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Sample records for replication stalling inducing

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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...

  6. 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...

  7. 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.

  8. 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.

  9. 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...

  10. 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)

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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...

  6. 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....

  7. 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...

  8. 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

  9. 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.

  10. 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

  11. Mammalian RAD52 Functions in Break-Induced Replication Repair of Collapsed DNA Replication Forks.

    Science.gov (United States)

    Sotiriou, Sotirios K; Kamileri, Irene; Lugli, Natalia; Evangelou, Konstantinos; Da-Ré, Caterina; Huber, Florian; Padayachy, Laura; Tardy, Sebastien; Nicati, Noemie L; Barriot, Samia; Ochs, Fena; Lukas, Claudia; Lukas, Jiri; Gorgoulis, Vassilis G; Scapozza, Leonardo; Halazonetis, Thanos D

    2016-12-15

    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 depletion inhibited G1 to S phase progression when oncogenic cyclin E was overexpressed. RAD52, a gene dispensable for normal development in mice, was among the top hits. In cells in which fork collapse was induced by oncogenes or chemicals, the Rad52 protein localized to DRS foci. Depletion of Rad52 by siRNA or knockout of the gene by CRISPR/Cas9 compromised restart of collapsed forks and led to DNA damage in cells experiencing DRS. Furthermore, in cancer-prone, heterozygous APC mutant mice, homozygous deletion of the Rad52 gene suppressed tumor growth and prolonged lifespan. We therefore propose that mammalian RAD52 facilitates repair of collapsed DNA replication forks in cancer cells. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  12. Suppression of inducer stall based on inlet recirculation in a centrifugal impeller. 1st Report. Improvement in stall limit by ring groove arrangement; Enshin haneguruma iriguchi junkanryu ni yoru inducer shissoku no yokusei. 1. kanjoko ni yoru shissoku genkai no kaizen

    Energy Technology Data Exchange (ETDEWEB)

    Ueki, H.; Ishida, M.; Sakaguchi, D.; Sun, Z. [Nagasaki University, Nagasaki (Japan). Faculty of Engineering

    2000-07-25

    A ring groove arrangement is proposed to suppress unstable flow or surge in a centrifugal blower. The ring groove arrangement connects the upstream position of impeller inlet and the inducer throat tip through a bypass. The recirculation flow 'vas formed by the pressure difference between the two positions, and the recirculation flow rate was changed by increasing the ring groove widths. The inlet recirculation results in a decrease in the flow rate of unstable flow inception, and an up to 800 improvement in stall limit was obtained by the ring groove arrangement at a small expense of the delivery pressure drop. The improvement of stall limit in the present experiment seems to be mainly due to decrease in flow incidence based on the inlet recirculation flow. Tre flow incidence decreases more as the recirculation flow rate increases, thus resulting in a larger improvement in stall limit. (author)

  13. Induction of UV-resistant DNA replication in Escherichia coli: Induced stable DNA replication as an SOS function

    International Nuclear Information System (INIS)

    Kogoma, T.; Torrey, T.A.; Connaughton, M.J.

    1979-01-01

    The striking similarity between the treatments that induce SOS functions and those that result in stable DNA replication (continuous DNA replication in the absence of protein synthesis) prompted us to examine the possibility of stable DNA replication being a recA + lexA + -dependent SOS function. In addition to the treatments previously reported, ultraviolet (UV) irradiation or treatment with mitomycin C was also found to induce stable DNA replication. The thermal treatment of tif-1 strains did not result in detectable levels of stable DNA replication, but nalidixic acid readily induced the activity in these strains. The induction of stable DNA replication with nalidixic acid was severely suppressed in tif-1 lex A mutant strains. The inhibitory activity of lexA3 was negated by the presence of the spr-5l mutation, an intragenic suppressor of lexA3. Induced stable DNA replication was found to be considerably more resistant to UV irradiation than normal replication both in a uvr A6 strain and a uvr + strain. The UV-resistant replication occurred mostly in the semiconservative manner. The possible roles of stable DNA replication in repair of damaged DNA are discussed. (orig.)

  14. Caffeine Abolishes the Ultraviolet-Induced REV3 Translesion Replication Pathway in Mouse Cells

    Directory of Open Access Journals (Sweden)

    Kouichi Yamada

    2011-11-01

    Full Text Available When a replicative DNA polymerase stalls upon encountering a photoproduct on the template strand, it is relieved by other low-processivity polymerase(s, which insert nucleotide(s opposite the lesion. Using an alkaline sucrose density gradient sedimentation technique, we previously classified this process termed UV-induced translesion replication (UV-TLS into two types. In human cancer cells or xeroderma pigmentosum variant (XP-V cells, UV-TLS was inhibited by caffeine or proteasome inhibitors. However, in normal human cells, the process was insensitive to these reagents. Reportedly, in yeast or mammalian cells, REV3 protein (a catalytic subunit of DNA polymerase ζ is predominantly involved in the former type of TLS. Here, we studied UV-TLS in fibroblasts derived from the Rev3-knockout mouse embryo (Rev3KO-MEF. In the wild-type MEF, UV-TLS was slow (similar to that of human cancer cells or XP-V cells, and was abolished by caffeine or MG-262. In 2 cell lines of Rev3KO-MEF (Rev3−/− p53−/−, UV-TLS was not observed. In p53KO-MEF, which is a strict control for Rev3KO-MEF, the UV-TLS response was similar to that of the wild-type. Introduction of the Rev3 expression plasmid into Rev3KO-MEF restored the UV-TLS response in selected stable transformants. In some transformants, viability to UV was the same as that in the wild-type, and the death rate was increased by caffeine. Our findings indicate that REV3 is predominantly involved in UV-TLS in mouse cells, and that the REV3 translesion pathway is suppressed by caffeine or proteasome inhibitors.

  15. Identification of 30 protein species involved in replicative senescence and stress-induced premature senescence

    DEFF Research Database (Denmark)

    Dierick, Jean François; Kalume, Dário E; Wenders, Frédéric

    2002-01-01

    Exposure of human proliferative cells to subcytotoxic stress triggers stress-induced premature senescence (SIPS) which is characterized by many biomarkers of replicative senescence. Proteomic comparison of replicative senescence and stress-induced premature senescence indicates that, at the level...

  16. DNA replication error-induced extinction of diploid yeast.

    Science.gov (United States)

    Herr, Alan J; Kennedy, Scott R; Knowels, Gary M; Schultz, Eric M; Preston, Bradley D

    2014-03-01

    Genetic defects in DNA polymerase accuracy, proofreading, or mismatch repair (MMR) induce mutator phenotypes that accelerate adaptation of microbes and tumor cells. Certain combinations of mutator alleles synergistically increase mutation rates to levels that drive extinction of haploid cells. The maximum tolerated mutation rate of diploid cells is unknown. Here, we define the threshold for replication error-induced extinction (EEX) of diploid Saccharomyces cerevisiae. Double-mutant pol3 alleles that carry mutations for defective DNA polymerase-δ proofreading (pol3-01) and accuracy (pol3-L612M or pol3-L612G) induce strong mutator phenotypes in heterozygous diploids (POL3/pol3-01,L612M or POL3/pol3-01,L612G). Both pol3-01,L612M and pol3-01,L612G alleles are lethal in the homozygous state; cells with pol3-01,L612M divide up to 10 times before arresting at random stages in the cell cycle. Antimutator eex mutations in the pol3 alleles suppress this lethality (pol3-01,L612M,eex or pol3-01,L612G,eex). MMR defects synergize with pol3-01,L612M,eex and pol3-01,L612G,eex alleles, increasing mutation rates and impairing growth. Conversely, inactivation of the Dun1 S-phase checkpoint kinase suppresses strong pol3-01,L612M,eex and pol3-01,L612G,eex mutator phenotypes as well as the lethal pol3-01,L612M phenotype. Our results reveal that the lethal error threshold in diploids is 10 times higher than in haploids and likely determined by homozygous inactivation of essential genes. Pronounced loss of fitness occurs at mutation rates well below the lethal threshold, suggesting that mutator-driven cancers may be susceptible to drugs that exacerbate replication errors.

  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. 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...

  19. Insulated hsp70B' promoter: stringent heat-inducible activity in replication-deficient, but not replication-competent adenoviruses.

    Science.gov (United States)

    Rohmer, Stanimira; Mainka, Astrid; Knippertz, Ilka; Hesse, Andrea; Nettelbeck, Dirk M

    2008-04-01

    Key to the realization of gene therapy is the development of efficient and targeted gene transfer vectors. Therapeutic gene transfer by replication-deficient or more recently by conditionally replication-competent/oncolytic adenoviruses has shown much promise. For specific applications, however, it will be advantageous to provide vectors that allow for external control of gene expression. The efficient cellular heat shock system in combination with available technology for focused and controlled hyperthermia suggests heat-regulated transcription control as a promising tool for this purpose. We investigated the feasibility of a short fragment of the human hsp70B' promoter, with and without upstream insulator elements, for the regulation of transgene expression by replication-deficient or oncolytic adenoviruses. Two novel adenoviral vectors with an insulated hsp70B' promoter were developed and showed stringent heat-inducible gene expression with induction ratios up to 8000-fold. In contrast, regulation of gene expression from the hsp70B' promoter without insulation was suboptimal. In replication-competent/oncolytic adenoviruses regulation of the hsp70B' promoter was lost specifically during late replication in permissive cells and could not be restored by the insulators. We developed novel adenovirus gene transfer vectors that feature improved and stringent regulation of transgene expression from the hsp70B' promoter using promoter insulation. These vectors have potential for gene therapy applications that benefit from external modulation of therapeutic gene expression or for combination therapy with hyperthermia. Furthermore, our study reveals that vector replication can deregulate inserted cellular promoters, an observation which is of relevance for the development of replication-competent/oncolytic gene transfer vectors. (c) 2008 John Wiley & Sons, Ltd.

  20. Identification of genes involved in low aminoglycoside-induced SOS response in Vibrio cholerae: a role for transcription stalling and Mfd helicase.

    Science.gov (United States)

    Baharoglu, Zeynep; Babosan, Anamaria; Mazel, Didier

    2014-02-01

    Sub-inhibitory concentrations (sub-MIC) of antibiotics play a very important role in selection and development of resistances. Unlike Escherichia coli, Vibrio cholerae induces its SOS response in presence of sub-MIC aminoglycosides. A role for oxidized guanine residues was observed, but the mechanisms of this induction remained unclear. To select for V. cholerae mutants that do not induce low aminoglycoside-mediated SOS induction, we developed a genetic screen that renders induction of SOS lethal. We identified genes involved in this pathway using two strategies, inactivation by transposition and gene overexpression. Interestingly, we obtained mutants inactivated for the expression of proteins known to destabilize the RNA polymerase complex. Reconstruction of the corresponding mutants confirmed their specific involvement in induction of SOS by low aminoglycoside concentrations. We propose that DNA lesions formed on aminoglycoside treatment are repaired through the formation of single-stranded DNA intermediates, inducing SOS. Inactivation of functions that dislodge RNA polymerase leads to prolonged stalling on these lesions, which hampers SOS induction and repair and reduces viability under antibiotic stress. The importance of these mechanisms is illustrated by a reduction of aminoglycoside sub-MIC. Our results point to a central role for transcription blocking at DNA lesions in SOS induction, so far underestimated.

  1. HCV-induced autophagosomes are generated via homotypic fusion of phagophores that mediate HCV RNA replication.

    Directory of Open Access Journals (Sweden)

    Linya Wang

    2017-09-01

    Full Text Available Hepatitis C virus (HCV induces autophagy to promote its replication, including its RNA replication, which can take place on double-membrane vesicles known as autophagosomes. However, how HCV induces the biogenesis of autophagosomes and how HCV RNA replication complex may be assembled on autophagosomes were largely unknown. During autophagy, crescent membrane structures known as phagophores first appear in the cytoplasm, which then progress to become autophagosomes. By conducting electron microscopy and in vitro membrane fusion assay, we found that phagophores induced by HCV underwent homotypic fusion to generate autophagosomes in a process dependent on the SNARE protein syntaxin 7 (STX7. Further analyses by live-cell imaging and fluorescence microscopy indicated that HCV-induced phagophores originated from the endoplasmic reticulum (ER. Interestingly, comparing with autophagy induced by nutrient starvation, the progression of phagophores to autophagosomes induced by HCV took significantly longer time, indicating fundamental differences in the biogenesis of autophagosomes induced by these two different stimuli. As the knockdown of STX7 to inhibit the formation of autophagosomes did not affect HCV RNA replication, and purified phagophores could mediate HCV RNA replication, the assembly of the HCV RNA replication complex on autophagosomes apparently took place during the formative stage of phagophores. These findings provided important information for understanding how HCV controlled and modified this important cellular pathway for its own replication.

  2. KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.

    Science.gov (United States)

    Betz, Karin; Malyshev, Denis A; Lavergne, Thomas; Welte, Wolfram; Diederichs, Kay; Dwyer, Tammy J; Ordoukhanian, Phillip; Romesberg, Floyd E; Marx, Andreas

    2012-07-01

    Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.

  3. 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.

  4. 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.

  5. Replicative Stress Induces Intragenic Transcription of the ASE1 Gene that Negatively Regulates Ase1 Activity

    OpenAIRE

    McKnight, Kelly; Liu, Hong; Wang, Yanchang

    2014-01-01

    Intragenic transcripts initiate within the coding region of a gene, thereby producing shorter mRNAs and proteins. Although intragenic transcripts are widely expressed [1], their role in the functional regulation of genes remains largely unknown. In budding yeast, DNA replication stress activates the S-phase checkpoint that stabilizes replication forks and arrests cells in S-phase with a short spindle [2-4]. When yeast cells were treated with hydroxyurea (HU) to block DNA synthesis and induce ...

  6. 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.

  7. The role of inducer cells in mediating in vitro suppression of feline immunodeficiency virus replication

    International Nuclear Information System (INIS)

    Phadke, Anagha P.; Choi, In-Soo; Li Zhongxia; Weaver, Eric; Collisson, Ellen W.

    2004-01-01

    CD8 + T-cell-mediated suppression of feline immunodeficiency virus (FIV) replication has been described by several groups, although the mechanisms of activation and conditions for viral suppression vary with the methodologies. We have previously reported that CD8 + T-cell-mediated suppression of FIV replication required inducer cell stimulation of the effector cells. The focus of the present study was to examine the essential role of inducer cells required for the induction of this soluble anti-FIV activity. Both FIV-PPR-infected T cells and feline skin fibroblasts (FSF) infected with an alphavirus vector expressing FIV capsid or the irrelevant antigen lacZ, stimulated autologous or heterologous effector cells to produce supernatants that suppressed FIV replication. Thus, induction of this suppression of FIV replication did not strictly require autologous inducer cells and did not require the presence of FIV antigen. Anti-viral activity correlated with the presence of CD8 + T cells. Suppression was maximal when the inducer cells and the effector cells were in contact with each other, because separation of the inducer and effector cells by a 0.45-μm membrane reduced FIV suppression by approximately 50%. These findings emphasize the importance for membrane antigen interactions and cytokines in the optimal induction of effector cell synthesis of the soluble anti-FIV activity

  8. 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...

  9. Rev1, Rev3, or Rev7 siRNA Abolishes Ultraviolet Light-Induced Translesion Replication in HeLa Cells: A Comprehensive Study Using Alkaline Sucrose Density Gradient Sedimentation

    Directory of Open Access Journals (Sweden)

    Jun Takezawa

    2010-01-01

    Full Text Available When a replicative DNA polymerase stalls upon encountering a lesion on the template strand, it is relieved by other low-processivity polymerase(s, which insert nucleotide(s opposite the lesion, extend by a few nucleotides, and dissociate from the 3′-OH. The replicative polymerase then resumes DNA synthesis. This process, termed translesion replication (TLS or replicative bypass, may involve at least five different polymerases in mammals, although the participating polymerases and their roles have not been entirely characterized. Using siRNAs originally designed and an alkaline sucrose density gradient sedimentation technique, we verified the involvement of several polymerases in ultraviolet (UV light-induced TLS in HeLa cells. First, siRNAs to Rev3 or Rev7 largely abolished UV-TLS, suggesting that these 2 gene products, which comprise Polζ, play a main role in mutagenic TLS. Second, Rev1-targeted siRNA also abrogated UV-TLS, indicating that Rev1 is also indispensable to mutagenic TLS. Third, Polη-targeted siRNA also prevented TLS to a greater extent than our expectations. Forth, although siRNA to Polι had no detectable effect, that to Polκ delayed UV-TLS. To our knowledge, this is the first study reporting apparent evidence for the participation of Polκ in UV-TLS.

  10. 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

  11. Effects of aphidicolin on repair replication and induced chromosomal aberrations in mammalian cells

    International Nuclear Information System (INIS)

    Zeeland, A.A. van; Filon, A.R.; Natarajan, A.T.; Bussmann, C.J.M.; Degrassi, F.; Kesteren-van Leeuwen, A.C. van; Palitti, F.; Rome Univ.

    1982-01-01

    The influence of aphidicolin, an inhibitor of polymerase α, on UV-induced repair replication in human skin fibroblasts, as well as in HeLa cells, was determined. In growing fibroblasts and in HeLa cells, aphidicolin had a potentiating effect on UV-induced repair replication, whereas in fibroblasts grown to confluency, aphidicolin had an inhibitory effect. This inhibitory effect was stronger when measured in the presence of hydroxyurea. In HeLa cells the presence of both aphidicolin and hydroxyurea also had an inhibitory effect, but in the presence of hydroxyurea alone, UV-induced repair replication was enhanced. The results of these studies can be explained on the basis of differences in deoxyribonucleotide triphosphate pool sizes in growing and confluent cells. Post-treatment of X-irradiated human lymphocytes in the G 0 and G 1 stages with aphidicolin increased the frequencies of X-ray-induced chromosomal aberrations. Such an increase was not observed in G 1 cells of CHO after similar treatment with X-rays and aphidicolin. However, treatment with aphidicolin, in the G 2 stage, increased the frequencies of induced chromatid breaks. The significance of these results is discussed. (orig.)

  12. Influenza Virus Induces Inflammatory Response in Mouse Primary Cortical Neurons with Limited Viral Replication

    Directory of Open Access Journals (Sweden)

    Gefei Wang

    2016-01-01

    Full Text Available Unlike stereotypical neurotropic viruses, influenza A viruses have been detected in the brain tissues of human and animal models. To investigate the interaction between neurons and influenza A viruses, mouse cortical neurons were isolated, infected with human H1N1 influenza virus, and then examined for the production of various inflammatory molecules involved in immune response. We found that replication of the influenza virus in neurons was limited, although early viral transcription was not affected. Virus-induced neuron viability decreased at 6 h postinfection (p.i. but increased at 24 h p.i. depending upon the viral strain. Virus-induced apoptosis and cytopathy in primary cortical neurons were not apparent at 24 h p.i. The mRNA levels of inflammatory cytokines, chemokines, and type I interferons were upregulated at 6 h and 24 h p.i. These results indicate that the influenza virus induces inflammatory response in mouse primary cortical neurons with limited viral replication. The cytokines released in viral infection-induced neuroinflammation might play critical roles in influenza encephalopathy, rather than in viral replication-induced cytopathy.

  13. 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...

  14. DNA lesions induced by replication stress trigger mitotic aberration and tetraploidy development.

    Directory of Open Access Journals (Sweden)

    Yosuke Ichijima

    Full Text Available During tumorigenesis, cells acquire immortality in association with the development of genomic instability. However, it is still elusive how genomic instability spontaneously generates during the process of tumorigenesis. Here, we show that precancerous DNA lesions induced by oncogene acceleration, which induce situations identical to the initial stages of cancer development, trigger tetraploidy/aneuploidy generation in association with mitotic aberration. Although oncogene acceleration primarily induces DNA replication stress and the resulting lesions in the S phase, these lesions are carried over into the M phase and cause cytokinesis failure and genomic instability. Unlike directly induced DNA double-strand breaks, DNA replication stress-associated lesions are cryptogenic and pass through cell-cycle checkpoints due to limited and ineffective activation of checkpoint factors. Furthermore, since damaged M-phase cells still progress in mitotic steps, these cells result in chromosomal mis-segregation, cytokinesis failure and the resulting tetraploidy generation. Thus, our results reveal a process of genomic instability generation triggered by precancerous DNA replication stress.

  15. RECQL5 Suppresses Oncogenic JAK2-Induced Replication Stress and Genomic Instability

    Directory of Open Access Journals (Sweden)

    Edwin Chen

    2015-12-01

    Full Text Available JAK2V617F is the most common oncogenic lesion in patients with myeloproliferative neoplasms (MPNs. Despite the ability of JAK2V617F to instigate DNA damage in vitro, MPNs are nevertheless characterized by genomic stability. In this study, we address this paradox by identifying the DNA helicase RECQL5 as a suppressor of genomic instability in MPNs. We report increased RECQL5 expression in JAK2V617F-expressing cells and demonstrate that RECQL5 is required to counteract JAK2V617F-induced replication stress. Moreover, RECQL5 depletion sensitizes JAK2V617F mutant cells to hydroxyurea (HU, a pharmacological inducer of replication stress and the most common treatment for MPNs. Using single-fiber chromosome combing, we show that RECQL5 depletion in JAK2V617F mutant cells impairs replication dynamics following HU treatment, resulting in increased double-stranded breaks and apoptosis. Cumulatively, these findings identify RECQL5 as a critical regulator of genome stability in MPNs and demonstrate that replication stress-associated cytotoxicity can be amplified specifically in JAK2V617F mutant cells through RECQL5-targeted synthetic lethality.

  16. 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...

  17. Leflunomide/teriflunomide inhibit Epstein-Barr virus (EBV)- induced lymphoproliferative disease and lytic viral replication.

    Science.gov (United States)

    Bilger, Andrea; Plowshay, Julie; Ma, Shidong; Nawandar, Dhananjay; Barlow, Elizabeth A; Romero-Masters, James C; Bristol, Jillian A; Li, Zhe; Tsai, Ming-Han; Delecluse, Henri-Jacques; Kenney, Shannon C

    2017-07-04

    EBV infection causes mononucleosis and is associated with specific subsets of B cell lymphomas. Immunosuppressed patients such as organ transplant recipients are particularly susceptible to EBV-induced lymphoproliferative disease (LPD), which can be fatal. Leflunomide (a drug used to treat rheumatoid arthritis) and its active metabolite teriflunomide (used to treat multiple sclerosis) inhibit de novo pyrimidine synthesis by targeting the cellular dihydroorotate dehydrogenase, thereby decreasing T cell proliferation. Leflunomide also inhibits the replication of cytomegalovirus and BK virus via both "on target" and "off target" mechanisms and is increasingly used to treat these viruses in organ transplant recipients. However, whether leflunomide/teriflunomide block EBV replication or inhibit EBV-mediated B cell transformation is currently unknown. We show that teriflunomide inhibits cellular proliferation, and promotes apoptosis, in EBV-transformed B cells in vitro at a clinically relevant dose. In addition, teriflunomide prevents the development of EBV-induced lymphomas in both a humanized mouse model and a xenograft model. Furthermore, teriflunomide inhibits lytic EBV infection in vitro both by preventing the initial steps of lytic viral reactivation, and by blocking lytic viral DNA replication. Leflunomide/teriflunomide might therefore be clinically useful for preventing EBV-induced LPD in patients who have high EBV loads yet require continued immunosuppression.

  18. Human Metapneumovirus Induces Formation of Inclusion Bodies for Efficient Genome Replication and Transcription.

    Science.gov (United States)

    Cifuentes-Muñoz, Nicolás; Branttie, Jean; Slaughter, Kerri Beth; Dutch, Rebecca Ellis

    2017-12-15

    induce the formation of large cytoplasmic granules, named inclusion bodies, for genome replication and transcription. Unlike other cytoplasmic structures, such as stress granules and processing bodies, inclusion bodies are exclusively present in infected cells and contain HMPV RNA and proteins to more efficiently transcribe and replicate the viral genome. Though inclusion body formation is nuanced, it corresponds to a more generalized strategy used by different viruses, including filoviruses and rhabdoviruses, for genome transcription and replication. Thus, an understanding of inclusion body formation is crucial for the discovery of innovative therapeutic targets. Copyright © 2017 American Society for Microbiology.

  19. Oncogenic Herpesvirus Utilizes Stress-Induced Cell Cycle Checkpoints for Efficient Lytic Replication.

    Directory of Open Access Journals (Sweden)

    Giuseppe Balistreri

    2016-02-01

    Full Text Available Kaposi's sarcoma herpesvirus (KSHV causes Kaposi's sarcoma and certain lymphoproliferative malignancies. Latent infection is established in the majority of tumor cells, whereas lytic replication is reactivated in a small fraction of cells, which is important for both virus spread and disease progression. A siRNA screen for novel regulators of KSHV reactivation identified the E3 ubiquitin ligase MDM2 as a negative regulator of viral reactivation. Depletion of MDM2, a repressor of p53, favored efficient activation of the viral lytic transcription program and viral reactivation. During lytic replication cells activated a p53 response, accumulated DNA damage and arrested at G2-phase. Depletion of p21, a p53 target gene, restored cell cycle progression and thereby impaired the virus reactivation cascade delaying the onset of virus replication induced cytopathic effect. Herpesviruses are known to reactivate in response to different kinds of stress, and our study now highlights the molecular events in the stressed host cell that KSHV has evolved to utilize to ensure efficient viral lytic replication.

  20. 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.

  1. 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...

  2. 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.

  3. The Tat protein of human immunodeficiency virus-1 enhances hepatitis C virus replication through interferon gamma-inducible protein-10

    Directory of Open Access Journals (Sweden)

    Qu Jing

    2012-04-01

    Full Text Available Abstract Background Co-infection with human immunodeficiency virus-1 (HIV-1 and hepatitis C virus (HCV is associated with faster progression of liver disease and an increase in HCV persistence. However, the mechanism by which HIV-1 accelerates the progression of HCV liver disease remains unknown. Results HIV-1/HCV co-infection is associated with increased expression of interferon gamma-induced protein-10 (IP-10 mRNA in peripheral blood mononuclear cells (PBMCs. HCV RNA levels were higher in PBMCs of patients with HIV-1/HCV co-infection than in patients with HCV mono-infection. HIV-1 Tat and IP-10 activated HCV replication in a time-dependent manner, and HIV-1 Tat induced IP-10 production. In addition, the effect of HIV-1 Tat on HCV replication was blocked by anti-IP-10 monoclonal antibody, demonstrating that the effect of HIV-1 Tat on HCV replication depends on IP-10. Taken together, these results suggest that HIV-1 Tat protein activates HCV replication by upregulating IP-10 production. Conclusions HIV-1/HCV co-infection is associated with increased expression of IP-10 mRNA and replication of HCV RNA. Furthermore, both HIV-1 Tat and IP-10 activate HCV replication. HIV-1 Tat activates HCV replication by upregulating IP-10 production. These results expand our understanding of HIV-1 in HCV replication and the mechanism involved in the regulation of HCV replication mediated by HIV-1 during co-infection.

  4. 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.

  5. 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.

