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Sample records for stratified replication timing

  1. Multiprocessor Real-Time Locking Protocols for Replicated Resources

    Science.gov (United States)

    2016-07-01

    assignment problem, the ac- tual identities of the allocated replicas must be known. When locking protocols are used, tasks may experience delays due to both...Multiprocessor Real-Time Locking Protocols for Replicated Resources ∗ Catherine E. Jarrett1, Kecheng Yang1, Ming Yang1, Pontus Ekberg2, and James H...replicas to execute. In prior work on replicated resources, k-exclusion locks have been used, but this restricts tasks to lock only one replica at a time. To

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

    Directory of Open Access Journals (Sweden)

    Majid Eshaghi

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

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

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

    2012-01-01

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

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

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    Thiriet, Christophe; Hayes, Jeffrey J.

    2009-01-01

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

  5. Replication Variance Estimation under Two-phase Sampling in the Presence of Non-response

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    Muqaddas Javed

    2014-09-01

    Full Text Available Kim and Yu (2011 discussed replication variance estimator for two-phase stratified sampling. In this paper estimators for mean have been proposed in two-phase stratified sampling for different situation of existence of non-response at first phase and second phase. The expressions of variances of these estimators have been derived. Furthermore, replication-based jackknife variance estimators of these variances have also been derived. Simulation study has been conducted to investigate the performance of the suggested estimators.

  6. Characterization of the replication timing program of 6 human model cell lines

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    Djihad Hadjadj

    2016-09-01

    Full Text Available During the S-phase, the DNA replication process is finely orchestrated and regulated by two programs: the spatial program that determines where replication will start in the genome (Cadoret et al. (2008 Oct 14, Cayrou et al. (2011 Sep, Picard et al. (2014 May 1 [1–3], and the temporal program that determines when during the S phase different parts of the genome are replicated and when origins are activated. The temporal program is so well conserved for each cell type from independent individuals [4] that it is possible to identify a cell type from an unknown sample just by determining its replication timing program. Moreover, replicative domains are strongly correlated with the partition of the genome into topological domains (determined by the Hi-C method, Lieberman-Aiden et al. (2009 Oct 9, Pope et al. (2014 Nov 20 [5,6]. On the one hand, replicative areas are well defined and participate in shaping the spatial organization of the genome for a given cell type. On the other hand, studies on the timing program during cell differentiation showed a certain plasticity of this program according to the stage of cell differentiation Hiratani et al. (2008 Oct 7, 2010 Feb [7,8]. Domains where a replication timing change was observed went through a nuclear re-localization. Thus the temporal program of replication can be considered as an epigenetic mark Hiratani and Gilbert (2009 Feb 16 [9]. We present the genomic data of replication timing in 6 human model cell lines: U2OS (GSM2111308, RKO (GSM2111309, HEK 293T (GSM2111310, HeLa (GSM2111311, MRC5-SV (GSM2111312 and K562 (GSM2111313. A short comparative analysis was performed that allowed us to define regions common to the 6 cell lines. These replication timing data can be taken into account when performing studies that use these model cell lines.

  7. Difference-based clustering of short time-course microarray data with replicates

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    Kim Jihoon

    2007-07-01

    Full Text Available Abstract Background There are some limitations associated with conventional clustering methods for short time-course gene expression data. The current algorithms require prior domain knowledge and do not incorporate information from replicates. Moreover, the results are not always easy to interpret biologically. Results We propose a novel algorithm for identifying a subset of genes sharing a significant temporal expression pattern when replicates are used. Our algorithm requires no prior knowledge, instead relying on an observed statistic which is based on the first and second order differences between adjacent time-points. Here, a pattern is predefined as the sequence of symbols indicating direction and the rate of change between time-points, and each gene is assigned to a cluster whose members share a similar pattern. We evaluated the performance of our algorithm to those of K-means, Self-Organizing Map and the Short Time-series Expression Miner methods. Conclusions Assessments using simulated and real data show that our method outperformed aforementioned algorithms. Our approach is an appropriate solution for clustering short time-course microarray data with replicates.

  8. Identifying significant temporal variation in time course microarray data without replicates

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    Porter Weston

    2009-03-01

    Full Text Available Abstract Background An important component of time course microarray studies is the identification of genes that demonstrate significant time-dependent variation in their expression levels. Until recently, available methods for performing such significance tests required replicates of individual time points. This paper describes a replicate-free method that was developed as part of a study of the estrous cycle in the rat mammary gland in which no replicate data was collected. Results A temporal test statistic is proposed that is based on the degree to which data are smoothed when fit by a spline function. An algorithm is presented that uses this test statistic together with a false discovery rate method to identify genes whose expression profiles exhibit significant temporal variation. The algorithm is tested on simulated data, and is compared with another recently published replicate-free method. The simulated data consists both of genes with known temporal dependencies, and genes from a null distribution. The proposed algorithm identifies a larger percentage of the time-dependent genes for a given false discovery rate. Use of the algorithm in a study of the estrous cycle in the rat mammary gland resulted in the identification of genes exhibiting distinct circadian variation. These results were confirmed in follow-up laboratory experiments. Conclusion The proposed algorithm provides a new approach for identifying expression profiles with significant temporal variation without relying on replicates. When compared with a recently published algorithm on simulated data, the proposed algorithm appears to identify a larger percentage of time-dependent genes for a given false discovery rate. The development of the algorithm was instrumental in revealing the presence of circadian variation in the virgin rat mammary gland during the estrous cycle.

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

    Science.gov (United States)

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

    2002-11-01

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

  10. Timing, coordination, and rhythm: Acrobatics at the DNA replication fork

    KAUST Repository

    Hamdan, Samir

    2010-04-09

    In DNA replication, the antiparallel nature of the parental duplex imposes certain constraints on the activity of the DNA polymerases that synthesize new DNA. The leading-strand polymerase advances in a continuous fashion, but the lagging-strand polymerase is forced to restart at short intervals. In several prokaryotic systems studied so far, this problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. The timing of Okazaki fragment synthesis and loop formation is determined by a subtle interplay of enzymatic activities at the fork. Recent developments in single-molecule techniques have enabled the direct observation of these processes and have greatly contributed to a better understanding of the dynamic nature of the replication fork. Here, we will review recent experimental advances, present the current models, and discuss some of the exciting developments in the field. 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Timing, coordination, and rhythm: Acrobatics at the DNA replication fork

    KAUST Repository

    Hamdan, Samir; van Oijen, Antoine M.

    2010-01-01

    In DNA replication, the antiparallel nature of the parental duplex imposes certain constraints on the activity of the DNA polymerases that synthesize new DNA. The leading-strand polymerase advances in a continuous fashion, but the lagging-strand polymerase is forced to restart at short intervals. In several prokaryotic systems studied so far, this problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. The timing of Okazaki fragment synthesis and loop formation is determined by a subtle interplay of enzymatic activities at the fork. Recent developments in single-molecule techniques have enabled the direct observation of these processes and have greatly contributed to a better understanding of the dynamic nature of the replication fork. Here, we will review recent experimental advances, present the current models, and discuss some of the exciting developments in the field. 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Real-time single-molecule observation of rolling-circle DNA replication

    NARCIS (Netherlands)

    Tanner, Nathan A.; Loparo, Joseph J.; Hamdan, Samir M.; Jergic, Slobodan; Dixon, Nicholas E.; Oijen, Antoine M. van

    2009-01-01

    We present a simple technique for visualizing replication of individual DNA molecules in real time. By attaching a rolling-circle substrate to a TIRF microscope-mounted flow chamber, we are able to monitor the progression of single-DNA synthesis events and accurately measure rates and processivities

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

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

    2007-09-01

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

  14. Centromere replication timing determines different forms of genomic instability in Saccharomyces cerevisiae checkpoint mutants during replication stress.

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    Feng, Wenyi; Bachant, Jeff; Collingwood, David; Raghuraman, M K; Brewer, Bonita J

    2009-12-01

    Yeast replication checkpoint mutants lose viability following transient exposure to hydroxyurea, a replication-impeding drug. In an effort to understand the basis for this lethality, we discovered that different events are responsible for inviability in checkpoint-deficient cells harboring mutations in the mec1 and rad53 genes. By monitoring genomewide replication dynamics of cells exposed to hydroxyurea, we show that cells with a checkpoint deficient allele of RAD53, rad53K227A, fail to duplicate centromeres. Following removal of the drug, however, rad53K227A cells recover substantial DNA replication, including replication through centromeres. Despite this recovery, the rad53K227A mutant fails to achieve biorientation of sister centromeres during recovery from hydroxyurea, leading to secondary activation of the spindle assembly checkpoint (SAC), aneuploidy, and lethal chromosome segregation errors. We demonstrate that cell lethality from this segregation defect could be partially remedied by reinforcing bipolar attachment. In contrast, cells with the mec1-1 sml1-1 mutations suffer from severely impaired replication resumption upon removal of hydroxyurea. mec1-1 sml1-1 cells can, however, duplicate at least some of their centromeres and achieve bipolar attachment, leading to abortive segregation and fragmentation of incompletely replicated chromosomes. Our results highlight the importance of replicating yeast centromeres early and reveal different mechanisms of cell death due to differences in replication fork progression.

  15. De novo identification of replication-timing domains in the human genome by deep learning.

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    Liu, Feng; Ren, Chao; Li, Hao; Zhou, Pingkun; Bo, Xiaochen; Shu, Wenjie

    2016-03-01

    The de novo identification of the initiation and termination zones-regions that replicate earlier or later than their upstream and downstream neighbours, respectively-remains a key challenge in DNA replication. Building on advances in deep learning, we developed a novel hybrid architecture combining a pre-trained, deep neural network and a hidden Markov model (DNN-HMM) for the de novo identification of replication domains using replication timing profiles. Our results demonstrate that DNN-HMM can significantly outperform strong, discriminatively trained Gaussian mixture model-HMM (GMM-HMM) systems and other six reported methods that can be applied to this challenge. We applied our trained DNN-HMM to identify distinct replication domain types, namely the early replication domain (ERD), the down transition zone (DTZ), the late replication domain (LRD) and the up transition zone (UTZ), using newly replicated DNA sequencing (Repli-Seq) data across 15 human cells. A subsequent integrative analysis revealed that these replication domains harbour unique genomic and epigenetic patterns, transcriptional activity and higher-order chromosomal structure. Our findings support the 'replication-domain' model, which states (1) that ERDs and LRDs, connected by UTZs and DTZs, are spatially compartmentalized structural and functional units of higher-order chromosomal structure, (2) that the adjacent DTZ-UTZ pairs form chromatin loops and (3) that intra-interactions within ERDs and LRDs tend to be short-range and long-range, respectively. Our model reveals an important chromatin organizational principle of the human genome and represents a critical step towards understanding the mechanisms regulating replication timing. Our DNN-HMM method and three additional algorithms can be freely accessed at https://github.com/wenjiegroup/DNN-HMM The replication domain regions identified in this study are available in GEO under the accession ID GSE53984. shuwj@bmi.ac.cn or boxc

  16. Analysis of Turbulent Combustion in Simplified Stratified Charge Conditions

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    Moriyoshi, Yasuo; Morikawa, Hideaki; Komatsu, Eiji

    The stratified charge combustion system has been widely studied due to the significant potentials for low fuel consumption rate and low exhaust gas emissions. The fuel-air mixture formation process in a direct-injection stratified charge engine is influenced by various parameters, such as atomization, evaporation, and in-cylinder gas motion at high temperature and high pressure conditions. It is difficult to observe the in-cylinder phenomena in such conditions and also challenging to analyze the following stratified charge combustion. Therefore, the combustion phenomena in simplified stratified charge conditions aiming to analyze the fundamental stratified charge combustion are examined. That is, an experimental apparatus which can control the mixture distribution and the gas motion at ignition timing was developed, and the effects of turbulence intensity, mixture concentration distribution, and mixture composition on stratified charge combustion were examined. As a result, the effects of fuel, charge stratification, and turbulence on combustion characteristics were clarified.

  17. The ESS and replicator equation in matrix games under time constraints.

    Science.gov (United States)

    Garay, József; Cressman, Ross; Móri, Tamás F; Varga, Tamás

    2018-06-01

    Recently, we introduced the class of matrix games under time constraints and characterized the concept of (monomorphic) evolutionarily stable strategy (ESS) in them. We are now interested in how the ESS is related to the existence and stability of equilibria for polymorphic populations. We point out that, although the ESS may no longer be a polymorphic equilibrium, there is a connection between them. Specifically, the polymorphic state at which the average strategy of the active individuals in the population is equal to the ESS is an equilibrium of the polymorphic model. Moreover, in the case when there are only two pure strategies, a polymorphic equilibrium is locally asymptotically stable under the replicator equation for the pure-strategy polymorphic model if and only if it corresponds to an ESS. Finally, we prove that a strict Nash equilibrium is a pure-strategy ESS that is a locally asymptotically stable equilibrium of the replicator equation in n-strategy time-constrained matrix games.

  18. High-resolution time-resolved Experiments on mixing and entrainment of buoyant jets in stratified environments

    Energy Technology Data Exchange (ETDEWEB)

    Manera, Annalisa; Bardet, Philippe; Petrov, Victor

    2018-03-29

    Fluid jets interacting with a stratified layer play an important role in the safety of several reactor designs. In the containment of nuclear power plants, fluid jets dominate the transport and mixing of gaseous species and consequent hydrogen distribution in case of a severe accident. The mixing phenomena in the containment are driven by buoyant high-momentum injections (jets) and low momentum injection plumes. Mixing near the postulated break is initially dominated by high flow velocities. Plumes with moderate flow velocities are instead relevant in the break compartment during the long-term pressurization phase, or in any of the apertures between two connected compartments if the mass flows are sufficiently high and the density differences between efflux and ambient are sufficiently low. Phenomena of interest include free plumes (as produced by the efflux from the break compartment in a larger room or directly from a break flow), wall plumes (such those produced by low mass flows through inter-compartment apertures), and propagating stratification fronts in the ambient (for any stably stratified conditions). These phenomena have been highly ranked about nuclear reactor design, especially regarding of safety protocols. During a Pressurized Thermal Shock (PTS) scenario, the interaction between the cold ECCS injection plume and the stratified fluid present in the cold (or hot) leg is important in order to determine the temperature at the time-dependent temperature at the inlet of the reactor pressure vessel (RPV) and the potential to cause a thermal shock on the RPV wall. In sodium-cooled fast reactors (SFRs), core channels are typically hydro-dynamically isolated so that there exists a considerable temperature variation at the exit of adjacent fuel assemblies. All the above phenomena are characterized by the interaction of buoyant jets with the stratified flow. In stratified layers baroclinic forces create significant redistribution of turbulent kinetic energy and

  19. 'Stratified Contraception': Emergency Contraceptive Pills and Women's Differential Experiences in Contemporary India.

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    Sheoran, Nayantara

    2015-01-01

    Available without prescriptions in India since 2005, emergency contraceptive pills (ECPs) and their advertisements have provided women with increased contraceptive options and a vocabulary to talk about their reproductive lives. I draw on long-term fieldwork with women in urban India about ECPs, demonstrating a new form of 'stratified contraception' enabled by these pills and their advertisements. I posit that there are within India spaces that replicate the luxuries and privileges of the global North. These material conditions, I suggest, are replicated when it comes to contraception as there are hubs of women consumers of contraception and contraceptive advertising that participate in an 'imagined cosmopolitanism' within the global South in close proximity to 'contraceptive ghettos.' Moving beyond simplistic binaries, I outline three major stratifications along which women experience this medical technology and outline the implications for women and their contraceptive choices when notions of northern privilege exist in the 'South.'

  20. 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...

  1. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates.

    Science.gov (United States)

    Xia, Li C; Steele, Joshua A; Cram, Jacob A; Cardon, Zoe G; Simmons, Sheri L; Vallino, Joseph J; Fuhrman, Jed A; Sun, Fengzhu

    2011-01-01

    The increasing availability of time series microbial community data from metagenomics and other molecular biological studies has enabled the analysis of large-scale microbial co-occurrence and association networks. Among the many analytical techniques available, the Local Similarity Analysis (LSA) method is unique in that it captures local and potentially time-delayed co-occurrence and association patterns in time series data that cannot otherwise be identified by ordinary correlation analysis. However LSA, as originally developed, does not consider time series data with replicates, which hinders the full exploitation of available information. With replicates, it is possible to understand the variability of local similarity (LS) score and to obtain its confidence interval. We extended our LSA technique to time series data with replicates and termed it extended LSA, or eLSA. Simulations showed the capability of eLSA to capture subinterval and time-delayed associations. We implemented the eLSA technique into an easy-to-use analytic software package. The software pipeline integrates data normalization, statistical correlation calculation, statistical significance evaluation, and association network construction steps. We applied the eLSA technique to microbial community and gene expression datasets, where unique time-dependent associations were identified. The extended LSA analysis technique was demonstrated to reveal statistically significant local and potentially time-delayed association patterns in replicated time series data beyond that of ordinary correlation analysis. These statistically significant associations can provide insights to the real dynamics of biological systems. The newly designed eLSA software efficiently streamlines the analysis and is freely available from the eLSA homepage, which can be accessed at http://meta.usc.edu/softs/lsa.

  2. Risk Factors for Emergency Department Short Time Readmission in Stratified Population

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    Ariadna Besga

    2015-01-01

    Full Text Available Background. Emergency department (ED readmissions are considered an indicator of healthcare quality that is particularly relevant in older adults. The primary objective of this study was to identify key factors for predicting patients returning to the ED within 30 days of being discharged. Methods. We analysed patients who attended our ED in June 2014, stratified into four groups based on the Kaiser pyramid. We collected data on more than 100 variables per case including demographic and clinical characteristics and drug treatments. We identified the variables with the highest discriminating power to predict ED readmission and constructed classifiers using machine learning methods to provide predictions. Results. Classifier performance distinguishing between patients who were and were not readmitted (within 30 days, in terms of average accuracy (AC. The variables with the greatest discriminating power were age, comorbidity, reasons for consultation, social factors, and drug treatments. Conclusions. It is possible to predict readmissions in stratified groups with high accuracy and to identify the most important factors influencing the event. Therefore, it will be possible to develop interventions to improve the quality of care provided to ED patients.

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  4. Evaluation of the minimal replication time of Cauliflower mosaic virus in different hosts

    International Nuclear Information System (INIS)

    Khelifa, Mounia; Masse, Delphine; Blanc, Stephane; Drucker, Martin

    2010-01-01

    Though the duration of a single round of replication is an important biological parameter, it has been determined for only few viruses. Here, this parameter was determined for Cauliflower mosaic virus (CaMV) in transfected protoplasts from different hosts: the highly susceptible Arabidopsis and turnip, and Nicotiana benthamiana, where CaMV accumulates only slowly. Four methods of differing sensitivity were employed: labelling of (1) progeny DNA and (2) capsid protein, (3) immunocapture PCR,, and (4) progeny-specific PCR. The first progeny virus was detected about 21 h after transfection. This value was confirmed by all methods, indicating that our estimate was not biased by the sensitivity of the detection method, and approximated the actual time required for one round of CaMV replication. Unexpectedly, the replication kinetics were similar in the three hosts; suggesting that slow accumulation of CaMV in Nicotiana plants is determined by non-optimal interactions in other steps of the infection cycle.

  5. 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.

  6. The AGIS metric and time of test: A replication study

    OpenAIRE

    Counsell, S; Swift, S; Tucker, A

    2016-01-01

    Visual Field (VF) tests and corresponding data are commonly used in clinical practices to manage glaucoma. The standard metric used to measure glaucoma severity is the Advanced Glaucoma Intervention Studies (AGIS) metric. We know that time of day when VF tests are applied can influence a patient’s AGIS metric value; a previous study showed that this was the case for a data set of 160 patients. In this paper, we replicate that study using data from 2468 patients obtained from Moorfields Eye Ho...

  7. DNA replication timing is maintained genome-wide in primary human myoblasts independent of D4Z4 contraction in FSH muscular dystrophy.

    Directory of Open Access Journals (Sweden)

    Benjamin D Pope

    Full Text Available Facioscapulohumeral muscular dystrophy (FSHD is linked to contraction of an array of tandem 3.3-kb repeats (D4Z4 at 4q35.2 from 11-100 copies to 1-10 copies. The extent to which D4Z4 contraction at 4q35.2 affects overall 4q35.2 chromatin organization remains unclear. Because DNA replication timing is highly predictive of long-range chromatin interactions, we generated genome-wide replication-timing profiles for FSHD and control myogenic precursor cells. We compared non-immortalized myoblasts from four FSHD patients and three control individuals to each other and to a variety of other human cell types. This study also represents the first genome-wide comparison of replication timing profiles in non-immortalized human cell cultures. Myoblasts from both control and FSHD individuals all shared a myoblast-specific replication profile. In contrast, male and female individuals were readily distinguished by monoallelic differences in replication timing at DXZ4 and other regions across the X chromosome affected by X inactivation. We conclude that replication timing is a robust cell-type specific feature that is unaffected by FSHD-related D4Z4 contraction.

  8. Timing of host feeding drives rhythms in parasite replication

    KAUST Repository

    Prior, Kimberley F.

    2018-02-26

    Circadian rhythms enable organisms to synchronise the processes underpinning survival and reproduction to anticipate daily changes in the external environment. Recent work shows that daily (circadian) rhythms also enable parasites to maximise fitness in the context of ecological interactions with their hosts. Because parasite rhythms matter for their fitness, understanding how they are regulated could lead to innovative ways to reduce the severity and spread of diseases. Here, we examine how host circadian rhythms influence rhythms in the asexual replication of malaria parasites. Asexual replication is responsible for the severity of malaria and fuels transmission of the disease, yet, how parasite rhythms are driven remains a mystery. We perturbed feeding rhythms of hosts by 12 hours (i.e. diurnal feeding in nocturnal mice) to desynchronise the host’s peripheral oscillators from the central, light-entrained oscillator in the brain and their rhythmic outputs. We demonstrate that the rhythms of rodent malaria parasites in day-fed hosts become inverted relative to the rhythms of parasites in night-fed hosts. Our results reveal that the host’s peripheral rhythms (associated with the timing of feeding and metabolism), but not rhythms driven by the central, light-entrained circadian oscillator in the brain, determine the timing (phase) of parasite rhythms. Further investigation reveals that parasite rhythms correlate closely with blood glucose rhythms. In addition, we show that parasite rhythms resynchronise to the altered host feeding rhythms when food availability is shifted, which is not mediated through rhythms in the host immune system. Our observations suggest that parasites actively control their developmental rhythms. Finally, counter to expectation, the severity of disease symptoms expressed by hosts was not affected by desynchronisation of their central and peripheral rhythms. Our study at the intersection of disease ecology and chronobiology opens up a new

  9. Timing of host feeding drives rhythms in parasite replication

    KAUST Repository

    Prior, Kimberley F

    2017-12-07

    Circadian rhythms enable organisms to synchronise the processes underpinning survival and reproduction to anticipate daily changes in the external environment. Recent work shows that daily (circadian) rhythms also enable parasites to maximise fitness in the context of ecological interactions with their hosts. Because parasite rhythms matter for their fitness, understanding how they are regulated could lead to innovative ways to reduce the severity and spread of diseases. Here, we examine how host circadian rhythms influence rhythms in the asexual replication of malaria parasites. Asexual replication is responsible for the severity of malaria and fuels transmission of the disease, yet, how parasite rhythms are driven remains a mystery. We perturbed feeding rhythms of hosts by 12 hours (i.e. diurnal feeding in nocturnal mice) to desynchronise the host\\'s peripheral oscillators from the central, light-entrained oscillator in the brain and their rhythmic outputs. We demonstrate that the rhythms of rodent malaria parasites in day-fed hosts become inverted relative to the rhythms of parasites in night-fed hosts. Our results reveal that the host\\'s peripheral rhythms (associated with the timing of feeding and metabolism), but not rhythms driven by the central, light-entrained circadian oscillator in the brain, determine the timing (phase) of parasite rhythms. Further investigation reveals that parasite rhythms correlate closely with blood glucose rhythms. In addition, we show that parasite rhythms resynchronise to the altered host feeding rhythms when food availability is shifted, which is not mediated through rhythms in the host immune system. Our observations suggest that parasites actively control their developmental rhythms. Finally, counter to expectation, the severity of disease symptoms expressed by hosts was not affected by desynchronisation of their central and peripheral rhythms. Our study at the intersection of disease ecology and chronobiology opens up a new

  10. Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters.

    Science.gov (United States)

    Hensman, James; Lawrence, Neil D; Rattray, Magnus

    2013-08-20

    Time course data from microarrays and high-throughput sequencing experiments require simple, computationally efficient and powerful statistical models to extract meaningful biological signal, and for tasks such as data fusion and clustering. Existing methodologies fail to capture either the temporal or replicated nature of the experiments, and often impose constraints on the data collection process, such as regularly spaced samples, or similar sampling schema across replications. We propose hierarchical Gaussian processes as a general model of gene expression time-series, with application to a variety of problems. In particular, we illustrate the method's capacity for missing data imputation, data fusion and clustering.The method can impute data which is missing both systematically and at random: in a hold-out test on real data, performance is significantly better than commonly used imputation methods. The method's ability to model inter- and intra-cluster variance leads to more biologically meaningful clusters. The approach removes the necessity for evenly spaced samples, an advantage illustrated on a developmental Drosophila dataset with irregular replications. The hierarchical Gaussian process model provides an excellent statistical basis for several gene-expression time-series tasks. It has only a few additional parameters over a regular GP, has negligible additional complexity, is easily implemented and can be integrated into several existing algorithms. Our experiments were implemented in python, and are available from the authors' website: http://staffwww.dcs.shef.ac.uk/people/J.Hensman/.

  11. Two-phase air-water stratified flow measurement using ultrasonic techniques

    International Nuclear Information System (INIS)

    Fan, Shiwei; Yan, Tinghu; Yeung, Hoi

    2014-01-01

    In this paper, a time resolved ultrasound system was developed for investigating two-phase air-water stratified flow. The hardware of the system includes a pulsed wave transducer, a pulser/receiver, and a digital oscilloscope. The time domain cross correlation method is used to calculate the velocity profile along ultrasonic beam. The system is able to provide velocities with spatial resolution of around 1mm and the temporal resolution of 200μs. Experiments were carried out on single phase water flow and two-phase air-water stratified flow. For single phase water flow, the flow rates from ultrasound system were compared with those from electromagnetic flow (EM) meter, which showed good agreement. Then, the experiments were conducted on two-phase air-water stratified flow and the results were given. Compared with liquid height measurement from conductance probe, it indicated that the measured velocities were explainable

  12. 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.

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

    Science.gov (United States)

    Smith, Owen K.; Aladjem, Mirit I.

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Michelle Hawkins

    2013-11-01

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

  15. Free Falling in Stratified Fluids

    Science.gov (United States)

    Lam, Try; Vincent, Lionel; Kanso, Eva

    2017-11-01

    Leaves falling in air and discs falling in water are examples of unsteady descents due to complex interaction between gravitational and aerodynamic forces. Understanding these descent modes is relevant to many branches of engineering and science such as estimating the behavior of re-entry space vehicles to studying biomechanics of seed dispersion. For regularly shaped objects falling in homogenous fluids, the motion is relatively well understood. However, less is known about how density stratification of the fluid medium affects the falling behavior. Here, we experimentally investigate the descent of discs in both pure water and in stable linearly stratified fluids for Froude numbers Fr 1 and Reynolds numbers Re between 1000 -2000. We found that stable stratification (1) enhances the radial dispersion of the disc at landing, (2) increases the descent time, (3) decreases the inclination (or nutation) angle, and (4) decreases the fluttering amplitude while falling. We conclude by commenting on how the corresponding information can be used as a predictive model for objects free falling in stratified fluids.

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

    Science.gov (United States)

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

    2016-10-21

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

  17. Design Optimization of Time- and Cost-Constrained Fault-Tolerant Embedded Systems with Checkpointing and Replication

    DEFF Research Database (Denmark)

    Pop, Paul; Izosimov, Viacheslav; Eles, Petru

    2009-01-01

    We present an approach to the synthesis of fault-tolerant hard real-time systems for safety-critical applications. We use checkpointing with rollback recovery and active replication for tolerating transient faults. Processes and communications are statically scheduled. Our synthesis approach deci...

  18. AN INVESTIGATION OF TIME LAG MAPS USING THREE-DIMENSIONAL SIMULATIONS OF HIGHLY STRATIFIED HEATING

    Energy Technology Data Exchange (ETDEWEB)

    Winebarger, Amy R. [NASA Marshall Space Flight Center, ZP 13, Huntsville, AL 35812 (United States); Lionello, Roberto; Downs, Cooper; Mikić, Zoran; Linker, Jon [Predictive Science, Inc., 9990 Mesa Rim Rd., Ste. 170, San Diego, CA 92121-2910 (United States); Mok, Yung, E-mail: amy.r.winebarger@nasa.gov, E-mail: lionel@predsci.com, E-mail: cdowns@predsci.com, E-mail: mikicz@predsci.com, E-mail: linkerj@predsci.com, E-mail: ymok@uci.edu [Department of Physics and Astronomy, University of California, Irvine, CA 92697 (United States)

    2016-11-10

    The location and frequency of coronal energy release provide a significant constraint on the coronal heating mechanism. The evolution of the intensity observed in coronal structures found from time lag analysis of Atmospheric Imaging Assembly (AIA) data has been used to argue that heating must occur sporadically. Recently, we have demonstrated that quasi-steady, highly stratified (footpoint) heating can produce results qualitatively consistent with the evolution of observed coronal structures. The goals of this paper are to demonstrate that time lag analysis of 3D simulations of footpoint heating are qualitatively consistent with time lag analysis of observations and to use the 3D simulations to further understand whether time lag analysis is a useful tool in defining the evolution of coronal structures. We find the time lag maps generated from simulated data are consistent with the observed time lag maps. We next investigate several example points. In some cases, the calculated time lag reflects the evolution of a unique loop along the line of sight, though there may be additional evolving structures along the line of sight. We confirm that using the multi-peak AIA channels can produce time lags that are difficult to interpret. We suggest using a different high temperature channel, such as an X-ray channel. Finally, we find that multiple evolving structures along the line of sight can produce time lags that do not represent the physical properties of any structure along the line of sight, although the cross-correlation coefficient of the lightcurves is high. Considering the projected geometry of the loops may reduce some of the line-of-sight confusion.

  19. Computing the transport time scales of a stratified lake on the basis of Tonolli’s model

    Directory of Open Access Journals (Sweden)

    Marco Pilotti

    2014-05-01

    Full Text Available This paper deals with a simple model to evaluate the transport time scales in thermally stratified lakes that do not necessarily completely mix on a regular annual basis. The model is based on the formalization of an idea originally proposed in Italian by Tonolli in 1964, who presented a mass balance of the water initially stored within a lake, taking into account the known seasonal evolution of its thermal structure. The numerical solution of this mass balance provides an approximation to the water age distribution for the conceptualised lake, from which an upper bound to the typical time scales widely used in limnology can be obtained. After discussing the original test case considered by Tonolli, we apply the model to Lake Iseo, a deep lake located in the North of Italy, presenting the results obtained on the basis of a 30 year series of data.

  20. Design of dry sand soil stratified sampler

    Science.gov (United States)

    Li, Erkang; Chen, Wei; Feng, Xiao; Liao, Hongbo; Liang, Xiaodong

    2018-04-01

    This paper presents a design of a stratified sampler for dry sand soil, which can be used for stratified sampling of loose sand under certain conditions. Our group designed the mechanical structure of a portable, single - person, dry sandy soil stratified sampler. We have set up a mathematical model for the sampler. It lays the foundation for further development of design research.

  1. 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...

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

    Science.gov (United States)

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

    2013-11-06

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

  3. 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.

  4. Fixed-location hydroacoustic monitoring designs for estimating fish passage using stratified random and systematic sampling

    International Nuclear Information System (INIS)

    Skalski, J.R.; Hoffman, A.; Ransom, B.H.; Steig, T.W.

    1993-01-01

    Five alternate sampling designs are compared using 15 d of 24-h continuous hydroacoustic data to identify the most favorable approach to fixed-location hydroacoustic monitoring of salmonid outmigrants. Four alternative aproaches to systematic sampling are compared among themselves and with stratified random sampling (STRS). Stratifying systematic sampling (STSYS) on a daily basis is found to reduce sampling error in multiday monitoring studies. Although sampling precision was predictable with varying levels of effort in STRS, neither magnitude nor direction of change in precision was predictable when effort was varied in systematic sampling (SYS). Furthermore, modifying systematic sampling to include replicated (e.g., nested) sampling (RSYS) is further shown to provide unbiased point and variance estimates as does STRS. Numerous short sampling intervals (e.g., 12 samples of 1-min duration per hour) must be monitored hourly using RSYS to provide efficient, unbiased point and interval estimates. For equal levels of effort, STRS outperformed all variations of SYS examined. Parametric approaches to confidence interval estimates are found to be superior to nonparametric interval estimates (i.e., bootstrap and jackknife) in estimating total fish passage. 10 refs., 1 fig., 8 tabs

  5. Information content of household-stratified epidemics

    Directory of Open Access Journals (Sweden)

    T.M. Kinyanjui

    2016-09-01

    Full Text Available Household structure is a key driver of many infectious diseases, as well as a natural target for interventions such as vaccination programs. Many theoretical and conceptual advances on household-stratified epidemic models are relatively recent, but have successfully managed to increase the applicability of such models to practical problems. To be of maximum realism and hence benefit, they require parameterisation from epidemiological data, and while household-stratified final size data has been the traditional source, increasingly time-series infection data from households are becoming available. This paper is concerned with the design of studies aimed at collecting time-series epidemic data in order to maximize the amount of information available to calibrate household models. A design decision involves a trade-off between the number of households to enrol and the sampling frequency. Two commonly used epidemiological study designs are considered: cross-sectional, where different households are sampled at every time point, and cohort, where the same households are followed over the course of the study period. The search for an optimal design uses Bayesian computationally intensive methods to explore the joint parameter-design space combined with the Shannon entropy of the posteriors to estimate the amount of information in each design. For the cross-sectional design, the amount of information increases with the sampling intensity, i.e., the designs with the highest number of time points have the most information. On the other hand, the cohort design often exhibits a trade-off between the number of households sampled and the intensity of follow-up. Our results broadly support the choices made in existing epidemiological data collection studies. Prospective problem-specific use of our computational methods can bring significant benefits in guiding future study designs.

  6. Information content of household-stratified epidemics.

    Science.gov (United States)

    Kinyanjui, T M; Pellis, L; House, T

    2016-09-01

    Household structure is a key driver of many infectious diseases, as well as a natural target for interventions such as vaccination programs. Many theoretical and conceptual advances on household-stratified epidemic models are relatively recent, but have successfully managed to increase the applicability of such models to practical problems. To be of maximum realism and hence benefit, they require parameterisation from epidemiological data, and while household-stratified final size data has been the traditional source, increasingly time-series infection data from households are becoming available. This paper is concerned with the design of studies aimed at collecting time-series epidemic data in order to maximize the amount of information available to calibrate household models. A design decision involves a trade-off between the number of households to enrol and the sampling frequency. Two commonly used epidemiological study designs are considered: cross-sectional, where different households are sampled at every time point, and cohort, where the same households are followed over the course of the study period. The search for an optimal design uses Bayesian computationally intensive methods to explore the joint parameter-design space combined with the Shannon entropy of the posteriors to estimate the amount of information in each design. For the cross-sectional design, the amount of information increases with the sampling intensity, i.e., the designs with the highest number of time points have the most information. On the other hand, the cohort design often exhibits a trade-off between the number of households sampled and the intensity of follow-up. Our results broadly support the choices made in existing epidemiological data collection studies. Prospective problem-specific use of our computational methods can bring significant benefits in guiding future study designs. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  7. The effect of surfactant on stratified and stratifying gas-liquid flows

    Science.gov (United States)

    Heiles, Baptiste; Zadrazil, Ivan; Matar, Omar

    2013-11-01

    We consider the dynamics of a stratified/stratifying gas-liquid flow in horizontal tubes. This flow regime is characterised by the thin liquid films that drain under gravity along the pipe interior, forming a pool at the bottom of the tube, and the formation of large-amplitude waves at the gas-liquid interface. This regime is also accompanied by the detachment of droplets from the interface and their entrainment into the gas phase. We carry out an experimental study involving axial- and radial-view photography of the flow, in the presence and absence of surfactant. We show that the effect of surfactant is to reduce significantly the average diameter of the entrained droplets, through a tip-streaming mechanism. We also highlight the influence of surfactant on the characteristics of the interfacial waves, and the pressure gradient that drives the flow. EPSRC Programme Grant EP/K003976/1.

  8. Electromagnetic waves in stratified media

    CERN Document Server

    Wait, James R; Fock, V A; Wait, J R

    2013-01-01

    International Series of Monographs in Electromagnetic Waves, Volume 3: Electromagnetic Waves in Stratified Media provides information pertinent to the electromagnetic waves in media whose properties differ in one particular direction. This book discusses the important feature of the waves that enables communications at global distances. Organized into 13 chapters, this volume begins with an overview of the general analysis for the electromagnetic response of a plane stratified medium comprising of any number of parallel homogeneous layers. This text then explains the reflection of electromagne

  9. Spatio-temporal re-organization of replication foci accompanies replication domain consolidation during human pluripotent stem cell lineage specification

    Science.gov (United States)

    Wilson, Korey A.; Elefanty, Andrew G.; Stanley, Edouard G.; Gilbert, David M.

    2016-01-01

    ABSTRACT Lineage specification of both mouse and human pluripotent stem cells (PSCs) is accompanied by spatial consolidation of chromosome domains and temporal consolidation of their replication timing. Replication timing and chromatin organization are both established during G1 phase at the timing decision point (TDP). Here, we have developed live cell imaging tools to track spatio-temporal replication domain consolidation during differentiation. First, we demonstrate that the fluorescence ubiquitination cell cycle indicator (Fucci) system is incapable of demarcating G1/S or G2/M cell cycle transitions. Instead, we employ a combination of fluorescent PCNA to monitor S phase progression, cytokinesis to demarcate mitosis, and fluorescent nucleotides to label early and late replication foci and track their 3D organization into sub-nuclear chromatin compartments throughout all cell cycle transitions. We find that, as human PSCs differentiate, the length of S phase devoted to replication of spatially clustered replication foci increases, coincident with global compartmentalization of domains into temporally clustered blocks of chromatin. Importantly, re-localization and anchorage of domains was completed prior to the onset of S phase, even in the context of an abbreviated PSC G1 phase. This approach can also be employed to investigate cell fate transitions in single PSCs, which could be seen to differentiate preferentially from G1 phase. Together, our results establish real-time, live-cell imaging methods for tracking cell cycle transitions during human PSC differentiation that can be applied to study chromosome domain consolidation and other aspects of lineage specification. PMID:27433885

  10. Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

    NARCIS (Netherlands)

    Tanner, Nathan A.; Loparo, Joseph J.; Oijen, Antoine M. van

    2009-01-01

    We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides. The

  11. Rif1 acts through Protein Phosphatase 1 but independent of replication timing to suppress telomere extension in budding yeast.

    Science.gov (United States)

    Kedziora, Sylwia; Gali, Vamsi K; Wilson, Rosemary H C; Clark, Kate R M; Nieduszynski, Conrad A; Hiraga, Shin-Ichiro; Donaldson, Anne D

    2018-05-04

    The Rif1 protein negatively regulates telomeric TG repeat length in the budding yeast Saccharomyces cerevisiae, but how it prevents telomere over-extension is unknown. Rif1 was recently shown to control DNA replication by acting as a Protein Phosphatase 1 (PP1)-targeting subunit. Therefore, we investigated whether Rif1 controls telomere length by targeting PP1 activity. We find that a Rif1 mutant defective for PP1 interaction causes a long-telomere phenotype, similar to that of rif1Δ cells. Tethering PP1 at a specific telomere partially substitutes for Rif1 in limiting TG repeat length, confirming the importance of PP1 in telomere length control. Ablating Rif1-PP1 interaction is known to cause precocious activation of telomere-proximal replication origins and aberrantly early telomere replication. However, we find that Rif1 still limits telomere length even if late replication is forced through deletion of nearby replication origins, indicating that Rif1 can control telomere length independent of replication timing. Moreover we find that, even at a de novo telomere created after DNA synthesis during a mitotic block, Rif1-PP1 interaction is required to suppress telomere lengthening and prevent inappropriate recruitment of Tel1 kinase. Overall, our results show that Rif1 controls telomere length by recruiting PP1 to directly suppress telomerase-mediated TG repeat lengthening.

  12. Electrical resistance imaging of a time-varying interface in stratified flows using an unscented Kalman filter

    International Nuclear Information System (INIS)

    Ijaz, Umer Zeeshan; Khambampati, Anil Kumar; Kim, Kyung Youn; Chung, Soon Il; Kim, Sin

    2008-01-01

    In this paper, we estimate a time-varying interfacial boundary in stratified flows of two immiscible liquids using electrical resistance tomography. The interfacial boundary is approximated with front points spaced discretely along the interface. The design variables to be estimated are the locations of the front points, which are varying with the moving interface. The inverse problem is treated as a stochastic nonlinear state estimation problem with the nonstationary phase boundary (state) being estimated with the aid of an unscented Kalman filter. Numerical experiments are performed to evaluate the performance of an unscented Kalman filter. Specifically, a detailed analysis has been done on the effect of the number of front points and contrast ratio on the reconstruction performance. The reconstruction results show that an unscented Kalman filter is better suited for estimation in comparison to the conventional extended Kalman filter

  13. Turning the Hands of Time Again: A Purely Confirmatory Replication Study and a Bayesian Analysis

    Directory of Open Access Journals (Sweden)

    Eric-Jan eWagenmakers

    2015-04-01

    Full Text Available In a series of four experiments, Topolinski and Sparenberg (2012; TS found support for the conjecture that clockwise movements induce psychological states of temporal progression and an orientation toward the future and novelty. Here we report the results of a preregistered replication attempt of Experiment 2 from TS. Participants turned kitchen rolls either clockwise or counterclockwise while answering items from a questionnaire assessing openness to experience. Data from 102 participants showed that the effect went slightly in the direction opposite to that predicted by TS, and a preregistered Bayes factor hypothesis test revealed that the data were 10.76 times more likely under the null hypothesis than under the alternative hypothesis. Our findings illustrate the theoretical importance and practical advantages of preregistered Bayes factor replication studies, both for psychological science and for empirical work in general.

  14. DNA replication and post-replication repair in U.V.-sensitive mouse neuroblastoma cells

    International Nuclear Information System (INIS)

    Lavin, M.F.; McCombe, P.; Kidson, C.

    1976-01-01

    Mouse neuroblastoma cells differentiated when grown in the absence of serum; differentiation was reversed on the addition of serum. Differentiated cells were more sensitive to U.V.-radiation than proliferating cells. Whereas addition of serum to differentiated neuroblastoma cells normally resulted in immediate, synchronous entry into S phase, irradiation just before the addition of serum resulted in a long delay in the onset of DNA replication. During this lag period, incorporated 3 H-thymidine appeared in the light density region of CsCl gradients, reflecting either repair synthesis or abortive replication. Post-replication repair (gap-filling) was found to be present in proliferating cells and at certain times in differentiated cells. It is suggested that the sensitivity of differentiated neuroblastoma cells to U.V.-radiation may have been due to ineffective post-replication repair or to deficiencies in more than one repair mechanism, with reduction in repair capacity beyond a critical threshold. (author)

  15. The Inherent Asymmetry of DNA Replication.

    Science.gov (United States)

    Snedeker, Jonathan; Wooten, Matthew; Chen, Xin

    2017-10-06

    Semiconservative DNA replication has provided an elegant solution to the fundamental problem of how life is able to proliferate in a way that allows cells, organisms, and populations to survive and replicate many times over. Somewhat lost, however, in our admiration for this mechanism is an appreciation for the asymmetries that occur in the process of DNA replication. As we discuss in this review, these asymmetries arise as a consequence of the structure of the DNA molecule and the enzymatic mechanism of DNA synthesis. Increasing evidence suggests that asymmetries in DNA replication are able to play a central role in the processes of adaptation and evolution by shaping the mutagenic landscape of cells. Additionally, in eukaryotes, recent work has demonstrated that the inherent asymmetries in DNA replication may play an important role in the process of chromatin replication. As chromatin plays an essential role in defining cell identity, asymmetries generated during the process of DNA replication may play critical roles in cell fate decisions related to patterning and development.

  16. Analysis of photonic band-gap structures in stratified medium

    DEFF Research Database (Denmark)

    Tong, Ming-Sze; Yinchao, Chen; Lu, Yilong

    2005-01-01

    in electromagnetic and microwave applications once the Maxwell's equations are appropriately modeled. Originality/value - The method validates its values and properties through extensive studies on regular and defective 1D PBG structures in stratified medium, and it can be further extended to solving more......Purpose - To demonstrate the flexibility and advantages of a non-uniform pseudo-spectral time domain (nu-PSTD) method through studies of the wave propagation characteristics on photonic band-gap (PBG) structures in stratified medium Design/methodology/approach - A nu-PSTD method is proposed...... in solving the Maxwell's equations numerically. It expands the temporal derivatives using the finite differences, while it adopts the Fourier transform (FT) properties to expand the spatial derivatives in Maxwell's equations. In addition, the method makes use of the chain-rule property in calculus together...

  17. Therapeutic Assessment for Preadolescent Boys with Oppositional Defiant Disorder: A Replicated Single-Case Time-Series Design

    Science.gov (United States)

    Smith, Justin D.; Handler, Leonard; Nash, Michael R.

    2010-01-01

    The Therapeutic Assessment (TA) model is a relatively new treatment approach that fuses assessment and psychotherapy. The study examines the efficacy of this model with preadolescent boys with oppositional defiant disorder and their families. A replicated single-case time-series design with daily measures is used to assess the effects of TA and to…

  18. Identification of distinct layers within the stratified squamous epithelium of the adult human true vocal fold.

    Science.gov (United States)

    Dowdall, Jayme R; Sadow, Peter M; Hartnick, Christopher; Vinarsky, Vladimir; Mou, Hongmei; Zhao, Rui; Song, Phillip C; Franco, Ramon A; Rajagopal, Jayaraj

    2015-09-01

    A precise molecular schema for classifying the different cell types of the normal human vocal fold epithelium is lacking. We hypothesize that the true vocal fold epithelium has a cellular architecture and organization similar to that of other stratified squamous epithelia including the skin, cornea, oral mucosa, and esophagus. In analogy to disorders of the skin and gastrointestinal tract, a molecular definition of the normal cell types within the human vocal fold epithelium and a description of their geometric relationships should serve as a foundation for characterizing cellular changes associated with metaplasia, dysplasia, and cancer. Qualitative study with adult human larynges. Histologic sections of normal human laryngeal tissue were analyzed for morphology (hematoxylin and eosin) and immunohistochemical protein expression profile, including cytokeratins (CK13 and CK14), cornified envelope proteins (involucrin), basal cells (NGFR/p75), and proliferation markers (Ki67). We demonstrated that three distinct cell strata with unique marker profiles are present within the stratified squamous epithelium of the true vocal fold. We used these definitions to establish that cell proliferation is restricted to certain cell types and layers within the epithelium. These distinct cell types are reproducible across five normal adult larynges. We have established that three layers of cells are present within the normal adult stratified squamous epithelium of the true vocal fold. Furthermore, replicating cell populations are largely restricted to the parabasal strata within the epithelium. This delineation of distinct cell populations will facilitate future studies of vocal fold regeneration and cancer. N/A. © 2015 The American Laryngological, Rhinological and Otological Society, Inc.

