA and the ASPECT aircraft. Casting about with a combination of airborne photography and infrared spectroscopy, the highly instrumented plane provides emergency responders on the ground with a clear concept of where danger lies, and the nature of the sometimes-invisible plumes that could otherwise kill them. ASPECT is the nations only 24/7 emergency response aircraft with chemical plume mapping capability. Bob Kroutil of Bioscience Division is the project leader, and while he said the team has put in long hours, both on the ground and in the air, its a worthwhile effort. The plane flew over 320 targeted sites in four days, he noted. Prior to the deployment to the Gulf Coast, the plane had been monitoring the Democratic National Convention in Denver, Colorado. Los Alamos National Laboratory Divisions that are supporting ASPECT include, in addition to B-Division, CTN-5: Networking Engineering and IRM-CAS: Communication, Arts, and Services. Leslie Mansell, CTN-5, and Marilyn Pruitt, IRM-CAS, were recognized the the U.S. EPA for their outstanding support to the hurricane response of Gustav in Louisiana and Ike in Texas. The information from the data collected in the most recent event, Hurricane Ike, was sent to the EPA Region 6 Rapid Needs Assessment and the State of Texas Joint Field Office in Austin, Texas. It appears that though there is considerable damage in Galveston and Texas City, there are fewer chemical leaks than during either hurricanes Katrina or Rita. Specific information gathered from the data was reported out to the U.S. Environmental Protection Agency Headquarters, the Federal Emergency Management Agency, the Department of Homeland Security, and the State of Texas Emergency Management Agency.

  15. ASPECT Emergency Response Chemical and Radiological Mapping

    SciTech Connect (OSTI)

    LANL

    2008-05-12

    A unique airborne emergency response tool, ASPECT is a Los Alamos/U.S. Environmental Protection Agency project that can put chemical and radiological mapping tools in the air over an accident scene. The name ASPECT is an acronym for Airborne Spectral Photometric Environmental Collection Technology. Update, Sept. 19, 2008: Flying over storm-damaged refineries and chemical factories, a twin-engine plane carrying the ASPECT (Airborne Spectral Photometric Environmental Collection Technology) system has been on duty throughout the recent hurricanes that have swept the Florida and Gulf Coast areas. ASPECT is a project of the U.S. U.S. Environmental Protection Agencys National Decontamination Team. Los Alamos National Laboratory leads a science and technology program supporting the EPA and the ASPECT aircraft. Casting about with a combination of airborne photography and infrared spectroscopy, the highly instrumented plane provides emergency responders on the ground with a clear concept of where danger lies, and the nature of the sometimes-invisible plumes that could otherwise kill them. ASPECT is the nations only 24/7 emergency response aircraft with chemical plume mapping capability. Bob Kroutil of Bioscience Division is the project leader, and while he said the team has put in long hours, both on the ground and in the air, its a worthwhile effort. The plane flew over 320 targeted sites in four days, he noted. Prior to the deployment to the Gulf Coast, the plane had been monitoring the Democratic National Convention in Denver, Colorado. Los Alamos National Laboratory Divisions that are supporting ASPECT include, in addition to B-Division, CTN-5: Networking Engineering and IRM-CAS: Communication, Arts, and Services. Leslie Mansell, CTN-5, and Marilyn Pruitt, IRM-CAS, were recognized the the U.S. EPA for their outstanding support to the hurricane response of Gustav in Louisiana and Ike in Texas. The information from the data collected in the most recent event, Hurricane Ike, was sent to the EPA Region 6 Rapid Needs Assessment and the State of Texas Joint Field Office in Austin, Texas. It appears that though there is considerable damage in Galveston and Texas City, there are fewer chemical leaks than during either hurricanes Katrina or Rita. Specific information gathered from the data was reported out to the U.S. Environmental Protection Agency Headquarters, the Federal Emergency Management Agency, the Department of Homeland Security, and the State of Texas Emergency Management Agency.

  16. Increase of bulk optical damage threshold fluences of KDP crystals by laser irradiation and heat treatment

    DOE Patents [OSTI]

    Swain, J.E.; Stokowski, S.E.; Milam, D.; Kennedy, G.C.; Rainer, F.

    1982-07-07

    The bulk optical damage threshold fluence of potassium dihydrogen phosphate (KDP) crystals is increased by irradiating the crystals with laser pulses of duration 1 to 20 nanoseconds of increasing fluence, below the optical damage threshold fluence for untreated crystals, or by baking the crystals for times of the order of 24 hours at temperatures of 110 to 165/sup 0/C, or by a combination of laser irradiation and baking.

  17. Probing Fukushima with cosmic rays should help speed cleanup of damaged

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

    plant Probing Fukushima with cosmic rays Probing Fukushima with cosmic rays should help speed cleanup of damaged plant The initiative could reduce the time required to clean up the disabled complex by at least a decade and greatly reduce radiation exposure to personnel working at the plant. December 22, 2014 Probing Fukushima with cosmic rays should help speed cleanup of damaged plant Los Alamos-generated computer animation of the Fukushima Diachi powerplant. Contact James Rickman

  18. Evaluation of ATWS core damage frequency for an earlier vintage BWR/4

    SciTech Connect (OSTI)

    Shiu, K.K.; Ilberg, D.; Hanan, N.

    1986-01-01

    In summary, this study evaluated the total core damage contribution due to ATWS events for an earlier vintage BWR/4. A realistic calculation was performed for a plant with a particular ATWS prevention and mitigation configuration and with some of the ATWS rule modifications implemented. Results are compared with the ATWS task force findings; three areas have been identified which could potentially have significant impact upon the ATWS core damage frequency contribution. 4 refs.