  6. Interferon-inducible MyD88 protein inhibits hepatitis B virus replication

    International Nuclear Information System (INIS)

    Xiong Wei; Wang Xun; Liu Xiaoying; Xiang Li; Zheng Lingjie; Yuan Zhenghong

    2004-01-01

    Myeloid differential primary response protein (MyD88) is a critical component in the signaling cascade through Toll-like receptors (TLRs) and is induced by α interferon (IFN-α). To examine the role of MyD88 in the antiviral activity of IFN-α against hepatitis B virus (HBV), we established MyD88 stably expressing cell lines and studied HBV replication in these lines after transient transfection. The levels of HBV proteins and viral replicative intermediates were effectively reduced in MyD88-expressing cells. A significant reduction of total and cytoplasmic viral RNAs in MyD88 stably expressing cells was also observed. Using a nuclear factor-κB (NF-κB) dependent reporter assay, it was shown that activation of NF-κB was moderately increased in the presence of expression of MyD88, and further significantly increased by co-expression of HBV. These results suggest a novel mechanism for the inhibition of HBV replication by IFN-α via expression of MyD88 protein involving activation of NF-κB signaling pathway and downregulation of viral transcription

  7. Identification and replication of loci involved in camptothecin-induced cytotoxicity using CEPH pedigrees.

    Directory of Open Access Journals (Sweden)

    Venita Gresham Watson

    2011-05-01

    Full Text Available To date, the Centre d'Etude Polymorphism Humain (CEPH cell line model has only been used as a pharmacogenomic tool to evaluate which genes are responsible for the disparity in response to a single drug. The purpose of this study was demonstrate the model's ability to establish a specific pattern of quantitative trait loci (QTL related to a shared mechanism for multiple structurally related drugs, the camptothecins, which are Topoisomerase 1 inhibitors. A simultaneous screen of six camptothecin analogues for in vitro sensitivity in the CEPH cell lines resulted in cytotoxicity profiles and orders of potency which were in agreement with the literature. For all camptothecins studied, heritability estimates for cytotoxic response averaged 23.1 ± 2.6%. Nonparametric linkage analysis was used to identify a relationship between genetic markers and response to the camptothecins. Ten QTLs on chromosomes 1, 3, 5, 6, 11, 12, 16 and 20 were identified as shared by all six camptothecin analogues. In a separate validation experiment, nine of the ten QTLs were replicated at the significant and suggestive levels using three additional camptothecin analogues. To further refine this list of QTLs, another validation study was undertaken and seven of the nine QTLs were independently replicated for all nine camptothecin analogues. This is the first study using the CEPH cell lines that demonstrates that a specific pattern of QTLs could be established for a class of drugs which share a mechanism of action. Moreover, it is the first study to report replication of linkage results for drug-induced cytotoxicity using this model. The QTLs, which have been identified as shared by all camptothecins and replicated across multiple datasets, are of considerable interest; they harbor genes related to the shared mechanism of action for the camptothecins, which are responsible for variation in response.

  8. 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...

  9. A subset of herpes simplex virus replication genes induces DNA amplification within the host cell genome

    Energy Technology Data Exchange (ETDEWEB)

    Heilbronn, R.; zur Hausen, H. (Deutsches Krebsforschungszentrum, Heidelberg (West Germany))

    1989-09-01

    Herpes simplex virus (HSV) induces DNA amplification of target genes within the host cell chromosome. To characterize the HSV genes that mediate the amplification effect, combinations of cloned DNA fragments covering the entire HSV genome were transiently transfected into simian virus 40 (SV40)-transformed hamster cells. This led to amplification of the integrated SV40 DNA sequences to a degree comparable to that observed after transfection of intact virion DNA. Transfection of combinations of subclones and of human cytomegalovirus immediate-early promoter-driven expression constructs for individual open reading frames led to the identification of sic HSV genes which together were necessary and sufficient for the induction of DNA amplification: UL30 (DNA polymerase), UL29 (major DNA-binding protein), UL5, UL8, UL42, and UL52. All of these genes encode proteins necessary for HSV DNA replication. However, an additional gene coding for an HSV origin-binding protein (UL9) was required for origin-dependent HSV DNA replication but was dispensable for SV40 DNA amplification. The results show that a subset of HSV replication genes is sufficient for the induction of DNA amplification. This opens the possibility that HSV expresses functions sufficient for DNA amplification but separate from those responsible for lytic viral growth. HSV infection may thereby induce DNA amplification within the host cell genome without killing the host by lytic viral growth. This may lead to persistence of a cell with a new genetic phenotype, which would have implications for the pathogenicity of the virus in vivo.

  10. Macrophage activation induced by Brucella DNA suppresses bacterial intracellular replication via enhancing NO production.

    Science.gov (United States)

    Liu, Ning; Wang, Lin; Sun, Changjiang; Yang, Li; Tang, Bin; Sun, Wanchun; Peng, Qisheng

    2015-12-01

    Brucella DNA can be sensed by TLR9 on endosomal membrane and by cytosolic AIM2-inflammasome to induce proinflammatory cytokine production that contributes to partially activate innate immunity. Additionally, Brucella DNA has been identified to be able to act as a major bacterial component to induce type I IFN. However, the role of Brucella DNA in Brucella intracellular growth remains unknown. Here, we showed that stimulation with Brucella DNA promote macrophage activation in TLR9-dependent manner. Activated macrophages can suppresses wild type Brucella intracellular replication at early stage of infection via enhancing NO production. We also reported that activated macrophage promotes bactericidal function of macrophages infected with VirB-deficient Brucella at the early or late stage of infection. This study uncovers a novel function of Brucella DNA, which can help us further elucidate the mechanism of Brucella intracellular survival. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Hydrogen peroxide induced loss of heterozygosity correlates with replicative lifespan and mitotic asymmetry in Saccharomyces cerevisiae

    Science.gov (United States)

    Jackson, Erin D.; Parker, Meighan C.; Gupta, Nilin; Rodrigues, Jenny

    2016-01-01

    Cellular aging in Saccharomyces cerevisiae can lead to genomic instability and impaired mitotic asymmetry. To investigate the role of oxidative stress in cellular aging, we examined the effect of exogenous hydrogen peroxide on genomic instability and mitotic asymmetry in a collection of yeast strains with diverse backgrounds. We treated yeast cells with hydrogen peroxide and monitored the changes of viability and the frequencies of loss of heterozygosity (LOH) in response to hydrogen peroxide doses. The mid-transition points of viability and LOH were quantified using sigmoid mathematical functions. We found that the increase of hydrogen peroxide dependent genomic instability often occurs before a drop in viability. We previously observed that elevation of genomic instability generally lags behind the drop in viability during chronological aging. Hence, onset of genomic instability induced by exogenous hydrogen peroxide treatment is opposite to that induced by endogenous oxidative stress during chronological aging, with regards to the midpoint of viability. This contrast argues that the effect of endogenous oxidative stress on genome integrity is well suppressed up to the dying-off phase during chronological aging. We found that the leadoff of exogenous hydrogen peroxide induced genomic instability to viability significantly correlated with replicative lifespan (RLS), indicating that yeast cells’ ability to counter oxidative stress contributes to their replicative longevity. Surprisingly, this leadoff is positively correlated with an inverse measure of endogenous mitotic asymmetry, indicating a trade-off between mitotic asymmetry and cell’s ability to fend off hydrogen peroxide induced oxidative stress. Overall, our results demonstrate strong associations of oxidative stress to genomic instability and mitotic asymmetry at the population level of budding yeast. PMID:27833823

  12. 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%.

  13. Soluble histone H2AX is induced by DNA replication stress and sensitizes cells to undergo apoptosis

    Directory of Open Access Journals (Sweden)

    Duensing Stefan

    2008-07-01

    Full Text Available Abstract Background Chromatin-associated histone H2AX is a key regulator of the cellular responses to DNA damage. However, non-nucleosomal functions of histone H2AX are poorly characterized. We have recently shown that soluble H2AX can trigger apoptosis but the mechanisms leading to non-chromatin-associated H2AX are unclear. Here, we tested whether stalling of DNA replication, a common event in cancer cells and the underlying mechanism of various chemotherapeutic agents, can trigger increased soluble H2AX. Results Transient overexpression of H2AX was found to lead to a detectable fraction of soluble H2AX and was associated with increased apoptosis. This effect was enhanced by the induction of DNA replication stress using the DNA polymerase α inhibitor aphidicolin. Cells manipulated to stably express H2AX did not contain soluble H2AX, however, short-term treatment with aphidicolin (1 h resulted in detectable amounts of H2AX in the soluble nuclear fraction and enhanced apoptosis. Similarly, soluble endogenous H2AX was detected under these conditions. We found that excessive soluble H2AX causes chromatin aggregation and inhibition of ongoing gene transcription as evidenced by the redistribution and/or loss of active RNA polymerase II as well as the transcriptional co-activators CBP and p300. Conclusion Taken together, these results show that DNA replication stress rapidly leads to increased soluble H2AX and that non-chromatin-associated H2AX can sensitize cells to undergo apoptosis. Our findings encourage further studies to explore H2AX and the cellular pathways that control its expression as anti-cancer drug targets.

  14. Proteasome inhibitors induce apoptosis and reduce viral replication in primary effusion lymphoma cells

    Energy Technology Data Exchange (ETDEWEB)

    Saji, Chiaki [Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060-0812 (Japan); Higashi, Chizuka; Niinaka, Yasufumi [Faculty of Medicine, University of Yamanashi, Chuoh-shi 409-3898 (Japan); Yamada, Koji [Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060-0812 (Japan); Noguchi, Kohji [Faculty of Pharmacy, Keio University, 1-5-30 Shiba-koen, Minato-ku, Tokyo 105-8512 (Japan); Fujimuro, Masahiro, E-mail: fuji2@mb.kyoto-phu.ac.jp [Department of Cell Biology, Kyoto Pharmaceutical University, Misasagi-Shichonocho 1, Yamashinaku, Kyoto 607-8412 (Japan)

    2011-12-02

    Highlights: Black-Right-Pointing-Pointer Constitutive NF-{kappa}B signaling is essential for the survival and growth of PEL cells. Black-Right-Pointing-Pointer NF-{kappa}B signaling is upregulated by the proteasome-dependent degradation of I{kappa}B{alpha}. Black-Right-Pointing-Pointer Proteasome inhibitors suppress NF-{kappa}B signaling and induce apoptosis in PEL cells through stabilization of I{kappa}B{alpha}. Black-Right-Pointing-Pointer Proteasome inhibitors suppress viral replication in PEL cells during lytic KSHV infection. -- Abstract: Primary effusion lymphoma (PEL) is an aggressive neoplasm caused by Kaposi's sarcoma-associated herpesvirus (KSHV). This study provides evidence that proteasomal activity is required for both survival of PEL cells stably harboring the KSHV genome and viral replication of KSHV. We evaluated the cytotoxic effects of proteasome inhibitors on PEL cells. The proteasome inhibitors MG132, lactacystin, and proteasome inhibitor I dramatically inhibited cell proliferation and induced apoptosis of PEL cells through the accumulation of p21 and p27. Furthermore, proteasome inhibitors induced the stabilization of NF-{kappa}B inhibitory molecule (I{kappa}B{alpha}) and suppressed the transcriptional activity of NF-{kappa}B in PEL cells. The NF-{kappa}B specific inhibitor BAY11-7082 also induced apoptosis in PEL cells. The constitutive activation of NF-{kappa}B signaling is essential for the survival and growth of B cell lymphoma cells, including PEL cells. NF-{kappa}B signaling is upregulated by proteasome-dependent degradation of I{kappa}B{alpha}. The suppression of NF-{kappa}B signaling by proteasome inhibitors may contribute to the induction of apoptosis in PEL cells. In addition, proteasome activity is required for KSHV replication in KSHV latently infected PEL cells. MG132 reduced the production of progeny virus from PEL cells at low concentrations, which do not affect PEL cell growth. These findings suggest that proteasome

  15. RPA Stabilization of Single-Stranded DNA Is Critical for Break-Induced Replication.

    Science.gov (United States)

    Ruff, Patrick; Donnianni, Roberto A; Glancy, Eleanor; Oh, Julyun; Symington, Lorraine S

    2016-12-20

    DNA double-strand breaks (DSBs) are cytotoxic lesions that must be accurately repaired to maintain genome stability. Replication protein A (RPA) plays an important role in homology-dependent repair of DSBs by protecting the single-stranded DNA (ssDNA) intermediates formed by end resection and by facilitating Rad51 loading. We found that hypomorphic mutants of RFA1 that support intra-chromosomal homologous recombination are profoundly defective for repair processes involving long tracts of DNA synthesis, in particular break-induced replication (BIR). The BIR defects of the rfa1 mutants could be partially suppressed by eliminating the Sgs1-Dna2 resection pathway, suggesting that Dna2 nuclease attacks the ssDNA formed during end resection when not fully protected by RPA. Overexpression of Rad51 was also found to suppress the rfa1 BIR defects. We suggest that Rad51 binding to the ssDNA formed by excessive end resection and during D-loop migration can partially compensate for dysfunctional RPA. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  16. In situ enzymology of DNA replication and ultraviolet-induced DNA repair synthesis in permeable human cells

    International Nuclear Information System (INIS)

    Dresler, S.; Frattini, M.G.; Robinson-Hill, R.M.

    1988-01-01

    Using permeable diploid human fibroblasts, the authors have studied the deoxyribonucleoside triphosphate concentration dependences of ultraviolet- (UV-) induced DNA repair synthesis and semiconservative DNA replication. In both cell types (AG1518 and IMR-90) examined, the apparent K m values for dCTP, dGTP, and dTTP for DNA replication were between 1.2 and 2.9 μM. For UV-induced DNA repair synthesis, the apparent K m values were substantially lower, ranging from 0.11 to 0.44 μM for AG1518 cells and from 0.06 to 0.24 μM for IMR-90 cells. Recent data implicate DNA polymerase δ in UV-induced repair synthesis and suggest that DNA polymerases α and δ are both involved in semiconservative replication. They measured K m values for dGTP and dTTP for polymerases α and δ, for comparison with the values for replication and repair synthesis. The deoxyribonucleotide K m values for DNA polymerase δ are much greater than the K m values for UV-induced repair synthesis, suggesting that when polymerase δ functions in DNA repair, its characteristics are altered substantially either by association with accessory proteins or by direct posttranslational modification. In contrast, the deoxyribonucleotide binding characteristics of the DNA replication machinery differ little from those of the isolated DNA polymerases. The K m values for UV-induced repair synthesis are 5-80-fold lower than deoxyribonucleotide concentrations that have been reported for intact cultured diploid human fibroblasts. For replication, however, the K m for dGTP is only slightly lower than the average cellular dGTP concentration that has been reported for exponentially growing human fibroblasts. This finding is consistent with the concept that nucleotide compartmentation is required for the attainment of high rates of DNA replication in vivo

  17. DNA Damage Response Resulting from Replication Stress Induced by Synchronization of Cells by Inhibitors of DNA Replication: Analysis by Flow Cytometry.

    Science.gov (United States)

    Halicka, Dorota; Zhao, Hong; Li, Jiangwei; Garcia, Jorge; Podhorecka, Monika; Darzynkiewicz, Zbigniew

    2017-01-01

    Cell synchronization is often achieved by transient inhibition of DNA replication. When cultured in the presence of such inhibitors as hydroxyurea, aphidicolin or excess of thymidine the cells that become arrested at the entrance to S-phase upon release from the block initiate progression through S then G 2 and M. However, exposure to these inhibitors at concentrations commonly used to synchronize cells leads to activation of ATR and ATM protein kinases as well as phosphorylation of Ser139 of histone H2AX. This observation of DNA damage signaling implies that synchronization of cells by these inhibitors is inducing replication stress. Thus, a caution should be exercised while interpreting data obtained with use of cells synchronized this way since they do not represent unperturbed cell populations in a natural metabolic state. This chapter critically outlines virtues and vices of most cell synchronization methods. It also presents the protocol describing an assessment of phosphorylation of Ser139 on H2AX and activation of ATM in cells treated with aphidicolin, as a demonstrative of one of several DNA replication inhibitors that are being used for cell synchronization. Phosphorylation of Ser139H2AX and Ser1981ATM in individual cells is detected immunocytochemically with phospho-specific Abs and intensity of immunofluorescence is measured by flow cytometry. Concurrent measurement of cellular DNA content followed by multiparameter analysis allows one to correlate the extent of phosphorylation of these proteins in response to aphidicolin with the cell cycle phase.

  18. A comparison of oncogene-induced senescence and replicative senescence: implications for tumor suppression and aging.

    Science.gov (United States)

    Nelson, David M; McBryan, Tony; Jeyapalan, Jessie C; Sedivy, John M; Adams, Peter D

    2014-06-01

    Cellular senescence is a stable proliferation arrest associated with an altered secretory pathway, the senescence-associated secretory phenotype. However, cellular senescence is initiated by diverse molecular triggers, such as activated oncogenes and shortened telomeres, and is associated with varied and complex physiological endpoints, such as tumor suppression and tissue aging. The extent to which distinct triggers activate divergent modes of senescence that might be associated with different physiological endpoints is largely unknown. To begin to address this, we performed gene expression profiling to compare the senescence programs associated with two different modes of senescence, oncogene-induced senescence (OIS) and replicative senescence (RS [in part caused by shortened telomeres]). While both OIS and RS are associated with many common changes in gene expression compared to control proliferating cells, they also exhibit substantial differences. These results are discussed in light of potential physiological consequences, tumor suppression and aging.

  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. The role of HBV-induced autophagy in HBV replication and HBV related-HCC.

    Science.gov (United States)

    Xie, Mingjie; Yang, Zhenggang; Liu, Yanning; Zheng, Min

    2018-04-27

    Hepatitis B virus (HBV) is infecting about 364 million people around the world. It can cause various diseases, such as chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). However, the present anti-viral treatment in clinics is limited; studies for new therapies are highly desired. Autophagy is a crucial and major catabolic process in the maintenance of normal intracellular homeostasis in host cells. Host cells use this unique process to degrade and recycle long-lived proteins, damaged organelles, and various pathogens for keeping the normal physiological functions. Recently, published studies indicated that HBV can induce autophagy in host cells; this autophagic response is involved in viral replication and pathogenesis. Several viral proteins, such as surface and X proteins, are assumed to be responsible for inducing autophagy in HBV infection. This review briefly summarizes some important mechanisms involved in HBV-induced autophagy and provides a novel perspective on therapies of HBV infection and HBV-related HCC. Copyright © 2017. Published by Elsevier Inc.

  1. 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.

  2. 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.

  3. ATM is required for the repair of Topotecan-induced replication-associated double-strand breaks

    International Nuclear Information System (INIS)

    Köcher, Sabrina; Spies-Naumann, Anja; Kriegs, Malte; Dahm-Daphi, Jochen; Dornreiter, Irena

    2013-01-01

    Purpose: DNA replication is a promising target for anti-cancer therapies. Therefore, the understanding of replication-associated DNA repair mechanisms is of great interest. One key factor of DNA double-strand break (DSB) repair is the PIK kinase Ataxia-Telangiectasia Mutated (ATM) but it is still unclear whether ATM is involved in the repair of replication-associated DSBs. Here, we focused on the involvement of ATM in homology-directed repair (HDR) of indirect DSBs associated with replication. Material and methods: Experiments were performed using ATM-deficient and -proficient human cells. Replication-associated DSBs were induced with Topotecan (TPT) and compared with γ-irradiation (IR). Cell survival was measured by clonogenic assay. Overall DSB repair and HDR were evaluated by detecting residual γH2AX/53BP1 and Rad51 foci, respectively. Cell cycle distribution was analysed by flow cytometry and protein expression by Western blot. Results: ATM-deficiency leads to enhanced numbers of residual DSBs, resulting in a pronounced S/G2-block and decreased survival upon TPT-treatment. In common with IR, persisting Rad51 foci were detected following TPT-treatment. Conclusions: These results demonstrate that ATM is essentially required for the completion of HR-mediated repair of TPT-induced DSBs formed indirectly at replication forks

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

    Directory of Open Access Journals (Sweden)

    P J Hastings

    2009-01-01

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

  5. 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

  6. 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...

  7. Replication of Merkel cell polyomavirus induces reorganization of promyelocytic leukemia nuclear bodies.

    Science.gov (United States)

    Neumann, Friederike; Czech-Sioli, Manja; Dobner, Thomas; Grundhoff, Adam; Schreiner, Sabrina; Fischer, Nicole

    2016-11-01

    Merkel cell polyomavirus (MCPyV) is associated with Merkel cell carcinoma (MCC), a rare but aggressive skin cancer. The virus is highly prevalent: 60-80 % of adults are seropositive; however, cells permissive for MCPyV infection are unknown. Consequently, very little information about the MCPyV life cycle is available. Until recently, MCPyV replication could only be studied using a semi-permissive in vitro replication system (Neumann et al., 2011; Feng et al., 2011, Schowalter et al., 2011). MCPyV replication most likely depends on subnuclear structures such as promyelocytic leukemia protein nuclear bodies (PML-NBs), which are known to play regulatory roles in the infection of many DNA viruses. Here, we investigated PML-NB components as candidate host factors to control MCPyV DNA replication. We showed that PML-NBs change in number and size in cells actively replicating MCPyV proviral DNA. We observed a significant increase in PML-NBs in cells positive for MCPyV viral DNA replication. Interestingly, a significant amount of cells actively replicating MCPyV did not show any Sp100 expression. While PML and Daxx had no effect on MCPyV DNA replication, MCPyV replication was increased in cells depleted for Sp100, strongly suggesting that Sp100 is a negative regulator of MCPyV DNA replication.

  8. Pyrimidine Pool Disequilibrium Induced by a Cytidine Deaminase Deficiency Inhibits PARP-1 Activity, Leading to the Under Replication of DNA.

    Directory of Open Access Journals (Sweden)

    Simon Gemble

    2015-07-01

    Full Text Available Genome stability is jeopardized by imbalances of the dNTP pool; such imbalances affect the rate of fork progression. For example, cytidine deaminase (CDA deficiency leads to an excess of dCTP, slowing the replication fork. We describe here a novel mechanism by which pyrimidine pool disequilibrium compromises the completion of replication and chromosome segregation: the intracellular accumulation of dCTP inhibits PARP-1 activity. CDA deficiency results in incomplete DNA replication when cells enter mitosis, leading to the formation of ultrafine anaphase bridges between sister-chromatids at "difficult-to-replicate" sites such as centromeres and fragile sites. Using molecular combing, electron microscopy and a sensitive assay involving cell imaging to quantify steady-state PAR levels, we found that DNA replication was unsuccessful due to the partial inhibition of basal PARP-1 activity, rather than slower fork speed. The stimulation of PARP-1 activity in CDA-deficient cells restores replication and, thus, chromosome segregation. Moreover, increasing intracellular dCTP levels generates under-replication-induced sister-chromatid bridges as efficiently as PARP-1 knockdown. These results have direct implications for Bloom syndrome (BS, a rare genetic disease combining susceptibility to cancer and genomic instability. BS results from mutation of the BLM gene, encoding BLM, a RecQ 3'-5' DNA helicase, a deficiency of which leads to CDA downregulation. BS cells thus have a CDA defect, resulting in a high frequency of ultrafine anaphase bridges due entirely to dCTP-dependent PARP-1 inhibition and independent of BLM status. Our study describes previously unknown pathological consequences of the distortion of dNTP pools and reveals an unexpected role for PARP-1 in preventing DNA under-replication and chromosome segregation defects.

  9. Mutator suppression and escape from replication error-induced extinction in yeast.

    Directory of Open Access Journals (Sweden)

    Alan J Herr

    2011-10-01

    Full Text Available Cells rely on a network of conserved pathways to govern DNA replication fidelity. Loss of polymerase proofreading or mismatch repair elevates spontaneous mutation and facilitates cellular adaptation. However, double mutants are inviable, suggesting that extreme mutation rates exceed an error threshold. Here we combine alleles that affect DNA polymerase δ (Pol δ proofreading and mismatch repair to define the maximal error rate in haploid yeast and to characterize genetic suppressors of mutator phenotypes. We show that populations tolerate mutation rates 1,000-fold above wild-type levels but collapse when the rate exceeds 10⁻³ inactivating mutations per gene per cell division. Variants that escape this error-induced extinction (eex rapidly emerge from mutator clones. One-third of the escape mutants result from second-site changes in Pol δ that suppress the proofreading-deficient phenotype, while two-thirds are extragenic. The structural locations of the Pol δ changes suggest multiple antimutator mechanisms. Our studies reveal the transient nature of eukaryotic mutators and show that mutator phenotypes are readily suppressed by genetic adaptation. This has implications for the role of mutator phenotypes in cancer.

  10. 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.

  11. 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.

  12. 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.

  13. 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...

  14. 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

  15. Enterovirus 71 induces autophagy by regulating has-miR-30a expression to promote viral replication.

    Science.gov (United States)

    Fu, Yuxuan; Xu, Wentao; Chen, Deyan; Feng, Chunhong; Zhang, Li; Wang, Xiaohui; Lv, Xiaowen; Zheng, Nan; Jin, Yu; Wu, Zhiwei

    2015-12-01

    Enterovirus 71 (EV71), the etiological agent of hand-foot-and-mouth disease, has increasingly become a public health challenge around the world. Previous studies reported that EV71 infection can induce autophagic machinery to enhance viral replication in vitro and in vivo, but did not address the underlying mechanisms. Increasing evidence suggests that autophagy, in a virus-specific manner, may function to degrade viruses or facilitate viral replication. In this study, we reported that EV71 infection of human epidermoid carcinoma (Hep2) and African green monkey kidney cells (Vero) induced autophagy, which is beneficial for viral replication. Our investigation of the mechanisms revealed that EV71 infection resulted in the reduction of cellular miR-30a, which led to the inhibition of Beclin-1, a key autophagy-promoting gene that plays important roles at the early phase of autophagosome formation. We provided further evidence that by modulating cellular miR-30a level through either overexpression or inhibition, one can inhibit or promote EV71 replication, respectively, through regulating autophagic activity. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Brucella suis vaccine strain 2 induces endoplasmic reticulum stress that affects intracellular replication in goat trophoblast cells in vitro

    Directory of Open Access Journals (Sweden)

    Xiangguo eWang

    2016-02-01

    Full Text Available Brucella has been reported to impair placental trophoblasts, a cellular target where Brucella efficiently replicates in association with the endoplasmic reticulum (ER, and ultimately trigger abortion in pregnant animals. However, the precise effects of Brucella on trophoblast cells remain unclear. Here, we describe the infection and replication of Brucella suis vaccine strain 2 (B.suis.S2 in goat trophoblast cells (GTCs and the cellular and molecular responses induced in vitro. Our studies demonstrated that B.suis.S2 was able to infect and proliferate to high titers, hamper the proliferation of GTCs and induce apoptosis due to ER stress. Tunicamycin (Tm, a pharmacological chaperone that strongly mounts ER stress-induced apoptosis, inhibited B.suis.S2 replication in GTCs. In addition, 4 phenyl butyric acid (4-PBA, a pharmacological chaperone that alleviates ER stress-induced apoptosis, significantly enhanced B.suis.S2 replication in GTCs. The Unfolded Protein Response (UPR chaperone molecule GRP78 also promoted B.suis.S2 proliferation in GTCs by inhibiting ER stress-induced apoptosis. We also discovered that the IRE1 pathway, but not the PERK or ATF6 pathway, was activated in the process. However, decreasing the expression of phosphoIRE1α and IRE1α proteins with Irestatin 9389 (IRE1 antagonist in GTCs did not affect the proliferation of B.suis.S2. Although GTC implantation was not affected upon B.suis.S2 infection, progesterone secretion was suppressed, and prolactin and estrogen secretion increased; these effects were accompanied by changes in the expression of genes encoding key steroidogenic enzymes. This study systematically explored the mechanisms of abortion in Brucella infection from the viewpoint of pathogen invasion, ER stress and reproductive endocrinology. Our findings may provide new insight for understanding the mechanisms involved in goat abortions caused by Brucella infection.

  17. 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.

  18. 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.