  19. 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...

  20. 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 ...

  1. Grain distinct stratified nanolayers in aluminium alloys

    Energy Technology Data Exchange (ETDEWEB)

    Donatus, U., E-mail: uyimedonatus@yahoo.com [School of Materials, The University of Manchester, Manchester, M13 9PL, England (United Kingdom); Thompson, G.E.; Zhou, X.; Alias, J. [School of Materials, The University of Manchester, Manchester, M13 9PL, England (United Kingdom); Tsai, I.-L. [Oxford Instruments NanoAnalysis, HP12 2SE, High Wycombe (United Kingdom)

    2017-02-15

    The grains of aluminium alloys have stratified nanolayers which determine their mechanical and chemical responses. In this study, the nanolayers were revealed in the grains of AA6082 (T6 and T7 conditions), AA5083-O and AA2024-T3 alloys by etching the alloys in a solution comprising 20 g Cr{sub 2}O{sub 3} + 30 ml HPO{sub 3} in 1 L H{sub 2}O. Microstructural examination was conducted on selected grains of interest using scanning electron microscopy and electron backscatter diffraction technique. It was observed that the nanolayers are orientation dependent and are parallel to the {100} planes. They have ordered and repeated tunnel squares that are flawed at the sides which are aligned in the <100> directions. These flawed tunnel squares dictate the tunnelling corrosion morphology as well as appearing to have an affect on the arrangement and sizes of the precipitation hardening particles. The inclination of the stratified nanolayers, their interpacing, and the groove sizes have significant influence on the corrosion behaviour and seeming influence on the strengthening mechanism of the investigated aluminium alloys. - Highlights: • Stratified nanolayers in aluminium alloy grains. • Relationship of the stratified nanolayers with grain orientation. • Influence of the inclinations of the stratified nanolayers on corrosion. • Influence of the nanolayers interspacing and groove sizes on hardness and corrosion.

  2. Timely binding of IHF and Fis to DARS2 regulates ATP–DnaA production and replication initiation

    Science.gov (United States)

    Kasho, Kazutoshi; Fujimitsu, Kazuyuki; Matoba, Toshihiro; Oshima, Taku; Katayama, Tsutomu

    2014-01-01

    In Escherichia coli, the ATP-bound form of DnaA (ATP–DnaA) promotes replication initiation. During replication, the bound ATP is hydrolyzed to ADP to yield the ADP-bound form (ADP–DnaA), which is inactive for initiation. The chromosomal site DARS2 facilitates the regeneration of ATP–DnaA by catalyzing nucleotide exchange between free ATP and ADP bound to DnaA. However, the regulatory mechanisms governing this exchange reaction are unclear. Here, using in vitro reconstituted experiments, we show that two nucleoid-associated proteins, IHF and Fis, bind site-specifically to DARS2 to activate coordinately the exchange reaction. The regenerated ATP–DnaA was fully active in replication initiation and underwent DnaA–ATP hydrolysis. ADP–DnaA formed heteromultimeric complexes with IHF and Fis on DARS2, and underwent nucleotide dissociation more efficiently than ATP–DnaA. Consistently, mutant analyses demonstrated that specific binding of IHF and Fis to DARS2 stimulates the formation of ATP–DnaA production, thereby promoting timely initiation. Moreover, we show that IHF–DARS2 binding is temporally regulated during the cell cycle, whereas Fis only binds to DARS2 in exponentially growing cells. These results elucidate the regulation of ATP–DnaA and replication initiation in coordination with the cell cycle and growth phase. PMID:25378325

  3. Timely binding of IHF and Fis to DARS2 regulates ATP-DnaA production and replication initiation.

    Science.gov (United States)

    Kasho, Kazutoshi; Fujimitsu, Kazuyuki; Matoba, Toshihiro; Oshima, Taku; Katayama, Tsutomu

    2014-12-01

    In Escherichia coli, the ATP-bound form of DnaA (ATP-DnaA) promotes replication initiation. During replication, the bound ATP is hydrolyzed to ADP to yield the ADP-bound form (ADP-DnaA), which is inactive for initiation. The chromosomal site DARS2 facilitates the regeneration of ATP-DnaA by catalyzing nucleotide exchange between free ATP and ADP bound to DnaA. However, the regulatory mechanisms governing this exchange reaction are unclear. Here, using in vitro reconstituted experiments, we show that two nucleoid-associated proteins, IHF and Fis, bind site-specifically to DARS2 to activate coordinately the exchange reaction. The regenerated ATP-DnaA was fully active in replication initiation and underwent DnaA-ATP hydrolysis. ADP-DnaA formed heteromultimeric complexes with IHF and Fis on DARS2, and underwent nucleotide dissociation more efficiently than ATP-DnaA. Consistently, mutant analyses demonstrated that specific binding of IHF and Fis to DARS2 stimulates the formation of ATP-DnaA production, thereby promoting timely initiation. Moreover, we show that IHF-DARS2 binding is temporally regulated during the cell cycle, whereas Fis only binds to DARS2 in exponentially growing cells. These results elucidate the regulation of ATP-DnaA and replication initiation in coordination with the cell cycle and growth phase. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. 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...

  5. Random forcing of geostrophic motion in rotating stratified turbulence

    Science.gov (United States)

    Waite, Michael L.

    2017-12-01

    Random forcing of geostrophic motion is a common approach in idealized simulations of rotating stratified turbulence. Such forcing represents the injection of energy into large-scale balanced motion, and the resulting breakdown of quasi-geostrophic turbulence into inertia-gravity waves and stratified turbulence can shed light on the turbulent cascade processes of the atmospheric mesoscale. White noise forcing is commonly employed, which excites all frequencies equally, including frequencies much higher than the natural frequencies of large-scale vortices. In this paper, the effects of these high frequencies in the forcing are investigated. Geostrophic motion is randomly forced with red noise over a range of decorrelation time scales τ, from a few time steps to twice the large-scale vortex time scale. It is found that short τ (i.e., nearly white noise) results in about 46% more gravity wave energy than longer τ, despite the fact that waves are not directly forced. We argue that this effect is due to wave-vortex interactions, through which the high frequencies in the forcing are able to excite waves at their natural frequencies. It is concluded that white noise forcing should be avoided, even if it is only applied to the geostrophic motion, when a careful investigation of spontaneous wave generation is needed.

  6. The stratified H-index makes scientific impact transparent

    DEFF Research Database (Denmark)

    Würtz, Morten; Schmidt, Morten

    2017-01-01

    The H-index is widely used to quantify and standardize researchers' scientific impact. However, the H-index does not account for the fact that co-authors rarely contribute equally to a paper. Accordingly, we propose the use of a stratified H-index to measure scientific impact. The stratified H......-index supplements the conventional H-index with three separate H-indices: one for first authorships, one for second authorships and one for last authorships. The stratified H-index takes scientific output, quality and individual author contribution into account....

  7. 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....

  8. [Causes of emergency dizziness stratified by etiology].

    Science.gov (United States)

    Qiao, Wenying; Liu, Jianguo; Zeng, Hong; Liu, Yugeng; Jia, Weihua; Wang, Honghong; Liu, Bo; Tan, Jing; Li, Changqing

    2014-06-03

    To explore the causes of emergency dizziness stratified to improve the diagnostic efficiency. A total of 1 857 cases of dizziness at our emergency department were collected and their etiologies stratified by age and gender. The top three diagnoses were benign paroxysmal positional vertigo (BPPV, 31.7%), hypertension (24.0%) and posterior circulation ischemia (PCI, 20.5%). Stratified by age, the main causes of dizziness included BPPV (n = 6), migraine-associated vertigo (n = 2), unknown cause (n = 1) for the group of vertigo (14.5%) and neurosis (7.3%) for 18-44 years; BPPV (36.8%), hypertension (22.4%) and migraine-associated vertigo (11.2%) for 45-59 years; hypertension (30.8%), PCI (29.8%) and BPPV (22.9%) for 60-74 years; PCI (30.7%), hypertension (28.6%) and BPPV (25.5%) for 75-92 years. BPPV, migraine and neurosis were more common in females while hypertension and PCI predominated in males (all P hypertension, neurosis and migraine showed the following significant demographic features: BPPV, PCI, hypertension, neurosis and migraine may be the main causes of dizziness. BPPV should be considered initially when vertigo was triggered repeatedly by positional change, especially for young and middle-aged women. And the other common causes of dizziness were migraine-associated vertigo, neurosis and Meniere's disease.Hypertension should be screened firstly in middle-aged and elderly patients presenting mainly with head heaviness and stretching. In elders with dizziness, BPPV is second in constituent ratio to PCI and hypertension.In middle-aged and elderly patients with dizziness, psychological factors should be considered and diagnosis and treatment should be offered timely.

  9. A New Replication Norm for Psychology

    Directory of Open Access Journals (Sweden)

    Etienne P LeBel

    2015-10-01

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

  10. Amplified Self-replication of DNA Origami Nanostructures through Multi-cycle Fast-annealing Process

    Science.gov (United States)

    Zhou, Feng; Zhuo, Rebecca; He, Xiaojin; Sha, Ruojie; Seeman, Nadrian; Chaikin, Paul

    We have developed a non-biological self-replication process using templated reversible association of components and irreversible linking with annealing and UV cycles. The current method requires a long annealing time, up to several days, to achieve the specific self-assembly of DNA nanostructures. In this work, we accomplished the self-replication with a shorter time and smaller replication rate per cycle. By decreasing the ramping time, we obtained the comparable replication yield within 90 min. Systematic studies show that the temperature and annealing time play essential roles in the self-replication process. In this manner, we can amplify the self-replication process to a factor of 20 by increasing the number of cycles within the same amount of time.

  11. Rotating Arc Jet Test Model: Time-Accurate Trajectory Heat Flux Replication in a Ground Test Environment

    Science.gov (United States)

    Laub, Bernard; Grinstead, Jay; Dyakonov, Artem; Venkatapathy, Ethiraj

    2011-01-01

    Though arc jet testing has been the proven method employed for development testing and certification of TPS and TPS instrumentation, the operational aspects of arc jets limit testing to selected, but constant, conditions. Flight, on the other hand, produces timevarying entry conditions in which the heat flux increases, peaks, and recedes as a vehicle descends through an atmosphere. As a result, we are unable to "test as we fly." Attempts to replicate the time-dependent aerothermal environment of atmospheric entry by varying the arc jet facility operating conditions during a test have proven to be difficult, expensive, and only partially successful. A promising alternative is to rotate the test model exposed to a constant-condition arc jet flow to yield a time-varying test condition at a point on a test article (Fig. 1). The model shape and rotation rate can be engineered so that the heat flux at a point on the model replicates the predicted profile for a particular point on a flight vehicle. This simple concept will enable, for example, calibration of the TPS sensors on the Mars Science Laboratory (MSL) aeroshell for anticipated flight environments.

  12. Temporal organization of cellular self-replication

    Science.gov (United States)

    Alexandrov, Victor; Pugatch, Rami

    Recent experiments demonstrate that single cells grow exponentially in time. A coarse grained model of cellular self-replication is presented based on a novel concept - the cell is viewed as a self-replicating queue. This allows to have a more fundamental look into various temporal organizations and, importantly, the inherent non-Markovianity of noise distributions. As an example, the distribution of doubling times can be inferred and compared to single cell experiments in bacteria. We observe data collapse upon scaling by the average doubling time for different environments and present an inherent task allocation trade-off. Support from the Simons Center for Systems Biology, IAS, Princeon.

  13. Timing, Coordination, and Rhythm : Acrobatics at the DNA Replication Fork

    NARCIS (Netherlands)

    Hamdan, Samir M.; Oijen, Antoine M. van

    2010-01-01

    In DNA replication, the antiparallel nature of the parental duplex imposes certain constraints on the activity of the DNA polymerases that synthesize new DNA. The leading-strand polymerase advances in a continuous fashion, but the lagging-strand polymerase is forced to restart at short intervals. In

  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. 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

  16. Perfusion of surgical cavity wall enhancement in early post-treatment MR imaging may stratify the time-to-progression in glioblastoma.

    Directory of Open Access Journals (Sweden)

    Ji Eun Park

    Full Text Available To determine if perfusion in surgical cavity wall enhancement (SCWE obtained in early post-treatment MR imaging can stratify time-to-progression (TTP in glioblastoma.This study enrolled 60 glioblastoma patients with more than 5-mm-thick SCWEs as detected on contrast-enhanced MR imaging after concurrent chemoradiation therapy. Two independent readers categorized the shape and perfusion state of SCWEs as nodular or non-nodular and as having positive or negative perfusion compared with the contralateral grey matter on arterial spin labeling (ASL. The perfusion fraction on ASL within the contrast-enhancing lesion was calculated. The independent predictability of TTP was analyzed using the Kaplan-Meier method and Cox proportional hazards modelling.The perfusion fraction was higher in the non-progression group, significantly for reader 2 (P = 0.03 and borderline significantly for reader 1 (P = 0.08. A positive perfusion state and (P = 0.02 a higher perfusion fraction of the SCWE were found to become an independent predictor of longer TTP (P = 0.001 for reader 1 and P < 0.001 for reader 2. The contrast enhancement pattern did not become a TTP predictor.Assessment of perfusion in early post-treatment MR imaging can stratify TTP in patients with glioblastoma for adjuvant temozolomide therapy. Positive perfusion in SCWEs can become a predictor of a longer TTP.

  17. Ethanol dehydration to ethylene in a stratified autothermal millisecond reactor.

    Science.gov (United States)

    Skinner, Michael J; Michor, Edward L; Fan, Wei; Tsapatsis, Michael; Bhan, Aditya; Schmidt, Lanny D

    2011-08-22

    The concurrent decomposition and deoxygenation of ethanol was accomplished in a stratified reactor with 50-80 ms contact times. The stratified reactor comprised an upstream oxidation zone that contained Pt-coated Al(2)O(3) beads and a downstream dehydration zone consisting of H-ZSM-5 zeolite films deposited on Al(2)O(3) monoliths. Ethanol conversion, product selectivity, and reactor temperature profiles were measured for a range of fuel:oxygen ratios for two autothermal reactor configurations using two different sacrificial fuel mixtures: a parallel hydrogen-ethanol feed system and a series methane-ethanol feed system. Increasing the amount of oxygen relative to the fuel resulted in a monotonic increase in ethanol conversion in both reaction zones. The majority of the converted carbon was in the form of ethylene, where the ethanol carbon-carbon bonds stayed intact while the oxygen was removed. Over 90% yield of ethylene was achieved by using methane as a sacrificial fuel. These results demonstrate that noble metals can be successfully paired with zeolites to create a stratified autothermal reactor capable of removing oxygen from biomass model compounds in a compact, continuous flow system that can be configured to have multiple feed inputs, depending on process restrictions. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. 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...

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

    Directory of Open Access Journals (Sweden)

    Bazilė Ravoitytė

    2017-01-01

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

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

    Science.gov (United States)

    Das, Shankar P; Rhind, Nicholas

    2016-07-01

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

  1. Ecosystem metabolism in a stratified lake

    DEFF Research Database (Denmark)

    Stæhr, Peter Anton; Christensen, Jesper Philip Aagaard; Batt, Ryan D.

    2012-01-01

    , differences were not significant. During stratification, daily variability in epilimnetic DO was dominated by metabolism (46%) and air-water gas exchange (44%). Fluxes related to mixed-layer deepening dominated in meta- and hypolimnic waters (49% and 64%), while eddy diffusion (1% and 14%) was less important....... Although air-water gas exchange rates differed among the three formulations of gas-transfer velocity, this had no significant effect on metabolic rates....... that integrates rates across the entire depth profile and includes DO exchange between depth layers driven by mixed-layer deepening and eddy diffusivity. During full mixing, NEP was close to zero throughout the water column, and GPP and R were reduced 2-10 times compared to stratified periods. When present...

  2. FDTD scattered field formulation for scatterers in stratified dispersive media.

    Science.gov (United States)

    Olkkonen, Juuso

    2010-03-01

    We introduce a simple scattered field (SF) technique that enables finite difference time domain (FDTD) modeling of light scattering from dispersive objects residing in stratified dispersive media. The introduced SF technique is verified against the total field scattered field (TFSF) technique. As an application example, we study surface plasmon polariton enhanced light transmission through a 100 nm wide slit in a silver film.

  3. Time-varying Entry Heating Profile Replication with a Rotating Arc Jet Test Article

    Science.gov (United States)

    Grinstead, Jay Henderson; Venkatapathy, Ethiraj; Noyes, Eric A.; Mach, Jeffrey J.; Empey, Daniel M.; White, Todd R.

    2014-01-01

    A new approach for arc jet testing of thermal protection materials at conditions approximating the time-varying conditions of atmospheric entry was developed and demonstrated. The approach relies upon the spatial variation of heat flux and pressure over a cylindrical test model. By slowly rotating a cylindrical arc jet test model during exposure to an arc jet stream, each point on the test model will experience constantly changing applied heat flux. The predicted temporal profile of heat flux at a point on a vehicle can be replicated by rotating the cylinder at a prescribed speed and direction. An electromechanical test model mechanism was designed, built, and operated during an arc jet test to demonstrate the technique.

  4. Exploring the role of wave drag in the stable stratified oceanic and atmospheric bottom boundary layer in the cnrs-toulouse (cnrm-game) large stratified water flume

    NARCIS (Netherlands)

    Kleczek, M.; Steeneveld, G.J.; Paci, A.; Calmer, R.; Belleudy, A.; Canonici, J.C.; Murguet, F.; Valette, V.

    2014-01-01

    This paper reports on a laboratory experiment in the CNRM-GAME (Toulouse) stratified water flume of a stably stratified boundary layer, in order to quantify the momentum transfer due to orographically induced gravity waves by gently undulating hills in a boundary layer flow. In a stratified fluid, a

  5. Late replication domains are evolutionary conserved in the Drosophila genome.

    Science.gov (United States)

    Andreyenkova, Natalya G; Kolesnikova, Tatyana D; Makunin, Igor V; Pokholkova, Galina V; Boldyreva, Lidiya V; Zykova, Tatyana Yu; Zhimulev, Igor F; Belyaeva, Elena S

    2013-01-01

    Drosophila chromosomes are organized into distinct domains differing in their predominant chromatin composition, replication timing and evolutionary conservation. We show on a genome-wide level that genes whose order has remained unaltered across 9 Drosophila species display late replication timing and frequently map to the regions of repressive chromatin. This observation is consistent with the existence of extensive domains of repressive chromatin that replicate extremely late and have conserved gene order in the Drosophila genome. We suggest that such repressive chromatin domains correspond to a handful of regions that complete replication at the very end of S phase. We further demonstrate that the order of genes in these regions is rarely altered in evolution. Substantial proportion of such regions significantly coincide with large synteny blocks. This indicates that there are evolutionary mechanisms maintaining the integrity of these late-replicating chromatin domains. The synteny blocks corresponding to the extremely late-replicating regions in the D. melanogaster genome consistently display two-fold lower gene density across different Drosophila species.

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

    Directory of Open Access Journals (Sweden)

    Amnon Koren

    2010-08-01

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

  7. Suspected survivor bias in case-control studies: stratify on survival time and use a negative control.

    Science.gov (United States)

    van Rein, Nienke; Cannegieter, Suzanne C; Rosendaal, Frits R; Reitsma, Pieter H; Lijfering, Willem M

    2014-02-01

    Selection bias in case-control studies occurs when control selection is inappropriate. However, selection bias due to improper case sampling is less well recognized. We describe how to recognize survivor bias (i.e., selection on exposed cases) and illustrate this with an example study. A case-control study was used to analyze the effect of statins on major bleedings during treatment with vitamin K antagonists. A total of 110 patients who experienced such bleedings were included 18-1,018 days after the bleeding complication and matched to 220 controls. A protective association of major bleeding for exposure to statins (odds ratio [OR]: 0.56; 95% confidence interval: 0.29-1.08) was found, which did not become stronger after adjustment for confounding factors. These observations lead us to suspect survivor bias. To identify this bias, results were stratified on time between bleeding event and inclusion, and repeated for a negative control (an exposure not related to survival): blood group non-O. The ORs for exposure to statins increased gradually to 1.37 with shorter time between outcome and inclusion, whereas ORs for the negative control remained constant, confirming our hypothesis. We recommend the presented method to check for overoptimistic results, that is, survivor bias in case-control studies. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Analysing stratified medicine business models and value systems: innovation-regulation interactions.

    Science.gov (United States)

    Mittra, James; Tait, Joyce

    2012-09-15

    Stratified medicine offers both opportunities and challenges to the conventional business models that drive pharmaceutical R&D. Given the increasingly unsustainable blockbuster model of drug development, due in part to maturing product pipelines, alongside increasing demands from regulators, healthcare providers and patients for higher standards of safety, efficacy and cost-effectiveness of new therapies, stratified medicine promises a range of benefits to pharmaceutical and diagnostic firms as well as healthcare providers and patients. However, the transition from 'blockbusters' to what might now be termed 'niche-busters' will require the adoption of new, innovative business models, the identification of different and perhaps novel types of value along the R&D pathway, and a smarter approach to regulation to facilitate innovation in this area. In this paper we apply the Innogen Centre's interdisciplinary ALSIS methodology, which we have developed for the analysis of life science innovation systems in contexts where the value creation process is lengthy, expensive and highly uncertain, to this emerging field of stratified medicine. In doing so, we consider the complex collaboration, timing, coordination and regulatory interactions that shape business models, value chains and value systems relevant to stratified medicine. More specifically, we explore in some depth two convergence models for co-development of a therapy and diagnostic before market authorisation, highlighting the regulatory requirements and policy initiatives within the broader value system environment that have a key role in determining the probable success and sustainability of these models. Copyright © 2012 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    1994-07-01

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

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

    Science.gov (United States)

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

    2016-06-01

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

  11. Aligning the Economic Value of Companion Diagnostics and Stratified Medicines

    Directory of Open Access Journals (Sweden)

    Edward D. Blair

    2012-11-01

    Full Text Available The twin forces of payors seeking fair pricing and the rising costs of developing new medicines has driven a closer relationship between pharmaceutical companies and diagnostics companies, because stratified medicines, guided by companion diagnostics, offer better commercial, as well as clinical, outcomes. Stratified medicines have created clinical success and provided rapid product approvals, particularly in oncology, and indeed have changed the dynamic between drug and diagnostic developers. The commercial payback for such partnerships offered by stratified medicines has been less well articulated, but this has shifted as the benefits in risk management, pricing and value creation for all stakeholders become clearer. In this larger healthcare setting, stratified medicine provides both physicians and patients with greater insight on the disease and provides rationale for providers to understand cost-effectiveness of treatment. This article considers how the economic value of stratified medicine relationships can be recognized and translated into better outcomes for all healthcare stakeholders.

  12. Large eddy simulation of stably stratified turbulence

    International Nuclear Information System (INIS)

    Shen Zhi; Zhang Zhaoshun; Cui Guixiang; Xu Chunxiao

    2011-01-01

    Stably stratified turbulence is a common phenomenon in atmosphere and ocean. In this paper the large eddy simulation is utilized for investigating homogeneous stably stratified turbulence numerically at Reynolds number Re = uL/v = 10 2 ∼10 3 and Froude number Fr = u/NL = 10 −2 ∼10 0 in which u is root mean square of velocity fluctuations, L is integral scale and N is Brunt-Vaïsälä frequency. Three sets of computation cases are designed with different initial conditions, namely isotropic turbulence, Taylor Green vortex and internal waves, to investigate the statistical properties from different origins. The computed horizontal and vertical energy spectra are consistent with observation in atmosphere and ocean when the composite parameter ReFr 2 is greater than O(1). It has also been found in this paper that the stratification turbulence can be developed under different initial velocity conditions and the internal wave energy is dominated in the developed stably stratified turbulence.

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

    Science.gov (United States)

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

    1995-01-01

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

  14. RAD52 Facilitates Mitotic DNA Synthesis Following Replication Stress

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  15. Stratified medicine and reimbursement issues

    NARCIS (Netherlands)

    Fugel, Hans-Joerg; Nuijten, Mark; Postma, Maarten

    2012-01-01

    Stratified Medicine (SM) has the potential to target patient populations who will most benefit from a therapy while reducing unnecessary health interventions associated with side effects. The link between clinical biomarkers/diagnostics and therapies provides new opportunities for value creation to

  16. The Impact of Implementation Fidelity on Mortality Under a CD4-Stratified Timing Strategy for Antiretroviral Therapy in Patients With Tuberculosis.

    Science.gov (United States)

    Patel, Monita R; Westreich, Daniel; Yotebieng, Marcel; Nana, Mbonze; Eron, Joseph J; Behets, Frieda; Van Rie, Annelies

    2015-05-01

    Among patients with tuberculosis and human immunodeficiency virus type 1, CD4-stratified initiation of antiretroviral therapy (ART) is recommended, with earlier ART in those with low CD4 counts. However, the impact of implementation fidelity to this recommendation is unknown. We examined a prospective cohort study of 395 adult patients diagnosed with tuberculosis and human immunodeficiency virus between August 2007 and November 2009 in Kinshasa, Democratic Republic of the Congo. ART was to be initiated after 1 month of tuberculosis treatment at a CD4 count of implementation fidelity on 6-month mortality. Observed implementation fidelity was low (46%); 54% of patients either experienced delays in ART initiation or did not initiate ART, which could be avoided under perfect implementation fidelity. The observed mortality risk was 12.0% (95% confidence interval (CI): 8.2, 15.7); under complete (counterfactual) implementation fidelity, the mortality risk was 7.8% (95% CI: 2.4, 12.3), corresponding to a risk reduction of 4.2% (95% CI: 0.3, 8.1) and a preventable fraction of 35.1% (95% CI: 2.9, 67.9). Strategies to achieve high implementation fidelity to CD4-stratified ART timing are needed to maximize survival benefit. © The Author 2015. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Sutudy on exchange flow under the unstably stratified field

    OpenAIRE

    文沢, 元雄

    2005-01-01

    This paper deals with the exchange flow under the unstably stratified field. The author developed the effective measurement system as well as the numerical analysis program. The system and the program are applied to the helium-air exchange flow in a rectangular channel with inclination. Following main features of the exchange flow were discussed based on the calculated results.(1) Time required for establishing a quasi-steady state exchange flow.(2) The relationship between the inclination an...

  18. Inhibition of DNA replication by ultraviolet light

    International Nuclear Information System (INIS)

    Edenberg, H.J.

    1976-01-01

    DNA replication in ultraviolet-irradiated HeLa cells was studied by two different techniques: measurements of the kinetics of semiconservative DNA synthesis, and DNA fiber autoradiography. In examining the kinetics of semiconservative DNA synthesis, density label was used to avoid measuring the incorporation due to repair replication. The extent of inhibition varied with time. After doses of less than 10 J/m 2 the rate was initially depressed but later showed some recovery. After higher doses, a constant, low rate of synthesis was seen for at least the initial 6 h. An analysis of these data indicated that the inhibition of DNA synthesis could be explained by replication forks halting at pyrimidine dimers. DNA fiber autoradiography was used to further characterize replication after ultraviolet irradiation. The average length of labeled segments in irradiated cells increased in the time immediately after irradiation, and then leveled off. This is the predicted pattern if DNA synthesis in each replicon continued at its previous rate until a lesion is reached, and then halted. The frequency of lesions that block synthesis is approximately the same as the frequency of pyrimidine dimers

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

    International Nuclear Information System (INIS)

    Frappier, L.; Zannis-Hadjopoulos, M.

    1987-01-01

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

  20. Economic viability of Stratified Medicine concepts: An investor perspective on drivers and conditions that favour using Stratified Medicine approaches in a cost-contained healthcare environment.

    Science.gov (United States)

    Fugel, Hans-Joerg; Nuijten, Mark; Postma, Maarten

    2016-12-25

    Stratified Medicine (SM) is becoming a natural result of advances in biomedical science and a promising path for the innovation-based biopharmaceutical industry to create new investment opportunities. While the use of biomarkers to improve R&D efficiency and productivity is very much acknowledged by industry, much work remains to be done to understand the drivers and conditions that favour using a stratified approach to create economically viable products and to justify the investment in SM interventions as a stratification option. In this paper we apply a decision analytical methodology to address the economic attractiveness of different SM development options in a cost-contained healthcare environment. For this purpose, a hypothetical business case in the oncology market has been developed considering four feasible development scenarios. The article outlines the effects of development time and time to peak sales as key economic value drivers influencing profitability of SM interventions under specific conditions. If regulatory and reimbursement challenges can be solved, decreasing development time and enhancing early market penetration would most directly improve the economic attractiveness of SM interventions. Appropriate tailoring of highly differentiated patient subgroups is the prerequisite to leverage potential efficiency gains in the R&D process. Also, offering a better targeted and hence ultimately more cost-effective therapy at reimbursable prices will facilitate time to market access and allow increasing market share gains within the targeted populations. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. The Stratified Legitimacy of Abortions.

    Science.gov (United States)

    Kimport, Katrina; Weitz, Tracy A; Freedman, Lori

    2016-12-01

    Roe v. Wade was heralded as an end to unequal access to abortion care in the United States. However, today, despite being common and safe, abortion is performed only selectively in hospitals and private practices. Drawing on 61 interviews with obstetrician-gynecologists in these settings, we examine how they determine which abortions to perform. We find that they distinguish between more and less legitimate abortions, producing a narrative of stratified legitimacy that privileges abortions for intended pregnancies, when the fetus is unhealthy, and when women perform normative gendered sexuality, including distress about the abortion, guilt about failure to contracept, and desire for motherhood. This stratified legitimacy can perpetuate socially-inflected inequality of access and normative gendered sexuality. Additionally, we argue that the practice by physicians of distinguishing among abortions can legitimate legislative practices that regulate and restrict some kinds of abortion, further constraining abortion access. © American Sociological Association 2016.

  2. Stratified charge rotary engine for general aviation

    Science.gov (United States)

    Mount, R. E.; Parente, A. M.; Hady, W. F.

    1986-01-01

    A development history, a current development status assessment, and a design feature and performance capabilities account are given for stratified-charge rotary engines applicable to aircraft propulsion. Such engines are capable of operating on Jet-A fuel with substantial cost savings, improved altitude capability, and lower fuel consumption by comparison with gas turbine powerplants. Attention is given to the current development program of a 400-hp engine scheduled for initial operations in early 1990. Stratified charge rotary engines are also applicable to ground power units, airborne APUs, shipboard generators, and vehicular engines.

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

    Science.gov (United States)

    Stroebe, Wolfgang; Strack, Fritz

    2014-01-01

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

  4. 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.

  5. 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.

  6. Replicative intermediates in UV-irradiated Simian virus 40

    International Nuclear Information System (INIS)

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

    1984-01-01

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

  7. Pyrimidine dimers block simian virus 40 replication forks

    International Nuclear Information System (INIS)

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

    1986-01-01

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

  8. Initiation preference at a yeast origin of replication.

    Science.gov (United States)

    Brewer, B J; Fangman, W L

    1994-04-12

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

  9. 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. Nitrogen transformations in stratified aquatic microbial ecosystems

    DEFF Research Database (Denmark)

    Revsbech, Niels Peter; Risgaard-Petersen, N.; Schramm, Andreas

    2006-01-01

    Abstract  New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a µm-mm scale. A large and ever-expanding knowledge base about n...... performing dissimilatory reduction of nitrate to ammonium have given new dimensions to the understanding of nitrogen cycling in nature, and the occurrence of these organisms and processes in stratified microbial communities will be described in detail.......Abstract  New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a µm-mm scale. A large and ever-expanding knowledge base about...... nitrogen fixation, nitrification, denitrification, and dissimilatory reduction of nitrate to ammonium, and about the microorganisms performing the processes, has been produced by use of these techniques. During the last decade the discovery of anammmox bacteria and migrating, nitrate accumulating bacteria...

  11. 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.

  12. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  13. Autophagy Facilitates Salmonella Replication in HeLa Cells

    Science.gov (United States)

    Yu, Hong B.; Croxen, Matthew A.; Marchiando, Amanda M.; Ferreira, Rosana B. R.; Cadwell, Ken; Foster, Leonard J.; Finlay, B. Brett

    2014-01-01

    ABSTRACT Autophagy is a process whereby a double-membrane structure (autophagosome) engulfs unnecessary cytosolic proteins, organelles, and invading pathogens and delivers them to the lysosome for degradation. We examined the fate of cytosolic Salmonella targeted by autophagy and found that autophagy-targeted Salmonella present in the cytosol of HeLa cells correlates with intracellular bacterial replication. Real-time analyses revealed that a subset of cytosolic Salmonella extensively associates with autophagy components p62 and/or LC3 and replicates quickly, whereas intravacuolar Salmonella shows no or very limited association with p62 or LC3 and replicates much more slowly. Replication of cytosolic Salmonella in HeLa cells is significantly decreased when autophagy components are depleted. Eventually, hyperreplication of cytosolic Salmonella potentiates cell detachment, facilitating the dissemination of Salmonella to neighboring cells. We propose that Salmonella benefits from autophagy for its cytosolic replication in HeLa cells. PMID:24618251

  14. X-irradiation affects all DNA replication intermediates when inhibiting replication initiation

    International Nuclear Information System (INIS)

    Loenn, U.; Karolinska Hospital, Stockholm

    1982-01-01

    When a human melanoma line was irradiated with 10 Gy, there was, after 30 to 60 min, a gradual reduction in the DNA replication rate. Ten to twelve hours after the irradiation, the DNA replication had returned to near normal rate. The results showed tht low dose-rate X-irradiation inhibits preferentially the formation of small DNA replication intermediates. There is no difference between the inhibition of these replication intermediates formed only in the irradiated cells and those formed also in untreated cells. (U.K.)

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

    Science.gov (United States)

    Raghuraman, M K; Brewer, Bonita J

    2010-01-01

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

  16. 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...

  17. Data from Investigating Variation in Replicability: A “Many Labs” Replication Project

    Directory of Open Access Journals (Sweden)

    Richard A. Klein

    2014-04-01

    Full Text Available This dataset is from the Many Labs Replication Project in which 13 effects were replicated across 36 samples and over 6,000 participants. Data from the replications are included, along with demographic variables about the participants and contextual information about the environment in which the replication was conducted. Data were collected in-lab and online through a standardized procedure administered via an online link. The dataset is stored on the Open Science Framework website. These data could be used to further investigate the results of the included 13 effects or to study replication and generalizability more broadly.

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

    Science.gov (United States)

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

    2012-10-01

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

  19. Low cost management of replicated data in fault-tolerant distributed systems

    Science.gov (United States)

    Joseph, Thomas A.; Birman, Kenneth P.

    1990-01-01

    Many distributed systems replicate data for fault tolerance or availability. In such systems, a logical update on a data item results in a physical update on a number of copies. The synchronization and communication required to keep the copies of replicated data consistent introduce a delay when operations are performed. A technique is described that relaxes the usual degree of synchronization, permitting replicated data items to be updated concurrently with other operations, while at the same time ensuring that correctness is not violated. The additional concurrency thus obtained results in better response time when performing operations on replicated data. How this technique performs in conjunction with a roll-back and a roll-forward failure recovery mechanism is also discussed.

  20. 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.

  1. 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

  2. A study of an adaptive replication framework for orchestrated composite web services.

    Science.gov (United States)

    Mohamed, Marwa F; Elyamany, Hany F; Nassar, Hamed M

    2013-01-01

    Replication is considered one of the most important techniques to improve the Quality of Services (QoS) of published Web Services. It has achieved impressive success in managing resource sharing and usage in order to moderate the energy consumed in IT environments. For a robust and successful replication process, attention should be paid to suitable time as well as the constraints and capabilities in which the process runs. The replication process is time-consuming since outsourcing some new replicas into other hosts is lengthy. Furthermore, nowadays, most of the business processes that might be implemented over the Web are composed of multiple Web services working together in two main styles: Orchestration and Choreography. Accomplishing a replication over such business processes is another challenge due to the complexity and flexibility involved. In this paper, we present an adaptive replication framework for regular and orchestrated composite Web services. The suggested framework includes a number of components for detecting unexpected and unhappy events that might occur when consuming the original published web services including failure or overloading. It also includes a specific replication controller to manage the replication process and select the best host that would encapsulate a new replica. In addition, it includes a component for predicting the incoming load in order to decrease the time needed for outsourcing new replicas, enhancing the performance greatly. A simulation environment has been created to measure the performance of the suggested framework. The results indicate that adaptive replication with prediction scenario is the best option for enhancing the performance of the replication process in an online business environment.

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

    OpenAIRE

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

    2010-01-01

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

  4. Simulation model of stratified thermal energy storage tank using finite difference method

    Science.gov (United States)

    Waluyo, Joko

    2016-06-01

    Stratified TES tank is normally used in the cogeneration plant. The stratified TES tanks are simple, low cost, and equal or superior in thermal performance. The advantage of TES tank is that it enables shifting of energy usage from off-peak demand for on-peak demand requirement. To increase energy utilization in a stratified TES tank, it is required to build a simulation model which capable to simulate the charging phenomenon in the stratified TES tank precisely. This paper is aimed to develop a novel model in addressing the aforementioned problem. The model incorporated chiller into the charging of stratified TES tank system in a closed system. The model was developed in one-dimensional type involve with heat transfer aspect. The model covers the main factors affect to degradation of temperature distribution namely conduction through the tank wall, conduction between cool and warm water, mixing effect on the initial flow of the charging as well as heat loss to surrounding. The simulation model is developed based on finite difference method utilizing buffer concept theory and solved in explicit method. Validation of the simulation model is carried out using observed data obtained from operating stratified TES tank in cogeneration plant. The temperature distribution of the model capable of representing S-curve pattern as well as simulating decreased charging temperature after reaching full condition. The coefficient of determination values between the observed data and model obtained higher than 0.88. Meaning that the model has capability in simulating the charging phenomenon in the stratified TES tank. The model is not only capable of generating temperature distribution but also can be enhanced for representing transient condition during the charging of stratified TES tank. This successful model can be addressed for solving the limitation temperature occurs in charging of the stratified TES tank with the absorption chiller. Further, the stratified TES tank can be

  5. 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…

  6. The Legal Road To Replicating Silicon Valley

    OpenAIRE

    John Armour; Douglas Cumming

    2004-01-01

    Must policymakers seeking to replicate the success of Silicon Valley’s venture capital market first replicate other US institutions, such as deep and liquid stock markets? Or can legal reforms alone make a significant difference? In this paper, we compare the economic and legal determinants of venture capital investment, fundraising and exits. We introduce a cross-sectional and time series empirical analysis across 15 countries and 13 years of data spanning an entire business cycle. We show t...

  7. Quantitative live imaging of endogenous DNA replication in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Andrew Burgess

    Full Text Available Historically, the analysis of DNA replication in mammalian tissue culture cells has been limited to static time points, and the use of nucleoside analogues to pulse-label replicating DNA. Here we characterize for the first time a novel Chromobody cell line that specifically labels endogenous PCNA. By combining this with high-resolution confocal time-lapse microscopy, and with a simplified analysis workflow, we were able to produce highly detailed, reproducible, quantitative 4D data on endogenous DNA replication. The increased resolution allowed accurate classification and segregation of S phase into early-, mid-, and late-stages based on the unique subcellular localization of endogenous PCNA. Surprisingly, this localization was slightly but significantly different from previous studies, which utilized over-expressed GFP tagged forms of PCNA. Finally, low dose exposure to Hydroxyurea caused the loss of mid- and late-S phase localization patterns of endogenous PCNA, despite cells eventually completing S phase. Taken together, these results indicate that this simplified method can be used to accurately identify and quantify DNA replication under multiple and various experimental conditions.

  8. Theory of hyperbolic stratified nanostructures for surface-enhanced Raman scattering

    Science.gov (United States)

    Wong, Herman M. K.; Dezfouli, Mohsen Kamandar; Axelrod, Simon; Hughes, Stephen; Helmy, Amr S.

    2017-11-01

    We theoretically investigate the enhancement of surface enhanced Raman spectroscopy (SERS) using hyperbolic stratified nanostructures and compare to metal nanoresonators. The photon Green function of each nanostructure within its environment is first obtained from a semianalytical modal theory, which is used in a quantum optics formalism of the molecule-nanostructure interaction to model the SERS spectrum. An intuitive methodology is presented for calculating the single-molecule enhancement factor (SMEF), which is also able to predict known experimental SERS enhancement factors of a gold nanodimer. We elucidate the important figures-of-merit of the enhancement and explore these for different designs. We find that the use of hyperbolic stratified materials can enhance the photonic local density of states (LDOS) by close to two times in comparison to pure metal nanostructures, when both designed to work at the same operating wavelengths. However, the increased LDOS is accompanied by higher electric field concentration within the lossy hyperbolic material, which leads to increased quenching that serves to reduce the overall detected SERS enhancement in the far field. For nanoresonators with resonant localized surface plasmon wavelengths in the near-infrared, the SMEF for the hyperbolic stratified nanostructure is approximately one order of magnitude lower than the pure metal counterpart. Conversely, we show that by detecting the Raman signal using a near-field probe, hyperbolic materials can provide an improvement in SERS enhancement compared to using pure metal nanostructures when the probe is sufficiently close (<50 nm ) to the Raman active molecule at the plasmonic hotspot.

  9. Electrochemically replicated smooth aluminum foils for anodic alumina nanochannel arrays

    International Nuclear Information System (INIS)

    Biring, Sajal; Tsai, K-T; Sur, Ujjal Kumar; Wang, Y-L

    2008-01-01

    A fast electrochemical replication technique has been developed to fabricate large-scale ultra-smooth aluminum foils by exploiting readily available large-scale smooth silicon wafers as the masters. Since the adhesion of aluminum on silicon depends on the time of surface pretreatment in water, it is possible to either detach the replicated aluminum from the silicon master without damaging the replicated aluminum and master or integrate the aluminum film to the silicon substrate. Replicated ultra-smooth aluminum foils are used for the growth of both self-organized and lithographically guided long-range ordered arrays of anodic alumina nanochannels without any polishing pretreatment

  10. 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.

  11. 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....

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

    Science.gov (United States)

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

    2014-04-07

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

  13. 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.

  14. Hierarchical Data Replication and Service Monitoring Methods in a Scientific Data Grid

    Directory of Open Access Journals (Sweden)

    Weizhong Lu

    2009-04-01

    Full Text Available In a grid and distributed computing environment, data replication is an effective way to improve data accessibility and data accessing efficiency. It is also significant in developing a real-time service monitoring system for a Chinese Scientific Data Grid to guarantee the system stability and data availability. Hierarchical data replication and service monitoring methods are proposed in this paper. The hierarchical data replication method divides the network into different domains and replicates data in local domains. The nodes in a local domain are classified into hierarchies to improve data accessibility according to bandwidth and storage memory space. An extensible agent-based prototype of a hierarchical service monitoring system is presented. The status information of services in the Chinese Scientific Data Grid is collected from the grid nodes based on agent technology and then is transformed into real-time operational pictures for management needs. This paper presents frameworks of the hierarchical data replication and service monitoring methods and gives detailed resolutions. Simulation analyses have demonstrated improved data accessing efficiency and verified the effectiveness of the methods at the same time.

  15. Thermal stratification built up in hot water tank with different inlet stratifiers

    DEFF Research Database (Denmark)

    Dragsted, Janne; Furbo, Simon; Dannemand, Mark

    2017-01-01

    Thermal stratification in a water storage tank can strongly increase the thermal performance of solar heating systems. Thermal stratification can be built up in a storage tank during charge, if the heated water enters through an inlet stratifier. Experiments with a test tank have been carried out...... in order to elucidate how well thermal stratification is established in the tank with differently designed inlet stratifiers under different controlled laboratory conditions. The investigated inlet stratifiers are from Solvis GmbH & Co KG and EyeCular Technologies ApS. The inlet stratifier from Solvis Gmb...... for Solvis GmbH & Co KG had a better performance at 4 l/min. In the intermediate charge test the stratifier from EyeCular Technologies ApS had a better performance in terms of maintaining the thermal stratification in the storage tank while charging with a relative low temperature. [All rights reserved...

  16. Parasites Sustain and Enhance RNA-Like Replicators through Spatial Self-Organisation.

    Directory of Open Access Journals (Sweden)

    Enrico Sandro Colizzi

    2016-04-01

    Full Text Available In a prebiotic RNA world, parasitic behaviour may be favoured because template dependent replication happens in trans, thus being altruistic. Spatially extended systems are known to reduce harmful effects of parasites. Here we present a spatial system to show that evolution of replication is (indirectly enhanced by strong parasites, and we characterise the phase transition that leads to this mode of evolution. Building on the insights of this analysis, we identify two scenarios, namely periodic disruptions and longer replication time-span, in which speciation occurs and an evolved parasite-like lineage enables the evolutionary increase of replication rates in replicators. Finally, we show that parasites co-evolving with replicators are selected to become weaker, i.e. worse templates for replication when the duration of replication is increased. We conclude that parasites may not be considered a problem for evolution in a prebiotic system, but a degree of freedom that can be exploited by evolution to enhance the evolvability of replicators, by means of emergent levels of selection.