  19. Self-Healing of Structural Damage to Restore Performance of Electrical

    Office of Science (SC) Website

    Circuits | U.S. DOE Office of Science (SC) Self-Healing of Structural Damage to Restore Performance of Electrical Circuits Energy Frontier Research Centers (EFRCs) EFRCs Home Centers Research Science Highlights Highlight Archives News & Events Publications History Contact BES Home 04.27.12 Self-Healing of Structural Damage to Restore Performance of Electrical Circuits Print Text Size: A A A FeedbackShare Page Scientific Achievement Designed chemical interactions of liquid-metal-filled

  20. Full-length high-temperature severe fuel damage test No. 2. Final safety analysis

    SciTech Connect (OSTI)

    Hesson, G.M.; Lombardo, N.J.; Pilger, J.P.; Rausch, W.N.; King, L.L.; Hurley, D.E.; Parchen, L.J.; Panisko, F.E.

    1993-09-01

    Hazardous conditions associated with performing the Full-Length High- Temperature (FLHT). Severe Fuel Damage Test No. 2 experiment have been analyzed. Major hazards that could cause harm or damage are (1) radioactive fission products, (2) radiation fields, (3) reactivity changes, (4) hydrogen generation, (5) materials at high temperature, (6) steam explosion, and (7) steam pressure pulse. As a result of this analysis, it is concluded that with proper precautions the FLHT- 2 test can be safely conducted.

  1. Damage prognosis of adhesively-bonded joints in laminated composite structural components of unmanned aerial vehicles

    SciTech Connect (OSTI)

    Farrar, Charles R; Gobbato, Maurizio; Conte, Joel; Kosmatke, John; Oliver, Joseph A

    2009-01-01

    The extensive use of lightweight advanced composite materials in unmanned aerial vehicles (UAVs) drastically increases the sensitivity to both fatigue- and impact-induced damage of their critical structural components (e.g., wings and tail stabilizers) during service life. The spar-to-skin adhesive joints are considered one of the most fatigue sensitive subcomponents of a lightweight UAV composite wing with damage progressively evolving from the wing root. This paper presents a comprehensive probabilistic methodology for predicting the remaining service life of adhesively-bonded joints in laminated composite structural components of UAVs. Non-destructive evaluation techniques and Bayesian inference are used to (i) assess the current state of damage of the system and, (ii) update the probability distribution of the damage extent at various locations. A probabilistic model for future loads and a mechanics-based damage model are then used to stochastically propagate damage through the joint. Combined local (e.g., exceedance of a critical damage size) and global (e.g.. flutter instability) failure criteria are finally used to compute the probability of component failure at future times. The applicability and the partial validation of the proposed methodology are then briefly discussed by analyzing the debonding propagation, along a pre-defined adhesive interface, in a simply supported laminated composite beam with solid rectangular cross section, subjected to a concentrated load applied at mid-span. A specially developed Eliler-Bernoulli beam finite element with interlaminar slip along the damageable interface is used in combination with a cohesive zone model to study the fatigue-induced degradation in the adhesive material. The preliminary numerical results presented are promising for the future validation of the methodology.

  2. Nonlinear Ultrasonic Techniques to Monitor Radiation Damage in RPV and Internal Components

    SciTech Connect (OSTI)

    Jacobs, Laurence; Kim, Jin-Yeon; Qu, Jisnmin; Ramuhalli, Pradeep; Wall, Joe

    2015-11-02

    The objective of this research is to demonstrate that nonlinear ultrasonics (NLU) can be used to directly and quantitatively measure the remaining life in radiation damaged reactor pressure vessel (RPV) and internal components. Specific damage types to be monitored are irradiation embrittlement and irradiation assisted stress corrosion cracking (IASCC). Our vision is to develop a technique that allows operators to assess damage by making a limited number of NLU measurements in strategically selected critical reactor components during regularly scheduled outages. This measured data can then be used to determine the current condition of these key components, from which remaining useful life can be predicted. Methods to unambiguously characterize radiation related damage in reactor internals and RPVs remain elusive. NLU technology has demonstrated great potential to be used as a material sensor – a sensor that can continuously monitor a material’s damage state. The physical effect being monitored by NLU is the generation of higher harmonic frequencies in an initially monochromatic ultrasonic wave. The degree of nonlinearity is quantified with the acoustic nonlinearity parameter, β, which is an absolute, measurable material constant. Recent research has demonstrated that nonlinear ultrasound can be used to characterize material state and changes in microscale characteristics such as internal stress states, precipitate formation and dislocation densities. Radiation damage reduces the fracture toughness of RPV steels and internals, and can leave them susceptible to IASCC, which may in turn limit the lifetimes of some operating reactors. The ability to characterize radiation damage in the RPV and internals will enable nuclear operators to set operation time thresholds for vessels and prescribe and schedule replacement activities for core internals. Such a capability will allow a more clear definition of reactor safety margins. The research consists of three tasks: (1) materials sensing and monitoring; (2) physics-based materials and damage evolution modeling; and (3) remaining life estimation by integrating sensing, modeling and uncertainty.

  3. Structural health and prognostics management for offshore wind turbines : case studies of rotor fault and blade damage with initial O&M cost modeling.

    SciTech Connect (OSTI)

    Myrent, Noah J.; Kusnick, Joshua F.; Barrett, Natalie C.; Adams, Douglas E.; Griffith, Daniel Todd

    2013-04-01

    Operations and maintenance costs for offshore wind plants are significantly higher than the current costs for land-based (onshore) wind plants. One way to reduce these costs would be to implement a structural health and prognostic management (SHPM) system as part of a condition based maintenance paradigm with smart load management and utilize a state-based cost model to assess the economics associated with use of the SHPM system. To facilitate the development of such a system a multi-scale modeling approach developed in prior work is used to identify how the underlying physics of the system are affected by the presence of damage and faults, and how these changes manifest themselves in the operational response of a full turbine. This methodology was used to investigate two case studies: (1) the effects of rotor imbalance due to pitch error (aerodynamic imbalance) and mass imbalance and (2) disbond of the shear web; both on a 5-MW offshore wind turbine in the present report. Based on simulations of damage in the turbine model, the operational measurements that demonstrated the highest sensitivity to the damage/faults were the blade tip accelerations and local pitching moments for both imbalance and shear web disbond. The initial cost model provided a great deal of insight into the estimated savings in operations and maintenance costs due to the implementation of an effective SHPM system. The integration of the health monitoring information and O&M cost versus damage/fault severity information provides the initial steps to identify processes to reduce operations and maintenance costs for an offshore wind farm while increasing turbine availability, revenue, and overall profit.

