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Sample records for affects replicative efficiency

  1. Efficient usage of Adabas replication

    CERN Document Server

    Storr, Dieter W

    2011-01-01

    In today's IT organization replication becomes more and more an essential technology. This makes Software AG's Event Replicator for Adabas an important part of your data processing. Setting the right parameters and establishing the best network communication, as well as selecting efficient target components, is essential for successfully implementing replication. This book provides comprehensive information and unique best-practice experience in the field of Event Replicator for Adabas. It also includes sample codes and configurations making your start very easy. It describes all components ne

  2. PB2 amino acid at position 627 affects replicative efficiency, but not cell tropism, of Hong Kong H5N1 influenza A viruses in mice

    International Nuclear Information System (INIS)

    A single amino acid substitution, from glutamic acid to lysine at position 627 of the PB2 protein, converts a nonlethal H5N1 influenza A virus isolated from a human to a lethal virus in mice. In contrast to the nonlethal virus, which replicates only in respiratory organs, the lethal isolate replicates in a variety of organs, producing systemic infection. Despite a clear difference in virulence and organ tropism between the two viruses, it remains unknown whether the dissimilarity is a result of differences in cell tropism or the reduced replicative ability of the nonlethal virus in mouse cells in general. To determine how this single amino acid change affects virulence and organ tropism in mice, we investigated the growth kinetics of the two H5N1 viruses both in vitro and in vivo. The identity of the PB2 amino acid at position 627 did not appreciably affect viral replicative efficiency in chicken embryo fibroblasts and a quail cell line; however, viruses with lysine at this position instead of glutamic acid grew better in the different mouse cells tested. When the effect of this substitution was investigated in mice, all of the test viruses showed the same cell tropism, but infection by viruses containing lysine at position 627 spread more rapidly than those viruses containing glutamic acid at this position. Further analysis showed a difference in local immune responses: neutrophil infiltration in lungs infected with viruses containing lysine at position 627 persisted longer than that associated with viruses lacking a glutamic acid substitution. Our data indicate that the amino acid at position 627 of the PB2 protein determines the efficiency of viral replication in mouse (not avian) cells, but not tropism among cells in different mouse organs. The presence of lysine leads to more aggressive viral replication, overwhelming the host's defense mechanisms and resulting in high mortality rates in mice

  3. Efficient Co-Replication of Defective Novirhabdovirus.

    Science.gov (United States)

    Rouxel, Ronan N; Mérour, Emilie; Biacchesi, Stéphane; Brémont, Michel

    2016-03-01

    We have generated defective Viral Hemorrhagic Septicemia Viruses (VHSV) which express either the green fluorescent protein (GFP) or a far-red fluorescent protein (mKate) by replacing the genes encoding the nucleoprotein N or the polymerase-associated P protein. To recover viable defective viruses, rVHSV-ΔN-Red and rVHSV-ΔP-Green, fish cells were co-transfected with both deleted cDNA VHSV genomes, together with plasmids expressing N, P and L of the RNA-dependent RNA polymerase. After one passage of the transfected cell supernatant, red and green cell foci were observed. Viral titer reached 10⁷ PFU/mL after three passages. Infected cells were always red and green with the very rare event of single red or green cell foci appearing. To clarify our understanding of how such defective viruses could be so efficiently propagated, we investigated whether (i) a recombination event between both defective genomes had occurred, (ii) whether both genomes were co-encapsidated in a single viral particle, and (iii) whether both defective viruses were always replicated together through a complementation phenomenon or even as conglomerate. To address these hypotheses, genome and viral particles have been fully characterized and, thus, allowing us to conclude that rVHSV-ΔN-Red and rVHSV-ΔP-Green are independent viral particles which could propagate only by simultaneously infecting the same cells. PMID:26959049

  4. Highly Efficient Self-Replicating RNA Enzymes

    OpenAIRE

    Robertson, Michael P; Joyce, Gerald F.

    2014-01-01

    An RNA enzyme has been developed that catalyzes the joining of oligonucleotide substrates to form additional copies of itself, undergoing self-replication with exponential growth. The enzyme also can cross-replicate with a partner enzyme, resulting in their mutual exponential growth and enabling self-sustained Darwinian evolution. The opportunity for inventive evolution within this synthetic genetic system depends on the diversity of the evolving population, which is limited by the catalytic ...

  5. A novel class of mutations that affect DNA replication in E. coli

    DEFF Research Database (Denmark)

    Nordman, Jared; Skovgaard, Ole; Wright, Andrew

    2007-01-01

    Over-initiation of DNA replication in cells containing the cold-sensitive dnaA(cos) allele has been shown to lead to extensive DNA damage, potentially due to head-to-tail replication fork collisions that ultimately lead to replication fork collapse, growth stasis and/or cell death. Based on the...... assumption that suppressors of the cold-sensitive phenotype of the cos mutant should include mutations that affect the efficiency and/or regulation of DNA replication, we subjected a dnaA(cos) mutant strain to transposon mutagenesis and selected mutant derivatives that could form colonies at 30°C. Four...... suppressors of the dnaA(cos)-mediated cold sensitivity were identified and further characterized. Based on origin to terminus ratios, chromosome content per cell, measured by flow cytometry, and sensitivity to the replication fork inhibitor hydroxyurea, the suppressors fell into two distinct categories: those...

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

    Directory of Open Access Journals (Sweden)

    Majid Eshaghi

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

  7. Drosophila Ctf4 is essential for efficient DNA replication and normal cell cycle progression

    OpenAIRE

    Christensen Tim W; Gosnell Justin A

    2011-01-01

    Abstract Background Proper coordination of the functions at the DNA replication fork is vital to the normal functioning of a cell. Specifically the precise coordination of helicase and polymerase activity is crucial for efficient passage though S phase. The Ctf4 protein has been shown to be a central member of the replication fork and links the replicative MCM helicase and DNA polymerase α primase. In addition, it has been implicated as a member of a complex that promotes replication fork sta...

  8. Factors affecting feed efficiency in dairy goats

    OpenAIRE

    Tadeu Silva de Oliveira; Fernando de Paula Leonel; Cássio José da Silva; Danielle Ferreira Baffa; José Carlos Pereira; Joanis Tilemahos Zervoudakis

    2014-01-01

    The objective of this study was to present some factors affecting feed efficiency in dairy goats. To develop our work, individual and average data from performance experiments with lactating goats were used. The following variables were evaluated: gross feed efficiency, adjusted feed efficiency, dry matter intake, milk-yield, 3.5% fat-corrected milk yield, dry matter digestibility, dietary neutral detergent fiber content, different roughage-to-concentrate ratios and body weight. The statistic...

  9. Identification of the determinants of efficient Pestivirus replication

    DEFF Research Database (Denmark)

    Risager, Peter Christian

    /Classical swine fever virus replication determinants, including a thorough presentation of the viral proteins, and the involvement of these in the infection progress. Part 3, "The manuscripts", includes the papers published and submitted on this work. These describe the outcome of experiments performed during the...... (Submitted paper, BMC genomics). Manuscript II describes the generation of replicons that express two different types of luciferases (Rluc and Gluc), and their application as a tool for easy monitoring of replication competence (published paper, Journal of General Virology (94), 1739-1748). Manuscript III...... three years. Manuscript I is a coauthored paper that describes a summary of the work I have been doing in my thesis dealing with the application of the Red/ET mediated homologous recombination method to modify viral cDNA. For proof of this method, CSFV/BDV chimeric clones were produced and characterized...

  10. Systematic identification of novel, essential host genes affecting bromovirus RNA replication.

    Directory of Open Access Journals (Sweden)

    Brandi L Gancarz

    Full Text Available Positive-strand RNA virus replication involves viral proteins and cellular proteins at nearly every replication step. Brome mosaic virus (BMV is a well-established model for dissecting virus-host interactions and is one of very few viruses whose RNA replication, gene expression and encapsidation have been reproduced in the yeast Saccharomyces cerevisiae. Previously, our laboratory identified ∼100 non-essential host genes whose loss inhibited or enhanced BMV replication at least 3-fold. However, our isolation of additional BMV-modulating host genes by classical genetics and other results underscore that genes essential for cell growth also contribute to BMV RNA replication at a frequency that may be greater than that of non-essential genes. To systematically identify novel, essential host genes affecting BMV RNA replication, we tested a collection of ∼900 yeast strains, each with a single essential gene promoter replaced by a doxycycline-repressible promoter, allowing repression of gene expression by adding doxycycline to the growth medium. Using this strain array of ∼81% of essential yeast genes, we identified 24 essential host genes whose depleted expression reproducibly inhibited or enhanced BMV RNA replication. Relevant host genes are involved in ribosome biosynthesis, cell cycle regulation and protein homeostasis, among other cellular processes. BMV 2a(Pol levels were significantly increased in strains depleted for a heat shock protein (HSF1 or proteasome components (PRE1 and RPT6, suggesting these genes may affect BMV RNA replication by directly or indirectly modulating 2a(Pol localization, post-translational modification or interacting partners. Investigating the diverse functions of these newly identified essential host genes should advance our understanding of BMV-host interactions and normal cellular pathways, and suggest new modes of virus control.

  11. Monitoring the determinants of efficient viral replication using Classical Swine Fever Virus-reporter replicons

    DEFF Research Database (Denmark)

    Risager, Peter Christian; Everett, Helen; Crooke, Helen;

    2012-01-01

    Classical swine fever virus (CSFV) is the etiological agent of the severe porcine disease, classical swine fever. Unraveling the molecular determinants of efficient replication is crucial for gaining improved knowledge of the pathogenic features of this virus. Monitoring the replication competence...

  12. Factors affecting feed efficiency in dairy goats

    Directory of Open Access Journals (Sweden)

    Tadeu Silva de Oliveira

    2014-10-01

    Full Text Available The objective of this study was to present some factors affecting feed efficiency in dairy goats. To develop our work, individual and average data from performance experiments with lactating goats were used. The following variables were evaluated: gross feed efficiency, adjusted feed efficiency, dry matter intake, milk-yield, 3.5% fat-corrected milk yield, dry matter digestibility, dietary neutral detergent fiber content, different roughage-to-concentrate ratios and body weight. The statistical analyses involved the application of descriptive and dispersion measures besides Pearson's correlation coefficient and linear regression analysis. The analyzed variables were highly correlated with feed efficiency. The feed efficiency of lactating goats was affected by the milk fat correction, dry matter digestibility, dietary fiber content, proportion of roughage in the diet and body weight. Among these factors, standardization of the milk fat appeared to be the most efficient in correcting the feed efficiency in lactating goats. Correction of some of these factors implies greater precision in the measurement of feed efficiency.

  13. Vaccinia virus replication is not affected by APOBEC3 family members

    Directory of Open Access Journals (Sweden)

    Sutter Gerd

    2006-10-01

    Full Text Available Abstract Background The APOBEC3G protein represents a novel innate defense mechanism against retroviral infection. It facilitates the deamination of the cytosine residues in the single stranded cDNA intermediate during early steps of retroviral infection. Most poxvirus genomes are relatively A/T-rich, which may indicate APOBEC3G-induced mutational pressure. In addition, poxviruses replicate exclusively in the cytoplasm where APOBEC3G is located. It was therefore tempting to analyze whether vaccinia virus replication is affected by APOBEC3G. Results The replication of vaccinia virus, a prototype poxvirus, was not, however, inhibited in APOBEC3G-expressing cells, nor did other members of the APOBEC3 family alter vaccinia virus replication. HIV counteracts APOBEC3G by inducing its degradation. However, Western blot analysis showed that the levels of APOBEC3G protein were not affected by vaccinia virus infection. Conclusion The data indicate that APOBEC3G is not a restriction factor for vaccinia virus replication nor is vaccinia virus able to degrade APOBEC3G.