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

    Science.gov (United States)

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

    2017-01-05

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

  18. Large eddy simulation of turbulent and stably-stratified flows

    International Nuclear Information System (INIS)

    Fallon, Benoit

    1994-01-01

    The unsteady turbulent flow over a backward-facing step is studied by mean of Large Eddy Simulations with structure function sub grid model, both in isothermal and stably-stratified configurations. Without stratification, the flow develops highly-distorted Kelvin-Helmholtz billows, undergoing to helical pairing, with A-shaped vortices shed downstream. We show that forcing injected by recirculation fluctuations governs this oblique mode instabilities development. The statistical results show good agreements with the experimental measurements. For stably-stratified configurations, the flow remains more bi-dimensional. We show with increasing stratification, how the shear layer growth is frozen by inhibition of pairing process then of Kelvin-Helmholtz instabilities, and the development of gravity waves or stable density interfaces. Eddy structures of the flow present striking analogies with the stratified mixing layer. Additional computations show the development of secondary Kelvin-Helmholtz instabilities on the vorticity layers between two primary structures. This important mechanism based on baroclinic effects (horizontal density gradients) constitutes an additional part of the turbulent mixing process. Finally, the feasibility of Large Eddy Simulation is demonstrated for industrial flows, by studying a complex stratified cavity. Temperature fluctuations are compared to experimental measurements. We also develop three-dimensional un-stationary animations, in order to understand and visualize turbulent interactions. (author) [fr

  19. 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.

  20. Virtual Machine Replication on Achieving Energy-Efficiency in a Cloud

    Directory of Open Access Journals (Sweden)

    Subrota K. Mondal

    2016-07-01

    Full Text Available The rapid growth in cloud service demand has led to the establishment of large-scale virtualized data centers in which virtual machines (VMs are used to handle user requests for service. A user’s request cannot be completed if the VM fails. Replication mechanisms can be used to mitigate the impact of failures. Further, data centers consume a large amount of energy resulting in high operating costs and contributing to significant greenhouse gas (GHG emissions. In this paper, we focus on Infrastructure as a Service (IaaS cloud where user job requests are processed by VMs and analyze the effectiveness of VM replications in terms of job completion time performance as well as energy consumption. Three different schemes: cold, warm, and hot replications are considered. The trade-offs between job completion time and energy consumption in different replication schemes are characterized through comprehensive analytical models which capture VM state transitions and associated power consumption patterns. The effectiveness of replication schemes are demonstrated through experimental results. To verify the validity of the proposed analytical models, we extend the widely used cloud simulator CloudSim and compare the simulation results with analytical solutions.

  1. Diversity of the DNA Replication System in the Archaea Domain

    Directory of Open Access Journals (Sweden)

    Felipe Sarmiento

    2014-01-01

    Full Text Available The precise and timely duplication of the genome is essential for cellular life. It is achieved by DNA replication, a complex process that is conserved among the three domains of life. Even though the cellular structure of archaea closely resembles that of bacteria, the information processing machinery of archaea is evolutionarily more closely related to the eukaryotic system, especially for the proteins involved in the DNA replication process. While the general DNA replication mechanism is conserved among the different domains of life, modifications in functionality and in some of the specialized replication proteins are observed. Indeed, Archaea possess specific features unique to this domain. Moreover, even though the general pattern of the replicative system is the same in all archaea, a great deal of variation exists between specific groups.

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

    International Nuclear Information System (INIS)

    Shavitt, O.; Livneh, Z.

    1989-01-01

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

  3. 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....

  4. The role of cooperation and parasites in non-linear replicator delayed extinctions

    International Nuclear Information System (INIS)

    Sardanyes, Josep; Sole, Ricard V.

    2007-01-01

    In the present work we study the role of cooperation and parasites on extinction delayed transitions for self-replicating species with catalytic activity. We first use a one-dimensional continuous equation to study the dynamics of both single autocatalytic replicator and symmetric two-member hypercycles, where two well-defined phases involving survival and extinction of replicators are shown to exist. Extinction dynamics is analyzed numerically and analytically and under both deterministic and stochastic scenarios. A ghost is also found for the single autocatalytic replicator and for the asymmetric hypercycle, with an extinction time delay following the square-root scaling law near bifurcation threshold. We find that the extinction delay is longer for the two-member hypercycle than for the single autocatalytic species, indicating that cooperation among replicators might involve to spend a longer time in the bottle-neck region of the ghost. The asymmetry of the network is shown to prolong the extinction time. We also show that an attached parasite decreases the time spent in the bottle-neck region of the ghost, thus accelerating extinction in these systems of replicators. Nevertheless the effect of the parasite is not so important when replicators catalytically cooperate, being the two-member hypercycle less sensitive to the parasite than the autocatalytic species. Here the hypercycle asymmetry can also significantly increase the delaying capacity. These features make the hypercycle to undergo a longer extinction delay, thus increasing the memory effect of the ghost. We finally explore the role of the ghost in fluctuating media, where the extinction delayed transition is shown to increase the survival probability of cooperating catalytic species

  5. Optimal energy growth in a stably stratified shear flow

    Science.gov (United States)

    Jose, Sharath; Roy, Anubhab; Bale, Rahul; Iyer, Krithika; Govindarajan, Rama

    2018-02-01

    Transient growth of perturbations by a linear non-modal evolution is studied here in a stably stratified bounded Couette flow. The density stratification is linear. Classical inviscid stability theory states that a parallel shear flow is stable to exponentially growing disturbances if the Richardson number (Ri) is greater than 1/4 everywhere in the flow. Experiments and numerical simulations at higher Ri show however that algebraically growing disturbances can lead to transient amplification. The complexity of a stably stratified shear flow stems from its ability to combine this transient amplification with propagating internal gravity waves (IGWs). The optimal perturbations associated with maximum energy amplification are numerically obtained at intermediate Reynolds numbers. It is shown that in this wall-bounded flow, the three-dimensional optimal perturbations are oblique, unlike in unstratified flow. A partitioning of energy into kinetic and potential helps in understanding the exchange of energies and how it modifies the transient growth. We show that the apportionment between potential and kinetic energy depends, in an interesting manner, on the Richardson number, and on time, as the transient growth proceeds from an optimal perturbation. The oft-quoted stabilizing role of stratification is also probed in the non-diffusive limit in the context of disturbance energy amplification.

  6. Stratified Medicine and Reimbursement Issues

    Directory of Open Access Journals (Sweden)

    Hans-Joerg eFugel

    2012-10-01

    Full Text Available Stratified Medicine (SM has the potential to target patient populations who will most benefit from a therapy while reducing unnecessary health interventions associated with side effects. The link between clinical biomarkers/diagnostics and therapies provides new opportunities for value creation to strengthen the value proposition to pricing and reimbursement (P&R authorities. However, the introduction of SM challenges current reimbursement schemes in many EU countries and the US as different P&R policies have been adopted for drugs and diagnostics. Also, there is a lack of a consistent process for value assessment of more complex diagnostics in these markets. New, innovative approaches and more flexible P&R systems are needed to reflect the added value of diagnostic tests and to stimulate investments in new technologies. Yet, the framework for access of diagnostic–based therapies still requires further development while setting the right incentives and appropriate align stakeholders interests when realizing long- term patient benefits. This article addresses the reimbursement challenges of SM approaches in several EU countries and the US outlining some options to overcome existing reimbursement barriers for stratified medicine.

  7. 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...

  8. Advanced liquid-cooled, turbocharged and intercooled stratified charge rotary engines for aircraft

    Science.gov (United States)

    Mount, Robert E.; Bartel, John; Hady, William F.

    1987-01-01

    Developments concerning stratified-charge rotary (SCR) engines over the past 10 years are reviewed. Aircraft engines being developed using SCR technology are shown and described, and the ability of such technology to meet general aviation engine needs is considered. Production timing and availability of SCR technology for the development of aviation rotary engines are discussed, and continuing efforts toward improving this technology, including NASA efforts, are described.

  9. Iterated function systems for DNA replication

    Science.gov (United States)

    Gaspard, Pierre

    2017-10-01

    The kinetic equations of DNA replication are shown to be exactly solved in terms of iterated function systems, running along the template sequence and giving the statistical properties of the copy sequences, as well as the kinetic and thermodynamic properties of the replication process. With this method, different effects due to sequence heterogeneity can be studied, in particular, a transition between linear and sublinear growths in time of the copies, and a transition between continuous and fractal distributions of the local velocities of the DNA polymerase along the template. The method is applied to the human mitochondrial DNA polymerase γ without and with exonuclease proofreading.

  10. Recommendations for Replication Research in Special Education: A Framework of Systematic, Conceptual Replications

    Science.gov (United States)

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

    2016-01-01

    Special education researchers conduct studies that can be considered replications. However, they do not often refer to them as replication studies. The purpose of this article is to consider the potential benefits of conceptualizing special education intervention research within a framework of systematic, conceptual replication. Specifically, we…

  11. 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....

  12. Late-replicating X-chromosome: replication patterns in mammalian females

    Directory of Open Access Journals (Sweden)

    Tunin Karen

    2002-01-01

    Full Text Available The GTG-banding and 5-BrdU incorporation patterns of the late-replicating X-chromosome were studied in female dogs and cattle, and compared to human female patterns. The replication patterns of the short arm of the X-chromosomes did not show any difference between human, dog and cattle females. As to the long arm, some bands showed differences among the three studied species regarding the replication kinetics pattern. These differences were observed in a restricted region of the X-chromosome, delimited by Xq11 -> q25 in humans, by Xq1 -> q8 in dogs, and by Xq12 -> q32 in cattle. In an attempt to find out if these differences in the replication kinetics could be a reflection of differences in the localization of genes in that region of the X-chromosome, we used the probe for the human androgen receptor gene (AR localized at Xq12, which is in the region where we observed differences among the three studied species. We did not, however, observe hybridization signals. Our study goes on, using other human probes for genes located in the region Xq11 -> Xq25.

  13. A Replication by Any Other Name: A Systematic Review of Replicative Intervention Studies

    Science.gov (United States)

    Cook, Bryan G.; Collins, Lauren W.; Cook, Sara C.; Cook, Lysandra

    2016-01-01

    Replication research is essential to scientific knowledge. Reviews of replication studies often electronically search for "replicat*" as a textword, which does not identify studies that replicate previous research but do not self-identify as such. We examined whether the 83 intervention studies published in six non-categorical research…

  14. Numerical simulation of stratified flows with different k-ε turbulence models

    International Nuclear Information System (INIS)

    Dagestad, S.

    1991-01-01

    The thesis comprises the numerical simulation of stratified flows with different k-ε models. When using the k-ε model, two equations are solved to describe the turbulence. The k-equation represents the turbulent kinetic energy of the turbulence and the ε-equation is the turbulent dissipation. Different k-ε models predict stratified flows differently. The standard k-ε model leads to higher turbulent mixing than the low-Reynolds model does. For lower Froude numbers, F 0 , this effect becomes enhanced. Buoyancy extension of the k-ε model also leads to less vertical mixing in cases with strong stratification. When the stratification increases, buoyancy-extension becomes larger influence. The turbulent Prandtl number effects have large impact on the transport of heat and the development of the flow. Two different formulae which express the turbulent Prandtl effects have been tested. For unstably stratified flows, the rapid mixing and three-dimensionality of the flow can in fact be computed using a k-ε model when buoyancy-extended is employed. The turbulent heat transfer and thus turbulent production in unstable stratified flows depends strongly upon the turbulent Prandtl number effect. The main conclusions are: Stable stratified flows should be computed with a buoyancy-extended low-Reynolds k-ε model; Unstable stratified flows should be computed with a buoyancy-extended standard k-ε model; The turbulent Prandtl number effects should be included in the computations; Buoyancy-extension has lead to more correct description of the physics for all of the investigated flows. 78 refs., 128 figs., 17 tabs

  15. PHOTOSPHERIC EMISSION FROM STRATIFIED JETS

    International Nuclear Information System (INIS)

    Ito, Hirotaka; Nagataki, Shigehiro; Ono, Masaomi; Lee, Shiu-Hang; Mao, Jirong; Yamada, Shoichi; Pe'er, Asaf; Mizuta, Akira; Harikae, Seiji

    2013-01-01

    We explore photospheric emissions from stratified two-component jets, wherein a highly relativistic spine outflow is surrounded by a wider and less relativistic sheath outflow. Thermal photons are injected in regions of high optical depth and propagated until the photons escape at the photosphere. Because of the presence of shear in velocity (Lorentz factor) at the boundary of the spine and sheath region, a fraction of the injected photons are accelerated using a Fermi-like acceleration mechanism such that a high-energy power-law tail is formed in the resultant spectrum. We show, in particular, that if a velocity shear with a considerable variance in the bulk Lorentz factor is present, the high-energy part of observed gamma-ray bursts (GRBs) photon spectrum can be explained by this photon acceleration mechanism. We also show that the accelerated photons might also account for the origin of the extra-hard power-law component above the bump of the thermal-like peak seen in some peculiar bursts (e.g., GRB 090510, 090902B, 090926A). We demonstrate that time-integrated spectra can also reproduce the low-energy spectrum of GRBs consistently using a multi-temperature effect when time evolution of the outflow is considered. Last, we show that the empirical E p -L p relation can be explained by differences in the outflow properties of individual sources

  16. 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...

  17. Universal Temporal Profile of Replication Origin Activation in Eukaryotes

    Science.gov (United States)

    Goldar, Arach

    2011-03-01

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

  18. Sterol Binding by the Tombusviral Replication Proteins Is Essential for Replication in Yeast and Plants.

    Science.gov (United States)

    Xu, Kai; Nagy, Peter D

    2017-04-01

    Membranous structures derived from various organelles are important for replication of plus-stranded RNA viruses. Although the important roles of co-opted host proteins in RNA virus replication have been appreciated for a decade, the equally important functions of cellular lipids in virus replication have been gaining full attention only recently. Previous work with Tomato bushy stunt tombusvirus (TBSV) in model host yeast has revealed essential roles for phosphatidylethanolamine and sterols in viral replication. To further our understanding of the role of sterols in tombusvirus replication, in this work we showed that the TBSV p33 and p92 replication proteins could bind to sterols in vitro The sterol binding by p33 is supported by cholesterol recognition/interaction amino acid consensus (CRAC) and CARC-like sequences within the two transmembrane domains of p33. Mutagenesis of the critical Y amino acids within the CRAC and CARC sequences blocked TBSV replication in yeast and plant cells. We also showed the enrichment of sterols in the detergent-resistant membrane (DRM) fractions obtained from yeast and plant cells replicating TBSV. The DRMs could support viral RNA synthesis on both the endogenous and exogenous templates. A lipidomic approach showed the lack of enhancement of sterol levels in yeast and plant cells replicating TBSV. The data support the notion that the TBSV replication proteins are associated with sterol-rich detergent-resistant membranes in yeast and plant cells. Together, the results obtained in this study and the previously published results support the local enrichment of sterols around the viral replication proteins that is critical for TBSV replication. IMPORTANCE One intriguing aspect of viral infections is their dependence on efficient subcellular assembly platforms serving replication, virion assembly, or virus egress via budding out of infected cells. These assembly platforms might involve sterol-rich membrane microdomains, which are

  19. MC3D modelling of stratified explosion

    International Nuclear Information System (INIS)

    Picchi, S.; Berthoud, G.

    1999-01-01

    It is known that a steam explosion can occur in a stratified geometry and that the observed yields are lower than in the case of explosion in a premixture configuration. However, very few models are available to quantify the amount of melt which can be involved and the pressure peak that can be developed. In the stratified application of the MC3D code, mixing and fragmentation of the melt are explained by the growth of Kelvin Helmholtz instabilities due to the shear flow of the two phase coolant above the melt. Such a model is then used to recalculate the Frost-Ciccarelli tin-water experiment. Pressure peak, speed of propagation, bubble shape and erosion height are well reproduced as well as the influence of the inertial constraint (height of the water pool). (author)

  20. MC3D modelling of stratified explosion

    Energy Technology Data Exchange (ETDEWEB)

    Picchi, S.; Berthoud, G. [DTP/SMTH/LM2, CEA, 38 - Grenoble (France)

    1999-07-01

    It is known that a steam explosion can occur in a stratified geometry and that the observed yields are lower than in the case of explosion in a premixture configuration. However, very few models are available to quantify the amount of melt which can be involved and the pressure peak that can be developed. In the stratified application of the MC3D code, mixing and fragmentation of the melt are explained by the growth of Kelvin Helmholtz instabilities due to the shear flow of the two phase coolant above the melt. Such a model is then used to recalculate the Frost-Ciccarelli tin-water experiment. Pressure peak, speed of propagation, bubble shape and erosion height are well reproduced as well as the influence of the inertial constraint (height of the water pool). (author)

  1. Reliability analysis of a replication with limited number of journaling files

    International Nuclear Information System (INIS)

    Kimura, Mitsutaka; Imaizumi, Mitsuhiro; Nakagawa, Toshio

    2013-01-01

    Recently, replication mechanisms using journaling files have been widely used for the server systems. We have already discussed the model of asynchronous replication system using journaling files [8]. This paper formulates a stochastic model of a server system with replication considering the number of transmitting journaling files. The server updates the storage database and transmits the journaling file when a client requests the data update. The server transmits the database content to a backup site either at a constant time or after a constant number of transmitting journaling files. We derive the expected number of the replication and of transmitting journaling files. Further, we calculate the expected cost and discuss optimal replication interval to minimize it. Finally, numerical examples are given

  2. Changes in nucleosome repeat lengths precede replication in the early replicating metallothionein II gene region of cells synchronized in early S phase

    International Nuclear Information System (INIS)

    D'Anna, J.A.; Tobey, R.A.

    1989-01-01

    Previous investigations showed that inhibition of DNA synthesis by hydroxyurea, aphidicolin, or 5-fluorodeoxyuridine produced large changes in the composition and nucleosome repeat lengths of bulk chromatin. There the authors report results of investigations to determine whether the changes in nucleosome repeat lengths might be localized in the initiated replicons, as postulated. In most experiments, Chinese hamster (line CHO) cells were synchronized in G1, or they were synchronized in early S phase by allowing G1 cells to enter S phase in medium containing 1 mM hydroxyurea or 5 μg mL -1 aphidicolin, a procedure believed to produce an accumulation of initiated replicons that arise from normally early replicating DNA. Measurements of nucleosome repeat lengths of bulk chromatin, the early replicating unexpressed metallothionein II (MTII) gene region, and a later replicating repeated sequence indicate that the changes in repeat lengths occur preferentially in the early replicating MTII gene region as G1 cells enter and become synchronized in early S phase. During that time, the MTII gene region is not replicated nor is there any evidence for induction of MTII messenger RNA. Thus, the results are consistent with the hypothesis that changes in chromatin structure occur preferentially in the early replicating (presumably initiated) replicons at initiation or that changes in chromatin structure can precede replication during inhibition of DNA synthesis. The shortened repeat lengths that precede MTII replication are, potentially, reversible, because they become elongated when the synchronized early S-phase cells are released to resume cell cycle progression

  3. The effect of existing turbulence on stratified shear instability

    Science.gov (United States)

    Kaminski, Alexis; Smyth, William

    2017-11-01

    Ocean turbulence is an essential process governing, for example, heat uptake by the ocean. In the stably-stratified ocean interior, this turbulence occurs in discrete events driven by vertical variations of the horizontal velocity. Typically, these events have been modelled by assuming an initially laminar stratified shear flow which develops wavelike instabilities, becomes fully turbulent, and then relaminarizes into a stable state. However, in the real ocean there is always some level of turbulence left over from previous events, and it is not yet understood how this turbulence impacts the evolution of future mixing events. Here, we perform a series of direct numerical simulations of turbulent events developing in stratified shear flows that are already at least weakly turbulent. We do so by varying the amplitude of the initial perturbations, and examine the subsequent development of the instability and the impact on the resulting turbulent fluxes. This work is supported by NSF Grant OCE1537173.

  4. Stratified source-sampling techniques for Monte Carlo eigenvalue analysis

    International Nuclear Information System (INIS)

    Mohamed, A.

    1998-01-01

    In 1995, at a conference on criticality safety, a special session was devoted to the Monte Carlo ''Eigenvalue of the World'' problem. Argonne presented a paper, at that session, in which the anomalies originally observed in that problem were reproduced in a much simplified model-problem configuration, and removed by a version of stratified source-sampling. In this paper, stratified source-sampling techniques are generalized and applied to three different Eigenvalue of the World configurations which take into account real-world statistical noise sources not included in the model problem, but which differ in the amount of neutronic coupling among the constituents of each configuration. It is concluded that, in Monte Carlo eigenvalue analysis of loosely-coupled arrays, the use of stratified source-sampling reduces the probability of encountering an anomalous result over that if conventional source-sampling methods are used. However, this gain in reliability is substantially less than that observed in the model-problem results

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

    Science.gov (United States)

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

    2017-02-01

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

  6. Hourly differences in air pollution and risk of respiratory disease in the elderly: a time-stratified case-crossover study.

    Science.gov (United States)

    Yorifuji, Takashi; Suzuki, Etsuji; Kashima, Saori

    2014-08-13

    Epidemiological studies have shown adverse effects of short-term exposure to air pollution on respiratory disease outcomes; however, few studies examined this association on an hourly time scale. We evaluated the associations between hourly changes in air pollution and the risk of respiratory disease in the elderly, using the time of the emergency call as the disease onset for each case. We used a time-stratified case-crossover design. Study participants were 6,925 residents of the city of Okayama, Japan, aged 65 or above who were taken to hospital emergency rooms between January 2006 and December 2010 for onset of respiratory disease. We calculated city-representative hourly average concentrations of air pollutants from several monitoring stations. By using conditional logistic regression models, we estimated odds ratios per interquartile-range increase in each pollutant by exposure period prior to emergency call, adjusting for hourly ambient temperature, hourly relative humidity, and weekly numbers of reported influenza cases aged ≥60. Suspended particulate matter (SPM) exposure 24 to respiratory disease. For example, following one interquartile-range increase, odds ratios were 1.05 (95% confidence interval: 1.01, 1.09) for SPM exposure 24 to respiratory disease of SPM or ozone. Overall, the effect estimates for chronic obstructive pulmonary disease and allied conditions were equivocal. This study provides further evidence that hourly changes in air pollution exposure increase the risks of respiratory disease, and that SO2 may be related with more immediate onset of the disease than other pollutants.

  7. Autoradiographic studies of chromosome replication during the cell cycle of Streptococcus faecium

    International Nuclear Information System (INIS)

    Higgins, M.L.; Koch, A.L.; Dicker, D.T.; Daneo-Moore, L.

    1986-01-01

    Analysis of the distribution of autoradiographic grains around cells of Streptococcus faecium which had been either continuously or pulse-labeled with tritiated thymidine (mass doubling time, 90 min) showed a non-Poisson distribution even when the distribution of cell sizes in the populations studied was taken into account. These non-Poisson distributions of grains were assumed to reflect the discontinuous nature of chromosome replication. To study this discontinuous process further, an equation was fitted to the grain distribution observed for the pulse-labeled cells that assumed that in any population of cells there were subpopulations in which there were zero, one, or two replicating chromosomes. This analysis predicted an average time for chromosome replication and for the period between completion of rounds of chromosome replication and division of 55 and 43 min, respectively, which were in excellent agreement with estimates made by other techniques. The present investigation extended past studies in indicating that the initiation and completion of rounds of chromosome replication are poorly phased with increases in cell volume and that the amount of chromosome replication may be different in different cell halves

  8. Enhanced replication of damaged SV40 DNA in carcinogen-treated monkey cells

    International Nuclear Information System (INIS)

    Maga, J.A.; Dixon, K.

    1984-01-01

    Treatment of mammalian cells with certain chemical or physical carcinogens prior to infection with ultraviolet-irradiated virus results in enhanced survival or reactivation of the damaged virus. To investigate the molecular basis of this enhanced reactivation (ER), Simian virus 40 DNA replication in carcinogen-treated cells was examined. Treatment of monkey kidney cells with N-acetoxy-2-acetylamino-fluorene or UV radiation 24 h prior to infection with ultraviolet-irradiated Simian virus 40 leads to enhancement of viral DNA replication measured at 36 h after infection by [ 3 H]thymidine incorporation or hybridization. The enhancement of DNA replication is observed when cells are treated from 1 to 60 h before infection or 1 to 16 h after infection. The fact that enhancement is observed also when cells are treated after infection rules out the possiblity that enhancement occurs at the level of adsorption or penetration of the virus. Measurements of the time course of viral DNA replication indicate that pretreatment of cells does not alter the time of onset of viral DNA replication. It is concluded that ER of Simain virus 40 occurs at the level of viral DNA replication. (author)

  9. Visualization of mole fraction distribution of slow jet forming stably stratified field

    International Nuclear Information System (INIS)

    Fumizawa, Motoo; Hishida, Makoto

    1990-01-01

    An experimental study has been performed to investigate the behavior of flow and mass transfer in gaseous slow jet in which buoyancy force opposed the flow forming stably stratified field. The study has been performed to understand the basic features of air ingress phenomena at pipe rupture accident of the high temperature gas-cooled reactor. A displacement fringe technique was adopted in Mach-Zehnder interferometer to visualize the mole fraction distribution. As the result, the followings were obtained: (1) The stably stratified fields were formed in the vicinity of the outlet of the slow jet. The penetration distance of the stably stratified fields increased with Froude number. (2) Mass fraction distributions in the stably stratified fields were well correlated with the present model using the ramp mole velocity profile. (author)

  10. Direct contact condensation induced transition from stratified to slug flow

    International Nuclear Information System (INIS)

    Strubelj, Luka; Ezsoel, Gyoergy; Tiselj, Iztok

    2010-01-01

    Selected condensation-induced water hammer experiments performed on PMK-2 device were numerically modelled with three-dimensional two-fluid models of computer codes NEPTUNE C FD and CFX. Experimental setup consists of the horizontal pipe filled with the hot steam that is being slowly flooded with cold water. In most of the experimental cases, slow flooding of the pipe was abruptly interrupted by a strong slugging and water hammer, while in the selected experimental runs performed at higher initial pressures and temperatures that are analysed in the present work, the transition from the stratified into the slug flow was not accompanied by the water hammer pressure peak. That makes these cases more suitable tests for evaluation of the various condensation models in the horizontally stratified flows and puts them in the range of the available CFD (Computational Fluid Dynamics) codes. The key models for successful simulation appear to be the condensation model of the hot vapour on the cold liquid and the interfacial momentum transfer model. The surface renewal types of condensation correlations, developed for condensation in the stratified flows, were used in the simulations and were applied also in the regions of the slug flow. The 'large interface' model for inter-phase momentum transfer model was compared to the bubble drag model. The CFD simulations quantitatively captured the main phenomena of the experiments, while the stochastic nature of the particular condensation-induced water hammer experiments did not allow detailed prediction of the time and position of the slug formation in the pipe. We have clearly shown that even the selected experiments without water hammer present a tough test for the applied CFD codes, while modelling of the water hammer pressure peaks in two-phase flow, being a strongly compressible flow phenomena, is beyond the capability of the current CFD codes.

  11. Simulation of steam explosion in stratified melt-coolant configuration

    International Nuclear Information System (INIS)

    Leskovar, Matjaž; Centrih, Vasilij; Uršič, Mitja

    2016-01-01

    Highlights: • Strong steam explosions may develop spontaneously in stratified configurations. • Considerable melt-coolant premixed layer formed in subcooled water with hot melts. • Analysis with MC3D code provided insight into stratified steam explosion phenomenon. • Up to 25% of poured melt was mixed with water and available for steam explosion. • Better instrumented experiments needed to determine dominant mixing process. - Abstract: A steam explosion is an energetic fuel coolant interaction process, which may occur during a severe reactor accident when the molten core comes into contact with the coolant water. In nuclear reactor safety analyses steam explosions are primarily considered in melt jet-coolant pool configurations where sufficiently deep coolant pool conditions provide complete jet breakup and efficient premixture formation. Stratified melt-coolant configurations, i.e. a molten melt layer below a coolant layer, were up to now believed as being unable to generate strong explosive interactions. Based on the hypothesis that there are no interfacial instabilities in a stratified configuration it was assumed that the amount of melt in the premixture is insufficient to produce strong explosions. However, the recently performed experiments in the PULiMS and SES (KTH, Sweden) facilities with oxidic corium simulants revealed that strong steam explosions may develop spontaneously also in stratified melt-coolant configurations, where with high temperature melts and subcooled water conditions a considerable melt-coolant premixed layer is formed. In the article, the performed study of steam explosions in a stratified melt-coolant configuration in PULiMS like conditions is presented. The goal of this analytical work is to supplement the experimental activities within the PULiMS research program by addressing the key questions, especially regarding the explosivity of the formed premixed layer and the mechanisms responsible for the melt-water mixing. To

  12. Development of a duplex real-time RT-qPCR assay to monitor genome replication, gene expression and gene insert stability during in vivo replication of a prototype live attenuated canine distemper virus vector encoding SIV gag.

    Science.gov (United States)

    Coleman, John W; Wright, Kevin J; Wallace, Olivia L; Sharma, Palka; Arendt, Heather; Martinez, Jennifer; DeStefano, Joanne; Zamb, Timothy P; Zhang, Xinsheng; Parks, Christopher L

    2015-03-01

    Advancement of new vaccines based on live viral vectors requires sensitive assays to analyze in vivo replication, gene expression and genetic stability. In this study, attenuated canine distemper virus (CDV) was used as a vaccine delivery vector and duplex 2-step quantitative real-time RT-PCR (RT-qPCR) assays specific for genomic RNA (gRNA) or mRNA have been developed that concurrently quantify coding sequences for the CDV nucleocapsid protein (N) and a foreign vaccine antigen (SIV Gag). These amplicons, which had detection limits of about 10 copies per PCR reaction, were used to show that abdominal cavity lymphoid tissues were a primary site of CDV vector replication in infected ferrets, and importantly, CDV gRNA or mRNA was undetectable in brain tissue. In addition, the gRNA duplex assay was adapted for monitoring foreign gene insert genetic stability during in vivo replication by analyzing the ratio of CDV N and SIV gag genomic RNA copies over the course of vector infection. This measurement was found to be a sensitive probe for assessing the in vivo genetic stability of the foreign gene insert. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    Zhong, Wei; Kim, Yushim

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

  15. RADIAL STABILITY IN STRATIFIED STARS

    International Nuclear Information System (INIS)

    Pereira, Jonas P.; Rueda, Jorge A.

    2015-01-01

    We formulate within a generalized distributional approach the treatment of the stability against radial perturbations for both neutral and charged stratified stars in Newtonian and Einstein's gravity. We obtain from this approach the boundary conditions connecting any two phases within a star and underline its relevance for realistic models of compact stars with phase transitions, owing to the modification of the star's set of eigenmodes with respect to the continuous case

  16. 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

  17. STRESS DISTRIBUTION IN THE STRATIFIED MASS CONTAINING VERTICAL ALVEOLE

    Directory of Open Access Journals (Sweden)

    Bobileva Tatiana Nikolaevna

    2017-08-01

    Full Text Available Almost all subsurface rocks used as foundations for various types of structures are stratified. Such heterogeneity may cause specific behaviour of the materials under strain. Differential equations describing the behaviour of such materials contain rapidly fluctuating coefficients, in view of this, solution of such equations is more time-consuming when using today’s computers. The method of asymptotic averaging leads to getting homogeneous medium under study to averaged equations with fixed factors. The present article is concerned with stratified soil mass consisting of pair-wise alternative isotropic elastic layers. In the results of elastic modules averaging, the present soil mass with horizontal rock stratification is simulated by homogeneous transversal-isotropic half-space with isotropy plane perpendicular to the standing axis. Half-space is loosened by a vertical alveole of circular cross-section, and virgin ground is under its own weight. For horizontal parting planes of layers, the following two types of surface conditions are set: ideal contact and backlash without cleavage. For homogeneous transversal-isotropic half-space received with a vertical alveole, the analytical solution of S.G. Lekhnitsky, well known in scientific papers, is used. The author gives expressions for stress components and displacements in soil mass for different marginal conditions on the alveole surface. Such research problems arise when constructing and maintaining buildings and when composite materials are used.

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

    Science.gov (United States)

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

    2016-07-01

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

  19. Soil mixing of stratified contaminated sands.

    Science.gov (United States)

    Al-Tabba, A; Ayotamuno, M J; Martin, R J

    2000-02-01

    Validation of soil mixing for the treatment of contaminated ground is needed in a wide range of site conditions to widen the application of the technology and to understand the mechanisms involved. Since very limited work has been carried out in heterogeneous ground conditions, this paper investigates the effectiveness of soil mixing in stratified sands using laboratory-scale augers. This enabled a low cost investigation of factors such as grout type and form, auger design, installation procedure, mixing mode, curing period, thickness of soil layers and natural moisture content on the unconfined compressive strength, leachability and leachate pH of the soil-grout mixes. The results showed that the auger design plays a very important part in the mixing process in heterogeneous sands. The variability of the properties measured in the stratified soils and the measurable variations caused by the various factors considered, highlighted the importance of duplicating appropriate in situ conditions, the usefulness of laboratory-scale modelling of in situ conditions and the importance of modelling soil and contaminant heterogeneities at the treatability study stage.

  20. Determination of selenium in food matrices by replicate sample neutron activation analysis

    International Nuclear Information System (INIS)

    Ventura, M.G.; Freitas, M.C.; Ventura, M.G.; Pacheco, A.M.G.

    2009-01-01

    The replicate sample instrumental neutron activation method was optimized and used for the determination of selenium in foodstuffs. The method was reliable, yielding accurate results. Lower detections limits were obtained after each successive irradiation. Different irradiation conditions were used depending on the type of sample. For samples with higher selenium contents (meat, fish, eggs), the measured selenium in the first replicate is in all cases larger than the detection limit, but a better accuracy was obtained with a larger number of replicates (2-3 replicates). For samples with extremely low selenium contents (vegetable samples), at least seven replicates were necessary to obtain a concentration value two times larger than the detection limit. (author)

  1. Stratified charge rotary aircraft engine technology enablement program

    Science.gov (United States)

    Badgley, P. R.; Irion, C. E.; Myers, D. M.

    1985-01-01

    The multifuel stratified charge rotary engine is discussed. A single rotor, 0.7L/40 cu in displacement, research rig engine was tested. The research rig engine was designed for operation at high speeds and pressures, combustion chamber peak pressure providing margin for speed and load excursions above the design requirement for a high is advanced aircraft engine. It is indicated that the single rotor research rig engine is capable of meeting the established design requirements of 120 kW, 8,000 RPM, 1,379 KPA BMEP. The research rig engine, when fully developed, will be a valuable tool for investigating, advanced and highly advanced technology components, and provide an understanding of the stratified charge rotary engine combustion process.

  2. Asynchronous DNA replication within the human β-globin gene locus

    International Nuclear Information System (INIS)

    Epner, E.; Forrester, W.C.; Groudine, M.

    1988-01-01

    The timing of DNA replication of the human β-globin gene locus has been studied by blot hybridization of newly synthesized BrdUrd-substituted DNA from cells in different stages of the S phase. Using probes that span >120 kilobases across the human β-globin gene locus, the authors show that the majority of this domain replicates in early S phase in the human erythroleukemia cell line K562 and in middle-to-late S phase in the lymphoid cell line Manca. However, in K562 cells three small regions display a strikingly different replication pattern than adjacent sequences. These islands, located in the inter-γ-globin gene region and approximately 20 kilobases 5' to the ε-globin gene and 20 kilobases 3' to the β-globin gene, replicate later and throughout S phase. A similar area is also present in the α-globin gene region in K562 cells. They suggest that these regions may represent sites of termination of replication forks

  3. A review of recent developments on turbulent entrainment in stratified flows

    International Nuclear Information System (INIS)

    Cotel, Aline J

    2010-01-01

    Stratified interfaces are present in many geophysical flow situations, and transport across such an interface is an essential factor for correctly evaluating the physical processes taking place at many spatial and temporal scales in such flows. In order to accurately evaluate vertical and lateral transport occurring when a turbulent flow impinges on a stratified interface, the turbulent entrainment and vorticity generation mechanisms near the interface must be understood and quantified. Laboratory experiments were performed for three flow configurations: a vertical thermal, a sloping gravity current and a vertical turbulent jet with various tilt angles and precession speeds. All three flows impinged on an interface separating a two-layer stably stratified environment. The entrainment rate is quantified for each flow using laser-induced fluorescence and compared to predictions of Cotel and Breidenthal (1997 Appl. Sci. Res. 57 349-66). The possible applications of transport across stratified interfaces include the contribution of hydrothermal plumes to the global ocean energy budget, turbidity currents on the ocean floor, the design of lake de-stratification systems, modeling gas leaks from storage reservoirs, weather forecasting and global climate change.

  4. Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq.

    Science.gov (United States)

    Marchal, Claire; Sasaki, Takayo; Vera, Daniel; Wilson, Korey; Sima, Jiao; Rivera-Mulia, Juan Carlos; Trevilla-García, Claudia; Nogues, Coralin; Nafie, Ebtesam; Gilbert, David M

    2018-05-01

    This protocol is an extension to: Nat. Protoc. 6, 870-895 (2014); doi:10.1038/nprot.2011.328; published online 02 June 2011Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early- and late-replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and subnuclear position. Moreover, RT is regulated during development and is altered in diseases. Here, we describe E/L Repli-seq, an extension of our Repli-chip protocol. E/L Repli-seq is a rapid, robust and relatively inexpensive protocol for analyzing RT by next-generation sequencing (NGS), allowing genome-wide assessment of how cellular processes are linked to RT. Briefly, cells are pulse-labeled with BrdU, and early and late S-phase fractions are sorted by flow cytometry. Labeled nascent DNA is immunoprecipitated from both fractions and sequenced. Data processing leads to a single bedGraph file containing the ratio of nascent DNA from early versus late S-phase fractions. The results are comparable to those of Repli-chip, with the additional benefits of genome-wide sequence information and an increased dynamic range. We also provide computational pipelines for downstream analyses, for parsing phased genomes using single-nucleotide polymorphisms (SNPs) to analyze RT allelic asynchrony, and for direct comparison to Repli-chip data. This protocol can be performed in up to 3 d before sequencing, and requires basic cellular and molecular biology skills, as well as a basic understanding of Unix and R.

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

    Science.gov (United States)

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

    1996-07-01

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

  6. Human cytomegalovirus replicates in gamma-irradiated fibroblasts

    International Nuclear Information System (INIS)

    Shanley, J.D.

    1986-01-01

    Because of the unique interdependence of human cytomegalovirus (HCMV) and the physiological state of the host cell, we evaluated the ability of human foreskin fibroblasts (HFF), exposed to gamma radiation, to support HCMV growth. Irradiation of HFF with 2,500 rADS prevented cellular proliferation and suppressed cellular DNA, but not RNA or protein synthesis. Treatment of HFF cells with 2,500 rADS 6 or 48 hours prior to infection did not alter the time course or virus yield during HCMV replication. Virus plaquing efficiency in irradiated cells was comparable to that of nonirradiated cells. As judged by thymidine incorporation and BUdR inhibition of virus replication, HCMV infection induced both thymidine kinase activity and host cell DNA synthesis in irradiated cells. In addition, virus could be recovered from HFF exposed to radiation 0-2 days after infection with HCMV. These studies indicate that the damage to cells by gamma irradiation does not alter the capacity of host cells to support HCMV replication

  7. 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.

  8. Stratified turbulent Bunsen flames : flame surface analysis and flame surface density modelling

    NARCIS (Netherlands)

    Ramaekers, W.J.S.; Oijen, van J.A.; Goey, de L.P.H.

    2012-01-01

    In this paper it is investigated whether the Flame Surface Density (FSD) model, developed for turbulent premixed combustion, is also applicable to stratified flames. Direct Numerical Simulations (DNS) of turbulent stratified Bunsen flames have been carried out, using the Flamelet Generated Manifold

  9. 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.)

  10. 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...

  11. 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.

  12. 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...

  13. Spinning phenomena and energetics of spherically pulsating patterns in stratified fluids

    International Nuclear Information System (INIS)

    Ibragimov, Ranis N; Dameron, Michael

    2011-01-01

    The nonlinear solutions of the two-dimensional Boussinesq equations describing internal waves in rotating stratified fluids were obtained as group invariant solutions. The latter nonlinear solutions correspond to the rotation transformation preserving the form of the original nonlinear equations of motion. It is shown that the obtained class of exact solutions can be associated with the spherically pulsating patterns observed in uniformly stratified fluids. It is also shown that the obtained rotationally symmetric solutions are bounded functions that can be visualized as spinning patterns in stratified fluids. It is also shown that the rotational transformation provides the energy conservation law together with other conservation laws for which the spinning phenomena is observed. The effects of nonlinearity and the Earth's rotation on such a phenomenon are also discussed.

  14. 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.

  15. 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.

  16. Legionella pneumophila-Derived Outer Membrane Vesicles Promote Bacterial Replication in Macrophages.

    Directory of Open Access Journals (Sweden)

    Anna Lena Jung

    2016-04-01

    Full Text Available The formation and release of outer membrane vesicles (OMVs is a phenomenon of Gram-negative bacteria. This includes Legionella pneumophila (L. pneumophila, a causative agent of severe pneumonia. Upon its transmission into the lung, L. pneumophila primarily infects and replicates within macrophages. Here, we analyzed the influence of L. pneumophila OMVs on macrophages. To this end, differentiated THP-1 cells were incubated with increasing doses of Legionella OMVs, leading to a TLR2-dependent classical activation of macrophages with the release of pro-inflammatory cytokines. Inhibition of TLR2 and NF-κB signaling reduced the induction of pro-inflammatory cytokines. Furthermore, treatment of THP-1 cells with OMVs prior to infection reduced replication of L. pneumophila in THP-1 cells. Blocking of TLR2 activation or heat denaturation of OMVs restored bacterial replication in the first 24 h of infection. With prolonged infection-time, OMV pre-treated macrophages became more permissive for bacterial replication than untreated cells and showed increased numbers of Legionella-containing vacuoles and reduced pro-inflammatory cytokine induction. Additionally, miRNA-146a was found to be transcriptionally induced by OMVs and to facilitate bacterial replication. Accordingly, IRAK-1, one of miRNA-146a's targets, showed prolonged activation-dependent degradation, which rendered THP-1 cells more permissive for Legionella replication. In conclusion, L. pneumophila OMVs are initially potent pro-inflammatory stimulators of macrophages, acting via TLR2, IRAK-1, and NF-κB, while at later time points, OMVs facilitate L. pneumophila replication by miR-146a-dependent IRAK-1 suppression. OMVs might thereby promote spreading of L. pneumophila in the host.

  17. Modeling the Conducting Stably-Stratified Layer of the Earth's Core

    Science.gov (United States)

    Petitdemange, L.; Philidet, J.; Gissinger, C.

    2017-12-01

    Observations of the Earth magnetic field as well as recent theoretical works tend to show that the Earth's outer liquid core is mostly comprised of a convective zone in which the Earth's magnetic field is generated - likely by dynamo action -, but also features a thin, stably stratified layer at the top of the core.We carry out direct numerical simulations by modeling this thin layer as an axisymmetric spherical Couette flow for a stably stratified fluid embedded in a dipolar magnetic field. The dynamo region is modeled by a conducting inner core rotating slightly faster than the insulating mantle due to magnetic torques acting on it, such that a weak differential rotation (low Rossby limit) can develop in the stably stratified layer.In the case of a non-stratified fluid, the combined action of the differential rotation and the magnetic field leads to the well known regime of `super-rotation', in which the fluid rotates faster than the inner core. Whereas in the classical case, this super-rotation is known to vanish in the magnetostrophic limit, we show here that the fluid stratification significantly extends the magnitude of the super-rotation, keeping this phenomenon relevant for the Earth core. Finally, we study how the shear layers generated by this new state might give birth to magnetohydrodynamic instabilities or waves impacting the secular variations or jerks of the Earth's magnetic field.

  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. Replication of simulated prebiotic amphiphile vesicles controlled by experimental lipid physicochemical properties

    International Nuclear Information System (INIS)

    Armstrong, Don L; Zidovetzki, Raphael; Markovitch, Omer; Lancet, Doron

    2011-01-01

    We present a new embodiment of the graded autocatalysis replication domain (GARD) for the growth, replication and evolution of lipid vesicles based on a semi-empirical foundation using experimentally measured kinetic values of selected extant lipid species. Extensive simulations using this formalism elucidated the details of the dependence of the replication and properties of the vesicles on the physicochemical properties and concentrations of the lipids, both in the environment and in the vesicle. As expected, the overall concentration and number of amphiphilic components strongly affect average replication time. Furthermore, variations in acyl chain length and unsaturation of vesicles also influence replication rate, as do the relative concentrations of individual lipid types. Understanding of the dependence of replication rates on physicochemical parameters opens a new direction in the study of prebiotic vesicles and lays the groundwork for future studies involving the competition between lipid vesicles for available amphiphilic monomers

  20. 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.

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

    NARCIS (Netherlands)

    Moolman, M.C.; Tiruvadi Krishnan, S; Kerssemakers, J.W.J.; de Leeuw, R.; Lorent, V.J.F.; Sherratt, David J.; Dekker, N.H.

    2016-01-01

    Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these

  2. Flock House virus subgenomic RNA3 is replicated and its replication correlates with transactivation of RNA2

    International Nuclear Information System (INIS)

    Eckerle, Lance D.; Albarino, Cesar G.; Ball, L. Andrew.

    2003-01-01

    The nodavirus Flock House virus has a bipartite genome composed of RNAs 1 and 2, which encode the catalytic component of the RNA-dependent RNA polymerase (RdRp) and the capsid protein precursor, respectively. In addition to catalyzing replication of the viral genome, the RdRp also transcribes from RNA1 a subgenomic RNA3, which is both required for and suppressed by RNA2 replication. Here, we show that in the absence of RNA1 replication, FHV RdRp replicated positive-sense RNA3 transcripts fully and copied negative-sense RNA3 transcripts into positive strands. The two nonstructural proteins encoded by RNA3 were dispensable for replication, but sequences in the 3'-terminal 58 nucleotides were required. RNA3 variants that failed to replicate also failed to transactivate RNA2. These results imply that RNA3 is naturally produced both by transcription from RNA1 and by subsequent RNA1-independent replication and that RNA3 replication may be necessary for transactivation of RNA2

  3. Background stratified Poisson regression analysis of cohort data.

    Science.gov (United States)

    Richardson, David B; Langholz, Bryan

    2012-03-01

    Background stratified Poisson regression is an approach that has been used in the analysis of data derived from a variety of epidemiologically important studies of radiation-exposed populations, including uranium miners, nuclear industry workers, and atomic bomb survivors. We describe a novel approach to fit Poisson regression models that adjust for a set of covariates through background stratification while directly estimating the radiation-disease association of primary interest. The approach makes use of an expression for the Poisson likelihood that treats the coefficients for stratum-specific indicator variables as 'nuisance' variables and avoids the need to explicitly estimate the coefficients for these stratum-specific parameters. Log-linear models, as well as other general relative rate models, are accommodated. This approach is illustrated using data from the Life Span Study of Japanese atomic bomb survivors and data from a study of underground uranium miners. The point estimate and confidence interval obtained from this 'conditional' regression approach are identical to the values obtained using unconditional Poisson regression with model terms for each background stratum. Moreover, it is shown that the proposed approach allows estimation of background stratified Poisson regression models of non-standard form, such as models that parameterize latency effects, as well as regression models in which the number of strata is large, thereby overcoming the limitations of previously available statistical software for fitting background stratified Poisson regression models.

