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Sample records for replicatory leading strand

  1. Dynamics of Leading-strand Lesion Skipping by the Replisome

    Science.gov (United States)

    Yeeles, Joseph T.P.; Marians, Kenneth J.

    2013-01-01

    SUMMARY The E. coli replisome stalls transiently when it encounters a lesion in the leading-strand template, skipping over the damage by reinitiating replication at a new primer synthesized downstream by the primase. We report here that template unwinding and lagging-strand synthesis continue downstream of the lesion at a reduced rate after replisome stalling, that one replisome is capable of skipping multiple lesions, and that the rate limiting steps of replication restart involve the synthesis and activation of the new primer downstream. We also find little support for the concept that polymerase uncoupling, where extensive lagging-strand synthesis proceeds downstream in the absence of leading-strand synthesis, involves physical separation of the leading-strand polymerase from the replisome. Instead, our data indicate that extensive uncoupled replication likely results from a failure of the leading-strand polymerase still associated with the DNA helicase and the lagging-strand polymerase that are proceeding downstream to reinitiate synthesis. PMID:24268579

  2. Flap Endonuclease 1 Limits Telomere Fragility on the Leading Strand.

    Science.gov (United States)

    Teasley, Daniel C; Parajuli, Shankar; Nguyen, Mai; Moore, Hayley R; Alspach, Elise; Lock, Ying Jie; Honaker, Yuchi; Saharia, Abhishek; Piwnica-Worms, Helen; Stewart, Sheila A

    2015-06-12

    The existence of redundant replication and repair systems that ensure genome stability underscores the importance of faithful DNA replication. Nowhere is this complexity more evident than in challenging DNA templates, including highly repetitive or transcribed sequences. Here, we demonstrate that flap endonuclease 1 (FEN1), a canonical lagging strand DNA replication protein, is required for normal, complete leading strand replication at telomeres. We find that the loss of FEN1 nuclease activity, but not DNA repair activities, results in leading strand-specific telomere fragility. Furthermore, we show that FEN1 depletion-induced telomere fragility is increased by RNA polymerase II inhibition and is rescued by ectopic RNase H1 expression. These data suggest that FEN1 limits leading strand-specific telomere fragility by processing RNA:DNA hybrid/flap intermediates that arise from co-directional collisions occurring between the replisome and RNA polymerase. Our data reveal the first molecular mechanism for leading strand-specific telomere fragility and the first known role for FEN1 in leading strand DNA replication. Because FEN1 mutations have been identified in human cancers, our findings raise the possibility that unresolved RNA:DNA hybrid structures contribute to the genomic instability associated with cancer. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Flap Endonuclease 1 Limits Telomere Fragility on the Leading Strand*

    Science.gov (United States)

    Teasley, Daniel C.; Parajuli, Shankar; Nguyen, Mai; Moore, Hayley R.; Alspach, Elise; Lock, Ying Jie; Honaker, Yuchi; Saharia, Abhishek; Piwnica-Worms, Helen; Stewart, Sheila A.

    2015-01-01

    The existence of redundant replication and repair systems that ensure genome stability underscores the importance of faithful DNA replication. Nowhere is this complexity more evident than in challenging DNA templates, including highly repetitive or transcribed sequences. Here, we demonstrate that flap endonuclease 1 (FEN1), a canonical lagging strand DNA replication protein, is required for normal, complete leading strand replication at telomeres. We find that the loss of FEN1 nuclease activity, but not DNA repair activities, results in leading strand-specific telomere fragility. Furthermore, we show that FEN1 depletion-induced telomere fragility is increased by RNA polymerase II inhibition and is rescued by ectopic RNase H1 expression. These data suggest that FEN1 limits leading strand-specific telomere fragility by processing RNA:DNA hybrid/flap intermediates that arise from co-directional collisions occurring between the replisome and RNA polymerase. Our data reveal the first molecular mechanism for leading strand-specific telomere fragility and the first known role for FEN1 in leading strand DNA replication. Because FEN1 mutations have been identified in human cancers, our findings raise the possibility that unresolved RNA:DNA hybrid structures contribute to the genomic instability associated with cancer. PMID:25922071

  4. Strand misalignments lead to quasipalindrome correction

    DEFF Research Database (Denmark)

    van Noort, V.; Worning, Peder; Ussery, David

    2003-01-01

    Quasipalindromes, or imperfect inverted repeats, undergo spontaneous mutation to more-perfect inverted repeats. These mutations have been observed in many organisms, ranging from bacteria to humans, where they are associated with mutations leading to disease. We determined the relative frequency...

  5. Mismatch repair balances leading and lagging strand DNA replication fidelity.

    Directory of Open Access Journals (Sweden)

    Scott A Lujan

    Full Text Available The two DNA strands of the nuclear genome are replicated asymmetrically using three DNA polymerases, α, δ, and ε. Current evidence suggests that DNA polymerase ε (Pol ε is the primary leading strand replicase, whereas Pols α and δ primarily perform lagging strand replication. The fact that these polymerases differ in fidelity and error specificity is interesting in light of the fact that the stability of the nuclear genome depends in part on the ability of mismatch repair (MMR to correct different mismatches generated in different contexts during replication. Here we provide the first comparison, to our knowledge, of the efficiency of MMR of leading and lagging strand replication errors. We first use the strand-biased ribonucleotide incorporation propensity of a Pol ε mutator variant to confirm that Pol ε is the primary leading strand replicase in Saccharomyces cerevisiae. We then use polymerase-specific error signatures to show that MMR efficiency in vivo strongly depends on the polymerase, the mismatch composition, and the location of the mismatch. An extreme case of variation by location is a T-T mismatch that is refractory to MMR. This mismatch is flanked by an AT-rich triplet repeat sequence that, when interrupted, restores MMR to > 95% efficiency. Thus this natural DNA sequence suppresses MMR, placing a nearby base pair at high risk of mutation due to leading strand replication infidelity. We find that, overall, MMR most efficiently corrects the most potentially deleterious errors (indels and then the most common substitution mismatches. In combination with earlier studies, the results suggest that significant differences exist in the generation and repair of Pol α, δ, and ε replication errors, but in a generally complementary manner that results in high-fidelity replication of both DNA strands of the yeast nuclear genome.

  6. Strand misalignments lead to quasipalindrome correction

    DEFF Research Database (Denmark)

    van Noort, V.; Worning, Peder; Ussery, David

    2003-01-01

    Quasipalindromes, or imperfect inverted repeats, undergo spontaneous mutation to more-perfect inverted repeats. These mutations have been observed in many organisms, ranging from bacteria to humans, where they are associated with mutations leading to disease. We determined the relative frequency...... of quasi palindromes and perfect palindromes in more than 100 sequenced prokaryotic genomes. In nearly all cases, perfect palindromes were relatively more frequent than quasipalindromes, suggesting that quasipalindrome correction is a general mechanism for mutation in prokaryotes....

  7. Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication.

    Science.gov (United States)

    Price, Morgan N; Alm, Eric J; Arkin, Adam P

    2005-01-01

    In bacteria, most genes are on the leading strand of replication, a phenomenon attributed to collisions between the DNA and RNA polymerases. In Escherichia coli, these collisions slow the movement of the replication fork through actively transcribed genes only if they are coded on the lagging strand. For genes on both strands, however, these collisions sever nascent transcripts and interrupt gene expression. Based on these observations, we propose a new theory to explain strand bias: genes whose expression is important for fitness are selected to the leading strand because this reduces the duration of these interruptions. Our theory predicts that multi-gene operons, which are subject to longer interruptions, should be more strongly selected to the leading strand than singleton transcripts. We show that this is true even after controlling for the tendency for essential genes, which are strongly biased to the leading strand, to occur in operons. Our theory also predicts that other factors that are associated with strand bias should have stronger effects for genes that are in operons. We find that expression level and phylogenetic ubiquity are correlated with strand bias for both essential and non-essential genes, but only for genes in operons.

  8. The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces

    Science.gov (United States)

    Mao, Xizeng; Zhang, Han; Yin, Yanbin; Xu, Ying

    2012-01-01

    The majority of bacterial genes are located on the leading strand, and the percentage of such genes has a large variation across different bacteria. Although some explanations have been proposed, these are at most partial explanations as they cover only small percentages of the genes and do not even consider the ones biased toward the lagging strand. We have carried out a computational study on 725 bacterial genomes, aiming to elucidate other factors that may have influenced the strand location of genes in a bacterium. Our analyses suggest that (i) genes of some functional categories such as ribosome have higher preferences to be on the leading strands; (ii) genes of some functional categories such as transcription factor have higher preferences on the lagging strands; (iii) there is a balancing force that tends to keep genes from all moving to the leading and more efficient strand and (iv) the percentage of leading-strand genes in an bacterium can be accurately explained based on the numbers of genes in the functional categories outlined in (i) and (ii), genome size and gene density, indicating that these numbers implicitly contain the information about the percentage of genes on the leading versus lagging strand in a genome. PMID:22735706

  9. Reconstitution of a eukaryotic replisome reveals suppression mechanisms that define leading/lagging strand operation

    Science.gov (United States)

    Georgescu, Roxana E; Schauer, Grant D; Yao, Nina Y; Langston, Lance D; Yurieva, Olga; Zhang, Dan; Finkelstein, Jeff; O'Donnell, Mike E

    2015-01-01

    We have reconstituted a eukaryotic leading/lagging strand replisome comprising 31 distinct polypeptides. This study identifies a process unprecedented in bacterial replisomes. While bacteria and phage simply recruit polymerases to the fork, we find that suppression mechanisms are used to position the distinct eukaryotic polymerases on their respective strands. Hence, Pol ε is active with CMG on the leading strand, but it is unable to function on the lagging strand, even when Pol δ is not present. Conversely, Pol δ-PCNA is the only enzyme capable of extending Okazaki fragments in the presence of Pols ε and α. We have shown earlier that Pol δ-PCNA is suppressed on the leading strand with CMG (Georgescu et al., 2014). We propose that CMG, the 11-subunit helicase, is responsible for one or both of these suppression mechanisms that spatially control polymerase occupancy at the fork. DOI: http://dx.doi.org/10.7554/eLife.04988.001 PMID:25871847

  10. BLM helicase facilitates telomere replication during leading strand synthesis of telomeres

    Science.gov (United States)

    Kosiyatrakul, Settapong T.

    2015-01-01

    Based on its in vitro unwinding activity on G-quadruplex (G4) DNA, the Bloom syndrome–associated helicase BLM is proposed to participate in telomere replication by aiding fork progression through G-rich telomeric DNA. Single molecule analysis of replicated DNA (SMARD) was used to determine the contribution of BLM helicase to telomere replication. In BLM-deficient cells, replication forks initiating from origins within the telomere, which copy the G-rich strand by leading strand synthesis, moved slower through the telomere compared with the adjacent subtelomere. Fork progression through the telomere was further slowed in the presence of a G4 stabilizer. Using a G4-specific antibody, we found that deficiency of BLM, or another G4-unwinding helicase, the Werner syndrome-associated helicase WRN, resulted in increased G4 structures in cells. Importantly, deficiency of either helicase led to greater increases in G4 DNA detected in the telomere compared with G4 seen genome-wide. Collectively, our findings are consistent with BLM helicase facilitating telomere replication by resolving G4 structures formed during copying of the G-rich strand by leading strand synthesis. PMID:26195664

  11. Coordinated leading and lagging strand DNA synthesis by using the herpes simplex virus 1 replication complex and minicircle DNA templates.

    Science.gov (United States)

    Stengel, Gudrun; Kuchta, Robert D

    2011-01-01

    The origin-specific replication of the herpes simplex virus 1 genome requires seven proteins: the helicase-primase (UL5-UL8-UL52), the DNA polymerase (UL30-UL42), the single-strand DNA binding protein (ICP8), and the origin-binding protein (UL9). We reconstituted these proteins, excluding UL9, on synthetic minicircular DNA templates and monitored leading and lagging strand DNA synthesis using the strand-specific incorporation of dTMP and dAMP. Critical features of the assays that led to efficient leading and lagging stand synthesis included high helicase-primase concentrations and a lagging strand template whose sequence resembled that of the viral DNA. Depending on the nature of the minicircle template, the replication complex synthesized leading and lagging strand products at molar ratios varying between 1:1 and 3:1. Lagging strand products (∼0.2 to 0.6 kb) were significantly shorter than leading strand products (∼2 to 10 kb), and conditions that stimulated primer synthesis led to shorter lagging strand products. ICP8 was not essential; however, its presence stimulated DNA synthesis and increased the length of both leading and lagging strand products. Curiously, human DNA polymerase α (p70-p180 or p49-p58-p70-p180), which improves the utilization of RNA primers synthesized by herpesvirus primase on linear DNA templates, had no effect on the replication of the minicircles. The lack of stimulation by polymerase α suggests the existence of a macromolecular assembly that enhances the utilization of RNA primers and may functionally couple leading and lagging strand synthesis. Evidence for functional coupling is further provided by our observations that (i) leading and lagging strand synthesis produce equal amounts of DNA, (ii) leading strand synthesis proceeds faster under conditions that disable primer synthesis on the lagging strand, and (iii) conditions that accelerate helicase-catalyzed DNA unwinding stimulate decoupled leading strand synthesis but not

  12. CMG helicase and DNA polymerase ε form a functional 15-subunit holoenzyme for eukaryotic leading-strand DNA replication.

    Science.gov (United States)

    Langston, Lance D; Zhang, Dan; Yurieva, Olga; Georgescu, Roxana E; Finkelstein, Jeff; Yao, Nina Y; Indiani, Chiara; O'Donnell, Mike E

    2014-10-28

    DNA replication in eukaryotes is asymmetric, with separate DNA polymerases (Pol) dedicated to bulk synthesis of the leading and lagging strands. Pol α/primase initiates primers on both strands that are extended by Pol ε on the leading strand and by Pol δ on the lagging strand. The CMG (Cdc45-MCM-GINS) helicase surrounds the leading strand and is proposed to recruit Pol ε for leading-strand synthesis, but to date a direct interaction between CMG and Pol ε has not been demonstrated. While purifying CMG helicase overexpressed in yeast, we detected a functional complex between CMG and native Pol ε. Using pure CMG and Pol ε, we reconstituted a stable 15-subunit CMG-Pol ε complex and showed that it is a functional polymerase-helicase on a model replication fork in vitro. On its own, the Pol2 catalytic subunit of Pol ε is inefficient in CMG-dependent replication, but addition of the Dpb2 protein subunit of Pol ε, known to bind the Psf1 protein subunit of CMG, allows stable synthesis with CMG. Dpb2 does not affect Pol δ function with CMG, and thus we propose that the connection between Dpb2 and CMG helps to stabilize Pol ε on the leading strand as part of a 15-subunit leading-strand holoenzyme we refer to as CMGE. Direct binding between Pol ε and CMG provides an explanation for specific targeting of Pol ε to the leading strand and provides clear mechanistic evidence for how strand asymmetry is maintained in eukaryotes.

  13. CMG helicase and DNA polymerase ε form a functional 15-subunit holoenzyme for eukaryotic leading-strand DNA replication

    Science.gov (United States)

    Langston, Lance D.; Zhang, Dan; Yurieva, Olga; Georgescu, Roxana E.; Finkelstein, Jeff; Yao, Nina Y.; Indiani, Chiara; O’Donnell, Mike E.

    2014-01-01

    DNA replication in eukaryotes is asymmetric, with separate DNA polymerases (Pol) dedicated to bulk synthesis of the leading and lagging strands. Pol α/primase initiates primers on both strands that are extended by Pol ε on the leading strand and by Pol δ on the lagging strand. The CMG (Cdc45-MCM-GINS) helicase surrounds the leading strand and is proposed to recruit Pol ε for leading-strand synthesis, but to date a direct interaction between CMG and Pol ε has not been demonstrated. While purifying CMG helicase overexpressed in yeast, we detected a functional complex between CMG and native Pol ε. Using pure CMG and Pol ε, we reconstituted a stable 15-subunit CMG–Pol ε complex and showed that it is a functional polymerase–helicase on a model replication fork in vitro. On its own, the Pol2 catalytic subunit of Pol ε is inefficient in CMG-dependent replication, but addition of the Dpb2 protein subunit of Pol ε, known to bind the Psf1 protein subunit of CMG, allows stable synthesis with CMG. Dpb2 does not affect Pol δ function with CMG, and thus we propose that the connection between Dpb2 and CMG helps to stabilize Pol ε on the leading strand as part of a 15-subunit leading-strand holoenzyme we refer to as CMGE. Direct binding between Pol ε and CMG provides an explanation for specific targeting of Pol ε to the leading strand and provides clear mechanistic evidence for how strand asymmetry is maintained in eukaryotes. PMID:25313033

  14. Partial strands synthesizing leads to inevitable aborting and complicated products in consecutive polymerase chain reactions (PCRs)

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Various abnormal phenomena have been observed during PCR so far. The present study performed a series of consecutive PCRs (including many rounds of re-amplification continuously) and found that the abortion of re-amplification was inevitable as long as a variety of complicated product appeared. The aborting stages varied, according to the lengths of targets. Longer targets reached the abortion earlier than the shorter ones, marked by appearance of the complex that was immobile in electropho-resis. Denatured gel-electrophoresis revealed that the complex was mainly made up of shorter or partially synthesized strands, together with small amounts of full-length ones. Able to be digested by S1 nuclease but unable by restriction endonucleases (REs), the complex was proved to consist of both single regions and double-helix regions that kept the complex stable thermodynamically. Simulations gave evidence that partial strands, even at lower concentration, could disturb re-amplification effec- tively and lead to the abortion of re-amplifications finally. It was pointed out that the partial strands formed chiefly via polymerase’s infidelity, and hence the solution to lighten the abnormality was also proposed.

  15. Partial strands synthesizing leads to inevitable aborting and complicated products in consecutive polymerase chain reactions (PCRs)

    Institute of Scientific and Technical Information of China (English)

    LUO Rui; ZHANG DaMing

    2007-01-01

    Various abnormal phenomena have been observed during PCR so far. The present study performed a series of consecutive PCRs (including many rounds of re-amplification continuously) and found that the abortion of re-amplification was inevitable as long as a variety of complicated product appeared.The aborting stages varied, according to the lengths of targets. Longer targets reached the abortion earlier than the shorter ones, marked by appearance of the complex that was immobile in electrophoresis. Denatured gel-electrophoresis revealed that the complex was mainly made up of shorter or partially synthesized strands, together with small amounts of full-length ones. Able to be digested by S1 nuclease but unable by restriction endonucleases (REs), the complex was proved to consist of both single regions and double-helix regions that kept the complex stable thermodynamically. Simulations gave evidence that partial strands, even at lower concentration, could disturb re-amplification effectively and lead to the abortion of re-amplifications finally. It was pointed out that the partial strands formed chiefly via polymerase's infidelity, and hence the solution to lighten the abnormality was also proposed.

  16. Formation of interference-sensitive meiotic cross-overs requires sufficient DNA leading-strand elongation.

    Science.gov (United States)

    Huang, Jiyue; Cheng, Zhihao; Wang, Cong; Hong, Yue; Su, Hang; Wang, Jun; Copenhaver, Gregory P; Ma, Hong; Wang, Yingxiang

    2015-10-06

    Meiosis halves diploid genomes to haploid and is essential for sexual reproduction in eukaryotes. Meiotic recombination ensures physical association of homologs and their subsequent accurate segregation and results in the redistribution of genetic variations among progeny. Most organisms have two classes of cross-overs (COs): interference-sensitive (type I) and -insensitive (type II) COs. DNA synthesis is essential for meiotic recombination, but whether DNA synthesis has a role in differentiating meiotic CO pathways is unknown. Here, we show that Arabidopsis POL2A, the homolog of the yeast DNA polymerase-ε (a leading-strand DNA polymerase), is required for plant fertility and meiosis. Mutations in POL2A cause reduced fertility and meiotic defects, including abnormal chromosome association, improper chromosome segregation, and fragmentation. Observation of prophase I cell distribution suggests that pol2a mutants likely delay progression of meiotic recombination. In addition, the residual COs in pol2a have reduced CO interference, and the double mutant of pol2a with mus81, which affects type II COs, displayed more severe defects than either single mutant, indicating that POL2A functions in the type I pathway. We hypothesize that sufficient leading-strand DNA elongation promotes formation of some type I COs. Given that meiotic recombination and DNA synthesis are conserved in divergent eukaryotes, this study and our previous study suggest a novel role for DNA synthesis in the differentiation of meiotic recombination pathways.

  17. Replisome-mediated Translesion Synthesis and Leading Strand Template Lesion Skipping Are Competing Bypass Mechanisms*

    Science.gov (United States)

    Gabbai, Carolina B.; Yeeles, Joseph T. P.; Marians, Kenneth J.

    2014-01-01

    A number of different enzymatic pathways have evolved to ensure that DNA replication can proceed past template base damage. These pathways include lesion skipping by the replisome, replication fork regression followed by either correction of the damage and origin-independent replication restart or homologous recombination-mediated restart of replication downstream of the lesion, and bypass of the damage by a translesion synthesis DNA polymerase. We report here that of two translesion synthesis polymerases tested, only DNA polymerase IV, not DNA polymerase II, could engage productively with the Escherichia coli replisome to bypass leading strand template damage, despite the fact that both enzymes are shown to be interacting with the replicase. Inactivation of the 3′ → 5′ proofreading exonuclease of DNA polymerase II did not enable bypass. Bypass by DNA polymerase IV required its ability to interact with the β clamp and act as a translesion polymerase but did not require its “little finger” domain, a secondary region of interaction with the β clamp. Bypass by DNA polymerase IV came at the expense of the inherent leading strand lesion skipping activity of the replisome, indicating that they are competing reactions. PMID:25301949

  18. Long inverted repeat transiently stalls DNA replication by forming hairpin structures on both leading and lagging strands.

    Science.gov (United States)

    Lai, Pey Jiun; Lim, Chew Theng; Le, Hang Phuong; Katayama, Tsutomu; Leach, David R F; Furukohri, Asako; Maki, Hisaji

    2016-02-01

    Long inverted repeats (LIRs), often found in eukaryotic genomes, are unstable in Escherichia coli where they are recognized by the SbcCD (the bacterial Mre11/Rad50 homologue), an endonuclease/exonuclease capable of cleaving hairpin DNA. It has long been postulated that LIRs form hairpin structures exclusively on the lagging-strand template during DNA replication, and SbcCD cleaves these hairpin-containing lagging strands to generate DNA double-strand breaks. Using a reconstituted oriC plasmid DNA replication system, we have examined how a replication fork behaves when it meets a LIR on DNA. We have shown that leading-strand synthesis stalls transiently within the upstream half of the LIR. Pausing of lagging-strand synthesis at the LIR was not clearly observed, but the pattern of priming sites for Okazaki fragment synthesis was altered within the downstream half of the LIR. We have found that the LIR on a replicating plasmid was cleaved by SbcCD with almost equal frequency on both the leading- and lagging-strand templates. These data strongly suggest that the LIR is readily converted to a cruciform DNA, before the arrival of the fork, creating SbcCD-sensitive hairpin structures on both leading and lagging strands. We propose a model for the replication-dependent extrusion of LIRs to form cruciform structures that transiently impede replication fork movement.

  19. A Major Role of DNA Polymerase δ in Replication of Both the Leading and Lagging DNA Strands.

    Science.gov (United States)

    Johnson, Robert E; Klassen, Roland; Prakash, Louise; Prakash, Satya

    2015-07-16

    Genetic studies with S. cerevisiae Polδ (pol3-L612M) and Polε (pol2-M644G) mutant alleles, each of which display a higher rate for the generation of a specific mismatch, have led to the conclusion that Polε is the primary leading strand replicase and that Polδ is restricted to replicating the lagging strand template. Contrary to this widely accepted view, here we show that Polδ plays a major role in the replication of both DNA strands, and that the paucity of pol3-L612M-generated errors on the leading strand results from their more proficient removal. Thus, the apparent lack of Polδ contribution to leading strand replication is due to differential mismatch removal rather than differential mismatch generation. Altogether, our genetic studies with Pol3 and Pol2 mutator alleles support the conclusion that Polδ, and not Polε, is the major DNA polymerase for carrying out both leading and lagging DNA synthesis. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. A major role of DNA polymerase δ in replication of both the leading and lagging DNA strands

    Science.gov (United States)

    Prakash, Louise; Prakash, Satya

    2015-01-01

    SUMMARY Genetic studies with S. cerevisiae Polδ (pol3-L612M) and Polε (pol2-M644G) mutant alleles, each of which display a higher rate for the generation of a specific mismatch, have led to the conclusion that Polε is the primary leading strand replicase and that Polδ is restricted to replicating the lagging strand template. Contrary to this widely accepted view, here we show that Polδ plays a major role in the replication of both DNA strands, and that the paucity of pol3-L612M generated errors on the leading strand results from their more proficient removal. Thus, the apparent lack of Polδ contribution to leading strand replication is due to differential mismatch removal rather than differential mismatch generation. Altogether, our genetic studies with Pol3 and Pol2 mutator alleles support the conclusion that Polδ, and not Polε, is the major DNA polymerase for carrying out both leading and lagging DNA synthesis. PMID:26145172

  1. Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes

    KAUST Repository

    Qu, Hongzhu

    2010-12-01

    Nucleotide compositional asymmetry (NCA) between leading and lagging strands (LeS and LaS) is dynamic and diverse among eubacterial genomes due to different mutation and selection forces. A thorough investigation is needed in order to study the relationship between nucleotide composition dynamics and gene distribution biases. Based on a collection of 364 eubacterial genomes that were grouped according to a DnaE-based scheme (DnaE1-DnaE1, DnaE2-DnaE1, and DnaE3-PolC), we investigated NCA and nucleotide composition gradients at three codon positions and found that there was universal G-enrichment on LeS among all groups. This was due to a strong selection for G-heading (codon position1 or cp1) codons and mutation pressure that led to more G-ending (cp3) codons. Moreover, a slight T-enrichment of LeS due to the mutation of cytosine deamination at cp3 was universal among DnaE1-DnaE1 and DnaE2-DnaE1 genomes, but was not clearly seen among DnaE3-PolC genomes, in which A-enrichment of LeS was proposed to be the effect of selections unique to polC and a mutation bias toward A-richness at cp1 that may be a result of transcription-coupled DNA repair mechanisms. Furthermore, strand-biased gene distribution enhances the purine-richness of LeS for DnaE3-PolC genomes and T-richness of LeS for DnaE1-DnaE1 and DnaE2-dnaE1 genomes. © 2010 Institut Pasteur.

  2. Single-molecule visualization of Saccharomyces cerevisiae leading-strand synthesis reveals dynamic interaction between MTC and the replisome.

    Science.gov (United States)

    Lewis, Jacob S; Spenkelink, Lisanne M; Schauer, Grant D; Hill, Flynn R; Georgescu, Roxanna E; O'Donnell, Michael E; van Oijen, Antoine M

    2017-09-18

    The replisome, the multiprotein system responsible for genome duplication, is a highly dynamic complex displaying a large number of different enzyme activities. Recently, the Saccharomyces cerevisiae minimal replication reaction has been successfully reconstituted in vitro. This provided an opportunity to uncover the enzymatic activities of many of the components in a eukaryotic system. Their dynamic behavior and interactions in the context of the replisome, however, remain unclear. We use a tethered-bead assay to provide real-time visualization of leading-strand synthesis by the S. cerevisiae replisome at the single-molecule level. The minimal reconstituted leading-strand replisome requires 24 proteins, forming the CMG helicase, the Pol ε DNA polymerase, the RFC clamp loader, the PCNA sliding clamp, and the RPA single-stranded DNA binding protein. We observe rates and product lengths similar to those obtained from ensemble biochemical experiments. At the single-molecule level, we probe the behavior of two components of the replication progression complex and characterize their interaction with active leading-strand replisomes. The Minichromosome maintenance protein 10 (Mcm10), an important player in CMG activation, increases the number of productive replication events in our assay. Furthermore, we show that the fork protection complex Mrc1-Tof1-Csm3 (MTC) enhances the rate of the leading-strand replisome threefold. The introduction of periods of fast replication by MTC leads to an average rate enhancement of a factor of 2, similar to observations in cellular studies. We observe that the MTC complex acts in a dynamic fashion with the moving replisome, leading to alternating phases of slow and fast replication.

  3. Cdc45 (cell division cycle protein 45) guards the gate of the Eukaryote Replisome helicase stabilizing leading strand engagement

    Science.gov (United States)

    Petojevic, Tatjana; Pesavento, James J.; Costa, Alessandro; Liang, Jingdan; Wang, Zhijun; Berger, James M.; Botchan, Michael R.

    2015-01-01

    DNA replication licensing is now understood to be the pathway that leads to the assembly of double hexamers of minichromosome maintenance (Mcm2–7) at origin sites. Cell division control protein 45 (Cdc45) and GINS proteins activate the latent Mcm2–7 helicase by inducing allosteric changes through binding, forming a Cdc45/Mcm2-7/GINS (CMG) complex that is competent to unwind duplex DNA. The CMG has an active gate between subunits Mcm2 and Mcm5 that opens and closes in response to nucleotide binding. The consequences of inappropriate Mcm2/5 gate actuation and the role of a side channel formed between GINS/Cdc45 and the outer edge of the Mcm2–7 ring for unwinding have remained unexplored. Here we uncover a novel function for Cdc45. Cross-linking studies trace the path of the DNA with the CMG complex at a fork junction between duplex and single strands with the bound CMG in an open or closed gate conformation. In the closed state, the lagging strand does not pass through the side channel, but in the open state, the leading strand surprisingly interacts with Cdc45. Mutations in the recombination protein J fold of Cdc45 that ablate this interaction diminish helicase activity. These data indicate that Cdc45 serves as a shield to guard against occasional slippage of the leading strand from the core channel. PMID:25561522

  4. Coordinated Leading and Lagging Strand DNA Synthesis by Using the Herpes Simplex Virus 1 Replication Complex and Minicircle DNA Templates ▿

    Science.gov (United States)

    Stengel, Gudrun; Kuchta, Robert D.

    2011-01-01

    The origin-specific replication of the herpes simplex virus 1 genome requires seven proteins: the helicase-primase (UL5-UL8-UL52), the DNA polymerase (UL30-UL42), the single-strand DNA binding protein (ICP8), and the origin-binding protein (UL9). We reconstituted these proteins, excluding UL9, on synthetic minicircular DNA templates and monitored leading and lagging strand DNA synthesis using the strand-specific incorporation of dTMP and dAMP. Critical features of the assays that led to efficient leading and lagging stand synthesis included high helicase-primase concentrations and a lagging strand template whose sequence resembled that of the viral DNA. Depending on the nature of the minicircle template, the replication complex synthesized leading and lagging strand products at molar ratios varying between 1:1 and 3:1. Lagging strand products (∼0.2 to 0.6 kb) were significantly shorter than leading strand products (∼2 to 10 kb), and conditions that stimulated primer synthesis led to shorter lagging strand products. ICP8 was not essential; however, its presence stimulated DNA synthesis and increased the length of both leading and lagging strand products. Curiously, human DNA polymerase α (p70-p180 or p49-p58-p70-p180), which improves the utilization of RNA primers synthesized by herpesvirus primase on linear DNA templates, had no effect on the replication of the minicircles. The lack of stimulation by polymerase α suggests the existence of a macromolecular assembly that enhances the utilization of RNA primers and may functionally couple leading and lagging strand synthesis. Evidence for functional coupling is further provided by our observations that (i) leading and lagging strand synthesis produce equal amounts of DNA, (ii) leading strand synthesis proceeds faster under conditions that disable primer synthesis on the lagging strand, and (iii) conditions that accelerate helicase-catalyzed DNA unwinding stimulate decoupled leading strand synthesis but not

  5. Bacillus subtilis DNA polymerases, PolC and DnaE, are required for both leading and lagging strand synthesis in SPP1 origin-dependent DNA replication.

    Science.gov (United States)

    Seco, Elena M; Ayora, Silvia

    2017-08-21

    Firmicutes have two distinct replicative DNA polymerases, the PolC leading strand polymerase, and PolC and DnaE synthesizing the lagging strand. We have reconstituted in vitro Bacillus subtilis bacteriophage SPP1 θ-type DNA replication, which initiates unidirectionally at oriL. With this system we show that DnaE is not only restricted to lagging strand synthesis as previously suggested. DnaG primase and DnaE polymerase are required for initiation of DNA replication on both strands. DnaE and DnaG synthesize in concert a hybrid RNA/DNA 'initiation primer' on both leading and lagging strands at the SPP1 oriL region, as it does the eukaryotic Pol α complex. DnaE, as a RNA-primed DNA polymerase, extends this initial primer in a reaction modulated by DnaG and one single-strand binding protein (SSB, SsbA or G36P), and hands off the initiation primer to PolC, a DNA-primed DNA polymerase. Then, PolC, stimulated by DnaG and the SSBs, performs the bulk of DNA chain elongation at both leading and lagging strands. Overall, these modulations by the SSBs and DnaG may contribute to the mechanism of polymerase switch at Firmicutes replisomes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method

    Directory of Open Access Journals (Sweden)

    Yu Xiu-Juan

    2007-10-01

    Full Text Available Abstract Background The nucleotide compositional asymmetry between the leading and lagging strands in bacterial genomes has been the subject of intensive study in the past few years. It is interesting to mention that almost all bacterial genomes exhibit the same kind of base asymmetry. This work aims to investigate the strand biases in Chlamydia muridarum genome and show the potential of the Z curve method for quantitatively differentiating genes on the leading and lagging strands. Results The occurrence frequencies of bases of protein-coding genes in C. muridarum genome were analyzed by the Z curve method. It was found that genes located on the two strands of replication have distinct base usages in C. muridarum genome. According to their positions in the 9-D space spanned by the variables u1 – u9 of the Z curve method, K-means clustering algorithm can assign about 94% of genes to the correct strands, which is a few percent higher than those correctly classified by K-means based on the RSCU. The base usage and codon usage analyses show that genes on the leading strand have more G than C and more T than A, particularly at the third codon position. For genes on the lagging strand the biases is reverse. The y component of the Z curves for the complete chromosome sequences show that the excess of G over C and T over A are more remarkable in C. muridarum genome than in other bacterial genomes without separating base and/or codon usages. Furthermore, for the genomes of Borrelia burgdorferi, Treponema pallidum, Chlamydia muridarum and Chlamydia trachomatis, in which distinct base and/or codon usages have been observed, closer phylogenetic distance is found compared with other bacterial genomes. Conclusion The nature of the strand biases of base composition in C. muridarum is similar to that in most other bacterial genomes. However, the base composition asymmetry between the leading and lagging strands in C. muridarum is more significant than that in

  7. Capillary electrophoresis-single strand conformation polymorphism for the detection of multiple mutations leading to tuberculosis drug resistance.

    Science.gov (United States)

    Krothapalli, Sowmya; May, Michael K; Hestekin, Christa N

    2012-10-01

    Drug resistant tuberculosis (TB) is a major health problem in both developed and developing countries. Mutations in the Mycobacterium (M.) tuberculosis bacterial genome, such as those to the rpoB gene and mabA-inhA promoter region, have been linked to TB drug resistance in against rifampicin and isoniazid, respectively. The rapid, accurate, and inexpensive identification of these and other mutations leading to TB drug resistance is an essential tool for improving human health. Capillary electrophoresis (CE) single strand conformation polymorphism (SSCP) can be a highly sensitive technique for the detection of genetic mutation that has not been previously explored for drug resistance mutations in M. tuberculosis. This work explores the potential of CE-SSCP through the optimization of variables such as polymer separation matrix concentration, capillary wall coating, electric field strength, and temperature on resolution of mutation detection. The successful detection of an rpoB gene mutation and two mabA-inhA promoter region mutations while simultaneously differentiating a TB-causing mycobacteria from a non-TB bacteria was accomplished using the optimum conditions of 4.5% (w/v) PDMA in a PDMA coated capillary at 20°C using a separation voltage of 278 V/cm. This multiplexed analysis that can be completed in a few hours demonstrates the potential of CE-SSCP to be an inexpensive and rapid analysis method.

  8. Oncogenic ras-driven cancer cell vesiculation leads to emission of double-stranded DNA capable of interacting with target cells

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Tae Hoon; Chennakrishnaiah, Shilpa [Montreal Children’s Hospital, Research Institute of McGill University Health Centre, McGill University, Montreal, Quebec (Canada); Audemard, Eric [McGill University and Genome Quebec Innovation Centre, Montreal, Quebec (Canada); Montermini, Laura; Meehan, Brian [Montreal Children’s Hospital, Research Institute of McGill University Health Centre, McGill University, Montreal, Quebec (Canada); Rak, Janusz, E-mail: janusz.rak@mcgill.ca [Montreal Children’s Hospital, Research Institute of McGill University Health Centre, McGill University, Montreal, Quebec (Canada)

    2014-08-22

    Highlights: • Oncogenic H-ras stimulates emission of extracellular vesicles containing double-stranded DNA. • Vesicle-associated extracellular DNA contains mutant N-ras sequences. • Vesicles mediate intercellular transfer of mutant H-ras DNA to normal fibroblasts where it remains for several weeks. • Fibroblasts exposed to vesicles containing H-ras DNA exhibit increased proliferation. - Abstract: Cell free DNA is often regarded as a source of genetic cancer biomarkers, but the related mechanisms of DNA release, composition and biological activity remain unclear. Here we show that rat epithelial cell transformation by the human H-ras oncogene leads to an increase in production of small, exosomal-like extracellular vesicles by viable cancer cells. These EVs contain chromatin-associated double-stranded DNA fragments covering the entire host genome, including full-length H-ras. Oncogenic N-ras and SV40LT sequences were also found in EVs emitted from spontaneous mouse brain tumor cells. Disruption of acidic sphingomyelinase and the p53/Rb pathway did not block emission of EV-related oncogenic DNA. Exposure of non-transformed RAT-1 cells to EVs containing mutant H-ras DNA led to the uptake and retention of this material for an extended (30 days) but transient period of time, and stimulated cell proliferation. Thus, our study suggests that H-ras-mediated transformation stimulates vesicular emission of this histone-bound oncogene, which may interact with non-transformed cells.

  9. Spontaneous tumor development in bone marrow-rescued DNA-PKcs(3A/3A) mice due to dysfunction of telomere leading strand deprotection.

    Science.gov (United States)

    Zhang, S; Matsunaga, S; Lin, Y-F; Sishc, B; Shang, Z; Sui, J; Shih, H-Y; Zhao, Y; Foreman, O; Story, M D; Chen, D J; Chen, B P C

    2016-07-28

    Phosphorylation of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) at the Thr2609 cluster is essential for its complete function in DNA repair and tissue stem cell homeostasis. This phenomenon is demonstrated by congenital bone marrow failure occurring in DNA-PKcs(3A/3A) mutant mice, which require bone marrow transplantation (BMT) to prevent early mortality. Surprisingly, an increased incidence of spontaneous tumors, especially skin cancer, was observed in adult BMT-rescued DNA-PKcs(3A/3A) mice. Upon further investigation, we found that spontaneous γH2AX foci occurred in DNA-PKcs(3A/3A) skin biopsies and primary keratinocytes and that these foci overlapped with telomeres during mitosis, indicating impairment of telomere replication and maturation. Consistently, we observed significantly elevated frequencies of telomere fusion events in DNA-PKcs(3A/3A) cells as compared with wild-type and DNA-PKcs-knockout cells. In addition, a previously identified DNA-PKcs Thr2609Pro mutation, found in breast cancer, also induces a similar impairment of telomere leading-end maturation. Taken together, our current analyses indicate that the functional DNA-PKcs T2609 cluster is required to facilitate telomere leading strand maturation and prevention of genomic instability and cancer development.

  10. Bypass of a 5',8-cyclopurine-2'-deoxynucleoside by DNA polymerase β during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks.

    Science.gov (United States)

    Jiang, Zhongliang; Xu, Meng; Lai, Yanhao; Laverde, Eduardo E; Terzidis, Michael A; Masi, Annalisa; Chatgilialoglu, Chryssostomos; Liu, Yuan

    2015-09-01

    5',8-Cyclopurine-2'-deoxynucleosides including 5',8-cyclo-dA (cdA) and 5',8-cyclo-dG (cdG) are induced by hydroxyl radicals resulting from oxidative stress such as ionizing radiation. 5',8-cyclopurine-2'-deoxynucleoside lesions are repaired by nucleotide excision repair with low efficiency, thereby leading to their accumulation in the human genome and lesion bypass by DNA polymerases during DNA replication and base excision repair (BER). In this study, for the first time, we discovered that DNA polymerase β (pol β) efficiently bypassed a 5'R-cdA, but inefficiently bypassed a 5'S-cdA during DNA replication and BER. We found that cell extracts from pol β wild-type mouse embryonic fibroblasts exhibited significant DNA synthesis activity in bypassing a cdA lesion located in replication and BER intermediates. However, pol β knock-out cell extracts exhibited little DNA synthesis to bypass the lesion. This indicates that pol β plays an important role in bypassing a cdA lesion during DNA replication and BER. Furthermore, we demonstrated that pol β inserted both a correct and incorrect nucleotide to bypass a cdA at a low concentration. Nucleotide misinsertion was significantly stimulated by a high concentration of pol β, indicating a mutagenic effect induced by pol β lesion bypass synthesis of a 5',8-cyclopurine-2'-deoxynucleoside. Moreover, we found that bypass of a 5'S-cdA by pol β generated an intermediate that failed to be extended by pol β, resulting in accumulation of single-strand DNA breaks. Our study provides the first evidence that pol β plays an important role in bypassing a 5',8-cyclo-dA during DNA replication and repair, as well as new insight into mutagenic effects and genome instability resulting from pol β bypassing of a cdA lesion.

  11. Lead

    Science.gov (United States)

    ... found? Who is at risk? What are the health effects of lead? Get educational material about lead Get certified as a Lead Abatement Worker, or other abatement discipline Lead in drinking water Lead air pollution Test your child Check and maintain your home ...

  12. Lead

    Science.gov (United States)

    ... Chapter 6 Chapter 7 Chapter 8 Chapter 9 Appendix I Appendix II Tables Figures State Programs Alabama Alaska Arizona ... Tool Kit Resources Healthy Homes and Lead Poisoning Prevention Training Center (HHLPPTC) Training Tracks File Formats Help: ...

  13. Fair Exchange in Strand Spaces

    Directory of Open Access Journals (Sweden)

    Joshua D. Guttman

    2009-10-01

    Full Text Available Many cryptographic protocols are intended to coordinate state changes among principals. Exchange protocols coordinate delivery of new values to the participants, e.g. additions to the set of values they possess. An exchange protocol is fair if it ensures that delivery of new values is balanced: If one participant obtains a new possession via the protocol, then all other participants will, too. Fair exchange requires progress assumptions, unlike some other protocol properties. The strand space model is a framework for design and verification of cryptographic protocols. A strand is a local behavior of a single principal in a single session of a protocol. A bundle is a partially ordered global execution built from protocol strands and adversary activities. The strand space model needs two additions for fair exchange protocols. First, we regard the state as a multiset of facts, and we allow strands to cause changes in this state via multiset rewriting. Second, progress assumptions stipulate that some channels are resilient-and guaranteed to deliver messages-and some principals are assumed not to stop at certain critical steps. This method leads to proofs of correctness that cleanly separate protocol properties, such as authentication and confidentiality, from invariants governing state evolution. G. Wang's recent fair exchange protocol illustrates the approach.

  14. Alaska Beluga Strandings

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NMFS is mandated by the Marine Mammal Protection Act (MMPA) to collect reports of marine mammal stranding events. This particular catalogue item is specific to the...

  15. Stranded Specimen Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Marine Mammal and Turtle Division collects data about individual cetaceans and sea turtles that come ashore, or strand on the beach. The date and location of...

  16. Whale strandings: hypothesis.

    Science.gov (United States)

    Mawson, A R

    1978-01-01

    The hypothesis is presented that whales become stranded inadvertently as a consequence of seeking stimulation. The animals enter shallow water in order to roll over, bask, and rub themselves in the sand, and are trapped by the receding tide. It suggested that stimulation-seeking behavior (and stranding) reflects a general sympathetic nervous system response which may be due to a number of factors such as pain, discomfort, reproductive state, and other biorhythmic changes.

  17. Bubbles in live-stranded dolphins.

    Science.gov (United States)

    Dennison, S; Moore, M J; Fahlman, A; Moore, K; Sharp, S; Harry, C T; Hoppe, J; Niemeyer, M; Lentell, B; Wells, R S

    2012-04-07

    Bubbles in supersaturated tissues and blood occur in beaked whales stranded near sonar exercises, and post-mortem in dolphins bycaught at depth and then hauled to the surface. To evaluate live dolphins for bubbles, liver, kidneys, eyes and blubber-muscle interface of live-stranded and capture-release dolphins were scanned with B-mode ultrasound. Gas was identified in kidneys of 21 of 22 live-stranded dolphins and in the hepatic portal vasculature of 2 of 22. Nine then died or were euthanized and bubble presence corroborated by computer tomography and necropsy, 13 were released of which all but two did not re-strand. Bubbles were not detected in 20 live wild dolphins examined during health assessments in shallow water. Off-gassing of supersaturated blood and tissues was the most probable origin for the gas bubbles. In contrast to marine mammals repeatedly diving in the wild, stranded animals are unable to recompress by diving, and thus may retain bubbles. Since the majority of beached dolphins released did not re-strand it also suggests that minor bubble formation is tolerated and will not lead to clinically significant decompression sickness.

  18. Strand SPA & Konverentsikeskus

    Index Scriptorium Estoniae

    2008-01-01

    Strand SPA & Konverentsikeskus on Pärnu suurim äri- ja konverentsiklientidele suunatud hotell, mis klientide seas on hinnatud just selle kompleksuse tõttu, kuna kõik, mida külaline vajab ja soovib, on olemas ühe katuse all

  19. Op het strand

    NARCIS (Netherlands)

    Boer, M.G. de

    2010-01-01

    SAMENVATTING Het woord spiaggia ‘strand’ wordt besproken binnen het veld van woorden die een scheiding tussen land en water aangeven. Hierbij worden historisch verschillende scenario’s (frames) onderscheiden, al naar de functie de het strand destijds had. Spiaggia wordt vergeleken met zijn synoniem

  20. Strand SPA & Konverentsikeskus

    Index Scriptorium Estoniae

    2008-01-01

    Strand SPA & Konverentsikeskus on Pärnu suurim äri- ja konverentsiklientidele suunatud hotell, mis klientide seas on hinnatud just selle kompleksuse tõttu, kuna kõik, mida külaline vajab ja soovib, on olemas ühe katuse all

  1. LHC superconducting strand

    CERN Multimedia

    Patrice Loiez

    1999-01-01

    This cross-section through a strand of superconducting matieral as used in the LHC shows the 8000 Niobium-Titanium filaments embedded like a honeycomb in copper. When cooled to 1.9 degrees above absolute zero in the LHC accelerator, these filaments will have zero resistance and so will carry a high electric current with no energy loss.

  2. Op het strand

    NARCIS (Netherlands)

    Boer, M.G. de

    2010-01-01

    SAMENVATTING Het woord spiaggia ‘strand’ wordt besproken binnen het veld van woorden die een scheiding tussen land en water aangeven. Hierbij worden historisch verschillende scenario’s (frames) onderscheiden, al naar de functie de het strand destijds had. Spiaggia wordt vergeleken met zijn

  3. Folding DNA origami from a double-stranded source of scaffold

    Science.gov (United States)

    Högberg, Björn; Liedl, Tim; Shih, William M.

    2009-01-01

    Combined heat and chemical denaturation of double-stranded DNA scaffold strands in the presence of staple strands, followed by a sudden temperature drop and then stepwise dialysis to remove the chemical denaturant, leads to self-assembly of two distinct DNA-origami structures. PMID:19566089

  4. The causes of whale strandings.

    Science.gov (United States)

    Cordes, D O

    1982-03-01

    Strandings of cetaceans (whales and dolphins) is probably the result of a sequence of events rather than a simple cause-and-effect relationship. Strandings of solitary animals are more common than massed and generally thought to be due to severe disease. Mass strandings (three to several hundred individuals) are less common, but very spectacular. Mass strandings are considered to be due to a complex of factors in which behavioural factors are probably important, severe disease making an unimportant, or negligible contribution. There may be interaction of physical conditions (weather, tides, currents, coastline) and biological conditions (predators, feeding, disturbance of echolocation and disease) which result in stranding. One postulated reason for stranding is that it is dependent on instinctive behaviour, deeply located in subcortical areas of the brain, which provokes cetaceans to seek refuge ashore when under stress.

  5. Single strand annealing and ATP-independent strand exchange activities of yeast and human DNA2: possible role in Okazaki fragment maturation.

    Science.gov (United States)

    Masuda-Sasa, Taro; Polaczek, Piotr; Campbell, Judith L

    2006-12-15

    The Dna2 protein is a multifunctional enzyme with 5'-3' DNA helicase, DNA-dependent ATPase, 3' exo/endonuclease, and 5' exo/endonuclease. The enzyme is highly specific for structures containing single-stranded flaps adjacent to duplex regions. We report here two novel activities of both the yeast and human Dna2 helicase/nuclease protein: single strand annealing and ATP-independent strand exchange on short duplexes. These activities are independent of ATPase/helicase and nuclease activities in that mutations eliminating either nuclease or ATPase/helicase do not inhibit strand annealing or strand exchange. ATP inhibits strand exchange. A model rationalizing the multiple catalytic functions of Dna2 and leading to its coordination with other enzymes in processing single-stranded flaps during DNA replication and repair is presented.

  6. Distinct signaling pathways leading to the induction of human β-defensin 2 by stimulating an electrolyticaly-generated acid functional water and double strand RNA in oral epithelial cells.

    Science.gov (United States)

    Gojoubori, Takahiro; Nishio, Yukina; Asano, Masatake; Nishida, Tetsuya; Komiyama, Kazuo; Ito, Koichi

    2014-04-01

    Defensins, a major family of cationic antimicrobial peptides, play important roles in innate immunity. In the present study, we investigated whether double-stranded RNA (dsRNA), a by-product of RNA virus replication, can induce human β-defensins-2 (hBD-2) expression in oral epithelial cells (OECs). We also examined the hBD-2-inducible activity of acid-electrolyzed functional water (FW). The results indicated that both dsRNA- and FW-induced hBD-2 expression in OECs. The induction efficiency was much higher for FW than for dsRNA. FW-induced production of hBD-2 was clearly observed by immunofluorescence staining. A luciferase assay was performed with 1.2 kb of the 5'-untranslated region (5'-UTR) of the hBD-2 gene. The results indicated that the nuclear factor-kappa B (NF-κB)-binding site proximal to the translation initiation site was indispensable for dsRNA-stimulated hBD-2 expression, but not in the case of FW. Moreover, FW-stimulated hBD-2 expression did not depend on NF-κB activity; instead, FW inhibited NF-κB activity. Pretreatment of the cells with specific inhibitors against NF-κB further confirmed NF-κB-independent hBD-2 induction by FW. In analogy to the results for intestinal epithelial cells (IECs), the dsRNA signal, but not FW, was sensed by toll-like receptor 3 (TLR3) in OECs. These results suggested that hBD-2 expression induced by dsRNA and FW is regulated by distinct mechanisms in OECs.

  7. Effect of subelement spacing in RRP Nb3Sn strands

    Energy Technology Data Exchange (ETDEWEB)

    Barzi, E.; Turrioni, D.; /Fermilab; Alsharo' a, M.; /MUONS Inc., Batavia; Field, M.; Hong, S.; Parrell, J.; Yamada, R.; /Fermilab; Zhang, Y.; Zlobin, A.; /Fermilab

    2007-10-01

    The Restacked Rod Process (RRP) is the Nb{sub 3}Sn strand technology presently producing the largest critical current densities at 4.2 K and 12 T. However, when subject to plastic deformation, RRP subelements (SE) were found to merge into each other, creating larger filaments with a somewhat continuous barrier. In this case, the strand sees a larger effective filament size, d{sub eff}, and its instability can dramatically increase locally leading to cable quench. To reduce and possibly eliminate this effect, Oxford Instruments Superconducting Technology (OST) developed for FNAL a modified RRP strand design with larger Cu spacing between SE's arranged in a 60/61 array. Strand samples of this design with sizes from 0.7 to 1 mm were first evaluated for transport current properties. A comparison study was then performed between the regular 54/61 and the modified 60/61 design using 0.7 mm round and deformed strands. Finite element modeling of the deformed strands was also performed with ANSYS.

  8. Hearing loss in stranded odontocete dolphins and whales.

    Directory of Open Access Journals (Sweden)

    David Mann

    Full Text Available The causes of dolphin and whale stranding can often be difficult to determine. Because toothed whales rely on echolocation for orientation and feeding, hearing deficits could lead to stranding. We report on the results of auditory evoked potential measurements from eight species of odontocete cetaceans that were found stranded or severely entangled in fishing gear during the period 2004 through 2009. Approximately 57% of the bottlenose dolphins and 36% of the rough-toothed dolphins had significant hearing deficits with a reduction in sensitivity equivalent to severe (70-90 dB or profound (>90 dB hearing loss in humans. The only stranded short-finned pilot whale examined had profound hearing loss. No impairments were detected in seven Risso's dolphins from three different stranding events, two pygmy killer whales, one Atlantic spotted dolphin, one spinner dolphin, or a juvenile Gervais' beaked whale. Hearing impairment could play a significant role in some cetacean stranding events, and the hearing of all cetaceans in rehabilitation should be tested.

  9. Cryptography with DNA binary strands.

    Science.gov (United States)

    Leier, A; Richter, C; Banzhaf, W; Rauhe, H

    2000-06-01

    Biotechnological methods can be used for cryptography. Here two different cryptographic approaches based on DNA binary strands are shown. The first approach shows how DNA binary strands can be used for steganography, a technique of encryption by information hiding, to provide rapid encryption and decryption. It is shown that DNA steganography based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages. The second approach shown here is based on steganography and a method of graphical subtraction of binary gel-images. It can be used to constitute a molecular checksum and can be combined with the first approach to support encryption. DNA cryptography might become of practical relevance in the context of labelling organic and inorganic materials with DNA 'barcodes'.

  10. Double stranded nucleic acid biochips

    Energy Technology Data Exchange (ETDEWEB)

    Chernov, Boris; Golova, Julia

    2006-05-23

    This invention describes a new method of constructing double-stranded DNA (dsDNA) microarrays based on the use of pre-synthesized or natural DNA duplexes without a stem-loop structure. The complementary oligonucleotide chains are bonded together by a novel connector that includes a linker for immobilization on a matrix. A non-enzymatic method for synthesizing double-stranded nucleic acids with this novel connector enables the construction of inexpensive and robust dsDNA/dsRNA microarrays. DNA-DNA and DNA-protein interactions are investigated using the microarrays.

  11. Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis

    NARCIS (Netherlands)

    Hamdan, Samir M.; Loparo, Joseph J.; Takahashi, Masateru; Richardson, Charles C.; Oijen, Antoine M. van

    2009-01-01

    In all organisms, the protein machinery responsible for the replication of DNA, the replisome, is faced with a directionality problem. The antiparallel nature of duplex DNA permits the leading-strand polymerase to advance in a continuous fashion, but forces the lagging-strand polymerase to

  12. Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis

    NARCIS (Netherlands)

    Hamdan, Samir M.; Loparo, Joseph J.; Takahashi, Masateru; Richardson, Charles C.; Oijen, Antoine M. van

    2009-01-01

    In all organisms, the protein machinery responsible for the replication of DNA, the replisome, is faced with a directionality problem. The antiparallel nature of duplex DNA permits the leading-strand polymerase to advance in a continuous fashion, but forces the lagging-strand polymerase to synthesiz

  13. Excess single-stranded DNA inhibits meiotic double-strand break repair.

    Directory of Open Access Journals (Sweden)

    Rebecca Johnson

    2007-11-01

    Full Text Available During meiosis, self-inflicted DNA double-strand breaks (DSBs are created by the protein Spo11 and repaired by homologous recombination leading to gene conversions and crossovers. Crossover formation is vital for the segregation of homologous chromosomes during the first meiotic division and requires the RecA orthologue, Dmc1. We analyzed repair during meiosis of site-specific DSBs created by another nuclease, VMA1-derived endonuclease (VDE, in cells lacking Dmc1 strand-exchange protein. Turnover and resection of the VDE-DSBs was assessed in two different reporter cassettes that can repair using flanking direct repeat sequences, thereby obviating the need for a Dmc1-dependent DNA strand invasion step. Access of the single-strand binding complex replication protein A, which is normally used in all modes of DSB repair, was checked in chromatin immunoprecipitation experiments, using antibody against Rfa1. Repair of the VDE-DSBs was severely inhibited in dmc1Delta cells, a defect that was associated with a reduction in the long tract resection required to initiate single-strand annealing between the flanking repeat sequences. Mutants that either reduce Spo11-DSB formation or abolish resection at Spo11-DSBs rescued the repair block. We also found that a replication protein A component, Rfa1, does not accumulate to expected levels at unrepaired single-stranded DNA (ssDNA in dmc1Delta cells. The requirement of Dmc1 for VDE-DSB repair using flanking repeats appears to be caused by the accumulation of large quantities of ssDNA that accumulate at Spo11-DSBs when Dmc1 is absent. We propose that these resected DSBs sequester both resection machinery and ssDNA binding proteins, which in wild-type cells would normally be recycled as Spo11-DSBs repair. The implication is that repair proteins are in limited supply, and this could reflect an underlying mechanism for regulating DSB repair in wild-type cells, providing protection from potentially harmful effects

  14. A methodology to identify stranded generation facilities and estimate stranded costs for Louisiana's electric utility industry

    Science.gov (United States)

    Cope, Robert Frank, III

    1998-12-01

    to each set of parameters, lead to the identification of stranded generation facilities. Stranded costs of non-dispatched and uneconomically dispatched generation facilities can then be estimated to indicate, arguably, the largest portion of restructuring transition costs as the industry is transformed from its present monopolistic structure to a competitive one.

  15. Southeast US Historical Marine Mammal Stranding Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data on marine mammal strandings are collected by the Southeast Marine Mammal Stranding Network. Basic data on the location, species identification, animal...

  16. Hyperchromicity and strand separation in bacterial DNA.

    Science.gov (United States)

    FREIFELDER, D; DAVISON, P F

    1962-05-01

    Studies of the per cent of strand separation of N(14)-N(15) hybrid coli DNA heated to various temperatures in formaldehyde have shown that the process of strand separation is a function of temperature and formaldehyde concentration and is directly related to the measured hyperchromicity. No strands separate until about 75 per cent of full hyperchromicity is obtained, and even at apparently full hyperchromicity a large fraction of the strands may be held together, possibly by guanine-cytosine-rich regions.

  17. ELASTIC DEFORMATION ANALYSIS OF MULTILA YERED STRANDS

    Institute of Scientific and Technical Information of China (English)

    王世文; 冯继玲; 杨兆建; 连香姣

    1999-01-01

    This paper describes a general model for the mechanical behavior studying of general wire rope strand. An exact solution of the deformation characteristics was given when the strands is under tensile and torsional loads. The theoretical results are useful in evaluating the extensional and torsional moduli of rigidity for the strands. Finally, a simple design criterion is established for the nonrotating ropes.

  18. Transient stability of LHC strands

    CERN Document Server

    Baynham, D Elwyn; Coombs, R C; Bauer, P; Wolf, R

    1999-01-01

    The Large Hadron Collider (LHC) machine will operate at 1.9 K in order to achieve the high bending fields required in the dipole magnets. The cable and coil matrix is designed to be 'porous' in order to allow the He II coolant to $9 penetrate within the cable for stability enhancement. This paper describes transient stability measurements and theoretical modelling carried out on single strands from the LHC cable. The experimental work has been carried out at the $9 Rutherford Appleton Laboratory under an agreement with CERN. The aim of the experimental work has been to measure the influence of the strand surface treatment on the quench energy. The surface treatment, oxidized copper, tin-silver, $9 nickel etc., determines the transient heat transfer coefficients to the He II under high heat flux, short timescale (approximately 20 microseconds) conditions. The test equipment, based on an inductive heating technique, is described $9 and quench energy measurements presented. The experimental results are compared ...

  19. Two-Domain DNA Strand Displacement

    CERN Document Server

    Cardelli, Luca

    2010-01-01

    We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose restrictions on the single strands they interact with: we consider only two-domain single strands consisting of one toehold domain and one recognition domain. We study fork and join signal-processing gates based on these structures, and we show that these systems are amenable to formalization and to mechanical verification.

  20. Flexural behavior of bonded post-tensioned concrete beams under strand corrosion

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xuhui [College of Civil Engineering and Mechanics, Xiangtan University, 411105 Xiangtan (China); School of Civil Engineering and Architecture, Changsha University of Science & Technology, 410114 Changsha (China); Industry Key Laboratory of Traffic Infrastructure Security Risk Management (CSUST), 410114 Changsha (China); Wang, Lei, E-mail: leiwlei@hotmail.com [School of Civil Engineering and Architecture, Changsha University of Science & Technology, 410114 Changsha (China); Industry Key Laboratory of Traffic Infrastructure Security Risk Management (CSUST), 410114 Changsha (China); Zhang, Jianren; Ma, Yafei [School of Civil Engineering and Architecture, Changsha University of Science & Technology, 410114 Changsha (China); Industry Key Laboratory of Traffic Infrastructure Security Risk Management (CSUST), 410114 Changsha (China); Liu, Yongming [School for Engineering of Matter, Transport and Energy, Arizona State University, 85281 Tempe, AZ (United States)

    2017-03-15

    Highlights: • Flexural behavior of bonded PT beams with strand corrosion is experimental tested. • Cracking, stiffness, ultimate strength, failure & ductility of beams are clarified. • A coefficient is proposed to measure incompatible strain between strand & concrete. - Abstract: An experimental test is performed to investigate the flexural behavior of bonded post-tensioned concrete beams under strand corrosion. Eight beams are designed and subjected to accelerated method to different corrosion levels. The initial stiffness of beams is observed by cyclic loading-unloading test during the corrosion procedure. Corrosion effects on concrete cracking, post-cracking stiffness, ultimate strength, failure mode and ductility are then clarified by the flexural test. And, a coefficient is introduced to quantify the incompatible strain between corroded strand and concrete. Results show that the prestress force loss of strand has almost the linear relation with corrosion loss. Strand corrosion affects slightly the initial stiffness of beam before flexural cracking, but degrades significantly the post-cracking stiffness of beam as the corrosion loss exceeds 27.0%. Slight corrosion of strand has little effects on beams flexural behavior. The severe corrosion, however, decreases the number of crack, changes the failure mode form the concrete crushing to strand rupture, degrades the ductility and the ultimate strength of beams, and leads to the incompatible strain between strand and concrete. In the present test, the incompatible strain decreases about 20% of the flexural strength as the corrosion loss exceeds 27.0%.

