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Sample records for firing replication origins

  1. Histone acetylation regulates the time of replication origin firing.

    Science.gov (United States)

    Vogelauer, Maria; Rubbi, Liudmilla; Lucas, Isabelle; Brewer, Bonita J; Grunstein, Michael

    2002-11-01

    The temporal firing of replication origins throughout S phase in yeast depends on unknown determinants within the adjacent chromosomal environment. We demonstrate here that the state of histone acetylation of surrounding chromatin is an important regulator of temporal firing. Deletion of RPD3 histone deacetylase causes earlier origin firing and concurrent binding of the replication factor Cdc45p to origins. In addition, increased acetylation of histones in the vicinity of the late origin ARS1412 by recruitment of the histone acetyltransferase Gcn5p causes ARS1412 alone to fire earlier. These data indicate that histone acetylation is a direct determinant of the timing of origin firing.

  2. The eukaryotic bell-shaped temporal rate of DNA replication origin firing emanates from a balance between origin activation and passivation.

    Science.gov (United States)

    Arbona, Jean-Michel; Goldar, Arach; Hyrien, Olivier; Arneodo, Alain; Audit, Benjamin

    2018-06-01

    The time-dependent rate I(t) of origin firing per length of unreplicated DNA presents a universal bell shape in eukaryotes that has been interpreted as the result of a complex time-evolving interaction between origins and limiting firing factors. Here we show that a normal diffusion of replication fork components towards localized potential replication origins (p-oris) can more simply account for the I(t) universal bell shape, as a consequence of a competition between the origin firing time and the time needed to replicate DNA separating two neighboring p-oris . We predict the I(t) maximal value to be the product of the replication fork speed with the squared p-ori density. We show that this relation is robustly observed in simulations and in experimental data for several eukaryotes. Our work underlines that fork-component recycling and potential origins localization are sufficient spatial ingredients to explain the universality of DNA replication kinetics. © 2018, Arbona et al.

  3. Protein Phosphatase 1 Recruitment by Rif1 Regulates DNA Replication Origin Firing by Counteracting DDK Activity

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    Anoushka Davé

    2014-04-01

    Full Text Available The firing of eukaryotic origins of DNA replication requires CDK and DDK kinase activities. DDK, in particular, is involved in setting the temporal program of origin activation, a conserved feature of eukaryotes. Rif1, originally identified as a telomeric protein, was recently implicated in specifying replication timing in yeast and mammals. We show that this function of Rif1 depends on its interaction with PP1 phosphatases. Mutations of two PP1 docking motifs in Rif1 lead to early replication of telomeres in budding yeast and misregulation of origin firing in fission yeast. Several lines of evidence indicate that Rif1/PP1 counteract DDK activity on the replicative MCM helicase. Our data suggest that the PP1/Rif1 interaction is downregulated by the phosphorylation of Rif1, most likely by CDK/DDK. These findings elucidate the mechanism of action of Rif1 in the control of DNA replication and demonstrate a role of PP1 phosphatases in the regulation of origin firing.

  4. Global profiling of DNA replication timing and efficiency reveals that efficient replication/firing occurs late during S-phase in S. pombe.

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    Majid Eshaghi

    Full Text Available BACKGROUND: During S. pombe S-phase, initiation of DNA replication occurs at multiple sites (origins that are enriched with AT-rich sequences, at various times. Current studies of genome-wide DNA replication profiles have focused on the DNA replication timing and origin location. However, the replication and/or firing efficiency of the individual origins on the genomic scale remain unclear. METHODOLOGY/PRINCIPAL FINDINGS: Using the genome-wide ORF-specific DNA microarray analysis, we show that in S. pombe, individual origins fire with varying efficiencies and at different times during S-phase. The increase in DNA copy number plotted as a function of time is approximated to the near-sigmoidal model, when considering the replication start and end timings at individual loci in cells released from HU-arrest. Replication efficiencies differ from origin to origin, depending on the origin's firing efficiency. We have found that DNA replication is inefficient early in S-phase, due to inefficient firing at origins. Efficient replication occurs later, attributed to efficient but late-firing origins. Furthermore, profiles of replication timing in cds1Delta cells are abnormal, due to the failure in resuming replication at the collapsed forks. The majority of the inefficient origins, but not the efficient ones, are found to fire in cds1Delta cells after HU removal, owing to the firing at the remaining unused (inefficient origins during HU treatment. CONCLUSIONS/SIGNIFICANCE: Taken together, our results indicate that efficient DNA replication/firing occurs late in S-phase progression in cells after HU removal, due to efficient late-firing origins. Additionally, checkpoint kinase Cds1p is required for maintaining the efficient replication/firing late in S-phase. We further propose that efficient late-firing origins are essential for ensuring completion of DNA duplication by the end of S-phase.

  5. Checkpoint independence of most DNA replication origins in fission yeast

    OpenAIRE

    Mickle, Katie L; Ramanathan, Sunita; Rosebrock, Adam; Oliva, Anna; Chaudari, Amna; Yompakdee, Chulee; Scott, Donna; Leatherwood, Janet; Huberman, Joel A

    2007-01-01

    Abstract Background In budding yeast, the replication checkpoint slows progress through S phase by inhibiting replication origin firing. In mammals, the replication checkpoint inhibits both origin firing and replication fork movement. To find out which strategy is employed in the fission yeast, Schizosaccharomyces pombe, we used microarrays to investigate the use of origins by wild-type and checkpoint-mutant strains in the presence of hydroxyurea (HU), which limits the pool of deoxyribonucleo...

  6. Interaction of RECQ4 and MCM10 is important for efficient DNA replication origin firing in human cells

    DEFF Research Database (Denmark)

    Kliszczak, Maciej; Sedlackova, Hana; Pitchai, Ganesha P

    2015-01-01

    DNA replication is a highly coordinated process that is initiated at multiple replication origins in eukaryotes. These origins are bound by the origin recognition complex (ORC), which subsequently recruits the Mcm2-7 replicative helicase in a Cdt1/Cdc6-dependent manner. In budding yeast, two...... essential replication factors, Sld2 and Mcm10, are then important for the activation of replication origins. In humans, the putative Sld2 homolog, RECQ4, interacts with MCM10. Here, we have identified two mutants of human RECQ4 that are deficient in binding to MCM10. We show that these RECQ4 variants...... are able to complement the lethality of an avian cell RECQ4 deletion mutant, indicating that the essential function of RECQ4 in vertebrates is unlikely to require binding to MCM10. Nevertheless, we show that the RECQ4-MCM10 interaction is important for efficient replication origin firing....

  7. Checkpoint independence of most DNA replication origins in fission yeast.

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    Mickle, Katie L; Ramanathan, Sunita; Rosebrock, Adam; Oliva, Anna; Chaudari, Amna; Yompakdee, Chulee; Scott, Donna; Leatherwood, Janet; Huberman, Joel A

    2007-12-19

    In budding yeast, the replication checkpoint slows progress through S phase by inhibiting replication origin firing. In mammals, the replication checkpoint inhibits both origin firing and replication fork movement. To find out which strategy is employed in the fission yeast, Schizosaccharomyces pombe, we used microarrays to investigate the use of origins by wild-type and checkpoint-mutant strains in the presence of hydroxyurea (HU), which limits the pool of deoxyribonucleoside triphosphates (dNTPs) and activates the replication checkpoint. The checkpoint-mutant cells carried deletions either of rad3 (which encodes the fission yeast homologue of ATR) or cds1 (which encodes the fission yeast homologue of Chk2). Our microarray results proved to be largely consistent with those independently obtained and recently published by three other laboratories. However, we were able to reconcile differences between the previous studies regarding the extent to which fission yeast replication origins are affected by the replication checkpoint. We found (consistent with the three previous studies after appropriate interpretation) that, in surprising contrast to budding yeast, most fission yeast origins, including both early- and late-firing origins, are not significantly affected by checkpoint mutations during replication in the presence of HU. A few origins (approximately 3%) behaved like those in budding yeast: they replicated earlier in the checkpoint mutants than in wild type. These were located primarily in the heterochromatic subtelomeric regions of chromosomes 1 and 2. Indeed, the subtelomeric regions defined by the strongest checkpoint restraint correspond precisely to previously mapped subtelomeric heterochromatin. This observation implies that subtelomeric heterochromatin in fission yeast differs from heterochromatin at centromeres, in the mating type region, and in ribosomal DNA, since these regions replicated at least as efficiently in wild-type cells as in checkpoint

  8. Checkpoint independence of most DNA replication origins in fission yeast

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    Mickle, Katie L; Ramanathan, Sunita; Rosebrock, Adam; Oliva, Anna; Chaudari, Amna; Yompakdee, Chulee; Scott, Donna; Leatherwood, Janet; Huberman, Joel A

    2007-01-01

    Background In budding yeast, the replication checkpoint slows progress through S phase by inhibiting replication origin firing. In mammals, the replication checkpoint inhibits both origin firing and replication fork movement. To find out which strategy is employed in the fission yeast, Schizosaccharomyces pombe, we used microarrays to investigate the use of origins by wild-type and checkpoint-mutant strains in the presence of hydroxyurea (HU), which limits the pool of deoxyribonucleoside triphosphates (dNTPs) and activates the replication checkpoint. The checkpoint-mutant cells carried deletions either of rad3 (which encodes the fission yeast homologue of ATR) or cds1 (which encodes the fission yeast homologue of Chk2). Results Our microarray results proved to be largely consistent with those independently obtained and recently published by three other laboratories. However, we were able to reconcile differences between the previous studies regarding the extent to which fission yeast replication origins are affected by the replication checkpoint. We found (consistent with the three previous studies after appropriate interpretation) that, in surprising contrast to budding yeast, most fission yeast origins, including both early- and late-firing origins, are not significantly affected by checkpoint mutations during replication in the presence of HU. A few origins (~3%) behaved like those in budding yeast: they replicated earlier in the checkpoint mutants than in wild type. These were located primarily in the heterochromatic subtelomeric regions of chromosomes 1 and 2. Indeed, the subtelomeric regions defined by the strongest checkpoint restraint correspond precisely to previously mapped subtelomeric heterochromatin. This observation implies that subtelomeric heterochromatin in fission yeast differs from heterochromatin at centromeres, in the mating type region, and in ribosomal DNA, since these regions replicated at least as efficiently in wild-type cells as in

  9. Checkpoint independence of most DNA replication origins in fission yeast

    Directory of Open Access Journals (Sweden)

    Scott Donna

    2007-12-01

    Full Text Available Abstract Background In budding yeast, the replication checkpoint slows progress through S phase by inhibiting replication origin firing. In mammals, the replication checkpoint inhibits both origin firing and replication fork movement. To find out which strategy is employed in the fission yeast, Schizosaccharomyces pombe, we used microarrays to investigate the use of origins by wild-type and checkpoint-mutant strains in the presence of hydroxyurea (HU, which limits the pool of deoxyribonucleoside triphosphates (dNTPs and activates the replication checkpoint. The checkpoint-mutant cells carried deletions either of rad3 (which encodes the fission yeast homologue of ATR or cds1 (which encodes the fission yeast homologue of Chk2. Results Our microarray results proved to be largely consistent with those independently obtained and recently published by three other laboratories. However, we were able to reconcile differences between the previous studies regarding the extent to which fission yeast replication origins are affected by the replication checkpoint. We found (consistent with the three previous studies after appropriate interpretation that, in surprising contrast to budding yeast, most fission yeast origins, including both early- and late-firing origins, are not significantly affected by checkpoint mutations during replication in the presence of HU. A few origins (~3% behaved like those in budding yeast: they replicated earlier in the checkpoint mutants than in wild type. These were located primarily in the heterochromatic subtelomeric regions of chromosomes 1 and 2. Indeed, the subtelomeric regions defined by the strongest checkpoint restraint correspond precisely to previously mapped subtelomeric heterochromatin. This observation implies that subtelomeric heterochromatin in fission yeast differs from heterochromatin at centromeres, in the mating type region, and in ribosomal DNA, since these regions replicated at least as efficiently in wild

  10. Prereplicative complexes assembled in vitro support origin-dependent and independent DNA replication

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    On, Kin Fan; Beuron, Fabienne; Frith, David; Snijders, Ambrosius P; Morris, Edward P; Diffley, John F X

    2014-01-01

    Eukaryotic DNA replication initiates from multiple replication origins. To ensure each origin fires just once per cell cycle, initiation is divided into two biochemically discrete steps: the Mcm2-7 helicase is first loaded into prereplicative complexes (pre-RCs) as an inactive double hexamer by the origin recognition complex (ORC), Cdt1 and Cdc6; the helicase is then activated by a set of “firing factors.” Here, we show that plasmids containing pre-RCs assembled with purified proteins support complete and semi-conservative replication in extracts from budding yeast cells overexpressing firing factors. Replication requires cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK). DDK phosphorylation of Mcm2-7 does not by itself promote separation of the double hexamer, but is required for the recruitment of firing factors and replisome components in the extract. Plasmid replication does not require a functional replication origin; however, in the presence of competitor DNA and limiting ORC concentrations, replication becomes origin-dependent in this system. These experiments indicate that Mcm2-7 double hexamers can be precursors of replication and provide insight into the nature of eukaryotic DNA replication origins. PMID:24566989

  11. The Hsk1(Cdc7) replication kinase regulates origin efficiency.

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    Patel, Prasanta K; Kommajosyula, Naveen; Rosebrock, Adam; Bensimon, Aaron; Leatherwood, Janet; Bechhoefer, John; Rhind, Nicholas

    2008-12-01

    Origins of DNA replication are generally inefficient, with most firing in fewer than half of cell cycles. However, neither the mechanism nor the importance of the regulation of origin efficiency is clear. In fission yeast, origin firing is stochastic, leading us to hypothesize that origin inefficiency and stochasticity are the result of a diffusible, rate-limiting activator. We show that the Hsk1-Dfp1 replication kinase (the fission yeast Cdc7-Dbf4 homologue) plays such a role. Increasing or decreasing Hsk1-Dfp1 levels correspondingly increases or decreases origin efficiency. Furthermore, tethering Hsk1-Dfp1 near an origin increases the efficiency of that origin, suggesting that the effective local concentration of Hsk1-Dfp1 regulates origin firing. Using photobleaching, we show that Hsk1-Dfp1 is freely diffusible in the nucleus. These results support a model in which the accessibility of replication origins to Hsk1-Dfp1 regulates origin efficiency and provides a potential mechanistic link between chromatin structure and replication timing. By manipulating Hsk1-Dfp1 levels, we show that increasing or decreasing origin firing rates leads to an increase in genomic instability, demonstrating the biological importance of appropriate origin efficiency.

  12. The Hsk1(Cdc7) Replication Kinase Regulates Origin Efficiency

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    Patel, Prasanta K.; Kommajosyula, Naveen; Rosebrock, Adam; Bensimon, Aaron; Leatherwood, Janet; Bechhoefer, John

    2008-01-01

    Origins of DNA replication are generally inefficient, with most firing in fewer than half of cell cycles. However, neither the mechanism nor the importance of the regulation of origin efficiency is clear. In fission yeast, origin firing is stochastic, leading us to hypothesize that origin inefficiency and stochasticity are the result of a diffusible, rate-limiting activator. We show that the Hsk1-Dfp1 replication kinase (the fission yeast Cdc7-Dbf4 homologue) plays such a role. Increasing or decreasing Hsk1-Dfp1 levels correspondingly increases or decreases origin efficiency. Furthermore, tethering Hsk1-Dfp1 near an origin increases the efficiency of that origin, suggesting that the effective local concentration of Hsk1-Dfp1 regulates origin firing. Using photobleaching, we show that Hsk1-Dfp1 is freely diffusible in the nucleus. These results support a model in which the accessibility of replication origins to Hsk1-Dfp1 regulates origin efficiency and provides a potential mechanistic link between chromatin structure and replication timing. By manipulating Hsk1-Dfp1 levels, we show that increasing or decreasing origin firing rates leads to an increase in genomic instability, demonstrating the biological importance of appropriate origin efficiency. PMID:18799612

  13. How and why multiple MCMs are loaded at origins of DNA replication.

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    Das, Shankar P; Rhind, Nicholas

    2016-07-01

    Recent work suggests that DNA replication origins are regulated by the number of multiple mini-chromosome maintenance (MCM) complexes loaded. Origins are defined by the loading of MCM - the replicative helicase which initiates DNA replication and replication kinetics determined by origin's location and firing times. However, activation of MCM is heterogeneous; different origins firing at different times in different cells. Also, more MCMs are loaded in G1 than are used in S phase. These aspects of MCM biology are explained by the observation that multiple MCMs are loaded at origins. Having more MCMs at early origins makes them more likely to fire, effecting differences in origin efficiency that define replication timing. Nonetheless, multiple MCM loading raises new questions, such as how they are loaded, where these MCMs reside at origins, and how their presence affects replication timing. In this review, we address these questions and discuss future avenues of research. © 2016 WILEY Periodicals, Inc.

  14. Regulated eukaryotic DNA replication origin firing with purified proteins.

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    Yeeles, Joseph T P; Deegan, Tom D; Janska, Agnieszka; Early, Anne; Diffley, John F X

    2015-03-26

    Eukaryotic cells initiate DNA replication from multiple origins, which must be tightly regulated to promote precise genome duplication in every cell cycle. To accomplish this, initiation is partitioned into two temporally discrete steps: a double hexameric minichromosome maintenance (MCM) complex is first loaded at replication origins during G1 phase, and then converted to the active CMG (Cdc45-MCM-GINS) helicase during S phase. Here we describe the reconstitution of budding yeast DNA replication initiation with 16 purified replication factors, made from 42 polypeptides. Origin-dependent initiation recapitulates regulation seen in vivo. Cyclin-dependent kinase (CDK) inhibits MCM loading by phosphorylating the origin recognition complex (ORC) and promotes CMG formation by phosphorylating Sld2 and Sld3. Dbf4-dependent kinase (DDK) promotes replication by phosphorylating MCM, and can act either before or after CDK. These experiments define the minimum complement of proteins, protein kinase substrates and co-factors required for regulated eukaryotic DNA replication.

  15. The Hsk1(Cdc7) Replication Kinase Regulates Origin Efficiency

    OpenAIRE

    Patel, Prasanta K.; Kommajosyula, Naveen; Rosebrock, Adam; Bensimon, Aaron; Leatherwood, Janet; Bechhoefer, John; Rhind, Nicholas

    2008-01-01

    Origins of DNA replication are generally inefficient, with most firing in fewer than half of cell cycles. However, neither the mechanism nor the importance of the regulation of origin efficiency is clear. In fission yeast, origin firing is stochastic, leading us to hypothesize that origin inefficiency and stochasticity are the result of a diffusible, rate-limiting activator. We show that the Hsk1-Dfp1 replication kinase (the fission yeast Cdc7-Dbf4 homologue) plays such a role. Increasing or ...

  16. Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress.

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    Macheret, Morgane; Halazonetis, Thanos D

    2018-03-01

    Oncogene-induced DNA replication stress contributes critically to the genomic instability that is present in cancer. However, elucidating how oncogenes deregulate DNA replication has been impeded by difficulty in mapping replication initiation sites on the human genome. Here, using a sensitive assay to monitor nascent DNA synthesis in early S phase, we identified thousands of replication initiation sites in cells before and after induction of the oncogenes CCNE1 and MYC. Remarkably, both oncogenes induced firing of a novel set of DNA replication origins that mapped within highly transcribed genes. These ectopic origins were normally suppressed by transcription during G1, but precocious entry into S phase, before all genic regions had been transcribed, allowed firing of origins within genes in cells with activated oncogenes. Forks from oncogene-induced origins were prone to collapse, as a result of conflicts between replication and transcription, and were associated with DNA double-stranded break formation and chromosomal rearrangement breakpoints both in our experimental system and in a large cohort of human cancers. Thus, firing of intragenic origins caused by premature S phase entry represents a mechanism of oncogene-induced DNA replication stress that is relevant for genomic instability in human cancer.

  17. Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe.

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    Marques, Catarina A; Dickens, Nicholas J; Paape, Daniel; Campbell, Samantha J; McCulloch, Richard

    2015-10-19

    DNA replication initiates on defined genome sites, termed origins. Origin usage appears to follow common rules in the eukaryotic organisms examined to date: all chromosomes are replicated from multiple origins, which display variations in firing efficiency and are selected from a larger pool of potential origins. To ask if these features of DNA replication are true of all eukaryotes, we describe genome-wide origin mapping in the parasite Leishmania. Origin mapping in Leishmania suggests a striking divergence in origin usage relative to characterized eukaryotes, since each chromosome appears to be replicated from a single origin. By comparing two species of Leishmania, we find evidence that such origin singularity is maintained in the face of chromosome fusion or fission events during evolution. Mapping Leishmania origins suggests that all origins fire with equal efficiency, and that the genomic sites occupied by origins differ from related non-origins sites. Finally, we provide evidence that origin location in Leishmania displays striking conservation with Trypanosoma brucei, despite the latter parasite replicating its chromosomes from multiple, variable strength origins. The demonstration of chromosome replication for a single origin in Leishmania, a microbial eukaryote, has implications for the evolution of origin multiplicity and associated controls, and may explain the pervasive aneuploidy that characterizes Leishmania chromosome architecture.

  18. Fragile genomic sites are associated with origins of replication.

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    Di Rienzi, Sara C; Collingwood, David; Raghuraman, M K; Brewer, Bonita J

    2009-09-09

    Genome rearrangements are mediators of evolution and disease. Such rearrangements are frequently bounded by transfer RNAs (tRNAs), transposable elements, and other repeated elements, suggesting a functional role for these elements in creating or repairing breakpoints. Though not well explored, there is evidence that origins of replication also colocalize with breakpoints. To investigate a potential correlation between breakpoints and origins, we analyzed evolutionary breakpoints defined between Saccharomyces cerevisiae and Kluyveromyces waltii and S. cerevisiae and a hypothetical ancestor of both yeasts, as well as breakpoints reported in the experimental literature. We find that origins correlate strongly with both evolutionary breakpoints and those described in the literature. Specifically, we find that origins firing earlier in S phase are more strongly correlated with breakpoints than are later-firing origins. Despite origins being located in genomic regions also bearing tRNAs and Ty elements, the correlation we observe between origins and breakpoints appears to be independent of these genomic features. This study lays the groundwork for understanding the mechanisms by which origins of replication may impact genome architecture and disease.

  19. Linker Histone Phosphorylation Regulates Global Timing of Replication Origin Firing*S⃞

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    Thiriet, Christophe; Hayes, Jeffrey J.

    2009-01-01

    Despite the presence of linker histone in all eukaryotes, the primary function(s) of this histone have been difficult to clarify. Knock-out experiments indicate that H1s play a role in regulation of only a small subset of genes but are an essential component in mouse development. Here, we show that linker histone (H1) is involved in the global regulation of DNA replication in Physarum polycephalum. We find that genomic DNA of H1 knock-down cells is more rapidly replicated, an effect due at least in part to disruption of the native timing of replication fork firing. Immunoprecipitation experiments demonstrate that H1 is transiently lost from replicating chromatin via a process facilitated by phosphorylation. Our results suggest that linker histones generate a chromatin environment refractory to replication and that their transient removal via protein phosphorylation during S phase is a critical step in the epigenetic regulation of replication timing. PMID:19015270

  20. DNA replication and cancer: From dysfunctional replication origin activities to therapeutic opportunities.

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    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

    2016-06-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways to promote genome integrity during DNA replication. This includes suppressing new replication origin firing, stabilization of replicating forks, and the safe restart of forks to prevent any loss of genetic information. Here, we describe mechanisms by which oncogenes can interfere with DNA replication thereby causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Cdc7 is required throughout the yeast S phase to activate replication origins.

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    Donaldson, A D; Fangman, W L; Brewer, B J

    1998-02-15

    The long-standing conclusion that the Cdc7 kinase of Saccharomyces cerevisiae is required only to trigger S phase has been challenged by recent data that suggests it acts directly on individual replication origins. We tested the possibility that early- and late-activated origins have different requirements for Cdc7 activity. Cells carrying a cdc7(ts) allele were first arrested in G1 at the cdc7 block by incubation at 37 degrees C, and then were allowed to enter S phase by brief incubation at 23 degrees C. During the S phase, after return to 37 degrees C, early-firing replication origins were activated, but late origins failed to fire. Similarly, a plasmid with a late-activated origin was defective in replication. As a consequence of the origin activation defect, duplication of chromosomal sequences that are normally replicated from late origins was greatly delayed. Early-replicating regions of the genome duplicated at approximately their normal time. The requirements of early and late origins for Cdc7 appear to be temporally rather than quantitatively different, as reducing overall levels of Cdc7 by growth at semi-permissive temperature reduced activation at early and late origins approximately equally. Our results show that Cdc7 activates early and late origins separately, with late origins requiring the activity later in S phase to permit replication initiation.

  2. Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae.

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    Soriano, Ignacio; Morafraile, Esther C; Vázquez, Enrique; Antequera, Francisco; Segurado, Mónica

    2014-09-13

    Eukaryotic genomes are replicated during S phase according to a temporal program. Several determinants control the timing of origin firing, including the chromatin environment and epigenetic modifications. However, how chromatin structure influences the timing of the activation of specific origins is still poorly understood. By performing high-resolution analysis of genome-wide nucleosome positioning we have identified different chromatin architectures at early and late replication origins. These different patterns are already established in G1 and are tightly correlated with the organization of adjacent transcription units. Moreover, specific early and late nucleosomal patterns are fixed robustly, even in rpd3 mutants in which histone acetylation and origin timing have been significantly altered. Nevertheless, higher histone acetylation levels correlate with the local modulation of chromatin structure, leading to increased origin accessibility. In addition, we conducted parallel analyses of replication and nucleosome dynamics that revealed that chromatin structure at origins is modulated during origin activation. Our results show that early and late replication origins present distinctive nucleosomal configurations, which are preferentially associated to different genomic regions. Our data also reveal that origin structure is dynamic and can be locally modulated by histone deacetylation, as well as by origin activation. These data offer novel insight into the contribution of chromatin structure to origin selection and firing in budding yeast.

  3. Robust Replication Control Is Generated by Temporal Gaps between Licensing and Firing Phases and Depends on Degradation of Firing Factor Sld2

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    Karl-Uwe Reusswig

    2016-10-01

    Full Text Available Temporal separation of DNA replication initiation into licensing and firing phases ensures the precise duplication of the genome during each cell cycle. Cyclin-dependent kinase (CDK is known to generate this separation by activating firing factors and at the same time inhibiting licensing factors but may not be sufficient to ensure robust separation at transitions between both phases. Here, we show that a temporal gap separates the inactivation of firing factors from the re-activation of licensing factors during mitosis in budding yeast. We find that gap size critically depends on phosphorylation-dependent degradation of the firing factor Sld2 mediated by CDK, DDK, Mck1, and Cdc5 kinases and the ubiquitin-ligases Dma1/2. Stable mutants of Sld2 minimize the gap and cause increased genome instability in an origin-dependent manner when combined with deregulation of other replication regulators or checkpoint mechanisms. Robust separation of licensing and firing phases therefore appears indispensable to safeguard genome stability.

  4. High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

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    Federico Comoglio

    2015-05-01

    Full Text Available At every cell cycle, faithful inheritance of metazoan genomes requires the concerted activation of thousands of DNA replication origins. However, the genetic and chromatin features defining metazoan replication start sites remain largely unknown. Here, we delineate the origin repertoire of the Drosophila genome at high resolution. We address the role of origin-proximal G-quadruplexes and suggest that they transiently stall replication forks in vivo. We dissect the chromatin configuration of replication origins and identify a rich spatial organization of chromatin features at initiation sites. DNA shape and chromatin configurations, not strict sequence motifs, mark and predict origins in higher eukaryotes. We further examine the link between transcription and origin firing and reveal that modulation of origin activity across cell types is intimately linked to cell-type-specific transcriptional programs. Our study unravels conserved origin features and provides unique insights into the relationship among DNA topology, chromatin, transcription, and replication initiation across metazoa.

  5. DNA replication origins-where do we begin?

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    Prioleau, Marie-Noëlle; MacAlpine, David M

    2016-08-01

    For more than three decades, investigators have sought to identify the precise locations where DNA replication initiates in mammalian genomes. The development of molecular and biochemical approaches to identify start sites of DNA replication (origins) based on the presence of defining and characteristic replication intermediates at specific loci led to the identification of only a handful of mammalian replication origins. The limited number of identified origins prevented a comprehensive and exhaustive search for conserved genomic features that were capable of specifying origins of DNA replication. More recently, the adaptation of origin-mapping assays to genome-wide approaches has led to the identification of tens of thousands of replication origins throughout mammalian genomes, providing an unprecedented opportunity to identify both genetic and epigenetic features that define and regulate their distribution and utilization. Here we summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages. © 2016 Prioleau and MacAlpine; Published by Cold Spring Harbor Laboratory Press.

  6. Mapping replication origins in yeast chromosomes.

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    Brewer, B J; Fangman, W L

    1991-07-01

    The replicon hypothesis, first proposed in 1963 by Jacob and Brenner, states that DNA replication is controlled at sites called origins. Replication origins have been well studied in prokaryotes. However, the study of eukaryotic chromosomal origins has lagged behind, because until recently there has been no method for reliably determining the identity and location of origins from eukaryotic chromosomes. Here, we review a technique we developed with the yeast Saccharomyces cerevisiae that allows both the mapping of replication origins and an assessment of their activity. Two-dimensional agarose gel electrophoresis and Southern hybridization with total genomic DNA are used to determine whether a particular restriction fragment acquires the branched structure diagnostic of replication initiation. The technique has been used to localize origins in yeast chromosomes and assess their initiation efficiency. In some cases, origin activation is dependent upon the surrounding context. The technique is also being applied to a variety of eukaryotic organisms.

  7. DNA Replication in Engineered Escherichia coli Genomes with Extra Replication Origins.

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    Milbredt, Sarah; Farmani, Neda; Sobetzko, Patrick; Waldminghaus, Torsten

    2016-10-21

    The standard outline of bacterial genomes is a single circular chromosome with a single replication origin. From the bioengineering perspective, it appears attractive to extend this basic setup. Bacteria with split chromosomes or multiple replication origins have been successfully constructed in the last few years. The characteristics of these engineered strains will largely depend on the respective DNA replication patterns. However, the DNA replication has not been investigated systematically in engineered bacteria with multiple origins or split replicons. Here we fill this gap by studying a set of strains consisting of (i) E. coli strains with an extra copy of the native replication origin (oriC), (ii) E. coli strains with an extra copy of the replication origin from the secondary chromosome of Vibrio cholerae (oriII), and (iii) a strain in which the E. coli chromosome is split into two linear replicons. A combination of flow cytometry, microarray-based comparative genomic hybridization (CGH), and modeling revealed silencing of extra oriC copies and differential timing of ectopic oriII copies compared to the native oriC. The results were used to derive construction rules for future multiorigin and multireplicon projects.

  8. Initiation preference at a yeast origin of replication.

    Science.gov (United States)

    Brewer, B J; Fangman, W L

    1994-04-12

    Replication origins in the yeast Saccharomyces cerevisiae are identified as autonomous replication sequence (ARS) elements. To examine the effect of origin density on replication initiation, we have analyzed the replication of a plasmid that contains two copies of the same origin, ARS1. The activation of origins and the direction that replication forks move through flanking sequences can be physically determined by analyzing replication intermediates on two-dimensional agarose gels. We find that only one of the two identical ARSs on the plasmid initiates replication on any given plasmid molecule; that is, this close spacing of ARSs results in an apparent interference between the potential origins. Moreover, in the particular plasmid that we constructed, one of the two identical copies of ARS1 is used four times more frequently than the other one. These results show that the plasmid context is critical for determining the preferred origin. This origin preference is also exhibited when the tandem copies of ARS1 are introduced into a yeast chromosome. The sequences responsible for establishing the origin preference have been identified by deletion analysis and are found to reside in a portion of the yeast URA3 gene.

  9. Structural diversity and dynamics of genomic replication origins in Schizosaccharomyces pombe

    Science.gov (United States)

    Cotobal, Cristina; Segurado, Mónica; Antequera, Francisco

    2010-01-01

    DNA replication origins (ORI) in Schizosaccharomyces pombe colocalize with adenine and thymine (A+T)-rich regions, and earlier analyses have established a size from 0.5 to over 3 kb for a DNA fragment to drive replication in plasmid assays. We have asked what are the requirements for ORI function in the chromosomal context. By designing artificial ORIs, we have found that A+T-rich fragments as short as 100 bp without homology to S. pombe DNA are able to initiate replication in the genome. On the other hand, functional dissection of endogenous ORIs has revealed that some of them span a few kilobases and include several modules that may be as short as 25–30 contiguous A+Ts capable of initiating replication from ectopic chromosome positions. The search for elements with these characteristics across the genome has uncovered an earlier unnoticed class of low-efficiency ORIs that fire late during S phase. These results indicate that ORI specification and dynamics varies widely in S. pombe, ranging from very short elements to large regions reminiscent of replication initiation zones in mammals. PMID:20094030

  10. Structural properties of replication origins in yeast DNA sequences

    International Nuclear Information System (INIS)

    Cao Xiaoqin; Zeng Jia; Yan Hong

    2008-01-01

    Sequence-dependent DNA flexibility is an important structural property originating from the DNA 3D structure. In this paper, we investigate the DNA flexibility of the budding yeast (S. Cerevisiae) replication origins on a genome-wide scale using flexibility parameters from two different models, the trinucleotide and the tetranucleotide models. Based on analyzing average flexibility profiles of 270 replication origins, we find that yeast replication origins are significantly rigid compared with their surrounding genomic regions. To further understand the highly distinctive property of replication origins, we compare the flexibility patterns between yeast replication origins and promoters, and find that they both contain significantly rigid DNAs. Our results suggest that DNA flexibility is an important factor that helps proteins recognize and bind the target sites in order to initiate DNA replication. Inspired by the role of the rigid region in promoters, we speculate that the rigid replication origins may facilitate binding of proteins, including the origin recognition complex (ORC), Cdc6, Cdt1 and the MCM2-7 complex

  11. Varicella-zoster virus (VZV) origin of DNA replication oriS influences origin-dependent DNA replication and flanking gene transcription.

    Science.gov (United States)

    Khalil, Mohamed I; Sommer, Marvin H; Hay, John; Ruyechan, William T; Arvin, Ann M

    2015-07-01

    The VZV genome has two origins of DNA replication (oriS), each of which consists of an AT-rich sequence and three origin binding protein (OBP) sites called Box A, C and B. In these experiments, the mutation in the core sequence CGC of the Box A and C not only inhibited DNA replication but also inhibited both ORF62 and ORF63 expression in reporter gene assays. In contrast the Box B mutation did not influence DNA replication or flanking gene transcription. These results suggest that efficient DNA replication enhances ORF62 and ORF63 transcription. Recombinant viruses carrying these mutations in both sites and one with a deletion of the whole oriS were constructed. Surprisingly, the recombinant virus lacking both copies of oriS retained the capacity to replicate in melanoma and HELF cells suggesting that VZV has another origin of DNA replication. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. ATR prohibits replication catastrophe by preventing global exhaustion of RPA.

    Science.gov (United States)

    Toledo, Luis Ignacio; Altmeyer, Matthias; Rask, Maj-Britt; Lukas, Claudia; Larsen, Dorthe Helena; Povlsen, Lou Klitgaard; Bekker-Jensen, Simon; Mailand, Niels; Bartek, Jiri; Lukas, Jiri

    2013-11-21

    ATR, activated by replication stress, protects replication forks locally and suppresses origin firing globally. Here, we show that these functions of ATR are mechanistically coupled. Although initially stable, stalled forks in ATR-deficient cells undergo nucleus-wide breakage after unscheduled origin firing generates an excess of single-stranded DNA that exhausts the nuclear pool of RPA. Partial reduction of RPA accelerated fork breakage, and forced elevation of RPA was sufficient to delay such "replication catastrophe" even in the absence of ATR activity. Conversely, unscheduled origin firing induced breakage of stalled forks even in cells with active ATR. Thus, ATR-mediated suppression of dormant origins shields active forks against irreversible breakage via preventing exhaustion of nuclear RPA. This study elucidates how replicating genomes avoid destabilizing DNA damage. Because cancer cells commonly feature intrinsically high replication stress, this study also provides a molecular rationale for their hypersensitivity to ATR inhibitors. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Universal Temporal Profile of Replication Origin Activation in Eukaryotes

    Science.gov (United States)

    Goldar, Arach

    2011-03-01

    The complete and faithful transmission of eukaryotic genome to daughter cells involves the timely duplication of mother cell's DNA. DNA replication starts at multiple chromosomal positions called replication origin. From each activated replication origin two replication forks progress in opposite direction and duplicate the mother cell's DNA. While it is widely accepted that in eukaryotic organisms replication origins are activated in a stochastic manner, little is known on the sources of the observed stochasticity. It is often associated to the population variability to enter S phase. We extract from a growing Saccharomyces cerevisiae population the average rate of origin activation in a single cell by combining single molecule measurements and a numerical deconvolution technique. We show that the temporal profile of the rate of origin activation in a single cell is similar to the one extracted from a replicating cell population. Taking into account this observation we exclude the population variability as the origin of observed stochasticity in origin activation. We confirm that the rate of origin activation increases in the early stage of S phase and decreases at the latter stage. The population average activation rate extracted from single molecule analysis is in prefect accordance with the activation rate extracted from published micro-array data, confirming therefore the homogeneity and genome scale invariance of dynamic of replication process. All these observations point toward a possible role of replication fork to control the rate of origin activation.

  14. Modeling inhomogeneous DNA replication kinetics.

    Directory of Open Access Journals (Sweden)

    Michel G Gauthier

    Full Text Available In eukaryotic organisms, DNA replication is initiated at a series of chromosomal locations called origins, where replication forks are assembled proceeding bidirectionally to replicate the genome. The distribution and firing rate of these origins, in conjunction with the velocity at which forks progress, dictate the program of the replication process. Previous attempts at modeling DNA replication in eukaryotes have focused on cases where the firing rate and the velocity of replication forks are homogeneous, or uniform, across the genome. However, it is now known that there are large variations in origin activity along the genome and variations in fork velocities can also take place. Here, we generalize previous approaches to modeling replication, to allow for arbitrary spatial variation of initiation rates and fork velocities. We derive rate equations for left- and right-moving forks and for replication probability over time that can be solved numerically to obtain the mean-field replication program. This method accurately reproduces the results of DNA replication simulation. We also successfully adapted our approach to the inverse problem of fitting measurements of DNA replication performed on single DNA molecules. Since such measurements are performed on specified portion of the genome, the examined DNA molecules may be replicated by forks that originate either within the studied molecule or outside of it. This problem was solved by using an effective flux of incoming replication forks at the model boundaries to represent the origin activity outside the studied region. Using this approach, we show that reliable inferences can be made about the replication of specific portions of the genome even if the amount of data that can be obtained from single-molecule experiments is generally limited.

  15. Dormant origins as a built-in safeguard in eukaryotic DNA replication against genome instability and disease development.

    Science.gov (United States)

    Shima, Naoko; Pederson, Kayla D

    2017-08-01

    DNA replication is a prerequisite for cell proliferation, yet it can be increasingly challenging for a eukaryotic cell to faithfully duplicate its genome as its size and complexity expands. Dormant origins now emerge as a key component for cells to successfully accomplish such a demanding but essential task. In this perspective, we will first provide an overview of the fundamental processes eukaryotic cells have developed to regulate origin licensing and firing. With a special focus on mammalian systems, we will then highlight the role of dormant origins in preventing replication-associated genome instability and their functional interplay with proteins involved in the DNA damage repair response for tumor suppression. Lastly, deficiencies in the origin licensing machinery will be discussed in relation to their influence on stem cell maintenance and human diseases. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Maintaining replication origins in the face of genomic change.

    Science.gov (United States)

    Di Rienzi, Sara C; Lindstrom, Kimberly C; Mann, Tobias; Noble, William S; Raghuraman, M K; Brewer, Bonita J

    2012-10-01

    Origins of replication present a paradox to evolutionary biologists. As a collection, they are absolutely essential genomic features, but individually are highly redundant and nonessential. It is therefore difficult to predict to what extent and in what regard origins are conserved over evolutionary time. Here, through a comparative genomic analysis of replication origins and chromosomal replication patterns in the budding yeasts Saccharomyces cerevisiae and Lachancea waltii, we assess to what extent replication origins survived genomic change produced from 150 million years of evolution. We find that L. waltii origins exhibit a core consensus sequence and nucleosome occupancy pattern highly similar to those of S. cerevisiae origins. We further observe that the overall progression of chromosomal replication is similar between L. waltii and S. cerevisiae. Nevertheless, few origins show evidence of being conserved in location between the two species. Among the conserved origins are those surrounding centromeres and adjacent to histone genes, suggesting that proximity to an origin may be important for their regulation. We conclude that, over evolutionary time, origins maintain sequence, structure, and regulation, but are continually being created and destroyed, with the result that their locations are generally not conserved.

  17. Non‐Canonical Replication Initiation: You’re Fired!

    Directory of Open Access Journals (Sweden)

    Bazilė Ravoitytė

    2017-01-01

    Full Text Available The division of prokaryotic and eukaryotic cells produces two cells that inherit a perfect copy of the genetic material originally derived from the mother cell. The initiation of canonical DNA replication must be coordinated to the cell cycle to ensure the accuracy of genome duplication. Controlled replication initiation depends on a complex interplay of cis‐acting DNA sequences, the so‐called origins of replication (ori, with trans‐acting factors involved in the onset of DNA synthesis. The interplay of cis‐acting elements and trans‐acting factors ensures that cells initiate replication at sequence‐specific sites only once, and in a timely order, to avoid chromosomal endoreplication. However, chromosome breakage and excessive RNA:DNA hybrid formation can cause breakinduced (BIR or transcription‐initiated replication (TIR, respectively. These non‐canonical replication events are expected to affect eukaryotic genome function and maintenance, and could be important for genome evolution and disease development. In this review, we describe the difference between canonical and non‐canonical DNA replication, and focus on mechanistic differences and common features between BIR and TIR. Finally, we discuss open issues on the factors and molecular mechanisms involved in TIR.

  18. Enzymatic recognition of DNA replication origins

    International Nuclear Information System (INIS)

    Stayton, M.M.; Bertsch, L.; Biswas, S.

    1983-01-01

    In this paper we discuss the process of recognition of the complementary-strand origin with emphasis on RNA polymerase action in priming M13 DNA replication, the role of primase in G4 DNA replication, and the function of protein n, a priming protein, during primosome assembly. These phage systems do not require several of the bacterial DNA replication enzymes, particularly those involved in the regulation of chromosome copy number of the initiatiion of replication of duplex DNA. 51 references, 13 figures, 1 table

  19. 3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression.

    Science.gov (United States)

    Löb, D; Lengert, N; Chagin, V O; Reinhart, M; Casas-Delucchi, C S; Cardoso, M C; Drossel, B

    2016-04-07

    DNA replication dynamics in cells from higher eukaryotes follows very complex but highly efficient mechanisms. However, the principles behind initiation of potential replication origins and emergence of typical patterns of nuclear replication sites remain unclear. Here, we propose a comprehensive model of DNA replication in human cells that is based on stochastic, proximity-induced replication initiation. Critical model features are: spontaneous stochastic firing of individual origins in euchromatin and facultative heterochromatin, inhibition of firing at distances below the size of chromatin loops and a domino-like effect by which replication forks induce firing of nearby origins. The model reproduces the empirical temporal and chromatin-related properties of DNA replication in human cells. We advance the one-dimensional DNA replication model to a spatial model by taking into account chromatin folding in the nucleus, and we are able to reproduce the spatial and temporal characteristics of the replication foci distribution throughout S-phase.

  20. Replication Catastrophe

    DEFF Research Database (Denmark)

    Toledo, Luis; Neelsen, Kai John; Lukas, Jiri

    2017-01-01

    Proliferating cells rely on the so-called DNA replication checkpoint to ensure orderly completion of genome duplication, and its malfunction may lead to catastrophic genome disruption, including unscheduled firing of replication origins, stalling and collapse of replication forks, massive DNA...... breakage, and, ultimately, cell death. Despite many years of intensive research into the molecular underpinnings of the eukaryotic replication checkpoint, the mechanisms underlying the dismal consequences of its failure remain enigmatic. A recent development offers a unifying model in which the replication...... checkpoint guards against global exhaustion of rate-limiting replication regulators. Here we discuss how such a mechanism can prevent catastrophic genome disruption and suggest how to harness this knowledge to advance therapeutic strategies to eliminate cancer cells that inherently proliferate under...

  1. ATR Prohibits Replication Catastrophe by Preventing Global Exhaustion of RPA

    DEFF Research Database (Denmark)

    Toledo Lazaro, Luis Ignacio; Altmeyer, Matthias; Rask, Maj-Britt

    2013-01-01

    origin firing generates an excess of single-stranded DNA that exhausts the nuclear pool of RPA. Partial reduction of RPA accelerated fork breakage, and forced elevation of RPA was sufficient to delay such "replication catastrophe" even in the absence of ATR activity. Conversely, unscheduled origin firing...... induced breakage of stalled forks even in cells with active ATR. Thus, ATR-mediated suppression of dormant origins shields active forks against irreversible breakage via preventing exhaustion of nuclear RPA. This study elucidates how replicating genomes avoid destabilizing DNA damage. Because cancer cells...

  2. Addressing the "Replication Crisis": Using Original Studies to Design Replication Studies with Appropriate Statistical Power.

    Science.gov (United States)

    Anderson, Samantha F; Maxwell, Scott E

    2017-01-01

    Psychology is undergoing a replication crisis. The discussion surrounding this crisis has centered on mistrust of previous findings. Researchers planning replication studies often use the original study sample effect size as the basis for sample size planning. However, this strategy ignores uncertainty and publication bias in estimated effect sizes, resulting in overly optimistic calculations. A psychologist who intends to obtain power of .80 in the replication study, and performs calculations accordingly, may have an actual power lower than .80. We performed simulations to reveal the magnitude of the difference between actual and intended power based on common sample size planning strategies and assessed the performance of methods that aim to correct for effect size uncertainty and/or bias. Our results imply that even if original studies reflect actual phenomena and were conducted in the absence of questionable research practices, popular approaches to designing replication studies may result in a low success rate, especially if the original study is underpowered. Methods correcting for bias and/or uncertainty generally had higher actual power, but were not a panacea for an underpowered original study. Thus, it becomes imperative that 1) original studies are adequately powered and 2) replication studies are designed with methods that are more likely to yield the intended level of power.

  3. Initiation at closely spaced replication origins in a yeast chromosome.

    Science.gov (United States)

    Brewer, B J; Fangman, W L

    1993-12-10

    Replication of eukaryotic chromosomes involves initiation at origins spaced an average of 50 to 100 kilobase pairs. In yeast, potential origins can be recognized as autonomous replication sequences (ARSs) that allow maintenance of plasmids. However, there are more ARS elements than active chromosomal origins. The possibility was examined that close spacing of ARSs can lead to inactive origins. Two ARSs located 6.5 kilobase pairs apart can indeed interfere with each other. Replication is initiated from one or the other ARS with equal probability, but rarely (< 5%) from both ARSs on the same DNA molecule.

  4. Structural changes in Mcm5 protein bypass Cdc7-Dbf4 function and reduce replication origin efficiency in Saccharomyces cerevisiae.

    Science.gov (United States)

    Hoang, Margaret L; Leon, Ronald P; Pessoa-Brandao, Luis; Hunt, Sonia; Raghuraman, M K; Fangman, Walton L; Brewer, Bonita J; Sclafani, Robert A

    2007-11-01

    Eukaryotic chromosomal replication is a complicated process with many origins firing at different efficiencies and times during S phase. Prereplication complexes are assembled on all origins in G(1) phase, and yet only a subset of complexes is activated during S phase by DDK (for Dbf4-dependent kinase) (Cdc7-Dbf4). The yeast mcm5-bob1 (P83L) mutation bypasses DDK but results in reduced intrinsic firing efficiency at 11 endogenous origins and at origins located on minichromosomes. Origin efficiency may result from Mcm5 protein assuming an altered conformation, as predicted from the atomic structure of an archaeal MCM (for minichromosome maintenance) homologue. Similarly, an intragenic mutation in a residue predicted to interact with P83L suppresses the mcm5-bob1 bypass phenotype. We propose DDK phosphorylation of the MCM complex normally results in a single, highly active conformation of Mcm5, whereas the mcm5-bob1 mutation produces a number of conformations, only one of which is permissive for origin activation. Random adoption of these alternate states by the mcm5-bob1 protein can explain both how origin firing occurs independently of DDK and why origin efficiency is reduced. Because similar mutations in mcm2 and mcm4 cannot bypass DDK, Mcm5 protein may be a unique Mcm protein that is the final target of DDK regulation.

  5. Origin of Fire.

    Science.gov (United States)

    Bennett, Ruth, Ed.

    Intended for use with college students, this booklet contains a traditional Hupa story (in Hupa and English) followed by information to aid in a critical literary analysis of the story and topics for student discussion. The introduction explains that "Origin of Fire"--first written down by P.E. Goddard in 1902 and still told by…

  6. Mechanism of Archaeal MCM Helicase Recruitment to DNA Replication Origins

    Science.gov (United States)

    Samson, Rachel Y.; Abeyrathne, Priyanka D.; Bell, Stephen D.

    2015-01-01

    Summary Cellular DNA replication origins direct the recruitment of replicative helicases via the action of initiator proteins belonging to the AAA+ superfamily of ATPases. Archaea have a simplified subset of the eukaryotic DNA replication machinery proteins and possess initiators that appear ancestral to both eukaryotic Orc1 and Cdc6. We have reconstituted origin-dependent recruitment of the homohexameric archaeal MCM in vitro with purified recombinant proteins. Using this system, we reveal that archaeal Orc1-1 fulfills both Orc1 and Cdc6 functions by binding to a replication origin and directly recruiting MCM helicase. We identify the interaction interface between these proteins and reveal how ATP binding by Orc1-1 modulates recruitment of MCM. Additionally, we provide evidence that an open-ring form of the archaeal MCM homohexamer is loaded at origins. PMID:26725007

  7. Mechanisms and regulation of DNA replication initiation in eukaryotes.

    Science.gov (United States)

    Parker, Matthew W; Botchan, Michael R; Berger, James M

    2017-04-01

    Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here, we review the molecular mechanisms that underpin eukaryotic DNA replication initiation - from selecting replication start sites to replicative helicase loading and activation - and describe how these events are often distinctly regulated across different eukaryotic model organisms.

  8. Causation and the origin of life. Metabolism or replication first?

    Science.gov (United States)

    Pross, Addy

    2004-06-01

    The conceptual gulf that separates the 'metabolism first' and 'replication first' mechanisms for the emergence of life continues to cloud the origin of life debate. In the present paper we analyze this aspect of the origin of life problem and offer arguments in favor of the 'replication first' school. Utilizing Wicken's two-tier approach to causation we argue that a causal connection between replication and metabolism can only be demonstrated if replication would have preceded metabolism. In conjunction with existing empirical evidence and theoretical reasoning, our analysis concludes that there is no substantive evidence for a 'metabolism first' mechanism for life's emergence, while a coherent case can be made for the 'replication first' group of mechanisms. The analysis reaffirms our conviction that life is an extreme expression of kinetic control, and that the emergence of metabolic pathways can be understood by considering life as a manifestation of 'replicative chemistry'.

  9. Chromatin Controls DNA Replication Origin Selection, Lagging-Strand Synthesis, and Replication Fork Rates.

    Science.gov (United States)

    Kurat, Christoph F; Yeeles, Joseph T P; Patel, Harshil; Early, Anne; Diffley, John F X

    2017-01-05

    The integrity of eukaryotic genomes requires rapid and regulated chromatin replication. How this is accomplished is still poorly understood. Using purified yeast replication proteins and fully chromatinized templates, we have reconstituted this process in vitro. We show that chromatin enforces DNA replication origin specificity by preventing non-specific MCM helicase loading. Helicase activation occurs efficiently in the context of chromatin, but subsequent replisome progression requires the histone chaperone FACT (facilitates chromatin transcription). The FACT-associated Nhp6 protein, the nucleosome remodelers INO80 or ISW1A, and the lysine acetyltransferases Gcn5 and Esa1 each contribute separately to maximum DNA synthesis rates. Chromatin promotes the regular priming of lagging-strand DNA synthesis by facilitating DNA polymerase α function at replication forks. Finally, nucleosomes disrupted during replication are efficiently re-assembled into regular arrays on nascent DNA. Our work defines the minimum requirements for chromatin replication in vitro and shows how multiple chromatin factors might modulate replication fork rates in vivo. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  10. Recent advances in the genome-wide study of DNA replication origins in yeast

    Directory of Open Access Journals (Sweden)

    Chong ePeng

    2015-02-01

    Full Text Available DNA replication, one of the central events in the cell cycle, is the basis of biological inheritance. In order to be duplicated, a DNA double helix must be opened at defined sites, which are called DNA replication origins (ORIs. Unlike in bacteria, where replication initiates from a single replication origin, multiple origins are utilized in the eukaryotic genome. Among them, the ORIs in budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe have been best characterized. In recent years, advances in DNA microarray and next-generation sequencing technologies have increased the number of yeast species involved in ORIs research dramatically. The ORIs in some nonconventional yeast species such as Kluyveromyces lactis and Pichia pastoris have also been genome-widely identified. Relevant databases of replication origins in yeast were constructed, then the comparative genomic analysis can be carried out. Here, we review several experimental approaches that have been used to map replication origins in yeast and some of the available web resources related to yeast ORIs. We also discuss the sequence characteristics and chromosome structures of ORIs in the four yeast species, which can be utilized to improve the replication origins prediction.

  11. Recent advances in the genome-wide study of DNA replication origins in yeast

    Science.gov (United States)

    Peng, Chong; Luo, Hao; Zhang, Xi; Gao, Feng

    2015-01-01

    DNA replication, one of the central events in the cell cycle, is the basis of biological inheritance. In order to be duplicated, a DNA double helix must be opened at defined sites, which are called DNA replication origins (ORIs). Unlike in bacteria, where replication initiates from a single replication origin, multiple origins are utilized in the eukaryotic genomes. Among them, the ORIs in budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe have been best characterized. In recent years, advances in DNA microarray and next-generation sequencing technologies have increased the number of yeast species involved in ORIs research dramatically. The ORIs in some non-conventional yeast species such as Kluyveromyces lactis and Pichia pastoris have also been genome-widely identified. Relevant databases of replication origins in yeast were constructed, then the comparative genomic analysis can be carried out. Here, we review several experimental approaches that have been used to map replication origins in yeast and some of the available web resources related to yeast ORIs. We also discuss the sequence characteristics and chromosome structures of ORIs in the four yeast species, which can be utilized to improve yeast replication origins prediction. PMID:25745419

  12. Loss of maintenance DNA methylation results in abnormal DNA origin firing during DNA replication

    Energy Technology Data Exchange (ETDEWEB)

    Haruta, Mayumi [Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601 (Japan); Shimada, Midori, E-mail: midorism@med.nagoya-cu.ac.jp [Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601 (Japan); Nishiyama, Atsuya; Johmura, Yoshikazu [Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601 (Japan); Le Tallec, Benoît; Debatisse, Michelle [Institut Curie, Centre de Recherche, 26 rue d’Ulm, CNRS UMR 3244, 75248 ParisCedex 05 (France); Nakanishi, Makoto, E-mail: mkt-naka@med.nagoya-cu.ac.jp [Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601 (Japan)

    2016-01-22

    The mammalian maintenance methyltransferase DNMT1 [DNA (cytosine-5-)-methyltransferase 1] mediates the inheritance of the DNA methylation pattern during replication. Previous studies have shown that depletion of DNMT1 causes a severe growth defect and apoptosis in differentiated cells. However, the detailed mechanisms behind this phenomenon remain poorly understood. Here we show that conditional ablation of Dnmt1 in murine embryonic fibroblasts (MEFs) resulted in an aberrant DNA replication program showing an accumulation of late-S phase replication and causing severely defective growth. Furthermore, we found that the catalytic activity and replication focus targeting sequence of DNMT1 are required for a proper DNA replication program. Taken together, our findings suggest that the maintenance of DNA methylation by DNMT1 plays a critical role in proper regulation of DNA replication in mammalian cells. - Highlights: • DNMT1 depletion results in an abnormal DNA replication program. • Aberrant DNA replication is independent of the DNA damage checkpoint in DNMT1cKO. • DNMT1 catalytic activity and RFT domain are required for proper DNA replication. • DNMT1 catalytic activity and RFT domain are required for cell proliferation.

  13. Loss of maintenance DNA methylation results in abnormal DNA origin firing during DNA replication

    International Nuclear Information System (INIS)

    Haruta, Mayumi; Shimada, Midori; Nishiyama, Atsuya; Johmura, Yoshikazu; Le Tallec, Benoît; Debatisse, Michelle; Nakanishi, Makoto

    2016-01-01

    The mammalian maintenance methyltransferase DNMT1 [DNA (cytosine-5-)-methyltransferase 1] mediates the inheritance of the DNA methylation pattern during replication. Previous studies have shown that depletion of DNMT1 causes a severe growth defect and apoptosis in differentiated cells. However, the detailed mechanisms behind this phenomenon remain poorly understood. Here we show that conditional ablation of Dnmt1 in murine embryonic fibroblasts (MEFs) resulted in an aberrant DNA replication program showing an accumulation of late-S phase replication and causing severely defective growth. Furthermore, we found that the catalytic activity and replication focus targeting sequence of DNMT1 are required for a proper DNA replication program. Taken together, our findings suggest that the maintenance of DNA methylation by DNMT1 plays a critical role in proper regulation of DNA replication in mammalian cells. - Highlights: • DNMT1 depletion results in an abnormal DNA replication program. • Aberrant DNA replication is independent of the DNA damage checkpoint in DNMT1cKO. • DNMT1 catalytic activity and RFT domain are required for proper DNA replication. • DNMT1 catalytic activity and RFT domain are required for cell proliferation.

  14. Mapping vaccinia virus DNA replication origins at nucleotide level by deep sequencing.

    Science.gov (United States)

    Senkevich, Tatiana G; Bruno, Daniel; Martens, Craig; Porcella, Stephen F; Wolf, Yuri I; Moss, Bernard

    2015-09-01

    Poxviruses reproduce in the host cytoplasm and encode most or all of the enzymes and factors needed for expression and synthesis of their double-stranded DNA genomes. Nevertheless, the mode of poxvirus DNA replication and the nature and location of the replication origins remain unknown. A current but unsubstantiated model posits only leading strand synthesis starting at a nick near one covalently closed end of the genome and continuing around the other end to generate a concatemer that is subsequently resolved into unit genomes. The existence of specific origins has been questioned because any plasmid can replicate in cells infected by vaccinia virus (VACV), the prototype poxvirus. We applied directional deep sequencing of short single-stranded DNA fragments enriched for RNA-primed nascent strands isolated from the cytoplasm of VACV-infected cells to pinpoint replication origins. The origins were identified as the switching points of the fragment directions, which correspond to the transition from continuous to discontinuous DNA synthesis. Origins containing a prominent initiation point mapped to a sequence within the hairpin loop at one end of the VACV genome and to the same sequence within the concatemeric junction of replication intermediates. These findings support a model for poxvirus genome replication that involves leading and lagging strand synthesis and is consistent with the requirements for primase and ligase activities as well as earlier electron microscopic and biochemical studies implicating a replication origin at the end of the VACV genome.

  15. Replication dynamics of the yeast genome.

    Science.gov (United States)

    Raghuraman, M K; Winzeler, E A; Collingwood, D; Hunt, S; Wodicka, L; Conway, A; Lockhart, D J; Davis, R W; Brewer, B J; Fangman, W L

    2001-10-05

    Oligonucleotide microarrays were used to map the detailed topography of chromosome replication in the budding yeast Saccharomyces cerevisiae. The times of replication of thousands of sites across the genome were determined by hybridizing replicated and unreplicated DNAs, isolated at different times in S phase, to the microarrays. Origin activations take place continuously throughout S phase but with most firings near mid-S phase. Rates of replication fork movement vary greatly from region to region in the genome. The two ends of each of the 16 chromosomes are highly correlated in their times of replication. This microarray approach is readily applicable to other organisms, including humans.

  16. Mapping yeast origins of replication via single-stranded DNA detection.

    Science.gov (United States)

    Feng, Wenyi; Raghuraman, M K; Brewer, Bonita J

    2007-02-01

    Studies in th Saccharomyces cerevisiae have provided a framework for understanding how eukaryotic cells replicate their chromosomal DNA to ensure faithful transmission of genetic information to their daughter cells. In particular, S. cerevisiae is the first eukaryote to have its origins of replication mapped on a genomic scale, by three independent groups using three different microarray-based approaches. Here we describe a new technique of origin mapping via detection of single-stranded DNA in yeast. This method not only identified the majority of previously discovered origins, but also detected new ones. We have also shown that this technique can identify origins in Schizosaccharomyces pombe, illustrating the utility of this method for origin mapping in other eukaryotes.

  17. Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase.

    Directory of Open Access Journals (Sweden)

    Amnon Koren

    2010-08-01

    Full Text Available Eukaryotic centromeres are maintained at specific chromosomal sites over many generations. In the budding yeast Saccharomyces cerevisiae, centromeres are genetic elements defined by a DNA sequence that is both necessary and sufficient for function; whereas, in most other eukaryotes, centromeres are maintained by poorly characterized epigenetic mechanisms in which DNA has a less definitive role. Here we use the pathogenic yeast Candida albicans as a model organism to study the DNA replication properties of centromeric DNA. By determining the genome-wide replication timing program of the C. albicans genome, we discovered that each centromere is associated with a replication origin that is the first to fire on its respective chromosome. Importantly, epigenetic formation of new ectopic centromeres (neocentromeres was accompanied by shifts in replication timing, such that a neocentromere became the first to replicate and became associated with origin recognition complex (ORC components. Furthermore, changing the level of the centromere-specific histone H3 isoform led to a concomitant change in levels of ORC association with centromere regions, further supporting the idea that centromere proteins determine origin activity. Finally, analysis of centromere-associated DNA revealed a replication-dependent sequence pattern characteristic of constitutively active replication origins. This strand-biased pattern is conserved, together with centromere position, among related strains and species, in a manner independent of primary DNA sequence. Thus, inheritance of centromere position is correlated with a constitutively active origin of replication that fires at a distinct early time. We suggest a model in which the distinct timing of DNA replication serves as an epigenetic mechanism for the inheritance of centromere position.

  18. Loss of maintenance DNA methylation results in abnormal DNA origin firing during DNA replication.

    Science.gov (United States)

    Haruta, Mayumi; Shimada, Midori; Nishiyama, Atsuya; Johmura, Yoshikazu; Le Tallec, Benoît; Debatisse, Michelle; Nakanishi, Makoto

    2016-01-22

    The mammalian maintenance methyltransferase DNMT1 [DNA (cytosine-5-)-methyltransferase 1] mediates the inheritance of the DNA methylation pattern during replication. Previous studies have shown that depletion of DNMT1 causes a severe growth defect and apoptosis in differentiated cells. However, the detailed mechanisms behind this phenomenon remain poorly understood. Here we show that conditional ablation of Dnmt1 in murine embryonic fibroblasts (MEFs) resulted in an aberrant DNA replication program showing an accumulation of late-S phase replication and causing severely defective growth. Furthermore, we found that the catalytic activity and replication focus targeting sequence of DNMT1 are required for a proper DNA replication program. Taken together, our findings suggest that the maintenance of DNA methylation by DNMT1 plays a critical role in proper regulation of DNA replication in mammalian cells. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Activation of a yeast replication origin near a double-stranded DNA break.

    Science.gov (United States)

    Raghuraman, M K; Brewer, B J; Fangman, W L

    1994-03-01

    Irradiation in the G1 phase of the cell cycle delays the onset of DNA synthesis and transiently inhibits the activation of replication origins in mammalian cells. It has been suggested that this inhibition is the result of the loss of torsional tension in the DNA after it has been damaged. Because irradiation causes DNA damage at an undefined number of nonspecific sites in the genome, it is not known how cells respond to limited DNA damage, and how replication origins in the immediate vicinity of a damage site would behave. Using the sequence-specific HO endonuclease, we have created a defined double-stranded DNA break in a centromeric plasmid in G1-arrested cells of the yeast Saccharomyces cerevisiae. We show that replication does initiate at the origin on the cut plasmid, and that the plasmid replicates early in the S phase after linearization in vivo. These observations suggest that relaxation of a supercoiled DNA domain in yeast need not inactivate replication origins within that domain. Furthermore, these observations rule out the possibility that the late replication context associated with chromosomal termini is a consequence of DNA ends.

  20. Multiple determinants controlling activation of yeast replication origins late in S phase.

    Science.gov (United States)

    Friedman, K L; Diller, J D; Ferguson, B M; Nyland, S V; Brewer, B J; Fangman, W L

    1996-07-01

    Analysis of a 131-kb segment of the left arm of yeast chromosome XIV beginning 157 kb from the telomere reveals four highly active origins of replication that initiate replication late in S phase. Previous work has shown that telomeres act as determinants for late origin activation. However, at least two of the chromosome XIV origins maintain their late activation time when located on large circular plasmids, indicating that late replication is independent of telomeres. Analysis of the replication time of plasmid derivatives containing varying amounts of chromosome XIV DNA show that a minimum of three chromosomal elements, distinct from each tested origin, contribute to late activation time. These late determinants are functionally equivalent, because duplication of one set of contributing sequences can compensate for the removal of another set. Furthermore, insertion of an origin that is normally early activated into this domain results in a shift to late activation, suggesting that the chromosome XIV origins are not unique in their ability to respond to the late determinants.

  1. Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication.

    Science.gov (United States)

    Feng, Wenyi; Collingwood, David; Boeck, Max E; Fox, Lindsay A; Alvino, Gina M; Fangman, Walton L; Raghuraman, Mosur K; Brewer, Bonita J

    2006-02-01

    During DNA replication one or both strands transiently become single stranded: first at the sites where initiation of DNA synthesis occurs (known as origins of replication) and subsequently on the lagging strands of replication forks as discontinuous Okazaki fragments are generated. We report a genome-wide analysis of single-stranded DNA (ssDNA) formation in the presence of hydroxyurea during DNA replication in wild-type and checkpoint-deficient rad53 Saccharomyces cerevisiae cells. In wild-type cells, ssDNA was first observed at a subset of replication origins and later 'migrated' bi-directionally, suggesting that ssDNA formation is associated with continuously moving replication forks. In rad53 cells, ssDNA was observed at virtually every known origin, but remained there over time, suggesting that replication forks stall. Telomeric regions seemed to be particularly sensitive to the loss of Rad53 checkpoint function. Replication origins in Schizosaccharomyces pombe were also mapped using our method.

  2. Intrinsically bent DNA in replication origins and gene promoters.

    Science.gov (United States)

    Gimenes, F; Takeda, K I; Fiorini, A; Gouveia, F S; Fernandez, M A

    2008-06-24

    Intrinsically bent DNA is an alternative conformation of the DNA molecule caused by the presence of dA/dT tracts, 2 to 6 bp long, in a helical turn phase DNA or with multiple intervals of 10 to 11 bp. Other than flexibility, intrinsic bending sites induce DNA curvature in particular chromosome regions such as replication origins and promoters. Intrinsically bent DNA sites are important in initiating DNA replication, and are sometimes found near to regions associated with the nuclear matrix. Many methods have been developed to localize bent sites, for example, circular permutation, computational analysis, and atomic force microscopy. This review discusses intrinsically bent DNA sites associated with replication origins and gene promoter regions in prokaryote and eukaryote cells. We also describe methods for identifying bent DNA sites for circular permutation and computational analysis.

