National Library of Energy BETA

Sample records for dna damage response

  1. Cellular responses to environmental DNA damage

    SciTech Connect

    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

    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

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

    SciTech Connect

    Ganesan, Shanthi Keating, Aileen F.

    2015-02-01

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

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  6. Sirtuin 7 promotes cellular survival following genomic stress by attenuation of DNA damage, SAPK activation and p53 response

    SciTech Connect

    Kiran, Shashi; Oddi, Vineesha; Ramakrishna, Gayatri

    2015-02-01

    Maintaining the genomic integrity is a constant challenge in proliferating cells. Amongst various proteins involved in this process, Sirtuins play a key role in DNA damage repair mechanisms in yeast as well as mammals. In the present work we report the role of one of the least explored Sirtuin viz., SIRT7, under conditions of genomic stress when treated with doxorubicin. Knockdown of SIRT7 sensitized osteosarcoma (U2OS) cells to DNA damage induced cell death by doxorubicin. SIRT7 overexpression in NIH3T3 delayed cell cycle progression by causing delay in G1 to S transition. SIRT7 overexpressing cells when treated with low dose of doxorubicin (0.25 µM) showed delayed onset of senescence, lesser accumulation of DNA damage marker γH2AX and lowered levels of growth arrest markers viz., p53 and p21 when compared to doxorubicin treated control GFP expressing cells. Resistance to DNA damage following SIRT7 overexpression was also evident by EdU incorporation studies where cellular growth arrest was significantly delayed. When treated with higher dose of doxorubicin (>1 µM), SIRT7 conferred resistance to apoptosis by attenuating stress activated kinases (SAPK viz., p38 and JNK) and p53 response thereby shifting the cellular fate towards senescence. Interestingly, relocalization of SIRT7 from nucleolus to nucleoplasm together with its co-localization with SAPK was an important feature associated with DNA damage. SIRT7 mediated resistance to doxorubicin induced apoptosis and senescence was lost when p53 level was restored by nutlin treatment. Overall, we propose SIRT7 attenuates DNA damage, SAPK activation and p53 response thereby promoting cellular survival under conditions of genomic stress. - Highlights: • Knockdown of SIRT7 sensitized cells to DNA damage induced apoptosis. • SIRT7 delayed onset of premature senescence by attenuating DNA damage response. • Overexpression of SIRT7 delayed cell cycle progression by delaying G1/S transition. • Upon DNA damage SIRT

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

    SciTech Connect

    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.

  8. Polychlorinated biphenyl quinone induces oxidative DNA damage and repair responses: The activations of NHEJ, BER and NER via ATM-p53 signaling axis

    SciTech Connect

    Dong, Hui; Shi, Qiong; Song, Xiufang; Fu, Juanli; Hu, Lihua; Xu, Demei; Su, Chuanyang; Xia, Xiaomin; Song, Erqun; Song, Yang

    2015-07-01

    Our previous studies demonstrated that polychlorinated biphenyl (PCB) quinone induced oxidative DNA damage in HepG2 cells. To promote genomic integrity, DNA damage response (DDR) coordinates cell-cycle transitions, DNA repair and apoptosis. PCB quinone-induced cell cycle arrest and apoptosis have been documented, however, whether PCB quinone insult induce DNA repair signaling is still unknown. In this study, we identified the activation of DDR and corresponding signaling events in HepG2 cells upon the exposure to a synthetic PCB quinone, PCB29-pQ. Our data illustrated that PCB29-pQ induces the phosphorylation of p53, which was mediated by ataxia telangiectasia mutated (ATM) protein kinase. The observed phosphorylated histone H2AX (γ-H2AX) foci and the elevation of 8-hydroxy-2′-deoxyguanosine (8-OHdG) indicated that DDR was stimulated by PCB29-pQ treatment. Additionally, we found PCB29-pQ activates non-homologous end joining (NHEJ), base excision repair (BER) and nucleotide excision repair (NER) signalings. However, these repair pathways are not error-free processes and aberrant repair of DNA damage may cause the potential risk of carcinogenesis and mutagenesis. - Highlights: • Polychlorinated biphenyl quinone induces oxidative DNA damage in HepG2 cells. • The elevation of γ-H2AX and 8-OHdG indicates the activation of DNA damage response. • ATM-p53 signaling acts as the DNA damage sensor and effector. • Polychlorinated biphenyl quinone activates NHEJ, BER and NER signalings.

  9. Method for assaying clustered DNA damages

    DOEpatents

    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.

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

    SciTech Connect

    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

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

    SciTech Connect

    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.

  12. ZRBA1, a Mixed EGFR/DNA Targeting Molecule, Potentiates Radiation Response Through Delayed DNA Damage Repair Process in a Triple Negative Breast Cancer Model

    SciTech Connect

    Heravi, Mitra; Kumala, Slawomir; Rachid, Zakaria; Jean-Claude, Bertrand J.; Radzioch, Danuta; Muanza, Thierry M.

    2015-06-01

    Purpose: ZRBA1 is a combi-molecule designed to induce DNA alkylating lesions and to block epidermal growth factor receptor (EGFR) TK domain. Inasmuch as ZRBA1 downregulates the EGFR TK-mediated antisurvival signaling and induces DNA damage, we postulated that it might be a radiosensitizer. The aim of this study was to further investigate the potentiating effect of ZRBA1 in combination with radiation and to elucidate the possible mechanisms of interaction between these 2 treatment modalities. Methods and Materials: The triple negative human breast MDA-MB-468 cancer cell line and mouse mammary cancer 4T1 cell line were used in this study. Clonogenic assay, Western blot analysis, and DNA damage analysis were performed at multiple time points after treatment. To confirm our in vitro findings, in vivo tumor growth delay assay was performed. Results: Our results show that a combination of ZRBA1 and radiation increases the radiation sensitivity of both cell lines significantly with a dose enhancement factor of 1.56, induces significant numbers of DNA strand breaks, prolongs higher DNA damage up to 24 hours after treatment, and significantly increases tumor growth delay in a syngeneic mouse model. Conclusions: Our data suggest that the higher efficacy of this combination could be partially due to increased DNA damage and delayed DNA repair process and to the inhibition of EGFR. The encouraging results of this combination demonstrated a significant improvement in treatment efficiency and therefore could be applicable in early clinical trial settings.

  13. DNA damage checkpoint recovery and cancer development

    SciTech Connect

    Wang, Haiyong; Zhang, Xiaoshan; Teng, Lisong; Legerski, Randy J.

    2015-06-10

    Cell cycle checkpoints were initially presumed to function as a regulator of cell cycle machinery in response to different genotoxic stresses, and later found to play an important role in the process of tumorigenesis by acting as a guard against DNA over-replication. As a counterpart of checkpoint activation, the checkpoint recovery machinery is working in opposition, aiming to reverse the checkpoint activation and resume the normal cell cycle. The DNA damage response (DDR) and oncogene induced senescence (OIS) are frequently found in precancerous lesions, and believed to constitute a barrier to tumorigenesis, however, the DDR and OIS have been observed to be diminished in advanced cancers of most tissue origins. These findings suggest that when progressing from pre-neoplastic lesions to cancer, DNA damage checkpoint barriers are overridden. How the DDR checkpoint is bypassed in this process remains largely unknown. Activated cytokine and growth factor-signaling pathways were very recently shown to suppress the DDR and to promote uncontrolled cell proliferation in the context of oncovirus infection. In recent decades, data from cell line and tumor models showed that a group of checkpoint recovery proteins function in promoting tumor progression; data from patient samples also showed overexpression of checkpoint recovery proteins in human cancer tissues and a correlation with patients' poor prognosis. In this review, the known cell cycle checkpoint recovery proteins and their roles in DNA damage checkpoint recovery are reviewed, as well as their implications in cancer development. This review also provides insight into the mechanism by which the DDR suppresses oncogene-driven tumorigenesis and tumor progression. - Highlights: • DNA damage checkpoint works as a barrier to cancer initiation. • DDR machinary response to genotoxic and oncogenic stress in similar way. • Checkpoint recovery pathways provide active signaling in cell cycle control. • Checkpoint

  14. 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

    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 β (TGFβ) 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 TGFβ pathways initiated by low and high LET radiation. We will characterize ATM and TGFβ 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 TGFβ 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

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

    SciTech Connect

    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.

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

    DOE PAGES [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 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

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

    SciTech Connect

    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 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

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    DOEpatents

    McCutchen-Maloney, Sandra L.

    2002-01-01

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

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

    DOE PAGES [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 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

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

    SciTech Connect

    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.

  3. Capturing snapshots of APE1 processing DNA damage

    SciTech Connect

    Freudenthal, Bret D.; Beard, William A.; Cuneo, Matthew J.; Dyrkheeva, Nadezhda S.; Wilson, Samuel H.

    2015-10-12

    DNA apurinic-apyrimidinic (AP) sites are prevalent noncoding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA-repair intermediate that is potentially cytotoxic. The molecular events of the incision reaction remain elusive, owing in part to limited structural information. Here we report multiple high-resolution human APE1-DNA structures that divulge new features of the APE1 reaction, including the metal-binding site, the nucleophile and the arginine clamps that mediate product release. We also report APE1-DNA structures with a T-G mismatch 5' to the AP site, representing a clustered lesion occurring in methylated CpG dinucleotides. Moreover, these structures reveal that APE1 molds the T-G mismatch into a unique Watson-Crick-like geometry that distorts the active site, thus reducing incision. Finally, these snapshots provide mechanistic clarity for APE1 while affording a rational framework to manipulate biological responses to DNA damage.

  4. Capturing snapshots of APE1 processing DNA damage

    DOE PAGES [OSTI]

    Freudenthal, Bret D.; Beard, William A.; Cuneo, Matthew J.; Dyrkheeva, Nadezhda S.; Wilson, Samuel H.

    2015-10-12

    DNA apurinic-apyrimidinic (AP) sites are prevalent noncoding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA-repair intermediate that is potentially cytotoxic. The molecular events of the incision reaction remain elusive, owing in part to limited structural information. Here we report multiple high-resolution human APE1-DNA structures that divulge new features of the APE1 reaction, including the metal-binding site, the nucleophile and the arginine clamps that mediate product release. We also report APE1-DNA structures with a T-G mismatch 5' to the AP site, representing a clustered lesion occurring in methylatedmore » CpG dinucleotides. Moreover, these structures reveal that APE1 molds the T-G mismatch into a unique Watson-Crick-like geometry that distorts the active site, thus reducing incision. Finally, these snapshots provide mechanistic clarity for APE1 while affording a rational framework to manipulate biological responses to DNA damage.« less

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    DOEpatents

    McCutchen-Maloney, Sandra L.

    2002-01-01

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

  8. 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 ... Sponsoring Org: USDOE Country of Publication: United States Language: ENGLISH Word Cloud ...

  9. The effects of male age on sperm DNA damage in healthy non-smokers

    SciTech Connect

    Schmid, T; Eskenazi, B; Baumgartner, A; Marchetti, F; Young, S; Weldon, R; Anderson, D; Wyrobek, A

    2006-03-08

    The trend for men to have children at older ages raises concerns that advancing age may increase the production of genetically defective sperm, increasing the risks of transmitting germ-line mutations. We investigated the associations between male age and sperm DNA damage and the influence of several lifestyle factors in a healthy non-clinical group of 80 non-smokers (age: 22-80) with no known fertility problems using the sperm Comet analyses. The average percent of DNA that migrated out of the sperm nucleus under alkaline electrophoresis increased with age (0.18% per year, p=0.006); but there was no age association for damage measured under neutral conditions (p=0.7). Men who consumed >3 cups coffee per day had {approx}20% higher % tail DNA under neutral but not alkaline conditions compared to men who consumed no caffeine (p=0.005). Our findings indicate that (a) older men have increased sperm DNA damage associated with alkali-labile sites or single-strand DNA breaks, and (b) independent of age, men with substantial daily caffeine consumption have increased sperm DNA damage associated with double-strand DNA breaks. DNA damage in sperm can be converted to chromosomal aberrations and gene mutations after fertilization increasing the risks for developmental defects and genetic diseases among offspring.

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

    Office of Scientific and Technical Information (OSTI)

    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) ...

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

    SciTech Connect

    Zheng, Yi; Tao, Shasha; Lian, Fangru; Chau, Binh T.; Chen, Jie; Sun, Guifan; Fang, Deyu; Lantz, R. Clark; 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.

  12. Suppression of autophagy enhances the cytotoxicity of the DNA-damaging aromatic amine p-anilinoaniline

    SciTech Connect

    Elliott, Althea; Reiners, John J.

    2008-10-15

    p-Anilinoaniline (pAA) is an aromatic amine that is widely used in hair dying applications. It is also a metabolite of metanil yellow, an azo dye that is commonly used as a food coloring agent. Concentrations of pAA between 10 and 25 {mu}M were cytostatic to cultures of the normal human mammary epithelia cell line MCF10A. Concentrations {>=} 50 {mu}M were cytotoxic. Cytostatic concentrations induced transient G{sub 1} and S cell cycle phase arrests; whereas cytotoxic concentrations induced protracted arrests. Cytotoxic concentrations of pAA caused DNA damage, as monitored by the alkaline single-cell gel electrophoresis (Comet) assay, and morphological changes consistent with cells undergoing apoptosis and/or autophagy. Enzymatic and western blot analyses, and binding analyses of fluorescent labeled VAD-FMK, suggested that caspase family members were activated by pAA. Western blot analyses documented the conversion of LC3-I to LC3-II, a post-translational modification involved in the development of the autophagosome. Suppression of autophagosome formation, via knockdown of ATG7 with shRNA, prevented pAA-induced vacuolization, enhanced the activation of pro-caspase-3, and increased susceptibility of ATG7-deficient cells to the cytostatic and cytotoxic activities of markedly lower concentrations of pAA. Cells stably transfected with a nonsense shRNA behaved like parental MCF10A cells. Collectively, these data suggest that MCF10A cultures undergo autophagy as a pro-survival response to concentrations of pAA sufficient to induce DNA damage.

  13. An immunochemical approach to the study of DNA damage and repair

    SciTech Connect

    Wallace, S.S.; Erlanger, B.F. . Dept. of Microbiology and Molecular Genetics; Columbia Univ., New York, NY . Dept. of Microbiology)

    1989-01-01

    The most studied radiation-induced modified DNA base is thymine glycol. Thymine glycols are produced in relatively high yields in irradiated DNA and are also formed as a consequence of oxidative stress. Thymine glycol has been shown to be an in vitro replicative block to DNA polymerases as well as a cytotoxic lesion. DNA glycosylases that remove thymine glycol from damaged DNA are found in both prokaryotes an deukaryotes. Thus this lesion provides a good model for studying the potential biological consequences of pyrimidine ring saturation products. In order to elicit antibodies that would react with unique modified base on a damaged DNA molecule, we have chosen to chemically synthesize the hapten of interest and conjugate it to a protein carrier. Thymine glycol monophosphate was synthesized, conjugated by the carbodiimide method to bovine serum albumin (BSA), and used as an immunogen. Initially, polyclonal antibodies were produced in rabbits. These antibodies had high affinity and specificity as measured by both albumin (RSA) and by enzyme immunoassay using either the conjugate or DNA oxidized inhibited by thymine glycol, thymidine glycol and thymine glycol monophosphate determinants for the phosphate group in addition to the thymidine glycol. In both the direct and competitive assays, this antibody reacts with osmium tetroxide-treated DNA containing cis-thymine glycols and DNA X-irradiated in vitro at a femtomole level of sensitivity. 24 refs.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  16. Radiation-induced DNA damage and the relative biological effectiveness of 18F-FDG in wild-type mice

    DOE PAGES [OSTI]

    Taylor, Kristina; Lemon, Jennifer A.; Boreham, Douglas R.

    2014-05-28

    Clinically, the most commonly used positron emission tomography (PET) radiotracer is the glucose analog 2-[18F] fluoro-2-deoxy-d-glucose (18F-FDG), however little research has been conducted on the biological effects of 18F-FDG injections. The induction and repair of DNA damage and the relative biological effectiveness (RBE) of radiation from 18F-FDG relative to 662 keV γ-rays were investigated. The study also assessed whether low-dose radiation exposure from 18F-FDG was capable of inducing an adaptive response. DNA damage to the bone marrow erythroblast population was measured using micronucleus formation and lymphocyte γH2A.X levels. To test the RBE of 18F-FDG, mice were injected with a rangemore » of activities of 18F-FDG (0–14.80 MBq) or irradiated with Cs-137 γ-rays (0–100 mGy). The adaptive response was investigated 24 h after the 18F-FDG injection by 1 Gy in vivo challenge doses for micronucleated reticulocyte (MN-RET) formation or 1, 2 and 4 Gy in vitro challenges doses for γH2A.X formation. A significant increase in MN-RET formation above controls occurred following injection activities of 3.70, 7.40 or 14.80 MBq (P < 0.001) which correspond to bone marrow doses of ~35, 75 and 150 mGy, respectively. Per unit dose, the Cs-137 radiation exposure induced significantly more damage than the 18F-FDG injections (RBE = 0.79 ± 0.04). A 20% reduction in γH2A.X fluorescence was observed in mice injected with a prior adapting low dose of 14.80 MBq 18F-FDG relative to controls (P < 0.019). A 0.74 MBq 18F-FDG injection, which gives mice a dose approximately equal to a typical human PET scan, did not cause a significant increase in DNA damage nor did it generate an adaptive response. Typical 18F-FDG injection activities used in small animal imaging (14.80 MBq) resulted in a decrease in DNA damage, as measured by γH2A.X formation, below spontaneous levels observed in control mice. Lastly, the 18F-FDG RBE was <1.0, indicating that the mixed radiation quality

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

    SciTech Connect

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

    2012-04-15

    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.

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

    SciTech Connect

    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.

  19. Hydroxychavicol, a betel leaf component, inhibits prostate cancer through ROS-driven DNA damage and apoptosis

    SciTech Connect

    Gundala, Sushma Reddy; Yang, Chunhua; Mukkavilli, Rao; Paranjpe, Rutugandha; Brahmbhatt, Meera; Pannu, Vaishali; Cheng, Alice; Reid, Michelle D.; Aneja, Ritu

    2014-10-01

    Dietary phytochemicals are excellent ROS-modulating agents and have been shown to effectively enhance ROS levels beyond toxic threshold in cancer cells to ensure their selective killing while leaving normal cells unscathed. Here we demonstrate that hydroxychavicol (HC), extracted and purified from Piper betel leaves, significantly inhibits growth and proliferation via ROS generation in human prostate cancer, PC-3 cells. HC perturbed cell-cycle kinetics and progression, reduced clonogenicity and mediated cytotoxicity by ROS-induced DNA damage leading to activation of several pro-apoptotic molecules. In addition, HC treatment elicited a novel autophagic response as evidenced by the appearance of acidic vesicular organelles and increased expression of autophagic markers, LC3-IIb and beclin-1. Interestingly, quenching of ROS with tiron, an antioxidant, offered significant protection against HC-induced inhibition of cell growth and down regulation of caspase-3, suggesting the crucial role of ROS in mediating cell death. The collapse of mitochondrial transmembrane potential by HC further revealed the link between ROS generation and induction of caspase-mediated apoptosis in PC-3 cells. Our data showed remarkable inhibition of prostate tumor xenografts by ∼ 72% upon daily oral administration of 150 mg/kg bw HC by quantitative tumor volume measurements and non-invasive real-time bioluminescent imaging. HC was well-tolerated at this dosing level without any observable toxicity. This is the first report to demonstrate the anti-prostate cancer efficacy of HC in vitro and in vivo, which is perhaps attributable to its selective prooxidant activity to eliminate cancer cells thus providing compelling grounds for future preclinical studies to validate its potential usefulness for prostate cancer management. - Highlights: • HC perturbs cell-cycle progression by induction of reactive oxygen species (ROS). • HC mediated cytotoxicity by ROS-induced DNA damage leading to

  20. Significant accumulation of persistent organic pollutants and dysregulation in multiple DNA damage repair pathways in the electronic-waste-exposed populations

    SciTech Connect

    He, Xiaobo; Jing, Yaqing; Wang, Jianhai; Li, Keqiu; Yang, Qiaoyun; Zhao, Yuxia; Li, Ran; Ge, Jie; Qiu, Xinghua; Li, Guang

    2015-02-15

    Electronic waste (e-waste) has created a worldwide environmental and health problem, by generating a diverse group of hazardous compounds such as persistent organic pollutants (POPs). Our previous studies demonstrated that populations from e-waste exposed region have a significantly higher level of chromosomal aberrancy and incidence of DNA damage. In this study, we further demonstrated that various POPs persisted at a significantly higher concentration in the exposed group than those in the unexposed group. The level of reactive oxygen species and micronucleus rate were also significantly elevated in the exposed group. RNA sequencing analysis revealed 31 genes in DNA damage responses and repair pathways that were differentially expressed between the two groups (Log 2 ratio >1 or <−1). Our data demonstrated that both females and males of the exposed group have activated a series of DNA damage response genes; however many important DNA repair pathways have been dysregulated. Expressions of NEIL1/3 and RPA3, which are critical in initiating base pair and nucleotide excision repairs respectively, have been downregulated in both females and males of the exposed group. In contrast, expression of RNF8, an E3 ligase involved in an error prone non-homologous end joining repair for DNA double strand break, was upregulated in both genders of the exposed group. The other genes appeared to be differentially expressed only when the males or females of the two groups were compared respectively. Importantly, the expression of cell cycle regulatory gene CDC25A that has been implicated in multiple kinds of malignant transformation was significantly upregulated among the exposed males while downregulated among the exposed females. In conclusion, our studies have demonstrated significant correlations between e-waste disposing and POPs accumulation, DNA lesions and dysregulation of multiple DNA damage repair mechanisms in the residents of the e-waste exposed region. - Highlights:

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

    SciTech Connect

    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).

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

    SciTech Connect

    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

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

    DOE PAGES [OSTI]

    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

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  7. Phorate-induced oxidative stress, DNA damage and transcriptional activation of p53 and caspase genes in male Wistar rats

    SciTech Connect

    Saquib, Quaiser; Attia, Sabry M.; Siddiqui, Maqsood A.; Aboul-Soud, Mourad A.M.; Biochemistry Department, Faculty of Agriculture, Cairo University, 12613 Giza ; Al-Khedhairy, Abdulaziz A.; Giesy, John P.; Department of Biomedical and Veterinary Biosciences and Toxicology Centre, University of Saskatchewan, Saskatoon, Canada S7N 5B3; Zoology Department and Center for Integrative Toxicology, Michigan State University, East Lansing 48824 ; Musarrat, Javed; Department of Microbiology, Faculty of Agricultural Sciences, AMU, Aligarh

    2012-02-15

    Male Wistar rats exposed to a systemic organophosphorus insecticide, phorate [O,O-diethyl S-[(ethylthio) methyl] phosphorothioate] at varying oral doses of 0.046, 0.092 or 0.184 mg phorate/kg bw for 14 days, exhibited substantial oxidative stress, cellular DNA damage and activation of apoptosis-related p53, caspase 3 and 9 genes. The histopathological changes including the pyknotic nuclei, inflammatory leukocyte infiltrations, renal necrosis, and cardiac myofiber degeneration were observed in the liver, kidney and heart tissues. Biochemical analysis of catalase and glutathione revealed significantly lesser activities of antioxidative enzymes and lipid peroxidation in tissues of phorate exposed rats. Furthermore, generation of intracellular reactive oxygen species and reduced mitochondrial membrane potential in bone marrow cells confirmed phorate-induced oxidative stress. Significant DNA damage was measured through comet assay in terms of the Olive tail moment in bone marrow cells of treated animals as compared to control. Cell cycle analysis also demonstrated the G{sub 2}/M arrest and appearance of a distinctive SubG{sub 1} peak, which signified induction of apoptosis. Up-regulation of tumor suppressor p53 and caspase 3 and 9 genes, determined by quantitative real-time PCR and enzyme-linked immunosorbent assay, elucidated the activation of intrinsic apoptotic pathways in response to cellular stress. Overall, the results suggest that phorate induces genetic alterations and cellular toxicity, which can adversely affect the normal cellular functioning in rats. -- Highlights: ► This is the first report on molecular toxicity of phorate in an in vivo test system. ► Phorate induces biochemical and histological changes in liver, kidney and heart. ► Rats treated with phorate exhibited DNA damage in bone marrow cells. ► Phorate induces apoptosis, oxidative stress and alters mitochondrial fluorescence. ► Phorate induces transcriptional changes and enhanced

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

    SciTech Connect

    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

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

    SciTech Connect

    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).