  14. Efficient Bulk Data Replication for the Earth System Grid

    Energy Technology Data Exchange (ETDEWEB)

    Sim, Alex [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Gunter, Dan [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Natarajan, Vijaya [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Shoshani, Arie [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Williams, Dean [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Long, Jeff [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Hick, Jason [National Energy Research Scientific Computing Center, Berkeley, CA (United States); Lee, Jason [National Energy Research Scientific Computing Center, Berkeley, CA (United States); Dart, Eli [Energy Sciences Network, Berkeley, CA (United States)

    2010-03-10

    The Earth System Grid (ESG) community faces the difficult challenge of managing the distribution of massive data sets to thousands of scientists around the world. To move data replicas efficiently, the ESG has developed a data transfer management tool called the Bulk Data Mover (BDM). We describe the performance results of the current system and plans towards extending the techniques developed so far for the up- coming project, in which the ESG will employ advanced networks to move multi-TB datasets with the ulti- mate goal of helping researchers understand climate change and its potential impacts on world ecology and society.

  15. Brucella suis Vaccine Strain 2 Induces Endoplasmic Reticulum Stress that Affects Intracellular Replication in Goat Trophoblast Cells In vitro.

    Science.gov (United States)

    Wang, Xiangguo; Lin, Pengfei; Li, Yang; Xiang, Caixia; Yin, Yanlong; Chen, Zhi; Du, Yue; Zhou, Dong; Jin, Yaping; Wang, Aihua

    2016-01-01

    Brucella has been reported to impair placental trophoblasts, a cellular target where Brucella efficiently replicates in association with the endoplasmic reticulum (ER), and ultimately trigger abortion in pregnant animals. However, the precise effects of Brucella on trophoblast cells remain unclear. Here, we describe the infection and replication of Brucella suis vaccine strain 2 (B.suis.S2) in goat trophoblast cells (GTCs) and the cellular and molecular responses induced in vitro. Our studies demonstrated that B.suis.S2 was able to infect and proliferate to high titers, hamper the proliferation of GTCs and induce apoptosis due to ER stress. Tunicamycin (Tm), a pharmacological chaperone that strongly mounts ER stress-induced apoptosis, inhibited B.suis.S2 replication in GTCs. In addition, 4 phenyl butyric acid (4-PBA), a pharmacological chaperone that alleviates ER stress-induced apoptosis, significantly enhanced B.suis.S2 replication in GTCs. The Unfolded Protein Response (UPR) chaperone molecule GRP78 also promoted B.suis.S2 proliferation in GTCs by inhibiting ER stress-induced apoptosis. We also discovered that the IRE1 pathway, but not the PERK or ATF6 pathway, was activated in the process. However, decreasing the expression of phosphoIRE1α and IRE1α proteins with Irestatin 9389 (IRE1 antagonist) in GTCs did not affect the proliferation of B.suis.S2. Although GTC implantation was not affected upon B.suis.S2 infection, progesterone secretion was suppressed, and prolactin and estrogen secretion increased; these effects were accompanied by changes in the expression of genes encoding key steroidogenic enzymes. This study systematically explored the mechanisms of abortion in Brucella infection from the viewpoint of pathogen invasion, ER stress and reproductive endocrinology. Our findings may provide new insight for understanding the mechanisms involved in goat abortions caused by Brucella infection. PMID:26904517

  16. Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E. coli.

    Directory of Open Access Journals (Sweden)

    Alex Boehm

    2016-04-01

    Full Text Available In bacteria, replicative aging manifests as a difference in growth or survival between the two cells emerging from division. One cell can be regarded as an aging mother with a decreased potential for future survival and division, the other as a rejuvenated daughter. Here, we aimed at investigating some of the processes involved in aging in the bacterium Escherichia coli, where the two types of cells can be distinguished by the age of their cell poles. We found that certain changes in the regulation of the carbohydrate metabolism can affect aging. A mutation in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative lifespan; csrA mutants stop dividing once their pole exceeds an age of about five divisions. These old-pole cells accumulate glycogen at their old cell poles; after their last division, they do not contain a chromosome, presumably because of spatial exclusion by the glycogen aggregates. The new-pole daughters produced by these aging mothers are born young; they only express the deleterious phenotype once their pole is old. These results demonstrate how manipulations of nutrient allocation can lead to the exclusion of the chromosome and limit replicative lifespan in E. coli, and illustrate how mutations can have phenotypic effects that are specific for cells with old poles. This raises the question how bacteria can avoid the accumulation of such mutations in their genomes over evolutionary times, and how they can achieve the long replicative lifespans that have recently been reported.

  17. Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E. coli.

    Science.gov (United States)

    Boehm, Alex; Arnoldini, Markus; Bergmiller, Tobias; Röösli, Thomas; Bigosch, Colette; Ackermann, Martin

    2016-04-01

    In bacteria, replicative aging manifests as a difference in growth or survival between the two cells emerging from division. One cell can be regarded as an aging mother with a decreased potential for future survival and division, the other as a rejuvenated daughter. Here, we aimed at investigating some of the processes involved in aging in the bacterium Escherichia coli, where the two types of cells can be distinguished by the age of their cell poles. We found that certain changes in the regulation of the carbohydrate metabolism can affect aging. A mutation in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative lifespan; csrA mutants stop dividing once their pole exceeds an age of about five divisions. These old-pole cells accumulate glycogen at their old cell poles; after their last division, they do not contain a chromosome, presumably because of spatial exclusion by the glycogen aggregates. The new-pole daughters produced by these aging mothers are born young; they only express the deleterious phenotype once their pole is old. These results demonstrate how manipulations of nutrient allocation can lead to the exclusion of the chromosome and limit replicative lifespan in E. coli, and illustrate how mutations can have phenotypic effects that are specific for cells with old poles. This raises the question how bacteria can avoid the accumulation of such mutations in their genomes over evolutionary times, and how they can achieve the long replicative lifespans that have recently been reported. PMID:27093302

  18. Drosophila Ctf4 is essential for efficient DNA replication and normal cell cycle progression

    Directory of Open Access Journals (Sweden)

    Christensen Tim W

    2011-04-01

    Full Text Available Abstract Background Proper coordination of the functions at the DNA replication fork is vital to the normal functioning of a cell. Specifically the precise coordination of helicase and polymerase activity is crucial for efficient passage though S phase. The Ctf4 protein has been shown to be a central member of the replication fork and links the replicative MCM helicase and DNA polymerase α primase. In addition, it has been implicated as a member of a complex that promotes replication fork stability, the Fork Protection Complex (FPC, and as being important for sister chromatid cohesion. As such, understanding the role of Ctf4 within the context of a multicellular organism will be integral to our understanding of its potential role in developmental and disease processes. Results We find that Drosophila Ctf4 is a conserved protein that interacts with members of the GINS complex, Mcm2, and Polymerase α primase. Using in vivo RNAi knockdown of CTF4 in Drosophila we show that Ctf4 is required for viability, S phase progression, sister chromatid cohesion, endoreplication, and coping with replication stress. Conclusions Ctf4 remains a central player in DNA replication. Our findings are consistent with what has been previously reported for CTF4 function in yeast, Xenopus extracts, and human tissue culture. We show that Ctf4 function is conserved and that Drosophila can be effectively used as a model to further probe the precise function of Ctf4 as a member of the replication fork and possible roles in development.

  19. Replisome speed determines the efficiency of the Tus−Ter replication termination barrier

    KAUST Repository

    Elshenawy, Mohamed M.

    2015-08-31

    In all domains of life, DNA synthesis occurs bidirectionally from replication origins. Despite variable rates of replication fork progression, fork convergence often occurs at specific sites. Escherichia coli sets a \\'replication fork trap\\' that allows the first arriving fork to enter but not to leave the terminus region. The trap is set by oppositely oriented Tus-bound Ter sites that block forks on approach from only one direction. However, the efficiency of fork blockage by Tus-Ter does not exceed 50% in vivo despite its apparent ability to almost permanently arrest replication forks in vitro. Here we use data from single-molecule DNA replication assays and structural studies to show that both polarity and fork-arrest efficiency are determined by a competition between rates of Tus displacement and rearrangement of Tus-Ter interactions that leads to blockage of slower moving replisomes by two distinct mechanisms. To our knowledge this is the first example where intrinsic differences in rates of individual replisomes have different biological outcomes. ©2015 Macmillan Publishers Limited. All rights reserved.

  20. Mutational Analysis of Influenza A Virus Nucleoprotein: Identification of Mutations That Affect RNA Replication

    OpenAIRE

    Mena, Ignacio; Jambrina, Enrique; Albo, Carmen; Perales, Beatriz; Ortín, Juan; Arrese, Marta; Vallejo, Dolores; Portela, Agustín

    1999-01-01

    The influenza A virus nucleoprotein (NP) is a multifunctional polypeptide which plays a pivotal role in virus replication. To get information on the domains and specific residues involved in the different NP activities, we describe here the preparation and characterization of 20 influenza A virus mutant NPs. The mutations, mostly single-amino-acid substitutions, were introduced in a cDNA copy of the A/Victoria/3/75 NP gene and, in most cases, affected residues located in regions that were hig...

  1. Activating Ras mutations fail to ensure efficient replication of adenovirus mutants lacking VA-RNA

    DEFF Research Database (Denmark)

    Schümann, Michael; Dobbelstein, Matthias

    2006-01-01

    Adenoviruses lacking their PKR-antagonizing VA RNAs replicate poorly in primary cells. It has been suggested that these virus recombinants still replicate efficiently in tumor cells with Ras mutations and might therefore be useful in tumor therapy. The ability of interferon-sensitive viruses to...... grow in Ras-mutant tumor cells is generally ascribed to a postulated inhibitory effect of mutant Ras on PKR. We have constructed a set of isogenic adenoviruses that lack either or both VA RNA species, and tested virus replication in a variety of cell species with different Ras status. In tendency, VA...... mutational status, upon infection with VA-less adenoviruses in the presence of interferon, but also upon addition of the PKR activator polyIC to cells. When comparing two isogenic cell lines that differ solely with regard to the presence or absence of mutant Ras, no difference was observed concerning the...

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

    Science.gov (United States)

    Balistreri, Giuseppe; Viiliäinen, Johanna; Turunen, Mikko; Diaz, Raquel; Lyly, Lauri; Pekkonen, Pirita; Rantala, Juha; Ojala, Krista; Sarek, Grzegorz; Teesalu, Mari; Denisova, Oxana; Peltonen, Karita; Julkunen, Ilkka; Varjosalo, Markku; Kainov, Denis; Kallioniemi, Olli; Laiho, Marikki; Taipale, Jussi; Hautaniemi, Sampsa; Ojala, Päivi M

    2016-02-01

    Kaposi's sarcoma herpesvirus (KSHV) causes Kaposi's sarcoma and certain lymphoproliferative malignancies. Latent infection is established in the majority of tumor cells, whereas lytic replication is reactivated in a small fraction of cells, which is important for both virus spread and disease progression. A siRNA screen for novel regulators of KSHV reactivation identified the E3 ubiquitin ligase MDM2 as a negative regulator of viral reactivation. Depletion of MDM2, a repressor of p53, favored efficient activation of the viral lytic transcription program and viral reactivation. During lytic replication cells activated a p53 response, accumulated DNA damage and arrested at G2-phase. Depletion of p21, a p53 target gene, restored cell cycle progression and thereby impaired the virus reactivation cascade delaying the onset of virus replication induced cytopathic effect. Herpesviruses are known to reactivate in response to different kinds of stress, and our study now highlights the molecular events in the stressed host cell that KSHV has evolved to utilize to ensure efficient viral lytic replication. PMID:26891221

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

    Directory of Open Access Journals (Sweden)

    Giuseppe Balistreri

    2016-02-01

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

  4. Mutagenesis in ORF AV2 affects viral replication in Mungbean yellow mosaic India virus

    Indian Academy of Sciences (India)

    A Rouhibakhsh; Q M I Haq; V G Malathi

    2011-06-01

    Mungbean yellow mosaic India virus (MYMIV) is a whitefly-transmitted begomovirus with a bipartite genome. We investigate the functions of the MYMIV-AV2 protein, the open reading frame present upstream of the coat protein gene in DNA A component. The ability of MYMIV-AV2 mutants to replicate, spread and cause symptoms in legume hosts, blackgram, cowpea and French bean was analysed. Plants agroinoculated with mutants K73R, C86S and the double mutant C84S, C86S showed increase in severity of symptoms compared with the wild type. However, mutants W2S and H14Q,G15E caused marked attenuation of symptoms. While the double mutants C84S,C86S caused a 50-fold increase in double-stranded supercoiled and single-stranded DNA accumulation, the mutations W2S and H14Q,G15E showed a decrease in double-stranded supercoiled and single-stranded viral DNA accumulation. Because AV2 mutants affect the ratio between open circular and supercoiled DNA forms, we hypothesize that these mutations may modulate the functions of the replication initiation protein.

