Sample records for dna damage response

  1. Cellular responses to environmental DNA damage

    SciTech Connect (OSTI)

    Not Available

    1994-08-01T23:59:59.000Z

    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. Ubiquitylation, neddylation and the DNA damage response

    E-Print Network [OSTI]

    Brown, Jessica S.; Jackson, Stephen P.

    2015-04-01T23:59:59.000Z

    major families: RING (really interesting new gene), HECT (homology to E6AP car- boxyl-terminus) and RBR (ring between ring) [102,103]. The transcription, respectively [88] trans-lesion synthesis (TLS) TLS is a DNA damage bypass mechanism tha It employs... depends on RNF4 binding to SUMO2/3 polymeric chains and subsequent RNF4 dimerization [183]. In addition to its role in promoting the turnover of proteins, RNF4 might also be important for the formation of hybrid SUMO/ubiquitin chains at DNA damage sites...

  3. Conserved and Unconventional Responses to DNA Damage in Tetrahymena 

    E-Print Network [OSTI]

    Sandoval Oporto, Pamela

    2012-07-16T23:59:59.000Z

    characterization of the response to genotoxic agents showed that Tetrahymena is able to activate a G1/S and intra-S phase DNA damage response. The results presented here suggest that a caffeine-dependent checkpoint activator protein modulates the response to DNA...

  4. DNA damage responses in the context of the cell division cycle

    E-Print Network [OSTI]

    Giunta, Simona

    2010-11-16T23:59:59.000Z

    During my PhD, I have investigated aspects of the DNA damage response (DDR) in the context of three different cellular scenarios: DNA damage signalling in response to double-strand breaks during mitosis, coordination of DNA replication with DNA...

  5. Functional role of p53 N-terminal phosphorylation in regulating the p53 response to DNA damage

    E-Print Network [OSTI]

    Chao, Connie

    2006-01-01T23:59:59.000Z

    the p53 Responses to DNA Damage. Proc. Natl. Acad. Sci. USAapoptosis following DNA damage. EMBO J. 19, 4967-4975. Chao,Herrlich, P. (1999). DNA damage induced p53 stabilization:

  6. ATM Phosphorylates and Activates the Transcription Factor MEF2D for Neuronal Survival in Response to DNA Damage

    E-Print Network [OSTI]

    Chan, Shing Fai

    2009-01-01T23:59:59.000Z

    by ATM in response to DNA damage. Science, 281, 1674-1677.J. and Kastan M. B. (2003). DNA damage activates ATM throughgene product causes oxidative damage in target organs. Proc.

  7. Cellular responses against DNA damaged by platinum anticancer drugs

    E-Print Network [OSTI]

    Jung, Yongwon, 1977-

    2005-01-01T23:59:59.000Z

    The anticancer activity of platinum-based drugs such as cisplatin, carboplatin, and oxaliplatin is mediated by their ability to attack DNA such that generated adducts trigger numerous cellular responses. A better understanding ...

  8. Conserved and Unconventional Responses to DNA Damage in Tetrahymena

    E-Print Network [OSTI]

    Sandoval Oporto, Pamela

    2012-07-16T23:59:59.000Z

    ongoing genome instability ............................................................ 60 Elevated levels of DNA damage in MMS-treated TIF1 mutants ... 61 Differential regulation of TIF1 and RAD51 in MMS-treated cells... ................................ 59 2.2 Micronuclear genome instability in TIF1-deficient T. thermophila .......... 62 2.3 Regulation of RAD51 and TIF1 by MMS ................................................. 66 2.4 Immunolocalization of Rad51p and Tif1p in control and MMS...

  9. Integration of the phosphorylation-dependent signaling in the DNA damage response network : implications for cancer

    E-Print Network [OSTI]

    Manke, Isaac Andrew

    2005-01-01T23:59:59.000Z

    The cellular response to DNA damage is an evolutionarily conserved process mediated by Ser/Thr kinases that results in the formation of multiple protein-protein complexes designed to control the cell cycle. The assembly ...

  10. Functional analysis of p53 N-terminal phosphorylation and C-terminal multiple posttranslational modifications in regulating p53 responses to DNA damage

    E-Print Network [OSTI]

    Feng, Lijin

    2006-01-01T23:59:59.000Z

    C. W. , and Appella, E. DNA damage activates p53 through aby ATM in Response to DNA Damage. Science 133.Shieh, S. Y. ,Y. , and Prives, C. DNA damage-induced phosphorylation of

  11. DNA damage response to different surface chemistry of silver nanoparticles in mammalian cells

    SciTech Connect (OSTI)

    Ahamed, Maqusood; Karns, Michael; Goodson, Michael; Rowe, John [Department of Biology, Centre for Tissue Regeneration and Engineering, University of Dayton, Dayton-45469, OH (United States); Hussain, Saber M.; Schlager, John J. [Applied Biotechnology Branch, Human Effectiveness Directorate Air Force Research Laboratory/HEPB, Wright-Patterson Air Force Base-45433, OH (United States); Hong Yiling [Department of Biology, Centre for Tissue Regeneration and Engineering, University of Dayton, Dayton-45469, OH (United States)], E-mail: Yiling.Hong@notes.udayton.edu

    2008-12-15T23:59:59.000Z

    Silver nanoparticles (Ag NPs) have recently received much attention for their possible applications in biotechnology and life sciences. Ag NPs are of interest to defense and engineering programs for new material applications as well as for commercial purposes as an antimicrobial. However, little is known about the genotoxicity of Ag NPs following exposure to mammalian cells. This study was undertaken to examine the DNA damage response to polysaccharide surface functionalized (coated) and non-functionalized (uncoated) Ag NPs in two types of mammalian cells; mouse embryonic stem (mES) cells and mouse embryonic fibroblasts (MEF). Both types of Ag NPs up-regulated the cell cycle checkpoint protein p53 and DNA damage repair proteins Rad51 and phosphorylated-H2AX expression. Furthermore both of them induced cell death as measured by the annexin V protein expression and MTT assay. Our observations also suggested that the different surface chemistry of Ag NPs induce different DNA damage response: coated Ag NPs exhibited more severe damage than uncoated Ag NPs. The results suggest that polysaccharide coated particles are more individually distributed while agglomeration of the uncoated particles limits the surface area availability and access to membrane bound organelles.

  12. A novel high-throughput in-cell Western assay for the quantitative measurement of signaling dynamics in DNA damage signaling networks : cell decision processes in response to DNA double strand breaks

    E-Print Network [OSTI]

    Tentner, Andrea R. (Andrea Ruth)

    2006-01-01T23:59:59.000Z

    Following exposure to DNA damage, cells initiate a stress response involving multiple protein kinase signaling cascades. The DNA damage response results in one of several possible cell-fate decisions, or cellular responses: ...

  13. RhoJ Regulates Melanoma Chemoresistance by Suppressing Pathways that Sense DNA Damage

    E-Print Network [OSTI]

    Ho, Hsiang; Aruri, Jayavani; Kapadia, Rubina; Mehr, Hootan; White, Michael A.; Ganesan, Anand K.

    2012-01-01T23:59:59.000Z

    Pathways that Sense DNA Damage $watermark-text Hsiang Ho 1 ,16. Roos WP, Kaina B. DNA damage-induced apoptosis: FromDNA lesions to the DNA damage response and apoptosis. Cancer

  14. The role of mismatch repair and recombination in cellular responses to the DNA damaging anticancer drug Cisplatin

    E-Print Network [OSTI]

    Zdraveski, Zoran Z. (Zoran Zare), 1969-

    2002-01-01T23:59:59.000Z

    Cisplatin (cis-diamminedichloroplatinum(ll)) is a successful DNA-damaging anticancer drug used in the treatment of testicular, ovarian and other tumors. In the past decade, several mutually non-exclusive hypotheses have ...

  15. Anc1 : a new player in the cellular response to DNA damage

    E-Print Network [OSTI]

    Erlich, Rachel L

    2007-01-01T23:59:59.000Z

    The continuity of living organisms depends on their ability to protect their genomes from a constant assault by internal and external sources of damage. To this end, cells have developed a variety of mechanisms to avoid ...

  16. Response of DNA repair and replication systems to exocyclic nucleic acid base damage

    E-Print Network [OSTI]

    ?r?v?stava, Nidhi

    2012-01-01T23:59:59.000Z

    Genomes experience an often hostile environment that creates a vast array of damages that can give rise to myriad biological outcomes. Fortunately, cells are equipped with networks such as direct reversal, base excision ...

  17. Method for assaying clustered DNA damages

    DOE Patents [OSTI]

    Sutherland, Betsy M.

    2004-09-07T23:59:59.000Z

    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.

  18. A DNA Damage-Induced, SOS-Independent Checkpoint Regulates Cell Division in Caulobacter crescentus

    E-Print Network [OSTI]

    Modell, Joshua W.

    Cells must coordinate DNA replication with cell division, especially during episodes of DNA damage. The paradigm for cell division control following DNA damage in bacteria involves the SOS response where cleavage of the ...

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

    SciTech Connect (OSTI)

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

    2005-07-29T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2009-01-01T23:59:59.000Z

    Kastan, M. B. (1997). DNA damage induces phosphorylation ofby ATM in response to DNA damage. Science 281, Barber, R. ,Nussenzweig, A. (2002). DNA damage-induced G2-M checkpoint

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

    SciTech Connect (OSTI)

    O'Neill, Peter [University of Oxford; Anderson, Jennifer [University of Oxford

    2014-10-02T23:59:59.000Z

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

  2. Micropatterned cell arrays for detecting DNA damage

    E-Print Network [OSTI]

    Mittal, Sukant

    2008-01-01T23:59:59.000Z

    Numerous agents are capable of interacting with DNA and damaging it. Permanent changes in the DNA structure can be both mutagenic and cytotoxic; therefore, methods to measure the susceptibility of cells to mutations are ...

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

    male germ cells handle DNA damage? Toxicol. Appl. Pharmacol.strand breaks and DNA base damage at different cellularrelationship to genetic damage, Mutat. Res. 216 (1989) 221-

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

    male germ cells handle DNA damage? Toxicol. Appl. Pharmacol.strand breaks and DNA base damage at different cellularrelationship to genetic damage, Mutat. Res. 216 (1989) 221-

  5. A DNA damage checkpoint in Caulobacter crescentus inhibits cell division through a direct interaction with FtsW

    E-Print Network [OSTI]

    Modell, Joshua Wexler

    Following DNA damage, cells typically delay cell cycle progression and inhibit cell division until their chromosomes have been repaired. The bacterial checkpoint systems responsible for these DNA damage responses are ...

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

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

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

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

    E-Print Network [OSTI]

    Woodruff, Rachel Van Etten

    2008-01-01T23:59:59.000Z

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

  8. Quantitative measurement and modeling of the DNA damage signaling network : DNA double-strand breaks

    E-Print Network [OSTI]

    Tentner, Andrea R. (Andrea Ruth)

    2009-01-01T23:59:59.000Z

    DNA double-strand breaks (DSB) are one of the major mediators of chemotherapy-induced cytotoxicity in tumors. Cells that experience DNA damage can initiate a DNA damage-mediated cell-cycle arrest, attempt to repair the ...

  9. The dynamic interplay between DNA damage and metabolism : the metabolic fate and transport of DNA lesions and novel DNA damage derived from intermediary metabolism

    E-Print Network [OSTI]

    Jumpathong, Watthanachai

    2014-01-01T23:59:59.000Z

    The work presented in this thesis explores two novel and complementary facets of endogenous DNA damage: the development of biomarkers of inflammation based on metabolites of DNA damage products and the formation of DNA ...

  10. DNA-damage-mediated remodeling of normal and tumor microenvironments modulates cell survival

    E-Print Network [OSTI]

    Gilbert, Luke A. (Luke Andrew)

    2012-01-01T23:59:59.000Z

    Chemotherapeutic regimens involve the systemic administration of genotoxic compounds that induce cancer cell death via well-established DNA damage response signaling networks. While modern chemotherapeutic regimens can be ...

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

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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.

  12. Spatially localized generation of nucleotide sequence-specific DNA damage

    E-Print Network [OSTI]

    Boxer, Steven G.

    Spatially localized generation of nucleotide sequence-specific DNA damage Dennis H. Oh* , Brett A- neously manipulated at the nucleotide level and in three dimen- sions. This approach for targeting

  13. Nanofoams Response to Radiation Damage

    SciTech Connect (OSTI)

    Fu, Engang [Los Alamos National Laboratory; Serrano De Caro, Magdalena [Los Alamos National Laboratory; Wang, Yongqiang [Los Alamos National Laboratory; Nastasi, Michael [Nebraska Center for Energy Sciences Research, University of Nebraska-Lincoln, NE 68508; Zepeda-Ruiz, Luis [PLS, Lawrence Livermore National Laboratory, Livermore, CA 94551; Bringa, Eduardo M. [CONICET and Inst. Ciencias Basicas, Universidad Nacional de Cuyo, Mendoza, 5500 Argentina; Baldwin, Jon K. [Los Alamos National Laboratory; Caro, Jose A. [Los Alamos National Laboratory

    2012-07-30T23:59:59.000Z

    Conclusions of this presentation are: (1) np-Au foams were successfully synthesized by de-alloying process; (2) np-Au foams remain porous structure after Ne ion irradiation to 1 dpa; (3) SFTs were observed in irradiated np-Au foams with highest and intermediate flux, while no SFTs were observed with lowest flux; (4) SFTs were observed in irradiated np-Au foams at RT, whereas no SFTs were observed at LNT irradiation; (5) The diffusivity of vacancies in Au at RT is high enough so that the vacancies have enough time to agglomerate and thus collapse. As a result, SFTs were formed; (6) The high flux created much more damage/time, vacancies don't have enough time to diffuse or recombine. As a result, SFTs were formed.

  14. Functional analysis of p53 N-terminal phosphorylation and C-terminal multiple posttranslational modifications in regulating p53 responses to DNA damage

    E-Print Network [OSTI]

    Feng, Lijin

    2006-01-01T23:59:59.000Z

    derived from the p53 C-terminal domain. Nat Med. 1997;3:632-core and nonspecific C-terminal DNA binding domains of p53:kinase coordinates N-terminal phosphorylation and apoptosis

  15. Identification and characterization of tac5, a telomerase activation mutant, characterization of DNA damage responses and assessment of interactions between telomere-related proteins in Arabidopsis thaliana

    E-Print Network [OSTI]

    Jasti, Madhuri

    2009-05-15T23:59:59.000Z

    in the genetically tractable Arabidopsis model may provide insight into the cellular response to dysfunctional telomeres. As explained in chapter IV, the yeast two-hybrid screen was utilized to confirm the interactions of ATR with AtPOT2 and Ku80 and to identify...

  16. Engineering a single cell microarray platform for high throughput DNA damage and repair analysis

    E-Print Network [OSTI]

    Weingeist, David McGregor

    2012-01-01T23:59:59.000Z

    DNA damage contributes to cancer, aging, and heritable diseases. Ironically, DNA damaging agents are also commonly used in current cancer treatment. We therefore need robust, high throughput, and inexpensive tools for ...

  17. DNA Strand Damage Product Analysis Provides Evidence That the Tumor Cell-Specific Cytotoxin Tirapazamine

    E-Print Network [OSTI]

    Gates, Kent. S.

    DNA Strand Damage Product Analysis Provides Evidence That the Tumor Cell-Specific Cytotoxin DNA strand damage that is initiated by the abstraction of hydrogen atoms from the deoxyribose damage. We find that the action of TPZ on duplex DNA under hypoxic conditions generates 5-methylene-2

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

    SciTech Connect (OSTI)

    Shen, Yan Nan; Shin, Hyun-Jin; Joo, Hyun-Yoo; Park, Eun-Ran; Kim, Su-Hyeon; Hwang, Sang-Gu [Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul 139-706 (Korea, Republic of)] [Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul 139-706 (Korea, Republic of); Park, Sang Jun; Kim, Chun-Ho [Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul 139-706 (Korea, Republic of)] [Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul 139-706 (Korea, Republic of); Lee, Kee-Ho, E-mail: khlee@kirams.re.kr [Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul 139-706 (Korea, Republic of)] [Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul 139-706 (Korea, Republic of)

    2014-01-17T23:59:59.000Z

    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.

  19. DNA Damage by Fasicularin Sanjay Dutta, Hideki Abe, Sakae Aoyagi, Chihiro Kibayashi, and Kent S. Gates*,

    E-Print Network [OSTI]

    Gates, Kent. S.

    DNA Damage by Fasicularin Sanjay Dutta, Hideki Abe, Sakae Aoyagi, Chihiro Kibayashi, and Kent S that a DNA repair- deficient cell line is hypersensitive to fasicularin suggest that an ability to damage DNA a putative aziridinium ion intermediate.2 Aziridinium ions are well-known DNA-alkylating species.3

  20. Tensile damage response from discrete element virtual testing

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Tensile damage response from discrete element virtual testing A. DELAPLACE LMT-Cachan, ENS Cachan conditions on brittle materials, damage can generally not be re- duced to a simple scalar. Microcrack into account the damage anisotropy in phenomenological models is a possible option, but the identification

  1. Regulatory pathways controlling cell division after DNA damage in Caulobacter crescentus

    E-Print Network [OSTI]

    Modell, Joshua Wexler

    2013-01-01T23:59:59.000Z

    All cells must coordinate DNA replication with cell division in order to faithfully propagate whole chromosomes to daughter cells. During episodes of DNA damage, cells often delay division until the lesions have been ...

  2. DNA damage tolerance and mutagenesis : the regulation of S. cerevisiae Rev1

    E-Print Network [OSTI]

    Wiltrout, Mary Ellen

    2009-01-01T23:59:59.000Z

    DNA damage constantly challenges the integrity of genetic material during the lifetime of every cell. Accurate duplication of DNA and its proper transmission to a new cell are critical to avoid mutations or loss of genetic ...

  3. GENETIC AND MOLECULAR ANALYSIS OF DNA DAMAGE REPAIR AND TOLERANCE PATHWAYS.

    SciTech Connect (OSTI)

    SUTHERLAND, B.M.

    2001-07-26T23:59:59.000Z

    Radiation can damage cellular components, including DNA. Organisms have developed a panoply of means of dealing with DNA damage. Some repair paths have rather narrow substrate specificity (e.g. photolyases), which act on specific pyrimidine photoproducts in a specific type (e.g., DNA) and conformation (double-stranded B conformation) of nucleic acid. Others, for example, nucleotide excision repair, deal with larger classes of damages, in this case bulky adducts in DNA. A detailed discussion of DNA repair mechanisms is beyond the scope of this article, but one can be found in the excellent book of Friedberg et al. [1] for further detail. However, some DNA damages and paths for repair of those damages important for photobiology will be outlined below as a basis for the specific examples of genetic and molecular analysis that will be presented below.

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

    SciTech Connect (OSTI)

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

    2002-01-01T23:59:59.000Z

    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.

  5. Potential effects of environmental contaminants on P450 aromatase activity and DNA damage in swallows

    E-Print Network [OSTI]

    Mora, Miguel A.

    Potential effects of environmental contaminants on P450 aromatase activity and DNA damage, to evaluate the potential effects of environmental contaminants on P450 aromatase activity in brain and gonads and DNA damage in blood cells. The tritiated water-release aromatase assay was used to measure aromatase

  6. Insulin signaling, dietary restriction and DNA damage : multiple roles for smk-1 in the mediation of C. elegans life span

    E-Print Network [OSTI]

    Wolff, Suzanne Christine

    2008-01-01T23:59:59.000Z

    role of oxidative damage and environmental stresses. Natureand environmental insults drive the accumulation of DNA damageenvironmental state. While age- related decay still occurs (due to oxidative damage and

  7. Chemical biology of mutagenesis and DNA repair: cellular responses to DNA alkylation

    E-Print Network [OSTI]

    Shrivastav, Nidhi

    The reaction of DNA-damaging agents with the genome results in a plethora of lesions, commonly referred to as adducts. Adducts may cause DNA to mutate, they may represent the chemical precursors of lethal events and they ...

  8. Structural damage detection using frequency response functions

    E-Print Network [OSTI]

    Dincal, Selcuk

    2006-04-12T23:59:59.000Z

    .........................90 5.1.2 Case 3: 1 st - 3 rd Story Braces Are Damaged .................................................92 5.1.2.1 All Four Modes Are Used for Damage Detection..........................95 5.1.2.2 The Last Two Modes... for Trial #2 with Hillclimbing #739 .......................................................................................................... 92 Figure 5.8 FRF for the 1 st Floor – 1 st - 3 rd Story Braces Are Broken SIMO – 12 DOF Symmetric...

  9. CometChip: A High-throughput 96-Well Platform for Measuring DNA Damage in Microarrayed Human Cells

    E-Print Network [OSTI]

    Ge, Jing

    DNA damaging agents can promote aging, disease and cancer and they are ubiquitous in the environment and produced within human cells as normal cellular metabolites. Ironically, at high doses DNA damaging agents are also ...

  10. DNA Damage, Repair & Replication Using E. Coli Model Systems

    E-Print Network [OSTI]

    Troll, Christopher

    2013-01-01T23:59:59.000Z

    431. Kunkel, T.A. (2004) DNA replication fidelity. J Biol1996) Generation of an endogenous DNA- methylating agent bypombe Mag1 alkylpurine DNA glycosylase. EMBO Rep, 12, 1286-

  11. DNA Damage, Repair & Replication Using E. Coli Model Systems

    E-Print Network [OSTI]

    Troll, Christopher

    2013-01-01T23:59:59.000Z

    from DNA containing dIMP residues by the Escherichia coli,from DNA containing dIMP residues by the Escherichia coli,

  12. DNA Base Damage by the Antitumor Agent 3-Amino-1,2,4-benzotriazine 1,4-Dioxide (Tirapazamine)

    E-Print Network [OSTI]

    Gates, Kent. S.

    DNA Base Damage by the Antitumor Agent 3-Amino-1,2,4-benzotriazine 1,4-Dioxide (Tirapazamine: Tirapazamine is a bioreductively activated DNA-damaging agent that selectively kills the hypoxic cells found cellular target for tirapazamine; however, the structural nature of the DNA damage inflicted by this drug

  13. Paraoxonase-1 genetic polymorphisms and susceptibility to DNA damage in workers occupationally exposed to organophosphate pesticides

    SciTech Connect (OSTI)

    Singh, Satyender [Division of Biochemistry and Biotechnology, National Centre for Disease Control, 22, Sham Nath Marg, Delhi-110054 (India); Kumar, Vivek [Environmental Biochemistry and Molecular Biology laboratory, Department of Biochemistry, University College of Medical Sciences and GTB Hospital, University of Delhi, Dilshad Garden, Delhi-110095 (India); Thakur, Sachin [Division of Biochemistry and Biotechnology, National Centre for Disease Control, 22, Sham Nath Marg, Delhi-110054 (India); Presently at, Department of Biochemistry, University of Texas Health Science Center at San Antonio (UTHSCSA), 7703 Floyd Curl Drive, San Antonio, TX 78229-3900 (United States); Banerjee, Basu Dev [Environmental Biochemistry and Molecular Biology laboratory, Department of Biochemistry, University College of Medical Sciences and GTB Hospital, University of Delhi, Dilshad Garden, Delhi-110095 (India); Rautela, Rajender Singh; Grover, Shyam Sunder; Rawat, Devendra Singh [Division of Biochemistry and Biotechnology, National Centre for Disease Control, 22, Sham Nath Marg, Delhi-110054 (India); Pasha, Syed Tazeen [National Programme for Prevention and Control of Fluorosis, DGHS, Ministry of Health and Family Welfare, Government of India, Nirman Bhavan, New Delhi 110011 (India); Jain, Sudhir Kumar [Centre for Epidemiology and Parasitic Diseases, National Centre for Disease Control, 22, Sham Nath Marg, Delhi-110054 (India); Ichhpujani, Rattan Lal [Division of Biochemistry and Biotechnology, National Centre for Disease Control, 22, Sham Nath Marg, Delhi-110054 (India); National Programme for Prevention and Control of Fluorosis, DGHS, Ministry of Health and Family Welfare, Government of India, Nirman Bhavan, New Delhi 110011 (India); Rai, Arvind, E-mail: arvindrai.nicd@gmail.com [Division of Biochemistry and Biotechnology, National Centre for Disease Control, 22, Sham Nath Marg, Delhi-110054 (India)

    2011-04-15T23:59:59.000Z

    Human paraoxonase 1 (PON1) is a lipoprotein-associated enzyme involved in the detoxification of organophosphate pesticides (OPs) by hydrolyzing the bioactive oxons. Polymorphisms of the PON1 gene are responsible for variation in the expression and catalytic activity of PON1 enzyme. In the present study, we have determined (a) the prevalence of two common PON1 polymorphisms, (b) the activity of PON1 and acetylcholinesterase enzymes, and (c) the influence of PON1 genotypes and phenotypes variation on DNA damage in workers exposed to OPs. We examined 230 subjects including 115 workers exposed to OPs and an equal number of normal healthy controls. The results revealed that PON1 activity toward paraoxon (179.19 {+-} 39.36 vs. 241.52 {+-} 42.32 nmol/min/ml in controls) and phenylacetate (112.74 {+-} 17.37 vs. 134.28 {+-} 25.49 {mu}mol/min/ml in controls) was significantly lower in workers than in control subjects (p < 0.001). No significant difference was observed in the distribution of genotypes and allelic frequencies of PON1{sub 192}QR (Gln/Arg) and PON1{sub 55}LM (Leu/Met) in workers and control subjects (p > 0.05). The PON1 activity toward paraoxonase was found to be significantly higher in the R/R (Arg/Arg) genotypes than Q/R (Gln/Arg) and lowest in Q/Q (Gln/Gln) genotypes in both workers and control subjects (p < 0.001). For PON1{sub 55}LM (Leu/Met), PON1 activity toward paraoxonase was observed to be higher in individuals with L/L (Leu/Leu) genotypes and lowest in individuals with M/M (Met/Met) genotypes in both groups (p < 0.001). No influence of PON1 genotypes and phenotypes was seen on the activity of acetylcholinesterase and arylesterase. The DNA damage was observed to be significantly higher in workers than in control subjects (p < 0.05). Further, the individuals who showed least paraoxonase activity i.e., those with (Q/Q [Gln/Gln] and M/M [Met/Met]) genotypes showed significantly higher DNA damage compared to other isoforms in workers exposed to OPs (p < 0.05). The results indicate that the individuals with PON1 Q/Q and M/M genotypes are more susceptible toward genotoxicity. In conclusion, the study suggests wide variation in enzyme activities and DNA damage due to polymorphisms in PON1 gene, which might have an important role in the identification of individual risk factors in workers occupationally exposed to OPs.

  14. The role of ClpXP-mediated proteolysis in resculpting the proteome after DNA damage

    E-Print Network [OSTI]

    Neher, Saskia B. (Saskia Byerly)

    2005-01-01T23:59:59.000Z

    When faced with environmental assaults, E. coli can take extreme measures to survive. For example, starving bacteria consume their own proteins, and bacteria with severe DNA damage introduce mutations into their genomes. ...

  15. Mechanistic investigation of an anticancer agent that damages DNA and interacts with the androgen receptor

    E-Print Network [OSTI]

    Proffitt, Kyle David

    2009-01-01T23:59:59.000Z

    The 11[beta] molecule comprises a ligand for the androgen receptor (AR), which is crucial to progression and survival of many prostate cancers, tethered to a DNA-damaging aniline mustard. The compound was designed to exhibit ...

  16. Mechanistic investigation of anticancer agents that damage DNA and interact with the estrogen receptor

    E-Print Network [OSTI]

    Gopal, Sreeja

    2009-01-01T23:59:59.000Z

    One of the primary goals of cancer chemotherapy is the design of antitumor agents that achieve selective targeting of tumor cells while minimizing toxicity to normal tissues. We have synthesized a series of DNA damaging ...

  17. To be submitted to Continuum Mechanics and Thermodynamics From the onset of damage to rupture: construction of responses with damage

    E-Print Network [OSTI]

    Boyer, Edmond

    To be submitted to Continuum Mechanics and Thermodynamics From the onset of damage to rupture: construction of responses with damage localization for a general class of gradient damage models Kim Pham solutions for the traction problem of an elastic damaging bar. This bar has a softening behavior which obeys

  18. alkaloid damages dna: Topics by E-print Network

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

    damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative...

  19. assessing dna damage: Topics by E-print Network

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

    damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative...

  20. affects dna damage: Topics by E-print Network

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

    damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative...

  1. alternative dna damage: Topics by E-print Network

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

    damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative...

  2. Controlled degradation by ClpXP protease tunes the levels of the excision repair protein UvrA to the extent of DNA damage

    E-Print Network [OSTI]

    Pruteanu, Mihaela

    UV irradiation damages DNA and activates expression of genes encoding proteins helpful for survival under DNA stress. These proteins are often deleterious in the absence of DNA damage. Here, we investigate mechanisms used ...

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

    SciTech Connect (OSTI)

    Gajski, Goran [Institute for Medical Research and Occupational Health, Mutagenesis Unit, 10000 Zagreb (Croatia)], E-mail: ggajski@imi.hr; Garaj-Vrhovac, Vera [Institute for Medical Research and Occupational Health, Mutagenesis Unit, 10000 Zagreb (Croatia); Orescanin, Visnja [Ruder Boskovic Institute, 10000 Zagreb (Croatia)

    2008-08-15T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

    van Buul, D.G. de Rooij, DNA double-strand breaks and gamma-for the transition proteins in DNA strand break repair, FEBSBoissonneault, Stimulation of DNA repair by the spermatidal

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

    van Buul, D.G. de Rooij, DNA double-strand breaks and gamma-for the transition proteins in DNA strand break repair, FEBSBoissonneault, Stimulation of DNA repair by the spermatidal

  6. Understanding cell fate decisions in response to 0?-Methylguanine DNA lesions

    E-Print Network [OSTI]

    Noonan, Ericka Marie

    2011-01-01T23:59:59.000Z

    The stability of the genome is constantly challenged by both endogenous and exogenous DNA damaging agents. DNA damage, if left unrepaired, can give rise to permanent genetic alterations that ultimately increase our risk ...

  7. Damage to Model DNA Fragments from Very Low-Energy (<1 eV) Electrons

    E-Print Network [OSTI]

    Simons, Jack

    Damage to Model DNA Fragments from Very Low-Energy ( of Chemistry, UniVersity of Gdansk ul. Sobieskiego 18, 80-952 Gdansk, Poland Received January 8, 2004; E-mail: simons@chemistry.utah.edu Abstract: Although electrons having enough energy to ionize or electronically

  8. Repair of gamma-ray-induced DNA base damage in xeroderma pigmentosum cells

    SciTech Connect (OSTI)

    Fornace, A.J. Jr.; Dobson, P.P.; Kinsella, T.J.

    1986-04-01T23:59:59.000Z

    The repair of DNA damage produced by /sup 137/Cs gamma irradiation was measured with a preparation from Micrococcus luteus containing DNA damage-specific endonucleases in combination with alkaline elution. The frequency of these endonuclease sensitive sites (ESS) was determined after 54 or 110 Gy of oxic irradiation in normal and xeroderma pigmentosum (XP) fibroblasts from complementation groups A, C, D, and G. Repair was rapid in all cell strains with greater than 50% repair after 1.5 h of repair incubation. At later repair times, 12-17 h, more ESS remained in XP than in normal cells. The frequency of excess ESS in XP cells was approximately 0.04 per 10(9) Da of DNA per Gy which was equivalent to 10% of the initial ESS produced. The removal of ESS was comparable in XP cells with normal radiosensitivity and XP3BR cells which have been reported to be moderately radiosensitive.

  9. RecA acts in trans to allow replication of damaged DNA by DNA polymerase V

    E-Print Network [OSTI]

    Cox, Michael M.

    , Michael M. Cox2 , Roger Woodgate3 & Myron F. Goodman1 The DNA polymerase V (pol V) and RecA proteins

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

    SciTech Connect (OSTI)

    Ruben A. Abagyan, PhD

    2004-04-15T23:59:59.000Z

    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).

  11. Structure and mechanism of the UvrA?UvrB DNA damage sensor

    SciTech Connect (OSTI)

    Pakotiprapha, Danaya; Samuels, Martin; Shen, Koning; Hu, Johnny H.; Jeruzalmi, David (Harvard)

    2012-04-17T23:59:59.000Z

    Nucleotide excision repair (NER) is used by all organisms to eliminate DNA lesions. We determined the structure of the Geobacillus stearothermophilus UvrA-UvrB complex, the damage-sensor in bacterial NER and a new structure of UvrA. We observe that the DNA binding surface of UvrA, previously found in an open shape that binds damaged DNA, also exists in a closed groove shape compatible with native DNA only. The sensor contains two UvrB molecules that flank the UvrA dimer along the predicted path for DNA, {approx}80 {angstrom} from the lesion. We show that the conserved signature domain II of UvrA mediates a nexus of contacts among UvrA, UvrB and DNA. Further, in our new structure of UvrA, this domain adopts an altered conformation while an adjacent nucleotide binding site is vacant. Our findings raise unanticipated questions about NER and also suggest a revised picture of its early stages.