  10. Shape-dependent bactericidal activity of copper oxide nanoparticle mediated by DNA and membrane damage

    SciTech Connect

    Laha, Dipranjan; Pramanik, Arindam; Laskar, Aparna; Jana, Madhurya; Pramanik, Panchanan; Karmakar, Parimal

    2014-11-15

    Highlights: • Spherical and sheet shaped copper oxide nanoparticles were synthesized. • Physical characterizations of these nanoparticles were done by TEM, DLS, XRD, FTIR. • They showed shape dependent antibacterial activity on different bacterial strain. • They induced both membrane damage and ROS mediated DNA damage in bacteria. - Abstract: In this work, we synthesized spherical and sheet shaped copper oxide nanoparticles and their physical characterizations were done by the X-ray diffraction, fourier transform infrared spectroscopy, transmission electron microscopy and dynamic light scattering. The antibacterial activity of these nanoparticles was determined on both gram positive and gram negative bacterial. Spherical shaped copper oxide nanoparticles showed more antibacterial property on gram positive bacteria where as sheet shaped copper oxide nanoparticles are more active on gram negative bacteria. We also demonstrated that copper oxide nanoparticles produced reactive oxygen species in both gram negative and gram positive bacteria. Furthermore, they induced membrane damage as determined by atomic force microscopy and scanning electron microscopy. Thus production of and membrane damage are major mechanisms of the bactericidal activity of these copper oxide nanoparticles. Finally it was concluded that antibacterial activity of nanoparticles depend on physicochemical properties of copper oxide nanoparticles and bacterial strain.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  13. SOLAR RADIATION AND INDUCTION OF DNA DAMAGE, MUTATIONS AND SKIN CANCERS.

    SciTech Connect

    SETLOW,R.B.

    2007-05-10

    An understanding of the effects of sunlight on human skin begins with the effects on DNA and extends to cells, animals and humans. The major DNA photoproducts arising from UVB (280-320 nm) exposures are cyclobutane pyrimidine dimers. If unrepaired, they may kill or mutate cells and result in basal and squamous cell carcinomas. Although UVA (320-400 nm) and visible wavelengths are poorly absorbed by DNA, the existing data indicate clearly that exposures to these wavelengths are responsible, in an animal model, for {approx}95 % of the incidence of cutaneous malignant melanoma (CMM). Six lines of evidence, to be discussed in detail, support the photosensitizing role of melanin in the induction of this cancer. They are: (1) Melanomas induced in backcross hybrids of small tropical fish of the genus Xiphophorus, exposed to wavelengths from 302-547 nm, indicate that {approx}95% of the cancers induced by exposure to sunlight would arise from UVA + visible wavelengths; (2) The action spectrum for inducing melanin-photosensitized oxidant production is very similar to the spectrum for inducing melanoma; (3) Albino whites and blacks, although very sensitive to sunburn and the sunlight induction of non-CMM, have very low incidences of CMM; (4) The incidence of CMM as a function of latitude is very similar to that of UVA, but not UVB; (5) Use of UVA-exposing sun-tanning parlors by the young increases the incidence rate of CMM and (6) Major mutations observed in CMM are not UVB-induced.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  16. Meiotic interstrand DNA damage escapes paternal repair and causes chromosomal aberrations in the zygote by maternal misrepair

    SciTech Connect

    Marchetti, Francesco; Bishop, Jack; Gingerich, John; Wyrobek, Andrew J.

    2015-01-08

    De novo point mutations and chromosomal structural aberrations (CSA) detected in offspring of unaffected parents show a preferential paternal origin with higher risk for older fathers. Studies in rodents suggest that heritable mutations transmitted from the father can arise from either paternal or maternal misrepair of damaged paternal DNA, and that the entire spermatogenic cycle can be at risk after mutagenic exposure. Understanding the susceptibility and mechanisms of transmission of paternal mutations is important in family planning after chemotherapy and donor selection for assisted reproduction. We report that treatment of male mice with melphalan (MLP), a bifunctional alkylating agent widely used in chemotherapy, induces DNA lesions during male mouse meiosis that persist unrepaired as germ cells progress through DNA repair-competent phases of spermatogenic development. After fertilization, unrepaired sperm DNA lesions are mis-repaired into CSA by the egg's DNA repair machinery producing chromosomally abnormal offspring. In conclusion, these findings highlight the importance of both pre- and post-fertilization DNA repair in assuring the genomic integrity of the conceptus.

  17. Meiotic interstrand DNA damage escapes paternal repair and causes chromosomal aberrations in the zygote by maternal misrepair

    DOE PAGES [OSTI]

    Marchetti, Francesco; Bishop, Jack; Gingerich, John; Wyrobek, Andrew J.

    2015-01-08

    De novo point mutations and chromosomal structural aberrations (CSA) detected in offspring of unaffected parents show a preferential paternal origin with higher risk for older fathers. Studies in rodents suggest that heritable mutations transmitted from the father can arise from either paternal or maternal misrepair of damaged paternal DNA, and that the entire spermatogenic cycle can be at risk after mutagenic exposure. Understanding the susceptibility and mechanisms of transmission of paternal mutations is important in family planning after chemotherapy and donor selection for assisted reproduction. We report that treatment of male mice with melphalan (MLP), a bifunctional alkylating agent widelymore » used in chemotherapy, induces DNA lesions during male mouse meiosis that persist unrepaired as germ cells progress through DNA repair-competent phases of spermatogenic development. After fertilization, unrepaired sperm DNA lesions are mis-repaired into CSA by the egg's DNA repair machinery producing chromosomally abnormal offspring. In conclusion, these findings highlight the importance of both pre- and post-fertilization DNA repair in assuring the genomic integrity of the conceptus.« less

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

    SciTech Connect

    Wolff, S.; Afzal, V.

    1996-06-11

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

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

    Office of Scientific and Technical Information (OSTI)

    DDB2 to detect lesions refractory to detection by other damage surveillance proteins. ... Issue: (7) ; 12, 2008 Research Org: Advanced Photon Source (APS), Argonne National ...

  20. Proton pump inhibitors suppress iNOS-dependent DNA damage in Barrett's esophagus by increasing Mn-SOD expression

    SciTech Connect

    Thanan, Raynoo; Ma, Ning; Iijima, Katsunori; Abe, Yasuhiko; Koike, Tomoyuki; Shimosegawa, Tooru; Pinlaor, Somchai; Hiraku, Yusuke; Oikawa, Shinji; Murata, Mariko; Kawanishi, Shosuke

    2012-05-04

    Highlights: Black-Right-Pointing-Pointer Inflammation by Barrett's esophagus (BE) is a risk factor of its adenocarcinoma (BEA). Black-Right-Pointing-Pointer 8-Nitroguanine and 8-oxodG are inflammation-related DNA lesions. Black-Right-Pointing-Pointer DNA lesions and iNOS expression were higher in the order, BEA > BE > normal tissues. Black-Right-Pointing-Pointer Proton pump inhibitors suppress DNA damage by increasing Mn-SOD via Nrf2 activation. Black-Right-Pointing-Pointer DNA lesions can be useful biomarkers to predict risk of BEA in BE patients. -- Abstract: Barrett's esophagus (BE), an inflammatory disease, is a risk factor for Barrett's esophageal adenocarcinoma (BEA). Treatment of BE patients with proton pump inhibitors (PPIs) is expected to reduce the risk of BEA. We performed an immunohistochemical study to examine the formation of nitrative and oxidative DNA lesions, 8-nitroguanine and 8-oxo-7,8-dihydro-2 Prime -deoxygaunosine (8-oxodG), in normal esophageal, BE with pre- and post-treatment by PPIs and BEA tissues. We also observed the expression of an oxidant-generating enzyme (iNOS) and its transcription factor NF-{kappa}B, an antioxidant enzyme (Mn-SOD), its transcription factor (Nrf2) and an Nrf2 inhibitor (Keap1). The immunoreactivity of DNA lesions was significantly higher in the order of BEA > BE > normal tissues. iNOS expression was significantly higher in the order of BEA > BE > normal tissues, while Mn-SOD expression was significantly lower in the order of BEA < BE < normal tissues. Interestingly, Mn-SOD expression and the nuclear localization of Nrf2 were significantly increased, and the formation of DNA lesions was significantly decreased in BE tissues after PPIs treatment for 3-6 months. Keap1 and iNOS expression was not significantly changed by the PPIs treatment in BE tissues. These results indicate that 8-nitroguanine and 8-oxodG play a role in BE-derived BEA. Additionally, PPIs treatment may trigger the activation and nuclear translocation

  1. Radiation-induced DNA damage and the relative biological effectiveness of 18F-FDG in wild-type mice

    SciTech Connect

    Taylor, Kristina; Lemon, Jennifer A.; Boreham, Douglas R.

    2014-05-28

    Clinically, the most commonly used positron emission tomography (PET) radiotracer is the glucose analog 2-[18F] fluoro-2-deoxy-d-glucose (18F-FDG), however little research has been conducted on the biological effects of 18F-FDG injections. The induction and repair of DNA damage and the relative biological effectiveness (RBE) of radiation from 18F-FDG relative to 662 keV γ-rays were investigated. The study also assessed whether low-dose radiation exposure from 18F-FDG was capable of inducing an adaptive response. DNA damage to the bone marrow erythroblast population was measured using micronucleus formation and lymphocyte γH2A.X levels. To test the RBE of 18F-FDG, mice were injected with a range of activities of 18F-FDG (0–14.80 MBq) or irradiated with Cs-137 γ-rays (0–100 mGy). The adaptive response was investigated 24 h after the 18F-FDG injection by 1 Gy in vivo challenge doses for micronucleated reticulocyte (MN-RET) formation or 1, 2 and 4 Gy in vitro challenges doses for γH2A.X formation. A significant increase in MN-RET formation above controls occurred following injection activities of 3.70, 7.40 or 14.80 MBq (P < 0.001) which correspond to bone marrow doses of ~35, 75 and 150 mGy, respectively. Per unit dose, the Cs-137 radiation exposure induced significantly more damage than the 18F-FDG injections (RBE = 0.79 ± 0.04). A 20% reduction in γH2A.X fluorescence was observed in mice injected with a prior adapting low dose of 14.80 MBq 18F-FDG relative to controls (P < 0.019). A 0.74 MBq 18F-FDG injection, which gives mice a dose approximately equal to a typical human PET scan, did not cause a significant increase in DNA damage nor did it generate an adaptive response. Typical 18F-FDG injection activities used in small animal imaging (14.80 MBq) resulted in a decrease in DNA damage, as measured by γH2A.X formation

  2. THAP5 is a DNA-binding transcriptional repressor that is regulated in melanoma cells during DNA damage-induced cell death

    SciTech Connect

    Balakrishnan, Meenakshi P.; Cilenti, Lucia; Ambivero, Camilla; Goto, Yamafumi; Takata, Minoru; Turkson, James; Li, Xiaoman Shawn; Zervos, Antonis S.

    2011-01-07

    Research highlights: {yields} THAP5 is a DNA-binding protein and a transcriptional repressor. {yields} THAP5 is induced in melanoma cells upon exposure to UV or treatment with cisplatin. {yields} THAP5 induction correlates with the degree of apoptosis in melanoma cell population. {yields} THAP5 is a pro-apoptotic protein involved in melanoma cell death. -- Abstract: THAP5 was originally isolated as a specific interactor and substrate of the mitochondrial pro-apoptotic Omi/HtrA2 protease. It is a human zinc finger protein characterized by a restricted pattern of expression and the lack of orthologs in mouse and rat. The biological function of THAP5 is unknown but our previous studies suggest it could regulate G2/M transition in kidney cells and could be involved in human cardiomyocyte cell death associated with coronary artery disease (CAD). In this report, we expanded our studies on the properties and function of THAP5 in human melanoma cells. THAP5 was expressed in primary human melanocytes as well as in all melanoma cell lines that were tested. THAP5 protein level was significantly induced by UV irradiation or cisplatin treatment, conditions known to cause DNA damage. The induction of THAP5 correlated with a significant increase in apoptotic cell death. In addition, we show that THAP5 is a nuclear protein that could recognize and bind a specific DNA motif. THAP5 could also repress the transcription of a reporter gene in a heterologous system. Our work suggests that THAP5 is a DNA-binding protein and a transcriptional repressor. Furthermore, THAP5 has a pro-apoptotic function and it was induced in melanoma cells under conditions that promoted cell death.

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

    SciTech Connect

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

    1993-08-01

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

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

    DOE PAGES [OSTI]

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

    2016-02-28

    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

  5. 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

    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.

  6. Cytotoxic and DNA-damaging effects of methyl tert-butyl ether and its metabolites on HL-60 cells in vitro

    SciTech Connect

    Tang, G.H.; Shen, Y.; Shen, H.M.

    1996-12-31

    Methyl tert-butyl ether (MTBE) is a widely used oxygenate in unleaded gasoline; however, few studies have been conducted on the toxicity of this compound. This study evaluates the cytotoxic and DNA-damaging effects of MTBE and its metabolites in a human haemopoietic cell line, HL-60. The metabolites of MTBE studied include tertiary butyl alcohol (TBA), {alpha}-hydroxyisobutyric acid (HIBA), and formaldehyde. Comet assay is used to assess DNA damage, and the cytotoxicity is investigated by lactate dehydrogenease (LDH) release. The results show no significant cytotoxic effects of MTBE, TBA, and HIBA over a concentration ranging from 1 to 30 mM. Formaldehyde, in contrast, causes a substantial LDH release at a concentration of 5 {mu}M. Hydrogen peroxide, a known oxidative agent, at concentrations ranging from 10 to 100 {mu}M, produces a significant dose-related increase in DNA damage, whereas a much higher concentration of MTBE (1 to 30 mM) is required to produce a similar observation. The genotoxic effects of TBA and HIBA appear to be identical to that of MTBE. Conversely, DNA damage is observed for formaldehyde at a relatively low concentration range (5 to 100 {mu}M). These findings suggest that MTBE and its metabolites, except formaldehyde, have relatively low cytotoxic and genotoxic effects. 16 refs., 4 figs.

  7. Final report [DNA Repair and Mutagenesis - 1999

    SciTech Connect

    Walker, Graham C.

    2001-05-30

    The meeting, titled ''DNA Repair and Mutagenesis: Mechanism, Control, and Biological Consequences'', was designed to bring together the various sub-disciplines that collectively comprise the field of DNA Repair and Mutagenesis. The keynote address was titled ''Mutability Doth Play Her Cruel Sports to Many Men's Decay: Variations on the Theme of Translesion Synthesis.'' Sessions were held on the following themes: Excision repair of DNA damage; Transcription and DNA excision repair; UmuC/DinB/Rev1/Rad30 superfamily of DNA polymerases; Cellular responses to DNA damage, checkpoints, and damage tolerance; Repair of mismatched bases, mutation; Genome-instability, and hypermutation; Repair of strand breaks; Replicational fidelity, and Late-breaking developments; Repair and mutation in challenging environments; and Defects in DNA repair: consequences for human disease and aging.

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

    DOE PAGES [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 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

    U.S. Department of Energy (DOE) - all 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

    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

    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. Mechanical Response of Stitched T300 Mat/Urethane 420 IMR Composite Laminates: Property/Orientation Dependence and Damage Evolution

    SciTech Connect

    Deng, S.; Weitsman, Y.J.

    2000-03-01

    This report presents experimental and analytical results of investigations on the mechanical response of stitched T300 mat/urethane 420 IMR composite laminates with three different lay-up configurations. Tensile tests and short-term creep and recovery tests were conducted on the laminate coupons at various orientations. The X-ray photographic technique was adopted to detect the internal damage due to external loading history. The tensile data of laminates with antisymmetric and symmetric lay-ups indicated that lay- up sequences of cross-ply laminates do not have much influence on their tensile properties. However, misalignments within the stitch-bonded plies disturb the symmetry of intended quasi-isotropic laminates and thereby cause the mechanical properties to exhibit a certain amount of angular dependence. Classic lamination theory was found to be able to provide a very good prediction of tensile properties for the stitched laminates within linear range. Creep and recovery response of laminate coupons is greatly dependent on loading angles and load levels. The internal damage of laminate coupons is also directly related to loading angles and load levels as well as loading history.

  13. DNA repair in spermatocytes and spermatids of the mouse

    SciTech Connect

    Sega, G.A.

    1982-01-01

    When male mice are exposed to chemical agents that reach the germ cells several outcomes are possible in terms of the germ cell unscheduled DNA synthesis (UDS) response and removal of DNA adducts. It is possible that: the chemical binds to the DNA and induces a UDS response with concomittant removal of DNA adducts; the chemical binds to the DNA but no UDS response is induced; or the chemical does not bind to DNA and no UDS is induced. Many mutagens have been shown to induce a UDS response in postgonial germ cell stages of the male mouse up through midspermatids, but the relationship between this UDS and the repair of genetic damage within the germ cells is still unknown. While some mutagens appear to have an effect only in germ-cell stages where no UDS occurs, others are able to induce genetic damage in stages where UDS has been induced.

  14. The cAMP signaling system inhibits the repair of {gamma}-ray-induced DNA damage by promoting Epac1-mediated proteasomal degradation of XRCC1 protein in human lung cancer cells

    SciTech Connect

    Cho, Eun-Ah; Juhnn, Yong-Sung

    2012-06-01

    Highlights: Black-Right-Pointing-Pointer cAMP signaling system inhibits repair of {gamma}-ray-induced DNA damage. Black-Right-Pointing-Pointer cAMP signaling system inhibits DNA damage repair by decreasing XRCC1 expression. Black-Right-Pointing-Pointer cAMP signaling system decreases XRCC1 expression by promoting its proteasomal degradation. Black-Right-Pointing-Pointer The promotion of XRCC1 degradation by cAMP signaling system is mediated by Epac1. -- Abstract: Cyclic AMP is involved in the regulation of metabolism, gene expression, cellular growth and proliferation. Recently, the cAMP signaling system was found to modulate DNA-damaging agent-induced apoptosis by regulating the expression of Bcl-2 family proteins and inhibitors of apoptosis. Thus, we hypothesized that the cAMP signaling may modulate DNA repair activity, and we investigated the effects of the cAMP signaling system on {gamma}-ray-induced DNA damage repair in lung cancer cells. Transient expression of a constitutively active mutant of stimulatory G protein (G{alpha}sQL) or treatment with forskolin, an adenylyl cyclase activator, augmented radiation-induced DNA damage and inhibited repair of the damage in H1299 lung cancer cells. Expression of G{alpha}sQL or treatment with forskolin or isoproterenol inhibited the radiation-induced expression of the XRCC1 protein, and exogenous expression of XRCC1 abolished the DNA repair-inhibiting effect of forskolin. Forskolin treatment promoted the ubiquitin and proteasome-dependent degradation of the XRCC1 protein, resulting in a significant decrease in the half-life of the protein after {gamma}-ray irradiation. The effect of forskolin on XRCC1 expression was not inhibited by PKA inhibitor, but 8-pCPT-2 Prime -O-Me-cAMP, an Epac-selective cAMP analog, increased ubiquitination of XRCC1 protein and decreased XRCC1 expression. Knockdown of Epac1 abolished the effect of 8-pCPT-2 Prime -O-Me-cAMP and restored XRCC1 protein level following {gamma}-ray irradiation. From

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  17. An evidence on G2/M arrest, DNA damage and caspase mediated apoptotic effect of biosynthesized gold nanoparticles on human cervical carcinoma cells (HeLa)

    SciTech Connect

    Jeyaraj, M.; Arun, R.; Sathishkumar, G.; MubarakAli, D.; Rajesh, M.; Sivanandhan, G.; Kapildev, G.; Manickavasagam, M.; Thajuddin, N.; Ganapathi, A.

    2014-04-01

    Highlights: • Gold nanoparticles (AuNPs) have been synthesized using Podophyllum hexandrum L. • AuNPs induces the oxidative stress to cell death in human cervical carcinoma cells. • It activates the caspase-cascade to cellular death. • It is actively blocks G2/M phase of cell cycle. - Abstract: Current prospect of nanobiotechnology involves in the greener synthesis of nanostructured materials particularly noble metal nanoparticles for various biomedical applications. In this study, biologically (Podophyllum hexandrum L.) synthesized crystalline gold nanoparticles (AuNPs) with the size range between 5 and 35 nm were screened for its anticancereous potential against human cervical carcinoma cells (HeLa). Stoichiometric proportion of the reaction mixture and conditions were optimized to attain stable nanoparticles with narrow size range. Different high throughput techniques like transmission electron microscope (TEM), X-ray diffraction (XRD) and UV–vis spectroscopy were adopted for the physio-chemical characterization of AuNPs. Additionally, Fourier transform infrared spectroscopy (FTIR) study revealed that the water soluble fractions present in the plant extract solely influences the reduction of AuNPs. Sublimely, synthesized AuNPs exhibits an effective in vitro anticancer activity against HeLa cells via induction of cell cycle arrest and DNA damage. Furthermore, it was evidenced that AuNPs treated cells are undergone apoptosis through the activation of caspase cascade which subsequently leads to mitochondrial dysfunction. Thereby, this study proves that biogenic colloidal AuNPs can be developed as a promising drug candidature for human cervical cancer therapy.

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

    DOE PAGES [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 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

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    DOE PAGES [OSTI]

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

    2014-04-01

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

  3. DNA ELECTROPHORESIS AT SURFACES

    SciTech Connect

    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.

  4. Probing Radiation Damage at the Molecular Level

    SciTech Connect

    Mason, N. J.; Smialek, M. A.; Moore, S. A.; Folkard, M.; Hoffmann, S. V.

    2006-12-01

    Radiation damage of DNA and other cellular components has traditionally been attributed to ionisation via direct impact of high-energy quanta or by complex radical chemistry. However recent research has shown that strand breaks in DNA may be initiated by secondary electrons and is strongly dependent upon the target DNA base identity. Such research provides the fascinating perspective that it is possible that radiation damage may be described and understood at an individual molecular level introducing new possibilites for therapy and perhaps providing an insight into the origins of life.

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

    SciTech Connect

    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.

  6. Temporal and spatial features of the formation of DNA adducts in sulfur mustard-exposed skin

    SciTech Connect

    Batal, Mohamed; Boudry, Isabelle; Mouret, Stéphane; Wartelle, Julien; Emorine, Sandy; Bertoni, Marine; Bérard, Izabel; and others

    2013-12-15

    Sulfur mustard (SM) is a chemical warfare agent that targets skin where it induces large blisters. DNA alkylation is a critical step to explain SM-induced cutaneous symptoms. We determined the kinetics of formation of main SM–DNA adducts and compare it with the development of the SM-induced pathogenesis in skin. SKH-1 mice were exposed to 2, 6 and 60 mg/kg of SM and treated skin was biopsied between 6 h and 21 days. Formation of SM DNA adducts was dose-dependent with a maximum immediately after exposure. However, adducts were persistent and still detectable 21 days post-exposure. The time-dependent formation of DNA adducts was also found to be correlated with the appearance of apoptotic cells. This temporal correlation suggests that these two early events are responsible for the severity of the damage to the skin. Besides, SM–DNA adducts were also detected in areas located next to contaminated zone, thus suggesting that SM diffuses in skin. Altogether, this work provides for the first time a clear picture of SM-induced genotoxicity using DNA adducts as a marker. - Highlights: • Sulfur mustard adducts are formed in DNA after skin exposure. • DNA damage formation is an early event in the pathological process of skin burn. • The amount of SM–DNA adducts is maximal at the earliest time point investigated. • Adducts are still detected 3 weeks after exposure. • Sulfur mustard diffuses in skin especially when large doses are applied.

  7. Identification and Characterization of a Small Inhibitory Peptide That Can Target DNA-PKcs Autophosphorylation and Increase Tumor Radiosensitivity

    SciTech Connect

    Sun Xiaonan; Yang Chunying; Liu Hai; Wang Qi; Wu Shixiu; Li Xia; Xie Tian; Brinkman, Kathryn L.; Teh, Bin S.; Butler, E. Brian; Xu Bo; Zheng, Shu

    2012-12-01

    Purpose: The DNA protein kinase catalytic subunit (DNA-PKcs) is one of the critical elements involved in the DNA damage repair process. Inhibition of DNA-PKcs results in hypersensitivity to ionizing radiation (IR); therefore, this approach has been explored to develop molecular targeted radiosensitizers. Here, we aimed to develop small inhibitory peptides that could specifically target DNA-PKcs autophosphorylation, a critical step for the enzymatic activation of the kinase in response to IR. Methods and Materials: We generated several small fusion peptides consisting of 2 functional domains, 1 an internalization domain and the other a DNA-PKcs autophosphorylation inhibitory domain. We characterized the internalization, toxicity, and radiosensitization activities of the fusion peptides. Furthermore, we studied the mechanisms of the inhibitory peptides on DNA-PKcs autophosphorylation and DNA repair. Results: We found that among several peptides, the biotin-labeled peptide 3 (BTW3) peptide, which targets DNA-PKcs threonine 2647 autophosphorylation, can abrogate IR-induced DNA-PKcs activation and cause prolonged {gamma}-H2AX focus formation. We demonstrated that BTW3 exposure led to hypersensitivity to IR in DNA-PKcs-proficient cells but not in DNA-PKcs-deficient cells. Conclusions: The small inhibitory peptide BTW3 can specifically target DNA-PKcs autophosphorylation and enhance radiosensitivity; therefore, it can be further developed as a novel class of radiosensitizer.