  4. Active investigation of material damage under load using micro-CT

    SciTech Connect (OSTI)

    Navalgund, Megha Mishra, Debasish; Manoharan, V.; Zunjarrao, Suraj

    2015-03-31

    Due the growth of composite materials across multiple industries such as Aviation, Wind there is an increasing need to not just standardize and improve manufacturing processes but also to design these materials for the specific applications. One of the things that this translates to is understanding how failure initiates and grows in these materials and at what loads, especially around internal flaws such as voids or features such as ply drops. Traditional methods of investigating internal damage such as CT lack the resolution to resolve ply level damage in composites. Interrupted testing with layer removal can be used to investigate internal damage using microscopy; however this is a destructive method. Advanced techniques such as such as DIC are useful for in-situ damage detection, however are limited to surface information and would not enable interrogating the volume. Computed tomography has become a state of the art technique for metrology and complete volumetric investigation especially for metallic components. However, its application to the composite world is still nascent. This paper demonstrates micro-CTs capability as a gauge to quantitatively estimate the extent of damage and understand the propagation of damage in PMC composites while the component is under stress.

  5. Finite element simulation of magnetic detection of creep damage at seam welds

    SciTech Connect (OSTI)

    Sablik, M.J.; Rubin, S.W.; Jiles, D.C.; Kaminski, D.; Bi, Y.

    1996-09-01

    Using appropriately modified magnetization curves for each element of creep-damaged material, a finite element calculation has been carried out to simulate magnetic detection of non-uniform creep damage around a seam weld in a 2.25 Cr 1 Mo steam pipe. The magnetization curves for the creep-damaged elements were obtained from an earlier model for the magnetic effect of a uniformly creep-damaged material as given by Chen, et al. In the finite element calculation, a magnetic C-core with primary and secondary coils was placed with its pole pieces flush against the specimen in the vicinity of the weld. The secondary emf was shown to be reduced when creep damage was present inside the pipe wall at the cusp of weld and in the vicinity of the cusp. The C-core detected the creep damage best if it completely spanned the weld seam width. Also, the current in the primary needed to be such that the C-core was not magnetically saturated.

  6. (Microstructural dependence of the cavitation damage function in the FCC materials: Annual report, 1990--1991)

    SciTech Connect (OSTI)

    Not Available

    1991-01-01

    The interface damage function (IDF) defines an area fraction of damage on crystallite interfaces. This function, which is material and condition dependent, sustains a complete geometrical description of grain boundaries and identifies those types of interfaces which are preferentially damaged. Included in the IDF is functional dependence, not only upon lattice orientations or misorientations, but also upon grain boundary normal; this dependence has been largely neglected in other studies examining damage inhomogeneity of polycrystals. The experimental method used in describing the damaged microstructures included random sectioning of the damaged specimen, and the manual or semi-automatic construction of grain maps describing the observed microstructure. The grain maps for the initial IDF determination were constructed from scanning electron micrographs. Several of these micrographs were joined together and the grain boundaries were traced. There were manually fed back into the computer using a digitizing pad with each grain boundary intersection defined by an (x,y) pair of coordinates. Using algorithms written as a part of this work, the computer then reconstructs the grain map from this series of points. Manual correction of the computer generated maps was required to obtain an acceptable digitized reproduction of the observed microstructure.

  7. Management of wildlife causing damage at Argonne National Laboratory-East, DuPage County, Illinois

    SciTech Connect (OSTI)

    1995-04-01

    The DOE, after an independent review, has adopted an Environmental Assessment (EA) prepared by the US Department of Agriculture (USDA) which evaluates use of an Integrated Wildlife Damage Management approach at Argonne National Laboratory-East (ANL-E) in DuPage County, Illinois (April 1995). In 1994, the USDA issued a programmatic Environmental Impact Statement (EIS) that covers nationwide animal damage control activities. The EA for Management of Wildlife Causing Damage at ANL-E tiers off this programmatic EIS. The USDA wrote the EA as a result of DOE`s request to USDA to prepare and implement a comprehensive Wildlife Management Damage Plan; the USDA has authority for animal damage control under the Animal Damage Control Act of 1931, as amended, and the Rural Development, Agriculture and Related Agencies Appropriations Act of 1988. DOE has determined, based on the analysis in the EA, that the proposed action does not constitute a major Federal action significantly affecting the quality of the human environment within the meaning of the National Environmental Policy Act of 1969 (NEPA). Therefore, the preparation of an EIS is not required. This report contains the Environmental Assessment, as well as the Finding of No Significant Impact (FONSI).

  8. Vehicle Technologies Office Merit Review 2014: Fleet DNA

    Broader source: Energy.gov [DOE]

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

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

    Office of Scientific and Technical Information (OSTI)

    tube surface and better interpret STM data. Our simulations clearly demonstrate the existence of a very stable DNA binding geometry for (6,5) CNT as evidenced by the presence of...

  10. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1998-11-03

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

  11. When DNA Needs to Stand Up and Be Counted

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

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

  12. Charge Transport within a Three-Dimensional DNA Nanostructure...

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

    Charge Transport within a Three-Dimensional DNA Nanostructure Framework Authors: Lu, N., Pei, H., Ge, Z., Simmons, C.R., Yan, H., and Fan, C. Title: Charge Transport within a...