  19. Replication of simian virus 40 in simian virus 40-transformed hamster kidney cells induced by mitomycin C or 60Co γ irradiation

    International Nuclear Information System (INIS)

    Rakusanova, T.; Smales, W.P.; Kaplan, J.C.; Black, P.H.

    1978-01-01

    Several clones of simian virus 40 (SV40)-transformed hamster kidney cells, which are heterogeneous for induction of infectious SV40, have been studied. SV40 yields are low after induction with 60 Co γ irradiation or mitomycin C. In order to clarify the mechanism(s) by which virus is produced in induced cells, we analyzed the replication of viral DNA and production of virion (V) antigen and infectious virus after induction in various clones as well as in lytically infected permissive cells. Cells replicating SV40 DNA or synthesizing V antigen were visualized by in situ hybridization and immunofluorescence techniques, respectively. Only some cells in induced cultures were found to produce SV40 and those which did were less efficient than lytically infected monkey cells. Mitomycin C or 60 Co γ irradiation acted by inducing more cells to replicate virus rather than by increasing the amount of SV40 released from individual cells. A greater proportion of cells could be induced to replicate SV40 DNA than to synthesize V antigen in all induced clones studied. Also, SV40 DNA replication was induced at lower doses of γ irradiation than the production of either V antigen or infectious virus suggesting that synthesis of late virus protein is more restricted in induced cells than is replication of SV40 DNA. These findings indicate that one of the effects of induction treatments on SV40-transformed hamster cells is an enhancement of the cells' capacity to support SV40 replication

  20. Molecular cloning of osteoma-inducing replication-competent murine leukemia viruses from the RFB osteoma virus stock

    DEFF Research Database (Denmark)

    Pedersen, Lene; Behnisch, Werner; Schmidt, Jörg

    1992-01-01

    We report the molecular cloning of two replication-competent osteoma-inducing murine leukemia viruses from the RFB osteoma virus stock (M. P. Finkel, C. A. Reilly, Jr., B. O. Biskis, and I. L. Greco, p. 353-366, in C. H. G. Price and F. G. M. Ross, ed., Bone--Certain Aspects of Neoplasia, 1973......). Like the original RFB osteoma virus stock, viruses derived from the molecular RFB clones induced multiple osteomas in mice of the CBA/Ca strain. The cloned RFB viruses were indistinguishable by restriction enzyme analysis and by nucleotide sequence analysis of their long-terminal-repeat regions...

  1. Radiation-induced inhibition of human endothelial cells replicating in culture

    International Nuclear Information System (INIS)

    DeGowin, R.L.; Lewis, L.J.; Mason, R.E.; Borke, M.K.; Hoak, J.C.

    1976-01-01

    The radiosensitivity of some tumors may depend upon the sensitivity of their microvasculature to radiation. Heretofore, the dose-response of human endothelial cells replicating in tissue culture has not been published. In studies reported here, we exposed flasks containing 4 to 7 x 10 4 genetically identical human endothelial cells to doses of x irradiation from 125 to 1000 rad. During the phase of logarithmic growth, cell counts were compared to those of an unirradiated control to construct a dose--response curve. Similar studies were performed with normal fibroblasts. We found that 160 rad suppressed endothelial cell replication by 37 percent. Although recovery was evident with doses of 500 rad, no net increase in cell number occurred in 3 weeks in flasks of endothelial cells that received 750 or 1000 rad. Fibroblasts were slightly less sensitive under these conditions. To our knowledge, this is the first report of a radiation dose--response curve for human endothelial cells replicating in culture

  2. A case with concurrent duplication, triplication, and uniparental isodisomy at 1q42.12-qter supporting microhomology-mediated break-induced replication model for replicative rearrangements.

    Science.gov (United States)

    Kohmoto, Tomohiro; Okamoto, Nana; Naruto, Takuya; Murata, Chie; Ouchi, Yuya; Fujita, Naoko; Inagaki, Hidehito; Satomura, Shigeko; Okamoto, Nobuhiko; Saito, Masako; Masuda, Kiyoshi; Kurahashi, Hiroki; Imoto, Issei

    2017-01-01

    Complex genomic rearrangements (CGRs) consisting of interstitial triplications in conjunction with uniparental isodisomy (isoUPD) have rarely been reported in patients with multiple congenital anomalies (MCA)/intellectual disability (ID). One-ended DNA break repair coupled with microhomology-mediated break-induced replication (MMBIR) has been recently proposed as a possible mechanism giving rise to interstitial copy number gains and distal isoUPD, although only a few cases providing supportive evidence in human congenital diseases with MCA have been documented. Here, we report on the chromosomal microarray (CMA)-based identification of the first known case with concurrent interstitial duplication at 1q42.12-q42.2 and triplication at 1q42.2-q43 followed by isoUPD for the remainder of chromosome 1q (at 1q43-qter). In distal 1q duplication/triplication overlapping with 1q42.12-q43, variable clinical features have been reported, and our 25-year-old patient with MCA/ID presented with some of these frequently described features. Further analyses including the precise mapping of breakpoint junctions within the CGR in a sequence level suggested that the CGR found in association with isoUPD in our case is a triplication with flanking duplications, characterized as a triplication with a particularly long duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) structure. Because microhomology was observed in both junctions between the triplicated region and the flanking duplicated regions, our case provides supportive evidence for recently proposed replication-based mechanisms, such as MMBIR, underlying the formation of CGRs + isoUPD implicated in chromosomal disorders. To the best of our knowledge, this is the first case of CGRs + isoUPD observed in 1q and having DUP-TRP/INV-DUP structure with a long proximal duplication, which supports MMBIR-based model for genomic rearrangements. Molecular cytogenetic analyses using CMA containing single

  3. 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.

  4. 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.

  5. 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)

  6. Oncogenic Herpesvirus Utilizes Stress-Induced Cell Cycle Checkpoints for Efficient Lytic Replication

    OpenAIRE

    Balistreri, Giuseppe; Viiliainen, Johanna; Turunen, Mikko; Diaz, Raquel; Lyly, Lauri; Pekkonen, Pirita; Rantala, Juha; Ojala, Krista; Sarek, Grzegorz; Teesalu, Mari; Denisova, Oxana; Peltonen, Karita; Julkunen, Ilkka; Varjosalo, Markku; Kainov, Denis

    2016-01-01

    Kaposi?s sarcoma herpesvirus (KSHV) causes Kaposi?s sarcoma and certain lymphoproliferative malignancies. Latent infection is established in the majority of tumor cells, whereas lytic replication is reactivated in a small fraction of cells, which is important for both virus spread and disease progression. A siRNA screen for novel regulators of KSHV reactivation identified the E3 ubiquitin ligase MDM2 as a negative regulator of viral reactivation. Depletion of MDM2, a repressor of p53, favored...

  7. 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

  8. 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

  9. Replicative age induces mitotic recombination in the ribosomal RNA gene cluster of Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Derek L Lindstrom

    2011-03-01

    Full Text Available Somatic mutations contribute to the development of age-associated disease. In earlier work, we found that, at high frequency, aging Saccharomyces cerevisiae diploid cells produce daughters without mitochondrial DNA, leading to loss of respiration competence and increased loss of heterozygosity (LOH in the nuclear genome. Here we used the recently developed Mother Enrichment Program to ask whether aging cells that maintain the ability to produce respiration-competent daughters also experience increased genomic instability. We discovered that this population exhibits a distinct genomic instability phenotype that primarily affects the repeated ribosomal RNA gene array (rDNA array. As diploid cells passed their median replicative life span, recombination rates between rDNA arrays on homologous chromosomes progressively increased, resulting in mutational events that generated LOH at >300 contiguous open reading frames on the right arm of chromosome XII. We show that, while these recombination events were dependent on the replication fork block protein Fob1, the aging process that underlies this phenotype is Fob1-independent. Furthermore, we provide evidence that this aging process is not driven by mechanisms that modulate rDNA recombination in young cells, including loss of cohesion within the rDNA array or loss of Sir2 function. Instead, we suggest that the age-associated increase in rDNA recombination is a response to increasing DNA replication stress generated in aging cells.

  10. 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.

  11. Endoplasmic Reticulum Stress Induced Synthesis of a Novel Viral Factor Mediates Efficient Replication of Genotype-1 Hepatitis E Virus.

    Directory of Open Access Journals (Sweden)

    Vidya P Nair

    2016-04-01

    Full Text Available Hepatitis E virus (HEV causes acute hepatitis in many parts of the world including Asia, Africa and Latin America. Though self-limiting in normal individuals, it results in ~30% mortality in infected pregnant women. It has also been reported to cause acute and chronic hepatitis in organ transplant patients. Of the seven viral genotypes, genotype-1 virus infects humans and is a major public health concern in South Asian countries. Sporadic cases of genotype-3 and 4 infection in human and animals such as pigs, deer, mongeese have been reported primarily from industrialized countries. Genotype-5, 6 and 7 viruses are known to infect animals such as wild boar and camel, respectively. Genotype-3 and 4 viruses have been successfully propagated in the laboratory in mammalian cell culture. However, genotype-1 virus replicates poorly in mammalian cell culture and no other efficient model exists to study its life cycle. Here, we report that endoplasmic reticulum (ER stress promotes genotype-1 HEV replication by inducing cap-independent, internal initiation mediated translation of a novel viral protein (named ORF4. Importantly, ORF4 expression and stimulatory effect of ER stress inducers on viral replication is specific to genotype-1. ORF4 protein sequence is mostly conserved among genotype-1 HEV isolates and ORF4 specific antibodies were detected in genotype-1 HEV patient serum. ORF4 interacted with multiple viral and host proteins and assembled a protein complex consisting of viral helicase, RNA dependent RNA polymerase (RdRp, X, host eEF1α1 (eukaryotic elongation factor 1 isoform-1 and tubulinβ. In association with eEF1α1, ORF4 stimulated viral RdRp activity. Furthermore, human hepatoma cells that stably express ORF4 or engineered proteasome resistant ORF4 mutant genome permitted enhanced viral replication. These findings reveal a positive role of ER stress in promoting genotype-1 HEV replication and pave the way towards development of an efficient

  12. IFN regulatory factor 1 restricts hepatitis E virus replication by activating STAT1 to induce antiviral IFN-stimulated genes.

    Science.gov (United States)

    Xu, Lei; Zhou, Xinying; Wang, Wenshi; Wang, Yijin; Yin, Yuebang; Laan, Luc J W van der; Sprengers, Dave; Metselaar, Herold J; Peppelenbosch, Maikel P; Pan, Qiuwei

    2016-10-01

    IFN regulatory factor 1 (IRF1) is one of the most important IFN-stimulated genes (ISGs) in cellular antiviral immunity. Although hepatitis E virus (HEV) is a leading cause of acute hepatitis worldwide, how ISGs counteract HEV infection is largely unknown. This study was conducted to investigate the effect of IRF1 on HEV replication. Multiple cell lines were used in 2 models that harbor HEV. In different HEV cell culture systems, IRF1 effectively inhibited HEV replication. IRF1 did not trigger IFN production, and chromatin immunoprecipitation sequencing data analysis revealed that IRF1 bound to the promoter region of signal transducers and activators of transcription 1 (STAT1). Functional assay confirmed that IRF1 could drive the transcription of STAT1, resulting in elevation of total and phosphorylated STAT1 proteins and further activating the transcription of a panel of downstream antiviral ISGs. By pharmacological inhibitors and RNAi-mediated gene-silencing approaches, we revealed that antiviral function of IRF1 is dependent on the JAK-STAT cascade. Furthermore, induction of ISGs and the anti-HEV effect of IRF1 overlapped that of IFNα, but was potentiated by ribavirin. We demonstrated that IRF1 effectively inhibits HEV replication through the activation of the JAK-STAT pathway, and the subsequent transcription of antiviral ISGs, but independent of IFN production.-Xu, L., Zhou, X., Wang, W., Wang, Y., Yin, Y., van der Laan, L. J. W., Sprengers, D., Metselaar, H. J., Peppelenbosch, M. P., Pan, Q. IFN regulatory factor 1 restricts hepatitis E virus replication by activating STAT1 to induce antiviral IFN-stimulated genes. © FASEB.

  13. 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.

  14. 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.

  15. 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.

  16. A Novel Agonist of the TRIF Pathway Induces a Cellular State Refractory to Replication of Zika, Chikungunya, and Dengue Viruses

    Directory of Open Access Journals (Sweden)

    Kara M. Pryke

    2017-05-01

    Full Text Available The ongoing concurrent outbreaks of Zika, Chikungunya, and dengue viruses in Latin America and the Caribbean highlight the need for development of broad-spectrum antiviral treatments. The type I interferon (IFN system has evolved in vertebrates to generate tissue responses that actively block replication of multiple known and potentially zoonotic viruses. As such, its control and activation through pharmacological agents may represent a novel therapeutic strategy for simultaneously impairing growth of multiple virus types and rendering host populations resistant to virus spread. In light of this strategy’s potential, we undertook a screen to identify novel interferon-activating small molecules. Here, we describe 1-(2-fluorophenyl-2-(5-isopropyl-1,3,4-thiadiazol-2-yl-1,2-dihydrochromeno[2,3-c]pyrrole-3,9-dione, which we termed AV-C. Treatment of human cells with AV-C activates innate and interferon-associated responses that strongly inhibit replication of Zika, Chikungunya, and dengue viruses. By utilizing genome editing, we investigated the host proteins essential to AV-C-induced cellular states. This showed that the compound requires a TRIF-dependent signaling cascade that culminates in IFN regulatory factor 3 (IRF3-dependent expression and secretion of type I interferon to elicit antiviral responses. The other canonical IRF3-terminal adaptor proteins STING and IPS-1/MAVS were dispensable for AV-C-induced phenotypes. However, our work revealed an important inhibitory role for IPS-1/MAVS, but not TRIF, in flavivirus replication, implying that TRIF-directed viral evasion may not occur. Additionally, we show that in response to AV-C, primary human peripheral blood mononuclear cells secrete proinflammatory cytokines that are linked with establishment of adaptive immunity to viral pathogens. Ultimately, synthetic innate immune activators such as AV-C may serve multiple therapeutic purposes, including direct antimicrobial responses and facilitation

  17. A Novel Agonist of the TRIF Pathway Induces a Cellular State Refractory to Replication of Zika, Chikungunya, and Dengue Viruses

    Science.gov (United States)

    Pryke, Kara M.; Abraham, Jinu; Sali, Tina M.; Gall, Bryan J.; Archer, Iris; Liu, Andrew; Bambina, Shelly; Baird, Jason; Gough, Michael; Chakhtoura, Marita; Haddad, Elias K.; Kirby, Ilsa T.; Nilsen, Aaron; Streblow, Daniel N.; Hirsch, Alec J.; Smith, Jessica L.

    2017-01-01

    ABSTRACT The ongoing concurrent outbreaks of Zika, Chikungunya, and dengue viruses in Latin America and the Caribbean highlight the need for development of broad-spectrum antiviral treatments. The type I interferon (IFN) system has evolved in vertebrates to generate tissue responses that actively block replication of multiple known and potentially zoonotic viruses. As such, its control and activation through pharmacological agents may represent a novel therapeutic strategy for simultaneously impairing growth of multiple virus types and rendering host populations resistant to virus spread. In light of this strategy’s potential, we undertook a screen to identify novel interferon-activating small molecules. Here, we describe 1-(2-fluorophenyl)-2-(5-isopropyl-1,3,4-thiadiazol-2-yl)-1,2-dihydrochromeno[2,3-c]pyrrole-3,9-dione, which we termed AV-C. Treatment of human cells with AV-C activates innate and interferon-associated responses that strongly inhibit replication of Zika, Chikungunya, and dengue viruses. By utilizing genome editing, we investigated the host proteins essential to AV-C-induced cellular states. This showed that the compound requires a TRIF-dependent signaling cascade that culminates in IFN regulatory factor 3 (IRF3)-dependent expression and secretion of type I interferon to elicit antiviral responses. The other canonical IRF3-terminal adaptor proteins STING and IPS-1/MAVS were dispensable for AV-C-induced phenotypes. However, our work revealed an important inhibitory role for IPS-1/MAVS, but not TRIF, in flavivirus replication, implying that TRIF-directed viral evasion may not occur. Additionally, we show that in response to AV-C, primary human peripheral blood mononuclear cells secrete proinflammatory cytokines that are linked with establishment of adaptive immunity to viral pathogens. Ultimately, synthetic innate immune activators such as AV-C may serve multiple therapeutic purposes, including direct antimicrobial responses and facilitation of

  18. 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...

  19. 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

  20. Adenovirus E4ORF1-induced MYC activation promotes host cell anabolic glucose metabolism and virus replication.

    Science.gov (United States)

    Thai, Minh; Graham, Nicholas A; Braas, Daniel; Nehil, Michael; Komisopoulou, Evangelia; Kurdistani, Siavash K; McCormick, Frank; Graeber, Thomas G; Christofk, Heather R

    2014-04-01

    Virus infections trigger metabolic changes in host cells that support the bioenergetic and biosynthetic demands of viral replication. Although recent studies have characterized virus-induced changes in host cell metabolism (Munger et al., 2008; Terry et al., 2012), the molecular mechanisms by which viruses reprogram cellular metabolism have remained elusive. Here, we show that the gene product of adenovirus E4ORF1 is necessary for adenovirus-induced upregulation of host cell glucose metabolism and sufficient to promote enhanced glycolysis in cultured epithelial cells by activation of MYC. E4ORF1 localizes to the nucleus, binds to MYC, and enhances MYC binding to glycolytic target genes, resulting in elevated expression of specific glycolytic enzymes. E4ORF1 activation of MYC promotes increased nucleotide biosynthesis from glucose intermediates and enables optimal adenovirus replication in primary lung epithelial cells. Our findings show how a viral protein exploits host cell machinery to reprogram cellular metabolism and promote optimal progeny virion generation. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Photosensitized UVA-Induced Cross-Linking between Human DNA Repair and Replication Proteins and DNA Revealed by Proteomic Analysis

    Science.gov (United States)

    2016-01-01

    Long wavelength ultraviolet radiation (UVA, 320–400 nm) interacts with chromophores present in human cells to induce reactive oxygen species (ROS) that damage both DNA and proteins. ROS levels are amplified, and the damaging effects of UVA are exacerbated if the cells are irradiated in the presence of UVA photosensitizers such as 6-thioguanine (6-TG), a strong UVA chromophore that is extensively incorporated into the DNA of dividing cells, or the fluoroquinolone antibiotic ciprofloxacin. Both DNA-embedded 6-TG and ciprofloxacin combine synergistically with UVA to generate high levels of ROS. Importantly, the extensive protein damage induced by these photosensitizer+UVA combinations inhibits DNA repair. DNA is maintained in intimate contact with the proteins that effect its replication, transcription, and repair, and DNA–protein cross-links (DPCs) are a recognized reaction product of ROS. Cross-linking of DNA metabolizing proteins would compromise these processes by introducing physical blocks and by depleting active proteins. We describe a sensitive and statistically rigorous method to analyze DPCs in cultured human cells. Application of this proteomics-based analysis to cells treated with 6-TG+UVA and ciprofloxacin+UVA identified proteins involved in DNA repair, replication, and gene expression among those most vulnerable to cross-linking under oxidative conditions. PMID:27654267

  2. 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

  3. 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.

  4. 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...

  5. FBH1 co-operates with MUS81 in inducing DNA double-strand breaks and cell death following replication stress

    DEFF Research Database (Denmark)

    Fugger, Kasper; Chu, Wai Kit; Haahr, Peter

    2013-01-01

    The molecular events occurring following the disruption of DNA replication forks are poorly characterized, despite extensive use of replication inhibitors such as hydroxyurea in the treatment of malignancies. Here, we identify a key role for the FBH1 helicase in mediating DNA double-strand break...... formation following replication inhibition. We show that FBH1-deficient cells are resistant to killing by hydroxyurea, and exhibit impaired activation of the pro-apoptotic factor p53, consistent with decreased DNA double-strand break formation. Similar findings were obtained in murine ES cells carrying...... of replication stress. Our data suggest that FBH1 helicase activity is required to eliminate cells with excessive replication stress through the generation of MUS81-induced DNA double-strand breaks....

  6. Direct Observation of Field and Temperature Induced Domain Replication in Dipolar Coupled Perpendicular Anisotropy Films

    Energy Technology Data Exchange (ETDEWEB)

    Hauet, T.; Gunther, C.M.; Pfau, B.; Eisebitt, S.; Fischer, P.; Rick, R. L.; Thiele, J.-U.; Hellwig, O.; Schabes, M.E.

    2007-07-01

    Dipolar interactions in a soft/Pd/hard [CoNi/Pd]{sub 30}/Pd/[Co/Pd]{sub 20} multilayer system, where a thick Pd layer between two ferromagnetic units prevents direct exchange coupling, are directly revealed by combining magnetometry and state-of-the-art layer resolving soft x-ray imaging techniques with sub-100-nm spatial resolution. The domains forming in the soft layer during external magnetic field reversal are found to match the domains previously trapped in the hard layer. The low Curie temperature of the soft layer allows varying its intrinsic parameters via temperature and thus studying the competition with dipolar fields due to the domains in the hard layer. Micromagnetic simulations elucidate the role of [CoNi/Pd] magnetization, exchange, and anisotropy in the duplication process. Finally, thermally driven domain replication in remanence during temperature cycling is demonstrated.

  7. 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.

  8. Experimentally-induced immune activation in natural hosts of SIV induces significant increases in viral replication and CD4+ T cell depletion

    Energy Technology Data Exchange (ETDEWEB)

    Ribeiro, Ruy M [Los Alamos National Laboratory

    2008-01-01

    Chronically SIVagm-infected African green monkeys (AGMs) have a remarkably stable non-pathogenic disease course, with levels of immune activation in chronic SIVagm infection similar to those observed in uninfected monkeys and stable viral loads (VLs) for long periods of time. In vivo administration of lipopolysaccharide (LPS) or an IL-2/diphtheria toxin fusion protein (Ontak) to chronically SIVagm-infected AGMs triggered increases in immune activation and subsequently of viral replication and depletion of intestinal CD4{sup +} T cells. Our study indicates that circulating microbial products can increase viral replication by inducing immune activation and increasing the number of viral target cells, thus demonstrating that immune activation and T cell prolifeation are key factors in AIDS pathogenesis.

  9. 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)

  10. 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.

  11. 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.

  12. 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

  13. Differential sensitivity to aphidicolin of replicative DNA synthesis and ultraviolet-induced unscheduled DNA synthesis in vivo in mammalian cells

    International Nuclear Information System (INIS)

    Seki, Shuji; Hosogi, Nobuo; Oda, Takuzo

    1984-01-01

    In vivo in mammalian cells, ultraviolet-induced unscheduled DNA synthesis was less sensitive to aphidicolin than was replicative DNA synthesis. Replicative DNA synthesis in HeLa, HEp-2, WI-38 VA-13 and CV-1 cells was inhibited more than 97 % by aphidicolin at 10 μg/ml, whereas aphidicolin inhibition of DNA synthesis in ultraviolet-irradiated cells varied between 30 % and 90 % depending on cell types and assay conditions. Aphidicolin inhibition of unscheduled DNA synthesis (UDS) in HeLa cells increased gradually with increasing aphidicolin concentration and reached approximately 90 % at 100 μg/ml aphidicolin. A significant fraction of UDS in ultraviolet-irradiated HEp-2 cells was resistant to aphidicolin even at 300 μg/ml. Considered along with related information reported previously, the present results suggest that both aphidicolin-sensitive and insensitive DNA polymerases, DNA polymerase α and a non-α DNA polymerase (possibly DNA polymerase β), are involved in in situ UDS in these ultraviolet-irradiated cells. Comparison of staphylococcal nuclease sensitivity between DNAs repaired in the presence and in the absence of aphidicolin in HEp-2 cells suggested that the involvement of DNA polymerase α in UDS favored DNA synthesis in the intranucleosomal region. (author)

  14. 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.

  15. Radiation-induced cross-link DNA damages: synthesis, measurement and insertion into oligonucleotides for replication and enzymatic repair studies

    International Nuclear Information System (INIS)

    Bellon, Sophie

    2003-01-01

    This research thesis addresses the synthesis, measurement and study of the biological impact of radio-induced DNA double damages. In the first part, the author reports the study of the reactivity and fate of the 5-(2'-desoxy-uridilyl)methyl radical which is one of the intermediates formed by oxidizing photo-sensitisation of thymine. The next part reports results of the formation and measurement of double damages of isolated and cellular DNA, notably in the case of γ irradiation. The third part reports the study of in vitro replication of one of the double damages. The behaviour of different polymerases with respect to the damage is reported. Finally, the modified oligonucleotide has been used as a substrate to highlight possible activities of enzymatic repair for this type of cross-link damages by purified proteins or proteins present within cellular extracts [fr

  16. Identification of rep-associated factors in herpes simplex virus type 1-induced adeno-associated virus type 2 replication compartments.

    Science.gov (United States)

    Nicolas, Armel; Alazard-Dany, Nathalie; Biollay, Coline; Arata, Loredana; Jolinon, Nelly; Kuhn, Lauriane; Ferro, Myriam; Weller, Sandra K; Epstein, Alberto L; Salvetti, Anna; Greco, Anna

    2010-09-01

    Adeno-associated virus (AAV) is a human parvovirus that replicates only in cells coinfected with a helper virus, such as adenovirus or herpes simplex virus type 1 (HSV-1). We previously showed that nine HSV-1 factors are able to support AAV rep gene expression and genome replication. To elucidate the strategy of AAV replication in the presence of HSV-1, we undertook a proteomic analysis of cellular and HSV-1 factors associated with Rep proteins and thus potentially recruited within AAV replication compartments (AAV RCs). This study resulted in the identification of approximately 60 cellular proteins, among which factors involved in DNA and RNA metabolism represented the largest functional categories. Validation analyses indicated that the cellular DNA replication enzymes RPA, RFC, and PCNA were recruited within HSV-1-induced AAV RCs. Polymerase delta was not identified but subsequently was shown to colocalize with Rep within AAV RCs even in the presence of the HSV-1 polymerase complex. In addition, we found that AAV replication is associated with the recruitment of components of the Mre11/Rad50/Nbs1 complex, Ku70 and -86, and the mismatch repair proteins MSH2, -3, and -6. Finally, several HSV-1 factors were also found to be associated with Rep, including UL12. We demonstrated for the first time that this protein plays a role during AAV replication by enhancing the resolution of AAV replicative forms and AAV particle production. Altogether, these analyses provide the basis to understand how AAV adapts its replication strategy to the nuclear environment induced by the helper virus.

  17. A Novel Agonist of the TRIF Pathway Induces a Cellular State Refractory to Replication of Zika, Chikungunya, and Dengue Viruses.

