WorldWideScience

Sample records for stalled replication sites

  1. DNA replication: stalling a fork for imprinting and switching

    DEFF Research Database (Denmark)

    Egel, Richard

    2004-01-01

    Mating-type switching in fission yeast has long been known to be directed by a DNA 'imprint'. This imprint has now been firmly characterized as a protected site-specific and strand-specific nick. New work also links the widely conserved Swi1-Swi3 complex to the protection of stalled replication...

  2. RECQ5 Helicase Cooperates with MUS81 Endonuclease in Processing Stalled Replication Forks at Common Fragile Sites during Mitosis

    DEFF Research Database (Denmark)

    Di Marco, Stefano; Hasanova, Zdenka; Kanagaraj, Radhakrishnan

    2017-01-01

    The MUS81-EME1 endonuclease cleaves late replication intermediates at common fragile sites (CFSs) during early mitosis to trigger DNA-repair synthesis that ensures faithful chromosome segregation. Here, we show that these DNA transactions are promoted by RECQ5 DNA helicase in a manner dependent...... on its Ser727 phosphorylation by CDK1. Upon replication stress, RECQ5 associates with CFSs in early mitosis through its physical interaction with MUS81 and promotes MUS81-dependent mitotic DNA synthesis. RECQ5 depletion or mutational inactivation of its ATP-binding site, RAD51-interacting domain...

  3. RFWD3-Dependent Ubiquitination of RPA Regulates Repair at Stalled Replication Forks.

    Science.gov (United States)

    Elia, Andrew E H; Wang, David C; Willis, Nicholas A; Boardman, Alexander P; Hajdu, Ildiko; Adeyemi, Richard O; Lowry, Elizabeth; Gygi, Steven P; Scully, Ralph; Elledge, Stephen J

    2015-10-15

    We have used quantitative proteomics to profile ubiquitination in the DNA damage response (DDR). We demonstrate that RPA, which functions as a protein scaffold in the replication stress response, is multiply ubiquitinated upon replication fork stalling. Ubiquitination of RPA occurs on chromatin, involves sites outside its DNA binding channel, does not cause proteasomal degradation, and increases under conditions of fork collapse, suggesting a role in repair at stalled forks. We demonstrate that the E3 ligase RFWD3 mediates RPA ubiquitination. RFWD3 is necessary for replication fork restart, normal repair kinetics during replication stress, and homologous recombination (HR) at stalled replication forks. Mutational analysis suggests that multisite ubiquitination of the entire RPA complex is responsible for repair at stalled forks. Multisite protein group sumoylation is known to promote HR in yeast. Our findings reveal a similar requirement for multisite protein group ubiquitination during HR at stalled forks in mammalian cells. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. FBH1 Catalyzes Regression of Stalled Replication Forks

    Directory of Open Access Journals (Sweden)

    Kasper Fugger

    2015-03-01

    Full Text Available DNA replication fork perturbation is a major challenge to the maintenance of genome integrity. It has been suggested that processing of stalled forks might involve fork regression, in which the fork reverses and the two nascent DNA strands anneal. Here, we show that FBH1 catalyzes regression of a model replication fork in vitro and promotes fork regression in vivo in response to replication perturbation. Cells respond to fork stalling by activating checkpoint responses requiring signaling through stress-activated protein kinases. Importantly, we show that FBH1, through its helicase activity, is required for early phosphorylation of ATM substrates such as CHK2 and CtIP as well as hyperphosphorylation of RPA. These phosphorylations occur prior to apparent DNA double-strand break formation. Furthermore, FBH1-dependent signaling promotes checkpoint control and preserves genome integrity. We propose a model whereby FBH1 promotes early checkpoint signaling by remodeling of stalled DNA replication forks.

  5. Checkpoint responses to replication stalling: inducing tolerance and preventing mutagenesis

    Energy Technology Data Exchange (ETDEWEB)

    Kai, Mihoko; Wang, Teresa S.-F

    2003-11-27

    Replication mutants often exhibit a mutator phenotype characterized by point mutations, single base frameshifts, and the deletion or duplication of sequences flanked by homologous repeats. Mutation in genes encoding checkpoint proteins can significantly affect the mutator phenotype. Here, we use fission yeast (Schizosaccharomyces pombe) as a model system to discuss the checkpoint responses to replication perturbations induced by replication mutants. Checkpoint activation induced by a DNA polymerase mutant, aside from delay of mitotic entry, up-regulates the translesion polymerase DinB (Pol{kappa}). Checkpoint Rad9-Rad1-Hus1 (9-1-1) complex, which is loaded onto chromatin by the Rad17-Rfc2-5 checkpoint complex in response to replication perturbation, recruits DinB onto chromatin to generate the point mutations and single nucleotide frameshifts in the replication mutator. This chain of events reveals a novel checkpoint-induced tolerance mechanism that allows cells to cope with replication perturbation, presumably to make possible restarting stalled replication forks. Fission yeast Cds1 kinase plays an essential role in maintaining DNA replication fork stability in the face of DNA damage and replication fork stalling. Cds1 kinase is known to regulate three proteins that are implicated in maintaining replication fork stability: Mus81-Eme1, a hetero-dimeric structure-specific endonuclease complex; Rqh1, a RecQ-family helicase involved in suppressing inappropriate recombination during replication; and Rad60, a protein required for recombinational repair during replication. These Cds1-regulated proteins are thought to cooperatively prevent mutagenesis and maintain replication fork stability in cells under replication stress. These checkpoint-regulated processes allow cells to survive replication perturbation by preventing stalled replication forks from degenerating into deleterious DNA structures resulting in genomic instability and cancer development.

  6. Checkpoint responses to replication stalling: inducing tolerance and preventing mutagenesis

    International Nuclear Information System (INIS)

    Kai, Mihoko; Wang, Teresa S.-F.

    2003-01-01

    Replication mutants often exhibit a mutator phenotype characterized by point mutations, single base frameshifts, and the deletion or duplication of sequences flanked by homologous repeats. Mutation in genes encoding checkpoint proteins can significantly affect the mutator phenotype. Here, we use fission yeast (Schizosaccharomyces pombe) as a model system to discuss the checkpoint responses to replication perturbations induced by replication mutants. Checkpoint activation induced by a DNA polymerase mutant, aside from delay of mitotic entry, up-regulates the translesion polymerase DinB (Polκ). Checkpoint Rad9-Rad1-Hus1 (9-1-1) complex, which is loaded onto chromatin by the Rad17-Rfc2-5 checkpoint complex in response to replication perturbation, recruits DinB onto chromatin to generate the point mutations and single nucleotide frameshifts in the replication mutator. This chain of events reveals a novel checkpoint-induced tolerance mechanism that allows cells to cope with replication perturbation, presumably to make possible restarting stalled replication forks. Fission yeast Cds1 kinase plays an essential role in maintaining DNA replication fork stability in the face of DNA damage and replication fork stalling. Cds1 kinase is known to regulate three proteins that are implicated in maintaining replication fork stability: Mus81-Eme1, a hetero-dimeric structure-specific endonuclease complex; Rqh1, a RecQ-family helicase involved in suppressing inappropriate recombination during replication; and Rad60, a protein required for recombinational repair during replication. These Cds1-regulated proteins are thought to cooperatively prevent mutagenesis and maintain replication fork stability in cells under replication stress. These checkpoint-regulated processes allow cells to survive replication perturbation by preventing stalled replication forks from degenerating into deleterious DNA structures resulting in genomic instability and cancer development

  7. 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.

  8. Stalled replication forks generate a distinct mutational signature in yeast

    DEFF Research Database (Denmark)

    Larsen, Nicolai B.; Liberti, Sascha E.; Vogel, Ivan

    2017-01-01

    Proliferating cells acquire genome alterations during the act of DNA replication. This leads to mutation accumulation and somatic cell mosaicism in multicellular organisms, and is also implicated as an underlying cause of aging and tumorigenesis. The molecular mechanisms of DNA replication...... Escherichia coli Tus/Ter complex) engineered into the yeast genome. We demonstrate that transient stalling at this barrier induces a distinct pattern of genome rearrangements in the newly replicated region behind the stalled fork, which primarily consist of localized losses and duplications of DNA sequences....... These genetic alterations arise through the aberrant repair of a single-stranded DNA gap, in a process that is dependent on Exo1- and Shu1-dependent homologous recombination repair (HRR). Furthermore, aberrant processing of HRR intermediates, and elevated HRR-associated mutagenesis, is detectable in a yeast...

  9. Both DNA Polymerases δ and ε Contact Active and Stalled Replication Forks Differently

    Science.gov (United States)

    Yu, Chuanhe; Gan, Haiyun

    2017-01-01

    ABSTRACT Three DNA polymerases, polymerases α, δ, and ε (Pol α, Pol δ, and Pol ε), are responsible for eukaryotic genome duplication. When DNA replication stress is encountered, DNA synthesis stalls until the stress is ameliorated. However, it is not known whether there is a difference in the association of each polymerase with active and stalled replication forks. Here, we show that each DNA polymerase has a distinct pattern of association with active and stalled replication forks. Pol α is enriched at extending Okazaki fragments of active and stalled forks. In contrast, although Pol δ contacts the nascent lagging strands of active and stalled forks, it binds to only the matured (and not elongating) Okazaki fragments of stalled forks. Pol ε has greater contact with the nascent single-stranded DNA (ssDNA) of the leading strand on active forks than on stalled forks. We propose that the configuration of DNA polymerases at stalled forks facilitates the resumption of DNA synthesis after stress removal. PMID:28784720

  10. 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

  11. Replication Stalling and Heteroduplex Formation within CAG/CTG Trinucleotide Repeats by Mismatch Repair

    KAUST Repository

    Viterbo, David

    2016-03-16

    Trinucleotide repeat expansions are responsible for at least two dozen neurological disorders. Mechanisms leading to these large expansions of repeated DNA are still poorly understood. It was proposed that transient stalling of the replication fork by the repeat tract might trigger slippage of the newly-synthesized strand over its template, leading to expansions or contractions of the triplet repeat. However, such mechanism was never formally proven. Here we show that replication fork pausing and CAG/CTG trinucleotide repeat instability are not linked, stable and unstable repeats exhibiting the same propensity to stall replication forks when integrated in a yeast natural chromosome. We found that replication fork stalling was dependent on the integrity of the mismatch-repair system, especially the Msh2p-Msh6p complex, suggesting that direct interaction of MMR proteins with secondary structures formed by trinucleotide repeats in vivo, triggers replication fork pauses. We also show by chromatin immunoprecipitation that Msh2p is enriched at trinucleotide repeat tracts, in both stable and unstable orientations, this enrichment being dependent on MSH3 and MSH6. Finally, we show that overexpressing MSH2 favors the formation of heteroduplex regions, leading to an increase in contractions and expansions of CAG/CTG repeat tracts during replication, these heteroduplexes being dependent on both MSH3 and MSH6. These heteroduplex regions were not detected when a mutant msh2-E768A gene in which the ATPase domain was mutated was overexpressed. Our results unravel two new roles for mismatch-repair proteins: stabilization of heteroduplex regions and transient blocking of replication forks passing through such repeats. Both roles may involve direct interactions between MMR proteins and secondary structures formed by trinucleotide repeat tracts, although indirect interactions may not be formally excluded.

  12. Replication Stalling and Heteroduplex Formation within CAG/CTG Trinucleotide Repeats by Mismatch Repair

    KAUST Repository

    Viterbo, David; Michoud, Gregoire; Mosbach, Valentine; Dujon, Bernard; Richard, Guy-Franck

    2016-01-01

    Trinucleotide repeat expansions are responsible for at least two dozen neurological disorders. Mechanisms leading to these large expansions of repeated DNA are still poorly understood. It was proposed that transient stalling of the replication fork by the repeat tract might trigger slippage of the newly-synthesized strand over its template, leading to expansions or contractions of the triplet repeat. However, such mechanism was never formally proven. Here we show that replication fork pausing and CAG/CTG trinucleotide repeat instability are not linked, stable and unstable repeats exhibiting the same propensity to stall replication forks when integrated in a yeast natural chromosome. We found that replication fork stalling was dependent on the integrity of the mismatch-repair system, especially the Msh2p-Msh6p complex, suggesting that direct interaction of MMR proteins with secondary structures formed by trinucleotide repeats in vivo, triggers replication fork pauses. We also show by chromatin immunoprecipitation that Msh2p is enriched at trinucleotide repeat tracts, in both stable and unstable orientations, this enrichment being dependent on MSH3 and MSH6. Finally, we show that overexpressing MSH2 favors the formation of heteroduplex regions, leading to an increase in contractions and expansions of CAG/CTG repeat tracts during replication, these heteroduplexes being dependent on both MSH3 and MSH6. These heteroduplex regions were not detected when a mutant msh2-E768A gene in which the ATPase domain was mutated was overexpressed. Our results unravel two new roles for mismatch-repair proteins: stabilization of heteroduplex regions and transient blocking of replication forks passing through such repeats. Both roles may involve direct interactions between MMR proteins and secondary structures formed by trinucleotide repeat tracts, although indirect interactions may not be formally excluded.

  13. Phosphorylated RPA recruits PALB2 to stalled DNA replication forks to facilitate fork recovery.

    Science.gov (United States)

    Murphy, Anar K; Fitzgerald, Michael; Ro, Teresa; Kim, Jee Hyun; Rabinowitsch, Ariana I; Chowdhury, Dipanjan; Schildkraut, Carl L; Borowiec, James A

    2014-08-18

    Phosphorylation of replication protein A (RPA) by Cdk2 and the checkpoint kinase ATR (ATM and Rad3 related) during replication fork stalling stabilizes the replisome, but how these modifications safeguard the fork is not understood. To address this question, we used single-molecule fiber analysis in cells expressing a phosphorylation-defective RPA2 subunit or lacking phosphatase activity toward RPA2. Deregulation of RPA phosphorylation reduced synthesis at forks both during replication stress and recovery from stress. The ability of phosphorylated RPA to stimulate fork recovery is mediated through the PALB2 tumor suppressor protein. RPA phosphorylation increased localization of PALB2 and BRCA2 to RPA-bound nuclear foci in cells experiencing replication stress. Phosphorylated RPA also stimulated recruitment of PALB2 to single-strand deoxyribonucleic acid (DNA) in a cell-free system. Expression of mutant RPA2 or loss of PALB2 expression led to significant DNA damage after replication stress, a defect accentuated by poly-ADP (adenosine diphosphate) ribose polymerase inhibitors. These data demonstrate that phosphorylated RPA recruits repair factors to stalled forks, thereby enhancing fork integrity during replication stress. © 2014 Murphy et al.

  14. Disruption of PCNA-lamins A/C interactions by prelamin A induces DNA replication fork stalling.

    Science.gov (United States)

    Cobb, Andrew M; Murray, Thomas V; Warren, Derek T; Liu, Yiwen; Shanahan, Catherine M

    2016-09-02

    The accumulation of prelamin A is linked to disruption of cellular homeostasis, tissue degeneration and aging. Its expression is implicated in compromised genome stability and increased levels of DNA damage, but to date there is no complete explanation for how prelamin A exerts its toxic effects. As the nuclear lamina is important for DNA replication we wanted to investigate the relationship between prelamin A expression and DNA replication fork stability. In this study we report that the expression of prelamin A in U2OS cells induced both mono-ubiquitination of proliferating cell nuclear antigen (PCNA) and subsequent induction of Pol η, two hallmarks of DNA replication fork stalling. Immunofluorescence microscopy revealed that cells expressing prelamin A presented with high levels of colocalisation between PCNA and γH2AX, indicating collapse of stalled DNA replication forks into DNA double-strand breaks. Subsequent protein-protein interaction assays showed prelamin A interacted with PCNA and that its presence mitigated interactions between PCNA and the mature nuclear lamina. Thus, we propose that the cytotoxicity of prelamin A arises in part, from it actively competing against mature lamin A to bind PCNA and that this destabilises DNA replication to induce fork stalling which in turn contributes to genomic instability.

  15. Stalled repair of lesions when present within a clustered DNA damage site

    International Nuclear Information System (INIS)

    Lomax, M.E.; Cunniffe, S.; O'Neill, P.

    2003-01-01

    Ionising radiation produces clustered DNA damages (two or more lesions within one or two helical turns of the DNA) which could challenge the repair mechanism(s) of the cell. Using purified base excision repair (BER) enzymes and synthetic oligonucleotides a number of recent studies have established the excision of a lesion within clustered damage sites is compromised. Evidence will be presented that the efficiency of repair of lesions within a clustered DNA damage site is reduced, relative to that of the isolated lesions, since the lifetime of both lesions is extended by up to four fold. Simple clustered damage sites, comprised of single-strand breaks, abasic sites and base damages, one or five bases 3' or 5' to each other, were synthesised in oligonucleotides and repair carried out in mammalian cell nuclear extracts. The rate of repair of the single-strand break/abasic site within these clustered damage sites is reduced, mainly due to inhibition of the DNA ligase. The mechanism of repair of the single-strand break/abasic site shows some asymmetry. Repair appears to be by the short-patch BER pathway when the lesions are 5' to each other. In contrast, when the lesions are 3' to each other repair appears to proceed along the long-patch BER pathway. The lesions within the cluster are processed sequentially, the single-strand break/abasic site being repaired before excision of 8-oxoG, limiting the formation of double-strand breaks to <2%. Stalled processing of clustered DNA damage extends the lifetime of the lesions to an extent that could have biological consequences, e.g. if the lesions are still present during transcription and/or at replication mutations could arise

  16. A ruthenium polypyridyl intercalator stalls DNA replication forks, radiosensitizes human cancer cells and is enhanced by Chk1 inhibition

    Science.gov (United States)

    Gill, Martin R.; Harun, Siti Norain; Halder, Swagata; Boghozian, Ramon A.; Ramadan, Kristijan; Ahmad, Haslina; Vallis, Katherine A.

    2016-08-01

    Ruthenium(II) polypyridyl complexes can intercalate DNA with high affinity and prevent cell proliferation; however, the direct impact of ruthenium-based intercalation on cellular DNA replication remains unknown. Here we show the multi-intercalator [Ru(dppz)2(PIP)]2+ (dppz = dipyridophenazine, PIP = 2-(phenyl)imidazo[4,5-f][1,10]phenanthroline) immediately stalls replication fork progression in HeLa human cervical cancer cells. In response to this replication blockade, the DNA damage response (DDR) cell signalling network is activated, with checkpoint kinase 1 (Chk1) activation indicating prolonged replication-associated DNA damage, and cell proliferation is inhibited by G1-S cell-cycle arrest. Co-incubation with a Chk1 inhibitor achieves synergistic apoptosis in cancer cells, with a significant increase in phospho(Ser139) histone H2AX (γ-H2AX) levels and foci indicating increased conversion of stalled replication forks to double-strand breaks (DSBs). Normal human epithelial cells remain unaffected by this concurrent treatment. Furthermore, pre-treatment of HeLa cells with [Ru(dppz)2(PIP)]2+ before external beam ionising radiation results in a supra-additive decrease in cell survival accompanied by increased γ-H2AX expression, indicating the compound functions as a radiosensitizer. Together, these results indicate ruthenium-based intercalation can block replication fork progression and demonstrate how these DNA-binding agents may be combined with DDR inhibitors or ionising radiation to achieve more efficient cancer cell killing.

  17. Stop Stalling: Mus81 Required for Efficient Replication | Center for Cancer Research

    Science.gov (United States)

    DNA replication is precisely controlled to ensure that daughter cells receive intact, accurate genetic information. Each segment of DNA must be copied only once, and the rate of replication coordinated genome-wide. Mild replication stress slows DNA synthesis and activates a pathway involving the Mus81 endonuclease, which generates a series of DNA breaks that are rapidly repaired, allowing the cell to avoid activating the S-phase checkpoint and its potentially damaging outcomes of apoptosis or error-prone repair. Mirit Aladjem, Ph.D., of CCR’s Developmental Therapeutics Branch, and her colleagues wondered whether Mus81 also plays a role in regulating the replication rate during growth in the absence of stress.

  18. Replication stalling by catalytically impaired Twinkle induces mitochondrial DNA rearrangements in cultured cells

    NARCIS (Netherlands)

    Pohjoismaki, J.L.; Goffart, S.; Spelbrink, J.N.

    2011-01-01

    Pathological mitochondrial DNA (mtDNA) rearrangements have been proposed to result from repair of double-strand breaks caused by blockage of mitochondrial DNA (mtDNA) replication. As mtDNA deletions are seen only in post-mitotic tissues, it has been suggested that they are selected out in actively

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

    Directory of Open Access Journals (Sweden)

    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.

  20. 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.

  1. The Escherichia coli Tus-Ter replication fork barrier causes site-specific DNA replication perturbation in yeast

    DEFF Research Database (Denmark)

    Larsen, Nicolai B; Sass, Ehud; Suski, Catherine

    2014-01-01

    Replication fork (RF) pausing occurs at both 'programmed' sites and non-physiological barriers (for example, DNA adducts). Programmed RF pausing is required for site-specific DNA replication termination in Escherichia coli, and this process requires the binding of the polar terminator protein, Tus...... as a versatile, site-specific, heterologous DNA replication-perturbing system, with a variety of potential applications....

  2. Nuclear insulin-like growth factor 1 receptor phosphorylates proliferating cell nuclear antigen and rescues stalled replication forks after DNA damage.

    Science.gov (United States)

    Waraky, Ahmed; Lin, Yingbo; Warsito, Dudi; Haglund, Felix; Aleem, Eiman; Larsson, Olle

    2017-11-03

    We have previously shown that the insulin-like growth factor 1 receptor (IGF-1R) translocates to the cell nucleus, where it binds to enhancer-like regions and increases gene transcription. Further studies have demonstrated that nuclear IGF-1R (nIGF-1R) physically and functionally interacts with some nuclear proteins, i.e. the lymphoid enhancer-binding factor 1 (Lef1), histone H3, and Brahma-related gene-1 proteins. In this study, we identified the proliferating cell nuclear antigen (PCNA) as a nIGF-1R-binding partner. PCNA is a pivotal component of the replication fork machinery and a main regulator of the DNA damage tolerance (DDT) pathway. We found that IGF-1R interacts with and phosphorylates PCNA in human embryonic stem cells and other cell lines. In vitro MS analysis of PCNA co-incubated with the IGF-1R kinase indicated tyrosine residues 60, 133, and 250 in PCNA as IGF-1R targets, and PCNA phosphorylation was followed by mono- and polyubiquitination. Co-immunoprecipitation experiments suggested that these ubiquitination events may be mediated by DDT-dependent E2/E3 ligases ( e.g. RAD18 and SHPRH/HLTF). Absence of IGF-1R or mutation of Tyr-60, Tyr-133, or Tyr-250 in PCNA abrogated its ubiquitination. Unlike in cells expressing IGF-1R, externally induced DNA damage in IGF-1R-negative cells caused G 1 cell cycle arrest and S phase fork stalling. Taken together, our results suggest a role of IGF-1R in DDT. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. 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.

  4. Dedicated education unit: implementing an innovation in replication sites.

    Science.gov (United States)

    Moscato, Susan R; Nishioka, Vicki M; Coe, Michael T

    2013-05-01

    An important measure of an innovation is the ease of replication and achievement of the same positive outcomes. The dedicated education unit (DEU) clinical education model uses a collaborative academic-service partnership to develop an optimal learning environment for students. The University of Portland adapted this model from Flinders University, Australia, to increase the teaching capacity and quality of nursing education. This article identifies DEU implementation essentials and reports on the outcomes of two replication sites that received consultation support from the University of Portland. Program operation information, including education requirements for clinician instructors, types of patient care units, and clinical faculty-to-student ratios is presented. Case studies of the three programs suggest the DEU model is adaptable to a range of different clinical settings and continues to show promise as one strategy for addressing the nurse faculty shortage and strengthening academic-clinical collaborations while maintaining quality clinical education for students. Copyright 2013, SLACK Incorporated.

  5. Inclusion bodies are a site of ebolavirus replication.

    Science.gov (United States)

    Hoenen, Thomas; Shabman, Reed S; Groseth, Allison; Herwig, Astrid; Weber, Michaela; Schudt, Gordian; Dolnik, Olga; Basler, Christopher F; Becker, Stephan; Feldmann, Heinz

    2012-11-01

    Inclusion bodies are a characteristic feature of ebolavirus infections in cells. They contain large numbers of preformed nucleocapsids, but their biological significance has been debated, and they have been suggested to be aggregates of viral proteins without any further biological function. However, recent data for other viruses that produce similar structures have suggested that inclusion bodies might be involved in genome replication and transcription. In order to study filovirus inclusion bodies, we fused mCherry to the ebolavirus polymerase L, which is found in inclusion bodies. The resulting L-mCherry fusion protein was functional in minigenome assays and incorporated into virus-like particles. Importantly, L-mCherry fluorescence in transfected cells was readily detectable and distributed in a punctate pattern characteristic for inclusion bodies. A recombinant ebolavirus encoding L-mCherry instead of L was rescued and showed virtually identical growth kinetics and endpoint titers to those for wild-type virus. Using this virus, we showed that the onset of inclusion body formation corresponds to the onset of viral genome replication, but that viral transcription occurs prior to inclusion body formation. Live-cell imaging further showed that inclusion bodies are highly dynamic structures and that they can undergo dramatic reorganization during cell division. Finally, by labeling nascent RNAs using click technology we showed that inclusion bodies are indeed the site of viral RNA synthesis. Based on these data we conclude that, rather than being inert aggregates of nucleocapsids, ebolavirus inclusion bodies are in fact complex and dynamic structures and an important site at which viral RNA replication takes place.

  6. Direct Binding to Replication Protein A (RPA)-coated Single-stranded DNA Allows Recruitment of the ATR Activator TopBP1 to Sites of DNA Damage*

    Science.gov (United States)

    Acevedo, Julyana; Yan, Shan; Michael, W. Matthew

    2016-01-01

    A critical event for the ability of cells to tolerate DNA damage and replication stress is activation of the ATR kinase. ATR activation is dependent on the BRCT (BRCA1 C terminus) repeat-containing protein TopBP1. Previous work has shown that recruitment of TopBP1 to sites of DNA damage and stalled replication forks is necessary for downstream events in ATR activation; however, the mechanism for this recruitment was not known. Here, we use protein binding assays and functional studies in Xenopus egg extracts to show that TopBP1 makes a direct interaction, via its BRCT2 domain, with RPA-coated single-stranded DNA. We identify a point mutant that abrogates this interaction and show that this mutant fails to accumulate at sites of DNA damage and that the mutant cannot activate ATR. These data thus supply a mechanism for how the critical ATR activator, TopBP1, senses DNA damage and stalled replication forks to initiate assembly of checkpoint signaling complexes. PMID:27129245

  7. A Molecular Toolbox to Engineer Site-Specific DNA Replication Perturbation.

    Science.gov (United States)

    Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

    2018-01-01

    Site-specific arrest of DNA replication is a useful tool for analyzing cellular responses to DNA replication perturbation. The E. coli Tus-Ter replication barrier can be reconstituted in eukaryotic cells as a system to engineer an unscheduled collision between a replication fork and an "alien" impediment to DNA replication. To further develop this system as a versatile tool, we describe a set of reagents and a detailed protocol that can be used to engineer Tus-Ter barriers into any locus in the budding yeast genome. Because the Tus-Ter complex is a bipartite system with intrinsic DNA replication-blocking activity, the reagents and protocols developed and validated in yeast could also be optimized to engineer site-specific replication fork barriers into other eukaryotic cell types.

  8. A Molecular Toolbox to Engineer Site-Specific DNA Replication Perturbation

    DEFF Research Database (Denmark)

    Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

    2018-01-01

    " impediment to DNA replication. To further develop this system as a versatile tool, we describe a set of reagents and a detailed protocol that can be used to engineer Tus-Ter barriers into any locus in the budding yeast genome. Because the Tus-Ter complex is a bipartite system with intrinsic DNA replication......Site-specific arrest of DNA replication is a useful tool for analyzing cellular responses to DNA replication perturbation. The E. coli Tus-Ter replication barrier can be reconstituted in eukaryotic cells as a system to engineer an unscheduled collision between a replication fork and an "alien......-blocking activity, the reagents and protocols developed and validated in yeast could also be optimized to engineer site-specific replication fork barriers into other eukaryotic cell types....

  9. The Escherichia coli Tus-Ter replication fork barrier causes site-specific DNA replication perturbation in yeast.

    Science.gov (United States)

    Larsen, Nicolai B; Sass, Ehud; Suski, Catherine; Mankouri, Hocine W; Hickson, Ian D

    2014-04-07

    Replication fork (RF) pausing occurs at both 'programmed' sites and non-physiological barriers (for example, DNA adducts). Programmed RF pausing is required for site-specific DNA replication termination in Escherichia coli, and this process requires the binding of the polar terminator protein, Tus, to specific DNA sequences called Ter. Here, we demonstrate that Tus-Ter modules also induce polar RF pausing when engineered into the Saccharomyces cerevisiae genome. This heterologous RF barrier is distinct from a number of previously characterized, protein-mediated, RF pause sites in yeast, as it is neither Tof1-dependent nor counteracted by the Rrm3 helicase. Although the yeast replisome can overcome RF pausing at Tus-Ter modules, this event triggers site-specific homologous recombination that requires the RecQ helicase, Sgs1, for its timely resolution. We propose that Tus-Ter can be utilized as a versatile, site-specific, heterologous DNA replication-perturbing system, with a variety of potential applications.

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

    Science.gov (United States)

    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.

  11. Tus-Ter as a tool to study site-specific DNA replication perturbation in eukaryotes

    DEFF Research Database (Denmark)

    Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

    2014-01-01

    The high-affinity binding of the Tus protein to specific 21-bp sequences, called Ter, causes site-specific, and polar, DNA replication fork arrest in E coli. The Tus-Ter complex serves to coordinate DNA replication with chromosome segregation in this organism. A number of recent and ongoing studies...... have demonstrated that Tus-Ter can be used as a heterologous tool to generate site-specific perturbation of DNA replication when reconstituted in eukaryotes. Here, we review these recent findings and explore the molecular mechanism by which Tus-Ter mediates replication fork (RF) arrest in the budding...... yeast, S. cerevisiae. We propose that Tus-Ter is a versatile, genetically tractable, and regulatable RF blocking system that can be utilized for disrupting DNA replication in a diverse range of host cells....

  12. Tus-Ter as a tool to study site-specific DNA replication perturbation in eukaryotes.

    Science.gov (United States)

    Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

    2014-01-01

    The high-affinity binding of the Tus protein to specific 21-bp sequences, called Ter, causes site-specific, and polar, DNA replication fork arrest in E coli. The Tus-Ter complex serves to coordinate DNA replication with chromosome segregation in this organism. A number of recent and ongoing studies have demonstrated that Tus-Ter can be used as a heterologous tool to generate site-specific perturbation of DNA replication when reconstituted in eukaryotes. Here, we review these recent findings and explore the molecular mechanism by which Tus-Ter mediates replication fork (RF) arrest in the budding yeast, S. cerevisiae. We propose that Tus-Ter is a versatile, genetically tractable, and regulatable RF blocking system that can be utilized for disrupting DNA replication in a diverse range of host cells.

  13. 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...

  14. Disaster recovery using VMware vSphere Replication and vCenter Site Recovery Manager

    CERN Document Server

    GB, Abhilash

    2014-01-01

    This is a step-by-step guide that will help you understand disaster recovery using VMware vSphere Replication 5.5 and VMware vCenter Site Recovery Manager (SRM) 5.5. The topics and configuration procedures are accompanied with relevant screenshots, flowcharts, and logical diagrams that makes grasping the concepts easier. This book is a guide for anyone who is keen on using vSphere Replication or vCenter Site Recovery Manager as a disaster recovery solution. This is an excellent handbook for solution architects, administrators, on-field engineers, and support professionals. Although the book as

  15. 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....

  16. 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.

  17. 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.

  18. Overcoming natural replication barriers: differential helicase requirements.

    Science.gov (United States)

    Anand, Ranjith P; Shah, Kartik A; Niu, Hengyao; Sung, Patrick; Mirkin, Sergei M; Freudenreich, Catherine H

    2012-02-01

    DNA sequences that form secondary structures or bind protein complexes are known barriers to replication and potential inducers of genome instability. In order to determine which helicases facilitate DNA replication across these barriers, we analyzed fork progression through them in wild-type and mutant yeast cells, using 2-dimensional gel-electrophoretic analysis of the replication intermediates. We show that the Srs2 protein facilitates replication of hairpin-forming CGG/CCG repeats and prevents chromosome fragility at the repeat, whereas it does not affect replication of G-quadruplex forming sequences or a protein-bound repeat. Srs2 helicase activity is required for hairpin unwinding and fork progression. Also, the PCNA binding domain of Srs2 is required for its in vivo role of replication through hairpins. In contrast, the absence of Sgs1 or Pif1 helicases did not inhibit replication through structural barriers, though Pif1 did facilitate replication of a telomeric protein barrier. Interestingly, replication through a protein barrier but not a DNA structure barrier was modulated by nucleotide pool levels, illuminating a different mechanism by which cells can regulate fork progression through protein-mediated stall sites. Our analyses reveal fundamental differences in the replication of DNA structural versus protein barriers, with Srs2 helicase activity exclusively required for fork progression through hairpin structures.

  19. 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.

  20. Wider stall space affects behavior, lesion scores, and productivity of gestating sows.

    Science.gov (United States)

    Salak-Johnson, J L; DeDecker, A E; Levitin, H A; McGarry, B M

    2015-10-01

    Limited space allowance within the standard gestation stall is an important welfare concern because it restricts the ability of the sow to make postural adjustments and hinders her ability to perform natural behaviors. Therefore, we evaluated the impacts of increasing stall space and/or providing sows the freedom to access a small pen area on sow well-being using multiple welfare metrics. A total of 96 primi- and multiparous crossbred sows were randomly assigned in groups of 4 sows/treatment across 8 replicates to 1 of 3 stall treatments (TRT): standard stall (CTL; dimensions: 61 by 216 cm), width-adjustable stall (flex stall [FLX]; dimensions: adjustable width of 56 to 79 cm by 216 cm), or an individual walk-in/lock-in stall with access to a small communal open-pen area at the rear of the stall (free-access stall [FAS]; dimensions: 69 by 226 cm). Lesion scores, behavior, and immune and productivity traits were measured at various gestational days throughout the study. Total lesion scores were greatest for sows in FAS and least for sows in FLX ( pregnancy progressed, lesion scores increased among sows in CTL ( postural behaviors and sham chew behavior were affected by TRT ( changes in postural behaviors, lesion severity scores, and other sow traits. Moreover, compromised welfare measures found among sows in various stall environments may be partly attributed to the specific constraints of each stall system such as restricted stall space in CTL, insufficient floor space in the open-pen area of the FAS system, and gate design of the FLX (e.g., direction of bars and feeder space). These results also indicate that parity and gestational day are additional factors that may exacerbate the effects of restricted stall space or insufficient pen space, further compromising sow well-being.

  1. 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.

  2. 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.

  3. Recruitment of Mcm10 to Sites of Replication Initiation Requires Direct Binding to the Minichromosome Maintenance (MCM) Complex*

    Science.gov (United States)

    Douglas, Max E.

    2016-01-01

    Mcm10 is required for the initiation of eukaryotic DNA replication and contributes in some unknown way to the activation of the Cdc45-MCM-GINS (CMG) helicase. How Mcm10 is localized to sites of replication initiation is unclear, as current models indicate that direct binding to minichromosome maintenance (MCM) plays a role, but the details and functional importance of this interaction have not been determined. Here, we show that purified Mcm10 can bind both DNA-bound double hexamers and soluble single hexamers of MCM. The binding of Mcm10 to MCM requires the Mcm10 C terminus. Moreover, the binding site for Mcm10 on MCM includes the Mcm2 and Mcm6 subunits and overlaps that for the loading factor Cdt1. Whether Mcm10 recruitment to replication origins depends on CMG helicase assembly has been unclear. We show that Mcm10 recruitment occurs via two modes: low affinity recruitment in the absence of CMG assembly (“G1-like”) and high affinity recruitment when CMG assembly takes place (“S-phase-like”). Mcm10 that cannot bind directly to MCM is defective in both modes of recruitment and is unable to support DNA replication. These findings indicate that Mcm10 is localized to replication initiation sites by directly binding MCM through the Mcm10 C terminus. PMID:26719337

  4. Recruitment of Mcm10 to Sites of Replication Initiation Requires Direct Binding to the Minichromosome Maintenance (MCM) Complex.

    Science.gov (United States)

    Douglas, Max E; Diffley, John F X

    2016-03-11

    Mcm10 is required for the initiation of eukaryotic DNA replication and contributes in some unknown way to the activation of the Cdc45-MCM-GINS (CMG) helicase. How Mcm10 is localized to sites of replication initiation is unclear, as current models indicate that direct binding to minichromosome maintenance (MCM) plays a role, but the details and functional importance of this interaction have not been determined. Here, we show that purified Mcm10 can bind both DNA-bound double hexamers and soluble single hexamers of MCM. The binding of Mcm10 to MCM requires the Mcm10 C terminus. Moreover, the binding site for Mcm10 on MCM includes the Mcm2 and Mcm6 subunits and overlaps that for the loading factor Cdt1. Whether Mcm10 recruitment to replication origins depends on CMG helicase assembly has been unclear. We show that Mcm10 recruitment occurs via two modes: low affinity recruitment in the absence of CMG assembly ("G1-like") and high affinity recruitment when CMG assembly takes place ("S-phase-like"). Mcm10 that cannot bind directly to MCM is defective in both modes of recruitment and is unable to support DNA replication. These findings indicate that Mcm10 is localized to replication initiation sites by directly binding MCM through the Mcm10 C terminus. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Exploiting replicative stress to treat cancer

    DEFF Research Database (Denmark)

    Dobbelstein, Matthias; Sørensen, Claus Storgaard

    2015-01-01

    DNA replication in cancer cells is accompanied by stalling and collapse of the replication fork and signalling in response to DNA damage and/or premature mitosis; these processes are collectively known as 'replicative stress'. Progress is being made to increase our understanding of the mechanisms...

  6. 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.

  7. Replication stress, a source of epigenetic aberrations in cancer?

    DEFF Research Database (Denmark)

    Jasencakova, Zusana; Groth, Anja

    2010-01-01

    . Chromatin organization is transiently disrupted during DNA replication and maintenance of epigenetic information thus relies on faithful restoration of chromatin on the new daughter strands. Acute replication stress challenges proper chromatin restoration by deregulating histone H3 lysine 9 mono......-methylation on new histones and impairing parental histone recycling. This could facilitate stochastic epigenetic silencing by laying down repressive histone marks at sites of fork stalling. Deregulation of replication in response to oncogenes and other tumor-promoting insults is recognized as a significant source...... of genome instability in cancer. We propose that replication stress not only presents a threat to genome stability, but also jeopardizes chromatin integrity and increases epigenetic plasticity during tumorigenesis....

  8. Enhancement of internal ribosome entry site-mediated translation and replication of hepatitis C virus by PD98059

    International Nuclear Information System (INIS)

    Murata, Takayuki; Hijikata, Makoto; Shimotohno, Kunitada

    2005-01-01

    Translation initiation of hepatitis C virus (HCV) occurs in an internal ribosome entry site (IRES)-dependent manner. We found that HCV IRES-dependent protein synthesis is enhanced by PD98059, an inhibitor of the extracellular signal-regulated kinase (ERK) signaling pathway, while cellular cap-dependent translation was relatively unaffected by the compound. Treatment of cells with PD98059 allowed for robust HCV replication following cellular incubation with HCV-positive serum. Though the molecular mechanism underlying IRES enhancement remains elusive, PD98059 is a potent accelerator of HCV RNA replication

  9. 14 CFR 25.203 - Stall characteristics.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Stall characteristics. 25.203 Section 25.203 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION AIRCRAFT AIRWORTHINESS STANDARDS: TRANSPORT CATEGORY AIRPLANES Flight Stalls § 25.203 Stall characteristics. (a) It must...

  10. Simulator Studies of the Deep Stall

    Science.gov (United States)

    White, Maurice D.; Cooper, George E.

    1965-01-01

    Simulator studies of the deep-stall problem encountered with modern airplanes are discussed. The results indicate that the basic deep-stall tendencies produced by aerodynamic characteristics are augmented by operational considerations. Because of control difficulties to be anticipated in the deep stall, it is desirable that adequate safeguards be provided against inadvertent penetrations.

  11. Acute Smc5/6 depletion reveals its primary role in rDNA replication by restraining recombination at fork pausing sites.

    Directory of Open Access Journals (Sweden)

    Xiao P Peng

    2018-01-01

    Full Text Available Smc5/6, a member of the conserved SMC family of complexes, is essential for growth in most organisms. Its exact functions in a mitotic cell cycle are controversial, as chronic Smc5/6 loss-of-function alleles produce varying phenotypes. To circumvent this issue, we acutely depleted Smc5/6 in budding yeast and determined the first cell cycle consequences of Smc5/6 removal. We found a striking primary defect in replication of the ribosomal DNA (rDNA array. Each rDNA repeat contains a programmed replication fork barrier (RFB established by the Fob1 protein. Fob1 removal improves rDNA replication in Smc5/6 depleted cells, implicating Smc5/6 in the management of programmed fork pausing. A similar improvement is achieved by removing the DNA helicase Mph1 whose recombinogenic activity can be inhibited by Smc5/6 under DNA damage conditions. DNA 2D gel analyses further show that Smc5/6 loss increases recombination structures at RFB regions; moreover, mph1∆ and fob1∆ similarly reduce this accumulation. These findings point to an important mitotic role for Smc5/6 in restraining recombination events when protein barriers in rDNA stall replication forks. As rDNA maintenance influences multiple essential cellular processes, Smc5/6 likely links rDNA stability to overall mitotic growth.

  12. Funding stalls ARETS work

    International Nuclear Information System (INIS)

    Anon.

    1997-01-01

    The current status of the Lethbridge Alberta Renewable Energy Test Site (ARETS) was described, following the Alberta Energy Department's failure to respond to the funding application of the Test Site. This forced the facility to be inactive for its 1997 field season. The site was established in 1982 to evaluate and demonstrate wind turbines for water pumping. It now includes solar and deep well pumping systems, and also wind-powered aeration. Up to now the site has been jointly financed by Alberta Energy and Natural Resources Canada. Both departments wanted ARETS to put more emphasis on research and development and on helping manufacturers commercialize their ideas. Despite the inactivity during the 1997 field season, one small project managed to continue, i.e., the wind project involving testing the new Delta Junior water-pumper by Dutch Industries. The Centre will also be working on a new submersible pump and DC motor system. For long-term survival, the Centre needs the support of its major financial backers. 1 fig

  13. Inhibition of Lassa virus glycoprotein cleavage and multicycle replication by site 1 protease-adapted alpha(1-antitrypsin variants.

    Directory of Open Access Journals (Sweden)

    Anna Maisa

    2009-06-01

    Full Text Available Proteolytic processing of the Lassa virus envelope glycoprotein precursor GP-C by the host proprotein convertase site 1 protease (S1P is a prerequisite for the incorporation of the subunits GP-1 and GP-2 into viral particles and, hence, essential for infectivity and virus spread. Therefore, we tested in this study the concept of using S1P as a target to block efficient virus replication.We demonstrate that stable cell lines inducibly expressing S1P-adapted alpha(1-antitrypsin variants inhibit the proteolytic maturation of GP-C. Introduction of the S1P recognition motifs RRIL and RRLL into the reactive center loop of alpha(1-antitrypsin resulted in abrogation of GP-C processing by endogenous S1P to a similar level observed in S1P-deficient cells. Moreover, S1P-specific alpha(1-antitrypsins significantly inhibited replication and spread of a replication-competent recombinant vesicular stomatitis virus expressing the Lassa virus glycoprotein GP as well as authentic Lassa virus. Inhibition of viral replication correlated with the ability of the different alpha(1-antitrypsin variants to inhibit the processing of the Lassa virus glycoprotein precursor.Our data suggest that glycoprotein cleavage by S1P is a promising target for the development of novel anti-arenaviral strategies.

  14. The onset of dynamic stall revisited

    Energy Technology Data Exchange (ETDEWEB)

    Mulleners, Karen; Raffel, Markus [German Aerospace Center (DLR), Goettingen (Germany)

    2012-03-15

    Dynamic stall on a helicopter rotor blade comprises a series of complex aerodynamic phenomena in response to the unsteady change of the blade's angle of attack. It is accompanied by a lift overshoot and delayed massive flow separation with respect to static stall. The classical hallmark of the dynamic stall phenomenon is the dynamic stall vortex. The flow over an oscillating OA209 airfoil under dynamic stall conditions was investigated by means of unsteady surface pressure measurements and time-resolved particle image velocimetry. The characteristic features of the unsteady flow field were identified and analysed utilising different coherent structure identification methods. An Eulerian and a Lagrangian procedure were adopted to locate the axes of vortices and the edges of Lagrangian coherent structures, respectively; a proper orthogonal decomposition of the velocity field revealed the energetically dominant coherent flow patterns and their temporal evolution. Based on the complementary information obtained by these methods the dynamics and interaction of vortical structures were analysed within a single dynamic stall life cycle leading to a classification of the unsteady flow development into five successive stages: the attached flow stage; the stall development stage; stall onset; the stalled stage; and flow reattachment. The onset of dynamic stall was specified here based on a characteristic mode of the proper orthogonal decomposition of the velocity field. Variations in the flow field topology that accompany the stall onset were verified by the Lagrangian coherent structure analysis. The instantaneous effective unsteadiness was defined as a single representative parameter to describe the influence of the motion parameters. Dynamic stall onset was found to be promoted by increasing unsteadiness. The mechanism that results in the detachment of the dynamic stall vortex from the airfoil was identified as vortex-induced separation caused by strong viscous

  15. Development of tooling suitable for stall regulated blades

    Energy Technology Data Exchange (ETDEWEB)

    Hancock, M.

    2001-07-01

    The objectives of the project were to make significant improvements in the production of stall regulated blades in the areas of (a) the tip box, its housing, its mechanism and small GRP parts; (b) mould technology; (c) resins and glues and (d) root tooling. Although wood composite had been identified as a competitive technology for blades, compared with GRP blades, production volumes had been lower; reasons are given. The way in which the four areas identified for investigation were tackled are discussed. The study showed that the mould cycle time can be reduced to two days for a stall regulated blade and the blade quality can be improved by using the composite tip box and new resins. The time required for replication of moulds can be reduced by 40%.

  16. Emissions trading stalls

    International Nuclear Information System (INIS)

    Milne, R.

    1998-01-01

    A brief article examines prospects for emission trading of greenhouse gas emissions in the UK. Topics covered include a checklist of principles for any trading system, plans for oil companies to do it internally, the possibility for carbon sinks as well as emissions and developments around the world. (UK) alt. Directly northward of the Sigsbee Escarpment, there is a relatively thin, low-velocity zone known as a ''gumbo zone''. Here two other pressure compartments are proposed. The origin of them is two-fold. First, initial sedimentation consists of pelagic clay draped over oceanic and transitional crust. Later, as the continental margin progrades nearer sedimentation becomes hemipelagic and coarser as gravity-driven sediments predominate. Secondly, as the salt wedge overrides a given spot of the basement, it is possible to develop a shear couple between the migrating salt and the stationary basement. The resultant shear (the site of the next strike-slip fault) may change pressures beneath the salt such that the shear may create two pressure compartments. The differences between the two compartments may be accentuated by lithologic changes caused by depositional mechanisms. (author)

  17. P1 plasmid replication: initiator sequestration is inadequate to explain control by initiator-binding sites.

    OpenAIRE

    Pal, S K; Chattoraj, D K

    1988-01-01

    The unit-copy plasmid replicon mini-P1 consists of an origin, a gene for an initiator protein, RepA, and a control locus, incA. Both the origin and the incA locus contain repeat sequences that bind RepA. It has been proposed that the incA repeats control replication by sequestering the rate-limiting RepA initiator protein. Here we show that when the concentration of RepA was increased about fourfold beyond its normal physiological level from an inducible source in trans, the copy number of a ...

  18. Towards observing the encounter of the T7 DNA replication fork with a lesion site at the Single molecule level

    KAUST Repository

    Shirbini, Afnan

    2017-05-01

    Single-molecule DNA flow-stretching assays have been a powerful approach to study various aspects on the mechanism of DNA replication for more than a decade. This technique depends on flow-induced force on a bead attached to a surface-tethered DNA. The difference in the elastic property between double-strand DNA (long) and single-strand DNA (short) at low regime force allows the observation of the beads motion when the dsDNA is converted to ssDNA by the replisome machinery during DNA replication. Here, I aim to develop an assay to track in real-time the encounter of the bacteriophage T7 replisome with abasic lesion site inserted on the leading strand template. I optimized methods to construct the DNA substrate that contains the abasic site and established the T7 leading strand synthesis at the single molecule level. I also optimized various control experiments to remove any interference from the nonspecific interactions of the DNA with the surface. My work established the foundation to image the encounter of the T7 replisome with abasic site and to characterize how the interactions between the helicase and the polymerase could influence the polymerase proofreading ability and its direct bypass of this highly common DNA damage type.

  19. FBH1 Catalyzes Regression of Stalled Replication Forks

    DEFF Research Database (Denmark)

    Fugger, Kasper; Mistrik, Martin; Neelsen, Kai J

    2015-01-01

    , is required for early phosphorylation of ATM substrates such as CHK2 and CtIP as well as hyperphosphorylation of RPA. These phosphorylations occur prior to apparent DNA double-strand break formation. Furthermore, FBH1-dependent signaling promotes checkpoint control and preserves genome integrity. We propose...

  20. Transition Process from Diffuser Stall to Stage Stall in a Centrifugal Compressor with a Vaned Diffuser

    Directory of Open Access Journals (Sweden)

    Nobumichi Fujisawa

    2017-01-01

    Full Text Available The transition process from a diffuser rotating stall to a stage stall in a centrifugal compressor with a vaned diffuser was investigated by experimental and numerical analyses. From the velocity measurements, it was found that the rotating stall existed on the shroud side of the diffuser passage in the off-design flow condition. The numerical results revealed the typical vortical structure of the diffuser stall. The diffuser stall cell was caused by the systematic vortical structure which consisted of the tornado-type vortex, the longitudinal vortex at the shroud/suction surface corner (i.e., leading edge vortex (LEV, and the vortex in the throat area of the diffuser passages. Furthermore, the stage stall, which rotated within both the impeller and diffuser passages, occurred instead of the diffuser stall as the mass flow rate was decreased. According to the velocity measurements at the diffuser inlet, the diffuser stall which rotated on the shroud side was shifted to the hub side. Then, the diffuser stall moved into the impeller passages and formed the stage stall. Therefore, the stage stall was caused by the development of the diffuser stall, which transferred from the shroud side to the hub side in the vaneless space and expanded to the impeller passages.

  1. DVC1 (C1orf124) is a DNA damage-targeting p97 adaptor that promotes ubiquitin-dependent responses to replication blocks

    DEFF Research Database (Denmark)

    Mosbech, Anna; Gibbs-Seymour, Ian; Kagias, Konstantinos

    2012-01-01

    Ubiquitin-mediated processes orchestrate critical DNA-damage signaling and repair pathways. We identify human DVC1 (C1orf124; Spartan) as a cell cycle-regulated anaphase-promoting complex (APC) substrate that accumulates at stalled replication forks. DVC1 recruitment to sites of replication stress...... synthesis (TLS) DNA polymerase η (Pol η) from monoubiquitylated PCNA. DVC1 knockdown enhances UV light-induced mutagenesis, and depletion of human DVC1 or the Caenorhabditis elegans ortholog DVC-1 causes hypersensitivity to replication stress-inducing agents. Our findings establish DVC1 as a DNA damage...

  2. Characterization of a Non-Canonical Signal Peptidase Cleavage Site in a Replication Protein from Tomato Ringspot Virus.

    Directory of Open Access Journals (Sweden)

    Ting Wei

    Full Text Available The NTB-VPg polyprotein from tomato ringspot virus is an integral membrane replication protein associated with endoplasmic reticulum membranes. A signal peptidase (SPase cleavage was previously detected in the C-terminal region of NTB-VPg downstream of a 14 amino acid (aa-long hydrophobic region (termed TM2. However, the exact location of the cleavage site was not determined. Using in vitro translation assays, we show that the SPase cleavage site is conserved in the NTB-VPg protein from various ToRSV isolates, although the rate of cleavage varies from one isolate to another. Systematic site-directed mutagenesis of the NTB-VPg SPase cleavage sites of two ToRSV isolates allowed the identification of sequences that affect cleavage efficiency. We also present evidence that SPase cleavage in the ToRSV-Rasp2 isolate occurs within a GAAGG sequence likely after the AAG (GAAG/G. Mutation of a downstream MAAV sequence to AAAV resulted in SPase cleavage at both the natural GAAG/G and the mutated AAA/V sequences. Given that there is a distance of seven aa between the two cleavage sites, this indicates that there is flexibility in the positioning of the cleavage sites relative to the inner surface of the membrane and the SPase active site. SPase cleavage sites are typically located 3-7 aa downstream of the hydrophobic region. However, the NTB-VPg GAAG/G cleavage site is located 17 aa downstream of the TM2 hydrophobic region, highlighting unusual features of the NTB-VPg SPase cleavage site. A putative 11 aa-long amphipathic helix was identified immediately downstream of the TM2 region and five aa upstream of the GAAG/G cleavage site. Based on these results, we present an updated topology model in which the hydrophobic and amphipathic domains form a long tilted helix or a bent helix in the membrane lipid bilayer, with the downstream cleavage site(s oriented parallel to the membrane inner surface.

  3. The analysis on centrifugal compressor rotating stall

    International Nuclear Information System (INIS)

    Kim, Ji Hwan; Kim, Kwang Ho; Shin, You Hwan

    2003-01-01

    In the present study, the performance characteristics and the number of stall cell during rotating stall of a centrifugal air compressor were experimentally investigated. Rotating stall in the vaneless diffuser were investigated by measuring unsteady pressure fluctuations at several different diffuser radius using a high frequency pressure transducer. The number of stall cell and their rotational speeds are distinctive features of the rotating stall phenomenon. The present study is mainly forced on the analysis for the stall cell number and its propagation speed unstable operating region of the compressor. The interpretation method of visualization is based on the pressure distribution in the circumference pressure fields while plotting the pressure and its harmonics variations in time in polar coordinates. To obtain the visualize the existence rotating stall, auto-correlation function and the frequency spectra of the pressure fluctuations were measured at r/r2=1.52. When the flow coefficient is lower than 0.150, the static pressure at impeller inlet is higher than that at inlet duct of the compressor. And the flow coefficient is lower than 0.086, several stall cell groups of discrete frequencies are observed

  4. Anaphase onset before complete DNA replication with intact checkpoint responses

    DEFF Research Database (Denmark)

    Torres-Rosell, Jordi; De Piccoli, Giacomo; Cordon-Preciado, Violeta

    2007-01-01

    Cellular checkpoints prevent mitosis in the presence of stalled replication forks. Whether checkpoints also ensure the completion of DNA replication before mitosis is unknown. Here, we show that in yeast smc5-smc6 mutants, which are related to cohesin and condensin, replication is delayed, most...

  5. Monitoring Replication Protein A (RPA) dynamics in homologous recombination through site-specific incorporation of non-canonical amino acids.

    Science.gov (United States)

    Pokhrel, Nilisha; Origanti, Sofia; Davenport, Eric Parker; Gandhi, Disha; Kaniecki, Kyle; Mehl, Ryan A; Greene, Eric C; Dockendorff, Chris; Antony, Edwin

    2017-09-19

    An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as a reporter of its dynamics on DNA in the presence of multiple other DNA binding proteins. Using RPAf, we describe the kinetics of facilitated self-exchange and exchange by Rad51 and mediator proteins during various stages in homologous recombination. RPAf is widely applicable to investigate its mechanism of action in processes such as DNA replication, repair and telomere maintenance. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. An unusual internal ribosomal entry site of inverted symmetry directs expression of a potato leafroll polerovirus replication-associated protein

    Science.gov (United States)

    Jaag, Hannah Miriam; Kawchuk, Lawrence; Rohde, Wolfgang; Fischer, Rainer; Emans, Neil; Prüfer, Dirk

    2003-01-01

    Potato leafroll polerovirus (PLRV) genomic RNA acts as a polycistronic mRNA for the production of proteins P0, P1, and P2 translated from the 5′-proximal half of the genome. Within the P1 coding region we identified a 5-kDa replication-associated protein 1 (Rap1) essential for viral multiplication. An internal ribosome entry site (IRES) with unusual structure and location was identified that regulates Rap1 translation. Core structural elements for internal ribosome entry include a conserved AUG codon and a downstream GGAGAGAGAGG motif with inverted symmetry. Reporter gene expression in potato protoplasts confirmed the internal ribosome entry function. Unlike known IRES motifs, the PLRV IRES is located completely within the coding region of Rap1 at the center of the PLRV genome. PMID:12835413

  7. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

    Directory of Open Access Journals (Sweden)

    Anil Raj

    Full Text Available Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue-specific DNase I cleavage patterns and genomic sequence content, leverages the hypersensitivity of factor-bound chromatin and the information in the DNase I spatial cleavage profile characteristic of each DNA binding protein to accurately infer functional factor binding sites. However, the model for the spatial profile in this framework fails to account for the substantial variation in the DNase I cleavage profiles across different binding sites. Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available. In this work, we introduce new methods, based on multi-scale models for inhomogeneous Poisson processes, to account for such variation in DNase I cleavage patterns both within and across binding sites. These models account for the spatial structure in the heterogeneity in DNase I cleavage patterns for each factor. Using DNase-seq measurements assayed in a lymphoblastoid cell line, we demonstrate the improved performance of this model for several transcription factors by comparing against the Chip-seq peaks for those factors. Finally, we explore the effects of DNase I sequence bias on inference of factor binding using a simple extension to our framework that allows for a more flexible background model. The proposed model can also be easily applied to paired-end ATAC-seq and DNase-seq data. msCentipede, a Python implementation of our algorithm, is available at http://rajanil.github.io/msCentipede.

  8. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

    Science.gov (United States)

    Raj, Anil; Shim, Heejung; Gilad, Yoav; Pritchard, Jonathan K; Stephens, Matthew

    2015-01-01

    Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue-specific DNase I cleavage patterns and genomic sequence content, leverages the hypersensitivity of factor-bound chromatin and the information in the DNase I spatial cleavage profile characteristic of each DNA binding protein to accurately infer functional factor binding sites. However, the model for the spatial profile in this framework fails to account for the substantial variation in the DNase I cleavage profiles across different binding sites. Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available. In this work, we introduce new methods, based on multi-scale models for inhomogeneous Poisson processes, to account for such variation in DNase I cleavage patterns both within and across binding sites. These models account for the spatial structure in the heterogeneity in DNase I cleavage patterns for each factor. Using DNase-seq measurements assayed in a lymphoblastoid cell line, we demonstrate the improved performance of this model for several transcription factors by comparing against the Chip-seq peaks for those factors. Finally, we explore the effects of DNase I sequence bias on inference of factor binding using a simple extension to our framework that allows for a more flexible background model. The proposed model can also be easily applied to paired-end ATAC-seq and DNase-seq data. msCentipede, a Python implementation of our algorithm, is available at http://rajanil.github.io/msCentipede.