  3. GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.

    Science.gov (United States)

    Liachko, Ivan; Youngblood, Rachel A; Tsui, Kyle; Bubb, Kerry L; Queitsch, Christine; Raghuraman, M K; Nislow, Corey; Brewer, Bonita J; Dunham, Maitreya J

    2014-03-01

    The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins--a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation.

  4. GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.

    Directory of Open Access Journals (Sweden)

    Ivan Liachko

    2014-03-01

    Full Text Available The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins--a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation.

  5. Loss of FANCC function is associated with failure to inhibit late firing replication origins after DNA cross-linking

    International Nuclear Information System (INIS)

    Phelps, Randall A.; Gingras, Helene; Hockenbery, David M.

    2007-01-01

    Fanconi anemia (FA) cells are abnormally sensitive to DNA cross-linking agents with increased levels of apoptosis and chromosomal instability. Defects in eight FA complementation groups inhibit monoubiquitination of FANCD2, and subsequent recruitment of FANCD2 to DNA damage and S-phase-associated nuclear foci. The specific functional defect in repair or response to DNA damage in FA cells remains unknown. Damage-resistant DNA synthesis is present 2.5-5 h after cross-linker treatment of FANCC, FANCA and FANCD2-deficient cells. Analysis of the size distribution of labeled DNA replication strands revealed that diepoxybutane treatment suppressed labeling of early but not late-firing replicons in FANCC-deficient cells. In contrast, normal responses to ionizing radiation were observed in FANCC-deficient cells. Absence of this late S-phase response in FANCC-deficient cells leads to activation of secondary checkpoint responses

  6. Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts

    Science.gov (United States)

    Newman, Timothy J.; Mamun, Mohammed A.; Nieduszynski, Conrad A.; Blow, J. Julian

    2013-01-01

    During S phase, the entire genome must be precisely duplicated, with no sections of DNA left unreplicated. Here, we develop a simple mathematical model to describe the probability of replication failing due to the irreversible stalling of replication forks. We show that the probability of complete genome replication is maximized if replication origins are evenly spaced, the largest inter-origin distances are minimized, and the end-most origins are positioned close to chromosome ends. We show that origin positions in the yeast Saccharomyces cerevisiae genome conform to all three predictions thereby maximizing the probability of complete replication if replication forks stall. Origin positions in four other yeasts—Kluyveromyces lactis, Lachancea kluyveri, Lachancea waltii and Schizosaccharomyces pombe—also conform to these predictions. Equating failure rates at chromosome ends with those in chromosome interiors gives a mean per nucleotide fork stall rate of ∼5 × 10−8, which is consistent with experimental estimates. Using this value in our theoretical predictions gives replication failure rates that are consistent with data from replication origin knockout experiments. Our theory also predicts that significantly larger genomes, such as those of mammals, will experience a much greater probability of replication failure genome-wide, and therefore will likely require additional compensatory mechanisms. PMID:23963700

  7. The Location of the Bacterial Origin of Replication is Critical for Initial Ciproflaxcin Antibiotic Resistance

    Science.gov (United States)

    Bos, Julia; Nehring, Ralph; Cruz, Diane; Austin, Doug; Rosenberg, Susan; Austin, Robert

    By using E. coli cells in which the unique origin of replication has been moved to a ectopic chromosome location distant from the native one, we probe how perturbation of gene order near the origin of replication impacts genome stability and survival under genomic attack. We find that when challenged with sub-inhibitory doses of ciprofloxacin, an antibiotic that generates replication fork stalling, cells with the ectopic origin show significant fitness loss. We show that genes functionally relevant to the cipro-induced stress response are largely located near the native origin, even in distantly related species. We show that while cipro induces increased copy number of genes proximal to the origin of replication as a direct consequence of replication fork stalling, gene copy number variation was reduced near the ectopic origin. Altered gene dosage in cells with an ectopic origin resulted in impaired replication fork repair and chromosome instability. We propose that gene distribution in the origin region acts as a fundamental first line of defense when the integrity of the genome is threatened and that genes proximal to the origin of replication serve as a mechanism of genetic innovation and a driving force of genome evolution in the presence of genotoxic antibiotics. Lewis Sigler Institute for Integrative Genomics and the Physics Department at Princeton University.

  8. Autonomous replication of plasmids bearing monkey DNA origin-enriched sequences

    International Nuclear Information System (INIS)

    Frappier, L.; Zannis-Hadjopoulos, M.

    1987-01-01

    Twelve clones of origin-enriched sequences (ORS) isolated from early replicating monkey (CV-1) DNA were examined for transient episomal replication in transfected CV-1, COS-7, and HeLa cells. Plasmid DNA was isolated at time intervals after transfection and screened by the Dpn I resistance assay or by the bromodeoxyuridine substitution assay to differentiate between input and replicated DNA. The authors have identified four monkey ORS (ORS3, -8, -9, and -12) that can support plasmid replication in mammalian cells. This replication is carried out in a controlled and semiconservative manner characteristic of mammalian replicons. ORS replication was most efficient in HeLa cells. Electron microscopy showed ORS8 and ORS12 plasmids of the correct size with replication bubbles. Using a unique restriction site in ORS12, we have mapped the replication bubble within the monkey DNA sequence

  9. A Cretaceous origin for fire adaptations in the Cape flora.

    Science.gov (United States)

    He, Tianhua; Lamont, Byron B; Manning, John

    2016-10-05

    Fire has had a profound effect on the evolution of worldwide biotas. The Cape Floristic Region is one of the world's most species-rich regions, yet it is highly prone to recurrent fires and fire-adapted species contribute strongly to the overall flora. It is hypothesized that the current fire regimes in the Cape could be as old as 6-8 million years (My), while indirect evidence indicates that the onset of fire could have reached 18 million years ago (Ma). Here, we trace the origin of fire-dependent traits in two monocot families that are significant elements in the fire-prone Cape flora. Our analysis shows that fire-stimulated flowering originated in the Cape Haemodoraceae 81 Ma, while fire-stimulated germination arose in the African Restionaceae at least 70 Ma, implying that wildfires have been a significant force in the evolution of the Cape flora at least 60 My earlier than previous estimates. Our results provide strong evidence for the presence of fire adaptations in the Cape from the Cretaceous, leading to the extraordinary persistence of a fire-adapted flora in this biodiversity hotspot, and giving support to the hypothesis that Cretaceous fire was a global phenomenon that shaped the evolution of terrestrial floras.

  10. Effects of a fire response trait on diversification in replicated radiations.

    Science.gov (United States)

    Litsios, Glenn; Wüest, Rafael O; Kostikova, Anna; Forest, Félix; Lexer, Christian; Linder, H Peter; Pearman, Peter B; Zimmermann, Niklaus E; Salamin, Nicolas

    2014-02-01

    Fire has been proposed as a factor explaining the exceptional plant species richness found in Mediterranean regions. A fire response trait that allows plants to cope with frequent fire by either reseeding or resprouting could differentially affect rates of species diversification. However, little is known about the generality of the effects of differing fire response on species evolution. We study this question in the Restionaceae, a family that radiated in Southern Africa and Australia. These radiations occurred independently and represent evolutionary replicates. We apply Bayesian approaches to estimate trait-specific diversification rates and patterns of climatic niche evolution. We also compare the climatic heterogeneity of South Africa and Australia. Reseeders diversify faster than resprouters in South Africa, but not in Australia. We show that climatic preferences evolve more rapidly in reseeder lineages than in resprouters and that the optima of these climatic preferences differ between the two strategies. We find that South Africa is more climatically heterogeneous than Australia, independent of the spatial scale we consider. We propose that rapid shifts between states of the fire response trait promote speciation by separating species ecologically, but this only happens when the landscape is sufficiently heterogeneous. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  11. Replication termination and chromosome dimer resolution in the archaeon Sulfolobus solfataricus.

    Science.gov (United States)

    Duggin, Iain G; Dubarry, Nelly; Bell, Stephen D

    2011-01-05

    Archaea of the genus Sulfolobus have a single-circular chromosome with three replication origins. All three origins fire in every cell in every cell cycle. Thus, three pairs of replication forks converge and terminate in each replication cycle. Here, we report 2D gel analyses of the replication fork fusion zones located between origins. These indicate that replication termination involves stochastic fork collision. In bacteria, replication termination is linked to chromosome dimer resolution, a process that requires the XerC and D recombinases, FtsK and the chromosomal dif site. Sulfolobus encodes a single-Xer homologue and its deletion gave rise to cells with aberrant DNA contents and increased volumes. Identification of the chromosomal dif site that binds Xer in vivo, and biochemical characterization of Xer/dif recombination revealed that, in contrast to bacteria, dif is located outside the fork fusion zones. Therefore, it appears that replication termination and dimer resolution are temporally and spatially distinct processes in Sulfolobus.

  12. Transcriptionally Driven DNA Replication Program of the Human Parasite Leishmania major.

    Science.gov (United States)

    Lombraña, Rodrigo; Álvarez, Alba; Fernández-Justel, José Miguel; Almeida, Ricardo; Poza-Carrión, César; Gomes, Fábia; Calzada, Arturo; Requena, José María; Gómez, María

    2016-08-09

    Faithful inheritance of eukaryotic genomes requires the orchestrated activation of multiple DNA replication origins (ORIs). Although origin firing is mechanistically conserved, how origins are specified and selected for activation varies across different model systems. Here, we provide a complete analysis of the nucleosomal landscape and replication program of the human parasite Leishmania major, building on a better evolutionary understanding of replication organization in Eukarya. We found that active transcription is a driving force for the nucleosomal organization of the L. major genome and that both the spatial and the temporal program of DNA replication can be explained as associated to RNA polymerase kinetics. This simple scenario likely provides flexibility and robustness to deal with the environmental changes that impose alterations in the genetic programs during parasitic life cycle stages. Our findings also suggest that coupling replication initiation to transcription elongation could be an ancient solution used by eukaryotic cells for origin maintenance. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  13. Transcriptionally Driven DNA Replication Program of the Human Parasite Leishmania major

    Directory of Open Access Journals (Sweden)

    Rodrigo Lombraña

    2016-08-01

    Full Text Available Faithful inheritance of eukaryotic genomes requires the orchestrated activation of multiple DNA replication origins (ORIs. Although origin firing is mechanistically conserved, how origins are specified and selected for activation varies across different model systems. Here, we provide a complete analysis of the nucleosomal landscape and replication program of the human parasite Leishmania major, building on a better evolutionary understanding of replication organization in Eukarya. We found that active transcription is a driving force for the nucleosomal organization of the L. major genome and that both the spatial and the temporal program of DNA replication can be explained as associated to RNA polymerase kinetics. This simple scenario likely provides flexibility and robustness to deal with the environmental changes that impose alterations in the genetic programs during parasitic life cycle stages. Our findings also suggest that coupling replication initiation to transcription elongation could be an ancient solution used by eukaryotic cells for origin maintenance.

  14. Singlet Oxygen-Mediated Oxidation during UVA Radiation Alters the Dynamic of Genomic DNA Replication.

    Directory of Open Access Journals (Sweden)

    Dany Graindorge

    Full Text Available UVA radiation (320-400 nm is a major environmental agent that can exert its deleterious action on living organisms through absorption of the UVA photons by endogenous or exogenous photosensitizers. This leads to the production of reactive oxygen species (ROS, such as singlet oxygen (1O2 and hydrogen peroxide (H2O2, which in turn can modify reversibly or irreversibly biomolecules, such as lipids, proteins and nucleic acids. We have previously reported that UVA-induced ROS strongly inhibit DNA replication in a dose-dependent manner, but independently of the cell cycle checkpoints activation. Here, we report that the production of 1O2 by UVA radiation leads to a transient inhibition of replication fork velocity, a transient decrease in the dNTP pool, a quickly reversible GSH-dependent oxidation of the RRM1 subunit of ribonucleotide reductase and sustained inhibition of origin firing. The time of recovery post irradiation for each of these events can last from few minutes (reduction of oxidized RRM1 to several hours (replication fork velocity and origin firing. The quenching of 1O2 by sodium azide prevents the delay of DNA replication, the decrease in the dNTP pool and the oxidation of RRM1, while inhibition of Chk1 does not prevent the inhibition of origin firing. Although the molecular mechanism remains elusive, our data demonstrate that the dynamic of replication is altered by UVA photosensitization of vitamins via the production of singlet oxygen.

  15. Singlet Oxygen-Mediated Oxidation during UVA Radiation Alters the Dynamic of Genomic DNA Replication

    Science.gov (United States)

    Graindorge, Dany; Martineau, Sylvain; Machon, Christelle; Arnoux, Philippe; Guitton, Jérôme; Francesconi, Stefania; Frochot, Céline; Sage, Evelyne; Girard, Pierre-Marie

    2015-01-01

    UVA radiation (320–400 nm) is a major environmental agent that can exert its deleterious action on living organisms through absorption of the UVA photons by endogenous or exogenous photosensitizers. This leads to the production of reactive oxygen species (ROS), such as singlet oxygen (1O2) and hydrogen peroxide (H2O2), which in turn can modify reversibly or irreversibly biomolecules, such as lipids, proteins and nucleic acids. We have previously reported that UVA-induced ROS strongly inhibit DNA replication in a dose-dependent manner, but independently of the cell cycle checkpoints activation. Here, we report that the production of 1O2 by UVA radiation leads to a transient inhibition of replication fork velocity, a transient decrease in the dNTP pool, a quickly reversible GSH-dependent oxidation of the RRM1 subunit of ribonucleotide reductase and sustained inhibition of origin firing. The time of recovery post irradiation for each of these events can last from few minutes (reduction of oxidized RRM1) to several hours (replication fork velocity and origin firing). The quenching of 1O2 by sodium azide prevents the delay of DNA replication, the decrease in the dNTP pool and the oxidation of RRM1, while inhibition of Chk1 does not prevent the inhibition of origin firing. Although the molecular mechanism remains elusive, our data demonstrate that the dynamic of replication is altered by UVA photosensitization of vitamins via the production of singlet oxygen. PMID:26485711

  16. A role for the weak DnaA binding sites in bacterial replication origins

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Løbner-Olesen, Anders

    2011-01-01

    DnaA initiates the chromosomal DNA replication in nearly all bacteria, and replication origins are characterized by binding sites for the DnaA protein (DnaA-boxes) along with an ‘AT-rich’ region. However, great variation in number, spatial organization and specificity of DnaA-boxes is observed...... between species. In the study by Taylor et al. (2011), new and unexpectedly weak DnaA-boxes were identified within the Caulobacter crescentus origin of replication (Cori). The position of weak and stronger DnaA-boxes follows a pattern seen in Escherichia coli oriC. This raises the possibility...... that bacterial origins might be more alike than previously thought....

  17. Relationship between mitochondrial gene rearrangements and stability of the origin of light strand replication

    Directory of Open Access Journals (Sweden)

    Miguel M. Fonseca

    2008-01-01

    Full Text Available Mitochondrial gene rearrangements are much more frequent in vertebrates than initially thought. It has been suggested that the origin of light strand replication could have an important role in the process of gene rearrangements, but this hypothesis has never been tested before. We used amphibians to test the correlation between light-strand replication origin thermodynamic stability and the occurrence of gene rearrangements. The two variables were correlated in a non-phylogenetic approach, but when tested in a phylogenetically based comparative method the correlation was not significant, although species with unstable light-strand replication origins were much more likely to have undergone gene rearrangements. This indicates that within amphibians there are stable and unstable phylogenetic groups regarding mitochondrial gene order. The species analyzed showed variability in the thermodynamic stability of the secondary structure, in the length of its stem and loop, and several species did not present the 5’-GCCGG-3’ motif reported to be necessary for efficient mitochondrial DNA replication. Future studies should focus on the role of the light-strand replication origin in mitochondrial DNA replication and gene rearrangements mechanisms.

  18. Function of BRCA1 at a DNA Replication Origin

    National Research Council Canada - National Science Library

    Lieberman, Paul

    2004-01-01

    ... and allow efficient repair of damaged DNA. In this proposal, we present preliminary data that BRCA1 functions in a DNA checkpoint response for the origin of Epstein-Barr Virus DNA replication (Ori P...

  19. Identifying sites of replication initiation in yeast chromosomes: looking for origins in all the right places.

    Science.gov (United States)

    van Brabant, A J; Hunt, S Y; Fangman, W L; Brewer, B J

    1998-06-01

    DNA fragments that contain an active origin of replication generate bubble-shaped replication intermediates with diverging forks. We describe two methods that use two-dimensional (2-D) agarose gel electrophoresis along with DNA sequence information to identify replication origins in natural and artificial Saccharomyces cerevisiae chromosomes. The first method uses 2-D gels of overlapping DNA fragments to locate an active chromosomal replication origin within a region known to confer autonomous replication on a plasmid. A variant form of 2-D gels can be used to determine the direction of fork movement, and the second method uses this technique to find restriction fragments that are replicated by diverging forks, indicating that a bidirectional replication origin is located between the two fragments. Either of these two methods can be applied to the analysis of any genomic region for which there is DNA sequence information or an adequate restriction map.

  20. Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq).

    Science.gov (United States)

    Langley, Alexander R; Gräf, Stefan; Smith, James C; Krude, Torsten

    2016-12-01

    Next-generation sequencing has enabled the genome-wide identification of human DNA replication origins. However, different approaches to mapping replication origins, namely (i) sequencing isolated small nascent DNA strands (SNS-seq); (ii) sequencing replication bubbles (bubble-seq) and (iii) sequencing Okazaki fragments (OK-seq), show only limited concordance. To address this controversy, we describe here an independent high-resolution origin mapping technique that we call initiation site sequencing (ini-seq). In this approach, newly replicated DNA is directly labelled with digoxigenin-dUTP near the sites of its initiation in a cell-free system. The labelled DNA is then immunoprecipitated and genomic locations are determined by DNA sequencing. Using this technique we identify >25,000 discrete origin sites at sub-kilobase resolution on the human genome, with high concordance between biological replicates. Most activated origins identified by ini-seq are found at transcriptional start sites and contain G-quadruplex (G4) motifs. They tend to cluster in early-replicating domains, providing a correlation between early replication timing and local density of activated origins. Origins identified by ini-seq show highest concordance with sites identified by SNS-seq, followed by OK-seq and bubble-seq. Furthermore, germline origins identified by positive nucleotide distribution skew jumps overlap with origins identified by ini-seq and OK-seq more frequently and more specifically than do sites identified by either SNS-seq or bubble-seq. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. MOF Suppresses Replication Stress and Contributes to Resolution of Stalled Replication Forks.

    Science.gov (United States)

    Singh, Dharmendra Kumar; Pandita, Raj K; Singh, Mayank; Chakraborty, Sharmistha; Hambarde, Shashank; Ramnarain, Deepti; Charaka, Vijaya; Ahmed, Kazi Mokim; Hunt, Clayton R; Pandita, Tej K

    2018-03-15

    The human MOF (hMOF) protein belongs to the MYST family of histone acetyltransferases and plays a critical role in transcription and the DNA damage response. MOF is essential for cell proliferation; however, its role during replication and replicative stress is unknown. Here we demonstrate that cells depleted of MOF and under replicative stress induced by cisplatin, hydroxyurea, or camptothecin have reduced survival, a higher frequency of S-phase-specific chromosome damage, and increased R-loop formation. MOF depletion decreased replication fork speed and, when combined with replicative stress, also increased stalled replication forks as well as new origin firing. MOF interacted with PCNA, a key coordinator of replication and repair machinery at replication forks, and affected its ubiquitination and recruitment to the DNA damage site. Depletion of MOF, therefore, compromised the DNA damage repair response as evidenced by decreased Mre11, RPA70, Rad51, and PCNA focus formation, reduced DNA end resection, and decreased CHK1 phosphorylation in cells after exposure to hydroxyurea or cisplatin. These results support the argument that MOF plays an important role in suppressing replication stress induced by genotoxic agents at several stages during the DNA damage response. Copyright © 2018 American Society for Microbiology.

  2. Rif1 Binding and Control of Chromosome-Internal DNA Replication Origins Is Limited by Telomere Sequestration.

    Science.gov (United States)

    Hafner, Lukas; Lezaja, Aleksandra; Zhang, Xu; Lemmens, Laure; Shyian, Maksym; Albert, Benjamin; Follonier, Cindy; Nunes, Jose Manuel; Lopes, Massimo; Shore, David; Mattarocci, Stefano

    2018-04-24

    The Saccharomyces cerevisiae telomere-binding protein Rif1 plays an evolutionarily conserved role in control of DNA replication timing by promoting PP1-dependent dephosphorylation of replication initiation factors. However, ScRif1 binding outside of telomeres has never been detected, and it has thus been unclear whether Rif1 acts directly on the replication origins that it controls. Here, we show that, in unperturbed yeast cells, Rif1 primarily regulates late-replicating origins within 100 kb of a telomere. Using the chromatin endogenous cleavage ChEC-seq technique, we robustly detect Rif1 at late-replicating origins that we show are targets of its inhibitory action. Interestingly, abrogation of Rif1 telomere association by mutation of its Rap1-binding module increases Rif1 binding and origin inhibition elsewhere in the genome. Our results indicate that Rif1 inhibits replication initiation by interacting directly with origins and suggest that Rap1-dependent sequestration of Rif1 increases its effective concentration near telomeres, while limiting its action at chromosome-internal sites. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  3. The fork and the kinase: a DNA replication tale from a CHK1 perspective.

    Science.gov (United States)

    González Besteiro, Marina A; Gottifredi, Vanesa

    2015-01-01

    Replication fork progression is being continuously hampered by exogenously introduced and naturally occurring DNA lesions and other physical obstacles. Checkpoint kinase 1 (Chk1) is activated at replication forks that encounter damaged DNA. Subsequently, Chk1 inhibits the initiation of new replication factories and stimulates the firing of dormant origins (those in the vicinity of stalled forks). Chk1 also avoids fork collapse into DSBs (double strand breaks) and promotes fork elongation. At the molecular level, the current model considers stalled forks as the site of Chk1 activation and the nucleoplasm as the location where Chk1 phosphorylates target proteins. This model certainly serves to explain how Chk1 modulates origin firing, but how Chk1 controls the fate of stalled forks is less clear. Interestingly, recent reports demonstrating that Chk1 phosphorylates chromatin-bound proteins and even holds kinase-independent functions might shed light on how Chk1 contributes to the elongation of damaged DNA. Indeed, such findings have unveiled a puzzling connection between Chk1 and DNA lesion bypass, which might be central to promoting fork elongation and checkpoint attenuation. In summary, Chk1 is a multifaceted and versatile signaling factor that acts at ongoing forks and replication origins to determine the extent and quality of the cellular response to replication stress. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. The hunt for origins of DNA replication in multicellular eukaryotes

    DEFF Research Database (Denmark)

    Urban, J. M.; Foulk, M. S.; Casella, Cinzia

    2015-01-01

    Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope...... that features for ORI specification might emerge. These methods are reviewed here with analysis of their advantages and shortcomings. The various factors that may influence ORI selection for initiation of DNA replication are discussed....

  5. Savanna fire and the origins of the 'underground forests' of Africa.

    Science.gov (United States)

    Maurin, Olivier; Davies, T Jonathan; Burrows, John E; Daru, Barnabas H; Yessoufou, Kowiyou; Muasya, A Muthama; van der Bank, Michelle; Bond, William J

    2014-10-01

    The origin of fire-adapted lineages is a long-standing question in ecology. Although phylogeny can provide a significant contribution to the ongoing debate, its use has been precluded by the lack of comprehensive DNA data. Here, we focus on the 'underground trees' (=geoxyles) of southern Africa, one of the most distinctive growth forms characteristic of fire-prone savannas. We placed geoxyles within the most comprehensive dated phylogeny for the regional flora comprising over 1400 woody species. Using this phylogeny, we tested whether African geoxyles evolved concomitantly with those of the South American cerrado and used their phylogenetic position to date the appearance of humid savannas. We found multiple independent origins of the geoxyle life-form mostly from the Pliocene, a period consistent with the origin of cerrado, with the majority of divergences occurring within the last 2 million yr. When contrasted with their tree relatives, geoxyles occur in regions characterized by higher rainfall and greater fire frequency. Our results indicate that the geoxylic growth form may have evolved in response to the interactive effects of frequent fires and high precipitation. As such, geoxyles may be regarded as markers of fire-maintained savannas occurring in climates suitable for forests. © 2014 The Authors New Phytologist © 2014 New Phytologist Trust.

  6. G-Quadruplexes in DNA Replication: A Problem or a Necessity?

    Science.gov (United States)

    Valton, Anne-Laure; Prioleau, Marie-Noëlle

    2016-11-01

    DNA replication is a highly regulated process that ensures the correct duplication of the genome at each cell cycle. A precise cell type-specific temporal program controls the duplication of complex vertebrate genomes in an orderly manner. This program is based on the regulation of both replication origin firing and replication fork progression. G-quadruplexes (G4s), DNA secondary structures displaying noncanonical Watson-Crick base pairing, have recently emerged as key controllers of genome duplication. Here we discuss the various means by which G4s affect this fundamental cellular process. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. DNA damage by X-rays and their impact on replication processes

    International Nuclear Information System (INIS)

    Parplys, Ann Christin; Petermann, Eva; Petersen, Cordula; Dikomey, Ekkehard; Borgmann, Kerstin

    2012-01-01

    Background: Replication-dependent radiosensitization of tumors ranks among the most promising tools for future improvements in tumor therapy. However, cell cycle checkpoint signaling during S phase is a key for maintaining genomic stability after ionizing irradiation allowing DNA damage repair by stabilizing replication forks, inhibiting new origin firing and recruiting DNA repair proteins. As the impact of the different types of DNA damage induced by ionizing radiation on replication fork functionality has not been investigated, this study was performed in tumor cells treated with various agents that induce specific DNA lesions. Methods: U2OS cells were exposed to methyl methanesulfonate (MMS) to induce base damage, low or high concentrations of hydrogen peroxide for the induction of SSBs, Topotecan to induce DSBs at replication, Mitomycin C (MMC) to induce interstrand cross-links or ionizing irradiation to analyze all damages. Chk1 phosphorylation, origin firing and replication fork progression, and cell cycle distribution were analyzed. Results: In our system, the extent of Chk1 phosphorylation was dependent on the type of damage induced and prolonged Chk1 phosphorylation correlated with the inhibition of replication initiation. Ionizing radiation, high concentrations of hydrogen peroxide, and Topotecan affected replication elongation much more strongly that the other agents. Almost all agents induced a slight increase in the S phase population but subsequent G2 arrest was only observed in response to those agents that strongly inhibited replication elongation and caused prolonged Chk1 phosphorylation. Conclusions: Our data suggest that to improve radiotherapy, radiosensitivity in S phase could be increased by combining irradiation with agents that induce secondary DSB or inhibit checkpoint signaling, such as inhibitors of PARP or Chk1.

  8. pUL34 binding near the human cytomegalovirus origin of lytic replication enhances DNA replication and viral growth.

    Science.gov (United States)

    Slayton, Mark; Hossain, Tanvir; Biegalke, Bonita J

    2018-05-01

    The human cytomegalovirus (HCMV) UL34 gene encodes sequence-specific DNA-binding proteins (pUL34) which are required for viral replication. Interactions of pUL34 with DNA binding sites represses transcription of two viral immune evasion genes, US3 and US9. 12 additional predicted pUL34-binding sites are present in the HCMV genome (strain AD169) with three binding sites concentrated near the HCMV origin of lytic replication (oriLyt). We used ChIP-seq analysis of pUL34-DNA interactions to confirm that pUL34 binds to the oriLyt region during infection. Mutagenesis of the UL34-binding sites in an oriLyt-containing plasmid significantly reduced viral-mediated oriLyt-dependent DNA replication. Mutagenesis of these sites in the HCMV genome reduced the replication efficiencies of the resulting viruses. Protein-protein interaction analyses demonstrated that pUL34 interacts with the viral proteins IE2, UL44, and UL84, that are essential for viral DNA replication, suggesting that pUL34-DNA interactions in the oriLyt region are involved in the DNA replication cascade. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. DNA replication origin function is promoted by H3K4 di-methylation in Saccharomyces cerevisiae.

    Science.gov (United States)

    Rizzardi, Lindsay F; Dorn, Elizabeth S; Strahl, Brian D; Cook, Jeanette Gowen

    2012-10-01

    DNA replication is a highly regulated process that is initiated from replication origins, but the elements of chromatin structure that contribute to origin activity have not been fully elucidated. To identify histone post-translational modifications important for DNA replication, we initiated a genetic screen to identify interactions between genes encoding chromatin-modifying enzymes and those encoding proteins required for origin function in the budding yeast Saccharomyces cerevisiae. We found that enzymes required for histone H3K4 methylation, both the histone methyltransferase Set1 and the E3 ubiquitin ligase Bre1, are required for robust growth of several hypomorphic replication mutants, including cdc6-1. Consistent with a role for these enzymes in DNA replication, we found that both Set1 and Bre1 are required for efficient minichromosome maintenance. These phenotypes are recapitulated in yeast strains bearing mutations in the histone substrates (H3K4 and H2BK123). Set1 functions as part of the COMPASS complex to mono-, di-, and tri-methylate H3K4. By analyzing strains lacking specific COMPASS complex members or containing H2B mutations that differentially affect H3K4 methylation states, we determined that these replication defects were due to loss of H3K4 di-methylation. Furthermore, histone H3K4 di-methylation is enriched at chromosomal origins. These data suggest that H3K4 di-methylation is necessary and sufficient for normal origin function. We propose that histone H3K4 di-methylation functions in concert with other histone post-translational modifications to support robust genome duplication.

  10. Origin Licensing Requires ATP Binding and Hydrolysis by the MCM Replicative Helicase

    Science.gov (United States)

    Coster, Gideon; Frigola, Jordi; Beuron, Fabienne; Morris, Edward P.; Diffley, John F.X.

    2014-01-01

    Summary Loading of the six related Minichromosome Maintenance (MCM) proteins as head-to-head double hexamers during DNA replication origin licensing is crucial for ensuring once-per-cell-cycle DNA replication in eukaryotic cells. Assembly of these prereplicative complexes (pre-RCs) requires the Origin Recognition Complex (ORC), Cdc6, and Cdt1. ORC, Cdc6, and MCM are members of the AAA+ family of ATPases, and pre-RC assembly requires ATP hydrolysis. Here we show that ORC and Cdc6 mutants defective in ATP hydrolysis are competent for origin licensing. However, ATP hydrolysis by Cdc6 is required to release nonproductive licensing intermediates. We show that ATP binding stabilizes the wild-type MCM hexamer. Moreover, by analyzing MCM containing mutant subunits, we show that ATP binding and hydrolysis by MCM are required for Cdt1 release and double hexamer formation. This work alters our view of how ATP is used by licensing factors to assemble pre-RCs. PMID:25087873

  11. Crystallization and preliminary crystallographic characterization of the origin-binding domain of the bacteriophage λ O replication initiator

    International Nuclear Information System (INIS)

    Struble, E. B.; Gittis, A. G.; Bianchet, M. A.; McMacken, R.

    2007-01-01

    Crystallization and preliminary diffraction data of the N-terminal 19–139 fragment of the origin-binding domain of bacteriophage λ O replication initiator are reported. The bacteriophage λ O protein binds to the λ replication origin (oriλ) and serves as the primary replication initiator for the viral genome. The binding energy derived from the binding of O to oriλ is thought to help drive DNA opening to facilitate initiation of DNA replication. Detailed understanding of this process is severely limited by the lack of high-resolution structures of O protein or of any lambdoid phage-encoded paralogs either with or without DNA. The production of crystals of the origin-binding domain of λ O that diffract to 2.5 Å is reported. Anomalous dispersion methods will be used to solve this structure

  12. Functional characterization of the origin of replication of pRN1 from Sulfolobus islandicus REN1H1.

    Directory of Open Access Journals (Sweden)

    Chijioke J Joshua

    Full Text Available Plasmid pRN1 from Sulfolobus islandicus REN1H1 is believed to replicate by a rolling circle mechanism but its origin and mechanism of replication are not well understood. We sought to create minimal expression vectors based on pRN1 that would be useful for heterologous gene expression in S. acidocaldarius, and in the process improve our understanding of the mechanism of replication. We constructed and transformed shuttle vectors that harbored different contiguous stretches of DNA from pRN1 into S. acidocaldarius E4-39, a uracil auxotroph. A 232-bp region 3' of orf904 was found to be critical for pRN1 replication and is therefore proposed to be the putative origin of replication. This 232-bp region contains a 100-bp stem-loop structure believed to be the double-strand origin of replication. The loop of the 100-bp structure contains a GTG tri-nucleotide motif, a feature that was previously reported to be important for the primase activity of Orf904. This putative origin and the associated orf56 and orf904 were identified as the minimal replicon of pRN1 because transformants of plasmids lacking any of these three features were not recovered. Plasmids lacking orf904 and orf56 but harboring the putative origin were transformable when orf904 and orf56 were provided in-trans; a 75-bp region 5' of the orf904 start codon was found to be essential for this complementation. Detailed knowledge of the pRN1 origin of replication will broaden the application of the plasmid as a genetic tool for Sulfolobus species.

  13. Aberrant allele-specific replication, independent of parental origin, in blood cells of cancer patients

    International Nuclear Information System (INIS)

    Dotan, Zohar A; Dotan, Aviva; Ramon, Jacob; Avivi, Lydia

    2008-01-01

    Allelic counterparts of biallelically expressed genes display an epigenetic symmetry normally manifested by synchronous replication, different from genes subjected to monoallelic expression, which normally are characterized by an asynchronous mode of replication (well exemplified by the SNRPN imprinted locus). Malignancy was documented to be associated with gross modifications in the inherent replication-timing coordination between allelic counterparts of imprinted genes as well as of biallelically expressed loci. The cancer-related allelic replication timing aberrations are non-disease specific and appear in peripheral blood cells of cancer patients, including those with solid tumors. As such they offer potential blood markers for non-invasive cancer test. The present study was aimed to gain some insight into the mechanism leading to the replication timing alterations of genes in blood lymphocytes of cancer patients. Peripheral blood samples derived from patients with prostate cancer were chosen to represent the cancerous status, and samples taken from patients with no cancer but with benign prostate hyperplasia were used to portray the normal status. Fluorescence In Situ Hybridization (FISH) replication assay, applied to phytohemagglutinin (PHA)-stimulated blood lymphocytes, was used to evaluate the temporal order (either synchronous or asynchronous) of genes in the patients' cells. We demonstrated that: (i) the aberrant epigenetic profile, as delineated by the cancer status, is a reversible modification, evidenced by our ability to restore the normal patterns of replication in three unrelated loci (CEN15, SNRPN and RB1) by introducing an archetypical demethylating agent, 5-azacytidine; (ii) following the rehabilitating effect of demethylation, an imprinted gene (SNRPN) retains its original parental imprint; and (iii) the choice of an allele between early or late replication in the aberrant asynchronous replication, delineated by the cancer status, is not

  14. Examining reproducibility in psychology : A hybrid method for combining a statistically significant original study and a replication

    NARCIS (Netherlands)

    Van Aert, R.C.M.; Van Assen, M.A.L.M.

    2018-01-01

    The unrealistically high rate of positive results within psychology has increased the attention to replication research. However, researchers who conduct a replication and want to statistically combine the results of their replication with a statistically significant original study encounter

  15. A microhomology-mediated break-induced replication model for the origin of human copy number variation.

    Directory of Open Access Journals (Sweden)

    P J Hastings

    2009-01-01

    Full Text Available Chromosome structural changes with nonrecurrent endpoints associated with genomic disorders offer windows into the mechanism of origin of copy number variation (CNV. A recent report of nonrecurrent duplications associated with Pelizaeus-Merzbacher disease identified three distinctive characteristics. First, the majority of events can be seen to be complex, showing discontinuous duplications mixed with deletions, inverted duplications, and triplications. Second, junctions at endpoints show microhomology of 2-5 base pairs (bp. Third, endpoints occur near pre-existing low copy repeats (LCRs. Using these observations and evidence from DNA repair in other organisms, we derive a model of microhomology-mediated break-induced replication (MMBIR for the origin of CNV and, ultimately, of LCRs. We propose that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (BIR. Under these circumstances, single-strand 3' tails from broken replication forks will anneal with microhomology on any single-stranded DNA nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.

  16. Interaction of the retinoblastoma protein with Orc1 and its recruitment to human origins of DNA replication.

    Directory of Open Access Journals (Sweden)

    Ramiro Mendoza-Maldonado

    Full Text Available BACKGROUND: The retinoblastoma protein (Rb is a crucial regulator of cell cycle progression by binding with E2F transcription factor and repressing the expression of a variety of genes required for the G1-S phase transition. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that Rb and E2F1 directly participate in the control of initiation of DNA replication in human HeLa, U2OS and T98G cells by specifically binding to origins of DNA replication in a cell cycle regulated manner. We show that, both in vitro and inside the cells, the largest subunit of the origin recognition complex (Orc1 specifically binds hypo-phosphorylated Rb and that this interaction is competitive with the binding of Rb to E2F1. The displacement of Rb-bound Orc1 by E2F1 at origins of DNA replication marks the progression of the G1 phase of the cell cycle toward the G1-S border. CONCLUSIONS/SIGNIFICANCE: The participation of Rb and E2F1 in the formation of the multiprotein complex that binds origins of DNA replication in mammalian cells appears to represent an effective mechanism to couple the expression of genes required for cell cycle progression to the activation of DNA replication.

  17. Chromatin Structure and Replication Origins: Determinants Of Chromosome Replication And Nuclear Organization

    Science.gov (United States)

    Smith, Owen K.; Aladjem, Mirit I.

    2014-01-01

    The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes on chromatin is illustrated by two recent sets of discoveries. First, chromatin-associated proteins that are not part of the core replication machinery were shown to affect the timing of DNA replication. These chromatin-associated proteins could be working in concert, or perhaps in competition, with the transcriptional machinery and with chromatin modifiers to determine the spatial and temporal organization of replication initiation events. Second, epigenetic interactions are mediated by DNA sequences that determine chromosomal replication. In this review we summarize recent findings and current models linking spatial and temporal regulation of the replication program with epigenetic signaling. We discuss these issues in the context of the genome’s three-dimensional structure with an emphasis on events occurring during the initiation of DNA replication. PMID:24905010

  18. Constructive Approaches for Understanding the Origin of Self-Replication and Evolution

    Directory of Open Access Journals (Sweden)

    Norikazu Ichihashi

    2016-07-01

    Full Text Available The mystery of the origin of life can be divided into two parts. The first part is the origin of biomolecules: under what physicochemical conditions did biomolecules such as amino acids, nucleotides, and their polymers arise? The second part of the mystery is the origin of life-specific functions such as the replication of genetic information, the reproduction of cellular structures, metabolism, and evolution. These functions require the coordination of many different kinds of biological molecules. A direct strategy to approach the second part of the mystery is the constructive approach, in which life-specific functions are recreated in a test tube from specific biological molecules. Using this approach, we are able to employ design principles to reproduce life-specific functions, and the knowledge gained through the reproduction process provides clues as to their origins. In this mini-review, we introduce recent insights gained using this approach, and propose important future directions for advancing our understanding of the origins of life.

  19. A DNA sequence element that advances replication origin activation time in Saccharomyces cerevisiae.

    Science.gov (United States)

    Pohl, Thomas J; Kolor, Katherine; Fangman, Walton L; Brewer, Bonita J; Raghuraman, M K

    2013-11-06

    Eukaryotic origins of DNA replication undergo activation at various times in S-phase, allowing the genome to be duplicated in a temporally staggered fashion. In the budding yeast Saccharomyces cerevisiae, the activation times of individual origins are not intrinsic to those origins but are instead governed by surrounding sequences. Currently, there are two examples of DNA sequences that are known to advance origin activation time, centromeres and forkhead transcription factor binding sites. By combining deletion and linker scanning mutational analysis with two-dimensional gel electrophoresis to measure fork direction in the context of a two-origin plasmid, we have identified and characterized a 19- to 23-bp and a larger 584-bp DNA sequence that are capable of advancing origin activation time.

  20. Calcein represses human papillomavirus 16 E1-E2 mediated DNA replication via blocking their binding to the viral origin of replication.

    Science.gov (United States)

    Das, Dipon; Smith, Nathan W; Wang, Xu; Richardson, Stacie L; Hartman, Matthew C T; Morgan, Iain M

    2017-08-01

    Human papillomaviruses are causative agents in several human diseases ranging from genital warts to ano-genital and oropharyngeal cancers. Currently only symptoms of HPV induced disease are treated; there are no antivirals available that directly target the viral life cycle. Previously, we determined that the cellular protein TopBP1 interacts with the HPV16 replication/transcription factor E2. This E2-TopBP1 interaction is essential for optimal E1-E2 DNA replication and for the viral life cycle. The drug calcein disrupts the interaction of TopBP1 with itself and other host proteins to promote cell death. Here we demonstrate that calcein blocks HPV16 E1-E2 DNA replication via blocking the viral replication complex forming at the origin of replication. This occurs at non-toxic levels of calcein and demonstrates specificity as it does not block the ability of E2 to regulate transcription. We propose that calcein or derivatives could be developed as an anti-HPV therapeutic. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Genetic variations in the DNA replication origins of human papillomavirus family correlate with their oncogenic potential.

    Science.gov (United States)

    Yilmaz, Gulden; Biswas-Fiss, Esther E; Biswas, Subhasis B

    2018-04-01

    Human papillomaviruses (HPVs) encompass a large family of viruses that range from benign to highly carcinogenic. The crucial differences between benign and carcinogenic types of HPV remain unknown, except that the two HPV types differ in the frequency of DNA replication. We have systematically analyzed the mechanism of HPV DNA replication initiation in low-risk and high-risk HPVs. Our results demonstrate that HPV-encoded E2 initiator protein and its four binding sites in the replication origin play pivotal roles in determining the destiny of the HPV-infected cell. We have identified strain-specific single nucleotide variations in E2 binding sites found only in the high-risk HPVs. We have demonstrated that these variations result in attenuated formation of the E2-DNA complex. E2 binding to these sites is linked to the activation of the DNA replication origin as well as initiation of DNA replication. Both electrophoretic mobility shift assay and atomic force microscopy studies demonstrated that binding of E2 from either low- or high-risk HPVs with variant binding sequences lacked multimeric E2-DNA complex formation in vitro. These results provided a molecular basis of differential DNA replication in the two types of HPVs and pointed to a correlation with the development of cancer. Copyright © 2017. Published by Elsevier B.V.

  2. Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding

    International Nuclear Information System (INIS)

    Tewary, Sunil K.; Liang, Lingfei; Lin, Zihan; Lynn, Annie; Cotmore, Susan F.; Tattersall, Peter; Zhao, Haiyan; Tang, Liang

    2015-01-01

    Members of the Parvoviridae family all encode a non-structural protein 1 (NS1) that directs replication of single-stranded viral DNA, packages viral DNA into capsid, and serves as a potent transcriptional activator. Here we report the X-ray structure of the minute virus of mice (MVM) NS1 N-terminal domain at 1.45 Å resolution, showing that sites for dsDNA binding, ssDNA binding and cleavage, nuclear localization, and other functions are integrated on a canonical fold of the histidine-hydrophobic-histidine superfamily of nucleases, including elements specific for this Protoparvovirus but distinct from its Bocaparvovirus or Dependoparvovirus orthologs. High resolution structural analysis reveals a nickase active site with an architecture that allows highly versatile metal ligand binding. The structures support a unified mechanism of replication origin recognition for homotelomeric and heterotelomeric parvoviruses, mediated by a basic-residue-rich hairpin and an adjacent helix in the initiator proteins and by tandem tetranucleotide motifs in the replication origins. - Highlights: • The structure of a parvovirus replication initiator protein has been determined; • The structure sheds light on mechanisms of ssDNA binding and cleavage; • The nickase active site is preconfigured for versatile metal ligand binding; • The binding site for the double-stranded replication origin DNA is identified; • A single domain integrates multiple functions in virus replication

  3. Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding

    Energy Technology Data Exchange (ETDEWEB)

    Tewary, Sunil K.; Liang, Lingfei; Lin, Zihan; Lynn, Annie [Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 (United States); Cotmore, Susan F. [Departments of Laboratory Medicine, Yale University Medical School, New Haven, CT 06510 (United States); Tattersall, Peter [Departments of Laboratory Medicine, Yale University Medical School, New Haven, CT 06510 (United States); Departments of Genetics, Yale University Medical School, New Haven, CT 06510 (United States); Zhao, Haiyan, E-mail: zhaohy@ku.edu [Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 (United States); Tang, Liang, E-mail: tangl@ku.edu [Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 (United States)

    2015-02-15

    Members of the Parvoviridae family all encode a non-structural protein 1 (NS1) that directs replication of single-stranded viral DNA, packages viral DNA into capsid, and serves as a potent transcriptional activator. Here we report the X-ray structure of the minute virus of mice (MVM) NS1 N-terminal domain at 1.45 Å resolution, showing that sites for dsDNA binding, ssDNA binding and cleavage, nuclear localization, and other functions are integrated on a canonical fold of the histidine-hydrophobic-histidine superfamily of nucleases, including elements specific for this Protoparvovirus but distinct from its Bocaparvovirus or Dependoparvovirus orthologs. High resolution structural analysis reveals a nickase active site with an architecture that allows highly versatile metal ligand binding. The structures support a unified mechanism of replication origin recognition for homotelomeric and heterotelomeric parvoviruses, mediated by a basic-residue-rich hairpin and an adjacent helix in the initiator proteins and by tandem tetranucleotide motifs in the replication origins. - Highlights: • The structure of a parvovirus replication initiator protein has been determined; • The structure sheds light on mechanisms of ssDNA binding and cleavage; • The nickase active site is preconfigured for versatile metal ligand binding; • The binding site for the double-stranded replication origin DNA is identified; • A single domain integrates multiple functions in virus replication.

  4. Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses.

    Science.gov (United States)

    Hamperl, Stephan; Bocek, Michael J; Saldivar, Joshua C; Swigut, Tomek; Cimprich, Karlene A

    2017-08-10

    Conflicts between transcription and replication are a potent source of DNA damage. Co-transcriptional R-loops could aggravate such conflicts by creating an additional barrier to replication fork progression. Here, we use a defined episomal system to investigate how conflict orientation and R-loop formation influence genome stability in human cells. R-loops, but not normal transcription complexes, induce DNA breaks and orientation-specific DNA damage responses during conflicts with replication forks. Unexpectedly, the replisome acts as an orientation-dependent regulator of R-loop levels, reducing R-loops in the co-directional (CD) orientation but promoting their formation in the head-on (HO) orientation. Replication stress and deregulated origin firing increase the number of HO collisions leading to genome-destabilizing R-loops. Our findings connect DNA replication to R-loop homeostasis and suggest a mechanistic basis for genome instability resulting from deregulated DNA replication, observed in cancer and other disease states. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Identification of Persistent RNA-DNA Hybrid Structures within the Origin of Replication of Human Cytomegalovirus

    OpenAIRE

    Prichard, Mark N.; Jairath, Sanju; Penfold, Mark E. T.; Jeor, Stephen St.; Bohlman, Marlene C.; Pari, Gregory S.

    1998-01-01

    Human cytomegalovirus (HCMV) lytic-phase DNA replication initiates at the cis-acting origin of replication, oriLyt. oriLyt is a structurally complex region containing repeat elements and transcription factor binding sites. We identified two site-specific alkali-labile regions within oriLyt which flank an alkali-resistant DNA segment. These alkali-sensitive regions were the result of the degradation of two RNA species embedded within oriLyt and covalently linked to viral DNA. The virus-associa...

  6. High-Resolution Replication Profiles Define the Stochastic Nature of Genome Replication Initiation and Termination

    Directory of Open Access Journals (Sweden)

    Michelle Hawkins

    2013-11-01

    Full Text Available Eukaryotic genome replication is stochastic, and each cell uses a different cohort of replication origins. We demonstrate that interpreting high-resolution Saccharomyces cerevisiae genome replication data with a mathematical model allows quantification of the stochastic nature of genome replication, including the efficiency of each origin and the distribution of termination events. Single-cell measurements support the inferred values for stochastic origin activation time. A strain, in which three origins were inactivated, confirmed that the distribution of termination events is primarily dictated by the stochastic activation time of origins. Cell-to-cell variability in origin activity ensures that termination events are widely distributed across virtually the whole genome. We propose that the heterogeneity in origin usage contributes to genome stability by limiting potentially deleterious events from accumulating at particular loci.

  7. Functions of mammalian Cdc7 kinase in initiation/monitoring of DNA replication and development

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jung Min; Yamada, Masayuki; Masai, Hisao

    2003-11-27

    Cdc7 kinase plays an essential role in firing of replication origins by phosphorylating components of the replication complexes. Cdc7 kinase has also been implicated in S phase checkpoint signaling downstream of the ATR and Chk1 kinases. Inactivation of Cdc7 in yeast results in arrest of cell growth with 1C DNA content after completion of the ongoing DNA replication. In contrast, conditional inactivation of Cdc7 in undifferentiated mouse embryonic stem (ES) cells leads to growth arrest with rapid cessation of DNA synthesis, suggesting requirement of Cdc7 functions for continuation of ongoing DNA synthesis. Furthermore, loss of Cdc7 function induces recombinational repair (nuclear Rad51 foci) and G2/M checkpoint responses (inhibition of Cdc2 kinase). Eventually, p53 becomes highly activated and the cells undergo massive p53-dependent apoptosis. Thus, defective origin activation in mammalian cells can generate DNA replication checkpoint signals. Efficient removal of those cells in which replication has been perturbed, through cell death, may be beneficial to maintain the highest level of genetic integrity in totipotent stem cells. Partial, rather than total, loss of Cdc7 kinase expression results in retarded growth at both cellular and whole body levels, with especially profound impairment of germ cell development.

  8. Functions of mammalian Cdc7 kinase in initiation/monitoring of DNA replication and development

    International Nuclear Information System (INIS)

    Kim, Jung Min; Yamada, Masayuki; Masai, Hisao

    2003-01-01

    Cdc7 kinase plays an essential role in firing of replication origins by phosphorylating components of the replication complexes. Cdc7 kinase has also been implicated in S phase checkpoint signaling downstream of the ATR and Chk1 kinases. Inactivation of Cdc7 in yeast results in arrest of cell growth with 1C DNA content after completion of the ongoing DNA replication. In contrast, conditional inactivation of Cdc7 in undifferentiated mouse embryonic stem (ES) cells leads to growth arrest with rapid cessation of DNA synthesis, suggesting requirement of Cdc7 functions for continuation of ongoing DNA synthesis. Furthermore, loss of Cdc7 function induces recombinational repair (nuclear Rad51 foci) and G2/M checkpoint responses (inhibition of Cdc2 kinase). Eventually, p53 becomes highly activated and the cells undergo massive p53-dependent apoptosis. Thus, defective origin activation in mammalian cells can generate DNA replication checkpoint signals. Efficient removal of those cells in which replication has been perturbed, through cell death, may be beneficial to maintain the highest level of genetic integrity in totipotent stem cells. Partial, rather than total, loss of Cdc7 kinase expression results in retarded growth at both cellular and whole body levels, with especially profound impairment of germ cell development

  9. Loss of Hda activity stimulates replication initiation from I-box, but not R4 mutant origins in Escherichia coli.

    Science.gov (United States)

    Riber, Leise; Fujimitsu, Kazuyuki; Katayama, Tsutomu; Løbner-Olesen, Anders

    2009-01-01

    Initiation of chromosome replication in Escherichia coli is limited by the initiator protein DnaA associated with ATP. Within the replication origin, binding sites for DnaA associated with ATP or ADP (R boxes) and the DnaA(ATP) specific sites (I-boxes, tau-boxes and 6-mer sites) are found. We analysed chromosome replication of cells carrying mutations in conserved regions of oriC. Cells carrying mutations in DnaA-boxes I2, I3, R2, R3 and R5 as well as FIS and IHF binding sites resembled wild-type cells with respect to origin concentration. Initiation of replication in these mutants occurred in synchrony or with slight asynchrony only. Furthermore, lack of Hda stimulated initiation in all these mutants. The DnaA(ATP) containing complex that leads to initiation can therefore be formed in the absence of several of the origin DnaA binding sites including both DnaA(ATP) specific I-boxes. However, competition between I-box mutant and wild-type origins, revealed a positive role of I-boxes on initiation. On the other hand, mutations affecting DnaA-box R4 were found to be compromised for initiation and could not be augmented by an increase in cellular DnaA(ATP)/DnaA(ADP) ratio. Compared with the sites tested here, R4 therefore seems to contribute to initiation most critically.

  10. Role for a region of helically unstable DNA within the Epstein-Barr virus latent cycle origin of DNA replication oriP in origin function

    International Nuclear Information System (INIS)

    Polonskaya, Zhanna; Benham, Craig J.; Hearing, Janet

    2004-01-01

    The minimal replicator of the Epstein-Barr virus (EBV) latent cycle origin of DNA replication oriP is composed of two binding sites for the Epstein-Barr virus nuclear antigen-1 (EBNA-1) and flanking inverted repeats that bind the telomere repeat binding factor TRF2. Although not required for minimal replicator activity, additional binding sites for EBNA-1 and TRF2 and one or more auxiliary elements located to the right of the EBNA-1/TRF2 sites are required for the efficient replication of oriP plasmids. Another region of oriP that is predicted to be destabilized by DNA supercoiling is shown here to be an important functional component of oriP. The ability of DNA fragments of unrelated sequence and possessing supercoiled-induced DNA duplex destabilized (SIDD) structures, but not fragments characterized by helically stable DNA, to substitute for this component of oriP demonstrates a role for the SIDD region in the initiation of oriP-plasmid DNA replication

  11. DNA replication origins—where do we begin?

    Science.gov (United States)

    Prioleau, Marie-Noëlle; MacAlpine, David M.

    2016-01-01

    For more than three decades, investigators have sought to identify the precise locations where DNA replication initiates in mammalian genomes. The development of molecular and biochemical approaches to identify start sites of DNA replication (origins) based on the presence of defining and characteristic replication intermediates at specific loci led to the identification of only a handful of mammalian replication origins. The limited number of identified origins prevented a comprehensive and exhaustive search for conserved genomic features that were capable of specifying origins of DNA replication. More recently, the adaptation of origin-mapping assays to genome-wide approaches has led to the identification of tens of thousands of replication origins throughout mammalian genomes, providing an unprecedented opportunity to identify both genetic and epigenetic features that define and regulate their distribution and utilization. Here we summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages. PMID:27542827

  12. Variability of fire behavior, fire effects, and emissions in Scotch pine forests of central Siberia

    Science.gov (United States)

    D. J. McRae; Susan Conard; G. A. Ivanova; A. I. Sukhinin; Steve Baker; Y. N. Samsonov; T. W. Blake; V. A. Ivanov; A. V. Ivanov; T. V. Churkina; WeiMin Hao; K. P. Koutzenogij; Nataly Kovaleva

    2006-01-01

    As part of the Russian FIRE BEAR (Fire Effects in the Boreal Eurasia Region) Project, replicated 4-ha experimental fires were conducted on a dry Scotch pine (Pinus sylvestris)/lichen (Cladonia sp.)/feathermoss (Pleurozeum schreberi) forest site in central Siberia. Observations from the initial seven surface fires (2000-2001) ignited under a range of burning...

  13. Histone hypoacetylation is required to maintain late replication timing of constitutive heterochromatin.

    Science.gov (United States)

    Casas-Delucchi, Corella S; van Bemmel, Joke G; Haase, Sebastian; Herce, Henry D; Nowak, Danny; Meilinger, Daniela; Stear, Jeffrey H; Leonhardt, Heinrich; Cardoso, M Cristina

    2012-01-01

    The replication of the genome is a spatio-temporally highly organized process. Yet, its flexibility throughout development suggests that this process is not genetically regulated. However, the mechanisms and chromatin modifications controlling replication timing are still unclear. We made use of the prominent structure and defined heterochromatic landscape of pericentric regions as an example of late replicating constitutive heterochromatin. We manipulated the major chromatin markers of these regions, namely histone acetylation, DNA and histone methylation, as well as chromatin condensation and determined the effects of these altered chromatin states on replication timing. Here, we show that manipulation of DNA and histone methylation as well as acetylation levels caused large-scale heterochromatin decondensation. Histone demethylation and the concomitant decondensation, however, did not affect replication timing. In contrast, immuno-FISH and time-lapse analyses showed that lowering DNA methylation, as well as increasing histone acetylation, advanced the onset of heterochromatin replication. While dnmt1(-)(/)(-) cells showed increased histone acetylation at chromocenters, histone hyperacetylation did not induce DNA demethylation. Hence, we propose that histone hypoacetylation is required to maintain normal heterochromatin duplication dynamics. We speculate that a high histone acetylation level might increase the firing efficiency of origins and, concomitantly, advances the replication timing of distinct genomic regions.

  14. Mortality due to Vegetation Fire-Originated PM2.5 Exposure in Europe-Assessment for the Years 2005 and 2008.

    Science.gov (United States)

    Kollanus, Virpi; Prank, Marje; Gens, Alexandra; Soares, Joana; Vira, Julius; Kukkonen, Jaakko; Sofiev, Mikhail; Salonen, Raimo O; Lanki, Timo

    2017-01-01

    Vegetation fires can release substantial quantities of fine particles (PM2.5), which are harmful to health. The fire smoke may be transported over long distances and can cause adverse health effects over wide areas. We aimed to assess annual mortality attributable to short-term exposures to vegetation fire-originated PM2.5 in different regions of Europe. PM2.5 emissions from vegetation fires in Europe in 2005 and 2008 were evaluated based on Moderate Resolution Imaging Spectroradiometer (MODIS) satellite data on fire radiative power. Atmospheric transport of the emissions was modeled using the System for Integrated modeLling of Atmospheric coMposition (SILAM) chemical transport model. Mortality impacts were estimated for 27 European countries based on a) modeled daily PM2.5 concentrations and b) population data, both presented in a 50 × 50 km2 spatial grid; c) an exposure-response function for short-term PM2.5 exposure and daily nonaccidental mortality; and d) country-level data for background mortality risk. In the 27 countries overall, an estimated 1,483 and 1,080 premature deaths were attributable to the vegetation fire-originated PM2.5 in 2005 and 2008, respectively. Estimated impacts were highest in southern and eastern Europe. However, all countries were affected by fire-originated PM2.5, and even the lower concentrations in western and northern Europe contributed substantially (~ 30%) to the overall estimate of attributable mortality. Our assessment suggests that air pollution caused by PM2.5 released from vegetation fires is a notable risk factor for public health in Europe. Moreover, the risk can be expected to increase in the future as climate change proceeds. This factor should be taken into consideration when evaluating the overall health and socioeconomic impacts of these fires. Citation: Kollanus V, Prank M, Gens A, Soares J, Vira J, Kukkonen J, Sofiev M, Salonen RO, Lanki T. 2017. Mortality due to vegetation fire-originated PM2.5 exposure in Europe

  15. What Should Researchers Expect When They Replicate Studies? A Statistical View of Replicability in Psychological Science.

    Science.gov (United States)

    Patil, Prasad; Peng, Roger D; Leek, Jeffrey T

    2016-07-01

    A recent study of the replicability of key psychological findings is a major contribution toward understanding the human side of the scientific process. Despite the careful and nuanced analysis reported, the simple narrative disseminated by the mass, social, and scientific media was that in only 36% of the studies were the original results replicated. In the current study, however, we showed that 77% of the replication effect sizes reported were within a 95% prediction interval calculated using the original effect size. Our analysis suggests two critical issues in understanding replication of psychological studies. First, researchers' intuitive expectations for what a replication should show do not always match with statistical estimates of replication. Second, when the results of original studies are very imprecise, they create wide prediction intervals-and a broad range of replication effects that are consistent with the original estimates. This may lead to effects that replicate successfully, in that replication results are consistent with statistical expectations, but do not provide much information about the size (or existence) of the true effect. In this light, the results of the Reproducibility Project: Psychology can be viewed as statistically consistent with what one might expect when performing a large-scale replication experiment. © The Author(s) 2016.

  16. New criteria for selecting the origin of DNA replication in Wolbachia and closely related bacteria

    DEFF Research Database (Denmark)

    Ioannidis, Panagiotis; Dunning Hotopp, Julie C; Sapountzis, Panagiotis

    2007-01-01

    , the origin of DNA replication (ori) regions were identified in silico for Wolbachia strains and eleven other related bacteria belonging to Ehrlichia, Anaplasma, and Rickettsia genera. These features include DnaA-, CtrA- and IHF-binding sites as well as the flanking genes in C. crescentus. The Wolbachia ori...

  17. Ecological effects of alternative fuel-reduction treatments: highlights of the National Fire and Fire Surrogate study (FFS)

    Science.gov (United States)

    James D. McIver; Scott L. Stephens; James K. Agee; Jamie Barbour; Ralph E. J. Boerner; Carl B. Edminster; Karen L. Erickson; Kerry L. Farris; Christopher J. Fettig; Carl E. Fiedler; Sally Haase; Stephen C. Hart; Jon E. Keeley; Eric E. Knapp; John F. Lehmkuhl; Jason J. Moghaddas; William Otrosina; Kenneth W. Outcalt; Dylan W. Schwilk; Carl N. Skinner; Thomas A. Waldrop; C. Phillip Weatherspoon; Daniel A. Yaussy; Andrew Youngblood; Steve Zack

    2012-01-01

    The 12-site National Fire and Fire Surrogate study (FFS) was a multivariate experiment that evaluated ecological consequences of alternative fuel-reduction treatments in seasonally dry forests of the US. Each site was a replicated experiment with a common design that compared an un-manipulated control, prescribed fire, mechanical and mechanical + fire treatments....

  18. Organization of the origins of replication of the chromosomes of Mycobacterium smegmatis, Mycobacterium leprae and Mycobacterium tuberculosis and isolation of a functional origin from M. smegmatis.

    Science.gov (United States)

    Salazar, L; Fsihi, H; de Rossi, E; Riccardi, G; Rios, C; Cole, S T; Takiff, H E

    1996-04-01

    The genus Mycobacterium is composed of species with widely differing growth rates ranging from approximately three hours in Mycobacterium smegmatis to two weeks in Mycobacterium leprae. As DNA replication is coupled to cell duplication, it may be regulated by common mechanisms. The chromosomal regions surrounding the origins of DNA replication from M. smegmatis, M. tuberculosis, and M. leprae have been sequenced, and show very few differences. The gene order, rnpA-rpmH-dnaA-dnaN-recF-orf-gyrB-gyrA, is the same as in other Gram-positive organisms. Although the general organization in M. smegmatis is very similar to that of Streptomyces spp., a closely related genus, M. tuberculosis and M. leprae differ as they lack an open reading frame, between dnaN and recF, which is similar to the gnd gene of Escherichia coli. Within the three mycobacterial species, there is extensive sequence conservation in the intergenic regions flanking dnaA, but more variation from the consensus DnaA box sequence was seen than in other bacteria. By means of subcloning experiments, the putative chromosomal origin of replication of M. smegmatis, containing the dnaA-dnaN region, was shown to promote autonomous replication in M. smegmatis, unlike the corresponding regions from M. tuberculosis or M. leprae.

  19. Strategic role of the ubiquitin-dependent segregase p97 (VCP or Cdc48) in DNA replication.

    Science.gov (United States)

    Ramadan, Kristijan; Halder, Swagata; Wiseman, Katherine; Vaz, Bruno

    2017-02-01

    Genome amplification (DNA synthesis) is one of the most demanding cellular processes in all proliferative cells. The DNA replication machinery (also known as the replisome) orchestrates genome amplification during S-phase of the cell cycle. Genetic material is particularly vulnerable to various events that can challenge the replisome during its assembly, activation (firing), progression (elongation) and disassembly from chromatin (termination). Any disturbance of the replisome leads to stalling of the DNA replication fork and firing of dormant replication origins, a process known as DNA replication stress. DNA replication stress is considered to be one of the main causes of sporadic cancers and other pathologies related to tissue degeneration and ageing. The mechanisms of replisome assembly and elongation during DNA synthesis are well understood. However, once DNA synthesis is complete, the process of replisome disassembly, and its removal from chromatin, remains unclear. In recent years, a growing body of evidence has alluded to a central role in replisome regulation for the ubiquitin-dependent protein segregase p97, also known as valosin-containing protein (VCP) in metazoans and Cdc48 in lower eukaryotes. By orchestrating the spatiotemporal turnover of the replisome, p97 plays an essential role in DNA replication. In this review, we will summarise our current knowledge about how p97 controls the replisome from replication initiation, to elongation and finally termination. We will also further examine the more recent findings concerning the role of p97 and how mutations in p97 cofactors, also known as adaptors, cause DNA replication stress induced genomic instability that leads to cancer and accelerated ageing. To our knowledge, this is the first comprehensive review concerning the mechanisms involved in the regulation of DNA replication by p97.

  20. A theory for the origin of a self-replicating chemical system. I - Natural selection of the autogen from short, random oligomers

    Science.gov (United States)

    White, D. H.

    1980-01-01

    A general theory is presented for the origin of a self-replicating chemical system, termed an autogen, which is capable of both crude replication and translation (protein synthesis). The theory requires the availability of free energy and monomers to the system, a significant background low-yield synthesis of kinetically stable oligopeptides and oligonucleotides, the localization of the oligomers, crude oligonucleotide selectivity of amino acids during oligopeptide synthesis, crude oligonucleotide replication, and two short peptide families which catalyze replication and translation, to produce a localized group of at least one copy each of two protogenes and two protoenzymes. The model posits a process of random oligomerization, followed by the random nucleation of functional components and the rapid autocatalytic growth of the functioning autogen to macroscopic amounts, to account for the origin of the first self-replicating system. Such a process contains steps of such high probability and short time periods that it is suggested that the emergence of an autogen in a laboratory experiment of reasonable time scale may be possible.

  1. Adenovirus sequences required for replication in vivo.

    OpenAIRE

    Wang, K; Pearson, G D

    1985-01-01

    We have studied the in vivo replication properties of plasmids carrying deletion mutations within cloned adenovirus terminal sequences. Deletion mapping located the adenovirus DNA replication origin entirely within the first 67 bp of the adenovirus inverted terminal repeat. This region could be further subdivided into two functional domains: a minimal replication origin and an adjacent auxillary region which boosted the efficiency of replication by more than 100-fold. The minimal origin occup...

  2. Childhood trauma and the origins of paranormal belief: a constructive replication.

    Science.gov (United States)

    Irwin, H J

    1994-02-01

    Previous research suggests that, as a group, people who believe in the paranormal tend to have a history of traumatic events in childhood. This relationship has been incorporated into Irwin's 1993 model of the psychological origins and functions of paranormal belief. A constructive replication of the relationship and a test of Irwin's model was undertaken in relation to a specific context, namely, a childhood spent with an alcoholic parent. Compared to 89 control participants, a sample of 32 adults who were children of alcoholics had stronger beliefs in witchcraft, superstitions, and precognition. The results are discussed in relation to two components of Irwin's model.