  5. Market conditions affecting energy efficiency investments

    International Nuclear Information System (INIS)

    The global energy efficiency market is growing, due in part to energy sector and macroeconomic reforms and increased awareness of the environmental benefits of energy efficiency. Many countries have promoted open, competitive markets, thereby stimulating economic growth. They have reduced or removed subsidies on energy prices, and governments have initiated energy conservation programs that have spurred the wider adoption of energy efficiency technologies. The market outlook for energy efficiency is quite positive. The global market for end-use energy efficiency in the industrial, residential and commercial sectors is now estimated to total more than $34 billion per year. There is still enormous technical potential to implement energy conservation measures and to upgrade to the best available technologies for new investments. For many technologies, energy-efficient designs now represent less than 10--20% of new product sales. Thus, creating favorable market conditions should be a priority. There are a number of actions that can be taken to create favorable market conditions for investing in energy efficiency. Fostering a market-oriented energy sector will lead to energy prices that reflect the true cost of supply. Policy initiatives should address known market failures and should support energy efficiency initiatives. And market transformation for energy efficiency products and services can be facilitated by creating an institutional and legal structure that favors commercially-oriented entities

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

    OpenAIRE

    Xiangguo eWang; pengfei elin; yang eli; caixia exiang; yanlong eyin; zhi echen; yue edu; dong ezhou; yaping ejin; Aihua eWang

    2016-01-01

    Brucella has been reported to impair placental trophoblasts, a cellular target where Brucella efficiently replicates in association with the endoplasmic reticulum (ER), and ultimately trigger abortion in pregnant animals. However, the precise effects of Brucella on trophoblast cells remain unclear. Here, we describe the infection and replication of Brucella suis vaccine strain 2 (B.suis.S2) in goat trophoblast cells (GTCs) and the cellular and molecular responses induced in vitro. Our studies...

  7. Brucella suis Vaccine Strain 2 Induces Endoplasmic Reticulum Stress that Affects Intracellular Replication in Goat Trophoblast Cells In vitro

    OpenAIRE

    Wang, Xiangguo; Lin, PengFei; Li, Yang; Xiang, Caixia; Yin, Yanlong; Chen, Zhi; Du, Yue; Zhou, dong; Jin, Yaping; Wang, Aihua

    2016-01-01

    Brucella has been reported to impair placental trophoblasts, a cellular target where Brucella efficiently replicates in association with the endoplasmic reticulum (ER), and ultimately trigger abortion in pregnant animals. However, the precise effects of Brucella on trophoblast cells remain unclear. Here, we describe the infection and replication of Brucella suis vaccine strain 2 (B.suis.S2) in goat trophoblast cells (GTCs) and the cellular and molecular responses induced in vitro. Our studies...

  8. A prophage-encoded actin-like protein required for efficient viral DNA replication in bacteria.

    Science.gov (United States)

    Donovan, Catriona; Heyer, Antonia; Pfeifer, Eugen; Polen, Tino; Wittmann, Anja; Krämer, Reinhard; Frunzke, Julia; Bramkamp, Marc

    2015-05-26

    In host cells, viral replication is localized at specific subcellular sites. Viruses that infect eukaryotic and prokaryotic cells often use host-derived cytoskeletal structures, such as the actin skeleton, for intracellular positioning. Here, we describe that a prophage, CGP3, integrated into the genome of Corynebacterium glutamicum encodes an actin-like protein, AlpC. Biochemical characterization confirms that AlpC is a bona fide actin-like protein and cell biological analysis shows that AlpC forms filamentous structures upon prophage induction. The co-transcribed adaptor protein, AlpA, binds to a consensus sequence in the upstream promoter region of the alpAC operon and also interacts with AlpC, thus connecting circular phage DNA to the actin-like filaments. Transcriptome analysis revealed that alpA and alpC are among the early induced genes upon excision of the CGP3 prophage. Furthermore, qPCR analysis of mutant strains revealed that both AlpA and AlpC are required for efficient phage replication. Altogether, these data emphasize that AlpAC are crucial for the spatio-temporal organization of efficient viral replication. This is remarkably similar to actin-assisted membrane localization of eukaryotic viruses that use the actin cytoskeleton to concentrate virus particles at the egress sites and provides a link of evolutionary conserved interactions between intracellular virus transport and actin. PMID:25916847

  9. The Impact of Positive Affect on Language Learning Efficiency

    Institute of Scientific and Technical Information of China (English)

    LU Pan

    2013-01-01

    To generate a further understanding of the impact of positive affective variables on foreign language learning efficiency, a theoretical analysis was conducted, from second language acquisition and cognitive psychology perspectives. Second language ac⁃quisition process is inevitably influenced by individual affective variables residing within the learner. To improve language learn⁃ing efficiency, positive and facilitative affect should be enhanced in language learning.

  10. Mutated primer binding sites interacting with different tRNAs allow efficient murine leukemia virus replication

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M; Lovmand, J;

    1993-01-01

    Two Akv murine leukemia virus-based retroviral vectors with primer binding sites matching tRNA(Gln-1) and tRNA(Lys-3) were constructed. The transduction efficiency of these mutated vectors was found to be comparable to that of a vector carrying the wild-type primer binding site matching t......RNA(Pro). Polymerase chain reaction amplification and sequence analysis of transduced proviruses confirmed the transfer of vectors with mutated primer binding sites and further showed that tRNA(Gln-2) may act efficiently in conjunction with the tRNA(Gln-1) primer binding site. We conclude that murine leukemia virus...... can replicate by using various tRNA molecules as primers and propose primer binding site-tRNA primer interactions to be of major importance for tRNA primer selection. However, efficient primer selection does not require perfect Watson-Crick base pairing at all 18 positions of the primer binding site....

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  12. High efficiency of replication and expression of foreign genes in SV40-transformed human fibroblasts.

    OpenAIRE

    Boast, S; La Mantia, G; Lania, L; Blasi, F

    1983-01-01

    Human fibroblasts (HF) were transformed in vitro with origin-defective SV40 DNA (ori-) using the calcium phosphate co-precipitation technique. The SV40 ori- transformed human cells (HSF) were able to replicate efficiently a recombinant DNA molecule containing the ori sequence of SV40 DNA. Transfection of HFS with pTBC1, a recombinant pi vx plasmid containing the herpes simplex virus thymidine kinase (HSV-TK) gene and the ori SV40 sequences, results in high levels of TK mRNA of correct size. T...

  13. Work-family enrichment and job performance: a constructive replication of affective events theory.

    Science.gov (United States)

    Carlson, Dawn; Kacmar, K Michele; Zivnuska, Suzanne; Ferguson, Merideth; Whitten, Dwayne

    2011-07-01

    Based on affective events theory (AET), we hypothesize a four-step model of the mediating mechanisms of positive mood and job satisfaction in the relationship between work-family enrichment and job performance. We test this model for both directions of enrichment (work-to-family and family-to-work). We used two samples to test the model using structural equation modeling. Results from Study 1, which included 240 full-time employees, were replicated in Study 2, which included 189 matched subordinate-supervisor dyads. For the work-to-family direction, results from both samples support our conceptual model and indicate mediation of the enrichment-performance relationship for the work-to-family direction of enrichment. For the family-to-work direction, results from the first sample support our conceptual model but results from the second sample do not. Our findings help elucidate mixed findings in the enrichment and job performance literatures and contribute to an understanding of the mechanisms linking these concepts. We conclude with a discussion of the practical and theoretical implications of our findings. PMID:21728437

  14. Genetic Elements in the VP Region of Porcine Parvovirus Are Critical to Replication Efficiency in Cell Culture▿

    OpenAIRE

    Fernandes, Sandra; Boisvert, Maude; Tijssen, Peter

    2011-01-01

    Factors controlling porcine parvovirus (PPV) replication efficiency are poorly characterized. Two prototype strains of PPV, NADL-2 and Kresse, differ greatly in pathogenic capacity both in vivo and in vitro, yet their genomic sequence is nearly identical (13 single-nucleotide substitutions and a 127-nucleotide noncoding repeated sequence). We have created a series of chimeras of these strains to identify the genetic elements involved in replication efficiency in the host porcine cell line. Wh...

  15. Neonicotinoid clothianidin adversely affects insect immunity and promotes replication of a viral pathogen in honey bees.

    Science.gov (United States)

    Di Prisco, Gennaro; Cavaliere, Valeria; Annoscia, Desiderato; Varricchio, Paola; Caprio, Emilio; Nazzi, Francesco; Gargiulo, Giuseppe; Pennacchio, Francesco

    2013-11-12

    Large-scale losses of honey bee colonies represent a poorly understood problem of global importance. Both biotic and abiotic factors are involved in this phenomenon that is often associated with high loads of parasites and pathogens. A stronger impact of pathogens in honey bees exposed to neonicotinoid insecticides has been reported, but the causal link between insecticide exposure and the possible immune alteration of honey bees remains elusive. Here, we demonstrate that the neonicotinoid insecticide clothianidin negatively modulates NF-κB immune signaling in insects and adversely affects honey bee antiviral defenses controlled by this transcription factor. We have identified in insects a negative modulator of NF-κB activation, which is a leucine-rich repeat protein. Exposure to clothianidin, by enhancing the transcription of the gene encoding this inhibitor, reduces immune defenses and promotes the replication of the deformed wing virus in honey bees bearing covert infections. This honey bee immunosuppression is similarly induced by a different neonicotinoid, imidacloprid, but not by the organophosphate chlorpyriphos, which does not affect NF-κB signaling. The occurrence at sublethal doses of this insecticide-induced viral proliferation suggests that the studied neonicotinoids might have a negative effect at the field level. Our experiments uncover a further level of regulation of the immune response in insects and set the stage for studies on neural modulation of immunity in animals. Furthermore, this study has implications for the conservation of bees, as it will contribute to the definition of more appropriate guidelines for testing chronic or sublethal effects of pesticides used in agriculture. PMID:24145453

  16. Elements in the canine distemper virus M 3' UTR contribute to control of replication efficiency and virulence.

    Directory of Open Access Journals (Sweden)

    Danielle E Anderson

    Full Text Available Canine distemper virus (CDV is a negative-sense, single-stranded RNA virus within the genus Morbillivirus and the family Paramyxoviridae. The Morbillivirus genome is composed of six transcriptional units that are separated by untranslated regions (UTRs, which are relatively uniform in length, with the exception of the UTR between the matrix (M and fusion (F genes. This UTR is at least three times longer and in the case of CDV also highly variable. Exchange of the M-F region between different CDV strains did not affect virulence or disease phenotype, demonstrating that this region is functionally interchangeable. Viruses carrying the deletions in the M 3' UTR replicated more efficiently, which correlated with a reduction of virulence, suggesting that overall length as well as specific sequence motifs distributed throughout the region contribute to virulence.