  13. Method for rapid base sequencing in DNA and RNA

    DOE Patents [OSTI]

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

    1987-10-07

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

  14. Method for rapid base sequencing in DNA and RNA

    DOE Patents [OSTI]

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

    1990-10-09

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

  15. Method for rapid base sequencing in DNA and RNA

    DOE Patents [OSTI]

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

    1990-01-01

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

  16. Flow cytomeric measurement of DNA and incorporated nucleoside analogs

    DOE Patents [OSTI]

    Dolbeare, Frank A. (Livermore, CA); Gray, Joe W. (Livermore, CA)

    1989-01-01

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

  17. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B. (New York, NY); Efstratiadis, Argiris (Englewood, NJ)

    1998-01-01

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

  18. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, N.V.

    1994-01-04

    Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties. GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon. .

  19. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, Natasha V.

    1994-01-04

    Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties. GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon.

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

    Office of Scientific and Technical Information (OSTI)

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

  1. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

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

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

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

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

  3. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

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

  4. DNA-Directed Artificial Light-Harvesting Antenna

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

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

  5. Surface state reconstruction in ion-damaged SmB6

    SciTech Connect (OSTI)

    Wakeham, N.; Wang, Y. Q.; Fisk, Z.; Ronning, F.; Thompson, J. D.

    2015-02-12

    We have used ion-irradiation to damage the (001) surfaces of SmB? single crystals to varying depths, and have measured the resistivity as a function of temperature for each depth of damage. We observe a reduction in the residual resistivity with increasing depth of damage. Our data are consistent with a model in which the surface state is not destroyed by the ion-irradiation, however instead the damaged layer is poorly conducting and the initial surface state is reconstructed below the damage. This behavior is consistent with a surface state that is topologically protected.

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

    SciTech Connect (OSTI)

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

    2009-06-08

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

  7. Demand Response Dispatch Tool

    Energy Science and Technology Software Center (OSTI)

    2012-08-31

    The Demand Response (DR) Dispatch Tool uses price profiles to dispatch demand response resources and create load modifying profiles. These annual profiles are used as inputs to production cost models and regional planning tools (e.g., PROMOD). The tool has been effectively implemented in transmission planning studies conducted by the Western Electricity Coordinating Council via its Transmission Expansion Planning and Policy Committee. The DR Dispatch Tool can properly model the dispatch of DR resources for bothmore » reliability and economic conditions.« less

  8. Mechanical and substructural response of incipiently spalled 316L stainless steel.

    SciTech Connect (OSTI)

    Gray, G. T. , III; Bourne, N. K.

    2004-01-01

    316L SS samples were shock prestrained to a peak stress of 6.6 GPa using a 0.75 {mu}sec pulse duration square-topped shock profile and 'soft' recovered while a second sample was similarly shock loaded, without spall momentum trapping, leading to incipient spall damage. Shock prestraining and 'soft' shock recovery to 6.6 GPa led to an increase in the post-shock flow strength of 316L SS by {approx}100 MPa over the starting material while the reload yield strength of the incipiently spall damaged sample increased by {approx}200 MPa. In this paper the sequential processes of defect generation and damage operative during the shock prestraining, spallation, and reloading of incipiently spalled 316L SS is presented. The influence of shock prestraining, using both triangular-wave loading, via both direct HE and triangular-wave pulses on a gas launcher, as well as 'square-topped' shock prestaining via conventional flyer-plate impact, is crucial to understanding the shock hardening and spallation responses of materials(Gray III, et al. [2003]). The development of predictive constitutive models to describe the mechanical response of incipiently damaged metals and alloys requires an understanding of the defect generation and storage due to shock hardening as well as the additional plasticity and damage evolution during spallation. In this paper the influence of shock-wave prestraining on the process of shock hardening and thereafterthe hardeningand damage evolution accompanying incipient spallation in 316L stainless steel (316L SS) on post-shock constitutive behavior is examined using 'soft' recovery techniques and mechanical behavior measurements.

  9. Roles & Responsibilities | Department of Energy

    Office of Environmental Management (EM)

    Responsibilities PDF icon Roles & Responsibilities.pdf Responsible Contacts Donna Friend HUMAN RESOURCES SPECIALIST E-mail donna.friend@hq.doe.dov Phone 202-586-5880 More...

  10. Demand Response | Department of Energy

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

    Demand Response Demand Response Demand Response Demand response provides an opportunity for consumers to play a significant role in the operation of the electric grid by reducing or shifting their electricity usage during peak periods in response to time-based rates or other forms of financial incentives. Demand response programs are being used by electric system planners and operators as resource options for balancing supply and demand. Such programs can lower the cost of electricity in

  11. Response Events | Department of Energy

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

    Response Events Response Events Emergency preparedness and response activities help to facilitate recovery from disruptions to the energy supply, thereby reducing the impact of these events. As such, the ISER approach for emergency response is to leverage a coordinated integration of several DOE capabilities and resources to emergency response situations. These capabilities and resources include personnel with emergency response and/or energy systems operations experience, leading-edge

  12. The Marginal Damage Costs of Different Greenhouse Gases: An Application of FUND

    SciTech Connect (OSTI)

    Waldhoff, Stephanie T.; Anthoff, David; Rose, Steven K.; Tol, Richard

    2014-01-01

    We use FUND 3.8 to estimate the social cost of four greenhouse gases: carbon dioxide, methane, nitrous oxide, and sulphur hexafluoride emissions. The damage potential for each gasthe ratio of the social cost of the non-carbon dioxide greenhouse gas to the social cost of carbon dioxideis also estimated. The damage potentials are compared to several metrics, focusing in particular on the global warming potentials, which are frequently used to measure the trade-off between gases in the form of carbon dioxide equivalents. We find that damage potentials could be significantly higher than global warming potentials. This finding implies that previous papers have underestimated the relative importance of reducing non-carbon dioxide greenhouse gas emissions from an economic damage perspective. We show results for a range of sensitivity analyses: carbon dioxide fertilization on agriculture productivity, terrestrial feedbacks, climate sensitivity, discounting, equity weighting, and socioeconomic and emissions scenarios. The sensitivity of the results to carbon dioxide fertilization is a primary focus as it is an important element of climate change that has not been considered in much of the previous literature. We estimate that carbon dioxide fertilization has a large positive impact that reduces the social cost of carbon dioxide with a much smaller effect on the other greenhouse gases. As a result, our estimates of the damage potentials of methane and nitrous oxide are much higher compared to estimates that ignore carbon dioxide fertilization. As a result, our base estimates of the damage potential for methane and nitrous oxide that include carbon dioxide fertilization are twice their respective global warming potentials. Our base estimate of the damage potential of sulphur hexafluoride is similar to the one previous estimate, both almost three times the global warming potential.