  4. Control of Initiation of DNA Replication in Bacillus subtilis and Escherichia coli

    Directory of Open Access Journals (Sweden)

    Katie H. Jameson

    2017-01-01

    Full Text Available Initiation of DNA Replication is tightly regulated in all cells since imbalances in chromosomal copy number are deleterious and often lethal. In bacteria such as Bacillus subtilis and Escherichia coli, at the point of cytokinesis, there must be two complete copies of the chromosome to partition into the daughter cells following division at mid-cell during vegetative growth. Under conditions of rapid growth, when the time taken to replicate the chromosome exceeds the doubling time of the cells, there will be multiple initiations per cell cycle and daughter cells will inherit chromosomes that are already undergoing replication. In contrast, cells entering the sporulation pathway in B. subtilis can do so only during a short interval in the cell cycle when there are two, and only two, chromosomes per cell, one destined for the spore and one for the mother cell. Here, we briefly describe the overall process of DNA replication in bacteria before reviewing initiation of DNA replication in detail. The review covers DnaA-directed assembly of the replisome at oriC and the multitude of mechanisms of regulation of initiation, with a focus on the similarities and differences between E. coli and B. subtilis.

  5. Control of Initiation of DNA Replication in Bacillus subtilis and Escherichia coli

    Science.gov (United States)

    Jameson, Katie H.; Wilkinson, Anthony J.

    2017-01-01

    Initiation of DNA Replication is tightly regulated in all cells since imbalances in chromosomal copy number are deleterious and often lethal. In bacteria such as Bacillus subtilis and Escherichia coli, at the point of cytokinesis, there must be two complete copies of the chromosome to partition into the daughter cells following division at mid-cell during vegetative growth. Under conditions of rapid growth, when the time taken to replicate the chromosome exceeds the doubling time of the cells, there will be multiple initiations per cell cycle and daughter cells will inherit chromosomes that are already undergoing replication. In contrast, cells entering the sporulation pathway in B. subtilis can do so only during a short interval in the cell cycle when there are two, and only two, chromosomes per cell, one destined for the spore and one for the mother cell. Here, we briefly describe the overall process of DNA replication in bacteria before reviewing initiation of DNA replication in detail. The review covers DnaA-directed assembly of the replisome at oriC and the multitude of mechanisms of regulation of initiation, with a focus on the similarities and differences between E. coli and B. subtilis. PMID:28075389

  6. Single molecular biology: coming of age in DNA replication.

    Science.gov (United States)

    Liu, Xiao-Jing; Lou, Hui-Qiang

    2017-09-20

    DNA replication is an essential process of the living organisms. To achieve precise and reliable replication, DNA polymerases play a central role in DNA synthesis. Previous investigations have shown that the average rates of DNA synthesis on the leading and lagging strands in a replisome must be similar to avoid the formation of significant gaps in the nascent strands. The underlying mechanism has been assumed to be coordination between leading- and lagging-strand polymerases. However, Kowalczykowski's lab members recently performed single molecule techniques in E. coli and showed the real-time behavior of a replisome. The leading- and lagging-strand polymerases function stochastically and independently. Furthermore, when a DNA polymerase is paused, the helicase slows down in a self-regulating fail-safe mechanism, akin to a ''dead-man's switch''. Based on the real-time single-molecular observation, the authors propose that leading- and lagging-strand polymerases synthesize DNA stochastically within a Gaussian distribution. Along with the development and application of single-molecule techniques, we will witness a new age of DNA replication and other biological researches.

  7. DNA Replication Control During Drosophila Development: Insights into the Onset of S Phase, Replication Initiation, and Fork Progression

    Science.gov (United States)

    Hua, Brian L.; Orr-Weaver, Terry L.

    2017-01-01

    Proper control of DNA replication is critical to ensure genomic integrity during cell proliferation. In addition, differential regulation of the DNA replication program during development can change gene copy number to influence cell size and gene expression. Drosophila melanogaster serves as a powerful organism to study the developmental control of DNA replication in various cell cycle contexts in a variety of differentiated cell and tissue types. Additionally, Drosophila has provided several developmentally regulated replication models to dissect the molecular mechanisms that underlie replication-based copy number changes in the genome, which include differential underreplication and gene amplification. Here, we review key findings and our current understanding of the developmental control of DNA replication in the contexts of the archetypal replication program as well as of underreplication and differential gene amplification. We focus on the use of these latter two replication systems to delineate many of the molecular mechanisms that underlie the developmental control of replication initiation and fork elongation. PMID:28874453

  8. Nitrogen transformations in stratified aquatic microbial ecosystems

    DEFF Research Database (Denmark)

    Revsbech, N. P.; Risgaard-Petersen, N.; Schramm, A.

    2006-01-01

    Abstract  New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a µm-mm scale. A large and ever-expanding knowledge base about n...

  9. Air Pollution and Suicide in 10 Cities in Northeast Asia: A Time-Stratified Case-Crossover Analysis.

    Science.gov (United States)

    Kim, Yoonhee; Ng, Chris Fook Sheng; Chung, Yeonseung; Kim, Ho; Honda, Yasushi; Guo, Yue Leon; Lim, Youn-Hee; Chen, Bing-Yu; Page, Lisa A; Hashizume, Masahiro

    2018-03-06

    There is growing evidence suggesting an association between air pollution and suicide. However, previous findings varied depending on the type of air pollutant and study location. We examined the association between air pollutants and suicide in 10 large cities in South Korea, Japan, and Taiwan. We used a two-stage meta-analysis. First, we conducted a time-stratified case-crossover analysis to estimate the short-term association between nitrogen dioxide (NO 2 ), sulfur dioxide (SO 2 ), and particulate matter [aerodynamic diameter ≤10μm (PM 10 ), aerodynamic diameter ≤2.5μm (PM 2.5 ), and PM 10–2.5 ] and suicide, adjusted for weather factors, day-of-week, long-term time trends, and season. Then, we conducted a meta-analysis to combine the city-specific effect estimates for NO 2 , SO 2 , and PM 10 across 10 cities and for PM 2.5 and PM 10–2.5 across 3 cities. We first fitted single-pollutant models, followed by two-pollutant models to examine the robustness of the associations. Higher risk of suicide was associated with higher levels of NO 2 , SO 2 , PM 10 , and PM 10–2.5 over multiple days. The combined relative risks (RRs) were 1.019 for NO 2 (95% confidence interval [CI]: 0.999, 1.039), 1.020 for SO 2 (95% CI: 1.005, 1.036), 1.016 for PM 10 (95% CI: 1.004, 1.029), and 1.019 for PM 10–2.5 (95% CI: 1.005, 1.033) per interquartile range (IQR) increase in the 0-1 d average level of each pollutant. We found no evidence of an association for PM 2.5 . Some of the associations, particularly for SO 2 and NO 2 , were attenuated after adjusting for a second pollutant. Our findings suggest that higher levels of air pollution may be associated with suicide, and further research is merited to understand the underlying mechanisms. https://doi.org/10.1289/EHP2223.

  10. Improved patient selection by stratified surgical intervention

    DEFF Research Database (Denmark)

    Wang, Miao; Bünger, Cody E; Li, Haisheng

    2015-01-01

    BACKGROUND CONTEXT: Choosing the best surgical treatment for patients with spinal metastases remains a significant challenge for spine surgeons. There is currently no gold standard for surgical treatments. The Aarhus Spinal Metastases Algorithm (ASMA) was established to help surgeons choose...... the most appropriate surgical intervention for patients with spinal metastases. PURPOSE: The purpose of this study was to evaluate the clinical outcome of stratified surgical interventions based on the ASMA, which combines life expectancy and the anatomical classification of patients with spinal metastases...... survival times in the five surgical groups determined by the ASMA were 2.1 (TS 0-4, TC 1-7), 5.1 (TS 5-8, TC 1-7), 12.1 (TS 9-11, TC 1-7 or TS 12-15, TC 7), 26.0 (TS 12-15, TC 4-6), and 36.0 (TS 12-15, TC 1-3) months. The 30-day mortality rate was 7.5%. Postoperative neurological function was maintained...

  11. Experimental study of unsteady thermally stratified flow

    International Nuclear Information System (INIS)

    Lee, Sang Jun; Chung, Myung Kyoon

    1985-01-01

    Unsteady thermally stratified flow caused by two-dimensional surface discharge of warm water into a oblong channel was investigated. Experimental study was focused on the rapidly developing thermal diffusion at small Richardson number. The basic objectives were to study the interfacial mixing between a flowing layer of warm water and an underlying body of cold water and to accumulate experimental data to test computational turbulence models. Mean velocity field measurements were carried out by using NMR-CT(Nuclear Magnetic Resonance-Computerized Tomography). It detects quantitative flow image of any desired section in any direction of flow in short time. Results show that at small Richardson number warm layer rapidly penetrates into the cold layer because of strong turbulent mixing and instability between the two layers. It is found that the transfer of heat across the interface is more vigorous than that of momentum. It is also proved that the NMR-CT technique is a very valuable tool to measure unsteady three dimensional flow field. (Author)

  12. Replication cycle of duck hepatitis A virus type 1 in duck embryonic hepatocytes

    International Nuclear Information System (INIS)

    Yao, Fangke; Chen, Yun; Shi, Jintong; Ming, Ke; Liu, Jiaguo; Xiong, Wen; Song, Meiyun; Du, Hongxu; Wang, Yixuan; Zhang, Shuaibin; Wu, Yi; Wang, Deyun; Hu, Yuanliang

    2016-01-01

    Duck hepatitis A virus type 1 (DHAV-1) is an important agent of duck viral hepatitis. Until recently, the replication cycle of DHAV-1 is still unknown. Here duck embryonic hepatocytes infected with DHAV-1 were collected at different time points, and dynamic changes of the relative DHAV-1 gene expression during replication were detected by real-time PCR. And the morphology of hepatocytes infected with DHAV was evaluated by electron microscope. The result suggested that the adsorption of DHAV-1 saturated at 90 min post-infection, and the virus particles with size of about 50 nm including more than 20 nm of vacuum drying gold were observed on the infected cells surface. What's more, the replication lasted around 13 h after the early protein synthesis for about 5 h, and the release of DHAV-1 was in steady state after 32 h. The replication cycle will enrich the data for DVH control and provide the foundation for future studies. - Highlights: • This is the first description of the replication cycle of DHAV-1. • Firstly find that DHAV-1 adsorption saturated at 90 min post-infection. • The replication lasted around 13 h after early protein synthesis for about 5 h. • The release of DHAV-1 was in steady state after 32 h.

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

    Science.gov (United States)

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

    2016-07-27

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

  14. The clinical and cost-effectiveness of stratified care for patients with sciatica: the SCOPiC randomised controlled trial protocol (ISRCTN75449581).

    Science.gov (United States)

    Foster, Nadine E; Konstantinou, Kika; Lewis, Martyn; Ogollah, Reuben; Dunn, Kate M; van der Windt, Danielle; Beardmore, Ruth; Artus, Majid; Bartlam, Bernadette; Hill, Jonathan C; Jowett, Sue; Kigozi, Jesse; Mallen, Christian; Saunders, Benjamin; Hay, Elaine M

    2017-04-26

    Sciatica has a substantial impact on patients, and is associated with high healthcare and societal costs. Although there is variation in the clinical management of sciatica, the current model of care usually involves an initial period of 'wait and see' for most patients, with simple measures of advice and analgesia, followed by conservative and/or more invasive interventions if symptoms fail to resolve. A model of care is needed that does not over-treat those with a good prognosis yet identifies patients who do need more intensive treatment to help with symptoms, and return to everyday function including work. The aim of the SCOPiC trial (SCiatica Outcomes in Primary Care) is to establish whether stratified care based on subgrouping using a combination of prognostic and clinical information, with matched care pathways, is more effective than non-stratified care, for improving time to symptom resolution in patients consulting with sciatica in primary care. We will also assess the impact of stratified care on service delivery and evaluate its cost-effectiveness compared to non-stratified care. Multicentre, pragmatic, parallel arm randomised trial, with internal pilot, cost-effectiveness analysis and embedded qualitative study. We will recruit 470 adult patients with sciatica from general practices in England and Wales, over 24 months. Patients will be randomised to stratified care or non-stratified care, and treated in physiotherapy and spinal specialist services, in participating NHS services. The primary outcome is time to first resolution of sciatica symptoms, measured on a 6-point ordered categorical scale, collected using text messaging. Secondary outcomes include physical function, pain intensity, quality of life, work loss, healthcare use and satisfaction with treatment, and will be collected using postal questionnaires at 4 and 12-month follow-up. Semi-structured qualitative interviews with a subsample of participants and clinicians will explore the

  15. Structural Insights into the Coupling of Virion Assembly and Rotavirus Replication

    Science.gov (United States)

    Trask, Shane D.; McDonald, Sarah M.; Patton, John T.

    2013-01-01

    Preface Viral replication is rapid and robust, but it is far from a chaotic process. Instead, successful production of infectious progeny requires that events occur in the correct place and at the correct time. Rotavirus, a segmented double-stranded RNA virus of the Reoviridae family, seems to govern its replication through ordered disassembly and assembly of a triple-layered icosahedral capsid. In recent years, high-resolution structural data have provided unprecedented insight into these events. In this Review, we explore the current understanding of rotavirus replication and how it compares to other Reoviridae family members. PMID:22266782

  16. Molecular polymorphism of a cell surface proteoglycan: distinct structures on simple and stratified epithelia.

    Science.gov (United States)

    Sanderson, R D; Bernfield, M

    1988-12-01

    Epithelial cells are organized into either a single layer (simple epithelia) or multiple layers (stratified epithelia). Maintenance of these cellular organizations requires distinct adhesive mechanisms involving many cell surface molecules. One such molecule is a cell surface proteoglycan, named syndecan, that contains both heparan sulfate and chondroitin sulfate chains. This proteoglycan binds cells to fibrillar collagens and fibronectin and thus acts as a receptor for interstitial matrix. The proteoglycan is restricted to the basolateral surface of simple epithelial cells, but is located over the entire surface of stratified epithelial cells, even those surfaces not contacting matrix. We now show that the distinct localization in simple and stratified epithelia correlates with a distinct proteoglycan structure. The proteoglycan from simple epithelia (modal molecular size, 160 kDa) is larger than that from stratified epithelia (modal molecular size, 92 kDa), but their core proteins are identical in size and immunoreactivity. The proteoglycan from simple epithelia has more and larger heparan sulfate and chondroitin sulfate chains than the proteoglycan from stratified epithelia. Thus, the cell surface proteoglycan shows a tissue-specific structural polymorphism due to distinct posttranslational modifications. This polymorphism likely reflects distinct proteoglycan functions in simple and stratified epithelia, potentially meeting the different adhesive requirements of the cells in these different organizations.

  17. Replicating Health Economic Models: Firm Foundations or a House of Cards?

    Science.gov (United States)

    Bermejo, Inigo; Tappenden, Paul; Youn, Ji-Hee

    2017-11-01

    Health economic evaluation is a framework for the comparative analysis of the incremental health gains and costs associated with competing decision alternatives. The process of developing health economic models is usually complex, financially expensive and time-consuming. For these reasons, model development is sometimes based on previous model-based analyses; this endeavour is usually referred to as model replication. Such model replication activity may involve the comprehensive reproduction of an existing model or 'borrowing' all or part of a previously developed model structure. Generally speaking, the replication of an existing model may require substantially less effort than developing a new de novo model by bypassing, or undertaking in only a perfunctory manner, certain aspects of model development such as the development of a complete conceptual model and/or comprehensive literature searching for model parameters. A further motivation for model replication may be to draw on the credibility or prestige of previous analyses that have been published and/or used to inform decision making. The acceptability and appropriateness of replicating models depends on the decision-making context: there exists a trade-off between the 'savings' afforded by model replication and the potential 'costs' associated with reduced model credibility due to the omission of certain stages of model development. This paper provides an overview of the different levels of, and motivations for, replicating health economic models, and discusses the advantages, disadvantages and caveats associated with this type of modelling activity. Irrespective of whether replicated models should be considered appropriate or not, complete replicability is generally accepted as a desirable property of health economic models, as reflected in critical appraisal checklists and good practice guidelines. To this end, the feasibility of comprehensive model replication is explored empirically across a small

  18. 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....

  19. Effects of solution chemistry and aging time on prion protein adsorption and replication of soil-bound prions.

    Directory of Open Access Journals (Sweden)

    Samuel E Saunders

    2011-04-01

    Full Text Available Prion interactions with soil may play an important role in the transmission of chronic wasting disease (CWD and scrapie. Prions are known to bind to a wide range of soil surfaces, but the effects of adsorption solution chemistry and long-term soil binding on prion fate and transmission risk are unknown. We investigated HY TME prion protein (PrP(Sc adsorption to soil minerals in aqueous solutions of phosphate buffered saline (PBS, sodium chloride, calcium chloride, and deionized water using western blotting. The replication efficiency of bound prions following adsorption in these solutions was also evaluated by protein misfolding cyclic amplification (PMCA. Aging studies investigated PrP(Sc desorption and replication efficiency up to one year following adsorption in PBS or DI water. Results indicate that adsorption solution chemistry can affect subsequent prion replication or desorption ability, especially after incubation periods of 30 d or longer. Observed effects were minor over the short-term (7 d or less. Results of long-term aging experiments demonstrate that unbound prions or prions bound to a diverse range of soil surfaces can readily replicate after one year. Our results suggest that while prion-soil interactions can vary with solution chemistry, prions bound to soil could remain a risk for transmitting prion diseases after months in the environment.

  20. Late replicating domains are highly recombining in females but have low male recombination rates: implications for isochore evolution.

    Directory of Open Access Journals (Sweden)

    Catherine J Pink

    Full Text Available In mammals sequences that are either late replicating or highly recombining have high rates of evolution at putatively neutral sites. As early replicating domains and highly recombining domains both tend to be GC rich we a priori expect these two variables to covary. If so, the relative contribution of either of these variables to the local neutral substitution rate might have been wrongly estimated owing to covariance with the other. Against our expectations, we find that sex-averaged recombination rates show little or no correlation with replication timing, suggesting that they are independent determinants of substitution rates. However, this result masks significant sex-specific complexity: late replicating domains tend to have high recombination rates in females but low recombination rates in males. That these trends are antagonistic explains why sex-averaged recombination is not correlated with replication timing. This unexpected result has several important implications. First, although both male and female recombination rates covary significantly with intronic substitution rates, the magnitude of this correlation is moderately underestimated for male recombination and slightly overestimated for female recombination, owing to covariance with replicating timing. Second, the result could explain why male recombination is strongly correlated with GC content but female recombination is not. If to explain the correlation between GC content and replication timing we suppose that late replication forces reduced GC content, then GC promotion by biased gene conversion during female recombination is partly countered by the antagonistic effect of later replicating sequence tending increase AT content. Indeed, the strength of the correlation between female recombination rate and local GC content is more than doubled by control for replication timing. Our results underpin the need to consider sex-specific recombination rates and potential covariates in

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

    Science.gov (United States)

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

    2006-02-01

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

  2. Background stratified Poisson regression analysis of cohort data

    International Nuclear Information System (INIS)

    Richardson, David B.; Langholz, Bryan

    2012-01-01

    Background stratified Poisson regression is an approach that has been used in the analysis of data derived from a variety of epidemiologically important studies of radiation-exposed populations, including uranium miners, nuclear industry workers, and atomic bomb survivors. We describe a novel approach to fit Poisson regression models that adjust for a set of covariates through background stratification while directly estimating the radiation-disease association of primary interest. The approach makes use of an expression for the Poisson likelihood that treats the coefficients for stratum-specific indicator variables as 'nuisance' variables and avoids the need to explicitly estimate the coefficients for these stratum-specific parameters. Log-linear models, as well as other general relative rate models, are accommodated. This approach is illustrated using data from the Life Span Study of Japanese atomic bomb survivors and data from a study of underground uranium miners. The point estimate and confidence interval obtained from this 'conditional' regression approach are identical to the values obtained using unconditional Poisson regression with model terms for each background stratum. Moreover, it is shown that the proposed approach allows estimation of background stratified Poisson regression models of non-standard form, such as models that parameterize latency effects, as well as regression models in which the number of strata is large, thereby overcoming the limitations of previously available statistical software for fitting background stratified Poisson regression models. (orig.)

  3. A 3D spectral anelastic hydrodynamic code for shearing, stratified flows

    Science.gov (United States)

    Barranco, Joseph A.; Marcus, Philip S.

    2006-11-01

    We have developed a three-dimensional (3D) spectral hydrodynamic code to study vortex dynamics in rotating, shearing, stratified systems (e.g., the atmosphere of gas giant planets, protoplanetary disks around newly forming protostars). The time-independent background state is stably stratified in the vertical direction and has a unidirectional linear shear flow aligned with one horizontal axis. Superposed on this background state is an unsteady, subsonic flow that is evolved with the Euler equations subject to the anelastic approximation to filter acoustic phenomena. A Fourier Fourier basis in a set of quasi-Lagrangian coordinates that advect with the background shear is used for spectral expansions in the two horizontal directions. For the vertical direction, two different sets of basis functions have been implemented: (1) Chebyshev polynomials on a truncated, finite domain, and (2) rational Chebyshev functions on an infinite domain. Use of this latter set is equivalent to transforming the infinite domain to a finite one with a cotangent mapping, and using cosine and sine expansions in the mapped coordinate. The nonlinear advection terms are time-integrated explicitly, the pressure/enthalpy terms are integrated semi-implicitly, and the Coriolis force and buoyancy terms are treated semi-analytically. We show that internal gravity waves can be damped by adding new terms to the Euler equations. The code exhibits excellent parallel performance with the message passing interface (MPI). As a demonstration of the code, we simulate the merger of two 3D vortices in the midplane of a protoplanetary disk.

  4. Theoretical study of evaporation heat transfer in horizontal microfin tubes: stratified flow model

    Energy Technology Data Exchange (ETDEWEB)

    Honda, H; Wang, Y S [Kyushu Univ., Inst. for Materials Chemistry and Engineering, Kasuga, Fukuoka (Japan)

    2004-08-01

    The stratified flow model of evaporation heat transfer in helically grooved, horizontal microfin tubes has been developed. The profile of stratified liquid was determined by a theoretical model previously developed for condensation in horizontal microfin tubes. For the region above the stratified liquid, the meniscus profile in the groove between adjacent fins was determined by a force balance between the gravity and surface tension forces. The thin film evaporation model was applied to predict heat transfer in the thin film region of the meniscus. Heat transfer through the stratified liquid was estimated by using an empirical correlation proposed by Mori et al. The theoretical predictions of the circumferential average heat transfer coefficient were compared with available experimental data for four tubes and three refrigerants. A good agreement was obtained for the region of Fr{sub 0}<2.5 as long as partial dry out of tube surface did not occur. (Author)

  5. Stratified prevention: opportunities and limitations. Report on the 1st interdisciplinary cardiovascular workshop in Augsburg.

    Science.gov (United States)

    Kirchhof, Gregor; Lindner, Josef Franz; Achenbach, Stephan; Berger, Klaus; Blankenberg, Stefan; Fangerau, Heiner; Gimpel, Henner; Gassner, Ulrich M; Kersten, Jens; Magnus, Dorothea; Rebscher, Herbert; Schunkert, Heribert; Rixen, Stephan; Kirchhof, Paulus

    2018-03-01

    Sufficient exercise and sleep, a balanced diet, moderate alcohol consumption and a good approach to handle stress have been known as lifestyles that protect health and longevity since the Middle Age. This traditional prevention quintet, turned into a sextet by smoking cessation, has been the basis of the "preventive personality" that formed in the twentieth century. Recent analyses of big data sets including genomic and physiological measurements have unleashed novel opportunities to estimate individual health risks with unprecedented accuracy, allowing to target preventive interventions to persons at high risk and at the same time to spare those in whom preventive measures may not be needed or even be harmful. To fully grasp these opportunities for modern preventive medicine, the established healthy life styles require supplementation by stratified prevention. The opportunities of these developments for life and health contrast with justified concerns: A "surveillance society", able to predict individual behaviour based on big data, threatens individual freedom and jeopardises equality. Social insurance law and the new German Disease Prevention Act (Präventionsgesetz) rightly stress the need for research to underpin stratified prevention which is accessible to all, ethical, effective, and evidence based. An ethical and acceptable development of stratified prevention needs to start with autonomous individuals who control and understand all information pertaining to their health. This creates a mandate for lifelong health education, enabled in an individualised form by digital technology. Stratified prevention furthermore requires the evidence-based development of a new taxonomy of cardiovascular diseases that reflects disease mechanisms. Such interdisciplinary research needs broad support from society and a better use of biosamples and data sets within an updated research governance framework.

  6. A novel technique with enhanced detection and quantitation of HPV-16 E1- and E2-mediated DNA replication

    International Nuclear Information System (INIS)

    Taylor, Ewan R.; Morgan, Iain M.

    2003-01-01

    Transient DNA replication assays to detect papillomavirus E1/E2-mediated DNA replication have depended upon Southern blotting. This technique is hazardous (radioactive), labour intensive, semiquantitative, and physically limited in the number of samples that can be processed at any one time. We have overcome these problems by developing a real-time PCR protocol for the detection of E1/E2-mediated transient DNA replication. The results demonstrate detection of replication at levels not seen using Southern blotting demonstrating enhanced sensitivity. This technique is also, by definition, highly quantitative. Therefore, the real-time PCR technique is the optimal method for the detection of E1/E2-mediated DNA replication

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

    Science.gov (United States)

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

    2016-03-01

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

  8. Dual Spark Plugs For Stratified-Charge Rotary Engine

    Science.gov (United States)

    Abraham, John; Bracco, Frediano V.

    1996-01-01

    Fuel efficiency of stratified-charge, rotary, internal-combustion engine increased by improved design featuring dual spark plugs. Second spark plug ignites fuel on upstream side of main fuel injector; enabling faster burning and more nearly complete utilization of fuel.

  9. Roles for Dam methylation in bacterial chromosome replication

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Koch, Birgit; Skovgaard, Ole

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

  10. 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.

  11. Implementing content constraints in alpha-stratified adaptive testing using a shadow test approach

    NARCIS (Netherlands)

    van der Linden, Willem J.; Chang, Hua-Hua

    2001-01-01

    The methods of alpha-stratified adaptive testing and constrained adaptive testing with shadow tests are combined in this study. The advantages are twofold. First, application of the shadow test allows the researcher to implement any type of constraint on item selection in alpha-stratified adaptive

  12. 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.

  13. 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

  14. Stratified coastal ocean interactions with tropical cyclones

    Science.gov (United States)

    Glenn, S. M.; Miles, T. N.; Seroka, G. N.; Xu, Y.; Forney, R. K.; Yu, F.; Roarty, H.; Schofield, O.; Kohut, J.

    2016-01-01

    Hurricane-intensity forecast improvements currently lag the progress achieved for hurricane tracks. Integrated ocean observations and simulations during hurricane Irene (2011) reveal that the wind-forced two-layer circulation of the stratified coastal ocean, and resultant shear-induced mixing, led to significant and rapid ahead-of-eye-centre cooling (at least 6 °C and up to 11 °C) over a wide swath of the continental shelf. Atmospheric simulations establish this cooling as the missing contribution required to reproduce Irene's accelerated intensity reduction. Historical buoys from 1985 to 2015 show that ahead-of-eye-centre cooling occurred beneath all 11 tropical cyclones that traversed the Mid-Atlantic Bight continental shelf during stratified summer conditions. A Yellow Sea buoy similarly revealed significant and rapid ahead-of-eye-centre cooling during Typhoon Muifa (2011). These findings establish that including realistic coastal baroclinic processes in forecasts of storm intensity and impacts will be increasingly critical to mid-latitude population centres as sea levels rise and tropical cyclone maximum intensities migrate poleward. PMID:26953963

  15. Properties of the endogenous post-stratified estimator using a random forests model

    Science.gov (United States)

    John Tipton; Jean Opsomer; Gretchen G. Moisen

    2012-01-01

    Post-stratification is used in survey statistics as a method to improve variance estimates. In traditional post-stratification methods, the variable on which the data is being stratified must be known at the population level. In many cases this is not possible, but it is possible to use a model to predict values using covariates, and then stratify on these predicted...

  16. Testing the Efficacy of a Tier 2 Mathematics Intervention: A Conceptual Replication Study

    Science.gov (United States)

    Doabler, Christian T.; Clarke, Ben; Kosty, Derek B.; Kurtz-Nelson, Evangeline; Fien, Hank; Smolkowski, Keith; Baker, Scott K.

    2016-01-01

    The purpose of this closely aligned conceptual replication study was to investigate the efficacy of a Tier 2 kindergarten mathematics intervention. The replication study differed from the initial randomized controlled trial on three important elements: geographical region, timing of the intervention, and instructional context of the…

  17. Characterization and modeling of turbidity density plume induced into stratified reservoir by flood runoffs.

    Science.gov (United States)

    Chung, S W; Lee, H S

    2009-01-01

    In monsoon climate area, turbidity flows typically induced by flood runoffs cause numerous environmental impacts such as impairment of fish habitat and river attraction, and degradation of water supply efficiency. This study was aimed to characterize the physical dynamics of turbidity plume induced into a stratified reservoir using field monitoring and numerical simulations, and to assess the effect of different withdrawal scenarios on the control of downstream water quality. Three different turbidity models (RUN1, RUN2, RUN3) were developed based on a two-dimensional laterally averaged hydrodynamic and transport model, and validated against field data. RUN1 assumed constant settling velocity of suspended sediment, while RUN2 estimated the settling velocity as a function of particle size, density, and water temperature to consider vertical stratification. RUN3 included a lumped first-order turbidity attenuation rate taking into account the effects of particles aggregation and degradable organic particles. RUN3 showed best performance in replicating the observed variations of in-reservoir and release turbidity. Numerical experiments implemented to assess the effectiveness of different withdrawal depths showed that the alterations of withdrawal depth can modify the pathway and flow regimes of the turbidity plume, but its effect on the control of release water quality could be trivial.

  18. Replication cycle of duck hepatitis A virus type 1 in duck embryonic hepatocytes

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Fangke; Chen, Yun; Shi, Jintong; Ming, Ke; Liu, Jiaguo, E-mail: liujiaguo@njau.edu.cn; Xiong, Wen; Song, Meiyun; Du, Hongxu; Wang, Yixuan; Zhang, Shuaibin; Wu, Yi; Wang, Deyun; Hu, Yuanliang

    2016-04-15

    Duck hepatitis A virus type 1 (DHAV-1) is an important agent of duck viral hepatitis. Until recently, the replication cycle of DHAV-1 is still unknown. Here duck embryonic hepatocytes infected with DHAV-1 were collected at different time points, and dynamic changes of the relative DHAV-1 gene expression during replication were detected by real-time PCR. And the morphology of hepatocytes infected with DHAV was evaluated by electron microscope. The result suggested that the adsorption of DHAV-1 saturated at 90 min post-infection, and the virus particles with size of about 50 nm including more than 20 nm of vacuum drying gold were observed on the infected cells surface. What's more, the replication lasted around 13 h after the early protein synthesis for about 5 h, and the release of DHAV-1 was in steady state after 32 h. The replication cycle will enrich the data for DVH control and provide the foundation for future studies. - Highlights: • This is the first description of the replication cycle of DHAV-1. • Firstly find that DHAV-1 adsorption saturated at 90 min post-infection. • The replication lasted around 13 h after early protein synthesis for about 5 h. • The release of DHAV-1 was in steady state after 32 h.

  19. 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.

  20. Study of MRI in stratified viscous plasma configuration

    Science.gov (United States)

    Carlevaro, Nakia; Montani, Giovanni; Renzi, Fabrizio

    2017-02-01

    We analyze the morphology of the magneto-rotational instability (MRI) for a stratified viscous plasma disk configuration in differential rotation, taking into account the so-called corotation theorem for the background profile. In order to select the intrinsic Alfvénic nature of MRI, we deal with an incompressible plasma and we adopt a formulation of the local perturbation analysis based on the use of the magnetic flux function as a dynamical variable. Our study outlines, as consequence of the corotation condition, a marked asymmetry of the MRI with respect to the equatorial plane, particularly evident in a complete damping of the instability over a positive critical height on the equatorial plane. We also emphasize how such a feature is already present (although less pronounced) even in the ideal case, restoring a dependence of the MRI on the stratified morphology of the gravitational field.

  1. 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...

  2. Chromatin maturation depends on continued DNA-replication

    International Nuclear Information System (INIS)

    Schlaeger, E.J.; Puelm, W.; Knippers, R.

    1983-01-01

    The structure of [ 3 H]thymidine pulse-labeled chromatin in lymphocytes differs from that of non-replicating chromatin by several operational criteria which are related to the higher nuclease sensitivity of replicating chromatin. These structural features of replicating chromatin rapidly disappear when the [ 3 H]thymidine pulse is followed by a chase in the presence of an excess of non-radioactive thymidine. However, when the rate of DNA replication is reduced, as in cycloheximide-treated lymphocytes, chromatin maturation is retarded. No chromatin maturation is observed when nuclei from pulse-labeled lymphocytes are incubated in vitro in the absence of DNA precursors. In contrast, when these nuclei are incubated under conditions known to be optimal for DNA replication, the structure of replicating chromatin is efficiently converted to that of 'mature', non-replicating chromatin. The authors conclude that the properties of nascent DNA and/or the distance from the replication fork are important factors in chromatin maturation. (Auth.)

  3. Synthesis of Fault-Tolerant Embedded Systems with Checkpointing and Replication

    DEFF Research Database (Denmark)

    Izosimov, Viacheslav; Pop, Paul; Eles, Petru

    2006-01-01

    We present an approach to the synthesis of fault-tolerant hard real-time systems for safety-critical applications. We use checkpointing with rollback recovery and active replication for tolerating transient faults. Processes are statically scheduled and communications are performed using the time...

  4. Reflection and transmission of electromagnetic waves in planarly stratified media

    International Nuclear Information System (INIS)

    Caviglia, G.

    1999-01-01

    Propagation of time-harmonic electromagnetic waves in planarly stratified multilayers is investigated. Each layer is allowed to be inhomogeneous and the layers are separated by interfaces. The procedure is based on the representation of the electromagnetic field in the basis of the eigenvectors of the matrix characterizing the first-order system. Hence the local reflection and transmission matrices are defined and the corresponding differential equations, in the pertinent space variable are determined. The jump conditions at interfaces are also established. The present model incorporates dissipative materials and the procedure holds without any restrictions to material symmetries. Differential equations appeared in the literature are shown to hold in particular (one-dimensional) cases or to represent homogeneous layers only

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  6. Characterizing the performance of an affordable, multichannel conductivity probe for density measurements in stratified flows

    Science.gov (United States)

    Subramanian, Balaji; Carminati, Marco; Luzzatto-Fegiz, Paolo

    2017-11-01

    In stratified flows, conductivity (combined with temperature) is often used to measure density. The conductivity probes typically used can resolve very fine spatial scales, but on the downside they are fragile, expensive, sensitive to environmental noise and have only single channel capability. Recently a low-cost, robust, arduino-based probe called Conduino was developed, which can be valuable in a wide range of applications where resolving extremely small spatial scales is not needed. This probe uses micro-USB connectors as actual conductivity sensors with a custom designed electronic board for simultaneous acquisition from multiple probes, with conductivity resolution comparable to commercially available PME conductivity probe. A detailed assessment of performance of this Conduino probe is described here. To establish time response and sensitivity as a function of electrode geometry, we build a variety of shapes for different kinds of applications, with tip spacing ranging from 0.5-2.5 mm, and with electrode length ranging from 2.3-6 mm. We set up a two-layer density profile and traverse it rapidly, yielding a time response comparable to PME. The Conduino's multi-channel capability is used to operate probe arrays, which helps to construct density fields in stratified flows.

  7. On Internal Waves in a Density-Stratified Estuary

    NARCIS (Netherlands)

    Kranenburg, C.

    1991-01-01

    In this article some field observations, made in recent years, of internal wave motions in a density-stratified estuary are presented, In order to facilitate the appreciation of the results, and to make some quantitative comparisons, the relevant theory is also summarized. Furthermore, the origins

  8. Prognosis research strategy (PROGRESS) 4: Stratified medicine research

    NARCIS (Netherlands)

    A. Hingorani (Aroon); D.A.W.M. van der Windt (Daniëlle); R.D. Riley (Richard); D. Abrams; K.G.M. Moons (Karel); E.W. Steyerberg (Ewout); S. Schroter (Sara); W. Sauerbrei (Willi); D.G. Altman (Douglas); H. Hemingway; A. Briggs (Andrew); N. Brunner; P. Croft (Peter); J. Hayden (Jill); P.A. Kyzas (Panayiotis); N. Malats (Núria); G. Peat; P. Perel (Pablo); I. Roberts (Ian); A. Timmis (Adam)

    2013-01-01

    textabstractIn patients with a particular disease or health condition, stratified medicine seeks to identify thosewho will have the most clinical benefit or least harm from a specific treatment. In this article, thefourth in the PROGRESS series, the authors discuss why prognosis research should form

  9. Repair replication in cultured normal and transformed human fibroblasts

    International Nuclear Information System (INIS)

    Smith, C.A.; Hanawalt, P.C.

    1976-01-01

    Repair replication in response to ultraviolet irradiation has been studied in normal human diploid fibroblast cultures, W138, and an SV40 transformant, VA13. Quantitative comparisons have been made using the combined isotopic and density labelling method for assaying repair replication. No significant difference was found in the amount of repair replication performed, its dose response, or the time course between growing and confluent W138 cells, early passage and senescent cells, or normal W138 cells and the transformed VA13 cells. When [ 3 H]dThd was employed as the isotopic label in the presence of a 30-200 fold excess of unlabelled BrdUrd apparent differences in repair replication were seen between W138 cells shortly after subcultivation and cells which had been allowed to reach confluence. These differences were the same over a wide dose range and regardless of the passage number of the cells, but could be influenced by using different serum lots. The differences were not seen, however, when [ 3 H]BrdUrd provided the isotopic label; thus they reflect either impurities in the [ 3 H]dThd or a slight discrimination by some cellular process

  10. Enzymatic recognition of DNA replication origins

    International Nuclear Information System (INIS)

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

    1983-01-01

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

  11. Surface Microstructure Replication in Injection Moulding

    DEFF Research Database (Denmark)

    Hansen, Hans Nørgaard; Arlø, Uffe Rolf

    2005-01-01

    topography is transcribed onto the plastic part through complex mechanisms. This replication however, is not perfect, and the replication quality depends on the plastic material properties, the topography itself, and the process conditions. This paper describes and discusses an investigation of injection...... moulding of surface microstructures. Emphasis is put on the ability to replicate surface microstructures under normal injection moulding conditions, notably with low cost materials at low mould temperatures. The replication of surface microstructures in injection moulding has been explored...... for Polypropylene at low mould temperatures. The process conditions were varied over the recommended process window for the material. The geometry of the obtained structures was analyzed. Evidence suggests that step height replication quality depends linearly on structure width in a certain range. Further...

  12. Energy Cascade from Internal Modes in Non-uniformly Stratified Fluid through Excitation of Superharmonic Disturbances

    Science.gov (United States)

    Sutherland, B. R.

    2016-02-01

    It is well established that two-dimensional internal plane waves and modes in uniformly stratified fluid efficiently transfer energy to smaller scale waves and ultimately turbulent mixing through parametric subharmonic instability (PSI). The numerical simulations of MacKinnon & Winters (GRL 2005) predicted PSI should act efficiently to disrupt the internal tide. However, while in situ observations showed the presence of PSI, it was not found to be appreciable. One reason for the discrepancy between simulations and observations is that the former examined an internal mode in uniformly stratified fluid whereas, in reality, the internal tide exists in non-uniform stratification and is manifest as sinusoidal oscillations of the thermocline. Through theory supported by numerical simulations, it is shown that internal modes in non-uniform stratification immediately excite superharmonics, not subharmonic disturbances. These have double the horizontal wavenumber and double the frequency of the parent mode and hence move with the same horizontal phase speed of the parent mode. As the disturbances grow in amplitude, however, they interact with the parent mode generating small-scale vertically propagating internal waves within the strongly stratified layer. The occurrence of PSI over very long times can occur, as in the simulations of Hazewinkel and Winters (JPO 2011). However, a comprehensive understanding of the energy cascade from the internal tide to small scales must consider the evolution of excited superharmonic disturbances.

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

    OpenAIRE

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

    2004-01-01

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

  14. 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.

  15. Stratified Simulations of Collisionless Accretion Disks

    Energy Technology Data Exchange (ETDEWEB)

    Hirabayashi, Kota; Hoshino, Masahiro, E-mail: hirabayashi-k@eps.s.u-tokyo.ac.jp [Department of Earth and Planetary Science, The University of Tokyo, Tokyo, 113-0033 (Japan)

    2017-06-10

    This paper presents a series of stratified-shearing-box simulations of collisionless accretion disks in the recently developed framework of kinetic magnetohydrodynamics (MHD), which can handle finite non-gyrotropy of a pressure tensor. Although a fully kinetic simulation predicted a more efficient angular-momentum transport in collisionless disks than in the standard MHD regime, the enhanced transport has not been observed in past kinetic-MHD approaches to gyrotropic pressure anisotropy. For the purpose of investigating this missing link between the fully kinetic and MHD treatments, this paper explores the role of non-gyrotropic pressure and makes the first attempt to incorporate certain collisionless effects into disk-scale, stratified disk simulations. When the timescale of gyrotropization was longer than, or comparable to, the disk-rotation frequency of the orbit, we found that the finite non-gyrotropy selectively remaining in the vicinity of current sheets contributes to suppressing magnetic reconnection in the shearing-box system. This leads to increases both in the saturated amplitude of the MHD turbulence driven by magnetorotational instabilities and in the resultant efficiency of angular-momentum transport. Our results seem to favor the fast advection of magnetic fields toward the rotation axis of a central object, which is required to launch an ultra-relativistic jet from a black hole accretion system in, for example, a magnetically arrested disk state.

  16. Dispersion of (light) inertial particles in stratified turbulence

    NARCIS (Netherlands)

    van Aartrijk, M.; Clercx, H.J.H.; Armenio, Vincenzo; Geurts, Bernardus J.; Fröhlich, Jochen

    2010-01-01

    We present a brief overview of a numerical study of the dispersion of particles in stably stratified turbulence. Three types of particles arc examined: fluid particles, light inertial particles ($\\rho_p/\\rho_f = \\mathcal{O}(1)$) and heavy inertial particles ($\\rho_p/\\rho_f \\gg 1$). Stratification

  17. Faithful replication of grating patterns in polymer through electrohydrodynamic instabilities

    International Nuclear Information System (INIS)

    Li, H; Yu, W; Wang, T; Zhang, H; Cao, Y; Abraham, E; Desmulliez, M P Y

    2014-01-01

    Electrohydrodynamic instability patterning (EHDIP) as an alternative patterning method has attracted a great deal of attention over the past decade. This article demonstrates the faithful transfer of patterns with a high aspect ratio onto a polymer film via electrohydrodynamic instabilities for a given patterned grating mask. We perform a simple mathematical analysis to determine the influence of process parameters on the pressure difference ▵P. Through numerical simulation, it is demonstrated that thick films subject to large electric fields are essential to realize this faithful replication. In particular, the influence of the material properties of the polymer on pattern replication is discussed in detail. It is found that, to achieve the smaller periodic patterns with a higher resolution, film with a larger value of the dielectric constant and smaller value of the surface tension should be chosen. In addition, an ideal replication of the mask pattern with a short evolution time is possible by reducing the viscosity of the polymer liquid. Finally, the experiments of the pattern replication with and without defects are demonstrated to compare with the numerical simulation results. It is found that experiments are in good agreement with the simulation results and prove that the numerical simulation method provides an effective way to predict faithful replication. (paper)

  18. Dengue virus replicates and accumulates in Aedes aegypti salivary glands

    Energy Technology Data Exchange (ETDEWEB)

    Raquin, Vincent, E-mail: vincent.raquin@univ-lyon1.fr [Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris (France); Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, 75015 Paris (France); Lambrechts, Louis, E-mail: louis.lambrechts@pasteur.fr [Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris (France); Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, 75015 Paris (France)

    2017-07-15

    Dengue virus (DENV) is an RNA virus transmitted among humans by mosquito vectors, mainly Aedes aegypti. DENV transmission requires viral dissemination from the mosquito midgut to the salivary glands. During this process the virus undergoes several population bottlenecks, which are stochastic reductions in population size that restrict intra-host viral genetic diversity and limit the efficiency of natural selection. Despite the implications for virus transmission and evolution, DENV replication in salivary glands has not been directly demonstrated. Here, we used a strand-specific quantitative RT-PCR assay to demonstrate that negative-strand DENV RNA is produced in Ae. aegypti salivary glands, providing conclusive evidence that viral replication occurs in this tissue. Furthermore, we showed that the concentration of DENV genomic RNA in salivary glands increases significantly over time, indicating that active replication likely replenishes DENV genetic diversity prior to transmission. These findings improve our understanding of the biological determinants of DENV fitness and evolution. - Highlights: •Strand-specific RT-qPCR allows accurate quantification of DENV (-) RNA in mosquito tissues. •Detection of DENV (-) RNA in salivary glands provides evidence of viral replication in this tissue. •Viral replication in salivary glands likely replenishes DENV genetic diversity prior to transmission.

  19. Dengue virus replicates and accumulates in Aedes aegypti salivary glands

    International Nuclear Information System (INIS)

    Raquin, Vincent; Lambrechts, Louis

    2017-01-01

    Dengue virus (DENV) is an RNA virus transmitted among humans by mosquito vectors, mainly Aedes aegypti. DENV transmission requires viral dissemination from the mosquito midgut to the salivary glands. During this process the virus undergoes several population bottlenecks, which are stochastic reductions in population size that restrict intra-host viral genetic diversity and limit the efficiency of natural selection. Despite the implications for virus transmission and evolution, DENV replication in salivary glands has not been directly demonstrated. Here, we used a strand-specific quantitative RT-PCR assay to demonstrate that negative-strand DENV RNA is produced in Ae. aegypti salivary glands, providing conclusive evidence that viral replication occurs in this tissue. Furthermore, we showed that the concentration of DENV genomic RNA in salivary glands increases significantly over time, indicating that active replication likely replenishes DENV genetic diversity prior to transmission. These findings improve our understanding of the biological determinants of DENV fitness and evolution. - Highlights: •Strand-specific RT-qPCR allows accurate quantification of DENV (-) RNA in mosquito tissues. •Detection of DENV (-) RNA in salivary glands provides evidence of viral replication in this tissue. •Viral replication in salivary glands likely replenishes DENV genetic diversity prior to transmission.