  17. Relationship between RNA polymerase II and efficiency of vaccinia virus replication

    International Nuclear Information System (INIS)

    It is clear from previous studies that host transcriptase or RNA polymerase II (pol II) has a role in poxvirus replication. To elucidate the participation of this enzyme further, in this study the authors examined several parameters related to pol II during the cycle of vaccinia virus infection in L-strain fibroblasts, HeLa cells, and L6H9 rat myoblasts. Nucleocytoplasmic transposition of pol II into virus factories and virions was assessed by immunofluorescence and immunoblotting by using anti-pol II immunoglobulin G. RNA polymerase activities were compared in nuclear extracts containing cured enzyme preparations. Rates of translation into cellular or viral polypeptides were ascertained by labeling with [35S]methionine. In L and HeLa cells, which produced vaccinia virus more abundantly, the rate of RNA polymerase and translation in controls and following infection were higher than in myoblasts. The data on synthesis and virus formation could be correlated with observations on transmigration of pol II, which was more efficient and complete in L and HeLa cells. The stimulus for pol II to leave the nucleus required the expression of both early and late viral functions. On the basis of current and past information, the authors suggest that mobilization of pol II depends on the efficiency of vaccinia virus replication and furthermore that control over vaccinia virus production by the host is related to the content or availability (or both) of pol II in different cell types

  18. A conserved OmpA-like protein in Legionella pneumophila required for efficient intracellular replication.

    Science.gov (United States)

    Goodwin, Ian P; Kumova, Ogan K; Ninio, Shira

    2016-08-01

    The OmpA-like protein domain has been associated with peptidoglycan-binding proteins, and is often found in virulence factors of bacterial pathogens. The intracellular pathogen Legionella pneumophila encodes for six proteins that contain the OmpA-like domain, among them the highly conserved uncharacterized protein we named CmpA. Here we set out to characterize the CmpA protein and determine its contribution to intracellular survival of L. pneumophila Secondary structure analysis suggests that CmpA is an inner membrane protein with a peptidoglycan-binding domain at the C-teminus. A cmpA mutant was able to replicate normally in broth, but failed to compete with an isogenic wild-type strain in an intracellular growth competition assay. The cmpA mutant also displayed significant intracellular growth defects in both the protozoan host Acanthamoeba castellanii and in primary bone marrow-derived macrophages, where uptake into the cells was also impaired. The cmpA phenotypes were completely restored upon expression of CmpA in trans The data presented here establish CmpA as a novel virulence factor of L. pneumophila that is required for efficient intracellular replication in both mammalian and protozoan hosts. PMID:27421957

  19. A Gossip-based optimistic replication for efficient delay-sensitive streaming using an interactive middleware support system

    CERN Document Server

    Mavromoustakis, Constandinos X; 10.1109/JSYST.2010.2047172

    2010-01-01

    While sharing resources the efficiency is substantially degraded as a result of the scarceness of availability of the requested resources in a multiclient support manner. These resources are often aggravated by many factors like the temporal constraints for availability or node flooding by the requested replicated file chunks. Thus replicated file chunks should be efficiently disseminated in order to enable resource availability on-demand by the mobile users. This work considers a cross layered middleware support system for efficient delay-sensitive streaming by using each device's connectivity and social interactions in a cross layered manner. The collaborative streaming is achieved through the epidemically replicated file chunk policy which uses a transition-based approach of a chained model of an infectious disease with susceptible, infected, recovered and death states. The Gossip-based stateful model enforces the mobile nodes whether to host a file chunk or not or, when no longer a chunk is needed, to pur...

  20. Generation of a human hepatoma cell line supporting efficient replication of a lamivudine resistant hepatitis B virus.

    Science.gov (United States)

    Zhang, Yijun; Zhang, Yongmei; Kang, Yaoyue; Wang, Jinyu; Liu, Hongyan; Zhu, Haoxiang; Qin, Yanli; Mao, Richeng; Lin, Xu; Lu, Mengji; Zhang, Jiming

    2014-06-01

    Emergence of lamivudine (LAM) resistance causes treatment failure in patients with chronic hepatitis B and compromise the efficacy of subsequent salvage therapies with other nucleot(s)ide analogs (NAs). Establishment of cell-based assays supporting LAM-resistant hepatitis B virus (HBV) replication will not only provide tools for investigating the replication property, but also screening for antiviral agents efficiently inhibiting the replication of LAM-resistant HBV variants. Accordingly, a human hepatoma (HepG2)-derived cell line was established by stable transfection of a plasmid containing a 1.2 unit length of HBV genome harboring rtL180M and rtM204V mutations that confer LAM resistance. In addition to support efficient viral genome replication, the cell line also produces high levels of HBV virions and subviral particles. As expected, HBV DNA replication in this cell line is completely resistant to lamivudine, but sensitive to adefovir (ADV), entecavir (ETV) and tenofovir (TDF). The cell line is suitable for screening for antiviral agents that inhibit LAM-resistant HBV replication and inhibitors of HBsAg biosynthesis and secretion, which may reduce HBsAg antigenemia and ultimately help to restore host antiviral immune response against HBV and cure chronic HBV infection. PMID:24583110

  1. Nucleolin interacts with influenza A nucleoprotein and contributes to viral ribonucleoprotein complexes nuclear trafficking and efficient influenza viral replication.

    Science.gov (United States)

    Terrier, Olivier; Carron, Coralie; De Chassey, Benoît; Dubois, Julia; Traversier, Aurélien; Julien, Thomas; Cartet, Gaëlle; Proust, Anaïs; Hacot, Sabine; Ressnikoff, Denis; Lotteau, Vincent; Lina, Bruno; Diaz, Jean-Jacques; Moules, Vincent; Rosa-Calatrava, Manuel

    2016-01-01

    Influenza viruses replicate their single-stranded RNA genomes in the nucleus of infected cells and these replicated genomes (vRNPs) are then exported from the nucleus to the cytoplasm and plasma membrane before budding. To achieve this export, influenza viruses hijack the host cell export machinery. However, the complete mechanisms underlying this hijacking remain not fully understood. We have previously shown that influenza viruses induce a marked alteration of the nucleus during the time-course of infection and notably in the nucleolar compartment. In this study, we discovered that a major nucleolar component, called nucleolin, is required for an efficient export of vRNPs and viral replication. We have notably shown that nucleolin interacts with the viral nucleoprotein (NP) that mainly constitutes vRNPs. Our results suggest that this interaction could allow vRNPs to "catch" the host cell export machinery, a necessary step for viral replication. PMID:27373907

  2. Nucleolin interacts with influenza A nucleoprotein and contributes to viral ribonucleoprotein complexes nuclear trafficking and efficient influenza viral replication

    Science.gov (United States)

    Terrier, Olivier; Carron, Coralie; De Chassey, Benoît; Dubois, Julia; Traversier, Aurélien; Julien, Thomas; Cartet, Gaëlle; Proust, Anaïs; Hacot, Sabine; Ressnikoff, Denis; Lotteau, Vincent; Lina, Bruno; Diaz, Jean-Jacques; Moules, Vincent; Rosa-Calatrava, Manuel

    2016-01-01

    Influenza viruses replicate their single-stranded RNA genomes in the nucleus of infected cells and these replicated genomes (vRNPs) are then exported from the nucleus to the cytoplasm and plasma membrane before budding. To achieve this export, influenza viruses hijack the host cell export machinery. However, the complete mechanisms underlying this hijacking remain not fully understood. We have previously shown that influenza viruses induce a marked alteration of the nucleus during the time-course of infection and notably in the nucleolar compartment. In this study, we discovered that a major nucleolar component, called nucleolin, is required for an efficient export of vRNPs and viral replication. We have notably shown that nucleolin interacts with the viral nucleoprotein (NP) that mainly constitutes vRNPs. Our results suggest that this interaction could allow vRNPs to “catch” the host cell export machinery, a necessary step for viral replication. PMID:27373907

  3. Degenerate in vitro genetic selection reveals mutations that diminish alfalfa mosaic virus RNA replication without affecting coat protein binding.

    Science.gov (United States)

    Rocheleau, Gail; Petrillo, Jessica; Guogas, Laura; Gehrke, Lee

    2004-08-01

    The alfalfa mosaic virus (AMV) RNAs are infectious only in the presence of the viral coat protein; however, the mechanisms describing coat protein's role during replication are disputed. We reasoned that mechanistic details might be revealed by identifying RNA mutations in the 3'-terminal coat protein binding domain that increased or decreased RNA replication without affecting coat protein binding. Degenerate (doped) in vitro genetic selection, based on a pool of randomized 39-mers, was used to select 30 variant RNAs that bound coat protein with high affinity. AUGC sequences that are conserved among AMV and ilarvirus RNAs were among the invariant nucleotides in the selected RNAs. Five representative clones were analyzed in functional assays, revealing diminished viral RNA expression resulting from apparent defects in replication and/or translation. These data identify a set of mutations, including G-U wobble pairs and nucleotide mismatches in the 5' hairpin, which affect viral RNA functions without significant impact on coat protein binding. Because the mutations associated with diminished function were scattered over the 3'-terminal nucleotides, we considered the possibility that RNA conformational changes rather than disruption of a precise motif might limit activity. Native polyacrylamide gel electrophoresis experiments showed that the 3' RNA conformation was indeed altered by nucleotide substitutions. One interpretation of the data is that coat protein binding to the AUGC sequences determines the orientation of the 3' hairpins relative to one another, while local structural features within these hairpins are also critical determinants of functional activity. PMID:15254175

  4. nfi-1 affects behavior and life-span in C. elegans but is not essential for DNA replication or survival

    Directory of Open Access Journals (Sweden)

    Hirono Keiko

    2005-10-01

    Full Text Available Abstract Background The Nuclear Factor I (one (NFI family of transcription/replication factors plays essential roles in mammalian gene expression and development and in adenovirus DNA replication. Because of its role in viral DNA replication NFI has long been suspected to function in host DNA synthesis. Determining the requirement for NFI proteins in mammalian DNA replication is complicated by the presence of 4 NFI genes in mice and humans. Loss of individual NFI genes in mice cause defects in brain, lung and tooth development, but the presence of 4 homologous NFI genes raises the issue of redundant roles for NFI genes in DNA replication. No NFI genes are present in bacteria, fungi or plants. However single NFI genes are present in several simple animals including Drosophila and C. elegans, making it possible to test for a requirement for NFI in multicellular eukaryotic DNA replication and development. Here we assess the functions of the single nfi-1 gene in C. elegans. Results C. elegans NFI protein (CeNFI binds specifically to the same NFI-binding site recognized by vertebrate NFIs. nfi-1 encodes alternatively-spliced, maternally-inherited transcripts that are expressed at the single cell stage, during embryogenesis, and in adult muscles, neurons and gut cells. Worms lacking nfi-1 survive but have defects in movement, pharyngeal pumping and egg-laying and have a reduced life-span. Expression of the muscle gene Ce titin is decreased in nfi-1 mutant worms. Conclusion NFI gene function is not needed for survival in C. elegans and thus NFI is likely not essential for DNA replication in multi-cellular eukaryotes. The multiple defects in motility, egg-laying, pharyngeal pumping, and reduced lifespan indicate that NFI is important for these processes. Reduction in Ce titin expression could affect muscle function in multiple tissues. The phenotype of nfi-1 null worms indicates that NFI functions in multiple developmental and behavioral systems in C

  5. DNA repair and replication fork helicases are differentially affected by alkyl phosphotriester lesion.

    Science.gov (United States)

    Suhasini, Avvaru N; Sommers, Joshua A; Yu, Stephen; Wu, Yuliang; Xu, Ting; Kelman, Zvi; Kaplan, Daniel L; Brosh, Robert M