  3. The scenario on the origin of translation in the RNA world: in principle of replication parsimony

    Directory of Open Access Journals (Sweden)

    Ma Wentao

    2010-11-01

    Full Text Available Abstract Background It is now believed that in the origin of life, proteins should have been "invented" in an RNA world. However, due to the complexity of a possible RNA-based proto-translation system, this evolving process seems quite complicated and the associated scenario remains very blurry. Considering that RNA can bind amino acids with specificity, it has been reasonably supposed that initial peptides might have been synthesized on "RNA templates" containing multiple amino acid binding sites. This "Direct RNA Template (DRT" mechanism is attractive because it should be the simplest mechanism for RNA to synthesize peptides, thus very likely to have been adopted initially in the RNA world. Then, how this mechanism could develop into a proto-translation system mechanism is an interesting problem. Presentation of the hypothesis Here an explanation to this problem is shown considering the principle of "replication parsimony" --- genetic information tends to be utilized in a parsimonious way under selection pressure, due to its replication cost (e.g., in the RNA world, nucleotides and ribozymes for RNA replication. Because a DRT would be quite long even for a short peptide, its replication cost would be great. Thus the diversity and the length of functional peptides synthesized by the DRT mechanism would be seriously limited. Adaptors (proto-tRNAs would arise to allow a DRT's complementary strand (called "C-DRT" here to direct the synthesis of the same peptide synthesized by the DRT itself. Because the C-DRT is a necessary part in the DRT's replication, fewer turns of the DRT's replication would be needed to synthesize definite copies of the functional peptide, thus saving the replication cost. Acting through adaptors, C-DRTs could transform into much shorter templates (called "proto-mRNAs" here and substitute the role of DRTs, thus significantly saving the replication cost. A proto-rRNA corresponding to the small subunit rRNA would then emerge

  4. Herpesvirus papio contains a plasmid origin of replication that acts in cis interspecies with an Epstein-Barr virus trans-acting function.

    Science.gov (United States)

    Pesano, R L; Pagano, J S

    1986-01-01

    Herpesvirus papio (HVP) and Epstein-Barr virus (EBV) are closely related biologically and biochemically; lymphoblastoid cells infected with either virus contain episomal viral DNA. The putative origin of replication for EBV plasmids (oriP) has been assigned to a 1,790-base-pair fragment (cis) in the short unique region of the genome which requires a viral function supplied in trans from elsewhere in the genome (J. Yates, N. Warren, D. Reisman, and B. Sugden, Proc. Natl. Acad. Sci. USA 81:3806-3810, 1984). We report here the identification of the putative origin of replication (cis) in HVP; we assigned it to the HVP EcoRI K fragment. The results indicate that the HVP replication process requires both a cis and a trans-acting function, analogous to that found in EBV. Images PMID:3023667

  5. The age and origin of carbon in fire aerosols during El Niño-induced haze events in Singapore

    Science.gov (United States)

    Wiggins, E. B.; Czimczik, C. I.; Santos, G. M.; Chen, Y.; Xu, X.; Randerson, J. T.

    2017-12-01

    During the onset of the 2015-2016 El Niño, fires in Indonesia and Malaysia created a massive regional haze event that severely degraded air quality in many urban centers and resulted in significant land-atmosphere CO2 emissions with average daily CO2 emissions of 11.2 Tg during September - October. Many lines of evidence indicate that peat fires are a dominant contributor to biomass burning emissions in the region. However, El Nino-induced drought is also known to increase deforestation fires and agricultural waste burning, and there are relatively few observational constraints that provide a quantitative partitioning of emissions among these fire types. Nor have there been regionally-integrated estimates of the age of carbon that is combusted in peatland fires. This information is critical for linking haze-related mortality with the anthropogenic build-up of atmospheric CO2. Measuring the age of carbon (14C content) in airborne particulate matter provides a mean to apportion how different fire types contribute to regional air pollution. Here we measured the 14C content of 39 particulate matter (PM2.5) samples collected in Singapore from September 2014 through October 2015, with the aim of assessing the age and origin of the haze-inducing carbonaceous aerosol. We found that the 14C content of the fire aerosols in Singapore was -59.8 ± 61.6‰, well below atmospheric background levels of 24 ± 3‰, and consistent with an age of 430 ± 520 years before present. Atmospheric transport modeling confirmed that fire emissions originating from Sumatra and Borneo were the dominant contributor to the elevated PM2.5 in Singapore. The 14C measurements provide independent confirmation that fire emissions in the region originate primarily from peat burning, and should be treated as a component of the net land use change flux that contributes to climate warming. Our analysis also highlights the dual benefits for air quality and climate mitigation of improving fire management

  6. Identification of a Single Strand Origin of Replication in the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.

    Directory of Open Access Journals (Sweden)

    Laurel D Wright

    2015-10-01

    Full Text Available We identified a functional single strand origin of replication (sso in the integrative and conjugative element ICEBs1 of Bacillus subtilis. Integrative and conjugative elements (ICEs, also known as conjugative transposons are DNA elements typically found integrated into a bacterial chromosome where they are transmitted to daughter cells by chromosomal replication and cell division. Under certain conditions, ICEs become activated and excise from the host chromosome and can transfer to neighboring cells via the element-encoded conjugation machinery. Activated ICEBs1 undergoes autonomous rolling circle replication that is needed for the maintenance of the excised element in growing and dividing cells. Rolling circle replication, used by many plasmids and phages, generates single-stranded DNA (ssDNA. In many cases, the presence of an sso enhances the conversion of the ssDNA to double-stranded DNA (dsDNA by enabling priming of synthesis of the second DNA strand. We initially identified sso1 in ICEBs1 based on sequence similarity to the sso of an RCR plasmid. Several functional assays confirmed Sso activity. Genetic analyses indicated that ICEBs1 uses sso1 and at least one other region for second strand DNA synthesis. We found that Sso activity was important for two key aspects of the ICEBs1 lifecycle: 1 maintenance of the plasmid form of ICEBs1 in cells after excision from the chromosome, and 2 stable acquisition of ICEBs1 following transfer to a new host. We identified sequences similar to known plasmid sso's in several other ICEs. Together, our results indicate that many other ICEs contain at least one single strand origin of replication, that these ICEs likely undergo autonomous replication, and that replication contributes to the stability and spread of these elements.

  7. Replicative Intermediates of Human Papillomavirus Type 11 in Laryngeal Papillomas: Site of Replication Initiation and Direction of Replication

    Science.gov (United States)

    Auborn, K. J.; Little, R. D.; Platt, T. H. K.; Vaccariello, M. A.; Schildkraut, C. L.

    1994-07-01

    We have examined the structures of replication intermediates from the human papillomavirus type 11 genome in DNA extracted from papilloma lesions (laryngeal papillomas). The sites of replication initiation and termination utilized in vivo were mapped by using neutral/neutral and neutral/alkaline two-dimensional agarose gel electrophoresis methods. Initiation of replication was detected in or very close to the upstream regulatory region (URR; the noncoding, regulatory sequences upstream of the open reading frames in the papillomavirus genome). We also show that replication forks proceed bidirectionally from the origin and converge 180circ opposite the URR. These results demonstrate the feasibility of analysis of replication of viral genomes directly from infected tissue.

  8. Set2 Methyltransferase Facilitates DNA Replication and Promotes Genotoxic Stress Responses through MBF-Dependent Transcription.

    Science.gov (United States)

    Pai, Chen-Chun; Kishkevich, Anastasiya; Deegan, Rachel S; Keszthelyi, Andrea; Folkes, Lisa; Kearsey, Stephen E; De León, Nagore; Soriano, Ignacio; de Bruin, Robertus Antonius Maria; Carr, Antony M; Humphrey, Timothy C

    2017-09-12

    Chromatin modification through histone H3 lysine 36 methylation by the SETD2 tumor suppressor plays a key role in maintaining genome stability. Here, we describe a role for Set2-dependent H3K36 methylation in facilitating DNA replication and the transcriptional responses to both replication stress and DNA damage through promoting MluI cell-cycle box (MCB) binding factor (MBF)-complex-dependent transcription in fission yeast. Set2 loss leads to reduced MBF-dependent ribonucleotide reductase (RNR) expression, reduced deoxyribonucleoside triphosphate (dNTP) synthesis, altered replication origin firing, and a checkpoint-dependent S-phase delay. Accordingly, prolonged S phase in the absence of Set2 is suppressed by increasing dNTP synthesis. Furthermore, H3K36 is di- and tri-methylated at these MBF gene promoters, and Set2 loss leads to reduced MBF binding and transcription in response to genotoxic stress. Together, these findings provide new insights into how H3K36 methylation facilitates DNA replication and promotes genotoxic stress responses in fission yeast. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Set2 Methyltransferase Facilitates DNA Replication and Promotes Genotoxic Stress Responses through MBF-Dependent Transcription

    Directory of Open Access Journals (Sweden)

    Chen-Chun Pai

    2017-09-01

    Full Text Available Chromatin modification through histone H3 lysine 36 methylation by the SETD2 tumor suppressor plays a key role in maintaining genome stability. Here, we describe a role for Set2-dependent H3K36 methylation in facilitating DNA replication and the transcriptional responses to both replication stress and DNA damage through promoting MluI cell-cycle box (MCB binding factor (MBF-complex-dependent transcription in fission yeast. Set2 loss leads to reduced MBF-dependent ribonucleotide reductase (RNR expression, reduced deoxyribonucleoside triphosphate (dNTP synthesis, altered replication origin firing, and a checkpoint-dependent S-phase delay. Accordingly, prolonged S phase in the absence of Set2 is suppressed by increasing dNTP synthesis. Furthermore, H3K36 is di- and tri-methylated at these MBF gene promoters, and Set2 loss leads to reduced MBF binding and transcription in response to genotoxic stress. Together, these findings provide new insights into how H3K36 methylation facilitates DNA replication and promotes genotoxic stress responses in fission yeast.

  10. DNA Replication Profiling Using Deep Sequencing.

    Science.gov (United States)

    Saayman, Xanita; Ramos-Pérez, Cristina; Brown, Grant W

    2018-01-01

    Profiling of DNA replication during progression through S phase allows a quantitative snap-shot of replication origin usage and DNA replication fork progression. We present a method for using deep sequencing data to profile DNA replication in S. cerevisiae.

  11. Phosphopeptide binding by Sld3 links Dbf4-dependent kinase to MCM replicative helicase activation.

    Science.gov (United States)

    Deegan, Tom D; Yeeles, Joseph Tp; Diffley, John Fx

    2016-05-02

    The initiation of eukaryotic DNA replication requires the assembly of active CMG (Cdc45-MCM-GINS) helicases at replication origins by a set of conserved and essential firing factors. This process is controlled during the cell cycle by cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), and in response to DNA damage by the checkpoint kinase Rad53/Chk1. Here we show that Sld3, previously shown to be an essential CDK and Rad53 substrate, is recruited to the inactive MCM double hexamer in a DDK-dependent manner. Sld3 binds specifically to DDK-phosphorylated peptides from two MCM subunits (Mcm4, 6) and then recruits Cdc45. MCM mutants that cannot bind Sld3 or Sld3 mutants that cannot bind phospho-MCM or Cdc45 do not support replication. Moreover, phosphomimicking mutants in Mcm4 and Mcm6 bind Sld3 without DDK and facilitate DDK-independent replication. Thus, Sld3 is an essential "reader" of DDK phosphorylation, integrating signals from three distinct protein kinase pathways to coordinate DNA replication during S phase. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

  12. Who Needs Replication?

    Science.gov (United States)

    Porte, Graeme

    2013-01-01

    In this paper, the editor of a recent Cambridge University Press book on research methods discusses replicating previous key studies to throw more light on their reliability and generalizability. Replication research is presented as an accepted method of validating previous research by providing comparability between the original and replicated…

  13. The world behind electricity from coal. The dubious origin of coal for Dutch coal-fired power plants

    International Nuclear Information System (INIS)

    2008-01-01

    Five energy companies in the Netherlands want to build additional coal-fired power plants: Essent and Nuon, the German company RWE and E.ON and the Belgian company Electrabel. Coal-fired power plants emit 70 percent more CO2 than gas-fired power plants. Especially because of the threat to the climate Greenpeace believes that no more coal-fired power plants should be built. In this publication Greenpeace explores the pollution, the working conditions and human rights with regard to the exploitation of coal. That has been elaborated for the three countries from which Dutch energy companies import coal: South Africa, Colombia and Indonesia. In addition to information about the origin of coal also insight is given into the coal market (stocks and use), the enormous coal transport and the world trade [nl

  14. Specificity and function of Archaeal DNA replication initiator proteins

    DEFF Research Database (Denmark)

    Samson, Rachel Y.; Xu, Yanqun; Gadelha, Catarina

    2013-01-01

    Chromosomes with multiple DNA replication origins are a hallmark of Eukaryotes and some Archaea. All eukaryal nuclear replication origins are defined by the origin recognition complex (ORC) that recruits the replicative helicase MCM(2-7) via Cdc6 and Cdt1. We find that the three origins...... to investigate the role of ATP binding and hydrolysis in initiator function in vivo and in vitro. We find that the ATP-bound form of Orc1-1 is proficient for replication and implicates hydrolysis of ATP in downregulation of origin activity. Finally, we reveal that ATP and DNA binding by Orc1-1 remodels...

  15. From the chromatin interaction network to the organization of the human genome into replication N/U-domains

    International Nuclear Information System (INIS)

    Boulos, Rasha E; Julienne, Hanna; Baker, Antoine; Jensen, Pablo; Arneodo, Alain; Audit, Benjamin; Chen, Chun-Long; D'Aubenton-Carafa, Yves; Thermes, Claude; Petryk, Nataliya; Kahli, Malik; Hyrien, Olivier; Goldar, Arach

    2014-01-01

    The three-dimensional (3D) architecture of the mammalian nucleus is now being unraveled thanks to the recent development of chromatin conformation capture (3C) technologies. Here we report the results of a combined multiscale analysis of genome-wide mean replication timing and chromatin conformation data that reveal some intimate relationships between chromatin folding and human DNA replication. We previously described megabase replication N/U-domains as mammalian multiorigin replication units, and showed that their borders are ‘master’ replication initiation zones that likely initiate cascades of origin firing responsible for the stereotypic replication of these domains. Here, we demonstrate that replication N/U-domains correspond to the structural domains of self-interacting chromatin, and that their borders act as insulating regions both in high-throughput 3C (Hi-C) data and high-resolution 3C (4C) experiments. Further analyses of Hi-C data using a graph-theoretical approach reveal that N/U-domain borders are long-distance, interconnected hubs of the chromatin interaction network. Overall, these results and the observation that a well-defined ordering of chromatin states exists from N/U-domain borders to centers suggest that ‘master’ replication initiation zones are at the heart of a high-order, epigenetically controlled 3D organization of the human genome. (paper)

  16. Uncoupling of Sister Replisomes during Eukaryotic DNA Replication

    NARCIS (Netherlands)

    Yardimci, Hasan; Loveland, Anna B.; Habuchi, Satoshi; van Oijen, Antoine M.; Walter, Johannes C.

    2010-01-01

    The duplication of eukaryotic genomes involves the replication of DNA from multiple origins of replication. In S phase, two sister replisomes assemble at each active origin, and they replicate DNA in opposite directions. Little is known about the functional relationship between sister replisomes.

  17. Regulatory cross-talk links Vibrio cholerae chromosome II replication and segregation.

    Directory of Open Access Journals (Sweden)

    Yoshiharu Yamaichi

    2011-07-01

    Full Text Available There is little knowledge of factors and mechanisms for coordinating bacterial chromosome replication and segregation. Previous studies have revealed that genes (and their products that surround the origin of replication (oriCII of Vibrio cholerae chromosome II (chrII are critical for controlling the replication and segregation of this chromosome. rctB, which flanks one side of oriCII, encodes a protein that initiates chrII replication; rctA, which flanks the other side of oriCII, inhibits rctB activity. The chrII parAB2 operon, which is essential for chrII partitioning, is located immediately downstream of rctA. Here, we explored how rctA exerts negative control over chrII replication. Our observations suggest that RctB has at least two DNA binding domains--one for binding to oriCII and initiating replication and the other for binding to rctA and thereby inhibiting RctB's ability to initiate replication. Notably, the inhibitory effect of rctA could be alleviated by binding of ParB2 to a centromere-like parS site within rctA. Furthermore, by binding to rctA, ParB2 and RctB inversely regulate expression of the parAB2 genes. Together, our findings suggest that fluctuations in binding of the partitioning protein ParB2 and the chrII initiator RctB to rctA underlie a regulatory network controlling both oriCII firing and the production of the essential chrII partitioning proteins. Thus, by binding both RctB and ParB2, rctA serves as a nexus for regulatory cross-talk coordinating chrII replication and segregation.

  18. Long-term effects of fire and fire-return interval on population structure and growth of longleaf pine (Pinus palustris)

    Science.gov (United States)

    Chelcy R. Ford; Emily S. Minor; Gordon A. Fox

    2010-01-01

    We investigated the effect of fire and fire frequency on stand structure and longleaf pine (Pinus palustris P. Mill.) growth and population demography in an experimental research area in a southwest Florida sandhill community. Data were collected from replicated plots that had prescribed fire-return intervals of 1, 2, 5, or 7 years or were left...

  19. Initiation of enzymatic replication at the origin of the Escherichia coli chromosome: primase as the sole priming enzyme

    NARCIS (Netherlands)

    van der Ende, A.; Baker, T. A.; Ogawa, T.; Kornberg, A.

    1985-01-01

    The enzymatic replication of plasmids containing the unique (245 base pair) origin of the Escherichia coli chromosome (oriC) can be initiated with any of three enzyme priming systems: primase alone, RNA polymerase alone, or both combined (Ogawa, T., Baker, T. A., van der Ende, A. & Kornberg, A.

  20. Post-disturbance plant community dynamics following a rare natural-origin fire in a Tsuga canadensis forest.

    Directory of Open Access Journals (Sweden)

    Bryan D Murray

    Full Text Available Opportunities to directly study infrequent forest disturbance events often lead to valuable information about vegetation dynamics. In mesic temperate forests of North America, stand-replacing crown fire occurs infrequently, with a return interval of 2000-3000 years. Rare chance events, however, may have profound impacts on the developmental trajectories of forest ecosystems. For example, it has been postulated that stand-replacing fire may have been an important factor in the establishment of eastern hemlock (Tsuga canadensis stands in the northern Great Lakes region. Nevertheless, experimental evidence linking hemlock regeneration to non-anthropogenic fire is limited. To clarify this potential relationship, we monitored vegetation dynamics following a rare lightning-origin crown fire in a Wisconsin hemlock-hardwood forest. We also studied vegetation in bulldozer-created fire breaks and adjacent undisturbed forest. Our results indicate that hemlock establishment was rare in the burned area but moderately common in the scarified bulldozer lines compared to the reference area. Early-successional, non-arboreal species including Rubus spp., Vaccinium angustifolium, sedges (Carex spp., grasses, Epilobium ciliatum, and Pteridium aquilinium were the most abundant post-fire species. Collectively, our results suggest that competing vegetation and moisture stress resulting from drought may reduce the efficacy of scarification treatments as well as the usefulness of fire for preparing a suitable seedbed for hemlock. The increasing prevalence of growing-season drought suggests that silvicultural strategies based on historic disturbance regimes may need to be reevaluated for mesic species.

  1. Nuclear mitochondrial DNA activates replication in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Laurent Chatre

    Full Text Available The nuclear genome of eukaryotes is colonized by DNA fragments of mitochondrial origin, called NUMTs. These insertions have been associated with a variety of germ-line diseases in humans. The significance of this uptake of potentially dangerous sequences into the nuclear genome is unclear. Here we provide functional evidence that sequences of mitochondrial origin promote nuclear DNA replication in Saccharomyces cerevisiae. We show that NUMTs are rich in key autonomously replicating sequence (ARS consensus motifs, whose mutation results in the reduction or loss of DNA replication activity. Furthermore, 2D-gel analysis of the mrc1 mutant exposed to hydroxyurea shows that several NUMTs function as late chromosomal origins. We also show that NUMTs located close to or within ARS provide key sequence elements for replication. Thus NUMTs can act as independent origins, when inserted in an appropriate genomic context or affect the efficiency of pre-existing origins. These findings show that migratory mitochondrial DNAs can impact on the replication of the nuclear region they are inserted in.

  2. Registered Replication Report

    DEFF Research Database (Denmark)

    Bouwmeester, S.; Verkoeijen, P. P.J.L.; Aczel, B.

    2017-01-01

    and colleagues. The results of studies using time pressure have been mixed, with some replication attempts observing similar patterns (e.g., Rand et al., 2014) and others observing null effects (e.g., Tinghög et al., 2013; Verkoeijen & Bouwmeester, 2014). This Registered Replication Report (RRR) assessed...... the size and variability of the effect of time pressure on cooperative decisions by combining 21 separate, preregistered replications of the critical conditions from Study 7 of the original article (Rand et al., 2012). The primary planned analysis used data from all participants who were randomly assigned...

  3. Bayesian evaluation of effect size after replicating an original study

    NARCIS (Netherlands)

    Van Aert, Robbie C M; Van Assen, Marcel A.L.M.

    2017-01-01

    The vast majority of published results in the literature is statistically significant, which raises concerns about their reliability. The Reproducibility Project Psychology (RPP) and Experimental Economics Replication Project (EE-RP) both replicated a large number of published studies in psychology

  4. Fire Risk Scoping Study: Investigation of nuclear power plant fire risk, including previously unaddressed issues

    International Nuclear Information System (INIS)

    Lambright, J.A.; Nowlen, S.P.; Nicolette, V.F.; Bohn, M.P.

    1989-01-01

    An investigation of nuclear power plant fire risk issues raised as a result of the USNRC sponsored Fire Protection Research Program at Sandia National Laboratories has been performed. The specific objectives of this study were (1) to review and requantify fire risk scenarios from four fire probabilistic risk assessments (PRAs) in light of updated data bases made available as a result of USNRC sponsored Fire Protection Research Program and updated computer fire modeling capabilities, (2) to identify potentially significant fire risk issues that have not been previously addressed in a fire risk context and to quantify the potential impact of those identified fire risk issues where possible, and (3) to review current fire regulations and plant implementation practices for relevance to the identified unaddressed fire risk issues. In performance of the fire risk scenario requantifications several important insights were gained. It was found that utilization of a more extensive operational experience base resulted in both fire occurrence frequencies and fire duration times (i.e., time required for fire suppression) increasing significantly over those assumed in the original works. Additionally, some thermal damage threshold limits assumed in the original works were identified as being nonconservative based on more recent experimental data. Finally, application of the COMPBRN III fire growth model resulted in calculation of considerably longer fire damage times than those calculated in the original works using COMPBRN I. 14 refs., 2 figs., 16 tabs

  5. Buffer layers grown by replicating the texture of an original template tape

    International Nuclear Information System (INIS)

    Lim, Sunme; Yoo, Jaeun; Park, Chan; Youm, Dojun

    2007-01-01

    We propose a fabrication method of the buffer layers, whose biaxial textures are replicated from an original template tape. The purpose of this method is economical texturing process for coated conductors. At first we prepared a biaxially textured metal tape (TM-tape). Then a sacrifice layer (SA), a buffer layer (BU) and a thick metallic layer (SM) were sequentially deposited on the TM-tape. SA-layer and BU-layer were deposited epitaxially to copy the texture of the TM-tape. SA-layer was dissoluble in water. SM-layer with the textured BU-layer was separated and could be used for a supporting tape for the further growth of a superconducting layer. In this way, it is possible to reuse the original textured TM-tape many times. In this paper, we report the results of our experiments, in which we used a biaxially Ni tape, BaO film, STO film, and a thick Ag film for TM-tape, SA-layer, BU-layer, and SM-layer, respectively. The Ag/STO layers were successfully separated form the Ni tape by dissolving the BaO layer in water. The texture quality of the STO layer was well secured after the separation

  6. A Novel Rrm3 Function in Restricting DNA Replication via an Orc5-Binding Domain Is Genetically Separable from Rrm3 Function as an ATPase/Helicase in Facilitating Fork Progression

    Science.gov (United States)

    Syed, Salahuddin; Desler, Claus; Rasmussen, Lene J.; Schmidt, Kristina H.

    2016-01-01

    In response to replication stress cells activate the intra-S checkpoint, induce DNA repair pathways, increase nucleotide levels, and inhibit origin firing. Here, we report that Rrm3 associates with a subset of replication origins and controls DNA synthesis during replication stress. The N-terminal domain required for control of DNA synthesis maps to residues 186–212 that are also critical for binding Orc5 of the origin recognition complex. Deletion of this domain is lethal to cells lacking the replication checkpoint mediator Mrc1 and leads to mutations upon exposure to the replication stressor hydroxyurea. This novel Rrm3 function is independent of its established role as an ATPase/helicase in facilitating replication fork progression through polymerase blocking obstacles. Using quantitative mass spectrometry and genetic analyses, we find that the homologous recombination factor Rdh54 and Rad5-dependent error-free DNA damage bypass act as independent mechanisms on DNA lesions that arise when Rrm3 catalytic activity is disrupted whereas these mechanisms are dispensable for DNA damage tolerance when the replication function is disrupted, indicating that the DNA lesions generated by the loss of each Rrm3 function are distinct. Although both lesion types activate the DNA-damage checkpoint, we find that the resultant increase in nucleotide levels is not sufficient for continued DNA synthesis under replication stress. Together, our findings suggest a role of Rrm3, via its Orc5-binding domain, in restricting DNA synthesis that is genetically and physically separable from its established catalytic role in facilitating fork progression through replication blocks. PMID:27923055

  7. A Novel Rrm3 Function in Restricting DNA Replication via an Orc5-Binding Domain Is Genetically Separable from Rrm3 Function as an ATPase/Helicase in Facilitating Fork Progression.

    Science.gov (United States)

    Syed, Salahuddin; Desler, Claus; Rasmussen, Lene J; Schmidt, Kristina H

    2016-12-01

    In response to replication stress cells activate the intra-S checkpoint, induce DNA repair pathways, increase nucleotide levels, and inhibit origin firing. Here, we report that Rrm3 associates with a subset of replication origins and controls DNA synthesis during replication stress. The N-terminal domain required for control of DNA synthesis maps to residues 186-212 that are also critical for binding Orc5 of the origin recognition complex. Deletion of this domain is lethal to cells lacking the replication checkpoint mediator Mrc1 and leads to mutations upon exposure to the replication stressor hydroxyurea. This novel Rrm3 function is independent of its established role as an ATPase/helicase in facilitating replication fork progression through polymerase blocking obstacles. Using quantitative mass spectrometry and genetic analyses, we find that the homologous recombination factor Rdh54 and Rad5-dependent error-free DNA damage bypass act as independent mechanisms on DNA lesions that arise when Rrm3 catalytic activity is disrupted whereas these mechanisms are dispensable for DNA damage tolerance when the replication function is disrupted, indicating that the DNA lesions generated by the loss of each Rrm3 function are distinct. Although both lesion types activate the DNA-damage checkpoint, we find that the resultant increase in nucleotide levels is not sufficient for continued DNA synthesis under replication stress. Together, our findings suggest a role of Rrm3, via its Orc5-binding domain, in restricting DNA synthesis that is genetically and physically separable from its established catalytic role in facilitating fork progression through replication blocks.

  8. Mapping autonomously replicating sequence elements in a 73-kb ...

    Indian Academy of Sciences (India)

    Autonomously replicating sequence (ARS) elements are the genetic determinants of replication origin function in yeasts. They can be easily identified as the plasmids containing them transform yeast cells at a high frequency. As the first step towards identifying all potential replication origins in a 73-kb region of the long arm ...

  9. Specificity and Function of Archaeal DNA Replication Initiator Proteins

    Directory of Open Access Journals (Sweden)

    Rachel Y. Samson

    2013-02-01

    Full Text Available Chromosomes with multiple DNA replication origins are a hallmark of Eukaryotes and some Archaea. All eukaryal nuclear replication origins are defined by the origin recognition complex (ORC that recruits the replicative helicase MCM(2-7 via Cdc6 and Cdt1. We find that the three origins in the single chromosome of the archaeon Sulfolobus islandicus are specified by distinct initiation factors. While two origins are dependent on archaeal homologs of eukaryal Orc1 and Cdc6, the third origin is instead reliant on an archaeal Cdt1 homolog. We exploit the nonessential nature of the orc1-1 gene to investigate the role of ATP binding and hydrolysis in initiator function in vivo and in vitro. We find that the ATP-bound form of Orc1-1 is proficient for replication and implicates hydrolysis of ATP in downregulation of origin activity. Finally, we reveal that ATP and DNA binding by Orc1-1 remodels the protein’s structure rather than that of the DNA template.

  10. Analysis of the temporal program of replication initiation in yeast chromosomes.

    Science.gov (United States)

    Friedman, K L; Raghuraman, M K; Fangman, W L; Brewer, B J

    1995-01-01

    The multiple origins of eukaryotic chromosomes vary in the time of their initiation during S phase. In the chromosomes of Saccharomyces cerevisiae the presence of a functional telomere causes nearby origins to delay initiation until the second half of S phase. The key feature of telomeres that causes the replication delay is the telomeric sequence (C(1-3)A/G(1-3)T) itself and not the proximity of the origin to a DNA end. A second group of late replicating origins has been found at an internal position on chromosome XIV. Four origins, spanning approximately 140 kb, initiate replication in the second half of S phase. At least two of these internal origins maintain their late replication time on circular plasmids. Each of these origins can be separated into two functional elements: those sequences that provide origin function and those that impose late activation. Because the assay for determining replication time is costly and laborious, it has not been possible to analyze in detail these 'late' elements. We report here the development of two new assays for determining replication time. The first exploits the expression of the Escherichia coli dam methylase in yeast and the characteristic period of hemimethylation that transiently follows the passage of a replication fork. The second uses quantitative hybridization to detect two-fold differences in the amount of specific restriction fragments as a function of progress through S phase. The novel aspect of this assay is the creation in vivo of a non-replicating DNA sequence by site-specific pop-out recombination. This non-replicating fragment acts as an internal control for copy number within and between samples. Both of these techniques are rapid and much less costly than the more conventional density transfer experiments that require CsCl gradients to detect replicated DNA. With these techniques it should be possible to identify the sequences responsible for late initiation, to search for other late replicating

  11. Replication, falsification, and the crisis of confidence in social psychology.

    Science.gov (United States)

    Earp, Brian D; Trafimow, David

    2015-01-01

    The (latest) crisis in confidence in social psychology has generated much heated discussion about the importance of replication, including how it should be carried out as well as interpreted by scholars in the field. For example, what does it mean if a replication attempt "fails"-does it mean that the original results, or the theory that predicted them, have been falsified? And how should "failed" replications affect our belief in the validity of the original research? In this paper, we consider the replication debate from a historical and philosophical perspective, and provide a conceptual analysis of both replication and falsification as they pertain to this important discussion. Along the way, we highlight the importance of auxiliary assumptions (for both testing theories and attempting replications), and introduce a Bayesian framework for assessing "failed" replications in terms of how they should affect our confidence in original findings.

  12. Replication, falsification, and the crisis of confidence in social psychology

    Science.gov (United States)

    Earp, Brian D.; Trafimow, David

    2015-01-01

    The (latest) crisis in confidence in social psychology has generated much heated discussion about the importance of replication, including how it should be carried out as well as interpreted by scholars in the field. For example, what does it mean if a replication attempt “fails”—does it mean that the original results, or the theory that predicted them, have been falsified? And how should “failed” replications affect our belief in the validity of the original research? In this paper, we consider the replication debate from a historical and philosophical perspective, and provide a conceptual analysis of both replication and falsification as they pertain to this important discussion. Along the way, we highlight the importance of auxiliary assumptions (for both testing theories and attempting replications), and introduce a Bayesian framework for assessing “failed” replications in terms of how they should affect our confidence in original findings. PMID:26042061

  13. Mechanisms of DNA replication termination.

    Science.gov (United States)

    Dewar, James M; Walter, Johannes C

    2017-08-01

    Genome duplication is carried out by pairs of replication forks that assemble at origins of replication and then move in opposite directions. DNA replication ends when converging replication forks meet. During this process, which is known as replication termination, DNA synthesis is completed, the replication machinery is disassembled and daughter molecules are resolved. In this Review, we outline the steps that are likely to be common to replication termination in most organisms, namely, fork convergence, synthesis completion, replisome disassembly and decatenation. We briefly review the mechanism of termination in the bacterium Escherichia coli and in simian virus 40 (SV40) and also focus on recent advances in eukaryotic replication termination. In particular, we discuss the recently discovered E3 ubiquitin ligases that control replisome disassembly in yeast and higher eukaryotes, and how their activity is regulated to avoid genome instability.

  14. Initiation of DNA replication: functional and evolutionary aspects

    Science.gov (United States)

    Bryant, John A.; Aves, Stephen J.

    2011-01-01

    Background The initiation of DNA replication is a very important and highly regulated step in the cell division cycle. It is of interest to compare different groups of eukaryotic organisms (a) to identify the essential molecular events that occur in all eukaryotes, (b) to start to identify higher-level regulatory mechanisms that are specific to particular groups and (c) to gain insights into the evolution of initiation mechanisms. Scope This review features a wide-ranging literature survey covering replication origins, origin recognition and usage, modification of origin usage (especially in response to plant hormones), assembly of the pre-replication complex, loading of the replisome, genomics, and the likely origin of these mechanisms and proteins in Archaea. Conclusions In all eukaryotes, chromatin is organized for DNA replication as multiple replicons. In each replicon, replication is initiated at an origin. With the exception of those in budding yeast, replication origins, including the only one to be isolated so far from a plant, do not appear to embody a specific sequence; rather, they are AT-rich, with short tracts of locally bent DNA. The proteins involved in initiation are remarkably similar across the range of eukaryotes. Nevertheless, their activity may be modified by plant-specific mechanisms, including regulation by plant hormones. The molecular features of initiation are seen in a much simpler form in the Archaea. In particular, where eukaryotes possess a number of closely related proteins that form ‘hetero-complexes’ (such as the origin recognition complex and the MCM complex), archaeans typically possess one type of protein (e.g. one MCM) that forms a homo-complex. This suggests that several eukaryotic initiation proteins have evolved from archaeal ancestors by gene duplication and divergence. PMID:21508040

  15. Two subunits of human ORC are dispensable for DNA replication and proliferation.

    Science.gov (United States)

    Shibata, Etsuko; Kiran, Manjari; Shibata, Yoshiyuki; Singh, Samarendra; Kiran, Shashi; Dutta, Anindya

    2016-12-01

    The six-subunit Origin Recognition Complex (ORC) is believed to be an essential eukaryotic ATPase that binds to origins of replication as a ring-shaped heterohexamer to load MCM2-7 and initiate DNA replication. We have discovered that human cell lines in culture proliferate with intact chromosomal origins of replication after disruption of both alleles of ORC2 or of the ATPase subunit, ORC1 . The ORC1 or ORC2 -depleted cells replicate with decreased chromatin loading of MCM2-7 and become critically dependent on another ATPase, CDC6, for survival and DNA replication. Thus, either the ORC ring lacking a subunit, even its ATPase subunit, can load enough MCM2-7 in partnership with CDC6 to initiate DNA replication, or cells have an ORC-independent, CDC6-dependent mechanism to load MCM2-7 on origins of replication.

  16. Influence of contemporary carbon originating from the 2003 Siberian forest fire on organic carbon in PM2.5 in Nagoya, Japan

    International Nuclear Information System (INIS)

    Ikemori, Fumikazu; Honjyo, Koji; Yamagami, Makiko; Nakamura, Toshio

    2015-01-01

    In May 2003, high concentrations of organic carbon (OC) in PM 2.5 were measured in Nagoya, a representative metropolitan area in Japan. To investigate the influence of possible forest fires on PM 2.5 in Japan via long-range aerosol transport, the radiocarbon ( 14 C) concentrations of PM 2.5 samples from April 2003 to March 2004 were measured. 14 C concentrations in total carbon (TC) from May to early June showed higher values than those in other periods. The OC/elemental carbon (EC) ratios from May to early June were also significantly higher than the ones in other periods. In addition, OC concentrations from May to early June were typically high. These results indicate that the abundant OC fraction from May to early June in Nagoya consisted predominantly of contemporary carbon. Furthermore, simulations of diffusion and transport of organic matter (OM) in East Asia showed that abundant OM originating from East Siberia spread over East Asia and Japan in May and early June. Backward air mass trajectories from this time frame indicate that the air mass in Nagoya likely first passed through East Siberia where fire events were prevalent. However, the backward trajectories showed that the air mass after early June did not originate mainly from Siberia, and correspondingly, the 14 C and OC concentrations showed lower values than those from May to early June. Therefore, the authors conclude that contemporary carbon originating from the forest fire in East Siberia was transported to Nagoya, where it significantly contributed to the high observed concentrations of both OC and 14 C. - Highlights: • We analyzed the radiocarbon ( 14 C) concentration of TC in PM 2.5 from Nagoya, Japan. • 14 C concentrations from May to early June in 2003 were elevated. • The air mass at this time in Nagoya likely first passed through East Siberia. • Fire location data from MODIS indicate that fire events were prevalent in East Siberia. • Contemporary carbon emitted from the Siberian

  17. A New Replication Norm for Psychology

    Directory of Open Access Journals (Sweden)

    Etienne P LeBel

    2015-10-01

    Full Text Available In recent years, there has been a growing concern regarding the replicability of findings in psychology, including a mounting number of prominent findings that have failed to replicate via high-powered independent replication attempts. In the face of this replicability “crisis of confidence”, several initiatives have been implemented to increase the reliability of empirical findings. In the current article, I propose a new replication norm that aims to further boost the dependability of findings in psychology. Paralleling the extant social norm that researchers should peer review about three times as many articles that they themselves publish per year, the new replication norm states that researchers should aim to independently replicate important findings in their own research areas in proportion to the number of original studies they themselves publish per year (e.g., a 4:1 original-to-replication studies ratio. I argue this simple approach could significantly advance our science by increasing the reliability and cumulative nature of our empirical knowledge base, accelerating our theoretical understanding of psychological phenomena, instilling a focus on quality rather than quantity, and by facilitating our transformation toward a research culture where executing and reporting independent direct replications is viewed as an ordinary part of the research process. To help promote the new norm, I delineate (1 how each of the major constituencies of the research process (i.e., funders, journals, professional societies, departments, and individual researchers can incentivize replications and promote the new norm and (2 any obstacles each constituency faces in supporting the new norm.

  18. The Sodium-Potassium Pump Controls the Intrinsic Firing of the Cerebellar Purkinje Neuron

    Science.gov (United States)

    Forrest, Michael D.; Wall, Mark J.; Press, Daniel A.; Feng, Jianfeng

    2012-01-01

    In vitro, cerebellar Purkinje cells can intrinsically fire action potentials in a repeating trimodal or bimodal pattern. The trimodal pattern consists of tonic spiking, bursting, and quiescence. The bimodal pattern consists of tonic spiking and quiescence. It is unclear how these firing patterns are generated and what determines which firing pattern is selected. We have constructed a realistic biophysical Purkinje cell model that can replicate these patterns. In this model, Na+/K+ pump activity sets the Purkinje cell's operating mode. From rat cerebellar slices we present Purkinje whole cell recordings in the presence of ouabain, which irreversibly blocks the Na+/K+ pump. The model can replicate these recordings. We propose that Na+/K+ pump activity controls the intrinsic firing mode of cerbellar Purkinje cells. PMID:23284664

  19. Plant Community and Soil Environment Response to Summer Fire in the Northern Great Plains

    Science.gov (United States)

    Fire is a keystone process in many ecosystems, especially grasslands. However, documentation of plant community and soil environment responses to fire is limited for semiarid grasslands relative to that for mesic grasslands. Replicated summer fire research is lacking, but much needed because summe...

  20. Chromatin Constrains the Initiation and Elongation of DNA Replication.

    Science.gov (United States)

    Devbhandari, Sujan; Jiang, Jieqing; Kumar, Charanya; Whitehouse, Iestyn; Remus, Dirk

    2017-01-05

    Eukaryotic chromosomal DNA is faithfully replicated in a complex series of cell-cycle-regulated events that are incompletely understood. Here we report the reconstitution of DNA replication free in solution with purified proteins from the budding yeast Saccharomyces cerevisiae. The system recapitulates regulated bidirectional origin activation; synthesis of leading and lagging strands by the three replicative DNA polymerases Pol α, Pol δ, and Pol ε; and canonical maturation of Okazaki fragments into continuous daughter strands. We uncover a dual regulatory role for chromatin during DNA replication: promoting origin dependence and determining Okazaki fragment length by restricting Pol δ progression. This system thus provides a functional platform for the detailed mechanistic analysis of eukaryotic chromosome replication. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Organization of Replication of Ribosomal DNA in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Linskens, Maarten H.K.; Huberman, Joel A.

    1988-01-01

    Using recently developed replicon mapping techniques, we have analyzed the replication of the ribosomal DNA in Saccharomyces cerevisiae. The results show that (i) the functional origin of replication colocalizes with an autonomously replicating sequence element previously mapped to the

  2. Genetic Analysis of a Mammalian Chromosomal Origin of Replication

    National Research Council Canada - National Science Library

    Altman, Amy

    2001-01-01

    The main goal of the research proposal was to develop an assay system for studying the specific genetic elements, if any, involved in the initiation of DNA replication in mammalian cells as outlined in Task 1...

  3. The Alleged Crisis and the Illusion of Exact Replication.

    Science.gov (United States)

    Stroebe, Wolfgang; Strack, Fritz

    2014-01-01

    There has been increasing criticism of the way psychologists conduct and analyze studies. These critiques as well as failures to replicate several high-profile studies have been used as justification to proclaim a "replication crisis" in psychology. Psychologists are encouraged to conduct more "exact" replications of published studies to assess the reproducibility of psychological research. This article argues that the alleged "crisis of replicability" is primarily due to an epistemological misunderstanding that emphasizes the phenomenon instead of its underlying mechanisms. As a consequence, a replicated phenomenon may not serve as a rigorous test of a theoretical hypothesis because identical operationalizations of variables in studies conducted at different times and with different subject populations might test different theoretical constructs. Therefore, we propose that for meaningful replications, attempts at reinstating the original circumstances are not sufficient. Instead, replicators must ascertain that conditions are realized that reflect the theoretical variable(s) manipulated (and/or measured) in the original study. © The Author(s) 2013.

  4. Origin of life in a digital microcosm

    Science.gov (United States)

    C G, Nitash; LaBar, Thomas; Hintze, Arend; Adami, Christoph

    2017-11-01

    While all organisms on Earth share a common descent, there is no consensus on whether the origin of the ancestral self-replicator was a one-off event or whether it only represented the final survivor of multiple origins. Here, we use the digital evolution system Avida to study the origin of self-replicating computer programs. By using a computational system, we avoid many of the uncertainties inherent in any biochemical system of self-replicators (while running the risk of ignoring a fundamental aspect of biochemistry). We generated the exhaustive set of minimal-genome self-replicators and analysed the network structure of this fitness landscape. We further examined the evolvability of these self-replicators and found that the evolvability of a self-replicator is dependent on its genomic architecture. We also studied the differential ability of replicators to take over the population when competed against each other, akin to a primordial-soup model of biogenesis, and found that the probability of a self-replicator outcompeting the others is not uniform. Instead, progenitor (most-recent common ancestor) genotypes are clustered in a small region of the replicator space. Our results demonstrate how computational systems can be used as test systems for hypotheses concerning the origin of life. This article is part of the themed issue 'Reconceptualizing the origins of life'.

  5. Geminin: a major DNA replication safeguard in higher eukaryotes

    DEFF Research Database (Denmark)

    Melixetian, Marina; Helin, Kristian

    2004-01-01

    Eukaryotes have evolved multiple mechanisms to restrict DNA replication to once per cell cycle. These mechanisms prevent relicensing of origins of replication after initiation of DNA replication in S phase until the end of mitosis. Most of our knowledge of mechanisms controlling prereplication...

  6. Prediction Interval: What to Expect When You're Expecting … A Replication.

    Directory of Open Access Journals (Sweden)

    Jeffrey R Spence

    Full Text Available A challenge when interpreting replications is determining whether the results of a replication "successfully" replicate the original study. Looking for consistency between two studies is challenging because individual studies are susceptible to many sources of error that can cause study results to deviate from each other and the population effect in unpredictable directions and magnitudes. In the current paper, we derive methods to compute a prediction interval, a range of results that can be expected in a replication due to chance (i.e., sampling error, for means and commonly used indexes of effect size: correlations and d-values. The prediction interval is calculable based on objective study characteristics (i.e., effect size of the original study and sample sizes of the original study and planned replication even when sample sizes across studies are unequal. The prediction interval provides an a priori method for assessing if the difference between an original and replication result is consistent with what can be expected due to sample error alone. We provide open-source software tools that allow researchers, reviewers, replicators, and editors to easily calculate prediction intervals.

  7. Gene organization inside replication domains in mammalian genomes

    Science.gov (United States)

    Zaghloul, Lamia; Baker, Antoine; Audit, Benjamin; Arneodo, Alain

    2012-11-01

    We investigate the large-scale organization of human genes with respect to "master" replication origins that were previously identified as bordering nucleotide compositional skew domains. We separate genes in two categories depending on their CpG enrichment at the promoter which can be considered as a marker of germline DNA methylation. Using expression data in mouse, we confirm that CpG-rich genes are highly expressed in germline whereas CpG-poor genes are in a silent state. We further show that, whether tissue-specific or broadly expressed (housekeeping genes), the CpG-rich genes are over-represented close to the replication skew domain borders suggesting some coordination of replication and transcription. We also reveal that the transcription of the longest CpG-rich genes is co-oriented with replication fork progression so that the promoter of these transcriptionally active genes be located into the accessible open chromatin environment surrounding the master replication origins that border the replication skew domains. The observation of a similar gene organization in the mouse genome confirms the interplay of replication, transcription and chromatin structure as the cornerstone of mammalian genome architecture.

  8. Influence of contemporary carbon originating from the 2003 Siberian forest fire on organic carbon in PM{sub 2.5} in Nagoya, Japan

    Energy Technology Data Exchange (ETDEWEB)

    Ikemori, Fumikazu, E-mail: ikemori@nagoyakankaken.net [Nagoya City Institute for Environmental Sciences, 5-16-8, Toyoda, Minami-ku, Nagoya 457-0841 (Japan); Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464–8601 (Japan); Honjyo, Koji [Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464–8601 (Japan); Yamagami, Makiko [Nagoya City Institute for Environmental Sciences, 5-16-8, Toyoda, Minami-ku, Nagoya 457-0841 (Japan); Nakamura, Toshio [Centre for Chronological Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan)

    2015-10-15

    In May 2003, high concentrations of organic carbon (OC) in PM{sub 2.5} were measured in Nagoya, a representative metropolitan area in Japan. To investigate the influence of possible forest fires on PM{sub 2.5} in Japan via long-range aerosol transport, the radiocarbon ({sup 14}C) concentrations of PM{sub 2.5} samples from April 2003 to March 2004 were measured. {sup 14}C concentrations in total carbon (TC) from May to early June showed higher values than those in other periods. The OC/elemental carbon (EC) ratios from May to early June were also significantly higher than the ones in other periods. In addition, OC concentrations from May to early June were typically high. These results indicate that the abundant OC fraction from May to early June in Nagoya consisted predominantly of contemporary carbon. Furthermore, simulations of diffusion and transport of organic matter (OM) in East Asia showed that abundant OM originating from East Siberia spread over East Asia and Japan in May and early June. Backward air mass trajectories from this time frame indicate that the air mass in Nagoya likely first passed through East Siberia where fire events were prevalent. However, the backward trajectories showed that the air mass after early June did not originate mainly from Siberia, and correspondingly, the {sup 14}C and OC concentrations showed lower values than those from May to early June. Therefore, the authors conclude that contemporary carbon originating from the forest fire in East Siberia was transported to Nagoya, where it significantly contributed to the high observed concentrations of both OC and {sup 14}C. - Highlights: • We analyzed the radiocarbon ({sup 14}C) concentration of TC in PM{sub 2.5} from Nagoya, Japan. • {sup 14}C concentrations from May to early June in 2003 were elevated. • The air mass at this time in Nagoya likely first passed through East Siberia. • Fire location data from MODIS indicate that fire events were prevalent in East Siberia.

  9. Termination of DNA replication forks: "Breaking up is hard to do".

    Science.gov (United States)

    Bailey, Rachael; Priego Moreno, Sara; Gambus, Agnieszka

    2015-01-01

    To ensure duplication of the entire genome, eukaryotic DNA replication initiates from thousands of replication origins. The replication forks move through the chromatin until they encounter forks from neighboring origins. During replication fork termination forks converge, the replisomes disassemble and topoisomerase II resolves the daughter DNA molecules. If not resolved efficiently, terminating forks result in genomic instability through the formation of pathogenic structures. Our recent findings shed light onto the mechanism of replisome disassembly upon replication fork termination. We have shown that termination-specific polyubiquitylation of the replicative helicase component - Mcm7, leads to dissolution of the active helicase in a process dependent on the p97/VCP/Cdc48 segregase. The inhibition of terminating helicase disassembly resulted in a replication termination defect. In this extended view we present hypothetical models of replication fork termination and discuss remaining and emerging questions in the DNA replication termination field.

  10. Characterization of the adenoassociated virus Rep protein complex formed on the viral origin of DNA replication

    International Nuclear Information System (INIS)

    Li Zengi; Brister, J. Rodney; Im, Dong-Soo; Muzyczka, Nicholas

    2003-01-01

    Interaction between the adenoassociated virus (AAV) replication proteins, Rep68 and 78, and the viral terminal repeats (TRs) is mediated by a DNA sequence termed the Rep-binding element (RBE). This element is necessary for Rep-mediated unwinding of duplex DNA substrates, directs Rep catalyzed cleavage of the AAV origin of DNA replication, and is required for viral transcription and proviral integration. Six discrete Rep complexes with the AAV TR substrates have been observed in vitro, and cross-linking studies suggest these complexes contain one to six molecules of Rep. However, the functional relationship between Rep oligomerization and biochemical activity is unclear. Here we have characterized Rep complexes that form on the AAV TR. Both Rep68 and Rep78 appear to form the same six complexes with the AAV TR, and ATP seems to stimulate formation of specific, higher order complexes. When the sizes of these Rep complexes were estimated on native polyacrylamide gels, the four slower migrating complexes were larger than predicted by an amount equivalent to one or two TRs. To resolve this discrepancy, the molar ratio of protein and DNA was calculated for the three largest complexes. Data from these experiments indicated that the larger complexes included multiple TRs in addition to multiple Rep molecules and that the Rep-to-TR ratio was approximately 2. The two largest complexes were also associated with increased Rep-mediated, origin cleavage activity. Finally, we characterized a second, Rep-mediated cleavage event that occurs adjacent to the normal nicking site, but on the opposite strand. This second site nicking event effectively results in double-stranded DNA cleavage at the normal nicking site

  11. Characterization of pMC11, a plasmid with dual origins of replication isolated from Lactobacillus casei MCJ and construction of shuttle vectors with each replicon

    DEFF Research Database (Denmark)

    Chen, Zhengjun; Lin, Jinzhong; Ma, Chengjie

    2014-01-01

    . These plasmids showed distinct properties: pEL5.7 was capable of replicating in L. casei MCJΔ1 and Lactobacillus delbrueckii subsp. lactic LBCH-1 but failed to do so in two other tested lactobacilli strains whereas pEL5.6 replicated in three different strains, including L. casei MCJΔ1, L. casei NJ, Lactobacillus......Many lactic acid bacteria carry different plasmids, particularly those that replicate via a theta mechanism. Here we describe Lactobacillus casei MCJ(CCTCC AB20130356), a new isolate that contains pMC11, carrying two distinct theta-type replicons. Each replicon contained an iteron in the origin...... of replication (oriV1 or oriV2) and a gene coding for the replicase (RepA_1 or RepB_1), both of which are essential for plasmid replication. Escherichia coli/Lactobacillus shuttle vectors were constructed with each replicon, yielding pEL5.7 and pEL5.6 that are based on oriV2 and oriV1 replicons, respectively...

  12. Assessment of direct radiological risk and indirect associated toxic risks originated by Coal-Fired Power Plants

    OpenAIRE

    Dinis, M. L.; Fiúza, António; Góis, Joaquim; Carvalho, José Soeiro de; Meira Castro, A C

    2011-01-01

    Over the past few decades there has been some discussion concerning the increase of the natural background radiation originated by coal-fired power plants, due to the uranium and thorium content present in combustion ashes. The radioactive decay products of uranium and thorium, such as radium, radon, polonium, bismuth and lead, are also released in addition to a significant amount of 40K. Since the measurement of radioactive elements released by the gaseous emissions of coal power plants i...

  13. Advanced fire information system

    CSIR Research Space (South Africa)

    Frost, PE

    2007-01-01

    Full Text Available The South African Advanced Fire Information System (AFIS) is the first near real-time satellite-based fire monitoring system in Africa. It was originally developed for, and funded by, the electrical power utility Eskom, to reduce the impact of wild...

  14. Managing Fire in the Northern Chihuahuan Desert: A Review and Analysis of the Literature

    Science.gov (United States)

    Gebow, Brooke S.; Halvorson, William L.

    2005-01-01

    Executive Summary This report began as a literature review (Gebow and Halvorson 2001) conducted for fire planners at Carlsbad Caverns National Park who were seeking information about (1) the natural state of park vegetation, (2) northern Chihuahuan Desert natural fire regimes, and (3) fire effects on park plant species. It is the goal of managers there to continue to refine the wildland and prescribed fire program as they learn more about the ecosystems at the park.The park has a history of grazing and then fire suppression in the 20th century. The current effort revisits questions asked by earlier workers at the park, Walter Kittams and Gary Ahlstrand, who began fire studies in the 1970s. This document addresses ecosystems and historical change to those systems in Chihuahuan Desert areas of southeast Arizona, southern New Mexico, west Texas, or in neighboring regions that share the same plant species. It examines fire literature for situations possibly analogous to those at Carlsbad Caverns. It also includes papers that offer advice on extrapolating future ecological trends from past ones (Swetnam et al. 1999) and on resource management decision-making (Grumbine 1997), and other pieces that address broader aspects of fire or landscape change (Goldman 1994; Marston 1996; Mutch 1994, 1995). These more philosophical works were included in the original review at the park's request and have been retained here because they discuss other issues relevant to fire management. Individual reviews of 35 papers, as requested originally by Carlsbad Caverns, appear in Appendix 1. The results section-summary of key findings-discusses historical changes to plant communities then focuses on burn intervals observed or recommended by workers for particular plant communities. Results from a search of the USDA Forest Service's Fire Effects Information System (www.fs.fed.us/database/feis) are also included in this report, supplemented with information from a review conducted by Ahlstrand

  15. Mcm10 regulates DNA replication elongation by stimulating the CMG replicative helicase.

    Science.gov (United States)

    Lõoke, Marko; Maloney, Michael F; Bell, Stephen P

    2017-02-01

    Activation of the Mcm2-7 replicative DNA helicase is the committed step in eukaryotic DNA replication initiation. Although Mcm2-7 activation requires binding of the helicase-activating proteins Cdc45 and GINS (forming the CMG complex), an additional protein, Mcm10, drives initial origin DNA unwinding by an unknown mechanism. We show that Mcm10 binds a conserved motif located between the oligonucleotide/oligosaccharide fold (OB-fold) and A subdomain of Mcm2. Although buried in the interface between these domains in Mcm2-7 structures, mutations predicted to separate the domains and expose this motif restore growth to conditional-lethal MCM10 mutant cells. We found that, in addition to stimulating initial DNA unwinding, Mcm10 stabilizes Cdc45 and GINS association with Mcm2-7 and stimulates replication elongation in vivo and in vitro. Furthermore, we identified a lethal allele of MCM10 that stimulates initial DNA unwinding but is defective in replication elongation and CMG binding. Our findings expand the roles of Mcm10 during DNA replication and suggest a new model for Mcm10 function as an activator of the CMG complex throughout DNA replication. © 2017 Lõoke et al.; Published by Cold Spring Harbor Laboratory Press.

  16. How MCM loading and spreading specify eukaryotic DNA replication initiation sites.

    Science.gov (United States)

    Hyrien, Olivier

    2016-01-01

    DNA replication origins strikingly differ between eukaryotic species and cell types. Origins are localized and can be highly efficient in budding yeast, are randomly located in early fly and frog embryos, which do not transcribe their genomes, and are clustered in broad (10-100 kb) non-transcribed zones, frequently abutting transcribed genes, in mammalian cells. Nonetheless, in all cases, origins are established during the G1-phase of the cell cycle by the loading of double hexamers of the Mcm 2-7 proteins (MCM DHs), the core of the replicative helicase. MCM DH activation in S-phase leads to origin unwinding, polymerase recruitment, and initiation of bidirectional DNA synthesis. Although MCM DHs are initially loaded at sites defined by the binding of the origin recognition complex (ORC), they ultimately bind chromatin in much greater numbers than ORC and only a fraction are activated in any one S-phase. Data suggest that the multiplicity and functional redundancy of MCM DHs provide robustness to the replication process and affect replication time and that MCM DHs can slide along the DNA and spread over large distances around the ORC. Recent studies further show that MCM DHs are displaced along the DNA by collision with transcription complexes but remain functional for initiation after displacement. Therefore, eukaryotic DNA replication relies on intrinsically mobile and flexible origins, a strategy fundamentally different from bacteria but conserved from yeast to human. These properties of MCM DHs likely contribute to the establishment of broad, intergenic replication initiation zones in higher eukaryotes.

  17. Performance of fire behavior fuel models developed for the Rothermel Surface Fire Spread Model

    Science.gov (United States)

    Robert Ziel; W. Matt Jolly

    2009-01-01

    In 2005, 40 new fire behavior fuel models were published for use with the Rothermel Surface Fire Spread Model. These new models are intended to augment the original 13 developed in 1972 and 1976. As a compiled set of quantitative fuel descriptions that serve as input to the Rothermel model, the selected fire behavior fuel model has always been critical to the resulting...

  18. Characteristic effects of stochastic oscillatory forcing on neural firing: analytical theory and comparison to paddlefish electroreceptor data.

    Science.gov (United States)

    Bauermeister, Christoph; Schwalger, Tilo; Russell, David F; Neiman, Alexander B; Lindner, Benjamin

    2013-01-01

    Stochastic signals with pronounced oscillatory components are frequently encountered in neural systems. Input currents to a neuron in the form of stochastic oscillations could be of exogenous origin, e.g. sensory input or synaptic input from a network rhythm. They shape spike firing statistics in a characteristic way, which we explore theoretically in this report. We consider a perfect integrate-and-fire neuron that is stimulated by a constant base current (to drive regular spontaneous firing), along with Gaussian narrow-band noise (a simple example of stochastic oscillations), and a broadband noise. We derive expressions for the nth-order interval distribution, its variance, and the serial correlation coefficients of the interspike intervals (ISIs) and confirm these analytical results by computer simulations. The theory is then applied to experimental data from electroreceptors of paddlefish, which have two distinct types of internal noisy oscillators, one forcing the other. The theory provides an analytical description of their afferent spiking statistics during spontaneous firing, and replicates a pronounced dependence of ISI serial correlation coefficients on the relative frequency of the driving oscillations, and furthermore allows extraction of certain parameters of the intrinsic oscillators embedded in these electroreceptors.

  19. BRPF3-HBO1 regulates replication origin activation and histone H3K14 acetylation

    DEFF Research Database (Denmark)

    Feng, Yunpeng; Vlassis, Arsenios; Roques, Céline

    2016-01-01

    implicated in replication control by measuring RPA accumulation upon replication stress. We identify six factors required for normal rates of DNA replication and characterize a function of the bromodomain and PHD finger-containing protein 3 (BRPF3) in replication initiation. BRPF3 forms a complex with HBO1...

  20. The rolling-circle melting-pot model for porcine circovirus DNA replication

    Science.gov (United States)

    A stem-loop structure, formed by a pair of inverted repeats during DNA replication, is a conserved feature at the origin of DNA replication (Ori) among plant and animal viruses, bacteriophages and plasmids that replicate their genomes via the rolling-circle replication (RCR) mechanism. Porcine circo...

  1. Three attempts to replicate the moral licensing effect

    NARCIS (Netherlands)

    Blanken, I.; van de Ven, N.; Zeelenberg, M.; Meijers, Marijn H. C.

    2014-01-01

    The present work includes three attempts to replicate the moral licensing effect by Sachdeva, Iliev, and Medin (2009). The original authors found that writing about positive traits led to lower donations to charity and decreased cooperative behavior. The first two replication attempts (student

  2. Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p

    Directory of Open Access Journals (Sweden)

    Greenblatt Jack F

    2007-09-01

    Full Text Available Abstract Background Histone modifications have been implicated in the regulation of transcription and, more recently, in DNA replication and repair. In yeast, a major conserved histone acetyltransferase, Hat1p, preferentially acetylates lysine residues 5 and 12 on histone H4. Results Here, we report that a nuclear sub-complex consisting of Hat1p and its partner Hat2p interacts physically and functionally with the origin recognition complex (ORC. While mutational inactivation of the histone acetyltransferase (HAT gene HAT1 alone does not compromise origin firing or initiation of DNA replication, a deletion in HAT1 (or HAT2 exacerbates the growth defects of conditional orc-ts mutants. Thus, the ORC-associated Hat1p-dependent histone acetyltransferase activity suggests a novel linkage between histone modification and DNA replication. Additional genetic and biochemical evidence points to the existence of partly overlapping histone H3 acetyltransferase activities in addition to Hat1p/Hat2p for proper DNA replication efficiency. Furthermore, we demonstrated a dynamic association of Hat1p with chromatin during S-phase that suggests a role of this enzyme at the replication fork. Conclusion We have found an intriguing new association of the Hat1p-dependent histone acetyltransferase in addition to its previously known role in nuclear chromatin assembly (Hat1p/Hat2p-Hif1p. The participation of a distinct Hat1p/Hat2p sub-complex suggests a linkage of histone H4 modification with ORC-dependent DNA replication.

  3. Burning phylogenies: fire, molecular evolutionary rates, and diversification.

    Science.gov (United States)

    Verdú, Miguel; Pausas, Juli G; Segarra-Moragues, José Gabriel; Ojeda, Fernando

    2007-09-01

    Mediterranean-type ecosystems are among the most remarkable plant biodiversity "hot spots" on the earth, and fire has traditionally been invoked as one of the evolutionary forces explaining this exceptional diversity. In these ecosystems, adult plants of some species are able to survive after fire (resprouters), whereas in other species fire kills the adults and populations are only maintained by an effective post-fire recruitment (seeders). Seeders tend to have shorter generation times than resprouters, particularly under short fire return intervals, thus potentially increasing their molecular evolutionary rates and, ultimately, their diversification. We explored whether seeder lineages actually have higher rates of molecular evolution and diversification than resprouters. Molecular evolutionary rates in different DNA regions were compared in 45 phylogenetically paired congeneric taxa from fire-prone Mediterranean-type ecosystems with contrasting seeder and resprouter life histories. Differential diversification was analyzed with both topological and chronological approaches in five genera (Banksia, Daviesia, Lachnaea, Leucadendron, and Thamnochortus) from two fire-prone regions (Australia and South Africa). We found that seeders had neither higher molecular rates nor higher diversification than resprouters. Such lack of differences in molecular rates between seeders and resprouters-which did not agree with theoretical predictions-may occur if (1) the timing of the switch from seeding to resprouting (or vice versa) occurs near the branch tip, so that most of the branch length evolves under the opposite life-history form; (2) resprouters suffer more somatic mutations and therefore counterbalancing the replication-induced mutations of seeders; and (3) the rate of mutations is not related to shorter generation times because plants do not undergo determinate germ-line replication. The absence of differential diversification is to be expected if seeders and resprouters

  4. Rolling replication of UV-irradiated duplex DNA in the phi X174 replicative-form----single-strand replication system in vitro

    International Nuclear Information System (INIS)

    Shavitt, O.; Livneh, Z.

    1989-01-01

    Cloning of the phi X174 viral origin of replication into phage M13mp8 produced an M13-phi X174 chimera, the DNA of which directed efficient replicative-form----single-strand rolling replication in vitro. This replication assay was performed with purified phi X174-encoded gene A protein, Escherichia coli rep helicase, single-stranded DNA-binding protein, and DNA polymerase III holoenzyme. The nicking of replicative-form I (RFI) DNA by gene A protein was essentially unaffected by the presence of UV lesions in the DNA. However, unwinding of UV-irradiated DNA by the rep helicase was inhibited twofold as compared with unwinding of the unirradiated substrate. UV irradiation of the substrate DNA caused a strong inhibition in its ability to direct DNA synthesis. However, even DNA preparations that contained as many as 10 photodimers per molecule still supported the synthesis of progeny full-length single-stranded DNA. The appearance of full-length radiolabeled products implied at least two full rounds of replication, since the first round released the unlabeled plus viral strand of the duplex DNA. Pretreatment of the UV-irradiated DNA substrate with purified pyrimidine dimer endonuclease from Micrococcus luteus, which converted photodimer-containing supercoiled RFI DNA into relaxed, nicked RFII DNA and thus prevented its replication, reduced DNA synthesis by 70%. Analysis of radiolabeled replication products by agarose gel electrophoresis followed by autoradiography revealed that this decrease was due to a reduction in the synthesis of progeny full-length single-stranded DNA. This implies that 70 to 80% of the full-length DNA products produced in this system were synthesized on molecules that carried photodimers

  5. Influence of contemporary carbon originating from the 2003 Siberian forest fire on organic carbon in PM2.5 in Nagoya, Japan.

    Science.gov (United States)

    Ikemori, Fumikazu; Honjyo, Koji; Yamagami, Makiko; Nakamura, Toshio

    2015-10-15

    In May 2003, high concentrations of organic carbon (OC) in PM2.5 were measured in Nagoya, a representative metropolitan area in Japan. To investigate the influence of possible forest fires on PM2.5 in Japan via long-range aerosol transport, the radiocarbon ((14)C) concentrations of PM2.5 samples from April 2003 to March 2004 were measured. (14)C concentrations in total carbon (TC) from May to early June showed higher values than those in other periods. The OC/elemental carbon (EC) ratios from May to early June were also significantly higher than the ones in other periods. In addition, OC concentrations from May to early June were typically high. These results indicate that the abundant OC fraction from May to early June in Nagoya consisted predominantly of contemporary carbon. Furthermore, simulations of diffusion and transport of organic matter (OM) in East Asia showed that abundant OM originating from East Siberia spread over East Asia and Japan in May and early June. Backward air mass trajectories from this time frame indicate that the air mass in Nagoya likely first passed through East Siberia where fire events were prevalent. However, the backward trajectories showed that the air mass after early June did not originate mainly from Siberia, and correspondingly, the (14)C and OC concentrations showed lower values than those from May to early June. Therefore, the authors conclude that contemporary carbon originating from the forest fire in East Siberia was transported to Nagoya, where it significantly contributed to the high observed concentrations of both OC and (14)C. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Origin of life. Primordial genetics: Information transfer in a pre-RNA world based on self-replicating beta-sheet amyloid conformers.