  1. The Drosophila HP1 homologue Rhino is required for transposon silencing and piRNA production by dual strand clusters

    Science.gov (United States)

    Klattenhoff, Carla; Xi, Hualin; Li, Chengjian; Lee, Soohyun; Xu, Jia; Khurana, Jaspreet S.; Zhang, Fan; Schultz, Nadine; Koppetsch, Birgit S.; Nowosielska, Anetta; Seitz, Herve; Zamore, Phillip D.; Weng, Zhiping; Theurkauf, William E.

    2009-01-01

    Summary piRNAs silence transposons and maintain genome integrity during germ-line development. In Drosophila, transposon-rich heterochromatic clusters encode piRNAs either on both genomic strands (dual-strand clusters) or predominantly one genomic strand (uni-strand clusters). Primary piRNAs derived from these clusters are proposed to drive a ping-pong amplification cycle catalyzed by proteins that localize to the perinuclear nuage. We show that the HP1 homologue Rhino is required for nuage organization, transposon silencing, and ping-pong amplification of piRNAs. rhi mutations virtually eliminate piRNAs from the dual-strand clusters and block production of putative precursor RNAs from both strands of the major 42AB dual-strand cluster, but do not block production of transcripts or piRNAs from the uni-strand clusters. Furthermore, Rhino protein associates with the 42AB dual-strand cluster, but does not bind to uni-strand cluster 2 or flamenco. Rhino thus appears to promote transcription of dual-strand clusters, leading to production of piRNAs that drive the ping-pong amplification cycle. PMID:19732946

  2. Why double-stranded RNA resists condensation

    Energy Technology Data Exchange (ETDEWEB)

    Tolokh, Igor S.; Pabit, Suzette; Katz, Andrea M.; Chen, Yujie; Drozdetski, Aleksander; Baker, Nathan A.; Pollack, Lois; Onufriev, Alexey

    2014-09-15

    The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to attraction between the negatively charged helices and eventually to condensation. Surprisingly, this effect is suppressed in double-stranded RNA, which carries the same charge as the DNA, but assumes a different double helical form. However, additional characterization of short (25 base-pairs) nucleic acid (NA) duplex structures by circular dichroism shows that measured differences in condensation are not solely determined by duplex helical geometry. Here we combine experiment, theory, and atomistic simulations to propose a mechanism that connects the observed variations in condensation of short NA duplexes with the spatial variation of cobalt hexammine (CoHex) binding at the NA duplex surface. The atomistic picture that emerged showed that CoHex distributions around the NA reveals two major NA-CoHex binding modes -- internal and external -- distinguished by the proximity of bound CoHex to the helical axis. Decreasing trends in experimentally observed condensation propensity of the four studied NA duplexes (from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA:RNA hybrid, to A-like RNA) are explained by the progressive decrease of a single quantity: the fraction of CoHex ions in the external binding mode. Thus, while NA condensation depends on a complex interplay between various structural and sequence features, our coupled experimental and theoretical results suggest a new model in which a single parameter connects the NA condensation propensity with geometry and sequence dependence of CoHex binding.

  3. Transcription-induced mutational strand bias and its effect on substitution rates in human genes.

    Science.gov (United States)

    Mugal, Carina F; von Grünberg, Hans-Hennig; Peifer, Martin

    2009-01-01

    If substitution rates are not the same on the two complementary DNA strands, a substitution is considered strand asymmetric. Such substitutional strand asymmetries are determined here for the three most frequent types of substitution on the human genome (C --> T, A --> G, and G --> T). Substitution rate differences between both strands are estimated for 4,590 human genes by aligning all repeats occurring within the introns with their ancestral consensus sequences. For 1,630 of these genes, both coding strand and noncoding strand rates could be compared with rates in gene-flanking regions. All three rates considered are found to be on average higher on the coding strand and lower on the transcribed strand in comparison to their values in the gene-flanking regions. This finding points to the simultaneous action of rate-increasing effects on the coding strand--such as increased adenine and cytosine deamination--and transcription-coupled repair as a rate-reducing effect on the transcribed strand. The common behavior of the three rates leads to strong correlations of the rate asymmetries: Whenever one rate is strand biased, the other two rates are likely to show the same bias. Furthermore, we determine all three rate asymmetries as a function of time: the A --> G and G --> T rate asymmetries are both found to be constant in time, whereas the C --> T rate asymmetry shows a pronounced time dependence, an observation that explains the difference between our results and those of an earlier work by Green et al. (2003. Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet. 33:514-517.). Finally, we show that in addition to transcription also the replication process biases the substitution rates in genes.

  4. Hyperchromicity and Strand Separation in Bacterial DNA

    Science.gov (United States)

    Freifelder, David; Davison, Peter F.

    1962-01-01

    Studies of the per cent of strand separation of N14-N15 hybrid coli DNA heated to various temperatures in formaldehyde have shown that the process of strand separation is a function of temperature and formaldehyde concentration and is directly related to the measured hyperchromicity. No strands separate until about 75 per cent of full hyperchromicity is obtained, and even at apparently full hyperchromicity a large fraction of the strands may be held together, possibly by guanine-cytosine-rich regions. PMID:13894962

  5. Tolerance of DNA Mismatches in Dmc1 Recombinase-mediated DNA Strand Exchange.

    Science.gov (United States)

    Borgogno, María V; Monti, Mariela R; Zhao, Weixing; Sung, Patrick; Argaraña, Carlos E; Pezza, Roberto J

    2016-03-04

    Recombination between homologous chromosomes is required for the faithful meiotic segregation of chromosomes and leads to the generation of genetic diversity. The conserved meiosis-specific Dmc1 recombinase catalyzes homologous recombination triggered by DNA double strand breaks through the exchange of parental DNA sequences. Although providing an efficient rate of DNA strand exchange between polymorphic alleles, Dmc1 must also guard against recombination between divergent sequences. How DNA mismatches affect Dmc1-mediated DNA strand exchange is not understood. We have used fluorescence resonance energy transfer to study the mechanism of Dmc1-mediated strand exchange between DNA oligonucleotides with different degrees of heterology. The efficiency of strand exchange is highly sensitive to the location, type, and distribution of mismatches. Mismatches near the 3' end of the initiating DNA strand have a small effect, whereas most mismatches near the 5' end impede strand exchange dramatically. The Hop2-Mnd1 protein complex stimulates Dmc1-catalyzed strand exchange on homologous DNA or containing a single mismatch. We observed that Dmc1 can reject divergent DNA sequences while bypassing a few mismatches in the DNA sequence. Our findings have important implications in understanding meiotic recombination. First, Dmc1 acts as an initial barrier for heterologous recombination, with the mismatch repair system providing a second level of proofreading, to ensure that ectopic sequences are not recombined. Second, Dmc1 stepping over infrequent mismatches is likely critical for allowing recombination between the polymorphic sequences of homologous chromosomes, thus contributing to gene conversion and genetic diversity.

  6. Thermophoresis of single stranded DNA.

    Science.gov (United States)

    Reineck, Philipp; Wienken, Christoph J; Braun, Dieter

    2010-01-01

    The manipulation and analysis of biomolecules in native bulk solution is highly desired; however, few methods are available. In thermophoresis, the thermal analog to electrophoresis, molecules are moved along a microscopic temperature gradient. Its theoretical foundation is still under debate, but practical applications for analytics in biology show considerable potential. Here we measured the thermophoresis of highly diluted single stranded DNA using an all-optical capillary approach. Temperature gradients were created locally by an infrared laser. The thermal depletion of oligonucleotides of between 5 and 50 bases in length were investigated by fluorescence at various salt concentrations. To a good approximation, the previously tested capacitor model describes thermophoresis: the Soret coefficient linearly depends on the Debye length and is proportional to the DNA length to the power of 0.35, dictated by the conformation-based size scaling of the diffusion coefficient. The results form the basis for quantitative DNA analytics using thermophoresis.

  7. THE THREE-STRANDED CORD

    Directory of Open Access Journals (Sweden)

    Walter Redmond

    2013-11-01

    Full Text Available The Schoolmen did much of their most interesting and original philosophizing in theology. An example is the dilemma in Renaissance Scholasticism on free will: how can we act freely if God causes and knows our actions? Basic issues are involved here: the antinomy between freedom and determination, modal semantics, tense logic, the logical status of counterfacts. Mexican Jesuits Matías Blanco (d. 1734 and Antonio Peralta (d. 1736 wrote books on the subject. We describe here the “disjunctive” solution that Blanco advanced in his Funiculus triplex (The Three-Stranded Cord, published posthumously in Mexico in 1746. When someone is faced with choosing between B and C, conjectures Blanco, God does not actualize either, but rather their disjunction B-or-C. Blanco calls for a truce in the “war” among the contending schools so that they may consider his solution–for he thinks it may indeed be acceptable to all.

  8. Control of contact resistance by strand surface coating in 36-strand NbTi CICCs

    NARCIS (Netherlands)

    Nijhuis, Arend; Kate, ten Herman H.J.; Duchateau, Jean-Luc; Decool, Patrick

    2001-01-01

    The stability and AC loss of NbTi cable-in-conduit conductors (CICCs) is largely determined by the interstrand contact resistance (Rc). Rc is predominantly established by the strand surface properties. Five 36-strand CICCs, fully identical except for the plating of the strand surface or the presence

  9. The Stranding Anomaly as Population Indicator

    DEFF Research Database (Denmark)

    Peltier, Helene; Baagøe, Hans J.; Camphuysen, Kees C.J.;

    2013-01-01

    in space and constant in time. We used a drift model to map stranding probabilities and predict stranding patterns of cetacean carcasses under H0 across the North Sea, the Channel and the Bay of Biscay, for the period 1990–2009. As the most common cetacean occurring in this area, we chose the harbour...

  10. Modelling toehold-mediated RNA strand displacement

    CERN Document Server

    Šulc, Petr; Romano, Flavio; Doye, Jonathan P K; Louis, Ard A

    2014-01-01

    We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5' end of the substrate and that the displacement slows down with increasing temperature for longer toeholds.

  11. Structure/function relationships in RecA protein-mediated homology recognition and strand exchange.

    Science.gov (United States)

    Prentiss, Mara; Prévost, Chantal; Danilowicz, Claudia

    2015-01-01

    RecA family proteins include RecA, Rad51, and Dmc1. These recombinases are responsible for homology search and strand exchange. Homology search and strand exchange occur during double-strand break repair and in eukaryotes during meiotic recombination. In bacteria, homology search begins when RecA binds an initiating single-stranded DNA (ssDNA) in the primary DNA-binding site to form the presynaptic filament. The filament is a right-handed helix, where the initiating strand is bound deep within the filament. Once the presynaptic filament is formed, it interrogates nearby double-stranded DNA (dsDNA) to find a homologous sequence; therefore, we provide a detailed discussion of structural features of the presynaptic filament that play important functional roles. The discussion includes many diagrams showing multiple filament turns. These diagrams illustrate interactions that are not evident in single turn structures. The first dsDNA interactions with the presynaptic filament are insensitive to mismatches. The mismatch insensitive interactions lead to dsDNA deformation that triggers a homology testing process governed by kinetics. The first homology test involves ∼8 bases. Almost all interactions are rejected by this initial rapid test, leading to a new cycle of homology testing. Interactions that pass the initial rapid test proceed to a slower testing stage. That slower stage induces nonhomologous dsDNA to reverse strand exchange and begin a new cycle of homology testing. In contrast, homologous dsDNA continues to extend the heteroduplex strand-exchange product until ATP hydrolysis makes strand exchange irreversible.

  12. Cetacean strandings in Costa Rica (1966-1999)

    OpenAIRE

    Rodríguez-Fonseca, Javier; Cubero-Pardo,Priscilla

    2014-01-01

    Cetacean strandings in Costa Rica are reported for a period of 33 years, with a total of 35 strandings, 13 species and 247 individuals involved. The vast majority of documented strandings occurred on the Pacific coast and correspond to single individuals (32 and 28 strandings respectively). The highest stranding number was in the period from 1990 to 1999 (n=24). Physeter catodon (cachalot or sperm whale) is the species with the highest frequency of strandings (n=8) and the family Delphinidae ...

  13. Marine mammal strandings in the New Caledonia region, Southwest Pacific.

    Science.gov (United States)

    Borsa, Philippe

    2006-04-01

    Four hundred twenty three marine mammals, in 72 stranding events, were recorded between 1877 and 2005 in New Caledonia, the Loyalty Islands, and Vanuatu in the southwest Pacific. Sixteen species were represented in this count, including: minke whale, Balaenoptera acutorostrata (1 single stranding), sei whale, B. borealis (1 single stranding), blue whale, B. musculus (1 single stranding), humpback whale, Megaptera novaeangliae (2 single strandings), giant sperm whale, Physeter macrocephalus (18 single strandings, 2 pair strandings), pygmy sperm whale, Kogia breviceps (5 single strandings), dwarf sperm whale, K. sima (2 single strandings, 1 triple stranding), Blainville's beaked whale, Mesoplodon densirostris (2 single strandings), short-finned pilot whale, Globicephala macrorhynchus (4 strandings, 56 individuals), melon-headed whale, Peponocephala electra (1 single stranding and 2 mass strandings totalling 231 individuals), common dolphin, Delphinus delphis (1 single stranding), spinner dolphin, Stenella longirostris (1 pair stranding and 2 mass strandings of groups of approximately 30 individuals each), Indian Ocean bottlenose dolphin, Tursiops aduncus (2 single strandings), dugong, Dugong dugon (14 single strandings), and New Zealand fur seal, Arctocephalus forsteri (3 single strandings). A stranded rorqual identified as an Antarctic minke whale (B. bonaerensis), with coloration patterns that did not match known descriptions, was also reported. Sei whale was recorded for the first time in the tropical Southwest Pacific region and Antarctic minke whale, melon-headed whale, and Indian Ocean bottlenose dolphin were recorded for the first time in New Caledonia. Strandings of sperm whales were most frequent in the spring, but also occurred in autumn months, suggesting a seasonal pattern of occurrence possibly related to seasonal migration. One stranded humpback whale bore the scars of a killer whale's attack and one dugong was injured by a shark. Scars left by

  14. The Stranding Anomaly as Population Indicator

    DEFF Research Database (Denmark)

    Peltier, Helene; Baagøe, Hans J.; Camphuysen, Kees C.J.

    2013-01-01

    Ecological indicators for monitoring strategies are expected to combine three major characteristics: ecological significance, statistical credibility, and cost-effectiveness. Strategies based on stranding networks rank highly in cost-effectiveness, but their ecological significance and statistical...... credibility are disputed. Our present goal is to improve the value of stranding data as population indicator as part of monitoring strategies by constructing the spatial and temporal null hypothesis for strandings. The null hypothesis is defined as: small cetacean distribution and mortality are uniform...... surveys, mostly SCANS surveys (1994 and 2005). This new indicator could be applied to cetacean populations across the world and more widely to marine megafauna....

  15. DNA strand displacement system running logic programs.

    Science.gov (United States)

    Rodríguez-Patón, Alfonso; Sainz de Murieta, Iñaki; Sosík, Petr

    2014-01-01

    The paper presents a DNA-based computing model which is enzyme-free and autonomous, not requiring a human intervention during the computation. The model is able to perform iterated resolution steps with logical formulae in conjunctive normal form. The implementation is based on the technique of DNA strand displacement, with each clause encoded in a separate DNA molecule. Propositions are encoded assigning a strand to each proposition p, and its complementary strand to the proposition ¬p; clauses are encoded comprising different propositions in the same strand. The model allows to run logic programs composed of Horn clauses by cascading resolution steps. The potential of the model is demonstrated also by its theoretical capability of solving SAT. The resulting SAT algorithm has a linear time complexity in the number of resolution steps, whereas its spatial complexity is exponential in the number of variables of the formula. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  16. Alaska Marine Mammal Strandings/Entanglements

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database represents a summary of information on stranded marine mammals reported to NMFS throughout the State of Alaska in fulfillment of Title IV of the Marine...

  17. Thermodynamic Analysis of Interacting Nucleic Acid Strands

    OpenAIRE

    Dirks, Robert M.; Bois, Justin S.; Schaeffer, Joseph M.; Winfree, Erik; Pierce, Niles A.

    2007-01-01

    Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures. We then derive the form of the partition function for a fixed...

  18. Study on Strand Space Model Theory

    Institute of Scientific and Technical Information of China (English)

    JI QingGuang(季庆光); QING SiHan(卿斯汉); ZHOU YongBin(周永彬); FENG DengGuo(冯登国)

    2003-01-01

    The growing interest in the application of formal methods of cryptographic pro-tocol analysis has led to the development of a number of different ways for analyzing protocol. Inthis paper, it is strictly proved that if for any strand, there exists at least one bundle containingit, then an entity authentication protocol is secure in strand space model (SSM) with some smallextensions. Unfortunately, the results of attack scenario demonstrate that this protocol and the Yahalom protocol and its modification are de facto insecure. By analyzing the reasons of failure offormal inference in strand space model, some deficiencies in original SSM are pointed out. In orderto break through these limitations of analytic capability of SSM, the generalized strand space model(GSSM) induced by some protocol is proposed. In this model, some new classes of strands, oraclestrands, high order oracle strands etc., are developed, and some notions are formalized strictly in GSSM, such as protocol attacks, valid protocol run and successful protocol run. GSSM can thenbe used to further analyze the entity authentication protocol. This analysis sheds light on why thisprotocol would be vulnerable while it illustrates that GSSM not only can prove security protocolcorrect, but also can be efficiently used to construct protocol attacks. It is also pointed out thatusing other protocol to attack some given protocol is essentially the same as the case of using themost of protocol itself.

  19. Mortality trends of stranded marine mammals on Cape Cod and southeastern Massachusetts, USA, 2000 to 2006.

    Science.gov (United States)

    Bogomolni, Andrea L; Pugliares, Katie R; Sharp, Sarah M; Patchett, Kristen; Harry, Charles T; LaRocque, Jane M; Touhey, Kathleen M; Moore, Michael

    2010-01-25

    To understand the cause of death of 405 marine mammals stranded on Cape Cod and southeastern Massachusetts between 2000 and 2006, a system for coding final diagnosis was developed and categorized as (1) disease, (2) human interaction, (3) mass-stranded with no significant findings, (4) single-stranded with no significant findings, (5) rock and/or sand ingestion, (6) predatory attack, (7) failure to thrive or dependent calf or pup, or (8) other. The cause of death for 91 animals could not be determined. For the 314 animals that could be assigned a cause of death, gross and histological pathology results and ancillary testing indicated that disease was the leading cause of mortality in the region, affecting 116/314 (37%) of cases. Human interaction, including harassment, entanglement, and vessel collision, fatally affected 31/314 (10%) of all animals. Human interaction accounted for 13/29 (45%) of all determined gray seal Halichoerus grypus mortalities. Mass strandings were most likely to occur in northeastern Cape Cod Bay; 97/106 (92%) of mass stranded animals necropsied presented with no significant pathological findings. Mass strandings were the leading cause of death in 3 of the 4 small cetacean species: 46/67 (69%) of Atlantic white-sided dolphin Lagenorhynchus acutus, 15/21 (71%) of long-finned pilot whale Globicephala melas, and 33/54 (61%) of short-beaked common dolphin Delphinus delphis. These baseline data are critical for understanding marine mammal population health and mortality trends, which in turn have significant conservation and management implications. They not only afford a better retrospective analysis of strandings, but ultimately have application for improving current and future response to live animal stranding.

  20. Cetacean strandings in Costa Rica (1966-1999).

    Science.gov (United States)

    Rodríguez-Fonseca, J; Cubero-Pardo, P

    2001-06-01

    Cetacean strandings in Costa Rica are reported for a period of 33 years, with a total of 35 strandings, 13 species and 247 individuals involved. The vast majority of documented strandings occurred on the Pacific coast and correspond to single individuals (32 and 28 strandings respectively). The highest stranding number was in the period from 1990 to 1999 (n = 24). Physeter catodon (cachalot or sperm whale) is the species with the highest frequency of strandings (n = 8) and the family Delphinidae has the majority of species (n = 8) and strandings (n = 22). No other general tendencies were determined with the existing data.

  1. The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters.

    Science.gov (United States)

    Klattenhoff, Carla; Xi, Hualin; Li, Chengjian; Lee, Soohyun; Xu, Jia; Khurana, Jaspreet S; Zhang, Fan; Schultz, Nadine; Koppetsch, Birgit S; Nowosielska, Anetta; Seitz, Herve; Zamore, Phillip D; Weng, Zhiping; Theurkauf, William E

    2009-09-18

    Piwi-interacting RNAs (piRNAs) silence transposons and maintain genome integrity during germline development. In Drosophila, transposon-rich heterochromatic clusters encode piRNAs either on both genomic strands (dual-strand clusters) or predominantly one genomic strand (uni-strand clusters). Primary piRNAs derived from these clusters are proposed to drive a ping-pong amplification cycle catalyzed by proteins that localize to the perinuclear nuage. We show that the HP1 homolog Rhino is required for nuage organization, transposon silencing, and ping-pong amplification of piRNAs. rhi mutations virtually eliminate piRNAs from the dual-strand clusters and block production of putative precursor RNAs from both strands of the major 42AB dual-strand cluster, but not of transcripts or piRNAs from the uni-strand clusters. Furthermore, Rhino protein associates with the 42AB dual-strand cluster,but does not bind to uni-strand cluster 2 or flamenco. Rhino thus appears to promote transcription of dual-strand clusters, leading to production of piRNAs that drive the ping-pong amplification cycle.

  2. Mechanical properties of rubberwood oriented strand lumber (OSL: The effect of strand length

    Directory of Open Access Journals (Sweden)

    Buhnnum Kyokong

    2005-09-01

    Full Text Available Effect of strand length on mechanical properties (tension, compression and bending of oriented strand lumber (OSL made of rubberwood (Hevea brasiliensis Muell. Arg. was reported. Three strand lengths of 50 mm, 100 mm, and 150 mm with 1 mm thickness and 15 mm width were used. The strands were mixed with 5% pMDI glue (weight basis in a tumble mixer. The OSL specimens were formed by hot pressing process of unidirectionally aligned strands. Average specific gravity and moisture content were 0.76 and 8.34%, respectively. Tension and compression tests were carried out for directions both parallel and perpendicular to grain while bending test was performed only in parallel direction. Ultimate stresses and moduli of elasticity were examined from the stress-strain curves. It was found that for the parallel-to-grain direction, the longer strand OSL gave higher strength. The role of the strand length did not appear for the direction normal to the grain. The relationship between the mechanical properties of OSL and strand length was well described by the modified Hankinson formula.

  3. Stranding of two sperm whales (Physeter macrocephalus) in the "North Sea trap" at Henne Strand, Denmark

    DEFF Research Database (Denmark)

    Hansen, Mette Sif; Alstrup, Aage K. O.; Hansen, Jørgen H.

    2016-01-01

    In February 2014 two male sperm whales (Physeter macrocephalus) stranded at Henne Strand, Denmark. One whale (MCE 1644) was found dead, while the other (MCE 1645) was still alive, but drowned during the high tide. To increase our knowledge of sperm whales, conduct forage investigations, post...

  4. Win-win measurement of stranded costs

    Energy Technology Data Exchange (ETDEWEB)

    Graniere, R.J. [Ohio State Univ., Columbus, OH (United States). National Regulatory Research Inst.

    1998-08-01

    While the underrecovery of stranded costs puts a portion of the utility`s investors` wealth at risk, the overrecovery of these costs causes the utility`s customers to shoulder an unnecessary financial burden. These opposing potential costs associated inevitably with stranded-cost recovery help insure that everyone involved in the production, sale, and use of electric power, for selfish reasons, wants to coordinate on the best measure of these costs. That is, in equilibrium, everyone in the electricity production chain does not want to deviate from a measurement approach that prevents either the overrecovery or underrecovery of stranded costs. An important task, then, is to determine the ad hoc rules that must be appended to ex ante and ex post measures of stranded costs in order to reasonably prevent overrecoveries and underrecoveries. While either ex ante or ex post measures of stranded facilities and costs can be implemented reasonably, appropriately constructed ex post measures are superior, so long as regulators follow a reasonable protocol for the securitization of these costs.

  5. Marine mammal strandings in the New Caledonia region, Southwest Pacific

    OpenAIRE

    Borsa, Philippe

    2006-01-01

    International audience; Four hundred twenty three marine mammals, in 72 stranding events, were recorded between 1877 and 2005 in New Caledonia, the Loyalty Islands, and Vanuatu in the southwest Pacific. Sixteen species were represented in this count, including: minke whale, Balaenoptera acutorostrata (1 single stranding), sei whale, B. borealis (1 single stranding), blue whale, B. musculus (1 single stranding), humpback whale, Megaptera novaeangliae (2 single strandings), giant sperm whale, P...

  6. DNA Strand Breaks in Mitotic Germ Cells of Caenorhabditis elegans Evaluated by Comet Assay.

    Science.gov (United States)

    Park, Sojin; Choi, Seoyun; Ahn, Byungchan

    2016-03-01

    DNA damage responses are important for the maintenance of genome stability and the survival of organisms. Such responses are activated in the presence of DNA damage and lead to cell cycle arrest, apoptosis, and DNA repair. In Caenorhabditis elegans, double-strand breaks induced by DNA damaging agents have been detected indirectly by antibodies against DSB recognizing proteins. In this study we used a comet assay to detect DNA strand breaks and to measure the elimination of DNA strand breaks in mitotic germline nuclei of C. elegans. We found that C. elegans brc-1 mutants were more sensitive to ionizing radiation and camptothecin than the N2 wild-type strain and repaired DNA strand breaks less efficiently than N2. This study is the first demonstration of direct measurement of DNA strand breaks in mitotic germline nuclei of C. elegans. This newly developed assay can be applied to detect DNA strand breaks in different C. elegans mutants that are sensitive to DNA damaging agents.

  7. Performance optimization of internal tin process multifilamentary Nb{sub 3}Sn strands

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ke, E-mail: zhangke@c-wst.com [State Key Laboratory of Solidification Processing, Northwestern Polytechnical University, Xi’an, Shaanxi 710072 (China); Western Superconducting Technologies Co. Ltd, Xi’an, Shaanxi 710018 (China); State Engineering Lab. of Superconducting Material Preparation, Xi’an, Shaanxi 710018 (China); Zhang, Pingxiang [State Key Laboratory of Solidification Processing, Northwestern Polytechnical University, Xi’an, Shaanxi 710072 (China); Western Superconducting Technologies Co. Ltd, Xi’an, Shaanxi 710018 (China); State Engineering Lab. of Superconducting Material Preparation, Xi’an, Shaanxi 710018 (China); Northwest Institute for Non-ferrous Metal Research, Xi’an, Shaanxi 710016 (China); Shi, Yigong; Liu, Jianwei; Gao, Huixian; Li, Jianfeng; Liu, Xianghong; Feng, Yong [Western Superconducting Technologies Co. Ltd, Xi’an, Shaanxi 710018 (China); State Engineering Lab. of Superconducting Material Preparation, Xi’an, Shaanxi 710018 (China)

    2016-11-01

    Highlights: • J{sub c} increases by adding Sn cores in the interspaces, hysteresis loss increases at the same time. • Enlarger the number of filaments with the same Sn proportion will increase J{sub c} and hysteresis loss. • Cu split adopted in each sub-element leads to a low hysteresis loss. - Abstract: In this study, internal tin process Nb{sub 3}Sn strands for the International Thermo-nuclear Experimental Reactor are developed in Western Superconducting Technologies. Short cable-in-conduit conductors manufactured with these strands have been qualified. Mass production is accomplished, and all the performances of the strands meet the requirement of ITER project. Besides, more researches on the effect of strand design on critical current density and hysteresis loss for Nb{sub 3}Sn strands are carried out. It is found that critical current density can be enhanced by reducing filament diameter and increasing Sn content, and hysteresis loss of the strands can be significantly reduced through Cu split adopted in sub-element.

  8. Human Stn1 protects telomere integrity by promoting efficient lagging-strand synthesis at telomeres and mediating C-strand fill-in

    Institute of Scientific and Technical Information of China (English)

    Chenhui Huang; Xueyu Dai; Weihang Chai

    2012-01-01

    Telomere maintenance is critical for genome stability.The newly-identified Ctc1/Stn1/Ten1 complex is important for telomere maintenance,though its precise role is unclear.We report here that depletion of hStn1 induces catastrophic telomere shortening,DNA damage response,and early senescence in human somatic cells.These phenotypes are likely due to the essential role of hStn1 in promoting efficient replication of lagging-strand telomeric DNA.Downregulation of hStn1 accumulates single-stranded G-rich DNA specifically at lagging-strand telomeres,increases telomere fragility,hinders telomere DNA synthesis,as well as delays and compromises telomeric C-strand synthesis.We further show that hStn1 deficiency leads to persistent and elevated association of DNA polymerase α(polα)to telomeres,suggesting that hStn1 may modulate the DNA synthesis activity of polα rather than controlling the loading of polα to telomeres.Additionally,our data suggest that hStn1 is unlikely to be part of the telomere capping complex.We propose that the hStn1 assists DNA polymerases to efficiently duplicate lagging-strand telomeres in order to achieve complete synthesis of telomeric DNA,therefore preventing rapid telomere loss.

  9. Fine strand-like structure in the solar corona from MHD transverse oscillations

    CERN Document Server

    Antolin, P; Van Doorsselaere, T

    2014-01-01

    Current analytical and numerical modelling suggest the existence of ubiquitous thin current sheets in the corona that could explain the observed heating requirements. On the other hand, new high resolution observations of the corona indicate that its magnetic field may tend to organise itself in fine strand-like structures of few hundred kilometres widths. The link between small structure in models and the observed widths of strand-like structure several orders of magnitude larger is still not clear. A popular theoretical scenario is the nanoflare model, in which each strand is the product of an ensemble of heating events. Here, we suggest an alternative mechanism for strand generation. Through forward modelling of 3D MHD simulations we show that small amplitude transverse MHD waves can lead in a few periods time to strand-like structure in loops in EUV intensity images. Our model is based on previous numerical work showing that transverse MHD oscillations can lead to Kelvin-Helmholtz instabilities that defor...

  10. Double-Stranded Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2001-01-01

    A novel class of compounds, known as peptide nucleic acids, form double-stranded structures with one another and with ssDNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  11. SAKAMATA : A tool to avoid whale strandings

    NARCIS (Netherlands)

    Benders, F.P.A.; Beerens, S.P.; Verboom, W.C.

    2002-01-01

    World-wide a concern exists about the influence of man-made noise on marine life, and particularly of high power sonar. Most concern lies with marine mammals that use acoustics for hunting, communication and/or navigation. This concern is fed by recent strandings of whales that could be related to m

  12. SAKAMATA : A tool to avoid whale strandings

    NARCIS (Netherlands)

    Benders, F.P.A.; Beerens, S.P.; Verboom, W.C.

    2004-01-01

    World-wide a concern exists about the influence of man-made noise on marine life, and particularly of high power sonar. Most concern lies with marine mammals that use acoustics for hunting, communication and/or navigation. This concern is fed by recent strandings of whales that could be related to m

  13. Lead Poisoning

    Science.gov (United States)

    Lead is a metal that occurs naturally in the earth's crust. Lead can be found in all parts of our ... from human activities such as mining and manufacturing. Lead used to be in paint; older houses may ...

  14. The evolution of strand preference in simulated RNA replicators with strand displacement: implications for the origin of transcription.

    Science.gov (United States)

    Takeuchi, Nobuto; Salazar, Laura; Poole, Anthony M; Hogeweg, Paulien

    2008-08-11

    The simplest conceivable example of evolving systems is RNA molecules that can replicate themselves. Since replication produces a new RNA strand complementary to a template, all templates would eventually become double-stranded and, hence, become unavailable for replication. Thus the problem of how to separate the two strands is considered a major issue for the early evolution of self-replicating RNA. One biologically plausible way to copy a double-stranded RNA is to displace a preexisting strand by a newly synthesized strand. Such copying can in principle be initiated from either the (+) or (-) strand of a double-stranded RNA. Assuming that only one of them, say (+), can act as replicase when single-stranded, strand displacement produces a new replicase if the (-) strand is the template. If, however, the (+) strand is the template, it produces a new template (but no replicase). Modern transcription exhibits extreme strand preference wherein anti-sense strands are always the template. Likewise, replication by strand displacement seems optimal if it also exhibits extreme strand preference wherein (-) strands are always the template, favoring replicase production. Here we investigate whether such strand preference can evolve in a simple RNA replicator system with strand displacement. We first studied a simple mathematical model of the replicator dynamics. Our results indicated that if the system is well-mixed, there is no selective force acting upon strand preference per se. Next, we studied an individual-based simulation model to investigate the evolution of strand preference under finite diffusion. Interestingly, the results showed that selective forces "emerge" because of finite diffusion. Strikingly, the direction of the strand preference that evolves [i.e. (+) or (-) strand excess] is a complex non-monotonic function of the diffusion intensity. The mechanism underlying this behavior is elucidated. Furthermore, a speciation-like phenomenon is observed under

  15. The evolution of strand preference in simulated RNA replicators with strand displacement: Implications for the origin of transcription

    Directory of Open Access Journals (Sweden)

    Poole Anthony M

    2008-08-01

    Full Text Available Abstract Background The simplest conceivable example of evolving systems is RNA molecules that can replicate themselves. Since replication produces a new RNA strand complementary to a template, all templates would eventually become double-stranded and, hence, become unavailable for replication. Thus the problem of how to separate the two strands is considered a major issue for the early evolution of self-replicating RNA. One biologically plausible way to copy a double-stranded RNA is to displace a preexisting strand by a newly synthesized strand. Such copying can in principle be initiated from either the (+ or (- strand of a double-stranded RNA. Assuming that only one of them, say (+, can act as replicase when single-stranded, strand displacement produces a new replicase if the (- strand is the template. If, however, the (+ strand is the template, it produces a new template (but no replicase. Modern transcription exhibits extreme strand preference wherein anti-sense strands are always the template. Likewise, replication by strand displacement seems optimal if it also exhibits extreme strand preference wherein (- strands are always the template, favoring replicase production. Here we investigate whether such strand preference can evolve in a simple RNA replicator system with strand displacement. Results We first studied a simple mathematical model of the replicator dynamics. Our results indicated that if the system is well-mixed, there is no selective force acting upon strand preference per se. Next, we studied an individual-based simulation model to investigate the evolution of strand preference under finite diffusion. Interestingly, the results showed that selective forces "emerge" because of finite diffusion. Strikingly, the direction of the strand preference that evolves [i.e. (+ or (- strand excess] is a complex non-monotonic function of the diffusion intensity. The mechanism underlying this behavior is elucidated. Furthermore, a speciation

  16. Analyses of point mutation repair and allelic heterogeneity generated by CRISPR/Cas9 and single-stranded DNA oligonucleotides

    OpenAIRE

    Pawel Bialk; Brett Sansbury; Natalia Rivera-Torres; Kevin Bloh; Dula Man; Kmiec, Eric B.

    2016-01-01

    The repair of a point mutation can be facilitated by combined activity of a single-stranded oligonucleotide and a CRISPR/Cas9 system. While the mechanism of action of combinatorial gene editing remains to be elucidated, the regulatory circuitry of nucleotide exchange executed by oligonucleotides alone has been largely defined. The presence of the appropriate CRISPR/Cas9 system leads to an enhancement in the frequency of gene editing directed by single-stranded DNA oligonucleotides. While CRIS...

  17. Analyses of point mutation repair and allelic heterogeneity generated by CRISPR/Cas9 and single-stranded DNA oligonucleotides

    OpenAIRE

    Pawel Bialk; Brett Sansbury; Natalia Rivera-Torres; Kevin Bloh; Dula Man; Kmiec, Eric B.

    2016-01-01

    The repair of a point mutation can be facilitated by combined activity of a single-stranded oligonucleotide and a CRISPR/Cas9 system. While the mechanism of action of combinatorial gene editing remains to be elucidated, the regulatory circuitry of nucleotide exchange executed by oligonucleotides alone has been largely defined. The presence of the appropriate CRISPR/Cas9 system leads to an enhancement in the frequency of gene editing directed by single-stranded DNA oligonucleotides. While CRIS...

  18. [Spectral analysis of self-oscillating motility in isolated plasmodial strand of Physarum polycephalum].

    Science.gov (United States)

    Proskurin, S G; Avsievich, T I

    2014-01-01

    In this study the experimental dependencies of the velocity of shuttle endoplasmic motion in the isolated plasmodial strand of Physarum polycephalum obtained by laser Doppler microscopy are presented. The spectral analysis of the time dependencies of the endoplasm allows obtaining two distinct harmonic components. Influence of KCN and SHAM--inhibitors of cellular respiration--leads to a complete cessation of endoplasmic motion in the strand. After removal of the inhibitors the respiratory system becomes normal, gradually restoring the activity of both harmonic oscillation sources. Based on the spectral analysis the simulated time-dependent velocity of the endoplasmic motion is rather good consistent with experimental data.

  19. KARAKTERISTIK ORIENTED STRAND BOARD DARI KAYU AKASIA DAN AFRIKA BERDASARKAN PENYUSUNAN ARAH STRAND

    Directory of Open Access Journals (Sweden)

    Nurhaida

    2008-04-01

    Full Text Available The research objectives arc to evaluate physical and mechanical properties of OSB based on strands orientation; and to evaluate physical and mechanical properties of OSB made from akasia wood (Acacia mangium Wild and afrika wood (Maesopsis eminii Engl. Akasia and afrika wood are used for OSB strand material with phenol formaldehyde (PF as adhesives and addition of paraffin. OSB made in this research is consist of three plies whereas are differed into eight (8 strand orientations. In the making process, hot press was carried out at 160OC and pressure 25kg.cm-2 for 15 minutes. Determination of OSB physical and mechanical properties is referred to JIS A 5908-2003. Result showed that strand orientations has no affect to OSB physical properties except for linicr swelling 24h, but it significantly influence all mechanical properties of OSB. Wood species have an effect on mechanical properties of OSB in the dry test, wet MOE lengthwise test and OSB physical properties, particularly to OSB density and water absorbing capability at 2h and 24h. All of OSB physical properties arc meet JIS A 5908-2003 standard, but not all of the mechanical properties such as dry MOE lengthwise, dry MOE and MOR widthwise. The best physical and mechanical properties is presented by OSB made from akasia wood in strand orientation F, G, Band C whereas all parameters meet JIS A 5908-2003 standard. In comparation with strand orientation B that is frequent used in industry, strand orientation F and G arc proficient to raise the modulus elasticity value (MOE and strength (MOR as much as 167.81-231.65% and 89.73-109.87%, respectively; especially in widthwise board application. Furthermore, strand orientation F and G arc more flexible as structural components

  20. Lead Toxicity

    Science.gov (United States)

    ... including some imported jewelry. What are the health effects of lead? • More commonly, lower levels of lead in children over time may lead to reduced IQ, slow learning, Attention Deficit Hyperactivity Disorder (ADHD), or behavioral issues. • Lead also affects other ...

  1. Slow conduction in mixed cultured strands of primary ventricular cells and stem cell-derived cardiomyocytes

    Directory of Open Access Journals (Sweden)

    Jan Pavel Kucera

    2015-09-01

    Full Text Available Modern concepts for the treatment of myocardial diseases focus on novel cell therapeutic strategies involving stem cell-derived cardiomyocytes (SCMs. However, functional integration of SCMs requires similar electrophysiological properties as primary cardiomyocytes (PCMs and the ability to establish intercellular connections with host myocytes in order to contribute to the electrical and mechanical activity of the heart. The aim of this project was to investigate the properties of cardiac conduction in a co-culture approach using SCMs and PCMs in cultured cell strands. Murine embryonic SCMs were pooled with fetal ventricular cells and seeded in predefined proportions on microelectrode arrays to form patterned strands of mixed cells. Conduction velocity (CV was measured during steady state pacing. SCM excitability was estimated from action potentials measured in single cells using the patch clamp technique. Experiments were complemented with computer simulations of conduction using a detailed model of cellular architecture in mixed cell strands.CV was significantly lower in strands composed purely of SCMs (5.5±1.5 cm/s, n=11 as compared to PCMs (34.9±2.9 cm/s, n=21 at similar refractoriness (100% SCMs: 122±25 ms, n=9; 100% PCMs: 139±67 ms, n=14. In mixed strands combining both cell types, CV was higher than in pure SCMs strands, but always lower than in 100% PCM strands. Computer simulations demonstrated that both intercellular coupling and electrical excitability limit CV.These data provide evidence that in cultures of murine ventricular cardiomyocytes, SCMs cannot restore CV to control levels resulting in slow conduction, which may lead to reentry circuits and arrhythmias.

  2. Targeting of single stranded oligonucleotides through metal-induced cyclization of short complementary strands : Targeting of single stranded oligonucleotides

    OpenAIRE

    Freville, Fabrice; Richard, Tristan; Bathany, Katell; Moreau, Serge

    2006-01-01

    International audience; A new strategy to cyclize a short synthetic oligonucleotide on a DNA or a RNA target strand is described. This one relies on a metal-mediated cyclization of short synthetic oligonucleotides conjugated with two chelating 2,2':6',2”-terpyridine moieties at their 3' and 5' ends. Cyclization following metal addition (Zn2+, Fe2+) was demonstrated using UV monitored thermal denaturation experiments, mass spectrometry analysis and gel shift assays. NMR experiments were used t...

  3. Southeast Region Level A Marine Mammal Stranding Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data on marine mammal strandings are collected by the Southeast Marine Mammal Stranding Network. Basic data on the location, species identification, animal...

  4. Charge Migration in DNA: A Double Stranded Model

    Institute of Scientific and Technical Information of China (English)

    BAO, Han; LU, Jing; FAN, Kang-Nian

    2006-01-01

    In particular, charge migration phenomena in DNA have attracted much interest because of relevance to the generation of damage and mutations which play important roles in most of life processes. In this paper a theory method was presented in which the DNA chain was treated as a double-stranded system, and the charge migration in DNA based on the donor-bridge-acceptor system was investigated by this model. After having obtained the Hamiltonian, the effects of the surrounding were explained and calculated. The double-strand calculation could lead to good exponential decay curves and this time two different falloff parameters were found respectively before and after 3 or 4 AT base pair bridge lengths as prediction. Lately theoretical study showed this result by addition of more parameter, and sequence effect was then concentrated on. The difference of transfer integral caused the different decay rate of unlike sequences, but bridge length was still proved to be the main factor on the decay rates.

  5. Quantitative assay of photoinduced DNA strand breaks by real-time PCR.

    Science.gov (United States)

    Wiczk, Justyna; Westphal, Kinga; Rak, Janusz

    2016-09-05

    Real-time PCR (qPCR) - a modern methodology primarily used for studying gene expression has been employed for the quantitative assay of an important class of DNA damage - single strand breaks. These DNA lesions which may lead to highly cytotoxic double strand breaks were quantified in a model system where double stranded DNA was sensitized to UV photons by labeling with 5-bromo-2'-deoxyuridine. The amount of breaks formed due to irradiation with several doses of 320nm photons was assayed by two independent methods: LC-MS and qPCR. A very good agreement between the relative damage measured by the two completely different analytical tools proves the applicability of qPCR for the quantitative analysis of SSBs. Our results suggest that the popularity of the hitherto underestimated though accurate and site-specific technique of real-time PCR may increase in future DNA damage studies.

  6. Evaluation and Application of the Strand-Specific Protocol for Next-Generation Sequencing

    Directory of Open Access Journals (Sweden)

    Kuo-Wang Tsai

    2015-01-01

    Full Text Available Next-generation sequencing (NGS has become a powerful sequencing tool, applied in a wide range of biological studies. However, the traditional sample preparation protocol for NGS is non-strand-specific (NSS, leading to biased estimates of expression for transcripts overlapped at the antisense strand. Strand-specific (SS protocols have recently been developed. In this study, we prepared the same RNA sample by using the SS and NSS protocols, followed by sequencing with Illumina HiSeq platform. Using real-time quantitative PCR as a standard, we first proved that the SS protocol more precisely estimates gene expressions compared with the NSS protocol, particularly for those overlapped at the antisense strand. In addition, we also showed that the sequence reads from the SS protocol are comparable with those from conventional NSS protocols in many aspects. Finally, we also mapped a fraction of sequence reads back to the antisense strand of the known genes, originally without annotated genes located. Using sequence assembly and PCR validation, we succeeded in identifying and characterizing the novel antisense genes. Our results show that the SS protocol performs more accurately than the traditional NSS protocol and can be applied in future studies.

  7. Implementation of a method to visualize noise-induced hearing loss in mass stranded cetaceans

    Science.gov (United States)

    Morell, Maria; Brownlow, Andrew; McGovern, Barry; Raverty, Stephen A.; Shadwick, Robert E.; André, Michel

    2017-02-01

    Assessment of the impact of noise over-exposure in stranded cetaceans is challenging, as the lesions that lead to hearing loss occur at the cellular level and inner ear cells are very sensitive to autolysis. Distinguishing ante-mortem pathology from post-mortem change has been a major constraint in diagnosing potential impact. Here, we outline a methodology applicable to the detection of noise-induced hearing loss in stranded cetaceans. Inner ears from two mass strandings of long-finned pilot whales in Scotland were processed for scanning electron microscopy observation. In one case, a juvenile animal, whose ears were fixed within 4 hours of death, revealed that many sensory cells at the apex of the cochlear spiral were missing. In this case, the absence of outer hair cells would be compatible with overexposure to underwater noise, affecting the region which transduces the lowest frequencies of the pilot whales hearing spectrum. Perfusion of cochlea with fixative greatly improved preservation and enabled diagnostic imaging of the organ of Corti, even 30 hours after death. This finding supports adopting a routine protocol to detect the pathological legacy of noise overexposure in mass stranded cetaceans as a key to understanding the complex processes and implications that lie behind such stranding events.

  8. Implementation of a method to visualize noise-induced hearing loss in mass stranded cetaceans

    Science.gov (United States)

    Morell, Maria; Brownlow, Andrew; McGovern, Barry; Raverty, Stephen A.; Shadwick, Robert E.; André, Michel

    2017-01-01

    Assessment of the impact of noise over-exposure in stranded cetaceans is challenging, as the lesions that lead to hearing loss occur at the cellular level and inner ear cells are very sensitive to autolysis. Distinguishing ante-mortem pathology from post-mortem change has been a major constraint in diagnosing potential impact. Here, we outline a methodology applicable to the detection of noise-induced hearing loss in stranded cetaceans. Inner ears from two mass strandings of long-finned pilot whales in Scotland were processed for scanning electron microscopy observation. In one case, a juvenile animal, whose ears were fixed within 4 hours of death, revealed that many sensory cells at the apex of the cochlear spiral were missing. In this case, the absence of outer hair cells would be compatible with overexposure to underwater noise, affecting the region which transduces the lowest frequencies of the pilot whales hearing spectrum. Perfusion of cochlea with fixative greatly improved preservation and enabled diagnostic imaging of the organ of Corti, even 30 hours after death. This finding supports adopting a routine protocol to detect the pathological legacy of noise overexposure in mass stranded cetaceans as a key to understanding the complex processes and implications that lie behind such stranding events. PMID:28165504

  9. Analog Computation by DNA Strand Displacement Circuits.

    Science.gov (United States)

    Song, Tianqi; Garg, Sudhanshu; Mokhtar, Reem; Bui, Hieu; Reif, John

    2016-08-19

    DNA circuits have been widely used to develop biological computing devices because of their high programmability and versatility. Here, we propose an architecture for the systematic construction of DNA circuits for analog computation based on DNA strand displacement. The elementary gates in our architecture include addition, subtraction, and multiplication gates. The input and output of these gates are analog, which means that they are directly represented by the concentrations of the input and output DNA strands, respectively, without requiring a threshold for converting to Boolean signals. We provide detailed domain designs and kinetic simulations of the gates to demonstrate their expected performance. On the basis of these gates, we describe how DNA circuits to compute polynomial functions of inputs can be built. Using Taylor Series and Newton Iteration methods, functions beyond the scope of polynomials can also be computed by DNA circuits built upon our architecture.

  10. DNA Strand-Displacement Timer Circuits.

    Science.gov (United States)

    Fern, Joshua; Scalise, Dominic; Cangialosi, Angelo; Howie, Dylan; Potters, Leo; Schulman, Rebecca

    2017-02-17

    Chemical circuits can coordinate elaborate sequences of events in cells and tissues, from the self-assembly of biological complexes to the sequence of embryonic development. However, autonomously directing the timing of events in synthetic systems using chemical signals remains challenging. Here we demonstrate that a simple synthetic DNA strand-displacement circuit can release target sequences of DNA into solution at a constant rate after a tunable delay that can range from hours to days. The rates of DNA release can be tuned to the order of 1-100 nM per day. Multiple timer circuits can release different DNA strands at different rates and times in the same solution. This circuit can thus facilitate precise coordination of chemical events in vitro without external stimulation.

  11. Lead Poisoning

    Science.gov (United States)

    ... lead is of microscopic size, invisible to the naked eye. More often than not, children with elevated ... majority of the childhood lead poisoning cases we see today. Children and adults too can get seriously ...

  12. Relational Leading

    DEFF Research Database (Denmark)

    2015-01-01

    This first chapter presents the exploratory and curious approach to leading as relational processes – an approach that pervades the entire book. We explore leading from a perspective that emphasises the unpredictable challenges and triviality of everyday life, which we consider an interesting......, relevant and realistic way to examine leading. The chapter brings up a number of concepts and contexts as formulated by researchers within the field, and in this way seeks to construct a first understanding of relational leading....

  13. Markers of Decompression Stress of Mass Stranded/Live Caught and Released vs. Single Stranded Marine Mammals

    Science.gov (United States)

    2014-09-30

    1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Markers of Decompression Stress of Mass Stranded /Live...Caught and Released vs. Single Stranded Marine Mammals Michael Moore Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543...analyze blood samples from captive, wild-caught, and stranded marine mammals in order to compare concentrations of Microparticles (MPs). If confirmed

  14. Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses.

    Science.gov (United States)

    Kim, Kyoung-Ho; Bae, Jin-Woo

    2011-11-01

    Investigation of viruses in the environment often requires the amplification of viral DNA before sequencing of viral metagenomes. In this study, two of the most widely used amplification methods, the linker amplified shotgun library (LASL) and multiple displacement amplification (MDA) methods, were applied to a sample from the seawater surface. Viral DNA was extracted from viruses concentrated by tangential flow filtration and amplified by these two methods. 454 pyrosequencing was used to read the metagenomic sequences from different libraries. The resulting taxonomic classifications of the viruses, their functional assignments, and assembly patterns differed substantially depending on the amplification method. Only double-stranded DNA viruses were retrieved from the LASL, whereas most sequences in the MDA library were from single-stranded DNA viruses, and double-stranded DNA viral sequences were minorities. Thus, the two amplification methods reveal different aspects of viral diversity.

  15. The multiple personalities of Watson and Crick strands

    Directory of Open Access Journals (Sweden)

    Graur Dan

    2011-02-01

    Full Text Available Abstract Background In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. Proposal The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. The Watson strand is always used as the reference strand in their database. Using this as the basis of our standard, we recommend that Watson and Crick strand terminology only be used in the context of genomics. When possible, the centromere or other genomic feature should be used as a reference point, dividing the chromosome into two arms of unequal lengths. Under our proposal, the Watson strand is standardized as the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Furthermore, the Watson strand should be retained as the reference (plus strand in a genomic database. This usage not only makes the determination of Watson and Crick unambiguous, but also allows unambiguous selection of reference stands for genomics. Reviewers This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky, and William Martin.

  16. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA

    DEFF Research Database (Denmark)

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela

    2015-01-01

    An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ss......DNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained...

  17. Are there three polynucleotide strands in the catalytic centre of DNA polymerases?

    Science.gov (United States)

    Lestienne, Patrick P

    2009-01-01

    Mitochondrial DNA may undergo large-scale rearrangements, thus leading to diseases. The mechanisms of these rearrangements are still the matter of debates. Several lines of evidence indicate that breakpoints are characterized by direct repeats (DR), one of them being eliminated from the normal genome. Analysis of DR showed their skewed nucleotide content compatible with the formation of known triple helices. Here, I propose a novel mechanism involving the formation of triplex structures that result from the dissociation of the [synthesized repeat-DNA polymerase] complex. Upon binding to the homologous sequence, replication is initiated from the primer bound in a triple helix manner. This feature implies the initiation of replication on the double-stranded DNA from the triple helix primer. Hereby, I review evidences supporting this model. Indeed, all short d(G)-rich primers 10 nucleotides long can be elongated on double-stranded DNA by phage, bacterial, reverse transcriptases and eukaryotic DNA polymerases. Mismatches may be tolerated between the primer and its double-stranded binding site. In contrast to previous studies, evidences for the parallel binding of the triple helix to its homologous strand are provided. This suggest the displacement of the non-template strand by the triple helix primer upon binding within the DNA polymerase catalytic centre. Computer modelling indicates that the triple helix primer lies within the major groove of the double helix, with its 3' hydroxyl end nearby the catalytic amino acids. Taken together, I bring new concepts on DNA rearrangements, and novel features of triple helices and DNA polymerases that can bind three polynucleotide strands similar to RNA polymerases.

  18. Lead Test

    Science.gov (United States)

    ... months, and at 3, 4, 5, and 6 years of age. A blood lead level test should be done only if the risk ... recommended if the person is symptomatic at any level below 70 mcg/dL. Because lead will pass through the blood to an unborn child, pregnant ...

  19. Improving strand quality of upland oaks for use in oriented strand board

    Science.gov (United States)

    David B. DeValliance; Jody D. Gray; Shawn T. Grushecky

    2013-01-01

    Past research estimates that more than 1 million tons of oak logging residues go unused in West Virginia each year. Much research has been done investigating potential products and markets for this underutilized resource. West Virginia is home to an oriented strand board (OSB) producer that consumes large volumes of small diameter, low quality round wood. However, the...

  20. Hole hopping rates in single strand oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Borrelli, Raffaele [Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, TO (Italy); Capobianco, Amedeo [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy); Peluso, Andrea, E-mail: apeluso@unisa.it [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy)

    2014-08-31

    Highlights: • DNA hole transfer rates have been computed. • Delocalized adenine domains significantly affect hole transfer rates in DNA. • Franck–Condon weighted density of state from DFT normal modes. • DNA application in molecular electronics. - Abstract: The rates of hole transfer between guanine and adenine in single strand DNA have been evaluated by using Fermi’s golden rule and Kubo’s generating function approach for the Franck–Condon weighted density of states. The whole sets of the normal modes and vibrational frequencies of the two nucleobases, obtained at DFT/B3LYP level of calculation, have been considered in computations. The results show that in single strand the pyramidalization/planarization mode of the amino groups of both nucleobases plays the major role. At room temperature, the Franck–Condon density of states extends over a wide range of hole site energy difference, 0–1 eV, giving some hints about the design of oligonucleotides of potential technological interest.

  1. Repair of DNA Double-Strand Breaks

    Science.gov (United States)

    Falk, Martin; Lukasova, Emilie; Kozubek, Stanislav

    The genetic information of cells continuously undergoes damage induced by intracellular processes including energy metabolism, DNA replication and transcription, and by environmental factors such as mutagenic chemicals and UV and ionizing radiation. This causes numerous DNA lesions, including double strand breaks (DSBs). Since cells cannot escape this damage or normally function with a damaged genome, several DNA repair mechanisms have evolved. Although most "single-stranded" DNA lesions are rapidly removed from DNA without permanent damage, DSBs completely break the DNA molecule, presenting a real challenge for repair mechanisms, with the highest risk among DNA lesions of incorrect repair. Hence, DSBs can have serious consequences for human health. Therefore, in this chapter, we will refer only to this type of DNA damage. In addition to the biochemical aspects of DSB repair, which have been extensively studied over a long period of time, the spatio-temporal organization of DSB induction and repair, the importance of which was recognized only recently, will be considered in terms of current knowledge and remaining questions.

  2. Magnetization measurements on LHC superconducting strands

    CERN Document Server

    Le Naour, S; Wolf, R; Puzniak, R; Szewczyk, A; Wisniewski, A; Fikis, H; Foitl, M; Kirchmayr, H

    1999-01-01

    When using superconducting magnets in particle accelerators like the LHC, persistent currents in the superconductor often determine the field quality at injection, where the magnetic field is low. This paper describes magnetization measurements made on LHC cable strands at the Technical University of Vienna and the Institute of Physics of the Polish Academy of Sciences in collaboration with CERN. Measurements were performed at T=2 K and T=4.2 K on more than 50 strands of 7 different manufacturers with NbTi filament diameter between 5 and 7 micrometer. Two different measurement set-ups were used: vibrating sample magnetometer, with a sample length of about 8 mm, and an integrating coil magnetometer, with sample length of about 1 m. The two methods were compared by measuring the same sample. Low field evidence of proximity effect is discussed. Statistics like ratio of the width of the magnetization loop at 4.2 K 2 K, and the initial slope dM/dB after cooldown are presented. Decrease of the magnetization with ti...

  3. Hypermutability of damaged single-strand DNA formed at double-strand breaks and uncapped telomeres in yeast Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Yong Yang

    2008-11-01

    Full Text Available The major DNA repair pathways operate on damage in double-strand DNA because they use the intact strand as a template after damage removal. Therefore, lesions in transient single-strand stretches of chromosomal DNA are expected to be especially threatening to genome stability. To test this hypothesis, we designed systems in budding yeast that could generate many kilobases of persistent single-strand DNA next to double-strand breaks or uncapped telomeres. The systems allowed controlled restoration to the double-strand state after applying DNA damage. We found that lesions induced by UV-light and methyl methanesulfonate can be tolerated in long single-strand regions and are hypermutagenic. The hypermutability required PCNA monoubiquitination and was largely attributable to translesion synthesis by the error-prone DNA polymerase zeta. In support of multiple lesions in single-strand DNA being a source of hypermutability, analysis of the UV-induced mutants revealed strong strand-specific bias and unexpectedly high frequency of alleles with widely separated multiple mutations scattered over several kilobases. Hypermutability and multiple mutations associated with lesions in transient stretches of long single-strand DNA may be a source of carcinogenesis and provide selective advantage in adaptive evolution.

  4. Hypermutability of Damaged Single-Strand DNA Formed at Double-Strand Breaks and Uncapped Telomeres in Yeast Saccharomyces cerevisiae

    Science.gov (United States)

    Yang, Yong; Sterling, Joan; Storici, Francesca; Resnick, Michael A.; Gordenin, Dmitry A.

    2008-01-01

    The major DNA repair pathways operate on damage in double-strand DNA because they use the intact strand as a template after damage removal. Therefore, lesions in transient single-strand stretches of chromosomal DNA are expected to be especially threatening to genome stability. To test this hypothesis, we designed systems in budding yeast that could generate many kilobases of persistent single-strand DNA next to double-strand breaks or uncapped telomeres. The systems allowed controlled restoration to the double-strand state after applying DNA damage. We found that lesions induced by UV-light and methyl methanesulfonate can be tolerated in long single-strand regions and are hypermutagenic. The hypermutability required PCNA monoubiquitination and was largely attributable to translesion synthesis by the error-prone DNA polymerase ζ. In support of multiple lesions in single-strand DNA being a source of hypermutability, analysis of the UV-induced mutants revealed strong strand-specific bias and unexpectedly high frequency of alleles with widely separated multiple mutations scattered over several kilobases. Hypermutability and multiple mutations associated with lesions in transient stretches of long single-strand DNA may be a source of carcinogenesis and provide selective advantage in adaptive evolution. PMID:19023402

  5. DNA Strand Breaks, Neurodegeneration and Aging in the Brain

    Science.gov (United States)

    Katyal, Sachin; McKinnon, Peter J.

    2013-01-01

    Defective responses to DNA single- or double-strand breaks can result in neurological disease, underscoring the critical importance of DNA repair for neural homeostasis. Human DNA repair-deficient syndromes are generally congenital, in which brain pathology reflects the consequences of developmentally incurred DNA damage. Although, it is unclear to what degree DNA strand-break repair defects in mature neural cells contributes to disease pathology. However, DNA single-strand breaks are a relatively common lesion which if not repaired can impact cells via interference with transcription. Thus, this lesion, and probably to a lesser extent DNA double strand breaks, may be particularly relevant to aging in the neural cell population. In this review we will examine the consequences of defective DNA strand break repair towards homeostasis in the brain. Further, we also consider the utility of mouse models as reagents to understand the connection between DNA strand breaks and aging in the brain. PMID:18455751

  6. Lead Poisoning

    Science.gov (United States)

    ... Topics Environment & Health Healthy Living Pollution Reduce, Reuse, Recycle Science – How It Works The Natural World Games ... OTHERS: Lead has recently been found in some plastic mini-blinds and vertical blinds which were made ...

  7. DNA Strand Breaks, Neurodegeneration and Aging in the Brain

    OpenAIRE

    Katyal, Sachin; McKinnon, Peter J

    2008-01-01

    Defective responses to DNA single- or double-strand breaks can result in neurological disease, underscoring the critical importance of DNA repair for neural homeostasis. Human DNA repair-deficient syndromes are generally congenital, in which brain pathology reflects the consequences of developmentally incurred DNA damage. Although, it is unclear to what degree DNA strand-break repair defects in mature neural cells contributes to disease pathology. However, DNA single-strand breaks are a relat...

  8. The multiple personalities of Watson and Crick strands

    OpenAIRE

    Graur Dan; Cartwright Reed A

    2011-01-01

    Abstract Background In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. Proposal The Saccharomyces Genome Database defines ...

  9. DNA double strand break repair via non-homologous end-joining

    OpenAIRE

    Davis, Anthony J.; Chen, David J.

    2013-01-01

    DNA double-stranded breaks (DSB) are among the most dangerous forms of DNA damage. Unrepaired DSBs results in cells undergoing apoptosis or senescence whereas mis-processing of DSBs can lead to genomic instability and carcinogenesis. One important pathway in eukaryotic cells responsible for the repair of DSBs is non-homologous end-joining (NHEJ). In this review we will discuss the interesting new insights into the mechanism of the NHEJ pathway and the proteins which mediate this repair proces...