    2012-06-01

    DNA helicases are directly responsible for catalytically unwinding duplex DNA in an ATP-dependent and directionally specific manner and play essential roles in cellular nucleic acid metabolism. It has been conventionally thought that DNA helicases are inhibited by bulky covalent DNA adducts in a strand-specific manner. However, the effects of highly stable alkyl phosphotriester (PTE) lesions that are induced by chemical mutagens and refractory to DNA repair have not been previously studied for their effects on helicases. In this study, DNA repair and replication helicases were examined for unwinding a forked duplex DNA substrate harboring a single isopropyl PTE specifically positioned in the helicase-translocating or -nontranslocating strand within the double-stranded region. A comparison of SF2 helicases (RecQ, RECQ1, WRN, BLM, FANCJ, and ChlR1) with a SF1 DNA repair helicase (UvrD) and two replicative helicases (MCM and DnaB) demonstrates unique differences in the effect of the PTE on the DNA unwinding reactions catalyzed by these enzymes. All of the SF2 helicases tested were inhibited by the PTE lesion, whereas UvrD and the replication fork helicases were fully tolerant of the isopropyl backbone modification, irrespective of strand. Sequestration studies demonstrated that RECQ1 helicase was trapped by the PTE lesion only when it resided in the helicase-translocating strand. Our results are discussed in light of the current models for DNA unwinding by helicases that are likely to encounter sugar phosphate backbone damage during biological DNA transactions. PMID:22500020

  6. Cellular DNA repair cofactors affecting hepatitis B virus infection and replication

    Institute of Scientific and Technical Information of China (English)

    Fan Zhao; Ning-Bo Hou; Ting Song; Xiang He; Zi-Rui Zheng; Qing-Jun Ma; Li Li; Yan-Hong Zhang; Hui Zhong

    2008-01-01

    AIM: To investigate whether hepatitis B virus (HBV)infection activates DNA damage response and DNA repair cofactors inhibit HBV infection and replication.METHODS: Human hepatocyte cell line HL7702 was studied. Immunoblotting was performed to test the expression of ataxia telangiectasia-mutated (ATM)-Rad3-related protein (ATR), p21 and the level of phosphorylation of Chk1, p53, H2AX, ATM in HBV-infected or non-infected-cells. Special short RNAi oligos was transfected to induce transient ATR knockdown in HL7702. ATR-ATM chemical inhibitors caffeine (CF) and theophylline (TP), or Chk1 inhibitor 7-hydroxystaurosporine (UCN01) was studied to determine whether they suppress cellular DNA damage response and MG132 inhibits proteasome.RESULTS: The ATR checkpoint pathway, responding to single-strand breaks in DNA, was activated in response to HBV infection. ATR knockdown cells decreased the HBV DNA yields, implying that HBV infection and replication could activate and exploit the activated DNA damage response. CF/TP or UCN01 reduced the HBV DNA yield by 70% and 80%, respectively. HBV abrogated the ATR-dependent DNA damage signaling pathway by degrading p21, and introduction of the p21 protein before HBV infection reduced the HBV DNA yield. Consistent with this result, p21 accumulation after MG132 treatment also sharply decreased the HBV DNA yield.CONCLUSION: HBV infection can be treated with therapeutic approaches targeting host cell proteins by inhibiting a cellular gene required for HBV replication or by restoring a response abrogated by HBV, thus providing a potential approach to the prevention and treatrnent of HBV infection.

  7. Extensive Replication of a Retroviral Replicating Vector Can Expand the A Bulge in the Encephalomyocarditis Virus Internal Ribosome Entry Site and Change Translation Efficiency of the Downstream Transgene.

    Science.gov (United States)

    Lin, Amy H; Liu, Yanzheng; Burrascano, Cynthia; Cunanan, Kathrina; Logg, Christopher R; Robbins, Joan M; Kasahara, Noriyuki; Gruber, Harry; Ibañez, Carlos; Jolly, Douglas J

    2016-04-01

    We have developed retroviral replicating vectors (RRV) derived from Moloney murine gammaretrovirus with an amphotropic envelope and an encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES)-transgene cassette downstream of the env gene. During long-term (180 days) replication of the vector in animals, a bulge of 7 adenosine residues (A's) in the J-K bifurcation domain sometimes serially added A's. Therefore, vectors with 4-12 A's in the A bulge in the J-K bifurcation domain were generated, and the impact of the variants on transgene protein expression, vector stability, and IRES sequence upon multiple infection cycles was assessed in RRV encoding yeast-derived cytosine deaminase and green fluorescent protein in vitro. For transgene protein expression, after multiple infection cycles, RRV-IRES with 5-7 A's gave roughly comparable levels, 4 and 8 A's were within about 4-5-fold of the 6 A's, whereas 10 and 12 A's were marked lower. In terms of stability, after 10 infection cycles, expansion of A's appeared to be a more frequent event affecting transgene protein expression than viral genome deletions or rearrangement: 4 and 5 A's appeared completely stable; 6, 7, and particularly 8 A's showed some level of expansion in the A bulge; 10 and 12 A's underwent both expansion and transgene deletion. The strong relative translational activity of the 5 A's in the EMCV IRES has not been reported previously. The 5A RRV-IRES may have utility for preclinical and clinical applications where extended replication is required. PMID:26918465

  8. Investigating factors affecting the efficiency of gas turbine power cycle

    Directory of Open Access Journals (Sweden)

    R. Ghaderi

    2014-05-01

    Full Text Available Today, the use of gas turbines in power generation cycles has been growing. Small size, easy installation, high power-to-mass ratio and the ability to load and unload the cycle quickly are the advantages of such systems. Low efficiency is considered as one of the major disadvantages of such power plants. Thus providing a way to increase cycle efficiency can be very effective in making the cycle more efficient and thus saving fuel consumed in such systems. In this paper the thermal efficiency of the cycle is introduced through describing the mechanism of gas turbine in power generation cycle. Then we will examine the factors affecting the efficiency of the cycle and finally practical solutions such as increasing the inlet temperature, recovery, internal cooling of the compressor and heat recovery for increasing efficiency will be explained. Evaluating the polytropic efficiency of cycles shows that increasing the inlet gas temperature has little effect on turbine efficiency and is limited at high levels of ηpoly. Water or steam injection into the gas turbines will not only lead to increased efficiency of the cycle, but also increases the flexibility of the turbine, too.

  9. Factors Affecting the Relative Efficiency of General Acid Catalysis

    Science.gov (United States)

    Kwan, Eugene E.

    2005-01-01

    A simple framework for evaluating experimental kinetic data to provide support for Specific Acid Catalysis (SAC) and General Acid Catalysis (GAC) is described based on the factors affecting their relative efficiency. Observations reveal that increasing the SAC-to-GAC rate constant ratio reduces the effective pH range for GAC.

  10. Efficient replication bypass of size-expanded DNA base pairs in bacterial cells

    OpenAIRE

    Delaney, James C.; GAO, JIANMIN; Liu, Haibo; Shrivastav, Nidhi; Essigmann, John M.; Kool, Eric T.

    2009-01-01

    Supersize me! Size-expanded DNA bases (xDNA) are able to encode natural DNA sequences in replication. In vitro experiments with a DNA polymerase show nucleotide incorporation opposite the xDNA bases with correct pairing. In vivo experiments using E. coli show that two xDNA bases (xA and xC, see picture) encode the correct replication partners.

  11. Efficient Replication of Severe Acute Respiratory Syndrome Coronavirus in Mouse Cells Is Limited by Murine Angiotensin-Converting Enzyme 2

    Science.gov (United States)

    Li, Wenhui; Greenough, Thomas C.; Moore, Michael J.; Vasilieva, Natalya; Somasundaran, Mohan; Sullivan, John L.; Farzan, Michael; Choe, Hyeryun

    2004-01-01

    Replication of viruses in species other than their natural hosts is frequently limited by entry and postentry barriers. The coronavirus that causes severe acute respiratory syndrome (SARS-CoV) utilizes the receptor angiotensin-converting enzyme 2 (ACE2) to infect cells. Here we compare human, mouse, and rat ACE2 molecules for their ability to serve as receptors for SARS-CoV. We found that, compared to human ACE2, murine ACE2 less efficiently bound the S1 domain of SARS-CoV and supported less-efficient S protein-mediated infection. Rat ACE2 was even less efficient, at near background levels for both activities. Murine 3T3 cells expressing human ACE2 supported SARS-CoV replication, whereas replication was less than 10% as efficient in the same cells expressing murine ACE2. These data imply that a mouse transgenically expressing human ACE2 may be a useful animal model of SARS. PMID:15452268

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

    Directory of Open Access Journals (Sweden)

    Subrota K. Mondal

    2016-07-01

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

  13. Physical Factors Affecting in Vitro Replication of Foot and Mouth Disease Virus (Serotype “O”

    Directory of Open Access Journals (Sweden)

    Muhammad Taslim Ghori*, Khushi Muhammad and Masood Rabbani1

    2011-10-01

    Full Text Available Effect of physical factors (temperature, pH and UV light on replicating ability of “O” type of Foot and Mouth Disease (FMD virus on Baby Hamster Kidney (BHK cell line was determined. The freshly grown FMD virus containing 106 units of tissue culture infective dose (TCID50 was divided into aliquots. Each of the 9 virus aliquots was exposed to 37, 57 or 77C for 15, 30 or 45 minutes, respectively. Each of the 5 virus aliquots was mixed with MEM-199 maintenance medium having pH 3, 5, 7, 9, or 11. Similarly, each of the 3 aliquots having 1 mm depth of the medium was exposed to ultraviolet light (252.7 nm wavelength: one foot distance for 15, 30 or 45 minutes. Each of the virus aliquot exposed to either of the temperature, pH or ultraviolet light (UV for either of the interaction time was inoculated to 8 wells of the 96-well cell culture plate containing complete monolayer of BHK cell line. One row of 8 wells served as virus control and other row of 8 wells served as control for monolayer of the BHK-21 cell line. The plates were incubated at 37°C for 48 hours. It was observed that temperature of 57 and 77C inactivated the virus within 15 minutes. The virus when admixed in the MEM-199 maintenance medium having pH 3, 5, 9 or 11, of the medium inactivated the virus while pH 7 did not show any detrimental effect on its survival. The ultraviolet light for 15, 30 or 45 minutes showed undetectable effect on survival of the virus as either of the virus aliquot exposed to the UV light for either of the interaction time showed cytopathogenic effects (CPE. It was concluded that the temperature of 57°C or higher for 15 minutes, acidic pH (below 5 or basic pH (more than 9 may inactivate the FMD virus.

  14. The exogenous factors affecting the cost efficiency of power generation

    International Nuclear Information System (INIS)

    This paper employs a stochastic frontier analysis (SFA) to examine cost efficiency and scale economies in Taiwan Power Company (TPC) by using the panel data covering the period of 1995-2006. In most previous studies, the efficiency estimated by the Panel Data without testing the endogeneity may bring about a biased estimator resulting from the correlation between input and individual effect. A Hausman test is conducted in this paper to examine the endogeneity of input variables and thus an appropriate model is selected based on the test result. This study finds that the power generation executes an increasing return to scale across all the power plants based on the pooled data. We also use installed capacity, service years of the power plant, and type of fuel as explanatory variable for accounting for the estimated cost efficiency of each plant by a logistic regression model to examine the factor affecting the individual efficiency estimates. The results demonstrate that the variable of installed capacity keeps a positive relationship with cost efficiency while the factor of working years has a negative relationship.

  15. Improved method for rapid and efficient determination of genome replication and protein expression of clinical hepatitis B virus isolates.