  9. Why do Cross-Flow Turbines Stall?

    Science.gov (United States)

    Cavagnaro, Robert; Strom, Benjamin; Polagye, Brian

    2015-11-01

    Hydrokinetic turbines are prone to instability and stall near their peak operating points under torque control. Understanding the physics of turbine stall may help to mitigate this undesirable occurrence and improve the robustness of torque controllers. A laboratory-scale two-bladed cross-flow turbine operating at a chord-based Reynolds number ~ 3 ×104 is shown to stall at a critical tip-speed ratio. Experiments are conducting bringing the turbine to this critical speed in a recirculating current flume by increasing resistive torque and allowing the rotor to rapidly decelerate while monitoring inflow velocity, torque, and drag. The turbine stalls probabilistically with a distribution generated from hundreds of such events. A machine learning algorithm identifies stall events and indicates the effectiveness of available measurements or combinations of measurements as predictors. Bubble flow visualization and PIV are utilized to observe fluid conditions during stall events including the formation, separation, and advection of leading-edge vortices involved in the stall process.

  10. Comfort zone-design free stalls: do they influence the stall use behavior of lame cows?

    Science.gov (United States)

    Cook, N B; Marin, M J; Mentink, R L; Bennett, T B; Schaefer, M J

    2008-12-01

    The behavior of 59 cows in 4 herds, each with Comfort Zone-design free stalls with dimensions suitable for 700-kg, mature Holstein dairy cows, was filmed for a 48-h period. Comparison was made between nonlame, slightly lame, and moderately lame cows on either rubber-crumb-filled mattress stall surfaces bedded with a small amount of sawdust (2 herds) or a Pack Mat design, which consisted of a rubber-crumb-filled mattress pad installed 5 cm below a raised rear curb, bedded with 5 to 8 cm of sand bedding (2 herds). All other stall design components were similar. Despite adequate resting space and freedom to perform normal rising and lying movements, lame cows on mattresses stood in the stall for >2 h longer than nonlame cows. Although a significant increase in stall standing behavior was observed in lame cows on Pack Mat stalls, the mean (95% confidence interval) standing time in the stall was only 0.7 (0 to 3.0) h/d for nonlame cows and 1.6 (0 to 4.2) h/d for moderately lame cows, which was less than the 2.1 (0 to 4.4), 4.3 (1.6 to 6.9), and 4.9 (2.5 to 7.3) h/d spent standing in the stall for nonlame, slightly lame, and moderately lame cows on mattresses, respectively. This observation supports the hypothesis that it is the nature of the stall surface that dictates changes in stall standing behavior observed in lame cows, rather than other components of stall design. The finding that only 5 to 8 cm of sand over a mattress pad provides most of the benefits of deep sand-bedded stalls, along with other advantages related to stall maintenance and manure handling, gives farmers another useful housing alternative with which to improve cow comfort and well-being.

  11. The Relevance of the Dynamic Stall Effect for Transient

    DEFF Research Database (Denmark)

    Jauch, Clemens; Sørensen, Poul; Bak-Jensen, Birgitte

    2005-01-01

    This article describes a methodology to quantify the influence of dynamic stall on transient fault operations of active-stall turbines. The model of the dynamic stall effect is introduced briefly. The behaviour of the dynamic stall model during a transient fault operation is described mathematica...

  12. Biomimetic Wind Turbine Design with Lift Enhancing Periodic Stall

    NARCIS (Netherlands)

    Stamhuis, Eize Jan

    2017-01-01

    A wind turbine includes a rotor; a blade; and a periodic stall system. The periodic stall system selectively moves at least part of the blade in an oscillating motion whereby an angle of incidence continuously varies to invoke periodic stall. The periodic stall system can move the entire blade or

  13. Viral replication. Structural basis for RNA replication by the hepatitis C virus polymerase.

    Science.gov (United States)

    Appleby, Todd C; Perry, Jason K; Murakami, Eisuke; Barauskas, Ona; Feng, Joy; Cho, Aesop; Fox, David; Wetmore, Diana R; McGrath, Mary E; Ray, Adrian S; Sofia, Michael J; Swaminathan, S; Edwards, Thomas E

    2015-02-13

    Nucleotide analog inhibitors have shown clinical success in the treatment of hepatitis C virus (HCV) infection, despite an incomplete mechanistic understanding of NS5B, the viral RNA-dependent RNA polymerase. Here we study the details of HCV RNA replication by determining crystal structures of stalled polymerase ternary complexes with enzymes, RNA templates, RNA primers, incoming nucleotides, and catalytic metal ions during both primed initiation and elongation of RNA synthesis. Our analysis revealed that highly conserved active-site residues in NS5B position the primer for in-line attack on the incoming nucleotide. A β loop and a C-terminal membrane-anchoring linker occlude the active-site cavity in the apo state, retract in the primed initiation assembly to enforce replication of the HCV genome from the 3' terminus, and vacate the active-site cavity during elongation. We investigated the incorporation of nucleotide analog inhibitors, including the clinically active metabolite formed by sofosbuvir, to elucidate key molecular interactions in the active site. Copyright © 2015, American Association for the Advancement of Science.

  14. Prediction of induced vibrations in stall

    Energy Technology Data Exchange (ETDEWEB)

    Thirstrup Petersen, J; Thomsen, K; Aagaard Madsen, H [Risoe National Lab., Wind Energy and Atmospheric Physics Dept., Roskilde (Denmark)

    1999-03-01

    The main results from recent research in stall induced vibrations are presented. The focus is on the edgewise blade vibrations, which during the last decade have turned out to be a potential threat against the stable operation of stall regulated wind turbines and a fact, which must be dealt with by the designer. The basic physical explanation for the phenomenon and examples of design precaution, which can be taken, are presented. (au)

  15. Stalling Tropical Cyclones over the Atlantic Basin

    Science.gov (United States)

    Nielsen-Gammon, J. W.; Emanuel, K.

    2017-12-01

    Hurricane Harvey produced massive amounts of rain over southeast Texas and southwest Louisiana. Average storm total rainfall amounts over a 10,000 square mile (26,000 square km) area exceeded 30 inches (750 mm). An important aspect of the storm that contributed to the large rainfall totals was its unusual motion. The storm stalled shortly after making landfall, then moved back offshore before once again making landfall five days later. This storm motion permitted heavy rainfall to occur in the same general area for an extended period of time. The unusual nature of this event motivates an investigation into the characteristics and potential climate change influences on stalled tropical cyclones in the Atlantic basin using the HURDAT 2 storm track database for 1866-2016 and downscaled tropical cyclones driven by simulations of present and future climate. The motion of cyclones is quantified as the size of a circle circumscribing all storm locations during a given length of time. For a three-day period, Harvey remained inside a circle with a radius of 123 km. This ranks within the top 0.6% of slowest-moving historical storm instances. Among the 2% of slowest-moving storm instances prior to Harvey, only 13 involved storms that stalled near the continental United States coast, where they may have produced substantial rainfall onshore while tapping into marine moisture. Only two such storms stalled in the month of September, in contrast to 20 September stalls out of the 36 storms that stalled over the nearby open Atlantic. Just four of the stalled coastal storms were hurricanes, implying a return frequency for such storms of much less than once per decade. The synoptic setting of these storms is examined for common features, and historical and projected trends in occurrences of stalled storms near the coast and farther offshore are investigated.

  16. Observations of the Growth and Decay of Stall Cells during Stall and Surge in an Axial Compressor

    Directory of Open Access Journals (Sweden)

    Adam R. Hickman

    2017-01-01

    Full Text Available This research investigated unsteady events such as stall inception, stall-cell development, and surge. Stall is characterized by a decrease in overall pressure rise and nonaxisymmetric throughflow. Compressor stall can lead to surge which is characterized by quasi-axisymmetric fluctuations in mass flow and pressure. Unsteady measurements of the flow field around the compressor rotor are examined. During the stall inception process, initial disturbances were found within the rotor passage near the tip region. As the stall cell develops, blade lift and pressure ratio decrease within the stall cell and increase ahead of the stall cell. The stall inception event, stall-cell development, and stall recovery event were found to be nearly identical for stable rotating stall and surge cases. As the stall cell grows, the leading edge of the cell will rotate at a higher rate than the trailing edge in the rotor frame. The opposite occurs during stall recovery. The trailing edge of the stall cell will rotate at the approximate speed as the fully developed stall cell, while the leading edge decreases in rotational speed in the rotor frame.

  17. 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.

  18. Dynamic Stall Control Using Plasma Actuators

    Science.gov (United States)

    Webb, Nathan; Singhal, Achal; Castaneda, David; Samimy, Mo

    2017-11-01

    Dynamic stall occurs in many applications, including sharp maneuvers of fixed wing aircraft, wind turbines, and rotorcraft and produces large unsteady aerodynamic loads that can lead to flutter and mechanical failure. This work uses flow control to reduce the unsteady loads by excitation of instabilities in the shear layer over the separated region using nanosecond pulse driven dielectric barrier discharge (NS-DBD) plasma actuators. These actuators have been shown to effectively delay or mitigate static stall. A wide range of flow parameters were explored in the current work: Reynolds number (Re = 167,000 to 500,000), reduced frequency (k = 0.025 to 0.075), and excitation Strouhal number (Ste = 0 to 10). Based on the results, three major conclusions were drawn: (a) Low Strouhal number excitation (Ste <0.5) results in oscillatory aerodynamic loads in the stalled stage of dynamic stall; (b) All excitation resulted in earlier flow reattachment; and (c) Excitation at progressively higher Ste weakened and eventually eliminated the dynamic stall vortex (DSV), thereby dramatically reducing the unsteady loading. The decrease in the strength of the DSV is achieved by the formation of shear layer coherent structures that bleed the leading-edge vorticity prior to the ejection of the DSV.

  19. The relevance of the dynamic stall effect for transient fault operations of active-stall wind turbines

    Energy Technology Data Exchange (ETDEWEB)

    Jauch, Clemens; Soerensen, Poul; Jensen, Birgitte Bak

    2005-06-15

    This article describes a methodology to quantify the influence of dynamic stall on transient fault operations of active-stall turbines. The model of the dynamic stall effect is introduced briefly. The behaviour of the dynamic stall model during a transient fault operation is described mathematically, and from this its effect quantified. Two quantities are chosen to describe the influence of the dynamic stall effect: one is active power and the other is time delay. Subsequently a transient fault scenario is simulated with and without the dynamic stall effect and the differences discussed. From this comparison, the conclusion is drawn that the dynamic stall effect has some influence on the post-fault behaviour of the wind turbine, and it is hence suggested that the dynamic stall effect is considered if an active-stall wind turbine is to be modelled realistically. (Author)

  20. Dynamic stall and 3D effects

    Energy Technology Data Exchange (ETDEWEB)

    Bjoerck, A.; Thor, S.E. [Aeronautical Research Inst. of Sweden, Bromma (Sweden)

    1996-12-01

    The JOULE II project `Dynamic stall and 3D effects` started in January 1994 and was completed in September 1995. The objective of the project has been to increase the understanding of the three-dimensional and unsteady aerodynamics of stall controlled HAWT`s. The objectives have also been to develop `engineering models` suitable for inclusion into aero-elastic codes. The project included the participation of 13 parties within Europe. This paper describes an overview of the work carried out within the project and key results. 3 refs, 4 figs

  1. Load prediction of stall regulated wind turbines

    Energy Technology Data Exchange (ETDEWEB)

    Bjoerck, A.; Dahlberg, J.Aa. [Aeronautical Research Inst. of Sweden, Bromma (Sweden); Carlen, I. [Chalmers Univ. of Technology, Goeteborg (Sweden). Div. of Marine Structural Engineering; Ganander, H. [Teknikgruppen AB, Sollentua (Sweden)

    1996-12-01

    Measurements of blade loads on a turbine situated in a small wind farm shows that the highest blade loads occur during operation close to the peak power i.e. when the turbine operates in the stall region. In this study the extensive experimental data base has been utilised to compare loads in selected campaigns with corresponding load predictions. The predictions are based on time domain simulations of the wind turbine structure, performed by the aeroelastic code VIDYN. In the calculations a model were adopted in order to include the effects of dynamic stall. This paper describes the work carried out so far within the project and key results. 5 refs, 10 figs

  2. Education stalls and subsequent stalls in African fertility: A descriptive overview

    Directory of Open Access Journals (Sweden)

    Anne Goujon

    2015-12-01

    Full Text Available Background: Recent stalls in fertility decline have been observed in a few countries in sub-Saharan Africa, and so far no plausible common reason has been identified in the literature. This paper develops the hypothesis that these fertility stalls could be associated with stalls in the progress of education among the women of the relevant cohorts, possibly resulting partly from the Structural Adjustment Programs (SAPs of the 1980s. Methods: We descriptively link the change in the education composition of successive cohorts of young women in sub-Saharan Africa and the recent fertility stalls. We use reconstructed data on population by age, gender, and level of education from www.wittgenstein centre.org/dataexplorer, and fertility rates from the United Nations. Results: In most sub-Saharan African countries, we observe that the same countries that had fertility stalls had a stall in the progress of education, particularly for young women who were of primary school age during the 1980s, when most of the countries were under structural adjustment. Conversely, stalls in fertility are less common in countries that did not have an education stall, possibly in relation to SAPs. Conclusions: The results point to the possibility of a link between the recent fertility stalls and discontinuities in the improvement of the education of the relevant cohorts, which in turn could be related to the SAPs in the 1980s. This descriptive finding now needs to be corroborated through more detailed cohort-specific fertility analysis. If the education-fertility link can be further established, it will have important implications for the projections of population growth in affected countries.

  3. Airfoil stall interpreted through linear stability analysis

    Science.gov (United States)

    Busquet, Denis; Juniper, Matthew; Richez, Francois; Marquet, Olivier; Sipp, Denis

    2017-11-01

    Although airfoil stall has been widely investigated, the origin of this phenomenon, which manifests as a sudden drop of lift, is still not clearly understood. In the specific case of static stall, multiple steady solutions have been identified experimentally and numerically around the stall angle. We are interested here in investigating the stability of these steady solutions so as to first model and then control the dynamics. The study is performed on a 2D helicopter blade airfoil OA209 at low Mach number, M 0.2 and high Reynolds number, Re 1.8 ×106 . Steady RANS computation using a Spalart-Allmaras model is coupled with continuation methods (pseudo-arclength and Newton's method) to obtain steady states for several angles of incidence. The results show one upper branch (high lift), one lower branch (low lift) connected by a middle branch, characterizing an hysteresis phenomenon. A linear stability analysis performed around these equilibrium states highlights a mode responsible for stall, which starts with a low frequency oscillation. A bifurcation scenario is deduced from the behaviour of this mode. To shed light on the nonlinear behavior, a low order nonlinear model is created with the same linear stability behavior as that observed for that airfoil.

  4. Picornaviruses and nuclear functions: targeting a cellular compartment distinct from the replication site of a positive-strand RNA virus

    Directory of Open Access Journals (Sweden)

    Dylan eFlather

    2015-06-01

    Full Text Available The compartmentalization of DNA replication and gene transcription in the nucleus and protein production in the cytoplasm is a defining feature of eukaryotic cells. The nucleus functions to maintain the integrity of the nuclear genome of the cell and to control gene expression based on intracellular and environmental signals received through the cytoplasm. The spatial separation of the major processes that lead to the expression of protein-coding genes establishes the necessity of a transport network to allow biomolecules to translocate between these two regions of the cell. The nucleocytoplasmic transport network is therefore essential for regulating normal cellular functioning. The Picornaviridae virus family is one of many viral families that disrupt the nucleocytoplasmic trafficking of cells to promote viral replication. Picornaviruses contain positive-sense, single-stranded RNA genomes and replicate in the cytoplasm of infected cells. As a result of the limited coding capacity of these viruses, cellular proteins are required by these intracellular parasites for both translation and genomic RNA replication. Being of messenger RNA polarity, a picornavirus genome can immediately be translated upon entering the cell cytoplasm. However, the replication of viral RNA requires the activity of RNA-binding proteins, many of which function in host gene expression, and are consequently localized to the nucleus. As a result, picornaviruses disrupt nucleocytoplasmic trafficking to exploit protein functions normally localized to a different cellular compartment from which they translate their genome to facilitate efficient replication. Furthermore, picornavirus proteins are also known to enter the nucleus of infected cells to limit host-cell transcription and down-regulate innate antiviral responses. The interactions of picornavirus proteins and host-cell nuclei are extensive, required for a productive infection, and are the focus of this review.

  5. 16 CFR 1505.50 - Stalled motor testing.

    Science.gov (United States)

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Stalled motor testing. 1505.50 Section 1505... USE BY CHILDREN Policies and Interpretations § 1505.50 Stalled motor testing. (a) § 1505.6(e)(4)(ii) requires that a motor-operated toy be tested with the motor stalled if the construction of the toy is such...

  6. Economic evaluation of stall stocking density of lactating dairy cows

    NARCIS (Netherlands)

    Vries, De Albert; Dechassa, Hailegziabher; Hogeveen, Henk

    2016-01-01

    An increase in stall stocking density (SSD), as measured by the number of lactating cows per stall in a freestall barn, reduces cow performance, such as milk yield and fertility, but may increase farm profitability. Our objectives were to calculate effects of varying SSD on profit per stall for a

  7. Identification of a divalent metal cation binding site in herpes simplex virus 1 (HSV-1) ICP8 required for HSV replication.

    Science.gov (United States)

    Bryant, Kevin F; Yan, Zhipeng; Dreyfus, David H; Knipe, David M

    2012-06-01

    Herpes simplex virus 1 (HSV-1) ICP8 is a single-stranded DNA-binding protein that is necessary for viral DNA replication and exhibits recombinase activity in vitro. Alignment of the HSV-1 ICP8 amino acid sequence with ICP8 homologs from other herpesviruses revealed conserved aspartic acid (D) and glutamic acid (E) residues. Amino acid residue D1087 was conserved in every ICP8 homolog analyzed, indicating that it is likely critical for ICP8 function. We took a genetic approach to investigate the functions of the conserved ICP8 D and E residues in HSV-1 replication. The E1086A D1087A mutant form of ICP8 failed to support the replication of an ICP8 mutant virus in a complementation assay. E1086A D1087A mutant ICP8 bound DNA, albeit with reduced affinity, demonstrating that the protein is not globally misfolded. This mutant form of ICP8 was also recognized by a conformation-specific antibody, further indicating that its overall structure was intact. A recombinant virus expressing E1086A D1087A mutant ICP8 was defective in viral replication, viral DNA synthesis, and late gene expression in Vero cells. A class of enzymes called DDE recombinases utilize conserved D and E residues to coordinate divalent metal cations in their active sites. We investigated whether the conserved D and E residues in ICP8 were also required for binding metal cations and found that the E1086A D1087A mutant form of ICP8 exhibited altered divalent metal binding in an in vitro iron-induced cleavage assay. These results identify a novel divalent metal cation-binding site in ICP8 that is required for ICP8 functions during viral replication.

  8. Factors affecting stall use for different freestall bases.

    Science.gov (United States)

    Wagner-Storch, A M; Palmer, R W; Kammel, D W

    2003-06-01

    The objective of this study was to compare stall use (stall occupancy and cow position) by barn side for factors affecting stall use. A closed circuit television system recorded stall use four times per day for a 9-mo period starting May 9, 2001. Six factors were analyzed: stall base, distance to water, stall location within stall base section, stall location within barn, inside barn temperature, and length of time cows were exposed to stall bases. Two barn sides with different stocking densities were analyzed: low (66%), with cows milked by robotic milker; and high (100%), with cows milked 2X in parlor. Six stall base types were tested: two mattresses, a waterbed, a rubber mat, concrete, and sand (high side only). The base types were grouped 3 to 7 stalls/section and randomly placed in each row. Cows spent more time in mattress-based stalls, but the highest percentage lying was in sand-based stalls. The following significant stall occupancy percentages were found: sand had the highest percentage of cows lying on the high stocking density side (69%), followed by mattress type 1 (65%) > mattress type 2 (57%) > waterbed (45%) > rubber mat (33%) > concrete (23%). Mattress type 1 had the highest percentage stalls occupied (88%), followed by mattress type 2 (84%) > sand (79%) > soft rubber mat (65%) > waterbed (62%) > concrete (39%). On the low stocking rate side, mattress type 1 had the highest percentage cows lying (45%) and occupied (59.6%), followed by mattress type 2 > waterbed > soft rubber mat > concrete. Cow lying and stalls occupied percentages were highest for stalls 1) not at the end of a section, and 2) on the outside row, and varied by base type for time cows exposed to stalls and inside barn temperature. Lying and occupied percentages were different for different mattress types. The percentage of stalls with cows standing was higher for mat and mattress-based stalls. Results show mattress type 1 and sand to be superior and rubber mats and concrete inferior

  9. Illuminating the Sites of Enterovirus Replication in Living Cells by Using a Split-GFP-Tagged Viral Protein

    NARCIS (Netherlands)

    van der Schaar, H M; Melia, C E; van Bruggen, J A C; Strating, J R P M; van Geenen, M E D; Koster, A J; Bárcena, M; van Kuppeveld, F J M

    2016-01-01

    Like all other positive-strand RNA viruses, enteroviruses generate new organelles (replication organelles [ROs]) with a unique protein and lipid composition on which they multiply their viral genome. Suitable tools for live-cell imaging of enterovirus ROs are currently unavailable, as recombinant

  10. Simulation model of an active stall wind turbine controller

    Energy Technology Data Exchange (ETDEWEB)

    Jauch, C.; Hansen, A.D.; Soerensen, P. [Risoe National Lab., Wind Energy Dept., Rosilde (Denmark); Blaabjerg, F. [Aalborg Univ., Inst. of Energy Technology (Denmark)

    2004-07-01

    This paper describes an active stall wind turbine controller. The objective is to develop a general model of an active stall controller in order to simulate the operation of grid connected active stall wind turbines. The active stall turbine concept and its control strategies are presented and evaluated on the basis of simulations. The presented controller is described for continuous operation under all wind speeds from start-up wind speed to shut doven wind speed. Due to its parametric implementation it is general i.e. it can represent different active stall wind turbine controllers and can be implemented in different simulation tools. (au)

  11. Rotating stall simulation for axial and centrifugal compressors

    Science.gov (United States)

    Halawa, Taher; Gadala, Mohamed S.

    2017-05-01

    This study presents a numerical simulation of the rotating stall phenomenon in axial and centrifugal compressors with detailed descriptions of stall precursors and its development with time. Results showed that the vaneless region of the centrifugal compressor is the most critical location affected by stall. It was found that the tip leakage flow and the back flow impingement are the main cause of the stall development at the impeller exit area for centrifugal compressors. The results of the axial compressor simulations indicated that the early separated flow combined with the tip leakage flow can block the impeller passages during stall.

  12. Progerin sequestration of PCNA promotes replication fork collapse and mislocalization of XPA in laminopathy-related progeroid syndromes.

    Science.gov (United States)

    Hilton, Benjamin A; Liu, Ji; Cartwright, Brian M; Liu, Yiyong; Breitman, Maya; Wang, Youjie; Jones, Rowdy; Tang, Hui; Rusinol, Antonio; Musich, Phillip R; Zou, Yue

    2017-09-01

    Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disorder that is caused by a point mutation in the LMNA gene, resulting in production of a truncated farnesylated-prelamin A protein (progerin). We previously reported that XPA mislocalized to the progerin-induced DNA double-strand break (DSB) sites, blocking DSB repair, which led to DSB accumulation, DNA damage responses, and early replication arrest in HGPS. In this study, the XPA mislocalization to DSBs occurred at stalled or collapsed replication forks, concurrent with a significant loss of PCNA at the forks, whereas PCNA efficiently bound to progerin. This PCNA sequestration likely exposed ds-ssDNA junctions at replication forks for XPA binding. Depletion of XPA or progerin each significantly restored PCNA at replication forks. Our results suggest that although PCNA is much more competitive than XPA in binding replication forks, PCNA sequestration by progerin may shift the equilibrium to favor XPA binding. Furthermore, we demonstrated that progerin-induced apoptosis could be rescued by XPA, suggesting that XPA-replication fork binding may prevent apoptosis in HGPS cells. Our results propose a mechanism for progerin-induced genome instability and accelerated replicative senescence in HGPS.-Hilton, B. A., Liu, J., Cartwright, B. M., Liu, Y., Breitman, M., Wang, Y., Jones, R., Tang, H., Rusinol, A., Musich, P. R., Zou, Y. Progerin sequestration of PCNA promotes replication fork collapse and mislocalization of XPA in laminopathy-related progeroid syndromes. © FASEB.

  13. Observations of dynamic stall on Darrieus wind turbine blades

    Energy Technology Data Exchange (ETDEWEB)

    Fujisawa, N.; Shibuya, S. [Department of Mechanical and Production Engineering, Niigata University, 8050 Ikarashi 2, 950-2181 Niigata (Japan)

    2001-02-01

    Flow field around a Darrieus wind turbine blade in dynamic stall is studied by flow visualization and particle image velocimetry (PIV) measurement in stationary and rotating frames of reference. The experiment is carried out using the small-scale Darrieus wind turbine in a water tunnel. The unsteady nature of the dynamic stall observed by the flow visualization is quantitatively reproduced in the instantaneous velocity distributions by PIV measurement, which describes the successive shedding of two pairs of stall vortices from the blade moving upstream. The mechanism of dynamic stall is due to the successive generation of separation on the inner surface of the blade followed by the formation of roll-up vortices from the outer surface. Although the qualitative nature of the dynamic stall is independent of the tip-speed ratios, the blade angle for stall appearance and the growth rate of the stall vortices are influenced by the change in tip-speed ratios.

  14. The cholesterol, fatty acid and triglyceride synthesis pathways regulated by site 1 protease (S1P) are required for efficient replication of severe fever with thrombocytopenia syndrome virus.

    Science.gov (United States)

    Urata, Shuzo; Uno, Yukiko; Kurosaki, Yohei; Yasuda, Jiro

    2018-06-12

    Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by the SFTS virus (SFTSV), which has a high mortality rate. Currently, no licensed vaccines or therapeutic agents have been approved for use against SFTSV infection. Here, we report that the cholesterol, fatty acid, and triglyceride synthesis pathways regulated by S1P is involved in SFTSV replication, using CHO-K1 cell line (SRD-12B) that is deficient in site 1 protease (S1P) enzymatic activity, PF-429242, a small compound targeting S1P enzymatic activity, and Fenofibrate and Lovastatin, which inhibit triglyceride and cholesterol synthesis, respectively. These results enhance our understanding of the SFTSV replication mechanism and may contribute to the development of novel therapies for SFTSV infection. Copyright © 2018. Published by Elsevier Inc.

  15. Numerical Investigations of Dynamic Stall Control

    Directory of Open Access Journals (Sweden)

    Florin FRUNZULICA

    2014-04-01

    Full Text Available In this paper we investigated numerically the dynamic stall phenomenon and the possibilities to control it, with application to vertical axis wind turbines (for urban users. The Phenomenon appear at low tip speed ratio (TSR<4 and it has a great impact on structural integrity of the wind turbine and power performances. For this reason we performed a computational study of dynamic stall around NACA 0012 airfoil in pitching motion at relative low Reynolds number (105. Also, we performed the same analysis for four flow control methods: two passive (Gurney flap and slot and two active (blowing jet on the rounded trailing edge and synthetic jet periodically activated. The Results are compared to those of an existing experimental case test.

  16. The stress granule component TIA-1 binds tick-borne encephalitis virus RNA and is recruited to perinuclear sites of viral replication to inhibit viral translation.

    Science.gov (United States)

    Albornoz, Amelina; Carletti, Tea; Corazza, Gianmarco; Marcello, Alessandro

    2014-06-01

    Flaviviruses are a major cause of disease in humans and animals worldwide. Tick-borne encephalitis virus (TBEV) is the most important arthropod-borne flavivirus endemic in Europe and is the etiological agent of tick-borne encephalitis, a potentially fatal infection of the central nervous system. However, the contributions of host proteins during TBEV infection are poorly understood. In this work, we investigate the cellular protein TIA-1 and its cognate factor TIAR, which are stress-induced RNA-binding proteins involved in the repression of initiation of translation of cellular mRNAs and in the formation of stress granules. We show that TIA-1 and TIAR interact with viral RNA in TBEV-infected cells. During TBEV infection, cytoplasmic TIA-1 and TIAR are recruited at sites of viral replication with concomitant depletion from stress granules. This effect is specific, since G3BP1, another component of these cytoplasmic structures, remains localized to stress granules. Moreover, heat shock induction of stress granules containing TIA-1, but not G3BP1, is inhibited in TBEV-infected cells. Infection of cells depleted of TIA-1 or TIAR by small interfering RNA (siRNA) or TIA-1(-/-) mouse fibroblasts, leads to a significant increase in TBEV extracellular infectivity. Interestingly, TIAR(-/-) fibroblasts show the opposite effect on TBEV infection, and this phenotype appears to be related to an excess of TIA-1 in these cells. Taking advantage of a TBE-luciferase replicon system, we also observed increased luciferase activity in TIA-1(-/-) mouse fibroblasts at early time points, consistent with TIA-1-mediated inhibition at the level of the first round of viral translation. These results indicate that, in response to TBEV infection, TIA-1 is recruited to sites of virus replication to bind TBEV RNA and modulate viral translation independently of stress granule (SG) formation. This study (i) extends previous work that showed TIA-1/TIAR recruitment at sites of flavivirus replication

  17. 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.

  18. Bacillus cereus in free-stall bedding.

    Science.gov (United States)

    Magnusson, M; Svensson, B; Kolstrup, C; Christiansson, A

    2007-12-01

    To increase the understanding of how different factors affect the bacterial growth in deep sawdust beds for dairy cattle, the microbiological status of Bacillus cereus and coliforms in deep sawdust-bedded free stalls was investigated over two 14-d periods on one farm. High counts of B. cereus and coliforms were found in the entire beds. On average, 4.1 log(10) B. cereus spores, 5.5 log(10) B. cereus, and 6.7 log(10) coliforms per gram of bedding could be found in the upper layers of the sawdust likely to be in contact with the cows' udders. The highest counts of B. cereus spores, B. cereus, and coliforms were found in the bedding before fresh bedding was added, and the lowest immediately afterwards. Different factors of importance for the growth of B. cereus in the bedding material were explored in laboratory tests. These were found to be the type of bedding, pH, and the type and availability of nutrients. Alternative bedding material such as peat and mixtures of peat and sawdust inhibited the bacterial growth of B. cereus. The extent of growth of B. cereus in the sawdust was increased in a dose-dependent manner by the availability of feces. Urine added to different bedding material raised the pH and also led to bacterial growth of B. cereus in the peat. In sawdust, a dry matter content greater than 70% was needed to lower the water activity to 0.95, which is needed to inhibit the growth of B. cereus. In an attempt to reduce the bacterial growth of B. cereus and coliforms in deep sawdust beds on the farm, the effect of giving bedding daily or a full replacement of the beds was studied. The spore count of B. cereus in the back part of the free stalls before fresh bedding was added was 0.9 log units lower in stalls given daily bedding than in stalls given bedding twice weekly. No effect on coliform counts was found. Replacement of the entire sawdust bedding had an effect for a short period, but by 1 to 2 mo after replacement, the counts of B. cereus spores in the

  19. The quest for stall-free dynamic lift

    Science.gov (United States)

    Tung, C.; Mcalister, K. W.; Carr, Lawrence W.; Duque, E.; Zinner, R.

    1992-01-01

    During the past decade, numerous major effects have addressed the question of how to control or alleviate dynamic stall effects on helicopter rotors, but little concrete evidence of any significant reduction of the adverse characteristics of the dynamic stall phenomenon has been demonstrated. Nevertheless, it is important to remember that the control of dynamic stall is an achievable goal. Experiments performed at the US Army Aeroflight-dynamics Directorate more than a decade ago demonstrated that dynamic stall is not an unavoidable penalty of high amplitude motion, and that airfoils can indeed operate dynamically at angles far above the static-stall angle without necessarily forming a stall vortex. These experiments, one of them featuring a slat that was designed from static airfoil considerations, showed that unsteadiness can be a very beneficial factor in the development of high-lift devices for helicopter rotors. The experience drawn from these early experiments is now being focused on a program for the alleviation of dynamic-stall effects on helicopter rotors. The purpose of this effort is to demonstrate that rotor stall can be controlled through an improved understanding of the unsteady effects on airfoil stall and to document the role of specific means that lead to stall alleviation in the three dimensional unsteady environment of helicopter rotors in forward flight. The first concept to be addressed in this program will be a slatted airfoil. A two dimensional unsteady Navier-Stokes code has been modified to compute the flow around a two-element airfoil.

  20. The kissing-loop motif is a preferred site of 5' leader recombination during replication of SL3-3 murine leukemia viruses in mice

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Mikkelsen, J G; Schmidt, J

    1999-01-01

    , and the upstream part of the 5' untranslated region, enabled us to map recombination sites, guided by distinct scattered nucleotide differences. In 30 of 44 analyzed sequences, recombination was mapped to a 33-nucleotide similarity window coinciding with the kissing-loop stem-loop motif implicated in dimerization...... of the diploid genome. Interestingly, the recombination pattern preference found in replication-competent viruses from T-cell tumors is very similar to the pattern previously reported for retroviral vectors in cell culture experiments. The data therefore sustain the hypothesis that the kissing loop, presumably...

  1. HuR and Ago2 Bind the Internal Ribosome Entry Site of Enterovirus 71 and Promote Virus Translation and Replication.

    Directory of Open Access Journals (Sweden)

    Jing-Yi Lin

    Full Text Available EV71 (enterovirus 71 RNA contains an internal ribosomal entry site (IRES that directs cap-independent initiation of translation. IRES-dependent translation requires the host's translation initiation factors and IRES-associated trans-acting factors (ITAFs. We reported recently that mRNA decay factor AUF1 is a negative-acting ITAF that binds IRES stem-loop II. We also reported that the small RNA-processing enzyme Dicer produces at least four small RNAs (vsRNAs from the EV71 IRES. One of these, vsRNA1, derived from IRES stem-loop II, reduces IRES activity and virus replication. Since its mechanism of action is unknown, we hypothesized that it might control association of ITAFs with the IRES. Here, we identified the mRNA stability factor HuR and the RISC subunit Argonaute 2 (Ago2 as two ITAFs that bind stem-loop II. In contrast to AUF1, HuR and Ago2 promote EV71 IRES activity and virus replication. In vitro RNA-binding assays revealed that vsRNA1 can alter association of Ago2, HuR, and AUF1 with stem-loop II. This presents a possible mechanism by which vsRNA1 could control viral translation and replication.

  2. 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...

  3. Role of DNA Repair Factor Xeroderma Pigmentosum Protein Group C in Response to Replication Stress As Revealed by DNA Fragile Site Affinity Chromatography and Quantitative Proteomics.

    Science.gov (United States)

    Beresova, Lucie; Vesela, Eva; Chamrad, Ivo; Voller, Jiri; Yamada, Masayuki; Furst, Tomas; Lenobel, Rene; Chroma, Katarina; Gursky, Jan; Krizova, Katerina; Mistrik, Martin; Bartek, Jiri

    2016-12-02

    Replication stress (RS) fuels genomic instability and cancer development and may contribute to aging, raising the need to identify factors involved in cellular responses to such stress. Here, we present a strategy for identification of factors affecting the maintenance of common fragile sites (CFSs), which are genomic loci that are particularly sensitive to RS and suffer from increased breakage and rearrangements in tumors. A DNA probe designed to match the high flexibility island sequence typical for the commonly expressed CFS (FRA16D) was used as specific DNA affinity bait. Proteins significantly enriched at the FRA16D fragment under normal and replication stress conditions were identified using stable isotope labeling of amino acids in cell culture-based quantitative mass spectrometry. The identified proteins interacting with the FRA16D fragment included some known CFS stabilizers, thereby validating this screening approach. Among the hits from our screen so far not implicated in CFS maintenance, we chose Xeroderma pigmentosum protein group C (XPC) for further characterization. XPC is a key factor in the DNA repair pathway known as global genomic nucleotide excision repair (GG-NER), a mechanism whose several components were enriched at the FRA16D fragment in our screen. Functional experiments revealed defective checkpoint signaling and escape of DNA replication intermediates into mitosis and the next generation of XPC-depleted cells exposed to RS. Overall, our results provide insights into an unexpected biological role of XPC in response to replication stress and document the power of proteomics-based screening strategies to elucidate mechanisms of pathophysiological significance.

  4. Recovery of arrested replication forks by homologous recombination is error-prone.

    Directory of Open Access Journals (Sweden)

    Ismail Iraqui

    Full Text Available Homologous recombination is a universal mechanism that allows repair of DNA and provides support for DNA replication. Homologous recombination is therefore a major pathway that suppresses non-homology-mediated genome instability. Here, we report that recovery of impeded replication forks by homologous recombination is error-prone. Using a fork-arrest-based assay in fission yeast, we demonstrate that a single collapsed fork can cause mutations and large-scale genomic changes, including deletions and translocations. Fork-arrest-induced gross chromosomal rearrangements are mediated by inappropriate ectopic recombination events at the site of collapsed forks. Inverted repeats near the site of fork collapse stimulate large-scale genomic changes up to 1,500 times over spontaneous events. We also show that the high accuracy of DNA replication during S-phase is impaired by impediments to fork progression, since fork-arrest-induced mutation is due to erroneous DNA synthesis during recovery of replication forks. The mutations caused are small insertions/duplications between short tandem repeats (micro-homology indicative of replication slippage. Our data establish that collapsed forks, but not stalled forks, recovered by homologous recombination are prone to replication slippage. The inaccuracy of DNA synthesis does not rely on PCNA ubiquitination or trans-lesion-synthesis DNA polymerases, and it is not counteracted by mismatch repair. We propose that deletions/insertions, mediated by micro-homology, leading to copy number variations during replication stress may arise by progression of error-prone replication forks restarted by homologous recombination.

  5. Close-loop Dynamic Stall Control on a Pitching Airfoil

    Science.gov (United States)

    Giles, Ian; Corke, Thomas

    2017-11-01

    A closed-loop control scheme utilizing a plasma actuator to control dynamic stall is presented. The plasma actuator is located at the leading-edge of a pitching airfoil. It initially pulses at an unsteady frequency that perturbs the boundary layer flow over the suction surface of the airfoil. As the airfoil approaches and enters stall, the amplification of the unsteady disturbance is detected by an onboard pressure sensor also located near the leading edge. Once detected, the actuator is switched to a higher voltage control state that in static airfoil experiments would reattach the flow. The threshold level of the detection is a parameter in the control scheme. Three stall regimes were examined: light, medium, and deep stall, that were defined by their stall penetration angles. The results showed that in general, the closed-loop control scheme was effective at controlling dynamic stall. The cycle-integrated lift improved in all cases, and increased by as much as 15% at the lowest stall penetration angle. As important, the cycle-integrated aerodynamic damping coefficient also increased in all cases, and was made to be positive at the light stall regime where it traditionally is negative. The latter is important in applications where negative damping can lead to stall flutter.

  6. Inviscid double wake model for stalled airfoils

    International Nuclear Information System (INIS)

    Marion, L; Ramos-García, N; Sørensen, J N

    2014-01-01

    An inviscid double wake model based on a steady two-dimensional panel method has been developed to predict aerodynamic loads of wind turbine airfoils in the deep stall region. The separated flow is modelled using two constant vorticity sheets which are released at the trailing edge and at the separation point. A calibration of the code through comparison with experiments has been performed using one set of airfoils. A second set of airfoils has been used for the validation of the calibrated model. Predicted aerodynamic forces for a wide range of angles of attack (0 to 90 deg) are in overall good agreement with wind tunnel measurements

  7. Stress induced by premature chromatin condensation triggers chromosome shattering and chromothripsis at DNA sites still replicating in micronuclei or multinucleate cells when primary nuclei enter mitosis.

    Science.gov (United States)

    Terzoudi, Georgia I; Karakosta, Maria; Pantelias, Antonio; Hatzi, Vasiliki I; Karachristou, Ioanna; Pantelias, Gabriel

    2015-11-01

    Combination of next-generation DNA sequencing, single nucleotide polymorphism array analyses and bioinformatics has revealed the striking phenomenon of chromothripsis, described as complex genomic rearrangements acquired in a single catastrophic event affecting one or a few chromosomes. Via an unproven mechanism, it is postulated that mechanical stress causes chromosome shattering into small lengths of DNA, which are then randomly reassembled by DNA repair machinery. Chromothripsis is currently examined as an alternative mechanism of oncogenesis, in contrast to the present paradigm that considers a stepwise development of cancer. While evidence for the mechanism(s) underlying chromosome shattering during cancer development remains elusive, a number of hypotheses have been proposed to explain chromothripsis, including ionizing radiation, DNA replication stress, breakage-fusion-bridge cycles, micronuclei formation and premature chromosome compaction. In the present work, we provide experimental evidence on the mechanistic basis of chromothripsis and on how chromosomes can get locally shattered in a single catastrophic event. Considering the dynamic nature of chromatin nucleoprotein complex, capable of rapid unfolding, disassembling, assembling and refolding, we first show that chromatin condensation at repairing or replicating DNA sites induces the mechanical stress needed for chromosome shattering to ensue. Premature chromosome condensation is then used to visualize the dynamic nature of interphase chromatin and demonstrate that such mechanical stress and chromosome shattering can also occur in chromosomes within micronuclei or asynchronous multinucleate cells when primary nuclei enter mitosis. Following an aberrant mitosis, chromosomes could find themselves in the wrong place at the wrong time so that they may undergo massive DNA breakage and rearrangement in a single catastrophic event. Specifically, our results support the hypothesis that premature chromosome

  8. 14 CFR 33.65 - Surge and stall characteristics.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Surge and stall characteristics. 33.65 Section 33.65 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION AIRCRAFT... stall characteristics. When the engine is operated in accordance with operating instructions required by...

  9. Compartmental HBV evolution and replication in liver and extrahepatic sites after nucleos/tide analogue therapy in chronic hepatitis B carriers.

    Science.gov (United States)

    Gao, Shan; Duan, Zhong-Ping; Chen, Yu; van der Meer, Frank; Lee, Samuel S; Osiowy, Carla; van Marle, Guido; Coffin, Carla S

    2017-09-01

    Hepatitis B virus (HBV) variants are associated with nucleos/tide analogue (NA) response and liver disease but it is unknown whether NA influences extrahepatic HBV persistence. To investigate HBV replication and genetic evolution in hepatic and extrahepatic sites of chronic hepatitis B (CHB) before and after NA therapy. A total of 13 paired plasma, peripheral blood mononuclear cells (PBMC), were collected from chronic HBV carriers at baseline and after a median 53 weeks NA therapy as well as liver biopsy (N=7 baseline, N=5 follow-up). HBV covalently closed circular DNA (cccDNA) and messenger (m) RNA in liver and PBMC were analyzed. HBV polymerase (P)/surface (S), basal core promoter (BCP)/pre-core (PC)/C gene clonal sequencing was done in plasma, peripheral blood mononuclear cells (PBMC), and liver. Compare to baseline, at ∼53 weeks follow-up, there was no significant change in HBV cccDNA levels in liver (0.2-0.08 copies/hepatocyte, p>0.05) or in PBMC 0.003-0.02 copies/PBMC, p>0.05), and HBV mRNA remained detectable in both sites. At baseline, BCP variants were higher in PBMC vs. liver and plasma. After therapy, drug resistant (DR) and immune escape (IE) variants increased in liver but IE and PC variants were more frequent in PBMC. HBV P/S diversity was significantly higher in PBMC compared to plasma. Continuous HBV replication occurs in liver and PBMC and shows compartmentalized evolution under selective pressure of potent NA therapy. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Early events in the pathogenesis of foot-and-mouth disease in pigs; identification of oropharyngeal tonsils as sites of primary and sustained viral replication.

    Directory of Open Access Journals (Sweden)

    Carolina Stenfeldt

    Full Text Available A time-course study was performed to elucidate the early events of foot-and-mouth disease virus (FMDV infection in pigs subsequent to simulated natural, intra-oropharyngeal, inoculation. The earliest detectable event was primary infection in the lingual and paraepiglottic tonsils at 6 hours post inoculation (hpi characterized by regional localization of viral RNA, viral antigen, and infectious virus. At this time FMDV antigen was localized in cytokeratin-positive epithelial cells and CD172a-expressing leukocytes of the crypt epithelium of the paraepiglottic tonsils. De novo replication of FMDV was first detected in oropharyngeal swab samples at 12 hpi and viremia occurred at 18-24 hpi, approximately 24 hours prior to the appearance of vesicular lesions. From 12 through 78 hpi, microscopic detection of FMDV was consistently localized to cytokeratin-positive cells within morphologically characteristic segments of oropharyngeal tonsil crypt epithelium. During this period, leukocyte populations expressing CD172a, SLA-DQ class II and/or CD8 were found in close proximity to infected epithelial cells, but with little or no co-localization with viral proteins. Similarly, M-cells expressing cytokeratin-18 did not co-localize with FMDV proteins. Intra-epithelial micro-vesicles composed of acantholytic epithelial cells expressing large amounts of structural and non-structural FMDV proteins were present within crypts of the tonsil of the soft palate during peak clinical infection. These findings inculpate the paraepiglottic tonsils as the primary site of FMDV infection in pigs exposed via the gastrointestinal tract. Furthermore, the continuing replication of FMDV in the oropharyngeal tonsils during viremia and peak clinical infection with no concurrent amplification of virus occurring in the lower respiratory tract indicates that these sites are the major source of shedding of FMDV from pigs.

  11. 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

  12. Effects of three types of free-stall surfaces on preferences and stall usage by dairy cows.

    Science.gov (United States)

    Tucker, C B; Weary, D M; Fraser, D

    2003-02-01

    One important criterion in choosing appropriate housing systems for dairy cattle is that the freestall provides a comfortable surface for the cow. This paper describes two experiments testing the effects of commonly used lying surfaces on stall preference and stall usage by Holstein cows. In both experiments, 12 cows were housed individually in separate pens. Each pen contained three free stalls with a different surface: deep-bedded sawdust, deep-bedded sand, and a geotextile mattress covered with 2 to 3 cm of sawdust. The animals were restricted to each surface in turn, in a random order for either 2 (Experiment 1) or 3 d (Experiment 2). Both before and after this restriction phase, the animals were allowed access to all three surfaces, and preference was determined, based on lying times. Of the 12 cows used in Experiment 1, 10 preferred sawdust before and nine after the restriction phase. During the restriction phase, average lying times and number of lying events during the restriction phase were significantly lower for the sand-bedded stalls (P sand bedded stalls. In this experiment, about half the cows preferred sand and half sawdust, after the restriction phase. During the restriction phase of experiment, lying times and number of lying events were lower, and standing times were higher when the animals were restricted to the mattresses compared to either sand or sawdust (P < or = 0.05). These results indicate that (1) free stall surface can affect both stall preferences and stall usage, and (2) mattresses are less preferred.

  13. Model of OSBP-Mediated Cholesterol Supply to Aichi Virus RNA Replication Sites Involving Protein-Protein Interactions among Viral Proteins, ACBD3, OSBP, VAP-A/B, and SAC1.

    Science.gov (United States)

    Ishikawa-Sasaki, Kumiko; Nagashima, Shigeo; Taniguchi, Koki; Sasaki, Jun

    2018-04-15

    Positive-strand RNA viruses, including picornaviruses, utilize cellular machinery for genome replication. Previously, we reported that each of the 2B, 2BC, 2C, 3A, and 3AB proteins of Aichi virus (AiV), a picornavirus, forms a complex with the Golgi apparatus protein ACBD3 and phosphatidylinositol 4-kinase IIIβ (PI4KB) at viral RNA replication sites (replication organelles [ROs]), enhancing PI4KB-dependent phosphatidylinositol 4-phosphate (PI4P) production. Here, we demonstrate AiV hijacking of the cellular cholesterol transport system involving oxysterol-binding protein (OSBP), a PI4P-binding cholesterol transfer protein. AiV RNA replication was inhibited by silencing cellular proteins known to be components of this pathway, OSBP, the ER membrane proteins VAPA and VAPB (VAP-A/B), the PI4P-phosphatase SAC1, and PI-transfer protein β. OSBP, VAP-A/B, and SAC1 were present at RNA replication sites. We also found various previously unknown interactions among the AiV proteins (2B, 2BC, 2C, 3A, and 3AB), ACBD3, OSBP, VAP-A/B, and SAC1, and the interactions were suggested to be involved in recruiting the component proteins to AiV ROs. Importantly, the OSBP-2B interaction enabled PI4P-independent recruitment of OSBP to AiV ROs, indicating preferential recruitment of OSBP among PI4P-binding proteins. Protein-protein interaction-based OSBP recruitment has not been reported for other picornaviruses. Cholesterol was accumulated at AiV ROs, and inhibition of OSBP-mediated cholesterol transfer impaired cholesterol accumulation and AiV RNA replication. Electron microscopy showed that AiV-induced vesicle-like structures were close to ER membranes. Altogether, we conclude that AiV directly recruits the cholesterol transport machinery through protein-protein interactions, resulting in formation of membrane contact sites between the ER and AiV ROs and cholesterol supply to the ROs. IMPORTANCE Positive-strand RNA viruses utilize host pathways to modulate the lipid composition of

  14. Stability Analysis for Rotating Stall Dynamics in Axial Flow Compressors

    Science.gov (United States)

    1999-01-01

    modes determines collectively local stability of the compressor model. Explicit conditions are obtained for local stability of rotating stall which...critical modes determines the stability for rotating stall collectively . We point out that although in a special case our stability condition for...strict crossing assumption implies that the zero solution changes its stability as ~, crosses ~’c. For instance, odk (yc ) > 0 implies that the zero

  15. Venture from the Interior-Herpesvirus pUL31 Escorts Capsids from Nucleoplasmic Replication Compartments to Sites of Primary Envelopment at the Inner Nuclear Membrane.

    Science.gov (United States)

    Bailer, Susanne M.

    2017-11-25

    Herpesviral capsid assembly is initiated in the nucleoplasm of the infected cell. Size constraints require that newly formed viral nucleocapsids leave the nucleus by an evolutionarily conserved vescular transport mechanism called nuclear egress. Mature capsids released from the nucleoplasm are engaged in a membrane-mediated budding process, composed of primary envelopment at the inner nuclear membrane and de-envelopment at the outer nuclear membrane. Once in the cytoplasm, the capsids receive their secondary envelope for maturation into infectious virions. Two viral proteins conserved throughout the herpesvirus family, the integral membrane protein pUL34 and the phosphoprotein pUL31, form the nuclear egress complex required for capsid transport from the infected nucleus to the cytoplasm. Formation of the nuclear egress complex results in budding of membrane vesicles revealing its function as minimal virus-encoded membrane budding and scission machinery. The recent structural analysis unraveled details of the heterodimeric nuclear egress complex and the hexagonal coat it forms at the inside of budding vesicles to drive primary envelopment. With this review, I would like to present the capsid-escort-model where pUL31 associates with capsids in nucleoplasmic replication compartments for escort to sites of primary envelopment thereby coupling capsid maturation and nuclear egress.

  16. 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

  17. Conducting Classroom Observations : Stallings 'Classroom Snapshot' Observation System for an Electronic Tablet

    OpenAIRE

    World Bank Group

    2017-01-01

    The “Stallings Classroom Snapshot” instrument, technically called the “Stanford Research Institute Classroom Observation System”, was developed by Professor Jane Stallings for research on the efficiency and quality of basic education teachers in the United States in the 1970s. (Stallings, 1977; Stallings and Mohlman, 1988). The Stallings instrument generates robust quantitative data on the interaction of teachers and students in the classroom, with a high degree of inter-rater rel...

  18. A numerical strategy for modelling rotating stall in core compressors

    Science.gov (United States)

    Vahdati, M.

    2007-03-01

    The paper will focus on one specific core-compressor instability, rotating stall, because of the pressing industrial need to improve current design methods. The determination of the blade response during rotating stall is a difficult problem for which there is no reliable procedure. During rotating stall, the blades encounter the stall cells and the excitation depends on the number, size, exact shape and rotational speed of these cells. The long-term aim is to minimize the forced response due to rotating stall excitation by avoiding potential matches between the vibration modes and the rotating stall pattern characteristics. Accurate numerical simulations of core-compressor rotating stall phenomena require the modelling of a large number of bladerows using grids containing several tens of millions of points. The time-accurate unsteady-flow computations may need to be run for several engine revolutions for rotating stall to get initiated and many more before it is fully developed. The difficulty in rotating stall initiation arises from a lack of representation of the triggering disturbances which are inherently present in aeroengines. Since the numerical model represents a symmetric assembly, the only random mechanism for rotating stall initiation is provided by numerical round-off errors. In this work, rotating stall is initiated by introducing a small amount of geometric mistuning to the rotor blades. Another major obstacle in modelling flows near stall is the specification of appropriate upstream and downstream boundary conditions. Obtaining reliable boundary conditions for such flows can be very difficult. In the present study, the low-pressure compression (LPC) domain is placed upstream of the core compressor. With such an approach, only far field atmospheric boundary conditions are specified which are obtained from aircraft speed and altitude. A chocked variable-area nozzle, placed after the last compressor bladerow in the model, is used to impose boundary

  19. Homologous regions of Fen1 and p21Cip1 compete for binding to the same site on PCNA: a potential mechanism to co-ordinate DNA replication and repair.

    Science.gov (United States)

    Warbrick, E; Lane, D P; Glover, D M; Cox, L S

    1997-05-15

    Following genomic damage, the cessation of DNA replication is co-ordinated with onset of DNA repair; this co-ordination is essential to avoid mutation and genomic instability. To investigate these phenomena, we have analysed proteins that interact with PCNA, which is required for both DNA replication and repair. One such protein is p21Cip1, which inhibits DNA replication through its interaction with PCNA, while allowing repair to continue. We have identified an interaction between PCNA and the structure specific nuclease, Fen1, which is involved in DNA replication. Deletion analysis suggests that p21Cip1 and Fen1 bind to the same region of PCNA. Within Fen1 and its homologues a small region (10 amino acids) is sufficient for PCNA binding, which contains an 8 amino acid conserved PCNA-binding motif. This motif shares critical residues with the PCNA-binding region of p21Cip1. A PCNA binding peptide from p21Cip1 competes with Fen1 peptides for binding to PCNA, disrupts the Fen1-PCNA complex in replicating cell extracts, and concomitantly inhibits DNA synthesis. Competition between homologous regions of Fen1 and p21Cip1 for binding to the same site on PCNA may provide a mechanism to co-ordinate the functions of PCNA in DNA replication and repair.

  20. Is Social Licence A Licence To Stall?

    Directory of Open Access Journals (Sweden)

    Mark Lowey

    2016-03-01

    Full Text Available The School of Public Policy at the University of Calgary organized a one-day symposium on Oct. 8, 2014 in Calgary, as part of the School’s TransCanada Corporation Energy Policy and Regulatory Frameworks Program. The symposium was titled “Is Social License a License to Stall?” Held at the Hotel Arts, the event attracted a full-capacity audience of about 110 people, including representatives from industry, government and environmental non-government organizations. The symposium included four moderated panel sessions and a keynote speaker at lunch. The School of Public Policy set the framework for discussion at the Calgary symposium with the following description: Canada’s regulators act in the public interest to review energy and infrastructure project applications. Regulators are guided by procedural fairness and follow a transparent application, review and hearing process with data filings and sworn testimony. But that’s changing. “Social license” is a relatively new term, which some interests are using to create a different standard for the approval of projects — especially energy projects. According to social license advocates, projects must meet often ill-defined requirements set up by non-governmental organizations, local residents or other interests — a new hurdle for project approval, but without the rigour and rule of law of a regulator. Is social license a meaningful addition to the regulatory process, or is it being used as a constantly moving goal-post designed to slow down regulatory processes, delay project implementation, frustrate energy infrastructure expansion and even enrich those advocates who promote it as a new model? This paper summarises the discussion and the themes that emerged throughout the day. Most notably, panellists concluded that “social licence” is a real and significant issue that presents both an opportunity and a problem, not only for regulators but for all parties involved in the

  1. Hock lesions and free-stall design.

    Science.gov (United States)

    Weary, D M; Taszkun, I

    2000-04-01

    We compared the prevalence and severity of skin lesions on the hocks of lactating dairy cows in southern British Columbia, comparing 20 farms using three common bedding surfaces: sawdust, sand, and geotextile mattresses. Skin lesions were scored at five positions on the hock. For each position we noted if the lesion showed inflammatory attributes, and then assigned a severity score. Of the 1752 lactating cows scored, 1267 cows (73%) had at least one hock lesion. Of those cows with lesions, 87% had lesions on both legs, 76% had lesions on more than one location on the hock, and 78% had a lesion of at least moderate severity (i.e., evidence of skin breakage or an area of hair loss >10 cm2). Lesions were most prevalent on farms that used geotextile mattresses (91% of cows) and least common on farms that used sand (24% of cows). Moreover, lesions on cows from farms using mattresses were more numerous and more severe than those on cows from sand-bedded farms. The prevalence and severity of lesions on farms using sawdust was intermediate. Lesions also varied in relation to location on the hock. For farms using geotextile mattresses, lesions were more common and more severe on the lateral surfaces of both the tuber calcis and the tarsal joint. On farms using sawdust, lesions were common on the dorsal surface of the tuber calcis and the lateral surfaces of both the tuber calcis and the tarsal joint. Lesions were rare on all five positions for cows from sand-bedded farms. Among the 10 farms sampled using sawdust, we found a significant negative relationship between the length of the stall and severity of lesions. For cows with lesions, the number and severity of lesions increased with age.

  2. Dynamic Stall Characteristics of Drooped Leading Edge Airfoils

    Science.gov (United States)

    Sankar, Lakshmi N.; Sahin, Mehmet; Gopal, Naveen

    2000-01-01

    Helicopters in high-speed forward flight usually experience large regions of dynamic stall over the retreating side of the rotor disk. The rapid variations in the lift and pitching moments associated with the stall process can result in vibratory loads, and can cause fatigue and failure of pitch links. In some instances, the large time lag between the aerodynamic forces and the blade motion can trigger stall flutter. A number of techniques for the alleviation of dynamic stall have been proposed and studied by researchers. Passive and active control techniques have both been explored. Passive techniques include the use of high solidity rotors that reduce the lift coefficients of individual blades, leading edge slots and leading edge slats. Active control techniques include steady and unsteady blowing, and dynamically deformable leading edge (DDLE) airfoils. Considerable amount of experimental and numerical data has been collected on the effectiveness of these concepts. One concept that has not received as much attention is the drooped-leading edge airfoil idea. It has been observed in wind tunnel studies and flight tests that drooped leading edge airfoils can have a milder dynamic stall, with a significantly milder load hysteresis. Drooped leading edge airfoils may not, however, be suitable at other conditions, e.g. in hover, or in transonic flow. Work needs to be done on the analysis and design of drooped leading edge airfoils for efficient operation in a variety of flight regimes (hover, dynamic stall, and transonic flow). One concept that is worthy of investigation is the dynamically drooping airfoil, where the leading edge shape is changed roughly once-per-rev to mitigate the dynamic stall.

  3. RPA-Binding Protein ETAA1 Is an ATR Activator Involved in DNA Replication Stress Response.

    Science.gov (United States)

    Lee, Yuan-Cho; Zhou, Qing; Chen, Junjie; Yuan, Jingsong

    2016-12-19

    ETAA1 (Ewing tumor-associated antigen 1), also known as ETAA16, was identified as a tumor-specific antigen in the Ewing family of tumors. However, the biological function of this protein remains unknown. Here, we report the identification of ETAA1 as a DNA replication stress response protein. ETAA1 specifically interacts with RPA (Replication protein A) via two conserved RPA-binding domains and is therefore recruited to stalled replication forks. Interestingly, further analysis of ETAA1 function revealed that ETAA1 participates in the activation of ATR signaling pathway via a conserved ATR-activating domain (AAD) located near its N terminus. Importantly, we demonstrate that both RPA binding and ATR activation are required for ETAA1 function at stalled replication forks to maintain genome stability. Therefore, our data suggest that ETAA1 is a new ATR activator involved in replication checkpoint control. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. FANCJ couples replication past natural fork barriers with maintenance of chromatin structure.