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

    SciTech Connect

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

    2014-10-03

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

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

    SciTech Connect

    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

  10. Decreased cell survival and DNA repair capacity after UVC irradiation in association with down-regulation of GRP78/BiP in human RSa cells

    SciTech Connect

    Zhai Ling; Kita, Kazuko . E-mail: kita@faculty.chiba-u.jp; Wano, Chieko; Wu Yuping; Sugaya, Shigeru; Suzuki, Nobuo

    2005-05-01

    In contrast to extensive studies on the roles of molecular chaperones, such as heat shock proteins, there are only a few reports about the roles of GRP78/BiP, an endoplasmic reticulum (ER) stress-induced molecular chaperone, in mammalian cell responses to DNA-damaging stresses. To investigate whether GRP78/BiP is involved in resistance to a DNA-damaging agent, UVC (principally 254 nm in wavelength), we established human cells with down-regulation of GRP78/BiP by transfection of human RSa cells with antisense cDNA for GRP78/BiP. We found that the transfected cells showed higher sensitivity to UVC-induced cell death than control cells transfected with the vector alone. In the antisense-cDNA transfected cells, the removal capacities of the two major types of UVC-damaged DNA (thymine dimers and (6-4) photoproducts) in vivo and DNA synthesis activity of whole cell extracts to repair UVC-irradiated plasmids in vitro were remarkably decreased compared with those in the control cells. Furthermore, the antisense-cDNA transfected cells also showed slightly higher sensitivity to cisplatin-induced cell death than the control cells. Cisplatin-induced DNA damage is primarily repaired by nucleotide excision repair, like UVC-induced DNA damage. The present results suggest that GRP78/BiP plays a protective role against UVC-induced cell death possibly via nucleotide excision repair, at least in the human RSa cells tested.

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

    SciTech Connect

    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.

  12. Radiation-induced p53 protein response in the A549 cell line is culture growth-phase dependent

    SciTech Connect

    Johnson, N.F.; Gurule, D.M.; Carpenter, T.R.

    1995-12-01

    One role of the p53 tumor suppressor protein has been recently revealed. Kastan, M.B. reported that p53 protein accumulates in cells exposed to ionizing radiation. The accumulation of p53 protein is in response to DNA damage, most importantly double-strand breaks, that results from exposure to ionizing radiation. The rise in cellular p53 levels is necessary for an arrest in the G{sub 1} phase of the cell cycle to provide additional time for DNA repair. The p53 response has also been demonstrated to enhance PCNA-dependent repair. p53 is thus an important regulator of the cellular response to DNA-damaging radiation. From this data, it can be concluded that the magnitude of the p53 response is not dependent on the phase of culture growth.

  13. Radiation Damage/Materials Modification

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    radiation damage materials modification Radiation DamageMaterials Modification High-energy ion irradiation is an important tool for studying radiation damage effects Materials in ...

  14. Damage identification and health monitoring of structural and...

    Office of Scientific and Technical Information (OSTI)

    Methods that use property (stiffness, mass, damping) matrix updating, detection of nonlinear response, and damage detection via neural networks are also summarized. The ...

  15. 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...

  16. 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

  17. Adaptive response induction by bacterial catalysis of nitrosation

    SciTech Connect

    Tsimis, J.; Yarosh, D.B. )

    1990-01-01

    A wide variety of distantly related bacteria have the adaptive response suggesting that they are frequently exposed to alkylating mutagens. However, the identity and source of the DNA damaging agents have not as yet been demonstrated. S-adenosyl-methionine has been proposed because it can weakly methylate DNA, but it produces only nitrogen adducts and is unlikely to induce adaptation. The authors have found that adaptive bacteria themselves produce oxygen-alkylating species by catalyzing the formation of nitroso compounds which in turn leads to induction of the adaptive response. Many strains of bacteria, especially those with the adaptive response, are able to nitrosate amines at neutral pH, where chemical nitrosation is negligible. Nitrosamines are metabolized to potent alkylating intermediates and produce DNA oxygen adducts (such as methyl phosphotriesters) in proportion to the (S{sub N}1) nature of the reaction.

  18. Response

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    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

  19. Dna Sequencing

    DOEpatents

    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.

  20. Special Section Guest Editorial: Laser Damage

    SciTech Connect

    Gruzdev, Vitaly E.; Shinn, Michelle D.

    2012-11-09

    Laser damage of optical materials, first reported in 1964, continues to limit the output energy and power of pulsed and continuous-wave laser systems. In spite of some 48 years of research in this area, interest from the international laser community to laser damage issues remains at a very high level and does not show any sign of decreasing. Moreover, it grows with the development of novel laser systems, for example, ultrafast and short-wavelength lasers that involve new damage effects and specific mechanisms not studied before. This interest is evident from the high level of attendance and presentations at the annual SPIE Laser Damage Symposium (aka, Boulder Damage Symposium) that has been held in Boulder, Colorado, since 1969. This special section of Optical Engineering is the first one devoted to the entire field of laser damage rather than to a specific part. It is prepared in response to growing interest from the international laser-damage community. Some papers in this special section were presented at the Laser Damage Symposium; others were submitted in response to the general call for papers for this special section. The 18 papers compiled into this special section represent many sides of the broad field of laser-damage research. They consider theoretical studies of the fundamental mechanisms of laser damage including laser-driven electron dynamics in solids (O. Brenk and B. Rethfeld; A. Nikiforov, A. Epifanov, and S. Garnov; T. Apostolova et al.), modeling of propagation effects for ultrashort high-intensity laser pulses (J. Gulley), an overview of mechanisms of inclusion-induced damage (M. Koldunov and A. Manenkov), the formation of specific periodic ripples on a metal surface by femtosecond laser pulses (M. Ahsan and M. Lee), and the laser-plasma effects on damage in glass (Y. Li et al). Material characterization is represented by the papers devoted to accurate and reliable measurements of absorption with special emphasis on thin films (C. Mühlig and S

  1. BuD, a helix–loop–helix DNA-binding domain for genome modification

    SciTech Connect

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

    2014-07-01

    Crystal structures of BurrH and the BurrH–DNA 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 protein–DNA 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 helix–loop–helix 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 β (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.

  2. Structure of the Human MutSa DNA Lesion Recognition Complex

    SciTech Connect

    Warren,J.; Pohlhaus, T.; Changela, A.; Iyer, R.; Modrich, P.; Beese, L.

    2007-01-01

    Mismatch repair (MMR) ensures the fidelity of DNA replication, initiates the cellular response to certain classes of DNA damage, and has been implicated in the generation of immune diversity. Each of these functions depends on MutS{alpha} (MSH2{center_dot}MSH6 heterodimer). Inactivation of this protein complex is responsible for tumor development in about half of known hereditary nonpolyposis colorectal cancer kindreds and also occurs in sporadic tumors in a variety of tissues. Here, we describe a series of crystal structures of human MutS{alpha} bound to different DNA substrates, each known to elicit one of the diverse biological responses of the MMR pathway. All lesions are recognized in a similar manner, indicating that diversity of MutS{alpha}-dependent responses to DNA lesions is generated in events downstream of this lesion recognition step. This study also allows rigorous mapping of cancer-causing mutations and furthermore suggests structural pathways for allosteric communication between different regions within the heterodimer.

  3. G2 Checkpoint Responses in Arabidopsis

    SciTech Connect

    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.

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

    DOE PAGES [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 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

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

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Presentation given at DEER 2006, August 20-24, 2006, Detroit, Michigan. Sponsored by the U.S. DOE's EERE FreedomCar and Fuel Partnership and 21st Century Truck Programs. ...

  6. Preserved DNA Damage Checkpoint Pathway Protects against Complications...

    Office of Scientific and Technical Information (OSTI)

    Ouaamari, Abdelfattah ; Dirice, Ercument ; Takatani, Tomozumi ; Keenan, Hillary A. ; Smith, Richard D. ; Church, George ; Weiss, Ron more ; Wagers, Amy J. ; Qian, Wei-Jun ; ...

  7. Quercitrin protects skin from UVB-induced oxidative damage

    SciTech Connect

    Yin, Yuanqin; Li, Wenqi; Son, Young-Ok; Sun, Lijuan; Lu, Jian; Kim, Donghern; Wang, Xin; Yao, Hua; Wang, Lei; Pratheeshkumar, Poyil; Hitron, Andrew J.; Luo, Jia; Gao, Ning; Shi, Xianglin; Zhang, Zhuo

    2013-06-01

    Exposure of the skin to ultraviolet B (UVB) radiation causes oxidative damage to skin, resulting in sunburn, photoaging, and skin cancer. It is generally believed that the skin damage induced by UV irradiation is a consequence of generation of reactive oxygen species (ROS). Recently, there is an increased interest in the use of natural products as chemopreventive agents for non-melanoma skin cancer (NMSC) due to their antioxidants and anti-inflammatory properties. Quercitrin, glycosylated form of quercetin, is the most common flavonoid in nature with antioxidant properties. The present study investigated the possible beneficial effects of quercitrin to inhibit UVB irradiation-induced oxidative damage in vitro and in vivo. Our results showed that quercitrin decreased ROS generation induced by UVB irradiation in JB6 cells. Quercitrin restored catalase expression and GSH/GSSG ratio reduced by UVB exposure, two major antioxidant enzymes, leading to reductions of oxidative DNA damage and apoptosis and protection of the skin from inflammation caused by UVB exposure. The present study demonstrated that quercitrin functions as an antioxidant against UVB irradiation-induced oxidative damage to skin. - Highlights: • Oxidative stress plays a key role in UV-induced cell and tissue injuries. • Quercitrin decreases ROS generation and restores antioxidants irradiated by UVB. • Quercitrin reduces UVB-irradiated oxidative DNA damage, apoptosis, and inflammation. • Quercitrin functions as an antioxidant against UVB-induced skin injuries.

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

    DOE PAGES [OSTI]

    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

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

    SciTech Connect

    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.; Yadava, N.; Chandra, D.

    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 mitochondrial 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

  10. Infant sex-specific placental cadmium and DNA methylation associations

    SciTech Connect

    Mohanty, April F.; Farin, Fred M.; Bammler, Theo K.; MacDonald, James W.; Afsharinejad, Zahra; Burbacher, Thomas M.; Siscovick, David S.; and others

    2015-04-15

    Background: Recent evidence suggests that maternal cadmium (Cd) burden and fetal growth associations may vary by fetal sex. However, mechanisms contributing to these differences are unknown. Objectives: Among 24 maternal-infant pairs, we investigated infant sex-specific associations between placental Cd and placental genome-wide DNA methylation. Methods: We used ANOVA models to examine sex-stratified associations of placental Cd (dichotomized into high/low Cd using sex-specific Cd median cutoffs) with DNA methylation at each cytosine-phosphate-guanine site or region. Statistical significance was defined using a false discovery rate cutoff (<0.10). Results: Medians of placental Cd among females and males were 5 and 2 ng/g, respectively. Among females, three sites (near ADP-ribosylation factor-like 9 (ARL9), siah E3 ubiquitin protein ligase family member 3 (SIAH3), and heparin sulfate (glucosamine) 3-O-sulfotransferase 4 (HS3ST4) and one region on chromosome 7 (including carnitine O-octanoyltransferase (CROT) and TP5S target 1 (TP53TG1)) were hypomethylated in high Cd placentas. Among males, high placental Cd was associated with methylation of three sites, two (hypomethylated) near MDS1 and EVI1 complex locus (MECOM) and one (hypermethylated) near spalt-like transcription factor 1 (SALL1), and two regions (both hypomethylated, one on chromosome 3 including MECOM and another on chromosome 8 including rho guanine nucleotide exchange factor (GEF) 10 (ARHGEF10). Differentially methylated sites were at or close to transcription start sites of genes involved in cell damage response (SIAH3, HS3ST4, TP53TG1) in females and cell differentiation, angiogenesis and organ development (MECOM, SALL1) in males. Conclusions: Our preliminary study supports infant sex-specific placental Cd-DNA methylation associations, possibly accounting for previously reported differences in Cd-fetal growth associations across fetal sex. Larger studies are needed to replicate and extend these

  11. Structural damage detection using the holder exponent.

    SciTech Connect

    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.

  12. Structural Damage Detection Using Slopes of Longitudinal Vibration Shapes

    DOE PAGES [OSTI]

    Xu, W.; Zhu, W. D.; Smith, S. A.; Cao, M. S.

    2016-03-18

    While structural damage detection based on flexural vibration shapes, such as mode shapes and steady-state response shapes under harmonic excitation, has been well developed, little attention is paid to that based on longitudinal vibration shapes that also contain damage information. This study originally formulates a slope vibration shape for damage detection in bars using longitudinal vibration shapes. To enhance noise robustness of the method, a slope vibration shape is transformed to a multiscale slope vibration shape in a multiscale domain using wavelet transform, which has explicit physical implication, high damage sensitivity, and noise robustness. These advantages are demonstrated in numericalmore » cases of damaged bars, and results show that multiscale slope vibration shapes can be used for identifying and locating damage in a noisy environment. A three-dimensional (3D) scanning laser vibrometer is used to measure the longitudinal steady-state response shape of an aluminum bar with damage due to reduced cross-sectional dimensions under harmonic excitation, and results show that the method can successfully identify and locate the damage. Slopes of longitudinal vibration shapes are shown to be suitable for damage detection in bars and have potential for applications in noisy environments.« less

  13. Uncertainty of silicon 1-MeV damage function

    SciTech Connect

    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.

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

    SciTech Connect

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

    2010-11-01

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

  15. BPA-2011-00384-FOIA Response

    U.S. Department of Energy (DOE) - all 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. Defects in the kinetics of the repair of DNA double-strand breaks and inhibition of DNA synthesis in the ataxia telangiectasia AT5Bl-VA cell line: Comparison to a corrected hybrid, atxbc

    SciTech Connect

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

    1995-12-01

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

  17. Convention on Supplementary Compensation for Nuclear Damage Contingent Cost Allocation, Section 934

    Energy.gov [DOE]

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

  18. Public Comment re NOI on Convention on Supplementary Compensation for Nuclear Damage

    Energy.gov [DOE]

    ENERGYSOLUTIONS' Comment in Response to Notice of Inquiry, Convention on Supplementary Compensation for Nuclear Damage Contingent Cost Allocation -75 FR 43945

  19. 8-Oxoguanine DNA glycosylase 1 (ogg1) maintains the function of cardiac progenitor cells during heart formation in zebrafish

    SciTech Connect

    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.

  20. DNA polymerase with modified processivity

    DOEpatents

    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.

  1. Microfluidic DNA sample preparation method and device

    DOEpatents

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

    2002-01-01

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

  2. Shock Initiation of Damaged Explosives

    SciTech Connect

    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.

  3. Synthesis of DNA

    DOEpatents

    Mariella, Jr., Raymond P.

    2008-11-18

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

  4. DNA encoding a DNA repair protein

    DOEpatents

    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.

  5. Cancer cells recovering from damage exhibit mitochondrial restructuring and increased aerobic glycolysis

    SciTech Connect

    Akakura, Shin; Ostrakhovitch, Elena; Sanokawa-Akakura, Reiko; Tabibzadeh, Siamak

    2014-06-13

    Highlights: • Some cancer cells recover from severe damage that causes cell death in majority of cells. • Damage-Recovered (DR) cancer cells show reduced mitochondria, mDNA and mitochondrial enzymes. • DR cells show increased aerobic glycolysis, ATP, cell proliferation, and resistance to damage. • DR cells recovered from in vivo damage also show increased glycolysis and proliferation rate. - Abstract: Instead of relying on mitochondrial oxidative phosphorylation, most cancer cells rely heavily on aerobic glycolysis, a phenomenon termed as “the Warburg effect”. We considered that this effect is a direct consequence of damage which persists in cancer cells that recover from damage. To this end, we studied glycolysis and rate of cell proliferation in cancer cells that recovered from severe damage. We show that in vitro Damage-Recovered (DR) cells exhibit mitochondrial structural remodeling, display Warburg effect, and show increased in vitro and in vivo proliferation and tolerance to damage. To test whether cancer cells derived from tumor microenvironment can show similar properties, we isolated Damage-Recovered (T{sup DR}) cells from tumors. We demonstrate that T{sup DR} cells also show increased aerobic glycolysis and a high proliferation rate. These findings show that Warburg effect and its consequences are induced in cancer cells that survive severe damage.

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

    SciTech Connect

    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.

  7. Acoustic emission sensor radiation damage threshold experiment

    SciTech Connect

    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.

  8. Quantitative DNA fiber mapping

    DOEpatents

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

    1998-01-01

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

  9. Rapid Damage Assessment Using High-resolution Remote Sensing Imagery: Tools and Techniques

    SciTech Connect

    Vatsavai, Raju; Tuttle, Mark A; Bhaduri, Budhendra L; Bright, Eddie A; Cheriyadat, Anil M; Chandola, Varun; Graesser, Jordan B

    2011-01-01

    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 growing population, as well as human migration to disaster prone regions of the world. Rapid damage assessment and dissemination of accurate information is critical for creating an effective emergency response. Remote sensing and geographic information systems (GIS) based techniques and tools are important in disaster damage assessment and reporting activities. In this review, we will look into the state of the art techniques in damage assessment using remote sensing and GIS.

  10. Diphenylarsinic acid, a chemical warfare-related neurotoxicant, promotes liver carcinogenesis via activation of aryl hydrocarbon receptor signaling and consequent induction of oxidative DAN damage in rats

    SciTech Connect

    Wei, Min; Yamada, Takanori; Yamano, Shotaro; Kato, Minoru; Kakehashi, Anna; Fujioka, Masaki; Tago, Yoshiyuki; Kitano, Mistuaki; Wanibuchi, Hideki

    2013-11-15

    Diphenylarsinic acid (DPAA), a chemical warfare-related neurotoxic organic arsenical, is present in the groundwater and soil in some regions of Japan due to illegal dumping after World War II. Inorganic arsenic is carcinogenic in humans and its organic arsenic metabolites are carcinogenic in animal studies, raising serious concerns about the carcinogenicity of DPAA. However, the carcinogenic potential of DPAA has not yet been evaluated. In the present study we found that DPAA significantly enhanced the development of diethylnitrosamine-induced preneoplastic lesions in the liver in a medium-term rat liver carcinogenesis assay. Evaluation of the expression of cytochrome P450 (CYP) enzymes in the liver revealed that DPAA induced the expression of CYP1B1, but not any other CYP1, CYP2, or CYP3 enzymes, suggesting that CYP1B1 might be the enzyme responsible for the metabolic activation of DPAA. We also found increased oxidative DNA damage, possibly due to elevated CYP1B1 expression. Induction of CYP1B1 has generally been linked with the activation of AhR, and we found that DPAA activates the aryl hydrocarbon receptor (AhR). Importantly, the promotion effect of DPAA was observed only at a dose that activated the AhR, suggesting that activation of AhR and consequent induction of AhR target genes and oxidative DNA damage plays a vital role in the promotion effects of DPAA. The present study provides, for the first time, evidence regarding the carcinogenicity of DPAA and indicates the necessity of comprehensive evaluation of its carcinogenic potential using long-term carcinogenicity studies. - Highlights: • DPAA, an environmental neurotoxicant, promotes liver carcinogenesis in rats. • DPAA is an activator of AhR signaling pathway. • DPAA promoted oxidative DNA damage in rat livers. • AhR target gene CYP 1B1 might be involved in the metabolism of DPAA.

  11. Sizing of DNA fragments by flow cytometry

    SciTech Connect

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

    1993-02-01

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

  12. Sizing of DNA fragments by flow cytometry

    SciTech Connect

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

    1993-01-01

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

  13. Boulder damage symposium annual thin film laser damage competition

    DOE PAGES [OSTI]

    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. Boulder damage symposium annual thin film laser damage competition

    SciTech Connect

    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 between 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.

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

    SciTech Connect

    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.

  16. Size selective absorption of DNA tetrahedra in ATO nanomaterials

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

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

  17. DNA tagged microparticles

    DOEpatents

    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.

  18. Incipient and Progressive Damage in Polyethylene Under Extreme Tensile Conditions

    SciTech Connect

    Furmanski, Jevan; Brown, Eric; Trujillo, Carl P.; Martinez, Daniel Tito; Gray, George T. III

    2012-06-07

    The Dynamic-Tensile-Extrusion (Dyn-Ten-Ext) test was developed at LANL by Gray and coworkers to probe the tensile response of materials at large strains (>1) and high strain-rates (>1000/s) by firing projectiles through a conical die at 300-700 m/s. This technique has recently been applied to various polymers, such as the fluoropolymers PTFE (Teflon) and the chemically similar PCTFE, which respectively exhibited catastrophic fragmentation and distributed dynamic necking. This work details investigations of the Dyn-Ten-Ext response of high density polyethylene, both to failure and sub-critical conditions. At large extrusion ratios ({approx}7.4) and high velocities, such as those previously employed, HDPE catastrophically fragmented in a craze-like manner in the extruded jet. At more modest extrusion ratios and high velocities the specimen extruded a stable jet that ruptured cleanly, and at lower velocities was recovered intact after sustaining substantial internal damage. Thermomechanical finite element simulations showed that the damage corresponded to a locus of shear stress in the presence of hydrostatic tension. X-ray computed tomography corroborated the prediction of a shear damage mechanism by finding the region of partially damaged material to consist of macroscopic shear-mode cracks nearly aligned with the extrusion axis, originating from the location of damage inception.

  19. LANL Natural Resource Damage Assessment

    Energy.gov [DOE]

    This Performance Work Statement (PWS) sets forth the tasks to be performed to complete a Natural Resource Damage Assessment (NRDA) and Restoration Plan based on injuries to natural resources from the release of hazardous substances from the Los Alamos National Laboratory (LANL).

  20. Disruption of Maternal DNA Repair Increases Sperm-DerivedChromosomal Aberrations

    SciTech Connect

    Marchetti, Francesco; Essers, Jeroun; Kanaar, Roland; Wyrobek,Andrew J.

    2007-02-07

    The final weeks of male germ cell differentiation occur in aDNA repair-deficient environment and normal development depends on theability of the egg to repair DNA damage in the fertilizing sperm. Geneticdisruption of maternal DNA double-strand break repair pathways in micesignificantly increased the frequency of zygotes with chromosomalstructural aberrations after paternal exposure to ionizing radiation.These findings demonstrate that radiation-induced DNA sperm lesions arerepaired after fertilization by maternal factors and suggest that geneticvariation in maternal DNA repair can modulate the risk of early pregnancylosses and of children with chromosomal aberrations of paternalorigin.

  1. DNA Sequencing apparatus

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1992-01-01

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

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

    SciTech Connect

    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.

  3. Damage detection in initially nonlinear systems

    SciTech Connect

    Bornn, Luke; Farrar, Charles; Park, Gyuhae

    2009-01-01

    The primary goal of Structural Health Monitoring (SHM) is to detect structural anomalies before they reach a critical level. Because of the potential life-safety and economic benefits, SHM has been widely studied over the past decade. In recent years there has been an effort to provide solid mathematical and physical underpinnings for these methods; however, most focus on systems that behave linearly in their undamaged state - a condition that often does not hold in complex 'real world' systems and systems for which monitoring begins mid-lifecycle. In this work, we highlight the inadequacy of linear-based methodology in handling initially nonlinear systems. We then show how the recently developed autoregressive support vector machine (AR-SVM) approach to time series modeling can be used for detecting damage in a system that exhibits initially nonlinear response. This process is applied to data acquired from a structure with induced nonlinearity tested in a laboratory environment.

  4. Method for producing damage resistant optics

    DOEpatents

    Hackel, Lloyd A.; Burnham, Alan K.; Penetrante, Bernardino M.; Brusasco, Raymond M.; Wegner, Paul J.; Hrubesh, Lawrence W.; Kozlowski, Mark R.; Feit, Michael D.

    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.

  5. Dynamically Driven Phase Transformations in Damaged Composite Materials

    SciTech Connect

    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.

  6. Public Comment re Convention on Supplementary Compensation for Nuclear Damage Contingent Cost Allocation

    Energy.gov [DOE]

    Comments by International Group on Nuclear Liability (CIGNL), in response to U.S. Department of Energy Notice of Inquiry on Convention on Supplementary Compensation for Nuclear Damage Contingent...

  7. EM, Tribal, and State Officials Receive Training on Restoring Damaged Natural Resources

    Energy.gov [DOE]

    NEW ORLEANS – Senior EM, Tribal, and state officials gathered for a training on the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) process for restoring resources damaged from oil spills or hazardous substance releases into the environment.

  8. Modeling of Damage, Permeability Changes and Pressure Responses...

    Office of Scientific and Technical Information (OSTI)

    ... DOE Contract Number: DE-AC02-05CH11231 Resource Type: Journal Article Resource Relation: Journal Name: Engineering Geology; Related Information: Journal Publication Date: 2009 ...