    Science.gov (United States)

    Qin, Yanli; Zhang, Jiming; Garcia, Tamako; Ito, Kiyoaki; Gutelius, Danielle; Li, Jisu; Wands, Jack; Tong, Shuping

    2011-04-01

    Different hepatitis B virus (HBV) genotypes and variants are associated with different clinical outcomes and/or response to antiviral therapy, yet the comparison of the in vitro replication capacity of a large number of clinical isolates remains technically challenging and time-consuming. Although the full-length HBV genome can be amplified from high-titer blood samples by PCR using High Fidelity(plus) DNA polymerase and primers targeting the conserved precore region, the HBV clones thus generated are replication deficient due to the inability to generate the terminally redundant pregenomic RNA essential for genome replication. The transfection experiment is further complicated by PCR errors and the presence of viral quasispecies. A previous study found that the precise removal of non-HBV sequence by SapI digestion led to HBV replication in transfected cells, possibly due to low-level genome circularization by a cellular enzyme. We released HBV genome from the cloning vector using BspQI, an inexpensive isoschizomer of SapI, and increased the efficiency of genome replication by an extra step of in vitro DNA ligation. The uncut plasmid DNA can be used for transfection if the sole purpose is to study envelope protein expression. We found significant PCR errors associated with the High Fidelity(plus) DNA polymerase, which could be greatly diminished using Phusion DNA polymerase or masked by the use of a clone pool. The reduced PCR error and modified enzymatic steps prior to transfection should facilitate a more widespread functional characterization of clinical HBV isolates, while the clone pool approach is useful for samples with significant sequence heterogeneity. PMID:21289153

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

    OpenAIRE

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

    2016-01-01

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

  17. High efficient generation of replication-defective adenoviruses containing thymidine kinase by homogeneous recombination in bacteria

    Institute of Scientific and Technical Information of China (English)

    CONG Tie-chuan; LU Zhe-ming; LI Yong; ZHENG Li; QIN Yong

    2007-01-01

    Background Suicide gene therapy is a widely used molecular treatment for head and neck cancer. In this study, we try to use the method of homogenous recombination in bacteria to clone thymidine kinase gene (tk)-a kind of suicide gene to adenovirus backbone vectors for the construction of replication-defective adenoviruses.Methods pAdTrack-CMV/tk was constructed through subclone of a restriction endonuclease fragment including thymidine kinase gene from plasmid pCMV-tk to another plasmid pAdTrack-CMV, and then co-transfected with supercoiled pAdEasy-1, which was an adenoviral backbone vector except for deletions of E1 and E3, to competent E.coli BJ5183 for homogenous recombination using electroporation procedure. With the same method, pAdTrack-CMV was also co-transformed with pAdEasy-1 for homogenous recombination in BJ5183. Identified with restriction endonuclease Pacl and polymerase chain reaction (PCR), plasmids pAd-GFP/tk and pAd-GFP were successfully constructed. Each of them was digested with Pacl and sequently transfected into human embryo kidney 293 cells (HEK293) using Lipofectamine 2000.Results Comet-like adenovirus-producing foci of Ad-GFP/tk and Ad-GFP were observed after 5 to 7 days of cell culture.After twelve days of packaging, the replication-defective adenoviruses were collected. Identified with PCR, thymidine kinase gene was successfully constructed into Ad-GFP/tk.Conclusion The replication-defective adenoviruses containing thymidine kinase can be constructed more easily by homogenous recombination in bacteria than conventional techniques.

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

    Science.gov (United States)

    Nair, Vidya P; Anang, Saumya; Subramani, Chandru; Madhvi, Abhilasha; Bakshi, Karishma; Srivastava, Akriti; Shalimar; Nayak, Baibaswata; Ct, Ranjith Kumar; Surjit, Milan

    2016-04-01

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

  19. Evidence that a polyhexameric genome length is preferred, but not strictly required, for efficient mumps virus replication.

    Science.gov (United States)

    Sauder, Christian J; Simonyan, Vahan; Ngo, Laurie; Karagiannis, Konstantinos; Cong, Yu; Zhang, Cheryl; Wang, Rong; Wu, Wells W; Malik, Tahir; Rubin, Steven A

    2016-06-01

    Mumps virus (MuV) is postulated to adhere to the "rule of six" for efficient replication. To examine the requirement for MuV, minigenomes of nonpolyhexameric length (6n-1 and 6n+1) were analyzed. Expression of the reporter gene CAT was significantly reduced with minigenomes of nonpolyhexameric length compared to the wild type 6n genome, and reduction was more pronounced for the 6n-1 than for the 6n+1 minigenome. That 6n-1 genomes are impacted by nonconformance with the rule of six to a greater degree as compared to 6n+1 genomes was also suggested with MuV derived from cDNA coding for 6n+1 or 6n-1 genomes. While viruses recovered from 6n+1 cDNAs maintained a nonpolyhexameric genome length over multiple replication cycles, viruses rescued from the 6n-1 cDNAs acquired length correcting mutations rapidly following rescue. Our data indicate that polyhexameric genomes are the preferred template for the MuV RNA polymerase, but that this requirement is not absolute. PMID:27058764

  20. Efficient Inhibition of HIV Replication in the Gastrointestinal and Female Reproductive Tracts of Humanized BLT Mice by EFdA.

    Directory of Open Access Journals (Sweden)

    Uma Shanmugasundaram

    Full Text Available The nucleoside reverse transcriptase inhibitor (NRTI 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA in preclinical development exhibits improved safety and antiviral activity profiles with minimal drug resistance compared to approved NRTIs. However, the systemic antiviral efficacy of EFdA has not been fully evaluated. In this study, we utilized bone marrow/liver/thymus (BLT humanized mice to investigate the systemic effect of EFdA treatment on HIV replication and CD4+ T cell depletion in the peripheral blood (PB and tissues. In particular, we performed a comprehensive analysis of the female reproductive tract (FRT and gastrointestinal (GI tract, major sites of transmission, viral replication, and CD4+ T cell depletion and where some current antiretroviral drugs have a sub-optimal effect.EFdA treatment resulted in reduction of HIV-RNA in PB to undetectable levels in the majority of treated mice by 3 weeks post-treatment. HIV-RNA levels in cervicovaginal lavage of EFdA-treated BLT mice also declined to undetectable levels demonstrating strong penetration of EFdA into the FRT. Our results also demonstrate a strong systemic suppression of HIV replication in all tissues analyzed. In particular, we observed more than a 2-log difference in HIV-RNA levels in the GI tract and FRT of EFdA-treated BLT mice compared to untreated HIV-infected control mice. In addition, HIV-RNA was also significantly lower in the lymph nodes, liver, lung, spleen of EFdA-treated BLT mice compared to untreated HIV-infected control mice. Furthermore, EFdA treatment prevented the depletion of CD4+ T cells in the PB, mucosal tissues and lymphoid tissues.Our findings indicate that EFdA is highly effective in controlling viral replication and preserving CD4+ T cells in particular with high efficiency in the GI and FRT tract. Thus, EFdA represents a strong potential candidate for further development as a part of antiretroviral therapy regimens.

  1. Efficient replication of genotype 3a and 4a hepatitis C virus replicons in human hepatoma cells

    DEFF Research Database (Denmark)

    Saeed, Mohsan; Scheel, Troels K H; Gottwein, Judith M;

    2012-01-01

    culture adaptive mutations originally reported for genotype 1b replicons. RNA replication was confirmed by quantitative reverse transcription-PCR and detection of viral protein. Sequencing of multiple independent replicon clones revealed the presence of additional nonsynonymous mutations. Interestingly......, all potentially adaptive mutations mapped to the NS3 protein. These mutations, when introduced back into original constructs, substantially increased colony formation efficiency. To make these replicons useful for high-throughput screening and evaluation of antiviral compounds, they were modified to...... express a chimeric fusion protein of firefly luciferase and neomycin phosphotransferase to yield stable replicon-expressing cells. Using these constructs, the inhibitory effects of beta interferon (IFN-β), an NS3 protease inhibitor, and an NS5B nucleoside polymerase inhibitor were readily detected by...

  2. Rad52 SUMOylation affects the efficiency of the DNA repair

    DEFF Research Database (Denmark)

    Altmannova, Veronika; Eckert-Boulet, Nadine; Arneric, Milica;

    2010-01-01

    Homologous recombination (HR) plays a vital role in DNA metabolic processes including meiosis, DNA repair, DNA replication and rDNA homeostasis. HR defects can lead to pathological outcomes, including genetic diseases and cancer. Recent studies suggest that the post-translational modification by...... recombination and DNA repair....... recombination mediator protein Rad52. Interestingly, Rad52 SUMOylation is enhanced by single-stranded DNA, and we show that SUMOylation of Rad52 also inhibits its DNA binding and annealing activities. The biochemical effects of SUMO modification in vitro are accompanied by a shorter duration of spontaneous Rad...

  3. Investigating factors affecting the efficiency of gas turbine power cycle

    OpenAIRE

    Ghaderi, R.; M. Damircheli

    2014-01-01

    Today, the use of gas turbines in power generation cycles has been growing. Small size, easy installation, high power-to-mass ratio and the ability to load and unload the cycle quickly are the advantages of such systems. Low efficiency is considered as one of the major disadvantages of such power plants. Thus providing a way to increase cycle efficiency can be very effective in making the cycle more efficient and thus saving fuel consumed in such systems. In this paper the thermal efficiency ...

  4. Do capital requirements affect bank efficiency? Evidence from China

    OpenAIRE

    Pessarossi, Pierre; Weill, Laurent

    2013-01-01

    This paper contributes to the debate on the effect of capital requirements on bank efficiency. We study the relation between capital ratio and bank efficiency for Chinese banks over the period 2004-2009, taking advantage of the profound regulatory changes in capital requirements that occurred during this period to measure the exogenous impact of an in-crease in the capital ratio on banks’ cost efficiency. We find that such an increase has a positive effect on cost efficiency, the size of whic...

  5. Efficient Gene Transfer Mediated by HIV-1-based Defective Lentivector and Inhibition of HIV-1 Replication

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Lentiviral vectors have drawn considerable attention recently and show great promise to become important delivery vehicles for future gene transfer manipulation. In the present study we have optimized a protocol for preparation of human immunodeficiency virus type-1 (HIV-1)-based defective lentiviral vectors (DLV) and characterized these vectors in terms of their transduction of different cells. Transient co-transfection of 293T packaging cells with DNA plasmids encoding lentiviral vector constituents resulted in production of high-titer DLV (0.5-1.2 × 107IU/mL), which can be further concentrated over 100-fold through a single step ultracentrifugation. These vectors were capable of transducing a variety of cells from both primate and non-primate sources and high transduction efficiency was achieved using concentrated vectors. Assessment of potential generation of RCV revealed no detection of infection by infectious particles in DLV-transduced CEM, SupT-1 and MT-2 cells. Long-term culture of transduced cells showed a stable expression of transgenes without apparent alteration in cellular morphology and growth kinetics. Vector mobilization to untransduced cells mediated by wild-type HIV-1 infection was confirmed in this test. Challenge of transduced human T-lymphocytes with wild-type HIV-1 showed these cells are totally resistant to the viral infection. Considering the effective gene transfer and stable gene expression, safety and anti-HIV activity, these DLV vectors warrant further exploration for their potential use as a gene transfer vehicle in the development of gene therapy protocols.

  6. Cisplatin-Induced DNA Damage Activates Replication Checkpoint Signaling Components that Differentially Affect Tumor Cell SurvivalS⃞

    OpenAIRE

    Wagner, Jill M.; Karnitz, Larry M.

    2009-01-01

    Cisplatin and other platinating agents are some of the most widely used chemotherapy agents. These drugs exert their antiproliferative effects by creating intrastrand and interstrand DNA cross-links, which block DNA replication. The cross-links mobilize signaling and repair pathways, including the Rad9-Hus1-Rad1-ATR-Chk1 pathway, a pathway that helps tumor cells survive the DNA damage inflicted by many chemotherapy agents. Here we show that Rad9 and ATR play critical r...

  7. Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo.

    Directory of Open Access Journals (Sweden)

    Lisa Marcinowski

    2012-02-01

    Full Text Available Cytomegaloviruses express large amounts of viral miRNAs during lytic infection, yet, they only modestly alter the cellular miRNA profile. The most prominent alteration upon lytic murine cytomegalovirus (MCMV infection is the rapid degradation of the cellular miR-27a and miR-27b. Here, we report that this regulation is mediated by the ∼1.7 kb spliced and highly abundant MCMV m169 transcript. Specificity to miR-27a/b is mediated by a single, apparently optimized, miRNA binding site located in its 3'-UTR. This site is easily and efficiently retargeted to other cellular and viral miRNAs by target site replacement. Expression of the 3'-UTR of m169 by an adenoviral vector was sufficient to mediate its function, indicating that no other viral factors are essential in this process. Degradation of miR-27a/b was found to be accompanied by 3'-tailing and -trimming. Despite its dramatic effect on miRNA stability, we found this interaction to be mutual, indicating potential regulation of m169 by miR-27a/b. Most interestingly, three mutant viruses no longer able to target miR-27a/b, either due to miRNA target site disruption or target site replacement, showed significant attenuation in multiple organs as early as 4 days post infection, indicating that degradation of miR-27a/b is important for efficient MCMV replication in vivo.