    Science.gov (United States)

    Schwab, Rebekka A; Nieminuszczy, Jadwiga; Shin-ya, Kazuo; Niedzwiedz, Wojciech

    2013-04-01

    Defective DNA repair causes Fanconi anemia (FA), a rare childhood cancer-predisposing syndrome. At least 15 genes are known to be mutated in FA; however, their role in DNA repair remains unclear. Here, we show that the FANCJ helicase promotes DNA replication in trans by counteracting fork stalling on replication barriers, such as G4 quadruplex structures. Accordingly, stabilization of G4 quadruplexes in ΔFANCJ cells restricts fork movements, uncouples leading- and lagging-strand synthesis and generates small single-stranded DNA gaps behind the fork. Unexpectedly, we also discovered that FANCJ suppresses heterochromatin spreading by coupling fork movement through replication barriers with maintenance of chromatin structure. We propose that FANCJ plays an essential role in counteracting chromatin compaction associated with unscheduled replication fork stalling and restart, and suppresses tumorigenesis, at least partially, in this replication-specific manner.

  5. Physical Interaction between Replication Protein A (RPA) and MRN: Involvement of RPA2 Phosphorylation and the N-terminus of RPA1

    OpenAIRE

    Oakley, Greg; Tillison, Kristin; Opiyo, Stephen; Glanzer, Jason; Horn, Jeffrey M.; Patrick, Steve M.

    2009-01-01

    Replication protein A (RPA) is a heterotrimeric protein consisting of RPA1, RPA2 and RPA3 subunits that binds to ssDNA with high affinity. The response to replication stress requires the recruitment of RPA and the MRE11/RAD50/NBS1 (MRN) complex. RPA bound to ssDNA stabilizes stalled replication forks by recruiting checkpoint proteins involved in fork stabilization. MRN can bind DNA structures encountered at stalled or collapsed replication forks, such as ssDNA-dsDNA junctions or breaks and pr...

  6. Managing Single-Stranded DNA during Replication Stress in Fission Yeast

    Directory of Open Access Journals (Sweden)

    Sarah A. Sabatinos

    2015-09-01

    Full Text Available Replication fork stalling generates a variety of responses, most of which cause an increase in single-stranded DNA. ssDNA is a primary signal of replication distress that activates cellular checkpoints. It is also a potential source of genome instability and a substrate for mutation and recombination. Therefore, managing ssDNA levels is crucial to chromosome integrity. Limited ssDNA accumulation occurs in wild-type cells under stress. In contrast, cells lacking the replication checkpoint cannot arrest forks properly and accumulate large amounts of ssDNA. This likely occurs when the replication fork polymerase and helicase units are uncoupled. Some cells with mutations in the replication helicase (mcm-ts mimic checkpoint-deficient cells, and accumulate extensive areas of ssDNA to trigger the G2-checkpoint. Another category of helicase mutant (mcm4-degron causes fork stalling in early S-phase due to immediate loss of helicase function. Intriguingly, cells realize that ssDNA is present, but fail to detect that they accumulate ssDNA, and continue to divide. Thus, the cellular response to replication stalling depends on checkpoint activity and the time that replication stress occurs in S-phase. In this review we describe the signs, signals, and symptoms of replication arrest from an ssDNA perspective. We explore the possible mechanisms for these effects. We also advise the need for caution when detecting and interpreting data related to the accumulation of ssDNA.

  7. A Comparative Study of Three Methodologies for Modeling Dynamic Stall

    Science.gov (United States)

    Sankar, L.; Rhee, M.; Tung, C.; ZibiBailly, J.; LeBalleur, J. C.; Blaise, D.; Rouzaud, O.

    2002-01-01

    During the past two decades, there has been an increased reliance on the use of computational fluid dynamics methods for modeling rotors in high speed forward flight. Computational methods are being developed for modeling the shock induced loads on the advancing side, first-principles based modeling of the trailing wake evolution, and for retreating blade stall. The retreating blade dynamic stall problem has received particular attention, because the large variations in lift and pitching moments encountered in dynamic stall can lead to blade vibrations and pitch link fatigue. Restricting to aerodynamics, the numerical prediction of dynamic stall is still a complex and challenging CFD problem, that, even in two dimensions at low speed, gathers the major difficulties of aerodynamics, such as the grid resolution requirements for the viscous phenomena at leading-edge bubbles or in mixing-layers, the bias of the numerical viscosity, and the major difficulties of the physical modeling, such as the turbulence models, the transition models, whose both determinant influences, already present in static maximal-lift or stall computations, are emphasized by the dynamic aspect of the phenomena.

  8. Compressible dynamic stall control using high momentum microjets

    Science.gov (United States)

    Beahan, James J.; Shih, Chiang; Krothapalli, Anjaneyulu; Kumar, Rajan; Chandrasekhara, Muguru S.

    2014-09-01

    Control of the dynamic stall process of a NACA 0015 airfoil undergoing periodic pitching motion is investigated experimentally at the NASA Ames compressible dynamic stall facility. Multiple microjet nozzles distributed uniformly in the first 12 % chord from the airfoil's leading edge are used for the dynamic stall control. Point diffraction interferometry technique is used to characterize the control effectiveness, both qualitatively and quantitatively. The microjet control has been found to be very effective in suppressing both the emergence of the dynamic stall vortex and the associated massive flow separation at the entire operating range of angles of attack. At the high Mach number ( M = 0.4), the use of microjets appears to eliminate the shock structures that are responsible for triggering the shock-induced separation, establishing the fact that the use of microjets is effective in controlling dynamic stall with a strong compressibility effect. In general, microjet control has an overall positive effect in terms of maintaining leading edge suction pressure and preventing flow separation.

  9. The Dynamics of SecM-Induced Translational Stalling

    Directory of Open Access Journals (Sweden)

    Albert Tsai

    2014-06-01

    Full Text Available SecM is an E. coli secretion monitor capable of stalling translation on the prokaryotic ribosome without cofactors. Biochemical and structural studies have demonstrated that the SecM nascent chain interacts with the 50S subunit exit tunnel to inhibit peptide bond formation. However, the timescales and pathways of stalling on an mRNA remain undefined. To provide a dynamic mechanism for stalling, we directly tracked the dynamics of elongation on ribosomes translating the SecM stall sequence (FSTPVWISQAQGIRAGP using single-molecule fluorescence techniques. Within 1 min, three peptide-ribosome interactions work cooperatively over the last five codons of the SecM sequence, leading to severely impaired elongation rates beginning from the terminal proline and lasting four codons. Our results suggest that stalling is tightly linked to the dynamics of elongation and underscore the roles that the exit tunnel and nascent chain play in controlling fundamental steps in translation.

  10. Time Accurate Unsteady Simulation of the Stall Inception Process in the Compression System of a US Army Helicopter Gas Turbine Engine

    National Research Council Canada - National Science Library

    Hathaway, Michael D; Herrick, Greg; Chen, Jenping; Webster, Robert

    2004-01-01

    .... Improved understanding of the stall inception process and how stall control technologies mitigate such will provide compressors with increased tolerance to stall, thereby expanding the operational...

  11. Site-directed mutagenesis of HIV-1 vpu gene demonstrates two clusters of replication-defective mutants with distinct ability to down-modulate cell surface CD4 and tetherin

    Directory of Open Access Journals (Sweden)

    Masako Nomaguchi

    2010-11-01

    Full Text Available HIV-1 Vpu acts positively on viral infectivity by mediating CD4 degradation in endoplasmic reticulum and enhances virion release by counteracting a virion release restriction factor, tetherin. In order to define the impact of Vpu activity on HIV-1 replication, we have generated a series of site-specific proviral vpu mutants. Of fifteen mutants examined, seven exhibited a replication-defect similar to that of a vpu-deletion mutant in a lymphocyte cell line H9. These mutations clustered in narrow regions within transmembrane domain (TMD and cytoplasmic domain (CTD. Replication-defective mutants displayed the reduced ability to enhance virion release from a monolayer cell line HEp2 without exception. Upon transfection with Vpu expression vectors, neither TMD mutants nor CTD mutants blocked CD4 expression at the cell surface in another monolayer cell line MAGI. While TMD mutants were unable to down-modulate cell surface tetherin in HEp2 cells, CTD mutants did quite efficiently. Confocal microscopy analysis revealed the difference of intracellular localization between TMD and CTD mutants. In total, replication capability of HIV-1 carrying vpu mutations correlates well with the ability of Vpu to enhance virion release and to impede the cell surface expression of CD4 but not with the ability to down-modulate cell surface tetherin. Our results here suggest that efficient viral replication requires not only down-regulation of cell surface tetherin but also its degradation.

  12. Active Suppression of Rotating Stall Inception with Distributed Jet Actuation

    Directory of Open Access Journals (Sweden)

    Huu Duc Vo

    2007-01-01

    Full Text Available An analytical and experimental investigation of the effectiveness of full-span distributed jet actuation for active suppression of long length-scale rotating stall inception is carried out. Detailed modeling and experimental verification highlight the important effects of mass addition, discrete injectors, and feedback dynamics, which may be overlooked in preliminary theoretical studies of active control with jet injection. A model of the compression system incorporating nonideal injection and feedback dynamics is verified with forced response measurements to predict the right trends in the movement of the critical pole associated with the stall precursor. Active control experiments with proportional feedback control show that the predicted stall precursors are suppressed to give a 5.5% range extension in compressor flow coefficient. In addition, results suggest that the proposed model could be used to design a more sophisticated controller to further improve performance while reducing actuator bandwidth requirements.

  13. Stall Recovery Guidance Algorithms Based on Constrained Control Approaches

    Science.gov (United States)

    Stepanyan, Vahram; Krishnakumar, Kalmanje; Kaneshige, John; Acosta, Diana

    2016-01-01

    Aircraft loss-of-control, in particular approach to stall or fully developed stall, is a major factor contributing to aircraft safety risks, which emphasizes the need to develop algorithms that are capable of assisting the pilots to identify the problem and providing guidance to recover the aircraft. In this paper we present several stall recovery guidance algorithms, which are implemented in the background without interfering with flight control system and altering the pilot's actions. They are using input and state constrained control methods to generate guidance signals, which are provided to the pilot in the form of visual cues. It is the pilot's decision to follow these signals. The algorithms are validated in the pilot-in-the loop medium fidelity simulation experiment.

  14. A dynamic stall model for airfoils with deformable trailing edges

    DEFF Research Database (Denmark)

    Andersen, Peter Bjørn; Gaunaa, Mac; Bak, Dan Christian

    2007-01-01

    on an airfoil section undergoing arbitrary motion in heave, lead-lag, pitch, Trailing Edge (TE) flapping. In the linear region, the model reduces to the inviscid model of Gaunaa [4], which includes the aerodynamic effect of a thin airfoil with a deformable camberline in inviscid flow. Therefore, the proposed......The present work contains an extension of the Beddoes-Leishman (B-L) type dynamic stall model, as described by Hansen et al. [7]. In this work a Deformable Trailing Edge Geometry (DTEG) has been added to the dynamic stall model. The model predicts the unsteady aerodynamic forces and moments...

  15. Miscoding-induced stalling of substrate translocation on the bacterial ribosome.

    Science.gov (United States)

    Alejo, Jose L; Blanchard, Scott C

    2017-10-10

    Directional transit of the ribosome along the messenger RNA (mRNA) template is a key determinant of the rate and processivity of protein synthesis. Imaging of the multistep translocation mechanism using single-molecule FRET has led to the hypothesis that substrate movements relative to the ribosome resolve through relatively long-lived late intermediates wherein peptidyl-tRNA enters the P site of the small ribosomal subunit via reversible, swivel-like motions of the small subunit head domain within the elongation factor G (GDP)-bound ribosome complex. Consistent with translocation being rate-limited by recognition and productive engagement of peptidyl-tRNA within the P site, we now show that base-pairing mismatches between the peptidyl-tRNA anticodon and the mRNA codon dramatically delay this rate-limiting, intramolecular process. This unexpected relationship between aminoacyl-tRNA decoding and translocation suggests that miscoding antibiotics may impact protein synthesis by impairing the recognition of peptidyl-tRNA in the small subunit P site during EF-G-catalyzed translocation. Strikingly, we show that elongation factor P (EF-P), traditionally known to alleviate ribosome stalling at polyproline motifs, can efficiently rescue translocation defects arising from miscoding. These findings help reveal the nature and origin of the rate-limiting steps in substrate translocation on the bacterial ribosome and indicate that EF-P can aid in resuming translation elongation stalled by miscoding errors.

  16. Damage-induced DNA replication stalling relies on MAPK-activated protein kinase 2 activity

    DEFF Research Database (Denmark)

    Köpper, Frederik; Bierwirth, Cathrin; Schön, Margarete

    2013-01-01

    knockdown of the MAP kinase-activated protein kinase 2 (MK2), a kinase currently implicated in p38 stress signaling and G2 arrest. Depletion or inhibition of MK2 also protected cells from DNA damage-induced cell death, and mice deficient for MK2 displayed decreased apoptosis in the skin upon UV irradiation...

  17. 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...

  18. LHCb experience with LFC replication

    International Nuclear Information System (INIS)

    Bonifazi, F; Carbone, A; D'Apice, A; Dell'Agnello, L; Re, G L; Martelli, B; Ricci, P P; Sapunenko, V; Vitlacil, D; Perez, E D; Duellmann, D; Girone, M; Peco, G; Vagnoni, V

    2008-01-01

    Database replication is a key topic in the framework of the LHC Computing Grid to allow processing of data in a distributed environment. In particular, the LHCb computing model relies on the LHC File Catalog, i.e. a database which stores information about files spread across the GRID, their logical names and the physical locations of all the replicas. The LHCb computing model requires the LFC to be replicated at Tier-1s. The LCG 3D project deals with the database replication issue and provides a replication service based on Oracle Streams technology. This paper describes the deployment of the LHC File Catalog replication to the INFN National Center for Telematics and Informatics (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements

  19. LHCb experience with LFC replication

    CERN Document Server

    Bonifazi, F; Perez, E D; D'Apice, A; dell'Agnello, L; Düllmann, D; Girone, M; Re, G L; Martelli, B; Peco, G; Ricci, P P; Sapunenko, V; Vagnoni, V; Vitlacil, D

    2008-01-01

    Database replication is a key topic in the framework of the LHC Computing Grid to allow processing of data in a distributed environment. In particular, the LHCb computing model relies on the LHC File Catalog, i.e. a database which stores information about files spread across the GRID, their logical names and the physical locations of all the replicas. The LHCb computing model requires the LFC to be replicated at Tier-1s. The LCG 3D project deals with the database replication issue and provides a replication service based on Oracle Streams technology. This paper describes the deployment of the LHC File Catalog replication to the INFN National Center for Telematics and Informatics (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements.

  20. Compressible dynamic stall vorticity flux control using a dynamic ...

    Indian Academy of Sciences (India)

    systems, such as a wind turbine, are prevented from ever entering dynamic stall, essentially disregarding potential ... future generations of such systems, an overwhelming need has developed to avail this benefit safely. ... approach must diffuse the vorticity prior to its coalescence, but keep the vorticity over the airfoil up to ...

  1. Dynamic Characteristics of Rotating Stall in Mixed Flow Pump

    Directory of Open Access Journals (Sweden)

    Xiaojun Li

    2013-01-01

    Full Text Available Rotating stall, a phenomenon that causes flow instabilities and pressure hysteresis by propagating at some fraction of the impeller rotational speed, can occur in centrifugal impellers, mixed impellers, radial diffusers, or axial diffusers. Despite considerable efforts devoted to the study of rotating stall in pumps, the mechanics of this phenomenon are not sufficiently understood. The propagation mechanism and onset of rotating stall are not only affected by inlet flow but also by outlet flow as well as the pressure gradient in the flow passage. As such, the complexity of these concepts is not covered by the classical explanation. To bridge this research gap, the current study investigated prerotation generated at the upstream of the impeller, leakage flow at the tip clearance between the casing and the impeller, and strong reserve flow at the inlet of the diffuser. Understanding these areas will clarify the origin of the positive slope of the head-flow performance curve for a mixed flow pump. Nonuniform pressure distribution and adverse pressure gradient were also introduced to evaluate the onset and development of rotating stall within the diffuser.

  2. Prediction of active control of subsonic centrifugal compressor rotating stall

    Science.gov (United States)

    Lawless, Patrick B.; Fleeter, Sanford

    1993-01-01

    A mathematical model is developed to predict the suppression of rotating stall in a centrifugal compressor with a vaned diffuser. This model is based on the employment of a control vortical waveform generated upstream of the impeller inlet to damp weak potential disturbances that are the early stages of rotating stall. The control system is analyzed by matching the perturbation pressure in the compressor inlet and exit flow fields with a model for the unsteady behavior of the compressor. The model was effective at predicting the stalling behavior of the Purdue Low Speed Centrifugal Compressor for two distinctly different stall patterns. Predictions made for the effect of a controlled inlet vorticity wave on the stability of the compressor show that for minimum control wave magnitudes, on the order of the total inlet disturbance magnitude, significant damping of the instability can be achieved. For control waves of sufficient amplitude, the control phase angle appears to be the most important factor in maintaining a stable condition in the compressor.

  3. A CFD Database for Airfoils and Wings at Post-Stall Angles of Attack

    Science.gov (United States)

    Petrilli, Justin; Paul, Ryan; Gopalarathnam, Ashok; Frink, Neal T.

    2013-01-01

    This paper presents selected results from an ongoing effort to develop an aerodynamic database from Reynolds-Averaged Navier-Stokes (RANS) computational analysis of airfoils and wings at stall and post-stall angles of attack. The data obtained from this effort will be used for validation and refinement of a low-order post-stall prediction method developed at NCSU, and to fill existing gaps in high angle of attack data in the literature. Such data could have potential applications in post-stall flight dynamics, helicopter aerodynamics and wind turbine aerodynamics. An overview of the NASA TetrUSS CFD package used for the RANS computational approach is presented. Detailed results for three airfoils are presented to compare their stall and post-stall behavior. The results for finite wings at stall and post-stall conditions focus on the effects of taper-ratio and sweep angle, with particular attention to whether the sectional flows can be approximated using two-dimensional flow over a stalled airfoil. While this approximation seems reasonable for unswept wings even at post-stall conditions, significant spanwise flow on stalled swept wings preclude the use of two-dimensional data to model sectional flows on swept wings. Thus, further effort is needed in low-order aerodynamic modeling of swept wings at stalled conditions.

  4. Distinct functions of human RecQ helicases during DNA replication.

    Science.gov (United States)

    Urban, Vaclav; Dobrovolna, Jana; Janscak, Pavel

    2017-06-01

    DNA replication is the most vulnerable process of DNA metabolism in proliferating cells and therefore it is tightly controlled and coordinated with processes that maintain genomic stability. Human RecQ helicases are among the most important factors involved in the maintenance of replication fork integrity, especially under conditions of replication stress. RecQ helicases promote recovery of replication forks being stalled due to different replication roadblocks of either exogenous or endogenous source. They prevent generation of aberrant replication fork structures and replication fork collapse, and are involved in proper checkpoint signaling. The essential role of human RecQ helicases in the genome maintenance during DNA replication is underlined by association of defects in their function with cancer predisposition. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Ward Valley transfer stalled by Babbitt

    International Nuclear Information System (INIS)

    Anon.

    1994-01-01

    Interior Secretary Bruce Babbitt announced on November 24 that he would not authorize the land transfer for the proposed low-level waste disposal site at Ward Valley, California, until a legal challenge to the facility's license and environmental impact statement is resolved. Even if the matter is resolved quickly, there exists the possibility that yet another hearing will be held on the project, even though state courts in California have stated flatly that no such hearings are required

  6. Ward Valley transfer stalled by Babbitt

    Energy Technology Data Exchange (ETDEWEB)

    1994-01-01

    Interior Secretary Bruce Babbitt announced on November 24 that he would not authorize the land transfer for the proposed low-level waste disposal site at Ward Valley, California, until a legal challenge to the facility's license and environmental impact statement is resolved. Even if the matter is resolved quickly, there exists the possibility that yet another hearing will be held on the project, even though state courts in California have stated flatly that no such hearings are required.

  7. Simulation model of an active-stall fixed-speed wind turbine controller

    Energy Technology Data Exchange (ETDEWEB)

    Jauch, C.; Hansen, A.D.; Sorensen, P.; Blaabjerg, F.

    2004-07-01

    This paper describes an active-stall wind turbine controller. The objective is to develop a general model of an active stall controller in order to simulate the operation of grid connected active stall wind turbines. The active stall turbine concept and its control strategies are presented and evaluated by simulations. The presented controller is described for continuous operation under all wind speeds from start-up wind speed to shut down wind speed. Due to its parametric implementation it is general i. e. it can represent different active stall wind turbine controllers and can be implemented in different simulation tools. (author)

  8. Identifying Functional Neighborhoods within the Cell Nucleus: Proximity Analysis of Early S-Phase Replicating Chromatin Domains to Sites of Transcription, RNA Polymerase II, HP1γ, Matrin 3 and SAF-A

    Science.gov (United States)

    Malyavantham, Kishore S; Bhattacharya, Sambit; Barbeitos, Marcos; Mukherjee, Lopamudra; Xu, Jinhui; Fackelmayer, Frank O; Berezney, Ronald

    2009-01-01

    Higher order chromatin organization in concert with epigenetic regulation is a key process that determines gene expression at the global level. The organization of dynamic chromatin domains and their associated protein factors is intertwined with nuclear function to create higher levels of functional zones within the cell nucleus. As a step towards elucidating the organization and dynamics of these functional zones, we have investigated the spatial proximities among a constellation of functionally related sites that are found within euchromatic regions of the cell nucleus including: HP1γ, nascent transcript sites (TS), active DNA replicating sites in early S phase (PCNA) and RNA polymerase II sites. We report close associations among these different sites with proximity values specific for each combination. Analysis of matrin 3 and SAF-A sites demonstrates that these nuclear matrix proteins are highly proximal with the functionally related sites as well as to each other and display closely aligned and overlapping regions following application of the minimal spanning tree (MST) algorithm to visualize higher order network-like patterns. Our findings suggest that multiple factors within the nuclear microenvironment collectively form higher order combinatorial arrays of function. We propose a model for the organization of these functional neighborhoods which takes into account the proximity values of the individual sites and their spatial organization within the nuclear architecture. PMID:18618731

  9. Visualization and PIV measurement of unsteady flow around a darrieus wind turbine in dynamic stall

    Energy Technology Data Exchange (ETDEWEB)

    Shibuya, Satoshi; Fujisawa, Nobuyuki; Takano, Tsuyoshi [Dept. of Mechanical and Production Engineering, Niigata Univ., Niigata (Japan)

    1999-07-01

    Flow around a Darrieus wind turbine in dynamic stall is studied by flow visualization and PIV (particle image velocimeter) measurement in a rotating frame of reference, which allows the successive observation of the dynamic stall over the blade. The qualitative features of the flow field in dynamic stall observed by the flow visualization, such as the formation and shedding of the stall vortices, are quantitatively reproduced in the instantaneous velocity distributions near the blade by using PIV. These results indicate that two pairs of stall vortices are generated from the blade during one rotation of the blade and that the size and the generating blade angle of the stall vortices are enlarged as the tip-speed ratio decreases. These stall vortices are produced by the in-flow motion from the outer surface to the inner surface through the trailing edge of the blade and the flow separation over the inner surface of the blade. (author)

  10. Flow and Noise Characteristics of Centrifugal Fan under Different Stall Conditions

    Directory of Open Access Journals (Sweden)

    Lei Zhang

    2014-01-01

    Full Text Available An implicit, time-accurate 3D Reynolds-averaged Navier-Stokes (RANS solver is used to simulate the rotating stall phenomenon in a centrifugal fan. The goal of the present work is to shed light on the flow field and particularly the aerodynamic noise at different stall conditions. Aerodynamic characteristics, frequency domain characteristics, and the contours of sound power level under two different stall conditions are discussed in this paper. The results show that, with the decrease of valve opening, the amplitude of full pressure and flow fluctuations tends to be larger and the stall frequency remains the same. The flow field analysis indicates that the area occupied by stall cells expands with the decrease of flow rate. The noise calculation based on the simulation underlines the role of vortex noise after the occurrence of rotating stall, showing that the high noise area rotates along with the stall cell in the circumferential direction.

  11. Mutation of the dengue virus type 2 envelope protein heparan sulfate binding sites or the domain III lateral ridge blocks replication in Vero cells prior to membrane fusion

    International Nuclear Information System (INIS)

    Roehrig, John T.; Butrapet, Siritorn; Liss, Nathan M.; Bennett, Susan L.; Luy, Betty E.; Childers, Thomas; Boroughs, Karen L.; Stovall, Janae L.; Calvert, Amanda E.; Blair, Carol D.; Huang, Claire Y.-H.

    2013-01-01

    Using an infectious cDNA clone we engineered seven mutations in the putative heparan sulfate- and receptor-binding motifs of the envelope protein of dengue virus serotype 2, strain 16681. Four mutant viruses, KK122/123EE, E202K, G304K, and KKK305/307/310EEE, were recovered following transfection of C6/36 cells. A fifth mutant, KK291/295EE, was recovered from C6/36 cells with a compensatory E295V mutation. All mutants grew in and mediated fusion of virus-infected C6/36 cells, but three of the mutants, KK122/123EE, E202K, G304K, did not grow in Vero cells without further modification. Two Vero cell lethal mutants, KK291/295EV and KKK307/307/310EEE, failed to replicate in DC-SIGN-transformed Raji cells and did not react with monoclonal antibodies known to block DENV attachment to Vero cells. Additionally, both mutants were unable to initiate negative-strand vRNA synthesis in Vero cells by 72 h post-infection, suggesting that the replication block occurred prior to virus-mediated membrane fusion. - Highlights: • Heparan sulfate- and receptor-binding motifs of DENV2 envelope protein were mutated. • Four mutant viruses were isolated—all could fuse C6/36 cells. • Two of these mutants were lethal in Vero cells without further modification. • Lethal mutations were KK291/295EV and KKK305/307/310EEE. • Cell attachment was implicated as the replication block for both mutants

  12. Mutation of the dengue virus type 2 envelope protein heparan sulfate binding sites or the domain III lateral ridge blocks replication in Vero cells prior to membrane fusion

    Energy Technology Data Exchange (ETDEWEB)

    Roehrig, John T., E-mail: jtr1@cdc.gov [Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521 (United States); Butrapet, Siritorn; Liss, Nathan M. [Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521 (United States); Bennett, Susan L. [Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523 (United States); Luy, Betty E.; Childers, Thomas; Boroughs, Karen L.; Stovall, Janae L.; Calvert, Amanda E. [Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521 (United States); Blair, Carol D. [Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523 (United States); Huang, Claire Y.-H. [Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521 (United States)

    2013-07-05

    Using an infectious cDNA clone we engineered seven mutations in the putative heparan sulfate- and receptor-binding motifs of the envelope protein of dengue virus serotype 2, strain 16681. Four mutant viruses, KK122/123EE, E202K, G304K, and KKK305/307/310EEE, were recovered following transfection of C6/36 cells. A fifth mutant, KK291/295EE, was recovered from C6/36 cells with a compensatory E295V mutation. All mutants grew in and mediated fusion of virus-infected C6/36 cells, but three of the mutants, KK122/123EE, E202K, G304K, did not grow in Vero cells without further modification. Two Vero cell lethal mutants, KK291/295EV and KKK307/307/310EEE, failed to replicate in DC-SIGN-transformed Raji cells and did not react with monoclonal antibodies known to block DENV attachment to Vero cells. Additionally, both mutants were unable to initiate negative-strand vRNA synthesis in Vero cells by 72 h post-infection, suggesting that the replication block occurred prior to virus-mediated membrane fusion. - Highlights: • Heparan sulfate- and receptor-binding motifs of DENV2 envelope protein were mutated. • Four mutant viruses were isolated—all could fuse C6/36 cells. • Two of these mutants were lethal in Vero cells without further modification. • Lethal mutations were KK291/295EV and KKK305/307/310EEE. • Cell attachment was implicated as the replication block for both mutants.

  13. Activity-based protein profiling of the hepatitis C virus replication in Huh-7 hepatoma cells using a non-directed active site probe

    Directory of Open Access Journals (Sweden)

    McKay Craig S

    2010-02-01

    Full Text Available Abstract Background Hepatitis C virus (HCV poses a growing threat to global health as it often leads to serious liver diseases and is one of the primary causes for liver transplantation. Currently, no vaccines are available to prevent HCV infection and clinical treatments have limited success. Since HCV has a small proteome, it relies on many host cell proteins to complete its life cycle. In this study, we used a non-directed phenyl sulfonate ester probe (PS4≡ to selectively target a broad range of enzyme families that show differential activity during HCV replication in Huh-7 cells. Results The PS4≡ probe successfully targeted 19 active proteins in nine distinct protein families, some that were predominantly labeled in situ compared to the in vitro labeled cell homogenate. Nine proteins revealed altered activity levels during HCV replication. Some candidates identified, such as heat shock 70 kDa protein 8 (or HSP70 cognate, have been shown to influence viral release and abundance of cellular lipid droplets. Other differentially active PS4≡ targets, such as electron transfer flavoprotein alpha, protein disulfide isomerase A5, and nuclear distribution gene C homolog, constitute novel proteins that potentially mediate HCV propagation. Conclusions These findings demonstrate the practicality and versatility of non-directed activity-based protein profiling (ABPP to complement directed methods and accelerate the discovery of altered protein activities associated with pathological states such as HCV replication. Collectively, these results highlight the ability of in situ ABPP approaches to facilitate the identification of enzymes that are either predominantly or exclusively labeled in living cells. Several of these differentially active enzymes represent possible HCV-host interactions that could be targeted for diagnostic or therapeutic purposes.

  14. Replication origins oriGNAI3 and oriB of the mammalian AMPD2 locus nested in a region of straight DNA flanked by intrinsically bent DNA sites.

    Science.gov (United States)

    Balani, Valério Américo; de Lima Neto, Quirino Alves; Takeda, Karen Izumi; Gimenes, Fabrícia; Fiorini, Adriana; Debatisse, Michelle; Fernandez, Maria Aparecida

    2010-11-01

    The aim of this work was to determine whether intrinsically bent DNA sites are present at, or close to, the mammalian replication origins oriGNAI3 and oriB in the Chinese hamster AMPD2 locus. Using an electrophoretic mobility shift assay and in silico analysis, we located four intrinsically bent DNA sites (b1 to b4) in a fragment that contains the oriGNAI3 and one site (b5) proximal to oriB. The helical parameters show that each bent DNA site is curved in a left-handed superhelical writhe. A 2D projection of 3D fragment trajectories revealed that oriGNAI3 is located in a relatively straight segment flanked by bent sites b1 and b2, which map in previously identified Scaffold/Matrix Attachment Region. Sites b3 and b4 are located approximately 2 kb downstream and force the fragment into a strong closed loop structure. The b5 site is also located in an S/MAR that is found just downstream of oriB.

  15. Dynamic stall - The case of the vertical axis wind turbine

    Science.gov (United States)

    Laneville, A.; Vittecoq, P.

    1986-05-01

    This paper presents the results of an experimental investigation on a driven Darrieus turbine rotating at different tip speed ratios. For a Reynolds number of 3.8 x 10 to the 4th, the results indicate the presence of dynamic stall at tip speed ratio less than 4, and that helicopter blade aerodynamics can be used in order to explain some aspects of the phenomenon. It was observed that in deep stall conditions, a vortex is formed at the leading edge; this vortex moves over the airfoil surface with 1/3 of the airfoil speed and then is shed at the trailing edge. After its shedding, the vortex can interact with the airfoil surface as the blade passes downstream.

  16. DYNSTALL: Subroutine package with a dynamic stall model

    Energy Technology Data Exchange (ETDEWEB)

    Bjoerck, Anders [Aeronautical Research Inst. of Sweden, Bromma (Sweden)

    2001-03-01

    A subroutine package, called DYNSTALL, for the calculation of 2D unsteady airfoil aerodynamics is described. The subroutines are written in FORTRAN. DYNSTALL is basically an implementation of the Beddoes-Leishman dynamic stall model. This model is a semi-empirical model for dynamic stall. It includes, however, also models for attached flow unsteady aerodynamics. It is complete in the sense that it treats attached flow as well as separated flow. Semi-empirical means that the model relies on empirically determined constants. Semi because the constants are constants in equations with some physical interpretation. It requires the input of 2D airfoil aerodynamic data via tables as function of angle of attack. The method is intended for use in an aeroelastic code with the aerodynamics solved by blade/element method. DYNSTALL was written to work for any 2D angles of attack relative to the airfoil, e.g. flow from the rear of an airfoil.

  17. A dynamic stall model for airfoils with deformable trailing edges

    DEFF Research Database (Denmark)

    Andersen, Peter Bjørn; Gaunaa, Mac; Bak, Christian

    2009-01-01

    , lead-lag, pitch, trailing-edge flapping. In the linear region, the model reduces to the inviscid model, which includes the aerodynamic effect of a thin airfoil with a deformable camberline in inviscid flow. Therefore, the proposed model can be considered a crossover between the work of Gaunaa......The present work contains an extension of the Beddoes-Leishman-type dynamic stall model. In this work, a deformable trailing-edge flap has been added to the dynamic stall model. The model predicts the unsteady aerodynamic forces and moments on an airfoil section undergoing arbitrary motion in heave...... for the attached flow region and Hansen et al. The model is compared qualitatively to wind tunnel measurements of a Riso/ B1-18 blade section equipped with deformable trailing-edge flap devices in the form of piezoelectric devices. Copyright © 2009 John Wiley & Sons, Ltd....

  18. A Dynamic Stall Model for Airfoils with Deformable Trailing Edges

    International Nuclear Information System (INIS)

    Andersen, Peter Bjoern; Gaunaa, Mac; Bak, Christian; Hansen, Morten Hartvig

    2007-01-01

    The present work contains an extension of the Beddoes-Leishman (B-L) type dynamic stall model, as described by Hansen et al. In this work a Deformable Trailing Edge Geometry (DTEG) has been added to the dynamic stall model. The model predicts the unsteady aerodynamic forces and moments on an airfoil section undergoing arbitrary motion in heave, lead-lag, pitch, Trailing Edge (TE) flapping. In the linear region, the model reduces to the inviscid model of Gaunaa, which includes the aerodynamic effect of a thin airfoil with a deformable camberline in inviscid flow. Therefore, the proposed model can be considered a crossover between the work of Gaunaa for the attached flow region and Hansen et al. The model will be compared to wind tunnel measurements from Velux described by Bak et al

  19. Detection of foot-and-mouth disease virus RNA in pharyngeal epithelium biopsy samples obtained from infected cattle: Investigation of possible sites of virus replication and persistence

    DEFF Research Database (Denmark)

    Stenfeldt, Anna Carolina; Belsham, Graham

    2012-01-01

    measurements of the levels of FMDV RNA in the DSP as well as mandibular and retropharyngeal lymph nodes beyond 28 days after infection. Results indicated only low levels of FMDV RNA present in samples of pharyngeal epithelia during both early and persistent phases of infection with significantly higher levels...... of virus detected in pharyngeal excretions. It is concluded that the targeted area for sampling within the DSP does not harbour significant levels of virus replication during acute or persistent FMDV infection in cattle. Furthermore, the DSP and the mandibular and retropharyngeal lymph nodes cannot...

  20. Dairy Cows Produce Less Milk and Modify Their Behaviour during the Transition between Tie-Stall to Free-Stall

    Science.gov (United States)

    Broucek, Jan; Uhrincat, Michal; Mihina, Stefan; Soch, Miloslav; Mrekajova, Andrea; Hanus, Anton

    2017-01-01

    Simple Summary The purpose of this study was to evaluate the influence of moving cows from the barn with stanchion-stall housing to free-stall housing on their behaviour and production. Cows lay down up to ten hours after removing. The cows in their second lactation and open cows tended to lie sooner after removing than cows in their first lactation and pregnant cows. The times of total lying and rumination were increasing from the first day to the tenth day after removing. Cows produced 23.3% less milk at the first day following the transfer than at the last day prior to moving (23.76 ± 7.20 kg vs. 30.97 ± 7.26 kg, p cows achieved maximum production. The difference was found in milk losses due to the shift between cows in first and second lactation. Abstract Transfer of cattle to an unknown barn may result in a reduction in its welfare. Housing and management practices can result in signs of stress that include a long-term suppression of milk efficiency. The purpose of this study was to evaluate the influence of moving cows from the stanchion-stall housing to free-stall housing on their behaviour and production. The Holstein cows were moved into the new facility with free-stall housing from the old barn with stanchion-stall housing. Cows lay down up to ten hours (596.3 ± 282.7 min) after removing. The cows in their second lactation and open cows tended to lie sooner after removing than cows in their first lactation and pregnant cows. The times of total lying and rumination were increasing from the first day to the tenth day after removing (23.76 ± 7.20 kg vs. 30.97 ± 7.26 kg, p Cows produced 23.3% less milk at the first day following the transfer than at the last day prior to moving (p cows on the first and second lactation (p cows’ milk production. However, when the cows are moved to a better environment, they rapidly adapt to the change. PMID:28273810

  1. 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.

  2. A kinesthetic-tactual display for stall deterrence

    Science.gov (United States)

    Gilson, R. D.; Ventola, R. W.; Fenton, R. E.

    1975-01-01

    A kinesthetic tactual display may be effectively used as a control aid per previous flight tests. Angle of attack information would be continuously presented to a pilot, via this display, during critical operational phases where stalls are probable. A two phase plan for evaluating this concept is presented. A first development phase would encompass: (1) display fabrication for a conventional control yoke; (2) its installation, together with other necessary instrumentation, in an experimental aircraft; and (3) preliminary flight testing by experienced pilots.

  3. 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....

  4. Study and Control of a Radial Vaned Diffuser Stall

    Directory of Open Access Journals (Sweden)

    Aurélien Marsan

    2012-01-01

    Full Text Available The aim of the present study is to evaluate the efficiency of a boundary layer suction technique in case of a centrifugal compressor stage in order to extend its stable operating range. First, an analysis of the flow pattern within the radial vaned diffuser is presented. It highlights the stall of the diffuser vanes when reaching a low massflow. A boundary layer separation in the hub-suction side corner grows when decreasing the massflow from the nominal operating point to the surge and finally leads to a massive stall. An aspiration strategy is investigated in order to control the stall. The suction slot is put in the vicinity of the saddle that originates the main separating skin-friction line, identified thanks to the analysis of the skin-friction pattern. Several aspiration massflow rates are tested, and two different modelings of the aspiration are evaluated. Finally, an efficient control is reached with a removal of only 0,1% of the global massflow and leads—from a steady-state calculations point of view—to an increase by 40% of the compressor operating range extent.

  5. Simulasi Numerik Dynamic Stall Pada Airfoil Yang Berosilasi

    Directory of Open Access Journals (Sweden)

    Galih S.T.A. Bangga

    2012-09-01

    Full Text Available Kebutuhan analisa pada sudu helikopter, kompresor, kincir angin dan struktur streamline lainya yang beroperasi pada angle of attack yang tinggi dan melibatkan instationary effects yang disebut dynamic stall menjadi semakin penting. Fenomena ini ditandai dengan naiknya dynamic lift melewati static lift maksimum pada critical static stall angle, vortex yang terbentuk pada leading edge mengakibatkan naiknya suction contribution yang kemudian terkonveksi sepanjang permukaan hingga mencapai trailling edge diikuti terbentuknya trailling edge vortex yang menunjukkan terjadinya lift stall. Fenomena ini sangat berbahaya terhadap struktur airfoil itu sendiri. Secara umum, beban fatique yang ditimbulkan oleh adanya efek histerisis karena fluktuasi gaya lift akibat induksi vibrasi lebih besar dibandingkan kondisi statis. Simulasi numerik dilakukan secara 2D dengan menggunakan profil Boeing-Vertol V23010-1.58 pada α0 = 14.92°. Standard-kω dan SST-kω digunakan sebagai URANS turbulence modelling. Model osilasi dari airfoil disusun dalam suatu user defined function (UDF. Gerakan meshing beserta airfoil diakomodasi dengan menggunakan dynamic mesh approach. Simulasi numerik menunjukkan bahwa, model SST-kω menunjukkan performa yang lebih baik dibandingkan dengan Standard-kω. Fenomena travelling vortex yang terjadi mampu ditangkap dengan baik, meski pada angle of attack yang tinggi URANS turbulence model gagal memprediksikan fenomena yang terjadi karena dominasi efek 3D.

  6. The SmpB C-terminal tail helps tmRNA to recognize and enter stalled ribosomes

    Directory of Open Access Journals (Sweden)

    Mickey R. Miller

    2014-09-01

    Full Text Available In bacteria, transfer-messenger RNA (tmRNA and SmpB comprise the most common and effective system for rescuing stalled ribosomes. Ribosomes stall on mRNA transcripts lacking stop codons and are rescued as the defective mRNA is swapped for the tmRNA template in a process known as trans-translation. The tmRNA–SmpB complex is recruited to the ribosome independent of a codon–anticodon interaction. Given that the ribosome uses robust discriminatory mechanisms to select against non-cognate tRNAs during canonical decoding, it has been hard to explain how this can happen. Recent structural and biochemical studies show that SmpB licenses tmRNA entry through its interactions with the decoding center and mRNA channel. In particular, the C-terminal tail of SmpB promotes both EFTu activation and accommodation of tmRNA, the former through interactions with 16S rRNA nucleotide G530 and the latter through interactions with the mRNA channel downstream of the A site. Here we present a detailed model of the earliest steps in trans-translation, and in light of these mechanistic considerations, revisit the question of how tmRNA preferentially reacts with stalled, non-translating ribosomes.

  7. Prediction of dynamic loads and induced vibrations in stall

    Energy Technology Data Exchange (ETDEWEB)

    Thirstrup Petersen, J.; Aagaard Madsen, H. [Risoe National Lab. (Denmark); Bjoerck, A. [Aeronautical Research Inst. of Sweden (Sweden); Enevoldsen, P. [Bonus Energy A/S (Denmark); Oeye, S. [The Technical Univ. of Denmark (Denmark); Ganander, H. [Teknikgruppen AB (Sweden); Winkelaar, D. [Netherlands Energy Research Foundation (Netherlands)

    1998-05-01

    Results from research in an EC Joule-III project and from national projects are presented. The objectives are improvement of design methods for stall regulated wind turbines with emphasis on stall induced vibrations and dynamic stall. The primary concern is limitation of the edgewise vibrations in the fundamental blade natural mode shape, which have caused trouble on modern wind turbines of approximate size 500 kW nominal power and 40 m rotor diameter. A theoretical study of quasi-steady aerodynamics confirms that the vibrations are driven basically by energy supplied from the aerodynamic forces during stalled operation. This energy exchange is equivalent to negative aerodynamic damping. The theoretical approach identifies the main parameters controlling the phenomenon. These parameters describe the steady and the dynamic airfoil characteristics, the overall aerodynamic layout of the blade, e.g. chord length and twist, the structural properties of the blade, e.g. structural damping and properties controlling the resulting vibration direction. Furthermore, full aeroelastic calculations and comparison with measurements show that the properties of the supporting structure, i.e. the main shaft, the nacelle and the tower, are important, as the global vibration of the rotor on its support may exchange energy with the blade vibration, when the blade natural frequency is close to one of the frequencies of the coupled rotor tilt-yaw mode shapes, usually denoted the global rotor whirl frequencies. It is confirmed that the influence of changing the primary design parameters can be determined by use of qualified aeroelastic calculations. Presented design guidelines therefore build on both the simple quasi-steady models, which can be used for the preliminary choice of the design variables mentioned above, and on full aeroelastic calculations. The aeroelastic calculations refine the design basis and should be used for choosing the final design variables and for final

  8. 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...

  9. Performance augmentation with vortex generators: Design and testing for stall-regulated AWT-26 turbine

    Energy Technology Data Exchange (ETDEWEB)

    Griffin, D.A. [Advanced Wind Turbines Inc., Seattle, WA (United States)

    1996-12-31

    A study investigated the use of vortex generators (VGs) for performance augmentation of the stall-regulated AWT-26 wind turbine. Based on wind-tunnel results and analysis, a VG array was designed for and tested on the AWT-26 prototype, designated Pt. Performance and loads data were measured for P1, both with and without VGs installed. The turbine performance with VGs met most of the design requirements; power output was increased at moderate wind speeds with a minimal effect on peak power. However, VG drag penalties caused a loss in power output for low wind speeds, such that performance with VGs resulted in a net decrease in AEP for wind speed sites up to 8.5 m/s. 8 refs., 8 figs., 3 tabs.

  10. RPA mediates recombination repair during replication stress and is displaced from DNA by checkpoint signalling in human cells

    DEFF Research Database (Denmark)

    Sleeth, Kate M; Sørensen, Claus Storgaard; Issaeva, Natalia

    2007-01-01

    The replication protein A (RPA) is involved in most, if not all, nuclear metabolism involving single-stranded DNA. Here, we show that RPA is involved in genome maintenance at stalled replication forks by the homologous recombination repair system in humans. Depletion of the RPA protein inhibited...... the formation of RAD51 nuclear foci after hydroxyurea-induced replication stalling leading to persistent unrepaired DNA double-strand breaks (DSBs). We demonstrate a direct role of RPA in homology directed recombination repair. We find that RPA is dispensable for checkpoint kinase 1 (Chk1) activation...... and that RPA directly binds RAD52 upon replication stress, suggesting a direct role in recombination repair. In addition we show that inhibition of Chk1 with UCN-01 decreases dissociation of RPA from the chromatin and inhibits association of RAD51 and RAD52 with DNA. Altogether, our data suggest a direct role...

  11. Systematic identification of fragile sites via genome-wide location analysis of γ-H2AX

    Science.gov (United States)

    Szilard, Rachel K.; Jacques, Pierre-Étienne; Laramée, Louise; Cheng, Benjamin; Galicia, Sarah; Bataille, Alain R.; Yeung, ManTek; Mendez, Megan; Bergeron, Maxime; Robert, François; Durocher, Daniel

    2011-01-01

    Phosphorylation of histone H2AX is an early response to DNA damage in eukaryotes. In Saccharomyces cerevisiae, DNA damage or replication fork stalling results in histone H2A phosphorylation to yield γ-H2A (yeast γ-H2AX) in a Mec1 (ATR)- and Tel1 (ATM)- dependent manner. Here, we describe the genome-wide location analysis of γ-H2A as a strategy to identify loci prone to engage the Mec1 and Tel1 pathways. Remarkably, γ-H2A enrichment overlaps with loci prone to replication fork stalling and is caused by the action of Mec1 and Tel1, indicating that these loci are prone to breakage. Moreover, about half the sites enriched for γ-H2A map to repressed protein-coding genes, and histone deacetylases are necessary for formation of γ-H2A at these loci. Finally, our work indicates that high resolution mapping of γ-H2AX is a fruitful route to map fragile sites in eukaryotic genomes. PMID:20139982

  12. Precautions against axial fan stall in reactor building to Tianwan NPP

    International Nuclear Information System (INIS)

    Liu Chunlong; Pei Junmin

    2011-01-01

    The paper introduces the mechanism and harm of rotating stall of axial fans, analyzes the necessity for prevention against axial fan stall in reactor building of Tianwan NPP, introduces the precautions, and then makes an assessment on anti-stall effect of flow separators. It can provide reference for model-selection or reconstruction of similar fans in power stations, and for operation and maintenance of axial fans. (authors)

  13. Preferences of dairy cows for three stall surface materials with small amounts of bedding.

    Science.gov (United States)

    Norring, M; Manninen, E; de Passillé, A M; Rushen, J; Saloniemi, H

    2010-01-01

    Farmers' concerns about the economy, cost of labor, and hygiene have resulted in reduced use of organic bedding in stalls for dairy cows; however, the reduced use of organic bedding possibly impairs cow comfort. The effects of different stall surface materials were evaluated in an unheated building in which only a small amount of bedding was used. The lying time and preferences of 18 cows using 3 stall surface materials (concrete, soft rubber mat, and sand) were compared. All materials were lightly bedded with a small amount of straw, and the amount of straw added to each stall was measured. The cows only had access to stalls of one surface type while their lying time was observed. Lying times were longest on the rubber mats compared with other surfaces (rubber mat 768; concrete 727; sand 707+/-16 min/d). In a preference test, cows had access to 2 of the 3 types of stalls for 10 d and their stall preference was measured. Cows preferred stalls with rubber mats to stalls with a concrete floor (median 73 vs. 18 from a total of 160 observations per day; interquartile range was 27 and 12, respectively), but showed no preference for sand stalls compared with stalls with a concrete floor or with rubber mats. More straw was needed on sand stalls compared with concrete or mat (638+/-13 g/d on sand, 468+/-10 g/d on concrete, and 464+/-8 g/d on rubber mats). Lying times on bedded mats indicated that mats were comfortable for the cows. If availability or cost of bedding material requires limiting the amount of bedding used, rubber mats may help maintain cow comfort. Copyright 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  14. Chemical shift changes provide evidence for overlapping single-stranded DNA and XPA binding sites on the 70 kDa subunit of human replication protein A

    Energy Technology Data Exchange (ETDEWEB)

    Daughdrill, Gary W.; Buchko, Garry W.; Botuyan, Maria V.; Arrowsmith, Cheryl H.; Wold, Marc S.; Kennedy, Michael A.; Lowry, David F.

    2003-07-15

    Replication protein A (RPA) is a heterotrimeric single-stranded DNA (ssDNA) binding protein that can form a complex with the xeroderma pigmentosum group A protein (XPA). This complex can preferentially recognize UV damaged DNA over undamaged DNA and has been implicated in the stabilization of open complex formation during nucleotide excision repair. In this report, NMR spectroscopy was used to investigate the interaction between a fragment of the 70 kDa subunit of human RPA, residues 1-326 (hRPA701-326), and a fragment of the human XPA protein, residues 98-219 (XPA-MBD). Intensity changes were observed for amide resonances in the 1H-15N correlation spectrum of uniformly 15N-labeled hRPA701-326 after the addition of unlabeled XPA-MBD. The intensity changes observed were restricted to an ssDNA binding domain that is between residues 183 and 296 of the hRPA701-326 fragment. The hRPA701-326 residues with the largest resonance intensity reductions were mapped onto the structure of the ssDNA binding domain to identify the binding surface with XPA-MBD. The XPA-MBD binding surface showed significant overlap with an ssDNA binding surface that was previously identified using NMR spectroscopy and X-ray crystallography.

  15. Replication and Comparison of the Newly Proposed ADOS-2, Module 4 Algorithm in ASD without ID: A Multi-Site Study

    Science.gov (United States)

    Pugliese, Cara E.; Kenworthy, Lauren; Bal, Vanessa Hus; Wallace, Gregory L.; Yerys, Benjamin E.; Maddox, Brenna B.; White, Susan W.; Popal, Haroon; Armour, Anna Chelsea; Miller, Judith; Herrington, John D.; Schultz, Robert T.; Martin, Alex; Anthony, Laura Gutermuth

    2015-01-01

    Recent updates have been proposed to the Autism Diagnostic Observation Schedule-2 Module 4 diagnostic algorithm. This new algorithm, however, has not yet been validated in an independent sample without intellectual disability (ID). This multi-site study compared the original and revised algorithms in individuals with ASD without ID. The revised…

  16. Monitoring indices of cow comfort in free-stall-housed dairy herds.

    Science.gov (United States)

    Cook, N B; Bennett, T B; Nordlund, K V

    2005-11-01

    Indices of cow comfort are used widely by consultants in the dairy industry, with a general understanding that they are representative of lying behavior. This study examines the influence of stall base type (sand or a geotextile mattress filled with rubber crumbs) and time of measurement on 4 indices of comfort collected at hourly intervals in 12 herds, aligned by morning and afternoon milking. Stall base type significantly influenced all indices of comfort. For example, the least squares mean (SE) cow comfort index (proportion of cows touching a stall that are lying down) was 0.76 (0.015) in herds with mattresses compared with 0.86 (0.015) in herds with sand stalls. Significant hourly variation was also identified suggesting that timing of measurement is important. None of the indices of cow comfort derived from the high-yielding group pen was associated with the mean 24-h lying time of 10 sentinel cows whose time budgets were known in each herd. However, the cow comfort index was associated with the herd mean 24-h stall standing time, with the strongest relationships occurring 2 h before the morning and afternoon milking, when stall base type did not significantly influence the association. When measured at these times, we recommend use of the stall standing index (proportion of cows touching a stall that are standing), with values greater than 0.20 being associated with abnormally long herd mean stall standing times greater than 2 h/d.

  17. Inception mechanism and suppression of rotating stall in an axial-flow fan

    International Nuclear Information System (INIS)

    Nishioka, T

    2013-01-01

    Inception patterns of rotating stall at two stagger-angle settings for the highly loaded rotor blades were experimentally investigated in a low-speed axial-flow fan. Rotor-tip flow fields were also numerically investigated to clarify the mechanism behind the rotating stall inception. The stall inception patterns depended on the rotor stagger-angle settings. The stall inception from a rotating instability was confirmed at the design stagger-angle settings. The stall inception from a short length-scale stall cell (spike) was also confirmed at the small stagger-angle setting. The spillage of tip-leakage flow and the tip-leakage vortex breakdown influence the rotating stall inception. An air-separator has been developed based on the clarified inception mechanism of rotating stall. The rotating stall was suppressed by the developed air-separator, and the operating range of fan was extended towards low flow rate. The effect of developed air-separator was also confirmed by application to a primary air fan used in a coal fired power plant. It is concluded from these results that the developed air-separator can provide a wide operating range for an axial-flow fan

  18. Enhancing BEM simulations of a stalled wind turbine using a 3D correction model

    Science.gov (United States)

    Bangga, Galih; Hutomo, Go; Syawitri, Taurista; Kusumadewi, Tri; Oktavia, Winda; Sabila, Ahmad; Setiadi, Herlambang; Faisal, Muhamad; Hendranata, Yongki; Lastomo, Dwi; Putra, Louis; Kristiadi, Stefanus; Bumi, Ilmi

    2018-03-01

    Nowadays wind turbine rotors are usually employed with pitch control mechanisms to avoid deep stall conditions. Despite that, wind turbines often operate under pitch fault situation causing massive flow separation to occur. Pure Blade Element Momentum (BEM) approaches are not designed for this situation and inaccurate load predictions are already expected. In the present studies, BEM predictions are improved through the inclusion of a stall delay model for a wind turbine rotor operating under pitch fault situation of -2.3° towards stall. The accuracy of the stall delay model is assessed by comparing the results with available Computational Fluid Dynamics (CFD) simulations data.

  19. Experimental study of dynamic stall on Darrieus wind turbine blades

    Science.gov (United States)

    Brochier, G.; Fraunie, P.; Beguier, C.; Paraschivoiu, I.

    1985-12-01

    An experimental study of periodic vortex phenomena was performed on a model of a two straight-bladed Darrieus wind turbine under controlled-rotation conditions in the IMST water tunnel. The main focus of interest was the tip-speed ratios at which dynamic stall appears. Observations of this phenomenon from dye emission and the formation of hydrogen bubbles were made in the form of photographs, film and video recordings. Velocity measurements were obtained using the Laser-Doppler Velocimeter and components of velocity fluctuations could be determined quantitatively.

  20. Numerical simulation of the RISOe1-airfoil dynamic stall

    Energy Technology Data Exchange (ETDEWEB)

    Bertagnolio, F.; Soerensen, N. [Risoe National Lab., Wind Energy and Atmospheric Physics Dept., Roskilde (Denmark)

    1997-12-31

    In this paper we are concerned with the numerical computation of the dynamic stall that occur in the viscous flowfield over an airfoil. These results are compared to experimental data that were obtained with the new designed RISOe1-airfoil, both for a motionless airfoil and for a pitching motion. Moreover, we present some numerical computations of the plunging and lead-lag motions. We also investigate the possibility of using the pitching motion to simulate the plunging and lead-lag situations. (au)

  1. MICROBIOLOGICAL STUDY ON ICE FROM A FISH STALL

    Directory of Open Access Journals (Sweden)

    E. Tirloni

    2012-08-01

    Full Text Available The ice used for exposure of fish products could be a source of secondary contamination due to ice machine, due to not respected good manufacturing practices, particularly when ice is left on the fish stall and the next day the new layer is deposited over the old one. Aim of this study was the verification of the hygienic risk of this procedure through analyses of the liquid produced by the zones “thawed cephalopods” and “fresh whole fish”. Almost the microorganisms found were Gram negative (in particular Pseudomonadaceae.

  2. Molecular basis for PrimPol recruitment to replication forks by RPA.

    Science.gov (United States)

    Guilliam, Thomas A; Brissett, Nigel C; Ehlinger, Aaron; Keen, Benjamin A; Kolesar, Peter; Taylor, Elaine M; Bailey, Laura J; Lindsay, Howard D; Chazin, Walter J; Doherty, Aidan J

    2017-05-23

    DNA damage and secondary structures can stall the replication machinery. Cells possess numerous tolerance mechanisms to complete genome duplication in the presence of such impediments. In addition to translesion synthesis (TLS) polymerases, most eukaryotic cells contain a multifunctional replicative enzyme called primase-polymerase (PrimPol) that is capable of directly bypassing DNA damage by TLS, as well as repriming replication downstream of impediments. Here, we report that PrimPol is recruited to reprime through its interaction with RPA. Using biophysical and crystallographic approaches, we identify that PrimPol possesses two RPA-binding motifs and ascertained the key residues required for these interactions. We demonstrate that one of these motifs is critical for PrimPol's recruitment to stalled replication forks in vivo. In addition, biochemical analysis reveals that RPA serves to stimulate the primase activity of PrimPol. Together, these findings provide significant molecular insights into PrimPol's mode of recruitment to stalled forks to facilitate repriming and restart.

  3. Replication and Comparison of the Newly Proposed ADOS-2, Module 4 Algorithm in ASD without ID: A Multi-site Study

    OpenAIRE

    Pugliese, Cara E.; Kenworthy, Lauren; Bal, Vanessa Hus; Wallace, Gregory L; Yerys, Benjamin E; Maddox, Brenna B.; White, Susan W.; Popal, Haroon; Armour, Anna Chelsea; Miller, Judith; Herrington, John D.; Schultz, Robert T.; Martin, Alex; Anthony, Laura Gutermuth

    2015-01-01

    Recent updates have been proposed to the Autism Diagnostic Observation Schedule-2 Module 4 diagnostic algorithm. This new algorithm, however, has not yet been validated in an independent sample without intellectual disability (ID). This multi-site study compared the original and revised algorithms in individuals with ASD without ID. The revised algorithm demonstrated increased sensitivity, but lower specificity in the overall sample. Estimates were highest for females, individuals with a verb...

  4. 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.

  5. Stalled RNAP-II molecules bound to non-coding rDNA spacers are required for normal nucleolus architecture.

    Science.gov (United States)

    Freire-Picos, M A; Landeira-Ameijeiras, V; Mayán, María D

    2013-07-01

    The correct distribution of nuclear domains is critical for the maintenance of normal cellular processes such as transcription and replication, which are regulated depending on their location and surroundings. The most well-characterized nuclear domain, the nucleolus, is essential for cell survival and metabolism. Alterations in nucleolar structure affect nuclear dynamics; however, how the nucleolus and the rest of the nuclear domains are interconnected is largely unknown. In this report, we demonstrate that RNAP-II is vital for the maintenance of the typical crescent-shaped structure of the nucleolar rDNA repeats and rRNA transcription. When stalled RNAP-II molecules are not bound to the chromatin, the nucleolus loses its typical crescent-shaped structure. However, the RNAP-II interaction with Seh1p, or cryptic transcription by RNAP-II, is not critical for morphological changes. Copyright © 2013 John Wiley & Sons, Ltd.