  12. DAMAGE DETECTION BASED ON STRUCTURAL RESPONSE TO TEMPERATURE CHANGES AND MODEL UPDATING

    E-Print Network [OSTI]

    Boyer, Edmond

    DAMAGE DETECTION BASED ON STRUCTURAL RESPONSE TO TEMPERATURE CHANGES AND MODEL UPDATING Marian The paper proposes use of measured structural response to temperature loads for purposes of damage identification. As opposed to the most common approaches, which rely on suppressing temperature effects in damage

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

    SciTech Connect (OSTI)

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

    2013-05-14T23:59:59.000Z

    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.

  14. Metabolites of arsenic and increased DNA damage of p53 gene in arsenic plant workers

    SciTech Connect (OSTI)

    Wen Weihua, E-mail: Dongsijiehua@sina.com [Department of Occupational Health, Yunnan Provincial Center for Disease Control and Prevention, No. 158, Dongsi Street, Kunming, Yunnan, 650022 (China); Public Health College, Huazhong University of Science and Technology, No. 13, Hangkong Road, Wuhan City, Hubei, 430030 (China); Wen Jinghua [Guizhou College of Finance and Economics, No. 276, Chongguan Road, Guiyang, Guizhou, 550004 (China); Lu Lin [Department of Occupational Health, Yunnan Provincial Center for Disease Control and Prevention, No. 158, Dongsi Street, Kunming, Yunnan, 650022 (China); Liu Hua [The First Affiliated Hospital of Kunming Medical College, No. 295 Xichang Road, Kunming, Yunnan, 650032 (China); Yang Jun; Cheng Huirong [Department of Occupational Health, Yunnan Provincial Center for Disease Control and Prevention, No. 158, Dongsi Street, Kunming, Yunnan, 650022 (China); Che Wangjun [The First Division of Public Health, Kunming Center for Disease Control and Prevention, No. 4, Ziyun Road, Xishan District, Kunming, Yunnan 650228 (China); Li Liang [Honghe Zhou Center for Disease Control and Prevention, No. 1, Guannan Road, Mengzi City, Yunnan, 661100 (China); Zhang Guanbei [Yunnan Institute for Drug Abuse, Kunming, 650028 (China)

    2011-07-01T23:59:59.000Z

    Recent studies have shown that monomethylarsonous acid is more cytotoxic and genotoxic than arsenate and arsenite, which may attribute to the increased levels of reactive oxygen species. In this study, we used hydride generation-atomic absorption spectrometry to determine three arsenic species in urine of workers who had been working in arsenic plants,and calculated primary and secondary methylation indexes. The damages of exon 5, 6, 8 of p53 gene were determined by the method developed by Sikorsky, et al. Results show that the concentrations of each urinary arsenic species,and damage indexes of exon 5 and 8 of p53 gene in the exposed population were significantly higher, but SMI was significantly lower than in the control group. The closely positive correlation between the damage index of exon 5 and PMI,MMA, DMA were found, but there was closely negative correlation between the damage index of exon 5 and SMI. Those findings suggested that DNA damage of exon 5 and 8 of p53 gene existed in the population occupationally exposed to arsenic. For exon 5, the important factors may include the model of arsenic metabolic transformation, the concentrations of MMA and DMA, and the MMA may be of great importance. - Research Highlights: > In our study, the mean SMI for workers came from arsenic plants is 4.06, so they may be in danger. > There are more MMA, there are more damage of exon 5 of p53 gene. > MMA and damage of exon 5 of p53 gene may be useful biomarkers to assess adverse health effects caused by arsenic.

  15. Generation of DNA-Damaging Reactive Oxygen Species via the Autoxidation of Hydrogen Sulfide under Physiologically Relevant

    E-Print Network [OSTI]

    Gates, Kent. S.

    Generation of DNA-Damaging Reactive Oxygen Species via the Autoxidation of Hydrogen Sulfide under found that micromolar concentrations of H2S generated single-strand DNA cleavage. Mechanistic studies indicate that this process involved autoxidation of H2S to generate superoxide, hydrogen peroxide, and

  16. Robust damage assessment of multiple cracks based on the Frequency Response Function and the Constitutive Relation

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Robust damage assessment of multiple cracks based on the Frequency Response Function a damage assessment technique for the non destructive detection and sizing of multiple open cracks in beams, many researchers have performed extensive investigations and damage assess- ment techniques based

  17. Total dose radiation response of plasma-damaged NMOS devices

    SciTech Connect (OSTI)

    Yue, J.; Lo, E.; Flanery, M. [Honeywell Solid-State Electronic Center, Plymouth, MN (United States)] [Honeywell Solid-State Electronic Center, Plymouth, MN (United States)

    1997-11-01T23:59:59.000Z

    Plasma-damaged NMOS devices were subjected to the X-ray total dose irradiation. Unlike the traditional hot-carrier or Fowler-Nordheim (F-N) stress where the hole trap generation is less pronounced, this study shows enhanced hole trap and interface trap generation on plasma-damaged devices after total dose irradiation.

  18. DNA Damage-inducible Genes as Biomarkers for Exposures to Environmental Agents

    E-Print Network [OSTI]

    Neil F. Johnson; Thomas R. Carpenter; Richard J. Jaramillo; Teresa A. Liberati

    A biodosimetric approach to determine alpha-particle dose to the respiratory tract epithelium from known exposures to radon has been developed in the rat. Cytotoxicity assays have been used to obtain dose-conversion factors for cumulative exposures typical of those encountered by underground uranium miners. However, this approach is not sensitive enough to derive doseconversion factors for indoor radon exposures. The expression of DNA damage-inducible genes is being investigated as a biomarker of exposure to radon progeny. Exposure of cultures of A549 cells to alpha particles resulted in an increase in the protein levels of the DNA damage-inducible genes, p53, Cip1, and Gadd45. These protein changes were associated with a transient arrest of cells passing through the cell cycle. This arrest was typified by an increase in the number of cells in the G, and G2 phases and a decrease in the number of cells in the S phase. The effect of inhaled alpha particles (radon progeny) in rats was examined in the epithelial cells of the lateral wall of the anterior nasal cavity. Exposures to radon progeny resulted in a significant increase in the number of cells in the G, phase and a decrease in the number of cells in the S phase. These cell-cycle changes were concomitant with an increase in the number of cells containing DNA strand breaks. These results suggest a commonality between cell-cycle events in vitro and in vivo following exposure to ionizing radiation. In addition to ionizing radiation, A549 cells were exposed to 4-nitroquinoline-1-oxide, methyl methanesulphonate, crocidolite asbestos, and glass microfiber. These studies showed that physical and chemical agents induce different expression patterns of p53, Cipl, and Gaddl 53 proteins and they could be used to discriminate between toxic and nontoxic materials such as asbestos and glass microfiber. The measurement of gene expression in A549 cells may provide a means to identify a broad spectrum of physical and chemical toxicants encountered in the environment. Environ Health Perspect 1 05(Suppl 4):913-918 (1997) Key words: radiation, fibers, chemicals, DNA damage-inducible genes

  19. DNA . DNA

    E-Print Network [OSTI]

    1. DNA . , . , . . DNA DNA . , DNA . DNA . DNA . DNA DNA DNA . DNA [6, 7, 8]. DNA . DNA NACST/Sim DNA/DNA

  20. A Mitotic Phosphorylation Feedback Network Connects Cdk1, Plk1, 53BP1, and Chk2 to Inactivate the G2/M DNA Damage Checkpoint

    E-Print Network [OSTI]

    Yaffe, Michael B.

    DNA damage checkpoints arrest cell cycle progression to facilitate DNA repair. The ability to survive genotoxic insults depends not only on the initiation of cell cycle checkpoints but also on checkpoint maintenance. While ...

  1. DNA Repair Biomarkers Predict Response to Neoadjuvant Chemoradiotherapy in Esophageal Cancer

    SciTech Connect (OSTI)

    Alexander, Brian M., E-mail: bmalexander@lroc.harvard.edu [Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (United States); Wang Xiaozhe [On-Q-ity, Inc., Waltham, Massachusetts (United States); Niemierko, Andrzej [Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts (United States); Weaver, David T. [On-Q-ity, Inc., Waltham, Massachusetts (United States); Mak, Raymond H. [Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (United States); Roof, Kevin S. [Southeast Radiation Oncology, Charlotte, North Carolina (United States); Fidias, Panagiotis [Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts (United States); Wain, John [Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts (United States); Choi, Noah C. [Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts (United States)

    2012-05-01T23:59:59.000Z

    Purpose: The addition of neoadjuvant chemoradiotherapy prior to surgical resection for esophageal cancer has improved clinical outcomes in some trials. Pathologic complete response (pCR) following neoadjuvant therapy is associated with better clinical outcome in these patients, but only 22% to 40% of patients achieve pCR. Because both chemotherapy and radiotherapy act by inducing DNA damage, we analyzed proteins selected from multiple DNA repair pathways, using quantitative immunohistochemistry coupled with a digital pathology platform, as possible biomarkers of treatment response and clinical outcome. Methods and Materials: We identified 79 patients diagnosed with esophageal cancer between October 1994 and September 2002, with biopsy tissue available, who underwent neoadjuvant chemoradiotherapy prior to surgery at the Massachusetts General Hospital and used their archived, formalin-fixed, paraffin-embedded biopsy samples to create tissue microarrays (TMA). TMA sections were stained using antibodies against proteins in various DNA repair pathways including XPF, FANCD2, PAR, MLH1, PARP1, and phosphorylated MAPKAP kinase 2 (pMK2). Stained TMA slides were evaluated using machine-based image analysis, and scoring incorporated both the intensity and the quantity of positive tumor nuclei. Biomarker scores and clinical data were assessed for correlations with clinical outcome. Results: Higher scores for MLH1 (p = 0.018) and lower scores for FANCD2 (p = 0.037) were associated with pathologic response to neoadjuvant chemoradiation on multivariable analysis. Staining of MLH1, PARP1, XPF, and PAR was associated with recurrence-free survival, and staining of PARP1 and FANCD2 was associated with overall survival on multivariable analysis. Conclusions: DNA repair proteins analyzed by immunohistochemistry may be useful as predictive markers for response to neoadjuvant chemoradiotherapy in patients with esophageal cancer. These results are hypothesis generating and need confirmation in an independent data set.

  2. Damage Threats and Response of Final Optics for Laser-Fusion Power Plants

    E-Print Network [OSTI]

    Tillack, Mark

    Damage Threats and Response of Final Optics for Laser-Fusion Power Plants M. S. Tillack1 , S. A-1597 The final optics for laser-IFE (inertial fusion energy) power plants will be exposed to a variety of damage to be the most serious concerns for a power plant. 1. Introduction Survival of the final optic is one of the most

  3. DNA damage in barn swallows (Hirundo rustica) from the Chernobyl region detected by use of the comet assay

    E-Print Network [OSTI]

    Mousseau, Timothy A.

    DNA damage in barn swallows (Hirundo rustica) from the Chernobyl region detected by use November 2009 Accepted 19 November 2009 Available online 24 November 2009 Keywords: Barn swallow Chernobyl swallows (Hirundo rustica) inhabiting the Chernobyl region to evaluate whether chronic exposure to low

  4. Distinct Ultraviolet-Signaling Pathways in Bean Leaves. DNA Damage Is Associated with -1,3-Glucanase Gene

    E-Print Network [OSTI]

    Leubner, Gerhard

    Distinct Ultraviolet-Signaling Pathways in Bean Leaves. DNA Damage Is Associated with -1 (UV-B; 280­320 nm) radiation in primary leaves of French bean (Phaseolus vulgaris to the expression of bean class I Glu ( Glu I). In contrast to other proteins of the family of pathogenesis

  5. RADIATION SENSITIVITY & PROCESSING OF DNA DAMAGE FOLLOWING LOW DOSES OF GAMMA-RAY ALPHA PARTICLES & HZE IRRADIATION OF NORMAL DSB REPAIR DEFICIENT CELLS

    SciTech Connect (OSTI)

    O'Neil, Peter

    2009-05-15T23:59:59.000Z

    Non-homologous end joining (NHEJ) predominates in the repair of DNA double strand breaks (DSB) over homologous recombination (HR). NHEJ occurs throughout the cell cycle whereas HR occurs in late S/G2 due to the requirement of a sister chromatid (Rothkamm et al, Mol Cell Biol 23 5706-15 [2003]). To date evidence obtained with DSB repair deficient cells using pulsed-field gel electrophoresis has revealed the major pathway throughout all phases of the cell cycle for processing high dose induced DSBs is NHEJ (Wang et al, Oncogene 20 2212-24 (2001); Pluth et al, Cancer Res. 61 2649-55 [2001]). These findings however were obtained at high doses when on average >> 20-30 DSBs are formed per cell. The contribution of the repair pathways (NHEJ and HR) induced in response to DNA damage during the various phases of the cell cycle may depend upon the dose (the level of initial DSBs) especially since low levels of DSBs are induced at low dose. To date, low dose studies using NHEJ and HR deficient mutants have not been carried out to address this important question with radiations of different quality. The work presented here leads us to suggest that HR plays a relatively minor role in the repair of radiation-induced prompt DSBs. SSBs lead to the induction of DSBs which are associated specifically with S-phase cells consistent with the idea that they are formed at stalled replication forks in which HR plays a major role in repair. That DNA-PKcs is in some way involved in the repair of the precursors to replication-induced DSB remains an open question. Persistent non-DSB oxidative damage also leads to an increase in RAD51 positive DSBs. Both simple and complex non-DSB DNA damage may therefore contribute to indirect DSBs induced by ionising radiation at replication forks.

  6. Removal of N-Alkyl Modifications from N[superscript 2]-Alkylguanine and N[superscript 4]-Alkylcytosine in DNA by the Adaptive Response Protein AlkB

    E-Print Network [OSTI]

    Li, Deyu

    The AlkB enzyme is an Fe(II)- and ?-ketoglutarate-dependent dioxygenase that repairs DNA alkyl lesions by a direct reversal of damage mechanism as part of the adaptive response in E. coli. The reported substrate scope of ...

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

    SciTech Connect (OSTI)

    Nakadate, Yusuke [Shien-Lab, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan) [Shien-Lab, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan); Department of Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585 (Japan); Kodera, Yasuo; Kitamura, Yuka [Shien-Lab, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan)] [Shien-Lab, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan); Tachibana, Taro [Department of Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585 (Japan)] [Department of Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585 (Japan); Tamura, Tomohide [Division of Thoracic Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan)] [Division of Thoracic Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan); Koizumi, Fumiaki, E-mail: fkoizumi@ncc.go.jp [Division of Thoracic Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan)] [Division of Thoracic Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan)

    2013-11-29T23:59:59.000Z

    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.

  8. Predictive storm damage modeling and optimizing crew response to improve storm response operations

    E-Print Network [OSTI]

    Whipple, Sean David

    2014-01-01T23:59:59.000Z

    Utility infrastructures are constantly damaged by naturally occurring weather. Such damage results in customer service interruption and repairs are necessary to return the system to normal operation. In most cases these ...

  9. Examination of the damage and failure response of tantalum and copper under varied shock loading conditions

    SciTech Connect (OSTI)

    Bronkhorst, Curt A [Los Alamos National Laboratory; Dennis - Koller, Darcie [Los Alamos National Laboratory; Cerreta, Ellen K [Los Alamos National Laboratory; Gray Ill, George T [Los Alamos National Laboratory; Bourne, Neil [AWE-ALDERMASTON

    2010-12-16T23:59:59.000Z

    A number of plate impact experiments have been conducted on high purity polycrystalline tantalum and copper samples using graded flyer plate configurations to alter the loading profile. These experiments are designed in a way so that a broad range of damage regimes are probed. The results show that the nucleation of damage primarily occurs at the grain boundaries of the materials. This affords us the opportunity to propose a porosity damage nucleation criterion which begins to account for the length scales of the microstructure (grain size distribution) and the mechanical response of the grain boundary regions (failure stress distribution). This is done in the context of a G-T-N type model for the ductile damage and failure response of both the materials examined. The role of micro-inertial effects on the porosity growth process is also considered.

  10. Reactive oxygen species and oxidative DNA damage mediate the cytotoxicity of tungsten-nickel-cobalt alloys in vitro

    SciTech Connect (OSTI)

    Harris, R.M.; Williams, T.D.; Hodges, N.J.; Waring, R.H., E-mail: R.H.Waring@bham.ac.uk

    2011-01-01T23:59:59.000Z

    Tungsten alloys (WA) have been introduced in an attempt to find safer alternatives to depleted uranium and lead munitions. However, it is known that at least one alloy, 91% tungsten-6% nickel-3% cobalt (WNC-91-6-3), causes rhabdomyosarcomas when fragments are implanted in rat muscle. This raises concerns that shrapnel, if not surgically removable, may result in similar tumours in humans. There is therefore a clear need to develop rapid and robust in vitro methods to characterise the toxicity of different WAs in order to identify those that are most likely to be harmful to human health and to guide development of new materials in the future. In the current study we have developed a rapid visual in vitro assay to detect toxicity mediated by individual WA particles in cultured L6-C11 rat muscle cells. Using a variety of techniques (histology, comet assay, caspase-3 activity, oxidation of 2'7'-dichlorofluorescin to measure the production of reactive oxygen species and whole-genome microarrays) we show that, in agreement with the in vivo rat carcinogenicity studies, WNC-91-6-3 was the most toxic of the alloys tested. On dissolution, it produces large amounts of reactive oxygen species, causes significant amounts of DNA damage, inhibits caspase-3, triggers a severe hypoxic response and kills the cells in the immediate vicinity of the alloy particles within 24 h. By combining these in vitro data we offer a mechanistic explanation of the effect of this alloy in vivo and show that in vitro tests are a viable alternative for assessing new alloys in the future.

  11. DNA DNA DNA (d)DNA DNA DNA

    E-Print Network [OSTI]

    Hagiya, Masami

    DNA DNA DNA DNA DNA DNA DNA DNA [ 2008] (d)DNA DNA DNA DNA 2 3 DNA DNA DNA DNA DNA DNA DNA (a) (c) (b) (d) #12;DNA DNA DNA DNA DNA DNA DNA DNA (b) DNA [Tanaka et al.2008] DNA DNA DNA DNA DNA DNA DNA #12;iGEM MIT MIT

  12. Earthquake Damage Detection in the Imperial County Services Building III: Analysis of Wave Travel Times via Impulse Response Functions

    E-Print Network [OSTI]

    Southern California, University of

    1 Earthquake Damage Detection in the Imperial County Services Building III: Analysis of Wave Travel characteristics of the structure, and are not sensitive to local damage. Wave travel times between selected changes in such characteristics of response are potentially more sensitive to local damage. In this paper

  13. Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress

    E-Print Network [OSTI]

    Tentner, Andrea R

    Following DNA damage, cells display complex multi-pathway signaling dynamics that connect cell-cycle arrest and DNA repair in G1, S, or G2/M phase with phenotypic fate decisions made between survival, cell-cycle re-entry ...

  14. Effects of Base -Stacking on Damage to DNA by Low-Energy Electrons Iwona Anusiewicz,,, Joanna Berdys,, Monika Sobczyk,, Piotr Skurski,, and

    E-Print Network [OSTI]

    Simons, Jack

    Effects of Base -Stacking on Damage to DNA by Low-Energy Electrons Iwona Anusiewicz,,,§ JoannaVersity of Gdansk, 80-952 Gdansk, Poland ReceiVed: June 16, 2004; In Final Form: July 28, 2004 In this work, we -stacking. In thsese studies, we consider SSBs induced by low-energy electrons that attach to DNA bases

  15. atr-mediated dna damage: Topics by E-print Network

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

    damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative...

  16. aluminium-induced dna damage: Topics by E-print Network

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

    damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative...

  17. atr-dependent dna damage: Topics by E-print Network

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

    damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative...

  18. Structural health monitoring (SHM) entails the use of structural response data to identify the existence, location, and severity of structural damage. However, damage

    E-Print Network [OSTI]

    Lynch, Jerome P.

    ABSTRACT Structural health monitoring (SHM) entails the use of structural response data to identify in the structural health monitoring (SHM) community seek means of detecting the onset of damage using structural response data. For example, early efforts in the structural health monitoring field concentrated

  19. Altered Mitochondrial Retrograde Signaling in Response to mtDNA Depletion or a Ketogenic Diet

    E-Print Network [OSTI]

    Selfridge, Jennifer Eva

    2012-12-31T23:59:59.000Z

    kinase kinase MCI Mild cognitive impairment MCT Monocarboxylate transporter Mfn Mitofusin mtDNA Mitochondrial DNA mTOR Mammalian target of rapamycin mTORC1 mTOR complex 1 MRC Mitochondrial Respiratory Complex NAD(H) Nicotinamide adenine...; Smith et al., 1991; Sultana et al., 2010). Many studies suggest that oxidative damage is also present in individuals with mild cognitive impairment (MCI), a syndromic state that in many cases represents a very early AD clinical stage (Aluise et al...

  20. Integrase-independent HIV-1 infection is augmented under conditions of DNA damage and produces a viral reservoir

    SciTech Connect (OSTI)

    Ebina, Hirotaka, E-mail: hebina@virus.kyoto-u.ac.jp; Kanemura, Yuka; Suzuki, Yasutsugu; Urata, Kozue; Misawa, Naoko; Koyanagi, Yoshio

    2012-05-25T23:59:59.000Z

    HIV-1 possesses a viral protein, integrase (IN), which is necessary for its efficient integration in target cells. However, it has been reported that an IN-defective HIV strain is still capable of integration. Here, we assessed the ability of wild type (WT) HIV-1 to establish infection in the presence of IN inhibitors. We observed a low, yet clear infection of inhibitor-incubated cells infected with WT HIV which was identical to cells infected with IN-deficient HIV, D64A. Furthermore, the IN-independent integration could be enhanced by the pretreatment of cells with DNA-damaging agents suggesting that integration is mediated by a DNA repair system. Moreover, significantly faster viral replication kinetics with augmented viral DNA integration was observed after infection in irradiated cells treated with IN inhibitor compared to nonirradiated cells. Altogether, our results suggest that HIV DNA has integration potential in the presence of an IN inhibitor and may serve as a virus reservoir.

  1. An unprecedented nucleic acid capture mechanism for excision of DNA damage

    SciTech Connect (OSTI)

    Rubinson, Emily H.; Prakasha Gowda, A.S.; Spratt, Thomas E.; Gold, Barry; Eichmanbrand, Brandt F. (Pitt); (Vanderbilt); (Penn)

    2010-11-18T23:59:59.000Z

    DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation, providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.

  2. DNA Damage Induced by Low-Energy Electrons: Electron Transfer and Diffraction

    SciTech Connect (OSTI)

    Zheng Yi; Wagner, J. Richard; Sanche, Leon [Groupe de Recherche en Sciences des Radiations, Faculte de Medecine, Universite de Sherbrooke, Sherbrooke, QC J1H 5N4 (Canada)

    2006-05-26T23:59:59.000Z

    Thin films of the short single strand of DNA, GCAT, in which guanine (G) or adenine (A) have been removed, were bombarded under vacuum by 4 to 15 eV electrons. The fragments corresponding to base release and strand breaks (SB) were analyzed by high performance liquid chromatography and their yields compared with those obtained from unmodified GCAT. From such a comparison, it is shown that, using GCAT as a model system (1) most SB result from electron capture by DNA bases followed by electron transfer to the phosphate group and (2) the initial capture probability depends on the coherence of the electron wave within the tetramer.

  3. DNA DNA . DNA

    E-Print Network [OSTI]

    1. DNA DNA , . . DNA ( ) DNA "exhaustive " . Boolean , 40 2 40 10 12 pico mole . DNA . 20 3-SAT DNA NP-complete [1]. [2, 3]. DNA

  4. Pliable DNA Conformation of Response Elements Bound to Transcription Factor p63

    SciTech Connect (OSTI)

    Chen, Chen; Gorlatova, Natalia; Herzberg, Osnat (Maryland)

    2012-05-02T23:59:59.000Z

    We show that changes in the nucleotide sequence alter the DNA conformation in the crystal structures of p63 DNA-binding domain (p63DBD) bound to its response element. The conformation of a 22-bp canonical response element containing an AT spacer between the two half-sites is unaltered compared with that containing a TA spacer, exhibiting superhelical trajectory. In contrast, a GC spacers abolishes the DNA superhelical trajectory and exhibits less bent DNA, suggesting that increased GC content accompanies increased double helix rigidity. A 19-bp DNA, representing an AT-rich response element with overlapping half-sites, maintains superhelical trajectory and reveals two interacting p63DBD dimers crossing one another at 120{sup o}. p63DBD binding assays to response elements of increasing length complement the structural studies. We propose that DNA deformation may affect promoter activity, that the ability of p63DBD to bind to superhelical DNA suggests that it is capable of binding to nucleosomes, and that overlapping response elements may provide a mechanism to distinguish between p63 and p53 promoters.

  5. Photochemistry and Photobiology, 2005, 81: 8995 Photoinduced DNA Cleavage and Cellular Damage in Human Dermal

    E-Print Network [OSTI]

    Turro, Claudia

    1 Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD . Furthermore, upon irradiation with visible light, DAP is able to nick plasmid DNA in the presence of oxygen. The concentration of DAP that resulted in 50% cell death was 172 6 9 lM in the dark and 13 6 1 lM after irradiation

  6. Non-ionic, thermo-responsive DEA/DMA nanogels: Synthesis, characterization, and use for DNA separations by microchip electrophoresis

    E-Print Network [OSTI]

    Barron, Annelise E.

    Non-ionic, thermo-responsive DEA/DMA nanogels: Synthesis, characterization, and use for DNA DNA separations a b s t r a c t Thermo-responsive polymer ``nanogels'' (crosslinked hydrogel particles-to-volume ratios, thermo-responsive nanogels can exhibit unusually rapid responses to micro-environmental stimuli

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

    SciTech Connect (OSTI)

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

    2011-06-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Tang, G.H. [Xian Medical Univ. (China); Shen, Y.; Shen, H.M. [National Univ. of Singapore (Singapore)] [and others

    1996-12-31T23:59:59.000Z

    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.

  9. (CANCER RESEARCH 53. I02.VI026. March I. 1993] Benzene and Its Phenolic Metabolites Produce Oxidative DNA Damage in HL60

    E-Print Network [OSTI]

    California at Berkeley, University of

    (CANCER RESEARCH 53. I02.VI026. March I. 1993] Benzene and Its Phenolic Metabolites Produce ABSTRACT Benzene, an important industrial chemical, is myelotoxic and leuke- mogenic in humans effects. Here we report the induction of oxida- tive DNA damage by benzene and its phenolic metabolites

  10. DNA Self-Assembly of Targeted Near-Infrared-Responsive Gold Nanoparticles for Cancer Thermo-Chemotherapy

    E-Print Network [OSTI]

    Xiao, Zeyu

    Targeted cancer therapy: Inspired by the ability of DNA hybridization, a targeted near-infrared (NIR) light-responsive delivery system has been developed through simple DNA self-assembly (see picture; PEG=polyethylene ...

  11. Molecular views of damaged DNA: Adaptation of the Program DUPLEX to parallel architectures

    SciTech Connect (OSTI)

    Hingerty, B.E.; Crawford, O.H. [Oak Ridge National Lab., TN (United States); Broyde, S. [New York Univ., NY (United States). Biology Dept.; Wagner, R.A. [Duke Univ., Durham, NC (United States). Dept. of Computer Science

    1994-09-01T23:59:59.000Z

    The nucleic acids molecular mechanics program DUPLEX has been designed with useful features for surveying the potential energy surface of polynucleotides, especially ones that are modified by polycyclic aromatic carcinogens. The program features helpful strategies for addressing the multiple minimum problem: (1) the reduced variable domain of torsion angle space; (2) search strategies that emphasize large scale searches for smaller subunits, followed by building to larger units by a variety of strategies; (3) the use of penalty functions to aid the minimizer in locating selected structural types in first stage minimizations; penalty functions are released in terminal minimizations to yield final unrestrained minimum energy conformations. Predictive capability is illustrated by DNA modified by activated benzo[a]pyrenes. The first stage of adaptation to parallel computers is described.

  12. Role of genetic polymorphisms of CYP1A1, CYP3A5, CYP2C9, CYP2D6, and PON1 in the modulation of DNA damage in workers occupationally exposed to organophosphate pesticides

    SciTech Connect (OSTI)

    Singh, Satyender [Division of Biochemistry and Biotechnology, National Centre for Disease Control 22, Sham Nath Marg, Delhi-110054 (India)] [Division of Biochemistry and Biotechnology, National Centre for Disease Control 22, Sham Nath Marg, Delhi-110054 (India); Kumar, Vivek [Environmental Biochemistry and Molecular Biology laboratory, Department of Biochemistry, University College of Medical Sciences and GTB Hospital, University of Delhi, Dilshad Garden, Delhi-110095 (India)] [Environmental Biochemistry and Molecular Biology laboratory, Department of Biochemistry, University College of Medical Sciences and GTB Hospital, University of Delhi, Dilshad Garden, Delhi-110095 (India); Vashisht, Kapil; Singh, Priyanka [Division of Biochemistry and Biotechnology, National Centre for Disease Control 22, Sham Nath Marg, Delhi-110054 (India)] [Division of Biochemistry and Biotechnology, National Centre for Disease Control 22, Sham Nath Marg, Delhi-110054 (India); Banerjee, Basu Dev, E-mail: banerjeebd@hotmail.com [Environmental Biochemistry and Molecular Biology laboratory, Department of Biochemistry, University College of Medical Sciences and GTB Hospital, University of Delhi, Dilshad Garden, Delhi-110095 (India); Rautela, Rajender Singh; Grover, Shyam Sunder; Rawat, Devendra Singh; Pasha, Syed Tazeen [Division of Biochemistry and Biotechnology, National Centre for Disease Control 22, Sham Nath Marg, Delhi-110054 (India)] [Division of Biochemistry and Biotechnology, National Centre for Disease Control 22, Sham Nath Marg, Delhi-110054 (India); Jain, Sudhir Kumar [Centre for Epidemiology and Parasitic Diseases, National Centre for Disease Control 22, Sham Nath Marg, Delhi-110054 (India)] [Centre for Epidemiology and Parasitic Diseases, National Centre for Disease Control 22, Sham Nath Marg, Delhi-110054 (India); Rai, Arvind [Division of Biochemistry and Biotechnology, National Centre for Disease Control 22, Sham Nath Marg, Delhi-110054 (India)] [Division of Biochemistry and Biotechnology, National Centre for Disease Control 22, Sham Nath Marg, Delhi-110054 (India)

    2011-11-15T23:59:59.000Z

    Organophosphate pesticides (OPs) are primarily metabolized by several xenobiotic metabolizing enzymes (XMEs). Very few studies have explored genetic polymorphisms of XMEs and their association with DNA damage in pesticide-exposed workers. The present study was designed to determine the role of genetic polymorphisms of CYP1A1, CYP3A5, CYP2C9, CYP2D6, and PON1 in the modulation of DNA damage in workers occupationally exposed to OPs. We examined 284 subjects including 150 workers occupationally exposed to OPs and 134 normal healthy controls. The DNA damage was evaluated using the alkaline comet assay and genotyping was done using PCR-RFLP. The results revealed that the PONase activity toward paraoxonase and AChE activity was found significantly lowered in workers as compared to control subjects (p < 0.001). Workers showed significantly higher DNA damage compared to control subjects (14.37 {+-} 2.15 vs. 6.24 {+-} 1.37 tail% DNA, p < 0.001). Further, the workers with CYP2D6*3 PM and PON1 (QQ and MM) genotypes were found to have significantly higher DNA damage when compared to other genotypes (p < 0.05). In addition, significant increase in DNA damage was also observed in workers with concomitant presence of certain CYP2D6 and PON1 (Q192R and L55M) genotypes which need further extensive studies. In conclusion, the results indicate that the PON1 and CYP2D6 genotypes can modulate DNA damage elicited by some OPs possibly through gene-environment interactions. -- Highlights: Black-Right-Pointing-Pointer Role of CYP1A1, CYP3A5, CYP2C, CYP2D6 and PON1 genotypes on DNA damage. Black-Right-Pointing-Pointer Workers exposed to some OPs demonstrated increased DNA damage. Black-Right-Pointing-Pointer CYP2D6 *3 PM and PON1 (Q192R and L55M) genotypes are associated with DNA damage. Black-Right-Pointing-Pointer Concomitant presence of certain CYP2D6 and PON1 genotypes can increase DNA damage.

  13. DNA -DNA--

    E-Print Network [OSTI]

    Glykos, Nikolaos

    #12;#12;#12;8.1 DNA - . DNA- - (DNA-binding domains) ( 100 ). - DNA- - -, DNA. - -- - DNA. 173 8 DNA : -- 8.1 8.2 8.3 Cro - 8.4 Cro 8.5 DNA- - 8.6 Cro DN 8

  14. Telomere Regulation in Arabidopsis thaliana by the CST Capping Complex and DNA Damage Response Proteins

    E-Print Network [OSTI]

    Boltz, Kara A.

    2013-09-11T23:59:59.000Z

    ). In the flowering plant, Arabidopsis thaliana telomeres are bound by the CST (CTC1/STN1/TEN1) heterotrimer. Loss of any CST component results in telomere shortening, telomere fusions, increased G-overhang length and telomere recombination. To understand...