  13. SIMULATION AND MOCKUP OF SNS JET-FLOW TARGET WITH WALL JET FOR CAVITATION DAMAGE MITIGATION

    SciTech Connect (OSTI)

    Wendel, Mark W; Geoghegan, Patrick J; Felde, David K

    2014-01-01

    Pressure waves created in liquid mercury pulsed spallation targets at the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory induce cavitation damage on the stainless steel target container. The cavitation damage is thought to limit the lifetime of the target for power levels at and above 1 MW. Severe through-wall cavitation damage on an internal wall near the beam entrance window has been observed in spent-targets. Surprisingly though, there is very little damage on the walls that bound an annular mercury channel that wraps around the front and outside of the target. The mercury flow through this channel is characterized by smooth, attached streamlines. One theory to explain this lack of damage is that the uni-directional flow biases the direction of the collapsing cavitation bubble, reducing the impact pressure and subsequent damage. The theory has been reinforced by in-beam separate effects data. For this reason, a second-generation SNS mercury target has been designed with an internal wall jet configuration intended to protect the concave wall where damage has been observed. The wall jet mimics the annular flow channel streamlines, but since the jet is bounded on only one side, the momentum is gradually diffused by the bulk flow interactions as it progresses around the cicular path of the target nose. Numerical simulations of the flow through this jet-flow target have been completed, and a water loop has been assembled with a transparent test target in order to visualize and measure the flow field. This paper presents the wall jet simulation results, as well as early experimental data from the test loop.

  14. Senescence responsive transcriptional element

    DOE Patents [OSTI]

    Campisi, Judith; Testori, Alessandro

    1999-01-01

    Recombinant polynucleotides have expression control sequences that have a senescence responsive element and a minimal promoter, and which are operatively linked to a heterologous nucleotide sequence. The molecules are useful for achieving high levels of expression of genes in senescent cells. Methods of inhibiting expression of genes in senescent cells also are provided.

  15. General Responsibilities and Requirements

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1999-07-09

    The material presented in this guide provides suggestions and acceptable ways of implementing DOE M 435.1-1 and should not be viewed as additional or mandatory requirements. The objective of the guide is to ensure that responsible individuals understand what is necessary and acceptable for implementing the requirements of DOE M 435.1-1.

  16. Supervisor Responsibilities at Berkeley Lab

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

    Supervisor Responsibilities at Berkeley Lab This online course will help both new and experienced supervisors better understand key knowledge and responsibilities needed to be an...

  17. First Responder Initial Response Procedure

    Broader source: Energy.gov [DOE]

    The purpose of this response flow chart is to provide first responders with guidance for response to a transportation accident involving radioactive material.

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

    SciTech Connect (OSTI)

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

    1991-05-01

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

  19. Structural dynamics and ssDNA binding activity of the three N-terminal domains of the large subunit of Replication Protein A from small angle X-ray scattering

    SciTech Connect (OSTI)

    Pretto, Dalyir I.; Tsutakawa, Susan; Brosey, Chris A.; Castillo, Amalchi; Chagot, Marie-Eve; Smith, Jarrod A.; Tainer, John A.; Chazin, Walter J.

    2010-03-11

    Replication Protein A (RPA) is the primary eukaryotic ssDNA binding protein utilized in diverse DNA transactions in the cell. RPA is a heterotrimeric protein with seven globular domains connected by flexible linkers, which enable substantial inter-domain motion that is essential to its function. Small angle X-ray scattering (SAXS) experiments on two multi-domain constructs from the N-terminus of the large subunit (RPA70) were used to examine the structural dynamics of these domains and their response to the binding of ssDNA. The SAXS data combined with molecular dynamics simulations reveal substantial interdomain flexibility for both RPA70AB (the tandem high affinity ssDNA binding domains A and B connected by a 10-residue linker) and RPA70NAB (RPA70AB extended by a 70-residue linker to the RPA70N protein interaction domain). Binding of ssDNA to RPA70NAB reduces the interdomain flexibility between the A and B domains, but has no effect on RPA70N. These studies provide the first direct measurements of changes in orientation of these three RPA domains upon binding ssDNA. The results support a model in which RPA70N remains structurally independent of RPA70AB in the DNA bound state and therefore freely available to serve as a protein recruitment module.

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

    Office of Scientific and Technical Information (OSTI)

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

  1. HF-based etching processes for improving laser damage resistance of fused silica optical surfaces

    SciTech Connect (OSTI)

    Suratwala, T I; Miller, P E; Bude, J D; Steele, R A; Shen, N; Monticelli, M V; Feit, M D; Laurence, T A; Norton, M A; Carr, C W; Wong, L L