  10. Acoustical dead zones and the spatial aggregation of whale strandings.

    Science.gov (United States)

    Sundaram, Bala; Poje, Andrew C; Veit, Richard R; Nganguia, Herve

    2006-02-21

    Cetacean strandings display a marked geographical clustering. We propose a simple, two-dimensional ray-dynamics model of cetacean echolocation to examine the role played by coastline topography in influencing the location and clustering of stranding sites. We find that a number of coastlines known to attract cetacean strandings produce acoustical "Dead Zones" where echolocation signals are severely distorted by purely geometric effects. Using available cetacean stranding data bases from four disparate areas, we show that the geographical clusters in the observations correlate strongly with the regions of distorted echolocation signals as predicted by the model.

  11. Branch migration prevents DNA loss during double-strand break repair.

    Directory of Open Access Journals (Sweden)

    Julia S P Mawer

    2014-08-01

    Full Text Available The repair of DNA double-strand breaks must be accurate to avoid genomic rearrangements that can lead to cell death and disease. This can be accomplished by promoting homologous recombination between correctly aligned sister chromosomes. Here, using a unique system for generating a site-specific DNA double-strand break in one copy of two replicating Escherichia coli sister chromosomes, we analyse the intermediates of sister-sister double-strand break repair. Using two-dimensional agarose gel electrophoresis, we show that when double-strand breaks are formed in the absence of RuvAB, 4-way DNA (Holliday junctions are accumulated in a RecG-dependent manner, arguing against the long-standing view that the redundancy of RuvAB and RecG is in the resolution of Holliday junctions. Using pulsed-field gel electrophoresis, we explain the redundancy by showing that branch migration catalysed by RuvAB and RecG is required for stabilising the intermediates of repair as, when branch migration cannot take place, repair is aborted and DNA is lost at the break locus. We demonstrate that in the repair of correctly aligned sister chromosomes, an unstable early intermediate is stabilised by branch migration. This reliance on branch migration may have evolved to help promote recombination between correctly aligned sister chromosomes to prevent genomic rearrangements.

  12. [Superparamagnetic Cobalt Ferrite Nanoparticles "Blow up" Spatial Ordering of Double-stranded DNA Molecules].

    Science.gov (United States)

    Yevdokimov, Yu M; Pershina, A G; Salyanov, V I; Magaeva, A A; Popenko, V I; Shtykova, E V; Dadinova, L A; Skuridin, S G

    2015-01-01

    The formation of cholesteric liquid-crystalline dispersions formed by double-stranded DNA molecules, handled by positively charged superparamagnetic cobalt ferrite nanoparticles, as well as action of these nanoparticles on DNA dispersion, are considered. The binding of magnetic nanoparticles to the linear double-stranded DNA in solution of high ionic strength (0.3 M NaCl) and subsequent phase exclusion of these complexes from polyethylene glycol-containing solutions lead to their inability to form dispersions, whose particles do possess the spatially twisted arrangement of neighboring double-stranded DNA molecules. The action of magnetic nanoparticles on DNA dispersion (one magnetic nanoparticle per one double-stranded DNA molecule) results in such "perturbation" of DNA structure at sites of magnetic nanoparticles binding that the regular spatial structure of DNA dispersion particles "blows up"; this process is accompanied by disappearance of both abnormal optical activity and characteristic Bragg maximum on the small-angle X-ray scattering curve. Allowing with the fact that the physicochemical properties of the DNA liquid-crystalline dispersion particles reflect features of spatial organization of these molecules in chromosomes of primitive organisms, it is possible, that the found effect can have the relevant biological consequences.

  13. Detection of the strand exchange reaction using DNAzyme and Thermotoga maritima recombinase A.

    Science.gov (United States)

    Jo, Hunho; Lee, Seonghwan; Min, Kyoungin; Ban, Changill

    2012-02-01

    We have designed multiple detection systems for the DNA strand exchange process. Thermostable Thermotoga maritima recombinase A (TmRecA), a core protein in homologous recombination, and DNAzyme, a catalytic DNA that can cleave a specific DNA sequence, are introduced in this work. In a colorimetric method, gold nanoparticles (AuNPs) modified with complementary DNAs (cDNAs) were assembled by annealing. Aggregated AuNPs were then separated irreversibly by TmRecA and DNAzyme, leading to a distinct color change in the particles from purple to red. For the case of fluorometric detection, fluorescein isothiocyanate (FITC)-labeled DNA as a fluorophore and black hole quencher 1 (BHQ1)-labeled DNA as a quencher were used; successful strand exchange was clearly detected by variations in fluorescence intensity. In addition, alterations in the impedance of a gold electrode with immobilized DNA were employed to monitor the regular exchange of DNA strands. All three methods provided sufficient evidence of efficient strand exchange reactions and have great potential for applications in the monitoring of recombination, discovery of new DNAzymes, detection of DNAzymes, and measurement of other protein activities.

  14. Domoic Acid Poisoning as a Possible Cause of Seasonal Cetacean Mass Stranding Events in Tasmania, Australia.

    Science.gov (United States)

    Bengtson Nash, S M; Baddock, M C; Takahashi, E; Dawson, A; Cropp, R

    2017-01-01

    The periodic trend to cetacean mass stranding events in the Australian island state of Tasmania remains unexplained. This article introduces the hypothesis that domoic acid poisoning may be a causative agent in these events. The hypothesis arises from the previously evidenced role of aeolian dust as a vector of iron input to the Southern Ocean; the role of iron enrichment in Pseudo-nitzschia bloom proliferation and domoic acid production; and importantly, the characteristic toxicosis of domoic acid poisoning in mammalian subjects leading to spatial navigation deficits. As a pre-requisite for quantitative evaluation, the plausibility of this hypothesis was considered through correlation analyses between historical monthly stranding event numbers, mean monthly chlorophyll concentration and average monthly atmospheric dust loading. Correlation of these variables, which under the domoic acid stranding scenario would be linked, revealed strong agreement (r = 0.80-0.87). We therefore advocate implementation of strategic quantitative investigation of the role of domoic acid in Tasmanian cetacean mass stranding events.

  15. Signalling of double strand breaks and deprotected telomeres in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Simon eAmiard

    2013-10-01

    Full Text Available Failure to repair DNA double strand breaks (DSB can lead to chromosomal rearrangements and eventually to cancer or cell death. Radiation and environmental pollutants induce DSB and this is of particular relevance to plants due to their sessile life style. DSB also occur naturally in cells during DNA replication and programmed induction of DSB initiates the meiotic recombination essential for gametogenesis in most eukaryotes. The linear nature of most eukaryotic chromosomes means that each chromosome has two "broken" ends. Chromosome ends, or telomeres, are protected by nucleoprotein caps which avoid their recognition as DSB by the cellular DNA repair machinery. Deprotected telomeres are recognized as DSB and become substrates for recombination leading to chromosome fusions, the "bridge-breakage-fusion" cycle, genome rearrangements and cell death. The importance of repair of DSB and the severity of the consequences of their misrepair have led to the presence of multiple, robust mechanisms for their detection and repair. After a brief overview of DSB repair pathways to set the context, we present here an update of current understanding of the detection and signalling of DSB in the plant, Arabidopsis thaliana.

  16. Conservative Repair of a Chromosomal Double-Strand Break by Single-Strand DNA through Two Steps of Annealing▿ †

    OpenAIRE

    Storici, Francesca; Snipe, Joyce R.; Chan, Godwin K.; Dmitry A Gordenin; Michael A Resnick

    2006-01-01

    The repair of chromosomal double-strand breaks (DSBs) is essential to normal cell growth, and homologous recombination is a universal process for DSB repair. We explored DSB repair mechanisms in the yeast Saccharomyces cerevisiae using single-strand oligonucleotides with homology to both sides of a DSB. Oligonucleotide-directed repair occurred exclusively via Rad52- and Rad59-mediated single-strand annealing (SSA). Even the SSA domain of human Rad52 provided partial complementation for a null...

  17. Ecotoxicology: Lead

    Science.gov (United States)

    Scheuhammer, A.M.; Beyer, W.N.; Schmitt, C.J.; Jorgensen, Sven Erik; Fath, Brian D.

    2008-01-01

    Lead (Pb) is a naturally occurring metallic element; trace concentrations are found in all environmental media and in all living things. However, certain human activities, especially base metal mining and smelting; combustion of leaded gasoline; the use of Pb in hunting, target shooting, and recreational angling; the use of Pb-based paints; and the uncontrolled disposal of Pb-containing products such as old vehicle batteries and electronic devices have resulted in increased environmental levels of Pb, and have created risks for Pb exposure and toxicity in invertebrates, fish, and wildlife in some ecosystems.

  18. CRISPR interference directs strand specific spacer acquisition.

    Directory of Open Access Journals (Sweden)

    Daan C Swarts

    Full Text Available BACKGROUND: CRISPR/Cas is a widespread adaptive immune system in prokaryotes. This system integrates short stretches of DNA derived from invading nucleic acids into genomic CRISPR loci, which function as memory of previously encountered invaders. In Escherichia coli, transcripts of these loci are cleaved into small RNAs and utilized by the Cascade complex to bind invader DNA, which is then likely degraded by Cas3 during CRISPR interference. RESULTS: We describe how a CRISPR-activated E. coli K12 is cured from a high copy number plasmid under non-selective conditions in a CRISPR-mediated way. Cured clones integrated at least one up to five anti-plasmid spacers in genomic CRISPR loci. New spacers are integrated directly downstream of the leader sequence. The spacers are non-randomly selected to target protospacers with an AAG protospacer adjacent motif, which is located directly upstream of the protospacer. A co-occurrence of PAM deviations and CRISPR repeat mutations was observed, indicating that one nucleotide from the PAM is incorporated as the last nucleotide of the repeat during integration of a new spacer. When multiple spacers were integrated in a single clone, all spacer targeted the same strand of the plasmid, implying that CRISPR interference caused by the first integrated spacer directs subsequent spacer acquisition events in a strand specific manner. CONCLUSIONS: The E. coli Type I-E CRISPR/Cas system provides resistance against bacteriophage infection, but also enables removal of residing plasmids. We established that there is a positive feedback loop between active spacers in a cluster--in our case the first acquired spacer--and spacers acquired thereafter, possibly through the use of specific DNA degradation products of the CRISPR interference machinery by the CRISPR adaptation machinery. This loop enables a rapid expansion of the spacer repertoire against an actively present DNA element that is already targeted, amplifying the

  19. Leading men

    DEFF Research Database (Denmark)

    Bekker-Nielsen, Tønnes

    2016-01-01

    Through a systematic comparison of c. 50 careers leading to the koinarchate or high priesthood of Asia, Bithynia, Galatia, Lycia, Macedonia and coastal Pontus, as described in funeral or honorary inscriptions of individual koinarchs, it is possible to identify common denominators but also...

  20. Lead grids

    CERN Multimedia

    1974-01-01

    One of the 150 lead grids used in the multiwire proportional chamber g-ray detector. The 0.75 mm diameter holes are spaced 1 mm centre to centre. The grids were made by chemical cutting techniques in the Godet Workshop of the SB Physics.

  1. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA.

    Science.gov (United States)

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela; Gamba, Cristina; Barnett, Ross; Samaniego, José Alfredo; Madrigal, Jazmín Ramos; Orlando, Ludovic; Gilbert, M Thomas P

    2015-12-01

    An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ssDNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained DNA, but this enrichment is less pronounced when dsDNA preparations successfully recover short endogenous DNA fragments (mean size < 70 bp). Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method.

  2. Catalysis of Strand Annealing by Replication Protein A Derives from Its Strand Melting Properties*

    OpenAIRE

    Bartos, Jeremy D.; Willmott, Lyndsay J.; Binz, Sara K.; Wold, Marc S.; Bambara, Robert A.

    2008-01-01

    Eukaryotic DNA-binding protein replication protein A (RPA) has a strand melting property that assists polymerases and helicases in resolving DNA secondary structures. Curiously, previous results suggested that human RPA (hRPA) promotes undesirable recombination by facilitating annealing of flaps produced transiently during DNA replication; however, the mechanism was not understood. We designed a series of substrates, representing displaced DNA flaps generated during ma...

  3. A New Form of Triple-Stranded Helicate Found in Uranyl Complexes of Aliphatic α,ω-Dicarboxylates.

    Science.gov (United States)

    Thuéry, Pierre; Harrowfield, Jack

    2015-11-16

    The reaction of uranyl ions with azelaic or dodecanedioic acids under solvohydrothermal conditions leads to crystallization of anionic dinuclear cage compounds with [M(bipy/phen)3](2+) counterions (M = 3d-block cation), while the smaller suberic acid yields heterometallic metallacycles. Complexes with the longer aliphatic chains are the first triple-stranded helicates reported in actinide chemistry.

  4. A Case Study on the Challenges and Opportunities for School Leaders Implementing a Dual Language Immersion Strand Program

    Science.gov (United States)

    Romero-Johnson, Silvia

    2011-01-01

    The purpose of this case study was to identify the challenges and opportunities that school principals face when leading the implementation of dual language immersion programs as instructional strands. This case study also sought to determine what skills and strategies principals utilized to facilitate the change process for all the stakeholders…

  5. Strategies underlying RNA silencing suppression by negative strand RNA viruses

    NARCIS (Netherlands)

    Hemmes, J.C.

    2007-01-01

    The research described in this thesis focused on the strategies of negative strand RNA viruses to counteract antiviral RNA silencing. In plants and insects, RNA silencing has been shown to act as a sequence specific antiviral defence mechanism that is characterised by the processing of double strand

  6. Strategies underlying RNA silencing suppression by negative strand RNA viruses

    NARCIS (Netherlands)

    Hemmes, J.C.

    2007-01-01

    The research described in this thesis focused on the strategies of negative strand RNA viruses to counteract antiviral RNA silencing. In plants and insects, RNA silencing has been shown to act as a sequence specific antiviral defence mechanism that is characterised by the processing of double strand

  7. A FORMAL SPECIFICATION LANGUAGE FOR DYNAMIC STRAND SPACE MODEL

    Institute of Scientific and Technical Information of China (English)

    刘东喜; 李晓勇; 白英彩

    2002-01-01

    Specification language is used to provide enough information for the model of the cryptographic protocol. This paper first extends strand space model to dynamic strand model, and then a formal specification language for this model is defined by using BNF grammar. Compared with those in literatures, it is simpler because of only concerning the algebraic properties of cryptographic protocols.

  8. Cetaceans stranded in the Netherlands in 2008-2014

    NARCIS (Netherlands)

    Keijl, Guido; Begeman, L.; Hiemstra, S.; IJsseldijk, L.L.; Kamminga, Pepijn

    2016-01-01

    We present a validated list of cetaceans stranded from 2008 up to and including 2014. A total of 4406 cetaceans was found on the Dutch coast during this period, comprising 4346 harbour porpoises (Phocoena phocoena) (98.6% of all strandings) and 59 individuals of twelve other species. The next most n

  9. Cetacean strandings along the coast of Izmir Bay, Turkey

    NARCIS (Netherlands)

    Guclusoy, H.; Veryeri, N.; Cirik, S.

    2004-01-01

    The present paper provides information on the stranding of cetaceans in Izmir Bay, Aegean Sea, between 1992 and 2004. The data were collected opportunistically during sightings and stranding data collection for Monk Seals. A total of 12 cetaceans, namely Bottle-nosed Dolphin, Tursiops truncatus (n=6

  10. The HSV-1 exonuclease, UL12, stimulates recombination by a single strand annealing mechanism.

    Science.gov (United States)

    Schumacher, April J; Mohni, Kareem N; Kan, Yinan; Hendrickson, Eric A; Stark, Jeremy M; Weller, Sandra K

    2012-01-01

    Production of concatemeric DNA is an essential step during HSV infection, as the packaging machinery must recognize longer-than-unit-length concatemers; however, the mechanism by which they are formed is poorly understood. Although it has been proposed that the viral genome circularizes and rolling circle replication leads to the formation of concatemers, several lines of evidence suggest that HSV DNA replication involves recombination-dependent replication reminiscent of bacteriophages λ and T4. Similar to λ, HSV-1 encodes a 5'-to-3' exonuclease (UL12) and a single strand annealing protein [SSAP (ICP8)] that interact with each other and can perform strand exchange in vitro. By analogy with λ phage, HSV may utilize viral and/or cellular recombination proteins during DNA replication. At least four double strand break repair pathways are present in eukaryotic cells, and HSV-1 is known to manipulate several components of these pathways. Chromosomally integrated reporter assays were used to measure the repair of double strand breaks in HSV-infected cells. Single strand annealing (SSA) was increased in HSV-infected cells, while homologous recombination (HR), non-homologous end joining (NHEJ) and alternative non-homologous end joining (A-NHEJ) were decreased. The increase in SSA was abolished when cells were infected with a viral mutant lacking UL12. Moreover, expression of UL12 alone caused an increase in SSA, which was completely eliminated when a UL12 mutant lacking exonuclease activity was expressed. UL12-mediated stimulation of SSA was decreased in cells lacking the cellular SSAP, Rad52, and could be restored by coexpressing the viral SSAP, ICP8, indicating that an SSAP is also required. These results demonstrate that UL12 can specifically stimulate SSA and that either ICP8 or Rad52 can function as an SSAP. We suggest that SSA is the homology-mediated repair pathway utilized during HSV infection.

  11. The HSV-1 exonuclease, UL12, stimulates recombination by a single strand annealing mechanism.

    Directory of Open Access Journals (Sweden)

    April J Schumacher

    Full Text Available Production of concatemeric DNA is an essential step during HSV infection, as the packaging machinery must recognize longer-than-unit-length concatemers; however, the mechanism by which they are formed is poorly understood. Although it has been proposed that the viral genome circularizes and rolling circle replication leads to the formation of concatemers, several lines of evidence suggest that HSV DNA replication involves recombination-dependent replication reminiscent of bacteriophages λ and T4. Similar to λ, HSV-1 encodes a 5'-to-3' exonuclease (UL12 and a single strand annealing protein [SSAP (ICP8] that interact with each other and can perform strand exchange in vitro. By analogy with λ phage, HSV may utilize viral and/or cellular recombination proteins during DNA replication. At least four double strand break repair pathways are present in eukaryotic cells, and HSV-1 is known to manipulate several components of these pathways. Chromosomally integrated reporter assays were used to measure the repair of double strand breaks in HSV-infected cells. Single strand annealing (SSA was increased in HSV-infected cells, while homologous recombination (HR, non-homologous end joining (NHEJ and alternative non-homologous end joining (A-NHEJ were decreased. The increase in SSA was abolished when cells were infected with a viral mutant lacking UL12. Moreover, expression of UL12 alone caused an increase in SSA, which was completely eliminated when a UL12 mutant lacking exonuclease activity was expressed. UL12-mediated stimulation of SSA was decreased in cells lacking the cellular SSAP, Rad52, and could be restored by coexpressing the viral SSAP, ICP8, indicating that an SSAP is also required. These results demonstrate that UL12 can specifically stimulate SSA and that either ICP8 or Rad52 can function as an SSAP. We suggest that SSA is the homology-mediated repair pathway utilized during HSV infection.

  12. Relationship between marine mammal stranding events and offshore earthquakes

    Science.gov (United States)

    Grant, Rachel; Savirina, Anna; Hoppit, Will

    2014-05-01

    The causes of marine mammal stranding events are largely unknown, but may relate to ocean currents, severe weather, anthropogenic noise pollution, and other factors. Large stranding events have been suggested to occur as a result of offshore earthquakes but there is little evidence as yet to support this hypothesis. Stranding events occur in hotspots, which are sometimes areas of high seismic activity, such as Taiwan, and other times, in areas that are removed from seismic zones, such as Cape Cod. We analyse a large and robust dataset of marine mammal stranding data collected off the coast of Washington and Oregon from 1999 to 2010, to look for statistical connections to offshore earthquakes. We looked forward, as well as backward in time from significant seismic events, to ascertain whether stranding occurrences, if connected to earthquakes, are a result of the earthquake preparation period or the earthquake itself. Possible mechanisms are discussed.

  13. The effect of base pair mismatch on DNA strand displacement

    CERN Document Server

    Broadwater, Bo

    2016-01-01

    DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single base pair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration, and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term, the concurrent displacement model, and used the first passage t...

  14. Computing in mammalian cells with nucleic acid strand exchange

    Science.gov (United States)

    Groves, Benjamin; Chen, Yuan-Jyue; Zurla, Chiara; Pochekailov, Sergii; Kirschman, Jonathan L.; Santangelo, Philip J.; Seelig, Georg

    2016-03-01

    DNA strand displacement has been widely used for the design of molecular circuits, motors, and sensors in cell-free settings. Recently, it has been shown that this technology can also operate in biological environments, but capabilities remain limited. Here, we look to adapt strand displacement and exchange reactions to mammalian cells and report DNA circuitry that can directly interact with a native mRNA. We began by optimizing the cellular performance of fluorescent reporters based on four-way strand exchange reactions and identified robust design principles by systematically varying the molecular structure, chemistry and delivery method. Next, we developed and tested AND and OR logic gates based on four-way strand exchange, demonstrating the feasibility of multi-input logic. Finally, we established that functional siRNA could be activated through strand exchange, and used native mRNA as programmable scaffolds for co-localizing gates and visualizing their operation with subcellular resolution.

  15. Who Leads China's Leading Universities?

    Science.gov (United States)

    Huang, Futao

    2017-01-01

    This study attempts to identify the major characteristics of two different groups of institutional leaders in China's leading universities. The study begins with a review of relevant literature and theory. Then, there is a brief introduction to the selection of party secretaries, deputy secretaries, presidents and vice presidents in leading…

  16. Leading Cities

    DEFF Research Database (Denmark)

    Pogner, Karl-Heinz

    2017-01-01

    and technical engineering; Smart Cities) is very prominent in the traditional mass media discourse, in PR / PA of tech companies and traditional municipal administrations; whereas the second one (participation; Livable Cities) is mostly enacted in social media, (local) initiatives, movements, (virtual......) communities, new forms of urban governance in municipal administration and co-competitive city networks. Both forms seem to struggle for getting voice and power in the discourses, negotiations, struggles, and conflicts in Urban Governance about the question how to manage or lead (in) a city. Talking about...

  17. Transformation-associated recombination between diverged and homologous DNA repeats is induced by strand breaks

    Energy Technology Data Exchange (ETDEWEB)

    Larionov, V.; Kouprina, N. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States)]|[Institute of Cytology, St. Petersburg, (Russian Federation); Edlarov, M. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States)]|[Center of Bioengineering, Moscow, (Russian Federation); Perkins, E.; Porter, G.; Resnick, M.A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States)

    1993-12-31

    Rearrangement and deletion within plasmid DNA is commonly observed during transformation. We have examined the mechanisms of transformation-associated recombination in the yeast Saccharomyces cerevisiae using a plasmid system which allowed the effects of physical state and/or extent of homology on recombination to be studied. The plasmid contains homologous or diverged (19%) DNA repeats separated by a genetically detectable color marker. Recombination during transformation for covalently closed circular plasmids was over 100-fold more frequent than during mitotic growth. The frequency of recombination is partly dependent on the method of transformation in that procedures involving lithium acetate or spheroplasting yield higher frequencies than electroporation. When present in the repeats, unique single-strand breaks that are ligatable, as well as double-strand breaks, lead to high levels of recombination between diverged and identical repeats. The transformation-associated recombination between repeat DNA`s is under the influence of the RADS2, RADI and the RNCI genes,

  18. Repair Pathway Choices and Consequences at the Double-Strand Break.

    Science.gov (United States)

    Ceccaldi, Raphael; Rondinelli, Beatrice; D'Andrea, Alan D

    2016-01-01

    DNA double-strand breaks (DSBs) are cytotoxic lesions that threaten genomic integrity. Failure to repair a DSB has deleterious consequences, including genomic instability and cell death. Indeed, misrepair of DSBs can lead to inappropriate end-joining events, which commonly underlie oncogenic transformation due to chromosomal translocations. Typically, cells employ two main mechanisms to repair DSBs: homologous recombination (HR) and classical nonhomologous end joining (C-NHEJ). In addition, alternative error-prone DSB repair pathways, namely alternative end joining (alt-EJ) and single-strand annealing (SSA), have been recently shown to operate in many different conditions and to contribute to genome rearrangements and oncogenic transformation. Here, we review the mechanisms regulating DSB repair pathway choice, together with the potential interconnections between HR and the annealing-dependent error-prone DSB repair pathways.

  19. Compound Poisson Processes and Clustered Damage of Radiation Induced DNA Double Strand Breaks

    Science.gov (United States)

    Gudowska-Nowak, E.; Ritter, S.; Taucher-Scholz, G.; Kraft, G.

    2000-05-01

    Recent experimental data have demonstrated that DNA damage induced by densely ionizing radiation in mammalian cells is distributed along the DNA molecule in the form of clusters. The principal constituent of DNA damage are double-strand breaks (DSB) which are formed when the breaks occur in both DNA strands and are directly opposite or separated by only a few base pairs. DSBs are believed to be most important lesions produced in chromosomes by radiation; interaction between DSBs can lead to cell killing, mutation or carcinogenesis. The paper discusses a model of clustered DSB formation viewed in terms of compound Poisson process along with the predictive essay of the formalism in application to experimental data.

  20. Mechanical and Electrical Modeling of Strands in Two ITER CS Cable Designs

    CERN Document Server

    Torre, A; Ciazynski, D

    2014-01-01

    Following the test of the first Central Solenoid (CS) conductor short samples for the International Thermonuclear Experimental Reactor (ITER) in the SULTAN facility, Iter Organization (IO) decided to manufacture and test two alternate samples using four different cable designs. These samples, while using the same Nb3Sn strand, were meant to assess the influence of various cable design parameters on the conductor performance and behavior under mechanical cycling. In particular, the second of these samples, CSIO2, aimed at comparing designs with modified cabling twist pitches sequences. This sample has been tested, and the two legs exhibited very different behaviors. To help understand what could lead to such a difference, these two cables were mechanically modeled using the MULTIFIL code, and the resulting strain map was used as an input into the CEA electrical code CARMEN. This article presents the main data extracted from the mechanical simulation and its use into the electrical modeling of individual strand...

  1. Uterine Leiomyoma and Prolapse in a Live-stranded Atlantic Spotted Dolphin (Stenella frontalis).

    Science.gov (United States)

    Díaz-Delgado, J; Fernández, A; Edwards, J F; Sierra, E; Xuriach, A; García-Álvarez, N; Sacchini, S; Groch, K R; Andrada, M; Arbelo, M

    2015-07-01

    A uterine prolapse associated with a leiomyoma (fibroid) was observed in a live-stranded Atlantic spotted dolphin (Stenella frontalis). A 7 cm segment of the reproductive tract including the cervix, uterine neck and caudal uterine body had intussuscepted and prolapsed into the cranial vaginal vault. In the leading edge of the intussuscepted/prolapsed uterine wall was a 6 × 3 × 3.5 cm leiomyoma expanding the myometrium. The leiomyoma and prolapse were associated with necrotizing exposure endometritis. This is the first report of a uterine prolapse associated with a leiomyoma in a cetacean. This lesion was believed to be the underlying cause of the live stranding. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Hela细胞端粒DNA断裂损伤%Strand breaks in telomeres in Hela cells

    Institute of Scientific and Technical Information of China (English)

    阳芳; 杨洁萍; 李清焕; 邵兰; 谭铮

    2003-01-01

    Telomeres are the repetitive G-rich DNA sequences at the end of chromosomes and shorten at each round of cell division.Besides the incomplete DNA synthesis,single and double DNA strand breaks,if not repaired, also contribute to the telomere shortening.To assess the frequency of strand breaks in proliferating Hela cells,telomere fragments were released by alkaline denaturing and electrophoresis from cells embedded in agarose,blotted onto membrane,and detected by probe specific to telomere sequence.The quantity of telomere fragments released was estimated to be less than 0.4% of the total telomere content,which corresponded to less than one break per cell.Since the mean length of the terminal restriction fragments of the cells was about 7 kbp,the fragments detected would lead to less than 19 bp in mean telomere shortening [Acta Zoologica Sinica 49(6):873-877,2003].

  3. Nampt is involved in DNA double-strand break repair

    Institute of Scientific and Technical Information of China (English)

    Bingtao Zhu; Xiaoli Deng; Yifan Sun; Lin Bai; Zhikai Xiahou; Yusheng Cong; Xingzhi Xu

    2012-01-01

    DNA double-strand break (DSB) is the most severe form of DNA damage,which is repaired mainly through high-fidelity homologous recombination (HR) or error-prone non-homologous end joining (NHEJ).Defects in the DNA damage response lead to genomic instability and ultimately predispose organs to cancer.Nicotinamide phosphoribosyltransferase (Nampt),which is involved in nicotinamide adenine dinucleotide metabolism,is overexpressed in a variety of tumors.In this report,we found that Nampt physically associated with CtlP and DNA-PKcs/Ku80,which are key factors in HR and NHEJ,respectively.Depletion of Nampt by small interfering RNA (siRNA) led to defective NHEJ-mediated DSB repair and enhanced HR-mediated repair.Furthermore,the inhibition of Nampt expression promoted proliferation of cancer cells and normal human fibroblasts and decreased β-galactosidase staining,indicating a delay in the onset of cellular senescence in normal human fibroblasts.Taken together,our results suggest that Nampt is a suppressor of HR-mediated DSB repair and an enhancer of NHEJ-mediated DSB repair,contributing to the acceleration of cellular senescence.

  4. A Spinach molecular beacon triggered by strand displacement.

    Science.gov (United States)

    Bhadra, Sanchita; Ellington, Andrew D

    2014-08-01

    We have re-engineered the fluorescent RNA aptamer Spinach to be activated in a sequence-dependent manner. The original Spinach aptamer was extended at its 5'- and 3'-ends to create Spinach.ST, which is predicted to fold into an inactive conformation and thus prevent association with the small molecule fluorophore DFHBI. Hybridization of a specific trigger oligonucleotide to a designed toehold leads to toehold-initiated strand displacement and refolds Spinach into the active, fluorophore-binding conformation. Spinach.ST not only specifically detects its target oligonucleotide but can discriminate readily against single-nucleotide mismatches. RNA amplicons produced during nucleic acid sequence-based amplification (NASBA) of DNA or RNA targets could be specifically detected and reported in real-time by conformational activation of Spinach.ST generated by in vitro transcription. In order to adapt any target sequence to detection by a Spinach reporter we used a primer design technique that brings together otherwise distal toehold sequences via hairpin formation. The same techniques could potentially be used to adapt common Spinach reporters to non-nucleic acid analytes, rather than by making fusions between aptamers and Spinach.

  5. submitter Hysteresis Losses and Effective $J_{c}(B)$ Scaling Law for ITER $Nb_{3}Sn$ Strands

    CERN Document Server

    Seiler, E; Bordini, B; Bottura, L; Bessette, D; Vostner, A; Devred, A

    2016-01-01

    Hysteresis losses of five $Nb_{3}Sn$ International Thermonuclear Experimental Reactor reference strands were investigated by means of magnetization loop measurements in a vibrating sample magnetometer in a perpendicularly applied magnetic field. The magnetization loops were recorded while continuously sweeping the applied field between the extreme values $±B_m$, covering a wide range of maximum applied fields (0.2-10 T). In this paper, we compare the directly determined hysteresis losses based on the area of the smaller measured loops and the losses calculated by the integration of the width ΔM of the $B_m$ = 10 T magnetization loop. A suitable fitting function is proposed to describe the ΔM(B) dependence, which leads, for each strand, to an excellent agreement with the experimentally determined hysteresis losses, magnetization, and pinning force. Transport critical current measurements in a perpendicularly applied magnetic field were also performed for all the strands, and on the basis of the comparison w...

  6. Crystal Structure of E. coli RecE Protein Reveals a Toroidal Tetramer for Processing Double-Stranded DNA Breaks

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jinjin; Xing, Xu; Herr, Andrew B.; Bell, Charles E.; (OSU); (UCIN)

    2009-07-21

    Escherichia coli RecE protein is part of the classical RecET recombination system that has recently been used in powerful new methods for genetic engineering. RecE binds to free double-stranded DNA (dsDNA) ends and processively digests the 5{prime}-ended strand to form 5{prime}-mononucleotides and a 3{prime}-overhang that is a substrate for single strand annealing promoted by RecT. Here, we report the crystal structure of the C-terminal nuclease domain of RecE at 2.8 {angstrom} resolution. RecE forms a toroidal tetramer with a central tapered channel that is wide enough to bind dsDNA at one end, but is partially plugged at the other end by the C-terminal segment of the protein. Four narrow tunnels, one within each subunit of the tetramer, lead from the central channel to the four active sites, which lie about 15 {angstrom} from the channel. The structure, combined with mutational studies, suggests a mechanism in which dsDNA enters through the open end of the central channel, the 5{prime}-ended strand passes through a tunnel to access one of the four active sites, and the 3{prime}-ended strand passes through the plugged end of the channel at the back of the tetramer.

  7. Strand critical current degradation in $Nb_{3}$ Sn Rutherford cables

    CERN Document Server

    Barzi, E; Higley, H C; Scanlan, R M; Yamada, R; Zlobin, A V

    2001-01-01

    Fermilab is developing 11 Tesla superconducting accelerator magnets based on Nb/sub 3/Sn superconductor. Multifilamentary Nb/sub 3/Sn strands produced using the modified jelly roll, internal tin, and powder-in-tube technologies were used for the development and test of the prototype cable. To optimize the cable geometry with respect to the critical current, short samples of Rutherford cable with packing factors in the 85 to 95% range were fabricated and studied. In this paper, the results of measurements of critical current, n-value and RRR made on the round virgin strands and on the strands extracted from the cable samples are presented. (5 refs).

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-02-01

    Probability {approx} Location + Kinetic Energy Proxy + Tidal Height + Salmonid Density + Kinetic energy proxy ? Tidal Height + Tidal Height x Salmonid Density. (2) Stranding Probability {approx} Location + Total Wave Distance + Salmonid Density Index. (3) Log(Total Wave Height) {approx} Ship Block + Tidal Height + Location + Ship Speed. (4) Log(Total Wave Excursion Across the Beach) {approx} Location + Kinetic Energy Proxy + Tidal Height The above equations form the basis for a conceptual model of the factors leading to salmon stranding. The equations also form the basis for an approach for assessing impacts of dredging under the before/after study design.

  9. Programmable energy landscapes for kinetic control of DNA strand displacement.

    Science.gov (United States)

    Machinek, Robert R F; Ouldridge, Thomas E; Haley, Natalie E C; Bath, Jonathan; Turberfield, Andrew J

    2014-11-10

    DNA is used to construct synthetic systems that sense, actuate, move and compute. The operation of many dynamic DNA devices depends on toehold-mediated strand displacement, by which one DNA strand displaces another from a duplex. Kinetic control of strand displacement is particularly important in autonomous molecular machinery and molecular computation, in which non-equilibrium systems are controlled through rates of competing processes. Here, we introduce a new method based on the creation of mismatched base pairs as kinetic barriers to strand displacement. Reaction rate constants can be tuned across three orders of magnitude by altering the position of such a defect without significantly changing the stabilities of reactants or products. By modelling reaction free-energy landscapes, we explore the mechanistic basis of this control mechanism. We also demonstrate that oxDNA, a coarse-grained model of DNA, is capable of accurately predicting and explaining the impact of mismatches on displacement kinetics.

  10. DNA strand exchange and RecA homologs in meiosis.

    Science.gov (United States)

    Brown, M Scott; Bishop, Douglas K

    2014-12-04

    Homology search and DNA strand-exchange reactions are central to homologous recombination in meiosis. During meiosis, these processes are regulated such that the probability of choosing a homolog chromatid as recombination partner is enhanced relative to that of choosing a sister chromatid. This regulatory process occurs as homologous chromosomes pair in preparation for assembly of the synaptonemal complex. Two strand-exchange proteins, Rad51 and Dmc1, cooperate in regulated homology search and strand exchange in most organisms. Here, we summarize studies on the properties of these two proteins and their accessory factors. In addition, we review current models for the assembly of meiotic strand-exchange complexes and the possible mechanisms through which the interhomolog bias of recombination partner choice is achieved.

  11. Recovery of stranded costs under electric deregulation: The Winstar doctrine

    Energy Technology Data Exchange (ETDEWEB)

    Person, J.C. [Person and Craver, Washington, DC (United States)

    1998-12-31

    This paper explores the applicability of the Winstar doctrine to the recovery of stranded costs arising from the deregulation of the electric utility industry. Such stranded costs, which have been widely estimated to be in the $100--200 billion range, represent those utility assets whose book value exceed their market value. Not addressed in this paper are the ongoing state and federal legislative initiatives to allow for the recovery of some or all of a utility`s stranded costs, such as through the assessment of competitive transmission charges (CTCs) or through stranded cost securitization. Rather, this paper presents one of several of legal arguments that could be utilized in those situations where a legislative solution either does not exist or does not allow for full book value recovery.

  12. Interaction of DAPI with double-stranded ribonucleic acids.

    OpenAIRE

    Manzini, G.; Xodo, L; Barcellona, M L; Quadrifoglio, F

    1985-01-01

    The interaction of DAPI with natural and synthetic double-stranded polyribonucleotides was studied with different optical and calorimetric methods. The results were similar to those obtained previously with double-stranded polydeoxynucleotides, i.e. two interaction modes, the first of which shows high affinity for AU clusters and consequent strong fluorescence enhancement. The results suggest caution in the use of DAPI as selective fluorescent staining agent for DNA in the presence of RNA. A ...

  13. The N-terminal strand modulates immunoglobulin light chain fibrillogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Pozo-Yauner, Luis del, E-mail: ldelpozo@inmegen.gob.mx [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico); Wall, Jonathan S. [Departments of Radiology and Medicine, The University of Tennessee Medical Center, 1924 Alcoa Highway, Knoxville, TN (United States); González Andrade, Martín [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico); Sánchez-López, Rosana [Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa Cuernavaca, Morelos C.P. 62210 (Mexico); Rodríguez-Ambriz, Sandra L. [Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Calle CEPROBI No. 8, Col. San Isidro, Yautepec, Morelos C.P. 62731 (Mexico); Pérez Carreón, Julio I. [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico); and others

    2014-01-10

    Highlights: •We evaluated the impact of mutations in the N-terminal strand of 6aJL2 protein. •Mutations destabilized the protein in a position-dependent manner. •Destabilizing mutations accelerated the fibrillogenesis by shortening the lag time. •The effect on the kinetic of fibril elongation by seeding was of different nature. •The N-terminal strand is buried in the fibrillar state of 6aJL2 protein. -- Abstract: It has been suggested that the N-terminal strand of the light chain variable domain (V{sub L}) protects the molecule from aggregation by hindering spurious intermolecular contacts. We evaluated the impact of mutations in the N-terminal strand on the thermodynamic stability and kinetic of fibrillogenesis of the V{sub L} protein 6aJL2. Mutations in this strand destabilized the protein in a position-dependent manner, accelerating the fibrillogenesis by shortening the lag time; an effect that correlated with the extent of destabilization. In contrast, the effect on the kinetics of fibril elongation, as assessed in seeding experiments was of different nature, as it was not directly dependant on the degree of destabilization. This finding suggests different factors drive the nucleation-dependent and elongation phases of light chain fibrillogenesis. Finally, taking advantage of the dependence of the Trp fluorescence upon environment, four single Trp substitutions were made in the N-terminal strand, and changes in solvent exposure during aggregation were evaluated by acrylamide-quenching. The results suggest that the N-terminal strand is buried in the fibrillar state of 6aJL2 protein. This finding suggest a possible explanation for the modulating effect exerted by the mutations in this strand on the aggregation behavior of 6aJL2 protein.

  14. A model capturing novel strand symmetries in bacterial DNA

    Energy Technology Data Exchange (ETDEWEB)

    Sobottka, Marcelo, E-mail: sobottka@mtm.ufsc.br [Departamento de Matematica, Universidade Federal de Santa Catarina (Brazil); Hart, Andrew G., E-mail: ahart@dim.uchile.cl [Departamento de Ingenieria Matematica and Centro de Modelamiento Matematico, Universidad de Chile (Chile)

    2011-07-15

    Highlights: {yields} We propose a simple stochastic model to construct primitive DNA sequences. {yields} The model provide an explanation for Chargaff's second parity rule in primitive DNA sequences. {yields} The model is also used to predict a novel type of strand symmetry in primitive DNA sequences. {yields} We extend the results for bacterial DNA sequences and compare distributional properties intrinsic to the model to statistical estimates from 1049 bacterial genomes. {yields} We find out statistical evidences that the novel type of strand symmetry holds for bacterial DNA sequences. -- Abstract: Chargaff's second parity rule for short oligonucleotides states that the frequency of any short nucleotide sequence on a strand is approximately equal to the frequency of its reverse complement on the same strand. Recent studies have shown that, with the exception of organellar DNA, this parity rule generally holds for double-stranded DNA genomes and fails to hold for single-stranded genomes. While Chargaff's first parity rule is fully explained by the Watson-Crick pairing in the DNA double helix, a definitive explanation for the second parity rule has not yet been determined. In this work, we propose a model based on a hidden Markov process for approximating the distributional structure of primitive DNA sequences. Then, we use the model to provide another possible theoretical explanation for Chargaff's second parity rule, and to predict novel distributional aspects of bacterial DNA sequences.

  15. G-Strands and Peakon Collisions on Diff(R

    Directory of Open Access Journals (Sweden)

    Darryl D. Holm

    2013-03-01

    Full Text Available A G-strand is a map g: R×R→G for a Lie group G that follows from Hamilton's principle for a certain class of G-invariant Lagrangians. Some G-strands on finite-dimensional groups satisfy 1+1 space-time evolutionary equations that admit soliton solutions as completely integrable Hamiltonian systems. For example, the SO(3-strand equations may be regarded physically as integrable dynamics for solitons on a continuous spin chain. Previous work has shown that G-strands for diffeomorphisms on the real line possess solutions with singular support (e.g. peakons. This paper studies collisions of such singular solutions of G-strands when G=Diff(R is the group of diffeomorphisms of the real line R, for which the group product is composition of smooth invertible functions. In the case of peakon-antipeakon collisions, the solution reduces to solving either Laplace's equation or the wave equation (depending on a sign in the Lagrangian and is written in terms of their solutions. We also consider the complexified systems of G-strand equations for G=Diff(R corresponding to a harmonic map g: C→Diff(R and find explicit expressions for its peakon-antipeakon solutions, as well.

  16. Protein-free parallel triple-stranded DNA complex formation

    Science.gov (United States)

    Shchyolkina, A. K.; Timofeev, E. N.; Lysov, Yu. P.; Florentiev, V. L.; Jovin, T. M.; Arndt-Jovin, D. J.

    2001-01-01

    A 14 nt DNA sequence 5′-AGAATGTGGCAAAG-3′ from the zinc finger repeat of the human KRAB zinc finger protein gene ZNF91 bearing the intercalator 2-methoxy,6-chloro,9-amino acridine (Acr) attached to the sugar–phosphate backbone in various positions has been shown to form a specific triple helix (triplex) with a 16 bp hairpin (intramolecular) or a two-stranded (intermolecular) duplex having the identical sequence in the same (parallel) orientation. Intramolecular targets with the identical sequence in the antiparallel orientation and a non-specific target sequence were tested as controls. Apparent binding constants for formation of the triplex were determined by quantitating electrophoretic band shifts. Binding of the single-stranded oligonucleotide probe sequence to the target led to an increase in the fluorescence anisotropy of acridine. The parallel orientation of the two identical sequence segments was confirmed by measurement of fluorescence resonance energy transfer between the acridine on the 5′-end of the probe strand as donor and BODIPY-Texas Red on the 3′-amino group of either strand of the target duplex as acceptor. There was full protection from OsO4-bipyridine modification of thymines in the probe strand of the triplex, in accordance with the presumed triplex formation, which excluded displacement of the homologous duplex strand by the probe–intercalator conjugate. The implications of these results for the existence of protein-independent parallel triplexes are discussed. PMID:11160932

  17. DNA Origami with Double Stranded DNA as a Unified Scaffold

    Science.gov (United States)

    Yang, Yang; Han, Dongran; Nangreave, Jeanette; Liu, Yan; Yan, Hao

    2013-01-01

    Scaffolded DNA origami is a widely used technology for self-assembling precisely structured nanoscale objects that contain a large number of addressable features. Typical scaffolds are long, single strands of DNA (ssDNA) that are folded into distinct shapes through the action of many, short ssDNA staples that are complementary to several different domains of the scaffold. However, sources of long single stranded DNA are scarce, limiting the size and complexity of structures that can be assembled. Here we demonstrated that dsDNA scaffolds can be directly used to fabricate integrated DNA origami structures that incorporate both of the constituent ssDNA molecules. Two basic principles were employed in the design of scaffold folding paths – folding path asymmetry and periodic convergence of the two ssDNA scaffold strands. Asymmetry in the folding path minimizes unwanted complementarity between staples, and incorporating an offset between the folding paths of each ssDNA scaffold strand reduces the number of times that complementary portions of the strands are brought into close proximity with one another, both of which decrease the likelihood of dsDNA scaffold recovery. Meanwhile, the folding paths of the two ssDNA scaffold strands were designed to periodically converge to promote the assembly of a single, unified structure rather than two individual ones. Our results reveal that this basic strategy can be used to reliably assemble integrated DNA nanostructures from dsDNA scaffolds. PMID:22830653

  18. The importance of becoming double-stranded: Innate immunity and the kinetic model of HIV-1 central plus strand synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Poeschla, Eric, E-mail: poeschla.eric@mayo.edu

    2013-06-20

    Central initiation of plus strand synthesis is a conserved feature of lentiviruses and certain other retroelements. This complication of the standard reverse transcription mechanism produces a transient “central DNA flap” in the viral cDNA, which has been proposed to mediate its subsequent nuclear import. This model has assumed that the important feature is the flapped DNA structure itself rather than the process that produces it. Recently, an alternative kinetic model was proposed. It posits that central plus strand synthesis functions to accelerate conversion to the double-stranded state, thereby helping HIV-1 to evade single-strand DNA-targeting antiviral restrictions such as APOBEC3 proteins, and perhaps to avoid innate immune sensor mechanisms. The model is consistent with evidence that lentiviruses must often synthesize their cDNAs when dNTP concentrations are limiting and with data linking reverse transcription and uncoating. There may be additional kinetic advantages for the artificial genomes of lentiviral gene therapy vectors. - Highlights: • Two main functional models for HIV central plus strand synthesis have been proposed. • In one, a transient central DNA flap in the viral cDNA mediates HIV-1 nuclear import. • In the other, multiple kinetic consequences are emphasized. • One is defense against APOBEC3G, which deaminates single-stranded DNA. • Future questions pertain to antiviral restriction, uncoating and nuclear import.

  19. Strength and reliability of Oriented Strand Lumber made from heat-treated Parawood strands

    Directory of Open Access Journals (Sweden)

    Veerapong Chotchuay

    2008-08-01

    Full Text Available This study was carried out to investigate engineering properties of one type of wood composites known as Oriented Strand Lumber (OSL. Heat-treated Parawood strands were used for producing OSL specimens (HOSL and compared to a control one (nonheat-treated or NOSL. The structural application as beams was selected to determine the effect of sheared volume to longitudinal shear strength since shear failure is a critical mode of OSL. The reliability concept was then employedto analyze the data to ensure that OSL structural members can be used for construction safely and economically. The results indicated that mean values of strength of HOSL subjected to axial loading, i.e., compression (39 MPa and tension (36 MPa parallel to the grain as well as bending in the flatwise (59 MPa and edgewise (61 MPa directions were significantly higher than those of NOSL. However, the differences between HOSL and NOSL subjected to normal loading, i.e., compression perpendicular to the grain (26 vs 25 MPa, shear parallel to the grain (4 vs 3 MPa and internal bonding (0.48 vs 0.47 MPa were non-significant. The results of shear strength studies showed that the shear strength ofHOSL beams was higher than that of NOSL beams and regression analysis revealed that the shear strength depended on sheared volume. It showed that shear strength decreased with increasing sheared volume. The results of the reliability analysis indicated that the fitted distribution of the flexural rigidity (EI could be represented well as normal. The coefficient of variation of the fitted EI distribution was found to be within the serviceability limit state required by the building codes. This implies that OSL beams can be used safely as an alternative structural material for wood construction. The safetyfactor and recommended allowable design stresses are also presented.

  20. SCAI promotes DNA double-strand break repair in distinct chromosomal contexts

    DEFF Research Database (Denmark)

    Hansen, Rebecca Kring; Mund, Andreas; Poulsen, Sara Lund

    2016-01-01

    DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions, whose accurate repair by non-homologous end-joining (NHEJ) or homologous recombination (HR) is crucial for genome integrity and is strongly influenced by the local chromatin environment. Here, we identify SCAI (suppressor of cancer...... in repressive chromatin environments. Moreover, we establish an important role of SCAI in meiotic recombination, as SCAI deficiency in mice leads to germ cell loss and subfertility associated with impaired retention of the DMC1 recombinase on meiotic chromosomes. Collectively, our findings uncover SCAI...

  1. Role of stranded gas in increasing global gas supplies

    Science.gov (United States)

    Attanasi, E.D.; Freeman, P.A.

    2013-01-01

    This report synthesizes the findings of three regional studies in order to evaluate, at the global scale, the contribution that stranded gas resources can make to global natural gas supplies. Stranded gas, as defined for this study, is natural gas in discovered conventional gas and oil fields that is currently not commercially producible for either physical or economic reasons. The regional studies evaluated the cost of bringing the large volumes of undeveloped gas in stranded gas fields to selected markets. In particular, stranded gas fields of selected Atlantic Basin countries, north Africa, Russia, and central Asia are screened to determine whether the volumes are sufficient to meet Europe’s increasing demand for gas imports. Stranded gas fields in Russia, central Asia, Southeast Asia, and Australia are also screened to estimate development, production, and transport costs and corresponding gas volumes that could be supplied to Asian markets in China, India, Japan, and South Korea. The data and cost analysis presented here suggest that for the European market and the markets examined in Asia, the development of stranded gas provides a way to meet projected gas import demands for the 2020-to-2040 period. Although this is a reconnaissance-type appraisal, it is based on volumes of gas that are associated with individual identified fields. Individual field data were carefully examined. Some fields were not evaluated because current technology was insufficient or it appeared the gas was likely to be held off the export market. Most of the evaluated stranded gas can be produced and delivered to markets at costs comparable to historical prices. Moreover, the associated volumes of gas are sufficient to provide an interim supply while additional technologies are developed to unlock gas diffused in shale and hydrates or while countries transition to making a greater use of renewable energy sources.

  2. Stranding Events of Kogia Whales along the Brazilian Coast.

    Directory of Open Access Journals (Sweden)

    Jailson F Moura

    Full Text Available The genus Kogia, which comprises only two extant species, Kogia sima and Kogia breviceps, represents one of the least known groups of cetaceans in the global ocean. In some coastal regions, however, stranding events of these species have been relatively common over the last decades. Stranding provides the opportunity to investigate the biology of these cetaceans and to explore the epidemiological aspects associated with the mortality of the organisms found on the beach. A number of disturbances (including pelagic fisheries, chemical pollution, boat strikes, and noise pollution have been confirmed to pose a particular threat to the Kogia species. However, no study has yet investigated potential relationships between environmental conditions and stranding events. Here we analyse how a collection of environmental, physical, and biological variables, such as wind, sea surface temperature (SST, water depth, and chlorophyll-a, correlate to Kogia stranding events along the Brazilian coast. The results of our statistical analyses suggest that K. sima is more likely found in warm tropical waters, which provide an explanation for the high frequency of stranding in northeastern Brazilian coast. In contrast, K. breviceps appears to have a preference for temperate and productive waters. Wind speed results to be also an important factor for predicting Kogia strandings in Brazilian coast. Additionally, literature information in combination with our own data and analyses of stomach contents confirms that oceanic cephalopods constitute the primary nutritional source of both Kogia species. By using the available information as a qualitative proxy for habitat preference and feeding ecology, our study provides a novel and comprehensive assessment of Kogia stranding data in relation to environmental conditions along the Brazilian coast.

  3. Stranding Events of Kogia Whales along the Brazilian Coast.

    Science.gov (United States)

    Moura, Jailson F; Acevedo-Trejos, Esteban; Tavares, Davi C; Meirelles, Ana C O; Silva, Cristine P N; Oliveira, Larissa R; Santos, Roberta A; Wickert, Janaína C; Machado, Rodrigo; Siciliano, Salvatore; Merico, Agostino

    2016-01-01

    The genus Kogia, which comprises only two extant species, Kogia sima and Kogia breviceps, represents one of the least known groups of cetaceans in the global ocean. In some coastal regions, however, stranding events of these species have been relatively common over the last decades. Stranding provides the opportunity to investigate the biology of these cetaceans and to explore the epidemiological aspects associated with the mortality of the organisms found on the beach. A number of disturbances (including pelagic fisheries, chemical pollution, boat strikes, and noise pollution) have been confirmed to pose a particular threat to the Kogia species. However, no study has yet investigated potential relationships between environmental conditions and stranding events. Here we analyse how a collection of environmental, physical, and biological variables, such as wind, sea surface temperature (SST), water depth, and chlorophyll-a, correlate to Kogia stranding events along the Brazilian coast. The results of our statistical analyses suggest that K. sima is more likely found in warm tropical waters, which provide an explanation for the high frequency of stranding in northeastern Brazilian coast. In contrast, K. breviceps appears to have a preference for temperate and productive waters. Wind speed results to be also an important factor for predicting Kogia strandings in Brazilian coast. Additionally, literature information in combination with our own data and analyses of stomach contents confirms that oceanic cephalopods constitute the primary nutritional source of both Kogia species. By using the available information as a qualitative proxy for habitat preference and feeding ecology, our study provides a novel and comprehensive assessment of Kogia stranding data in relation to environmental conditions along the Brazilian coast.

  4. Methods for DNA Strand Breaks Detection

    Directory of Open Access Journals (Sweden)

    Gholamreza Motalleb

    2012-07-01

    Full Text Available The study of Deoxyribonucleic Acid (DNA damage holds a wide interest within both basic and applied fields of research. Elucidating the mechanisms involved in the generation of DNA damage and the consequences of this damage, will have an enormous impact on multiple fields of scientific research and will ultimately lead to a better understanding of human disease. In this review article, a variety of experimental molecular biology techniques will be described.

  5. Accurate strand-specific quantification of viral RNA.

    Directory of Open Access Journals (Sweden)

    Nicole E Plaskon

    Full Text Available The presence of full-length complements of viral genomic RNA is a hallmark of RNA virus replication within an infected cell. As such, methods for detecting and measuring specific strands of viral RNA in infected cells and tissues are important in the study of RNA viruses. Strand-specific quantitative real-time PCR (ssqPCR assays are increasingly being used for this purpose, but the accuracy of these assays depends on the assumption that the amount of cDNA measured during the quantitative PCR (qPCR step accurately reflects amounts of a specific viral RNA strand present in the RT reaction. To specifically test this assumption, we developed multiple ssqPCR assays for the positive-strand RNA virus o'nyong-nyong (ONNV that were based upon the most prevalent ssqPCR assay design types in the literature. We then compared various parameters of the ONNV-specific assays. We found that an assay employing standard unmodified virus-specific primers failed to discern the difference between cDNAs generated from virus specific primers and those generated through false priming. Further, we were unable to accurately measure levels of ONNV (- strand RNA with this assay when higher levels of cDNA generated from the (+ strand were present. Taken together, these results suggest that assays of this type do not accurately quantify levels of the anti-genomic strand present during RNA virus infectious cycles. However, an assay permitting the use of a tag-specific primer was able to distinguish cDNAs transcribed from ONNV (- strand RNA from other cDNAs present, thus allowing accurate quantification of the anti-genomic strand. We also report the sensitivities of two different detection strategies and chemistries, SYBR(R Green and DNA hydrolysis probes, used with our tagged ONNV-specific ssqPCR assays. Finally, we describe development, design and validation of ssqPCR assays for chikungunya virus (CHIKV, the recent cause of large outbreaks of disease in the Indian Ocean

  6. The superconducting strand for the CMS solenoid conductor

    CERN Document Server

    Curé, B; Campi, D; Goodrich, L F; Horváth, I L; Kircher, F; Liikamaa, R; Seppälä, J; Smith, R P; Teuho, J; Vieillard, L

    2002-01-01

    The Compact Muon Solenoid (CMS) is one of the general-purpose detectors to be provided for the LHC project at CERN. The design field of the CMS superconducting magnet is 4 T, the magnetic length is 12.5 m and the free bore is 6 m. Approximately 2000 km of superconducting strand is under procurement for the conductor of the CMS superconducting solenoid. Each strand length is required to be an integral multiple of 2.75 km. The strand is composed of copper- stabilized multifilamentary Nb-Ti with Nb barrier. Individual strands are identified by distinctive patterns of Nb-Ti filaments selected during stacking of the monofilaments. The statistics of piece length, measurements of I/sub c/, n-value, copper RRR, (Cu+Nb)/Nb-Ti ratio, as well as the results of independent cross checks of these quantities, are presented. A study was performed on the CMS strands to investigate the critical current degradation due to various heat treatments. The degradation versus annealing temperature and duration are reported. (4 refs).

  7. Heavy ion induced double strand breaks in bacteria and bacteriophages

    Science.gov (United States)

    Micke, U.; Schäfer, M.; Anton, A.; Horneck, G.; Bücker, H.

    DNA damage induced by heavy ions in bacterial cells and bacteriophages such as Bacillus subtilis, E. coli and Bacteriophage Tl were investigated by analyzing the double strand breaks in the chromosomal DNA. This kind of lesion is considered as one of the main reasons for lethal events. To analyze double strand breaks in long molecules of DNA - up to some Mbp in length - the technique of pulse field agarose gel electrophoresis has been used. This allows the detection of one double strand break per genome. Cell lysis and DNA isolation were performed in small agarose blocks directly. This procedure secured minimum DNA destruction by shearing forces. After running a gel, the DNA was stained with ethidium bromide. The light intensity of ethidium bromide fluorescence for both the outcoming (running) DNA and the remaining intact DNA were measured by scanning. The mean number of double strand breaks was calculated by determining the quotient of these intensities. Strand break induction after heavy ion and X-ray irradiation was compared.

  8. Single strand DNA binding proteins 1 and 2 protect newly replicated telomeres

    Institute of Scientific and Technical Information of China (English)

    Peili Gu; Wei Deng; Ming Lei; Sandy Chang

    2013-01-01

    Human single-strand (ss) DNA binding proteins 1 and 2 (hSSB1 and 2) are components of the hSSB1/2-INTS3-C9orf80 heterotrimeric protein complex shown to participate in DNA damage response and maintenance of genome stability.However,their roles at telomeres remain unknown.Here,we generated murine SSB1 conditional knockout mice and cells and found that mSSB1 plays a critical role in telomere end protection.Both mSSB1 and mSSB2 localize to a subset of telomeres and are required to repair TRF2-deficient telomeres.Deletion of mSSB1 resulted in increased chromatid-type fusions involving both leading-and lagging-strand telomeric DNA,suggesting that it is required for the protection of G-overhangs.mSSB1's interaction with INTS3 is required for its localization to damaged DNA.mSSB1 interacts with Potla,but not Potlb,and its association with telomeric ssDNA requires Potla.mSSB1△/△ mice die at birth with developmental abnormalities,while mice with the hypomorphic mSSB1F/F allele are born alive and display increased sensitivity to ionizing radiation (IR).Our results suggest that mSSB1 is required to maintain genome stability,and document a previously unrecognized role for mSSB1/2 in the protection of newly replicated leading-and lagging-strand telomeres.

  9. PROPERTIES OF DOUBLE-STRANDED DNA AS A POLYELECTROLYTE.

    Science.gov (United States)

    OHNISHI, T

    1963-11-01

    The stability of the structure of double-stranded DNA in the salt-free solution is discussed on the basis of the polyelectrolyte theory. Assuming that DNA is an infinitely long rod, and the formation of double strands is divided into combining process and folding process, the free energy changes required in these processes are calculated by the use of the exact solutions of two-dimensional Poisson-Boltzmann equation for the one rod and the two rod systems.By strong depression of electrostatic interaction due to counter-ion condensation phenomena, the free energy change is remarkably decreased so that the double-stranded structure of DNA can be stabilized by energy of hydrogen bonds between base pairs. The increase of the activity coefficient of a counterion upon heat denaturation of DNA is also explained.

  10. Analyses of point mutation repair and allelic heterogeneity generated by CRISPR/Cas9 and single-stranded DNA oligonucleotides.

    Science.gov (United States)

    Bialk, Pawel; Sansbury, Brett; Rivera-Torres, Natalia; Bloh, Kevin; Man, Dula; Kmiec, Eric B

    2016-09-09

    The repair of a point mutation can be facilitated by combined activity of a single-stranded oligonucleotide and a CRISPR/Cas9 system. While the mechanism of action of combinatorial gene editing remains to be elucidated, the regulatory circuitry of nucleotide exchange executed by oligonucleotides alone has been largely defined. The presence of the appropriate CRISPR/Cas9 system leads to an enhancement in the frequency of gene editing directed by single-stranded DNA oligonucleotides. While CRISPR/Cas9 executes double-stranded DNA cleavage efficiently, closure of the broken chromosomes is dynamic, as varying degrees of heterogeneity of the cleavage products appear to accompany the emergence of the corrected base pair. We provide a detailed analysis of allelic variance at and surrounding the target site. In one particular case, we report sequence alteration directed by a distinct member of the same gene family. Our data suggests that single-stranded DNA molecules may influence DNA junction heterogeneity created by CRISPR/Cas9.

  11. Interaction of DAPI with double-stranded ribonucleic acids.

    Science.gov (United States)

    Manzini, G; Xodo, L; Barcellona, M L; Quadrifoglio, F

    1985-01-01

    The interaction of DAPI with natural and synthetic double-stranded polyribonucleotides was studied with different optical and calorimetric methods. The results were similar to those obtained previously with double-stranded polydeoxynucleotides, i.e. two interaction modes, the first of which shows high affinity for AU clusters and consequent strong fluorescence enhancement. The results suggest caution in the use of DAPI as selective fluorescent staining agent for DNA in the presence of RNA. A narrow groove binding model with hydrogen bonds between DAPI and AU pairs is proposed. An intercalation mechanism can be excluded because of the non planarity of DAPI molecule. PMID:4080554

  12. Crystal structure of four-stranded Oxytricha telomeric DNA

    Science.gov (United States)

    Kang, C.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A.

    1992-01-01

    The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

  13. [Effect of single-stranded and double-stranded breaks on the melting temperature of phage T2 DNA].