  20. Internal circle uplifts, transversality and stratified G-structures

    Energy Technology Data Exchange (ETDEWEB)

    Babalic, Elena Mirela [Department of Theoretical Physics, National Institute of Physics and Nuclear Engineering,Str. Reactorului no.30, P.O.BOX MG-6, Postcode 077125, Bucharest-Magurele (Romania); Department of Physics, University of Craiova,13 Al. I. Cuza Str., Craiova 200585 (Romania); Lazaroiu, Calin Iuliu [Center for Geometry and Physics, Institute for Basic Science,Pohang 790-784 (Korea, Republic of)

    2015-11-24

    We study stratified G-structures in N=2 compactifications of M-theory on eight-manifolds M using the uplift to the auxiliary nine-manifold M̂=M×S{sup 1}. We show that the cosmooth generalized distribution D̂ on M̂ which arises in this formalism may have pointwise transverse or non-transverse intersection with the pull-back of the tangent bundle of M, a fact which is responsible for the subtle relation between the spinor stabilizers arising on M and M̂ and for the complicated stratified G-structure on M which we uncovered in previous work. We give a direct explanation of the latter in terms of the former and relate explicitly the defining forms of the SU(2) structure which exists on the generic locus U of M to the defining forms of the SU(3) structure which exists on an open subset Û of M̂, thus providing a dictionary between the eight- and nine-dimensional formalisms.

  1. Dyadic Green's function of an eccentrically stratified sphere.

    Science.gov (United States)

    Moneda, Angela P; Chrissoulidis, Dimitrios P

    2014-03-01

    The electric dyadic Green's function (dGf) of an eccentrically stratified sphere is built by use of the superposition principle, dyadic algebra, and the addition theorem of vector spherical harmonics. The end result of the analytical formulation is a set of linear equations for the unknown vector wave amplitudes of the dGf. The unknowns are calculated by truncation of the infinite sums and matrix inversion. The theory is exact, as no simplifying assumptions are required in any one of the analytical steps leading to the dGf, and it is general in the sense that any number, position, size, and electrical properties can be considered for the layers of the sphere. The point source can be placed outside of or in any lossless part of the sphere. Energy conservation, reciprocity, and other checks verify that the dGf is correct. A numerical application is made to a stratified sphere made of gold and glass, which operates as a lens.

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

    Science.gov (United States)

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

    2014-09-13

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

  3. Surface microstructure replication in injection molding

    DEFF Research Database (Denmark)

    Theilade, Uffe Arlø; Hansen, Hans Nørgaard

    2006-01-01

    topography is transcribed onto the plastic part through complex mechanisms. This replication, however, is not perfect, and the replication quality depends on the plastic material properties, the topography itself, and the process conditions. This paper describes and discusses an investigation of injection...... molding of surface microstructures. The fundamental problem of surface microstructure replication has been studied. The research is based on specific microstructures as found in lab-on-a-chip products and on rough surfaces generated from EDM (electro discharge machining) mold cavities. Emphasis is put...... on the ability to replicate surface microstructures under normal injection-molding conditions, i.e., with commodity materials within typical process windows. It was found that within typical process windows the replication quality depends significantly on several process parameters, and especially the mold...

  4. Process chain validation in micro and nano replication

    DEFF Research Database (Denmark)

    Calaon, Matteo

    to quantification of replication quality over large areas of surface topography based on areal detection technique and angular diffraction measurements were developed. A series of injection molding and compression molding experiments aimed at process analysis and optimization showed the possibility to control...... features dimensional accuracy variation through the identification of relevant process parameters. Statistical design of experiment results, showed the influence of both process parameters (mold temperature, packing time, packing pressure) and design parameters (channel width and direction with respect......Innovations in nanotechnology propose applications integrating micro and nanometer structures fabricated as master geometries for final replication on polymer substrates. The possibility for polymer materials of being processed with technologies enabling large volume production introduces solutions...

  5. Stratified B-trees and versioning dictionaries

    OpenAIRE

    Twigg, Andy; Byde, Andrew; Milos, Grzegorz; Moreton, Tim; Wilkes, John; Wilkie, Tom

    2011-01-01

    A classic versioned data structure in storage and computer science is the copy-on-write (CoW) B-tree -- it underlies many of today's file systems and databases, including WAFL, ZFS, Btrfs and more. Unfortunately, it doesn't inherit the B-tree's optimality properties; it has poor space utilization, cannot offer fast updates, and relies on random IO to scale. Yet, nothing better has been developed since. We describe the `stratified B-tree', which beats all known semi-external memory versioned B...

  6. Vorticity generation and evolution in shock-accelerated density-stratified interfaces

    International Nuclear Information System (INIS)

    Yang, X.; Chern, I.; Zabusky, N.J.; Samtaney, R.; Hawley, J.F.

    1992-01-01

    The results of direct numerical simulations of inviscid planar shock-accelerated density-stratified interfaces in two dimensions are presented and compared with shock tube experiments of Haas [(private communication, 1988)] and Sturtevant [in Shock Tubes and Waves, edited by H. Gronig (VCH, Berlin, 1987), p. 89] . Heavy-to-light (''slow/fast or s/f) and light-to-heavy (''fast/slow,'' or f/s) gas interfaces are examined and early-time impulsive vorticity deposition and the evolution of coherent vortex structures are emphasized and quantified. The present second-order Godunov scheme yields excellent agreement with shock-polar analyses at early time. A more physical vortex interpretation explains the commonly used (i.e., linear paradigm) designations of ''unstable'' and ''stable'' for the f/s and s/f interfaces, respectively. The later time events are Rayleigh--Taylor like and can be described in terms of the evolution of a vortex layer (large-scale translation and rotation): asymmetric tip vortex ''roll-up'' and ''binding;'' layer ''instability;'' convective mixing; and baroclinic vorticity generation from secondary shock--interface interactions

  7. The Values of Combined and Sub-Stratified Imaging Scores with Ultrasonography and Mammography in Breast Cancer Subtypes.

    Directory of Open Access Journals (Sweden)

    Tsun-Hou Chang

    Full Text Available The Breast Imaging Reporting and Data System (BI-RADS of Mammography (MG and Ultrasonography (US were equivalent to the "5-point score" and applied for combined and sub-stratified imaging assessments. This study evaluated the value of combined and sub-stratified imaging assessments with MG and US over breast cancer subtypes (BCS.Medical records of 5,037 cases having imaging-guided core biopsy, performed from 2009 to 2012, were retrospectively reviewed. This study selected 1,995 cases (1,457 benign and 538 invasive cancer having both MG and US before biopsy. These cases were categorized with the "5-point score" for their MG and US, and applied for combined and sub-stratified imaging assessments. Invasive cancers were classified on the basis of BCS, and correlated with combined and sub-stratified imaging assessments.These selected cases were evaluated by the "5-point score." MG, US, and combined and sub-stratified imaging assessments all revealed statistically significant (P < 0.001 incidence of malignancy. The sensitivity was increased in the combined imaging score (99.8%, and the specificity was increased in the sub-stratified combined score (75.4%. In the sub-stratified combined imaging assessment, all BCS can be classified with higher scores (abnormality hierarchy, and luminal B subtype showed the most salient result (hierarchy: higher, 95%; lower, 5%.Combined and sub-stratified imaging assessments can increase sensitivity and specificity of breast cancer diagnosis, respectively, and Luminal B subtype shows the best identification by sub-stratified combined imaging scoring.

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  9. Exponential growth and selection in self-replicating materials from DNA origami rafts

    Science.gov (United States)

    He, Xiaojin; Sha, Ruojie; Zhuo, Rebecca; Mi, Yongli; Chaikin, Paul M.; Seeman, Nadrian C.

    2017-10-01

    Self-replication and evolution under selective pressure are inherent phenomena in life, and but few artificial systems exhibit these phenomena. We have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temperature and ultraviolet illumination, producing more than 7 million copies in 24 cycles. We demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent-daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating. At pH 5.3, the replication rate of species I is ~1.3-1.4 times faster than that of species II. At pH 7.8, the replication rates are reversed. When mixed together in the same vial, the progeny of species I replicate preferentially at pH 7.8 similarly at pH 5.3, the progeny of species II take over the system. This addressable selectivity should be adaptable to the selection and evolution of multi-component self-replicating materials in the nanoscopic-to-microscopic size range.

  10. 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.

  11. Anatomy of the epidemiological literature on the 2003 SARS outbreaks in Hong Kong and Toronto: a time-stratified review.

    Directory of Open Access Journals (Sweden)

    Weijia Xing

    2010-05-01

    Full Text Available BACKGROUND: Outbreaks of emerging infectious diseases, especially those of a global nature, require rapid epidemiological analysis and information dissemination. The final products of those activities usually comprise internal memoranda and briefs within public health authorities and original research published in peer-reviewed journals. Using the 2003 severe acute respiratory syndrome (SARS epidemic as an example, we conducted a comprehensive time-stratified review of the published literature to describe the different types of epidemiological outputs. METHODS AND FINDINGS: We identified and analyzed all published articles on the epidemiology of the SARS outbreak in Hong Kong or Toronto. The analysis was stratified by study design, research domain, data collection, and analytical technique. We compared the SARS-case and matched-control non-SARS articles published according to the timeline of submission, acceptance, and publication. The impact factors of the publishing journals were examined according to the time of publication of SARS articles, and the numbers of citations received by SARS-case and matched-control articles submitted during and after the epidemic were compared. Descriptive, analytical, theoretical, and experimental epidemiology concerned, respectively, 54%, 30%, 11%, and 6% of the studies. Only 22% of the studies were submitted, 8% accepted, and 7% published during the epidemic. The submission-to-acceptance and acceptance-to-publication intervals of the SARS articles submitted during the epidemic period were significantly shorter than the corresponding intervals of matched-control non-SARS articles published in the same journal issues (p<0.001 and p<0.01, respectively. The differences of median submission-to-acceptance intervals and median acceptance-to-publication intervals between SARS articles and their corresponding control articles were 106.5 d (95% confidence interval [CI] 55.0-140.1 and 63.5 d (95% CI 18

  12. 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

  13. DNA replication origins—where do we begin?

    Science.gov (United States)

    Prioleau, Marie-Noëlle; MacAlpine, David M.

    2016-01-01

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

  14. ATAD2 is an epigenetic reader of newly synthesized histone marks during DNA replication.

    Science.gov (United States)

    Koo, Seong Joo; Fernández-Montalván, Amaury E; Badock, Volker; Ott, Christopher J; Holton, Simon J; von Ahsen, Oliver; Toedling, Joern; Vittori, Sarah; Bradner, James E; Gorjánácz, Mátyás

    2016-10-25

    ATAD2 (ATPase family AAA domain-containing protein 2) is a chromatin regulator harboring an AAA+ ATPase domain and a bromodomain, previously proposed to function as an oncogenic transcription co-factor. Here we suggest that ATAD2 is also required for DNA replication. ATAD2 is co-expressed with genes involved in DNA replication in various cancer types and predominantly expressed in S phase cells where it localized on nascent chromatin (replication sites). Our extensive biochemical and cellular analyses revealed that ATAD2 is recruited to replication sites through a direct interaction with di-acetylated histone H4 at K5 and K12, indicative of newly synthesized histones during replication-coupled chromatin reassembly. Similar to ATAD2-depletion, ectopic expression of ATAD2 mutants that are deficient in binding to these di-acetylation marks resulted in reduced DNA replication and impaired loading of PCNA onto chromatin, suggesting relevance of ATAD2 in DNA replication. Taken together, our data show a novel function of ATAD2 in cancer and for the first time identify a reader of newly synthesized histone di-acetylation-marks during replication.

  15. Barriers and facilitators to replicating an evidence-based palliative care model.

    Science.gov (United States)

    Davis, E Maxwell; Jamison, Paula; Brumley, Richard; Enguídanos, Susan

    2006-01-01

    Recognition of the difficulties involved in replicating evidence- based interventions is well documented in the literature within the medical field. Promising research findings are often not translated into practice, and if they are, there is a significant time gap between study conclusion and practice adoption. The purpose of this article is to describe the barriers and facilitators encountered by two managed care organizations while replicating an evidence-based end of life in-home palliative care model. Using Diffusion of Innovation Theory as a theoretical framework, results from focus groups and interviews with the project's clinical, administrative and research teams are presented and recommendations made for improving translational efforts. The process of replicating the end of life in-home palliative care model clearly illustrated the key elements required for successfully diffusing innovation. These key elements include marketing and communication, leadership, organizational support and training and mentorship. This qualitative process study provides clear, real world perspectives of the myriad of challenges encountered in replicating an evidence-based project.

  16. Diagnostic accuracy of the STRATIFY clinical prediction rule for falls: A systematic review and meta-analysis

    LENUS (Irish Health Repository)

    Billington, Jennifer

    2012-08-07

    AbstractBackgroundThe STRATIFY score is a clinical prediction rule (CPR) derived to assist clinicians to identify patients at risk of falling. The purpose of this systematic review and meta-analysis is to determine the overall diagnostic accuracy of the STRATIFY rule across a variety of clinical settings.MethodsA literature search was performed to identify all studies that validated the STRATIFY rule. The methodological quality of the studies was assessed using the Quality Assessment of Diagnostic Accuracy Studies tool. A STRATIFY score of ≥2 points was used to identify individuals at higher risk of falling. All included studies were combined using a bivariate random effects model to generate pooled sensitivity and specificity of STRATIFY at ≥2 points. Heterogeneity was assessed using the variance of logit transformed sensitivity and specificity.ResultsSeventeen studies were included in our meta-analysis, incorporating 11,378 patients. At a score ≥2 points, the STRATIFY rule is more useful at ruling out falls in those classified as low risk, with a greater pooled sensitivity estimate (0.67, 95% CI 0.52–0.80) than specificity (0.57, 95% CI 0.45 – 0.69). The sensitivity analysis which examined the performance of the rule in different settings and subgroups also showed broadly comparable results, indicating that the STRATIFY rule performs in a similar manner across a variety of different ‘at risk’ patient groups in different clinical settings.ConclusionThis systematic review shows that the diagnostic accuracy of the STRATIFY rule is limited and should not be used in isolation for identifying individuals at high risk of falls in clinical practice.

  17. Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes

    KAUST Repository

    Cui, Peng; Ding, Feng; Lin, Qiang; Zhang, Lingfang; Li, Ang; Zhang, Zhang; Hu, Songnian; Yu, Jun

    2012-01-01

    Here, we evaluate the contribution of two major biological processes—DNA replication and transcription—to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expression breadth, replication time in local regions and SNP density. SNP density of tissue-specific (TS) genes is significantly higher than that of housekeeping (HK) genes. TS genes tend to locate in late-replicating genomic regions and genes in such regions have a higher SNP density compared to those in early-replication regions. In addition, SNP density is found to be positively correlated with expression level among HK genes. We conclude that the process of DNA replication generates stronger mutational pressure than transcription-associated biological processes do, resulting in an increase of mutation rate in TS genes while having weaker effects on HK genes. In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes.

  18. Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes

    KAUST Repository

    Cui, Peng

    2012-03-23

    Here, we evaluate the contribution of two major biological processes—DNA replication and transcription—to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expression breadth, replication time in local regions and SNP density. SNP density of tissue-specific (TS) genes is significantly higher than that of housekeeping (HK) genes. TS genes tend to locate in late-replicating genomic regions and genes in such regions have a higher SNP density compared to those in early-replication regions. In addition, SNP density is found to be positively correlated with expression level among HK genes. We conclude that the process of DNA replication generates stronger mutational pressure than transcription-associated biological processes do, resulting in an increase of mutation rate in TS genes while having weaker effects on HK genes. In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes.

  19. The Impact of the Implementation Cost of Replication in Data Grid Job Scheduling

    Directory of Open Access Journals (Sweden)

    Babar Nazir

    2018-05-01

    Full Text Available Data Grids deal with geographically-distributed large-scale data-intensive applications. Schemes scheduled for data grids attempt to not only improve data access time, but also aim to improve the ratio of data availability to a node, where the data requests are generated. Data replication techniques manage large data by storing a number of data files efficiently. In this paper, we propose centralized dynamic scheduling strategy-replica placement strategies (CDSS-RPS. CDSS-RPS schedule the data and task so that it minimizes the implementation cost and data transfer time. CDSS-RPS consists of two algorithms, namely (a centralized dynamic scheduling (CDS and (b replica placement strategy (RPS. CDS considers the computing capacity of a node and finds an appropriate location for the job. RPS attempts to improve file access time by using replication on the basis of number of accesses, storage capacity of a computing node, and response time of a requested file. Extensive simulations are carried out to demonstrate the effectiveness of the proposed strategy. Simulation results demonstrate that the replication and scheduling strategies improve the implementation cost and average access time significantly.

  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. Surface micro topography replication in injection moulding

    DEFF Research Database (Denmark)

    Arlø, Uffe Rolf

    Thermoplastic injection moulding is a widely used industrial process that involves surface generation by replication. The surface topography of injection moulded plastic parts can be important for aesthetical or technical reasons. With the emergence of microengineering and nanotechnology additional...... importance of surface topography follows. In general the replication is not perfect and the topography of the plastic part differs from the inverse topography of the mould cavity. It is desirable to be able to control the degree of replication perfection or replication quality. This requires an understanding...... of the physical mechanisms of replication. Such understanding can lead to improved process design and facilitate in-line process quality control with respect to surface properties. The purpose of the project is to identify critical factors that affect topography replication quality and to obtain an understanding...

  2. DNA replication in ultraviolet light irradiated Chinese hamster cells: the nature of replicon inhibition and post-replication repair

    International Nuclear Information System (INIS)

    Doniger, J.

    1978-01-01

    DNA replication in ultraviolet light irradiated Chinese hamster cells was studied using techniques of DNA fiber autoradiography and alkaline sucrose sedimentation. Bidirectionally growing replicons were observed in the autoradiograms independent of the irradiation conditions. After a dose of 5 J/m 2 at 254 nm the rate of fork progression was the same as in unirradiated cells, while the rate of replication was reduced by 50%. After a dose of 10J/m 2 the rate of fork progression was reduced 40%, while the replication rate was only 25% of normal. Therefore, at low doses of ultraviolet light irradiation, the inhibition of DNA replication is due to reduction in the number of functioning replicons, while at higher doses the rate of fork progression is also slowed. Those replicons which no longer function after irradiation are blocked in fork movement rather than replicon initiation. After irradiation, pulse label was first incorporated into short nascent strands, the average size of which was approximately equal to the distance between pyrimidine dimers. Under conditions where post-replication repair occurs these short strands were eventually joined into larger pieces. Finally, the data show that slowing post-replication repair with caffeine does not slow fork movement. The results presented here support the post-replication repair model of 'gapped synthesis' and rule out a major role for 'replicative bypass'. (author)

  3. General Practitioners' and patients' perceptions towards stratified care: a theory informed investigation.

    Science.gov (United States)

    Saunders, Benjamin; Bartlam, Bernadette; Foster, Nadine E; Hill, Jonathan C; Cooper, Vince; Protheroe, Joanne

    2016-08-31

    Stratified primary care involves changing General Practitioners' (GPs) clinical behaviour in treating patients, away from the current stepped care approach to instead identifying early treatment options that are matched to patients' risk of persistent disabling pain. This article explores the perspectives of UK-based GPs and patients about a prognostic stratified care model being developed for patients with the five most common primary care musculoskeletal pain presentations. The focus was on views about acceptability, and anticipated barriers and facilitators to the use of stratified care in routine practice. Four focus groups and six semi-structured telephone interviews were conducted with GPs (n = 23), and three focus groups with patients (n = 20). Data were analysed thematically; and identified themes examined in relation to the Theoretical Domains Framework (TDF), which facilitates comprehensive identification of behaviour change determinants. A critical approach was taken in using the TDF, examining the nuanced interrelationships between theoretical domains. Four key themes were identified: Acceptability of clinical decision-making guided by stratified care; impact on the therapeutic relationship; embedding a prognostic approach within a biomedical model; and practical issues in using stratified care. Whilst within each theme specific findings are reported, common across themes was the identified relationships between the theoretical domains of knowledge, skills, professional role and identity, environmental context and resources, and goals. Through analysis of these identified relationships it was found that, for GPs and patients to perceive stratified care as being acceptable, it must be seen to enhance GPs' knowledge and skills, not undermine GPs' and patients' respective identities and be integrated within the environmental context of the consultation with minimal disruption. Findings highlight the importance of taking into account the context of

  4. Yield and quality of ground water from stratified-drift aquifers, Taunton River basin, Massachusetts : executive summary

    Science.gov (United States)

    Lapham, Wayne W.; Olimpio, Julio C.

    1989-01-01

    Water shortages are a chronic problem in parts of the Taunton River basin and are caused by a combination of factors. Water use in this part of the Boston metropolitan area is likely to increase during the next decade. The Massachusetts Division of Water Resources projects that about 50% of the cities and towns within and on the perimeter of the basin may have water supply deficits by 1990 if water management projects are not pursued throughout the 1980s. Estimates of the long-term yield of the 26 regional aquifers indicate that the yields of the two most productive aquifers equal or exceed 11.9 and 11.3 cu ft/sec, 90% of the time, respectively, if minimum stream discharge is maintained at 99.5% flow duration. Eighteen of the 26 aquifers were pumped for public water supply during 1983. Further analysis of the yield characteristics of these 18 aquifers indicates that the 1983 pumping rate of each of these 18 aquifers can be sustained at least 70% of the time. Selected physical properties and concentrations of major chemical constituents in groundwater from the stratified-drift aquifers at 80 sampling sites were used to characterize general water quality in aquifers throughout the basin. The pH of the groundwater ranged from 5.4 to 7.0. Natural elevated concentrations of Fe and Mn in water in the stratified-drift aquifers are present locally in the basin. Natural concentrations of these two metals commonly exceed the limits of 0.3 mg/L for Fe and 0.05 mg/L for Mn recommended for drinking water. Fifty-one analyses of selected trace metals in groundwater samples from stratified-drift aquifers throughout the basin were used to characterize trace metal concentrations in the groundwater. Of the 10 constituents sampled that have US EPA limits recommended for drinking water, only the Pb concentration in water at one site (60 micrograms/L) exceeded the recommended limit of 50 micrograms/L. Analyses of selected organic compounds in water in the stratified-drift aquifers at 74

  5. Dynamics of Escherichia coli Chromosome Segregation during Multifork Replication

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  6. Nonequilibrium Entropic Bounds for Darwinian Replicators

    Directory of Open Access Journals (Sweden)

    Jordi Piñero

    2018-01-01

    Full Text Available Life evolved on our planet by means of a combination of Darwinian selection and innovations leading to higher levels of complexity. The emergence and selection of replicating entities is a central problem in prebiotic evolution. Theoretical models have shown how populations of different types of replicating entities exclude or coexist with other classes of replicators. Models are typically kinetic, based on standard replicator equations. On the other hand, the presence of thermodynamical constraints for these systems remain an open question. This is largely due to the lack of a general theory of statistical methods for systems far from equilibrium. Nonetheless, a first approach to this problem has been put forward in a series of novel developements falling under the rubric of the extended second law of thermodynamics. The work presented here is twofold: firstly, we review this theoretical framework and provide a brief description of the three fundamental replicator types in prebiotic evolution: parabolic, malthusian and hyperbolic. Secondly, we employ these previously mentioned techinques to explore how replicators are constrained by thermodynamics. Finally, we comment and discuss where further research should be focused on.

  7. Rescue from replication stress during mitosis.

    Science.gov (United States)

    Fragkos, Michalis; Naim, Valeria

    2017-04-03

    Genomic instability is a hallmark of cancer and a common feature of human disorders, characterized by growth defects, neurodegeneration, cancer predisposition, and aging. Recent evidence has shown that DNA replication stress is a major driver of genomic instability and tumorigenesis. Cells can undergo mitosis with under-replicated DNA or unresolved DNA structures, and specific pathways are dedicated to resolving these structures during mitosis, suggesting that mitotic rescue from replication stress (MRRS) is a key process influencing genome stability and cellular homeostasis. Deregulation of MRRS following oncogene activation or loss-of-function of caretaker genes may be the cause of chromosomal aberrations that promote cancer initiation and progression. In this review, we discuss the causes and consequences of replication stress, focusing on its persistence in mitosis as well as the mechanisms and factors involved in its resolution, and the potential impact of incomplete replication or aberrant MRRS on tumorigenesis, aging and disease.

  8. Surface Replication of Molded Products with Microneedle Features in Injection Molding

    Science.gov (United States)

    Uchiumi, Kazuyasu; Takayama, Tetsuo; Ito, Hiroshi; Inou, Akinori

    Micro-molding of microneedle features was conducted using several injection-molding techniques. Injection compression molding and injection molding were performed with supercritical carbon dioxide fluid and with or without vacuum processing inside the mold cavity. Effects of process parameters on processability and surface replication of the molded parts were evaluated. The height replication ratio for microneedles was improved using injection compression molding. At a shorter compression stroke, the needle height was improved, and the influence of compression delay time was also small. Moreover, the effects of vacuum processing inside the mold cavity under the filling process were slight. The height replication ratio for microneedles showed the highest values using injection molding using supercritical carbon dioxide fluid with vacuum inside the mold cavity.

  9. 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…

  10. Spectral transfer functions of body waves propagating through a stratified medium. Part 1: Basic theory by means of matrix propagators

    International Nuclear Information System (INIS)

    Macia, R.; Correig, A.M.

    1987-01-01

    Seismic wave propagation is described by a second order differential equation for medium displacement. By Fourier transforming with respect to time and space, wave equation transforms into a system of first order linear differential equations for the Fourier transform of displacement and stress. This system of differential equations is solved by means of Matrix Propagator and applied to the propagation of body waves in stratified media. The matrix propagators corresponding to P-SV and SH waves in homogeneous medium are found as an intermediate step to obtain the spectral response of body waves propagating through a stratified medium with homogeneous layers. (author) 14 refs

  11. Inviscid incompressible limits of strongly stratified fluids

    Czech Academy of Sciences Publication Activity Database

    Feireisl, Eduard; Jin, B.J.; Novotný, A.

    2014-01-01

    Roč. 89, 3-4 (2014), s. 307-329 ISSN 0921-7134 R&D Projects: GA ČR GA201/09/0917 Institutional support: RVO:67985840 Keywords : compressible Navier-Stokes system * anelastic approximation * stratified fluid Subject RIV: BA - General Mathematics Impact factor: 0.528, year: 2014 http://iospress.metapress.com/content/d71255745tl50125/?p=969b60ae82634854ab8bd25505ce1f71&pi=3

  12. DNA replication origins-where do we begin?

    Science.gov (United States)

    Prioleau, Marie-Noëlle; MacAlpine, David M

    2016-08-01

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

  13. 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

  14. Measurements of density profile evolution during the stably-stratified filling of an open enclosure

    International Nuclear Information System (INIS)

    Tarawneh, Constantine M.; Homan, K.O.

    2008-01-01

    The stably-stratified filling of an open enclosure produces an interfacial gradient layer which is transported through the enclosure with the bulk flow. The evolution of this interfacial layer is strongly time-dependent and is driven by the nature of the interaction between the internal gravity waves and the inlet-driven interfacial shear. Measurements of density profile evolution have been completed for a rectangular enclosure with a single corner inlet and density variation produced by saline concentration. This system serves as a mass transfer analog to large-scale, thermally-stratified energy storage devices, preserving dynamic similitude in a laboratory-scale system. The experiments covered jet Reynolds numbers of 200-2200 and Froude numbers of 0.06-0.6 in an enclosure with a width 23 times the jet inlet height. The density profiles are seen to be strongly asymmetric and exhibit growth rates significantly different than due to simple one-dimensional molecular diffusion. In addition, shadowgraph and hydrogen bubble visualizations of the density and velocity fields in the gradient layer show the persistence of complex multi-dimensional flow structure even at relatively late stages of the filling process when the gradient layer has been transported well away from the enclosure inlet. The evolution of the vertical density profile has been compared quantitatively to a quasi one-dimensional model based upon empirical diffusivity coefficients

  15. Cross-cultural adaptation of the STRATIFY tool in detecting and predicting risk of falling.

    Science.gov (United States)

    Enríquez de Luna-Rodríguez, Margarita; Aranda-Gallardo, Marta; Canca-Sánchez, José Carlos; Vazquez-Blanco, M José; Moya-Suárez, Ana Belén; Morales-Asencio, José Miguel

    To adapt to Spanish language the STRATIFY tool for clinical use in the Spanish-speaking World. A multicenter, 2 care settings cross-sectional study cultural adaptation study in acute care hospitals and nursing homes was performed in Andalusia during 2014. The adaptation process was divided into 4 stages: translation, back-translation, equivalence between the 2 back-translations and piloting of the Spanish version, thus obtaining the final version. The validity of appearance, content validity and the time required to complete the scale were taken into account. For analysis, the median, central tendency and dispersion of scores, the interquartile range, and the interquartile deviation for the possible variability in responses it was calculated. Content validity measured by content validity index reached a profit of 1. For the validity aspect the clarity and comprehensibility of the questions were taken into account. Of the 5 questions of the instrument, 2 had a small disagreement solved with the introduction of an explanatory phrase to achieve conceptual equivalence. Median both questions were equal or superior to 5. The average time for completion of the scale was less than 3 minutes. The process of adaptation to Spanish of STRATIFY has led to a semantic version and culturally equivalent to the original for easy filling and understanding for use in the Spanish-speaking world. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

  16. Emergence of cooperation in phenotypically heterogeneous populations: a replicator dynamics analysis

    International Nuclear Information System (INIS)

    Barreira da Silva Rocha, A; Escobedo, R; Laruelle, A

    2015-01-01

    The emergence of cooperation is analyzed in heterogeneous populations where two kinds of individuals exist according to their phenotypic appearance. Phenotype recognition is assumed for all individuals: individuals are able to identify the type of every other individual, but fail to recognize their own type. Individuals thus behave under partial information conditions. The interactions between individuals are described by the snowdrift game, where individuals can either cooperate or defect. The evolution of such populations is studied in the framework of evolutionary game theory by means of the replicator dynamics. Overlapping generations are considered, so the replicator equations are formulated in discrete-time form. The stability analysis of the dynamical system is carried out and a detailed description of the behavior of trajectories starting from the interior of the state-space is given. We find that the four monomorphic states are unstable and that a polymorphic state exists which is a global attractor for non-degenerate initial states of the population. The result for the discrete-time replicator coincides with the one of the continuous case. (paper)

  17. 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....

  18. 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...

  19. A dynamic replicator model of the players' bids in an oligopolistic electricity market

    International Nuclear Information System (INIS)

    Sahraei-Ardakani, Mostafa; Rahimi-Kian, Ashkan

    2009-01-01

    In this paper, the replicator dynamics of the power suppliers' bids in an oligopolistic electricity market are derived for both the fixed and variable demand cases. The replicator dynamics stability analysis is also performed. The dynamics of the electricity markets are the results of players' decisions. The physical parameters of the power systems (such as the lines capacities, voltage limitations, etc.) also affect the market dynamics indirectly, through the changes in players' behaviors. Assuming rational players, an optimal bidding strategy for constructing the supply function (SF) of a generating firm is presented and based on that, the dynamics of the bid replicators are studied. Both fixed demands and price sensitive demands are taken into account. The replicator model is presented in the well-known state space structure. A case study is presented to show the applicability of the developed dynamic replicator bid model, and also to show how the Nash-SFE equilibrium evolves over time. (author)

  20. Quality of life in survivors of hematological malignancies stratified by cancer type, time since diagnosis and stem cell transplantation.

    Science.gov (United States)

    Esser, Peter; Kuba, Katharina; Mehnert, Anja; Johansen, Christoffer; Hinz, Andreas; Lordick, Florian; Götze, Heide

    2018-06-01

    Quality of life (QoL) has become an important tool to guide decision making in oncology. Given the heterogeneity among hematological cancer survivors, however, clinicians need comparative data across different subsets. This study recruited survivors of hematological malignancies (≥ 2.5 years after diagnosis) from two German cancer registries. QoL was assessed with the EORTC QLQ-C30. The sample was stratified by cancer type, time since diagnosis, treatment with stem cell transplantation (SCT) and type of SCT. First, levels of QoL were compared across subsamples when controlling for several covariates. Second, we contrasted subsamples with gender- and age-matched population controls obtained from the general population. Of 2001 survivors contacted by mail, 922 (46%) participated in the study. QoL did not significantly differ between the subsamples. All subsamples scored significantly lower in functioning and significantly higher in symptom burden compared to population controls (all p < .001). Almost all of these group effects reached clinically meaningful sizes (Cohen's d ≥ .5). Group differences in global health/QoL were mostly non-significant. Hematological cancer survivors are associated with practically relevant impairments irrespective of differences in central medical characteristics. Nevertheless, survivors seem to evaluate their overall situation as relatively well. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  1. Short-term effects of floods on Japanese encephalitis in Nanchong, China, 2007-2012: A time-stratified case-crossover study.

    Science.gov (United States)

    Zhang, Feifei; Liu, Zhidong; Zhang, Caixia; Jiang, Baofa

    2016-09-01

    This time-stratified case-crossover study aimed to quantify the impact of floods on daily Japanese encephalitis (JE) cases from 2007 to 2012 in Nanchong city of Sichuan Province, China. Using conditional logistic regression analysis, we calculated the odds ratios (ORs) and 95% confidence intervals (CIs) at different lagged days, adjusting for daily average temperature (AT) and daily average relative humidity (ARH). A total of 370 JE cases were notified during the study period, with the median patient age being 4.2years. The seasonal pattern of JE cases clustered in July and August during the study period. Floods were significantly associated with an increased number of JE cases from lag 23 to lag 24, with the strongest lag effect at lag 23 (OR=2.00, 95% CI: 1.14-3.52). Similarly, AT and ARH were positively associated with daily JE cases from lag 0 to lag 8 and from lag 0 to lag 9, respectively. Floods, with AT and ARH, can be used to forecast JE outbreaks in the study area. Based on the results of this study, recommendations include undertaking control measures before the number of cases increases, especially for regions with similar geographic, climatic, and socio-economic conditions as those in the study area. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Experimental investigation and physical description of stratified flow in horizontal channels

    International Nuclear Information System (INIS)

    Staebler, T.

    2007-05-01

    The interaction between a liquid film and turbulent gas flows plays an important role in many technical applications (e.g. in hydraulic engineering, process engineering and nuclear engineering). The local kinematic and turbulent time-averaged flow quantities for counter-current stratified flows (supercritical and subcritical flows with and without flow reversal) have been measured for the first time. Therefore, the method of Particle Image Velocimetry was applied. By using fluorescent particles in combination with an optical filter it was possible to determine the flow quantities of the liquid phase up to the free surface. Additionally, the gaseous phase was investigated by using the scattering of light of conventional particles. With a further measurement technique the void fraction distribution along the channel height has been determined. For this purpose, a single-tip conductivity probe was developed. Furthermore, water delivery rates and pressure losses along the test section were measured over a wide range of parameters. The measurements also revealed new details on the hysteresis effect after the occurrence of flow reversal. The experimental findings were used to develop and validate a statistical model in which the liquid phase is considered to be an agglomeration of interacting particles. The statistical consideration of the particle interactions delivers a differential equation which can be used to predict the local void fraction distribution with the local turbulent kinematic energies of the liquid phase. Beyond that, an additional statistical description is presented in which the probability density functions of the local void fraction are described by beta-functions. Both theoretical approaches can be used for numerical modelling whereas the statistical model can be used to describe the phase interactions and the statistical description to describe the turbulent fluctuations of the local void fraction. Thus, this work has made available all necessary

  3. 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.

  4. Suppression of Poxvirus Replication by Resveratrol.

    Science.gov (United States)

    Cao, Shuai; Realegeno, Susan; Pant, Anil; Satheshkumar, Panayampalli S; Yang, Zhilong

    2017-01-01

    Poxviruses continue to cause serious diseases even after eradication of the historically deadly infectious human disease, smallpox. Poxviruses are currently being developed as vaccine vectors and cancer therapeutic agents. Resveratrol is a natural polyphenol stilbenoid found in plants that has been shown to inhibit or enhance replication of a number of viruses, but the effect of resveratrol on poxvirus replication is unknown. In the present study, we found that resveratrol dramatically suppressed the replication of vaccinia virus (VACV), the prototypic member of poxviruses, in various cell types. Resveratrol also significantly reduced the replication of monkeypox virus, a zoonotic virus that is endemic in Western and Central Africa and causes human mortality. The inhibitory effect of resveratrol on poxviruses is independent of VACV N1 protein, a potential resveratrol binding target. Further experiments demonstrated that resveratrol had little effect on VACV early gene expression, while it suppressed VACV DNA synthesis, and subsequently post-replicative gene expression.

  5. Suppression of Poxvirus Replication by Resveratrol

    Directory of Open Access Journals (Sweden)

    Shuai Cao

    2017-11-01

    Full Text Available Poxviruses continue to cause serious diseases even after eradication of the historically deadly infectious human disease, smallpox. Poxviruses are currently being developed as vaccine vectors and cancer therapeutic agents. Resveratrol is a natural polyphenol stilbenoid found in plants that has been shown to inhibit or enhance replication of a number of viruses, but the effect of resveratrol on poxvirus replication is unknown. In the present study, we found that resveratrol dramatically suppressed the replication of vaccinia virus (VACV, the prototypic member of poxviruses, in various cell types. Resveratrol also significantly reduced the replication of monkeypox virus, a zoonotic virus that is endemic in Western and Central Africa and causes human mortality. The inhibitory effect of resveratrol on poxviruses is independent of VACV N1 protein, a potential resveratrol binding target. Further experiments demonstrated that resveratrol had little effect on VACV early gene expression, while it suppressed VACV DNA synthesis, and subsequently post-replicative gene expression.

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

    Science.gov (United States)

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

    2018-06-01

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

  7. 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

  8. Effector-Triggered Self-Replication in Coupled Subsystems.

    Science.gov (United States)

    Komáromy, Dávid; Tezcan, Meniz; Schaeffer, Gaël; Marić, Ivana; Otto, Sijbren

    2017-11-13

    In living systems processes like genome duplication and cell division are carefully synchronized through subsystem coupling. If we are to create life de novo, similar control over essential processes such as self-replication need to be developed. Here we report that coupling two dynamic combinatorial subsystems, featuring two separate building blocks, enables effector-mediated control over self-replication. The subsystem based on the first building block shows only self-replication, whereas that based on the second one is solely responsive toward a specific external effector molecule. Mixing the subsystems arrests replication until the effector molecule is added, resulting in the formation of a host-effector complex and the liberation of the building block that subsequently engages in self-replication. The onset, rate and extent of self-replication is controlled by the amount of effector present. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

    Anderson, Samantha F; Maxwell, Scott E

    2017-01-01

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

  10. 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

    Human metapneumovirus (HMPV) causes significant upper and lower respiratory disease in all age groups worldwide. The virus possesses a negative-sense single-stranded RNA genome of approximately 13.3 kb encapsidated by multiple copies of the nucleoprotein (N), giving rise to helical nucleocapsids. In addition, copies of the phosphoprotein (P) and the large RNA polymerase (L) decorate the viral nucleocapsids. After viral attachment, endocytosis, and fusion mediated by the viral glycoproteins, HMPV nucleocapsids are released into the cell cytoplasm. To visualize the subsequent steps of genome transcription and replication, a fluorescence in situ hybridization (FISH) protocol was established to detect different viral RNA subpopulations in infected cells. The FISH probes were specific for detection of HMPV positive-sense RNA (+RNA) and viral genomic RNA (vRNA). Time course analysis of human bronchial epithelial BEAS-2B cells infected with HMPV revealed the formation of inclusion bodies (IBs) from early times postinfection. HMPV IBs were shown to be cytoplasmic sites of active transcription and replication, with the translation of viral proteins being closely associated. Inclusion body formation was consistent with an actin-dependent coalescence of multiple early replicative sites. Time course quantitative reverse transcription-PCR analysis suggested that the coalescence of inclusion bodies is a strategy to efficiently replicate and transcribe the viral genome. These results provide a better understanding of the steps following HMPV entry and have important clinical implications. IMPORTANCE Human metapneumovirus (HMPV) is a recently discovered pathogen that affects human populations of all ages worldwide. Reinfections are common throughout life, but no vaccines or antiviral treatments are currently available. In this work, a spatiotemporal analysis of HMPV replication and transcription in bronchial epithelial cell-derived immortal cells was performed. HMPV was shown to

  11. Performance of a supercharged direct-injection stratified-charge rotary combustion engine

    Science.gov (United States)

    Bartrand, Timothy A.; Willis, Edward A.

    1990-01-01

    A zero-dimensional thermodynamic performance computer model for direct-injection stratified-charge rotary combustion engines was modified and run for a single rotor supercharged engine. Operating conditions for the computer runs were a single boost pressure and a matrix of speeds, loads and engine materials. A representative engine map is presented showing the predicted range of efficient operation. After discussion of the engine map, a number of engine features are analyzed individually. These features are: heat transfer and the influence insulating materials have on engine performance and exhaust energy; intake manifold pressure oscillations and interactions with the combustion chamber; and performance losses and seal friction. Finally, code running times and convergence data are presented.

  12. Replicability of time-varying connectivity patterns in large resting state fMRI samples.

    Science.gov (United States)

    Abrol, Anees; Damaraju, Eswar; Miller, Robyn L; Stephen, Julia M; Claus, Eric D; Mayer, Andrew R; Calhoun, Vince D

    2017-12-01

    The past few years have seen an emergence of approaches that leverage temporal changes in whole-brain patterns of functional connectivity (the chronnectome). In this chronnectome study, we investigate the replicability of the human brain's inter-regional coupling dynamics during rest by evaluating two different dynamic functional network connectivity (dFNC) analysis frameworks using 7 500 functional magnetic resonance imaging (fMRI) datasets. To quantify the extent to which the emergent functional connectivity (FC) patterns are reproducible, we characterize the temporal dynamics by deriving several summary measures across multiple large, independent age-matched samples. Reproducibility was demonstrated through the existence of basic connectivity patterns (FC states) amidst an ensemble of inter-regional connections. Furthermore, application of the methods to conservatively configured (statistically stationary, linear and Gaussian) surrogate datasets revealed that some of the studied state summary measures were indeed statistically significant and also suggested that this class of null model did not explain the fMRI data fully. This extensive testing of reproducibility of similarity statistics also suggests that the estimated FC states are robust against variation in data quality, analysis, grouping, and decomposition methods. We conclude that future investigations probing the functional and neurophysiological relevance of time-varying connectivity assume critical importance. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  13. RANS Modeling of Stably Stratified Turbulent Boundary Layer Flows in OpenFOAM®

    Directory of Open Access Journals (Sweden)

    Wilson Jordan M.

    2015-01-01

    Full Text Available Quantifying mixing processes relating to the transport of heat, momentum, and scalar quantities of stably stratified turbulent geophysical flows remains a substantial task. In a stably stratified flow, such as the stable atmospheric boundary layer (SABL, buoyancy forces have a significant impact on the flow characteristics. This study investigates constant and stability-dependent turbulent Prandtl number (Prt formulations linking the turbulent viscosity (νt and diffusivity (κt for modeling applications of boundary layer flows. Numerical simulations of plane Couette flow and pressure-driven channel flow are performed using the Reynolds-averaged Navier-Stokes (RANS framework with the standard k-ε turbulence model. Results are compared with DNS data to evaluate model efficacy for predicting mean velocity and density fields. In channel flow simulations, a Prandtl number formulation for wall-bounded flows is introduced to alleviate overmixing of the mean density field. This research reveals that appropriate specification of Prt can improve predictions of stably stratified turbulent boundary layer flows.

  14. Replication and robustness in developmental research.

    Science.gov (United States)

    Duncan, Greg J; Engel, Mimi; Claessens, Amy; Dowsett, Chantelle J

    2014-11-01

    Replications and robustness checks are key elements of the scientific method and a staple in many disciplines. However, leading journals in developmental psychology rarely include explicit replications of prior research conducted by different investigators, and few require authors to establish in their articles or online appendices that their key results are robust across estimation methods, data sets, and demographic subgroups. This article makes the case for prioritizing both explicit replications and, especially, within-study robustness checks in developmental psychology. It provides evidence on variation in effect sizes in developmental studies and documents strikingly different replication and robustness-checking practices in a sample of journals in developmental psychology and a sister behavioral science-applied economics. Our goal is not to show that any one behavioral science has a monopoly on best practices, but rather to show how journals from a related discipline address vital concerns of replication and generalizability shared by all social and behavioral sciences. We provide recommendations for promoting graduate training in replication and robustness-checking methods and for editorial policies that encourage these practices. Although some of our recommendations may shift the form and substance of developmental research articles, we argue that they would generate considerable scientific benefits for the field. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

  15. How many bootstrap replicates are necessary?

    Science.gov (United States)

    Pattengale, Nicholas D; Alipour, Masoud; Bininda-Emonds, Olaf R P; Moret, Bernard M E; Stamatakis, Alexandros

    2010-03-01

    Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reconstruction approaches, but we focus here on one of the most popular, maximum likelihood (ML). Because ML inference is so computationally demanding, it has proved too expensive to date to assess the impact of the number of replicates used in BS on the relative accuracy of the support values. For the same reason, a rather small number (typically 100) of BS replicates are computed in real-world studies. Stamatakis et al. recently introduced a BS algorithm that is 1 to 2 orders of magnitude faster than previous techniques, while yielding qualitatively comparable support values, making an experimental study possible. In this article, we propose stopping criteria--that is, thresholds computed at runtime to determine when enough replicates have been generated--and we report on the first large-scale experimental study to assess the effect of the number of replicates on the quality of support values, including the performance of our proposed criteria. We run our tests on 17 diverse real-world DNA--single-gene as well as multi-gene--datasets, which include 125-2,554 taxa. We find that our stopping criteria typically stop computations after 100-500 replicates (although the most conservative criterion may continue for several thousand replicates) while producing support values that correlate at better than 99.5% with the reference values on the best ML trees. Significantly, we also find that the stopping criteria can recommend very different numbers of replicates for different datasets of comparable sizes. Our results are thus twofold: (i) they give the first experimental assessment of the effect of the number of BS replicates on the quality of support values returned through BS, and (ii) they validate our proposals for

  16. Stability of Miscible Displacements Across Stratified Porous Media

    Energy Technology Data Exchange (ETDEWEB)

    Shariati, Maryam; Yortsos, Yanis C.