  6. The FFA dynamic stall model. The Beddoes-Leishman dynamic stall model modified for lead-lag oscillations

    Energy Technology Data Exchange (ETDEWEB)

    Bjoerck, A. [FFA, The Aeronautical Research Institute of Sweden, Bromma (Sweden)

    1997-08-01

    For calculations of the dynamics of wind turbines the inclusion of a dynamic stall model is necessary in order to obtain reliable results at high winds. For blade vibrations in the lead-lag motion the velocity relative to the blade will vary in time. In the present paper modifications to the Beddoes-Leishman model is presented in order to improve the model for calculations of cases with a varying relative velocity. Comparisons with measurement are also shown and the influence on the calculated aerodynamic damping by the modifications are investigated. (au)

  7. Design of advanced airfoil for stall-regulated wind turbines

    Directory of Open Access Journals (Sweden)

    F. Grasso

    2017-07-01

    Full Text Available Nowadays, all the modern megawatt-class wind turbines make use of pitch control to optimise the rotor performance and control the turbine. However, for kilowatt-range machines, stall-regulated solutions are still attractive and largely used for their simplicity and robustness. In the design phase, the aerodynamics plays a crucial role, especially concerning the selection/design of the necessary airfoils. This is because the airfoil performance is supposed to guarantee high wind turbine performance but also the necessary machine control capabilities. In the present work, the design of a new airfoil dedicated to stall machines is discussed. The design strategy makes use of a numerical optimisation scheme, where a gradient-based algorithm is coupled with the RFOIL code and an original Bezier-curves-based parameterisation to describe the airfoil shape. The performances of the new airfoil are compared in free- and fixed-transition conditions. In addition, the performance of the rotor is analysed, comparing the impact of the new geometry with alternative candidates. The results show that the new airfoil offers better performance and control than existing candidates do.

  8. Ingestive behavior of lambs confined in individual and group stalls.

    Science.gov (United States)

    Filho, A Eustáquio; Carvalho, G G P; Pires, A J V; Silva, R R; Santos, P E F; Murta, R M; Pereira, F M

    2014-02-01

    The experiment was conducted to evaluate the ingestive behavior of lambs confined in individual and group stalls. We used thirty-four lambs in their growing phase, aged an average of three months, with mean initial live weight of 17.8±5.2 kg. They were allotted in a completely randomized design with 24 animals kept in individual stalls and 10 animals confined as a group. The experiment lasted for a total of 74 days, and the first 14 days were dedicated to the animals' adaption to the management, facilities and diets. The data collection period lasted 60 days, divided into three 20-d periods for the behavior evaluation. The animals were subjected to five days of visual observation during the experiment period, by the quantification of 24 h a day, with evaluations on the 15th day of each period and an interim evaluation consisting of two consecutive days on the 30th and 31st day of the experiment. The animals confined as a group consumed less (pbehavior.

  9. Associations between cow hygiene, hock injuries, and free stall usage on US dairy farms.

    Science.gov (United States)

    Lombard, J E; Tucker, C B; von Keyserlingk, M A G; Kopral, C A; Weary, D M

    2010-10-01

    This cross-sectional study evaluated cow comfort measures in free stall dairies across the United States as part of the National Animal Health Monitoring System's Dairy 2007 study. The study was conducted in 17 states and evaluations were completed between March 5 and September 5, 2007. Assessors recorded hygiene and hock scores, number of cows housed in the pen, the number of cows standing with only the front feet in a stall, standing fully in a stall, and lying in a stall. Facility design measures included bedding type, bedding quantity, stall length and width, presence of a neck rail or brisket locator, and relevant distances from the rear and bed of the stall. Of the 491 operations that completed the cow comfort assessment, 297 had Holstein cows housed in free stalls and were included in this analysis. Negative binomial models were constructed to evaluate the following outcomes: the number of cows that were very dirty, had severe hock injuries, stood with front feet in the stall, stood with all feet in the stall, and were lying in the stall. Hygiene was better on farms that did not tail dock cows compared with those that did (5.7 vs. 8.8% were dirty) and on farms located in the study's west region compared with those located in the east region (5.2 vs. 9.7% were dirty). Severe hock injuries were less common on farms in the west than those in the east (0.5 vs. 4.1%). In addition, severe hock injuries were less common on farms that used dirt as a stall base or sand as bedding compared with farms that did not. A higher percentage of cows was standing with front feet in the stall at higher ambient temperatures (incidence rate ratio=1.016) and as time since feeding increased (incidence rate ratio=1.030). A lower percentage of cows were standing with front feet in the stall when the stalls were shorter and when there were fewer cows per stall. Standing fully in a stall was performed by a higher percentage of cows during the summer than during the spring (13.6 vs. 8

  10. Evaluating Classroom Interaction with the iPad®: An Updated Stalling's Tool

    Science.gov (United States)

    MacKinnon, Gregory; Schep, Lourens; Borden, Lisa Lunney; Murray-Orr, Anne; Orr, Jeff; MacKinnon, Paula

    2016-01-01

    A large study of classrooms in the Caribbean context necessitated the use of a validated classroom observation tool. In practice, the paper-version Stalling's instrument (Stallings & Kaskowitz 1974) presented specific challenges with respect to (a) facile data collection and (b) qualitative observations of classrooms. In response to these…

  11. Simulation of Broadband Noise Sources of an Axial Fan under Rotating Stall Conditions

    Directory of Open Access Journals (Sweden)

    Lei Zhang

    2014-11-01

    Full Text Available Study on the influence of rotating stall on the aerodynamic noise of axial fan has important value to warn of the occurrence of stall through monitoring the noise variations. The present work is to analyze the aerodynamic noise before and after the phenomenon of rotating stall by solving Navier-Stokes equations, coupled with the throttle condition and the broadband noise sources model. The impeller exit rotational Mach number and rotational Reynolds number are separately 0.407 and 8.332 × 106. The results show that the aerodynamic noise source of the fan is mainly the rotation noise under the design condition. The vortex noise accounts for the major part of fan noise after the occurrence of stall, and the maximum acoustic power level of the fan appears in the rotor domains. In the evolution process from the stall inception to the stall cell, the high noise regions of the rotor develop along the radial, circumferential, and axial directions, and the area occupied by high noise regions increases from 33% to 46% impeller channels area. On rotating stall condition, the high noise regions occupying about 46% impeller channels area propagate with the stall cell along the circumferential direction at a half of rotor speed.

  12. Simulation of Entropy Generation under Stall Conditions in a Centrifugal Fan

    Directory of Open Access Journals (Sweden)

    Lei Zhang

    2014-06-01

    Full Text Available Rotating stalls are generally the first instability met in turbomachinery, before surges. This 3D phenomenon is characterized by one or more stalled flow cells which rotate at a fraction of the impeller speed. The goal of the present work is to shed some light on the entropy generation in a centrifugal fan under rotating stall conditions. A numerical simulation of entropy generation is carried out with the ANSYS Fluent software which solves the Navier-Stokes equations and user defined function (UDF. The entropy generation characteristics in the centrifugal fan for five typical conditions are presented and discussed, involving the design condition, conditions on occurrence and development of stall inception, the rotating stall conditions with two throttle coefficients. The results show that the entropy generation increases after the occurrence of stall inception. The high entropy generation areas move along the circumferential and axial directions, and finally merge into one stall cell. The entropy generation rate during circumferential propagation of the stall cell is also discussed, showing that the entropy generation history is similar to sine curves in impeller and volute, and the volute tongue has a great influence on entropy generation in the centrifugal fan.

  13. Escherichia coli DinB inhibits replication fork progression without significantly inducing the SOS response.

    Science.gov (United States)

    Mori, Tetsuya; Nakamura, Tatsuro; Okazaki, Naoto; Furukohri, Asako; Maki, Hisaji; Akiyama, Masahiro Tatsumi

    2012-01-01

    The SOS response is readily triggered by replication fork stalling caused by DNA damage or a dysfunctional replicative apparatus in Escherichia coli cells. E. coli dinB encodes DinB DNA polymerase and its expression is upregulated during the SOS response. DinB catalyzes translesion DNA synthesis in place of a replicative DNA polymerase III that is stalled at a DNA lesion. We showed previously that DNA replication was suppressed without exogenous DNA damage in cells overproducing DinB. In this report, we confirm that this was due to a dose-dependent inhibition of ongoing replication forks by DinB. Interestingly, the DinB-overproducing cells did not significantly induce the SOS response even though DNA replication was perturbed. RecA protein is activated by forming a nucleoprotein filament with single-stranded DNA, which leads to the onset of the SOS response. In the DinB-overproducing cells, RecA was not activated to induce the SOS response. However, the SOS response was observed after heat-inducible activation in strain recA441 (encoding a temperature-sensitive RecA) and after replication blockage in strain dnaE486 (encoding a temperature-sensitive catalytic subunit of the replicative DNA polymerase III) at a non-permissive temperature when DinB was overproduced in these cells. Furthermore, since catalytically inactive DinB could avoid the SOS response to a DinB-promoted fork block, it is unlikely that overproduced DinB takes control of primer extension and thus limits single-stranded DNA. These observations suggest that DinB possesses a feature that suppresses DNA replication but does not abolish the cell's capacity to induce the SOS response. We conclude that DinB impedes replication fork progression in a way that does not activate RecA, in contrast to obstructive DNA lesions and dysfunctional replication machinery.

  14. Mutations within Four Distinct Gag Proteins Are Required To Restore Replication of Human Immunodeficiency Virus Type 1 after Deletion Mutagenesis within the Dimerization Initiation Site

    Science.gov (United States)

    Liang, Chen; Rong, Liwei; Quan, Yudong; Laughrea, Michael; Kleiman, Lawrence; Wainberg, Mark A.

    1999-01-01

    Human immunodeficiency virus type 1 (HIV-1) genomic RNA segments at nucleotide (nt) positions +240 to +274 are thought to form a stem-loop secondary structure, termed SL1, that serves as a dimerization initiation site for viral genomic RNA. We have generated two distinct deletion mutations within this region, termed BH10-LD3 and BH10-LD4, involving nt positions +238 to +253 and +261 to +274, respectively, and have shown that each of these resulted in significant diminutions in levels of viral infectiousness. However, long-term culture of each of these viruses in MT-2 cells resulted in a restoration of infectiousness, due to a series of compensatory point mutations within four distinct proteins that are normally cleaved from the Gag precursor. In the case of BH10-LD3, these four mutations were MA1, CA1, MP2, and MNC, and they involved changes of amino acid Val-35 to Ile within the matrix protein (MA), Ile-91 to Thr within the capsid (CA), Thr-12 to Ile within p2, and Thr-24 to Ile within the nucleocapsid (NC). The order in which these mutations were acquired by the mutated BH10-LD3 was MNC > CA1 > MP2 > MA1. The results of site-directed mutagenesis studies confirmed that each of these four substitutions contributed to the increased viability of the mutated BH10-LD3 viruses and that the MNC substitution, which was acquired first, played the most important role in this regard. Three point mutations, MP2, MNC, and MA2, were also shown to be sequentially acquired by viruses that had emerged in culture from the BH10-LD4 deletion. The first two of these were identical to those described above, while the last involved a change of Val-35 to Leu. All three of these substitutions were necessary to restore the infectiousness of mutated BH10-LD4 viruses to wild-type levels, although the MP2 mutation alone, but neither of the other two substitutions, was able to confer some viability on BH10-LD4 viruses. Studies of viral RNA packaging showed that the BH10-LD4 deletion only

  15. Dynamic stall study of a multi-element airfoil

    Science.gov (United States)

    Tung, Chee; Mcalister, Kenneth W.; Wang, Clin M.

    1992-01-01

    Unsteady flow behavior and load characteristics of a VR-7 airfoil with and without a slat were studied in the water tunnel of the Aeroflightdynamics Directorate, NASA Ames Research Center. Both airfoils were oscillated sinusoidally between 5 and 25 degrees at a Reynolds number of 200,000 to obtain the unsteady lift, drag and pitching moment data. A fluorescing dye was released from an orifice located at the leading edge of the airfoil for the purpose of visualizing the boundary layer and wake flow. The flow field and load predictions of an incompressible Navier-Stokes code based on a velocity-vorticity formulation were compared with the test data. The test and predictions both confirm that the slatted VR-7 airfoil delays both static and dynamic stall as compared to the VR-7 airfoil alone.

  16. Proposed Chevron Tengiz venture stalls amid Soviet political squabble

    International Nuclear Information System (INIS)

    Anon.

    1991-01-01

    This paper reports on the status of foreign investment in Soviet oil and gas joint ventures which has reached a critical juncture. Just as the U.S. is considering granting most favored nation trade status to the U.S.S.R., the joint venture petroleum deal seen as the litmus test for such deals-Chevron Corp.'s proposed addition of supergiant Tengiz oil field to its Caspian Sea joint venture-has stalled amid controversy. Unconfirmed reports from Soviet officials and other foreign joint venture participants in the U.S.S.R. have Chevron pulling out of the long negotiated, multibillion dollar project after the Soviets rejected the company's terms. Chevron, however, insists the project is still alive

  17. Optimal parameters for the FFA-Beddoes dynamic stall model

    Energy Technology Data Exchange (ETDEWEB)

    Bjoerck, A; Mert, M [FFA, The Aeronautical Research Institute of Sweden, Bromma (Sweden); Madsen, H A [Risoe National Lab., Roskilde (Denmark)

    1999-03-01

    Unsteady aerodynamic effects, like dynamic stall, must be considered in calculation of dynamic forces for wind turbines. Models incorporated in aero-elastic programs are of semi-empirical nature. Resulting aerodynamic forces therefore depend on values used for the semi-empiricial parameters. In this paper a study of finding appropriate parameters to use with the Beddoes-Leishman model is discussed. Minimisation of the `tracking error` between results from 2D wind tunnel tests and simulation with the model is used to find optimum values for the parameters. The resulting optimum parameters show a large variation from case to case. Using these different sets of optimum parameters in the calculation of blade vibrations, give rise to quite different predictions of aerodynamic damping which is discussed. (au)

  18. Analysis of Vaneless Diffuser Stall Instability in a Centrifugal Compressor

    Directory of Open Access Journals (Sweden)

    Elias Sundström

    2017-11-01

    Full Text Available Numerical simulations based on the large eddy simulation approach were conducted with the aim to explore vaneless diffuser rotating stall instability in a centrifugal compressor. The effect of the impeller blade passage was included as an inlet boundary condition with sufficiently low flow angle relative to the tangent to provoke the instability and cause circulation in the diffuser core flow. Flow quantities, velocity and pressure, were extracted to accumulate statistics for calculating mean velocity and mean Reynolds stresses in the wall-to-wall direction. The paper focuses on the assessment of the complex response of the system to the velocity perturbations imposed, the resulting pressure gradient and flow curvature effects.

  19. Genome-wide alterations of the DNA replication program during tumor progression

    Science.gov (United States)

    Arneodo, A.; Goldar, A.; Argoul, F.; Hyrien, O.; Audit, B.

    2016-08-01

    Oncogenic stress is a major driving force in the early stages of cancer development. Recent experimental findings reveal that, in precancerous lesions and cancers, activated oncogenes may induce stalling and dissociation of DNA replication forks resulting in DNA damage. Replication timing is emerging as an important epigenetic feature that recapitulates several genomic, epigenetic and functional specificities of even closely related cell types. There is increasing evidence that chromosome rearrangements, the hallmark of many cancer genomes, are intimately associated with the DNA replication program and that epigenetic replication timing changes often precede chromosomic rearrangements. The recent development of a novel methodology to map replication fork polarity using deep sequencing of Okazaki fragments has provided new and complementary genome-wide replication profiling data. We review the results of a wavelet-based multi-scale analysis of genomic and epigenetic data including replication profiles along human chromosomes. These results provide new insight into the spatio-temporal replication program and its dynamics during differentiation. Here our goal is to bring to cancer research, the experimental protocols and computational methodologies for replication program profiling, and also the modeling of the spatio-temporal replication program. To illustrate our purpose, we report very preliminary results obtained for the chronic myelogeneous leukemia, the archetype model of cancer. Finally, we discuss promising perspectives on using genome-wide DNA replication profiling as a novel efficient tool for cancer diagnosis, prognosis and personalized treatment.

  20. Direct numerical simulation of a NACA0012 in full stall

    International Nuclear Information System (INIS)

    Rodríguez, I.; Lehmkuhl, O.; Borrell, R.; Oliva, A.

    2013-01-01

    Highlights: • Coherent structures at transitional and supercritical wake modes are presented. • Vortex shedding is detected in both wake modes. • KH instabilities and vortex shedding frequencies are identified. • Low-frequency flapping of the shear-layer is also detected after stall. • Local pressure distribution at both AOA is coherent with experimental observations. -- Abstract: This work aims at investigating the mechanisms of separation and the transition to turbulence in the separated shear-layer of aerodynamic profiles, while at the same time to gain insight into coherent structures formed in the separated zone at low-to-moderate Reynolds numbers. To do this, direct numerical simulations of the flow past a NACA0012 airfoil at Reynolds numbers Re = 50,000 (based on the free-stream velocity and the airfoil chord) and angles of attack AOA = 9.25° and AOA = 12° have been carried out. At low-to-moderate Reynolds numbers, NACA0012 exhibits a combination of leading-edge/trailing-edge stall which causes the massive separation of the flow on the suction side of the airfoil. The initially laminar shear layer undergoes transition to turbulence and vortices formed are shed forming a von Kármán like vortex street in the airfoil wake. The main characteristics of this flow together with its main features, including power spectra of a set of selected monitoring probes at different positions on the suction side and in the wake of the airfoil are provided and discussed in detail

  1. Prevalence of lameness among dairy cattle in Wisconsin as a function of housing type and stall surface.

    Science.gov (United States)

    Cook, Nigel B

    2003-11-01

    To determine the prevalence of lameness as a function of season (summer vs winter), housing type (free stalls vs tie stalls), and stall surface (sand vs any other surface) among lactating dairy cows in Wisconsin. Epidemiologic survey. 3,621 lactating dairy cows in 30 herds. Herds were visited once during the summer and once during the winter, and a locomotion score ranging from 1 (no gait abnormality) to 4 (severe lameness) was assigned to all lactating cows. Cows with a score of 3 or 4 were considered to be clinically lame. Mean +/- SD herd lameness prevalence was 21.1 +/- 10.5% during the summer and 23.9 +/- 10.7% during the winter; these values were significantly different. During the winter, mean prevalence of lameness in free-stall herds with non-sand stall surfaces (33.7%) was significantly higher than prevalences in free-stall herds with sand stall surfaces (21.2%), tie-stall herds with non-sand stall surfaces (21.7%), and tie-stall herds with sand stall surfaces (12.1%). Results suggest that the prevalence of lameness among dairy cattle in Wisconsin is higher than previously thought and that lameness prevalence is associated with season, housing type, and stall surface.

  2. Flight Measurements of the Flying Qualities of a Lockheed P-80A Airplane (Army No. 44-85099) - Stalling Characteristics

    Science.gov (United States)

    Anderson, Seth B.; Cooper, George E.

    1947-01-01

    This report contains the flight-test results of the stalling characteristics measured during the flying-qualities investigation of the Lockheed P-8OA airplane (Army No. 44-85099). The tests were conducted in straight and turning flight with and without wing-tip tanks. These tests showed satisfactory stalling characteristics and adequate stall warning for all configurations and conditions tested.

  3. Replication fork stability confers chemoresistance in BRCA-deficient cells

    DEFF Research Database (Denmark)

    Chaudhuri, Arnab Ray; Callen, Elsa; Ding, Xia

    2016-01-01

    /4 complex protein, PTIP, protects Brca1/2-deficient cells from DNA damage and rescues the lethality of Brca2-deficient embryonic stem cells. However, PTIP deficiency does not restore homologous recombination activity at double-strand breaks. Instead, its absence inhibits the recruitment of the MRE11......Cells deficient in the Brca1 and Brca2 genes have reduced capacity to repair DNA double-strand breaks by homologous recombination and consequently are hypersensitive to DNA-damaging agents, including cisplatin and poly(ADP-ribose) polymerase (PARP) inhibitors. Here we show that loss of the MLL3...... nuclease to stalled replication forks, which in turn protects nascent DNA strands from extensive degradation. More generally, acquisition of PARP inhibitors and cisplatin resistance is associated with replication fork protection in Brca2-deficient tumour cells that do not develop Brca2 reversion mutations...

  4. Replication of kinetoplast minicircle DNA

    International Nuclear Information System (INIS)

    Sheline, C.T.

    1989-01-01

    These studies describe the isolation and characterization of early minicircle replication intermediates from Crithidia fasciculata, and Leishmania tarentolae, the mitochondrial localization of a type II topoisomerase (TIImt) in C. fasciculata, and the implication of the aforementioned TIImt in minicircle replication in L. tarentolae. Early minicircle replication intermediates from C. fasciculata were identified and characterized using isolated kinetoplasts to incorporate radiolabeled nucleotides into its DNA. The pulse-label in an apparent theta-type intermediate chase into two daughter molecules. A uniquely gapped, ribonucleotide primed, knotted molecule represents the leading strand in the model proposed, and a highly gapped molecule represents the lagging strand. This theta intermediate is repaired in vitro to a doubly nicked catenated dimer which was shown to result from the replication of a single parental molecule. Very similar intermediates were found in the heterogeneous population of minicircles of L. tarentolae. The sites of the Leishmania specific discontinuities were mapped and shown to lie within the universally conserved sequence blocks in identical positions as compared to C. fasciculata and Trypanosoma equiperdum

  5. Manual of Cupule Replication Technology

    Directory of Open Access Journals (Sweden)

    Giriraj Kumar

    2015-09-01

    Full Text Available Throughout the world, iconic rock art is preceded by non-iconic rock art. Cupules (manmade, roughly semi-hemispherical depressions on rocks form the major bulk of the early non-iconic rock art globally. The antiquity of cupules extends back to the Lower Paleolithic in Asia and Africa, hundreds of thousand years ago. When one observes these cupules, the inquisitive mind poses so many questions with regard to understanding their technology, reasons for selecting the site, which rocks were used to make the hammer stones used, the skill and cognitive abilities employed to create the different types of cupules, the objective of their creation, their age, and so on. Replication of the cupules can provide satisfactory answers to some of these questions. Comparison of the hammer stones and cupules produced by the replication process with those obtained from excavation can provide support to observations. This paper presents a manual of cupule replication technology based on our experience of cupule replication on hard quartzite rock near Daraki-Chattan in the Chambal Basin, India.

  6. Analysis of Low Speed Stall Aerodynamics of a Swept Wing with Laminar Flow Glove

    Science.gov (United States)

    Bui, Trong T.

    2014-01-01

    Reynolds-Averaged Navier-Stokes (RANS) computational fluid dynamics (CFD) analysis was conducted to study the low-speed stall aerodynamics of a GIII aircraft's swept wing modified with a laminar-flow wing glove. The stall aerodynamics of the gloved wing were analyzed and compared with the unmodified wing for the flight speed of 120 knots and altitude of 2300 ft above mean sea level (MSL). The Star-CCM+ polyhedral unstructured CFD code was first validated for wing stall predictions using the wing-body geometry from the First American Institute of Aeronautics and Astronautics (AIAA) CFD High-Lift Prediction Workshop. It was found that the Star-CCM+ CFD code can produce results that are within the scattering of other CFD codes considered at the workshop. In particular, the Star-CCM+ CFD code was able to predict wing stall for the AIAA wing-body geometry to within 1 degree of angle of attack as compared to benchmark wind-tunnel test data. Current results show that the addition of the laminar-flow wing glove causes the gloved wing to stall much earlier than the unmodified wing. Furthermore, the gloved wing has a different stall characteristic than the clean wing, with no sharp lift drop-off at stall for the gloved wing.

  7. Analysis of Low-Speed Stall Aerodynamics of a Swept Wing with Laminar-Flow Glove

    Science.gov (United States)

    Bui, Trong T.

    2014-01-01

    Reynolds-Averaged Navier-Stokes (RANS) computational fluid dynamics (CFD) analysis was conducted to study the low-speed stall aerodynamics of a GIII aircraft's swept wing modified with a laminar-flow wing glove. The stall aerodynamics of the gloved wing were analyzed and compared with the unmodified wing for the flight speed of 120 knots and altitude of 2300 ft above mean sea level (MSL). The Star-CCM+ polyhedral unstructured CFD code was first validated for wing stall predictions using the wing-body geometry from the First American Institute of Aeronautics and Astronautics (AIAA) CFD High-Lift Prediction Workshop. It was found that the Star-CCM+ CFD code can produce results that are within the scattering of other CFD codes considered at the workshop. In particular, the Star-CCM+ CFD code was able to predict wing stall for the AIAA wing-body geometry to within 1 degree of angle of attack as compared to benchmark wind-tunnel test data. Current results show that the addition of the laminar-flow wing glove causes the gloved wing to stall much earlier than the unmodified wing. Furthermore, the gloved wing has a different stall characteristic than the clean wing, with no sharp lift drop-off at stall for the gloved wing.

  8. Identify the Rotating Stall in Centrifugal Compressors by Fractal Dimension in Reconstructed Phase Space

    Directory of Open Access Journals (Sweden)

    Le Wang

    2015-11-01

    Full Text Available Based on phase space reconstruction and fractal dynamics in nonlinear dynamics, a method is proposed to extract and analyze the dynamics of the rotating stall in the impeller of centrifugal compressor, and some numerical examples are given to verify the results as well. First, the rotating stall of an existing low speed centrifugal compressor (LSCC is numerically simulated, and the time series of pressure in the rotating stall is obtained at various locations near the impeller outlet. Then, the phase space reconstruction is applied to these pressure time series, and a low-dimensional dynamical system, which the dynamics properties are included in, is reconstructed. In phase space reconstruction, C–C method is used to obtain the key parameters, such as time delay and the embedding dimension of the reconstructed phase space. Further, the fractal characteristics of the rotating stall are analyzed in detail, and the fractal dimensions are given for some examples to measure the complexity of the flow in the post-rotating stall. The results show that the fractal structures could reveal the intrinsic dynamics of the rotating stall flow and could be considered as a characteristic to identify the rotating stall.

  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. A comparison of free-stall barns used by modernized Wisconsin dairies.

    Science.gov (United States)

    Bewley, J; Palmer, R W; Jackson-Smith, D B

    2001-02-01

    A primary objective of the Wisconsin Dairy Modernization Survey was to compare features of free-stall barns available to dairy producers. This study used data from a large random sample of expanding dairy farms to determine whether the theoretical benefits of particular free-stall configurations bear out under on-farm conditions. Comparisons were made among herds using free-stall barns as their primary housing for new versus remodeled facilities, barn design, bedding used, feed-delivery design, manure removal strategies, animal restraint, maternity areas, overcrowding, and cooling methods. Producers who made the transition from tie-stall housing to free-stall housing were satisfied with this decision. New free-stall barns provided a more desirable environment for the herds than remodeled free-stall barns, although initial investments were higher. When new free-stall barns were compared, herds with four-row barns had higher production, lower somatic cell count, and higher stocking rates than herds with six-row barns. Respondents were more satisfied with four- and six-row barns than with two- and three-row barns. Respondents felt sand provided some advantages for cow comfort, while satisfaction with bedding cost and manure handling was higher with mattresses. Dairy Herd Improvement data showed no difference in milk production or somatic cell count for producers who chose sand or mattress-based free stalls. Respondents were more satisfied with the use of drive-through feeding than other feed-delivery designs. Most producers chose to use tractor scrapers to remove manure; however, producers who used automated systems were more satisfied with manure management. Few differences were observed when comparing self-locking head gates to palpation rails. Overcrowding did not have any adverse affect on production or user satisfaction with feed intake or cow comfort. Using supplemental cooling appeared to facilitate higher production.

  11. Experimental investigation on the effects of non-cyclical frequency and amplitude variation on dynamic stall

    Science.gov (United States)

    Heintz, Kyle C.

    An experimental study of a cambered airfoil undergoing non-cyclical, transient pitch trajectories and the resulting effects on the dynamic stall phenomenon is presented. Surface pressure measurements and airfoil incidence angle are acquired simultaneously to resolve instantaneous aerodynamic load coefficients at Mach numbers ranging from 0.2 to 0.4. Derived from these coefficients are various formulations of the aerodynamic damping factor, referred to copiously throughout. Using a two-motor mechanism, each providing independent frequency and amplitude input to the airfoil, unique pitch motions can be implemented by actively controlling the phase between inputs. This work primarily focuses on three pitch motion schemas, the first of which is a "chirp" style trajectory featuring concurrent exponential frequency growth and amplitude decay. Second, these parameters are tested separately to determine their individual contributions. Lastly, a novel dual harmonic pitch motion is devised which rapidly traverses dynamic stall regimes on an inter-cycle basis by modulating the static-stall penetration angle. Throughout all results presented, there is evidence that for consecutive pitch-cycles, the process of dynamic stall is affected when prior oscillations prior have undergone deeper stall-penetration angles. In other words when stall-penetration is descending, retreating from a regime of light or deep stall, statistics of load coefficients, such as damping coefficient, maximum lift, minimum quarter-chord moment, and their phase relationships, do not match the values seen when stall-penetration was growing. The outcomes herein suggest that the airfoil retains some memory of previous flow separation which has the potential to change the influence of the dynamic stall vortex.

  12. Effects of laminar separation bubbles and turbulent separation on airfoil stall

    Energy Technology Data Exchange (ETDEWEB)

    Dini, P. [Carleton College, Northfield, MN (United States); Coiro, D.P. [Universita di Napoli (Italy)

    1997-12-31

    An existing two-dimensional, interactive, stall prediction program is extended by improving its laminar separation bubble model. The program now accounts correctly for the effects of the bubble on airfoil performance characteristics when it forms at the mid-chord and on the leading edge. Furthermore, the model can now predict bubble bursting on very sharp leading edges at high angles of attack. The details of the model are discussed in depth. Comparisons of the predicted stall and post-stall pressure distributions show excellent agreement with experimental measurements for several different airfoils at different Reynolds numbers.

  13. Analysis of Low-Speed Stall Aerodynamics of a Business Jets Wing Using STAR-CCM+

    Science.gov (United States)

    Bui, Trong

    2016-01-01

    Reynolds-Averaged Navier-Stokes (RANS) computational fluid dynamics (CFD) analysis was conducted: to study the low-speed stall aerodynamics of a GIII aircrafts swept wing modified with (1) a laminar-flow wing glove, or (2) a seamless flap. The stall aerodynamics of these two different wing configurations were analyzed and compared with the unmodified baseline wing for low-speed flight. The Star-CCM+ polyhedral unstructured CFD code was first validated for wing stall predictions using the wing-body geometry from the First AIAA CFD High-Lift Prediction Workshop.

  14. Stall inception and warning in a single-stage transonic axial compressor with axial skewed slot casing treatment

    International Nuclear Information System (INIS)

    Lim, Byeung Jun; Kwon, Se Jin; Park, Tae Choon

    2014-01-01

    Characteristic changes in the stall inception in a single-stage transonic axial compressor with an axial skewed slot casing treatment were investigated experimentally. A rotating stall occurred intermittently in a compressor with an axial skewed slot, whereas spike-type rotating stalls occurred in the case of smooth casing. The axial skewed slot suppressed stall cell growth and increased the operating range. A mild surge, the frequency of which is the Helmholtz frequency of the compressor system, occurred with the rotating stall. The irregularity in the pressure signals at the slot bottom increased decreasing flow rate. An autocorrelation-based stall warning method was applied to the measured pressure signals. Results estimate and warn against the stall margin in a compressor with an axial skewed slot.

  15. 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.

  16. 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…

  17. Replication Protein A (RPA) Phosphorylation Prevents RPA Association with Replication Centers

    OpenAIRE

    Vassin, Vitaly M.; Wold, Marc S.; Borowiec, James A.

    2004-01-01

    Mammalian replication protein A (RPA) undergoes DNA damage-dependent phosphorylation at numerous sites on the N terminus of the RPA2 subunit. To understand the functional significance of RPA phosphorylation, we expressed RPA2 variants in which the phosphorylation sites were converted to aspartate (RPA2D) or alanine (RPA2A). Although RPA2D was incorporated into RPA heterotrimers and supported simian virus 40 DNA replication in vitro, the RPA2D mutant was selectively unable to associate with re...

  18. Crinivirus replication and host interactions

    Directory of Open Access Journals (Sweden)

    Zsofia A Kiss

    2013-05-01

    Full Text Available Criniviruses comprise one of the genera within the family Closteroviridae. Members in this family are restricted to the phloem and rely on whitefly vectors of the genera Bemisia and/or Trialeurodes for plant-to-plant transmission. All criniviruses have bipartite, positive-sense ssRNA genomes, although there is an unconfirmed report of one having a tripartite genome. Lettuce infectious yellows virus (LIYV is the type species of the genus, the best studied so far of the criniviruses and the first for which a reverse genetics system was available. LIYV RNA 1 encodes for proteins predicted to be involved in replication, and alone is competent for replication in protoplasts. Replication results in accumulation of cytoplasmic vesiculated membranous structures which are characteristic of most studied members of the Closteroviridae. These membranous structures, often referred to as BYV-type vesicles, are likely sites of RNA replication. LIYV RNA 2 is replicated in trans when co-infecting cells with RNA 1, but is temporally delayed relative to RNA1. Efficient RNA 2 replication also is dependent on the RNA 1-encoded RNA binding protein, P34. No LIYV RNA 2-encoded proteins have been shown to affect RNA replication, but at least four, CP, CPm, Hsp70h, and p59 are virion structural components and CPm is a determinant of whitefly transmissibility. Roles of other LIYV RNA 2-encoded proteins are largely as yet unknown, but P26 is a non-virion protein that accumulates in cells as characteristic plasmalemma deposits which in plants are localized within phloem parenchyma and companion cells over plasmodesmata connections to sieve elements. The two remaining crinivirus-conserved RNA 2-encoded proteins are P5 and P9. P5 is 39 amino acid protein and is encoded at the 5’ end of RNA 2 as ORF1 and is part of the hallmark closterovirus gene array. The orthologous gene in BYV has been shown to play a role in cell-to-cell movement and indicated to be localized to the

  19. Modeling dynamic stall on wind turbine blades under rotationally augmented flow fields

    DEFF Research Database (Denmark)

    Guntur, Srinivas; Sørensen, Niels N.; Schreck, Scott

    2016-01-01

    a reduced order dynamic stall model that uses rotationally augmented steady-state polars obtained from steady Phase VI experimental sequences, instead of the traditional two-dimensional, non-rotating data. The aim of this work is twofold. First, the blade loads estimated by the DDES simulations are compared...... Experiment Phase VI experimental data, including constant as well as continuously pitching blade conditions during axial operation; (2) data from unsteady delayed detached eddy simulations (DDES) carried out using the Technical University of Denmark’s in-house flow solver Ellipsys3D; and (3) data from...... with those from the dynamic stall model. This allowed the differences between the stall phenomenon on the inboard parts of harmonically pitching blades on a rotating wind turbine and the classic dynamic stall representation in two-dimensional flow to be investigated. Results indicated a good qualitative...

  20. A theory of post-stall transients in axial compression systems. I - Development of equations

    Science.gov (United States)

    Moore, F. K.; Greitzer, E. M.

    1985-01-01

    An approximate theory is presented for post-stall transients in multistage axial compression systems. The theory leads to a set of three simultaneous nonlinear third-order partial differential equations for pressure rise, and average and disturbed values of flow coefficient, as functions of time and angle around the compressor. By a Galerkin procedure, angular dependence is averaged, and the equations become first order in time. These final equations are capable of describing the growth and possible decay of a rotating-stall cell during a compressor mass-flow transient. It is shown how rotating-stall-like and surgelike motions are coupled through these equations, and also how the instantaneous compressor pumping characteristic changes during the transient stall process.

  1. Computer modeling of the stalled flow of a rotating cylinder and the reverse magnus effect

    Science.gov (United States)

    Belotserkovskii, S. M.; Kotovskii, V. N.; Nisht, M. I.; Fedorov, R. M.

    1985-02-01

    Unsteady stalled flow around a rotating cylinder is investigated in a numerical experiment. Attention is mostly given to the reverse Magnus effect which was discovered in tube experiments at some critical rotational speed of the cylinder.

  2. Stalling HIV through social marketing: prospects in Pakistan.

    Science.gov (United States)

    Husain, Sara; Shaikh, Babar T

    2005-07-01

    Over the last two decades HIV/AIDS has evolved from a series of interesting case-reports to a growing epidemic that threatens the entire world. It is feared to cause devastation among large pockets of populations and may roll back more than thirty years of public health achievements. This killer disease has been more amenable to behavioral change than by provision of curative services and attempts are being made to educate the public about this threat. Various techniques of promotion have been tried through out the world including television dramas/soaps, mass media and school curricula. Social marketing is an evolving strategy used to influence human behavior and choices. By using the principles of marketing and promoting behavior as a product, social marketers attempt to understand the dynamics of human behaviour and devise messages and products to change, modify, accept or reject unsafe behaviors or practices. Thus, social marketers provide an effective force to combat the spread of HIV and may serve to be invaluable allies in health promotion efforts. In a complex and diversified cultural milieu of Pakistan, social marketing can have a significant impact on health determinants and the conditions that will facilitate the adoption of health-oriented behaviors and practices. This paper gives an account of the elements needed for the success of a health promotion strategy adopted in a developing country and makes a case for social marketing to be adopted as the lead strategy for stalling HIV/AIDS in Pakistan.

  3. Initial design of a stall-controlled wind turbine rotor

    Energy Technology Data Exchange (ETDEWEB)

    Nygaard, T.A. [Inst. for Energiteknikk, Kjeller (Norway)

    1997-08-01

    A model intended for initial design of stall-controlled wind turbine rotors is described. The user specifies relative radial position of an arbitrary number of airfoil sections, referring to a data file containing lift-and drag curves. The data file is on the same format as used in the commercial blade-element code BLADES-/2/, where lift- and drag coefficients are interpolated from tables as function of Reynolds number, relative thickness and angle of attack. The user can set constraints on a selection of the following: Maximum power; Maximum thrust in operation; Maximum root bending moment in operation; Extreme root bending moment, parked rotor; Tip speed; Upper and lower bounds on optimisation variables. The optimisation variables can be selected from: Blade radius; Rotational speed; Chord and twist at an arbitrary number of radial positions. The user can chose linear chord distribution and a hyperbola-like twist distribution to ensure smooth planform and twist, or cubic spline interpolation for one or both. The aerodynamic model is based on classical strip theory with Prandtl tip loss correction, supplemented by empirical data for high induction factors. (EG)

  4. Cow comfort in tie-stalls: increased depth of shavings or straw bedding increases lying time.

    Science.gov (United States)

    Tucker, C B; Weary, D M; von Keyserlingk, M A G; Beauchemin, K A

    2009-06-01

    Over half of US dairy operations use tie-stalls, but these farming systems have received relatively little research attention in terms of stall design and management. The current study tested the effects of the amount of 2 bedding materials, straw and shavings, on dairy cattle lying behavior. The effects of 4 levels of shavings, 3, 9, 15, and 24 kg/stall (experiment 1, n = 12), and high and low levels of straw in 2 separate experiments: 1, 3, 5, and 7 kg/stall (experiment 2, n = 12) and 0.5, 1, 2, and 3 kg/stall (experiment 3, n = 12) were assessed. Treatments were compared using a crossover design with lactating cows housed in tie-stalls fitted with mattresses. Treatments were applied for 1 wk. Total lying time, number of lying bouts, and the length of each lying bout was recorded with data loggers. In experiment 1, cows spent 3 min more lying down for each additional kilogram of shavings (11.0, 11.7, 11.6, and 12.1 +/- 0.24 h/d for 3, 9, 15, and 24 kg/stall shavings, respectively). In experiment 2, cows increased lying time by 12 min for every additional kilogram of straw (11.2, 12.0, 11.8, and 12.4 +/- 0.24 h/d for 1, 3, 5, and 7 kg/stall of straw, respectively). There were no differences in lying behavior among the lower levels of straw tested in experiment 3 (11.7 +/- 0.32 h/d). These results indicated that additional bedding above a scant amount improves cow comfort, as measured by lying time, likely because a well-bedded surface is more compressible.

  5. 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...

  6. Dynamic stall characterization using modal analysis of phase-averaged pressure distributions

    Science.gov (United States)

    Harms, Tanner; Nikoueeyan, Pourya; Naughton, Jonathan

    2017-11-01

    Dynamic stall characterization by means of surface pressure measurements can simplify the time and cost associated with experimental investigation of unsteady airfoil aerodynamics. A unique test capability has been developed at University of Wyoming over the past few years that allows for time and cost efficient measurement of dynamic stall. A variety of rotorcraft and wind turbine airfoils have been tested under a variety of pitch oscillation conditions resulting in a range of dynamic stall behavior. Formation, development and separation of different flow structures are responsible for the complex aerodynamic loading behavior experienced during dynamic stall. These structures have unique signatures on the pressure distribution over the airfoil. This work investigates the statistical behavior of phase-averaged pressure distribution for different types of dynamic stall by means of modal analysis. The use of different modes to identify specific flow structures is being investigated. The use of these modes for different types of dynamic stall can provide a new approach for understanding and categorizing these flows. This work uses airfoil data acquired under Army contract W911W60160C-0021, DOE Grant DE-SC0001261, and a gift from BP Alternative Energy North America, Inc.

  7. 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

  8. 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

  9. Replication protein A and γ-H2AX foci assembly is triggered by cellular response to DNA double-strand breaks

    International Nuclear Information System (INIS)

    Balajee, Adayabalam S.; Geard, Charles R.

    2004-01-01

    Human replication protein A (RPA p34), a crucial component of diverse DNA excision repair pathways, is implicated in DNA double-strand break (DSB) repair. To evaluate its role in DSB repair, the intranuclear dynamics of RPA was investigated after DNA damage and replication blockage in human cells. Using two different agents [ionizing radiation (IR) and hydroxyurea (HU)] to generate DSBs, we found that RPA relocated into distinct nuclear foci and colocalized with a well-known DSB binding factor, γ-H2AX, at the sites of DNA damage in a time-dependent manner. Colocalization of RPA and γ-H2AX foci peaked at 2 h after IR treatment and subsequently declined with increasing postrecovery times. The time course of RPA and γ-H2AX foci association correlated well with the DSB repair activity detected by a neutral comet assay. A phosphatidylinositol-3 (PI-3) kinase inhibitor, wortmannin, completely abolished both RPA and γ-H2AX foci formation triggered by IR. Additionally, radiosensitive ataxia telangiectasia (AT) cells harboring mutations in ATM gene product were found to be deficient in RPA and γ-H2AX colocalization after IR. Transfection of AT cells with ATM cDNA fully restored the association of RPA foci with γ-H2AX illustrating the requirement of ATM gene product for this process. The exact coincidence of RPA and γ-H2AX in response to HU specifically in S-phase cells supports their role in DNA replication checkpoint control. Depletion of RPA by small interfering RNA (SiRNA) substantially elevated the frequencies of IR-induced micronuclei (MN) and apoptosis in human cells suggestive of a role for RPA in DSB repair. We propose that RPA in association with γ-H2AX contributes to both DNA damage checkpoint control and repair in response to strand breaks and stalled replication forks in human cells

  10. Eukaryotic DNA Replication Fork.

    Science.gov (United States)

    Burgers, Peter M J; Kunkel, Thomas A

    2017-06-20

    This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

  11. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  12. 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 ...

  13. Mode of transgene expression after fusion to early or late viral genes of a conditionally replicating adenovirus via an optimized internal ribosome entry site in vitro and in vivo

    International Nuclear Information System (INIS)

    Rivera, Angel A.; Wang Minghui; Suzuki, Kaori; Uil, Taco G.; Krasnykh, Victor; Curiel, David T.; Nettelbeck, Dirk M.

    2004-01-01

    The expression of therapeutic genes by oncolytic viruses is a promising strategy to improve viral oncolysis, to augment gene transfer compared with a nonreplicating adenoviral vector, or to combine virotherapy and gene therapy. Both the mode of transgene expression and the locale of transgene insertion into the virus genome critically determine the efficacy of this approach. We report here on the properties of oncolytic adenoviruses which contain the luciferase cDNA fused via an optimized internal ribosome entry site (IRES) to the immediate early adenoviral gene E1A (AdΔE1AIL), the early gene E2B (AdΔE2BIL), or the late fiber gene (AdΔfiberIL). These viruses showed distinct kinetics of transgene expression and luciferase activity. Early after infection, luciferase activities were lower for these viruses, especially for AdΔE2BIL, compared with nonreplicating AdTL, which contained the luciferase gene expressed from the strong CMV promoter. However, 6 days after infection, luciferase activities were approximately four (AdΔE1AIL) to six (AdΔfiberIL) orders of magnitude higher than for AdTL, reflecting virus replication and efficient transgene expression. Similar results were obtained in vivo after intratumoral injection of AdΔE2BIL, AdΔfiberIL, and AdTL. AdΔfiberIL and the parental virus, Ad5-Δ24, resulted in similar cytotoxicity, but AdΔE2BIL and AdΔE1AIL were slightly attenuated. Disruption of the expression of neighboring viral genes by insertion of the transgene was minimal for AdΔE2BIL and AdΔfiberIL, but substantial for AdΔE1AIL. Our observations suggest that insertion of IRES-transgene cassettes into viral transcription units is an attractive strategy for the development of armed oncolytic adenoviruses with defined kinetics and strength of transgene expression

  14. Mapping replication origins in yeast chromosomes.

    Science.gov (United States)

    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.

  15. Alleviation of spike stall in axial compressors utilizing grooved casing treatment

    Directory of Open Access Journals (Sweden)

    Reza Taghavi-Zenouz

    2015-06-01

    Full Text Available This article deals with application of grooved type casing treatment for suppression of spike stall in an isolated axial compressor rotor blade row. The continuous grooved casing treatment covering the whole compressor circumference is of 1.8 mm in depth and located between 90% and 108% chord of the blade tip as measured from leading edge. The method of investigation is based on time-accurate three-dimensional full annulus numerical simulations for cases with and without casing treatment. Discretization of the Navier–Stokes equations has been carried out based on an upwind second-order scheme and k-ω-SST (Shear Stress Transport turbulence modeling has been used for estimation of eddy viscosity. Time-dependent flow structure results for the smooth casing reveal that there are two criteria for spike stall inception known as leading edge spillage and trailing edge backflow, which occur at specific mass flow rates in near-stall conditions. In this case, two dominant stall cells of different sizes could be observed. The larger one is caused by the spike stall covering roughly two blade passages in the circumferential direction and about 25% span in the radial direction. Spike stall disturbances are accompanied by lower frequencies and higher amplitudes of the pressure signals. Casing treatment causes flow blockages to reduce due to alleviation of backflow regions, which in turn reduces the total pressure loss and increases the axial velocity in the blade tip gap region, as well as tip leakage flow fluctuation at higher frequencies and lower amplitudes. Eventually, it can be concluded that the casing treatment of the stepped tip gap type could increase the stall margin of the compressor. This fact is basically due to retarding the movement of the interface region between incoming and tip leakage flows towards the rotor leading edge plane and suppressing the reversed flow around the blade trailing edge.

  16. Shallow and deep dynamic stall for flapping low Reynolds number airfoils

    Energy Technology Data Exchange (ETDEWEB)

    Ol, Michael V. [Wright-Patterson AFB, Air Force Research Lab., Dayton, OH (United States); Bernal, Luis; Kang, Chang-Kwon; Shyy, Wei [University of Michigan, Department of Aerospace Engineering, Ann Arbor, MI (United States)

    2009-05-15

    We consider a combined experimental (based on flow visualization, direct force measurement and phase-averaged 2D particle image velocimetry in a water tunnel), computational (2D Reynolds-averaged Navier-Stokes) and theoretical (Theodorsen's formula) approach to study the fluid physics of rigid-airfoil pitch-plunge in nominally two-dimensional conditions. Shallow-stall (combined pitch-plunge) and deep-stall (pure-plunge) are compared at a reduced frequency commensurate with flapping-flight in cruise in nature. Objectives include assessment of how well attached-flow theory can predict lift coefficient even in the presence of significant separation, and how well 2D velocimetry and 2D computation can mutually validate one another. The shallow-stall case shows promising agreement between computation and experiment, while in the deep-stall case, the computation's prediction of flow separation lags that of the experiment, but eventually evinces qualitatively similar leading edge vortex size. Dye injection was found to give good qualitative match with particle image velocimetry in describing leading edge vortex formation and return to flow reattachment, and also gave evidence of strong spanwise growth of flow separation after leading-edge vortex formation. Reynolds number effects, in the range of 10,000-60,000, were found to influence the size of laminar separation in those phases of motion where instantaneous angle of attack was well below stall, but have limited effect on post-stall flowfield behavior. Discrepancy in lift coefficient time history between experiment, theory and computation was mutually comparable, with no clear failure of Theodorsen's formula. This is surprising and encouraging, especially for the deep-stall case, because the theory's assumptions are clearly violated, while its prediction of lift coefficient remains useful for capturing general trends. (orig.)

  17. Mutations in DONSON disrupt replication fork stability and cause microcephalic dwarfism.

    Science.gov (United States)

    Reynolds, John J; Bicknell, Louise S; Carroll, Paula; Higgs, Martin R; Shaheen, Ranad; Murray, Jennie E; Papadopoulos, Dimitrios K; Leitch, Andrea; Murina, Olga; Tarnauskaitė, Žygimantė; Wessel, Sarah R; Zlatanou, Anastasia; Vernet, Audrey; von Kriegsheim, Alex; Mottram, Rachel M A; Logan, Clare V; Bye, Hannah; Li, Yun; Brean, Alexander; Maddirevula, Sateesh; Challis, Rachel C; Skouloudaki, Kassiani; Almoisheer, Agaadir; Alsaif, Hessa S; Amar, Ariella; Prescott, Natalie J; Bober, Michael B; Duker, Angela; Faqeih, Eissa; Seidahmed, Mohammed Zain; Al Tala, Saeed; Alswaid, Abdulrahman; Ahmed, Saleem; Al-Aama, Jumana Yousuf; Altmüller, Janine; Al Balwi, Mohammed; Brady, Angela F; Chessa, Luciana; Cox, Helen; Fischetto, Rita; Heller, Raoul; Henderson, Bertram D; Hobson, Emma; Nürnberg, Peter; Percin, E Ferda; Peron, Angela; Spaccini, Luigina; Quigley, Alan J; Thakur, Seema; Wise, Carol A; Yoon, Grace; Alnemer, Maha; Tomancak, Pavel; Yigit, Gökhan; Taylor, A Malcolm R; Reijns, Martin A M; Simpson, Michael A; Cortez, David; Alkuraya, Fowzan S; Mathew, Christopher G; Jackson, Andrew P; Stewart, Grant S

    2017-04-01

    To ensure efficient genome duplication, cells have evolved numerous factors that promote unperturbed DNA replication and protect, repair and restart damaged forks. Here we identify downstream neighbor of SON (DONSON) as a novel fork protection factor and report biallelic DONSON mutations in 29 individuals with microcephalic dwarfism. We demonstrate that DONSON is a replisome component that stabilizes forks during genome replication. Loss of DONSON leads to severe replication-associated DNA damage arising from nucleolytic cleavage of stalled replication forks. Furthermore, ATM- and Rad3-related (ATR)-dependent signaling in response to replication stress is impaired in DONSON-deficient cells, resulting in decreased checkpoint activity and the potentiation of chromosomal instability. Hypomorphic mutations in DONSON substantially reduce DONSON protein levels and impair fork stability in cells from patients, consistent with defective DNA replication underlying the disease phenotype. In summary, we have identified mutations in DONSON as a common cause of microcephalic dwarfism and established DONSON as a critical replication fork protein required for mammalian DNA replication and genome stability.

  18. Transcription-replication conflicts at chromosomal fragile sites—consequences in M phase and beyond

    DEFF Research Database (Denmark)

    Østergaard, Vibe Hallundbæk; Lisby, Michael

    2017-01-01

    transcription and replication patterns. At the same time, these chromosomal fragile sites engage in aberrant DNA structures in mitosis. Here, we discuss the mechanistic details of transcription–replication conflicts including putative scenarios for R-loop-induced replication inhibition to understand how...... transcription–replication conflicts transition from S phase into various aberrant DNA structures in mitosis....

  19. An archival analysis of stall warning system effectiveness during airborne icing encounters

    Science.gov (United States)

    Maris, John Michael

    An archival study was conducted to determine the influence of stall warning system performance on aircrew decision-making outcomes during airborne icing encounters. A Conservative Icing Response Bias (CIRB) model was developed to explain the historical variability in aircrew performance in the face of airframe icing. The model combined Bayes' Theorem with Signal Detection Theory (SDT) concepts to yield testable predictions that were evaluated using a Binary Logistic Regression (BLR) multivariate technique applied to two archives: the NASA Aviation Safety Reporting System (ASRS) incident database, and the National Transportation Safety Board (NTSB) accident databases, both covering the period January 1, 1988 to October 2, 2015. The CIRB model predicted that aircrew would experience more incorrect response outcomes in the face of missed stall warnings than with stall warning False Alarms. These predicted outcomes were observed at high significance levels in the final sample of 132 NASA/NTSB cases. The CIRB model had high sensitivity and specificity, and explained 71.5% (Nagelkerke R2) of the variance of aircrew decision-making outcomes during the icing encounters. The reliability and validity metrics derived from this study suggest indicate that the findings are generalizable to the population of U.S. registered turbine-powered aircraft. These findings suggest that icing-related stall events could be reduced if the incidence of stall warning Misses could be minimized. Observed stall warning Misses stemmed from three principal causes: aerodynamic icing effects, which reduced the stall angle-of-attack (AoA) to below the stall warning calibration threshold; tail stalls, which are not monitored by contemporary protection systems; and icing-induced system issues (such as frozen pitot tubes), which compromised stall warning system effectiveness and airframe envelope protections. Each of these sources of missed stall warnings could be addressed by Aerodynamic Performance

  20. Effect of artificial UV irradiation on spore content of stall air and fattening pig breeding

    International Nuclear Information System (INIS)

    Kalich, J.; Blendl, H.M.

    1978-01-01

    The influence of a continuous UV irradiation (emitter NN 33/89 original Hanau) during the fattening periods primarily in the bactericide region of 253.7 nm of various intensities on the spore content of air, on the state of health and on the fattening breeding of pigs was tested in two fattening procedures. The high spore number per m 3 air of over 700 000 upon occupying the stall in the first fattening procedure was reduced by 90.5% to about 70 000 after 1 week of UV irradiation, and in the second procedure, from 111 500 to 16 000, i.e. a reduction of 85.5%. The spore content of the stall air then exhibited large deviations reducing and increasing. The same deviations were recorded for dust content. There was no absolute correlation between dust and spore content of the air until the 11th week after starting UV irradiation in either test. The spore content sank in the reference stalls also without UV irradiation, by 29.9% in the first fattening procedure 1 week after occupying the stall and even by 75% in the second procedure. The spore content of the air in the reference stalls also then exhibited deviations sinking and rising as in the test stalls with UV irradiation. Here too, there was no correlation between dust and spore content of the air. The spore content in the air was 2 to 7 times higher in the reference stalls than in the test stalls. One may conclude from the tests that the promoting irradiation strength is between 15 and 20 μW/cm 2 and that short-term stool production in danish stalling, 60 μW/cm 2 are not harmful. Air disinfection with UV irradiation, can only be part of the total hygiene measures taken in veterinary medicine and may only be considered as an important link in the chain of the health promoting and increased efficient hygiene measures in the intensification of aggriculturally useful animals. (orig./AJ) [de

  1. Revision 2 of the NPP Krsko Decommissioning Program Is Stalled

    International Nuclear Information System (INIS)

    Levanat, I.; Lokner, V.; Rapic, A.; Zeleznik, N.; Kralj, M.

    2012-01-01

    Revision 2 of the joint Slovenian-Croatian Program of NPP Krsko Decommissioning and SF andLILW Disposal was scheduled to be finished and formally approved by the end of 2009, in accordance with the bilateral Agreement on the NPP. Slightly behind the schedule, the Project team completed the entire document during spring of 2010, and in June 2010 drafted a proposal for a peer review of the Program by a dedicated IAEA expert mission. This procedure was agreed upon at the last session (May 2010) of the Intergovernmental Commission for implementation of the Agreement, when the Commission was acquainted with the five scenarios of the Revision 2 and with the estimates of their costs/financing. It was expected that the peer review would be performed soon, and that formal adoption of the Revision 2 would follow. Although in this process of approval some decisions remained to be made by the stakeholders, the Project team did select and recommend one scenario to be used for costing purposes, in order to ensure that most necessary corrections in Program financing would be timely adopted. However, the planned IAEA review was cancelled by the Advisory board, the body nominated by the Commission ''to supervise the activities and resolve the issues raised by the Project team''. By this cancellation, the process of Program revision was effectively stalled, because the Advisory board could not clearly define further course of action: differing views between the Slovenian and the Croatian part of the Advisory board appeared, in particular regarding the set of Program scenarios and regarding the appropriateness of the Revision 2 document for the IAEA review; nonetheless, the Advisory board sent to the Project team a compilation of requests to modify Revision 2 document. The Project team determined that some minor requests were easy to fulfill, but other modifications could only be carried out after changes in the boundary conditions (approved by the Commission), or changes in national

  2. Comparison of driven and simulated "free" stall flutter in a wind tunnel

    Science.gov (United States)

    Culler, Ethan; Farnsworth, John; Fagley, Casey; Seidel, Jurgen

    2016-11-01

    Stall flutter and dynamic stall have received a significant amount of attention over the years. To experimentally study this problem, the body undergoing stall flutter is typically driven at a characteristic, single frequency sinusoid with a prescribed pitching amplitude and mean angle of attack offset. This approach allows for testing with repeatable kinematics, however it effectively decouples the structural motion from the aerodynamic forcing. Recent results suggest that this driven approach could misrepresent the forcing observed in a "free" stall flutter scenario. Specifically, a dynamically pitched rigid NACA 0018 wing section was tested in the wind tunnel under two modes of operation: (1) Cyber-Physical where "free" stall flutter was physically simulated through a custom motor-control system modeling a torsional spring and (2) Direct Motor-Driven Dynamic Pitch at a single frequency sinusoid representative of the cyber-physical motion. The time-resolved pitch angle and moment were directly measured and compared for each case. It was found that small deviations in the pitch angle trajectory between these two operational cases generate significantly different aerodynamic pitching moments on the wing section, with the pitching moments nearly 180o out of phase in some cases. This work is supported by the Air Force Office of Scientific Research through the Flow Interactions and Control Program and by the National Defense Science and Engineering Graduate Fellowship Program.

  3. Development and application of a dynamic stall model for rotating wind turbine blades

    International Nuclear Information System (INIS)

    Xu, B F; Yuan, Y; Wang, T G

    2014-01-01

    In unsteady conditions of wind turbines, both the dynamic stall phenomenon and the three-dimensional (3D) rotational effect affect the rotor aerodynamics. The dynamic stall mechanism for rotating wind turbine blades is first investigated. Through the comparison of the aerodynamic data between the rotating blade and the two-dimensional (2D) airfoil, the normal force slope in the attached flow and the separation point expression in the separated flow are modified in the Beddoes-Leishman (B-L) dynamic stall model for rotating NREL wind turbine blades. The modified model is validated by the comparison between the calculation results and the experimental results of the lift and drag coefficients at different radial positions. Both the hysteresis loop shapes and the calculation values are closer to the experiment than the 2D dynamic stall model. The present dynamic stall model is then coupled to a free vortex wake model. The coupled model is used to calculate the unsteady blade aerodynamic loads and the low speed shaft torque of the NREL wind turbine in a yawed condition. The accuracy is greatly improved by the corrections presented in the paper

  4. A time-varying subjective quality model for mobile streaming videos with stalling events

    Science.gov (United States)

    Ghadiyaram, Deepti; Pan, Janice; Bovik, Alan C.