    Science.gov (United States)

    Iurgaĭtis, A P; Lazurkin, Iu S; Bannikov, Iu A

    1979-01-01

    The effect of single- and double-stranded breaks in DNA phage T2, on the melting temperature of this DNA in the 0,05 M SSC solution, was investigated. The number of cleavages per 1000 nucleotide pairs varied in the range of 0 to 10. It is shown that single- and double-stranded breaks affect the melting temperature with approximately (within 20%) the same efficiency. The relationship between the melting temperature shift (delta Tm) and the number of cleavages is non-linear. The magnitude of the effect is characterized by delta Tm of 2 +/- 0.4 degrees C for the average inter-cleavage distance of 200 base pairs. It is shown that the observed melting curves are non-equilibrium ones, which is probably due to the fact that the effect of cleavages on the melting temperature is largely results from the complete and practically irreversible separation of strands.

  14. Ligation of double-stranded and single-stranded [Oligo(dT)] DNA by vaccinia virus DNA ligase

    OpenAIRE

    1996-01-01

    Vaccinia virus DNA ligase has been expressed in Escherichia coli, purified, and biochemically characterized. The enzyme ligates double-stranded (ds) DNA substrates with either cohesive or blunt-end termini and the latter reaction is stimulated by PEG. Vaccinia virus DNA ligase can also ligate oligo(dT) when annealed to either a poly(dA) or a poly(rA) backbone and, remarkably, free oligo(dT). This ligation of a single-stranded (ss) substrate is unique among eukaryotic DNA ligases. The enzyme r...

  15. DNA replication of single-stranded Escherichia coli DNA phages

    NARCIS (Netherlands)

    Baas, P.D.

    1985-01-01

    Research on single-stranded DNA phages has contributed tremendously to our knowledge of several fundamental life-processes. The small size of their genomes and the fast rate at which they multiply in their host, Escherichia coil, made them attractive candidates for various studies. There are two cla

  16. Chromatin remodelers in the DNA double strand break response

    NARCIS (Netherlands)

    Smeenk, Godelieve

    2012-01-01

    During my PhD project, I studied the role of several chromatin remodelers in the DNA double strand break (DSB) response. We discovered that both CHD4 and SMARCA5 are required for ubiquitin signaling through the E3 ubiquitin ligases RNF8 and RNF168, which is a central signaling event in the response

  17. Polarity, Continuity, and Alignment in Plant Vascular Strands

    Institute of Scientific and Technical Information of China (English)

    Megan G. Sawchuk; Enrico Scarpella

    2013-01-01

    Plant vascular cells are joined end to end along uninterrupted lines to connect shoot organs with roots;vascular strands are thus polar, continuous, and internally aligned. What controls the formation of vascular strands with these properties? The “auxin canalization hypothesis”-based on positive feedback between auxin flow through a cell and the cell’s capacity for auxin transport-predicts the selection of continuous files of cells that transport auxin polarly, thus accounting for the polarity and continuity of vascular strands. By contrast, polar, continuous auxin transport-though required-is insufficient to promote internal alignment of vascular strands, implicating additional factors. The auxin canalization hypothesis was derived from the response of mature tissue to auxin application but is consistent with molecular and cellular events in embryo axis formation and shoot organ development. Objections to the hypothesis have been raised based on vascular organizations in callus tissue and shoot organs but seem unsupported by available evidence. Other objections call instead for further research; yet the inductive and orienting influence of auxin on continuous vascular differentiation remains unique.

  18. DNA strand exchange catalyzed by molecular crowding in PEG solutions

    KAUST Repository

    Feng, Bobo

    2010-01-01

    DNA strand exchange is catalyzed by molecular crowding and hydrophobic interactions in concentrated aqueous solutions of polyethylene glycol, a discovery of relevance for understanding the function of recombination enzymes and with potential applications to DNA nanotechnology. © 2010 The Royal Society of Chemistry.

  19. Nucleic Acid Analogue Induced Transcription of Double Stranded DNA

    DEFF Research Database (Denmark)

    1998-01-01

    RNA is transcribed from a double stranded DNA template by forming a complex by hybridizing to the template at a desired transcription initiation site one or more oligonucleic acid analogues of the PNA type capable of forming a transcription initiation site with the DNA and exposing the complex...

  20. Targeting DNA double-strand breaks with TAL effector nucleases.

    Science.gov (United States)

    Christian, Michelle; Cermak, Tomas; Doyle, Erin L; Schmidt, Clarice; Zhang, Feng; Hummel, Aaron; Bogdanove, Adam J; Voytas, Daniel F

    2010-10-01

    Engineered nucleases that cleave specific DNA sequences in vivo are valuable reagents for targeted mutagenesis. Here we report a new class of sequence-specific nucleases created by fusing transcription activator-like effectors (TALEs) to the catalytic domain of the FokI endonuclease. Both native and custom TALE-nuclease fusions direct DNA double-strand breaks to specific, targeted sites.

  1. Negative-strand RNA viruses: The plant-infecting counterparts

    NARCIS (Netherlands)

    Kormelink, R.J.M.; Garcia, M.L.; Goodin, M.; Sasaya, T.; Haenni, A.L.

    2011-01-01

    While a large number of negative-strand (-)RNA viruses infect animals and humans, a relative small number have plants as their primary host. Some of these have been classified within families together with animal/human infecting viruses due to similarities in particle morphology and genome organizat

  2. On the Distinction between Preposition Stranding and Orphan Prepositions

    Science.gov (United States)

    Roberge, Yves

    2012-01-01

    Poplack, Zentz and Dion (PZD; Poplack, Zentz & Dion, 2011, this issue) examine the often unquestioned assumption that the existence of preposition stranding (PS) in Canadian French is linked to the presence of a contact situation with English in the North American context. Although this issue has been the topic of previous research from a…

  3. Cetaceans stranded in the Netherlands from 1998 to 2007

    NARCIS (Netherlands)

    Camphuysen, C.J.; Smeenk, C.; Addink, M.; Jansen, O.E.

    2008-01-01

    Between 1998 and 2007, 2063 cetaceans were found stranded in the Netherlands, representing at least 14 species. Two species, humpback whale (Megaptera novaeangliae) and Blainville’s beaked whale (Mesoplodon densirostris), are additions to the Dutch list. Apart from the first humpback whales, relativ

  4. Cetaceans stranded in the Netherlands from 1998 to 2007

    NARCIS (Netherlands)

    Camphuysen, C.J.; Smeenk, C.; Addink, M.; Grouw, van H.; Jansen, O.E.

    2008-01-01

    Between 1998 and 2007, 2063 cetaceans were found stranded in the Netherlands, representing at least 14 species. Two species, humpback whale (Megaptera novaeangliae) and Blainville's beaked whale (Mesoplodon densirostris), are additions to the Dutch list. Apart from the first humpback whales, relativ

  5. Chromatin remodelers in the DNA double strand break response

    NARCIS (Netherlands)

    Smeenk, Godelieve

    2012-01-01

    During my PhD project, I studied the role of several chromatin remodelers in the DNA double strand break (DSB) response. We discovered that both CHD4 and SMARCA5 are required for ubiquitin signaling through the E3 ubiquitin ligases RNF8 and RNF168, which is a central signaling event in the response

  6. Double strand break repair functions of histone H2AX

    Energy Technology Data Exchange (ETDEWEB)

    Scully, Ralph, E-mail: rscully@bidmc.harvard.edu; Xie, Anyong

    2013-10-15

    Chromosomal double strand breaks provoke an extensive reaction in neighboring chromatin, characterized by phosphorylation of histone H2AX on serine 139 of its C-terminal tail (to form “γH2AX”). The γH2AX response contributes to the repair of double strand breaks encountered in a variety of different contexts, including those induced by ionizing radiation, physiologically programmed breaks that characterize normal immune cell development and the pathological exposure of DNA ends triggered by telomere dysfunction. γH2AX also participates in the evolutionarily conserved process of sister chromatid recombination, a homologous recombination pathway involved in the suppression of genomic instability during DNA replication and directly implicated in tumor suppression. At a biochemical level, the γH2AX response provides a compelling example of how the “histone code” is adapted to the regulation of double strand break repair. Here, we review progress in research aimed at understanding how γH2AX contributes to double strand break repair in mammalian cells.

  7. Sensitive, Specific Complementary - Strand Optical Detection of Viral RNA

    Science.gov (United States)

    1997-06-01

    promise Its components have been characterized and proven to show unparalleled sensitivity; in addition, an innovative method for improving...sensing. 14. SUBJECT TERMS 15. NUMBER OF PAGES RNA, enterovirii, biosensor, evanscent waves, refractometry , 31 phase detection, complementary strand...Phase Measurements (10) Tri-Phase Detection Method . (11) Phase Detectors (12) Phase Processor Board (13) Laboratory Experim ents

  8. Excited states in DNA strands investigated by ultrafast laser spectroscopy.

    Science.gov (United States)

    Chen, Jinquan; Zhang, Yuyuan; Kohler, Bern

    2015-01-01

    Ultrafast laser experiments on carefully selected DNA model compounds probe the effects of base stacking, base pairing, and structural disorder on excited electronic states formed by UV absorption in single and double DNA strands. Direct π-orbital overlap between two stacked bases in a dinucleotide or in a longer single strand creates new excited states that decay orders of magnitude more slowly than the generally subpicosecond excited states of monomeric bases. Half or more of all excited states in single strands decay in this manner. Ultrafast mid-IR transient absorption experiments reveal that the long-lived excited states in a number of model compounds are charge transfer states formed by interbase electron transfer, which subsequently decay by charge recombination. The lifetimes of the charge transfer states are surprisingly independent of how the stacked bases are oriented, but disruption of π-stacking, either by elevating temperature or by adding a denaturing co-solvent, completely eliminates this decay channel. Time-resolved emission measurements support the conclusion that these states are populated very rapidly from initial excitons. These experiments also reveal the existence of populations of emissive excited states that decay on the nanosecond time scale. The quantum yield of these states is very small for UVB/UVC excitation, but increases at UVA wavelengths. In double strands, hydrogen bonding between bases perturbs, but does not quench, the long-lived excited states. Kinetic isotope effects on the excited-state dynamics suggest that intrastrand electron transfer may couple to interstrand proton transfer. By revealing how structure and non-covalent interactions affect excited-state dynamics, on-going experimental and theoretical studies of excited states in DNA strands can advance understanding of fundamental photophysics in other nanoscale systems.

  9. RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

    Directory of Open Access Journals (Sweden)

    Andronescu Mirela

    2008-08-01

    Full Text Available Abstract Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. Results In this paper we describe RNA STRAND – the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. Conclusion RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.

  10. Same-strand overlapping genes in bacteria: compositional determinants of phase bias

    Directory of Open Access Journals (Sweden)

    Landan Giddy

    2008-08-01

    Full Text Available Abstract Background Same-strand overlapping genes may occur in frameshifts of one (phase 1 or two nucleotides (phase 2. In previous studies of bacterial genomes, long phase-1 overlaps were found to be more numerous than long phase-2 overlaps. This bias was explained by either genomic location or an unspecified selection advantage. Models that focused on the ability of the two genes to evolve independently did not predict this phase bias. Here, we propose that a purely compositional model explains the phase bias in a more parsimonious manner. Same-strand overlapping genes may arise through either a mutation at the termination codon of the upstream gene or a mutation at the initiation codon of the downstream gene. We hypothesized that given these two scenarios, the frequencies of initiation and termination codons in the two phases may determine the number for overlapping genes. Results We examined the frequencies of initiation- and termination-codons in the two phases, and found that termination codons do not significantly differ between the two phases, whereas initiation codons are more abundant in phase 1. We found that the primary factors explaining the phase inequality are the frequencies of amino acids whose codons may combine to form start codons in the two phases. We show that the frequencies of start codons in each of the two phases, and, hence, the potential for the creation of overlapping genes, are determined by a universal amino-acid frequency and species-specific codon usage, leading to a correlation between long phase-1 overlaps and genomic GC content. Conclusion Our model explains the phase bias in same-strand overlapping genes by compositional factors without invoking selection. Therefore, it can be used as a null model of neutral evolution to test selection hypotheses concerning the evolution of overlapping genes. Reviewers This article was reviewed by Bill Martin, Itai Yanai, and Mikhail Gelfand.

  11. Different Pathways Leading to Integrase Inhibitors Resistance

    Science.gov (United States)

    Thierry, Eloïse; Deprez, Eric; Delelis, Olivier

    2017-01-01

    Integrase strand-transfer inhibitors (INSTIs), such as raltegravir (RAL), elvitegravir, or dolutegravir (DTG), are efficient antiretroviral agents used in HIV treatment in order to inhibit retroviral integration. By contrast to RAL treatments leading to well-identified mutation resistance pathways at the integrase level, recent clinical studies report several cases of patients failing DTG treatment without clearly identified resistance mutation in the integrase gene raising questions for the mechanism behind the resistance. These compounds, by impairing the integration of HIV-1 viral DNA into the host DNA, lead to an accumulation of unintegrated circular viral DNA forms. This viral DNA could be at the origin of the INSTI resistance by two different ways. The first one, sustained by a recent report, involves 2-long terminal repeat circles integration and the second one involves expression of accumulated unintegrated viral DNA leading to a basal production of viral particles maintaining the viral information. PMID:28123383

  12. Critical current and strand stiffness of three types Nb3Sn strand subjected to spatial periodic bending

    NARCIS (Netherlands)

    Nijhuis, Arend; Ilyin, Y.; Wessel, Wilhelm A.J.; Abbas, Wouter

    2006-01-01

    Knowledge of the influence of bending on the critical current (Ic) of Nb3Sn strands is essential for the understanding of the reduction in performance due to transverse electromagnetic load. In particular, for the large cable-in-conduit conductors (CICCs) meant for the international thermonuclear

  13. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication.

    Science.gov (United States)

    Shinbrot, Eve; Henninger, Erin E; Weinhold, Nils; Covington, Kyle R; Göksenin, A Yasemin; Schultz, Nikolaus; Chao, Hsu; Doddapaneni, HarshaVardhan; Muzny, Donna M; Gibbs, Richard A; Sander, Chris; Pursell, Zachary F; Wheeler, David A

    2014-11-01

    Tumors with somatic mutations in the proofreading exonuclease domain of DNA polymerase epsilon (POLE-exo*) exhibit a novel mutator phenotype, with markedly elevated TCT→TAT and TCG→TTG mutations and overall mutation frequencies often exceeding 100 mutations/Mb. Here, we identify POLE-exo* tumors in numerous cancers and classify them into two groups, A and B, according to their mutational properties. Group A mutants are found only in POLE, whereas Group B mutants are found in POLE and POLD1 and appear to be nonfunctional. In Group A, cell-free polymerase assays confirm that mutations in the exonuclease domain result in high mutation frequencies with a preference for C→A mutation. We describe the patterns of amino acid substitutions caused by POLE-exo* and compare them to other tumor types. The nucleotide preference of POLE-exo* leads to increased frequencies of recurrent nonsense mutations in key tumor suppressors such as TP53, ATM, and PIK3R1. We further demonstrate that strand-specific mutation patterns arise from some of these POLE-exo* mutants during genome duplication. This is the first direct proof of leading strand-specific replication by human POLE, which has only been demonstrated in yeast so far. Taken together, the extremely high mutation frequency and strand specificity of mutations provide a unique identifier of eukaryotic origins of replication.

  14. Detection of bacteriophage phi 6 minus-strand RNA and novel mRNA isoconformers synthesized in vivo and in vitro, by strand-separating agarose gels

    Energy Technology Data Exchange (ETDEWEB)

    Pagratis, N.; Revel, H.R. (Univ. of Chicago, IL (USA))

    1990-07-01

    Two urea-free agarose gel protocols that resolve the six individual strands of bacteriophage phi 6 dsRNA were developed and used to analyze phage RNA synthesis in vivo and in vitro. Citrate gels separate strands of the large and medium chromosomes while Tris-borate-EDTA (TBE) gels resolve the medium and small dsRNA segments. Minus strands migrate faster than plus strands on citrate gels but are retarded on TBE gels. A study of electrophoretic conditions showed that pH affects strand resolution on citrate gels, and that voltage gradient, agarose concentration, and ethidium bromide significantly alter strand migration on TBE gels. Analysis of native phi 6 RNA synthesized in vivo and in vitro showed that the large and medium message RNAs comigrate with the corresponding plus strands of denatured virion dsRNA. The small messenger RNA is exceptional. Native small mRNA was detected as three isoconformers in vivo and in vitro. The isoconformers were converted by heat denaturation to a single RNA species that comigrates with the virion s+ strand. Minus strands labeled in vivo were detected only after heat denaturation. Minus strand synthesis was detected also in heat-denatured samples from in vitro phi 6 nucleocapsid RNA polymerase reactions at pH values suboptimal for transcription.

  15. A New Powerful Method for Site-Specific Transgene Stabilization Based on Chromosomal Double-Strand Break Repair

    Science.gov (United States)

    Kravchuk, Oksana; Savitsky, Mikhail

    2011-01-01

    Transgenic insects are a promising tool in sterile insect techniques and population replacement strategies. Such transgenic insects can be created using nonautonomous transposons, which cannot be transferred without a transposase source. In biocontrol procedures where large numbers of insects are released, there is increased risk of transgene remobilization caused by external transposase sources that can alter the characteristics of the transgenic organisms lead horizontal transgene transfer to other species. Here we describe a novel, effective method for transgene stabilization based on the introduction of directed double-strand breaks (DSB) into a genome-integrated sequence and their subsequent repair by the single-strand annealing (SSA) pathway. Due to the construct's organization, the repair pathway is predictable, such that all transposon and marker sequences can be deleted, while preserving integration of exogenous DNA in the genome. The exceptional conservation of DNA repair pathways makes this method suitable for a broad range of organisms. PMID:22022613

  16. A new powerful method for site-specific transgene stabilization based on chromosomal double-strand break repair.

    Directory of Open Access Journals (Sweden)

    Artem Tkachuk

    Full Text Available Transgenic insects are a promising tool in sterile insect techniques and population replacement strategies. Such transgenic insects can be created using nonautonomous transposons, which cannot be transferred without a transposase source. In biocontrol procedures where large numbers of insects are released, there is increased risk of transgene remobilization caused by external transposase sources that can alter the characteristics of the transgenic organisms lead horizontal transgene transfer to other species. Here we describe a novel, effective method for transgene stabilization based on the introduction of directed double-strand breaks (DSB into a genome-integrated sequence and their subsequent repair by the single-strand annealing (SSA pathway. Due to the construct's organization, the repair pathway is predictable, such that all transposon and marker sequences can be deleted, while preserving integration of exogenous DNA in the genome. The exceptional conservation of DNA repair pathways makes this method suitable for a broad range of organisms.

  17. An S-Transform and Support Vector Machine (SVM-Based Online Method for Diagnosing Broken Strands in Transmission Lines

    Directory of Open Access Journals (Sweden)

    Caxin Sun

    2011-08-01

    Full Text Available During their long-term outdoor field service, overhead transmission lines will be exposed to strikes by lightning, corrosion by chemical contaminants, ice-shedding, wind vibration of conductors, line galloping, external destructive forces and so on, which will generally cause a series of latent faults such as aluminum strand fracture. This may lead to broken transmission lines which will have a very strong impact on the safe operation of power grids that if the latent faults cannot be recognized and fixed as soon as possible. The detection of broken strands in transmission lines using inspection robots equipped with suitable detectors is a method with good prospects. In this paper, a method for detecting broken strands in transmission lines using an eddy current transducer (ECT carried by a robot is developed, and an approach for identifying broken strands in transmission lines based on an S-transform is proposed. The proposed approach utilizes the S-transform to extract the module and phase information at each frequency point from detection signals. Through module phase and comparison, the characteristic frequency points are ascertained, and the fault information of the detection signal is constructed. The degree of confidence of broken strand identification is defined by the Shannon fuzzy entropy (SFE-BSICD. The proposed approach combines module information while utilizing phase information, SFE-BSICD, and the energy, so the reliability is greatly improved. These characteristic qualities of broken strands in transmission lines are used as the input of a multi-classification SVM, allowing the number of broken strands to be determined. Through experimental field verification, it can be shown that the proposed approach displays high accuracy and the SFE-BSICD is defined reasonably.

  18. The invariance of the total direct DNA strand break yield

    Energy Technology Data Exchange (ETDEWEB)

    Bernal, M. A.; Almeida, C. E. de; Sampaio, C.; Incerti, S.; Champion, C.; Nieminen, P. [Laboratorio de Ciencias Radiologicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-90 (Brazil); Universite Bordeaux 1, CNRS/IN2P3, Centre d' Etudes Nucleaires de Bordeaux-Gradignan, CENBG, Chemin du Solarium, BP 120, 33175 Gradignan (France); Laboratoire de Physique Moleculaire et des Collisions, Universite Paul Verlaine-Metz, 1 Boulevard Arago, Technopole 2000, 57078 Metz (France); ESA-ESTEC, 2200 AG Noordwijk (Netherlands)

    2011-07-15

    Purpose: The invariance of the total direct strand break yield when DNA is irradiated by different types of particles and energies has been reported by previous works. This study is intended to explain the physical causes of this behavior. Methods: The geant4-dna extension of the geant4 general purpose Monte Carlo simulation toolkit has been used to determine direct strand break yields induced by protons and alpha particles impacting on a B-DNA geometrical model, including five organization levels of the human genetic material. The linear energy transfer (LET) of such particles ranges from 4.8 keV/{mu}m (10 MeV protons) to about 235 keV/{mu}m (2 MeV alpha particles), at 5.225 {mu}m depth (near the center of the region of interest). Direct total, single and double strand break probabilities have been determined in a liquid water homogeneous medium with a 1.06 g/cm {sup 3} density. The energetic spectra of single strand breaks (SSB), the number of energy deposition events, and the SSB/event ratio were determined. Results: The target-hit probability was found to be independent of both the type and the energy of the incident particle, even if this latter is a secondary electron. This probability is determined by the geometrical properties of the system. The total strand break yield and the number of energy deposition events required to reach a certain absorbed dose were found nearly independent of the type and energy of the incident ion (proton or alpha). In contrast, the double strand break (DSB) yield was found strongly dependent on the LET of the incident radiation. Conclusions: The SSB generation process is homogeneous and independent of the LET of the particles involved, at least within the proton and alpha particle energy range here studied. The target-hit probability is only determined by the ratio between the total volume occupied by targets and that of the ROI where the radiation deposits its energy. The maximum separation distance between two adjacent SSBs to

  19. 蛋白质中strand-loop-strand模体的分类%THE CLASSIFICATION OF STRAND-LOOP-STRAND MOTIFS IN PROTEINS

    Institute of Scientific and Technical Information of China (English)

    高苏娟; 胡秀珍

    2009-01-01

    从蛋白质一级序列出发,以氨基酸紧邻关联为参数,用离散量的方法,采用5交叉检验,对蛋白质中的strand-loop-strand模体进行了分类.文中使用了两个数据库,采用了不同的截取方式和序列模式长,均得到了较好的预测效果.

  20. Transformation-associated recombination between diverged and homologous DNA repeats is induced by strand breaks

    Energy Technology Data Exchange (ETDEWEB)

    Larionov, V.; Kouprina, N. [National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC (United States)]|[Institute of Cytology, St. Petersburg (Russian Federation); Eldarov, M. [National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC (United States)]|[Center for Bioengineering, Moscow (Russian Federation); Perkins, E.; Porter, G.; Resnick, M.A. [National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC (United States)

    1994-10-01

    Rearrangement and deletion within plasmid DNA is commonly observed during transformation. We have examined the mechanisms of transformation-associated recombination in the yeast Saccharomyces cerevisiae using a plasmid system which allowed the effects of physical state and/or extent of homology on recombination to be studied. The plasmid contains homologous or diverged (19%) DNA repeats separated by a genetically detectable color marker. Recombination during transformation for covalently closed circular plasmids was over 100-fold more frequent than during mitotic-growth. The frequency of recombination is partly dependent on the method of transformation In that procedures involving lithium acetate or spheroplasting yield higher frequencies than electroporation. When present in the repeats, unique single-strand breaks that are ligatable, as well as double-strand breaks, lead to high levels of recombination between diverged and identical repeats. The transformation-associated recombination between repeat DNA`s is under the influence of the RAD52, RAD1 and the RNC1 genes.

  1. The hair strand test - a new method for testing antifungal effects of antidandruff preparations.

    Science.gov (United States)

    Mayser, Peter; Argembeaux, Horst; Rippke, Frank

    2003-01-01

    Seborrheic dermatitis and its minimal variant, dandruff (pityriasis simplex capillitii), are among the most frequent diseases caused by Malassezia (M.) yeasts. Treatment studies have shown that antimycotics achieve clinical improvement, while recolonization leads to recurrent symptoms. Among the antimycotics used are azoles, hydroxypyridones, and various agents such as zinc pyrithione, tar, and selenium disulfide. However, comparative efficacy studies in vitro should not only consider the minimal inhibitory concentrations against Malassezia yeasts but also the bioavailability of the individual substances with regard to hair and scalp. By means of a new method, the hair strand test, hairs from ten volunteers were subjected to standardized 5-min incubation with different shampoo formulations. Thereafter they were rinsed with running water for 1 min and dried. Two hundred each of these hairs (length 1 cm) were given into a medium (olive oil on selective agar for pathogenic fungi) inoculated with M. sympodialis or M. globosa (5 x 10(3) CFU/microl), and the influence on growth was semiquantitatively determined over a period of up to 18 days. According to preliminary results, 1% climbazole proved to be particularly effective. The hair strand test, which can also be performed ex vivo, is a new method to find out whether antimycotic agents bind differently to the hair substance and, via a depot effect, may influence the growth of Malassezia yeasts and thus affect dandruff. This allows conclusions about the efficacy of antidandruff formulations.

  2. Fracture behavior of filament in Nb{sub 3}Sn strands with crack-bridging model

    Energy Technology Data Exchange (ETDEWEB)

    Yong, Huadong, E-mail: yonghd@lzu.edu.cn; Yang, Penglei; Xue, Cun; Zhou, Youhe

    2016-01-15

    Highlights: • The crack-bridging model is used to study the fracture behavior of filaments. • Two different fracture modes are characterized by the number of bridging bronzes. • Short twist pitch has better mechanical stability for the tensile loadings. • The widths of bridging bronze and filament have different effects for the central crack and two collinear cracks. - Abstract: The Nb{sub 3}Sn strands which have high critical field are used in cable-in-conduit conductors (CICCs). The superconducting strands are twisted multistage and experience complex thermal and electromagnetic loadings. Due to their brittleness, the cracking of the Nb{sub 3}Sn filaments will occur under mechanical loading. In this paper, based on the linear elastic fracture theory, we study the effects of tension loading on the fracture behavior of central crack firstly. The strain energy release rates for different twist pitches and cabling stages are presented. As the triplet is subjected to the uniaxial strain, the cracking probability will increase with the twist pitch. The crack number increases with the applied strain, and wider filament or bronze can lead to smaller crack number under the same applied strain. In addition, multistage cabling has better mechanical stability. Next, the two collinear crack problem is considered. The variations of microcrack number show that the wider bronze can provide more resistance for the propagating of the large cracks. We can conclude that the bronze plays an important role in improving the stability and strength.

  3. Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA

    Science.gov (United States)

    Savelyev, Alexey; Papoian, Garegin A.

    2009-01-01

    Coarse-graining of atomistic force fields allows us to investigate complex biological problems, occurring at long timescales and large length scales. In this work, we have developed an accurate coarse-grained model for double-stranded DNA chain, derived systematically from atomistic simulations. Our approach is based on matching correlators obtained from atomistic and coarse-grained simulations, for observables that explicitly enter the coarse-grained Hamiltonian. We show that this requirement leads to equivalency of the corresponding partition functions, resulting in a one-step renormalization. Compared to prior works exploiting similar ideas, the main novelty of this work is the introduction of a highly compact set of Hamiltonian basis functions, based on molecular interaction potentials. We demonstrate that such compactification allows us to reproduce many-body effects, generated by one-step renormalization, at low computational cost. In addition, compact Hamiltonians greatly increase the likelihood of finding unique solutions for the coarse-grained force-field parameter values. By successfully applying our molecular renormalization group coarse-graining technique to double-stranded DNA, we solved, for the first time, a long-standing problem in coarse-graining polymer systems, namely, how to accurately capture the correlations among various polymeric degrees of freedom. Excellent agreement is found among atomistic and coarse-grained distribution functions for various structural observables, including those not included in the Hamiltonian. We also suggest higher-order generalization of this method, which may allow capturing more subtle correlations in biopolymer dynamics. PMID:19450476

  4. New tools to study DNA double-strand break repair pathway choice.

    Directory of Open Access Journals (Sweden)

    Daniel Gomez-Cabello

    Full Text Available A broken DNA molecule is difficult to repair, highly mutagenic, and extremely cytotoxic. Such breaks can be repaired by homology-independent or homology-directed mechanisms. Little is known about the network that controls the repair pathway choice except that a licensing step for homology-mediated repair exists, called DNA-end resection. The choice between these two repair pathways is a key event for genomic stability maintenance, and an imbalance of the ratio is directly linked with human diseases, including cancer. Here we present novel reporters to study the balance between both repair options in human cells. In these systems, a double-strand break can be alternatively repaired by homology-independent or -dependent mechanisms, leading to the accumulation of distinct fluorescent proteins. These reporters thus allow the balance between both repair pathways to be analyzed in different experimental setups. We validated the reporters by analyzing the effect of protein downregulation of the DNA end resection and non-homologous end-joining pathways. Finally, we analyzed the role of the DNA damage response on double-strand break (DSB repair mechanism selection. Our reporters could be used in the future to understand the roles of specific factors, whole pathways, or drugs in DSB repair pathway choice, or for genome-wide screening. Moreover, our findings can be applied to increase gene-targeting efficiency, making it a beneficial tool for a broad audience in the biological sciences.

  5. Heat transfer and friction characteristics of rotor-assembled strand heat exchanger studied by uniform design experiment

    Directory of Open Access Journals (Sweden)

    Yan Wei

    2015-10-01

    Full Text Available The uniform distribution and experimental design is employed to study the thermo-hydraulic characteristics of a heat exchanger, which consists of the rotor-assembled strands mounted in circular smooth tubes. The uniform distribution and experimental design parameters include multiple rotor parameters such as rotor diameters, rotor lead, and height of blade, with the aim of studying their influence on the PEC, that is, ( ( Nu z / Nu g / ( f g / f z 1 / 3 , which stands for the heat transfer and friction characteristics. The best matching schemes of rotor-assembled strand, which significantly improves PEC to 2.01, are given by the regression analysis of uniform distribution and experimental design table. The single-factor experiments are performed to compare a tube installed with different kinds of rotor-assembled strands with a smooth tube without any strands when the Reynolds number changes between 20,000 and 60,000. The experimental result is in good agreement with the result obtained by the regression analysis of uniform distribution and experimental design. It is shown that the rotor diameters play important role in the heat transfer, and the optimal PEC value is obtained under the case that the rotor diameter is 21 mm. The rotor lead also contributes to the improvement of heat transfer and its optimal value is 700 mm in this study. The Nusselt number, friction factor and PEC increase with the increase in blade height. It shows that the uniform distribution and experimental design is an efficient method to find out the optimal parameters.

  6. Multi-Quality Properties Capability Analysis for Prestressing Strand of Prestressed Concrete

    Institute of Scientific and Technical Information of China (English)

    Wen; Pei; Sung; Kuen; Suan; Chen; Cheer; Germ; Go

    2002-01-01

    Prestressed concrete structures are main conformati on for the construction of high way bridges. The quality of prestressed concrete s tructures is mainly affected by the tensile strength of prestressing strand. In order to attain the purpose of economic design and long life span of prestressin g strand, the less relaxation property of strand type is suitable for constructi on and usage. Thus, the research and development of prestressing strand is requi red to reach the goals of high tensile strength and ...

  7. Unusual Mortality Events of Harbor Porpoise Strandings in North Carolina, 1997–2009

    OpenAIRE

    Aleta A. Hohn; Rotstein, David S.; Byrd, Barbie L.

    2013-01-01

    A marked increase in the frequency of harbor porpoises (Phocoena phocoena) stranded in North Carolina in 2005 was declared as an Unusual Mortality Event (UME). Strandings occurred in January through May when harbor porpoises are seasonally present. Increased stranding rates were measured relative to a threshold to determine that the UME was occurring. The threshold analysis also revealed elevated strandings during 1999, an undeclared UME year. Recovered carcasses during 1999 and 2005 accounte...

  8. Lead Poisoning Prevention Tips

    Science.gov (United States)

    ... or removed safely. How are children exposed to lead? Lead-based paint and lead contaminated dust are ... What can be done to prevent exposure to lead? It is important to determine the construction year ...

  9. Lead (Pb) Air Pollution

    Science.gov (United States)

    ... States Environmental Protection Agency Search Search Lead (Pb) Air Pollution Share Facebook Twitter Google+ Pinterest Contact Us As ... and protect aquatic and terrestrial ecosystems. Lead (Pb) Air Pollution Lead Air Pollution Basics How does lead get ...

  10. Extended minus-strand DNA as template for R-U5-mediated second-strand transfer in recombinational rescue of primer binding site-modified retroviral vectors

    DEFF Research Database (Denmark)

    Mikkelsen, J G; Lund, Anders Henrik; Dybkaer, K

    1998-01-01

    We have previously demonstrated recombinational rescue of primer binding site (PBS)-impaired Akv murine leukemia virus-based vectors involving initial priming on endogenous viral sequences and template switching during cDNA synthesis to obtain PBS complementarity in second-strand transfer...... of reverse transcription (Mikkelsen et al., J. Virol. 70:1439-1447, 1996). By use of the same forced recombination system, we have now found recombinant proviruses of different structures, suggesting that PBS knockout vectors may be rescued through initial priming on endogenous virus RNA, read......-through of the mutated PBS during minus-strand synthesis, and subsequent second-strand transfer mediated by the R-U5 complementarity of the plus strand and the extended minus-strand DNA acceptor template. Mechanisms for R-U5-mediated second-strand transfer and its possible role in retrovirus replication and evolution...

  11. 77 FR 2958 - Prestressed Concrete Steel Wire Strand From Thailand: Correction to Notice of Opportunity To...

    Science.gov (United States)

    2012-01-20

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE International Trade Administration Prestressed Concrete Steel Wire Strand From Thailand: Correction to Notice of... administrative review of the antidumping duty order on prestressed concrete steel wire strand (``PC Strand...

  12. Oriented-strand-board- the wave of the future- for the building trade

    Science.gov (United States)

    Linda Ashton

    1984-01-01

    Move over, plywood. Oriented-strand board is here. It's less expensive. It's as durable. It has as many uses. And it is the wave of the future. "Oriented-strand board is a direct substitute for plywood" said Jerry Buckner, plant manager for the Martco oriented-strand board plant in Lemoyen. OSB, as it is commonly called, is a structural panel made...

  13. Torsional regulation of hRPA-induced unwinding of double-stranded DNA

    NARCIS (Netherlands)

    De Vlaminck, I.; Vidic, I.; Van Loenhout, M.T.J.; Kanaar, R.; Lebbink, J.H.G.; Dekker, C.

    2010-01-01

    All cellular single-stranded (ss) DNA is rapidly bound and stabilized by single stranded DNA-binding proteins (SSBs). Replication protein A, the main eukaryotic SSB, is able to unwind double-stranded (ds) DNA by binding and stabilizing transiently forming bubbles of ssDNA. Here, we study the dynamic

  14. 7 CFR 1755.370 - RUS specification for seven wire galvanized steel strand.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 11 2010-01-01 2010-01-01 false RUS specification for seven wire galvanized steel... steel strand. (a) RUS incorporates by reference ASTM A475-78, Standard Specification for Zinc-Coated Steel Wire Strand, issued May 1978. All seven wire galvanized steel strand purchased after April 1,...

  15. Probing electronic coupling between adenine bases in RNA strands from synchrotron radiation circular dichroism experiments

    DEFF Research Database (Denmark)

    Nielsen, Lisbeth Munksgård; Hoffmann, Søren Vrønning; Nielsen, Steen Brøndsted

    2012-01-01

    Circular dichroism spectra (176–330 nm) of RNA adenine oligomers, (rA)n (n = 1–10, 12, 15, and 20), reveal electronic coupling between two bases in short strands. The number of interacting bases in long strands is more and larger than that reported previously for the corresponding DNA strands....

  16. 75 FR 28560 - Prestressed Concrete Steel Wire Strand From the People's Republic of China: Final Determination...

    Science.gov (United States)

    2010-05-21

    ... International Trade Administration Prestressed Concrete Steel Wire Strand From the People's Republic of China... less than fair value (``LTFV'') in the antidumping investigation of prestressed concrete steel strand...'' section of this notice. \\1\\ See Prestressed Concrete Steel Wire Strand From the People's Republic of...

  17. 75 FR 32747 - Prestressed Concrete Steel Wire Strand from Mexico: Rescission of Antidumping Duty Administrative...

    Science.gov (United States)

    2010-06-09

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE INTERNATIONAL TRADE ADMINISTRATION Prestressed Concrete Steel Wire Strand from Mexico: Rescission of Antidumping... prestressed concrete steel wire strand (``PC Strand'') from Mexico for the period January 1, 2009...

  18. Hybrid fur rendering: combining volumetric fur with explicit hair strands

    DEFF Research Database (Denmark)

    Andersen, Tobias Grønbeck; Falster, Viggo; Frisvad, Jeppe Revall

    2016-01-01

    Hair is typically modeled and rendered using either explicitly defined hair strand geometry or a volume texture of hair densities. Taken each on their own, these two hair representations have difficulties in the case of animal fur as it consists of very dense and thin undercoat hairs in combination...... with coarse guard hairs. Explicit hair strand geometry is not well-suited for the undercoat hairs, while volume textures are not well-suited for the guard hairs. To efficiently model and render both guard hairs and undercoat hairs, we present a hybrid technique that combines rasterization of explicitly...... defined guard hairs with ray marching of a prismatic shell volume with dynamic resolution. The latter is the key to practical combination of the two techniques, and it also enables a high degree of detail in the undercoat. We demonstrate that our hybrid technique creates a more detailed and soft fur...

  19. Implementing Nonlinear Feedback Controllers Using DNA Strand Displacement Reactions.

    Science.gov (United States)

    Sawlekar, Rucha; Montefusco, Francesco; Kulkarni, Vishwesh V; Bates, Declan G

    2016-07-01

    We show how an important class of nonlinear feedback controllers can be designed using idealized abstract chemical reactions and implemented via DNA strand displacement (DSD) reactions. Exploiting chemical reaction networks (CRNs) as a programming language for the design of complex circuits and networks, we show how a set of unimolecular and bimolecular reactions can be used to realize input-output dynamics that produce a nonlinear quasi sliding mode (QSM) feedback controller. The kinetics of the required chemical reactions can then be implemented as enzyme-free, enthalpy/entropy driven DNA reactions using a toehold mediated strand displacement mechanism via Watson-Crick base pairing and branch migration. We demonstrate that the closed loop response of the nonlinear QSM controller outperforms a traditional linear controller by facilitating much faster tracking response dynamics without introducing overshoots in the transient response. The resulting controller is highly modular and is less affected by retroactivity effects than standard linear designs.

  20. HOMFLY polynomials in representation [3, 1] for 3-strand braids

    Science.gov (United States)

    Mironov, A.; Morozov, A.; Morozov, An.; Sleptsov, A.

    2016-09-01

    This paper is a new step in the project of systematic description of colored knot polynomials started in [1]. In this paper, we managed to explicitly find the inclusive Racah matrix, i.e. the whole set of mixing matrices in channels R ⊗3 -→ Q with all possible Q, for R = [3 , 1]. The calculation is made possible by the use of a newly-developed efficient highest-weight method, still it remains tedious. The result allows one to evaluate and investigate [3 , 1]-colored polynomials for arbitrary 3-strand knots, and this confirms many previous conjectures on various factorizations, universality, and differential expansions. We consider in some detail the next-to-twist-knots three-strand family ( n, -1 | 1 , -1) and deduce its colored HOMFLY. Also confirmed and clarified is the eigenvalue hypothesis for the Racah matrices, which promises to provide a shortcut to generic formulas for arbitrary representations.

  1. Hybrid fur rendering: combining volumetric fur with explicit hair strands

    DEFF Research Database (Denmark)

    Andersen, Tobias Grønbeck; Falster, Viggo; Frisvad, Jeppe Revall

    2016-01-01

    Hair is typically modeled and rendered using either explicitly defined hair strand geometry or a volume texture of hair densities. Taken each on their own, these two hair representations have difficulties in the case of animal fur as it consists of very dense and thin undercoat hairs in combination...... with coarse guard hairs. Explicit hair strand geometry is not well-suited for the undercoat hairs, while volume textures are not well-suited for the guard hairs. To efficiently model and render both guard hairs and undercoat hairs, we present a hybrid technique that combines rasterization of explicitly...... defined guard hairs with ray marching of a prismatic shell volume with dynamic resolution. The latter is the key to practical combination of the two techniques, and it also enables a high degree of detail in the undercoat. We demonstrate that our hybrid technique creates a more detailed and soft fur...

  2. Identification of Cis-Acting Elements on Positive-Strand Subgenomic mRNA Required for the Synthesis of Negative-Strand Counterpart in Bovine Coronavirus

    Directory of Open Access Journals (Sweden)

    Po-Yuan Yeh

    2014-07-01

    Full Text Available It has been demonstrated that, in addition to genomic RNA, sgmRNA is able to serve as a template for the synthesis of the negative-strand [(−-strand] complement. However, the cis-acting elements on the positive-strand [(+-strand] sgmRNA required for (−-strand sgmRNA synthesis have not yet been systematically identified. In this study, we employed real-time quantitative reverse transcription polymerase chain reaction to analyze the cis-acting elements on bovine coronavirus (BCoV sgmRNA 7 required for the synthesis of its (−-strand counterpart by deletion mutagenesis. The major findings are as follows. (1 Deletion of the 5'-terminal leader sequence on sgmRNA 7 decreased the synthesis of the (−-strand sgmRNA complement. (2 Deletions of the 3' untranslated region (UTR bulged stem-loop showed no effect on (−-strand sgmRNA synthesis; however, deletion of the 3' UTR pseudoknot decreased the yield of (−-strand sgmRNA. (3 Nucleotides positioned from −15 to −34 of the sgmRNA 7 3'-terminal region are required for efficient (−-strand sgmRNA synthesis. (4 Nucleotide species at the 3'-most position (−1 of sgmRNA 7 is correlated to the efficiency of (−-strand sgmRNA synthesis. These results together suggest, in principle, that the 5'- and 3'-terminal sequences on sgmRNA 7 harbor cis-acting elements are critical for efficient (−-strand sgmRNA synthesis in BCoV.

  3. What Governs the Unzipping Process of Double-Stranded DNA

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-Feng; LEI Xiao-Ling; FANG Hai-Ping

    2006-01-01

    @@ The unzipping process of double-stranded DNA is analysed using a discrete model at the base level [Chin. Phys.Lett. 22 (2005)1540]. The numerical results are consistent with the experimental observations on the force-displacement behaviour including the sequence-dependence. We find that the hydrogen bond interaction in a base pair is crucially important to the force-displacement profile.

  4. Electrostatic Origin of Single-Stranded Genome Packing in Viruses

    Science.gov (United States)

    Belyi, Vladimir; Muthukumar, M.

    2006-03-01

    We develop an electrostatic model for single-stranded RNA/DNA viruses that bind their genome via highly basic semiflexible peptide arms. We show that genome-capsid binding is dominated by non-specific electrostatic interactions, rather than actual amino-acid content. Proposed model explains many universal features of the viral genome. Good agreement is found with wide range of qualified wild-type and mutant viruses.

  5. Five strands of math tasks big book : grades pk-2

    CERN Document Server

    Reed, Nat; Forest, Chris

    2009-01-01

    For grades PK-2, our Common Core State Standards-based resource meets the five strands of math concepts addressed by the NCTM standards and encourages the students to learn and review the concepts in unique ways. Included are challenging problem-solving tasks which will push the boundaries of critical thought and demonstrate to students the importance of mathematical problems in Number & Operations, Geometry, Measurement, Data Analysis & Probability and Algebra using real world situations.

  6. Five strands of math drills big book : grades PK-2

    CERN Document Server

    Reed, Nat; Forest, Chris

    2011-01-01

    For grades PK-2, our Common Core State Standards-based resource meets the five strands of math concepts addressed by the NCTM standards and encourages the students to review the concepts in unique ways. Included are warm-up and timed drill activities which will push the boundaries of critical thought and demonstrate to students the importance of mathematical problems in Number & Operations, Geometry, Measurement, Data Analysis & Probability and Algebra using real world situations.

  7. Commercial possibilities for stranded conventional gas from Alaska's North Slope

    Science.gov (United States)

    Attanasi, E.D.; Freeman, P.A.

    2014-01-01

    Stranded gas resources are defined for this study as gas resources in discrete accumulations that are not currently commercially producible, or producible at full potential, for either physical or economic reasons. Approximately 35 trillion cubic feet (TCF) of stranded gas was identified on Alaska’s North Slope. The commercialization of this resource requires facilities to transport gas to markets where sales revenue will be sufficient to offset the cost of constructing and operating a gas delivery system. With the advent of the shale gas revolution, plans for a gas pipeline to the conterminous US have been shelved (at least temporarily) and the State and resource owners are considering a liquefied natural gas (LNG) export project that targets Asian markets. This paper focuses on competitive conditions for Asian gas import markets by estimating delivered costs of competing supplies from central Asia, Russia, Indonesia, Malaysia, and Australia in the context of a range of import gas demand projections for the period from 2020 to 2040. These suppliers’ costs are based on the cost of developing, producing, and delivering to markets tranches of the nearly 600 TCF of recoverable gas from their own conventional stranded gas fields. The results of these analyses imply that Alaska’s gas exports to Asia will likely encounter substantial competitive challenges. The sustainability of Asia’s oil-indexed LNG pricing is also discussed in light of a potentially intense level of competition.

  8. Euler buckling and nonlinear kinking of double-stranded DNA.

    Science.gov (United States)

    Fields, Alexander P; Meyer, Elisabeth A; Cohen, Adam E

    2013-11-01

    The bending stiffness of double-stranded DNA (dsDNA) at high curvatures is fundamental to its biological activity, yet this regime has been difficult to probe experimentally, and literature results have not been consistent. We created a 'molecular vise' in which base-pairing interactions generated a compressive force on sub-persistence length segments of dsDNA. Short dsDNA strands (Euler buckling'. We monitored the buckling transition via Förster Resonance Energy Transfer (FRET) between appended fluorophores. For low-to-moderate concentrations of monovalent salt (up to ∼150 mM), our results are in quantitative agreement with the worm-like chain (WLC) model of DNA elasticity, without the need to invoke any 'kinked' states. Greater concentrations of monovalent salts or 1 mM Mg(2+) induced an apparent softening of the dsDNA, which was best accounted for by a kink in the region of highest curvature. We tested the effects of all single-nucleotide mismatches on the DNA bending. Remarkably, the propensity to kink correlated with the thermodynamic destabilization of the mismatched DNA relative the perfectly complementary strand, suggesting that the kinked state is locally melted. The molecular vise is exquisitely sensitive to the sequence-dependent linear and nonlinear elastic properties of dsDNA.

  9. Structure of the guide-strand-containing argonaute silencing complex

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-15

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

  10. A novel bio-sensor based on DNA strand displacement.

    Directory of Open Access Journals (Sweden)

    Xiaolong Shi

    Full Text Available DNA strand displacement technology performs well in sensing and programming DNA segments. In this work, we construct DNA molecular systems based on DNA strand displacement performing computation of logic gates. Specifically, a class of so-called "DNA neurons" are achieved, in which a "smart" way inspired by biological neurons encoding information is developed to encode and deliver information using DNA molecules. The "DNA neuron" is bistable, that is, it can sense DNA molecules as input signals, and release "negative" or "positive" signals DNA molecules. We design intelligent DNA molecular systems that are constructed by cascading some particularly organized "DNA neurons", which could perform logic computation, including AND, OR, XOR logic gates, automatically. Both simulation results using visual DSD (DNA strand displacement software and experimental results are obtained, which shows that the proposed systems can detect DNA signals with high sensitivity and accretion; moreover, the systems can process input signals automatically with complex nonlinear logic. The method proposed in this work may provide a new way to construct a sensitive molecular signal detection system with neurons spiking behavior in vitro, and can be used to develop intelligent molecular processing systems in vivo.

  11. Paul Strand y las paradojas de la modernidad americana

    Directory of Open Access Journals (Sweden)

    Vicente Sánchez Biosca

    2010-06-01

    Full Text Available As contribuições de Strand para o cinema estão estreitamente relacionadas com seus trabalhos fotográficos da época e mesmo com um olhar que, apesar de suas múltiplas diferenças, possui muitos pontos em comum. Se em Manhatta (1920, Strand (em colaboração com Sheeler oferece uma síntese da natureza e da modernidade, em Redes (1934 o que predomina, em contrapartida, é a experiência da arte muralista mexicana e a influência de Eisenstein (em suas andanças por México são os fatores que determinam seus esforços na construção de uma épica dos operários. Mas sem dúvida, o projeto mais ambicioso de Strand (ao mando da produtora Frontier Films foi Native Land, o filme que atendeu às demandas do American Popular Front e as moldou nas palavras dos fundadores da pátria americana.

  12. Spectroscopic characterization of the interaction of phenosafranin and safranin O with double stranded, heat denatured and single stranded calf thymus DNA.

    Science.gov (United States)

    Saha, Ishita; Kumar, Gopinatha Suresh

    2011-01-01

    Interaction of phenosafranin and safranin O with double stranded, heat denatured and single stranded calf thymus DNA has been studied by fluorescence, absorbance and circular dichroic techniques. Binding to the double stranded and heat denatured DNA conformations induced strong quenching in the fluorescence spectra of both dyes. Linear Scatchard plots indicated the binding to be of one type and the affinity evaluated to be of the order of 10(5) M(-1) with double stranded and heat denatured DNAs. Fluorescence quenching was much weaker with the single stranded DNA and the binding affinity was one order lower. Ferrocyanide quenching studies revealed that the fluorescence emission of the dye molecules bound to the double stranded and heat denatured DNAs was quenched much less compared to that bound to the single stranded DNA. Further, there was significant emission polarization for the bound dyes and strong energy transfer from the DNA base pairs to the dye molecules indicating intercalative binding. Salt dependence of the binding phenomenon revealed that electrostatic forces have significant role in the binding process. The intercalation of these molecules to double stranded and heat denatured DNA and simple stacking to single strands was proved by these fluorescence techniques. Support to the fluorescence results have been derived from absorption and circular dichroic results. Phenosafranin was revealed to be a stronger binding species compared to safranin O.

  13. Autonomous parvovirus LuIII encapsidates equal amounts of plus and minus DNA strands

    Energy Technology Data Exchange (ETDEWEB)

    Bates, R.C.; Snyder, C.E.; Banerjee, P.T.; Mitra, S.

    1984-02-01

    Autonomous parvoviruses are thought to uniquely encapsidate single-stranded DNA of minus polarity. In contrast, the defective adeno-associated viruses separately encapsidate equal amounts of plus and minus DNA strands. The uniqueness of minus strand encapsidation is reexamined for the autonomous parvoviruses. Although it was found that Kilham rat virus and H-1 virus encapsidate varying but small amounts of complementary-strand DNA, it was unexpected to find that LuIII virus encapsidated equal amounts of plus and minus DNA. The extracted LuIII DNA possessed properties of double-stranded replicative-form DNA, including insensitivity to S1 endonuclease, cleavage by restriction enzymes, and conversion to unit-length, single-stranded DNA when electrophoresed under denaturing conditions. However, the inability of this DNA to form single-stranded DNA circles when denatured and then renatured in the presence of formamide and the lack of double-stranded DNA circle formation after treatment with exonuclease III and reannealing shows a lack of sequence homology of the 3' and 5' termini of LuIII DNA, in contrast to adeno-associated virus DNA. Digestion of LuIII double-stranded DNA with EcoRI and HincII and separation of plus and minus DNA strands on composite agarose-acrylamide gels identified a heterogeneity present only in the plus DNA strand. These results suggest that strand specificity of viral DNA encapsidation is not a useful property for differentiation between the autonomous and defective parvoviruses. Furthermore, encapsidation by LuIII of equal amounts of complementary DNA strands in contrast to encapsidation of minus strands by H-1 virus, when propagated in the same host cell type, suggests that selection of strands for encapsidation is a virus-coded rather than host-controlled event.

  14. Stranding of Two Sperm Whales (Physeter macrocephalus) in the “North Sea Trap” at Henne Strand, Denmark

    DEFF Research Database (Denmark)

    Hansen, Mette Siv; Alstrup, Aage Kristian Olsen; Hansen, Jørgen H.

    2016-01-01

    In February 2014 two male sperm whales (Physeter macrocephalus) stranded at Henne Strand, Denmark. One whale (MCE 1644) was found dead, while the other (MCE 1645) was still alive, but drowned during the high tide. To increase our knowledge of sperm whales, conduct forage investigations, post......-mortem and diagnostic examinations were carried out. The decay of the carcasses progressed quickly. The whales had large (MCE 1644) or moderate (MCE 1645) numbers of squid beaks (Gonatus fabricii) in the stomachventricles, but no evidence of recentfresh feeding. Both whales had acute dermatitis probably due to trauma...... severe localized or systemic infections. The finding of large volumes of bloody pleural fluid with large quantities of C. septicum suggests that MCE 1644 died of infection. However, reservations must be taken due to the pronounced decay of the carcass. Sperm whales have strong social bonds where...

  15. GTL or LNG: Which is the best way to monetize "stranded" natural gas?

    Institute of Scientific and Technical Information of China (English)

    Dong Lichun; Wei Shun'an; Tan Shiyu; Zhang Hongjing

    2008-01-01

    A large portion of world's natural gas reserves are "stranded" resources, the drive to monetize these resources leads to the development of gas-to-liquids (GTL) and liquefied natural gas (LNG) technologies. LNG has the advantage of having been developed for the past 40 years and having an excellent safety record. GTL on the other hand is another option with substantial benefits, but its development stage and commercial viability are far behind LNG. This paper presents a techno-economic comparison of GTL with LNG, including technical development, plant efficiency, market potential for the products, and capital cost for the infrastructure. The aim is to give an overall view on both LNG and GTL and provide a perspective on the profitability of these two technologies.

  16. Gin-mediated DNA inversion: product structure and the mechanism of strand exchange.

    Science.gov (United States)

    Kanaar, R; van de Putte, P; Cozzarelli, N R

    1988-02-01

    Inversion of the G loop of bacteriophage Mu requires the phage-encoded Gin protein and a host factor. The topological changes in a supercoiled DNA substrate generated by the two purified proteins were analyzed. More than 99% of the inversion products were unknotted rings. This result excludes synapsis by way of a random collision of recombination sites, because the resulting entrapped supercoils would be converted into knots by recombination. Instead, the recombination sites must come together in the synaptic complex in an ordered fashion with a fixed number of supercoils between the sites. The linking number of the substrate DNA increases by four during recombination. Thus, in three successive rounds of inversion, the change in linking number was +4, +8, and +12, respectively. These results lead to a quantitative model for the mechanism of Gin recombination that includes the distribution of supercoils in the synaptic complex, their alteration by strand exchange, and specific roles for the two proteins needed for recombination.

  17. Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy

    Science.gov (United States)

    Salari, H.; Eslami-Mossallam, B.; Ranjbar, H. F.; Ejtehadi, M. R.

    2016-12-01

    Using analytical approach and Monte Carlo (MC) simulations, we study the elastic behavior of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We show that, due to the bending anisotropy, the persistence length of dsDNA in 2D conformations is always greater than three-dimensional (3D) conformations. This result is in consistence with the measured values for DNA persistence length in 2D and 3D in equal biological conditions. We also show that in two dimensions, an anisotropic, intrinsically twisted polymer exhibits an implicit twist-bend coupling, which leads to the transient curvature increasing with a half helical turn periodicity along the bent polymer.

  18. Have a break: determinants of meiotic DNA double strand break (DSB) formation and processing in plants.

    Science.gov (United States)

    Edlinger, Bernd; Schlögelhofer, Peter

    2011-03-01

    Meiosis is an essential process for sexually reproducing organisms, leading to the formation of specialized generative cells. This review intends to highlight current knowledge of early events during meiosis derived from various model organisms, including plants. It will particularly focus on cis- and trans-requirements of meiotic DNA double strand break (DSB) formation, a hallmark event during meiosis and a prerequisite for recombination of genetic traits. Proteins involved in DSB formation in different organisms, emphasizing the known factors from plants, will be introduced and their functions outlined. Recent technical advances in DSB detection and meiotic recombination analysis will be reviewed, as these new tools now allow analysis of early meiotic recombination in plants with incredible accuracy. To anticipate future directions in plant meiosis research, unpublished results will be included wherever possible.

  19. RNF4 is required for DNA double-strand break repair in vivo

    DEFF Research Database (Denmark)

    Vyas, R; Kumar, R; Clermont, F

    2013-01-01

    for both homologous recombination (HR) and non-homologous end joining repair. To establish a link between Rnf4 and the DNA damage response (DDR) in vivo, we generated an Rnf4 allelic series in mice. We show that Rnf4-deficiency causes persistent ionizing radiation-induced DNA damage and signaling......Unrepaired DNA double-strand breaks (DSBs) cause genetic instability that leads to malignant transformation or cell death. Cells respond to DSBs with the ordered recruitment of signaling and repair proteins to the sites of DNA lesions. Coordinated protein SUMOylation and ubiquitylation have crucial......, and that Rnf4-deficient cells and mice exhibit increased sensitivity to genotoxic stress. Mechanistically, we show that Rnf4 targets SUMOylated MDC1 and SUMOylated BRCA1, and is required for the loading of Rad51, an enzyme required for HR repair, onto sites of DNA damage. Similarly to inactivating mutations...

  20. Lead Aprons Are a Lead Exposure Hazard.

    Science.gov (United States)

    Burns, Kevin M; Shoag, Jamie M; Kahlon, Sukhraj S; Parsons, Patrick J; Bijur, Polly E; Taragin, Benjamin H; Markowitz, Morri

    2017-05-01

    To determine whether lead-containing shields have lead dust on the external surface. Institutional review board approval was obtained for this descriptive study of a convenience sample of 172 shields. Each shield was tested for external lead dust via a qualitative rapid on-site test and a laboratory-based quantitative dust wipe analysis, flame atomic absorption spectrometry (FAAS). The χ(2) test was used to test the association with age, type of shield, lead sheet thickness, storage method, and visual and radiographic appearance. Sixty-three percent (95% confidence interval [CI]: 56%-70%) of the shields had detectable surface lead by FAAS and 50% (95% CI: 43%-57%) by the qualitative method. Lead dust by FAAS ranged from undetectable to 998 μg/ft(2). The quantitative detection of lead was significantly associated with the following: (1) visual appearance of the shield (1 = best, 3 = worst): 88% of shields that scored 3 had detectable dust lead; (2) type of shield: a greater proportion of the pediatric patient, full-body, and thyroid shields were positive than vests and skirts; (3) use of a hanger for storage: 27% of shields on a hanger were positive versus 67% not on hangers. Radiographic determination of shield intactness, thickness of interior lead sheets, and age of shield were unrelated to presence of surface dust lead. Sixty-three percent of shields had detectable surface lead that was associated with visual appearance, type of shield, and storage method. Lead-containing shields are a newly identified, potentially widespread source of lead exposure in the health industry. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

  1. Bottlenose dolphin (Tursiops truncatus) strandings in South Carolina, 1992-1996

    OpenAIRE

    McFee, Wayne E.; Hopkins-Murphy, Sally R.

    2002-01-01

    From 1992 to 1996, 153 bottlenose dolphin stranded in South Carolina, accounting for 73% of all marine mammal strandings during this period. The objectives of our study were to evaluate data from these strandings to deter-mine 1) annual trends in strandings, 2) seasonal and spatial distribution trends, 3) life history parameters such as sex ratio and age classes, 3) seasonal trends in reproduction, and 4) the extent to which humans have played a role in causing these strandings (human inter-a...

  2. Cetacean stranding records in the Turkish Western Black Sea coast during October 2012 - September 2013

    Directory of Open Access Journals (Sweden)

    Arda M. Tonay

    2016-11-01

    Full Text Available Between October 2012 and September 2013, a research has been conducted on marine mammal strandings on Turkish western Black Sea coast. In total, 54 stranded cetaceans were found, which included 22 bottlenose dolphins (41%, 19 harbour porpoises (35%, 11 common dolphins (20%, and 4% unidentified individuals. Most strandings were observed in May and June. Bycaught carcases were found especially in April, June and July. The aim of the study is to collect first-hand data on the monthly stranding rates in order to understand the seasonal variation of stranding cases in a year.

  3. Experimental study on the ac loss properties of two-strand parallel conductors composed of superconducting multifilamentary strands

    CERN Document Server

    Iwakuma, M; Funaki, K

    2002-01-01

    The ac loss properties of two-strand superconducting parallel conductors were experimentally investigated by using NbTi multifilamentary strands with a rectangular cross section. We prepared the simple situation that was supposed in the previous theoretical study (M Iwakuma et al 2002 Supercond. Sci. Technol. 15 1525-36). The two insulated strands were sparsely co-wound into one-layer solenoidal coils. They were transposed only once and soldered at both ends. The ac losses in the sample coils were measured by a pick-up-coil method by applying uniform ac magnetic field parallel to the coil axis and comparing it with the theoretical results. The validity of the theoretical expressions derived in the previous paper was verified by the quantitative agreement with experiment in all the aspects, i.e. the dependencies on frequency, field amplitude and the deviation length in transposition in both the non-saturation and saturation cases and also the threshold condition between them. The results obtained support the t...

  4. The isothermal amplification detection of double-stranded DNA based on a double-stranded fluorescence probe.

    Science.gov (United States)

    Shi, Chao; Shang, Fanjin; Pan, Mei; Liu, Sen; Ma, Cuiping

    2016-06-15

    Here we have developed a novel method of isothermal amplification detection of double-stranded DNA (dsDNA) based on double-stranded fluorescence probe (ds-probe). Target dsDNA repeatedly generated single-stranded DNA (ssDNA) with polymerase and nicking enzyme. The ds-probe as a primer hybridized with ssDNA and extended to its 5'-end. The displaced ssDNA served as a new detection target to initiate above-described reaction. Meanwhile, the extended ds-probe could dynamically dissociate from ssDNA and self-hybridize, converting into a turn-back structure to initiate another amplification reaction. In particular, the ds-probe played a key role in the entire experimental process, which not only was as a primer but also produced the fluorescent signal by an extension and displacement reaction. Our method could detect the pBluescript II KS(+) plasmid with a detection limit of 2.3 amol, and it was also verified to exhibit a high specificity, even one-base mismatch. Overall, it was a true isothermal dsDNA detection strategy with a strongly anti-jamming capacity and one-pot, only requiring one ds-probe, which greatly reduced the cost and the probability of contamination. With its advantages, the approach of dsDNA detection will offer a promising tool in the field of point-of-care testing (POCT).