    Science.gov (United States)

    Maury, Carl Peter J

    2015-10-07

    The question of the origin of life on Earth can largely be reduced to the question of what was the first molecular replicator system that was able to replicate and evolve under the presumably very harsh conditions on the early Earth. It is unlikely that a functional RNA could have existed under such conditions and it is generally assumed that some other kind of information system preceded the RNA world. Here, I present an informational molecular system that is stable, self-replicative, environmentally responsive, and evolvable under conditions characterized by high temperatures, ultraviolet and cosmic radiation. This postulated pregenetic system is based on the amyloid fold, a functionally unique polypeptide fold characterized by a cross beta-sheet structure in which the beta strands are arranged perpendicular to the fiber axis. Beside an extraordinary structural robustness, the amyloid fold possesses a unique ability to transmit information by a three-dimensional templating mechanism. In amyloidogenesis short peptide monomers are added one by one to the growing end of the fiber. From the same monomeric subunits several structural variants of amyloid may be formed. Then, in a self-replicative mode, a specific amyloid conformer can act as a template and confer its spatially encoded information to daughter molecular entities in a repetitive way. In this process, the specific conformational information, the spatially changed organization, is transmitted; the coding element is the steric zipper structure, and recognition occurs by amino acid side chain complementarity. The amyloid information system fulfills several basic requirements of a primordial evolvable replicator system: (i) it is stable under the presumed primitive Earth conditions, (ii) the monomeric building blocks of the informational polymer can be formed from available prebiotic compounds, (iii) the system is self-assembling and self-replicative and (iv) it is adaptive to changes in the environment and

  7. Fire PRA requantification studies. Final report

    International Nuclear Information System (INIS)

    Parkinson, W.

    1993-03-01

    This report describes the requantification of two existing fire probabilistic risk assessments (PRAs) using a fire PRA method and data that are being developed by the Electric Power Research Institute (EPRI). The two existing studies are the Seabrook Station Probabilistic Safety Assessment that was made in 1983 and the 1989 NUREG-1150 analysis of the Peach Bottom Plant. Except for the fire methods and data, the original assumptions were used. The results from the requantification show that there were excessive conservatisms in the original studies. The principal reason for a hundredfold reduction in the Peach Bottom core- damage frequency is the determination that no electrical cabinet fire in a switchgear room would damage both offsite power feeds. Past studies often overestimated the heat release from electrical cabinet fires. EPRI's electrical cabinet heat release rates are based on tests that were conducted for Sandia's fire research program. The rates are supported by the experience in the EPRI Fire Events Database for U.S. nuclear plants. Test data and fire event experience also removed excessive conservatisms in the Peach Bottom control and cable spreading rooms, and the Seabrook primary component cooling pump, turbine building relay and cable spreading rooms. The EPRI fire PRA method and data will show that there are excessive conservatisms in studies that were made for many plants and can benefit them accordingly

  8. Are Psychology Journals Anti-replication? A Snapshot of Editorial Practices

    OpenAIRE

    Martin, G. N.; Clarke, Richard M.

    2017-01-01

    Recent research in psychology has highlighted a number of replication problems in the discipline, with publication bias – the preference for publishing original and positive results, and a resistance to publishing negative results and replications- identified as one reason for replication failure. However, little empirical research exists to demonstrate that journals explicitly refuse to publish replications. We reviewed the instructions to authors and the published aims of 1151 psychology jo...

  9. The Role of Low-severity Fire and Thermal Alteration of Soil Organic Matter in Carbon Preservation and GHG Flux From Global Peatlands

    Science.gov (United States)

    Flanagan, N. E.; Wang, H.; Hodgkins, S. B.; Richardson, C. J.

    2017-12-01

    Many global peatlands are dominated by fire-adapted plant communities and are subject to frequent wildfires with return intervals ranging between 3 to 100 years. Wildfires in peatlands are typically low-severity events that occur in winter and spring when vegetation is desiccated and soil moisture content is high. As a result, most wildfires consume aboveground fuels in a matter of minutes without igniting the nearly saturated peat. In such fires, surface soil layers are subjected to flash heating with a rapid loss of soil moisture but little loss of soil organic matter (SOM). Such fires have the potential to alter the chemical structure of SOM, even in the absence of combustion, through Maillard's Reaction and similar chemical processes, and through structural changes that protect SOM from decomposition. This study examines the effects of low-intensity surface fires on the recalcitrance of SOM from fire-adapted communities located in subtropical, temperate and sub-boreal peatlands. In addition, soil from a non-fire-adapted Peruvian palm peatland was examined for response to thermal alteration. The timing and temperatures of low-intensity fires were measured in the field during prescribed burns and replicated in simulated fires. The effects of fire on the chemical structure of SOM were examined with FTIR, SEM and XPS. Burned and unburned peat replicates were incubated at three temperatures (5oC, 15oC, 25oC) in controlled chambers for more than six months. Burned replicates initially showed higher CO2, CH4 and NO2 emissions. Yet, within four weeks emissions from the burned replicates dropped below those of unburned replicates and remained significantly lower (10-50%) for the duration of the experiment. In addition, thermal alteration significantly reduced the temperature sensitivity (Q10) of thermally altered peat. After accounting for small initial losses of organic matter (<10 %) during the fire simulations, thermal alteration of SOM resulted in a net long

  10. MYC and the Control of DNA Replication

    Science.gov (United States)

    Dominguez-Sola, David; Gautier, Jean

    2014-01-01

    The MYC oncogene is a multifunctional protein that is aberrantly expressed in a significant fraction of tumors from diverse tissue origins. Because of its multifunctional nature, it has been difficult to delineate the exact contributions of MYC’s diverse roles to tumorigenesis. Here, we review the normal role of MYC in regulating DNA replication as well as its ability to generate DNA replication stress when overexpressed. Finally, we discuss the possible mechanisms by which replication stress induced by aberrant MYC expression could contribute to genomic instability and cancer. PMID:24890833

  11. Fire debris analysis for forensic fire investigation using laser induced breakdown spectroscopy (LIBS)

    Science.gov (United States)

    Choi, Soojin; Yoh, Jack J.

    2017-08-01

    The possibility verification of the first attempt to apply LIBS to arson investigation was performed. LIBS has capabilities for real time in-situ analysis and depth profiling. It can provide valuable information about the fire debris that are complementary to the classification of original sample components and combustion residues. In this study, fire debris was analyzed to determine the ignition source and existence of a fire accelerant using LIBS spectra and depth profiling analysis. Fire debris chemical composition and carbon layer thickness determines the possible ignition source while the carbon layer thickness of combusted samples represents the degree of sample carbonization. When a sample is combusted with fire accelerants, a thicker carbon layer is formed because the burning rate is increased. Therefore, depth profiling can confirm the existence of combustion accelerants, which is evidence of arson. Also investigation of fire debris by depth profiling is still possible when a fire is extinguished with water from fire hose. Such data analysis and in-situ detection of forensic signals via the LIBS may assist fire investigation at crime scenes.

  12. The progression of replication forks at natural replication barriers in live bacteria.

    Science.gov (United States)

    Moolman, M Charl; Tiruvadi Krishnan, Sriram; Kerssemakers, Jacob W J; de Leeuw, Roy; Lorent, Vincent; Sherratt, David J; Dekker, Nynke H

    2016-07-27

    Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these Tus-ter barriers in the cell are poorly understood. By performing quantitative fluorescence microscopy with microfuidics, we investigate the effect on the replisome when encountering these barriers in live Escherichia coli cells. We make use of an E. coli variant that includes only an ectopic origin of replication that is positioned such that one of the two replisomes encounters a Tus-ter barrier before the other replisome. This enables us to single out the effect of encountering a Tus-ter roadblock on an individual replisome. We demonstrate that the replisome remains stably bound after encountering a Tus-ter complex from the non-permissive direction. Furthermore, the replisome is only transiently blocked, and continues replication beyond the barrier. Additionally, we demonstrate that these barriers affect sister chromosome segregation by visualizing specific chromosomal loci in the presence and absence of the Tus protein. These observations demonstrate the resilience of the replication fork to natural barriers and the sensitivity of chromosome alignment to fork progression. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Chronic DNA Replication Stress Reduces Replicative Lifespan of Cells by TRP53-Dependent, microRNA-Assisted MCM2-7 Downregulation.

    Directory of Open Access Journals (Sweden)

    Gongshi Bai

    2016-01-01

    Full Text Available Circumstances that compromise efficient DNA replication, such as disruptions to replication fork progression, cause a state known as DNA replication stress (RS. Whereas normally proliferating cells experience low levels of RS, excessive RS from intrinsic or extrinsic sources can trigger cell cycle arrest and senescence. Here, we report that a key driver of RS-induced senescence is active downregulation of the Minichromosome Maintenance 2-7 (MCM2-7 factors that are essential for replication origin licensing and which constitute the replicative helicase core. Proliferating cells produce high levels of MCM2-7 that enable formation of dormant origins that can be activated in response to acute, experimentally-induced RS. However, little is known about how physiological RS levels impact MCM2-7 regulation. We found that chronic exposure of primary mouse embryonic fibroblasts (MEFs to either genetically-encoded or environmentally-induced RS triggered gradual MCM2-7 repression, followed by inhibition of replication and senescence that could be accelerated by MCM hemizygosity. The MCM2-7 reduction in response to RS is TRP53-dependent, and involves a group of Trp53-dependent miRNAs, including the miR-34 family, that repress MCM expression in replication-stressed cells before they undergo terminal cell cycle arrest. miR-34 ablation partially rescued MCM2-7 downregulation and genomic instability in mice with endogenous RS. Together, these data demonstrate that active MCM2-7 repression is a physiologically important mechanism for RS-induced cell cycle arrest and genome maintenance on an organismal level.

  14. Replication in hydroxyurea: it's a matter of time.

    Science.gov (United States)

    Alvino, Gina M; Collingwood, David; Murphy, John M; Delrow, Jeffrey; Brewer, Bonita J; Raghuraman, M K

    2007-09-01

    Hydroxyurea (HU) is a DNA replication inhibitor that negatively affects both the elongation and initiation phases of replication and triggers the "intra-S phase checkpoint." Previous work with budding yeast has shown that, during a short exposure to HU, MEC1/RAD53 prevent initiation at some late S phase origins. In this study, we have performed microarray experiments to follow the fate of all origins over an extended exposure to HU. We show that the genome-wide progression of DNA synthesis, including origin activation, follows the same pattern in the presence of HU as in its absence, although the time frames are very different. We find no evidence for a specific effect that excludes initiation from late origins. Rather, HU causes S phase to proceed in slow motion; all temporal classes of origins are affected, but the order in which they become active is maintained. We propose a revised model for the checkpoint response to HU that accounts for the continued but slowed pace of the temporal program of origin activation.

  15. CRISPR-mediated control of the bacterial initiation of replication.

    Science.gov (United States)

    Wiktor, Jakub; Lesterlin, Christian; Sherratt, David J; Dekker, Cees

    2016-05-05

    Programmable control of the cell cycle has been shown to be a powerful tool in cell-biology studies. Here, we develop a novel system for controlling the bacterial cell cycle, based on binding of CRISPR/dCas9 to the origin-of-replication locus. Initiation of replication of bacterial chromosomes is accurately regulated by the DnaA protein, which promotes the unwinding of DNA at oriC We demonstrate that the binding of CRISPR/dCas9 to any position within origin or replication blocks the initiation of replication. Serial-dilution plating, single-cell fluorescence microscopy, and flow-cytometry experiments show that ongoing rounds of chromosome replication are finished upon CRISPR/dCas9 binding, but no new rounds are initiated. Upon arrest, cells stay metabolically active and accumulate cell mass. We find that elevating the temperature from 37 to 42°C releases the CRISR/dCas9 replication inhibition, and we use this feature to recover cells from the arrest. Our simple and robust method of controlling the bacterial cell cycle is a useful asset for synthetic biology and DNA-replication studies in particular. The inactivation of CRISPR/dCas9 binding at elevated temperatures may furthermore be of wide interest for CRISPR/Cas9 applications in genomic engineering. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. PAST AND PRESENT FOREST FIRES IN ITATIAIA NATIONAL PARK

    Directory of Open Access Journals (Sweden)

    Izar Aximoff

    2011-03-01

    Full Text Available This study was conducted with the aim of evaluating the fire reports occurring in the Itatiaia National Park (INP between 1937 and 2008 and aiming to show information about the total number of fires occurred, and the annual burnt areas, in relation with climate and biodiversity, the months of highest occurrence, the origins and causes of fires. A survey of 323 reports of forest fires showed the highest incidence of forest fires in the months of winter, during the dry season, between July and October. The most affected vegetation was that of the “campos de altitude” (high-altitude grasslands, a native ecosystem of Atlantic Rainforest restricted to the isolated southeastern high peaks and plateaus. Most of the fires had unknown origins and causes, and only twice were examinations by experts carried out. Data revealed INP fragility against forest fires and the importance and the need of Forest Fire Privation and Control Plans for effective biodiversity protection.

  17. Reduced frequency and severity of residential fires following delivery of fire prevention education by on-duty fire fighters: cluster randomized controlled study.

    Science.gov (United States)

    Clare, Joseph; Garis, Len; Plecas, Darryl; Jennings, Charles

    2012-04-01

    In 2008, Surrey Fire Services, British Columbia, commenced a firefighter-delivered, door-to-door fire-prevention education and smoke alarm examination/installation initiative with the intention of reducing the frequency and severity of residential structure fires in the City of Surrey. High-risk zones within the city were identified and 18,473 home visits were undertaken across seven temporal delivery cohorts (13.8% of non-apartment dwellings in the city). The frequency and severity of fires pre- and post- the home visit intervention was examined in comparison to randomized high-risk cluster controls. Overall, the frequency of fires was found to have reduced in the city overall, however, the reduction in the intervention cohorts was significantly larger than for controls. Furthermore, when fires did occur within the intervention cohorts, smoke detectors were activated more frequently and the fires were confined to the object of origin more often post-home visits. No equivalent pattern was observed for the cluster control. On-duty fire fighters can reduce the frequency and severity of residential fires through targeted, door-to-door distribution of fire prevention education in high-risk areas. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. Dynamics of Escherichia coli Chromosome Segregation during Multifork Replication

    DEFF Research Database (Denmark)

    Nielsen, Henrik Jørck; Youngren, Brenda; Hansen, Flemming G.

    2007-01-01

    Slowly growing Escherichia coli cells have a simple cell cycle, with replication and progressive segregation of the chromosome completed before cell division. In rapidly growing cells, initiation of replication occurs before the previous replication rounds are complete. At cell division, the chro......Slowly growing Escherichia coli cells have a simple cell cycle, with replication and progressive segregation of the chromosome completed before cell division. In rapidly growing cells, initiation of replication occurs before the previous replication rounds are complete. At cell division......, the chromosomes contain multiple replication forks and must be segregated while this complex pattern of replication is still ongoing. Here, we show that replication and segregation continue in step, starting at the origin and progressing to the replication terminus. Thus, early-replicated markers on the multiple......-branched chromosomes continue to separate soon after replication to form separate protonucleoids, even though they are not segregated into different daughter cells until later generations. The segregation pattern follows the pattern of chromosome replication and does not follow the cell division cycle. No extensive...

  19. R-loops and initiation of DNA replication in human cells: a missing link?

    Directory of Open Access Journals (Sweden)

    Rodrigo eLombraña

    2015-04-01

    Full Text Available The unanticipated widespread occurrence of stable hybrid DNA/RNA structures (R-loops in human cells and the increasing evidence of their involvement in several human malignancies have invigorated the research on R-loop biology in recent years. Here we propose that physiological R-loop formation at CpG island promoters can contribute to DNA replication origin specification at these regions, the most efficient replication initiation sites in mammalian cells. Quite likely, this occurs by the strand-displacement reaction activating the formation of G-quadruplex structures that target the Origin Recognition Complex (ORC in the single-stranded conformation. In agreement with this, we found that R-loops co-localize with the ORC within the same CpG island region in a significant fraction of these efficient replication origins, precisely at the position displaying the highest density of G4 motifs. This scenario builds on the connection between transcription and replication in human cells and suggests that R-loop dysregulation at CpG island promoter-origins might contribute to the phenotype of DNA replication abnormalities and loss of genome integrity detected in cancer cells.

  20. DNA adenine methylation is required to replicate both Vibrio cholerae chromosomes once per cell cycle.

    Science.gov (United States)

    Demarre, Gaëlle; Chattoraj, Dhruba K

    2010-05-06

    DNA adenine methylation is widely used to control many DNA transactions, including replication. In Escherichia coli, methylation serves to silence newly synthesized (hemimethylated) sister origins. SeqA, a protein that binds to hemimethylated DNA, mediates the silencing, and this is necessary to restrict replication to once per cell cycle. The methylation, however, is not essential for replication initiation per se but appeared so when the origins (oriI and oriII) of the two Vibrio cholerae chromosomes were used to drive plasmid replication in E. coli. Here we show that, as in the case of E. coli, methylation is not essential for oriI when it drives chromosomal replication and is needed for once-per-cell-cycle replication in a SeqA-dependent fashion. We found that oriII also needs SeqA for once-per-cell-cycle replication and, additionally, full methylation for efficient initiator binding. The requirement for initiator binding might suffice to make methylation an essential function in V. cholerae. The structure of oriII suggests that it originated from a plasmid, but unlike plasmids, oriII makes use of methylation for once-per-cell-cycle replication, the norm for chromosomal but not plasmid replication.

  1. From structure to mechanism—understanding initiation of DNA replication

    Science.gov (United States)

    Riera, Alberto; Barbon, Marta; Noguchi, Yasunori; Reuter, L. Maximilian; Schneider, Sarah; Speck, Christian

    2017-01-01

    DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2–7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability. PMID:28717046

  2. Fire Perimeters (2012)

    Data.gov (United States)

    Department of Homeland Security — The Geospatial Multi-Agency Coordination Group, or GeoMAC, is an internet-based mapping tool originally designed for fire managers to access online maps of current...

  3. The analysis of fire losses and characteristics of residential fires based on investigation data in Selangor, 2012-2014

    Directory of Open Access Journals (Sweden)

    Tan Yi Rong

    2016-01-01

    Full Text Available This is a research in progress where authors seek to investigate the factors of residential fires. As part of the research, this paper aims to analyse the fire problems faced by the community of Malaysia. Data regarding residential fires between 2012 and 2014 was collected from fire investigation reports prepared by the Selangor Fire and Rescue Department. Descriptive analysis is conducted to summarize the data collected and describe the common phenomenon of residential fires. The distributions of the fire characteristics suggested that residential fires are commonly occurred during daytime, confined within the room of fire origin, caused by electrical failure and cooking negligence, started from kitchen, and occurred in multi-units housing. Further analysis will be conducted in order to investigate the relationships between the characteristics and residential fires.

  4. Severity of an uncharacteristically large wildfire, the Rim Fire, in forests with relatively restored frequent fire regimes

    Science.gov (United States)

    Jamie Lydersen; Malcolm North; Brandon M. Collins

    2014-01-01

    The 2013 Rim Fire, originating on Forest Service land, burned into old-growth forests within Yosemite National Park with relatively restored frequent-fire regimes (¡Ý2 predominantly low and moderate severity burns within the last 35 years). Forest structure and fuels data were collected in the field 3-4 years before the fire, providing a rare chance to use pre-existing...

  5. Fire, herbicide, and chainsaw felling effects on arthropods in fire-suppressed longleaf pine sandhills at Eglin Air Force Base, Florida

    Science.gov (United States)

    Louis Provencher; Krista E. M. Galley; Andrea R. Litt; Doria R. Gordon; Leonard A. Brennan; George W. Tanner; Jeffrey L. Hardesty

    2002-01-01

    Experimentally evaluating the success of hardwood reduction techniques against a "model" reference condition of longleaf pine sandhill communities is not directly possible because reference sites are not randomized or replicated. We addressed this issue by measuring the similarity of arthropods in treatment (fire, herbicide, felling/girdling, and control) and...

  6. Role of the hydrophilic channels of simian virus 40 T-antigen helicase in DNA replication.

    Science.gov (United States)

    Wang, Weiping; Manna, David; Simmons, Daniel T

    2007-05-01

    The simian virus 40 (SV40) hexameric helicase consists of a central channel and six hydrophilic channels located between adjacent large tier domains within each hexamer. To study the function of the hydrophilic channels in SV40 DNA replication, a series of single-point substitutions were introduced at sites not directly involved in protein-protein contacts. The mutants were characterized biochemically in various ways. All mutants oligomerized normally in the absence of DNA. Interestingly, 8 of the 10 mutants failed to unwind an origin-containing DNA fragment and nine of them were totally unable to support SV40 DNA replication in vitro. The mutants fell into four classes based on their biochemical properties. Class A mutants bound DNA normally and had normal ATPase and helicase activities but failed to unwind origin DNA and support SV40 DNA replication. Class B mutants were compromised in single-stranded DNA and origin DNA binding at low protein concentrations. They were defective in helicase activity and unwinding of the origin and in supporting DNA replication. Class C and D mutants possessed higher-than-normal single-stranded DNA binding activity at low protein concentrations. The class C mutants failed to separate origin DNA and support DNA replication. The class D mutants unwound origin DNA normally but were compromised in their ability to support DNA replication. Taken together, these results suggest that the hydrophilic channels have an active role in the unwinding of SV40 DNA from the origin and the placement of the resulting single strands within the helicase.

  7. An assessment of the impact of home safety assessments on fires and fire-related injuries: a case study of Cheshire Fire and Rescue Service.

    Science.gov (United States)

    Arch, B N; Thurston, M N

    2013-06-01

    Deaths and injuries related to fires are largely preventable events. In the UK, a plethora of community-based fire safety initiatives have been introduced over the last 25 years, often led by fire and rescue services, to address this issue. This paper focuses on one such initiative--home safety assessments (HSAs). Cheshire Fire and Rescue Service (in England) implemented a uniquely large-scale HSA intervention. This paper assesses its effectiveness. The impact of HSAs was assessed in relation to three outcomes: accidental dwelling fires (ADFs), ADFs contained and injuries arising from ADFs. A two-period comparison in fire-related rates of incidences in Cheshire between 2002 and 2011 was implemented, using Poisson regression and adjusting for the national temporal trend using a control group comprising the 37 other English non-metropolitan fire-services. Significant reductions were observed in rates of ADFs [incidence rate ratios (IRR): 0.79, 95% confidence interval (CI): 0.74-0.83, P fires contained to room of origin. There is strong evidence to suggest that the intervention was successful in reducing domestic fires and related injuries.

  8. Initiation of Replication in Escherichia coli

    DEFF Research Database (Denmark)

    Frimodt-Møller, Jakob

    The circular chromosome of Escherichia coli is replicated by two replisomes assembled at the unique origin and moving in the opposite direction until they meet in the less well defined terminus. The key protein in initiation of replication, DnaA, facilitates the unwinding of double-stranded DNA...... to single-stranded DNA in oriC. Although DnaA is able to bind both ADP and ATP, DnaA is only active in initiation when bound to ATP. Although initiation of replication, and the regulation of this, is thoroughly investigated it is still not fully understood. The overall aim of the thesis was to investigate...... the regulation of initiation, the effect on the cell when regulation fails, and if regulation was interlinked to chromosomal organization. This thesis uncovers that there exists a subtle balance between chromosome replication and reactive oxygen species (ROS) inflicted DNA damage. Thus, failure in regulation...

  9. Megabase replication domains along the human genome: relation to chromatin structure and genome organisation.

    Science.gov (United States)

    Audit, Benjamin; Zaghloul, Lamia; Baker, Antoine; Arneodo, Alain; Chen, Chun-Long; d'Aubenton-Carafa, Yves; Thermes, Claude

    2013-01-01

    In higher eukaryotes, the absence of specific sequence motifs, marking the origins of replication has been a serious hindrance to the understanding of (i) the mechanisms that regulate the spatio-temporal replication program, and (ii) the links between origins activation, chromatin structure and transcription. In this chapter, we review the partitioning of the human genome into megabased-size replication domains delineated as N-shaped motifs in the strand compositional asymmetry profiles. They collectively span 28.3% of the genome and are bordered by more than 1,000 putative replication origins. We recapitulate the comparison of this partition of the human genome with high-resolution experimental data that confirms that replication domain borders are likely to be preferential replication initiation zones in the germline. In addition, we highlight the specific distribution of experimental and numerical chromatin marks along replication domains. Domain borders correspond to particular open chromatin regions, possibly encoded in the DNA sequence, and around which replication and transcription are highly coordinated. These regions also present a high evolutionary breakpoint density, suggesting that susceptibility to breakage might be linked to local open chromatin fiber state. Altogether, this chapter presents a compartmentalization of the human genome into replication domains that are landmarks of the human genome organization and are likely to play a key role in genome dynamics during evolution and in pathological situations.

  10. Shaping the landscape of the Escherichia coli chromosome: replication-transcription encounters in cells with an ectopic replication origin

    DEFF Research Database (Denmark)

    Ivanova, Darja; Taylor, Toni; Smith, Sarah L

    2015-01-01

    Each cell division requires the unwinding of millions of DNA base pairs to allow chromosome duplication and gene transcription. As DNA replication and transcription share the same template, conflicts between both processes are unavoidable and head-on collisions are thought to be particularly...

  11. From structure to mechanism-understanding initiation of DNA replication.

    Science.gov (United States)

    Riera, Alberto; Barbon, Marta; Noguchi, Yasunori; Reuter, L Maximilian; Schneider, Sarah; Speck, Christian

    2017-06-01

    DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2-7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability. © 2017 Riera et al.; Published by Cold Spring Harbor Laboratory Press.

  12. CRISPR-mediated control of the bacterial initiation of replication

    NARCIS (Netherlands)

    Wiktor, J.M.; Lesterlin, Christian; Sherratt, David J.; Dekker, C.

    2016-01-01

    Programmable control of the cell cycle has been shown to be a powerful tool in cell-biology studies. Here, we develop a novel system for controlling the bacterial cell cycle, based on binding of CRISPR/dCas9 to the origin-of-replication locus. Initiation of replication of bacterial chromosomes is

  13. DNA adenine methylation is required to replicate both Vibrio cholerae chromosomes once per cell cycle.

    Directory of Open Access Journals (Sweden)

    Gaëlle Demarre

    2010-05-01

    Full Text Available DNA adenine methylation is widely used to control many DNA transactions, including replication. In Escherichia coli, methylation serves to silence newly synthesized (hemimethylated sister origins. SeqA, a protein that binds to hemimethylated DNA, mediates the silencing, and this is necessary to restrict replication to once per cell cycle. The methylation, however, is not essential for replication initiation per se but appeared so when the origins (oriI and oriII of the two Vibrio cholerae chromosomes were used to drive plasmid replication in E. coli. Here we show that, as in the case of E. coli, methylation is not essential for oriI when it drives chromosomal replication and is needed for once-per-cell-cycle replication in a SeqA-dependent fashion. We found that oriII also needs SeqA for once-per-cell-cycle replication and, additionally, full methylation for efficient initiator binding. The requirement for initiator binding might suffice to make methylation an essential function in V. cholerae. The structure of oriII suggests that it originated from a plasmid, but unlike plasmids, oriII makes use of methylation for once-per-cell-cycle replication, the norm for chromosomal but not plasmid replication.

  14. Quantifying black carbon deposition over the Greenland ice sheet from forest fires in Canada: BC DEPOSITION FROM FOREST FIRES

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, J. L. [LATMOS/IPSL, UPMC University Paris 6 Sorbonne Universités, UVSQ, CNRS, Paris France; Polashenski, C. M. [USACE-CRREL, Fort Wainwright Alaska USA; Thayer School of Engineering, Dartmouth College, Hanover New Hampshire USA; Soja, A. J. [National Institute of Aerospace, NASA Langley Research Center, Hampton Virginia USA; Marelle, L. [Center for International Climate and Environmental Research-Oslo (CICERO), Oslo Norway; Casey, K. A. [Thayer School of Engineering, Dartmouth College, Hanover New Hampshire USA; Cryospheric Sciences Laboratory, NASA Goddard Space Flight Center, Greenbelt Maryland USA; Choi, H. D. [National Institute of Aerospace, NASA Langley Research Center, Hampton Virginia USA; Raut, J. -C. [LATMOS/IPSL, UPMC University Paris 6 Sorbonne Universités, UVSQ, CNRS, Paris France; Wiedinmyer, C. [National Center for Atmospheric Research, Boulder Colorado USA; Emmons, L. K. [National Center for Atmospheric Research, Boulder Colorado USA; Fast, J. D. [Pacific Northwest National Laboratory, Richland Washington USA; Pelon, J. [LATMOS/IPSL, UPMC University Paris 6 Sorbonne Universités, UVSQ, CNRS, Paris France; Law, K. S. [LATMOS/IPSL, UPMC University Paris 6 Sorbonne Universités, UVSQ, CNRS, Paris France; Flanner, M. G. [Department of Climate and Space Sciences and Engineering, University of Michigan, Ann Arbor Michigan USA; Dibb, J. E. [Earth Systems Research Center, EOS, University of New Hampshire, Durham New Hampshire USA

    2017-08-05

    We identify an important Black Carbon (BC) aerosol deposition event that was observed in snow stratigraphy and dated to between 27 July 2013 – 2 August 2013. This event comprises a significant portion (~60%) of total deposition over a 10 month period (July 2013 – April 2014). Here we link this event to forest fires burning in Canada during summer 2013 using modeling and remote sensing tools. Aerosols were detected by both the CALIOP and MODIS instruments during transport between Canada and Greenland, confirming that this event involved emissions from forest fires in Canada. We use high-resolution regional chemical transport mod-eling (WRF-Chem) combined with high-resolution fire emissions (FINNv1.5) to study aerosol emissions, transport, and deposition during this event. The model accurately captures the timing of the BC deposition event and shows that the major contribution to deposition during this event is emissions originating from fires in Canada. However, the model under-predicts aerosol deposition compared to measurements at all sites by a factor of 2–100. Under-prediction of modeled BC deposition originates from uncertainties in fire emissions combined with uncertainties in aerosol scavenging by clouds. This study suggests that it is possible to describe the transport of an exceptional smoke event on regional and continental scales. Improvements in model descriptions of precipitation scavenging and emissions from wildfires are needed to correctly predict deposition, which is critical for determining the climate impacts of aerosols that originate from fires.

  15. Molecular analysis of the replication program in unicellular model organisms

    OpenAIRE

    Raghuraman, M. K.; Brewer, Bonita J.

    2010-01-01

    Eukaryotes have long been reported to show temporal programs of replication, different portions of the genome being replicated at different times in S phase, with the added possibility of developmentally regulated changes in this pattern depending on species and cell type. Unicellular model organisms, primarily the budding yeast Saccharomyces cerevisiae, have been central to our current understanding of the mechanisms underlying the regulation of replication origins and the temporal program o...

  16. A new MCM modification cycle regulates DNA replication initiation.

    Science.gov (United States)

    Wei, Lei; Zhao, Xiaolan

    2016-03-01

    The MCM DNA helicase is a central regulatory target during genome replication. MCM is kept inactive during G1, and it initiates replication after being activated in S phase. During this transition, the only known chemical change to MCM is the gain of multisite phosphorylation that promotes cofactor recruitment. Because replication initiation is intimately linked to multiple biological cues, additional changes to MCM can provide further regulatory points. Here, we describe a yeast MCM SUMOylation cycle that regulates replication. MCM subunits undergo SUMOylation upon loading at origins in G1 before MCM phosphorylation. MCM SUMOylation levels then decline as MCM phosphorylation levels rise, thus suggesting an inhibitory role of MCM SUMOylation during replication. Indeed, increasing MCM SUMOylation impairs replication initiation, partly through promoting the recruitment of a phosphatase that decreases MCM phosphorylation and activation. We propose that MCM SUMOylation counterbalances kinase-based regulation, thus ensuring accurate control of replication initiation.

  17. MMSET is dynamically regulated during cell-cycle progression and promotes normal DNA replication.

    Science.gov (United States)

    Evans, Debra L; Zhang, Haoxing; Ham, Hyoungjun; Pei, Huadong; Lee, SeungBaek; Kim, JungJin; Billadeau, Daniel D; Lou, Zhenkun

    2016-01-01

    The timely and precise duplication of cellular DNA is essential for maintaining genome integrity and is thus tightly-regulated. During mitosis and G1, the Origin Recognition Complex (ORC) binds to future replication origins, coordinating with multiple factors to load the minichromosome maintenance (MCM) complex onto future replication origins as part of the pre-replication complex (pre-RC). The pre-RC machinery, in turn, remains inactive until the subsequent S phase when it is required for replication fork formation, thereby initiating DNA replication. Multiple myeloma SET domain-containing protein (MMSET, a.k.a. WHSC1, NSD2) is a histone methyltransferase that is frequently overexpressed in aggressive cancers and is essential for normal human development. Several studies have suggested a role for MMSET in cell-cycle regulation; however, whether MMSET is itself regulated during cell-cycle progression has not been examined. In this study, we report that MMSET is degraded during S phase in a cullin-ring ligase 4-Cdt2 (CRL4(Cdt2)) and proteasome-dependent manner. Notably, we also report defects in DNA replication and a decreased association of pre-RC factors with chromatin in MMSET-depleted cells. Taken together, our results suggest a dynamic regulation of MMSET levels throughout the cell cycle, and further characterize the role of MMSET in DNA replication and cell-cycle progression.

  18. Molecular analysis of the replication program in unicellular model organisms.

    Science.gov (United States)

    Raghuraman, M K; Brewer, Bonita J

    2010-01-01

    Eukaryotes have long been reported to show temporal programs of replication, different portions of the genome being replicated at different times in S phase, with the added possibility of developmentally regulated changes in this pattern depending on species and cell type. Unicellular model organisms, primarily the budding yeast Saccharomyces cerevisiae, have been central to our current understanding of the mechanisms underlying the regulation of replication origins and the temporal program of replication in particular. But what exactly is a temporal program of replication, and how might it arise? In this article, we explore this question, drawing again on the wealth of experimental information in unicellular model organisms.

  19. The influence of mortality and socioeconomic status on risk and delayed rewards: a replication with British participants

    Directory of Open Access Journals (Sweden)

    Gillian V. Pepper

    2017-07-01

    Full Text Available Here, we report three attempts to replicate a finding from an influential psychological study (Griskevicius et al., 2011b. The original study found interactions between childhood SES and experimental mortality-priming condition in predicting risk acceptance and delay discounting outcomes. The original study used US student samples. We used British university students (replication 1 and British online samples (replications 2 and 3 with a modified version of the original priming material, which was tailored to make it more credible to a British audience. We did not replicate the interaction between childhood SES and mortality-priming condition in any of our three experiments. The only consistent trend of note was an interaction between sex and priming condition for delay discounting. We note that psychological priming effects are considered fragile and often fail to replicate. Our failure to replicate the original finding could be due to demographic differences in study participants, alterations made to the prime, or other study limitations. However, it is also possible that the previously reported interaction is not a robust or generalizable finding.

  20. Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replication

    Energy Technology Data Exchange (ETDEWEB)

    Hood, Iris V.; Berger, James M.

    2016-05-31

    Replisome assembly requires the loading of replicative hexameric helicases onto origins by AAA+ ATPases. How loader activity is appropriately controlled remains unclear. Here, we use structural and biochemical analyses to establish how an antimicrobial phage protein interferes with the function of theStaphylococcus aureusreplicative helicase loader, DnaI. The viral protein binds to the loader’s AAA+ ATPase domain, allowing binding of the host replicative helicase but impeding loader self-assembly and ATPase activity. Close inspection of the complex highlights an unexpected locus for the binding of an interdomain linker element in DnaI/DnaC-family proteins. We find that the inhibitor protein is genetically coupled to a phage-encoded homolog of the bacterial helicase loader, which we show binds to the host helicase but not to the inhibitor itself. These findings establish a new approach by which viruses can hijack host replication processes and explain how loader activity is internally regulated to prevent aberrant auto-association.

  1. Prescribed-fire effects on an aquatic community of a southwest montane grassland system

    Science.gov (United States)

    Caldwell, Colleen A.; Jacobi, Gerald Z.; Anderson, Michael C.; Parmenter, Robert R.; McGann, Jeanine; Gould, William R.; DuBey, Robert; Jacobi, M. Donna

    2013-01-01

    The use of prescription fire has long been recognized as a reliable management tool to suppress vegetative succession processes and to reduce fuel loading to prevent catastrophic wildfires, but very little attention has been paid to the effects on aquatic systems. A late-fall prescribed burn was implemented to characterize effects on an aquatic community within a montane grassland system in north-central New Mexico. The fire treatment was consistent with protocols of a managed burn except that the fire was allowed to burn through the riparian area to the treatment stream to replicate natural fire behavior. In addition to summer and fall preburn assessment of the treatment and reference stream, we characterized immediate postfire effects (within a week for macroinvertebrates and within 6 months for fish) and seasonal effects over a 2-year period. Responses within the treatment stream were compared with an unburned reference stream adjacent to the prescription burn. During the burn, the diel range in air temperature increased by 5°C while diel range in water temperature did not change. Carbon–nitrogen ratios did not differ between treatment and reference streams, indicating the contribution of ash from the surrounding grassland was negligible. Although total taxa and species richness of aquatic macroinvertebrates were not altered, qualitative indices revealed departure from preburn condition due to loss of sensitive taxa (mayflies [order Ephemeroptera] and stoneflies [order Plecoptera]) and an increase in tolerant taxa (midges [order Chironomidae]) following the burn. Within 1 year of the burn, these attributes returned to preburn conditions. The density and recruitment of adult Brown Trout Salmo trutta did not differ between pre- and postburn collections, nor did fish condition differ. Fire is rarely truly replicated within a given study. Although our study represents one replication, the results will inform managers about the importance in timing (seasonality

  2. MCM Paradox: Abundance of Eukaryotic Replicative Helicases and Genomic Integrity.

    Science.gov (United States)

    Das, Mitali; Singh, Sunita; Pradhan, Satyajit; Narayan, Gopeshwar

    2014-01-01

    As a crucial component of DNA replication licensing system, minichromosome maintenance (MCM) 2-7 complex acts as the eukaryotic DNA replicative helicase. The six related MCM proteins form a heterohexamer and bind with ORC, CDC6, and Cdt1 to form the prereplication complex. Although the MCMs are well known as replicative helicases, their overabundance and distribution patterns on chromatin present a paradox called the "MCM paradox." Several approaches had been taken to solve the MCM paradox and describe the purpose of excess MCMs distributed beyond the replication origins. Alternative functions of these MCMs rather than a helicase had also been proposed. This review focuses on several models and concepts generated to solve the MCM paradox coinciding with their helicase function and provides insight into the concept that excess MCMs are meant for licensing dormant origins as a backup during replication stress. Finally, we extend our view towards the effect of alteration of MCM level. Though an excess MCM constituent is needed for normal cells to withstand stress, there must be a delineation of the threshold level in normal and malignant cells. This review also outlooks the future prospects to better understand the MCM biology.

  3. Intrinsic bent DNA sites in the chromosomal replication origin of Xylella fastidiosa 9a5c

    Directory of Open Access Journals (Sweden)

    F. Gimenes

    2008-04-01

    Full Text Available The features of the nucleotide sequences in both replication and promoter regions have been investigated in many organisms. Intrinsically bent DNA sites associated with transcription have been described in several prokaryotic organisms. The aim of the present study was to investigate intrinsic bent DNA sites in the segment that holds the chromosomal replication origin, oriC, of Xylella fastidiosa 9a5c. Electrophoretic behavior analyses, as well as in silico analyses of both the 2-D projection and helical parameters, were performed. The chromosomal segment analyzed contains the initial sequence of the rpmH gene, an intergenic region, the dnaA gene, the oriC sequence, and the 5' partial sequence of the dnaN gene. The analysis revealed fragments with reduced electrophoretic mobility, which indicates the presence of curved DNA segments. The analysis of the helical parameter ENDS ratio revealed three bent DNA sites (b1, b2, and b3 located in the rpmH-dnaA intergenic region, the dnaA gene, and the oriC 5' end, respectively. The chromosomal segment of X. fastidiosa analyzed here is rich in phased AT tracts and in CAnT motifs. The 2-D projection indicated a segment whose structure was determined by the cumulative effect of all bent DNA sites. Further, the in silico analysis of the three different bacterial oriC sequences indicated similar negative roll and twist >34.00° values. The DnaA box sequences, and other motifs in them, may be associated with the intrinsic DNA curvature.

  4. New insights into HCV replication in original cells from Aedes mosquitoes.

    Science.gov (United States)

    Fallecker, Catherine; Caporossi, Alban; Rechoum, Yassine; Garzoni, Frederic; Larrat, Sylvie; François, Olivier; Fender, Pascal; Morand, Patrice; Berger, Imre; Petit, Marie-Anne; Drouet, Emmanuel

    2017-08-22

    The existing literature about HCV association with, and replication in mosquitoes is extremely poor. To fill this gap, we performed cellular investigations aimed at exploring (i) the capacity of HCV E1E2 glycoproteins to bind on Aedes mosquito cells and (ii) the ability of HCV serum particles (HCVsp) to replicate in these cell lines. First, we used purified E1E2 expressing baculovirus-derived HCV pseudo particles (bacHCVpp) so we could investigate their association with mosquito cell lines from Aedes aegypti (Aag-2) and Aedes albopictus (C6/36). We initiated a series of infections of both mosquito cells (Ae aegypti and Ae albopictus) with the HCVsp (Lat strain - genotype 3) and we observed the evolution dynamics of viral populations within cells over the course of infection via next-generation sequencing (NGS) experiments. Our binding assays revealed bacHCVpp an association with the mosquito cells, at comparable levels obtained with human hepatocytes (HepaRG cells) used as a control. In our infection experiments, the HCV RNA (+) were detectable by RT-PCR in the cells between 21 and 28 days post-infection (p.i.). In human hepatocytes HepaRG and Ae aegypti insect cells, NGS experiments revealed an increase of global viral diversity with a selection for a quasi-species, suggesting a structuration of the population with elimination of deleterious mutations. The evolutionary pattern in Ae albopictus insect cells is different (stability of viral diversity and polymorphism). These results demonstrate for the first time that natural HCV could really replicate within Aedes mosquitoes, a discovery which may have major consequences for public health as well as in vaccine development.

  5. Natural radionuclides in coal and waste material originating from coal fired power plant

    International Nuclear Information System (INIS)

    Marovic, Gordana; Franic, Zdenko; Sencar, Jasminka; Petrinec, Branko; Bituh, Tomislav; Kovac, Jadranka

    2008-01-01

    This paper presents long-term investigations of natural radioactivity in coal, used for power production in the coal-fired power plant (CFPP) situated on the Adriatic coast, and resulting slag and ash. Activity concentrations of 40 K, 232 Th, 226 Ra and 238 U in used coal and resulting waste material have been measured for 25 years. As expected, it was demonstrated that the content of radionuclides in deposited bottom and filter ash material are closely related with radionuclide activity concentrations and mineral matter fraction in used coals. The external hazard index has been calculated and discussed for the slag and ash depository. During the first decade of operation of the CFPP has been used domestic coal produced in nearby area characterized by higher background radiation compared with the rest of Croatia. Therefore, the coal itself had relatively high 226 Ra and 238 U activity concentrations while potassium and thorium content was very low, 40 K activity concentrations being 2-9% and those of 232 Th 1-3% of total activity. As, in addition, the sulphur concentrations in coal were very high use of domestic coal was gradually abandoned till it was completely substituted by imported coal originated from various sources and of low natural radioactivity. Upon this, activity concentrations of uranium series radionuclides in deposited waste materials decreased significantly. Consequently, waste material i.e., slag and ash, generated in the last several years of coal fired power plant operation could be readily used in cement industry and as additive to other building materials, without any special restrictions according to the Croatian regulations dealing with building materials and European directives. (author)

  6. Use of Video Modeling to Teach Extinguishing of Cooking Related Fires to Individuals with Moderate Intellectual Disabilities

    Science.gov (United States)

    Mechling, Linda C.; Gast, David L.; Gustafson, Melissa R.

    2009-01-01

    This study evaluated the effectiveness of video modeling to teach fire extinguishing behaviors to three young adults with moderate intellectual disabilities. A multiple probe design across three fire extinguishing behaviors and replicated across three students was used to evaluate the effectiveness of the video-based program. Results indicate that…

  7. Enzymes involved in organellar DNA replication in photosynthetic eukaryotes.

    Science.gov (United States)

    Moriyama, Takashi; Sato, Naoki

    2014-01-01

    Plastids and mitochondria possess their own genomes. Although the replication mechanisms of these organellar genomes remain unclear in photosynthetic eukaryotes, several organelle-localized enzymes related to genome replication, including DNA polymerase, DNA primase, DNA helicase, DNA topoisomerase, single-stranded DNA maintenance protein, DNA ligase, primer removal enzyme, and several DNA recombination-related enzymes, have been identified. In the reference Eudicot plant Arabidopsis thaliana, the replication-related enzymes of plastids and mitochondria are similar because many of them are dual targeted to both organelles, whereas in the red alga Cyanidioschyzon merolae, plastids and mitochondria contain different replication machinery components. The enzymes involved in organellar genome replication in green plants and red algae were derived from different origins, including proteobacterial, cyanobacterial, and eukaryotic lineages. In the present review, we summarize the available data for enzymes related to organellar genome replication in green plants and red algae. In addition, based on the type and distribution of replication enzymes in photosynthetic eukaryotes, we discuss the transitional history of replication enzymes in the organelles of plants.

  8. A 4-study replication of the moderating effects of greed on socioeconomic status and unethical behaviour.

    Science.gov (United States)

    Balakrishnan, Anjana; Palma, Paolo A; Patenaude, Joshua; Campbell, Lorne

    2017-01-31

    Four replications of Piff and colleagues' study examined the moderating effects of greed attitudes on the relationship between socio-economic status (SES) and unethical behaviour (Study 7). In the original study, the researchers found that both greed and SES predicted increased propensity to engage in unethical behavior. Furthermore, this association was moderated such that the effects of SES on unethical behaviour were no longer present in the greed prime condition versus the neutral condition. In replication 1 of the original study main effects of greed attitudes and SES were found, but no interaction was found. Main effects for greed emerged in replications 3 and 4. However no main effects for SES or interactions emerged for replications 2-4. A meta-analysis was conducted with all replications and the original study, and found no moderating effect of greed on the relationship between SES and unethical behavior.

  9. Americans Still Overestimate Social Class Mobility: A Pre-Registered Self-Replication.

    Science.gov (United States)

    Kraus, Michael W

    2015-01-01

    Kraus and Tan (2015) hypothesized that Americans tend to overestimate social class mobility in society, and do so because they seek to protect the self. This paper reports a pre-registered exact replication of Study 3 from this original paper and finds, consistent with the original study, that Americans substantially overestimate social class mobility, that people provide greater overestimates when made while thinking of similar others, and that high perceived social class is related to greater overestimates. The current results provide additional evidence consistent with the idea that people overestimate class mobility to protect their beliefs in the promise of equality of opportunity. Discussion considers the utility of pre-registered self-replications as one tool for encouraging replication efforts and assessing the robustness of effect sizes.

  10. Active role of a human genomic insert in replication of a yeast artificial chromosome.

    Science.gov (United States)

    van Brabant, A J; Fangman, W L; Brewer, B J

    1999-06-01

    Yeast artificial chromosomes (YACs) are a common tool for cloning eukaryotic DNA. The manner by which large pieces of foreign DNA are assimilated by yeast cells into a functional chromosome is poorly understood, as is the reason why some of them are stably maintained and some are not. We examined the replication of a stable YAC containing a 240-kb insert of DNA from the human T-cell receptor beta locus. The human insert contains multiple sites that serve as origins of replication. The activity of these origins appears to require the yeast ARS consensus sequence and, as with yeast origins, additional flanking sequences. In addition, the origins in the human insert exhibit a spacing, a range of activation efficiencies, and a variation in times of activation during S phase similar to those found for normal yeast chromosomes. We propose that an appropriate combination of replication origin density, activation times, and initiation efficiencies is necessary for the successful maintenance of YAC inserts.

  11. How MCM loading and spreading specify eukaryotic DNA replication initiation sites [version 1; referees: 4 approved

    Directory of Open Access Journals (Sweden)

    Olivier Hyrien

    2016-08-01

    Full Text Available DNA replication origins strikingly differ between eukaryotic species and cell types. Origins are localized and can be highly efficient in budding yeast, are randomly located in early fly and frog embryos, which do not transcribe their genomes, and are clustered in broad (10-100 kb non-transcribed zones, frequently abutting transcribed genes, in mammalian cells. Nonetheless, in all cases, origins are established during the G1-phase of the cell cycle by the loading of double hexamers of the Mcm 2-7 proteins (MCM DHs, the core of the replicative helicase. MCM DH activation in S-phase leads to origin unwinding, polymerase recruitment, and initiation of bidirectional DNA synthesis. Although MCM DHs are initially loaded at sites defined by the binding of the origin recognition complex (ORC, they ultimately bind chromatin in much greater numbers than ORC and only a fraction are activated in any one S-phase. Data suggest that the multiplicity and functional redundancy of MCM DHs provide robustness to the replication process and affect replication time and that MCM DHs can slide along the DNA and spread over large distances around the ORC. Recent studies further show that MCM DHs are displaced along the DNA by collision with transcription complexes but remain functional for initiation after displacement. Therefore, eukaryotic DNA replication relies on intrinsically mobile and flexible origins, a strategy fundamentally different from bacteria but conserved from yeast to human. These properties of MCM DHs likely contribute to the establishment of broad, intergenic replication initiation zones in higher eukaryotes.

  12. Readability of self-illuminated signs obscured by black fuel-fire smoke.

    Science.gov (United States)

    1980-07-01

    This study, using black fuel-fire generated smoke, is a partial replication of an earlier study using an inert white smoke as the obscuring agent in the study of the readability of smoke-obscured, self-illuminated emergency exit signs. : The results ...

  13. Fire decreases arthropod abundance but increases diversity: Early and late season prescribed fire effects in a Sierra Nevada mixed-conifer forest

    Science.gov (United States)

    Ferrenberg, Scott; Schwilk, Dylan W.; Knapp, Eric E.; Groth, Eric; Keeley, Jon E.

    2006-01-01

    Prior to fire suppression in the 20th century, the mixed-conifer forests of the Sierra Nevada, California, U.S.A., historically burned in frequent fires that typically occurred during the late summer and early fall. Fire managers have been attempting to restore natural ecosystem processes through prescription burning, and have often favored burning during the fall in order to mimic historical fire regimes. Increasingly, however, prescription burning is also being done during the late spring and early summer in order to expand the window of opportunity for needed fuel reduction burning. The effect of prescribed fires outside of the historical fire season on forest arthropods is not known. The objective of this study was to compare the short-term effects of prescribed fires ignited in the early and late fire season on forest floor arthropods. Arthropod abundance and diversity were assessed using pitfall trapping in replicated burn units in Sequoia National Park, California. Overall, abundance of arthropods was lower in the burn treatments than in the unburned control. However, diversity tended to be greater in the burn treatments. Fire also altered the relative abundances of arthropod feeding guilds. No significant differences in arthropod community structure were found between early and late season burn treatments. Instead, changes in the arthropod community appeared to be driven largely by changes in fuel loading, vegetation, and habitat heterogeneity, all of which differed more between the burned and unburned treatments than between early and late season burn treatments.

  14. Replication stress activates DNA repair synthesis in mitosis

    DEFF Research Database (Denmark)

    Minocherhomji, Sheroy; Ying, Songmin; Bjerregaard, Victoria A

    2015-01-01

    Oncogene-induced DNA replication stress has been implicated as a driver of tumorigenesis. Many chromosomal rearrangements characteristic of human cancers originate from specific regions of the genome called common fragile sites (CFSs). CFSs are difficult-to-replicate loci that manifest as gaps...... into mitotic prophase triggers the recruitment of MUS81 to CFSs. The nuclease activity of MUS81 then promotes POLD3-dependent DNA synthesis at CFSs, which serves to minimize chromosome mis-segregation and non-disjunction. We propose that the attempted condensation of incompletely duplicated loci in early...... mitosis serves as the trigger for completion of DNA replication at CFS loci in human cells. Given that this POLD3-dependent mitotic DNA synthesis is enhanced in aneuploid cancer cells that exhibit intrinsically high levels of chromosomal instability (CIN(+)) and replicative stress, we suggest...

  15. A complex-valued firing-rate model that approximates the dynamics of spiking networks.

    Directory of Open Access Journals (Sweden)

    Evan S Schaffer

    2013-10-01

    Full Text Available Firing-rate models provide an attractive approach for studying large neural networks because they can be simulated rapidly and are amenable to mathematical analysis. Traditional firing-rate models assume a simple form in which the dynamics are governed by a single time constant. These models fail to replicate certain dynamic features of populations of spiking neurons, especially those involving synchronization. We present a complex-valued firing-rate model derived from an eigenfunction expansion of the Fokker-Planck equation and apply it to the linear, quadratic and exponential integrate-and-fire models. Despite being almost as simple as a traditional firing-rate description, this model can reproduce firing-rate dynamics due to partial synchronization of the action potentials in a spiking model, and it successfully predicts the transition to spike synchronization in networks of coupled excitatory and inhibitory neurons.

  16. A complex-valued firing-rate model that approximates the dynamics of spiking networks.

    Science.gov (United States)

    Schaffer, Evan S; Ostojic, Srdjan; Abbott, L F

    2013-10-01

    Firing-rate models provide an attractive approach for studying large neural networks because they can be simulated rapidly and are amenable to mathematical analysis. Traditional firing-rate models assume a simple form in which the dynamics are governed by a single time constant. These models fail to replicate certain dynamic features of populations of spiking neurons, especially those involving synchronization. We present a complex-valued firing-rate model derived from an eigenfunction expansion of the Fokker-Planck equation and apply it to the linear, quadratic and exponential integrate-and-fire models. Despite being almost as simple as a traditional firing-rate description, this model can reproduce firing-rate dynamics due to partial synchronization of the action potentials in a spiking model, and it successfully predicts the transition to spike synchronization in networks of coupled excitatory and inhibitory neurons.

  17. Pyrimidine dimers block simian virus 40 replication forks

    International Nuclear Information System (INIS)

    Berger, C.A.; Edenberg, H.J.

    1986-01-01

    UV light produces lesions, predominantly pyrimidine dimers, which inhibit DNA replication in mammalian cells. The mechanism of inhibition is controversial: is synthesis of a daughter strand halted at a lesion while the replication fork moves on and reinitiates downstream, or is fork progression itself blocked for some time at the site of a lesion? We directly addressed this question by using electron microscopy to examine the distances of replication forks from the origin in unirradiated and UV-irradiated simian virus 40 chromosomes. If UV lesions block replication fork progression, the forks should be asymmetrically located in a large fraction of the irradiated molecules; if replication forks move rapidly past lesions, the forks should be symmetrically located. A large fraction of the simian virus 40 replication forks in irradiated molecules were asymmetrically located, demonstrating that UV lesions present at the frequency of pyrimidine dimers block replication forks. As a mechanism for this fork blockage, we propose that polymerization of the leading strand makes a significant contribution to the energetics of fork movement, so any lesion in the template for the leading strand which blocks polymerization should also block fork movement

  18. Controlled Experiment Replication in Evaluation of E-Learning System's Educational Influence

    Science.gov (United States)

    Grubisic, Ani; Stankov, Slavomir; Rosic, Marko; Zitko, Branko

    2009-01-01

    We believe that every effectiveness evaluation should be replicated at least in order to verify the original results and to indicate evaluated e-learning system's advantages or disadvantages. This paper presents the methodology for conducting controlled experiment replication, as well as, results of a controlled experiment and an internal…

  19. Phosphorylation of Large T Antigen Regulates Merkel Cell Polyomavirus Replication

    International Nuclear Information System (INIS)

    Diaz, Jason; Wang, Xin; Tsang, Sabrina H.; Jiao, Jing; You, Jianxin

    2014-01-01

    Merkel Cell Polyomavirus (MCPyV) was recently discovered as a novel human polyomavirus that is associated with ~80% of Merkel Cell Carcinomas. The Large Tumor antigen (LT) is an early viral protein which has a variety of functions, including manipulation of the cell cycle and initiating viral DNA replication. Phosphorylation plays a critical regulatory role for polyomavirus LT proteins, but no investigation of MCPyV LT phosphorylation has been performed to date. In this report mass spectrometry analysis reveals three unique phosphorylation sites: T271, T297 and T299. In vivo replication assays confirm that phosphorylation of T271 does not play a role in viral replication, while modification at T297 and T299 have dramatic and opposing effects on LT’s ability to initiate replication from the viral origin. We test these mutants for their ability to bind, unwind, and act as a functional helicase at the viral origin. These studies provide a framework for understanding how phosphorylation of LT may dynamically regulate viral replication. Although the natural host cell of MCPyV has not yet been established, this work provides a foundation for understanding how LT activity is regulated and provides tools for better exploring this regulation in both natural host cells and Merkel cells

  20. Phosphorylation of Large T Antigen Regulates Merkel Cell Polyomavirus Replication

    Energy Technology Data Exchange (ETDEWEB)

    Diaz, Jason; Wang, Xin; Tsang, Sabrina H. [Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 (United States); Jiao, Jing [Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 (United States); You, Jianxin, E-mail: jianyou@mail.med.upenn.edu [Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 (United States)

    2014-07-08

    Merkel Cell Polyomavirus (MCPyV) was recently discovered as a novel human polyomavirus that is associated with ~80% of Merkel Cell Carcinomas. The Large Tumor antigen (LT) is an early viral protein which has a variety of functions, including manipulation of the cell cycle and initiating viral DNA replication. Phosphorylation plays a critical regulatory role for polyomavirus LT proteins, but no investigation of MCPyV LT phosphorylation has been performed to date. In this report mass spectrometry analysis reveals three unique phosphorylation sites: T271, T297 and T299. In vivo replication assays confirm that phosphorylation of T271 does not play a role in viral replication, while modification at T297 and T299 have dramatic and opposing effects on LT’s ability to initiate replication from the viral origin. We test these mutants for their ability to bind, unwind, and act as a functional helicase at the viral origin. These studies provide a framework for understanding how phosphorylation of LT may dynamically regulate viral replication. Although the natural host cell of MCPyV has not yet been established, this work provides a foundation for understanding how LT activity is regulated and provides tools for better exploring this regulation in both natural host cells and Merkel cells.

  1. BehavePlus fire modeling system, version 5.0: Variables

    Science.gov (United States)

    Patricia L. Andrews

    2009-01-01

    This publication has been revised to reflect updates to version 4.0 of the BehavePlus software. It was originally published as the BehavePlus fire modeling system, version 4.0: Variables in July, 2008.The BehavePlus fire modeling system is a computer program based on mathematical models that describe wildland fire behavior and effects and the...

  2. Applying Open Source Game Engine for Building Visual Simulation Training System of Fire Fighting

    Science.gov (United States)

    Yuan, Diping; Jin, Xuesheng; Zhang, Jin; Han, Dong

    There's a growing need for fire departments to adopt a safe and fair method of training to ensure that the firefighting commander is in a position to manage a fire incident. Visual simulation training systems, with their ability to replicate and interact with virtual fire scenarios through the use of computer graphics or VR, become an effective and efficient method for fire ground education. This paper describes the system architecture and functions of a visual simulated training system of fire fighting on oil storage, which adopting Delat3D, a open source game and simulation engine, to provide realistic 3D views. It presents that using open source technology provides not only the commercial-level 3D effects but also a great reduction of cost.

  3. Are Psychology Journals Anti-replication? A Snapshot of Editorial Practices.

    Science.gov (United States)

    Martin, G N; Clarke, Richard M

    2017-01-01

    Recent research in psychology has highlighted a number of replication problems in the discipline, with publication bias - the preference for publishing original and positive results, and a resistance to publishing negative results and replications- identified as one reason for replication failure. However, little empirical research exists to demonstrate that journals explicitly refuse to publish replications. We reviewed the instructions to authors and the published aims of 1151 psychology journals and examined whether they indicated that replications were permitted and accepted. We also examined whether journal practices differed across branches of the discipline, and whether editorial practices differed between low and high impact journals. Thirty three journals (3%) stated in their aims or instructions to authors that they accepted replications. There was no difference between high and low impact journals. The implications of these findings for psychology are discussed.

  4. Americans Still Overestimate Social Class Mobility: A Pre-Registered Self-Replication

    Directory of Open Access Journals (Sweden)

    Michael W. Kraus

    2015-11-01

    Full Text Available Kraus and Tan (2015 hypothesized that Americans tend to overestimate social class mobility in society, and do so because they seek to protect the self. This paper reports a pre-registered exact replication of Study 3 from this original paper and finds, consistent with the original study, that Americans substantially overestimate social class mobility, that people provide greater overestimates when made while thinking of similar others, and that high perceived social class is related to greater overestimates. The current results provide additional evidence consistent with the idea that people overestimate class mobility to protect their beliefs in the promise of equality of opportunity. Discussion considers the utility of pre-registered self-replications as one tool for encouraging replication efforts and assessing the robustness of effect sizes.

  5. Seasonality of fire weather strongly influences fire regimes in South Florida savanna-grassland landscapes.

    Directory of Open Access Journals (Sweden)

    William J Platt

    Full Text Available Fire seasonality, an important characteristic of fire regimes, commonly is delineated using seasons based on single weather variables (rainfall or temperature. We used nonparametric cluster analyses of a 17-year (1993-2009 data set of weather variables that influence likelihoods and spread of fires (relative humidity, air temperature, solar radiation, wind speed, soil moisture to explore seasonality of fire in pine savanna-grassland landscapes at the Avon Park Air Force Range in southern Florida. A four-variable, three-season model explained more variation within fire weather variables than models with more seasons. The three-season model also delineated intra-annual timing of fire more accurately than a conventional rainfall-based two-season model. Two seasons coincided roughly with dry and wet seasons based on rainfall. The third season, which we labeled the fire season, occurred between dry and wet seasons and was characterized by fire-promoting conditions present annually: drought, intense solar radiation, low humidity, and warm air temperatures. Fine fuels consisting of variable combinations of pyrogenic pine needles, abundant C4 grasses, and flammable shrubs, coupled with low soil moisture, and lightning ignitions early in the fire season facilitate natural landscape-scale wildfires that burn uplands and across wetlands. We related our three season model to fires with different ignition sources (lightning, military missions, and prescribed fires over a 13-year period with fire records (1997-2009. Largest wildfires originate from lightning and military ignitions that occur within the early fire season substantially prior to the peak of lightning strikes in the wet season. Prescribed ignitions, in contrast, largely occur outside the fire season. Our delineation of a pronounced fire season provides insight into the extent to which different human-derived fire regimes mimic lightning fire regimes. Delineation of a fire season associated with

  6. Seasonality of Fire Weather Strongly Influences Fire Regimes in South Florida Savanna-Grassland Landscapes

    Science.gov (United States)

    Platt, William J.; Orzell, Steve L.; Slocum, Matthew G.

    2015-01-01

    Fire seasonality, an important characteristic of fire regimes, commonly is delineated using seasons based on single weather variables (rainfall or temperature). We used nonparametric cluster analyses of a 17-year (1993–2009) data set of weather variables that influence likelihoods and spread of fires (relative humidity, air temperature, solar radiation, wind speed, soil moisture) to explore seasonality of fire in pine savanna-grassland landscapes at the Avon Park Air Force Range in southern Florida. A four-variable, three-season model explained more variation within fire weather variables than models with more seasons. The three-season model also delineated intra-annual timing of fire more accurately than a conventional rainfall-based two-season model. Two seasons coincided roughly with dry and wet seasons based on rainfall. The third season, which we labeled the fire season, occurred between dry and wet seasons and was characterized by fire-promoting conditions present annually: drought, intense solar radiation, low humidity, and warm air temperatures. Fine fuels consisting of variable combinations of pyrogenic pine needles, abundant C4 grasses, and flammable shrubs, coupled with low soil moisture, and lightning ignitions early in the fire season facilitate natural landscape-scale wildfires that burn uplands and across wetlands. We related our three season model to fires with different ignition sources (lightning, military missions, and prescribed fires) over a 13-year period with fire records (1997–2009). Largest wildfires originate from lightning and military ignitions that occur within the early fire season substantially prior to the peak of lightning strikes in the wet season. Prescribed ignitions, in contrast, largely occur outside the fire season. Our delineation of a pronounced fire season provides insight into the extent to which different human-derived fire regimes mimic lightning fire regimes. Delineation of a fire season associated with timing of

  7. RNase H and replication of ColE1 DNA in Escherichia coli.

    OpenAIRE

    Naito, S; Uchida, H

    1986-01-01

    Amber mutations within the rnh (RNase H) gene of Escherichia coli K-12 were isolated by selecting for bacteria capable of replicating in a sup+ background replication-defective cer-6 mutant of the ColE1 replicon. The cer-6 mutation is an alteration of one base pair located 160 nucleotides upstream of the unique replication origin of this plasmid. Subsequently, we determined the DNA alterations present within these mutants. ColE1 DNA replicated in rnh(Am) recA cells, indicating that (i) RNase ...

  8. Opposite replication polarities of transcribed and nontranscribed histone H5 genes

    International Nuclear Information System (INIS)

    Trempe, J.P.; Lindstrom, Y.I.; Leffak, M.

    1988-01-01

    The authors used an in vitro nuclear runoff replication assay to analyze the direction of replication of the active and inactive histone H5 genes in avian cells. In embryonic erythrocytes the transcribed histone H5 gene displayed sensitivity to endogenous nuclease cleavage. In contrast, this gene was insensitive to endogenous nuclease digestion under the same conditions in nuclei of the lymphoblastoid cell line MSB-1, and histone H5 gene transcripts were not detectable by dot-blot analysis of MSB-1 cell RNA. When nuclei were isolated from embryonic erythrocyctes and incubated with bromodeoxyuridine triphosphate, runoff replication from endogenous nuclease cleavage sites led to a relative enrichment for fragments near the 3' end of the histone H5 gene in the density-labeled DNA. In nuclei of MSB-1 cells or chicken embryo fibroblasts, however, runoff replication from restriction enzyme-cut sites (or induced endogenous nuclease-cut sites in MSB-1 nuclei) led to a relative enrichment for fragments near the 5' end of the H5 gene in dense DNA. Based on the enhanced incorporation of bromodeoxyuridine into origin-distal regions of DNA during the in vitro runoff replication assay, the authors conclude that the active histone H5 gene in embryonic erythrocytes is preferentially replicated in the transcriptional direction from an origin in the 5'-flanking DNA, whereas its inactive counterparts in MSB-1 cells and chicken embryo fibroblasts are preferentially replicated in the opposite direction

  9. Non-Equilibrium Thermodynamics of Self-Replicating Protocells

    DEFF Research Database (Denmark)

    Fellermann, Harold; Corominas-Murtra, Bernat; Hansen, Per Lyngs

    2018-01-01

    We provide a non-equilibrium thermodynamic description of the life-cycle of a droplet based, chemically feasible, system of protocells. By coupling the protocells metabolic kinetics with its thermodynamics, we demonstrate how the system can be driven out of equilibrium to ensure protocell growth...... and replication. This coupling allows us to derive the equations of evolution and to rigorously demonstrate how growth and replication life-cycle can be understood as a non-equilibrium thermodynamic cycle. The process does not appeal to genetic information or inheritance, and is based only on non......-equilibrium physics considerations. Our non-equilibrium thermodynamic description of simple, yet realistic, processes of protocell growth and replication, represents an advance in our physical understanding of a central biological phenomenon both in connection to the origin of life and for modern biology....