    2015-09-01

    Over-the-top mobile video streaming is invariably influenced by volatile network conditions which cause playback interruptions (stalling events), thereby impairing users' quality of experience (QoE). Developing models that can accurately predict users' QoE could enable the more efficient design of quality-control protocols for video streaming networks that reduce network operational costs while still delivering high-quality video content to the customers. Existing objective models that predict QoE are based on global video features, such as the number of stall events and their lengths, and are trained and validated on a small pool of ad hoc video datasets, most of which are not publicly available. The model we propose in this work goes beyond previous models as it also accounts for the fundamental effect that a viewer's recent level of satisfaction or dissatisfaction has on their overall viewing experience. In other words, the proposed model accounts for and adapts to the recency, or hysteresis effect caused by a stall event in addition to accounting for the lengths, frequency of occurrence, and the positions of stall events - factors that interact in a complex way to affect a user's QoE. On the recently introduced LIVE-Avvasi Mobile Video Database, which consists of 180 distorted videos of varied content that are afflicted solely with over 25 unique realistic stalling events, we trained and validated our model to accurately predict the QoE, attaining standout QoE prediction performance.

  5. An airloads theory for morphing airfoils in dynamic stall with experimental correlation

    Science.gov (United States)

    Ahaus, Loren A.

    Helicopter rotor blades frequently encounter dynamic stall during normal flight conditions, limiting the applicability of classical thin-airfoil theory at large angles of attack. Also, it is evident that because of the largely different conditions on the advancing and retreating sides of the rotor, future rotorcraft may incorporate dynamically morphing airfoils (trailing-edge aps, dynamic camber, dynamic droop, etc.). Reduced-order aerodynamic models are needed for preliminary design and ight simulation. A unified model for predicting the airloads on a morphing airfoil in dynamic stall is presented, consisting of three components. First, a linear airloads theory allows for arbitrary airfoil deformations consistent with a morphing airfoil. Second, to capture the effects of the wake, the airloads theory is coupled to an induced ow model. Third, the overshoot and time delay associated with dynamic stall are modeled by a second-order dynamic filter, along the lines of the ONERA dynamic stall model. This paper presents a unified airloads model that allows arbitrary airfoil morphing with dynamic stall. Correlations with experimental data validate the theory.

  6. An experimental description of the flow in a centrifugal compressor from alternate stall to surge

    Science.gov (United States)

    Moënne-Loccoz, V.; Trébinjac, I.; Benichou, E.; Goguey, S.; Paoletti, B.; Laucher, P.

    2017-08-01

    The present paper gives the experimental results obtained in a centrifugal compressor stage designed and built by SAFRAN Helicopter Engines. The compressor is composed of inlet guide vanes, a backswept splittered unshrouded impeller, a splittered vaned radial diffuser and axial outlet guide vanes. Previous numerical simulations revealed a particular S-shape pressure rise characteristic at partial rotation speed and predicted an alternate flow pattern in the vaned radial diffuser at low mass flow rate. This alternate flow pattern involves two adjacent vane passages. One passage exhibits very low momentum and a low pressure recovery, whereas the adjacent passage has very high momentum in the passage inlet and diffuses efficiently. Experimental measurements confirm the S-shape of the pressure rise characteristic even if the stability limit experimentally occurs at higher mass flow than numerically predicted. At low mass flow the alternate stall pattern is confirmed thanks to the data obtained by high-frequency pressure sensors. As the compressor is throttled the path to instability has been registered and a first scenario of the surge inception is given. The compressor first experiences a steady alternate stall in the diffuser. As the mass flow decreases, the alternate stall amplifies and triggers the mild surge in the vaned diffuser. An unsteady behavior results from the interaction of the alternate stall and the mild surge. Finally, when the pressure gradient becomes too strong, the alternate stall blows away and the compressor enters into deep surge.

  7. Stall Margin Improvement in a Centrifugal Compressor through Inducer Casing Treatment

    Directory of Open Access Journals (Sweden)

    V. V. N. K. Satish Koyyalamudi

    2016-01-01

    Full Text Available The increasing trend of high stage pressure ratio with increased aerodynamic loading has led to reduction in stable operating range of centrifugal compressors with stall and surge initiating at relatively higher mass flow rates. The casing treatment technique of stall control is found to be effective in axial compressors, but very limited research work is published on the application of this technique in centrifugal compressors. Present research was aimed to investigate the effect of casing treatment on the performance and stall margin of a high speed, 4 : 1 pressure ratio centrifugal compressor through numerical simulations using ANSYS CFX software. Three casing treatment configurations were developed and incorporated in the shroud over the inducer of the impeller. The predicted performance of baseline compressor (without casing treatment was in good agreement with published experimental data. The compressor with different inducer casing treatment geometries showed varying levels of stall margin improvement, up to a maximum of 18%. While the peak efficiency of the compressor with casing treatment dropped by 0.8%–1% compared to the baseline compressor, the choke mass flow rate was improved by 9.5%, thus enhancing the total stable operating range. The inlet configuration of the casing treatment was found to play an important role in stall margin improvement.

  8. Evolution of Replication Machines

    Science.gov (United States)

    Yao, Nina Y.; O'Donnell, Mike E.

    2016-01-01

    The machines that decode and regulate genetic information require the translation, transcription and replication pathways essential to all living cells. Thus, it might be expected that all cells share the same basic machinery for these pathways that were inherited from the primordial ancestor cell from which they evolved. A clear example of this is found in the translation machinery that converts RNA sequence to protein. The translation process requires numerous structural and catalytic RNAs and proteins, the central factors of which are homologous in all three domains of life, bacteria, archaea and eukarya. Likewise, the central actor in transcription, RNA polymerase, shows homology among the catalytic subunits in bacteria, archaea and eukarya. In contrast, while some “gears” of the genome replication machinery are homologous in all domains of life, most components of the replication machine appear to be unrelated between bacteria and those of archaea and eukarya. This review will compare and contrast the central proteins of the “replisome” machines that duplicate DNA in bacteria, archaea and eukarya, with an eye to understanding the issues surrounding the evolution of the DNA replication apparatus. PMID:27160337

  9. Replication studies in longevity

    DEFF Research Database (Denmark)

    Varcasia, O; Garasto, S; Rizza, T

    2001-01-01

    In Danes we replicated the 3'APOB-VNTR gene/longevity association study previously carried out in Italians, by which the Small alleles (less than 35 repeats) had been identified as frailty alleles for longevity. In Danes, neither genotype nor allele frequencies differed between centenarians and 20...

  10. ATR-Chk1-APC/C-dependent stabilization of Cdc7-ASK (Dbf4) kinase is required for DNA lesion bypass under replication stress

    DEFF Research Database (Denmark)

    Yamada, M.; Watanabe, K.; Mistrik, M.

    2013-01-01

    replication. Stalled DNA replication evoked stabilization of the Cdc7-ASK (Dbf4) complex in a manner dependent on ATR-Chk1-mediated checkpoint signaling and its interplay with the anaphase-promoting complex/cyclosomeCdh1 (APC/C) ubiquitin ligase. Mechanistically, Chk1 kinase inactivates APC/C through...... degradation of Cdh1 upon replication block, thereby stabilizing APC/C substrates, including Cdc7-ASK (Dbf4). Furthermore, motif C of ASK (Dbf4) interacts with the N-terminal region of RAD18 ubiquitin ligase, and this interaction is required for chromatin binding of RAD18. Impaired interaction of ASK (Dbf4...

  11. Simulating Dynamic Stall Effects for Vertical Axis Wind Turbines Applying a Double Multiple Streamtube Model

    Directory of Open Access Journals (Sweden)

    Eduard Dyachuk

    2015-02-01

    Full Text Available The complex unsteady aerodynamics of vertical axis wind turbines (VAWT poses significant challenges to the simulation tools. Dynamic stall is one of the phenomena associated with the unsteady conditions for VAWTs, and it is in the focus of the study. Two dynamic stall models are compared: the widely-used Gormont model and a Leishman–Beddoes-type model. The models are included in a double multiple streamtube model. The effects of flow curvature and flow expansion are also considered. The model results are assessed against the measured data on a Darrieus turbine with curved blades. To study the dynamic stall effects, the comparison of force coefficients between the simulations and experiments is done at low tip speed ratios. Simulations show that the Leishman–Beddoes model outperforms the Gormont model for all tested conditions.

  12. The computation of the post-stall behavior of a circulation controlled airfoil

    Science.gov (United States)

    Linton, Samuel W.

    1993-01-01

    The physics of the circulation controlled airfoil is complex and poorly understood, particularly with regards to jet stall, which is the eventual breakdown of lift augmentation by the jet at some sufficiently high blowing rate. The present paper describes the numerical simulation of stalled and unstalled flows over a two-dimensional circulation controlled airfoil using a fully implicit Navier-Stokes code, and the comparison with experimental results. Mach numbers of 0.3 and 0.5 and jet total to freestream pressure ratios of 1.4 and 1.8 are investigated. The Baldwin-Lomax and k-epsilon turbulence models are used, each modified to include the effect of strong streamline curvature. The numerical solutions of the post-stall circulation controlled airfoil show a highly regular unsteady periodic flowfield. This is the result of an alternation between adverse pressure gradient and shock induced separation of the boundary layer on the airfoil trailing edge.

  13. Effect of summer grazing on welfare of dairy cows reared in mountain tie-stall barns

    Directory of Open Access Journals (Sweden)

    Simonetta Dovier

    2010-09-01

    Full Text Available Traditional mountain farms have an important economic, social and environmental role. The Alps management system for dairy cows consists of animals kept indoors from autumn to spring, mostly in tie-stalls, and moved to mountain pasture in summer. The aim of our study was to assess the effect of mountain summer grazing on the welfare of dairy cows housed in tie-stall barns. Twenty-four farms were considered. In twelve of them, animals were reared in tie-stalls and moved to mountain pasture for three months in summer; they were visited three times: (i four weeks before grazing during the indoor period in the stall; (ii about three weeks after the start of grazing; and (iii in the stall, in autumn, at least three weeks after returning from grazing. The other twelve farms kept the animals in tie-stalls all year; they were visited once in autumn. Data were collected following a protocol that considers animal-based measures and structure information on the basis of Quality Welfare Consortium® indications. Data allowed the calculation of both the Animal Needs Index score (ANI 35L and an overall assessment of the cows’ welfare obtained from three general aspects: housing, animal’s physical condition, and animal’s behaviour. Summer grazing had a significant positive effect on injuries, lameness and animal’s rising duration but a negative effect on faeces consistency. Moreover, a reduction of tongue playing was observed. The ANI 35L and the overall assessment did not show significant differences linked to summer grazing, which tended to have a positive but temporary effect on animal behaviour.

  14. Dynamic Stall Vortex Formation of OA-209 Airfoil at Low Reynolds Number

    OpenAIRE

    Aung Myo Thu; Sang Eon Jeon; Yung Hwan Byun; Soo Hyung Park

    2014-01-01

    The unsteady flow field around oscillating OA-209 airfoil at a Reynolds number of 3.5×105 were investigated. Three different reduced frequencies were tested in order to see how it affects the hysteresis loop of an airfoil. At a reduced frequency of 0.05 the deep dynamic stall phenomenon was observed. Lift overshooting was observed as a result of dynamic stall vortex (DSV) shedding. Further investigation was carried out to find out the cause of DSV formation and shedding over airfoil. Particle...

  15. The influence of elevated feed stalls on feeding behaviour of lactating dairy cows

    Directory of Open Access Journals (Sweden)

    Barbara Benz

    2014-10-01

    Full Text Available The performance level of high yielding cows can only be guaranteed by high quality forage and high feed intake. An about 15–20 cm elevated and 160 cm long feed stall with rubber flooring doesn’t only offer undisturbed meals but also a yielding and dry standing surface. In a pilot stable with 130 dairy cows (German Simmental the feeding alley was subsequently equipped with elevated feed stalls. The results show that animals frequented the feeding barn less often while the duration of single meals prolonged. The specific behavioural changes differed depending on milk yield and number of lactation.

  16. Diagnosis of voltage collapse due to induction motor stalling using static analysis

    International Nuclear Information System (INIS)

    Karbalaei, F.; Kalantar, M.; Kazemi, A.

    2008-01-01

    Induction motor stalling is one of the important reasons for voltage collapse. This paper presents that, for induction motor stalling diagnosis, it is not necessary to use a third or first order dynamic model of induction motors. Instead, a method is presented based on algebraic calculations for which the steady state model of the induction motor considering different kinds of mechanical loads (constant and variable torque) is added to the power flow equations. Simulation results for a simple system confirm the correctness of the proposed method as compared to dynamic simulation results

  17. Power control of a wind farm with active stall wind turbines and AC grid connection

    DEFF Research Database (Denmark)

    Hansen, Anca Daniela; Sørensen, Poul; Iov, Florin

    both the control on wind turbine level as well as the central control on the wind farm level. The ability of active stall wind farms with AC grid connection to regulate the power production to the reference power ordered by the operators is assessed and discussed by means of simulations.......This paper describes the design of a centralised wind farm controller for a wind farm made-up exclusively of active stall wind turbines with AC grid connection. The overall aim of such controller is to enable the wind farms to provide the best grid support. The designed wind farm control involves...

  18. Analysis of compressible light dynamic stall flow at transitional Reynolds numbers

    DEFF Research Database (Denmark)

    Dyken, R.D. Van; Ekaterinaris, John A.; Chandrasekhara, M.S.

    1996-01-01

    Numerical and experimental results of steady and light dynamic stall flow over an oscillating NACA 0012 airfoil at a freestream Mach number of 0.3 and Reynolds number of 0.54 x 10(6) are compared, The experimental observation that dynamic stall is induced from the bursting of a laminar separation...... point is specified suitably and a simple transition length model is incorporated to determine the extent of the laminar separation bubble. The thin-layer approximations of compressible, Reynolds-averaged, Navier-Stokes equations are used for the numerical solution, with an implicit, upwind-biased, third...

  19. Checkpoint-dependent RNR induction promotes fork restart after replicative stress.

    Science.gov (United States)

    Morafraile, Esther C; Diffley, John F X; Tercero, José Antonio; Segurado, Mónica

    2015-01-20

    The checkpoint kinase Rad53 is crucial to regulate DNA replication in the presence of replicative stress. Under conditions that interfere with the progression of replication forks, Rad53 prevents Exo1-dependent fork degradation. However, although EXO1 deletion avoids fork degradation in rad53 mutants, it does not suppress their sensitivity to the ribonucleotide reductase (RNR) inhibitor hydroxyurea (HU). In this case, the inability to restart stalled forks is likely to account for the lethality of rad53 mutant cells after replication blocks. Here we show that Rad53 regulates replication restart through the checkpoint-dependent transcriptional response, and more specifically, through RNR induction. Thus, in addition to preventing fork degradation, Rad53 prevents cell death in the presence of HU by regulating RNR-expression and localization. When RNR is induced in the absence of Exo1 and RNR negative regulators, cell viability of rad53 mutants treated with HU is increased and the ability of replication forks to restart after replicative stress is restored.

  20. Effects of alley and stall surfaces on indices of claw and leg health in dairy cattle housed in a free-stall barn.

    Science.gov (United States)

    Vokey, F J; Guard, C L; Erb, H N; Galton, D M

    2001-12-01

    A 15-wk 2 x 3 factorial trial in a university dairy herd compared the effects of two alley surfaces and three free-stall beds on indices of lameness. Alley surfaces were grooved concrete (Ct) or 1.9-cm-thick interlocking rubber mats (R). Stalls were deep sand (S), rubber mattresses (M), or concrete (C). Mattress and concrete stalls were bedded with sawdust. At wk 1 and 15, the hind claws and hocks of 120 primi- (n = 69) and multiparous (n = 51) cows were scored for lesions and three claw measurements (dorsal wall length, heel depth, and toe angle) were recorded. Rates of lateral and medial claw growth and wear were calculated by measuring the migration of a reference mark away from the coronet. Digital photographs of claw surfaces were used to rescore claw lesions. Clinical lameness was evaluated by assigning a locomotion score from 1 to 4 to each cow during wk 1, 5, 10, and 14. Digital dermatitis (present/not present) and interdigital dermatitis (mild, moderate, or severe) were recorded at wk 15. The number of days that cows spent in a hospital barn was recorded. Before assignment, cows were professionally foot trimmed, sorted by initial claw lesion score, and then randomized in consecutive blocks of three to stall treatments. Photograph scores were highly repeatable. Nonparametric statistical techniques were used for analyses of rank data. Claw lesion score increased significantly for all treatment groups except RC and RS; however, when early lactation cows were excluded, no differences were found between treatment groups. Hock scores increased significantly more for cows in CtC than in CtS or RS. Significantly more animals from RC spent more than 10 d in the hospital pen compared with RM and RS. Groups did not significantly differ for clinical lameness. Cows in RS and RC had significantly lower rates for lateral claw net growth than those in CtM. Having moderate or severe interdigital dermatitis at wk 15 was associated with greater increases in claw lesion score

  1. Questionnaire-based study to assess the association between management practices and mastitis within tie-stall and free-stall dairy housing systems in Switzerland

    Science.gov (United States)

    2013-01-01

    Background Prophylactic measures are key components of dairy herd mastitis control programs, but some are only relevant in specific housing systems. To assess the association between management practices and mastitis incidence, data collected in 2011 by a survey among 979 randomly selected Swiss dairy farms, and information from the regular test day recordings from 680 of these farms was analyzed. Results The median incidence of farmer-reported clinical mastitis (ICM) was 11.6 (mean 14.7) cases per 100 cows per year. The median annual proportion of milk samples with a composite somatic cell count (PSCC) above 200,000 cells/ml was 16.1 (mean 17.3) %. A multivariable negative binomial regression model was fitted for each of the mastitis indicators for farms with tie-stall and free-stall housing systems separately to study the effect of other (than housing system) management practices on the ICM and PSCC events (above 200,000 cells/ml). The results differed substantially by housing system and outcome. In tie-stall systems, clinical mastitis incidence was mainly affected by region (mountainous production zone; incidence rate ratio (IRR) = 0.73), the dairy herd replacement system (1.27) and farmers age (0.81). The proportion of high SCC was mainly associated with dry cow udder controls (IRR = 0.67), clean bedding material at calving (IRR = 1.72), using total merit values to select bulls (IRR = 1.57) and body condition scoring (IRR = 0.74). In free-stall systems, the IRR for clinical mastitis was mainly associated with stall climate/temperature (IRR = 1.65), comfort mats as resting surface (IRR = 0.75) and when no feed analysis was carried out (IRR = 1.18). The proportion of high SSC was only associated with hand and arm cleaning after calving (IRR = 0.81) and beef producing value to select bulls (IRR = 0.66). Conclusions There were substantial differences in identified risk factors in the four models. Some of the factors were in agreement with the reported literature

  2. RAD52 Facilitates Mitotic DNA Synthesis Following Replication Stress

    DEFF Research Database (Denmark)

    Bhowmick, Rahul; Minocherhomji, Sheroy; Hickson, Ian D

    2016-01-01

    Homologous recombination (HR) is necessary to counteract DNA replication stress. Common fragile site (CFS) loci are particularly sensitive to replication stress and undergo pathological rearrangements in tumors. At these loci, replication stress frequently activates DNA repair synthesis in mitosis...... replication stress at CFS loci during S-phase. In contrast, MiDAS is RAD52 dependent, and RAD52 is required for the timely recruitment of MUS81 and POLD3 to CFSs in early mitosis. Our results provide further mechanistic insight into MiDAS and define a specific function for human RAD52. Furthermore, selective...

  3. High-resolution LES of the rotating stall in a reduced scale model pump-turbine

    International Nuclear Information System (INIS)

    Pacot, Olivier; Avellan, François; Kato, Chisachi

    2014-01-01

    Extending the operating range of modern pump-turbines becomes increasingly important in the course of the integration of renewable energy sources in the existing power grid. However, at partial load condition in pumping mode, the occurrence of rotating stall is critical to the operational safety of the machine and on the grid stability. The understanding of the mechanisms behind this flow phenomenon yet remains vague and incomplete. Past numerical simulations using a RANS approach often led to inconclusive results concerning the physical background. For the first time, the rotating stall is investigated by performing a large scale LES calculation on the HYDRODYNA pump-turbine scale model featuring approximately 100 million elements. The computations were performed on the PRIMEHPC FX10 of the University of Tokyo using the overset Finite Element open source code FrontFlow/blue with the dynamic Smagorinsky turbulence model and the no-slip wall condition. The internal flow computed is the one when operating the pump-turbine at 76% of the best efficiency point in pumping mode, as previous experimental research showed the presence of four rotating cells. The rotating stall phenomenon is accurately reproduced for a reduced Reynolds number using the LES approach with acceptable computing resources. The results show an excellent agreement with available experimental data from the reduced scale model testing at the EPFL Laboratory for Hydraulic Machines. The number of stall cells as well as the propagation speed corroborates the experiment

  4. Visualization by PIV of dynamic stall on a vertical axis wind turbine

    NARCIS (Netherlands)

    Ferreira, C.J.S.; Kuik, van G.A.M.; Bussel, van G.J.W.; Scarano, F.

    2009-01-01

    The aerodynamic behavior of a vertical axis wind turbine (VAWT) is analyzed by means of 2D particle image velocimetry (PIV), focusing on the development of dynamic stall at different tip speed ratios. The VAWT has an unsteady aerodynamic behavior due to the variation with the azimuth angle ¿ of the

  5. Stall Recovery in a Centrifuge-Based Flight Simulator With an Extended Aerodynamic Model

    NARCIS (Netherlands)

    Ledegang, W.D.; Groen, E.L.

    2015-01-01

    We investigated the performance of 12 airline pilots in recovering from an asymmetrical stall in a flight simulator featuring an extended aerodynamic model of a transport-category aircraft, and a centrifuge-based motion platform capable of generating enhanced buffet motion and g-cueing. All pilots

  6. Identification of phlebovirus and arenavirus RNA sequences that stall and repress the exoribonuclease XRN1.

    Science.gov (United States)

    Charley, Phillida A; Wilusz, Carol J; Wilusz, Jeffrey

    2018-01-05

    Regulated mRNA decay plays a vital role in determining both the level and quality of cellular gene expression. Viral RNAs must successfully evade this host RNA decay machinery to establish a productive infection. One way for RNA viruses to accomplish this is to target the cellular exoribonuclease XRN1, because this enzyme is accessible in the cytoplasm and plays a major role in mRNA decay. Members of the Flaviviridae use RNA structures in their 5'- or 3'-untranslated regions to stall and repress XRN1, effectively stabilizing viral RNAs while also causing significant dysregulation of host cell mRNA stability. Here, we use a series of biochemical assays to demonstrate that the 3'-terminal portion of the nucleocapsid (N) mRNA of Rift Valley fever virus, a phlebovirus of the Bunyaviridae family, also can effectively stall and repress XRN1. The region responsible for impeding XRN1 includes a G-rich portion that likely forms a G-quadruplex structure. The 3'-terminal portions of ambisense-derived transcripts of multiple arenaviruses also stalled XRN1. Therefore, we conclude that RNAs from two additional families of mammalian RNA viruses stall and repress XRN1. This observation. emphasizes the importance and commonality of this viral strategy to interfere with the 5'-to-3'-exoribonuclease component of the cytoplasmic RNA decay machinery. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Power reduction and the radial limit of stall delay in revolving wings of different aspect ratio

    NARCIS (Netherlands)

    Kruyt, J.W.; Heijst, Van G.F.; Altshuler, D.L.; Lentink, David

    2015-01-01

    Airplanes and helicopters use high aspect ratio wings to reduce the power required to fly, but must operate at low angle of attack to prevent flow separation and stall. Animals capable of slow sustained flight, such as hummingbirds, have low aspect ratio wings and flap their wings at high angle

  8. Physics of Prestall Propagating Disturbances in Axial Compressors and Their Potential as a Stall Warning Indicator

    Directory of Open Access Journals (Sweden)

    Mario Eck

    2017-03-01

    Full Text Available Axial compressors in aero engines are prone to suffering a breakdown of orderly flow when operating at the peak of the pressure rise characteristic. The damaging potential of separated flows is why a safe distance has to be left between every possible operating point and an operating point at which stall occurs. During earlier investigations of stall inception mechanisms, a new type of prestall instability has been found. In this study, it could be demonstrated that the prestall instability characterised by discrete flow disturbances can be clearly assigned to the subject of “Rotating Instabilities”. Propagating disturbances are responsible for the rise in blade passing irregularity. If the mass flow is reduced successively, the level of irregularity increases until the prestall condition devolves into rotating stall. The primary objective of the current work is to highlight the basic physics behind these prestall disturbances by complementary experimental and numerical investigations. Before reaching the peak of the pressure rise characteristic flow, disturbances appear as small vortex tubes with one end attached to the casing and the other attached to the suction surface of the rotor blade. These vortex structures arise when the entire tip region is affected by blockage and at the same time the critical rotor incidence is not exceeded in this flow regime. Furthermore, a new stall indicator was developed by applying statistical methods to the unsteady pressure signal measured over the rotor blade tips, thus granting a better control of the safety margin.

  9. Combustion-Powered Actuation for Dynamic Stall Suppression - Simulations and Low-Mach Experiments

    Science.gov (United States)

    Matalanis, Claude G.; Min, Byung-Young; Bowles, Patrick O.; Jee, Solkeun; Wake, Brian E.; Crittenden, Tom; Woo, George; Glezer, Ari

    2014-01-01

    An investigation on dynamic-stall suppression capabilities of combustion-powered actuation (COMPACT) applied to a tabbed VR-12 airfoil is presented. In the first section, results from computational fluid dynamics (CFD) simulations carried out at Mach numbers from 0.3 to 0.5 are presented. Several geometric parameters are varied including the slot chordwise location and angle. Actuation pulse amplitude, frequency, and timing are also varied. The simulations suggest that cycle-averaged lift increases of approximately 4% and 8% with respect to the baseline airfoil are possible at Mach numbers of 0.4 and 0.3 for deep and near-deep dynamic-stall conditions. In the second section, static-stall results from low-speed wind-tunnel experiments are presented. Low-speed experiments and high-speed CFD suggest that slots oriented tangential to the airfoil surface produce stronger benefits than slots oriented normal to the chordline. Low-speed experiments confirm that chordwise slot locations suitable for Mach 0.3-0.4 stall suppression (based on CFD) will also be effective at lower Mach numbers.

  10. Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation.

    Science.gov (United States)

    Artieri, Carlo G; Fraser, Hunter B

    2014-12-01

    The recent advent of ribosome profiling-sequencing of short ribosome-bound fragments of mRNA-has offered an unprecedented opportunity to interrogate the sequence features responsible for modulating translational rates. Nevertheless, numerous analyses of the first riboprofiling data set have produced equivocal and often incompatible results. Here we analyze three independent yeast riboprofiling data sets, including two with much higher coverage than previously available, and find that all three show substantial technical sequence biases that confound interpretations of ribosomal occupancy. After accounting for these biases, we find no effect of previously implicated factors on ribosomal pausing. Rather, we find that incorporation of proline, whose unique side-chain stalls peptide synthesis in vitro, also slows the ribosome in vivo. We also reanalyze a method that implicated positively charged amino acids as the major determinant of ribosomal stalling and demonstrate that it produces false signals of stalling in low-coverage data. Our results suggest that any analysis of riboprofiling data should account for sequencing biases and sparse coverage. To this end, we establish a robust methodology that enables analysis of ribosome profiling data without prior assumptions regarding which positions spanned by the ribosome cause stalling. © 2014 Artieri and Fraser; Published by Cold Spring Harbor Laboratory Press.

  11. Aerodynamic shape optimization for alleviating dynamic stall characteristics of helicopter rotor airfoil

    Directory of Open Access Journals (Sweden)

    Wang Qing

    2015-04-01

    Full Text Available In order to alleviate the dynamic stall effects in helicopter rotor, the sequential quadratic programming (SQP method is employed to optimize the characteristics of airfoil under dynamic stall conditions based on the SC1095 airfoil. The geometry of airfoil is parameterized by the class-shape-transformation (CST method, and the C-topology body-fitted mesh is then automatically generated around the airfoil by solving the Poisson equations. Based on the grid generation technology, the unsteady Reynolds-averaged Navier-Stokes (RANS equations are chosen as the governing equations for predicting airfoil flow field and the highly-efficient implicit scheme of lower–upper symmetric Gauss–Seidel (LU-SGS is adopted for temporal discretization. To capture the dynamic stall phenomenon of the rotor more accurately, the Spalart–Allmaras turbulence model is employed to close the RANS equations. The optimized airfoil with a larger leading edge radius and camber is obtained. The leading edge vortex and trailing edge separation of the optimized airfoil under unsteady conditions are obviously weakened, and the dynamic stall characteristics of optimized airfoil at different Mach numbers, reduced frequencies and angles of attack are also obviously improved compared with the baseline SC1095 airfoil. It is demonstrated that the optimized method is effective and the optimized airfoil is suitable as the helicopter rotor airfoil.

  12. High-resolution LES of the rotating stall in a reduced scale model pump-turbine

    Science.gov (United States)

    Pacot, Olivier; Kato, Chisachi; Avellan, François

    2014-03-01

    Extending the operating range of modern pump-turbines becomes increasingly important in the course of the integration of renewable energy sources in the existing power grid. However, at partial load condition in pumping mode, the occurrence of rotating stall is critical to the operational safety of the machine and on the grid stability. The understanding of the mechanisms behind this flow phenomenon yet remains vague and incomplete. Past numerical simulations using a RANS approach often led to inconclusive results concerning the physical background. For the first time, the rotating stall is investigated by performing a large scale LES calculation on the HYDRODYNA pump-turbine scale model featuring approximately 100 million elements. The computations were performed on the PRIMEHPC FX10 of the University of Tokyo using the overset Finite Element open source code FrontFlow/blue with the dynamic Smagorinsky turbulence model and the no-slip wall condition. The internal flow computed is the one when operating the pump-turbine at 76% of the best efficiency point in pumping mode, as previous experimental research showed the presence of four rotating cells. The rotating stall phenomenon is accurately reproduced for a reduced Reynolds number using the LES approach with acceptable computing resources. The results show an excellent agreement with available experimental data from the reduced scale model testing at the EPFL Laboratory for Hydraulic Machines. The number of stall cells as well as the propagation speed corroborates the experiment.

  13. Nonlinear Aeroelastic Study of Stall Induced Oscillation in a Symmetric Airfoil

    NARCIS (Netherlands)

    Sarkar, S.; Bijl, H.

    2006-01-01

    In this paper the aeroelastic stability of a wind turbine rotor in the dynamic stall regime is investigated. Increased flexibility of modern turbine blades makes them more susceptible to aeroelastic instabilities. Complex oscillation modes like flap/lead-lag are of particular concern, which give way

  14. 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.

  15. Modeling dynamic stall on wind turbine blades under rotationally augmented flow fields

    Energy Technology Data Exchange (ETDEWEB)

    Guntur, S. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Schreck, S. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Sorensen, N. N. [Technical Univ. of Denmark, Lyngby (Denmark); Bergami, L. [Technical Univ. of Denmark, Lyngby (Denmark)

    2015-04-22

    It is well known that airfoils under unsteady flow conditions with a periodically varying angle of attack exhibit aerodynamic characteristics different from those under steady flow conditions, a phenomenon commonly known as dynamic stall. It is also well known that the steady aerodynamic characteristics of airfoils in the inboard region of a rotating blade differ from those under steady two-dimensional (2D) flow conditions, a phenomenon commonly known as rotational augmentation. This paper presents an investigation of these two phenomena together in the inboard parts of wind turbine blades. This analysis is carried out using data from three sources: (1) the National Renewable Energy Laboratory’s Unsteady Aerodynamics Experiment Phase VI experimental data, including constant as well as continuously pitching blade conditions during axial operation, (2) data from unsteady Delayed Detached Eddy Simulations (DDES) carried out using the Technical University of Denmark’s in-house flow solver Ellipsys3D, and (3) data from a simplified model based on the blade element momentum method with a dynamic stall subroutine that uses rotationally augmented steady-state polars obtained from steady Phase VI experimental sequences, instead of the traditional 2D nonrotating data. The aim of this work is twofold. First, the blade loads estimated by the DDES simulations are compared to three select cases of the N sequence experimental data, which serves as a validation of the DDES method. Results show reasonable agreement between the two data in two out of three cases studied. Second, the dynamic time series of the lift and the moment polars obtained from the experiments are compared to those from the dynamic stall subroutine that uses the rotationally augmented steady polars. This allowed the differences between the stall phenomenon on the inboard parts of harmonically pitching blades on a rotating wind turbine and the classic dynamic stall representation in 2D flow to be

  16. Conical Magnetic Bearings Developed for Active Stall Control in Gas Turbine Engines

    Science.gov (United States)

    Trudell, Jeffrey J.; Kascak, Albert F.; Provenza, Andrew J.; Buccieri, Carl J.

    2004-01-01

    Active stall control is a current research area at the NASA Glenn Research Center that offers a great benefit in specific fuel consumption by allowing the gas turbine to operate beyond the onset of stall. Magnetic bearings are being investigated as a new method to perform active stall control. This enabling global aviation safety technology would result in improved fuel efficiency and decreased carbon dioxide emissions, as well as improve safety and reliability by eliminating oil-related delays and failures of engine components, which account for 40 percent of the commercial aircraft departure delays. Active stall control works by perturbing the flow in front of the compressor stage such that it cancels the pressure wave, which causes the compressor to go into stall. Radial magnetic bearings are able to whirl the shaft so that variations in blade tip leakage would flow upstream causing a perturbation wave that could cancel the rotating stall cell. Axial or thrust magnetic bearings cannot be used to cancel the surge mode in the compressor because they have a very low bandwidth and thus cannot modulate at a high enough frequency. Frequency response is limited because the thrust runner cannot be laminated. To improve the bandwidth of magnetic thrust bearings, researchers must use laminations to suppress the eddy currents. A conical magnetic bearing can be laminated, resulting in increased bandwidth in the axial direction. In addition, this design can produce both radial and thrust force in a single bearing, simplifying the installation. The proposed solution combines the radial and thrust bearing into one design that can be laminated--a conical magnetic bearing. The new conical magnetic bearing test rig, funded by a Glenn fiscal year 2002 Director's Discretionary Fund, was needed because none of the existing rigs has an axial degree of freedom. The rotor bearing configuration will simulate that of the main shaft on a gas turbine engine. One conical magnetic bearing

  17. 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.

  18. Development of High Speed Imaging and Analysis Techniques Compressible Dynamics Stall

    Science.gov (United States)

    Chandrasekhara, M. S.; Carr, L. W.; Wilder, M. C.; Davis, Sanford S. (Technical Monitor)

    1996-01-01

    Dynamic stall has limited the flight envelope of helicopters for many years. The problem has been studied in the laboratory as well as in flight, but most research, even in the laboratory, has been restricted to surface measurement techniques such as pressure transducers or skin friction gauges, except at low speed. From this research, it became apparent that flow visualization tests performed at Mach numbers representing actual flight conditions were needed if the complex physics associated with dynamic stall was to be properly understood. However, visualization of the flow field during compressible conditions required carefully aligned and meticulously reconstructed holographic interferometry. As part of a long-range effort focused on exposing of the physics of compressible dynamic stall, a research wind tunnel was developed at NASA Ames Research Center which permits visual access to the full flow field surrounding an oscillating airfoil during compressible dynamic stall. Initially, a stroboscopic schlieren technique was used for visualization of the stall process, but the primary research tool has been point diffraction interferometry(PDI), a technique carefully optimized for use in th is project. A review of the process of development of PDI will be presented in the full paper. One of the most valuable aspects of PDI is the fact that interferograms are produced in real time on a continuous basis. The use of a rapidly-pulsed laser makes this practical; a discussion of this approach will be presented in the full paper. This rapid pulsing(up to 40,000 pulses/sec) produces interferograms of the rapidly developing dynamic stall field in sufficient resolution(both in space and time) that the fluid physics of the compressible dynamic stall flowfield can be quantitatively determined, including the gradients of pressure in space and time. This permits analysis of the influence of the effect of pitch rate, Mach number, Reynolds number, amplitude of oscillation, and other

  19. DNA Replication Dynamics of the GGGGCC Repeat of the C9orf72 Gene.

    Science.gov (United States)

    Thys, Ryan Griffin; Wang, Yuh-Hwa

    2015-11-27

    DNA has the ability to form a variety of secondary structures in addition to the normal B-form DNA, including hairpins and quadruplexes. These structures are implicated in a number of neurological diseases and cancer. Expansion of a GGGGCC repeat located at C9orf72 is associated with familial amyotrophic lateral sclerosis and frontotemporal dementia. This repeat expands from two to 24 copies in normal individuals to several hundreds or thousands of repeats in individuals with the disease. Biochemical studies have demonstrated that as little as four repeats have the ability to form a stable DNA secondary structure known as a G-quadruplex. Quadruplex structures have the ability to disrupt normal DNA processes such as DNA replication and transcription. Here we examine the role of GGGGCC repeat length and orientation on DNA replication using an SV40 replication system in human cells. Replication through GGGGCC repeats leads to a decrease in overall replication efficiency and an increase in instability in a length-dependent manner. Both repeat expansions and contractions are observed, and replication orientation is found to influence the propensity for expansions or contractions. The presence of replication stress, such as low-dose aphidicolin, diminishes replication efficiency but has no effect on instability. Two-dimensional gel electrophoresis analysis demonstrates a replication stall with as few as 20 GGGGCC repeats. These results suggest that replication of the GGGGCC repeat at C9orf72 is perturbed by the presence of expanded repeats, which has the potential to result in further expansion, leading to disease. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication...... initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

  1. Nonlinear control of rotating stall and surge with axisymmetric bleed and air injection on axial flow compressors

    Science.gov (United States)

    Yeung, Chung-Hei (Simon)

    The study of compressor instabilities in gas turbine engines has received much attention in recent years. In particular, rotating stall and surge are major causes of problems ranging from component stress and lifespan reduction to engine explosion. In this thesis, modeling and control of rotating stall and surge using bleed valve and air injection is studied and validated on a low speed, single stage, axial compressor at Caltech. Bleed valve control of stall is achieved only when the compressor characteristic is actuated, due to the fast growth rate of the stall cell compared to the rate limit of the valve. Furthermore, experimental results show that the actuator rate requirement for stall control is reduced by a factor of fourteen via compressor characteristic actuation. Analytical expressions based on low order models (2--3 states) and a high fidelity simulation (37 states) tool are developed to estimate the minimum rate requirement of a bleed valve for control of stall. A comparison of the tools to experiments show a good qualitative agreement, with increasing quantitative accuracy as the complexity of the underlying model increases. Air injection control of stall and surge is also investigated. Simultaneous control of stall and surge is achieved using axisymmetric air injection. Three cases with different injector back pressure are studied. Surge control via binary air injection is achieved in all three cases. Simultaneous stall and surge control is achieved for two of the cases, but is not achieved for the lowest authority case. This is consistent with previous results for control of stall with axisymmetric air injection without a plenum attached. Non-axisymmetric air injection control of stall and surge is also studied. Three existing control algorithms found in literature are modeled and analyzed. A three-state model is obtained for each algorithm. For two cases, conditions for linear stability and bifurcation criticality on control of rotating stall are

  2. Power reduction and the radial limit of stall delay in revolving wings of different aspect ratio.

    Science.gov (United States)

    Kruyt, Jan W; van Heijst, GertJan F; Altshuler, Douglas L; Lentink, David

    2015-04-06

    Airplanes and helicopters use high aspect ratio wings to reduce the power required to fly, but must operate at low angle of attack to prevent flow separation and stall. Animals capable of slow sustained flight, such as hummingbirds, have low aspect ratio wings and flap their wings at high angle of attack without stalling. Instead, they generate an attached vortex along the leading edge of the wing that elevates lift. Previous studies have demonstrated that this vortex and high lift can be reproduced by revolving the animal wing at the same angle of attack. How do flapping and revolving animal wings delay stall and reduce power? It has been hypothesized that stall delay derives from having a short radial distance between the shoulder joint and wing tip, measured in chord lengths. This non-dimensional measure of wing length represents the relative magnitude of inertial forces versus rotational accelerations operating in the boundary layer of revolving and flapping wings. Here we show for a suite of aspect ratios, which represent both animal and aircraft wings, that the attachment of the leading edge vortex on a revolving wing is determined by wing aspect ratio, defined with respect to the centre of revolution. At high angle of attack, the vortex remains attached when the local radius is shorter than four chord lengths and separates outboard on higher aspect ratio wings. This radial stall limit explains why revolving high aspect ratio wings (of helicopters) require less power compared with low aspect ratio wings (of hummingbirds) at low angle of attack and vice versa at high angle of attack. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  3. Parametric analyses on dynamic stall control of rotor airfoil via synthetic jet

    Directory of Open Access Journals (Sweden)

    Qijun ZHAO

    2017-12-01

    Full Text Available The effects of synthetic jet control on unsteady dynamic stall over rotor airfoil are investigated numerically. A moving-embedded grid method and an Unsteady Reynolds Averaged Navier-Stokes (URANS solver coupled with k-ω Shear Stress Transport (SST turbulence model are established for predicting the complex flowfields of oscillatory airfoil under jet control. Additionally, a velocity boundary condition modeled by sinusoidal function has been developed to fulfill the perturbation effect of periodic jet. The validity of present CFD method is evaluated by comparisons of the calculated results of baseline dynamic stall case for rotor airfoil and jet control case for VR-7B airfoil with experimental data. Then, parametric analyses are conducted emphatically for an OA212 rotor airfoil to investigate the effects of jet control parameters (jet location, dimensionless frequency, momentum coefficient, jet angle, jet type and dual-jet on dynamic stall characteristics of rotor airfoil. It is demonstrated by the calculated results that efficiency of jet control could be improved with specific momentum coefficient and jet angle when the jet is located near separation point of rotor airfoil. Furthermore, the dual-jet could improve control efficiency more obviously on dynamic stall of rotor airfoil with respect to the unique jet, and the influence laws of dual-jet’s angles and momentum coefficients on control effects are similar to those of the unique jet. Finally, unsteady aerodynamic characteristics of rotor via synthetic jet which is located on the upper surface of rotor blade in forward flight are calculated, and as a result, the aerodynamic characteristics of rotor are improved compared with the baseline. The results indicate that synthetic jet has the capability in improving aerodynamic characteristics of rotor. Keywords: Airfoil, Dynamic stall characteristics, Flow control, Moving-embedded grid methodology, Navier-Stokes equations, Parametric

  4. Stalling autophagy: a new function for Listeria phospholipases

    Directory of Open Access Journals (Sweden)

    Ivan Tattoli

    2014-01-01

    Full Text Available Listeria monocytogenes is a Gram-positive bacterial pathogen that induces its own uptake in non-phagocytic cells. Following invasion, Listeria escapes from the entry vacuole through the secretion of a pore-forming toxin, listeriolysin O (LLO that acts to damage and disrupt the vacuole membrane. Listeria then replicates in the cytosol and is able to spread from cell-to-cell using actin-based motility. In addition to LLO, Listeria produces two phospholipase toxins, a phosphatidylinositol-specific phospholipase C (PI-PLC, encoded by plcB and a broad-range phospholipase C (PC-PLC, encoded by plcA, which contribute to bacterial virulence. It has long been recognized that secretion of PI- and PC-PLC enables the disruption of the double membrane vacuole during cell-to-cell spread, and those phospholipases have also been shown to augment LLO-dependent escape from the entry endosome. However, a specific role for Listeria phospholipases during the cytosolic stage of infection has not been previously reported. In a recent study, we demonstrated that Listeria PI-PLC and PC-PLC contribute to the bacterial escape from autophagy through a mechanism that involves direct inhibition of the autophagic flux in the infected cells [Tattoli et al. EMBO J (2013, 32, 3066-3078].

  5. Replication Research and Special Education

    Science.gov (United States)

    Travers, Jason C.; Cook, Bryan G.; Therrien, William J.; Coyne, Michael D.

    2016-01-01

    Replicating previously reported empirical research is a necessary aspect of an evidence-based field of special education, but little formal investigation into the prevalence of replication research in the special education research literature has been conducted. Various factors may explain the lack of attention to replication of special education…

  6. Flooding of S. Dakota mine stalls plans for laboratory

    CERN Multimedia

    Chang, K

    2003-01-01

    The owner of a former gold mine in South Dakota turned off the pumps allowing water to begin accumulating in the tunnels below ground. The site had previously been proposed as the location for a new underground particle physics and astronomy laboratory (1 page).

  7. Internal Flow of a High Specific-Speed Diagonal-Flow Fan (Rotor Outlet Flow Fields with Rotating Stall

    Directory of Open Access Journals (Sweden)

    Norimasa Shiomi

    2003-01-01

    Full Text Available We carried out investigations for the purpose of clarifying the rotor outlet flow fields with rotating stall cell in a diagonal-flow fan. The test fan was a high–specific-speed (ns=1620 type of diagonal-flow fan that had 6 rotor blades and 11 stator blades. It has been shown that the number of the stall cell is 1, and its propagating speed is approximately 80% of its rotor speed, although little has been known about the behavior of the stall cell because a flow field with a rotating stall cell is essentially unsteady. In order to capture the behavior of the stall cell at the rotor outlet flow fields, hot-wire surveys were performed using a single-slant hotwire probe. The data obtained by these surveys were processed by means of a double phase-locked averaging technique, which enabled us to capture the flow field with the rotating stall cell in the reference coordinate system fixed to the rotor. As a result, time-dependent ensemble averages of the three-dimensional velocity components at the rotor outlet flow fields were obtained. The behavior of the stall cell was shown for each velocity component, and the flow patterns on the meridional planes were illustrated.

  8. 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...

  9. 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.

  10. A flight investigation of the ultra-deep-stall descent and spin recovery characteristics of a 1/6 scale radiocontrolled model of the Piper PA38 Tomahawk

    Science.gov (United States)

    Blanchard, W. S., Jr.

    1981-01-01

    Ultradeep stall descent and spin recovery characteristics of a 1/6 scale radio controlled model of the Piper PA38 Tomahawk aircraft was investigated. It was shown that the full scale PA38 is a suitable aircraft for conducting ultradeep stall research. Spin recovery was accomplished satisfactorily by entry to the ultradeep stall mode, followed by the exit from the ultradeep stall mode. It is concluded that since the PA38 has excellent spin recovery characteristics using normal recovery techniques (opposite rudder and forward control colum pressure), recovery using ultradeep stall would be beneficial only if the pilot suffered from disorientation.

  11. Hepatitis C Virus Replication Depends on Endosomal Cholesterol Homeostasis.

    Science.gov (United States)

    Stoeck, Ina Karen; Lee, Ji-Young; Tabata, Keisuke; Romero-Brey, Inés; Paul, David; Schult, Philipp; Lohmann, Volker; Kaderali, Lars; Bartenschlager, Ralf

    2018-01-01

    Similar to other positive-strand RNA viruses, hepatitis C virus (HCV) causes massive rearrangements of intracellular membranes, resulting in a membranous web (MW) composed of predominantly double-membrane vesicles (DMVs), the presumed sites of RNA replication. DMVs are enriched for cholesterol, but mechanistic details on the source and recruitment of cholesterol to the viral replication organelle are only partially known. Here we focused on selected lipid transfer proteins implicated in direct lipid transfer at various endoplasmic reticulum (ER)-membrane contact sites. RNA interference (RNAi)-mediated knockdown identified several hitherto unknown HCV dependency factors, such as steroidogenic acute regulatory protein-related lipid transfer domain protein 3 (STARD3), oxysterol-binding protein-related protein 1A and -B (OSBPL1A and -B), and Niemann-Pick-type C1 (NPC1), all residing at late endosome and lysosome membranes and required for efficient HCV RNA replication but not for replication of the closely related dengue virus. Focusing on NPC1, we found that knockdown or pharmacological inhibition caused cholesterol entrapment in lysosomal vesicles concomitant with decreased cholesterol abundance at sites containing the viral replicase factor NS5A. In untreated HCV-infected cells, unesterified cholesterol accumulated at the perinuclear region, partially colocalizing with NS5A at DMVs, arguing for NPC1-mediated endosomal cholesterol transport to the viral replication organelle. Consistent with cholesterol being an important structural component of DMVs, reducing NPC1-dependent endosomal cholesterol transport impaired MW integrity. This suggests that HCV usurps lipid transfer proteins, such as NPC1, at ER-late endosome/lysosome membrane contact sites to recruit cholesterol to the viral replication organelle, where it contributes to MW functionality. IMPORTANCE A key feature of the replication of positive-strand RNA viruses is the rearrangement of the host cell

  12. 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.

  13. SUMO and KSHV Replication

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Pei-Ching [Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan (China); Kung, Hsing-Jien, E-mail: hkung@nhri.org.tw [Institute for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan (China); Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 (United States); UC Davis Cancer Center, University of California, Davis, CA 95616 (United States); Division of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan (China)

    2014-09-29

    Small Ubiquitin-related MOdifier (SUMO) modification was initially identified as a reversible post-translational modification that affects the regulation of diverse cellular processes, including signal transduction, protein trafficking, chromosome segregation, and DNA repair. Increasing evidence suggests that the SUMO system also plays an important role in regulating chromatin organization and transcription. It is thus not surprising that double-stranded DNA viruses, such as Kaposi’s sarcoma-associated herpesvirus (KSHV), have exploited SUMO modification as a means of modulating viral chromatin remodeling during the latent-lytic switch. In addition, SUMO regulation allows the disassembly and assembly of promyelocytic leukemia protein-nuclear bodies (PML-NBs), an intrinsic antiviral host defense, during the viral replication cycle. Overcoming PML-NB-mediated cellular intrinsic immunity is essential to allow the initial transcription and replication of the herpesvirus genome after de novo infection. As a consequence, KSHV has evolved a way as to produce multiple SUMO regulatory viral proteins to modulate the cellular SUMO environment in a dynamic way during its life cycle. Remarkably, KSHV encodes one gene product (K-bZIP) with SUMO-ligase activities and one gene product (K-Rta) that exhibits SUMO-targeting ubiquitin ligase (STUbL) activity. In addition, at least two viral products are sumoylated that have functional importance. Furthermore, sumoylation can be modulated by other viral gene products, such as the viral protein kinase Orf36. Interference with the sumoylation of specific viral targets represents a potential therapeutic strategy when treating KSHV, as well as other oncogenic herpesviruses. Here, we summarize the different ways KSHV exploits and manipulates the cellular SUMO system and explore the multi-faceted functions of SUMO during KSHV’s life cycle and pathogenesis.

  14. 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.

  15. Histone Modification Associated with Initiation of DNA Replication | Center for Cancer Research

    Science.gov (United States)

    Before cells are able to divide, they must first duplicate their chromosomes accurately. DNA replication and packaging of DNA into chromosomes by histone proteins need to be coordinated by the cell to ensure proper transmission of genetic and epigenetic information to the next generation. Mammalian DNA replication begins at specific chromosomal sites, called replication

  16. 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.

  17. 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.

  18. A Beddoes-Leishman type dynamic stall model in state-space and indicial formulations

    DEFF Research Database (Denmark)

    Hansen, M.H.; Gaunaa, Mac; Aagaard Madsen, Helge

    2004-01-01

    This report contains a description of a Beddoes-Leishman type dynamic stall model in both a state-space and an indicial function formulation. The model predicts the unsteady aerodynamic forces and moment on an airfoil section undergoing arbitrary motionin heave, lead-lag, and pitch. The model...... features, such as overshoot of the lift, in the stall region. The linearized model is shown to give identicalresults to the full model for small amplitude oscillations. Furthermore, it is shown that the response of finite thichkness airfoils can be reproduced to a high accuracy by the use of specific...... is carried out by comparing the response of the model with inviscid solutions and observing the general behavior of the model using known airfoil data as input. Theproposed dynamic model gives results identical to inviscid solutions within the attached-flow region; and it exhibits the expected dynamic...

  19. Wave energy plants: Control strategies for avoiding the stalling behaviour in the Wells turbine

    Energy Technology Data Exchange (ETDEWEB)

    Amundarain, Modesto; Alberdi, Mikel; Garrido, Aitor J.; Garrido, Izaskun; Maseda, Javier [Dept. of Automatic Control and Systems Engineering, EUITI Bilbao, University of the Basque Country, Plaza de la Casilla 3, 48012 Bilbao (Spain)

    2010-12-15

    This study analyzes the problem of the stalling behaviour in Wells turbines, one of the most widely used turbines in wave energy plants. For this purpose two different control strategies are presented and compared. In the first one, a rotational speed control system is employed to appropriately adapt the speed of the double-fed induction generator coupling to the turbine, according to the pressure drop entry. In the second control strategy, an airflow control regulates the power generated by the turbine generator module by means of the modulation valve avoiding the stalling behaviour. It is demonstrated that the proposed rotational speed control design adequately matches the desired relationship between the slip of the double-fed induction generator and the pressure drop input, whilst the valve control using a traditional PID controller successfully governs the flow that modulates the pressure drop across the turbine. (author)

  20. Grid support of a wind farm with active stall wind turbines and AC grid connection

    DEFF Research Database (Denmark)

    Hansen, Anca Daniela; Sørensen, Poul Ejnar; Iov, F.

    2006-01-01

    grid connection. The designed control system has the task of enabling such a wind farm to provide the best grid support. It is based on two control levels: a supervisory control level, which controls the power production of the whole farm by sending out reference signals to each individual wind turbine......One of the main concerns in the grid integration of large wind farms is their ability to behave as active controllable components in the power system. This article presents the design of a new integrated power control system for a wind farm made up exclusively of active stall wind turbines with AC......, and a local control level, which ensures that the reference power signals at the wind turbine level are reached. The ability of active stall wind farms with AC grid connection to control the power production to the reference power ordered by the operators is assessed and discussed by means of simulations....

  1. Why Do Promising Therapies Stall in Development and How Can We Move Them Forward?

    Science.gov (United States)

    Wegner, Craig D; Goodwin, Andrew; Cook, Jon C; Allamneni, Krishna; Sohn, Jane; McVean, Maralee

    There are many reasons that molecules fail to progress to market and various principles of risk-benefit decisions that can help drive the molecule through development. This symposium included discussions on global strategies involved in pushing promising molecules to market, what to do when a molecule stalls in its progress to market, and options for rescuing the molecule and pushing it forward again. Innovative partnerships that bring stalled drugs back into clinical development were also addressed. A regulatory perspective on common reasons for a molecule to fail in its forward progress was presented. In addition, situations arise when a third-party advisory committee can provide input to help overcome issues identified by a regulatory agency. Using examples from the private and public domain, presentations centered on how to repurpose a molecule and when more science is needed.

  2. A Detailed Study of the Rotational Augmentation and Dynamic Stall Phenomena for Wind Turbines

    DEFF Research Database (Denmark)

    Guntur, Srinivas

    This thesis presents investigations into the aerodynamics of wind turbine rotors, with a focus on the in-board sections of the rotor. Two important aerodynamic phenomena that have challenged scientists over nearly the last half a century are the so-called rotational augmentation and dynamic stall....... This thesis presents an investigation into these two phenomena, using data from the MEXICO and the NREL UAE Phase VI experiments, as well as data obtained from full rotor CFD computations carried out using the in-house flow solver Ellipsys3D. The experimental data, CFD data and that from some of the existing...... on wind turbine blades using the N-sequence data of the NREL UAE Phase VI experiment. The experimental data is compared with the results from unsteady Delayed Detached Eddy Simulations (DDES). The same conditions are also modelled using a Beddoes-Leishman type dynamic stall model by Hansen et al. (2004...

  3. Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data

    DEFF Research Database (Denmark)

    Chen, Yun; Jørgensen, Mette; Kolde, Raivo

    2011-01-01

    of RNAPII stalling. CONCLUSIONS: In this study we introduce a general framework to accurately predict the level of RNAPII recruitment, elongation, stalling and mRNA expression from chromatin signals. The versatility of the method also makes it ideally suited to investigate other genomic data....... strategies are needed to progress from descriptive annotation of data to quantitative, predictive models. RESULTS: Here, we describe a computational framework which with high accuracy can predict the locations of core promoters, the amount of recruited RNAPII at the promoter, the amount of elongating RNAPII...... of these four marks are found to be necessary for recruitment of RNAPII but not sufficient for the elongation. We also show that the spatial distributions of histone marks are almost as predictive as the signal strength and that a set of histone marks immediately downstream of the TSS is highly predictive...

  4. DATABASE REPLICATION IN HETEROGENOUS PLATFORM

    OpenAIRE

    Hendro Nindito; Evaristus Didik Madyatmadja; Albert Verasius Dian Sano

    2014-01-01

    The application of diverse database technologies in enterprises today is increasingly a common practice. To provide high availability and survavibality of real-time information, a database replication technology that has capability to replicate databases under heterogenous platforms is required. The purpose of this research is to find the technology with such capability. In this research, the data source is stored in MSSQL database server running on Windows. The data will be replicated to MyS...

  5. Robust post-stall perching with a simple fixed-wing glider using LQR-Trees

    International Nuclear Information System (INIS)

    Moore, Joseph; Cory, Rick; Tedrake, Russ

    2014-01-01

    Birds routinely execute post-stall maneuvers with a speed and precision far beyond the capabilities of our best aircraft control systems. One remarkable example is a bird exploiting post-stall pressure drag in order to rapidly decelerate to land on a perch. Stall is typically associated with a loss of control authority, and it is tempting to attribute this agility of birds to the intricate morphology of the wings and tail, to their precision sensing apparatus, or their ability to perform thrust vectoring. Here we ask whether an extremely simple fixed-wing glider (no propeller) with only a single actuator in the tail is capable of landing precisely on a perch from a large range of initial conditions. To answer this question, we focus on the design of the flight control system; building upon previous work which used linear feedback control design based on quadratic regulators (LQR), we develop nonlinear feedback control based on nonlinear model-predictive control and ‘LQR-Trees’. Through simulation using a flat-plate model of the glider, we find that both nonlinear methods are capable of achieving an accurate bird-like perching maneuver from a large range of initial conditions; the ‘LQR-Trees’ algorithm is particularly useful due to its low computational burden at runtime and its inherent performance guarantees. With this in mind, we then implement the ‘LQR-Trees’ algorithm on real hardware and demonstrate a 95 percent perching success rate over 147 flights for a wide range of initial speeds. These results suggest that, at least in the absence of significant disturbances like wind gusts, complex wing morphology and sensing are not strictly required to achieve accurate and robust perching even in the post-stall flow regime. (papers)

  6. Simulation model of a transient fault controller for an active-stall wind turbine

    Energy Technology Data Exchange (ETDEWEB)

    Jauch, C.; Soerensen, P.; Bak Jensen, B.

    2005-01-01

    This paper describes the simulation model of a controller that enables an active-stall wind turbine to ride through transient faults. The simulated wind turbine is connected to a simple model of a power system. Certain fault scenarios are specified and the turbine shall be able to sustain operation in case of such faults. The design of the controller is described and its performance assessed by simulations. The control strategies are explained and the behaviour of the turbine discussed. (author)

  7. Fluid mechanics of dynamic stall. II - Prediction of full scale characteristics

    Science.gov (United States)

    Ericsson, L. E.; Reding, J. P.

    1988-01-01

    Analytical extrapolations are made from experimental subscale dynamics to predict full scale characteristics of dynamic stall. The method proceeds by establishing analytic relationships between dynamic and static aerodynamic characteristics induced by viscous flow effects. The method is then validated by predicting dynamic test results on the basis of corresponding static test data obtained at the same subscale flow conditions, and the effect of Reynolds number on the static aerodynamic characteristics are determined from subscale to full scale flow conditions.