  8. Efficient generation of long-distance conditional alleles using recombineering and a dual selection strategy in replicate plates

    Directory of Open Access Journals (Sweden)

    Liang Hong-Erh

    2009-07-01

    Full Text Available Abstract Background Conditional knockout mice are a useful tool to study the function of gene products in a tissue-specific or inducible manner. Classical approaches to generate targeting vectors for conditional alleles are often limited by the availability of suitable restriction sites. Furthermore, plasmid-based targeting vectors can only cover a few kB of DNA which precludes the generation of targeting vectors where the two loxP sites are placed far apart. These limitations have been overcome in the recent past by using homologous recombination of bacterial artificial chromosomes (BACs in Escherichia coli to produce large targeting vector containing two different loxP-flanked selection cassettes so that a single targeting event is sufficient to introduce loxP-sites a great distances into the mouse genome. However, the final targeted allele should be free of selection cassettes and screening for correct removal of selection cassettes can be a laborious task. Therefore, we developed a new strategy to rapidly identify ES cells containing the desired allele. Results Using BAC recombineering we generated a single targeting vector which contained two different selection cassettes that were flanked by loxP-loxP sites or by FRT-FRT/loxP sites so that they could be deleted sequentially by Cre- and FLPe-recombinases, respectively. Transfected ES cells were first selected in the presence of both antibiotics in vitro before correctly targeted clones were identified by Southern blot. After transfection of a Cre recombinase expression plasmid ES cell clones were selected on replicate plates to identify those clones which maintained the FRT-FRT/loxP flanked cassette and lost the loxP-loxP flanked cassette. Using this strategy facilitated the identification of ES cell clones containing the desired allele before blastocyst injection. Conclusion The strategy of ES cell cultures in replicate plates proved to be very efficient in identifying ES cells that had

  9. FACTORS AFFECTING THE VEGETABLE FARMING EFFICIENCY IN BULGARIA

    Directory of Open Access Journals (Sweden)

    Teodora STOEVA

    2012-01-01

    Full Text Available The efficiency is the major economic category, which measures the final result and the expenses related to the production and provides value expression. The article aims to analyze the prospects and conditions for the development of field vegetable production in Bulgaria. Field vegetable farming is a traditional and fast developing sector of the Bulgarian agriculture. Its condition and development is determined by the various natural and geographic conditions in the country and the experience in cultivating and farming vegetable crops, which are traditional for the Bulgarian population. The vegetable farming is organized in individual private agricultural farms and agricultural farming cooperatives and is performed in small areas. The crisis in the vegetable farming raised a lot of questions that need to be answered. It is necessary to overcome the decrease in vegetable production. This can happen by establishing efficiently operating organizational companies. The most important reasons for the reported decrease are the result of the improperly conducted reforms in the agriculture industry as a result of which the economic condition of the sector is declining. A serious flaw is that the farmers are selecting certain crop production without conducting any preliminary marketing and without any signed contracts for produce realization.

  10. Efficiency, specificity and DNA polymerase-dependence of translesion replication across the oxidative DNA lesion 8-oxoguanine in human cells

    International Nuclear Information System (INIS)

    The oxidation product of guanine, 8-oxoguanine, is a major lesion formed in DNA by intracellular metabolism, ionizing radiation, and tobacco smoke. Using a recently developed method for the quantitative analysis of translesion replication, we have studied the bypass of 8-oxoguanine in vivo by transfecting human cells with a gapped plasmid carrying a site-specific 8-oxoguanine in the ssDNA region. The efficiency of bypass in the human large-cell lung carcinoma cell line H1299 was 80%, and it was similar when assayed in the presence of aphidicolin, an inhibitor of DNA polymerases α, δ and ε. A similar extent of bypass was observed also in XP-V cells, defective in pol η, both in the absence and presence of aphidicolin. DNA sequence analysis indicated that the major nucleotide inserted opposite the 8-oxoguanine was the correct nucleotide C, both in H1299 cells (81%) and in XP-V cells (77%). The major mutagenic event was the insertion of an A, both in H1299 and XP-V cells, and it occurred at a frequency of 16-17%, significantly higher than previously reported. Interestingly, the misinsertion frequency of A opposite 8-oxoguanine was decreased in XP-V cells in the presence of aphidicolin, and misinsertion of G was observed. This modulation of the mutagenic specificity at 8-oxoguanine is consistent with the notion that while not essential for the bypass reaction, pol η and pol δ, when present, are involved in bypass of 8-oxoguanine in vivo

  11. Mutations that abrogate transactivational activity of the feline leukemia virus long terminal repeat do not affect virus replication

    International Nuclear Information System (INIS)

    The U3 region of the LTR of oncogenic Moloney murine leukemia virus (Mo-MuLV) and feline leukemia viruses (FeLV) have been previously reported to activate expression of specific cellular genes in trans, such as MHC class I, collagenase IV, and MCP-1, in an integration-independent manner. It has been suggested that transactivation of these specific cellular genes by leukemia virus U3-LTR may contribute to the multistage process of leukemogenesis. The U3-LTR region, necessary for gene transactivational activity, also contains multiple transcription factor-binding sites that are essential for normal virus replication. To dissect the promoter activity and the gene transactivational activity of the U3-LTR, we conducted mutational analysis of the U3-LTR region of FeLV-A molecular clone 61E. We identified minimal nucleotide substitution mutants on the U3 LTR that did not disturb transcription factor-binding sites but abrogated its ability to transactivate the collagenase gene promoter. To determine if these mutations actually have altered any uncharacterized important transcription factor-binding site, we introduced these U3-LTR mutations into the full-length infectious molecular clone 61E. We demonstrate that the mutant virus was replication competent but could not transactivate cellular gene expression. These results thus suggest that the gene transactivational activity is a distinct property of the LTR and possibly not related to its promoter activity. The cellular gene transactivational activity-deficient mutant FeLV generated in this study may also serve as a valuable reagent for testing the biological significance of LTR-mediated cellular gene activation in the tumorigenesis caused by leukemia viruses

  12. Dual effect of nitric oxide on SARS-CoV replication: Viral RNA production and palmitoylation of the S protein are affected

    International Nuclear Information System (INIS)

    Nitric oxide is an important molecule playing a key role in a broad range of biological process such as neurotransmission, vasodilatation and immune responses. While the anti-microbiological properties of nitric oxide-derived reactive nitrogen intermediates (RNI) such as peroxynitrite, are known, the mechanism of these effects are as yet poorly studied. Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) belongs to the family Coronaviridae, was first identified during 2002-2003. Mortality in SARS patients ranges from between 6 to 55%. We have previously shown that nitric oxide inhibits the replication cycle of SARS-CoV in vitro by an unknown mechanism. In this study, we have further investigated the mechanism of the inhibition process of nitric oxide against SARS-CoV. We found that peroxynitrite, an intermediate product of nitric oxide in solution formed by the reaction of NO with superoxide, has no effect on the replication cycle of SARS-CoV, suggesting that the inhibition is either directly effected by NO or a derivative other than peroxynitrite. Most interestingly, we found that NO inhibits the replication of SARS-CoV by two distinct mechanisms. Firstly, NO or its derivatives cause a reduction in the palmitoylation of nascently expressed spike (S) protein which affects the fusion between the S protein and its cognate receptor, angiotensin converting enzyme 2. Secondly, NO or its derivatives cause a reduction in viral RNA production in the early steps of viral replication, and this could possibly be due to an effect on one or both of the cysteine proteases encoded in Orf1a of SARS-CoV.

  13. Nuclear localization of Vpr is crucial for the efficient replication of HIV-1 in primary CD4+ T cells

    International Nuclear Information System (INIS)

    The human immunodeficiency virus type 1 (HIV-1) accessory protein Vpr appears to make a substantial contribution to the replication of HIV-1 in established T cell lines when HIV-1 is present at very low multiplicities of infection. However, the role of Vpr in viral replication in primary CD4+ T cells remains to be clarified. In this study, we generated a panel of viruses that encoded mutant forms of Vpr that lacked either the ability to accumulate in the nucleus and induce G2 arrest or the ability to induce apoptosis, which has been shown to occur independently of G2 arrest of the cell cycle. We demonstrate here that the nuclear localization of Vpr and consequent G2 arrest but not the induction of apoptosis by Vpr are important for viral replication in primary CD4+ T cells at both high and low multiplicities of infection. Viruses that encoded mutant forms of Vpr that failed to be imported into the nucleus in the presence of cytoplasmic extracts from primary CD4+ T cells in an in vitro nuclear import assay replicated at drastically reduced rates. Thus, Vpr might be a key regulator of the viral nuclear import process during infection in primary CD4+ T cells. By contrast, a mutant form of Vpr that exhibited diffuse cytosolic staining exclusively in an immunofluorescence assay of HeLa cells and was not imported into nucleus by the cytosol from HeLa cells was effectively imported into the nucleus by cytosol from primary CD4+ T cells. This Vpr mutant virus replicated well in primary CD4+ T cells, indicating that cellular factors in primary CD4+ T cells are indispensable for the accumulation of Vpr in the nucleus and, thus, for viral replication. Our results suggest that the nuclear import of Vpr might be a good target in efforts to block the early stages of replication of HIV-1

  14. An Exploratory Study of Critical Factors Affecting the Efficiency of Sorting Techniques (Shell, Heap and Treap)

    CERN Document Server

    Folorunso, Olusegun; Salako, Oluwatimilehin

    2012-01-01

    The efficiency of sorting techniques has a significant impact on the overall efficiency of a program. The efficiency of Shell, Heap and Treap sorting techniques in terms of both running time and memory usage was studied, experiments conducted and results subjected to factor analysis by SPSS. The study revealed the main factor affecting these sorting techniques was time taken to sort.

  15. A conserved amphipathic helix in the N-terminal regulatory region of the papillomavirus E1 helicase is required for efficient viral DNA replication.