  9. Modeling of Damage, Permeability Changes and Pressure Responses...

    Office of Scientific and Technical Information (OSTI)

    the TSX Tunnel in Granitic Rock at URL, Canada Citation Details In-Document Search ... the TSX Tunnel in Granitic Rock at URL, Canada This paper presents numerical modeling of ...

  10. CO/sub 2/ formation damage study. Final report

    SciTech Connect

    Patton, J.T.

    1983-07-01

    The literature did provide insight into four possible damage mechanisms, namely: (1) precipitation of reservoir mineral in the vicinity around the producing well as carbon dioxide escapes from the water phase due to pressure draw down; (2) plugging of reservoir interstices by insoluble organic solids precipitated as the carbon dioxide dissolves in crude oil; (3) formation of an immobile gas phase, predominately CO/sub 2/, which would drastically lower the effective permeability to oil and, especially water; and (4) dissolution of cementation, especially carbonates or feldspars, that could allow fines to migrate in the reservoir and plug tiny flow passages. Each of these mechanisms was investigated in depth during the laboratory experiments. Occasional reports from industry suggested that the use of carbon dioxide to enhance the recovery of tertiary oil might be causing formation damage. This project was undertaken to define the mechanisms responsible for such occurrences. The objectives were threefold: (1) provide a comprehensive literature survey to elicit all that is currently known or suspected, relative to formation damage that might occur during the injection of carbon dioxide into an oil reservoir; (2) under simulated reservoir conditions, demonstrate in the laboratory each of the damage mechanisms and quantify the degree to which each mechanism could cause damage; and (3) for those damage mechanisms identified to be significant, develop a feasible remedy, easily applied in actual field operations. The third mechanism, related to the presence of an immobile gas phase, is a real problem but not unique to the injection of carbon dioxide. In the case of carbon dioxide, the damage should be self-correcting, as the solubility of carbon dioxide in water will eventually allow the water to dissolve away the gas and, hence, the blocking effect.

  11. A Mechanistic Approach to Damage in Short-Fiber Composites Based on Micromechanical and Continuum Damage Mechanics Descriptions

    SciTech Connect

    Nguyen, Ba Nghiep; Khaleel, Mohammad A.

    2004-04-01

    A micro-macro mechanistic approach to matrix cracking in randomly oriented short-fiber composites is developed in this paper. At the micro-scale, the virgin and reduced elastic properties of the reference aligned fiber composite are determined using micromechanical models [1-5], and are then distributed over all possible orientations in order to compute the stiffness of the random fiber composite containing random matrix microcracks. After that the macroscopic response is obtained by means of a continuum damage mechanics formulation, which extends the thermodynamics based approach in [6] to randomly oriented short-fiber composites. Damage accumulations leading to initiation and propagation of a macroscopic crack are modeled using a vanishing element technique. The model is validated against the published experimental data and results [7]. Finally, its practical application is illustrated through the damage analysis of a random glass/epoxy composite plate containing a central hole and under tensile loading.

  12. Controlling DNA Methylation

    U.S. Department of Energy (DOE) - all 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

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

    SciTech Connect

    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.

  14. DNA-cell conjugates

    DOEpatents

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

    2016-05-03

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

  15. Quantitive DNA Fiber Mapping

    SciTech Connect

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

    2008-01-28

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

  16. Correlating cookoff violence with pre-ignition damage.

    SciTech Connect

    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.

  17. DNA-PK assay

    DOEpatents

    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.

  18. Irradiation damage behavior of low alloy steel wrought and weld materials

    SciTech Connect

    Stofanak, R.J.; Poskie, T.J.; Li, Y.Y.; Wire, G.L.

    1993-10-01

    A study was undertaken to evaluate the irradiation damage response of several different types of low alloy steel: vintage type ASTM A302 Grade B (A302B) plates and welds containing different Ni and Cu concentrations, 3.5% Ni steels similar to ASTM A508 Class 4, welds containing about 1% Ni (similar to type 105S), and 3.5% Ni steels with ``superclean`` composition. All materials were irradiated at several different irradiation damage levels ranging from 0.0003 to 0.06 dpa at 232C (450F). Complete Charpy V-notch impact energy transition temperature curves were generated for all materials before and after irradiation to determine transition temperature at 4IJ (30 ft-lb) or 47J (35 ft-lb) and the upper shelf energy. Irradiation damage behavior was measured by shift in Charpy 41J or 47J transition temperature ({Delta}TT4{sub 41J} or {Delta}TT{sub 47J}) and lowering of upper shelf Charpy energy at a given irradiation damage level. It was found that chemical composition greatly influenced irradiation damage behavior; highest irradiation damage (greatest {Delta}TT) was found in an A302B type weld containing 1.28% Ni and 0.20% Cu while the least damage was found in 3.5% Ni, 0.05% Cu, superclean wrought materials. Combination of Ni and Cu was found to affect irradiation damage behavior at higher irradiation damage levels in the A302B welds where the 1.28% Ni, 0.20% Cu weld showed more damage than a 0.60% Ni, 0.31% Cu weld. For the 3.5% Ni steels, fabrication influenced irradiation behavior in that a silicon (Si) killed material showed greater irradiation damage than a low silicon material. In general, the 3.5% Ni materials with low copper showed less irradiation damage than the A302B materials.

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

    DOEpatents

    Weiss, Jonathan D.

    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.

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

    DOEpatents

    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.

  1. Multiplex analysis of DNA

    DOEpatents

    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.

  2. DNA | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

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

    SciTech Connect

    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. Patterning nanocrystals using DNA

    SciTech Connect

    Williams, Shara Carol

    2003-09-01

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

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

    SciTech Connect

    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

  6. Earthquake damage to underground facilities (Technical Report...

    Office of Scientific and Technical Information (OSTI)

    The potential seismic risk for an underground nuclear waste repository will be one of the ... Damage from documented nuclear events was also included in the study where applicable. ...

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

    SciTech Connect

    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.

  8. Quantifying uncertainty in material damage from vibrational data

    SciTech Connect

    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.

  9. Determination of laser damage initiation probability and growth on fused silica scratches

    SciTech Connect

    Norton, M A; Carr, C W; Cross, D A; Negres, R A; Bude, J D; Steele, W A; Monticelli, M V; Suratwala, T I

    2010-10-26

    Current methods for the manufacture of optical components inevitably leaves a variety of sub-surface imperfections including scratches of varying lengths and widths on even the finest finishes. It has recently been determined that these finishing imperfections are responsible for the majority of laser-induced damage for fluences typically used in ICF class lasers. We have developed methods of engineering subscale parts with a distribution of scratches mimicking those found on full scale fused silica parts. This much higher density of scratches provides a platform to measure low damage initiation probabilities sufficient to describe damage on large scale optics. In this work, damage probability per unit scratch length was characterized as a function of initial scratch width and post fabrication processing including acid-based etch mitigation processes. The susceptibility of damage initiation density along scratches was found to be strongly affected by the post etching material removal and initial scratch width. We have developed an automated processing procedure to document the damage initiations per width and per length of theses scratches. We show here how these tools can be employed to provide predictions of the performance of full size optics in laser systems operating at 351 nm. In addition we use these tools to measure the growth rate of a damage site initiated along a scratch and compare this to the growth measured on an isolated damage site.

  10. Testing model for predicting spillway cavitation damage

    SciTech Connect

    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.

  11. Tamoxifen Forms DNA Adducts In Human Colon After Administration Of A Single [14C]-Labeled Therapeutic Dose.

    SciTech Connect

    Brown, K; Tompkins, E M; Boocock, D J; Martin, E A; Farmer, P B; Turteltaub, K W; Ubick, E; Hemingway, D; Horner-Glister, E; White, I H

    2007-05-23

    Tamoxifen is widely prescribed for the treatment of breast cancer and is also licensed in the U.S. for the prevention of this disease. However, tamoxifen therapy is associated with an increased occurrence of endometrial cancer in women and there is also evidence that it may elevate the risk of colorectal cancer. The underlying mechanisms responsible for tamoxifen-induced carcinogenesis in women have not yet been elucidated but much interest has focussed on the role of DNA adduct formation. We investigated the propensity of tamoxifen to bind irreversibly to colorectal DNA when given to ten women as a single [{sup 14}C]-labeled therapeutic (20 mg) dose, {approx}18 h prior to undergoing colon resections. Using the sensitive technique of accelerator mass spectrometry, coupled with HPLC separation of enzymatically digested DNA, a peak corresponding to authentic dG-N{sup 2}-tamoxifen adduct was detected in samples from three patients, at levels ranging from 1-7 adducts/10{sup 9} nucleotides. No [{sup 14}C]-radiolabel associated with tamoxifen or its major metabolites was detected. The presence of detectable CYP3A4 protein in all colon samples suggests this tissue has the potential to activate tamoxifen to {alpha}-hydroxytamoxifen, in addition to that occurring in the systemic circulation, and direct interaction of this metabolite with DNA could account for the binding observed. Although the level of tamoxifeninduced damage displayed a degree of inter-individual variability, when present it was {approx}10-100 times higher than that reported for other suspect human colon carcinogens such as PhIP. These findings provide a mechanistic basis through which tamoxifen could increase the incidence of colon cancers in women.

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

    SciTech Connect

    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.

  13. Underground infrastructure damage for a Chicago scenario

    SciTech Connect

    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.

  14. War damages and reconstruction of Peruca dam

    SciTech Connect

    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.

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

    DOEpatents

    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.

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

    DOEpatents

    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.

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

    SciTech Connect

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

    1991-01-01

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

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

    SciTech Connect

    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.

  19. DNA tagged microparticles

    DOEpatents

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

    2016-03-22

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

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

    SciTech Connect

    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. Thin Film Femtosecond Laser Damage Competition

    SciTech Connect

    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.

  2. Laser Damage Precursors in Fused Silica

    SciTech Connect

    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.

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

    SciTech Connect

    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).

  4. Quantitative damage evaluation of localized deep pitting

    SciTech Connect

    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.

  5. Controlled ion implant damage profile for etching

    DOEpatents

    Arnold, Jr., George W.; Ashby, Carol I. H.; Brannon, Paul J.

    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.

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

    SciTech Connect

    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.

  7. Fleet DNA (Presentation)

    SciTech Connect

    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.

  8. Hardware Controller DNA Synthesizer

    Energy Science and Technology Software Center

    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.

  9. Damaged Surface Hydrodynamics (DSH) Flash Report (Technical Report...

    Office of Scientific and Technical Information (OSTI)

    Technical Report: Damaged Surface Hydrodynamics (DSH) Flash Report Citation Details In-Document Search Title: Damaged Surface Hydrodynamics (DSH) Flash Report You are accessing ...

  10. Cable Damage Detection System and Algorithms Using Time Domain Reflectometry

    SciTech Connect

    Clark, G A; Robbins, C L; Wade, K A; Souza, P R

    2009-03-24

    This report describes the hardware system and the set of algorithms we have developed for detecting damage in cables for the Advanced Development and Process Technologies (ADAPT) Program. This program is part of the W80 Life Extension Program (LEP). The system could be generalized for application to other systems in the future. Critical cables can undergo various types of damage (e.g. short circuits, open circuits, punctures, compression) that manifest as changes in the dielectric/impedance properties of the cables. For our specific problem, only one end of the cable is accessible, and no exemplars of actual damage are available. This work addresses the detection of dielectric/impedance anomalies in transient time domain reflectometry (TDR) measurements on the cables. The approach is to interrogate the cable using time domain reflectometry (TDR) techniques, in which a known pulse is inserted into the cable, and reflections from the cable are measured. The key operating principle is that any important cable damage will manifest itself as an electrical impedance discontinuity that can be measured in the TDR response signal. Machine learning classification algorithms are effectively eliminated from consideration, because only a small number of cables is available for testing; so a sufficient sample size is not attainable. Nonetheless, a key requirement is to achieve very high probability of detection and very low probability of false alarm. The approach is to compare TDR signals from possibly damaged cables to signals or an empirical model derived from reference cables that are known to be undamaged. This requires that the TDR signals are reasonably repeatable from test to test on the same cable, and from cable to cable. Empirical studies show that the repeatability issue is the 'long pole in the tent' for damage detection, because it is has been difficult to achieve reasonable repeatability. This one factor dominated the project. The two-step model-based approach is

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

    SciTech Connect

    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.

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

    SciTech Connect

    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

  13. Results from computational and experimental modeling of runaway electron damage on plasma facing components

    SciTech Connect

    Niemer, K.A.; Gilligan, J.G.; Croessmann, C.D.

    1994-11-01

    The purpose of this research was to extend the theoretical and experimental knowledge of runaway electron damage-impact-bombardment on plasma facing components and materials in magnetic fusion devices. The emphasis of this work involved computational modeling and experimental studies to investigate runaway electron energy deposition and thermal response in plasma facing materials. The goals were: (1) to develop a computational model to study and analyze runaway electron damage; (2) to characterize runaway electron parameters; and (3) to perform experiments to analyze runaway electron damage. These goals were accomplished by first assembling the PTA code package. PTA is a unique application of PATRAN, the Integrated TIGER Series (ITS), and ABAQUS for modeling high energy electron impact on magnetic fusion materials and components. The PTA code package provides a three-dimensional, time dependent, computational code package which predicts material response from runaway bombardment under most runaway conditions (i.e., electron energy, incident angle, energy density, and deposition time). As part of this research, PTA was used to study energy deposition and material response in several design applications, to analyze damaged material, and to analyze several experiments. Runaway electron characterization was determined through parametric studies, analysis of damaged materials, and analysis of experimental results. Characterization provided information on electron energy, incident angle, current, deposition time, and volume of material impacted by runaway electrons. Finally an experiment was performed on the Advanced Toroidal Facility (ATF) at Oak Ridge National Laboratory to study runaway electron damage. The experiment provided information on the runaway electron energy and current in ATF, as well as supplemented the existing experimental knowledge of runaway electron damage.

  14. Identification of Human Repetitive DNA Elements

    Energy Science and Technology Software Center

    1995-11-01

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

  15. Development of a cyclic damage evaluation method

    SciTech Connect

    Nakagawa, Y.G.; Yoshizawa, H.; Umemoto, T. )

    1990-07-01

    An effective method of measuring the state of fatigue damage accumulation in a pressure vessel, steel, A508, was identified by microstructural examinations. Selective angle diffraction (SAD), based on electron beam technique is utilized. SAD had been proved to be effective for detecting cumulative damage (CD) in samples cyclicly deformed at two levels of constant strain amplitudes. The objectives of this study are to validate the SAD method with a composite of cyclic strains simulating LWR plant service strains, and to transform the SAD method, which requires expert operation and data analysis of electron microscopy, to a nonexpert inspection procedure. Fatigue damage was induced in test bars under cyclic conditions intended to simulate the service conditions of a BWR feedwater nozzle. Three types (A, B, C) of cyclic strains were superimposed. B and C represent events associated with scram and normal transients, respectively. The degree of damage due to those events are insignificant, and thus used as pre-fatigue conditions. Type A damage originates from pressure tests and startup/shutdown events, and control the usage factor. One of the samples (Sample 11) was made to represent the case of probable CD (0.7%), for the plant life time ({approximately}40 years). Three other samples (12, 13, 14) represented the cases of cycle up to failure, having CD of 15, 43, and 100%, respectively. 19 figs., 3 tabs.

  16. Biological response modifiers

    SciTech Connect

    Weller, R.E.

    1991-10-01

    Much of what used to be called immunotherapy is now included in the term biological response modifiers. Biological response modifiers (BRMs) are defined as those agents or approaches that modify the relationship between the tumor and host by modifying the host's biological response to tumor cells with resultant therapeutic effects.'' Most of the early work with BRMs centered around observations of spontaneous tumor regression and the association of tumor regression with concurrent bacterial infections. The BRM can modify the host response in the following ways: Increase the host's antitumor responses through augmentation and/or restoration of effector mechanisms or mediators of the host's defense or decrease the deleterious component by the host's reaction; Increase the host's defenses by the administration of natural biologics (or the synthetic derivatives thereof) as effectors or mediators of an antitumor response; Augment the host's response to modified tumor cells or vaccines, which might stimulate a greater response by the host or increase tumor-cell sensitivity to an existing response; Decrease the transformation and/or increase differentiation (maturation) of tumor cells; or Increase the ability of the host to tolerate damage by cytotoxic modalities of cancer treatment.

  17. Thermal Damage Characterization of Energetic Materials

    SciTech Connect

    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.

  18. Method to reduce damage to backing plate

    DOEpatents

    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.

  19. Damage mapping in structural health monitoring using a multi-grid architecture

    SciTech Connect

    Mathews, V. John

    2015-03-31

    This paper presents a multi-grid architecture for tomography-based damage mapping of composite aerospace structures. The system employs an array of piezo-electric transducers bonded on the structure. Each transducer may be used as an actuator as well as a sensor. The structure is excited sequentially using the actuators and the guided waves arriving at the sensors in response to the excitations are recorded for further analysis. The sensor signals are compared to their baseline counterparts and a damage index is computed for each actuator-sensor pair. These damage indices are then used as inputs to the tomographic reconstruction system. Preliminary damage maps are reconstructed on multiple coordinate grids defined on the structure. These grids are shifted versions of each other where the shift is a fraction of the spatial sampling interval associated with each grid. These preliminary damage maps are then combined to provide a reconstruction that is more robust to measurement noise in the sensor signals and the ill-conditioned problem formulation for single-grid algorithms. Experimental results on a composite structure with complexity that is representative of aerospace structures included in the paper demonstrate that for sufficiently high sensor densities, the algorithm of this paper is capable of providing damage detection and characterization with accuracy comparable to traditional C-scan and A-scan-based ultrasound non-destructive inspection systems quickly and without human supervision.

  20. Impact of substrate surface scratches on the laser damage resistance of multilayer coatings

    SciTech Connect

    Qiu, S; Wolfe, J; Monterrosa, A; Teslich, N; Feit, M; Pistor, T; Stolz, C

    2010-11-03

    Substrate scratches can limit the laser resistance of multilayer mirror coatings on high-peak-power laser systems. To date, the mechanism by which substrate surface defects affect the performance of coating layers under high power laser irradiation is not well defined. In this study, we combine experimental approaches with theoretical simulations to delineate the correlation between laser damage resistance of coating layers and the physical properties of the substrate surface defects including scratches. A focused ion beam technique is used to reveal the morphological evolution of coating layers on surface scratches. Preliminary results show that coating layers initially follow the trench morphology on the substrate surface, and as the thickness increases, gradually overcoat voids and planarize the surface. Simulations of the electrical-field distribution of the defective layers using the finite-difference time-domain (FDTD) method show that field intensification exists mostly near the top surface region of the coating near convex focusing structures. The light intensification could be responsible for the reduced damage threshold. Damage testing under 1064 nm, 3 ns laser irradiation over coating layers on substrates with designed scratches show that damage probability and threshold of the multilayer depend on substrate scratch density and width. Our preliminary results show that damage occurs on the region of the coating where substrate scratches reside and etching of the substrate before coating does not seem to improve the laser damage resistance.

  1. How do energetic ions damage metallic surfaces?

    DOE PAGES [OSTI]

    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 <100> vacancy loops beneath the free surface was observed, which may explain some earlier experimental observations.« less

  2. How do energetic ions damage metallic surfaces?

    SciTech Connect

    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 with (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 <100> vacancy loops beneath the free surface was observed, which may explain some earlier experimental observations.

  3. Undulator Radiation Damage Experience at LCLS

    SciTech Connect

    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 µm, 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.

  4. The tomato DWD motif-containing protein DDI1 interacts with the CUL4–DDB1-based ubiquitin ligase and plays a pivotal role in abiotic stress responses

    SciTech Connect

    Miao, Min; Zhu, Yunye; Qiao, Maiju; Tang, Xiaofeng; Zhao, Wei; Xiao, Fangming; Liu, Yongsheng

    2014-08-08

    Highlights: • We identify DDI1 as a DAMAGED DNA BINDING PROTEIN1 (DDB1)-interacting protein. • DDI1 interacts with the CUL4–DDB1-based ubiquitin ligase in the nucleus. • DDI1 plays a positive role in regulating abiotic stress response in tomato. - Abstract: CULLIN4(CUL4)–DAMAGED DNA BINDING PROTEIN1 (DDB1)-based ubiquitin ligase plays significant roles in multiple physiological processes via ubiquitination-mediated degradation of relevant target proteins. The DDB1–CUL4-associated factor (DCAF) acts as substrate receptor in the CUL4–DDB1 ubiquitin ligase complex and determines substrate specificity. In this study, we identified a tomato (Solanum lycopersicum) DDB1-interacting (DDI1) protein as a DCAF protein involved in response to abiotic stresses, including UV radiation, high salinity and osmotic stress. Co-immunoprecipitation and bimolecular fluorescence complementation assay indicated that DDI1 associates with CUL4–DDB1 in the nucleus. Quantitative RT-PCR analysis indicated the DDI1 gene is induced by salt, mannitol and UV-C treatment. Moreover, transgenic tomato plants with overexpression or knockdown of the DDI1 gene exhibited enhanced or attenuated tolerance to salt/mannitol/UV-C, respectively. Thus, our data suggest that DDI1 functions as a substrate receptor of the CUL4–DDB1 ubiquitin ligase, positively regulating abiotic stress response in tomato.

  5. 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...

  6. Human Genome Research: Decoding DNA

    Office of Scientific and Technical Information (OSTI)

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

  7. DNA attachment to support structures

    DOEpatents

    Balhorn, Rodney L.; Barry, Christopher H.

    2002-01-01

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

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

    SciTech Connect

    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 NFκB in response to low doses irradiation. We found in our recent study that low dose IR induces a reciprocal p53 suppression and NFκB 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 HIF1α activation was in sharp contrast with the high-dose IR-induced p53 activation and HIF1α inhibition. HIF1α and p53 seem to play distinct roles in mediating the radiation dose-dependent metabolic response. The induction of HIF1α-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, HIF1α 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 HIF1α 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 HIF1α activity as a potential reliable biological readout of radiation exposure in humans. The

  9. Damage Identification of Wind Turbine Blades Using Piezoelectric Transducers

    DOE PAGES [OSTI]

    Choi, Seong-Won; Farinholt, Kevin M.; Taylor, Stuart G.; Light-Marquez, Abraham; Park, Gyuhae

    2014-01-01

    This paper presents the experimental results of active-sensing structural health monitoring (SHM) techniques, which utilize piezoelectric transducers as sensors and actuators, for determining the structural integrity of wind turbine blades. Specifically, Lamb wave propagations and frequency response functions at high frequency ranges are used to estimate the condition of wind turbine blades. For experiments, a 1 m section of a CX-100 blade is used. The goal of this study is to assess and compare the performance of each method in identifying incipient damage with a consideration given to field deployability. Overall, these methods yielded a sufficient damage detection capability to warrantmore » further investigation. This paper also summarizes the SHM results of a full-scale fatigue test of a 9 m CX-100 blade using piezoelectric active sensors. This paper outlines considerations needed to design such SHM systems, experimental procedures and results, and additional issues that can be used as guidelines for future investigations.« less

  10. Frequency Response Tool

    Energy Science and Technology Software Center

    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

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  14. Nonuniform radiation damage in permanent magnet quadrupoles

    SciTech Connect

    Danly, C. R.; Merrill, F. E.; Barlow, D.; Mariam, F. G.

    2014-08-15

    We present data that indicate nonuniform magnetization loss due to radiation damage in neodymium-iron-boron Halbach-style permanent magnet quadrupoles. The proton radiography (pRad) facility at Los Alamos uses permanent-magnet quadrupoles for magnifying lenses, and a system recently commissioned at GSI-Darmsdadt uses permanent magnets for its primary lenses. Large fluences of spallation neutrons can be produced in close proximity to these magnets when the proton beam is, intentionally or unintentionally, directed into the tungsten beam collimators; imaging experiments at LANL’s pRad have shown image degradation with these magnetic lenses at proton beam doses lower than those expected to cause damage through radiation-induced reduction of the quadrupole strength alone. We have observed preferential degradation in portions of the permanent magnet quadrupole where the field intensity is highest, resulting in increased high-order multipole components.

  15. Radiation damage in cubic-stabilized zirconia

    SciTech Connect

    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.

  16. When DNA Needs to Stand Up and Be Counted

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

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

  17. Assessing thermal damage in silicon PN-junctions using Raman thermometry

    SciTech Connect

    Beechem, Thomas E.; Serrano, Justin R.; McDonald, Anthony; Mani, Seethambal

    2013-03-28

    Laser machining is frequently utilized in the manufacture of photovoltaics. A natural by-product of these fabrication processes, heat, not only serves as a means of material removal but also modifies the material in an extended region beyond that ideally intended for alteration. This modified region, termed the heat affected zone, is detrimental to performance and should therefore be minimized. While undoubtedly thermal in origin, it is unclear exactly how the thermal environment during laser machining correlates to changes in the PN-junction that reduce performance. In response, we combine in-situ Raman based thermometry measurements with post-event failure analysis to identify the physical mechanisms damaging the junction during laser machining. From this approach, damage is shown to initiate prior to melting and be driven primarily by the diffusion of dopants for fluences that do not induce ablation. Additionally, comparatively small regions of damage are shown to have a large impact on operation.