    2000-09-11

    This report studied macro-scale heterogeneity effects. Reflecting on their importance, current simulation practices of flow and displacement in porous media were invariably based on heterogeneous permeability fields. Here, it was focused on a specific aspect of such problems, namely the stability of miscible displacements in stratified porous media, where the displacement is perpendicular to the direction of stratification.

  17. Mechanisms and Variability of Salt Transport in Partially-Stratified Estuaries

    National Research Council Canada - National Science Library

    Bowen, Melissa

    2000-01-01

    .... Analysis of salt transport from observations in the Hudson Estuary show that stratified periods with elevated estuarine salt transport occur in five-day intervals once a month during apogean neap tides...

  18. Factors influencing microinjection molding replication quality

    Science.gov (United States)

    Vera, Julie; Brulez, Anne-Catherine; Contraires, Elise; Larochette, Mathieu; Trannoy-Orban, Nathalie; Pignon, Maxime; Mauclair, Cyril; Valette, Stéphane; Benayoun, Stéphane

    2018-01-01

    In recent years, there has been increased interest in producing and providing high-precision plastic parts that can be manufactured by microinjection molding: gears, pumps, optical grating elements, and so on. For all of these applications, the replication quality is essential. This study has two goals: (1) fabrication of high-precision parts using the conventional injection molding machine; (2) identification of robust parameters that ensure production quality. Thus, different technological solutions have been used: cavity vacuuming and the use of a mold coated with DLC or CrN deposits. AFM and SEM analyses were carried out to characterize the replication profile. The replication quality was studied in terms of the process parameters, coated and uncoated molds and crystallinity of the polymer. Specific studies were processed to quantify the replicability of injection molded parts (ABS, PC and PP). Analysis of the Taguchi experimental designs permits prioritization of the impact of each parameter on the replication quality. A discussion taking into account these new parameters and the thermal and spreading properties on the coatings is proposed. It appeared that, in general, increasing the mold temperature improves the molten polymer fill in submicron features except for the steel insert (for which the presence of a vacuum is the most important factor). Moreover, the DLC coating was the best coating to increase the quality of the replication. This result could be explained by the lower thermal diffusivity of this coating. We noted that the viscosity of the polymers is not a primordial factor of the replication quality.

  19. Realistic Vascular Replicator for TAVR Procedures.

    Science.gov (United States)

    Rotman, Oren M; Kovarovic, Brandon; Sadasivan, Chander; Gruberg, Luis; Lieber, Baruch B; Bluestein, Danny

    2018-04-13

    Transcatheter aortic valve replacement (TAVR) is an over-the-wire procedure for treatment of severe aortic stenosis (AS). TAVR valves are conventionally tested using simplified left heart simulators (LHS). While those provide baseline performance reliably, their aortic root geometries are far from the anatomical in situ configuration, often overestimating the valves' performance. We report on a novel benchtop patient-specific arterial replicator designed for testing TAVR and training interventional cardiologists in the procedure. The Replicator is an accurate model of the human upper body vasculature for training physicians in percutaneous interventions. It comprises of fully-automated Windkessel mechanism to recreate physiological flow conditions. Calcified aortic valve models were fabricated and incorporated into the Replicator, then tested for performing TAVR procedure by an experienced cardiologist using the Inovare valve. EOA, pressures, and angiograms were monitored pre- and post-TAVR. A St. Jude mechanical valve was tested as a reference that is less affected by the AS anatomy. Results in the Replicator of both valves were compared to the performance in a commercial ISO-compliant LHS. The AS anatomy in the Replicator resulted in a significant decrease of the TAVR valve performance relative to the simplified LHS, with EOA and transvalvular pressures comparable to clinical data. Minor change was seen in the mechanical valve performance. The Replicator showed to be an effective platform for TAVR testing. Unlike a simplified geometric anatomy LHS, it conservatively provides clinically-relevant outcomes and complement it. The Replicator can be most valuable for testing new valves under challenging patient anatomies, physicians training, and procedural planning.

  20. Rock bream iridovirus (RBIV) replication in rock bream (Oplegnathus fasciatus) exposed for different time periods to susceptible water temperatures.

    Science.gov (United States)

    Jung, Myung-Hwa; Nikapitiya, Chamilani; Vinay, Tharabenahalli-Nagaraju; Lee, Jehee; Jung, Sung-Ju

    2017-11-01

    Rock bream iridovirus (RBIV) is a member of the Megalocytivirus genus that causes severe mortality to rock bream. Water temperature is known to affect the immune system and susceptibility of fish to RBIV infection. In this study, we evaluated the time dependent virus replication pattern and time required to completely eliminate virus from the rock bream body against RBIV infection at different water temperature conditions. The rock bream was exposed to the virus and held at 7 (group A1), 4 (group A2) and 2 days (group A3) at 23 °C before the water temperature was reduced to 17 °C. A total of 28% mortality was observed 24-35 days post infection (dpi) in only the 7 day exposure group at 23 °C. In all 23 °C exposure groups, virus replication peaked at 20 to 22 dpi (10 6 -10 7 /μl). In recovery stages (30-100 dpi), the virus copy number was gradually reduced, from 10 6 to 10 1 with faster decreases in the shorter exposure period group at 23 °C. When the water temperature was increased in surviving fish from 17 to 26 °C at 70 dpi, they did not show any mortality or signs of disease and had low virus copy numbers (below 10 2 /μl). Thus, fish need at least 50 days from peaked RBIV levels (approximately 20-25 dpi) to inhibit the virus. This indicates that maintaining the fish at low water temperature (17 °C) for 70 days is sufficient to eradicate RBIV from fish body. Thus, RBIV could be eliminated slowly from the fish body and the virus may be completely eliminated under the threshold of causing mortality. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Unit Stratified Sampling as a Tool for Approximation of Stochastic Optimization Problems

    Czech Academy of Sciences Publication Activity Database

    Šmíd, Martin

    2012-01-01

    Roč. 19, č. 30 (2012), s. 153-169 ISSN 1212-074X R&D Projects: GA ČR GAP402/11/0150; GA ČR GAP402/10/0956; GA ČR GA402/09/0965 Institutional research plan: CEZ:AV0Z10750506 Institutional support: RVO:67985556 Keywords : Stochastic programming * approximation * stratified sampling Subject RIV: BB - Applied Statistics, Operational Research http://library.utia.cas.cz/separaty/2013/E/smid-unit stratified sampling as a tool for approximation of stochastic optimization problems.pdf

  2. Monitoring oil persistence on beaches : SCAT versus stratified random sampling designs

    International Nuclear Information System (INIS)

    Short, J.W.; Lindeberg, M.R.; Harris, P.M.; Maselko, J.M.; Pella, J.J.; Rice, S.D.

    2003-01-01

    In the event of a coastal oil spill, shoreline clean-up assessment teams (SCAT) commonly rely on visual inspection of the entire affected area to monitor the persistence of the oil on beaches. Occasionally, pits are excavated to evaluate the persistence of subsurface oil. This approach is practical for directing clean-up efforts directly following a spill. However, sampling of the 1989 Exxon Valdez oil spill in Prince William Sound 12 years later has shown that visual inspection combined with pit excavation does not offer estimates of contaminated beach area of stranded oil volumes. This information is needed to statistically evaluate the significance of change with time. Assumptions regarding the correlation of visually-evident surface oil and cryptic subsurface oil are usually not evaluated as part of the SCAT mandate. Stratified random sampling can avoid such problems and could produce precise estimates of oiled area and volume that allow for statistical assessment of major temporal trends and the extent of the impact. The 2001 sampling of the shoreline of Prince William Sound showed that 15 per cent of surface oil occurrences were associated with subsurface oil. This study demonstrates the usefulness of the stratified random sampling method and shows how sampling design parameters impact statistical outcome. Power analysis based on the study results, indicate that optimum power is derived when unnecessary stratification is avoided. It was emphasized that sampling effort should be balanced between choosing sufficient beaches for sampling and the intensity of sampling

  3. Yeast as a model host to study replication and recombination of defective interfering RNA of Tomato bushy stunt virus

    International Nuclear Information System (INIS)

    Panavas, Tadas; Nagy, Peter D.

    2003-01-01

    Defective interfering (DI) RNA associated with Tomato bushy stunt virus (TBSV), which is a plus-strand RNA virus, requires p33 and p92 proteins of TBSV or the related Cucumber necrosis virus (CNV), for replication in plants. To test if DI RNA can replicate in a model host, we coexpressed TBSV DI RNA and p33/p92 of CNV in yeast. We show evidence for replication of DI RNA in yeast, including (i) dependence on p33 and p92 for DI replication; (ii) presence of active CNV RNA-dependent RNA polymerase in isolated membrane-containing preparations; (iii) increasing amount of DI RNA(+) over time; (iv) accumulation of (-)stranded DI RNA; (v) presence of correct 5' and 3' ends in DI RNA; (vi) inhibition of replication by mutations in the replication enhancer; and (vii) evolution of DI RNA over time, as shown by sequence heterogeneity. We also produced evidence supporting the occurrence of DI RNA recombinants in yeast. In summary, development of yeast as a host for replication of TBSV DI RNA will facilitate studies on the roles of viral and host proteins in replication/recombination

  4. Hydrodynamics of stratified epithelium: Steady state and linearized dynamics

    Science.gov (United States)

    Yeh, Wei-Ting; Chen, Hsuan-Yi

    2016-05-01

    A theoretical model for stratified epithelium is presented. The viscoelastic properties of the tissue are assumed to be dependent on the spatial distribution of proliferative and differentiated cells. Based on this assumption, a hydrodynamic description of tissue dynamics at the long-wavelength, long-time limit is developed, and the analysis reveals important insights into the dynamics of an epithelium close to its steady state. When the proliferative cells occupy a thin region close to the basal membrane, the relaxation rate towards the steady state is enhanced by cell division and cell apoptosis. On the other hand, when the region where proliferative cells reside becomes sufficiently thick, a flow induced by cell apoptosis close to the apical surface enhances small perturbations. This destabilizing mechanism is general for continuous self-renewal multilayered tissues; it could be related to the origin of certain tissue morphology, tumor growth, and the development pattern.

  5. Prospective elementary teachers' conceptions of multidigit number: exemplifying a replication framework for mathematics education

    Science.gov (United States)

    Jacobson, Erik; Simpson, Amber

    2018-04-01

    Replication studies play a critical role in scientific accumulation of knowledge, yet replication studies in mathematics education are rare. In this study, the authors replicated Thanheiser's (Educational Studies in Mathematics 75:241-251, 2010) study of prospective elementary teachers' conceptions of multidigit number and examined the main claim that most elementary pre-service teachers think about digits incorrectly at least some of the time. Results indicated no statistically significant difference in the distribution of conceptions between the original and replication samples and, moreover, no statistically significant differences in the distribution of sub-conceptions among prospective teachers with the most common conception. These results suggest confidence is warranted both in the generality of the main claim and in the utility of the conceptions framework for describing prospective elementary teachers' conceptions of multidigit number. The report further contributes a framework for replication of mathematics education research adapted from the field of psychology.

  6. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural...... framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures...

  7. Inhibition of Rho-associated kinases disturbs the collective cell migration of stratified TE-10 cells

    Directory of Open Access Journals (Sweden)

    Taro Mikami

    2015-01-01

    Full Text Available BACKGROUND: The collective cell migration of stratified epithelial cells is considered to be an important phenomenon in wound healing, development, and cancer invasion; however, little is known about the mechanisms involved. Furthermore, whereas Rho family proteins, including RhoA, play important roles in cell migration, the exact role of Rho-associated coiled coil-containing protein kinases (ROCKs in cell migration is controversial and might be cell-type dependent. Here, we report the development of a novel modified scratch assay that was used to observe the collective cell migration of stratified TE-10 cells derived from a human esophageal cancer specimen. RESULTS: Desmosomes were found between the TE-10 cells and microvilli of the surface of the cell sheet. The leading edge of cells in the cell sheet formed a simple layer and moved forward regularly; these rows were followed by the stratified epithelium. ROCK inhibitors and ROCK small interfering RNAs (siRNAs disturbed not only the collective migration of the leading edge of this cell sheet, but also the stratified layer in the rear. In contrast, RhoA siRNA treatment resulted in more rapid migration of the leading rows and disturbed movement of the stratified portion. CONCLUSIONS: The data presented in this study suggest that ROCKs play an important role in mediating the collective migration of TE-10 cell sheets. In addition, differences between the effects of siRNAs targeting either RhoA or ROCKs suggested that distinct mechanisms regulate the collective cell migration in the simple epithelium of the wound edge versus the stratified layer of the epithelium.

  8. Stereo imaging and random array stratified imaging for cargo radiation inspecting

    International Nuclear Information System (INIS)

    Wang Jingjin; Zeng Yu

    2003-01-01

    This paper presents a Stereo Imaging and Random Array Stratified Imaging for cargo container radiation Inspecting. By using dual-line vertical detector array scan, a stereo image of inspected cargo can be obtained and watched with virtual reality view. The random detector array has only one-row of detectors but distributed in a certain horizontal dimension randomly. To scan a cargo container with this random array detector, a 'defocused' image is obtained. By using 'anti-random focusing', one layer of the image can be focused on the background of all defocused images from other layers. A stratified X-ray image of overlapped bike wheels is presented

  9. Cytology of DNA Replication Reveals Dynamic Plasticity of Large-Scale Chromatin Fibers.

    Science.gov (United States)

    Deng, Xiang; Zhironkina, Oxana A; Cherepanynets, Varvara D; Strelkova, Olga S; Kireev, Igor I; Belmont, Andrew S

    2016-09-26

    In higher eukaryotic interphase nuclei, the 100- to >1,000-fold linear compaction of chromatin is difficult to reconcile with its function as a template for transcription, replication, and repair. It is challenging to imagine how DNA and RNA polymerases with their associated molecular machinery would move along the DNA template without transient decondensation of observed large-scale chromatin "chromonema" fibers [1]. Transcription or "replication factory" models [2], in which polymerases remain fixed while DNA is reeled through, are similarly difficult to conceptualize without transient decondensation of these chromonema fibers. Here, we show how a dynamic plasticity of chromatin folding within large-scale chromatin fibers allows DNA replication to take place without significant changes in the global large-scale chromatin compaction or shape of these large-scale chromatin fibers. Time-lapse imaging of lac-operator-tagged chromosome regions shows no major change in the overall compaction of these chromosome regions during their DNA replication. Improved pulse-chase labeling of endogenous interphase chromosomes yields a model in which the global compaction and shape of large-Mbp chromatin domains remains largely invariant during DNA replication, with DNA within these domains undergoing significant movements and redistribution as they move into and then out of adjacent replication foci. In contrast to hierarchical folding models, this dynamic plasticity of large-scale chromatin organization explains how localized changes in DNA topology allow DNA replication to take place without an accompanying global unfolding of large-scale chromatin fibers while suggesting a possible mechanism for maintaining epigenetic programming of large-scale chromatin domains throughout DNA replication. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2015-07-01

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

  11. Stratified charge rotary engine combustion studies

    Science.gov (United States)

    Shock, H.; Hamady, F.; Somerton, C.; Stuecken, T.; Chouinard, E.; Rachal, T.; Kosterman, J.; Lambeth, M.; Olbrich, C.

    1989-07-01

    Analytical and experimental studies of the combustion process in a stratified charge rotary engine (SCRE) continue to be the subject of active research in recent years. Specifically to meet the demand for more sophisticated products, a detailed understanding of the engine system of interest is warranted. With this in mind the objective of this work is to develop an understanding of the controlling factors that affect the SCRE combustion process so that an efficient power dense rotary engine can be designed. The influence of the induction-exhaust systems and the rotor geometry are believed to have a significant effect on combustion chamber flow characteristics. In this report, emphasis is centered on Laser Doppler Velocimetry (LDV) measurements and on qualitative flow visualizations in the combustion chamber of the motored rotary engine assembly. This will provide a basic understanding of the flow process in the RCE and serve as a data base for verification of numerical simulations. Understanding fuel injection provisions is also important to the successful operation of the stratified charge rotary engine. Toward this end, flow visualizations depicting the development of high speed, high pressure fuel jets are described. Friction is an important consideration in an engine from the standpoint of lost work, durability and reliability. MSU Engine Research Laboratory efforts in accessing the frictional losses associated with the rotary engine are described. This includes work which describes losses in bearing, seal and auxillary components. Finally, a computer controlled mapping system under development is described. This system can be used to map shapes such as combustion chamber, intake manifolds or turbine blades accurately.

  12. Gaseous air pollution and emergency hospital visits for hypertension in Beijing, China: a time-stratified case-crossover study

    Directory of Open Access Journals (Sweden)

    Zhang Yanshen

    2010-10-01

    Full Text Available Abstract Background A number of epidemiological studies have been conducted to research the adverse effects of air pollution on mortality and morbidity. Hypertension is the most important risk factor for cardiovascular mortality. However, few previous studies have examined the relationship between gaseous air pollution and morbidity for hypertension. Methods Daily data on emergency hospital visits (EHVs for hypertension were collected from the Peking University Third Hospital. Daily data on gaseous air pollutants (sulfur dioxide (SO2 and nitrogen dioxide (NO2 and particulate matter less than 10 μm in aerodynamic diameter (PM10 were collected from the Beijing Municipal Environmental Monitoring Center. A time-stratified case-crossover design was conducted to evaluate the relationship between urban gaseous air pollution and EHVs for hypertension. Temperature and relative humidity were controlled for. Results In the single air pollutant models, a 10 μg/m3 increase in SO2 and NO2 were significantly associated with EHVs for hypertension. The odds ratios (ORs were 1.037 (95% confidence interval (CI: 1.004-1.071 for SO2 at lag 0 day, and 1.101 (95% CI: 1.038-1.168 for NO2 at lag 3 day. After controlling for PM10, the ORs associated with SO2 and NO2 were 1.025 (95% CI: 0.987-1.065 and 1.114 (95% CI: 1.037-1.195, respectively. Conclusion Elevated urban gaseous air pollution was associated with increased EHVs for hypertension in Beijing, China.

  13. Plume Splitting in a Two-layer Stratified Ambient Fluid

    Science.gov (United States)

    Ma, Yongxing; Flynn, Morris; Sutherland, Bruce

    2017-11-01

    A line-source plume descending into a two-layer stratified ambient fluid in a finite sized tank is studied experimentally. Although the total volume of ambient fluid is fixed, lower- and upper-layer fluids are respectively removed and added at a constant rate mimicking marine outfall through diffusers and natural and hybrid ventilated buildings. The influence of the plume on the ambient depends on the value of λ, defined as the ratio of the plume buoyancy to the buoyancy loss of the plume as it crosses the ambient interface. Similar to classical filling-box experiments, the plume can always reach the bottom of the tank if λ > 1 . By contrast, if λ < 1 , an intermediate layer eventually forms as a result of plume splitting. Eventually all of the plume fluid spreads within the intermediate layer. The starting time, tv, and the ending time, tt, of the transition process measured from experiments correlate with the value of λ. A three-layer ambient fluid is observed after transition, and the mean value of the measured densities of the intermediate layer fluid is well predicted using plume theory. Acknowledgments: Funding for this study was provided by NSERC.

  14. 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.

  15. 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.)

  16. 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…

  17. Formation and repair of DNA-protein cross-links (DPCs) in newly replicated DNA

    International Nuclear Information System (INIS)

    Chiu, S.; Friedman, L.R.; Oleinick, N.L.

    1987-01-01

    DPCs preferentially involve proteins of the nuclear matrix, the site of replication and transcription. To elucidate the relationship with replication, the formation and repair of DPCs has been studied in newly replicated DNA. Log-phase V79 cells were pulsed with /sup 3/H-TdR (10-20 μCi/ml) for 30-90 sec at 22 0 followed by up to a 60 min chase at 37 0 . Irradiation (0-100 Gy) immediately after the pulse increases the labeled DNA in DPCs with a dose-dependence that is unaffected by the initial level of labeled DPC or by chase time. When cells are irradiated before the pulse, DNA synthesis is inhibited; however, release of pulse-labeled DPCs appears normal. The data suggest that during replication, DNA is cross-linked to (matrix) protein, contributing to background DPCs

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

    Science.gov (United States)

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

    2016-01-01

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

  19. 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

  20. 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.

  1. Equipment for extracting and conveying stratified minerals

    Energy Technology Data Exchange (ETDEWEB)

    Blumenthal, G.; Kunzer, H.; Plaga, K.

    1991-08-14

    This invention relates to equipment for extracting stratified minerals and conveying the said minerals along the working face, comprising a trough shaped conveyor run assembled from lengths, a troughed extraction run in lengths matching the lengths of conveyor troughing, which is linked to the top edge of the working face side of the conveyor troughing with freedom to swivel vertically, and a positively guided chain carrying extraction tools and scrapers along the conveyor and extraction runs.

  2. 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.

  3. Applying a multi-replication framework to support dynamic situation assessment and predictive capabilities

    Science.gov (United States)

    Lammers, Craig; McGraw, Robert M.; Steinman, Jeffrey S.

    2005-05-01

    Technological advances and emerging threats reduce the time between target detection and action to an order of a few minutes. To effectively assist with the decision-making process, C4I decision support tools must quickly and dynamically predict and assess alternative Courses Of Action (COAs) to assist Commanders in anticipating potential outcomes. These capabilities can be provided through the faster-than-real-time predictive simulation of plans that are continuously re-calibrating with the real-time picture. This capability allows decision-makers to assess the effects of re-tasking opportunities, providing the decision-maker with tremendous freedom to make time-critical, mid-course decisions. This paper presents an overview and demonstrates the use of a software infrastructure that supports DSAP capabilities. These DSAP capabilities are demonstrated through the use of a Multi-Replication Framework that supports (1) predictivie simulations using JSAF (Joint Semi-Automated Forces); (2) real-time simulation, also using JSAF, as a state estimation mechanism; and, (3) real-time C4I data updates through TBMCS (Theater Battle Management Core Systems). This infrastructure allows multiple replications of a simulation to be executed simultaneously over a grid faster-than-real-time, calibrated with live data feeds. A cost evaluator mechanism analyzes potential outcomes and prunes simulations that diverge from the real-time picture. In particular, this paper primarily serves to walk a user through the process for using the Multi-Replication Framework providing an enhanced decision aid.

  4. Replicated Data Management for Mobile Computing

    CERN Document Server

    Douglas, Terry

    2008-01-01

    Managing data in a mobile computing environment invariably involves caching or replication. In many cases, a mobile device has access only to data that is stored locally, and much of that data arrives via replication from other devices, PCs, and services. Given portable devices with limited resources, weak or intermittent connectivity, and security vulnerabilities, data replication serves to increase availability, reduce communication costs, foster sharing, and enhance survivability of critical information. Mobile systems have employed a variety of distributed architectures from client-server

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

    Science.gov (United States)

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

    2018-05-01

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

  6. A mechanically enhanced hybrid nano-stratified barrier with a defect suppression mechanism for highly reliable flexible OLEDs.

    Science.gov (United States)

    Jeong, Eun Gyo; Kwon, Seonil; Han, Jun Hee; Im, Hyeon-Gyun; Bae, Byeong-Soo; Choi, Kyung Cheol

    2017-05-18

    Understanding the mechanical behaviors of encapsulation barriers under bending stress is important when fabricating flexible organic light-emitting diodes (FOLEDs). The enhanced mechanical characteristics of a nano-stratified barrier were analyzed based on a defect suppression mechanism, and then experimentally demonstrated. Following the Griffith model, naturally-occurring cracks, which were caused by Zn etching at the interface of the nano-stratified structure, can curb the propagation of defects. Cross-section images after bending tests provided remarkable evidence to support the existence of a defect suppression mechanism. Many visible cracks were found in a single Al 2 O 3 layer, but not in the nano-stratified structure, due to the mechanism. The nano-stratified structure also enhanced the barrier's physical properties by changing the crystalline phase of ZnO. In addition, experimental results demonstrated the effect of the mechanism in various ways. The nano-stratified barrier maintained a low water vapor transmission rate after 1000 iterations of a 1 cm bending radius test. Using this mechanically enhanced hybrid nano-stratified barrier, FOLEDs were successfully encapsulated without losing mechanical or electrical performance. Finally, comparative lifetime measurements were conducted to determine reliability. After 2000 hours of constant current driving and 1000 iterations with a 1 cm bending radius, the FOLEDs retained 52.37% of their initial luminance, which is comparable to glass-lid encapsulation, with 55.96% retention. Herein, we report a mechanically enhanced encapsulation technology for FOLEDs using a nano-stratified structure with a defect suppression mechanism.

  7. Replication of urban innovations - prioritization of strategies for the replication of Dhaka's community-based decentralized composting model.

    Science.gov (United States)

    Yedla, Sudhakar

    2012-01-01

    Dhaka's community-based decentralized composting (DCDC) is a successful demonstration of solid waste management by adopting low-cost technology, local resources community participation and partnerships among the various actors involved. This paper attempts to understand the model, necessary conditions, strategies and their priorities to replicate DCDC in the other developing cities of Asia. Thirteen strategies required for its replication are identified and assessed based on various criteria, namely transferability, longevity, economic viability, adaptation and also overall replication. Priority setting by multi-criteria analysis by applying analytic hierarchy process revealed that immediate transferability without long-term and economic viability consideration is not advisable as this would result in unsustainable replication of DCDC. Based on the analysis, measures to ensure the product quality control; partnership among stakeholders (public-private-community); strategies to achieve better involvement of the private sector in solid waste management (entrepreneurship in approach); simple and low-cost technology; and strategies to provide an effective interface among the complementing sectors are identified as important strategies for its replication.

  8. 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

  9. Evaluation of a Stratified National Breast Screening Program in the United Kingdom : An Early Model-Based Cost-Effectiveness Analysis

    NARCIS (Netherlands)

    Gray, Ewan; Donten, Anna; Karssemeijer, Nico; van Gils, Carla; Evans, D. Gareth R.; Astley, Sue; Payne, Katherine

    Objectives: To identify the incremental costs and consequences of stratified national breast screening programs (stratified NBSPs) and drivers of relative cost-effectiveness. Methods: A decision-analytic model (discrete event simulation) was conceptualized to represent four stratified NBSPs (risk 1,

  10. Evaluation of a Stratified National Breast Screening Program in the United Kingdom: An Early Model-Based Cost-Effectiveness Analysis

    NARCIS (Netherlands)

    Gray, E.; Donten, A.; Karssemeijer, N.; Gils, C. van; Evans, D.G.; Astley, S.; Payne, K.

    2017-01-01

    OBJECTIVES: To identify the incremental costs and consequences of stratified national breast screening programs (stratified NBSPs) and drivers of relative cost-effectiveness. METHODS: A decision-analytic model (discrete event simulation) was conceptualized to represent four stratified NBSPs (risk 1,

  11. Direct Visualization of DNA Replication Dynamics in Zebrafish Cells.

    Science.gov (United States)

    Kuriya, Kenji; Higashiyama, Eriko; Avşar-Ban, Eriko; Tamaru, Yutaka; Ogata, Shin; Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

    2015-12-01

    Spatiotemporal regulation of DNA replication in the S-phase nucleus has been extensively studied in mammalian cells because it is tightly coupled with the regulation of other nuclear processes such as transcription. However, little is known about the replication dynamics in nonmammalian cells. Here, we analyzed the DNA replication processes of zebrafish (Danio rerio) cells through the direct visualization of replicating DNA in the nucleus and on DNA fiber molecules isolated from the nucleus. We found that zebrafish chromosomal DNA at the nuclear interior was replicated first, followed by replication of DNA at the nuclear periphery, which is reminiscent of the spatiotemporal regulation of mammalian DNA replication. However, the relative duration of interior DNA replication in zebrafish cells was longer compared to mammalian cells, possibly reflecting zebrafish-specific genomic organization. The rate of replication fork progression and ori-to-ori distance measured by the DNA combing technique were ∼ 1.4 kb/min and 100 kb, respectively, which are comparable to those in mammalian cells. To our knowledge, this is a first report that measures replication dynamics in zebrafish cells.

  12. 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.

  13. Theoretical models for the regulation of DNA replication in fast-growing bacteria

    Science.gov (United States)

    Creutziger, Martin; Schmidt, Mischa; Lenz, Peter

    2012-09-01

    Growing in always changing environments, Escherichia coli cells are challenged by the task to coordinate growth and division. In particular, adaption of their growth program to the surrounding medium has to guarantee that the daughter cells obtain fully replicated chromosomes. Replication is therefore to be initiated at the right time, which is particularly challenging in media that support fast growth. Here, the mother cell initiates replication not only for the daughter but also for the granddaughter cells. This is possible only if replication occurs from several replication forks that all need to be correctly initiated. Despite considerable efforts during the last 40 years, regulation of this process is still unknown. Part of the difficulty arises from the fact that many details of the relevant molecular processes are not known. Here, we develop a novel theoretical strategy for dealing with this general problem: instead of analyzing a single model, we introduce a wide variety of 128 different models that make different assumptions about the unknown processes. By comparing the predictions of these models we are able to identify the key quantities that allow the experimental discrimination of the different models. Analysis of these quantities yields that out of the 128 models 94 are not consistent with available experimental data. From the remaining 34 models we are able to conclude that mass growth and DNA replication need either to be truly coupled, by coupling DNA replication initiation to the event of cell division, or to the amount of accumulated mass. Finally, we make suggestions for experiments to further reduce the number of possible regulation scenarios.

  14. [Late-replicating regions in salivary gland polytene chromosomes of Drosophila melanogaster].

    Science.gov (United States)

    Kolesnikov, T D; Andreenkova, N G; Beliaeva, E S; Goncharov, F P; Zykova, T Iu; Boldyreva, L V; Pokholkova, g V; Zhimulev, I F

    2013-01-01

    About 240 specific regions that are replicated at the very end of the S-phase have been identified in D. melanogaster polytene chromosomes. These regions have a repressive chromatine state, low gene density, long intergenic distances and are enriched in tissue specific genes. In polytene chromosomes, about a quarter of these regions have no enough time to complete replication. As a result, underreplication zones represented by fewer DNA copy number, appear. We studied 60 chromosome regions that demonstrated the most pronounced under-replication. By comparing the location of these regions on a molecular map with syntenic blocks found earlier for Drosophila species by von Grotthuss et al., 2010, we have shown that across the genus Drosophila, these regions tend to have conserved gene order. This forces us to assume the existence of evolutionary mechanisms aimed at maintaining the integrity of these regions.

  15. 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...

  16. From Near-Neutral to Strongly Stratified: Adequately Modelling the Clear-Sky Nocturnal Boundary Layer at Cabauw.

    Science.gov (United States)

    Baas, P; van de Wiel, B J H; van der Linden, S J A; Bosveld, F C

    2018-01-01

    The performance of an atmospheric single-column model (SCM) is studied systematically for stably-stratified conditions. To this end, 11 years (2005-2015) of daily SCM simulations were compared to observations from the Cabauw observatory, The Netherlands. Each individual clear-sky night was classified in terms of the ambient geostrophic wind speed with a [Formula: see text] bin-width. Nights with overcast conditions were filtered out by selecting only those nights with an average net radiation of less than [Formula: see text]. A similar procedure was applied to the observational dataset. A comparison of observed and modelled ensemble-averaged profiles of wind speed and potential temperature and time series of turbulent fluxes showed that the model represents the dynamics of the nocturnal boundary layer (NBL) at Cabauw very well for a broad range of mechanical forcing conditions. No obvious difference in model performance was found between near-neutral and strongly-stratified conditions. Furthermore, observed NBL regime transitions are represented in a natural way. The reference model version performs much better than a model version that applies excessive vertical mixing as is done in several (global) operational models. Model sensitivity runs showed that for weak-wind conditions the inversion strength depends much more on details of the land-atmosphere coupling than on the turbulent mixing. The presented results indicate that in principle the physical parametrizations of large-scale atmospheric models are sufficiently equipped for modelling stably-stratified conditions for a wide range of forcing conditions.

  17. From Near-Neutral to Strongly Stratified: Adequately Modelling the Clear-Sky Nocturnal Boundary Layer at Cabauw

    Science.gov (United States)

    Baas, P.; van de Wiel, B. J. H.; van der Linden, S. J. A.; Bosveld, F. C.

    2018-02-01

    The performance of an atmospheric single-column model (SCM) is studied systematically for stably-stratified conditions. To this end, 11 years (2005-2015) of daily SCM simulations were compared to observations from the Cabauw observatory, The Netherlands. Each individual clear-sky night was classified in terms of the ambient geostrophic wind speed with a 1 m s^{-1} bin-width. Nights with overcast conditions were filtered out by selecting only those nights with an average net radiation of less than - 30 W m^{-2}. A similar procedure was applied to the observational dataset. A comparison of observed and modelled ensemble-averaged profiles of wind speed and potential temperature and time series of turbulent fluxes showed that the model represents the dynamics of the nocturnal boundary layer (NBL) at Cabauw very well for a broad range of mechanical forcing conditions. No obvious difference in model performance was found between near-neutral and strongly-stratified conditions. Furthermore, observed NBL regime transitions are represented in a natural way. The reference model version performs much better than a model version that applies excessive vertical mixing as is done in several (global) operational models. Model sensitivity runs showed that for weak-wind conditions the inversion strength depends much more on details of the land-atmosphere coupling than on the turbulent mixing. The presented results indicate that in principle the physical parametrizations of large-scale atmospheric models are sufficiently equipped for modelling stably-stratified conditions for a wide range of forcing conditions.

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

    Science.gov (United States)

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

    2017-04-01

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

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

    Science.gov (United States)

    Hyrien, Olivier

    2016-01-01

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

  20. Crenothrix are major methane consumers in stratified lakes.

    Science.gov (United States)

    Oswald, Kirsten; Graf, Jon S; Littmann, Sten; Tienken, Daniela; Brand, Andreas; Wehrli, Bernhard; Albertsen, Mads; Daims, Holger; Wagner, Michael; Kuypers, Marcel Mm; Schubert, Carsten J; Milucka, Jana

    2017-09-01

    Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth's natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870, but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an 'unusual' methane monooxygenase (MMO), which was only distantly related to 'classical' MMO of gamma-proteobacterial methanotrophs. We now correct this assignment and show that Crenothrix encode a typical gamma-proteobacterial PmoA. Stable isotope labeling in combination swith single-cell imaging mass spectrometry revealed methane-dependent growth of the lacustrine Crenothrix with oxygen as well as under oxygen-deficient conditions. Crenothrix genomes encoded pathways for the respiration of oxygen as well as for the reduction of nitrate to N 2 O. The observed abundance and planktonic growth of Crenothrix suggest that these methanotrophs can act as a relevant biological sink for methane in stratified lakes and should be considered in the context of environmental removal of methane.

  1. Crystallization of a compositionally stratified basal magma ocean

    Science.gov (United States)

    Laneuville, Matthieu; Hernlund, John; Labrosse, Stéphane; Guttenberg, Nicholas

    2018-03-01

    Earth's ∼3.45 billion year old magnetic field is regenerated by dynamo action in its convecting liquid metal outer core. However, convection induces an isentropic thermal gradient which, coupled with a high core thermal conductivity, results in rapid conducted heat loss. In the absence of implausibly high radioactivity or alternate sources of motion to drive the geodynamo, the Earth's early core had to be significantly hotter than the melting point of the lower mantle. While the existence of a dense convecting basal magma ocean (BMO) has been proposed to account for high early core temperatures, the requisite physical and chemical properties for a BMO remain controversial. Here we relax the assumption of a well-mixed convecting BMO and instead consider a BMO that is initially gravitationally stratified owing to processes such as mixing between metals and silicates at high temperatures in the core-mantle boundary region during Earth's accretion. Using coupled models of crystallization and heat transfer through a stratified BMO, we show that very high temperatures could have been trapped inside the early core, sequestering enough heat energy to run an ancient geodynamo on cooling power alone.

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

    Science.gov (United States)

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

    2008-12-01

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

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

    Science.gov (United States)

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

    2008-01-01

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

  4. Commercial Building Partnerships Replication and Diffusion

    Energy Technology Data Exchange (ETDEWEB)

    Antonopoulos, Chrissi A.; Dillon, Heather E.; Baechler, Michael C.

    2013-09-16

    This study presents findings from survey and interview data investigating replication efforts of Commercial Building Partnership (CBP) partners that worked directly with the Pacific Northwest National Laboratory (PNNL). PNNL partnered directly with 12 organizations on new and retrofit construction projects, which represented approximately 28 percent of the entire U.S. Department of Energy (DOE) CBP program. Through a feedback survey mechanism, along with personal interviews, PNNL gathered quantitative and qualitative data relating to replication efforts by each organization. These data were analyzed to provide insight into two primary research areas: 1) CBP partners’ replication efforts of technologies and approaches used in the CBP project to the rest of the organization’s building portfolio (including replication verification), and, 2) the market potential for technology diffusion into the total U.S. commercial building stock, as a direct result of the CBP program. The first area of this research focused specifically on replication efforts underway or planned by each CBP program participant. Factors that impact replication include motivation, organizational structure and objectives firms have for implementation of energy efficient technologies. Comparing these factors between different CBP partners revealed patterns in motivation for constructing energy efficient buildings, along with better insight into market trends for green building practices. The second area of this research develops a diffusion of innovations model to analyze potential broad market impacts of the CBP program on the commercial building industry in the United States.

  5. Extremal dynamics in random replicator ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Kärenlampi, Petri P., E-mail: petri.karenlampi@uef.fi

    2015-10-02

    The seminal numerical experiment by Bak and Sneppen (BS) is repeated, along with computations with replicator models, including a greater amount of features. Both types of models do self-organize, and do obey power-law scaling for the size distribution of activity cycles. However species extinction within the replicator models interferes with the BS self-organized critical (SOC) activity. Speciation–extinction dynamics ruins any stationary state which might contain a steady size distribution of activity cycles. The BS-type activity appears as a dissimilar phenomenon in comparison to speciation–extinction dynamics in the replicator system. No criticality is found from the speciation–extinction dynamics. Neither are speciations and extinctions in real biological macroevolution known to contain any diverging distributions, or self-organization towards any critical state. Consequently, biological macroevolution probably is not a self-organized critical phenomenon. - Highlights: • Extremal Dynamics organizes random replicator ecosystems to two phases in fitness space. • Replicator systems show power-law scaling of activity. • Species extinction interferes with Bak–Sneppen type mutation activity. • Speciation–extinction dynamics does not show any critical phase transition. • Biological macroevolution probably is not a self-organized critical phenomenon.

  6. Unsteady natural convection flow past an accelerated vertical plate in a thermally stratified fluid

    Directory of Open Access Journals (Sweden)

    Deka Rudra Kt.

    2009-01-01

    Full Text Available An exact solution to one-dimensional unsteady natural convection flow past an infinite vertical accelerated plate, immersed in a viscous thermally stratified fluid is investigated. Pressure work term and the vertical temperature advection are considered in the thermodynamic energy equation. The dimensionless governing equations are solved by Laplace Transform techniques for the Prandtl number unity. The velocity and temperature profiles as well as the skin-friction and the rate of heat transfer are presented graphically and discussed the effects of the Grashof number Gr, stratification parameter S at various times t.

  7. Evidence of Ebola Virus Replication and High Concentration in Semen of a Patient During Recovery.

    Science.gov (United States)

    Barnes, Kayla G; Kindrachuk, Jason; Lin, Aaron E; Wohl, Shirlee; Qu, James; Tostenson, Samantha D; Dorman, William R; Busby, Michele; Siddle, Katherine J; Luo, Cynthia Y; Matranga, Christian B; Davey, Richard T; Sabeti, Pardis C; Chertow, Daniel S

    2017-10-15

    In one patient over time, we found that concentration of Ebola virus RNA in semen during recovery is remarkably higher than blood at peak illness. Virus in semen is replication-competent with no change in viral genome over time. Presence of sense RNA suggests replication in cells present in semen. Published by Oxford University Press for the Infectious Diseases Society of America 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  8. Turbulent circulation above the surface heat source in stably stratified atmosphere

    Science.gov (United States)

    Kurbatskii, A. F.; Kurbatskaya, L. I.

    2016-10-01

    The 3-level RANS approach for simulating a turbulent circulation over the heat island in a stably stratified environment under nearly calm conditions is formulated. The turbulent kinetic energy its spectral consumption (dissipation) and the dispersion of turbulent fluctuations of temperature are found from differential equations, thus the correct modeling of transport processes in the interface layer with the counter-gradient heat flux is assured. The three-parameter turbulence RANS approach minimizes difficulties in simulating the turbulent transport in a stably stratified environment and reduces efforts needed for the numerical implementation of the 3-level RANS approach. Numerical simulation of the turbulent structure of the penetrative convection over the heat island under conditions of stably stratified atmosphere demonstrates that the three-equation model is able to predict the thermal circulation induced by the heat island. The temperature distribution, root-mean-square fluctuations of the turbulent velocity and temperature fields and spectral turbulent kinetic energy flux are in good agreement with the experimental data. The model describes such thin physical effects, as a crossing of vertical profiles of temperature of a thermal plume with the formation of the negative buoyancy area testifying to development of the dome-shaped form at the top part of a plume in the form of "hat".

  9. The Genomic Replication of the Crenarchaeal Virus SIRV2

    DEFF Research Database (Denmark)

    Martinez Alvarez, Laura

    reinitiation events may partially explain the branched topology of the viral replication intermediates. We also analyzed the intracellular location of viral replication, showing the formation of viral peripheral replication centers in SIRV2-infected cells, where viral DNA synthesis and replication...

  10. Degradation of organic dyes using spray deposited nanocrystalline stratified WO3/TiO2 photoelectrodes under sunlight illumination

    Science.gov (United States)

    Hunge, Y. M.; Yadav, A. A.; Mahadik, M. A.; Bulakhe, R. N.; Shim, J. J.; Mathe, V. L.; Bhosale, C. H.

    2018-02-01

    The need to utilize TiO2 based metal oxide hetero nanostructures for the degradation of environmental pollutants like Rhodamine B and reactive red 152 from the wastewater using stratified WO3/TiO2 catalyst under sunlight illumination. WO3, TiO2 and stratified WO3/TiO2 catalysts were prepared by a spray pyrolysis method. It was found that the stratified WO3/TiO2 heterostructure has high crystallinity, no mixed phase formation occurs, strong optical absorption in the visible region of the solar spectrum, and large surface area. The photocatalytic activity was tested for degradation of Rhodamine B (Rh B) and reactive red 152 in an aqueous medium. TiO2 layer in stratified WO3/TiO2 catalyst helps to extend its absorption spectrum in the solar light region. Rh B and Reactive red 152is eliminated up to 98 and 94% within the 30 and 40 min respectively at optimum experimental condition by stratified WO3/TiO2. Moreover, stratified WO3/TiO2 photoelectrode has good stability and reusability than individual TiO2 and WO3 thin film in the degradation of Rh B and reactive red 152. The photoelectrocatalytic experimental results indicate that stratified WO3/TiO2 photoelectrode is a promising material for dye removal.

  11. Automated interpretable computational biology in the clinic: a framework to predict disease severity and stratify patients from clinical data

    Directory of Open Access Journals (Sweden)

    Soumya Banerjee

    2017-10-01

    Full Text Available We outline an automated computational and machine learning framework that predicts disease severity and stratifies patients. We apply our framework to available clinical data. Our algorithm automatically generates insights and predicts disease severity with minimal operator intervention. The computational framework presented here can be used to stratify patients, predict disease severity and propose novel biomarkers for disease. Insights from machine learning algorithms coupled with clinical data may help guide therapy, personalize treatment and help clinicians understand the change in disease over time. Computational techniques like these can be used in translational medicine in close collaboration with clinicians and healthcare providers. Our models are also interpretable, allowing clinicians with minimal machine learning experience to engage in model building. This work is a step towards automated machine learning in the clinic.

  12. Identification of major planktonic sulfur oxidizers in stratified freshwater lake.

    Directory of Open Access Journals (Sweden)

    Hisaya Kojima

    Full Text Available Planktonic sulfur oxidizers are important constituents of ecosystems in stratified water bodies, and contribute to sulfide detoxification. In contrast to marine environments, taxonomic identities of major planktonic sulfur oxidizers in freshwater lakes still remain largely unknown. Bacterioplankton community structure was analyzed in a stratified freshwater lake, Lake Mizugaki in Japan. In the clone libraries of 16S rRNA gene, clones very closely related to a sulfur oxidizer isolated from this lake, Sulfuritalea hydrogenivorans, were detected in deep anoxic water, and occupied up to 12.5% in each library of different water depth. Assemblages of planktonic sulfur oxidizers were specifically analyzed by constructing clone libraries of genes involved in sulfur oxidation, aprA, dsrA, soxB and sqr. In the libraries, clones related to betaproteobacteria were detected with high frequencies, including the close relatives of Sulfuritalea hydrogenivorans.

  13. Mixing of stratified flow around bridge piers in steady current

    DEFF Research Database (Denmark)

    Jensen, Bjarne; Carstensen, Stefan; Christensen, Erik Damgaard

    2018-01-01

    This paper presents the results of an experimental and numerical investigation of the mixing of stratified flow around bridge pier structures. In this study, which was carried out in connection with the Fehmarnbelt Fixed Link environmental impact assessment, the mixing processes of two-layer stra......This paper presents the results of an experimental and numerical investigation of the mixing of stratified flow around bridge pier structures. In this study, which was carried out in connection with the Fehmarnbelt Fixed Link environmental impact assessment, the mixing processes of two......-layer stratification was studied in which the lower level had a higher salinity than the upper layer. The physical experiments investigated two different pier designs. A general study was made regarding forces on the piers in which the effect of the current angle relative to the structure was also included...

  14. Quantum image pseudocolor coding based on the density-stratified method

    Science.gov (United States)

    Jiang, Nan; Wu, Wenya; Wang, Luo; Zhao, Na

    2015-05-01

    Pseudocolor processing is a branch of image enhancement. It dyes grayscale images to color images to make the images more beautiful or to highlight some parts on the images. This paper proposes a quantum image pseudocolor coding scheme based on the density-stratified method which defines a colormap and changes the density value from gray to color parallel according to the colormap. Firstly, two data structures: quantum image GQIR and quantum colormap QCR are reviewed or proposed. Then, the quantum density-stratified algorithm is presented. Based on them, the quantum realization in the form of circuits is given. The main advantages of the quantum version for pseudocolor processing over the classical approach are that it needs less memory and can speed up the computation. Two kinds of examples help us to describe the scheme further. Finally, the future work are analyzed.

  15. Improvement of replication fidelity in injection moulding of nano structures using an induction heating system

    DEFF Research Database (Denmark)

    Menotti, Stefano; Hansen, Hans Nørgaard; Bissacco, Giuliano

    2014-01-01

    In today’s industry, applications involving surface pattering with sub-μm scale structures have shown a high interest. The replication of these structures by injection molding leads to special requirements for the mold in order to ensure proper replication and an acceptable cycle time. A tool ins...... quantitatively characterized by atomic force microscopy comparing the measurement in the nickel insert with the corresponding polymer nano-features. The experimental results show that the use of the induction heating system is an efficient way to improve the pattern replication....