    Science.gov (United States)

    Pryke, Kara M; Abraham, Jinu; Sali, Tina M; Gall, Bryan J; Archer, Iris; Liu, Andrew; Bambina, Shelly; Baird, Jason; Gough, Michael; Chakhtoura, Marita; Haddad, Elias K; Kirby, Ilsa T; Nilsen, Aaron; Streblow, Daniel N; Hirsch, Alec J; Smith, Jessica L; DeFilippis, Victor R

    2017-05-02

    The ongoing concurrent outbreaks of Zika, Chikungunya, and dengue viruses in Latin America and the Caribbean highlight the need for development of broad-spectrum antiviral treatments. The type I interferon (IFN) system has evolved in vertebrates to generate tissue responses that actively block replication of multiple known and potentially zoonotic viruses. As such, its control and activation through pharmacological agents may represent a novel therapeutic strategy for simultaneously impairing growth of multiple virus types and rendering host populations resistant to virus spread. In light of this strategy's potential, we undertook a screen to identify novel interferon-activating small molecules. Here, we describe 1-(2-fluorophenyl)-2-(5-isopropyl-1,3,4-thiadiazol-2-yl)-1,2-dihydrochromeno[2,3- c ]pyrrole-3,9-dione, which we termed AV-C. Treatment of human cells with AV-C activates innate and interferon-associated responses that strongly inhibit replication of Zika, Chikungunya, and dengue viruses. By utilizing genome editing, we investigated the host proteins essential to AV-C-induced cellular states. This showed that the compound requires a TRIF-dependent signaling cascade that culminates in IFN regulatory factor 3 (IRF3)-dependent expression and secretion of type I interferon to elicit antiviral responses. The other canonical IRF3-terminal adaptor proteins STING and IPS-1/MAVS were dispensable for AV-C-induced phenotypes. However, our work revealed an important inhibitory role for IPS-1/MAVS, but not TRIF, in flavivirus replication, implying that TRIF-directed viral evasion may not occur. Additionally, we show that in response to AV-C, primary human peripheral blood mononuclear cells secrete proinflammatory cytokines that are linked with establishment of adaptive immunity to viral pathogens. Ultimately, synthetic innate immune activators such as AV-C may serve multiple therapeutic purposes, including direct antimicrobial responses and facilitation of pathogen

  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. 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...

  1. Vitamin D represses rhinovirus replication in cystic fibrosis cells by inducing LL-37.

    Science.gov (United States)

    Schögler, Aline; Muster, Ricardo J; Kieninger, Elisabeth; Casaulta, Carmen; Tapparel, Caroline; Jung, Andreas; Moeller, Alexander; Geiser, Thomas; Regamey, Nicolas; Alves, Marco P

    2016-02-01

    Vitamin D has immunomodulatory properties in the defence against pathogens. Its insufficiency is a widespread feature of cystic fibrosis (CF) patients, which are repeatedly suffering from rhinovirus (RV)-induced pulmonary exacerbations.To investigate whether vitamin D has antiviral activity, primary bronchial epithelial cells from CF children were pre-treated with vitamin D and infected with RV16. Antiviral and anti-inflammatory activity of vitamin D was assessed. RV and LL-37 levels were measured in bronchoalveolar lavage (BAL) of CF children infected with RV.Vitamin D reduced RV16 load in a dose-dependent manner in CF cells (10(-7 )M, pvitamin D in CF cells. Vitamin D did not exert anti-inflammatory properties in RV-infected CF cells. Vitamin D increased the expression of the antimicrobial peptide LL-37 up to 17.4-fold (pvitamin D through the induction of LL-37. Clinical studies are needed to determine the importance of an adequate control of vitamin D for prevention of virus-induced pulmonary CF exacerbations. Copyright ©ERS 2016.

  2. 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.

  3. Pur-Alpha Induces JCV Gene Expression and Viral Replication by Suppressing SRSF1 in Glial Cells.

    Directory of Open Access Journals (Sweden)

    Ilker Kudret Sariyer

    Full Text Available PML is a rare and fatal demyelinating disease of the CNS caused by the human polyomavirus, JC virus (JCV, which occurs in AIDS patients and those on immunosuppressive monoclonal antibody therapies (mAbs. We sought to identify mechanisms that could stimulate reactivation of JCV in a cell culture model system and targeted pathways which could affect early gene transcription and JCV T-antigen production, which are key steps of the viral life cycle for blocking reactivation of JCV. Two important regulatory partners we have previously identified for T-antigen include Pur-alpha and SRSF1 (SF2/ASF. SRSF1, an alternative splicing factor, is a potential regulator of JCV whose overexpression in glial cells strongly suppresses viral gene expression and replication. Pur-alpha has been most extensively characterized as a sequence-specific DNA- and RNA-binding protein which directs both viral gene transcription and mRNA translation, and is a potent inducer of the JCV early promoter through binding to T-antigen.Pur-alpha and SRSF1 both act directly as transcriptional regulators of the JCV promoter and here we have observed that Pur-alpha is capable of ameliorating SRSF1-mediated suppression of JCV gene expression and viral replication. Interestingly, Pur-alpha exerted its effect by suppressing SRSF1 at both the protein and mRNA levels in glial cells suggesting this effect can occur independent of T-antigen. Pur-alpha and SRSF1 were both localized to oligodendrocyte inclusion bodies by immunohistochemistry in brain sections from patients with HIV-1 associated PML. Interestingly, inclusion bodies were typically positive for either Pur-alpha or SRSF1, though some cells appeared to be positive for both proteins.Taken together, these results indicate the presence of an antagonistic interaction between these two proteins in regulating of JCV gene expression and viral replication and suggests that they play an important role during viral reactivation leading to

  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. uvsF RFC1, the large subunit of replication factor C in Aspergillus nidulans, is essential for DNA replication, functions in UV repair and is upregulated in response to MMS-induced DNA damage.

    Science.gov (United States)

    Kafer, Etta; Chae, Suhn-Kee

    2008-09-01

    uvsF201 was the first highly UV-sensitive repair-defective mutation isolated in Aspergillus nidulans. It showed epistasis only with postreplication repair mutations, but caused lethal interactions with many other repair-defective strains. Unexpectedly, closest homology of uvsF was found to the large subunit of human DNA replication factor RFC that is essential for DNA replication. Sequencing of the uvsF201 region identified changes at two close base pairs and the corresponding amino acids in the 5'-region of uvsF(RFC1). This viable mutant represents a novel and possibly important type. Additional sequencing of the uvsF region confirmed a mitochondrial ribosomal protein gene, mrpA(L16), closely adjacent, head-to-head with a 0.2kb joint promoter region. MMS-induced transcription of both the genes, but especially uvsF(RFC1), providing evidence for a function in DNA damage response.

  6. 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.

  7. 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

  8. Effect of the uvr D3 mutation on ultraviolet radiation-induced DNA-repair replication in Escherichia coli K12

    International Nuclear Information System (INIS)

    Carlson, K.M.; Smith, K.C.

    1981-01-01

    Ultraviolet-radiation-induced DNA-repair replication was measured in wild-type, polA1, uvrD3, and polA1 uvrD3 strains of Escherichia coli K 12. A large stimulation of repair replication was observed in the uvrD3 strain, compared to the wild-type and polA1 strains. This enhanced repair replication was reduced in the polA1 uvrD3 strain. Therefore, a uvrD3 mutation appears to affect the amount of repair replication performed by DNA polymerase I. In the polA1 strain, there also appears to be an effect of the uvrD3 mutation on the amount of repair replication performed by DNA polymerase III (and/or II). The enhanced repair replication observed for the uvrD3 strains appears to be in response to the enhanced DNA degradation observed for these strains. (orig.)

  9. Replication and virus-induced transcriptome of HAdV-5 in normal host cells versus cancer cells--differences of relevance for adenoviral oncolysis.

    Directory of Open Access Journals (Sweden)

    Dominik E Dorer

    Full Text Available Adenoviruses (Ads, especially HAdV-5, have been genetically equipped with tumor-restricted replication potential to enable applications in oncolytic cancer therapy. Such oncolytic adenoviruses have been well tolerated in cancer patients, but their anti-tumor efficacy needs to be enhanced. In this regard, it should be considered that cancer cells, dependent on their tissue of origin, can differ substantially from the normal host cells to which Ads are adapted by complex virus-host interactions. Consequently, viral replication efficiency, a key determinant of oncolytic activity, might be suboptimal in cancer cells. Therefore, we have analyzed both the replication kinetics of HAdV-5 and the virus-induced transcriptome in human bronchial epithelial cells (HBEC in comparison to cancer cells. This is the first report on genome-wide expression profiling of Ads in their native host cells. We found that E1A expression and onset of viral genome replication are most rapid in HBEC and considerably delayed in melanoma cells. In squamous cell lung carcinoma cells, we observed intermediate HAdV-5 replication kinetics. Infectious particle production, viral spread and lytic activity of HAdV-5 were attenuated in melanoma cells versus HBEC. Expression profiling at the onset of viral genome replication revealed that HAdV-5 induced the strongest changes in the cellular transcriptome in HBEC, followed by lung cancer and melanoma cells. We identified prominent regulation of genes involved in cell cycle and DNA metabolism, replication and packaging in HBEC, which is in accord with the necessity to induce S phase for viral replication. Strikingly, in melanoma cells HAdV-5 triggered opposing regulation of said genes and, in contrast to lung cancer cells, no weak S phase induction was detected when using the E2F promoter as reporter. Our results provide a rationale for improving oncolytic adenoviruses either by adaptation of viral infection to target tumor cells or by

  10. Blood CXCR3+ CD4 T Cells Are Enriched in Inducible Replication Competent HIV in Aviremic Antiretroviral Therapy-Treated Individuals.

    Science.gov (United States)

    Banga, Riddhima; Procopio, Francesco A; Ruggiero, Alessandra; Noto, Alessandra; Ohmiti, Khalid; Cavassini, Matthias; Corpataux, Jean-Marc; Paxton, William A; Pollakis, Georgios; Perreau, Matthieu

    2018-01-01

    We recently demonstrated that lymph nodes (LNs) PD-1 + /T follicular helper (Tfh) cells from antiretroviral therapy (ART)-treated HIV-infected individuals were enriched in cells containing replication competent virus. However, the distribution of cells containing inducible replication competent virus has been only partially elucidated in blood memory CD4 T-cell populations including the Tfh cell counterpart circulating in blood (cTfh). In this context, we have investigated the distribution of (1) total HIV-infected cells and (2) cells containing replication competent and infectious virus within various blood and LN memory CD4 T-cell populations of conventional antiretroviral therapy (cART)-treated HIV-infected individuals. In the present study, we show that blood CXCR3-expressing memory CD4 T cells are enriched in cells containing inducible replication competent virus and contributed the most to the total pool of cells containing replication competent and infectious virus in blood. Interestingly, subsequent proviral sequence analysis did not indicate virus compartmentalization between blood and LN CD4 T-cell populations, suggesting dynamic interchanges between the two compartments. We then investigated whether the composition of blood HIV reservoir may reflect the polarization of LN CD4 T cells at the time of reservoir seeding and showed that LN PD-1 + CD4 T cells of viremic untreated HIV-infected individuals expressed significantly higher levels of CXCR3 as compared to CCR4 and/or CCR6, suggesting that blood CXCR3-expressing CD4 T cells may originate from LN PD-1 + CD4 T cells. Taken together, these results indicate that blood CXCR3-expressing CD4 T cells represent the major blood compartment containing inducible replication competent virus in treated aviremic HIV-infected individuals.

  11. Hepatitis C virus (HCV) induces formation of stress granules whose proteins regulate HCV RNA replication and virus assembly and egress.

    Science.gov (United States)

    Garaigorta, Urtzi; Heim, Markus H; Boyd, Bryan; Wieland, Stefan; Chisari, Francis V

    2012-10-01

    Stress granules (SGs) are cytoplasmic structures that are induced in response to environmental stress, including viral infections. Here we report that hepatitis C virus (HCV) triggers the appearance of SGs in a PKR- and interferon (IFN)-dependent manner. Moreover, we show an inverse correlation between the presence of stress granules and the induction of IFN-stimulated proteins, i.e., MxA and USP18, in HCV-infected cells despite high-level expression of the corresponding MxA and USP18 mRNAs, suggesting that interferon-stimulated gene translation is inhibited in stress granule-containing HCV-infected cells. Finally, in short hairpin RNA (shRNA) knockdown experiments, we found that the stress granule proteins T-cell-restricted intracellular antigen 1 (TIA-1), TIA1-related protein (TIAR), and RasGAP-SH3 domain binding protein 1 (G3BP1) are required for efficient HCV RNA and protein accumulation at early time points in the infection and that G3BP1 and TIA-1 are required for intracellular and extracellular infectious virus production late in the infection, suggesting that they are required for virus assembly. In contrast, TIAR downregulation decreases extracellular infectious virus titers with little effect on intracellular RNA content or infectivity late in the infection, suggesting that it is required for infectious particle release. Collectively, these results illustrate that HCV exploits the stress granule machinery at least two ways: by inducing the formation of SGs by triggering PKR phosphorylation, thereby downregulating the translation of antiviral interferon-stimulated genes, and by co-opting SG proteins for its replication, assembly, and egress.

  12. 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.

  13. 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...

  14. Inhibition of Poliovirus-Induced Cleavage of Cellular Protein PCBP2 Reduces the Levels of Viral RNA Replication

    Science.gov (United States)

    Chase, Amanda J.; Daijogo, Sarah

    2014-01-01

    ABSTRACT Due to their small genome size, picornaviruses must utilize host proteins to mediate cap-independent translation and viral RNA replication. The host RNA-binding protein poly(rC) binding protein 2 (PCBP2) is involved in both processes in poliovirus infected cells. It has been shown that the viral proteinase 3CD cleaves PCBP2 and contributes to viral translation inhibition. However, cleaved PCBP2 remains active in viral RNA replication. This would suggest that both cleaved and intact forms of PCBP2 have a role in the viral RNA replication cycle. The picornavirus genome must act as a template for both translation and RNA replication. However, a template that is actively being translated cannot function as a template for RNA replication, suggesting that there is a switch in template usage from translation to RNA replication. We demonstrate that the cleavage of PCBP2 by the poliovirus 3CD proteinase is a necessary step for efficient viral RNA replication and, as such, may be important for mediating a switch in template usage from translation to RNA replication. IMPORTANCE Poliovirus, like all positive-strand RNA viruses that replicate in the cytoplasm of eukaryotic cells, uses its genomic RNA as a template for both viral protein synthesis and RNA replication. Given that these processes cannot occur simultaneously on the same template, poliovirus has evolved a mechanism(s) to facilitate the switch from using templates for translation to using them for RNA synthesis. This study explores one possible scenario for how the virus alters the functions of a host cell RNA binding protein to mediate, in part, this important transition. PMID:24371074

  15. 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.

  16. 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

  17. Genome-Wide Search for Competing Endogenous RNAs Responsible for the Effects Induced by Ebola Virus Replication and Transcription Using a trVLP System

    Directory of Open Access Journals (Sweden)

    Zhong-Yi Wang

    2017-11-01

    Full Text Available Understanding how infected cells respond to Ebola virus (EBOV and how this response changes during the process of viral replication and transcription are very important for establishing effective antiviral strategies. In this study, we conducted a genome-wide screen to identify long non-coding RNAs (lncRNAs, circular RNAs (circRNAs, micro RNAs (miRNAs, and mRNAs differentially expressed during replication and transcription using a tetracistronic transcription and replication-competent virus-like particle (trVLP system that models the life cycle of EBOV in 293T cells. To characterize the expression patterns of these differentially expressed RNAs, we performed a series cluster analysis, and up- or down-regulated genes were selected to establish a gene co-expression network. Competing endogenous RNA (ceRNA networks based on the RNAs responsible for the effects induced by EBOV replication and transcription in human cells, including circRNAs, lncRNAs, miRNAs, and mRNAs, were constructed for the first time. Based on these networks, the interaction details of circRNA-chr19 were explored. Our results demonstrated that circRNA-chr19 targeting miR-30b-3p regulated CLDN18 expression by functioning as a ceRNA. These findings may have important implications for further studies of the mechanisms of EBOV replication and transcription. These RNAs potentially have important functions and may be promising targets for EBOV therapy.

  18. 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.

  19. Overexpression of pig selenoprotein S blocks OTA-induced promotion of PCV2 replication by inhibiting oxidative stress and p38 phosphorylation in PK15 cells

    Science.gov (United States)

    Gan, Fang; Hu, Zhihua; Huang, Yu; Xue, Hongxia; Huang, Da; Qian, Gang; Hu, Junfa; Chen, Xingxiang; Wang, Tian; Huang, Kehe

    2016-01-01

    Porcine circovirus type 2 (PCV2) is the primary cause of porcine circovirus disease, and ochratoxin A (OTA)-induced oxidative stress promotes PCV2 replication. In humans, selenoprotein S (SelS) has antioxidant ability, but it is unclear whether SelS affects viral infection. Here, we stably transfected PK15 cells with pig pCDNA3.1-SelS to overexpress SelS. Selenium (Se) at 2 or 4 μM and SelS overexpression blocked the OTA-induced increases of PCV2 DNA copy number and infected cell numbers. SelS overexpression also increased glutathione (GSH), NF-E2-related factor 2 (Nrf2) mRNA, and γ-glutamyl-cysteine synthetase mRNA levels; decreased reactive oxygen species (ROS) levels; and inhibited p38 phosphorylation in PCV2-infected PK15 cells, regardless of OTA treatment. Buthionine sulfoximine reversed all of the above SelS-induced changes. siRNA-mediated SelS knockdown decreased Nrf2 mRNA and GSH levels, increased ROS levels, and promoted PCV2 replication in OTA-treated PK15 cells. These data indicate that pig SelS blocks OTA-induced promotion of PCV2 replication by inhibiting the oxidative stress and p38 phosphorylation in PK15 cells. PMID:26943035

  20. Synthesis of modified oligonucleotides for repair and replication studies of single and double radio-induced DNA lesions

    International Nuclear Information System (INIS)

    Muller, E.

    2002-01-01

    Several oxidative processes induce the formation of DNA lesions. In order to evaluate the biological and structural significance of such damage, several DNA lesions were inserted into synthetic oligonucleotides at defined sites. The research work aimed at describing the preparation of oligonucleotides t hat contained DNA damage and the evaluation of the biological properties of the lesions. A first part described the incorporation of radiation-induced lesions, namely (5'S,6S)-5',6-cyclo-5,6-dihydro-2'-deoxyuridine and (5'S,5S,6S)-5',6-cyclo-5-hydroxy-5,6-dihydro-2'-desoxyuridine into oligonucleotides. The modified DNA fragments were characterised by several spectroscopic and biochemical analyses including ESI MS, MALDI-TOF MS, CLHP and enzymatic digestions. During in vitro DNA synthesis by Taq DNA polymerase and Klenow exo fragment, the pyrimidine cyclo-nucleosides were found to block the progression of the enzymes. Then, repair studies by ADN N glycosylases, operating in the base excision repair pathway, have shown that the anhydro-nucleoside lesions were not recognised nor excised by Fpg, endo III, endo VIII, yNtg1 yNtg2 and yOgg1. Interestingly, the Latococcus lactis Fpg protein recognises (formation of a non covalent complex) but do not excise the damage. The incorporation into oligonucleotides of the (5R*) and (5S*) diastereoisomers of 1-[2-deoxy-β-D-erythro-pentofuranosyl]-5-hydroxy-hydantoin, generated by several oxidative processes was then described. In vitro DNA replication assays using modified oligonucleotides matrix showed a lethal potential of the latter base damage. Repair studies by ADN N-glycosylases showed that the damage was substrate for Fpg, endo III, endo VIII, Ntg1, Ntg2 and Fpg-L1. The rates of excision as inferred from the determination of the Michaelis kinetics constants were found to be affected by the presence of the damage. MALDI-TOF MS was used in order to gain insights into mechanistic aspects of oligonucleotides cleavage by the

  1. 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.

  2. Effective Respiratory CD8 T-Cell Immunity to Influenza Virus Induced by Intranasal Carbomer-Lecithin-Adjuvanted Non-replicating Vaccines

    Science.gov (United States)

    Gasper, David J.; Neldner, Brandon; Plisch, Erin H.; Rustom, Hani; Imai, Hirotaka; Kawaoka, Yoshihiro; Suresh, M.

    2016-01-01

    CD8+ cytotoxic T lymphocytes (CTLs) are critical for clearing many viral infections, and protective CTL memory can be induced by vaccination with attenuated viruses and vectors. Non-replicating vaccines are typically potentiated by the addition of adjuvants that enhance humoral responses, however few are capable of generating CTL responses. Adjuplex is a carbomer-lecithin-based adjuvant demonstrated to elicit robust humoral immunity to non-replicating antigens. We report that mice immunized with non-replicating Adjuplex-adjuvanted vaccines generated robust antigen-specific CTL responses. Vaccination by the subcutaneous or the intranasal route stimulated systemic and mucosal CTL memory respectively. However, only CTL memory induced by intranasal vaccination was protective against influenza viral challenge, and correlated with an enhancement of memory CTLs in the airways and CD103+ CD69+ CXCR3+ resident memory-like CTLs in the lungs. Mechanistically, Myd88-deficient mice mounted primary CTL responses to Adjuplex vaccines that were similar in magnitude to wild-type mice, but exhibited altered differentiation of effector cell subsets. Immune potentiating effects of Adjuplex entailed alterations in the frequency of antigen-presenting-cell subsets in vaccine draining lymph nodes, and in the lungs and airways following intranasal vaccination. Further, Adjuplex enhanced the ability of dendritic cells to promote antigen-induced proliferation of naïve CD8 T cells by modulating antigen uptake, its intracellular localization, and rate of processing. Taken together, we have identified an adjuvant that elicits both systemic and mucosal CTL memory to non-replicating antigens, and engenders protective CTL-based heterosubtypic immunity to influenza A virus in the respiratory tract. Further, findings presented in this manuscript have provided key insights into the mechanisms and factors that govern the induction and programming of systemic and protective memory CTLs in the

  3. 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

  4. Influenza A Virus-Induced Expression of a GalNAc Transferase, GALNT3, via MicroRNAs Is Required for Enhanced Viral Replication.

    Science.gov (United States)

    Nakamura, Shoko; Horie, Masayuki; Daidoji, Tomo; Honda, Tomoyuki; Yasugi, Mayo; Kuno, Atsushi; Komori, Toshihisa; Okuzaki, Daisuke; Narimatsu, Hisashi; Nakaya, Takaaki; Tomonaga, Keizo

    2016-02-15

    Influenza A virus (IAV) affects the upper and lower respiratory tracts and rapidly induces the expression of mucins, which are common O-glycosylated proteins, on the epithelial surfaces of the respiratory tract. Although mucin production is associated with the inhibition of virus transmission as well as characteristic clinical symptoms, little is known regarding how mucins are produced on the surfaces of respiratory epithelial cells and how they affect IAV replication. In this study, we found that two microRNAs (miRNAs), miR-17-3p and miR-221, which target GalNAc transferase 3 (GALNT3) mRNA, are rapidly downregulated in human alveolar basal epithelial cells during the early stage of IAV infection. We demonstrated that the expression of GALNT3 mRNA is upregulated in an IAV replication-dependent fashion and leads to mucin production in bronchial epithelial cells. A lectin microarray analysis revealed that the stable expression of GALNT3 by human alveolar basal epithelial cells induces mucin-type O-glycosylation modifications similar to those present in IAV-infected cells, suggesting that GALNT3 promotes mucin-type O-linked glycosylation in IAV-infected cells. Notably, analyses using short interfering RNAs and miRNA mimics showed that GALNT3 knockdown significantly reduces IAV replication. Furthermore, IAV replication was markedly decreased in embryonic fibroblast cells obtained from galnt3-knockout mice. Interestingly, IAV-infected galnt3-knockout mice exhibited high mortality and severe pathological alterations in the lungs compared to those of wild-type mice. Our results demonstrate not only the molecular mechanism underlying rapid mucin production during IAV infection but also the contribution of O-linked glycosylation to the replication and propagation of IAV in lung cells. Viral infections that affect the upper or lower respiratory tracts, such as IAV, rapidly induce mucin production on the epithelial surfaces of respiratory cells. However, the details of how

  5. Laser-induced heating integrated with a microfluidic platform for real-time DNA replication and detection

    Science.gov (United States)

    Hung, Min-Sheng; Ho, Chia-Chin; Chen, Chih-Pin

    2016-08-01

    This study developed a microfluidic platform for replicating and detecting DNA in real time by integrating a laser and a microfluidic device composed of polydimethylsiloxane. The design of the microchannels consisted of a laser-heating area and a detection area. An infrared laser was used as the heating source for DNA replication, and the laser power was adjusted to heat the solutions directly. In addition, strong biotin-avidin binding was used to capture and detect the replicated products. The biotin on one end was bound to avidin and anchored to the surface of the microchannels, whereas the biotin on the other end was bound to the quantum dots (Qdots). The results showed that the fluorescent intensity of the Qdots bound to the replicated products in the detection area increased with the number of thermal cycles created by the laser. When the number of thermal cycles was ≥10, the fluorescent intensity of the Qdots was directly detectable on the surface of the microchannels. The proposed method is more sensitive than detection methods entailing gel electrophoresis.

  6. 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...

  7. 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

  8. 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

  9. 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.

  10. DNA Damage Signaling Is Induced in the Absence of Epstein-Barr Virus (EBV) Lytic DNA Replication and in Response to Expression of ZEBRA.

    Science.gov (United States)

    Wang'ondu, Ruth; Teal, Stuart; Park, Richard; Heston, Lee; Delecluse, Henri; Miller, George

    2015-01-01

    Epstein Barr virus (EBV), like other oncogenic viruses, modulates the activity of cellular DNA damage responses (DDR) during its life cycle. Our aim was to characterize the role of early lytic proteins and viral lytic DNA replication in activation of DNA damage signaling during the EBV lytic cycle. Our data challenge the prevalent hypothesis that activation of DDR pathways during the EBV lytic cycle occurs solely in response to large amounts of exogenous double stranded DNA products generated during lytic viral DNA replication. In immunofluorescence or immunoblot assays, DDR activation markers, specifically phosphorylated ATM (pATM), H2AX (γH2AX), or 53BP1 (p53BP1), were induced in the presence or absence of viral DNA amplification or replication compartments during the EBV lytic cycle. In assays with an ATM inhibitor and DNA damaging reagents in Burkitt lymphoma cell lines, γH2AX induction was necessary for optimal expression of early EBV genes, but not sufficient for lytic reactivation. Studies in lytically reactivated EBV-positive cells in which early EBV proteins, BGLF4, BGLF5, or BALF2, were not expressed showed that these proteins were not necessary for DDR activation during the EBV lytic cycle. Expression of ZEBRA, a viral protein that is necessary for EBV entry into the lytic phase, induced pATM foci and γH2AX independent of other EBV gene products. ZEBRA mutants deficient in DNA binding, Z(R183E) and Z(S186E), did not induce foci of pATM. ZEBRA co-localized with HP1β, a heterochromatin associated protein involved in DNA damage signaling. We propose a model of DDR activation during the EBV lytic cycle in which ZEBRA induces ATM kinase phosphorylation, in a DNA binding dependent manner, to modulate gene expression. ATM and H2AX phosphorylation induced prior to EBV replication may be critical for creating a microenvironment of viral and cellular gene expression that enables lytic cycle progression.

  11. 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.

  12. Molecular mechanisms of induced mutagenesis. Replication in vivo of bacteriophage phiX174 single-stranded, ultraviolet light-irradiated DNA in intact and irradiated host cells

    Energy Technology Data Exchange (ETDEWEB)

    Caillet-Fauquet, P; Defais, M; Radman, M [Brussels Univ. (Belgium)

    1977-11-25

    Genetic analysis has revealed that radiation and many chemical mutagens induce in bacteria an error-prone DNA repair process which is responsible for their mutagenic effect. The biochemical mechanism of this inducible error-prone repair has been studied by analysis of the first round of DNA synthesis on ultraviolet light-irradiated phiX174 DNA in both intact and ultraviolet light-irradiated host cells. Intracellular phiX174 DNA was extracted, subjected to isopycnic CsCl density-gradient analysis, hydroxylapatite chromatography and digestion by single-strand-specific endonuclease S/sub 1/. Ultraviolet light-induced photolesions in viral DNA cause a permanent blockage of DNA synthesis in intact Escherichia coli cells. However, when host cells were irradiated and incubated to induce fully the error-prone repair system, a significant fraction of irradiated phiX174 DNA molecules can be fully replicated. Thus, inducible error-prone repair in E.coli is manifested by an increased capacity for DNA synthesis on damaged phiX174 DNA. Chloramphenicol (100 ..mu.. g/ml), which is an inhibitor of the inducible error-prone DNA repair, is also an inhibitor of this particular inducible DNA synthesis.