  18. Alkylation damage repair in mammalian genomes

    SciTech Connect

    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.

  19. Alkylation damage repair in mammalian genomes

    SciTech Connect

    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.

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

    Office of Scientific and Technical Information (OSTI)

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

  1. The Initiation of Bacterial DNA Replication

    U.S. Department of Energy (DOE) - all 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...

  2. The Initiation of Bacterial DNA Replication

    U.S. Department of Energy (DOE) - all 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...

  3. Forensic DNA data banking by state crime labortaories

    SciTech Connect

    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.

  4. Normalized cDNA libraries

    DOEpatents

    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.

  5. Normalized cDNA libraries

    DOEpatents

    Soares, Marcelo B.; Efstratiadis, Argiris

    1997-01-01

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

  6. Sequence independent amplification of DNA

    DOEpatents

    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

    DOEpatents

    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. Using DNA to Build Nanomaterials

    DOE R&D Accomplishments

    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.

  9. Minimizing radiation damage in nonlinear optical crystals

    DOEpatents

    Cooke, D. Wayne; Bennett, Bryan L.; Cockroft, Nigel J.

    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.

  10. Minimizing radiation damage in nonlinear optical crystals

    DOEpatents

    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.

  11. Survey of four damage models for concrete.

    SciTech Connect

    Leelavanichkul, Seubpong; Brannon, Rebecca Moss

    2009-08-01

    Four conventional damage plasticity models for concrete, the Karagozian and Case model (K&C), the Riedel-Hiermaier-Thoma model (RHT), the Brannon-Fossum model (BF1), and the Continuous Surface Cap Model (CSCM) are compared. The K&C and RHT models have been used in commercial finite element programs many years, whereas the BF1 and CSCM models are relatively new. All four models are essentially isotropic plasticity models for which 'plasticity' is regarded as any form of inelasticity. All of the models support nonlinear elasticity, but with different formulations. All four models employ three shear strength surfaces. The 'yield surface' bounds an evolving set of elastically obtainable stress states. The 'limit surface' bounds stress states that can be reached by any means (elastic or plastic). To model softening, it is recognized that some stress states might be reached once, but, because of irreversible damage, might not be achievable again. In other words, softening is the process of collapse of the limit surface, ultimately down to a final 'residual surface' for fully failed material. The four models being compared differ in their softening evolution equations, as well as in their equations used to degrade the elastic stiffness. For all four models, the strength surfaces are cast in stress space. For all four models, it is recognized that scale effects are important for softening, but the models differ significantly in their approaches. The K&C documentation, for example, mentions that a particular material parameter affecting the damage evolution rate must be set by the user according to the mesh size to preserve energy to failure. Similarly, the BF1 model presumes that all material parameters are set to values appropriate to the scale of the element, and automated assignment of scale-appropriate values is available only through an enhanced implementation of BF1 (called BFS) that regards scale effects to be coupled to statistical variability of material

  12. Helium damage in austenitic stainless steels

    SciTech Connect

    Caskey, G.R. Jr.; Mezzanotte, D.A. Jr.; Rawl, D.E. Jr.

    1983-01-01

    Helium produced by tritium decay was first shown to embrittle austenitic stainless steel at ambient temperature in tensile specimens of Nitronic-40 steel (Armco, Inc.). A long-term study was initiated to study this form of helium damage in five austenitic alloys. Results from this study have been analyzed by the J-integral technique and show a decrease in ductile fracture toughness with increasing He-3 concentration. Sustained-load cracking tests indicate that the stress intensity required to initiate and propagate a crack also decreases with increasing He-3 concentration. 9 figures, 3 tables.

  13. Development of subsidence damage criteria. Final report

    SciTech Connect

    Bhattacharya, S.; Singh, M.M.

    1985-10-01

    In the process of coal mining it is certain that some degree of disturbance of the overlying strata and consequent subsidence of the surface will result. The problem of land subsidence has faced engineers and geologists for many years and, when widespread movements and damage to surface structures occurred, systematic investigations were undertaken. The term subsidence, as used in the report, implies the total phenomenon of surface effects associated with the mining of minerals, and not only vertical displacement of the surface as is sometimes inferred in the literature.

  14. Natural Resource Damage Assessment Cooperation and Integration

    Directives, Delegations, and Other 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.

  15. Surface state reconstruction in ion-damaged SmB?

    DOE PAGES [OSTI]

    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.

  16. Analyses of containment structures with corrosion damage

    SciTech Connect

    Cherry, J.L.

    1997-01-01

    Corrosion damage that has been found in a number of nuclear power plant containment structures can degrade the pressure capacity of the vessel. This has prompted concerns regarding the capacity of corroded containments to withstand accident loadings. To address these concerns, finite element analyses have been performed for a typical PWR Ice Condenser containment structure. Using ABAQUS, the pressure capacity was calculated for a typical vessel with no corrosion damage. Multiple analyses were then performed with the location of the corrosion and the amount of corrosion varied in each analysis. Using a strain-based failure criterion, a {open_quotes}lower bound{close_quotes}, {open_quotes}best estimate{close_quotes}, and {open_quotes}upper bound{close_quotes} failure level was predicted for each case. These limits were established by: determining the amount of variability that exists in material properties of typical containments, estimating the amount of uncertainty associated with the level of modeling detail and modeling assumptions, and estimating the effect of corrosion on the material properties.

  17. High damage tolerance of electrochemically lithiated silicon

    DOE PAGES [OSTI]

    Wang, Xueju; Fan, Feifei; Wang, Jiangwei; Wang, Haoran; Tao, Siyu; Yang, Avery; Liu, Yang; Beng Chew, Huck; Mao, Scott X.; Zhu, Ting; et al

    2015-09-24

    Mechanical degradation and resultant capacity fade in high-capacity electrode materials critically hinder their use in high-performance rechargeable batteries. Despite tremendous efforts devoted to the study of the electro–chemo–mechanical behaviours of high-capacity electrode materials, their fracture properties and mechanisms remain largely unknown. In this paper, we report a nanomechanical study on the damage tolerance of electrochemically lithiated silicon. Our in situ transmission electron microscopy experiments reveal a striking contrast of brittle fracture in pristine silicon versus ductile tensile deformation in fully lithiated silicon. Quantitative fracture toughness measurements by nanoindentation show a rapid brittle-to-ductile transition of fracture as the lithium-to-silicon molar ratiomore » is increased to above 1.5. Molecular dynamics simulations elucidate the mechanistic underpinnings of the brittle-to-ductile transition governed by atomic bonding and lithiation-induced toughening. Finally, our results reveal the high damage tolerance in amorphous lithium-rich silicon alloys and have important implications for the development of durable rechargeable batteries.« less

  18. High damage tolerance of electrochemically lithiated silicon

    SciTech Connect

    Wang, Xueju; Fan, Feifei; Wang, Jiangwei; Wang, Haoran; Tao, Siyu; Yang, Avery; Liu, Yang; Beng Chew, Huck; Mao, Scott X.; Zhu, Ting; Xia, Shuman

    2015-09-24

    Mechanical degradation and resultant capacity fade in high-capacity electrode materials critically hinder their use in high-performance rechargeable batteries. Despite tremendous efforts devoted to the study of the electro–chemo–mechanical behaviours of high-capacity electrode materials, their fracture properties and mechanisms remain largely unknown. In this paper, we report a nanomechanical study on the damage tolerance of electrochemically lithiated silicon. Our in situ transmission electron microscopy experiments reveal a striking contrast of brittle fracture in pristine silicon versus ductile tensile deformation in fully lithiated silicon. Quantitative fracture toughness measurements by nanoindentation show a rapid brittle-to-ductile transition of fracture as the lithium-to-silicon molar ratio is increased to above 1.5. Molecular dynamics simulations elucidate the mechanistic underpinnings of the brittle-to-ductile transition governed by atomic bonding and lithiation-induced toughening. Finally, our results reveal the high damage tolerance in amorphous lithium-rich silicon alloys and have important implications for the development of durable rechargeable batteries.

  19. [Studies of the repair of radiation-induced genetic damage in Drosophila]. Annual progress report, July 1, 1991--June 1, 1992

    SciTech Connect

    1992-12-31

    The primary goal of this program is to achieve a more thorough understanding of the mechanisms employed by higher organisms to resist DNA damage. Concurrently this effort contributes to an improved understanding of the processes of mutagenesis and carcinogenesis in higher eukaryotes. Drosophila was initially chosen as a model organism for investigating functions that control mutagen resistance because of the ease with which one can isolate and characterize mutagen-sensitive mutants in this multicellular organism. This laboratory then went on to investigate the DNA repair defects of such mutants while others performed complementary genetic and cytogenetic studies which relate DNA repair processes to mutagenesis and chromosome stability. Currently, recombinant DNA technology is being employed to investigate the mechanisms of mutagen resistance defined by those mutants. The following two studies experienced the most significant progress during the past year: cloning and genetic characterization of the mus209 gene, and genetic and molecular analysis of the mus308 gene.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  3. Accident Response Group | National Nuclear Security Administration | (NNSA)

    National Nuclear Security Administration (NNSA)

    Accident Response Group NNSA's Accident Response Group (ARG) provides technical guidance and responds to U.S. nuclear weapons accidents. ARG_Logo The team assists in assessing weapons damage and risk, and in developing and implementing procedures for safe weapon recovery, packaging, transportation, and disposal of damaged weapons. The ARG headquarters is located in Albuquerque, New Mexico and is supported by Lawrence Livermore National Laboratory, Los Alamos National Laboratory, Sandia National

  4. Damage from the impacts of small asteroids

    SciTech Connect

    Hills, J.G.; Goda, M.P.

    1996-08-15

    The fragmentation of a small asteroid in the atmosphere greatly increases its aerodynamic drag and rate of energy dissipation. The differential atmospheric pressure across it disperses its fragments at a velocity that increases with atmospheric density and impact velocity and decreases with asteroid density. Extending our previous work, we use a spherical atmosphere and a fitted curve to its density profile to find the damage done by an asteroid entering the atmosphere at various zenith angles. In previous work we estimated the blast damage by scaling from data on nuclear explosions in the atmosphere during the 1940s, 1950s and early 1960s. This underestimated the blast from asteroid impacts because nuclear fireballs radiate away a larger fraction of their energy than do meteors, so less of their energy goes into the blast wave. We have redone the calculations to allow for this effect. We have found the area of destruction around the impact point in which the over pressure in the blast wave exceeds 4 pounds/inch{sup 2} = 2.8 X 10{sup 5} dynes/cm{sup 3}, which is enough to knock over trees and destroy buildings. About every 100 years an impactor should blast an area of 300 km{sup 2} or more somewhere on the land area of Earth. The optical flux from asteroids 60 meters or more in diameter is enough to ignite pine forests. However, the blast from an impacting asteroid goes beyond the radius within which the fire starts. It tends to blow out the fire, so it is likely that the impact will char the forest (as at Tunguska), but it will not produce a sustained fire. Because of the atmosphere, asteroids less than about 200 m in diameter are not effective in producing craters and earthquakes. They are also not effective in producing water waves and tsunami in ocean impacts. Tsunami is probably the most devastating type of damage for asteroids that are between 200 meters and 1 km in diameter.

  5. Interconnecting gold islands with DNA origami

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

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

  6. DNA polymorphism identity determination using flow cytometry

    DOEpatents

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

    2001-01-01

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

  7. DNA analysis conference in Santa Fe

    U.S. Department of Energy (DOE) - all 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

  8. Techniques for preventing accidental damage to pipelines

    SciTech Connect

    Lothon, A.; Akel, S.

    1996-12-31

    Following a survey of all of the techniques capable of preventing third-party damage to its gas transmission pipelines, Gaz de France has selected two of them, Electromagnetic Detection and Positioning by Satellite. The first technique is based on detection of the magnetic field existing around transmission pipes excited by a driving current. A receiver is mounted on the excavation equipment to detect the magnetic field, thereby preventing any risk of hitting the pipe. The second technique consists in locating excavators by satellite. Each excavator needs to be equipped with a GPS beacon to know its position. Using the map of the transmission network stored in data-base form, i.e., digitized, the system calculates the position of the excavator relative to the pipes buried in its vicinity so as to avoid any accidental contact. The main features, advantages and drawbacks of the two techniques are presented in this paper.

  9. Final report on optical damage tests

    SciTech Connect

    Not Available

    1990-05-18

    This report presents the data resulting from a series of mirror damage tests conducted with the FLEX laser at KMS Fusion on March 14 through March 20, 1990 for Los Alamos National Laboratory. The FLEX laser consists of a ND:YLF master oscillator and four Nd:glass rod amplifiers operating at 1.05 {mu}m. For this program, the laser was configured to produce a 3 ms long square wave envelope of mode locked pulses which was focused onto Los Alamos supplied targets via a 1200 mm focal length (f/20) lens at approximately normal incidence. The pulse energy and spot size were specified by Los Alamos personnel, the energy varying from approximately 10--40 Joules and the spot size ranging from approximately 100--300 {mu}m. A total of 63 target shots and 19 calibration and/or test shots were conducted.

  10. A damage mechanics based approach to structural deterioration and reliability

    SciTech Connect

    Bhattcharya, B.; Ellingwood, B.

    1998-02-01

    Structural deterioration often occurs without perceptible manifestation. Continuum damage mechanics defines structural damage in terms of the material microstructure, and relates the damage variable to the macroscopic strength or stiffness of the structure. This enables one to predict the state of damage prior to the initiation of a macroscopic flaw, and allows one to estimate residual strength/service life of an existing structure. The accumulation of damage is a dissipative process that is governed by the laws of thermodynamics. Partial differential equations for damage growth in terms of the Helmholtz free energy are derived from fundamental thermodynamical conditions. Closed-form solutions to the equations are obtained under uniaxial loading for ductile deformation damage as a function of plastic strain, for creep damage as a function of time, and for fatigue damage as function of number of cycles. The proposed damage growth model is extended into the stochastic domain by considering fluctuations in the free energy, and closed-form solutions of the resulting stochastic differential equation are obtained in each of the three cases mentioned above. A reliability analysis of a ring-stiffened cylindrical steel shell subjected to corrosion, accidental pressure, and temperature is performed.

  11. Stacking interactions and DNA intercalation

    SciTech Connect

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

    2009-01-01

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

  12. Apparatus for improved DNA sequencing

    DOEpatents

    Douthart, Richard J.; Crowell, Shannon L.

    1996-01-01

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

  13. Apparatus for improved DNA sequencing

    DOEpatents

    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.

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

    SciTech Connect

    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.

  15. Damage-free vibrational spectroscopy of biological materials in the

    Office of Scientific and Technical Information (OSTI)

    electron microscope (Journal Article) | SciTech Connect Damage-free vibrational spectroscopy of biological materials in the electron microscope Citation Details In-Document Search Title: Damage-free vibrational spectroscopy of biological materials in the electron microscope Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy

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

    SciTech Connect

    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.

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

    Office of Scientific and Technical Information (OSTI)

    Predicting seismic or shock loading damage of the soil-concrete interface where an ... erosion process, and deposition within interface cracks; and (2) to investigate the ...

  18. Guest Editorial: Laser Damage (Journal Article) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    the output energy and power of pulsed and ... studies based on third-harmonic generation microscopy). ... Another paper is devoted to thermal annealing of damage ...

  19. Unlimited Damage Accumulation in Metallic Materials Under Cascade-Damage Conditions

    SciTech Connect

    Barashev, Aleksandr; Golubov, Stanislav I

    2008-09-01

    Most experiments on neutron or heavy-ion cascade-produced irradiation of pure metals and metallic alloys demonstrate unlimited void growth as well as development of the dislocation structure. In contrast, the theory of radiation damage predicts saturation of void swelling at sufficiently high irradiation doses and, accordingly, termination of accumulation of interstitial-type defects. It is shown in the present paper that, under conditions of steady production of one-dimensionally (1-D) mobile clusters of self-interstitial atoms (SIAs) in displacement cascades, any one of the following three conditions can result in indefinite damage accumulation. First, if the fraction of SIAs generated in the clustered form is smaller than some finite value of the order of the dislocation bias factor. Second, if solute, impurity or transmuted atoms form atmospheres around voids and repel the SIA clusters. Third, if spatial correlations between voids and other defects, such as second-phase precipitates and dislocations, exist that provide shadowing of voids from the SIA clusters. The driving force for the development of such correlations is the same as for void lattice formation and is argued to be always present under cascade-damage conditions. It is emphasised that the mean-free path of 1-D migrating SIA clusters is typically at least an order of magnitude longer than the average distance between microstructural defects; hence spatial correlations on the same scale should be taken into consideration. A way of developing a predictive theory is discussed. An interpretation

  20. Revision of laser-induced damage threshold evaluation from damage probability data

    SciTech Connect

    Bataviciute, Gintare; Grigas, Povilas; Smalakys, Linas; Melninkaitis, Andrius

    2013-04-15

    In this study, the applicability of commonly used Damage Frequency Method (DFM) is addressed in the context of Laser-Induced Damage Threshold (LIDT) testing with pulsed lasers. A simplified computer model representing the statistical interaction between laser irradiation and randomly distributed damage precursors is applied for Monte Carlo experiments. The reproducibility of LIDT predicted from DFM is examined under both idealized and realistic laser irradiation conditions by performing numerical 1-on-1 tests. A widely accepted linear fitting resulted in systematic errors when estimating LIDT and its error bars. For the same purpose, a Bayesian approach was proposed. A novel concept of parametric regression based on varying kernel and maximum likelihood fitting technique is introduced and studied. Such approach exhibited clear advantages over conventional linear fitting and led to more reproducible LIDT evaluation. Furthermore, LIDT error bars are obtained as a natural outcome of parametric fitting which exhibit realistic values. The proposed technique has been validated on two conventionally polished fused silica samples (355 nm, 5.7 ns).

  1. The Replication Focus Targeting Sequence (RFTS) Domain Is a DNA-competitive Inhibitor of Dnmt1

    SciTech Connect

    Syeda, Farisa; Fagan, Rebecca L.; Wean, Matthew; Avvakumov, George V.; Walker, John R.; Xue, Sheng; Dhe-Paganon, Sirano; Brenner, Charles

    2015-11-30

    Dnmt1 (DNA methyltransferase 1) is the principal enzyme responsible for maintenance of cytosine methylation at CpG dinucleotides in the mammalian genome. The N-terminal replication focus targeting sequence (RFTS) domain of Dnmt1 has been implicated in subcellular localization, protein association, and catalytic function. However, progress in understanding its function has been limited by the lack of assays for and a structure of this domain. Here, we show that the naked DNA- and polynucleosome-binding activities of Dnmt1 are inhibited by the RFTS domain, which functions by virtue of binding the catalytic domain to the exclusion of DNA. Kinetic analysis with a fluorogenic DNA substrate established the RFTS domain as a 600-fold inhibitor of Dnmt1 enzymatic activity. The crystal structure of the RFTS domain reveals a novel fold and supports a mechanism in which an RFTS-targeted Dnmt1-binding protein, such as Uhrf1, may activate Dnmt1 for DNA binding.

  2. Chromosome specific repetitive DNA sequences

    DOEpatents

    Moyzis, Robert K.; Meyne, Julianne

    1991-01-01

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

  3. Modeling and characterization of recompressed damaged materials

    SciTech Connect

    Becker, R; Cazamias, J U; Kalantar, D H; LeBlanc, M M; Springer, H K

    2004-02-11

    Experiments have been performed to explore conditions under which spall damage is recompressed with the ultimate goal of developing a predictive model. Spall is introduced through traditional gas gun techniques or with laser ablation. Recompression techniques producing a uniaxial stress state, such as a Hopkinson bar, do not create sufficient confinement to close the porosity. Higher stress triaxialities achieved through a gas gun or laser recompression can close the spall. Characterization of the recompressed samples by optical metallography and electron microscopy reveal a narrow, highly deformed process zone. At the higher pressures achieved in the gas gun, little evidence of spall remains other than differentially etched features in the optical micrographs. With the very high strain rates achieved with laser techniques there is jetting from voids and other signs of turbulent metal flow. Simulations of spall and recompression on micromechanical models containing a single void suggest that it might be possible to represent the recompression using models similar to those employed for void growth. Calculations using multiple, randomly distributed voids are needed to determine if such models will yield the proper behavior for more realistic microstructures.

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

    SciTech Connect

    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.

  7. Amplification of chromosomal DNA in situ

    DOEpatents

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

    2002-01-01

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

  8. DNA Origami: A History and Current Perspective

    U.S. Department of Energy (DOE) - all 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

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

    SciTech Connect

    James, Conrad D.; Derzon, Mark Steven

    2005-10-01

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

  10. Micro-mechanical modeling of perforating shock damage

    SciTech Connect

    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. Radiation Damage In Reactor Cavity Concrete

    SciTech Connect

    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 [1]. Much of the historical mechanical performance data of irradiated concrete [2] does not accurately reflect typical radiation conditions in NPPs or conditions out to 60 or 80 years of radiation exposure [3]. 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.

  12. Radiation Damage In Reactor Cavity Concrete

    SciTech Connect

    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.

  13. Antibody specific for a DNA repair protein

    DOEpatents

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

    2006-07-11

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

  14. Probe and method for DNA detection

    SciTech Connect

    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.

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

    SciTech Connect

    Burian, Tomáš; Hájková, Věra; Chalupský, Jaromír; Vyšín, Luděk; Boháček, Pavel; Přeček, Martin; Wild, Jan; Özkan, Cigdem; Coppola, Nicola; Farahani, Shafagh Dastjani; Schulz, Joachim; Sinn, Harald; Tschentscher, Thomas; Gaudin, Jérôme; Bajt, Saša; Tiedtke, Kai; Toleikis, Sven; Chapman, Henry N.; Loch, Rolf A.; Jurek, Marek; Sobierajski, Ryszard; Krzywinski, Jacek; Moeller, Stefan; Harmand, Marion; Galasso, Germano; Nagasono, Mitsuru; Saskl, Karel; Sovák, Pavol; Juha, Libor

    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 determined 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.

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

    DOE PAGES [OSTI]

    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

  17. Electronic effects in high-energy radiation damage in tungsten

    DOE PAGES [OSTI]

    Zarkadoula, Eva; Duffy, Dorothy M.; Nordlund, Kai; Seaton, M. A.; Todorov, I. T.; Weber, William J.; Trachenko, Kostya

    2015-01-01

    Even though the effects of the electronic excitations during high-energy radiation damage processes are not currently understood, it is shown that their role in the interaction of radiation with matter is important. We perform molecular dynamics simulations of high-energy collision cascades in bcc-tungsten using the coupled two-temperature molecular dynamics (2T-MD) model that incorporates both the effects of electronic stopping and electron–phonon interaction. We compare the combination of these effects on the induced damage with only the effect of electronic stopping, and conclude in several novel insights. In the 2T-MD model, the electron–phonon coupling results in less damage production in themore » molten region and in faster relaxation of the damage at short times. We show these two effects lead to a significantly smaller amount of the final damage at longer times.« less

  18. Mesoscale polycrystal calculations of damage in spallation in metals

    SciTech Connect

    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.

  19. Analysis of 1w Bulk Laser Damage in KDP

    SciTech Connect

    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.

  20. Nuclear sensing of viral DNA, epigenetic regulation of herpes simplex virus infection, and innate immunity

    SciTech Connect

    Knipe, David M.

    2015-05-15

    Herpes simplex virus (HSV) undergoes a lytic infection in epithelial cells and a latent infection in neuronal cells, and epigenetic mechanisms play a major role in the differential gene expression under the two conditions. HSV viron DNA is not associated with histones but is rapidly loaded with heterochromatin upon entry into the cell. Viral proteins promote reversal of the epigenetic silencing in epithelial cells while the viral latency-associated transcript promotes additional heterochromatin in neuronal cells. The cellular sensors that initiate the chromatinization of foreign DNA have not been fully defined. IFI16 and cGAS are both essential for innate sensing of HSV DNA, and new evidence shows how they work together to initiate innate signaling. IFI16 also plays a role in the heterochromatinization of HSV DNA, and this review will examine how IFI16 integrates epigenetic regulation and innate sensing of foreign viral DNA to show how these two responses are related. - Highlights: • HSV lytic and latent gene expression is regulated differentially by epigenetic processes. • The sensors of foreign DNA have not been defined fully. • IFI16 and cGAS cooperate to sense viral DNA in HSV-infected cells. • IFI16 plays a role in both innate sensing of HSV DNA and in restricting its expression.