    2010-02-23

    The effect of various HF-based etching processes on the laser damage resistance of scratched fused silica surfaces has been investigated. Conventionally polished and subsequently scratched fused silica plates were treated by submerging in various HF-based etchants (HF or NH{sub 4}F:HF at various ratios and concentrations) under different process conditions (e.g., agitation frequencies, etch times, rinse conditions, and environmental cleanliness). Subsequently, the laser damage resistance (at 351 or 355 nm) of the treated surface was measured. The laser damage resistance was found to be strongly process dependent and scaled inversely with scratch width. The etching process was optimized to remove or prevent the presence of identified precursors (chemical impurities, fracture surfaces, and silica-based redeposit) known to lead to laser damage initiation. The redeposit precursor was reduced (and hence the damage threshold was increased) by: (1) increasing the SiF{sub 6}{sup 2-} solubility through reduction in the NH4F concentration and impurity cation impurities, and (2) improving the mass transport of reaction product (SiF{sub 6}{sup 2-}) (using high frequency ultrasonic agitation and excessive spray rinsing) away from the etched surface. A 2D finite element crack-etching and rinsing mass transport model (incorporating diffusion and advection) was used to predict reaction product concentration. The predictions are consistent with the experimentally observed process trends. The laser damage thresholds also increased with etched amount (up to {approx}30 {micro}m), which has been attributed to: (1) etching through lateral cracks where there is poor acid penetration, and (2) increasing the crack opening resulting in increased mass transport rates. With the optimized etch process, laser damage resistance increased dramatically; the average threshold fluence for damage initiation for 30 {micro}m wide scratches increased from 7 to 41 J/cm{sup 2}, and the statistical probability of damage initiation at 12 J/cm{sup 2} of an ensemble of scratches decreased from {approx}100 mm{sup -1} of scratch length to {approx}0.001 mm{sup -1}.

  2. Attenuation due to hysteretic damage in the free vibration of a beam

    SciTech Connect (OSTI)

    Mendelsohn, Daniel A.; Pecorari, Claudio

    2014-02-18

    We present an asymptotic analysis of nonlinear free vibration of a beam with a damage plane represented by nonlinear hysteretic bending and shear springs. The perturbation parameter is the product of the ratio of the nonlinear to linear parts of the stiffness times the amplitude of the free vibration. The loss of energy and ensuing attenuation due to hysteresis is accounted for by reducing the amplitude of vibration after each cycle by an amount such that the loss in total system energy equals the work done to traverse the hysteresis loop. A new Fourier representation for each cycle of the hysteresis and the deflection solution is used for this purpose and leads to higher harmonics, an evolving complex stiffness and corrected natural frequency that are linked to the attenuation. The frequency increases to its linear value from an initially reduced value. The damage parameter, frequency shift and fundamental amplitudes are presented as functions of the initial damage parameter and time (cycles of vibration). The amplitudes of several of the higher harmonics are also presented as functions of time. Many of the results exhibit sufficient sensitivity with respect to the damage parameter that they should be able to be used to characterize the damage.

  3. Damaged Spent Nuclear Fuel at U.S. DOE Facilities Experience and Lessons Learned

    SciTech Connect (OSTI)

    Brett W. Carlsen; Eric Woolstenhulme; Roger McCormack

    2005-11-01

    From a handling perspective, any spent nuclear fuel (SNF) that has lost its original technical and functional design capabilities with regard to handling and confinement can be considered as damaged. Some SNF was damaged as a result of experimental activities and destructive examinations; incidents during packaging, handling, and transportation; or degradation that has occurred during storage. Some SNF was mechanically destroyed to protect proprietary SNF designs. Examples of damage to the SNF include failed cladding, failed fuel meat, sectioned test specimens, partially reprocessed SNFs, over-heated elements, dismantled assemblies, and assemblies with lifting fixtures removed. In spite of the challenges involved with handling and storage of damaged SNF, the SNF has been safely handled and stored for many years at DOE storage facilities. This report summarizes a variety of challenges encountered at DOE facilities during interim storage and handling operations along with strategies and solutions that are planned or were implemented to ameliorate those challenges. A discussion of proposed paths forward for moving damaged and nondamaged SNF from interim storage to final disposition in the geologic repository is also presented.

  4. Thermal conductivity measurements via time-domain thermoreflectance for the characterization of radiation induced damage

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

    Cheaito, Ramez; Gorham, Caroline S.; Carnegie Mellon Univ., Pittsburgh, PA; Misra, Amit; Hattar, Khalid; Hopkins, Patrick E.

    2015-05-01

    The progressive build up of displacement damage and fission products inside different systems and components of a nuclear reactor can lead to significant defect formation, degradation, and damage of the constituent materials. This structural modification can highly influence the thermal transport mechanisms and various mechanical properties of solids. In this paper we demonstrate the use of time-domain thermoreflectance (TDTR), a non-destructive method capable of measuring the thermal transport in material systems from nano to bulk scales, to study the effect of radiation damage and the subsequent changes in the thermal properties of materials. We use TDTR to show that displacementmore » damage from ion irradiation can significantly reduce the thermal conductivity of Optimized ZIRLO, a material used as fuel cladding in several current nuclear reactors. We find that the thermal conductivity of copper-niobium nanostructured multilayers does not change with helium ion irradiation doses of up to 1015 cm-2 and ion energy of 200 keV suggesting that these structures can be used and radiation tolerant materials in nuclear reactors. We compare the effect of ion doses and ion beam energies on the measured thermal conductivity of bulk silicon. Results demonstrate that TDTR thermal measurements can be used to quantify depth dependent damage.« less

  5. Thermal conductivity measurements via time-domain thermoreflectance for the characterization of radiation induced damage

    SciTech Connect (OSTI)

    Cheaito, Ramez; Gorham, Caroline S.; Misra, Amit; Hattar, Khalid; Hopkins, Patrick E.

    2015-05-01

    The progressive build up of displacement damage and fission products inside different systems and components of a nuclear reactor can lead to significant defect formation, degradation, and damage of the constituent materials. This structural modification can highly influence the thermal transport mechanisms and various mechanical properties of solids. In this paper we demonstrate the use of time-domain thermoreflectance (TDTR), a non-destructive method capable of measuring the thermal transport in material systems from nano to bulk scales, to study the effect of radiation damage and the subsequent changes in the thermal properties of materials. We use TDTR to show that displacement damage from ion irradiation can significantly reduce the thermal conductivity of Optimized ZIRLO, a material used as fuel cladding in several current nuclear reactors. We find that the thermal conductivity of copper-niobium nanostructured multilayers does not change with helium ion irradiation doses of up to 1015 cm-2 and ion energy of 200 keV suggesting that these structures can be used and radiation tolerant materials in nuclear reactors. We compare the effect of ion doses and ion beam energies on the measured thermal conductivity of bulk silicon. Results demonstrate that TDTR thermal measurements can be used to quantify depth dependent damage.