  13. 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.

  14. 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.

  15. 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...

  16. Influence of some radioprotective and radiosensitizing compounds on the replicative and repair induced DNA synthesis of rats spleen cells in vitro

    International Nuclear Information System (INIS)

    Goette, A.

    1982-01-01

    The effect of cysteine, dithiothreitol, N-ethylmaleimide, cytosinearabinoside, ethidiumbromide, bleomycine and diethyldithiocarbamate on the replicative and repair induced DNA synthesis in vitro was tested by using rats spleen cells. Besides the incorporation of a labeled DNA precursor (TdR- 3 H) the sedimentation of DNA in sucrose gradients was inquired. With respect to the DNA synthesis an uniform mechanism of action for the radioprotective substances can't be seen. Thymocytes and spleen cells seem to possess different systems of repair; this may be an explanation for their different sensibility against ionizing radiation. (orig./MG) [de

  17. 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.

  18. Label-free Proteomic Analysis of Exosomes Derived from Inducible Hepatitis B Virus-Replicating HepAD38 Cell Line.

    Science.gov (United States)

    Jia, Xiaofang; Chen, Jieliang; Megger, Dominik A; Zhang, Xiaonan; Kozlowski, Maya; Zhang, Lijun; Fang, Zhong; Li, Jin; Chu, Qiaofang; Wu, Min; Li, Yaming; Sitek, Barbara; Yuan, Zhenghong

    2017-04-01

    Hepatitis B virus (HBV) infection is a major health problem worldwide. Recent evidence suggests that some viruses can manipulate the infection process by packing specific viral and cellular components into exosomes, small nanometer-sized (30-150 nm) vesicles secreted from various cells. However, the impact of HBV replication on the content of exosomes produced by hepatocytes has not been fully delineated. In this work, an HBV-inducible cell line HepAD38 was used to directly compare changes in the protein content of exosomes secreted from HepAD38 cells with or without HBV replication. Exosomes were isolated from supernantants of HepAD38 cells cultured with or without doxycycline (dox) and their purity was confirmed by transmission electron microscopy (TEM) and Western immunoblotting assays. Ion-intensity based label-free LC-MS/MS quantitation technologies were applied to analyze protein content of exosomes from HBV replicating cells [referred as HepAD38 (dox - )-exo] and from HBV nonreplicating cells [referred as HepAD38 (dox + )-exo]. A total of 1412 exosomal protein groups were identified, among which the abundance of 35 proteins was significantly changed following HBV replication. Strikingly, 5 subunit proteins from the 26S proteasome complex, including PSMC1, PSMC2, PSMD1, PSMD7 and PSMD14 were consistently enhanced in HepAD38 (dox - )-exo. Bioinformatic analysis of differential exosomal proteins confirmed the significant enrichment of components involved in the proteasomal catabolic process. Proteasome activity assays further suggested that HepAD38 (dox - )-exo had enhanced proteolytic activity compared with HepAD38 (dox + )-exo. Furthermore, human peripheral monocytes incubated with HepAD38 (dox - )-exo induced a significantly lower level of IL-6 secretion compared with IL-6 levels from HepAD38 (dox + )-exo. Irreversible inhibition of proteasomal activity within exosomes restored higher production of IL-6 by monocytes, suggesting that transmission of

  19. 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.

  20. 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.

  1. 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...

  2. 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

  3. Inspirations on Virus Replication and Cell-to-Cell Movement from Studies Examining the Cytopathology Induced by Lettuce infectious yellows virus in Plant Cells

    Directory of Open Access Journals (Sweden)

    Wenjie Qiao

    2017-09-01

    Full Text Available Lettuce infectious yellows virus (LIYV is the type member of the genus Crinivirus in the family Closteroviridae. Like many other positive-strand RNA viruses, LIYV infections induce a number of cytopathic changes in plant cells, of which the two most characteristic are: Beet yellows virus-type inclusion bodies composed of vesicles derived from cytoplasmic membranes; and conical plasmalemma deposits (PLDs located at the plasmalemma over plasmodesmata pit fields. The former are not only found in various closterovirus infections, but similar structures are known as ‘viral factories’ or viroplasms in cells infected with diverse types of animal and plant viruses. These are generally sites of virus replication, virion assembly and in some cases are involved in cell-to-cell transport. By contrast, PLDs induced by the LIYV-encoded P26 non-virion protein are not involved in replication but are speculated to have roles in virus intercellular movement. These deposits often harbor LIYV virions arranged to be perpendicular to the plasma membrane over plasmodesmata, and our recent studies show that P26 is required for LIYV systemic plant infection. The functional mechanism of how LIYV P26 facilitates intercellular movement remains unclear, however, research on other plant viruses provides some insights on the possible ways of viral intercellular movement through targeting and modifying plasmodesmata via interactions between plant cellular components and viral-encoded factors. In summary, beginning with LIYV, we review the studies that have uncovered the biological determinants giving rise to these cytopathological effects and their importance in viral replication, virion assembly and intercellular movement during the plant infection by closteroviruses, and compare these findings with those for other positive-strand RNA viruses.

  4. HBV subgenotypes F1b and F4 replication induces an incomplete autophagic process in hepatocytes: Role of BCP and preCore mutations.

    Science.gov (United States)

    Elizalde, María Mercedes; Pérez, Paula Soledad; Sevic, Ina; Grasso, Daniel; Ropolo, Alejandro; Barbini, Luciana; Campos, Rodolfo Héctor; Vaccaro, María Inés; Flichman, Diego Martín

    2018-01-01

    Hepatitis B virus (HBV) genotypes and mutants have been associated with differences in clinical and virological characteristics. Autophagy is a cellular process that degrades long-lived proteins and damaged organelles. Viruses have evolved mechanisms to alter this process to survive in host cells. In this work, we studied the modulation of autophagy by the replication of HBV subgenotypes F1b and F4, and the naturally occurring mutants BCP and preCore. HBV subgenotypes F1b and F4 replication induced accumulation of autophagosomes in hepatoma cells. However, no autophagic protein degradation was observed, indicating a blockage of autophagic flux at later stages. This inhibition of autophagy flux might be due to an impairment of lysosomal acidification in hepatoma cells. Moreover, HBV-mediated autophagy modulation was independent of the viral subgenotypes and enhanced in viruses with BCP and preCore naturally occurring mutations. These results contribute to understand the mechanisms by which different HBV variants contribute to the pathogenesis of HBV infections. In addition, this study is the first to describe the role that two highly prevalent naturally occurring mutations exert on the modulation of HBV-induced autophagy.

  5. Human hepatocytes apoptosis induced by replication of hepatitis B virus subgenotypes F1b and F4: Role of basal core promoter and preCore mutations.

    Science.gov (United States)

    Elizalde, María Mercedes; Sevic, Ina; González López Ledesma, María Mora; Campos, Rodolfo Héctor; Barbini, Luciana; Flichman, Diego Martin

    2018-01-01

    In the context of pathogenesis of HBV infection, HBV genotypes and mutants have been shown to affect the natural course of chronic infection and treatment outcomes. In this work, we studied the induction of apoptosis by the replication of HBV subgenotypes F1b and F4, and the naturally occurring mutants BCP and preCore. Both subgenotypes F1b and F4 HBV genome transfections induced cell death by apoptosis in human hepatocytes. The BCPdm (A1762T/G1764A) and preCore (G1896A) mutants induced higher levels of apoptosis than the wt virus. This increase in apoptosis was not associated with the enhanced viral replication of the variants. HBV-mediated apoptosis was independent of viral subgenotypes, and associated with the modulation of members of the regulatory Bcl-2 family proteins expression in the mitochondrial apoptotic pathway. Finally, the apoptosis induction increase observed for the preCore mutants suggests that HBeAg might have an anti-apoptotic effect in human hepatocytes. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Glycoprotein from street rabies virus BD06 induces early and robust immune responses when expressed from a non-replicative adenovirus recombinant.

    Science.gov (United States)

    Wang, Shuchao; Sun, Chenglong; Zhang, Shoufeng; Zhang, Xiaozhuo; Liu, Ye; Wang, Ying; Zhang, Fei; Wu, Xianfu; Hu, Rongliang

    2015-09-01

    The rabies virus (RABV) glycoprotein (G) is responsible for inducing neutralizing antibodies against rabies virus. Development of recombinant vaccines using the G genes from attenuated strains rather than street viruses is a regular practice. In contrast to this scenario, we generated three human adenovirus type 5 recombinants using the G genes from the vaccine strains SRV9 and Flury-LEP, and the street RABV strain BD06 (nrAd5-SRV9-G, nrAd5-Flury-LEP-G, and nrAd5-BD06-G). These recombinants were non-replicative, but could grow up to ~10(8) TCID50/ml in helper HEK293AD cells. Expression of the G protein was verified by immunostaining, quantitative PCR and cytometry. Animal experiments revealed that immunization with nrAd5-BD06-G can induce a higher seroconversion rate, a higher neutralizing antibody level, and a longer survival time after rabies virus challenge in mice when compared with the other two recombinants. Moreover, the expression of granulocyte-macrophage colony-stimulating factor (GM-CSF) was significantly higher in mice immunized with nrAd5-BD06-G, which might also contribute to the increased protection. These results show that the use of street RABV G for non-replicative systems may be an alternative for developing effective recombinant rabies vaccines.

  7. 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.

  8. 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.

  9. 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

  10. Epigallocatechin-3-Gallate Suppresses Human Herpesvirus 8 Replication and Induces ROS Leading to Apoptosis and Autophagy in Primary Effusion Lymphoma Cells

    Directory of Open Access Journals (Sweden)

    Ching-Yi Tsai

    2017-12-01

    Full Text Available Epigallocatechin-3-gallate (EGCG, the major constituent of green tea, has been shown to induce cell death in cancer cells. Primary effusion lymphoma (PEL is an aggressive neoplasm caused by human herpesvirus 8 (HHV8. In this study, we examined the role of EGCG on PEL cells in cell death and HHV8 replication. We performed trypan blue exclusion assay to assess the cell viability of PEL cells, flow cytometry analysis to examine the cell cycle distribution and reactive oxygen species (ROS generation, caspase-3 activity to assay apoptosis, acridine orange staining to determine autophagy, and immunoblotting to detect the protein levels involved in apoptosis and autophagy as well as mitogen activated protein kinases (MAPKs activation upon EGCG treatment. The expression of the HHV8 lytic gene was determined by luciferase reporter assay and reverse transcription-PCR, and viral progeny production was determined by PCR. Results revealed that EGCG induced cell death and ROS generation in PEL cells in a dose-dependent manner. N-acetylcysteine (NAC inhibited the EGCG-induced ROS and rescued the cell from EGCG-induced cell death. Even though EGCG induced ROS generation in PEL cells, it reduced the production of progeny virus from PEL cells without causing HHV8 reactivation. These results suggest that EGCG may represent a novel strategy for the treatment of HHV8 infection and HHV8-associated lymphomas.

  11. 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...

  12. Vaccinia virus, herpes simplex virus, and carcinogens induce DNA amplification in a human cell line and support replication of a helpervirus dependent parvovirus

    International Nuclear Information System (INIS)

    Schlehofer, J.R.; Ehrbar, M.; zur Hausen, H.

    1986-01-01

    The SV40-transformed human kidney cell line, NB-E, amplifies integrated as well as episomal SV40 DNA upon treatment with chemical (DMBA) or physical (uv irradiation) carcinogens (initiators) as well as after infection with herpes simplex virus (HSV) type 1 or with vaccinia virus. In addition it is shown that vaccinia virus induces SV40 DNA amplification also in the SV40-transformed Chinese hamster embryo cell line, CO631. These findings demonstrate that human cells similar to Chinese hamster cells amplify integrated DNA sequences after treatment with carcinogens or infection with specific viruses. Furthermore, a poxvirus--vaccinia virus--similar to herpes group viruses induces DNA amplification. As reported for other systems, the vaccinia virus-induced DNA amplification in NB-E cells is inhibited by coinfection with adeno-associated virus (AAV) type 5. This is in line with previous studies on inhibition of carcinogen- or HSV-induced DNA amplification in CO631 cells. The experiments also demonstrate that vaccinia virus, in addition to herpes and adenoviruses acts as a helper virus for replication and structural antigen synthesis of AAV-5 in NB-E cells

  13. 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 ...

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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)

  19. A Respiratory Syncytial Virus Vaccine Vectored by a Stable Chimeric and Replication-Deficient Sendai Virus Protects Mice without Inducing Enhanced Disease.

    Science.gov (United States)

    Wiegand, Marian Alexander; Gori-Savellini, Gianni; Gandolfo, Claudia; Papa, Guido; Kaufmann, Christine; Felder, Eva; Ginori, Alessandro; Disanto, Maria Giulia; Spina, Donatella; Cusi, Maria Grazia

    2017-05-15

    Respiratory syncytial virus (RSV) is a major cause of severe respiratory infections in children and elderly people, and no marketed vaccine exists. In this study, we generated and analyzed a subunit vaccine against RSV based on a novel genome replication-deficient Sendai virus (SeV) vector. We inserted the RSV F protein, known to be a genetically stable antigen, into our vector in a specific way to optimize the vaccine features. By exchanging the ectodomain of the SeV F protein for its counterpart from RSV, we created a chimeric vectored vaccine that contains the RSV F protein as an essential structural component. In this way, the antigen is actively expressed on the surfaces of vaccine particles in its prefusion conformation, and as recently reported for other vectored vaccines, the occurrence of silencing mutations of the transgene in the vaccine genome can be prevented. In addition, its active gene expression contributes to further stimulation of the immune response. In order to understand the best route of immunization, we compared vaccine efficacies after intranasal (i.n.) or intramuscular (i.m.) immunization of BALB/c mice. Via both routes, substantial RSV-specific immune responses were induced, consisting of serum IgG and neutralizing antibodies, as well as cytotoxic T cells. Moreover, i.n. immunization was also able to stimulate specific mucosal IgA in the upper and lower respiratory tract. In virus challenge experiments, animals were protected against RSV infection after both i.n. and i.m. immunization without inducing vaccine-enhanced disease. Above all, the replication-deficient SeV appeared to be safe and well tolerated. IMPORTANCE Respiratory syncytial virus (RSV) is a major cause of respiratory diseases in young children and elderly people worldwide. There is a great demand for a licensed vaccine. Promising existing vaccine approaches based on live-attenuated vaccines or viral vectors have suffered from unforeseen drawbacks related to immunogenicity

  20. 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....

  1. 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)

  2. DNA replication in necessary for fixing induced mutations to streptomycin-resistance in UV-irradiated Escherichia coli cells

    Energy Technology Data Exchange (ETDEWEB)

    Dubinin, N P; Filippov, V D

    1986-01-01

    A suspension of E.coli cells has been subjected to UV radiation, then it has been incubated in the growth medium for 15 min. After that one of the portions was incubated with nalidixic acid (NA), and the other one without it in the presence of an antibiotic. Frequency of mutations depending on or irrespective of photoactivation, has been determined. Dependence of Str mutation fixing, induced by low UV radiation doses, on DNA synthesis is determined. Results indicate that both photoreactivation of mutations and its senstivity to mfd system are simultaneously lost.

  3. Specific interaction of the nonstructural protein NS1 of minute virus of mice (MVM) with [ACCA](2) motifs in the centre of the right-end MVM DNA palindrome induces hairpin-primed viral DNA replication.

    Science.gov (United States)

    Willwand, Kurt; Moroianu, Adela; Hörlein, Rita; Stremmel, Wolfgang; Rommelaere, Jean

    2002-07-01

    The linear single-stranded DNA genome of minute virus of mice (MVM) is replicated via a double-stranded replicative form (RF) intermediate DNA. Amplification of viral RF DNA requires the structural transition of the right-end palindrome from a linear duplex into a double-hairpin structure, which serves for the repriming of unidirectional DNA synthesis. This conformational transition was found previously to be induced by the MVM nonstructural protein NS1. Elimination of the cognate NS1-binding sites, [ACCA](2), from the central region of the right-end palindrome next to the axis of symmetry was shown to markedly reduce the efficiency of hairpin-primed DNA replication, as measured in a reconstituted in vitro replication system. Thus, [ACCA](2) sequence motifs are essential as NS1-binding elements in the context of the structural transition of the right-end MVM palindrome.

  4. Plate assay for chemical- and radiation-induced mutagenesis of CAN1 in yeast as a function of post-treatment DNA replication: The effect of rad6-1

    International Nuclear Information System (INIS)

    Lemontt, J.F.; Lair, S.V.

    1982-01-01

    An agar post-treatment method was used to monitor levels of ultraviolet light- and hydrazine-induced mutagenesis at CAN1 in Saccharomyces cerevisiae as a function of post-treatment cell division prior to selection for canavanine-resistant mutants with a top-agar overlay containing canavanine. The advantage of this method is that its permits reliable measurements of mutation induction during the early period before, during, and after the first round of post-treatment DNA replication. In strains that are wild-type for DNA repair, ultraviolet light mutagenesis appears to be a pre-replicative phenomenon, while mutation by hydrazine involves a replicative or post-replicative mechanism. Most chemical mutagenesis in yeast requires a functional RAD6 gene. Hydrazine mutability is also reduced by rad6-1, suggesting a possible misrepair mechanism. (orig.)

  5. 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)

  6. 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.

  7. A Model of Chronic Exposure to Unpredictable Mild Socio-Environmental Stressors Replicates Some Spaceflight-Induced Immunological Changes

    Directory of Open Access Journals (Sweden)

    Fanny Gaignier

    2018-05-01

    Full Text Available During spaceflight, astronauts face radiations, mechanical, and socio-environmental stressors. To determine the impact of chronic socio-environmental stressors on immunity, we exposed adult male mice to chronic unpredictable mild psychosocial and environmental stressors (CUMS model for 3 weeks. This duration was chosen to simulate a long flight at the human scale. Our data show that this combination of stressors induces an increase of serum IgA, a reduction of normalized splenic mass and tends to reduce the production of pro-inflammatory cytokines, as previously reported during or after space missions. However, CUMS did not modify major splenic lymphocyte sub-populations and the proliferative responses of splenocytes suggesting that these changes could be due to other factors such as gravity changes. Thus, CUMS, which is an easy to implement model, could contribute to deepen our understanding of some spaceflight-associated immune alterations and could be useful to test countermeasures.

  8. Sodium phenylbutyrate abrogates African swine fever virus replication by disrupting the virus-induced hypoacetylation status of histone H3K9/K14.

    Science.gov (United States)

    Frouco, Gonçalo; Freitas, Ferdinando B; Martins, Carlos; Ferreira, Fernando

    2017-10-15

    African swine fever virus (ASFV) causes a highly lethal disease in swine for which neither a vaccine nor treatment are available. Recently, a new class of drugs that inhibit histone deacetylases enzymes (HDACs) has received an increasing interest as antiviral agents. Considering studies by others showing that valproic acid, an HDAC inhibitor (HDACi), blocks the replication of enveloped viruses and that ASFV regulates the epigenetic status of the host cell by promoting heterochromatinization and recruitment of class I HDACs to viral cytoplasmic factories, the antiviral activity of four HDACi against ASFV was evaluated in this study. Results showed that the sodium phenylbutyrate fully abrogates the ASFV replication, whereas the valproic acid leads to a significant reduction of viral progeny at 48h post-infection (-73.9%, p=0.046), as the two pan-HDAC inhibitors tested (Trichostatin A: -82.2%, p=0.043; Vorinostat: 73.9%, p=0.043). Further evaluation showed that protective effects of NaPB are dose-dependent, interfering with the expression of late viral genes and reversing the ASFV-induced histone H3 lysine 9 and 14 (H3K9K14) hypoacetylation status, compatible to an open chromatin state and possibly enabling the expression of host genes non-beneficial to infection progression. Additionally, a synergic antiviral effect was detected when NaPB is combined with an ASFV-topoisomerase II poison (Enrofloxacin). Altogether, our results strongly suggest that cellular HDACs are involved in the establishment of ASFV infection and emphasize that further in vivo studies are needed to better understand the antiviral activity of HDAC inhibitors. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. 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.

  10. 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.

  11. 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....

  12. 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

  13. Analysis of the Unsteady Flow Field in a Centrifugal Compressor from Peak Efficiency to Near Stall with Full-Annulus Simulations

    Directory of Open Access Journals (Sweden)

    Yannick Bousquet

    2014-01-01

    Full Text Available This study concerns a 2.5 pressure ratio centrifugal compressor stage consisting of a splittered unshrouded impeller and a vaned diffuser. The aim of this paper is to investigate the modifications of the flow structure when the operating point moves from peak efficiency to near stall. The investigations are based on the results of unsteady three-dimensional simulations, in a calculation domain comprising all the blade. A detailed analysis is given in the impeller inducer and in the vaned diffuser entry region through time-averaged and unsteady flow field. In the impeller inducer, this study demonstrates that the mass flow reduction from peak efficiency to near stall leads to intensification of the secondary flow effects. The low momentum fluid accumulated near the shroud interacts with the main flow through a shear layer zone. At near stall condition, the interface between the two flow structures becomes unstable leading to vortices development. In the diffuser entry region, by reducing the mass flow, the high incidence angle from the impeller exit induces a separation on the diffuser vane suction side. At near stall operating point, vorticity from the separation is shed into vortex cores which are periodically formed and convected downstream along the suction side.

  14. 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

  15. 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.

  16. 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....

  17. 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.

  18. 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.

  19. 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.

  20. Trovafloxacin-induced replication stress sensitizes HepG2 cells to tumor necrosis factor-alpha-induced cytotoxicity mediated by extracellular signal-regulated kinase and ataxia telangiectasia and Rad3-related

    International Nuclear Information System (INIS)

    Beggs, Kevin M.; Maiuri, Ashley R.; Fullerton, Aaron M.; Poulsen, Kyle L.; Breier, Anna B.; Ganey, Patricia E.; Roth, Robert A.

    2015-01-01

    Use of the fluoroquinolone antibiotic trovafloxacin (TVX) was restricted due to idiosyncratic, drug-induced liver injury (IDILI). Previous studies demonstrated that tumor necrosis factor-alpha (TNF) and TVX interact to cause death of hepatocytes in vitro that was associated with prolonged activation of c-Jun N-terminal kinase (JNK), activation of caspases 9 and 3, and DNA damage. The purpose of this study was to explore further the mechanism by which TVX interacts with TNF to cause cytotoxicity. Treatment with TVX caused cell cycle arrest, enhanced expression of p21 and impaired proliferation, but cell death only occurred after cotreatment with TVX and TNF. Cell death involved activation of extracellular signal-related kinase (ERK), which in turn activated caspase 3 and ataxia telangiectasia and Rad3-related (ATR), both of which contributed to cytotoxicity. Cotreatment of HepG2 cells with TVX and TNF caused double-strand breaks in DNA, and ERK contributed to this effect. Inhibition of caspase activity abolished the DNA strand breaks. The data suggest a complex interaction of TVX and TNF in which TVX causes replication stress, and the downstream effects are exacerbated by TNF, leading to hepatocellular death. These results raise the possibility that IDILI from TVX results from MAPK and ATR activation in hepatocytes initiated by interaction of cytokine signaling with drug-induced replication stress

  1. Herpes Simplex Virus 1 Mutant with Point Mutations in UL39 Is Impaired for Acute Viral Replication in Mice, Establishment of Latency, and Explant-Induced Reactivation.

    Science.gov (United States)

    Mostafa, Heba H; Thompson, Thornton W; Konen, Adam J; Haenchen, Steve D; Hilliard, Joshua G; Macdonald, Stuart J; Morrison, Lynda A; Davido, David J

    2018-04-01

    In the process of generating herpes simplex virus 1 (HSV-1) mutations in the viral regulatory gene encoding infected cell protein 0 (ICP0), we isolated a viral mutant, termed KOS-NA, that was severely impaired for acute replication in the eyes and trigeminal ganglia (TG) of mice, defective in establishing a latent infection, and reactivated poorly from explanted TG. To identify the secondary mutation(s) responsible for the impaired phenotypes of this mutant, we sequenced the KOS-NA genome and noted that it contained two nonsynonymous mutations in UL39 , which encodes the large subunit of ribonucleotide reductase, ICP6. These mutations resulted in lysine-to-proline (residue 393) and arginine-to-histidine (residue 950) substitutions in ICP6. To determine whether alteration of these amino acids was responsible for the KOS-NA phenotypes in vivo , we recombined the wild-type UL39 gene into the KOS-NA genome and rescued its acute replication phenotypes in mice. To further establish the role of UL39 in KOS-NA's decreased pathogenicity, the UL39 mutations were recombined into HSV-1 (generating UL39 mut ), and this mutant virus showed reduced ocular and TG replication in mice comparable to that of KOS-NA. Interestingly, ICP6 protein levels were reduced in KOS-NA-infected cells relative to the wild-type protein. Moreover, we observed that KOS-NA does not counteract caspase 8-induced apoptosis, unlike wild-type strain KOS. Based on alignment studies with other HSV-1 ICP6 homologs, our data suggest that amino acid 950 of ICP6 likely plays an important role in ICP6 accumulation and inhibition of apoptosis, consequently impairing HSV-1 pathogenesis in a mouse model of HSV-1 infection. IMPORTANCE HSV-1 is a major human pathogen that infects ∼80% of the human population and can be life threatening to infected neonates or immunocompromised individuals. Effective therapies for treatment of recurrent HSV-1 infections are limited, which emphasizes a critical need to understand in

  2. Bayesian tests to quantify the result of a replication attempt

    NARCIS (Netherlands)

    Verhagen, J.; Wagenmakers, E.-J.

    2014-01-01

    Replication attempts are essential to the empirical sciences. Successful replication attempts increase researchers’ confidence in the presence of an effect, whereas failed replication attempts induce skepticism and doubt. However, it is often unclear to what extent a replication attempt results in

  3. 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...

  4. 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...

  5. 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)

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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)

  12. 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.

  13. 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.

  14. Telomere healing following DNA polymerase arrest-induced breakages is likely the main mechanism generating chromosome 4p terminal deletions.

    Science.gov (United States)

    Hannes, Femke; Van Houdt, Jeroen; Quarrell, Oliver W; Poot, Martin; Hochstenbach, Ron; Fryns, Jean-Pierre; Vermeesch, Joris R

    2010-12-01

    Constitutional developmental disorders are frequently caused by terminal chromosomal deletions. The mechanisms and/or architectural features that might underlie those chromosome breakages remain largely unexplored. Because telomeres are the vital DNA protein complexes stabilizing linear chromosomes against chromosome degradation, fusion, and incomplete replication, those terminal-deleted chromosomes acquired new telomeres either by telomere healing or by telomere capture. To unravel the mechanisms leading to chromosomal breakage and healing, we sequenced nine chromosome 4p terminal deletion boundaries. A computational analysis of the breakpoint flanking region, including 12 previously published pure terminal breakage sites, was performed in order to identify architectural features that might be involved in this process. All terminal 4p truncations were likely stabilized by telomerase-mediated telomere healing. In the majority of breakpoints multiple genetic elements have a potential to induce secondary structures and an enrichment in replication stalling site motifs were identified. These findings suggest DNA replication stalling-induced chromosome breakage during early development is the first mechanistic step leading toward terminal deletion syndromes. © 2010 Wiley-Liss, Inc.

  15. Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain.