  5. Extensive ssDNA end formation at DNA double-strand breaks in non-homologous end-joining deficient cells during the S phase

    Directory of Open Access Journals (Sweden)

    Stenerlöw Bo

    2007-10-01

    Full Text Available Abstract Background Efficient and correct repair of DNA damage, especially DNA double-strand breaks, is critical for cellular survival. Defects in the DNA repair may lead to cell death or genomic instability and development of cancer. Non-homologous end-joining (NHEJ is the major repair pathway for DNA double-strand breaks in mammalian cells. The ability of other repair pathways, such as homologous recombination, to compensate for loss of NHEJ and the ways in which contributions of different pathways are regulated are far from fully understood. Results In this report we demonstrate that long single-stranded DNA (ssDNA ends are formed at radiation-induced DNA double-strand breaks in NHEJ deficient cells. At repair times ≥ 1 h, processing of unrejoined DNA double-strand breaks generated extensive ssDNA at the DNA ends in cells lacking the NHEJ protein complexes DNA-dependent protein kinase (DNA-PK or DNA Ligase IV/XRCC4. The ssDNA formation was cell cycle dependent, since no ssDNA ends were observed in G1-synchronized NHEJ deficient cells. Furthermore, in wild type cells irradiated in the presence of DNA-PKcs (catalytic subunit of DNA-PK inhibitors, or in DNA-PKcs deficient cells complemented with DNA-PKcs mutated in six autophosphorylation sites (ABCDE, no ssDNA was formed. The ssDNA generation also greatly influences DNA double-strand break quantification by pulsed-field gel electrophoresis, resulting in overestimation of the DNA double-strand break repair capability in NHEJ deficient cells when standard protocols for preparing naked DNA (i. e., lysis at 50°C are used. Conclusion We provide evidence that DNA Ligase IV/XRCC4 recruitment by DNA-PK to DNA double-strand breaks prevents the formation of long ssDNA ends at double-strand breaks during the S phase, indicating that NHEJ components may downregulate an alternative repair process where ssDNA ends are required.

  6. DNA cleavage by Type ISP Restriction-Modification enzymes is initially targeted to the 3'-5' strand.

    Science.gov (United States)

    van Aelst, Kara; Šišáková, Eva; Szczelkun, Mark D

    2013-01-01

    The mechanism by which a double-stranded DNA break is produced following collision of two translocating Type I Restriction-Modification enzymes is not fully understood. Here, we demonstrate that the related Type ISP Restriction-Modification enzymes LlaGI and LlaBIII can cooperate to cleave DNA following convergent translocation and collision. When one of these enzymes is a mutant protein that lacks endonuclease activity, DNA cleavage of the 3'-5' strand relative to the wild-type enzyme still occurs, with the same kinetics and at the same collision loci as for a reaction between two wild-type enzymes. The DNA nicking activity of the wild-type enzyme is still activated by a protein variant entirely lacking the Mrr nuclease domain and by a helicase mutant that cannot translocate. However, the helicase mutant cannot cleave the DNA despite the presence of an intact nuclease domain. Cleavage by the wild-type enzyme is not activated by unrelated protein roadblocks. We suggest that the nuclease activity of the Type ISP enzymes is activated following collision with another Type ISP enzyme and requires adenosine triphosphate binding/hydrolysis but, surprisingly, does not require interaction between the nuclease domains. Following the initial rapid endonuclease activity, additional DNA cleavage events then occur more slowly, leading to further processing of the initial double-stranded DNA break.

  7. Metallographic investigation of fracture behavior in ITER-style Nb$_{3}$Sn superconducting strands

    CERN Document Server

    Jewell, M C; Larbalestier, D C; Nijhuis, A

    2009-01-01

    In this work we specify the extent to which fracture in two ITER-style Nb3Sn composite strands occurs in a collective or individual manner, under mechanical tension and bending from the TARSIS apparatus at the University of Twente. A bronze-route strand from European Advanced Superconductors (EAS), which has very uniform, well-spaced filaments, has a widely distributed (200 μm) fracture field and exhibits a composite of individual and collective cracks. An internal tin strand from Oxford Instruments – Superconducting Technology (OST) demonstrates much more localized, collective fracture behavior. The filaments in this strand are about four times larger (in area) than the filaments in the EAS strand, and also agglomerate significantly during heat treatment upon conversion of the Nb to Nb3Sn. These results demonstrate that the architecture of the strand can play a significant role in determining the mechanical toughness of the composite, and that strand design should incorporate mechanical considerations in ...

  8. Lead and the Romans

    Science.gov (United States)

    Reddy, Aravind; Braun, Charles L.

    2010-01-01

    Lead poisoning has been a problem since early history and continues into modern times. An appealing characteristic of lead is that many lead salts are sweet. In the absence of cane and beet sugars, early Romans used "sugar of lead" (lead acetate) to sweeten desserts, fruits, and sour wine. People most at risk would have been those who…

  9. Lead and the Romans

    Science.gov (United States)

    Reddy, Aravind; Braun, Charles L.

    2010-01-01

    Lead poisoning has been a problem since early history and continues into modern times. An appealing characteristic of lead is that many lead salts are sweet. In the absence of cane and beet sugars, early Romans used "sugar of lead" (lead acetate) to sweeten desserts, fruits, and sour wine. People most at risk would have been those who consumed the…

  10. Excited State Pathways Leading to Formation of Adenine Dimers.

    Science.gov (United States)

    Banyasz, Akos; Martinez-Fernandez, Lara; Ketola, Tiia-Maaria; Muñoz-Losa, Aurora; Esposito, Luciana; Markovitsi, Dimitra; Improta, Roberto

    2016-06-02

    The reaction intermediate in the path leading to UV-induced formation of adenine dimers A═A and AA* is identified for the first time quantum mechanically, using PCM/TD-DFT calculations on (dA)2 (dA: 2'deoxyadenosine). In parallel, its fingerprint is detected in the absorption spectra recorded on the millisecond time-scale for the single strand (dA)20 (dA: 2'deoxyadenosine).

  11. Cryopreservation and in vitro culture of primary cell types from lung tissue of a stranded pygmy sperm whale (Kogia breviceps).

    Science.gov (United States)

    Annalaura Mancia; Spyropoulos, Demetri D; McFee, Wayne E; Newton, Danforth A; Baatz, John E

    2012-01-01

    Current models for in vitro studies of tissue function and physiology, including responses to hypoxia or environmental toxins, are limited and rely heavily on standard 2-dimensional (2-D) cultures with immortalized murine or human cell lines. To develop a new more powerful model system, we have pursued methods to establish and expand cultures of primary lung cell types and reconstituted tissues from marine mammals. What little is known about the physiology of the deep-sea diving pygmy sperm whale (PSW), Kogia breviceps, comes primarily from stranding events that occur along the coast of the southeastern United States. Thus, development of a method for preserving live tissues and retrieving live cells from deceased stranded individuals was initiated. This report documents successful cryopreservation of PSW lung tissue. We established in vitro cultures of primary lung cell types from tissue fragments that had been cryopreserved several months earlier at the stranding event. Dissociation of cryopreserved lung tissues readily provides a variety of primary cell types that, to varying degrees, can be expanded and further studied/manipulated in cell culture. In addition, PSW-specific molecular markers have been developed that permitted the monitoring of fibroblast, alveolar type II, and vascular endothelial cell types. Reconstitution of 3-D cultures of lung tissues with these cell types is now underway. This novel system may facilitate the development of rare or disease-specific lung tissue models (e.g., to test causes of PSW stranding events and lead to improved treatments for pulmonary hypertension or reperfusion injury in humans). Also, the establishment of a "living" tissue bank biorepository for rare/endangered species could serve multiple purposes as surrogates for freshly isolated samples.

  12. Jinde Lead lead smelting project starts construction

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    <正>On Dec.20,the lead smelting project of Jiangxi Jinde Lead started construction in Dexin as a technical renovation project on environmental treatment of Jiangxi Metallurgical Group.The project is the one with the largest investment of Provincial Metallurgical Group in non-ferrous

  13. Lead - nutritional considerations

    Science.gov (United States)

    Lead poisoning - nutritional considerations; Toxic metal - nutritional considerations ... Markowitz M. Lead poisoning. In: Kliegman RM, Behrman RE, Jenson HB, ... Emergency Medicine: Concepts and Clinical Practice . 8th ed. ...

  14. Single-stranded heteroduplex intermediates in λ Red homologous recombination

    Directory of Open Access Journals (Sweden)

    Zhang Youming

    2010-07-01

    Full Text Available Abstract Background The Red proteins of lambda phage mediate probably the simplest and most efficient homologous recombination reactions yet described. However the mechanism of dsDNA recombination remains undefined. Results Here we show that the Red proteins can act via full length single stranded intermediates to establish single stranded heteroduplexes at the replication fork. We created asymmetrically digestible dsDNA substrates by exploiting the fact that Redα exonuclease activity requires a 5' phosphorylated end, or is blocked by phosphothioates. Using these substrates, we found that the most efficient configuration for dsDNA recombination occurred when the strand that can prime Okazaki-like synthesis contained both homology regions on the same ssDNA molecule. Furthermore, we show that Red recombination requires replication of the target molecule. Conclusions Hence we propose a new model for dsDNA recombination, termed 'beta' recombination, based on the formation of ssDNA heteroduplexes at the replication fork. Implications of the model were tested using (i an in situ assay for recombination, which showed that recombination generated mixed wild type and recombinant colonies; and (ii the predicted asymmetries of the homology arms, which showed that recombination is more sensitive to non-homologies attached to 5' than 3' ends. Whereas beta recombination can generate deletions in target BACs of at least 50 kb at about the same efficiency as small deletions, the converse event of insertion is very sensitive to increasing size. Insertions up to 3 kb are most efficiently achieved using beta recombination, however at greater sizes, an alternative Red-mediated mechanism(s appears to be equally efficient. These findings define a new intermediate in homologous recombination, which also has practical implications for recombineering with the Red proteins.

  15. Heavy Metal Exposure Influences Double Strand Break DNA Repair Outcomes.

    Directory of Open Access Journals (Sweden)

    Maria E Morales

    Full Text Available Heavy metals such as cadmium, arsenic and nickel are classified as carcinogens. Although the precise mechanism of carcinogenesis is undefined, heavy metal exposure can contribute to genetic damage by inducing double strand breaks (DSBs as well as inhibiting critical proteins from different DNA repair pathways. Here we take advantage of two previously published culture assay systems developed to address mechanistic aspects of DNA repair to evaluate the effects of heavy metal exposures on competing DNA repair outcomes. Our results demonstrate that exposure to heavy metals significantly alters how cells repair double strand breaks. The effects observed are both specific to the particular metal and dose dependent. Low doses of NiCl2 favored resolution of DSBs through homologous recombination (HR and single strand annealing (SSA, which were inhibited by higher NiCl2 doses. In contrast, cells exposed to arsenic trioxide preferentially repaired using the "error prone" non-homologous end joining (alt-NHEJ while inhibiting repair by HR. In addition, we determined that low doses of nickel and cadmium contributed to an increase in mutagenic recombination-mediated by Alu elements, the most numerous family of repetitive elements in humans. Sequence verification confirmed that the majority of the genetic deletions were the result of Alu-mediated non-allelic recombination events that predominantly arose from repair by SSA. All heavy metals showed a shift in the outcomes of alt-NHEJ repair with a significant increase of non-templated sequence insertions at the DSB repair site. Our data suggest that exposure to heavy metals will alter the choice of DNA repair pathway changing the genetic outcome of DSBs repair.

  16. Reachability bounds for chemical reaction networks and strand displacement systems.

    Science.gov (United States)

    Condon, Anne; Kirkpatrick, Bonnie; Maňuch, Ján

    2014-01-01

    Chemical reaction networks (CRNs) and DNA strand displacement systems (DSDs) are widely-studied and useful models of molecular programming. However, in order for some DSDs in the literature to behave in an expected manner, the initial number of copies of some reagents is required to be fixed. In this paper we show that, when multiple copies of all initial molecules are present, general types of CRNs and DSDs fail to work correctly if the length of the shortest sequence of reactions needed to produce any given molecule exceeds a threshold that grows polynomially with attributes of the system.

  17. Strand Breaks in DNA Samples Induced with LASERIX

    Science.gov (United States)

    Zielbauer, B.; Habib, J.; Kazamias, S.; Guilbaud, O.; Pittman, M.; Ros, D.; Hervé du Penhoat, M.-A.; Touati, A.; Sech, C. Le; Porcel, E.; Lacombe, S.

    Samples of plasmid DNA were irradiated with pulsed 18.9 nm radiation originating from a Mo X-ray laser pumped in GRIP configuration at the LASERIX facility [1]. Surface doses of up to 500 kGray were delivered with a repetition rate of 10 Hz and average pulse energy of 200 nJ. The occurrence of single and double strand breaks not present in controls having undergone the same treatment except for the XRL irradiation can be seen as a clear effect of the XRL irradiation. This confirms the role of direct effects in DNA damages as previously seen with low energy ions [2, 3] and electrons.

  18. 75 FR 38977 - Pre-Stressed Concrete Steel Wire Strand from the People's Republic of China: Notice of Amended...

    Science.gov (United States)

    2010-07-07

    ... International Trade Administration Pre-Stressed Concrete Steel Wire Strand from the People's Republic of China... concrete steel wire strand (PC strand) from the People's Republic of China (PRC). On June 22, 2010, the ITC...-Stressed Concrete Steel Wire Strand from the People's Republic of China, USITC Pub. 4162, Inv. Nos....

  19. Mechanical behaviors of multi-filament twist superconducting strand under tensile and cyclic loading

    Science.gov (United States)

    Wang, Xu; Li, Yingxu; Gao, Yuanwen

    2016-01-01

    The superconducting strand, serving as the basic unit cell of the cable-in-conduit-conductors (CICCs), is a typical multi-filament twist composite which is always subjected to a cyclic loading under the operating condition. Meanwhile, the superconducting material Nb3Sn in the strand is sensitive to strain frequently relating to the performance degradation of the superconductivity. Therefore, a comprehensive study on the mechanical behavior of the strand helps understanding the superconducting performance of the strained Nb3Sn strands. To address this issue, taking the LMI (internal tin) strand as an example, a three-dimensional structural finite element model, named as the Multi-filament twist model, of the strand with the real configuration of the LMI strand is built to study the influences of the plasticity of the component materials, the twist of the filament bundle, the initial thermal residual stress and the breakage and its evolution of the filaments on the mechanical behaviors of the strand. The effective properties of superconducting filament bundle with random filament breakage and its evolution versus strain are obtained based on the damage theory of fiber-reinforced composite materials proposed by Curtin and Zhou. From the calculation results of this model, we find that the occurrence of the hysteresis loop in the cyclic loading curve is determined by the reverse yielding of the elastic-plastic materials in the strand. Both the initial thermal residual stress in the strand and the pitch length of the filaments have significant impacts on the axial and hysteretic behaviors of the strand. The damage of the filaments also affects the axial mechanical behavior of the strand remarkably at large axial strain. The critical current of the strand is calculated by the scaling law with the results of the Multi-filament twist model. The predicted results of the Multi-filament twist model show an acceptable agreement with the experiment.

  20. Cryogenic current leads

    Energy Technology Data Exchange (ETDEWEB)

    Zizek, F.

    1982-01-01

    Theoretical, technical and design questions are examined of cryogenic current leads for SP of magnetic systems. Simplified mathematical models are presented for the current leads. To illustrate modeling, the calculation is made of the real current leads for 500 A and three variants of current leads for 1500 A for the enterprise ''Shkoda.''

  1. Learn about Lead

    Science.gov (United States)

    ... old and younger are most susceptible to the effects of lead. Children Even low levels of lead in the blood ... simple blood test to check you or your child for lead exposure. You may also want to test your home for sources ... and Technology Lead Laws and Regulations Outreach and Grants En ...

  2. Mapping meiotic single-strand DNA reveals a new landscape of DNA double-strand breaks in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Cyril Buhler

    2007-12-01

    Full Text Available DNA double-strand breaks (DSBs, which are formed by the Spo11 protein, initiate meiotic recombination. Previous DSB-mapping studies have used rad50S or sae2Delta mutants, which are defective in break processing, to accumulate Spo11-linked DSBs, and report large (> or = 50 kb "DSB-hot" regions that are separated by "DSB-cold" domains of similar size. Substantial recombination occurs in some DSB-cold regions, suggesting that DSB patterns are not normal in rad50S or sae2Delta mutants. We therefore developed a novel method to map genome-wide, single-strand DNA (ssDNA-associated DSBs that accumulate in processing-capable, repair-defective dmc1Delta and dmc1Delta rad51Delta mutants. DSBs were observed at known hot spots, but also in most previously identified "DSB-cold" regions, including near centromeres and telomeres. Although approximately 40% of the genome is DSB-cold in rad50S mutants, analysis of meiotic ssDNA from dmc1Delta shows that most of these regions have substantial DSB activity. Southern blot assays of DSBs in selected regions in dmc1Delta, rad50S, and wild-type cells confirm these findings. Thus, DSBs are distributed much more uniformly than was previously believed. Comparisons of DSB signals in dmc1, dmc1 rad51, and dmc1 spo11 mutant strains identify Dmc1 as a critical strand-exchange activity genome-wide, and confirm previous conclusions that Spo11-induced lesions initiate all meiotic recombination.

  3. Activation of 2'-5' oligoadenylate synthetase by single-stranded and double-stranded RNA aptamers

    DEFF Research Database (Denmark)

    Hartmann, R; Norby, P L; Martensen, P M

    1998-01-01

    A number of small RNA molecules that are high affinity ligands for the 46-kDa form of human 2'-5' oligoadenylate synthetase have been identified by the SELEX method. Surface plasmon resonance analysis indicates that these RNAs bind to the enzyme with dissociation constants in the nanomolar range......-stranded RNA, can also be activated by RNA ligands with little secondary structure. Since 2'-5' oligoadenylate synthetase possesses no homology to other known RNA-binding proteins, the development of small specific ligands by SELEX should facilitate studies of RNA-protein interactions and may reveal novel...

  4. Protection of DNA strand breakage by radiation exposure

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jeong Ho; Kim, In Gyu; Lee, Kang Suk; Kim, Kug Chan; Shim, Hae Won

    1997-12-01

    Human ceruloplasmin, the plasma copper containing protein, is thought to play an essential role in iron metabolism, but it also has antioxidant properties. Ceruloplasmin directly scavenged hydroxyl radicals (.OH) generated in dithiothreitol/FeCl{sub 3} system besides inhibitory function of hydroxyl radical formation and lipid peroxidation. Polyamines, spermidine and spermine, significantly protected the supercoiled DNA strand breakage by hydroxyl radicals and DNA strand breakage by UV was highly protected by all four polyamines used in this study. In polyamine deficient mutant KL527. It was shown that cell survivability following UV irradiation was slightly increased by exogenous polyamines putrescine and spermidine supplement. However the cell survivability of wild type (MG 1655) was not influenced by polyamine supplement. In {gamma}-irradiated cells, cell survivability of polyamine-deficient mutant strain KL527 was significantly increased by exogenous putrescine supplement and that of wild type strain MG1655 was similar irrespective of polyamine supplement. These results implicate the possibility that polyamines play a potent role in radioprotection of cell and DNA level. (author). 32 refs., 8 figs

  5. The RNA synthesis machinery of negative-stranded RNA viruses

    Energy Technology Data Exchange (ETDEWEB)

    Ortín, Juan, E-mail: jortin@cnb.csic.es [Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CSIC) and CIBER de Enfermedades Respiratorias (ISCIII), Madrid (Spain); Martín-Benito, Jaime, E-mail: jmartinb@cnb.csic.es [Department of Macromolecular Structures, Centro Nacional de Biotecnología (CSIC), Madrid (Spain)

    2015-05-15

    The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and function of the ribonucleoprotein components: Atomic structure of the RNA polymerase complex. • Commonalities and differences between segmented- and non-segmented NSVs. • Transcription versus replication programmes.

  6. Genome-wide mapping of DNA strand breaks.

    Directory of Open Access Journals (Sweden)

    Frédéric Leduc

    Full Text Available Determination of cellular DNA damage has so far been limited to global assessment of genome integrity whereas nucleotide-level mapping has been restricted to specific loci by the use of specific primers. Therefore, only limited DNA sequences can be studied and novel regions of genomic instability can hardly be discovered. Using a well-characterized yeast model, we describe a straightforward strategy to map genome-wide DNA strand breaks without compromising nucleotide-level resolution. This technique, termed "damaged DNA immunoprecipitation" (dDIP, uses immunoprecipitation and the terminal deoxynucleotidyl transferase-mediated dUTP-biotin end-labeling (TUNEL to capture DNA at break sites. When used in combination with microarray or next-generation sequencing technologies, dDIP will allow researchers to map genome-wide DNA strand breaks as well as other types of DNA damage and to establish a clear profiling of altered genes and/or intergenic sequences in various experimental conditions. This mapping technique could find several applications for instance in the study of aging, genotoxic drug screening, cancer, meiosis, radiation and oxidative DNA damage.

  7. An effective mesoscopic model of double-stranded DNA.

    Science.gov (United States)

    Jeon, Jae-Hyung; Sung, Wokyung

    2014-01-01

    Watson and Crick's epochal presentation of the double helix structure in 1953 has paved the way to intense exploration of DNA's vital functions in cells. Also, recent advances of single molecule techniques have made it possible to probe structures and mechanics of constrained DNA at length scales ranging from nanometers to microns. There have been a number of atomistic scale quantum chemical calculations or molecular level simulations, but they are too computationally demanding or analytically unfeasible to describe the DNA conformation and mechanics at mesoscopic levels. At micron scales, on the other hand, the wormlike chain model has been very instrumental in describing analytically the DNA mechanics but lacks certain molecular details that are essential in describing the hybridization, nano-scale confinement, and local denaturation. To fill this fundamental gap, we present a workable and predictive mesoscopic model of double-stranded DNA where the nucleotides beads constitute the basic degrees of freedom. With the inter-strand stacking given by an interaction between diagonally opposed monomers, the model explains with analytical simplicity the helix formation and produces a generalized wormlike chain model with the concomitant large bending modulus given in terms of the helical structure and stiffness. It also explains how the helical conformation undergoes overstretch transition to the ladder-like conformation at a force plateau, in agreement with the experiment.

  8. Single-Stranded DNA Curtains for Studying Homologous Recombination.

    Science.gov (United States)

    Ma, C J; Steinfeld, J B; Greene, E C

    2017-01-01

    Homologous recombination is an important pathway involved in the repair of double-stranded DNA breaks. Genetic studies form the foundation of our knowledge on homologous recombination. Significant progress has also been made toward understanding the biochemical and biophysical properties of the proteins, complexes, and reaction intermediates involved in this essential DNA repair pathway. However, heterogeneous or transient recombination intermediates remain extremely difficult to assess through traditional ensemble methods, leaving an incomplete mechanistic picture of many steps that take place during homologous recombination. To help overcome some of these limitations, we have established DNA curtain methodologies as an experimental platform for studying homologous DNA recombination in real-time at the single-molecule level. Here, we present a detailed overview describing the preparation and use of single-stranded DNA curtains in applications related to the study of homologous DNA recombination with emphasis on recent work related to the study of the eukaryotic recombinase Rad51. © 2017 Elsevier Inc. All rights reserved.

  9. Tip Heater for Minimum Quench Energy Measurements on Superconducting Strands

    CERN Document Server

    Bauer, P; Oberli, L R

    1999-01-01

    Superconducting strands can be characterized by their Minimum Quench Energy (MQE), i.e. the minimum heat pulse needed to trigger a quench in operation conditions (field, temperature, current), in the limit of a (temporally and spatially) d-shaped disturbance. The sub-mm/µs range of perturbation space has only recently been achieved using the electrical graphite-paste heater technique [1]. The present work has put this technique into practice for the strands of the LHC main magnets, which are designed to operate at 1.9K in peak fields of up to 9T [1]. No way has been found yet to calibrate MQE measurements. To make relative statements on the MQE of different samples possible, the reproducibility of the measurements was emphasized. First heater prototypes did not come up to this stipulation. Finally the tip-heater configuration was found to meet the requirements. It generates a heat pulse in a thin resistive graphite paste deposit on top of a small tip that is pressed against the sample with a clamp. The clamp...

  10. Dynamics of single-stranded DNA tethered to a solid

    Science.gov (United States)

    Radiom, Milad; Paul, Mark R.; Ducker, William A.

    2016-06-01

    Tethering is used to deliver specific biological and industrial functions. For example, single-stranded DNA (ssDNA) is tethered to polymerases and long sequences of double-stranded DNA (dsDNA) during replication, and to solids in DNA microarrays. However, tethering ssDNA to a large object limits not only the available ssDNA conformations, but also the range of time-scales over which the mechanical responses of ssDNA are important. In this work we examine the effect of tethering by measurement of the mechanical response of ssDNA that is tethered at each end to two separate atomic force microscope cantilevers in aqueous solution. Thermal motion of the cantilevers drives the ends of the ssDNA chain at frequencies near 2 kHz. The presence of a tethered molecule makes a large difference to the asymmetric cross-correlation of two cantilevers, which enables resolution of the mechanical properties in our experiments. By analysis of the correlated motion of the cantilevers we extract the friction and stiffness of the ssDNA. We find that the measured friction is much larger than the friction that is usually associated with the unencumbered motion of ssDNA. We also find that the measured relaxation time, ∼30 μs, is much greater than prior measurements of the free-molecule relaxation time. We attribute the difference to the loss of conformational possibilities as a result of constraining the ends of the ssDNA.

  11. Disseminated mycobacteriosis in a stranded loggerhead sea turtle (Caretta caretta).

    Science.gov (United States)

    Nardini, Giordano; Florio, Daniela; Di Girolamo, Nicola; Gustinelli, Andrea; Quaglio, Francesco; Fiorentini, Laura; Leopardi, Stefania; Fioravanti, Maria Letizia

    2014-06-01

    A loggerhead sea turtle (Caretta caretta) was found stranded alive along the Adriatic coast close to Ancona, Italy, displaying obtundation, tachypnea, and increased respiratory effort. It died a few hours after admission, and a postmortem examination was immediately performed. Miliary yellowish nodules were evident in the liver, and a lower number in the heart, stomach, and gut wall. Hundreds of whitish nodules were scattered in the lungs, with the majority of the pulmonary parenchyma being replaced by the lesions. Histologically, all nodular lesions consisted of a small central area of necrosis with acid-fast bacilli surrounded by epithelioid cells, macrophages, and lymphocytes. Giant cells were found in the spleen and the liver. Kidneys, lungs, liver, spleen, brain, and skin lesions were inoculated aseptically onto general isolation media and selective isolation media for mycobacteria. The isolate showed a restriction pattern identical to Mycobacterium chelonae by polymerase chain reaction-restriction fragment length polymorphism. To the best of the authors' knowledge, this is the first description of a disseminated infection caused by a potentially pathogenic mycobacteria in a stranded, free-ranging loggerhead sea turtle. Veterinary staff and biologists who handle sea turtles with suspected mycobacterial disease should protect themselves appropriately.

  12. Assessing Disease and Mortality among Small Cetaceans Stranded at a World Heritage Site in Southern Brazil.

    Directory of Open Access Journals (Sweden)

    Isabela G Domiciano

    Full Text Available Cetaceans are considered environmental sentinels and their health often reflects either anthropogenic or natural spatio-temporal disturbances. This study investigated the pathological findings and mortality of small cetaceans with the aim of detecting hazards and monitoring health trends in a high-biodiversity area. Between 2007 and 2012, 218 stranded cetaceans were recorded on the Paraná coast, southern Brazil. Fifty-seven (26.1% of these animals, including 50 Sotalia guianensis, 2 Pontoporia blainvillei, 2 Stenella frontalis, 1 Stenella longirostris, 1 Tursiops truncatus and 1 Globicephala melas were necropsied and samples were collected for histopathology. Causes of death were determined in 46 of the 57 (80.7% animals and most (30 or 65.2% were ascribed to anthropogenic activities, including fisheries bycatch (28/30 and trauma (2/30. The remaining 16 fatalities were considered natural, and attributed to pneumonia (10/16, emaciation (3/16, septicemia (1/16, neonatal pathology (1/16 and choking via food obstruction (1/16. Irrespective of the cause, bronchointerstitial pneumonia, associated with parasitism, lymphadenitis and membranous glomerulonephritis were common findings among all fatalities. These results suggest, that while anthropogenic activities are a leading cause of cetacean strandings in Paraná, underlying pre-existing diseases may contribute towards deaths. Although the studied area is considered a biosphere reserve by UNESCO, complex anthropogenic and natural interactions might be occurring, increasing cetacean susceptibility to hazards. This study may help facilitate developing an effective conservation plan for coastal cetaceans focusing on reducing fisheries interactions, habitat degradation and pollution as mechanisms for ultimately increasing species resilience.

  13. Binding by TRBP-dsRBD2 Does Not Induce Bending of Double-Stranded RNA.

    Science.gov (United States)

    Acevedo, Roderico; Evans, Declan; Penrod, Katheryn A; Showalter, Scott A

    2016-06-21

    Protein-nucleic acid interactions are central to a variety of biological processes, many of which involve large-scale conformational changes that lead to bending of the nucleic acid helix. Here, we focus on the nonsequence-specific protein TRBP, whose double-stranded RNA-binding domains (dsRBDs) interact with the A-form geometry of double-stranded RNA (dsRNA). Crystal structures of dsRBD-dsRNA interactions suggest that the dsRNA helix must bend in such a way that its major groove expands to conform to the dsRBD's binding surface. We show through isothermal titration calorimetry experiments that dsRBD2 of TRBP binds dsRNA with a temperature-independent observed binding affinity (KD ∼500 nM). Furthermore, a near-zero observed heat capacity change (ΔCp = 70 ± 40 cal·mol(-1)·K(-1)) suggests that large-scale conformational changes do not occur upon binding. This result is bolstered by molecular-dynamics simulations in which dsRBD-dsRNA interactions generate only modest bending of the RNA along its helical axis. Overall, these results suggest that this particular dsRBD-dsRNA interaction produces little to no change in the A-form geometry of dsRNA in solution. These results further support our previous hypothesis, based on extensive gel-shift assays, that TRBP preferentially binds to sites of nearly ideal A-form structure while being excluded from sites of local deformation in the RNA helical structure. The implications of this mechanism for efficient micro-RNA processing will be discussed.

  14. Residual Resistivity Ratio (RRR) Measurements of LHC Superconducting NbTi Cable Strands

    CERN Document Server

    Charifoulline, Z

    2006-01-01

    The Rutherford-type superconducting NbTi cables of the LHC accelerator are currently manufactured by six industrial companies. As a part of the acceptance tests, the Residual Resistivity Ratio (RRR) of superconducting strands is systematically measured on virgin strands to qualify the strands before cabling and on extracted strands to qualify the cables and to check the final heat treatment (controlled oxidation to control interstrand resistance). More than 12000 samples of virgin and extracted strands have been measured during last five years. Results show good correlation with the measurements done by the companies and reflect well the technological process of cable production (strand annealing, cabling, cable heat treatment). This paper presents a description of the RRR-test station and the measurement procedure, the summary of the results over all suppliers and finally the correlation between RRR-values of the cables and the magnets.

  15. Simulation of 125I induced DNA strand breaks in a CAP-DNA complex.

    Science.gov (United States)

    Li, W; Friedland, W; Jacob, P; Paretzke, H G; Panyutin, I; Neumann, R D

    2002-01-01

    The E. coli catabolite gene activator protein (CAP)-DNA complex with 125I located at the position of the H5 atom of the cytosine near the centre was incorporated into the PARTRAC track structure code. DNA strand breaks due to irradiation were calculated by track structure and radical attack simulations; strand breaks due to neutralisation of the highly charged 125Te ion were derived from a semi-empirical distribution. According to the calculations, the neutralisation effect dominates the strand breakage frequency at 2 bases away from the 125I decay site on both strands. The first breakage distribution counted from a 32P labelled end on the strand with 125I agreed well with experimental data, but on the opposite strand, the calculated distribution is more concentrated around the decay site and its yield is about 20% larger than the measured data.

  16. Estimation of Prestress Force Distribution in the Multi-Strand System of Prestressed Concrete Structures

    Directory of Open Access Journals (Sweden)

    Keunhee Cho

    2015-06-01

    Full Text Available Prestressed concrete (PSC is one of the most reliable, durable and widely used construction materials, which overcomes the weakness of concrete in tension by the introduction of a prestress force. Smart strands enabling measurement of the prestress force have recently been developed to maintain PSC structures throughout their lifetime. However, the smart strand cannot give a representative indication of the whole prestress force when used in multi-strand systems since each strand sustains a different prestress force. In this paper, the actual distribution of the prestress force in a multi-strand system is examined using elastomagnetic (EM sensors to develop a method for tracking representative indicators of the prestress force using smart strands.

  17. Strand Burner Results of AFP-001 Propellant with Inert Coating for Temperature Compensation

    Science.gov (United States)

    2015-10-01

    ARL-MR-0907 ● OCT 2015 US Army Research Laboratory Strand Burner Results of AFP -001 Propellant with Inert Coating for Temperature...Laboratory Strand Burner Results of AFP -001 Propellant with Inert Coating for Temperature Compensation by John J Ritter and Anthony Canami...COVERED (From - To) February 2015 4. TITLE AND SUBTITLE Strand Burner Results of AFP -001 Propellant with Inert Coating for Temperature Compensation

  18. A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology.

    OpenAIRE

    Marcel Ander; Sivaraman Subramaniam; Karim Fahmy; Francis Stewart, A.; Erik Schäffer

    2015-01-01

    Repair of DNA breaks by single-strand annealing (SSA) is a major mechanism for the maintenance of genomic integrity. SSA is promoted by proteins (single-strand-annealing proteins [SSAPs]), such as eukaryotic RAD52 and λ phage Redβ. These proteins use a short single-stranded region to find sequence identity and initiate homologous recombination. However, it is unclear how SSAPs detect homology and catalyze annealing. Using single-molecule experiments, we provide evidence that homology is recog...

  19. Analysis of Cable-in-Conduit Conductors' DC Performance in Light of Strand's Experimental Properties

    Institute of Scientific and Technical Information of China (English)

    TAN Yunfei; WENG Peide; LIU Fang; LI Shaolei

    2007-01-01

    Conductor qualification will be carried out with four Cable-in-Conduit Conductor (CICC) samples made of superconducting strands. The direct current (DC) performance of these samples will be tested in the SULTAN facility. The critical current densities of the strands can be well simulated by empirical equations. In this paper, a model is illustrated to predict the DC behaviour of the cable in light of the single strand's experimental properties. The simulation results were compared with experimental results.

  20. Interpreting the spatio-temporal patterns of sea turtle strandings: Going with the flow

    Science.gov (United States)

    Hart, K.M.; Mooreside, P.; Crowder, L.B.

    2006-01-01

    Knowledge of the spatial and temporal distribution of specific mortality sources is crucial for management of species that are vulnerable to human interactions. Beachcast carcasses represent an unknown fraction of at-sea mortalities. While a variety of physical (e.g., water temperature) and biological (e.g., decomposition) factors as well as the distribution of animals and their mortality sources likely affect the probability of carcass stranding, physical oceanography plays a major role in where and when carcasses strand. Here, we evaluate the influence of nearshore physical oceanographic and wind regimes on sea turtle strandings to decipher seasonal trends and make qualitative predictions about stranding patterns along oceanfront beaches. We use results from oceanic drift-bottle experiments to check our predictions and provide an upper limit on stranding proportions. We compare predicted current regimes from a 3D physical oceanographic model to spatial and temporal locations of both sea turtle carcass strandings and drift bottle landfalls. Drift bottle return rates suggest an upper limit for the proportion of sea turtle carcasses that strand (about 20%). In the South Atlantic Bight, seasonal development of along-shelf flow coincides with increased numbers of strandings of both turtles and drift bottles in late spring and early summer. The model also predicts net offshore flow of surface waters during winter - the season with the fewest relative strandings. The drift bottle data provide a reasonable upper bound on how likely carcasses are to reach land from points offshore and bound the general timeframe for stranding post-mortem (strandings follow a seasonal regime predictable from physical oceanography and mimicked by drift bottle experiments. Managers can use these findings to reevaluate incidental strandings limits and fishery takes for both nearshore and offshore mortality sources. ?? 2005 Elsevier Ltd. All rights reserved.

  1. Analysis of heavy-ion-induced DNA strand breaks in plasmid pUC18

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Plasmid DNA was irradiated or implanted by mixed particle field(CR) or lithium-ion-beam to detect strand breaks.The primary results showed that mixed particle field could induce single and double strand breaks with positive linear-dose-effects;most of sequence changes induced by CR were point mutant.Lithium-ion-beam could induce strand breaks also,but it was only at dose of 20Gy.

  2. Edwardsiella tarda sepsis in a live-stranded sperm whale (Physeter macrocephalus).

    Science.gov (United States)

    Cools, Piet; Haelters, Jan; Lopes dos Santos Santiago, Guido; Claeys, Geert; Boelens, Jerina; Leroux-Roels, Isabel; Vaneechoutte, Mario; Deschaght, Pieter

    2013-09-27

    Whale strandings remain poorly understood, although bacterial infections have been suggested to contribute. We isolated Edwardsiella tarda from the blood of a stranded sperm whale. The pathogen was identified with MALDI-TOF MS, confirmed by 16S rRNA gene sequencing and quantified in blood by qPCR. We report the first case of sepsis in a sperm whale. The zoonotic potential of E. tarda and the possible role of bacterial infections in the enigmatic strandings of cetaceans are discussed.

  3. Refinement of Propellant Strand Burning Method to Suit Aluminised Composite Rocket Propellant

    Science.gov (United States)

    2014-12-01

    ABSTRACT An epoxy coating was trialled as an inhibitor for composite rocket propellant strands burned in a Crawford–style bomb . The epoxy coating...into the Crawford bomb and pressurised with nitrogen to the specified pressure. Once pressure and temperature were stable at the required set- point...aggressive propellant. This method involved the coating of strands of propellant with a two-part epoxy polymer. Strands were dipped into a bath of epoxy

  4. Structure-spectrophotometric selectivity relationship in interactions of quercetin related flavonoids with double stranded and single stranded RNA

    Science.gov (United States)

    Piantanida, Ivo; Mašić, Lozika; Rusak, Gordana

    2009-04-01

    Interactions of five flavonoids with dsRNA and single stranded ssRNA were studied by UV/vis titrations. The results obtained supported the intercalative binding mode as a dominant interaction of studied flavonoids with dsRNA as well as major interaction with ssRNA. Furthermore, changes of the UV/vis spectra of flavonoids induced by addition of poly G or poly C, respectively, are significantly stronger than changes induced by double stranded poly G-poly C, pointing to essential role of the free poly G or poly C sequence (not hydrogen bonded in double helix). Exclusively poly G caused significant batochromic shift of the UV/vis maxima of all studied flavonoids, whereby the intensity of batochromic shift is nicely correlated to the number of OH groups of flavonoid. Unlikely to poly G, addition of poly A and poly U induced measurable changes only in the UV/vis spectra of flavonoids characterised by no OH (galangin) or three OH groups (myricetin) on the phenyl part of the molecule. Consequently, flavonoids with one- or two-OH groups on the phenyl part of the molecule (luteolin, fisetin, kaempferol) specifically differentiate between poly A, poly U (negligible changes in the UV/Vis spectra) and poly G (strong changes in the UV/Vis spectra) as well as poly C (moderate changes in the UV/Vis spectra).

  5. Genetic requirements for the single-strand annealing pathway of double-strand break repair in Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, E.L.; Sugawara, N.; Haber, J.E. [Brandeis Univ., Waltham, MA (United States)] [and others

    1996-03-01

    HO endonuclease-induced double-strand breaks (DSBs) within a direct duplication of Escherichia coli lacZ genes are repaired either by gene conversion or by single-strand annealing (SSA), with >80% being SSA. Previously it was demonstrated that the RAD52 gene is required for DSB-induced SSA. In the present study, the effects of other genes belonging to the RAD52 epistasis group were analyzed. We show that RAD51, RAD54, RAD55, and RAD57 genes are not required for SSA irrespective of whether recombination occurred in plasmid or chromosomal DNA. In both plasmid and chromosomal constructs with homologous sequences in direct orientation, the proportion of SSA events over gene conversion was significantly elevated in the mutant strains. However, gene conversion was not affected when the two lacZ sequences were in inverted orientation. These results suggest that there is a competition between SSA and gene conversion processes that favors SSA in the absence of RAD51, RAD54, RAD55 and RAD57. Mutations in RAD50 and XRS2 genes do not prevent the completion, but markedly retard the kinetics, of DSB repair by both mechanisms in the lacZ direct repeat plasmid, a result resembling the effects of these genes during mating-type (MAT) switching. 43 refs., 8 figs., 3 tabs.

  6. NUMERICAL ANALYSIS OF THE STRESS-STRAIN STATE OF A ROPE STRAND WITH LINEAR CONTACT UNDER TENSION AND TORSION LOADING CONDITIONS

    Directory of Open Access Journals (Sweden)

    Evgenij Kalentev

    2017-06-01

    Full Text Available The paper presents the results of a numerical analysis of the stress-strain state of a rope strand with linear contact under tension and torsion loading conditions. Calculations are done using the ANSYS software package. Different approaches to calculation of the stress-strain state of ropes are reviewed, and their advantages and deficiencies are considered. The analysis of the obtained results leads us to the conclusion that the proposed method can be used in engineering calculations.

  7. To Nick or Not to Nick: Comparison of I-SceI Single- and Double-Strand Break-Induced Recombination in Yeast and Human Cells

    OpenAIRE

    2014-01-01

    Genetic modification of a chromosomal locus to replace an existing dysfunctional allele with a corrected sequence can be accomplished through targeted gene correction using the cell's homologous recombination (HR) machinery. Gene targeting is stimulated by generation of a DNA double-strand break (DSB) at or near the site of correction, but repair of the break via non-homologous end-joining without using the homologous template can lead to deleterious genomic changes such as in/del mutations, ...

  8. Transport AC loss characteristics of a nine strand YBCO Roebel cable

    Science.gov (United States)

    Jiang, Zhenan; Badcock, R. A.; Long, N. J.; Staines, Mike; Thakur, K. P.; Lakshmi, L. S.; Wright, A.; Hamilton, K.; Sidorov, G. N.; Buckley, R. G.; Amemiya, Naoyuki; Caplin, A. D.

    2010-02-01

    Transport AC loss in a short length of 9/2 YBCO Roebel cable (nine 2 mm wide strands) is measured. The AC loss data are compared with those in a 5/2 YBCO Roebel cable (five 2 mm wide strands) as well as that in a single strand. All the strands composing the cables and the single strand are insulated and cut from the same stock material. The validity of the measurement method was reconfirmed by results at a range of frequencies. At a wide range of It/Ic, the normalized AC losses in the Roebel cable were around 6.2-6.7 times of those in the single strand. This is less than the nine times predicted for a tight bundle of nine conductors. The normalized transport AC losses in the 5/2 Roebel cable are much smaller than those in the 9/2 Roebel. This should be due to larger superposition of magnetic field in the 9/2 Roebel. The Ic of the 9/2 and 5/2 Roebel cables is determined by serial connection of the strands. This eliminates the effect where differing resistances in the current terminations cause uneven current sharing between strands when the strands are connected in parallel.

  9. Sequence Conversion by Single Strand Oligonucleotide Donors via Non-homologous End Joining in Mammalian Cells*

    OpenAIRE

    Liu, Jia; Majumdar, Alokes; Liu, Jilan; Thompson, Lawrence H.; Seidman, Michael M.

    2010-01-01

    Double strand breaks (DSBs) can be repaired by homology independent nonhomologous end joining (NHEJ) pathways involving proteins such as Ku70/80, DNAPKcs, Xrcc4/Ligase 4, and the Mre11/Rad50/Nbs1 (MRN) complex. DSBs can also be repaired by homology-dependent pathways (HDR), in which the MRN and CtIP nucleases produce single strand ends that engage homologous sequences either by strand invasion or strand annealing. The entry of ends into HDR pathways underlies protocols for genomic manipulatio...

  10. Sequence conversion by single strand oligonucleotide donors via non-homologous end joining in mammalian cells.

    Science.gov (United States)

    Liu, Jia; Majumdar, Alokes; Liu, Jilan; Thompson, Lawrence H; Seidman, Michael M

    2010-07-23

    Double strand breaks (DSBs) can be repaired by homology independent nonhomologous end joining (NHEJ) pathways involving proteins such as Ku70/80, DNAPKcs, Xrcc4/Ligase 4, and the Mre11/Rad50/Nbs1 (MRN) complex. DSBs can also be repaired by homology-dependent pathways (HDR), in which the MRN and CtIP nucleases produce single strand ends that engage homologous sequences either by strand invasion or strand annealing. The entry of ends into HDR pathways underlies protocols for genomic manipulation that combine site-specific DSBs with appropriate informational donors. Most strategies utilize long duplex donors that participate by strand invasion. Work in yeast indicates that single strand oligonucleotide (SSO) donors are also active, over considerable distance, via a single strand annealing pathway. We examined the activity of SSO donors in mammalian cells at DSBs induced either by a restriction nuclease or by a targeted interstrand cross-link. SSO donors were effective immediately adjacent to the break, but activity declined sharply beyond approximately 100 nucleotides. Overexpression of the resection nuclease CtIP increased the frequency of SSO-mediated sequence modulation distal to the break site, but had no effect on the activity of an SSO donor adjacent to the break. Genetic and in vivo competition experiments showed that sequence conversion by SSOs in the immediate vicinity of the break was not by strand invasion or strand annealing pathways. Instead these donors competed for ends that would have otherwise entered NHEJ pathways.

  11. Necropsy report of a fin whale (Balaenoptera physalus) stranded in Denmark in 2010

    DEFF Research Database (Denmark)

    Alstrup, Aage K. O.; Hedayat, Abdi; Jensen, Trine Hammer;

    2013-01-01

    There is little detailed information on stranded fin whales (Balaenoptera physalus) in the scientific literature (Notarbartolo di Sciara et al., 2003). In Denmark, at least eight fin whales stranded between the years 1603 and 1958 (Kinze, 1995). On 16 June 2010, a live subadult or adult male fin...... whale stranded in the Bay of Vejle (55º 69' N, 9º 58' E), Denmark. Despite several attempts, it was not possible to rescue the fin whale, which was only partially exposed by the water. The fin whale succumbed after 5 d stranded in shallow water. The dead fin whale was transported to a nearby pier...

  12. Trends in Marine Turtle Strandings along the East Queensland, Australia Coast, between 1996 and 2013

    Directory of Open Access Journals (Sweden)

    Jaylene Flint

    2015-01-01

    Full Text Available In-water monitoring of marine vertebrates is usually expensive while the use of stranding data can be used to provide a cost-effective estimation of disease and mortality. Strandings for Queensland are recorded in a web based database (StrandNet managed by the Queensland Government’s Department of Environment and Heritage Protection (EHP. Data recorded in StrandNet from the east coast of Queensland between 1996 and 2013 were investigated for patterns of stranding. Significant trends in Queensland over this time were (i an increase in the number of animals reported stranded within this study site; (ii a species (loggerhead and green marine turtles prevalence; (iii a seasonal effect on different age classes stranding with most overall strandings occurring between August and November; and (iv stranding hotspots (Moreton Bay, Hervey Bay, Rockhampton region, and Cleveland Bays persisting throughout the study timeframe. This study suggested that intervention strategies, such as rehabilitation, should be able to be focussed on periods of heightened importance and specific localities to minimize health risks and contribute to sustainable use of resources.

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

    Energy Technology Data Exchange (ETDEWEB)

    1994-04-12

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

  14. Necropsy report of a fin whale (Balaenoptera physalus) stranded in Denmark in 2010

    DEFF Research Database (Denmark)

    Alstrup, Aage K. O.; Hedayat, Abdi; Jensen, Trine Hammer

    2013-01-01

    There is little detailed information on stranded fin whales (Balaenoptera physalus) in the scientific literature (Notarbartolo di Sciara et al., 2003). In Denmark, at least eight fin whales stranded between the years 1603 and 1958 (Kinze, 1995). On 16 June 2010, a live subadult or adult male fin...... whale stranded in the Bay of Vejle (55º 69' N, 9º 58' E), Denmark. Despite several attempts, it was not possible to rescue the fin whale, which was only partially exposed by the water. The fin whale succumbed after 5 d stranded in shallow water. The dead fin whale was transported to a nearby pier...

  15. Polycation graft copolymers accelerating DNA strand exchange: involvement of ionic interaction.

    Science.gov (United States)

    Kim, W J; Ishihara, T; Akaike, T; Maruyama, A

    2001-01-01

    In the previous study (Chem. Eur. J., 7, 176 (2001)) we demonstrated that the comb-type polycationic copolymer (PLL-g-Dex) which is composed of poly (L-lysine) backbone and dextran graft chains expedited the DNA strand exchange reaction. In this study, fluorescence resonance energy transfer (FRET) was employed to explore the copolymer-mediated DNA strand exchange with higher time-resolution. To initiate strand exchange reaction the duplex prepared from 3'-fluorescein isothiocyanate (FITC)--and 5'-carboxytetramethylrhodamine(TAMRA)-labeled complementary DNAs was added to its non-labeled complementary single strand. DNA strand exchange was monitored by observing the recovery of the FITC quenching. More than 20,000 times increase in strand exchange rate at 37 degrees C by the copolymer was estimated. To investigate the accelerating mechanisms of the copolymer, the same reactions but at various ionic strenghts were studied. With increasing ionic strengths the strand exchange rate in the absence of the copolymer increased, suggesting that ionic repulsion among DNAs is unfavorable for the strand exchange to occur. Hence, alleviation of the electrostatic repulsion through interpolyelectrolyte complex formation is probably a role of the copolymer for accelerating the strand exchange reaction.

  16. Single-stranded regions in transforming deoxyribonucleic acid after uptake by competent Haemophilus influenzae

    Energy Technology Data Exchange (ETDEWEB)

    Sedgwick, B.; Setlow, J.K.

    1976-02-01

    About 15% of donor deoxyribonucleic acid (DNA) is single stranded immediately after uptake into competent Haemophilus influenzae wild-type cells, as judged by its sensitivity to S1 endonuclease. This amount decreases to 4 to 5% by 30 min after uptake. Mutants which are defective in the covalent association of recipient and donor DNA form little or no S1 endonuclease-sensitive donor. At 17 C donor DNA taken up by the wild type contains single-stranded regions although there is no observable association, either covalent or noncovalent. The single-stranded regions are at the ends of donor DNA molecules, as judged by the unchanged sedimentation velocity after S1 endonuclease digestion. The amount of single-stranded donor remains constant at 17 C for more than 60 min after uptake, suggesting that the decrease observed at 37 C is the result of association of single-stranded ends with single-stranded regions of recipient cell DNA. Three sequential steps necessary for the integration of donor DNA into recipient DNA are proposed: the synthesis of single-stranded regions in recipient DNA, the interaction of donor DNA with recipient DNA resulting in the production of single-stranded ends on donor DNA, and the stable pairing of homologous single-stranded regions. (auth)

  17. A euryarchaeal histone modulates strand displacement synthesis by replicative DNA polymerases.

    Science.gov (United States)

    Sun, Fei; Huang, Li

    2016-07-01

    Euryarchaeota and Crenarchaeota, the two main lineages of the domain Archaea, encode different chromatin proteins and differ in the use of replicative DNA polymerases. Crenarchaea possess a single family B DNA polymerase (PolB), which is capable of strand displacement modulated by the chromatin proteins Cren7 and Sul7d. Euryarchaea have two distinct replicative DNA polymerases, PolB and PolD, a family D DNA polymerase. Here we characterized the strand displacement activities of PolB and PolD from the hyperthermophilic euryarchaeon Pyrococcus furiosus and investigated the influence of HPfA1, a homolog of eukaryotic histones from P. furiosus, on these activities. We showed that both PolB and PolD were efficient in strand displacement. HPfA1 inhibited DNA strand displacement by both DNA polymerases but exhibited little effect on the displacement of a RNA strand annealed to single-stranded template DNA. This is consistent with the finding that HPfA1 bound more tightly to double-stranded DNA than to a RNA:DNA hybrid. Our results suggest that, although crenarchaea and euryarchaea differ in chromosomal packaging, they share similar mechanisms in modulating strand displacement by DNA polymerases during lagging strand DNA synthesis.

  18. Lead and tap water

    Science.gov (United States)

    Water contaminated with lead ... The Environmental Protection Agency (EPA) monitors drinking water in the United States. It requires water suppliers to produce annual water quality reports. These reports include information about lead amounts, and they ...

  19. Lead and Your Baby

    Science.gov (United States)

    ... who works with lead, like in auto repair, construction or in a plant that makes paint, batteries, ... who works with lead, like in auto repair, construction or in a plant that makes paint, batteries, ...

  20. Exposures to lead.

    Science.gov (United States)

    Callan, Anna C; Hinwood, Andrea L

    2011-01-01

    The Pacific Basin Consortium for Environment and Health hosted a workshop on Exposures to Lead. Speakers from Australia and the United States of America addressed current research knowledge on lead exposures and health effects in children, risk assessment and communication issues in dealing with lead exposure sources, different methods for assessing exposure, and the variety of scenarios where lead still remains a pollutant of concern. Mining continues to be a source of lead for many communities, and approaches to reducing exposures in these settings present particular challenges. A Perth Declaration for the Global Reduction of Childhood Lead Exposure was signed by participants of the meeting and is aimed at increasing attention to the need to continue to assess lead in the environment and to develop strategies to reduce lead in the environment and exposure by communities.

  1. Rapid Lead Screening Test

    Science.gov (United States)

    ... Vitro Diagnostics Tests Used In Clinical Care Rapid Lead Screening Test Share Tweet Linkedin Pin it More ... reducing the need for a follow-up visit. Lead Risk Links Centers for Disease Control and Prevention ( ...

  2. Lead Poisoning (For Parents)

    Science.gov (United States)

    ... organs and tissues that need it, thus causing anemia. Most lead ends up in the bone, where it causes ... vomiting or nausea constipation pallor (pale skin) from ... look for lead poisoning or other health problems. Treatment Treatment for ...

  3. Immunofluorescent Detection of DNA Double Strand Breaks induced by High-LET Radiation

    Science.gov (United States)

    Cucinotta, Francis A.; Wu, Honglu; Desai, Nirav

    2004-01-01

    Within cell nuclei, traversing charged heavy ion particles lead to the accumulation of proteins related to DNA lesions and repair along the ion trajectories. Irradiation using a standard geometric setup with the beam path perpendicular to the cell monolayer generates discrete foci of several proteins known to localize at sites of DNA double strand breaks (DSBs). One such molecule is the histone protein H2AX (gamma-H2AX), which gets rapidly phosphorylated in response to ionizing radiation. Here we present data obtained with a modified irradiation geometry characterized by a beam path parallel to a monolayer of human fibroblast cells. This new irradiation geometry leads to the formation of gamma-H2AX aggregates in the shape of streaks stretching over several micrometers in the x/y plane, thus enabling the analysis of the fluorescence distributions along the particle trajectories. Qualitative analysis of these distributions presented insights into the DNA repair kinetics along the primary track structure and visualization of possible chromatin movement. We also present evidence of colocalization of gamma-H2AX with several other proteins in responses to ionizing radiation exposure. Analysis of gamma-H2AX has the potential to provide useful information on human cell responses to high LET radiation after exposure to space-like radiation.

  4. Targeting collagen strands by photo-triggered triple-helix hybridization.

    Science.gov (United States)

    Li, Yang; Foss, Catherine A; Summerfield, Daniel D; Doyle, Jefferson J; Torok, Collin M; Dietz, Harry C; Pomper, Martin G; Yu, S Michael

    2012-09-11

    Collagen remodeling is an integral part of tissue development, maintenance, and regeneration, but excessive remodeling is associated with various pathologic conditions. The ability to target collagens undergoing remodeling could lead to new diagnostics and therapeutics as well as applications in regenerative medicine; however, such collagens are often degraded and denatured, making them difficult to target with conventional approaches. Here, we present caged collagen mimetic peptides (CMPs) that can be photo-triggered to fold into triple helix and bind to collagens denatured by heat or by matrix metalloproteinase (MMP) digestion. Peptide-binding assays indicate that the binding is primarily driven by stereo-selective triple-helical hybridization between monomeric CMPs of high triple-helical propensity and denatured collagen strands. Photo-triggered hybridization allows specific staining of collagen chains in protein gels as well as photo-patterning of collagen and gelatin substrates. In vivo experiments demonstrate that systemically delivered CMPs can bind to collagens in bones, as well as prominently in articular cartilages and tumors characterized by high MMP activity. We further show that CMP-based probes can detect abnormal bone growth activity in a mouse model of Marfan syndrome. This is an entirely new way to target the microenvironment of abnormal tissues and could lead to new opportunities for management of numerous pathologic conditions associated with collagen remodeling and high MMP activity.

  5. NA49: lead-lead collision

    CERN Multimedia

    1996-01-01

    This is an image of an actual lead ion collision taken from tracking detectors on the NA49 experiment, part of the heavy ion project at CERN. These collisions produce a very complicated array of hadrons as the heavy ions break up. It is hoped that one of these collisions will eventually create a new state of matter known as quark-gluon plasma.

  6. Occupational lead poisoning

    OpenAIRE

    Ramírez, Augusto V; Médico del Trabajo. American College of Occupational and Environmental Medicine.

    2013-01-01

    Lead, a ubiquitous heavy metal, has been found in places as unlikely as Greenland’s fossil ice. Egyptians and Hebrews used it. In Spain, Phoenicians c. 2000 BC worked ores of lead. At the end of the XX century, occupational lead’s poisoning became a public health problem in developed countries. In non-developed countries occupational lead poisoning is still frequent. Diagnosis is directed to recognize lead existence at the labor environment and good clinical and occupational documentation. Di...

  7. Lead Poisoning in Children.

    Science.gov (United States)

    Drummond, A. H., Jr.

    1981-01-01

    Early symptoms of lead poisoning in children are often overlooked. Lead poisoning has its greatest effects on the brain and nervous system. The obvious long-term solution to the lead poisoning problem is removal of harmful forms of the metal from the environment. (JN)

  8. Atrioventricular Pacemaker Lead Reversal

    Directory of Open Access Journals (Sweden)

    Mehmet K Aktas, MD

    2007-01-01

    Full Text Available During cardiac surgery temporary epicardial atrial and ventricular leads are placed in case cardiac pacing is required postoperatively. We present the first reported series of patients with reversal of atrioventricular electrodes in the temporary pacemaker without any consequent deleterious hemodynamic effect. We review the electrocardiographic findings and discuss the findings that lead to the discovery of atrioventricular lead reversal.

  9. Molecular dynamics simulations of a single stranded (ss) DNA

    CERN Document Server

    Chatterjee, Subhasish; Thakur, Siddarth; Burin, Alexander

    2012-01-01

    The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon sequence of the p53 gene. Various thermodynamic macroscopic observables such as temperature, energy distributions, as well as root mean square deviation (RMSD) of the nucleic acid backbone of the ssDNA were studied using molecular dynamics (MD) simulations. The AMBER program was used for building the structural model of the ssDNA, and atomistic MD simulations in three different ensembles were carried out using the NAMD program. The microcanonical (NVE), conical (NVT) and isobaric-isothermal (NPT) ensembles were employed to compare the equilibrium characteristics of ssDNA in aqueous solutions. Our results indicate that the conformational stability of the ssDNA is dependent on the thermodynamic conditions.

  10. Using both strands: The fundamental nature of antisense transcription.

    Science.gov (United States)

    Murray, Struan C; Mellor, Jane

    2016-01-01

    Non-coding transcription across the antisense strands of genes is an abundant, pervasive process in eukaryotes from yeast to humans, however its biological function remains elusive. Here, we provide commentary on a recent study of ours, which demonstrates a genome-wide role for antisense transcription: establishing a unique, dynamic chromatin architecture over genes. Antisense transcription increases the level of nucleosome occupancy and histone acetylation at the promoter and body of genes, without necessarily modulating the level of protein-coding sense transcription. It is also associated with high levels of histone turnover. By allowing genes to sample a wider range of chromatin configurations, antisense transcription could serve to make genes more sensitive to changing signals, priming them for responses to developmental programs or stressful cellular environments. Given the abundance of antisense transcription and the breadth of these chromatin changes, we propose that antisense transcription represents a fundamental, canonical feature of eukaryotic genes.

  11. Electronic transport in double-strand DNA segments

    Science.gov (United States)

    Albuquerque, E. L.; Mauriz, P. W.; Moreira, D. A.

    2008-03-01

    We report in this work a numerical study of the electronic density of states in π-stacked arrays of DNA double-strand segments made up from the nucleotides guanine G, adenine A, cytosine C and thymine T. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for a genomic DNA sequence, considering a segment of the first sequenced human chromosome 22 (Ch 22), with those of two artificial sequences forming a Rudin-Shapiro (RS) as well as a Fibonacci (FB) polyGC quasiperiodic sequences. Our theoretical method uses an electronic tight-binding Hamiltonian suitable to describe the DNA segments modeled by the quasiperiodic chains.

  12. Current-voltage characteristics of double-strand DNA sequences

    Science.gov (United States)

    Bezerril, L. M.; Moreira, D. A.; Albuquerque, E. L.; Fulco, U. L.; de Oliveira, E. L.; de Sousa, J. S.

    2009-09-01

    We use a tight-binding formulation to investigate the transmissivity and the current-voltage (I-V) characteristics of sequences of double-strand DNA molecules. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for the genomic DNA sequence with those of artificial sequences (the long-range correlated Fibonacci and Rudin-Shapiro one) and a random sequence, which is a kind of prototype of a short-range correlated system. The random sequence is presented here with the same first neighbors pair correlations of the human DNA sequence. We found that the long-range character of the correlations is important to the transmissivity spectra, although the I-V curves seem to be mostly influenced by the short-range correlations.