  15. Regulation of epithelial-mesenchymal transition and DNA damage responses by singleminded-2s 

    E-Print Network [OSTI]

    Laffin, Brian Edward

    2009-05-15T23:59:59.000Z

    such as TGF-beta receptor ligands (141-143, 147) Wnts (176, 177), FGFs (178-181), and Notch ligands (149). TGF-beta and BMP signaling results both in broad chromatin remodeling via HMGA2 (182, 183) 16 and the assembly of numerous transcriptional complexes...-cadherin repression (127-129, 161, 182, 188). One or more of these proteins are the eventual targets of all EMT-promoting signaling pathways. 1.6 Transforming growth factor (TGF)-beta signaling TGF-? signaling (Fig. 2) begins with the synthesis of one of 30...

  16. Characterization of Biological Effects of Computed Tomography by Assessing the DNA Damage Response

    E-Print Network [OSTI]

    Elgart, Shona Robin

    2014-01-01T23:59:59.000Z

    Brenner DJ, Hall EJ. Computed Tomography - An IncreasingSmith-Bindman R. Is Computed Tomography Safe? New Englandof X-ray Trends: Computed Tomography 2005 – 06 Preliminary

  17. Regulation of epithelial-mesenchymal transition and DNA damage responses by singleminded-2s

    E-Print Network [OSTI]

    Laffin, Brian Edward

    2009-05-15T23:59:59.000Z

    and progression in breast cancer, we depleted SIM2 RNA in MCF-7 cells using a retroviral shRNA system and examined gene expression and functional abilities of the SIM2-depleted MCF-7 cells (SIM2i) relative to a control MCF line expressing a non-specific “scrambled...

  18. 3-amino thioacridone inhibits DNA synthesis and induces DNA damage in T-cell acute lymphoblastic leukemia (T-ALL) in a p16-dependent manner

    E-Print Network [OSTI]

    2005-01-01T23:59:59.000Z

    T-lineage acute lymphoblastic leukemia. Blood 91:735-746,damage in T-cell acute lymphoblastic leukemia (T-ALL) in arelapse in T-cell acute lymphoblastic leukemia patients with

  19. IH Report #04-010 April 2004 Water Damage Response (Mold Prevention)

    E-Print Network [OSTI]

    , discard books and papers Photocopy important/valuable items, discard originals or Freeze in frost-free freezer or meat locker and consult with a restoration/water damage professional. Carpet and backing ­ dry

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

    E-Print Network [OSTI]

    Rutqvist, Jonny

    2009-01-01T23:59:59.000Z

    Modeling of Damage, Permeability Changes and Pressureof excavation-induced damage, permeability changes, andrange of approaches to model damage and permeability changes

  1. Insulin signaling, dietary restriction and DNA damage : multiple roles for smk-1 in the mediation of C. elegans life span

    E-Print Network [OSTI]

    Wolff, Suzanne Christine

    2008-01-01T23:59:59.000Z

    involved in resistance to heat stress, a common correlatedamage, UV damage, and heat stress are tightly coupled to2003), and induced by heat stress (mtl-1 and hsp-12.6) (

  2. p63 and p73 Transcriptionally Regulate Genes Involved in DNA Repair

    E-Print Network [OSTI]

    Lin, Yu-Li

    The p53 family activates many of the same genes in response to DNA damage. Because p63 and p73 have structural differences from p53 and play distinct biological functions in development and metastasis, it is likely that ...

  3. Expanded breadth of the T-cell response to mosaic HIV-1 envelope DNA vaccination

    SciTech Connect (OSTI)

    Korber, Bette [Los Alamos National Laboratory; Fischer, William [Los Alamos National Laboratory; Wallstrom, Timothy [Los Alamos National Laboratory

    2009-01-01T23:59:59.000Z

    An effective AIDS vaccine must control highly diverse circulating strains of HIV-1. Among HIV -I gene products, the envelope (Env) protein contains variable as well as conserved regions. In this report, an informatic approach to the design of T-cell vaccines directed to HIV -I Env M group global sequences was tested. Synthetic Env antigens were designed to express mosaics that maximize the inclusion of common potential Tcell epitope (PTE) 9-mers and minimize the inclusion of rare epitopes likely to elicit strain-specific responses. DNA vaccines were evaluated using intracellular cytokine staining (ICS) in inbred mice with a standardized panel of highly conserved 15-mer PTE peptides. I, 2 and 3 mosaic sets were developed that increased theoretical epitope coverage. The breadth and magnitude ofT-cell immunity stimulated by these vaccines were compared to natural strain Env's; additional comparisons were performed on mutant Env's, including gpl60 or gpl45 with or without V regions and gp41 deletions. Among them, the 2 or 3 mosaic Env sets elicited the optimal CD4 and CD8 responses. These responses were most evident in CD8 T cells; the 3 mosaic set elicited responses to an average of 8 peptide pools compared to 2 pools for a set of3 natural Env's. Synthetic mosaic HIV -I antigens can therefore induce T-cell responses with expanded breadth and may facilitate the development of effective T -cell-based HIV -1 vaccines.

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

    SciTech Connect (OSTI)

    Prieto, A.M. [UNESP — Univ. Estadual Paulista, College of Pharmaceutical Sciences, Department of Clinical Analysis, Rua Expedicionários do Brasil, 1621, Araraquara (Brazil)] [UNESP — Univ. Estadual Paulista, College of Pharmaceutical Sciences, Department of Clinical Analysis, Rua Expedicionários do Brasil, 1621, Araraquara (Brazil); Santos, A.G. [UNESP — Univ. Estadual Paulista, College of Pharmaceutical Sciences, Department of Natural Principles and Toxicology, Rodovia Araraquara-Jau, km 01, Araraquara (Brazil)] [UNESP — Univ. Estadual Paulista, College of Pharmaceutical Sciences, Department of Natural Principles and Toxicology, Rodovia Araraquara-Jau, km 01, Araraquara (Brazil); Csipak, A.R.; Caliri, C.M.; Silva, I.C. [UNESP — Univ. Estadual Paulista, College of Pharmaceutical Sciences, Department of Clinical Analysis, Rua Expedicionários do Brasil, 1621, Araraquara (Brazil)] [UNESP — Univ. Estadual Paulista, College of Pharmaceutical Sciences, Department of Clinical Analysis, Rua Expedicionários do Brasil, 1621, Araraquara (Brazil); Arbex, M.A. [UNIFESP — Federal University of Săo Paulo, Paulista College of Medicine, Department of Internal Medicine, Rua Pedro de Toledo, 720, Săo Paulo (Brazil)] [UNIFESP — Federal University of Săo Paulo, Paulista College of Medicine, Department of Internal Medicine, Rua Pedro de Toledo, 720, Săo Paulo (Brazil); Silva, F.S.; Marchi, M.R.R. [UNESP — Univ. Estadual Paulista, Chemistry Institute, Department of Analytical Chemistry, Rua Francisco Degni, S/N, Araraquara (Brazil)] [UNESP — Univ. Estadual Paulista, Chemistry Institute, Department of Analytical Chemistry, Rua Francisco Degni, S/N, Araraquara (Brazil); Cavalheiro, A.J.; Silva, D.H.S.; Bolzani, V.S. [UNESP — Univ. Estadual Paulista, Chemistry Institute, Department of Organic Chemistry, Rua Francisco Degni, S/N, Araraquara (Brazil)] [UNESP — Univ. Estadual Paulista, Chemistry Institute, Department of Organic Chemistry, Rua Francisco Degni, S/N, Araraquara (Brazil); Soares, C.P., E-mail: soarescp@hotmail.com [UNESP — Univ. Estadual Paulista, College of Pharmaceutical Sciences, Department of Clinical Analysis, Rua Expedicionários do Brasil, 1621, Araraquara (Brazil)

    2012-12-15T23:59:59.000Z

    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 extract—3.9, 7.5, or 15.0 mg/kg body weight (BW)—or with casearin X—0.3, 0.25, or 1.2 mg/kg BW—after 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.

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

    SciTech Connect (OSTI)

    Quirk, W.A.

    1993-04-01T23:59:59.000Z

    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.

  6. Tissue responses to low protracted doses of high let radiations or photons: Early and late damage relevant to radio-protective countermeasures

    SciTech Connect (OSTI)

    Ainsworth, E.J.; Afzal, S.M.J.; Crouse, D.A.; Hanson, W.R.; Fry, R.J.M.

    1988-01-01T23:59:59.000Z

    Early and late murine tissue responses to single or fractionated low doses of heavy charged particles, fission-spectrum neutrons or gamma rays are considered. Damage to the hematopoietic system is emphasized, but results on acute lethality, host response to challenge with transplanted leukemia cells and life-shortening are presented. Low dose rates per fraction were used in some neutron experiments. Split-dose lethality studies (LD 50/30) with fission neutrons indicated greater accumulation of injury during a 9 fraction course (over 17 days) than was the case for ..gamma..-radiation. When total doses of 96 or 247 cGy of neutrons or ..gamma.. rays were given as a single dose or in 9 fractions, a significant sparing effect on femur CFU-S depression was observed for both radiation qualities during the first 11 days, but there was not an earlier return to normal with dose fractionation. During the 9 fraction sequence, a significant sparing effect of low dose rate on CFU-S depression was observed in both neutron and ..gamma..-irradiated mice. CFU-S content at the end of the fractionation sequence did not correlate with measured LD 50/30. Sustained depression of femur and spleen CFU-S and a significant thrombocytopenia were observed when a total neutron dose of 240 cGy was given in 72 fractions over 24 weeks at low dose rates. The temporal aspects of CFU-S repopulation were different after a single versus fractionated neutron doses. The sustained reduction in the size of the CFU-S population was accompanied by an increase in the fraction in DNA synthesis. The proliferation characteristics and effects of age were different for radial CFU-S population closely associated with bone, compared with the axial population that can be readily aspirated from the femur. In aged irradiated animals, the CFU-S proliferation/redistribution response to typhoid vaccine showed both an age and radiation effect. 63 refs., 6 figs., 7 tabs.

  7. DNA repair is the target of novel antibiotics

    E-Print Network [OSTI]

    Gunderson, Carl Wayne

    2007-01-01T23:59:59.000Z

    W. & A. M. Segall, (2006) DNA repair, a novel antibacterialjunction-trapping peptides induce DNA damage and chromosomePeptide inhibitors of DNA cleavage by tyrosine recombinases

  8. Species Discovery versus Species Identification in DNA Barcoding Efforts: Response to Rubinoff

    E-Print Network [OSTI]

    DeSalle, Rob

    in the discus- sion. I start with Rubinoff's second point that there are "problems with DNA barcodes and species needs to be tested in a scientific context (Goldstein et al. 2000; Lipscomb et al. 2003; Sites of taxonomy (Dunn 2003; Lipscomb et al. 2003; Seberg et al. 2003). On the other hand DNA sequences can be used

  9. Functional role of p53 N-terminal phosphorylation in regulating the p53 response to DNA damage

    E-Print Network [OSTI]

    Chao, Connie

    2006-01-01T23:59:59.000Z

    and JNK3 are p53 n- terminal serine 34 kinases. Oncogene 15,and Vousden, K. H. (2001). C-Terminal Ubiquitination of p53Lysine Mutations in the C-Terminal Domain of p53 Interfere

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

    E-Print Network [OSTI]

    Chappell, Lori J.

    2011-01-01T23:59:59.000Z

    software (TreeStar Inc. , Ashland, OR. ) and analyzed assoftware (TreeStar Inc. , Ashland, OR. ) and resulting

  11. Cell cycle and DNA damage response regulation by Spy1, and the intersection of FGFR and NFkappaB pathways

    E-Print Network [OSTI]

    McAndrew, Christopher William

    2010-01-01T23:59:59.000Z

    in FGFR2, including Antley-Bixler-like syndrome (ABS), Apertsyndromes, including Antley-Bixler-like syndrome (ABS),

  12. ATM Phosphorylates and Activates the Transcription Factor MEF2D for Neuronal Survival in Response to DNA Damage

    E-Print Network [OSTI]

    Chan, Shing Fai

    2009-01-01T23:59:59.000Z

    Biol. , 4, Schwartz E. I. , Smilenov L. B. , Price M. A. ,FEBS Lett. , 472, 53-56. Smilenov L. B. , Morgan S. E. ,Metcalfe et al. , 1996; Smilenov et al. , 1997). Cancer

  13. Comment on `Nanoconfinement-enhanced conformational response of single DNA molecules to changes in ionic environment'

    E-Print Network [OSTI]

    Madhavi Krishnan; Eugene P. Petrov

    2008-05-14T23:59:59.000Z

    In the present Comment we show that, contrary to the recent findings of Reisner et al. [Phys. Rev. Lett. 99, 058302 (2007)], the excluded volume effect does not play an important role in determining DNA behavior in nanochannels at low ionic strength. We argue that the DNA extension data are described very well without the notion of an effective polymer width using the entropic depletion theory due to Odijk.

  14. . DNA, RNA, Protein

    E-Print Network [OSTI]

    Yoo, SukIn

    1. , . DNA, RNA, Protein [1-4]. DNA . DNA A, T, G, C . DNA , DNA DNA . , DNA DNA . DNA DNA . , PCR , , DNA [5]. DNA DNA , DNA

  15. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    a nucleotide from the DNA double helix to its active site to access damaged nucleotides. But unlike AGT and most other known DNA nucleotide-flipping proteins, this...

  16. How the DNA sequence affects the Hill curve of transcriptional response

    E-Print Network [OSTI]

    M. Sheinman; Y. Kafri

    2011-11-16T23:59:59.000Z

    The Hill coefficient is often used as a direct measure of the cooperativity of binding processes. It is an essential tool for probing properties of reactions in many biochemical systems. Here we analyze existing experimental data and demonstrate that the Hill coefficient characterizing the binding of transcription factors to their cognate sites can in fact be larger than one -- the standard indication of cooperativity -- even in the absence of any standard cooperative binding mechanism. By studying the problem analytically, we demonstrate that this effect occurs due to the disordered binding energy of the transcription factor to the DNA molecule and the steric interactions between the different copies of the transcription factor. We show that the enhanced Hill coefficient implies a significant reduction in the number of copies of the transcription factors which is needed to occupy a cognate site and, in many cases, can explain existing estimates for numbers of the transcription factors in cells. The mechanism is general and should be applicable to other biological recognition processes.

  17. IMPULSE RESPONSE ANALYSIS OF THE VAN NUYS 7-STORY HOTEL DURING 11 EARTHQUAKES AND EARTHQUAKE DAMAGE DETECTION

    E-Print Network [OSTI]

    Southern California, University of

    propagating waves are measured in the Van Nuys 7- story hotel, located in the Los Angeles metropolitan area response data from 11 earthquakes over a period of 24 years are analyzed. Changes in wave travel times). Also, wave travel times are used to estimate the fundamental fixed-base frequency of the building, 1f

  18. Strandwise translocation of a DNA glycosylase on undamaged DNA

    SciTech Connect (OSTI)

    Qi, Yan; Nam, Kwangho; Spong, Marie C.; Banerjee, Anirban; Sung, Rou-Jia; Zhang, Michael; Karplus, Martin; Verdine, Gregory L. (Harvard)

    2012-05-14T23:59:59.000Z

    Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process. Considerable interest surrounds the question of how DNA glycosylases translocate efficiently along DNA while maintaining their vigilance for target damaged sites. Here, we report the observation of strandwise translocation of 8-oxoguanine DNA glycosylase, MutM, along undamaged DNA. In these complexes, the protein is observed to translocate by one nucleotide on one strand while remaining untranslocated on the complementary strand. We further report that alterations of single base-pairs or a single amino acid substitution (R112A) can induce strandwise translocation. Molecular dynamics simulations confirm that MutM can translocate along DNA in a strandwise fashion. These observations reveal a previously unobserved mode of movement for a DNA-binding protein along the surface of DNA.

  19. Human AlkB Homolog ABH8 Is a tRNA Methyltransferase Required for Wobble Uridine Modification and DNA Damage Survival

    E-Print Network [OSTI]

    Fu, Dragony

    tRNA nucleosides are extensively modified to ensure their proper function in translation. However, many of the enzymes responsible for tRNA modifications in mammals await identification. Here, we show that human AlkB homolog ...

  20. Nonlocal Damage Models 8.1 Basic Types of Nonlocal Damage Formulations

    E-Print Network [OSTI]

    Jirasek, Milan

    Chapter 8 Nonlocal Damage Models 8.1 Basic Types of Nonlocal Damage Formulations 8.1.1 Formulations Motivated by Isotropic Damage A number of nonlocal concepts giving local response in the linear elastic damage model from Section 5.2. Certain models use a formulation in which the role of the equivalent

  1. DNA ELECTROPHORESIS AT SURFACES

    SciTech Connect (OSTI)

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01T23:59:59.000Z

    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.

  2. Property Loss / Damage Report Damage Loss Details

    E-Print Network [OSTI]

    Ponce, V. Miguel

    Property Loss / Damage Report Damage Loss Details Date & Time of Damage / Loss: Type of damage / loss: Location - specific address / room: Project / Grant associated with damage / loss - grant Police: When was damage / loss first discovered - BY WHOM: Pictures available or attached? Was personal

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

    SciTech Connect (OSTI)

    Peng, Jamy C.

    2007-05-05T23:59:59.000Z

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

  4. A General Method for Quantifying Sequence Effects on Nucleobase Oxidation in DNA

    E-Print Network [OSTI]

    Margolin, Yelena

    2010-01-01T23:59:59.000Z

    Oxidative damage to DNA has long been associated with aging and disease, with guanine serving as the

  5. Nanotechnology with DNA DNA Nanodevices

    E-Print Network [OSTI]

    Ludwig-Maximilians-Universität, München

    Nanotechnology with DNA DNA Nanodevices Friedrich C. Simmel* and Wendy U. Dittmer A DNA actuator. Introduction.............285 2. Overview: DNA Nanotechnology.......285 3. Prototypes of Nanomechanical DNA overview of DNA nanotechnology as a whole is given. The most important properties of DNA molecules

  6. Infection-induced colitis in mice causes dynamic and tissue-specific changes in stress response and DNA damage leading to colon cancer

    E-Print Network [OSTI]

    Mangerich, Aswin

    Helicobacter hepaticus-infected Rag2-/- mice emulate many aspects of human inflammatory bowel disease, including the development of colitis and colon cancer. To elucidate mechanisms of inflammation-induced carcinogenesis, ...

  7. DNA microarray (spot) .

    E-Print Network [OSTI]

    1. DNA microarray DNA (spot) . DNA probe , probe (hybridization) . DNA microarray cDNA oligonucleotide oligonucleotide cDNA probe . oligonucleotide microarray , DNA , probe . oligonucleotide microarray probe

  8. Role of DNA repair protein ERCC1 in skin cancer 

    E-Print Network [OSTI]

    Song, Liang

    2009-01-01T23:59:59.000Z

    Nucleotide excision repair (NER) is one of the major repair systems for removal of DNA lesions. The NER pathway has evolved mainly to repair UV-induced DNA damage and is also active against a broad range of endogenously ...

  9. DAMAGE ESTIMATION USING MULTI-OBJECTIVE GENETIC ALGORITHMS Faisal Shabbir

    E-Print Network [OSTI]

    Boyer, Edmond

    DAMAGE ESTIMATION USING MULTI-OBJECTIVE GENETIC ALGORITHMS Faisal Shabbir 1 , Piotr Omenzetter 2 1.omenzetter@abdn.ac.uk ABSTRACT It is common to estimate structural damage severity by updating a structural model against experimental responses at different damage states. When experimental results from the healthy and damaged

  10. Excitation optimization for damage detection

    SciTech Connect (OSTI)

    Bement, Matthew T [Los Alamos National Laboratory; Bewley, Thomas R [UCSD

    2009-01-01T23:59:59.000Z

    A technique is developed to answer the important question: 'Given limited system response measurements and ever-present physical limits on the level of excitation, what excitation should be provided to a system to make damage most detectable?' Specifically, a method is presented for optimizing excitations that maximize the sensitivity of output measurements to perturbations in damage-related parameters estimated with an extended Kalman filter. This optimization is carried out in a computationally efficient manner using adjoint-based optimization and causes the innovations term in the extended Kalman filter to be larger in the presence of estimation errors, which leads to a better estimate of the damage-related parameters in question. The technique is demonstrated numerically on a nonlinear 2 DOF system, where a significant improvement in the damage-related parameter estimation is observed.

  11. DNA Computing Hamiltonian path

    E-Print Network [OSTI]

    Hagiya, Masami

    2014 DNA DNA #12;DNA Computing · Feynman · Adleman · DNASIMD · ... · · · · · DNADNA #12;DNA · DNA · · · · DNA · · #12;2000 2005 2010 1995 Hamiltonian path DNA tweezers DNA tile DNA origami DNA box Sierpinski DNA tile self assembly DNA logic gates Whiplash PCR DNA automaton DNA spider MAYA

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

    SciTech Connect (OSTI)

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

    2009-01-01T23:59:59.000Z

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

  13. Damage experiments in a cylindrical geometry

    SciTech Connect (OSTI)

    Kaul, Ann M [Los Alamos National Laboratory

    2010-09-21T23:59:59.000Z

    Studying spallation damage with a cylindrical configuration allows for a natural recollection of the damaged material under proper driving conditions. Additionally, the damaged material can come to a complete rest without the application of further stopping forces. Specific areas of research include the damage initiation regime in convergent geometry, behavior of material recollected after damage, and effects of convergent geometry on the material response. Such experiments produce unique strain and shear stress states, motivating improvements in existing computational material models and increasing the predictive capabilities of codes. A LANL/VNIIEF joint experimental series has produced cylindrical aluminum failure initiation data and studied the behavior of material recollected after damage initiation and after complete failure. In addition to post-shot collection of the damaged target material for subsequent metallographic analysis, dynamic in-situ experimental diagnostics include velocimetry and transverse radial radiography. This paper will discuss the current experimental status.

  14. Nowcasting Disaster Damage

    E-Print Network [OSTI]

    Kryvasheyeu, Yury; Obradovich, Nick; Moro, Esteban; Van Hentenryck, Pascal; Fowler, James; Cebrian, Manuel

    2015-01-01T23:59:59.000Z

    Could social media data aid in disaster response and damage assessment? Countries face both an increasing frequency and intensity of natural disasters due to climate change. And during such events, citizens are turning to social media platforms for disaster-related communication and information. Social media improves situational awareness, facilitates dissemination of emergency information, enables early warning systems, and helps coordinate relief efforts. Additionally, spatiotemporal distribution of disaster-related messages helps with real-time monitoring and assessment of the disaster itself. Here we present a multiscale analysis of Twitter activity before, during, and after Hurricane Sandy. We examine the online response of 50 metropolitan areas of the United States and find a strong relationship between proximity to Sandy's path and hurricane-related social media activity. We show that real and perceived threats -- together with the physical disaster effects -- are directly observable through the intens...

  15. Environmental Stigma Damages: Speculative Damages in Environmental Tort Cases

    E-Print Network [OSTI]

    Johnson, E. Jean

    1997-01-01T23:59:59.000Z

    contami- nation causing environmental damage cannot be seen,Damages: Speculative Damages in Environmental Tort Cases E.in cases of environmental damage, primar- ily because it is

  16. Transcriptional Control of DNA-Based Nanomachines

    E-Print Network [OSTI]

    Ludwig-Maximilians-Universität, München

    on responses to stimuli or the cell's environ- ment. So far, nanomachines have been controlled with DNA rather be performed by these devices in well-defined steps. Recently, a DNA machine that binds, carries, and releases the manual addition of a "fuel" strand, consisting of single stranded DNA (ssDNA) that affects

  17. The DNA Single-Strand Break Repair Machinery Facilitates CAF-1-Mediated Histone Deposition at Oxidative DNA Strand Breaks

    E-Print Network [OSTI]

    Arman Nabatiyan; Zhihong Zeng; Keith W. Caldecott

    2012-02-01T23:59:59.000Z

    Oxidative DNA single strand breaks arise continuously in cells and defects in their repair have been implicated in neurological disease. While much progress has been made in understanding how chromosomal single strand breaks are repaired little is known about the changes chromatin structure that accompany this process. Here, we show that nascent recombinant histone H3.1 protein accumulates and is deposited into chromatin at sites of DNA strand breakage in quiescent human cells following oxidative stress, and that core components of the single-strand break repair machinery are required for this process. We show that the SSBR sensor and scaffold proteins poly (ADP-ribose) polymerase and XRCC1 facilitate accumulation of chromatin assembly factor-1 (CAF-1) at sites of oxidative DNA strand breakage, which in turn mediates the deposition of Histone H3.1. We also demonstrate that depletion of CAF-1 slows global rates of DNA strand break repair in quiescent cells following oxidative stress, demonstrating that single-strand break repair and histone deposition are tightly coordinated processes. These data describe a novel role for the DNA singlestrand break repair machinery and implicate histone turnover as a core component of the cellular response of quiescent cells to oxidative damage.

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

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

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

  19. Structural basis for the inhibition of human alkyladenine DNA by 3,N4-ethenocytosine containing DNA

    E-Print Network [OSTI]

    Lingaraju, Gondichatnahalli M.

    Reactive oxygen and nitrogen species, generated by neutrophils and macrophages in chronically inflamed tissues, readily damage DNA, producing a variety of potentially genotoxic etheno base lesions; such inflammation-related ...

  20. Response

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn'tOrigin ofEnergy at Waste-to-Energy usingof Enhanced Dr. JuliaPOINTRespond to theResponse SEAB

  1. Chemical compositions responsible for inflammation and tissue damage in the mouse lung by coarse and fine particulate samples from contrasting air pollution in Europe

    SciTech Connect (OSTI)

    Happo, M.S.; Hirvonen, M.R.; Halinen, A.I.; Jalava, P.I.; Pennanen, A.S.; Sillanpaa, M.; Hillamo, R.; Salonen, R.O. [National Public Health Institute, Kuopio (Finland). Dept. of Environmental Health

    2008-07-01T23:59:59.000Z

    Inflammation is regarded as an important mechanism in mortality and morbidity associated with exposures of cardiorespiratory patients to urban air particulate matter. We investigated the association of the chemical composition and sources of urban air fine (PM2.5-0.2) and coarse (PM10-2.5) particulate samples with the inflammatory activity in the mouse lung. The particulate samples were collected during selected seasons in six European cities using a high-volume cascade impactor. Healthy C57BL/6J mice were intratracheally instilled with a single dose (10 mg/kg) of the particulate samples. At 4, 12, and 24 h after the exposure, the lungs were lavaged and the bronchoalveolar lavage fluid (BALF) was assayed for indicators of inflammation and tissue damage: cell number, total protein, and cytokines (tumor necrosis factor (TNF)-alpha, interleukin (IL)-6, and KC). Dicarboxylic acids and transition metals, especially Ni and V, in PM2.5-0.2 correlated positively and some secondary inorganic ions (NO{sub 3}{sup -}, NH{sub 4}{sup +}) negatively with the inflammatory activity. Total organic matter and SO{sub 4}{sup 2-} had no consistent correlations. In addition, the soil-derived constituents (Ca{sup 2+}, Al, Fe, Si) showed positive correlations with the PM2.5-0.2-induced inflammatory activity, but their role in PM10 (2.5) remained obscure, possibly due to largely undefined biogenic material. Markers of poor biomass and coal combustion, i.e., monosaccharide anhydrides and As, were associated with elevated PAH contents in PM2.5 (0.2) and a consistent immunosuppressive effect. Overall, our results support epidemiological findings that the local sources of incomplete combustion and resuspended road dust are important in urban air particulate pollution-related health effects.

  2. DNA Copyright

    E-Print Network [OSTI]

    Torrance, Andrew W.

    2011-01-01T23:59:59.000Z

    of architecture and computer software. Sequences of DNA should also be acknowledged as eligible for copyright protection. Unaltered genomic DNA sequences would seem poor candidates for copyright protection. The case is stronger for copyright protection...

  3. Damage susceptibility tables

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

    conditions, 3) that x-ray induced damage rates for a common material (relatively pure PVC in this example 7,8 ) can be used to normalize different sets of XPS damage...

  4. DNA demethylation by DNA repair

    E-Print Network [OSTI]

    Gehring, Mary

    Active DNA demethylation underlies key facets of reproduction in flowering plants and mammals and serves a general genome housekeeping function in plants. A family of 5-methylcytosine DNA glycosylases catalyzes plant ...

  5. System and damage identification of civil structures

    E-Print Network [OSTI]

    Moaveni, Babak

    2007-01-01T23:59:59.000Z

    12 Damage Index Methods. . . . . . . . . . . . . . . .Model Updating for Damage Identification . . . . . . . .298 x Damage Factors and Residual

  6. DNA repair modulates the vulnerability of the developing brain to alkylating agents

    E-Print Network [OSTI]

    Samson, Leona D.

    Neurons of the developing brain are especially vulnerable to environmental agents that damage DNA (i.e., genotoxicants), but the mechanism is poorly understood. The focus of the present study is to demonstrate that DNA ...

  7. Photoaffinity Labeling Reveals Nuclear Proteins That Uniquely Recognize Cisplatin?DNA Interstrand Cross-Links

    E-Print Network [OSTI]

    Zhu, Guangyu

    The DNA-binding inorganic compound cisplatin is one of the most successful anticancer drugs. The detailed mechanism by which cells recognize and process cisplatin?DNA damage is of great interest. Although the family of ...

  8. DNA Pendant

    E-Print Network [OSTI]

    Hacker, Randi; Tsutsui, William

    2007-11-14T23:59:59.000Z

    Broadcast Transcript: It's a symbol of commitment. It's a memento mori. It's the DNA pendant offered by Japan's Eiwa Industry and it's two, two, two things in one. Using genetic extraction, Eiwa removes the DNA from, say, a strand of hair or a...

  9. Antaphid interactions on Asclepias syriaca are mediated by plant genotype and caterpillar damage

    E-Print Network [OSTI]

    Mooney, Kailen A.

    1 Ant­aphid interactions on Asclepias syriaca are mediated by plant genotype and caterpillar damage in induced responses to herbivory. Here we test whether induced responses to leaf damage and genotypic-way factorial field experiment manipulating plant genotype, leaf damage by specialist monarch caterpillars

  10. Comparative Analysis of Four Oxidized Guanine Lesions from Reactions of DNA with Peroxynitrite, Singlet Oxygen, and ?-Radiation

    E-Print Network [OSTI]

    Cui, Liang

    Oxidative damage to DNA has many origins, including irradiation, inflammation, and oxidative stress, but the chemistries are not the same. The most oxidizable base in DNA is 2-deoxyguanosine (dG), and the primary oxidation ...

  11. Regulation of DNA repair by parkin

    SciTech Connect (OSTI)

    Kao, Shyan-Yuan, E-mail: shyan-yuan_kao@meei.harvard.edu [Eaton Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114 (United States)] [Eaton Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114 (United States)

    2009-05-01T23:59:59.000Z

    Mutation of parkin is one of the most prevalent causes of autosomal recessive Parkinson's disease (PD). Parkin is an E3 ubiquitin ligase that acts on a variety of substrates, resulting in polyubiquitination and degradation by the proteasome or monoubiquitination and regulation of biological activity. However, the cellular functions of parkin that relate to its pathological involvement in PD are not well understood. Here we show that parkin is essential for optimal repair of DNA damage. Parkin-deficient cells exhibit reduced DNA excision repair that can be restored by transfection of wild-type parkin, but not by transfection of a pathological parkin mutant. Parkin also protects against DNA damage-induced cell death, an activity that is largely lost in the pathological mutant. Moreover, parkin interacts with the proliferating cell nuclear antigen (PCNA), a protein that coordinates DNA excision repair. These results suggest that parkin promotes DNA repair and protects against genotoxicity, and implicate DNA damage as a potential pathogenic mechanism in PD.

  12. DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics

    E-Print Network [OSTI]

    DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics Soo­Yong Shin 1 , Eun Jeong the complexity of DNA computing. The complexity of any computational algorithm is typically measured in terms of time and space. In DNA computing, the time complexity can be measured by the total reaction time

  13. DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics

    E-Print Network [OSTI]

    DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics Soo-Yong Shin1 , Eun Jeong of DNA computing. The complexity of any computational algorithm is typically measured in terms of time and space. In DNA computing, the time complexity can be measured by the total reaction time

  14. RADIATION DAMAGE OF GERMANIUM DETECTORS

    E-Print Network [OSTI]

    Pehl, Richard H.

    2011-01-01T23:59:59.000Z

    the high-energy proton damage than was the planar detector.as far as radiation damage is concerned. Unfortunately, some28-29, 1978 LBL-7967 RADIATION DAMAGE OF GERMANIUM DETECTORS

  15. Composite heat damage assessment

    SciTech Connect (OSTI)

    Janke, C.J.; Wachter, E.A. [Oak Ridge National Lab., TN (United States); Philpot, H.E. [Oak Ridge K-25 Site, TN (United States); Powell, G.L. [Oak Ridge Y-12 Plant, TN (United States)

    1993-12-31T23:59:59.000Z

    The effects of heat damage were determined on the residual mechanical, physical, and chemical properties of IM6/3501-6 laminates, and potential nondestructive techniques to detect and assess material heat damage were evaluated. About one thousand preconditioned specimens were exposed to elevated temperatures, then cooled to room temperature and tested in compression, flexure, interlaminar shear, shore-D hardness, weight loss, and change in thickness. Specimens experienced significant and irreversible reduction in their residual properties when exposed to temperatures exceeding the material upper service temperature of this material (350{degrees}F). The Diffuse Reflectance Infrared Fourier Transform and Laser-Pumped Fluorescence techniques were found to be capable of rapid, in-service, nondestructive detection and quantitation of heat damage in IM6/3501- 6. These techniques also have the potential applicability to detect and assess heat damage effects in other polymer matrix composites.