  6. Assessment of damage to the desert surfaces of Kuwait due to the Gulf War

    SciTech Connect (OSTI)

    El-Baz, F. . Center for Remote Sensing); Al-Ajmi, D. . Environmental and Earth Sciences Div.)

    1993-01-01

    This is a preliminary report on a joint research project by Boston University and the Kuwait Institute for Scientific Research that commenced in April 1992. The project aim is to establish the extent and nature of environmental damage to the desert surface and coastal zone of Kuwait due to the Gulf War and its aftermath. Change detection image enhancement techniques were employed to enhance environmental change by comparison of Landsat Thematic Mapper images obtained before the wars and after the cessation of the oil and well fires. Higher resolution SPOT images were also utilized to evaluate the nature of the environmental damage to specific areas. The most prominent changes were due to: (1) the deposition of oil and course-grained soot on the desert surface as a result of oil rain'' from the plume that emanated from the oil well fires; (2) the formation of hundreds of oil lakes, from oil seepage at the damaged oil well heads; (3) the mobilization of sand and dust and (4) the pollution of segments of the coastal zone by the deposition of oil from several oil spills. Interpretation of satellite image data are checked in the field to confirm the observations, and to assess the nature of the damage. Final results will be utilized in establishing the needs for remedial action to counteract the harmful effects of the various types of damage to the environment of Kuwait.

  7. The Uniaxial Tensile Response of Porous and Microcracked Ceramic Materials

    SciTech Connect (OSTI)

    Pandey, Amit; Shyam, Amit; Watkins, Thomas R; Lara-Curzio, Edgar; Lara-Curzio, Edgar; Stafford, Randall; Hemker, Kevin J

    2014-01-01

    The uniaxial tensile stress-strain behavior of three porous ceramic materials was determined at ambient conditions. Test specimens in the form of thin beams were obtained from the walls of diesel particulate filter honeycombs and tested using a microtesting system. A digital image correlation technique was used to obtain full-field 2D in-plane surface displacement maps during tensile loading, and in turn, the 2D strains obtained from displacement fields were used to determine the Secant modulus, Young s modulus and initial Poisson s ratio of the three porous ceramic materials. Successive unloading-reloading experiments were performed at different levels of stress to decouple the linear elastic, anelastic and inelastic response in these materials. It was found that the stress-strain response of these materials was non-linear and that the degree of nonlinearity is related to the initial microcrack density and evolution of damage in the material.

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

    SciTech Connect (OSTI)

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

    2013-01-17

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

  9. Structural response synthesis

    SciTech Connect (OSTI)

    Ozisik, H.; Keltie, R.F.

    1988-12-01

    The open loop control technique of predicting a conditioned input signal based on a specified output response for a second order system has been analyzed both analytically and numerically to gain a firm understanding of the method. Differences between this method of control and digital closed loop control using pole cancellation were investigated as a follow up to previous experimental work. Application of the technique to diamond turning using a fast tool is also discussed.

  10. Response Resources Demonstration

    Energy Savers [EERE]

    Interoperability of Demand Response Resources Demonstration in NY Final Technical Report Award Number: DE-FC26-08NT02869 Project Type: Regional Demonstration Principal Investigator: Andre Wellington, Project Manager, Smart Grid Implementation Group Recipient: Consolidated Edison Company of New York, Inc. Team members: Innoventive Power and Verizon Communications Consolidated Edison Company of New York, Inc. Taxpayer ID Number: 13-5009340 Organizational DUNS: 00-698-2359 4 Irving Place New York,

  11. Roles and Responsibilities

    Energy Savers [EERE]

    Partnership Ombudsman - Roles, Responsibilities, Authorities and Accountabilities Prepared by the Technology Partnership Ombudsman The purpose of this document is to provide guidance for the performance of the Technology Partnership Ombudsman function at the national laboratories and facilities within the Department of Energy, and to implement the requirements of the Technology Transfer Commercialization Act of 2000. Each national laboratory is required, and other facilities may be required, to

  12. Climate Change Response

    Office of Environmental Management (EM)

    Interior Climate Change Response "From the Everglades to the Great Lakes to Alaska and everywhere in between, climate change is a leading threat to natural and cultural resources across America, and tribal communities are often the hardest hit by severe weather events such as droughts, floods and wildfires" - Secretary of the Interior Sally Jewell "Impacts of climate change are increasingly evident for American Indian and Alaska Native communities and, in some cases, threaten the

  13. Process of labeling specific chromosomes using recombinant repetitive DNA

    DOE Patents [OSTI]

    Moyzis, R.K.; Meyne, J.

    1988-02-12

    Chromosome preferential nucleotide sequences are first determined from a library of recombinant DNA clones having families of repetitive sequences. Library clones are identified with a low homology with a sequence of repetitive DNA families to which the first clones respectively belong and variant sequences are then identified by selecting clones having a pattern of hybridization with genomic DNA dissimilar to the hybridization pattern shown by the respective families. In another embodiment, variant sequences are selected from a sequence of a known repetitive DNA family. The selected variant sequence is classified as chromosome specific, chromosome preferential, or chromosome nonspecific. Sequences which are classified as chromosome preferential are further sequenced and regions are identified having a low homology with other regions of the chromosome preferential sequence or with known sequences of other family members and consensus sequences of the repetitive DNA families for the chromosome preferential sequences. The selected low homology regions are then hybridized with chromosomes to determine those low homology regions hybridized with a specific chromosome under normal stringency conditions.

