WorldWideScience

Sample records for split-plot design replicated

  1. Split-plot designs for multistage experimentation

    DEFF Research Database (Denmark)

    Kulahci, Murat; Tyssedal, John

    2016-01-01

    Most of today’s complex systems and processes involve several stages through which input or the raw material has to go before the final product is obtained. Also in many cases factors at different stages interact. Therefore, a holistic approach for experimentation that considers all stages...... on the Kronecker product representation of orthogonal designs and can be used for any number of stages, for various numbers of subplots and for different number of subplots for each stage. The procedure is demonstrated on both regular and nonregular designs and provides the maximum number of factors that can...... be accommodated in each stage. Furthermore, split-plot designs for multistage experiments with good projective properties are also provided....

  2. Constructing General Orthogonal Fractional Factorial Split-Plot Designs

    NARCIS (Netherlands)

    Sartono, B.; Goos, P.; Schoen, E.

    2015-01-01

    While the orthogonal design of split-plot fractional factorial experiments has received much attention already, there are still major voids in the literature. First, designs with one or more factors acting at more than two levels have not yet been considered. Second, published work on nonregular

  3. Split-Plot Designs with Mirror Image Pairs as Subplots

    DEFF Research Database (Denmark)

    Tyssedal, John; Kulahci, Murat; Bisgaard, Soren

    2011-01-01

    In this article we investigate two-level split-plot designs where the sub-plots consist of only two mirror image trials. Assuming third and higher order interactions negligible, we show that these designs divide the estimated effects into two orthogonal sub-spaces, separating sub-plot main effects...... appealing with effects of major interest free from full aliasing assuming that 3rd and higher order interactions are negligible....

  4. Incomplete split-plot designs based on alpha-designs: a compromise between traditional split-plot designs and randomised complete block design

    DEFF Research Database (Denmark)

    Kristensen, Kristian

    2012-01-01

    The paper shows how the α-design (also known as generalised lattice) may be used for constructing incomplete split-plot designs and describes four different methods (A, B, C and D) of construction. Intra-block efficiency factors and theoretical considerations are used to compare the methods. Based...... of data. The three types were simulated data with known covariance structure, data from uniformity trials and data from actual trials using incomplete split-plot designs for comparing cereal varieties under different growing conditions. It is concluded that the incomplete split-plot designs may be a good...

  5. The Use of Plackett-Burman Designs to Construct Split Plot Designs.

    NARCIS (Netherlands)

    Kulahci, M.; Bisgaard, S.

    2005-01-01

    Abstract When some factors are hard to change and others are relatively easier, split-plot experiments are often an economic alternative to fully randomized designs. Split-plot experiments, with their structure of subplot arrays imbedded within whole-plot arrays, have a tendency to become large,

  6. Follow-up Designs to Resolve Confounding in Split-Plot Experiments

    DEFF Research Database (Denmark)

    Almimi, Ashraf A.; Kulahci, Murat; Montgomery, Douglas C.

    2008-01-01

    Split-plot designs are effective in industry due to time and/or cost constraints, restriction on randomization of the treatment combinations of the hard-to-change factors, and different sizes of experimental units. Some of the results of fractional factorial split-plot experiments can be ambiguous......-alias certain effects. Six rules are provided to develop foldovers for minimum aberration resolution III and resolution IV fractional factorial split-plot designs....

  7. Incomplete split-plots in designs with many entries – a compromise between split-plots and randomized complete block designs

    OpenAIRE

    Kristensen, Kristian

    2012-01-01

    The paper shows how the Alpha-design (also known as generalised lattice) may be used for constructing incomplete split-plot designs and describes 4 different methods (A, B, C and D) of construction. Intra-block efficiency factors and theoretical considerations are used to compare the methods. Based on those considerations method B was considered to be the most appropriate method for trials where tests for interaction between the two factors were important and thus this method was used and mos...

  8. Designing fractional factorial split-plot experiments using integer programming

    DEFF Research Database (Denmark)

    Capehart, Shay R.; Keha, Ahmet; Kulahci, Murat

    2011-01-01

    factorial (FF) design, with the restricted randomisation structure to account for the whole plots and subplots. We discuss the formulation of FFSP designs using integer programming (IP) to achieve various design criteria. We specifically look at the maximum number of clear two-factor interactions...

  9. Checking the Adequacy of Fit of Models from Split-Plot Designs

    DEFF Research Database (Denmark)

    Almini, A. A.; Kulahci, Murat; Montgomery, D. C.

    2009-01-01

    One of the main features that distinguish split-plot experiments from other experiments is that they involve two types of experimental errors: the whole-plot (WP) error and the subplot (SP) error. Taking this into consideration is very important when computing measures of adequacy of fit for split......-plot models. In this article, we propose the computation of two R-2, R-2-adjusted, prediction error sums of squares (PRESS), and R-2-prediction statistics to measure the adequacy of fit for the WP and the SP submodels in a split-plot design. This is complemented with the graphical analysis of the two types...... of errors to check for any violation of the underlying assumptions and the adequacy of fit of split-plot models. Using examples, we show how computing two measures of model adequacy of fit for each split-plot design model is appropriate and useful as they reveal whether the correct WP and SP effects have...

  10. The application of the split-plot design in the analysis of ...

    African Journals Online (AJOL)

    The Split-plot design model was used to analyze rabbit feeds data obtained from the Department of Agricultural Science, Federal College of Education Pankshin in order to determine whether there is significant variation in the categories of feeds given. The result shows that there was no significant effect in the different ...

  11. Classes of Split-Plot Response Surface Designs for Equivalent Estimation

    Science.gov (United States)

    Parker, Peter A.; Kowalski, Scott M.; Vining, G. Geoffrey

    2006-01-01

    When planning an experimental investigation, we are frequently faced with factors that are difficult or time consuming to manipulate, thereby making complete randomization impractical. A split-plot structure differentiates between the experimental units associated with these hard-to-change factors and others that are relatively easy-to-change and provides an efficient strategy that integrates the restrictions imposed by the experimental apparatus. Several industrial and scientific examples are presented to illustrate design considerations encountered in the restricted randomization context. In this paper, we propose classes of split-plot response designs that provide an intuitive and natural extension from the completely randomized context. For these designs, the ordinary least squares estimates of the model are equivalent to the generalized least squares estimates. This property provides best linear unbiased estimators and simplifies model estimation. The design conditions that allow for equivalent estimation are presented enabling design construction strategies to transform completely randomized Box-Behnken, equiradial, and small composite designs into a split-plot structure.

  12. Estimation of Missing Observations in Two-Level Split-Plot Designs

    DEFF Research Database (Denmark)

    Almimi, Ashraf A.; Kulahci, Murat; Montgomery, Douglas C.

    2008-01-01

    Inserting estimates for the missing observations from split-plot designs restores their balanced or orthogonal structure and alleviates the difficulties in the statistical analysis. In this article, we extend a method due to Draper and Stoneman to estimate the missing observations from unreplicated...... to the number of the missing observations. These estimates are inserted into the design table and the estimates for the remaining effects (or alias chains of effects as the case with FFSP designs) are plotted on two half-normal plots: one for the whole-plot effects and the other for the subplot effects...

  13. Analysis of a Split-Plot Experimental Design Applied to a Low-Speed Wind Tunnel Investigation

    Science.gov (United States)

    Erickson, Gary E.

    2013-01-01

    A procedure to analyze a split-plot experimental design featuring two input factors, two levels of randomization, and two error structures in a low-speed wind tunnel investigation of a small-scale model of a fighter airplane configuration is described in this report. Standard commercially-available statistical software was used to analyze the test results obtained in a randomization-restricted environment often encountered in wind tunnel testing. The input factors were differential horizontal stabilizer incidence and the angle of attack. The response variables were the aerodynamic coefficients of lift, drag, and pitching moment. Using split-plot terminology, the whole plot, or difficult-to-change, factor was the differential horizontal stabilizer incidence, and the subplot, or easy-to-change, factor was the angle of attack. The whole plot and subplot factors were both tested at three levels. Degrees of freedom for the whole plot error were provided by replication in the form of three blocks, or replicates, which were intended to simulate three consecutive days of wind tunnel facility operation. The analysis was conducted in three stages, which yielded the estimated mean squares, multiple regression function coefficients, and corresponding tests of significance for all individual terms at the whole plot and subplot levels for the three aerodynamic response variables. The estimated regression functions included main effects and two-factor interaction for the lift coefficient, main effects, two-factor interaction, and quadratic effects for the drag coefficient, and only main effects for the pitching moment coefficient.

  14. Mixed-strain housing for female C57BL/6, DBA/2, and BALB/c mice: validating a split-plot design that promotes refinement and reduction.

    Science.gov (United States)

    Walker, Michael; Fureix, Carole; Palme, Rupert; Newman, Jonathan A; Ahloy Dallaire, Jamie; Mason, Georgia

    2016-01-27

    enhanced statistical power of split-plot designs, allowing many fewer animals to be used. More powerful designs can also increase the chances of replicable findings, and increase the ability of small-scale studies to yield significant results. Using mixed-strain housing for female C57BL/6, DBA/2 and BALB/c mice is therefore an effective, efficient way to promote both refinement and the reduction of animal-use in research.

  15. Mixed-strain housing for female C57BL/6, DBA/2, and BALB/c mice: validating a split-plot design that promotes refinement and reduction

    Directory of Open Access Journals (Sweden)

    Michael Walker

    2016-01-01

    for research mice. Furthermore, it dramatically illustrates the enhanced statistical power of split-plot designs, allowing many fewer animals to be used. More powerful designs can also increase the chances of replicable findings, and increase the ability of small-scale studies to yield significant results. Using mixed-strain housing for female C57BL/6, DBA/2 and BALB/c mice is therefore an effective, efficient way to promote both refinement and the reduction of animal-use in research.

  16. Split-plot Experiments with Unusual Numbers of Subplot Runs

    DEFF Research Database (Denmark)

    Kulahci, Murat

    2007-01-01

    In many experimental situations, it may not be feasible or even possible to run experiments in a completely randomized fashion as usually recommended. Under these circumstances, split-plot experiments in which certain factors are changed less frequently than the others are often used. Most...... of the literature on split-plot designs is based on 2-level factorials. For those designs, the number of subplots is a power of 2. There may however be some situations where for cost purposes or physical constraints, we may need to have unusual number of subplots such as 3, 5, 6, etc. In this article, we explore...

  17. Trellis plots as visual aids for analyzing split plot experiments

    DEFF Research Database (Denmark)

    Kulahci, Murat; Menon, Anil

    2017-01-01

    The analysis of split plot experiments can be challenging due to a complicated error structure resulting from restrictions on complete randomization. Similarly, standard visualization methods do not provide the insight practitioners desire to understand the data, think of explanations, generate h...

  18. Relative Efficiency of Split-plot Design (SPD) to Randomized ...

    African Journals Online (AJOL)

    PROF. O. E. OSUAGWU

    2013-06-01

    Datafield .... abn. −. −. −. +. −. = −. The correction factor is given as: ( )(. ) (. )( ) 1. 2. 1. 2. 1. 3. 3. 1. F. F m. F. F. +. +. = +. + where ,m is the correction factor; F1 = d.f of mean square error for SPD; F2 = d.f of mean square error for ...

  19. A study of split plot design in balanced in complete blocks

    OpenAIRE

    Iemma, A.F.; Campos, H.

    1982-01-01

    Com o objetivo de ampliar o uso dos ensaios com parcelas subdivididas na pesquisa agropecuária, realizou-se um estudo de tais ensaios delineados em blocos incompletos balanceados. Adotou-se, para tanto, o modelo tradicionalmente usado no delineamento completo. Optou-se pela existência de correlação constante entre subparcelas distintas. A obtenção das estimativas para efeitos de blocos ocorreu como nos ensaios em blocos incompletos balanceados, enquanto que as estimativas para efeitos de trat...

  20. Estimation of the Box Correction for Degrees of Freedom from Sample Data in Randomized Block and Split-Plot Designs

    Science.gov (United States)

    Huynh, Huynh; Feldt, Leonard S.

    1976-01-01

    When the variance assumptions of a repeated measures ANOVA are not met, the F distribution of the mean square ratio should be adjusted by the sample estimate of the Box correction factor. An alternative is proposed which is shown by Monte Carlo methods to be less biased for a moderately large factor. (RC)

  1. 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.

  2. Replication protocol analysis: a method for the study of real-world design thinking

    DEFF Research Database (Denmark)

    Galle, Per; Kovacs, L. B.

    1996-01-01

    ’ is refined into a method called ‘replication protocol analysis’ (RPA), and discussed from a methodological perspective of design research. It is argued that for the study of real-world design thinking this method offers distinct advantages over traditional ‘design protocol analysis’, which seeks to capture......Given the brief of an architectural competition on site planning, and the design awarded the first prize, the first author (trained as an architect but not a participant in the competition) produced a line of reasoning that might have led from brief to design. In the paper, such ‘design replication...... the designer’s authentic line of reasoning. To illustrate how RPA can be used, the site planning case is briefly presented, and part of the replicated line of reasoning analysed. One result of the analysis is a glimpse of a ‘logic of design’; another is an insight which sheds new light on Darke’s classical...

  3. Replication protocol analysis: a method for the study of real-world design thinking

    DEFF Research Database (Denmark)

    Galle, Per; Kovacs, L. B.

    1996-01-01

    ’ is refined into a method called ‘replication protocol analysis’ (RPA), and discussed from a methodological perspective of design research. It is argued that for the study of real-world design thinking this method offers distinct advantages over traditional ‘design protocol analysis’, which seeks to capture...

  4. Fertilizer Response Curves for Commercial Southern Forest Species Defined with an Un-Replicated Experimental Design.

    Energy Technology Data Exchange (ETDEWEB)

    Coleman, Mark; Aubrey, Doug; Coyle, David, R.; Daniels, Richard, F.

    2005-11-01

    There has been recent interest in use of non-replicated regression experimental designs in forestry, as the need for replication in experimental design is burdensome on limited research budgets. We wanted to determine the interacting effects of soil moisture and nutrient availability on the production of various southeastern forest trees (two clones of Populus deltoides, open pollinated Platanus occidentalis, Liquidambar styraciflua and Pinus taeda). Additionally, we required an understanding of the fertilizer response curve. To accomplish both objectives we developed a composite design that includes a core ANOVA approach to consider treatment interactions, with the addition of non-replicated regression plots receiving a range of fertilizer levels for the primary irrigation treatment.

  5. Comparative analysis between intergradient and interblock in randomized complete block design with replication

    OpenAIRE

    Mubarak, Fadhlul

    2015-01-01

    Interblock and intergradient analyses obtaining alternative for mean square error in complex design likes factorial randomized complete blocks design with replication. The best analysis between interblok and intergradient analyses with using relative eficience. Relative eficience intergradient and interblock analyses within untractor???s line are 0.79 and 0.25, so intergradient and interblock analyses more anova for this case. Relative eficience intergradient and interblock ana...

  6. Image design and replication for image-plane disk-type multiplex holograms

    Science.gov (United States)

    Chen, Chih-Hung; Cheng, Yih-Shyang

    2017-09-01

    The fabrication methods and parameter design for both real-image generation and virtual-image display in image-plane disk-type multiplex holography are introduced in this paper. A theoretical model of a disk-type hologram is also presented and is then used in our two-step holographic processes, including the production of a non-image-plane master hologram and optical replication using a single-beam copying system for the production of duplicated holograms. Experimental results are also presented to verify the possibility of mass production using the one-shot holographic display technology described in this study.

  7. Analysis of Wind Tunnel Polar Replicates Using the Modern Design of Experiments

    Science.gov (United States)

    Deloach, Richard; Micol, John R.

    2010-01-01

    The role of variance in a Modern Design of Experiments analysis of wind tunnel data is reviewed, with distinctions made between explained and unexplained variance. The partitioning of unexplained variance into systematic and random components is illustrated, with examples of the elusive systematic component provided for various types of real-world tests. The importance of detecting and defending against systematic unexplained variance in wind tunnel testing is discussed, and the random and systematic components of unexplained variance are examined for a representative wind tunnel data set acquired in a test in which a missile is used as a test article. The adverse impact of correlated (non-independent) experimental errors is described, and recommendations are offered for replication strategies that facilitate the quantification of random and systematic unexplained variance.

  8. Teaching the Mixed Model Design: A Flowchart to Facilitate Understanding.

    Science.gov (United States)

    Mills, Jamie D.

    2005-01-01

    The Mixed Model (MM) design, sometimes known as a Split-Plot design, is very popular in educational research. This model can be used to examine the effects of several independent variables on a dependent variable and it offers a more powerful alternative to the completely randomized design. The MM design considers both a between-subjects factor,…

  9. Evaluation of some properties of individual bioequivalence (IBE) from replicate-design studies.

    Science.gov (United States)

    Tothfalusi, L; Endrenyi, L

    2001-04-01

    One of the claimed benefits of the individual bioequivalence (IBE) approach has been that the aggregate regulatory model rewards a test formulation when it has a within-subject variation smaller than the reference product. Hauck et al. [1996] demonstrated that, in the absence of random variations, this property of IBE was due to the tradeoff between the difference of the means and the deviation between the intrasubject variances of the two formulations. The tradeoff was a consequence of the aggregate regulatory model. However, calculations of Endrenyi and Hao [1998] showed that, in the presence of random variations, not only rewards but also penalties can arise due to chance alone. A data set of 55 investigations made public by the FDA in 1999 and containing replicate crossover designs was analyzed. Two parameters, AUC and Cmax, were determined in each investigation. The analyses of the FDA data indicate that: rewards and penalties occur at similar frequencies, large rewards and penalties are recorded quite often, and the aggregate IBE model is rather insensitive to the difference between the estimated means and is compatible with the frequent occurrence of large deviations. Rewards and penalties, apparently arising from random variations, can affect regulatory decisions on the acceptance of IBE and can lead to incorrect conclusions.

  10. Professional Development to Increase Teacher Behavior-Specific Praise: A Single-Case Design Replication

    Science.gov (United States)

    Gage, Nicholas A.; Grasley-Boy, Nicolette M.; MacSuga-Gage, Ashley S.

    2018-01-01

    Effective classroom instruction is contingent upon successful classroom management. Unfortunately, not all teachers successfully manage classroom behavior and need in-service professional development. In this study, we replicated a targeted professional development approach that included a brief one-on-one training session and emailed visual…

  11. Designing simulation experiments with controllable and uncontrollable factors for applications in healthcare

    DEFF Research Database (Denmark)

    Dehlendorff, Christian; Kulahci, Murat; Andersen, Klaus Kaae

    2011-01-01

    We propose a new methodology for designing computer experiments that was inspired by the split-plot designs that are often used in physical experimentation.The methodology has been developed for a simulation model of a surgical unit in a Danish hospital.We classify the factors as controllable and...

  12. 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...... increased DNA replication stress....

  13. A limited sampling approach in bioequivalence studies: application to long half-life drugs and replicate design studies.

    Science.gov (United States)

    Mahmood, I; Mahayni, H

    1999-06-01

    The objectives of this study was to develop a limited sampling model (LSM) to predict the area under the curve (AUC) and the maximum plasma concentration (Cmax) for the assessment of bioequivalence studies. Two drugs (A and B) were selected for this purpose. Drug A was chosen to test bioequivalence of two formulations with a long half-life (> 35 hours), whereas drug B was chosen to test the bioequivalence of two formulations (half-life = 12 hrs) with a replicate design study. The LSM for both drugs was developed using 5 blood samples each from 15 healthy subjects. The relationship between plasma concentration (independent variable) at selected time points with the AUC or Cmax (dependent variable) was evaluated by multiple linear regression analysis. The multiple linear regression which gave the best correlation coefficient (r) for 5 sampling time vs AUC or Cmax was chosen as the LSM. The predicted AUC and Cmax from the LSM were then used to assess bioequivalence of two different formulations of each drug following a single oral dose. The model provided good estimates of both AUC and Cmax for both drugs. The 90% confidence intervals on log-transformed observed and predicted AUC and Cmax were comparable for both drugs. The method described here may be used to estimate AUC and Cmax for bioequivalence studies for drugs with long half-lives or for highly variable drugs which may require replicate design studies without detailed blood sampling.

  14. VIRUS-P: A Powerful Integral Field Spectrograph Designed For Replication

    Science.gov (United States)

    Hill, Gary J.; MacQueen, P. J.; Adams, J.; Tufts, J.; Blanc, G.; Smith, M. P.; Roth, M. M.; Kelz, A.; Segura, P.; Gebhardt, K.; Good, J.; Drory, N.

    2007-12-01

    The Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) will outfit the 10 m HET with a new wide field and an array of 145 integral-field spectrographs to survey a 400 sq. degree area in the north galactic cap. Each fiber-coupled unit spectrograph will cover 350-590 nm, simultaneously at 5 A resolution, providing 40,000 spectra per exposure. This instrument, called VIRUS, will open up surveys of the emission-line universe for the first time, and in particular will be used to detect 1 million Lyman-alpha emitting (LAE) galaxies with 1.9 powerful instrument in its own right. Used on the McDonald 2.7 m Smith reflector, it covers the largest area of any integral field spectrograph, and has coverage down to 340 nm. It is currently in use for a pilot survey to better measure the properties of LAE galaxies in support of HETDEX, among other investigations where it is uniquely powerful. We report details of the VIRUS-P design and its performance. VIRUS-P has been made possible by a generous donation from the Cynthia and George Mitchell Foundation. This work is supported by Texas Advanced Research Program Grant No. 003658-0005-2006

  15. 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

  16. Database Replication

    Directory of Open Access Journals (Sweden)

    Marius Cristian MAZILU

    2010-12-01

    Full Text Available For someone who has worked in an environment in which the same database is used for data entry and reporting, or perhaps managed a single database server that was utilized by too many users, the advantages brought by data replication are clear. The main purpose of this paper is to emphasize those advantages as well as presenting the different types of Database Replication and the cases in which their use is recommended.

  17. Implications of “too good to be true” for replication, theoretical claims, and experimental design: An example using prominent studies of racial bias

    Directory of Open Access Journals (Sweden)

    Greg Francis

    2016-09-01

    Full Text Available In response to concerns about the validity of empirical findings in psychology, some scientists use replication studies as a way to validate good science and to identify poor science. Such efforts are resource intensive and are sometimes controversial (with accusations of researcher incompetence when a replication fails to show a previous result. An alternative approach is to examine the statistical properties of the reported literature to identify some cases of poor science. This review discusses some details of this process for prominent findings about racial bias, where a set of studies seems too good to be true. This kind of analysis is based on the original studies, so it avoids criticism from the original authors about the validity of replication studies. The analysis is also much easier to perform than a new empirical study. A variation of the analysis can also be used to explore whether it makes sense to run a replication study. As demonstrated here, there are situations where the existing data suggest that a direct replication of a set of studies is not worth the effort. Such a conclusion should motivate scientists to generate alternative experimental designs that better test theoretical ideas.

  18. 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...

  19. CENTRIOLE REPLICATION

    Science.gov (United States)

    Mizukami, Ikuko; Gall, Joseph

    1966-01-01

    Sperm formation was studied in the fern, Marsilea, and the cycad, Zamia, with particular emphasis on the centrioles. In Marsilea, the mature sperm possesses over 100 flagella, the basal bodies of which have the typical cylindrical structure of centrioles. Earlier observations by light microscopy suggested that these centrioles arise by fragmentation of a body known as the blepharoplast. In the youngest spermatids the blepharoplast is a hollow sphere approximately 0.8 µ in diameter. Its wall consists of closely packed immature centrioles, or procentrioles. The procentrioles are short cylinders which progressively lengthen during differentiation of the spermatid. At the same time they migrate to the surface of the cell, where each of them puts out a flagellum. A blepharoplast is found at each pole of the spindle during the last antheridial mitosis, and two blepharoplasts are found in the cytoplasm before this mitosis. Blepharoplasts are also found in the preceding cell generation, but their ultimate origin is obscure. Before the last mitosis the blepharoplasts are solid, consisting of a cluster of radially arranged tubules which bear some structural similarity to centrioles. In Zamia, similar stages are found during sperm formation, although here the number of flagella on each sperm is close to 20,000 and the blepharoplast measures about 10 µ in diameter. These observations are discussed in relation to theories of centriole replication. PMID:5950730

  20. Bioequivalence evaluation of two brands of amoxicillin/clavulanic acid 250/125 mg combination tablets in healthy human volunteers: use of replicate design approach.

    Science.gov (United States)

    Idkaidek, Nasir M; Al-Ghazawi, Ahmad; Najib, Naji M

    2004-12-01

    The purpose of this study was to apply a replicate design approach to a bioequivalence study of amoxicillin/clavulanic acid combination following a 250/125 mg oral dose to 23 subjects, and to compare the analysis of individual bioequivalence with average bioequivalence. This was conducted as a 2-treatment 2-sequence 4-period crossover study. Average bioequivalence was shown, while the results from the individual bioequivalence approach had no success in showing bioequivalence. In conclusion, the individual bioequivalence approach is a strong statistical tool to test for intra-subject variances and also subject-by-formulation interaction variance compared with the average bioequivalence approach. copyright (c) 2004 John Wiley & Sons, Ltd.

  1. ROUTE PLAN DESIGNER FOR TRACTOR GUIDANCE SYSTEMS

    DEFF Research Database (Denmark)

    Sveistrup, Daniel; Jørgensen, Rasmus Nyholm; Green, Ole

    2010-01-01

    in their file formats and operationalrequirements, thereby creating an unnecessary burden for the field trial managers and researchersoperating on different computational platforms such as Windows, Mac or Linux.This paper demonstrates a methodological proof of concept for a software solution for assisting...... the benefits of the software. 1- a modified fullscalerandomized split-plot design of 840 parcels and 15 treatment combinations. 2 - a maize fieldsetup ensuring a prototype crop-weed detection camera to experience as many crops, weed and soilcolor conditions as possible. For both cases, after the overall layout...

  2. 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.

  3. Superior control of HIV-1 replication by CD8+ T cells targeting conserved epitopes: implications for HIV vaccine design.

    Directory of Open Access Journals (Sweden)

    Pratima Kunwar

    Full Text Available A successful HIV vaccine will likely induce both humoral and cell-mediated immunity, however, the enormous diversity of HIV has hampered the development of a vaccine that effectively elicits both arms of the adaptive immune response. To tackle the problem of viral diversity, T cell-based vaccine approaches have focused on two main strategies (i increasing the breadth of vaccine-induced responses or (ii increasing vaccine-induced responses targeting only conserved regions of the virus. The relative extent to which set-point viremia is impacted by epitope-conservation of CD8(+ T cell responses elicited during early HIV-infection is unknown but has important implications for vaccine design. To address this question, we comprehensively mapped HIV-1 CD8(+ T cell epitope-specificities in 23 ART-naïve individuals during early infection and computed their conservation score (CS by three different methods (prevalence, entropy and conseq on clade-B and group-M sequence alignments. The majority of CD8(+ T cell responses were directed against variable epitopes (p<0.01. Interestingly, increasing breadth of CD8(+ T cell responses specifically recognizing conserved epitopes was associated with lower set-point viremia (r = - 0.65, p = 0.009. Moreover, subjects possessing CD8(+ T cells recognizing at least one conserved epitope had 1.4 log10 lower set-point viremia compared to those recognizing only variable epitopes (p = 0.021. The association between viral control and the breadth of conserved CD8(+ T cell responses may be influenced by the method of CS definition and sequences used to determine conservation levels. Strikingly, targeting variable versus conserved epitopes was independent of HLA type (p = 0.215. The associations with viral control were independent of functional avidity of CD8(+ T cell responses elicited during early infection. Taken together, these data suggest that the next-generation of T-cell based HIV-1 vaccines should focus

  4. Artificial Warming of Arctic Meadow under Pollution Stress: Experimental design

    Science.gov (United States)

    Moni, Christophe; Silvennoinen, Hanna; Fjelldal, Erling; Brenden, Marius; Kimball, Bruce; Rasse, Daniel

    2014-05-01

    Boreal and arctic terrestrial ecosystems are central to the climate change debate, notably because future warming is expected to be disproportionate as compared to world averages. Likewise, greenhouse gas (GHG) release from terrestrial ecosystems exposed to climate warming is expected to be the largest in the arctic. Artic agriculture, in the form of cultivated grasslands, is a unique and economically relevant feature of Northern Norway (e.g. Finnmark Province). In Eastern Finnmark, these agro-ecosystems are under the additional stressor of heavy metal and sulfur pollution generated by metal smelters of NW Russia. Warming and its interaction with heavy metal dynamics will influence meadow productivity, species composition and GHG emissions, as mediated by responses of soil microbial communities. Adaptation and mitigation measurements will be needed. Biochar application, which immobilizes heavy metal, is a promising adaptation method to promote positive growth response in arctic meadows exposed to a warming climate. In the MeadoWarm project we conduct an ecosystem warming experiment combined to biochar adaptation treatments in the heavy-metal polluted meadows of Eastern Finnmark. In summary, the general objective of this study is twofold: 1) to determine the response of arctic agricultural ecosystems under environmental stress to increased temperatures, both in terms of plant growth, soil organisms and GHG emissions, and 2) to determine if biochar application can serve as a positive adaptation (plant growth) and mitigation (GHG emission) strategy for these ecosystems under warming conditions. Here, we present the experimental site and the designed open-field warming facility. The selected site is an arctic meadow located at the Svanhovd Research station less than 10km west from the Russian mining city of Nikel. A splitplot design with 5 replicates for each treatment is used to test the effect of biochar amendment and a 3oC warming on the Arctic meadow. Ten circular

  5. A comparison of the intrasubject variation in drug exposure between generic and brand-name drugs: a retrospective analysis of replicate design trials.

    Science.gov (United States)

    Yu, Yang; Teerenstra, Steven; Neef, Cees; Burger, David; Maliepaard, Marc

    2016-04-01

    The aim of the present study was to investigate whether differences in total and peak drug exposure upon generic substitution are due to differences between formulations or to intrasubject pharmacokinetic variability of the active substance. The study was designed as a retrospective reanalysis of existing studies. Nine replicate design bioequivalence studies representing six drug classes - i.e. for alendronate, atorvastatin, cyclosporin, ebastine, exemestane, mycophenolate mofetil, and ropinirole - were retrieved from the Dutch Medicines Regulatory Authority. In most studies, the intrasubject variability in total and peak drug exposure was comparable for the brand-name [in the range 0.01-0.24 for area under the concentration-time curve (AUCt ) and 0.02-0.29 for peak plasma concentration (Cmax ) on a log scale] and generic (0.01-0.23 for AUCt and 0.08-0.33 for Cmax ) drugs, and was comparable with the intrasubject variability upon switching between those drugs (0.01-0.23 for AUCt and 0.06-0.33 for Cmax ). The variance related to subject-by-formulation interaction could be considered negligible (-0.069 to 0.047 for AUCt and -0.091 to 0.02 for Cmax ). In the investigated studies, the variation in total and peak exposure seen when a patient is switched from a brand-name to a generic drug is comparable with that seen following repeated administration of the brand-name drug in the patient. Only the intrasubject variability seems to play a crucial and decisive role in the variation in drug exposure seen; no additional formulation-dependent variation in exposure is observed upon switching. Thus, our data support that, for the medicines that were included in the present investigation, from a clinical pharmacological perspective, the benefit-risk balance of a generic drug is comparable with that of the brand-name drug. © 2015 The British Pharmacological Society.

  6. EAT-UP™ Family-Centered Feeding Intervention to Promote Food Acceptance and Decrease Challenging Behaviors: A Single-Case Experimental Design Replicated across Three Families of Children with Autism Spectrum Disorder

    Science.gov (United States)

    Cosbey, Joanna; Muldoon, Deirdre

    2017-01-01

    This study evaluated the effectiveness of a family-centered feeding intervention, Easing Anxiety Together with Understanding and Perseverance (EAT-UP™), for promoting food acceptance of children with autism spectrum disorder at home. A concurrent multiple-baseline design was used with systematic replication across three families. Baseline was…

  7. Design of a factorial experiment with randomization restrictions to assess medical device performance on vascular tissue.

    Science.gov (United States)

    Diestelkamp, Wiebke S; Krane, Carissa M; Pinnell, Margaret F

    2011-05-20

    Energy-based surgical scalpels are designed to efficiently transect and seal blood vessels using thermal energy to promote protein denaturation and coagulation. Assessment and design improvement of ultrasonic scalpel performance relies on both in vivo and ex vivo testing. The objective of this work was to design and implement a robust, experimental test matrix with randomization restrictions and predictive statistical power, which allowed for identification of those experimental variables that may affect the quality of the seal obtained ex vivo. The design of the experiment included three factors: temperature (two levels); the type of solution used to perfuse the artery during transection (three types); and artery type (two types) resulting in a total of twelve possible treatment combinations. Burst pressures of porcine carotid and renal arteries sealed ex vivo were assigned as the response variable. The experimental test matrix was designed and carried out as a split-plot experiment in order to assess the contributions of several variables and their interactions while accounting for randomization restrictions present in the experimental setup. The statistical software package SAS was utilized and PROC MIXED was used to account for the randomization restrictions in the split-plot design. The combination of temperature, solution, and vessel type had a statistically significant impact on seal quality. The design and implementation of a split-plot experimental test-matrix provided a mechanism for addressing the existing technical randomization restrictions of ex vivo ultrasonic scalpel performance testing, while preserving the ability to examine the potential effects of independent factors or variables. This method for generating the experimental design and the statistical analyses of the resulting data are adaptable to a wide variety of experimental problems involving large-scale tissue-based studies of medical or experimental device efficacy and performance.

  8. 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...... 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....

  9. A flexible genome-wide bootstrap method that accounts for ranking and threshold-selection bias in GWAS interpretation and replication study design.

    Science.gov (United States)

    Faye, Laura L; Sun, Lei; Dimitromanolakis, Apostolos; Bull, Shelley B

    2011-07-10

    The phenomenon known as the winner's curse is a form of selection bias that affects estimates of genetic association. In genome-wide association studies (GWAS) the bias is exacerbated by the use of stringent selection thresholds and ranking over hundreds of thousands of single nucleotide polymorphisms (SNPs). We develop an improved multi-locus bootstrap point estimate and confidence interval, which accounts for both ranking- and threshold-selection bias in the presence of genome-wide SNP linkage disequilibrium structure. The bootstrap method easily adapts to various study designs and alternative test statistics as well as complex SNP selection criteria. The latter is demonstrated by our application to the Wellcome Trust Case Control Consortium findings, in which the selection criterion was the minimum of the p-values for the additive and genotypic genetic effect models. In contrast, existing likelihood-based bias-reduced estimators account for the selection criterion applied to an SNP as if it were the only one tested, and so are more simple computationally, but do not address ranking across SNPs. Our simulation studies show that the bootstrap bias-reduced estimates are usually closer to the true genetic effect than the likelihood estimates and are less variable with a narrower confidence interval. Replication study sample size requirements computed from the bootstrap bias-reduced estimates are adequate 75-90 per cent of the time compared to 53-60 per cent of the time for the likelihood method. The bootstrap methods are implemented in a user-friendly package able to provide point and interval estimation for both binary and quantitative phenotypes in large-scale GWAS. Copyright © 2011 John Wiley & Sons, Ltd.

  10. A comparison of the intrasubject variation in drug exposure between generic and brand‐name drugs: a retrospective analysis of replicate design trials

    Science.gov (United States)

    Teerenstra, Steven; Neef, Cees; Burger, David; Maliepaard, Marc

    2016-01-01

    AIMS The aim of the present study was to investigate whether differences in total and peak drug exposure upon generic substitution are due to differences between formulations or to intrasubject pharmacokinetic variability of the active substance. Methods The study was designed as a retrospective reanalysis of existing studies. Nine replicate design bioequivalence studies representing six drug classes – i.e. for alendronate, atorvastatin, cyclosporin, ebastine, exemestane, mycophenolate mofetil, and ropinirole – were retrieved from the Dutch Medicines Regulatory Authority. Results In most studies, the intrasubject variability in total and peak drug exposure was comparable for the brand‐name [in the range 0.01–0.24 for area under the concentration–time curve (AUCt) and 0.02–0.29 for peak plasma concentration (Cmax) on a log scale] and generic (0.01–0.23 for AUCt and 0.08–0.33 for Cmax) drugs, and was comparable with the intrasubject variability upon switching between those drugs (0.01–0.23 for AUCt and 0.06–0.33 for Cmax). The variance related to subject‐by‐formulation interaction could be considered negligible (–0.069 to 0.047 for AUCt and –0.091 to 0.02 for Cmax). Conclusion In the investigated studies, the variation in total and peak exposure seen when a patient is switched from a brand‐name to a generic drug is comparable with that seen following repeated administration of the brand‐name drug in the patient. Only the intrasubject variability seems to play a crucial and decisive role in the variation in drug exposure seen; no additional formulation‐dependent variation in exposure is observed upon switching. Thus, our data support that, for the medicines that were included in the present investigation, from a clinical pharmacological perspective, the benefit–risk balance of a generic drug is comparable with that of the brand‐name drug. PMID:26574160

  11. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  12. Effects of drought stress and different densities on oil yield and ...

    African Journals Online (AJOL)

    For evaluation of water deficit stress and planting density effects on the oil and biological yield attributes of sunflower, an experiment was conducted in a randomized complete block design (RCBD) based split plot factorial design in three replications in the research field of Baku State University, Baku, Azerbaijan, in 2009.

  13. Nitrogen dose and plant density effects on popcorn grain yield ...

    African Journals Online (AJOL)

    and plant densities on grain yield and yield-related plant characteristics of popcorn in Hatay, located at Southern Mediterranean region of Turkey, during 2002 and 2003. The experiment was designed in a randomized complete block design with a split-plot arrangement with three replications. Nitrogen doses of 0, 120, 180 ...

  14. Interaction of micro and macro elements with manure on barley feed ...

    African Journals Online (AJOL)

    In order to study the effect of interaction of 'micro' and 'macro' elements on soil chemical properties, grain yield and feed yield in barley, an experiment was conducted as split plot design on randomized complete block design with three replications in the research field of Zabol University 2009. The different proportions of ...

  15. Effects of irrigation regimes and polymer on dry matter yield and ...

    African Journals Online (AJOL)

    The experimental design was a split-plot with two factors including four irrigation regime (providing 40, 60, 80 and 100% from consumptive (ET crop) of sorghum) as main plots and four amounts of SAP (0, 75, 150 and 225 kg ha-1) as subplots in a completely randomized block design with three replications. Irrigation level ...

  16. DNA Virus Replication Compartments

    Science.gov (United States)

    Schmid, Melanie; Speiseder, Thomas; Dobner, Thomas

    2014-01-01

    Viruses employ a variety of strategies to usurp and control cellular activities through the orchestrated recruitment of macromolecules to specific cytoplasmic or nuclear compartments. Formation of such specialized virus-induced cellular microenvironments, which have been termed viroplasms, virus factories, or virus replication centers, complexes, or compartments, depends on molecular interactions between viral and cellular factors that participate in viral genome expression and replication and are in some cases associated with sites of virion assembly. These virus-induced compartments function not only to recruit and concentrate factors required for essential steps of the viral replication cycle but also to control the cellular mechanisms of antiviral defense. In this review, we summarize characteristic features of viral replication compartments from different virus families and discuss similarities in the viral and cellular activities that are associated with their assembly and the functions they facilitate for viral replication. PMID:24257611

  17. Adenovirus DNA Replication

    Science.gov (United States)

    Hoeben, Rob C.; Uil, Taco G.

    2013-01-01

    Adenoviruses have attracted much attention as probes to study biological processes such as DNA replication, transcription, splicing, and cellular transformation. More recently these viruses have been used as gene-transfer vectors and oncolytic agents. On the other hand, adenoviruses are notorious pathogens in people with compromised immune functions. This article will briefly summarize the basic replication strategy of adenoviruses and the key proteins involved and will deal with the new developments since 2006. In addition, we will cover the development of antivirals that interfere with human adenovirus (HAdV) replication and the impact of HAdV on human disease. PMID:23388625

  18. Effects of salicylic acid on morphological and physiological ...

    African Journals Online (AJOL)

    To evaluate the effect of different levels of salicylic acid (SA) on yield and some morphological and physiological characteristics of sweet corn hybrids under water stress, this study was conducted in 2015 using split plots in the base of randomized complete block design with three replications. Treatments were included ...

  19. The effect of zinc application methods on seed cotton yield, lint and ...

    African Journals Online (AJOL)

    The effect of different zinc application methods on seed cotton yield, yield components, lint and seed quality of cotton was investigated under east Mediterranean region conditions (Kahramanmaras, Turkey) in 2008. Experimental design was split plots with three replications. The cotton varieties: Agdas-3, Agdas-17 and ...

  20. Effects of disking, bedding, and subsoiling on survival and growth of three oak species in central Mississippi

    Science.gov (United States)

    J. Paul Jeffreys; Emily B. Schultz; Thomas G. Matney; W. Cade Booth; Jason M. Morris

    2010-01-01

    A replicated split-plot design experiment to evaluate the effects of three site preparation methods (disking, bedding, and subsoiling plus bedding) on survival and growth of three oak species (cherrybark, Quercus pagoda Raf.; Shumard, Quercus shumardii Buckl.; and Nuttall, Quercus texana Buckl.) was established...

  1. Incidence des infestations du foreur de tiges Eldana saccharina ...

    African Journals Online (AJOL)

    SARAH

    30 juin 2016 ... Methodology and Results: A field experiment under sprinkler irrigation was carried out at Ferké 1 Sugar Estate over three consecutive crop cycles. The experiment was designed following a split-plot in three replications with three harvest periods as main plots (early, mid, late) and 8 cane varieties as ...

  2. Growth and yield of barley (Hordeum vulgare L.) as affected by ...

    African Journals Online (AJOL)

    Bheema

    Nitrogen (N) and phosphorus (P) fertilizers were applied under three water regimes to 'Sasa' barley variety using split - split plot design with three replications ..... (1999) on maize. Increasing the dosage of both fertilizers was not necessarily increase grain yield of the crop though significant increase was obtained over the ...

  3. Canola traits and some soil biological parameters in response to ...

    African Journals Online (AJOL)

    This study describes the effects of fertilization and tillage methods on soil microbial community and canola traits. A field experiment was carried out in 2009 to 2010 growing season. Experiments were arranged in a split plot based on randomized complete block design with three replications. Main plots consisted of no ...

  4. Moringa extracts used in sugarcane juice treatment and effects on ...

    African Journals Online (AJOL)

    The objective of this study was to evaluate the effects of sugarcane juice treatment using Moringa oleifera leaf and seeds extracts on ethanolic fermentation. The experiment was arranged in a split plot statistical design, with four replications. Main treatments were three sedimentation agents (synthetic polyelectrolyte, ...

  5. Responses of phenological and physiological stages of spring ...

    African Journals Online (AJOL)

    In order to investigate impact of complementary irrigation on phenological stages, chlorophyll content, radiation absorption and extinction coefficient, as well as some aspects concerning the yield of spring safflower, a split-plot experiment based on randomized complete block design with three replication was conducted at ...

  6. Effects of tillage, organic resources and nitrogen fertiliser on soil carbon dynamics and crop nitrogen uptake in semi-arid West Africa

    NARCIS (Netherlands)

    Ouédraogo, E.; Mando, A.; Stroosnijder, L.

    2006-01-01

    Tillage, organic resources and fertiliser effects on soil carbon (C) dynamics were investigated in 2000 and 2001 in Burkina Faso (West Africa). A split plot design with four replications was laid-out on a loamy-sand Ferric Lixisol with till and no-till as main treatments and fertiliser types as

  7. Potential of Azolla as a Nitrogenous Biofertiliser for Irrigated Rice at ...

    African Journals Online (AJOL)

    These treatments were tested on Wahiwahi (indigenous) and IR54 (improved) rice varieties in a split-plot design with 3 replications, in 18 m2 plots each of which received a basal phosphate dose of 20 Kg P ha-1 as Tripe super phospate (TSP). Rice plant height, tiller number, panicles per m2, grains per panicle, grain mass ...

  8. The effect of municipal compost application on the amount of micro ...

    African Journals Online (AJOL)

    The aim of this study was to investigate the effect of municipal compost (MC) application on micro elements concentration in soil and tissues of medicinal plant of mint. This study was carried out in a split plot based on complete randomized block design in three replications in the field of the University of Agricultural Sciences ...