  16. Controlling Beaver Damage

    E-Print Network [OSTI]

    Texas Wildlife Services

    2007-03-13T23:59:59.000Z

    Beavers are important because their dams stabilize creek flow, slow runoff and create ponds. However, these same dams can negatively alter the flow of creeks. Damage prevention, control and various trapping methods are discussed in this publication....

  17. Controlling Opossum Damage

    E-Print Network [OSTI]

    Texas Wildlife Services

    2007-05-23T23:59:59.000Z

    damage; however, their pelts can be sold only during the furbearer season and with the proper licenses. Other furbearers include beaver, otter, mink, nutria, ringtailed cat, badger, skunk, weasel, raccoon, muskrat, fox and civet cat. Homeowners...

  18. (gene expression) DNA (DNA microarrays).

    E-Print Network [OSTI]

    Athens, University of

    Lymphoblastic Leukemia - ALL, 25 Acute Myeloid Leukemia - AML) µ 7129 [10]. µ µ µ µ µ µ µ µ DNA. 62 µ, 22 40 , µ 2000 [6]. µ 72 µ µ (47 Acute

  19. Oxidative stress and oxidative damage in chemical carcinogenesis

    SciTech Connect (OSTI)

    Klaunig, James E., E-mail: jklauni@indiana.edu; Wang Zemin; Pu Xinzhu; Zhou Shaoyu

    2011-07-15T23:59:59.000Z

    Reactive oxygen species (ROS) are induced through a variety of endogenous and exogenous sources. Overwhelming of antioxidant and DNA repair mechanisms in the cell by ROS may result in oxidative stress and oxidative damage to the cell. This resulting oxidative stress can damage critical cellular macromolecules and/or modulate gene expression pathways. Cancer induction by chemical and physical agents involves a multi-step process. This process includes multiple molecular and cellular events to transform a normal cell to a malignant neoplastic cell. Oxidative damage resulting from ROS generation can participate in all stages of the cancer process. An association of ROS generation and human cancer induction has been shown. It appears that oxidative stress may both cause as well as modify the cancer process. Recently association between polymorphisms in oxidative DNA repair genes and antioxidant genes (single nucleotide polymorphisms) and human cancer susceptibility has been shown.

  20. A UNIFIED FAILURE/DAMAGE APPROACH TO BATTLE DAMAGE REGENERATION

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    A UNIFIED FAILURE/DAMAGE APPROACH TO BATTLE DAMAGE REGENERATION : APPLICATION TO GROUND MILITARY-availability. Military weapon systems availability can be affected by system failures or by damage to the system damage into account in their more general dependability studies. This paper takes a look at the issues

  1. Atomistic simulations of radiation damage in amorphous metal alloys

    E-Print Network [OSTI]

    Baumer, Richard E. (Richard Edward)

    2013-01-01T23:59:59.000Z

    While numerous fundamental studies have characterized the atomic-level radiation response mechanisms in irradiated crystalline alloys, comparatively little is known regarding the mechanisms of radiation damage in amorphous ...

  2. ##### SAT Engine ####### _ ############ DNA ###### _

    E-Print Network [OSTI]

    Hagiya, Masami

    ##### SAT Engine ####### _ ############ DNA ###### _ # # # #y # # #yy # # # #yy ###### DNA #################################### ############### ##################### 6 ## 10 ##### ### DNA ############### (Sakamoto et al., Science, Vol.288, pp.1223-122* *6

  3. Damage monitoring in sandwich beams by modal parameter shifts: A comparative study of burst random and sine dwell

    E-Print Network [OSTI]

    Mailhes, Corinne

    1 Damage monitoring in sandwich beams by modal parameter shifts: A comparative study of burst Abstract: This paper presents an experimental study on the effects of multi-site damage on the vibration response of honeycomb sandwich beams, damaged by two different ways i.e., impact damage and core

  4. Adleman[1] 1994 DNA Hamiltonian Path Problem , DNA

    E-Print Network [OSTI]

    1. Adleman[1] 1994 DNA Hamiltonian Path Problem , DNA DNA [2]. DNA DNA , . , , 2 , DNA 4 . DNA 4 A(Adenine), C(Cytosine), G(Guanine), T(Thymine) 2 4 . , . 1 mole 6x10 23 DNA DNA . , . DNA NP-complete [1, 2], [2

  5. DNA Topology: Fundamentals

    E-Print Network [OSTI]

    Mirkin, Sergei

    DNA Topology: Fundamentals Sergei M Mirkin, University of Illinois at Chicago, Illinois, USA Topological characteristics of DNA and specifically DNA supercoiling influence all major DNA transactions in living cells. DNA supercoiling induces the formation of unusual secondary structure by specific DNA

  6. Damage detection on a full-scale highway sign structure with a distributed wireless sensor network

    E-Print Network [OSTI]

    Lu, Chenyang

    Damage detection on a full-scale highway sign structure with a distributed wireless sensor network highway sign support structure to investigate the ability to use vibration response data to detect damage induced in the structure. A multi-level damage detection strategy is employed for this structure

  7. Ectopic ERK Expression Induces Phenotypic Conversion of C10 Cells and Alters DNA Methyltransferase Expression

    SciTech Connect (OSTI)

    Sontag, Ryan L.; Weber, Thomas J.

    2012-05-04T23:59:59.000Z

    In some model systems constitutive extracellular signal regulated kinase (ERK) activation is sufficient to promote an oncogenic phenotype. Here we investigate whether constitutive ERK expression influences phenotypic conversion in murine C10 type II alveolar epithelial cells. C10 cells were stably transduced with an ERK1-green fluorescent protein (ERK1-GFP) chimera or empty vector and ectopic ERK expression was associated with the acquisition of soft agar focus-forming potential in late passage, but not early passage cells. Late passage ERK1-GFP cells exhibited a significant increase in the expression of DNA methyl transferases (DNMT1 and 3b) and a marked increase in sensitivity to 5-azacytidine (5-azaC)-mediated toxicity, relative to early passage ERK1-GFP cells and vector controls. The expression of xeroderma pigmentosum complementation group A (XPA) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) were significantly increased in late passage cells, suggesting enhanced DNA damage recognition and repair activity which we interpret as a reflection of genomic instability. Phospho-ERK levels were dramatically decreased in late passage ERK1-GFP cells, relative to early passage and vector controls, and phospho-ERK levels were restored by treatment with sodium orthovanadate, indicating a role for phosphatase activity in this response. Collectively these observations suggest that ectopic ERK expression promotes phenotypic conversion of C10 cells that is associated with latent effects on epigenetic programming and phosphatase activities.

  8. Microfluidic DNA sample preparation method and device

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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.

  9. ancient dna damage: Topics by E-print Network

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

    religion in the ancient Mediterranean permeated aspects of everyday life, including seafaring. Besides cargo, ships transported mariners' religious beliefs from port to port,...

  10. Impact of DNA damage proteins on the adenoviral lifecycle

    E-Print Network [OSTI]

    Lakdawala, Seema Sailesh

    2009-01-01T23:59:59.000Z

    4858-4866. Barbeau, D. , Marcellus, R.C. , Bacchetti, S. ,3104- Querido, E. , Marcellus, R.C. , Lai, A. , Charbonneau,

  11. Nucleotide capacitance calculation for DNA sequencing

    SciTech Connect (OSTI)

    Lu, Jun-Qiang [ORNL; Zhang, Xiaoguang [ORNL

    2008-01-01T23:59:59.000Z

    Using a first-principles linear response theory, the capacitance of the DNA nucleotides, adenine, cytosine, guanine and thymine, are calculated. The difference in the capacitance between the nucleotides is studied with respect to conformational distortion. The result suggests that although an alternate current capacitance measurement of a single-stranded DNA chain threaded through a nano-gap electrodes may not sufficient to be used as a stand alone method for rapid DNA sequencing, the capacitance of the nucleotides should be taken into consideration in any GHz-frequency electric measurements and may also serve as an additional criterion for identifying the DNA sequence.

  12. One-electron Oxidation of a Pyrenyl Photosensitizer Covalently Attached to DNA and Competition Between its Further Oxidation and DNA Hole Injection

    E-Print Network [OSTI]

    Yun, Byeong Hwa

    The photosensitized hole injection and guanine base damage phenomena have been investigated in the DNA sequence, 5?-d(CATG[subscript 1] [superscript Py]CG[subscript 2]TCCTAC) with a site-specifically positioned pyrene-like ...

  13. DNA polymerase with modified processivity

    DOE Patents [OSTI]

    Bedford, Ella (Brookline, MA); Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

    1999-01-01T23:59:59.000Z

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

  14. Radiation damage evolution in ceramics. | EMSL

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

    Radiation damage evolution in ceramics. Radiation damage evolution in ceramics. Abstract: A review is presented of recent results on radiation damage production, defect...

  15. Regulation with anticipated learning about environmental damages

    E-Print Network [OSTI]

    Karp, L; Zhang, J

    2006-01-01T23:59:59.000Z

    abatement costs and environmental damages, and a generalemissions. 2.2 Environmental damages and learning Let S t begas stocks and environmental damages. In some respects these

  16. Advance the DNA computing 

    E-Print Network [OSTI]

    Qiu, Zhiquan Frank

    2004-09-30T23:59:59.000Z

    DNA computer. The existing models from which a few DNA computing algorithms have been developed are not sufficiently powerful and robust, however, to attract potential users. This thesis has described research performed to build a new DNA computing...

  17. 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 (OSTI)

    Wei, Min; Yamada, Takanori; Yamano, Shotaro; Kato, Minoru; Kakehashi, Anna; Fujioka, Masaki; Tago, Yoshiyuki; Kitano, Mistuaki; Wanibuchi, Hideki, E-mail: wani@med.osaka-cu.ac.jp

    2013-11-15T23:59:59.000Z

    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.

  18. Stress Response & Adaptation: A New Molecular Toolkit

    E-Print Network [OSTI]

    Storey, Kenneth B.

    · Covalent attachment of: Antibodies, Oligonucleotides · Capture of proteins, peptides, coding and non pathways that are responsible for responding to &/or repairing cellular damage. E.g. antioxidant enzymes

  19. Synthesis of DNA

    DOE Patents [OSTI]

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

    2008-11-18T23:59:59.000Z

    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.

  20. LONG-CIRCULATING DNA LIPID NANOCAPSULES AS NEW VECTOR FOR PASSIVE TUMOR , Montier T.

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    genetic material to target cells. To this end, DNA, complexed with cationic lipids i.e DOTAP causing any hepatic damage. Keywords: poly (ethylene glycol) - non-viral vector - stealth properties

  1. DNA encoding a DNA repair protein

    DOE Patents [OSTI]

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

    2006-08-15T23:59:59.000Z

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

  2. Quantification of the 2-Deoxyribonolactone and Nucleoside 5 '-Aldehyde Products of 2-Deoxyribose Oxidation in DNA and Cells by Isotope-Dilution Gas Chromatography Mass Spectrometry: Differential Effects of gamma-Radiation and Fe[superscript 2+]-EDTA

    E-Print Network [OSTI]

    Chan, Wan Simon

    The oxidation of 2-deoxyribose in DNA has emerged as a critical determinant of the cellular toxicity of oxidative damage to DNA, with oxidation of each carbon producing a unique spectrum of electrophilic products. We have ...

  3. Quantitative DNA fiber mapping

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

    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.

  4. Damage-prone regions in structural composite materials are difficult to detect and even harder to repair. Damage is preceded by complex spatial and temporal changes in stress state, and it is

    E-Print Network [OSTI]

    Wisconsin at Madison, University of

    Materials Seminar Damage-prone regions in structural composite materials are difficult to detect and even harder to repair. Damage is preceded by complex spatial and temporal changes in stress state about in response to damage or high-stress conditions include: (1) signal generation to warn of ensuing

  5. Shock Initiation of Damaged Explosives

    SciTech Connect (OSTI)

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

    2009-10-22T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2010-06-29T23:59:59.000Z

    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.

  7. DNA-nuclear matrix interactions and ionizing radiation sensitivity

    SciTech Connect (OSTI)

    Schwartz, J.L. (Argonne National Lab., IL (United States) Chicago Univ., IL (United States). Dept. of Radiation and Cellular Oncology); Vaughan, A.T.M. (Loyola Univ., Hines, IL (United States). Dept. of Radiotherapy)

    1993-01-01T23:59:59.000Z

    The association between inherent ionizing radiation sensitivity and DNA supercoil unwinding in mammalian cells suggests that the DNA-nuclear matrix attachment region (MAR) plays an important role in radiation response. In radioresistant cells, the MAR structure may exist in a more stable, open configuration, limiting DNA unwinding following strand break induction and maintaining DNA ends in close proximity for more rapid and accurate rejoining. In addition, the open configuration at these matrix attachment sites may serve to facilitate rapid DNA processing of breaks by providing (1) sites for repair proteins to collect and (2) energy to drive enzymatic reactions.

  8. DNA-nuclear matrix interactions and ionizing radiation sensitivity

    SciTech Connect (OSTI)

    Schwartz, J.L. [Argonne National Lab., IL (United States)]|[Chicago Univ., IL (United States). Dept. of Radiation and Cellular Oncology; Vaughan, A.T.M. [Loyola Univ., Hines, IL (United States). Dept. of Radiotherapy

    1993-03-01T23:59:59.000Z

    The association between inherent ionizing radiation sensitivity and DNA supercoil unwinding in mammalian cells suggests that the DNA-nuclear matrix attachment region (MAR) plays an important role in radiation response. In radioresistant cells, the MAR structure may exist in a more stable, open configuration, limiting DNA unwinding following strand break induction and maintaining DNA ends in close proximity for more rapid and accurate rejoining. In addition, the open configuration at these matrix attachment sites may serve to facilitate rapid DNA processing of breaks by providing (1) sites for repair proteins to collect and (2) energy to drive enzymatic reactions.

  9. XRCC1 & DNA MTases : direct and indirect modulation of inflammation-induced DNA damage

    E-Print Network [OSTI]

    Mutamba, James T. (James Tendai)

    2011-01-01T23:59:59.000Z

    Cancer causes 13% of all deaths worldwide. Inflammation-mediated cancer accounts for ~15% of all malignancies, strongly necessitating investigation of the molecular interactions at play. Inflammatory reactive oxygen and ...

  10. Natural DNA sequencing by synthesis

    E-Print Network [OSTI]

    Roller, Eric E.

    2011-01-01T23:59:59.000Z

    labeled nucleotides by DNA polymerases. Biotechniques, 2005.S.A. , et al. , Multiplexed DNA sequencing-by-synthesis.Assembly of High-Density DNA Arrays for Genomic Analyses.

  11. DNA Functionalized Single-Walled Carbon Nanotubes for Electrochemical Detection Chenguo Hu,, Yiyi Zhang, Gang Bao, Yuelan Zhang, Meilin Liu, and Zhong Lin Wang*,

    E-Print Network [OSTI]

    Wang, Zhong L.

    DNA Functionalized Single-Walled Carbon Nanotubes for Electrochemical Detection Chenguo Hu,, Yiyi dispersed and functionalized by wrapping with single-stranded DNA (ssDNA). The ssDNA-SWNTs attach strongly responses, and quick electron transfer for a Fe(CN)6 3- /Fe(CN)6 4 system, indicating that the ssDNA

  12. DNA conjugation andDNA conjugation and reversibility onreversibility on

    E-Print Network [OSTI]

    Rubloff, Gary W.

    DNA conjugation andDNA conjugation and reversibility onreversibility on chitosan surfaceschitosan surfaceschitosan surfaceschitosan surfaces Rubloff Research Group Accomplishments #12;DNA conjugation and reversibility onDNA conjugation and reversibility on chitosan surfaceschitosan surfaces Accomplishment Single

  13. Electrochemical Characterization of Escherichia coli Adaptive Response Protein AidB

    E-Print Network [OSTI]

    Hamill, Michael J.

    When exposed to known DNA-damaging alkylating agents, Escherichia coli cells increase production of four DNA repair enzymes: Ada, AlkA, AlkB, and AidB. The role of three enzymes (Ada, AlkA, and AlkB) in repairing DNA lesions ...

  14. Damage and Damage Prediction for Wood Shearwalls Subjected to Simulated Earthquake Loads

    E-Print Network [OSTI]

    Gupta, Rakesh

    Damage and Damage Prediction for Wood Shearwalls Subjected to Simulated Earthquake Loads John W damaged resulting in large financial losses. Societal demands for damage-limiting design philosophies and better predict damage to woodframe structures. This paper examines damage to the lateral load carrying

  15. Meta-DNA: synthetic biology via DNA nanostructures and

    E-Print Network [OSTI]

    Reif, John H.

    Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions Harish Chandran1 of DNA manipulations achieved by protein enzymes be simulated via simple DNA hybridization chemistry? In this work, we develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based on strands

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

    E-Print Network [OSTI]

    Hang, Bo

    2010-01-01T23:59:59.000Z

    P-postlabeling. Carcinogenesis Malta, E. , Moolenaar, G.F. ,J Biol Chem 281, 2184-2194. Malta, E. , Verhagen, C.P. ,interactions with damaged DNA (Malta et al. , 2006; Malta et

  17. Molecular dissection of the roles of the SOD genes in mammalian response to low dose irradiation

    SciTech Connect (OSTI)

    Eric Y. Chuang

    2006-08-31T23:59:59.000Z

    It has been long recognized that a significant fraction of the radiation-induced genetic damage to cells are caused by secondary oxidative species. Internal cellular defense systems against oxidative stress play significant roles in countering genetic damage induced by ionizing radiation. The role of the detoxifying enzymes may be even more prominent in the case of low-dose, low-LET irradiation, as the majority of genetic damage may be caused by secondary oxidative species. In this study we have attempted to decipher the roles of the superoxide dismutase (SOD) genes, which are responsible for detoxifying the superoxide anions. We used adenovirus vectors to deliver RNA interference (RNAi or siRNA) technology to down-regulate the expression levels of the SOD genes. We have also over-expressed the SOD genes by use of recombinant adenovirus vectors. Cells infected with the vectors were then subjected to low dose ?-irradiation. Total RNA were extracted from the exposed cells and the expression of 9000 genes were profiled by use of cDNA microarrays. The result showed that low dose radiation had clear effects on gene expression in HCT116 cells. Both over-expression and down-regulation of the SOD1 gene can change the expression profiles of sub-groups of genes. Close to 200 of the 9000 genes examined showed over two-fold difference in expression under various conditions. Genes with changed expression pattern belong to many categories that include: early growth response, DNA-repair, ion transport, apoptosis, and cytokine response.

  18. Quantitive DNA Fiber Mapping

    E-Print Network [OSTI]

    Lu, Chun-Mei

    2009-01-01T23:59:59.000Z

    of California. Lu et al. : DNA Fiber Mapping page - 35 Lu etal. : DNA Fiber Mapping page - 36 a b c d e f g OV P1 cloneSp6 end T7 end Lu et al. : DNA Fiber Mapping page - 37 a b c

  19. Damage in porous media due to salt crystallization

    E-Print Network [OSTI]

    Noushine Shahidzadeh-Bonn; Julie Desarnaud; François Bertrand; Xavier Chateau; Daniel Bonn

    2010-07-13T23:59:59.000Z

    We investigate the origins of salt damage in sandstones for the two most common salts: sodium chloride and sulfate. The results show that the observed difference in damage between the two salts is directly related to the kinetics of crystallization and the interfacial properties of the salt solutions and crystals with respect to the stone. We show that, for sodium sulfate, the existence of hydrated and anhydrous crystals and specifically their dissolution and crystallization kinetics are responsible for the damage. Using magnetic resonance imaging and optical microscopy we show that when water imbibes sodium sulfate contaminated sandstones, followed by drying at room temperature, large damage occurs in regions where pores are fully filled with salts. After partial dissolution, anhydrous sodium sulfate salt present in these regions gives rise to a very rapid growth of the hydrated phase of sulfate in the form of clusters that form on or close to the remaining anhydrous microcrystals. The rapid growth of these clusters generates stresses in excess of the tensile strength of the stone leading to the damage. Sodium chloride only forms anhydrous crystals that consequently do not cause damage in the experiments.

  20. The Application of Flow Cytometry to Examine Damage Clearance in Stem Cells From Whole-Body Irradiated Mice

    SciTech Connect (OSTI)

    Marples, Brian; Kovalchuk, Olga; McGonagle, Michele; Martinez, Alvaro; Wilson, George, D.

    2010-02-26T23:59:59.000Z

    The bone marrow contains many types of cells. Approximately 1-2% of these cells are critical for life, these are the so-called ‘bone marrow stem cells’ which divide indefinitely to produce platelets, red blood cells and white blood cells. Death of the bone marrow stem cells results in a diminished ability of the organism to make new blood cell components and can be fatal without medical intervention, such as a bone marrow transplant. Bone marrow stem cells are considered to be particularly sensitive to radiation injury. Therefore, it is important to understand how these cells response to total body radiation exposure and how these cells can be protected from radiation damage. The aim of this project was to determine if these critical cells in the bone marrow are susceptible to short-term and long-term injury after a whole-body exposure to a sub-lethal low dose of ionizing radiation. The overall aims were to determine if the extent of injury produced by the sub-lethal radiation exposure would be cleared from the stem cells and therefore present no long- term genetic risk to the organism, or if the radiation injury persisted and had an adverse long-term consequences for the cell genome. This research question is of interest in order to define the risks to exposed persons after occupational, accidental or terrorism-related sub-lethal low-dose radiation exposures. The novel aspect of this project was the methodology used to obtain the bone marrow stem cell-like cells and examining the outcomes of sub-lethal low-dose radiation in a mammalian animal model. Four radiation treatments were used: single treatments of 0.01Gy, 0.1 Gy, 1 Gy and ten treatments of 0.1 Gy given over 10 days. Bone marrow stem cell-like cells were then harvested 6 hours, 24 hours and 24 days later. The levels of radiation-induced cell death, damage to DNA and permanent changes to cellular DNA were measured in the isolated stem cell-like cells after each radiation treatment and time point and then the results were compared. As expected, the largest radiation dose produced the greatest level of damage but a linear relationship did not exist between cellular effects and radiation dose. The low dose exposures appeared to be more efficient at producing damage than the highest dose when normalized for the initial extent of damage. Additionally, immune stimulation given prior to radiation exposure appeared to protect the critical bone marrow stem cell population from radiation injury. The data suggest that the response of bone marrow stem-cell like cells to radiation injury is dependent on the extent of the initial levels of damage and the effects of total-body low-dose exposures can not be predicted by extrapolating from high dose exposures. This research has provided new information about the radiation sensitivity of bone marrow stem cell-like cells following total-body exposures, and suggests that these critical cells might be more sensitive to radiation than more mature cells in the bone marrow. Further work is need with intermediate radiation doses to confirm this conclusion.

  1. DNA Sequencing apparatus

    DOE Patents [OSTI]

    Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

    1992-01-01T23:59:59.000Z

    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. DNA: structure, dense phases, charges, interactions

    E-Print Network [OSTI]

    Potsdam, Universität

    DNA: structure, dense phases, charges, interactions #12;Outline 1. DNA: structure, charges, dense phases 2. Counterion and DNA condensation 3. ES DNA-DNA interactions 4. DNA toroidal structures 5. Interactions of real DNA helices 6. DNA-DNA ES recognition 7. DNA melting in aggregates 8. Azimuthal

  3. Laser induced damage of fused silica polished optics due to a droplet forming organic contaminant

    SciTech Connect (OSTI)

    Bien-Aime, Karell; Neauport, Jerome; Tovena-Pecault, Isabelle; Fargin, Evelyne; Labrugere, Christine; Belin, Colette; Couzi, Michel

    2009-04-20T23:59:59.000Z

    We report on the effect of organic molecular contamination on single shot laser induced damage density at the wavelength of 351 nm, with a 3 ns pulse length. Specific contamination experiments were made with dioctylphthalate (DOP) in liquid or gaseous phase, on the surface of fused silica polished samples, bare or solgel coated. Systematic laser induced damage was observed only in the case of liquid phase contamination. Different chemical and morphological characterization methods were used to identify and understand the damage process. We demonstrate that the contaminant morphology, rather than its physicochemical nature, can be responsible for the decrease of laser induced damage threshold of optics.

  4. Inhibition of DNA Supercoiling-dependent Transcriptional Activation by a Distant B-DNA to Z-DNA Transition*

    E-Print Network [OSTI]

    Benham, Craig J.

    that a supercoiling-dependent, DNA structural transmission mechanism of this type is responsible for the integration over other alterna- tives, primarily because the change from right-handed helix to left-handed helix). In this way one can alter the destabilization characteristics of other local regions without changing

  5. DAMAGE LOCALIZATION USING LOAD VECTORS Dionisio Bernal

    E-Print Network [OSTI]

    Bernal, Dionisio

    DAMAGE LOCALIZATION USING LOAD VECTORS Dionisio Bernal Associate Professor Department of Civil: A technique to localize damage in structures that can be treated as linear in the pre and post-damage state is presented. Central to the approach is the computation of a set of vectors, designated as Damage Locating

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

    SciTech Connect (OSTI)

    Byers, Loren W. [Los Alamos National Laboratory; Ten Cate, James A. [Los Alamos National Laboratory; Johnson, Paul A. [Los Alamos National Laboratory

    2012-06-28T23:59:59.000Z

    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.

  7. Unexpected irreversible damage of an asymmetric bismuth silicate photorefractive spatial light modulator

    SciTech Connect (OSTI)

    Li Xiujian; Yang Jiankun; Yang Juncai; Chang Shengli; Liu Ju; Hu Wenhua

    2007-06-20T23:59:59.000Z

    Unexpected irreversible damage occurred repeatedly in the asymmetric bismuth silicate (BSO)photorefractive spatial light modulator under some operation modes, even though thepower of the write-light beam does not exceed the optical damage threshold. Accordingto the microscopic surface images and the Raman spectra of the BSO film, suddenrising of temperature in local areas caused by the drift of the photon-induced electronsis responsible for the damage; the damage exists not only on the surface but also insidethe BSO crystal. The damage is relative to the structure of the spatial lightmodulator, the operation mode, and the growth of the BSO crystal. The informationprovided by the damage is useful for optimizing the structure, the operation modes, and the performance of the photorefractive spatial light modulators.

  8. A transfection assay for the biological activity of irradiated PM2 DNA

    E-Print Network [OSTI]

    Newman, Andrew Drennan

    1982-01-01T23:59:59.000Z

    Transfection and Gel Electrophores1s Data for Form I PN2 DNA Exposed to X-Ray Radiation . Transfection and Gel Electrophoresis Data for Form I PN2 DNA Exposed to Ultraviolet Radiation Neasur1ng the Effect of moi of X-Ray Irradiated ONA... of Texas at Dallas Chairman of Advisory Committee: Dr. R. D. Neff A transfection assay was developed to detect radiation-damaged PM2 DNA. By varying growth and incubation condit1ons, the calcium heat shock technique was optimized for PM2 DNA and its...

  9. (2) DNA O(n^5) Quorum-Sensing Lux

    E-Print Network [OSTI]

    Hagiya, Masami

    - 1 - ( ) ( ) DNA RNA DNA RNA DNA DNA 2 DNA #12;- 2 - 17 6 (1) (2) DNA O(n^5) (3) Quorum-Sensing Lux (4) (5) LMNtal ambient LMNtal (1) (2) DNA (3) DNA (4) DNA (5) DNA (1) DNA ANP-96 (Precision System Science ) (2) RTRACS DNA RTRACS (3) in vivo in vivo (4) DNA trans cis 1/10 (5) DNA-PNA DNA DNA DNA DNA DNA

  10. 4698 Biochemistry 1993, 32, 4698-4701 Sequence-Specific Cleavage of DNA via Nucleophilic Attack of Hydrogen

    E-Print Network [OSTI]

    Tullius, Thomas D.

    4698 Biochemistry 1993, 32, 4698-4701 Sequence-Specific Cleavage of DNA via Nucleophilic Attack by oxidative damage of the DNA backbone but instead is the result of nucleophilic attack by peroxide. A singleSaccharomyces cerevisae, whichactivatesthephosphodiester for attack by thediffusible smallnucleophile. While Flp

  11. Electrochemical DNA Hybridization Detection Using DNA Dohyoung Kwon,a

    E-Print Network [OSTI]

    Kwak, Juhyoun

    Full Paper Electrochemical DNA Hybridization Detection Using DNA Cleavage Dohyoung Kwon,a Kyuwon method for detection of DNA hybridization using enzymatic cleavage. The strategy is based on that S1 nuclease is able to specifically cleave only single strand DNA, but not double strand DNA. The capture

  12. Damage detection in initially nonlinear systems

    SciTech Connect (OSTI)

    Bornn, Luke [Los Alamos National Laboratory; Farrar, Charles [Los Alamos National Laboratory; Park, Gyuhae [Los Alamos National Laboratory

    2009-01-01T23:59:59.000Z

    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.

  13. Remote sensing and forest damage

    SciTech Connect (OSTI)

    Reid, N.J.

    1987-05-01T23:59:59.000Z

    Each year, damage to North American forests caused by insects, diseases, pollution, and fire results in multibillion dollar losses of revenue and resources. To respond to these losses effectively, forest managers need timely information on the location, extent, and spread of the damage. Traditional techniques for monitoring forest damage include high-resolution aerial photography, color infrared photography, and visual reconnaissance mapping. These techniques require visual interpretation of the data and often are somewhat subjective. In addition, because such analyses are time-consuming and costly, many areas of forest are never mapped, and in cases where maps exist, they often are obsolete or incomplete. An airborne imager has been developed to solve the problems of time-consuming visual analysis and interpretations. The Programmable Multispectral Imager measures small changes - invisible by conventional detection methods - in light reflected by the forest canopy. The PMI measures the color an intensity of reflected light and records this information digitally in computer tape aboard an aircraft. This information is then available for later entry into a computer for processing and enhancement. Although airborne imagers have been available for nearly three decades, they have not been used extensively for forest damage assessment or other forestry applications because of their poor sensitivity and their limited number of fixed spectral channels. The PMI is the first of a new generation of imagers that combine high sensitivity with the flexibility of continuous spectral coverage. This allows scientists to evaluate the potential causes and effects of stress on vegetation.

  14. 2010 MICROBIAL STRESS RESPONSE GORDON RESEARCH CONFERENCE, JULY 18-23, 2010

    SciTech Connect (OSTI)

    Sarah Ades

    2011-07-23T23:59:59.000Z

    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.

  15. Multiprotein DNA looping

    E-Print Network [OSTI]

    Jose M. G. Vilar; Leonor Saiz

    2006-06-19T23:59:59.000Z

    DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switch-like transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.

  16. Collateral damage: Evolution with displacement of fracture distribution and secondary fault strands in fault damage zones

    E-Print Network [OSTI]

    Savage, Heather M.; Brodsky, Emily E.

    2011-01-01T23:59:59.000Z

    E. McCallum (1999), Reservoir damage around faults: OutcropSkar (2005), Controls on damage zone asymmetry of a normal2007), The evolution of the damage zone with fault growth in

  17. Structural Changes in Gill DNA Reveal the Effects of Contaminants on Puget Sound Fish

    SciTech Connect (OSTI)

    Malins, Donald C.; Stegeman, John J.; Anderson, Jack W.; Johnson, Paul M.; Gold, Jordan; Anderson, Katie M.

    2004-04-01T23:59:59.000Z

    Structural differences were identified in gill DNA from two groups of English sole collected from Puget Sound, Washington, in October 2000. One group was from the industrialized Duwamish River (DR) in Seattle and the other from relatively clean Quartermaster Harbor (QMH). Chemical markets of sediment contamination [e.g., polynuclear aromatic hydrocarbons (PAHS) and polychlorinated biphenyls (PCBs)] established that the DR was substantially more contaminated than QMH. The levels of these chemicals in the sediments of both sites were consistent with levels of cytochrome P450 IA (CYPIA) expression in the gills of English sole from the same sites. Structural differences in gill DNA between the groups were evinced via statistical models of Fourier transform-infrared (FT-IR) spectra. Marked structural damage was found in the gill DNA of the DR fish as reflected in differences in base functional groups (e.g., C-0 and NH2) and conformational properties (e.g., arising from perturbations in vertical base stacking interactions). These DNA differences were used to discriminate between the two fish groups through principal components analysis of mean FT-IR spectra In addition, logistic recession analysis allowed for the development of a ''DNA damage index'' to assess the effects of contaminants on the gill. The evidence implies that environmental chemicals contribute to the DNA changes in the gill. The damaged DNA is a promising marker for identifying, through gill biopsies, contaminant effects on fish.

  18. Method for producing damage resistant optics

    DOE Patents [OSTI]

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

    2003-01-01T23:59:59.000Z

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

  19. Visualizing DNA What is it?

    E-Print Network [OSTI]

    Rose, Michael R.

    Visualizing DNA #12;What is it? Gel electrophoresis is one of the techniques scientists use to look at the DNA they have. This technique separates DNA by size. #12;How does it work? First a gel is prepared. Gels

  20. Insulator damage endangers public, power reliability; ratepayers...

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

    for tips about multiple incidents of insulators damaged by firearms on its high-voltage power line near Joint Base Lewis-McChord in Tacoma, Wash. Damaged insulators can put...