  13. Regulatory RNA design through evolutionary computation and strand displacement.

    Science.gov (United States)

    Rostain, William; Landrain, Thomas E; Rodrigo, Guillermo; Jaramillo, Alfonso

    2015-01-01

    The discovery and study of a vast number of regulatory RNAs in all kingdoms of life over the past decades has allowed the design of new synthetic RNAs that can regulate gene expression in vivo. Riboregulators, in particular, have been used to activate or repress gene expression. However, to accelerate and scale up the design process, synthetic biologists require computer-assisted design tools, without which riboregulator engineering will remain a case-by-case design process requiring expert attention. Recently, the design of RNA circuits by evolutionary computation and adapting strand displacement techniques from nanotechnology has proven to be suited to the automated generation of DNA sequences implementing regulatory RNA systems in bacteria. Herein, we present our method to carry out such evolutionary design and how to use it to create various types of riboregulators, allowing the systematic de novo design of genetic control systems in synthetic biology.

  14. Stranded cost recovery presents stumbling block to open access

    Energy Technology Data Exchange (ETDEWEB)

    Del Roccili, J.A.

    1996-04-01

    Much of the impetus for the movement to competitive power markets is a result of the tremendous variance in energy prices across the country. Large commercial and industrial customers are becoming increasingly aware of these discrepancies and are marshaling the market and political forces required to guarantee the eventual development of a national open-access transmission policy. Such a policy will facilitate competition and equalize prices on a regional, and to some extent, national level. The stumbling block, however, is the recovery of stranded investment. Under traditional regulation, historical costs could be collected through approved rates for a bundled service. With the protection of a monopoly franchise, average electricity prices provide the possibility of cost recovery for assets that might not be recoverable in a competitive market.

  15. Membranous Replication Factories Induced by Plus-Strand RNA Viruses

    Directory of Open Access Journals (Sweden)

    Inés Romero-Brey

    2014-07-01

    Full Text Available In this review, we summarize the current knowledge about the membranous replication factories of members of plus-strand (+ RNA viruses. We discuss primarily the architecture of these complex membrane rearrangements, because this topic emerged in the last few years as electron tomography has become more widely available. A general denominator is that two “morphotypes” of membrane alterations can be found that are exemplified by flaviviruses and hepaciviruses: membrane invaginations towards the lumen of the endoplasmatic reticulum (ER and double membrane vesicles, representing extrusions also originating from the ER, respectively. We hypothesize that either morphotype might reflect common pathways and principles that are used by these viruses to form their membranous replication compartments.

  16. Phosphorylation: The Molecular Switch of Double-Strand Break Repair

    Directory of Open Access Journals (Sweden)

    K. C. Summers

    2011-01-01

    Full Text Available Repair of double-stranded breaks (DSBs is vital to maintaining genomic stability. In mammalian cells, DSBs are resolved in one of the following complex repair pathways: nonhomologous end-joining (NHEJ, homologous recombination (HR, or the inclusive DNA damage response (DDR. These repair pathways rely on factors that utilize reversible phosphorylation of proteins as molecular switches to regulate DNA repair. Many of these molecular switches overlap and play key roles in multiple pathways. For example, the NHEJ pathway and the DDR both utilize DNA-PK phosphorylation, whereas the HR pathway mediates repair with phosphorylation of RPA2, BRCA1, and BRCA2. Also, the DDR pathway utilizes the kinases ATM and ATR, as well as the phosphorylation of H2AX and MDC1. Together, these molecular switches regulate repair of DSBs by aiding in DSB recognition, pathway initiation, recruitment of repair factors, and the maintenance of repair mechanisms.

  17. Electronic transport in double-strand DNA segments

    Energy Technology Data Exchange (ETDEWEB)

    Albuquerque, E L; Moreira, D A [Departamento de Fisica, Universidade Federal do Rio Grande do Norte 59072-970 Natal-RN (Brazil); Mauriz, P W [Departamento de Ciencias Exatas, Centro Federal de Educacao Tecnologica do Maranhao 65025-001 Sao Luis-MA (Brazil)], E-mail: eudenilson@dfte.ufrn.br

    2008-03-15

    We report in this work a numerical study of the electronic density of states in {pi}-stacked arrays of DNA double-strand segments made up from the nucleotides guanine G, adenine A, cytosine C and thymine T. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for a genomic DNA sequence, considering a segment of the first sequenced human chromosome 22 (Ch 22), with those of two artificial sequences forming a Rudin-Shapiro (RS) as well as a Fibonacci (FB) polyGC quasiperiodic sequences. Our theoretical method uses an electronic tight-binding Hamiltonian suitable to describe the DNA segments modeled by the quasiperiodic chains.

  18. Current-voltage characteristics of double-strand DNA sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bezerril, L.M.; Moreira, D.A. [Departamento de Fisica, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN (Brazil); Albuquerque, E.L., E-mail: eudenilson@dfte.ufrn.b [Departamento de Fisica, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN (Brazil); Fulco, U.L. [Departamento de Biofisica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN (Brazil); Oliveira, E.L. de; Sousa, J.S. de [Departamento de Fisica, Universidade Federal do Ceara, 60455-760, Fortaleza-CE (Brazil)

    2009-09-07

    We use a tight-binding formulation to investigate the transmissivity and the current-voltage (I-V) characteristics of sequences of double-strand DNA molecules. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for the genomic DNA sequence with those of artificial sequences (the long-range correlated Fibonacci and Rudin-Shapiro one) and a random sequence, which is a kind of prototype of a short-range correlated system. The random sequence is presented here with the same first neighbors pair correlations of the human DNA sequence. We found that the long-range character of the correlations is important to the transmissivity spectra, although the I-V curves seem to be mostly influenced by the short-range correlations.

  19. Sulforaphane induces DNA single strand breaks in cultured human cells

    Energy Technology Data Exchange (ETDEWEB)

    Sestili, Piero, E-mail: piero.sestili@uniurb.it [Dipartimento di Scienze Biomolecolari, Via Maggetti, 21, Universita degli Studi di Urbino ' Carlo Bo' , 61029 Urbino, PU (Italy); Paolillo, Marco [Dipartimento di Scienze Biomolecolari, Via Maggetti, 21, Universita degli Studi di Urbino ' Carlo Bo' , 61029 Urbino, PU (Italy); Lenzi, Monia [Dipartimento di Farmacologia, Universita degli Studi di Bologna, Via Irnerio 48, 40126 Bologna (Italy); Colombo, Evelin; Vallorani, Luciana; Casadei, Lucia; Martinelli, Chiara [Dipartimento di Scienze Biomolecolari, Via Maggetti, 21, Universita degli Studi di Urbino ' Carlo Bo' , 61029 Urbino, PU (Italy); Fimognari, Carmela [Dipartimento di Farmacologia, Universita degli Studi di Bologna, Via Irnerio 48, 40126 Bologna (Italy)

    2010-07-07

    Sulforaphane (SFR), an isothiocyanate from cruciferous vegetables, possesses growth-inhibiting and apoptosis-inducing activities in cancer cell lines. Recently, SFR has been shown to promote the mitochondrial formation of reactive oxygen species (ROS) in human cancer cell lines. The present study was undertaken to see whether SFR-derived ROS might cause DNA damage in cultured human cells, namely T limphoblastoid Jurkat and human umbilical vein endothelial cells (HUVEC). 1-3 h treatments with 10-30 {mu}M SFR elicited intracellular ROS formation (as assayed with dihydrorhodamine, DHR, oxidation) as well as DNA breakage (as assessed with fast halo assay, FHA). These effects lacked cell-type specificity, since could be observed in both Jurkat and HUVEC. Differential-pH FHA analysis of damaged DNA showed that SFR causes frank DNA single strand breaks (SSBs); no DNA double strand breaks (DSBs) were found within the considered treatment times (up to 3 h). SFR-derived ROS were formed at the mitochondrial respiratory chain (MRC) level: indeed rotenone or myxothiazol (MRC Complex I and III inhibitors, respectively) abrogated ROS formation. Furthermore ROS were not formed in Jurkat cells pharmacologically depleted of respiring mitochondria (MRC-/Jurkat). Formation of ROS was causally linked to the induction of SSBs: indeed all the experimental conditions capable of preventing ROS formation also prevented the damage of nuclear DNA from SFR-intoxicated cells. As to the toxicological relevance of SSBs, we found that their prevention slightly but significantly attenuated SFR cytotoxicity, suggesting that high-dose SFR toxicity is the result of a complex series of events among which GSH depletion seems to play a pivotal role. In conclusion, the present study identifies a novel mechanism contributing to SFR toxicity which - since DNA damage is a prominent mechanism underlying the cytotoxic activity of established antineoplastic agents - might help to exploit the therapeutic value

  20. ISI支付协议的Strand Space模型及其公平性分析%Strand Space Model of ISI Payment Protocol and Its Fairness Analysis

    Institute of Scientific and Technical Information of China (English)

    陈浩; 程娜; 何大可

    2006-01-01

    文章利用Strand Space模型对ISI支付协议进行了分析,得出了与卿_周逻辑分析方法相同的结论,并将Strand Space模型对认证协议协定性的分析方法应用到了电子商务协议公平性的分析.

  1. ALICE: Simulated lead-lead collision

    CERN Multimedia

    2003-01-01

    This track is an example of simulated data modelled for the ALICE detector on the Large Hadron Collider (LHC) at CERN, which will begin taking data in 2008. ALICE will focus on the study of collisions between nuclei of lead, a heavy element that produces many different particles when collided. It is hoped that these collisions will produce a new state of matter known as the quark-gluon plasma, which existed billionths of a second after the Big Bang.

  2. Absorption by DNA single strands of adenine isolated in vacuo: The role of multiple chromophores

    DEFF Research Database (Denmark)

    Nielsen, L.M.; Pedersen, S.O.; Kirketerp, M.-B.S.;

    2012-01-01

    strands of adenine reveal sign of exciton coupling between stacked bases from blueshifted absorption bands (~3 nm) relative to that of the dAMP mononucleotide (one adenine base). The bands are blueshifted by about 10 nm compared to those of solvated strands, which is a shift similar...

  3. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

    NARCIS (Netherlands)

    Falconer, Ester; Hills, Mark; Naumann, Ulrike; Poon, Steven S. S.; Chavez, Elizabeth A.; Sanders, Ashley D.; Zhao, Yongjun; Hirst, Martin; Lansdorp, Peter M.

    2012-01-01

    DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive indicators of genomic stress and instability, but they are typically masked by single-cell sequencing techniques. We developed Strand-seq to independently sequence parental DNA template strands from single cells, making it po

  4. Mouse RAD54 affects DNA double-strand break repair and sister chromatid exchange

    NARCIS (Netherlands)

    H.B. Beverloo (Berna); R.D. Johnson (Roger); M. Jasin (Maria); R. Kanaar (Roland); J.H.J. Hoeijmakers (Jan); M.L.G. Dronkert (Mies)

    2000-01-01

    textabstractCells can achieve error-free repair of DNA double-strand breaks (DSBs) by homologous recombination through gene conversion with or without crossover. In contrast, an alternative homology-dependent DSB repair pathway, single-strand annealing (SSA), results in deletions. In this study, we

  5. Antibiotic efficacy in eliminating leptospiruria in California sea lions (Zalophus californianus) stranding with leptospirosis

    Science.gov (United States)

    Infection of California sea lions with leptospirosis can result in stranding and death of the animals. Shedding of the infectious organism contributes to spread of the disease to other animals and also poses a threat to human health. This is both for the public interacting with stranded animals and ...

  6. Unusual Mortality Events of Harbor Porpoise Strandings in North Carolina, 1997–2009

    Directory of Open Access Journals (Sweden)

    Aleta A. Hohn

    2013-01-01

    Full Text Available A marked increase in the frequency of harbor porpoises (Phocoena phocoena stranded in North Carolina in 2005 was declared as an Unusual Mortality Event (UME. Strandings occurred in January through May when harbor porpoises are seasonally present. Increased stranding rates were measured relative to a threshold to determine that the UME was occurring. The threshold analysis also revealed elevated strandings during 1999, an undeclared UME year. Recovered carcasses during 1999 and 2005 accounted for 39% of 261 strandings during 1997–2009. During 2005, of 43 strandings, primary or secondary causes of mortality included fishery interactions, emaciation, and interspecific aggression. Apart from small but significant differences in timing and condition of strandings, composition of strandings during UME and non-UME years was similar, with most being young-of-the-year and occurring during March and April, north of Cape Hatteras. Porpoises had high levels of parasitic infestation typical for this species. However, no indication of infectious disease and no cause of the 2005 event were found from gross and histologic findings. Response to UMEs is challenging, particularly along the expanses of North Carolina beaches, requiring additional effort to obtain carcasses in sufficiently fresh condition to determine the cause of these events.

  7. Dolphin Morbillivirus Associated with a Mass Stranding of Sperm Whales, Italy

    Science.gov (United States)

    Centelleghe, Cinzia; Di Provvido, Andrea; Di Renzo, Ludovica; Cardeti, Giusy; Cersini, Antonella; Fichi, Gianluca; Petrella, Antonio; Di Francesco, Cristina Esmeralda; Mignone, Walter; Casalone, Cristina; Di Guardo, Giovanni

    2017-01-01

    In September 2014, seven sperm whales were stranded along Italy’s Adriatic coastline. Postmortem investigations on 3 female adult whales and 1 male fetus carried by the largest female revealed molecular and immunohistochemical evidence of dolphin morbillivirus infection. A possible role of the virus in the stranding event was considered. PMID:27983493

  8. Parasitism as a factor (?) in single strandings of southern California cetaceans.

    Science.gov (United States)

    Dailey, M D; Walker, W A

    1978-08-01

    From 1970 to 1976 a total of 91 cetaceans was examined for parasites and associated pathology. Sixty of the animals were found stranded along a 100-mile section of southern California coastline while 31 were taken at sea. Parasites from 5 species of cetaceans are reported along with their possible role as a contributing factor in stranding behavior.

  9. Spatial periodic contact stress and critical current of a Nb3Sn strand measured in TARSIS

    NARCIS (Netherlands)

    Nijhuis, Arend; Ilyin, Y.; Wessel, Wilhelm A.J.

    2006-01-01

    We have developed a new probe for testing the influence of local contact load from crossing superconducting Nb3Sn strands. The probe is part of the TARSIS setup for strand stress–strain characterization. The results from the TARSIS setup with different probes developed for the characterization of

  10. Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays

    DEFF Research Database (Denmark)

    Keller, Adrian; Rackwitz, Jenny; Cauët, Emilie;

    2014-01-01

    sections for electron induced single strand breaks in specific 13 mer oligonucleotides we used atomic force microscopy analysis of DNA origami based DNA nanoarrays. We investigated the DNA sequences 5'-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections...

  11. Alkylation base damage is converted into repairable double-strand breaks and complex intermediates in G2 cells lacking AP endonuclease.

    Directory of Open Access Journals (Sweden)

    Wenjian Ma

    2011-04-01

    Full Text Available DNA double-strand breaks (DSBs are potent sources of genome instability. While there is considerable genetic and molecular information about the disposition of direct DSBs and breaks that arise during replication, relatively little is known about DSBs derived during processing of single-strand lesions, especially for the case of single-strand breaks (SSBs with 3'-blocked termini generated in vivo. Using our recently developed assay for detecting end-processing at random DSBs in budding yeast, we show that single-strand lesions produced by the alkylating agent methyl methanesulfonate (MMS can generate DSBs in G2-arrested cells, i.e., S-phase independent. These derived DSBs were observed in apn1/2 endonuclease mutants and resulted from aborted base excision repair leading to 3' blocked single-strand breaks following the creation of abasic (AP sites. DSB formation was reduced by additional mutations that affect processing of AP sites including ntg1, ntg2, and, unexpectedly, ogg1, or by a lack of AP sites due to deletion of the MAG1 glycosylase gene. Similar to direct DSBs, the derived DSBs were subject to MRX (Mre11, Rad50, Xrs2-determined resection and relied upon the recombinational repair genes RAD51, RAD52, as well as on the MCD1 cohesin gene, for repair. In addition, we identified a novel DNA intermediate, detected as slow-moving chromosomal DNA (SMD in pulsed field electrophoresis gels shortly after MMS exposure in apn1/2 cells. The SMD requires nicked AP sites, but is independent of resection/recombination processes, suggesting that it is a novel structure generated during processing of 3'-blocked SSBs. Collectively, this study provides new insights into the potential consequences of alkylation base damage in vivo, including creation of novel structures as well as generation and repair of DSBs in nonreplicating cells.

  12. Alkylation base damage is converted into repairable double-strand breaks and complex intermediates in G2 cells lacking AP endonuclease.

    Directory of Open Access Journals (Sweden)

    Wenjian Ma

    2011-04-01

    Full Text Available DNA double-strand breaks (DSBs are potent sources of genome instability. While there is considerable genetic and molecular information about the disposition of direct DSBs and breaks that arise during replication, relatively little is known about DSBs derived during processing of single-strand lesions, especially for the case of single-strand breaks (SSBs with 3'-blocked termini generated in vivo. Using our recently developed assay for detecting end-processing at random DSBs in budding yeast, we show that single-strand lesions produced by the alkylating agent methyl methanesulfonate (MMS can generate DSBs in G2-arrested cells, i.e., S-phase independent. These derived DSBs were observed in apn1/2 endonuclease mutants and resulted from aborted base excision repair leading to 3' blocked single-strand breaks following the creation of abasic (AP sites. DSB formation was reduced by additional mutations that affect processing of AP sites including ntg1, ntg2, and, unexpectedly, ogg1, or by a lack of AP sites due to deletion of the MAG1 glycosylase gene. Similar to direct DSBs, the derived DSBs were subject to MRX (Mre11, Rad50, Xrs2-determined resection and relied upon the recombinational repair genes RAD51, RAD52, as well as on the MCD1 cohesin gene, for repair. In addition, we identified a novel DNA intermediate, detected as slow-moving chromosomal DNA (SMD in pulsed field electrophoresis gels shortly after MMS exposure in apn1/2 cells. The SMD requires nicked AP sites, but is independent of resection/recombination processes, suggesting that it is a novel structure generated during processing of 3'-blocked SSBs. Collectively, this study provides new insights into the potential consequences of alkylation base damage in vivo, including creation of novel structures as well as generation and repair of DSBs in nonreplicating cells.

  13. Monitoring of DNA breakage in embryonic stages of the African catfish Clarias gariepinus (Burchell, 1822) after exposure to lead nitrate using alkaline comet assay

    NARCIS (Netherlands)

    Osman, A.G.M.; Mekkawy, Imam A.; Verreth, J.A.J.; Wuertz, S.; Kloas, W.; Kirschbaum, Frank

    2008-01-01

    Increasing lead contamination in Egyptian ecosystems and high lead concentrations in food items have raised concern for human health and stimulated studies on monitoring ecotoxicological impact of lead-caused genotoxicity. In this work, the alkaline comet assay was modified for monitoring DNA strand

  14. Lead-Free Piezoelectrics

    CERN Document Server

    Nahm, Sahn

    2012-01-01

    Ecological restrictions in many parts of the world are demanding the elimination of Pb from all consumer items. At this moment in the piezoelectric ceramics industry, there is no issue of more importance than the transition to lead-free materials. The goal of Lead-Free Piezoelectrics is to provide a comprehensive overview of the fundamentals and developments in the field of lead-free materials and products to leading researchers in the world. The text presents chapters on demonstrated applications of the lead-free materials, which will allow readers to conceptualize the present possibilities and will be useful for both students and professionals conducting research on ferroelectrics, piezoelectrics, smart materials, lead-free materials, and a variety of applications including sensors, actuators, ultrasonic transducers and energy harvesters.

  15. Statistical analysis of the Nb3Sn strand production for the ITER toroidal field coils

    Science.gov (United States)

    Vostner, A.; Jewell, M.; Pong, I.; Sullivan, N.; Devred, A.; Bessette, D.; Bevillard, G.; Mitchell, N.; Romano, G.; Zhou, C.

    2017-04-01

    The ITER toroidal field (TF) strand procurement initiated the largest Nb3Sn superconducting strand production hitherto. The industrial-scale production started in Japan in 2008 and finished in summer 2015. Six ITER partners (so-called Domestic Agencies, or DAs) are in charge of the procurement and involved eight different strand suppliers all over the world, of which four are using the bronze route (BR) process and four the internal-tin (IT) process. In total more than 500 tons have been produced including excess material covering losses during the conductor manufacturing process, in particular the cabling. The procurement is based on a functional specification where the main strand requirements like critical current, hysteresis losses, Cu ratio and residual resistance ratio are specified but not the strand production process or layout. This paper presents the analysis on the data acquired during the quality control (QC) process that was carried out to ensure the same conductor performance requirements are met by the different strand suppliers regardless of strand design. The strand QC is based on 100% billet testing and on applying statistical process control (SPC) limits. Throughout the production, samples adjacent to the strand pieces tested by the suppliers are cross-checked (‘verified’) by their respective DAs reference labs. The level of verification was lowered from 100% at the beginning of the procurement progressively to approximately 25% during the final phase of production. Based on the complete dataset of the TF strand production, an analysis of the SPC limits of the critical strand parameters is made and the related process capability indices are calculated. In view of the large-scale production and costs, key manufacturing parameters such as billet yield, number of breakages and piece-length distribution are also discussed. The results are compared among all the strand suppliers, focusing on the difference between BR and IT processes. Following

  16. Double-stranded RNA-activated protein kinase PKR of fishes and amphibians: Varying the number of double-stranded RNA binding domains and lineage-specific duplications

    Directory of Open Access Journals (Sweden)

    Dever Thomas E

    2008-03-01

    Full Text Available Abstract Background Double-stranded (ds RNA, generated during viral infection, binds and activates the mammalian anti-viral protein kinase PKR, which phosphorylates the translation initiation factor eIF2α leading to the general inhibition of protein synthesis. Although PKR-like activity has been described in fish cells, the responsible enzymes eluded molecular characterization until the recent discovery of goldfish and zebrafish PKZ, which contain Z-DNA-binding domains instead of dsRNA-binding domains (dsRBDs. Fish and amphibian PKR genes have not been described so far. Results Here we report the cloning and identification of 13 PKR genes from 8 teleost fish and amphibian species, including zebrafish, demonstrating the coexistence of PKR and PKZ in this latter species. Analyses of their genomic organization revealed up to three tandemly arrayed PKR genes, which are arranged in head-to-tail orientation. At least five duplications occurred independently in fish and amphibian lineages. Phylogenetic analyses reveal that the kinase domains of fish PKR genes are more closely related to those of fish PKZ than to the PKR kinase domains of other vertebrate species. The duplication leading to fish PKR and PKZ genes occurred early during teleost fish evolution after the divergence of the tetrapod lineage. While two dsRBDs are found in mammalian and amphibian PKR, one, two or three dsRBDs are present in fish PKR. In zebrafish, both PKR and PKZ were strongly upregulated after immunostimulation with some tissue-specific expression differences. Using genetic and biochemical assays we demonstrate that both zebrafish PKR and PKZ can phosphorylate eIF2α in yeast. Conclusion Considering the important role for PKR in host defense against viruses, the independent duplication and fixation of PKR genes in different lineages probably provided selective advantages by leading to the recognition of an extended spectrum of viral nucleic acid structures, including both ds

  17. Lead Poison Detection

    Science.gov (United States)

    1976-01-01

    With NASA contracts, Whittaker Corporations Space Science division has developed an electro-optical instrument to mass screen for lead poisoning. Device is portable and detects protoporphyrin in whole blood. Free corpuscular porphyrins occur as an early effect of lead ingestion. Also detects lead in urine used to confirm blood tests. Test is inexpensive and can be applied by relatively unskilled personnel. Similar Whittaker fluorometry device called "drug screen" can measure morphine and quinine in urine much faster and cheaper than other methods.

  18. Acute hypoxia and hypoxic exercise induce DNA strand breaks and oxidative DNA damage in humans

    DEFF Research Database (Denmark)

    Møller, P; Loft, S; Lundby, C

    2001-01-01

    ; lymphocytes were isolated for analysis of DNA strand breaks and oxidatively altered nucleotides, detected by endonuclease III and formamidipyridine glycosylase (FPG) enzymes. Urine was collected for 24 h periods for analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a marker of oxidative DNA damage....... Urinary excretion of 8-oxodG increased during the first day in altitude hypoxia, and there were more endonuclease III-sensitive sites on day 3 at high altitude. The subjects had more DNA strand breaks in altitude hypoxia than at sea level. The level of DNA strand breaks further increased immediately after...... exercise in altitude hypoxia. Exercise-induced generation of DNA strand breaks was not seen at sea level. In both environments, the level of FPG and endonuclease III-sensitive sites remained unchanged immediately after exercise. DNA strand breaks and oxidative DNA damage are probably produced by reactive...

  19. World-Wide Benchmarking of ITER Nb3Sn Strand Test Facilities

    CERN Document Server

    Jewell, MC; Takahashi, Yoshikazu; Shikov, Alexander; Devred, Arnaud; Vostner, Alexander; Liu, Fang; Wu, Yu; Jewell, Matthew C; Boutboul, Thierry; Bessette, Denis; Park, Soo-Hyeon; Isono, Takaaki; Vorobieva, Alexandra; Martovetsky, Nicolai; Seo, Kazutaka

    2010-01-01

    The world-wide procurement of Nb3Sn and NbTi for the ITER superconducting magnet systems will involve eight to ten strand suppliers from six Domestic Agencies (DAs) on three continents. To ensure accurate and consistent measurement of the physical and superconducting properties of the composite strand, a strand test facility benchmarking effort was initiated in August 2008. The objectives of this effort are to assess and improve the superconducting strand test and sample preparation technologies at each DA and supplier, in preparation for the more than ten thousand samples that will be tested during ITER procurement. The present benchmarking includes tests for critical current (I-c), n-index, hysteresis loss (Q(hys)), residual resistivity ratio (RRR), strand diameter, Cu fraction, twist pitch, twist direction, and metal plating thickness (Cr or Ni). Nineteen participants from six parties (China, EU, Japan, South Korea, Russia, and the United States) have participated in the benchmarking. This round, conducted...

  20. Magnetization Losses of Roebel Cable Samples with 2G YBCO Coated Conductor Strands

    CERN Document Server

    Yang, Y.; Falorio, I.; Young, E.A.; Kario, A.; Goldacker, W.; Dhallé, M. M. J.; van Nugteren, J.; Kirby, G.; Bottura, L.; Ballarino, A.

    2016-01-01

    Roebel cable with 2G YBCO strands is one of the promising HTS solutions of fully transposed high current conductors for high field accelerator magnets. Following the considerable research effort on the manufacturing of Roebel cables in recent years, sample conductors are now available in useful lengths with reproducible performances to allow detailed characterizations beyond the standard critical current measurements. The ac loss and strands coupling are of significant interest for the field quality of the accelerator magnets. We report a set of systematic ac loss measurements on two different Roebel cable samples prepared for the EuCARD2 collaboration. The measurements were performed over a wide range of temperature between 5 K and 90 K and the results were analyzed in the context of strands architecture and coupling. The results show that the transposed bundles are partially decoupled and the strands in transposition sections behave as an isolated single tape if the strands are insulated.

  1. DNA strand breaks (comet assay) in blood lymphocytes from wild bottlenose dolphins.

    Science.gov (United States)

    Lee, Richard F; Bulski, Karrie; Adams, Jeffrey D; Peden-Adams, Margie; Bossart, Gregory D; King, Lydia; Fair, Patricia A

    2013-12-15

    The comet assay was carried out on blood lymphocytes from a large number of wild dolphins (71 from Indian River Lagoon, FL, USA; 51 from Charleston Harbor, SC, USA) and provides a baseline study of DNA strand breaks in wild dolphin populations. There were no significant differences in the comet assay (% DNA in tail) results between the different age and sex categories. Significant difference in DNA strand breaks were found between Charleston Harbor dolphins (median--17.4% DNA in tail) and Indian River Lagoon dolphins (median--14.0% DNA in tail). A strong correlation found between T-cell proliferation and DNA strand breaks in dolphin lymphocytes suggests that dolphins with a high numbers of DNA strand breaks have a decreased ability to respond to infection. Higher concentrations of genotoxic agents in Charleston Harbor compared with Indian River lagoon may have been one of the causes of higher DNA strand breaks in these dolphins.

  2. Synchronization in a Plasmodial Strand of Physarum Polycephalum as a One-Dimensionally Coupled Oscillator System

    Science.gov (United States)

    Hu, Zi-Song; Takahashi, Kengo; Tsuchiya, Yoshimi

    1994-02-01

    Transient behaviors in self-sustained oscillation of a plasmodial strand of Physarum polycephalum have been investigated for various external loads under isotonic conditions. Synchronization between divisions of the strand has been observed in its formation process, which shows that the plasmodial strand can be considered as a one-dimensionally coupled oscillator system. The synchronization has been found to proceed faster with increasing external load applied to the strand. It has furthermore been found that the rate of increase of the amplitude of oscillation increases with the load, whereas the temporal behavior of its period is independent of the load. These results show that the oscillators themselves in the plasmodial strand do not depend on the external load, but the coupling between these oscillators is strongly affected with the external load. The experimental results have also been simulated on the basis of one-dimensionally coupled van der Pol equations.

  3. Third-strand in situ hybridization (TISH) to non-denatured metaphase spreads and interphase nuclei.

    Science.gov (United States)

    Johnson, M D; Fresco, J R

    1999-07-01

    A methodology has been developed for binding oligodeoxyribonucleotide 'third strands' to duplex DNA targets in fixed but not additionally denatured metaphase spreads and interphase nuclei under conditions found to be optimal in solution. Third-strand in situ hybridization (TISH) at pH 6.0 of a psoralen- and biotin-modified 16-nucleotide homopyrimidine third strand to a unique multicopy target sequence in human chromosome 17 alpha-satellite (D17Z1 locus) is described. UVA-photofixed third strands, rendered fluorescent by fluorescein isothiocyanate-labeled avidin, are reproducibly centromere-specific for chromosome 17, and visible without amplification of the signal in lymphocyte and somatic cell hybrid spreads and interphase nuclei. Two third-strand-specific D17Z1 haplotypes were identified. TISH has potential diagnostic, biochemical, and flow cytometric applicability to native metaphase and interphase chromatin.

  4. Enzyme-free colorimetric detection systems based on the DNA strand displacement competition reaction

    Science.gov (United States)

    Zhang, Z.; Birkedal, V.; Gothelf, K. V.

    2016-05-01

    The strand displacement competition assay is based on the dynamic equilibrium of the competitive hybridization of two oligonucleotides (A and B) to a third oligonucleotide (S). In the presence of an analyte that binds to a specific affinity-moiety conjugated to strand B, the equilibrium shifts, which can be detected by a shift in the fluorescence resonance energy transfer signal between dyes attached to the DNA strands. In the present study we have integrated an ATP aptamer in the strand B and demonstrated the optical detection of ATP. Furthermore we explore a new readout method using a split G-quadruplex DNAzyme for colorimetric readout of the detection of streptavidin by the naked eye. Finally, we integrate the whole G-quadruplex DNAzyme system in a single DNA strand and show that it is applicable to colorimetric detection.

  5. Structure of the replicative form of bacteriophage φX174 : VI. Studies on alkali-denatured double-stranded φX DNA

    NARCIS (Netherlands)

    Pouwels, P.H.; Knijnenburg, C.M.; Rotterdam, J. van; Cohen, J.A.; Jansz, H.S.

    1968-01-01

    Double-stranded φX DNA which accumulates after infection with bacteriophage φX174 in the presence of chloramphenicol consists mainly of twisted circular double-stranded DNA with no single-strand breaks (component I) and of circular double-stranded DNA, in which single-strand breaks are present (comp

  6. Position-specific propensities of amino acids in the β-strand

    Directory of Open Access Journals (Sweden)

    Biswas Parbati

    2010-09-01

    Full Text Available Abstract Background Despite the importance of β-strands as main building blocks in proteins, the propensity of amino acid in β-strands is not well-understood as it has been more difficult to determine experimentally compared to α-helices. Recent studies have shown that most of the amino acids have significantly high or low propensity towards both ends of β-strands. However, a comprehensive analysis of the sequence dependent amino acid propensities at positions between the ends of the β-strand has not been investigated. Results The propensities of the amino acids calculated from a large non-redundant database of proteins are found to be highly position-specific and vary continuously throughout the length of the β-strand. They follow an unexpected characteristic periodic pattern in inner positions with respect to the cap residues in both termini of β-strands; this periodic nature is markedly different from that of the α-helices with respect to the strength and pattern in periodicity. This periodicity is not only different for different amino acids but it also varies considerably for the amino acids belonging to the same physico-chemical group. Average hydrophobicity is also found to be periodic with respect to the positions from both termini of β-strands. Conclusions The results contradict the earlier perception of isotropic nature of amino acid propensities in the middle region of β-strands. These position-specific propensities should be of immense help in understanding the factors responsible for β-strand design and efficient prediction of β-strand structure in unknown proteins.

  7. Characteristics of Cu stabilized Nb3Al strands with low Cu ratio

    Energy Technology Data Exchange (ETDEWEB)

    Kikuchi, A.; Yamada, R.; Barzi, E.; Kobayashi, M.; Lamm, M.; Nakagawa, K.; Sasaki, K.; Takeuchi, T.; Turrioni, D.; Zlobin, A.V.; /NIMC, Tsukuba /Fermilab /Hitachi, Tsuchiura Works /KEK, Tsukuba

    2008-12-01

    Characteristics of recently developed F4-Nb{sub 3}Al strand with low Cu ratio are described. The overall J{sub c} of the Nb{sub 3}Al strand could be easily increased by decreasing of the Cu ratio. Although the quench of a pulse-like voltage generation is usually observed in superconducting unstable conductor, the F4 strand with a low Cu ratio of 0.61 exhibited an ordinary critical transition of gradual voltage generation. The F4 strand does not have magnetic instabilities at 4.2 K because of the tantalum interfilament matrix. The overall J{sub c} of the F4 strand achieved was 80-85% of the RRP strand. In the large mechanical stress above 100 MPa, the overall J{sub c} of the F4 strand might be comparable to that of high J{sub c} RRP-Nb{sub 3}Sn strands. The Rutherford cable with a high packing factor of 86.5% has been fabricated using F4 strands. The small racetrack magnet, SR07, was also fabricated by a 14 m F4 cable. The quench current, I{sub q}, of SR07 were obtained 22.4 kA at 4.5 K and 25.2 kA at 2.2 K. The tantalum matrix Nb{sub 3}Al strands are promising for the application of super-cooled high-field magnets as well as 4.2 K operation magnets.

  8. High resolution atomic force microscopy of double-stranded RNA

    Science.gov (United States)

    Ares, Pablo; Fuentes-Perez, Maria Eugenia; Herrero-Galán, Elías; Valpuesta, José M.; Gil, Adriana; Gomez-Herrero, Julio; Moreno-Herrero, Fernando

    2016-06-01

    Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to resolve the A-form sub-helical pitch periodicity. We have employed different high-sensitive force-detection methods and obtained images with similar spatial resolution. Therefore, we show here that the limiting factors for high-resolution AFM imaging of soft materials in liquid medium are, rather than the imaging mode, the force between the tip and the sample and the sharpness of the tip apex.Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to

  9. Materials, Strands, and Cables for Superconducting Accelerator Magnets. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Sumption, Mike D. [Ohio State University, Columbia, OH (United States); Collings, Edward W. [Ohio State University, Columbia, OH (United States)

    2014-09-19

    This report focuses on Materials, Strands and Cables for High Energy Physics Particle accelerators. In the materials area, work has included studies of basic reactions, diffusion, transformations, and phase assemblage of Nb3Sn. These materials science aspects have been married to results, in the form of flux pinning, Bc2, Birr, and transport Jc, with an emphasis on obtaining the needed Jc for HEP needs. Attention has also been paid to the “intermediate-temperature superconductor”, magnesium diboride emphasis being placed on (i) irreversibility field enhancement, (ii) critical current density and flux pinning, and (iii) connectivity. We also report on studies of Bi-2212. The second area of the program has been in the area of “Strands” in which, aside from the materials aspect of the conductor, its physical properties and their influence on performance have been studied. Much of this work has been in the area of magnetization estimation and flux jump calculation and control. One of the areas of this work was strand instabilities in high-performance Nb3Sn conductors due to combined fields and currents. Additionally, we investigated quench and thermal propagation in YBCO coated conductors at low temperatures and high fields. The last section, “Cables”, focussed on interstrand contact resistance, ICR, it origins, control, and implications. Following on from earlier work in NbTi, the present work in Nb3Sn has aimed to make ICR intermediate between the two extremes of too little contact (no current sharing) and too much (large and unacceptable magnetization and associated beam de-focussing). Interstrand contact and current sharing measurements are being made on YBCO based Roebel cables using transport current methods. Finally, quench was investigated for YBCO cables and the magnets wound from them, presently with a focus on 50 T solenoids for muon collider applications.

  10. Lead toxicity: Current concerns

    Energy Technology Data Exchange (ETDEWEB)

    Goyer, R.A. (Univ. of Western Ontario, London (Canada))

    1993-04-01

    Over the 20-year period since the first issue of Environmental Health Perspectives was published, there has been considerable progress in the understanding of the potential toxicity of exposure to lead. Many of these advances have been reviewed in published symposia, conferences, and review papers in EHP. This brief review identifies major advances as well as a number of current concerns that present opportunities for prevention and intervention strategies. The major scientific advance has been the demonstration that blood lead (PbB) levels of 10-15 micrograms/dL in newborn and very young infants result in cognitive and behavioral deficits. Further support for this observation is being obtained by prospective or longitudinal studies presently in progress. The mechanism(s) for the central nervous system effects of lead is unclear but involve lead interactions within calcium-mediated intracellular messenger systems and neurotransmission. Effects of low-level lead exposure on blood pressure, particularly in adult men, may be related to the effect of lead on calcium-mediated control of vascular smooth muscle contraction and on the renin-angiotensin system. Reproductive effects of lead have long been suspected, but low-level effects have not been well studied. Whether lead is a carcinogen or its association with renal adenocarcinoma is a consequence of cystic nephropathy is uncertain. Major risk factors for lead toxicity in children in the United States include nutrition, particularly deficiencies of essential metals, calcium, iron, and zinc, and housing and socioeconomic status. A goal for the year 2000 is to reduce prevalence of blood lead levels exceeding 15 micrograms/dL. 97 refs.

  11. Single-strand conformation polymorphism analysis for differentiating phytoplasma strains.

    Science.gov (United States)

    Musić, Martina Seruga; Skorić, Dijana

    2013-01-01

    Single-strand conformation polymorphism (SSCP) analysis is a sensitive and rapid technique for detecting DNA polymorphisms and mutations in PCR-amplified fragments. Due to its technical simplicity, it is widely used as a screening tool in various investigations, ranging from clinical diagnosis of human hereditary diseases to the characterization of microbial communities. This method can also be used successfully on phytoplasmas as a tool for the detection of molecular variability in conserved housekeeping genes such as 16S rRNA and tuf, as well as in more variable genes, revealing the presence of polymorphisms undetected by routine RFLP analyses. The reliability of SSCP has been confirmed by multiple alignments and phylogenetic analyses of representative sequences showing different SSCP profiles. However, it is not broadly applied in phytoplasma research yet. The technique provides an inexpensive, convenient, and sensitive method for determining sequence variation and to differentiate phytoplasma strains, and is particularly suitable for epidemiological studies or as a fast screening, typing tool when dealing with a large number of field samples.

  12. PIEZOELECTRIC PROPERTIES OF SINGLE-STRAND DNA MOLECULAR BRUSH BIOLAYERS

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The paper is devoted to investigations on nanomechanical behaviors of biochips in label-free biodetections. The chip consists of Si-layer, Ti-layer, Au-layer and single-strand DNA (ssDNA) molecular brush biolayer immobilized by self-assembly technology of thiol group. Unlike previous viewpoints, such as force-bending, entropy-bending and curvature electricity effect, etc.,the piezoelectric effect of the biopolymer brush layer is viewed as the main factor that induces nanomechanical bending of biochips, and a classical macroscopic piezoelectric constitutive relation is used to describe the piezoelectric effect. A new laminated cantilever beam model with a piezoelectric biolayer in continuum mechanics, the linearized Poisson-Boltzmann equation in statistical mechanics and the scaling method in polyelectrolyte brush theory are combined to establish a relationship between the nanomechanical deflection of DNA chips and the factors such as nanoscopic structural features of ssDNA molecules, buffer salt concentration, macroscopic mechanical/piezoelectric parameters of DNA chips etc. Curve fitting of experimental data shows that the sign of the piezoelectric constant of the biolayer may control the deflection direction of DNA chips during the packaging process.

  13. Habitat structure and zonation patterns of northwestern Mediterranean shoreline strands

    Directory of Open Access Journals (Sweden)

    Simone Mariani

    2017-06-01

    Full Text Available We studied the habitat structure (macrofaunal assemblages and bottom types and zonation patterns of 29 unvegetated shoreline strands along the 900-km coast of Catalonia (NW Mediterranean Sea. Organisms were sampled with grabs, pitfall traps, sticky traps, clam nets and spades to ensure capture of the different proportions of macrofaunal assemblages from the supra-, medio- and infralittoral levels. We collected 211 taxa: 194 animals and 17 algae. The most abundant and dominant organisms collected with van Veen grabs were Nematoda, Oligochaeta and Collembola at the supralittoral level; the polychaetes Saccocirrus spp. and Pisione remota, the amphipod Corophium orientale, Nematoda, and Turbellaria at the mediolittoral level; and Nematoda at the upper infralittoral level. SIMPER analysis revealed great dissimilarity between the organisms inhabiting the supralittoral and the other littoral levels. Regarding the epifauna, the sticky traps used at the supralittoral level mainly collected Collembola, which were nearly absent in pitfall traps. The qualitative study performed with a clam net and a small spade revealed that Nematoda, Saccocirrus spp., Turbellaria, Nemertea and the polychaete P. remota were the most abundant animals at both the medio- and the infralittoral levels and no differences were found between these levels. Different qualitative sampling methodologies showed that in fine sediments the bivalves Donax trunculus and D. semistriatus determined more than 97% of dissimilarity from coarse-sand sites. Richness increased in protected sandy and cobble shores. Littoral level and bottom-type features were only to a certain extent valid indicators of specific biotic components for a specific habitat.

  14. Patterns of evolution of research strands in the hydrologic sciences

    Science.gov (United States)

    Schwartz, F. W.; Fang, Y. C.; Parthasarathy, S.

    2005-03-01

    This paper examines issues of impact and innovation in groundwater research by using bibliometric data and citation analysis.The analysis is based on 3120 papers from the journal Water Resources Research with full contents and their citation data from the ISI Web of Science. The research is designed to develop a better understanding of the way citation numbers can be interpreted by scientists. Not surprisingly, the most highly cited papers appear to be pioneers in the field with papers departing significantly from what has come before and to be effective in creating similar, follow-on papers. Papers that are early contributions to a new research strand that is highly influential will be on average highly cited. However, the importance of a research strand as measured by citations seems to fall with time. The citation patterns of some classic papers show that the activity in the topical area and impact of follow-on papers gradually decline with time, which has similarities with Kuhn's ideas of revolutionary and normal science. The results of this study reinforce the importance of being a pioneer in a research strand, strategically shifting research strands, adopting strategies that can facilitate really major research breakthroughs. L'article examine les problèmes d'impact et d'innovation dans la recherche des eaux souterraines en utilisant les données bibliométriques et l'analyse des citations. L'analyse a été faite sur 3120 articles parus dans Water Resources Research en tenant compte de leur texte complet et de toutes citations parues dans l' ISI Web de la Science. Le but de la recherche a été de mieux comprendre comment le nombre des citations peut être interprété par les scientifiques. Ce n'est pas une surprise que les plus cités articles soient les articles-pionniers dans leurs domaines, qui s'écartent d'une manière significative de ce qui a été écrit auparavant et qui ont été suivi par des nouveaux articles. Les articles qui présentent une

  15. Prion search and cellular prion protein expression in stranded dolphins.

    Science.gov (United States)

    Di Guardo, G; Cocumelli, C; Meoli, R; Barbaro, K; Terracciano, G; Di Francesco, C E; Mazzariol, S; Eleni, C

    2012-01-01

    The recent description of a prion disease (PD) case in a free-ranging bottlenose dolphin (Tursiops truncatus) prompted us to carry out an extensive search for the disease-associated isoform (PrPSc) of the cellular prion protein (PrPC) in the brain and in a range of lymphoid tissues from 23 striped dolphins (Stenella coeruleoalba), 5 bottlenose dolphins and 2 Risso s dolphins (Grampus griseus) found stranded between 2007 and 2012 along the Italian coastline. Three striped dolphins and one bottlenose dolphin showed microscopic lesions of encephalitis, with no evidence of spongiform brain lesions being detected in any of the 30 free-ranging cetaceans investigated herein. Nevertheless, we could still observe a prominent PrPC immunoreactivity in the brain as well as in lymphoid tissues from these dolphins. Although immunohistochemical and Western blot investigations yielded negative results for PrPSc deposition in all tissues from the dolphins under study, the reported occurrence of a spontaneous PD case in a wild dolphin is an intriguing issue and a matter of concern for both prion biology and intra/inter-species transmissibility, as well as for cetacean conservation medicine.

  16. Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses

    Energy Technology Data Exchange (ETDEWEB)

    Lloyd, Richard E., E-mail: rlloyd@bcm.edu

    2015-05-15

    Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. - Highlights: • Nuclear shuttling host proteins are commonly hijacked by RNA viruses to support replication. • A limited group of ubiquitous RNA binding proteins are commonly hijacked by a broad range of viruses. • Key virus proteins alter roles of RNA binding proteins in different stages of virus replication.

  17. DNA double strand break repair, aging and the chromatin connection.

    Science.gov (United States)

    Gorbunova, Vera; Seluanov, Andrei

    2016-06-01

    Are DNA damage and mutations possible causes or consequences of aging? This question has been hotly debated by biogerontologists for decades. The importance of DNA damage as a possible driver of the aging process went from being widely recognized to then forgotten, and is now slowly making a comeback. DNA double strand breaks (DSBs) are particularly relevant to aging because of their toxicity, increased frequency with age and the association of defects in their repair with premature aging. Recent studies expand the potential impact of DNA damage and mutations on aging by linking DNA DSB repair and age-related chromatin changes. There is overwhelming evidence that increased DNA damage and mutations accelerate aging. However, an ultimate proof of causality would be to show that enhanced genome and epigenome stability delays aging. This is not an easy task, as improving such complex biological processes is infinitely more difficult than disabling it. We will discuss the possibility that animal models with enhanced DNA repair and epigenome maintenance will be generated in the near future.

  18. Divalent counterion-induced condensation of triple-strand DNA.

    Science.gov (United States)

    Qiu, Xiangyun; Parsegian, V Adrian; Rau, Donald C

    2010-12-14

    Understanding and manipulation of the forces assembling DNA/RNA helices have broad implications for biology, medicine, and physics. One subject of significance is the attractive force between dsDNA mediated by polycations of valence ≥ 3. Despite extensive studies, the physical origin of the "like-charge attraction" remains unsettled among competing theories. Here we show that triple-strand DNA (tsDNA), a more highly charged helix than dsDNA, is precipitated by alkaline-earth divalent cations that are unable to condense dsDNA. We further show that our observation is general by examining several cations (Mg(2+), Ba(2+), and Ca(2+)) and two distinct tsDNA constructs. Cation-condensed tsDNA forms ordered hexagonal arrays that redissolve upon adding monovalent salts. Forces between tsDNA helices, measured by osmotic stress, follow the form of hydration forces observed with condensed dsDNA. Probing a well-defined system of point-like cations and tsDNAs with more evenly spaced helical charges, the counterintuitive observation that the more highly charged tsDNA (vs. dsDNA) is condensed by cations of lower valence provides new insights into theories of polyelectrolytes and the biological and pathological roles of tsDNA. Cations and tsDNAs also hold promise as a model system for future studies of DNA-DNA interactions and electrostatic interactions in general.

  19. DNA strand breakage by bivalent metal ions and ionizing radiation.

    Science.gov (United States)

    Ayene, Iraimoudi S; Koch, Cameron J; Krisch, Robert E

    2007-03-01

    To investigate mechanisms of DNA breakage via the interaction of bivalent metal ion, thiol reducing agent and ionizing radiation, in *OH scavenging abilities comparable to those in cells. We measured the effects of 10 min exposure to 200 microM Fe2+ vs. Fe3+ on the induction of single (SSB) and double (DSB) strand breaks in unirradiated and oxically irradiated SV40 DNA, in aqueous solution containing 75 or 750 mM glycerol and/or 5 mM glutathione (GSH). Fe2+ or GSH alone produced little DNA damage. However, their combination produced a dramatic increase in the production of both SSB and DSB. Experiments with ferric ion suggest that it produces DNA damage only after partial reduction to ferrous by GSH. Induction efficiencies for SSB in the presence of Fe2+/GSH showed additivity of the effects of radiation alone with those from Fe2+/GSH. However, the corresponding induction efficiencies for DSB demonstrated a 2.5-fold enhancement. Our results are consistent with a model in which reduced bivalent metal ions plus thiols, in the presence of O2, produce DSB in DNA primarily via local clusters of hydroxyl radicals arising from site specific Fenton reactions. The synergism observed between DSB production by Fe/GSH and by ionizing radiation, also believed to occur via local clusters of hydroxyl radicals, is consistent with this model. Our results suggest that both normally present intracellular iron and ionizing radiation may be important sources of oxidative stress in cells.

  20. Plant somatic hybrid cytoplasmic DNA characterization by single-strand conformation polymorphism.

    Science.gov (United States)

    Olivares-Fuster, Oscar; Hernández-Garrido, María; Guerri, José; Navarro, Luis

    2007-06-01

    Unlike maternal inheritance in sexual hybridization, plant somatic hybridization allows transfer, mixing and recombination of cytoplasmic genomes. In addition to the use of somatic hybridization in plant breeding programs, application of this unique tool should lead to a better understanding of the roles played by the chloroplastic and mitochondrial genomes in determining agronomically important traits. The nucleotide sequences of cytoplasmic genomes are much more conserved than those of nuclear genomes. Cytoplasmic DNA composition in somatic hybrids is commonly elucidated either by length polymorphism analysis of restricted genome regions amplified with universal primers (PCR-RF) or by hybridization of total DNA using universal cytoplasmic probes. In this study, we demonstrate that single-stranded conformational polymorphism (SSCP) analysis is a powerful, quick and easy alternative method for cytoplasmic DNA characterization of somatic hybrids, especially for mitochondrial DNA. The technique allows detection of polymorphisms based on both size and sequence of amplified targets. Twenty-two species of the subfamily Aurantioideae were analyzed with eight universal primers (four from chloroplastic and four from mitochondrial regions). Differences in chloroplastic DNA composition were scored in 98% of all possible two-parent combinations, and different mitochondrial DNA profiles were found in 87% of them. Analysis by SSCP was also successfully used to characterize somatic hybrids and cybrids obtained by fusion of Citrus sinensis (L.) Osb. and C. excelsa Wester protoplasts.

  1. Cohesin protects genes against γH2AX Induced by DNA double-strand breaks.

    Directory of Open Access Journals (Sweden)

    Pierre Caron

    2012-01-01

    Full Text Available Chromatin undergoes major remodeling around DNA double-strand breaks (DSB to promote repair and DNA damage response (DDR activation. We recently reported a high-resolution map of γH2AX around multiple breaks on the human genome, using a new cell-based DSB inducible system. In an attempt to further characterize the chromatin landscape induced around DSBs, we now report the profile of SMC3, a subunit of the cohesin complex, previously characterized as required for repair by homologous recombination. We found that recruitment of cohesin is moderate and restricted to the immediate vicinity of DSBs in human cells. In addition, we show that cohesin controls γH2AX distribution within domains. Indeed, as we reported previously for transcription, cohesin binding antagonizes γH2AX spreading. Remarkably, depletion of cohesin leads to an increase of γH2AX at cohesin-bound genes, associated with a decrease in their expression level after DSB induction. We propose that, in agreement with their function in chromosome architecture, cohesin could also help to isolate active genes from some chromatin remodelling and modifications such as the ones that occur when a DSB is detected on the genome.

  2. Zinc Finger Nuclease induced DNA double stranded breaks and rearrangements in MLL

    Energy Technology Data Exchange (ETDEWEB)

    Do, To Uyen [Graduate Group in Immunology, University of California Davis, Davis, CA 95616 (United States); Department of Radiation Oncology, University of California Davis, Sacramento CA 95817 (United States); Ho, Bay; Shih, Shyh-Jen [Department of Radiation Oncology, University of California Davis, Sacramento CA 95817 (United States); Vaughan, Andrew, E-mail: Andrew.vaughan@ucdmc.ucdavis.edu [Graduate Group in Immunology, University of California Davis, Davis, CA 95616 (United States); Department of Radiation Oncology, University of California Davis, Sacramento CA 95817 (United States)

    2012-12-15

    Highlights: ► A Zinc Finger Nuclease (ZFN) targeting a leukemogenic hot spot for rearrangement in MLL is created. ► The novel ZFN efficiently cleaves MLL exon 13. ► Despite MLL cleavage and evidence of mis-repair, no leukemogenic translocations were produced. ► MLL cleavage alone is insufficient to generate leukemogenic translocations. - Abstract: Radiation treatment or chemotherapy has been linked with a higher risk of secondary cancers such as therapy related Acute Myeloid Leukemia (tAML). Several of these cancers have been shown to be correlated to the introduction of double stranded breaks (DSB) and rearrangements within the Mixed Lineage Leukemia (MLL) gene. We used Zinc Finger Nucleases (ZFNs) to introduce precise cuts within MLL to examine how a single DNA DSB might lead to chromosomal rearrangements. A ZFN targeting exon 13 within the Breakpoint Cluster Region of MLL was transiently expressed in a human lymphoblast cell line originating from a CML patient. Although FISH analysis showed ZFN DSB at this region increased the rate of MLL fragmentation, we were unable to detect leukemogenic rearrangements or translocations via inverse PCR. Interestingly, gene fragmentation as well as small interstitial deletions, insertions and base substitutions increased with the inhibition of DNA-PK, suggesting repair of this particular DSB is linked to non-homologous end joining (NHEJ). Although mis-repair of DSBs may be necessary for the initiation of leukemogenic translocations, a MLL targeted DNA break alone is insufficient.

  3. Noise assisted excitation energy transfer in a linear model of a selectivity filter backbone strand

    Science.gov (United States)

    Bassereh, Hassan; Salari, Vahid; Shahbazi, Farhad

    2015-07-01

    In this paper, we investigate the effect of noise and disorder on the efficiency of excitation energy transfer (EET) in a N=5 sites linear chain with ‘static’ dipole-dipole couplings. In fact, here, the disordered chain is a toy model for one strand of the selectivity filter backbone in ion channels. It has recently been discussed that the presence of quantum coherence in the selectivity filter is possible and can play a role in mediating ion-conduction and ion-selectivity in the selectivity filter. The question is ‘how a quantum coherence can be effective in such structures while the environment of the channel is dephasing (i.e. noisy)?’ Basically, we expect that the presence of the noise should have a destructive effect in the quantum transport. In fact, we show that such expectation is valid for ordered chains. However, our results indicate that introducing the dephasing in the disordered chains leads to the weakening of the localization effects, arising from the multiple back-scatterings due to the randomness, and then increases the efficiency of quantum energy transfer. Thus, the presence of noise is crucial for the enhancement of EET efficiency in disordered chains. We also show that the contribution of both classical and quantum mechanical effects are required to improve the speed of energy transfer along the chain. Our analysis may help for better understanding of fast and efficient functioning of the selectivity filters in ion channels.

  4. Noise assisted excitation energy transfer in a linear model of a selectivity filter backbone strand.

    Science.gov (United States)

    Bassereh, Hassan; Salari, Vahid; Shahbazi, Farhad

    2015-07-15

    In this paper, we investigate the effect of noise and disorder on the efficiency of excitation energy transfer (EET) in a N = 5 sites linear chain with 'static' dipole-dipole couplings. In fact, here, the disordered chain is a toy model for one strand of the selectivity filter backbone in ion channels. It has recently been discussed that the presence of quantum coherence in the selectivity filter is possible and can play a role in mediating ion-conduction and ion-selectivity in the selectivity filter. The question is 'how a quantum coherence can be effective in such structures while the environment of the channel is dephasing (i.e. noisy)?' Basically, we expect that the presence of the noise should have a destructive effect in the quantum transport. In fact, we show that such expectation is valid for ordered chains. However, our results indicate that introducing the dephasing in the disordered chains leads to the weakening of the localization effects, arising from the multiple back-scatterings due to the randomness, and then increases the efficiency of quantum energy transfer. Thus, the presence of noise is crucial for the enhancement of EET efficiency in disordered chains. We also show that the contribution of both classical and quantum mechanical effects are required to improve the speed of energy transfer along the chain. Our analysis may help for better understanding of fast and efficient functioning of the selectivity filters in ion channels.

  5. Pull-Out Strength and Bond Behavior of Prestressing Strands in Prestressed Self-Consolidating Concrete.

    Science.gov (United States)

    Long, Wu-Jian; Khayat, Kamal Henri; Lemieux, Guillaume; Hwang, Soo-Duck; Xing, Feng

    2014-10-10

    With the extensive use of self-consolidating concrete (SCC) worldwide, it is important to ensure that such concrete can secure uniform in-situ mechanical properties that are similar to those obtained with properly consolidated concrete of conventional fluidity. Ensuring proper stability of SCC is essential to enhance the uniformity of in-situ mechanical properties, including bond to embedded reinforcement, which is critical for structural engineers considering the specification of SCC for prestressed applications. In this investigation, Six wall elements measuring 1540 mm × 2150 mm × 200 mm were cast using five SCC mixtures and one reference high-performance concrete (HPC) of normal consistency to evaluate the uniformity of bond strength between prestressing strands and concrete as well as the distribution of compressive strength obtained from cores along wall elements. The evaluated SCC mixtures used for casting wall elements were proportioned to achieve a slump flow consistency of 680 ± 15 mm and minimum caisson filling capacity of 80%, and visual stability index of 0.5 to 1. Given the spreads in viscosity and static stability of the SCC mixtures, the five wall elements exhibited different levels of homogeneity in in-situ compressive strength and pull-out bond strength. Test results also indicate that despite the high fluidity of SCC, stable concrete can lead to more homogenous in-situ properties than HPC of normal consistency subjected to mechanical vibration.

  6. ATM release at resected double-strand breaks provides heterochromatin reconstitution to facilitate homologous recombination.

    Directory of Open Access Journals (Sweden)

    Verena Geuting

    Full Text Available Non-homologous end-joining (NHEJ and homologous recombination (HR represent the two main pathways for repairing DNA double-strand breaks (DSBs. During the G2 phase of the mammalian cell cycle, both processes can operate and chromatin structure is one important factor which determines DSB repair pathway choice. ATM facilitates the repair of heterochromatic DSBs by phosphorylating and inactivating the heterochromatin building factor KAP-1, leading to local chromatin relaxation. Here, we show that ATM accumulation and activity is strongly diminished at DSBs undergoing end-resection during HR. Such DSBs remain unrepaired in cells devoid of the HR factors BRCA2, XRCC3 or RAD51. Strikingly, depletion of KAP-1 or expression of phospho-mimic KAP-1 allows repair of resected DSBs in the absence of BRCA2, XRCC3 or RAD51 by an erroneous PARP-dependent alt-NHEJ process. We suggest that DSBs in heterochromatin elicit initial local heterochromatin relaxation which is reversed during HR due to the release of ATM from resection break ends. The restored heterochromatic structure facilitates HR and prevents usage of error-prone alternative processes.

  7. The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape.

    Science.gov (United States)

    Petrov, Anton S; Boz, Mustafa Burak; Harvey, Stephen C

    2007-11-01

    The packaging of double-stranded DNA into bacteriophages leads to the arrangement of the genetic material into highly-packed and ordered structures. Although modern experimental techniques reveal the most probable location of DNA inside viral capsids, the individual conformations of DNA are yet to be determined. In the current study we present the results of molecular dynamics simulations of the DNA packaging into several bacteriophages performed within the framework of a coarse-grained model. The final DNA conformations depend on the size and shape of the capsid, as well as the size of the protein portal, if any. In particular, isometric capsids with small or absent portals tend to form concentric spools, whereas the presence of a large portal favors coaxial spooling; slightly and highly elongated capsids result in folded and twisted toroidal conformations, respectively. The results of the simulations also suggest that the predominant factor in defining the global DNA arrangement inside bacteriophages is the minimization of the bending stress upon packaging.

  8. Sequence-specific double strand breaks trigger P-TEFb-dependent Rpb1-CTD hyperphosphorylation

    Energy Technology Data Exchange (ETDEWEB)

    Napolitano, Giuliana; Amente, Stefano; Lavadera, Miriam Lubrano; Di Palo, Giacomo; Ambrosio, Susanna; Lania, Luigi [Department of Biology, University of Naples ‘Federico II’, Naples (Italy); Dellino, Gaetano Ivan; Pelicci, Pier Giuseppe [Department of Experimental Oncology, European Institute of Oncology, Milan (Italy); Majello, Barbara, E-mail: majello@unina.it [Department of Biology, University of Naples ‘Federico II’, Naples (Italy)

    2013-09-15

    Highlights: • Using an inducible restriction enzyme, hundreds of site-specific DSBs are generated across the genome. • Site-specific DSBs trigger activation of P-TEFb and consequent Rpb1-CTD hyperphosphorylation. • Site-specific DSBs induce activation of p53-transcriptional axis. - Abstract: Double strand DNA breaks (DSBs) are one of the most challenging forms of DNA damage which, if left unrepaired, can trigger cellular death and can contribute to cancer. A number of studies have been focused on DNA-damage response (DDR) mechanisms, and most of them rely on the induction of DSBs triggered by chemical compounds or radiations. However, genotoxic drugs and radiation treatments of cultured cell lines induce random DSBs throughout the genome, thus heterogeneously across the cell population, leading to variability of the cellular response. To overcome this aspect, we used here a recently described cell-based DSBs system whereby, upon induction of an inducible restriction enzyme, hundreds of site-specific DSBs are generated across the genome. We show here that sequence-specific DSBs are sufficient to activate the positive transcription elongation factor b (P-TEFb), to trigger hyperphosphorylation of the largest RNA polymerase II carboxyl-terminal-domain (Rpb1-CTD) and to induce activation of p53-transcriptional axis resulting in cell cycle arrest.