  9. The effect of the interaction of varying chicken manure supplement ...

    African Journals Online (AJOL)

    user

    2011-02-14

    Feb 14, 2011 ... 10, 15, 20 and 25% using solid-state fermentation bioreactors. The results .... MATERIALS AND METHODS. Origin of materials. Coprinus cinereus (Schaeff) S. Gray s.lat and sisal decortications wastes and chicken manure. Although C. .... split-split plot design with three replicates comprised of sisal waste.

  10. Untitled

    African Journals Online (AJOL)

    Perry, were tested for the control of major insect pests of cowpea using split plot fitted into a randomised complete block design and replicated 3 times in 2000. In this, the 5 plants and 2 synthetic Insecticides. (dimethoate and deltamethrin) were tested in main plots while the rates of applications were assigned in sub plots.

  11. Effect of municipal wastewater with manure and fertilizer on yield ...

    African Journals Online (AJOL)

    The experiment was conducted in split plot design with three replications. The treatment were comprised of two ... Treatment of treated wastewater also had a significant influence on crude protein content, ash percentage and macro elements (N, P and K) contents in corn forage (P < 5%). But wastewater had no significant ...

  12. Drought stress mitigation using supplemental irrigation in rainfed ...

    African Journals Online (AJOL)

    An experiment was carried out in 2007 to investigate the effects of different irrigation regimes, and chickpea cultivars on chickpea production in the Agricultural Research Station, College of Agriculture, Islamic Azad University, Kermanshah Branch, Iran. The experimental design was split-plot with three replications.

  13. Response of cucumber ( Cucumis sativus L.) To different rates of ...

    African Journals Online (AJOL)

    The growth and yield of cucumber (Cucumus sativus L.) in response to application of goat dung and poultry dropping rates was investigated in 2010 and 2011. The experiment was laid out in randomized complete block design replicated three times in a split plot arrangement. The main plot treatment was organic manure ...

  14. Effect of tillage and poultry manure application on soil infiltration rate ...

    African Journals Online (AJOL)

    This study was carried out in Abeokuta, South-western Nigeria in 2008 and 2009 to assess the impact of tillage and poultry manure (PM) on soil infiltration rate and maize root growth. The experiment was a split-plot design with three replications. The main plot consisted of three tillage treatments: zero tillage (ZT), minimum ...

  15. Evaluation of sorghum genotypes under drought stress conditions ...

    African Journals Online (AJOL)

    Seven genotypes of sorghum (Sorghum bicolour (L.) Moench) were studied in both drought and normal conditions. In each condition, the genotypes were evaluated using a split plot based randomized complete block design with three replications. Drought tolerance indices including stability tolerance index (STI), mean ...

  16. Lower seed rates favor seed multiplication ratio with minimal impact ...

    African Journals Online (AJOL)

    Field and laboratory studies were conducted in split plot design of three replications to determine effects of four sowing rates (50, 75, 100, 125 kg ha-1) and three row spacing (10, 20, 30 cm) on seed multiplication ratio, seed yield, and seed quality of wheat at Kulumsa and Assasa from 2012 to 2014. Results indicated that ...

  17. Lower Seed Rates Favor Seed Multiplication Ratio with Minimal ...

    African Journals Online (AJOL)

    else

    Field and laboratory studies were conducted in split plot design of three replications to determine effects of four ... row space of 20 cm to accelerate early generation seed supply within the fast track variety release program in .... of a standard germination paper (400 g/m2) saturated with distilled water and placed in bowls ...

  18. Loblolly pine growth response to mid-rotational treatments in an Eastern Texas plantation

    Science.gov (United States)

    Mohammad M. Bataineh; Amanda L. Bataineh; Brian P. Oswald; Kenneth W. Farrish; Hans M. Williams

    2006-01-01

    The effects of mid-rotational treatments (herbicide, prescribed burn, combination of herbicide and burn, and fertilization) on growth of loblolly pine were evaluated. Five replicates were established in a split-plot experimental design with fertilizer treatments as the whole-plot factor and competition control treatments as the sub-plot factor. Growth response was...

  19. Use of two-part regression calibration model to correct for measurement error in episodically consumed foods in a single-replicate study design: EPIC case study.

    Science.gov (United States)

    Agogo, George O; van der Voet, Hilko; van't Veer, Pieter; Ferrari, Pietro; Leenders, Max; Muller, David C; Sánchez-Cantalejo, Emilio; Bamia, Christina; Braaten, Tonje; Knüppel, Sven; Johansson, Ingegerd; van Eeuwijk, Fred A; Boshuizen, Hendriek

    2014-01-01

    In epidemiologic studies, measurement error in dietary variables often attenuates association between dietary intake and disease occurrence. To adjust for the attenuation caused by error in dietary intake, regression calibration is commonly used. To apply regression calibration, unbiased reference measurements are required. Short-term reference measurements for foods that are not consumed daily contain excess zeroes that pose challenges in the calibration model. We adapted two-part regression calibration model, initially developed for multiple replicates of reference measurements per individual to a single-replicate setting. We showed how to handle excess zero reference measurements by two-step modeling approach, how to explore heteroscedasticity in the consumed amount with variance-mean graph, how to explore nonlinearity with the generalized additive modeling (GAM) and the empirical logit approaches, and how to select covariates in the calibration model. The performance of two-part calibration model was compared with the one-part counterpart. We used vegetable intake and mortality data from European Prospective Investigation on Cancer and Nutrition (EPIC) study. In the EPIC, reference measurements were taken with 24-hour recalls. For each of the three vegetable subgroups assessed separately, correcting for error with an appropriately specified two-part calibration model resulted in about three fold increase in the strength of association with all-cause mortality, as measured by the log hazard ratio. Further found is that the standard way of including covariates in the calibration model can lead to over fitting the two-part calibration model. Moreover, the extent of adjusting for error is influenced by the number and forms of covariates in the calibration model. For episodically consumed foods, we advise researchers to pay special attention to response distribution, nonlinearity, and covariate inclusion in specifying the calibration model.

  20. Use of two-part regression calibration model to correct for measurement error in episodically consumed foods in a single-replicate study design: EPIC case study.

    Directory of Open Access Journals (Sweden)

    George O Agogo

    Full Text Available In epidemiologic studies, measurement error in dietary variables often attenuates association between dietary intake and disease occurrence. To adjust for the attenuation caused by error in dietary intake, regression calibration is commonly used. To apply regression calibration, unbiased reference measurements are required. Short-term reference measurements for foods that are not consumed daily contain excess zeroes that pose challenges in the calibration model. We adapted two-part regression calibration model, initially developed for multiple replicates of reference measurements per individual to a single-replicate setting. We showed how to handle excess zero reference measurements by two-step modeling approach, how to explore heteroscedasticity in the consumed amount with variance-mean graph, how to explore nonlinearity with the generalized additive modeling (GAM and the empirical logit approaches, and how to select covariates in the calibration model. The performance of two-part calibration model was compared with the one-part counterpart. We used vegetable intake and mortality data from European Prospective Investigation on Cancer and Nutrition (EPIC study. In the EPIC, reference measurements were taken with 24-hour recalls. For each of the three vegetable subgroups assessed separately, correcting for error with an appropriately specified two-part calibration model resulted in about three fold increase in the strength of association with all-cause mortality, as measured by the log hazard ratio. Further found is that the standard way of including covariates in the calibration model can lead to over fitting the two-part calibration model. Moreover, the extent of adjusting for error is influenced by the number and forms of covariates in the calibration model. For episodically consumed foods, we advise researchers to pay special attention to response distribution, nonlinearity, and covariate inclusion in specifying the calibration model.

  1. Use of Two-Part Regression Calibration Model to Correct for Measurement Error in Episodically Consumed Foods in a Single-Replicate Study Design: EPIC Case Study

    Science.gov (United States)

    Agogo, George O.; van der Voet, Hilko; Veer, Pieter van’t; Ferrari, Pietro; Leenders, Max; Muller, David C.; Sánchez-Cantalejo, Emilio; Bamia, Christina; Braaten, Tonje; Knüppel, Sven; Johansson, Ingegerd; van Eeuwijk, Fred A.; Boshuizen, Hendriek

    2014-01-01

    In epidemiologic studies, measurement error in dietary variables often attenuates association between dietary intake and disease occurrence. To adjust for the attenuation caused by error in dietary intake, regression calibration is commonly used. To apply regression calibration, unbiased reference measurements are required. Short-term reference measurements for foods that are not consumed daily contain excess zeroes that pose challenges in the calibration model. We adapted two-part regression calibration model, initially developed for multiple replicates of reference measurements per individual to a single-replicate setting. We showed how to handle excess zero reference measurements by two-step modeling approach, how to explore heteroscedasticity in the consumed amount with variance-mean graph, how to explore nonlinearity with the generalized additive modeling (GAM) and the empirical logit approaches, and how to select covariates in the calibration model. The performance of two-part calibration model was compared with the one-part counterpart. We used vegetable intake and mortality data from European Prospective Investigation on Cancer and Nutrition (EPIC) study. In the EPIC, reference measurements were taken with 24-hour recalls. For each of the three vegetable subgroups assessed separately, correcting for error with an appropriately specified two-part calibration model resulted in about three fold increase in the strength of association with all-cause mortality, as measured by the log hazard ratio. Further found is that the standard way of including covariates in the calibration model can lead to over fitting the two-part calibration model. Moreover, the extent of adjusting for error is influenced by the number and forms of covariates in the calibration model. For episodically consumed foods, we advise researchers to pay special attention to response distribution, nonlinearity, and covariate inclusion in specifying the calibration model. PMID:25402487

  2. Animal Mitochondrial DNA Replication

    Science.gov (United States)

    Ciesielski, Grzegorz L.; Oliveira, Marcos T.; Kaguni, Laurie S.

    2016-01-01

    Recent advances in the field of mitochondrial DNA (mtDNA) replication highlight the diversity of both the mechanisms utilized and the structural and functional organization of the proteins at mtDNA replication fork, despite the simplicity of the animal mtDNA genome. DNA polymerase γ, mtDNA helicase and mitochondrial single-stranded DNA-binding protein- the key replisome proteins, have evolved distinct structural features and biochemical properties. These appear to be correlated with mtDNA genomic features in different metazoan taxa and with their modes of DNA replication, although a substantial integrative research is warranted to establish firmly these links. To date, several modes of mtDNA replication have been described for animals: rolling circle, theta, strand-displacement, and RITOLS/bootlace. Resolution of a continuing controversy relevant to mtDNA replication in mammals/vertebrates will have a direct impact on the mechanistic interpretation of mtDNA-related human diseases. Here we review these subjects, integrating earlier and recent data to provide a perspective on the major challenges for future research. PMID:27241933

  3. Psychology, replication & beyond.

    Science.gov (United States)

    Laws, Keith R

    2016-06-01

    Modern psychology is apparently in crisis and the prevailing view is that this partly reflects an inability to replicate past findings. If a crisis does exists, then it is some kind of 'chronic' crisis, as psychologists have been censuring themselves over replicability for decades. While the debate in psychology is not new, the lack of progress across the decades is disappointing. Recently though, we have seen a veritable surfeit of debate alongside multiple orchestrated and well-publicised replication initiatives. The spotlight is being shone on certain areas and although not everyone agrees on how we should interpret the outcomes, the debate is happening and impassioned. The issue of reproducibility occupies a central place in our whig history of psychology.

  4. Registered Replication Report

    DEFF Research Database (Denmark)

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

    2017-01-01

    In an anonymous 4-person economic game, participants contributed more money to a common project (i.e., cooperated) when required to decide quickly than when forced to delay their decision (Rand, Greene & Nowak, 2012), a pattern consistent with the social heuristics hypothesis proposed by Rand...... 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...

  5. Replication, refinement & reachability

    DEFF Research Database (Denmark)

    Debois, Søren; Hildebrandt, Thomas T.; Slaats, Tijs

    2018-01-01

    We explore the complexity of reachability and run-time refinement under safety and liveness constraints in event-based process models. Our study is framed in the DCR? process language, which supports modular specification through a compositional operational semantics. DCR? encompasses the “Dynamic...... Condition Response (DCR) graphs” declarative process model for analysis, execution and safe run-time refinement of process-aware information systems; including replication of sub-processes. We prove that event-reachability and refinement are np-hard for DCR? processes without replication...

  6. Constructing an Evidence-Base for Future CALL Design with "Engineering Power": The Need for More Basic Research and Instrumental Replication

    Science.gov (United States)

    Handley, Zöe

    2014-01-01

    This paper argues that the goal of Computer-Assisted Language Learning (CALL) research should be to construct a reliable evidence-base with "engineering power" and generality upon which the design of future CALL software and activities can be based. In order to establish such an evidence base for future CALL design, it suggests that CALL…

  7. 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.

  8. Bispidine-amino acid conjugates act as a novel scaffold for the design of antivirals that block Japanese encephalitis virus replication.

    Directory of Open Access Journals (Sweden)

    V Haridas

    Full Text Available Japanese encephalitis virus (JEV is a major cause of viral encephalitis in South and South-East Asia. Lack of antivirals and non-availability of affordable vaccines in these endemic areas are a major setback in combating JEV and other closely related viruses such as West Nile virus and dengue virus. Protein secondary structure mimetics are excellent candidates for inhibiting the protein-protein interactions and therefore serve as an attractive tool in drug development. We synthesized derivatives containing the backbone of naturally occurring lupin alkaloid, sparteine, which act as protein secondary structure mimetics and show that these compounds exhibit antiviral properties.In this study we have identified 3,7-diazabicyclo[3.3.1]nonane, commonly called bispidine, as a privileged scaffold to synthesize effective antiviral agents. We have synthesized derivatives of bispidine conjugated with amino acids and found that hydrophobic amino acid residues showed antiviral properties against JEV. We identified a tryptophan derivative, Bisp-W, which at 5 µM concentration inhibited JEV infection in neuroblastoma cells by more than 100-fold. Viral inhibition was at a stage post-entry and prior to viral protein translation possibly at viral RNA replication. We show that similar concentration of Bisp-W was capable of inhibiting viral infection of two other encephalitic viruses namely, West Nile virus and Chandipura virus.We have demonstrated that the amino-acid conjugates of 3,7-diazabicyclo[3.3.1]nonane can serve as a molecular scaffold for development of potent antivirals against encephalitic viruses. Our findings will provide a novel platform to develop effective inhibitors of JEV and perhaps other RNA viruses causing encephalitis.

  9. 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

  10. Human Mitochondrial DNA Replication

    Science.gov (United States)

    Holt, Ian J.; Reyes, Aurelio

    2012-01-01

    Elucidation of the process of DNA replication in mitochondria is in its infancy. For many years, maintenance of the mitochondrial genome was regarded as greatly simplified compared to the nucleus. Mammalian mitochondria were reported to lack all DNA repair systems, to eschew DNA recombination, and to possess but a single DNA polymerase, polymerase γ. Polγ was said to replicate mitochondrial DNA exclusively via one mechanism, involving only two priming events and a handful of proteins. In this “strand-displacement model,” leading strand DNA synthesis begins at a specific site and advances approximately two-thirds of the way around the molecule before DNA synthesis is initiated on the “lagging” strand. Although the displaced strand was long-held to be coated with protein, RNA has more recently been proposed in its place. Furthermore, mitochondrial DNA molecules with all the features of products of conventional bidirectional replication have been documented, suggesting that the process and regulation of replication in mitochondria is complex, as befits a genome that is a core factor in human health and longevity. PMID:23143808

  11. Replication studies in longevity

    DEFF Research Database (Denmark)

    Varcasia, O; Garasto, S; Rizza, T

    2001-01-01

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

  12. A comparison of the intrasubject variation in drug exposure between generic and brand-name drugs: a retrospective analysis of replicate design trials

    NARCIS (Netherlands)

    Yu, Y.; Teerenstra, S.; Neef, C.; Burger, D.M.; Maliepaard, M.

    2016-01-01

    AIMS: The aim of the present study was to investigate whether differences in total and peak drug exposure upon generic substitution are due to differences between formulations or to intrasubject pharmacokinetic variability of the active substance. METHODS: The study was designed as a retrospective

  13. Soil Carbon Characteristics of a Fluvisol Affected by Aggregates ...

    African Journals Online (AJOL)

    The experimental design was a split-split plot arranged in a randomized complete block design, with tillage technique serving as main plot; crop regime was the split plot and NPK fertilizer as split – split plot. Tillage techniques used were conventional tillage (CT) and minimum tillage (MT) while maize and soybean were ...

  14. 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…

  15. DNA replication origins in archaea

    Directory of Open Access Journals (Sweden)

    Zhenfang eWu

    2014-04-01

    Full Text Available DNA replication initiation, which starts at specific chromosomal site (known as replication origins, is the key regulatory stage of chromosome replication. Archaea, the third domain of life, use a single or multiple origin(s to initiate replication of their circular chromosomes. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several conserved repeats (origin recognition box, ORB that are located adjacent to a replication initiator gene. Both the ORB sequence and the adjacent initiator gene are considerably diverse among different replication origins, while in silico and genetic analyses have indicated the specificity between the initiator genes and their cognate origins. These replicator-initiator pairings are reminiscent of the oriC-dnaA system in bacteria, and a model for the negative regulation of origin activity by a downstream cluster of ORB elements has been recently proposed in haloarchaea. Moreover, comparative genomic analyses have revealed that the mosaics of replicator-initiator pairings in archaeal chromosomes originated from the integration of extrachromosomal elements. This review summarizes the research progress in understanding of archaeal replication origins with particular focus on the utilization, control and evolution of multiple replication origins in haloarchaea.

  16. Signal replication in a DNA nanostructure

    Science.gov (United States)

    Mendoza, Oscar; Houmadi, Said; Aimé, Jean-Pierre; Elezgaray, Juan

    2017-01-01

    Logic circuits based on DNA strand displacement reaction are the basic building blocks of future nanorobotic systems. The circuits tethered to DNA origami platforms present several advantages over solution-phase versions where couplings are always diffusion-limited. Here we consider a possible implementation of one of the basic operations needed in the design of these circuits, namely, signal replication. We show that with an appropriate preparation of the initial state, signal replication performs in a reproducible way. We also show the existence of side effects concomitant to the high effective concentrations in tethered circuits, such as slow leaky reactions and cross-activation.

  17. 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.

  18. The replication of expansive production knowledge

    DEFF Research Database (Denmark)

    Wæhrens, Brian Vejrum; Yang, Cheng; Madsen, Erik Skov

    2012-01-01

    Purpose – With the aim to support offshore production line replication, this paper specifically aims to explore the use of templates and principles to transfer expansive productive knowledge embedded in a production line and understand the contingencies that influence the mix of these approaches....... Design/methodology/approach – Two case studies are introduced. Empirical data were collected over a period of two years based on interviews and participating observations. Findings – The findings show that (1) knowledge transfer within the replication of a production line is a stepwise expansive process......; and (2) rather than being viewed as alternative approaches, templates and principles should be seen as complementary once the transfer motive moves beyond pure replication. Research limitations – The concepts introduced in this paper were derived from two Danish cases. While acceptable for theory...

  19. SUMO and KSHV Replication

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-09-29

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

  20. Computational Design of Nanomaterials by Pattern Replication

    Data.gov (United States)

    National Aeronautics and Space Administration — Nanotechnology is a rapidly growing field with a plethora of novel applications and potential breakthroughs on the horizon. Some of the most exciting technologies...

  1. Reconsidering Replication: New Perspectives on Large-Scale School Improvement

    Science.gov (United States)

    Peurach, Donald J.; Glazer, Joshua L.

    2012-01-01

    The purpose of this analysis is to reconsider organizational replication as a strategy for large-scale school improvement: a strategy that features a "hub" organization collaborating with "outlet" schools to enact school-wide designs for improvement. To do so, we synthesize a leading line of research on commercial replication to construct a…

  2. 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...

  3. 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...... synthesis is perturbed, cells can suffer loss of both genome and epigenome integrity with severe consequences for the organism....

  4. Optical tweezers reveal how proteins alter replication

    Science.gov (United States)

    Chaurasiya, Kathy

    acids. We use single molecule DNA stretching to show that the nucleocapsid protein (NC) of the yeast retrotransposon Ty3, which is likely to be an ancestor of HIV NC, has optimal nucleic acid chaperone activity with only a single zinc finger. We also show that the chaperone activity of the ORF1 protein is responsible for successful replication of the mouse LINE-1 retrotransposon. LINE-1 is also 17% of the human genome, where it generates insertion mutations and alters gene expression. Retrotransposons such as LINE-1 and Ty3 are likely to be ancestors of retroviruses such as HIV. Human APOBEC3G (A3G) inhibits HIV-1 replication via cytidine deamination of the viral ssDNA genome, as well as via a distinct deamination-independent mechanism. Efficient deamination requires rapid on-off binding kinetics, but a slow dissociation rate is required for the proposed deaminase-independent mechanism. We resolve this apparent contradiction with a new quantitative single molecule method, which shows that A3G initially binds ssDNA with fast on-off rates and subsequently converts to a slow binding mode. This suggests that oligomerization transforms A3G from a fast enzyme to a slow binding protein, which is the biophysical mechanism that allows A3G to inhibit HIV replication. A complete understanding of the mechanism of A3G-mediated antiviral activity is required to design drugs that disrupt the viral response to A3G, enhance A3G packaging inside the viral core, and other potential strategies for long-term treatment of HIV infection. We use single molecule biophysics to explore the function of proteins involved in bacterial DNA replication, endogenous retrotransposition of retroelements in eukaryotic hosts such yeast and mice, and HIV replication in human cells. Our quantitative results provide insight into protein function in a range of complex biological systems and have wide-ranging implications for human health.

  5. 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

  6. Replication-uncoupled histone deposition during adenovirus DNA replication.

    Science.gov (United States)

    Komatsu, Tetsuro; Nagata, Kyosuke

    2012-06-01

    In infected cells, the chromatin structure of the adenovirus genome DNA plays critical roles in its genome functions. Previously, we reported that in early phases of infection, incoming viral DNA is associated with both viral core protein VII and cellular histones. Here we show that in late phases of infection, newly synthesized viral DNA is also associated with histones. We also found that the knockdown of CAF-1, a histone chaperone that functions in the replication-coupled deposition of histones, does not affect the level of histone H3 bound on viral chromatin, although CAF-1 is accumulated at viral DNA replication foci together with PCNA. Chromatin immunoprecipitation assays using epitope-tagged histone H3 demonstrated that histone variant H3.3, which is deposited onto the cellular genome in a replication-independent manner, is selectively associated with both incoming and newly synthesized viral DNAs. Microscopic analyses indicated that histones but not USF1, a transcription factor that regulates viral late gene expression, are excluded from viral DNA replication foci and that this is achieved by the oligomerization of the DNA binding protein (DBP). Taken together, these results suggest that histone deposition onto newly synthesized viral DNA is most likely uncoupled with viral DNA replication, and a possible role of DBP oligomerization in this replication-uncoupled histone deposition is discussed.

  7. MODIFIKASI MEAs DENGAN MENGGUNAKAN DIDACTICAL DESIGN RESEARCH UNTUK MENINGKATKAN KEMAMPUAN BERPIKIR STATISTIS MAHASISWA

    Directory of Open Access Journals (Sweden)

    Bambang Avip Priatna Martadiputra cakrawala

    2014-08-01

    Full Text Available Abstrak: Artikel ini berisi hasil penelitian tentang bagaimana cara memodifikasi pembelajaran Model- Eliciting Activities (MEAs dengan menggunakan Didactical Design Research (DDR. Metode yang digunakan adalah Research & Development melalui tahap-tahap: persiapan untuk mengetahui efektivitas bahan ajar, pembelajaran MEAs yang dimodifikasi, tingkat validitas, reliabilitas, daya pembeda, dan indeks kesukaran instrumen tes; pelaksanaan penelitian berupa uji coba pembelajaran MEAs yang dimodifikasi terhadap seluruh mahasiswa S1 pendidikan matematika yang mengikuti mata kuliah Statistika Dasar pada semester genap TA. 2011/2012 di sebuah PTN di Kota Bandung dengan metode kuasi-eksperimen menggunakan Split-Plot Nested Design. Hasil penelitian menunjukkan bahwa peningkatan kemampuan berpikir statistis mahasiswa reguler dan mahasiswa mengulang yang memperoleh pembelajaran MEAs yang dimodifikasi lebih tinggi secara signifikan dari mahasiswa yang memperoleh pembelajaran konvensional. Kata Kunci: Model-Eliciting Activities (MEAs yang dimodifikasi, didactical disain research

  8. Chromatin replication and histone dynamics

    DEFF Research Database (Denmark)

    Alabert, Constance; Jasencakova, Zuzana; Groth, Anja

    2017-01-01

    organization into chromatin. We reveal how specialized replication-coupled mechanisms rapidly assemble newly synthesized DNA into nucleosomes, while the complete restoration of chromatin organization including histone marks is a continuous process taking place throughout the cell cycle. Because failure...

  9. Synchronous replication of remote storage

    OpenAIRE

    Mirzoev, Dr. Timur

    2014-01-01

    Storage replication is one of the essential requirements for network environments. While many forms of Network Attached Storage (NAS), Storage Area Networks (SAN) and other forms of network storage exist, there is a need for a reliable synchronous storage replication technique between distant sites (less than 1 mile). Such technology allows setting new standards for network failover and failback systems for virtual servers; specifically, addressing the growing need for effective disaster reco...

  10. Optimal covariate designs theory and applications

    CERN Document Server

    Das, Premadhis; Mandal, Nripes Kumar; Sinha, Bikas Kumar

    2015-01-01

    This book primarily addresses the optimality aspects of covariate designs. A covariate model is a combination of ANOVA and regression models. Optimal estimation of the parameters of the model using a suitable choice of designs is of great importance; as such choices allow experimenters to extract maximum information for the unknown model parameters. The main emphasis of this monograph is to start with an assumed covariate model in combination with some standard ANOVA set-ups such as CRD, RBD, BIBD, GDD, BTIBD, BPEBD, cross-over, multi-factor, split-plot and strip-plot designs, treatment control designs, etc. and discuss the nature and availability of optimal covariate designs. In some situations, optimal estimations of both ANOVA and the regression parameters are provided. Global optimality and D-optimality criteria are mainly used in selecting the design. The standard optimality results of both discrete and continuous set-ups have been adapted, and several novel combinatorial techniques have been applied for...

  11. Comparative study between Federer and Gomez method for number of replication in complete randomized design using simulation: study of Areca Palm (Areca catechu) as organic waste for producing handicraft paper

    Science.gov (United States)

    Ihwah, A.; Deoranto, P.; Wijana, S.; Dewi, I. A.

    2018-03-01

    The part of Areca Palm (Areca catechu) that economical is the seed. It is commercially available in dried, cured and fresh forms, while the fibre is usually thrown away. Cellulose fibers from agricultural waste can be utilized as raw material for handicraft paper. Laboratory research showed that Areca palm fibre contained 70.2% of cellulose, 10.92% of water, and 6.02% of ash. This indicated that Areca palm fibre is very potential to be processed as handicraft paper. Handicraft paper is made of wastepaper or plants which cointain celluloce to produce rough-textured paper. In order to obtain preferred sensory quality of handicraft paper such as color, fiber appearance and texture as well as good physical quantity such as tensile strength, tear resistance and grammage, the addition of wastepaper to provide secondary fibre and sometimes adhesive are needed in making handicraft paper. Handicraft paper making was one alternative to treat the solid waste and to reduce the use of wood fiber as paper raw material. The aim of this study is to compare the two most famous method, i.e. Federer and Gomez Method, for calculate the number of replications. This study is preliminary research before do the research in order to get the best treatment to produce handicraft paper. The Gomez method calculates fewer replications than the Federer method. Based on data simulation the error generated using 3 replicates of 0.0876 while using 2 replicates of 0.1032.

  12. Replicable effects of primes on human behavior.

    Science.gov (United States)

    Payne, B Keith; Brown-Iannuzzi, Jazmin L; Loersch, Chris

    2016-10-01

    [Correction Notice: An Erratum for this article was reported online in Journal of Experimental Psychology: General on Oct 31 2016 (see record 2016-52334-001). ] The effect of primes (i.e., incidental cues) on human behavior has become controversial. Early studies reported counterintuitive findings, suggesting that primes can shape a wide range of human behaviors. Recently, several studies failed to replicate some earlier priming results, raising doubts about the reliability of those effects. We present a within-subjects procedure for priming behavior, in which participants decide whether to bet or pass on each trial of a gambling game. We report 6 replications (N = 988) showing that primes consistently affected gambling decisions when the decision was uncertain. Decisions were influenced by primes presented visibly, with a warning to ignore the primes (Experiments 1 through 3) and with subliminally presented masked primes (Experiment 4). Using a process dissociation procedure, we found evidence that primes influenced responses through both automatic and controlled processes (Experiments 5 and 6). Results provide evidence that primes can reliably affect behavior, under at least some conditions, without intention. The findings suggest that the psychological question of whether behavior priming effects are real should be separated from methodological issues affecting how easily particular experimental designs will replicate. PsycINFO Database Record (c) 2016 APA, all rights reserved

  13. The molecular biology of Bluetongue virus replication.

    Science.gov (United States)

    Patel, Avnish; Roy, Polly

    2014-03-01

    The members of Orbivirus genus within the Reoviridae family are arthropod-borne viruses which are responsible for high morbidity and mortality in ruminants. Bluetongue virus (BTV) which causes disease in livestock (sheep, goat, cattle) has been in the forefront of molecular studies for the last three decades and now represents the best understood orbivirus at a molecular and structural level. The complex nature of the virion structure has been well characterised at high resolution along with the definition of the virus encoded enzymes required for RNA replication; the ordered assembly of the capsid shell as well as the protein and genome sequestration required for it; and the role of host proteins in virus entry and virus release. More recent developments of Reverse Genetics and Cell-Free Assembly systems have allowed integration of the accumulated structural and molecular knowledge to be tested at meticulous level, yielding higher insight into basic molecular virology, from which the rational design of safe efficacious vaccines has been possible. This article is centred on the molecular dissection of BTV with a view to understanding the role of each protein in the virus replication cycle. These areas are important in themselves for BTV replication but they also indicate the pathways that related viruses, which includes viruses that are pathogenic to man and animals, might also use providing an informed starting point for intervention or prevention. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. 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...

  15. Defects of mitochondrial DNA replication.

    Science.gov (United States)

    Copeland, William C

    2014-09-01

    Mitochondrial DNA is replicated by DNA polymerase γ in concert with accessory proteins such as the mitochondrial DNA helicase, single-stranded DNA binding protein, topoisomerase, and initiating factors. Defects in mitochondrial DNA replication or nucleotide metabolism can cause mitochondrial genetic diseases due to mitochondrial DNA deletions, point mutations, or depletion, which ultimately cause loss of oxidative phosphorylation. These genetic diseases include mitochondrial DNA depletion syndromes such as Alpers or early infantile hepatocerebral syndromes, and mitochondrial DNA deletion disorders, such as progressive external ophthalmoplegia, ataxia-neuropathy, or mitochondrial neurogastrointestinal encephalomyopathy. This review focuses on our current knowledge of genetic defects of mitochondrial DNA replication (POLG, POLG2, C10orf2, and MGME1) that cause instability of mitochondrial DNA and mitochondrial disease. © The Author(s) 2014.

  16. 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...

  17. 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…

  18. International Expansion through Flexible Replication

    DEFF Research Database (Denmark)

    Jonsson, Anna; Foss, Nicolai Juul

    2011-01-01

    to local environments and under the impact of new learning. To illuminate these issues, we draw on a longitudinal in-depth study of Swedish home furnishing giant IKEA, involving more than 70 interviews. We find that IKEA has developed organizational mechanisms that support an ongoing learning process aimed...... at frequent modification of the format for replication. Another finding is that IKEA treats replication as hierarchical: lower-level features (marketing efforts, pricing, etc.) are allowed to vary across IKEA stores in response to market-based learning, while higher-level features (fundamental values, vision...

  19. Leaf miner incidence in coffee plants under different drip irrigation regimes and planting densities

    OpenAIRE

    Assis,Gleice Aparecida; Assis,Franscinely Aparecida; Scalco,Myriane Stella; Parolin,Francisco José Toloza; Fidelis,Iraci; Moraes,Jair Campos; Guimarães,Rubens José

    2012-01-01

    The objective of this work was to evaluate the effect of different drip irrigation regimes and planting densities on the incidence of the leaf miner, Leucoptera coffeella, in arabica coffee plants for one year. The experiment was carried out in 2008, in a complete randomized block design, in a split-plot in time arrangement, with four replicates. The treatments consisted of four drip irrigation regimes - soil water balance, irrigations at 20 and 60 kPa soil tensions, and a nonirrigated treatm...

  20. Effect of Salinity Stress and Iron Spraying on Leaf Area Index, Light Absorption and Relations with Yield in Sunflower (Helianthus annuns L.)

    OpenAIRE

    M.H Shariatmadari; G.R Zamani; M.H Sayari

    2012-01-01

    Salinity stress results to decreasing leaf area index (LAI) and light absorption in plant leading in yield decrease. In order to study effect of salinity and iron sulphate on LAI, absorbed light percentage and yield of sunflower (Euroflor cultivar), an experiment was carried out as split plot based on complete randomized block design with four replications in the Research Field of University of Birjand on 2009. In this experiment main plots were different levels of irrigation with saline wate...

  1. Methane mitigation in transplanting and direct-wet seeding rice fields treated with fertilizers under condition of alternately flooding and soil aerating

    OpenAIRE

    Sanwangsi, M.; Saenjan, P.; Prongjunteak, K.

    2006-01-01

    Rice is main staple crop of the world. Growing rice in flooded water entails methane (CH4) emission. CH4 is one of greenhouse gases contributing to global warming. The experiment aimed to clarify the influence of fertilizer and water management on total methane emission (TME), methane mitigation and rice yields (RY). The experimental design was a split - split plot with 3 replications taking 2 cultivation in main plots, transplanting (TP) rice and direct-wet seeding (DWS) rice fields; 2 basal...

  2. Effects of Sowing Date and Limited Irrigation on Yield and Yield Components of Five Rainfed Wheat Varieties in Maragheh Region

    OpenAIRE

    A. R. Tavakkoli

    2013-01-01

    In order to investigate the effects of sowing date (SD) and single irrigation (SI) amounts on yield and yield components of rainfed wheat varieties, a field experiment was conducted as split-split plots arranged in a randomized complete blocks design with three replications during 2002-2004 at main station of Dryland Agricultural Research Institute in Maragheh, Iran. Treatments included three sowing dates (early, normal and late), three levels of single irrigation (rainfed, 50 mm and 100 mm o...

  3. Response of Wheat Physiological and Agronomic Traits to Water Stress and Zeolite Application

    OpenAIRE

    M Mirzakhani; Z Hemmati; N Sajedi

    2015-01-01

    With increasing water deficit in agricultural production, quantity and quality of these products will be affected. In order to evaluate the response of wheat physiological and agronomic characteristics to water stress and zeolite application, this study was carried out in field of Arak Payam Noor University in 2009. A split-plot arrangement of treatments in a randomized complete block design with three replications was used. Water stress (I0= Control irrigation, I1= Irrigation about 85% plant...

  4. Indicators of soil quality in the implantation of no-till system with winter crops.

    OpenAIRE

    NOGUEIRA, M. A.; TELLES, T. S.; FAGOTTI, D. dos S. L.; BRITO, O. R.; PRETE, C. E. C.; GUIMARÃES, M. de F.

    2014-01-01

    We assessed the effect of different winter crops on indicators of soil quality related to C and N cycling and C fractions in a Rhodic Kandiudult under no-till system at implantation, during two growing seasons, in Londrina PR Brazil. The experimental design was randomized blocks with split-plot in time arrangement, with four replications. The parcels were the winter crops: multicropping of cover crops with black oat (Avena strigosa), hairy vetch (Vicia villosa) and fodder radish (Raphanus sat...

  5. The Influence of Tilletia spp. Inoculum Source and Enviromental Conditions on the Frequency of Infected Wheat Spikes

    OpenAIRE

    Mirjana Koprivica; Radivoje Jevtić; Ivana Dulić-Marković

    2009-01-01

    The influence of inoculum source on the incidence of common bunt, caused by fungi from the genus Tilletia, was estimated based on the frequency of bunt infected wheat spikes in our agroecological conditions. The cultivar Novosadska rana 5 was sown in a random split plot design with four replicates at Rimski Sancevi on three sawing dates in 1999/2000 and 2000/2001. The following variables were evaluated: I - control, II - soilborne inoculum (4 g teliospores/1 l soil), III - seedborne inoculum ...

  6. Tolerance of melon cultivars to irrigation water salinity

    OpenAIRE

    Pereira, Francisco A. de L.; Medeiros, José F. de; Gheyi, Hans R.; Dias, Nildo da S.; Preston, Welka; Vasconcelos, Cybelle B. e L.

    2017-01-01

    ABSTRACT The use of saline water for irrigation causes severe restriction to nutritional balance, growth and production in many crops due to the effect of salts on plant and soil. The objective of this study was to investigate the response of melon (Cucumis melo L.) cultivars to various levels of irrigation water salinity on yield and fruit quality. A field experiment was conducted in a split-plot randomized block design with four replicates. The factors were five levels of irrigation water s...

  7. Effect of organic fertilizers on quality and quantity characteristics of blond psyllium (Plantago ovata Forssk.) clasping peperweed (Lepidium perfoilatum L.), qodumeh Shirazi (Alyssum homolocarpum L.) and dragon's head (Lalementia iberica L.)

    OpenAIRE

    A. Koocheki; S. Amirmoradi; J. Shabahng; S. Kalantari Khandani

    2016-01-01

    This experiment was carried out in experimental farm of Agricultural Faculty of Ferdowsi University of Mashhad, Iran during 2010. The design was split plot with three replications. Main plots were the medicinal plant species consist of: blond psyllium (Plantago ovate Forssk.), clasping peperweed (Lepidium perfoilatum L.), qodumeh Shirazi (Alyssum homolocarpum L.) dragon's head (Lalementia iberica L.) and subplots were various organic fertilizer consist of cow manure, vermicompost (based on c...

  8. Effect of Drought Stress in Remobilization of Dry Matter in Five Varieties ofBread Wheat

    OpenAIRE

    M. Mirtaheri; S. Syadat; ms Najafi; Gh Fathi; Kh Alami Saeed

    2011-01-01

    Abstract In a field experiment conducted in Ramin Agriculture and Natural Resources University, remobilization of dry matter (DM) after anthesis of five wheat cultivars evaluated in severe and moderate stresses. The statistical design was split plot in RCB (Randomized Complete Blocks) with four replications. In moderate and severe stresses conditions, Falat cv. produced the highest grain yield. However, Chamran cv. had the highest grain yield in control condition. The stress treatment had ...

  9. The effects of super absorbent polymer application into soil and humic acid foliar application on some agrophysiological criteria and quantitative and qualitative yield of sugar beet (Beta vulgaris L.) under Mashhad conditions

    OpenAIRE

    M Jahan; M Nassiri Mahallati; F Ranjbar; M Aryaee; N Kamayestani

    2016-01-01

    Drought stress is the most limiting factor of agricultural production through the world. To evaluate the effect of super absorbent and humic acid to reduce drought stress in sugar beet production, a strip split plot arrangement based on randomized complete block design with three replications was conducted at Research Field of Faculty Agriculture, Ferdowsi University of Mashhad, Iran during growing season of 2010-2011. The main plot factor was application and no application of super absorbent...

  10. Fertilizantes para produção de Daphnia sp. (Crustacea, Cladocera) em tanques experimentais

    OpenAIRE

    Cunha, Patrícia de Souza Lima; Lanna, Eduardo Arruda Teixeira; Bastos, Rafael Kopschitz Xavier; Quadros, Moisés; Rezende, Fabrício Pereira; Freitas, Leandro Monteiro de

    2010-01-01

    The current study was aimed at investigating the use of different fertilizers - dicalcium phosphate, biosolid and quail feces - as a strategy for water fertilization in Daphnia sp production. It was used twenty-four 100-L tanks of asbestos cement distributed in a completely randomized split-plot design with six replicates, with plots in the three kinds of fertilizers (biosolid, dicalcium phosphate, and quail feces) and a control without fertilization (WF) and subplots at the times of assessme...

  11. DATABASE OF MIGRATION AND REPLICATION WITH ORACLE GOLDEN GATE

    Directory of Open Access Journals (Sweden)

    Suharjito Suharjito

    2014-10-01

    Full Text Available The main goal of this research is to analyze and design a database configuration of migration and replication in PT Metro Batavia. Research methodologies used in this research are data collecting, analysis and design model. Data collecting method is conducted with library research and direct survey in the company. Analysis method is conducted by analyzing hangar system, migration and reflection process and the available problems. Design method is conducted by designing a prototype for migration process with the implementation of Oracle SQL Developer and replication process with implementation of Oracle Golden Gate. The result of this research is a prototype for configuration of migration and replication process by using Oracle Golden Gate, which can produce two sets of identical data for the purpose of backup and recovery, and also design a simple tool that is expected to help active-active or active-passive replication process. The conclusion of this research is migration process of MySQL database to Oracle database by using Oracle Golden Gate hasn’t been conducted, because Oracle Golden Gate still has bug related to binary log, so database of migration is conducted by using Oracle Golden Gate. However, replication of bi-directional in between database of Oracle by using Oracle SQL Developer can guarantee data availability and reduce work burden from primary database.

  12. 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.

  13. Chameleon Chasing II: A Replication.

    Science.gov (United States)

    Newsom, Doug A.; And Others

    1993-01-01

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

  14. 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.

  15. Can Coloring Mandalas Reduce Anxiety? A Replication Study

    Science.gov (United States)

    van der Vennet, Renee; Serice, Susan

    2012-01-01

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

  16. DATABASE OF MIGRATION AND REPLICATION WITH ORACLE GOLDEN GATE

    OpenAIRE

    Suharjito Suharjito; Raymond Raymond; Ida Ratna

    2014-01-01

    The main goal of this research is to analyze and design a database configuration of migration and replication in PT Metro Batavia. Research methodologies used in this research are data collecting, analysis and design model. Data collecting method is conducted with library research and direct survey in the company. Analysis method is conducted by analyzing hangar system, migration and reflection process and the available problems. Design method is conducted by designing a prototype for migrati...

  17. Process chain validation in micro and nano replication

    DEFF Research Database (Denmark)

    Calaon, Matteo

    tranches a standard deviation of 4 % around the calculated average value was assessed. The work is concluded validating the deterministic test structures as a tool to predict, through relocation of measuring positions, replication quality of critical geometries of specific LoC devices. The study showed...... to the polymer flow) on the final quality of replicated sub-µm features. For cross test structure with target design height dimension of 62 nm and width of 500 nm, the largest depth deviation was measured. For an average measured polymer channel depth corresponding to 94 % replication of the corresponding nickel...... nm and process reproducibility within a range of ±8 nm. Therefore test structures provide a process calibration tool enabling definition of tolerance limits within micro and nano replication...

  18. Replicator dynamics in value chains

    DEFF Research Database (Denmark)

    Cantner, Uwe; Savin, Ivan; Vannuccini, Simone

    2016-01-01

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

  19. Replication Clamps and Clamp Loaders

    Science.gov (United States)

    Hedglin, Mark; Kumar, Ravindra; Benkovic, Stephen J.

    2013-01-01

    To achieve the high degree of processivity required for DNA replication, DNA polymerases associate with ring-shaped sliding clamps that encircle the template DNA and slide freely along it. The closed circular structure of sliding clamps necessitates an enzyme-catalyzed mechanism, which not only opens them for assembly and closes them around DNA, but specifically targets them to sites where DNA synthesis is initiated and orients them correctly for replication. Such a feat is performed by multisubunit complexes known as clamp loaders, which use ATP to open sliding clamp rings and place them around the 3′ end of primer–template (PT) junctions. Here we discuss the structure and composition of sliding clamps and clamp loaders from the three domains of life as well as T4 bacteriophage, and provide our current understanding of the clamp-loading process. PMID:23545418

  20. 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...... that govern replicative stress, thus providing ample opportunities to enhance replicative stress for therapeutic purposes. Rather than trying to halt cell cycle progression, cancer therapeutics could aim to increase replicative stress by further loosening the checkpoints that remain available to cancer cells...