    Science.gov (United States)

    Koch, Miriam; Willi, Jessica; Pradère, Ugo; Hall, Jonathan; Polacek, Norbert

    2017-06-20

    The nascent peptide exit tunnel has recently been identified as a functional region of ribosomes contributing to translation regulation and co-translational protein folding. Inducible expression of the erm resistance genes depends on ribosome stalling at specific codons of an upstream open reading frame in the presence of an exit tunnel-bound macrolide antibiotic. The molecular basis for this translation arrest is still not fully understood. Here, we used a nucleotide analog interference approach to unravel important functional groups on 23S rRNA residues in the ribosomal exit tunnel for ribosome stalling on the ErmC leader peptide. By replacing single nucleobase functional groups or even single atoms we were able to demonstrate the importance of A2062, A2503 and U2586 for drug-dependent ribosome stalling. Our data show that the universally conserved A2062 and A2503 are capable of forming a non-Watson-Crick base pair that is critical for sensing and transmitting the stalling signal from the exit tunnel back to the peptidyl transferase center of the ribosome. The nucleobases of A2062, A2503 as well as U2586 do not contribute significantly to the overall mechanism of protein biosynthesis, yet their elaborate role for co-translational monitoring of nascent peptide chains inside the exit tunnel can explain their evolutionary conservation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. 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.

  17. 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)

  18. 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.

  19. 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.

  20. Cell-Free and Cell-Based Approaches to Explore the Roles of Host Membranes and Lipids in the Formation of Viral Replication Compartment Induced by Tombusviruses.

    Science.gov (United States)

    Nagy, Peter D; Pogany, Judit; Xu, Kai

    2016-03-03

    Plant positive strand RNA viruses are intracellular infectious agents that take advantage of cellular lipids and membranes to support replication and protect viral RNA from degradation by host antiviral responses. In this review, we discuss how Tomato bushy stunt virus (TBSV) co-opts lipid transfer proteins and modulates lipid metabolism and transport to facilitate the assembly of the membrane-bound viral replicase complexes within intricate replication compartments. Identification and characterization of the proviral roles of specific lipids and proteins involved in lipid metabolism based on results from yeast (Saccharomyces cerevisiae) model host and cell-free approaches are discussed. The review also highlights the advantage of using liposomes with chemically defined composition to identify specific lipids required for TBSV replication. Remarkably, all the known steps in TBSV replication are dependent on cellular lipids and co-opted membranes.

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

    Directory of Open Access Journals (Sweden)

    Petra Mooij

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

  2. 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

  3. Glycoprotein 5 of porcine reproductive and respiratory syndrome virus strain SD16 inhibits viral replication and causes G2/M cell cycle arrest, but does not induce cellular apoptosis in Marc-145 cells

    International Nuclear Information System (INIS)

    Mu, Yang; Li, Liangliang; Zhang, Beibei; Huang, Baicheng; Gao, Jiming

    2015-01-01

    Cell apoptosis is common after infection with porcine reproductive and respiratory syndrome virus (PRRSV). PRRSV GP5 has been reported to induce cell apoptosis. To further understand the role of GP5 in PRRSV induced cell apoptosis, we established Marc-145 cell lines stably expressing full-length GP5, GP5 Δ84-96 (aa 84-96 deletion), and GP5 Δ97-119 (aa 97-119 deletion). Cell proliferation, cell cycle progression, cell apoptosis and virus replication in these cell lines were evaluated. Neither truncated nor full-length GP5 induced cell apoptosis in Marc-145 cells. However, GP5 Δ97-119 , but not full-length or GP5 Δ84-96 , induced a cell cycle arrest at the G2/M phase resulting in a reduction in the growth of Marc-145 cells. Additionally, GP5 Δ84-96 inhibited the replication of PRRSV in Marc-145 cells through induction of IFN-β. These findings suggest that PRRSV GP5 is not responsible for inducing cell apoptosis in Marc-145 cells under these experimental conditions; however it has other important roles in virus/host cell biology. - Highlights: • Marc-145 cell lines stable expression PRRSV GP5 or truncated GP5 were constructed. • GP5 Δ97-119 expression in Marc-145 cell induced cell cycle arrest at G2/M phase. • Expression of GP5 and truncated GP5 could not induce Marc-145 cells apoptosis. • PRRSV replication in Marc-145-GP5 Δ84-96 was significantly inhibited

  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. 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…

  6. 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.

  7. 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.

  8. The Role of the Transcriptional Response to DNA Replication Stress.

    Science.gov (United States)

    Herlihy, Anna E; de Bruin, Robertus A M

    2017-03-02

    During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage.

  9. The Role of the Transcriptional Response to DNA Replication Stress

    Science.gov (United States)

    Herlihy, Anna E.; de Bruin, Robertus A.M.

    2017-01-01

    During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage. PMID:28257104

  10. 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.

  11. 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.

  12. 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

  13. 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)

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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...

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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....

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. The cyclin-dependent kinase inhibitor 5, 6-dichloro-1-beta-D-ribofuranosylbenzimidazole induces nongenotoxic, DNA replication-independent apoptosis of normal and leukemic cells, regardless of their p53 status

    International Nuclear Information System (INIS)

    Turinetto, Valentina; Porcedda, Paola; Orlando, Luca; De Marchi, Mario; Amoroso, Antonio; Giachino, Claudia

    2009-01-01

    Current chemotherapy of human cancers focuses on the DNA damage pathway to induce a p53-mediated cellular response leading to either G1 arrest or apoptosis. However, genotoxic treatments may induce mutations and translocations that result in secondary malignancies or recurrent disease. In addition, about 50% of human cancers are associated with mutations in the p53 gene. Nongenotoxic activation of apoptosis by targeting specific molecular pathways thus provides an attractive therapeutic approach. Normal and leukemic cells were evaluated for their sensitivity to 5, 6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) through cell viability and caspase activation tests. The apoptotic pathway induced by DRB was analysed by immunfluorescence and immunoblot analysis. H2AX phosphorylation and cell cycle analysis were performed to study the dependance of apoptosis on DNA damage and DNA replication, respectively. To investigate the role of p53 in DRB-induced apoptosis, specific p53 inhibitors were used. Statistical analysis on cell survival was performed with the test of independence. Here we report that DRB, an inhibitor of the transcriptional cyclin-dependent kinases (CDKs) 7 and 9, triggers DNA replication-independent apoptosis in normal and leukemic human cells regardless of their p53 status and without inducing DNA damage. Our data indicate that (i) in p53-competent cells, apoptosis induced by DRB relies on a cytosolic accumulation of p53 and subsequent Bax activation, (ii) in the absence of p53, it may rely on p73, and (iii) it is independent of ATM and NBS1 proteins. Notably, even apoptosis-resistant leukemic cells such as Raji were sensitive to DRB. Our results indicate that DRB represents a potentially useful cancer chemotherapeutic strategy that employs both the p53-dependent and -independent apoptotic pathways without inducing genotoxic stress, thereby decreasing the risk of secondary malignancies

  9. Human Parvovirus B19 Utilizes Cellular DNA Replication Machinery for Viral DNA Replication.

    Science.gov (United States)

    Zou, Wei; Wang, Zekun; Xiong, Min; Chen, Aaron Yun; Xu, Peng; Ganaie, Safder S; Badawi, Yomna; Kleiboeker, Steve; Nishimune, Hiroshi; Ye, Shui Qing; Qiu, Jianming

    2018-03-01

    Human parvovirus B19 (B19V) infection of human erythroid progenitor cells (EPCs) induces a DNA damage response and cell cycle arrest at late S phase, which facilitates viral DNA replication. However, it is not clear exactly which cellular factors are employed by this single-stranded DNA virus. Here, we used microarrays to systematically analyze the dynamic transcriptome of EPCs infected with B19V. We found that DNA metabolism, DNA replication, DNA repair, DNA damage response, cell cycle, and cell cycle arrest pathways were significantly regulated after B19V infection. Confocal microscopy analyses revealed that most cellular DNA replication proteins were recruited to the centers of viral DNA replication, but not the DNA repair DNA polymerases. Our results suggest that DNA replication polymerase δ and polymerase α are responsible for B19V DNA replication by knocking down its expression in EPCs. We further showed that although RPA32 is essential for B19V DNA replication and the phosphorylated forms of RPA32 colocalized with the replicating viral genomes, RPA32 phosphorylation was not necessary for B19V DNA replication. Thus, this report provides evidence that B19V uses the cellular DNA replication machinery for viral DNA replication. IMPORTANCE Human parvovirus B19 (B19V) infection can cause transient aplastic crisis, persistent viremia, and pure red cell aplasia. In fetuses, B19V infection can result in nonimmune hydrops fetalis and fetal death. These clinical manifestations of B19V infection are a direct outcome of the death of human erythroid progenitors that host B19V replication. B19V infection induces a DNA damage response that is important for cell cycle arrest at late S phase. Here, we analyzed dynamic changes in cellular gene expression and found that DNA metabolic processes are tightly regulated during B19V infection. Although genes involved in cellular DNA replication were downregulated overall, the cellular DNA replication machinery was tightly

  10. 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

  11. 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.

  12. 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.

  13. 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…

  14. Replication-deficient mutant Herpes Simplex Virus-1 targets professional antigen presenting cells and induces efficient CD4+ T helper responses.

    Science.gov (United States)

    Fiorentini, Simona; Marconi, Peggy; Avolio, Manuela; Marini, Elena; Garrafa, Emirena; Caracciolo, Sonia; Rossi, Daniele; Bozac, Alexandra; Becker, Pablo D; Gentili, Francesca; Facchetti, Fabio; Guzman, Carlos A; Manservigi, Roberto; Caruso, Arnaldo

    2007-07-01

    Both neutralizing antibodies and cytotoxic T-cells are necessary to control a viral infection. However, vigorous T helper responses are essential for their elicitation and maintenance. Here we show that a recombinant replication-deficient Herpes Simplex Virus (HSV)-1 vector encoding the Human Immunodeficiency Virus (HIV)-1 matrix protein p17 (T0-p17) was capable of infecting professional antigen presenting cells (APCs) in vitro and in vivo. The injection of T0-p17 in the mouse dermis generated a strong p17-specific CD4+ T helper response preceding both p17-specific humoral and effector T cell responses. Moreover, we show that T0-p17 infection did not interfere with the endogenous processing of the transgene encoded antigen, since infected APCs were able to evoke a strong recall response in vitro. Our results demonstrate that replication-deficient HSV vectors can be appealing candidates for the development of vaccines able to trigger T helper responses.

  15. Replication-deficient mutant Herpes Simplex Virus-1 targets professional antigen presenting cells and induces efficient CD4+ T helper responses.

    OpenAIRE

    Fiorentini, Simona; Marconi, Peggy; Avolio, Manuela; Marini, Elena; Garrafa, Emirena; Caracciolo, Sonia; Rossi, Daniele; Bozac, Alexandra; Becker, Pablo D; Gentili, Francesca; Facchetti, Fabio; Guzman, Carlos A; Manservigi, Roberto; Caruso, Arnaldo

    2007-01-01

    Both neutralizing antibodies and cytotoxic T-cells are necessary to control a viral infection. However, vigorous T helper responses are essential for their elicitation and maintenance. Here we show that a recombinant replication-deficient Herpes Simplex Virus (HSV)-1 vector encoding the Human Immunodeficiency Virus (HIV)-1 matrix protein p17 (T0-p17) was capable of infecting professional antigen presenting cells (APCs) in vitro and in vivo. The injection of T0-p17 in the mouse dermis generate...

  16. Involvement of Autophagy in Coronavirus Replication

    Directory of Open Access Journals (Sweden)

    Paul Britton

    2012-11-01

    Full Text Available Coronaviruses are single stranded, positive sense RNA viruses, which induce the rearrangement of cellular membranes upon infection of a host cell. This provides the virus with a platform for the assembly of viral replication complexes, improving efficiency of RNA synthesis. The membranes observed in coronavirus infected cells include double membrane vesicles. By nature of their double membrane, these vesicles resemble cellular autophagosomes, generated during the cellular autophagy pathway. In addition, coronavirus infection has been demonstrated to induce autophagy. Here we review current knowledge of coronavirus induced membrane rearrangements and the involvement of autophagy or autophagy protein microtubule associated protein 1B light chain 3 (LC3 in coronavirus replication.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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...

  2. 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.

  3. 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.

  4. 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.

  5. 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)

  6. 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.

  7. Fine-tuning synthesis of Yersinia pestis LcrV from runaway-like replication balanced-lethal plasmid in a Salmonella enterica serovar typhimurium vaccine induces protection against a lethal Y. pestis challenge in mice.

    Science.gov (United States)

    Torres-Escobar, Ascención; Juárez-Rodríguez, María Dolores; Gunn, Bronwyn M; Branger, Christine G; Tinge, Steven A; Curtiss, Roy

    2010-06-01

    A balanced-lethal plasmid expression system that switches from low-copy-number to runaway-like high-copy-number replication (pYA4534) was constructed for the regulated delayed in vivo synthesis of heterologous antigens by vaccine strains. This is an antibiotic resistance-free maintenance system containing the asdA gene (essential for peptidoglycan synthesis) as a selectable marker to complement the lethal chromosomal DeltaasdA allele in live recombinant attenuated Salmonella vaccines (RASVs) such as Salmonella enterica serovar Typhimurium strain chi9447. pYA4534 harbors two origins of replication, pSC101 and pUC (low and high copy numbers, respectively). The pUC replication origin is controlled by a genetic switch formed by the operator/promoter of the P22 cro gene (O/P(cro)) (P(R)), which is negatively regulated by an arabinose-inducible P22 c2 gene located on both the plasmid and the chromosome (araC P(BAD) c2). The absence of arabinose, which is unavailable in vivo, triggers replication to a high-copy-number plasmid state. To validate these vector attributes, the Yersinia pestis virulence antigen LcrV was used to develop a vaccine against plague. An lcrV sequence encoding amino acids 131 to 326 (LcrV196) was optimized for expression in Salmonella, flanked with nucleotide sequences encoding the signal peptide (SS) and the carboxy-terminal domain (CT) of beta-lactamase, and cloned into pYA4534 under the control of the P(trc) promoter to generate plasmid pYA4535. Our results indicate that the live Salmonella vaccine strain chi9447 harboring pYA4535 efficiently stimulated a mixed Th1/Th2 immune response that protected mice against lethal challenge with Y. pestis strain CO92 introduced through either the intranasal or subcutaneous route.

  8. Fine-Tuning Synthesis of Yersinia pestis LcrV from Runaway-Like Replication Balanced-Lethal Plasmid in a Salmonella enterica Serovar Typhimurium Vaccine Induces Protection against a Lethal Y. pestis Challenge in Mice▿

    Science.gov (United States)

    Torres-Escobar, Ascención; Juárez-Rodríguez, María Dolores; Gunn, Bronwyn M.; Branger, Christine G.; Tinge, Steven A.; Curtiss, Roy

    2010-01-01

    A balanced-lethal plasmid expression system that switches from low-copy-number to runaway-like high-copy-number replication (pYA4534) was constructed for the regulated delayed in vivo synthesis of heterologous antigens by vaccine strains. This is an antibiotic resistance-free maintenance system containing the asdA gene (essential for peptidoglycan synthesis) as a selectable marker to complement the lethal chromosomal ΔasdA allele in live recombinant attenuated Salmonella vaccines (RASVs) such as Salmonella enterica serovar Typhimurium strain χ9447. pYA4534 harbors two origins of replication, pSC101 and pUC (low and high copy numbers, respectively). The pUC replication origin is controlled by a genetic switch formed by the operator/promoter of the P22 cro gene (O/Pcro) (PR), which is negatively regulated by an arabinose-inducible P22 c2 gene located on both the plasmid and the chromosome (araC PBAD c2). The absence of arabinose, which is unavailable in vivo, triggers replication to a high-copy-number plasmid state. To validate these vector attributes, the Yersinia pestis virulence antigen LcrV was used to develop a vaccine against plague. An lcrV sequence encoding amino acids 131 to 326 (LcrV196) was optimized for expression in Salmonella, flanked with nucleotide sequences encoding the signal peptide (SS) and the carboxy-terminal domain (CT) of β-lactamase, and cloned into pYA4534 under the control of the Ptrc promoter to generate plasmid pYA4535. Our results indicate that the live Salmonella vaccine strain χ9447 harboring pYA4535 efficiently stimulated a mixed Th1/Th2 immune response that protected mice against lethal challenge with Y. pestis strain CO92 introduced through either the intranasal or subcutaneous route. PMID:20308296

  9. 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.

  10. 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...

  11. 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.

  12. Early viral replication and induced or constitutive immunity in rainbow trout families with differential resistance to Infectious hematopoietic necrosis virus (IHNV)

    Science.gov (United States)

    Purcell, M.K.; LaPatra, S.E.; Woodson, J.C.; Kurath, G.; Winton, J.R.

    2010-01-01

    The main objective of this study was to assess correlates of innate resistance in rainbow trout full-sibling families that differ in susceptibility to Infectious hematopoietic necrosis virus (IHNV). As part of a commercial breeding program, full-sibling families were challenged with IHNV by waterborne exposure at the 1 g size to determine susceptibility to IHNV. Progeny from select families (N = 7 families) that varied in susceptibility (ranging from 32 to 90% cumulative percent mortality (CPM)) were challenged again at the 10 g size by intra-peritoneal injection and overall mortality, early viral replication and immune responses were evaluated. Mortality challenges included 20–40 fish per family while viral replication and immune response studies included 6 fish per family at each time point (24, 48 and 72 h post-infection (hpi)). CPM at the 1 g size was significantly correlated with CPM at the 10 g size, indicating that inherent resistance was a stable trait irrespective of size. In the larger fish, viral load was measured by quantitative reverse-transcriptase PCR in the anterior kidney and was a significant predictor of family disease outcome at 48 hpi. Type I interferon (IFN) transcript levels were significantly correlated with an individual's viral load at 48 and 72 hpi, while type II IFN gene expression was significantly correlated with an individual's viral load at 24 and 48 hpi. Mean family type I but not type II IFN gene expression was weakly associated with susceptibility at 72 hpi. There was no association between mean family susceptibility and the constitutive expression of a range of innate immune genes (e.g. type I and II IFN pathway genes, cytokine and viral recognition receptor genes). The majority of survivors from the challenge had detectable serum neutralizing antibody titers but no trend was observed among families. This result suggests that even the most resistant families experienced sufficient levels of viral replication to trigger specific

  13. 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

  14. 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

  15. NS Segment of a 1918 Influenza A Virus-Descendent Enhances Replication of H1N1pdm09 and Virus-Induced Cellular Immune Response in Mammalian and Avian Systems

    Science.gov (United States)

    Petersen, Henning; Mostafa, Ahmed; Tantawy, Mohamed A.; Iqbal, Azeem A.; Hoffmann, Donata; Tallam, Aravind; Selvakumar, Balachandar; Pessler, Frank; Beer, Martin; Rautenschlein, Silke; Pleschka, Stephan

    2018-01-01

    The 2009 pandemic influenza A virus (IAV) H1N1 strain (H1N1pdm09) has widely spread and is circulating in humans and swine together with other human and avian IAVs. This fact raises the concern that reassortment between H1N1pdm09 and co-circulating viruses might lead to an increase of H1N1pdm09 pathogenicity in different susceptible host species. Herein, we explored the potential of different NS segments to enhance the replication dynamics, pathogenicity and host range of H1N1pdm09 strain A/Giessen/06/09 (Gi-wt). The NS segments were derived from (i) human H1N1- and H3N2 IAVs, (ii) highly pathogenic- (H5- or H7-subtypes) or (iii) low pathogenic avian influenza viruses (H7- or H9-subtypes). A significant increase of growth kinetics in A549 (human lung epithelia) and NPTr (porcine tracheal epithelia) cells was only noticed in vitro for the reassortant Gi-NS-PR8 carrying the NS segment of the 1918-descendent A/Puerto Rico/8/34 (PR8-wt, H1N1), whereas all other reassortants showed either reduced or comparable replication efficiencies. Analysis using ex vivo tracheal organ cultures of turkeys (TOC-Tu), a species susceptible to IAV H1N1 infection, demonstrated increased replication of Gi-NS-PR8 compared to Gi-wt. Also, Gi-NS-PR8 induced a markedly higher expression of immunoregulatory and pro-inflammatory cytokines, chemokines and interferon-stimulated genes in A549 cells, THP-1-derived macrophages (dHTP) and TOC-Tu. In vivo, Gi-NS-PR8 induced an earlier onset of mortality than Gi-wt in mice, whereas, 6-week-old chickens were found to be resistant to both viruses. These data suggest that the specific characteristics of the PR8 NS segments can impact on replication, virus induced cellular immune responses and pathogenicity of the H1N1pdm09 in different avian and mammalian host species. PMID:29623073

  16. 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.

  17. 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)

  18. 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 ...

  19. A recombinant anchorless respiratory syncytial virus (RSV) fusion (F) protein/monophosphoryl lipid A (MPL) vaccine protects against RSV-induced replication and lung pathology.

    Science.gov (United States)

    Blanco, Jorge C G; Boukhvalova, Marina S; Pletneva, Lioubov M; Shirey, Kari Ann; Vogel, Stefanie N

    2014-03-14

    We previously demonstrated that the severe cytokine storm and pathology associated with RSV infection following intramuscular vaccination of cotton rats with FI-RSV Lot 100 could be completely abolished by formulating the vaccine with the mild TLR4 agonist and adjuvant, monophosphoryl lipid A (MPL). Despite this significant improvement, the vaccine failed to blunt viral replication in the lungs. Since MPL is a weak TLR4 agonist, we hypothesized that its adjuvant activity was mediated by modulating the innate immune response of respiratory tract resident macrophages. Therefore, we developed a new vaccine preparation with purified, baculovirus expressed, partially purified, anchorless RSV F protein formulated with synthetic MPL that was administered to cotton rats intranasally, followed by an intradermal boost. This novel formulation and heterologous "prime/boost" route of administration resulted in decreased viral titers compared to that seen in animals vaccinated with F protein alone. Furthermore, animals vaccinated by this route showed no evidence of enhanced lung pathology upon RSV infection. This indicates that MPL acts as an immune modulator that protects the host from vaccine-enhanced pathology, and reduces RSV replication in the lower respiratory tract when administered by a heterologous prime/boost immunization regimen. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Hoechst 33258 dye generates DNA-protein cross-links during ultraviolet light-induced photolysis of bromodeoxyuridine in replicated and repaired DNA

    Energy Technology Data Exchange (ETDEWEB)

    Guo Xicang; Morgan, W.F.; Cleaver, J.E.

    1986-08-01

    Substitution of bromodeoxyuridine for thymidine in the DNA of mammalian cells sensitizes them to a range of wavelengths of ultraviolet light. Cells are also sensitized to photochemical reactions involving dyes such as Hoechst 33258, which is used to produce differential staining of chromatids according to their bromodeoxyuridine content. Irradiation with 313 nm light of human and hamster cells containing bromodeoxyuridine in their DNA produced single-strand breaks but no DNA-protein cross-links. Irradiation with 360 nm light in the presence of Hoechst 33258 produced extensive DNA-protein cross-linkage as well as single-strand breaks. These cross-links were observed in DNA containing bromodeoxyuridine incorporated by either semiconservative or repair replication. When the protein was removed with proteinase K, bromodeoxyuridine in repair patches after irradiation by doses of ultraviolet (254 nm) light as low as 0.26 J/m/sup 2/ could readily be detected. Hoechst 33258-mediated photolysis, therefore, provides a sensitive new technique for measuring repair replication after ultraviolet light irradiation.

  1. Interleukin-7 induces HIV replication in primary naive T cells through a nuclear factor of activated T cell (NFAT)-dependent pathway

    International Nuclear Information System (INIS)

    Managlia, Elizabeth Z.; Landay, Alan; Al-Harthi, Lena

    2006-01-01

    Interleukin (IL)-7 plays several roles critical to T cell maturation, survival, and homeostasis. Because of these functions, IL-7 is under investigation as an immune-modulator for therapeutic use in lymphopenic clinical conditions, including HIV. We reported that naive T cells, typically not permissive to HIV, can be productively infected when pre-treated with IL-7. We evaluated the mechanism by which IL-7-mediates this effect. IL-7 potently up-regulated the transcriptional factor NFAT, but had no effect on NFκB. Blocking NFAT activity using a number of reagents, such as Cyclosporin A, FK-506, or the NFAT-specific inhibitor known as VIVIT peptide, all markedly reduced IL-7-mediated induction of HIV replication in naive T cells. Additional neutralization of cytokines present in IL-7-treated cultures and/or those that have NFAT-binding sequences within their promotors indicated that IL-10, IL-4, and most significantly IFNγ, all contribute to IL-7-induction of HIV productive replication in naive T cells. These data clarify the mechanism by which IL-7 can overcome the block to HIV productive infection in naive T cells, despite their quiescent cell status. These findings are relevant to the treatment of HIV disease and understanding HIV pathogenesis in the naive CD4+ T cell compartment, especially in light of the vigorous pursuit of IL-7 as an in vivo immune modulator

  2. 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

  3. Replication assessment of surface texture at sub-micrometre scale

    DEFF Research Database (Denmark)

    Quagliotti, Danilo; Tosello, Guido; Hansen, Hans Nørgaard

    2017-01-01

    [2]. A replication process requires reproducing a master geometry by conveying it to a substrate material. It is typically induced by means of different energy sources (usually heat and force) and a direct physical contact between the master and the substrate. Furthermore, concepts of advanced......, because of the replication nature of molding processes, the required specifications for the manufacture of micro molded components must be ensured by means of a metrological approach to surface replication and dimensional control of both master geometry and replicated substrate [3]-[4]. Therefore...... replication was assessed by the replication fidelity, i.e., comparing the produced parts with the tool used to replicate the geometry. Furthermore, the uncertainty of the replication fidelity was achieved by propagating the uncertainties evaluated for both masters and replicas. Finally, despite the specimens...

  4. 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.

  5. 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.)

  6. Vaccination with Replication Deficient Adenovectors Encoding YF-17D Antigens Induces Long-Lasting Protection from Severe Yellow Fever Virus Infection in Mice

    DEFF Research Database (Denmark)

    Bassi, Maria R; Larsen, Mads Andreas Bay; Kongsgaard, Michael

    2016-01-01

    The live attenuated yellow fever vaccine (YF-17D) has been successfully used for more than 70 years. It is generally considered a safe vaccine, however, recent reports of serious adverse events following vaccination have raised concerns and led to suggestions that even safer YF vaccines should...... be developed. Replication deficient adenoviruses (Ad) have been widely evaluated as recombinant vectors, particularly in the context of prophylactic vaccination against viral infections in which induction of CD8+ T-cell mediated immunity is crucial, but potent antibody responses may also be elicited using......, which afforded a high degree of protection from subsequent intracranial challenge of vaccinated mice. However, full protection was only observed using a vector encoding the structural proteins from YF-17D. This vector elicited virus-specific CD8+ T cells as well as neutralizing antibodies, and both...

  7. Vaccination with Replication Deficient Adenovectors Encoding YF-17D Antigens Induces Long-Lasting Protection from Severe Yellow Fever Virus Infection in Mice.