  9. Analysis of DNA Double-strand Break (DSB) Repair in Mammalian Cells

    Science.gov (United States)

    Seluanov, Andrei; Mao, Zhiyong; Gorbunova, Vera

    2010-01-01

    DNA double-strand breaks are the most dangerous DNA lesions that may lead to massive loss of genetic information and cell death. Cells repair DSBs using two major pathways: nonhomologous end joining (NHEJ) and homologous recombination (HR). Perturbations of NHEJ and HR are often associated with premature aging and tumorigenesis, hence it is important to have a quantitative way of measuring each DSB repair pathway. Our laboratory has developed fluorescent reporter constructs that allow sensitive and quantitative measurement of NHEJ and HR. The constructs are based on an engineered GFP gene containing recognition sites for a rare-cutting I-SceI endonuclease for induction of DSBs. The starting constructs are GFP negative as the GFP gene is inactivated by an additional exon, or by mutations. Successful repair of the I-SceI-induced breaks by NHEJ or HR restores the functional GFP gene. The number of GFP positive cells counted by flow cytometry provides quantitative measure of NHEJ or HR efficiency. PMID:20864925

  10. Analysis of DNA double-strand break (DSB) repair in mammalian cells.

    Science.gov (United States)

    Seluanov, Andrei; Mao, Zhiyong; Gorbunova, Vera

    2010-09-08

    DNA double-strand breaks are the most dangerous DNA lesions that may lead to massive loss of genetic information and cell death. Cells repair DSBs using two major pathways: nonhomologous end joining (NHEJ) and homologous recombination (HR). Perturbations of NHEJ and HR are often associated with premature aging and tumorigenesis, hence it is important to have a quantitative way of measuring each DSB repair pathway. Our laboratory has developed fluorescent reporter constructs that allow sensitive and quantitative measurement of NHEJ and HR. The constructs are based on an engineered GFP gene containing recognition sites for a rare-cutting I-SceI endonuclease for induction of DSBs. The starting constructs are GFP negative as the GFP gene is inactivated by an additional exon, or by mutations. Successful repair of the I-SceI-induced breaks by NHEJ or HR restores the functional GFP gene. The number of GFP positive cells counted by flow cytometry provides quantitative measure of NHEJ or HR efficiency.

  11. Analysis of DNA double-strand break repair pathways in mice

    Energy Technology Data Exchange (ETDEWEB)

    Brugmans, Linda [Department of Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, PO Box 1738, Rotterdam 3015GE (Netherlands); Kanaar, Roland [Department of Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, PO Box 1738, Rotterdam 3015GE (Netherlands); Department of Radiation Oncology, Erasmus MC, PO Box 1738, 3000 DR Rotterdam (Netherlands); Essers, Jeroen [Department of Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, PO Box 1738, Rotterdam 3015GE (Netherlands) and Department of Radiation Oncology, Erasmus MC, PO Box 1738, 3000 DR Rotterdam (Netherlands)]. E-mail: j.essers@erasmusmc.nl

    2007-01-03

    During the last years significant new insights have been gained into the mechanism and biological relevance of DNA double-strand break (DSB) repair in relation to genome stability. DSBs are a highly toxic DNA lesion, because they can lead to chromosome fragmentation, loss and translocations, eventually resulting in cancer. DSBs can be induced by cellular processes such as V(D)J recombination or DNA replication. They can also be introduced by exogenous agents DNA damaging agents such as ionizing radiation or mitomycin C. During evolution several pathways have evolved for the repair of these DSBs. The most important DSB repair mechanisms in mammalian cells are nonhomologous end-joining and homologous recombination. By using an undamaged repair template, homologous recombination ensures accurate DSB repair, whereas the untemplated nonhomologous end-joining pathway does not. Although both pathways are active in mammals, the relative contribution of the two repair pathways to genome stability differs in the different cell types. Given the potential differences in repair fidelity, it is of interest to determine the relative contribution of homologous recombination and nonhomologous end-joining to DSB repair. In this review, we focus on the biological relevance of DSB repair in mammalian cells and the potential overlap between nonhomologous end-joining and homologous recombination in different tissues.

  12. Binding of DNA hairpins to an assembler-strand as part of a primordial translation device

    Science.gov (United States)

    Baumann, Ulrich

    1987-09-01

    A crucial event in the process leading to the origin of life is the emergence of a simple translation device. To approach experimental realization of this device the binding ability of short DNA hairpins to complementary oligonucleotides fixed on a solid support was investigated. The binding is achieved by base pairing between the loop nucleotides of the hairpins containing different numbers of adenosine residues and oligothymidylates covalently linked to cellulose. The loop has to consist of at least five nucleotides to achieve binding. The exact number of established base pairs was determined in two ways. First, the elution temperatures of hairpins and those of oligoadenylates which had the length of the loop were compared. Secondly, the architecture of the loop was analyzed by means of the single-strand-specific nuclease from mung bean acting as structural probe. Onlyn-2 of n loop nucleotides of a hairpin are able to form base pairs. Therefore, a strong evidence for the formation of a triplet of base pairs between primeval tRNA and mRNA sufficient to stabilize the complex enzyme-free is given.

  13. Generation of Gross Chromosomal Rearrangements by a Single Engineered DNA Double Strand Break

    Science.gov (United States)

    Qiu, Zhijun; Zhang, Zhenhua; Roschke, Anna; Varga, Tamas; Aplan, Peter D.

    2017-01-01

    Gross chromosomal rearrangements (GCRs), including translocations, inversions amplifications, and deletions, can be causal events leading to malignant transformation. GCRs are thought to be triggered by DNA double strand breaks (DSBs), which in turn can be spontaneous or induced by external agents (eg. cytotoxic chemotherapy, ionizing radiation). It has been shown that induction of DNA DSBs at two defined loci can produce stable balanced chromosomal translocations, however, a single engineered DNA DSB could not. Herein, we report that although a single engineered DNA DSB in H2AX “knockdown” cells did not generate GCRs, repair of a single engineered DNA DSB in fibroblasts that had ablated H2ax did produce clonal, stable GCRs, including balanced translocations and megabase-pair inversions. Upon correction of the H2ax deficiency, cells no longer generated GCRs following a single engineered DNA DSB. These findings demonstrate that clonal, stable GCRs can be produced by a single engineered DNA DSB in H2ax knockout cells, and that the production of these GCRs is ameliorated by H2ax expression. PMID:28225067

  14. Phosphorylation of Ku dictates DNA double-strand break (DSB) repair pathway choice in S phase.

    Science.gov (United States)

    Lee, Kyung-Jong; Saha, Janapriya; Sun, Jingxin; Fattah, Kazi R; Wang, Shu-Chi; Jakob, Burkhard; Chi, Linfeng; Wang, Shih-Ya; Taucher-Scholz, Gisela; Davis, Anthony J; Chen, David J

    2016-02-29

    Multiple DNA double-strand break (DSB) repair pathways are active in S phase of the cell cycle; however, DSBs are primarily repaired by homologous recombination (HR) in this cell cycle phase. As the non-homologous end-joining (NHEJ) factor, Ku70/80 (Ku), is quickly recruited to DSBs in S phase, we hypothesized that an orchestrated mechanism modulates pathway choice between HR and NHEJ via displacement of the Ku heterodimer from DSBs to allow HR. Here, we provide evidence that phosphorylation at a cluster of sites in the junction of the pillar and bridge regions of Ku70 mediates the dissociation of Ku from DSBs. Mimicking phosphorylation at these sites reduces Ku's affinity for DSB ends, suggesting that phosphorylation of Ku70 induces a conformational change responsible for the dissociation of the Ku heterodimer from DNA ends. Ablating phosphorylation of Ku70 leads to the sustained retention of Ku at DSBs, resulting in a significant decrease in DNA end resection and HR, specifically in S phase. This decrease in HR is specific as these phosphorylation sites are not required for NHEJ. Our results demonstrate that the phosphorylation-mediated dissociation of Ku70/80 from DSBs frees DNA ends, allowing the initiation of HR in S phase and providing a mechanism of DSB repair pathway choice in mammalian cells.

  15. Double-strand breaks associated with repetitive DNA can reshape the genome

    Science.gov (United States)

    Argueso, Juan Lucas; Westmoreland, James; Mieczkowski, Piotr A.; Gawel, Malgorzata; Petes, Thomas D.; Resnick, Michael A.

    2008-01-01

    Ionizing radiation is an established source of chromosome aberrations (CAs). Although double-strand breaks (DSBs) are implicated in radiation-induced and other CAs, the underlying mechanisms are poorly understood. Here, we show that, although the vast majority of randomly induced DSBs in G2 diploid yeast cells are repaired efficiently through homologous recombination (HR) between sister chromatids or homologous chromosomes, ≈2% of all DSBs give rise to CAs. Complete molecular analysis of the genome revealed that nearly all of the CAs resulted from HR between nonallelic repetitive elements, primarily Ty retrotransposons. Nonhomologous end-joining (NHEJ) accounted for few, if any, of the CAs. We conclude that only those DSBs that fall at the 3–5% of the genome composed of repetitive DNA elements are efficient at generating rearrangements with dispersed small repeats across the genome, whereas DSBs in unique sequences are confined to recombinational repair between the large regions of homology contained in sister chromatids or homologous chromosomes. Because repeat-associated DSBs can efficiently lead to CAs and reshape the genome, they could be a rich source of evolutionary change. PMID:18701715

  16. Lesions associated with Halocercus brasiliensis Lins de Almeida, 1933 in the lungs of dolphins stranded in the Northeast of Brazil.

    Science.gov (United States)

    Guimarães, J P; Febronio, A M B; Vergara-Parente, J E; Werneck, M R

    2015-04-01

    The parasitic fauna of cetaceans is an important tool for ecological studies, including analyses on the causes of death. Halocercus brasiliensis is a nematode frequently found in the bronchi and bronchioles of some cetaceans, and it is commonly associated with focal inflammation of the respiratory tract leading to bacterial pneumonia and septicemia and, sometimes, to death. The objective of this study was to report infections by H. brasiliensis in the respiratory tract of Delphinidae stranded on the northern seaside of Bahia, Sergipe, and south of Alagoas, all states in the northeast region of Brazil. A total of 30 individuals, 1 Feresa attenuate (pygmy killer whale), 9 Stenella clymene (Clymene dolphin), and 20 Sotalia guianensis (Guiana dolphin) were studied. In 16 of them, the presence of H. brasiliensis was observed with a mean intensity of 3.5 ± 0.6 (range 1-9) in the hosts. Macroscopically, parasitic calcified nodules, lung congestion, edema, and emphysema were observed. Histopathological examination showed interstitial and granulomatous pneumonia with multifocal infiltrates, discrete to moderate edema, congestion, diffuse hemorrhage, and foci of calcification. We conclude that parasitic pneumonia in the sampled individuals may have directly contributed to stranding and death of the animals.

  17. Contribution of DNA double-strand break repair gene XRCC3 genotypes to oral cancer susceptibility in Taiwan.

    Science.gov (United States)

    Tsai, Chia-Wen; Chang, Wen-Shin; Liu, Juhn-Cherng; Tsai, Ming-Hsui; Lin, Cheng-Chieh; Bau, Da-Tian

    2014-06-01

    The DNA repair gene X-ray repair cross complementing protein 3 (XRCC3) is thought to play a major role in double-strand break repair and in maintaining genomic stability. Very possibly, defective double-strand break repair of cells can lead to carcinogenesis. Therefore, a case-control study was performed to reveal the contribution of XRCC3 genotypes to individual oral cancer susceptibility. In this hospital-based research, the association of XRCC3 rs1799794, rs45603942, rs861530, rs3212057, rs1799796, rs861539, rs28903081 genotypes with oral cancer risk in a Taiwanese population was investigated. In total, 788 patients with oral cancer and 956 age- and gender-matched healthy controls were genotyped. The results showed that there was significant differential distribution among oral cancer and controls in the genotypic (p=0.001428) and allelic (p=0.0013) frequencies of XRCC3 rs861539. As for the other polymorphisms, there was no difference between case and control groups. In gene-lifestyle interaction analysis, we have provided the first evidence showing that there is an obvious joint effect of XRCC3 rs861539 genotype with individual areca chewing habits on oral cancer risk. In conclusion, the T allele of XRCC3 rs861539, which has an interaction with areca chewing habit in oral carcinogenesis, may be an early marker for oral cancer in Taiwanese.

  18. Enhancement of RecA-mediated self-assembly in DNA nanostructures through basepair mismatches and single-strand nicks

    Science.gov (United States)

    Corbett, Sybilla Louise; Sharma, Rajan; Davies, Alexander Giles; Wälti, Christoph

    2017-01-01

    The use of DNA as a structural material for nanometre-scale construction has grown extensively over the last decades. The development of more advanced DNA-based materials would benefit from a modular approach enabling the direct assembly of additional elements onto nanostructures after fabrication. RecA-based nucleoprotein filaments encapsulating short ssDNA have been demonstrated as a tool for highly efficient and fully programmable post-hoc patterning of duplex DNA scaffold. However, the underlying assembly process is not fully understood, in particular when patterning complex DNA topologies. Here, we report the effect of basepair-mismatched regions and single-strand nicks in the double-stranded DNA scaffold on the yield of RecA-based assembly. Significant increases in assembly yield are observed upon the introduction of unpaired basepairs directly adjacent to the assembly region. However, when the unpaired regions were introduced further from the assembly site the assembly yield initially decreased as the length of the unpaired region was increased. These results suggest that an unpaired region acts as a kinetic trap for RecA-based nucleoprotein filaments, impeding the assembly mechanism. Conversely, when the unpaired region is located directly adjacent to the assembly site, it leads to an increase in efficiency of RecA patterning owing to increased breathing of the assembly site.

  19. Lead Time Study,

    Science.gov (United States)

    1982-05-01

    AD-A128 318 LEAD TIME STUDY (U) ARMY ARMAMENT RESEARCH AND DEVELOPMENT CDMMAND DOVER NJ SYSTEMS ANALYSIS DIV dI-T~~ CHU MAY 82 ARRAA 82- 3/ /l N...EhhEEE--E 1111.0 U 1 - I 1120 1.25I1,,-. 11.6 MICROCOPY RESOLUTION TESI CHARI NATIONAL BUREAU 01 STANDARDt 19t,3 A co LEAD TIME STUDY c*A JULIE CHU MAY...188 D I.-f . . .... .. - r - .. " ’- -~ L - - _ _ __ ARRAA 82-3 LEAD TIME STUDY Prepared by:_ JL CHU Reviewed by:Li t’ ( LAWRENCE J. QWUNI Chief, Sys

  20. Lead effects on fungi

    Energy Technology Data Exchange (ETDEWEB)

    Gullino, M.L.; Fiussello, N.

    1976-01-01

    Addition of 0.01M lead nitrate to media caused complete inhibition of most of a group of 80 strains of fungi of several genera. Those which did grow at all had an extended lag period in comparison to controls. At 0.001M all the fungi grew, but had thinner-than-normal mycelia and delayed fruiting body formation. Fusarium species and members of Class Basidiomycetes were among the most sensitive, and Penicillium and Aspergillus species were the most tolerant. Lead uptake rates varied positively with lead nitrate concentration in the media. 9 references, 2 figures, 3 tables.

  1. [Cytomechanics of oscillatory contractions. Modeling the longitudinal dynamics of Physarum polycephalum protoplasmic strands].

    Science.gov (United States)

    Teplov, V A

    2010-01-01

    A mathematical model of the longitudinal dynamics of an isolated strand of the Physarum polycephalum plasmodium has been constructed. Its contractile system is considered as a continual viscoelastic medium with passive and active components. The mathematical description of the longitudinal dynamics of the plasmodial strand is reduced to a system of three first-order differential equations, whose variables are its active stress, deformation, and the intracellular concentration of calcium ions. The model is based on the hypothesis that there exists a feedback loop, which appears because of the influence of strand stretching on the rate of the release of calcium ions, which in turn controls the active contraction and deformation of the strand. Nonlinear interactions between the variables evoke a loss of the stationary state stability and a self-excitation of mechanochemical autooscillations when the external load exceeds some critical value. The results of numerical solutions of the model with the empirically determined viscoelastic parameters are in good agreement with the available experimental data and testify to the adequacy of the description of strand dynamics by the mathematical model in which the contractile apparatus is a part of the cellular control system. In particular, this model well simulates the form and duration of transient mechanochemical processes observed under isotonic and isometric conditions immediately after strand isolation, as well as the subsequent excitation of autooscillations of the contractile activity and their activation by strand stretching.

  2. The kinetics of force-dependent hybridization and strand-peeling of short DNA fragments

    Science.gov (United States)

    Yang, ZhouJie; Yuan, GuoHua; Zhai, WeiLi; Yan, Jie; Chen, Hu

    2016-08-01

    Deoxyribonucleic acid (DNA) carries the genetic information in all living organisms. It consists of two interwound single-stranded (ss) strands, forming a double-stranded (ds) DNA with a right-handed double-helical conformation. The two strands are held together by highly specific basepairing interactions and are further stabilized by stacking between adjacent basepairs. A transition from a dsDNA to two separated ssDNA is called melting and the reverse transition is called hybridization. Applying a tensile force to a dsDNA can result in a particular type of DNA melting, during which one ssDNA strand is peeled away from the other. In this work, we studied the kinetics of strand-peeling and hybridization of short DNA under tensile forces. Our results show that the force-dependent strand-peeling and hybridization can be described with a simple two-state model. Importantly, detailed analysis of the force-dependent transition rates revealed that the transition state consists of several basepairs dsDNA.

  3. FTIR study of CPD photolyase with substrate in single strand DNA.

    Science.gov (United States)

    Mahaputra Wijaya, I M; Iwata, Tatsuya; Yamamoto, Junpei; Hitomi, Kenichi; Iwai, Shigenori; Getzoff, Elizabeth D; Kandori, Hideki

    2015-01-01

    Photolyases (PHRs) utilize near UV/blue light to specifically repair the major photoproducts (PPs) of UV-induced damaged DNA. The cyclobutane pyrimidine dimer (CPD)-PHR binds flavin adenine dinucleotide (FAD) as a cofactor and repairs CPD lesions in double-stranded DNA. To understand the activation and repair mechanism of CPD-PHR, we applied light-induced difference Fourier transform infrared (FTIR) spectroscopy to CPD-PHR, whose signals were identified by use of isotope-labeling. To further investigate the enzymatic function, here we study the activation and repair mechanism of CPD-PHR with the substrate in single strand DNA, and the obtained FTIR spectra are compared with those in double-stranded DNA, the natural substrate. The difference spectra of photoactivation, the fully-reduced (FADH(-)) minus semiquinone (FADH(•)) spectra, are almost identical in the presence of single strand and double-stranded DNA, except for slight spectral modification in the amide-I region. On the other hand, the difference spectra of photorepair were highly substrate dependent. Strong bands of the C=O stretch (1,720-1,690 cm(-1)) and phosphate vibrations (1,090-1,060 cm(-1)) of double-stranded DNA may have disappeared in the case of single strand DNA. However, an isotope-labeled enzyme study revealed that spectral features upon DNA repair are similar between both substrates, and the main reason for the apparent spectral difference originates from structural flexibility of DNA after repair.

  4. Life cycle assessment of oriented strand boards (OSB): from process innovation to ecodesign.

    Science.gov (United States)

    Benetto, Enrico; Becker, Marko; Welfring, Joëlle

    2009-08-01

    Oriented strand boards (OSBs) are wood panels that are used worldwide mainly in the packaging and the building sectors. Their market share is rapidly increasing thanks to their outstanding mechanical properties and to a renewed interest for wood based products. The OSB production process generates, nonetheless, emissions of volatile organic compounds (VOCs) during the air-drying of wood strands. This known problem in the literature leads to an odorous nuisance in the surrounding area of the production site. In order to address this problem, a novel application to wood drying of an innovative vapor drying technology is successfully operated at the production site of Kronospan Luxembourg S.A. In addition to the reduced odorous nuisance, a significant environmental added value is expected because of the other modifications induced by the vapor-drying technique on the OSB production process viz. the reduced energy and raw materials demands and the change of adhesive mixture, with the addition of phenol resin. The potential impact of this technology on the OSB market is therefore very significant. This study was aimed at assessing the environmental added value provided by the vapor-drying technique through a life cycle assessment (LCA) according to ISO 14040-44 standards. The objective was to compare the environmental performances of the former and the current OSB production processes. Considering only the pollutant emissions from the OSB production process, the reduction of climate change impact and human health damage is significant respectively, 15-20% and 50-75%. When the lifecycle processes related to the OSB production are included, the reduction of damages does not exceed 3-7%. Following an uncertainty analysis,this reduction was nevertheless proven to be statistically significant. However, it is observed that the reduction of environmental impacts and damages allowed by the vapor-drying technology is counterbalanced by the change of adhesive mixture. Indeed the

  5. Lead Exposure Induces Telomere Instability in Human Cells.

    Directory of Open Access Journals (Sweden)

    Géraldine Pottier

    Full Text Available Lead (Pb is an important environmental contaminant due to its widespread use over many centuries. While it affects primarily every organ system of the body, the most pernicious effects of Pb are on the central nervous system leading to cognitive and behavioral modification. Despite decades of research, the mechanisms responsible for Pb toxicity remain poorly understood. Recent work has suggested that Pb exposure may have consequences on chromosomal integrity as it was shown that Pb exposure leads to the generation of γH2Ax foci, a well-established biomarker for DNA double stranded break (DSB formation. As the chromosomal localization of γH2Ax foci plays an important role in determining the molecular mechanism responsible for their formation, we examined the localization of Pb-induced foci with respect to telomeres. Indeed, short or dysfunctional telomeres (uncapped or damaged telomeres may be recognized as DSB by the DNA repair machinery, leading to "telomere-Induced Foci" (TIFs. In the current study, we show that while Pb exposure did not increase intra-chromosomal foci, it significantly induced TIFs, leading in some cases, to chromosomal abnormalities including telomere loss. The evidence suggests that these chromosomal abnormalities are likely due to perturbation of telomere replication, in particular on the lagging DNA strand. We propose a mechanism by which Pb exposure leads to the loss of telomere maintenance. As numerous studies have demonstrated a role for telomere maintenance in brain development and tissue homeostasis, our results suggest a possible mechanism for lead-induced neurotoxicity.

  6. The role of cytosine methylation on charge transport through a DNA strand

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Jianqing, E-mail: jqqi@uw.edu; Anantram, M. P., E-mail: anantmp@uw.edu [Department of Electrical Engineering, University of Washington, Seattle, Washington 98195-2500 (United States); Govind, Niranjan, E-mail: niri.govind@pnnl.gov [William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)

    2015-09-07

    Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Büttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter-strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchange-correlation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit.

  7. Electro-mechanical behaviors of composite superconducting strand with filament breakage

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xu [Key Laboratory of Mechanics on Environment and Disaster in Western China, The Ministry of Education of China, Lanzhou, Gansu 730000 (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China); Gao, Yuanwen, E-mail: ywgao@lzu.edu.cn [Key Laboratory of Mechanics on Environment and Disaster in Western China, The Ministry of Education of China, Lanzhou, Gansu 730000 (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China); Zhou, Youhe [Key Laboratory of Mechanics on Environment and Disaster in Western China, The Ministry of Education of China, Lanzhou, Gansu 730000 (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China)

    2016-10-15

    Highlights: • The electromechanical behaviors of the superconducting (SC) strand are investigated. • A 3D FEM model for bending behaviors and electric properties of strand is developed. • The influence of breakage of filaments on the critical current of SC strand is calculated. • The impact of current transfer length on the electric properties of SC strand is discussed. - Abstract: The bending behaviors of superconducting strand with typical multi-filament twist configuration are investigated based on a three-dimensional finite element method (FEM) model, named as the Multi-filament twist model, of the strand. In this 3D FEM model, the impacts of initial thermal residual stress, filament-breakage and its evaluation are taken into accounts. The mechanical responses of the strand under bending load are studied with the factors taken into consideration one by one. The distribution of the damage of the filaments and its evolution and the movement of the neutral axis caused by it are studied and displayed in detail. Besides, taking the advantages of the Multi-filament twist model, the normalized critical current of the strand under bending load is also calculated based on the invariant temperature and field strain functions. In addition, the non-negligible influences of the pitch length of the filaments on both the mechanical behaviors and the normalized critical current are discussed. The stress-strain characteristics of the strand under tensile load and the normalized critical current of it under axial and bending loads resulting from the Multi-filament twist model show good agreement with the experimental data.

  8. A Sensor-Type PC Strand with an Embedded FBG Sensor for Monitoring Prestress Forces

    Directory of Open Access Journals (Sweden)

    Sung Tae Kim

    2015-01-01

    Full Text Available Prestressed Concrete Wire and Strand (PC strands are the most used materials to introduce prestress in a Pre-Stressed Concrete (PSC structure. However, it is difficult to evaluate the final prestress force of the PC strand after prestressing or its residual prestress force after completion of the structure on site. This impossibility to assess eventual loss of prestress of the PC strand has resulted in a number of serious accidents and even in the collapse of several structures. This situation stresses the necessity to maintain the prestress force residual or after prestressing for the evaluation of the health of the concrete structure throughout its lifespan. Recently, several researchers have studied methods enabling one to verify the prestress force by inserting an optical fiber sensor inside the strand but failed to provide simple techniques for the fabrication of these devices to fulfill measurement performance from the design prestress to failure. Moreover, these methods require the additional installation of electrical resistance strain gages, displacement sensors and load cells on the outer surface of the structure for long-term precise measurement. This paper proposes a method enabling one to evaluate precisely and effectively the prestress force of the PC strand and intends to verify the applicability of the proposed method on actual concrete structures. To that end, an innovative PC strand is developed by embedding a Fiber Bragg Grating (FBG sensor in the core wire of the PC strand so as to enable short term as well as long term monitoring. The measurement performance of the developed strand is then evaluated experimentally and the reliability of the monitoring data is assessed.

  9. Factors affecting harp seal (Pagophilus groenlandicus) strandings in the Northwest Atlantic.

    Science.gov (United States)

    Soulen, Brianne K; Cammen, Kristina; Schultz, Thomas F; Johnston, David W

    2013-01-01

    The effects of climate change on high latitude regions are becoming increasingly evident, particularly in the rapid decline of sea ice cover in the Arctic. Many high latitude species dependent on sea ice are being forced to adapt to changing habitats. Harp seals (Pagophilus groenlandicus) are an indicator species for changing high-latitude ecosystems. This study analyzed multiple factors including ice cover, demographics, and genetic diversity, which could affect harp seal stranding rates along the eastern coast of the United States. Ice cover assessments were conducted for the month of February in the Gulf of St. Lawrence whelping region from 1991-2010 using remote sensing data, and harp seal stranding data were collected over the same time period. Genetic diversity, which may affect how quickly species can adapt to changing climates, was assessed using ten microsatellite markers to determine mean d (2) in a subset of stranded and by-caught (presumably healthy) seals sampled along the northeast U.S. coast. Our study found a strong negative correlation (R (2) = 0.49) between ice cover in the Gulf of St. Lawrence and yearling harp seal strandings, but found no relationship between sea ice conditions and adult strandings. Our analysis revealed that male seals stranded more frequently than females during the study period and that this relationship was strongest during light ice years. In contrast, we found no significant difference in mean d (2) between stranded and by-caught harp seals. The results demonstrate that sea ice cover and demographic factors have a greater influence on harp seal stranding rates than genetic diversity, with only a little of the variance in mean d (2) among stranded seals explained by ice cover. Any changes in these factors could have major implications for harp seals, and these findings should be considered in the development of future management plans for the Arctic that incorporate climate variability.

  10. Factors affecting harp seal (Pagophilus groenlandicus strandings in the Northwest Atlantic.

    Directory of Open Access Journals (Sweden)

    Brianne K Soulen

    Full Text Available The effects of climate change on high latitude regions are becoming increasingly evident, particularly in the rapid decline of sea ice cover in the Arctic. Many high latitude species dependent on sea ice are being forced to adapt to changing habitats. Harp seals (Pagophilus groenlandicus are an indicator species for changing high-latitude ecosystems. This study analyzed multiple factors including ice cover, demographics, and genetic diversity, which could affect harp seal stranding rates along the eastern coast of the United States. Ice cover assessments were conducted for the month of February in the Gulf of St. Lawrence whelping region from 1991-2010 using remote sensing data, and harp seal stranding data were collected over the same time period. Genetic diversity, which may affect how quickly species can adapt to changing climates, was assessed using ten microsatellite markers to determine mean d (2 in a subset of stranded and by-caught (presumably healthy seals sampled along the northeast U.S. coast. Our study found a strong negative correlation (R (2 = 0.49 between ice cover in the Gulf of St. Lawrence and yearling harp seal strandings, but found no relationship between sea ice conditions and adult strandings. Our analysis revealed that male seals stranded more frequently than females during the study period and that this relationship was strongest during light ice years. In contrast, we found no significant difference in mean d (2 between stranded and by-caught harp seals. The results demonstrate that sea ice cover and demographic factors have a greater influence on harp seal stranding rates than genetic diversity, with only a little of the variance in mean d (2 among stranded seals explained by ice cover. Any changes in these factors could have major implications for harp seals, and these findings should be considered in the development of future management plans for the Arctic that incorporate climate variability.

  11. The structure-specific endonuclease Mus81-Eme1 promotes conversion of interstrand DNA crosslinks into double-strands breaks

    NARCIS (Netherlands)

    K. Hanada (Katsuhiro); M. Budzowska (Magdalena); M. Modesti (Mauro); A. Maas (Alex); C. Wyman (Claire); J. Essers (Jeroen); R. Kanaar (Roland)

    2006-01-01

    textabstractRepair of interstrand crosslinks (ICLs) requires multiple-strand incisions to separate the two covalently attached strands of DNA. It is unclear how these incisions are generated. DNA double-strand breaks (DSBs) have been identified as intermediates in ICL repair, but enzymes responsible

  12. The stranding anomaly as population indicator: the case of harbour porpoise Phocoena phocoena in North-Western Europe.

    Science.gov (United States)

    Peltier, Helene; Baagøe, Hans J; Camphuysen, Kees C J; Czeck, Richard; Dabin, Willy; Daniel, Pierre; Deaville, Rob; Haelters, Jan; Jauniaux, Thierry; Jensen, Lasse F; Jepson, Paul D; Keijl, Guido O; Siebert, Ursula; Van Canneyt, Olivier; Ridoux, Vincent

    2013-01-01

    Ecological indicators for monitoring strategies are expected to combine three major characteristics: ecological significance, statistical credibility, and cost-effectiveness. Strategies based on stranding networks rank highly in cost-effectiveness, but their ecological significance and statistical credibility are disputed. Our present goal is to improve the value of stranding data as population indicator as part of monitoring strategies by constructing the spatial and temporal null hypothesis for strandings. The null hypothesis is defined as: small cetacean distribution and mortality are uniform in space and constant in time. We used a drift model to map stranding probabilities and predict stranding patterns of cetacean carcasses under H0 across the North Sea, the Channel and the Bay of Biscay, for the period 1990-2009. As the most common cetacean occurring in this area, we chose the harbour porpoise Phocoena phocoena for our modelling. The difference between these strandings expected under H0 and observed strandings is defined as the stranding anomaly. It constituted the stranding data series corrected for drift conditions. Seasonal decomposition of stranding anomaly suggested that drift conditions did not explain observed seasonal variations of porpoise strandings. Long-term stranding anomalies increased first in the southern North Sea, the Channel and Bay of Biscay coasts, and finally the eastern North Sea. The hypothesis of changes in porpoise distribution was consistent with local visual surveys, mostly SCANS surveys (1994 and 2005). This new indicator could be applied to cetacean populations across the world and more widely to marine megafauna.

  13. The stranding anomaly as population indicator: the case of harbour porpoise Phocoena phocoena in North-Western Europe.

    Directory of Open Access Journals (Sweden)

    Helene Peltier

    Full Text Available Ecological indicators for monitoring strategies are expected to combine three major characteristics: ecological significance, statistical credibility, and cost-effectiveness. Strategies based on stranding networks rank highly in cost-effectiveness, but their ecological significance and statistical credibility are disputed. Our present goal is to improve the value of stranding data as population indicator as part of monitoring strategies by constructing the spatial and temporal null hypothesis for strandings. The null hypothesis is defined as: small cetacean distribution and mortality are uniform in space and constant in time. We used a drift model to map stranding probabilities and predict stranding patterns of cetacean carcasses under H0 across the North Sea, the Channel and the Bay of Biscay, for the period 1990-2009. As the most common cetacean occurring in this area, we chose the harbour porpoise Phocoena phocoena for our modelling. The difference between these strandings expected under H0 and observed strandings is defined as the stranding anomaly. It constituted the stranding data series corrected for drift conditions. Seasonal decomposition of stranding anomaly suggested that drift conditions did not explain observed seasonal variations of porpoise strandings. Long-term stranding anomalies increased first in the southern North Sea, the Channel and Bay of Biscay coasts, and finally the eastern North Sea. The hypothesis of changes in porpoise distribution was consistent with local visual surveys, mostly SCANS surveys (1994 and 2005. This new indicator could be applied to cetacean populations across the world and more widely to marine megafauna.

  14. DMPD: Transcriptional signaling by double-stranded RNA: role of TLR3. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 15733829 Transcriptional signaling by double-stranded RNA: role of TLR3. Sen GC, Sa... signaling by double-stranded RNA: role of TLR3. PubmedID 15733829 Title Transcriptional signaling by double-stranded RNA: role

  15. 75 FR 28557 - Pre-Stressed Concrete Steel Wire Strand from the People's Republic of China: Final Affirmative...

    Science.gov (United States)

    2010-05-21

    ... International Trade Administration Pre-Stressed Concrete Steel Wire Strand from the People's Republic of China... countervailable subsidies are being provided to producers and exporters of pre-stressed concrete steel wire strand... Determination on October 27, 2009. See Pre-Stressed Concrete Steel Wire Strand from the People's Republic...

  16. Lead levels - blood

    Science.gov (United States)

    Blood lead levels ... A blood sample is needed. Most of the time blood is drawn from a vein located on the inside ... may be used to puncture the skin. The blood collects in a small glass tube called a ...

  17. Lead User Innovation

    DEFF Research Database (Denmark)

    Brem, Alexander; Larsen, Henry

    2015-01-01

    , deliver and capture the value of an innovatively new device together. From the perspective of the lead user, we show antecedents and effects of social interaction between organizational actors and the lead user on the development of social capital, especially trust and shared imagination. The second case......User innovation and especially the integration of lead users is a key topic in the innovation management literature of recent years. This paper contributes by providing a rare perspective into what easily could be seen as innovation failure, shown from two perspectives. We show how a lack of shared...... imagination hampers participation and kills innovation between interdependent stakeholders at the threshold between invention and innovation in practice. We present a first case in the fun-sport industry where an external lead user and diverse firm representatives in different functions fail to create...

  18. Double-strand break repair-adox: Restoration of suppressed double-strand break repair during mitosis induces genomic instability.

    Science.gov (United States)

    Terasawa, Masahiro; Shinohara, Akira; Shinohara, Miki

    2014-12-01

    Double-strand breaks (DSBs) are one of the severest types of DNA damage. Unrepaired DSBs easily induce cell death and chromosome aberrations. To maintain genomic stability, cells have checkpoint and DSB repair systems to respond to DNA damage throughout most of the cell cycle. The failure of this process often results in apoptosis or genomic instability, such as aneuploidy, deletion, or translocation. Therefore, DSB repair is essential for maintenance of genomic stability. During mitosis, however, cells seem to suppress the DNA damage response and proceed to the next G1 phase, even if there are unrepaired DSBs. The biological significance of this suppression is not known. In this review, we summarize recent studies of mitotic DSB repair and discuss the mechanisms of suppression of DSB repair during mitosis. DSB repair, which maintains genomic integrity in other phases of the cell cycle, is rather toxic to cells during mitosis, often resulting in chromosome missegregation and aberration. Cells have multiple safeguards to prevent genomic instability during mitosis: inhibition of 53BP1 or BRCA1 localization to DSB sites, which is important to promote non-homologous end joining or homologous recombination, respectively, and also modulation of the non-homologous end joining core complex to inhibit DSB repair. We discuss how DSBs during mitosis are toxic and the multiple safeguard systems that suppress genomic instability.

  19. DNA Double Strand Break Response and Limited Repair Capacity in Mouse Elongated Spermatids

    Directory of Open Access Journals (Sweden)

    Emad A. Ahmed

    2015-12-01

    Full Text Available Spermatids are extremely sensitive to genotoxic exposures since during spermiogenesis only error-prone non homologous end joining (NHEJ repair pathways are available. Hence, genomic damage may accumulate in sperm and be transmitted to the zygote. Indirect, delayed DNA fragmentation and lesions associated with apoptotic-like processes have been observed during spermatid elongation, 27 days after irradiation. The proliferating spermatogonia and early meiotic prophase cells have been suggested to retain a memory of a radiation insult leading later to this delayed fragmentation. Here, we used meiotic spread preparations to localize phosphorylate histone H2 variant (γ-H2AX foci marking DNA double strand breaks (DSBs in elongated spermatids. This technique enabled us to determine the background level of DSB foci in elongated spermatids of RAD54/RAD54B double knockout (dko mice, severe combined immunodeficiency SCID mice, and poly adenosine diphosphate (ADP-ribose polymerase 1 (PARP1 inhibitor (DPQ-treated mice to compare them with the appropriate wild type controls. The repair kinetics data and the protein expression patterns observed indicate that the conventional NHEJ repair pathway is not available for elongated spermatids to repair the programmed and the IR-induced DSBs, reflecting the limited repair capacity of these cells. However, although elongated spermatids express the proteins of the alternative NHEJ, PARP1-inhibition had no effect on the repair kinetics after IR, suggesting that DNA damage may be passed onto sperm. Finally, our genetic mutant analysis suggests that an incomplete or defective meiotic recombinational repair of Spo11-induced DSBs may lead to a carry-over of the DSB damage or induce a delayed nuclear fragmentation during the sensitive programmed chromatin remodeling occurring in elongated spermatids.

  20. Lead-210 contamination

    Energy Technology Data Exchange (ETDEWEB)

    Gray, P. [Peter Gray and Associates, Tulsa, OK (United States)

    1997-12-31

    Nearly all scrap dealers, smelters and other recyclers routinely monitor for radioactivity in shipments entering their facility. These sensitive radiation gate monitors easily detect radium-226 and most other radioactive nuclides. However, the type of detector normally used, sodium iodide scintillation crystals, will not detect the low energy gamma radiation emitted by lead-210 and its progeny. Since lead-210 is a common radioactive contaminant in certain industries, contaminated scrap metal from these industries may avoid detection at the recycler. Lead-210 is a decay product of radon-222 which is produced in small concentrations with natural gas. As the natural gas liquids, particularly ethane and propane, are separated from the natural gas, the radon concentrates in the ethane/propane fraction. The natural gas industry, particularly gas processing facilities and industries using ethane and propane as feed stocks can be significantly contaminated with the radon decay products, especially lead-210, bismuth-210 and polonium-210. Unless the scrap metal is decontaminated before sending to the recycler, the lead-210 contaminated scrap may be processed, resulting in some degree of radioactive contamination of the recycling facilities. Methods of detecting the low energy gamma radiation associated with lead-210 include the pancake G-M detector and the thin crystal-thin window scintillation detector.

  1. Enzyme-free colorimetric detection systems based on the DNA strand displacement competition reaction

    DEFF Research Database (Denmark)

    Zhang, Zhao; Birkedal, Victoria; Gothelf, Kurt Vesterager

    2016-01-01

    The strand displacement competition assay is based on the dynamic equilibrium of the competitive hybridization of two oligonucleotides (A and B) to a third oligonucleotide (S). In the presence of an analyte that binds to a specific affinity-moiety conjugated to strand B, the equilibrium shifts, w...... G-quadruplex DNAzyme for colorimetric readout of the detection of streptavidin by the naked eye. Finally, we integrate the whole G-quadruplex DNAzyme system in a single DNA strand and show that it is applicable to colorimetric detection....

  2. The effects of strand transposition on the stiffness matrix of superconductor core elements

    Energy Technology Data Exchange (ETDEWEB)

    Schnefler, B.; Gori, R.

    1988-03-01

    The axial and torsional components of the stiffness matrix of superconductor core elements are derived taking into account the effects of the wrapping of superconductor strands around the internal insulating strip. It is shown that the inclination of the strands referred to the longitudinal axis of the superconductor produces a reduction of the axial stiffness and a considerable increase in torsional stiffness. Examples relating to superconductors proposed for the NET Toroidal Field Coil are shown. In that instance the strand transposition is carried out by roebling.

  3. Long-Term Seasonal and Interannual Patterns of Marine Mammal Strandings in Subtropical Western South Atlantic

    Science.gov (United States)

    Prado, Jonatas H. F.; Mattos, Paulo H.; Silva, Kleber G.; Secchi, Eduardo R.

    2016-01-01

    Understanding temporal patterns of marine mammal occurrence is useful for establishing conservation strategies. We used a 38 yr-long dataset spanning 1976 to 2013 to describe temporal patterns and trends in marine mammal strandings along a subtropical stretch of the east coast of South America. This region is influenced by a transitional zone between tropical and temperate waters and is considered an important fishing ground off Brazil. Generalized Additive Models were used to evaluate the temporal stranding patterns of the most frequently stranded species. Forty species were documented in 12,540 stranding events. Franciscana (n = 4,574), South American fur seal, (n = 3,419), South American sea lion (n = 2,049), bottlenose dolphins (n = 293) and subantarctic fur seal (n = 219) were the most frequently stranded marine mammals. The seasonality of strandings of franciscana and bottlenose dolphin coincided with periods of higher fishing effort and strandings of South American and subantarctic fur seals with post-reproductive dispersal. For South American sea lion the seasonality of strandings is associated with both fishing effort and post-reproductive dispersal. Some clear seasonal patterns were associated with occurrence of cold- (e.g. subantarctic fur seal) and warm-water (e.g. rough-toothed dolphin) species in winter and summer, respectively. Inter-annual increases in stranding rate were observed for franciscana and South American fur seal and these are likely related to increased fishing effort and population growth, respectively. For subantarctic fur seal the stranding rate showed a slight decline while for bottlenose dolphin it remained steady. No significant year to year variation in stranding rate was observed for South American sea lion. The slight decrease in frequency of temperate/polar marine mammals and the increased occurrence of subtropical/tropical species since the late 1990s might be associated with environmental changes linked to climate change

  4. DC measurement of electrical contacts between strands in superconducting cables for the LHC main magnets

    CERN Document Server

    Richter, D; Depond, J M; Leroy, D; Oberli, L R

    1996-01-01

    In the LHC main magnets, using Rutherford type cable, the eddy current loss and dynamic magnetic field error depend largely on the electrical resistance between crossing (Rc) and adjacent (Ra) strands. Cables made of strands with pre-selected coatings have been studied at low temperature using a DC electrical method. The significance of the inter-strand contact is explained. The properties of resistive barriers, the DC method used for the resistance measurement on the cable, and sample preparation are described. Finally the resistances are presented under various conditions, and the effect is discussed that the cable treatment has on the contact resistance.

  5. Validation of 3D RANS-SA Calculations on Strand/Cartesian Meshes

    Science.gov (United States)

    2014-01-07

    and scalability are presented in Section IV. With more complex 3D geometries the traditional strand grid generation approach used today can break down...from a from a solid model, such as geometry from a modern CAD system, around geometric nodes and edges. The new multi-strand strand mesh generation...rely on a reconstruction upwind formula for the numerical flux based on the approximate Riemann solver of Roe,16 F̂ = 1 2 (F(QR) + F(QL))− 1 2 |A(QR

  6. A kinetic analysis of strand breaks on large DNA induced by cigarette smoke extract

    Science.gov (United States)

    Kurita, Hirofumi; Takata, Tatsuya; Yasuda, Hachiro; Takashima, Kazunori; Mizuno, Akira

    2010-06-01

    We report a kinetic analysis of strand breakages on large DNA molecules induced by cigarette smoke extract (CSE), an extract of soluble cigarette smoke components. Previously, this DNA damage was analyzed by agarose gel electrophoresis, whereas we used fluorescence to kinetically analyze damage to individual DNA molecules. CSE caused a marked change in length of DNA molecules. The rate of CSE-induced double-strand breakage on large random-coiled DNA molecules was determined using a simple theoretical model, allowing the facile estimation of the rate of double-strand breaks on large DNA molecules.

  7. Facile synthesis of Graphene Oxide/Double-stranded DNA composite liquid crystals and Hydrogels

    Indian Academy of Sciences (India)

    Rajendra Kurapati; Ashok M Raichur; U Venkateswara Reddy; N Suryaprakash

    2016-03-01

    Investigation of the interactions between graphene oxide (GO) and biomolecules is very crucialfor the development of biomedical applications based on GO. This study reports the first observation of thespontaneous formation of self-assembled liquid crystals and three-dimensional hydrogels of graphene oxidewith double-stranded DNA by simple mixing in an aqueous buffer media without unwinding double-strandedDNA to single-stranded DNA. The GO/dsDNA hydrogels have shown controlled porosity by changing the concentration of the components. The strong binding between dsDNA and graphene is proved by Ramanspectroscopy

  8. Repair of radiation-induced DNA double-strand breaks in isolated nuclei of Physarum polycephalum

    Energy Technology Data Exchange (ETDEWEB)

    Brewer, E.N.

    1979-08-01

    Radiation-induced DNA double-strand breaks are rejoined in homogenates and isolated nuclei of Physarum polycephalum. In agreement with results obtained previously for intact plasmodia, double-strand breaks are less extensively repaired in nuclei isolated from S-phase, as compared to G/sub 2/-phase, cultures. A corresponding propensity of DNA present in unirradiated nuclei of S-phase plasmodia toward breakage during incubation in vitro was observed. Repair of putative single-strand breaks, as ascertained from alkaline sucrose density-gradient centrifugation analysis, was not observed. The possible relationships between these phenomena are discussed.

  9. Recent Progress in Application of Internal Oxidation Technique in Nb3Sn Strands

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Xingchen [Fermilab; Peng, Xuan [Hyper Tech Research Inc.; Sumption, Michael [Ohio State U.; Collings, E. W. [Ohio State U.

    2016-10-13

    The internal oxidation technique can generate ZrO2 nano particles in Nb3Sn strands, which markedly refine the Nb3Sn grain size and boost the high-field critical current density (Jc). This article summarizes recent efforts on implementing this technique in practical Nb3Sn wires and adding Ti as a dopant. It is demonstrated that this technique can be readily incorporated into the present Nb3Sn conductor manufacturing technology. Powder-in-tube (PIT) strands with fine subelements (~25 µm) based on this technique were successfully fabricated, and proper heat treatments for oxygen transfer were explored. Future work for producing strands ready for applications is proposed.

  10. Stenting of the Portal Vein Combined with Different Numbers of Iodine-125 Seed Strands: Dosimetric Analyses

    Directory of Open Access Journals (Sweden)

    Li-Hong Yao

    2017-01-01

    Conclusions: A portal-vein stent combined with a single 125I seed strand could not meet dosimetry requirements. For a stent combined with two 125I seed strands, when the PD was 105 Gy and seed activity was 0.7 mCi, the dose distribution could satisfy dosimetry requirements. For a stent combined with three 125I seed strands, if the PD was 105, 125, or 145 Gy, the recommended seed activities were 0.5, 0.5, and 0.6 mCi, respectively.

  11. Asymmetric Quantum Transport in a Double-Stranded Kronig-Penney Model

    Science.gov (United States)

    Cheon, Taksu; Poghosyan, Sergey S.

    2015-06-01

    We introduce a double-stranded Kronig-Penney model and analyze its transport properties. Asymmetric fluxes between two strands with suddenly alternating localization patterns are found as the energy is varied. The zero-size limit of the internal lines connecting two strands is examined using quantum graph vertices with four edges. We also consider a two-dimensional Kronig-Penney lattice with two types of alternating layer with δ and δ' connections, and show the existence of energy bands in which the quantum flux can flow only in selected directions.

  12. Long-Term Seasonal and Interannual Patterns of Marine Mammal Strandings in Subtropical Western South Atlantic.

    Science.gov (United States)

    Prado, Jonatas H F; Mattos, Paulo H; Silva, Kleber G; Secchi, Eduardo R

    2016-01-01

    Understanding temporal patterns of marine mammal occurrence is useful for establishing conservation strategies. We used a 38 yr-long dataset spanning 1976 to 2013 to describe temporal patterns and trends in marine mammal strandings along a subtropical stretch of the east coast of South America. This region is influenced by a transitional zone between tropical and temperate waters and is considered an important fishing ground off Brazil. Generalized Additive Models were used to evaluate the temporal stranding patterns of the most frequently stranded species. Forty species were documented in 12,540 stranding events. Franciscana (n = 4,574), South American fur seal, (n = 3,419), South American sea lion (n = 2,049), bottlenose dolphins (n = 293) and subantarctic fur seal (n = 219) were the most frequently stranded marine mammals. The seasonality of strandings of franciscana and bottlenose dolphin coincided with periods of higher fishing effort and strandings of South American and subantarctic fur seals with post-reproductive dispersal. For South American sea lion the seasonality of strandings is associated with both fishing effort and post-reproductive dispersal. Some clear seasonal patterns were associated with occurrence of cold- (e.g. subantarctic fur seal) and warm-water (e.g. rough-toothed dolphin) species in winter and summer, respectively. Inter-annual increases in stranding rate were observed for franciscana and South American fur seal and these are likely related to increased fishing effort and population growth, respectively. For subantarctic fur seal the stranding rate showed a slight decline while for bottlenose dolphin it remained steady. No significant year to year variation in stranding rate was observed for South American sea lion. The slight decrease in frequency of temperate/polar marine mammals and the increased occurrence of subtropical/tropical species since the late 1990s might be associated with environmental changes linked to climate change

  13. Summary of recorded cetacean strandings in the Commonwealth of the Northern Mariana Islands

    Directory of Open Access Journals (Sweden)

    Tenorio, M.C.

    2012-05-01

    Full Text Available Documented strandings in the Commonwealth of the Northern Mariana Islands over the past 17 years are reviewed with recorded autopsy information provided. Most of the strandings occurred on the island of Saipan, although two whales were noted to have stranded during this period on Tinian, one identified as Balaenoptera edeni, the Byrdes whale, while the other was not identified. The planned expansion of military activities in the Marianas Archipelago, particularly the use of sonar and the potential impact on cetaceans, is noted.

  14. Long-Term Seasonal and Interannual Patterns of Marine Mammal Strandings in Subtropical Western South Atlantic.

    Directory of Open Access Journals (Sweden)

    Jonatas H F Prado

    Full Text Available Understanding temporal patterns of marine mammal occurrence is useful for establishing conservation strategies. We used a 38 yr-long dataset spanning 1976 to 2013 to describe temporal patterns and trends in marine mammal strandings along a subtropical stretch of the east coast of South America. This region is influenced by a transitional zone between tropical and temperate waters and is considered an important fishing ground off Brazil. Generalized Additive Models were used to evaluate the temporal stranding patterns of the most frequently stranded species. Forty species were documented in 12,540 stranding events. Franciscana (n = 4,574, South American fur seal, (n = 3,419, South American sea lion (n = 2,049, bottlenose dolphins (n = 293 and subantarctic fur seal (n = 219 were the most frequently stranded marine mammals. The seasonality of strandings of franciscana and bottlenose dolphin coincided with periods of higher fishing effort and strandings of South American and subantarctic fur seals with post-reproductive dispersal. For South American sea lion the seasonality of strandings is associated with both fishing effort and post-reproductive dispersal. Some clear seasonal patterns were associated with occurrence of cold- (e.g. subantarctic fur seal and warm-water (e.g. rough-toothed dolphin species in winter and summer, respectively. Inter-annual increases in stranding rate were observed for franciscana and South American fur seal and these are likely related to increased fishing effort and population growth, respectively. For subantarctic fur seal the stranding rate showed a slight decline while for bottlenose dolphin it remained steady. No significant year to year variation in stranding rate was observed for South American sea lion. The slight decrease in frequency of temperate/polar marine mammals and the increased occurrence of subtropical/tropical species since the late 1990s might be associated with environmental changes linked to

  15. Review of the Effects of Offshore Seismic Surveys in Cetaceans: Are Mass Strandings a Possibility?

    Science.gov (United States)

    Castellote, Manuel; Llorens, Carlos

    2016-01-01

    Displacement of cetaceans is commonly reported during offshore seismic surveys. Speculation concerning possible links between seismic survey noise and cetacean strandings is available for a dozen events but without convincing causal evidence. This lack of evidence should not be considered conclusive but rather as reflecting the absence of a comprehensive analysis of the circumstances. Current mitigation guidelines are inadequate for long-range effects such as displacements and the potential for strandings. This review presents the available information for ten documented strandings that were possibly linked to seismic surveys and recommends initial measures and actions to further evaluate this potential link.

  16. Polynomial Invariants for Arbitrary Rank D Weakly-Colored Stranded Graphs

    Science.gov (United States)

    Avohou, Remi Cocou

    2016-03-01

    Polynomials on stranded graphs are higher dimensional generalization of Tutte and Bollobás-Riordan polynomials [Math. Ann. 323 (2002), 81-96]. Here, we deepen the analysis of the polynomial invariant defined on rank 3 weakly-colored stranded graphs introduced in arXiv:1301.1987. We successfully find in dimension D≥3 a modified Euler characteristic with D-2 parameters. Using this modified invariant, we extend the rank 3 weakly-colored graph polynomial, and its main properties, on rank 4 and then on arbitrary rank D weakly-colored stranded graphs.

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

    Energy Technology Data Exchange (ETDEWEB)

    Martovetsky, N N

    2007-12-06

    ITER TF coils will see a significant longitudinal magnetic field in the event of the plasma disruption. This abrupt change of magnetic fields results in the appearance of an additional electrical field in the strands. The mechanism of this electrical field is the induced currents that expel the flux from the strands. This effect was known since the late 1970's [1-3] and most of the details necessary for the analyses given in this report are presented in [4]. Let's assume for simplicity a zero transport current in the strand. When a longitudinal pulsed field is applied, the outer filaments will carry an induced current repelling the change of flux. The current density of this current is 'critical' in the simplification of Bean's critical state model, where superconducting transition is represented as j=j{sub c} at any non-zero electrical field and zero where the electrical field has not penetrated. In reality, since the current density is roughly logarithmic with the electrical field, E=E{sub c}*exp[(j-j{sub c})/jo], Bean's model is just a simplification, and current density is slightly nonuniform in the outer filament and more so for the interior strands. The inner portion of the filaments will carry a current of the opposite sign. Even in the Bean's model it is not uniform, but the assumption that it is uniform and less than critical simplifies mathematics significantly and does not deviate far from the real current density distribution. In certain circumstances, the average electrical field in the strands will be high enough to exceed the take-off electrical field averaged across the cross section. In this case, the multifilamentary strand will become unstable and will experience transition to the normal state. With zero transport current, it will eventually recover, of course. This phenomenon is analogous to the flux jump. If the strand carries a transport current, the situation becomes more complicated. If it goes unstable and

  18. Comparative Genotoxicity of Cadmium and Lead in Earthworm Coelomocytes

    Directory of Open Access Journals (Sweden)

    Ptumporn Muangphra

    2011-01-01

    Full Text Available To determine genotoxicity to coelomocytes, Pheretima peguana earthworms were exposed in filter paper studies to cadmium (Cd and lead (Pb for 48 h, at concentrations less than the LC10—Cd: 0.09, 0.19, 0.38, 0.75, and 1.50 μg cm−2; Pb: 1.65, 3.29, 6.58, 13.16, and 26.32 μg cm−2. For Cd at 0.75 μg cm−2, in the micronucleus test (detects chromosomal aberrations, significant increases (<.05 in micronuclei and binucleate cells were observed, and in the comet assay (detects DNA single-strand breaks, tail DNA% was significantly increased. Lead was less toxic with minimal effects on DNA, but the binucleates were significantly increased by Pb at 3.29 μg cm−2. This study shows that Cd is more acutely toxic and sublethally genotoxic than Pb to P. peguana. Cadmium caused chromosomal aberrations and DNA single-strand breaks at 45% of the LC10 concentration. Lead, in contrast, did not induce DNA damage but caused cytokinesis defects.

  19. Magnesium Diboride Current Leads

    Science.gov (United States)

    Panek, John

    2010-01-01

    A recently discovered superconductor, magnesium diboride (MgB2), can be used to fabricate conducting leads used in cryogenic applications. Dis covered to be superconducting in 2001, MgB2 has the advantage of remaining superconducting at higher temperatures than the previously used material, NbTi. The purpose of these leads is to provide 2 A of electricity to motors located in a 1.3 K environment. The providing environment is a relatively warm 17 K. Requirements for these leads are to survive temperature fluctuations in the 5 K and 11 K heat sinks, and not conduct excessive heat into the 1.3 K environment. Test data showed that each lead in the assembly could conduct 5 A at 4 K, which, when scaled to 17 K, still provided more than the required 2 A. The lead assembly consists of 12 steelclad MgB2 wires, a tensioned Kevlar support, a thermal heat sink interface at 4 K, and base plates. The wires are soldered to heavy copper leads at the 17 K end, and to thin copper-clad NbTi leads at the 1.3 K end. The leads were designed, fabricated, and tested at the Forschungszentrum Karlsruhe - Institut foer Technische Physik before inclusion in Goddard's XRS (X-Ray Spectrometer) instrument onboard the Astro-E2 spacecraft. A key factor is that MgB2 remains superconducting up to 30 K, which means that it does not introduce joule heating as a resistive wire would. Because the required temperature ranges are 1.3-17 K, this provides a large margin of safety. Previous designs lost superconductivity at around 8 K. The disadvantage to MgB2 is that it is a brittle ceramic, and making thin wires from it is challenging. The solution was to encase the leads in thin steel tubes for strength. Previous designs were so brittle as to risk instrument survival. MgB2 leads can be used in any cryogenic application where small currents need to be conducted at below 30 K. Because previous designs would superconduct only at up to 8 K, this new design would be ideal for the 8-30 K range.

  20. Global organization of a positive-strand RNA virus genome.

    Directory of Open Access Journals (Sweden)

    Baodong Wu

    Full Text Available The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2'-hydroxyl acylation analysed by primer extension (i.e. SHAPE, which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context.

  1. Regulation of DNA double-strand break repair pathway choice

    Institute of Scientific and Technical Information of China (English)

    Meena Shrivastav; Leyma P De Haro; Jac A Nickoloff

    2008-01-01

    DNA double-strand breaks (DSBs) are critical lesions that can result in cell death or a wide variety of genetic alterations including large- or small-scale deletions, loss of heterozygosity, translocations, and chromosome loss. DSBs are repaired by non-homologous end-joining (NHEJ) and homologous recombination (HR), and defects in these pathways cause genome instability and promote tumorigenesis. DSBs arise from endogenous sources includ-ing reactive oxygen species generated during cellular metabolism, collapsed replication forks, and nucleases, and from exogenous sources including ionizing radiation and chemicals that directly or indirectly damage DNA and are commonly used in cancer therapy. The DSB repair pathways appear to compete for DSBs, but the balance between them differs widely among species, between different cell types of a single species, and during different cell cycle phases of a single cell type. Here we review the regulatory factors that regulate DSB repair by NHEJ and HR in yeast and higher eukaryotes. These factors include regulated expression and phosphorylation of repair proteins, chromatin modulation of repair factor accessibility, and the availability of homologous repair templates. While most DSB repair proteins appear to function exclusively in NHEJ or HR, a number of proteins influence both pathways, including the MRE11/RAD50/NBS1 (XRS2) complex, BRCA1, histone H2AX, PARP-1, RAD18, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and ATM. DNA-PKcs plays a role in mammalian NHEJ, but it also influences HR through a complex regulatory network that may involve crosstalk with ATM, and the regulation of at least 12 proteins involved in HR that are phosphorylated by DNA-PKcs and/or ATM.

  2. Study of Interaction between Red-tide Toxin, Domoic Acid and Double -stranded DNA by Capillary Zone Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    Da Zhi LI; Xin Ya HE; Hui WANG; Li SUN; Bing Cheng LIN

    2004-01-01

    The interactions between amnesic red-tide toxin, domoic acid (DA) and 14mer double-stranded DNA (dsDNA with three kinds of sequences) were studied by capillary zone electrophoresis (CZE). For the dsDNA with a sequence of 5'-CCCCCTATACCCGC-3', the amount of free dsDNA decreases with the increase of added DA; and the signal of DA-dsDNA complex was observed. Meanwhile, the other two dsDNAs, 5'-(C)12GC-3' and 5'-(AT)7-3', the existence of DA could not lead to the change of dsDNA signal and indicated that there is no interaction between DA and these two dsDNAs.

  3. Mechanisms of a novel anticancer therapeutic strategy involving atmospheric pressure plasma-mediated apoptosis and DNA strand break formation.

    Science.gov (United States)

    Chung, Woo-Hyun

    2016-01-01

    Atmospheric pressure plasma has been developed for a variety of biomedical applications due to its chemically reactive components. Recently, the plasma has emerged as a promising novel cancer therapy based on its ability to selectively ablate cancer cells while leaving normal cells essentially unaffected. The therapeutic effect of plasma is attributed to intracellular generation of reactive oxygen/nitrogen species (ROS/RNS) leading to mitochondria-mediated apoptosis and to activation of the DNA damage checkpoint signaling pathway via severe DNA strand break formation. However, the biochemical mechanisms responsible for appropriate activation of these physiological events and which pathway is more crucial for plasma-mediated cytotoxicity have not been clarified. Understanding the molecular link between ROS/RNS-mediated apoptosis and DNA damage-involved chromosome instability is critical for the development of more efficacious therapeutic strategies for selective killing of diverse cancer cells.

  4. Cationic lipids and cationic ligands induce DNA helix denaturation: detection of single stranded regions by KMnO4 probing.

    Science.gov (United States)

    Prasad, T K; Gopal, Vijaya; Rao, N Madhusudhana

    2003-09-25

    Cationic lipids and cationic polymers are widely used in gene delivery. Using 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) as a cationic lipid, we have investigated the stability of the DNA in DOTAP:DNA complexes by probing with potassium permanganate (KMnO4). Interestingly, thymidines followed by a purine showed higher susceptibility to cationic ligand-mediated melting. Similar studies performed with other water-soluble cationic ligands such as polylysine, protamine sulfate and polyethyleneimine also demonstrated melting of the DNA but with variations. Small cations such as spermine and spermidine and a cationic detergent, cetyl trimethylammonium bromide, also rendered the DNA susceptible to modification by KMnO4. The data presented here provide direct proof for melting of DNA upon interaction with cationic lipids. Structural changes subsequent to binding of cationic lipids/ligands to DNA may lead to instability and formation of DNA bubbles in double-stranded DNA.