  16. 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.

  17. 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

  18. Suppression of stratified explosive interactions

    Energy Technology Data Exchange (ETDEWEB)

    Meeks, M.K.; Shamoun, B.I.; Bonazza, R.; Corradini, M.L. [Wisconsin Univ., Madison, WI (United States). Dept. of Nuclear Engineering and Engineering Physics

    1998-01-01

    Stratified Fuel-Coolant Interaction (FCI) experiments with Refrigerant-134a and water were performed in a large-scale system. Air was uniformly injected into the coolant pool to establish a pre-existing void which could suppress the explosion. Two competing effects due to the variation of the air flow rate seem to influence the intensity of the explosion in this geometrical configuration. At low flow rates, although the injected air increases the void fraction, the concurrent agitation and mixing increases the intensity of the interaction. At higher flow rates, the increase in void fraction tends to attenuate the propagated pressure wave generated by the explosion. Experimental results show a complete suppression of the vapor explosion at high rates of air injection, corresponding to an average void fraction of larger than 30%. (author)

  19. Monte Carlo stratified source-sampling

    International Nuclear Information System (INIS)

    Blomquist, R.N.; Gelbard, E.M.

    1997-01-01

    In 1995, at a conference on criticality safety, a special session was devoted to the Monte Carlo open-quotes eigenvalue of the worldclose quotes problem. Argonne presented a paper, at that session, in which the anomalies originally observed in that problem were reproduced in a much simplified model-problem configuration, and removed by a version of stratified source-sampling. The original test-problem was treated by a special code designed specifically for that purpose. Recently ANL started work on a method for dealing with more realistic eigenvalue of the world configurations, and has been incorporating this method into VIM. The original method has been modified to take into account real-world statistical noise sources not included in the model problem. This paper constitutes a status report on work still in progress

  20. DNA Copy-Number Control through Inhibition of Replication Fork Progression

    Directory of Open Access Journals (Sweden)

    Jared T. Nordman

    2014-11-01

    Full Text Available Proper control of DNA replication is essential to ensure faithful transmission of genetic material and prevent chromosomal aberrations that can drive cancer progression and developmental disorders. DNA replication is regulated primarily at the level of initiation and is under strict cell-cycle regulation. Importantly, DNA replication is highly influenced by developmental cues. In Drosophila, specific regions of the genome are repressed for DNA replication during differentiation by the SNF2 domain-containing protein SUUR through an unknown mechanism. We demonstrate that SUUR is recruited to active replication forks and mediates the repression of DNA replication by directly inhibiting replication fork progression instead of functioning as a replication fork barrier. Mass spectrometry identification of SUUR-associated proteins identified the replicative helicase member CDC45 as a SUUR-associated protein, supporting a role for SUUR directly at replication forks. Our results reveal that control of eukaryotic DNA copy number can occur through the inhibition of replication fork progression.

  1. Psychology's Replication Crisis and the Grant Culture: Righting the Ship.

    Science.gov (United States)

    Lilienfeld, Scott O

    2017-07-01

    The past several years have been a time for soul searching in psychology, as we have gradually come to grips with the reality that some of our cherished findings are less robust than we had assumed. Nevertheless, the replication crisis highlights the operation of psychological science at its best, as it reflects our growing humility. At the same time, institutional variables, especially the growing emphasis on external funding as an expectation or de facto requirement for faculty tenure and promotion, pose largely unappreciated hazards for psychological science, including (a) incentives for engaging in questionable research practices, (b) a single-minded focus on programmatic research, (c) intellectual hyperspecialization, (d) disincentives for conducting direct replications, (e) stifling of creativity and intellectual risk taking, (f) researchers promising more than they can deliver, and (g) diminished time for thinking deeply. Preregistration should assist with (a), but will do little about (b) through (g). Psychology is beginning to right the ship, but it will need to confront the increasingly deleterious impact of the grant culture on scientific inquiry.

  2. PRC1 Prevents Replication Stress during Chondrogenic Transit Amplification

    Directory of Open Access Journals (Sweden)

    Frank Spaapen

    2017-12-01

    Full Text Available Transit amplification (TA, a state of combined, rapid proliferative expansion and differentiation of stem cell-descendants, remains poorly defined at the molecular level. The Polycomb Repressive Complex 1 (PRC1 protein BMI1 has been localized to TA compartments, yet its exact role in TA is unclear. PRC1 proteins control gene expression, cell proliferation and DNA-damage repair. Coordination of such DNA-templated activities during TA is predicted to be crucial to support DNA replication and differentiation-associated transcriptional programming. We here examined whether chondrogenesis provides a relevant biological context for synchronized coordination of these chromatin-based tasks by BMI1. Taking advantage of a prominently featuring TA-phase during chondrogenesis in vitro and in vivo, we here report that TA is completely dependent on intact PRC1 function. BMI1-depleted chondrogenic progenitors rapidly accumulate double strand DNA breaks during DNA replication, present massive non-H3K27me3-directed transcriptional deregulation and fail to undergo chondrogenic TA. Genome-wide accumulation of Topoisomerase 2α and Geminin suggests a model in which PRC1 synchronizes replication and transcription during rapid chondrogenic progenitor expansion. Our combined data reveals for the first time a vital cell-autonomous role for PRC1 during chondrogenesis. We provide evidence that chondrocyte hyper-replication and hypertrophy represent a unique example of programmed senescence in vivo. These findings provide new perspectives on PRC1 function in development and disease.

  3. Error threshold ghosts in a simple hypercycle with error prone self-replication

    International Nuclear Information System (INIS)

    Sardanyes, Josep

    2008-01-01

    A delayed transition because of mutation processes is shown to happen in a simple hypercycle composed by two indistinguishable molecular species with error prone self-replication. The appearance of a ghost near the hypercycle error threshold causes a delay in the extinction and thus in the loss of information of the mutually catalytic replicators, in a kind of information memory. The extinction time, τ, scales near bifurcation threshold according to the universal square-root scaling law i.e. τ ∼ (Q hc - Q) -1/2 , typical of dynamical systems close to a saddle-node bifurcation. Here, Q hc represents the bifurcation point named hypercycle error threshold, involved in the change among the asymptotic stability phase and the so-called Random Replication State (RRS) of the hypercycle; and the parameter Q is the replication quality factor. The ghost involves a longer transient towards extinction once the saddle-node bifurcation has occurred, being extremely long near the bifurcation threshold. The role of this dynamical effect is expected to be relevant in fluctuating environments. Such a phenomenon should also be found in larger hypercycles when considering the hypercycle species in competition with their error tail. The implications of the ghost in the survival and evolution of error prone self-replicating molecules with hypercyclic organization are discussed

  4. Initiation of Replication in Escherichia coli

    DEFF Research Database (Denmark)

    Frimodt-Møller, Jakob

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

  5. LHCb Data Replication During SC3

    CERN Multimedia

    Smith, A

    2006-01-01

    LHCb's participation in LCG's Service Challenge 3 involves testing the bulk data transfer infrastructure developed to allow high bandwidth distribution of data across the grid in accordance with the computing model. To enable reliable bulk replication of data, LHCb's DIRAC system has been integrated with gLite's File Transfer Service middleware component to make use of dedicated network links between LHCb computing centres. DIRAC's Data Management tools previously allowed the replication, registration and deletion of files on the grid. For SC3 supplementary functionality has been added to allow bulk replication of data (using FTS) and efficient mass registration to the LFC replica catalog.Provisional performance results have shown that the system developed can meet the expected data replication rate required by the computing model in 2007. This paper details the experience and results of integration and utilisation of DIRAC with the SC3 transfer machinery.

  6. Restoring chromatin after replication: How new and old histone marks come together

    DEFF Research Database (Denmark)

    Jasencakova, Zusana; Groth, Anja

    2010-01-01

    In dividing cells genome stability and function rely on faithful transmission of both DNA sequence and its organization into chromatin. In the course of DNA replication chromatin undergoes transient genome-wide disruption followed by restoration on new DNA. This involves tight coordination of DNA...... replication and chromatin assembly processes in time and space. Dynamic recycling and de novo deposition of histones are fundamental for chromatin restoration. Histone post-translational modifications (PTMs) are thought to have a causal role in establishing distinct chromatin structures. Here we discuss PTMs...... present on new and parental histones and how they influence genome stability and restoration of epigenetically defined domains. Newly deposited histones must change their signature in the process of chromatin restoration, this may occur in a step-wise fashion involving replication-coupled processes...

  7. 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

  8. Tombusviruses upregulate phospholipid biosynthesis via interaction between p33 replication protein and yeast lipid sensor proteins during virus replication in yeast

    International Nuclear Information System (INIS)

    Barajas, Daniel; Xu, Kai; Sharma, Monika; Wu, Cheng-Yu; Nagy, Peter D.

    2014-01-01

    Positive-stranded RNA viruses induce new membranous structures and promote membrane proliferation in infected cells to facilitate viral replication. In this paper, the authors show that a plant-infecting tombusvirus upregulates transcription of phospholipid biosynthesis genes, such as INO1, OPI3 and CHO1, and increases phospholipid levels in yeast model host. This is accomplished by the viral p33 replication protein, which interacts with Opi1p FFAT domain protein and Scs2p VAP protein. Opi1p and Scs2p are phospholipid sensor proteins and they repress the expression of phospholipid genes. Accordingly, deletion of OPI1 transcription repressor in yeast has a stimulatory effect on TBSV RNA accumulation and enhanced tombusvirus replicase activity in an in vitro assay. Altogether, the presented data convincingly demonstrate that de novo lipid biosynthesis is required for optimal TBSV replication. Overall, this work reveals that a (+)RNA virus reprograms the phospholipid biosynthesis pathway in a unique way to facilitate its replication in yeast cells. - Highlights: • Tombusvirus p33 replication protein interacts with FFAT-domain host protein. • Tombusvirus replication leads to upregulation of phospholipids. • Tombusvirus replication depends on de novo lipid synthesis. • Deletion of FFAT-domain host protein enhances TBSV replication. • TBSV rewires host phospholipid synthesis

  9. 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.

  10. Uncoupling of Sister Replisomes during Eukaryotic DNA Replication

    NARCIS (Netherlands)

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

    2010-01-01

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

  11. Dynamic behavior of DNA replication domains

    NARCIS (Netherlands)

    Manders, E. M.; Stap, J.; Strackee, J.; van Driel, R.; Aten, J. A.

    1996-01-01

    Like many nuclear processes, DNA replication takes place in distinct domains that are scattered throughout the S-phase nucleus. Recently we have developed a fluorescent double-labeling procedure that allows us to visualize nascent DNA simultaneously with "newborn" DNA that had replicated earlier in

  12. A Role of hIPI3 in DNA Replication Licensing in Human Cells.

    Science.gov (United States)

    Huang, Yining; Amin, Aftab; Qin, Yan; Wang, Ziyi; Jiang, Huadong; Liang, Lu; Shi, Linjing; Liang, Chun

    2016-01-01

    The yeast Ipi3p is required for DNA replication and cell viability in Sacharomyces cerevisiae. It is an essential component of the Rix1 complex (Rix1p/Ipi2p-Ipi1p-Ipi3p) that is required for the processing of 35S pre-rRNA in pre-60S ribosomal particles and for the initiation of DNA replication. The human IPI3 homolog is WDR18 (WD repeat domain 18), which shares significant homology with yIpi3p. Here we report that knockdown of hIPI3 resulted in substantial defects in the chromatin association of the MCM complex, DNA replication, cell cycle progression and cell proliferation. Importantly, hIPI3 silencing did not result in a reduction of the protein level of hCDC6, hMCM7, or the ectopically expressed GFP protein, indicating that protein synthesis was not defective in the same time frame of the DNA replication and cell cycle defects. Furthermore, the mRNA and protein levels of hIPI3 fluctuate in the cell cycle, with the highest levels from M phase to early G1 phase, similar to other pre-replicative (pre-RC) proteins. Moreover, hIPI3 interacts with other replication-initiation proteins, co-localizes with hMCM7 in the nucleus, and is important for the nuclear localization of hMCM7. We also found that hIPI3 preferentially binds to the origins of DNA replication including those at the c-Myc, Lamin-B2 and β-Globin loci. These results indicate that hIPI3 is involved in human DNA replication licensing independent of its role in ribosome biogenesis.

  13. The evolutionary ecology of molecular replicators.

    Science.gov (United States)

    Nee, Sean

    2016-08-01

    By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology.

  14. Implementasi Highly Available Website Dengan Distributed Replicated Block Device

    Directory of Open Access Journals (Sweden)

    Mulyanto Mulyanto

    2016-07-01

    Full Text Available As an important IT infrastructure, website is a system which requires high reliability and availability levels. Website meets the criteria as a highly available system because website must provide services to clients in real time, handle a large amount of data, and not lose data during transaction. A highly available system must meet the condition of being able to run continuously as well as guaranteeing consistency on data requests. This study designed a website with high availability. The approach was building network cluster with failover and replicated block device functions. Failover was built to provide service availability, while replicated block device provides data consistency during failure of service.  With failover cluster and replicated block device approaches, a cluster which is able to handle service failures of web server and database server on the website. The result of this study was the services of the website could run well if there was any failure in node members of the cluster. The system was able to provide 99,999 (five nines availability on database server services and 99,98  (three nines on web server services.

  15. A Fuzzy Modeling Approach for Replicated Response Measures Based on Fuzzification of Replications with Descriptive Statistics and Golden Ratio

    Directory of Open Access Journals (Sweden)

    Özlem TÜRKŞEN

    2018-03-01

    Full Text Available Some of the experimental designs can be composed of replicated response measures in which the replications cannot be identified exactly and may have uncertainty different than randomness. Then, the classical regression analysis may not be proper to model the designed data because of the violation of probabilistic modeling assumptions. In this case, fuzzy regression analysis can be used as a modeling tool. In this study, the replicated response values are newly formed to fuzzy numbers by using descriptive statistics of replications and golden ratio. The main aim of the study is obtaining the most suitable fuzzy model for replicated response measures through fuzzification of the replicated values by taking into account the data structure of the replications in statistical framework. Here, the response and unknown model coefficients are considered as triangular type-1 fuzzy numbers (TT1FNs whereas the inputs are crisp. Predicted fuzzy models are obtained according to the proposed fuzzification rules by using Fuzzy Least Squares (FLS approach. The performances of the predicted fuzzy models are compared by using Root Mean Squared Error (RMSE criteria. A data set from the literature, called wheel cover component data set, is used to illustrate the performance of the proposed approach and the obtained results are discussed. The calculation results show that the combined formulation of the descriptive statistics and the golden ratio is the most preferable fuzzification rule according to the well-known decision making method, called TOPSIS, for the data set.

  16. Rapid transient production in plants by replicating and non-replicating vectors yields high quality functional anti-HIV antibody.

    Directory of Open Access Journals (Sweden)

    Frank Sainsbury

    2010-11-01

    Full Text Available The capacity of plants and plant cells to produce large amounts of recombinant protein has been well established. Due to advantages in terms of speed and yield, attention has recently turned towards the use of transient expression systems, including viral vectors, to produce proteins of pharmaceutical interest in plants. However, the effects of such high level expression from viral vectors and concomitant effects on host cells may affect the quality of the recombinant product.To assess the quality of antibodies transiently expressed to high levels in plants, we have expressed and characterised the human anti-HIV monoclonal antibody, 2G12, using both replicating and non-replicating systems based on deleted versions of Cowpea mosaic virus (CPMV RNA-2. The highest yield (approximately 100 mg/kg wet weight leaf tissue of affinity purified 2G12 was obtained when the non-replicating CPMV-HT system was used and the antibody was retained in the endoplasmic reticulum (ER. Glycan analysis by mass-spectrometry showed that the glycosylation pattern was determined exclusively by whether the antibody was retained in the ER and did not depend on whether a replicating or non-replicating system was used. Characterisation of the binding and neutralisation properties of all the purified 2G12 variants from plants showed that these were generally similar to those of the Chinese hamster ovary (CHO cell-produced 2G12.Overall, the results demonstrate that replicating and non-replicating CPMV-based vectors are able to direct the production of a recombinant IgG similar in activity to the CHO-produced control. Thus, a complex recombinant protein was produced with no apparent effect on its biochemical properties using either high-level expression or viral replication. The speed with which a recombinant pharmaceutical with excellent biochemical characteristics can be produced transiently in plants makes CPMV-based expression vectors an attractive option for

  17. Bacterial production, protozoan grazing, and mineralization in stratified Lake Vechten

    NARCIS (Netherlands)

    Bloem, J.

    1989-01-01

    The role of heterotrophic nanoflagellates (HNAN, size 2-20 μm) in grazing on bacteria and mineralization of organic matter in stratified Lake Vechten was studied.

    Quantitative effects of manipulation and fixation on HNAN were checked. Considerable losses were caused by

  18. Internal wave patterns in enclosed density-stratified and rotating fluids

    NARCIS (Netherlands)

    Manders, A.M.A.

    2003-01-01

    Stratified fluids support internal waves, which propagate obliquely through the fluid. The angle with respectto the stratification direction is contrained: it is purely determined by the wave frequency and the strength of the density stratification (internal gravity waves) or the rotation rate

  19. Computational Fluid Dynamics model of stratified atmospheric boundary-layer flow

    DEFF Research Database (Denmark)

    Koblitz, Tilman; Bechmann, Andreas; Sogachev, Andrey

    2015-01-01

    For wind resource assessment, the wind industry is increasingly relying on computational fluid dynamics models of the neutrally stratified surface-layer. So far, physical processes that are important to the whole atmospheric boundary-layer, such as the Coriolis effect, buoyancy forces and heat...

  20. Dynamics of picornavirus RNA replication within infected cells

    DEFF Research Database (Denmark)

    Belsham, Graham; Normann, Preben

    2008-01-01

    Replication of many picornaviruses is inhibited by low concentrations of guanidine. Guanidine-resistant mutants are readily isolated and the mutations map to the coding region for the 2C protein. Using in vitro replication assays it has been determined previously that guanidine blocks the initiat......Replication of many picornaviruses is inhibited by low concentrations of guanidine. Guanidine-resistant mutants are readily isolated and the mutations map to the coding region for the 2C protein. Using in vitro replication assays it has been determined previously that guanidine blocks...... the initiation of negative-strand synthesis. We have now examined the dynamics of RNA replication, measured by quantitative RT-PCR, within cells infected with either swine vesicular disease virus (an enterovirus) or foot-and-mouth disease virus as regulated by the presence or absence of guanidine. Following...... the removal of guanidine from the infected cells, RNA replication occurs after a significant lag phase. This restoration of RNA synthesis requires de novo protein synthesis. Viral RNA can be maintained for at least 72 h within cells in the absence of apparent replication but guanidine-resistant virus can...

  1. Autonomous model protocell division driven by molecular replication.

    Science.gov (United States)

    Taylor, J W; Eghtesadi, S A; Points, L J; Liu, T; Cronin, L

    2017-08-10

    The coupling of compartmentalisation with molecular replication is thought to be crucial for the emergence of the first evolvable chemical systems. Minimal artificial replicators have been designed based on molecular recognition, inspired by the template copying of DNA, but none yet have been coupled to compartmentalisation. Here, we present an oil-in-water droplet system comprising an amphiphilic imine dissolved in chloroform that catalyses its own formation by bringing together a hydrophilic and a hydrophobic precursor, which leads to repeated droplet division. We demonstrate that the presence of the amphiphilic replicator, by lowering the interfacial tension between droplets of the reaction mixture and the aqueous phase, causes them to divide. Periodic sampling by a droplet-robot demonstrates that the extent of fission is increased as the reaction progresses, producing more compartments with increased self-replication. This bridges a divide, showing how replication at the molecular level can be used to drive macroscale droplet fission.Coupling compartmentalisation and molecular replication is essential for the development of evolving chemical systems. Here the authors show an oil-in-water droplet containing a self-replicating amphiphilic imine that can undergo repeated droplet division.

  2. Gene organization inside replication domains in mammalian genomes

    Science.gov (United States)

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

    2012-11-01

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

  3. Experimental CFD grade data for stratified two-phase flows

    Energy Technology Data Exchange (ETDEWEB)

    Vallee, Christophe, E-mail: c.vallee@fzd.d [Forschungszentrum Dresden-Rossendorf e.V., Institute of Safety Research, D-01314 Dresden (Germany); Lucas, Dirk; Beyer, Matthias; Pietruske, Heiko; Schuetz, Peter; Carl, Helmar [Forschungszentrum Dresden-Rossendorf e.V., Institute of Safety Research, D-01314 Dresden (Germany)

    2010-09-15

    Stratified two-phase flows were investigated at two test facilities with horizontal test-sections. For both, rectangular channel cross-sections were chosen to provide optimal observation possibilities for the application of optical measurement techniques. In order to show the local flow structure, high-speed video observation was applied, which delivers the high-resolution in space and time needed for CFD code validation. The first investigations were performed in the Horizontal Air/Water Channel (HAWAC), which is made of acrylic glass and allows the investigation of air/water co-current flows at atmospheric pressure and room temperature. At the channel inlet, a special device was designed for well-defined and adjustable inlet boundary conditions. For the quantitative analysis of the optical measurements performed at the HAWAC, an algorithm was developed to recognise the stratified interface in the camera frames. This allows to make statistical treatments for comparison with CFD calculation results. As an example, the unstable wave growth leading to slug flow is shown from the test-section inlet. Moreover, the hydraulic jump as the quasi-stationary discontinuous transition between super- and subcritical flow was investigated in this closed channel. The structure of the hydraulic jump over time is revealed by the calculation of the probability density of the water level. A series of experiments show that the hydraulic jump profile and its position from the inlet vary substantially with the inlet boundary conditions due to the momentum exchange between the phases. The second channel is built in the pressure chamber of the TOPFLOW test facility, which is used to perform air/water and steam/water experiments at pressures of up to 5.0 MPa and temperatures of up to 264 {sup o}C, but under pressure equilibrium with the vessel inside. In the present experiment, the test-section represents a flat model of the hot leg of the German Konvoi pressurised water reactor scaled at

  4. Experimental CFD grade data for stratified two-phase flows

    International Nuclear Information System (INIS)

    Vallee, Christophe; Lucas, Dirk; Beyer, Matthias; Pietruske, Heiko; Schuetz, Peter; Carl, Helmar

    2010-01-01

    Stratified two-phase flows were investigated at two test facilities with horizontal test-sections. For both, rectangular channel cross-sections were chosen to provide optimal observation possibilities for the application of optical measurement techniques. In order to show the local flow structure, high-speed video observation was applied, which delivers the high-resolution in space and time needed for CFD code validation. The first investigations were performed in the Horizontal Air/Water Channel (HAWAC), which is made of acrylic glass and allows the investigation of air/water co-current flows at atmospheric pressure and room temperature. At the channel inlet, a special device was designed for well-defined and adjustable inlet boundary conditions. For the quantitative analysis of the optical measurements performed at the HAWAC, an algorithm was developed to recognise the stratified interface in the camera frames. This allows to make statistical treatments for comparison with CFD calculation results. As an example, the unstable wave growth leading to slug flow is shown from the test-section inlet. Moreover, the hydraulic jump as the quasi-stationary discontinuous transition between super- and subcritical flow was investigated in this closed channel. The structure of the hydraulic jump over time is revealed by the calculation of the probability density of the water level. A series of experiments show that the hydraulic jump profile and its position from the inlet vary substantially with the inlet boundary conditions due to the momentum exchange between the phases. The second channel is built in the pressure chamber of the TOPFLOW test facility, which is used to perform air/water and steam/water experiments at pressures of up to 5.0 MPa and temperatures of up to 264 o C, but under pressure equilibrium with the vessel inside. In the present experiment, the test-section represents a flat model of the hot leg of the German Konvoi pressurised water reactor scaled at 1

  5. Mapping replication origins in yeast chromosomes.

    Science.gov (United States)

    Brewer, B J; Fangman, W L

    1991-07-01

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

  6. Assembly of Slx4 signaling complexes behind DNA replication forks.

    Science.gov (United States)

    Balint, Attila; Kim, TaeHyung; Gallo, David; Cussiol, Jose Renato; Bastos de Oliveira, Francisco M; Yimit, Askar; Ou, Jiongwen; Nakato, Ryuichiro; Gurevich, Alexey; Shirahige, Katsuhiko; Smolka, Marcus B; Zhang, Zhaolei; Brown, Grant W

    2015-08-13

    Obstructions to replication fork progression, referred to collectively as DNA replication stress, challenge genome stability. In Saccharomyces cerevisiae, cells lacking RTT107 or SLX4 show genome instability and sensitivity to DNA replication stress and are defective in the completion of DNA replication during recovery from replication stress. We demonstrate that Slx4 is recruited to chromatin behind stressed replication forks, in a region that is spatially distinct from that occupied by the replication machinery. Slx4 complex formation is nucleated by Mec1 phosphorylation of histone H2A, which is recognized by the constitutive Slx4 binding partner Rtt107. Slx4 is essential for recruiting the Mec1 activator Dpb11 behind stressed replication forks, and Slx4 complexes are important for full activity of Mec1. We propose that Slx4 complexes promote robust checkpoint signaling by Mec1 by stably recruiting Dpb11 within a discrete domain behind the replication fork, during DNA replication stress. © 2015 The Authors.

  7. 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.

  8. 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

  9. A criterion for the onset of slugging in horizontal stratified air-water countercurrent flow

    International Nuclear Information System (INIS)

    Chun, Moon-Hyun; Lee, Byung-Ryung; Kim, Yang-Seok

    1995-01-01

    This paper presents an experimental and theoretical investigation of wave height and transition criterion from wavy to slug flow in horizontal air-water countercurrent stratified flow conditions. A theoretical formula for the wave height in a stratified wavy flow regime has been developed using the concept of total energy balance over a wave crest to consider the shear stress acting on the interface of two fluids. From the limiting condition of the formula for the wave height, a necessary criterion for transition from a stratified wavy flow to a slug flow has been derived. A series of experiments have been conducted changing the non-dimensional water depth and the flow rates of air in a horizontal pipe and a duct. Comparisons between the measured data and the predictions of the present theory show that the agreement is within ±8%

  10. A criterion for the onset of slugging in horizontal stratified air-water countercurrent flow

    Energy Technology Data Exchange (ETDEWEB)

    Chun, Moon-Hyun; Lee, Byung-Ryung; Kim, Yang-Seok [Korea Advanced Institute of Science and Technology, Taejon (Korea, Republic of)] [and others

    1995-09-01

    This paper presents an experimental and theoretical investigation of wave height and transition criterion from wavy to slug flow in horizontal air-water countercurrent stratified flow conditions. A theoretical formula for the wave height in a stratified wavy flow regime has been developed using the concept of total energy balance over a wave crest to consider the shear stress acting on the interface of two fluids. From the limiting condition of the formula for the wave height, a necessary criterion for transition from a stratified wavy flow to a slug flow has been derived. A series of experiments have been conducted changing the non-dimensional water depth and the flow rates of air in a horizontal pipe and a duct. Comparisons between the measured data and the predictions of the present theory show that the agreement is within {plus_minus}8%.

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

    Science.gov (United States)

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

    1998-02-15

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

  12. Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli.

    Science.gov (United States)

    Kato , J; Katayama, T

    2001-08-01

    The bacterial DnaA protein binds to the chromosomal origin of replication to trigger a series of initiation reactions, which leads to the loading of DNA polymerase III. In Escherichia coli, once this polymerase initiates DNA synthesis, ATP bound to DnaA is efficiently hydrolyzed to yield the ADP-bound inactivated form. This negative regulation of DnaA, which occurs through interaction with the beta-subunit sliding clamp configuration of the polymerase, functions in the temporal blocking of re-initiation. Here we show that the novel DnaA-related protein, Hda, from E.coli is essential for this regulatory inactivation of DnaA in vitro and in vivo. Our results indicate that the hda gene is required to prevent over-initiation of chromosomal replication and for cell viability. Hda belongs to the chaperone-like ATPase family, AAA(+), as do DnaA and certain eukaryotic proteins essential for the initiation of DNA replication. We propose that the once-per-cell-cycle rule of replication depends on the timely interaction of AAA(+) proteins that comprise the apparatus regulating the activity of the initiator of replication.

  13. Generation of stratified squamous epithelial progenitor cells from mouse induced pluripotent stem cells.

    Directory of Open Access Journals (Sweden)

    Satoru Yoshida

    Full Text Available BACKGROUND: Application of induced pluripotent stem (iPS cells in regenerative medicine will bypass ethical issues associated with use of embryonic stem cells. In addition, patient-specific IPS cells can be useful to elucidate the pathophysiology of genetic disorders, drug screening, and tailor-made medicine. However, in order to apply iPS cells to mitotic tissue, induction of tissue stem cells that give rise to progeny of the target organ is required. METHODOLOGY/PRINCIPAL FINDINGS: We induced stratified epithelial cells from mouse iPS cells by co-culture with PA6 feeder cells (SDIA-method with use of BMP4. Clusters of cells positive for the differentiation markers KRT1 or KRT12 were observed in KRT14-positive colonies. We successfully cloned KRT14 and p63 double-positive stratified epithelial progenitor cells from iPS-derived epithelial cells, which formed stratified epithelial sheets consisting of five- to six-polarized epithelial cells in vitro. When these clonal cells were cultured on denuded mouse corneas, a robust stratified epithelial layer was observed with physiological cell polarity including high levels of E-cadherin, p63 and K15 expression in the basal layer and ZO-1 in the superficial layer, recapitulating the apico-basal polarity of the epithelium in vivo. CONCLUSIONS/SIGNIFICANCE: These results suggest that KRT14 and p63 double-positive epithelial progenitor cells can be cloned from iPS cells in order to produce polarized multilayer epithelial cell sheets.

  14. Enhanced replication of herpes simplex virus type 1 in human cells

    International Nuclear Information System (INIS)

    Miller, C.S.; Smith, K.O.

    1991-01-01

    The effects of DNA-damaging agents on the replication of herpes simplex virus type 1 (HSV-1) were assessed in vitro. Monolayers of human lung fibroblast cell lines were exposed to DNA-damaging agents (methyl methanesulfonate [MMS], methyl methanethiosulfonate [MMTS], ultraviolet light [UV], or gamma radiation [GR]) at specific intervals, before or after inoculation with low levels of HSV-1. The ability of cell monolayers to support HSV-1 replication was measured by direct plaque assay and was compared with that of untreated control samples. In this system, monolayers of different cell lines infected with identical HSV-1 strains demonstrated dissimilar levels of recovery of the infectious virus. Exposure of DNA-repair-competent cell cultures to DNA-damaging agents produced time-dependent enhanced virus replication. Treatment with agent before virus inoculation significantly (p less than 0.025) increased the number of plaques by 10 to 68%, compared with untreated control cultures, while treatment with agent after virus adsorption significantly increased (p less than 0.025) the number of plaques by 7 to 15%. In a parallel series of experiments, cells deficient in DNA repair (xeroderma pigmentosum) failed to support enhanced virus replication. These results suggest that after exposure to DNA-damaging agents, fibroblasts competent in DNA repair amplify the replication of HSV-1, and that DNA-repair mechanisms that act on a variety of chromosomal lesions may be involved in the repair and biological activation of HSV-1 genomes

  15. Experimental Validation of a Domestic Stratified Hot Water Tank Model in Modelica for Annual Performance Assessment

    DEFF Research Database (Denmark)

    Carmo, Carolina; Dumont, Olivier; Nielsen, Mads Pagh

    2015-01-01

    The use of stratified hot water tanks in solar energy systems - including ORC systems - as well as heat pump systems is paramount for a better performance of these systems. However, the availability of effective and reliable models to predict the annual performance of stratified hot water tanks...

  16. 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.

  17. Evidence that DNA polymerase δ contributes to initiating leading strand DNA replication in Saccharomyces cerevisiae.

    Science.gov (United States)

    Garbacz, Marta A; Lujan, Scott A; Burkholder, Adam B; Cox, Phillip B; Wu, Qiuqin; Zhou, Zhi-Xiong; Haber, James E; Kunkel, Thomas A

    2018-02-27

    To investigate nuclear DNA replication enzymology in vivo, we have studied Saccharomyces cerevisiae strains containing a pol2-16 mutation that inactivates the catalytic activities of DNA polymerase ε (Pol ε). Although pol2-16 mutants survive, they present very tiny spore colonies, increased doubling time, larger than normal cells, aberrant nuclei, and rapid acquisition of suppressor mutations. These phenotypes reveal a severe growth defect that is distinct from that of strains that lack only Pol ε proofreading (pol2-4), consistent with the idea that Pol ε is the major leading-strand polymerase used for unstressed DNA replication. Ribonucleotides are incorporated into the pol2-16 genome in patterns consistent with leading-strand replication by Pol δ when Pol ε is absent. More importantly, ribonucleotide distributions at replication origins suggest that in strains encoding all three replicases, Pol δ contributes to initiation of leading-strand replication. We describe two possible models.

  18. Replication and Robustness in Developmental Research

    Science.gov (United States)

    Duncan, Greg J.; Engel, Mimi; Claessens, Amy; Dowsett, Chantelle J.

    2014-01-01

    Replications and robustness checks are key elements of the scientific method and a staple in many disciplines. However, leading journals in developmental psychology rarely include explicit replications of prior research conducted by different investigators, and few require authors to establish in their articles or online appendices that their key…

  19. 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...

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

    Science.gov (United States)

    Moriyama, Takashi; Sato, Naoki

    2014-01-01

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

  1. Visualization and measurement of ATP levels in living cells replicating hepatitis C virus genome RNA.

    Directory of Open Access Journals (Sweden)

    Tomomi Ando

    Full Text Available Adenosine 5'-triphosphate (ATP is the primary energy currency of all living organisms and participates in a variety of cellular processes. Although ATP requirements during viral lifecycles have been examined in a number of studies, a method by which ATP production can be monitored in real-time, and by which ATP can be quantified in individual cells and subcellular compartments, is lacking, thereby hindering studies aimed at elucidating the precise mechanisms by which viral replication energized by ATP is controlled. In this study, we investigated the fluctuation and distribution of ATP in cells during RNA replication of the hepatitis C virus (HCV, a member of the Flaviviridae family. We demonstrated that cells involved in viral RNA replication actively consumed ATP, thereby reducing cytoplasmic ATP levels. Subsequently, a method to measure ATP levels at putative subcellular sites of HCV RNA replication in living cells was developed by introducing a recently-established Förster resonance energy transfer (FRET-based ATP indicator, called ATeam, into the NS5A coding region of the HCV replicon. Using this method, we were able to observe the formation of ATP-enriched dot-like structures, which co-localize with non-structural viral proteins, within the cytoplasm of HCV-replicating cells but not in non-replicating cells. The obtained FRET signals allowed us to estimate ATP concentrations within HCV replicating cells as ∼5 mM at possible replicating sites and ∼1 mM at peripheral sites that did not appear to be involved in HCV replication. In contrast, cytoplasmic ATP levels in non-replicating Huh-7 cells were estimated as ∼2 mM. To our knowledge, this is the first study to demonstrate changes in ATP concentration within cells during replication of the HCV genome and increased ATP levels at distinct sites within replicating cells. ATeam may be a powerful tool for the study of energy metabolism during replication of the viral genome.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hood, Iris V.; Berger, James M.

    2016-05-31

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

  3. The transcription elongation factor Bur1-Bur2 interacts with replication protein A and maintains genome stability during replication stress

    DEFF Research Database (Denmark)

    Clausing, Emanuel; Mayer, Andreas; Chanarat, Sittinan

    2010-01-01

    Multiple DNA-associated processes such as DNA repair, replication, and recombination are crucial for the maintenance of genome integrity. Here, we show a novel interaction between the transcription elongation factor Bur1-Bur2 and replication protein A (RPA), the eukaryotic single-stranded DNA......-binding protein with functions in DNA repair, recombination, and replication. Bur1 interacted via its C-terminal domain with RPA, and bur1-¿C mutants showed a deregulated DNA damage response accompanied by increased sensitivity to DNA damage and replication stress as well as increased levels of persisting Rad52...... foci. Interestingly, the DNA damage sensitivity of an rfa1 mutant was suppressed by bur1 mutation, further underscoring a functional link between these two protein complexes. The transcription elongation factor Bur1-Bur2 interacts with RPA and maintains genome integrity during DNA replication stress....

  4. [The effects of TorR protein on initiation of DNA replication in Escherichia coli].

    Science.gov (United States)

    Yuan, Yao; Jiaxin, Qiao; Jing, Li; Hui, Li; Morigen, Morigen

    2015-03-01

    The two-component systems, which could sense and respond to environmental changes, widely exist in bacteria as a signal transduction pathway. The bacterial CckA/CtrA, ArcA/ArcB and PhoP/PhoQ two-component systems are associated with initiation of DNA replication and cell division, however, the effects of the TorS/TorR system on cell cycle and DNA replication remains unknown. The TorS/TorR system in Escherichia coli can sense changes in trimethylamine oxide (TMAO) concentration around the cells. However, it is unknown if it also affects initiation of DNA replication. We detected DNA replication patterns in ΔtorS and ΔtorR mutant strains by flow cytometry. We found that the average number of replication origins (oriCs) per cell and doubling time in ΔtorS mutants were the same while the average number of oriCs in ΔtorR mutants was increased compared with that in wild-type cells. These results indicated that absence of TorR led to an earlier initiation of DNA replication than that in wild-type cells. Strangely, neither overexpression of TorR nor co-expression of TorR and TorS could restore ΔtorR mutant phenotype to the wild type. However, overexpression of SufD in both wild type and ΔtorR mutants promoted initiation of DNA replication, while mutation of SufD delayed it in ΔtorR mutants. Thus, TorR may affect initiation of DNA replication indirectly through regulating gene expression of sufD.

  5. 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)

  6. Large Eddy Simulation of stratified flows over structures

    OpenAIRE

    Brechler J.; Fuka V.

    2013-01-01

    We tested the ability of the LES model CLMM (Charles University Large-Eddy Microscale Model) to model the stratified flow around three dimensional hills. We compared the quantities, as the height of the dividing streamline, recirculation zone length or length of the lee waves with experiments by Hunt and Snyder[3] and numerical computations by Ding, Calhoun and Street[5]. The results mostly agreed with the references, but some important differences are present.

  7. Large Eddy Simulation of stratified flows over structures

    Science.gov (United States)

    Fuka, V.; Brechler, J.

    2013-04-01

    We tested the ability of the LES model CLMM (Charles University Large-Eddy Microscale Model) to model the stratified flow around three dimensional hills. We compared the quantities, as the height of the dividing streamline, recirculation zone length or length of the lee waves with experiments by Hunt and Snyder[3] and numerical computations by Ding, Calhoun and Street[5]. The results mostly agreed with the references, but some important differences are present.

  8. 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.

  9. Evolution of complexity in RNA-like replicator systems

    Directory of Open Access Journals (Sweden)

    Hogeweg Paulien

    2008-03-01

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

  10. Molecular Mechanisms of DNA Replication Checkpoint Activation

    Directory of Open Access Journals (Sweden)

    Bénédicte Recolin

    2014-03-01

    Full Text Available The major challenge of the cell cycle is to deliver an intact, and fully duplicated, genetic material to the daughter cells. To this end, progression of DNA synthesis is monitored by a feedback mechanism known as replication checkpoint that is untimely linked to DNA replication. This signaling pathway ensures coordination of DNA synthesis with cell cycle progression. Failure to activate this checkpoint in response to perturbation of DNA synthesis (replication stress results in forced cell division leading to chromosome fragmentation, aneuploidy, and genomic instability. In this review, we will describe current knowledge of the molecular determinants of the DNA replication checkpoint in eukaryotic cells and discuss a model of activation of this signaling pathway crucial for maintenance of genomic stability.

  11. DCOMP Award Lecture (Metropolis): A 3D Spectral Anelastic Hydrodynamic Code for Shearing, Stratified Flows

    Science.gov (United States)

    Barranco, Joseph

    2006-03-01

    We have developed a three-dimensional (3D) spectral hydrodynamic code to study vortex dynamics in rotating, shearing, stratified systems (eg, the atmosphere of gas giant planets, protoplanetary disks around newly forming protostars). The time-independent background state is stably stratified in the vertical direction and has a unidirectional linear shear flow aligned with one horizontal axis. Superposed on this background state is an unsteady, subsonic flow that is evolved with the Euler equations subject to the anelastic approximation to filter acoustic phenomena. A Fourier-Fourier basis in a set of quasi-Lagrangian coordinates that advect with the background shear is used for spectral expansions in the two horizontal directions. For the vertical direction, two different sets of basis functions have been implemented: (1) Chebyshev polynomials on a truncated, finite domain, and (2) rational Chebyshev functions on an infinite domain. Use of this latter set is equivalent to transforming the infinite domain to a finite one with a cotangent mapping, and using cosine and sine expansions in the mapped coordinate. The nonlinear advection terms are time integrated explicitly, whereas the Coriolis force, buoyancy terms, and pressure/enthalpy gradient are integrated semi- implicitly. We show that internal gravity waves can be damped by adding new terms to the Euler equations. The code exhibits excellent parallel performance with the Message Passing Interface (MPI). As a demonstration of the code, we simulate vortex dynamics in protoplanetary disks and the Kelvin-Helmholtz instability in the dusty midplanes of protoplanetary disks.

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

    Science.gov (United States)

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

    1999-06-01

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

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

    Science.gov (United States)

    Wei, Lei; Zhao, Xiaolan

    2016-03-01

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

  14. Bifurcation from stable holes to replicating holes in vibrated dense suspensions.

    Science.gov (United States)

    Ebata, H; Sano, M

    2013-11-01

    In vertically vibrated starch suspensions, we observe bifurcations from stable holes to replicating holes. Above a certain acceleration, finite-amplitude deformations of the vibrated surface continue to grow until void penetrates fluid layers, and a hole forms. We studied experimentally and theoretically the parameter dependence of the holes and their stabilities. In suspensions of small dispersed particles, the circular shapes of the holes are stable. However, we find that larger particles or lower surface tension of water destabilize the circular shapes; this indicates the importance of capillary forces acting on the dispersed particles. Around the critical acceleration for bifurcation, holes show intermittent large deformations as a precursor to hole replication. We applied a phenomenological model for deformable domains, which is used in reaction-diffusion systems. The model can explain the basic dynamics of the holes, such as intermittent behavior, probability distribution functions of deformation, and time intervals of replication. Results from the phenomenological model match the linear growth rate below criticality that was estimated from experimental data.

  15. Zika Virus RNA Replication and Persistence in Brain and Placental Tissue

    Science.gov (United States)

    Rabeneck, Demi B.; Martines, Roosecelis B.; Reagan-Steiner, Sarah; Ermias, Yokabed; Estetter, Lindsey B.C.; Suzuki, Tadaki; Ritter, Jana; Keating, M. Kelly; Hale, Gillian; Gary, Joy; Muehlenbachs, Atis; Lambert, Amy; Lanciotti, Robert; Oduyebo, Titilope; Meaney-Delman, Dana; Bolaños, Fernando; Saad, Edgar Alberto Parra; Shieh, Wun-Ju; Zaki, Sherif R.

    2017-01-01

    Zika virus is causally linked with congenital microcephaly and may be associated with pregnancy loss. However, the mechanisms of Zika virus intrauterine transmission and replication and its tropism and persistence in tissues are poorly understood. We tested tissues from 52 case-patients: 8 infants with microcephaly who died and 44 women suspected of being infected with Zika virus during pregnancy. By reverse transcription PCR, tissues from 32 (62%) case-patients (brains from 8 infants with microcephaly and placental/fetal tissues from 24 women) were positive for Zika virus. In situ hybridization localized replicative Zika virus RNA in brains of 7 infants and in placentas of 9 women who had pregnancy losses during the first or second trimester. These findings demonstrate that Zika virus replicates and persists in fetal brains and placentas, providing direct evidence of its association with microcephaly. Tissue-based reverse transcription PCR extends the time frame of Zika virus detection in congenital and pregnancy-associated infections. PMID:27959260

  16. The difference between LSMC and replicating portfolio in insurance liability modeling.

    Science.gov (United States)

    Pelsser, Antoon; Schweizer, Janina

    2016-01-01

    Solvency II requires insurers to calculate the 1-year value at risk of their balance sheet. This involves the valuation of the balance sheet in 1 year's time. As for insurance liabilities, closed-form solutions to their value are generally not available, insurers turn to estimation procedures. While pure Monte Carlo simulation set-ups are theoretically sound, they are often infeasible in practice. Therefore, approximation methods are exploited. Among these, least squares Monte Carlo (LSMC) and portfolio replication are prominent and widely applied in practice. In this paper, we show that, while both are variants of regression-based Monte Carlo methods, they differ in one significant aspect. While the replicating portfolio approach only contains an approximation error, which converges to zero in the limit, in LSMC a projection error is additionally present, which cannot be eliminated. It is revealed that the replicating portfolio technique enjoys numerous advantages and is therefore an attractive model choice.

  17. 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

  18. Direct numerical simulations of exhaust gas recirculation effect on multistage autoignition in the negative temperature combustion regime for stratified HCCI flow conditions by using H2O2 addition

    Science.gov (United States)

    El-Asrag, Hossam A.; Ju, Yiguang

    2013-04-01

    Direct numerical simulations (DNSs) of a stratified flow in a homogeneous compression charge ignition (HCCI) engine are performed to investigate the exhaust gas recirculation (EGR) and temperature/mixture stratification effects on the autoignition of synthetic dimethyl ether (DME) in the negative temperature combustion region. Detailed chemistry for a DME/air mixture is employed and solved by a hybrid multi-time scale (HMTS) algorithm to reduce the computational cost. The effect of ? to mimic the EGR effect on autoignition are studied. The results show that adding ? enhances autoignition by rapid OH radical pool formation (34-46% reduction in ignition delay time) and changes the ignition heat release rates at different ignition stages. Sensitivity analysis is performed and the important reactions pathways affecting the autoignition are specified. The DNS results show that the scales introduced by thermal and mixture stratifications have a strong effect after the low temperature chemistry (LTC) ignition especially at the locations of high scalar dissipation rates. Compared to homogenous ignition, stratified ignitions show similar first autoignition delay times, but 18% reduction in the second and third ignition delay times. The results also show that molecular transport plays an important role in stratified low temperature ignition, and that the scalar mixing time scale is strongly affected by local ignition in the stratified flow. Two ignition-kernel propagation modes are observed: a wave-like, low-speed, deflagrative mode and a spontaneous, high-speed, ignition mode. Three criteria are introduced to distinguish these modes by different characteristic time scales and Damkhöler numbers using a progress variable conditioned by an ignition kernel indicator. The low scalar dissipation rate flame front is characterized by high displacement speeds and high mixing Damkhöler number. The proposed criteria are applied successfully at the different ignition stages and

  19. Replication of cultured lung epithelial cells

    International Nuclear Information System (INIS)

    Guzowski, D.; Bienkowski, R.