  1. Particle sizer and DNA sequencer

    DOEpatents

    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.

  2. Fleet DNA Project (Fact Sheet)

    SciTech Connect

    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. Human Genome Research: Decoding DNA

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

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

  4. Channel plate for DNA sequencing

    DOEpatents

    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.

  5. Channel plate for DNA sequencing

    DOEpatents

    Douthart, Richard J.; Crowell, Shannon L.

    1998-01-01

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

  8. Method for sequencing DNA base pairs

    DOEpatents

    Sessler, Andrew M.; Dawson, John

    1993-01-01

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

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

    SciTech Connect

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

    2015-06-02

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

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

    DOE PAGES [OSTI]

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

    2015-06-02

    Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. Results: This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This 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

  11. Neutron Damage and MAX Phase Ternary Compounds

    SciTech Connect

    Barsoum, Michael; Hoffman, Elizabeth; Sindelar, Robert; Garcua-Duaz, Brenda; Kohse, Gordon

    2014-06-17

    The Demands of Gen IV nuclear power plants for long service life under neutron radiation at high temperature are severe. Advanced materials that would withstand high temperatures (up to 1000+ C) to high doses in a neutron field would be ideal for reactor internal structures and would add to the long service life and reliability of the reactors. The objective of this work is to investigate the response of a new class of machinable, conductive, layered, ternary transition metal carbides and nitrides - the so-called MAX phases - to low and moderate neutron dose levels.

  12. Common trenching reduces damage to buried utilities

    SciTech Connect

    Alfiere, E.P.

    1982-09-01

    Since 1972 Niagara Mohawk Power Co. has established a utility corridor, installing 503 miles of buried gas mains and electric cables in a common trench. Their guidelines for common trenching included (1) the developer's responsibility for providing a subdivision map showing the location of each sidewalk, lot, and roadway, (2) an easement strip paralleling the front lot (street) line that is to be cleared and graded by the developer before construction is started, (3) an electric planning department to prepare detailed construction drawings, coordinate plans with other utilities, determine the responsibility for trenching and backfilling, and determine that all the necessary easements have been secured, and (4) construction specifications varying the width and depth of the trench with the number and type of utilties occupying the joint trench. Advantages of the common trench program comprise reduced exposure to digups, communication and concern for each utility's facility, water and sewer construction installed before the common trench, and cost sharing that would reduce each facility's construction and restoration costs.

  13. DNA

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

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

  14. Departmental Response:

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Departmental Response: Assessment of the Report of the SEAB Task Force on National Laboratories Introduction The Department of Energy (DOE) and its network or national laboratories (labs) are responsible for advancing the national, economic. energy. and nuclear security of the U.S.: promoting innovative and transformative scientific and technological solutions in support or those missions: sponsoring basic research in the physical sciences: and ensuring environmental cleanup of the nation's

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

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    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

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

    DOE PAGES [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.; 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. Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  20. Thalidomide Ameliorates Inflammation and Vascular Injury but Aggravates Tubular Damage in the Irradiated Mouse Kidney

    SciTech Connect

    Scharpfenecker, Marion; Floot, Ben; Russell, Nicola S.; Coppes, Rob P.; Stewart, Fiona A.

    2014-07-01

    Purpose: The late side effects of kidney irradiation include vascular damage and fibrosis, which are promoted by an irradiation-induced inflammatory response. We therefore treated kidney-irradiated mice with the anti-inflammatory and angiogenesis-modulating drug thalidomide in an attempt to prevent the development of late normal tissue damage and radiation nephropathy in the mouse kidney. Methods and Materials: Kidneys of C57Bl/6 mice were irradiated with a single dose of 14 Gy. Starting from week 16 after irradiation, the mice were fed with thalidomide-containing chow (100 mg/kg body weight/day). Gene expression and kidney histology were analyzed at 40 weeks and blood samples at 10, 20, 30, and 40 weeks after irradiation. Results: Thalidomide improved the vascular structure and vessel perfusion after irradiation, associated with a normalization of pericyte coverage. The drug also reduced infiltration of inflammatory cells but could not suppress the development of fibrosis. Irradiation-induced changes in hematocrit and blood urea nitrogen levels were not rescued by thalidomide. Moreover, thalidomide worsened tubular damage after irradiation and also negatively affected basal tubular function. Conclusions: Thalidomide improved the inflammatory and vascular side effects of kidney irradiation but could not reverse tubular toxicity, which probably prevented preservation of kidney function.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  3. DNA Sequencing Using capillary Electrophoresis

    SciTech Connect

    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

  4. Damage identification and health monitoring of structural and mechanical systems from changes in their vibration characteristics: A literature review

    SciTech Connect

    Doebling, S.W.; Farrar, C.R.; Prime, M.B.; Shevitz, D.W.

    1996-05-01

    This report contains a review of the technical literature concerning the detection, location, and characterization of structural damage via techniques that examine changes in measured structural vibration response. The report first categorizes the methods according to required measured data and analysis technique. The analysis categories include changes in modal frequencies, changes in measured mode shapes (and their derivatives), and changes in measured flexibility coefficients. Methods that use property (stiffness, mass, damping) matrix updating, detection of nonlinear response, and damage detection via neural networks are also summarized. The applications of the various methods to different types of engineering problems are categorized by type of structure and are summarized. The types of structures include beams, trusses, plates, shells, bridges, offshore platforms, other large civil structures, aerospace structures, and composite structures. The report describes the development of the damage-identification methods and applications and summarizes the current state-of-the-art of the technology. The critical issues for future research in the area of damage identification are also discussed.

  5. Enhancing the DNA Patent Database

    SciTech Connect

    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.

  6. NMSLO Water Lease Damage Bond | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

  7. Neutron and gamma irradiation damage to organic materials.

    SciTech Connect

    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.

  8. Damage threshold of platinum coating used for optics for self...

    Office of Scientific and Technical Information (OSTI)

    used for optics for self-seeding of soft x-ray free electron laser Citation Details In-Document Search Title: Damage threshold of platinum coating used for optics for ...

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

    SciTech Connect

    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.

  10. Los Alamos offers new insights into radiation damage evolution

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    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 ...

  11. 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...

  12. 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...

  13. DNA-guided nanoparticle assemblies

    DOEpatents

    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.

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

    SciTech Connect

    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

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

    DOEpatents

    Siekhaus, Wigbert

    1987-01-01

    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 comprising, a focused and pulsed laser, an 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.

  16. Los Alamos National Laboratory describes storm damage to environmental

    U.S. Department of Energy (DOE) - all 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

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

    SciTech Connect

    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.

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

    SciTech Connect

    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 Recognition by a σ54 Transcriptional Activator from Aquifex aeolicus

    DOE PAGES [OSTI]

    Vidangos, Natasha K.; Heideker, Johanna; Lyubimov, Artem; Lamers, Meindert; Huo, Yixin; Pelton, Jeffrey G.; Ton, Jimmy; Gralla, Jay; Berger, James; Wemmer, David E.

    2014-08-23

    Transcription initiation by bacterial σ54-polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain. The structurally characterized DNA-binding domains from activators all belong to the Factor for Inversion Stimulation (Fis) family of helix-turn-helix DNA-binding proteins. We report here structures of the free and DNA-bound forms of the DNA-binding domain of NtrC4 (4DBD) from Aquifex aeolicus, a member of the NtrC family of σ54 activators. Two NtrC4 binding sites were identified upstream (-145 and -85 base pairs) from the start of the lpxC gene, which is responsible for themore » first committed step in Lipid A biosynthesis. This is the first experimental evidence for σ54 regulation in lpxC expression. 4DBD was crystallized both without DNA and in complex with the -145 binding site. The structures, together with biochemical data, indicate that NtrC4 binds to DNA in a manner that is similar to that of its close homologue, Fis. Ultimately, the greater sequence specificity for the binding of 4DBD relative to Fis seems to arise from a larger number of base specific contacts contributing to affinity than for Fis.« less

  20. Polycyclic aromatic hydrocarbon-DNA adducts and the CYP1A1 restriction fragment length polymorphism

    SciTech Connect

    Shields, P.G.; Bowman, E.D.; Weston, A.; Harris, C.C.; Sugimura, H.; Caporaso, N.E.; Petruzzelli, S.F. ); Trump, B.F. )

    1992-11-01

    Human cancer risk assessment at a genetic level involves the investigation of carcinogen metabolism and DNA adduct formation. Wide interindividual differences in metabolism result in different DNA adduct levels. For this and other reasons, many laboratories have considered DNA adducts to be a measure of the biologically effective dose of a carcinogen. Techniques for studying DNA adducts using chemically specific assays are becoming available. A modification of the [sup 32]P-postlabeling assay for polycyclic aromatic hydrocarbon DNA adducts described here provides potential improvements in quantification. DNA adducts, however, reflect only recent exposure to carcinogens; in contrast, genetic testing for metabolic capacity indicates the extent to which carcinogens can be activated and exert genotoxic effects. Such studies may reflect both separate and integrated risk factors together with DNA adduct levels. A recently described restriction fragment length polymorphism for the CYP1A1, which codes for the cytochrome P450 enzyme primarily responsible for the metabolic activation of carcinogenic polycyclic aromatic hydrocarbons, has been found to be associated with lung cancer risk in a Japanese population. In a subset of individuals enrolled in a US lung cancer case-control study, no association with lung cancer was found. 17 refs., 3 figs.

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

    SciTech Connect

    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.

  2. Corporate Responsibility

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Corporate Responsibility Corporate Responsibility Motivated to serve our nation and the world 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 a sense of service At the Lab, we are motivated by service to our nation and a desire to keep our nation and the world secure. That same sense of service compels us to be

  3. Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA and lengthen linear DNA

    SciTech Connect

    Verebová, Valéria; Adamcik, Jozef; Danko, Patrik; Podhradský, Dušan; Miškovský, Pavol; Staničová, Jana

    2014-01-31

    Highlights: • Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA. • Anthraquinones quinizarin and danthron lengthen linear DNA. • Anthraquinones quinizarin and danthron possess middle binding affinity to DNA. • Anthraquinones quinizarin and danthron interact with DNA by intercalating mode. - Abstract: The intercalating drugs possess a planar aromatic chromophore unit by which they insert between DNA bases causing the distortion of classical B-DNA form. The planar tricyclic structure of anthraquinones belongs to the group of chromophore units and enables anthraquinones to bind to DNA by intercalating mode. The interactions of simple derivatives of anthraquinone, quinizarin (1,4-dihydroxyanthraquinone) and danthron (1,8-dihydroxyanthraquinone), with negatively supercoiled and linear DNA were investigated using a combination of the electrophoretic methods, fluorescence spectrophotometry and single molecule technique an atomic force microscopy. The detection of the topological change of negatively supercoiled plasmid DNA, unwinding of negatively supercoiled DNA, corresponding to appearance of DNA topoisomers with the low superhelicity and an increase of the contour length of linear DNA in the presence of quinizarin and danthron indicate the binding of both anthraquinones to DNA by intercalating mode.

  4. Assembling semiconductor nanocomposites using DNA replication technologies.

    SciTech Connect

    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.

  5. 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"

  6. DNA sequencing using fluorescence background electroblotting membrane

    DOEpatents

    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

  7. DNA sequencing using fluorescence background electroblotting membrane

    DOEpatents

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

    1992-01-01

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

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

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

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

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

    SciTech Connect

    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

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

    SciTech Connect

    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.

  11. Differential effects of nitro-PAHs and amino-PAHs on cytokine and chemokine responses in human bronchial epithelial BEAS-2B cells

    SciTech Connect

    Ovrevik, J.; Arlt, V.M.; Oya, E.; Nagy, E.; Mollerup, S.; Phillips, D.H.; Lag, M.; Holme, J.A.

    2010-02-01

    Nitro-polycyclic aromatic hydrocarbons (nitro-PAHs) are found in diesel exhaust and air pollution particles. Along with other PAHs, many nitro-PAHs possess mutagenic and carcinogenic properties, but their effects on pro-inflammatory processes and cell death are less known. In the present study we examined the effects of 1-nitropyrene (1-NP), 3-nitrofluoranthene (3-NF) and 3-nitrobenzanthrone (3-NBA) and their corresponding amino forms, 1-AP, 3-AF and 3-ABA, in human bronchial epithelial BEAS-2B cells. The effects of the different nitro- and amino-PAHs were compared to the well-characterized PAH benzo[a]pyrene (B[a]P). Expression of 17 cytokine and chemokine genes, measured by real-time PCR, showed that 1-NP and 3-NF induced a completely different cytokine/chemokine gene expression pattern to that of their amino analogues. 1-NP/3-NF-induced responses were dominated by maximum effects on CXCL8 (IL-8) and TNF-alpha expression, while 1-AP-/3-AF-induced responses were dominated by CCL5 (RANTES) and CXCL10 (IP-10) expression. 3-NBA and 3-ABA induced only marginal cytokine/chemokine responses. However, 3-NBA exposure induced considerable DNA damage resulting in accumulation of cells in S-phase and a marked increase in apoptosis. B[a]P was the only compound to induce expression of aryl hydrocarbon receptor (AhR)-regulated genes, such as CYP1A1 and CYP1B1, but did not induce cytokine/chemokine responses in BEAS-2B cells. Importantly, nitro-PAHs and amino-PAHs induced both qualitatively and quantitatively different effects on cytokine/chemokine expression, DNA damage, cell cycle alterations and cytotoxicity. The cytokine/chemokine responses appeared to be triggered, at least partly, through mechanisms separate from the other examined endpoints. These results confirm and extend previous studies indicating that certain nitro-PAHs have a considerable pro-inflammatory potential.

  12. Interacting damage models mapped onto ising and percolation models

    SciTech Connect

    Toussaint, Renaud; Pride, Steven R.

    2004-03-23

    The authors introduce a class of damage models on regular lattices with isotropic interactions between the broken cells of the lattice. Quasistatic fiber bundles are an example. The interactions are assumed to be weak, in the sense that the stress perturbation from a broken cell is much smaller than the mean stress in the system. The system starts intact with a surface-energy threshold required to break any cell sampled from an uncorrelated quenched-disorder distribution. The evolution of this heterogeneous system is ruled by Griffith's principle which states that a cell breaks when the release in potential (elastic) energy in the system exceeds the surface-energy barrier necessary to break the cell. By direct integration over all possible realizations of the quenched disorder, they obtain the probability distribution of each damage configuration at any level of the imposed external deformation. They demonstrate an isomorphism between the distributions so obtained and standard generalized Ising models, in which the coupling constants and effective temperature in the Ising model are functions of the nature of the quenched-disorder distribution and the extent of accumulated damage. In particular, they show that damage models with global load sharing are isomorphic to standard percolation theory, that damage models with local load sharing rule are isomorphic to the standard ising model, and draw consequences thereof for the universality class and behavior of the autocorrelation length of the breakdown transitions corresponding to these models. they also treat damage models having more general power-law interactions, and classify the breakdown process as a function of the power-law interaction exponent. Last, they also show that the probability distribution over configurations is a maximum of Shannon's entropy under some specific constraints related to the energetic balance of the fracture process, which firmly relates this type of quenched-disorder based damage model

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

    SciTech Connect

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

    2007-02-15

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

  14. Response Elements

    Directives, Delegations, and Other 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.

  15. Departmental Response:

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    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

  16. Departmental Response:

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Departmental Response: Assessment of the Report of the SEAB Task Force on Methane Hydrates 1. Introduction Recent research confirms that gas hydrates are abundant in nature and exist in a wide variety of forms with varying relevance to future energy, long-term global carbon cycling, near-term climate change, and both natural and operational geohazards. Further, recent assessments within the Department of the Interior suggest large potential resources in gas hydrate deposits onshore Alaska and

  17. Damage mechanisms avoided or managed for NIF large optics

    DOE PAGES [OSTI]

    Manes, K. R.; Spaeth, M. L.; Adams, J. J.; Bowers, M. W.; Bude, J. D.; Carr, C. W.; Conder, A. D.; DiNicola, J. M. G.; Dixit, S. N.; Feigenbaum, E.; et al

    2016-02-09

    After every other failure mode has been considered, in the end, the high-performance limit of all lasers is set by optical damage. The demands of inertial confinement fusion (ICF) pushed lasers designed as ICF drivers into this limit from their very earliest days. The first ICF lasers were small, and their pulses were short. Their goal was to provide as much power to the target as possible. Typically, they faced damage due to high intensity on their optics. As requests for higher laser energy, longer pulse lengths, and better symmetry appeared, new kinds of damage also emerged, some of themmore » anticipated and others unexpected. This paper will discuss the various types of damage to large optics that had to be considered, avoided to the extent possible, or otherwise managed as the National Ignition Facility (NIF) laser was designed, fabricated, and brought into operation. Furthermore, it has been possible for NIF to meet its requirements because of the experience gained in previous ICF systems and because NIF designers have continued to be able to avoid or manage new damage situations as they have appeared.« less

  18. Investigation of subsidence damages above abandoned mine lands

    SciTech Connect

    Lin, Po-Ming.

    1988-01-01

    Abandoned mine lands (AML) subsidence is one of the most hazardous problems for personal property and community development. In order to improve the technique for subsidence diagnosis and the effectiveness of remedial measures, several methods and techniques have been developed in this research. A subsidence site investigation checklist is developed to guide the investigators with or without hands-on experience to collect a complete and necessary information for subsidence analysis during site investigation. A subsidence cause identification system is developed to streamline the process of analysis and for subsidence cause differentiation and identification over AML. A damage severity system is developed to evaluate the intensity of the damage to structures. A subsidence deduction model is developed based on the probability function integration method to reconstruct subsidence profile and subsurface failure zone for AML subsidence. The study is based on the case studies which include site investigation, surface subsidence survey, subsurface instrumentation, damage severity evaluation, subsidence deduction and statistical analysis. The results show that geologic conditions such as seam depth, seam height, ratios of strong and weak rocks do affect the subsidence damage area, subsidence factor, and damage severity. The relationship between above parameters can be expressed by a second order polynomial with correlation coefficients ranging from 0.7 to 0.9.

  19. Allostery through protein-induced DNA bubbles

    DOE PAGES [OSTI]

    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

  20. Recombinant DNA encoding a desulfurization biocatalyst

    DOEpatents

    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. Recombinant DNA encoding a desulfurization biocatalyst

    DOEpatents

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

    1994-01-01

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

  2. PHMC post-NPH emergency response training

    SciTech Connect

    Conrads, T.J.

    1997-04-08

    This document describes post-Natural Phenomena Hazard (NPH) emergency response training that was provided to two teams of Project Hanford Management Contractors (PHMC) staff that will be used to assess potential structural damage that may occur as a result of a significant natural phenomena event. This training supports recent plans and procedures to use trained staff to inspect structures following an NPH event on the Hanford Site.

  3. Flow cytometric detection method for DNA samples

    DOEpatents

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

    2006-08-01

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

  4. Storing data encoded DNA in living organisms

    DOEpatents

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

    2006-06-06

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

  5. Flow cytometric detection method for DNA samples

    DOEpatents

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

    2011-07-05

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

  6. Method for sequencing DNA base pairs

    DOEpatents

    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.

  7. Damage rates for FFTF structural components and surveillance assemblies

    SciTech Connect

    Simons, R.L.

    1993-08-01

    The Fast Flux Test Facility (FFTF) surveillance program provides coupon surveillance materials that are irradiated to the expected lifetime damage dose that the represented component will experience. This methodology requires a knowledge of the damage dose rates to the surveillance assemblies and to the critical locations of the structural components. This analysis updates the predicted exposures from a total fluence to a displacement per atom (dpa) basis using Monte Carlo (computer code for) neutron photon (transport) code (MCNP). The MCNP calculation improves the relative consistency and lowers the predicted damage rates uncertainty in a number of out-of-core locations. The results were used an part of the evaluation to extend the lifetime of the invessel components to 30 years in support of multiple missions for FFTF.

  8. Analysis of bending properties for damaged laminated pipes

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

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

    2010-06-21

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

  14. Commercial & Industrial Demand Response

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

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

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

    SciTech Connect

    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.

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

    SciTech Connect

    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

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

    SciTech Connect

    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.

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

    DOEpatents

    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.

  19. Laser damage in silicon: Energy absorption, relaxation, and transport

    SciTech Connect

    Rämer, A. Rethfeld, B.; Osmani, O.

    2014-08-07

    Silicon irradiated with an ultrashort 800 nm-laser pulse is studied theoretically using a two temperature description that considers the transient free carrier density during and after irradiation. A Drude model is implemented to account for the highly transient optical parameters. We analyze the importance of considering these density-dependent parameters as well as the choice of the Drude collision frequency. In addition, degeneracy and transport effects are investigated. The importance of each of these processes for resulting calculated damage thresholds is studied. We report damage thresholds calculations that are in very good agreement with experimental results over a wide range of pulse durations.

  20. BDS Thin Film UV Antireflection Laser Damage Competition

    SciTech Connect

    Stolz, C J

    2010-10-26

    UV antireflection coatings are a challenging coating for high power laser applications as exemplified by the use of uncoated Brewster's windows in laser cavities. In order to understand the current laser resistance of UV AR coatings in the industrial and university sectors, a double blind laser damage competition was performed. The coatings have a maximum reflectance of 0.5% at 355 nm at normal incidence. Damage testing will be performed using the raster scan method with a 7.5 ns pulse length on a single testing facility to facilitate direct comparisons. In addition to the laser resistance results, details of deposition processes and coating materials will also be shared.

  1. 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...

  2. Property:NEPA DNA Worksheet | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

  3. A physiologically based biodynamic (PBBD) model for estragole DNA binding in rat liver based on in vitro kinetic data and estragole DNA adduct formation in primary hepatocytes

    SciTech Connect

    Paini, Alicia; Punt, Ans; Viton, Florian; Scholz, Gabriele; Delatour, Thierry; Marin-Kuan, Maricel; Schilter, Benoit; Bladeren, Peter J. van; Rietjens, Ivonne M.C.M.

    2010-05-15

    Estragole has been shown to be hepatocarcinogenic in rodent species at high-dose levels. Translation of these results into the likelihood of formation of DNA adducts, mutation, and ultimately cancer upon more realistic low-dose exposures remains a challenge. Recently we have developed physiologically based biokinetic (PBBK) models for rat and human predicting bioactivation of estragole. These PBBK models, however, predict only kinetic characteristics. The present study describes the extension of the PBBK model to a so-called physiologically based biodynamic (PBBD) model predicting in vivo DNA adduct formation of estragole in rat liver. This PBBD model was developed using in vitro data on DNA adduct formation in rat primary hepatocytes exposed to 1'-hydroxyestragole. The model was extended by linking the area under the curve for 1'-hydroxyestragole formation predicted by the PBBK model to the area under the curve for 1'-hydroxyestragole in the in vitro experiments. The outcome of the PBBD model revealed a linear increase in DNA adduct formation with increasing estragole doses up to 100 mg/kg bw. Although DNA adduct formation of genotoxic carcinogens is generally seen as a biomarker of exposure rather than a biomarker of response, the PBBD model now developed is one step closer to the ultimate toxic effect of estragole than the PBBK model described previously. Comparison of the PBBD model outcome to available data showed that the model adequately predicts the dose-dependent level of DNA adduct formation. The PBBD model predicts DNA adduct formation at low levels of exposure up to a dose level showing to cause cancer in rodent bioassays, providing a proof of principle for modeling a toxicodynamic in vivo endpoint on the basis of solely in vitro experimental data.

  4. Mechanical Response of Thermoelectric Materials

    SciTech Connect

    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.

  5. Gel Electrophoresis of Gold-DNA Nanoconjugates

    DOE PAGES [OSTI]

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

    2007-01-01

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

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

    SciTech Connect

    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.

  7. Method of quantitating dsDNA

    DOEpatents

    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.

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

    SciTech Connect

    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.

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

    DOEpatents

    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.

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

    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."

  11. DOE and State Sign Natural Resources Damages Settlement Agreement

    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.

  12. When DNA Needs to Stand Up and Be Counted

    U.S. Department of Energy (DOE) - all 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...

  13. 6.7 Engineered Enzyme Accelerates DNA Sequencing

    U.S. Department of Energy (DOE) - all 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...

  14. When DNA Needs to Stand Up and Be Counted

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Understanding both the attachment and orientation of DNA on gold surfaces was the goal of ... Schematic of DNA structures in various conformations on a gold surface. Differences in ...

  15. DNA-mediated engineering of multicomponent enzyme crystals (Journal...

    Office of Scientific and Technical Information (OSTI)

    DNA-mediated engineering of multicomponent enzyme crystals Citation Details In-Document Search Title: DNA-mediated engineering of multicomponent enzyme crystals Authors: Brodin, ...

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

    Office of Scientific and Technical Information (OSTI)

    Microfluidics: Kinetics of Hybridized DNA With Fluid Flow Variations. Citation Details In-Document Search Title: Microfluidics: Kinetics of Hybridized DNA With Fluid Flow ...