  1. Replication, Communication, and the Population Dynamics of Scientific Discovery.

    Science.gov (United States)

    McElreath, Richard; Smaldino, Paul E

    2015-01-01

    Many published research results are false (Ioannidis, 2005), and controversy continues over the roles of replication and publication policy in improving the reliability of research. Addressing these problems is frustrated by the lack of a formal framework that jointly represents hypothesis formation, replication, publication bias, and variation in research quality. We develop a mathematical model of scientific discovery that combines all of these elements. This model provides both a dynamic model of research as well as a formal framework for reasoning about the normative structure of science. We show that replication may serve as a ratchet that gradually separates true hypotheses from false, but the same factors that make initial findings unreliable also make replications unreliable. The most important factors in improving the reliability of research are the rate of false positives and the base rate of true hypotheses, and we offer suggestions for addressing each. Our results also bring clarity to verbal debates about the communication of research. Surprisingly, publication bias is not always an obstacle, but instead may have positive impacts-suppression of negative novel findings is often beneficial. We also find that communication of negative replications may aid true discovery even when attempts to replicate have diminished power. The model speaks constructively to ongoing debates about the design and conduct of science, focusing analysis and discussion on precise, internally consistent models, as well as highlighting the importance of population dynamics.

  2. Recombination-dependent concatemeric viral DNA replication.

    Science.gov (United States)

    Lo Piano, Ambra; Martínez-Jiménez, María I; Zecchi, Lisa; Ayora, Silvia

    2011-09-01

    The initiation of viral double stranded (ds) DNA replication involves proteins that recruit and load the replisome at the replication origin (ori). Any block in replication fork progression or a programmed barrier may act as a factor for ori-independent remodelling and assembly of a new replisome at the stalled fork. Then replication initiation becomes dependent on recombination proteins, a process called recombination-dependent replication (RDR). RDR, which is recognized as being important for replication restart and stability in all living organisms, plays an essential role in the replication cycle of many dsDNA viruses. The SPP1 virus, which infects Bacillus subtilis cells, serves as a paradigm to understand the links between replication and recombination in circular dsDNA viruses. SPP1-encoded initiator and replisome assembly proteins control the onset of viral replication and direct the recruitment of host-encoded replisomal components at viral oriL. SPP1 uses replication fork reactivation to switch from ori-dependent θ-type (circle-to-circle) replication to σ-type RDR. Replication fork arrest leads to a double strand break that is processed by viral-encoded factors to generate a D-loop into which a new replisome is assembled, leading to σ-type viral replication. SPP1 RDR proteins are compared with similar proteins encoded by other viruses and their possible in vivo roles are discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. 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....

  4. Evaluating replicability of laboratory experiments in economics.

    Science.gov (United States)

    Camerer, Colin F; Dreber, Anna; Forsell, Eskil; Ho, Teck-Hua; Huber, Jürgen; Johannesson, Magnus; Kirchler, Michael; Almenberg, Johan; Altmejd, Adam; Chan, Taizan; Heikensten, Emma; Holzmeister, Felix; Imai, Taisuke; Isaksson, Siri; Nave, Gideon; Pfeiffer, Thomas; Razen, Michael; Wu, Hang

    2016-03-25

    The replicability of some scientific findings has recently been called into question. To contribute data about replicability in economics, we replicated 18 studies published in the American Economic Review and the Quarterly Journal of Economics between 2011 and 2014. All of these replications followed predefined analysis plans that were made publicly available beforehand, and they all have a statistical power of at least 90% to detect the original effect size at the 5% significance level. We found a significant effect in the same direction as in the original study for 11 replications (61%); on average, the replicated effect size is 66% of the original. The replicability rate varies between 67% and 78% for four additional replicability indicators, including a prediction market measure of peer beliefs. Copyright © 2016, American Association for the Advancement of Science.

  5. Field replication of classwide peer tutoring.

    Science.gov (United States)

    Greenwood, C R; Dinwiddie, G; Bailey, V; Carta, J J; Dorsey, D; Kohler, F W; Nelson, C; Rotholz, D; Schulte, D

    1987-01-01

    We conducted a large-scale field replication study of classwide peer tutoring applied to spelling instruction (Greenwood, Delquadri, & Hall, 1984). Two hundred and eleven inner-city students in four schools participated during their first- and second-grade school years. The effects of classwide peer tutoring were compared to teacher instructional procedures and pretest probes using a group replication design (Barlow, Hayes, & Nelson, 1984). Analysis of group and individual results indicated that (a) both teacher instructional procedures and classwide peer tutoring were effective in increasing spelling performance above pretest levels, (b) peer tutoring produced statistically greater gains relative to the teachers' procedures for both low and high student groups formed on pretest levels, (c) these outcomes were representative of groups, classes, individuals, and years during the project, and (d) participant satisfaction with the program was generally high. A separate analysis of the social importance of treatment outcome revealed differential findings for low and high groups related to pretest levels. Implications of these findings are discussed.

  6. Field replication of classwide peer tutoring.

    Science.gov (United States)

    Greenwood, C R; Dinwiddie, G; Bailey, V; Carta, J J; Dorsey, D; Kohler, F W; Nelson, C; Rotholz, D; Schulte, D

    1987-01-01

    We conducted a large-scale field replication study of classwide peer tutoring applied to spelling instruction (Greenwood, Delquadri, & Hall, 1984). Two hundred and eleven inner-city students in four schools participated during their first- and second-grade school years. The effects of classwide peer tutoring were compared to teacher instructional procedures and pretest probes using a group replication design (Barlow, Hayes, & Nelson, 1984). Analysis of group and individual results indicated that (a) both teacher instructional procedures and classwide peer tutoring were effective in increasing spelling performance above pretest levels, (b) peer tutoring produced statistically greater gains relative to the teachers' procedures for both low and high student groups formed on pretest levels, (c) these outcomes were representative of groups, classes, individuals, and years during the project, and (d) participant satisfaction with the program was generally high. A separate analysis of the social importance of treatment outcome revealed differential findings for low and high groups related to pretest levels. Implications of these findings are discussed. PMID:3610894

  7. 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.

  8. The Persuasiveness of Metaphor: A Replication and Extension.

    Science.gov (United States)

    Siltanen, Susan A.

    A study was conducted to replicate and extend an earlier investigation of the persuasive effects of extended, intense concluding sex and death metaphors by using a more controlled design and by mixing metaphors. Fifty-eight high school students completed pretests assessing their attitudes toward a speech topic (legalization of marijuana). Two…

  9. Physically Embedded Minimal Self-Replicating Systems

    DEFF Research Database (Denmark)

    Fellermann, Harold

    Self-replication is a fundamental property of all living organisms, yet has only been accomplished to limited extend in manmade systems. This thesis is part of the ongoing research endeavor to bridge the two sides of this gap. In particular, we present simulation results of a minimal life...... for any model above the atomistic scale. This is achieved by deriving an alternative scaling procedure for interaction parameters in the model. We perform system-level simulations of the design which attempt to account for theoretical, and experimental knowledge, as well as results from other...... other life-like features can be achieved in systems of formerly unanticipated simplicity – if these systems exploit physicochemical principles that are immanent to their physical scale....

  10. Data Service: Distributed Data Capture and Replication

    Science.gov (United States)

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

    2007-10-01

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

  11. 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.

  12. Adressing Replication and Model Uncertainty

    DEFF Research Database (Denmark)

    Ebersberger, Bernd; Galia, Fabrice; Laursen, Keld

    innovation survey data for France, Germany and the UK, we conduct a ‘large-scale’ replication using the Bayesian averaging approach of classical estimators. Our method tests a wide range of determinants of innovation suggested in the prior literature, and establishes a robust set of findings on the variables...... which shape the introduction of new to the firm and new to the world innovations. We provide some implications for innovation research, and explore the potential application of our approach to other domains of research in strategic management.......Many fields of strategic management are subject to an important degree of model uncertainty. This is because the true model, and therefore the selection of appropriate explanatory variables, is essentially unknown. Drawing on the literature on the determinants of innovation, and by analyzing...

  13. Addressing voice recording replications for tracking Parkinson's disease progression.

    Science.gov (United States)

    Naranjo, Lizbeth; Pérez, Carlos J; Martín, Jacinto

    2017-03-01

    Tracking Parkinson's disease symptom severity by using characteristics automatically extracted from voice recordings is a very interesting and challenging problem. In this context, voice features are automatically extracted from multiple voice recordings from the same subjects. In principle, for each subject, the features should be identical at a concrete time, but the imperfections in technology and the own biological variability result in nonidentical replicated features. The involved within-subject variability must be addressed since replicated measurements from voice recordings can not be directly used in independence-based pattern recognition methods as they have been routinely used through the scientific literature. Besides, the time plays a key role in the experimental design. In this paper, for the first time, a Bayesian linear regression approach suitable to handle replicated measurements and time is proposed. Moreover, a version favoring the best predictors and penalizing the worst ones is also presented. Computational difficulties have been avoided by developing Gibbs sampling-based approaches.

  14. Dissection of a replication origin of Xenopus DNA

    Energy Technology Data Exchange (ETDEWEB)

    Chambers, J.C.; Watanabe, S.; Taylor, J.H.

    1982-09-01

    A previously cloned 503-base pair (bp) EcoRI segment of genomic DNA from Xenopus laevis selected for enhancement of replication of its vector plasmid was moved to the EcoRI site of pBR322. This plasmid designated pJCC31 and five other clones, which were made by cleaving the 503-bp segment in relation to a dispersed repeated sequence and subcloning, were compared with pBR322 for replication by microinjection into Xenopus eggs. The replication measured by incorporation of a /sup 32/P-labeled nucleotide as well as semiconservative segregation and dilution of N/sup 6/-methyladenine at the EcoRI sites showed pJCC31 to be about 15 times as efficient as pBR322. The next most efficient subclone, pJCC31-2, contains an insert with a complete 320-bp dispersed repeated sequence bracketed by an 8-bp direct repeat. This observation, along with the authors' previous report that repeated sequences of the Alu family in the human genome enhanced replication of the vector plasmid nearly as much as that of the presumptive Xenopus origin, leads to the hypothesis that members of a subset of the short dispersed repeated sequences in vertebrates function as origins for chromosomal replication. Preliminary studies also show that the presumptive Xenopus origin contains a RNA polymerase promoter that increases the transcription of the plasmid when it is microinjected into Xenopus oocytes.

  15. 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.

  16. Bioequivalence of two lansoprazole delayed release capsules 30 mg in healthy male volunteers under fasting, fed and fasting-applesauce conditions: a partial replicate crossover study design to estimate the pharmacokinetics of highly variable drugs.

    Science.gov (United States)

    Thota, S; Khan, S M; Tippabhotla, S K; Battula, R; Gadiko, C; Vobalaboina, V

    2013-11-01

    An open-label, 2-treatment, 3-sequence, 3-period, single-dose, partial replicate crossover studies under fasting (n=48), fed (n=60) and fasting-applesauce (n=48) (sprinkled on one table spoonful of applesauce) modalities were conducted in healthy adult male volunteers to evaluate bioequivalence between 2 formulations of lansoprazole delayed release capsules 30 mg. In all the 3 studies, as per randomization, either test or reference formulations were administered in a crossover manner with a required washout period of at least 7 days. Blood samples were collected adequately (0-24 h) to determine lansoprazole plasma concentrations using a validated LC-MS/MS analytical method. To characterize the pharmacokinetic parameters (Cmax, AUC0-t, AUC0-∞, Tmax, Kel and T1/2) of lansoprazole, non-compartmental analysis and ANOVA was applied on ln-transformed values. The bioequivalence was tested based on within-subject variability of the reference formulation. In fasting and fed studies (within-subject variability>30%) bioequivalence was evaluated with scaled average bioequivalence, hence for the pharmacokinetic parameters Cmax, AUC0-t and AUC0-∞, the 95% upper confidence bound for (μT-μR)2-θσ2 WR was ≤0, and the point estimates (test-to-reference ratio) were within the regulatory acceptance limit 80.00-125.00%. In fasting-applesauce study (within-subject variability<30%) bioequivalence was evaluated with average bioequivalence, the 90% CI of ln-transformed data of Cmax, AUC0-t and AUC0-∞ were within the regulatory acceptance limit 80.00-125.00%. Based on these aforesaid statistical inferences, it was concluded that the test formulation is bioequivalent to reference formulation. © Georg Thieme Verlag KG Stuttgart · New York.

  17. Replication of a Continuing Education Workshop in the Evidence-Based Practice Process

    Science.gov (United States)

    Gromoske, Andrea N.; Berger, Lisa K.

    2017-01-01

    Objective: To replicate the results of Parrish and Rubin's continuing education workshop in the evidence-based practice (EBP) process utilizing different workshop facilitators with participants in a different geographic location. Methods: We used a replicated, one-group pretest-posttest design with 3-month follow-up to evaluate the effectiveness…

  18. Replication of Muscle Cell Using Bioimprint

    Science.gov (United States)

    Samsuri, Fahmi; Mitchell, John S.; Alkaisi, Maan M.; Evans, John J.

    2009-07-01

    In our earlier study a heat-curable PDMS or a UV curable elastomer, was used as the replicating material to introduce Bioimprint methodology to facilitate cell imaging [1-2] But, replicating conditions for thermal polymerization is known to cause cell dehydration during curing. In this study, a new type of polymer was developed for use in living cell replica formation, and it was tested on human muscle cells. The cells were incubated and cultured according to standard biological culturing procedures, and they were grown for about 10 days. The replicas were then separated from the muscle cells and taken for analysis under an Atomic Force Microscope (AFM). The new polymer was designed to be biocompatible with higher resolution and fast curing process compared to other types of silicon-based organic polymers such as polydimethylsiloxane (PDMS). Muscle cell imprints were achieved and higher resolution images were able to show the micro structures of the muscle cells, including the cellular fibers and cell membranes. The AFM is able to image features at nanoscale resolution. This capacity enables a number of characteristics of biological cells to be visualized in a unique manner. Polymer and muscle cells preparations were developed at Hamilton, in collaboration between Plant and Food Research and the Department of Electrical and Computer Engineering, University of Canterbury. Tapping mode was used for the AFM image analysis as it has low tip-sample forces and non-destructive imaging capability. We will be presenting the bioimprinting processes of muscle cells, their AFM imaging and characterization of the newly developed polymer.

  19. Replication and efficiency in experiments for marketable emissions permits

    Energy Technology Data Exchange (ETDEWEB)

    Cason, T.N. [Univ. of Southern California, Los Angeles, CA (United States). Dept. of Economics; Elliott, S.R. [Oak Ridge National Lab., TN (United States); Kundra, I. [Dept. of Energy, Washington, DC (United States). Energy Information Administration; Van Boening, M.V. [Univ. of Mississippi, Oxford, MS (United States). Dept. of Economics and Finance

    1996-04-01

    The Energy Information Administration (EIA) funded the universities of Colorado and Arizona to define an experimental institution that captures the salient features of the sulfur dioxide allowance market created by the Clean Air Act Amendments of 1990 (CAAA); to develop and document a transportable software that implements the experimental institutions; and to replicate experiments. Subsequently, EIA, in conjunction with the Oak Ridge National Laboratory (ORNL) funded the universities of Mississippi and Southern California to test the replicability of these experiments using statistically sound experimental design and the standardized software developed by the University of Arizona. The present experiment is designed to identify any differences in the results of the two laboratory sites. It is designed to determine whether market outcomes are reproducible across different laboratories and experimenters and to determine if any behavior patterns exist across a large set of independent experimental sessions.

  20. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    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...... reassembly on nascent DNA strands. The aim of this review is to discuss how histones - new and old - are handled at the replication fork, highlighting new mechanistic insights and revisiting old paradigms....

  1. 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

  2. Replication initiatives will not salvage the trustworthiness of psychology.

    Science.gov (United States)

    Coyne, James C

    2016-05-31

    Replication initiatives in psychology continue to gather considerable attention from far outside the field, as well as controversy from within. Some accomplishments of these initiatives are noted, but this article focuses on why they do not provide a general solution for what ails psychology. There are inherent limitations to mass replications ever being conducted in many areas of psychology, both in terms of their practicality and their prospects for improving the science. Unnecessary compromises were built into the ground rules for design and publication of the Open Science Collaboration: Psychology that undermine its effectiveness. Some ground rules could actually be flipped into guidance for how not to conduct replications. Greater adherence to best publication practices, transparency in the design and publishing of research, strengthening of independent post-publication peer review and firmer enforcement of rules about data sharing and declarations of conflict of interest would make many replications unnecessary. Yet, it has been difficult to move beyond simple endorsement of these measures to consistent implementation. Given the strong institutional support for questionable publication practices, progress will depend on effective individual and collective use of social media to expose lapses and demand reform. Some recent incidents highlight the necessity of this.

  3. Design

    DEFF Research Database (Denmark)

    Volf, Mette

    This publication is unique in its demystification and operationalization of the complex and elusive nature of the design process. The publication portrays the designer’s daily work and the creative process, which the designer is a part of. Apart from displaying the designer’s work methods...... and design parameters, the publication shows examples from renowned Danish design firms. Through these examples the reader gets an insight into the designer’s reality....

  4. ATM and ATR Activities Maintain Replication Fork Integrity during SV40 Chromatin Replication

    Science.gov (United States)

    Sowd, Gregory A.; Li, Nancy Yan; Fanning, Ellen

    2013-01-01

    Mutation of DNA damage checkpoint signaling kinases ataxia telangiectasia-mutated (ATM) or ATM- and Rad3-related (ATR) results in genomic instability disorders. However, it is not well understood how the instability observed in these syndromes relates to DNA replication/repair defects and failed checkpoint control of cell cycling. As a simple model to address this question, we have studied SV40 chromatin replication in infected cells in the presence of inhibitors of ATM and ATR activities. Two-dimensional gel electrophoresis and southern blotting of SV40 chromatin replication products reveal that ATM activity prevents accumulation of unidirectional replication products, implying that ATM promotes repair of replication-associated double strand breaks. ATR activity alleviates breakage of a functional fork as it converges with a stalled fork. The results suggest that during SV40 chromatin replication, endogenous replication stress activates ATM and ATR signaling, orchestrating the assembly of genome maintenance machinery on viral replication intermediates. PMID:23592994

  5. Host factors involved in chikungunya virus replication

    NARCIS (Netherlands)

    Scholte, Florine Elisabeth Maria

    2015-01-01

    In this thesis the interplay of CHIKV with cellular (host) factors involved in its replication is addressed. An in-depth understanding of the interactions between the viral proteins and those of their host is required for the elucidation of molecular mechanisms underlying viral replication. A

  6. Using Replication Projects in Teaching Research Methods

    Science.gov (United States)

    Standing, Lionel G.; Grenier, Manuel; Lane, Erica A.; Roberts, Meigan S.; Sykes, Sarah J.

    2014-01-01

    It is suggested that replication projects may be valuable in teaching research methods, and also address the current need in psychology for more independent verification of published studies. Their use in an undergraduate methods course is described, involving student teams who performed direct replications of four well-known experiments, yielding…

  7. 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…

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

    OpenAIRE

    Klein, Richard A.; Ratliff, Kate A; Vianello, Michelangelo; Adams Jr., Reginald B; Bahník, Stĕpán; Bernstein, Michael J; Bocian, Konrad; Brandt, Mark J; Brooks, Beach; Brumbaugh, Claudia Chloe; Cemalcilar, Zeynep; Chandler, Jesse; Cheong, Winnee; Davis, William E; Devos, Thierry

    2014-01-01

    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 da...

  9. Nuclear safety aspects of exported replicate nuclear power plants and associated problems

    International Nuclear Information System (INIS)

    Kern, H.G.

    1978-01-01

    The standardization of the export nuclear power plant is being pursued with the concept of replication. This concept entails using another exported Nuclear Power Plant (NPP) as the base design and adapting it to a new site. The general ground rule applied to this concept is upgrading the design where necessary and duplicating the design where it is superior. Such continuous improvement will result in a standard export NPP that incorporates design features which will make it essentially acceptable for any suitable site. The advantages of replication are, therefore, boundless. However, the replication mode requires superior design control by the engineer to assure that only improvements alter the base design. With this concept, the replicating engineer is essentially assigned the responsiblity of safeguarding the standard export plant design. He is delegated the task of filtering the design such that only the conservative aspects prevail. Tight control of design changes via properly administered procedures is necessary to assure that no unforeseen compromises are made in designs which have already achieved optimization. Techniques to accomplish successful replication include, among others, the use of PCNs, system cognizant engineers, design verfication review, and the participation of all engineering disciplines in the development of the project schedule. (author)

  10. 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.

  11. 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.

  12. Characteristics of the poliovirus replication complex.

    Science.gov (United States)

    Bienz, K; Egger, D; Pfister, T

    1994-01-01

    In the infected cell, the poliovirus replication complex (RC) is found in the center of a rosette formed by many virus-induced vesicles. The RC is attached to the vesicular membranes and contains a compact central part which encloses the replication forks of the replicative intermediate and all proteins necessary for strand elongation. The growing plus strands of the replicative intermediate protrude from the central part of the RC, but are still enclosed by membraneous structures of the rosette. After completion, progeny 36S RNA is set free at the surface of the rosette. In an in vitro transcription system, isolated replication complex-containing rosettes are active in initiation, elongation and maturation (release) of plus strand progeny RNA. Full functionality of the RC depends on an intact structural framework of all membraneous components of the rosette.

  13. 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…

  14. Registered Replication Report: Dijksterhuis and van Knippenberg (1998).

    Science.gov (United States)

    O'Donnell, Michael; Nelson, Leif D; Ackermann, Evi; Aczel, Balazs; Akhtar, Athfah; Aldrovandi, Silvio; Alshaif, Nasseem; Andringa, Ronald; Aveyard, Mark; Babincak, Peter; Balatekin, Nursena; Baldwin, Scott A; Banik, Gabriel; Baskin, Ernest; Bell, Raoul; Białobrzeska, Olga; Birt, Angie R; Boot, Walter R; Braithwaite, Scott R; Briggs, Jessie C; Buchner, Axel; Budd, Desiree; Budzik, Kathryn; Bullens, Lottie; Bulley, Richard L; Cannon, Peter R; Cantarero, Katarzyna; Cesario, Joseph; Chambers, Stephanie; Chartier, Christopher R; Chekroun, Peggy; Chong, Clara; Cleeremans, Axel; Coary, Sean P; Coulthard, Jacob; Cramwinckel, Florien M; Denson, Thomas F; Díaz-Lago, Marcos; DiDonato, Theresa E; Drummond, Aaron; Eberlen, Julia; Ebersbach, Titus; Edlund, John E; Finnigan, Katherine M; Fisher, Justin; Frankowska, Natalia; García-Sánchez, Efraín; Golom, Frank D; Graves, Andrew J; Greenberg, Kevin; Hanioti, Mando; Hansen, Heather A; Harder, Jenna A; Harrell, Erin R; Hartanto, Andree; Inzlicht, Michael; Johnson, David J; Karpinski, Andrew; Keller, Victor N; Klein, Olivier; Koppel, Lina; Krahmer, Emiel; Lantian, Anthony; Larson, Michael J; Légal, Jean-Baptiste; Lucas, Richard E; Lynott, Dermot; Magaldino, Corey M; Massar, Karlijn; McBee, Matthew T; McLatchie, Neil; Melia, Nadhilla; Mensink, Michael C; Mieth, Laura; Moore-Berg, Samantha; Neeser, Geraldine; Newell, Ben R; Noordewier, Marret K; Ali Özdoğru, Asil; Pantazi, Myrto; Parzuchowski, Michał; Peters, Kim; Philipp, Michael C; Pollmann, Monique M H; Rentzelas, Panagiotis; Rodríguez-Bailón, Rosa; Philipp Röer, Jan; Ropovik, Ivan; Roque, Nelson A; Rueda, Carolina; Rutjens, Bastiaan T; Sackett, Katey; Salamon, Janos; Sánchez-Rodríguez, Ángel; Saunders, Blair; Schaafsma, Juliette; Schulte-Mecklenbeck, Michael; Shanks, David R; Sherman, Martin F; Steele, Kenneth M; Steffens, Niklas K; Sun, Jessie; Susa, Kyle J; Szaszi, Barnabas; Szollosi, Aba; Tamayo, Ricardo M; Tinghög, Gustav; Tong, Yuk-Yue; Tweten, Carol; Vadillo, Miguel A; Valcarcel, Deisy; Van der Linden, Nicolas; van Elk, Michiel; van Harreveld, Frenk; Västfjäll, Daniel; Vazire, Simine; Verduyn, Philippe; Williams, Matt N; Willis, Guillermo B; Wood, Sarah E; Yang, Chunliang; Zerhouni, Oulmann; Zheng, Robert; Zrubka, Mark

    2018-03-01

    Dijksterhuis and van Knippenberg (1998) reported that participants primed with a category associated with intelligence ("professor") subsequently performed 13% better on a trivia test than participants primed with a category associated with a lack of intelligence ("soccer hooligans"). In two unpublished replications of this study designed to verify the appropriate testing procedures, Dijksterhuis, van Knippenberg, and Holland observed a smaller difference between conditions (2%-3%) as well as a gender difference: Men showed the effect (9.3% and 7.6%), but women did not (0.3% and -0.3%). The procedure used in those replications served as the basis for this multilab Registered Replication Report. A total of 40 laboratories collected data for this project, and 23 of these laboratories met all inclusion criteria. Here we report the meta-analytic results for those 23 direct replications (total N = 4,493), which tested whether performance on a 30-item general-knowledge trivia task differed between these two priming conditions (results of supplementary analyses of the data from all 40 labs, N = 6,454, are also reported). We observed no overall difference in trivia performance between participants primed with the "professor" category and those primed with the "hooligan" category (0.14%) and no moderation by gender.

  15. DBR1 siRNA inhibition of HIV-1 replication

    Directory of Open Access Journals (Sweden)

    Naidu Yathi

    2005-10-01

    Full Text Available Abstract Background HIV-1 and all retroviruses are related to retroelements of simpler organisms such as the yeast Ty elements. Recent work has suggested that the yeast retroelement Ty1 replicates via an unexpected RNA lariat intermediate in cDNA synthesis. The putative genomic RNA lariat intermediate is formed by a 2'-5' phosphodiester bond, like that found in pre-mRNA intron lariats and it facilitates the minus-strand template switch during cDNA synthesis. We hypothesized that HIV-1 might also form a genomic RNA lariat and therefore that siRNA-mediated inhibition of expression of the human RNA lariat de-branching enzyme (DBR1 expression would specifically inhibit HIV-1 replication. Results We designed three short interfering RNA (siRNA molecules targeting DBR1, which were capable of reducing DBR1 mRNA expression by 80% and did not significantly affect cell viability. We assessed HIV-1 replication in the presence of DBR1 siRNA and found that DBR1 knockdown led to decreases in viral cDNA and protein production. These effects could be reversed by cotransfection of a DBR1 cDNA indicating that the inhibition of HIV-1 replication was a specific effect of DBR1 underexpression. Conclusion These data suggest that DBR1 function may be needed to debranch a putative HIV-1 genomic RNA lariat prior to completion of reverse transcription.

  16. Modelling the Replication Management in Information Systems

    Directory of Open Access Journals (Sweden)

    Cezar TOADER

    2017-01-01

    Full Text Available In the modern economy, the benefits of Web services are significant because they facilitates the activities automation in the framework of Internet distributed businesses as well as the cooperation between organizations through interconnection process running in the computer systems. This paper presents the development stages of a model for a reliable information system. This paper describes the communication between the processes within the distributed system, based on the message exchange, and also presents the problem of distributed agreement among processes. A list of objectives for the fault-tolerant systems is defined and a framework model for distributed systems is proposed. This framework makes distinction between management operations and execution operations. The proposed model promotes the use of a central process especially designed for the coordination and control of other application processes. The execution phases and the protocols for the management and the execution components are presented. This model of a reliable system could be a foundation for an entire class of distributed systems models based on the management of replication process.

  17. 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.

  18. 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

  19. 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

  20. Replication and Analysis of Ebbinghaus' Forgetting Curve.

    Science.gov (United States)

    Murre, Jaap M J; Dros, Joeri

    2015-01-01

    We present a successful replication of Ebbinghaus' classic forgetting curve from 1880 based on the method of savings. One subject spent 70 hours learning lists and relearning them after 20 min, 1 hour, 9 hours, 1 day, 2 days, or 31 days. The results are similar to Ebbinghaus' original data. We analyze the effects of serial position on forgetting and investigate what mathematical equations present a good fit to the Ebbinghaus forgetting curve and its replications. We conclude that the Ebbinghaus forgetting curve has indeed been replicated and that it is not completely smooth but most probably shows a jump upwards starting at the 24 hour data point.

  1. Replication and Analysis of Ebbinghaus’ Forgetting Curve

    Science.gov (United States)

    Murre, Jaap M. J.; Dros, Joeri

    2015-01-01

    We present a successful replication of Ebbinghaus’ classic forgetting curve from 1880 based on the method of savings. One subject spent 70 hours learning lists and relearning them after 20 min, 1 hour, 9 hours, 1 day, 2 days, or 31 days. The results are similar to Ebbinghaus' original data. We analyze the effects of serial position on forgetting and investigate what mathematical equations present a good fit to the Ebbinghaus forgetting curve and its replications. We conclude that the Ebbinghaus forgetting curve has indeed been replicated and that it is not completely smooth but most probably shows a jump upwards starting at the 24 hour data point. PMID:26148023

  2. Replication and Analysis of Ebbinghaus' Forgetting Curve.

    Directory of Open Access Journals (Sweden)

    Jaap M J Murre

    Full Text Available We present a successful replication of Ebbinghaus' classic forgetting curve from 1880 based on the method of savings. One subject spent 70 hours learning lists and relearning them after 20 min, 1 hour, 9 hours, 1 day, 2 days, or 31 days. The results are similar to Ebbinghaus' original data. We analyze the effects of serial position on forgetting and investigate what mathematical equations present a good fit to the Ebbinghaus forgetting curve and its replications. We conclude that the Ebbinghaus forgetting curve has indeed been replicated and that it is not completely smooth but most probably shows a jump upwards starting at the 24 hour data point.

  3. Replication-Competent Controlled Herpes Simplex Virus.

    Science.gov (United States)

    Bloom, David C; Feller, Joyce; McAnany, Peterjon; Vilaboa, Nuria; Voellmy, Richard

    2015-10-01

    We present the development and characterization of a replication-competent controlled herpes simplex virus 1 (HSV-1). Replication-essential ICP4 and ICP8 genes of HSV-1 wild-type strain 17syn+ were brought under the control of a dually responsive gene switch. The gene switch comprises (i) a transactivator that is activated by a narrow class of antiprogestins, including mifepristone and ulipristal, and whose expression is mediated by a promoter cassette that comprises an HSP70B promoter and a transactivator-responsive promoter and (ii) transactivator-responsive promoters that drive the ICP4 and ICP8 genes. Single-step growth experiments in different cell lines demonstrated that replication of the recombinant virus, HSV-GS3, is strictly dependent on an activating treatment consisting of administration of a supraphysiological heat dose in the presence of an antiprogestin. The replication-competent controlled virus replicates with an efficiency approaching that of the wild-type virus from which it was derived. Essentially no replication occurs in the absence of activating treatment or if HSV-GS3-infected cells are exposed only to heat or antiprogestin. These findings were corroborated by measurements of amounts of viral DNA and transcripts of the regulated ICP4 gene and the glycoprotein C (gC) late gene, which was not regulated. Similar findings were made in experiments with a mouse footpad infection model. The alphaherpesviruses have long been considered vectors for recombinant vaccines and oncolytic therapies. The traditional approach uses vector backbones containing attenuating mutations that restrict replication to ensure safety. The shortcoming of this approach is that the attenuating mutations tend to limit both the immune presentation and oncolytic properties of these vectors. HSV-GS3 represents a novel type of vector that, when activated, replicates with the efficiency of a nonattenuated virus and whose safety is derived from deliberate, stringent regulation of

  4. 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.

  5. 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......In recent years polymer components with surface microstructures have been in rising demand for applications such as lab-on-a-chip and optical components. Injection moulding has proven to be a feasible and efficient way to manufacture such components. In injection moulding the mould surface...... 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...

  6. Lipid Tales of Viral Replication and Transmission.

    Science.gov (United States)

    Altan-Bonnet, Nihal

    2017-03-01

    Positive-strand RNA viruses are the largest group of RNA viruses on Earth and cellular membranes are critical for all aspects of their life cycle, from entry and replication to exit. In particular, membranes serve as platforms for replication and as carriers to transmit these viruses to other cells, the latter either as an envelope surrounding a single virus or as the vesicle containing a population of viruses. Notably, many animal and human viruses appear to induce and exploit phosphatidylinositol 4-phosphate/cholesterol-enriched membranes for replication, whereas many plant and insect-vectored animal viruses utilize phosphatidylethanolamine/cholesterol-enriched membranes for the same purpose; and phosphatidylserine-enriched membrane carriers are widely used by both single and populations of viruses for transmission. Here I discuss the implications for viral pathogenesis and therapeutic development of this remarkable convergence on specific membrane lipid blueprints for replication and transmission. Published by Elsevier Ltd.

  7. Surface Micro Topography Replication in Injection Moulding

    DEFF Research Database (Denmark)

    Arlø, Uffe Rolf; Hansen, Hans Nørgaard; Kjær, Erik Michael

    2005-01-01

    carried out with rough EDM (electrical discharge machining) mould surfaces, a PS grade, and by applying established three-dimensional topography parameters. Significant quantitative relationships between process parameters and topography parameters were established. It further appeared that replication...

  8. 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.

  9. Is psychology suffering from a replication crisis? What does "failure to replicate" really mean?

    Science.gov (United States)

    Maxwell, Scott E; Lau, Michael Y; Howard, George S

    2015-09-01

    Psychology has recently been viewed as facing a replication crisis because efforts to replicate past study findings frequently do not show the same result. Often, the first study showed a statistically significant result but the replication does not. Questions then arise about whether the first study results were false positives, and whether the replication study correctly indicates that there is truly no effect after all. This article suggests these so-called failures to replicate may not be failures at all, but rather are the result of low statistical power in single replication studies, and the result of failure to appreciate the need for multiple replications in order to have enough power to identify true effects. We provide examples of these power problems and suggest some solutions using Bayesian statistics and meta-analysis. Although the need for multiple replication studies may frustrate those who would prefer quick answers to psychology's alleged crisis, the large sample sizes typically needed to provide firm evidence will almost always require concerted efforts from multiple investigators. As a result, it remains to be seen how many of the recently claimed failures to replicate will be supported or instead may turn out to be artifacts of inadequate sample sizes and single study replications. (PsycINFO Database Record (c) 2015 APA, all rights reserved).

  10. Replication and Analysis of Ebbinghaus? Forgetting Curve

    OpenAIRE

    Murre, Jaap M. J.; Dros, Joeri

    2015-01-01

    We present a successful replication of Ebbinghaus’ classic forgetting curve from 1880 based on the method of savings. One subject spent 70 hours learning lists and relearning them after 20 min, 1 hour, 9 hours, 1 day, 2 days, or 31 days. The results are similar to Ebbinghaus' original data. We analyze the effects of serial position on forgetting and investigate what mathematical equations present a good fit to the Ebbinghaus forgetting curve and its replications. We conclude that the Ebbingha...

  11. Evolution of Database Replication Technologies for WLCG

    OpenAIRE

    Baranowski, Zbigniew; Pardavila, Lorena Lobato; Blaszczyk, Marcin; Dimitrov, Gancho; Canali, Luca

    2015-01-01

    In this article we summarize several years of experience on database replication technologies used at WLCG and we provide a short review of the available Oracle technologies and their key characteristics. One of the notable changes and improvement in this area in recent past has been the introduction of Oracle GoldenGate as a replacement of Oracle Streams. We report in this article on the preparation and later upgrades for remote replication done in collaboration with ATLAS and Tier 1 databas...

  12. 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...

  13. Design

    DEFF Research Database (Denmark)

    Jensen, Ole B.; Pettiway, Keon

    2017-01-01

    by designers, planners, etc. (staging from above) and mobile subjects (staging from below). A research agenda for studying situated practices of mobility and mobilities design is outlined in three directions: foci of studies, methods and approaches, and epistemologies and frames of thinking. Jensen begins......In this chapter, Ole B. Jensen takes a situational approach to mobilities to examine how ordinary life activities are structured by technology and design. Using “staging mobilities” as a theoretical approach, Jensen considers mobilities as overlapping, actions, interactions and decisions...... with a brief description of how movement is studied within social sciences after the “mobilities turn” versus the idea of physical movement in transport geography and engineering. He then explains how “mobilities design” was derived from connections between traffic and architecture. Jensen concludes...

  14. Design

    DEFF Research Database (Denmark)

    Volf, Mette

    Design - proces & metode iBog®  er enestående i sit fokus på afmystificering og operationalisering af designprocessens flygtige og komplekse karakter. Udgivelsen går bag om designerens daglige arbejde og giver et indblik i den kreative skabelsesproces, som designeren er en del af. Udover et bredt...... indblik i designerens arbejdsmetoder og designparametre giver Design - proces & metode en række eksempler fra anerkendte designvirksomheder, der gør det muligt at komme helt tæt på designerens virkelighed....

  15. 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.

  16. Engineering attenuated virus vaccines by controlling replication fidelity.

    Science.gov (United States)

    Vignuzzi, Marco; Wendt, Emily; Andino, Raul

    2008-02-01

    Long-lasting protection against viral infection is best achieved by vaccination with attenuated viruses. Obtaining stably attenuated vaccine strains has traditionally been an empirical process, which greatly restricts the number of effective vaccines for viral diseases. Here we describe a rational approach for engineering stably attenuated viruses that can serve as safe and effective vaccines. Our approach exploits the observation that restricting viral population diversity by increasing replication fidelity greatly reduces viral tissue tropism and pathogenicity. We show that poliovirus variants with reduced genetic diversity elicit a protective immune response in an animal model of infection. Indeed, these novel vaccine candidates are comparable in efficacy to the currently available Sabin type 1 vaccine strain, but have the added advantage of being more stable, as their increased replication fidelity prevents reversion to the pathogenic wild-type phenotype. We propose that restricting viral quasispecies diversity provides a general approach for the rational design of stable, attenuated vaccines for a wide variety of viruses.

  17. Replicated x-ray optics for space applications

    Science.gov (United States)

    Hudec, René; Pína, Ladislav; Inneman, Adolf

    2017-11-01

    We report on the program of design and development of X-ray optics for space applications in the Czech Republic. Having more than 30 years background in X-ray optics development for space applications (for use in astronomical X-ray telescopes onboard spacecrafts, before 1989 mostly for Soviet and East European INTERKOSMOS program), we focus nowadays on novel technologies and approaches, thin shell replicated mirrors, as well as studies of light-weight mirrors based on innovative materials such as ceramics. The collaboration includes teams from the Academy of Sciences, Universities, and industry. We will describe and discuss both the history of the development of Xray optics in the Czech Republic and the developed technologies and approaches (with focus on replication technology) as well as recent activities and developments including our participation on the ESA XEUS mirror technology development based on the Agreement between ESA and Czech Government.

  18. 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

  19. Design

    Science.gov (United States)

    Buchanan, Richard; Cross, Nigel; Durling, David; Nelson, Harold; Owen, Charles; Valtonen, Anna; Boling, Elizabeth; Gibbons, Andrew; Visscher-Voerman, Irene

    2013-01-01

    Scholars representing the field of design were asked to identify what they considered to be the most exciting and imaginative work currently being done in their field, as well as how that work might change our understanding. The scholars included Richard Buchanan, Nigel Cross, David Durling, Harold Nelson, Charles Owen, and Anna Valtonen. Scholars…

  20. Design

    DEFF Research Database (Denmark)

    Jensen, Ole B.; Pettiway, Keon

    2017-01-01

    In this chapter, Ole B. Jensen takes a situational approach to mobilities to examine how ordinary life activities are structured by technology and design. Using “staging mobilities” as a theoretical approach, Jensen considers mobilities as overlapping, actions, interactions and decisions by desig......In this chapter, Ole B. Jensen takes a situational approach to mobilities to examine how ordinary life activities are structured by technology and design. Using “staging mobilities” as a theoretical approach, Jensen considers mobilities as overlapping, actions, interactions and decisions...... by designers, planners, etc. (staging from above) and mobile subjects (staging from below). A research agenda for studying situated practices of mobility and mobilities design is outlined in three directions: foci of studies, methods and approaches, and epistemologies and frames of thinking. Jensen begins...... with a brief description of how movement is studied within social sciences after the “mobilities turn” versus the idea of physical movement in transport geography and engineering. He then explains how “mobilities design” was derived from connections between traffic and architecture. Jensen concludes...

  1. Promotion of Hendra virus replication by microRNA 146a.

    Science.gov (United States)

    Stewart, Cameron R; Marsh, Glenn A; Jenkins, Kristie A; Gantier, Michael P; Tizard, Mark L; Middleton, Deborah; Lowenthal, John W; Haining, Jessica; Izzard, Leonard; Gough, Tamara J; Deffrasnes, Celine; Stambas, John; Robinson, Rachel; Heine, Hans G; Pallister, Jackie A; Foord, Adam J; Bean, Andrew G; Wang, Lin-Fa

    2013-04-01

    Hendra virus is a highly pathogenic zoonotic paramyxovirus in the genus Henipavirus. Thirty-nine outbreaks of Hendra virus have been reported since its initial identification in Queensland, Australia, resulting in seven human infections and four fatalities. Little is known about cellular host factors impacting Hendra virus replication. In this work, we demonstrate that Hendra virus makes use of a microRNA (miRNA) designated miR-146a, an NF-κB-responsive miRNA upregulated by several innate immune ligands, to favor its replication. miR-146a is elevated in the blood of ferrets and horses infected with Hendra virus and is upregulated by Hendra virus in human cells in vitro. Blocking miR-146a reduces Hendra virus replication in vitro, suggesting a role for this miRNA in Hendra virus replication. In silico analysis of miR-146a targets identified ring finger protein (RNF)11, a member of the A20 ubiquitin editing complex that negatively regulates NF-κB activity, as a novel component of Hendra virus replication. RNA interference-mediated silencing of RNF11 promotes Hendra virus replication in vitro, suggesting that increased NF-κB activity aids Hendra virus replication. Furthermore, overexpression of the IκB superrepressor inhibits Hendra virus replication. These studies are the first to demonstrate a host miRNA response to Hendra virus infection and suggest an important role for host miRNAs in Hendra virus disease.

  2. Effects of ultraviolet irradiation on the rate and sequence of DNA replication in synchronized Chinese hamster cells

    Energy Technology Data Exchange (ETDEWEB)

    Meyn, R.E.; Hewitt, R.R.; Thomson, L.F.; Humphrey, R.M.

    1976-05-01

    The effects of ultraviolet light (uv) irradiation on the rate of DNA replication in synchronized Chinese hamster ovary (CHO) cells were investigated. A technique for measuring semiconservative DNA replication was employed that involved growing the cells in medium containing 5-bromodeoxyuridine and subsequently determining the amount of DNA that acquired hybrid buoyant density in CsCl density gradients. One of the advantages of this technique was that it allowed a characterization of the extent of DNA replication as well as rate after irradiation. It was found that while there was a dose-dependent reduction in the rate of DNA replication following uv-irradiation, doses of up to 10 J/m/sup 2/ (which produce many dimers per replicon) did not prevent the ultimate replication of the entire genome. Hence, we conclude that dimers cannot be absolute blocks to DNA replication. In order to account for the total genome replication observed, a mechanism must exist that allows genome replication between dimers. The degree of reduction in the rate of replication by uv was the same whether the cells were irradiated at the Gl-S boundary or 1 h into S-phase. Previous work had shown that cells in early S-phase are considerably more sensitive to uv than cells at the G1-S boundary. Experiments specifically designed to test for reiterative replication showed that uv does not induce a second round of DNA replication within the same S-phase.