  10. A CI-Independent Form of Replicative Inhibition: Turn Off of Early Replication of Bacteriophage Lambda

    Science.gov (United States)

    Hayes, Sidney; Horbay, Monique A.; Hayes, Connie

    2012-01-01

    Several earlier studies have described an unusual exclusion phenotype exhibited by cells with plasmids carrying a portion of the replication region of phage lambda. Cells exhibiting this inhibition phenotype (IP) prevent the plating of homo-immune and hybrid hetero-immune lambdoid phages. We have attempted to define aspects of IP, and show that it is directed to repλ phages. IP was observed in cells with plasmids containing a λ DNA fragment including oop, encoding a short OOP micro RNA, and part of the lambda origin of replication, oriλ, defined by iteron sequences ITN1-4 and an adjacent high AT-rich sequence. Transcription of the intact oop sequence from its promoter, pO is required for IP, as are iterons ITN3–4, but not the high AT-rich portion of oriλ. The results suggest that IP silencing is directed to theta mode replication initiation from an infecting repλ genome, or an induced repλ prophage. Phage mutations suppressing IP, i.e., Sip, map within, or adjacent to cro or in O, or both. Our results for plasmid based IP suggest the hypothesis that there is a natural mechanism for silencing early theta-mode replication initiation, i.e. the buildup of λ genomes with oop + oriλ+ sequence. PMID:22590552

  11. A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae

    DEFF Research Database (Denmark)

    Val, Marie-Eve; Marbouty, Martial; Martins, Francisco de Lemos

    2016-01-01

    Bacteria with multiple chromosomes represent up to 10% of all bacterial species. Unlike eukaryotes, these bacteria use chromosome-specific initiators for their replication. In all cases investigated, the machineries for secondary chromosome replication initiation are of plasmid origin. One of the...

  12. Fire resistance of extruded hollow-core slabs

    DEFF Research Database (Denmark)

    Hertz, Kristian Dahl; Sørensen, Lars Schiøtt; Giuliani, Luisa

    2017-01-01

    to the structural codes with data derived from a standard fire test and from a thorough examination of the comprehensive test documentation available on fire exposed hollow-core slabs. Findings – Mechanisms for loss of load-bearing capacity are clarified, and evidence of the fire resistance is found. Originality......Purpose – Prefabricated extruded hollow-core slabs are preferred building components for floor structures in several countries. It is therefore important to be able to document the fire resistance of these slabs proving fulfilment of standard fire resistance requirements of 60 and 120 min found...... in most national building regulations. The paper aims to present a detailed analysis of the mechanisms responsible for the loss of loadbearing capacity of hollow-core slabs when exposed to fire. Design/methodology/approach – Furthermore, it compares theoretica calculation and assessment according...

  13. 46 CFR 28.820 - Fire pumps, fire mains, fire hydrants, and fire hoses.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false Fire pumps, fire mains, fire hydrants, and fire hoses... REQUIREMENTS FOR COMMERCIAL FISHING INDUSTRY VESSELS Aleutian Trade Act Vessels § 28.820 Fire pumps, fire mains, fire hydrants, and fire hoses. (a) Each vessel must be equipped with a self-priming, power driven fire...

  14. Nucleotide sequence analysis of regions of adenovirus 5 DNA containing the origins of DNA replication

    International Nuclear Information System (INIS)

    Steenbergh, P.H.

    1979-01-01

    The purpose of the investigations described is the determination of nucleotide sequences at the molecular ends of the linear adenovirus type 5 DNA. Knowledge of the primary structure at the termini of this DNA molecule is of particular interest in the study of the mechanism of replication of adenovirus DNA. The initiation- and termination sites of adenovirus DNA replication are located at the ends of the DNA molecule. (Auth.)

  15. Floristic patterns and disturbance history in karri ( Eucalyptus diversicolor: Myrtaceae) forest, south-western Australia: 2. Origin, growth form and fire response

    Science.gov (United States)

    Wardell-Johnson, Grant W.; Williams, M. R.; Mellican, A. E.; Annells, A.

    2007-03-01

    We examined the influence of disturbance history on the floristic composition of a single community type in karri forest, south-western Australia. Cover-abundance of 224 plant species and six disturbance and site-based environmental variables were recorded in 91, 20 m × 20 m quadrats. Numerical taxonomic and correlation approaches were used to relate these and 10 plant species-group variables based on origin, growth form and fire response. Ordination revealed no discernable pattern of sites based on floristic composition. However, all 10 species-group variables were significantly correlated with the ordination axes. Species richness within these groups varied with category and with respect to many of the disturbance and site variables. We encountered low diversity of vascular plants at the community level and limited diversity of growth forms. Thus most species were herbs (62.1%) or shrubs (30.3%), and there were no epiphytes and few species of trees or climbers. Although many introduced species were recorded (18.3% of all taxa), virtually all (83%) were herbs that demonstrated little persistence in the community, and there was limited evidence of transformer species. Time-since-fire (and other disturbance) influenced species richness more than the number of recent past fires because of a high proportion of ephemerals associated with the immediate post-fire period. Long-lived shrubs with soil stored seed dominate numerically, and in understorey biomass in comparison with neighboring vegetation types because of their greater flexibility of response following irregular, but intense disturbance events. However, interactions between nutrient status, regeneration mechanisms and community composition may be worthy of further investigation.

  16. Deterministic analysis of mid scale outdoor fire

    International Nuclear Information System (INIS)

    Vidmar, P.; Petelin, S.

    2003-01-01

    The idea behind the article is how to define fire behaviour. The work is based on an analytical study of fire origin, its development and spread. Mathematical fire model called FDS (Fire Dynamic Simulator) is used in the presented work. A CFD (Computational Fluid Dynamic) model using LES (Large Eddie Simulation) is used to calculate fire development and spread of combustion products in the environment. The fire source is located in the vicinity of the hazardous plant, power, chemical etc. The article presents the brief background of the FDS computer program and the initial and boundary conditions used in the mathematical model. Results discuss output data and check the validity of results. The work also presents some corrections of the physical model used, which influence the quality of results. The obtained results were discussed and compared with the Fire Safety Analysis report included in the Probabilistic Safety Assessment of Krsko nuclear power plant. (author)

  17. 46 CFR 28.315 - Fire pumps, fire mains, fire hydrants, and fire hoses.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false Fire pumps, fire mains, fire hydrants, and fire hoses... After September 15, 1991, and That Operate With More Than 16 Individuals on Board § 28.315 Fire pumps, fire mains, fire hydrants, and fire hoses. (a) Each vessel 36 feet (11.8 meters) or more in length must...

  18. Partial Purification of a Megadalton DNA Replication Complex by Free Flow Electrophoresis.

    Directory of Open Access Journals (Sweden)

    Caroline M Li

    Full Text Available We describe a gentle and rapid method to purify the intact multiprotein DNA replication complex using free flow electrophoresis (FFE. In particular, we applied FFE to purify the human cell DNA synthesome, which is a multiprotein complex that is fully competent to carry-out all phases of the DNA replication process in vitro using a plasmid containing the simian virus 40 (SV40 origin of DNA replication and the viral large tumor antigen (T-antigen protein. The isolated native DNA synthesome can be of use in studying the mechanism by which mammalian DNA replication is carried-out and how anti-cancer drugs disrupt the DNA replication or repair process. Partially purified extracts from HeLa cells were fractionated in a native, liquid based separation by FFE. Dot blot analysis showed co-elution of many proteins identified as part of the DNA synthesome, including proliferating cell nuclear antigen (PCNA, DNA topoisomerase I (topo I, DNA polymerase δ (Pol δ, DNA polymerase ɛ (Pol ɛ, replication protein A (RPA and replication factor C (RFC. Previously identified DNA synthesome proteins co-eluted with T-antigen dependent and SV40 origin-specific DNA polymerase activity at the same FFE fractions. Native gels show a multiprotein PCNA containing complex migrating with an apparent relative mobility in the megadalton range. When PCNA containing bands were excised from the native gel, mass spectrometric sequencing analysis identified 23 known DNA synthesome associated proteins or protein subunits.

  19. Partial Purification of a Megadalton DNA Replication Complex by Free Flow Electrophoresis.

    Science.gov (United States)

    Li, Caroline M; Miao, Yunan; Lingeman, Robert G; Hickey, Robert J; Malkas, Linda H

    2016-01-01

    We describe a gentle and rapid method to purify the intact multiprotein DNA replication complex using free flow electrophoresis (FFE). In particular, we applied FFE to purify the human cell DNA synthesome, which is a multiprotein complex that is fully competent to carry-out all phases of the DNA replication process in vitro using a plasmid containing the simian virus 40 (SV40) origin of DNA replication and the viral large tumor antigen (T-antigen) protein. The isolated native DNA synthesome can be of use in studying the mechanism by which mammalian DNA replication is carried-out and how anti-cancer drugs disrupt the DNA replication or repair process. Partially purified extracts from HeLa cells were fractionated in a native, liquid based separation by FFE. Dot blot analysis showed co-elution of many proteins identified as part of the DNA synthesome, including proliferating cell nuclear antigen (PCNA), DNA topoisomerase I (topo I), DNA polymerase δ (Pol δ), DNA polymerase ɛ (Pol ɛ), replication protein A (RPA) and replication factor C (RFC). Previously identified DNA synthesome proteins co-eluted with T-antigen dependent and SV40 origin-specific DNA polymerase activity at the same FFE fractions. Native gels show a multiprotein PCNA containing complex migrating with an apparent relative mobility in the megadalton range. When PCNA containing bands were excised from the native gel, mass spectrometric sequencing analysis identified 23 known DNA synthesome associated proteins or protein subunits.

  20. The Reputational Consequences of Failed Replications and Wrongness Admission among Scientists.

    Directory of Open Access Journals (Sweden)

    Adam K Fetterman

    Full Text Available Scientists are dedicating more attention to replication efforts. While the scientific utility of replications is unquestionable, the impact of failed replication efforts and the discussions surrounding them deserve more attention. Specifically, the debates about failed replications on social media have led to worry, in some scientists, regarding reputation. In order to gain data-informed insights into these issues, we collected data from 281 published scientists. We assessed whether scientists overestimate the negative reputational effects of a failed replication in a scenario-based study. Second, we assessed the reputational consequences of admitting wrongness (versus not as an original scientist of an effect that has failed to replicate. Our data suggests that scientists overestimate the negative reputational impact of a hypothetical failed replication effort. We also show that admitting wrongness about a non-replicated finding is less harmful to one's reputation than not admitting. Finally, we discovered a hint of evidence that feelings about the replication movement can be affected by whether replication efforts are aimed one's own work versus the work of another. Given these findings, we then present potential ways forward in these discussions.

  1. The Reputational Consequences of Failed Replications and Wrongness Admission among Scientists.

    Science.gov (United States)

    Fetterman, Adam K; Sassenberg, Kai

    2015-01-01

    Scientists are dedicating more attention to replication efforts. While the scientific utility of replications is unquestionable, the impact of failed replication efforts and the discussions surrounding them deserve more attention. Specifically, the debates about failed replications on social media have led to worry, in some scientists, regarding reputation. In order to gain data-informed insights into these issues, we collected data from 281 published scientists. We assessed whether scientists overestimate the negative reputational effects of a failed replication in a scenario-based study. Second, we assessed the reputational consequences of admitting wrongness (versus not) as an original scientist of an effect that has failed to replicate. Our data suggests that scientists overestimate the negative reputational impact of a hypothetical failed replication effort. We also show that admitting wrongness about a non-replicated finding is less harmful to one's reputation than not admitting. Finally, we discovered a hint of evidence that feelings about the replication movement can be affected by whether replication efforts are aimed one's own work versus the work of another. Given these findings, we then present potential ways forward in these discussions.

  2. Characterization of the Fire Regime and Drivers of Fires in the West African Tropical Forest

    Science.gov (United States)

    Dwomoh, F. K.; Wimberly, M. C.

    2016-12-01

    The Upper Guinean forest (UGF), encompassing the tropical regions of West Africa, is a globally significant biodiversity hotspot and a critically important socio-economic and ecological resource for the region. However, the UGF is one of the most human-disturbed tropical forest ecosystems with the only remaining large patches of original forests distributed in protected areas, which are embedded in a hotspot of climate stress & land use pressures, increasing their vulnerability to fire. We hypothesized that human impacts and climate interact to drive spatial and temporal variability in fire, with fire exhibiting distinctive seasonality and sensitivity to drought in areas characterized by different population densities, agricultural practices, vegetation types, and levels of forest degradation. We used the MODIS active fire product to identify and characterize fire activity in the major ecoregions of the UGF. We used TRMM rainfall data to measure climatic variability and derived indicators of human land use from a variety of geospatial datasets. We employed time series modeling to identify the influences of drought indices and other antecedent climatic indicators on temporal patterns of active fire occurrence. We used a variety of modeling approaches to assess the influences of human activities and land cover variables on the spatial pattern of fire activity. Our results showed that temporal patterns of fire activity in the UGF were related to precipitation, but these relationships were spatially heterogeneous. The pattern of fire seasonality varied geographically, reflecting both climatological patterns and agricultural practices. The spatial pattern of fire activity was strongly associated with vegetation gradients and anthropogenic activities occurring at fine spatial scales. The Guinean forest-savanna mosaic ecoregion had the most fires. This study contributes to our understanding of UGF fire regime and the spatio-temporal dynamics of tropical forest fires in

  3. Hda inactivation of DnaA is the predominant mechanism preventing hyperinitiation of Escherichia coli DNA replication.

    Science.gov (United States)

    Camara, Johanna E; Breier, Adam M; Brendler, Therese; Austin, Stuart; Cozzarelli, Nicholas R; Crooke, Elliott

    2005-08-01

    Initiation of DNA replication from the Escherichia coli chromosomal origin is highly regulated, assuring that replication occurs precisely once per cell cycle. Three mechanisms for regulation of replication initiation have been proposed: titration of free DnaA initiator protein by the datA locus, sequestration of newly replicated origins by SeqA protein and regulatory inactivation of DnaA (RIDA), in which active ATP-DnaA is converted to the inactive ADP-bound form. DNA microarray analyses showed that the level of initiation in rapidly growing cells that lack datA was indistinguishable from that in wild-type cells, and that the absence of SeqA protein caused only a modest increase in initiation, in agreement with flow-cytometry data. In contrast, cells lacking Hda overinitiated replication twofold, implicating RIDA as the predominant mechanism preventing extra initiation events in a cell cycle.

  4. Fire in the Plio-Pleistocene: the functions of hominin fire use, and the mechanistic, developmental and evolutionary consequences.

    Science.gov (United States)

    Attwell, Laura; Kovarovic, Kris; Kendal, Jeremy

    2015-07-20

    Fire is a powerful natural force that can change landscapes extremely quickly. Hominins have harnessed this resource for their own purposes, with mechanistic and developmental physiological consequences. In addition, the use of fire has niche constructive effects, altering selective environments for genetic and cultural evolution. We review the record for hominin fire use in the Plio-Pleistocene, before considering the various functions for its use, and the resultant mechanistic and developmental consequences. We also adopt the niche construction framework to consider how the use of fire can modify selective environments, and thus have evolutionary consequences at genetic and cultural levels. The light that fire produces may influence photoperiodicity and alter hormonally-controlled bodily rhythms. Fire used for cooking could have extended the range of foods hominins were able to consume, and reduced digestion costs. This may have contributed to the expansion of the hominin brain and facial anatomy, influenced by a higher quality cooked diet. Fire may also have allowed dispersal into northern areas with much cooler climates than the hominin African origin, posing novel problems that affected diet and social behaviour.

  5. Replication of Vibrio cholerae chromosome I in Escherichia coli: dependence on dam methylation

    DEFF Research Database (Denmark)

    Koch, Birgit; Ma, Xiaofang; Løbner-Olesen, Anders

    2010-01-01

    . cholerae chromosome I replication, which similar to what is observed for E. coli. No hda homologue has been identified in V. cholerae yet. In V. cholerae, dam is essential for viability, whereas in E. coli, dam mutants are viable. Replacement of E. coli oriC with oriCIVc allowed us to specifically address...... the role of the Dam methyltransferase and SeqA in replication initiation from oriCIVc. We show that when E. coli's origin of replication is substituted by oriCIVc, dam, but not seqA, becomes important for growth, arguing that Dam methylation exerts a critical function at the origin of replication itself....... We propose that Dam methylation promotes DnaA-assisted successful duplex opening and replisome assembly at oriCIVc in E. coli. In this model, methylation at oriCIVc would ease DNA melting. This is supported by the fact that the requirement for dam can be alleviated by increasing negative supercoiling...

  6. Using Model Replication to Improve the Reliability of Agent-Based Models

    Science.gov (United States)

    Zhong, Wei; Kim, Yushim

    The basic presupposition of model replication activities for a computational model such as an agent-based model (ABM) is that, as a robust and reliable tool, it must be replicable in other computing settings. This assumption has recently gained attention in the community of artificial society and simulation due to the challenges of model verification and validation. Illustrating the replication of an ABM representing fraudulent behavior in a public service delivery system originally developed in the Java-based MASON toolkit for NetLogo by a different author, this paper exemplifies how model replication exercises provide unique opportunities for model verification and validation process. At the same time, it helps accumulate best practices and patterns of model replication and contributes to the agenda of developing a standard methodological protocol for agent-based social simulation.

  7. Fire safety

    International Nuclear Information System (INIS)

    Keski-Rahkonen, O.; Bjoerkman, J.; Hostikka, S.; Mangs, J.; Huhtanen, R.; Palmen, H.; Salminen, A.; Turtola, A.

    1998-01-01

    According to experience and probabilistic risk assessments, fires present a significant hazard in a nuclear power plant. Fires may be initial events for accidents or affect safety systems planned to prevent accidents and to mitigate their consequences. The project consists of theoretical work, experiments and simulations aiming to increase the fire safety at nuclear power plants. The project has four target areas: (1) to produce validated models for numerical simulation programmes, (2) to produce new information on the behavior of equipment in case of fire, (3) to study applicability of new active fire protecting systems in nuclear power plants, and (4) to obtain quantitative knowledge of ignitions induced by important electric devices in nuclear power plants. These topics have been solved mainly experimentally, but modelling at different level is used to interpret experimental data, and to allow easy generalisation and engineering use of the obtained data. Numerical fire simulation has concentrated in comparison of CFD modelling of room fires, and fire spreading on cables on experimental data. So far the success has been good to fair. A simple analytical and numerical model has been developed for fire effluents spreading beyond the room of origin in mechanically strongly ventilated compartments. For behaviour of equipment in fire several full scale and scaled down calorimetric experiments were carried out on electronic cabinets, as well as on horizontal and vertical cable trays. These were carried out to supply material for CFD numerical simulation code validation. Several analytical models were developed and validated against obtained experimental results to allow quick calculations for PSA estimates as well as inter- and extrapolations to slightly different objects. Response times of different commercial fire detectors were determined for different types of smoke, especially emanating from smoldering and flaming cables to facilitate selection of proper detector

  8. A critique of the historical-fire-regime concept in conservation.

    Science.gov (United States)

    Freeman, Johanna; Kobziar, Leda; Rose, Elizabeth White; Cropper, Wendell

    2017-10-01

    Prescribed fire is widely accepted as a conservation tool because fire is essential to the maintenance of native biodiversity in many terrestrial communities. Approaches to this land-management technique vary greatly among continents, and sharing knowledge internationally can inform application of prescribed fire worldwide. In North America, decisions about how and when to apply prescribed fire are typically based on the historical-fire-regime concept (HFRC), which holds that replicating the pattern of fires ignited by lightning or preindustrial humans best promotes native species in fire-prone regions. The HFRC rests on 3 assumptions: it is possible to infer historical fire regimes accurately; fire-suppressed communities are ecologically degraded; and reinstating historical fire regimes is the best course of action despite the global shift toward novel abiotic and biotic conditions. We examined the underpinnings of these assumptions by conducting a literature review on the use of historical fire regimes to inform the application of prescribed fire. We found that the practice of inferring historical fire regimes for entire regions or ecosystems often entails substantial uncertainty and can yield equivocal results; ecological outcomes of fire suppression are complex and may not equate to degradation, depending on the ecosystem and context; and habitat fragmentation, invasive species, and other modern factors can interact with fire to produce novel and in some cases negative ecological outcomes. It is therefore unlikely that all 3 assumptions will be fully upheld for any landscape in which prescribed fire is being applied. Although the HFRC is a valuable starting point, it should not be viewed as the sole basis for developing prescribed fire programs. Rather, fire prescriptions should also account for other specific, measurable ecological parameters on a case-by-case basis. To best achieve conservation goals, researchers should seek to understand contemporary fire

  9. Metrology for fire experiments in outdoor conditions

    CERN Document Server

    Silvani, Xavier

    2013-01-01

    Natural fires can be considered as scale-dependant, non-linear processes of mass, momentum and heat transport, resulting from a turbulent reactive and radiative fluid medium flowing over a complex medium, the vegetal fuel. In natural outdoor conditions, the experimental study of natural fires at real scale needs the development of an original metrology, one able to capture the large range of time and length scales involved in its dynamic nature and also able to resist the thermal, mechanical and chemical aggression of flames on devices. Robust, accurate and poorly intrusive tools must be carefully set-up and used for gaining very fluctuating data over long periods. These signals also need the development of original post-processing tools that take into account the non-steady nature of their stochastic components. Metrology for Fire Experiments in Outdoor Conditions closely analyzes these features, and also describes measurements techniques, the thermal insulation of fragile electronic systems, data acquisitio...

  10. Historical Fire Perimeters (2000 to 2011)

    Data.gov (United States)

    Department of Homeland Security — The Geospatial Multi-Agency Coordination Group, or GeoMAC, is an internet-based mapping tool originally designed for fire managers to access online maps of current...

  11. Pipeline oil fire detection with MODIS active fire products

    Science.gov (United States)

    Ogungbuyi, M. G.; Martinez, P.; Eckardt, F. D.

    2017-12-01

    We investigate 85 129 MODIS satellite active fire events from 2007 to 2015 in the Niger Delta of Nigeria. The region is the oil base for Nigerian economy and the hub of oil exploration where oil facilities (i.e. flowlines, flow stations, trunklines, oil wells and oil fields) are domiciled, and from where crude oil and refined products are transported to different Nigerian locations through a network of pipeline systems. Pipeline and other oil facilities are consistently susceptible to oil leaks due to operational or maintenance error, and by acts of deliberate sabotage of the pipeline equipment which often result in explosions and fire outbreaks. We used ground oil spill reports obtained from the National Oil Spill Detection and Response Agency (NOSDRA) database (see www.oilspillmonitor.ng) to validate MODIS satellite data. NOSDRA database shows an estimate of 10 000 spill events from 2007 - 2015. The spill events were filtered to include largest spills by volume and events occurring only in the Niger Delta (i.e. 386 spills). By projecting both MODIS fire and spill as `input vector' layers with `Points' geometry, and the Nigerian pipeline networks as `from vector' layers with `LineString' geometry in a geographical information system, we extracted the nearest MODIS events (i.e. 2192) closed to the pipelines by 1000m distance in spatial vector analysis. The extraction process that defined the nearest distance to the pipelines is based on the global practices of the Right of Way (ROW) in pipeline management that earmarked 30m strip of land to the pipeline. The KML files of the extracted fires in a Google map validated their source origin to be from oil facilities. Land cover mapping confirmed fire anomalies. The aim of the study is to propose a near-real-time monitoring of spill events along pipeline routes using 250 m spatial resolution of MODIS active fire detection sensor when such spills are accompanied by fire events in the study location.

  12. Assessing Wildland Fire Risk Transmission to Communities in Northern Spain

    Directory of Open Access Journals (Sweden)

    Fermín J. Alcasena

    2017-01-01

    Full Text Available We assessed potential economic losses and transmission to residential houses from wildland fires in a rural area of central Navarra (Spain. Expected losses were quantified at the individual structure level (n = 306 in 14 rural communities by combining fire model predictions of burn probability and fire intensity with susceptibility functions derived from expert judgement. Fire exposure was estimated by simulating 50,000 fire events that replicated extreme (97th percentile historical fire weather conditions. Spatial ignition probabilities were used in the simulations to account for non-random ignitions, and were estimated from a fire occurrence model generated with an artificial neural network. The results showed that ignition probability explained most of spatial variation in risk, with economic value of structures having only a minor effect. Average expected loss to residential houses from a single wildfire event in the study area was 7955€, and ranged from a low of 740 to the high of 28,725€. Major fire flow-paths were analyzed to understand fire transmission from surrounding municipalities and showed that incoming fires from the north exhibited strong pathways into the core of the study area, and fires spreading from the south had the highest likelihood of reaching target residential structures from the longest distances (>5 km. Community firesheds revealed the scale of risk to communities and extended well beyond administrative boundaries. The results provided a quantitative risk assessment that can be used by insurance companies and local landscape managers to prioritize and allocate investments to treat wildland fuels and identify clusters of high expected loss within communities. The methodological framework can be extended to other fire-prone southern European Union countries where communities are threatened by large wildland fires.

  13. A Fire-Retardant Composite Made from Domestic Waste and PVA

    Directory of Open Access Journals (Sweden)

    Neni Surtiyeni

    2016-01-01

    Full Text Available We report the synthesis of a composite from domestic waste with the strength of wood building materials. We used original domestic waste with only a simple pretreatment to reduce the processing cost. The wastes were composed of organic components (generally originating from foods, paper, plastics, and clothes; the average fraction of each type of waste mirrored the corresponding fractions of wastes in the city of Bandung, Indonesia. An initial survey of ten landfills scattered through Bandung was conducted to determine the average fraction of each component in the waste. The composite was made using a hot press. A large number of synthesis parameters were tested to determine the optimum ones. The measured mechanical strength of the produced composite approached the mechanical properties of wood building materials. A fire-retardant powder was added to retard fire so that the composite could be useful for the construction of residential homes of lower-income people who often have problems with fire. Fire tests showed that the composites were more resistant to fire than widely used wood building materials.

  14. Coupled atmosphere-wildland fire modelling

    Directory of Open Access Journals (Sweden)

    Jacques Henri Balbi

    2009-10-01

    Full Text Available Simulating the interaction between fire and atmosphere is critical to the estimation of the rate of spread of the fire. Wildfire’s convection (i.e., entire plume can modify the local meteorology throughout the atmospheric boundary layer and consequently affect the fire propagation speed and behaviour. In this study, we use for the first time the Méso-NH meso-scale numerical model coupled to the point functional ForeFire simplified physical front-tracking wildfire model to investigate the differences introduced by the atmospheric feedback in propagation speed and behaviour. Both numerical models have been developed as research tools for operational models and are currently used to forecast localized extreme events. These models have been selected because they can be run coupled and support decisions in wildfire management in France and Europe. The main originalities of this combination reside in the fact that Méso-NH is run in a Large Eddy Simulation (LES configuration and that the rate of spread model used in ForeFire provides a physical formulation to take into account the effect of wind and slope. Simulations of typical experimental configurations show that the numerical atmospheric model is able to reproduce plausible convective effects of the heat produced by the fire. Numerical results are comparable to estimated values for fire-induced winds and present behaviour similar to other existing numerical approaches.

  15. Towards adaptive fire management for biodiversity conservation: experience in South African national parks

    CSIR Research Space (South Africa)

    Van Wilgen, BW

    2011-05-01

    Full Text Available heterogeneity in fires, the effects of fire on vegetation structure and on animals, and historic fire patterns. Ultimately, the goal was to use this understanding to develop an informed context for fire management. The original fire-related thresholds..., and to apply a single set of fire-related thresholds over the entire area. Mean annual rainfall varies from between approximately 350 mm in the north and approximately 750 mm in the south, and the effects of fire are far more marked in areas of higher...

  16. Insights into the Initiation of Eukaryotic DNA Replication.

    Science.gov (United States)

    Bruck, Irina; Perez-Arnaiz, Patricia; Colbert, Max K; Kaplan, Daniel L

    2015-01-01

    The initiation of DNA replication is a highly regulated event in eukaryotic cells to ensure that the entire genome is copied once and only once during S phase. The primary target of cellular regulation of eukaryotic DNA replication initiation is the assembly and activation of the replication fork helicase, the 11-subunit assembly that unwinds DNA at a replication fork. The replication fork helicase, called CMG for Cdc45-Mcm2-7, and GINS, assembles in S phase from the constituent Cdc45, Mcm2-7, and GINS proteins. The assembly and activation of the CMG replication fork helicase during S phase is governed by 2 S-phase specific kinases, CDK and DDK. CDK stimulates the interaction between Sld2, Sld3, and Dpb11, 3 initiation factors that are each required for the initiation of DNA replication. DDK, on the other hand, phosphorylates the Mcm2, Mcm4, and Mcm6 subunits of the Mcm2-7 complex. Sld3 recruits Cdc45 to Mcm2-7 in a manner that depends on DDK, and recent work suggests that Sld3 binds directly to Mcm2-7 and also to single-stranded DNA. Furthermore, recent work demonstrates that Sld3 and its human homolog Treslin substantially stimulate DDK phosphorylation of Mcm2. These data suggest that the initiation factor Sld3/Treslin coordinates the assembly and activation of the eukaryotic replication fork helicase by recruiting Cdc45 to Mcm2-7, stimulating DDK phosphorylation of Mcm2, and binding directly to single-stranded DNA as the origin is melted.

  17. Literature study regarding fire protection in nuclear power plants. Part I: Fire rated separations

    International Nuclear Information System (INIS)

    Isaksson, S.

    1995-06-01

    This literature study has been made on behalf of the Swedish Nuclear Power Inspectorate. The aim is to describe different aspects of fire protection in nuclear power plants. Conventional building codes can not give guidance on where to make fire rated separations in order to separate redundant trains of safety systems. The separation must originate in functional demands from the authorities on what functions are essential during and after a fire, and under what circumstances these functions shall be retained, i.e. the number of independent faults and initiating events. As a basic demand it is suggested to rate the strength of separations according to conventional building code, based on fire load. The whole separating construction shall have the same fire rating, including the ventilation system. Deviations from the basic demand can de done in case it can be proven that it is possible to compensate some or all of the fire rating with other measures. There is a general lack of statistical information regarding the reliability of fire separating constructions such as walls, fire doors, penetration seals and fire dampers. The amount of cables penetrating a seal is in many cases much higher in real installations than what has been tested for type approval. It would therefore be valuable to perform a furnace test with a more representative amount of cables passing through a penetration seal. Tests have shown that the 20 foot horizontal separation distance stipulated by NRC is not a guarantee against fire damage. Spatial separations based on general requirements shall not be allowed, but considered from case to case based on actual circumstances. For fire protection by isolation or coatings, it is of great importance to choose the method of protection carefully, to be compatible with the material it shall be applied on, and the environment and types of fire that may occur. 48 refs, 2 figs, 5 tabs

  18. An Introduction to Replication Research in Gifted Education: Shiny and New Is Not the Same as Useful

    Science.gov (United States)

    Makel, Matthew C.; Plucker, Jonathan A.

    2015-01-01

    This methodological brief introduces readers to replication methods and their uses. Broadly defined, replication is the duplication of previously conducted research to verify or expand the original findings. Replication is particularly useful in the gifted education context because so much education theory and research are based on general…

  19. Does it actually feel right? A replication attempt of the rounded price effect.

    Science.gov (United States)

    Harms, Christopher; Genau, Hanna A; Meschede, Carolin; Beauducel, André

    2018-04-01

    How does the roundedness of prices affect product evaluations? The 'rounded price effect' postulates that depending on the context, rounded or non-rounded prices increase the purchase likelihood of consumers. The study presented here is a replication attempt of these findings and the proposed mediation of the effect through a sense of 'feeling right' when evaluating the product. p -Curve analysis and the R-Index are used to assess the robustness of the originally reported statistics since original data were not available. A pre-registered replication of study 5 from the original article was conducted in a sample of N =588 participants. For both the original product and one alternative product neither an interaction between price roundedness and context, nor a mediation through 'a sense of feeling right' was found. Our results suggest that the effect is either smaller than originally reported or contingent on other, not investigated factors. Further studies might investigate contingencies in larger samples.

  20. BRD4 Phosphorylation Regulates HPV E2-Mediated Viral Transcription, Origin Replication, and Cellular MMP-9 Expression

    Directory of Open Access Journals (Sweden)

    Shwu-Yuan Wu

    2016-08-01

    Full Text Available Post-translational modification can modulate protein conformation and alter binding partner recruitment within gene regulatory regions. Here, we report that bromodomain-containing protein 4 (BRD4, a transcription co-factor and chromatin regulator, uses a phosphorylation-induced switch mechanism to recruit E2 protein encoded by cancer-associated human papillomavirus (HPV to viral early gene and cellular matrix metalloproteinase-9 (MMP-9 promoters. Enhanced MMP-9 expression, induced upon keratinocyte differentiation, occurs via BRD4-dependent recruitment of active AP-1 and NF-κB to their target sequences. This is triggered by replacement of AP-1 family members JunB and JunD by c-Jun and by re-localization of NF-κB from the cytoplasm to the nucleus. In addition, BRD4 phosphorylation is critical for E2- and origin-dependent HPV DNA replication. A class of phospho-BRD4-targeting compounds, distinct from the BET bromodomain inhibitors, effectively blocks BRD4 phosphorylation-specific functions in transcription and factor recruitment.

  1. Fire regime in Mediterranean ecosystem

    Science.gov (United States)

    Biondi, Guido; Casula, Paolo; D'Andrea, Mirko; Fiorucci, Paolo

    2010-05-01

    The analysis of burnt areas time series in Mediterranean regions suggests that ecosystems characterising this area consist primarily of species highly vulnerable to the fire but highly resilient, as characterized by a significant regenerative capacity after the fire spreading. In a few years the area burnt may once again be covered by the same vegetation present before the fire. Similarly, Mediterranean conifer forests, which often refers to plantations made in order to reforest the areas most severely degraded with high erosion risk, regenerate from seed after the fire resulting in high resilience to the fire as well. Only rarely, and usually with negligible damages, fire affects the areas covered by climax species in relation with altitude and soil types (i.e, quercus, fagus, abies). On the basis of these results, this paper shows how the simple Drossel-Schwabl forest fire model is able to reproduce the forest fire regime in terms of number of fires and burned area, describing whit good accuracy the actual fire perimeters. The original Drossel-Schwabl model has been slightly modified in this work by introducing two parameters (probability of propagation and regrowth) specific for each different class of vegetation cover. Using model selection methods based on AIC, the model with the optimal number of classes with different fire behaviour was selected. Two different case studies are presented in this work: Regione Liguria and Regione Sardegna (Italy). Both regions are situated in the center of the Mediterranean and are characterized by a high number of fires and burned area. However, the two regions have very different fire regimes. Sardinia is affected by the fire phenomenon only in summer whilst Liguria is affected by fires also in winter, with higher number of fires and larger burned area. In addition, the two region are very different in vegetation cover. The presence of Mediterranean conifers, (Pinus Pinaster, Pinus Nigra, Pinus halepensis) is quite spread in

  2. USP37 deubiquitinates Cdt1 and contributes to regulate DNA replication.

    Science.gov (United States)

    Hernández-Pérez, Santiago; Cabrera, Elisa; Amoedo, Hugo; Rodríguez-Acebes, Sara; Koundrioukoff, Stephane; Debatisse, Michelle; Méndez, Juan; Freire, Raimundo

    2016-10-01

    DNA replication control is a key process in maintaining genomic integrity. Monitoring DNA replication initiation is particularly important as it needs to be coordinated with other cellular events and should occur only once per cell cycle. Crucial players in the initiation of DNA replication are the ORC protein complex, marking the origin of replication, and the Cdt1 and Cdc6 proteins, that license these origins to replicate by recruiting the MCM2-7 helicase. To accurately achieve its functions, Cdt1 is tightly regulated. Cdt1 levels are high from metaphase and during G1 and low in S/G2 phases of the cell cycle. This control is achieved, among other processes, by ubiquitination and proteasomal degradation. In an overexpression screen for Cdt1 deubiquitinating enzymes, we isolated USP37, to date the first ubiquitin hydrolase controlling Cdt1. USP37 overexpression stabilizes Cdt1, most likely a phosphorylated form of the protein. In contrast, USP37 knock down destabilizes Cdt1, predominantly during G1 and G1/S phases of the cell cycle. USP37 interacts with Cdt1 and is able to de-ubiquitinate Cdt1 in vivo and, USP37 is able to regulate the loading of MCM complexes onto the chromatin. In addition, downregulation of USP37 reduces DNA replication fork speed. Taken together, here we show that the deubiquitinase USP37 plays an important role in the regulation of DNA replication. Whether this is achieved via Cdt1, a central protein in this process, which we have shown to be stabilized by USP37, or via additional factors, remains to be tested. Copyright © 2016 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  3. Primer retention owing to the absence of RNase H1 is catastrophic for mitochondrial DNA replication.

    Science.gov (United States)

    Holmes, J Bradley; Akman, Gokhan; Wood, Stuart R; Sakhuja, Kiran; Cerritelli, Susana M; Moss, Chloe; Bowmaker, Mark R; Jacobs, Howard T; Crouch, Robert J; Holt, Ian J

    2015-07-28

    Encoding ribonuclease H1 (RNase H1) degrades RNA hybridized to DNA, and its function is essential for mitochondrial DNA maintenance in the developing mouse. Here we define the role of RNase H1 in mitochondrial DNA replication. Analysis of replicating mitochondrial DNA in embryonic fibroblasts lacking RNase H1 reveals retention of three primers in the major noncoding region (NCR) and one at the prominent lagging-strand initiation site termed Ori-L. Primer retention does not lead immediately to depletion, as the persistent RNA is fully incorporated in mitochondrial DNA. However, the retained primers present an obstacle to the mitochondrial DNA polymerase γ in subsequent rounds of replication and lead to the catastrophic generation of a double-strand break at the origin when the resulting gapped molecules are copied. Hence, the essential role of RNase H1 in mitochondrial DNA replication is the removal of primers at the origin of replication.

  4. French position paper on sodium fires, design and testing

    International Nuclear Information System (INIS)

    Malet, J.C.; Casselman, C.; Charpenel, J.; Duverger de Cuy, G.; Rzekiecki, R.; Dufresne, J.; Lo Pinto, P.; Montaignac de; Herault, A.

    1983-01-01

    This document gives an up-to-date account of studies carried out in France in the fields of sodium fires, extinction, filtration and prefiltration of aerosols originating from a sodium fire, and of sodium concrete reactions. It also indicates how the CEA, in collaboration with the CNEN, intends to deal with scale effects. (author)

  5. ATR kinase regulates its attenuation via PPM1D phosphatase ...

    Indian Academy of Sciences (India)

    In eukaryotes, in response to replication stress, DNA damage response kinase, ATR is activated, whose signalling abrogationleads to cell lethality due to aberrant fork remodelling and excessive origin firing. Here we report that inhibition ofATR kinase activity specifically during replication stress recovery results in persistent ...

  6. Forest fires and lightning activity during the outstanding 2003 and 2005 fire seasons

    Science.gov (United States)

    Russo, Ana; Ramos, Alexandre; Trigo, Ricardo

    2013-04-01

    Wildfires in southern Europe cause frequent extensive economical and ecological losses and, even human casualties. Comparatively to other Mediterranean countries, Portugal is the country with more burnt area and fires per unit area in the last decade, mainly during the summer season (Pereira et al., 2011). According to the fire records available, between 1980 and 2009, wildfires have affected over 3 million hectares in Portugal (JRC, 2011), which corresponds to approximately a third of the Portuguese Continental territory. The main factors that influence fire ignition and propagation are: (1) the presence of fuel (i.e. vegetation); (2) climate and weather; (3) socioeconomic conditions that affect land use/land cover patterns, fire-prevention and fire-fighting capacity and (4) topography. Specifically, weather (e.g. wind, temperature, precipitation, humidity, and lightning occurrence) plays an important role in fire behavior, affecting both ignition and spread of wildfires. Some countries have a relatively large fraction of fires caused by lightning, e.g. northwestern USA, Canada, Russia (). In contrast, Portugal has only a small percentage of fire records caused by lightning. Although significant doubts remain for the majority of fires in the catalog since they were cataloged without a likely cause. The recent years of 2003 and 2005 were particularly outstanding for fire activity in Portugal, registering, respectively, total burned areas of 425 726 ha and 338 262 ha. However, while the 2003 was triggered by an exceptional heatwave that struck the entire western Europe, the 2005 fire season registered was coincident with one of the most severe droughts of the 20th century. In this work we have used mainly two different databases: 1) the Portuguese Rural Fire Database (PRFD) which is representative of rural fires that have occurred in Continental Portugal, 2001-2011, with the original data provided by the Autoridade Florestal Nacional (AFN, 2011); 2) lightning

  7. Distributional Replication

    OpenAIRE

    Beare, Brendan K.

    2009-01-01

    Suppose that X and Y are random variables. We define a replicating function to be a function f such that f(X) and Y have the same distribution. In general, the set of replicating functions for a given pair of random variables may be infinite. Suppose we have some objective function, or cost function, defined over the set of replicating functions, and we seek to estimate the replicating function with the lowest cost. We develop an approach to estimating the cheapest replicating function that i...

  8. Chromatin Immunoprecipitation of Replication Factors Moving with the Replication Fork

    OpenAIRE

    Rapp, Jordan B.; Ansbach, Alison B.; Noguchi, Chiaki; Noguchi, Eishi

    2009-01-01

    Replication of chromosomes involves a variety of replication proteins including DNA polymerases, DNA helicases, and other accessory factors. Many of these proteins are known to localize at replication forks and travel with them as components of the replisome complex. Other proteins do not move with replication forks but still play an essential role in DNA replication. Therefore, in order to understand the mechanisms of DNA replication and its controls, it is important to examine localization ...

  9. Fidelity of DNA Replication in Normal and Malignant Human Breast Cells.

    Science.gov (United States)

    1997-08-01

    enzyme) into the multiple cloning site (MCS). This template will not only replicate inside a mammalian cell (utilizing the E-B virus origin), and...Maniatis, T. Commonly used techniques in molecular cloning . In: Molecular cloning : REFERENCES a laboratory manual, 2nd edition. Cold Spring Harbor...A vatit"Y Of DNA synthesis and the typt of DNA replica~tion Products " celular prca including DNA rsplicatlon. DNA repsair. R~NA formed in experiments

  10. Analysis of Architectural Building Design Influences on Fire Spread in Densely Urban Settlement using Cellular Automata

    Science.gov (United States)

    Tambunan, L.; Salamah, H.; Asriana, N.

    2017-03-01

    This study aims to determine the influence of architectural design on the risk of fire spread in densely urban settlement area. Cellular Automata (CA) is used to analyse the fire spread pattern, speed, and the extent of damage. Four cells represent buildings, streets, and fields characteristic in the simulated area, as well as their flammability level and fire spread capabilities. Two fire scenarios are used to model the spread of fire: (1) fire origin in a building with concrete and wood material majority, and (2) fire origin in building with wood material majority. Building shape, building distance, road width, and total area of wall openings are considered constant, while wind is ignored. The result shows that fire spread faster in the building area with wood majority than with concrete majority. Significant amount of combustible building material, absence of distance between buildings, narrow streets and limited fields are factors which influence fire spread speed and pattern as well as extent of damage when fire occurs in the densely urban settlement area.

  11. Different interest group views of fuels treatments: survey results from fire and fire surrogate treatments in a Sierran mixed conifer forest, California, USA

    Science.gov (United States)

    Sarah McCaffrey; Jason J. Moghaddas; Scott L. Stephens

    2008-01-01

    The present paper discusses results from a survey about the acceptance of and preferences for fuels treatments of participants following a field tour of the University of California Blodgett Forest Fire and Fire Surrogate Study Site. Although original expectations were that tours would be composed of general members of the public, individual tour groups ultimately were...

  12. Regulation of DNA replication in irradiated cells by trans-acting factors

    International Nuclear Information System (INIS)

    Wang, Y.; Huq, M.S.; Cheng, X.; Iliakis, G.

    1995-01-01

    We compared DNA replication activity in cytoplasmic extracts prepared from irradiated and nonirradiated HeLa cells using a simian virus 40 (SV40)-based in vitro replication assay. The assay measures semi-conservative DNA replication in a plasmid carrying the SV40 origin of replication and requires SV40 T antigen as the sole noncellular protein. The plasmid DNA used in the replication reaction is never exposed to radiation. We find that replication of plasmid DNA is significantly reduced when cytoplasmic extracts from irradiated cells are used. Since plasmid replication proceeds to completion in extracts from irradiated cells, the observed reduction in the overall replication activity is probably due to a reduction in the efficiency of initiation events. The degree of inhibition of DNA replication after exposure to 10, 30 and 50 Gy X rays as measured in vitro using this assay is similar to that measured in intact cells immediately before processing for extract preparation. These observations are compatible with the induction or activation by ionizing radiation of a factor(s) that inhibits in trans DNA replication. The results contribute to our understanding of the mechanism(s) developed by the cells to regulate DNA replication when exposed to clastogenic agents. Such processes may be of significance in the restoration of DNA integrity, and may define yet another checkpoint operating during S at the level of clusters of replicons. 26 refs., 4 figs

  13. Amplification of the Kaposi's sarcoma-associated herpesvirus/human herpesvirus 8 lytic origin of DNA replication is dependent upon a cis-acting AT-rich region and an ORF50 response element and the trans-acting factors ORF50 (K-Rta) and K8 (K-bZIP)

    International Nuclear Information System (INIS)

    AuCoin, David P.; Colletti, Kelly S.; Cei, Sylvia A.; Papouskova, Iva; Tarrant, Margaret; Pari, Gregory S.

    2004-01-01

    Kaposi's sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus 8 (HHV8), has significant sequence homology to Epstein-Barr virus (EBV). In cell culture, HHV8 is primarily latent, and viral genes associated with lytic replication are not expressed. Two lytic origins of DNA replication (oriLyt) are present within the HHV8 genome and are composed of an AT-rich region adjacent to GC-rich DNA sequences. We have now identified essential cis- and trans-acting elements required for oriLyt-dependent DNA replication. The transient replication assay was used to show that two AT-rich elements, three consensus AP1 transcription factor-binding sites, an ORF50 response element (RE), and a consensus TATA box motif are essential for efficient origin-dependent DNA replication. Transient transfection of luciferase reporter constructs indicated that the downstream region of the HHV8 oriLyt responds to ORF50 and suggests that part of the oriLyt may be an enhancer/promoter. In addition, a transient cotransfection-replication assay elucidated the set of trans-acting factors required for lytic DNA replication. These factors consist of homologues to the core replication proteins: ORF6 (ssDNA binding protein), ORF9 (DNA polymerase), ORF40-41 (primase-associated factor), ORF44 (helicase), ORF56 (primase), and ORF59 (polymerase processivity factor) common to all herpesviruses along with ORF50 (K-Rta) and K8 (K-bZIP)

  14. Derivatives. Replication and (auto)plagiarism in the social sciences

    NARCIS (Netherlands)

    R. Tweehuysen (Rolandt ); J. den Haan (Joost); K. Berkhout (Karel ); P.A.G. van Bergeijk (Peter)

    2012-01-01

    textabstractThis working paper reports on the travelling exhibition “Derivatives”. This exhibition investigates the issue of originality in the context of (self) plagiarism and replication. The different views in the Arts and the scientific discourse form the point of departure for discovering how

  15. Replicative intermediates in UV-irradiated Simian virus 40

    International Nuclear Information System (INIS)

    Clark, J.M.; Hanawalt, P.C.

    1984-01-01

    The authors have used Simian virus 40 (SV40) as a probe to study the replication of UV-damaged DNA in mammalian cells. Viral DNA replication in infected monkey kidney cells was synchronized by incubating a mutant of SV40 (tsA58) temperature-sensitive for the initiation of DNA synthesis at the restrictive temperature and then adding aphidicolin to temporarily inhibit DNA synthesis at the permissive temperature while permitting pre-replicative events to occur. After removal of the drug, the infected cells were irradiated at 100 J/m 2 (254 nm) to produce 6-7 pyrimidine dimers per SV40 genome, and returned to the restrictive temperature to prevent reinitiation of replication from the SV40 origin. Replicative intermediates (RI) were labeled with [ 3 H]thymidine. The size distribution of daughter DNA strands in RI isolated shortly after irradiation was skewed towards lengths less than the interdimer spacing in parental DNA; this bias persisted for at least 1 h after irradiation, but disappeared within 3 h by which time the size of the newly-synthesized DNA exceeded the interdimer distance. Evidence was obtained for the generation at late times after irradiation, of Form I molecules in which the daughter DNA strand contain dimers. Thus DNA strand exchange as well as trans-dimer synthesis may be involved in the generation of supercoiled Form I DNA from 0V-damaged SV40 replicative intermediates. (Auth.)

  16. Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index

    Directory of Open Access Journals (Sweden)

    Suzuki Haruo

    2009-12-01

    Full Text Available Abstract Background Due to their bi-directional replication machinery starting from a single finite origin, bacterial genomes show characteristic nucleotide compositional bias between the two replichores, which can be visualised through GC skew or (C-G/(C+G. Although this polarisation is used for computational prediction of replication origins in many bacterial genomes, the degree of GC skew visibility varies widely among different species, necessitating a quantitative measurement of GC skew strength in order to provide confidence measures for GC skew-based predictions of replication origins. Results Here we discuss a quantitative index for the measurement of GC skew strength, named the generalised GC skew index (gGCSI, which is applicable to genomes of any length, including bacterial chromosomes and plasmids. We demonstrate that gGCSI is independent of the window size and can thus be used to compare genomes with different sizes, such as bacterial chromosomes and plasmids. It can suggest the existence of different replication mechanisms in archaea and of rolling-circle replication in plasmids. Correlation of gGCSI values between plasmids and their corresponding host chromosomes suggests that within the same strain, these replicons have reproduced using the same replication machinery and thus exhibit similar strengths of replication strand skew. Conclusions gGCSI can be applied to genomes of any length and thus allows comparative study of replication-related mutation and selection pressures in genomes of different lengths such as bacterial chromosomes and plasmids. Using gGCSI, we showed that replication-related mutation or selection pressure is similar for replicons with similar machinery.

  17. Analysis of JC virus DNA replication using a quantitative and high-throughput assay

    Science.gov (United States)

    Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert; Gagnon, David; Gjoerup, Ole; Archambault, Jacques; Bullock, Peter A.

    2015-01-01

    Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. PMID:25155200

  18. The avian-origin PB1 gene segment facilitated replication and transmissibility of the H3N2/1968 pandemic influenza virus.

    Science.gov (United States)

    Wendel, Isabel; Rubbenstroth, Dennis; Doedt, Jennifer; Kochs, Georg; Wilhelm, Jochen; Staeheli, Peter; Klenk, Hans-Dieter; Matrosovich, Mikhail

    2015-04-01

    The H2N2/1957 and H3N2/1968 pandemic influenza viruses emerged via the exchange of genomic RNA segments between human and avian viruses. The avian hemagglutinin (HA) allowed the hybrid viruses to escape preexisting immunity in the human population. Both pandemic viruses further received the PB1 gene segment from the avian parent (Y. Kawaoka, S. Krauss, and R. G. Webster, J Virol 63:4603-4608, 1989), but the biological significance of this observation was not understood. To assess whether the avian-origin PB1 segment provided pandemic viruses with some selective advantage, either on its own or via cooperation with the homologous HA segment, we modeled by reverse genetics the reassortment event that led to the emergence of the H3N2/1968 pandemic virus. Using seasonal H2N2 virus A/California/1/66 (Cal) as a surrogate precursor human virus and pandemic virus A/Hong Kong/1/68 (H3N2) (HK) as a source of avian-derived PB1 and HA gene segments, we generated four reassortant recombinant viruses and compared pairs of viruses which differed solely by the origin of PB1. Replacement of the PB1 segment of Cal by PB1 of HK facilitated viral polymerase activity, replication efficiency in human cells, and contact transmission in guinea pigs. A combination of PB1 and HA segments of HK did not enhance replicative fitness of the reassortant virus compared with the single-gene PB1 reassortant. Our data suggest that the avian PB1 segment of the 1968 pandemic virus served to enhance viral growth and transmissibility, likely by enhancing activity of the viral polymerase complex. Despite the high impact of influenza pandemics on human health, some mechanisms underlying the emergence of pandemic influenza viruses still are poorly understood. Thus, it was unclear why both H2N2/1957 and H3N2/1968 reassortant pandemic viruses contained, in addition to the avian HA, the PB1 gene segment of the avian parent. Here, we addressed this long-standing question by modeling the emergence of the H3N2

  19. Database Replication Prototype

    OpenAIRE

    Vandewall, R.

    2000-01-01

    This report describes the design of a Replication Framework that facilitates the implementation and com-parison of database replication techniques. Furthermore, it discusses the implementation of a Database Replication Prototype and compares the performance measurements of two replication techniques based on the Atomic Broadcast communication primitive: pessimistic active replication and optimistic active replication. The main contributions of this report can be split into four parts....

  20. Deciphering DNA replication dynamics in eukaryotic cell populations in relation with their averaged chromatin conformations

    Science.gov (United States)

    Goldar, A.; Arneodo, A.; Audit, B.; Argoul, F.; Rappailles, A.; Guilbaud, G.; Petryk, N.; Kahli, M.; Hyrien, O.

    2016-03-01

    We propose a non-local model of DNA replication that takes into account the observed uncertainty on the position and time of replication initiation in eukaryote cell populations. By picturing replication initiation as a two-state system and considering all possible transition configurations, and by taking into account the chromatin’s fractal dimension, we derive an analytical expression for the rate of replication initiation. This model predicts with no free parameter the temporal profiles of initiation rate, replication fork density and fraction of replicated DNA, in quantitative agreement with corresponding experimental data from both S. cerevisiae and human cells and provides a quantitative estimate of initiation site redundancy. This study shows that, to a large extent, the program that regulates the dynamics of eukaryotic DNA replication is a collective phenomenon that emerges from the stochastic nature of replication origins initiation.

  1. Multiple regulatory systems coordinate DNA replication with cell growth in Bacillus subtilis.

    Science.gov (United States)

    Murray, Heath; Koh, Alan

    2014-10-01

    In many bacteria the rate of DNA replication is linked with cellular physiology to ensure that genome duplication is coordinated with growth. Nutrient-mediated growth rate control of DNA replication initiation has been appreciated for decades, however the mechanism(s) that connects these cell cycle activities has eluded understanding. In order to help address this fundamental question we have investigated regulation of DNA replication in the model organism Bacillus subtilis. Contrary to the prevailing view we find that changes in DnaA protein level are not sufficient to account for nutrient-mediated growth rate control of DNA replication initiation, although this regulation does require both DnaA and the endogenous replication origin. We go on to report connections between DNA replication and several essential cellular activities required for rapid bacterial growth, including respiration, central carbon metabolism, fatty acid synthesis, phospholipid synthesis, and protein synthesis. Unexpectedly, the results indicate that multiple regulatory systems are involved in coordinating DNA replication with cell physiology, with some of the regulatory systems targeting oriC while others act in a oriC-independent manner. We propose that distinct regulatory systems are utilized to control DNA replication in response to diverse physiological and chemical changes.

  2. Replicating an Intervention: The Tension between Fidelity and Adaptation

    Science.gov (United States)

    Morrison, Diane M.; Hoppe, Marilyn J.; Gillmore, Mary Rogers; Kluver, Carisa; Higa, Darrel; Wells, Elizabeth A.

    2009-01-01

    Increased awareness of the importance of tailoring interventions to participants' cultures has focused attention on the limited generalizability of a single test of an intervention to determine efficacy. Adaptation is often necessary to replicate interventions across cultures. This produces a tension between fidelity to the original intervention…

  3. An Mcm10 Mutant Defective in ssDNA Binding Shows Defects in DNA Replication Initiation.

    Science.gov (United States)

    Perez-Arnaiz, Patricia; Kaplan, Daniel L

    2016-11-20

    Mcm10 is an essential protein that functions to initiate DNA replication after the formation of the replication fork helicase. In this manuscript, we identified a budding yeast Mcm10 mutant (Mcm10-m2,3,4) that is defective in DNA binding in vitro. Moreover, this Mcm10-m2,3,4 mutant does not stimulate the phosphorylation of Mcm2 by Dbf4-dependent kinase (DDK) in vitro. When we expressed wild-type levels of mcm10-m2,3,4 in budding yeast cells, we observed a severe growth defect and a substantially decreased DNA replication. We also observed a substantially reduced replication protein A- chromatin immunoprecipitation signal at origins of replication, reduced levels of DDK-phosphorylated Mcm2, and diminished Go, Ichi, Ni, and San (GINS) association with Mcm2-7 in vivo. mcm5-bob1 bypasses the growth defect conferred by DDK-phosphodead Mcm2 in budding yeast. However, the growth defect observed by expressing mcm10-m2,3,4 is not bypassed by the mcm5-bob1 mutation. Furthermore, origin melting and GINS association with Mcm2-7 are substantially decreased for cells expressing mcm10-m2,3,4 in the mcm5-bob1 background. Thus, the origin melting and GINS-Mcm2-7 interaction defects we observed for mcm10-m2,3,4 are not explained by decreased Mcm2 phosphorylation by DDK, since the defects persist in an mcm5-bob1 background. These data suggest that DNA binding by Mcm10 is essential for the initiation of DNA replication. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Wildland fire limits subsequent fire occurrence

    Science.gov (United States)

    Sean A. Parks; Carol Miller; Lisa M. Holsinger; Scott Baggett; Benjamin J. Bird

    2016-01-01

    Several aspects of wildland fire are moderated by site- and landscape-level vegetation changes caused by previous fire, thereby creating a dynamic where one fire exerts a regulatory control on subsequent fire. For example, wildland fire has been shown to regulate the size and severity of subsequent fire. However, wildland fire has the potential to influence...

  5. Roles for Dam methylation in bacterial chromosome replication

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Koch, Birgit; Skovgaard, Ole

    GATC sequences in the DNA of Escherichia coli and related species are methylated at the adenine residue by DNA adenine methyltransferase (DamMT). These methylated residues and/or the level of DamMT influence initiation of chromosome replication from the replication origin, oriC, which contain...... for about one third of the cell cycle. During sequestration at least three mechanisms operate to lower the activity of the initiator protein, DnaA. First, the dnaA promoter, which also contains an excess of GATC sequences, is sequestered for the same period of time as oriC to prevent de novo DnaA synthesis....... Second, new DnaA binding sites outside oriC are generated by replication which serve to titrate free DNA protein. Third, after initiation, DnaA-ATP is converted to inactive DnaA-ADP by a process called RIDA (regulatory inactivation of DnaA), which is dependent on the beta-clamp of DNA polymerase III...

  6. Nuclear Power Plant Fire Protection Research Program

    International Nuclear Information System (INIS)

    Datta, A.

    1985-07-01

    The goal is to develop test data and analytical capabilities to support the evaluation of: (1) the contribution of fires to the risk from nuclear power plants; (2) the effects of fires on control room equipment and operations; and (3) the effects of actuation of fire suppression systems on safety equipment. A range of fire sources will be characterized with respect to their energy and mass evolution, including smoke, corrosion products, and electrically conductive products of combustion. An analytical method for determining the environment resulting from fire will be developed. This method will account for the source characteristics, the suppression action following detection of the fire, and certain parameters specific to the plant enclosure in which the fire originates, such as the geometry of the enclosure and the ventilation rate. The developing local environment in the vicinity of safety-related equipment will be expressed in terms of temperatures, temperature rise rates, heat fluxes, and moisture and certain species content. The response of certain safe shutdown equipment and components to the environmental conditions will be studied. The objective will be to determine the limits of environmental conditions that a component may be exposed to without impairment of its ability to function

  7. GEMC1 is a TopBP1 interacting protein required for chromosomal DNA replication

    Science.gov (United States)

    Balestrini, Alessia; Cosentino, Claudia; Errico, Alessia; Garner, Elizabeth; Costanzo, Vincenzo

    2010-01-01

    Many factors required for chromosomal DNA replication have been identified in unicellular eukaryotes. However, DNA replication in complex multicellular organisms is poorly understood. Here, we report the identification of GEMC1, a novel vertebrate protein required for chromosomal DNA replication. GEMC1 is highly conserved in vertebrates and is preferentially expressed in proliferating cells. Using Xenopus egg extract we show that Xenopus GEMC1 (xGEMC1) binds to checkpoint and replication factor TopBP1, which promotes xGEMC1 binding to chromatin during pre-replication complex (pre-RC) formation. We demonstrate that xGEMC1 directly interacts with replication factors such as Cdc45 and Cdk2-CyclinE by which it is heavily phosphorylated. Phosphorylated xGEMC1 stimulates initiation of DNA replication whereas depletion of xGEMC1 prevents DNA replication onset due to impairment of Cdc45 loading onto chromatin. Likewise, inhibition of GEMC1 expression by morpholino and siRNA oligos prevents DNA replication in embryonic and somatic vertebrate cells. These data suggest that GEMC1 promotes initiation of chromosomal DNA replication in higher eukaryotes by mediating TopBP1 and Cdk2 dependent recruitment of Cdc45 onto replication origins. PMID:20383140

  8. Fires in the Cenozoic: a late flowering of flammable ecosystems

    Directory of Open Access Journals (Sweden)

    William John Bond

    2015-01-01

    Full Text Available Modern flammable ecosystems include tropical and subtropical savannas, steppe grasslands, boreal forests and temperate sclerophyll shrublands. Despite the apparent fiery nature of much contemporary vegetation, terrestrial fossil evidence would suggest we live in a time of low fire activity relative to the deep past. The inertinite content of coal, fossil charcoal, is strikingly low from the Eocene to the Pleistocene and no charcoalified mesofossils have been reported for the Cenozoic. Marine cores have been analysed for charcoal in the North Pacific, the north and south Atlantic off Africa, and the south China sea. These tell a different story with the oldest records indicating low levels of fire activity from the Eocene but a surge of fire from the late Miocene (~7 Ma. Phylogenetic studies of woody plants adapted to frequent savanna fires show them beginning to appear from the Late Miocene with peak origins in the late Pliocene in both South American and African lineages. Phylogenetic studies indicate ancient origins (60 Ma+ for clades characteristic of flammable sclerophyll vegetation from Australia and the Cape region of South Africa. However, as for savannas, there was a surge of speciation from the Late Miocene associated with the retreat of closed fire-intolerant forests. The wide geographic spread of increased fire activity in the last few million years suggests a global cause. However none of the potential global factors (oxygen, rainfall seasonality, CO2 , novel flammable growth forms provides an adequate explanation as yet. The global patterns and processes of fire and flammable vegetation in the Cenozoic, especially since the Late Miocene, deserve much more attention to better understand fire in the earth system.

  9. Fires in the Cenozoic: a late flowering of flammable ecosystems.

    Science.gov (United States)

    Bond, William J

    2014-01-01

    Modern flammable ecosystems include tropical and subtropical savannas, steppe grasslands, boreal forests, and temperate sclerophyll shrublands. Despite the apparent fiery nature of much contemporary vegetation, terrestrial fossil evidence would suggest we live in a time of low fire activity relative to the deep past. The inertinite content of coal, fossil charcoal, is strikingly low from the Eocene to the Pleistocene and no charcoalified mesofossils have been reported for the Cenozoic. Marine cores have been analyzed for charcoal in the North Pacific, the north and south Atlantic off Africa, and the south China sea. These tell a different story with the oldest records indicating low levels of fire activity from the Eocene but a surge of fire from the late Miocene (~7 Ma). Phylogenetic studies of woody plants adapted to frequent savanna fires show them beginning to appear from the Late Miocene with peak origins in the late Pliocene in both South American and African lineages. Phylogenetic studies indicate ancient origins (60 Ma+) for clades characteristic of flammable sclerophyll vegetation from Australia and the Cape region of South Africa. However, as for savannas, there was a surge of speciation from the Late Miocene associated with the retreat of closed fire-intolerant forests. The wide geographic spread of increased fire activity in the last few million years suggests a global cause. However, none of the potential global factors (oxygen, rainfall seasonality, CO2, novel flammable growth forms) provides an adequate explanation as yet. The global patterns and processes of fire and flammable vegetation in the Cenozoic, especially since the Late Miocene, deserve much more attention to better understand fire in the earth system.

  10. Evaluation Logic of Main Control Board Fire Risk

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Dae Il; Kim, Kilyoo; Lim, Ho Gon [KAERI, Daejeon (Korea, Republic of)

    2015-05-15

    The main control board (MCB) is defined as the collection of control panels inside the main control room (MCR) of a nuclear power plant (NPP). As the MCB has the control and instrumentation circuits of redundant trains for almost all plant systems, small fires within the control panels may be detrimental to the safe shutdown capability. A big fire affecting many panels in the MCB can cause a forced MCR abandonment of the operators as well as function failures or spurious operations of the control and instrumentation-related components. If the MCR cannot be habitable, a safe shutdown from outside the MCR can be achieved and maintained at an alternate shutdown panel electrically and physically independent from the MCR. Because the MCB consist of many electrical panels, it may have internal barriers between them to prevent a fire from spreading from its origin to neighboring locations. However, most MCBs of domestic NPPs do not have internal barriers within them. If the MCB cabinets are not separated by a double wall with an air gap, the fire propagation of an MCB panel fire cannot be ruled out. Recently, Joglar et al. proposed a new evaluation logic for the MCB panel fires and mentioned that an MCB fire can be divided into propagation and non-propagating fires for abandonment and non-abandonment fire scenarios. However, they did not present the details on the fire modeling approaches and probability formulas for the fire scenarios. In this paper, a decision tree for evaluating the risk of an MCB fire is proposed to systematically determine the fire scenarios in terms of the fire modeling approaches. This paper proposed a decision tree for evaluating the risk of an MCB fire to systematically determine the fire scenarios in terms of fire modeling approaches.

  11. The Replication Recipe: What makes for a convincing replication?

    NARCIS (Netherlands)

    Brandt, M.J.; IJzerman, H.; Dijksterhuis, A.J.; Farach, F.J.; Geller, J.; Giner-Sorolla, R.; Grange, J.A.; Perugini, M.; Spies, J.R.; Veer, A. van 't

    2014-01-01

    Psychological scientists have recently started to reconsider the importance of close replications in building a cumulative knowledge base; however, there is no consensus about what constitutes a convincing close replication study. To facilitate convincing close replication attempts we have developed

  12. The replication recipe : What makes for a convincing replication?

    NARCIS (Netherlands)

    Brandt, M.J.; IJzerman, H.; Dijksterhuis, Ap; Farach, Frank J.; Geller, Jason; Giner-Sorolla, Roger; Grange, James A.; Perugini, Marco; Spies, Jeffrey R.; van 't Veer, Anna

    Psychological scientists have recently started to reconsider the importance of close replications in building a cumulative knowledge base; however, there is no consensus about what constitutes a convincing close replication study. To facilitate convincing close replication attempts we have developed

  13. Multiple DNA binding proteins contribute to timing of chromosome replication in E. coli

    DEFF Research Database (Denmark)

    Riber, Leise; Frimodt-Møller, Jakob; Charbon, Godefroid

    2016-01-01

    Chromosome replication in Escherichia coli is initiated from a single origin, oriC. Initiation involves a number of DNA binding proteins, but only DnaA is essential and specific for the initiation process. DnaA is an AAA+ protein that binds both ATP and ADP with similar high affinities. Dna...... replication is initiated, or the time window in which all origins present in a single cell are initiated, i.e. initiation synchrony, or both. Overall, these DNA binding proteins modulate the initiation frequency from oriC by: (i) binding directly to oriC to affect DnaA binding, (ii) altering the DNA topology...... in or around oriC, (iii) altering the nucleotide bound status of DnaA by interacting with non-coding chromosomal sequences, distant from oriC, that are important for DnaA activity. Thus, although DnaA is the key protein for initiation of replication, other DNA-binding proteins act not only on ori...

  14. Pandemic Swine-Origin H1N1 Influenza Virus Replicates to Higher Levels and Induces More Fever and Acute Inflammatory Cytokines in Cynomolgus versus Rhesus Monkeys and Can Replicate in Common Marmosets.