    Science.gov (United States)

    Bassi, Maria R; Larsen, Mads A B; Kongsgaard, Michael; Rasmussen, Michael; Buus, Søren; Stryhn, Anette; Thomsen, Allan R; Christensen, Jan P

    2016-02-01

    The live attenuated yellow fever vaccine (YF-17D) has been successfully used for more than 70 years. It is generally considered a safe vaccine, however, recent reports of serious adverse events following vaccination have raised concerns and led to suggestions that even safer YF vaccines should be developed. Replication deficient adenoviruses (Ad) have been widely evaluated as recombinant vectors, particularly in the context of prophylactic vaccination against viral infections in which induction of CD8+ T-cell mediated immunity is crucial, but potent antibody responses may also be elicited using these vectors. In this study, we present two adenobased vectors targeting non-structural and structural YF antigens and characterize their immunological properties. We report that a single immunization with an Ad-vector encoding the non-structural protein 3 from YF-17D could elicit a strong CD8+ T-cell response, which afforded a high degree of protection from subsequent intracranial challenge of vaccinated mice. However, full protection was only observed using a vector encoding the structural proteins from YF-17D. This vector elicited virus-specific CD8+ T cells as well as neutralizing antibodies, and both components were shown to be important for protection thus mimicking the situation recently uncovered in YF-17D vaccinated mice. Considering that Ad-vectors are very safe, easy to produce and highly immunogenic in humans, our data indicate that a replication deficient adenovector-based YF vaccine may represent a safe and efficient alternative to the classical live attenuated YF vaccine and should be further tested.

  8. Distinct cell clusters touching islet cells induce islet cell replication in association with over-expression of Regenerating Gene (REG protein in fulminant type 1 diabetes.

    Directory of Open Access Journals (Sweden)

    Kaoru Aida

    Full Text Available BACKGROUND: Pancreatic islet endocrine cell-supporting architectures, including islet encapsulating basement membranes (BMs, extracellular matrix (ECM, and possible cell clusters, are unclear. PROCEDURES: The architectures around islet cell clusters, including BMs, ECM, and pancreatic acinar-like cell clusters, were studied in the non-diabetic state and in the inflamed milieu of fulminant type 1 diabetes in humans. RESULT: Immunohistochemical and electron microscopy analyses demonstrated that human islet cell clusters and acinar-like cell clusters adhere directly to each other with desmosomal structures and coated-pit-like structures between the two cell clusters. The two cell-clusters are encapsulated by a continuous capsule composed of common BMs/ECM. The acinar-like cell clusters have vesicles containing regenerating (REG Iα protein. The vesicles containing REG Iα protein are directly secreted to islet cells. In the inflamed milieu of fulminant type 1 diabetes, the acinar-like cell clusters over-expressed REG Iα protein. Islet endocrine cells, including beta-cells and non-beta cells, which were packed with the acinar-like cell clusters, show self-replication with a markedly increased number of Ki67-positive cells. CONCLUSION: The acinar-like cell clusters touching islet endocrine cells are distinct, because the cell clusters are packed with pancreatic islet clusters and surrounded by common BMs/ECM. Furthermore, the acinar-like cell clusters express REG Iα protein and secrete directly to neighboring islet endocrine cells in the non-diabetic state, and the cell clusters over-express REG Iα in the inflamed milieu of fulminant type 1 diabetes with marked self-replication of islet cells.

  9. Modification of the Host Cell Lipid Metabolism Induced by Hypolipidemic Drugs Targeting the Acetyl Coenzyme A Carboxylase Impairs West Nile Virus Replication.

    Science.gov (United States)

    Merino-Ramos, Teresa; Vázquez-Calvo, Ángela; Casas, Josefina; Sobrino, Francisco; Saiz, Juan-Carlos; Martín-Acebes, Miguel A

    2016-01-01

    West Nile virus (WNV) is a neurotropic flavivirus transmitted by the bite of mosquitoes that causes meningitis and encephalitis in humans, horses, and birds. Several studies have highlighted that flavivirus infection is highly dependent on cellular lipids for virus replication and infectious particle biogenesis. The first steps of lipid synthesis involve the carboxylation of acetyl coenzyme A (acetyl-CoA) to malonyl-CoA that is catalyzed by the acetyl-CoA carboxylase (ACC). This makes ACC a key enzyme of lipid synthesis that is currently being evaluated as a therapeutic target for different disorders, including cancers, obesity, diabetes, and viral infections. We have analyzed the effect of the ACC inhibitor 5-(tetradecyloxy)-2-furoic acid (TOFA) on infection by WNV. Lipidomic analysis of TOFA-treated cells confirmed that this drug reduced the cellular content of multiple lipids, including those directly implicated in the flavivirus life cycle (glycerophospholipids, sphingolipids, and cholesterol). Treatment with TOFA significantly inhibited the multiplication of WNV in a dose-dependent manner. Further analysis of the antiviral effect of this drug showed that the inhibitory effect was related to a reduction of viral replication. Furthermore, treatment with another ACC inhibitor, 3,3,14,14-tetramethylhexadecanedioic acid (MEDICA 16), also inhibited WNV infection. Interestingly, TOFA and MEDICA 16 also reduced the multiplication of Usutu virus (USUV), a WNV-related flavivirus. These results point to the ACC as a druggable cellular target suitable for antiviral development against WNV and other flaviviruses. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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....

  20. DEB025 (Alisporivir inhibits hepatitis C virus replication by preventing a cyclophilin A induced cis-trans isomerisation in domain II of NS5A.

    Directory of Open Access Journals (Sweden)

    Lotte Coelmont

    2010-10-01

    Full Text Available DEB025/Debio 025 (Alisporivir is a cyclophilin (Cyp-binding molecule with potent anti-hepatitis C virus (HCV activity both in vitro and in vivo. It is currently being evaluated in phase II clinical trials. DEB025 binds to CypA, a peptidyl-prolyl cis-trans isomerase which is a crucial cofactor for HCV replication. Here we report that it was very difficult to select resistant replicons (genotype 1b to DEB025, requiring an average of 20 weeks (four independent experiments, compared to the typically <2 weeks with protease or polymerase inhibitors. This indicates a high genetic barrier to resistance for DEB025. Mutation D320E in NS5A was the only mutation consistently selected in the replicon genome. This mutation alone conferred a low-level (3.9-fold resistance. Replacing the NS5A gene (but not the NS5B gene from the wild type (WT genome with the corresponding sequence from the DEB025(res replicon resulted in transfer of resistance. Cross-resistance with cyclosporine A (CsA was observed, whereas NS3 protease and NS5B polymerase inhibitors retained WT-activity against DEB025(res replicons. Unlike WT, DEB025(res replicon replicated efficiently in CypA knock down cells. However, DEB025 disrupted the interaction between CypA and NS5A regardless of whether the NS5A protein was derived from WT or DEB025(res replicon. NMR titration experiments with peptides derived from the WT or the DEB025(res domain II of NS5A corroborated this observation in a quantitative manner. Interestingly, comparative NMR studies on two 20-mer NS5A peptides that contain D320 or E320 revealed a shift in population between the major and minor conformers. These data suggest that D320E conferred low-level resistance to DEB025 probably by reducing the need for CypA-dependent isomerisation of NS5A. Prolonged DEB025 treatment and multiple genotypic changes may be necessary to generate significant resistance to DEB025, underlying the high barrier to resistance.

  1. Pre-existing vector immunity does not prevent replication deficient adenovirus from inducing efficient CD8 T-cell memory and recall responses

    DEFF Research Database (Denmark)

    Steffensen, Maria Abildgaard; Jensen, Benjamin Anderschou Holbech; Holst, Peter Johannes

    2012-01-01

    directed against epitopes in the adenoviral vector seemed to correlate with repression of the induced response in re-vaccinated B-cell deficient mice. More importantly, despite a repressed primary effector CD8 T-cell response in Ad5-immune animals subjected to vaccination, memory T cells were generated...... that provided the foundation for an efficient recall response and protection upon subsequent viral challenge. Furthermore, the transgene specific response could be efficiently boosted by homologous re-immunization. Taken together, these studies indicate that adenoviral vectors can be used to induce efficient CD......8 T-cell memory even in individuals with pre-existing vector immunity....

  2. 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

  3. 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...

  4. 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...

  5. 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.

  6. Cell Death of Gamma Interferon-Stimulated Human Fibroblasts upon Toxoplasma gondii Infection Induces Early Parasite Egress and Limits Parasite Replication

    NARCIS (Netherlands)

    Niedelman, Wendy; Sprokholt, Joris K.; Clough, Barbara; Frickel, Eva-Maria; Saeij, Jeroen P. J.

    2013-01-01

    The intracellular protozoan parasite Toxoplasma gondii is a major food-borne illness and opportunistic infection for the immunosuppressed. Resistance to Toxoplasma is dependent on gamma interferon (IFN-γ) activation of both hematopoietic and nonhematopoietic cells. Although IFN-γ-induced innate

  7. Cell death of gamma interferon-stimulated human fibroblasts upon toxoplasma gondii infection induces early parasite egress and limits parasite replication

    NARCIS (Netherlands)

    Niedelman, W.; Sprokholt, J.K.; Clough, B.; Frickel, E.; Saeij, J.P.J.

    2013-01-01

    The intracellular protozoan parasite Toxoplasma gondii is a major food-borne illness and opportunistic infection for the immunosuppressed. Resistance to Toxoplasma is dependent on gamma interferon (IFN-¿) activation of both hematopoietic and nonhematopoietic cells. Although IFN-¿-induced innate

  8. Modes of DNA repair and replication

    International Nuclear Information System (INIS)

    Hanawalt, P.; Kondo, S.

    1979-01-01

    Modes of DNA repair and replication require close coordination as well as some overlap of enzyme functions. Some classes of recovery deficient mutants may have defects in replication rather than repair modes. Lesions such as the pyrimidine dimers produced by ultraviolet light irradiation are the blocks to normal DNA replication in vivo and in vitro. The DNA synthesis by the DNA polymerase 1 of E. coli is blocked at one nucleotide away from the dimerized pyrimidines in template strands. Thus, some DNA polymerases seem to be unable to incorporate nucleotides opposite to the non-pairing lesions in template DNA strands. The lesions in template DNA strands may block the sequential addition of nucleotides in the synthesis of daughter strands. Normal replication utilizes a constitutive ''error-free'' mode that copies DNA templates with high fidelity, but which may be totally blocked at a lesion that obscures the appropriate base pairing specificity. It might be expected that modified replication system exhibits generally high error frequency. The error rate of DNA polymerases may be controlled by the degree of phosphorylation of the enzyme. Inducible SOS system is controlled by recA genes that also control the pathways for recombination. It is possible that SOS system involves some process other than the modification of a blocked replication apparatus to permit error-prone transdimer synthesis. (Yamashita, S.)

  9. 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.

  10. PA from an H5N1 highly pathogenic avian influenza virus activates viral transcription and replication and induces apoptosis and interferon expression at an early stage of infection

    Directory of Open Access Journals (Sweden)

    Wang Qiang

    2012-06-01

    Full Text Available Abstract Background Although gene exchange is not likely to occur freely, reassortment between the H5N1 highly pathogenic avian influenza virus (HPAIV and currently circulating human viruses is a serious concern. The PA polymerase subunit of H5N1 HPAIV was recently reported to activate the influenza replicon activity. Methods The replicon activities of PR8 and WSN strains (H1N1 of influenza containing PA from HPAIV A/Cambodia/P0322095/2005 (H5N1 and the activity of the chimeric RNA polymerase were analyzed. A reassortant WSN virus containing the H5N1 Cambodia PA (C-PA was then reconstituted and its growth in cells and pathogenicity in mice examined. The interferon promoter, TUNEL, and caspase 3, 8, and 9 activities of C-PA-infected cells were compared with those of WSN-infected cells. Results The activity of the chimeric RNA polymerase was slightly higher than that of WSN, and C-PA replicated better than WSN in cells. However, the multi-step growth of C-PA and its pathogenicity in mice were lower than those of WSN. The interferon promoter, TUNEL, and caspase 3, 8, and 9 activities were strongly induced in early infection in C-PA-infected cells but not in WSN-infected cells. Conclusions Apoptosis and interferon were strongly induced early in C-PA infection, which protected the uninfected cells from expansion of viral infection. In this case, these classical host-virus interactions contributed to the attenuation of this strongly replicating virus.

  11. 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...

  12. 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.

  13. 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

  14. 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...

  15. Pre-existing vector immunity does not prevent replication deficient adenovirus from inducing efficient CD8 T-cell memory and recall responses.

    Directory of Open Access Journals (Sweden)

    Maria Abildgaard Steffensen

    Full Text Available Adenoviral vectors have shown a great potential for vaccine development due to their inherent ability to induce potent and protective CD8 T-cell responses. However, a critical issue regarding the use of these vectors is the existence of inhibitory immunity against the most commonly used Ad5 vector in a large part of the human population. We have recently developed an improved adenoviral vaccine vector system in which the vector expresses the transgene tethered to the MHC class II associated invariant chain (Ii. To further evaluate the potential of this system, the concept of pre-existing inhibitory immunity to adenoviral vectors was revisited to investigate whether the inhibition previously seen with the Ad5 vector also applied to the optimized vector system. We found this to be the case, and antibodies dominated as the mechanism underlying inhibitory vector immunity. However, presence of CD8 T cells directed against epitopes in the adenoviral vector seemed to correlate with repression of the induced response in re-vaccinated B-cell deficient mice. More importantly, despite a repressed primary effector CD8 T-cell response in Ad5-immune animals subjected to vaccination, memory T cells were generated that provided the foundation for an efficient recall response and protection upon subsequent viral challenge. Furthermore, the transgene specific response could be efficiently boosted by homologous re-immunization. Taken together, these studies indicate that adenoviral vectors can be used to induce efficient CD8 T-cell memory even in individuals with pre-existing vector immunity.

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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...

  14. 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

  15. 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.

  16. 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

  17. COPI is required for enterovirus 71 replication.

    Directory of Open Access Journals (Sweden)

    Jianmin Wang

    Full Text Available Enterovirus 71 (EV71, a member of the Picornaviridae family, is found in Asian countries where it causes a wide range of human diseases. No effective therapy is available for the treatment of these infections. Picornaviruses undergo RNA replication in association with membranes of infected cells. COPI and COPII have been shown to be involved in the formation of picornavirus-induced vesicles. Replication of several picornaviruses, including poliovirus and Echovirus 11 (EV11, is dependent on COPI or COPII. Here, we report that COPI, but not COPII, is required for EV71 replication. Replication of EV71 was inhibited by brefeldin A and golgicide A, inhibitors of COPI activity. Furthermore, we found EV71 2C protein interacted with COPI subunits by co-immunoprecipitation and GST pull-down assay, indicating that COPI coatomer might be directed to the viral replication complex through viral 2C protein. Additionally, because the pathway is conserved among different species of enteroviruses, it may represent a novel target for antiviral therapies.

  18. 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…

  19. Persistent Low-Level Replication of SIVΔnef Drives Maturation of Antibody and CD8 T Cell Responses to Induce Protective Immunity against Vaginal SIV Infection.

    Directory of Open Access Journals (Sweden)

    Sama Adnan

    2016-12-01

    Full Text Available Defining the correlates of immune protection conferred by SIVΔnef, the most effective vaccine against SIV challenge, could enable the design of a protective vaccine against HIV infection. Here we provide a comprehensive assessment of immune responses that protect against SIV infection through detailed analyses of cellular and humoral immune responses in the blood and tissues of rhesus macaques vaccinated with SIVΔnef and then vaginally challenged with wild-type SIV. Despite the presence of robust cellular immune responses, animals at 5 weeks after vaccination displayed only transient viral suppression of challenge virus, whereas all macaques challenged at weeks 20 and 40 post-SIVΔnef vaccination were protected, as defined by either apparent sterile protection or significant suppression of viremia in infected animals. Multiple parameters of CD8 T cell function temporally correlated with maturation of protection, including polyfunctionality, phenotypic differentiation, and redistribution to gut and lymphoid tissues. Importantly, we also demonstrate the induction of a tissue-resident memory population of SIV-specific CD8 T cells in the vaginal mucosa, which was dependent on ongoing low-level antigenic stimulation. Moreover, we show that vaginal and serum antibody titers inversely correlated with post-challenge peak viral load, and we correlate the accumulation and affinity maturation of the antibody response to the duration of the vaccination period as well as to the SIVΔnef antigenic load. In conclusion, maturation of SIVΔnef-induced CD8 T cell and antibody responses, both propelled by viral persistence in the gut mucosa and secondary lymphoid tissues, results in protective immune responses that are able to interrupt viral transmission at mucosal portals of entry as well as potential sites of viral dissemination.

  20. Persistent Low-Level Replication of SIVΔnef Drives Maturation of Antibody and CD8 T Cell Responses to Induce Protective Immunity against Vaginal SIV Infection.

    Science.gov (United States)

    Adnan, Sama; Reeves, R Keith; Gillis, Jacqueline; Wong, Fay E; Yu, Yi; Camp, Jeremy V; Li, Qingsheng; Connole, Michelle; Li, Yuan; Piatak, Michael; Lifson, Jeffrey D; Li, Wenjun; Keele, Brandon F; Kozlowski, Pamela A; Desrosiers, Ronald C; Haase, Ashley T; Johnson, R Paul

    2016-12-01

    Defining the correlates of immune protection conferred by SIVΔnef, the most effective vaccine against SIV challenge, could enable the design of a protective vaccine against HIV infection. Here we provide a comprehensive assessment of immune responses that protect against SIV infection through detailed analyses of cellular and humoral immune responses in the blood and tissues of rhesus macaques vaccinated with SIVΔnef and then vaginally challenged with wild-type SIV. Despite the presence of robust cellular immune responses, animals at 5 weeks after vaccination displayed only transient viral suppression of challenge virus, whereas all macaques challenged at weeks 20 and 40 post-SIVΔnef vaccination were protected, as defined by either apparent sterile protection or significant suppression of viremia in infected animals. Multiple parameters of CD8 T cell function temporally correlated with maturation of protection, including polyfunctionality, phenotypic differentiation, and redistribution to gut and lymphoid tissues. Importantly, we also demonstrate the induction of a tissue-resident memory population of SIV-specific CD8 T cells in the vaginal mucosa, which was dependent on ongoing low-level antigenic stimulation. Moreover, we show that vaginal and serum antibody titers inversely correlated with post-challenge peak viral load, and we correlate the accumulation and affinity maturation of the antibody response to the duration of the vaccination period as well as to the SIVΔnef antigenic load. In conclusion, maturation of SIVΔnef-induced CD8 T cell and antibody responses, both propelled by viral persistence in the gut mucosa and secondary lymphoid tissues, results in protective immune responses that are able to interrupt viral transmission at mucosal portals of entry as well as potential sites of viral dissemination.

  1. 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.

  2. 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.

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. A replicating modified vaccinia tiantan strain expressing an avian-derived influenza H5N1 hemagglutinin induce broadly neutralizing antibodies and cross-clade protective immunity in mice.

    Directory of Open Access Journals (Sweden)

    Haixia Xiao

    Full Text Available To combat the possibility of a zoonotic H5N1 pandemic in a timely fashion, it is necessary to develop a vaccine that would confer protection against homologous and heterologous human H5N1 influenza viruses. Using a replicating modified vaccinia virus Tian Tan strain (MVTT as a vaccine vector, we constructed MVTTHA-QH and MVTTHA-AH, which expresses the H5 gene of a goose-derived Qinghai strain A/Bar-headed Goose/Qinghai/1/2005 or human-derived Anhui Strain A/Anhui/1/2005. The immunogenicity profiles of both vaccine candidates were evaluated. Vaccination with MVTTHA-QH induced a significant level of neutralizing antibodies (Nabs against a homologous strain and a wide range of H5N1 pseudoviruses (clades 1, 2.1, 2.2, 2.3.2, and 2.3.4. Neutralization tests (NT and Haemagglutination inhibition (HI antibodies inhibit the live autologous virus as well as a homologous A/Xingjiang/1/2006 and a heterologous A/Vietnam/1194/2004, representing two human isolates from clade 2.2 and clade 1, respectively. Importantly, mice vaccinated with intranasal MVTTHA-QH were completely protected from challenge with lethal dosages of A/Bar-headed Goose/Qinghai/1/2005 and the A/Viet Nam/1194/2004, respectively, but not control mice that received a mock MVTTS vaccine. However, MVTTHA-AH induced much lower levels of NT against its autologous strain. Our results suggest that it is feasible to use the H5 gene from A/Bar-headed Goose/Qinghai/1/2005 to construct an effective vaccine, when using MVTT as a vector, to prevent infections against homologous and genetically divergent human H5N1 influenza viruses.

  8. MMS exposure promotes increased MtDNA mutagenesis in the presence of replication-defective disease-associated DNA polymerase γ variants.

    Science.gov (United States)

    Stumpf, Jeffrey D; Copeland, William C

    2014-10-01

    Mitochondrial DNA (mtDNA) encodes proteins essential for ATP production. Mutant variants of the mtDNA polymerase cause mutagenesis that contributes to aging, genetic diseases, and sensitivity to environmental agents. We interrogated mtDNA replication in Saccharomyces cerevisiae strains with disease-associated mutations affecting conserved regions of the mtDNA polymerase, Mip1, in the presence of the wild type Mip1. Mutant frequency arising from mtDNA base substitutions that confer erythromycin resistance and deletions between 21-nucleotide direct repeats was determined. Previously, increased mutagenesis was observed in strains encoding mutant variants that were insufficient to maintain mtDNA and that were not expected to reduce polymerase fidelity or exonuclease proofreading. Increased mutagenesis could be explained by mutant variants stalling the replication fork, thereby predisposing the template DNA to irreparable damage that is bypassed with poor fidelity. This hypothesis suggests that the exogenous base-alkylating agent, methyl methanesulfonate (MMS), would further increase mtDNA mutagenesis. Mitochondrial mutagenesis associated with MMS exposure was increased up to 30-fold in mip1 mutants containing disease-associated alterations that affect polymerase activity. Disrupting exonuclease activity of mutant variants was not associated with increased spontaneous mutagenesis compared with exonuclease-proficient alleles, suggesting that most or all of the mtDNA was replicated by wild type Mip1. A novel subset of C to G transversions was responsible for about half of the mutants arising after MMS exposure implicating error-prone bypass of methylated cytosines as the predominant mutational mechanism. Exposure to MMS does not disrupt exonuclease activity that suppresses deletions between 21-nucleotide direct repeats, suggesting the MMS-induce mutagenesis is not explained by inactivated exonuclease activity. Further, trace amounts of CdCl2 inhibit mtDNA replication but

  9. 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.

  10. 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...

  11. 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)

  12. 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....

  13. 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.

  14. 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...

  15. 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...

  16. 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...

  17. 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)

  18. 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)

  19. 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.

  20. 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)

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. Role of oxidative stress and intracellular calcium in nickel carbonate hydroxide-induced sister-chromatid exchange, and alterations in replication index and mitotic index in cultured human peripheral blood lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    M' Bemba-Meka, Prosper [Universite de Montreal, Human Toxicology Research Group (TOXHUM), Department of Environmental and Occupational Health, Main Station, P.O. Box 6128, Montreal, QC (Canada); University of Louisville, Department of Pharmacology and Toxicology, Center for Genetics and Molecular Medicine, Louisville, KY (United States); Lemieux, Nicole [Universite de Montreal, Department of Pathology and Cellular Biology, Faculty of Medicine, Main Station, P.O. Box 6128, Montreal, QC (Canada); Chakrabarti, Saroj K. [Universite de Montreal, Human Toxicology Research Group (TOXHUM), Department of Environmental and Occupational Health, Main Station, P.O. Box 6128, Montreal, QC (Canada)

    2007-02-15

    Human peripheral lymphocytes from whole blood cultures were exposed to either soluble form of nickel carbonate hydroxide (NiCH) (0-60 {mu}M), or of nickel subsulfide (Ni{sub 3}S{sub 2}) (0-120 {mu}M), or of nickel oxide (NiO) (0-120 {mu}M), or nickel sulfate (NiSO{sub 4}) (0-120 {mu}M) for a short duration of 2 h. The treatments occurred 46 h after the beginning of the cultures. The cultures were harvested after a total incubation of 72 h, and sister-chromatid exchange (SCE), replication index (RI), and mitotic index (MI) were measured for each nickel compound. The soluble form of NiCH at 30 {mu}M but those of Ni{sub 3}S{sub 2} and NiO at 120 {mu}M produced significant increase in the SCE per cell compared to the control value, whereas NiSO{sub 4} failed to produce any such significant increase. Except NiSO{sub 4}, the soluble forms of NiCH, Ni{sub 3}S{sub 2}, and NiO produced significant cell-cycle delay (as measured by the inhibition of RI) as well as significant inhibition of the MI at respective similar concentrations as mentioned above. Pretreatment of human blood lymphocytes with catalase (H{sub 2}O{sub 2} scavenger), or superoxide dismutase (superoxide anion scavenger), or dimethylthiourea (hydroxyl radical scavenger), or deferoxamine (iron chelator), or N-acetylcysteine (general antioxidant) inhibited NiCH-induced SCE, and changes in RI and MI. This suggests the participation of oxidative stress involving H{sub 2}O{sub 2}, the superoxide anion radical, the hydroxyl radical, and iron in the NiCH-induced genotoxic responses. Cotreatment of NiCH with either verapamil (inhibitor of intracellular calcium ion ([Ca{sup 2+}]{sub i}) movement through plasma membranes), or dantrolene (inhibitor of [Ca{sup 2+}]{sub i} release from sarcoplasmic reticulum), or BAPTA (Ca{sup 2+} chelator) also inhibited the NiCH-induced responses. These results suggest that [Ca{sup 2+}]{sub i} is also implicated in the genotoxicity of NiCH. Overall these data indicate that various types

  9. Cytoplasmic ATR Activation Promotes Vaccinia Virus Genome Replication

    Directory of Open Access Journals (Sweden)

    Antonio Postigo

    2017-05-01

    Full Text Available In contrast to most DNA viruses, poxviruses replicate their genomes in the cytoplasm without host involvement. We find that vaccinia virus induces cytoplasmic activation of ATR early during infection, before genome uncoating, which is unexpected because ATR plays a fundamental nuclear role in maintaining host genome integrity. ATR, RPA, INTS7, and Chk1 are recruited to cytoplasmic DNA viral factories, suggesting canonical ATR pathway activation. Consistent with this, pharmacological and RNAi-mediated inhibition of canonical ATR signaling suppresses genome replication. RPA and the sliding clamp PCNA interact with the viral polymerase E9 and are required for DNA replication. Moreover, the ATR activator TOPBP1 promotes genome replication and associates with the viral replisome component H5. Our study suggests that, in contrast to long-held beliefs, vaccinia recruits conserved components of the eukaryote DNA replication and repair machinery to amplify its genome in the host cytoplasm.