  3. The structure and function of replication protein A in DNA replication.

    Science.gov (United States)

    Prakash, Aishwarya; Borgstahl, Gloria E O

    2012-01-01

    In all organisms from bacteria and archaea to eukarya, single-stranded DNA binding proteins play an essential role in most, if not all, nuclear metabolism involving single-stranded DNA (ssDNA). Replication protein A (RPA), the major eukaryotic ssDNA binding protein, has two important roles in DNA metabolism: (1) in binding ssDNA to protect it and to keep it unfolded, and (2) in coordinating the assembly and disassembly of numerous proteins and protein complexes during processes such as DNA replication. Since its discovery as a vital player in the process of replication, RPAs roles in recombination and DNA repair quickly became evident. This chapter summarizes the current understanding of RPA's roles in replication by reviewing the available structural data, DNA-binding properties, interactions with various replication proteins, and interactions with DNA repair proteins when DNA replication is stalled.

  4. 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...

  5. Replication ofVibrio choleraeclassical CTX phage.

    Science.gov (United States)

    Kim, Eun Jin; Yu, Hyun Jin; Lee, Je Hee; Kim, Jae-Ouk; Han, Seung Hyun; Yun, Cheol-Heui; Chun, Jongsik; Nair, G Balakrish; Kim, Dong Wook

    2017-02-28

    The toxigenic classical and El Tor biotype Vibrio cholerae serogroup O1 strains are generated by lysogenization of host-type-specific cholera toxin phages (CTX phages). Experimental evidence of the replication and transmission of an El Tor biotype-specific CTX phage, CTX-1, has explained the evolution of V. cholerae El Tor biotype strains. The generation of classical biotype strains has not been demonstrated in the laboratory, and the classical biotype-specific CTX phage, CTX-cla, is considered to be defective with regard to replication. However, the identification of atypical El Tor strains that contain CTX-cla-like phage, CTX-2, indicates that CTX-cla and CTX-2 replicate and can be transmitted to V. cholerae strains. The replication of CTX-cla and CTX-2 phages and the transduction of El Tor biotype strains by various CTX phages under laboratory conditions are demonstrated in this report. We have established a plasmid-based CTX phage replication system that supports the replication of CTX-1, CTX-cla, CTX-2, and CTX-O139. The replication of CTX-2 from the tandem repeat of lysogenic CTX-2 in Wave 2 El Tor strains is also presented. El Tor biotype strains can be transduced by CTX phages in vitro by introducing a point mutation in toxT , the transcriptional activator of the tcp (toxin coregulated pilus) gene cluster and the cholera toxin gene. This mutation also increases the expression of cholera toxin in El Tor strains in a sample single-phase culture. Our results thus constitute experimental evidence of the genetic mechanism of the evolution of V. cholerae .

  6. Prevention of natural grassland invasion by Eragrostis plana Nees using ecological management practices

    Directory of Open Access Journals (Sweden)

    Telmo Focht

    2012-08-01

    Full Text Available The objective of this research was to evaluate the effects of different types of disturbance on the ability of the natural grassland to avoid the invasion of Eragrostis plana Nees (South African lovegrass. The experiment was carried out in Dom Pedrito, Rio Grande do Sul, Brazil, in an area free of South African lovegrass, from Feb. 2004 to Apr. 2007. The treatments were: 1 grassland management regimes: exclusion; low grazing intensity (rotational grazing, ±10 cm; and high grazing intensity (continuous grazing, ±5 cm; 2 initial levels of soil disturbance: high grassland, ±10 cm; low grassland, ±5 cm height; and low grassland with scarified soil; 3 fertilization regimes: without fertilization; phosphorus; and nitrogen. The experimental design was a split-split-plot type in complete blocks, with three replicates. Three winter cultivated species - Trefoil repens L., Lotus corniculatus L., Lolium multiflorum Lam. and South African lovegrass -were sown in 54 split-splitplots (split-plots: low grassland, and low grassland with scarified soil. The other 27 split-split-plots (split-plots: high grassland were sown only with South African lovegrass. The grassland height, plant number of South African lovegrass, grassland dry mass and photosynthetic active radiation intercepted (FARint at the soil level were recorded. The fertilization regimes did not influence the South African lovegrass plant number. The initial levels of soil disturbance and grassland management regimes influenced the invasion of South African lovegrass. The invasion was favored by the lower grassland height and lower forage mass, higher intensity of the soil disturbance, and higher FARint due to the continuous grazing. On the contrary, higher grassland height, higher forage mass, lower soil disturbance and lower FARint, associated with rotational grazing or exclusion, showed higher potential to control the invasion of South African lovegrass in the natural grassland.

  7. Effect of Functional Nano Channel Structures Different Widths on Injection Molding and Compression Molding Replication Capabilities

    DEFF Research Database (Denmark)

    Calaon, M.; Tosello, G.; Garnaes, J.

    The present study investigates the capabilities of the two employed processes, injection molding (IM) and injection compression molding (ICM) on replicating different channel cross sections. Statistical design of experiment was adopted to optimize replication quality of produced polymer parts...... with the two different molding technologies. Focus of the experimental work was the assessment of the IM and ICM processes capabilities to replicate different channels widths (240 nm, 440 nm and 1040 nm) at different positions from the gate based on the deviations of their dimensions from the corresponding...

  8. Design and Performance Analysis of a Relational Replicated Database System

    Science.gov (United States)

    1988-01-01

    Machine (RDBM) .. ......... . 21 Stonebraker’s Machine ..... ............... . 25 Teradata DBC/1012 ...... ................. . 28 DBMAC...22 V 8. Stonebraker’s Machine Architecture .. ........ .. 26 9. Teradata DBC/1012 Architecture ... .......... . 29 10. DBMAC Architecture...backends, control message traffic, controller limitation, and device limitation. Teradata DBC/1012 The DBC/1012 ( Teradata 1986), a commercially

  9. Design and synthesis of compounds that extend yeast replicative lifespan

    Science.gov (United States)

    Yang, Hongying; Baur, Joseph A.; Chen, Allen; Miller, Christine; Sinclair, David A.

    2011-01-01

    Summary This past decade has seen the identification of numerous conserved genes that extend lifespan in diverse species, yet the number of compounds that extend lifespan is relatively small. A class of compounds called STACs, which were identified as activators of Sir2/SIRT1 NAD+-dependent deacetylases, extend the lifespans of multiple species in a Sir2-dependent manner and can delay the onset of age-related diseases such as cancer, diabetes and neurodegeneration in model organisms. Plant-derived STACs such as fisetin and resveratrol have several liabilities, including poor stability and relatively low potency as SIRT1 activators. To develop improved STACs, stilbene derivatives with modifications at the 4′ position of the B ring were synthesized using a Horner-Emmons-based synthetic route or by hydrolyzing deoxyrhapontin. Here, we describe synthetic STACs with lower toxicity toward human cells, and higher potency with respect to SIRT1 activation and lifespan extension in Saccharomyces cerevisiae. These studies show that it is possible to improve upon naturally occurring STACs based on a number of criteria including lifespan extension. PMID:17156081

  10. Autophagy Negatively Regulates Transmissible Gastroenteritis Virus Replication.

    Science.gov (United States)

    Guo, Longjun; Yu, Haidong; Gu, Weihong; Luo, Xiaolei; Li, Ren; Zhang, Jian; Xu, Yunfei; Yang, Lijun; Shen, Nan; Feng, Li; Wang, Yue

    2016-03-31

    Autophagy is an evolutionarily ancient pathway that has been shown to be important in the innate immune defense against several viruses. However, little is known about the regulatory role of autophagy in transmissible gastroenteritis virus (TGEV) replication. In this study, we found that TGEV infection increased the number of autophagosome-like double- and single-membrane vesicles in the cytoplasm of host cells, a phenomenon that is known to be related to autophagy. In addition, virus replication was required for the increased amount of the autophagosome marker protein LC3-II. Autophagic flux occurred in TGEV-infected cells, suggesting that TGEV infection triggered a complete autophagic response. When autophagy was pharmacologically inhibited by wortmannin or LY294002, TGEV replication increased. The increase in virus yield via autophagy inhibition was further confirmed by the use of siRNA duplexes, through which three proteins required for autophagy were depleted. Furthermore, TGEV replication was inhibited when autophagy was activated by rapamycin. The antiviral response of autophagy was confirmed by using siRNA to reduce the expression of gene p300, which otherwise inhibits autophagy. Together, the results indicate that TGEV infection activates autophagy and that autophagy then inhibits further TGEV replication.

  11. Methadone enhances human influenza A virus replication.

    Science.gov (United States)

    Chen, Yun-Hsiang; Wu, Kuang-Lun; Tsai, Ming-Ta; Chien, Wei-Hsien; Chen, Mao-Liang; Wang, Yun

    2017-01-01

    Growing evidence has indicated that opioids enhance replication of human immunodeficiency virus and hepatitis C virus in target cells. However, it is unknown whether opioids can enhance replication of other clinically important viral pathogens. In this study, the interaction of opioid agonists and human influenza A/WSN/33 (H1N1) virus was examined in human lung epithelial A549 cells. Cells were exposed to morphine, methadone or buprenorphine followed by human H1N1 viral infection. Exposure to methadone differentially enhanced viral propagation, consistent with an increase in virus adsorption, susceptibility to virus infection and viral protein synthesis. In contrast, morphine or buprenorphine did not alter H1N1 replication. Because A549 cells do not express opioid receptors, methadone-enhanced H1N1 replication in human lung cells may not be mediated through these receptors. The interaction of methadone and H1N1 virus was also examined in adult mice. Treatment with methadone significantly increased H1N1 viral replication in lungs. Our data suggest that use of methadone facilitates influenza A viral infection in lungs and might raise concerns regarding the possible consequence of an increased risk of serious influenza A virus infection in people who receive treatment in methadone maintenance programs. © 2015 Society for the Study of Addiction.

  12. 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.

  13. Replicating viruses for gynecologic cancer therapy.

    Science.gov (United States)

    Park, J W; Kim, M

    2016-01-01

    Despite advanced therapeutic treatments, gynecologic malignancies such as cervical and ovarian cancers are still the top ten leading cause of cancer death among women in South Korea. Thus a novel and innovative approach is urgently needed. Naturally occurring viruses are live, replication-proficient viruses that specifically infect human cancer cells while sparing normal cell counterparts. Since the serendipitous discovery of the naturally oncotropic virus targeting gynecologic cancer in 1920s, various replicating viruses have shown various degrees of safety and efficacy in preclinical or clinical applications for gynecologic cancer therapy. Cellular oncogenes and tumor suppressor genes, which are frequently dysregulated in gynecologic malignancies, play an important role in determining viral oncotropism. Published articles describing replicating, oncolytic viruses for gynecologic cancers are thoroughly reviewed. This review outlines the discovery of replication-proficient virus strains for targeting gynecologic malignancies, recent progresses elucidating molecular connections between oncogene/tumor suppressor gene abnormalities and viral oncotropism, and the associated preclinical/clinical implications. The authors would also like to propose future directions in the utility of the replicating viruses for gynecologic cancer therapy.

  14. 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.

  15. Stocking rate and fuels reduction effects on beef cattle diet composition and quality

    Science.gov (United States)

    Abe Clark; Tim DelCurto; Martin Vavra; Brian L. Dick

    2013-01-01

    An experiment was conducted to evaluate the influence of forest fuels reduction on diet quality, botanical composition, relative preference, and foraging efficiency of beef cattle grazing at different stocking rates. A split plot factorial design was used, with whole plots (3 ha) being fuel reduced or no treatment (control), and split plots (1 ha) within whole plots...

  16. PTEN Regulates DNA Replication Progression and Stalled Fork Recovery

    Science.gov (United States)

    He, Jinxue; Kang, Xi; Yin, Yuxin; Chao, K.S. Clifford; Shen, Wen H.

    2015-01-01

    Faithful DNA replication is a cornerstone of genomic integrity. PTEN plays multiple roles in genome protection and tumor suppression. Here we report on the importance of PTEN in DNA replication. PTEN depletion leads to impairment of replication progression and stalled fork recovery, indicating an elevation of endogenous replication stress. Exogenous replication inhibition aggravates replication-originated DNA lesions without inducing S-phase arrest in cells lacking PTEN, representing replication stress tolerance. Our analysis reveals the physical association of PTEN with DNA replication forks and PTEN-dependent recruitment of Rad51. PTEN deletion results in Rad51 dissociation from replication forks. Stalled replication forks in Pten null cells can be reactivated by ectopic Rad51 or PTEN, the latter facilitating chromatin loading of Rad51. These data highlight the interplay of PTEN with Rad51 in promoting stalled fork restart. We propose that loss of PTEN may initiate a replication stress cascade that progressively deteriorates through the cell cycle. PMID:26158445

  17. 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.

  18. Towards scalable Byzantine fault-tolerant replication

    Science.gov (United States)

    Zbierski, Maciej

    2017-08-01

    Byzantine fault-tolerant (BFT) replication is a powerful technique, enabling distributed systems to remain available and correct even in the presence of arbitrary faults. Unfortunately, existing BFT replication protocols are mostly load-unscalable, i.e. they fail to respond with adequate performance increase whenever new computational resources are introduced into the system. This article proposes a universal architecture facilitating the creation of load-scalable distributed services based on BFT replication. The suggested approach exploits parallel request processing to fully utilize the available resources, and uses a load balancer module to dynamically adapt to the properties of the observed client workload. The article additionally provides a discussion on selected deployment scenarios, and explains how the proposed architecture could be used to increase the dependability of contemporary large-scale distributed systems.

  19. The replication of expansive production knowledge

    DEFF Research Database (Denmark)

    Wæhrens, Brian Vejrum; Yang, Cheng; Madsen, Erik Skov

    2012-01-01

    Purpose – With the aim to support offshore production line replication, this paper specifically aims to explore the use of templates and principles to transfer expansive productive knowledge embedded in a production line and understand the contingencies that influence the mix of these approaches...... exploration, the small sample size is an obvious limitation for generalisation. Practical implications – A roadmap for knowledge transfer within the replication of a production line is suggested, which, together with four managerial suggestions, provides strong support and clear directions to managers....... Originality/value – Research in replication to date has mostly focused on templates and has mainly taken an organizational perspective. This paper shows its potential contribution on bridging the relevant theoretical gaps by (1) addressing the effects of principles; and (2) exploring how to use templates...

  20. Evolution of Database Replication Technologies for WLCG

    CERN Document Server

    Baranowski, Zbigniew; Blaszczyk, Marcin; Dimitrov, Gancho; Canali, Luca

    2015-01-01

    In this article we summarize several years of experience on database replication technologies used at WLCG and we provide a short review of the available Oracle technologies and their key characteristics. One of the notable changes and improvement in this area in recent past has been the introduction of Oracle GoldenGate as a replacement of Oracle Streams. We report in this article on the preparation and later upgrades for remote replication done in collaboration with ATLAS and Tier 1 database administrators, including the experience from running Oracle GoldenGate in production. Moreover, we report on another key technology in this area: Oracle Active Data Guard which has been adopted in several of the mission critical use cases for database replication between online and offline databases for the LHC experiments.

  1. Effectiveness of strategies to increase the validity of findings from association studies: size vs. replication

    Directory of Open Access Journals (Sweden)

    Kallischnigg Gerd

    2010-05-01

    Full Text Available Abstract Background The capacity of multiple comparisons to produce false positive findings in genetic association studies is abundantly clear. To address this issue, the concept of false positive report probability (FPRP measures "the probability of no true association between a genetic variant and disease given a statistically significant finding". This concept involves the notion of prior probability of an association between a genetic variant and a disease, making it difficult to achieve acceptable levels for the FPRP when the prior probability is low. Increasing the sample size is of limited efficiency to improve the situation. Methods To further clarify this problem, the concept of true report probability (TRP is introduced by analogy to the positive predictive value (PPV of diagnostic testing. The approach is extended to consider the effects of replication studies. The formula for the TRP after k replication studies is mathematically derived and shown to be only dependent on prior probability, alpha, power, and number of replication studies. Results Case-control association studies are used to illustrate the TRP concept for replication strategies. Based on power considerations, a relationship is derived between TRP after k replication studies and sample size of each individual study. That relationship enables study designers optimization of study plans. Further, it is demonstrated that replication is efficient in increasing the TRP even in the case of low prior probability of an association and without requiring very large sample sizes for each individual study. Conclusions True report probability is a comprehensive and straightforward concept for assessing the validity of positive statistical testing results in association studies. By its extension to replication strategies it can be demonstrated in a transparent manner that replication is highly effective in distinguishing spurious from true associations. Based on the generalized TRP

  2. Chromatin structure and replication origins: determinants of chromosome replication and nuclear organization.

    Science.gov (United States)

    Smith, Owen K; Aladjem, Mirit I

    2014-10-09

    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. Published by Elsevier Ltd.

  3. 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

  4. Chromatin challenges during DNA replication and repair

    DEFF Research Database (Denmark)

    Groth, Anja; Rocha, Walter; Verreault, Alain

    2007-01-01

    Inheritance and maintenance of the DNA sequence and its organization into chromatin are central for eukaryotic life. To orchestrate DNA-replication and -repair processes in the context of chromatin is a challenge, both in terms of accessibility and maintenance of chromatin organization. To meet...... the challenge of maintenance, cells have evolved efficient nucleosome-assembly pathways and chromatin-maturation mechanisms that reproduce chromatin organization in the wake of DNA replication and repair. The aim of this Review is to describe how these pathways operate and to highlight how the epigenetic...... landscape may be stably maintained even in the face of dramatic changes in chromatin structure....

  5. 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.

  6. Involvement of Autophagy in Coronavirus Replication

    Directory of Open Access Journals (Sweden)

    Paul Britton

    2012-11-01

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

  7. A Highly Concurrent Replicated Data Structure EAI Endorsed Transactions

    Directory of Open Access Journals (Sweden)

    Mumtaz Ahmad

    2015-12-01

    Full Text Available Well defined concurrent replicated data structure is very important to design collaborative editing system, particularly, certain properties like out-of-order execution of concurrent operations and data convergence. In this paper, we introduce novel linear data structure based on unique identifier scheme required for indexed communication. These identifiers are real numbers holding specific pattern of precision. Based on the uniqueness and the total order of these identifiers, here, we present two concurrency control techniques to achieve high degree of concurrency according to strong and lazy happened-before relations. Our data structure preserves data convergence, yields better performance and avoids overheads as compared to existing approaches.

  8. Suppression of Coronavirus Replication by Cyclophilin Inhibitors

    Directory of Open Access Journals (Sweden)

    Takashi Sasaki

    2013-05-01

    Full Text Available Coronaviruses infect a variety of mammalian and avian species and cause serious diseases in humans, cats, mice, and birds in the form of severe acute respiratory syndrome (SARS, feline infectious peritonitis (FIP, mouse hepatitis, and avian infectious bronchitis, respectively. No effective vaccine or treatment has been developed for SARS-coronavirus or FIP virus, both of which cause lethal diseases. It has been reported that a cyclophilin inhibitor, cyclosporin A (CsA, could inhibit the replication of coronaviruses. CsA is a well-known immunosuppressive drug that binds to cellular cyclophilins to inhibit calcineurin, a calcium-calmodulin-activated serine/threonine-specific phosphatase. The inhibition of calcineurin blocks the translocation of nuclear factor of activated T cells from the cytosol into the nucleus, thus preventing the transcription of genes encoding cytokines such as interleukin-2. Cyclophilins are peptidyl-prolyl isomerases with physiological functions that have been described for many years to include chaperone and foldase activities. Also, many viruses require cyclophilins for replication; these include human immunodeficiency virus, vesicular stomatitis virus, and hepatitis C virus. However, the molecular mechanisms leading to the suppression of viral replication differ for different viruses. This review describes the suppressive effects of CsA on coronavirus replication.

  9. Replication and analysis of Ebbinghaus' forgetting curve

    NARCIS (Netherlands)

    Murre, J.M.J.; Dros, J.

    2015-01-01

    We present a successful replication of Ebbinghaus’ classic forgetting curve from 1880 based on the method of savings. One subject spent 70 hours learning lists and relearning them after 20 min, 1 hour, 9 hours, 1 day, 2 days, or 31 days. The results are similar to Ebbinghaus' original data. We

  10. Optical replication techniques for image slicers

    Czech Academy of Sciences Publication Activity Database

    Schmoll, J.; Robertson, D.J.; Dubbeldam, C.M.; Bortoletto, F.; Pína, L.; Hudec, René; Prieto, E.; Norrie, C.; Ramsay- Howat, S.

    2006-01-01

    Roč. 50, 4-5 (2006), s. 263-266 ISSN 1387-6473 Institutional research plan: CEZ:AV0Z10030501 Keywords : smart focal planes * image slicers * replication Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 1.914, year: 2006

  11. Surface microstructure replication in injection molding

    DEFF Research Database (Denmark)

    Theilade, Uffe Arlø; Hansen, Hans Nørgaard

    2006-01-01

    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...

  12. Conditionally replicating HIV and SIV variants

    NARCIS (Netherlands)

    Das, Atze T.; Berkhout, Ben

    2016-01-01

    Conditionally replicating human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) variants that can be switched on and off at will are attractive tools for HIV and SIV research. We constructed HIV and SIV variants in which the natural transcription control mechanism was replaced

  13. Inhibition of DNA replication by ultraviolet light

    Energy Technology Data Exchange (ETDEWEB)

    Edenberg, H.J.

    1976-08-01

    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/sup 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.

  14. Genome Replication in Thermococcus kodakarensis Independent of Cdc6 and an Origin of Replication

    Directory of Open Access Journals (Sweden)

    Alexandra M. Gehring

    2017-10-01

    Full Text Available The initiation of DNA replication is typically tightly regulated by proteins that form initiation complexes at specific sequences known as replication origins. In Archaea and Eukaryotes, Cdc6, a near-universally conserved protein binds and facilitates the origin-dependent assembly of the replicative apparatus. TK1901 encodes Cdc6 in Thermococcus kodakarensis but, as we report here, TK1901 and the presumed origin of replication can be deleted from the genome of this hyperthermophilic Archaeon without any detectable effects on growth, genetic competence or the ability to support autonomous plasmid replication. All regions of the genome were equally represented in the sequences generated by whole genome sequencing of DNA isolated from T. kodakarensis strains with or without TK1901, inconsistent with DNA initiation occurring at one or few origins, and instead suggestive of replication initiating at many sites distributed throughout the genome. We were unable to generate strains lacking the recombination factors, RadA or RadB, consistent with T. kodakarensis cells, that are oligoploid (7–19 genomes per cell, employing a recombination-based mechanism of DNA replication. Deletion of the previously presumed origin region reduced the long-term viability of cultures supporting the possibility that retaining an origin-based mechanism of DNA initiation provides a survival mechanism for stationary phase cells with only one genome.

  15. 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.

  16. Bacteriophage SPP1 DNA replication strategies promote viral and disable host replication in vitro.

    Science.gov (United States)

    Seco, Elena M; Zinder, John C; Manhart, Carol M; Lo Piano, Ambra; McHenry, Charles S; Ayora, Silvia

    2013-02-01

    Complex viruses that encode their own initiation proteins and subvert the host's elongation apparatus have provided valuable insights into DNA replication. Using purified bacteriophage SPP1 and Bacillus subtilis proteins, we have reconstituted a rolling circle replication system that recapitulates genetically defined protein requirements. Eleven proteins are required: phage-encoded helicase (G40P), helicase loader (G39P), origin binding protein (G38P) and G36P single-stranded DNA-binding protein (SSB); and host-encoded PolC and DnaE polymerases, processivity factor (β(2)), clamp loader (τ-δ-δ') and primase (DnaG). This study revealed a new role for the SPP1 origin binding protein. In the presence of SSB, it is required for initiation on replication forks that lack origin sequences, mimicking the activity of the PriA replication restart protein in bacteria. The SPP1 replisome is supported by both host and viral SSBs, but phage SSB is unable to support B. subtilis replication, likely owing to its inability to stimulate the PolC holoenzyme in the B. subtilis context. Moreover, phage SSB inhibits host replication, defining a new mechanism by which bacterial replication could be regulated by a viral factor.

  17. Replication of somatic micronuclei in bovine enucleated oocytes

    Directory of Open Access Journals (Sweden)

    Canel Natalia

    2012-11-01

    Full Text Available Abstract Background Microcell-mediated chromosome transfer (MMCT was developed to introduce a low number of chromosomes into a host cell. We have designed a novel technique combining part of MMCT with somatic cell nuclear transfer, which consists of injecting a somatic micronucleus into an enucleated oocyte, and inducing its cellular machinery to replicate such micronucleus. It would allow the isolation and manipulation of a single or a low number of somatic chromosomes. Methods Micronuclei from adult bovine fibroblasts were produced by incubation in 0.05 μg/ml demecolcine for 46 h followed by 2 mg/ml mitomycin for 2 h. Cells were finally treated with 10 μg/ml cytochalasin B for 1 h. In vitro matured bovine oocytes were mechanically enucleated and intracytoplasmatically injected with one somatic micronucleus, which had been previously exposed [Micronucleus- injected (+] or not [Micronucleus- injected (−] to a transgene (50 ng/μl pCX-EGFP during 5 min. Enucleated oocytes [Enucleated (+] and parthenogenetic [Parthenogenetic (+] controls were injected into the cytoplasm with less than 10 pl of PVP containing 50 ng/μl pCX-EGFP. A non-injected parthenogenetic control [Parthenogenetic (−] was also included. Two hours after injection, oocytes and reconstituted embryos were activated by incubation in 5 μM ionomycin for 4 min + 1.9 mM 6-DMAP for 3 h. Cleavage stage and egfp expression were evaluated. DNA replication was confirmed by DAPI staining. On day 2, Micronucleus- injected (−, Parthenogenetic (− and in vitro fertilized (IVF embryos were karyotyped. Differences among treatments were determined by Fisher′s exact test (p≤0.05. Results All the experimental groups underwent the first cell divisions. Interestingly, a low number of Micronucleus-injected embryos showed egfp expression. DAPI staining confirmed replication of micronuclei in most of the evaluated embryos. Karyotype analysis revealed that all Micronucleus-injected embryos had

  18. Replication and reconfiguration in a distributed mail repository

    Science.gov (United States)

    Day, Mark S.

    1987-04-01

    Conventional approaches to programming produce centralized programs that run on a single computer. However, an unconventional approach can take advantage of low-cost communication and small, inexpensive computers. A distributed program provides service through programs executing at several nodes of a distributed system. Distributed programs can offer two important advantages over centralized programs: high availability and scalability. In a highly-available system, it is very likely that a randomly-chosen transaction will complete successfully. A scalable system's capacity can be increased or decreased to match changes in the demands placed on the system. When a node is unavailable because of maintenance or a crash, transactions may fail unless copies of the node's information are stored at other nodes. Thus, high availability requires replication of data. This thesis considers the problem of building scalable and highly-available distributed programs without using special processors with redundant hardware and software. It describes a design and implementation of an example distributed program, an electronic mail repository. The thesis focuses on how to design and implement replication and reconfiguration for the distributed mail repository.

  19. 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.

  20. Determination of Soil and Plant Water Balance and Its Critical Stages for Rainfed Wheat Using Crop Water Stress Index (CWSI)

    OpenAIRE

    V. Feiziasl; A. Fotovat; A. Astaraei; A. Lakzian; M.A. Mousavi Shalmani

    2014-01-01

    In order to determination of water stress threshold and dryland wheat genotypes water status in different nitrogen managements, this experiment was carried out in split split plot RCBD design in three replications in 2010-2011 cropping year. Treatments included: N application time (whole fertilization of N at planting time , and its split fertilization as 2/3 at planting time and 1/3 in early spring), N rates (0, 30, 60 and 90 kg ha-1) and 7 wheat genotypes. Also these genotypes were grown in...

  1. Effect of Chemical Fertilizer, Cow Manure and Municipal Compost on Yield, Yield Components and Oil Quantity of three Sesame (Sesamum indicum L. Cultivars in Mashhad

    Directory of Open Access Journals (Sweden)

    P Rezvani Moghaddam

    2013-10-01

    Full Text Available In order to evaluate the effects of different organic and chemical fertilizers on yield, yield components and seed oil content of sesame an experiment was conducted in a split plot layout based on randomized complete block design with four replications at Research Station, Faculty of Agriculture, Ferdowsi University of Mashhad in year 2006. Four types of fertilizer, including chemical fertilizer, cow manure, municipal compost and no fertilizer (control were allocated as main plots and three sesame cultivars (two local varieties of Kalat and Esfarayen, and Oltan cultivar were used as sub plots. The results showed that fertilizer treatments had significant effect (P

  2. QUALIDADE DE GOIABAS CV. 'PALUMA' SUBMETIDAS A INJÚRIAS MECÂNICAS E FRIGOARMAZENAMENTO

    OpenAIRE

    HELTON DE SOUZA SILVA; RAILENE HÉRICA CARLOS ROCHA; FRANCISCO DE ASSIS DE SOUSA

    2013-01-01

    This work aimed to evaluate the effect of mechanical injuries caused by impact, abrasion and cut in guavas cv. 'Paluma' under fruit quality during cold storage at 10°C, and at environment temperature. Was to adopt the completely randomized design in a split-plot in time considering as plots, the mechanical injuries and subplots, the storage periods (0, 5, 8, 11, 14 and 17 days) with four replicates of two fruits per experimental unit. The mechanical injuries were induced considering the follo...

  3. Assay for applying super absorbent polymer in a low input corn (Zea mays L.) production system aimed to reduce drought stress under Mashhad conditions

    OpenAIRE

    M. Jahan; N. Kamayestani; F. Ranjbar

    2016-01-01

    In order to investigate the effects of super absorbent polymer application on reduction of drought stress to corn, a split plot arrangement based on randomized complete block design with three replications was conducted at Research Field of Agriculture Faculty of Ferdowsi University of Mashhad during growing season of 2010-11. The main plot treatments were 1) application of 40 kg.ha-1 super absorbent, 2) application of 80 kg.ha-1 super absorbent and 3) no application of super absorbent polyme...

  4. 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.

  5. DNA replication and repair in Tilapia cells

    International Nuclear Information System (INIS)

    Yew, F.H.; Chang, L.M.

    1984-01-01

    The effect of ultraviolet radiation on a cell line established from the warm water fish Tilapia has been assessed by measuring the rate of DNA synthesis, excision repair, post-replication repair and cell survival. The cells tolerate ultraviolet radiation better than mammalian cells with respect to DNA synthesis, post-replication repair and cell survival. They are also efficient in excision repair, which in other fish cell lines has been found to be at a low level or absent. Their response to the inhibitors hydroxyurea and 1-β-D-arabinofuranosylcytosine is less sensitive than that of other cell lines, yet the cells seem to have very small pools of DNA precursor. (author)

  6. Gene- and protein-delivered zinc finger-staphylococcal nuclease hybrid for inhibition of DNA replication of human papillomavirus.

    Science.gov (United States)

    Mino, Takashi; Mori, Tomoaki; Aoyama, Yasuhiro; Sera, Takashi

    2013-01-01

    Previously, we reported that artificial zinc-finger proteins (AZPs) inhibited virus DNA replication in planta and in mammalian cells by blocking binding of a viral replication protein to its replication origin. However, the replication mechanisms of viruses of interest need to be disentangled for the application. To develop more widely applicable methods for antiviral therapy, we explored the feasibility of inhibition of HPV-18 replication as a model system by cleaving its viral genome. To this end, we fused the staphylococcal nuclease cleaving DNA as a monomer to an AZP that binds to the viral genome. The resulting hybrid nuclease (designated AZP-SNase) cleaved its target DNA plasmid efficiently and sequence-specifically in vitro. Then, we confirmed that transfection with a plasmid expressing AZP-SNase inhibited HPV-18 DNA replication in transient replication assays using mammalian cells. Linker-mediated PCR analysis revealed that the AZP-SNase cleaved an HPV-18 ori plasmid around its binding site. Finally, we demonstrated that the protein-delivered AZP-SNase inhibited HPV-18 DNA replication as well and did not show any significant cytotoxicity. Thus, both gene- and protein-delivered hybrid nucleases efficiently inhibited HPV-18 DNA replication, leading to development of a more universal antiviral therapy for human DNA viruses.

  7. Ultrastructural Characterization of Zika Virus Replication Factories.

    Science.gov (United States)

    Cortese, Mirko; Goellner, Sarah; Acosta, Eliana Gisela; Neufeldt, Christopher John; Oleksiuk, Olga; Lampe, Marko; Haselmann, Uta; Funaya, Charlotta; Schieber, Nicole; Ronchi, Paolo; Schorb, Martin; Pruunsild, Priit; Schwab, Yannick; Chatel-Chaix, Laurent; Ruggieri, Alessia; Bartenschlager, Ralf

    2017-02-28

    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. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  8. Molecular Biology of Rotavirus Entry and Replication

    Science.gov (United States)

    Ruiz, Marie Christine; Leon, Theresa; Diaz, Yuleima; Michelangeli, Fabian

    2009-01-01

    Rotavirus is a nonenveloped, double-stranded, RNA virus belonging to the Reoviridae family and is the major etiological agent of viral gastroenteritis in young children and young animals. Remarkable progress in the understanding of the rotavirus cycle has been made in the last 10 years. The knowledge of viral replication thus far acquired is based on structural studies, the expression and coexpression of individual viral proteins, silencing of individual genes by siRNAs, and the effects that these manipulations have on the physiology of the infected cell. The functions of the individual rotavirus proteins have been largely dissected; however, the interactions between them and with cell proteins, and the molecular mechanisms of virus replication, are just beginning to be understood. These advancements represent the basis for the development of effective vaccination and rational therapeutic strategies to combat rotavirus infection and diarrhea syndromes. In this paper, we review and try to integrate the new knowledge about rotavirus entry, replication, and assembly, and pose some of the questions that remain to be solved. PMID:20024520

  9. The Impact of Message Replication on the Performance of Opportunistic Networks for Sensed Data Collection

    Directory of Open Access Journals (Sweden)

    Tekenate E. Amah

    2017-11-01

    Full Text Available Opportunistic networks (OppNets provide a scalable solution for collecting delay‑tolerant data from sensors for their respective gateways. Portable handheld user devices contribute significantly to the scalability of OppNets since their number increases according to user population and they closely follow human movement patterns. Hence, OppNets for sensed data collection are characterised by high node population and degrees of spatial locality inherent to user movement. We study the impact of these characteristics on the performance of existing OppNet message replication techniques. Our findings reveal that the existing replication techniques are not specifically designed to cope with these characteristics. This raises concerns regarding excessive message transmission overhead and throughput degradations due to resource constraints and technological limitations associated with portable handheld user devices. Based on concepts derived from the study, we suggest design guidelines to augment existing message replication techniques. We also follow our design guidelines to propose a message replication technique, namely Locality Aware Replication (LARep. Simulation results show that LARep achieves better network performance under high node population and degrees of spatial locality as compared with existing techniques.

  10. Pressure tube replication techniques using the advanced NDE system

    International Nuclear Information System (INIS)

    Isherwood, A.; Jarron, D.; Travers, J.; Hanley, K.

    2006-01-01

    Periodic and in-service inspections of fuel channels are essential for the proper assessment of the structural integrity of these vital components. The arrival of new delivery devices for fuel channel inspections has driven new tooling for gathering and analyzing NDE data. The Advanced Non-Destructive Examination (ANDE) Replication System has been designed to compliment the ANDE Inspection System by providing a two plate replica system. These plates deliver a compound that makes a positive 3D mould of known ID flaws to gather information for flaw assessment. The two plate system, and the ability to retrieve and recharge the moulds in the reactor vault allows for gathering defect information with minimal critical path time. The ANDE Replication System was built on the foundation of CIGAR experience by a solid design team familiar with 3D CAD and manufacturing techniques. The tooling and controls went through a series of integration stages in the laboratory and then later with the Universal Delivery Machine (UDM) before being used on reactor starting in 2003. Once the inspection phase of an outage has been completed, the analysis team provides a list of flaw candidates that require 'root radius' information to complete the flaw assessment. This is a measure of how sharp the corners are in the defect. This data is used as part of the stress calculation that ultimately determines how many shutdown cycles that the reactor can have before that flaw must be re-inspected. The inspection tool is then swapped out of the delivery machine in the reactor vault using the versatile connectorized umbilical. The replication tool is loaded on the machine, charged with replica compound on each of the two plates, and then sent to the target channel(s). On channel, the operators use the same console as the ANDE Inspection System, but have a separate control system with a graphical display of the tool that shows its position in the channel with respect to the E-face. The axial and

  11. Gravel admix, vegetation, and soil water interactions in protective barriers: Experimental design, construction, and initial conditions

    International Nuclear Information System (INIS)

    Waugh, W.J.

    1989-05-01

    The purpose of this study is to measure the interactive effects of gravel admix and greater precipitation on soil water storage and plant abundance. The study is one of many tasks in the Protective Barrier Development Program for the disposal of Hanford defense waste. A factorial field-plot experiment was set up at the site selected as the borrow area for barrier topsoil. Gravel admix, vegetation, and enhanced precipitation treatments were randomly assigned to the plots using a split-split plot design structure. Changes in soil water storage and plant cover were monitored using neutron probe and point intercept methods, respectively. The first-year results suggest that water extraction by plants will offset gravel-caused increases in soil water storage. Near-surface soil water contents were much lower in graveled plots with plants than in nongraveled plots without plants. Large inherent variability in deep soil water storage masked any effects gravel may have had on water content below the root zone. In the future, this source of variation will be removed by differencing monthly data series and testing for changes in soil water storage. Tests of the effects of greater precipitation on soil water storage were inconclusive. A telling test will be possible in the spring of 1988, following the first wet season during which normal precipitation is doubled. 26 refs., 9 figs., 9 tabs

  12. Gravel admix, vegetation, and soil water interactions in protective barriers: Experimental design, construction, and initial conditions

    Energy Technology Data Exchange (ETDEWEB)

    Waugh, W.J.

    1989-05-01

    The purpose of this study is to measure the interactive effects of gravel admix and greater precipitation on soil water storage and plant abundance. The study is one of many tasks in the Protective Barrier Development Program for the disposal of Hanford defense waste. A factorial field-plot experiment was set up at the site selected as the borrow area for barrier topsoil. Gravel admix, vegetation, and enhanced precipitation treatments were randomly assigned to the plots using a split-split plot design structure. Changes in soil water storage and plant cover were monitored using neutron probe and point intercept methods, respectively. The first-year results suggest that water extraction by plants will offset gravel-caused increases in soil water storage. Near-surface soil water contents were much lower in graveled plots with plants than in nongraveled plots without plants. Large inherent variability in deep soil water storage masked any effects gravel may have had on water content below the root zone. In the future, this source of variation will be removed by differencing monthly data series and testing for changes in soil water storage. Tests of the effects of greater precipitation on soil water storage were inconclusive. A telling test will be possible in the spring of 1988, following the first wet season during which normal precipitation is doubled. 26 refs., 9 figs., 9 tabs.

  13. 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.

  14. Replicates in high dimensions, with applications to latent variable graphical models.

    Science.gov (United States)

    Tan, Kean Ming; Ning, Yang; Witten, Daniela M; Liu, Han

    2016-12-01

    In classical statistics, much thought has been put into experimental design and data collection. In the high-dimensional setting, however, experimental design has been less of a focus. In this paper, we stress the importance of collecting multiple replicates for each subject in this setting. We consider learning the structure of a graphical model with latent variables, under the assumption that these variables take a constant value across replicates within each subject. By collecting multiple replicates for each subject, we are able to estimate the conditional dependence relationships among the observed variables given the latent variables. To test the null hypothesis of conditional independence between two observed variables, we propose a pairwise decorrelated score test. Theoretical guarantees are established for parameter estimation and for this test. We show that our proposal is able to estimate latent variable graphical models more accurately than some existing proposals, and apply the proposed method to a brain imaging dataset.

  15. Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization.

    Science.gov (United States)

    Farkash-Amar, Shlomit; David, Yaara; Polten, Andreas; Hezroni, Hadas; Eldar, Yonina C; Meshorer, Eran; Yakhini, Zohar; Simon, Itamar

    2012-01-01

    DNA replication is a highly regulated process, with each genomic locus replicating at a distinct time of replication (ToR). Advances in ToR measurement technology enabled several genome-wide profiling studies that revealed tight associations between ToR and general genomic features and a remarkable ToR conservation in mammals. Genome wide studies further showed that at the hundreds kb-to-megabase scale the genome can be divided into constant ToR regions (CTRs) in which the replication process propagates at a faster pace due to the activation of multiple origins and temporal transition regions (TTRs) in which the replication process propagates at a slower pace. We developed a computational tool that assigns a ToR to every measured locus and determines its replication activity type (CTR versus TTR). Our algorithm, ARTO (Analysis of Replication Timing and Organization), uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. We tested our algorithm and provide performance and usability results. A Matlab implementation of ARTO is available at http://bioinfo.cs.technion.ac.il/people/zohar/ARTO/. Applying our algorithm to ToR data measured in multiple mouse and human samples allowed precise genome-wide ToR determination and replication activity type characterization. Analysis of the results highlighted the plasticity of the replication program. For example, we observed significant ToR differences in 10-25% of the genome when comparing different tissue types. Our analyses also provide evidence for activity type differences in up to 30% of the probes. Integration of the ToR data with multiple aspects of chromosome organization characteristics suggests that ToR plays a role in shaping the regional chromatin structure. Namely, repressive chromatin marks, are associated with late ToR both in TTRs and CTRs. Finally, characterization of the differences between TTRs and CTRs, with matching ToR, revealed that TTRs are associated with

  16. Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization.

    Directory of Open Access Journals (Sweden)

    Shlomit Farkash-Amar

    Full Text Available DNA replication is a highly regulated process, with each genomic locus replicating at a distinct time of replication (ToR. Advances in ToR measurement technology enabled several genome-wide profiling studies that revealed tight associations between ToR and general genomic features and a remarkable ToR conservation in mammals. Genome wide studies further showed that at the hundreds kb-to-megabase scale the genome can be divided into constant ToR regions (CTRs in which the replication process propagates at a faster pace due to the activation of multiple origins and temporal transition regions (TTRs in which the replication process propagates at a slower pace. We developed a computational tool that assigns a ToR to every measured locus and determines its replication activity type (CTR versus TTR. Our algorithm, ARTO (Analysis of Replication Timing and Organization, uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. We tested our algorithm and provide performance and usability results. A Matlab implementation of ARTO is available at http://bioinfo.cs.technion.ac.il/people/zohar/ARTO/. Applying our algorithm to ToR data measured in multiple mouse and human samples allowed precise genome-wide ToR determination and replication activity type characterization. Analysis of the results highlighted the plasticity of the replication program. For example, we observed significant ToR differences in 10-25% of the genome when comparing different tissue types. Our analyses also provide evidence for activity type differences in up to 30% of the probes. Integration of the ToR data with multiple aspects of chromosome organization characteristics suggests that ToR plays a role in shaping the regional chromatin structure. Namely, repressive chromatin marks, are associated with late ToR both in TTRs and CTRs. Finally, characterization of the differences between TTRs and CTRs, with matching ToR, revealed that TTRs are

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

    DEFF Research Database (Denmark)

    Jasencakova, Zusana; Groth, Anja

    2010-01-01

    . Chromatin organization is transiently disrupted during DNA replication and maintenance of epigenetic information thus relies on faithful restoration of chromatin on the new daughter strands. Acute replication stress challenges proper chromatin restoration by deregulating histone H3 lysine 9 mono...

  18. 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.

  19. Reliable Date-Replication Using Grid Computing Tools

    CERN Document Server

    Sonnick, D

    2009-01-01

    The LHCb detector at CERN is a physical experiment to measure rare b-decays after the collision of protons in the Large Hadron Collider ring. The measured collisions are called “Events”. These events are containing the data which are necessary to analyze and reconstruct the decays. The events are send to speed optimized writer processes which are writing the events into files on a local hard disk cluster. Because the space is limited on the hard disk cluster, the data needs to be replicated to a long term storage system. This diploma thesis will present the design and implementation of a software which replicates the data in a reliable manner. In addition this software registers the data in special databases to prepare the following analyzes and reconstructions. Because the software which is used in the LHCb experiment is still under development, there is a special need for reliability to deal with error situations or inconsistent data. The subject of this diploma thesis was also presented at the “17th ...