    Directory of Open Access Journals (Sweden)

    Petra Mooij

    Full Text Available The close immunological and physiological resemblance with humans makes non-human primates a valuable model for studying influenza virus pathogenesis and immunity and vaccine efficacy against infection. Although both cynomolgus and rhesus macaques are frequently used in influenza virus research, a direct comparison of susceptibility to infection and disease has not yet been performed. In the current study a head-to-head comparison was made between these species, by using a recently described swine-origin pandemic H1N1 strain, A/Mexico/InDRE4487/2009. In comparison to rhesus macaques, cynomolgus macaques developed significantly higher levels of virus replication in the upper airways and in the lungs, involving both peak level and duration of virus production, as well as higher increases in body temperature. In contrast, clinical symptoms, including respiratory distress, were more easily observed in rhesus macaques. Expression of sialyl-α-2,6-Gal saccharides, the main receptor for human influenza A viruses, was 50 to 73 times more abundant in trachea and bronchus of cynomolgus macaques relative to rhesus macaques. The study also shows that common marmosets, a New World non-human primate species, are susceptible to infection with pandemic H1N1. The study results favor the cynomolgus macaque as model for pandemic H1N1 influenza virus research because of the more uniform and high levels of virus replication, as well as temperature increases, which may be due to a more abundant expression of the main human influenza virus receptor in the trachea and bronchi.

  15. Topology optimization for simplified structural fire safety

    DEFF Research Database (Denmark)

    Madsen, Søren; Lange, Nis P.; Giuliani, Luisa

    2016-01-01

    Topology optimization is applied in an idealized structural fire safety model, where the minimum compliance problem is constrained by temperature-controlled structural degradation. The constraint ensures a certain structural stiffness after a prescribed time. As this time period is extended......, resulting optimized topologies tend to become thicker or introduce redundant members that can take over when structural parts near the origin of the fire lose their load carrying capability. Hence, the structural degradation model acts as an erosion operator on the topology and indirectly enforces a minimum...

  16. Evolution of complexity in RNA-like replicator systems

    Directory of Open Access Journals (Sweden)

    Hogeweg Paulien

    2008-03-01

    Full Text Available Abstract Background The evolution of complexity is among the most important questions in biology. The evolution of complexity is often observed as the increase of genetic information or that of the organizational complexity of a system. It is well recognized that the formation of biological organization – be it of molecules or ecosystems – is ultimately instructed by the genetic information, whereas it is also true that the genetic information is functional only in the context of the organization. Therefore, to obtain a more complete picture of the evolution of complexity, we must study the evolution of both information and organization. Results Here we investigate the evolution of complexity in a simulated RNA-like replicator system. The simplicity of the system allows us to explicitly model the genotype-phenotype-interaction mapping of individual replicators, whereby we avoid preconceiving the functionality of genotypes (information or the ecological organization of replicators in the model. In particular, the model assumes that interactions among replicators – to replicate or to be replicated – depend on their secondary structures and base-pair matching. The results showed that a population of replicators, originally consisting of one genotype, evolves to form a complex ecosystem of up to four species. During this diversification, the species evolve through acquiring unique genotypes with distinct ecological functionality. The analysis of this diversification reveals that parasitic replicators, which have been thought to destabilize the replicator's diversity, actually promote the evolution of diversity through generating a novel "niche" for catalytic replicators. This also makes the current replicator system extremely stable upon the evolution of parasites. The results also show that the stability of the system crucially depends on the spatial pattern formation of replicators. Finally, the evolutionary dynamics is shown to

  17. Tree mortality from fire and bark beetles following early and late season prescribed fires in a Sierra Nevada mixed-conifer forest

    Science.gov (United States)

    Schwilk, Dylan W.; Knapp, Eric E.; Ferrenberg, Scott; Keeley, Jon E.; Caprio, Anthony C.

    2006-01-01

    Over the last century, fire exclusion in the forests of the Sierra Nevada has allowed surface fuels to accumulate and has led to increased tree density. Stand composition has also been altered as shade tolerant tree species crowd out shade intolerant species. To restore forest structure and reduce the risk of large, intense fires, managers have increasingly used prescription burning. Most fires prior to EuroAmerican settlement occurred during the late summer and early fall and most prescribed burning has taken place during the latter part of this period. Poor air quality and lack of suitable burn windows during the fall, however, have resulted in a need to conduct more prescription burning earlier in the season. Previous reports have suggested that burning during the time when trees are actively growing may increase mortality rates due to fine root damage and/or bark beetle activity. This study examines the effects of fire on tree mortality and bark beetle attacks under prescription burning during early and late season. Replicated early season burn, late season burn and unburned control plots were established in an old-growth mixed conifer forest in the Sierra Nevada that had not experienced a fire in over 120 years. Although prescribed burns resulted in significant mortality of particularly the smallest tree size classes, no difference between early and late season burns was detected. Direct mortality due to fire was associated with fire intensity. Secondary mortality due to bark beetles was not significantly correlated with fire intensity. The probability of bark beetle attack on pines did not differ between early and late season burns, while the probability of bark beetle attack on firs was greater following early season burns. Overall tree mortality appeared to be primarily the result of fire intensity rather than tree phenology at the time of the burns. Early season burns are generally conducted under higher fuel moisture conditions, leading to less fuel

  18. Sustainability of a Compartmentalized Host-Parasite Replicator System under Periodic Washout-Mixing Cycles

    Directory of Open Access Journals (Sweden)

    Taro Furubayashi

    2018-01-01

    Full Text Available The emergence and dominance of parasitic replicators are among the major hurdles for the proliferation of primitive replicators. Compartmentalization of replicators is proposed to relieve the parasite dominance; however, it remains unclear under what conditions simple compartmentalization uncoupled with internal reaction secures the long-term survival of a population of primitive replicators against incessant parasite emergence. Here, we investigate the sustainability of a compartmentalized host-parasite replicator (CHPR system undergoing periodic washout-mixing cycles, by constructing a mathematical model and performing extensive simulations. We describe sustainable landscapes of the CHPR system in the parameter space and elucidate the mechanism of phase transitions between sustainable and extinct regions. Our findings revealed that a large population size of compartments, a high mixing intensity, and a modest amount of nutrients are important factors for the robust survival of replicators. We also found two distinctive sustainable phases with different mixing intensities. These results suggest that a population of simple host–parasite replicators assumed before the origin of life can be sustained by a simple compartmentalization with periodic washout-mixing processes.

  19. Multiple regulatory systems coordinate DNA replication with cell growth in Bacillus subtilis.

    Directory of Open Access Journals (Sweden)

    Heath Murray

    2014-10-01

    Full Text Available In many bacteria the rate of DNA replication is linked with cellular physiology to ensure that genome duplication is coordinated with growth. Nutrient-mediated growth rate control of DNA replication initiation has been appreciated for decades, however the mechanism(s that connects these cell cycle activities has eluded understanding. In order to help address this fundamental question we have investigated regulation of DNA replication in the model organism Bacillus subtilis. Contrary to the prevailing view we find that changes in DnaA protein level are not sufficient to account for nutrient-mediated growth rate control of DNA replication initiation, although this regulation does require both DnaA and the endogenous replication origin. We go on to report connections between DNA replication and several essential cellular activities required for rapid bacterial growth, including respiration, central carbon metabolism, fatty acid synthesis, phospholipid synthesis, and protein synthesis. Unexpectedly, the results indicate that multiple regulatory systems are involved in coordinating DNA replication with cell physiology, with some of the regulatory systems targeting oriC while others act in a oriC-independent manner. We propose that distinct regulatory systems are utilized to control DNA replication in response to diverse physiological and chemical changes.

  20. Multiple Regulatory Systems Coordinate DNA Replication with Cell Growth in Bacillus subtilis

    Science.gov (United States)

    Murray, Heath; Koh, Alan

    2014-01-01

    In many bacteria the rate of DNA replication is linked with cellular physiology to ensure that genome duplication is coordinated with growth. Nutrient-mediated growth rate control of DNA replication initiation has been appreciated for decades, however the mechanism(s) that connects these cell cycle activities has eluded understanding. In order to help address this fundamental question we have investigated regulation of DNA replication in the model organism Bacillus subtilis. Contrary to the prevailing view we find that changes in DnaA protein level are not sufficient to account for nutrient-mediated growth rate control of DNA replication initiation, although this regulation does require both DnaA and the endogenous replication origin. We go on to report connections between DNA replication and several essential cellular activities required for rapid bacterial growth, including respiration, central carbon metabolism, fatty acid synthesis, phospholipid synthesis, and protein synthesis. Unexpectedly, the results indicate that multiple regulatory systems are involved in coordinating DNA replication with cell physiology, with some of the regulatory systems targeting oriC while others act in a oriC-independent manner. We propose that distinct regulatory systems are utilized to control DNA replication in response to diverse physiological and chemical changes. PMID:25340815

  1. Learning causes reorganization of neuronal firing patterns to represent related experiences within a hippocampal schema.

    Science.gov (United States)

    McKenzie, Sam; Robinson, Nick T M; Herrera, Lauren; Churchill, Jordana C; Eichenbaum, Howard

    2013-06-19

    According to schema theory as proposed by Piaget and Bartlett, learning involves the assimilation of new memories into networks of preexisting knowledge, as well as alteration of the original networks to accommodate the new information. Recent evidence has shown that rats form a schema of goal locations and that the hippocampus plays an essential role in adding new memories to the spatial schema. Here we examined the nature of hippocampal contributions to schema updating by monitoring firing patterns of multiple CA1 neurons as rats learned new goal locations in an environment in which there already were multiple goals. Before new learning, many neurons that fired on arrival at one goal location also fired at other goals, whereas ensemble activity patterns also distinguished different goal events, thus constituting a neural representation that linked distinct goals within a spatial schema. During new learning, some neurons began to fire as animals approached the new goals. These were primarily the same neurons that fired at original goals, the activity patterns at new goals were similar to those associated with the original goals, and new learning also produced changes in the preexisting goal-related firing patterns. After learning, activity patterns associated with the new and original goals gradually diverged, such that initial generalization was followed by a prolonged period in which new memories became distinguished within the ensemble representation. These findings support the view that consolidation involves assimilation of new memories into preexisting neural networks that accommodate relationships among new and existing memories.

  2. Unearthing belowground bud banks in fire-prone ecosystems.

    Science.gov (United States)

    Pausas, Juli G; Lamont, Byron B; Paula, Susana; Appezzato-da-Glória, Beatriz; Fidelis, Alessandra

    2018-03-01

    Despite long-time awareness of the importance of the location of buds in plant biology, research on belowground bud banks has been scant. Terms such as lignotuber, xylopodium and sobole, all referring to belowground bud-bearing structures, are used inconsistently in the literature. Because soil efficiently insulates meristems from the heat of fire, concealing buds below ground provides fitness benefits in fire-prone ecosystems. Thus, in these ecosystems, there is a remarkable diversity of bud-bearing structures. There are at least six locations where belowground buds are stored: roots, root crown, rhizomes, woody burls, fleshy swellings and belowground caudexes. These support many morphologically distinct organs. Given their history and function, these organs may be divided into three groups: those that originated in the early history of plants and that currently are widespread (bud-bearing roots and root crowns); those that also originated early and have spread mainly among ferns and monocots (nonwoody rhizomes and a wide range of fleshy underground swellings); and those that originated later in history and are strictly tied to fire-prone ecosystems (woody rhizomes, lignotubers and xylopodia). Recognizing the diversity of belowground bud banks is the starting point for understanding the many evolutionary pathways available for responding to severe recurrent disturbances. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

  3. H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication.

    Science.gov (United States)

    Wu, Rentian; Wang, Zhiquan; Zhang, Honglian; Gan, Haiyun; Zhang, Zhiguo

    2017-01-09

    DNA replication is tightly regulated to occur once and only once per cell cycle. How chromatin, the physiological substrate of DNA replication machinery, regulates DNA replication remains largely unknown. Here we show that histone H3 lysine 9 demethylase Kdm4d regulates DNA replication in eukaryotic cells. Depletion of Kdm4d results in defects in DNA replication, which can be rescued by the expression of H3K9M, a histone H3 mutant transgene that reverses the effect of Kdm4d on H3K9 methylation. Kdm4d interacts with replication proteins, and its recruitment to DNA replication origins depends on the two pre-replicative complex components (origin recognition complex [ORC] and minichromosome maintenance [MCM] complex). Depletion of Kdm4d impairs the recruitment of Cdc45, proliferating cell nuclear antigen (PCNA), and polymerase δ, but not ORC and MCM proteins. These results demonstrate a novel mechanism by which Kdm4d regulates DNA replication by reducing the H3K9me3 level to facilitate formation of pre-initiative complex. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. GEMC1 is a TopBP1-interacting protein required for chromosomal DNA replication.

    Science.gov (United States)

    Balestrini, Alessia; Cosentino, Claudia; Errico, Alessia; Garner, Elizabeth; Costanzo, Vincenzo

    2010-05-01

    Many of the factors required for chromosomal DNA replication have been identified in unicellular eukaryotes. However, DNA replication is poorly understood in multicellular organisms. Here, we report the identification of GEMC1 (geminin coiled-coil containing protein 1), a novel vertebrate protein required for chromosomal DNA replication. GEMC1 is highly conserved in vertebrates and is preferentially expressed in proliferating cells. Using Xenopus laevis egg extract we show that Xenopus GEMC1 (xGEMC1) binds to the checkpoint and replication factor TopBP1, which promotes binding of xGEMC1 to chromatin during pre-replication complex (pre-RC) formation. We demonstrate that xGEMC1 interacts directly with replication factors such as Cdc45 and the kinase Cdk2-CyclinE, through which it is heavily phosphorylated. Phosphorylated xGEMC1 stimulates initiation of DNA replication, whereas depletion of xGEMC1 prevents the onset of DNA replication owing to the impairment of Cdc45 loading onto chromatin. Similarly, inhibition of GEMC1 expression with morpholino and siRNA oligos prevents DNA replication in embryonic and somatic vertebrate cells. These data suggest that GEMC1 promotes initiation of chromosomal DNA replication in multicellular organisms by mediating TopBP1- and Cdk2-dependent recruitment of Cdc45 onto replication origins.

  5. Applying genetic algorithms to set the optimal combination of forest fire related variables and model forest fire susceptibility based on data mining models. The case of Dayu County, China.

    Science.gov (United States)

    Hong, Haoyuan; Tsangaratos, Paraskevas; Ilia, Ioanna; Liu, Junzhi; Zhu, A-Xing; Xu, Chong

    2018-07-15

    The main objective of the present study was to utilize Genetic Algorithms (GA) in order to obtain the optimal combination of forest fire related variables and apply data mining methods for constructing a forest fire susceptibility map. In the proposed approach, a Random Forest (RF) and a Support Vector Machine (SVM) was used to produce a forest fire susceptibility map for the Dayu County which is located in southwest of Jiangxi Province, China. For this purpose, historic forest fires and thirteen forest fire related variables were analyzed, namely: elevation, slope angle, aspect, curvature, land use, soil cover, heat load index, normalized difference vegetation index, mean annual temperature, mean annual wind speed, mean annual rainfall, distance to river network and distance to road network. The Natural Break and the Certainty Factor method were used to classify and weight the thirteen variables, while a multicollinearity analysis was performed to determine the correlation among the variables and decide about their usability. The optimal set of variables, determined by the GA limited the number of variables into eight excluding from the analysis, aspect, land use, heat load index, distance to river network and mean annual rainfall. The performance of the forest fire models was evaluated by using the area under the Receiver Operating Characteristic curve (ROC-AUC) based on the validation dataset. Overall, the RF models gave higher AUC values. Also the results showed that the proposed optimized models outperform the original models. Specifically, the optimized RF model gave the best results (0.8495), followed by the original RF (0.8169), while the optimized SVM gave lower values (0.7456) than the RF, however higher than the original SVM (0.7148) model. The study highlights the significance of feature selection techniques in forest fire susceptibility, whereas data mining methods could be considered as a valid approach for forest fire susceptibility modeling

  6. Speculations on the initiation of chromosome replication in Escherichia coli: the dualism hypothesis.

    Science.gov (United States)

    Norris, Vic

    2011-05-01

    The exact nature of the mechanism that triggers initiation of chromosome replication in the best understood of all organisms, Escherichia coli, remains mysterious. Here, I suggest that this mechanism evolved in response to the problems that arise if chromosome replication does not occur. E. coli is now known to be highly structured. This leads me to propose a mechanism for initiation of replication based on the dynamics of large assemblies of molecules and macromolecules termed hyperstructures. In this proposal, hyperstructures and their constituents are put into two classes, non-equilibrium and equilibrium, that spontaneously separate and that are appropriate for life in either good or bad conditions. Maintaining the right ratio(s) of non-equilibrium to equilibrium hyperstructures is therefore a major challenge for cells. I propose that this maintenance entails a major transfer of material from equilibrium to non-equilibrium hyperstructures once per cell and I further propose that this transfer times the cell cycle. More specifically, I speculate that the dialogue between hyperstructures involves the structuring of water and the condensation of cations and that one of the outcomes of ion condensation on ribosomal hyperstructures and decondensation from the origin hyperstructure is the separation of strands at oriC responsible for triggering initiation of replication. The dualism hypothesis that comes out of these speculations may help integrate models for initiation of replication, chromosome segregation and cell division with the 'prebiotic ecology' scenario of the origins of life. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. Contribution to the discussions on the origin of the cerrado biome: Brazilian savanna

    Directory of Open Access Journals (Sweden)

    MHO. Pinheiro

    Full Text Available Theories that attempt to explain the origin of the cerrado biome are mostly based on the isolated action of three major factors: climate, fire and soil. Another factor that has been mentioned is that of human interference. We hypothesise that the evolutionary origin of this biome resulted from the complex interaction of climate, fire and soil, with climate being the triggering agent of this assumed interaction. Fire, as well as acid and dystrophic soils, would be factors involved in the selection of savanna species throughout climatic events, during the Tertiary and the Quaternary, e.g. Pliocene and Pleistocene. The genesis of the physiognomies that would give rise to cerrado sensu lato, rather than forest formations, could have occurred due to the strong pressure exerted by the reduction in water availability, and the selection of the species adapted to the new conditions imposed by the environment. The characteristics of cerrado sensu lato soil, originated from edaphic impoverishment caused by lixiviation and successive past fires, would remain, even after hydric availability increased following the Pleistocene glaciations.

  8. Phosphorylated STAT5 directly facilitates parvovirus B19 DNA replication in human erythroid progenitors through interaction with the MCM complex.

    Science.gov (United States)

    Ganaie, Safder S; Zou, Wei; Xu, Peng; Deng, Xuefeng; Kleiboeker, Steve; Qiu, Jianming

    2017-05-01

    Productive infection of human parvovirus B19 (B19V) exhibits high tropism for burst forming unit erythroid (BFU-E) and colony forming unit erythroid (CFU-E) progenitor cells in human bone marrow and fetal liver. This exclusive restriction of the virus replication to human erythroid progenitor cells is partly due to the intracellular factors that are essential for viral DNA replication, including erythropoietin signaling. Efficient B19V replication also requires hypoxic conditions, which upregulate the signal transducer and activator of transcription 5 (STAT5) pathway, and phosphorylated STAT5 is essential for virus replication. In this study, our results revealed direct involvement of STAT5 in B19V DNA replication. Consensus STAT5-binding elements were identified adjacent to the NS1-binding element within the minimal origins of viral DNA replication in the B19V genome. Phosphorylated STAT5 specifically interacted with viral DNA replication origins both in vivo and in vitro, and was actively recruited within the viral DNA replication centers. Notably, STAT5 interacted with minichromosome maintenance (MCM) complex, suggesting that STAT5 directly facilitates viral DNA replication by recruiting the helicase complex of the cellular DNA replication machinery to viral DNA replication centers. The FDA-approved drug pimozide dephosphorylates STAT5, and it inhibited B19V replication in ex vivo expanded human erythroid progenitors. Our results demonstrated that pimozide could be a promising antiviral drug for treatment of B19V-related diseases.

  9. Complex Dynamic Development of Poliovirus Membranous Replication Complexes

    Science.gov (United States)

    Nair, Vinod; Hansen, Bryan T.; Hoyt, Forrest H.; Fischer, Elizabeth R.; Ehrenfeld, Ellie

    2012-01-01

    Replication of all positive-strand RNA viruses is intimately associated with membranes. Here we utilize electron tomography and other methods to investigate the remodeling of membranes in poliovirus-infected cells. We found that the viral replication structures previously described as “vesicles” are in fact convoluted, branching chambers with complex and dynamic morphology. They are likely to originate from cis-Golgi membranes and are represented during the early stages of infection by single-walled connecting and branching tubular compartments. These early viral organelles gradually transform into double-membrane structures by extension of membranous walls and/or collapsing of the luminal cavity of the single-membrane structures. As the double-membrane regions develop, they enclose cytoplasmic material. At this stage, a continuous membranous structure may have double- and single-walled membrane morphology at adjacent cross-sections. In the late stages of the replication cycle, the structures are represented mostly by double-membrane vesicles. Viral replication proteins, double-stranded RNA species, and actively replicating RNA are associated with both double- and single-membrane structures. However, the exponential phase of viral RNA synthesis occurs when single-membrane formations are predominant in the cell. It has been shown previously that replication complexes of some other positive-strand RNA viruses form on membrane invaginations, which result from negative membrane curvature. Our data show that the remodeling of cellular membranes in poliovirus-infected cells produces structures with positive curvature of membranes. Thus, it is likely that there is a fundamental divergence in the requirements for the supporting cellular membrane-shaping machinery among different groups of positive-strand RNA viruses. PMID:22072780

  10. Chromosomal context and replication properties of ARS plasmids in ...

    Indian Academy of Sciences (India)

    2015-11-28

    Nov 28, 2015 ... plasmid but only a subset of them functions as replication origins in their ... except that they are rich in A + T content (As on one strand and Ts .... different unique, terminal, PCR-generated restriction sites used for cloning each fragment are ..... Hall TA 1999 BioEdit: a user-friendly biological sequence align-.

  11. Numerical study of fire whirlwind taking into account radiative heat transfer

    Science.gov (United States)

    Sakai, S.; Miyagi, N.

    2010-06-01

    The fire whirlwind is a strong swirling flow with flame and spark, which may occur in the case of, widespread fire in the urban region by an earthquake disaster or an air raid, and a large-scale fire such as a forest fire. Fire whirlwind moves and promotes spread of fire and may extend serious damage rapidly. In this study, performing the numerical analysis of fire whirlwind with respect to scale effect, it is examined whether a relationship exists between a real phenomenon and the phenomenon in the reduction model with taking into account radiative heat transfer. Three dimensional analyses are performed to investigate the thermal and flow fields by using the analytical software FLUENT6.3. It is analyzed that those swirling flow in original scale, 1/10 scale, 1/50 scale, 1/100 scale from the original brake out to vanish. As an analytical condition, parameter calculation is repeated to get the velocity of a parallel flow which is the easiest to occur the swirling flow for each reduction model, and then scale effect is discussed by comparing the velocity of the natural convection, the velocity of the parallel flow, the center pressure of the whirlwind and the continuance time of the swirling flow. The analysis model of C-character heat source model is performed as well as the analysis in L-character model, which is one of the representative example of the fire whirlwind occurred at Tokyo in the Great Kanto Earthquake (1923). The result of the numerical analysis shows that there is a scale effect to the speed of the parallel flow to generate the swirling flow.

  12. Numerical study of fire whirlwind taking into account radiative heat transfer

    International Nuclear Information System (INIS)

    Sakai, S; Miyagi, N

    2010-01-01

    The fire whirlwind is a strong swirling flow with flame and spark, which may occur in the case of, widespread fire in the urban region by an earthquake disaster or an air raid, and a large-scale fire such as a forest fire. Fire whirlwind moves and promotes spread of fire and may extend serious damage rapidly. In this study, performing the numerical analysis of fire whirlwind with respect to scale effect, it is examined whether a relationship exists between a real phenomenon and the phenomenon in the reduction model with taking into account radiative heat transfer. Three dimensional analyses are performed to investigate the thermal and flow fields by using the analytical software FLUENT6.3. It is analyzed that those swirling flow in original scale, 1/10 scale, 1/50 scale, 1/100 scale from the original brake out to vanish. As an analytical condition, parameter calculation is repeated to get the velocity of a parallel flow which is the easiest to occur the swirling flow for each reduction model, and then scale effect is discussed by comparing the velocity of the natural convection, the velocity of the parallel flow, the center pressure of the whirlwind and the continuance time of the swirling flow. The analysis model of C-character heat source model is performed as well as the analysis in L-character model, which is one of the representative example of the fire whirlwind occurred at Tokyo in the Great Kanto Earthquake (1923). The result of the numerical analysis shows that there is a scale effect to the speed of the parallel flow to generate the swirling flow.

  13. Using the sensor web to detect and monitor the spread of wild fires

    CSIR Research Space (South Africa)

    Moodley, D

    2006-09-01

    Full Text Available is facilitated by the Sensor Web Registry Service – an extended version of the OGC Catalog Service. 3 THE ADVANCED FIRE INFORMATION SYSTEM The Advanced Fire Information System (AFIS) is the first near real-time satellite-based fire monitoring system in Africa.... It was originally developed for the South African electrical power util- ity, ESKOM to mitigate the impact of wild fires on regional elec- tricity supply (Fleming et al., 2005, Frost and Vosloo, 2006). AFIS was first implemented using propriety GIS technology...

  14. Replicating a study of collaborative use of mobile phones for photo sharing in a different cultural context

    DEFF Research Database (Denmark)

    Sandoval, Carolina; Montero, Camila; Jokela, Tero

    2014-01-01

    In this paper, we replicate a study of collaborative mobile phone use to share personal photos in groups of collocated people. The replication study was conducted in a different cultural context to check the generalizability of the findings from the original study in terms of the proposed...

  15. Inhibition of in vitro SV40 DNA replication by ultraviolet light

    International Nuclear Information System (INIS)

    Gough, G.; Wood, R.W.

    1989-01-01

    Ultraviolet light-induced DNA damage was found to inhibit SV40 origin-dependent DNA synthesis carried out by soluble humancell extracts. Replication of SV40-based plasmids was reduced to approx. 35% of that in unirradiated controls after irradiation with 50-100 J/m 2 germicidal ultraviolet light, where an average of 3-6 pyrimidine dimer photoproducts were formed per plasmid circle. Inhibition of the DNA helicase activity of T antigen (required for initiation of replication in the in vitro system) was also investigated, and was only significant after much higher fluences, 1000-5000 J/m 2 . The data indicate that DNA damage by ultraviolet light inhibits DNA synthesis in cell-free extracts principally by affecting components of the replication complex other than the DNA helicase activity of T antigen. The soluble system could be used to biochemically investigate the possible bypass or tolerance of DNA damage during replication (author). 21 refs.; 2 figs

  16. Analysis of JC virus DNA replication using a quantitative and high-throughput assay

    International Nuclear Information System (INIS)

    Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert; Gagnon, David; Gjoerup, Ole; Archambault, Jacques; Bullock, Peter A.

    2014-01-01

    Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication

  17. Analysis of JC virus DNA replication using a quantitative and high-throughput assay

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States); Gagnon, David [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Gjoerup, Ole [Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111 (United States); Archambault, Jacques [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Bullock, Peter A., E-mail: Peter.Bullock@tufts.edu [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States)

    2014-11-15

    Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication.

  18. Evidence for an unorthodox firing sequence employed by the Berlin Painter : deciphering ancient ceramic firing conditions through high-resolution material characterization and replication

    NARCIS (Netherlands)

    Cianchetta, I.; Trentelman, K.; Maish, J.; Saunders, D.; Foran, B.; Walton, M.; Sciau, Ph.; Wang, T.; Pouyet, E.; Cotte, M.; Meirer, F.; Liu, Y.; Pianetta, P.; Mehta, A.

    2015-01-01

    XANES spectroscopy was used to complement the results previously obtained with Raman spectroscopy by the same group to determine the firing conditions used in the production of a single vessel painted by the Berlin Painter in the 5th century B.C. The vessel, part of the collection of the J. Paul

  19. Model of fire spread around Krsko Power Plant

    International Nuclear Information System (INIS)

    Vidmar, P.; Petelin, S.

    2001-01-01

    The idea behind the article is how to define fire behaviour. The work is based on an analytical study of fire origin, its development and spread. The study is based on thermodynamics, heat transfer and the study of hydrodynamics and combustion, which represent the bases of fire dynamics. The article shows a practical example of a leak of hazardous chemicals from a tank. Because of the inflammability of the fluid, fire may start. We have tried to model fire propagation around the Krsko power plant, and show what extended surrounding area could be affected. The model also considers weather conditions, in particular wind speed and direction. For this purpose we have used the computer code Safer Trace, which is based on zone models. That means that phenomena are described by physical and empirical equations. An imperfection in this computer code is the inability to consider ground topology. However in the case of the Krsko power plant, topology is not so important, as the plan is located in a relatively flat region. Mathematical models are presented. They show the propagation of hazardous fluid in the environment considering meteorological data. The work also shows which data are essential to define fire spread and shows the main considerations of Probabilistic Safety Assessment for external fire event.(author)

  20. FIRE

    International Nuclear Information System (INIS)

    Brtis, J.S.; Hausheer, T.G.

    1990-01-01

    FIRE, a microcomputer based program to assist engineers in reviewing and documenting the fire protection impact of design changes has been developed. Acting as an electronic consultant, FIRE is designed to work with an experienced nuclear system engineer, who may not have any detailed fire protection expertise. FIRE helps the engineer to decide if a modification might adversely affect the fire protection design of the station. Since its first development, FIRE has been customized to reflect the fire protection philosophy of the Commonwealth Edison Company. That program is in early production use. This paper discusses the FIRE program in light of its being a useful application of expert system technologies in the power industry

  1. Wildland Fire Management Plan for Brookhaven National Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Green,T.

    2009-10-23

    This Wildland Fire Management Plan (FMP) for Brookhaven National Lab (BNL) updates the 2003 plan incorporating changes necessary to comply with DOE Order 450.1 and DOE P 450.4, Federal Wildland Fire Management Policy and Program Review; Wildland and Prescribed Fire Management Policy and implementation Procedures Reference Guide. This current plan incorporates changes since the original draft of the FMP that result from new policies on the national level. This update also removes references and dependence on the U.S. Fish & Wildlife Service and Department of the Interior, fully transitioning Wildland Fire Management responsibilities to BNL. The Department of Energy policy for managing wildland fires requires that all areas, managed by the DOE and/or its various contractors, that can sustain fire must have a FMP that details fire management guidelines for operational procedures associated with wild fire, operational, and prescribed fires. Fire management plans provide guidance on fire preparedness, fire prevention, wildfire suppression, and the use of controlled, 'prescribed' fires and mechanical means to control the amount of available combustible material. Values reflected in the BNL Wildland FMP include protecting life and public safety; Lab properties, structures and improvements; cultural and historical sites; neighboring private and public properties; and endangered, threatened, and species of concern. Other values supported by the plan include the enhancement of fire-dependent ecosystems at BNL. This FMP will be reviewed periodically to ensure the fire program advances and evolves with the missions of the DOE and BNL. This Fire Management Plan is presented in a format that coverers all aspects specified by DOE guidance documents which are based on the national template for fire management plans adopted under the National Fire Plan. The DOE is one of the signatory agencies on the National Fire Plan. This FMP is to be used and implemented for the

  2. A Review of Fire Interactions and Mass Fires

    Directory of Open Access Journals (Sweden)

    Mark A. Finney

    2011-01-01

    Full Text Available The character of a wildland fire can change dramatically in the presence of another nearby fire. Understanding and predicting the changes in behavior due to fire-fire interactions cannot only be life-saving to those on the ground, but also be used to better control a prescribed fire to meet objectives. In discontinuous fuel types, such interactions may elicit fire spread where none otherwise existed. Fire-fire interactions occur naturally when spot fires start ahead of the main fire and when separate fire events converge in one location. Interactions can be created intentionally during prescribed fires by using spatial ignition patterns. Mass fires are among the most extreme examples of interactive behavior. This paper presents a review of the detailed effects of fire-fire interaction in terms of merging or coalescence criteria, burning rates, flame dimensions, flame temperature, indraft velocity, pulsation, and convection column dynamics. Though relevant in many situations, these changes in fire behavior have yet to be included in any operational-fire models or decision support systems.

  3. Long-term ecosystem nitrogen storage and soil nitrogen availability in post-fire lodgepole pine ecosystems

    Science.gov (United States)

    Erica A. H. Smithwick; Daniel M. Kashian; Michael G. Ryan; Monica G.  Turner

    2009-01-01

    Long-term, landscape patterns in inorganic nitrogen (N) availability and N stocks following infrequent, stand-replacing fire are unknown but are important for interpreting the effect of disturbances on ecosystem function. Here, we present results from a replicated chronosequence study in the Greater Yellowstone Ecosystem (Wyoming, USA) directed at measuring inorganic N...

  4. The state of the residential fire fatality problem in Sweden: Epidemiology, risk factors, and event typologies.

    Science.gov (United States)

    Jonsson, Anders; Bonander, Carl; Nilson, Finn; Huss, Fredrik

    2017-09-01

    Residential fires represent the largest category of fatal fires in Sweden. The purpose of this study was to describe the epidemiology of fatal residential fires in Sweden and to identify clusters of events. Data was collected from a database that combines information on fatal fires with data from forensic examinations and the Swedish Cause of Death-register. Mortality rates were calculated for different strata using population statistics and rescue service turnout reports. Cluster analysis was performed using multiple correspondence analysis with agglomerative hierarchical clustering. Male sex, old age, smoking, and alcohol were identified as risk factors, and the most common primary injury diagnosis was exposure to toxic gases. Compared to non-fatal fires, fatal residential fires more often originated in the bedroom, were more often caused by smoking, and were more likely to occur at night. Six clusters were identified. The first two clusters were both smoking-related, but were separated into (1) fatalities that often involved elderly people, usually female, whose clothes were ignited (17% of the sample), (2) middle-aged (45-64years old), (often) intoxicated men, where the fire usually originated in furniture (30%). Other clusters that were identified in the analysis were related to (3) fires caused by technical fault, started in electrical installations in single houses (13%), (4) cooking appliances left on (8%), (5) events with unknown cause, room and object of origin (25%), and (6) deliberately set fires (7%). Fatal residential fires were unevenly distributed in the Swedish population. To further reduce the incidence of fire mortality, specialized prevention efforts that focus on the different needs of each cluster are required. Cooperation between various societal functions, e.g. rescue services, elderly care, psychiatric clinics and other social services, with an application of both human and technological interventions, should reduce residential fire

  5. A conserved MCM single-stranded DNA binding element is essential for replication initiation.

    Science.gov (United States)

    Froelich, Clifford A; Kang, Sukhyun; Epling, Leslie B; Bell, Stephen P; Enemark, Eric J

    2014-04-01

    The ring-shaped MCM helicase is essential to all phases of DNA replication. The complex loads at replication origins as an inactive double-hexamer encircling duplex DNA. Helicase activation converts this species to two active single hexamers that encircle single-stranded DNA (ssDNA). The molecular details of MCM DNA interactions during these events are unknown. We determined the crystal structure of the Pyrococcus furiosus MCM N-terminal domain hexamer bound to ssDNA and define a conserved MCM-ssDNA binding motif (MSSB). Intriguingly, ssDNA binds the MCM ring interior perpendicular to the central channel with defined polarity. In eukaryotes, the MSSB is conserved in several Mcm2-7 subunits, and MSSB mutant combinations in S. cerevisiae Mcm2-7 are not viable. Mutant Mcm2-7 complexes assemble and are recruited to replication origins, but are defective in helicase loading and activation. Our findings identify an important MCM-ssDNA interaction and suggest it functions during helicase activation to select the strand for translocation. DOI: http://dx.doi.org/10.7554/eLife.01993.001.

  6. Different rates of DNA replication at early versus late S-phase sections: multiscale modeling of stochastic events related to DNA content/EdU (5-ethynyl-2'deoxyuridine) incorporation distributions.

    Science.gov (United States)

    Li, Biao; Zhao, Hong; Rybak, Paulina; Dobrucki, Jurek W; Darzynkiewicz, Zbigniew; Kimmel, Marek

    2014-09-01

    Mathematical modeling allows relating molecular events to single-cell characteristics assessed by multiparameter cytometry. In the present study we labeled newly synthesized DNA in A549 human lung carcinoma cells with 15-120 min pulses of EdU. All DNA was stained with DAPI and cellular fluorescence was measured by laser scanning cytometry. The frequency of cells in the ascending (left) side of the "horseshoe"-shaped EdU/DAPI bivariate distributions reports the rate of DNA replication at the time of entrance to S phase while their frequency in the descending (right) side is a marker of DNA replication rate at the time of transition from S to G2 phase. To understand the connection between molecular-scale events and scatterplot asymmetry, we developed a multiscale stochastic model, which simulates DNA replication and cell cycle progression of individual cells and produces in silico EdU/DAPI scatterplots. For each S-phase cell the time points at which replication origins are fired are modeled by a non-homogeneous Poisson Process (NHPP). Shifted gamma distributions are assumed for durations of cell cycle phases (G1, S and G2 M), Depending on the rate of DNA synthesis being an increasing or decreasing function, simulated EdU/DAPI bivariate graphs show predominance of cells in left (early-S) or right (late-S) side of the horseshoe distribution. Assuming NHPP rate estimated from independent experiments, simulated EdU/DAPI graphs are nearly indistinguishable from those experimentally observed. This finding proves consistency between the S-phase DNA-replication rate based on molecular-scale analyses, and cell population kinetics ascertained from EdU/DAPI scatterplots and demonstrates that DNA replication rate at entrance to S is relatively slow compared with its rather abrupt termination during S to G2 transition. Our approach opens a possibility of similar modeling to study the effect of anticancer drugs on DNA replication/cell cycle progression and also to quantify other

  7. FIRES: Fire Information Retrieval and Evaluation System - A program for fire danger rating analysis

    Science.gov (United States)

    Patricia L. Andrews; Larry S. Bradshaw

    1997-01-01

    A computer program, FIRES: Fire Information Retrieval and Evaluation System, provides methods for evaluating the performance of fire danger rating indexes. The relationship between fire danger indexes and historical fire occurrence and size is examined through logistic regression and percentiles. Historical seasonal trends of fire danger and fire occurrence can be...

  8. Fire propagation equation for the explicit identification of fire scenarios in a fire PSA

    International Nuclear Information System (INIS)

    Lim, Ho Gon; Han, Sang Hoon; Moon, Joo Hyun

    2011-01-01

    When performing fire PSA in a nuclear power plant, an event mapping method, using an internal event PSA model, is widely used to reduce the resources used by fire PSA model development. Feasible initiating events and component failure events due to fire are identified to transform the fault tree (FT) for an internal event PSA into one for a fire PSA using the event mapping method. A surrogate event or damage term method is used to condition the FT of the internal PSA. The surrogate event or the damage term plays the role of flagging whether the system/component in a fire compartment is damaged or not, depending on the fire being initiated from a specified compartment. These methods usually require explicit states of all compartments to be modeled in a fire area. Fire event scenarios, when using explicit identification, such as surrogate or damage terms, have two problems: there is no consideration of multiple fire propagation beyond a single propagation to an adjacent compartment, and there is no consideration of simultaneous fire propagations in which an initiating fire event is propagated to multiple paths simultaneously. The present paper suggests a fire propagation equation to identify all possible fire event scenarios for an explicitly treated fire event scenario in the fire PSA. Also, a method for separating fire events was developed to make all fire events a set of mutually exclusive events, which can facilitate arithmetic summation in fire risk quantification. A simple example is given to confirm the applicability of the present method for a 2x3 rectangular fire area. Also, a feasible asymptotic approach is discussed to reduce the computational burden for fire risk quantification

  9. [Fire worship on Soratte: form prehistory to present days].

    Science.gov (United States)

    Falchetti, Mario; Ottini, Laura

    2013-01-01

    Fire has always been involved in human thoughts, believes and actions. For many psychological reasons fire has been considered as living power: red as the human blood, warm as the human body, clearly shines in the night. Fire worship is very common, especially in regions where terrestrial fire is believed to be the image of the heavenly fire. Fire worship has represented the base for symbolic systems involved in the cultural-anthropological evolution of populations settled close to mount Soratte. Fire cults in this region have originated in independent and long-time separated contexts, according to available knowledge. Hirpi Sorani, ancient inhabitants of mount Soratte territory, celebrated Sorano Apollo by a famous fire walking ceremony, with a likely cathartic and apotropaic meaning, as reported by ancient Roman writers. The victory of Christianity over paganism caused the decline of these religious practices. The beginning of the XIX century witnessed the establishment ofa new kind of devotion to the Virgin Mary at the mount Soratte. Today, this religious piety-linked identity has weakened due to changes in lifestyles,from an agricultural to one based on outside home employment, and has been largely shifted on cultural and anthropological bases. In conclusion, fire worship at mount Soratte has evolved because of external influences and local inhabitants have reacted by asserting their own identity.

  10. Replisome speed determines the efficiency of the Tus−Ter replication termination barrier

    KAUST Repository

    Elshenawy, Mohamed; Jergic, Slobodan; Xu, Zhi Qiang; Sobhy, Mohamed Abdelmaboud; Takahashi, Masateru; Oakley, Aaron J.; Dixon, Nicholas E.; Hamdan, Samir

    2015-01-01

    In all domains of life, DNA synthesis occurs bidirectionally from replication origins. Despite variable rates of replication fork progression, fork convergence often occurs at specific sites. Escherichia coli sets a 'replication fork trap' that allows the first arriving fork to enter but not to leave the terminus region. The trap is set by oppositely oriented Tus-bound Ter sites that block forks on approach from only one direction. However, the efficiency of fork blockage by Tus-Ter does not exceed 50% in vivo despite its apparent ability to almost permanently arrest replication forks in vitro. Here we use data from single-molecule DNA replication assays and structural studies to show that both polarity and fork-arrest efficiency are determined by a competition between rates of Tus displacement and rearrangement of Tus-Ter interactions that leads to blockage of slower moving replisomes by two distinct mechanisms. To our knowledge this is the first example where intrinsic differences in rates of individual replisomes have different biological outcomes. ©2015 Macmillan Publishers Limited. All rights reserved.

  11. Replisome speed determines the efficiency of the Tus−Ter replication termination barrier

    KAUST Repository

    Elshenawy, Mohamed

    2015-08-31

    In all domains of life, DNA synthesis occurs bidirectionally from replication origins. Despite variable rates of replication fork progression, fork convergence often occurs at specific sites. Escherichia coli sets a \\'replication fork trap\\' that allows the first arriving fork to enter but not to leave the terminus region. The trap is set by oppositely oriented Tus-bound Ter sites that block forks on approach from only one direction. However, the efficiency of fork blockage by Tus-Ter does not exceed 50% in vivo despite its apparent ability to almost permanently arrest replication forks in vitro. Here we use data from single-molecule DNA replication assays and structural studies to show that both polarity and fork-arrest efficiency are determined by a competition between rates of Tus displacement and rearrangement of Tus-Ter interactions that leads to blockage of slower moving replisomes by two distinct mechanisms. To our knowledge this is the first example where intrinsic differences in rates of individual replisomes have different biological outcomes. ©2015 Macmillan Publishers Limited. All rights reserved.

  12. The Origin, Dynamic Morphology, and PI4P-Independent Formation of Encephalomyocarditis Virus Replication Organelles

    Directory of Open Access Journals (Sweden)

    C. E. Melia

    2018-04-01

    Full Text Available Picornaviruses induce dramatic rearrangements of endomembranes in the cells that they infect to produce dedicated platforms for viral replication. These structures, termed replication organelles (ROs, have been well characterized for the Enterovirus genus of the Picornaviridae. However, it is unknown whether the diverse RO morphologies associated with enterovirus infection are conserved among other picornaviruses. Here, we use serial electron tomography at different stages of infection to assess the three-dimensional architecture of ROs induced by encephalomyocarditis virus (EMCV, a member of the Cardiovirus genus of the family of picornaviruses that is distantly related. Ultrastructural analyses revealed connections between early single-membrane EMCV ROs and the endoplasmic reticulum (ER, establishing the ER as a likely donor organelle for their formation. These early single-membrane ROs appear to transform into double-membrane vesicles (DMVs as infection progresses. Both single- and double-membrane structures were found to support viral RNA synthesis, and progeny viruses accumulated in close proximity, suggesting a spatial association between RNA synthesis and virus assembly. Further, we explored the role of phosphatidylinositol 4-phosphate (PI4P, a critical host factor for both enterovirus and cardiovirus replication that has been recently found to expedite enterovirus RO formation rather than being strictly required. By exploiting an EMCV escape mutant, we found that low-PI4P conditions could also be overcome for the formation of cardiovirus ROs. Collectively, our data show that despite differences in the membrane source, there are striking similarities in the biogenesis, morphology, and transformation of cardiovirus and enterovirus ROs, which may well extend to other picornaviruses.

  13. An origin-deficient yeast artificial chromosome triggers a cell cycle checkpoint.

    Science.gov (United States)

    van Brabant, A J; Buchanan, C D; Charboneau, E; Fangman, W L; Brewer, B J

    2001-04-01

    Checkpoint controls coordinate entry into mitosis with the completion of DNA replication. Depletion of nucleotide precursors by treatment with the drug hydroxyurea triggers such a checkpoint response. However, it is not clear whether the signal for this hydroxyurea-induced checkpoint pathway is the presence of unreplicated DNA, or rather the persistence of single-stranded or damaged DNA. In a yeast artificial chromosome (YAC) we have engineered an approximately 170 kb region lacking efficient replication origins that allows us to explore the specific effects of unreplicated DNA on cell cycle progression. Replication of this YAC extends the length of S phase and causes cells to engage an S/M checkpoint. In the absence of Rad9 the YAC becomes unstable, undergoing deletions within the origin-free region.

  14. Internal fire analysis screening methodology for the Salem Nuclear Generating Station

    International Nuclear Information System (INIS)

    Eide, S.; Bertucio, R.; Quilici, M.; Bearden, R.

    1989-01-01

    This paper reports on an internal fire analysis screening methodology that has been utilized for the Salem Nuclear Generating Station (SNGS) Probabilistic Risk Assessment (PRA). The methodology was first developed and applied in the Brunswick Steam Electric Plant (BSEP) PRA. The SNGS application includes several improvements and extensions to the original methodology. The SNGS approach differs significantly from traditional fire analysis methodologies by providing a much more detailed treatment of transient combustibles. This level of detail results in a model which is more usable for assisting in the management of fire risk at the plant

  15. Fire protection research for DOE facilities: FY 83 year-end report

    International Nuclear Information System (INIS)

    Hasegawa, H.K.; Alvares, N.J.; Lipska-Quinn, A.E.; Beason, D.G.; Foote, K.L.; Priante, S.J.; Stagge, K.

    1984-01-01

    We summarize our research in FY 83 for the DOE-sponsored project, Fire Protection Research for DOE Facilities. This research program was initiated in 1977 to advance fire-protection strategies of energy technology facilities in order to keep abreast of the unique fire problems that develop along with energy technology research. Since 1977, the program has broadened its original scope, as reflected in previous year-end reports. We are developing an analytical methodology through detailed study of fusion energy experiments at Lawrence Livermore National Laboratory (LLNL). Using these experiments as models for methodology development, we are currently advancing three major task areas: (1) the identification of fire hazards unique to fusion energy facilities, (2) the evaluation of accepted fire-management measures to meet the negate hazards, and (3) the performance of unique research into problem areas we have identified to provide input into analytical fire-growth and damage-assessment models

  16. Fire-protection research for DOE facilities: FY 82 year-end report

    International Nuclear Information System (INIS)

    Hasegawa, H.K.; Alvares, N.J.; Lipska-Quinn, A.E.; Beason, D.G.; Priante, S.J.; Foote, K.L.

    1983-01-01

    We summarize our research in FY 82 for the DOE-sponsored project, Fire Protection Research for DOE Facilities. This research program was initiated in 1977 to advance fire-protection strategies for energy technology facilities to keep abreast of the unique fire problems that develop along with energy technology research. Since 1977, the program has broadened its original scope, as reflected in previous year-end reports. We are developing an analytical methodology through detailed study of fusion energy experiments at Lawrence Livermore National Laboratory (LLNL). Using these experiments as models for methodology development, we are concurrently advancing three major task areas: (1) the identification of fire hazards unique to current fusion energy facilities; (2) the evaluation of accepted fire-management measures to meet and negate hazards; and (3) the performance of unique research into problem areas we have identified to provide input into analytical fire-growth and damage-assessment models

  17. Prospective elementary teachers' conceptions of multidigit number: exemplifying a replication framework for mathematics education

    Science.gov (United States)

    Jacobson, Erik; Simpson, Amber

    2018-04-01

    Replication studies play a critical role in scientific accumulation of knowledge, yet replication studies in mathematics education are rare. In this study, the authors replicated Thanheiser's (Educational Studies in Mathematics 75:241-251, 2010) study of prospective elementary teachers' conceptions of multidigit number and examined the main claim that most elementary pre-service teachers think about digits incorrectly at least some of the time. Results indicated no statistically significant difference in the distribution of conceptions between the original and replication samples and, moreover, no statistically significant differences in the distribution of sub-conceptions among prospective teachers with the most common conception. These results suggest confidence is warranted both in the generality of the main claim and in the utility of the conceptions framework for describing prospective elementary teachers' conceptions of multidigit number. The report further contributes a framework for replication of mathematics education research adapted from the field of psychology.

  18. Fire protection in nuclear power plants

    International Nuclear Information System (INIS)

    1992-01-01

    The Code on Design (Safety Series 50-C-D (Rev. 1)) within the NUSS (Nuclear Safety Standards) programme of the IAEA points out the necessity of measures for protecting plant items which are important to safety against fires of internal and external origin. Experience of the past two decades in the operation of nuclear power plants and modern analysis techniques confirm that fire may be a real threat to nuclear safety and should receive adequate attention from the beginning of the design process throughout the life of the plant. Within the framework of the NUSS programme, a Safety Guide on fire protection had therefore been developed to enlarge on the general requirements given in the Code. Since its first publication in 1979, there has been considerable development in protection technology and analysis methods and after the Chernobyl accident it was decided to revise the existing Guide. The present Safety Guide is intended to advise designers, safety assessors and regulators on the concept of fire protection in the design of nuclear power plants and on recommended ways of implementing the concept in some detail in practice. Figs, 1 tab

  19. Comparison of the characteristics of fire and non-fire households in the 2004-2005 survey of fire department-attended and unattended fires.

    Science.gov (United States)

    Greene, Michael A

    2012-06-01

    Comparison of characteristics of fire with non-fire households to determine factors differentially associated with fire households (fire risk factors). National household telephone survey in 2004-2005 by the US Consumer Product Safety Commission with 916 fire households and a comparison sample of 2161 non-fire households. There were an estimated 7.4 million fires (96.6% not reported to fire departments) with 130,000 injuries. Bivariate analysis and multivariate logistic regression analyses to assess differences in household characteristics. Significant factors associated with fire households were renting vs. owning (OR 1.988 pfire households with non-cooking fires (OR 1.383 p=0.0011). Single family houses were associated with non-fire households in the bivariate analysis but not in the multivariate analyses. Renting, household members under 18 years old and smokers are risk factors for unattended fires, similar to the literature for fatal and injury fires. Differences included household members over 65 years old (associated with non-fire households), college/postgraduate education (associated with fire households) and lack of significance of income. Preventing cooking fires (64% of survey incidents), smoking prevention efforts and fire prevention education for families with young children have the potential for reducing unattended fires and injuries.

  20. Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life.

    Science.gov (United States)

    Vasas, Vera; Szathmáry, Eörs; Santos, Mauro

    2010-01-26

    A basic property of life is its capacity to experience Darwinian evolution. The replicator concept is at the core of genetics-first theories of the origin of life, which suggest that self-replicating oligonucleotides or their similar ancestors may have been the first "living" systems and may have led to the evolution of an RNA world. But problems with the nonenzymatic synthesis of biopolymers and the origin of template replication have spurred the alternative metabolism-first scenario, where self-reproducing and evolving proto-metabolic networks are assumed to have predated self-replicating genes. Recent theoretical work shows that "compositional genomes" (i.e., the counts of different molecular species in an assembly) are able to propagate compositional information and can provide a setup on which natural selection acts. Accordingly, if we stick to the notion of replicator as an entity that passes on its structure largely intact in successive replications, those macromolecular aggregates could be dubbed "ensemble replicators" (composomes) and quite different from the more familiar genes and memes. In sharp contrast with template-dependent replication dynamics, we demonstrate here that replication of compositional information is so inaccurate that fitter compositional genomes cannot be maintained by selection and, therefore, the system lacks evolvability (i.e., it cannot substantially depart from the asymptotic steady-state solution already built-in in the dynamical equations). We conclude that this fundamental limitation of ensemble replicators cautions against metabolism-first theories of the origin of life, although ancient metabolic systems could have provided a stable habitat within which polymer replicators later evolved.

  1. Fire debris analysis and scene reconstruction.

    Science.gov (United States)

    Sturaro, Alberto; Vianello, Alvise; Denti, Pablo; Rella, Rocco

    2013-06-01

    During the summer of 2010 near a little village in the south of Italy, a fire destroyed a piece of brushland without any apparent economic importance. The remains of a fire-setting tool were found at the point of origin of the fire. It was started using a well-planned and methodical approach. The analytical results demonstrated a sophisticated and effective incendiary tool designed to leave little evidence that could identify the offender. The action and the purpose of the arsonist were clear but the basic motivation was unpredictable. The burned area was without any relevant economical interest. It was burnt during the past and has not been used for any cultivation or sheep farming but in the region there was evidence of bushfires that had been lit to stimulate the growth of forest fruits to be harvested for sale. Copyright © 2012 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

  2. Discovery of modern (post-1850 CE) lavas in south-central British Columbia, Canada: Origin from coal fires or intraplate volcanism?

    Science.gov (United States)

    Canil, Dante; Mihalynuk, Mitch; Lacourse, Terri

    2018-01-01

    We describe three unusual lavas in the Northern Cordillera in south-central British Columbia, Canada, occurring as spatter, scoria and blocks over small 400 m2 areas. The lavas coat and weld cobbles and pebbles in glacial till and are vesicular and glassy with microlites of clinopyroxene and plagioclase, and xenocrysts of quartz, feldspar or clinopyroxene. Chemically the lavas are basaltic trachyandesite (55-61 wt% SiO2) with trace element patterns similar to average British Columbia upper crust, except for having higher V and lower Zr, Hf, Nb, Th and U. Melting experiments and plagioclase-melt thermometry on the glasses, and phase equilibrium in simple systems, require liquidus temperatures of 1150-1300 °C. Interaction of the liquids with carbonaceous matter at low pressure formed Fe metal spherules and SiC. Radiocarbon ages of charcoal and dendrochronology show the lavas are modern, emplaced in the last 120 years. The similar bulk composition of these lavas to several other Quaternary-aged volcanic centers in the North American Cordillera, some of which show recent seismic activity, could suggest a possible tectonic origin, but the deposits are unusually small and show no central vent for emplacement. Conversely, the balance of evidence would suggest an origin from coal fires or hot gas venting, but is less consistent with the observed calc- and per-alkaline lava compositions, and the lack of known local coal-bearing strata as a heat source. Other anthropogenic origins for the lavas are considered less plausible.

  3. Registered Replication Report: Strack, Martin, & Stepper (1988).

    Science.gov (United States)

    Acosta, Alberto; Adams, Reginald B; Albohn, Daniel N; Allard, Eric S; Beek, Titia; Benning, Stephen D; Blouin- Hudon, Eve-Marie; Bulnes, Luis Carlo; Caldwell, Tracy L; Calin-Jageman, Robert J; Capaldi, Colin A; Carfagno, Nicholas S; Chasten, Kelsie T; Cleeremans, Axel; Connell, Louise; DeCicco, Jennifer M.; Dijkhoff, Laura; Dijkstra, Katinka; Fischer, Agneta H; Foroni, Francesco; Gronau, Quentin F; Hess, Ursula; Holmes, Kevin J; Jones, Jacob L H; Klein, Olivier; Koch, Christopher; Korb, Sebastian; Lewinski, Peter; Liao, Julia D; Lund, Sophie; Lupiáñez, Juan; Lynott, Dermot; Nance, Christin N; Oosterwijk, Suzanne; Özdog˘ru, Asil Ali; Pacheco-Unguetti, Antonia Pilar; Pearson, Bethany; Powis, Christina; Riding, Sarah; Roberts, Tomi-Ann; Rumiati, Raffaella I; Senden, Morgane; Shea-Shumsky, Noah B; Sobocko, Karin; Soto, Jose A; Steiner, Troy G; Talarico, Jennifer M; vanAllen, Zack M; Wagenmakers, E-J; Vandekerckhove, Marie; Wainwright, Bethany; Wayand, Joseph F; Zeelenberg, Rene; Zetzer, Emily E; Zwaan, Rolf A

    2016-11-01

    According to the facial feedback hypothesis, people's affective responses can be influenced by their own facial expression (e.g., smiling, pouting), even when their expression did not result from their emotional experiences. For example, Strack, Martin, and Stepper (1988) instructed participants to rate the funniness of cartoons using a pen that they held in their mouth. In line with the facial feedback hypothesis, when participants held the pen with their teeth (inducing a "smile"), they rated the cartoons as funnier than when they held the pen with their lips (inducing a "pout"). This seminal study of the facial feedback hypothesis has not been replicated directly. This Registered Replication Report describes the results of 17 independent direct replications of Study 1 from Strack et al. (1988), all of which followed the same vetted protocol. A meta-analysis of these studies examined the difference in funniness ratings between the "smile" and "pout" conditions. The original Strack et al. (1988) study reported a rating difference of 0.82 units on a 10-point Likert scale. Our meta-analysis revealed a rating difference of 0.03 units with a 95% confidence interval ranging from -0.11 to 0.16. © The Author(s) 2016.

  4. Repair replication in replicating and nonreplicating DNA after irradiation with uv light

    Energy Technology Data Exchange (ETDEWEB)

    Slor, H.; Cleaver, J.E.

    1978-06-01

    Ultraviolet light induces more pyrimidine dimers and more repair replication in DNA that replicates within 2 to 3 h of irradiation than in DNA that does not replicate during this period. This difference may be due to special conformational changes in DNA and chromatin that might be associated with semiconservative DNA replication.

  5. A study of an adaptive replication framework for orchestrated composite web services.

    Science.gov (United States)

    Mohamed, Marwa F; Elyamany, Hany F; Nassar, Hamed M

    2013-01-01

    Replication is considered one of the most important techniques to improve the Quality of Services (QoS) of published Web Services. It has achieved impressive success in managing resource sharing and usage in order to moderate the energy consumed in IT environments. For a robust and successful replication process, attention should be paid to suitable time as well as the constraints and capabilities in which the process runs. The replication process is time-consuming since outsourcing some new replicas into other hosts is lengthy. Furthermore, nowadays, most of the business processes that might be implemented over the Web are composed of multiple Web services working together in two main styles: Orchestration and Choreography. Accomplishing a replication over such business processes is another challenge due to the complexity and flexibility involved. In this paper, we present an adaptive replication framework for regular and orchestrated composite Web services. The suggested framework includes a number of components for detecting unexpected and unhappy events that might occur when consuming the original published web services including failure or overloading. It also includes a specific replication controller to manage the replication process and select the best host that would encapsulate a new replica. In addition, it includes a component for predicting the incoming load in order to decrease the time needed for outsourcing new replicas, enhancing the performance greatly. A simulation environment has been created to measure the performance of the suggested framework. The results indicate that adaptive replication with prediction scenario is the best option for enhancing the performance of the replication process in an online business environment.

  6. p53 Maintains Genomic Stability by Preventing Interference between Transcription and Replication

    Directory of Open Access Journals (Sweden)

    Constance Qiao Xin Yeo

    2016-04-01

    Full Text Available p53 tumor suppressor maintains genomic stability, typically acting through cell-cycle arrest, senescence, and apoptosis. We discovered a function of p53 in preventing conflicts between transcription and replication, independent of its canonical roles. p53 deficiency sensitizes cells to Topoisomerase (Topo II inhibitors, resulting in DNA damage arising spontaneously during replication. Topoisomerase IIα (TOP2A-DNA complexes preferentially accumulate in isogenic p53 mutant or knockout cells, reflecting an increased recruitment of TOP2A to regulate DNA topology. We propose that p53 acts to prevent DNA topological stress originating from transcription during the S phase and, therefore, promotes normal replication fork progression. Consequently, replication fork progression is impaired in the absence of p53, which is reversed by transcription inhibition. Pharmacologic inhibition of transcription also attenuates DNA damage and decreases Topo-II-DNA complexes, restoring cell viability in p53-deficient cells. Together, our results demonstrate a function of p53 that may underlie its role in tumor suppression.

  7. Heat shields for aircraft - A new concept to save lives in crash fires.

    Science.gov (United States)

    Neel, C. B.; Parker, J. A.; Fish, R. H.; Henshaw, J.; Newland, J. H.; Tempesta, F. L.

    1971-01-01

    A passenger compartment surrounded by a fire-retardant shell, to protect the occupants long enough for the fire to burn out or for fire-fighting equipment to reach the aircraft and extinguish it, is proposed as a new concept for saving lives in crash fires. This concept is made possible by the recent development of two new fire-retardant materials: a very lightweight foam plastic, called polyisocyanurate foam, and an intumescent paint. Exposed to heat, the intumescent paint expands to many times its original thickness and insulates the surface underneath it. Demonstration tests are illustrated, described and discussed. However, some problems, such as preventing fuselage rupture and protecting windows, must be solved before such a system can be used.

  8. Failed Replication of Oxytocin Effects on Trust: The Envelope Task Case.

    Directory of Open Access Journals (Sweden)

    Anthony Lane

    Full Text Available The neurohormone Oxytocin (OT has been one of the most studied peptides in behavioral sciences over the past two decades. Many studies have suggested that OT could increase trusting behaviors. A previous study, based on the "Envelope Task" paradigm, where trust is assessed by the degree of openness of an envelope containing participant's confidential information, showed that OT increases trusting behavior and reported one of the most powerful effects of OT on a behavioral variable. In this paper we present two failed replications of this effect, despite sufficient power to replicate the original large effect. The non-significant results of these two failed replications clearly exclude a large effect of OT on trust in this paradigm but are compatible with either a null effect of OT on trust, or a small effect, undetectable with small sample size (N = 95 and 61 in Study 1 and 2, respectively. Taken together, our results question the purported size of OT's effect on trust and emphasize the need for replications.

  9. Human Parvovirus B19 Utilizes Cellular DNA Replication Machinery for Viral DNA Replication.

    Science.gov (United States)

    Zou, Wei; Wang, Zekun; Xiong, Min; Chen, Aaron Yun; Xu, Peng; Ganaie, Safder S; Badawi, Yomna; Kleiboeker, Steve; Nishimune, Hiroshi; Ye, Shui Qing; Qiu, Jianming

    2018-03-01

    Human parvovirus B19 (B19V) infection of human erythroid progenitor cells (EPCs) induces a DNA damage response and cell cycle arrest at late S phase, which facilitates viral DNA replication. However, it is not clear exactly which cellular factors are employed by this single-stranded DNA virus. Here, we used microarrays to systematically analyze the dynamic transcriptome of EPCs infected with B19V. We found that DNA metabolism, DNA replication, DNA repair, DNA damage response, cell cycle, and cell cycle arrest pathways were significantly regulated after B19V infection. Confocal microscopy analyses revealed that most cellular DNA replication proteins were recruited to the centers of viral DNA replication, but not the DNA repair DNA polymerases. Our results suggest that DNA replication polymerase δ and polymerase α are responsible for B19V DNA replication by knocking down its expression in EPCs. We further showed that although RPA32 is essential for B19V DNA replication and the phosphorylated forms of RPA32 colocalized with the replicating viral genomes, RPA32 phosphorylation was not necessary for B19V DNA replication. Thus, this report provides evidence that B19V uses the cellular DNA replication machinery for viral DNA replication. IMPORTANCE Human parvovirus B19 (B19V) infection can cause transient aplastic crisis, persistent viremia, and pure red cell aplasia. In fetuses, B19V infection can result in nonimmune hydrops fetalis and fetal death. These clinical manifestations of B19V infection are a direct outcome of the death of human erythroid progenitors that host B19V replication. B19V infection induces a DNA damage response that is important for cell cycle arrest at late S phase. Here, we analyzed dynamic changes in cellular gene expression and found that DNA metabolic processes are tightly regulated during B19V infection. Although genes involved in cellular DNA replication were downregulated overall, the cellular DNA replication machinery was tightly

  10. Maintaining epigenetic inheritance during DNA replication in plants

    Directory of Open Access Journals (Sweden)

    Francisco eIglesias

    2016-02-01

    Full Text Available Biotic and abiotic stresses alter the pattern of gene expression in plants. Depending on the frequency and duration of stress events, the effects on the transcriptional state of genes are remembered temporally or transmitted to daughter cells and, in some instances, even to offspring (transgenerational epigenetic inheritance. This memory effect, which can be found even in the absence of the original stress, has an epigenetic basis, through molecular mechanisms that take place at the chromatin and DNA level but do not imply changes in the DNA sequence. Many epigenetic mechanisms have been described and involve covalent modifications on the DNA and histones, such as DNA methylation, histone acetylation and methylation, and RNAi dependent silencing mechanisms. Some of these chromatin modifications need to be stable through cell division in order to be truly epigenetic. During DNA replication, histones are recycled during the formation of the new nucleosomes and this process is tightly regulated. Perturbations to the DNA replication process and/or the recycling of histones lead to epigenetic changes. In this mini-review, we discuss recent evidence aimed at linking DNA replication process to epigenetic inheritance in plants.

  11. Response of different-sized herbivores to fire history

    NARCIS (Netherlands)

    Hagenah, N.; Cromsigt, J.P.G.M.; Olff, H.; Prins, H.H.T.

    2006-01-01

    Retrieve original file from: http://edepot.wur.nl/121801 High herbivore densities and re-occurring fires are natural phenomenons that determine the structure and functioning of African savannas. Traditional burning practices have been intensified over the past years due to increased herbivore

  12. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  13. Characterizing the Final Steps of Chromosomal Replication at the Single-molecule Level in the Model System Escherichia coli

    KAUST Repository

    Elshenawy, Mohamed

    2015-01-01

    In the circular Escherichia coli chromosome, two replisomes are assembled at the unique origin of replication and drive DNA synthesis in opposite directions until they meet in the terminus region across from the origin. Despite the difference

  14. Calculation of Fire Severity Factors and Fire Non-Suppression Probabilities For A DOE Facility Fire PRA

    International Nuclear Information System (INIS)

    Elicson, Tom; Harwood, Bentley; Lucek, Heather; Bouchard, Jim

    2011-01-01

    Over a 12 month period, a fire PRA was developed for a DOE facility using the NUREG/CR-6850 EPRI/NRC fire PRA methodology. The fire PRA modeling included calculation of fire severity factors (SFs) and fire non-suppression probabilities (PNS) for each safe shutdown (SSD) component considered in the fire PRA model. The SFs were developed by performing detailed fire modeling through a combination of CFAST fire zone model calculations and Latin Hypercube Sampling (LHS). Component damage times and automatic fire suppression system actuation times calculated in the CFAST LHS analyses were then input to a time-dependent model of fire non-suppression probability. The fire non-suppression probability model is based on the modeling approach outlined in NUREG/CR-6850 and is supplemented with plant specific data. This paper presents the methodology used in the DOE facility fire PRA for modeling fire-induced SSD component failures and includes discussions of modeling techniques for: Development of time-dependent fire heat release rate profiles (required as input to CFAST), Calculation of fire severity factors based on CFAST detailed fire modeling, and Calculation of fire non-suppression probabilities.