    1986-01-01

    The authors have investigated the conditions necessary to support replication of lung type 2 epithelial cells in culture. Cells were isolated from mature fetal rabbit lungs (29d gestation) and cultured on feeder layers of mitotically inactivated 3T3 fibroblasts. The epithelial nature of the cells was demonstrated by indirect immunofluorescent staining for keratin and by polyacid dichrome stain. Ultrastructural examination during the first week showed that the cells contained myofilaments, microvilli and lamellar bodies (markers for type 2 cells). The following changes were observed after the first week: increase in cell size; loss of lamellar bodies and appearance of multivesicular bodies; increase in rough endoplasmic reticulum and golgi; increase in tonafilaments and well-defined junctions. General cell morphology was good for up to 10 wk. Cells cultured on plastic surface degenerated after 1 wk. Cell replication was assayed by autoradiography of cultures exposed to ( 3 H)-thymidine and by direct cell counts. The cells did not replicate during the first week; however, between 2-10 wk the cells incorporated the label and went through approximately 6 population doublings. They have demonstrated that lung alveolar epithelial cells can replicate in culture if they are maintained on an appropriate substrate. The coincidence of ability to replicate and loss of markers for differentiation may reflect the dichotomy between growth and differentiation commonly observed in developing systems

  20. Dynamic measurement of liquid film thickness in stratified flow by using ultrasonic echo technique

    International Nuclear Information System (INIS)

    Serizawa, A.; Nagane, K.; Kamei, T.; Kawara, Z.; Ebisu, T.; Torikoshi, K.

    2004-01-01

    We developed a technique to measure time-dependent local film thickness in stratified air-water flow over a horizontal plate by using a time of flight of ultrasonic transmission. The ultrasonic echoes reflected at the liquid/air interfaces are detected by a conventional ultrasonic instrumentation, and the signals are analyzed by a personal computer after being digitalized by an A/D converter to give the time of flight for the ultrasonic waves to run over a distance of twice of the film thickness. A 3.8 mm diameter probe type ultrasonic transducer was used in the present work which transmits and receives 10 MHz frequency ultrasonic waves. The estimated spatial resolution with this arrangement is 0.075 mm in film thickness for water. The time resolution, which depends on both the A/D converter and the memory capacity was up to several tens Hz. We also discussed the sensitivity of the method to the inclination angle of the interfaces. (author)

  1. Spacetime replication of continuous variable quantum information

    International Nuclear Information System (INIS)

    Hayden, Patrick; Nezami, Sepehr; Salton, Grant; Sanders, Barry C

    2016-01-01

    The theory of relativity requires that no information travel faster than light, whereas the unitarity of quantum mechanics ensures that quantum information cannot be cloned. These conditions provide the basic constraints that appear in information replication tasks, which formalize aspects of the behavior of information in relativistic quantum mechanics. In this article, we provide continuous variable (CV) strategies for spacetime quantum information replication that are directly amenable to optical or mechanical implementation. We use a new class of homologically constructed CV quantum error correcting codes to provide efficient solutions for the general case of information replication. As compared to schemes encoding qubits, our CV solution requires half as many shares per encoded system. We also provide an optimized five-mode strategy for replicating quantum information in a particular configuration of four spacetime regions designed not to be reducible to previously performed experiments. For this optimized strategy, we provide detailed encoding and decoding procedures using standard optical apparatus and calculate the recovery fidelity when finite squeezing is used. As such we provide a scheme for experimentally realizing quantum information replication using quantum optics. (paper)

  2. 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.

  3. Economic viability of Stratified Medicine concepts : An investor perspective on drivers and conditions that favour using Stratified Medicine approaches in a cost-contained healthcare environment

    NARCIS (Netherlands)

    Fugel, Hans-Joerg; Nuijten, Mark; Postma, Maarten

    2016-01-01

    RATIONALE: Stratified Medicine (SM) is becoming a natural result of advances in biomedical science and a promising path for the innovation-based biopharmaceutical industry to create new investment opportunities. While the use of biomarkers to improve R&D efficiency and productivity is very much

  4. A study of stratified gas-liquid pipe flow

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, George W.

    2005-07-01

    This work includes both theoretical modelling and experimental observations which are relevant to the design of gas condensate transport lines. Multicomponent hydrocarbon gas mixtures are transported in pipes over long distances and at various inclinations. Under certain circumstances, the heavier hydrocarbon components and/or water vapour condense to form one or more liquid phases. Near the desired capacity, the liquid condensate and water is efficiently transported in the form of a stratified flow with a droplet field. During operating conditions however, the flow rate may be reduced allowing liquid accumulation which can create serious operational problems due to large amounts of excess liquid being expelled into the receiving facilities during production ramp-up or even in steady production in severe cases. In particular, liquid tends to accumulate in upward inclined sections due to insufficient drag on the liquid from the gas. To optimize the transport of gas condensates, a pipe diameters should be carefully chosen to account for varying flow rates and pressure levels which are determined through the knowledge of the multiphase flow present. It is desirable to have a reliable numerical simulation tool to predict liquid accumulation for various flow rates, pipe diameters and pressure levels which is not presently accounted for by industrial flow codes. A critical feature of the simulation code would include the ability to predict the transition from small liquid accumulation at high flow rates to large liquid accumulation at low flow rates. A semi-intermittent flow regime of roll waves alternating with a partly backward flowing liquid film has been observed experimentally to occur for a range of gas flow rates. Most of the liquid is transported in the roll waves. The roll wave regime is not well understood and requires fundamental modelling and experimental research. The lack of reliable models for this regime leads to inaccurate prediction of the onset of

  5. Replication protein A in nonearly ovarian adenocarcinomas: correlation with MCM-2, MCM-5, Ki-67 index and prognostic significance.

    Science.gov (United States)

    Levidou, Georgia; Ventouri, Kiriaki; Nonni, Afroditi; Gakiopoulou, Hariklia; Bamias, Aristotle; Sotiropoulou, Maria; Papaspirou, Irene; Dimopoulos, Meletios A; Patsouris, Efstratios; Korkolopoulou, Penelope

    2012-07-01

    Replication protein A (RPA) is an ssDNA-binding protein required for the initiation of DNA replication and the stabilization of ssDNA. Collaboration with several molecules, that is, the MCM2-7 complex, has been suggested to be imperative for its multifaceted role. In this study, we investigated the immunohistochemical expression of the RPA2 subunit in correlation with the MCM-2 and MCM-5 and Ki67 index, and assessed its prognostic significance in 76 patients with nonearly ovarian adenocarcinomas, the majority of whom had a serous histotype. RPA2 protein expression was observed in all cases, whereas the staining intensity varied from weak to strong. RPA2 expression was correlated with the tumor stage in the entire cohort and in serous tumors (P=0.0053 in both relationships). Moreover, RPA2 immunoexpression was positively correlated with MCM-2 (P=0.0001) and MCM-5 (P0.10). In multivariate survival analysis, RPA2 expression emerged as an independent predictor of adverse outcome (PMCM-2 and MCM-5 expression and when analysis was restricted to serous carcinomas (P=0.004). Our results further support the interrelation of RPA2 protein with MCM-2 and MCM-5 in OCs. Moreover, RPA2 protein may play an important role in ovarian tumorigenesis, and may serve as a useful independent molecular marker for stratifying patients with OC in terms of prognosis.

  6. The Design of Finite State Machine for Asynchronous Replication Protocol

    Science.gov (United States)

    Wang, Yanlong; Li, Zhanhuai; Lin, Wei; Hei, Minglei; Hao, Jianhua

    Data replication is a key way to design a disaster tolerance system and to achieve reliability and availability. It is difficult for a replication protocol to deal with the diverse and complex environment. This means that data is less well replicated than it ought to be. To reduce data loss and to optimize replication protocols, we (1) present a finite state machine, (2) run it to manage an asynchronous replication protocol and (3) report a simple evaluation of the asynchronous replication protocol based on our state machine. It's proved that our state machine is applicable to guarantee the asynchronous replication protocol running in the proper state to the largest extent in the event of various possible events. It also can helpful to build up replication-based disaster tolerance systems to ensure the business continuity.

  7. Experimental analysis of an oblique turbulent flame front propagating in a stratified flow

    Energy Technology Data Exchange (ETDEWEB)

    Galizzi, C.; Escudie, D. [Universite de Lyon, CNRS, CETHIL, INSA-Lyon, UMR5008, F-69621 Cedex (France)

    2010-12-15

    This paper details the experimental study of a turbulent V-shaped flame expanding in a nonhomogeneous premixed flow. Its aim is to characterize the effects of stratification on turbulent flame characteristics. The setup consists of a stationary V-shaped flame stabilized on a rod and expanding freely in a lean premixed methane-air flow. One of the two oblique fronts interacts with a stratified slice, which has an equivalence ratio close to one and a thickness greater than that of the flame front. Several techniques such as PIV and CH{sup *} chemiluminescence are used to investigate the instantaneous fields, while laser Doppler anemometry and thermocouples are combined with a concentration probe to provide information on the mean fields. First, in order to provide a reference, the homogeneous turbulent case is studied. Next, the stratified turbulent premixed flame is investigated. Results show significant modifications of the whole flame and of the velocity field upstream of the flame front. The analysis of the geometric properties of the stratified flame indicates an increase in flame brush thickness, closely related to the local equivalence ratio. (author)

  8. DNA replication stress restricts ribosomal DNA copy number.

    Science.gov (United States)

    Salim, Devika; Bradford, William D; Freeland, Amy; Cady, Gillian; Wang, Jianmin; Pruitt, Steven C; Gerton, Jennifer L

    2017-09-01

    Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

  9. DNA replication stress restricts ribosomal DNA copy number

    Science.gov (United States)

    Salim, Devika; Bradford, William D.; Freeland, Amy; Cady, Gillian; Wang, Jianmin

    2017-01-01

    Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100–200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how “normal” copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a “normal” rDNA copy number. PMID:28915237

  10. DNA replication stress restricts ribosomal DNA copy number.

    Directory of Open Access Journals (Sweden)

    Devika Salim

    2017-09-01

    Full Text Available Ribosomal RNAs (rRNAs in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

  11. Improvements to TRAC models of condensing stratified flow. Pt. 1

    International Nuclear Information System (INIS)

    Zhang, Q.; Leslie, D.C.

    1991-12-01

    Direct contact condensation in stratified flow is an important phenomenon in LOCA analyses. In this report, the TRAC interfacial heat transfer model for stratified condensing flow has been assessed against the Bankoff experiments. A rectangular channel option has been added to the code to represent the experimental geometry. In almost all cases the TRAC heat transfer coefficient (HTC) over-predicts the condensation rates and in some cases it is so high that the predicted steam is sucked in from the normal outlet in order to conserve mass. Based on their cocurrent and countercurrent condensing flow experiments, Bankoff and his students (Lim 1981, Kim 1985) developed HTC models from the two cases. The replacement of the TRAC HTC with either of Bankoff's models greatly improves the predictions of condensation rates in the experiment with cocurrent condensing flow. However, the Bankoff HTC for countercurrent flow is preferable because it is based only on the local quantities rather than on the quantities averaged from the inlet. (author)

  12. Chaotic interactions of self-replicating RNA.

    Science.gov (United States)

    Forst, C V

    1996-03-01

    A general system of high-order differential equations describing complex dynamics of replicating biomolecules is given. Symmetry relations and coordinate transformations of general replication systems leading to topologically equivalent systems are derived. Three chaotic attractors observed in Lotka-Volterra equations of dimension n = 3 are shown to represent three cross-sections of one and the same chaotic regime. Also a fractal torus in a generalized three-dimensional Lotka-Volterra Model has been linked to one of the chaotic attractors. The strange attractors are studied in the equivalent four-dimensional catalytic replicator network. The fractal torus has been examined in adapted Lotka-Volterra equations. Analytic expressions are derived for the Lyapunov exponents of the flow in the replicator system. Lyapunov spectra for different pathways into chaos has been calculated. In the generalized Lotka-Volterra system a second inner rest point--coexisting with (quasi)-periodic orbits--can be observed; with an abundance of different bifurcations. Pathways from chaotic tori, via quasi-periodic tori, via limit cycles, via multi-periodic orbits--emerging out of periodic doubling bifurcations--to "simple" chaotic attractors can be found.

  13. Insights into the Initiation of Eukaryotic DNA Replication.

    Science.gov (United States)

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

    2015-01-01

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

  14. Large Eddy Simulation of stratified flows over structures

    Directory of Open Access Journals (Sweden)

    Brechler J.

    2013-04-01

    Full Text Available We tested the ability of the LES model CLMM (Charles University Large-Eddy Microscale Model to model the stratified flow around three dimensional hills. We compared the quantities, as the height of the dividing streamline, recirculation zone length or length of the lee waves with experiments by Hunt and Snyder[3] and numerical computations by Ding, Calhoun and Street[5]. The results mostly agreed with the references, but some important differences are present.

  15. Materials Chemistry and Performance of Silicone-Based Replicating Compounds.

    Energy Technology Data Exchange (ETDEWEB)

    Brumbach, Michael T.; Mirabal, Alex James; Kalan, Michael; Trujillo, Ana B; Hale, Kevin

    2014-11-01

    Replicating compounds are used to cast reproductions of surface features on a variety of materials. Replicas allow for quantitative measurements and recordkeeping on parts that may otherwise be difficult to measure or maintain. In this study, the chemistry and replicating capability of several replicating compounds was investigated. Additionally, the residue remaining on material surfaces upon removal of replicas was quantified. Cleaning practices were tested for several different replicating compounds. For all replicating compounds investigated, a thin silicone residue was left by the replica. For some compounds, additional inorganic species could be identified in the residue. Simple solvent cleaning could remove some residue.

  16. Mixed Convection Flow along a Stretching Cylinder in a Thermally Stratified Medium

    Directory of Open Access Journals (Sweden)

    Swati Mukhopadhyay

    2012-01-01

    Full Text Available An analysis for the axisymmetric laminar boundary layer mixed convection flow of a viscous and incompressible fluid towards a stretching cylinder immersed in a thermally stratified medium is presented in this paper. Similarity transformation is employed to convert the governing partial differential equations into highly nonlinear ordinary differential equations. Numerical solutions of these equations are obtained by a shooting method. It is found that the heat transfer rate at the surface is lower for flow in a thermally stratified medium compared to that of an unstratified medium. Moreover, both the skin friction coefficient and the heat transfer rate at the surface are larger for a cylinder compared to that for a flat plate.

  17. Plane Stratified Flow in a Room Ventilated by Displacement Ventilation

    DEFF Research Database (Denmark)

    Nielsen, Peter Vilhelm; Nickel, J.; Baron, D. J. G.

    2004-01-01

    The air movement in the occupied zone of a room ventilated by displacement ventilation exists as a stratified flow along the floor. This flow can be radial or plane according to the number of wall-mounted diffusers and the room geometry. The paper addresses the situations where plane flow...

  18. 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

  19. White dwarf stars with chemically stratified atmospheres

    Science.gov (United States)

    Muchmore, D.

    1982-01-01

    Recent observations and theory suggest that some white dwarfs may have chemically stratified atmospheres - thin layers of hydrogen lying above helium-rich envelopes. Models of such atmospheres show that a discontinuous temperature inversion can occur at the boundary between the layers. Model spectra for layered atmospheres at 30,000 K and 50,000 K tend to have smaller decrements at 912 A, 504 A, and 228 A than uniform atmospheres would have. On the basis of their continuous extreme ultraviolet spectra, it is possible to distinguish observationally between uniform and layered atmospheres for hot white dwarfs.

  20. 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.

  1. Measuring mixing efficiency in experiments of strongly stratified turbulence

    Science.gov (United States)

    Augier, P.; Campagne, A.; Valran, T.; Calpe Linares, M.; Mohanan, A. V.; Micard, D.; Viboud, S.; Segalini, A.; Mordant, N.; Sommeria, J.; Lindborg, E.

    2017-12-01

    Oceanic and atmospheric models need better parameterization of the mixing efficiency. Therefore, we need to measure this quantity for flows representative of geophysical flows, both in terms of types of flows (with vortices and/or waves) and of dynamical regimes. In order to reach sufficiently large Reynolds number for strongly stratified flows, experiments for which salt is used to produce the stratification have to be carried out in a large rotating platform of at least 10-meter diameter.We present new experiments done in summer 2017 to study experimentally strongly stratified turbulence and mixing efficiency in the Coriolis platform. The flow is forced by a slow periodic movement of an array of large vertical or horizontal cylinders. The velocity field is measured by 3D-2C scanned horizontal particles image velocimetry (PIV) and 2D vertical PIV. Six density-temperature probes are used to measure vertical and horizontal profiles and signals at fixed positions.We will show how we rely heavily on open-science methods for this study. Our new results on the mixing efficiency will be presented and discussed in terms of mixing parameterization.

  2. Mean-field theory of differential rotation in density stratified turbulent convection

    Science.gov (United States)

    Rogachevskii, I.

    2018-04-01

    A mean-field theory of differential rotation in a density stratified turbulent convection has been developed. This theory is based on the combined effects of the turbulent heat flux and anisotropy of turbulent convection on the Reynolds stress. A coupled system of dynamical budget equations consisting in the equations for the Reynolds stress, the entropy fluctuations and the turbulent heat flux has been solved. To close the system of these equations, the spectral approach, which is valid for large Reynolds and Péclet numbers, has been applied. The adopted model of the background turbulent convection takes into account an increase of the turbulence anisotropy and a decrease of the turbulent correlation time with the rotation rate. This theory yields the radial profile of the differential rotation which is in agreement with that for the solar differential rotation.

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

    Science.gov (United States)

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

    2018-01-01

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

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

    DEFF Research Database (Denmark)

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

    2018-01-01

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

  5. Monkey Viperin Restricts Porcine Reproductive and Respiratory Syndrome Virus Replication.

    Science.gov (United States)

    Fang, Jianyu; Wang, Haiyan; Bai, Juan; Zhang, Qiaoya; Li, Yufeng; Liu, Fei; Jiang, Ping

    2016-01-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen which causes huge economic damage globally in the swine industry. Current vaccination strategies provide only limited protection against PRRSV infection. Viperin is an interferon (IFN) stimulated protein that inhibits some virus infections via IFN-dependent or IFN-independent pathways. However, the role of viperin in PRRSV infection is not well understood. In this study, we cloned the full-length monkey viperin (mViperin) complementary DNA (cDNA) from IFN-α-treated African green monkey Marc-145 cells. It was found that the mViperin is up-regulated following PRRSV infection in Marc-145 cells along with elevated IRF-1 gene levels. IFN-α induced mViperin expression in a dose- and time-dependent manner and strongly inhibits PRRSV replication in Marc-145 cells. Overexpression of mViperin suppresses PRRSV replication by blocking the early steps of PRRSV entry and genome replication and translation but not inhibiting assembly and release. And mViperin co-localized with PRRSV GP5 and N protein, but only interacted with N protein in distinct cytoplasmic loci. Furthermore, it was found that the 13-16 amino acids of mViperin were essential for inhibiting PRRSV replication, by disrupting the distribution of mViperin protein from the granular distribution to a homogeneous distribution in the cytoplasm. These results could be helpful in the future development of novel antiviral therapies against PRRSV infection.

  6. An improved algorithm of image processing technique for film thickness measurement in a horizontal stratified gas-liquid two-phase flow

    Energy Technology Data Exchange (ETDEWEB)

    Kuntoro, Hadiyan Yusuf, E-mail: hadiyan.y.kuntoro@mail.ugm.ac.id; Majid, Akmal Irfan; Deendarlianto, E-mail: deendarlianto@ugm.ac.id [Center for Energy Studies, Gadjah Mada University, Sekip K-1A Kampus UGM, Yogyakarta 55281 (Indonesia); Department of Mechanical and Industrial Engineering, Faculty of Engineering, Gadjah Mada University, Jalan Grafika 2, Yogyakarta 55281 (Indonesia); Hudaya, Akhmad Zidni; Dinaryanto, Okto [Department of Mechanical and Industrial Engineering, Faculty of Engineering, Gadjah Mada University, Jalan Grafika 2, Yogyakarta 55281 (Indonesia)

    2016-06-03

    Due to the importance of the two-phase flow researches for the industrial safety analysis, many researchers developed various methods and techniques to study the two-phase flow phenomena on the industrial cases, such as in the chemical, petroleum and nuclear industries cases. One of the developing methods and techniques is image processing technique. This technique is widely used in the two-phase flow researches due to the non-intrusive capability to process a lot of visualization data which are contain many complexities. Moreover, this technique allows to capture direct-visual information data of the flow which are difficult to be captured by other methods and techniques. The main objective of this paper is to present an improved algorithm of image processing technique from the preceding algorithm for the stratified flow cases. The present algorithm can measure the film thickness (h{sub L}) of stratified flow as well as the geometrical properties of the interfacial waves with lower processing time and random-access memory (RAM) usage than the preceding algorithm. Also, the measurement results are aimed to develop a high quality database of stratified flow which is scanty. In the present work, the measurement results had a satisfactory agreement with the previous works.

  7. Cathepsin B & L are not required for ebola virus replication.

    Science.gov (United States)

    Marzi, Andrea; Reinheckel, Thomas; Feldmann, Heinz

    2012-01-01

    Ebola virus (EBOV), family Filoviridae, emerged in 1976 on the African continent. Since then it caused several outbreaks of viral hemorrhagic fever in humans with case fatality rates up to 90% and remains a serious Public Health concern and biothreat pathogen. The most pathogenic and best-studied species is Zaire ebolavirus (ZEBOV). EBOV encodes one viral surface glycoprotein (GP), which is essential for replication, a determinant of pathogenicity and an important immunogen. GP mediates viral entry through interaction with cellular surface molecules, which results in the uptake of virus particles via macropinocytosis. Later in this pathway endosomal acidification activates the cysteine proteases Cathepsin B and L (CatB, CatL), which have been shown to cleave ZEBOV-GP leading to subsequent exposure of the putative receptor-binding and fusion domain and productive infection. We studied the effect of CatB and CatL on in vitro and in vivo replication of EBOV. Similar to previous findings, our results show an effect of CatB, but not CatL, on ZEBOV entry into cultured cells. Interestingly, cell entry by other EBOV species (Bundibugyo, Côte d'Ivoire, Reston and Sudan ebolavirus) was independent of CatB or CatL as was EBOV replication in general. To investigate whether CatB and CatL have a role in vivo during infection, we utilized the mouse model for ZEBOV. Wild-type (control), catB(-/-) and catL(-/-) mice were equally susceptible to lethal challenge with mouse-adapted ZEBOV with no difference in virus replication and time to death. In conclusion, our results show that CatB and CatL activity is not required for EBOV replication. Furthermore, EBOV glycoprotein cleavage seems to be mediated by an array of proteases making targeted therapeutic approaches difficult.

  8. Cathepsin B & L are not required for ebola virus replication.

    Directory of Open Access Journals (Sweden)

    Andrea Marzi

    Full Text Available Ebola virus (EBOV, family Filoviridae, emerged in 1976 on the African continent. Since then it caused several outbreaks of viral hemorrhagic fever in humans with case fatality rates up to 90% and remains a serious Public Health concern and biothreat pathogen. The most pathogenic and best-studied species is Zaire ebolavirus (ZEBOV. EBOV encodes one viral surface glycoprotein (GP, which is essential for replication, a determinant of pathogenicity and an important immunogen. GP mediates viral entry through interaction with cellular surface molecules, which results in the uptake of virus particles via macropinocytosis. Later in this pathway endosomal acidification activates the cysteine proteases Cathepsin B and L (CatB, CatL, which have been shown to cleave ZEBOV-GP leading to subsequent exposure of the putative receptor-binding and fusion domain and productive infection. We studied the effect of CatB and CatL on in vitro and in vivo replication of EBOV. Similar to previous findings, our results show an effect of CatB, but not CatL, on ZEBOV entry into cultured cells. Interestingly, cell entry by other EBOV species (Bundibugyo, Côte d'Ivoire, Reston and Sudan ebolavirus was independent of CatB or CatL as was EBOV replication in general. To investigate whether CatB and CatL have a role in vivo during infection, we utilized the mouse model for ZEBOV. Wild-type (control, catB(-/- and catL(-/- mice were equally susceptible to lethal challenge with mouse-adapted ZEBOV with no difference in virus replication and time to death. In conclusion, our results show that CatB and CatL activity is not required for EBOV replication. Furthermore, EBOV glycoprotein cleavage seems to be mediated by an array of proteases making targeted therapeutic approaches difficult.

  9. Structural properties of replication origins in yeast DNA sequences

    International Nuclear Information System (INIS)

    Cao Xiaoqin; Zeng Jia; Yan Hong

    2008-01-01

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

  10. The dynamics of small inertial particles in weakly stratified turbulence

    NARCIS (Netherlands)

    van Aartrijk, M.; Clercx, H.J.H.

    We present an overview of a numerical study on the small-scale dynamics and the large-scale dispersion of small inertial particles in stably stratified turbulence. Three types of particles are examined: fluid particles, light inertial particles (with particle-to-fluid density ratio 1Ͽp/Ͽf25) and

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

    Science.gov (United States)

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

    2017-01-01

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

  12. 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

  13. Organization of Replication of Ribosomal DNA in Saccharomyces cerevisiae

    NARCIS (Netherlands)

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

    1988-01-01

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

  14. Cyclophilin B facilitates the replication of Orf virus.

    Science.gov (United States)

    Zhao, Kui; Li, Jida; He, Wenqi; Song, Deguang; Zhang, Ximu; Zhang, Di; Zhou, Yanlong; Gao, Feng

    2017-06-15

    Viruses interact with host cellular factors to construct a more favourable environment for their efficient replication. Expression of cyclophilin B (CypB), a cellular peptidyl-prolyl cis-trans isomerase (PPIase), was found to be significantly up-regulated. Recently, a number of studies have shown that CypB is important in the replication of several viruses, including Japanese encephalitis virus (JEV), hepatitis C virus (HCV) and human papillomavirus type 16 (HPV 16). However, the function of cellular CypB in ORFV replication has not yet been explored. Suppression subtractive hybridization (SSH) technique was applied to identify genes differentially expressed in the ORFV-infected MDBK cells at an early phase of infection. Cellular CypB was confirmed to be significantly up-regulated by quantitative reverse transcription-PCR (qRT-PCR) analysis and Western blotting. The role of CypB in ORFV infection was further determined using Cyclosporin A (CsA) and RNA interference (RNAi). Effect of CypB gene silencing on ORFV replication by 50% tissue culture infectious dose (TCID 50 ) assay and qRT-PCR detection. In the present study, CypB was found to be significantly up-regulated in the ORFV-infected MDBK cells at an early phase of infection. Cyclosporin A (CsA) exhibited suppressive effects on ORFV replication through the inhibition of CypB. Silencing of CypB gene inhibited the replication of ORFV in MDBK cells. In conclusion, these data suggest that CypB is critical for the efficient replication of the ORFV genome. Cellular CypB was confirmed to be significantly up-regulated in the ORFV-infected MDBK cells at an early phase of infection, which could effectively facilitate the replication of ORFV.

  15. Dipole formation by two interacting shielded monopoles in a stratified fluid

    NARCIS (Netherlands)

    Beckers, M.; Clercx, H.J.H.; Heijst, van G.J.F.; Verzicco, R.

    2002-01-01

    The interaction between two shielded monopolar vortices has been investigated experimentally in a nonrotating linearly stratified fluid and by full three-dimensional (3D) numerical simulations. The characteristic Reynolds and Froude numbers in the experiments are approximately Re [[approximate

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  17. Stabilization of Reversed Replication Forks by Telomerase Drives Telomere Catastrophe.

    Science.gov (United States)

    Margalef, Pol; Kotsantis, Panagiotis; Borel, Valerie; Bellelli, Roberto; Panier, Stephanie; Boulton, Simon J

    2018-01-25

    Telomere maintenance critically depends on the distinct activities of telomerase, which adds telomeric repeats to solve the end replication problem, and RTEL1, which dismantles DNA secondary structures at telomeres to facilitate replisome progression. Here, we establish that reversed replication forks are a pathological substrate for telomerase and the source of telomere catastrophe in Rtel1 -/- cells. Inhibiting telomerase recruitment to telomeres, but not its activity, or blocking replication fork reversal through PARP1 inhibition or depleting UBC13 or ZRANB3 prevents the rapid accumulation of dysfunctional telomeres in RTEL1-deficient cells. In this context, we establish that telomerase binding to reversed replication forks inhibits telomere replication, which can be mimicked by preventing replication fork restart through depletion of RECQ1 or PARG. Our results lead us to propose that telomerase inappropriately binds to and inhibits restart of reversed replication forks within telomeres, which compromises replication and leads to critically short telomeres. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Gongshi Bai

    2016-01-01

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

  19. Numerical simulations of the stratified oceanic bottom boundary layer

    Science.gov (United States)

    Taylor, John R.

    Numerical simulations are used to consider several problems relevant to the turbulent oceanic bottom boundary layer. In the first study, stratified open channel flow is considered with thermal boundary conditions chosen to approximate a shallow sea. Specifically, a constant heat flux is applied at the free surface and the lower wall is assumed to be adiabatic. When the surface heat flux is strong, turbulent upwellings of low speed fluid from near the lower wall are inhibited by the stable stratification. Subsequent studies consider a stratified bottom Ekman layer over a non-sloping lower wall. The influence of the free surface is removed by using an open boundary condition at the top of the computational domain. Particular attention is paid to the influence of the outer layer stratification on the boundary layer structure. When the density field is initialized with a linear profile, a turbulent mixed layer forms near the wall, which is separated from the outer layer by a strongly stable pycnocline. It is found that the bottom stress is not strongly affected by the outer layer stratification. However, stratification reduces turbulent transport to the outer layer and strongly limits the boundary layer height. The mean shear at the top of the boundary layer is enhanced when the outer layer is stratified, and this shear is strong enough to cause intermittent instabilities above the pycnocline. Turbulence-generated internal gravity waves are observed in the outer layer with a relatively narrow frequency range. An explanation for frequency content of these waves is proposed, starting with an observed broad-banded turbulent spectrum and invoking linear viscous decay to explain the preferential damping of low and high frequency waves. During the course of this work, an open-source computational fluid dynamics code has been developed with a number of advanced features including scalar advection, subgrid-scale models for large-eddy simulation, and distributed memory

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

    Science.gov (United States)

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

    2018-01-01

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

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

    DEFF Research Database (Denmark)

    Melixetian, Marina; Helin, Kristian

    2004-01-01

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

  2. Optical tweezers reveal how proteins alter replication

    Science.gov (United States)

    Chaurasiya, Kathy

    Single molecule force spectroscopy is a powerful method that explores the DNA interaction properties of proteins involved in a wide range of fundamental biological processes such as DNA replication, transcription, and repair. We use optical tweezers to capture and stretch a single DNA molecule in the presence of proteins that bind DNA and alter its mechanical properties. We quantitatively characterize the DNA binding mechanisms of proteins in order to provide a detailed understanding of their function. In this work, we focus on proteins involved in replication of Escherichia coli (E. coli ), endogenous eukaryotic retrotransposons Ty3 and LINE-1, and human immunodeficiency virus (HIV). DNA polymerases replicate the entire genome of the cell, and bind both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) during DNA replication. The replicative DNA polymerase in the widely-studied model system E. coli is the DNA polymerase III subunit alpha (DNA pol III alpha). We use optical tweezers to determine that UmuD, a protein that regulates bacterial mutagenesis through its interactions with DNA polymerases, specifically disrupts alpha binding to ssDNA. This suggests that UmuD removes alpha from its ssDNA template to allow DNA repair proteins access to the damaged DNA, and to facilitate exchange of the replicative polymerase for an error-prone translesion synthesis (TLS) polymerase that inserts nucleotides opposite the lesions, so that bacterial DNA replication may proceed. This work demonstrates a biophysical mechanism by which E. coli cells tolerate DNA damage. Retroviruses and retrotransposons reproduce by copying their RNA genome into the nuclear DNA of their eukaryotic hosts. Retroelements encode proteins called nucleic acid chaperones, which rearrange nucleic acid secondary structure and are therefore required for successful replication. The chaperone activity of these proteins requires strong binding affinity for both single- and double-stranded nucleic

  3. Flow and mixing of gas in cylinder of a stratified charge engine with two intake valves. Effects of late closing valve timing and intake port configurations; Kyuki nibenshiki sojo kyuki engine no cylinder nai gas ryudo to kongo. Osotoji valve timing oyobi port keijo ni yoru eikyo

    Energy Technology Data Exchange (ETDEWEB)

    Charoenphonphanich, C; Niwa, H; Ennoji, H; Iijima, T [Tokai University, Tokyo (Japan)

    1997-10-01

    A numerical analysis of the flow and mixing of rich mixture and air inducted into the cylinder through each of the two intake ports of a stratified charge engine have been carried out. Numerical calculations were performed by finite volume method for three types of the intake port configurations: inverse V type, parallel type and V type and two types of valve timing; conventional and late closing (Miller cycle). Velocity field, turbulent kinetic energy and distribution of mixture concentration in the cylinder were examined. 3 refs., 10 figs.

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

    Science.gov (United States)

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

    2017-06-01

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

  5. Murine leukemia virus (MLV replication monitored with fluorescent proteins

    Directory of Open Access Journals (Sweden)

    Bittner Alexandra

    2004-12-01

    Full Text Available Abstract Background Cancer gene therapy will benefit from vectors that are able to replicate in tumor tissue and cause a bystander effect. Replication-competent murine leukemia virus (MLV has been described to have potential as cancer therapeutics, however, MLV infection does not cause a cytopathic effect in the infected cell and viral replication can only be studied by immunostaining or measurement of reverse transcriptase activity. Results We inserted the coding sequences for green fluorescent protein (GFP into the proline-rich region (PRR of the ecotropic envelope protein (Env and were able to fluorescently label MLV. This allowed us to directly monitor viral replication and attachment to target cells by flow cytometry. We used this method to study viral replication of recombinant MLVs and split viral genomes, which were generated by replacement of the MLV env gene with the red fluorescent protein (RFP and separately cloning GFP-Env into a retroviral vector. Co-transfection of both plasmids into target cells resulted in the generation of semi-replicative vectors, and the two color labeling allowed to determine the distribution of the individual genomes in the target cells and was indicative for the occurrence of recombination events. Conclusions Fluorescently labeled MLVs are excellent tools for the study of factors that influence viral replication and can be used to optimize MLV-based replication-competent viruses or vectors for gene therapy.

  6. 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.

  7. Replication and interaction of herpes simplex virus and human papillomavirus in differentiating host epithelial tissue

    International Nuclear Information System (INIS)

    Meyers, Craig; Andreansky, Samita S.; Courtney, Richard J.

    2003-01-01

    We have investigated the interactions and consequences of superinfecting and coreplication of human papillomavirus (HPV) and herpes simplex virus (HSV) in human epithelial organotypic (raft) culture tissues. In HPV-positive tissues, HSV infection and replication induced significant cytopathic effects (CPE), but the tissues were able to recover and maintain a certain degree of tissue integrity and architecture. HPV31b not only maintained the episomal state of its genomic DNA but also maintained its genomic copy number even during times of extensive HSV-induced CPE. E2 transcripts encoded by HPV31b were undetectable even though HPV31b replication was maintained in HSV- infected raft tissues. Expression of HPV31b oncogenes (E6 and E7) was also repressed but to a lesser degree than was E2 expression. The extent of CPE induced by HSV is dependent on the magnitude of HPV replication and gene expression at the time of HSV infection. During active HSV infection, HPV maintains its genomic copy number even though genes required for its replication were repressed. These studies provide new insight into the complex interaction between two common human sexually transmitted viruses in an in vitro system, modeling their natural host tissue in vivo

  8. The DNA Replication Stress Hypothesis of Alzheimer’s Disease

    Directory of Open Access Journals (Sweden)

    Yuri B. Yurov

    2011-01-01

    Full Text Available A well-recognized theory of Alzheimer’s disease (AD pathogenesis suggests ectopic cell cycle events to mediate neurodegeneration. Vulnerable neurons of the AD brain exhibit biomarkers of cell cycle progression and DNA replication suggesting a reentry into the cell cycle. Chromosome reduplication without proper cell cycle completion and mitotic division probably causes neuronal cell dysfunction and death. However, this theory seems to require some inputs in accordance with the generally recognized amyloid cascade theory as well as to explain causes and consequences of genomic instability (aneuploidy in the AD brain. We propose that unscheduled and incomplete DNA replication (replication stress destabilizes (epigenomic landscape in the brain and leads to DNA replication “catastrophe” causing cell death during the S phase (replicative cell death. DNA replication stress can be a key element of the pathogenetic cascade explaining the interplay between ectopic cell cycle events and genetic instabilities in the AD brain. Abnormal cell cycle reentry and somatic genome variations can be used for updating the cell cycle theory introducing replication stress as a missing link between cell genetics and neurobiology of AD.

  9. Can concurrent memory load reduce distraction? A replication study and beyond.

    Science.gov (United States)

    Gil-Gómez de Liaño, Beatriz; Stablum, Franca; Umiltà, Carlo

    2016-01-01

    The effects of concurrent working memory load in attentional processes have been 1 of the most puzzling issues in cognitive psychology. Studies have shown detrimental effects, no effects, and even beneficial effects of working memory load in different attentional tasks. In the present study we attempted to replicate Kim, Kim, and Chun's (2005, Experiment 3b) findings of beneficial effects of concurrent working memory load in a spatial Stroop-like task. In 3 experiments in which our sample was 3 times larger than that in the original Kim et al. study, we could not replicate their findings. The results are discussed in terms of what may have produced the conflicting results, trying to shed light on how working memory load affects attentional tasks. Also, we emphasize the importance of using adequately large samples in cognitive research. Although we acknowledge the relevance of meta-analyses to analyze conflicting results, in the present article we stress (perhaps more important) the power of an essential trademark in science for research development: replicability. (c) 2015 APA, all rights reserved).

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

    Science.gov (United States)

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

    2018-04-24

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

  11. Stratified sampling design based on data mining.

    Science.gov (United States)

    Kim, Yeonkook J; Oh, Yoonhwan; Park, Sunghoon; Cho, Sungzoon; Park, Hayoung

    2013-09-01

    To explore classification rules based on data mining methodologies which are to be used in defining strata in stratified sampling of healthcare providers with improved sampling efficiency. We performed k-means clustering to group providers with similar characteristics, then, constructed decision trees on cluster labels to generate stratification rules. We assessed the variance explained by the stratification proposed in this study and by conventional stratification to evaluate the performance of the sampling design. We constructed a study database from health insurance claims data and providers' profile data made available to this study by the Health Insurance Review and Assessment Service of South Korea, and population data from Statistics Korea. From our database, we used the data for single specialty clinics or hospitals in two specialties, general surgery and ophthalmology, for the year 2011 in this study. Data mining resulted in five strata in general surgery with two stratification variables, the number of inpatients per specialist and population density of provider location, and five strata in ophthalmology with two stratification variables, the number of inpatients per specialist and number of beds. The percentages of variance in annual changes in the productivity of specialists explained by the stratification in general surgery and ophthalmology were 22% and 8%, respectively, whereas conventional stratification by the type of provider location and number of beds explained 2% and 0.2% of variance, respectively. This study demonstrated that data mining methods can be used in designing efficient stratified sampling with variables readily available to the insurer and government; it offers an alternative to the existing stratification method that is widely used in healthcare provider surveys in South Korea.

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

    Science.gov (United States)

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

    2015-03-26

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

  13. DNA replication stress and cancer chemotherapy.

    Science.gov (United States)

    Kitao, Hiroyuki; Iimori, Makoto; Kataoka, Yuki; Wakasa, Takeshi; Tokunaga, Eriko; Saeki, Hiroshi; Oki, Eiji; Maehara, Yoshihiko

    2018-02-01

    DNA replication is one of the fundamental biological processes in which dysregulation can cause genome instability. This instability is one of the hallmarks of cancer and confers genetic diversity during tumorigenesis. Numerous experimental and clinical studies have indicated that most tumors have experienced and overcome the stresses caused by the perturbation of DNA replication, which is also referred to as DNA replication stress (DRS). When we consider therapeutic approaches for tumors, it is important to exploit the differences in DRS between tumor and normal cells. In this review, we introduce the current understanding of DRS in tumors and discuss the underlying mechanism of cancer therapy from the aspect of DRS. © 2017 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

  14. Weight of fitness deviation governs strict physical chaos in replicator dynamics

    Science.gov (United States)

    Pandit, Varun; Mukhopadhyay, Archan; Chakraborty, Sagar

    2018-03-01

    Replicator equation—a paradigm equation in evolutionary game dynamics—mathematizes the frequency dependent selection of competing strategies vying to enhance their fitness (quantified by the average payoffs) with respect to the average fitnesses of the evolving population under consideration. In this paper, we deal with two discrete versions of the replicator equation employed to study evolution in a population where any two players' interaction is modelled by a two-strategy symmetric normal-form game. There are twelve distinct classes of such games, each typified by a particular ordinal relationship among the elements of the corresponding payoff matrix. Here, we find the sufficient conditions for the existence of asymptotic solutions of the replicator equations such that the solutions—fixed points, periodic orbits, and chaotic trajectories—are all strictly physical, meaning that the frequency of any strategy lies inside the closed interval zero to one at all times. Thus, we elaborate on which of the twelve types of games are capable of showing meaningful physical solutions and for which of the two types of replicator equation. Subsequently, we introduce the concept of the weight of fitness deviation that is the scaling factor in a positive affine transformation connecting two payoff matrices such that the corresponding one-shot games have exactly same Nash equilibria and evolutionary stable states. The weight also quantifies how much the excess of fitness of a strategy over the average fitness of the population affects the per capita change in the frequency of the strategy. Intriguingly, the weight's variation is capable of making the Nash equilibria and the evolutionary stable states, useless by introducing strict physical chaos in the replicator dynamics based on the normal-form game.

  15. Weight of fitness deviation governs strict physical chaos in replicator dynamics.

    Science.gov (United States)

    Pandit, Varun; Mukhopadhyay, Archan; Chakraborty, Sagar

    2018-03-01

    Replicator equation-a paradigm equation in evolutionary game dynamics-mathematizes the frequency dependent selection of competing strategies vying to enhance their fitness (quantified by the average payoffs) with respect to the average fitnesses of the evolving population under consideration. In this paper, we deal with two discrete versions of the replicator equation employed to study evolution in a population where any two players' interaction is modelled by a two-strategy symmetric normal-form game. There are twelve distinct classes of such games, each typified by a particular ordinal relationship among the elements of the corresponding payoff matrix. Here, we find the sufficient conditions for the existence of asymptotic solutions of the replicator equations such that the solutions-fixed points, periodic orbits, and chaotic trajectories-are all strictly physical, meaning that the frequency of any strategy lies inside the closed interval zero to one at all times. Thus, we elaborate on which of the twelve types of games are capable of showing meaningful physical solutions and for which of the two types of replicator equation. Subsequently, we introduce the concept of the weight of fitness deviation that is the scaling factor in a positive affine transformation connecting two payoff matrices such that the corresponding one-shot games have exactly same Nash equilibria and evolutionary stable states. The weight also quantifies how much the excess of fitness of a strategy over the average fitness of the population affects the per capita change in the frequency of the strategy. Intriguingly, the weight's variation is capable of making the Nash equilibria and the evolutionary stable states, useless by introducing strict physical chaos in the replicator dynamics based on the normal-form game.

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

    Science.gov (United States)

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

    2015-01-01

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

  17. Proposed catalog of the neuroanatomy and the stratified anatomy for the 361 acupuncture points of 14 channels.

    Science.gov (United States)

    Chapple, Will

    2013-10-01

    In spite of the extensive research on acupuncture mechanisms, no comprehensive and systematic peer-reviewed reference list of the stratified anatomical and the neuroanatomical features of all 361 acupuncture points exists. This study creates a reference list of the neuroanatomy and the stratified anatomy for each of the 361 acupuncture points on the 14 classical channels and for 34 extra points. Each acupuncture point was individually assessed to relate the point's location to anatomical and neuroanatomical features. The design of the catalogue is intended to be useful for any style of acupuncture or Oriental medicine treatment modality. The stratified anatomy was divided into shallow, intermediate and deep insertion. A separate stratified anatomy was presented for different needle angles and directions. The following are identified for each point: additional specifications for point location, the stratified anatomy, motor innervation, cutaneous nerve and sensory innervation, dermatomes, Langer's lines, and somatotopic organization in the primary sensory and motor cortices. Acupuncture points for each muscle, dermatome and myotome are also reported. This reference list can aid clinicians, practitioners and researchers in furthering the understanding and accurate practice of acupuncture. Additional research on the anatomical variability around acupuncture points, the frequency of needle contact with an anatomical structure in a clinical setting, and conformational imaging should be done to verify this catalogue. Copyright © 2013. Published by Elsevier B.V.

  18. A Case Study of Offshore Advection of Boundary Layer Rolls over a Stably Stratified Sea Surface

    DEFF Research Database (Denmark)

    Svensson, Nina; Sahlée, Erik; Bergström, Hans

    2017-01-01

    originate from boundary layer rolls generated over the convective air above Swedish mainland, also supported by visual satellite images showing the typical signature cloud streets. The simulations indicate that the rolls are advected and maintained at least 30–80 km off the coast, in agreement...... considerably for long times and over large areas in coastal regions. Although boundary layer rolls are a well-studied feature, no previous study has presented results concerning their persistence during situations with advection to a strongly stratified boundary layer. Such conditions are commonly encountered...

  19. Bayesian stratified sampling to assess corpus utility

    Energy Technology Data Exchange (ETDEWEB)

    Hochberg, J.; Scovel, C.; Thomas, T.; Hall, S.

    1998-12-01

    This paper describes a method for asking statistical questions about a large text corpus. The authors exemplify the method by addressing the question, ``What percentage of Federal Register documents are real documents, of possible interest to a text researcher or analyst?`` They estimate an answer to this question by evaluating 200 documents selected from a corpus of 45,820 Federal Register documents. Bayesian analysis and stratified sampling are used to reduce the sampling uncertainty of the estimate from over 3,100 documents to fewer than 1,000. A possible application of the method is to establish baseline statistics used to estimate recall rates for information retrieval systems.

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

    Science.gov (United States)

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

    2017-01-05

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