  1. A damage model for fracking

    E-Print Network [OSTI]

    Norris, J Quinn; Rundle, John B

    2015-01-01T23:59:59.000Z

    Injections of large volumes of water into tight shale reservoirs allows the extraction of oil and gas not previously accessible. This large volume "super" fracking induces damage that allows the oil and/or gas to flow to an extraction well. The purpose of this paper is to provide a model for understanding super fracking. We assume that water is injected from a small spherical cavity into a homogeneous elastic medium. The high pressure of the injected water generates hoop stresses that reactivate natural fractures in the tight shales. These fractures migrate outward as water is added creating a spherical shell of damaged rock. The porosity associated with these fractures is equal to the water volume injected. We obtain an analytic expression for this volume. We apply our model to a typical tight shale reservoir and show that the predicted water volumes are in good agreement with the volumes used in super fracking.

  2. Damaged Fuel Experiment DF-1

    SciTech Connect (OSTI)

    Gasser, R.D.; Fryer, C.P.; Gauntt, R.O.; Marshall, A.C.; Reil, K.O.; Stalker, K.T.

    1990-01-01T23:59:59.000Z

    A series of in-pile experiments addressing LWR severe fuel damage phenomena has been conducted in the Annular Core Research Reactor (ACRR) at Sandia National Laboratories. The ACRR Debris Formation and Relocation (DF) experiments are quasi-separate effects tests that provide a data base for the development and verification of models for LWR severe core damage accidents. The first experiment in this series, DF-1, was performed on March 15, 1984, and the results are presented in this report. The DF-1 experiment examined the effects of low initial clad oxidation conditions on fuel damage and relocation processes. The DF-1 test assembly consisted of a nine-rod square-matrix bundle that employed PWR-type fuel rods with a 0.5-m fissile length. The fuel rods were composed of 10% enriched UO{sub 2} pellets within a zircaloy-4 cladding. Steam flowed through the test bundle at flow rates varying between 0.5 and 3 g/s, and the ACRR maintained a peak power level of 1.5 MW during the high temperature oxidation phase of the test inducing {approximately}8.5 kW fission power and {approximately}20 kW peak oxidation power in the assembly. Visual observation showed early clad relocation and partial blockage formation at the grid spacer location accompanied by production of a dense aerosol. Posttest cross sections show liquefaction losses of fuel in excess of 10 volume percent, as well as large fractional losses of cladding material from the upper two-thirds of the bundle. The quantity of hydrogen measured during the test was consistent with the observed magnitude of cladding oxidation. Oxidation driven heating rates of 25 K/s and peak temperatures in excess of 2525 K were observed. The analyses, interpretation, and application of these results to severe fuel damage accidents are discussed. 27 refs., 118 figs., 23 tabs.

  3. Nondestructive Damage Detection in General Beams 

    E-Print Network [OSTI]

    Dincal, Selcuk

    2010-12-08T23:59:59.000Z

    Representation of the First Damage Case on the Finite Element Mesh of the Slender Beam ...................................................... 41 Figure 3.12 Schematic Representation of the Second Damage Case on the Finite Element Mesh... of the Slender Beam ...................................................... 42 Figure 3.13 Schematic Representation of the Third Damage Case on the Finite Element Mesh of the Slender Beam ...................................................... 44...

  4. Multiscale Modeling of Radiation Damage in

    E-Print Network [OSTI]

    Multiscale Modeling of Radiation Damage in Fusion Reactor Materials Brian D. Wirth, R.J. Kurtz-7405-Eng-48. #12;Presentation overview · Introduction to fusion reactor materials and radiation damage. tailor He HFIR isotopic tailor He HFIR target/RB He appmHe displacement damage (dpa) ffuussiioonn

  5. Density Functional Theory Models for Radiation Damage

    E-Print Network [OSTI]

    Density Functional Theory Models for Radiation Damage S.L. Dudarev EURATOM/CCFE Fusion Association and informative as the most advanced experimental techniques developed for the observation of radiation damage investigation and assessment of radiation damage effects, offering new insight into the origin of temperature

  6. Structural Damage Detection and Localization Using NETSHM

    E-Print Network [OSTI]

    Gnawali, Omprakash

    Structural Damage Detection and Localization Using NETSHM Krishna Chintalapudi, Jeongyeup Paek and localize damage in large civil structures. Structural engineers often implement and test SHM algorithms the intricacies of wireless networking, or the details of sensor data acquisition. We have implemented a damage

  7. Damage Detection in Plate Structures using Guided Ultrasonic Waves

    E-Print Network [OSTI]

    Jarmer, Gregory James Sylvester

    2009. “Evaluation of the Damage Detection Capability of alikelihood Estimation of Damage Location in Guided- waveStatistically-based Damage Detection in Geometrically-

  8. Micromechanical Damage Models for Continuous Fiber Reinforced Composite Materials

    E-Print Network [OSTI]

    Wu, Yi

    2013-01-01T23:59:59.000Z

    2008). Micromechanical modeling of damage and fracture ofmatrix viscoplasticity and evolving damage, Journal of theW.A. (1998). Stochastic damage evolution and failure in

  9. Blast damage mitigation of steel structures from near- contact charges

    E-Print Network [OSTI]

    Wolfson, Janet Crumrine

    2008-01-01T23:59:59.000Z

    OF CALIFORNIA, SAN DIEGO Blast Damage Mitigation of Steel35  Damage Levels Observed in LaboratoryFigure 3.34: Progression of damage for a Ballistic Loading

  10. Cognitive Empathy Following Orbitofrontal Cortex and Dorsolateral Prefrontal Cortex Damage

    E-Print Network [OSTI]

    Goodkind, Madeleine Shirley

    2010-01-01T23:59:59.000Z

    following bilateral damage to the human amygdala. Nature,as a measure of frontal lobe damage. Journal of Clinical andcaused by frontal damage fail to respond autonomically to

  11. International Trade and the Internalization of Environmental Damages

    E-Print Network [OSTI]

    Karp, Larry; Dumas, Christopher F.; Koo, Bonwoo; Sacheti, Sandeep

    1995-01-01T23:59:59.000Z

    estimates of environmental damages efficiently and quickly,an overview of environmental damages and internalizationdo little to decrease environmental damage, and may actually

  12. The Role of Nucleotide Excision Repair in Restoring Replication Following UV-Induced Damage in Escherichia coli

    E-Print Network [OSTI]

    Courcelle, Justin

    The Role of Nucleotide Excision Repair in Restoring Replication Following UV-Induced Damage DNA synthesis in the absence of nucleotide excision repair does not promote cell survivalA mutants....................... 26 Following low doses of UV irradiation cells lacking nucleotide excision

  13. DNA-PK assay

    DOE Patents [OSTI]

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12T23:59:59.000Z

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

  14. DNA chips --Integrated Chemical Circuits for DNADiagnosis and DNA computers

    E-Print Network [OSTI]

    Hagiya, Masami

    DNA chips -- Integrated Chemical Circuits for DNADiagnosis and DNA computers Akira Suyama, Associate Professor Institute of Physics, Graduate School of Arts and Sciences, The University of Tokyo DNA chips are si l i con­ or glass­based smal l surfaces on which many DNA ol i gonuc l eotides are i

  15. Focus: DNA probes

    SciTech Connect (OSTI)

    Not Available

    1986-11-01T23:59:59.000Z

    Progress in the development of DNA probes for the identification and quantitation of specific genetic sequences in biological samples is reviewed. Current research efforts in the development of DNA probes for the diagnosis of a wide variety of bacterial, viral, and other infectious diseases, such as herpes simplex and cytomegalovirus, and inherited genetic diseases such as cystic fibrosis and sickle cell anemia are discussed. Progress in development of DNA probe assays for cancer diagnosis, detection of Salmonella food poisoning, tissue typing (detection of histocompatibility antigens), mutagen screening, and animal diseases, among other applications is included.

  16. 28-nm laser damage testing of LIF

    SciTech Connect (OSTI)

    Foltyn, S.R.; Newman, B.E.

    1981-01-01T23:59:59.000Z

    We have tested several samples of LIF, both single crystal and press forged, for damage resistance to 10-ns 248-nm pulses at 35 pps. The damage thresholds - the highest levels at which no damage could be produced - ranged from 4 to 6 J/cm/sup 2/ although some test sites survived irradiation at approx. 30 J/cm/sup 2/. We observed that bulk damage is the primary failure mechanism in single crystal and press forged samples and that both types exhibit the same resistance to laser damage.

  17. Structural-Damage Detection by Distributed Piezoelectric Transducers and Tuned Electric Circuits

    E-Print Network [OSTI]

    F. dell'Isola; F. Vestroni; S. Vidoli

    2010-07-13T23:59:59.000Z

    A novel technique for damage detection of structures is introduced and discussed. It is based on purely electric measurements of the state variables of an electric network coupled to the main structure through a distributed set of piezoelectric patches. The constitutive parameters of this auxiliary network are optimized to increase the sensitivity of global measurements- as the frequency, response functions relative to selected electric degrees of freedom-with respect to a given class of variations in the structural-mechanical properties. Because the proposed method is based on purely electric input and output measurements, it allows for accurate results in the identification and localization of damages. Use of the electric frequency-response function to identify the mechanical damage leads to nonconvex optimization problems; therefore the proposed sensitivity-enhanced identification procedure becomes computationally efficient if an a priori knowledge about the damage is available.

  18. A micro to macro approach to polymer matrix composites damage modeling : final LDRD report.

    SciTech Connect (OSTI)

    English, Shawn Allen; Brown, Arthur A.; Briggs, Timothy M.

    2013-12-01T23:59:59.000Z

    Capabilities are developed, verified and validated to generate constitutive responses using material and geometric measurements with representative volume elements (RVE). The geometrically accurate RVEs are used for determining elastic properties and damage initiation and propagation analysis. Finite element modeling of the meso-structure over the distribution of characterizing measurements is automated and various boundary conditions are applied. Plain and harness weave composites are investigated. Continuum yarn damage, softening behavior and an elastic-plastic matrix are combined with known materials and geometries in order to estimate the macroscopic response as characterized by a set of orthotropic material parameters. Damage mechanics and coupling effects are investigated and macroscopic material models are demonstrated and discussed. Prediction of the elastic, damage, and failure behavior of woven composites will aid in macroscopic constitutive characterization for modeling and optimizing advanced composite systems.

  19. DNA microarray analyses reveal a post-irradiation differential time-dependent gene expression profile in yeast cells exposed to X-rays and {gamma}-rays

    SciTech Connect (OSTI)

    Kimura, Shinzo [Laboratory of Environmental Biology, Department of Preventive Medicine, Hokkaido University School of Medicine, Sapporo 060-8638 (Japan); Ishidou, Emi [Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science and Technology (AIST) WEST, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 (Japan); Kurita, Sakiko [Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science and Technology (AIST) WEST, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 (Japan); Suzuki, Yoshiteru [Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science and Technology (AIST) WEST, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 (Japan); Shibato, Junko [Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science and Technology (AIST) WEST, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 (Japan); Rakwal, Randeep [Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science and Technology (AIST) WEST, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 (Japan)]. E-mail: rakwal-68@aist.go.jp; Iwahashi, Hitoshi [Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science and Technology (AIST) WEST, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 (Japan)

    2006-07-21T23:59:59.000Z

    Ionizing radiation (IR) is the most enigmatic of genotoxic stress inducers in our environment that has been around from the eons of time. IR is generally considered harmful, and has been the subject of numerous studies, mostly looking at the DNA damaging effects in cells and the repair mechanisms therein. Moreover, few studies have focused on large-scale identification of cellular responses to IR, and to this end, we describe here an initial study on the transcriptional responses of the unicellular genome model, yeast (Saccharomyces cerevisiae strain S288C), by cDNA microarray. The effect of two different IR, X-rays, and gamma ({gamma})-rays, was investigated by irradiating the yeast cells cultured in YPD medium with 50 Gy doses of X- and {gamma}-rays, followed by resuspension of the cells in YPD for time-course experiments. The samples were collected for microarray analysis at 20, 40, and 80 min after irradiation. Microarray analysis revealed a time-course transcriptional profile of changed gene expressions. Up-regulated genes belonged to the functional categories mainly related to cell cycle and DNA processing, cell rescue defense and virulence, protein and cell fate, and metabolism (X- and {gamma}-rays). Similarly, for X- and {gamma}-rays, the down-regulated genes belonged to mostly transcription and protein synthesis, cell cycle and DNA processing, control of cellular organization, cell fate, and C-compound and carbohydrate metabolism categories, respectively. This study provides for the first time a snapshot of the genome-wide mRNA expression profiles in X- and {gamma}-ray post-irradiated yeast cells and comparatively interprets/discusses the changed gene functional categories as effects of these two radiations vis-a-vis their energy levels.

  20. Differences in Electrostatic Potential Around DNA Fragments Containing Guanine and 8-oxo-Guanine

    SciTech Connect (OSTI)

    Haranczyk, Maciej; Gutowski, Maciej S.

    2007-02-01T23:59:59.000Z

    hanges of electrostatic potential (EP) around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through large scale density functional theory computations. Quantum mechanical structural optimizations of DNA fragments with three pairs of nucleotoides and accompanying counteractions were performed with a B3LYP exchange-correlation functional and 6-31G** basis sets. The “intact” DNA fragment contained guanine in the middle layer, while the “damaged” fragment had the guanine replaced with 8-oxo-guanine. The electrostatic potential around these DNA fragments was projected on a surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were analyzed to identify these modifications of EP that result from the occurrence of 8-oxo-guanine. It was found that distortions of the phosphate groups and displacements of the accompanying countercations are clearly reflected in the EP maps.

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

    DOE Patents [OSTI]

    Weiss, J.D.

    1995-02-07T23:59:59.000Z

    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.

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

    DOE Patents [OSTI]

    Weiss, Jonathan D. (Albuquerque, NM)

    1995-01-01T23:59:59.000Z

    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.

  3. -DNA 1217 BK21-IT,

    E-Print Network [OSTI]

    - DNA 1217 BK21-IT, (MEC) (NRL) . . : : : : syshin@bi.snu.ac.kr ihlee@bi.snu.ac.kr btzhang@bi.snu.ac.kr 2004 9 16 2005 10 14 - DNA (DNA Sequence Design using -Multiobjective Evolutionary Algorithm) (Soo-Yong Shin) (In-Hee Lee) (Byoung-Tak Zhang) DNA

  4. Continuum limits of bistable spring models of carbon nanotube arrays accounting for material damage

    E-Print Network [OSTI]

    T. Blesgen; F. Fraternali; J. R. Raney; A. Amendola; C. Daraio

    2011-12-10T23:59:59.000Z

    Using chains of bistable springs, a model is derived to investigate the plastic behavior of carbon nanotube arrays with damage. We study the preconditioning effect due to the loading history by computing analytically the stress-strain pattern corresponding to a fatigue-type damage of the structure. We identify the convergence of the discrete response to the limiting case of infinitely many springs, both analytically in the framework of Gamma-convergence, as well as numerically.

  5. Shear Unzipping of DNA

    E-Print Network [OSTI]

    Buddhapriya Chakrabarti; David R. Nelson

    2009-04-09T23:59:59.000Z

    We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder model of shear unzipping proposed earlier by deGennes [deGennes P. G. C. R. Acad. Sci., Ser. IV; Phys., Astrophys. 2001, 1505]. Using this model and a combination of analytical and numerical methods, we study the DNA "unzipping" transition when the shearing force exceeds a critical threshold at zero temperature. We also explore the effects of sequence heterogeneity and finite temperature and discuss possible applications to determine the strength of colloidal nanoparticle assemblies functionalized by DNA.

  6. Conformational Manipulation of DNA in Nanochannels Using Hydrodynamics

    E-Print Network [OSTI]

    Qihao He; Hubert Ranchon; Pascal Carrivain; Yannick Viero; Joris Lacroix; Charline Blatché; Emmanuelle Daran; Jean-Marc Victor; Aurélien Bancaud

    2014-09-01T23:59:59.000Z

    The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics, although the physics of soft matter in nanoscale flows has raised considerable interest over the past decade. In this report the migration of DNA is studied in nanochannels of lateral dimension spanning 100 to 500 nm using both actuation principles. We show that the relaxation kinetics are 3-fold slowed down and the extension increases up to 3-fold using hydrodynamics. We propose a model to account for the onset in elongation with the flow, which assumes that DNA response is determined by the shear-driven lift forces mediated by the proximity of the channels' walls. Overall, we suggest that hydrodynamic actuation allows for an improved manipulation of DNA in nanochannels.

  7. Crystal structure of a p53 core tetramer bound to DNA

    SciTech Connect (OSTI)

    Malecka, K.A.; Ho, W.C.; Marmorstein, R.; (Penn)

    2009-09-02T23:59:59.000Z

    The tumor suppressor p53 regulates downstream genes in response to many cellular stresses and is frequently mutated in human cancers. Here, we report the use of a crosslinking strategy to trap a tetrameric p53 DNA-binding domain (p53DBD) bound to DNA and the X-ray crystal structure of the protein/DNA complex. The structure reveals that two p53DBD dimers bind to B form DNA with no relative twist and that a p53 tetramer can bind to DNA without introducing significant DNA bending. The numerous dimer-dimer interactions involve several strictly conserved residues, thus suggesting a molecular basis for p53DBD-DNA binding cooperativity. Surface residue conservation of the p53DBD tetramer bound to DNA highlights possible regions of other p53 domain or p53 cofactor interactions.

  8. Simulated Fatigue Damage Index on Mooring Lines of a Gulf of Mexico Truss Spar Determined from Recorded Field Data

    E-Print Network [OSTI]

    Kiecke, Adam Fuller

    2012-07-16T23:59:59.000Z

    . The platform is equipped with an Environmental Platform Response Monitoring System (EPRMS) which records real-time motions, environmental parameters and loads. These measurements were used to hind-cast the platform mooring tensions and estimate fatigue damage...

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

    SciTech Connect (OSTI)

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

    2012-09-17T23:59:59.000Z

    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).

  10. Intermediate DNA at low added salt: DNA bubbles slow the diffusion of short DNA fragments

    E-Print Network [OSTI]

    Tomislav Vuletic; Sanja Dolanski Babic; Ticijana Ban; Joachim Raedler; Francoise Livolant; Silvia Tomic

    2011-01-05T23:59:59.000Z

    We report a study of DNA (150 bp fragments) conformations in very low added salt $DNA concentration range $0.0015\\leq c \\leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 DNA has the diffusion coefficient, $D_p$ reduced below the values for both ssDNA coils and native dsDNA helices of similar polymerization degree $N$. Thus, this DNA population can not be a simple mix of dsDNA and of ssDNA which results from DNA melting. Here, melting occurs due to a reduction in screening concomitant with DNA concentration being reduced, in already very low salt conditions. The intermediate DNA is rationalized through the well known concept of fluctuational openings (DNA bubbles) which we postulate to form in AT-rich portions of the sequence, without the strands coming apart. Within the bubbles, DNA is locally stretched, while the whole molecule remains rod-like due to very low salt environment. Therefore, such intermediate DNA is elongated, in comparison to dsDNA, which accounts for its reduced $D_p$.

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

    SciTech Connect (OSTI)

    Claytor, Thomas N [Los Alamos National Laboratory; Ammerman, Curtt N [Los Alamos National Laboratory; Park, Gyu Hae [Los Alamos National Laboratory; Farinholt, Kevin M [Los Alamos National Laboratory; Farrar, Charles R [Los Alamos National Laboratory; Atterbury, Marie K [Los Alamos National Laboratory

    2010-01-01T23:59:59.000Z

    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.

  12. DNA Repair Alterations in Children With Pediatric Malignancies: Novel Opportunities to Identify Patients at Risk for High-Grade Toxicities

    SciTech Connect (OSTI)

    Ruebe, Claudia E., E-mail: claudia.ruebe@uks.e [Department of Radiation Oncology, Saarland University, Homburg/Saar (Germany); Fricke, Andreas; Schneider, Ruth; Simon, Karin; Kuehne, Martin; Fleckenstein, Jochen [Department of Radiation Oncology, Saarland University, Homburg/Saar (Germany); Graeber, Stefan [Institute of Medical Biometrics, Epidemiology and Medical Informatics, Saarland University, Homburg/Saar (Germany); Graf, Norbert [Department of Pediatric Hematology and Oncology, Saarland University, Homburg/Saar (Germany); Ruebe, Christian [Department of Radiation Oncology, Saarland University, Homburg/Saar (Germany)

    2010-10-01T23:59:59.000Z

    Purpose: To evaluate, in a pilot study, the phosphorylated H2AX ({gamma}H2AX) foci approach for identifying patients with double-strand break (DSB) repair deficiencies, who may overreact to DNA-damaging cancer therapy. Methods and Materials: The DSB repair capacity of children with solid cancers was analyzed compared with that of age-matched control children and correlated with treatment-related normal-tissue responses (n = 47). Double-strand break repair was investigated by counting {gamma}H2AX foci in blood lymphocytes at defined time points after irradiation of blood samples. Results: Whereas all healthy control children exhibited proficient DSB repair, 3 children with tumors revealed clearly impaired DSB repair capacities, and 2 of these repair-deficient children developed life-threatening or even lethal normal-tissue toxicities. The underlying mutations affecting regulatory factors involved in DNA repair pathways were identified. Moreover, significant differences in mean DSB repair capacity were observed between children with tumors and control children, suggesting that childhood cancer is based on genetic alterations affecting DSB repair function. Conclusions: Double-strand break repair alteration in children may predispose to cancer formation and may affect children's susceptibility to normal-tissue toxicities. Phosphorylated H2AX analysis of blood samples allows one to detect DSB repair deficiencies and thus enables identification of children at risk for high-grade toxicities.

  13. Coarse-graining DNA for simulations of DNA nanotechnology

    E-Print Network [OSTI]

    Doye, Jonathan P K; Louis, Ard A; Romano, Flavio; Sulc, Petr; Matek, Christian; Snodin, Benedict E K; Rovigatti, Lorenzo; Schreck, John S; Harrison, Ryan M; Smith, William P J

    2013-01-01T23:59:59.000Z

    To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.

  14. Hairpin DNA Switch for Ultrasensitive Spectrophotometric Detection...

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

    Hairpin DNA Switch for Ultrasensitive Spectrophotometric Detection of DNA Hybridization Based on Gold Nanoparticles and Enzyme Hairpin DNA Switch for Ultrasensitive...

  15. Synthetic-viability genomic screening defines Sae2 function in DNA repair

    E-Print Network [OSTI]

    Puddu, Fabio; Oelschlaegel, Tobias; Guerini, Ilaria; Geisler, Nicola J.; Niu, Hengyao; Herzog, Mareike; Salguero, Israel; Ochoa-Montańo, Bernardo; Viré, Emmanuelle; Sung, Patrick; Adams, David J.; Keane, Thomas M.; Jackson, Stephen P.

    2015-04-21T23:59:59.000Z

    are led to a model that resolves apparent para- doxes regarding Sae2 and MRX functions, namely the fact that while deletion of either SAE2 or MRE11 causes hypersensitivity to DNA- damaging agents, the resection defect of sae2? strains is negligible...

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

    DOE Patents [OSTI]

    Tabor, Stanley (Cambridge, MA); Richardson, Charles (Chestnut Hill, MA)

    1997-01-01T23:59:59.000Z

    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.

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

    DOE Patents [OSTI]

    Tabor, S.; Richardson, C.

    1997-03-25T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Drennan, Catherine L.

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

  19. Integrating natural resource damage assessment and environmental restoration activities at DOE facilities

    SciTech Connect (OSTI)

    NONE

    1993-10-01T23:59:59.000Z

    Environmental restoration activities are currently under way at many U.S. Department of Energy (DOE) sites under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), as amended. DOE is the CERCLA lead response agency for these activities. Section 120 of CERCLA also could subject DOE to liability for natural resource damages resulting from hazardous substance releases at its sites. A Natural Resource Damage Assessment (NRDA) process is used to determine whether natural resources have been injured and to calculate compensatory monetary damages to be used to restore the natural resources. In addition to restoration costs, damages may include costs of conducting the damage assessment and compensation for interim losses of natural resource services that occur before resource restoration is complete. Natural resource damages represent a potentially significant source of additional monetary claims under CERCLA, but are not well known or understood by many DOE staff and contractors involved in environmental restoration activities. This report describes the requirements and procedures of NRDA in order to make DOE managers aware of what the process is designed to do. It also explains how to integrate the NRDA and CERCLA Remedial Investigation/Feasibility Study processes, showing how the technical and cost analysis concepts of NRDA can be borrowed at strategic points in the CERCLA process to improve decisionmaking and more quickly restore natural resource services at the lowest total cost to the public.

  20. Integrating Natural Resource Damage Assessment and environmental restoration activities at DOE facilities

    SciTech Connect (OSTI)

    Not Available

    1993-10-01T23:59:59.000Z

    Environmental restoration activities are currently under way at many US Department of Energy (DOE) sites under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA). DOE is the CERCLA lead response agency for these activities. Section 120 of CERCLA also could subject DOE to liability for natural resource damages resulting from hazardous substance releases at its sites. A Natural Resource Damage Assessment (NRDA) process is used to determine whether natural resources have been injured and to calculate compensatory monetary damages to be used to restore the natural resources. In addition to restoration costs, damages may include costs of conducting the damage assessment and compensation for interim losses of natural resource services that occur before resource restoration is complete. Natural resource damages represent a potentially significant source of additional monetary claims under CERCLA, but are not well known or understood by many DOE staff and contractors involved in environmental restoration activities. This report describes the requirements and procedures of NRDA in order to make DOE managers aware of what the process is designed to do. It also explains how to integrate the NRDA and CERCLA Remedial Investigation/Feasibility Study processes, showing how the technical and cost analysis concepts of NRDA can be borrowed at strategic points in the CERCLA process to improve decisionmaking and more quickly restore natural resource services at the lowest total cost to the public.

  1. KU Public Safety Office Criminal Damage

    E-Print Network [OSTI]

    in the damage of a Coca-Cola vending machine in the Parking Services lobby at 1501 Irving Hill Drive and damage to Coca-Cola vending machines across the campus. Suspect Description: W/M, 5 feet 10 inches, 150

  2. Damage and plastic deformation of reservoir rocks

    E-Print Network [OSTI]

    Ze'ev, Reches

    Damage and plastic deformation of reservoir rocks: Part 1. Damage fracturing Seth Busetti, Kyran mechanics, fluid flow in fractured reservoirs, and geomechanics in nonconventional reservoirs. Kyran Mish finite deformation of reservoir rocks. We present an at- tempt to eliminate the main limitations

  3. MODELING LONGITUDINAL DAMAGE IN SHIP COLLISIONS

    E-Print Network [OSTI]

    Brown, Alan

    . Performing Organization Name and Address Department of Aerospace and Ocean Engineering. 10. Work Unit No made excellent progress towards predicting damage penetration in ship collisions. This project focuses collision data for penetrating collisions. 17. Key Words ship collisions, longitudinal ship damage 18

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

    SciTech Connect (OSTI)

    Pineda-porras, Omar Andrey [Los Alamos National Laboratory; Najafi, Mohammand [U. OF TEXAS

    2009-01-01T23:59:59.000Z

    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.

  5. DNA Structural Nanotechnology Duke University

    E-Print Network [OSTI]

    Reif, John H.

    DNA Structural Nanotechnology John Reif Duke University Graduate Students: Harish Chandran&Caltech Tube Lattices #12;Ned Seeman New York University, USA Ned Seeman: Father of DNA Nanotechnology His Initial Ideas & Motivation for DNA Nanotechnology #12;Cube Chen & Seeman, Nature350:631 (1991) Truncated

  6. Floating intake reduces pump damage

    SciTech Connect (OSTI)

    Kronig, A.

    1993-12-31T23:59:59.000Z

    The solution to a costly sand erosion problem at the Grande Dixence hydroelectric project in Switzerland turned out to be as simple as a floating pump. The 726-MW Grande Dixence project drains a 350-square-kilometer reach of the Zermatt and Herens valleys in the southwestern Swiss Alps. About half of the drainage area is covered by active glaciers. Because the glaciers in Zermatt Valley are so low in altitude, their water is collected in Z`mutt Reservoir at the base of the Matterhorn, then pumped up 500 meters for transport to the main Grande Disence Reservoir near Sion. The glacier water is heavily laden with sand. In spite of a gravel pass and a desilter, the 700,000-acubic-meter Z`mutt Reservoir receives large quantities of sand. The sand tends to remain in solution because of the low water temperatures (1 to 2 degrees Centigrade). In the original intake system, the sand would be sucked into the pump intakes, causing extensive erosion to the pump wheels and an expensive yearly program of repair. (Pump damage averaged 200,000 Swiss Francs ($284,000 U.S.) per year between 1980 and 1985.)

  7. Sensing DNA - DNA as nanosensor: a perspective towards nanobiotechnology

    E-Print Network [OSTI]

    Ralf Metzler; Tobias Ambjoernsson

    2005-08-20T23:59:59.000Z

    Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA may be used as a local sensor. Employing single molecule fluorescence methods, we propose to make use of the physics of DNA denaturation nanoregions to find out about the solvent conditions such as ionic strength, presence of binding proteins, etc. By measuring dynamical quantities in particular, rather sensitive nanoprobes may be constructed with contemporary instruments.

  8. Extreme bendability of DNA double helix due to bending asymmetry

    E-Print Network [OSTI]

    Salari, Hossein; Naderi, M S; Ejtehadi, M R

    2015-01-01T23:59:59.000Z

    Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study (B. Eslami-Mossallam and M. Ejtehadi, Phys. Rev. E 80, 011919 (2009)). Exploiting a coarse grained representation of DNA molecule at base pair (bp) level, and using the Monte Carlo simulation method in combination with the umbrella sampling technique, we calculate the loop formation probability of DNA in the AER model. We show that, for DNA molecule has a larger J-factor compared to the WLC model w...

  9. Underground infrastructure damage for a Chicago scenario

    SciTech Connect (OSTI)

    Dey, Thomas N [Los Alamos National Laboratory; Bos, Rabdall J [Los Alamos National Laboratory

    2011-01-25T23:59:59.000Z

    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.

  10. DNA Methylation as a Biomarker for Preeclampsia

    SciTech Connect (OSTI)

    Anderson, Cindy M.; Ralph, Jody L.; Wright, Michelle L.; Linggi, Bryan E.; Ohm, Joyce E.

    2014-10-01T23:59:59.000Z

    Background: Preeclampsia contributes significantly to pregnancy-associated morbidity and mortality as well as future risk of cardiovascular disease in mother and offspring, and preeclampsia in offspring. The lack of reliable methods for early detection limits the opportunities for prevention, diagnosis, and timely treatment. Purpose: The purpose of this study was to explore distinct DNA methylation patterns associated with preeclampsia in both maternal cells and fetal-derived tissue that represent potential biomarkers to predict future preeclampsia and inheritance in children. Method: A convenience sample of nulliparous women (N = 55) in the first trimester of pregnancy was recruited for this prospective study. Genome-wide DNA methylation was quantified in first-trimester maternal peripheral white blood cells and placental chorionic tissue from normotensive women and those with preeclampsia (n = 6/group). Results: Late-onset preeclampsia developed in 12.7% of women. Significant differences in DNA methylation were identified in 207 individual linked cytosine and guanine (CpG) sites in maternal white blood cells collected in the first trimester (132 sites with gain and 75 sites with loss of methylation), which were common to approximately 75% of the differentially methylated CpG sites identified in chorionic tissue of fetal origin. Conclusion: This study is the first to identify maternal epigenetic targets and common targets in fetal-derived tissue that represent putative biomarkers for early detection and heritable risk of preeclampsia. Findings may pave the way for diagnosis of preeclampsia prior to its clinical presentation and acute damaging effects, and the potential for prevention of the detrimental long-term sequelae.

  11. War damages and reconstruction of Peruca dam

    SciTech Connect (OSTI)

    Nonveiller, E. [Univ. of Zagreb (Croatia). Faculty of Civil Engineering] [Univ. of Zagreb (Croatia). Faculty of Civil Engineering; Rupcic, J. [Univ. of Zagreb (Croatia). Faculty of Civil Engineering] [Univ. of Zagreb (Croatia). Faculty of Civil Engineering; [Elektroprojekt Consulting Engineering, Zagreb (Croatia); Sever, Z. [Elektroprojekt Consulting Engineering, Zagreb (Croatia)] [Elektroprojekt Consulting Engineering, Zagreb (Croatia)

    1999-04-01T23:59:59.000Z

    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.

  12. DNA decontamination: DNA-ExitusPlus in comparison with conventional reagents

    E-Print Network [OSTI]

    Cai, Long

    DNA decontamination: DNA-ExitusPlus in comparison with conventional reagents Here we present a completely new DNA decontamination reagent DNA-ExitusPlus. In comparison with conventional products, DNA solutions for effective DNA decontamination. DNA decontamination reagents use three different molecular prin

  13. Structural rehabilitation of a fossil power station after major fire damage

    SciTech Connect (OSTI)

    Freskakis, G.N.; Archer, J.C. (Burns and Roe, Inc., Oradell, NJ (USA)); Shipskie, W.P. (Seminole Electric Cooperative, Inc., Tampa, FL (US))

    1989-01-01T23:59:59.000Z

    This paper discusses the eruption and course of a fire at a fossil power station. Focus is on the damage to the building and the reinforced concrete pedestal, and the assessments and repairs involved in the restoration. Emphasis is given to the pedestal since, both the response to fire and the repair for such a massive structure are of particular interest.