  15. Short-term responses of reptile assemblages to fire in native and weedy tropical savannah

    Directory of Open Access Journals (Sweden)

    Rickard Abom

    2016-04-01

    Full Text Available Fire is frequently used as a management tool to reduce the cover of weeds, to reduce the amount of fuel available for future fires, and to create succession mosaics that may enhance biodiversity. We determined the influence of fire on wildlife, by quantifying reptile assemblage composition in response to fire in a weedy environment characterised by very short-term fire return intervals (<2 years. We used reptiles because they are often understudied, and are only moderately vagile compared to other vertebrates, and they respond strongly to changes in vegetation structure. We repeatedly sampled 24 replicate sampling sites after they had been unburned for two years, just prior to burning (pre-burnt, just after burning (post-burnt, and up to 15 months after burning (revegetated and monitored vegetation structure and reptile richness, abundance and assemblage composition. Our sites were not spatially auto-correlated, and were covered by native kangaroo grass (Themeda triandra, black spear grass (Heteropogon contortus, or an invasive weed (grader grass, Themeda quadrivalvis. Reptile abundance and richness were highest when sites had been unburned for 2 years, and greatly reduced in all areas post burning. The lowest reptile abundances occurred in sites dominated by the weed. Reptile abundance and richness had recovered in all grass types 15 months after burning, but assemblage composition changed. Some species were present only in before our focus fire in native grass, and their populations did not recover even 15 months post-burning. Even in fire-prone, often-burnt habitats such as our study sites, in which faunal richness and abundance were not strongly influenced by fire, reptile assemblage composition was altered. To maintain faunal biodiversity in fire-prone systems, we suggest reducing the frequency of prescribed fires, and (if possible excluding fire from weedy invasions if it allows native grasses to return.

  16. Evaluating fire danger in Brazilian biomes: present and future patterns

    Science.gov (United States)

    Silva, Patrícia; Bastos, Ana; DaCamara, Carlos; Libonati, Renata

    2017-04-01

    Climate change is expected to have a significant impact on fire occurrence and activity, particularly in Brazil, a region known to be fire-prone [1]. The Brazilian savanna, commonly referred to as cerrado, is a fire-adapted biome covering more than 20% of the country's total area. It presents the highest numbers of fire events, making it particularly susceptible to changes in climate. It is thus essential to understand the present fire regimes in Brazilian biomes, in order to better evaluate future patterns. The CPTEC/INPE, the Brazilian Center for Weather Forecasting and Climate Research at the Brazilian National Institute of Space Research developed a fire danger index based on the occurrence of hundreds of thousands of fire events in the main Brazilian biomes [2]: the Meteorological Fire Danger Index (MFDI). This index indicates the predisposition of vegetation to be burned on a given day, for given climate conditions preceding that day. It relies on daily values of air temperature, relative humidity, accumulated precipitation and vegetation cover. In this study we aim to access the capability of the MFDI to accurately replicate present fire conditions for different biomes, with a special focus on cerrado. To this end, we assess the link between the MFDI as calculated by three different reanalysis (ERA-Interim, NCEP/DOE Reanalysis 2 and MERRA-2) and the observed burned area. We further calculate the validated MFDI using a regional climate model, the RCA4 as forced by EC-Earth from CORDEX, to understand the ability of the model to characterize present fire danger. Finally, the need to calibrate the model to better characterize future fire danger was also evaluated. This work was developed within the framework of the Brazilian Fire-Land-Atmosphere System (BrFLAS) Project financed by the Portuguese and Brazilian science foundations, FCT and FAPESP (project references FAPESP/1389/2014 and 2014/20042-2). [1] KRAWCHUK, M.A.; MORITZ, M.A.; PARISIEN, M.A.; VAN DORN, J

  17. A review of fire interactions and mass fires

    Science.gov (United States)

    Mark A. Finney; Sara S. McAllister

    2011-01-01

    The character of a wildland fire can change dramatically in the presence of another nearby fire. Understanding and predicting the changes in behavior due to fire-fire interactions cannot only be life-saving to those on the ground, but also be used to better control a prescribed fire to meet objectives. In discontinuous fuel types, such interactions may elicit fire...

  18. X-irradiation affects all DNA replication intermediates when inhibiting replication initiation

    International Nuclear Information System (INIS)

    Loenn, U.; Karolinska Hospital, Stockholm

    1982-01-01

    When a human melanoma line was irradiated with 10 Gy, there was, after 30 to 60 min, a gradual reduction in the DNA replication rate. Ten to twelve hours after the irradiation, the DNA replication had returned to near normal rate. The results showed tht low dose-rate X-irradiation inhibits preferentially the formation of small DNA replication intermediates. There is no difference between the inhibition of these replication intermediates formed only in the irradiated cells and those formed also in untreated cells. (U.K.)

  19. Fire characteristics charts for fire behavior and U.S. fire danger rating

    Science.gov (United States)

    Faith Ann Heinsch; Pat Andrews

    2010-01-01

    The fire characteristics chart is a graphical method of presenting U.S. National Fire Danger Rating indices or primary surface or crown fire behavior characteristics. A desktop computer application has been developed to produce fire characteristics charts in a format suitable for inclusion in reports and presentations. Many options include change of scales, colors,...

  20. Prelife catalysts and replicators

    OpenAIRE

    Ohtsuki, Hisashi; Nowak, Martin A.

    2009-01-01

    Life is based on replication and evolution. But replication cannot be taken for granted. We must ask what there was prior to replication and evolution. How does evolution begin? We have proposed prelife as a generative system that produces information and diversity in the absence of replication. We model prelife as a binary soup of active monomers that form random polymers. ‘Prevolutionary’ dynamics can have mutation and selection prior to replication. Some sequences might have catalytic acti...

  1. Collaborative Strategic Reading: Replications with Consideration of the Role of Fidelity

    Science.gov (United States)

    Vaughn, Sharon; Roberts, Greg; Reutebuch, Colleen

    2013-01-01

    Collaborative Strategic Reading (CSR) is a multicomponent reading intervention aimed at improving students' text comprehension. Two 1-year randomized controlled trials were conducted to determine the efficacy of CSR with seventh and eighth grade students. The Year 2 replication study was identical to the original Year 1 study except that the…

  2. Rhythmic Engagement with Music in Early Childhood: A Replication and Extension

    Science.gov (United States)

    Ilari, Beatriz

    2015-01-01

    The purpose of this study was to replicate and extend previous findings on spontaneous movement and rhythmic engagement with music in infancy. Using the identical stimuli and procedures from the original study, I investigated spontaneous rhythmic movements in response to music, infant-directed speech, and contrasting rhythmic patterns in 30…

  3. Data from Investigating Variation in Replicability: A “Many Labs” Replication Project

    Directory of Open Access Journals (Sweden)

    Richard A. Klein

    2014-04-01

    Full Text Available This dataset is from the Many Labs Replication Project in which 13 effects were replicated across 36 samples and over 6,000 participants. Data from the replications are included, along with demographic variables about the participants and contextual information about the environment in which the replication was conducted. Data were collected in-lab and online through a standardized procedure administered via an online link. The dataset is stored on the Open Science Framework website. These data could be used to further investigate the results of the included 13 effects or to study replication and generalizability more broadly.

  4. Fire protection and fire fighting in nuclear installations

    International Nuclear Information System (INIS)

    1989-01-01

    Fires are a threat to all technical installations. While fire protection has long been a well established conventional discipline, its application to nuclear facilities requires special considerations. Nevertheless, for a long time fire engineering has been somewhat neglected in the design and operation of nuclear installations. In the nuclear industry, the Browns Ferry fire in 1975 brought about an essential change in the attention paid to fire problems. Designers and plant operators, as well as insurance companies and regulators, increased their efforts to develop concepts and methods for reducing fire risks, not only to protect the capital investment in nuclear plants but also to consider the potential secondary effects which could lead to nuclear accidents. Although the number of fires in nuclear installations is still relatively large, their overall importance to the safety of nuclear power plants was not considered to be very high. Only more recently have probabilistic analyses changed this picture. The results may well have to be taken into account more carefully. Various aspects of fire fighting and fire protection were discussed during the Symposium, the first of its kind to be organized by the IAEA. It was convened in co-operation with several organizations working in the nuclear or fire protection fields. The intention was to gather experts from nuclear engineering areas and the conventional fire protection field at one meeting with a view to enhancing the exchange of information and experience and to presenting current knowledge on the various disciplines involved. The presentations at the meeting were subdivided into eight sessions: standards and licensing (6 papers); national fire safety practices (7 papers); fire safety by design (11 papers); fire fighting (2 papers); computer fire modeling (7 papers); fire safety in fuel center facilities (7 papers); fire testing of materials (3 papers); fire risk assessment (5 papers). A separate abstract was

  5. Resolving vorticity-driven lateral fire spread using the WRF-Fire coupled atmosphere–fire numerical model

    OpenAIRE

    Simpson, C. C.; Sharples, J. J.; Evans, J. P.

    2014-01-01

    Fire channelling is a form of dynamic fire behaviour, during which a wildland fire spreads rapidly across a steep lee-facing slope in a direction transverse to the background winds, and is often accompanied by a downwind extension of the active flaming region and extreme pyro-convection. Recent work using the WRF-Fire coupled atmosphere-fire model has demonstrated that fire channelling can be characterised as vorticity-driven lateral fire spread (VDLS). In t...

  6. Post-fire soil functionality and microbial community structure in a Mediterranean shrubland subjected to experimental drought.

    Science.gov (United States)

    Hinojosa, M Belén; Parra, Antonio; Laudicina, Vito Armando; Moreno, José M

    2016-12-15

    Fire may cause significant alterations in soil properties. Post-fire soil dynamics can vary depending, among other factors, on rainfall patterns. However, little is known regarding variations in response to post-fire drought. This is relevant in arid and semiarid areas with poor soils, like much of the western Mediterranean. Furthermore, climate change projections in such areas anticipate reduced precipitation and longer annual drought periods, together with an increase in fire severity and frequency. This research evaluates the effects of experimental drought after fire on soil dynamics of a Cistus-Erica shrubland (Central Spain). A replicated (n=4) field experiment was conducted in which the total rainfall and its patterns were manipulated by means of a rain-out shelters and irrigation system. The treatments were: environmental control (natural rainfall), historical control (average rainfall, 2months drought), moderate drought (25% reduction of historical control, 5months drought) and severe drought (45% reduction, 7months drought). After one growing season under these rainfall treatments, the plots were burned. One set of unburned plots under natural rainfall served as an additional control. Soils were collected seasonally. Fire increased soil P and N availability. Post-fire drought treatments reduced available soil P but increased N concentration (mainly nitrate). Fire reduced available K irrespective of drought treatments. Fire reduced enzyme activities and carbon mineralization rate, a reduction that was higher in post-fire drought-treated soils. Fire decreased soil microbial biomass and the proportion of fungi, while that of actinomycetes increased. Post-fire drought decreased soil total microbial biomass and fungi, with bacteria becoming more abundant. Our results support that increasing drought after fire could compromise the resilience of Mediterranean ecosystems to fire. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Sensitivity Analysis on Fire Modeling of Main Control Board Fire Using Fire Dynamics Simulator

    International Nuclear Information System (INIS)

    Kang, Dae Il; Lim, Ho Gon

    2015-01-01

    In this study, sensitivity analyses for an MCB fire were performed to identify the effects on the MCR forced abandonment time according to the changes of height and number for fire initiation places. Hanul Unit 3 NPP was selected as a reference plant for this study. In this study, sensitivity analyses for an MCB fire were performed to identify the effects on the MCR forced abandonment time according to the changes of height and number of fire initiation places. A main control board (MCB) fire can cause a forced main control room (MCR) abandonment of the operators as well as the function failures or spurious operations of the control and instrumentation-related components. If the MCR cannot be habitable, a safe shutdown from outside the MCR can be achieved and maintained at an alternate shutdown panel independent from the MCR. When the fire modeling for an electrical cabinet such as an MCB was performed, its many input parameters can affect the fire simulation results. This study results showed that the decrease in the height of fire ignition place and the use of single fire ignition place in fire modeling for the propagating fire shortened MCR abandonment time

  8. Sensitivity Analysis on Fire Modeling of Main Control Board Fire Using Fire Dynamics Simulator

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Dae Il; Lim, Ho Gon [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2015-10-15

    In this study, sensitivity analyses for an MCB fire were performed to identify the effects on the MCR forced abandonment time according to the changes of height and number for fire initiation places. Hanul Unit 3 NPP was selected as a reference plant for this study. In this study, sensitivity analyses for an MCB fire were performed to identify the effects on the MCR forced abandonment time according to the changes of height and number of fire initiation places. A main control board (MCB) fire can cause a forced main control room (MCR) abandonment of the operators as well as the function failures or spurious operations of the control and instrumentation-related components. If the MCR cannot be habitable, a safe shutdown from outside the MCR can be achieved and maintained at an alternate shutdown panel independent from the MCR. When the fire modeling for an electrical cabinet such as an MCB was performed, its many input parameters can affect the fire simulation results. This study results showed that the decrease in the height of fire ignition place and the use of single fire ignition place in fire modeling for the propagating fire shortened MCR abandonment time.

  9. Safety improvements made at the Loviisa nuclear power plant to reduce fire risks originating from the turbine generators

    International Nuclear Information System (INIS)

    Virolainen, T.; Marttila, J.; Aulamo, H.

    1998-01-01

    Comprehensive upgrading measures have been completed for the Loviisa Nuclear Power Plant (modified VVER440/V213). These were carried out from the start of the design phase and during operation to ensure safe plant shutdown in the event of a large turbine generator oil fire. These modifications were made mainly on a deterministic basis according to specific risk studies and fire analyses. As part of the probabilistic safety assessment, a fire risk analysis was made that confirmed the importance of these upgrading measures. In fact, they should be considered as design basis modifications for all VVER440 plants. (author)

  10. Land surveys show regional variability of historical fire regimes and dry forest structure of the western United States.

    Science.gov (United States)

    Baker, William L; Williams, Mark A

    2018-03-01

    An understanding of how historical fire and structure in dry forests (ponderosa pine, dry mixed conifer) varied across the western United States remains incomplete. Yet, fire strongly affects ecosystem services, and forest restoration programs are underway. We used General Land Office survey reconstructions from the late 1800s across 11 landscapes covering ~1.9 million ha in four states to analyze spatial variation in fire regimes and forest structure. We first synthesized the state of validation of our methods using 20 modern validations, 53 historical cross-validations, and corroborating evidence. These show our method creates accurate reconstructions with low errors. One independent modern test reported high error, but did not replicate our method and made many calculation errors. Using reconstructed parameters of historical fire regimes and forest structure from our validated methods, forests were found to be non-uniform across the 11 landscapes, but grouped together in three geographical areas. Each had a mixture of fire severities, but dominated by low-severity fire and low median tree density in Arizona, mixed-severity fire and intermediate to high median tree density in Oregon-California, and high-severity fire and intermediate median tree density in Colorado. Programs to restore fire and forest structure could benefit from regional frameworks, rather than one size fits all. © 2018 by the Ecological Society of America.

  11. Functions of Ubiquitin and SUMO in DNA Replication and Replication Stress

    Science.gov (United States)

    García-Rodríguez, Néstor; Wong, Ronald P.; Ulrich, Helle D.

    2016-01-01

    Complete and faithful duplication of its entire genetic material is one of the essential prerequisites for a proliferating cell to maintain genome stability. Yet, during replication DNA is particularly vulnerable to insults. On the one hand, lesions in replicating DNA frequently cause a stalling of the replication machinery, as most DNA polymerases cannot cope with defective templates. This situation is aggravated by the fact that strand separation in preparation for DNA synthesis prevents common repair mechanisms relying on strand complementarity, such as base and nucleotide excision repair, from working properly. On the other hand, the replication process itself subjects the DNA to a series of hazardous transformations, ranging from the exposure of single-stranded DNA to topological contortions and the generation of nicks and fragments, which all bear the risk of inducing genomic instability. Dealing with these problems requires rapid and flexible responses, for which posttranslational protein modifications that act independently of protein synthesis are particularly well suited. Hence, it is not surprising that members of the ubiquitin family, particularly ubiquitin itself and SUMO, feature prominently in controlling many of the defensive and restorative measures involved in the protection of DNA during replication. In this review we will discuss the contributions of ubiquitin and SUMO to genome maintenance specifically as they relate to DNA replication. We will consider cases where the modifiers act during regular, i.e., unperturbed stages of replication, such as initiation, fork progression, and termination, but also give an account of their functions in dealing with lesions, replication stalling and fork collapse. PMID:27242895

  12. Fire protection

    International Nuclear Information System (INIS)

    Janetzky, E.

    1980-01-01

    Safety and fire prevention measurements have to be treated like the activities developing, planning, construction and erection. Therefore it is necessary that these measurements have to be integrated into the activities mentioned above at an early stage in order to guarantee their effectiveness. With regard to fire accidents the statistics of the insurance companies concerned show that the damage caused increased in the last years mainly due to high concentration of material. Organization of fire prevention and fire fighting, reasons of fire break out, characteristics and behaviour of fire, smoke and fire detection, smoke and heat venting, fire extinguishers (portable and stationary), construction material in presence of fire, respiratory protection etc. will be discussed. (orig./RW)

  13. Systems and models of fire blight (Erwinia amylovora prediction

    Directory of Open Access Journals (Sweden)

    Krzysztof Kielak

    2013-12-01

    Full Text Available The paper presents fire blight prediction models and systems, developed in Europe (system Billing - versions: BOS, BRS, BIS95 and originated from this system: Firescreen, FEUERBRA and ANLAFBRA and in United States (Californian system, model Maryblyt and system Cougarblight. Use of above models and systems in various climatic-geographic conditions and comparison of obtained prognostic data to real fire blight occurrence is reviewed. The newest trends in research on improvement of prognostic analyses parameters with their adjustment to particular conditions and consideration of infection source occurrence are also presented.

  14. NACSA Charter School Replication Guide: The Spectrum of Replication Options. Authorizing Matters. Replication Brief 1

    Science.gov (United States)

    O'Neill, Paul

    2010-01-01

    One of the most important and high-profile issues in public education reform today is the replication of successful public charter school programs. With more than 5,000 failing public schools in the United States, there is a tremendous need for strong alternatives for parents and students. Replicating successful charter school models is an…

  15. Evidence of fuels management and fire weather influencing fire severity in an extreme fire event.

    Science.gov (United States)

    Lydersen, Jamie M; Collins, Brandon M; Brooks, Matthew L; Matchett, John R; Shive, Kristen L; Povak, Nicholas A; Kane, Van R; Smith, Douglas F

    2017-10-01

    Following changes in vegetation structure and pattern, along with a changing climate, large wildfire incidence has increased in forests throughout the western United States. Given this increase, there is great interest in whether fuels treatments and previous wildfire can alter fire severity patterns in large wildfires. We assessed the relative influence of previous fuels treatments (including wildfire), fire weather, vegetation, and water balance on fire-severity in the Rim Fire of 2013. We did this at three different spatial scales to investigate whether the influences on fire severity changed across scales. Both fuels treatments and previous low to moderate-severity wildfire reduced the prevalence of high-severity fire. In general, areas without recent fuels treatments and areas that previously burned at high severity tended to have a greater proportion of high-severity fire in the Rim Fire. Areas treated with prescribed fire, especially when combined with thinning, had the lowest proportions of high severity. The proportion of the landscape burned at high severity was most strongly influenced by fire weather and proportional area previously treated for fuels or burned by low to moderate severity wildfire. The proportion treated needed to effectively reduce the amount of high severity fire varied by spatial scale of analysis, with smaller spatial scales requiring a greater proportion treated to see an effect on fire severity. When moderate and high-severity fire encountered a previously treated area, fire severity was significantly reduced in the treated area relative to the adjacent untreated area. Our results show that fuels treatments and low to moderate-severity wildfire can reduce fire severity in a subsequent wildfire, even when burning under fire growth conditions. These results serve as further evidence that both fuels treatments and lower severity wildfire can increase forest resilience. © 2017 by the Ecological Society of America.

  16. Evacuation of a mental health center during a forest fire in Israel.

    Science.gov (United States)

    Kreinin, Anatoly; Shakera, Tatiana; Sheinkman, Ayala; Levi, Tamar; Tal, Vered; Polakiewicz, Jacob

    2014-08-01

    Tirat Carmel Mental Health Center was successfully evacuated in December 2010 during a ravaging forest fire in the nearby Carmel Mountains. A total of 228 patients were successfully evacuated from the center within 45 minutes. No fatalities or injuries associated with the evacuation occurred. We believe that the efficient functioning of the administrative and medical staff provides a replicable model that can contribute to the level of awareness and readiness of hospital staff members for natural and manmade disasters.

  17. DNA replication restart and cellular dynamics of Hef helicase/nuclease protein in Haloferax volcanii.

    Science.gov (United States)

    Lestini, Roxane; Delpech, Floriane; Myllykallio, Hannu

    2015-11-01

    Understanding how frequently spontaneous replication arrests occur and how archaea deal with these arrests are very interesting and challenging research topics. Here we will described how genetic and imaging studies have revealed the central role of the archaeal helicase/nuclease Hef belonging to the XPF/MUS81/FANCM family of endonucleases in repair of arrested replication forks. Special focus will be on description of a recently developed combination of genetic and imaging tools to study the dynamic localization of a functional Hef::GFP (Green Fluorescent Protein) fusion protein in the living cells of halophilic archaea Haloferax volcanii. As Archaea provide an excellent and unique model for understanding how DNA replication is regulated to allow replication of a circular DNA molecule either from single or multiple replication origins, we will also summarize recent studies that have revealed peculiar features regarding DNA replication, particularly in halophilic archaea. We strongly believe that fundamental knowledge of our on-going studies will shed light on the evolutionary history of the DNA replication machinery and will help to establish general rules concerning replication restart and the key role of recombination proteins not only in bacteria, yeast and higher eukaryotes but also in archaea. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  18. Sequential steps in DNA replication are inhibited to ensure reduction of ploidy in meiosis

    Science.gov (United States)

    Hua, Hui; Namdar, Mandana; Ganier, Olivier; Gregan, Juraj; Méchali, Marcel; Kearsey, Stephen E.

    2013-01-01

    Meiosis involves two successive rounds of chromosome segregation without an intervening S phase. Exit from meiosis I is distinct from mitotic exit, in that replication origins are not licensed by Mcm2-7 chromatin binding, but spindle disassembly occurs during a transient interphase-like state before meiosis II. The absence of licensing is assumed to explain the block to DNA replication, but this has not been formally tested. Here we attempt to subvert this block by expressing the licensing control factors Cdc18 and Cdt1 during the interval between meiotic nuclear divisions. Surprisingly, this leads only to a partial round of DNA replication, even when these factors are overexpressed and effect clear Mcm2-7 chromatin binding. Combining Cdc18 and Cdt1 expression with modulation of cyclin-dependent kinase activity, activation of Dbf4-dependent kinase, or deletion of the Spd1 inhibitor of ribonucleotide reductase has little additional effect on the extent of DNA replication. Single-molecule analysis indicates this partial round of replication results from inefficient progression of replication forks, and thus both initiation and elongation replication steps may be inhibited in late meiosis. In addition, DNA replication or damage during the meiosis I–II interval fails to arrest meiotic progress, suggesting absence of checkpoint regulation of meiosis II entry. PMID:23303250

  19. GINS complex protein Sld5 recruits SIK1 to activate MCM helicase during DNA replication.

    Science.gov (United States)

    Joshi, Kiranmai; Shah, Varun Jayeshkumar; Maddika, Subbareddy

    2016-12-01

    In eukaryotes, proper loading and activation of MCM helicase at chromosomal origins plays a central role in DNA replication. Activation of MCM helicase requires its association with CDC45-GINS complex, but the mechanism of how this complex activates MCM helicase is poorly understood. Here we identified SIK1 (salt-inducible kinase 1), an AMPK related protein kinase, as a molecular link that connects GINS complex with MCM helicase activity. We demonstrated that Sld5 a component of GINS complex interacts with SIK1 and recruits it to the sites of DNA replication at the onset of S phase. Depletion of SIK1 leads to defective DNA replication. Further, we showed that SIK1 phosphorylates MCM2 at five conserved residues at its N-terminus, which is essential for the activation of MCM helicase. Collectively, our results suggest SIK1 as a novel integral component of CMG replicative helicase during eukaryotic DNA replication. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Evidence that DNA polymerase δ contributes to initiating leading strand DNA replication in Saccharomyces cerevisiae.

    Science.gov (United States)

    Garbacz, Marta A; Lujan, Scott A; Burkholder, Adam B; Cox, Phillip B; Wu, Qiuqin; Zhou, Zhi-Xiong; Haber, James E; Kunkel, Thomas A

    2018-02-27

    To investigate nuclear DNA replication enzymology in vivo, we have studied Saccharomyces cerevisiae strains containing a pol2-16 mutation that inactivates the catalytic activities of DNA polymerase ε (Pol ε). Although pol2-16 mutants survive, they present very tiny spore colonies, increased doubling time, larger than normal cells, aberrant nuclei, and rapid acquisition of suppressor mutations. These phenotypes reveal a severe growth defect that is distinct from that of strains that lack only Pol ε proofreading (pol2-4), consistent with the idea that Pol ε is the major leading-strand polymerase used for unstressed DNA replication. Ribonucleotides are incorporated into the pol2-16 genome in patterns consistent with leading-strand replication by Pol δ when Pol ε is absent. More importantly, ribonucleotide distributions at replication origins suggest that in strains encoding all three replicases, Pol δ contributes to initiation of leading-strand replication. We describe two possible models.

  1. Laboratory fire behavior measurements of chaparral crown fire

    Science.gov (United States)

    C. Sanpakit; S. Omodan; D. Weise; M Princevac

    2015-01-01

    In 2013, there was an estimated 9,900 wildland fires that claimed more than 577,000 acres of land. That same year, about 542 prescribed fires were used to treat 48,554 acres by several agencies in California. Being able to understand fires using laboratory models can better prepare individuals to combat or use fires. Our research focused on chaparral crown fires....

  2. Wildland fire in ecosystems: effects of fire on flora

    Science.gov (United States)

    James K. Brown; Jane Kapler Smith

    2000-01-01

    VOLUME 2: This state-of-knowledge review about the effects of fire on flora and fuels can assist land managers with ecosystem and fire management planning and in their efforts to inform others about the ecological role of fire. Chapter topics include fire regime classification, autecological effects of fire, fire regime characteristics and postfire plant community...

  3. Hydroxyurea-Induced Replication Stress

    Directory of Open Access Journals (Sweden)

    Kenza Lahkim Bennani-Belhaj

    2010-01-01

    Full Text Available Bloom's syndrome (BS displays one of the strongest known correlations between chromosomal instability and a high risk of cancer at an early age. BS cells combine a reduced average fork velocity with constitutive endogenous replication stress. However, the response of BS cells to replication stress induced by hydroxyurea (HU, which strongly slows the progression of replication forks, remains unclear due to publication of conflicting results. Using two different cellular models of BS, we showed that BLM deficiency is not associated with sensitivity to HU, in terms of clonogenic survival, DSB generation, and SCE induction. We suggest that surviving BLM-deficient cells are selected on the basis of their ability to deal with an endogenous replication stress induced by replication fork slowing, resulting in insensitivity to HU-induced replication stress.

  4. Origins of gene, genetic code, protein and life: comprehensive view ...

    Indian Academy of Sciences (India)

    Unknown

    production, suggesting that proteins were originally produced by random peptide formation of amino acids restricted in specific amino acid compositions .... using random numbers by a computer, to confirm whether main chains of ...... world on the origin of life by the pseudo-replication of. [GADV]-proteins in the absence of ...

  5. The importance of fire simulation in fire prediction

    Directory of Open Access Journals (Sweden)

    Jevtić Radoje B.

    2014-01-01

    Full Text Available The appearance of fire in objects with lot of humans inside represents very possible real situation that could be very danger and could cause destructive consequences on human lives and material properties. Very important influence in fire prediction, fire protection, human and material properties safety could be a fire simulation in object. This simulation could give many useful information of possible fire propagation; possible and existed evacuation routes; possible and exited placing of fire, smoke, temperature conditions in object and many other information of crucial importance for human lives and material properties, such as the best places for sensors position, optimal number of sensors, projection of possible evacuation routes etc. There are many different programs for fire simulation. This paper presents complete fire simulation in Electrotechnical school Nikola Tesla in Niš in FDS.

  6. Replication of swine and human influenza viruses in juvenile and layer turkey hens.

    Science.gov (United States)

    Ali, Ahmed; Yassine, Hadi; Awe, Olusegun O; Ibrahim, Mahmoud; Saif, Yehia M; Lee, Chang-Won

    2013-04-12

    Since the first reported isolation of swine influenza viruses (SIVs) in turkeys in the 1980s, transmission of SIVs to turkeys was frequently documented. Recently, the 2009 pandemic H1N1 virus, that was thought to be of swine origin, was detected in turkeys with a severe drop in egg production. In this study, we assessed the infectivity of different mammalian influenza viruses including swine, pandemic H1N1 and seasonal human influenza viruses in both juvenile and layer turkeys. In addition, we investigated the potential influenza virus dissemination in the semen of experimentally infected turkey toms. Results showed that all mammalian origin influenza viruses tested can infect turkeys. SIVs were detected in respiratory and digestive tracts of both juvenile and layer turkeys. Variations in replication efficiencies among SIVs were observed especially in the reproductive tract of layer turkeys. Compared to SIVs, limited replication of seasonal human H1N1 and no detectable replication of recent human-like swine H1N2, pandemic H1N1 and seasonal human H3N2 viruses was noticed. All birds seroconverted to all tested viruses regardless of their replication level. In turkey toms, we were able to detect swine H3N2 virus in semen and reproductive tract of infected toms by real-time RT-PCR although virus isolation was not successful. These data suggest that turkey hens could be affected by diverse influenza strains especially SIVs. Moreover, the differences in the replication efficiency we demonstrated among SIVs and between SIV and human influenza viruses in layer turkeys suggest a possible use of turkeys as an animal model to study host tropism and pathogenesis of influenza viruses. Our results also indicate a potential risk of venereal transmission of influenza viruses in turkeys. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. RTEL1 is a replisome-associated helicase that promotes telomere and genome-wide replication.

    Science.gov (United States)

    Vannier, Jean-Baptiste; Sandhu, Sumit; Petalcorin, Mark I R; Wu, Xiaoli; Nabi, Zinnatun; Ding, Hao; Boulton, Simon J

    2013-10-11

    Regulator of telomere length 1 (RTEL1) is an essential DNA helicase that disassembles telomere loops (T loops) and suppresses telomere fragility to maintain the integrity of chromosome ends. We established that RTEL1 also associates with the replisome through binding to proliferating cell nuclear antigen (PCNA). Mouse cells disrupted for the RTEL1-PCNA interaction (PIP mutant) exhibited accelerated senescence, replication fork instability, reduced replication fork extension rates, and increased origin usage. Although T-loop disassembly at telomeres was unaffected in the mutant cells, telomere replication was compromised, leading to fragile sites at telomeres. RTEL1-PIP mutant mice were viable, but loss of the RTEL1-PCNA interaction accelerated the onset of tumorigenesis in p53-deficient mice. We propose that RTEL1 plays a critical role in both telomere and genome-wide replication, which is crucial for genetic stability and tumor avoidance.

  8. Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli.

    Science.gov (United States)

    Kato , J; Katayama, T

    2001-08-01

    The bacterial DnaA protein binds to the chromosomal origin of replication to trigger a series of initiation reactions, which leads to the loading of DNA polymerase III. In Escherichia coli, once this polymerase initiates DNA synthesis, ATP bound to DnaA is efficiently hydrolyzed to yield the ADP-bound inactivated form. This negative regulation of DnaA, which occurs through interaction with the beta-subunit sliding clamp configuration of the polymerase, functions in the temporal blocking of re-initiation. Here we show that the novel DnaA-related protein, Hda, from E.coli is essential for this regulatory inactivation of DnaA in vitro and in vivo. Our results indicate that the hda gene is required to prevent over-initiation of chromosomal replication and for cell viability. Hda belongs to the chaperone-like ATPase family, AAA(+), as do DnaA and certain eukaryotic proteins essential for the initiation of DNA replication. We propose that the once-per-cell-cycle rule of replication depends on the timely interaction of AAA(+) proteins that comprise the apparatus regulating the activity of the initiator of replication.

  9. Rif1 acts through Protein Phosphatase 1 but independent of replication timing to suppress telomere extension in budding yeast.

    Science.gov (United States)

    Kedziora, Sylwia; Gali, Vamsi K; Wilson, Rosemary H C; Clark, Kate R M; Nieduszynski, Conrad A; Hiraga, Shin-Ichiro; Donaldson, Anne D

    2018-05-04

    The Rif1 protein negatively regulates telomeric TG repeat length in the budding yeast Saccharomyces cerevisiae, but how it prevents telomere over-extension is unknown. Rif1 was recently shown to control DNA replication by acting as a Protein Phosphatase 1 (PP1)-targeting subunit. Therefore, we investigated whether Rif1 controls telomere length by targeting PP1 activity. We find that a Rif1 mutant defective for PP1 interaction causes a long-telomere phenotype, similar to that of rif1Δ cells. Tethering PP1 at a specific telomere partially substitutes for Rif1 in limiting TG repeat length, confirming the importance of PP1 in telomere length control. Ablating Rif1-PP1 interaction is known to cause precocious activation of telomere-proximal replication origins and aberrantly early telomere replication. However, we find that Rif1 still limits telomere length even if late replication is forced through deletion of nearby replication origins, indicating that Rif1 can control telomere length independent of replication timing. Moreover we find that, even at a de novo telomere created after DNA synthesis during a mitotic block, Rif1-PP1 interaction is required to suppress telomere lengthening and prevent inappropriate recruitment of Tel1 kinase. Overall, our results show that Rif1 controls telomere length by recruiting PP1 to directly suppress telomerase-mediated TG repeat lengthening.

  10. Adsorber fires

    International Nuclear Information System (INIS)

    Holmes, W.

    1987-01-01

    The following conclusions are offered with respect to activated charcoal filter systems in nuclear power plants: (1) The use of activated charcoal in nuclear facilities presents a potential for deep-seated fires. (2) The defense-in-depth approach to nuclear fire safety requires that if an ignition should occur, fires must be detected quickly and subsequently suppressed. (3) Deep-seated fires in charcoal beds are difficult to extinguish. (4) Automatic water sprays can be used to extinguish fires rapidly and reliably when properly introduced into the burning medium. The second part of the conclusions offered are more like challenges: (1) The problem associated with inadvertent actuations of fire protection systems is not a major one, and it can be reduced further by proper design review, installation, testing, and maintenance. Eliminating automatic fire extinguishing systems for the protection of charcoal adsorbers is not justified. (2) Removal of automatic fire protection systems due to fear of inadvertent fire protection system operation is a case of treating the effect rather than the cause. On the other hand, properly maintaining automatic fire protection systems will preserve the risk of fire loss at acceptable levels while at the same time reducing the risk of damage presented by inadvertent operation of fire protection systems

  11. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  12. The Acid Test for Biological Science: STAP Cells, Trust, and Replication.

    Science.gov (United States)

    Lancaster, Cheryl

    2016-02-01

    In January 2014, a letter and original research article were published in Nature describing a process whereby somatic mouse cells could be converted into stem cells by subjecting them to stress. These "stimulus-triggered acquisition of pluripotency" (STAP) cells were shown to be capable of contributing to all cell types of a developing embryo, and extra-embryonic tissues. The lead author of the publications, Haruko Obokata, became an overnight celebrity in Japan, where she was dubbed the new face of Japanese science. However, in the weeks that followed publication of the research, issues arose. Other laboratories and researchers (including authors on the original papers) found that they were unable to replicate Obokata et al.'s work. Closer scrutiny of the papers by the scientific community also suggested that there was manipulation of images that had been published, and Obokata was accused of misconduct. Those who should have been supervising her work (also her co-authors on the publications) were also heavily criticised. The STAP cell saga of 2014 is used as an example to highlight the importance of trust and replication in twenty-first century biological science. The role of trust in the scientific community is highlighted, and the effects on interactions between science and the public examined. Similarly, this essay aims to highlight the importance of replication, and how this is understood by researchers, the media, and the public. The expected behaviour of scientists in the twenty-first century is now more closely scrutinised.

  13. Twenty Years After the 1988 Yellowstone Fires: Lessons About Disturbance and Ecosystems

    Science.gov (United States)

    Romme, W.H.; Boyce, M.S.; Gresswell, R.; Merrill, E.H.; Minshall, G.W.; Whitlock, C.; Turner, M.G.

    2011-01-01

    The 1988 Yellowstone fires were among the first in what has proven to be an upsurge in large severe fires in the western USA during the past 20 years. At the time of the fires, little was known about the impacts of such a large severe disturbance because scientists had had few previous opportunities to study such an event. Ecologists predicted short- and long-term effects of the 1988 fires on vegetation, biogeochemistry, primary productivity, wildlife, and aquatic ecosystems based on scientific understanding of the time. Twenty-plus years of subsequent study allow these early predictions to be evaluated. Most of the original predictions were at least partially supported, but some predictions were refuted, others nuanced, and a few postfire phenomena were entirely unexpected. Post-1988 Yellowstone studies catalyzed advances in ecology focused on the importance of spatial and temporal heterogeneity, contingent influences, and multiple interacting drivers. Post-1988 research in Yellowstone also has changed public perceptions of fire as an ecological process and attitudes towards fire management. Looking ahead to projected climate change and more frequent large fires, the well-documented ecological responses to the 1988 Yellowstone fires provide a foundation for detecting and evaluating potential changes in fire regimes of temperate mountainous regions. ?? 2011 Springer Science+Business Media, LLC.

  14. On the Social Cost of Distributed Selfish Content Replication

    DEFF Research Database (Denmark)

    Pollatos, Gerasimos G.; Telelis, Orestis A.; Zissimopoulos, Vassilis

    2008-01-01

    We study distributed content replication networks formed voluntarily by selfish autonomous users, seeking access to information objects that originate form distant servers. Each user caters to minimization of its individual access cost by replicating locally (up to constrained storage capacity......) a subset of objects, and accessing the rest form the nearest possible location. We show existence of stable networks by proving existence of pure strategy Nash equilibria for a game-theoretic formulation of this situation. Social (overall) cost of stable networks is measured by the average...... or by the maximum access cost experienced by any user. We study socially most and least expensive stable networks by means of tight bounds on the ratios of the Price of Anarchy and Stability respectively. Although in the worst case the ratios may coincide, we identify cases where they differ significantly. We...

  15. A replication and methodological critique of the study "Evaluating drug trafficking on the Tor Network".

    Science.gov (United States)

    Munksgaard, Rasmus; Demant, Jakob; Branwen, Gwern

    2016-09-01

    The development of cryptomarkets has gained increasing attention from academics, including growing scientific literature on the distribution of illegal goods using cryptomarkets. Dolliver's 2015 article "Evaluating drug trafficking on the Tor Network: Silk Road 2, the Sequel" addresses this theme by evaluating drug trafficking on one of the most well-known cryptomarkets, Silk Road 2.0. The research on cryptomarkets in general-particularly in Dolliver's article-poses a number of new questions for methodologies. This commentary is structured around a replication of Dolliver's original study. The replication study is not based on Dolliver's original dataset, but on a second dataset collected applying the same methodology. We have found that the results produced by Dolliver differ greatly from our replicated study. While a margin of error is to be expected, the inconsistencies we found are too great to attribute to anything other than methodological issues. The analysis and conclusions drawn from studies using these methods are promising and insightful. However, based on the replication of Dolliver's study, we suggest that researchers using these methodologies consider and that datasets be made available for other researchers, and that methodology and dataset metrics (e.g. number of downloaded pages, error logs) are described thoroughly in the context of web-o-metrics and web crawling. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Risk assessment of main control board fire using fire dynamics simulator

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Dae Il, E-mail: dikang@kaeri.re.kr [KAERI, 1045 Daedeokdaero, Yuseong-Gu, Daejeon 305-353 (Korea, Republic of); Kim, Kilyoo; Jang, Seung-Cheol [KAERI, 1045 Daedeokdaero, Yuseong-Gu, Daejeon 305-353 (Korea, Republic of); Yoo, Seong Yeon [Chungnam National University, 79, Daehagro, Yuseong-Gu, Daejeon (Korea, Republic of)

    2015-08-15

    Highlights: • A decision tree for evaluating the risk of a main control board (MCB) fire was proposed to systematically determine the MCB fire scenarios. • Fire simulations using fire dynamics simulator (FDS) were performed to estimate the time to MCR abandonment. • Non-propagating and propagating fire scenarios were considered for fire simulations. • The current study indicates that the quantification of the MCB fire risk should address the propagating fire and non-propagating fire scenarios if the MCB has no internal barriers between the panels. - Abstract: This paper presents the process and results of a risk assessment for a main control board (MCB) fire using fire dynamics simulator (FDS). A decision tree for evaluating the risk of a MCB fire was proposed to systematically determine the MCB fire scenarios, and fire simulations using FDS were performed to estimate the time to MCR abandonment. As a reference NPP for this study, Hanul unit 3 in Korea was selected and its core damage frequency (CDF) owing to the MCB fire was quantified. Two types of fire scenarios were considered for fire simulations: non-propagating fire scenarios occurring within a single MCB panel and propagating fire scenarios spreading from one control panel to the adjacent panels. Further, the fire scenarios were classified into fires with and without a heating, ventilation, and air conditioning system (HVACS). The fire simulation results showed that the major factor causing the MCR evacuation was the optical density irrelevant to the availability of the HVACS. The risk assessment results showed that the abandonment fire scenario risk was less than the non-abandonment fire scenario risk and the propagating fire scenario risk was greater than the non-propagating fire scenario risk.

  17. Risk assessment of main control board fire using fire dynamics simulator

    International Nuclear Information System (INIS)

    Kang, Dae Il; Kim, Kilyoo; Jang, Seung-Cheol; Yoo, Seong Yeon

    2015-01-01

    Highlights: • A decision tree for evaluating the risk of a main control board (MCB) fire was proposed to systematically determine the MCB fire scenarios. • Fire simulations using fire dynamics simulator (FDS) were performed to estimate the time to MCR abandonment. • Non-propagating and propagating fire scenarios were considered for fire simulations. • The current study indicates that the quantification of the MCB fire risk should address the propagating fire and non-propagating fire scenarios if the MCB has no internal barriers between the panels. - Abstract: This paper presents the process and results of a risk assessment for a main control board (MCB) fire using fire dynamics simulator (FDS). A decision tree for evaluating the risk of a MCB fire was proposed to systematically determine the MCB fire scenarios, and fire simulations using FDS were performed to estimate the time to MCR abandonment. As a reference NPP for this study, Hanul unit 3 in Korea was selected and its core damage frequency (CDF) owing to the MCB fire was quantified. Two types of fire scenarios were considered for fire simulations: non-propagating fire scenarios occurring within a single MCB panel and propagating fire scenarios spreading from one control panel to the adjacent panels. Further, the fire scenarios were classified into fires with and without a heating, ventilation, and air conditioning system (HVACS). The fire simulation results showed that the major factor causing the MCR evacuation was the optical density irrelevant to the availability of the HVACS. The risk assessment results showed that the abandonment fire scenario risk was less than the non-abandonment fire scenario risk and the propagating fire scenario risk was greater than the non-propagating fire scenario risk

  18. The effect of intraoral suction on oxygen-enriched surgical environments: a mechanism for reducing the risk of surgical fires.

    Science.gov (United States)

    VanCleave, Andrea M; Jones, James E; McGlothlin, James D; Saxen, Mark A; Sanders, Brian J; Vinson, LaQuia A

    2014-01-01

    In this study, a mechanical model was applied in order to replicate potential surgical fire conditions in an oxygen-enriched environment with and without high-volume suction typical for dental surgical applications. During 41 trials, 3 combustion events were measured: an audible pop, a visible flash of light, and full ignition. In at least 11 of 21 trials without suction, all 3 conditions were observed, sometimes with an extent of fire that required early termination of the experimental trial. By contrast, in 18 of 20 with-suction trials, ignition did not occur at all, and in the 2 cases where ignition did occur, the fire was qualitatively a much smaller, candle-like flame. Statistically comparing these 3 combustion events in the no-suction versus with-suction trials, ignition (P = .0005), audible pop (P = .0211), and flash (P = .0092) were all significantly more likely in the no-suction condition. These results suggest a possible significant and new element to be added to existing surgical fire safety protocols toward making surgical fires the "never-events" they should be.

  19. Fire-Walking

    Science.gov (United States)

    Willey, David

    2010-01-01

    This article gives a brief history of fire-walking and then deals with the physics behind fire-walking. The author has performed approximately 50 fire-walks, took the data for the world's hottest fire-walk and was, at one time, a world record holder for the longest fire-walk (www.dwilley.com/HDATLTW/Record_Making_Firewalks.html). He currently…

  20. Forest-fire models

    Science.gov (United States)

    Haiganoush Preisler; Alan Ager

    2013-01-01

    For applied mathematicians forest fire models refer mainly to a non-linear dynamic system often used to simulate spread of fire. For forest managers forest fire models may pertain to any of the three phases of fire management: prefire planning (fire risk models), fire suppression (fire behavior models), and postfire evaluation (fire effects and economic models). In...

  1. Fire Perimeters

    Data.gov (United States)

    California Natural Resource Agency — The Fire Perimeters data consists of CDF fires 300 acres and greater in size and USFS fires 10 acres and greater throughout California from 1950 to 2003. Some fires...

  2. Fire History

    Data.gov (United States)

    California Natural Resource Agency — The Fire Perimeters data consists of CDF fires 300 acres and greater in size and USFS fires 10 acres and greater throughout California from 1950 to 2002. Some fires...

  3. Electronic firing systems and methods for firing a device

    Science.gov (United States)

    Frickey, Steven J [Boise, ID; Svoboda, John M [Idaho Falls, ID

    2012-04-24

    An electronic firing system comprising a control system, a charging system, an electrical energy storage device, a shock tube firing circuit, a shock tube connector, a blasting cap firing circuit, and a blasting cap connector. The control system controls the charging system, which charges the electrical energy storage device. The control system also controls the shock tube firing circuit and the blasting cap firing circuit. When desired, the control system signals the shock tube firing circuit or blasting cap firing circuit to electrically connect the electrical energy storage device to the shock tube connector or the blasting cap connector respectively.

  4. Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand.

    Science.gov (United States)

    Yasukawa, Takehiro; Reyes, Aurelio; Cluett, Tricia J; Yang, Ming-Yao; Bowmaker, Mark; Jacobs, Howard T; Holt, Ian J

    2006-11-15

    Using two-dimensional agarose gel electrophoresis, we show that mitochondrial DNA (mtDNA) replication of birds and mammals frequently entails ribonucleotide incorporation throughout the lagging strand (RITOLS). Based on a combination of two-dimensional agarose gel electrophoretic analysis and mapping of 5' ends of DNA, initiation of RITOLS replication occurs in the major non-coding region of vertebrate mtDNA and is effectively unidirectional. In some cases, conversion of nascent RNA strands to DNA starts at defined loci, the most prominent of which maps, in mammalian mtDNA, in the vicinity of the site known as the light-strand origin.

  5. Fire weather conditions and fire-atmosphere interactions observed during low-intensity prescribed fires - RxCADRE 2012

    Science.gov (United States)

    Craig B. Clements; Neil P. Lareau; Daisuke Seto; Jonathan Contezac; Braniff Davis; Casey Teske; Thomas J. Zajkowski; Andrew T. Hudak; Benjamin C. Bright; Matthew B. Dickinson; Bret W. Butler; Daniel Jimenez; J. Kevin. Hiers

    2016-01-01

    The role of fire-atmosphere coupling on fire behaviour is not well established, and to date few field observations have been made to investigate the interactions between fire spread and fire-induced winds. Therefore, comprehensive field observations are needed to better understand micrometeorological aspects of fire spread. To address this need, meteorological...

  6. Community participation in fire management planning: The Trinity county fire safe council's fire plan

    Science.gov (United States)

    Yvonne Everett

    2008-01-01

    In 1999, Trinity County CA, initiated a participatory fire management planning effort. Since that time, the Trinity County Fire Safe Council has completed critical portions of a fire safe plan and has begun to implement projects defined in the plan. Completion of a GIS based, landscape scale fuels reduction element in the plan defined by volunteer fire fighters, agency...

  7. Epoxy replication for Wolter x-ray microscope fabrication

    International Nuclear Information System (INIS)

    Priedhorsky, W.

    1981-01-01

    An epoxy replica of a test piece designed to simulate a Wolter x-ray microscope geometry showed no loss of x-ray reflectivity or resolution, compared to the original. The test piece was a diamond-turned cone with 1.5 0 half angle. A flat was fly-cut on one side, then super- and conventionally polished. The replica was separated at the 1.5 0 -draft angle, simulating a shallow angle Wolter microscope geometry. A test with 8.34 A x rays at 0.9 0 grazing angle showed a reflectivity of 67% for the replica flat surface, and 70% for the original. No spread of the reflected beam was observed with a 20-arc second wide test beam. This test verifies the epoxy replication technique for production of Wolter x-ray microscopes

  8. DNA moves sequentially towards the nuclear matrix during DNA replication in vivo

    Directory of Open Access Journals (Sweden)

    Aranda-Anzaldo Armando

    2011-01-01

    Full Text Available Abstract Background In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM. There is varied evidence indicating that DNA replication occurs in replication factories organized upon the NM and that DNA loops may correspond to the actual replicons in vivo. In normal rat liver the hepatocytes are arrested in G0 but they synchronously re-enter the cell cycle after partial-hepatectomy leading to liver regeneration in vivo. We have previously determined in quiescent rat hepatocytes that a 162 kbp genomic region containing members of the albumin gene family is organized into five structural DNA loops. Results In the present work we tracked down the movement relative to the NM of DNA sequences located at different points within such five structural DNA loops during the S phase and after the return to cellular quiescence during liver regeneration. Our results indicate that looped DNA moves sequentially towards the NM during replication and then returns to its original position in newly quiescent cells, once the liver regeneration has been achieved. Conclusions Looped DNA moves in a sequential fashion, as if reeled in, towards the NM during DNA replication in vivo thus supporting the notion that the DNA template is pulled progressively towards the replication factories on the NM so as to be replicated. These results provide further evidence that the structural DNA loops correspond to the actual replicons in vivo.

  9. Literature study regarding fire protection in nuclear power plants. Part I: Fire rated separations; Litteraturstudie angaaende brandskydd i kaernkraftverk. Del I: Brandteknisk separation

    Energy Technology Data Exchange (ETDEWEB)

    Isaksson, S [Swedish Testing and Research Inst., Boraas (Sweden)

    1995-06-01

    This literature study has been made on behalf of the Swedish Nuclear Power Inspectorate. The aim is to describe different aspects of fire protection in nuclear power plants. Conventional building codes can not give guidance on where to make fire rated separations in order to separate redundant trains of safety systems. The separation must originate in functional demands from the authorities on what functions are essential during and after a fire, and under what circumstances these functions shall be retained, i.e. the number of independent faults and initiating events. As a basic demand it is suggested to rate the strength of separations according to conventional building code, based on fire load. The whole separating construction shall have the same fire rating, including the ventilation system. Deviations from the basic demand can de done in case it can be proven that it is possible to compensate some or all of the fire rating with other measures. There is a general lack of statistical information regarding the reliability of fire separating constructions such as walls, fire doors, penetration seals and fire dampers. The amount of cables penetrating a seal is in many cases much higher in real installations than what has been tested for type approval. It would therefore be valuable to perform a furnace test with a more representative amount of cables passing through a penetration seal. Tests have shown that the 20 foot horizontal separation distance stipulated by NRC is not a guarantee against fire damage. Spatial separations based on general requirements shall not be allowed, but considered from case to case based on actual circumstances. For fire protection by isolation or coatings, it is of great importance to choose the method of protection carefully, to be compatible with the material it shall be applied on, and the environment and types of fire that may occur. 48 refs, 2 figs, 5 tabs.

  10. Characterization of the replication timing program of 6 human model cell lines

    Directory of Open Access Journals (Sweden)

    Djihad Hadjadj

    2016-09-01

    Full Text Available During the S-phase, the DNA replication process is finely orchestrated and regulated by two programs: the spatial program that determines where replication will start in the genome (Cadoret et al. (2008 Oct 14, Cayrou et al. (2011 Sep, Picard et al. (2014 May 1 [1–3], and the temporal program that determines when during the S phase different parts of the genome are replicated and when origins are activated. The temporal program is so well conserved for each cell type from independent individuals [4] that it is possible to identify a cell type from an unknown sample just by determining its replication timing program. Moreover, replicative domains are strongly correlated with the partition of the genome into topological domains (determined by the Hi-C method, Lieberman-Aiden et al. (2009 Oct 9, Pope et al. (2014 Nov 20 [5,6]. On the one hand, replicative areas are well defined and participate in shaping the spatial organization of the genome for a given cell type. On the other hand, studies on the timing program during cell differentiation showed a certain plasticity of this program according to the stage of cell differentiation Hiratani et al. (2008 Oct 7, 2010 Feb [7,8]. Domains where a replication timing change was observed went through a nuclear re-localization. Thus the temporal program of replication can be considered as an epigenetic mark Hiratani and Gilbert (2009 Feb 16 [9]. We present the genomic data of replication timing in 6 human model cell lines: U2OS (GSM2111308, RKO (GSM2111309, HEK 293T (GSM2111310, HeLa (GSM2111311, MRC5-SV (GSM2111312 and K562 (GSM2111313. A short comparative analysis was performed that allowed us to define regions common to the 6 cell lines. These replication timing data can be taken into account when performing studies that use these model cell lines.

  11. Mammalian RAD52 Functions in Break-Induced Replication Repair of Collapsed DNA Replication Forks

    DEFF Research Database (Denmark)

    Sotiriou, Sotirios K; Kamileri, Irene; Lugli, Natalia

    2016-01-01

    Human cancers are characterized by the presence of oncogene-induced DNA replication stress (DRS), making them dependent on repair pathways such as break-induced replication (BIR) for damaged DNA replication forks. To better understand BIR, we performed a targeted siRNA screen for genes whose...... RAD52 facilitates repair of collapsed DNA replication forks in cancer cells....

  12. Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems

    Science.gov (United States)

    Szilágyi, András; Kun, Ádám; Könnyű, Balázs; Czárán, Tamás

    2017-01-01

    As of today, the most credible scientific paradigm pertaining to the origin of life on Earth is undoubtedly the RNA World scenario. It is built on the assumption that catalytically active replicators (most probably RNA-like macromolecules) may have been responsible for booting up life almost four billion years ago. The many different incarnations of nucleotide sequence (string) replicator models proposed recently are all attempts to explain on this basis how the genetic information transfer and the functional diversity of prebiotic replicator systems may have emerged, persisted and evolved into the first living cell. We have postulated three necessary conditions for an RNA World model system to be a dynamically feasible representation of prebiotic chemical evolution: (1) it must maintain and transfer a sufficient diversity of information reliably and indefinitely, (2) it must be ecologically stable and (3) it must be evolutionarily stable. In this review, we discuss the best-known prebiotic scenarios and the corresponding models of string-replicator dynamics and assess them against these criteria. We suggest that the most popular of prebiotic replicator systems, the hypercycle, is probably the worst performer in almost all of these respects, whereas a few other model concepts (parabolic replicator, open chaotic flows, stochastic corrector, metabolically coupled replicator system) are promising candidates for development into coherent models that may become experimentally accessible in the future. PMID:29186916

  13. The Italian National Guidelines for the fire safety of facades

    Directory of Open Access Journals (Sweden)

    Lamberto Mazziotti

    2013-11-01

    Full Text Available Traditionally, the facades' design buildings where once only focused on architectural or aesthetic purposes (in addition, of course, of whether protective issues. Nowadays, thanks to the technological development of the construction works and the use of new types of materials, the facades' design should also address fire safety related aspects. In Europe and especially in Italy – where the types of building façades are built with windows of small surface and natural stone coverings – the green building/sustainability movement has resulted in the development of new concepts in facade or curtain wall design that intended to enhance the energy efficiency of building façades. These new building surfaces are covered by extensive panelling fitted with insulating materials or by wide glass surfaces, capable of carry out the most diverse purposes including, just to name a few: energy reduction, climate comfort, recovery of electricity through photovoltaic panels that convert sunlight into electricity, large space for advertising purpose. One of the main fire safety goal for a building design is to restrict the vertical fire spread so that the smoke and flames are limited to the fire origin floor. The new building façade and curtain wall topologies could overwhelms concerns for fire safety, therefore the Italian National fire service has released a Fire Code Guideline in order to address the fire safety design for an high rise building façade. This paper aims to show the guideline contents and the related fire safety façades concerns.

  14. Managing wildland fires: integrating weather models into fire projections

    Science.gov (United States)

    Anne M. Rosenthal; Francis Fujioka

    2004-01-01

    Flames from the Old Fire sweep through lands north of San Bernardino during late fall of 2003. Like many Southern California fires, the Old Fire consumed susceptible forests at the urban-wildland interface and spread to nearby city neighborhoods. By incorporating weather models into fire perimeter projections, scientist Francis Fujioka is improving fire modeling as a...

  15. Levels of the E2 interacting protein TopBP1 modulate papillomavirus maintenance stage replication

    International Nuclear Information System (INIS)

    Kanginakudru, Sriramana; DeSmet, Marsha; Thomas, Yanique; Morgan, Iain M.; Androphy, Elliot J.

    2015-01-01

    The evolutionarily conserved DNA topoisomerase II beta-binding protein 1 (TopBP1) functions in DNA replication, DNA damage response, and cell survival. We analyzed the role of TopBP1 in human and bovine papillomavirus genome replication. Consistent with prior reports, TopBP1 co-localized in discrete nuclear foci and was in complex with papillomavirus E2 protein. Similar to E2, TopBP1 is recruited to the region of the viral origin of replication during G1/S and early S phase. TopBP1 knockdown increased, while over-expression decreased transient virus replication, without affecting cell cycle. Similarly, using cell lines harboring HPV-16 or HPV-31 genome, TopBP1 knockdown increased while over-expression reduced viral copy number relative to genomic DNA. We propose a model in which TopBP1 serves dual roles in viral replication: it is essential for initiation of replication yet it restricts viral copy number. - Highlights: • Protein interaction study confirmed In-situ interaction between TopBP1 and E2. • TopBP1 present at papillomavirus ori in G1/S and early S phase of cell cycle. • TopBP1 knockdown increased, over-expression reduced virus replication. • TopBP1 protein level change did not influence cell survival or cell cycle. • TopBP1 displaced from papillomavirus ori after initiation of replication

  16. Levels of the E2 interacting protein TopBP1 modulate papillomavirus maintenance stage replication

    Energy Technology Data Exchange (ETDEWEB)

    Kanginakudru, Sriramana, E-mail: skangina@iu.edu [Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN (United States); DeSmet, Marsha, E-mail: mdesmet@iupui.edu [Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN (United States); Thomas, Yanique, E-mail: ysthomas@umail.iu.edu [Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN (United States); Morgan, Iain M., E-mail: immorgan@vcu.edu [VCU Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia (United States); Androphy, Elliot J., E-mail: eandro@iu.edu [Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN (United States); Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN (United States)

    2015-04-15

    The evolutionarily conserved DNA topoisomerase II beta-binding protein 1 (TopBP1) functions in DNA replication, DNA damage response, and cell survival. We analyzed the role of TopBP1 in human and bovine papillomavirus genome replication. Consistent with prior reports, TopBP1 co-localized in discrete nuclear foci and was in complex with papillomavirus E2 protein. Similar to E2, TopBP1 is recruited to the region of the viral origin of replication during G1/S and early S phase. TopBP1 knockdown increased, while over-expression decreased transient virus replication, without affecting cell cycle. Similarly, using cell lines harboring HPV-16 or HPV-31 genome, TopBP1 knockdown increased while over-expression reduced viral copy number relative to genomic DNA. We propose a model in which TopBP1 serves dual roles in viral replication: it is essential for initiation of replication yet it restricts viral copy number. - Highlights: • Protein interaction study confirmed In-situ interaction between TopBP1 and E2. • TopBP1 present at papillomavirus ori in G1/S and early S phase of cell cycle. • TopBP1 knockdown increased, over-expression reduced virus replication. • TopBP1 protein level change did not influence cell survival or cell cycle. • TopBP1 displaced from papillomavirus ori after initiation of replication.

  17. Fire Effects at the Tundra-Boreal Ecotone in Interior Alaska

    Science.gov (United States)

    Howard, B. K.; Mack, M. C.; Johnstone, J. F.; Walker, X. J.; Roland, C.

    2016-12-01

    Climate warming in northern latitudes has led to an intensification of disturbance by wildfire. Little is known about the effects of fire on tundra vegetation. Changes in vegetation composition could have important implications for carbon cycling , and may feedback positively or negatively to future climate change (Randerson et al., 2006). Our study utilizes extensive pre-fire ecological data collected by the National Park Service (NPS) Inventory and Monitoring (I&M) program to assess the prefire conditions important in driving successional pathways within Denali National Park and Preserve. In 2013, the East Toklat fire burned 30,000 acres of tussock tundra and mixed white and black spruce forest at a high severity, which encompassed 50 NPS plots that were originally monitored in 2003. Our sampling occurred the summer of 2016 following the same NPS protocols to assess post-fire vegetation composition. In addition, we conducted a seeding experiment using locally collected white and black spruce seed to assess natural and potential tree regeneration in unburned and post fire environments. Seed traps were established along our transects to assess seed rain. A multivariate approach will be used to assess post-fire community dynamics and future field seasons will address tree germination and survival rates. These data will then be coupled with pre and post-fire ecological data to parse out important factors driving secondary succession.

  18. Dayton Aircraft Cabin Fire Model, Version 3, Volume I. Physical Description.

    Science.gov (United States)

    1982-06-01

    contact to any surface directly above a burning element, provided that the current flame length makes contact possible. For fires originating on the...no extension of the flames horizontally beneath the surface is considered. The equation for computing the flame length is presented in Section 5. For...high as 0.3. The values chosen for DACFIR3 are 0.15 for Ec and 0.10 for E P. The Steward model is also used to compute flame length , hf, for the fire

  19. Measuring Radiant Emissions from Entire Prescribed Fires with Ground, Airborne and Satellite Sensors RxCADRE 2012

    Science.gov (United States)

    Dickinson, Matthew B.; Hudak, Andrew T.; Zajkowski, Thomas; Loudermilk, E. Louise; Schroeder, Wilfrid; Ellison, Luke; Kremens, Robert L.; Holley, William; Martinez, Otto; Paxton, Alexander; hide

    2015-01-01

    Characterising radiation from wildland fires is an important focus of fire science because radiation relates directly to the combustion process and can be measured across a wide range of spatial extents and resolutions. As part of a more comprehensive set of measurements collected during the 2012 Prescribed Fire Combustion and Atmospheric Dynamics Research (RxCADRE) field campaign, we used ground, airborne and spaceborne sensors to measure fire radiative power (FRP) from whole fires, applying different methods to small (2 ha) and large (.100 ha) burn blocks. For small blocks (n1/46), FRP estimated from an obliquely oriented long-wave infrared (LWIR) camera mounted on a boom lift were compared with FRP derived from combined data from tower-mounted radiometers and remotely piloted aircraft systems (RPAS). For large burn blocks (n1/43), satellite FRP measurements from the Moderate-resolution Imaging Spectroradiometer (MODIS) and Visible Infrared Imaging Radiometer Suite (VIIRS) sensors were compared with near-coincident FRP measurements derived from a LWIR imaging system aboard a piloted aircraft. We describe measurements and consider their strengths and weaknesses. Until quantitative sensors exist for small RPAS, their use in fire research will remain limited. For oblique, airborne and satellite sensors, further FRP measurement development is needed along with greater replication of coincident measurements, which we show to be feasible.

  20. Enhancing adaptive capacity for restoring fire-dependent ecosystems: the Fire Learning Network's Prescribed Fire Training Exchanges

    Directory of Open Access Journals (Sweden)

    Andrew G. Spencer

    2015-09-01

    Full Text Available Prescribed fire is a critical tool for promoting restoration and increasing resilience in fire-adapted ecosystems, but there are barriers to its use, including a shortage of personnel with adequate ecological knowledge and operational expertise to implement prescribed fire across multijurisdictional landscapes. In the United States, recognized needs for both professional development and increased use of fire are not being met, often because of institutional limitations. The Fire Learning Network has been characterized as a multiscalar, collaborative network that works to enhance the adaptive capacity of fire management institutions, and this network developed the Prescribed Fire Training Exchanges (TREXs to address persistent challenges in increasing the capacity for prescribed fire implementation. Our research was designed to investigate where fire professionals face professional barriers, how the TREX addresses these, and in what ways the TREX may be contributing to the adaptive capacity of fire management institutions. We evaluated the training model using surveys, interviews, focus groups, and participant observation. We found that, although the training events cannot overcome all institutional barriers, they incorporate the key components of professional development in fire; foster collaboration, learning, and network building; and provide flexible opportunities with an emphasis on local context to train a variety of professionals with disparate needs. The strategy also offers an avenue for overcoming barriers faced by contingent and nonfederal fire professionals in attaining training and operational experience, thereby increasing the variety of actors and resources involved in fire management. Although it is an incremental step, the TREX is contributing to the adaptive capacity of institutions in social-ecological systems in which fire is a critical ecological process.

  1. REPLICATION TOOL AND METHOD OF PROVIDING A REPLICATION TOOL

    DEFF Research Database (Denmark)

    2016-01-01

    The invention relates to a replication tool (1, 1a, 1b) for producing a part (4) with a microscale textured replica surface (5a, 5b, 5c, 5d). The replication tool (1, 1a, 1b) comprises a tool surface (2a, 2b) defining a general shape of the item. The tool surface (2a, 2b) comprises a microscale...... energy directors on flange portions thereof uses the replication tool (1, 1a, 1b) to form an item (4) with a general shape as defined by the tool surface (2a, 2b). The formed item (4) comprises a microscale textured replica surface (5a, 5b, 5c, 5d) with a lateral arrangement of polydisperse microscale...

  2. Application of an Image Tracking Algorithm in Fire Ant Motion Experiment

    Directory of Open Access Journals (Sweden)

    Lichuan Gui

    2009-04-01

    Full Text Available An image tracking algorithm, which was originally used with the particle image velocimetry (PIV to determine velocities of buoyant solid particles in water, is modified and applied in the presented work to detect motion of fire ant on a planar surface. A group of fire ant workers are put to the bottom of a tub and excited with vibration of selected frequency and intensity. The moving fire ants are captured with an image system that successively acquires image frames of high digital resolution. The background noise in the imaging recordings is extracted by averaging hundreds of frames and removed from each frame. The individual fire ant images are identified with a recursive digital filter, and then they are tracked between frames according to the size, brightness, shape, and orientation angle of the ant image. The speed of an individual ant is determined with the displacement of its images and the time interval between frames. The trail of the individual fire ant is determined with the image tracking results, and a statistical analysis is conducted for all the fire ants in the group. The purpose of the experiment is to investigate the response of fire ants to the substrate vibration. Test results indicate that the fire ants move faster after being excited, but the number of active ones are not increased even after a strong excitation.

  3. US Fire Administration Fire Statistics

    Data.gov (United States)

    Department of Homeland Security — The U.S. Fire Administration collects data from a variety of sources to provide information and analyses on the status and scope of the fire problem in the United...