  20. A dynamic replication management strategy in distributed GIS

    Science.gov (United States)

    Pan, Shaoming; Xiong, Lian; Xu, Zhengquan; Chong, Yanwen; Meng, Qingxiang

    2018-03-01

    Replication strategy is one of effective solutions to meet the requirement of service response time by preparing data in advance to avoid the delay of reading data from disks. This paper presents a brand-new method to create copies considering the selection of replicas set, the number of copies for each replica and the placement strategy of all copies. First, the popularities of all data are computed considering both the historical access records and the timeliness of the records. Then, replica set can be selected based on their recent popularities. Also, an enhanced Q-value scheme is proposed to assign the number of copies for each replica. Finally, a reasonable copies placement strategy is designed to meet the requirement of load balance. In addition, we present several experiments that compare the proposed method with techniques that use other replication management strategies. The results show that the proposed model has better performance than other algorithms in all respects. Moreover, the experiments based on different parameters also demonstrated the effectiveness and adaptability of the proposed algorithm.

  1. Replication Fidelity Assessment in Nano Moulding

    DEFF Research Database (Denmark)

    Calaon, Matteo; Hansen, Hans Nørgaard; Tosello, Guido

    2015-01-01

    to remove technology barrier between lab-scale proof-of-principle and high-volume low-cost production of nanotechnology-based products. In the current study research work has been devoted to develop methods and approaches to process chain characterization for final polymer micro and nano structures......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...

  2. Exception Handling in a Replicated Agent Environment

    OpenAIRE

    Azmeh, Zeina; Dony, Christophe; Tibermacine, Chouki; Urtado, Christelle; Vauttier, Sylvain

    2008-01-01

    This document is the semestrial report of the Lirmm partner for the Facoma project. It concludes semester 2 - out of 6 - for the project. During this semester, partners from Lirmm and Lgi2p have worked on: i) defining an exception handling system for agents. This work is based on previous work that has been done by these partners on the Sage exception handling system that was adapted to the context of the Facoma pro ject; ii) refining their knowledge and understanding of the Dimax replicated ...

  3. Implementing e-Transactions with Asynchronous Replication

    OpenAIRE

    Frolund, Svend; Guerraoui, Rachid

    2000-01-01

    An e-Transaction is one that executes exactly-once despite failures. This paper describes a distributed protocol that implements the abstraction of e-Transactionsin three-tier architectures. Three-tier architectures are typically Internet-oriented architectures, where the end-user interacts with front-end clients (e.g., browsers) that invoke middle-tier application servers (e.g., web servers) to access back-end databases. We implement the e-Transaction abstraction using an asynchronous replic...

  4. Replication of DNA during barley endosperm development

    DEFF Research Database (Denmark)

    Giese, H.

    1992-01-01

    The incorporation of [6-H-3]-thymidine into DNA of developing barley end sperm was examined by autoradiography of cross sections of seeds and DNA analysis. The majority of nuclear divisions took place in the very young endosperm, but as late as 25 days after anthesis there was evidence for DNA...... replication. The DNA content of the endosperm increases during development and in response to nitrogen application in parallel to the storage protein synthesis profile. The hordein genes were hypersensitive to DNase I treatment throughout development....

  5. Accounting for PDMS shrinkage when replicating structures

    DEFF Research Database (Denmark)

    Madsen, Morten Hannibal; Feidenhans'l, Nikolaj Agentoft; Hansen, Poul-Erik

    2014-01-01

    are seldom applied to counteract the shrinkage of PDMS. Also, to perform metrological measurements using replica techniques one has to take the shrinkage into account. Thus we report a study of the shrinkage of PDMS with several different mixing ratios and curing temperatures. The shrinkage factor, with its...... associated uncertainty, for PDMS in the range 40 to 120 °C is provided. By applying this correction factor, it is possible to replicate structures with a standard uncertainty of less than 0.2% in lateral dimensions using typical curing temperatures and PDMS mixing ratios in the range 1:6 to 1:20 (agent:base)....

  6. Lattice gas simulations of replicating domains

    International Nuclear Information System (INIS)

    Dawson, S.P.; Hasslacher, B.; Pearson, J.E.

    1993-01-01

    We use the lattice gas cellular automation (LGCA) developed to simulate a process of pattern-formation recently observed in reaction-diffusion systems. We study the reaction mechanism, which is an extension of the Selkov model for glycolytic oscillations. We are able to reproduce the self-replicating domains observed in this work. We use the LGCA simulation to estimate the smallest length-scale on which this process can occur under conditions encountered in the cell. These estimates are similar to those obtained for Turing patterns in the same setting

  7. The Nature of Stability in Replicating Systems

    Directory of Open Access Journals (Sweden)

    Addy Pross

    2011-02-01

    Full Text Available We review the concept of dynamic kinetic stability, a type of stability associated specifically with replicating entities, and show how it differs from the well-known and established (static kinetic and thermodynamic stabilities associated with regular chemical systems. In the process we demonstrate how the concept can help bridge the conceptual chasm that continues to separate the physical and biological sciences by relating the nature of stability in the animate and inanimate worlds, and by providing additional insights into the physicochemical nature of abiogenesis.

  8. Lattice gas simulations of replicating domains

    Energy Technology Data Exchange (ETDEWEB)

    Dawson, S.P.; Hasslacher, B.; Pearson, J.E.

    1993-12-31

    We use the lattice gas cellular automation (LGCA) developed to simulate a process of pattern-formation recently observed in reaction-diffusion systems. We study the reaction mechanism, which is an extension of the Selkov model for glycolytic oscillations. We are able to reproduce the self-replicating domains observed in this work. We use the LGCA simulation to estimate the smallest length-scale on which this process can occur under conditions encountered in the cell. These estimates are similar to those obtained for Turing patterns in the same setting.

  9. Building up and breaking down: mechanisms controlling recombination during replication.

    Science.gov (United States)

    Branzei, Dana; Szakal, Barnabas

    2017-08-01

    The complete and faithful duplication of the genome is an essential prerequisite for proliferating cells to maintain genome integrity. This objective is greatly challenged by DNA damage encountered during replication, which causes fork stalling and in certain cases, fork breakage. DNA damage tolerance (DDT) pathways mitigate the effects on fork stability induced by replication fork stalling by mediating damage-bypass and replication fork restart. These DDT mechanisms, largely relying on homologous recombination (HR) and specialized polymerases, can however contribute to genome rearrangements and mutagenesis. There is a profound connection between replication and recombination: recombination proteins protect replication forks from nuclease-mediated degradation of the nascent DNA strands and facilitate replication completion in cells challenged by DNA damage. Moreover, in case of fork collapse and formation of double strand breaks (DSBs), the recombination factors present or recruited to the fork facilitate HR-mediated DSB repair, which is primarily error-free. Disruption of HR is inexorably linked to genome instability, but the premature activation of HR during replication often leads to genome rearrangements. Faithful replication necessitates the downregulation of HR and disruption of active RAD51 filaments at replication forks, but upon persistent fork stalling, building up of HR is critical for the reorganization of the replication fork and for filling-in of the gaps associated with discontinuous replication induced by DNA lesions. Here we summarize and reflect on our understanding of the mechanisms that either suppress recombination or locally enhance it during replication, and the principles that underlie this regulation.

  10. 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...

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

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

    Indian Academy of Sciences (India)

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

  13. DNA replication in pathogens: Unique properties and possible ...

    Indian Academy of Sciences (India)

    asd

    Eukaryotic DNA Replication Initiation and Elongation. 1. 2. 3 5. 4. 6. ARS. Origin Recognition. Complex (ORC). MCM2-7. CDC6. 1. 2. 3 5. 4. ARS. Replication Initiation. ATP Hydrolysis? Yeast. 6. 2. 2. Replication Elongation. Is ORC function and cell cycle regulation is conserved in. Plasmodium falciparum?

  14. 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.

  15. Utilidad clínica de la terapia metacognitiva en pacientes con trastorno obsesivo compulsivo: un diseño de caso único con replicación directa Clinical utility of metacognitive therapy for obsessive compulsive disorder patients: a single case design with direct replication

    Directory of Open Access Journals (Sweden)

    Ricardo Rodríguez Biglieri

    2006-12-01

    Full Text Available El artículo presenta los resultados preliminares de una investigación tendiente a evaluar la utilidad clínica de dos vertientes de terapia cognitiva en pacientes con Trastorno obsesivo compulsivo (TOC. Una terapia metacognitiva fue aplicada a dos pacientes con TOC en comorbilidad con Trastorno Depresivo Mayor (TDM. Se utilizó un diseño de caso único (A-B con replicación directa entre sujetos. Los resultados son parciales ya que no se contaba todavía con datos de seguimiento. No obstante, los mismos muestran una mejoría significativa en la sintomatología obsesiva y depresiva tras la aplicación del tratamiento, así como un cambio significativo en las creencias relacionadas con el TOC. Al final del período de tratamiento los pacientes no cumplían criterios diagnósticos para TOC ni TDM; además, habían registrado una mejoría en la calidad de vida relacionada con aspectos emocionales. Se discuten las implicaciones teóricas y prácticas de los resultados y se sugieren nuevas líneas de investigación.The article presents preliminary outcomes from an investigation aimed to evaluate the clinical utility of two kinds of cognitive therapy in Obsesive Compulsive Disorder (OCD patients. Metacognitive therapy was applied to two OCD comorbid with Major Depression (MD patients. A single case design (A-B between subjetst with direct replication was used.The findings are limited since we have not follow-up data yet. Nevertheless, outcomes show a significant improvement in obsessive and depressive sympthomatology after the treatment application, as well as a significant change in OCD related beliefs. At the end point of treatment patients no longer met OCD or MD diagnostic criteria. Besides, patients shows an improvement in emotional related aspects of they quality of life.Theoretical and practical implications are discussed, as well as further investigation lines are suggested.

  16. Baculovirus DNA Replication-Specific Expression Factors Trigger Apoptosis and Shutoff of Host Protein Synthesis during Infection▿

    Science.gov (United States)

    Schultz, Kimberly L. W.; Friesen, Paul D.

    2009-01-01

    Apoptosis is an important antivirus defense. To define the poorly understood pathways by which invertebrates respond to viruses by inducing apoptosis, we have identified replication events that trigger apoptosis in baculovirus-infected cells. We used RNA silencing to ablate factors required for multiplication of Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV). Transfection with double-stranded RNA (dsRNA) complementary to the AcMNPV late expression factors (lefs) that are designated as replicative lefs (lef-1, lef-2, lef-3, lef-11, p143, dnapol, and ie-1/ie-0) blocked virus DNA synthesis and late gene expression in permissive Spodoptera frugiperda cells. dsRNAs specific to designated nonreplicative lefs (lef-8, lef-9, p47, and pp31) blocked late gene expression without affecting virus DNA replication. Thus, both classes of lefs functioned during infection as defined. Silencing the replicative lefs prevented AcMNPV-induced apoptosis of Spodoptera cells, whereas silencing the nonreplicative lefs did not. Thus, the activity of replicative lefs or virus DNA replication is sufficient to trigger apoptosis. Confirming this conclusion, AcMNPV-induced apoptosis was suppressed by silencing the replicative lefs in cells from a divergent species, Drosophila melanogaster. Silencing replicative but not nonreplicative lefs also abrogated AcMNPV-induced shutdown of host protein synthesis, suggesting that virus DNA replication triggers inhibition of host biosynthetic processes and that apoptosis and translational arrest are linked. Our findings suggest that baculovirus DNA replication triggers a host cell response similar to the DNA damage response in vertebrates, which causes translational arrest and apoptosis. Pathways for detecting virus invasion and triggering apoptosis may therefore be conserved between insects and mammals. PMID:19706708

  17. Baculovirus DNA replication-specific expression factors trigger apoptosis and shutoff of host protein synthesis during infection.

    Science.gov (United States)

    Schultz, Kimberly L W; Friesen, Paul D

    2009-11-01

    Apoptosis is an important antivirus defense. To define the poorly understood pathways by which invertebrates respond to viruses by inducing apoptosis, we have identified replication events that trigger apoptosis in baculovirus-infected cells. We used RNA silencing to ablate factors required for multiplication of Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV). Transfection with double-stranded RNA (dsRNA) complementary to the AcMNPV late expression factors (lefs) that are designated as replicative lefs (lef-1, lef-2, lef-3, lef-11, p143, dnapol, and ie-1/ie-0) blocked virus DNA synthesis and late gene expression in permissive Spodoptera frugiperda cells. dsRNAs specific to designated nonreplicative lefs (lef-8, lef-9, p47, and pp31) blocked late gene expression without affecting virus DNA replication. Thus, both classes of lefs functioned during infection as defined. Silencing the replicative lefs prevented AcMNPV-induced apoptosis of Spodoptera cells, whereas silencing the nonreplicative lefs did not. Thus, the activity of replicative lefs or virus DNA replication is sufficient to trigger apoptosis. Confirming this conclusion, AcMNPV-induced apoptosis was suppressed by silencing the replicative lefs in cells from a divergent species, Drosophila melanogaster. Silencing replicative but not nonreplicative lefs also abrogated AcMNPV-induced shutdown of host protein synthesis, suggesting that virus DNA replication triggers inhibition of host biosynthetic processes and that apoptosis and translational arrest are linked. Our findings suggest that baculovirus DNA replication triggers a host cell response similar to the DNA damage response in vertebrates, which causes translational arrest and apoptosis. Pathways for detecting virus invasion and triggering apoptosis may therefore be conserved between insects and mammals.

  18. Improving Student Confidence in Using Group Work Standards: A Controlled Replication

    Science.gov (United States)

    Macgowan, Mark J.; Wong, Stephen E.

    2017-01-01

    Objective: This is a replication of a study that examined the effects of teaching foundation competencies in group work to social work students and assessed their self-confidence in applying these skills. This study improves on the first by utilizing a controlled design. Method: Twenty-six master of social work students were taught group work…

  19. Teen Outreach: Data from the Second Year of a National Replication.

    Science.gov (United States)

    Philliber, Susan

    Teen Outreach is a school-based teenage pregnancy prevention program designed to decrease the incidence of teenage pregnancy and to increase the number of at-risk teenagers who successfully complete their high school education. Begun in 1981 in St. Louis, Missouri, Teen Outreach was implemented as a national replication study in 1983. There are…

  20. Teaching about Prejudice with a Bogardus Social Distance Scale Activity: Replication and Extension

    Science.gov (United States)

    Maurer, Trent W.; Keim, Cassidy

    2018-01-01

    This study presents a three-year replication and extension of Maurer's (2013) evaluation of a classroom activity to reduce prejudice and discrimination. Students in six sections of an introductory family science course were assigned to one of three conditions and one of two target marginalized groups for a 3x2 design. Results differed…

  1. 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.

  2. Replicative DNA polymerase mutations in cancer☆

    Science.gov (United States)

    Heitzer, Ellen; Tomlinson, Ian

    2014-01-01

    Three DNA polymerases — Pol α, Pol δ and Pol ɛ — are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol ɛ take over on the lagging and leading strand respectively. Pol δ and Pol ɛ perform the bulk of replication with very high fidelity, which is ensured by Watson–Crick base pairing and 3′exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol ɛ homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to ‘polymerase proofreading associated polyposis’ (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an ‘ultramutator’ phenotype, with a dramatic increase in base substitutions. PMID:24583393

  3. Replicative DNA polymerase mutations in cancer.

    Science.gov (United States)

    Heitzer, Ellen; Tomlinson, Ian

    2014-02-01

    Three DNA polymerases - Pol α, Pol δ and Pol ɛ - are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol ɛ take over on the lagging and leading strand respectively. Pol δ and Pol ɛ perform the bulk of replication with very high fidelity, which is ensured by Watson-Crick base pairing and 3'exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol ɛ homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to 'polymerase proofreading associated polyposis' (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an 'ultramutator' phenotype, with a dramatic increase in base substitutions. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. 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.

  5. The role of dimerization in prion replication.

    Science.gov (United States)

    Tompa, Peter; Tusnády, Gábor E; Friedrich, Peter; Simon, István

    2002-04-01

    The central theme in prion diseases is the conformational transition of a cellular protein from a physiologic to a pathologic (so-called scrapie) state. Currently, two alternative models exist for the mechanism of this autocatalytic process; in the template assistance model the prion is assumed to be a monomer of the scrapie conformer, whereas in the nucleated polymerization model it is thought to be an amyloid rod. A recent variation on the latter assumes disulfide reshuffling as the mechanism of polymerization. The existence of stable dimers, let alone their mechanistic role, is not taken into account in either of these models. In this paper we review evidence supporting that the dimerization of either the normal or the scrapie state, or both, has a decisive role in prion replication. The contribution of redox changes, i.e., the temporary opening and possible rearrangement of the intramolecular disulfide bridge is also considered. We present a model including these features largely ignored so far and show that it adheres satisfactorily to the observed phenomenology of prion replication.

  6. Multiaxial yield behaviour of Al replicated foam

    Science.gov (United States)

    Combaz, E.; Bacciarini, C.; Charvet, R.; Dufour, W.; Mortensen, A.

    2011-09-01

    Multiaxial experiments are performed on replicated aluminium foam using a custom-built apparatus. The foam structure is isotropic, and features open monomodal pores 75 μm in average diameter. Plane stress ( σ1, σ2, σ3=0) and axisymmetric ( σ1, σ2=σ3) yield envelopes are measured using cubical specimens, supplemented by tests on hollow cylindrical and uniaxial samples. In addition to the three stress components at 0.2% offset strain, the computer-controlled testing apparatus also measures the three instantaneous displacement vectors. Results show that the shape of the yield surface is independent of the relative density of the foam in the explored range (13-28%). Strain increment vectors lie, within error, roughly normal to the line traced through data points in stress space. Replicated foams feature asymmetric yield behaviour between tension and compression. The data additionally show an influence on the yield surface of the third stress tensor invariant (i.e., of the Lode angle). Simple general expressions for the yield surface are fitted to the data, leading to conclude that their behaviour is slightly better captured by parabolic rather than elliptic expressions dependent on all three stress invariants.

  7. Endoplasmic reticulum stress causes EBV lytic replication.

    Science.gov (United States)

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

    2011-11-17

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

  8. Replication strategy of human hepatitis B virus

    International Nuclear Information System (INIS)

    Will, H.; Reiser, W.; Weimer, T.; Pfaff, E.; Buescher, M.; Sprengel, R.; Cattaneo, R.; Schaller, H.

    1987-01-01

    To study the replication strategy of the human hepatitis B virus, the 5' end of the RNA pregenome and the initiation sites of DNA plus and minus strands have been mapped. The RNA pregenome was found to be terminally redundant by 120 nucleotides; it is initiated within the pre-C region and may also function as mRNA for synthesis of the major core protein and the hepatitis B virus reverse transcriptase. The hepatitis B virus DNA minus strand is initiated within the direct repeat sequence DR1, it contains a terminal redundancy of up to eight nucleotides, and its synthesis does not require any template switch. The DNA plus strand is primed by a short oligoribonucleotide probably derived from the 5' end of the RNA pregenome, and its synthesis is initiated close to the direct repeat sequence DR2. For its elongation to pass the discontinuity in the DNA minus strand an intramolecular template switch occurs using the terminal redundancy of this template. Thus, the route of reverse transcription and DNA replication of hepatitis B viruses is fundamentally different from that of retroviruses

  9. How to securely replicate services (preliminary version)

    Science.gov (United States)

    Reiter, Michael; Birman, Kenneth

    1992-01-01

    A method is presented for constructing replicated services that retain their availability and integrity despite several servers and clients being corrupted by an intruder, in addition to others failing benignly. More precisely, a service is replicated by 'n' servers in such a way that a correct client will accept a correct server's response if, for some prespecified parameter, k, at least k servers are correct and fewer than k servers are correct. The issue of maintaining causality among client requests is also addressed. A security breach resulting from an intruder's ability to effect a violation of causality in the sequence of requests processed by the service is illustrated. An approach to counter this problem is proposed that requires that fewer than k servers are corrupt and, to ensure liveness, that k is less than or = n - 2t, where t is the assumed maximum total number of both corruptions and benign failures suffered by servers in any system run. An important and novel feature of these schemes is that the client need not be able to identify or authenticate even a single server. Instead, the client is required only to possess at most two public keys for the service.

  10. Epoxy replication for Wolter x-ray microscope fabrication

    International Nuclear Information System (INIS)

    Priedhorsky, W.

    1981-01-01

    An epoxy replica of a test piece designed to simulate a Wolter x-ray microscope geometry showed no loss of x-ray reflectivity or resolution, compared to the original. The test piece was a diamond-turned cone with 1.5 0 half angle. A flat was fly-cut on one side, then super- and conventionally polished. The replica was separated at the 1.5 0 -draft angle, simulating a shallow angle Wolter microscope geometry. A test with 8.34 A x rays at 0.9 0 grazing angle showed a reflectivity of 67% for the replica flat surface, and 70% for the original. No spread of the reflected beam was observed with a 20-arc second wide test beam. This test verifies the epoxy replication technique for production of Wolter x-ray microscopes

  11. ATLAS Replica Management in Rucio: Replication Rules and Subscriptions

    CERN Document Server

    Barisits, M; The ATLAS collaboration; Garonne, V; Lassnig, M; Stewart, G; Beermann, T; Vigne, R; Goossens, L; Nairz, A; Molfetas, A

    2013-01-01

    The ATLAS Distributed Data Management system stores more than 150PB of physics data across 120 sites globally. To cope with the anticipated ATLAS workload of the coming decade, Rucio, the next-generation data management system has been developed. Replica management, as one of the keys aspects of the system, has to satisfy critical performance requirements in order to keep pace with the experiment’s high rate of continual data generation. The challenge lies in meeting these performance objectives while still giving the system users and applications a powerful toolkit to control their data workflows. In this work we present the concept, design and implementation of the replica management in Rucio. We will specifically introduce the workflows behind replication rules, their formal language definition, weighting and site selection. Furthermore we will present the subscription component, which offers functionality for users to proclaim interest in data that has not been created yet. This contribution describes t...

  12. ATLAS Replica Management in Rucio: Replication Rules and Subscriptions

    CERN Document Server

    Barisits, M; The ATLAS collaboration; Garonne, V; Lassnig, M; Stewart, G; Beermann, T; Vigne, R; Goossens, L; Nairz, A; Molfetas, A

    2014-01-01

    The ATLAS Distributed Data Management system stores more than 150PB of physics data across 120 sites globally. To cope with the anticipated ATLAS workload of the coming decade, Rucio, the next-generation data management system has been developed. Replica management, as one of the keys aspects of the system, has to satisfy critical performance requirements in order to keep pace with the experiment’s high rate of continual data generation. The challenge lies in meeting these performance objectives while still giving the system users and applications a powerful toolkit to control their data workflows. In this work we present the concept, design and implementation of the replica management in Rucio. We will specifically introduce the workflows behind replication rules, their formal language definition, weighting and site selection. Furthermore we will present the subscription component, which offers functionality for users to proclaim interest in data that has not been created yet. This contribution describes t...

  13. Regulation of replication fork progression through histone supply and demand

    DEFF Research Database (Denmark)

    Groth, Anja; Corpet, Armelle; Cook, Adam J L

    2007-01-01

    DNA replication in eukaryotes requires nucleosome disruption ahead of the replication fork and reassembly behind. An unresolved issue concerns how histone dynamics are coordinated with fork progression to maintain chromosomal stability. Here, we characterize a complex in which the human histone c...... progression and histone supply and demand.......1 chaperone function, histone supply, and replicative unwinding of DNA in chromatin. We propose that Asf1, as a histone acceptor and donor, handles parental and new histones at the replication fork via an Asf1-(H3-H4)-MCM2-7 intermediate and thus provides a means to fine-tune replication fork...

  14. 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.

  15. Late-replicating CNVs as a source of new genes

    Directory of Open Access Journals (Sweden)

    David Juan

    2013-11-01

    Asynchronous replication of the genome has been associated with different rates of point mutation and copy number variation (CNV in human populations. Here, our aim was to investigate whether the bias in the generation of CNV that is associated with DNA replication timing might have conditioned the birth of new protein-coding genes during evolution. We show that genes that were duplicated during primate evolution are more commonly found among the human genes located in late-replicating CNV regions. We traced the relationship between replication timing and the evolutionary age of duplicated genes. Strikingly, we found that there is a significant enrichment of evolutionary younger duplicates in late-replicating regions of the human and mouse genome. Indeed, the presence of duplicates in late-replicating regions gradually decreases as the evolutionary time since duplication extends. Our results suggest that the accumulation of recent duplications in late-replicating CNV regions is an active process influencing genome evolution.

  16. Eukaryotic Mismatch Repair in Relation to DNA Replication

    Science.gov (United States)

    Erie, Dorothy A.

    2017-01-01

    Three processes act in series to accurately replicate the eukaryotic nuclear genome. The major replicative DNA polymerases strongly prevent mismatch formation, occasional mismatches that do form are proofread during replication, and rare mismatches that escape proofreading are corrected by mismatch repair (MMR). This review focuses on MMR in light of increasing knowledge about nuclear DNA replication enzymology and the rate and specificity with which mismatches are generated during leading- and lagging-strand replication. We consider differences in MMR efficiency in relation to mismatch recognition, signaling to direct MMR to the nascent strand, mismatch removal, and the timing of MMR. These studies are refining our understanding of relationships between generating and repairing replication errors to achieve accurate replication of both DNA strands of the nuclear genome. PMID:26436461

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

    Science.gov (United States)

    Earp, Brian D.; Trafimow, David

    2015-01-01

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

  18. Recruitment of Brd4 to the human papillomavirus type 16 DNA replication complex is essential for replication of viral DNA.

    Science.gov (United States)

    Wang, Xin; Helfer, Christine M; Pancholi, Neha; Bradner, James E; You, Jianxin

    2013-04-01

    Replication of the human papillomavirus (HPV) DNA genome relies on viral factors E1 and E2 and the cellular replication machinery. Bromodomain-containing protein 4 (Brd4) interacts with viral E2 protein to mediate papillomavirus (PV) genome maintenance and viral transcription. However, the functional role of Brd4 in the HPV life cycle remains to be clearly defined. In this study, we provide the first look into the E2-Brd4 interaction in the presence of other important viral factors, such as the HPV16 E1 protein and the viral genome. We show that Brd4 is recruited to actively replicating HPV16 origin foci together with HPV16 E1, E2, and a number of the cellular replication factors: replication protein A70 (RPA70), replication factor C1 (RFC1), and DNA polymerase δ. Mutagenesis disrupting the E2-Brd4 interaction abolishes the formation of the HPV16 replication complex and impairs HPV16 DNA replication in cells. Brd4 was further demonstrated to be necessary for HPV16 viral DNA replication using a cell-free replication system in which depletion of Brd4 by small interfering RNA (siRNA) silencing leads to impaired HPV16 viral DNA replication and recombinant Brd4 protein is able to rescue viral DNA replication. In addition, releasing endogenous Brd4 from cellular chromatin by using the bromodomain inhibitor JQ1(+) enhances HPV16 DNA replication, demonstrating that the role of Brd4 in HPV DNA replication could be uncoupled from its function in chromatin-associated transcriptional regulation and cell cycle control. Our study reveals a new role for Brd4 in HPV genome replication, providing novel insights into understanding the life cycle of this oncogenic DNA virus.

  19. Do Neuroscience Journals Accept Replications? A Survey of Literature

    Directory of Open Access Journals (Sweden)

    Andy W. K. Yeung

    2017-09-01

    Full Text Available Background: Recent reports in neuroscience, especially those concerning brain-injury and neuroimaging, have revealed low reproducibility of results within the field and urged for more replication studies. However, it is unclear if the neuroscience journals welcome or discourage the submission of reports on replication studies. Therefore, the current study assessed the explicit position of neuroscience journals on replications.Methods: A list of active neuroscience journals publishing in English was compiled from Scopus database. These journal websites were accessed to read their aims and scope and instructions to authors, and to assess if they: (1 explicitly stated that they accept replications; (2 did not state their position on replications; (3 implicitly discouraged replications by emphasizing on the novelty of the manuscripts; or (4 explicitly stated that they reject replications. For journals that explicitly stated they accept or reject replications, their subcategory within neuroscience and their 5-year impact factor were recorded. The distribution of neuroscience replication studies published was also recorded by searching and extracting data from Scopus.Results: Of the 465 journals reviewed, 28 (6.0% explicitly stated that they accept replications, 394 (84.7% did not state their position on replications, 40 (8.6% implicitly discouraged replications by emphasizing on the novelty of the manuscripts, and 3 (0.6% explicitly stated that they reject replications. For the 28 journals that explicitly welcomed replications, three (10.7% stated their position in the aims and scope, whereas 25 (89.3% stated in within the detailed instructions to authors. The five-year impact factor (2015 of these journals ranged from 1.655 to 10.799, and nine of them (32.1% did not receive a 5-year or annual impact factor in 2015. There was no significant difference in the proportions of journals explicitly welcomed replications (journals with vs. without impact

  20. Do Neuroscience Journals Accept Replications? A Survey of Literature

    Science.gov (United States)

    Yeung, Andy W. K.

    2017-01-01

    Background: Recent reports in neuroscience, especially those concerning brain-injury and neuroimaging, have revealed low reproducibility of results within the field and urged for more replication studies. However, it is unclear if the neuroscience journals welcome or discourage the submission of reports on replication studies. Therefore, the current study assessed the explicit position of neuroscience journals on replications. Methods: A list of active neuroscience journals publishing in English was compiled from Scopus database. These journal websites were accessed to read their aims and scope and instructions to authors, and to assess if they: (1) explicitly stated that they accept replications; (2) did not state their position on replications; (3) implicitly discouraged replications by emphasizing on the novelty of the manuscripts; or (4) explicitly stated that they reject replications. For journals that explicitly stated they accept or reject replications, their subcategory within neuroscience and their 5-year impact factor were recorded. The distribution of neuroscience replication studies published was also recorded by searching and extracting data from Scopus. Results: Of the 465 journals reviewed, 28 (6.0%) explicitly stated that they accept replications, 394 (84.7%) did not state their position on replications, 40 (8.6%) implicitly discouraged replications by emphasizing on the novelty of the manuscripts, and 3 (0.6%) explicitly stated that they reject replications. For the 28 journals that explicitly welcomed replications, three (10.7%) stated their position in the aims and scope, whereas 25 (89.3%) stated in within the detailed instructions to authors. The five-year impact factor (2015) of these journals ranged from 1.655 to 10.799, and nine of them (32.1%) did not receive a 5-year or annual impact factor in 2015. There was no significant difference in the proportions of journals explicitly welcomed replications (journals with vs. without impact factors

  1. Replicability and generalizability of PTSD networks

    DEFF Research Database (Denmark)

    Eiko I., Fried; Eidhof, Marloes B.; Palic, Sabina

    2018-01-01

    The growing literature conceptualizing mental disorders like Posttraumatic Stress Disorder (PTSD) as networks of interacting symptoms faces three key challenges. Prior studies predominantly used (a) small samples with low power for precise estimation, (b) non-clinical samples, and (c) single...... samples. This renders network structures in clinical data, and the extent to which networks replicate across datasets, unknown. To overcome these limitations, the present cross-cultural multisite study estimated regularized partial correlation networks of 16 PTSD symptoms across four datasets...... of traumatized patients receiving treatment for PTSD (total N=2,782). Despite differences in culture, trauma-type and severity of the samples, considerable similarities emerged, with moderate to high correlations between symptom profiles (0.43-0.82), network structures (0.62-0.74), and centrality estimates (0...

  2. Security in a Replicated Metadata Catalogue

    CERN Document Server

    Koblitz, B

    2007-01-01

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

  3. Parametrised Constants and Replication for Spatial Mobility

    DEFF Research Database (Denmark)

    Hüttel, Hans; Haagensen, Bjørn

    2009-01-01

    and the calculus of mobile ambients. Here, processes are located at sites and can migrate between them. In this paper we say that an encoding is local if it does not introduce extra migration. We first study this property for the distributed π-calculus where locations can be dynamically created. If the set...... of reachable sites is static an encoding exists, but we also show that parametrised constants can not be encoded in the full calculus. The locality requirement supplements widely accepted encoding criteria. It appears to be a natural property in spatial calculi where links and locations can fail. The versions...... 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....

  4. Replicator dynamics for optional public good games

    DEFF Research Database (Denmark)

    Hauert, C.; De Monte, Silvia; Hofbauer, J.

    2002-01-01

    The public goods game represents a straightforward generalization of the prisoner's dilemma to an arbitrary number of players. Since the dominant strategy is to defect, both classical and evolutionary game theory predict the asocial outcome that no player contributes to the public goods....... In contrast to the compulsory public goods game, optional participation provides a natural way to avoid deadlocks in the state of mutual defection. The three resulting strategies-collaboration or defection in the public goods game, as well as not joining at all-are studied by means of a replicator dynamics...... participation makes cooperation feasible. But for each strategy, the average payoff value remains equal to the earnings of those not participating in the public goods game....

  5. Filovirus proteins for antiviral drug discovery: Structure/function bases of the replication cycle.

    Science.gov (United States)

    Martin, Baptiste; Canard, Bruno; Decroly, Etienne

    2017-05-01

    Filoviruses are important pathogens that cause severe and often fatal hemorrhagic fever in humans, for which no approved vaccines and antiviral treatments are yet available. In an earlier article (Martin et al., Antiviral Research, 2016), we reviewed the role of the filovirus surface glycoprotein in replication and as a target for drugs and vaccines. In this review, we focus on recent findings on the filovirus replication machinery and how they could be used for the identification of new therapeutic targets and the development of new antiviral compounds. First, we summarize the recent structural and functional advances on the molecules involved in filovirus replication/transcription cycle, particularly the NP, VP30, VP35 proteins, and the "large" protein L, which harbors the RNA-dependent RNA polymerase (RdRp) and mRNA capping activities. These proteins are essential for viral mRNA synthesis and genome replication, and consequently they constitute attractive targets for drug design. We then describe how these insights into filovirus replication mechanisms and the structure/function characterization of the involved proteins have led to the development of new and innovative antiviral strategies that may help reduce the filovirus disease case fatality rate through post-exposure or prophylactic treatments. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Origin-independent plasmid replication occurs in vaccinia virus cytoplasmic factories and requires all five known poxvirus replication factors

    Directory of Open Access Journals (Sweden)

    Moss Bernard

    2005-03-01

    Full Text Available Abstract Background Replication of the vaccinia virus genome occurs in cytoplasmic factory areas and is dependent on the virus-encoded DNA polymerase and at least four additional viral proteins. DNA synthesis appears to start near the ends of the genome, but specific origin sequences have not been defined. Surprisingly, transfected circular DNA lacking specific viral sequences is also replicated in poxvirus-infected cells. Origin-independent plasmid replication depends on the viral DNA polymerase, but neither the number of additional viral proteins nor the site of replication has been determined. Results Using a novel real-time polymerase chain reaction assay, we detected a >400-fold increase in newly replicated plasmid in cells infected with vaccinia virus. Studies with conditional lethal mutants of vaccinia virus indicated that each of the five proteins known to be required for viral genome replication was also required for plasmid replication. The intracellular site of replication was determined using a plasmid containing 256 repeats of the Escherichia coli lac operator and staining with an E. coli lac repressor-maltose binding fusion protein followed by an antibody to the maltose binding protein. The lac operator plasmid was localized in cytoplasmic viral factories delineated by DNA staining and binding of antibody to the viral uracil DNA glycosylase, an essential replication protein. In addition, replication of the lac operator plasmid was visualized continuously in living cells infected with a recombinant vaccinia virus that expresses the lac repressor fused to enhanced green fluorescent protein. Discrete cytoplasmic fluorescence was detected in cytoplasmic juxtanuclear sites at 6 h after infection and the area and intensity of fluorescence increased over the next several hours. Conclusion Replication of a circular plasmid lacking specific poxvirus DNA sequences mimics viral genome replication by occurring in cytoplasmic viral factories

  7. Software for Replicating Data Between X.500 and LDAP Directories

    Science.gov (United States)

    Wolfe, Thomas

    2003-01-01

    X500/LDAP Directory Replication Utility is a computer program for replicating information between X.500 and LDAP directories. [X.500 is an international standard for on-line directory services. LDAP (Lightweight Directory Access Protocol) is a simple directory access protocol.] The utility can be used to replicate an object of any type from X.500 to LDAP or from LDAP to X.500. The program uses the LDAP version 2 protocol, which is capable of working with both X.500 and LDAP directories. The program can provide any or all of the following services: (1) replicate only modified objects; (2) force replication of all objects; (3) replicate individual objects, one level of objects, or a subtree of objects; (4) filter sets of objects to select ones to be replicated; (5) remove and/or modify object classes from objects that are replicated; and (6) select and/or limit attributes that are replicated. The program includes a separate program that is used to remove objects that are no longer required to be replicated.

  8. Individual and Contextual Factors Influencing Engagement in Learning Activities after Errors at Work: A Replication Study in a German Retail Bank

    Science.gov (United States)

    Leicher, Veronika; Mulder, Regina H.

    2016-01-01

    Purpose: The purpose of this replication study is to identify relevant individual and contextual factors influencing learning from errors at work and to determine if the predictors for learning activities are the same for the domains of nursing and retail banking. Design/methodology/approach: A cross-sectional replication study was carried out in…

  9. Short hairpin-loop-structured oligodeoxynucleotides reduce HSV-1 replication

    Directory of Open Access Journals (Sweden)

    Heinrich Jochen

    2009-04-01

    Full Text Available Abstract The Herpes simplex virus (HSV is known as an infectious agent and widespread in the human population. The symptoms of HSV infections can range from mild to life threatening, especially in immune-compromised individuals. HSV infections are commonly treated with the guanosine analogue Aciclovir, but reports of resistance are increasing. Efforts are made to establish single-stranded antisense oligodeoxynucleotides (as and small interfering ribonucleic acids (siRNAs for antiviral treatment. Recently, another class of short interfering nucleic acids, partially double-stranded hairpin loop-structured 54 mer oligodeoxynucleotides (ODNs, was shown to allow hydrolysis of HIV RNA by binding to the viral RNA. This leads to a substrate for the viral RNase H. To assess the potential of such ODNs for inhibition of HSV-1 replication, five partially double-stranded ODNs were designed based on the sequences of known siRNAs against HSV-1 with antiviral activity. Three of them are directed against early and two against leaky late genes. Primary human lung fibroblasts, MRC-5, and African green monkey kidney cells, Vero, were transfected with ODNs and subsequently infected. The effect on HSV-1 replication was determined by analyzing the virus titer in cell culture supernatants by quantitative PCR and plaque assays. An inhibitory effect was observed with all five selected ODNs, with two cases showing statistical significance in both cell types. The observed effect was sequence-specific and dose dependent. In one case the ODN was more efficient than a previously described siRNA directed against the same target site in the mRNA of UL5, a component of the helicase/primase complex. HSV-1 virions and ODNs can be applied simultaneously without transfection reagent, but at a 50-fold higher concentration to Vero cells with similar efficiencies. The results underline the potential of partially double-stranded hairpin loop-structured ODNs as antiviral agents.

  10. Capitalizing on disaster: Establishing chromatin specificity behind the replication fork.

    Science.gov (United States)

    Ramachandran, Srinivas; Ahmad, Kami; Henikoff, Steven

    2017-04-01

    Eukaryotic genomes are packaged into nucleosomal chromatin, and genomic activity requires the precise localization of transcription factors, histone modifications and nucleosomes. Classic work described the progressive reassembly and maturation of bulk chromatin behind replication forks. More recent proteomics has detailed the molecular machines that accompany the replicative polymerase to promote rapid histone deposition onto the newly replicated DNA. However, localized chromatin features are transiently obliterated by DNA replication every S phase of the cell cycle. Genomic strategies now observe the rebuilding of locus-specific chromatin features, and reveal surprising delays in transcription factor binding behind replication forks. This implies that transient chromatin disorganization during replication is a central juncture for targeted transcription factor binding within genomes. We propose that transient occlusion of regulatory elements by disorganized nucleosomes during chromatin maturation enforces specificity of factor binding. © 2017 WILEY Periodicals, Inc.

  11. Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome.

    Directory of Open Access Journals (Sweden)

    Guillaume Guilbaud

    2011-12-01

    Full Text Available Genome-wide replication timing studies have suggested that mammalian chromosomes consist of megabase-scale domains of coordinated origin firing separated by large originless transition regions. Here, we report a quantitative genome-wide analysis of DNA replication kinetics in several human cell types that contradicts this view. DNA combing in HeLa cells sorted into four temporal compartments of S phase shows that replication origins are spaced at 40 kb intervals and fire as small clusters whose synchrony increases during S phase and that replication fork velocity (mean 0.7 kb/min, maximum 2.0 kb/min remains constant and narrowly distributed through S phase. However, multi-scale analysis of a genome-wide replication timing profile shows a broad distribution of replication timing gradients with practically no regions larger than 100 kb replicating at less than 2 kb/min. Therefore, HeLa cells lack large regions of unidirectional fork progression. Temporal transition regions are replicated by sequential activation of origins at a rate that increases during S phase and replication timing gradients are set by the delay and the spacing between successive origin firings rather than by the velocity of single forks. Activation of internal origins in a specific temporal transition region is directly demonstrated by DNA combing of the IGH locus in HeLa cells. Analysis of published origin maps in HeLa cells and published replication timing and DNA combing data in several other cell types corroborate these findings, with the interesting exception of embryonic stem cells where regions of unidirectional fork progression seem more abundant. These results can be explained if origins fire independently of each other but under the control of long-range chromatin structure, or if replication forks progressing from early origins stimulate initiation in nearby unreplicated DNA. These findings shed a new light on the replication timing program of mammalian genomes and

  12. Influence of Injection-Molding Process Parameters on Part Replication of Microstructures with Additively-Manufactured Soft Tooling Inserts WCMNM 2017 No

    DEFF Research Database (Denmark)

    Mischkot, Michael; Zhang, Yang; Segebrecht Gøtje, Asger

    The objective of this research is to investigate the influence of injection molding parameters on the dimensional replication of microstructure surfaces in injection molding with additively manufactured soft tooling inserts in a photopolymer material. The replication degree of micropillars...... on injection-molded tine rings was assessed and a Design of Experiments (DOE) approach was used to investigate which factors influence the replication. A full factorial analysis with three factors at two levels lead to the conclusion that a high mold temperature increases the replication degree of the pillar...... in the replication degree between inserts on the injection side and the ejector side of the mold respectively. Also, a position closer to the injection gate supports a higher replication degree. Insert wear was found insignificant within the experimental range of up to 100 injection cycles....

  13. Non-determinism in Byzantine Fault-Tolerant Replication

    OpenAIRE

    Cachin, Christian; Vukolic, Marko; Schubert, Simon

    2016-01-01

    Service replication distributes an application over many processes for tolerating faults, attacks, and misbehavior among a subset of the processes. With the recent interest in blockchain technologies, distributed execution of one logical application has become a prominent topic. The established state-machine replication paradigm inherently requires the application to be deterministic. This paper distinguishes three models for dealing with non-determinism in replicated services, where some pro...

  14. Intracellular Detection of Viral Transcription and Replication Using RNA FISH

    Science.gov (United States)

    2016-05-26

    Chapter 14. Intracellular detection of viral transcription and replication using RNA FISH i. Summary/Abstract Many hemorrhagic fever viruses...resolution. However, viral RNA tends to cluster in specific subcellular sites (e.g. viral replication factories). Thus while true single-molecule...assays [4]. Detection of viral RNA allows for in depth interrogation of the subcellular sites of viral replication and such experiments will help further

  15. PTEN regulates RPA1 and protects DNA replication forks

    Science.gov (United States)

    Wang, Guangxi; Li, Yang; Wang, Pan; Liang, Hui; Cui, Ming; Zhu, Minglu; Guo, Limei; Su, Qian; Sun, Yujie; McNutt, Michael A; Yin, Yuxin

    2015-01-01

    Tumor suppressor PTEN regulates cellular activities and controls genome stability through multiple mechanisms. In this study, we report that PTEN is necessary for the protection of DNA replication forks against replication stress. We show that deletion of PTEN leads to replication fork collapse and chromosomal instability upon fork stalling following nucleotide depletion induced by hydroxyurea. PTEN is physically associated with replication protein A 1 (RPA1) via the RPA1 C-terminal domain. STORM and iPOND reveal that PTEN is localized at replication sites and promotes RPA1 accumulation on replication forks. PTEN recruits the deubiquitinase OTUB1 to mediate RPA1 deubiquitination. RPA1 deletion confers a phenotype like that observed in PTEN knockout cells with stalling of replication forks. Expression of PTEN and RPA1 shows strong correlation in colorectal cancer. Heterozygous disruption of RPA1 promotes tumorigenesis in mice. These results demonstrate that PTEN is essential for DNA replication fork protection. We propose that RPA1 is a target of PTEN function in fork protection and that PTEN maintains genome stability through regulation of DNA replication. PMID:26403191

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    ATR, activated by replication stress, protects replication forks locally and suppresses origin firing globally. Here, we show that these functions of ATR are mechanistically coupled. Although initially stable, stalled forks in ATR-deficient cells undergo nucleus-wide breakage after unscheduled...... origin firing generates an excess of single-stranded DNA that exhausts the nuclear pool of RPA. Partial reduction of RPA accelerated fork breakage, and forced elevation of RPA was sufficient to delay such "replication catastrophe" even in the absence of ATR activity. Conversely, unscheduled origin firing...... commonly feature intrinsically high replication stress, this study also provides a molecular rationale for their hypersensitivity to ATR inhibitors....