  8. The Relationships between Selection and Processing Food with Escherichia coli Contaminant on Food Stall Serving

    Directory of Open Access Journals (Sweden)

    Tris Eryando

    2014-04-01

    Full Text Available Escherichia coli in food stalls surrounding the X Campuss in Depok, year 2012. The research conducted to examine food safety, which were served in surrounding the campus X in Depok. Escherichia coli (E. coli existence was used to indicate the quality of hygiene and sanitation of the food that was served. Using the cross sectional method, the research examined the persons who served the food to be sold in the food stalls in the campus. There were 173 food servers chosen as the respondents from 10 different food stalls around the university. The existence of E. coli examined in the microbiology laboratory in the Faculty of Public Health. Using the most probable number (MPN method found that 59.54% of the food served in the campus were contaminated E. coli. Factors affecting the existence of E. coli were the raw materials (vegetables treated and the length of cooking of the materials (rice/beens. The improper treatment such as washing with no running water or even unwashed vegetables had 5 times risk of the E. coli contamination. Cooking less than 15 minutes was also more risky than cooking more than 15 minutes. As a result, this is very important to find a method to improve knowledge and to increase practical skills in food safety. Furthermore, in this research area may give contribution to avoid E. coli contamination which will prevent unnecessary illness among students in the campus.

  9. An insight into the separate flow and stall delay for HAWT

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Guohua; Shen, Xin; Zhu, Xiaocheng; Du, Zhaohui [School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240 (China)

    2011-01-15

    The flow characteristics and the stall delay phenomenon of wind turbine rotor due to blade rotation in the steady state non-yawed conditions are investigated. An incompressible Reynolds-averaged Navier-Stokes solver is applied to carry out all the cases at different wind speeds from 5 m/s to 10 m/s with an interval of 1 m/s. CFD results turn out to agree well with experimental ones at incoming wind speeds below 10 m/s, though at 10 m/s some deviations exist due to the relative large flow separation and 3D spanwise flow over the suction surface of the blade. In the meanwhile, a lifting surface code with and without Du-Selig stall delay model is used to predict the power. A MATLAB code is developed to extract aerodynamic force coefficients from 3D CFD computations which are compared with the 2D airfoil wind tunnel experiment to demonstrate the stall delay and augmented lift phenomenon particularly at inboard span locations of the blade. The computational results are compared with the corrected value by the Du-Selig model and a lifting surface method derived data based on the measurements of the Unsteady Aerodynamic Experiment at the NASA Ames wind tunnel. (author)

  10. An automatic system for the detection of dairy cows lying behaviour in free-stall barns

    Directory of Open Access Journals (Sweden)

    Simona M.C. Porto

    2013-09-01

    Full Text Available In this paper, a method for the automatic detection of dairy cow lying behaviour in free-stall barns is proposed. A computer visionbased system (CVBS composed of a video-recording system and a cow lying behaviour detector based on the Viola Jones algorithm was developed. The CVBS performance was tested in a head-to-head free stall barn. Two classifiers were implemented in the software component of the CVBS to obtain the cow lying behaviour detector. The CVBS was validated by comparing its detection results with those generated from visual recognition. This comparison allowed the following accuracy indices to be calculated: the branching factor (BF, the miss factor (MF, the sensitivity, and the quality percentage (QP. The MF value of approximately 0.09 showed that the CVBS missed one cow every 11 well detected cows. Conversely, the BF value of approximately 0.08 indicated that one false positive was detected every 13 well detected cows. The high value of approximately 0.92 obtained for the sensitivity index and that obtained for QP of about 0.85 revealed the ability of the proposed system to detect cows lying in the stalls.

  11. Microbiological quality of air in free-range and box-stall stable horse keeping systems.

    Science.gov (United States)

    Wolny-Koładka, Katarzyna

    2018-04-07

    The aim of this study was to assess the microbiological quality of air in three horse riding centers differing in the horse keeping systems. The air samples were collected in one facility with free-range horse keeping system and two with box stalls of different sizes. The samples were collected over a period of 3 years (2015-2017), four times per year (spring, summer, autumn, winter) to assess the effect of seasonal changes. The prevalence of aerobic mesophilic bacteria, mold fungi, actinomycetes, Staphylococcus spp., and Escherichia coli was determined by the air collision method on Petri dishes with appropriate microbiological media. At the same time, air temperature, relative humidity, and particulate matter concentration (PM 10 , PM 2.5 ) were measured. It was found that the horse keeping system affects the occurrence of the examined airborne microorganisms. Over the 3-year period of study, higher temperature and humidity, as well as particulate matter concentration-which notoriously exceeded limit values-were observed in the facilities with the box-stall system. The air sampled from the largest horse riding center, with the largest number of horses and the box-stall system of horse keeping, was also characterized by the heaviest microbiological contamination. Among others, bacteria from the following genera: Staphylococcus spp., Streptococcus spp., Bacillus spp., and E. coli and fungi from the genera Aspergillus, Fusarium, Mucor, Rhizopus, Penicillium, Trichothecium, Cladosporium, and Alternaria were identified in the analyzed samples.

  12. Dynamic Stall Control on the Wind Turbine Airfoil via a Co-Flow Jet

    Directory of Open Access Journals (Sweden)

    He-Yong Xu

    2016-06-01

    Full Text Available Dynamic stall control of a S809 airfoil is numerically investigated by implementing a co-flow jet (CFJ. The numerical methods of the solver are validated by comparing results with the baseline experiment as well as a NACA 6415-based CFJ experiment, showing good agreement in both static and dynamic characteristics. The CFJ airfoil with inactive jet is simulated to study the impact that the jet channel imposes upon the dynamic characteristics. It is shown that the presence of a long jet channel could cause a negative effect of decreasing lift and increasing drag, leading to fluctuating extreme loads in terms of drag and moment. The main focus of the present research is the investigation of the dynamic characteristics of the CFJ airfoil with three different jet momentum coefficients, which are compared with the baseline, giving encouraging results. Dynamic stall can be greatly suppressed, showing a very good control performance of significantly increased lift and reduced drag and moment. Analysis of the amplitude of variation in the aerodynamic coefficients indicates that the fluctuating extreme aerodynamic loads are significantly alleviated, which is conducive to structural reliability and improved life cycle. The energy consumption analysis shows that the CFJ concept is applicable and economical in controlling dynamic stall.

  13. Short revolving wings enable hovering animals to avoid stall and reduce drag

    Science.gov (United States)

    Lentink, David; Kruyt, Jan W.; Heijst, Gertjan F.; Altshuler, Douglas L.

    2014-11-01

    Long and slender wings reduce the drag of airplanes, helicopters, and gliding animals, which operate at low angle of attack (incidence). Remarkably, there is no evidence for such influence of wing aspect ratio on the energetics of hovering animals that operate their wings at much higher incidence. High incidence causes aircraft wings to stall, hovering animals avoid stall by generating an attached vortex along the leading edge of their wings that elevates lift. Hypotheses that explain this capability include the necessity for a short radial distance between the shoulder joint and wing tip, measured in chord lengths, instead of the long tip-to-tip distance that elevates aircraft performance. This stems from how hovering animals revolve their wings around a joint, a condition for which the precise effect of aspect ratio on stall performance is unknown. Here we show that the attachment of the leading edge vortex is determined by wing aspect ratio with respect to the center of rotation-for a suite of aspect ratios that represent both animal and aircraft wings. The vortex remains attached when the local radius is shorter than 4 chord lengths, and separates outboard on more slender wings. Like most other hovering animals, hummingbirds have wing aspect ratios between 3 and 4, much stubbier than helicopters. Our results show this makes their wings robust against flow separation, which reduces drag below values obtained with more slender wings. This revises our understanding of how aspect ratio improves performance at low Reynolds numbers.

  14. Piloted Simulator Evaluation Results of Flight Physics Based Stall Recovery Guidance

    Science.gov (United States)

    Lombaerts, Thomas; Schuet, Stefan; Stepanyan, Vahram; Kaneshige, John; Hardy, Gordon; Shish, Kimberlee; Robinson, Peter

    2018-01-01

    In recent studies, it has been observed that loss of control in flight is the most frequent primary cause of accidents. A significant share of accidents in this category can be remedied by upset prevention if possible, and by upset recovery if necessary, in this order of priorities. One of the most important upsets to be recovered from is stall. Recent accidents have shown that a correct stall recovery maneuver remains a big challenge in civil aviation, partly due to a lack of pilot training. A possible strategy to support the flight crew in this demanding context is calculating a recovery guidance signal, and showing this signal in an intuitive way on one of the cockpit displays, for example by means of the flight director. Different methods for calculating the recovery signal, one based on fast model predictive control and another using an energy based approach, have been evaluated in four relevant operational scenarios by experienced commercial as well as test pilots in the Vertical Motion Simulator at NASA Ames Research Center. Evaluation results show that this approach could be able to assist the pilots in executing a correct stall recovery maneuver.

  15. A Method to Predict Compressor Stall in the TF34-100 Turbofan Engine Utilizing Real-Time Performance Data

    Science.gov (United States)

    2015-06-01

    A METHOD TO PREDICT COMPRESSOR STALL IN THE TF34-100 TURBOFAN ENGINE UTILIZING REAL-TIME PERFORMANCE...THE TF34-100 TURBOFAN ENGINE UTILIZING REAL-TIME PERFORMANCE DATA THESIS Presented to the Faculty Department of Systems Engineering and...036 A METHOD TO PREDICT COMPRESSOR STALL IN THE TF34-100 TURBOFAN ENGINE UTILIZING REAL-TIME PERFORMANCE DATA Shuxiang ‘Albert’ Li, BS

  16. Prediction of rotating stall within an impeller of a centrifugal pump based on spectral analysis of pressure and velocity data

    International Nuclear Information System (INIS)

    Ullum, Ulrik; Wright, Jennifer; Dayi, Oguz; Ecder, Ali; Soulaimani, Azzeddine; Piche, Robert; Kamath, Hemant

    2006-01-01

    Experimental data, which was acquired in two centrifugal pumps and provided by Grundfos A/S, were analysed to determine if rotating stall could be detected from the velocity and pressure time series. The pressure data, which were uniformly acquired in time at high sample rates(10 kHz), were measured simultaneously in four adjacent di.user channels just downstream of the impeller outlet. The velocity data, which were non-uniformly sampled in time at fairly low rates(100 Hz to 3.5 kHz), were acquired either in or downstream of the impeller. Two di.erent methodologies were employed for detection of stall. The first method, which involved direct analysis of raw data, yielded qualitatively useful flow reversal information from the time series for the radial velocity. The second approach, which was based on power spectrum analysis of velocity and pressure data, could detect the onset and identify the frequency of rotating stall to a satisfactory extent in one of the two pumps. Nearly identical stall frequencies were observed in both velocity and pressure power spectra and this rotating stall phenomenon, which occurred at a very low frequency relative to the impeller speed, did not reveal any noticeable degree of sensitivity to the flow rate. In the other pump, where the available data was limited to velocity time series, the power spectrum analysis was successful in detecting stationary stall for a 6 bladed impeller but did not provide conclusive results for the existence of stall in the case of the 7 bladed impeller. Recommendations on the type of experimental data required for accurate detection of stall are provided based upon the present study

  17. USP7 is a SUMO deubiquitinase essential for DNA replication

    DEFF Research Database (Denmark)

    Lecona, Emilio; Rodriguez-Acebes, Sara; Specks, Julia

    2016-01-01

    Post-translational modification of proteins by ubiquitin (Ub) and Ub-like modifiers regulates DNA replication. We have previously shown that chromatin around replisomes is rich in SUMO and poor in Ub, whereas mature chromatin exhibits an opposite pattern. How this SUMO-rich, Ub-poor environment...... is maintained at sites of DNA replication in mammalian cells remains unexplored. Here we identify USP7 as a replisome-enriched SUMO deubiquitinase that is essential for DNA replication. By acting on SUMO and SUMOylated proteins, USP7 counteracts their ubiquitination. Inhibition or genetic deletion of USP7 leads...... to the accumulation of Ub on SUMOylated proteins, which are displaced away from replisomes. Our findings provide a model explaining the differential accumulation of SUMO and Ub at replication forks and identify an essential role of USP7 in DNA replication that should be considered in the development of USP7...

  18. 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.

  19. A Crystallographic Study of the Role of Sequence Context in Thymine Glycol Bypass by a Replicative DNA Polymerase Serendipitously Sheds Light on the Exonuclease Complex

    Energy Technology Data Exchange (ETDEWEB)

    Aller, Pierre; Duclos, Stéphanie; Wallace, Susan S.; Doublié, Sylvie (Vermont)

    2012-06-27

    Thymine glycol (Tg) is the most common oxidation product of thymine and is known to be a strong block to replicative DNA polymerases. A previously solved structure of the bacteriophage RB69 DNA polymerase (RB69 gp43) in complex with Tg in the sequence context 5'-G-Tg-G shed light on how Tg blocks primer elongation: The protruding methyl group of the oxidized thymine displaces the adjacent 5'-G, which can no longer serve as a template for primer elongation [Aller, P., Rould, M. A., Hogg, M, Wallace, S. S. and Doublie S. (2007). A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol. Proc. Natl. Acad. Sci. USA, 104, 814-818.]. Several studies showed that in the sequence context 5'-C-Tg-purine, Tg is more likely to be bypassed by Klenow fragment, an A-family DNA polymerase. We set out to investigate the role of sequence context in Tg bypass in a B-family polymerase and to solve the crystal structures of the bacteriophage RB69 DNA polymerase in complex with Tg-containing DNA in the three remaining sequence contexts: 5'-A-Tg-G, 5'-T-Tg-G, and 5'-C-Tg-G. A combination of several factors - including the associated exonuclease activity, the nature of the 3' and 5' bases surrounding Tg, and the cis-trans interconversion of Tg - influences Tg bypass. We also visualized for the first time the structure of a well-ordered exonuclease complex, allowing us to identify and confirm the role of key residues (Phe123, Met256, and Tyr257) in strand separation and in the stabilization of the primer strand in the exonuclease site.

  20. DNA breaks early in replication in B cell cancers

    Science.gov (United States)

    Research by scientists at the NCI has identified a new class of DNA sites in cells that break early in the replication process. They found that these break sites correlate with damage often seen in B cell cancers, such as diffuse large B cell lymphoma.

  1. Dynamics and Control of Three-Dimensional Perching Maneuver under Dynamic Stall Influence

    Science.gov (United States)

    Feroskhan, Mir Alikhan Bin Mohammad

    Perching is a type of aggressive maneuver performed by the class 'Aves' species to attain precision point landing with a generally short landing distance. Perching capability is desirable on unmanned aerial vehicles (UAVs) due to its efficient deceleration process that potentially expands the functionality and flight envelope of the aircraft. This dissertation extends the previous works on perching, which is mostly limited to two-dimensional (2D) cases, to its state-of-the-art threedimensional (3D) variety. This dissertation presents the aerodynamic modeling and optimization framework adopted to generate unprecedented variants of the 3D perching maneuver that include the sideslip perching trajectory, which ameliorates the existing 2D perching concept by eliminating the undesirable undershoot and reliance on gravity. The sideslip perching technique methodically utilizes the lateral and longitudinal drag mechanisms through consecutive phases of yawing and pitching-up motion. Since perching maneuver involves high rates of change in the angles of attack and large turn rates, introduction of three internal variables thus becomes necessary for addressing the influence of dynamic stall delay on the UAV's transient post-stall behavior. These variables are then integrated into a static nonlinear aerodynamic model, developed using empirical and analytical methods, and into an optimization framework that generates a trajectory of sideslip perching maneuver, acquiring over 70% velocity reduction. An impact study of the dynamic stall influence on the optimal perching trajectories suggests that consideration of dynamic stall delay is essential due to the significant discrepancies in the corresponding control inputs required. A comparative study between 2D and 3D perching is also conducted to examine the different drag mechanisms employed by 2D and 3D perching respectively. 3D perching is presented as a more efficient deceleration technique with respect to spatial costs and

  2. Dairy cows welfare quality in tie-stall housing system with or without access to exercise

    Science.gov (United States)

    2013-01-01

    Background Tie-stall housing of dairy cows is used extensively worldwide, despite of the welfare concerns regarding the restriction of voluntary movement and limitation of expression of the cows’ natural behaviour. The aim of this study was to compare the welfare quality of dairy cows kept in two types of tie-stall housing systems: with regular outdoor exercise and without access to exercise. In addition, the study investigated the relationship between different welfare measures of dairy cows kept in tie-stalls. Methods 3,192 lactating cows were assessed using the Welfare Quality® assessment protocol for cattle in 80 commercial dairy farms, half of the farms providing outdoor access for the animals to exercise. The descriptive statistical indicators were determined for the assessed measures and for the welfare criteria and principle scores. The data obtained in the two housing types were compared and the correlation coefficients were calculated between the different welfare measures. Results The significant differences found between the two housing systems for the majority of the animal based measures indicate the positive effect of exercise on the welfare of tethered cows. Many of the animal welfare parameters correlated with each other. For the farms allowing the cows’ turnout in a paddock, pasture or both, the mean scores for the welfare criteria and principles were higher than for the farms with permanent tethering of the cows, except the criteria absence of prolonged hunger and expression of social behaviours. The lowest scores were obtained for the criterion positive emotional state, in both housing systems. With regard to the overall classification, none of the farms were considered excellent. In the not classified category were only farms with all-year-round tethering of the animals and in the enhanced category only farms where the cows had outdoor access. Conclusions The welfare quality of the investigated dairy cows was significantly better in the

  3. Human CST Facilitates Genome-wide RAD51 Recruitment to GC-Rich Repetitive Sequences in Response to Replication Stress.

    Science.gov (United States)

    Chastain, Megan; Zhou, Qing; Shiva, Olga; Fadri-Moskwik, Maria; Whitmore, Leanne; Jia, Pingping; Dai, Xueyu; Huang, Chenhui; Ye, Ping; Chai, Weihang

    2016-08-02

    The telomeric CTC1/STN1/TEN1 (CST) complex has been implicated in promoting replication recovery under replication stress at genomic regions, yet its precise role is unclear. Here, we report that STN1 is enriched at GC-rich repetitive sequences genome-wide in response to hydroxyurea (HU)-induced replication stress. STN1 deficiency exacerbates the fragility of these sequences under replication stress, resulting in chromosome fragmentation. We find that upon fork stalling, CST proteins form distinct nuclear foci that colocalize with RAD51. Furthermore, replication stress induces physical association of CST with RAD51 in an ATR-dependent manner. Strikingly, CST deficiency diminishes HU-induced RAD51 foci formation and reduces RAD51 recruitment to telomeres and non-telomeric GC-rich fragile sequences. Collectively, our findings establish that CST promotes RAD51 recruitment to GC-rich repetitive sequences in response to replication stress to facilitate replication restart, thereby providing insights into the mechanism underlying genome stability maintenance. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  4. Replication of bacteriophage lambda DNA

    International Nuclear Information System (INIS)

    Tsurimoto, T.; Matsubara, K.

    1983-01-01

    In this paper results of studies on the mechanism of bacteriophage lambda replication using molecular biological and biochemical approaches are reported. The purification of the initiator proteins, O and P, and the role of the O and P proteins in the initiation of lambda DNA replication through interactions with specific DNA sequences are described. 47 references, 15 figures

  5. Pattern replication by confined dewetting

    NARCIS (Netherlands)

    Harkema, S.; Schäffer, E.; Morariu, M.D.; Steiner, U

    2003-01-01

    The dewetting of a polymer film in a confined geometry was employed in a pattern-replication process. The instability of dewetting films is pinned by a structured confining surface, thereby replicating its topographic pattern. Depending on the surface energy of the confining surface, two different

  6. Charter School Replication. Policy Guide

    Science.gov (United States)

    Rhim, Lauren Morando

    2009-01-01

    "Replication" is the practice of a single charter school board or management organization opening several more schools that are each based on the same school model. The most rapid strategy to increase the number of new high-quality charter schools available to children is to encourage the replication of existing quality schools. This policy guide…

  7. 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…

  8. Phosphorylation of NS5A Serine-235 is essential to hepatitis C virus RNA replication and normal replication compartment formation

    Energy Technology Data Exchange (ETDEWEB)

    Eyre, Nicholas S., E-mail: nicholas.eyre@adelaide.edu.au [School of Biological Sciences and Research Centre for Infectious Diseases, University of Adelaide, Adelaide (Australia); Centre for Cancer Biology, SA Pathology, Adelaide (Australia); Hampton-Smith, Rachel J.; Aloia, Amanda L. [School of Biological Sciences and Research Centre for Infectious Diseases, University of Adelaide, Adelaide (Australia); Centre for Cancer Biology, SA Pathology, Adelaide (Australia); Eddes, James S. [Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide (Australia); Simpson, Kaylene J. [Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne (Australia); The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville (Australia); Hoffmann, Peter [Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide (Australia); Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide (Australia); Beard, Michael R. [School of Biological Sciences and Research Centre for Infectious Diseases, University of Adelaide, Adelaide (Australia); Centre for Cancer Biology, SA Pathology, Adelaide (Australia)

    2016-04-15

    Hepatitis C virus (HCV) NS5A protein is essential for HCV RNA replication and virus assembly. Here we report the identification of NS5A phosphorylation sites Ser-222, Ser-235 and Thr-348 during an infectious HCV replication cycle and demonstrate that Ser-235 phosphorylation is essential for HCV RNA replication. Confocal microscopy revealed that both phosphoablatant (S235A) and phosphomimetic (S235D) mutants redistribute NS5A to large juxta-nuclear foci that display altered colocalization with known replication complex components. Using electron microscopy (EM) we found that S235D alters virus-induced membrane rearrangements while EM using ‘APEX2’-tagged viruses demonstrated S235D-mediated enrichment of NS5A in irregular membranous foci. Finally, using a customized siRNA screen of candidate NS5A kinases and subsequent analysis using a phospho-specific antibody, we show that phosphatidylinositol-4 kinase III alpha (PI4KIIIα) is important for Ser-235 phosphorylation. We conclude that Ser-235 phosphorylation of NS5A is essential for HCV RNA replication and normal replication complex formation and is regulated by PI4KIIIα. - Highlights: • NS5A residues Ser-222, Ser-235 and Thr-348 are phosphorylated during HCV infection. • Phosphorylation of Ser-235 is essential to HCV RNA replication. • Mutation of Ser-235 alters replication compartment localization and morphology. • Phosphatidylinositol-4 kinase III alpha is important for Ser-235 phosphorylation.

  9. Replication stress-induced chromosome breakage is correlated with replication fork progression and is preceded by single-stranded DNA formation.

    Science.gov (United States)

    Feng, Wenyi; Di Rienzi, Sara C; Raghuraman, M K; Brewer, Bonita J

    2011-10-01

    Chromosome breakage as a result of replication stress has been hypothesized to be the direct consequence of defective replication fork progression, or "collapsed" replication forks. However, direct and genome-wide evidence that collapsed replication forks give rise to chromosome breakage is still lacking. Previously we showed that a yeast replication checkpoint mutant mec1-1, after transient exposure to replication impediment imposed by hydroxyurea (HU), failed to complete DNA replication, accumulated single-stranded DNA (ssDNA) at the replication forks, and fragmented its chromosomes. In this study, by following replication fork progression genome-wide via ssDNA detection and by direct mapping of chromosome breakage after HU exposure, we have tested the hypothesis that the chromosome breakage in mec1 cells occurs at collapsed replication forks. We demonstrate that sites of chromosome breakage indeed correlate with replication fork locations. Moreover, ssDNA can be detected prior to chromosome breakage, suggesting that ssDNA accumulation is the common precursor to double strand breaks at collapsed replication forks.

  10. Animal hygiene assessment of microclimate in semi open free-stall barns for dairy cows

    Directory of Open Access Journals (Sweden)

    D. Dimov

    2017-03-01

    Full Text Available Abstract. The study was conducted in three semi open free-stall barns (B1, B2, and B3 for dairy cows with capacities for 120, 120 and 500 cows, respectively, from three different dairy farms (F-1, F-2 and F-3, situated in Central Southern Bulgaria. The investigated farms had the same production system – loose housing in semi open free-stall dairy barn. For each of the farms the main microclimatic parameters – air temperature, relative humidity and speed of airflow were recorded twice a month at 10.00 h 12.00 h, 14.00 h, 16.00 h and 18.00 h of the day inside the barns in three main technological zones - above the stalls, above manure and feed alleys and outside the buildings. It was found that: a Microclimatic parameters (air temperature, air relative humidity and speed of airflow in technological zones (above the stalls, the manure and feed alleys of three semi open free-stall dairy barns meet the animal hygienic requirements for all seasons according to Regulation No. 44 (2006. Exceptions are some values of relative humidity in B1 and B2 in the spring, and in B1 in winter and summer, which are lower than the minimum humidity (50% according to the standard. b The investigated barns are characterized with poor insulation and do not provide enough isolation from the external ambient temperatures. With the exception of winter, the temperature of the air inside the buildings was lower than that outside, with minor differences for all seasons. The fans in the barns have no effect on the inside air temperature, especially in summer. There was a risk of higher temperatures mainly during the summer period. c There is no significant difference between the average temperatures, air humidity and speed of airflow in all technological zones of the investigated barns. d The largest and statistically significant is the difference between the relative air humidity outside and inside the building in Farm 3, followed by buildings in Farm 1 and 2, where the

  11. Airborne Microorganisms in Tie-stall Dairy Barns from Brasov County

    Directory of Open Access Journals (Sweden)

    Silvana Popescu

    2011-05-01

    Full Text Available The aim of this study was the assessment of the airborne microorganisms in tie-stall dairy cattle barns, through determination of the total number of bacteria (mesophilic bacteria, staphylococci, streptococci and gram-negative bacteria and fungi. We investigated 8 dairy cattle barns with tie-stalls in Brasov County during the winter of 2009. The mean numbers of bacteria and fungi in the morning and in the evening were: 1.02 °— 105 - 1.26 °— 105 CFU/m3 for mesophilic bacteria, 5.34 °— 104 - 5.91 °— 104 CFU/m3 for staphylococci, 2.93 °— 104 - 3.60 °— 104 CFU/m3 for streptococci, 2.17 °— 103 - 3.48 °— 103 CFU/m3 for gram-negative bacteria and 1.54 °— 104 - 2.75 °— 104 CFU/m3 for fungi. In the investigated cattle houses staphylococci represented 52.35 – 46.90%, streptococci were 28.73 – 28.57%, and the gram-negative bacteria were 2.13 – 2.76% within the overall number of mesophilic bacteria. The numbers of bacteria and fungi were slightly elevated in the evening comparative to the morning, but the differences were statistically insignificant (p>0.05. The great numbers of bacteria and fungi in the air of dairy cattle tie-stall barns indicate an elevated risk of disease for animals and human workers.

  12. Cooling systems of the resting area in free stall dairy barn

    Science.gov (United States)

    Calegari, F.; Calamari, L.; Frazzi, E.

    2016-04-01

    A study during the summer season evaluated the effect of different cooling systems on behavioral and productive responses of Italian Friesian dairy cows kept in an experimental-free stall barn located in the Po Valley in Italy. The study involved 30 lactating dairy cows subdivided into two groups kept in two pens with external hard court paddock in each free stall. The same cooling system was applied in the feeding area in both pens. A different cooling system in the resting area was applied to the two pens: in the pen SW, the resting area was equipped with fans and misters; in the other, there was simple ventilation (SV). Breathing rate, rectal temperature, milk yield, and milk characteristics (fat, protein, and somatic cell count) were measured. Behavioral activities (standing and lying cows in the different areas, as well as the animals in the feed bunk) were recorded. Mild to moderate heat waves during the trial were observed. On average, the breathing rate was numerically greater in SV compared with SW cows (60.2 and 55.8 breath/min, respectively), and mean rectal temperature remained below 39 °C in both groups during the trial (on average 38.7 and 38.8 °C in SV and SW, respectively. During the hotter periods of the trial, the time spent lying indoor in the free stall was greater in SW (11.8 h/day) than SV (10.7 h/day). Conversely, the time spent standing indoor without feeding was greater in SV (4.3 h/day) than SW (3.8 h/day). Milk yield was slightly better maintained during hotter period in SW compared with SV and somatic cell count was also slightly greater in the former. In conclusion, the adoption of the cooling system by means of evaporative cooling also in the resting area reduces the alteration of time budget caused by heat stress.

  13. 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.

  14. Constitutive role of the Fanconi anemia D2 gene in the replication stress response.

    Science.gov (United States)

    Tian, Yanyan; Shen, Xi; Wang, Rui; Klages-Mundt, Naeh L; Lynn, Erica J; Martin, Sara K; Ye, Yin; Gao, Min; Chen, Junjie; Schlacher, Katharina; Li, Lei

    2017-12-08

    In response to DNA cross-linking damage, the Fanconi anemia (FA) core complex activates the FA pathway by monoubiquitinating Fanconi anemia complementation group D2 (FANCD2) for the initiation of the nucleolytic processing of the DNA cross-links and stabilization of stalled replication forks. Given that all the classic FA proteins coordinately monoubiquitinate FANCD2, it is unclear why losses of individual classic FA genes yield varying cellular sensitivities to cross-linking damage. To address this question, we generated cellular knock-out models of FA core complex components and FANCD2 and found that FANCD2-null mutants display higher levels of spontaneous chromosomal damage and hypersensitivity to replication-blocking lesions than Fanconi anemia complementation group L (FANCL)-null mutants, suggesting that FANCD2 provides a basal level of DNA protection countering endogenous lesions in the absence of monoubiquitination. FANCD2's ubiquitination-independent function is likely involved in optimized recruitment of nucleolytic activities for the processing and protection of stressed replication forks. Our results reveal that FANCD2 has a ubiquitination-independent role in countering endogenous levels of replication stress, a function that is critical for the maintenance of genomic stability. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. 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

  16. 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.

  17. A stochastic model for the simulation of wind turbine blades in static stall

    DEFF Research Database (Denmark)

    Bertagnolio, Franck; Rasmussen, Flemming; Sørensen, Niels N.

    2010-01-01

    The aim of this work is to improve aeroelastic simulation codes by accounting for the unsteady aerodynamic forces that a blade experiences in static stall. A model based on a spectral representation of the aerodynamic lift force is defined. The drag and pitching moment are derived using...... a conditional simulation technique for stochastic processes. The input data for the model can be collected either from measurements or from numerical results from a Computational Fluid Dynamics code for airfoil sections at constant angles of attack. An analysis of such data is provided, which helps to determine...

  18. Prediction of H.A.W.T. blade stall and performance

    Energy Technology Data Exchange (ETDEWEB)

    Giannakidis, G.; Graham, J.M.R. [Imperial College, Dept. of Aeronautics, London (United Kingdom)

    1996-09-01

    A model is being developed for the prediction of Horizontal Axis Wind Turbine blade stall and performance coupled with a simple aeroelastic analysis model. For the aerodynamic calculation a two dimensional unsteady Navier-Stokes solver on a sectional basis on the blade is coupled with a three dimensional vortex lattice wake. Pressure coefficient distributions are calculated from the two dimensional viscous flow in each blade section. The aerodynamic computations are coupled with a vibrating beam model in order to incorporate flapwise deformations of the blade. (au) 17 refs.

  19. A model for the selective amplification of spatially coherent waves in a centrifugal compressor on the verge of rotating stall

    Science.gov (United States)

    Lawless, Patrick B.; Fleeter, Sanford

    1993-01-01

    A simple model for the stability zones of a low speed centrifugal compressor is developed, with the goal of understanding the driving mechanism for the changes in stalling behavior predicted for, and observed in, the Purdue Low Speed Centrifugal Research Compressor Facility. To this end, earlier analyses of rotating stall suppression in centrifugal compressors are presented in a reduced form that preserves the essential parameters of the model that affect the stalling behavior of the compressor. The model is then used to illuminate the relationship between compressor geometry, expected mode shape, and regions of amplification for weak waves which are indicative of the susceptibility of the system to rotating stall. The results demonstrate that increasing the stagger angle of the diffuser vanes, and consequently the diffusion path length, results in the compressor moving towards a condition where higher-order spatial modes are excited during stall initiation. Similarly, flow acceleration in the diffuser section caused by an increase in the number of diffuser vanes also results in the excitation of higher modes.

  20. DNA replication origins-where do we begin?

    Science.gov (United States)

    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.

  1. 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

  2. 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

  3. 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.

  4. Cell lethality after selective irradiation of the DNA replication fork

    International Nuclear Information System (INIS)

    Hofer, K.G.; Warters, R.L.

    1985-01-01

    It has been suggested that nascent DNA located at the DNA replication fork may exhibit enhanced sensitivity to radiation damage. To evaluate this hypothesis, Chinese hamster ovary cells (CHO) were labeled with 125 I-iododeoxyuridine ( 125 IUdR) either in the presence or absence of aphidicolin. Aphidicolin (5 μg/ml) reduced cellular 125 IUdR incorporation to 3-5% of the control value. The residual 125 I incorporation appeared to be restricted to low molecular weight (sub-replicon sized) fragments of DNA which were more sensitive to micrococcal nuclease attack and less sensitive to high salt DNase I digestion than randomly labeled DNA. These findings suggest that DNA replicated in the presence of aphidicolin remains localized at the replication fork adjacent to the nuclear matrix. Based on these observations an attempt was made to compare the lethal consequences of 125 I decays at the replication fork to that of 125 I decays randomly distributed over the entire genome. Regardless of the distribution of decay events, all treatment groups exhibited identical dose-response curves (D 0 : 101 125 I decays/cell). Since differential irradiation of the replication complex did not result in enhanced cell lethality, it can be concluded that neither the nascent DNA nor the protein components (replicative enzymes, nuclear protein matrix) associated with the DNA replication site constitute key radiosensitive targets within the cellular genome. (orig.)

  5. 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

  6. 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...

  7. Modelling of multiple short-length-scale stall cells in an axial compressor using evolved GMDH neural networks

    International Nuclear Information System (INIS)

    Amanifard, N.; Nariman-Zadeh, N.; Farahani, M.H.; Khalkhali, A.

    2008-01-01

    Over the past 15 years there have been several research efforts to capture the stall inception nature in axial flow compressors. However previous analytical models could not explain the formation of short-length-scale stall cells. This paper provides a new model based on evolved GMDH neural network for transient evolution of multiple short-length-scale stall cells in an axial compressor. Genetic Algorithms (GAs) are also employed for optimal design of connectivity configuration of such GMDH-type neural networks. In this way, low-pass filter (LPF) pressure trace near the rotor leading edge is modelled with respect to the variation of pressure coefficient, flow rate coefficient, and number of rotor rotations which are defined as inputs

  8. Blade tip, finite aspect ratio, and dynamic stall effects on the Darrieus rotor

    Science.gov (United States)

    Paraschivoiu, I.; Desy, P.; Masson, C.

    1988-02-01

    The objective of the work described in this paper was to apply the Boeing-Vertol dynamic stall model in an asymmetric manner to account for the asymmetry of the flow between the left and right sides of the rotor. This phenomenon has been observed by the flow visualization of a two-straight-bladed Darrieus rotor in the IMST water tunnel. Also introduced into the aerodynamic model are the effects of the blade tip and finite aspect ratio on the aerodynamic performance of the Darrieus wind turbine. These improvements are compatible with the double-multiple-streamtube model and have been included in the CARDAAV computer code for predicting the aerodynamic performance. Very good agreement has been observed between the test data (Sandia 17 m) and theoretical predictions; a significant improvement over the previous dynamic stall model was obtained for the rotor power at low tip speed ratios, while the inclusion of the finite aspect ratio effects enhances the prediction of the rotor power for high tip speed ratios. The tip losses and finite aspect ratio effects were also calculated for a small-scale vertical-axis wind turbine, with a two-straight-bladed (NACA 0015) rotor.

  9. Experimental Methods Applied in a Study of Stall Flutter in an Axial Flow Fan

    Directory of Open Access Journals (Sweden)

    John D. Gill

    2004-01-01

    Full Text Available Flutter testing is an integral part of aircraft gas turbine engine development. In typical flutter testing blade mounted sensors in the form of strain gages and casing mounted sensors in the form of light probes (NSMS are used. Casing mounted sensors have the advantage of being non-intrusive and can detect the vibratory response of each rotating blade. Other types of casing mounted sensors can also be used to detect flutter of rotating blades. In this investigation casing mounted high frequency response pressure transducers are used to characterize the part-speed stall flutter response of a single stage unshrouded axial-flow fan. These dynamic pressure transducers are evenly spaced around the circumference at a constant axial location upstream of the fan blade leading edge plane. The pre-recorded experimental data at 70% corrected speed is analyzed for the case where the fan is back-pressured into the stall flutter zone. The experimental data is analyzed using two probe and multi-probe techniques. The analysis techniques for each method are presented. Results from these two analysis methods indicate that flutter occurred at a frequency of 411 Hz with a dominant nodal diameter of 2. The multi-probe analysis technique is a valuable method that can be used to investigate the initiation of flutter in turbomachines.

  10. ATEFlap aerodynamic model, a dynamic stall model including the effects of trailing edge flap deflection

    Energy Technology Data Exchange (ETDEWEB)

    Bergami, L.; Gaunaa, M.

    2012-02-15

    The report presents the ATEFlap aerodynamic model, which computes the unsteady lift, drag and moment on a 2D airfoil section equipped with Adaptive Trailing Edge Flap. The model captures the unsteady response related to the effects of the vorticity shed into the wake, and the dynamics of flow separation a thin-airfoil potential flow model is merged with a dynamic stall model of the Beddoes-Leishmann type. The inputs required by the model are steady data for lift, drag, and moment coefficients as function of angle of attack and flap deflection. Further steady data used by the Beddoes- Leishmann dynamic stall model are computed in an external preprocessor application, which gives the user the possibility to verify, and eventually correct, the steady data passed to the aerodynamic model. The ATEFlap aerodynamic model is integrated in the aeroelastic simulation tool HAWC2, thus al- lowing to simulate the response of a wind turbine with trailing edge flaps on the rotor. The algorithms used by the preprocessor, and by aerodynamic model are presented, and modifications to previous implementations of the aerodynamic model are briefly discussed. The performance and the validity of the model are verified by comparing the dynamic response computed by the ATEFlap with solutions from CFD simulations. (Author)

  11. Suppression of dynamic stall with a leading-edge slat on a VR-7 airfoil

    Science.gov (United States)

    Mcalister, K. W.; Tung, C.

    1993-01-01

    The VR-7 airfoil was experimentally studied with and without a leading-edge slat at fixed angles of attack from 0 deg to 30 deg at Re = 200,000 and for unsteady pitching motions described by alpha equals alpha(sub m) + 10 deg(sin(wt)). The models were two dimensional, and the test was performed in a water tunnel at Ames Research Center. The unsteady conditions ranged over Re equals 100,000 to 250,000, k equals 0.001 to 0.2, and alpha(sub m) = 10 deg to 20 deg. Unsteady lift, drag, and pitching-moment measurements were obtained along with fluorescent-dye flow visualizations. The addition of the slat was found to delay the static-drag and static-moment stall by about 5 degrees and to eliminate completely the development of a dynamic-stall vortex during unsteady motions that reached angles as high as 25 degrees. In all of the unsteady cases studied, the slat caused a significant reduction in the force and moment hysteresis amplitudes. The reduced frequency was found to have the greatest effect on the results, whereas the Reynolds number had little effect on the behavior of either the basic or the slatted airfoil. The slat caused a slight drag penalty at low angles of attack, but generally increased the lift/drag ratio when averaged over the full cycle of oscillation.

  12. Pressure-based high-order TVD methodology for dynamic stall control

    Science.gov (United States)

    Yang, H. Q.; Przekwas, A. J.

    1992-01-01

    The quantitative prediction of the dynamics of separating unsteady flows, such as dynamic stall, is of crucial importance. This six-month SBIR Phase 1 study has developed several new pressure-based methodologies for solving 3D Navier-Stokes equations in both stationary and moving (body-comforting) coordinates. The present pressure-based algorithm is equally efficient for low speed incompressible flows and high speed compressible flows. The discretization of convective terms by the presently developed high-order TVD schemes requires no artificial dissipation and can properly resolve the concentrated vortices in the wing-body with minimum numerical diffusion. It is demonstrated that the proposed Newton's iteration technique not only increases the convergence rate but also strongly couples the iteration between pressure and velocities. The proposed hyperbolization of the pressure correction equation is shown to increase the solver's efficiency. The above proposed methodologies were implemented in an existing CFD code, REFLEQS. The modified code was used to simulate both static and dynamic stalls on two- and three-dimensional wing-body configurations. Three-dimensional effect and flow physics are discussed.

  13. Numerical study on a single bladed vertical axis wind turbine under dynamic stall

    Energy Technology Data Exchange (ETDEWEB)

    Bangga, Galih [Institute of Aerodynamics and Gas Dynamics, University of Stuttgart, Stuttgart (Germany); Hutomo, Go; Sasongko, Herman [Dept. of Mechanical Engineering, Institut Teknologi Sepuluh Nopember, Surabaya (Indonesia); Wiranegara, Raditya [School of Mechanical Aerospace and Civil Engineering, University of Manchester, Manchester (United Kingdom)

    2017-01-15

    The aim of this study is to investigate the flow development of a single bladed vertical axis wind turbine using Computational fluid dynamics (CFD) methods. The blade is constructed using the NACA 0012 profile and is operating under stalled conditions at tip speed ratio of 2. Two dimensional simulations are performed using a commercial CFD package, ANSYS Fluent 15.0, employing the Menter-SST turbulence model. For the preliminary study, simulations of the NACA 0012 airfoil under static conditions are carried out and compared with available measurement data and calculations using the boundary layer code XFOIL. The CFD results under the dynamic case are presented and the resulting aerodynamic forces are evaluated. The turbine is observed to generate negative power at certain azimuth angles which can be divided into three main zones. The blade vortex interaction is observed to strongly influence the flow behavior near the blade and contributes to the power production loss. However, the impact is considered small since it covers only 6.4 % of the azimuth angle range where the power is negative compared to the dynamic stall impact which covers almost 22 % of the azimuth angle range.

  14. Lift hysteresis at stall as an unsteady boundary-layer phenomenon

    Science.gov (United States)

    Moore, Franklin K

    1956-01-01

    Analysis of rotating stall of compressor blade rows requires specification of a dynamic lift curve for the airfoil section at or near stall, presumably including the effect of lift hysteresis. Consideration of the magnus lift of a rotating cylinder suggests performing an unsteady boundary-layer calculation to find the movement of the separation points of an airfoil fixed in a stream of variable incidence. The consideration of the shedding of vorticity into the wake should yield an estimate of lift increment proportional to time rate of change of angle of attack. This increment is the amplitude of the hysteresis loop. An approximate analysis is carried out according to the foregoing ideas for a 6:1 elliptic airfoil at the angle of attack for maximum lift. The assumptions of small perturbations from maximum lift are made, permitting neglect of distributed vorticity in the wake. The calculated hysteresis loop is counterclockwise. Finally, a discussion of the forms of hysteresis loops is presented; and, for small reduced frequency of oscillation, it is concluded that the concept of a viscous "time lag" is appropriate only for harmonic variations of angle of attack with time at mean conditions other than maximum lift.

  15. Active unsteady aerodynamic suppression of rotating stall in an incompressible flow centrifugal compressor with vaned diffuser

    Science.gov (United States)

    Lawless, Patrick B.; Fleeter, Sanford

    1991-01-01

    A mathematical model is developed to analyze the suppression of rotating stall in an incompressible flow centrifugal compressor with a vaned diffuser, thereby addressing the important need for centrifugal compressor rotating stall and surge control. In this model, the precursor to to instability is a weak rotating potential velocity perturbation in the inlet flow field that eventually develops into a finite disturbance. To suppress the growth of this potential disturbance, a rotating control vortical velocity disturbance is introduced into the impeller inlet flow. The effectiveness of this control is analyzed by matching the perturbation pressure in the compressor inlet and exit flow fields with a model for the unsteady behavior of the compressor. To demonstrate instability control, this model is then used to predict the control effectiveness for centrifugal compressor geometries based on a low speed research centrifugal compressor. These results indicate that reductions of 10 to 15 percent in the mean inlet flow coefficient at instability are possible with control waveforms of half the magnitude of the total disturbance at the inlet.

  16. Active flow control of the laminar separation bubble on a plunging airfoil near stall

    Science.gov (United States)

    Pande, Arth; Agate, Mark; Little, Jesse; Fasel, Hermann

    2017-11-01

    The effects of small amplitude (A/c = 0.048) high frequency (πfc/U∞ = 0.70) plunging motion on the X-56A airfoil are examined experimentally at Re = 200,000 for 12° angle of attack (CL,MAX = 12.25°) . The purpose of this research is to study the aerodynamic influence of structural motion when the wing is vibrating close to its eigenfrequency near static stall. Specific focus is placed on the laminar separation bubble (LSB) near the leading edge and its control via plasma actuation. In the baseline case, the leading edge bubble bursts during the oscillation cycle causing moment stall. A collaborative computational effort has shown that small amplitude forcing at a frequency that is most amplified by the primary instability of the LSB (FLSB+= 1, Fc+= 52) generates coherent spanwise vortices that entrain freestream momentum, thus reducing separation all while maintaining a laminar flow state. Results (PIV and surface pressure) indicate that a similar control mechanism is effective in the experiments. This is significant given the existence of freestream turbulence in the wind tunnel which has been shown to limit the efficacy of this active flow control technique in a model problem using Direct Numerical Simulation. The implications of these results are discussed.

  17. Compliance with NAGCAT work practices recommendations for youth cleaning service alleys in stall barns.

    Science.gov (United States)

    Canan, B D; Asti, L; Heaney, C; Ashida, S; Renick, K; Xiang, H; Stallones, L; Jepsen, S D; Crawford, J M; Wilkins, J R

    2011-04-01

    Unintentional injury is the leading cause of death in the U.S. among persons 1 to 44 years of age. Over one million children and adolescents in the U.S. live, work, and/or play on farms, where injury risk is relatively high compared to other settings. In an attempt to reduce the number of childhood agricultural injuries occurring on farms, the North American Guidelines for Children's Agricultural Tasks (NAGCAT) was developed to assist parents or other caregivers in assigning developmentally appropriate chores to youth exposed to agricultural hazards. The results presented here are from a longitudinal study in which we obtained (self-reported) daily chore, injury, and safety behavior data from children and adolescents. We focused on one NAGCAT chore, cleaning a service alley in a stall barn, in order to estimate the extent of compliance with specific work practice recommendations contained in the NAGCAT. Our results indicated that among the four NAGCAT-recommended safety practices for cleaning service alleys in stall barns (wearing nonskid shoes, leather gloves, a respirator, and eye protection), wearing non-skid shoes was the only safety practice reported with any degree of regularity. Overall, boys were more likely to wear non-skid shoes compared to girls. In addition, older youth were generally more likely to report higher work practice compliance compared to younger youth.

  18. 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...

  19. Effect of free stall surface on daily activity patterns in dairy cows with relevance to lameness prevalence.

    Science.gov (United States)

    Cook, N B; Bennett, T B; Nordlund, K V

    2004-09-01

    Differences in behavior of nonlame cows, slightly lame cows, and moderately lame cows in 6 free stall barns with sand bedding (SAND) vs. 6 free stall barns with rubber-crumb geotextile mattress surfaces (MAT) were documented in Wisconsin dairy herds. All lactating cows in the 12 herds were observed and given a locomotion score based on a 4-point scale: 1 = nonlame, 2 = slightly lame, 3 = moderately lame, and 4 = severely lame. Herd least square means +/-SE for prevalence of clinical lameness (locomotion scores = 3 and 4) were 11.1 vs. 24.0 +/- 1.7% for herds using SAND vs. MAT surfaces, respectively. Subsets of 10 cows per herd with locomotion scores of 1 to 3 were observed via video cameras for 24-h periods. Cows in MAT herds spent more time standing in free stalls per day than cows in SAND herds. Differences in standing times were 0.73 h/d for cows that were not lame, 2.32 h/d for cows that were slightly lame, and 4.31 h/d for cows that were moderately lame in MAT herds compared with equivalent cows in SAND herds. In MAT herds, the increase in time spent standing in the stall in moderately lame cows was associated with a significant reduction in stall use sessions per day, which impacted daily lying time. Although cause and effect are not clear, these findings have implications for housing, comfort, and care of cows in dairy herds with different types of free stall surfaces.

  20. Band-pass filtering algorithms for adaptive control of compressor pre-stall modes in aircraft gas-turbine engine

    Science.gov (United States)

    Kuznetsova, T. A.

    2018-05-01

    The methods for increasing gas-turbine aircraft engines' (GTE) adaptive properties to interference based on empowerment of automatic control systems (ACS) are analyzed. The flow pulsation in suction and a discharge line of the compressor, which may cause the stall, are considered as the interference. The algorithmic solution to the problem of GTE pre-stall modes’ control adapted to stability boundary is proposed. The aim of the study is to develop the band-pass filtering algorithms to provide the detection functions of the compressor pre-stall modes for ACS GTE. The characteristic feature of pre-stall effect is the increase of pressure pulsation amplitude over the impeller at the multiples of the rotor’ frequencies. The used method is based on a band-pass filter combining low-pass and high-pass digital filters. The impulse response of the high-pass filter is determined through a known low-pass filter impulse response by spectral inversion. The resulting transfer function of the second order band-pass filter (BPF) corresponds to a stable system. The two circuit implementations of BPF are synthesized. Designed band-pass filtering algorithms were tested in MATLAB environment. Comparative analysis of amplitude-frequency response of proposed implementation allows choosing the BPF scheme providing the best quality of filtration. The BPF reaction to the periodic sinusoidal signal, simulating the experimentally obtained pressure pulsation function in the pre-stall mode, was considered. The results of model experiment demonstrated the effectiveness of applying band-pass filtering algorithms as part of ACS to identify the pre-stall mode of the compressor for detection of pressure fluctuations’ peaks, characterizing the compressor’s approach to the stability boundary.

  1. SV40 utilizes ATM kinase activity to prevent non-homologous end joining of broken viral DNA replication products.

    Directory of Open Access Journals (Sweden)

    Gregory A Sowd

    2014-12-01

    Full Text Available Simian virus 40 (SV40 and cellular DNA replication rely on host ATM and ATR DNA damage signaling kinases to facilitate DNA repair and elicit cell cycle arrest following DNA damage. During SV40 DNA replication, ATM kinase activity prevents concatemerization of the viral genome whereas ATR activity prevents accumulation of aberrant genomes resulting from breakage of a moving replication fork as it converges with a stalled fork. However, the repair pathways that ATM and ATR orchestrate to prevent these aberrant SV40 DNA replication products are unclear. Using two-dimensional gel electrophoresis and Southern blotting, we show that ATR kinase activity, but not DNA-PK(cs kinase activity, facilitates some aspects of double strand break (DSB repair when ATM is inhibited during SV40 infection. To clarify which repair factors associate with viral DNA replication centers, we examined the localization of DSB repair proteins in response to SV40 infection. Under normal conditions, viral replication centers exclusively associate with homology-directed repair (HDR and do not colocalize with non-homologous end joining (NHEJ factors. Following ATM inhibition, but not ATR inhibition, activated DNA-PK(cs and KU70/80 accumulate at the viral replication centers while CtIP and BLM, proteins that initiate 5' to 3' end resection during HDR, become undetectable. Similar to what has been observed during cellular DSB repair in S phase, these data suggest that ATM kinase influences DSB repair pathway choice by preventing the recruitment of NHEJ factors to replicating viral DNA. These data may explain how ATM prevents concatemerization of the viral genome and promotes viral propagation. We suggest that inhibitors of DNA damage signaling and DNA repair could be used during infection to disrupt productive viral DNA replication.

  2. SV40 Utilizes ATM Kinase Activity to Prevent Non-homologous End Joining of Broken Viral DNA Replication Products

    Science.gov (United States)

    Sowd, Gregory A.; Mody, Dviti; Eggold, Joshua; Cortez, David; Friedman, Katherine L.; Fanning, Ellen

    2014-01-01

    Simian virus 40 (SV40) and cellular DNA replication rely on host ATM and ATR DNA damage signaling kinases to facilitate DNA repair and elicit cell cycle arrest following DNA damage. During SV40 DNA replication, ATM kinase activity prevents concatemerization of the viral genome whereas ATR activity prevents accumulation of aberrant genomes resulting from breakage of a moving replication fork as it converges with a stalled fork. However, the repair pathways that ATM and ATR orchestrate to prevent these aberrant SV40 DNA replication products are unclear. Using two-dimensional gel electrophoresis and Southern blotting, we show that ATR kinase activity, but not DNA-PKcs kinase activity, facilitates some aspects of double strand break (DSB) repair when ATM is inhibited during SV40 infection. To clarify which repair factors associate with viral DNA replication centers, we examined the localization of DSB repair proteins in response to SV40 infection. Under normal conditions, viral replication centers exclusively associate with homology-directed repair (HDR) and do not colocalize with non-homologous end joining (NHEJ) factors. Following ATM inhibition, but not ATR inhibition, activated DNA-PKcs and KU70/80 accumulate at the viral replication centers while CtIP and BLM, proteins that initiate 5′ to 3′ end resection during HDR, become undetectable. Similar to what has been observed during cellular DSB repair in S phase, these data suggest that ATM kinase influences DSB repair pathway choice by preventing the recruitment of NHEJ factors to replicating viral DNA. These data may explain how ATM prevents concatemerization of the viral genome and promotes viral propagation. We suggest that inhibitors of DNA damage signaling and DNA repair could be used during infection to disrupt productive viral DNA replication. PMID:25474690

  3. 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.

  4. Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication.

    Science.gov (United States)

    Bj Rås, Karine Ø; Sousa, Mirta M L; Sharma, Animesh; Fonseca, Davi M; S Gaard, Caroline K; Bj Rås, Magnar; Otterlei, Marit

    2017-08-21

    Base lesions in DNA can stall the replication machinery or induce mutations if bypassed. Consequently, lesions must be repaired before replication or in a post-replicative process to maintain genomic stability. Base excision repair (BER) is the main pathway for repair of base lesions and is known to be associated with DNA replication, but how BER is organized during replication is unclear. Here we coupled the iPOND (isolation of proteins on nascent DNA) technique with targeted mass-spectrometry analysis, which enabled us to detect all proteins required for BER on nascent DNA and to monitor their spatiotemporal orchestration at replication forks. We demonstrate that XRCC1 and other BER/single-strand break repair (SSBR) proteins are enriched in replisomes in unstressed cells, supporting a cellular capacity of post-replicative BER/SSBR. Importantly, we identify for the first time the DNA glycosylases MYH, UNG2, MPG, NTH1, NEIL1, 2 and 3 on nascent DNA. Our findings suggest that a broad spectrum of DNA base lesions are recognized and repaired by BER in a post-replicative process. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Ethnic Dimensions of Guatemala's Stalled Transition: A Parity-Specific Analysis of Ladino and Indigenous Fertility Regimes.

    Science.gov (United States)

    Grace, Kathryn; Sweeney, Stuart

    2016-02-01

    In some contemporary populations, fertility levels appear to plateau, with women maintaining a consistently high level of fertility for a relatively extended period. Because this plateau does not reflect the historical patterns observed in Europe, the focus of most studies on fertility patterns, mechanisms underlying the plateau and the reinstatement of a decline have not been fully explored and are not fully understood. Through the construction of fertility histories of 25,000 women using multiple years of health survey data, we analyze some of the components of stalled fertility as they pertain to Guatemala, the only Central American country to have experienced a stalled fertility decline.

  6. Biomarkers of replicative senescence revisited

    DEFF Research Database (Denmark)

    Nehlin, Jan

    2016-01-01

    Biomarkers of replicative senescence can be defined as those ultrastructural and physiological variations as well as molecules whose changes in expression, activity or function correlate with aging, as a result of the gradual exhaustion of replicative potential and a state of permanent cell cycle...... arrest. The biomarkers that characterize the path to an irreversible state of cell cycle arrest due to proliferative exhaustion may also be shared by other forms of senescence-inducing mechanisms. Validation of senescence markers is crucial in circumstances where quiescence or temporary growth arrest may...... be triggered or is thought to be induced. Pre-senescence biomarkers are also important to consider as their presence indicate that induction of aging processes is taking place. The bona fide pathway leading to replicative senescence that has been extensively characterized is a consequence of gradual reduction...

  7. Regulation of beta cell replication

    DEFF Research Database (Denmark)

    Lee, Ying C; Nielsen, Jens Høiriis

    2008-01-01

    Beta cell mass, at any given time, is governed by cell differentiation, neogenesis, increased or decreased cell size (cell hypertrophy or atrophy), cell death (apoptosis), and beta cell proliferation. Nutrients, hormones and growth factors coupled with their signalling intermediates have been...... suggested to play a role in beta cell mass regulation. In addition, genetic mouse model studies have indicated that cyclins and cyclin-dependent kinases that determine cell cycle progression are involved in beta cell replication, and more recently, menin in association with cyclin-dependent kinase...... inhibitors has been demonstrated to be important in beta cell growth. In this review, we consider and highlight some aspects of cell cycle regulation in relation to beta cell replication. The role of cell cycle regulation in beta cell replication is mostly from studies in rodent models, but whether...

  8. Personality and Academic Motivation: Replication, Extension, and Replication

    Science.gov (United States)

    Jones, Martin H.; McMichael, Stephanie N.

    2015-01-01

    Previous work examines the relationships between personality traits and intrinsic/extrinsic motivation. We replicate and extend previous work to examine how personality may relate to achievement goals, efficacious beliefs, and mindset about intelligence. Approximately 200 undergraduates responded to the survey with a 150 participants replicating…

  9. 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-.

  10. Chameleon Chasing II: A Replication.

    Science.gov (United States)

    Newsom, Doug A.; And Others

    1993-01-01

    Replicates a 1972 survey of students, educators, and Public Relations Society of America members regarding who the public relations counselor really serves. Finds that, in 1992, most respondents thought primary responsibility was to the client, then to the client's relevant publics, then to self, then to society, and finally to media. Compares…

  11. Hyperthermia stimulates HIV-1 replication.

    Directory of Open Access Journals (Sweden)

    Ferdinand Roesch

    Full Text Available HIV-infected individuals may experience fever episodes. Fever is an elevation of the body temperature accompanied by inflammation. It is usually beneficial for the host through enhancement of immunological defenses. In cultures, transient non-physiological heat shock (42-45°C and Heat Shock Proteins (HSPs modulate HIV-1 replication, through poorly defined mechanisms. The effect of physiological hyperthermia (38-40°C on HIV-1 infection has not been extensively investigated. Here, we show that culturing primary CD4+ T lymphocytes and cell lines at a fever-like temperature (39.5°C increased the efficiency of HIV-1 replication by 2 to 7 fold. Hyperthermia did not facilitate viral entry nor reverse transcription, but increased Tat transactivation of the LTR viral promoter. Hyperthermia also boosted HIV-1 reactivation in a model of latently-infected cells. By imaging HIV-1 transcription, we further show that Hsp90 co-localized with actively transcribing provirus, and this phenomenon was enhanced at 39.5°C. The Hsp90 inhibitor 17-AAG abrogated the increase of HIV-1 replication in hyperthermic cells. Altogether, our results indicate that fever may directly stimulate HIV-1 replication, in a process involving Hsp90 and facilitation of Tat-mediated LTR activity.

  12. Adressing Replication and Model Uncertainty

    DEFF Research Database (Denmark)

    Ebersberger, Bernd; Galia, Fabrice; Laursen, Keld

    innovation survey data for France, Germany and the UK, we conduct a ‘large-scale’ replication using the Bayesian averaging approach of classical estimators. Our method tests a wide range of determinants of innovation suggested in the prior literature, and establishes a robust set of findings on the variables...