  14. Gurson's plasticity coupled to damage as a CAP model for concrete compaction in dynamics

    E-Print Network [OSTI]

    1 Gurson's plasticity coupled to damage as a CAP model for concrete compaction in dynamics Fabrice (compaction) but also the plastic strains in compression and cracking in tension. Recently, new dynamic is generally described by means of the plasticity theory where the spherical and the deviatoric responses

  15. Fleet DNA (Presentation)

    SciTech Connect (OSTI)

    Walkokwicz, K.; Duran, A.

    2014-06-01T23:59:59.000Z

    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.

  16. Tops and Writhing DNA

    E-Print Network [OSTI]

    Joseph Samuel; Supurna Sinha

    2010-11-30T23:59:59.000Z

    The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the dynamics of tops to show that when subjected to stretch and twist, the polymer configurations which dominate the partition function admit a local writhe formulation in the spirit of Fuller and thus provide an underlying justification for the use of Fuller's "local writhe expression" which leads to considerable mathematical simplification in solving theoretical models of DNA and elucidating their predictions. Our result facilitates comparison of the theoretical models with single molecule micromanipulation experiments and computer simulations.

  17. Assessing United States hurricane damage under different environmental conditions

    E-Print Network [OSTI]

    Maheras, Anastasia Francis

    2012-01-01T23:59:59.000Z

    Hurricane activity between 1979 and 2011 was studied to determine damage statistics under different environmental conditions. Hurricanes cause billions of dollars of damage every year in the United States, but damage ...

  18. Beam damage of poly(2-chloroethyl methylacrylate) [PCEMA] films...

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

    evaluating x-ray damage. PCEMA has been shown to be more sensitive to degradation than PVC which has also been used as a damage sensitive material useful for comparison of damage...

  19. Radiation Damage Studies with Hadrons on Materials and Electronics

    E-Print Network [OSTI]

    2004-01-01T23:59:59.000Z

    PUB-10534 July 2004 Radiation Damage Studies with Hadrons oncontract DE–AC03–76SF00515. Radiation Damage Studies withand Zachary R. Wolf, “Radiation Damage Studies of Materials

  20. DAMAGE ASSESSMENT OF COMPOSITE PLATE STRUCTURES WITH UNCERTAINTY

    E-Print Network [OSTI]

    Boyer, Edmond

    DAMAGE ASSESSMENT OF COMPOSITE PLATE STRUCTURES WITH UNCERTAINTY Chandrashekhar M.* , Ranjan Uncertainties associated with a structural model and measured vibration data may lead to unreliable damage that material uncertainties in composite structures cause considerable problem in damage assessment which can

  1. New navel orangeworm sanitation standards ?could reduce almond damage

    E-Print Network [OSTI]

    Higbee, Bradley S.; Siegel, Joel P

    2009-01-01T23:59:59.000Z

    disruption, dispersal and damage prediction. Proc 34thtype and amount of insect damage. J Ag Food Chem 49:4513–9.standards could reduce almond damage by Bradley S. Higbee

  2. RADIATION DAMAGE TO BSCCO-2223 FROM 50 MEV PROTONS

    E-Print Network [OSTI]

    Zeller, A.F.; Ronningen, R.M.; Godeke, A.; Heilbronn, L.H.; McMahan-Norris, P.; Gupta, R.

    2007-01-01T23:59:59.000Z

    RADIATION DAMAGE TO BSCCO-2223 FROM 50 MEV PROTONS A. F.BSCCO-2223. Radiation damage. INTRODUCTION The magnets incomponents be resistant to damage. One solution [1] is to

  3. A Damage-Revelation Rationale for Coupon Remedies

    E-Print Network [OSTI]

    Polinsky, A. Mitchell; Rubinfeld, Daniel L.

    2006-01-01T23:59:59.000Z

    Bargaining and the Design of Damage Awards,” 10 Journal ofpage 1 Revised: March 2006 A DAMAGE-REVELATION RATIONALE FORin a setting in which damages vary among plaintiffs and are

  4. INSTANTANEOUS DAMAGE IDENTIFICATION AND LOCALIZATION THROUGH SPARSE LASER ULTRASONIC SCANNING

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    INSTANTANEOUS DAMAGE IDENTIFICATION AND LOCALIZATION THROUGH SPARSE LASER ULTRASONIC SCANNING This study proposes an instantaneous damage identification and localization technique through sparse laser ultrasonic signals are obtained, a damage index (DI) representing the violation of the linear reciprocity

  5. A Damage-Revelation Rationale for Coupon Remedies

    E-Print Network [OSTI]

    Polinsky, A. Mitchell; Rubinfeld, Daniel L

    2007-01-01T23:59:59.000Z

    Bargaining and the Design of Damage Awards,’’ 10 Journal ofGramlich, Fred. 1986. ‘‘Scrip Damages in Antitrust Cases,’’in the Assessment of Damages,’’ 39 Journal of Law and

  6. Earthquake Damage Identification using High-Resolution Satellite

    E-Print Network [OSTI]

    Shinozuka, Masanobu

    Earthquake Damage Identification using High-Resolution Satellite Images from the 2003 Northern & evaluation · High-resolution satellite imagery · Images from Boumerdes, Algeria · Semi-automated damage are most damaged? ­ Effects in less populated areas · Earthquake reconnaissance time wasted "looking

  7. DNA waves and water

    E-Print Network [OSTI]

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

    2010-12-23T23:59:59.000Z

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

  8. In Situ Analysis of 8-Oxo-7,8-dihydro-2?-deoxyguanosine Oxidation Reveals Sequence- and Agent-Specific Damage Spectra

    E-Print Network [OSTI]

    Lim, Kok Seong

    Guanine is a major target for oxidation in DNA, with 8-oxo-7,8-dihydro-2?-deoxyguanosine (8-oxodG) as a major product. 8-oxodG is itself significantly more susceptible to oxidation than guanine, with the resulting damage ...

  9. Apollo 324TM PrepX-32i DNA Library

    E-Print Network [OSTI]

    Apollo 324TM System PrepX-32i DNA Library Protocol D R AFT #12;© Copyright 2012, IntegenX Inc. All no responsibility for any errors that may appear in this document. RESEARCH USE ONLY The Apollo 324 System and conditions of sale. TRADEMARKS Apollo 324, BeadX and PrepX are trademarks of IntegenX Inc. (IXI) AMPure

  10. Gas condensate damage in hydraulically fractured wells

    E-Print Network [OSTI]

    Adeyeye, Adedeji Ayoola

    2004-09-30T23:59:59.000Z

    Company. The well was producing a gas condensate reservoir and questions were raised about how much drop in flowing bottomhole pressure below dewpoint would be appropriate. Condensate damage in the hydraulic fracture was expected to be of significant...

  11. Dealing with Storm-Damaged Trees

    E-Print Network [OSTI]

    Kirk, Melanie; Taylor, Eric; Foster, C. Darwin

    2005-10-25T23:59:59.000Z

    Many homeowners need help caring for or removing damaged trees after a natural disaster. This publication explains what a certified arborist is and how to select one. It also cautions against burning debris downed by a storm....

  12. Dealing with Storm-Damaged Trees 

    E-Print Network [OSTI]

    Kirk, Melanie; Taylor, Eric; Foster, C. Darwin

    2005-10-25T23:59:59.000Z

    ER-040 5-06 Dealing with Storm-Damaged Trees Melanie R. Kirk, Extension Program Specialist, Eric L. Taylor, Assistant Professor and Extension Specialist, and C. Darwin Foster, Associate Department Head and Extension Program Leader for Forestry...

  13. Damage spreading and coupling in Markov chains

    E-Print Network [OSTI]

    Etienne P. Bernard; Cédric Chanal; Werner Krauth

    2011-06-23T23:59:59.000Z

    In this paper, we relate the coupling of Markov chains, at the basis of perfect sampling methods, with damage spreading, which captures the chaotic nature of stochastic dynamics. For two-dimensional spin glasses and hard spheres we point out that the obstacle to the application of perfect-sampling schemes is posed by damage spreading rather than by the survey problem of the entire configuration space. We find dynamical damage-spreading transitions deeply inside the paramagnetic and liquid phases, and show that critical values of the transition temperatures and densities depend on the coupling scheme. We discuss our findings in the light of a classic proof that for arbitrary Monte Carlo algorithms damage spreading can be avoided through non-Markovian coupling schemes.

  14. Formation damage in underbalanced drilling operations

    E-Print Network [OSTI]

    Reyes Serpa, Carlos Alberto

    2003-01-01T23:59:59.000Z

    Formation damage has long been recognized as a potential source of reduced productivity and injectivity in both horizontal and vertical wells. From the moment that the pay zone is being drilled until the well is put on production, a formation...

  15. Nondestructive Damage Detection in General Beams

    E-Print Network [OSTI]

    Dincal, Selcuk

    2010-12-08T23:59:59.000Z

    is also vital for a nation’s economy. Substantial sums of money may be saved upon detecting structural deterioration in a timely manner. Nondestructive damage evaluation (NDE) offers effective and economically feasible solutions to perform such tasks...

  16. Los Alamos National Laboratory describes storm damage to environmental...

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

    Los Alamos National Laboratory describes storm damage Los Alamos National Laboratory describes storm damage to environmental monitoring stations, canyons Stations supporting Santa...

  17. area damage detection: Topics by E-print Network

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

    answer Cherkaev, Andrej 10 DAMAGE DETECTION IN STIFFENED AIRCRAFT PANELS VIA VIBRATION TESTING CiteSeer Summary: SUMMARY: The problem of damage detection in stiffened aircraft...

  18. Controlled ion implant damage profile for etching

    DOE Patents [OSTI]

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

    1990-01-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Niklas, Martin, E-mail: m.niklas@dkfz.de [Division of Medical Physics in Radiation Oncology, German Cancer Research Center, Heidelberg (Germany); German Cancer Consortium, National Center for Radiation Research in Oncology, Heidelberg Institute of Radiation Oncology, Heidelberg (Germany); Abdollahi, Amir [German Cancer Consortium, National Center for Radiation Research in Oncology, Heidelberg Institute of Radiation Oncology, Heidelberg (Germany); Molecular and Translational Radiation Oncology, Heidelberg Ion-Beam Therapy Center, University of Heidelberg Medical School and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg (Germany); Department of Radiation Oncology and Radiation Therapy, University Hospital Heidelberg, Heidelberg (Germany); Heidelberg Ion-Beam Therapy Center, Heidelberg (Germany); Akselrod, Mark S. [Stillwater Crystal Growth Division, Landauer Inc, Stillwater, Oklahoma (United States); Debus, Jürgen [German Cancer Consortium, National Center for Radiation Research in Oncology, Heidelberg Institute of Radiation Oncology, Heidelberg (Germany); Molecular and Translational Radiation Oncology, Heidelberg Ion-Beam Therapy Center, University of Heidelberg Medical School and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg (Germany); Department of Radiation Oncology and Radiation Therapy, University Hospital Heidelberg, Heidelberg (Germany); Heidelberg Ion-Beam Therapy Center, Heidelberg (Germany); Jäkel, Oliver [Division of Medical Physics in Radiation Oncology, German Cancer Research Center, Heidelberg (Germany); German Cancer Consortium, National Center for Radiation Research in Oncology, Heidelberg Institute of Radiation Oncology, Heidelberg (Germany); Department of Radiation Oncology and Radiation Therapy, University Hospital Heidelberg, Heidelberg (Germany); Heidelberg Ion-Beam Therapy Center, Heidelberg (Germany); and others

    2013-12-01T23:59:59.000Z

    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.

  20. Interstrand DNA-DNA Cross-Link Formation Between Adenine Residues and Abasic Sites in Duplex DNA

    E-Print Network [OSTI]

    Gates, Kent. S.

    Interstrand DNA-DNA Cross-Link Formation Between Adenine Residues and Abasic Sites in Duplex DNA of DNA is a common event that generates an abasic (Ap) site (1). Ap sites exist as an equilibrating that can form covalent adducts with nucleophilic sites in DNA. Thus, Ap sites present a potentially

  1. Effect of impurities and stress on the damage distributions of rapidly grown KDP crystals

    SciTech Connect (OSTI)

    Runkel, M.; Tan, M.; De Yoreo, J.; Zaitseva, N.

    1997-12-20T23:59:59.000Z

    Development of high damage threshold, 50 cm, rapidly grown KF*P frequency triplers for operation of the National Ignition Facility (NIF) in the 14 J/cm2, 351 nm, 3 ns regime requires a thorough understanding of how the crystal growth parameters and technologies affect laser induced damage. Of particular importance is determining the effect of ionic impurities (e.g. Cr3+, Fe3+, Al3+) which may be introduced in widely varying concentrations via starting salts. In addition, organic particulates can contaminate the solution as leachants from growth platforms or via mechanical ablation. Mechanical stresses in the crystals may also play a strong role in the laser-induced damage distribution (LIDD), particularly in the cases of large boules where hydrodynamic forces in the growth tank may be quite high. WE have developed a dedicated, automated damage test system with diagnostic capabilities specifically designed for measured time resolved bulk damage onset and evolution. The data obtained make it possible to construct characteristic damage threshold distributions for each sample. Test results obtained for a variety of KDP samples grown from high purity starting salts and individually doped with Lucite and Teflon, iron, chromium, and aluminium show that the LIDD drops with increasing contamination content. The results also show that solution filtration leads to increased damage performance for undoped crystals but is not solely responsibility for producing the high LIDDs required by the NIF. The highest LIDD measured on a rapidly grown sample indicate that it is possible to produce high damage threshold material using ultrahigh purity, recrystallized starting salts, continuous filtration and a platform designed to minimize internal stress during growth.

  2. Flavin-Induced Oligomerization in Escherichia coli Adaptive Response Protein AidB

    SciTech Connect (OSTI)

    Hamill, Michael J.; Jost, Marco; Wong, Cintyu; Elliott, Sean J.; Drennan, Catherine L. (MIT); (BU)

    2011-11-21T23:59:59.000Z

    The process known as 'adaptive response' allows Escherichia coli to respond to small doses of DNA-methylating agents by upregulating the expression of four proteins. While the role of three of these proteins in mitigating DNA damage is well understood, the function of AidB is less clear. Although AidB is a flavoprotein, no catalytic role has been established for the bound cofactor. Here we investigate the possibility that flavin plays a structural role in the assembly of the AidB tetramer. We report the generation and biophysical characterization of deflavinated AidB and of an AidB mutant that has greatly reduced affinity for flavin adenine dinucleotide (FAD). Using fluorescence quenching and analytical ultracentrifugation, we find that apo AidB has a high affinity for FAD, as indicated by an apparent dissociation constant of 402.1 {+-} 35.1 nM, and that binding of substoichiometric amounts of FAD triggers a transition in the AidB oligomeric state. In particular, deflavinated AidB is dimeric, whereas the addition of FAD yields a tetramer. We further investigate the dimerization and tetramerization interfaces of AidB by determining a 2.8 {angstrom} resolution crystal structure in space group P3{sub 2} that contains three intact tetramers in the asymmetric unit. Taken together, our findings provide strong evidence that FAD plays a structural role in the formation of tetrameric AidB.

  3. DNA attachment to support structures

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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).

  4. A Model for Structure and Thermodynamics of ssDNA and dsDNA Near...

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

    Structure and Thermodynamics of ssDNA and dsDNA Near a Surface:A Coarse Grained Approach. A Model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface:A Coarse...

  5. B-DNA Under Stress: Over- and Untwisting of DNA during MolecularDynami...

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

    B-DNA Under Stress: Over- and Untwisting of DNA during MolecularDynamics Simulations. B-DNA Under Stress: Over- and Untwisting of DNA during MolecularDynamics Simulations....

  6. Controlling DNA Methylation

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power Administration would likeConstitution And BylawsMetal-Organic FrameworksControlling DNA

  7. 8-oxoguainine enhances bending of DNA that favors binding of glycosylases

    SciTech Connect (OSTI)

    John H. Miller

    2003-04-23T23:59:59.000Z

    Molecular dynamics (MD) simulations were carried out on the DNA oligonucleotide GGGAACAACTAG:CTAGTTGTTCCC in its native form and with guanine in the central G19:C6 base pair replaced by 8-oxoguanine (8oxoG). A box of explicit water molecules was used for solvation and Na+ counterions were added to neutralize the system. The direction and magnitude of global bending were assessed by a technique used previously to analyze simulations of DNA containing a thymine dimer. The presence of 8oxoG did not greatly affect the magnitude of DNA bending; however, bending into the major groove was significantly more probable when 8oxoG replaced G19. Crystal structures of glycosylases bound to damaged-DNA substrates consistently show a sharp bend into the major groove at the damage site. We conclude that changes in bending dynamics that assist the formation of this kink are a part of the mechanism by which glycosylases of the base excision repair pathway recognize the presence of 8oxoG in DNA.

  8. Implications for Damage Recognition during Dpo4-Mediated Mutagenic Bypass of m1G and m3C Lesions

    SciTech Connect (OSTI)

    Rechkoblit, Olga; Delaney, James C.; Essigmann, John M.; Patel, Dinshaw J. (MIT); (MSKCC)

    2012-05-08T23:59:59.000Z

    DNA is susceptible to alkylation damage by a number of environmental agents that modify the Watson-Crick edge of the bases. Such lesions, if not repaired, may be bypassed by Y-family DNA polymerases. The bypass polymerase Dpo4 is strongly inhibited by 1-methylguanine (m1G) and 3-methylcytosine (m3C), with nucleotide incorporation opposite these lesions being predominantly mutagenic. Further, extension after insertion of both correct and incorrect bases, introduces additional base substitution and deletion errors. Crystal structures of the Dpo4 ternary extension complexes with correct and mismatched 3'-terminal primer bases opposite the lesions reveal that both m1G and m3C remain positioned within the DNA template/primer helix. However, both correct and incorrect pairing partners exhibit pronounced primer terminal nucleotide distortion, being primarily evicted from the DNA helix when opposite m1G or misaligned when pairing with m3C. Our studies provide insights into mechanisms related to hindered and mutagenic bypass of methylated lesions and models associated with damage recognition by repair demethylases.

  9. Forensic DNA data banking by state crime labortaories

    SciTech Connect (OSTI)

    McEwen, J.E. [Eunice Kennedy Shrive Center for Mental Retardation, Waltham, MA (United States)

    1995-06-01T23:59:59.000Z

    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.

  10. RUPTURE BY DAMAGE ACCUMULATION IN ROCKS David Amitrano

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    RUPTURE BY DAMAGE ACCUMULATION IN ROCKS David Amitrano LIRIGM, Université J. Fourier, Grenoble of rocks is associated with microcracks nucleation and propagation, i.e. damage. The accumulation of damage as strength and modulus. The damage process can be studied both statically by direct observation of thin

  11. Ductile damage parameters identification for cold metal forming applications

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Ductile damage parameters identification for cold metal forming applications Pierre damage mechanics is essential to predict failure during cold metal forming applications. Several damage models can be found in the literature. These damage models are coupled with the mechanical behavior so

  12. Damage from pulses with arbitrary temporal shapes

    SciTech Connect (OSTI)

    Trenholme, J.B.

    1994-06-06T23:59:59.000Z

    In fusion laser designs, the laser pulse has a complicated temporal shape which undergoes significant change as it passes through the laser. Our damage data, however, was taken with pulses whose temporal shapes were (more or less) Gaussian. We want to determine the damage propensity of a material exposed to a pulse of arbitrary temporal shape , given data taken with Gaussian pulses of different pulse widths. To do so, we must adopt a physical model of damage. This model will contain some number of parameters that depend on material properties, geometry, and so forth. We determine the parameters of the model appropriate to each material by fitting the model to the Gaussian data for that material. The resulting normalized model is then applied, using the appropriate pulse shape, to find the damage level for a specific material subjected to a specific pulse. The model we shall assume is related to diffusion, although (as we shall see) the experimental results do not fit any simple diffusion model. Initially, we will discuss simple diffusion models. We then examine some experimental data, and then develop a modified diffusive model from that data. That modified model is then used to predict damage levels in various portions of the NIF laser design.

  13. Fretting Corrosion Damage of Total Hip Prosthesis: Friction Coefficient and Damage Rate Constant Approach

    E-Print Network [OSTI]

    Boyer, Edmond

    1 Fretting Corrosion Damage of Total Hip Prosthesis: Friction Coefficient and Damage Rate Constant Building, University Park 16802 PA USA 4 Chair Professor Center for Research Excellence in Corrosion hip prosthesis. Fretting corrosion tests were conducted with stainless steel and poly (methyl

  14. DNA-DNA interactions Helmut H Strey*t, Rudi Podgornik* ,

    E-Print Network [OSTI]

    Podgornik, Rudolf

    309 DNA-DNA interactions Helmut H Strey*t, Rudi Podgornik* , Parsegian The forces that govern DNA interactions - such as electrostatic interactions, hydration, and fluctuation forces - that treat DNA about the physical forces and energies that involve DNA molecules is to ask whether there is more to DNA

  15. Spatiotemporal characterization of ionizing radiation induced DNA damage foci and their relation to chromatin organization

    E-Print Network [OSTI]

    Costes, Sylvain V

    2010-01-01T23:59:59.000Z

    to ionizing radiation are nuclear marks of permanentto ionizing radiation are nuclear marks of permanentvisible nuclear domains referred to as radiation-induced

  16. Neddylation promotes ubiquitylation and release of Ku from DNA damage sites

    E-Print Network [OSTI]

    Brown, Jessica S.; Lukashchuk, Natalia; Sczaniecka-Clift, Matylda; Britton, Sébastien; le Sage, Carlos; Calsou, Patrick; Beli, Petra; Galanty, Yaron; Jackson, Stephen P.

    2015-04-23T23:59:59.000Z

    observed in BrdU pretreated cells (Figure S1E), implying that in our system, NEDD8 accrual was largely promoted by DSBs rather than other forms of dam- age (Lukas et al., 2003). NEDD8 recruitment did not require the activity of PARP or the DDR kinases ATM... representsthe time taken for neddylation to be completely inhibited in cells by MLN4924 (which occurs within 5 min; Brownell et al., 2010). These data therefore suggested that neddylation is a dynamic modification that occurs and turns over at DSBs, although we...

  17. DNA Damage Causes p27^(Kip1) Accumulation Through COP1 Signaling

    E-Print Network [OSTI]

    Choi, Hyun Ho

    2014-05-06T23:59:59.000Z

    (Deng XW et al., 1991). The COP1 protein comprises three recognizable domains: a RING-finger motif, followed by a coiled-coil domain and seven WD40 repeats, all of which have been implicated in mediating the interaction of COP1 with other... Figure 2. Schematic diagram of COP1 structural domains. NES NIS 1 NIS 733 WD40 Coil RING Human COP1 1 675 WD40 AtCOP1 Coil RING NIS NIS NES 8 MG et al., 2000). The AtCOP1 C-terminal WD40 domain, by contrast, led to repression...

  18. RhoJ Regulates Melanoma Chemoresistance by Suppressing Pathways that Sense DNA Damage

    E-Print Network [OSTI]

    Ho, Hsiang; Aruri, Jayavani; Kapadia, Rubina; Mehr, Hootan; White, Michael A.; Ganesan, Anand K.

    2012-01-01T23:59:59.000Z

    Lowe SW. Apoptosis and melanoma chemoresistance. Oncogene.reactivation therapy in melanoma. J Invest Dermatol. 2012;amplified in malignant melanoma. Nature. 2005; 436:117–

  19. DOE contractors' workshop: Cellular and molecular aspects of radiation induced DNA damage and repair

    SciTech Connect (OSTI)

    Not Available

    1987-01-01T23:59:59.000Z

    For four decades the US Department of Energy and its predecessors have been the lead federal agency in supporting radiation biology research. Over the years emphasis in this program has gradually shifted from dose-effect studies on animals to research on the effects of radiations of various qualities on cells and molecules. Mechanistic studies on the action of radiation at the subcellular level are few in number and there is a need for more research in this area if we are to gain a better understanding of how radiation affects living cells. The intent of this workshop was to bring together DOE contractors and grantees who are investigating the effects of radiation at the cellular and molecular levels. The aims were to foster the exchange of information on research projects and experimental results, promote collaborative research efforts, and obtain an overview of research currently supported by the Health Effects Research Division of the Office of Health and Environmental Research. The latter is needed by the Office for program planning purposes. This report on the workshop which took place in Albuquerque, New Mexico on March 10-11, 1987, includes an overview with future research recommendations, extended abstracts of the plenary presentations, shorter abstracts of each poster presentation, a workshop agenda and the names and addresses of the attendees.

  20. Rat colonic reactive oxygen species production and DNA damage are mediated by diet and age

    E-Print Network [OSTI]

    Henderson, Cara Aletha Everett

    2001-01-01T23:59:59.000Z

    diacetate docosahexanoic acid diphenyliodonium chloride ethylenediaminetetraacetic acid eicosapentanoic acid ethidium homodiner ? 1 fragment length analysis using repair enzymes Fapy glycosylase Hanks' balanced salt solution hydrogen peroxide lipid... the elimination of cancer cells. Production and Functions of Reactive Oxygen Species Formation of reactive oxygen species Reactive oxygen species are a by-product of normal metabolism and include superoxide (Ot' ), hydrogen peroxide (HzO&), and the hydroxyl...

  1. Recommendations for Standardized Description of and Nomenclature Concerning Oxidatively Damaged Nucleobases in DNA

    E-Print Network [OSTI]

    Cooke, Marcus S.

    Despite being a relatively young field, the study of oxidative stress has attracted huge interest. With the advent of simple and relatively inexpensive assays (sometimes from commercial suppliers), a growing number of ...

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(Fact Sheet), GeothermalGridHYDROGEND DTechnologiesFinding U.CY2009 |DISPERSION OR

  3. Inhibition of uracil-DNA glycosylase increases SCEs in BrdU-treated and visible light-irradiated cells

    SciTech Connect (OSTI)

    Maldonado, A.; Hernandez, P.; Gutierrez, C.

    1985-11-01T23:59:59.000Z

    The authors have approached the study of the ability of different types of lesions produced by DNA-damaging agents to develop sister-chromatid exchanges (SCEs) by analyzing SCE levels observed in Allium cepa L cells with BrdU-substituted DNA and exposed to visible light (VL), an irradiation which produces uracil residues in DNA after debromination of bromouracil and enhances SCE levels but only above a certain dose. They have partially purified an uracil-DNA glycosylase activity from A. cepa L root meristem cells, which removes uracil from DNA, the first step in the excision repair of this lesion. This enzyme was inhibited in vitro by 6-amino-uracil and uracil but not by thymine. When cells exposed to VL, at a dose that did not produce per se an SCE increase, were immediately post-treated with these inhibitors of uracil-DNA glycosylase, a significant increase in SCE levels was obtained. Moreover, SCE levels in irradiated cells dropped to control level when a short holding time elapsed between exposure to VL and the beginning of post-treatment with the inhibitor. Thus, our results showed that inhibitors of uracil-DNA glycosylase enhanced SCE levels in cells with unifilarly BrdU-substituted DNA exposed to visible light; and indicated the existence of a very rapid repair of SCE-inducing lesions produced by visible light irradiation of cells with unifilarly BrdU-containing DNA.

  4. Method to reduce damage to backing plate

    DOE Patents [OSTI]

    Perry, Michael D. (Livermore, CA); Banks, Paul S. (Livermore, CA); Stuart, Brent C. (Fremont, CA)

    2001-01-01T23:59:59.000Z

    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.

  5. Delay-active damage versus non-local enhancement for anisotropic damage dynamics computations with alternated loading

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Delay-active damage versus non-local enhancement for anisotropic damage dynamics computations, Laboratoire d'´etudes dynamiques F-91191 GIF-SUR-YVETTE Abstract Anisotropic damage thermodynamics framework of anisotropic visco-damage, by introducing a material strain rate effect in the cases of positive hydro- static

  6. Damage mechanisms in the dynamic fracture of nominally brittle polymers

    E-Print Network [OSTI]

    Davy Dalmas; Claudia Guerra; Julien Scheibert; Daniel Bonamy

    2013-04-23T23:59:59.000Z

    Linear Elastic Fracture Mechanics (LEFM) provides a consistent framework to evaluate quantitatively the energy flux released to the tip of a growing crack. Still, the way in which the crack selects its velocity in response to this energy flux remains far from completely understood. To uncover the underlying mechanisms, we experimentally studied damage and dissipation processes that develop during the dynamic failure of polymethylmethacrylate (PMMA), classically considered as the archetype of brittle amorphous materials. We evidenced a well-defined critical velocity along which failure switches from nominally-brittle to quasi-brittle, where crack propagation goes hand in hand with the nucleation and growth of microcracks. Via post-mortem analysis of the fracture surfaces, we were able to reconstruct the complete spatiotemporal microcracking dynamics with micrometer/nanosecond resolution. We demonstrated that the true local propagation speed of individual crack fronts is limited to a fairly low value, which can be much smaller than the apparent speed measured at the continuum-level scale. By coalescing with the main front, microcracks boost the macroscale velocity through an acceleration factor of geometrical origin. We discuss the key role of damage-related internal variables in the selection of macroscale fracture dynamics.

  7. Seawater can damage Saudi sandstone oil reservoirs

    SciTech Connect (OSTI)

    Dahab, A.S. (King Saud Univ., Riyadh (SA))

    1990-12-10T23:59:59.000Z

    Experiments have shown that formation damage from waterflooding of the Aramco and Alkhafji sandstones of Saudi Arabia will not occur if the salinity of the injected brines is higher than 20% NaCl. Because the connate water in these reservoirs has a high salt content of up to 231,000 ppm, Saudi oil fields are almost always susceptible to formation damage when flooded with seawater (about 38,500 ppm). The productive behavior of a reservoir can be affected by clay crystals developed within rock pores.

  8. Condensation of circular DNA

    E-Print Network [OSTI]

    E. L. Starostin

    2013-04-05T23:59:59.000Z

    A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and torsional elastic components and the effective self-attraction energy. The model includes a relative orientation or sequence dependence of the effective attraction forces between different pieces of the polymer chain. Two series of conformations are analysed: a multicovered circle (a toroid) and a multifold two-headed racquet. The results are presented as a diagram of state. It is suggested that the stability of particular conformations may be controlled by proper adjustment of the primary structure. Application of the model to other semi-flexible polymers is considered.

  9. Damage detection technique by measuring laser-based mechanical impedance

    SciTech Connect (OSTI)

    Lee, Hyeonseok; Sohn, Hoon [Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (Daehak-ro 291, Yuseong-gu, Daejeon 305-701) (Korea, Republic of)

    2014-02-18T23:59:59.000Z

    This study proposes a method for measurement of mechanical impedance using noncontact laser ultrasound. The measurement of mechanical impedance has been of great interest in nondestructive testing (NDT) or structural health monitoring (SHM) since mechanical impedance is sensitive even to small-sized structural defects. Conventional impedance measurements, however, have been based on electromechanical impedance (EMI) using contact-type piezoelectric transducers, which show deteriorated performances induced by the effects of a) Curie temperature limitations, b) electromagnetic interference (EMI), c) bonding layers and etc. This study aims to tackle the limitations of conventional EMI measurement by utilizing laser-based mechanical impedance (LMI) measurement. The LMI response, which is equivalent to a steady-state ultrasound response, is generated by shooting the pulse laser beam to the target structure, and is acquired by measuring the out-of-plane velocity using a laser vibrometer. The formation of the LMI response is observed through the thermo-mechanical finite element analysis. The feasibility of applying the LMI technique for damage detection is experimentally verified using a pipe specimen under high temperature environment.

  10. Damage to unburied flowlines in the Gulf of Mexico during Hurricane Andrew

    SciTech Connect (OSTI)

    Collins, J.I.

    1995-12-31T23:59:59.000Z

    The US Minerals Management Service reported that 454 sub-sea pipelines were damaged during Hurricane Andrew. Previously, damage to pipelines and flowlines has been reported in a series of papers by Blumberg (1964). In the present paper a formulation of the hydrodynamic loads acting on a flowline which is lying on the seafloor in the presence of waves and currents is summarized. In general, the line dynamics can be represented by a fourth order differential equation with nonlinear forcing but a method is presented which assumes that the complete response can be broken down into distinct phases from ``early motion`` to ``taut line`` to ``yield and breaking``. The selection of appropriate force coefficients and boundary layer interactions is discussed. The initial stages of pipeline migration across the seafloor is shown to be followed by loading of the flowline once all of the ``slack`` is taken up. The loads are shown to be a function of the current orientation and the maximum tension is approximately proportional to the square of the distance between risers. Comparisons of predicted and observed damages confirm that ``effective`` boundary layer thicknesses at the seafloor and typical drag and lift coefficients which were selected based on available literature are consistent with observed flowline damage. The results of sidescan sonar mosaics of pipeline migrations and reported damage are consistent with the loads predicted by relatively simple hydrodynamic/structural models. The material presented in this paper permits the evaluation of the risk of damage to unburied flowlines using relatively simple tools. Guidelines to the assumptions of force coefficients and flowline responses are provided. 20 refs., 11 figs., 2 tabs.

  11. The Status of Radiation Damage Experiments

    SciTech Connect (OSTI)

    Strachan, Denis M.; Scheele, Randall D.; Icenhower, Jonathan P.; Kozelisky, Anne E.; Sell, Richard L.; Legore, Virginia L.; Schaef, Herbert T.; O'Hara, Matthew J.; Brown, Christopher F.; Buchmiller, William C.

    2001-11-20T23:59:59.000Z

    Experiments have been on-going for about two years to determine the effects that radiation damage have on the physical and chemical properties of candidate titanate ceramics for the immobilization of plutonium. We summarize the results of these experiments in this document.