  17. The architecture and function of the chromatin replication machinery.

    Science.gov (United States)

    Miller, Thomas Cr; Costa, Alessandro

    2017-12-01

    Genomic DNA in eukaryotic cells is packaged into nucleosome arrays. During replication, nucleosomes need to be dismantled ahead of the advancing replication fork and reassembled on duplicated DNA. The architecture and function of the core replisome machinery is now beginning to be elucidated, with recent insights shaping our view on DNA replication processes. Simultaneously, breakthroughs in our mechanistic understanding of epigenetic inheritance allow us to build new models of how histone chaperones integrate with the replisome to reshuffle nucleosomes. The emerging picture indicates that the core eukaryotic DNA replication machinery has evolved elements that handle nucleosomes to facilitate chromatin duplication. Copyright © 2017. Published by Elsevier Ltd.

  18. 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

  19. USP7 is a SUMO deubiquitinase essential for DNA replication

    DEFF Research Database (Denmark)

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

    2016-01-01

    to the accumulation of Ub on SUMOylated proteins, which are displaced away from replisomes. Our findings provide a model explaining the differential accumulation of SUMO and Ub at replication forks and identify an essential role of USP7 in DNA replication that should be considered in the development of USP7...... is maintained at sites of DNA replication in mammalian cells remains unexplored. Here we identify USP7 as a replisome-enriched SUMO deubiquitinase that is essential for DNA replication. By acting on SUMO and SUMOylated proteins, USP7 counteracts their ubiquitination. Inhibition or genetic deletion of USP7 leads...

  20. 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...

  1. Human Cytomegalovirus Induces JC Virus DNA Replication in Human Fibroblasts

    Science.gov (United States)

    Heilbronn, Regine; Albrecht, Ingrid; Stephan, Sonja; Burkle, Alexander; Zur Hausen, Harald

    1993-12-01

    JC virus, a human papovavirus, is the causative agent of the demyelinating brain disease progressive multifocal leucoencephalopathy (PML). PML is a rare but fatal disease which develops as a complication of severe immunosuppression. Latent JC virus is harbored by many asymptomatic carriers and is transiently reactivated from the latent state upon immunosuppression. JC virus has a very restricted host range, with human glial cells being the only tissue in which it can replicate at reasonable efficiency. Evidence that latent human cytomegalovirus is harbored in the kidney similar to latent JC virus led to the speculation that during episodes of impaired immunocompetence, cytomegalovirus might serve as helper virus for JC virus replication in otherwise nonpermissive cells. We show here that cytomegalovirus infection indeed leads to considerable JC virus DNA replication in cultured human fibroblasts that are nonpermissive for the replication of JC virus alone. Cytomegalovirus-mediated JC virus replication is dependent on the JC virus origin of replication and T antigen. Ganciclovir-induced inhibition of cytomegalovirus replication is associated with a concomitant inhibition of JC virus replication. These results suggest that reactivation of cytomegalovirus during episodes of immunosuppression might lead to activation of latent JC virus, which would enhance the probability of subsequent PML development. Ganciclovir-induced repression of both cytomegalovirus and JC virus replication may form the rational basis for the development of an approach toward treatment or prevention of PML.

  2. Energy Proportionality for Disk Storage Using Replication

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jinoh; Rotem, Doron

    2010-09-09

    Energy saving has become a crucial concern in datacenters as several reports predict that the anticipated energy costs over a three year period will exceed hardware acquisition. In particular, saving energy for storage is of major importance as storage devices (and cooling them off) may contribute over 25 percent of the total energy consumed in a datacenter. Recent work introduced the concept of energy proportionality and argued that it is a more relevant metric than just energy saving as it takes into account the tradeoff between energy consumption and performance. In this paper, we present a novel approach, called FREP (Fractional Replication for Energy Proportionality), for energy management in large datacenters. FREP includes areplication strategy and basic functions to enable flexible energy management. Specifically, our method provides performance guarantees by adaptively controlling the power states of a group of disks based on observed and predicted workloads. Our experiments, using a set of real and synthetic traces, show that FREP dramatically reduces energy requirements with a minimal response time penalty.

  3. Synaptic theory of Replicator-like melioration

    Directory of Open Access Journals (Sweden)

    Yonatan Loewenstein

    2010-06-01

    Full Text Available According to the theory of Melioration, organisms in repeated choice settings shift their choice preference in favor of the alternative that provides the highest return. The goal of this paper is to explain how this learning behavior can emerge from microscopic changes in the efficacies of synapses, in the context of two-alternative repeated-choice experiment. I consider a large family of synaptic plasticity rules in which changes in synaptic efficacies are driven by the covariance between reward and neural activity. I construct a general framework that predicts the learning dynamics of any decision-making neural network that implements this synaptic plasticity rule and show that melioration naturally emerges in such networks. Moreover, the resultant learning dynamics follows the Replicator equation which is commonly used to phenomenologically describe changes in behavior in operant conditioning experiments. Several examples demonstrate how the learning rate of the network is affected by its properties and by the specifics of the plasticity rule. These results help bridge the gap between cellular physiology and learning behavior.

  4. Factor Copula Models for Replicated Spatial Data

    KAUST Repository

    Krupskii, Pavel

    2016-12-19

    We propose a new copula model that can be used with replicated spatial data. Unlike the multivariate normal copula, the proposed copula is based on the assumption that a common factor exists and affects the joint dependence of all measurements of the process. Moreover, the proposed copula can model tail dependence and tail asymmetry. The model is parameterized in terms of a covariance function that may be chosen from the many models proposed in the literature, such as the Matérn model. For some choice of common factors, the joint copula density is given in closed form and therefore likelihood estimation is very fast. In the general case, one-dimensional numerical integration is needed to calculate the likelihood, but estimation is still reasonably fast even with large data sets. We use simulation studies to show the wide range of dependence structures that can be generated by the proposed model with different choices of common factors. We apply the proposed model to spatial temperature data and compare its performance with some popular geostatistics models.

  5. Minority games, evolving capitals and replicator dynamics

    Science.gov (United States)

    Galla, Tobias; Zhang, Yi-Cheng

    2009-11-01

    We discuss a simple version of the minority game (MG) in which agents hold only one strategy each, but in which their capitals evolve dynamically according to their success and in which the total trading volume varies in time accordingly. This feature is known to be crucial for MGs to reproduce stylized facts of real market data. The stationary states and phase diagram of the model can be computed, and we show that the ergodicity breaking phase transition common for MGs, and marked by a divergence of the integrated response, is present also in this simplified model. An analogous majority game turns out to be relatively void of interesting features, and the total capital is found to diverge in time. Introducing a restraining force leads to a model akin to the replicator dynamics of evolutionary game theory, and we demonstrate that here a different type of phase transition is observed. Finally we briefly discuss the relation of this model with one strategy per player to more sophisticated minority games with dynamical capitals and several trading strategies per agent.

  6. Inference by replication in densely connected systems.

    Science.gov (United States)

    Neirotti, Juan P; Saad, David

    2007-10-01

    An efficient Bayesian inference method for problems that can be mapped onto dense graphs is presented. The approach is based on message passing where messages are averaged over a large number of replicated variable systems exposed to the same evidential nodes. An assumption about the symmetry of the solutions is required for carrying out the averages; here we extend the previous derivation based on a replica-symmetric- (RS)-like structure to include a more complex one-step replica-symmetry-breaking-like (1RSB-like) ansatz. To demonstrate the potential of the approach it is employed for studying critical properties of the Ising linear perceptron and for multiuser detection in code division multiple access (CDMA) under different noise models. Results obtained under the RS assumption in the noncritical regime give rise to a highly efficient signal detection algorithm in the context of CDMA; while in the critical regime one observes a first-order transition line that ends in a continuous phase transition point. Finite size effects are also observed. While the 1RSB ansatz is not required for the original problems, it was applied to the CDMA signal detection problem with a more complex noise model that exhibits RSB behavior, resulting in an improvement in performance.

  7. The Cell Cycle Timing of Human Papillomavirus DNA Replication.

    Science.gov (United States)

    Reinson, Tormi; Henno, Liisi; Toots, Mart; Ustav, Mart; Ustav, Mart

    2015-01-01

    Viruses manipulate the cell cycle of the host cell to optimize conditions for more efficient viral genome replication. One strategy utilized by DNA viruses is to replicate their genomes non-concurrently with the host genome; in this case, the viral genome is amplified outside S phase. This phenomenon has also been described for human papillomavirus (HPV) vegetative genome replication, which occurs in G2-arrested cells; however, the precise timing of viral DNA replication during initial and stable replication phases has not been studied. We developed a new method to quantitate newly synthesized DNA levels and used this method in combination with cell cycle synchronization to show that viral DNA replication is initiated during S phase and is extended to G2 during initial amplification but follows the replication pattern of cellular DNA during S phase in the stable maintenance phase. E1 and E2 protein overexpression changes the replication time from S only to both the S and G2 phases in cells that stably maintain viral episomes. These data demonstrate that the active synthesis and replication of the HPV genome are extended into the G2 phase to amplify its copy number and the duration of HPV genome replication is controlled by the level of the viral replication proteins E1 and E2. Using the G2 phase for genome amplification may be an important adaptation that allows exploitation of changing cellular conditions during cell cycle progression. We also describe a new method to quantify newly synthesized viral DNA levels and discuss its benefits for HPV research.

  8. Design and analysis of experiments with SAS

    CERN Document Server

    Lawson, John

    2010-01-01

    IntroductionStatistics and Data Collection Beginnings of Statistically Planned Experiments Definitions and Preliminaries Purposes of Experimental Design Types of Experimental Designs Planning Experiments Performing the Experiments Use of SAS SoftwareCompletely Randomized Designs with One Factor Introduction Replication and Randomization A Historical Example Linear Model for Completely Randomized Design (CRD) Verifying Assumptions of the Linear Model Analysis Strategies When Assumptions Are Violated Determining the Number of Replicates Comparison of Treatments after the F-TestFactorial Designs

  9. Hypotension and Environmental Noise: A Replication Study

    Directory of Open Access Journals (Sweden)

    Peter Lercher

    2014-08-01

    Full Text Available Up to now, traffic noise effect studies focused on hypertension as health outcome. Hypotension has not been considered as a potential health outcome although in experiments some people also responded to noise with decreases of blood pressure. Currently, the characteristics of these persons are not known and whether this down regulation of blood pressure is an experimental artifact, selection, or can also be observed in population studies is unanswered. In a cross-sectional replication study, we randomly sampled participants (age 20–75, N = 807 from circular areas (radius = 500 m around 31 noise measurement sites from four noise exposure strata (35–44, 45–54, 55–64, >64 Leq, dBA. Repeated blood pressure measurements were available for a smaller sample (N = 570. Standardized information on socio-demographics, housing, life style and health was obtained by door to door visits including anthropometric measurements. Noise and air pollution exposure was assigned by GIS based on both calculation and measurements. Reported hypotension or hypotension medication past year was the main outcome studied. Exposure-effect relationships were modeled with multiple non-linear logistic regression techniques using separate noise estimations for total, highway and rail exposure. Reported hypotension was significantly associated with rail and total noise exposure and strongly modified by weather sensitivity. Reported hypotension medication showed associations of similar size with rail and total noise exposure without effect modification by weather sensitivity. The size of the associations in the smaller sample with BMI as additional covariate was similar. Other important cofactors (sex, age, BMI, health and moderators (weather sensitivity, adjacent main roads and associated annoyance need to be considered as indispensible part of the observed relationship. This study confirms a potential new noise effect pathway and discusses potential patho

  10. Bypass of a protein barrier by a replicative DNA helicase

    NARCIS (Netherlands)

    Yardimci, Hasan; Wang, Xindan; Loveland, Anna B.; Tappin, Inger; Rudner, David Z.; Hurwitz, Jerard; van Oijen, Antoine M.; Walter, Johannes C.

    2012-01-01

    Replicative DNA helicases generally unwind DNA as a single hexamer that encircles and translocates along one strand of the duplex while excluding the complementary strand (known as steric exclusion). By contrast, large T antigen, the replicative DNA helicase of the simian virus 40 (SV40), is

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    Proliferating cells acquire genome alterations during the act of DNA replication. This leads to mutation accumulation and somatic cell mosaicism in multicellular organisms, and is also implicated as an underlying cause of aging and tumorigenesis. The molecular mechanisms of DNA replication-associ...

  12. Trajectory of Externalizing Child Behaviors in a KEEP Replication

    Science.gov (United States)

    Uretsky, Mathew C.; Lee, Bethany R.; Greeno, Elizabeth J.; Barth, Richard P.

    2017-01-01

    Objective: The purpose of this study is to examine the correlates of child behavior change over time in a replication of the KEEP intervention. Method: The study sample was drawn from the treatment group of the Maryland replication of KEEP (n=65). Change over time was analyzed using multilevel linear mixed modeling. Results: Parents' use of…

  13. Parallelizing Federated SPARQL Queries in Presence of Replicated Data

    DEFF Research Database (Denmark)

    Minier, Thomas; Montoya, Gabriela; Skaf-Molli, Hala

    2017-01-01

    Federated query engines have been enhanced to exploit new data localities created by replicated data, e.g., Fedra. However, existing replication aware federated query engines mainly focus on pruning sources during the source selection and query decomposition in order to reduce intermediate results...

  14. The Causes and Consequences of Topological Stress during DNA Replication.

    Science.gov (United States)

    Keszthelyi, Andrea; Minchell, Nicola E; Baxter, Jonathan

    2016-12-21

    The faithful replication of sister chromatids is essential for genomic integrity in every cell division. The replication machinery must overcome numerous difficulties in every round of replication, including DNA topological stress. Topological stress arises due to the double-stranded helical nature of DNA. When the strands are pulled apart for replication to occur, the intertwining of the double helix must also be resolved or topological stress will arise. This intrinsic problem is exacerbated by specific chromosomal contexts encountered during DNA replication. The convergence of two replicons during termination, the presence of stable protein-DNA complexes and active transcription can all lead to topological stresses being imposed upon DNA replication. Here we describe how replication forks respond to topological stress by replication fork rotation and fork reversal. We also discuss the genomic contexts where topological stress is likely to occur in eukaryotes, focusing on the contribution of transcription. Finally, we describe how topological stress, and the ways forks respond to it, may contribute to genomic instability in cells.

  15. Replication stress in Mammalian cells and its consequences for mitosis.

    Science.gov (United States)

    Gelot, Camille; Magdalou, Indiana; Lopez, Bernard S

    2015-05-22

    The faithful transmission of genetic information to daughter cells is central to maintaining genomic stability and relies on the accurate and complete duplication of genetic material during each cell cycle. However, the genome is routinely exposed to endogenous and exogenous stresses that can impede the progression of replication. Such replication stress can be an early cause of cancer or initiate senescence. Replication stress, which primarily occurs during S phase, results in consequences during mitosis, jeopardizing chromosome segregation and, in turn, genomic stability. The traces of replication stress can be detected in the daughter cells during G1 phase. Alterations in mitosis occur in two types: 1) local alterations that correspond to breaks, rearrangements, intertwined DNA molecules or non-separated sister chromatids that are confined to the region of the replication dysfunction; 2) genome-wide chromosome segregation resulting from centrosome amplification (although centrosomes do not contain DNA), which amplifies the local replication stress to the entire genome. Here, we discuss the endogenous causes of replication perturbations, the mechanisms of replication fork restart and the consequences for mitosis, chromosome segregation and genomic stability.

  16. 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.

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

    Indian Academy of Sciences (India)

    2015-11-28

    Nov 28, 2015 ... mously Replicating Sequence (ARS) elements (reviewed in Campbell and Newlon 1991) function as replication origins in plasmids as well as in chromosomes. ARS elements can be identified by cloning and transformation analysis (also called ARS assay) as plasmids bearing them transform yeast cells.

  18. The Genomic Replication of the Crenarchaeal Virus SIRV2

    DEFF Research Database (Denmark)

    Martinez Alvarez, Laura

    Archaeal viruses have been found to be remarkably diverse in terms of their morphologies and genomes. But knowledge about their replication cycles and interactions with their hosts is still lacking. The aim of this work was to gain insight about the molecular mechanism of the genomic replication ...

  19. Unveiling the mystery of mitochondrial DNA replication in yeasts.

    Science.gov (United States)

    Chen, Xin Jie; Clark-Walker, George Desmond

    2018-01-01

    Conventional DNA replication is initiated from specific origins and requires the synthesis of RNA primers for both the leading and lagging strands. In contrast, the replication of yeast mitochondrial DNA is origin-independent. The replication of the leading strand is likely primed by recombinational structures and proceeded by a rolling circle mechanism. The coexistent linear and circular DNA conformers facilitate the recombination-based initiation. The replication of the lagging strand is poorly understood. Re-evaluation of published data suggests that the rolling circle may also provide structures for the synthesis of the lagging-strand by mechanisms such as template switching. Thus, the coupling of recombination with rolling circle replication and possibly, template switching, may have been selected as an economic replication mode to accommodate the reductive evolution of mitochondria. Such a replication mode spares the need for conventional replicative components, including those required for origin recognition/remodelling, RNA primer synthesis and lagging-strand processing. Copyright © 2017 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

  20. Fidelity of a human cell DNA replication complex

    International Nuclear Information System (INIS)

    Roberts, J.D.; Kunkel, T.A.

    1988-01-01

    The authors have measured the fidelity of bidirectional, semiconservative DNA synthesis by a human DNA replication complex in vitro. Replication was performed by extracts of HeLa cells in the presence of simian virus 40 (SV40) large tumor antigen by using a double-stranded phage M13mp2 DNA template containing the SV40 origin of replication and either of two different target sequences for scoring mutations in the lacZα-complementation gene, which encodes the α region (specifying the amino-terminal portion) of β-galactosidase. Replicative synthesis was substantially more accurate than synthesis by the human DNA polymerase α-DNA primase complex purified from HeLa cell extracts by immunoaffinity chromatography, suggesting that additional factors or activities in the extract may increase fidelity during bidirectional replication. However, by using a sensitive opal codon reversion assay, single-base substitution errors were readily detected in the replication products at frequencies significantly higher than estimated spontaneous mutation rates in vivo. These data suggest that additional fidelity factors may be present during chromosomal replication in vivo and/or that the fidelity of replication alone does not account for the low spontaneous mutation rates in eukaryotes

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

    NARCIS (Netherlands)

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

    2016-01-01

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

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

    Indian Academy of Sciences (India)

    2015-11-28

    Nov 28, 2015 ... ImageJ and Adobe Photoshop 7 soft-wares. 3. Results and discussion. To study the effect of the chromosomal context on replication origin activity and replication timing of ars2004 and ars727, our first goal was to make context specific clones containing the ura4 gene as a selectable marker. This was ...

  3. Three attempts to replicate the moral licensing effect

    NARCIS (Netherlands)

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

    2014-01-01

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

  4. Nidovirus replication structures : hijacking membranes to support viral RNA synthesis

    NARCIS (Netherlands)

    Knoops, Kèvin

    2011-01-01

    Positive-stranded RNA viruses replicate in the cytoplasm of host cells and their replication complexes are associated with modified cell membranes. We investigated the structure of the nidovirus-induced membrane modifications and found that nidoviruses transform the endoplasmic reticulum into a

  5. Fidelity of a human cell DNA replication complex

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, J.D.; Kunkel, T.A. (National Institute of Environmental Health Sciences, Research Triangle Park, NC (USA))

    1988-10-01

    The authors have measured the fidelity of bidirectional, semiconservative DNA synthesis by a human DNA replication complex in vitro. Replication was performed by extracts of HeLa cells in the presence of simian virus 40 (SV40) large tumor antigen by using a double-stranded phage M13mp2 DNA template containing the SV40 origin of replication and either of two different target sequences for scoring mutations in the lacZ{alpha}-complementation gene, which encodes the {alpha} region (specifying the amino-terminal portion) of {beta}-galactosidase. Replicative synthesis was substantially more accurate than synthesis by the human DNA polymerase {alpha}-DNA primase complex purified from HeLa cell extracts by immunoaffinity chromatography, suggesting that additional factors or activities in the extract may increase fidelity during bidirectional replication. However, by using a sensitive opal codon reversion assay, single-base substitution errors were readily detected in the replication products at frequencies significantly higher than estimated spontaneous mutation rates in vivo. These data suggest that additional fidelity factors may be present during chromosomal replication in vivo and/or that the fidelity of replication alone does not account for the low spontaneous mutation rates in eukaryotes.

  6. Poverty and suicide among native Canadians: a replication.

    Science.gov (United States)

    Bagley, C

    1991-08-01

    In replication of USA research, poverty and suicide were shown to have strong positive correlations in an ecological study of males, aged 15 to 34 years, in 26 Native reservations in Alberta, Canada. The importance of cross-cultural research in replicating and refining psychological research is stressed.

  7. Replication of Psycholinguistic Experiments and the Resolution of Inconsistencies

    Science.gov (United States)

    Rákosi, Csilla

    2017-01-01

    Non-exact replications are regarded as effective tools of problem solving in psycholinguistic research because they lead to more plausible experimental results; however, they are also ineffective tools of problem solving because they trigger cumulative contradictions among different replications of an experiment. This paper intends to resolve this…

  8. 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

  9. Template role of double-stranded RNA in tombusvirus replication.

    Science.gov (United States)

    Kovalev, Nikolay; Pogany, Judit; Nagy, Peter D

    2014-05-01

    Replication of plus-strand RNA [(+)RNA] viruses of plants is a relatively simple process that involves complementary minus-strand RNA [(-)RNA] synthesis and subsequent (+)RNA synthesis. However, the actual replicative form of the (-)RNA template in the case of plant (+)RNA viruses is not yet established unambiguously. In this paper, using a cell-free replication assay supporting a full cycle of viral replication, we show that replication of Tomato bushy stunt virus (TBSV) leads to the formation of double-stranded RNA (dsRNA). Using RNase digestion, DNAzyme, and RNA mobility shift assays, we demonstrate the absence of naked (-)RNA templates during replication. Time course experiments showed the rapid appearance of dsRNA earlier than the bulk production of new (+)RNAs, suggesting an active role for dsRNA in replication. Radioactive nucleotide chase experiments showed that the mechanism of TBSV replication involves the use of dsRNA templates in strand displacement reactions, where the newly synthesized plus strand replaces the original (+)RNA in the dsRNA. We propose that the use of dsRNA as a template for (+)RNA synthesis by the viral replicase is facilitated by recruited host DEAD box helicases and the viral p33 RNA chaperone protein. Altogether, this replication strategy allows TBSV to separate minus- and plus-strand syntheses in time and regulate asymmetrical RNA replication that leads to abundant (+)RNA progeny. Positive-stranded RNA viruses of plants use their RNAs as the templates for replication. First, the minus strand is synthesized by the viral replicase complex (VRC), which then serves as a template for new plus-strand synthesis. To characterize the nature of the (-)RNA in the membrane-bound viral replicase, we performed complete RNA replication of Tomato bushy stunt virus (TBSV) in yeast cell-free extracts and in plant extracts. The experiments demonstrated that the TBSV (-)RNA is present as a double-stranded RNA that serves as the template for TBSV

  10. 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.

  11. 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.

  12. 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

  13. Viral trans-factor independent replication of human papillomavirus genomes

    Directory of Open Access Journals (Sweden)

    Angeletti Peter C

    2010-06-01

    Full Text Available Abstract Background Papillomaviruses (PVs establish a persistent infection in the proliferating basal cells of the epithelium. The viral genome is replicated and maintained as a low-copy nuclear plasmid in basal keratinocytes. Bovine and human papillomaviruses (BPV and HPV are known to utilize two viral proteins; E1, a DNA helicase, and E2, a transcription factor, which have been considered essential for viral DNA replication. However, growing evidence suggests that E1 and E2 are not entirely essential for stable replication of HPV. Results Here we report that multiple HPV16 mutants, lacking either or both E1 and E2 open reading frame (ORFs and the long control region (LCR, still support extrachromosomal replication. Our data clearly indicate that HPV16 has a mode of replication, independent of viral trans-factors, E1 and E2, which is achieved by origin activity located outside of the LCR.

  14. Replication-Coupled Modulation of Early Replicating Chromatin Domains Detected by an Anti-Actin Antibody

    Czech Academy of Sciences Publication Activity Database

    Fidlerová, Helena; Mašata, Martin; Malínský, Jan; Fialová, Markéta; Cvačková, Zuzana; Loužecká, A.; Koberna, Karel; Berezney, R.; Raška, Ivan

    2005-01-01

    Roč. 94, č. 5 (2005), 899-916 ISSN 0730-2312 R&D Projects: GA ČR GA304/00/1622; GA ČR GA304/03/1121; GA ČR GA304/04/0692; GA ČR GA304/02/0342; GA AV ČR IAA5039103 Institutional research plan: CEZ:AV0Z5039906; MSM111100003 Keywords : DNA replication * chromatin * cell cycle Subject RIV: EA - Cell Biology Impact factor: 3.591, year: 2005

  15. Estimating Effect Sizes and Expected Replication Probabilities from GWAS Summary Statistics

    DEFF Research Database (Denmark)

    Holland, Dominic; Wang, Yunpeng; Thompson, Wesley K

    2016-01-01

    9.3 million SNP z-scores in both cases. We show that, over a broad range of z-scores and sample sizes, the model accurately predicts expectation estimates of true effect sizes and replication probabilities in multistage GWAS designs. We assess the degree to which effect sizes are over-estimated when......-scores, as such knowledge would enhance causal SNP and gene discovery, help elucidate mechanistic pathways, and inform future study design. Here we present a parsimonious methodology for modeling effect sizes and replication probabilities, relying only on summary statistics from GWAS substudies, and a scheme allowing...... for direct empirical validation. We show that modeling z-scores as a mixture of Gaussians is conceptually appropriate, in particular taking into account ubiquitous non-null effects that are likely in the datasets due to weak linkage disequilibrium with causal SNPs. The four-parameter model allows...

  16. 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.

  17. 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, Tu...

  18. 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

  19. Establishing a coherent and replicable measurement model of the Edinburgh Postnatal Depression Scale.

    Science.gov (United States)

    Martin, Colin R; Redshaw, Maggie

    2018-03-23

    The 10-item Edinburgh Postnatal Depression Scale (EPDS) is an established screening tool for postnatal depression. Inconsistent findings in factor structure and replication difficulties have limited the scope of development of the measure as a multi-dimensional tool. The current investigation sought to robustly determine the underlying factor structure of the EPDS and the replicability and stability of the most plausible model identified. A between-subjects design was used. EPDS data were collected postpartum from two independent cohorts using identical data capture methods. Datasets were examined with confirmatory factor analysis, model invariance testing and systematic evaluation of relational and internal aspects of the measure. Participants were two samples of postpartum women in England assessed at three months (n = 245) and six months (n = 217). The findings showed a three-factor seven-item model of the EPDS offered an excellent fit to the data, and was observed to be replicable in both datasets and invariant as a function of time point of assessment. Some EPDS sub-scale scores were significantly higher at six months. The EPDS is multi-dimensional and a robust measurement model comprises three factors that are replicable. The potential utility of the sub-scale components identified requires further research to identify a role in contemporary screening practice. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

  20. NMR structure of the N-terminal domain of the replication initiator protein DnaA

    Energy Technology Data Exchange (ETDEWEB)

    Wemmer, David E.; Lowery, Thomas J.; Pelton, Jeffrey G.; Chandonia, John-Marc; Kim, Rosalind; Yokota, Hisao; Wemmer, David E.

    2007-08-07

    DnaA is an essential component in the initiation of bacterial chromosomal replication. DnaA binds to a series of 9 base pair repeats leading to oligomerization, recruitment of the DnaBC helicase, and the assembly of the replication fork machinery. The structure of the N-terminal domain (residues 1-100) of DnaA from Mycoplasma genitalium was determined by NMR spectroscopy. The backbone r.m.s.d. for the first 86 residues was 0.6 +/- 0.2 Angstrom based on 742 NOE, 50 hydrogen bond, 46 backbone angle, and 88 residual dipolar coupling restraints. Ultracentrifugation studies revealed that the domain is monomeric in solution. Features on the protein surface include a hydrophobic cleft flanked by several negative residues on one side, and positive residues on the other. A negatively charged ridge is present on the opposite face of the protein. These surfaces may be important sites of interaction with other proteins involved in the replication process. Together, the structure and NMR assignments should facilitate the design of new experiments to probe the protein-protein interactions essential for the initiation of DNA replication.

  1. A replicated association between polymorphisms near TNFα and risk for adverse reactions to radiotherapy

    Science.gov (United States)

    Talbot, C J; Tanteles, G A; Barnett, G C; Burnet, N G; Chang-Claude, J; Coles, C E; Davidson, S; Dunning, A M; Mills, J; Murray, R J S; Popanda, O; Seibold, P; West, C M L; Yarnold, J R; Symonds, R P

    2012-01-01

    Background: Response to radiotherapy varies between individuals both in terms of efficacy and adverse reactions. Finding genetic determinants of radiation response would allow the tailoring of the treatment, either by altering the radiation dose or by surgery. Despite a growing number of studies in radiogenomics, there are no well-replicated genetic association results. Methods: We carried out a candidate gene association study and replicated the result using three additional large cohorts, a total of 2036 women scored for adverse reactions to radiotherapy for breast cancer. Results: Genetic variation near the tumour necrosis factor alpha gene is shown to affect several clinical endpoints including breast induration, telangiectasia and overall toxicity. In the combined analysis homozygosity for the rare allele increases overall toxicity (P=0.001) and chance of being in the upper quartile of risk with odds ratio of 2.46 (95% confidence interval 1.52–3.98). Conclusion: We have identified that alleles of the class III major histocompatibility complex region associate with overall radiotherapy toxicity in breast cancer patients by using internal replication through a staged design. This is the first well-replicated report of a genetic predictor for radiotherapy reactions. PMID:22767148

  2. Efficient inhibition of HIV-1 replication by an artificial polycistronic miRNA construct

    Directory of Open Access Journals (Sweden)

    Zhang Tao

    2012-06-01

    Full Text Available Abstract Background RNA interference (RNAi has been used as a promising approach to inhibit human immunodeficiency virus type 1 (HIV-1 replication for both in vitro and in vivo animal models. However, HIV-1 escape mutants after RNAi treatment have been reported. Expressing multiple small interfering RNAs (siRNAs against conserved viral sequences can serve as a genetic barrier for viral escape, and optimization of the efficiency of this process was the aim of this study. Results An artificial polycistronic transcript driven by a CMV promoter was designed to inhibit HIV-1 replication. The artificial polycistronic transcript contained two pre-miR-30a backbones and one pre-miR-155 backbone, which are linked by a sequence derived from antisense RNA sequence targeting the HIV-1 env gene. Our results demonstrated that this artificial polycistronic transcript simultaneously expresses three anti-HIV siRNAs and efficiently inhibits HIV-1 replication. In addition, the biosafety of MT-4 cells expressing this polycistronic miRNA transcript was evaluated, and no apparent impacts on cell proliferation rate, interferon response, and interruption of native miRNA processing were observed. Conclusions The strategy described here to generate an artificial polycistronic transcript to inhibit viral replication provided an opportunity to select and optimize many factors to yield highly efficient constructs expressing multiple siRNAs against viral infection.

  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. Lattice and compact family block designs in forest genetics

    Science.gov (United States)

    E. Bayne Snyder

    1966-01-01

    One of the principles of experimental design is that replicates be relatively homogeneous. Thus, in forest research a replicate is often assigned to a single crew for planting in a single day on a uniform site. When treatments are numerous, a large area is required per replication, and homogeneity of site is difficult to achieve. In this situation, crop scientists (...

  5. Implicit and explicit memory bias in anxiety: a conceptual replication.

    Science.gov (United States)

    MacLeod, C; McLaughlin, K

    1995-01-01

    Williams, Watts, MacLeod and Mathews' (1988) [Cognitive psychology and the emotional disorders. Chichester, Wiley] model of anxiety and cognition leads to the prediction that anxious subjects will show an implicit, but not an explicit, memory advantage for threat-related information. Mathews, Mogg, May and Eysenck (1989) [Journal of Abnormal Psychology, 98, 401-407] obtained marginally significant support for this prediction in an experiment that tested memory using word stem completion tasks following a self-referent encoding procedure. However, neither the reliability nor generality of these findings have been established. The current experiment was designed to provide a conceptual replication of Mathews et al.'s study, using different tests of implicit memory (i.e. tachistoscopic identification) and explicit memory (i.e. recognition) and an alternative type of encoding task (i.e. colour naming stimulus words). 16 generalised anxiety disorder patients, and 16 non-anxious control subjects were tested. As predicted, the anxiety patients showed a relative implicit memory advantage for threat-related stimulus words, while the two subject groups did not differ in their pattern of explicit memory performance. These results support the predictions generated by Williams et al.'s model of anxiety and cognition.

  6. A comprehensive family-based replication study of schizophrenia genes

    DEFF Research Database (Denmark)

    Aberg, Karolina A; Liu, Youfang; Bukszár, Jozsef

    2013-01-01

    (P = 9.01 × 10-7), CNNM2 (P = 6.07 × 10-7), and NT5C2 (P = 4.09 × 10-7). To explore the many small effects, we performed pathway analyses. The most significant pathways involved neuronal function (axonal guidance, neuronal systems, and L1 cell adhesion molecule interaction) and the immune system...... genes. DESIGN We integrated results from a meta-analysis of 18 genome-wide association studies (GWAS) involving 1 085 772 single-nucleotide polymorphisms (SNPs) and 6 databases that showed significant informativeness for SCZ. The 9380 most promising SNPs were then specifically genotyped...... in an independent family-based replication study that, after quality control, consisted of 8107 SNPs. SETTING Linkage meta-analysis, brain transcriptome meta-analysis, candidate gene database, OMIM, relevant mouse studies, and expression quantitative trait locus databases. PATIENTS We included 11 185 cases and 10...

  7. 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.

  8. Inhibitors of Nucleotidyltransferase Superfamily Enzymes Suppress Herpes Simplex Virus Replication

    Science.gov (United States)

    Wang, Hong; Tollefson, Ann E.; Ying, Baoling; Korom, Maria; Cheng, Xiaohong; Cao, Feng; Davis, Katie L.; Wold, William S. M.

    2014-01-01

    Herpesviruses are large double-stranded DNA viruses that cause serious human diseases. Herpesvirus DNA replication depends on multiple processes typically catalyzed by nucleotidyltransferase superfamily (NTS) enzymes. Therefore, we investigated whether inhibitors of NTS enzymes would suppress replication of herpes simplex virus 1 (HSV-1) and HSV-2. Eight of 42 NTS inhibitors suppressed HSV-1 and/or HSV-2 replication by >10-fold at 5 μM, with suppression at 50 μM reaching ∼1 million-fold. Five compounds in two chemical families inhibited HSV replication in Vero and human foreskin fibroblast cells as well as the approved drug acyclovir did. The compounds had 50% effective concentration values as low as 0.22 μM with negligible cytotoxicity in the assays employed. The inhibitors suppressed accumulation of viral genomes and infectious particles and blocked events in the viral replication cycle before and during viral DNA replication. Acyclovir-resistant mutants of HSV-1 and HSV-2 remained highly sensitive to the NTS inhibitors. Five of six NTS inhibitors of the HSVs also blocked replication of another herpesvirus pathogen, human cytomegalovirus. Therefore, NTS enzyme inhibitors are promising candidates for new herpesvirus treatments that may have broad efficacy against members of the herpesvirus family. PMID:25267681

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

    Science.gov (United States)

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

    2016-05-05

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

  10. Specificity and function of Archaeal DNA replication initiator proteins

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  11. On the Growth Rate of Non-Enzymatic Molecular Replicators

    Directory of Open Access Journals (Sweden)

    Harold Fellermann

    2011-10-01

    Full Text Available It is well known that non-enzymatic template directed molecular replicators X + nO -> 2X exhibit parabolic growth d[X]/dt -> k[X]1/2. Here, we analyze the dependence of the effective replication rate constant k on hybridization energies, temperature, strand length, and sequence composition. First we derive analytical criteria for the replication rate k based on simple thermodynamic arguments. Second we present a Brownian dynamics model for oligonucleotides that allows us to simulate their diffusion and hybridization behavior. The simulation is used to generate and analyze the effect of strand length, temperature, and to some extent sequence composition, on the hybridization rates and the resulting optimal overall rate constant k. Combining the two approaches allows us to semi-analytically depict a replication rate landscape for template directed replicators. The results indicate a clear replication advantage for longer strands at lower temperatures in the regime where the ligation rate is rate limiting. Further the results indicate the existence of an optimal replication rate at the boundary between the two regimes where the ligation rate and the dehybridization rates are rate limiting.

  12. The High Energy Replicated Optics to Explore the Sun (HEROES)

    Science.gov (United States)

    Christe, Steven; Shih, A. Y.; Rodriguez, M.; Cramer, A.; Gregory, K.; Gaskin, J.; Chavis, K.; Smith, L.; HOPE/HEROES Team

    2013-07-01

    Set to fly in the Fall of 2013 from Ft. Sumner, NM, the High Energy Replicated Optics to Explore the Sun (HEROES) mission is a collaboration between NASA Marshall Space Flight Center and Goddard Space Flight Center to upgrade an existing payload to make unique scientific measurements of the Sun (during the day) and astrophysical targets (at night) during a single flight. HEROES will use grazing-incidence x-ray focusing optics combined with position-sensitive detectors to make new high energy 20 keV to 75 keV) observations of the Sun in order to understand particle acceleration in solar flares. The HEROES science payload consists of 8 mirror modules, housing 109 grazing incidence replicated optics, mounted on a carbon-fiber-Aluminum optical bench 6 m from a matching array of focal-plane detectors (high pressure xenon gas scintillation proportional counters). HEROES will investigate electron acceleration and transport in the solar corona both in the solar flares and in the non-flaring quiet Sun. HEROES will image the Sun with an angular resolution of 20 arcsec (FWHM) and will have a sensitivity up to ~50 times better than RHESSI at 20 keV. During 6 hours of solar observations (a minimum requirement for a typical balloon flight), HEROES has a ~75% chance of observing at least one flare with a GOES class above C1, and a ~20% chance of at least one flare above M1. HEROES is expected to observe the faint HXR emission from electrons streaming down the legs of magnetic loops or escaping along open magnetic field lines. Experience on this flight will be used to design of new balloon payload (Super HERO) capable of capable of observing the Sun for 2-4 weeks using a Long Duration Balloon (LDB). This mission is funded by the NASA HOPE (Hands On Project Experience) Training Opportunity awarded by the NASA Academy of Program/Project and Engineering Leadership in partnership with NASA's Science Mission Directorate, Office of the Chief Engineer, and Office of the Chief

  13. 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...... complex (preRC) formation are based on studies from yeast and Xenopus, while much less is known for mammalian cells. Here we discuss our recent data demonstrating that Geminin is required for preventing rereplication in human normal and cancer cells....

  14. The Bimodal Lifestyle of Intracellular Salmonella in Epithelial Cells: Replication in the Cytosol Obscures Defects in Vacuolar Replication

    Science.gov (United States)

    Steele-Mortimer, Olivia

    2012-01-01

    Salmonella enterica serovar Typhimurium invades and proliferates within epithelial cells. Intracellular bacteria replicate within a membrane bound vacuole known as the Salmonella containing vacuole. However, this bacterium can also replicate efficiently in the cytosol of epithelial cells and net intracellular growth is a product of both vacuolar and cytosolic replication. Here we have used semi-quantitative single-cell analyses to investigate the contribution of each of these replicative niches to intracellular proliferation in cultured epithelial cells. We show that cytosolic replication can account for the majority of net replication even though it occurs in less than 20% of infected cells. Consequently, assays for net growth in a population of infected cells, for example by recovery of colony forming units, are not good indicators of vacuolar proliferation. We also show that the Salmonella Type III Secretion System 2, which is required for SCV biogenesis, is not required for cytosolic replication. Altogether this study illustrates the value of single cell analyses when studying intracellular pathogens. PMID:22719929

  15. LPEseq: Local-Pooled-Error Test for RNA Sequencing Experiments with a Small Number of Replicates.

    Science.gov (United States)

    Gim, Jungsoo; Won, Sungho; Park, Taesung

    2016-01-01

    RNA-Sequencing (RNA-Seq) provides valuable information for characterizing the molecular nature of the cells, in particular, identification of differentially expressed transcripts on a genome-wide scale. Unfortunately, cost and limited specimen availability often lead to studies with small sample sizes, and hypothesis testing on differential expression between classes with a small number of samples is generally limited. The problem is especially challenging when only one sample per each class exists. In this case, only a few methods among many that have been developed are applicable for identifying differentially expressed transcripts. Thus, the aim of this study was to develop a method able to accurately test differential expression with a limited number of samples, in particular non-replicated samples. We propose a local-pooled-error method for RNA-Seq data (LPEseq) to account for non-replicated samples in the analysis of differential expression. Our LPEseq method extends the existing LPE method, which was proposed for microarray data, to allow examination of non-replicated RNA-Seq experiments. We demonstrated the validity of the LPEseq method using both real and simulated datasets. By comparing the results obtained using the LPEseq method with those obtained from other methods, we found that the LPEseq method outperformed the others for non-replicated datasets, and showed a similar performance with replicated samples; LPEseq consistently showed high true discovery rate while not increasing the rate of false positives regardless of the number of samples. Our proposed LPEseq method can be effectively used to conduct differential expression analysis as a preliminary design step or for investigation of a rare specimen, for which a limited number of samples is available.

  16. A loss of function analysis of host factors influencing Vaccinia virus replication by RNA interference.

    Directory of Open Access Journals (Sweden)

    Philippa M Beard

    Full Text Available Vaccinia virus (VACV is a large, cytoplasmic, double-stranded DNA virus that requires complex interactions with host proteins in order to replicate. To explore these interactions a functional high throughput small interfering RNA (siRNA screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF influencing the replication and spread of an eGFP-tagged VACV. The experimental design incorporated a low multiplicity of infection, thereby enhancing detection of cellular proteins involved in cell-to-cell spread of VACV. The screen revealed 153 pro- and 149 anti-viral HFs that strongly influenced VACV replication. These HFs were investigated further by comparisons with transcriptional profiling data sets and HFs identified in RNAi screens of other viruses. In addition, functional and pathway analysis of the entire screen was carried out to highlight cellular mechanisms involved in VACV replication. This revealed, as anticipated, that many pro-viral HFs are involved in translation of mRNA and, unexpectedly, suggested that a range of proteins involved in cellular transcriptional processes and several DNA repair pathways possess anti-viral activity. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. This advancement in our understanding of the VACV life cycle provides a reliable knowledge base for the improvement of poxvirus-based vaccine vectors and development of anti-viral theraputics.

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    Precision molding and micro injection molding (μIM) have been the main replication technologies allowing for a rapid reduction of the dimensions of the products and, consequently, for the realization of new advanced micro and nano systems. Such miniaturization in the manufacture of polymer micro......, 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......, a detailed knowledge is necessary of not only absolute dimensions and geometrical quantities, but also of the measurement uncertainty, which is a decisive parameter to deal with the quality assurance of micro and nano manufactured components [5].In this context, the quality of the achieved surface texture...

  18. Advanced Optical Metrology for XRAY Replication Mandrels and Mirrors Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Advanced x-ray observatories such as IXO and GenX will require thousands of thin shell mirror segments produced by replication using convex mandrels. Quality and...