  13. Human ribonuclease H1 resolves R-loops and thereby enables progression of the DNA replication fork.

    Science.gov (United States)

    Parajuli, Shankar; Teasley, Daniel C; Murali, Bhavna; Jackson, Jessica; Vindigni, Alessandro; Stewart, Sheila A

    2017-09-15

    Faithful DNA replication is essential for genome stability. To ensure accurate replication, numerous complex and redundant replication and repair mechanisms function in tandem with the core replication proteins to ensure DNA replication continues even when replication challenges are present that could impede progression of the replication fork. A unique topological challenge to the replication machinery is posed by RNA-DNA hybrids, commonly referred to as R-loops. Although R-loops play important roles in gene expression and recombination at immunoglobulin sites, their persistence is thought to interfere with DNA replication by slowing or impeding replication fork progression. Therefore, it is of interest to identify DNA-associated enzymes that help resolve replication-impeding R-loops. Here, using DNA fiber analysis, we demonstrate that human ribonuclease H1 (RNH1) plays an important role in replication fork movement in the mammalian nucleus by resolving R-loops. We found that RNH1 depletion results in accumulation of RNA-DNA hybrids, slowing of replication forks, and increased DNA damage. Our data uncovered a role for RNH1 in global DNA replication in the mammalian nucleus. Because accumulation of RNA-DNA hybrids is linked to various human cancers and neurodegenerative disorders, our study raises the possibility that replication fork progression might be impeded, adding to increased genomic instability and contributing to disease. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Identification of Thrust, Lift, and Drag for Deep-stall Flight Data of a Fixed-wing Unmanned Aircraft

    DEFF Research Database (Denmark)

    Cunis, Torbjørn; Leth, Tobias; Totu, Luminita Cristiana

    2018-01-01

    In this paper, we consider a small unmanned aircraft and data collected during regular and deep-stall flight. We present an identification method for the thrust force generated by the propulsion system based on the in-flight measurements where we make use of the well-known linear and quadratic...... force estimation in the full flight envelope....

  15. Unsteady behavior of leading-edge vortex and diffuser stall in a centrifugal compressor with vaned diffuser

    Science.gov (United States)

    Fujisawa, Nobumichi; Hara, Shotaro; Ohta, Yutaka

    2016-02-01

    The characteristics of a rotating stall of an impeller and diffuser and the evolution of a vortex generated at the diffuser leading-edge (i.e., the leading-edge vortex (LEV)) in a centrifugal compressor were investigated by experiments and numerical analysis. The results of the experiments revealed that both the impeller and diffuser rotating stalls occurred at 55 and 25 Hz during off-design flow operation. For both, stall cells existed only on the shroud side of the flow passages, which is very close to the source location of the LEV. According to the CFD results, the LEV is made up of multiple vortices. The LEV is a combination of a separated vortex near the leading- edge and a longitudinal vortex generated by the extended tip-leakage flow from the impeller. Therefore, the LEV is generated by the accumulation of vorticity caused by the velocity gradient of the impeller discharge flow. In partial-flow operation, the spanwise extent and the position of the LEV origin are temporarily transmuted. The LEV develops with a drop in the velocity in the diffuser passage and forms a significant blockage within the diffuser passage. Therefore, the LEV may be regarded as being one of the causes of a diffuser stall in a centrifugal compressor.

  16. Self-induced vibrations of a DU96-W-180 airfoil in stall

    DEFF Research Database (Denmark)

    Skrzypinski, Witold Robert; Gaunaa, Mac; Sørensen, Niels N.

    2014-01-01

    This work presents an analysis of two-dimensional (2D) and three-dimensional (3D) non-moving, prescribed motion and elastically mounted airfoil computational fluid dynamics (CFD) computations. The elastically mounted airfoil computations were performed by means of a 2D structural model with two...... degrees of freedom. The computations aimed at investigating the mechanisms of both vortex-induced and stall-induced vibrations related to a wind turbine blade at standstill conditions. In this work, a DU96-W-180 airfoil was used in the angle-of-attack region potentially corresponding to stallinduced...... vibrations. The analysis showed significant differences between the aerodynamic stability limits predicted by 2D and 3D CFD computations. A general agreement was reached between the prescribed motion and elastically mounted airfoil computations. 3D computations indicated that vortex-induced vibrations...

  17. Spins, Stalls, and Shutdowns: Pitfalls of Qualitative Policing and Security Research

    Directory of Open Access Journals (Sweden)

    Randy K. Lippert

    2015-11-01

    Full Text Available This article explores key elements of qualitative research on policing and security agencies, including barriers encountered and strategies to prevent them. While it is oft-assumed that policing/security agencies are difficult to access due to their clandestine or bureaucratic nature, this article demonstrates this is not necessarily the case, as access was gained for three distinct qualitative research projects. Yet, access and subsequent research were not without pitfalls, which we term security spins, security stalls, and security shutdowns. We illustrate how each was encountered and argue these pitfalls are akin to researchers falling into risk categories, not unlike those used by policing/security agents in their work. Before concluding we discuss methodological strategies for scholars to avoid these pitfalls and to advance research that critically interrogates the immense policing/security realm. URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs1601108

  18. Study of Near-Stall Flow Behavior in a Modern Transonic Fan with Composite Sweep

    Science.gov (United States)

    Hah, Chunill; Shin, Hyoun-Woo

    2011-01-01

    Detailed flow behavior in a modern transonic fan with a composite sweep is investigated in this paper. Both unsteady Reynolds-averaged Navier-Stokes (URANS) and Large Eddy Simulation (LES) methods are applied to investigate the flow field over a wide operating range. The calculated flow fields are compared with the data from an array of high-frequency response pressure transducers embedded in the fan casing. The current study shows that a relatively fine computational grid is required to resolve the flow field adequately and to calculate the pressure rise across the fan correctly. The calculated flow field shows detailed flow structure near the fan rotor tip region. Due to the introduction of composite sweep toward the rotor tip, the flow structure at the rotor tip is much more stable compared to that of the conventional blade design. The passage shock stays very close to the leading edge at the rotor tip even at the throttle limit. On the other hand, the passage shock becomes stronger and detaches earlier from the blade passage at the radius where the blade sweep is in the opposite direction. The interaction between the tip clearance vortex and the passage shock becomes intense as the fan operates toward the stall limit, and tip clearance vortex breakdown occurs at near-stall operation. URANS calculates the time-averaged flow field fairly well. Details of measured RMS static pressure are not calculated with sufficient accuracy with URANS. On the other hand, LES calculates details of the measured unsteady flow features in the current transonic fan with composite sweep fairly well and reveals the flow mechanism behind the measured unsteady flow field.

  19. Reducing Respiratory Health Risks to Horses and Workers: A Comparison of Two Stall Bedding Materials

    Directory of Open Access Journals (Sweden)

    Markku Saastamoinen

    2015-10-01

    Full Text Available Stable air quality and the choice of bedding material are an important health issue both in horses and people working or visiting horse stables. Risks of impaired respiratory health are those that can especially be avoided by improving air quality in the stable. The choice of bedding material is particularly important in cold climate conditions; where horses are kept most of the day and year indoors throughout their life. This study examined the effect of two bedding materials; wood shavings and peat; on stable air quality and health of horses. Ammonia and dust levels were also measured to assess conditions in the stable. Ammonia was not detected or was at very low levels (<0.25 ppm in the boxes in which peat was used as bedding; but its concentration was clearly higher (1.5–7.0 ppm in stalls with wood shavings as bedding. Personal measurements of workers revealed quite high ammonia exposure (5.9 ppm8h in the boxes in which wood shavings were used; but no exposure was Animals 2015, 5 966 observed in stalls bedded with peat. The respiratory symptoms in horses increased regardless of the bedding material at the beginning of the study. The health status of the horses in the peat bedding group returned to the initial level in the end of the trial but horses bedded with wood shavings continued to be symptomatic. The hooves of the horses with peat bedding had a better moisture content than those of the horses bedded with wood shavings. The results suggest that peat is a better bedding material for horses than wood shavings regarding the health of both horses and stable workers.

  20. Low-Order Modeling of Dynamic Stall on Airfoils in Incompressible Flow

    Science.gov (United States)

    Narsipur, Shreyas

    Unsteady aerodynamics has been a topic of research since the late 1930's and has increased in popularity among researchers studying dynamic stall in helicopters, insect/bird flight, micro air vehicles, wind-turbine aerodynamics, and ow-energy harvesting devices. Several experimental and computational studies have helped researchers gain a good understanding of the unsteady ow phenomena, but have proved to be expensive and time-intensive for rapid design and analysis purposes. Since the early 1970's, the push to develop low-order models to solve unsteady ow problems has resulted in several semi-empirical models capable of effectively analyzing unsteady aerodynamics in a fraction of the time required by high-order methods. However, due to the various complexities associated with time-dependent flows, several empirical constants and curve fits derived from existing experimental and computational results are required by the semi-empirical models to be an effective analysis tool. The aim of the current work is to develop a low-order model capable of simulating incompressible dynamic-stall type ow problems with a focus on accurately modeling the unsteady ow physics with the aim of reducing empirical dependencies. The lumped-vortex-element (LVE) algorithm is used as the baseline unsteady inviscid model to which augmentations are applied to model unsteady viscous effects. The current research is divided into two phases. The first phase focused on augmentations aimed at modeling pure unsteady trailing-edge boundary-layer separation and stall without leading-edge vortex (LEV) formation. The second phase is targeted at including LEV shedding capabilities to the LVE algorithm and combining with the trailing-edge separation model from phase one to realize a holistic, optimized, and robust low-order dynamic stall model. In phase one, initial augmentations to theory were focused on modeling the effects of steady trailing-edge separation by implementing a non-linear decambering

  1. Effect of stall design on dairy calf transition to voluntary feeding on an automatic milk feeder after introduction to group housing.

    Science.gov (United States)

    Wilson, Tanya R; LeBlanc, Stephen J; DeVries, Trevor J; Haley, Derek B

    2018-06-01

    Automatic milk feeders (AMF) for young dairy calves are widely used in the dairy industry. These feeders are thought to have benefits for calf health and welfare and may reduce labor required for feeding; however, little is known about how calves adapt to feeding with AMF. The objective of this study was to observe the effects of feeding stall design on calves learning to use the AMF. The hypothesis was that solid side stalls, compared with steel bar stalls, would result in a longer latency to approach and feed from the AMF without assistance. A total of 147 Holstein calves (80 male and 67 female) were enrolled at 4 d of age, introduced to a group pen, and, at the same time, trained on an AMF. For training, calves were allowed to suck on the trainer's fingers and guided to the teat. Calves were allocated to 1 of 2 stall designs at the pen level, depending on which treatment cohort they were born into, either with steel bar stall walls (n = 46 male, 34 female calves) or with solid side stall walls (n = 34 male, 33 female calves). For 72 h after introductory training on the AMF, data from the feeders were collected and calf behavior was monitored by video. Outcomes measured included latency to first voluntary visit to the feeder and to first feeding, time spent in the feeder, amount of milk consumed over 72 h, number of retraining sessions required (retrained if linear regression models or a Poisson model for the outcome of retraining. For certain outcomes the effects of stall design interacted with difficulty of training (willingness to enter feeder and drink); for the 38% of calves that were scored as moderately difficult to train on a scale of easy, moderate, or difficult, treatment (stall design) differences were detected. These calves took 2× longer to lick or bite toward the nipple, 2× longer to first voluntarily feeding, and consumed less milk over 72 h following training when trained on the steel bar stall design. These results suggest simple features of a

  2. Power and precision of replicated helicopter surveys in mixed bushveld

    Directory of Open Access Journals (Sweden)

    B.K. Reilly

    1998-07-01

    Full Text Available It is well known that aerial game counts in South Africa are often applied in a non-standardised, unreplicated fashion. They contribute to poor management decisions based on their results as they may be subject to large statistical Type I and II errors. Replicate counts of large herbivores were conducted in a 8 500 ha sample site in the Loskop Dam Nature Reserve in July 1991. These data were used to estimate precision of the counts and estimate statistical power to detect population changes for different combinations of replications and significance levels.

  3. 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

  4. Data Service: Distributed Data Capture and Replication

    Science.gov (United States)

    Warner, P. B.; Pietrowicz, S. R.

    2007-10-01

    Data Service is a critical component of the NOAO Data Management and Science Support (DMaSS) Solutions Platform, which is based on a service-oriented architecture, and is to replace the current NOAO Data Transport System. Its responsibilities include capturing data from NOAO and partner telescopes and instruments and replicating the data across multiple (currently six) storage sites. Java 5 was chosen as the implementation language, and Java EE as the underlying enterprise framework. Application metadata persistence is performed using EJB and Hibernate on the JBoss Application Server, with PostgreSQL as the persistence back-end. Although potentially any underlying mass storage system may be used as the Data Service file persistence technology, DTS deployments and Data Service test deployments currently use the Storage Resource Broker from SDSC. This paper presents an overview and high-level design of the Data Service, including aspects of deployment, e.g., for the LSST Data Challenge at the NCSA computing facilities.

  5. Security in a Replicated Metadata Catalogue

    CERN Document Server

    Koblitz, B

    2007-01-01

    The gLite-AMGA metadata has been developed by NA4 to provide simple relational metadata access for the EGEE user community. As advanced features, which will be the focus of this presentation, AMGA provides very fine-grained security also in connection with the built-in support for replication and federation of metadata. AMGA is extensively used by the biomedical community to store medical images metadata, digital libraries, in HEP for logging and bookkeeping data and in the climate community. The biomedical community intends to deploy a distributed metadata system for medical images consisting of various sites, which range from hospitals to computing centres. Only safe sharing of the highly sensitive metadata as provided in AMGA makes such a scenario possible. Other scenarios are digital libraries, which federate copyright protected (meta-) data into a common catalogue. The biomedical and digital libraries have been deployed using a centralized structure already for some time. They now intend to decentralize ...

  6. The yeast replicative aging model.

    Science.gov (United States)

    He, Chong; Zhou, Chuankai; Kennedy, Brian K

    2018-03-08

    It has been nearly three decades since the budding yeast Saccharomyces cerevisiae became a significant model organism for aging research and it has emerged as both simple and powerful. The replicative aging assay, which interrogates the number of times a "mother" cell can divide and produce "daughters", has been a stalwart in these studies, and genetic approaches have led to the identification of hundreds of genes impacting lifespan. More recently, cell biological and biochemical approaches have been developed to determine how cellular processes become altered with age. Together, the tools are in place to develop a holistic view of aging in this single-celled organism. Here, we summarize the current state of understanding of yeast replicative aging with a focus on the recent studies that shed new light on how aging pathways interact to modulate lifespan in yeast. Copyright © 2018. Published by Elsevier B.V.

  7. Replicator dynamics in value chains

    DEFF Research Database (Denmark)

    Cantner, Uwe; Savin, Ivan; Vannuccini, Simone

    2016-01-01

    The pure model of replicator dynamics though providing important insights in the evolution of markets has not found much of empirical support. This paper extends the model to the case of firms vertically integrated in value chains. We show that i) by taking value chains into account, the replicator...... dynamics may revert its effect. In these regressive developments of market selection, firms with low fitness expand because of being integrated with highly fit partners, and the other way around; ii) allowing partner's switching within a value chain illustrates that periods of instability in the early...... stage of industry life-cycle may be the result of an 'optimization' of partners within a value chain providing a novel and simple explanation to the evidence discussed by Mazzucato (1998); iii) there are distinct differences in the contribution to market selection between the layers of a value chain...

  8. Replication confers β cell immaturity.

    Science.gov (United States)

    Puri, Sapna; Roy, Nilotpal; Russ, Holger A; Leonhardt, Laura; French, Esra K; Roy, Ritu; Bengtsson, Henrik; Scott, Donald K; Stewart, Andrew F; Hebrok, Matthias

    2018-02-02

    Pancreatic β cells are highly specialized to regulate systemic glucose levels by secreting insulin. In adults, increase in β-cell mass is limited due to brakes on cell replication. In contrast, proliferation is robust in neonatal β cells that are functionally immature as defined by a lower set point for glucose-stimulated insulin secretion. Here we show that β-cell proliferation and immaturity are linked by tuning expression of physiologically relevant, non-oncogenic levels of c-Myc. Adult β cells induced to replicate adopt gene expression and metabolic profiles resembling those of immature neonatal β that proliferate readily. We directly demonstrate that priming insulin-producing cells to enter the cell cycle promotes a functionally immature phenotype. We suggest that there exists a balance between mature functionality and the ability to expand, as the phenotypic state of the β cell reverts to a less functional one in response to proliferative cues.

  9. Chromatin replication and histone dynamics

    DEFF Research Database (Denmark)

    Alabert, Constance; Jasencakova, Zuzana; Groth, Anja

    2017-01-01

    Inheritance of the DNA sequence and its proper organization into chromatin is fundamental for genome stability and function. Therefore, how specific chromatin structures are restored on newly synthesized DNA and transmitted through cell division remains a central question to understand cell fate...... choices and self-renewal. Propagation of genetic information and chromatin-based information in cycling cells entails genome-wide disruption and restoration of chromatin, coupled with faithful replication of DNA. In this chapter, we describe how cells duplicate the genome while maintaining its proper...... organization into chromatin. We reveal how specialized replication-coupled mechanisms rapidly assemble newly synthesized DNA into nucleosomes, while the complete restoration of chromatin organization including histone marks is a continuous process taking place throughout the cell cycle. Because failure...

  10. Indoor and outdoor concentrations of RSP, NO2 and selected volatile organic compounds at 32 shoe stalls located near busy roadways in Seoul, Korea

    International Nuclear Information System (INIS)

    Bae, Hyunjoo; Chung, Moonho; Yang, Wonho

    2004-01-01

    It is suspected that persons who work in indoor environments near busy roadways are exposed to elevated levels of air pollutants during working hours. This study evaluated the potential exposure and source contribution associated with traffic-related air pollution for workers (polishers and repairmen) in shoe stalls from each of 32 districts during working hours in Seoul, Korea. The shoe stalls have been located at very close distances to the busy roadways. In this study, shoe stall workers could be exposed to high levels of respirable suspended particulate (RSP), nitrogen dioxide (NO 2 ) and volatile organic compounds (VOCs) from outdoor sources such as traffic exhaust, as well as indoor sources in the shoe stalls such as dust on the shoes, portable gas ranges, organic solvents, adhesives and shoe polish. Compounds of particular note included indoor mean concentrations of benzene, toluene, m/p-xylene and o-xylene were 0.732, 6.777, 4.080 and 1.302 mg/m 3 , respectively, in all shoe stalls. Mean indoor/outdoor ratios for toluene and m/p-xylene concentrations were 54.52 and 20.84, respectively. The contribution of vehicle exhaust emissions to indoor air quality of shoe stalls was identified by means of correlating the relationships between simultaneously measured air pollutant concentrations indoors and outdoors. Unlike RSP and NO 2 , indoor VOCs concentrations of shoe stalls mainly originated from indoor sources vs. outdoor sources

  11. Live Replication of Paravirtual Machines

    OpenAIRE

    Stodden, Daniel

    2009-01-01

    Virtual machines offer a fair degree of system state encapsulation, which promotes practical advances in fault tolerance, system debugging, profiling and security applications. This work investigates deterministic replay and semi-active replication for system paravirtualization, a software discipline trading guest kernel binar compatibility for reduced dependency on costly trap-and-emulate techniques. A primary contribution is evidence that trace capturing under a piecewise deterministic exec...

  12. In vitro replication of poliovirus

    International Nuclear Information System (INIS)

    Lubinski, J.M.

    1986-01-01

    Poliovirus is a member of the Picornaviridae whose genome is a single stranded RNA molecule of positive polarity surrounded by a proteinaceous capsid. Replication of poliovirus occurs via negative strand intermediates in infected cells using a virally encoded RNA-dependent RNA polymerase and host cell proteins. The authors have exploited the fact that complete cDNA copies of the viral genome when transfected onto susceptible cells generate virus. Utilizing the bacteriophage SP6 DNA dependent RNA polymerase system to synthesize negative strands in vitro and using these in an in vitro reaction the authors have generated full length infectious plus strands. Mutagenesis of the 5' and 3' ends of the negative and positive strands demonstrated that replication could occur either de novo or be extensions of the templates from their 3' ends or from nicks occurring during replication. The appearance of dimeric RNA molecules generated in these reactions was not dependent upon the same protein required for de novo initiation. Full length dimeric RNA molecules using a 5' 32 P end-labelled oligo uridylic acid primer and positive strand template were demonstrated in vitro containing only the 35,000 Mr host protein and the viral RNA-dependent RNA polymerase. A model for generating positive strands without protein priming by cleavage of dimeric RNA molecules was proposed

  13. Flow Observations with Tufts and Lampblack of the Stalling of Four Typical Airfoil Sections in the NACA Variable-density Tunnel

    Science.gov (United States)

    Abbott, Ira H; Sherman, Albert

    1938-01-01

    A preliminary investigation of the stalling processes of four typical airfoil sections was made over the critical range of the Reynolds Number. Motion pictures were taken of the movements of small silk tufts on the airfoil surface as the angle of attack increased through a range of angles including the stall. The boundary-layer flow also at certain angles of attack was indicated by the patterns formed by a suspension of lampblack in oil brushed onto the airfoil surface. These observations were analyzed together with corresponding force-test measurements to derive a picture of the stalling processes of airfoils.

  14. Replication of micro and nano surface geometries

    DEFF Research Database (Denmark)

    Hansen, Hans Nørgaard; Hocken, R.J.; Tosello, Guido

    2011-01-01

    The paper describes the state-of-the-art in replication of surface texture and topography at micro and nano scale. The description includes replication of surfaces in polymers, metals and glass. Three different main technological areas enabled by surface replication processes are presented......: manufacture of net-shape micro/nano surfaces, tooling (i.e. master making), and surface quality control (metrology, inspection). Replication processes and methods as well as the metrology of surfaces to determine the degree of replication are presented and classified. Examples from various application areas...... are given including replication for surface texture measurements, surface roughness standards, manufacture of micro and nano structured functional surfaces, replicated surfaces for optical applications (e.g. optical gratings), and process chains based on combinations of repeated surface replication steps....

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

    Directory of Open Access Journals (Sweden)

    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.

  16. USP7 is a SUMO deubiquitinase essential for DNA replication

    Science.gov (United States)

    Lecona, Emilio; Rodriguez-Acebes, Sara; Specks, Julia; Lopez-Contreras, Andres J; Ruppen, Isabel; Murga, Matilde; Muñoz, Javier; Mendez, Juan; Fernandez-Capetillo, Oscar

    2016-01-01

    Post-translational modification of proteins by ubiquitin (Ub) and Ub-like modifiers regulates various aspects of DNA replication. We previously showed that the chromatin around replisomes is rich in SUMO and depleted in Ub, whereas an opposite pattern is observed in mature chromatin. How this SUMO-rich/Ub-low environment is maintained at sites of DNA replication is not known. Here we identify USP7 as a replisome-enriched SUMO deubiquitinase that is essential for DNA replication. By acting on SUMO and SUMOylated proteins, USP7 counteracts their ubiquitination. Chemical inhibition or genetic deletion of USP7 leads to the accumulation of Ub on SUMOylated proteins, which are displaced to chromatin away from replisomes. Our findings provide a model to explain the differential accumulation of SUMO and Ub at replication forks, and identify an essential role of USP7 in DNA replication that should be taken into account for the use of USP7 inhibitors as anticancer agents. PMID:26950370

  17. 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

  18. 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.

  19. 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...

  20. Parametrised Constants and Replication for Spatial Mobility

    DEFF Research Database (Denmark)

    Hüttel, Hans; Haagensen, Bjørn

    2009-01-01

    Parametrised replication and replication are common ways of expressing infinite computation in process calculi. While parametrised constants can be encoded using replication in the π-calculus, this changes in the presence of spatial mobility as found in e.g. the distributed π- calculus...... of the distributed π-calculus with parametrised constants and replication are incomparable. On the other hand, we shall see that there exists a simple encoding of recursion in mobile ambients....

  1. Broken silence restored-remodeling primes for deacetylation at replication forks

    DEFF Research Database (Denmark)

    Jasencakova, Zuzana; Groth, Anja

    2011-01-01

    Faithful propagation of chromatin structures requires assimilation of new histones to the modification profile of individual loci. In this issue of Molecular Cell, Rowbotham and colleagues identify a remodeler, SMARCAD1, acting at replication sites to facilitate histone deacetylation and restorat......Faithful propagation of chromatin structures requires assimilation of new histones to the modification profile of individual loci. In this issue of Molecular Cell, Rowbotham and colleagues identify a remodeler, SMARCAD1, acting at replication sites to facilitate histone deacetylation...

  2. 36 CFR 910.64 - Replication.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Replication. 910.64 Section 910.64 Parks, Forests, and Public Property PENNSYLVANIA AVENUE DEVELOPMENT CORPORATION GENERAL... DEVELOPMENT AREA Glossary of Terms § 910.64 Replication. Replication means the process of using modern methods...

  3. Variance Swap Replication: Discrete or Continuous?

    Directory of Open Access Journals (Sweden)

    Fabien Le Floc’h

    2018-02-01

    Full Text Available The popular replication formula to price variance swaps assumes continuity of traded option strikes. In practice, however, there is only a discrete set of option strikes traded on the market. We present here different discrete replication strategies and explain why the continuous replication price is more relevant.

  4. 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.

  5. 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.

  6. Physical interaction between replication protein A (RPA) and MRN: involvement of RPA2 phosphorylation and the N-terminus of RPA1.

    Science.gov (United States)

    Oakley, Greg G; Tillison, Kristin; Opiyo, Stephen A; Glanzer, Jason G; Horn, Jeffrey M; Patrick, Steve M

    2009-08-11

    Replication protein A (RPA) is a heterotrimeric protein consisting of RPA1, RPA2, and RPA3 subunits that binds to single-stranded DNA (ssDNA) with high affinity. The response to replication stress requires the recruitment of RPA and the MRE11-RAD50-NBS1 (MRN) complex. RPA bound to ssDNA stabilizes stalled replication forks by recruiting checkpoint proteins involved in fork stabilization. MRN can bind DNA structures encountered at stalled or collapsed replication forks, such as ssDNA-double-stranded DNA (dsDNA) junctions or breaks, and promote the restart of DNA replication. Here, we demonstrate that RPA2 phosphorylation regulates the assembly of DNA damage-induced RPA and MRN foci. Using purified proteins, we observe a direct interaction between RPA with both NBS1 and MRE11. By utilizing RPA bound to ssDNA, we demonstrate that substituting RPA with phosphorylated RPA or a phosphomimetic weakens the interaction with the MRN complex. Also, the N-terminus of RPA1 is a critical component of the RPA-MRN protein-protein interaction. Deletion of the N-terminal oligonucleotide-oligosaccharide binding fold (OB-fold) of RPA1 abrogates interactions of RPA with MRN and individual proteins of the MRN complex. Further identification of residues critical for MRN binding in the N-terminus of RPA1 shows that substitution of Arg31 and Arg41 with alanines disrupts the RPA-MRN interaction and alters cell cycle progression in response to DNA damage. Thus, the N-terminus of RPA1 and phosphorylation of RPA2 regulate RPA-MRN interactions and are important in the response to DNA damage.

  7. Associations of soft flooring materials in free stalls with milk yield, clinical mastitis, teat lesions, and removal of dairy cows.

    Science.gov (United States)

    Ruud, L E; Bøe, K E; Osterås, O

    2010-04-01

    The objective was to test if there was an association between free-stall base softness and milk yield, incidence of clinical mastitis (CM), teat lesions, and removal of cows. In a questionnaire sent to 1,923 dairy farms presumed to be using free-stall housing, farmers were asked for information regarding housing and stall base; for example, the year of installation and the product name or brand of their mats or mattresses. This information was merged with data for milk yield, CM, teat lesions, and removal of cows extracted from the Norwegian Dairy Herd Recording System for the years after installation of mats or mattresses. After exclusion of invalid contributions, the data set consisted of 29,326 lactations for milk yield distributed over 363 free-stalled herds in Norway. The farms were stratified into 5 categories according to the softness of the stall surface measured as millimeter impact of a sphere with a diameter of 120 mm at 2-kN load: 1=concrete, softness of 0mm; 2=rubber, softness of 1 to 8mm; 3=soft mats, softness of 9 to 16 mm; 4=multilayer mats, softness of 17 to 24 mm; and 5=mattresses, softness over 24 mm. Lactation curves were estimated as modified Wood's lactation curves using test-day data and mixed models with repeated measurements, adjusting for days in milk, parity, and softness of free-stall flooring. Herds on concrete free-stall bases yielded 6,727+/-146 kg of milk from 5 to 305 days in milk. In comparison, herds showed a decrease of 0.3% on rubber, an increase of 2.4% on soft mats, an increase of 4.5% on multilayer mats, and an increase of 3.9% on mattresses. Compared with concrete, the hazard ratio (HR) of CM was less on rubber, multilayer mats, and mattresses [HR=0.89 (0.79-0.99), 0.85 (0.73-0.996), and 0.80 (0.73-0.88), respectively]. Compared with concrete, the HR of teat lesions was less on rubber, soft mats, multilayer mats, and mattresses [HR=0.41 (0.26-0.65), 0.33 (0.24-0.44), 0.12 (0.04-0.38), and 0.47 (0.33-0.67), respectively]. The

  8. Visualization and image analysis of dynamic stall phenomenon for a Darrieus wind turbine; Darrieus fusha ni okeru doteki shissoku gensho no kashika to gazo kaisekini kansuru kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    Fujisawa, N.; Shibuya, S.; Takano, T. [Niigata University, Niigata (Japan)

    1999-10-25

    The flow field around a Darrieus wind turbine is studied by flow visualization and PIV measurement in a rotating frame of reference to understand the unsteady nature of dynamic stall appearing at low tip-speed ratios. The qualitative nature of the dynamic stall observed by the flow visualization using dye injection technique is quantitatively reproduced in the instantaneous velocity distributions around the blade measured by PIV technique. These results indicate that two pairs of stall vortices are generated in one cycle of the turbine rotation and they grow in size as the tip-speed ratio decreases. The mechanism of the dynamic stall is found to be due to the flow separation over the suction side of the blade followed by the generation of in-flow motion from the pressure side to the suction side of the blade through the trailing edge. (author)

  9. Chromosomal DNA replication of Vicia faba cells

    International Nuclear Information System (INIS)

    Ikushima, Takaji

    1976-01-01

    The chromosomal DNA replication of higher plant cells has been investigated by DNA fiber autoradiography. The nuclear DNA fibers of Vicia root meristematic cells are organized into many tandem arrays of replication units or replicons which exist as clusters with respect to replication. DNA is replicated bidirectionally from the initiation points at the average rate of 0.15 μm/min at 20 0 C, and the average interinitiation interval is about 16 μm. The manner of chromosomal DNA replication in this higher plant is similar to that found in other eukaryotic cells at a subchromosomal level. (auth.)

  10. Exploring farmers’ seasonal and full year adoption of stall feeding of livestock in Tigrai region, Ethiopia

    Directory of Open Access Journals (Sweden)

    Hadush Muuz

    2017-01-01

    Full Text Available Adoption of stall feeding (SF of livestock was assessed in northern Ethiopia based on a household survey conducted in 2015. The study covered 21 communities in Tigrai to account for differences in agroecology. The purpose of this study was to understand the driving factors of full or seasonal SF adoption and its intensity. A Heckman selection model was used to estimate adoption and extent of adoption based on a model of technology adoption within an agricultural household framework, and Poisson Model for explaining the number of SF adopting seasons. The descriptive results indicate that 36% of the farmers were actually practicing SF in a full year whereas 55.6% were seasonal adopters in the study area. Empirical results of this study showed that our result is in favor of the Boserupian hypothesis indicating that small grazing land and large exclosure are associated with a higher probability of use of SF and with a higher number of SF adopting seasons. In a similar vein, small average village farm size stimulated SF adoption and adopting seasons, Availability of labor and a number of breed cows significantly increased the probability of using SF by 0.01% and 66% respectively. While animal shock had a marginal effect of 14%, factors such as access to information and early exposure increased SF adoption by about 18% and 6%. Similarly, the positive marginal effect of real milk price is 15%. However, SF appears to be less attractive to those farmers with more herd size and less crop residue.

  11. Welfare assessment of dairy cows housed in a tie-stall system

    Directory of Open Access Journals (Sweden)

    Marija Vučemilo

    2012-03-01

    Full Text Available Welfare assessment methods and techniques developed as a result of great interest of scientific and consumer populations regarding the welfare of animals housed in farms. In view of the fact that welfare by definition includes both physical and mental health, the welfare quality assessment includes an extensive number of measures. Welfare assessment was performed in two stables in which cows are kept in tie-stall by using the specific method described in the Welfare Quality® Assessment Protocol for Cattle. The measures included body condition score, qualitative behaviour assessment and body hygiene. The welfare assessment confirmed the importance of quality housing for ensuring better performance from animals, thus also affecting their health and productivity. It also pointed out the necessity of freeing animals by providing them with the possibility of free movement, whereat they can exhibit their physiological behaviour. It is definitely important to continue research, expand the number of researched measures in order to confirm the most useful indicators for welfare assessment and to identify the factors that within the animals’ physical and social environment affect the increase of their welfare.

  12. Flow-around modes for a rhomboid wing with a stall vortex in the shock layer

    Science.gov (United States)

    Zubin, M. A.; Maximov, F. A.; Ostapenko, N. A.

    2017-12-01

    The results of theoretical and experimental investigation of an asymmetrical hypersonic flow around a V-shaped wing with the opening angle larger than π on the modes with attached shockwaves on forward edges, when the stall flow is implemented on the leeward wing cantilever behind the kink point of the cross contour. In this case, a vortex of nonviscous nature is formed in which the velocities on the sphere exceeding the speed of sound and resulting in the occurrence of pressure shocks with an intensity sufficient for the separation of the turbulent boundary layer take place in the reverse flow according to the calculations within the framework of the ideal gas. It is experimentally established that a separation boundary layer can exist in the reverse flow, and its structure is subject to the laws inherent to the reverse flow in the separation region of the turbulent boundary layer arising in the supersonic conic flow under the action of a shockwave incident to the boundary layer.

  13. Fan cooling of the resting area in a free stalls dairy barn

    Science.gov (United States)

    Calegari, Ferdinando; Calamari, Luigi; Frazzi, Ermes

    2014-08-01

    This summer study evaluated the effect of providing additional fans (cooling) in the resting area within a free-stall dairy barn that had fans and sprinklers in the feeding area and paddock availability. Thirty cows were divided into two homogenous groups and kept in two pens: one had the resting area equipped with two fans (FAN) while no fans were added to the other resting area (CON). Microclimatic parameters, rectal temperature (RT), breathing rate (BR), milk yield, and milk pH traits were recorded. Time budgeting and the behaviour of the cows (time spent in the feeding area, standing and lying in other areas) were also recorded using digital video technology. Two slight-to-moderate heat waves were observed. During the hottest period the daily maximum temperature recorded was 33.5 °C and the daily maximum THI was 81.6. During this period, the BR and RT increased only slightly in both groups, with lower BR (n.s.) in FAN compared with CON. Milk yield was better maintained (n.s.) in FAN compared with CON during the hottest period. The FAN cows showed a greater ( P FAN and CON, respectively), whereas CON cows made greater ( P fans in the resting area improves cow comfort, which increases use of the resting area. The lying time results also suggest that the benefits of providing ventilation in the resting area might be more evident in barns where there is no paddock.

  14. Why commercialization of gene therapy stalled; examining the life cycles of gene therapy technologies.

    Science.gov (United States)

    Ledley, F D; McNamee, L M; Uzdil, V; Morgan, I W

    2014-02-01

    This report examines the commercialization of gene therapy in the context of innovation theories that posit a relationship between the maturation of a technology through its life cycle and prospects for successful product development. We show that the field of gene therapy has matured steadily since the 1980s, with the congruent accumulation of >35 000 papers, >16 000 US patents, >1800 clinical trials and >$4.3 billion in capital investment in gene therapy companies. Gene therapy technologies comprise a series of dissimilar approaches for gene delivery, each of which has introduced a distinct product architecture. Using bibliometric methods, we quantify the maturation of each technology through a characteristic life cycle S-curve, from a Nascent stage, through a Growing stage of exponential advance, toward an Established stage and projected limit. Capital investment in gene therapy is shown to have occurred predominantly in Nascent stage technologies and to be negatively correlated with maturity. Gene therapy technologies are now achieving the level of maturity that innovation research and biotechnology experience suggest may be requisite for efficient product development. Asynchrony between the maturation of gene therapy technologies and capital investment in development-focused business models may have stalled the commercialization of gene therapy.

  15. Numerical study of the static and pitching RISOe-B1-18 airfoil[STALL

    Energy Technology Data Exchange (ETDEWEB)

    Bertagnolio, F.

    2004-01-01

    The objective of this report is the better understanding of the physics of the aeroelastic motion of wind turbine blades in order to improve the numerical models used for their design. In this study, the case of the RISOe-B1-18 airfoil which was equipped and measured in an open jet wind tunnel is studied. Two and three dimensional Navier-Stokes calculations using the k-w SST and Detached Eddy Simulation turbulence models are conducted. An engineering semi-empirical dynamic stall model is also used for performing calculations. Computational results are compared to the experimental results that are available both for the static airfoil and in the case of pitching motions. It is shown that the Navier-Stokes simulations can reproduced the main characteristic features of the flow. The DES model seems also to be able to reproduce some details of the unsteady aerodynamics. The Navier-Stokes computations can then be used to improve the performance of the engineering model. (au)

  16. Parametric analyses for synthetic jet control on separation and stall over rotor airfoil

    Directory of Open Access Journals (Sweden)

    Zhao Guoqing

    2014-10-01

    Full Text Available Numerical simulations are performed to investigate the effects of synthetic jet control on separation and stall over rotor airfoils. The preconditioned and unsteady Reynolds-averaged Navier–Stokes equations coupled with a k − ω shear stream transport turbulence model are employed to accomplish the flowfield simulation of rotor airfoils under jet control. Additionally, a velocity boundary condition modeled by a sinusoidal function is developed to fulfill the perturbation effect of periodic jets. The validity of the present CFD procedure is evaluated by the simulated results of an isolated synthetic jet and the jet control case for airfoil NACA0015. Then, parametric analyses are conducted specifically for an OA213 rotor airfoil to investigate the effects of jet parameters (forcing frequency, jet location and momentum coefficient, jet direction, and distribution of jet arrays on the control effect of the aerodynamic characteristics of a rotor airfoil. Preliminary results indicate that the efficiency of jet control can be improved with specific frequencies (the best lift-drag ratio at F+ = 2.0 and jet angles (40° or 75° when the jets are located near the separation point of the rotor airfoil. Furthermore, as a result of a suitable combination of jet arrays, the lift coefficient of the airfoil can be improved by nearly 100%, and the corresponding drag coefficient decreased by 26.5% in comparison with the single point control case.

  17. Inferential misconceptions and replication crisis

    Directory of Open Access Journals (Sweden)

    Norbert Hirschauer

    2016-12-01

    Full Text Available Misinterpretations of the p value and the introduction of bias through arbitrary analytical choices have been discussed in the literature for decades. Nonetheless, they seem to have persisted in empirical research, and criticisms of p value misuses have increased in the recent past due to the non-replicability of many studies. Unfortunately, the critical concerns that have been raised in the literature are scattered over many disciplines, often linguistically confusing, and differing in their main reasons for criticisms. Misuses and misinterpretations of the p value are currently being discussed intensely under the label “replication crisis” in many academic disciplines and journals, ranging from specialized scientific journals to Nature and Science. In a drastic response to the crisis, the editors of the journal Basic and Applied Social Psychology even decided to ban the use of p values from future publications at the beginning of 2015, a fact that has certainly added fuel to the discussions in the relevant scientific forums. Finally, in early March, the American Statistical Association released a brief formal statement on p values that explicitly addresses misuses and misinterpretations. In this context, we systematize the most serious flaws related to the p value and discuss suggestions of how to prevent them and reduce the rate of false discoveries in the future.

  18. 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....

  19. 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.

  20. Aerodynamic loads calculation and analysis for large scale wind turbine based on combining BEM modified theory with dynamic stall model

    Energy Technology Data Exchange (ETDEWEB)

    Dai, J.C. [College of Mechanical and Electrical Engineering, Central South University, Changsha (China); School of Electromechanical Engineering, Hunan University of Science and Technology, Xiangtan (China); Hu, Y.P.; Liu, D.S. [School of Electromechanical Engineering, Hunan University of Science and Technology, Xiangtan (China); Long, X. [Hara XEMC Windpower Co., Ltd., Xiangtan (China)

    2011-03-15

    The aerodynamic loads for MW scale horizontal-axis wind turbines are calculated and analyzed in the established coordinate systems which are used to describe the wind turbine. In this paper, the blade element momentum (BEM) theory is employed and some corrections, such as Prandtl and Buhl models, are carried out. Based on the B-L semi-empirical dynamic stall (DS) model, a new modified DS model for NACA63-4xx airfoil is adopted. Then, by combing BEM modified theory with DS model, a set of calculation method of aerodynamic loads for large scale wind turbines is proposed, in which some influence factors such as wind shear, tower, tower and blade vibration are considered. The research results show that the presented dynamic stall model is good enough for engineering purpose; the aerodynamic loads are influenced by many factors such as tower shadow, wind shear, dynamic stall, tower and blade vibration, etc, with different degree; the single blade endures periodical changing loads but the variations of the rotor shaft power caused by the total aerodynamic torque in edgewise direction are very small. The presented study approach of aerodynamic loads calculation and analysis is of the university, and helpful for thorough research of loads reduction on large scale wind turbines. (author)

  1. Validation of an Actuator Line Model Coupled to a Dynamic Stall Model for Pitching Motions Characteristic to Vertical Axis Turbines

    International Nuclear Information System (INIS)

    Mendoza, Victor; Goude, Anders; Bachant, Peter; Wosnik, Martin

    2016-01-01

    Vertical axis wind turbines (VAWT) can be used to extract renewable energy from wind flows. A simpler design, low cost of maintenance, and the ability to accept flow from all directions perpendicular to the rotor axis are some of the most important advantages over conventional horizontal axis wind turbines (HAWT). However, VAWT encounter complex and unsteady fluid dynamics, which present significant modeling challenges. One of the most relevant phenomena is dynamic stall, which is caused by the unsteady variation of angle of attack throughout the blade rotation, and is the focus of the present study. Dynamic stall is usually used as a passive control for VAWT operating conditions, hence the importance of predicting its effects. In this study, a coupled model is implemented with the open-source CFD toolbox OpenFOAM for solving the Navier-Stokes equations, where an actuator line model and dynamic stall model are used to compute the blade loading and body force. Force coefficients obtained from the model are validated with experimental data of pitching airfoil in similar operating conditions as an H-rotor type VAWT. Numerical results show reasonable agreement with experimental data for pitching motion. (paper)

  2. Validation of an Actuator Line Model Coupled to a Dynamic Stall Model for Pitching Motions Characteristic to Vertical Axis Turbines

    Science.gov (United States)

    Mendoza, Victor; Bachant, Peter; Wosnik, Martin; Goude, Anders

    2016-09-01

    Vertical axis wind turbines (VAWT) can be used to extract renewable energy from wind flows. A simpler design, low cost of maintenance, and the ability to accept flow from all directions perpendicular to the rotor axis are some of the most important advantages over conventional horizontal axis wind turbines (HAWT). However, VAWT encounter complex and unsteady fluid dynamics, which present significant modeling challenges. One of the most relevant phenomena is dynamic stall, which is caused by the unsteady variation of angle of attack throughout the blade rotation, and is the focus of the present study. Dynamic stall is usually used as a passive control for VAWT operating conditions, hence the importance of predicting its effects. In this study, a coupled model is implemented with the open-source CFD toolbox OpenFOAM for solving the Navier-Stokes equations, where an actuator line model and dynamic stall model are used to compute the blade loading and body force. Force coefficients obtained from the model are validated with experimental data of pitching airfoil in similar operating conditions as an H-rotor type VAWT. Numerical results show reasonable agreement with experimental data for pitching motion.

  3. RANS study of unsteady flow around a profile blade : application to stall of horizontal axis wind turbine

    Energy Technology Data Exchange (ETDEWEB)

    Belkheir, N. [Khemis Miliana Univ., Ain Defla (Algeria); Dizene, R. [Univ. des Sciences et de la Technologie Houari Boumediene, Algiers (Algeria). Laboratoire de Mecanique Avancee; Khelladi, S.; Massouh, F.; Dobrev, I. [Arts et Metiers Paris Tech., Paris (France)

    2010-07-01

    The shape of an airfoil is designed to achieve the best aerodynamic performance. An aerofoil section undergoes dynamic stall when subjected to any form of unsteady angle of pitch. The study of a horizontal-axis wind turbine (HAWT) under wind operating conditions is complex because it is subject to instantaneous speed and wind direction variation. When turbine blades are driven into a dynamic stall, the lift coefficient drops suddenly resulting in a degradation in aerodynamic performance. This study presented steady and unsteady wind load predictions over an oscillating S809 airfoil tested in a subsonic wind tunnel. A model of sinusoidal pitch oscillations was used. The values for the angles of attack in steady state ranged from -20 to +40 degrees. The model considered 3 frequencies and 2 amplitudes. The two-dimensional numerical model simulated the instantaneous change of wind direction with respect to the turbine blade. Results were compared with data measurements of S809 aerofoil. Reasonable deviations were obtained between the predicted and experimental results for pitch oscillations. The URANS approach was used to predict the stall while the software FLUENT was used for the numerical solution. It was concluded that the behaviour of the unsteady flow in the wind farm must be considered in order to obtain an accurate estimate of the wind turbine aerodynamic load. 12 refs., 5 figs.

  4. Unsteady performance of a cavitating hydrofoil in stall conditions. Shissoku jotai ni okeru yokukei no hiteijo tokusei

    Energy Technology Data Exchange (ETDEWEB)

    Ogata, H. (Tohoku University, Sendai (Japan)); Ito, Y. (Hachinoe Institutea of Technology, Aomori (Japan)); Oba, R. (Tohoku University, Sendai (Japan). Institute of Fluid Science); Sunayama, Y.; Abe, J. (Suzuki Co. Ltd., Shizuoka (Japan))

    1991-11-25

    To elucidate the unsteady performance of cavitating hydrofoils in a stall condition, this paper describes a survey on unsteady conditions without cavitations and stall conditions as to their characteristics from a cavitation to a supercavitation, lift and drag. Flows with cavitations were also analyzed. As a result of comparing also data for the subcavitation regions, it was found that a large-scale vortex generation on the hydrofoil back-pressure plane in near stall condition has a close relation with the changes in lifts and drags or the cavitation breakdown. The experiment used a testing water tank of circulation flow type having a rectangular measuring cross section (70 mm in width and 190 mm in height), and the hydrofoil specimens of two-dimensional symmetric type with a chord length of 70 mm and an aspect ratio of 1.0. The test condition used a cavitation coefficient of 0.18-6.33 (from a supercavitation to non-cavitation). A numerical analysis proved that the power spectra around the hydrofoils having no cavitations agreed with the experimental results, and verified the reasonability of the application. 18 refs., 8 figs., 2 tabs.

  5. Zonal RANS/LES coupling simulation of a transitional and separated flow around an airfoil near stall

    Energy Technology Data Exchange (ETDEWEB)

    Richez, F.; Mary, I.; Gleize, V. [ONERA, Department of Computational Fluid Dynamics and Aeroacoustics, 29 Avenue de la Division Leclerc, BP 72, Chatillon (France); Basdevant, C. [Universite Paris-Nord, Laboratoire d' Analyse, Geometrie et Applications, CNRS, Villetaneuse (France)

    2008-05-15

    The objective of the current study is to examine the course of events leading to stall just before its occurrence. The stall mechanisms are very sensitive to the transition that the boundary layer undergoes near the leading edge of the profile by a so-called laminar separation bubble (LSB). In order to provide helpful insights into this complex flow, a zonal Reynolds-averaged Navier-Stokes (RANS)/large-eddy simulation (LES) simulation of the flow around an airfoil near stall has been achieved and its results are presented and analyzed in this paper. LSB has already been numerically studied by direct numerical simulation (DNS) or LES, but for a flat plate with an adverse pressure gradient only. We intend, in this paper, to achieve a detailed analysis of the transition process by a LSB in more realistic conditions. The comparison with a linear instability analysis has shown that the numerical instability mechanism in the LSB provides the expected frequency of the perturbations. Furthermore, the right order of magnitude for the turbulence intensities at the reattachment point is found. (orig.)

  6. Hepatitis C virus translation preferentially depends on active RNA replication.

    Directory of Open Access Journals (Sweden)

    Helene Minyi Liu

    Full Text Available Hepatitis C virus (HCV RNA initiates its replication on a detergent-resistant membrane structure derived from the endoplasmic reticulum (ER in the HCV replicon cells. By performing a pulse-chase study of BrU-labeled HCV RNA, we found that the newly-synthesized HCV RNA traveled along the anterograde-membrane traffic and moved away from the ER. Presumably, the RNA moved to the site of translation or virion assembly in the later steps of viral life cycle. In this study, we further addressed how HCV RNA translation was regulated by HCV RNA trafficking. When the movement of HCV RNA from the site of RNA synthesis to the Golgi complex was blocked by nocodazole, an inhibitor of ER-Golgi transport, HCV protein translation was surprisingly enhanced, suggesting that the translation of viral proteins occurred near the site of RNA synthesis. We also found that the translation of HCV proteins was dependent on active RNA synthesis: inhibition of viral RNA synthesis by an NS5B inhibitor resulted in decreased HCV viral protein synthesis even when the total amount of intracellular HCV RNA remained unchanged. Furthermore, the translation activity of the replication-defective HCV replicons or viral RNA with an NS5B mutation was greatly reduced as compared to that of the corresponding wildtype RNA. By performing live cell labeling of newly synthesized HCV RNA and proteins, we further showed that the newly synthesized HCV proteins colocalized with the newly synthesized viral RNA, suggesting that HCV RNA replication and protein translation take place at or near the same site. Our findings together indicate that the translation of HCV RNA is coupled to RNA replication and that the both processes may occur at the same subcellular membrane compartments, which we term the replicasome.

  7. Inhibition and recovery of the replication of depurinated parvovirus DNA in mouse fibroblasts

    International Nuclear Information System (INIS)

    Vos, J.M.; Avalosse, B.; Su, Z.Z.; Rommelaere, J.

    1984-01-01

    Apurinic sites were introduced in the single-stranded DNA of parvovirus minute-virus-of-mice (MVM) and their effect on viral DNA synthesis was measured in mouse fibroblasts. Approximately one apurinic site per viral genome, is sufficient to block its replication in untreated cells. The exposure of host cells to a sublethal dose of UV-light 15 hours prior to virus infection, enhances their ability to support the replication of depurinated MVM. Cell preirradiation induces the apparent overcome of 10-15% of viral DNA replication blocks. These results indicate that apurinic sites prevent mammalian cells from replicating single-stranded DNA unless a recovery process is activated by cell UV-irradiation

  8. Initiation of chromosomal replication in predatory bacterium Bdellovibrio bacteriovorus

    Directory of Open Access Journals (Sweden)

    Lukasz Makowski

    2016-11-01

    Full Text Available Bdellovibrio bacteriovorus is a small Gram-negative predatory bacterium that attacks other Gram-negative bacteria, including many animal, human, and plant pathogens. This bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase and replicating cells (the intracellular-growth phase. The process of chromosomal replication in B. bacteriovorus must therefore be temporally and spatially regulated to ensure that it is coordinated with cell differentiation and cell cycle progression. Recently, B. bacteriovorus has received considerable research interest due to its intriguing life cycle and great potential as a prospective antimicrobial agent. Although we know that chromosomal replication in bacteria is mainly regulated at the initiation step, no data exists about this process in B. bacteriovorus. We report the first characterization of key elements of initiation of chromosomal replication – DnaA protein and oriC region from the predatory bacterium, B. bacteriovorus. In vitro studies using different approaches demonstrate that the B. bacteriovorus oriC (BdoriC is specifically bound and unwound by the DnaA protein. Sequence comparison of the DnaA-binding sites enabled us to propose a consensus sequence for the B. bacteriovorus DnaA box (5’-NN(A/TTCCACA-3’. Surprisingly, in vitro analysis revealed that BdoriC is also bound and unwound by the host DnaA proteins (relatively distantly related from B. bacteriovorus. We compared the architecture of the DnaA–oriC complexes (orisomes in homologous (oriC and DnaA from B. bacteriovorus and heterologous (BdoriC and DnaA from prey, E. coli or P. aeruginosa systems. This work provides important new entry points toward improving our understanding of the initiation of chromosomal replication in this predatory bacterium.

  9. Association between stall surface and some animal welfare measurements in freestall dairy herds using recycled manure solids for bedding.

    Science.gov (United States)

    Husfeldt, A W; Endres, M I

    2012-10-01

    The objective of this cross-sectional study was to investigate the association between stall surface and some animal welfare measurements in upper Midwest US dairy operations using recycled manure solids as bedding material. The study included 34 dairy operations with herd sizes ranging from 130 to 3,700 lactating cows. Forty-five percent of the herds had mattresses and 55% had deep-bedded stalls. Farms were visited once between July and October 2009. At the time of visit, at least 50% of the cows in each lactating pen were scored for locomotion, hygiene, and hock lesions. On-farm herd records were collected for the entire year and used to investigate mortality, culling, milk production, and mastitis incidence. Stall surface was associated with lameness and hock lesion prevalence. Lameness prevalence (locomotion score ≥ 3 on a 1 to 5 scale) was lower in deep-bedded freestalls (14.4%) than freestalls with mattresses (19.8%). Severe lameness prevalence (locomotion score ≥ 4) was also lower for cows housed in deep-bedded freestalls (3.6%) than for cows housed in freestalls with mattresses (5.9%). In addition, the prevalence of hock lesions (hock lesion scores ≥ 2 on a 1 to 3 scale, with 1=no lesion, 2=hair loss or mild lesion, and 3=swelling or severe lesion) and severe hock lesions (hock lesion score=3) was lower in herds with deep-bedded freestalls (49.4%; 6.4%) than in herds with mattresses (67.3%; 13.2%). Herd turnover rates were not associated with stall surface; however, the percentage of removals due to voluntary (low milk production, disposition, and dairy) and involuntary (death, illness, injury, and reproductive) reasons was different between deep-bedded and mattress-based freestalls. Voluntary removals averaged 16% of all herd removals in deep-bedded herds, whereas in mattress herds, these removals were 8%. Other welfare measurements such as cow hygiene, mortality rate, mastitis incidence, and milk production were not associated with stall surface

  10. Plasticity of DNA replication initiation in Epstein-Barr virus episomes.

    Directory of Open Access Journals (Sweden)

    Paolo Norio

    2004-06-01

    Full Text Available In mammalian cells, the activity of the sites of initiation of DNA replication appears to be influenced epigenetically, but this regulation is not fully understood. Most studies of DNA replication have focused on the activity of individual initiation sites, making it difficult to evaluate the impact of changes in initiation activity on the replication of entire genomic loci. Here, we used single molecule analysis of replicated DNA (SMARD to study the latent duplication of Epstein-Barr virus (EBV episomes in human cell lines. We found that initiation sites are present throughout the EBV genome and that their utilization is not conserved in different EBV strains. In addition, SMARD shows that modifications in the utilization of multiple initiation sites occur across large genomic regions (tens of kilobases in size. These observations indicate that individual initiation sites play a limited role in determining the replication dynamics of the EBV genome. Long-range mechanisms and the genomic context appear to play much more important roles, affecting the frequency of utilization and the order of activation of multiple initiation sites. Finally, these results confirm that initiation sites are extremely redundant elements of the EBV genome. We propose that these conclusions also apply to mammalian chromosomes.

  11. Feline coronavirus replication is affected by both cyclophilin A and cyclophilin B.

    Science.gov (United States)

    Tanaka, Yoshikazu; Sato, Yuka; Sasaki, Takashi

    2017-02-01

    Feline coronavirus (FCoV) causes the fatal disease feline infectious peritonitis, which is currently incurable by drug treatment, and no effective vaccines are available. Cyclosporin A (CsA), a cyclophilin (Cyp) inhibitor, inhibits the replication of FCoV in vitro and in vivo as well as the replication of human and animal coronaviruses. However, the mechanism underlying the regulation of coronavirus replication by CsA is unknown. In this study, we analysed the role of Cyps in FCoV replication using knockdown and knockout cells specific to Cyps. Inhibition of CypA and CypB reduced FCoV replication, with replication in knockout cells being much less than that in knockdown cells. Furthermore, the proteins expressed by CypA and CypB harbouring mutations in their respective predicted peptidyl-prolyl cis-transisomerase active sites, which also alter the affinities between Cyps and CsA, inhibited FCoV replication. These findings indicate that the peptidyl-prolyl cis-transisomerase active sites of Cyps might be required for FCoV replication.

  12. ATAD2 is an epigenetic reader of newly synthesized histone marks during DNA replication.

    Science.gov (United States)

    Koo, Seong Joo; Fernández-Montalván, Amaury E; Badock, Volker; Ott, Christopher J; Holton, Simon J; von Ahsen, Oliver; Toedling, Joern; Vittori, Sarah; Bradner, James E; Gorjánácz, Mátyás

    2016-10-25

    ATAD2 (ATPase family AAA domain-containing protein 2) is a chromatin regulator harboring an AAA+ ATPase domain and a bromodomain, previously proposed to function as an oncogenic transcription co-factor. Here we suggest that ATAD2 is also required for DNA replication. ATAD2 is co-expressed with genes involved in DNA replication in various cancer types and predominantly expressed in S phase cells where it localized on nascent chromatin (replication sites). Our extensive biochemical and cellular analyses revealed that ATAD2 is recruited to replication sites through a direct interaction with di-acetylated histone H4 at K5 and K12, indicative of newly synthesized histones during replication-coupled chromatin reassembly. Similar to ATAD2-depletion, ectopic expression of ATAD2 mutants that are deficient in binding to these di-acetylation marks resulted in reduced DNA replication and impaired loading of PCNA onto chromatin, suggesting relevance of ATAD2 in DNA replication. Taken together, our data show a novel function of ATAD2 in cancer and for the first time identify a reader of newly synthesized histone di-acetylation-marks during replication.

  13. An active site aromatic triad in Escherichia coli DNA Pol IV coordinates cell survival and mutagenesis in different DNA damaging agents.

    Directory of Open Access Journals (Sweden)

    Ryan W Benson

    Full Text Available DinB (DNA Pol IV is a translesion (TLS DNA polymerase, which inserts a nucleotide opposite an otherwise replication-stalling N(2-dG lesion in vitro, and confers resistance to nitrofurazone (NFZ, a compound that forms these lesions in vivo. DinB is also known to be part of the cellular response to alkylation DNA damage. Yet it is not known if DinB active site residues, in addition to aminoacids involved in DNA synthesis, are critical in alkylation lesion bypass. It is also unclear which active site aminoacids, if any, might modulate DinB's bypass fidelity of distinct lesions. Here we report that along with the classical catalytic residues, an active site "aromatic triad", namely residues F12, F13, and Y79, is critical for cell survival in the presence of the alkylating agent methyl methanesulfonate (MMS. Strains expressing dinB alleles with single point mutations in the aromatic triad survive poorly in MMS. Remarkably, these strains show fewer MMS- than NFZ-induced mutants, suggesting that the aromatic triad, in addition to its role in TLS, modulates DinB's accuracy in bypassing distinct lesions. The high bypass fidelity of prevalent alkylation lesions is evident even when the DinB active site performs error-prone NFZ-induced lesion bypass. The analyses carried out with the active site aromatic triad suggest that the DinB active site residues are poised to proficiently bypass distinctive DNA lesions, yet they are also malleable so that the accuracy of the bypass is lesion-dependent.