  10. 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

  11. 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

  12. Registered Replication Report: Strack, Martin, & Stepper (1988).

    Science.gov (United States)

    Acosta, Alberto; Adams, Reginald B; Albohn, Daniel N; Allard, Eric S; Beek, Titia; Benning, Stephen D; Blouin- Hudon, Eve-Marie; Bulnes, Luis Carlo; Caldwell, Tracy L; Calin-Jageman, Robert J; Capaldi, Colin A; Carfagno, Nicholas S; Chasten, Kelsie T; Cleeremans, Axel; Connell, Louise; DeCicco, Jennifer M.; Dijkhoff, Laura; Dijkstra, Katinka; Fischer, Agneta H; Foroni, Francesco; Gronau, Quentin F; Hess, Ursula; Holmes, Kevin J; Jones, Jacob L H; Klein, Olivier; Koch, Christopher; Korb, Sebastian; Lewinski, Peter; Liao, Julia D; Lund, Sophie; Lupiáñez, Juan; Lynott, Dermot; Nance, Christin N; Oosterwijk, Suzanne; Özdog˘ru, Asil Ali; Pacheco-Unguetti, Antonia Pilar; Pearson, Bethany; Powis, Christina; Riding, Sarah; Roberts, Tomi-Ann; Rumiati, Raffaella I; Senden, Morgane; Shea-Shumsky, Noah B; Sobocko, Karin; Soto, Jose A; Steiner, Troy G; Talarico, Jennifer M; vanAllen, Zack M; Wagenmakers, E-J; Vandekerckhove, Marie; Wainwright, Bethany; Wayand, Joseph F; Zeelenberg, Rene; Zetzer, Emily E; Zwaan, Rolf A

    2016-11-01

    According to the facial feedback hypothesis, people's affective responses can be influenced by their own facial expression (e.g., smiling, pouting), even when their expression did not result from their emotional experiences. For example, Strack, Martin, and Stepper (1988) instructed participants to rate the funniness of cartoons using a pen that they held in their mouth. In line with the facial feedback hypothesis, when participants held the pen with their teeth (inducing a "smile"), they rated the cartoons as funnier than when they held the pen with their lips (inducing a "pout"). This seminal study of the facial feedback hypothesis has not been replicated directly. This Registered Replication Report describes the results of 17 independent direct replications of Study 1 from Strack et al. (1988), all of which followed the same vetted protocol. A meta-analysis of these studies examined the difference in funniness ratings between the "smile" and "pout" conditions. The original Strack et al. (1988) study reported a rating difference of 0.82 units on a 10-point Likert scale. Our meta-analysis revealed a rating difference of 0.03 units with a 95% confidence interval ranging from -0.11 to 0.16. © The Author(s) 2016.

  13. 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

  14. 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

  15. 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…

  16. 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

  17. 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.

  18. DNA replication after mutagenic treatment in Hordeum vulgare.

    Science.gov (United States)

    Kwasniewska, Jolanta; Kus, Arita; Swoboda, Monika; Braszewska-Zalewska, Agnieszka

    2016-12-01

    The temporal and spatial properties of DNA replication in plants related to DNA damage and mutagenesis is poorly understood. Experiments were carried out to explore the relationships between DNA replication, chromatin structure and DNA damage in nuclei from barley root tips. We quantitavely analysed the topological organisation of replication foci using pulse EdU labelling during the S phase and its relationship with the DNA damage induced by mutagenic treatment with maleic hydrazide (MH), nitroso-N-methyl-urea (MNU) and gamma ray. Treatment with mutagens did not change the characteristic S-phase patterns in the nuclei; however, the frequencies of the S-phase-labelled cells after treatment differed from those observed in the control cells. The analyses of DNA replication in barley nuclei were extended to the micronuclei induced by mutagens. Replication in the chromatin of the micronuclei was rare. The results of simultanous TUNEL reaction to identify cells with DNA strand breaks and the labelling of the S-phase cells with EdU revealed the possibility of DNA replication occurring in damaged nuclei. For the first time, the intensity of EdU fluorescence to study the rate of DNA replication was analysed. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Structural aspects of DNA in its replication and repair

    International Nuclear Information System (INIS)

    Mitra, S.; Pal, B.C.; Foote, R.S.; Bates, R.C.; Bhattacharyya, A.; Snow, E.T.; Wobbe, C.R.; Morse, C.C.; Snyder, C.E.

    1984-01-01

    The research objective of this laboratory is to investigate the structure of DNA, the mechanism of DNA replication and its regulation, and the mechanism and role of repair of the altered DNA in the expression of heritable changes. This research has two broad aims, namely investigation of (a) the regulation of DNA replication in mammals, using parvovirus DNA as a model system and (b) the role of DNA repair in mutagenesis and carcinogenesis induced by simple alkylating mutagens

  20. 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…

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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...

  7. 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.

  8. 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.

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

    Science.gov (United States)

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

    2012-01-01

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

  10. 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

  11. Repair of human DNA in molecules that replicate or remain unreplicated following ultraviolet irradiation

    International Nuclear Information System (INIS)

    Waters, R.

    1980-01-01

    The extent of DNA replication, the incidence of uv induced pyrimidine dimers and the repair replication observed after their excision was monitored in human fibroblasts uv irradiated with single or split uv doses. The excision repair processes were measured in molecules that remained unreplicated or in those that replicated after the latter uv irradiation. Less DNA replication was observed after a split as opposed to single uv irradiation. Furthermore, a split dose did not modify the excision parameters measured after a single irradiation, regardless of whether the DNA had replicated or not

  12. 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.

  13. 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.

  14. 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)

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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...

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. Endoplasmic reticulum stress causes EBV lytic replication.

    Science.gov (United States)

    Taylor, Gwen Marie; Raghuwanshi, Sandeep K; Rowe, David T; Wadowsky, Robert M; Rosendorff, Adam

    2011-11-17

    Endoplasmic reticulum (ER) stress triggers a homeostatic cellular response in mammalian cells to ensure efficient folding, sorting, and processing of client proteins. In lytic-permissive lymphoblastoid cell lines (LCLs), pulse exposure to the chemical ER-stress inducer thapsigargin (TG) followed by recovery resulted in the activation of the EBV immediate-early (BRLF1, BZLF1), early (BMRF1), and late (gp350) genes, gp350 surface expression, and virus release. The protein phosphatase 1 a (PP1a)-specific phosphatase inhibitor Salubrinal (SAL) synergized with TG to induce EBV lytic genes; however, TG treatment alone was sufficient to activate EBV lytic replication. SAL showed ER-stress-dependent and -independent antiviral effects, preventing virus release in human LCLs and abrogating gp350 expression in 12-O-tetradecanoylphorbol-13-acetate (TPA)-treated B95-8 cells. TG resulted in sustained BCL6 but not BLIMP1 or CD138 expression, which is consistent with maintenance of a germinal center B-cell, rather than plasma-cell, phenotype. Microarray analysis identified candidate genes governing lytic replication in LCLs undergoing ER stress.

  10. 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...

  11. 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…

  12. DNA replication stress as a hallmark of cancer.

    Science.gov (United States)

    Macheret, Morgane; Halazonetis, Thanos D

    2015-01-01

    Human cancers share properties referred to as hallmarks, among which sustained proliferation, escape from apoptosis, and genomic instability are the most pervasive. The sustained proliferation hallmark can be explained by mutations in oncogenes and tumor suppressors that regulate cell growth, whereas the escape from apoptosis hallmark can be explained by mutations in the TP53, ATM, or MDM2 genes. A model to explain the presence of the three hallmarks listed above, as well as the patterns of genomic instability observed in human cancers, proposes that the genes driving cell proliferation induce DNA replication stress, which, in turn, generates genomic instability and selects for escape from apoptosis. Here, we review the data that support this model, as well as the mechanisms by which oncogenes induce replication stress. Further, we argue that DNA replication stress should be considered as a hallmark of cancer because it likely drives cancer development and is very prevalent.

  13. Acute inactivation of the replicative helicase in human cells triggers MCM8-9-dependent DNA synthesis

    DEFF Research Database (Denmark)

    Natsume, Toyoaki; Nishimura, Kohei; Minocherhomji, Sheroy

    2017-01-01

    stemming from replisome dissociation during DNA replication perturbation, we used a degron-based system for inducible proteolysis of a subunit of the replicative helicase. We show that MCM2-depleted cells activate a DNA damage response pathway and generate replication-associated DNA double-strand breaks...

  14. 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…

  15. 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.

  16. 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...

  17. 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

  18. 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.

  19. Quality of topographical micro replication in injection moulding

    DEFF Research Database (Denmark)

    Arlø, Uffe Rolf; Hansen, Hans Nørgaard; Bariani, Paolo

    2003-01-01

    The quality of tool-to-part rough surface topography replication in injection moulding has been investigated. Quantitative descriptors suitable for detecting process conditions induced topography changes have been identified using a statistical criterion. The experimental work is based on a tool ...

  20. Can Coloring Mandalas Reduce Anxiety? A Replication Study

    Science.gov (United States)

    van der Vennet, Renee; Serice, Susan

    2012-01-01

    This experimental study replicated Curry and Kasser's (2005) research that tested whether coloring a mandala would reduce anxiety. After inducing an anxious mood via a writing activity, participants were randomly assigned to three groups that colored either on a mandala design, on a plaid design, or on a blank paper. Anxiety level was measured…

  1. 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

  2. X-ray repair replication in L1210 leukemia cells

    International Nuclear Information System (INIS)

    Lee, Y.C.; Byfield, J.E.; Bennett, L.R.; Chan, P.Y.M.

    1974-01-01

    Repair replication has been studied in detail in mouse L1210 leukemia cells. A method of identifying and quantitating repair replication using a pre- and postradiation block of normal replication with cytosine arabinoside is illustrated. The method derived does not require isolation of DNA per se and appears to be satisfactory for screening for inhibitors of repair replication. Repair replication can be demonstrated at doses in the 1000-rad range in bromouridine deoxyriboside-substituted cells and at slightly higher doses in nonsubstituted cells. Drugs that are known to bind to DNA inhibit this x-ray-induced repair replication. Drugs with these properties may be identified by the methods described and compared quantitatively in their ability to inhibit this type of x-ray damage. Since these phenomena can be demonstrated for low radiation doses and at drug concentrations attainable in vivo during human cancer chemotherapy this class of anticancer agent may be worthy of closer study. Application to the L1210 leukemia system should permit comparison of in vitro and in vivo drug effects in the context of the extensive in vivo pharmacological data already available for L1210 cells. (U.S.)

  3. The cytoprotective enzyme heme oxygenase-1 suppresses Ebola virus replication.

    Science.gov (United States)

    Hill-Batorski, Lindsay; Halfmann, Peter; Neumann, Gabriele; Kawaoka, Yoshihiro

    2013-12-01

    Ebola virus (EBOV) is the causative agent of a severe hemorrhagic fever in humans with reported case fatality rates as high as 90%. There are currently no licensed vaccines or antiviral therapeutics to combat EBOV infections. Heme oxygenase-1 (HO-1), an enzyme that catalyzes the rate-limiting step in heme degradation, has antioxidative properties and protects cells from various stresses. Activated HO-1 was recently shown to have antiviral activity, potently inhibiting the replication of viruses such as hepatitis C virus and human immunodeficiency virus. However, the effect of HO-1 activation on EBOV replication remains unknown. To determine whether the upregulation of HO-1 attenuates EBOV replication, we treated cells with cobalt protoporphyrin (CoPP), a selective HO-1 inducer, and assessed its effects on EBOV replication. We found that CoPP treatment, pre- and postinfection, significantly suppressed EBOV replication in a manner dependent upon HO-1 upregulation and activity. In addition, stable overexpression of HO-1 significantly attenuated EBOV growth. Although the exact mechanism behind the antiviral properties of HO-1 remains to be elucidated, our data show that HO-1 upregulation does not attenuate EBOV entry or budding but specifically targets EBOV transcription/replication. Therefore, modulation of the cellular enzyme HO-1 may represent a novel therapeutic strategy against EBOV infection.

  4. 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....

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. SMC1-Mediated Intra-S-Phase Arrest Facilitates Bocavirus DNA Replication

    Science.gov (United States)

    Luo, Yong; Deng, Xuefeng; Cheng, Fang; Li, Yi

    2013-01-01

    Activation of a host DNA damage response (DDR) is essential for DNA replication of minute virus of canines (MVC), a member of the genus Bocavirus of the Parvoviridae family; however, the mechanism by which DDR contributes to viral DNA replication is unknown. In the current study, we demonstrate that MVC infection triggers the intra-S-phase arrest to slow down host cellular DNA replication and to recruit cellular DNA replication factors for viral DNA replication. The intra-S-phase arrest is regulated by ATM (ataxia telangiectasia-mutated kinase) signaling in a p53-independent manner. Moreover, we demonstrate that SMC1 (structural maintenance of chromosomes 1) is the key regulator of the intra-S-phase arrest induced during infection. Either knockdown of SMC1 or complementation with a dominant negative SMC1 mutant blocks both the intra-S-phase arrest and viral DNA replication. Finally, we show that the intra-S-phase arrest induced during MVC infection was caused neither by damaged host cellular DNA nor by viral proteins but by replicating viral genomes physically associated with the DNA damage sensor, the Mre11-Rad50-Nbs1 (MRN) complex. In conclusion, the feedback loop between MVC DNA replication and the intra-S-phase arrest is mediated by ATM-SMC1 signaling and plays a critical role in MVC DNA replication. Thus, our findings unravel the mechanism underlying DDR signaling-facilitated MVC DNA replication and demonstrate a novel strategy of DNA virus-host interaction. PMID:23365434

  13. Hili Inhibits HIV Replication in Activated T Cells.

    Science.gov (United States)

    Peterlin, B Matija; Liu, Pingyang; Wang, Xiaoyun; Cary, Daniele; Shao, Wei; Leoz, Marie; Hong, Tian; Pan, Tao; Fujinaga, Koh

    2017-06-01

    P-element-induced wimpy-like (Piwil) proteins restrict the replication of mobile genetic elements in the germ line. They are also expressed in many transformed cell lines. In this study, we discovered that the human Piwil 2 (Hili) protein can also inhibit HIV replication, especially in activated CD4 + T cells that are the preferred target cells for this virus in the infected host. Although resting cells did not express Hili, its expression was rapidly induced following T cell activation. In these cells and transformed cell lines, depletion of Hili increased levels of viral proteins and new viral particles. Further studies revealed that Hili binds to tRNA. Some of the tRNAs represent rare tRNA species, whose codons are overrepresented in the viral genome. Targeting tRNA Arg (UCU) with an antisense oligonucleotide replicated effects of Hili and also inhibited HIV replication. Finally, Hili also inhibited the retrotransposition of the endogenous intracysternal A particle (IAP) by a similar mechanism. Thus, Hili joins a list of host proteins that inhibit the replication of HIV and other mobile genetic elements. IMPORTANCE Piwil proteins inhibit the movement of mobile genetic elements in the germ line. In their absence, sperm does not form and male mice are sterile. This inhibition is thought to occur via small Piwi-interacting RNAs (piRNAs). However, in some species and in human somatic cells, Piwil proteins bind primarily to tRNA. In this report, we demonstrate that human Piwil proteins, especially Hili, not only bind to select tRNA species, including rare tRNAs, but also inhibit HIV replication. Importantly, T cell activation induces the expression of Hili in CD4 + T cells. Since Hili also inhibited the movement of an endogenous retrovirus (IAP), our finding shed new light on this intracellular resistance to exogenous and endogenous retroviruses as well as other mobile genetic elements. Copyright © 2017 American Society for Microbiology.

  14. 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

  15. Le Chatelier's principle in replicator dynamics

    Science.gov (United States)

    Allahverdyan, Armen E.; Galstyan, Aram

    2011-10-01

    The Le Chatelier principle states that physical equilibria are not only stable, but they also resist external perturbations via short-time negative-feedback mechanisms: a perturbation induces processes tending to diminish its results. The principle has deep roots, e.g., in thermodynamics it is closely related to the second law and the positivity of the entropy production. Here we study the applicability of the Le Chatelier principle to evolutionary game theory, i.e., to perturbations of a Nash equilibrium within the replicator dynamics. We show that the principle can be reformulated as a majorization relation. This defines a stability notion that generalizes the concept of evolutionary stability. We determine criteria for a Nash equilibrium to satisfy the Le Chatelier principle and relate them to mutualistic interactions (game-theoretical anticoordination) showing in which sense mutualistic replicators can be more stable than (say) competing ones. There are globally stable Nash equilibria, where the Le Chatelier principle is violated even locally: in contrast to the thermodynamic equilibrium a Nash equilibrium can amplify small perturbations, though both types of equilibria satisfy the detailed balance condition.

  16. 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

  17. 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.

  18. 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...

  19. 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...

  20. 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

  1. 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...

  2. 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

  3. 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.

  4. 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.

  5. 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....

  6. 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...

  7. 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....

  8. TDP1 repairs nuclear and mitochondrial DNA damage induced by chain-terminating anticancer and antiviral nucleoside analogs

    Science.gov (United States)

    Huang, Shar-yin N.; Murai, Junko; Dalla Rosa, Ilaria; Dexheimer, Thomas S.; Naumova, Alena; Gmeiner, William H.; Pommier, Yves

    2013-01-01

    Chain-terminating nucleoside analogs (CTNAs) that cause stalling or premature termination of DNA replication forks are widely used as anticancer and antiviral drugs. However, it is not well understood how cells repair the DNA damage induced by these drugs. Here, we reveal the importance of tyrosyl–DNA phosphodiesterase 1 (TDP1) in the repair of nuclear and mitochondrial DNA damage induced by CTNAs. On investigating the effects of four CTNAs—acyclovir (ACV), cytarabine (Ara-C), zidovudine (AZT) and zalcitabine (ddC)—we show that TDP1 is capable of removing the covalently linked corresponding CTNAs from DNA 3′-ends. We also show that Tdp1−/− cells are hypersensitive and accumulate more DNA damage when treated with ACV and Ara-C, implicating TDP1 in repairing CTNA-induced DNA damage. As AZT and ddC are known to cause mitochondrial dysfunction, we examined whether TDP1 repairs the mitochondrial DNA damage they induced. We find that AZT and ddC treatment leads to greater depletion of mitochondrial DNA in Tdp1−/− cells. Thus, TDP1 seems to be critical for repairing nuclear and mitochondrial DNA damage caused by CTNAs. PMID:23775789

  9. 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...

  10. 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.

  11. Stwl modifies chromatin compaction and is required to maintain DNA integrity in the presence of perturbed DNA replication

    NARCIS (Netherlands)

    Yi, X.; Vries, de H.I.; Siudeja, K.; Rana, A.; Lemstra, W.; Brunsting, J.F.; Kok, R.J.M.; Smulders, Y.M.; Schaefer, M.; Dijk, F.; Shang, Y.F.; Eggen, B.J.L.; Kampinga, H.H.; Sibon, O.C.M.

    2009-01-01

    Hydroxyurea, a well-known DNA replication inhibitor, induces cell cycle arrest and intact checkpoint functions are required to survive DNA replication stress induced by this genotoxic agent. Perturbed DNA synthesis also results in elevated levels of DNA damage. It is unclear how organisms prevent

  12. Stwl Modifies Chromatin Compaction and Is Required to Maintain DNA Integrity in the Presence of Perturbed DNA Replication

    NARCIS (Netherlands)

    Yi, Xia; Vries, Hilda I. de; Siudeja, Katarzyna; Rana, Anil; Lemstra, Willy; Brunsting, Jeanette F.; Kok, Rob M.; Smulders, Yvo M.; Schaefer, Matthias; Dijk, Freark; Shang, Yongfeng; Eggen, Bart J.L.; Kampinga, Harm H.; Sibon, Ody C.M.

    Hydroxyurea, a well-known DNA replication inhibitor, induces cell cycle arrest and intact checkpoint functions are required to survive DNA replication stress induced by this genotoxic agent. Perturbed DNA synthesis also results in elevated levels of DNA damage. It is unclear how organisms prevent

  13. 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

  14. HSV-1 Remodels Host Telomeres to Facilitate Viral Replication

    Directory of Open Access Journals (Sweden)

    Zhong Deng

    2014-12-01

    Full Text Available Telomeres protect the ends of cellular chromosomes. We show here that infection with herpes simplex virus 1 (HSV-1 results in chromosomal structural aberrations at telomeres and the accumulation of telomere dysfunction-induced DNA damage foci (TIFs. At the molecular level, HSV-1 induces transcription of telomere repeat-containing RNA (TERRA, followed by the proteolytic degradation of the telomere protein TPP1 and loss of the telomere repeat DNA signal. The HSV-1-encoded E3 ubiquitin ligase ICP0 is required for TERRA transcription and facilitates TPP1 degradation. Small hairpin RNA (shRNA depletion of TPP1 increases viral replication, indicating that TPP1 inhibits viral replication. Viral replication protein ICP8 forms foci that coincide with telomeric proteins, and ICP8-null virus failed to degrade telomere DNA signal. These findings suggest that HSV-1 reorganizes telomeres to form ICP8-associated prereplication foci and to promote viral genomic replication.

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  16. 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)

  17. Reactivation of DNA replication of the parvovirus MVM in UV preirradiated mouse cells

    Energy Technology Data Exchange (ETDEWEB)

    Vos, J.M.; Rommelaere, J. (Universite Libre de Bruxelles, Rhode-St-Genese (Belgium))

    1982-07-01

    The parvovirus Minute-Virus-of-Mice (MVM) was used to probe the DNA replication activities expressed by mouse fibroblasts. This system allowed us to study quantitatively the effect of UV-induced DNA lesions on the progression of DNA replication in vivo. MVM was UV-irradiated prior to infection. Pyrimidine dimers induced in the viral genome account for the reduced level of intracellular viral DNA synthesis, assuming that most of these lesions block viral DNA replication in unirradiated cells. The inhibition of damaged MVM DNA synthesis is less severe if the host cells themselves are irradiated prior to virus infection. This stimulation of viral DNA replication in pretreated cells might account for the UV-enhanced viral reactivation phenomenon, i.e. the increased survival of nuclear-replicating viruses propagated in cells preexposed to various genotoxic agents.

  18. Reactivation of DNA replication of the parvovirus MVM in UV preirradiated mouse cells

    International Nuclear Information System (INIS)

    Vos, J.M.; Rommelaere, Jean

    1982-01-01

    The parvovirus Minute-Virus-of-Mice (MVM) was used to probe the DNA replication activities expressed by mouse fibroblasts. This system allowed us to study quantitatively the effect of UV-induced DNA lesions on the progression of DNA replication in vivo. MVM was UV-irradiated prior to infection. Pyrimidine dimers induced in the viral genome account for the reduced level of intracellular viral DNA synthesis, assuming that most of these lesions block viral DNA replication in unirradiated cells. The inhibition of damaged MVM DNA synthesis is less severe if the host cells themselves are irradiated prior to virus infection. This stimulation of viral DNA replication in pretreated cells might account for the UV-enhanced viral reactivation phenomenon, i.e. the increased survival of nuclear-replicating viruses propagated in cells preexposed to various genotoxic agents [fr

  19. 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.

  20. 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.)

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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)

  7. 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.

  8. 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.

  9. 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)

  10. 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)

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.)

  16. BPIFB6 Regulates Secretory Pathway Trafficking and Enterovirus Replication.

    Science.gov (United States)

    Morosky, Stefanie; Lennemann, Nicholas J; Coyne, Carolyn B

    2016-05-15

    Bactericidal/permeability-increasing protein (BPI) fold-containing family B, member 3 (BPIFB3) is an endoplasmic reticulum (ER)-localized host factor that negatively regulates coxsackievirus B (CVB) replication through its control of the autophagic pathway. Here, we show that another member of the BPIFB family, BPIFB6, functions as a positive regulator of CVB, and other enterovirus, replication by controlling secretory pathway trafficking and Golgi complex morphology. We show that similar to BPIFB3, BPIFB6 localizes exclusively to the ER, where it associates with other members of the BPIFB family. However, in contrast to our findings that RNA interference (RNAi)-mediated silencing of BPIFB3 greatly enhances CVB replication, we show that silencing of BPIFB6 expression dramatically suppresses enterovirus replication in a pan-viral manner. Mechanistically, we show that loss of BPIFB6 expression induces pronounced alterations in retrograde and anterograde trafficking, which correlate with dramatic fragmentation of the Golgi complex. Taken together, these data implicate BPIFB6 as a key regulator of secretory pathway trafficking and viral replication and suggest that members of the BPIFB family participate in diverse host cell functions to regulate virus infections. Enterovirus infections are associated with a number of severe pathologies, such as aseptic meningitis, dilated cardiomyopathy, type I diabetes, paralysis, and even death. These viruses, which include coxsackievirus B (CVB), poliovirus (PV), and enterovirus 71 (EV71), co-opt the host cell secretory pathway, which controls the transport of proteins from the endoplasmic reticulum to the Golgi complex, to facilitate their replication. Here we report on the identification of a novel regulator of the secretory pathway, bactericidal/permeability-increasing protein (BPI) fold-containing family B, member 6 (BPIFB6), whose expression is required for enterovirus replication. We show that loss of BPIFB6 expression

  17. BPIFB6 Regulates Secretory Pathway Trafficking and Enterovirus Replication

    Science.gov (United States)

    Morosky, Stefanie; Lennemann, Nicholas J.

    2016-01-01

    ABSTRACT Bactericidal/permeability-increasing protein (BPI) fold-containing family B, member 3 (BPIFB3) is an endoplasmic reticulum (ER)-localized host factor that negatively regulates coxsackievirus B (CVB) replication through its control of the autophagic pathway. Here, we show that another member of the BPIFB family, BPIFB6, functions as a positive regulator of CVB, and other enterovirus, replication by controlling secretory pathway trafficking and Golgi complex morphology. We show that similar to BPIFB3, BPIFB6 localizes exclusively to the ER, where it associates with other members of the BPIFB family. However, in contrast to our findings that RNA interference (RNAi)-mediated silencing of BPIFB3 greatly enhances CVB replication, we show that silencing of BPIFB6 expression dramatically suppresses enterovirus replication in a pan-viral manner. Mechanistically, we show that loss of BPIFB6 expression induces pronounced alterations in retrograde and anterograde trafficking, which correlate with dramatic fragmentation of the Golgi complex. Taken together, these data implicate BPIFB6 as a key regulator of secretory pathway trafficking and viral replication and suggest that members of the BPIFB family participate in diverse host cell functions to regulate virus infections. IMPORTANCE Enterovirus infections are associated with a number of severe pathologies, such as aseptic meningitis, dilated cardiomyopathy, type I diabetes, paralysis, and even death. These viruses, which include coxsackievirus B (CVB), poliovirus (PV), and enterovirus 71 (EV71), co-opt the host cell secretory pathway, which controls the transport of proteins from the endoplasmic reticulum to the Golgi complex, to facilitate their replication. Here we report on the identification of a novel regulator of the secretory pathway, bactericidal/permeability-increasing protein (BPI) fold-containing family B, member 6 (BPIFB6), whose expression is required for enterovirus replication. We show that loss of

  18. Autophagic machinery activated by dengue virus enhances virus replication

    International Nuclear Information System (INIS)

    Lee, Y.-R.; Lei, H.-Y.; Liu, M.-T.; Wang, J.-R.; Chen, S.-H.; Jiang-Shieh, Y.-F.; Lin, Y.-S.; Yeh, T.-M.; Liu, C.-C.; Liu, H.-S.

    2008-01-01

    Autophagy is a cellular response against stresses which include the infection of viruses and bacteria. We unravel that Dengue virus-2 (DV2) can trigger autophagic process in various infected cell lines demonstrated by GFP-LC3 dot formation and increased LC3-II formation. Autophagosome formation was also observed under the transmission electron microscope. DV2-induced autophagy further enhances the titers of extracellular and intracellular viruses indicating that autophagy can promote viral replication in the infected cells. Moreover, our data show that ATG5 protein is required to execute DV2-induced autophagy. All together, we are the first to demonstrate that DV can activate autophagic machinery that is favorable for viral replication

  19. Phenolic extract of Parkia biglobosa fruit pulp stalls aflatoxin B1 – mediated oxidative rout in the liver of male rats

    Directory of Open Access Journals (Sweden)

    Taofeek O. Ajiboye

    Full Text Available The effect of phenolic extract of Parkia biglobosa (Jacq. R. Br. ex G. Don, Fabaceae, pulp on aflatoxin B1 induced oxidative imbalance in rat liver was evaluated. Thirty-five male rats were randomized into seven groups of five animals each. Rats in group A served as control and received vehicle for drug administration (0.5% DMSO once daily at 24 h intervals for six weeks. Rats in groups B, D, E, F and G, received aflatoxin B1 (167 μg/kg body weight in 0.5% DMSO for three weeks, starting from the third week of the experimental pe