  19. Viral and Cellular Components of AAV2 Replication Compartments

    Science.gov (United States)

    Vogel, Rebecca; Seyffert, Michael; Pereira, Bruna de Andrade; Fraefel, Cornel

    2013-01-01

    Adeno-associated virus 2 (AAV2) is a helpervirus-dependent parvovirus with a bi-phasic life cycle comprising latency in absence and lytic replication in presence of a helpervirus, such as adenovirus (Ad) or herpes simplex virus type 1 (HSV-1). Helpervirus-supported AAV2 replication takes place in replication compartments (RCs) in the cell nucleus where virus DNA replication and transcription occur. RCs consist of a defined set of helper virus-, AAV2-, and cellular proteins. Here we compare the profile of cellular proteins recruited into AAV2 RCs or identified in Rep78-associated complexes when either Ad or HSV-1 is the helpervirus, and we discuss the potential roles of some of these proteins in AAV2 and helpervirus infection. PMID:24222808

  20. Submicron Composite Mirror Replication (PDRT08-027), Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR program will identify and address the primary technical issues that limit the current precision of replicated CFRP optics. These issues must be resolved to...

  1. RAD51 Interconnects Between DNA Replication DNA Repair and Immunity

    Data.gov (United States)

    National Aeronautics and Space Administration — RAD51 a multifunctional protein plays a central role in DNA replication and homologous recombination repair and is known to be involved in cancer development. We...

  2. Function of BRCA1 at a DNA Replication Origin

    National Research Council Canada - National Science Library

    Lieberman, Paul

    2004-01-01

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

  3. EPA Lean Government Initiative: How to Replicate Lean Successes

    Science.gov (United States)

    This Lean Replication Primer describes how EPA Offices and Regions can identify and adapt successful practices from previous Lean projects to “replicate” their successes and generate further improvements.

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

    Science.gov (United States)

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

    2015-01-01

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

  5. DNA replication, development and cancer: a homeotic connection?

    Science.gov (United States)

    Falaschi, Arturo; Abdurashidova, Gulnara; Biamonti, Giuseppe

    2010-02-01

    The homeotic proteins are transcription factors, highly conserved in metazoan organisms, exerting a pivotal role in development and differentiation. They individually display a loose specificity for the DNA sequence they can bind, but operate mainly in multi-molecular associations that assure their target and function specificity. Homeotic proteins are known to play a role in the positive or negative regulation of cell proliferation. Furthermore, many homeotic proteins are actually proto-oncogenes, since different translocations involving their genes cause tumors, particularly in the hematopoietic system. A one-hybrid screen to detect proteins with affinity for the lamin B2 replication origin identified three homeotic proteins, namely HoxA13, HoxC10 and HoxC13. Recent data demonstrate that the HoxC13 oncoprotein specifically associates with replication foci and binds in vitro and in vivo to several human DNA replication origins. Moreover, Hox proteins interact with geminin, a regulator of cell cycle progression, and control the interaction of this protein with the DNA replication licensing factor Ctd1. Thus, the homeotic proteins, by participating directly in the function of DNA replication origins, may provide a direct link between the accurate regulation of DNA replication required by the morphogenetic program and the deregulation of this process typical of cancer.

  6. 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. Thus, the guanidine-sensitive step in RNA synthesis is important throughout the virus life cycle in cells....... 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...

  7. The INO80 remodeller in transcription, replication and repair.

    Science.gov (United States)

    Poli, Jérôme; Gasser, Susan M; Papamichos-Chronakis, Manolis

    2017-10-05

    The accessibility of eukaryotic genomes to the action of enzymes involved in transcription, replication and repair is maintained despite the organization of DNA into nucleosomes. This access is often regulated by the action of ATP-dependent nucleosome remodellers. The INO80 class of nucleosome remodellers has unique structural features and it is implicated in a diverse array of functions, including transcriptional regulation, DNA replication and DNA repair. Underlying these diverse functions is the catalytic activity of the main ATPase subunit, which in the context of a multisubunit complex can shift nucleosomes and carry out histone dimer exchange. In vitro studies showed that INO80 promotes replication fork progression on a chromatin template, while in vivo it was shown to facilitate replication fork restart after stalling and to help evict RNA polymerase II at transcribed genes following the collision of a replication fork with transcription. More recent work in yeast implicates INO80 in the general eviction and degradation of nucleosomes following high doses of oxidative DNA damage. Beyond these replication and repair functions, INO80 was shown to repress inappropriate transcription at promoters in the opposite direction to the coding sequence. Here we discuss the ways in which INO80's diverse functions help maintain genome integrity.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'. © 2017 The Author(s).

  8. ATM Couples Replication Stress and Metabolic Reprogramming during Cellular Senescence

    Directory of Open Access Journals (Sweden)

    Katherine M. Aird

    2015-05-01

    Full Text Available Replication stress induced by nucleotide deficiency plays an important role in cancer initiation. Replication stress in primary cells typically activates the cellular senescence tumor-suppression mechanism. Senescence bypass correlates with development of cancer, a disease characterized by metabolic reprogramming. However, the role of metabolic reprogramming in the cellular response to replication stress has been little explored. Here, we report that ataxia telangiectasia mutated (ATM plays a central role in regulating the cellular response to replication stress by shifting cellular metabolism. ATM inactivation bypasses senescence induced by replication stress triggered by nucleotide deficiency. This was due to restoration of deoxyribonucleotide triphosphate (dNTP levels through both upregulation of the pentose phosphate pathway via increased glucose-6-phosphate dehydrogenase (G6PD activity and enhanced glucose and glutamine consumption. These phenotypes were mediated by a coordinated suppression of p53 and upregulation of c-MYC downstream of ATM inactivation. Our data indicate that ATM status couples replication stress and metabolic reprogramming during senescence.

  9. SMARCAL1 Resolves Replication Stress at ALT Telomeres.

    Science.gov (United States)

    Cox, Kelli E; Maréchal, Alexandre; Flynn, Rachel Litman

    2016-02-09

    Cancer cells overcome replicative senescence by exploiting mechanisms of telomere elongation, a process often accomplished by reactivation of the enzyme telomerase. However, a subset of cancer cells lack telomerase activity and rely on the alternative lengthening of telomeres (ALT) pathway, a recombination-based mechanism of telomere elongation. Although the mechanisms regulating ALT are not fully defined, chronic replication stress at telomeres might prime these fragile regions for recombination. Here, we demonstrate that the replication stress response protein SMARCAL1 is a critical regulator of ALT activity. SMARCAL1 associates with ALT telomeres to resolve replication stress and ensure telomere stability. In the absence of SMARCAL1, persistently stalled replication forks at ALT telomeres deteriorate into DNA double-strand breaks promoting the formation of chromosome fusions. Our studies not only define a role for SMARCAL1 in ALT telomere maintenance, but also demonstrate that resolution of replication stress is a crucial step in the ALT mechanism. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  10. 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.)

  11. 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.

  12. Break induced replication in eukaryotes: mechanisms, functions, and consequences.

    Science.gov (United States)

    Sakofsky, Cynthia J; Malkova, Anna

    2017-08-01

    Break-induced replication (BIR) is an important pathway specializing in repair of one-ended double-strand DNA breaks (DSBs). This type of DSB break typically arises at collapsed replication forks or at eroded telomeres. BIR initiates by invasion of a broken DNA end into a homologous template followed by initiation of DNA synthesis that can proceed for hundreds of kilobases. This synthesis is drastically different from S-phase replication in that instead of a replication fork, BIR proceeds via a migrating bubble and is associated with conservative inheritance of newly synthesized DNA. This unusual mode of DNA replication is responsible for frequent genetic instabilities associated with BIR, including hyper-mutagenesis, which can lead to the formation of mutation clusters, extensive loss of heterozygosity, chromosomal translocations, copy-number variations and complex genomic rearrangements. In addition to budding yeast experimental systems that were initially employed to investigate eukaryotic BIR, recent studies in different organisms including humans, have provided multiple examples of BIR initiated within different cellular contexts, including collapsed replication fork and telomere maintenance in the absence of telomerase. In addition, significant progress has been made towards understanding microhomology-mediated BIR (MMBIR) that can promote complex chromosomal rearrangements, including those associated with cancer and those leading to a number of neurological disorders in humans.

  13. CTCF driven TERRA transcription facilitates completion of telomere DNA replication.

    Science.gov (United States)

    Beishline, Kate; Vladimirova, Olga; Tutton, Stephen; Wang, Zhuo; Deng, Zhong; Lieberman, Paul M

    2017-12-13

    Telomere repeat DNA forms a nucleo-protein structure that can obstruct chromosomal DNA replication, especially under conditions of replication stress. Transcription of telomere repeats can initiate at subtelomeric CTCF-binding sites to generate telomere repeat-encoding RNA (TERRA), but the role of transcription, CTCF, and TERRA in telomere replication is not known. Here, we have used CRISPR/Cas9 gene editing to mutate CTCF-binding sites at the putative start site of TERRA transcripts for a class of subtelomeres. Under replication stress, telomeres lacking CTCF-driven TERRA exhibit sister-telomere loss and upon entry into mitosis, exhibit the formation of ultra-fine anaphase bridges and micronuclei. Importantly, these phenotypes could be rescued by the forced transcription of TERRA independent of CTCF binding. Our findings indicate that subtelomeric CTCF facilitates telomeric DNA replication by promoting TERRA transcription. Our findings also demonstrate that CTCF-driven TERRA transcription acts in cis to facilitate telomere repeat replication and chromosome stability.

  14. Generalised deletion designs | Gachii | African Journal of Science ...

    African Journals Online (AJOL)

    In this paper asymmetrical single replicate factorial designs are constructed from symmetrical single replicate factorial designs using the deletion technique. The study is along the lines of Voss(1986), Chauhan(1989) and Gachii and Odhiambo(1997). We give results for the general order deletion designs of the form sn-m1(s ...

  15. Effects of Concept Mapping Instruction on the Vocabulary Acquisition Skills of Seventh-Graders with Mild Disabilities: A Replication Study

    Science.gov (United States)

    Palmer, Jessica; Boon, Richard T.; Spencer, Vicky G.

    2014-01-01

    The present investigation replicates and extends an earlier study comparing 2 conditions, a dictionary approach versus a concept mapping model, on the learning of vocabulary words among 4 students with mild disabilities (i.e., emotional and/or behavioral disorders and other health impairments) attending a middle school. An A-B-A-B design was used…

  16. A dimeric Rep protein initiates replication of a linear archaeal virus genome: implications for the Rep mechanism and viral replication

    DEFF Research Database (Denmark)

    Oke, Muse; Kerou, Melina; Liu, Huanting

    2011-01-01

    that a protein encoded in the 34-kbp genome of the rudivirus SIRV1 is a member of the replication initiator (Rep) superfamily of proteins, which initiate rolling-circle replication (RCR) of diverse viruses and plasmids. We show that SIRV Rep nicks the viral hairpin terminus, forming a covalent adduct between...... positioned active sites, each with a single tyrosine residue, work in tandem to catalyze DNA nicking and joining. We propose a novel mechanism for rudivirus DNA replication, incorporating the first known example of a Rep protein that is not linked to RCR. The implications for Rep protein function and viral......The Rudiviridae are a family of rod-shaped archaeal viruses with covalently closed, linear double-stranded DNA (dsDNA) genomes. Their replication mechanisms remain obscure, although parallels have been drawn to the Poxviridae and other large cytoplasmic eukaryotic viruses. Here we report...

  17. Analysis of replication intermediates indicates that Drosophila melanogaster mitochondrial DNA replicates by a strand-coupled theta mechanism.

    Directory of Open Access Journals (Sweden)

    Priit Jõers

    Full Text Available Mitochondrial DNA synthesis is necessary for the normal function of the organelle and for the eukaryotic organism as a whole. Here we demonstrate, using two-dimensional agarose gel electrophoresis to analyse replication intermediates, that unidirectional, strand-coupled DNA synthesis is the prevalent mode of mtDNA replication in Drosophila melanogaster. Commencing within the single, extended non-coding region (NCR, replication proceeds around the circular genome, manifesting an irregular rate of elongation, and pausing frequently in specific regions. Evidence for a limited contribution of strand-asynchronous DNA synthesis was found in a subset of mtDNA molecules, but confined to the ribosomal RNA gene region, just downstream of the NCR. Our findings imply that strand-coupled replication is widespread amongst metazoans, and should inform future research on mtDNA metabolism in D. melanogaster.

  18. Wine glass size and wine sales: a replication study in two bars.

    Science.gov (United States)

    Pechey, Rachel; Couturier, Dominique-Laurent; Hollands, Gareth J; Mantzari, Eleni; Zupan, Zorana; Marteau, Theresa M

    2017-08-01

    Wine glass size may influence perceived volume and subsequently purchasing and consumption. Using a larger glass to serve the same portions of wine was found to increase wine sales by 9.4% (95% CI 1.9, 17.5) in a recent study conducted in one bar. The current study aimed to replicate this previous work in two other bars using a wider range of glass sizes. To match the previous study, a repeated multiple treatment reversal design, during which wine was served in glasses of the same design but different sizes, was used. The study was conducted in two bars in Cambridge, England, using glass sizes of 300, 370, 510 ml (Bar 1) and 300 and 510 ml (Bar 2). Customers purchased their choice of a 750 ml bottle, or standard UK measures of 125, 175 or 250 ml of wine, each of which was served with the same glass. Bar 1 Daily wine volume (ml) purchased was 10.5% (95% CI 1.0, 20.9) higher when sold in 510 ml compared to 370 ml glasses; but sales were not significantly higher with 370 ml versus 300 ml glasses (6.5%, 95% CI -5.2, 19.6). Bar 2 Findings were inconclusive as to whether daily wine purchased differed when using 510 ml versus 300 ml glasses (-1.1%, 95% CI -12.6, 11.9). These results provide a partial replication of previous work showing that introducing larger glasses (without manipulating portion size) increases purchasing. Understanding the mechanisms by which wine glass size influences consumption may elucidate when the effect can be expected and when not. Trial registration This study is a replication study, based on the procedure set out in the trial registration for the study that it attempts to replicate (ISRCTN registry: ISRCTN12018175).

  19. 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

  20. Evaluation of the soil-seed environment through computerized tomography

    International Nuclear Information System (INIS)

    Modolo, Alcir Jose; Fernandes, Haroldo Carlos; Schaefer, Carlos Ernesto G.R.; Santos, Nerilson Terra; Silveira, Joao Cleber Modernel da

    2008-01-01

    The physical conditioning of the soil around seeds is of great importance for an adequate initial development of a crop, ensuring a healthy plant population. A suitable soil-seed contact is a prerequisite for a fast crop germination and good establishment. In this study, computerized tomography of millimeter resolution was used to determine the soil-seed environment in a no tillage system, immediately after soybean planting. A split plot design was used, in which the plots consisted of three contents of soil water, corresponding to 0.27; 0,31 and 0.36 kg kg -1 , respectively, and the split plots of four load levels applied by the compaction wheel, corresponding to 0, 50, 90 and 140 N, respectively. It was used a random block design, with four replications. The medium soil density in the seed area and the medium density profile in the sowing furrow were evaluated. According to the results, it may be concluded that: the loads applied by the compaction wheel increased soil density at the vertical planting level beneath planting depth as compared with values obtained before planting, and; the combination of wheel loads and soil water contents did not influence the mean soil density in the seed area. (author)

  1. Replication-Coupled Dilution of H4K20me2 Guides 53BP1 to Pre-replicative Chromatin.

    Science.gov (United States)

    Pellegrino, Stefania; Michelena, Jone; Teloni, Federico; Imhof, Ralph; Altmeyer, Matthias

    2017-05-30

    The bivalent histone modification reader 53BP1 accumulates around DNA double-strand breaks (DSBs), where it dictates repair pathway choice decisions by limiting DNA end resection. How this function is regulated locally and across the cell cycle to channel repair reactions toward non-homologous end joining (NHEJ) in G1 and promote homology-directed repair (HDR) in S/G2 is insufficiently understood. Here, we show that the ability of 53BP1 to accumulate around DSBs declines as cells progress through S phase and reveal that the inverse relationship between 53BP1 recruitment and replicated chromatin is linked to the replication-coupled dilution of 53BP1's target mark H4K20me2. Consistently, premature maturation of post-replicative chromatin restores H4K20me2 and rescues 53BP1 accumulation on replicated chromatin. The H4K20me2-mediated chromatin association of 53BP1 thus represents an inbuilt mechanism to distinguish DSBs in pre- versus post-replicative chromatin, allowing for localized repair pathway choice decisions based on the availability of replication-generated template strands for HDR. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  2. Dissection of the beta-globin replication-initiation region reveals specific requirements for replicator elements during gene amplification.

    Directory of Open Access Journals (Sweden)

    Naoya Okada

    Full Text Available Gene amplification plays a pivotal role in malignant transformation of human cells. A plasmid with both a mammalian replication-initiation region (IR/origin/replicator and a nuclear matrix-attachment region (MAR is spontaneously amplified in transfected cells by a mechanism that involves amplification at the extrachromosomal site, followed by amplification at the chromosomal arm, ultimately generating a long homogeneously staining region (HSR. Several observations suggest that replication initiation from IR sequences might mediate amplification. To test this idea, we previously dissected c-myc and DHFR IRs to identify the minimum sequence required to support amplification. In this study, we applied an improved analysis that discriminates between two amplification steps to the ß-globin RepP IR, which contains separate elements already known to be essential for initiation on the chromosome arm. The IR sequence was required at least for the extrachromosomal amplification step. In addition to the vector-encoded MAR, amplification also required an AT-rich region and a MAR-like element, consistent with the results regarding replicator activity on the chromosome. However, amplification did not require the AG-rich tract necessary for replicator activity, but instead required a novel sequence containing another AG-rich tract. The differential sequence requirement might be a consequence of extrachromosomal replication.

  3. Mental toughness and behavioural perseverance: A conceptual replication and extension.

    Science.gov (United States)

    Giles, Brandon; Goods, Paul S R; Warner, Dylan R; Quain, Dale; Peeling, Peter; Ducker, Kagan J; Dawson, Brian; Gucciardi, Daniel F

    2017-11-08

    The purpose of this study was to conduct a conceptual replication of the proposition that mental toughness is associated positively with behavioural perseverance. Repeated-measures design. In total, 38 male Australian rules footballers took part in this study (age, 21±3 y; mass, 82.7±11.0kg; height, 1.84±.07m; football experience, 13±4 y). Participants self-reported mental toughness approximately one week prior to their first testing session where we assessed their aerobic capacity via the measurement of peak oxygen consumption (V˙O 2peak ). Approximately one week later, participants completed a 20m shuttle run test (MST). The final testing session took place approximately one week later, where participants completed a simulated team game circuit (STGC; 60min) to simulate game-relevant level of fatigue, which was followed immediately by a 20m MST. Mental toughness was a salient determinant of the variation in behavioural perseverance under typical circumstances, when prior knowledge from past research was incorporated directly into the estimation process. However, the positive association between mental toughness and behavioural perseverance did not generalise to a performance context in which participants were fatigued. The results of the current study suggest that mental toughness represents a salient psychological correlate of behavioural perseverance in a discrete physical task that taxes the aerobic energy system in some but not all situations. When fatigued, the effect of mental toughness is outweighed by greater underlying fitness. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  4. The influence of partner-specific memory associations on picture naming: a failure to replicate Horton (2007).

    Science.gov (United States)

    Brown-Schmidt, Sarah; Horton, William S

    2014-01-01

    The results of two experiments by Horton (2007) show that speakers name a pictured object faster when in the presence of another person with whom the speaker has previously associated that object name. The first of those two experiments (Horton, 2007, Experiment 1) is the focus of the present research. This paper presents the results of three experiments designed to replicate and extend Horton's (2007) Experiment 1. The original findings were not replicated. These findings do not support the hypothesis that partner-specific memory associations facilitate object naming.

  5. Quorum-based Data Replication in Grid Environment

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    Rohaya Latip

    2009-12-01

    Full Text Available Replication is a useful technique for distributed database systems and can be implemented in a grid computation environment to provide a high availability, fault tolerant, and enhance the performance of the system. This paper discusses a new protocol named Diagonal Data Replication in 2D Mesh structure (DR2M protocol where the performance addressed are data availability which is compared with the previous replication protocols, Read-One Write-All (ROWA, Voting (VT, Tree Quorum (TQ, Grid Configuration (GC, and Neighbor Replication on Grid (NRG. DR2M protocol is organized in a logical two dimensional mesh structure and by using quorums and voting techniques to improve the performance and availability of the replication protocol where it reduce the number of copies of data replication for read or write operations. The data file is copied at the selected node of the diagonal site in a quorum. The selection of a replica depends on the diagonal location of the structured two dimensional mesh quorum where the middle node is selected because it is the best location to get a copy of the data if every node has the equal number of request and data accessing in the network. The algorithm in this paper also calculates the best number of nodes in each quorum and how many quorums are needed for N number of nodes in a network. DR2M protocol also ensures that the data for read and write operations is consistency, by proofing the quorum must not have a nonempty intersection quorum. To evaluate DR2M protocol, we developed a simulation model in Java. Our results prove that DR2M protocol improves the performance of the data availability compare to the previous data replication protocol, ROWA, VT, TQ, GC and NRG.

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

    Directory of Open Access Journals (Sweden)

    Scott A Lujan

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

  7. BPIFB6 Regulates Secretory Pathway Trafficking and Enterovirus Replication

    Science.gov (United States)

    Morosky, Stefanie; Lennemann, Nicholas J.

    2016-01-01

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

  8. Oncolytic Replication of E1b-Deleted Adenoviruses

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    Pei-Hsin Cheng

    2015-11-01

    Full Text Available Various viruses have been studied and developed for oncolytic virotherapies. In virotherapy, a relatively small amount of viruses used in an intratumoral injection preferentially replicate in and lyse cancer cells, leading to the release of amplified viral particles that spread the infection to the surrounding tumor cells and reduce the tumor mass. Adenoviruses (Ads are most commonly used for oncolytic virotherapy due to their infection efficacy, high titer production, safety, easy genetic modification, and well-studied replication characteristics. Ads with deletion of E1b55K preferentially replicate in and destroy cancer cells and have been used in multiple clinical trials. H101, one of the E1b55K-deleted Ads, has been used for the treatment of late-stage cancers as the first approved virotherapy agent. However, the mechanism of selective replication of E1b-deleted Ads in cancer cells is still not well characterized. This review will focus on three potential molecular mechanisms of oncolytic replication of E1b55K-deleted Ads. These mechanisms are based upon the functions of the viral E1B55K protein that are associated with p53 inhibition, late viralmRNAexport, and cell cycle disruption.

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

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    Mitali Das

    2014-01-01

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

  10. Electron microscopic analysis of rotavirus assembly-replication intermediates

    Energy Technology Data Exchange (ETDEWEB)

    Boudreaux, Crystal E.; Kelly, Deborah F. [Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA (United States); McDonald, Sarah M., E-mail: mcdonaldsa@vtc.vt.edu [Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA (United States); Department of Biomedical Sciences and Pathobiology, Virginia—Maryland Regional College of Veterinary Medicine, Blacksburg, VA (United States)

    2015-03-15

    Rotaviruses (RVs) replicate their segmented, double-stranded RNA genomes in tandem with early virion assembly. In this study, we sought to gain insight into the ultrastructure of RV assembly-replication intermediates (RIs) using transmission electron microscopy (EM). Specifically, we examined a replicase-competent, subcellular fraction that contains all known RV RIs. Three never-before-seen complexes were visualized in this fraction. Using in vitro reconstitution, we showed that ~15-nm doughnut-shaped proteins in strings were nonstructural protein 2 (NSP2) bound to viral RNA transcripts. Moreover, using immunoaffinity-capture EM, we revealed that ~20-nm pebble-shaped complexes contain the viral RNA polymerase (VP1) and RNA capping enzyme (VP3). Finally, using a gel purification method, we demonstrated that ~30–70-nm electron-dense, particle-shaped complexes represent replicase-competent core RIs, containing VP1, VP3, and NSP2 as well as capsid proteins VP2 and VP6. The results of this study raise new questions about the interactions among viral proteins and RNA during the concerted assembly–replicase process. - Highlights: • Rotaviruses replicate their genomes in tandem with early virion assembly. • Little is known about rotavirus assembly-replication intermediates. • Assembly-replication intermediates were imaged using electron microscopy.

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Jason Diaz

    2014-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-08

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

  14. Replication of genetic associations as pseudoreplication due to shared genealogy.

    Science.gov (United States)

    Rosenberg, Noah A; Vanliere, Jenna M

    2009-09-01

    The genotypes of individuals in replicate genetic association studies have some level of correlation due to shared descent in the complete pedigree of all living humans. As a result of this genealogical sharing, replicate studies that search for genotype-phenotype associations using linkage disequilibrium between marker loci and disease-susceptibility loci can be considered as "pseudoreplicates" rather than true replicates. We examine the size of the pseudoreplication effect in association studies simulated from evolutionary models of the history of a population, evaluating the excess probability that both of a pair of studies detect a disease association compared to the probability expected under the assumption that the two studies are independent. Each of nine combinations of a demographic model and a penetrance model leads to a detectable pseudoreplication effect, suggesting that the degree of support that can be attributed to a replicated genetic association result is less than that which can be attributed to a replicated result in a context of true independence.

  15. Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors

    Directory of Open Access Journals (Sweden)

    Victor M. Bii

    2016-10-01

    Full Text Available Identifying novel genes that drive tumor metastasis and drug resistance has significant potential to improve patient outcomes. High-throughput sequencing approaches have identified cancer genes, but distinguishing driver genes from passengers remains challenging. Insertional mutagenesis screens using replication-incompetent retroviral vectors have emerged as a powerful tool to identify cancer genes. Unlike replicating retroviruses and transposons, replication-incompetent retroviral vectors lack additional mutagenesis events that can complicate the identification of driver mutations from passenger mutations. They can also be used for almost any human cancer due to the broad tropism of the vectors. Replication-incompetent retroviral vectors have the ability to dysregulate nearby cancer genes via several mechanisms including enhancer-mediated activation of gene promoters. The integrated provirus acts as a unique molecular tag for nearby candidate driver genes which can be rapidly identified using well established methods that utilize next generation sequencing and bioinformatics programs. Recently, retroviral vector screens have been used to efficiently identify candidate driver genes in prostate, breast, liver and pancreatic cancers. Validated driver genes can be potential therapeutic targets and biomarkers. In this review, we describe the emergence of retroviral insertional mutagenesis screens using replication-incompetent retroviral vectors as a novel tool to identify cancer driver genes in different cancer types.

  16. Asymmetrical DNA replication promotes evolution: disparity theory of evolution.

    Science.gov (United States)

    Furusawa, M; Doi, H

    1998-01-01

    Heredity is guaranteed by faithful DNA replication whereas evolution depends upon errors accompanying DNA replication. This contradiction existing between heredity and evolution cannot be resolved in an individual organism, but only in terms of a population, in that a delicate balance exists between wild type and variants in a population which is necessary for the survival of the species. Namely, there seems to be a key in the mechanism of DNA replication to solve some problems of evolution. DNA is replicated semiconservatively using the leading and discontinuous lagging strands. According to our 'disparity theory of evolution', the existence of a sufficient fidelity difference between the leading and lagging strands is advantageous in terms of evolution, because the diversity of genotypes is enlarged but genotypes that have occurred in the past are guaranteed. In theory, by artificially increasing the fidelity difference between the leading and lagging strand ('disparity mutator'), evolution is accelerated while avoiding the extinction of the population. Using a disparity mutator, we should be able to improve living things, including multicellular organisms, within constrained conditions. A double-stranded algorithm, which mimics the structure and replication manner of DNA, is promising for solving optimization problems.

  17. Automatic detection and measurement of viral replication compartments by ellipse adjustment

    Science.gov (United States)

    Garcés, Yasel; Guerrero, Adán; Hidalgo, Paloma; López, Raul Eduardo; Wood, Christopher D.; Gonzalez, Ramón A.; Rendón-Mancha, Juan Manuel

    2016-11-01

    Viruses employ a variety of strategies to hijack cellular activities through the orchestrated recruitment of macromolecules to specific virus-induced cellular micro-environments. Adenoviruses (Ad) and other DNA viruses induce extensive reorganization of the cell nucleus and formation of nuclear Replication Compartments (RCs), where the viral genome is replicated and expressed. In this work an automatic algorithm designed for detection and segmentation of RCs using ellipses is presented. Unlike algorithms available in the literature, this approach is deterministic, automatic, and can adjust multiple RCs using ellipses. The proposed algorithm is non iterative, computationally efficient and is invariant to affine transformations. The method was validated over both synthetic images and more than 400 real images of Ad-infected cells at various timepoints of the viral replication cycle obtaining relevant information about the biogenesis of adenoviral RCs. As proof of concept the algorithm was then used to quantitatively compare RCs in cells infected with the adenovirus wild type or an adenovirus mutant that is null for expression of a viral protein that is known to affect activities associated with RCs that result in deficient viral progeny production.

  18. Influenza virus replication in macrophages: balancing protection and pathogenesis.

    Science.gov (United States)

    Cline, Troy D; Beck, Donald; Bianchini, Elizabeth

    2017-10-01

    Macrophages are essential for protection against influenza A virus infection, but are also implicated in the morbidity and mortality associated with severe influenza disease, particularly during infection with highly pathogenic avian influenza (HPAI) H5N1 virus. While influenza virus infection of macrophages was once thought to be abortive, it is now clear that certain virus strains can replicate productively in macrophages. This may have important consequences for the antiviral functions of macrophages, the course of disease and the outcome of infection for the host. In this article, we review findings related to influenza virus replication in macrophages and the impact of productive replication on macrophage antiviral functions. A clear understanding of the interactions between influenza viruses and macrophages may lead to new antiviral therapies to relieve the burden of severe disease associated with influenza viruses.

  19. Topography measurements for determining the decay factors in surface replication

    International Nuclear Information System (INIS)

    Song, J; Zheng, A; Vorburger, T V; Rubert, P

    2008-01-01

    The electro-forming technique is used at National Institute of Standards and Technology (NIST) for the production of standard reference material (SRM) 2461 standard casings to support nationwide ballistics measurement traceability and measurement quality control in the US. In order to ensure that the SRM casings are produced with virtually the same surface topography, it is necessary to test the decay factors of the replication process. Twenty-six replica casings are replicated from the same master casing for the decay factor tests. The NIST topography measurement system is used for measurements and correlations of surface topography. The topography decays are quantified by the cross-correlation function maximum CCF max . Based on the test, it is expected that 256 SRM casings can be replicated from the same master with CCF max values higher than 95%

  20. STUDIES ON CHLOROPLAST DEVELOPMENT AND REPLICATION IN EUGLENA

    Science.gov (United States)

    Carell, Edgar F.

    1969-01-01

    When Euglena gracilis is grown under vitamin B12 deficiency conditions, the amount of protein and of chlorophyll per cell increase with decrease of B12 in the medium and consequently in the cell. The increase in cell protein is proportional to and precedes an increase in the number of chloroplasts per cell. This replication of the chloroplasts under deficiency conditions is not accompanied by nuclear or cell division. It is concluded that chloroplast replication in Euglena gracilis is independent of nuclear and cellular replication, at least under B12 deficiency conditions. We established a graph of the growth of Euglena under different concentrations of vitamin B12 added to the growth medium, which permitted us to calculate that at least 22,000 molecules of vitamin B12 per cell are required to give normal growth. PMID:5783865

  1. Non-Equilibrium Thermodynamics of Self-Replicating Protocells

    DEFF Research Database (Denmark)

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

    2018-01-01

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

  2. New histone supply regulates replication fork speed and PCNA unloading

    DEFF Research Database (Denmark)

    Mejlvang, Jakob; Feng, Yunpeng; Alabert, Constance

    2014-01-01

    Correct duplication of DNA sequence and its organization into chromatin is central to genome function and stability. However, it remains unclear how cells coordinate DNA synthesis with provision of new histones for chromatin assembly to ensure chromosomal stability. In this paper, we show...... that replication fork speed is dependent on new histone supply and efficient nucleosome assembly. Inhibition of canonical histone biosynthesis impaired replication fork progression and reduced nucleosome occupancy on newly synthesized DNA. Replication forks initially remained stable without activation...... of conventional checkpoints, although prolonged histone deficiency generated DNA damage. PCNA accumulated on newly synthesized DNA in cells lacking new histones, possibly to maintain opportunity for CAF-1 recruitment and nucleosome assembly. Consistent with this, in vitro and in vivo analysis showed that PCNA...

  3. Inhibition of Human Immunodeficiency Virus Replication by Antisense Oligodeoxynucleotides

    Science.gov (United States)

    Goodchild, John; Agrawal, Sudhir; Civeira, Maria P.; Sarin, Prem S.; Sun, Daisy; Zamecnik, Paul C.

    1988-08-01

    Twenty different target sites within human immunodeficiency virus (HIV) RNA were selected for studies of inhibition of HIV replication by antisense oligonucleotides. Target sites were selected based on their potential capacity to block recognition functions during viral replication. Antisense oligomers complementary to sites within or near the sequence repeated at the ends of retrovirus RNA (R region) and to certain splice sites were most effective. The effect of antisense oligomer length on inhibiting virus replication was also investigated, and preliminary toxicity studies in mice show that these compounds are toxic only at high levels. The results indicate potential usefulness for these oligomers in the treatment of patients with acquired immunodeficiency syndrome (AIDS) and AIDS-related complex either alone or in combination with other drugs.

  4. How many replicate tests do I need?$-$ Variability of cookstove performance and emissions has implications for obtaining useful results

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yungang [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Energy Technologies Division; Sohn, Michael D. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Energy Technologies Division; Gadgil, Ashok J. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Energy Technologies Division; Wang, Yilun [ISO Innovative Analytics San Francisco, CA (United States); Lask, Kathleen M. [Univ. of California, Berkeley, CA (United States). College of Engineering Applied Science and Technology Program; Kirchstetter, Thomas W. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Energy Technologies Division

    2013-02-01

    Almost half of the world’s population still cooks on biomass cookstoves of poor efficiency and primitive design, such as three stone fires (TSF). Emissions from biomass cookstoves contribute to adverse health effects and climate change. A number of “improved cookstoves” with higher energy efficiency and lower emissions have been designed and promoted across the world. During the design development, and for selection of a stove for dissemination, the stove performance and emissions are commonly evaluated, communicated and compared using the arithmetic average of replicate tests made using a standardized laboratory-based test, commonly the water boiling test (WBT). However, published literature shows different WBT results reported from different laboratories for the same stove technology. Also, there is no agreement in the literature on how many replicate tests should be performed to ensure “significance” in the reported average performance. This matter has not received attention in the rapidly growing literature on stoves, and yet is crucial for estimating and communicating the performance of a stove, and for comparing the performance between stoves. We present results of statistical analyses using data from a number of replicate tests of performance and emission of the Berkeley-Darfur Stove (BDS) and the TSF under well-controlled laboratory conditions. We observed moderate variability in the test results for the TSF and BDS when measuring several characteristics. Here we focus on two as illustrative: time-to-boil and PM2.5 (particulate matter less than or equal to 2.5 micrometers in diameter) emissions. We demonstrate that interpretation of the results comparing these stoves could be misleading if only a small number of replicates had been conducted. We then describe a practical approach, useful to both stove testers and designers, to assess the number of replicates needed to obtain useful data. Caution should be exercised in attaching high credibility to

  5. Nitrogen symbiotically fixed by cowpea and gliricidia in traditional and agroforestry systems under semiarid conditions

    Directory of Open Access Journals (Sweden)

    Júlio César Rodrigues Martins

    2015-02-01

    Full Text Available The objective of this work was to estimate the amounts of N fixed by cowpea in a traditional system and by cowpea and gliricidia in an agroforestry system in the Brazilian Northeast semiarid. The experiment was carried out in a randomized complete block design, in a split-plot arrangement, with four replicates, in the semiarid region of the state of Paraíba, Brazil. Plots consisted of agroforestry and traditional systems (no trees, and split-plots of the three crops planted between the tree rows in the agroforestry system. To estimate N fixation, plant samples were collected in the fourth growth cycle of the perennial species and in the fourth planting cycle of the annual species. In the agroforestry system with buffel grass and prickly-pear cactus, gliricidia plants symbiotically fix high proportions of N (>50% and contribute with higher N amounts (40 kg ha-1 in leaves than in the traditional system (11 kg ha-1 in grain and 18 kg ha-1 in straw. In the agroforestry system with maize and cowpea, gliricidia plants do not fix nitrogen, and N input is limited to the fixation by cowpea (2.7 kg ha-1, which is lower than in the traditional system due to its lower biomass production.

  6. Soil preparation and forage sowing time for crop-livestock integration in corn culture

    Directory of Open Access Journals (Sweden)

    Luiz Fernando de Andrade Fritsch

    2012-01-01

    Full Text Available This work was carried out during the 2008/2009 crop season, in an Oxisol. It was used a split-plot arrangement design, with each plot corresponding to a different soil preparation system and each split-plot corresponding to a different sowing time of the forage Brachiaria brizantha Stapf. The soil preparation systems were: heavy harrowing (HH, disk plough (DP, chisel plough (CP and no-till (NT, and the forage sowing times were: 0, 8, 16 and 25 days after sowing (DAS of corn, arranged in 16 treatments with 3 replicates. The productive and vegetative characteristics of the corn were evaluated. Soil preparations have influenced plant height and the first ear height, with the highest value found for the heavy harrow treatment. Forage sowing time had no influence on vegetative characteristics of the corn and productive characteristics were not influenced by the soil preparations. The forage sowing time had influence on corn productivity, causing decrease in competition with corn forage from 5 DAS. The productivity was highly correlated with the number of grains per ear.

  7. Degradabilidade in situ da silagem de quatro genótipos de sorgo com e sem tanino: I - Matéria seca e proteína bruta In situ degradability of four sorgum silages with or without tannin: I - Dry mater and crude protein

    Directory of Open Access Journals (Sweden)

    W.E. Campos

    2003-04-01

    Full Text Available Avaliaram-se a degradabilidade in situ da matéria seca (MS e da proteína bruta (PB da silagem de quatro genótipos de sorgo, dois com tanino (CMS XS 210 e BR 701 e dois sem tanino (CMS XS 214 e BR007 em um delineamento de blocos inteiramente ao acaso, com três repetições (animais, em arranjo de parcelas subdivididas. Os genótipos constituíram as parcelas e os tempos de digestão as subparcelas. O genótipo CMS XS 210 apresentou menor degradabilidade da MS em relação aos demais e os genótipos que continham tanino (CMS XS 210 e BR 701 apresentaram menores degradabilidades da PB em relação aos que não o continham.The in situ procedure was used to evaluate the disappearance of dry matter (DM and crude protein (CP of four sorghum genotypes with (CMS XS 210 and BR 701 or without (CMS XS 214 and BR 007 tannin in a completely randomized block design experiment with three replicates (animals, in a split plot arrangement. The four genotypes were allotted to the plots and the time of disappearance to the split plot. The DM of CMS XS210 was less degraded when compared to the others and sorghums with tannin showed lower CP degradability when compared to the sorghums without tannin.

  8. Redefining bacterial origins of replication as centralized information processors.

    Science.gov (United States)

    Marczynski, Gregory T; Rolain, Thomas; Taylor, James A

    2015-01-01

    In this review we stress the differences between eukaryotes and bacteria with respect to their different cell cycles, replication mechanisms and genome organizations. One of the most basic and underappreciated differences is that a bacterial chromosome uses only one ori while eukaryotic chromosome uses multiple oris. Consequently, eukaryotic oris work redundantly in a cell cycle divided into separate phases: First inactive replication proteins assemble on eukaryotic oris, and then they await conditions (in the separate "S-phase") that activate only the ori-bound and pre-assembled replication proteins. S-phase activation (without re-assembly) ensures that a eukaryotic ori "fires" (starts replication) only once and that each chromosome consistently duplicates only once per cell cycle. This precise chromosome duplication does not require precise multiple ori firing in S-phase. A eukaryotic ori can fire early, late or not at all. The single bacterial ori has no such margin for error and a comparable imprecision is lethal. Single ori usage is not more primitive; it is a totally different strategy that distinguishes bacteria. We further argue that strong evolutionary pressures created more sophisticated single ori systems because bacteria experience extreme and rapidly changing conditions. A bacterial ori must rapidly receive and process much information in "real-time" and not just in "cell cycle time." This redefinition of bacterial oris as centralized information processors makes at least two important predictions: First that bacterial oris use many and yet to be discovered control mechanisms and second that evolutionarily distinct bacteria will use many very distinct control mechanisms. We review recent literature that supports both predictions. We will highlight three key examples and describe how negative-feedback, phospho-relay, and chromosome-partitioning systems act to regulate chromosome replication. We also suggest future studies and discuss using replication

  9. Inhibition of Monkeypox virus replication by RNA interference

    Directory of Open Access Journals (Sweden)

    Jahrling Peter B

    2009-11-01

    Full Text Available Abstract The Orthopoxvirus genus of Poxviridae family is comprised of several human pathogens, including cowpox (CPXV, Vaccinia (VACV, monkeypox (MPV and Variola (VARV viruses. Species of this virus genus cause human diseases with various severities and outcome ranging from mild conditions to death in fulminating cases. Currently, vaccination is the only protective measure against infection with these viruses and no licensed antiviral drug therapy is available. In this study, we investigated the potential of RNA interference pathway (RNAi as a therapeutic approach for orthopox virus infections using MPV as a model. Based on genome-wide expression studies and bioinformatic analysis, we selected 12 viral genes and targeted them by small interference RNA (siRNA. Forty-eight siRNA constructs were developed and evaluated in vitro for their ability to inhibit viral replication. Two genes, each targeted with four different siRNA constructs in one pool, were limiting to viral replication. Seven siRNA constructs from these two pools, targeting either an essential gene for viral replication (A6R or an important gene in viral entry (E8L, inhibited viral replication in cell culture by 65-95% with no apparent cytotoxicity. Further analysis with wild-type and recombinant MPV expressing green fluorescence protein demonstrated that one of these constructs, siA6-a, was the most potent and inhibited viral replication for up to 7 days at a concentration of 10 nM. These results emphasis the essential role of A6R gene in viral replication, and demonstrate the potential of RNAi as a therapeutic approach for developing oligonucleotide-based drug therapy for MPV and other orthopox viruses.

  10. Cell size and the initiation of DNA replication in bacteria.

    Directory of Open Access Journals (Sweden)

    Norbert S Hill

    Full Text Available In eukaryotes, DNA replication is coupled to the cell cycle through the actions of cyclin-dependent kinases and associated factors. In bacteria, the prevailing view, based primarily from work in Escherichia coli, is that growth-dependent accumulation of the highly conserved initiator, DnaA, triggers initiation. However, the timing of initiation is unchanged in Bacillus subtilis mutants that are ~30% smaller than wild-type cells, indicating that achievement of a particular cell size is not obligatory for initiation. Prompted by this finding, we re-examined the link between cell size and initiation in both E. coli and B. subtilis. Although changes in DNA replication have been shown to alter both E. coli and B. subtilis cell size, the converse (the effect of cell size on DNA replication has not been explored. Here, we report that the mechanisms responsible for coordinating DNA replication with cell size vary between these two model organisms. In contrast to B. subtilis, small E. coli mutants delayed replication initiation until they achieved the size at which wild-type cells initiate. Modest increases in DnaA alleviated the delay, supporting the view that growth-dependent accumulation of DnaA is the trigger for replication initiation in E. coli. Significantly, although small E. coli and B. subtilis cells both maintained wild-type concentration of DnaA, only the E. coli mutants failed to initiate on time. Thus, rather than the concentration, the total amount of DnaA appears to be more important for initiation timing in E. coli. The difference in behavior of the two bacteria appears to lie in the mechanisms that control the activity of DnaA.