  14. New Catalytic DNA Biosensors for Radionuclides and Metal ion

    SciTech Connect (OSTI)

    Yi Lu

    2008-03-01

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

  15. Load responsive hydrodynamic bearing

    DOE Patents [OSTI]

    Kalsi, Manmohan S. (Houston, TX); Somogyi, Dezso (Sugar Land, TX); Dietle, Lannie L. (Stafford, TX)

    2002-01-01

    A load responsive hydrodynamic bearing is provided in the form of a thrust bearing or journal bearing for supporting, guiding and lubricating a relatively rotatable member to minimize wear thereof responsive to relative rotation under severe load. In the space between spaced relatively rotatable members and in the presence of a liquid or grease lubricant, one or more continuous ring shaped integral generally circular bearing bodies each define at least one dynamic surface and a plurality of support regions. Each of the support regions defines a static surface which is oriented in generally opposed relation with the dynamic surface for contact with one of the relatively rotatable members. A plurality of flexing regions are defined by the generally circular body of the bearing and are integral with and located between adjacent support regions. Each of the flexing regions has a first beam-like element being connected by an integral flexible hinge with one of the support regions and a second beam-like element having an integral flexible hinge connection with an adjacent support region. A least one local weakening geometry of the flexing region is located intermediate the first and second beam-like elements. In response to application of load from one of the relatively rotatable elements to the bearing, the beam-like elements and the local weakening geometry become flexed, causing the dynamic surface to deform and establish a hydrodynamic geometry for wedging lubricant into the dynamic interface.

  16. Optimization of a low noise detection circuit for probing the structure of damage cascades with IBIC

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

    Auden, Elizabeth C.; Doyle, Barney L.; Bielejec, Edward; Vizkelethy, Gyorgy; Wampler, William R.

    2015-06-18

    Optimal detector / pre-amplifier combinations have been identified for the use of light ion IBIC (ion beam induced charge) to probe the physical structure of electrically active defects in damage cascades caused by heavy ion implantation. The ideal detector must have a sufficiently thin dead layer that incident ions will produce the majority of damage cascades in the depletion region of the detector rather than the dead layer. Detector and circuit noise must be low enough to detect the implantation of a single heavy ion as well as the decrease in the light ion IBIC signal caused by Shockley-Read-Hall recombinationmore » when the beam scans regions of the detector damaged by the heavy ion. The IBIC signals from three detectors irradiated with 750 keV He⁺ ions are measured with commercial and bespoke charge sensitive pre-amplifiers to identify the combination with the lowest noise.« less

  17. Full-length high-temperature severe fuel damage test No. 1

    SciTech Connect (OSTI)

    Rausch, W.N.; Hesson, G.M.; Pilger, J.P.; King, L.L.; Goodman, R.L.; Panisko, F.E.

    1993-08-01

    This report describes the first full-length high-temperature test (FLHT-1) performed by Pacific Northwest Laboratory (PNL) in the National Research Universal (NRU) reactor at Chalk River, Ontario, Canada. The test is part of a series of experiments being performed for the NRC as a part of their Severe Fuel Damage Program and is one of several planned for PNL`s Coolant Boilaway and Damage Progression Program. The report summarizes the test design and test plan. it also provides a summary and discussion of the data collected during the test and of the photos taken during the post-test examination. All objectives for the test were met. The key objective was to demonstrate that severe fuel damage tests on full-length fuel bundles can be safely conducted in the NRU reactor.

  18. Investigation of damage behavior of thermally sprayed coatings depending on coating thickness

    SciTech Connect (OSTI)

    Crostack, H.A.; Beller, U.

    1995-12-31

    In order to increase the lifetime of components used for diesel engines or gas turbines surfaces are coated by ceramics. In recent years it succeeded in spraying thermal barrier coatings based on zirconia up to a thickness of a few millimeters. A comparison of the damage behavior between yttria partially stabilized zirconia coatings with different thickness will be presented. The coatings are produced by atmospheric plasma spraying. The thickness is varied from 0.5 mm up to 2 mm. In order to characterize the mechanical as well as the damage processes different methods of destructive testing (tensile, bending, and loading test) are applied. Additionally, non-destructive testing methods were used to investigate the damage processes on micro structural level. The results will be discussed according to the microstructure.

  19. New perspectives on the damage estimation for buried pipeline systems due to seismic wave propagation

    SciTech Connect (OSTI)

    Pineda Porras, Omar Andrey

    2009-01-01

    Over the past three decades, seismic fragility fonnulations for buried pipeline systems have been developed following two tendencies: the use of earthquake damage scenarios from several pipeline systems to create general pipeline fragility functions; and, the use of damage scenarios from one pipeline system to create specific-system fragility functions. In this paper, the advantages and disadvantages of both tendencies are analyzed and discussed; in addition, a summary of what can be considered the new challenges for developing better pipeline seismic fragility formulations is discussed. The most important conclusion of this paper states that more efforts are needed to improve the estimation of transient ground strain -the main cause of pipeline damage due to seismic wave propagation; with relevant advances in that research field, new and better fragility formulations could be developed.

  20. Measurement of underfilm corrosion propagation by use of spotface paint damage

    SciTech Connect (OSTI)

    Jordan, D.L; Franks, L.L.; Kallend, J.S.

    1995-11-01

    A new method of paint damage for underfilm corrosion testing of painted galvanized steel was introduced. The method was based on the observation that the onset of underfilm creepback propagation in atmospheric exposures is preceded by the formation of red rust at the paint defect. Spotface panel damage, i.e., milling through organic and metallic coatings to create a large, unprotected source of red rust, was used to shorten the time needed to produce underfilm creepback in atmospheric exposures. The traditional scribe method of paint damage was used in the same tests. Statistical techniques were used to rank underfilm creepback performance on a variety of painted metallic coated steels and to provide rank correlations between scribe and spotface data. Spotface data collected at six months provided similar rankings and discriminating ability as scribe data collected after a 30 month atmospheric exposure.