  4. Spatio-temporal evolution of forest fires in Portugal

    Science.gov (United States)

    Tonini, Marj; Pereira, Mário G.; Parente, Joana

    2017-04-01

    A key issue in fire management is the ability to explore and try to predict where and when fires are more likely to occur. This information can be useful to understand the triggering factors of ignitions and for planning strategies to reduce forest fires, to manage the sources of ignition and to identify areas and frame period at risk. Therefore, producing maps displaying forest fires location and their occurrence in time can be of great help for accurately forecasting these hazardous events. In a fire prone country as Portugal, where thousands of events occurs each year, it is involved to drive information about fires over densities and recurrences just by looking at the original arrangement of the mapped ignition points or burnt areas. In this respect, statistical methods originally developed for spatio-temporal stochastic point processes can be employed to find a structure within these large datasets. In the present study, the authors propose an approach to analyze and visualize the evolution in space and in time of forest fires occurred in Portugal during a long frame period (1990 - 2013). Data came from the Portuguese mapped burnt areas official geodatabase (by the Institute for the Conservation of Nature and Forests), which is the result of interpreted satellite measurements. The following statistical analyses were performed: the geographically-weighted summary statistics, to analyze the local variability of the average burned area; the space-time Kernel density, to elaborate smoothed density surfaces representing over densities of fires classed by size and on North vs South region. Finally, we emploied the volume rendering thecnique to visualize the spatio-temporal evolution of these events into a unique map: this representation allows visually inspecting areas and time-step more affected from a high aggregation of forest fires. It results that during the whole investigated period over densities are mainly located in the northern regions, while in the

  5. Recommendations for Replication Research in Special Education: A Framework of Systematic, Conceptual Replications

    Science.gov (United States)

    Coyne, Michael D.; Cook, Bryan G.; Therrien, William J.

    2016-01-01

    Special education researchers conduct studies that can be considered replications. However, they do not often refer to them as replication studies. The purpose of this article is to consider the potential benefits of conceptualizing special education intervention research within a framework of systematic, conceptual replication. Specifically, we…

  6. Experimental study of fire barriers preventing vertical fire spread in ETISs

    Directory of Open Access Journals (Sweden)

    Xin Huang

    2013-11-01

    Full Text Available In recent years, the external thermal insulation system (ETIS has been applied increasingly in a large amount of buildings for energy conservation purpose. However, the increase use of combustible insulation materials in the ETIS has raised serious fire safety problems. Fires involving this type of ETIS have caused severe damage and loss. In order to improve its fire safety, fire barriers were suggested to be installed. This paper introduces fire experiments that have been done to study the effects of fire barriers on preventing vertical fire spread along the ETIS. The experiments were performed according to BS 8414-1:2002 “Fire performance of external cladding systems – Part 1: Test method for non-loadbearing external cladding systems applied to the face of the building”. The test facility consists of a 9 m high wall. The fire sources were wood cribs with a fire size of 3 ± 0.5 MW. The insulation materials were expanded polystyrene foam (EPS. The fire barrier was a horizontal strip of rockwool with a width of 300 mm. Thermocouples were used to measure temperatures outside and inside the ETIS. A series of experiments with different fire scenarios were done: no fire barrier, two fire barriers and three fire barriers at different heights. Test results were compared. The results show that the ETIS using EPS without fire barriers almost burned out, while the ETIS with fire barriers performed well in preventing fire spread. The temperatures above the fire barrier were much lower than those below the fire barrier, and most of the insulation materials above the top fire barrier stayed in place.

  7. Large-proportional shrunken bio-replication of shark skin based on UV-curing shrinkage

    International Nuclear Information System (INIS)

    Chen, Huawei; Che, Da; Zhang, Xin; Yue, Yue; Zhang, Deyuan

    2015-01-01

    The shark skin effect has attracted worldwide attention because of its superior drag reduction. As the product of natural selection, the maximum drag reduction of shark skin is found in its normal living environment. Large-proportional shrinkage of shark skin morphology is greatly anticipated for its adaptation to faster fluid flow. One novel approach, large-proportional shrunken bio-replication, is proposed as a method to adjust the optimal drag reduction region of shark skin based on the shrinkage of UV-cured material. The shark skin is taken as a replica template to allow large-proportional shrinking in the drag reduction morphology by taking advantage of the shrinkage of UV-curable material. The accuracy of the large-proportional shrunken bio-replication approach is verified by a comparison between original and shrunken bio-replicated shark skin, which shows that the shrinking ratio can reach 23% and the bio-replication accuracy is higher than 95%. In addition, the translation of the optimum drag reduction peak of natural surface function to various applications and environments is proved by drag reduction experiments. (technical note)

  8. EFFECTS OF FIRE FUMES ON ALMOND SAFETY AND QUALITY

    Directory of Open Access Journals (Sweden)

    Amanda Ramírez-Gandolfo

    2011-08-01

    Full Text Available A fire originated and burnt two cold chambers; the present study focused on almonds stored in adjacent chambers (4, 5, 6 and 13 and evaluated both their food safety and quality. Testing for polycyclic aromatic hydrocarbons, polychlorinated dibenzo-p-dioxins and dibenzofurans was carried out in affected facilities, packaging and almonds. Experimental results proved that fire fumes did not reach chambers 4-6, but traces were found in bin packaging of chamber 13; thus, packaging from this chamber were changed. Concentrations of benzo(apyrene were low enough to prove that fire fumes did not get in contact with the stored almonds. Later, only volatile compounds typical of nuts were identified in both raw and toasted almonds. Finally, a trained panel concluded that no sensory signal of fumes reaching almonds was found. This manuscript could be taken as a model protocol to establish whether fire fumes have reached and affected the safety and/or quality of foods. This information will be especially useful for insurance companies.

  9. DNA replication and cancer

    DEFF Research Database (Denmark)

    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

    2016-01-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

  10. Exposure to radionuclides in smoke from vegetation fires

    International Nuclear Information System (INIS)

    Carvalho, Fernando P.; Oliveira, João M.; Malta, Margarida

    2014-01-01

    Naturally occurring radionuclides of uranium, thorium, radium, lead and polonium were determined in bushes and trees and in the smoke from summer forest fires. Activity concentrations of radionuclides in smoke particles were much enriched when compared to original vegetation. Polonium-210 ( 210 Po) in smoke was measured in concentrations much higher than all other radionuclides, reaching 7255 ± 285 Bq kg −1 , mostly associated with the smaller size smoke particles ( 210 Po in surface air near forest fires displayed volume concentrations up to 70 mBq m −3 , while in smoke-free air 210 Po concentration was about 30 μBq m −3 . The estimated absorbed radiation dose to an adult member of the public or a firefighter exposed for 24 h to inhalation of smoke near forest fires could exceed 5 μSv per day, i.e, more than 2000 times above the radiation dose from background radioactivity in surface air, and also higher than the radiation dose from 210 Po inhalation in a chronic cigarette smoker. It is concluded that prolonged exposure to smoke allows for enhanced inhalation of radionuclides associated with smoke particles. Due to high radiotoxicity of alpha emitting radionuclides, and in particular of 210 Po, the protection of respiratory tract of fire fighters is strongly recommended. - Highlights: • Natural radionuclides in vegetation are in low concentrations. • Forest fires release natural radionuclides from vegetation and concentrate them in inhalable ash particles. • Prolonged inhalation of smoke from forest fires gives rise enhanced radiation exposure of lungs especially due to polonium. • Respiratory protection of fire fighters and members of public is highly recommended for radioprotection reasons

  11. Registered Replication Report: Testing Disruptive Effects of Irrelevant Speech on Visual-Spatial Working Memory

    Directory of Open Access Journals (Sweden)

    Tatiana Kvetnaya

    2018-04-01

    Full Text Available A Partial Replication of “Functional Equivalence of Verbal and Spatial Information in Serial Short-Term Memory (Jones, Farrand, Stuart, & Morris, 1995; Experiment 4” The irrelevant speech effect (ISE—the phenomenon that background speech impairs serial recall of visually presented material—has been widely used for examining the structure of short-term memory. In Experiment 4, Jones, Farrand, Stuart, and Morris (1995 employed the ISE to demonstrate that impairment of performance is determined by the changing-state characteristics of the material, rather than its modality of origin. The present study directly replicated the spatial condition of Experiment 4 with 'N' = 40 German participants. In contrast to the original findings, no main effect of sound type was observed, 'F'(2, 78 = 0.81, 'p' = .450, η2'p' = .02. The absence of an ISE in the spatial domain does not support the changing state hypothesis.

  12. Late-replicating X-chromosome: replication patterns in mammalian females

    Directory of Open Access Journals (Sweden)

    Tunin Karen

    2002-01-01

    Full Text Available The GTG-banding and 5-BrdU incorporation patterns of the late-replicating X-chromosome were studied in female dogs and cattle, and compared to human female patterns. The replication patterns of the short arm of the X-chromosomes did not show any difference between human, dog and cattle females. As to the long arm, some bands showed differences among the three studied species regarding the replication kinetics pattern. These differences were observed in a restricted region of the X-chromosome, delimited by Xq11 -> q25 in humans, by Xq1 -> q8 in dogs, and by Xq12 -> q32 in cattle. In an attempt to find out if these differences in the replication kinetics could be a reflection of differences in the localization of genes in that region of the X-chromosome, we used the probe for the human androgen receptor gene (AR localized at Xq12, which is in the region where we observed differences among the three studied species. We did not, however, observe hybridization signals. Our study goes on, using other human probes for genes located in the region Xq11 -> Xq25.

  13. Group Therapy for Repeated Deliberate Self-Harm in Adolescents: Failure of Replication of a Randomized Trial

    Science.gov (United States)

    Hazell, Philip L.; Martin, Graham; McGill, Katherine; Kay, Tracey; Wood, Alison; Trainor, Gemma; Harrington, Richard

    2009-01-01

    A study revealing the superiority of group therapy to routine care in preventing the recurrence of self-harming behavior among adolescents is unsuccessfully replicated. The study's findings contradicted those of the original study.

  14. A Replication by Any Other Name: A Systematic Review of Replicative Intervention Studies

    Science.gov (United States)

    Cook, Bryan G.; Collins, Lauren W.; Cook, Sara C.; Cook, Lysandra

    2016-01-01

    Replication research is essential to scientific knowledge. Reviews of replication studies often electronically search for "replicat*" as a textword, which does not identify studies that replicate previous research but do not self-identify as such. We examined whether the 83 intervention studies published in six non-categorical research…

  15. RI E-911 Fire Hydrants; e911Hydrants13q1

    Data.gov (United States)

    University of Rhode Island Geospatial Extension Program — These data were originally developed and designed for Rhode Island Enhanced 9-1-1 purposes only. These data represents every known fire hydrant in the state of Rhode...

  16. WebGIS Platform Adressed to Forest Fire Management Methodologies

    Science.gov (United States)

    André Ramos-Simões, Nuno; Neto Paixão, Helena Maria; Granja Martins, Fernando Miguel; Pedras, Celestina; Lança, Rui; Silva, Elisa; Jordán, António; Zavala, Lorena; Soares, Cristina

    2015-04-01

    Forest fires are one of the natural disasters that causes more damages in nature, as well as high material costs, and sometimes, a significant losses in human lives. In summer season, when high temperatures are attained, fire may rapidly progress and destroy vast areas of forest and also rural and urban areas. The forest fires have effect on forest species, forest composition and structure, soil properties and soil capacity for nutrient retention. In order to minimize the negative impact of the forest fires in the environment, many studies have been developed, e.g. Jordán et al (2009), Cerdà & Jordán (2010), and Gonçalves & Vieira (2013). Nowadays, Remote Sensing (RS) and Geographic Information System (GIS) technologies are used as support tools in fire management decisions, namely during the fire, but also before and after. This study presents the development of a user-friendly WebGIS dedicated to share data, maps and provide updated information on forest fire management for stakeholders in Iberia Peninsula. The WebGIS platform was developed with ArcGIS Online, ArcGIS for Desktop; HyperText Markup Language (HTML) and Javascript. This platform has a database that includes spatial and alphanumeric information, such as: origin, burned areas, vegetation change over time, terrain natural slope, land use, soil erosion and fire related hazards. The same database contains also the following relevant information: water sources, forest tracks and traffic ways, lookout posts and urban areas. The aim of this study is to provide the authorities with a tool to assess risk areas and manage more efficiently forest fire hazards, giving more support to their decisions and helping the populations when facing this kind of phenomena.

  17. An evaluation of the fire barrier system thermo-lag 330-1

    International Nuclear Information System (INIS)

    Nowlen, S.P.

    1994-09-01

    This report presents the results of three fire endurance tests and one ampacity derating test set of the fire barrier system Thermo-Lag 330-1 Subliming Coating. Each test was performed using cable tray specimens protected by a nominal three-hour fire barrier envelope comprised of two layers of nominal 1/2 inch thick material. The fire barrier systems for two of the three fire endurance test articles and for the ampacity derating test article were installed in accordance with the manufacturer's installations procedures. The barrier system for the third fire endurance test article was a full reproduction of one of the original manufacturer's qualification test articles. This final test article included certain installation enhancements not considered typical of current nuclear power plant installations. The primary criteria for fire endurance performance evaluation was based on cable circuit integrity testing. Secondary consideration was also given to the temperature rise limits set forth in the ASTM E119 standard fire barrier test procedure. All three of the fire endurance specimens failed prematurely. Circuit integrity failures for the two fire endurance test articles with procedures-based installations were recorded at approximately 76 and 59 minutes into the exposures for a 6 inch wide and 12 inch wide cable tray respectively. Temperature excursion failures (single point) for these two test articles were noted at approximately 65 and 56 minutes respectively. The first circuit integrity failure for the full reproduction test article was recorded approximately 119 minutes into the exposure, and the first temperature excursion failure for this test article was recorded approximately 110 minutes into the exposure

  18. Optimizing prescribed fire allocation for managing fire risk in central Catalonia.

    Science.gov (United States)

    Alcasena, Fermín J; Ager, Alan A; Salis, Michele; Day, Michelle A; Vega-Garcia, Cristina

    2018-04-15

    We used spatial optimization to allocate and prioritize prescribed fire treatments in the fire-prone Bages County, central Catalonia (northeastern Spain). The goal of this study was to identify suitable strategic locations on forest lands for fuel treatments in order to: 1) disrupt major fire movements, 2) reduce ember emissions, and 3) reduce the likelihood of large fires burning into residential communities. We first modeled fire spread, hazard and exposure metrics under historical extreme fire weather conditions, including node influence grid for surface fire pathways, crown fraction burned and fire transmission to residential structures. Then, we performed an optimization analysis on individual planning areas to identify production possibility frontiers for addressing fire exposure and explore alternative prescribed fire treatment configurations. The results revealed strong trade-offs among different fire exposure metrics, showed treatment mosaics that optimize the allocation of prescribed fire, and identified specific opportunities to achieve multiple objectives. Our methods can contribute to improving the efficiency of prescribed fire treatment investments and wildfire management programs aimed at creating fire resilient ecosystems, facilitating safe and efficient fire suppression, and safeguarding rural communities from catastrophic wildfires. The analysis framework can be used to optimally allocate prescribed fire in other fire-prone areas within the Mediterranean region and elsewhere. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Advancements in Hydrology and Erosion Process Understanding and Post-Fire Hydrologic and Erosion Model Development for Semi-Arid Landscapes

    Science.gov (United States)

    Williams, C. Jason; Pierson, Frederick B.; Al-Hamdan, Osama Z.; Robichaud, Peter R.; Nearing, Mark A.; Hernandez, Mariano; Weltz, Mark A.; Spaeth, Kenneth E.; Goodrich, David C.

    2017-04-01

    Fire activity continues to increase in semi-arid regions around the globe. Private and governmental land management entities are challenged with predicting and mitigating post-fire hydrologic and erosion responses on these landscapes. For more than a decade, a team of scientists with the US Department of Agriculture has collaborated on extensive post-fire hydrologic field research and the application of field research to development of post-fire hydrology and erosion predictive technologies. Experiments funded through this research investigated the impacts of fire on vegetation and soils and the effects of these fire-induced changes on infiltration, runoff generation, erodibility, and soil erosion processes. The distribution of study sites spans diverse topography across grassland, shrubland, and woodland landscapes throughout the western United States. Knowledge gleaned from the extensive field experiments was applied to develop and enhance physically-based models for hillslope- to watershed-scale runoff and erosion prediction. Our field research and subsequent data syntheses have identified key knowledge gaps and challenges regarding post-fire hydrology and erosion modeling. Our presentation details some consistent trends across a diverse domain and varying landscape conditions based on our extensive field campaigns. We demonstrate how field data have advanced our understanding of post-fire hydrology and erosion for semi-arid landscapes and highlight remaining key knowledge gaps. Lastly, we briefly show how our well-replicated experimental methodologies have contributed to advancements in hydrologic and erosion model development for the post-fire environment.

  20. Enhanced Fire Events Database to Support Fire PRA

    International Nuclear Information System (INIS)

    Baranowsky, Patrick; Canavan, Ken; St. Germain, Shawn

    2010-01-01

    This paper provides a description of the updated and enhanced Fire Events Data Base (FEDB) developed by the Electric Power Research Institute (EPRI) in cooperation with the U.S. Nuclear Regulatory Commission (NRC). The FEDB is the principal source of fire incident operational data for use in fire PRAs. It provides a comprehensive and consolidated source of fire incident information for nuclear power plants operating in the U.S. The database classification scheme identifies important attributes of fire incidents to characterize their nature, causal factors, and severity consistent with available data. The database provides sufficient detail to delineate important plant specific attributes of the incidents to the extent practical. A significant enhancement to the updated FEDB is the reorganization and refinement of the database structure and data fields and fire characterization details added to more rigorously capture the nature and magnitude of the fire and damage to the ignition source and nearby equipment and structures.

  1. International Expansion through Flexible Replication

    DEFF Research Database (Denmark)

    Jonsson, Anna; Foss, Nicolai Juul

    2011-01-01

    Business organizations may expand internationally by replicating a part of their value chain, such as a sales and marketing format, in other countries. However, little is known regarding how such “international replicators” build a format for replication, or how they can adjust it in order to ada......, etc.) are replicated in a uniform manner across stores, and change only very slowly (if at all) in response to learning (“flexible replication”). We conclude by discussing the factors that influence the approach to replication adopted by an international replicator.......Business organizations may expand internationally by replicating a part of their value chain, such as a sales and marketing format, in other countries. However, little is known regarding how such “international replicators” build a format for replication, or how they can adjust it in order to adapt...

  2. Analysis of cis and trans Requirements for DNA Replication at the Right-End Hairpin of the Human Bocavirus 1 Genome.

    Science.gov (United States)

    Shen, Weiran; Deng, Xuefeng; Zou, Wei; Engelhardt, John F; Yan, Ziying; Qiu, Jianming

    2016-09-01

    Parvoviruses are single-stranded DNA viruses that use the palindromic structures at the ends of the viral genome for their replication. The mechanism of parvovirus replication has been studied mostly in the dependoparvovirus adeno-associated virus 2 (AAV2) and the protoparvovirus minute virus of mice (MVM). Here, we used human bocavirus 1 (HBoV1) to understand the replication mechanism of bocaparvovirus. HBoV1 is pathogenic to humans, causing acute respiratory tract infections, especially in young children under 2 years old. By using the duplex replicative form of the HBoV1 genome in human embryonic kidney 293 (HEK293) cells, we identified the HBoV1 minimal replication origin at the right-end hairpin (OriR). Mutagenesis analyses confirmed the putative NS1 binding and nicking sites within the OriR. Of note, unlike the large nonstructural protein (Rep78/68 or NS1) of other parvoviruses, HBoV1 NS1 did not specifically bind OriR in vitro, indicating that other viral and cellular components or the oligomerization of NS1 is required for NS1 binding to the OriR. In vivo studies demonstrated that residues responsible for NS1 binding and nicking are within the origin-binding domain. Further analysis identified that the small nonstructural protein NP1 is required for HBoV1 DNA replication at OriR. NP1 and other viral nonstructural proteins (NS1 to NS4) colocalized within the viral DNA replication centers in both OriR-transfected cells and virus-infected cells, highlighting a direct involvement of NP1 in viral DNA replication at OriR. Overall, our study revealed the characteristics of HBoV1 DNA replication at OriR, suggesting novel characteristics of autonomous parvovirus DNA replication. Human bocavirus 1 (HBoV1) causes acute respiratory tract infections in young children. The duplex HBoV1 genome replicates in HEK293 cells and produces progeny virions that are infectious in well-differentiated airway epithelial cells. A recombinant AAV2 vector pseudotyped with an HBoV1

  3. Fire Behavior (FB)

    Science.gov (United States)

    Robert E. Keane

    2006-01-01

    The Fire Behavior (FB) method is used to describe the behavior of the fire and the ambient weather and fuel conditions that influence the fire behavior. Fire behavior methods are not plot based and are collected by fire event and time-date. In general, the fire behavior data are used to interpret the fire effects documented in the plot-level sampling. Unlike the other...

  4. Emerging critical roles of Fe-S clusters in DNA replication and repair

    Science.gov (United States)

    Fuss, Jill O.; Tsai, Chi-Lin; Ishida, Justin P.; Tainer, John A.

    2015-01-01

    Fe-S clusters are partners in the origin of life that predate cells, acetyl-CoA metabolism, DNA, and the RNA world. The double helix solved the mystery of DNA replication by base pairing for accurate copying. Yet, for genome stability necessary to life, the double helix has equally important implications for damage repair. Here we examine striking advances that uncover Fe-S cluster roles both in copying the genetic sequence by DNA polymerases and in crucial repair processes for genome maintenance, as mutational defects cause cancer and degenerative disease. Moreover, we examine an exciting, controversial role for Fe-S clusters in a third element required for life – the long-range coordination and regulation of replication and repair events. By their ability to delocalize electrons over both Fe and S centers, Fe-S clusters have unbeatable features for protein conformational control and charge transfer via double-stranded DNA that may fundamentally transform our understanding of life, replication, and repair. PMID:25655665

  5. A Role of hIPI3 in DNA Replication Licensing in Human Cells.

    Science.gov (United States)

    Huang, Yining; Amin, Aftab; Qin, Yan; Wang, Ziyi; Jiang, Huadong; Liang, Lu; Shi, Linjing; Liang, Chun

    2016-01-01

    The yeast Ipi3p is required for DNA replication and cell viability in Sacharomyces cerevisiae. It is an essential component of the Rix1 complex (Rix1p/Ipi2p-Ipi1p-Ipi3p) that is required for the processing of 35S pre-rRNA in pre-60S ribosomal particles and for the initiation of DNA replication. The human IPI3 homolog is WDR18 (WD repeat domain 18), which shares significant homology with yIpi3p. Here we report that knockdown of hIPI3 resulted in substantial defects in the chromatin association of the MCM complex, DNA replication, cell cycle progression and cell proliferation. Importantly, hIPI3 silencing did not result in a reduction of the protein level of hCDC6, hMCM7, or the ectopically expressed GFP protein, indicating that protein synthesis was not defective in the same time frame of the DNA replication and cell cycle defects. Furthermore, the mRNA and protein levels of hIPI3 fluctuate in the cell cycle, with the highest levels from M phase to early G1 phase, similar to other pre-replicative (pre-RC) proteins. Moreover, hIPI3 interacts with other replication-initiation proteins, co-localizes with hMCM7 in the nucleus, and is important for the nuclear localization of hMCM7. We also found that hIPI3 preferentially binds to the origins of DNA replication including those at the c-Myc, Lamin-B2 and β-Globin loci. These results indicate that hIPI3 is involved in human DNA replication licensing independent of its role in ribosome biogenesis.

  6. The discovery of fire by humans: a long and convoluted process.

    Science.gov (United States)

    Gowlett, J A J

    2016-06-05

    Numbers of animal species react to the natural phenomenon of fire, but only humans have learnt to control it and to make it at will. Natural fires caused overwhelmingly by lightning are highly evident on many landscapes. Birds such as hawks, and some other predators, are alert to opportunities to catch animals including invertebrates disturbed by such fires and similar benefits are likely to underlie the first human involvements with fires. Early hominins would undoubtedly have been aware of such fires, as are savanna chimpanzees in the present. Rather than as an event, the discovery of fire use may be seen as a set of processes happening over the long term. Eventually, fire became embedded in human behaviour, so that it is involved in almost all advanced technologies. Fire has also influenced human biology, assisting in providing the high-quality diet which has fuelled the increase in brain size through the Pleistocene. Direct evidence of early fire in archaeology remains rare, but from 1.5 Ma onward surprising numbers of sites preserve some evidence of burnt material. By the Middle Pleistocene, recognizable hearths demonstrate a social and economic focus on many sites. The evidence of archaeological sites has to be evaluated against postulates of biological models such as the 'cooking hypothesis' or the 'social brain', and questions of social cooperation and the origins of language. Although much remains to be worked out, it is plain that fire control has had a major impact in the course of human evolution.This article is part of the themed issue 'The interaction of fire and mankind'. © 2016 The Authors.

  7. Sterol Binding by the Tombusviral Replication Proteins Is Essential for Replication in Yeast and Plants.

    Science.gov (United States)

    Xu, Kai; Nagy, Peter D

    2017-04-01

    Membranous structures derived from various organelles are important for replication of plus-stranded RNA viruses. Although the important roles of co-opted host proteins in RNA virus replication have been appreciated for a decade, the equally important functions of cellular lipids in virus replication have been gaining full attention only recently. Previous work with Tomato bushy stunt tombusvirus (TBSV) in model host yeast has revealed essential roles for phosphatidylethanolamine and sterols in viral replication. To further our understanding of the role of sterols in tombusvirus replication, in this work we showed that the TBSV p33 and p92 replication proteins could bind to sterols in vitro The sterol binding by p33 is supported by cholesterol recognition/interaction amino acid consensus (CRAC) and CARC-like sequences within the two transmembrane domains of p33. Mutagenesis of the critical Y amino acids within the CRAC and CARC sequences blocked TBSV replication in yeast and plant cells. We also showed the enrichment of sterols in the detergent-resistant membrane (DRM) fractions obtained from yeast and plant cells replicating TBSV. The DRMs could support viral RNA synthesis on both the endogenous and exogenous templates. A lipidomic approach showed the lack of enhancement of sterol levels in yeast and plant cells replicating TBSV. The data support the notion that the TBSV replication proteins are associated with sterol-rich detergent-resistant membranes in yeast and plant cells. Together, the results obtained in this study and the previously published results support the local enrichment of sterols around the viral replication proteins that is critical for TBSV replication. IMPORTANCE One intriguing aspect of viral infections is their dependence on efficient subcellular assembly platforms serving replication, virion assembly, or virus egress via budding out of infected cells. These assembly platforms might involve sterol-rich membrane microdomains, which are

  8. Replication and Pedagogy in the History of Psychology IV: Patrick and Gilbert (1896) on Sleep Deprivation

    Science.gov (United States)

    Fuchs, Thomas; Burgdorf, Jeffrey

    2008-05-01

    We report an attempted replication of G. T. W. Patrick and J. A. Gilbert’s pioneering sleep deprivation experiment ‘Studies from the psychological laboratory of the University of Iowa. On the effects of loss of sleep’, conducted in 1895/96. Patrick and Gilbert’s study was the first sleep deprivation experiment of its kind, performed by some of the first formally trained psychologists. We attempted to recreate the original experience in two subjects, using similar apparatus and methodology, and drawing direct comparisons to the original study whenever possible. We argue for a strong influence of an ‘Americanized’ Wundtian psychology on Patrick and Gilbert, a claim supported biographically by their education and by their experimental methods. The replication thus opens interesting new perspectives, which are unlikely to be generated by any other historical approach.

  9. Endogenous hepatitis C virus homolog fragments in European rabbit and hare genomes replicate in cell culture.

    Directory of Open Access Journals (Sweden)

    Eliane Silva

    Full Text Available Endogenous retroviruses, non-retroviral RNA viruses and DNA viruses have been found in the mammalian genomes. The origin of Hepatitis C virus (HCV, the major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma in humans, remains unclear since its discovery. Here we show that fragments homologous to HCV structural and non-structural (NS proteins present in the European rabbit (Oryctolagus cuniculus and hare (Lepus europaeus genomes replicate in bovine cell cultures. The HCV genomic homolog fragments were demonstrated by RT-PCR, PCR, mass spectrometry, and replication in bovine cell cultures by immunofluorescence assay (IFA and immunogold electron microscopy (IEM using specific MAbs for HCV NS3, NS4A, and NS5 proteins. These findings may lead to novel research approaches on the HCV origin, genesis, evolution and diversity.

  10. Plasmid origin of replication of herpesvirus papio: DNA sequence and enhancer function.

    Science.gov (United States)

    Loeb, D D; Sung, N S; Pesano, R L; Sexton, C J; Hutchison, C; Pagano, J S

    1990-01-01

    Herpesvirus papio (HVP) is a lymphotropic virus of baboons which is related to Epstein-Barr virus (EBV) and produces latent infection. The nucleotide sequence of the 5,775-base-pair (bp) EcoRI K fragment of HVP, which has previously been shown to confer the ability to replicate autonomously, has been determined. Within this DNA fragment is a region which bears structural and sequence similarity to the ori-P region of EBV. The HVP ori-P region has a 10- by 26-bp tandem array which is related to the 20- by 30-bp tandem array from the EBV ori-P region. In HVP there is an intervening region of 764 bp followed by five partial copies of the 26-bp monomer. Both the EBV and HVP 3' regions have the potential to form dyad structures which, however, differ in arrangement. We also demonstrate that a transcriptional enhancer which requires transactivation by a virus-encoded factor is present in the HVP ori-P. Images PMID:2159548

  11. Elements in the transcriptional regulatory region flanking herpes simplex virus type 1 oriS stimulate origin function.

    Science.gov (United States)

    Wong, S W; Schaffer, P A

    1991-05-01

    Like other DNA-containing viruses, the three origins of herpes simplex virus type 1 (HSV-1) DNA replication are flanked by sequences containing transcriptional regulatory elements. In a transient plasmid replication assay, deletion of sequences comprising the transcriptional regulatory elements of ICP4 and ICP22/47, which flank oriS, resulted in a greater than 80-fold decrease in origin function compared with a plasmid, pOS-822, which retains these sequences. In an effort to identify specific cis-acting elements responsible for this effect, we conducted systematic deletion analysis of the flanking region with plasmid pOS-822 and tested the resulting mutant plasmids for origin function. Stimulation by cis-acting elements was shown to be both distance and orientation dependent, as changes in either parameter resulted in a decrease in oriS function. Additional evidence for the stimulatory effect of flanking sequences on origin function was demonstrated by replacement of these sequences with the cytomegalovirus immediate-early promoter, resulting in nearly wild-type levels of oriS function. In competition experiments, cotransfection of cells with the test plasmid, pOS-822, and increasing molar concentrations of a competitor plasmid which contained the ICP4 and ICP22/47 transcriptional regulatory regions but lacked core origin sequences resulted in a significant reduction in the replication efficiency of pOS-822, demonstrating that factors which bind specifically to the oriS-flanking sequences are likely involved as auxiliary proteins in oriS function. Together, these studies demonstrate that trans-acting factors and the sites to which they bind play a critical role in the efficiency of HSV-1 DNA replication from oriS in transient-replication assays.

  12. Detection and Characterization of Low Temperature Peat Fires during the 2015 Fire Catastrophe in Indonesia Using a New High-Sensitivity Fire Monitoring Satellite Sensor (FireBird).

    Science.gov (United States)

    Atwood, Elizabeth C; Englhart, Sandra; Lorenz, Eckehard; Halle, Winfried; Wiedemann, Werner; Siegert, Florian

    2016-01-01

    Vast and disastrous fires occurred on Borneo during the 2015 dry season, pushing Indonesia into the top five carbon emitting countries. The region was affected by a very strong El Niño-Southern Oscillation (ENSO) climate phenomenon, on par with the last severe event in 1997/98. Fire dynamics in Central Kalimantan were investigated using an innovative sensor offering higher sensitivity to a wider range of fire intensities at a finer spatial resolution (160 m) than heretofore available. The sensor is onboard the TET-1 satellite, part of the German Aerospace Center (DLR) FireBird mission. TET-1 images (acquired every 2-3 days) from the middle infrared were used to detect fires continuously burning for almost three weeks in the protected peatlands of Sebangau National Park as well as surrounding areas with active logging and oil palm concessions. TET-1 detection capabilities were compared with MODIS active fire detection and Landsat burned area algorithms. Fire dynamics, including fire front propagation speed and area burned, were investigated. We show that TET-1 has improved detection capabilities over MODIS in monitoring low-intensity peatland fire fronts through thick smoke and haze. Analysis of fire dynamics revealed that the largest burned areas resulted from fire front lines started from multiple locations, and the highest propagation speeds were in excess of 500 m/day (all over peat > 2m deep). Fires were found to occur most often in concessions that contained drainage infrastructure but were not cleared prior to the fire season. Benefits of implementing this sensor system to improve current fire management techniques are discussed. Near real-time fire detection together with enhanced fire behavior monitoring capabilities would not only improve firefighting efforts, but also benefit analysis of fire impact on tropical peatlands, greenhouse gas emission estimations as well as mitigation measures to reduce severe fire events in the future.

  13. Absence of Non-histone Protein Complexes at Natural Chromosomal Pause Sites Results in Reduced Replication Pausing in Aging Yeast Cells

    Directory of Open Access Journals (Sweden)

    Marleny Cabral

    2016-11-01

    Full Text Available There is substantial evidence that genomic instability increases during aging. Replication pausing (and stalling at difficult-to-replicate chromosomal sites may induce genomic instability. Interestingly, in aging yeast cells, we observed reduced replication pausing at various natural replication pause sites (RPSs in ribosomal DNA (rDNA and non-rDNA locations (e.g., silent replication origins and tRNA genes. The reduced pausing occurs independent of the DNA helicase Rrm3p, which facilitates replication past these non-histone protein-complex-bound RPSs, and is independent of the deacetylase Sir2p. Conditions of caloric restriction (CR, which extend life span, also cause reduced replication pausing at the 5S rDNA and at tRNA genes. In aged and CR cells, the RPSs are less occupied by their specific non-histone protein complexes (e.g., the preinitiation complex TFIIIC, likely because members of these complexes have primarily cytosolic localization. These conditions may lead to reduced replication pausing and may lower replication stress at these sites during aging.

  14. Replication of UV-irradiated DNA in human cell extracts: Evidence for mutagenic bypass of pyrimidine dimers

    International Nuclear Information System (INIS)

    Thomas, D.C.; Kunkel, T.A.

    1993-01-01

    The authors have examined the efficiency and fidelity of simian virus 40-origin-dependent replication of UV-irradiated double-stranded DNA in extracts of human cells. Using as a mutational target the α-complementation domain of the Escherichia coli lacZ gene in bacteriophage M13mp2DNA, replication of undamaged DNA in HeLa cell extracts was highly accurate, whereas replication of DNA irradiated with UV light (280-320 nm) was both less efficient and less accurate. Replication was inhibited by irradiation in a dose-dependent manner. Nonetheless, covalently closed, monomer-length circular products were generated that were resistant to digestion by Dpn I, showing that they resulted from semiconservative replication. These products were incised by T4 endonuclease V, whereas the undamaged replication products were not, suggesting that pyrimidine dimers were bypassed during replication. When replicated, UV-irradiated DNA was used to transfect an E. coli α-complementation host strain to score mutant M13mp2 plaques, the mutant plaque frequency was substantially higher than that obtained with either unirradiated, replicated DNA, or unreplicated, UV-irradiated DNA. Both the increased mutagenicity and the inhibition of replication associated with UV irradiation were reversed by treatment of the irradiated DNA with photolyase before replication. Sequence analysis of mutants resulting from replication of UV-irradiated DNA demonstrated that most mutants contained C → T transition errors at dipyrimidine sites. A few mutants contained 1-nt frameshift errors or tandem double CC → TT substitutions. The data are consistent with the interpretation that pyrimidine dimers are bypassed during replication by the multiprotein replication apparatus in human cell extracts and that this bypass is mutagenic primarily via misincorporation of dAMP opposite a cytosine (or uracil) in the dimer. 56 refs., 2 figs., 3 tabs

  15. Can concurrent memory load reduce distraction? A replication study and beyond.

    Science.gov (United States)

    Gil-Gómez de Liaño, Beatriz; Stablum, Franca; Umiltà, Carlo

    2016-01-01

    The effects of concurrent working memory load in attentional processes have been 1 of the most puzzling issues in cognitive psychology. Studies have shown detrimental effects, no effects, and even beneficial effects of working memory load in different attentional tasks. In the present study we attempted to replicate Kim, Kim, and Chun's (2005, Experiment 3b) findings of beneficial effects of concurrent working memory load in a spatial Stroop-like task. In 3 experiments in which our sample was 3 times larger than that in the original Kim et al. study, we could not replicate their findings. The results are discussed in terms of what may have produced the conflicting results, trying to shed light on how working memory load affects attentional tasks. Also, we emphasize the importance of using adequately large samples in cognitive research. Although we acknowledge the relevance of meta-analyses to analyze conflicting results, in the present article we stress (perhaps more important) the power of an essential trademark in science for research development: replicability. (c) 2015 APA, all rights reserved).

  16. Integrated data lookup and replication scheme in mobile ad hoc networks

    Science.gov (United States)

    Chen, Kai; Nahrstedt, Klara

    2001-11-01

    Accessing remote data is a challenging task in mobile ad hoc networks. Two problems have to be solved: (1) how to learn about available data in the network; and (2) how to access desired data even when the original copy of the data is unreachable. In this paper, we develop an integrated data lookup and replication scheme to solve these problems. In our scheme, a group of mobile nodes collectively host a set of data to improve data accessibility for all members of the group. They exchange data availability information by broadcasting advertising (ad) messages to the group using an adaptive sending rate policy. The ad messages are used by other nodes to derive a local data lookup table, and to reduce data redundancy within a connected group. Our data replication scheme predicts group partitioning based on each node's current location and movement patterns, and replicates data to other partitions before partitioning occurs. Our simulations show that data availability information can quickly propagate throughout the network, and that the successful data access ratio of each node is significantly improved.

  17. Fire-driven alien invasion in a fire-adapted ecosystem

    Science.gov (United States)

    Keeley, Jon E.; Brennan, Teresa J.

    2012-01-01

    Disturbance plays a key role in many alien plant invasions. However, often the main driver of invasion is not disturbance per se but alterations in the disturbance regime. In some fire-adapted shrublands, the community is highly resilient to infrequent, high-intensity fires, but changes in the fire regime that result in shorter fire intervals may make these communities more susceptible to alien plant invasions. This study examines several wildfire events that resulted in short fire intervals in California chaparral shrublands. In one study, we compared postfire recovery patterns in sites with different prefire stand ages (3 and 24 years), and in another study we compared sites that had burned once in four years with sites that had burned twice in this period. The population size of the dominant native shrub Adenostoma fasciculatum was drastically reduced following fire in the 3-year sites relative to the 24-year sites. The 3-year sites had much greater alien plant cover and significantly lower plant diversity than the 24-year sites. In a separate study, repeat fires four years apart on the same sites showed that annual species increased significantly after the second fire, and alien annuals far outnumbered native annuals. Aliens included both annual grasses and annual forbs and were negatively correlated with woody plant cover. Native woody species regenerated well after the first fire but declined after the second fire, and one obligate seeding shrub was extirpated from two sites by the repeat fires. It is concluded that some fire-adapted shrublands are vulnerable to changes in fire regime, and this can lead to a loss of native diversity and put the community on a trajectory towards type conversion from a woody to an herbaceous system. Such changes result in alterations in the proportion of natives to non-natives, changes in functional types from deeply rooted shrubs to shallow rooted grasses and forbs, increased fire frequency due to the increase in fine fuels

  18. Fire-driven alien invasion in a fire-adapted ecosystem.

    Science.gov (United States)

    Keeley, Jon E; Brennan, Teresa J

    2012-08-01

    Disturbance plays a key role in many alien plant invasions. However, often the main driver of invasion is not disturbance per se but alterations in the disturbance regime. In some fire-adapted shrublands, the community is highly resilient to infrequent, high-intensity fires, but changes in the fire regime that result in shorter fire intervals may make these communities more susceptible to alien plant invasions. This study examines several wildfire events that resulted in short fire intervals in California chaparral shrublands. In one study, we compared postfire recovery patterns in sites with different prefire stand ages (3 and 24 years), and in another study we compared sites that had burned once in four years with sites that had burned twice in this period. The population size of the dominant native shrub Adenostoma fasciculatum was drastically reduced following fire in the 3-year sites relative to the 24-year sites. The 3-year sites had much greater alien plant cover and significantly lower plant diversity than the 24-year sites. In a separate study, repeat fires four years apart on the same sites showed that annual species increased significantly after the second fire, and alien annuals far outnumbered native annuals. Aliens included both annual grasses and annual forbs and were negatively correlated with woody plant cover. Native woody species regenerated well after the first fire but declined after the second fire, and one obligate seeding shrub was extirpated from two sites by the repeat fires. It is concluded that some fire-adapted shrublands are vulnerable to changes in fire regime, and this can lead to a loss of native diversity and put the community on a trajectory towards type conversion from a woody to an herbaceous system. Such changes result in alterations in the proportion of natives to non-natives, changes in functional types from deeply rooted shrubs to shallow rooted grasses and forbs, increased fire frequency due to the increase in fine fuels

  19. Earth, Air, Fire and Water in Our Elements

    Science.gov (United States)

    Lievesley, Tara

    2007-01-01

    The idea that everything is made of the four "elements", earth, air, fire and water, goes back to the ancient Greeks. In this article, the author talks about the origins of ideas about the elements. The author provides an account that attempts to summarise thousands of years of theoretical development of the elements in a thousand words or so.

  20. [The effects of TorR protein on initiation of DNA replication in Escherichia coli].

    Science.gov (United States)

    Yuan, Yao; Jiaxin, Qiao; Jing, Li; Hui, Li; Morigen, Morigen

    2015-03-01

    The two-component systems, which could sense and respond to environmental changes, widely exist in bacteria as a signal transduction pathway. The bacterial CckA/CtrA, ArcA/ArcB and PhoP/PhoQ two-component systems are associated with initiation of DNA replication and cell division, however, the effects of the TorS/TorR system on cell cycle and DNA replication remains unknown. The TorS/TorR system in Escherichia coli can sense changes in trimethylamine oxide (TMAO) concentration around the cells. However, it is unknown if it also affects initiation of DNA replication. We detected DNA replication patterns in ΔtorS and ΔtorR mutant strains by flow cytometry. We found that the average number of replication origins (oriCs) per cell and doubling time in ΔtorS mutants were the same while the average number of oriCs in ΔtorR mutants was increased compared with that in wild-type cells. These results indicated that absence of TorR led to an earlier initiation of DNA replication than that in wild-type cells. Strangely, neither overexpression of TorR nor co-expression of TorR and TorS could restore ΔtorR mutant phenotype to the wild type. However, overexpression of SufD in both wild type and ΔtorR mutants promoted initiation of DNA replication, while mutation of SufD delayed it in ΔtorR mutants. Thus, TorR may affect initiation of DNA replication indirectly through regulating gene expression of sufD.

  1. Chromosome replication, cell growth, division and shape: a personal perspective

    Directory of Open Access Journals (Sweden)

    Arieh eZaritsky

    2015-08-01

    Full Text Available The origins of Molecular Biology and Bacterial Physiology are reviewed, from our personal standpoints, emphasizing the coupling between bacterial growth, chromosome replication and cell division, dimensions and shape. Current knowledge is discussed with historical perspective, summarizing past and present achievements and enlightening ideas for future studies. An interactive simulation program of the Bacterial Cell Division Cycle (BCD, described as The Central Dogma in Bacteriology, is briefly represented. The coupled process of transcription/translation of genes encoding membrane proteins and insertion into the membrane (so-called transertion is invoked as the functional relationship between the only two unique macromolecules in the cell, DNA and peptidoglycan embodying the nucleoid and the sacculus respectively. We envision that nucleoid complexity, defined as the weighted-mean DNA content associated with the replication terminus, is directly related to cell shape through the transertion process. Accordingly, the primary signal for cell division transmitted by DNA dynamics (replication, transcription and segregation to the peptidoglycan biosynthetic machinery is of a physico-chemical nature, eg stress in the plasma membrane, relieving nucleoid occlusion in the cell's center hence enabling the divisome to assemble and function between segregated daughter nucleoids.

  2. Long and Short-Term Effects of Fire on Soil Charcoal of a Conifer Forest in Southwest Oregon

    Directory of Open Access Journals (Sweden)

    Brett Morrissette

    2012-06-01

    Full Text Available In 2002, the Biscuit Wildfire burned a portion of the previously established, replicated conifer unthinned and thinned experimental units of the Siskiyou Long-Term Ecosystem Productivity (LTEP experiment, southwest Oregon. Charcoal C in pre and post-fire O horizon and mineral soil was quantified by physical separation and a peroxide-acid digestion method. The abrupt, short-term fire event caused O horizon charcoal C to increase by a factor of ten to >200 kg C ha−1. The thinned wildfire treatment produced less charcoal C than unthinned wildfire and thinned prescribed fire treatments. The charcoal formation rate was 1 to 8% of woody fuels consumed, and this percentage was negatively related to woody fuels consumed, resulting in less charcoal formation with greater fire severity. Charcoal C averaged 2000 kg ha−1 in 0–3 cm mineral soil and may have decreased as a result of fire, coincident with convective or erosive loss of mineral soil. Charcoal C in 3–15 cm mineral soil was stable at 5500 kg C ha−1. Long-term soil C sequestration in the Siskiyou LTEP soils is greatly influenced by the contribution of charcoal C, which makes up 20% of mineral soil organic C. This research reiterates the importance of fire to soil C in a southwestern Oregon coniferous forest ecosystem.

  3. Evaluation of Criteria for the Detection of Fires in Underground Conveyor Belt Haulageways.

    Science.gov (United States)

    Litton, Charles D; Perera, Inoka Eranda

    2012-07-01

    Large-scale experiments were conducted in an above-ground gallery to simulate typical fires that develop along conveyor belt transport systems within underground coal mines. In the experiments, electrical strip heaters, imbedded ~5 cm below the top surface of a large mass of coal rubble, were used to ignite the coal, producing an open flame. The flaming coal mass subsequently ignited 1.83-meter-wide conveyor belts located approximately 0.30 m above the coal surface. Gas samples were drawn through an averaging probe located approximately 20 m downstream of the coal for continuous measurement of CO, CO 2 , and O 2 as the fire progressed through the stages of smoldering coal, flaming coal, and flaming conveyor belt. Also located approximately 20 m from the fire origin and approximately 0.5 m below the roof of the gallery were two commercially available smoke detectors, a light obscuration meter, and a sampling probe for measurement of total mass concentration of smoke particles. Located upstream of the fire origin and also along the wall of the gallery at approximately 14 m and 5 m upstream were two video cameras capable of both smoke and flame detection. During the experiments, alarm times of the smoke detectors and video cameras were measured while the smoke obscuration and total smoke mass were continually measured. Twelve large-scale experiments were conducted using three different types of fire-resistant conveyor belts and four air velocities for each belt. The air velocities spanned the range from 1.0 m/s to 6.9 m/s. The results of these experiments are compared to previous large-scale results obtained using a smaller fire gallery and much narrower (1.07-m) conveyor belts to determine if the fire detection criteria previously developed (1) remained valid for the wider conveyor belts. Although some differences between these and the previous experiments did occur, the results, in general, compare very favorably. Differences are duly noted and their impact on fire

  4. Post-fire vegetation and fuel development influences fire severity patterns in reburns.

    Science.gov (United States)

    Coppoletta, Michelle; Merriam, Kyle E; Collins, Brandon M

    2016-04-01

    In areas where fire regimes and forest structure have been dramatically altered, there is increasing concern that contemporary fires have the potential to set forests on a positive feedback trajectory with successive reburns, one in which extensive stand-replacing fire could promote more stand-replacing fire. Our study utilized an extensive set of field plots established following four fires that occurred between 2000 and 2010 in the northern Sierra Nevada, California, USA that were subsequently reburned in 2012. The information obtained from these field plots allowed for a unique set of analyses investigating the effect of vegetation, fuels, topography, fire weather, and forest management on reburn severity. We also examined the influence of initial fire severity and time since initial fire on influential predictors of reburn severity. Our results suggest that high- to moderate-severity fire in the initial fires led to an increase in standing snags and shrub vegetation, which in combination with severe fire weather promoted high-severity fire effects in the subsequent reburn. Although fire behavior is largely driven by weather, our study demonstrates that post-fire vegetation composition and structure are also important drivers of reburn severity. In the face of changing climatic regimes and increases in extreme fire weather, these results may provide managers with options to create more fire-resilient ecosystems. In areas where frequent high-severity fire is undesirable, management activities such as thinning, prescribed fire, or managed wildland fire can be used to moderate fire behavior not only prior to initial fires, but also before subsequent reburns.

  5. HCV-induced autophagosomes are generated via homotypic fusion of phagophores that mediate HCV RNA replication.

    Directory of Open Access Journals (Sweden)

    Linya Wang

    2017-09-01

    Full Text Available Hepatitis C virus (HCV induces autophagy to promote its replication, including its RNA replication, which can take place on double-membrane vesicles known as autophagosomes. However, how HCV induces the biogenesis of autophagosomes and how HCV RNA replication complex may be assembled on autophagosomes were largely unknown. During autophagy, crescent membrane structures known as phagophores first appear in the cytoplasm, which then progress to become autophagosomes. By conducting electron microscopy and in vitro membrane fusion assay, we found that phagophores induced by HCV underwent homotypic fusion to generate autophagosomes in a process dependent on the SNARE protein syntaxin 7 (STX7. Further analyses by live-cell imaging and fluorescence microscopy indicated that HCV-induced phagophores originated from the endoplasmic reticulum (ER. Interestingly, comparing with autophagy induced by nutrient starvation, the progression of phagophores to autophagosomes induced by HCV took significantly longer time, indicating fundamental differences in the biogenesis of autophagosomes induced by these two different stimuli. As the knockdown of STX7 to inhibit the formation of autophagosomes did not affect HCV RNA replication, and purified phagophores could mediate HCV RNA replication, the assembly of the HCV RNA replication complex on autophagosomes apparently took place during the formative stage of phagophores. These findings provided important information for understanding how HCV controlled and modified this important cellular pathway for its own replication.

  6. Fire intensity impacts on post-fire temperate coniferous forest net primary productivity

    Science.gov (United States)

    Sparks, Aaron M.; Kolden, Crystal A.; Smith, Alistair M. S.; Boschetti, Luigi; Johnson, Daniel M.; Cochrane, Mark A.

    2018-02-01

    Fire is a dynamic ecological process in forests and impacts the carbon (C) cycle through direct combustion emissions, tree mortality, and by impairing the ability of surviving trees to sequester carbon. While studies on young trees have demonstrated that fire intensity is a determinant of post-fire net primary productivity, wildland fires on landscape to regional scales have largely been assumed to either cause tree mortality, or conversely, cause no physiological impact, ignoring the impacted but surviving trees. Our objective was to understand how fire intensity affects post-fire net primary productivity in conifer-dominated forested ecosystems on the spatial scale of large wildland fires. We examined the relationships between fire radiative power (FRP), its temporal integral (fire radiative energy - FRE), and net primary productivity (NPP) using 16 years of data from the MOderate Resolution Imaging Spectrometer (MODIS) for 15 large fires in western United States coniferous forests. The greatest NPP post-fire loss occurred 1 year post-fire and ranged from -67 to -312 g C m-2 yr-1 (-13 to -54 %) across all fires. Forests dominated by fire-resistant species (species that typically survive low-intensity fires) experienced the lowest relative NPP reductions compared to forests with less resistant species. Post-fire NPP in forests that were dominated by fire-susceptible species were not as sensitive to FRP or FRE, indicating that NPP in these forests may be reduced to similar levels regardless of fire intensity. Conversely, post-fire NPP in forests dominated by fire-resistant and mixed species decreased with increasing FRP or FRE. In some cases, this dose-response relationship persisted for more than a decade post-fire, highlighting a legacy effect of fire intensity on post-fire C dynamics in these forests.

  7. A Method of Fire Scenarios Identification in a Consolidated Fire Risk Analysis

    International Nuclear Information System (INIS)

    Lim, Ho Gon; Han, Sang Hoon; Yang, Joon Eon

    2010-01-01

    Conventional fire PSA consider only two cases of fire scenarios, that is one for fire without propagation and the other for single propagation to neighboring compartment. Recently, a consolidated fire risk analysis using single fault tree (FT) was developed. However, the fire scenario identification in the new method is similar to conventional fire analysis method. The present study develops a new method of fire scenario identification in a consolidated fire risk analysis method. An equation for fire propagation is developed to identify fire scenario and a mapping method of fire scenarios into internal event risk model is discussed. Finally, an algorithm for automatic program is suggested

  8. Reduced predation risk for melanistic pygmy grasshoppers in post-fire environments

    Science.gov (United States)

    Karpestam, Einat; Merilaita, Sami; Forsman, Anders

    2012-01-01

    The existence of melanistic (black) color forms in many species represents interesting model systems that have played important roles for our understanding of selective processes, evolution of adaptations, and the maintenance of variation. A recent study reported on rapid evolutionary shifts in frequencies of the melanistic forms in replicated populations of Tetrix subulata pygmy grasshoppers; the incidence of the melanistic form was higher in recently burned areas with backgrounds blackened by fire than in nonburned areas, and it declined over time in postfire environments. Here, we tested the hypothesis that the frequency shifts of the black color variant were driven, at least in part, by changes in the selective regime imposed by visual predators. To study detectability of the melanistic form, we presented human “predators” with images of black grasshoppers and samples of the natural habitat on computer screens. We demonstrate that the protective value of black coloration differs between burnt and nonburnt environments and gradually increases in habitats that have been more blackened by fire. These findings support the notion that a black color pattern provides improved protection from visually oriented predators against blackened backgrounds and implicate camouflage and predation as important drivers of fire melanism in pygmy grasshoppers. PMID:23139879

  9. Fire and fire ecology: Concepts and principles

    Science.gov (United States)

    Mark A. Cochrane; Kevin C. Ryan

    2009-01-01

    Fire has been central to terrestrial life ever since early anaerobic microorganisms poisoned the atmosphere with oxygen and multicellular plant life moved onto land. The combination of fuels, oxygen, and heat gave birth to fire on Earth. Fire is not just another evolutionary challenge that life needed to overcome, it is, in fact, a core ecological process across much...

  10. Forest fires

    International Nuclear Information System (INIS)

    Fuller, M.

    1991-01-01

    This book examines the many complex and sensitive issues relating to wildland fires. Beginning with an overview of the fires of 1980s, the book discusses the implications of continued drought and considers the behavior of wildland fires, from ignition and spread to spotting and firestorms. Topics include the effects of weather, forest fuels, fire ecology, and the effects of fire on plants and animals. In addition, the book examines firefighting methods and equipment, including new minimum impact techniques and compressed air foam; prescribed burning; and steps that can be taken to protect individuals and human structures. A history of forest fire policies in the U.S. and a discussion of solutions to fire problems around the world completes the coverage. With one percent of the earth's surface burning every year in the last decade, this is a penetrating book on a subject of undeniable importance

  11. Detection and Characterization of Low Temperature Peat Fires during the 2015 Fire Catastrophe in Indonesia Using a New High-Sensitivity Fire Monitoring Satellite Sensor (FireBird)

    Science.gov (United States)

    Atwood, Elizabeth C.; Englhart, Sandra; Lorenz, Eckehard; Halle, Winfried; Wiedemann, Werner; Siegert, Florian

    2016-01-01

    Vast and disastrous fires occurred on Borneo during the 2015 dry season, pushing Indonesia into the top five carbon emitting countries. The region was affected by a very strong El Niño-Southern Oscillation (ENSO) climate phenomenon, on par with the last severe event in 1997/98. Fire dynamics in Central Kalimantan were investigated using an innovative sensor offering higher sensitivity to a wider range of fire intensities at a finer spatial resolution (160 m) than heretofore available. The sensor is onboard the TET-1 satellite, part of the German Aerospace Center (DLR) FireBird mission. TET-1 images (acquired every 2–3 days) from the middle infrared were used to detect fires continuously burning for almost three weeks in the protected peatlands of Sebangau National Park as well as surrounding areas with active logging and oil palm concessions. TET-1 detection capabilities were compared with MODIS active fire detection and Landsat burned area algorithms. Fire dynamics, including fire front propagation speed and area burned, were investigated. We show that TET-1 has improved detection capabilities over MODIS in monitoring low-intensity peatland fire fronts through thick smoke and haze. Analysis of fire dynamics revealed that the largest burned areas resulted from fire front lines started from multiple locations, and the highest propagation speeds were in excess of 500 m/day (all over peat > 2m deep). Fires were found to occur most often in concessions that contained drainage infrastructure but were not cleared prior to the fire season. Benefits of implementing this sensor system to improve current fire management techniques are discussed. Near real-time fire detection together with enhanced fire behavior monitoring capabilities would not only improve firefighting efforts, but also benefit analysis of fire impact on tropical peatlands, greenhouse gas emission estimations as well as mitigation measures to reduce severe fire events in the future. PMID:27486664

  12. Plum Pox Virus 6K1 Protein Is Required for Viral Replication and Targets the Viral Replication Complex at the Early Stage of Infection.

    Science.gov (United States)

    Cui, Hongguang; Wang, Aiming

    2016-05-15

    The potyviral RNA genome encodes two polyproteins that are proteolytically processed by three viral protease domains into 11 mature proteins. Extensive molecular studies have identified functions for the majority of the viral proteins. For example, 6K2, one of the two smallest potyviral proteins, is an integral membrane protein and induces the endoplasmic reticulum (ER)-originated replication vesicles that target the chloroplast for robust viral replication. However, the functional role of 6K1, the other smallest protein, remains uncharacterized. In this study, we developed a series of recombinant full-length viral cDNA clones derived from a Canadian Plum pox virus (PPV) isolate. We found that deletion of any of the short motifs of 6K1 (each of which ranged from 5 to 13 amino acids), most of the 6K1 sequence (but with the conserved sequence of the cleavage sites being retained), or all of the 6K1 sequence in the PPV infectious clone abolished viral replication. The trans expression of 6K1 or the cis expression of a dislocated 6K1 failed to rescue the loss-of-replication phenotype, suggesting the temporal and spatial requirement of 6K1 for viral replication. Disruption of the N- or C-terminal cleavage site of 6K1, which prevented the release of 6K1 from the polyprotein, either partially or completely inhibited viral replication, suggesting the functional importance of the mature 6K1. We further found that green fluorescent protein-tagged 6K1 formed punctate inclusions at the viral early infection stage and colocalized with chloroplast-bound viral replicase elements 6K2 and NIb. Taken together, our results suggest that 6K1 is required for viral replication and is an important viral element of the viral replication complex at the early infection stage. Potyviruses account for more than 30% of known plant viruses and consist of many agriculturally important viruses. The genomes of potyviruses encode two polyproteins that are proteolytically processed into 11 mature

  13. Initiation of simian virus 40 DNA replication in vitro: Pulse-chase experiments identify the first labeled species as topologically unwound

    International Nuclear Information System (INIS)

    Bullock, P.A.; Seo, Yeon Soo; Hurwitz, J.

    1989-01-01

    A distinct unwound form of DNA containing the simian virus 40 (SV40) origin is produced in replication reactions carried out in mixtures containing crude fractions prepared from HeLa cells. This species, termed form U R , comigrates on chloroquine-containing agarose gels with the upper part of the previously described heterogeneous highly unwound circular DNA, form U. As with form U, formation of form U R is dependent upon the SV40 tumor (T) antigen. Pulse-chase experiments demonstrate that the first species to incorporate labeled deoxyribonucleotides comigrates with form U R . Restriction analyses of the products of the pulse-chase experiments show that initiation occurs at the SV40 origin and then proceeds outward in a bidirectional manner. These experiments establish form U R as the earliest detectable substrate for SV40 DNA replication and suggest that SV40 DNA replication initiates on an unwound species

  14. Browns Ferry fire

    International Nuclear Information System (INIS)

    Harkleroad, J.R.

    1983-01-01

    A synopsis of the March 22, 1975 fire at Browns Ferry Nuclear Plant is discussed. Emphasis is placed on events prior to and during the fire. How the fire started, fire fighting activities, fire and smoke development, and restoration activities are discussed

  15. Overview of the 2013 FireFlux II grass fire field experiment

    Science.gov (United States)

    C.B. Clements; B. Davis; D. Seto; J. Contezac; A. Kochanski; J.-B. Fillipi; N. Lareau; B. Barboni; B. Butler; S. Krueger; R. Ottmar; R. Vihnanek; W.E. Heilman; J. Flynn; M.A. Jenkins; J. Mandel; C. Teske; D. Jimenez; J. O' Brien; B. Lefer

    2014-01-01

    In order to better understand the dynamics of fire-atmosphere interactions and the role of micrometeorology on fire behaviour the FireFlux campaign was conducted in 2006 on a coastal tall-grass prairie in southeast Texas, USA. The FireFlux campaign dataset has become the international standard for evaluating coupled fire-atmosphere model systems. While FireFlux is one...

  16. Exposure to radionuclides in smoke from vegetation fires

    Energy Technology Data Exchange (ETDEWEB)

    Carvalho, Fernando P., E-mail: carvalho@itn.pt; Oliveira, João M.; Malta, Margarida

    2014-02-01

    Naturally occurring radionuclides of uranium, thorium, radium, lead and polonium were determined in bushes and trees and in the smoke from summer forest fires. Activity concentrations of radionuclides in smoke particles were much enriched when compared to original vegetation. Polonium-210 ({sup 210}Po) in smoke was measured in concentrations much higher than all other radionuclides, reaching 7255 ± 285 Bq kg{sup −1}, mostly associated with the smaller size smoke particles (< 1.0 μm). Depending on smoke particle concentration, {sup 210}Po in surface air near forest fires displayed volume concentrations up to 70 mBq m{sup −3}, while in smoke-free air {sup 210}Po concentration was about 30 μBq m{sup −3}. The estimated absorbed radiation dose to an adult member of the public or a firefighter exposed for 24 h to inhalation of smoke near forest fires could exceed 5 μSv per day, i.e, more than 2000 times above the radiation dose from background radioactivity in surface air, and also higher than the radiation dose from {sup 210}Po inhalation in a chronic cigarette smoker. It is concluded that prolonged exposure to smoke allows for enhanced inhalation of radionuclides associated with smoke particles. Due to high radiotoxicity of alpha emitting radionuclides, and in particular of {sup 210}Po, the protection of respiratory tract of fire fighters is strongly recommended. - Highlights: • Natural radionuclides in vegetation are in low concentrations. • Forest fires release natural radionuclides from vegetation and concentrate them in inhalable ash particles. • Prolonged inhalation of smoke from forest fires gives rise enhanced radiation exposure of lungs especially due to polonium. • Respiratory protection of fire fighters and members of public is highly recommended for radioprotection reasons.

  17. Fire Risk Assessment of Adaptive Re-Use of Historic Shop Houses for Sleeping Accommodations in Malaysia

    Directory of Open Access Journals (Sweden)

    Mydin M.A.O.

    2014-01-01

    Full Text Available Heritage buildings were generally constructed without regard for fire risks or the requirements for fire protection, as are obligatory in new constructions. When a heritage building undergoes a change to its original function, improvements to the building’s fire safety are necessary to meet the needs of possible increases in occupancy loads and to account for fire risks related to the new usage. This research focuses on fire safety risks, fire protection and safety systems as well as the rules and regulations that an adaptive reuse heritage shop house is bound to when transitioning to a sleeping accommodation, which, in this case, means becoming a hotel. In this research, six heritage shop houses were chosen as case studies. The objectives of this research were to evaluate current fire emergency plans as well as to identify and assess possible fire hazards created by adaptive reuse of heritage shop houses to sleeping accommodations in Penang through a series of observations and interviews. The results of the research show that most of the buildings were provided with inadequate fire safety systems.

  18. Evidence supporting a role for TopBP1 and Brd4 in the initiation but not continuation of human papillomavirus 16 E1/E2-mediated DNA replication.

    Science.gov (United States)

    Gauson, Elaine J; Donaldson, Mary M; Dornan, Edward S; Wang, Xu; Bristol, Molly; Bodily, Jason M; Morgan, Iain M

    2015-05-01

    To replicate the double-stranded human papillomavirus 16 (HPV16) DNA genome, viral proteins E1 and E2 associate with the viral origin of replication, and E2 can also regulate transcription from adjacent promoters. E2 interacts with host proteins in order to regulate both transcription and replication; TopBP1 and Brd4 are cellular proteins that interact with HPV16 E2. Previous work with E2 mutants demonstrated the Brd4 requirement for the transactivation properties of E2, while TopBP1 is required for DNA replication induced by E2 from the viral origin of replication in association with E1. More-recent studies have also implicated Brd4 in the regulation of DNA replication by E2 and E1. Here, we demonstrate that both TopBP1 and Brd4 are present at the viral origin of replication and that interaction with E2 is required for optimal initiation of DNA replication. Both cellular proteins are present in E1-E2-containing nuclear foci, and the viral origin of replication is required for the efficient formation of these foci. Short hairpin RNA (shRNA) against either TopBP1 or Brd4 destroys the E1-E2 nuclear bodies but has no effect on E1-E2-mediated levels of DNA replication. An E2 mutation in the context of the complete HPV16 genome that compromises Brd4 interaction fails to efficiently establish episomes in primary human keratinocytes. Overall, the results suggest that interactions between TopBP1 and E2 and between Brd4 and E2 are required to correctly initiate DNA replication but are not required for continuing DNA replication, which may be mediated by alternative processes such as rolling circle amplification and/or homologous recombination. Human papillomavirus 16 (HPV16) is causative in many human cancers, including cervical and head and neck cancers, and is responsible for the annual deaths of hundreds of thousands of people worldwide. The current vaccine will save lives in future generations, but antivirals targeting HPV16 are required for the alleviation of disease

  19. Mechanisms of bacterial DNA replication restart

    Science.gov (United States)

    Windgassen, Tricia A; Wessel, Sarah R; Bhattacharyya, Basudeb

    2018-01-01

    Abstract Multi-protein DNA replication complexes called replisomes perform the essential process of copying cellular genetic information prior to cell division. Under ideal conditions, replisomes dissociate only after the entire genome has been duplicated. However, DNA replication rarely occurs without interruptions that can dislodge replisomes from DNA. Such events produce incompletely replicated chromosomes that, if left unrepaired, prevent the segregation of full genomes to daughter cells. To mitigate this threat, cells have evolved ‘DNA replication restart’ pathways that have been best defined in bacteria. Replication restart requires recognition and remodeling of abandoned replication forks by DNA replication restart proteins followed by reloading of the replicative DNA helicase, which subsequently directs assembly of the remaining replisome subunits. This review summarizes our current understanding of the mechanisms underlying replication restart and the proteins that drive the process in Escherichia coli (PriA, PriB, PriC and DnaT). PMID:29202195

  20. Fire models for assessment of nuclear power plant fires

    International Nuclear Information System (INIS)

    Nicolette, V.F.; Nowlen, S.P.

    1989-01-01

    This paper reviews the state-of-the-art in available fire models for the assessment of nuclear power plants fires. The advantages and disadvantages of three basic types of fire models (zone, field, and control volume) and Sandia's experience with these models will be discussed. It is shown that the type of fire model selected to solve a particular problem should be based on the information that is required. Areas of concern which relate to all nuclear power plant fire models are identified. 17 refs., 6 figs