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

    SciTech Connect

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

    2014-06-21

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

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

    SciTech Connect

    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.

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

    DOEpatents

    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.

  20. Scar-less multi-part DNA assembly design automation

    DOEpatents

    Hillson, Nathan J.

    2016-06-07

    The present invention provides a method of a method of designing an implementation of a DNA assembly. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding flanking homology sequences to each of the DNA oligos. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding optimized overhang sequences to each of the DNA oligos.

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

    DOEpatents

    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.

  2. Extracting biological knowledge from DNA sequences

    SciTech Connect

    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.

  3. Intriguing DNA Editor Has a Structural Trigger

    U.S. Department of Energy (DOE) - all 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...

  4. DNA Assembly Line for Nano-Construction

    ScienceCinema

    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

  5. Multiple tag labeling method for DNA sequencing

    DOEpatents

    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.

  6. Multiple tag labeling method for DNA sequencing

    DOEpatents

    Mathies, Richard A.; Huang, Xiaohua C.; Quesada, Mark A.

    1995-01-01

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

  7. A DNA tweezer-actuated enzyme nanoreactor

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    A DNA tweezer-actuated enzyme nanoreactor Authors: Liu, M., Fu, J., Hejesen, C., Yang, Y., Woodbury, N.W., Gothelf, K., Liu, Y., and Yan, H. Title: A DNA tweezer-actuated enzyme nanoreactor Source: Nature Communications Year: 2013 Volume: 4 Pages: article 2127 ABSTRACT: Date of online publication: Wed, 2013-07-03 Link online: http://dx.doi.org/10.1038/ncomms3127

  8. Oligonucleotide and Long Polymeric DNA Encoding

    SciTech Connect

    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.

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

    Office of Scientific and Technical Information (OSTI)

    Sponsoring Org: USDOE Country of Publication: United States Language: ENGLISH Subject: 60 APPLIED LIFE SCIENCES; ATP-ASE; ATP; CRYSTAL STRUCTURE; DNA; ESCHERICHIA COLI; FILAMENTS; ...

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

    SciTech Connect

    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.

  11. Technical Scope of Work: Proton Induced Radiation Damage in Crystal Scintillators

    SciTech Connect

    Zhu, Ren-Yuan; Zhang, Liyuan; Yang, Fan; Ramberg, Eric; Nebel, Todd

    2014-03-11

    This is a technical scope of work (TSW) between the Fermi National Accelerator Laboratory (Fermilab) and the experimenters of California Institute of Technology who have committed to participate in beam tests to be carried out during the 2014 Fermilab Test Beam Facility program. The goal of this investigation is to understand the proton induced radiation damage in candidate fast crystal scintillators for future HEP experiments. Degradations of the optical and scintillation properties, including emission and transmittance spectra, light output, decay time and light response uniformity, will be measured before and after each step of proton irradiation at Fermilab with a defined fluence. The irradiation will start with a fluence of 1010/cm2 and going up in four steps to 1013/cm2.

  12. Strenuous exercise induces mitochondrial damage in skeletal muscle of old mice

    SciTech Connect

    Lee, Sangho; Kim, Minjung; Lim, Wonchung; Kim, Taeyoung; Kang, Chounghun

    2015-05-29

    Strenuous exercise is known to cause excessive ROS generation and inflammation. However, the mechanisms responsible for the regulation of mitochondrial integrity in the senescent muscle during high-intensity exercise (HE) are not well studied. Here, we show that HE suppresses up-regulation of mitochondrial function despite increase in mitochondrial copy number, following excessive ROS production, proinflammatory cytokines and NFκB activation. Moreover, HE in the old group resulted in the decreasing of both fusion (Mfn2) and fission (Drp1) proteins that may contribute to alteration of mitochondrial morphology. This study suggests that strenuous exercise does not reverse age-related mitochondrial damage and dysfunction by the increased ROS and inflammation. - Highlights: • Effect of exercise on mitochondrial function of aged skeletal muscles was studied. • Strenuous exercise triggered excessive ROS production and inflammatory cytokines. • Strenuous exercise suppressed mitochondrial function in senescent muscle.

  13. Development and Application of a Strength and Damage Model for Rock under Dynamic Loading

    SciTech Connect

    Antoun, T H; Lomov, I N; Glenn, L A

    2001-03-12

    Simulating the behavior of geologic materials under impact loading conditions requires the use of a constitutive model that includes the effects of bulking, yielding, damage, porous compaction and loading rate on the material response. This paper describes the development, implementation and calibration of a thermodynamically consistent constitutive model that incorporates these features. The paper also describes a computational study in which the model was used to perform numerical simulations of PILE DRIVER, a deeply-buried underground nuclear explosion detonated in granite at the Nevada Test Site. Particle velocity histories, peak velocity and peak displacement as a function of slant range obtained from the code simulations compare favorably with PILE DRIVER data. The simulated attenuation of peak velocity and peak displacement also agrees with the results from several other spherical wave experiments in granite.

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

    SciTech Connect

    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.

  15. The simulation of the fourth spinning cylinder test using damage mechanics

    SciTech Connect

    Howard, I.C.; Li, Z.H.; Sheikh, M.A.; Lidbury, D.P.G.; Sherry, A.H.

    1996-12-01

    During the last decade, several large-scale tests programs have been mounted world-wide to validate the fracture mechanics principles employed in the structural integrity assessment of LWR pressure vessels. The fourth spinning cylinder test was a thermal shock experiment conducted at AEA Technology on a slowly spinning cylinder that contained two semi-circular cracks on the inner surface, one of 60 mm radius and the other, 40 mm. A small amount of ductile tearing at the position of maximum driving force of each defect triggered a cleavage event, which arrested leaving a thin ligament of uncracked material on the inner surface. The Damage Mechanics parameters of the A508 Class 3 steel from which the cylinder was made have been tuned on compact tension data obtained in the cleavage and transition regimes. A full model of the cylinder using the tuned material response provides the simulated ductile crack growth performance of this test.

  16. Targeting the Renin–Angiotensin System Combined With an Antioxidant Is Highly Effective in Mitigating Radiation-Induced Lung Damage

    SciTech Connect

    Mahmood, Javed; Jelveh, Salomeh; Zaidi, Asif; Doctrow, Susan R.; Medhora, Meetha; Hill, Richard P.

    2014-07-15

    Purpose: To investigate the outcome of suppression of the renin angiotensin system using captopril combined with an antioxidant (Eukarion [EUK]-207) for mitigation of radiation-induced lung damage in rats. Methods and Materials: The thoracic cavity of female Sprague-Dawley rats was irradiated with a single dose of 11 Gy. Treatment with captopril at a dose of 40 mg/kg/d in drinking water and EUK-207 given by subcutaneous injection (8 mg/kg daily) was started 1 week after irradiation (PI) and continuing until 14 weeks PI. Breathing rate was monitored until the rats were killed at 32 weeks PI, when lung fibrosis was assessed by lung hydroxyproline content. Lung levels of the cytokine transforming growth factor-β1 and macrophage activation were analyzed by immunohistochemistry. Oxidative DNA damage was assessed by 8-hydroxy-2-deoxyguanosine levels, and lipid peroxidation was measured by a T-BARS assay. Results: The increase in breathing rate in the irradiated rats was significantly reduced by the drug treatments. The drug treatment also significantly decreased the hydroxyproline content, 8-hydroxy-2-deoxyguanosine and malondialdehyde levels, and levels of activated macrophages and the cytokine transforming growth factor-β1 at 32 weeks. Almost complete mitigation of these radiation effects was observed by combining captopril and EUK-207. Conclusion: Captopril and EUK-207 can provide mitigation of radiation-induced lung damage out to at least 32 weeks PI after treatment given 1-14 weeks PI. Overall the combination of captopril and EUK-207 was more effective than the individual drugs used alone.

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

    Energy Science and Technology Software Center

    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

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

    DOE PAGES [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 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

  19. Representing ductile damage with the dual domain material point method

    DOE PAGES [OSTI]

    Long, C. C.; Zhang, D. Z.; Bronkhorst, C. A.; Gray, III, G. T.

    2015-12-14

    In this study, we incorporate a ductile damage material model into a computational framework based on the Dual Domain Material Point (DDMP) method. As an example, simulations of a flyer plate experiment involving ductile void growth and material failure are performed. The results are compared with experiments performed on high purity tantalum. We also compare the numerical results obtained from the DDMP method with those obtained from the traditional Material Point Method (MPM). Effects of an overstress model, artificial viscosity, and physical viscosity are investigated. Our results show that a physical bulk viscosity and overstress model are important in thismore » impact and failure problem, while physical shear viscosity and artificial shock viscosity have negligible effects. A simple numerical procedure with guaranteed convergence is introduced to solve for the equilibrium plastic state from the ductile damage model.« less

  20. Representing ductile damage with the dual domain material point method

    SciTech Connect

    Long, C. C.; Zhang, D. Z.; Bronkhorst, C. A.; Gray, III, G. T.

    2015-12-14

    In this study, we incorporate a ductile damage material model into a computational framework based on the Dual Domain Material Point (DDMP) method. As an example, simulations of a flyer plate experiment involving ductile void growth and material failure are performed. The results are compared with experiments performed on high purity tantalum. We also compare the numerical results obtained from the DDMP method with those obtained from the traditional Material Point Method (MPM). Effects of an overstress model, artificial viscosity, and physical viscosity are investigated. Our results show that a physical bulk viscosity and overstress model are important in this impact and failure problem, while physical shear viscosity and artificial shock viscosity have negligible effects. A simple numerical procedure with guaranteed convergence is introduced to solve for the equilibrium plastic state from the ductile damage model.

  1. Radiation damage studies for the D0 silicon detector

    SciTech Connect

    Lehner, F.; /Zurich U.

    2004-01-01

    We report on irradiation studies performed on spare production silicon detector modules for the current D0 silicon detector. The lifetime expectations due to radiation damage effects of the existing silicon detector are reviewed. A new upgrade project was started with the goal of a complete replacement of the existing silicon detector. In that context, several investigations on the radiation hardness of new prototype silicon microstrip detectors were carried out. The irradiation on different detector types was performed with 10 MeV protons up to fluences of 10{sup 14} p/cm{sup 2} at the J.R. Mcdonald Laboratory at Kansas State University. The flux calibration was carefully checked using different normalization techniques. As a result, we observe roughly 40-50% less radiation damage in silicon for 10 MeV p exposure than it is expected by the predicted NIEL scaling.

  2. Sources of fatigue damage to passive yaw wind turbine blades

    SciTech Connect

    Laino, D.J.

    1997-12-31

    Using an integrated computer analysis approach developed at the University of Utah, fatigue damage sources to passive yaw wind turbine blades have been investigated. Models of a rigid hub and teetering hub machine reveal the parameters important to the fatigue design of each type. The teetering hub proved much less susceptible to fatigue damage from normal operation loads. As a result, extreme events were critical to the teetering hub fatigue life. The rigid hub blades experienced extremely large gyroscopic load cycles induced by rapid yaw rates during normal operation. These yaw rates stem from turbulence activity which is shown to be dependent upon atmospheric stability. Investigation revealed that increasing yaw damping is an effective way of significantly reducing these gyroscopic fatigue loads.

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

    SciTech Connect

    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.

  4. DNA Extraction by Isotachophoresis in a Microfluidic Channel

    SciTech Connect

    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

  5. Fractal mechanism for characterizing singularity of mode shape for damage detection

    SciTech Connect

    Cao, M. S.; Ostachowicz, W.; Bai, R. B.; Radzieński, M.

    2013-11-25

    Damage is an ordinary physical phenomenon jeopardizing structural safety; damage detection is an ongoing interdisciplinary issue. Waveform fractal theory has provided a promising resource for detecting damage in plates while presenting a concomitant problem: susceptibility to false features of damage. This study proposes a fractal dimension method based on affine transformation to address this problem. Physical experiments using laser measurement demonstrate that this method can substantially eliminate false features of damage and accurately identify complex cracks in plates, providing a fundamental mechanism that brings the merits of waveform fractal theory into full play in structural damage detection applications.

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

    DOE PAGES [OSTI]

    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. Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana

    DOE PAGES [OSTI]

    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

    Humore » man 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 characterized ApPol η from the thermophilic worm Alvinella pompejana , which inhabits deep-sea hydrothermal vent chimneys. ApPol η shares sequence homology with HsPol η and contains domains for binding ubiquitin and proliferating cell nuclear antigen. Sun-induced UV does not penetrate Alvinella's environment; 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 η is more thermostable than HsPol η , as expected from its habitat temperature. Moreover, the activity of this enzyme was retained in the presence of a higher concentration of organic solvents. Therefore, ApPol η provides a robust, human-like Pol η that is more active after exposure to high temperatures and organic solvents.« less

  8. Facilities for studying radiation damage in nonmetals during irradiation

    SciTech Connect

    Levy, P.W.

    1984-08-01

    Two facilities have been developed for making optical absorption, luminescence and other measurements on a single sample before, during and after irradiation. One facility uses /sup 60/Co gamma rays and the other 0.5 to 3 MeV electrons from an accelerator. Optical relays function as spectrophotometers, luminescenc detectors, etc. All radiation sensitive components are outside of walk-in irradiation chambers; all measurement control and data recording is computerized. Irradiations are made at controlled temperatures between 5K and 900/sup 0/C. The materials studied include glasses, quartz, alkali halides (especially natural rock salt), organic crystals, etc. As determined from color center measurements the damage formation rate in all materials studied at 25/sup 0/C or above is strongly temperature dependent. The defect concentration during irradiation is usually much greater than that measured after irradiation. The fraction of defects annealing after irradiation and the annealing rate usually increases as the irradiation temperature increases. The completed studies demonstrate that, in most cases, the extent of maximum damage and the damage formation and annealing kinetics can be determined only by making measurements during irradiation.

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

    SciTech Connect

    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.

  10. DNA Probe Pooling for Rapid Delineation of Chromosomal Breakpoints

    SciTech Connect

    Lu, Chun-Mei; Kwan, Johnson; Baumgartner, Adolf; Weier, Jingly F.; Wang, Mei; Escudero, Tomas; Munne', Santiago; Zitzelsberger, Horst F.; Weier, Heinz-Ulrich

    2009-01-30

    Structural chromosome aberrations are hallmarks of many human genetic diseases. The precise mapping of translocation breakpoints in tumors is important for identification of genes with altered levels of expression, prediction of tumor progression, therapy response, or length of disease-free survival as well as the preparation of probes for detection of tumor cells in peripheral blood. Similarly, in vitro fertilization (IVF) and preimplantation genetic diagnosis (PGD) for carriers of balanced, reciprocal translocations benefit from accurate breakpoint maps in the preparation of patient-specific DNA probes followed by a selection of normal or balanced oocytes or embryos. We expedited the process of breakpoint mapping and preparation of case-specific probes by utilizing physically mapped bacterial artificial chromosome (BAC) clones. Historically, breakpoint mapping is based on the definition of the smallest interval between proximal and distal probes. Thus, many of the DNA probes prepared for multi-clone and multi-color mapping experiments do not generate additional information. Our pooling protocol described here with examples from thyroid cancer research and PGD accelerates the delineation of translocation breakpoints without sacrificing resolution. The turnaround time from clone selection to mapping results using tumor or IVF patient samples can be as short as three to four days.

  11. Optical selection and collection of DNA fragments

    DOEpatents

    Roslaniec, Mary C.; Martin, John C.; Jett, James H.; Cram, L. Scott

    1998-01-01

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

  12. DNA Persistence in a Sink Drain Environment

    SciTech Connect

    Winder, Eric M.; Bonheyo, George T.

    2015-07-31

    Biofilms are organized structures composed mainly of cells and extracellular polymeric substances produced by the constituent microorganisms. Ubiquitous in nature, biofilms have an innate ability to capture and retain passing material and may therefore act as natural collectors of contaminants or signatures of upstream activities. To determine the persistence and detectability of DNA passing through a sink drain environment, Bacillus anthracis strain Ames35 was cultured (6.35 x 107 CFU/mL), sterilized, and disposed of by addition to a sink drain apparatus with an established biofilm. The sink drain apparatus was sampled before and for several days after the addition of the sterilized B. anthracis culture to detect the presence of B. anthracis DNA. Multiple PCR primer pairs were used to screen for chromosomal and plasmid DNA with primers targeting shorter sequences showing greater amplification efficiency and success. PCR amplification and detection of target sequences indicate persistence of chromosomal DNA and plasmid DNA in the biofilm for 5 or more and 14 or more days, respectively.

  13. DNA Persistence in a Sink Drain Environment

    DOE PAGES [OSTI]

    Winder, Eric M.; Bonheyo, George T.

    2015-07-31

    Biofilms are organized structures composed mainly of cells and extracellular polymeric substances produced by the constituent microorganisms. Ubiquitous in nature, biofilms have an innate ability to capture and retain passing material and may therefore act as natural collectors of contaminants or signatures of upstream activities. To determine the persistence and detectability of DNA passing through a sink drain environment, Bacillus anthracis strain Ames35 was cultured (6.35 x 107 CFU/mL), sterilized, and disposed of by addition to a sink drain apparatus with an established biofilm. The sink drain apparatus was sampled before and for several days after the addition of themore » sterilized B. anthracis culture to detect the presence of B. anthracis DNA. Multiple PCR primer pairs were used to screen for chromosomal and plasmid DNA with primers targeting shorter sequences showing greater amplification efficiency and success. PCR amplification and detection of target sequences indicate persistence of chromosomal DNA and plasmid DNA in the biofilm for 5 or more and 14 or more days, respectively.« less

  14. Role of retinoic acid in the modulation of benzo(a)pyrene-DNA adducts in human hepatoma cells: Implications for cancer prevention

    SciTech Connect

    Zhou Guodong; Richardson, Molly; Fazili, Inayat S.; Wang, Jianbo; Donnelly, Kirby C.; Wang Fen; Amendt, Brad; Moorthy, Bhagavatula

    2010-12-15

    Carcinogen-DNA adducts could lead to mutations in critical genes, eventually resulting in cancer. Many studies have shown that retinoic acid (RA) plays an important role in inducing cell apoptosis. Here we have tested the hypothesis that levels of carcinogen-DNA adducts can be diminished by DNA repair and/or by eliminating damaged cells through apoptosis. Our results showed that the levels of total DNA adducts in HepG2 cells treated with benzo(a)pyrene (BP, 2 {mu}M) + RA (1 {mu}M) were significantly reduced compared to those treated with BP only (P = 0.038). In order to understand the mechanism of attenuation of DNA adducts, further experiments were performed. Cells were treated with BP (4 {mu}M) for 24 h to initiate DNA adduct formation, following which the medium containing BP was removed, and fresh medium containing 1 {mu}M RA was added. The cells were harvested 24 h after RA treatment. Interestingly, the levels of total DNA adducts were lower in the BP/RA group (390 {+-} 34) than those in the BP/DMSO group (544 {+-} 33), P = 0.032. Analysis of cell apoptosis showed an increase in BP + RA group, compared to BP or RA only groups. Our results also indicated that attenuation of BP-DNA adducts by RA was not primarily due to its effects on CYP1A1 expression. In conclusion, our results suggest a mechanistic link between cellular apoptosis and DNA adduct formation, phenomena that play important roles in BP-mediated carcinogenesis. Furthermore, these results help understand the mechanisms of carcinogenesis, especially in relation to the chemopreventive properties of nutritional apoptosis inducers.

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

    SciTech Connect

    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.

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

    DOEpatents

    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.

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

    DOEpatents

    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.

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

    DOEpatents

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

    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.

  19. Laser damage threshold measurements of optical materials for direct laser accelerators

    SciTech Connect

    Soong, Ken; Byer, R. L.; Colby, E. R.; England, R. J.; Peralta, E. A.

    2012-12-21

    The laser-damage threshold is a fundamental limit for any dielectric laser-driven accelerator and is set by the material of the structure. In this paper, we present a theoretical model of the laser damage mechanism, in comparison with experimental data on the damage threshold of silicon. Additionally, we present damage threshold measurement data of various optical materials, most of which have not been previously characterized in the picosecond-regime.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  2. SuppCompensationNuclearDamage_ExtensionComments.PDF | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    SuppCompensationNuclearDamage_ExtensionComments.PDF SuppCompensationNuclearDamage_ExtensionComments.PDF (131.46 KB) 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.

  3. DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

    DOE PAGES [OSTI]

    Hancock, Stephen P.; Stella, Stefano; Cascio, Duilio; Johnson, Reid C.; Leng, Fenfei

    2016-03-09

    The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequencesmore » in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.« less

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

    DOEpatents

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

    2011-01-18

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

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

    SciTech Connect

    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.

  6. Radiation damage in silicon trackers at the Tevatron experiments

    SciTech Connect

    Gonzalez, Oscar; /Madrid, CIEMAT

    2009-01-01

    An overview of the studies performed on the radiation damage affecting the silicon detectors at the CDF and D0 experiments is presented. These detectors have been exposed to a much larger radiation dose (and operating for a longer time) than originally planned and therefore these studies are fundamental to assess the status and future of the sensors. Results are summarized with special emphasis on the techniques used and their complementarity to achieve a complete picture of the effect of the radiation on the sensors and their performance for physics analysis.

  7. Analysis of damage and failure in metal matrix composites

    SciTech Connect

    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.

  8. DDT modeling and shock compression experiments of porous or damaged energetic materials

    SciTech Connect

    Baer, M.R.; Anderson, M.U.; Graham, R.A.

    1994-05-01

    In this presentation, we present modeling of DDT in porous energetic materials and experimental studies of a time-resolved, shock compression of highly porous inert and reactive materials. This combined theoretical and experimental studies explore the nature of the microscale processes of consolidation, deformation and reaction which are key features of the shock response of porous or damaged energetic materials. The theoretical modeling is based on the theory of mixtures in which multiphase mixtures are treated in complete nonequilibrium allowing for internal boundary effects associated mass/momentum and energy exchange between phases, relative flow, rate-dependent compaction behavior, multistage chemistry and interphase boundary effects. Numerous studies of low-velocity impacts using a high resolution adaptive finite element method are presented which replicate experimental observations. The incorporation of this model into multi-material hydrocode analysis will be discussed to address the effects of confinement and its influence on accelerated combustion behavior. The experimental studies will focus on the use of PVDF piezoelectric polymer stress-rate gauge to precisely measure the input and propagating shock stress response of porous materials. In addition to single constituent porous materials, such as granular HMX, we have resolved shock waves in porous composite intermetallic powders that confirm a dispersive wave nature which is highly morphologically and material dependent. This document consists of viewgraphs from the poster session.

  9. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOEpatents

    Dolbeare, Frank A.; Gray, Joe W.

    1986-01-01

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

  10. Surface state reconstruction in ion-damaged SmB6

    DOE PAGES [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 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.

  11. Laser damage resistant pits in dielectric coatings created by femtosecond laser machining

    SciTech Connect

    Wolfe, J; Roger Qiu, ,; Stolz, C; Thomas, M; Martinez, C; Ozkan, A

    2009-11-03

    Replacing growing damage sites with benign, laser damage resistant features in multilayer dielectric films may enable large mirrors to be operated at significantly higher fluences. Laser damage resistant features have been created in high reflecting coatings on glass substrates using femtosecond laser machining. These prototype features have been damage tested to over 40 J/cm{sup 2} (1064nm, 3ns pulselength) and have been shown not to damage upon repeated irradiation at 40J/cm{sup 2}. Further work to optimize feature shape and laser machining parameters is ongoing.

  12. Suspending DNA origami between four gold nanodots

    DOE PAGES [OSTI]

    Morales, Piero; Wang, Liqian; Krissanaprasit, Abhichart; Dalmastri, Claudia; Caruso, Mario N.; De Stefano, Mattia; Mosiello, Lucia; Rapone, Bruno; Rinaldi, Antonio; Vespucci, Stefano; et al

    2015-01-01

    Here, connecting DNA nanostructures to metallic nanostructures at specific positions is a relatively rarely addressed issue in nanotechnology.[1-5] It is of high importance for application of the origami structures as breadboards for molecular electronics and nanosensing arrays since the metallic nanostructures may potentially serve as electrodes.

  13. Chromosome-specific DNA Repeat Probes

    SciTech Connect

    Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.

    2006-03-16

    In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

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

    SciTech Connect

    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.