  14. The cellular Mre11 protein interferes with adenovirus E4 mutant DNA replication

    International Nuclear Information System (INIS)

    Mathew, Shomita S.; Bridge, Eileen

    2007-01-01

    Adenovirus type 5 (Ad5) relocalizes and degrades the host DNA repair protein Mre11, and efficiently initiates viral DNA replication. Mre11 associates with Ad E4 mutant DNA replication centers and is important for concatenating viral genomes. We have investigated the role of Mre11 in the E4 mutant DNA replication defect. RNAi-mediated knockdown of Mre11 dramatically rescues E4 mutant DNA replication in cells that do or do not concatenate viral genomes, suggesting that Mre11 inhibits DNA replication independent of genome concatenation. The mediator of DNA damage checkpoint 1 (Mdc1) protein is involved in recruiting and sustaining Mre11 at sites of DNA damage following ionizing radiation. We observe foci formation by Mdc1 in response to viral infection, indicating that this damage response protein is activated. However, knockdown of Mdc1 does not prevent Mre11 from localizing at viral DNA replication foci or rescue E4 mutant DNA replication. Our results are consistent with a model in which Mre11 interferes with DNA replication when it is localized at viral DNA replication foci

  15. 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

  16. Influence of free-stall base on tarsal joint lesions and hygiene in dairy cows.

    Science.gov (United States)

    Fulwider, W K; Grandin, T; Garrick, D J; Engle, T E; Lamm, W D; Dalsted, N L; Rollin, B E

    2007-07-01

    The objective was to quantify the incidence of tarsal lesions and level of hygiene by stall bed type. Cows were scored on 100 dairies from Wisconsin, Minnesota, Indiana, Iowa, and New York in the fall and winter. Thirty-eight dairies used rubber-filled mattresses (RFM), 27 had sand beds, 29 had waterbeds, and 6 used compost packs (CPk). Stocking density, stall dimensions, bedding amount, bedding frequency, and type of bedding were recorded. One pen of early-lactation multiparous cows on each dairy was scored based on injury of the tarsal joints at the lateral and medial surfaces and tuber calcis at the dorsal, lateral, and medial surfaces. A tarsal score of 1 represented hair loss, 2 was moderate, and 3 indicated severe swelling. Differences between bed types in the percentages of cows with lesions were tested with one-way ANOVA by lesion severity and incidence, with farm as the experimental unit. Cows on sand beds or waterbeds had fewer lesion scores of 1, 2, and 3 than those on RFM. The percentages of score 1 were 54.6 +/- 4.4 (RFM), 22.5 +/- 4.7 (sand), and 29.8 +/- 4.3 (waterbed), whereas the percentages of score 2 were 14.0 +/- 1.4, 2.3 +/- 1.5, and 5.0 +/- 1.4, and of score 3 were 3.0 +/- 0.4, 0.2 +/- 0.4, and 0.4 +/- 0.4. Cows on CPk had no lesions. Hygiene scores ranged from 1 to 5, with 1 being clean and 5 soiled. The percentages of hygiene score 1 were 0 (compost), 0.4 (RFM), 0.4 (sand), and 0.4 (waterbeds); those with score 2 were 79.0, 84.0 +/- 0.01, 73.2 +/- 0.01, and 80.4 +/- 0.01; with score 3 were 20.3, 15.2 +/- 0.01, 23.8 +/- 0.01, and 18.6 +/- 0.01; with score 4 were 0.8, 0.005 +/- 0.001, 0.006 +/- 0.001, and 0.025 +/- 0.003; and with score 5 was 0 for all bed types. Cows on RFM and waterbeds had improved hygiene compared with cows on sand beds. There was no difference in somatic cell count (SCC) by bed type. The percentage of cows in fourth lactation or greater on waterbeds (19.8 +/- 1.8) was greater than those on RFM (13.3 +/- 1.6) or on sand

  17. CFD study of a NACA 63-415 aerofoil fitted with stall strips

    Energy Technology Data Exchange (ETDEWEB)

    Zahle, F.; Soerensen, N.N.; Johansen, J.

    2002-09-01

    The present work describes a thorough investigation of 2D computations of the flow around a NACA 63-415 aerofoil fitted with stall strips (SS). A mesh study as well as a time step study is carried out and all computations are compared with experiments. Two different SS, 5mm and 7mm are investigated at several positions. Furthermore the influence of laminar to turbulent transition and the effect of a rounded SS were tested. There is not sufficient agreement between the experimental results and the simulations to draw any conclusions of optimum position and geometry of the SS. The 7mm SS's placed at P00 and P-02 has the greatest effect on the max lift followed by SS P02. The 5mm SS's does, as in the experiment, not change the lift curve noticeably. Even though this investigation does not conclusively succeed in verifying the experimental results with CFD, many useful conclusions can be drawn from the results. It is observed in the experiment that the vertical force fluctuates at higher angles of attack. This indicates that small bubbles are being shed off the profile causing the force to vary. This property is observed when transition is included in the model and also when the tip of the SS is rounded. From this result it could be concluded that the level of turbulence produced on the tip of the SS is very important for the development of the flow downstream. In the sharp tip calculations using fully turbulent computations, this is most likely too high, which resulted in the fine structures being damped out, with only one bubble appearing. (au)

  18. Evaluation of free-stall mattress bedding treatments to reduce mastitis bacterial growth

    Energy Technology Data Exchange (ETDEWEB)

    Kristula, M A; Dou, Z; Toth, J D; Smith, B I; Harvey, N; Sabo, M [University of Penn, Kennett Square, PA (United States)

    2008-05-15

    Bacterial counts were compared in free-stall mattresses and teat ends exposed to 5 treatments in a factorial study design on 1 dairy farm. Mattresses in five 30-cow groups were subjected to 1 of 5 bedding treatments every other day: 0.5 kg of hydrated limestone, 120 mL of commercial acidic conditioner, 1 kg of coal fly ash, 1 kg of kiln-dried wood shavings, and control (no bedding). Counts of coliforms, Klebsiella spp., Escherichia coli, and Streptococcus spp. were lowest on mattresses bedded with lime. Mattresses bedded with the commercial acidic conditioner had the next lowest counts for coliforms, Klebsiella spp., and Streptococcus spp. Wood shavings and the no-bedding control had the highest counts for coliform and Klebsiella spp. Compared with wood shavings or control, fly ash reduced the counts of coliforms, whereas for the other 3 bacterial groups, the reduction was not always significant. Streptococcus spp. counts were greatest in the control group and did not differ among the shavings and fly ash groups. Teat swab results indicated that hydrated lime was the only bedding treatment that significantly decreased the counts of both coliforms and Klebsiella spp. There were no differences in Streptococcus spp. numbers on the teats between any of the bedding treatments. Bacterial populations grew steadily on mattresses and were generally higher at 36 to 48 h than at 12 to 24 h, whereas bacterial populations on teats grew rapidly by 12 h and then remained constant. Hydrated lime was the only treatment that significantly reduced bacterial counts on both mattresses and teat ends, but it caused some skin irritation.

  19. Evaluation of rice mutant lines for resistance to brown planthopper, nilaparvata lugens stall

    International Nuclear Information System (INIS)

    Mugiono

    1985-01-01

    The most important and common insect in rice cultivation in South East Asia is brown planthopper, nilaparvata lugens stall. Seven rice mutant lines produced by the National Atomic Energy Agency, Indonesia, were tested at IRRI, the Philippines for resistance to brown planthopper. Those mutant lines were Atomita 1, 627/10-3/PsJ, Atomita 2 and 627/4-E/PsJ originated from Pelita 1/1 which was irradiated with 0.2 kGy of gamma rays and A227/2/PsJ, A227/3/PsJ and A227/5/PsJ, originated from early maturing mutant A23/PsJ/72K from irradiated Pelita 1/1 which was irradiated with 0.1 kGy of gamma rays. Evaluation of resistance was carried out by seedling bulk screening, honeydew excretion, survival and population build up tests by using brown planthopper biotype 1, 2 and 3. Results of these tests showed that the seven tested mutant lines were resistant to biotype 1 but susceptible to biotype 2. Reaction to biotype 3 showed that six mutant lines tested were moderately resistant and only one mutant of 627/4-E/PsJ was susceptible. Reactions of the mutant lines to biotype 1, 2 and 3 were different from the resistant varieties, Mudgo or ASD-7. This indicated that mutant lines might have gene(s) for resistance which differed from those of resistant varieties. The results showed that resistance to brown planthopper is possible to be introduced in Indonesian rice varieties by means of mutations. (author)

  20. Mcm2 phosphorylation and the response to replicative stress

    Directory of Open Access Journals (Sweden)

    Stead Brent E

    2012-05-01

    Full Text Available Abstract Background The replicative helicase in eukaryotic cells is comprised of minichromosome maintenance (Mcm proteins 2 through 7 (Mcm2-7 and is a key target for regulation of cell proliferation. In addition, it is regulated in response to replicative stress. One of the protein kinases that targets Mcm2-7 is the Dbf4-dependent kinase Cdc7 (DDK. In a previous study, we showed that alanine mutations of the DDK phosphorylation sites at S164 and S170 in Saccharomyces cerevisiae Mcm2 result in sensitivity to caffeine and methyl methanesulfonate (MMS leading us to suggest that DDK phosphorylation of Mcm2 is required in response to replicative stress. Results We show here that a strain with the mcm2 allele lacking DDK phosphorylation sites (mcm2AA is also sensitive to the ribonucleotide reductase inhibitor, hydroxyurea (HU and to the base analogue 5-fluorouracil (5-FU but not the radiomimetic drug, phleomycin. We screened the budding yeast non-essential deletion collection for synthetic lethal interactions with mcm2AA and isolated deletions that include genes involved in the control of genome integrity and oxidative stress. In addition, the spontaneous mutation rate, as measured by mutations in CAN1, was increased in the mcm2AA strain compared to wild type, whereas with a phosphomimetic allele (mcm2EE the mutation rate was decreased. These results led to the idea that the mcm2AA strain is unable to respond properly to DNA damage. We examined this by screening the deletion collection for suppressors of the caffeine sensitivity of mcm2AA. Deletions that decrease spontaneous DNA damage, increase homologous recombination or slow replication forks were isolated. Many of the suppressors of caffeine sensitivity suppressed other phenotypes of mcm2AA including sensitivity to genotoxic drugs, the increased frequency of cells with RPA foci and the increased mutation rate. Conclusions Together these observations point to a role for DDK-mediated phosphorylation

  1. Surface micro topography replication in injection moulding

    DEFF Research Database (Denmark)

    Arlø, Uffe Rolf

    Thermoplastic injection moulding is a widely used industrial process that involves surface generation by replication. The surface topography of injection moulded plastic parts can be important for aesthetical or technical reasons. With the emergence of microengineering and nanotechnology additional...... importance of surface topography follows. In general the replication is not perfect and the topography of the plastic part differs from the inverse topography of the mould cavity. It is desirable to be able to control the degree of replication perfection or replication quality. This requires an understanding...... of the physical mechanisms of replication. Such understanding can lead to improved process design and facilitate in-line process quality control with respect to surface properties. The purpose of the project is to identify critical factors that affect topography replication quality and to obtain an understanding...

  2. Distribution of DNA replication proteins in Drosophila cells

    Science.gov (United States)

    Easwaran, Hariharan P; Leonhardt, Heinrich; Cardoso, M Cristina

    2007-01-01

    Background DNA replication in higher eukaryotic cells is organized in discrete subnuclear sites called replication foci (RF). During the S phase, most replication proteins assemble at the RF by interacting with PCNA via a PCNA binding domain (PBD). This has been shown to occur for many mammalian replication proteins, but it is not known whether this mechanism is conserved in evolution. Results Fluorescent fusions of mammalian replication proteins, Dnmt1, HsDNA Lig I and HsPCNA were analyzed for their ability to target to RF in Drosophila cells. Except for HsPCNA, none of the other proteins and their deletions showed any accumulation at RF in Drosophila cells. We hypothesized that in Drosophila cells there might be some other peptide sequence responsible for targeting proteins to RF. To test this, we identified the DmDNA Lig I and compared the protein sequence with HsDNA Lig I. The two orthologs shared the PBD suggesting a functionally conserved role for this domain in the Drosophila counterpart. A series of deletions of DmDNA Lig I were analyzed for their ability to accumulate at RF in Drosophila and mammalian cells. Surprisingly, no accumulation at RF was observed in Drosophila cells, while in mammalian cells DmDNA Lig I accumulated at RF via its PBD. Further, GFP fusions with the PBD domains from Dnmt1, HsDNA Lig I and DmDNA Lig I, were able to target to RF only in mammalian cells but not in Drosophila cells. Conclusion We show that S phase in Drosophila cells is characterized by formation of RF marked by PCNA like in mammalian cells. However, other than PCNA none of the replication proteins and their deletions tested here showed accumulation at RF in Drosophila cells while the same proteins and deletions are capable of accumulating at RF in mammalian cells. We hypothesize that unlike mammalian cells, in Drosophila cells, replication proteins do not form long-lasting interactions with the replication machinery, and rather perform their functions via very

  3. Timeless links replication termination to mitotic kinase activation.

    Directory of Open Access Journals (Sweden)

    Jayaraju Dheekollu

    2011-05-01

    Full Text Available The mechanisms that coordinate the termination of DNA replication with progression through mitosis are not completely understood. The human Timeless protein (Tim associates with S phase replication checkpoint proteins Claspin and Tipin, and plays an important role in maintaining replication fork stability at physical barriers, like centromeres, telomeres and ribosomal DNA repeats, as well as at termination sites. We show here that human Tim can be isolated in a complex with mitotic entry kinases CDK1, Auroras A and B, and Polo-like kinase (Plk1. Plk1 bound Tim directly and colocalized with Tim at a subset of mitotic structures in M phase. Tim depletion caused multiple mitotic defects, including the loss of sister-chromatid cohesion, loss of mitotic spindle architecture, and a failure to exit mitosis. Tim depletion caused a delay in mitotic kinase activity in vivo and in vitro, as well as a reduction in global histone H3 S10 phosphorylation during G2/M phase. Tim was also required for the recruitment of Plk1 to centromeric DNA and formation of catenated DNA structures at human centromere alpha satellite repeats. Taken together, these findings suggest that Tim coordinates mitotic kinase activation with termination of DNA replication.

  4. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural...... framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures...

  5. 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

  6. Visualization and measurement of ATP levels in living cells replicating hepatitis C virus genome RNA.

    Directory of Open Access Journals (Sweden)

    Tomomi Ando

    Full Text Available Adenosine 5'-triphosphate (ATP is the primary energy currency of all living organisms and participates in a variety of cellular processes. Although ATP requirements during viral lifecycles have been examined in a number of studies, a method by which ATP production can be monitored in real-time, and by which ATP can be quantified in individual cells and subcellular compartments, is lacking, thereby hindering studies aimed at elucidating the precise mechanisms by which viral replication energized by ATP is controlled. In this study, we investigated the fluctuation and distribution of ATP in cells during RNA replication of the hepatitis C virus (HCV, a member of the Flaviviridae family. We demonstrated that cells involved in viral RNA replication actively consumed ATP, thereby reducing cytoplasmic ATP levels. Subsequently, a method to measure ATP levels at putative subcellular sites of HCV RNA replication in living cells was developed by introducing a recently-established Förster resonance energy transfer (FRET-based ATP indicator, called ATeam, into the NS5A coding region of the HCV replicon. Using this method, we were able to observe the formation of ATP-enriched dot-like structures, which co-localize with non-structural viral proteins, within the cytoplasm of HCV-replicating cells but not in non-replicating cells. The obtained FRET signals allowed us to estimate ATP concentrations within HCV replicating cells as ∼5 mM at possible replicating sites and ∼1 mM at peripheral sites that did not appear to be involved in HCV replication. In contrast, cytoplasmic ATP levels in non-replicating Huh-7 cells were estimated as ∼2 mM. To our knowledge, this is the first study to demonstrate changes in ATP concentration within cells during replication of the HCV genome and increased ATP levels at distinct sites within replicating cells. ATeam may be a powerful tool for the study of energy metabolism during replication of the viral genome.

  7. Preliminary Results of the Determination of Inlet-Pressure Distortion Effects on Compressor Stall and Altitude Operating Limits of the J57-P-1 Turbojet Engine

    Science.gov (United States)

    Wallner, L. E.; Lubick, R. J.; Chelko, L. J.

    1955-01-01

    During an investigation of the J57-P-1 turbojet engine in the Lewis altitude wind tunnel, effects of inlet-flow distortion on engine stall characteristics and operating limits were determined. In addition to a uniform inlet-flow profile, the inlet-pressure distortions imposed included two radial, two circumferential, and one combined radial-circumferential profile. Data were obtained over a range of compressor speeds at an altitude of 50,000 and a flight Mach number of 0.8; in addition, the high- and low-speed engine operating limits were investigated up to the maximum operable altitude. The effect of changing the compressor bleed position on the stall and operating limits was determined for one of the inlet distortions. The circumferential distortions lowered the compressor stall pressure ratios; this resulted in less fuel-flow margin between steady-state operation and compressor stall. Consequently, the altitude operating Limits with circumferential distortions were reduced compared with the uniform inlet profile. Radial inlet-pressure distortions increased the pressure ratio required for compressor stall over that obtained with uniform inlet flow; this resulted in higher altitude operating limits. Likewise, the stall-limit fuel flows required with the radial inlet-pressure distortions were considerably higher than those obtained with the uniform inlet-pressure profile. A combined radial-circumferential inlet distortion had effects on the engine similar to the circumferential distortion. Bleeding air between the two compressors eliminated the low-speed stall limit and thus permitted higher altitude operation than was possible without compressor bleed.

  8. Cellular Aspects of Prion Replication In Vitro

    Science.gov (United States)

    Grassmann, Andrea; Wolf, Hanna; Hofmann, Julia; Graham, James; Vorberg, Ina

    2013-01-01

    Prion diseases or transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative disorders in mammals that are caused by unconventional agents predominantly composed of aggregated misfolded prion protein (PrP). Prions self-propagate by recruitment of host-encoded PrP into highly ordered β-sheet rich aggregates. Prion strains differ in their clinical, pathological and biochemical characteristics and are likely to be the consequence of distinct abnormal prion protein conformers that stably replicate their alternate states in the host cell. Understanding prion cell biology is fundamental for identifying potential drug targets for disease intervention. The development of permissive cell culture models has greatly enhanced our knowledge on entry, propagation and dissemination of TSE agents. However, despite extensive research, the precise mechanism of prion infection and potential strain effects remain enigmatic. This review summarizes our current knowledge of the cell biology and propagation of prions derived from cell culture experiments. We discuss recent findings on the trafficking of cellular and pathologic PrP, the potential sites of abnormal prion protein synthesis and potential co-factors involved in prion entry and propagation. PMID:23340381

  9. Stuck in Neutral: Stalled Progress in Statewide Comprehensive Smoke-Free Laws and Cigarette Excise Taxes, United States, 2000–2014

    Science.gov (United States)

    King, Brian A.; Babb, Stephen D.

    2016-01-01

    Introduction Increasing tobacco excise taxes and implementing comprehensive smoke-free laws are two of the most effective population-level strategies to reduce tobacco use, prevent tobacco use initiation, and protect nonsmokers from secondhand smoke. We examined state laws related to smoke-free buildings and to cigarette excise taxes from 2000 through 2014 to see how implementation of these laws from 2000 through 2009 differs from implementation in more recent years (2010–2014). Methods We used legislative data from LexisNexis, an online legal research database, to examine changes in statewide smoke-free laws and cigarette excise taxes in effect from January 1, 2000, through December 31, 2014. A comprehensive smoke-free law was defined as a statewide law prohibiting smoking in all indoor areas of private work sites, restaurants, and bars. Results From 2000 through 2009, 21 states and the District of Columbia implemented comprehensive smoke-free laws prohibiting smoking in work sites, restaurants, and bars. In 2010, 4 states implemented comprehensive smoke-free laws. The last state to implement a comprehensive smoke-free law was North Dakota in 2012, bringing the total number to 26 states and the District of Columbia. From 2000 through 2009, 46 states and the District of Columbia implemented laws increasing their cigarette excise tax, which increased the national average state excise tax rate by $0.92. However, from 2010 through 2014, only 14 states and the District of Columbia increased their excise tax, which increased the national average state excise tax rate by $0.20. Conclusion The recent stall in progress in enacting and implementing statewide comprehensive smoke-free laws and increasing cigarette excise taxes may undermine tobacco prevention and control efforts in the United States, undercutting efforts to reduce tobacco use, exposure to secondhand smoke, health disparities, and tobacco-related illness and death. PMID:27309417

  10. Proteomics Reveals Global Regulation of Protein SUMOylation by ATM and ATR Kinases during Replication Stress

    Directory of Open Access Journals (Sweden)

    Stephanie Munk

    2017-10-01

    Full Text Available The mechanisms that protect eukaryotic DNA during the cumbersome task of replication depend on the precise coordination of several post-translational modification (PTM-based signaling networks. Phosphorylation is a well-known regulator of the replication stress response, and recently an essential role for SUMOs (small ubiquitin-like modifiers has also been established. Here, we investigate the global interplay between phosphorylation and SUMOylation in response to replication stress. Using SUMO and phosphoproteomic technologies, we identify thousands of regulated modification sites. We find co-regulation of central DNA damage and replication stress responders, of which the ATR-activating factor TOPBP1 is the most highly regulated. Using pharmacological inhibition of the DNA damage response kinases ATR and ATM, we find that these factors regulate global protein SUMOylation in the protein networks that protect DNA upon replication stress and fork breakage, pointing to integration between phosphorylation and SUMOylation in the cellular systems that protect DNA integrity.

  11. Reliability analysis of a replication with limited number of journaling files

    International Nuclear Information System (INIS)

    Kimura, Mitsutaka; Imaizumi, Mitsuhiro; Nakagawa, Toshio

    2013-01-01

    Recently, replication mechanisms using journaling files have been widely used for the server systems. We have already discussed the model of asynchronous replication system using journaling files [8]. This paper formulates a stochastic model of a server system with replication considering the number of transmitting journaling files. The server updates the storage database and transmits the journaling file when a client requests the data update. The server transmits the database content to a backup site either at a constant time or after a constant number of transmitting journaling files. We derive the expected number of the replication and of transmitting journaling files. Further, we calculate the expected cost and discuss optimal replication interval to minimize it. Finally, numerical examples are given

  12. 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.

  13. 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.

  14. New paradigms in the repair of oxidative damage in human genome: mechanisms ensuring repair of mutagenic base lesions during replication and involvement of accessory proteins.

    Science.gov (United States)

    Dutta, Arijit; Yang, Chunying; Sengupta, Shiladitya; Mitra, Sankar; Hegde, Muralidhar L

    2015-05-01

    Oxidized bases in the mammalian genome, which are invariably mutagenic due to their mispairing property, are continuously induced by endogenous reactive oxygen species and more abundantly after oxidative stress. Unlike bulky base adducts induced by UV and other environmental mutagens in the genome that block replicative DNA polymerases, oxidatively damaged bases such as 5-hydroxyuracil, produced by oxidative deamination of cytosine in the template strand, do not block replicative polymerases and thus need to be repaired prior to replication to prevent mutation. Following up our earlier studies, which showed that the Nei endonuclease VIII like 1 (NEIL1) DNA glycosylase, one of the five base excision repair (BER)-initiating enzymes in mammalian cells, has enhanced expression during the S-phase and higher affinity for replication fork-mimicking single-stranded (ss) DNA substrates, we recently provided direct experimental evidence for NEIL1's role in replicating template strand repair. The key requirement for this event, which we named as the 'cow-catcher' mechanism of pre-replicative BER, is NEIL1's non-productive binding (substrate binding without product formation) to the lesion base in ss DNA template to stall DNA synthesis, causing fork regression. Repair of the lesion in reannealed duplex is then carried out by NEIL1 in association with the DNA replication proteins. NEIL1 (and other BER-initiating enzymes) also interact with several accessory and non-canonical proteins including the heterogeneous nuclear ribonucleoprotein U and Y-box-binding protein 1 as well as high mobility group box 1 protein, whose precise roles in BER are still obscure. In this review, we have discussed the recent advances in our understanding of oxidative genome damage repair pathways with particular focus on the pre-replicative template strand repair and the role of scaffold factors like X-ray repairs cross-complementing protein 1 and poly (ADP-ribose) polymerase 1 and other accessory

  15. Activation of human herpesvirus replication by apoptosis.

    Science.gov (United States)

    Prasad, Alka; Remick, Jill; Zeichner, Steven L

    2013-10-01

    A central feature of herpesvirus biology is the ability of herpesviruses to remain latent within host cells. Classically, exposure to inducing agents, like activating cytokines or phorbol esters that stimulate host cell signal transduction events, and epigenetic agents (e.g., butyrate) was thought to end latency. We recently showed that Kaposi's sarcoma-associated herpesvirus (KSHV, or human herpesvirus-8 [HHV-8]) has another, alternative emergency escape replication pathway that is triggered when KSHV's host cell undergoes apoptosis, characterized by the lack of a requirement for the replication and transcription activator (RTA) protein, accelerated late gene kinetics, and production of virus with decreased infectivity. Caspase-3 is necessary and sufficient to initiate the alternative replication program. HSV-1 was also recently shown to initiate replication in response to host cell apoptosis. These observations suggested that an alternative apoptosis-triggered replication program might be a general feature of herpesvirus biology and that apoptosis-initiated herpesvirus replication may have clinical implications, particularly for herpesviruses that almost universally infect humans. To explore whether an alternative apoptosis-initiated replication program is a common feature of herpesvirus biology, we studied cell lines latently infected with Epstein-Barr virus/HHV-4, HHV-6A, HHV-6B, HHV-7, and KSHV. We found that apoptosis triggers replication for each HHV studied, with caspase-3 being necessary and sufficient for HHV replication. An alternative apoptosis-initiated replication program appears to be a common feature of HHV biology. We also found that commonly used cytotoxic chemotherapeutic agents activate HHV replication, which suggests that treatments that promote apoptosis may lead to activation of latent herpesviruses, with potential clinical significance.

  16. Recombination at DNA replication fork barriers is not universal and is differentially regulated by Swi1.

    Science.gov (United States)

    Pryce, David W; Ramayah, Soshila; Jaendling, Alessa; McFarlane, Ramsay J

    2009-03-24

    DNA replication stress has been implicated in the etiology of genetic diseases, including cancers. It has been proposed that genomic sites that inhibit or slow DNA replication fork progression possess recombination hotspot activity and can form potential fragile sites. Here we used the fission yeast, Schizosaccharomyces pombe, to demonstrate that hotspot activity is not a universal feature of replication fork barriers (RFBs), and we propose that most sites within the genome that form RFBs do not have recombination hotspot activity under nonstressed conditions. We further demonstrate that Swi1, the TIMELESS homologue, differentially controls the recombination potential of RFBs, switching between being a suppressor and an activator of recombination in a site-specific fashion.

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

    Science.gov (United States)

    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.

  18. Herpes simplex virus replication compartments can form by coalescence of smaller compartments

    International Nuclear Information System (INIS)

    Taylor, Travis J; McNamee, Elizabeth E.; Day, Cheryl; Knipe, David M.

    2003-01-01

    Herpes simplex virus (HSV) uses intranuclear compartmentalization to concentrate the viral and cellular factors required for the progression of the viral life cycle. Processes as varied as viral DNA replication, late gene expression, and capsid assembly take place within discrete structures within the nucleus called replication compartments. Replication compartments are hypothesized to mature from a few distinct structures, called prereplicative sites, that form adjacent to cellular nuclear matrix-associated ND10 sites. During productive infection, the HSV single-stranded DNA-binding protein ICP8 localizes to replication compartments. To further the understanding of replication compartment maturation, we have constructed and characterized a recombinant HSV-1 strain that expresses an ICP8 molecule with green fluorescent protein (GFP) fused to its C terminus. In transfected Vero cells that were infected with HSV, the ICP8-GFP protein localized to prereplicative sites in the presence of the viral DNA synthesis inhibitor phosphonoacetic acid (PAA) or to replication compartments in the absence of PAA. A recombinant HSV-1 strain expressing the ICP8-GFP virus replicated in Vero cells, but the yield was increased by 150-fold in an ICP8-complementing cell line. Using the ICP8-GFP protein as a marker for replication compartments, we show here that these structures start as punctate structures early in infection and grow into large, globular structures that eventually fill the nucleus. Large replication compartments were formed by small structures that either moved through the nucleus to merge with adjacent compartments or remained relatively stationary within the nucleus and grew by accretion and fused with neighboring structures

  19. Effect of paddock vs. stall housing on 24 hour gastric pH within the proximal and ventral equine stomach.

    Science.gov (United States)

    Husted, L; Sanchez, L C; Olsen, S N; Baptiste, K E; Merritt, A M

    2008-06-01

    Stall housing has been suggested as a risk factor for ulcer development in the equine stomach; however, the exact pathogenesis for this has not been established. To investigate the effect of 3 environmental situations (grass paddock, stall alone or stall with adjacent companion) on pH in the proximal and the ventral stomach. Six horses with permanently implanted gastric cannulae were used in a randomised, cross-over, block design. Each horse rotated through each of three 24 h environmental situations. Horses remained on their normal diet (grass hay ad libitum and grain b.i.d.) throughout the study. Intragastric pH was measured continuously for 72 h just inside the lower oesophageal sphincter (proximal stomach) and via a pH probe in the gastric cannula (ventral stomach). Neither proximal nor ventral 24 h gastric pH changed significantly between the 3 environmental situations. Mean hourly proximal gastric pH decreased significantly in the interval from 01.00-09.00 h compared to the interval from 13.00-20.00 h, regardless of environmental situation. Median hourly proximal pH only differed in the interval from 06.00-07.00 h compared to the interval 14.00-19.00 h. Neither mean nor median hourly ventral gastric pH varied significantly with the time of day. The change in housing status used in the current study did not affect acid exposure within either region of the equine stomach. The pH in the ventral stomach was uniformly stable throughout the study, while the proximal pH demonstrated a 24 h circadian pattern.

  20. Replication and Robustness in Developmental Research

    Science.gov (United States)

    Duncan, Greg J.; Engel, Mimi; Claessens, Amy; Dowsett, Chantelle J.

    2014-01-01

    Replications and robustness checks are key elements of the scientific method and a staple in many disciplines. However, leading journals in developmental psychology rarely include explicit replications of prior research conducted by different investigators, and few require authors to establish in their articles or online appendices that their key…

  1. Three Conceptual Replication Studies in Group Theory

    Science.gov (United States)

    Melhuish, Kathleen

    2018-01-01

    Many studies in mathematics education research occur with a nonrepresentative sample and are never replicated. To challenge this paradigm, I designed a large-scale study evaluating student conceptions in group theory that surveyed a national, representative sample of students. By replicating questions previously used to build theory around student…

  2. Using Replication Projects in Teaching Research Methods

    Science.gov (United States)

    Standing, Lionel G.; Grenier, Manuel; Lane, Erica A.; Roberts, Meigan S.; Sykes, Sarah J.

    2014-01-01

    It is suggested that replication projects may be valuable in teaching research methods, and also address the current need in psychology for more independent verification of published studies. Their use in an undergraduate methods course is described, involving student teams who performed direct replications of four well-known experiments, yielding…

  3. Dynamic behavior of DNA replication domains

    NARCIS (Netherlands)

    Manders, E. M.; Stap, J.; Strackee, J.; van Driel, R.; Aten, J. A.

    1996-01-01

    Like many nuclear processes, DNA replication takes place in distinct domains that are scattered throughout the S-phase nucleus. Recently we have developed a fluorescent double-labeling procedure that allows us to visualize nascent DNA simultaneously with "newborn" DNA that had replicated earlier in

  4. Injury scores and locomotor disorders of Holstein cows in a free-stall facility with different beds

    OpenAIRE

    Cecchin, Daiane; Universidade Federal de Lavras - UFLA Lavras - MG; Campos, Alessandro Torres; Universidade Federal de Lavras - UFLA Lavras - MG; Pires, Maria de Fátima Ávila; Sousa, Francine Aparecida; Universidade Federal de Lavras - UFLA Lavras - MG; Amaral, Pedro Ivo Sodré; Universidade Federal de Lavras - UFLA Lavras - MG; Yanagi Junior, Tadayuki; Universidade Federal de Lavras - UFLA Lavras - MG; Ferreira, Suane Alves; Médica Veterinária – UNIPAC Juiz de Fora, MG.; Souza, Myriam Cristiane Morais; Graduanda em Medicina Veterinária – UNIPAC Juiz de Fora, MG.; Cecchin, Diego; Especialista em Gestão – UPF, Passo Fundo, RS

    2015-01-01

    The aim of the present study was to evaluate hock and knee injuries and locomotor disorders in 36 multiparous Holstein cows confined in a free-stall model system with two types of beds at Embrapa Dairy Cattle in the city of Coronel Pacheco / MG. Rubber composite beds and sand beds were compared and the hock and knee injuries and locomotor disorders were assessed for severity scores. There was no difference between the scores or hock lesions observed at the beginning and end of the trial perio...

  5. REVIVAL OF THE STALLED CORE-COLLAPSE SUPERNOVA SHOCK TRIGGERED BY PRECOLLAPSE ASPHERICITY IN THE PROGENITOR STAR

    International Nuclear Information System (INIS)

    Couch, Sean M.; Ott, Christian D.

    2013-01-01

    Multi-dimensional simulations of advanced nuclear burning stages of massive stars suggest that the Si/O layers of presupernova stars harbor large deviations from the spherical symmetry typically assumed for presupernova stellar structure. We carry out three-dimensional core-collapse supernova simulations with and without aspherical velocity perturbations to assess their potential impact on the supernova hydrodynamics in the stalled-shock phase. Our results show that realistic perturbations can qualitatively alter the postbounce evolution, triggering an explosion in a model that fails to explode without them. This finding underlines the need for a multi-dimensional treatment of the presupernova stage of stellar evolution

  6. REVIVAL OF THE STALLED CORE-COLLAPSE SUPERNOVA SHOCK TRIGGERED BY PRECOLLAPSE ASPHERICITY IN THE PROGENITOR STAR

    Energy Technology Data Exchange (ETDEWEB)

    Couch, Sean M. [Flash Center for Computational Science, Department of Astronomy and Astrophysics, University of Chicago, Chicago, IL 60637 (United States); Ott, Christian D., E-mail: smc@flash.uchichago.edu, E-mail: cott@tapir.caltech.edu [TAPIR, Mailcode 350-17, California Institute of Technology, Pasadena, CA 91125 (United States)

    2013-11-20

    Multi-dimensional simulations of advanced nuclear burning stages of massive stars suggest that the Si/O layers of presupernova stars harbor large deviations from the spherical symmetry typically assumed for presupernova stellar structure. We carry out three-dimensional core-collapse supernova simulations with and without aspherical velocity perturbations to assess their potential impact on the supernova hydrodynamics in the stalled-shock phase. Our results show that realistic perturbations can qualitatively alter the postbounce evolution, triggering an explosion in a model that fails to explode without them. This finding underlines the need for a multi-dimensional treatment of the presupernova stage of stellar evolution.

  7. Hepatitis A Virus Genome Organization and Replication Strategy.

    Science.gov (United States)

    McKnight, Kevin L; Lemon, Stanley M

    2018-04-02

    Hepatitis A virus (HAV) is a positive-strand RNA virus classified in the genus Hepatovirus of the family Picornaviridae It is an ancient virus with a long evolutionary history and multiple features of its capsid structure, genome organization, and replication cycle that distinguish it from other mammalian picornaviruses. HAV proteins are produced by cap-independent translation of a single, long open reading frame under direction of an inefficient, upstream internal ribosome entry site (IRES). Genome replication occurs slowly and is noncytopathic, with transcription likely primed by a uridylated protein primer as in other picornaviruses. Newly produced quasi-enveloped virions (eHAV) are released from cells in a nonlytic fashion in a unique process mediated by interactions of capsid proteins with components of the host cell endosomal sorting complexes required for transport (ESCRT) system. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

  8. 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…

  9. 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…

  10. Stall margin improvement of an axial flow fan with end wall injection and suction; Hekimen fukidashi suidashi ni yoru han'yo jikuryu sofuki no shissoku kaizen

    Energy Technology Data Exchange (ETDEWEB)

    Nishioka, K.; Kuroda, H.; Obata, S.; Chimura, O. [National Defense Academy, Kanagawa (Japan)

    1999-06-25

    The experimental studies are conducted to reveal the mechanism of stall margin improvement of an axial flow fan by injection or suction from the end wall. In case of injection, the largest improvement is obtained by the injection at about 0. 14 {approx} 0 .21 times axial chord length downstream from leading edge. The reason for large improvement is that stall vortex, shed intermittent separation vortex and tip leakage vortex are dissipated by this injection, and also that this blowing suppresses the separation of boundary layer. In case of suction, the largest improvement is found for the suction from the end wall near leading edge. The amplitude of periodic static pressure after stall inception becomes smaller in comparison with injection cases. These effects are increased with the increase of suction flow rate, because the discharge of the vortex occurs more easily. On the other hand, the suction from the upstream of leading edge reduces the axial velocity near rotor tip, and then it induces stall. Also we tried to visualize the tip region flow, The suppression mechanism is discussed based on the visualization. The suppression of stall is successfully photographed. (author)

  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. P-body proteins regulate transcriptional rewiring to promote DNA replication stress resistance.

    Science.gov (United States)

    Loll-Krippleber, Raphael; Brown, Grant W

    2017-09-15

    mRNA-processing (P-) bodies are cytoplasmic granules that form in eukaryotic cells in response to numerous stresses to serve as sites of degradation and storage of mRNAs. Functional P-bodies are critical for the DNA replication stress response in yeast, yet the repertoire of P-body targets and the mechanisms by which P-bodies promote replication stress resistance are unknown. In this study we identify the complete complement of mRNA targets of P-bodies during replication stress induced by hydroxyurea treatment. The key P-body protein Lsm1 controls the abundance of HHT1, ACF4, ARL3, TMA16, RRS1 and YOX1 mRNAs to prevent their toxic accumulation during replication stress. Accumulation of YOX1 mRNA causes aberrant downregulation of a network of genes critical for DNA replication stress resistance and leads to toxic acetaldehyde accumulation. Our data reveal the scope and the targets of regulation by P-body proteins during the DNA replication stress response.P-bodies form in response to stress and act as sites of mRNA storage and degradation. Here the authors identify the mRNA targets of P-bodies during DNA replication stress, and show that P-body proteins act to prevent toxic accumulation of these target transcripts.

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

    Science.gov (United States)

    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.

  14. Surface Microstructure Replication in Injection Moulding

    DEFF Research Database (Denmark)

    Hansen, Hans Nørgaard; Arlø, Uffe Rolf

    2005-01-01

    topography is transcribed onto the plastic part through complex mechanisms. This replication however, is not perfect, and the replication quality depends on the plastic material properties, the topography itself, and the process conditions. This paper describes and discusses an investigation of injection...... moulding of surface microstructures. Emphasis is put on the ability to replicate surface microstructures under normal injection moulding conditions, notably with low cost materials at low mould temperatures. The replication of surface microstructures in injection moulding has been explored...... for Polypropylene at low mould temperatures. The process conditions were varied over the recommended process window for the material. The geometry of the obtained structures was analyzed. Evidence suggests that step height replication quality depends linearly on structure width in a certain range. Further...

  15. Surface microstructure replication in injection molding

    DEFF Research Database (Denmark)

    Theilade, Uffe Arlø; Hansen, Hans Nørgaard

    2006-01-01

    topography is transcribed onto the plastic part through complex mechanisms. This replication, however, is not perfect, and the replication quality depends on the plastic material properties, the topography itself, and the process conditions. This paper describes and discusses an investigation of injection...... molding of surface microstructures. The fundamental problem of surface microstructure replication has been studied. The research is based on specific microstructures as found in lab-on-a-chip products and on rough surfaces generated from EDM (electro discharge machining) mold cavities. Emphasis is put...... on the ability to replicate surface microstructures under normal injection-molding conditions, i.e., with commodity materials within typical process windows. It was found that within typical process windows the replication quality depends significantly on several process parameters, and especially the mold...

  16. Rescue from replication stress during mitosis.

    Science.gov (United States)

    Fragkos, Michalis; Naim, Valeria

    2017-04-03

    Genomic instability is a hallmark of cancer and a common feature of human disorders, characterized by growth defects, neurodegeneration, cancer predisposition, and aging. Recent evidence has shown that DNA replication stress is a major driver of genomic instability and tumorigenesis. Cells can undergo mitosis with under-replicated DNA or unresolved DNA structures, and specific pathways are dedicated to resolving these structures during mitosis, suggesting that mitotic rescue from replication stress (MRRS) is a key process influencing genome stability and cellular homeostasis. Deregulation of MRRS following oncogene activation or loss-of-function of caretaker genes may be the cause of chromosomal aberrations that promote cancer initiation and progression. In this review, we discuss the causes and consequences of replication stress, focusing on its persistence in mitosis as well as the mechanisms and factors involved in its resolution, and the potential impact of incomplete replication or aberrant MRRS on tumorigenesis, aging and disease.

  17. Suppression of Poxvirus Replication by Resveratrol.

    Science.gov (United States)

    Cao, Shuai; Realegeno, Susan; Pant, Anil; Satheshkumar, Panayampalli S; Yang, Zhilong

    2017-01-01

    Poxviruses continue to cause serious diseases even after eradication of the historically deadly infectious human disease, smallpox. Poxviruses are currently being developed as vaccine vectors and cancer therapeutic agents. Resveratrol is a natural polyphenol stilbenoid found in plants that has been shown to inhibit or enhance replication of a number of viruses, but the effect of resveratrol on poxvirus replication is unknown. In the present study, we found that resveratrol dramatically suppressed the replication of vaccinia virus (VACV), the prototypic member of poxviruses, in various cell types. Resveratrol also significantly reduced the replication of monkeypox virus, a zoonotic virus that is endemic in Western and Central Africa and causes human mortality. The inhibitory effect of resveratrol on poxviruses is independent of VACV N1 protein, a potential resveratrol binding target. Further experiments demonstrated that resveratrol had little effect on VACV early gene expression, while it suppressed VACV DNA synthesis, and subsequently post-replicative gene expression.

  18. Suppression of Poxvirus Replication by Resveratrol

    Directory of Open Access Journals (Sweden)

    Shuai Cao

    2017-11-01

    Full Text Available Poxviruses continue to cause serious diseases even after eradication of the historically deadly infectious human disease, smallpox. Poxviruses are currently being developed as vaccine vectors and cancer therapeutic agents. Resveratrol is a natural polyphenol stilbenoid found in plants that has been shown to inhibit or enhance replication of a number of viruses, but the effect of resveratrol on poxvirus replication is unknown. In the present study, we found that resveratrol dramatically suppressed the replication of vaccinia virus (VACV, the prototypic member of poxviruses, in various cell types. Resveratrol also significantly reduced the replication of monkeypox virus, a zoonotic virus that is endemic in Western and Central Africa and causes human mortality. The inhibitory effect of resveratrol on poxviruses is independent of VACV N1 protein, a potential resveratrol binding target. Further experiments demonstrated that resveratrol had little effect on VACV early gene expression, while it suppressed VACV DNA synthesis, and subsequently post-replicative gene expression.

  19. Defective replication initiation results in locus specific chromosome breakage and a ribosomal RNA deficiency in yeast.

    Directory of Open Access Journals (Sweden)

    Joseph C Sanchez

    2017-10-01

    Full Text Available A form of dwarfism known as Meier-Gorlin syndrome (MGS is caused by recessive mutations in one of six different genes (ORC1, ORC4, ORC6, CDC6, CDT1, and MCM5. These genes encode components of the pre-replication complex, which assembles at origins of replication prior to S phase. Also, variants in two additional replication initiation genes have joined the list of causative mutations for MGS (Geminin and CDC45. The identity of the causative MGS genetic variants strongly suggests that some aspect of replication is amiss in MGS patients; however, little evidence has been obtained regarding what aspect of chromosome replication is faulty. Since the site of one of the missense mutations in the human ORC4 alleles is conserved between humans and yeast, we sought to determine in what way this single amino acid change affects the process of chromosome replication, by introducing the comparable mutation into yeast (orc4Y232C. We find that yeast cells with the orc4Y232C allele have a prolonged S-phase, due to compromised replication initiation at the ribosomal DNA (rDNA locus located on chromosome XII. The inability to initiate replication at the rDNA locus results in chromosome breakage and a severely reduced rDNA copy number in the survivors, presumably helping to ensure complete replication of chromosome XII. Although reducing rDNA copy number may help ensure complete chromosome replication, orc4Y232C cells struggle to meet the high demand for ribosomal RNA synthesis. This finding provides additional evidence linking two essential cellular pathways-DNA replication and ribosome biogenesis.

  20. Defective replication initiation results in locus specific chromosome breakage and a ribosomal RNA deficiency in yeast.

    Science.gov (United States)

    Sanchez, Joseph C; Kwan, Elizabeth X; Pohl, Thomas J; Amemiya, Haley M; Raghuraman, M K; Brewer, Bonita J

    2017-10-01

    A form of dwarfism known as Meier-Gorlin syndrome (MGS) is caused by recessive mutations in one of six different genes (ORC1, ORC4, ORC6, CDC6, CDT1, and MCM5). These genes encode components of the pre-replication complex, which assembles at origins of replication prior to S phase. Also, variants in two additional replication initiation genes have joined the list of causative mutations for MGS (Geminin and CDC45). The identity of the causative MGS genetic variants strongly suggests that some aspect of replication is amiss in MGS patients; however, little evidence has been obtained regarding what aspect of chromosome replication is faulty. Since the site of one of the missense mutations in the human ORC4 alleles is conserved between humans and yeast, we sought to determine in what way this single amino acid change affects the process of chromosome replication, by introducing the comparable mutation into yeast (orc4Y232C). We find that yeast cells with the orc4Y232C allele have a prolonged S-phase, due to compromised replication initiation at the ribosomal DNA (rDNA) locus located on chromosome XII. The inability to initiate replication at the rDNA locus results in chromosome breakage and a severely reduced rDNA copy number in the survivors, presumably helping to ensure complete replication of chromosome XII. Although reducing rDNA copy number may help ensure complete chromosome replication, orc4Y232C cells struggle to meet the high demand for ribosomal RNA synthesis. This finding provides additional evidence linking two essential cellular pathways-DNA replication and ribosome biogenesis.

  1. Transcription and replication result in distinct epigenetic marks following repression of early gene expression

    OpenAIRE

    Kallestad, Les; Woods, Emily; Christensen, Kendra; Gefroh, Amanda; Balakrishnan, Lata; Milavetz, Barry

    2013-01-01

    Simian Virus 40 (SV40) early transcription is repressed when the product of early transcription, T-antigen, binds to its cognate regulatory sequence, Site I, in the promoter of the SV40 minichromosome. Because SV40 minichromosomes undergo replication and transcription potentially repression could occur during active transcription or during DNA replication. Since repression is frequently epigenetically marked by the introduction of specific forms of methylated histone H3, we characterized th...

  2. 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.)

  3. 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

  4. The DNA replication checkpoint directly regulates MBF-dependent G1/S transcription.

    Science.gov (United States)

    Dutta, Chaitali; Patel, Prasanta K; Rosebrock, Adam; Oliva, Anna; Leatherwood, Janet; Rhind, Nicholas

    2008-10-01

    The DNA replication checkpoint transcriptionally upregulates genes that allow cells to adapt to and survive replication stress. Our results show that, in the fission yeast Schizosaccharomyces pombe, the replication checkpoint regulates the entire G(1)/S transcriptional program by directly regulating MBF, the G(1)/S transcription factor. Instead of initiating a checkpoint-specific transcriptional program, the replication checkpoint targets MBF to maintain the normal G(1)/S transcriptional program during replication stress. We propose a mechanism for this regulation, based on in vitro phosphorylation of the Cdc10 subunit of MBF by the Cds1 replication-checkpoint kinase. Replacement of two potential phosphorylation sites with phosphomimetic amino acids suffices to promote the checkpoint transcriptional program, suggesting that Cds1 phosphorylation directly regulates MBF-dependent transcription. The conservation of MBF between fission and budding yeast, and recent results implicating MBF as a target of the budding yeast replication checkpoint, suggests that checkpoint regulation of the MBF transcription factor is a conserved strategy for coping with replication stress. Furthermore, the structural and regulatory similarity between MBF and E2F, the metazoan G(1)/S transcription factor, suggests that this checkpoint mechanism may be broadly conserved among eukaryotes.

  5. The DNA Replication Checkpoint Directly Regulates MBF-Dependent G1/S Transcription▿

    Science.gov (United States)

    Dutta, Chaitali; Patel, Prasanta K.; Rosebrock, Adam; Oliva, Anna; Leatherwood, Janet; Rhind, Nicholas

    2008-01-01

    The DNA replication checkpoint transcriptionally upregulates genes that allow cells to adapt to and survive replication stress. Our results show that, in the fission yeast Schizosaccharomyces pombe, the replication checkpoint regulates the entire G1/S transcriptional program by directly regulating MBF, the G1/S transcription factor. Instead of initiating a checkpoint-specific transcriptional program, the replication checkpoint targets MBF to maintain the normal G1/S transcriptional program during replication stress. We propose a mechanism for this regulation, based on in vitro phosphorylation of the Cdc10 subunit of MBF by the Cds1 replication-checkpoint kinase. Replacement of two potential phosphorylation sites with phosphomimetic amino acids suffices to promote the checkpoint transcriptional program, suggesting that Cds1 phosphorylation directly regulates MBF-dependent transcription. The conservation of MBF between fission and budding yeast, and recent results implicating MBF as a target of the budding yeast replication checkpoint, suggests that checkpoint regulation of the MBF transcription factor is a conserved strategy for coping with replication stress. Furthermore, the structural and regulatory similarity between MBF and E2F, the metazoan G1/S transcription factor, suggests that this checkpoint mechanism may be broadly conserved among eukaryotes. PMID:18662996

  6. 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.

  7. Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability

    NARCIS (Netherlands)

    Wanzek, Katharina; Schwindt, Eike; Capra, John A.; Paeschke, Katrin

    2017-01-01

    The regulation of replication is essential to preserve genome integrity. Mms1 is part of the E3 ubiquitin ligase complex that is linked to replication fork progression. By identifying Mms1 binding sites genome-wide in Saccharomyces cerevisiae we connected Mms1 function to genome integrity and

  8. 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.

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

    Science.gov (United States)

    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.

  10. 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.

  11. Targeting DNA Replication Stress for Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    2016-08-01

    Full Text Available The human cellular genome is under constant stress from extrinsic and intrinsic factors, which can lead to DNA damage and defective replication. In normal cells, DNA damage response (DDR mediated by various checkpoints will either activate the DNA repair system or induce cellular apoptosis/senescence, therefore maintaining overall genomic integrity. Cancer cells, however, due to constitutive growth signaling and defective DDR, may exhibit “replication stress” —a phenomenon unique to cancer cells that is described as the perturbation of error-free DNA replication and slow-down of DNA synthesis. Although replication stress has been proven to induce genomic instability and tumorigenesis, recent studies have counterintuitively shown that enhancing replicative stress through further loosening of the remaining checkpoints in cancer cells to induce their catastrophic failure of proliferation may provide an alternative therapeutic approach. In this review, we discuss the rationale to enhance replicative stress in cancer cells, past approaches using traditional radiation and chemotherapy, and emerging approaches targeting the signaling cascades induced by DNA damage. We also summarize current clinical trials exploring these strategies and propose future research directions including the use of combination therapies, and the identification of potential new targets and biomarkers to track and predict treatment responses to targeting DNA replication stress.

  12. Factors influencing microinjection molding replication quality

    Science.gov (United States)

    Vera, Julie; Brulez, Anne-Catherine; Contraires, Elise; Larochette, Mathieu; Trannoy-Orban, Nathalie; Pignon, Maxime; Mauclair, Cyril; Valette, Stéphane; Benayoun, Stéphane

    2018-01-01

    In recent years, there has been increased interest in producing and providing high-precision plastic parts that can be manufactured by microinjection molding: gears, pumps, optical grating elements, and so on. For all of these applications, the replication quality is essential. This study has two goals: (1) fabrication of high-precision parts using the conventional injection molding machine; (2) identification of robust parameters that ensure production quality. Thus, different technological solutions have been used: cavity vacuuming and the use of a mold coated with DLC or CrN deposits. AFM and SEM analyses were carried out to characterize the replication profile. The replication quality was studied in terms of the process parameters, coated and uncoated molds and crystallinity of the polymer. Specific studies were processed to quantify the replicability of injection molded parts (ABS, PC and PP). Analysis of the Taguchi experimental designs permits prioritization of the impact of each parameter on the replication quality. A discussion taking into account these new parameters and the thermal and spreading properties on the coatings is proposed. It appeared that, in general, increasing the mold temperature improves the molten polymer fill in submicron features except for the steel insert (for which the presence of a vacuum is the most important factor). Moreover, the DLC coating was the best coating to increase the quality of the replication. This result could be explained by the lower thermal diffusivity of this coating. We noted that the viscosity of the polymers is not a primordial factor of the replication quality.

  13. The Inherent Asymmetry of DNA Replication.

    Science.gov (United States)

    Snedeker, Jonathan; Wooten, Matthew; Chen, Xin

    2017-10-06

    Semiconservative DNA replication has provided an elegant solution to the fundamental problem of how life is able to proliferate in a way that allows cells, organisms, and populations to survive and replicate many times over. Somewhat lost, however, in our admiration for this mechanism is an appreciation for the asymmetries that occur in the process of DNA replication. As we discuss in this review, these asymmetries arise as a consequence of the structure of the DNA molecule and the enzymatic mechanism of DNA synthesis. Increasing evidence suggests that asymmetries in DNA replication are able to play a central role in the processes of adaptation and evolution by shaping the mutagenic landscape of cells. Additionally, in eukaryotes, recent work has demonstrated that the inherent asymmetries in DNA replication may play an important role in the process of chromatin replication. As chromatin plays an essential role in defining cell identity, asymmetries generated during the process of DNA replication may play critical roles in cell fate decisions related to patterning and development.

  14. Ultrastructural Characterization of Zika Virus Replication Factories

    Directory of Open Access Journals (Sweden)

    Mirko Cortese

    2017-02-01

    Full Text Available Summary: A global concern has emerged with the pandemic spread of Zika virus (ZIKV infections that can cause severe neurological symptoms in adults and newborns. ZIKV is a positive-strand RNA virus replicating in virus-induced membranous replication factories (RFs. Here we used various imaging techniques to investigate the ultrastructural details of ZIKV RFs and their relationship with host cell organelles. Analyses of human hepatic cells and neural progenitor cells infected with ZIKV revealed endoplasmic reticulum (ER membrane invaginations containing pore-like openings toward the cytosol, reminiscent to RFs in Dengue virus-infected cells. Both the MR766 African strain and the H/PF/2013 Asian strain, the latter linked to neurological diseases, induce RFs of similar architecture. Importantly, ZIKV infection causes a drastic reorganization of microtubules and intermediate filaments forming cage-like structures surrounding the viral RF. Consistently, ZIKV replication is suppressed by cytoskeleton-targeting drugs. Thus, ZIKV RFs are tightly linked to rearrangements of the host cell cytoskeleton. : Cortese et al. show that ZIKV infection in both human hepatoma and neuronal progenitor cells induces drastic structural modification of the cellular architecture. Microtubules and intermediate filaments surround the viral replication factory composed of vesicles corresponding to ER membrane invagination toward the ER lumen. Importantly, alteration of microtubule flexibility impairs ZIKV replication. Keywords: Zika virus, flavivirus, human neural progenitor cells, replication factories, replication organelles, microtubules, intermediate filaments, electron microscopy, electron tomography, live-cell imaging

  15. A Beddoes-Leishman type dynamic stall model in state-space and indicial formulations[Wind turbines

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, M.H.; Gaunaa, M.; Aagaard Madsen, H.

    2004-06-01

    This report contains a description of a Beddoes-Leishman type dynamic stall model in both a state-space and an indicial function formulation. The m odel predicts the unsteady aerodynamic foreces and moment on an airfoil section undergoing arbitrary motion in heavy, lead-lag, and pitch. The model includes the effects of shed vorticity from the trailing edge (Theodorsen Theory), and the effects of an instationary trailing edge separation point. The governing equations of the model are nonlinear, and they are linearized about a steady state for application in stability analyzes. A validation is carried out by comparing the response of the model with inviscid solutions and observing the general behavior of the model using known airfoil data as input. The proposed dyanmic model gives results identical to inviscid solutions within the attached-flow region; and it exhibits the expected dynamic features, such as overshoot of the lift, in the stall region. The linearized model is shown to give identical results to the full model for small amplitude oscillations. furthermore, it is shown that the response of finite thickness airfoils can be reproduced to a high accuracy by the use of specific inviscid response functions. (au)

  16. A model for roll stall and the inherent stability modes of low aspect ratio wings at low Reynolds numbers

    Science.gov (United States)

    Shields, Matt

    The development of Micro Aerial Vehicles has been hindered by the poor understanding of the aerodynamic loading and stability and control properties of the low Reynolds number regime in which the inherent low aspect ratio (LAR) wings operate. This thesis experimentally evaluates the static and damping aerodynamic stability derivatives to provide a complete aerodynamic model for canonical flat plate wings of aspect ratios near unity at Reynolds numbers under 1 x 105. This permits the complete functionality of the aerodynamic forces and moments to be expressed and the equations of motion to solved, thereby identifying the inherent stability properties of the wing. This provides a basis for characterizing the stability of full vehicles. The influence of the tip vortices during sideslip perturbations is found to induce a loading condition referred to as roll stall, a significant roll moment created by the spanwise induced velocity asymmetry related to the displacement of the vortex cores relative to the wing. Roll stall is manifested by a linearly increasing roll moment with low to moderate angles of attack and a subsequent stall event similar to a lift polar; this behavior is not experienced by conventional (high aspect ratio) wings. The resulting large magnitude of the roll stability derivative, Cl,beta and lack of roll damping, Cl ,rho, create significant modal responses of the lateral state variables; a linear model used to evaluate these modes is shown to accurately reflect the solution obtained by numerically integrating the nonlinear equations. An unstable Dutch roll mode dominates the behavior of the wing for small perturbations from equilibrium, and in the presence of angle of attack oscillations a previously unconsidered coupled mode, referred to as roll resonance, is seen develop and drive the bank angle? away from equilibrium. Roll resonance requires a linear time variant (LTV) model to capture the behavior of the bank angle, which is attributed to the

  17. 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

  18. Replicated Data Management for Mobile Computing

    CERN Document Server

    Douglas, Terry

    2008-01-01

    Managing data in a mobile computing environment invariably involves caching or replication. In many cases, a mobile device has access only to data that is stored locally, and much of that data arrives via replication from other devices, PCs, and services. Given portable devices with limited resources, weak or intermittent connectivity, and security vulnerabilities, data replication serves to increase availability, reduce communication costs, foster sharing, and enhance survivability of critical information. Mobile systems have employed a variety of distributed architectures from client-server

  19. 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

  20. Avaliação de diferentes materiais para recobrimento de camas em baias de galpão modelo free-stall

    OpenAIRE

    Cecchin, Daiane; Campos, Alessandro T.; Pires, Maria de F. A.; Lima, Renato R. de; Yanagi Junior, Tadayuki; Souza, Myriam C. M.

    2014-01-01

    Objetivou-se, com o presente trabalho, comparar o uso de cama de colchão de borracha e de areia no recobrimento da superfície de baias para confinamento tipo free-stall. Foram monitoradas 18 vacas holandesas confinadas em galpão modelo free-stall cujas baias foram recobertas com camas de areia e colchão de borracha (tratamentos). O delineamento experimental foi em blocos casualizados. Os parâmetros comportamentais estudados foram os tempos despendidos nas atividades: deitada em ócio e deitada...