  5. Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double strand break ends

    OpenAIRE

    Zhu, Zhu; Chung, Woo-Hyun; Shim, Eun Yong; Lee, Sang Eun; Ira, Grzegorz

    2008-01-01

    Formation of single-strand DNA (ssDNA) tails at a double-strand break (DSB) is a key step in homologous recombination and DNA damage signaling. The enzyme(s) producing ssDNA at DSBs in eukaryotes remains unknown. We monitored 5’-strand resection at inducible DSB ends and identified proteins required for two stages of resection: initiation and long-range 5’-strand resection. The Mre11-Rad50-Xrs2 complex (MRX) initiates 5’ degradation, whereas Sgs1 and Dna2 degrade 5’-strands exposing long 3’-s...

  6. Leading healthcare in complexity.

    Science.gov (United States)

    Cohn, Jeffrey

    2014-12-01

    Healthcare institutions and providers are in complexity. Networks of interconnections from relationships and technology create conditions in which interdependencies and non-linear dynamics lead to surprising, unpredictable outcomes. Previous effective approaches to leadership, focusing on top-down bureaucratic methods, are no longer effective. Leading in complexity requires leaders to accept the complexity, create an adaptive space in which innovation and creativity can flourish and then integrate the successful practices that emerge into the formal organizational structure. Several methods for doing adaptive space work will be discussed. Readers will be able to contrast traditional leadership approaches with leading in complexity. They will learn new behaviours that are required of complexity leaders, along with challenges they will face, often from other leaders within the organization.

  7. Strandings of Marine Mammals in Alabama from 16 Dec 1978 - 31 Dec 2015 (NODC Accession 0117461)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains information about marine mammal strandings documented in Alabama waters between 1978 and 2015. Data include identity, size, condition, sex, and...

  8. Non-Ideality and Kinetics of a Strand Displacement AND Gate

    CERN Document Server

    Svaneborg, Carsten; Rasmussen, Steen

    2012-01-01

    We perform a spatially resolved simulation study of an AND gate based on DNA strand displacement. DNA strands are modelled using a coarse-grained dynamic bonding model [C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012)]. We simulate the operation of the AND gate using several lengths of the toehold and the adjacent domains. Our simulations exhibit non-ideal behaviour as expected in an experimental implementation of strand displacement operations. We characterize this non-ideal behaviour in detail and characterize how the kinetic operation of the gate depends on the toehold and adjacent domain lengths. In particular, we observe that, while the final output state is reached with high fidelity when both input strands are present, our simulations exhibit numerous long-lived transition paths from the initial input state to the final output state.

  9. Single-strand conformation polymorphism analysis using capillary array electrophoresis for large-scale mutation detection.

    Science.gov (United States)

    Larsen, Lars Allan; Jespersgaard, Cathrine; Andersen, Paal Skytt

    2007-01-01

    This protocol describes capillary array electrophoresis single-strand conformation polymorphism (CAE-SSCP), a screening method for detection of unknown and previously identified mutations. The method detects 98% of mutations in a sample material and can be applied to any organism where the goal is to determine genetic variation. This protocol describes how to screen for mutations in 192 singleplex or up to 768 multiplex samples over 3 days. The protocol is based on the principle of sequence-specific mobility of single-stranded DNA in a native polymer, and covers all stages in the procedure, from initial DNA purification to final CAE-SSCP data analysis, as follows: DNA is purified, followed by PCR amplification using fluorescent primers. After PCR amplification, double-stranded DNA is heat-denatured to separate the strands and subsequently cooled on ice to avoid reannealing. Finally, samples are analyzed by capillary electrophoresis and appropriate analysis software.

  10. Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

    Science.gov (United States)

    Thubagere, Anupama J.; Thachuk, Chris; Berleant, Joseph; Johnson, Robert F.; Ardelean, Diana A.; Cherry, Kevin M.; Qian, Lulu

    2017-02-01

    Biochemical circuits made of rationally designed DNA molecules are proofs of concept for embedding control within complex molecular environments. They hold promise for transforming the current technologies in chemistry, biology, medicine and material science by introducing programmable and responsive behaviour to diverse molecular systems. As the transformative power of a technology depends on its accessibility, two main challenges are an automated design process and simple experimental procedures. Here we demonstrate the use of circuit design software, combined with the use of unpurified strands and simplified experimental procedures, for creating a complex DNA strand displacement circuit that consists of 78 distinct species. We develop a systematic procedure for overcoming the challenges involved in using unpurified DNA strands. We also develop a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data. Our methods now enable even novice researchers to successfully design and construct complex DNA strand displacement circuits.

  11. Biocomposites from abaca strands and polypropylene. Part I: Evaluation of the tensile properties.

    Science.gov (United States)

    Vilaseca, Fabiola; Valadez-Gonzalez, Alex; Herrera-Franco, Pedro J; Pèlach, M Angels; López, Joan Pere; Mutjé, Pere

    2010-01-01

    In this paper, abaca strands were used as reinforcement of polypropylene matrix and their tensile mechanical properties were studied. It was found relevant increments on the tensile properties of the abaca strand-PP composites despite the lack of good adhesion at fiber-matrix interface. Afterwards, it was stated the influence of using maleated polypropylene (MAPP) as compatibilizer to promote the interaction between abaca strands and polypropylene. The intrinsic mechanical properties of the reinforcement were evaluated and used for modeling both the tensile strength and elastic modulus of the composites. For these cases, the compatibility factor for the ultimate tensile strength was deduced from the modified rule of mixtures. Additionally, the experimental fiber orientation coefficient was measured, allowing determining the interfacial shear strengths of the composites and the critical fiber length of the abaca strand reinforcement. The mechanical improvement was compared to that obtained for fiberglass-reinforced PP composites and evaluated under an economical and technical point of view.

  12. The stranding anomaly as population indicator: the case of Harbour Porpoise

    NARCIS (Netherlands)

    Peltier, H.; Baagøe, H.J.; Camphuysen, K.C.J.; Czeck, R.; Dabin, W.; Daniel, P.; Deaville, R.; Haelters, J.; Jauniaux, T.; Jensen, L.F.; Jepson, P.D.; Keijl, G.O.; Siebert, U.; Van Canneyt, O.; Ridoux, V.

    2013-01-01

    Ecological indicators for monitoring strategies are expected to combine three major characteristics: ecological significance, statistical credibility, and cost-effectiveness. Strategies based on stranding networks rank highly in cost-effectiveness, but their ecological significance and statistical c

  13. Bubble-bound state of triple-stranded DNA: Efimov physics in DNA with repulsion

    Science.gov (United States)

    Maji, Jaya; Seno, Flavio; Trovato, Antonio; Bhattacharjee, Somendra M.

    2017-07-01

    The presence of a thermodynamic phase of a three-stranded DNA, namely, a mixed phase of bubbles of two bound strands and a single one, is established for large dimensions (d≥slant 5 ) by using exact real space renormalization group transformations and exact computations of specific heat for finite length chains. Similar exact computations for the fractal Sierpinski gasket of dimension d  <  2 establish the stability of the phase in the presence of a repulsive three chain interaction. Although, for d  <  2, cooperativity factors for bubbles or noncrossing conditions are needed for the melting transition, the mixed phase may exist even in absence of those. In contrast to the Efimov DNA, where three strands are bound though no two are bound, the mixed phase appears at temperatures less than the two chain melting temperature. Both the Efimov-DNA and the mixed phase are formed essentially due to the strand exchange mechanism.

  14. Formation of the triple-stranded polynucleotide helix, poly(A.A.U).

    Science.gov (United States)

    Broitman, S L; Im, D D; Fresco, J R

    1987-08-01

    A polynucleotide helical structure containing two strands of poly(A) and one of poly(U) is reported. As shown by spectroscopic observations, the complex only forms when the poly(A) strands are of Mr between 9000 and 50,000 (degree of polymerization congruent to 28-150), whereas the size of the poly(U) strand has no effect. This limitation may explain why poly(A.A.U) was not seen in previous investigations. The potential of the poly(A) tails of mRNA for formation of this triple helix and of A.A.U or/and A.A.T triplet formation to contribute to the binding of specific RNA strands to gene-encoding nucleic acid double helices are noted.

  15. Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins.

    Science.gov (United States)

    Vendome, Jeremie; Posy, Shoshana; Jin, Xiangshu; Bahna, Fabiana; Ahlsen, Goran; Shapiro, Lawrence; Honig, Barry

    2011-06-01

    Cell adhesion by classical cadherins is mediated by dimerization of their EC1 domains through the 'swapping' of N-terminal β-strands. We use molecular simulations, measurements of binding affinities and X-ray crystallography to provide a detailed picture of the structural and energetic factors that control the adhesive dimerization of cadherins. We show that strand swapping in EC1 is driven by conformational strain in cadherin monomers that arises from the anchoring of their short N-terminal strand at one end by the conserved Trp2 and at the other by ligation to Ca(2+) ions. We also demonstrate that a conserved proline-proline motif functions to avoid the formation of an overly tight interface where affinity differences between different cadherins, crucial at the cellular level, are lost. We use these findings to design site-directed mutations that transform a monomeric EC2-EC3 domain cadherin construct into a strand-swapped dimer.

  16. A New Quaternary Strand of the Karakoram Fault System, Ladakh Himalayas

    Science.gov (United States)

    Bohon, W.; Hodges, K.; Arrowsmith, R.; Tripathy, A.

    2009-12-01

    The NW-SE striking, dextral Karakoram fault system stretches for more than 1200 km from the Pamirs of Central Asia at least as far southeast as the Kailas area of Tibet. Estimates for the total lateral displacement along the fault system range from 150-1000 km, and estimated Quaternary rates of slip range from 1 to 30 mm/yr. In the Ladakh region of NW India (~ 33°28’N, 78°45’E), the fault system expresses as northern and southern strands bounding the Pangong Range. Studies of ductile deformation fabrics along these strands suggest that slip began in the Miocene, and Brown et al. (2002) documented Quaternary right-lateral slip along the northern strand at ~4 mm/yr on the basis of offset geomorphic features. The lack of documented Quaternary offset along the southern strand has led most researchers to assume that Quaternary slip on the Karakoram fault system in this region was partitioned exclusively to the northern strand. Our summer 2009 field work in the Pangong Range and adjacent Nubra Valley provides the first documentation of significant Quaternary activity along the southern strand. In the valley between the villages of Tangste (34°01’ N, 78°10’ E) and Durbuk (34°06’ N, 78°07’), the fault is visible high on the northeastern mountain side as a break in slope with offset Quaternary paleosurfaces and beheaded and offset stream channels, the largest of which have been displaced by as much as 250 m. Field mapping north of Durbuk, near the town of Tangyar (34°15’N, 77°52’E), shows that the southern strand continues northwest and cuts across the landscape as a sinuous, continuous trace with shutter ridges, offset alluvial fan surfaces, and sag ponds developed along its length. In this region, the northern and southern strands are linked by a Quaternary, E-directed thrust fault that places high-grade metamorphic rocks over poorly consolidated Quaternary alluvium. The partitioning of dextral slip between two strands of the Karakoram system

  17. Survey of stranded gas and delivered costs to Europe of selected gas resources

    Science.gov (United States)

    Attanasi, E.D.; Freeman, P.A.

    2011-01-01

    Two important trends affecting the expected growth of global gas markets are (1) the shift by many industrialized countries from coal-fired electricity generation to the use of natural gas to generate electricity and (2) the industrialization of the heavily populated Asian countries of India and China. This paper surveys discovered gas in stranded conventional gas accumulations and presents estimates of the cost of developing and producing stranded gas in selected countries. Stranded gas is natural gas in discovered or identified fields that is not currently commercially producible for either physical or economic reasons. Published reserves of gas at the global level do not distinguish between volumes of gas in producing fields and volumes in nonproducing fields. Data on stranded gas reported here-that is the volumes, geographical distribution, and size distributions of stranded gas fields at the country and regional level-are based on the examination of individual-field data and represent a significant improvement in information available to industry and government decision makers. Globally, stranded gas is pervasive, but large volumes in large accumulations are concentrated in only a few areas. The cost component of the paper focuses on stranded conventional gas accumulations in Africa and South America that have the potential to augment supplies to Europe. The methods described for the computation of extraction and transport costs are innovative in that they use information on the sizes and geographical distribution of the identified stranded gas fields. The costs are based on industry data specific to the country and geologic basin where the stranded gas is located. Gas supplies to Europe can be increased significantly at competitive costs by the development of stranded gas. Net extraction costs of producing the identified gas depend critically on the natural-gas-liquids (NGLs) content, the prevailing prices of liquids, the size of the gas accumulation, and the

  18. Repair on the go: E. coli maintains a high proliferation rate while repairing a chronic DNA double-strand break.

    Directory of Open Access Journals (Sweden)

    Elise Darmon

    Full Text Available DNA damage checkpoints exist to promote cell survival and the faithful inheritance of genetic information. It is thought that one function of such checkpoints is to ensure that cell division does not occur before DNA damage is repaired. However, in unicellular organisms, rapid cell multiplication confers a powerful selective advantage, leading to a dilemma. Is the activation of a DNA damage checkpoint compatible with rapid cell multiplication? By uncoupling the initiation of DNA replication from cell division, the Escherichia coli cell cycle offers a solution to this dilemma. Here, we show that a DNA double-strand break, which occurs once per replication cycle, induces the SOS response. This SOS induction is needed for cell survival due to a requirement for an elevated level of expression of the RecA protein. Cell division is delayed, leading to an increase in average cell length but with no detectable consequence on mutagenesis and little effect on growth rate and viability. The increase in cell length caused by chronic DNA double-strand break repair comprises three components: two types of increase in the unit cell size, one independent of SfiA and SlmA, the other dependent of the presence of SfiA and the absence of SlmA, and a filamentation component that is dependent on the presence of either SfiA or SlmA. These results imply that chronic checkpoint induction in E. coli is compatible with rapid cell multiplication. Therefore, under conditions of chronic low-level DNA damage, the SOS checkpoint operates seamlessly in a cell cycle where the initiation of DNA replication is uncoupled from cell division.

  19. Herpesvirus infection with severe lymphoid necrosis affecting a beaked whale stranded in the Canary Islands.

    Science.gov (United States)

    Arbelo, Manuel; Sierra, Eva; Esperón, Fernando; Watanabe, Tatiane T N; Bellière, Edwige N; Espinosa de los Monteros, Antonio; Fernández, Antonio

    2010-04-01

    This report describes the pathologic findings in a single, adult female Cuvier's beaked whale Ziphius cavirostris stranded in the Canary Islands. The study indicated that this whale died with a severe, systemic, herpesviral infection and clearly exhibited lesions different from those of the fat and gas embolic syndrome described in beaked whale mass strandings associated with sonar exposure. This is the first report of a cetacean alphaherpesvirus infection of the lymphoid system in a beaked whale.

  20. Self-consisting modeling of entangled network strands and dangling ends

    DEFF Research Database (Denmark)

    Jensen, Mette Krog; Schieber, Jay D.; Khaliullin, Renat N.;

    2009-01-01

    of dangling ends and soluble structures. Energy dissipation is increased by adding a fraction of dangling ends, wDE, to the ensemble. We find that when wDE=0.6, G0 is about 75% lower than GN0, this suggests that the fraction of network strands, wNS=1-wDE, largely influences the plateau value at low...... frequencies. Soluble strands can also be added to the theory which is expected to increase energy dissipation further....

  1. Analysis of marine turtle strandings (Reptilia: Testudine occurring on coast of Bahia State, Brazil

    Directory of Open Access Journals (Sweden)

    Aline Lopes-Souza

    2015-09-01

    Full Text Available This study provides an analysis of the occurrence and the spatial and temporal distribution of marine turtle strandings found in the south of the State of Bahia. Data was collected between January 2006 and June 2008. This study covers an area of 220 km of the southern coast of Bahia State (northeastern Brazil, and spatial analyses were made considering data collected in three bases suported by Petrobras-Petróleo Brasileiro S/A distributed in the area. The records were sorted according to month and year, species, age group and sex. A total of 260 stranding were reported: 183 of Chelonia mydas (74.1%, the most frequent species. The highest number of strandings was recorded in Gamboa do Morro Base. Juveniles presented the highest densities, but no differences between adults and small juveniles were detected. Males were more frequently stranded in Gamboa do Morro Base, while females were more frequent in Ilhéus Base. An increase in the number of stranding between 2006 and 2008 was noted; moreover, the months with more records were January, February, March, October and December. The number of stranding events was discontinuously distributed in the study area. This study also demonstrated the usefulness of implement different strategies of recording marine turtle strandings: direct monitoring efforts (patrol in remote beaches and educational campaigns applied on beaches frequented by tourists. This study demonstrated that, despite spatial nearby, the three bases attend independent biological systems and show different stranding dynamics, thus different conservancy actions should be implemented in order to improve the knowledge on natural history of sea-turtles in the southern coast of Bahia State.

  2. Marine Mammal Strandings and Environmental Changes: A 15-Year Study in the St. Lawrence Ecosystem

    OpenAIRE

    Marie-Hélène Truchon; Lena Measures; Vincent L'Hérault; Jean-Claude Brêthes; Peter S Galbraith; Michel Harvey; Sylvie Lessard; Michel Starr; Nicolas Lecomte

    2013-01-01

    Understanding the effects of climatic variability on marine mammals is challenging due to the complexity of ecological interactions. We used general linear models to analyze a 15-year database documenting marine mammal strandings (1994-2008; n = 1,193) and nine environmental parameters known to affect marine mammal survival, from regional (sea ice) to continental scales (North Atlantic Oscillation, NAO). Stranding events were more frequent during summer and fall than other seasons, and have i...

  3. DNA Single-Strand Break Repair and Spinocerebellar Ataxia with Axonal Neuropathy-1

    OpenAIRE

    Caldecott, K. W.

    2007-01-01

    DNA single-strand breaks (SSBs) are the commonest DNA lesions arising spontaneously in cells, and if not repaired may block transcription or may be converted into potentially lethal/clastogenic DNA double-strand breaks (DSBs). Recently, evidence has emerged that defects in the rapid repair of SSBs preferentially impact the nervous system. In particular, spinocerebellar ataxia with axonal neuropathy (SCAN1) is a human disease that is associated with mutation of TDP1 (tyrosyl DNA phosphodiester...

  4. DNA single-strand break repair and spinocerebellar ataxia with axonal neuropathy-1

    OpenAIRE

    El-Khamisy, S.F.; Caldecott, K. W.

    2007-01-01

    DNA single-strand breaks (SSBs) are the commonest DNA lesions arising spontaneously in cells, and if not repaired may block transcription or may be converted into potentially lethal/clastogenic DNA double-strand breaks (DSBs). Recently, evidence has emerged that defects in the rapid repair of SSBs preferentially impact the nervous system. In particular, spinocerebellar ataxia with axonal neuropathy (SCAN1) is a human disease that is associated with mutation of TDP1 (tyrosyl DNA phosphodiester...

  5. Recognizing a Single Base in an Individual DNA Strand: A Step Toward Nanopore DNA Sequencing**

    Science.gov (United States)

    Ashkenasy, N.; Sánchez-Quesada, J.; Ghadiri, M. R.; Bayley, H.

    2007-01-01

    Functional supramolecular chemistry at the single-molecule level. Single strands of DNA can be captured inside α-hemolysin transmembrane pore protein to form single-species α-HL·DNA pseudorotaxanes. This process can be used to identify a single adenine nucleotide at a specific location on a strand of DNA by the characteristic reductions in the α-HL ion conductance. This study suggests that α-HL-mediated single-molecule DNA sequencing might be fundamentally feasible. PMID:15666419

  6. Recognizing a Single Base in an Individual DNA Strand: A Step Toward Nanopore DNA Sequencing**

    OpenAIRE

    Ashkenasy, N.; Sánchez-Quesada, J.; Ghadiri, M. R.; Bayley, H

    2005-01-01

    Functional supramolecular chemistry at the single-molecule level. Single strands of DNA can be captured inside α-hemolysin transmembrane pore protein to form single-species α-HL·DNA pseudorotaxanes. This process can be used to identify a single adenine nucleotide at a specific location on a strand of DNA by the characteristic reductions in the α-HL ion conductance. This study sug...

  7. Cascaded strand displacement for non-enzymatic target recycling amplification and label-free electronic detection of microRNA from tumor cells

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Kai; Dou, Baoting; Yang, Jianmei; Yuan, Ruo; Xiang, Yun, E-mail: yunatswu@swu.edu.cn

    2016-04-15

    The monitoring of microRNA (miRNA) expression levels is of great importance in cancer diagnosis. In the present work, based on two cascaded toehold-mediated strand displacement reactions (TSDRs), we have developed a label- and enzyme-free target recycling signal amplification approach for sensitive electronic detection of miRNA-21 from human breast cancer cells. The junction probes containing the locked G-quadruplex forming sequences are self-assembled on the senor surface. The presence of the target miRNA-21 initiates the first TSDR and results in the disassembly of the junction probes and the release of the active G-quadruplex forming sequences. Subsequently, the DNA fuel strand triggers the second TSDR and leads to cyclic reuse of the target miRNA-21. The cascaded TSDRs thus generate many active G-quadruplex forming sequences on the sensor surface, which associate with hemin to produce significantly amplified current response for sensitive detection of miRNA-21 at 1.15 fM. The sensor is also selective and can be employed to monitor miRNA-21 from human breast cancer cells. - Highlights: • Amplified and sensitive detection of microRNA from tumor cells is achieved. • Signal amplification is realized by two cascaded strand displacement reactions. • The developed sensor is selective and label-free without involving any enzymes.

  8. Crude oil as a stranding cause among loggerhead sea turtles (Caretta caretta) in the Canary Islands, Spain (1998-2011).

    Science.gov (United States)

    Camacho, María; Calabuig, Pascual; Luzardo, Octavio P; Boada, Luis D; Zumbado, Manuel; Orós, Jorge

    2013-07-01

    We report the number of strandings caused by crude oil among loggerhead turtles (Caretta caretta) in the Canary Islands between 1998 and 2011 and analyze the impact of the designation of the Canary Islands as a Particularly Sensitive Sea Area (PSSA) in 2005. Among 1,679 stranded loggerhead turtles, 52 turtles stranded due to crude oil (3.1%). The survival rate of the turtles stranded by crude oil was 88%. All turtles that died because of crude oil stranding had signs of ingestion of crude oil and lesions, included esophageal impaction, necrotizing gastroenteritis, necrotizing hepatitis, and tubulonephrosis. The number of strandings caused by crude oil after 2005 was significantly lower than it was before 2006. We show that the designation of the Canary Islands as a PSSA in 2005 by the International Maritime Organization was associated with a reduction of sea turtle strandings caused by crude oil.

  9. Both strands of siRNA have potential to guide posttranscriptional gene silencing in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Jun-Xia Wei

    Full Text Available Despite the widespread application of RNA interference (RNAi as a research tool for diverse purposes, the key step of strand selection of siRNAs during the formation of RNA-induced silencing complex (RISC remains poorly understood. Here, using siRNAs targeted to the complementary region of Survivin and the effector protease receptor 1 (EPR-1, we show that both strands of the siRNA duplex can find their target mRNA and are equally eligible for assembly into Argonaute 2 (Ago2 of RISC in HEK293 cells. Transfection of the synthetic siRNA duplexes with different thermodynamic profiles or short hairpin RNA (shRNA vectors that generate double-stranded RNAs (dsRNAs, permitting processing specifically from either the 5' or 3' end of the incipient siRNA, results in the degradation of the respective target mRNAs of either strand of the siRNA duplex with comparable efficiencies. Thus, while most RNAi reactions may follow the thermodynamic asymmetry rule in strand selection, our study suggests an exceptional mode for certain siRNAs in which both strands of the duplex are competent in sponsoring RNAi, and implies additional factors that might dictate the RNAi targets.

  10. Sequential strand displacement beacon for detection of DNA coverage on functionalized gold nanoparticles.

    Science.gov (United States)

    Paliwoda, Rebecca E; Li, Feng; Reid, Michael S; Lin, Yanwen; Le, X Chris

    2014-06-17

    Functionalizing nanomaterials for diverse analytical, biomedical, and therapeutic applications requires determination of surface coverage (or density) of DNA on nanomaterials. We describe a sequential strand displacement beacon assay that is able to quantify specific DNA sequences conjugated or coconjugated onto gold nanoparticles (AuNPs). Unlike the conventional fluorescence assay that requires the target DNA to be fluorescently labeled, the sequential strand displacement beacon method is able to quantify multiple unlabeled DNA oligonucleotides using a single (universal) strand displacement beacon. This unique feature is achieved by introducing two short unlabeled DNA probes for each specific DNA sequence and by performing sequential DNA strand displacement reactions. Varying the relative amounts of the specific DNA sequences and spacing DNA sequences during their coconjugation onto AuNPs results in different densities of the specific DNA on AuNP, ranging from 90 to 230 DNA molecules per AuNP. Results obtained from our sequential strand displacement beacon assay are consistent with those obtained from the conventional fluorescence assays. However, labeling of DNA with some fluorescent dyes, e.g., tetramethylrhodamine, alters DNA density on AuNP. The strand displacement strategy overcomes this problem by obviating direct labeling of the target DNA. This method has broad potential to facilitate more efficient design and characterization of novel multifunctional materials for diverse applications.

  11. Simulating mechanisms for dispersal, production and stranding of small forage fish in temporary wetland habitats

    Science.gov (United States)

    Yurek, Simeon; DeAngelis, Donald L.; Trexler, Joel C.; Jopp, Fred; Donalson, Douglas D.

    2013-01-01

    Movement strategies of small forage fish (stranded fish in accessible depths. Expansion and contraction of seasonal wetlands induce a sequential alternation between rapid biomass growth and concentration, creating the conditions for local stranding of small fish as they move in response to varying water levels. To better understand how landscape topography, hydrology, and fish behavior interact to create high densities of stranded fish, we first simulated population dynamics of small fish, within a dynamic food web, with different traits for movement strategy and growth rate, across an artificial, spatially explicit, heterogeneous, two-dimensional marsh slough landscape, using hydrologic variability as the driver for movement. Model output showed that fish with the highest tendency to invade newly flooded marsh areas built up the largest populations over long time periods with stable hydrologic patterns. A higher probability to become stranded had negative effects on long-term population size, and offset the contribution of that species to stranded biomass. The model was next applied to the topography of a 10 km × 10 km area of Everglades landscape. The details of the topography were highly important in channeling fish movements and creating spatiotemporal patterns of fish movement and stranding. This output provides data that can be compared in the future with observed locations of fish biomass concentrations, or such surrogates as phosphorus ‘hotspots’ in the marsh.

  12. PROPAGATION CHARACTERISTICS OF HIGH ORDER LONGITUDINAL MODES IN STEEL STRANDS AND THEIR APPLICATIONS

    Institute of Scientific and Technical Information of China (English)

    Zenghua Liu; Su Liu; Bin Wu; Yinong Zhang; Cunfu He

    2008-01-01

    Propagation characteristics of high order longitudinal modes of ultrasonic guided waves in seven-wire steel strands are investigated theoretically and experimentally. According to these analysis results, proper longitudinal modes are selected for defect detection in steel strands.Dispersion curves for helical and central wires in a 17.80 mm nominal diameter seven-wire steel strand are numerically obtained firstly, and propagation characteristics of high-order longitudinal modes, such as wave structures, attenuation and dispersion, are analyzed. In experiments, the signals of ultrasonic guided wave at different high frequencies are excited and received at one end of a steel strand by using the same single piezoelectric transducer. The identification of longitudinal modes in the received signals is achieved based on short time Fourier transform. Furthermore,appropriate L(0, 5) mode at 2.54 MHz is chosen for detecting an artificial defect in a helical wire of the steel strand. Results show that high order longitudinal modes in a high frequency range with low dispersion and attenuation whose energy propagates mainly in the center of the wires can be used for defect detection in long range steel strands.

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

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Xuan

    2012-12-17

    During Phase I, our efforts were focusing on improving the array of subelement in the tube type strands by hardening the Sn core and the subelement matrix to effectively increase the Jc of the strands. Below is a summary of the results. 1) We were unsuccessful in improving the array using a Cu-Sn matrix approach. 2) We slightly improved the array using Sn with 1.5at%Ti doped core, and a 217-subelement restacked strand was made and drawn down without any breakage. 3) We greatly improved the array using the Glidcop Al-15 to replace the pure Cu sheath in the subelement, and a 217-subelement restacked strand was made and drawn down. Both strands have very good drawability and the array showed good improvement. 4) We also improved the array using improved wire drawing techniques using Hyper Tech's new caterpillar wire drawing machines to enable straight wire drawing for the entire wire drawing process. 5) The 919-subelement restack strand shows its non-Cu Jc over 2100 A/mm2 at 12 T/4.2 K and AC loss of 508 mJ/cm3.

  14. A requirement for polymerized actin in DNA double-strand break repair.

    Science.gov (United States)

    Andrin, Christi; McDonald, Darin; Attwood, Kathleen M; Rodrigue, Amélie; Ghosh, Sunita; Mirzayans, Razmik; Masson, Jean-Yves; Dellaire, Graham; Hendzel, Michael J

    2012-07-01

    Nuclear actin is involved in several nuclear processes from chromatin remodeling to transcription. Here we examined the requirement for actin polymerization in DNA double-strand break repair. Double-strand breaks are considered the most dangerous type of DNA lesion. Double-strand break repair consists of a complex set of events that are tightly regulated. Failure at any step can have catastrophic consequences such as genomic instability, oncogenesis or cell death. Many proteins involved in this repair process have been identified and their roles characterized. We discovered that some DNA double-strand break repair factors are capable of associating with polymeric actin in vitro and specifically, that purified Ku70/80 interacts with polymerized actin under these conditions. We find that the disruption of polymeric actin inhibits DNA double strand break repair both in vitro and in vivo. Introduction of nuclear targeted mutant actin that cannot polymerize, or the depolymerization of endogenous actin filaments by the addition of cytochalasin D, alters the retention of Ku80 at sites of DNA damage in live cells. Our results suggest that polymeric actin is required for proper DNA double-strand break repair and may function through the stabilization of the Ku heterodimer at the DNA damage site.

  15. Relational Perspectives on Leading

    DEFF Research Database (Denmark)

    Larsen, Mette Vinther; Rasmussen, Jørgen Gulddahl

    2015-01-01

    Relational Perspectives on Leading discusses leadership from a relational and social constructionism perspective as practiced on an everyday basis between people. The book pursues a fast growing, practice-based approach - particularly within the Anglo-Saxon parts of the world - to organization...... studies and organizational phenomena....

  16. lead glass brick

    CERN Multimedia

    As well as accelerators to boost particles up to high energy, physicists need detectors to see what happens when those particles collide. This lead glass block is part of a CERN detector called OPAL. OPAL uses some 12 000 blocks of glass like this to measure particle energies.

  17. Girls Leading Outward

    Science.gov (United States)

    Hamed, Heather; Reyes, Jazmin; Moceri, Dominic C.; Morana, Laura; Elias, Maurice J.

    2011-01-01

    The authors describe a program implemented in Red Bank Middle School in New Jersey to help at-risk, minority middle school girls realize their leadership potential. The GLO (Girls Leading Outward) program was developed by the Developing Safe and Civil Schools Project at Rutgers University and is facilitated by university students. Selected middle…

  18. Leading by Learning

    Science.gov (United States)

    Brookhart, Susan M.; Moss, Connie M.

    2013-01-01

    A lot has changed in the principalship since the principal was the head teacher in a school. Current principals are building administrators and that is likely to continue, the authors posit. Nonetheless, they report their study focusing on leadership's role in formative assessment concluded that in order to lead learning the principal must become…

  19. Change, Lead, Succeed

    Science.gov (United States)

    Munger, Linda; von Frank, Valerie

    2010-01-01

    Redefine leadership in your school, and create capacity through school leadership teams that successfully coordinate professional learning. "Change, Lead, Succeed" shows school leaders and teachers in leadership roles what they need to know to effectively create a culture for change. Find out what distinguishes a school leadership team from other…

  20. SU-E-T-241: Monte Carlo Simulation Study About the Prediction of Proton-Induced DNA Strand Breakage On the Double Helix Structure

    Energy Technology Data Exchange (ETDEWEB)

    Shin, J; Park, S; Jeong, J; Jeong, C [National Cancer Center, Goyang, Gyeonggi-do (Korea, Republic of); Lim, Y; Lee, S [National Cancer Center in Korea, Goyang, Gyeonggi-do (Korea, Republic of); SHIN, D [National Cancer Center, Goyangsi, Gyeonggi-do (Korea, Republic of); Incerti, S [Universite Bordeaux 1, CNRS.IN2P3, Centres d’Etudes Nucleaires de Bordeau, Gradignan, Gradignan (France)

    2014-06-01

    Purpose: In particle therapy and radiobiology, the investigation of mechanisms leading to the death of target cancer cells induced by ionising radiation is an active field of research. Recently, several studies based on Monte Carlo simulation codes have been initiated in order to simulate physical interactions of ionising particles at cellular scale and in DNA. Geant4-DNA is the one of them; it is an extension of the general purpose Geant4 Monte Carlo simulation toolkit for the simulation of physical interactions at sub-micrometre scale. In this study, we present Geant4-DNA Monte Carlo simulations for the prediction of DNA strand breakage using a geometrical modelling of DNA structure. Methods: For the simulation of DNA strand breakage, we developed a specific DNA geometrical structure. This structure consists of DNA components, such as the deoxynucleotide pairs, the DNA double helix, the nucleosomes and the chromatin fibre. Each component is made of water because the cross sections models currently available in Geant4-DNA for protons apply to liquid water only. Also, at the macroscopic-scale, protons were generated with various energies available for proton therapy at the National Cancer Center, obtained using validated proton beam simulations developed in previous studies. These multi-scale simulations were combined for the validation of Geant4-DNA in radiobiology. Results: In the double helix structure, the deposited energy in a strand allowed to determine direct DNA damage from physical interaction. In other words, the amount of dose and frequency of damage in microscopic geometries was related to direct radiobiological effect. Conclusion: In this report, we calculated the frequency of DNA strand breakage using Geant4- DNA physics processes for liquid water. This study is now on-going in order to develop geometries which use realistic DNA material, instead of liquid water. This will be tested as soon as cross sections for DNA material become available in Geant4

  1. [Analysis of polyA, polyU and double-stranded complex polyA x polyU via Raman spectroscopy].

    Science.gov (United States)

    Liao, Yu-bo; Meng, Yao-yong; Lei, Hao-dong; Wang, Ying

    2007-05-01

    The Raman spectra of PolyA, PolyU and their double-stranded complex were measured, and the spectral changes upon the formation of double-stranded complex were studied. The experimental results show: (1) Under the experimental conditions used in the present work (0.14 mol x L(-1) NaCl, 1 mmol x L(-1) Tris solution, neutral pH and 15 degrees C), PolyU, PolyA and PolyA x PolyU occur as random-coiled, A-single-stranded helical and A-double-stranded helical conformations, respectively. One of the main spectral differences between the latter two conformations and the former one is the Raman band near 814 cm(-1) of ordered structures. Another difference is in the full width at half the maximum (i.e. FWHM) of the band near 1100 cm(-1). The FWHM of the band 1100 cm(-1) of PolyA is the same as that of PolyA x PolyU, while the band of PolyU shows remarkable broadening. In addition, we found that the conformation of PolyA is somewhat not so ordered as that of its duplex, which can be concluded from the value of I814/I1100 of the two polynucleotides. (2) The formation of duplex makes base-base stacking interactions much stronger, and the conformation of the backbone more ordered, which leads to obvious Raman hypochromic effect with some corresponding band shift. In this process, PolyU underwent more significant spectral changes than PolyA. As spectral markers, these results can be of great importance in Raman spectral signal detection of gene-chips.

  2. Advances in ITER-relevant Nb-Ti and $Nb_{3}Sn$ strands and low-loss Nb-Ti strands in RF

    CERN Document Server

    Pantsyrny, V; Vorobieva, A; Potanina, L; Drobyshev, V; Kozlenkova, N; Dergunova, E; Gubkin, I; Sudyev, S

    2009-01-01

    The review of the main results of R&D directed on the enhancement of ITER relevant NbTi and Nb3Sn strands performance recently carried out in Russia (the Bochvar Institute) are presented. For ITER PF type (NbTi) strands with Cu/non Cu ratio of 1.6 the attainment of ITER specified critical current density (Jc) ≥ 2900 A/mm2 (5 T, 4.2 K) has been shown. For Toroidal Field (TF) strands (Nb3Sn) the influence of doping and layout peculiarities of the wires produced by bronze method on their current-carrying ability has been investigated. It was shown that with non-doped matrix and doped filaments Jc exceeds 800 A/mm2 (12 T, 4.2 K) while with the application of the doped bronze and nondoped filaments it exceeds 900 A/mm2. Internal-tin Nb3Sn strand meeting the ITER TF specification requirements was also developed and fabricated. The results of testing of CICC samples in a SULTAN facility have shown that performance parameters are higher than ITER qualification requirements Low loss model fine filament NbTi stra...

  3. Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex

    KAUST Repository

    Ghosh, Sharmistha

    2010-04-06

    The DNA polymerase encoded by bacteriophage T7 has low processivity. Escherichia coli thioredoxin binds to a segment of 76 residues in the thumb subdomain of the polymerase and increases the processivity. The binding of thioredoxin leads to the formation of two basic loops, loops A and B, located within the thioredoxin-binding domain (TBD). Both loops interact with the acidic C terminus of the T7 helicase. A relatively weak electrostatic mode involves the C-terminal tail of the helicase and the TBD, whereas a high affinity interaction that does not involve the C-terminal tail occurs when the polymerase is in a polymerization mode. T7 gene 2.5 single-stranded DNA-binding protein (gp2.5) also has an acidic C-terminal tail. gp2.5 also has two modes of interaction with the polymerase, but both involve the C-terminal tail of gp2.5. An electrostatic interaction requires the basic residues in loops A and B, and gp2.5 binds to both loops with similar affinity as measured by surface plasmon resonance. When the polymerase is in a polymerization mode, the C terminus of gene 2.5 protein interacts with the polymerase in regions outside the TBD.gp2.5 increases the processivity of the polymerase-helicase complex during leading strand synthesis. When loop B of the TBD is altered, abortive DNA products are observed during leading strand synthesis. Loop B appears to play an important role in communication with the helicase and gp2.5, whereas loop A plays a stabilizing role in these interactions. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. CMS lead tungstate crystals

    CERN Multimedia

    Laurent Guiraud

    2000-01-01

    These crystals are made from lead tungstate, a crystal that is as clear as glass yet with nearly four times the density. They have been produced in Russia to be used as scintillators in the electromagnetic calorimeter on the CMS experiment, part of the LHC project at CERN. When an electron, positron or photon passes through the calorimeter it will cause a cascade of particles that will then be absorbed by these scintillating crystals, allowing the particle's energy to be measured.

  5. Leading Generation Y

    Science.gov (United States)

    2008-04-01

    ensure the success of their child, failure is not often experienced. These successes and the ease of childhood lead to not only confidence but an...Messaging, chatting on the cell phone and working on homework is a common place scene for teens and college students. “The level of multiprocessing...to Gen Yers entering the workforce with unrealistic expectations and a sense of entitlement. Barbara Dwyer, CEO of the Job Journey, states that

  6. Superconductivity of lead

    Energy Technology Data Exchange (ETDEWEB)

    Boorse, H.A.; Cook, D.B.; Zemansky, W.M.

    1950-06-01

    Numerous determinations of the zero-field transition temperature of lead have been made. All of these observations except that of Daunt were made by the direct measurement of electrical resistance. Daunt`s method involved the shielding effect of persistent currents in a hollow cylinder. In the authors work on columbium to be described in a forthcoming paper an a.c. induction method was used for the measurement of superconducting transitions. The superconductor was mounted as a cylindrical core of a coil which functioned as the secondary of a mutual inductance. The primary coil was actuated by an oscillator which provided a maximum a.c. field within the secondary of 1.5 oersteds at a frequency of 1000 cycles per second. The secondary e.m.f. which was dependent for its magnitude on the permeability of the core was amplified, rectifie, and observed on a recording potentiometer. During the application of this method to the study of columbium it appeared that a further check on the zero-field transition temperature of lead would be worth while especially if agreement between results for very pure samples could be obtained using this method. Such result would help in establishing the lead transition temperature as a reasonably reproducible reference point in the region between 4 deg and 10 deg K.

  7. A regulatory role for NBS1 in strand-specific mutagenesis during somatic hypermutation.

    Directory of Open Access Journals (Sweden)

    Likun Du

    Full Text Available Activation-induced cytidine deaminase (AID is believed to initiate somatic hypermutation (SHM by deamination of deoxycytidines to deoxyuridines within the immunoglobulin variable regions genes. The deaminated bases can subsequently be replicated over, processed by base excision repair or mismatch repair, leading to introduction of different types of point mutations (G/C transitions, G/C transversions and A/T mutations. It is evident that the base excision repair pathway is largely dependent on uracil-DNA glycosylase (UNG through its uracil excision activity. It is not known, however, which endonuclease acts in the step immediately downstream of UNG, i.e. that cleaves at the abasic sites generated by the latter. Two candidates have been proposed, an apurinic/apyrimidinic endonuclease (APE and the Mre11-Rad50-NBS1 complex. The latter is intriguing as this might explain how the mutagenic pathway is primed during SHM. We have investigated the latter possibility by studying the in vivo SHM pattern in B cells from ataxia-telangiectasia-like disorder (Mre11 deficient and Nijmegen breakage syndrome (NBS1 deficient patients. Our results show that, although the pattern of mutations in the variable heavy chain (V(H genes was altered in NBS1 deficient patients, with a significantly increased number of G (but not C transversions occurring in the SHM and/or AID targeting hotspots, the general pattern of mutations in the V(H genes in Mre11 deficient patients was only slightly altered, with an increased frequency of A to C transversions. The Mre11-Rad50-NBS1 complex is thus unlikely to be the major nuclease involved in cleavage of the abasic sites during SHM, whereas NBS1 might have a specific role in regulating the strand-biased repair during phase Ib mutagenesis.

  8. Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein

    Directory of Open Access Journals (Sweden)

    Biswas-Fiss Esther E

    2012-06-01

    Full Text Available Abstract Background Single-stranded DNA binding proteins (SSB are essential for DNA replication, repair, and recombination in all organisms. SSB works in concert with a variety of DNA metabolizing enzymes such as DNA polymerase. Results We have cloned and purified SSB from Bacillus anthracis (SSBBA. In the absence of DNA, at concentrations ≤100 μg/ml, SSBBA did not form a stable tetramer and appeared to resemble bacteriophage T4 gene 32 protein. Fluorescence anisotropy studies demonstrated that SSBBA bound ssDNA with high affinity comparable to other prokaryotic SSBs. Thermodynamic analysis indicated both hydrophobic and ionic contributions to ssDNA binding. FRET analysis of oligo(dT70 binding suggested that SSBBA forms a tetrameric assembly upon ssDNA binding. This report provides evidence of a bacterial SSB that utilizes a novel mechanism for DNA binding through the formation of a transient tetrameric structure. Conclusions Unlike other prokaryotic SSB proteins, SSBBA from Bacillus anthracis appeared to be monomeric at concentrations ≤100 μg/ml as determined by SE-HPLC. SSBBA retained its ability to bind ssDNA with very high affinity, comparable to SSB proteins which are tetrameric. In the presence of a long ssDNA template, SSBBA appears to form a transient tetrameric structure. Its unique structure appears to be due to the cumulative effect of multiple key amino acid changes in its sequence during evolution, leading to perturbation of stable dimer and tetramer formation. The structural features of SSBBA could promote facile assembly and disassembly of the protein-DNA complex required in processes such as DNA replication.

  9. DNA double-strand breaks activate ATM independent of mitochondrial dysfunction in A549 cells.

    Science.gov (United States)

    Kalifa, Lidza; Gewandter, Jennifer S; Staversky, Rhonda J; Sia, Elaine A; Brookes, Paul S; O'Reilly, Michael A

    2014-10-01

    Excessive nuclear or mitochondrial DNA damage can lead to mitochondrial dysfunction, decreased energy production, and increased generation of reactive oxygen species (ROS). Although numerous cell signaling pathways are activated when cells are injured, the ataxia telangiectasia mutant (ATM) protein has emerged as a major regulator of the response to both mitochondrial dysfunction and nuclear DNA double-strand breaks (DSBs). Because mitochondrial dysfunction is often a response to excessive DNA damage, it has been difficult to determine whether nuclear and/or mitochondrial DNA DSBs activate ATM independent of mitochondrial dysfunction. In this study, mitochondrial and nuclear DNA DSBs were generated in the A549 human lung adenocarcinoma cell line by infecting with retroviruses expressing the restriction endonuclease PstI fused to a mitochondrial targeting sequence (MTS) or nuclear localization sequence (NLS) and a hemagglutinin antigen epitope tag (HA). Expression of MTS-PstI-HA or NLS-PstI-HA activated the DNA damage response defined by phosphorylation of ATM, the tumor suppressor protein p53 (TP53), KRAB-associated protein (KAP)-1, and structural maintenance of chromosomes (SMC)-1. Phosphorylated ATM and SMC1 were detected in nuclear fractions, whereas phosphorylated TP53 and KAP1 were detected in both mitochondrial and nuclear fractions. PstI also enhanced expression of the cyclin-dependent kinase inhibitor p21 and inhibited cell growth. This response to DNA damage occurred in the absence of detectable mitochondrial dysfunction and excess production of ROS. These findings reveal that DNA DSBs are sufficient to activate ATM independent of mitochondrial dysfunction and suggest that the activated form of ATM and some of its substrates are restricted to the nuclear compartment, regardless of the site of DNA damage.

  10. c-Myc Suppression of DNA Double-strand Break Repair12

    Science.gov (United States)

    Li, Zhaozhong; Owonikoko, Taofeek K; Sun, Shi-Yong; Ramalingam, Suresh S; Doetsch, Paul W; Xiao, Zhi-Qiang; Khuri, Fadlo R; Curran, Walter J; Deng, Xingming

    2012-01-01

    c-Myc is a transcriptional factor that functions as a central regulator of cell growth, proliferation, and apoptosis. Overexpression of c-Myc also enhances DNA double-strand breaks (DSBs), genetic instability, and tumorigenesis. However, the mechanism(s) involved remains elusive. Here, we discovered that γ-ray ionizing radiation-induced DSBs promote c-Myc to form foci and to co-localize with γ-H2AX. Conditional expression of c-Myc in HO15.19 c-Myc null cells using the Tet-Off/Tet-On inducible system results in down-regulation of Ku DNA binding and suppressed activities of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and DNA end-joining, leading to inhibition of DSB repair and enhanced chromosomal and chromatid breaks. Expression of c-Myc reduces both signal and coding joins with decreased fidelity during V(D)J recombination. Mechanistically, c-Myc directly interacts with Ku70 protein through its Myc box II (MBII) domain. Removal of the MBII domain from c-Myc abrogates its inhibitory effects on Ku DNA binding, DNA-PKcs, and DNA end-joining activities, which results in loss of c-Myc's ability to block DSB repair and V(D)J recombination. Interestingly, c-Myc directly disrupts the Ku/DNA-PKcs complex in vitro and in vivo. Thus, c-Myc suppression of DSB repair and V(D)J recombination may occur through inhibition of the nonhomologous end-joining pathway, which provides insight into the mechanism of c-Myc in the development of tumors through promotion of genomic instability. PMID:23308051

  11. Evolution of susceptibility to ingested double-stranded RNAs in Caenorhabditis nematodes.

    Directory of Open Access Journals (Sweden)

    Isabelle Nuez

    Full Text Available BACKGROUND: The nematode Caenorhabditis elegans is able to take up external double-stranded RNAs (dsRNAs and mount an RNA interference response, leading to the inactivation of specific gene expression. The uptake of ingested dsRNAs into intestinal cells has been shown to require the SID-2 transmembrane protein in C. elegans. By contrast, C. briggsae was shown to be naturally insensitive to ingested dsRNAs, yet could be rendered sensitive by transgenesis with the C. elegans sid-2 gene. Here we aimed to elucidate the evolution of the susceptibility to external RNAi in the Caenorhabditis genus. PRINCIPAL FINDINGS: We study the sensitivity of many new species of Caenorhabditis to ingested dsRNAs matching a conserved actin gene sequence from the nematode Oscheius tipulae. We find ample variation in the Caenorhabditis genus in the ability to mount an RNAi response. We map this sensitivity onto a phylogenetic tree, and show that sensitivity or insensitivity have evolved convergently several times. We uncover several evolutionary losses in sensitivity, which may have occurred through distinct mechanisms. We could render C. remanei and C. briggsae sensitive to ingested dsRNAs by transgenesis of the Cel-sid-2 gene. We thus provide tools for RNA interference studies in these species. We also show that transgenesis by injection is possible in many Caenorhabditis species. CONCLUSIONS: The ability of animals to take up dsRNAs or to respond to them by gene inactivation is under rapid evolution in the Caenorhabditis genus. This study provides a framework and tools to use RNA interference and transgenesis in various Caenorhabditis species for further comparative and evolutionary studies.

  12. Tying the loose ends together in DNA double strand break repair with 53BP1

    Directory of Open Access Journals (Sweden)

    Carpenter Phillip B

    2006-08-01

    Full Text Available Abstract To maintain genomic stability and ensure the fidelity of chromosomal transmission, cells respond to various forms of genotoxic stress, including DNA double-stranded breaks (DSBs, through the activation of DNA damage response signaling networks. In response to DSBs as induced by ionizing radiation (IR, during DNA replication, or through immunoglobulin heavy chain (IgH rearrangements in B cells of lymphoid origin, the phosphatidyl inositol-like kinase (PIK kinases ATM (mutated in ataxia telangiectasia, ATR (ATM and Rad3-related kinase, and the DNA-dependent protein kinase (DNA-PK activate signaling pathways that lead to DSB repair. DSBs are repaired by either of two major, non-mutually exclusive pathways: homologous recombination (HR that utilizes an undamaged sister chromatid template (or homologous chromosome and non- homologous end joining (NHEJ, an error prone mechanism that processes and joins broken DNA ends through the coordinated effort of a small set of ubiquitous factors (DNA-PKcs, Ku70, Ku80, artemis, Xrcc4/DNA lig IV, and XLF/Cernunnos. The PIK kinases phosphorylate a variety of effector substrates that propagate the DNA damage signal, ultimately resulting in various biological outputs that influence cell cycle arrest, transcription, DNA repair, and apoptosis. A variety of data has revealed a critical role for p53-binding protein 1 (53BP1 in the cellular response to DSBs including various aspects of p53 function. Importantly, 53BP1 plays a major role in suppressing translocations, particularly in B and T cells. This report will review past experiments and current knowledge regarding the role of 53BP1 in the DNA damage response.

  13. Recognition of double strand breaks by a mutator protein (MU2 in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Raghuvar Dronamraju

    2009-05-01

    Full Text Available Telomere capture, a rare event that stabilizes chromosome breaks, is associated with certain genetic abnormalities in humans. Studies pertaining to the generation, maintenance, and biological effects of telomere formation are limited in metazoans. A mutation, mu2(a, in Drosophila melanogaster decreases the rate of repair of double strand DNA breaks in oocytes, thus leading to chromosomes that have lost a natural telomere and gained a new telomere. Amino acid sequence, domain architecture, and protein interactions suggest that MU2 is an ortholog of human MDC1. The MU2 protein is a component of meiotic recombination foci and localizes to repair foci in S2 cells after irradiation in a manner similar to that of phosphorylated histone variant H2Av. Domain searches indicated that the protein contains an N-terminal FHA domain and a C-terminal tandem BRCT domain. Peptide pull-down studies showed that the BRCT domain interacts with phosphorylated H2Av, while the FHA domain interacts with the complex of MRE11, RAD50, and NBS. A frameshift mutation that eliminates the MU2 BRCT domain decreases the number and size of meiotic phospho-H2Av foci. MU2 is also required for the intra-S checkpoint in eye-antennal imaginal discs. MU2 participates at an early stage in the recognition of DNA damage at a step that is prerequisite for both DNA repair and cell cycle checkpoint control. We propose a model suggesting that neotelomeres may arise when radiation-induced chromosome breaks fail to be repaired, fail to arrest progression through meiosis, and are deposited in the zygote, where cell cycle control is absent and rapid rounds of replication and telomere formation ensue.

  14. Electronic excited states responsible for dimer formation upon UV absorption directly by thymine strands: joint experimental and theoretical study.

    Science.gov (United States)

    Banyasz, Akos; Douki, Thierry; Improta, Roberto; Gustavsson, Thomas; Onidas, Delphine; Vayá, Ignacio; Perron, Marion; Markovitsi, Dimitra

    2012-09-12

    The study addresses interconnected issues related to two major types of cycloadditions between adjacent thymines in DNA leading to cyclobutane dimers (TTs) and (6-4) adducts. Experimental results are obtained for the single strand (dT)(20) by steady-state and time-resolved optical spectroscopy, as well as by HPLC coupled to mass spectrometry. Calculations are carried out for the dinucleoside monophosphate in water using the TD-M052X method and including the polarizable continuum model; the reliability of TD-M052X is checked against CASPT2 calculations regarding the behavior of two stacked thymines in the gas phase. It is shown that irradiation at the main absorption band leads to cyclobutane dimers (TTs) and (6-4) adducts via different electronic excited states. TTs are formed via (1)ππ* excitons; [2 + 2] dimerization proceeds along a barrierless path, in line with the constant quantum yield (0.05) with the irradiation wavelength, the contribution of the (3)ππ* state to this reaction being less than 10%. The formation of oxetane, the reaction intermediate leading to (6-4) adducts, occurs via charge transfer excited states involving two stacked thymines, whose fingerprint is detected in the fluorescence spectra; it involves an energy barrier explaining the important decrease in the quantum yield of (6-4) adducts with the irradiation wavelength.

  15. Defective DNA single-strand break repair is responsible for senescence and neoplastic escape of epithelial cells.

    Science.gov (United States)

    Nassour, Joe; Martien, Sébastien; Martin, Nathalie; Deruy, Emeric; Tomellini, Elisa; Malaquin, Nicolas; Bouali, Fatima; Sabatier, Laure; Wernert, Nicolas; Pinte, Sébastien; Gilson, Eric; Pourtier, Albin; Pluquet, Olivier; Abbadie, Corinne

    2016-01-29

    The main characteristic of senescence is its stability which relies on the persistence of DNA damage. We show that unlike fibroblasts, senescent epithelial cells do not activate an ATM-or ATR-dependent DNA damage response (DDR), but accumulate oxidative-stress-induced DNA single-strand breaks (SSBs). These breaks remain unrepaired because of a decrease in PARP1 expression and activity. This leads to the formation of abnormally large and persistent XRCC1 foci that engage a signalling cascade involving the p38MAPK and leading to p16 upregulation and cell cycle arrest. Importantly, the default in SSB repair also leads to the emergence of post-senescent transformed and mutated precancerous cells. In human-aged skin, XRCC1 foci accumulate in the epidermal cells in correlation with a decline of PARP1, whereas DDR foci accumulate mainly in dermal fibroblasts. These findings point SSBs as a DNA damage encountered by epithelial cells with aging which could fuel the very first steps of carcinogenesis.

  16. The Role of Cytosine Methylation on Charge Transport through a DNA Strand

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Jianqing; Govind, Niranjan; Anantram, M.P.

    2015-09-04

    Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modifi-cation remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Buttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. Specifically, we compare the results generated with the widely used B3LYP exchange-correlation (XC) functional and CAM-B3LYP based tuned range-separated hybrid density functional. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that with both functionals, the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and interstrand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital (HOMO) level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with both functionals. We also study the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit. Our results suggest that the effect of the two different functionals is to alter the on-site energies of the DNA bases at the HOMO level, while the transport properties don't depend much on the two

  17. Genetic Kinship Analyses Reveal That Gray's Beaked Whales Strand in Unrelated Groups.

    Science.gov (United States)

    Patel, Selina; Thompson, Kirsten F; Santure, Anna W; Constantine, Rochelle; Millar, Craig D

    2017-06-01

    Some marine mammals are so rarely seen that their life history and social structure remain a mystery. Around New Zealand, Gray's beaked whales (Mesoplodon grayi) are almost never seen alive, yet they are a commonly stranded species. Gray's are unique among the beaked whales in that they frequently strand in groups, providing an opportunity to investigate their social organization. We examined group composition and genetic kinship in 113 Gray's beaked whales with samples collected over a 20-year period. Fifty-six individuals stranded in 19 groups (2 or more individuals), and 57 whales stranded individually. Mitochondrial control region haplotypes and microsatellite genotypes (16 loci) were obtained for 103 whales. We estimated pairwise relatedness between all pairs of individuals and average relatedness within, and between, groups. We identified 6 mother-calf pairs and 2 half-siblings, including 2 whales in different strandings 17 years and 1500 km apart. Surprisingly, none of the adults stranding together were related suggesting that groups are not formed through the retention of kin. These data suggest that both sexes may disperse from their mothers, and groups consisting of unrelated subadults are common. We also found no instances of paternity within the groups. Our results provide the first insights into dispersal, social organization, and the mating system in this rarely sighted species. Why whales strand is still unknown but, in Gray's beaked whales, the dead can tell us much about the living. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Possible causes of a harbour porpoise mass stranding in Danish waters in 2005.

    Directory of Open Access Journals (Sweden)

    Andrew J Wright

    Full Text Available An unprecedented 85 harbour porpoises stranded freshly dead along approximately 100 km of Danish coastline from 7-15 April, 2005. This total is considerably above the mean weekly stranding rate for the whole of Denmark, both for any time of year, 1.23 animals/week (ranging from 0 to 20 during 2003-2008, excluding April 2005, and specifically in April, 0.65 animals/week (0 to 4, same period. Bycatch was established as the cause of death for most of the individuals through typical indications of fisheries interactions, including net markings in the skin and around the flippers, and loss of tail flukes. Local fishermen confirmed unusually large porpoise bycatch in nets set for lumpfish (Cyclopterus lumpus and the strandings were attributed to an early lumpfish season. However, lumpfish catches for 2005 were not unusual in terms of season onset, peak or total catch, when compared to 2003-2008. Consequently, human activity was combined with environmental factors and the variation in Danish fisheries landings (determined through a principal component analysis in a two-part statistical model to assess the correlation of these factors with both the presence of fresh strandings and the numbers of strandings on the Danish west coast. The final statistical model (which was forward selected using Akaike information criterion; AIC indicated that naval presence is correlated with higher rates of porpoise strandings, particularly in combination with certain fisheries, although it is not correlated with the actual presence of strandings. Military vessels from various countries were confirmed in the area from the 7th April, en route to the largest naval exercise in Danish waters to date (Loyal Mariner 2005, 11-28 April. Although sonar usage cannot be confirmed, it is likely that ships were testing various equipment prior to the main exercise. Thus naval activity cannot be ruled out as a possible contributing factor.

  19. Possible causes of a harbour porpoise mass stranding in Danish waters in 2005.

    Science.gov (United States)

    Wright, Andrew J; Maar, Marie; Mohn, Christian; Nabe-Nielsen, Jacob; Siebert, Ursula; Jensen, Lasse Fast; Baagøe, Hans J; Teilmann, Jonas

    2013-01-01

    An unprecedented 85 harbour porpoises stranded freshly dead along approximately 100 km of Danish coastline from 7-15 April, 2005. This total is considerably above the mean weekly stranding rate for the whole of Denmark, both for any time of year, 1.23 animals/week (ranging from 0 to 20 during 2003-2008, excluding April 2005), and specifically in April, 0.65 animals/week (0 to 4, same period). Bycatch was established as the cause of death for most of the individuals through typical indications of fisheries interactions, including net markings in the skin and around the flippers, and loss of tail flukes. Local fishermen confirmed unusually large porpoise bycatch in nets set for lumpfish (Cyclopterus lumpus) and the strandings were attributed to an early lumpfish season. However, lumpfish catches for 2005 were not unusual in terms of season onset, peak or total catch, when compared to 2003-2008. Consequently, human activity was combined with environmental factors and the variation in Danish fisheries landings (determined through a principal component analysis) in a two-part statistical model to assess the correlation of these factors with both the presence of fresh strandings and the numbers of strandings on the Danish west coast. The final statistical model (which was forward selected using Akaike information criterion; AIC) indicated that naval presence is correlated with higher rates of porpoise strandings, particularly in combination with certain fisheries, although it is not correlated with the actual presence of strandings. Military vessels from various countries were confirmed in the area from the 7th April, en route to the largest naval exercise in Danish waters to date (Loyal Mariner 2005, 11-28 April). Although sonar usage cannot be confirmed, it is likely that ships were testing various equipment prior to the main exercise. Thus naval activity cannot be ruled out as a possible contributing factor.

  20. Marine mammal strandings and environmental changes: a 15-year study in the St. Lawrence ecosystem.

    Science.gov (United States)

    Truchon, Marie-Hélène; Measures, Lena; L'Hérault, Vincent; Brêthes, Jean-Claude; Galbraith, Peter S; Harvey, Michel; Lessard, Sylvie; Starr, Michel; Lecomte, Nicolas

    2013-01-01

    Understanding the effects of climatic variability on marine mammals is challenging due to the complexity of ecological interactions. We used general linear models to analyze a 15-year database documenting marine mammal strandings (1994-2008; n = 1,193) and nine environmental parameters known to affect marine mammal survival, from regional (sea ice) to continental scales (North Atlantic Oscillation, NAO). Stranding events were more frequent during summer and fall than other seasons, and have increased since 1994. Poor ice conditions observed during the same period may have affected marine mammals either directly, by modulating the availability of habitat for feeding and breeding activities, or indirectly, through changes in water conditions and marine productivity (krill abundance). For most species (75%, n = 6 species), a low volume of ice was correlated with increasing frequency of stranding events (e.g. R(2)adj = 0.59, hooded seal, Cystophora cristata). This likely led to an increase in seal mortality during the breeding period, but also to increase habitat availability for seasonal migratory cetaceans using ice-free areas during winter. We also detected a high frequency of stranding events for mysticete species (minke whale, Balaenoptera acutorostrata) and resident species (beluga, Delphinapterus leucas), correlated with low krill abundance since 1994. Positive NAO indices were positively correlated with high frequencies of stranding events for resident and seasonal migratory cetaceans, as well as rare species (R(2)adj = 0.53, 0.81 and 0.34, respectively). This contrasts with seal mass stranding numbers, which were negatively correlated with a positive NAO index. In addition, an unusual multiple species mortality event (n = 114, 62% of total annual mortality) in 2008 was caused by a harmful algal bloom. Our findings provide an empirical baseline in understanding marine mammal survival when faced with climatic variability. This is a promising