  11. Initiation of chromosomal replication in predatory bacterium Bdellovibrio bacteriovorus

    Directory of Open Access Journals (Sweden)

    Lukasz Makowski

    2016-11-01

    Full Text Available Bdellovibrio bacteriovorus is a small Gram-negative predatory bacterium that attacks other Gram-negative bacteria, including many animal, human, and plant pathogens. This bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase and replicating cells (the intracellular-growth phase. The process of chromosomal replication in B. bacteriovorus must therefore be temporally and spatially regulated to ensure that it is coordinated with cell differentiation and cell cycle progression. Recently, B. bacteriovorus has received considerable research interest due to its intriguing life cycle and great potential as a prospective antimicrobial agent. Although we know that chromosomal replication in bacteria is mainly regulated at the initiation step, no data exists about this process in B. bacteriovorus. We report the first characterization of key elements of initiation of chromosomal replication – DnaA protein and oriC region from the predatory bacterium, B. bacteriovorus. In vitro studies using different approaches demonstrate that the B. bacteriovorus oriC (BdoriC is specifically bound and unwound by the DnaA protein. Sequence comparison of the DnaA-binding sites enabled us to propose a consensus sequence for the B. bacteriovorus DnaA box (5’-NN(A/TTCCACA-3’. Surprisingly, in vitro analysis revealed that BdoriC is also bound and unwound by the host DnaA proteins (relatively distantly related from B. bacteriovorus. We compared the architecture of the DnaA–oriC complexes (orisomes in homologous (oriC and DnaA from B. bacteriovorus and heterologous (BdoriC and DnaA from prey, E. coli or P. aeruginosa systems. This work provides important new entry points toward improving our understanding of the initiation of chromosomal replication in this predatory bacterium.

  12. 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.

  13. Implementing three evidence-based program models: early lessons from the Teen Pregnancy Prevention Replication Study.

    Science.gov (United States)

    Kelsey, Meredith; Layzer, Jean

    2014-03-01

    This article describes some of the early implementation challenges faced by nine grantees participating in the Teen Pregnancy Prevention Replication Study and their response to them. The article draws on information collected as part of a comprehensive implementation study. Sources include site and program documents; program officer reports; notes from site investigation, selection and negotiation; ongoing communications with grantees as part of putting the study into place; and semi-structured interviews with program staff. The issues faced by grantees in implementing evidence-based programs designed to prevent teen pregnancy varied by program model. Grantees implementing a classroom-based curriculum faced challenges in delivering the curriculum within the constraints of school schedules and calendars (program length and size of class). Grantees implementing a culturally tailored curriculum faced a series of challenges, including implementing the intervention as part of the regular school curriculum in schools with diverse populations; low attendance when delivered as an after-school program; and resistance on the part of schools to specific curriculum content. The third set of grantees, implementing a program in clinics, faced challenges in identifying and recruiting young women into the program and in retaining young women once they were in the program. The experiences of these grantees reflect some of the complexities that should be carefully considered when choosing to replicate evidence-based programs. The Teen Pregnancy Prevention replication study will provide important context for assessing the effectiveness of some of the more widely replicated evidence-based programs. Copyright © 2014 Society for Adolescent Health and Medicine. All rights reserved.

  14. "Replicable effects of primes on human behavior": Correction to Payne et al. (2016).

    Science.gov (United States)

    2016-12-01

    Reports an error in "Replicable effects of primes on human behavior" by B. Keith Payne, Jazmin L. Brown-Iannuzzi and Chris Loersch ( Journal of Experimental Psychology: General , 2016[Oct], Vol 145[10], 1269-1279). In the article, the graph in Figure 5 did not contain the asterisk mentioned in the figure caption, which was intended to indicate a statistically significant difference between bet and pass prime. The online version of this article has been corrected. (The following abstract of the original article appeared in record 2016-46925-002.) The effect of primes (i.e., incidental cues) on human behavior has become controversial. Early studies reported counterintuitive findings, suggesting that primes can shape a wide range of human behaviors. Recently, several studies failed to replicate some earlier priming results, raising doubts about the reliability of those effects. We present a within-subjects procedure for priming behavior, in which participants decide whether to bet or pass on each trial of a gambling game. We report 6 replications (N = 988) showing that primes consistently affected gambling decisions when the decision was uncertain. Decisions were influenced by primes presented visibly, with a warning to ignore the primes (Experiments 1 through 3) and with subliminally presented masked primes (Experiment 4). Using a process dissociation procedure, we found evidence that primes influenced responses through both automatic and controlled processes (Experiments 5 and 6). Results provide evidence that primes can reliably affect behavior, under at least some conditions, without intention. The findings suggest that the psychological question of whether behavior priming effects are real should be separated from methodological issues affecting how easily particular experimental designs will replicate. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  15. Characterization of the theta replication plasmid pGR7 from Acetobacter aceti CCM 3610.

    Science.gov (United States)

    Grones, Peter; Grones, Jozef

    2012-07-01

    A cryptic plasmid of Acetobacter aceti CCM 3610, designated pGR7, was sequenced and characterized. It is a 2446-bp circular molecule with a G + C content of 30%, which is unusual when compared to the already known plasmids isolated from Acetobacter genera. Sequence analysis of pGR7 revealed three putative open reading frames (ORFs). ORF1 displays low similarity with other Acetobacter plasmid replication proteins. The other two ORFs show similarities only to hypothetical proteins and do not encode any important protein. The replication module comprises a DnaA box-like sequence, indirect repeats, a potential prokaryotic promoter and the rep gene. The rep module organization is similar to that found in other theta-replicating plasmids from acetic acid bacteria that stably maintain in both Acetobacter and Escherichia coli, with two repeated sequences containing modules. Nevertheless, the pGR7 plasmid could replicate and be stably maintained only in Acetobacter strains and not in E. coli, another uncommon feature of this plasmid. The Rep protein was cloned into the pET30a + expression vector and purified by high-performance liquid chromatography. The helicase activity was determined and the ability of the protein to bind to the plasmid regulation region was confirmed by an electrophoretic mobility shift assay. The plasmid was stable in the Acetobacter cells after cultivation under nonselective conditions. By real-time polymerase chain reaction, the relative copy number of pGR7 was estimated to be seven copies per host chromosome equivalent. Copyright © 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    B.K. Reilly

    1998-07-01

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

  17. The Interstellar Ethics of Self-Replicating Probes

    Science.gov (United States)

    Cooper, K.

    Robotic spacecraft have been our primary means of exploring the Universe for over 50 years. Should interstellar travel become reality it seems unlikely that humankind will stop using robotic probes. These probes will be able to replicate themselves ad infinitum by extracting raw materials from the space resources around them and reconfiguring them into replicas of themselves, using technology such as 3D printing. This will create a colonising wave of probes across the Galaxy. However, such probes could have negative as well as positive consequences and it is incumbent upon us to factor self-replicating probes into our interstellar philosophies and to take responsibility for their actions.

  18. Replication of avian influenza A viruses in mammals.

    OpenAIRE

    Hinshaw, V S; Webster, R G; Easterday, B C; Bean, W J

    1981-01-01

    The recent appearance of an avian influenza A virus in seals suggests that viruses are transmitted from birds to mammals in nature. To examine this possibility, avian viruses of different antigenic subtypes were evaluated for their ability to replicate in three mammals-pigs, ferrets, and cats. In each of these mammals, avian strains replicated to high titers in the respiratory tract (10(5) to 10(7) 50% egg infective doses per ml of nasal wash), with peak titers at 2 to 4 days post-inoculation...

  19. Reliable self-replicating machines in asynchronous cellular automata.

    Science.gov (United States)

    Lee, Jia; Adachi, Susumu; Peper, Ferdinand

    2007-01-01

    We propose a self-replicating machine that is embedded in a two-dimensional asynchronous cellular automaton with von Neumann neighborhood. The machine dynamically encodes its shape into description signals, and despite the randomness of cell updating, it is able to successfully construct copies of itself according to the description signals. Self-replication on asynchronously updated cellular automata may find application in nanocomputers, where reconfigurability is an essential property, since it allows avoidance of defective parts and simplifies programming of such computers.

  20. Functional analysis of replication determinantsin classical swine fever virus

    DEFF Research Database (Denmark)

    Hadsbjerg, Johanne

    and animal pathogens should facilitate finding new approaches for efficient disease control. The principal aim of this thesis is to characterise determinants involved in the replication of classical swine fever virus (CSFV). Classical swine fever is a highly contagious virus disease of domestic pigs and wild...... in cell culture. Knowledge of these sequence variations and putative long-range interactions will provide valuable insights into mechanisms underlying virustranslation and replication. In manuscript 3, a selection marker has been inserted into a CSFV-based replicon making it suitable for screening...

  1. Sabin-to-Mahoney Transition Model of Quasispecies Replication

    Energy Technology Data Exchange (ETDEWEB)

    2009-05-31

    Qspp is an agent-based stochastic simulation model of the Poliovirus Sabin-to-Mahoney transition. This code simulates a cell-to-cell model of Poliovirus replication. The model tracks genotypes (virus genomes) as they are replicated in cells, and as the cells burst and release particles into the medium of a culture dish. An inoculum is then taken from the pool of virions and is used to inoculate cells on a new dish. This process repeats. The Sabin genotype comprises the initial inoculum. Nucleotide positions that match the Sabin1 (vaccine strain) and Mahoney (wild type) genotypes, as well as the neurovirulent phenotype (from the literature) are enumerated as constants.

  2. Plasmid P1 replication: negative control by repeated DNA sequences.

    OpenAIRE

    Chattoraj, D; Cordes, K; Abeles, A

    1984-01-01

    The incompatibility locus, incA, of the unit-copy plasmid P1 is contained within a fragment that is essentially a set of nine 19-base-pair repeats. One or more copies of the fragment destabilizes the plasmid when present in trans. Here we show that extra copies of incA interfere with plasmid DNA replication and that a deletion of most of incA increases plasmid copy number. Thus, incA is not essential for replication but is required for its control. When cloned in a high-copy-number vector, pi...

  3. Promotion of Hendra Virus Replication by MicroRNA 146a

    OpenAIRE

    Stewart, Cameron R.; Marsh, Glenn A.; Jenkins, Kristie A.; Gantier, Michael P.; Tizard, Mark L.; Middleton, Deborah; Lowenthal, John W.; Haining, Jessica; Izzard, Leonard; Gough, Tamara J.; Deffrasnes, Celine; Stambas, John; Robinson, Rachel; Heine, Hans G.; Pallister, Jackie A.

    2013-01-01

    Hendra virus is a highly pathogenic zoonotic paramyxovirus in the genus Henipavirus. Thirty-nine outbreaks of Hendra virus have been reported since its initial identification in Queensland, Australia, resulting in seven human infections and four fatalities. Little is known about cellular host factors impacting Hendra virus replication. In this work, we demonstrate that Hendra virus makes use of a microRNA (miRNA) designated miR-146a, an NF-κB-responsive miRNA upregulated by several innate imm...

  4. A replicable and customizable approach to improve ambulatory care and research.

    Science.gov (United States)

    Wasson, J H; Jette, A M; Johnson, D J; Mohr, J J; Nelson, E C

    1997-01-01

    Health care is a service industry. A fundamental attribute of many successful service industries is the "small replicable unit (SRU)." There are three essential elements of an SRU: (1) the smallest core unit of activity, (2) micromeasures designed to help manage the core activities, and (3) combinations of the activities and measures to match local customer needs. In this article, we describe a model for geriatric care based on "SRU thinking." We demonstrate how this approach places measurement of patient values, clinical improvement strategies, and research objectives into day-to-day health care delivery.

  5. A replication-casting device for manufacturing open-cell Mg foams

    OpenAIRE

    Lara-Rodriguez, G.A.; Figueroa, I.A.; Suarez, M.A.; Novelo-Peralta, O.; Alfonso, I.; Goodall, R.

    2016-01-01

    The development of a replication casting device with the capability of manufacturing open-cell pure Mg and Mg alloys foams, with melting points lower than 950 °C is described. The device consists of three basic parts: a cylindrical reaction chamber, a valve system for controlling the vacuum and the gas injection, and a heating system. The purpose of the present design was to improve the existing laboratory-scale devices, making them simpler than those reported in the literature, as well as to...

  6. 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

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

    Science.gov (United States)

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

  8. Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components

    DEFF Research Database (Denmark)

    Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Po

    2014-01-01

    replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3,995 proteins. The replication machinery and 485 chromatin factors...

  9. Discussing the Need of Experimental Replication with 5th Grade Students Conducting a Mealworm Experiment

    Science.gov (United States)

    Asshoff, Roman

    2017-01-01

    Scientific inquiry requires the replication of results in experimental studies. Recent studies draw a severe picture on the need of replication and the difficulties in replicating already published studies. As replicated confirmation of results is the basis of scientific and medical research, there may be a need to introduce the topic of…

  10. Host factors in HIV-1 replication: The good, the bad and the ugly

    NARCIS (Netherlands)

    Booiman, T.

    2015-01-01

    The ability of HIV-1 to replicate in its target cells is influenced by numerous host factors that act on different steps of the viral replication cycle. The effects of these host factors on the replication cycle can be cell type specific and they can either support or restrict viral replication.

  11. Recruitment of Brd4 to the Human Papillomavirus Type 16 DNA Replication Complex Is Essential for Replication of Viral DNA

    OpenAIRE

    Wang, Xin; Helfer, Christine M.; Pancholi, Neha; Bradner, James E.; You, Jianxin

    2013-01-01

    Replication of the human papillomavirus (HPV) DNA genome relies on viral factors E1 and E2 and the cellular replication machinery. Bromodomain-containing protein 4 (Brd4) interacts with viral E2 protein to mediate papillomavirus (PV) genome maintenance and viral transcription. However, the functional role of Brd4 in the HPV life cycle remains to be clearly defined. In this study, we provide the first look into the E2-Brd4 interaction in the presence of other important viral factors, such as t...

  12. Rapid Transient Production in Plants by Replicating and Non-Replicating Vectors Yields High Quality Functional Anti-HIV Antibody

    Science.gov (United States)

    Sainsbury, Frank; Sack, Markus; Stadlmann, Johannes; Quendler, Heribert; Fischer, Rainer; Lomonossoff, George P.

    2010-01-01

    Background 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. Methodology/Principal Findings 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. Conclusions 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

  13. The oncolytic poxvirus JX-594 selectively replicates in and destroys cancer cells driven by genetic pathways commonly activated in cancers.

    Science.gov (United States)

    Parato, Kelley A; Breitbach, Caroline J; Le Boeuf, Fabrice; Wang, Jiahu; Storbeck, Chris; Ilkow, Carolina; Diallo, Jean-Simon; Falls, Theresa; Burns, Joseph; Garcia, Vanessa; Kanji, Femina; Evgin, Laura; Hu, Kang; Paradis, Francois; Knowles, Shane; Hwang, Tae-Ho; Vanderhyden, Barbara C; Auer, Rebecca; Kirn, David H; Bell, John C

    2012-04-01

    Oncolytic viruses are generally designed to be cancer selective on the basis of a single genetic mutation. JX-594 is a thymidine kinase (TK) gene-inactivated oncolytic vaccinia virus expressing granulocyte-macrophage colony-stimulating factor (GM-CSF) and lac-Z transgenes that is designed to destroy cancer cells through replication-dependent cell lysis and stimulation of antitumoral immunity. JX-594 has demonstrated a favorable safety profile and reproducible tumor necrosis in a variety of solid cancer types in clinical trials. However, the mechanism(s) responsible for its cancer-selectivity have not yet been well described. We analyzed the replication of JX-594 in three model systems: primary normal and cancer cells, surgical explants, and murine tumor models. JX-594 replication, transgene expression, and cytopathic effects were highly cancer-selective, and broad spectrum activity was demonstrated. JX-594 cancer-selectivity was multi-mechanistic; replication was activated by epidermal growth factor receptor (EGFR)/Ras pathway signaling, cellular TK levels, and cancer cell resistance to type-I interferons (IFNs). These findings confirm a large therapeutic index for JX-594 that is driven by common genetic abnormalities in human solid tumors. This appears to be the first description of multiple selectivity mechanisms, both inherent and engineered, for an oncolytic virus. These findings have implications for oncolytic viruses in general, and suggest that their cancer targeting is a complex and multifactorial process.

  14. A two-stage variable selection and classification approach for Parkinson's disease detection by using voice recording replications.

    Science.gov (United States)

    Naranjo, Lizbeth; Pérez, Carlos J; Martín, Jacinto; Campos-Roca, Yolanda

    2017-04-01

    In the scientific literature, there is a lack of variable selection and classification methods considering replicated data. The problem motivating this work consists in the discrimination of people suffering Parkinson's disease from healthy subjects based on acoustic features automatically extracted from replicated voice recordings. A two-stage variable selection and classification approach has been developed to properly match the replication-based experimental design. The way the statistical approach has been specified allows that the computational problems are solved by using an easy-to-implement Gibbs sampling algorithm. The proposed approach produces an acceptable predictive capacity for PD discrimination with the considered database, despite the fact that the sample size is relatively small. Specifically, the accuracy rate, sensitivity and specificity are 86.2%, 82.5%, and 90.0%, respectively. However, the most important fact is that there is an improvement in the interpretability of the results at the same time that it is shown a better chain mixing and a lower computation time with respect to the only-classification approaches presented in the scientific literature. To the best of the authors' knowledge, this is the first approach developed to properly consider intra-subject variability for variable selection and classification. Although the proposed approach has been applied for PD discrimination, it can be applied in other contexts with similar replication-based experimental designs. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. The big five as tendencies in situations : A replication study

    NARCIS (Netherlands)

    Hendriks, AAJ

    1996-01-01

    Van Heck, Perugini, Caprara and Froger (1994) report the average generalizability coefficient reflecting the consistent ordering of persons across different situations and different trait markers (items) to be in the order of 0.70. We performed a replication study in which we improved on their

  16. Modeling HIV-1 intracellular replication: two simulation approaches

    NARCIS (Netherlands)

    Zarrabi, N.; Mancini, E.; Tay, J.; Shahand, S.; Sloot, P.M.A.

    2010-01-01

    Many mathematical and computational models have been developed to investigate the complexity of HIV dynamics, immune response and drug therapy. However, there are not many models which consider the dynamics of virus intracellular replication at a single level. We propose a model of HIV intracellular

  17. Localization of adenovirus DNA replication in KB cells

    NARCIS (Netherlands)

    Vlak, J.M.; Rozijn, Th.H.; Spies, F.

    1975-01-01

    The localization of adenovirus type 5 DNA replication has been investigated by both fractionation of isolated nuclei and electron-microscope autoradiography. Nuclear fractionation by means of the M-band-technique of Tremblay et al. (Tremblay, G. Y., Daniels, M. J., and Schaechter, M. (1969). J. Mol.

  18. Failure to Replicate the "Work Ethic" Effect in Pigeons

    Science.gov (United States)

    Vasconcelos, Marco; Urcuioli, Peter J.; Lionello-DeNolf, Karen M.

    2007-01-01

    We report six unsuccessful attempts to replicate the "work ethic" phenomenon reported by Clement, Feltus, Kaiser, and Zentall (2000). In Experiments 1-5, pigeons learned two simultaneous discriminations in which the S+ and S- stimuli were obtained by pecking an initial stimulus once or multiple (20 or 40) times. Subsequent preference tests between…

  19. Replicating Data for Better Performances in X10

    DEFF Research Database (Denmark)

    Andrić, Marina; De Nicola, Rocco; Lluch Lafuente, Alberto

    2015-01-01

    used to experiment with X10, a parallel programming language primarily targeting clusters of multi-core processors linked in a large-scale system via high-performance networks. Our approach aims at allowing the programmer to specify and coordinate the replication of shared data items by taking...

  20. 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

  1. Across-Task Conflict Regulation: A Replication Failure

    Science.gov (United States)

    Runger, Dennis; Schwager, Sabine; Frensch, Peter A.

    2010-01-01

    Fernandez-Duque and Knight (2008, Experiment 4) described an across-task effect of endogenously generated, anticipatory control: A cue that predicted conflict in an upcoming Eriksen flanker task modulated conflict regulation in a subsequent number Stroop task. In 3 experiments, 1 of which included an exact replication condition, we failed to…

  2. DNA breaks early in replication in B cell cancers

    Science.gov (United States)

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

  3. Children's Understanding of Their Emotionally Disturbed Peers: A Replication

    Science.gov (United States)

    Hoffman, Edward; And Others

    1977-01-01

    Despite increasing recognition of the early importance of peer relations, virtually no systematic information exists on the way in which normal children view their emotionally disturbed peers. This research reports a replication of recent findings on children's use of the concept of emotional disturbance. (Editor/RK)

  4. Quality of topographical micro replication in injection moulding

    DEFF Research Database (Denmark)

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

    2003-01-01

    surface with Sq = 4.6 ƒÝm manufactured by EDM and a commercial polypropylene grade. 3D surface characterisation was carried out with a laser focus detection profiler. The investigation reveals that replication quality indices as measured with several established 3D topographical parameters...

  5. Automated Anxiety Control Promotes Student Retention: A Replication

    Science.gov (United States)

    Driscoll, Richard; Holt, Bruce

    2012-01-01

    This study was undertaken to replicate prior findings in which a test-anxiety control training produced substantial test gains among students on academic probation. Twelve first semester students with marginal achievement were identified, screened for test anxiety, and found to have substantially higher anxiety than other students. Ten of the…

  6. On Node Replication Attack in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Mumtaz Qabulio

    2016-04-01

    Full Text Available WSNs (Wireless Sensor Networks comprise a large number of small, inexpensive, low power and memory constrained sensing devices (called sensor nodes that are densely deployed to measure a given physical phenomenon. Since WSNs are commonly deployed in a hostile and unattended environment, it is easy for an adversary to physically capture one or more legitimate sensor nodes, re-program and redeploy them in the network. As a result, the adversary becomes able to deploy several identical copies of physically captured nodes in the network in order to perform illegitimate activities. This type of attack is referred to as Node Replication Attack or Clone Node Attack. By launching node replication attack, an adversary can easily get control on the network which consequently is the biggest threat to confidentiality, integrity and availability of data and services. Thus, detection and prevention of node replication attack in WSNs has become an active area of research and to date more than two dozen schemes have been proposed, which address this issue. In this paper, we present a comprehensive review, classification and comparative analysis of twenty five of these schemes which help to detect and/or prevent node replication attack in WSNs

  7. Evolution of DNA replication protein complexes in eukaryotes and Archaea.

    Directory of Open Access Journals (Sweden)

    Nicholas Chia

    Full Text Available BACKGROUND: The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA, replication factor C (RFC, and the minichromosome maintenance (MCM complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best. METHODOLOGY/PRINCIPAL FINDINGS: While the structures of each of the complexes do not differ significantly between the archaeal and eukaryotic versions thereof, the evolutionary dynamic in the two cases does. The number of subunits in each complex is constant across all taxa. However, they vary subtly with regard to composition. In some taxa the subunits are all identical in sequence, while in others some are homologous rather than identical. In the case of eukaryotes, there is no phylogenetic variation in the makeup of each complex-all appear to derive from a common eukaryotic ancestor. This is not the case in Archaea, where the relationship between the subunits within each complex varies taxon-to-taxon. We have performed a detailed phylogenetic analysis of these relationships in order to better understand the gene duplications and divergences that gave rise to the homologous subunits in Archaea. CONCLUSION/SIGNIFICANCE: This domain level difference in evolution suggests that different forces have driven the evolution of DNA replication proteins in each of these two domains. In addition, the phylogenies of all three gene families support the distinctiveness of the proposed archaeal phylum Thaumarchaeota.

  8. Gender Effects on Loyalty: A Replication in an Emerging Market

    NARCIS (Netherlands)

    Babah Daouda, Falylath; Ingenbleek, Paul T.M.; Trijp, van Hans C.M.

    2017-01-01

    This paper replicates the gender-effect on object of loyalty found by
    Melnyk et al. (2009), suggesting that females are more loyal towards
    individuals and males are more loyal to groups and organizations. Results
    from Benin (West Africa) support this but find that the results

  9. Global bifurcations at the onset of pulse self-replication

    Science.gov (United States)

    Yue, Baozeng

    2007-11-01

    In this work, we carried out an extensive numerical exploration of the delicate global dynamics of pulse self-replication and analyzed the stability of singular homoclinic stationary solutions and their bifurcations in the one-dimensional Gray-Scott model. This stability analysis has several implications for understanding the recently discovered phenomena of self-replicating pulses. The solutions of the ordinary differential equation are organized around a codimension-2 global bifurcation from which two or N branches of homoclinic orbits originate, corresponding to solitary pulse solutions in the partial differential equation. A careful analysis of the bifurcation scenarios in the global bifurcation diagram suggests that the dynamics of the self-replicating system are related to a hierarchy structure of folding bifurcation branches in parameter space. The numerical simulation suggests that the Bogdanov-Takens points, together with the presence of critical points emanating from a particular codimension-2 homoclinic orbit, play a central role for the global bifurcation of periodic orbits, the homoclinic solutions, and the complex chaotic dynamics. The numerical simulation also reveals the existence of a modulating two-pulse or multipulse, which accompanies the procedure of pulse self-replication in reaction-diffusion systems.

  10. Timeless links replication termination to mitotic kinase activation.

    Directory of Open Access Journals (Sweden)

    Jayaraju Dheekollu

    2011-05-01

    Full Text Available The mechanisms that coordinate the termination of DNA replication with progression through mitosis are not completely understood. The human Timeless protein (Tim associates with S phase replication checkpoint proteins Claspin and Tipin, and plays an important role in maintaining replication fork stability at physical barriers, like centromeres, telomeres and ribosomal DNA repeats, as well as at termination sites. We show here that human Tim can be isolated in a complex with mitotic entry kinases CDK1, Auroras A and B, and Polo-like kinase (Plk1. Plk1 bound Tim directly and colocalized with Tim at a subset of mitotic structures in M phase. Tim depletion caused multiple mitotic defects, including the loss of sister-chromatid cohesion, loss of mitotic spindle architecture, and a failure to exit mitosis. Tim depletion caused a delay in mitotic kinase activity in vivo and in vitro, as well as a reduction in global histone H3 S10 phosphorylation during G2/M phase. Tim was also required for the recruitment of Plk1 to centromeric DNA and formation of catenated DNA structures at human centromere alpha satellite repeats. Taken together, these findings suggest that Tim coordinates mitotic kinase activation with termination of DNA replication.

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

    Directory of Open Access Journals (Sweden)

    Zhong Deng

    2014-12-01

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

  12. A non-replicative adenovirus vaccine platform for poultry diseases ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2018-04-09

    Apr 9, 2018 ... Using a non-replicative adenovirus to transfer genetic material into cells, researchers will generate two proteins (HN and F) that are known targets of protective immunity against ND. Unlike traditional ND vaccines that are produced using eggs, the resulting vaccine will be produced in a cell culture system, ...

  13. Chromosomal replication incompatibility in Dam methyltransferase deficient Escherichia coli cells

    DEFF Research Database (Denmark)

    Freiesleben, Ulrik Von

    1996-01-01

    Dam methyltransferase deficient Escherichia coli cells containing minichromosomes were constructed. Free plasmid DNA could not be detected in these cells and the minichromosomes were found to be integrated in multiple copies in the origin of replication (oriC) region of the host chromosome...

  14. Psychological type and attitude toward Christianity: a replication.

    Science.gov (United States)

    Francis, Leslie J; Robbins, Mandy; Boxer, Anna; Lewis, Christopher Alan; McGuckin, Conor; McDaid, Charles J

    2003-02-01

    A sample of 149 university students completed the Francis Psychological Type Scales together with the Francis Scale of Attitude Toward Christianity. The data indicated that university students classified as Feeling Types hold a more positive attitude toward Christianity than those classified as Thinking Types. These findings replicate the 1999 report of Jones and Francis.

  15. Personality and attitude toward Christianity among churchgoers: a replication.

    Science.gov (United States)

    Williams, Emyr; Francis, Leslie J

    2006-08-01

    A sample of 158 churchgoers attending eight Anglican churches in the United Kingdom completed the abbreviated Revised Eysenck Personality Questionnaire together with the Francis Scale of Attitude toward Christianity to replicate a 1996 study by Carter, Kay, and Francis. Data confirm that scores on Attitude toward Christianity were significantly negatively related to Psychoticism, but to neither Extraversion nor Neuroticism scores.

  16. Web Services Solution on Replication Oriented Architecture (ROA ...

    African Journals Online (AJOL)

    ROA an acronym for Replication Oriented Architecture is speculated as capable of attenuating the scalability defect of Web Services and help application programmers build scalable Web Services solution. For this claim to be considered, it is ordinarily necessary to establish that Web Services solution can be built on ROA; ...

  17. Autonomous Technology: Rhetoric of the Replicants in Contemporary Cinema.

    Science.gov (United States)

    Frentz, Thomas S.; Rushing, Janice H.

    Developing a theme drawn from speculative writing of the nineteenth century--that technology, like biological species, undergoes a process of evolution--this paper explores the thesis that if technology divides from its human creators and perfects itself until it gains the capacity for self replication, it cannot return to its creator. Using…

  18. Clade-specific differences in active viral replication and compartmentalization

    NARCIS (Netherlands)

    Sala, Monica; Centlivre, Mireille; Wain-Hobson, Simon

    2006-01-01

    This review focuses on the impact of HIV-1 clade-specific polymorphisms on the dynamics of viral replication and compartmentalization in vivo. HIV-1 transcription and compartmentalization are essentially modulated by interconnected parameters: cellular activation by T-cell receptor engagement or

  19. Lytic Replication of Epstein-Barr Virus During Space Flight

    Science.gov (United States)

    Stowe, R. P.; Pierson, D. L.; Barrett, A. D. T.

    1999-01-01

    Reactivation of latent Epstein-Barr virus (EBV) may be an important threat to crew health during extended space missions. Cellular immunity, which is decreased during and after space flight, is responsible for controlling EBV replication in vivo. In this study, we investigated the effects of short-term space flight on latent EBV reactivation.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope...

  1. Revisiting Mental Simulation in Language Comprehension: Six Replication Attempts

    NARCIS (Netherlands)

    R.A. Zwaan (Rolf); D. Pecher (Diane)

    2012-01-01

    textabstractThe notion of language comprehension as mental simulation has become popular in cognitive science. We revisit some of the original empirical evidence for this. Specifically, we attempted to replicate the findings from earlier studies that examined the mental simulation of object

  2. DnaA and ORC : more than DNA replication initiators

    NARCIS (Netherlands)

    Scholefield, Graham; Veening, Jan-Willem; Murray, Heath

    Mutations in DNA replication initiator genes in both prokaryotes and eukaryotes lead to a pleiotropic array of phenotypes, including defects in chromosome segregation, cytokinesis, cell cycle regulation and gene expression. For years, it was not clear whether these diverse effects were indirect

  3. Specificity and Function of Archaeal DNA Replication Initiator Proteins

    Directory of Open Access Journals (Sweden)

    Rachel Y. Samson

    2013-02-01

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

  4. Mesoscopic superstructures of flexible porous coordination polymers synthesizedviacoordination replication.

    Science.gov (United States)

    Sumida, Kenji; Moitra, Nirmalya; Reboul, Julien; Fukumoto, Shotaro; Nakanishi, Kazuki; Kanamori, Kazuyoshi; Furukawa, Shuhei; Kitagawa, Susumu

    2015-10-01

    The coordination replication technique is employed for the direct conversion of a macro- and mesoporous Cu(OH) 2 -polyacrylamide composite to three-dimensional superstructures consisting of the flexible porous coordination polymers, Cu 2 (bdc) 2 (MeOH) 2 and Cu 2 (bdc) 2 (bpy) (bdc 2- = 1,4-benzenedicarboxylate, bpy = 4,4'-bipyridine). Detailed characterization of the replicated systems reveals that the structuralization plays an important role in determining the adsorptive properties of the replicated systems, and that the immobilization of the crystals within a higher-order architecture also affects its structural and dynamic properties. The polyacrylamide polymer is also found to be crucial for maintaining the structuralization of the monolithic systems, and in providing the mechanical robustness required for manual handling. In all, the results discussed here demonstrate a significant expansion in the scope of the coordination replication strategy, and further confirms its utility as a highly versatile platform for the preparation of functional three-dimensional superstructures of porous coordination polymers.

  5. Mathematical Analysis of Replication by Cash Flow Matching

    Directory of Open Access Journals (Sweden)

    Jan Natolski

    2017-02-01

    Full Text Available The replicating portfolio approach is a well-established approach carried out by many life insurance companies within their Solvency II framework for the computation of risk capital. In this note,weelaborateononespecificformulationofareplicatingportfolioproblem. Incontrasttothetwo most popular replication approaches, it does not yield an analytic solution (if, at all, a solution exists andisunique. Further,althoughconvex,theobjectivefunctionseemstobenon-smooth,andhencea numericalsolutionmightthusbemuchmoredemandingthanforthetwomostpopularformulations. Especially for the second reason, this formulation did not (yet receive much attention in practical applications, in contrast to the other two formulations. In the following, we will demonstrate that the (potential non-smoothness can be avoided due to an equivalent reformulation as a linear second order cone program (SOCP. This allows for a numerical solution by efficient second order methods like interior point methods or similar. We also show that—under weak assumptions—existence and uniqueness of the optimal solution can be guaranteed. We additionally prove that—under a further similarly weak condition—the fair value of the replicating portfolio equals the fair value of liabilities. Based on these insights, we argue that this unloved stepmother child within the replication problem family indeed represents an equally good formulation for practical purposes.

  6. The Green Revolution in Indonesia: A Replicable Success?

    NARCIS (Netherlands)

    Frankema, E.H.P.

    2015-01-01

    This chapter aims to disentangle the causal complex underpinning Indonesia’s ‘green revolution’ in order to assess which aspects of it are, in principle, replicable in other parts of the world and which aspects are not. More in particular this study focuses on the question which elements of the

  7. The absence of a DNA replication checkpoint in porcine zygotes

    Czech Academy of Sciences Publication Activity Database

    Vacková, I.; Křen, Radomír; Loi, P.; Krylov, V.; Fulka Jr., J.

    2006-01-01

    Roč. 14, 1 (2006), s. 33-37 ISSN 0967-1994 Institutional research plan: CEZ:AV0Z50450515 Keywords : checkpoint * DNA replication * fertilization Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.782, year: 2006

  8. Fear of AIDS : are there replicable, invariant questionnaire dimensions?

    NARCIS (Netherlands)

    Arrindell, W.A.; Ross, M.W.; Bridges, K.Robert; van Hout, W.; Hofman, A.; Sanderman, R.

    1989-01-01

    Explored the dimensional structure of the 38-item Fear of acquired immune deficiency syndrome (AIDS) Schedule with 684 American students. Principal components analysis with VARIMAX rotation revealed 2 separate but related, internally consistent, and replicable dimensions of AIDS fear. These were (1)

  9. Complement receptor mediates enhanced flavivirus replication in macrophages

    OpenAIRE

    1983-01-01

    Evidence is presented that M phi complement receptors (CR3) mediate IgM- dependent enhancement of flavivirus replication in the presence of complement. Enhancement is blocked by pretreatment of macrophages with monoclonal antibody Ml/70, which inhibits CR3 binding, but not by pretreatment with monoclonal antibody 2.4G2, which inhibits FcR binding.

  10. Precision in systematic trawl surveys as assessed from replicate ...

    African Journals Online (AJOL)

    Precision in systematic trawl surveys as assessed from replicate sampling by parallel trawling off Namibia. ... The main statistical techniques applied were less susceptible to outlier catches than straightforward correlations or regressions and could therefore, perhaps with some advantage, also be used to estimate the vessel ...

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

    NARCIS (Netherlands)

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

    2012-01-01

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

  12. DNA replication at the single-molecule level

    NARCIS (Netherlands)

    Stratmann, S.A.; Oijen, A.M. van

    2014-01-01

    A cell can be thought of as a highly sophisticated micro factory: in a pool of billions of molecules – metabolites, structural proteins, enzymes, oligonucleotides – multi-subunit complexes assemble to perform a large number of basic cellular tasks, such as DNA replication, RNA/protein synthesis or

  13. 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.

  14. Mcm2 phosphorylation and the response to replicative stress

    Directory of Open Access Journals (Sweden)

    Stead Brent E

    2012-05-01

    Full Text Available Abstract Background The replicative helicase in eukaryotic cells is comprised of minichromosome maintenance (Mcm proteins 2 through 7 (Mcm2-7 and is a key target for regulation of cell proliferation. In addition, it is regulated in response to replicative stress. One of the protein kinases that targets Mcm2-7 is the Dbf4-dependent kinase Cdc7 (DDK. In a previous study, we showed that alanine mutations of the DDK phosphorylation sites at S164 and S170 in Saccharomyces cerevisiae Mcm2 result in sensitivity to caffeine and methyl methanesulfonate (MMS leading us to suggest that DDK phosphorylation of Mcm2 is required in response to replicative stress. Results We show here that a strain with the mcm2 allele lacking DDK phosphorylation sites (mcm2AA is also sensitive to the ribonucleotide reductase inhibitor, hydroxyurea (HU and to the base analogue 5-fluorouracil (5-FU but not the radiomimetic drug, phleomycin. We screened the budding yeast non-essential deletion collection for synthetic lethal interactions with mcm2AA and isolated deletions that include genes involved in the control of genome integrity and oxidative stress. In addition, the spontaneous mutation rate, as measured by mutations in CAN1, was increased in the mcm2AA strain compared to wild type, whereas with a phosphomimetic allele (mcm2EE the mutation rate was decreased. These results led to the idea that the mcm2AA strain is unable to respond properly to DNA damage. We examined this by screening the deletion collection for suppressors of the caffeine sensitivity of mcm2AA. Deletions that decrease spontaneous DNA damage, increase homologous recombination or slow replication forks were isolated. Many of the suppressors of caffeine sensitivity suppressed other phenotypes of mcm2AA including sensitivity to genotoxic drugs, the increased frequency of cells with RPA foci and the increased mutation rate. Conclusions Together these observations point to a role for DDK-mediated phosphorylation

  15. Human Genome Replication Proceeds through Four Chromatin States

    Science.gov (United States)

    Julienne, Hanna; Zoufir, Azedine; Audit, Benjamin; Arneodo, Alain

    2013-01-01

    Advances in genomic studies have led to significant progress in understanding the epigenetically controlled interplay between chromatin structure and nuclear functions. Epigenetic modifications were shown to play a key role in transcription regulation and genome activity during development and differentiation or in response to the environment. Paradoxically, the molecular mechanisms that regulate the initiation and the maintenance of the spatio-temporal replication program in higher eukaryotes, and in particular their links to epigenetic modifications, still remain elusive. By integrative analysis of the genome-wide distributions of thirteen epigenetic marks in the human cell line K562, at the 100 kb resolution of corresponding mean replication timing (MRT) data, we identify four major groups of chromatin marks with shared features. These states have different MRT, namely from early to late replicating, replication proceeds though a transcriptionally active euchromatin state (C1), a repressive type of chromatin (C2) associated with polycomb complexes, a silent state (C3) not enriched in any available marks, and a gene poor HP1-associated heterochromatin state (C4). When mapping these chromatin states inside the megabase-sized U-domains (U-shaped MRT profile) covering about 50% of the human genome, we reveal that the associated replication fork polarity gradient corresponds to a directional path across the four chromatin states, from C1 at U-domains borders followed by C2, C3 and C4 at centers. Analysis of the other genome half is consistent with early and late replication loci occurring in separate compartments, the former correspond to gene-rich, high-GC domains of intermingled chromatin states C1 and C2, whereas the latter correspond to gene-poor, low-GC domains of alternating chromatin states C3 and C4 or long C4 domains. This new segmentation sheds a new light on the epigenetic regulation of the spatio-temporal replication program in human and provides a

  16. Host DNA damage response factors localize to merkel cell polyomavirus DNA replication sites to support efficient viral DNA replication.

    Science.gov (United States)

    Tsang, Sabrina H; Wang, Xin; Li, Jing; Buck, Christopher B; You, Jianxin

    2014-03-01

    Accumulating evidence indicates a role for Merkel cell polyomavirus (MCPyV) in the development of Merkel cell carcinoma (MCC), making MCPyV the first polyomavirus to be clearly associated with human cancer. With the high prevalence of MCPyV infection and the increasing amount of MCC diagnosis, there is a need to better understand the virus and its oncogenic potential. In this study, we examined the relationship between the host DNA damage response (DDR) and MCPyV replication. We found that components of the ATM- and ATR-mediated DDR pathways accumulate in MCPyV large T antigen (LT)-positive nuclear foci in cells infected with native MCPyV virions. To further study MCPyV replication, we employed our previously established system, in which recombinant MCPyV episomal DNA is autonomously replicated in cultured cells. Similar to native MCPyV infection, where both MCPyV origin and LT are present, the host DDR machinery colocalized with LT in distinct nuclear foci. Immunofluorescence in situ hybridization and bromodeoxyuridine (BrdU) incorporation analysis showed that these DDR proteins and MCPyV LT in fact colocalized at the actively replicating MCPyV replication complexes, which were absent when a replication-defective LT mutant or an MCPyV-origin mutant was introduced in place of wild-type LT or wild-type viral origin. Inhibition of DDR kinases using chemical inhibitors and ATR/ATM small interfering RNA (siRNA) knockdown reduced MCPyV DNA replication without significantly affecting LT expression or the host cell cycle. This study demonstrates that these host DDR factors are important for MCPyV DNA replication, providing new insight into the host machinery involved in the MCPyV life cycle. MCPyV is the first polyomavirus to be clearly associated with human cancer. However, the MCPyV life cycle and its oncogenic mechanism remain poorly understood. In this report, we show that, in cells infected with native MCPyV virions, components of the ATM- and ATR-mediated DDR

  17. Chromosome length influences replication-induced topological stress.

    Science.gov (United States)

    Kegel, Andreas; Betts-Lindroos, Hanna; Kanno, Takaharu; Jeppsson, Kristian; Ström, Lena; Katou, Yuki; Itoh, Takehiko; Shirahige, Katsuhiko; Sjögren, Camilla

    2011-03-17

    During chromosome duplication the parental DNA molecule becomes overwound, or positively supercoiled, in the region ahead of the advancing replication fork. To allow fork progression, this superhelical tension has to be removed by topoisomerases, which operate by introducing transient DNA breaks. Positive supercoiling can also be diminished if the advancing fork rotates along the DNA helix, but then sister chromatid intertwinings form in its wake. Despite these insights it remains largely unknown how replication-induced superhelical stress is dealt with on linear, eukaryotic chromosomes. Here we show that this stress increases with the length of Saccharomyces cerevisiae chromosomes. This highlights the possibility that superhelical tension is handled on a chromosome scale and not only within topologically closed chromosomal domains as the current view predicts. We found that inhibition of type I topoisomerases leads to a late replication delay of longer, but not shorter, chromosomes. This phenotype is also displayed by cells expressing mutated versions of the cohesin- and condensin-related Smc5/6 complex. The frequency of chromosomal association sites of the Smc5/6 complex increases in response to chromosome lengthening, chromosome circularization, or inactivation of topoisomerase 2, all having the potential to increase the number of sister chromatid intertwinings. Furthermore, non-functional Smc6 reduces the accumulation of intertwined sister plasmids after one round of replication in the absence of topoisomerase 2 function. Our results demonstrate that the length of a chromosome influences the need of superhelical tension release in Saccharomyces cerevisiae, and allow us to propose a model where the Smc5/6 complex facilitates fork rotation by sequestering nascent chromatid intertwinings that form behind the replication machinery.

  18. 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.

  19. Asynchronous Replication, Mono-Allelic Expression, and Long Range Cis-Effects of ASAR6

    OpenAIRE

    Donley, Nathan; Stoffregen, Eric P.; Smith, Leslie; Montagna, Christina; Thayer, Mathew J.

    2013-01-01

    Mammalian chromosomes initiate DNA replication at multiple sites along their length during each S phase following a temporal replication program. The majority of genes on homologous chromosomes replicate synchronously. However, mono-allelically expressed genes such as imprinted genes, allelically excluded genes, and genes on female X chromosomes replicate asynchronously. We have identified a cis-acting locus on human chromosome 6 that controls this replication-timing program. This locus encod...

  20. Cytosine methylation inhibits replication of African cassava mosaic virus by two distinct mechanisms.

    OpenAIRE

    Ermak, G; Paszkowski, U; Wohlmuth, M; Scheid, O M; Paszkowski, J

    1993-01-01

    Extrachromosomally replicating viral DNA is usually free of cytosine methylation and viral templates methylated in vitro are poor substrates when used in replication assays. We have investigated the mechanism of inhibition of viral replication by DNA methylation using as a model the DNA A of African cassava mosaic virus. We have constructed two component helper systems which allow for separation of the transcriptional inhibition of viral genes necessary for replication from replication inhibi...