  15. The role of nickel in radiation damage of ferritic alloys

    DOE PAGES [OSTI]

    Osetskiy, Yury N.; Anento, Napoleon; Serra, Anna; Terentyev, Dmitry

    2014-11-26

    According to the modern theory damage evolution under neutron irradiation depends on the fraction of self interstitial atoms (SIAs) produced in the form of one-dimensionally (1-D) glissile clusters. These clusters, having a low interaction cross-section with other defects, sink mainly on grain boundaries and dislocations creating the so-called production bias. It is known empirically that addition of certain alloying elements affect many radiation effects, including swelling, however the mechanisms are unknown in many cases. In this paper we report the results of an extensive multi-technique atomistic level modeling of SIA clusters mobility in bcc Fe-Ni alloys with Ni content frommore » 0.8 to 10 at.%. We have found that Ni interacts strongly with periphery of clusters affecting their mobility. The total effect is defined by all Ni atoms interacting with the cluster at the same time and can be significant even in low-Ni alloys. Thus 1nm (37SIAs) cluster is practically immobile at T < 500K in the Fe-0.8at.% Ni alloy. Increasing cluster size and Ni content enhance cluster immobilization. Furthermore, this effect should have quite broad consequences in swelling rate, matrix damage accumulation, radiation induced hardening, etc. and the results obtained help in better understanding and prediction of radiation effects in Fe-Ni ferritic alloys.« less

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

    SciTech Connect

    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.

  17. Combined Effects of Temperature and Irradiation on Concrete Damage

    SciTech Connect

    Le Pape, Yann; Giorla, Alain; Sanahuja, Julien

    2016-01-01

    Aggregate radiation-induced volumetric expansion (RIVE) is a predominant mechanism in the formation of mechanical damage in the hardened cement paste (hcp) of irradiated concrete under fast-neutron flux (Giorla et al. 2015). Among the operating conditions difference between test reactors and light water reactors (LWRs), the difference of irradiation flux and temperature is significant. While a temperature increase is quite generally associated with a direct, or indirect (e.g., by dehydration) loss of mechanical properties (Maruyama et al. 2014), we found that it causes a partial annealing of irradiation amorphization of α-quartz, hence, reducing RIVE rate. Based on data collected by Bykov et al. (1981), an incremental RIVE model coupling neutron fluence and temperature is developed. The elastic properties and coefficient of thermal expansion (CTE) of irradiated polycrystalline quartz are interpreted through analytical homogenization of experimental data on irradiated α-quartz published by Mayer and Lecomte (1960). Moreover, the proposed model, implemented in the meso-scale simulation code AMIE, is compared to experimental data obtained on ordinary concrete made of quartz/quartzite aggregate (Dubrovskii et al. 1967). Substantial discrepancy, in terms of damage and volumetric expansion developments, is found when comparing irradiation scenarios assuming constant flux and temperature, as opposed to more realistic test reactor operation conditions.

  18. Emulation of reactor irradiation damage using ion beams

    SciTech Connect

    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, 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.

  19. Emulation of reactor irradiation damage using ion beams

    DOE PAGES [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 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

  20. Characterization of swift heavy ion irradiation damage in ceria

    DOE PAGES [OSTI]

    Yablinsky, Clarissa A.; Devanathan, Ram; Pakarinen, Janne; Gan, Jian; Severin, Daniel; Trautmann, Christina; Allen, Todd R.

    2015-03-04

    Swift heavy ion induced radiation damage is investigated for ceria (CeO2), which serves as a UO2 fuel surrogate. Microstructural changes resulting from an irradiation with 940 MeV gold ions of 42 keV/nm electronic energy loss are investigated by means of electron microscopy accompanied by electron energy loss spectroscopy showing that there exists a small density reduction in the ion track core. While chemical changes in the ion track are not precluded, evidence of them was not observed. Classical molecular dynamics simulations of thermal spikes in CeO2 with an energy deposition of 12 and 36 keV/nm show damage consisting of isolatedmore » point defects at 12 keV/nm, and defect clusters at 36 keV/nm, with no amorphization at either energy. Furthermore, inferences are drawn from modeling about density changes in the ion track and the formation of interstitial loops that shed light on features observed by electron microscopy of swift heavy ion irradiated ceria.« less

  1. The Role of Nickel in Radiation Damage of Ferritic Alloys.

    SciTech Connect

    Osetskiy, Yury N; Anento, Napoleon; Serra, Anna; Terentyev, Dmitry

    2015-01-01

    According to the modern theory damage evolution under neutron irradiation depends on the fraction of self interstitial atoms (SIAs) produced in the form of one-dimensionally (1-D) glissile clusters. These clusters, having a low interaction cross-section with other defects, sink mainly on grain boundaries and dislocations creating the so-called production bias. It is known empirically that addition of certain alloying elements affect many radiation effects, including swelling, however the mechanisms are unknown in many cases. In this paper we report the results of an extensive multi-technique atomistic level modeling of SIA clusters mobility in bcc Fe-Ni alloys with Ni content from 0.8 to 10 at.%. We have found that Ni interacts strongly with periphery of clusters affecting their mobility. The total effect is defined by all Ni atoms interacting with the cluster at the same time and can be significant even in low-Ni alloys. Thus 1nm (37SIAs) cluster is practically immobile at T<500K in the Fe-0.8at.% Ni alloy. Increasing cluster size and Ni content enhance cluster immobilization. This effect should have quite broad consequences in swelling rate, matrix damage accumulation, radiation induced hardening, etc. and the results obtained help in better understanding and prediction of radiation effects in Fe-Ni ferritic alloys.

  2. Combined Effects of Temperature and Irradiation on Concrete Damage

    DOE PAGES [OSTI]

    Le Pape, Yann; Giorla, Alain; Sanahuja, Julien

    2016-01-01

    Aggregate radiation-induced volumetric expansion (RIVE) is a predominant mechanism in the formation of mechanical damage in the hardened cement paste (hcp) of irradiated concrete under fast-neutron flux (Giorla et al. 2015). Among the operating conditions difference between test reactors and light water reactors (LWRs), the difference of irradiation flux and temperature is significant. While a temperature increase is quite generally associated with a direct, or indirect (e.g., by dehydration) loss of mechanical properties (Maruyama et al. 2014), we found that it causes a partial annealing of irradiation amorphization of α-quartz, hence, reducing RIVE rate. Based on data collected by Bykovmore » et al. (1981), an incremental RIVE model coupling neutron fluence and temperature is developed. The elastic properties and coefficient of thermal expansion (CTE) of irradiated polycrystalline quartz are interpreted through analytical homogenization of experimental data on irradiated α-quartz published by Mayer and Lecomte (1960). Moreover, the proposed model, implemented in the meso-scale simulation code AMIE, is compared to experimental data obtained on ordinary concrete made of quartz/quartzite aggregate (Dubrovskii et al. 1967). Substantial discrepancy, in terms of damage and volumetric expansion developments, is found when comparing irradiation scenarios assuming constant flux and temperature, as opposed to more realistic test reactor operation conditions.« less

  3. Characterization of swift heavy ion irradiation damage in ceria

    SciTech Connect

    Yablinsky, Clarissa A.; Devanathan, Ram; Pakarinen, Janne; Gan, Jian; Severin, Daniel; Trautmann, Christina; Allen, Todd R.

    2015-03-04

    Swift heavy ion induced radiation damage is investigated for ceria (CeO2), which serves as a UO2 fuel surrogate. Microstructural changes resulting from an irradiation with 940 MeV gold ions of 42 keV/nm electronic energy loss are investigated by means of electron microscopy accompanied by electron energy loss spectroscopy showing that there exists a small density reduction in the ion track core. While chemical changes in the ion track are not precluded, evidence of them was not observed. Classical molecular dynamics simulations of thermal spikes in CeO2 with an energy deposition of 12 and 36 keV/nm show damage consisting of isolated point defects at 12 keV/nm, and defect clusters at 36 keV/nm, with no amorphization at either energy. Furthermore, inferences are drawn from modeling about density changes in the ion track and the formation of interstitial loops that shed light on features observed by electron microscopy of swift heavy ion irradiated ceria.

  4. Emulation of reactor irradiation damage using ion beams

    SciTech Connect

    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.

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

    U.S. Department of Energy (DOE) - all 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...

  6. Encapsulation of Gold Nanoparticles in a DNA Origami Cage

    U.S. Department of Energy (DOE) - all 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 ...

  7. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    these processes; however, the DNA cleavage chemistry used to resolve these altered DNA structures can also operate as a weak link that can be exploited to kill cells-in a good way. ...

  8. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOEpatents

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

    1983-10-18

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

  9. Lectin cDNA and transgenic plants derived therefrom

    DOEpatents

    Raikhel, Natasha V.

    2000-10-03

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

  10. DNA release from lipoplexes by anionic lipids: correlation with...

    Office of Scientific and Technical Information (OSTI)

    The separation of DNA from lipid measured this way was considerably slower and less ... This result was confirmed by centrifugal separation of released DNA and lipid. X-ray ...

  11. DNA origami with Complex Curvatures in 3D

    U.S. Department of Energy (DOE) - all 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

  12. Response_289.pdf

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    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

  13. Methods to alter levels of a DNA repair protein

    DOEpatents

    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.

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

    SciTech Connect

    Not Available

    1982-09-01

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

  15. Monitoring genetic damage to ecosystems from hazardous waste

    SciTech Connect

    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.

  16. Radiation Damage Study in Natural Zircon Using Neutrons Irradiation

    SciTech Connect

    Lwin, Maung Tin Moe; Amin, Yusoff Mohd.; Kassim, Hasan Abu; Mohamed, Abdul Aziz; Karim, Julia Abdul

    2011-03-30

    Changes of atomic displacements in crystalline structure of natural zircon (ZrSiO{sub 4}) can be studied by using neutron irradiation on the surface of zircon and compared the data from XRD measurements before and after irradiation. The results of neutron irradiation on natural zircon using Pneumatic Transfer System (PTS) at PUSPATI TRIGA Research Reactor in the Malaysian Nuclear Agency are discussed in this work. The reactor produces maximum thermal power output of 1 MWatt and the neutron flux of up to 1x10{sup 13} ncm{sup -2}s{sup -1}. From serial decay processes of uranium and thorium radionuclides in zircon crystalline structure, the emission of alpha particles can produce damage in terms of atomic displacements in zircon. Hence, zircon has been extensively studied as a possible candidate for immobilization of fission products and actinides.

  17. Molecular dynamics simulation of radiation damage cascades in diamond

    SciTech Connect

    Buchan, J. T.; Robinson, M.; Christie, H. J.; Roach, D. L.; Ross, D. K.; Marks, N. A.

    2015-06-28

    Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.

  18. One call systems can limit third party damage exposure

    SciTech Connect

    Meadows, R.C.; Sage, J.W.

    1985-10-01

    This paper describes how the Olympic Pipeline Co., in Washington, uses computers to handle more than 13,000 One Call messages annually. One call systems give contractors and the general public the ability to make one phone call and have all the utilities contacted in the general area of planned work. All the 1984 One Call messages were hand-researched and checked against system maps to determine if conflicts existed. Out of the 13,262 messages received, 12,763 were determined by a map search to be outside of the pipe line right of way. This represents, on the average, 4.4 man hours per day of clerical time spent checking the messages on the maps. Participating in a One Call system will definitely increase the work load of existing company personnel, and the system does not guarantee a company will never notified of all encroachment activity or never incur line damage as a result of encroachment.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  1. Sirtuin 6 protects the heart from hypoxic damage

    SciTech Connect

    Maksin-Matveev, Anna; Kanfi, Yariv; Hochhauser, Edith; Isak, Ahuva; Cohen, Haim Y.; Shainberg, Asher

    2015-01-01

    Sirtuin 6 (SIRT6) is a protein associated with prolonged life expectancy. We investigated whether life extension is associated with cardioprotection against hypoxia. The proposed study is to develop approaches to reduce hypoxic damage through the use of the sirtuin pathway and to elucidate the mechanism involved. For that purpose we subjected cardiomyocytes from transgenic mice (TG) with over-expression of SIRT6, to hypoxic stress in cell cultures. We hypothesized that cardiomyocytes from transgenic mice subjected to prolonged hypoxia may release survival factors or fewer damage markers to protect them from hypoxic stress compared with wild type (WT) mice. Lactate dehydrogenase (LDH) and creatine kinase (CK) released to the medium and propidium iodide (PI) binding, were markedly decreased following hypoxia in TG cardiomyocytes. The protective mechanism of SIRT6 over-expression includes the activation of pAMPKα pathway, the increased protein level of B-cell lymphoma 2 (Bcl2), the inhibition of nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB), the decrease of reactive oxygen species (ROS) and the reduction in the protein level of phospho-protein kinase B (pAkt) during hypoxia. Together, all these processes impede the necrosis/apoptosis pathways leading to the improved survival of cardiomyocytes following hypoxia, which might explain life extension. - Highlights: • Sirtuin 6 is a protein associated with prolonged life expectancy. • Over-expression of sirtuin 6 protects cardiocytes from hypoxia and oxidative stress. • Over-expression of sirtuin 6 activates the pAMPKα pathway and the Bcl2 expression. • Over-expression of sirtuin 6 decreases ROS formation and pAkt level during hypoxia. • These pathways protect cardiocytes from hypoxia and might explain lifespan extension.

  2. Catastrophic nanosecond laser induced damage in the bulk of potassium titanyl phosphate crystals

    SciTech Connect

    Wagner, Frank R. Natoli, Jean-Yves; Akhouayri, Hassan; Commandré, Mireille; Duchateau, Guillaume

    2014-06-28

    Due to its high effective nonlinearity and the possibility to produce periodically poled crystals, potassium titanyl phosphate (KTiOPO{sub 4}, KTP) is still one of the economically important nonlinear optical materials. In this overview article, we present a large study on catastrophic nanosecond laser induced damage in this material and the very similar RbTiOPO{sub 4} (RTP). Several different systematic studies are included: multiple pulse laser damage, multi-wavelength laser damage in KTP, damage resistance anisotropy, and variations of the laser damage thresholds for RTP crystals of different qualities. All measurements were carried out in comparable experimental conditions using a 1064 nm Q-switched laser and some were repeated at 532 nm. After summarizing the experimental results, we detail the proposed model for laser damage in this material and discuss the experimental results in this context. According to the model, nanosecond laser damage is caused by light-induced generation of transient laser-damage precursors which subsequently provide free electrons that are heated by the same nanosecond pulse. We also present a stimulated Raman scattering measurement and confront slightly different models to the experimental data. Finally, the physical nature of the transient damage precursors is discussed and similarities and differences to laser damage in other crystals are pointed out.

  3. DNA-Guided Crystallization of Colloidal Nanoparticles

    SciTech Connect

    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.

  4. Modeling the mechanical response of PBX 9501

    SciTech Connect

    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.

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

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

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

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

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

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

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

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

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

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

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

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

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

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

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

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

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

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

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

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

  15. Determining orientation and direction of DNA sequences

    DOEpatents

    Goodwin, Edwin H.; Meyne, Julianne

    2000-01-01

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

  16. Preparation of DNA-containing extract for PCR amplification

    DOEpatents

    Dunbar, John M.; Kuske, Cheryl R.

    2006-07-11

    Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 5–10 minutes.

  17. Stepped electrophoresis for movement and concentration of DNA

    DOEpatents

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

    2005-03-15

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

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

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

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

  19. Preparation of DNA-containing extract for PCR amplification

    DOEpatents

    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.

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

    U.S. Department of Energy (DOE) - all 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

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  3. Direct comparison of defect ensembles extracted from damage probability and raster scan measurements

    SciTech Connect

    Batavičiūtė, G. Ščiuka, M.; Melninkaitis, A.

    2015-09-14

    The presented study addresses the characterization of nanometer sized defects acting as damage precursors in nanosecond laser pulse duration regime. Two approaches are used to extract distributions of localized damage precursors, namely, damage probability and damage density measurements. Testing is performed on uncoated and SiO{sub 2} monolayer film deposited fused silica substrate exposed with pulsed UV irradiation (355 nm, 4.8 ns). Then, a direct comparison of damage precursor ensembles obtained from both methods is carried out. Our analysis indicates apparent differences between both methods that are discussed in detail. Contamination by ablation products is identified as one of the key factors that influence damage density measurements.

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

    SciTech Connect

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

    2009-05-11

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

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

    SciTech Connect

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

    2015-09-13

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

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

    DOE PAGES [OSTI]

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

    2015-09-13

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

  7. WILD PIGS: BIOLOGY, DAMAGE, CONTROL TECHINQUES AND MANAGEMENT

    SciTech Connect

    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

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

    SciTech Connect

    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.

  9. Demand Response | Department of Energy

    Energy Saver

    Technology Development Smart Grid Demand Response Demand Response Demand Response Demand response provides an opportunity for consumers to play a significant role in the ...

  10. Cross-sector Demand Response

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

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

  11. Transcription-Driven Twin Supercoiling of a DNA Loop: A Brownian Dynamics Study

    SciTech Connect

    Mielke, S P; Fink, W H; Krishnan, K; Gronbech-Jensen, N; Benham, C J

    2004-06-30

    The torque generated by RNA polymerase as it tracks along double-stranded DNA can potentially induce long-range structural deformations integral to mechanisms of biological significance in both prokaryotes and eukaryotes. In this report, we introduce a dynamic computer model for investigating this phenomenon. Duplex DNA is represented as a chain of hydrodynamic bends interacting through elastic potentials. The chain, linear when relaxed, is looped to form two open but topologically constrained subdomains. This permits the dynamic introduction of torsional stress via a centrally applied torque. We simulate by Brownian dynamics the 100 {micro}s response of a 477-basepair B-DNA template to the localized torque generated by the prokaryotic transcription ensemble. Following a sharp rise at early times, the distributed twist assumes a nearly constant value in both subdomains, and a succession of supercoiling deformations occurs as superhelical stress is increasingly partitioned to writhe. The magnitude of writhe surpasses that of twist before also leveling off when the structure reaches mechanical equilibrium with the torsional load. Superhelicity is simultaneously right-handed in one subdomain and left-handed in the other. The properties of the chain at the onset of writhing agree well with predictions from theory, and the generated stress is ample for driving secondary structural transitions in physiological DNA. These results suggest that the torsional stress generated by transcription can significantly deform the DNA template over short times. This highlights the potential of transcription and other tracking processes to play a central role in gene regulation, and prompts further investigation of dynamically-generated supercoiling.

  12. Mechanisms of formation damage in matrix-permeability geothermal wells

    SciTech Connect

    Bergosh, J.L.; Wiggins, R.B.; Enniss, D.O.

    1982-04-01

    Tests were conducted to determine mechanisms of formation damage that can occur in matrix permeability geothermal wells. Two types of cores were used in the testing, actual cores from the East Mesa Well 78-30RD and cores from a fairly uniform generic sandstone formation. Three different types of tests were run. The East Mesa cores were used in the testing of the sensitivity of core to filtrate chemistry. The tests began with the cores exposed to simulated East Mesa brine and then different filtrates were introduced and the effects of the fluid contrast on core permeability were measured. The East Mesa cores were also used in the second series of tests which tested formation sandstone cores were used in the third test series which investigated the effects of different sizes of entrained particles in the fluid. Tests were run with both single-particle sizes and distributions of particle mixes. In addition to the testing, core preparation techniques for simulating fracture permeability were evaluated. Three different fracture formation mechanisms were identified and compared. Measurement techniques for measuring fracture size and permeability were also developed.

  13. Influence of sweeping detonation-wave loading on damage evolution during spallation loading of tantalum in both a planar and curved geometry

    SciTech Connect

    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

  14. DNA Persistence in Sink Drain Environment

    SciTech Connect

    Winder, Eric M.; Bonheyo, George T.

    2015-07-31

    Biofilms are organized structures composed mainly of cells and extracellular polymeric substances produced by the constituent microorganisms. Ubiquitous in nature, biofilms have an innate ability to capture and retain passing material and may therefore act as natural collectors of contaminants or signatures of upstream activities. To determine the persistence and detectability of DNA passing through a sink drain environment, Bacillus anthracis strain Ames35 was cultured (6.35 x 107 CFU/mL), sterilized, and disposed of by addition to a sink drain apparatus with an established biofilm.

  15. Challenges and opportunities for structural DNA nanotechnology

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    ChallengeHER 2016-10-26 Event ChallengeHER 2016-10-26 Event October 26, 2016 8:00AM to 12:30PM MDT CNM Workforce Leaning Center 5600 Eagle Rock Avenue NE Albuquerque, NM 87113 Opportunities for Women in Federal Contracting Successfully navigate the federal contracting industry and win federal contracts by knowing the rules and understanding the strategies. To view or download the flyer click here.

    Challenges and opportunities for structural DNA nanotechnology Authors: Pinheiro, A. V., Han,

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

    SciTech Connect

    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.

  17. Beam test evaluation of electromagnetic calorimeter modules made from proton-damaged PbWO4 crystals

    DOE PAGES [OSTI]

    Adams, T.; Adzic, P.; Ahuja, S.; Anderson, D.; Andrews, M. B.; Antropov, I.; Antunovic, Z.; Arcidiacono, R.; Arenton, M. W.; Argirò, S.; et al

    2016-04-11

    The performance of electromagnetic calorimeter modules made of proton-irradiated PbWO4 crystals has been studied in beam tests. The modules, similar to those used in the Endcaps of the CMS electromagnetic calorimeter (ECAL), were formed from 5×5 matrices of PbWO4 crystals, which had previously been exposed to 24 GeV protons up to integrated fluences between 2.1 × 1013 and 1.3 × 1014 cm–2. These correspond to the predicted charged-hadron fluences in the ECAL Endcaps at pseudorapidity η = 2.6 after about 500 fb–1 and 3000 fb–1 respectively, corresponding to the end of the LHC and High Luminosity LHC operation periods. Themore » irradiated crystals have a lower light transmission for wavelengths corresponding to the scintillation light, and a correspondingly reduced light output. A comparison with four crystals irradiated in situ in CMS showed no significant rate dependence of hadron-induced damage. A degradation of the energy resolution and a non-linear response to electron showers are observed in damaged crystals. Direct measurements of the light output from the crystals show the amplitude decreasing and pulse becoming faster as the fluence increases. The latter is interpreted, through comparison with simulation, as a side-effect of the degradation in light transmission. In conclusion, the experimental results obtained can be used to estimate the long term performance of the CMS ECAL.« less

  18. Accident Response Group | National Nuclear Security Administration

    National Nuclear Security Administration (NNSA)

    Accident Response Group

  19. Characterization of irradiation damage distribution near TiO{sub 2}/SrTiO{sub 3} interfaces using coherent acoustic phonon interferometry

    SciTech Connect

    Yarotski, Dmitry; Yan Li; Jia Quanxi; Taylor, Antoinette J.; Fu Engang; Wang Yongqiang; Uberuaga, Blas P.

    2012-06-18

    We apply ultrafast coherent acoustic phonon interferometry to characterize the distribution of the radiation damage near the TiO{sub 2}/SrTiO{sub 3} interfaces. We show that the optical and mechanical properties of anatase TiO{sub 2} remain unaffected by the radiation dosages in the 0.1 Division-Sign 5 dpa (displacements per atom) range, while the degraded optical response indicates a significant defect accumulation in the interfacial region of SrTiO{sub 3} at 0.1 dpa and subsequent amorphization at 3 dpa. Comparison between the theoretical simulations and the experimental results reveals an almost threefold reduction of the sound velocity in the irradiated SrTiO{sub 3} layer with peak damage levels of 3 and 5 dpa.

  20. Bacterial CRISPR/Cas DNA endonucleases: A revolutionary technology that could dramatically impact viral research and treatment

    SciTech Connect

    Kennedy, Edward M.; Cullen, Bryan R.

    2015-05-15

    CRISPR/Cas systems mediate bacterial adaptive immune responses that evolved to protect bacteria from bacteriophage and other horizontally transmitted genetic elements. Several CRISPR/Cas systems exist but the simplest variant, referred to as Type II, has a single effector DNA endonuclease, called Cas9, which is guided to its viral DNA target by two small RNAs, the crRNA and the tracrRNA. Initial efforts to adapt the CRISPR/Cas system for DNA editing in mammalian cells, which focused on the Cas9 protein from Streptococcus pyogenes (Spy), demonstrated that Spy Cas9 can be directed to DNA targets in mammalian cells by tracrRNA:crRNA fusion transcripts called single guide RNAs (sgRNA). Upon binding, Cas9 induces DNA cleavage leading to mutagenesis as a result of error prone non-homologous end joining (NHEJ). Recently, the Spy Cas9 system has been adapted for high throughput screening of genes in human cells for their relevance to a particular phenotype and, more generally, for the targeted inactivation of specific genes, in cell lines and in vivo in a number of model organisms. The latter aim seems likely to be greatly enhanced by the recent development of Cas9 proteins from bacterial species such as Neisseria meningitidis and Staphyloccus aureus that are small enough to be expressed using adeno-associated (AAV)-based vectors that can be readily prepared at very high titers. The evolving Cas9-based DNA editing systems therefore appear likely to not only impact virology by allowing researchers to screen for human genes that affect the replication of pathogenic human viruses of all types but also to derive clonal human cell lines that lack individual gene products that either facilitate or restrict viral replication. Moreover, high titer AAV-based vectors offer the possibility of directly targeting DNA viruses that infect discrete sites in the human body, such as herpes simplex virus and hepatitis B virus, with the hope that the entire population of viral DNA genomes