  12. Damage and plastic deformation of reservoir rocks

    E-Print Network [OSTI]

    Ze'ev, Reches

    Damage and plastic deformation of reservoir rocks: Part 2. Propagation of a hydraulic fracture Seth fracture and fault mechanics, fluid flow in fractured reservoirs, and geome- chanics in nonconventional the development of complex hydraulic fractures (HFs) that are commonly ob- served in the field and in experiments

  13. Gas condensate damage in hydraulically fractured wells

    E-Print Network [OSTI]

    Reza, Rostami Ravari

    2004-11-15T23:59:59.000Z

    of this research are a step forward in helping to improve the management of gas condensate reservoirs by understanding the mechanics of liquid build-up. It also provides methodology for quantifying the condensate damage that impairs linear flow of gas...

  14. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, Stefan K. (Chicago, IL)

    1998-01-01T23:59:59.000Z

    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.

  15. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1997-06-10T23:59:59.000Z

    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.

  16. Normalized cDNA libraries

    DOE Patents [OSTI]

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

    1997-01-01T23:59:59.000Z

    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.

  17. DNA UPTAKE BY TRANSFORMABLE BACTERIA

    SciTech Connect (OSTI)

    LACKS,S.A.

    1999-09-07T23:59:59.000Z

    The various processes of DNA uptake by cells can be categorized as: viral DNA entry, conjugation, or transformation. Within each category, a variety of mechanisms have been found. However, considerable similarities occur among the different mechanisms of conjugation and, especially, transformation. All of these natural mechanisms of DNA transfer are quite elaborate and involve multiple protein components, as the case may be, of the virus, the donor cell, and the recipient cell. The mechanisms of viral infection and conjugation will be discussed mainly with respect to their relevance to transformation.

  18. Structure and Energetics of Clustered Damage Sites

    SciTech Connect (OSTI)

    Miller, J H.; Aceves Gaona, Alejandro; Ernst, Matthew B.; Haranczyk, Maciej; Gutowski, Maciej S.; Vorpagel, Erich R.; Dupuis, Michel

    2005-10-17T23:59:59.000Z

    Quantum calculations on duplex DNA trimers were used to model the changes in structure, hydrogen bonding, stacking properties, and electrostatic potential induced by oxidized purine bases and abasic (AP) sites. Results for oxidized purine bases were consistent with experimental data that show small structural and energetic perturbations induced by isolated 8-oxoGC and 8-oxoAT. In contrast, AP sites caused substantial distortions of the DNA backbone that were accompanied by relocation of counterions. New inter- and intra-strand hydrogen bonds formed after removal of a nucleic acid base that significantly affected the energy of AP site and introduced a strong dependence of sequence context. Quantum calculations on small DNA fragments provided starting conformations and force-field parameters for classical molecular dynamics (MD) simulations of radiation-induced single strand breaks that most often combine cleavage of a phosphate-oxygen (PO) bond with an AP site and fully or partially degraded sugar ring. PO bond cleavage increased the freedom in backbone torsion angles, which allowed the broken strand to compress fill the hole in the DNA created by the AP site. Results for strand breaks with a 3? phosphoglycolate were similar to those with 3? and 5? phosphate end groups.

  19. Autoregressive modeling with state-space embedding vectors for damage detection under operational and environmental variability

    SciTech Connect (OSTI)

    Farrar, Charles [Los Alamos National Laboratory; Figueiredo, Eloi [UNIV OF PORTO; Todd, Michael [UCSD; Flynn, Eric [UCSD

    2010-01-01T23:59:59.000Z

    A nonlinear time series approach is presented to detect damage in systems by using a state-space reconstruction to infer the geometrical structure of a deterministic dynamical system from observed time series response at multiple locations. The unique contribution of this approach is using a Multivariate Autoregressive (MAR) model of a baseline condition to predict the state space, where the model encodes the embedding vectors rather than scalar time series. A hypothesis test is established that the MAR model will fail to predict future response if damage is present in the test condition, and this test is investigated for robustness in the context of operational and environmental variability. The applicability of this approach is demonstrated using acceleration time series from a base-excited 3-story frame structure.

  20. Radiation Damage in Nanostructured Metallic Films 

    E-Print Network [OSTI]

    Yu, Kaiyuan

    2013-04-15T23:59:59.000Z

    with favorable microstructures and to investigate their response to radiation. The goals of this thesis are to study the radiation responses of several nanostructured metallic thin film systems, including Ag/Ni multilayers, nanotwinned Ag and nanocrystalline Fe...

  1. Radiation Damage in Nanostructured Metallic Films

    E-Print Network [OSTI]

    Yu, Kaiyuan

    2013-04-15T23:59:59.000Z

    with favorable microstructures and to investigate their response to radiation. The goals of this thesis are to study the radiation responses of several nanostructured metallic thin film systems, including Ag/Ni multilayers, nanotwinned Ag and nanocrystalline Fe...

  2. Climate change risk and response

    E-Print Network [OSTI]

    Kahrl, Fredrich; Roland-Holst, David

    2008-01-01T23:59:59.000Z

    electric power outages. Storm damage to transmission lineselectric power and transportation sectors. Storm damage to transmission lines

  3. Unnatural nucleotides for DNA sequencing

    E-Print Network [OSTI]

    Jacutin, Swanee E

    1997-01-01T23:59:59.000Z

    Fluorescent nucleotide analogs were prepared and tested to find surrogate structures that are: (i) incorporated by DNA polymerases; (ii) spectroscopically distinct for each fluorescent tag; and (iii) easily deprotected at the 3'-position under mild...

  4. Mammalian DNA Repair. Final Report

    SciTech Connect (OSTI)

    None

    2003-01-24T23:59:59.000Z

    The Gordon Research Conference (GRC) on Mammalian DNA Repair was held at Harbortown Resort, Ventura Beach, CA. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  5. Preliminary development of a constitutive model for metal matrix composites with damage 

    E-Print Network [OSTI]

    Nottorf, Eric Walter

    1985-01-01T23:59:59.000Z

    aphs and mechanical test data do not indicate a significant amount of modulus degr adation or change in damage state for this orientation of Al/SiC composite. The most dramatic photomicrographs of the micro- structural response of the Al... incr easing attention as a viable material for structural applications. Along with the normal advantages associated with tailorability of directional strength, these compos- ites can be used at elevated temper atures that would ad- verselyy affect...

  6. Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions Possible and Is DNA Leaching a Factor?

    E-Print Network [OSTI]

    Shapiro, Beth

    reported the successful extraction of ancient DNA (aDNA) from both frozen and nonfrozen sediments (even for vertical migration of aDNA across strata. To assess the extent of this problem, we extracted aDNA from (Lydolph et al. 2005). Also uncertain is whether the DNA is extracellular and bound to clay minerals

  7. Meta-DNA: A DNA-Based Approach to Synthetic Harish Chandran1

    E-Print Network [OSTI]

    Reif, John H.

    Meta-DNA: A DNA-Based Approach to Synthetic Biology Harish Chandran1 harish@cs.duke.edu Nikhil taken here is to develop a biochemical system which we call meta-DNA (abbre- viated as mDNA), based entirely on strands of DNA as the only component molecules. Our work leverages prior work

  8. Meta-DNA: Synthetic Biology via DNA Nanostructures and Hybridization Reactions

    E-Print Network [OSTI]

    Reif, John H.

    Meta-DNA: Synthetic Biology via DNA Nanostructures and Hybridization Reactions Harish Chandran for desired functionality. The approach of this paper is to develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based entirely on strands of DNA as the only component molecule. Our work leverages

  9. Impact of DNA Twist Accumulation on Progressive Helical Wrapping of Torsionally Constrained DNA

    E-Print Network [OSTI]

    Wang, Wei Hua

    Impact of DNA Twist Accumulation on Progressive Helical Wrapping of Torsionally Constrained DNA Wei (Received 17 July 2012; published 20 November 2012) DNA wrapping is an important mechanism for chromosomal DNA packaging in cells and viruses. Previous studies of DNA wrapping have been performed mostly

  10. DNA Word Design Strategy for Creating Sets of Non-interacting Oligonucleotides for DNA Microarrays

    E-Print Network [OSTI]

    DNA Word Design Strategy for Creating Sets of Non-interacting Oligonucleotides for DNA Microarrays-interacting DNA oligonucleotides for applications in DNA arrays and biosensors is demonstrated. This strategy mismatches with the complements of all the other members in the set. These "DNA word" sets are denoted as nbm

  11. Low energy electron stimulated desorption from DNA films dosed with oxygen

    SciTech Connect (OSTI)

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

    2012-06-21T23:59:59.000Z

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

  12. The spindle checkpoint : Bubs, Mads, and chromosome-microtubule attachment in budding yeast

    E-Print Network [OSTI]

    Gillett, Emily S., 1976-

    2005-01-01T23:59:59.000Z

    (cont.) DNA damage response, we hypothesize that the perinuclear pool of Mad proteins may be required for spindle checkpoint-independent functions such as invoking metaphase arrest following DNA damage.

  13. Identification of new functions for BRCT domains

    E-Print Network [OSTI]

    Mohammad, Duaa H

    2008-01-01T23:59:59.000Z

    Our lab identified the tandem BRCT domains of PTIP function as a DNA damage responsive phospho binding domain that recognizes proteins phosphorylated by ATM and ATR after DNA damage. The PTIP tandem BRCT domains are ...

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

    SciTech Connect (OSTI)

    Torok, Tamas

    2003-05-19T23:59:59.000Z

    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.

  15. Viscoelastic{Viscoplastic Damage Model for Asphalt Concrete

    E-Print Network [OSTI]

    Graham, Michael A.

    2010-10-12T23:59:59.000Z

    This thesis presents a continuum model for asphalt concrete incorporating non- linear viscoelasticity, viscoplasticity, mechanically-induced damage and moisture- induced damage. The Schapery single-integral viscoelastic model describes the nonlinear...

  16. Evaluation of moisture damage within asphalt concrete mixes 

    E-Print Network [OSTI]

    Shah, Brij D.

    2004-09-30T23:59:59.000Z

    as bond energy in order to predict moisture damage. Mixtures with the two types of bitumen and each aggregate with and without hydrated lime were evaluated. The hydrated lime substantially improved the resistance of the mixture to moisture damage....

  17. Damage analysis in asphalt concrete mixtures based on parameter relationships 

    E-Print Network [OSTI]

    Song, Injun

    2004-11-15T23:59:59.000Z

    Asphalt pavements experience damage due to traffic loading under various environmental conditions. Damage can be caused by viscopl microcracks, fracture due to fatigue cracking, or fracture due to thermal cracking. Asphalt ...

  18. Nonuniform radiation damage in permanent magnet quadrupoles

    SciTech Connect (OSTI)

    Danly, C. R.; Merrill, F. E.; Barlow, D.; Mariam, F. G. [Los Alamos National Laboratory, Los Alamos, New Mexico 87544 (United States)

    2014-08-15T23:59:59.000Z

    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.

  19. Evaluation of radiation damage using nonlinear ultrasound

    SciTech Connect (OSTI)

    Matlack, K. H. [G.W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); Wall, J. J. [G.W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); Electric Power Research Institute, Charlotte, North Carolina 28262 (United States); Kim, J.-Y. [School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); Qu, J. [Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois 60208 (United States); Jacobs, L. J. [G.W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); Viehrig, H.-W. [Department of Structural Materials, Helmholtz Zentrum Dresden-Rossendorf, Institute of Ion-Beam Physics and Materials Research, P.O. Box 510119, 01314 Dresden (Germany)

    2012-03-01T23:59:59.000Z

    Nonlinear ultrasound was used to monitor radiation damage in two reactor pressure vessel (RPV) steels. The microstructural changes associated with radiation damage include changes in dislocation density and the formation of precipitates, and nonlinear ultrasonic waves are known to be sensitive to such changes. Six samples each of two different RPV steels were previously irradiated in the Rheinsberg power reactor to two fluence levels, up to 10{sup 20} n/cm{sup 2} (E > 1 MeV). Longitudinal waves were used to measure the acoustic nonlinearity in these samples, and the results show a clear increase in the measured acoustic nonlinearity from the unirradiated state to the medium dose, and then a decrease from medium dose to high dose.

  20. Drill-in fluids control formation damage

    SciTech Connect (OSTI)

    Halliday, W.S. (Baker Hughes Inteq, Houston, TX (United States))

    1994-12-01T23:59:59.000Z

    Several factors led to development, oil company interest in, and use of payzone drilling fluids, including operator concern about maximizing well production, increasing acceptance of horizontal drilling and openhole completion popularity. This article discusses water-base drill-in'' fluid systems and applications. Payzone damage, including fine solids migration, clay swelling and solids invasion, reduces effective formation permeability, which results in lower production rates. Formation damage is often caused by invasion of normal drilling fluids that contain barite or bentonite. Drill-in systems are designed with special bridging agents to minimize invasion. Several bridging materials designed to form effective filter cake for instantaneous leak-off control can be used. Bridging materials are also designed to minimize stages and time required to clean up wells before production. Fluids with easy-to-remove bridging agents reduce completion costs. Drill-in fluid bridging particles can often be removed more thoroughly than those in standard fluids.

  1. Carbon Fiber Damage in Particle Beam

    E-Print Network [OSTI]

    Dehning, B; Kroyer, T; Meyer, M; Sapinski, M

    2011-01-01T23:59:59.000Z

    Carbon fibers are commonly used as moving targets in beam wire scanners. The heating of the fiber due to energy loss of the particles travelling through is simulated with Geant4. The heating induced by the beam electromagnetic field is estimated with ANSYS. The heat transfer and sublimation processes are modelled. Due to the model nonlinearity, a numerical approach based on discretization of the wire movement is used to solve it for particular beams. Radiation damage to the fiber is estimated with SRIM. The model is tested with available SPS and LEP data and a dedicated damage test on the SPS beam is performed followed by a post-mortem analysis of the wire remnants. Predictions for the LHC beams are made.

  2. DNA polymorphism identity determination using flow cytometry

    DOE Patents [OSTI]

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

    2001-01-01T23:59:59.000Z

    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.

  3. Effective charge and free energy of DNA inside an ion channel

    E-Print Network [OSTI]

    Jingshan Zhang; B. I. Shklovskii

    2008-03-03T23:59:59.000Z

    Translocation of a single stranded DNA (ssDNA) through an alpha-hemolysin channel in a lipid membrane driven by applied transmembrane voltage V was extensively studied recently. While the bare charge of the ssDNA piece inside the channel is approximately 12 (in units of electron charge) measurements of different effective charges resulted in values between one and two. We explain these challenging observations by a large self-energy of a charge in the narrow water filled gap between ssDNA and channel walls, related to large difference between dielectric constants of water and lipid, and calculate effective charges of ssDNA. We start from the most fundamental stall charge $q_s$, which determines the force $F_s= q_s V/L$ stalling DNA against the voltage V (L is the length of the channel). We show that the stall charge $q_s$ is proportional to the ion current blocked by DNA, which is small due to the self-energy barrier. Large voltage V reduces the capture barrier which DNA molecule should overcome in order to enter the channel by $|q_c|V$, where $q_c$ is the effective capture charge. We expressed it through the stall charge $q_s$. We also relate the stall charge $q_s$ to two other effective charges measured for ssDNA with a hairpin in the back end: the charge $q_u$ responsible for reduction of the barrier for unzipping of the hairpin and the charge $q_e$ responsible for DNA escape in the direction of hairpin against the voltage. At small V we explain reduction of the capture barrier with the salt concentration.

  4. Saga of Glass Damage in Urban Environments Continues

    E-Print Network [OSTI]

    Kareem, Ahsan

    Saga of Glass Damage in Urban Environments Continues: Consequences of Aerodynamics and Debris Laboratory University of Notre Dame The Saga of Glass Damage in Urban Environments Continues: Consequences east of the city of Houston. Initial reconnaissance suggested that the observed glass/cladding damage

  5. Assessing Hail and Freeze Damage to Field Corn and Sorghum

    E-Print Network [OSTI]

    Livingston, Stephen

    1995-11-30T23:59:59.000Z

    When a crop has been damaged by hail, it is important to be able to gauge the extent of the damage, the potential for recovery of the damaged crop, and the actions that might be necessary to maximize the recovery process. This publication tells how...

  6. Ice Storm Damage Greater Along the Terrestrial-Aquatic Interface

    E-Print Network [OSTI]

    Kraft, Clifford E.

    Ice Storm Damage Greater Along the Terrestrial-Aquatic Interface in Forested Landscapes Andrew A- tems. In 1998, a severe ice storm damaged over ten million hectares of forest across northern New York investigated the spatial arrangement of forest damage at the terrestrial-aquatic interface, an ecological edge

  7. Probabilistic Damage Detection Based on Large Area Electronics Sensing Sheets

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Probabilistic Damage Detection Based on Large Area Electronics Sensing Sheets Yao Yao and Branko-stage damage detection and characterization requires continuous sensing over large areas of structure are not sensitive to damage. In this research, a probabilistic approach based on Monte Carlo (MC) simulations

  8. Photogrammetry Assisted Rapid Measurement of Earthquake-Induced Building Damage

    E-Print Network [OSTI]

    Kamat, Vineet R.

    Photogrammetry Assisted Rapid Measurement of Earthquake-Induced Building Damage Fei Dai, PhD Hong for rapidly measuring structural damage induced in tall buildings by seismic events such as earthquakes) sustained at key floors along the edge of a damaged building. The measured drift can then be used to compute

  9. DAMAGE AND ROCKVOLATILE MIXTURE EFFECTS ON IMPACT CRATER FORMATION

    E-Print Network [OSTI]

    Stewart, Sarah T.

    DAMAGE AND ROCK­VOLATILE MIXTURE EFFECTS ON IMPACT CRATER FORMATION JOHN D. O'KEEFE, SARAH T models for material damage, dilatancy, and inhomogeneous materials (mixtures). We found that a strength degradation (damage) model was necessary to produce faulting in homogeneous materials. Both normal and thrust

  10. DAMAGE LOCALIZATION IN PLATES USING DLVs Dionisio Bernal1

    E-Print Network [OSTI]

    Bernal, Dionisio

    DAMAGE LOCALIZATION IN PLATES USING DLVs Dionisio Bernal1 and Ariel Levy2 Department of Civil Associate Professor, 2 Graduate Student ABSTRACT The performance of a technique to localize damage based on the computation of load vectors that create stress fields that bypass the damaged region is investigated

  11. A BAYESIAN PROBABILISTIC APPROACH TO DAMAGE DETECTION FOR CIVIL

    E-Print Network [OSTI]

    Stanford University

    damage or other environmental e ects. Results based on the eld vibration test of a bridge indicate on the vibration parameters can be di erentiated from other environmental e ects or potential structural damage. vA BAYESIAN PROBABILISTIC APPROACH TO DAMAGE DETECTION FOR CIVIL STRUCTURES a dissertation submitted

  12. An analysis of the kinetics of thermal damage and movement of damage front in laser irradiated egg white 

    E-Print Network [OSTI]

    Azeemi, Aamer Amjed

    1993-01-01T23:59:59.000Z

    Some of the major applications of laser surgery involve the photocoagulation of diseased tissue, with minimal or no damage to the surrounding healthy tissue. There is a growing need for a model for the quantification of thermal damage. The models...

  13. An analysis of the kinetics of thermal damage and movement of damage front in laser irradiated egg white

    E-Print Network [OSTI]

    Azeemi, Aamer Amjed

    1993-01-01T23:59:59.000Z

    Some of the major applications of laser surgery involve the photocoagulation of diseased tissue, with minimal or no damage to the surrounding healthy tissue. There is a growing need for a model for the quantification of thermal damage. The models...

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

    SciTech Connect (OSTI)

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

    2001-03-01T23:59:59.000Z

    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.

  15. DNA Strands Attached Inside Single Conical Nanopores: Ionic Pore Characteristics and Insight into DNA Biophysics

    E-Print Network [OSTI]

    Nguyen, Gael; Howorka, Stefan; Siwy, Zuzanna S.

    2011-01-01T23:59:59.000Z

    Nonexponential kinetics of DNA escape from alpha-hemolysin2010), (iii) the speed of DNA transport (Meller et al. 2001;0AJ, UK G. Nguyen et al. : DNA Strands in Single Nanopores

  16. DNA binding specificity of the p73 DNA-binding domain

    E-Print Network [OSTI]

    Tse, Pui Wah

    2011-01-01T23:59:59.000Z

    interactions of p53 with DNA: when flexibility serves2006). Structural basis of DNA recognition by p53 tetramers.Z. (2010). Diversity in DNA recognition by p53 revealed by

  17. Abdominal damage control surgery and reconstruction: world society of emergency surgery position paper

    E-Print Network [OSTI]

    Godat, Laura; Kobayashi, Leslie; Costantini, Todd; Coimbra, Raul

    2013-01-01T23:59:59.000Z

    as: Godat et al. : Abdominal damage control surgery andAD, Feliciano DV: Trauma damage control. In Trauma. 6thpatient which indicate damage control and predict outcome.

  18. Mechanical Damage from Cavitation in High Intensity Focused Ultrasound Accelerated Thrombolysis

    E-Print Network [OSTI]

    Weiss, Hope

    2012-01-01T23:59:59.000Z

    Mechanical Damage . . . . . . . . . . . . . . . . . .iiiMethod for Estimation of Cavitation Damage for an EmbeddedMethod for Estimation of Cavitation Damage for an Embedded

  19. Damage, Fear, and Transformation: International Currency Systems and Postwar Japan's Currency Policies

    E-Print Network [OSTI]

    Lee, Sangbaik

    2012-01-01T23:59:59.000Z

    will suffer a serious damage. ” 291 Above, we have surveyedparticularly for alleviating the damage incurred by the yenDamage, Fear, and Transformation: International Currency

  20. Damage Identification of a Composite Beam Using Finite Element Model Updating

    E-Print Network [OSTI]

    Moaveni, Babak; He, Xianfei; Conte, Joel P; De Callafon, Raymond A.

    2008-01-01T23:59:59.000Z

    Shevitz, D. W. (1996), Damage identification in structuresreview of vibration-based damage identification methods, TheM. , & Samman, M. M. (1991), Damage detection from changes

  1. Conformational Dynamics of Bacteriophage T7 DNA Polymerase and its Processivity Factor, Escherichia coli thioredoxin

    SciTech Connect (OSTI)

    Akabayov, B.; Akabayov, S; Lee , S; Tabor, S; Kulczyk , A; Richardson, C

    2010-01-01T23:59:59.000Z

    Gene 5 of bacteriophage T7 encodes a DNA polymerase (gp5) responsible for the replication of the phage DNA. Gp5 polymerizes nucleotides with low processivity, dissociating after the incorporation of 1 to 50 nucleotides. Thioredoxin (trx) of Escherichia coli binds tightly (Kd = 5 nM) to a unique segment in the thumb subdomain of gp5 and increases processivity. We have probed the molecular basis for the increase in processivity. A single-molecule experiment reveals differences in rates of enzymatic activity and processivity between gp5 and gp5/trx. Small angle X-ray scattering studies combined with nuclease footprinting reveal two conformations of gp5, one in the free state and one upon binding to trx. Comparative analysis of the DNA binding clefts of DNA polymerases and DNA binding proteins show that the binding surface contains more hydrophobic residues than other DNA binding proteins. The balanced composition between hydrophobic and charged residues of the binding site allows for efficient sliding of gp5/trx on the DNA. We propose a model for trx-induced conformational changes in gp5 that enhance the processivity by increasing the interaction of gp5 with DNA.

  2. 7th International Workshop on Microbeam Probes of Cellular Radiation Response

    SciTech Connect (OSTI)

    Brenner, David J.

    2009-07-21T23:59:59.000Z

    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.

  3. Natural Resource Damage Assessment Cooperation and Integration

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

    2012-06-19T23:59:59.000Z

    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.

  4. Surface state reconstruction in ion-damaged SmB?

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

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

    2015-02-01T23:59:59.000Z

    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.

  5. DNA Guided Self-Assembly of Nanocrystals for Optoelectronic Devices /

    E-Print Network [OSTI]

    Noh, Hyunwoo

    2013-01-01T23:59:59.000Z

    Lithographically Confined DNA Origami. Nat. Nanotech. 2010,and Orientation of Individual DNA Shapes on LithographicallyB. ; Yan, H. ; Liu, Y. DNA-Origami-Directed Self- Assembly

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

    SciTech Connect (OSTI)

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

    2004-11-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2005-01-01T23:59:59.000Z

    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.

  8. Survey of four damage models for concrete.

    SciTech Connect (OSTI)

    Leelavanichkul, Seubpong (University of Utah, Salt Lake City, UT); Brannon, Rebecca Moss (University of Utah, Salt Lake City, UT)

    2009-08-01T23:59:59.000Z

    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 properties. The RHT model appears to similarly support optional uncertainty and automated settings for scale-dependent material parameters. The K&C, RHT, and CSCM models support rate dependence by allowing the strength to be a function of strain rate, whereas the BF1 model uses Duvaut-Lion viscoplasticity theory to give a smoother prediction of transient effects. During softening, all four models require a certain amount of strain to develop before allowing significant damage accumulation. For the K&C, RHT, and CSCM models, the strain-to-failure is tied to fracture energy release, whereas a similar effect is achieved indirectly in the BF1 model by a time-based criterion that is tied to crack propagation speed.

  9. Minimizing radiation damage in nonlinear optical crystals

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

    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

    DOE Patents [OSTI]

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

    1998-09-08T23:59:59.000Z

    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. Radiation damage by neutrons to plastic scintillators

    SciTech Connect (OSTI)

    Buss, G.; Dannemann, A.; Holm, U.; Wick, K. [Univ. Hamburg (Germany). Inst. fuer Experimentalphysik] [Univ. Hamburg (Germany). Inst. fuer Experimentalphysik

    1995-08-01T23:59:59.000Z

    Polystyrene based scintillator SCSN38, wavelength shifter Y7 with polymethylmethacrylate matrix and pure PM-MA light guide GS218 have been irradiated in the mixed radiation field of a pool reactor. About 77% of the dose released in SCSN38 was caused by the {gamma}-field, 23% by fast neutrons. The total dose ranged from 2 to 105 kGy. The dose measurements were made using alanine dosimeters. Transmission and fluorescence of the samples have been measured before and several times after irradiation. The radiation damage results shown o differences to irradiations in pure {gamma}-fields with corresponding released doses.

  12. High-Fidelity DNA Hybridization Using Programmable Molecular DNA Devices

    E-Print Network [OSTI]

    Reif, John H.

    of complementary nucleic acid strands is the most basic of all reactions involving nucleic acids, but has a major specific high-fidelity DNA hybridization reactions for tar- get strands of arbitrary length. Our protocol acid strands is the most basic of all reactions involving nucleic acids and a major component of most

  13. Integrating Natural Resource Damage Assessment and environmental restoration activities at DOE facilities

    SciTech Connect (OSTI)

    Bascietto, J.J. [Dept. of Energy, Washington, DC (US). RCRA/CERCLA Div.; Dunford, R.W. [Research Triangle Inst., Research Triangle Park, NC (US); Sharples, F.E.; Suter, G.W. II [Oak Ridge National Lab., TN (US)

    1993-06-01T23:59:59.000Z

    Environmental restoration activities are currently under way at several sites owned by the US Department of Energy (DOE) under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), as amended. DOE is the CERCLA lead response agency for these activities. Section 120(a) of the Superfund Amendments and Reauthorization Act also subjects DOE to liability under Section 107 of CERCLA for natural resource damages resulting from hazardous substance releases at its sites. The Natural Resource Damage Assessment (NRDA) process, by which natural resource injuries are determined and compensatory monetary damages are calculated, is not well known or understood by DOE staff and contractors involved in environmental restoration activities. Nevertheless, natural resource liabilities are potentially a significant source of additional monetary claims for CERCLA hazardous substance releases. This paper describes the requirements of NRDA and explains how to integrate the NRDA and CERCLA Remedial Investigation/Feasibility Study processes, in order to more quickly restore environmental services at the lowest total cost to the public. The first section of the paper explains the statutory and regulatory mandates for the NRDA process. The second section briefly describes the four phases of the NRDA process, while the third section examines the three steps in the assessment phase in considerable detail. Finally, the last section focuses on the integration of the CERCLA and NRDA processes.

  14. Towards Privacy Preserving of Forensic DNA Databases

    E-Print Network [OSTI]

    Liu, Sanmin

    2012-02-14T23:59:59.000Z

    Protecting privacy of individuals is critical for forensic genetics. In a kinship/identity testing, related DNA profiles between user's query and the DNA database need to be extracted. However, unrelated profiles cannot be revealed to each other...

  15. Amplification of chromosomal DNA in situ

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

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

  16. DNA Microarrays An R Tutorial

    E-Print Network [OSTI]

    Qiu, Weigang

    Analysis & R Tutorial #12;DNA Microarrays An R Tutorial R: Graphics and Statistics beyond Excel R: an Open Source statistical package (http://www.r-project.org) RStudio: a Graphic User Interface to R (http(stock) # median > range(stock) # mim and max > sum(stock) # sum > var(stock) # variance > sd(stock) # standard

  17. Chromosome specific repetitive DNA sequences

    DOE Patents [OSTI]

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

    1991-01-01T23:59:59.000Z

    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).

  18. Protein-DNA Interactions Determine the Shapes of DNA Toroids Condensed in Virus Capsids

    E-Print Network [OSTI]

    Podgornik, Rudolf

    Protein-DNA Interactions Determine the Shapes of DNA Toroids Condensed in Virus Capsids Ame, University of Ljubljana, Ljubljana, Slovenia ABSTRACT DNA toroids that form inside the bacteriophage capsid glycol to the bathing solution. Spermine-DNA toroids present a convex, faceted section with no or minor

  19. Probe and method for DNA detection

    SciTech Connect (OSTI)

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

    2013-07-02T23:59:59.000Z

    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.

  20. DNA Sequencing via Electron Tunneling Michael Zwolak

    E-Print Network [OSTI]

    Zwolak, Michael

    DNA Sequencing via Electron Tunneling Michael Zwolak Department of Physics Oregon State University-cost DNA sequencing methods would revolutionize medicine: a person could have his/her full genome sequenced of "personalized medicine" is hampered today by the high cost and slow speed of DNA sequencing methods. We

  1. Antibody specific for a DNA repair protein

    DOE Patents [OSTI]

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

    2006-07-11T23:59:59.000Z

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

  2. Damage from the impacts of small asteroids

    SciTech Connect (OSTI)

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

    1996-08-15T23:59:59.000Z

    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.

  3. DNA and the Genetic Code June 14, 2011

    E-Print Network [OSTI]

    Guevara-Vasquez, Fernando

    DNA and the Genetic Code June 14, 2011 DNA and the Genetic Code #12;Protein synthesis The genetic synthesis requires two steps: transcription and translation. DNA and the Genetic Code #12;DNA DNA development. DNA is comprised of 4 bases: guanine (G), adenine (A), cytosine (C), and thymine (T). The bases

  4. Radiation Damage in Polarized Ammonia Solids

    E-Print Network [OSTI]

    K. Slifer

    2007-11-28T23:59:59.000Z

    Solid NH3 and ND3 provide a highly polarizable, radiation resistant source of polarized protons and deuterons and have been used extensively in high luminosity experiments investigating the spin structure of the nucleon. Over the past twenty years, the UVA polarized target group has been instrumental in producing and polarizing much of the material used in these studies, and many practical considerations have been learned in this time. In this discussion, we analyze the polarization performance of the solid ammonia targets used during the recent JLab Eg4 run. Topics include the rate of polarization decay with accumulated charge, the annealing procedure for radiation damaged targets to recover polarization, and the radiation induced change in optimum microwave frequency used to polarize the sample. We also discuss the success we have had in implementing frequency modulation of the polarizing microwave frequency.

  5. Thermal Decomposition of Radiation-Damaged Polystyrene

    SciTech Connect (OSTI)

    Abrefah, John; Klinger, George S.

    2000-09-26T23:59:59.000Z

    The radiation-damaged polystyrene (given the identification name of 'polycube') was fabricated by mixing high-density polystyrene material ("Dylene Fines # 100") with plutonium and uranium oxides. The polycubes were used in the 1960s for criticality studies during processing of spent nuclear fuel. The polycubes have since been stored for almost 40 years at the Hanford Plutonium Finishing Plant (PFP) after failure of two processes to reclaim the plutonium and uranium oxides from the polystyrene matrix. Thermal decomposition products from this highly cross-linked polystyrene matrix were characterized using Gas Chromatograph/Mass Spectroscopy (GC/MS) system coupled to a horizontal furnace. The decomposition studies were performed in air and helium atmospheres at about 773 K. The volatile and semi-volatile organic products for the radiation-damaged polystyrene were different compared to virgin polystyrene. The differences were in the number of organic species generated and their concentrations. In the inert (i.e., helium) atmosphere, the major volatile organic products identified (in order of decreasing concentrations) were styrene, benzene, toluene, ethylbenzene, xylene, nathphalene, propane, .alpha.-methylbenzene, indene and 1,2,3-trimethylbenzene. But in air, the major volatile organic species identified changed slightly. Concentrations of the organic species in the inert atmosphere were significantly higher than those for the air atmosphere processing. Overall, 38 volatile organic species were identified in the inert atmosphere compared to 49 species in air. Twenty of the 38 species in the inert conditions were also products in the air atmosphere. Twenty-two oxidized organic products were identified during thermal processing in air.

  6. assessing tubal damage: Topics by E-print Network

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

    State University, Deborah French, Applied Sciences Associates, Bruce Wright 5 Natural Resource Damage Assessment for the Deepwater BP Oil Spill Environmental Sciences and...

  7. Demonstration of damage with a wireless sensor network

    SciTech Connect (OSTI)

    Tanner, Neal A.; Farrar, C. R. (Charles R.)

    2001-01-01T23:59:59.000Z

    A damage detection system was developed with commercially available wireless sensors. Statistical process control methods were used to monitor the correlation of vibration data from two accelerometers mounted across a joint. Changes in correlation were used to detect damage to the joint. All data processing was done remotely on a microprocessor integrated with the wireless sensors to allow for the transmission of a simple damaged or undamaged status for each monitored joint. Additionally, a portable demonstration structure was developed to showcase the capabilities of the damage detection system to monitor joint failure in real time.

  8. Poroelastic damage rheology: Dilation, compaction, and failure of rocks

    E-Print Network [OSTI]

    Lyakhovsky, Vladimir

    Poroelastic damage rheology: Dilation, compaction, and failure of rocks Yariv Hamiel Institute December 2004; Published 26 January 2005. Hamiel, Y., V. Lyakhovsky, and A. Agnon (2005), Poroelastic

  9. Thermomechanics of damage and fatigue by a phase field model

    E-Print Network [OSTI]

    Giovambattista Amendola; Mauro Fabrizio

    2014-10-26T23:59:59.000Z

    In the paper we present an isothermal model for describing damage and fatigue by the use of the Ginzburg-Landau (G-L) equation. Fatigue produces progressive damage, which is related with a variation of the internal structure of the material. The G-L equation studies the evolution of the order parameter, which describes the constitutive arrangement of the system and, in this framework, the evolution of damage. The thermodynamic coherence of the model is proved. In the last part of the work, we extend the results of the paper to a non-isothermal system, where fatigue contains thermal effects, which increase the damage of materials.

  10. Damage Detection and Characterization in Smart Material Structures \\Lambda y

    E-Print Network [OSTI]

    ­maps'' as done in the thermal based tomography techniques of [BK1, BK2, BKW] wherein the damaged physical domain

  11. attack damage due: Topics by E-print Network

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

    Cell damage extent due to irradiation with nanosecond laser pulses under cell culturing medium and dry environment Engineering Websites Summary: Autnoma de Mxico; Av....

  12. acari eriophyidae damage: Topics by E-print Network

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

    resistant to particle beams. Their strength deteriorates with time due to radiation damage and low-cycle thermal fatigue. In case of high intensity beams this process can...

  13. aeroengines surface damage: Topics by E-print Network

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

    composition is compatible with a collisional sputtering model. At lower of radiation damage at oxide surfaces, induced by inert gas ions with energies typical of sputter...

  14. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

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

    1993-01-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    James, Conrad D.; Derzon, Mark Steven

    2005-10-01T23:59:59.000Z

    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.

  16. Fleet DNA Project (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2012-10-01T23:59:59.000Z

    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.

  17. Particle sizer and DNA sequencer

    DOE Patents [OSTI]

    Olivares, Jose A.; Stark, Peter C.

    2005-09-13T23:59:59.000Z

    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.

  18. Flavin-Induced Oligomerization in Escherichia coli Adaptive Response Protein AidB

    E-Print Network [OSTI]

    Drennan, Catherine L.

    The process known as “adaptive response” allows Escherichia coli to respond to small doses of DNA-methylating agents by upregulating the expression of four proteins. While the role of three of these proteins in mitigating ...

  19. Channel plate for DNA sequencing

    DOE Patents [OSTI]

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

    1998-01-13T23:59:59.000Z

    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.

  20. How Do Bacteria Repair Damage from the Sun? | Advanced Photon...

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

    of premature aging), and trichothiodystrophy (an inherited condition in which hair is brittle, sparse, and easily broken). Previous work had shown that the bacterial DNA...

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

    SciTech Connect (OSTI)

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

    1996-05-01T23:59:59.000Z

    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.

  2. Damage detection in mechanical structures using extreme value statistic.

    SciTech Connect (OSTI)

    Worden, K.; Allen, D. W. (David W.); Sohn, H. (Hoon); Farrar, C. R. (Charles R.)

    2002-01-01T23:59:59.000Z

    The first and most important objective of any damage identification algorithms is to ascertain with confidence if damage is present or not. Many methods have been proposed for damage detection based on ideas of novelty detection founded in pattern recognition and multivariate statistics. The philosophy of novelty detection is simple. Features are first extracted from a baseline system to be monitored, and subsequent data are then compared to see if the new features are outliers, which significantly depart from the rest of population. In damage diagnosis problems, the assumption is that outliers are generated from a damaged condition of the monitored system. This damage classification necessitates the establishment of a decision boundary. Choosing this threshold value is often based on the assumption that the parent distribution of data is Gaussian in nature. While the problem of novelty detection focuses attention on the outlier or extreme values of the data i.e. those points in the tails of the distribution, the threshold selection using the normality assumption weighs the central population of data. Therefore, this normality assumption might impose potentially misleading behavior on damage classification, and is likely to lead the damage diagnosis astray. In this paper, extreme value statistics is integrated with the novelty detection to specifically model the tails of the distribution of interest. Finally, the proposed technique is demonstrated on simulated numerical data and time series data measured from an eight degree-of-freedom spring-mass system.

  3. Real Time Computational Algorithms for Eddy Current Based Damage Detection

    E-Print Network [OSTI]

    Real Time Computational Algorithms for Eddy Current Based Damage Detection H. T. Banks y, Michele L such damages by application of an eddy current based technique coupled with reduced order modeling. We begin by developing a model for a speci#12;c eddy current method in which we make some simplifying assumptions

  4. Ris-R-1334(EN) Identification of Damage to Wind

    E-Print Network [OSTI]

    Risř-R-1334(EN) Identification of Damage to Wind Turbine Blades by Modal Parameter Estimation April 2002 #12;Risř-R-1334(EN) Identification of Damage to Wind Turbine Blades by Modal Parameter condition monitoring of wind turbine blades (Phase I)". The goal of Phase I is to make a pre

  5. Permeability of WIPP Salt During Damage Evolution and Healing

    SciTech Connect (OSTI)

    BODNER,SOL R.; CHAN,KWAI S.; MUNSON,DARRELL E.

    1999-12-03T23:59:59.000Z

    The presence of damage in the form of microcracks can increase the permeability of salt. In this paper, an analytical formulation of the permeability of damaged rock salt is presented for both initially intact and porous conditions. The analysis shows that permeability is related to the connected (i.e., gas accessible) volumetric strain and porosity according to two different power-laws, which may be summed to give the overall behavior of a porous salt with damage. This relationship was incorporated into a constitutive model, known as the Multimechanism Deformation Coupled Fracture (MDCF) model, which has been formulated to describe the inelastic flow behavior of rock salt due to coupled creep, damage, and healing. The extended model was used to calculate the permeability of rock salt from the Waste Isolation Pilot Plant (WIPP) site under conditions where damage evolved with stress over a time period. Permeability changes resulting from both damage development under deviatoric stresses and damage healing under hydrostatic pressures were considered. The calculated results were compared against experimental data from the literature, which indicated that permeability in damaged intact WIPP salt depends on the magnitude of the gas accessible volumetric strain and not on the total volumetric strain. Consequently, the permeability of WIPP salt is significantly affected by the kinetics of crack closure, but shows little dependence on the kinetics of crack removal by sintering.

  6. Genetic Algorithm Based Damage Control For Shipboard Power Systems

    E-Print Network [OSTI]

    Amba, Tushar

    2010-07-14T23:59:59.000Z

    The work presented in this thesis was concerned with the implementation of a damage control method for U.S. Navy shipboard power systems (SPS). In recent years, the Navy has been seeking an automated damage control and power system management...

  7. AFM CHARACTERIZATION OF LASER INDUCED DAMAGE ON CDZNTE CRYSTAL SURFACES

    SciTech Connect (OSTI)

    Hawkins, S; Lucile Teague, L; Martine Duff, M; Eliel Villa-Aleman, E

    2008-06-10T23:59:59.000Z

    Semi-conducting CdZnTe (or CZT) crystals can be used in a variety of detector-type applications. CZT shows great promise for use as a gamma radiation spectrometer. However, its performance is adversely affected by point defects, structural and compositional heterogeneities within the crystals, such as twinning, pipes, grain boundaries (polycrystallinity), secondary phases and in some cases, damage caused by external forces. One example is damage that occurs during characterization of the surface by a laser during Raman spectroscopy. Even minimal laser power can cause Te enriched areas on the surface to appear. The Raman spectra resulting from measurements at moderate intensity laser power show large increases in peak intensity that is attributed to Te. Atomic Force Microscopy (AFM) was used to characterize the extent of damage to the CZT crystal surface following exposure to the Raman laser. AFM data reveal localized surface damage in the areas exposed to the Raman laser beam. The degree of surface damage to the crystal is dependent on the laser power, with the most observable damage occurring at high laser power. Moreover, intensity increases in the Te peaks of the Raman spectra are observed even at low laser power with little to no visible damage observed by AFM. AFM results also suggest that exposure to the same amount of laser power yields different amounts of surface damage depending on whether the exposed surface is the Te terminating face or the Cd terminating face of CZT.

  8. Response Elements

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

    2007-07-11T23:59:59.000Z

    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. Cancels 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.

  9. Mesoscale polycrystal calculations of damage in spallation in metals

    SciTech Connect (OSTI)

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

    2010-01-01T23:59:59.000Z

    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.

  10. How Damage Diversification Can Reduce Systemic Risk

    E-Print Network [OSTI]

    Burkholz, Rebekka; Schweitzer, Frank

    2015-01-01T23:59:59.000Z

    We consider the problem of risk diversification in complex networks. Nodes represent e.g. financial actors, whereas weighted links represent e.g. financial obligations (credits/debts). Each node has a risk to fail because of losses resulting from defaulting neighbors, which may lead to large failure cascades. Classical risk diversification strategies usually neglect network effects and therefore suggest that risk can be reduced if possible losses (i.e., exposures) are split among many neighbors (exposure diversification, ED). But from a complex networks perspective diversification implies higher connectivity of the system as a whole which can also lead to increasing failure risk of a node. To cope with this, we propose a different strategy (damage diversification, DD), i.e. the diversification of losses that are imposed on neighboring nodes as opposed to losses incurred by the node itself. Here, we quantify the potential of DD to reduce systemic risk in comparison to ED. For this, we develop a branching proce...

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

    SciTech Connect (OSTI)

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

    1997-04-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Belles, R.J.; Cletcher, J.W.; Copinger, D.A.; Muhlheim, M.D. [Oak Ridge National Lab., TN (United States); Dolan, B.W.; Minarick, J.W. [Science Applications International Corp., Oak Ridge, TN (United States)

    1998-11-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    Belles, R.J.; Cletcher, J.W.; Copinger, D.A.; Vanden Heuvel, L.N. [Oak Ridge National Lab., TN (United States)] [Oak Ridge National Lab., TN (United States); Dolan, B.W.; Minarick, J.W. [Oak Ridge National Lab., TN (United States)] [Oak Ridge National Lab., TN (United States); [Science Applications International Corp., Oak Ridge, TN (United States)

    1995-12-01T23:59:59.000Z

    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.

  14. DNA Microarray Technologies: A Novel Approach to Geonomic Research

    SciTech Connect (OSTI)

    Hinman, R.; Thrall, B.; Wong, K,

    2002-01-01T23:59:59.000Z

    A cDNA microarray allows biologists to examine the expression of thousands of genes simultaneously. Researchers may analyze the complete transcriptional program of an organism in response to specific physiological or developmental conditions. By design, a cDNA microarray is an experiment with many variables and few controls. One question that inevitably arises when working with a cDNA microarray is data reproducibility. How easy is it to confirm mRNA expression patterns? In this paper, a case study involving the treatment of a murine macrophage RAW 264.7 cell line with tumor necrosis factor alpha (TNF) was used to obtain a rough estimate of data reproducibility. Two trials were examined and a list of genes displaying either a > 2-fold or > 4-fold increase in gene expression was compiled. Variations in signal mean ratios between the two slides were observed. We can assume that erring in reproducibility may be compensated by greater inductive levels of similar genes. Steps taken to obtain results included serum starvation of cells before treatment, tests of mRNA for quality/consistency, and data normalization.

  15. Real-Time damage localization by means of MEMS sensors and use of wireless data transmission

    E-Print Network [OSTI]

    Shinozuka, Masanobu

    Real-Time damage localization by means of MEMS sensors and use of wireless data transmission such as water delivery networks are damaged, it is critical to pinpoint the location of the damage, to assess the extent of the damage, and to mitigate the damage in real-time. We propose a wireless sensor network

  16. DNA Bubble Life Time in Denaturation

    E-Print Network [OSTI]

    Zh. S. Gevorkian; Chin-Kun Hu

    2010-10-11T23:59:59.000Z

    We have investigated the denaturation bubble life time for a homogeneous as well as for a heterogeneous DNA within a Poland-Scheraga model. It is shown that at criticality the bubble life time for a homogeneous DNA is finite provided that the loop entropic exponent c>2 and has a scaling dependence on DNA length for c<2. Heterogeneity in the thermodynamical limit makes the bubble life time infinite for any entropic exponent.

  17. Assembling semiconductor nanocomposites using DNA replication technologies.

    SciTech Connect (OSTI)

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

    2005-11-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2008-08-15T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Ng, Jin Kiat

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

  20. Optical Recognition of Converted DNA Nucleotides for Single-Molecule DNA

    E-Print Network [OSTI]

    Optical Recognition of Converted DNA Nucleotides for Single-Molecule DNA Sequencing Using Nanopore among individual nucleotides (nt). The system must be capable of differentiating among the four bases

  1. DNA binding specificity of the p73 DNA-binding domain

    E-Print Network [OSTI]

    Tse, Pui Wah

    2011-01-01T23:59:59.000Z

    of DNA recognition by p53 tetramers. Mol Cell 22, 741-753.site as a self-assembled tetramer. Structure 18, 246- Chene,structure of a p53 core tetramer bound to DNA. Oncogene 28,

  2. INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis

    SciTech Connect (OSTI)

    Ausin, Israel; Greenberg, Maxim V.C.; Simanshu, Dhirendra K.; Hale, Christopher J.; Vashisht, Ajay A.; Simon, Stacey A.; Lee, Tzuu-fen; Feng, Suhua; Espańola, Sophia D.; Meyers, Blake C.; Wohlschlegel, James A.; Patel, Dinshaw J.; Jacobsen, Steven E. (UCLA); (MSKCC); (Delaware)

    2012-10-23T23:59:59.000Z

    At least three pathways control maintenance of DNA cytosine methylation in Arabidopsis thaliana. However, the RNA-directed DNA methylation (RdDM) pathway is solely responsible for establishment of this silencing mark. We previously described INVOLVED IN DE NOVO 2 (IDN2) as being an RNA-binding RdDM component that is required for DNA methylation establishment. In this study, we describe the discovery of two partially redundant proteins that are paralogous to IDN2 and that form a stable complex with IDN2 in vivo. Null mutations in both genes, termed IDN2-LIKE 1 and IDN2-LIKE 2 (IDNL1 and IDNL2), result in a phenotype that mirrors, but does not further enhance, the idn2 mutant phenotype. Genetic analysis suggests that this complex acts in a step in the downstream portion of the RdDM pathway. We also have performed structural analysis showing that the IDN2 XS domain adopts an RNA recognition motif (RRM) fold. Finally, genome-wide DNA methylation and expression analysis confirms the placement of the IDN proteins in an RdDM pathway that affects DNA methylation and transcriptional control at many sites in the genome. Results from this study identify and describe two unique components of the RdDM machinery, adding to our understanding of DNA methylation control in the Arabidopsis genome.

  3. Calibration of damage parameters is an important issue for the use of damage laws, and particularly for industrial manufacturing processes. This paper deals with an

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    1 Abstract Calibration of damage parameters is an important issue for the use of damage laws Lemaitre damage parameters using tensile tests. An adapted objective function is built, and Efficient, ductile damage, global measurement. 1 Introduction An actual industrial issue is the study of material

  4. Characterization of Damage in Sandstones along the Mojave Section of the San Andreas Fault: Implications for the Shallow Extent of Damage

    E-Print Network [OSTI]

    Ben-Zion, Yehuda

    Characterization of Damage in Sandstones along the Mojave Section of the San Andreas Fault: Implications for the Shallow Extent of Damage Generation ORY DOR,1,5 JUDITH S. CHESTER,2 YEHUDA BEN-ZION,1 shallow generation of rock damage during an earthquake rupture, we measure the degree of fracture damage

  5. Enhancing the DNA Patent Database

    SciTech Connect (OSTI)

    Walters, LeRoy B.

    2008-02-18T23:59:59.000Z

    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. DNA: The Strand that Connects Us All

    SciTech Connect (OSTI)

    Kaplan, Matt (University of Arizona Genetics Core) [University of Arizona Genetics Core

    2011-03-29T23:59:59.000Z

    Learn how the methods and discoveries of human population genetics are applied for personal genealogical reconstruction and anthropological testing. Dr. Kaplan starts with a short general review of human genetics and the biology behind this form of DNA testing. He looks at how DNA testing is performed and how samples are processed in the University of Arizona laboratory. He also examines examples of personal genealogical results from Family Tree DNA and personal anthropological results from the Genographic Project. Finally, he describes the newest project in the UA laboratory, the DNA Shoah Project.

  7. SnapShot: DNA Polymerases II Mammals

    E-Print Network [OSTI]

    Foti, James J.

    DNA polymerases ensure the faithful duplication of genetic information inside the nuclease and mitochondria of eukaryotic cells and the nucleoid of prokaryotic cells. These remarkable enzymes synthesize polynucleotide ...

  8. DNA sequencing using fluorescence background electroblotting membrane

    DOE Patents [OSTI]

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

    1992-01-01T23:59:59.000Z

    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.

  9. DNA-guided nanoparticle assemblies

    DOE Patents [OSTI]

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

    2013-07-16T23:59:59.000Z

    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.

  10. DNA

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

    algorithms that we have developed to see the inner workings of molecular machines," said Thomas Terwilliger, a senior Los Alamos scientist and Laboratory Fellow. In this case,...

  11. DNA

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power Administration wouldDECOMPOSITION OF CALCIUM SULFATE: A REVIEWThis rcportJ it cdrives

  12. Introduction Organisms exhibit a heat shock response in which

    E-Print Network [OSTI]

    Robertson, Meldrum

    Introduction Organisms exhibit a heat shock response in which increased expression of stress proteins (or heat shock proteins, HSPs) is coincident with the induction of thermotolerance (the ability tissue because heat shock (HS) can protect neurons against ischaemic damage1 and this protection may

  13. DNA nanotechnology DOI: 10.1002/smll.200500464

    E-Print Network [OSTI]

    Li, Jiali

    DNA nanotechnology DOI: 10.1002/smll.200500464 Towards Rapid DNA Sequencing: Detecting Single- Stranded DNA with a Solid-State Nanopore Hao Yan* and Bingqian Xu* Keywords: · DNA · sequencing · single for rapid detection of single DNA molecules and their sequences. Two types of nanopores have been used

  14. Sequence specific alkylation of DNA by hairpin pyrroleimidazole polyamide conjugates

    E-Print Network [OSTI]

    Stoltz, Brian M.

    Sequence specific alkylation of DNA by hairpin pyrrole­imidazole polyamide conjugates Nicholas R predetermined sequences in the minor groove of DNA with affinities and specificities comparable to those of DNA for covalent reaction at specific DNA sequences and thereby inhibit DNA­protein interactions. Site

  15. Sequence Recognition of DNA by Protein-Induced Conformational Transitions

    E-Print Network [OSTI]

    Williams, Loren

    Sequence Recognition of DNA by Protein-Induced Conformational Transitions Derrick Watkins1 The binding of proteins to specific sequences of DNA is an important feature of virtually all DNA transactions. Proteins recognize specific DNA sequences using both direct readout (sensing types and positions of DNA

  16. Computational Hydrocode Study of Target Damage due to Fragment-Blast Impact

    SciTech Connect (OSTI)

    Hatch-Aguilar, T; Najjar, F; Szymanski, E

    2011-03-24T23:59:59.000Z

    A target's terminal ballistic effects involving explosively generated fragments, along with the original blast, are of critical importance for many different security and safety related applications. Personnel safety and protective building design are but a few of the practical disciplines that can gain from improved understanding combined loading effects. Traditionally, any engineering level analysis or design effort involving explosions would divide the target damage analysis into two correspondingly critical areas: blast wave and fragment related impact effects. The hypothesis of this paper lies in the supposition that a linear combination of a blast-fragment loading, coupled with an accurate target response description, can lead to a non-linear target damage effect. This non-linear target response could then stand as the basis of defining what a synergistic or combined frag-blast loading might actually look like. The table below, taken from Walters, et. al. categorizes some of the critical parameters driving any combined target damage effect and drives the evaluation of results. Based on table 1 it becomes clear that any combined frag-blast analysis would need to account for the target response matching similar ranges for the mechanics described above. Of interest are the critical times upon which a blast event or fragment impact loading occurs relative to the target's modal response. A blast, for the purposes of this paper is defined as the sudden release of chemical energy from a given material (henceforth referred to as an energetic material) onto its surrounding medium. During the coupling mechanism a discrete or discontinuous shockwave is generated. This shockwave travels outward from the source transferring energy and momentum to any surrounding objects including personnel and engineering structures. From an engineering perspective blast effects are typically characterized by way of physical characteristics such as Peak Pressure (PP), Time of Arrival (TOA), Pressure-Impulse (PI) and Time of Duration (TD). Other peculiarities include the radial decrease in pressure from the source, any fireball size measurement, and subsequent increase in temperature from the passing of the shockwave through the surrounding medium. In light of all of these metrics, the loading any object receives from a blast event becomes intricately connected to the distance between itself and the source. Because of this, a clear distinction is made between close-in effects and those from a source far away from the object of interest. Explosively generated fragments on the other hand are characterized by means of their localized damage potential. Metrics such as whether the fragment penetrates or perforates a given object is quantified as well as other variables including fragment's residual velocity, % kinetic energy decrease, residual fragment mass and other exit criteria. A fragment launched under such violent conditions could easily be traveling at speeds in excess of 2500 ft/s. Given these speeds it is conceivable to imagine how any given fragment could deliver a concentrated load to a target and penetrates through walls, vehicles or even the protection systems of nearby personnel. This study will focus on the individual fragment-target impact event with the hopes of expanding it to eventually include statistical procedures. Since this is a modeling excursion into the combined frag-blast target damage effects the numerical methods used to frame this problem become important in-so-far as the simulations are done in a consistent manner. For this study a Finite-Element based Hydrocode solution called ALE3D (ALE=Arbitrary Lagrangian-Eulerian) was utilized. ALE3D is developed by Lawrence Livermore National Laboratory (Livermore, CA), and as this paper will show, successfully implemented a converged ALE formulation including as many of the different aspects needed to query the synergistic damage on a given target. Further information on the modeling setup is included.

  17. Demand Response and Open Automated Demand Response

    E-Print Network [OSTI]

    LBNL-3047E Demand Response and Open Automated Demand Response Opportunities for Data Centers G described in this report was coordinated by the Demand Response Research Center and funded by the California. Demand Response and Open Automated Demand Response Opportunities for Data Centers. California Energy

  18. DNA Profiling Using Solid-State Nanopores: Detection of DNA-Binding

    E-Print Network [OSTI]

    Meller, Amit

    a 3.5 nm pore results from threading of a dye-intercalated DNA molecule, as compared to the typical for drug development, necessitating new in vitro methods for rapid and low-cost assessment of the binding molecules, which give the DNA/intercalator complex a bulkier structure than that of native DNA. Furthermore

  19. A DNA Based Implementation of an Evolutionary Search for Good Encodings for DNA Computation

    E-Print Network [OSTI]

    Deaton, Russell J.

    lelism, capacity, and power. This potential, however, is limited by the constraints imposed by the DNA chemistry 1]. Adleman 2] introduced a way to solve combina- torial optimization problems with DNA- mental reaction in DNA based computation is hydro- gen bonding between Watson-Crick complement base pairs

  20. Mathematical analysis of fully coupled approach to creep damage

    E-Print Network [OSTI]

    A. V. Shutov; A. -M. Saendig

    2006-01-25T23:59:59.000Z

    We prove the existence and uniqueness of solution to a classical creep damage problem. We formulate a sufficient condition for the problem to have a unique smooth solution, locally in time. This condition is stated in terms of smoothness of given data, such as solid geometry, boundary conditions, applied loads, and initial conditions. Counterexamples with an arbitrary small lifetime of a structure are also given, showing the mechanical interpretation of imposed smoothness conditions. The proposed theory gives a rigorous framework for a strain localization analysis. The influence of the damage gradient on the strain localization process is characterized within this framework and a measure of the damage localization is proposed.

  1. Repairs for damaged bolt holes in continuous fiber reinforced plastics 

    E-Print Network [OSTI]

    Copps, Kevin Daniel

    1992-01-01T23:59:59.000Z

    repair method for damaged bolt holes in such composites. Bolt holes in three types of graphite-epoxy were purposely damaged and then repaired. Each was tested to characterize its static and fatigue behavior. The tests used a special fixture to simulate... composite joints . Bearing-bypass ratio can change the failure mode of bolted composite joints 7 Drilling defects in graphite-epoxy coupons 12 26 The exit side of a IM7/8551-7A 18 ply tape coupon showing the damage due to drilling 27 9 Resin filled...

  2. Damage to HDPE geomembrane from interface shear over gravelly compacted clay liner

    E-Print Network [OSTI]

    Thielmann, Stuart

    2012-01-01T23:59:59.000Z

    R. S. (2011). “Geomembrane damage due to static and cyclic66 Figure 4.10. GM damage results after shearing for Testsshear displacement on shear strength and GM damage for test

  3. ENVIRONMENTAL DAMAGE AS NEGATIVE EXTERNALITY: UNCERTAINTY, MORAL COMPLEXITY AND THE LIMITS OF THE MARKET

    E-Print Network [OSTI]

    Boyer, Edmond

    21 ENVIRONMENTAL DAMAGE AS NEGATIVE EXTERNALITY: UNCERTAINTY, MORAL COMPLEXITY AND THE LIMITS environmental damage with a sociological approach, I show how the process of externalities definition inclusive and democratic public deliberation on environmental damage and its reparation. Key Words

  4. 3-amino thioacridone inhibits DNA synthesis and induces DNA damage in T-cell acute lymphoblastic leukemia (T-ALL) in a p16-dependent manner

    E-Print Network [OSTI]

    2005-01-01T23:59:59.000Z

    sequential therapy of acute leukemia with flavopiridol: indamage in T-cell acute lymphoblastic leukemia (T-ALL) in aT-lineage acute lymphoblastic leukemia. Blood 91:735-746,

  5. Neutron and gamma irradiation damage to organic materials.

    SciTech Connect (OSTI)

    White, Gregory Von, II; Bernstein, Robert

    2012-04-01T23:59:59.000Z

    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.

  6. Salvaging Timber: What should I do with my damaged timber?

    E-Print Network [OSTI]

    Taylor, Eric; Foster, C. Darwin

    2005-10-31T23:59:59.000Z

    ER-041 5-06 Salvaging Timber: What should I do with my damaged timber? Eric L. Taylor, Assistant Professor and Extension Specialist?Forestry, and C. Darwin Foster, Associate Department Head and Extension Program Leader for Forestry, The Texas...

  7. Effects of ballistic damage on the dynamics of composite driveshafts

    E-Print Network [OSTI]

    Ayers, Thomas Ray

    1993-01-01T23:59:59.000Z

    The objective of this research program is to study the dynamics of a composite driveshaft before and after ballistic damage is incurred. Driveshafts are tested under static and dynamic loads to obtain material, mechanical, and vibrational...

  8. Hail Ice Damage of Stringer-Stiffened Curved Composite Panels /

    E-Print Network [OSTI]

    Le, Jacqueline Linh

    2013-01-01T23:59:59.000Z

    Damage. Composite Structures 2003;62:213–21. Ice Drop.How to make clear ice. 28 February 2011. Victoria, BC,2011/02/how-to- make-clear-ice-that-actually-works/ Graham,

  9. Multiscale modeling of damage in multidirectional composite laminates

    E-Print Network [OSTI]

    Singh, Chandra Veer

    2009-05-15T23:59:59.000Z

    provides reasonable predictions for multidirectional laminatesin which intralaminar cracks may form in multiple orientations. Nevertheless, theprediction of damage accumulation and its effect on structural performance is a verydifficult problem due...

  10. Visual Indication of Mechanical Damage Using Core-Shell Microcapsules

    E-Print Network [OSTI]

    Sottos, Nancy R.

    -7 Changes in pH have been used to detect compression in polymer brushes,8 and microcapsules containing a p have been incorporated into filled hollow fibers to enhance damage visibility in the structure

  11. DAMAGE TOLERANCE ISSUES PECULIAR TO SUPERSONIC CIVIL TRANSPORT AIRCRAFT

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    investigations on creep, fatigue and creep-fatigue crack growth behaviour of the 2650-T6 aluminium alloy to investigate the damage tolerance of the new aluminium alloy succeeding as 2218A. LMPM has to examinate

  12. Lengthscale effects in the damage and failure of composites

    E-Print Network [OSTI]

    Chambers, Jeffrey Thomas

    2014-01-01T23:59:59.000Z

    The primary objective of this work is to investigate and identify lengthscale effects associated with damage in composite materials and their structures, and to determine how these lengthscales vary across levels of ...

  13. Drag amplification and fatigue damage in vortex-induced vibrations

    E-Print Network [OSTI]

    Jhingran, Vikas Gopal

    2008-01-01T23:59:59.000Z

    Fatigue damage and drag force amplification due to Vortex-Induced-Vibrations (VIV) continue to cause significant problems in the design of structures which operate in ocean current environments. These problems are magnified ...

  14. air pollution damage: Topics by E-print Network

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

    14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Health Damages from Air Pollution in China MIT - DSpace Summary: In China, elevated levels of urban air...

  15. Existence and Regularity for Dynamic Viscoelastic Adhesive Contact with Damage

    SciTech Connect (OSTI)

    Kuttler, Kenneth L. [Department of Mathematics, Brigham Young University, Provo, UT 84602 (United States)], E-mail: klkuttler@math.byu.edu; Shillor, Meir [Department of Mathematics and Statistics, Oakland University, Rochester, MI 48309 (United States)], E-mail: shillor@oakland.edu; Fernandez, Jose R. [Departamento de Matematica Aplicada, Facultade de Matematicas, University of Santiago de Compostela, 15706 Santiago de Compostela (Spain)], E-mail: jramon@usc.es

    2006-01-15T23:59:59.000Z

    A model for the dynamic process of frictionless adhesive contact between a viscoelastic body and a reactive foundation, which takes into account the damage of the material resulting from tension or compression, is presented. Contact is described by the normal compliance condition. Material damage is modelled by the damage field, which measures the pointwise fractional decrease in the load-carrying capacity of the material, and its evolution is described by a differential inclusion. The model allows for different damage rates caused by tension or compression. The adhesion is modelled by the bonding field, which measures the fraction of active bonds on the contact surface. The existence of the unique weak solution is established using the theory of set-valued pseudomonotone operators introduced by Kuttler and Shillor (1999). Additional regularity of the solution is obtained when the problem data is more regular and satisfies appropriate compatibility conditions.

  16. alkyladenine dna glycosylase: Topics by E-print Network

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

    recognition and repair by 3-methyladenine DNA glycosylase I (TAG) Audrey H Metz1II), Helicobacter pylori 3mA DNA glycosylase (MagIII), yeast methyladenine DNA glycosylase...

  17. Single Stranded DNA Induced Assembly of Gold Nanoparticles

    E-Print Network [OSTI]

    Yang, Jun

    The binding affinity of single stranded DNA (ssDNA) for gold nanoparticle surface is studied in this work. The data indicate that the strength of interaction between ssDNA and Au particle surface is closely related to the ...

  18. Single molecule analysis of DNA electrophoresis in microdevices

    E-Print Network [OSTI]

    Randall, Greg C

    2006-01-01T23:59:59.000Z

    Given that current electrophoresis technology is inadequate for mapping large O[100 kilobasepair] DNA, several promising lab-on-chip designs for DNA mapping have been recently proposed that require either 1) a DNA molecule ...

  19. DNA topology confers sequence specificity to nonspecific architectural proteins

    E-Print Network [OSTI]

    Swigon, David

    DNA topology confers sequence specificity to nonspecific architectural proteins Juan Weia , Luke of DNA change the disorder found in chain molecules randomly decorated by nonspecific, architectural, counter to expectations, in greater quantities and at particular sites along simulated DNA minicircles

  20. Electrokinetic Concentration of DNA Polymers in Nanofluidic Channels

    E-Print Network [OSTI]

    Dekker, Cees

    Electrokinetic Concentration of DNA Polymers in Nanofluidic Channels Derek Stein,, Zeno Deurvorst on this understanding by demonstrating how a nanofluidic device with integrated electrodes can preconcentrate DNA. KEYWORDS Nanofluidic, DNA, electrokinetic, concentration M iniature fluidic devices are having an important