    Science.gov (United States)

    Morin, Geneviève; Fradet-Turcotte, Amélie; Di Lello, Paola; Bergeron-Labrecque, Fanny; Omichinski, James G; Archambault, Jacques

    2011-06-01

    The papillomavirus E1 helicase, with the help of E2, assembles at the viral origin into a double hexamer that orchestrates replication of the viral genome. The N-terminal region (NTR) of E1 is essential for DNA replication in vivo but dispensable in vitro, suggesting that it has a regulatory function. By deletion analysis, we identified a conserved region of the E1 NTR needed for efficient replication of viral DNA. This region is predicted to form an amphipathic α-helix (AH) and shows sequence similarity to portions of the p53 and herpes simplex virus (HSV) VP16 transactivation domains known as transactivation domain 2 (TAD2) and VP16C, which fold into α-helices upon binding their target proteins, including the Tfb1/p62 (Saccharomyces cerevisiae/human) subunit of general transcription factor TFIIH. By nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry (ITC), we found that a peptide spanning the E1 AH binds Tfb1 on the same surface as TAD2/VP16C and with a comparable affinity, suggesting that it does bind as an α-helix. Furthermore, the E1 NTRs from several human papillomavirus (HPV) types could activate transcription in yeast, and to a lesser extent in mammalian cells, when fused to a heterologous DNA-binding domain. Mutation of the three conserved hydrophobic residues in the E1 AH, analogous to those in TAD2/VP16C that directly contact their target proteins, decreased transactivation activity and, importantly, also reduced by 50% the ability of E1 to support transient replication of DNA in C33A cells, at a step following assembly of the E1-E2-ori preinitiation complex. These results demonstrate the existence of a conserved TAD2/VP16C-like AH in E1 that is required for efficient replication of viral DNA. PMID:21450828

  16. Rec-8 dimorphism affects longevity, stress resistance and X-chromosome nondisjunction in C. elegans, and replicative lifespan in yeast

    Directory of Open Access Journals (Sweden)

    Srinivas eAyyadevara

    2014-08-01

    Full Text Available A quantitative trait locus (QTL in the nematode C. elegans, lsq4, was recently implicated by mapping longevity genes. QTLs for lifespan and 3 stress-resistance traits coincided within a span of <300 kbp, later narrowed to <200 kbp. A single gene in this interval is now shown to modulate all lsq4-associated traits. Full-genome analysis of transcript levels indicates that lsq4 contains a dimorphic gene governing expression of sperm-specific genes, suggesting effects on spermatogenesis. Quantitation of allele-specific transcripts encoded within the lsq4 interval revealed significant, 2- to 15-fold expression differences for 10 of 33 genes. Fourteen genes, implicated by both position and expression, were tested for RNA-interference effects on QTL-linked traits. In a strain carrying the shorter-lived allele, knockdown of rec-8 (encoding a meiotic cohesin reduced its transcripts 4-fold, to a level similar to the longer-lived strain, and extended lifespan 25–26% whether begun before fertilization or at maturity. The short-lived lsq4 allele also conferred sensitivity to oxidative and thermal stresses, and lower male frequency, traits reversed uniquely by rec-8 knockdown. A strain bearing the longer-lived lsq4 allele, differing from the short-lived strain at <0.3% of its genome, derived no lifespan or stress-survival benefit from rec-8 knockdown. We consider two possible explanations: high rec-8 expression may include increased leaky expression in mitotic cells, leading to deleterious destabilization of somatic genomes; or REC-8 may act entirely in germ-line meiotic cells to reduce aberrations such as nondisjunction, thereby blunting a stress-resistance response mediated by innate immunity. Replicative lifespan was extended 20% in haploid S. cerevisiae (BY4741 by deletion of REC8, orthologous to nematode rec-8, implying that REC8 disruption of mitotic-cell survival is widespread, reflecting antagonistic pleiotropy and/or balancing selection.

  17. Expression of porcine fusion protein IRF7/3(5D) efficiently controls foot-and-mouth disease virus replication

    Science.gov (United States)

    Several studies have demonstrated that administration of type I, II, or III interferons (IFN) delivered using a replication defective human adenovirus 5 (Ad5) vector is effective to control Foot-and-Mouth Disease (FMD) in cattle and swine during experimental infections. However, high doses are requi...

  18. The 1:1 N-NS protein complex of vesicular stomatitis virus is essential for efficient genome replication.

    Science.gov (United States)

    La Ferla, F M; Peluso, R W

    1989-01-01

    We studied the effect pH had on the N-NS protein complex to determine its role in vesicular stomatitis virus (VSV) genome replication, as we had previously shown that VSV genome replication in vitro requires the interaction of the viral N and NS proteins into a 1:1 complex. A previous report showed that the growth of VSV in L cells was sensitive to the pH of the environment (M. Fiszman, J. B. Leaute, C. Chany, and M. Girard, J. Virol. 13:801-808, 1974). We hypothesized that low pH might disrupt the N-NS protein complex, and so we investigated the molecular events leading to inhibition of viral RNA replication in vitro from extracts that were prepared from VSV-infected cells incubated at pH 6.6. We found that viral genome RNA synthesis in vitro was reduced when infected cells were maintained at pH 6.6. Through immunoprecipitation analysis of the viral soluble protein pool, we found that a complex that usually exists between the N and NS proteins at pH 7.4 was altered in extracts from infected cells maintained at pH 6.6, and this was responsible for the observed effects on viral replication. The effect of low pH on the N-NS protein complex could not be abolished by increasing the concentration of the altered complex, indicating that the effects is more than simply a decrease in the level of the protein complex in the cell. Our data provide additional evidence that the 1:1 N-NS protein complex, and not the N protein alone, serves as the substrate for viral RNA replication in vivo. Images PMID:2548001

  19. Selection affects genes involved in replication during long-term evolution in experimental populations of the bacteriophage φX174.

    Directory of Open Access Journals (Sweden)

    Celeste J Brown

    Full Text Available Observing organisms that evolve in response to strong selection over very short time scales allows the determination of the molecular mechanisms underlying adaptation. Although dissecting these molecular mechanisms is expensive and time-consuming, general patterns can be detected from repeated experiments, illuminating the biological processes involved in evolutionary adaptation. The bacteriophage φX174 was grown for 50 days in replicate chemostats under two culture conditions: Escherichia coli C as host growing at 37°C and Salmonella typhimurium as host growing at 43.5°C. After 50 days, greater than 20 substitutions per chemostat had risen to detectable levels. Of the 97 substitutions, four occurred in all four chemostats, five arose in both culture conditions, eight arose in only the high temperature S. typhimurium chemostats, and seven arose only in the E. coli chemostats. The remaining substitutions were detected only in a single chemostat, however, almost half of these have been seen in other similar experiments. Our findings support previous studies that host recognition and capsid stability are two biological processes that are modified during adaptation to novel hosts and high temperature. Based upon the substitutions shared across both environments, it is apparent that genome replication and packaging are also affected during adaptation to the chemostat environment, rather than to temperature or host per se. This environment is characterized by a large number of phage and very few hosts, leading to competition among phage within the host. We conclude from these results that adaptation to a high density environment selects for changes in genome replication at both protein and DNA sequence levels.

  20. Efficient data replication for the delivery of high-quality video content over P2P VoD advertising networks

    Science.gov (United States)

    Ho, Chien-Peng; Yu, Jen-Yu; Lee, Suh-Yin

    2011-12-01

    Recent advances in modern television systems have had profound consequences for the scalability, stability, and quality of transmitted digital data signals. This is of particular significance for peer-to-peer (P2P) video-on-demand (VoD) related platforms, faced with an immediate and growing demand for reliable service delivery. In response to demands for high-quality video, the key objectives in the construction of the proposed framework were user satisfaction with perceived video quality and the effective utilization of available resources on P2P VoD networks. This study developed a peer-based promoter to support online advertising in P2P VoD networks based on an estimation of video distortion prior to the replication of data stream chunks. The proposed technology enables the recovery of lost video using replicated stream chunks in real time. Load balance is achieved by adjusting the replication level of each candidate group according to the degree-of-distortion, thereby enabling a significant reduction in server load and increased scalability in the P2P VoD system. This approach also promotes the use of advertising as an efficient tool for commercial promotion. Results indicate that the proposed system efficiently satisfies the given fault tolerances.

  1. Improved Method for Rapid and Efficient Determination of Genome Replication and Protein Expression of Clinical Hepatitis B Virus Isolates▿

    OpenAIRE

    Qin, Yanli; Zhang, Jiming; Garcia, Tamako; Ito, Kiyoaki; Gutelius, Danielle; Li, Jisu; Wands, Jack; Tong, Shuping

    2011-01-01

    Different hepatitis B virus (HBV) genotypes and variants are associated with different clinical outcomes and/or response to antiviral therapy, yet the comparison of the in vitro replication capacity of a large number of clinical isolates remains technically challenging and time-consuming. Although the full-length HBV genome can be amplified from high-titer blood samples by PCR using High Fidelityplus DNA polymerase and primers targeting the conserved precore region, the HBV clones thus genera...

  2. Mutations Designed by Ensemble Defect to Misfold Conserved RNA Structures of Influenza A Segments 7 and 8 Affect Splicing and Attenuate Viral Replication in Cell Culture

    Science.gov (United States)

    Jiang, Tian; Nogales, Aitor; Baker, Steven F; Martinez-Sobrido, Luis; Turner, Douglas H

    2016-01-01

    Influenza A virus is a significant public health threat, but little is understood about the viral RNA structure and function. Current vaccines and therapeutic options to control influenza A virus infections are mostly protein-centric and of limited effectiveness. Here, we report using an ensemble defect approach to design mutations to misfold regions of conserved mRNA structures in influenza A virus segments 7 and 8. Influenza A mutant viruses inhibit pre-mRNA splicing and attenuate viral replication in cell culture, thus providing evidence for functions of the targeted regions. Targeting these influenza A viral RNA regions provides new possibilities for designing vaccines and therapeutics against this important human respiratory pathogen. The results also demonstrate that the ensemble defect approach is an efficient way to test for function of RNA sequences. PMID:27272307

  3. Factors Affecting the Technical Efficiency Level of Inshore Fisheries in Kuala Terengganu, Malaysia

    OpenAIRE

    Ismail Latiff; Mohd. Ariff Hussein; Nalini Arumugam; Nurul Aisyah

    2012-01-01

    The objective of this study is to determine factors affecting the technical efficiency of the inshore fisheries in Kuala Terengganu. Data for the study was collected from a survey conducted between June and August 2007 where 100 fishermen in 14 villages were chosen by stratified sampling. Data envelopment analysis (DEA) and Tobit analysis were employed to determine the technical efficiency level and factors influencing technical efficiency among the fishermen. Results of the study show that, ...

  4. Intracytoplasmic stable expression of IgG1 antibody targeting NS3 helicase inhibits replication of highly efficient hepatitis C Virus 2a clone

    Directory of Open Access Journals (Sweden)

    Clementi Massimo

    2010-06-01

    Full Text Available Abstract Background Hepatitis C virus (HCV infection is a major public health problem with more than 170 million cases of chronic infections worldwide. There is no protective vaccine currently available for HCV, therefore the development of novel strategy to prevent chronic infection is important. We reported earlier that a recombinant human antibody clone blocks viral NS3 helicase activity and inhibits replication of HCV 1b virus. This study was performed further to explore the mechanism of action of this recombinant antibody and to determine whether or not this antibody inhibits replication and infectivity of a highly efficient JFH1 HCV 2a virus clone. Results The antiviral effect of intracellular expressed antibody against the HCV 2a virus strain was examined using a full-length green fluorescence protein (GFP labeled infectious cell culture system. For this purpose, a Huh-7.5 cell line stably expressing the NS3 helicase gene specific IgG1 antibody was prepared. Replication of full-length HCV-GFP chimera RNA and negative-strand RNA was strongly inhibited in Huh-7.5 cells stably expressing NS3 antibody but not in the cells expressing an unrelated control antibody. Huh-7.5 cells stably expressing NS3 helicase antibody effectively suppressed infectious virus production after natural infection and the level of HCV in the cell free supernatant remained undetectable after first passage. In contrast, Huh-7.5 cells stably expressing an control antibody against influenza virus had no effect on virus production and high-levels of infectious HCV were detected in culture supernatants over four rounds of infectivity assay. A recombinant adenovirus based expression system was used to demonstrate that Huh-7.5 replicon cell line expressing the intracellular antibody strongly inhibited the replication of HCV-GFP RNA. Conclusion Recombinant human anti-HCV NS3 antibody clone inhibits replication of HCV 2a virus and infectious virus production. Intracellular

  5. Studies of Some Parameters Affecting The Efficiency and Accuracy of The Neutron Activation Analysis Technique

    International Nuclear Information System (INIS)

    The present studies deal with the optimum physical conditions which seriously affect the neutron activation analysis technique efficiency. An experimental work for the efficiency calibration of hyper pure germanium detectors especially for environmental studies is presented. This work showed that the tested parameters, under consideration, distance, mass and measured time, reveal a significant effect on the obtained data. These results, intern, affect the accuracy of the measurements. Further work on the test of other parameters is planned in our laboratory using special treatments and applying special computer programs

  6. Modulation of HIV-1 Gag NC/p1 cleavage efficiency affects protease inhibitor resistance and viral replicative capacity

    Czech Academy of Sciences Publication Activity Database

    Maarseveen van, N. M.; Andersson, Dan; Lepšík, Martin; Fun, A.; Schipper, P. J.; Jong de, D.; Boucher, Ch. A. B.; Nijhuis, M.

    2012-01-01

    Roč. 9, č. 29 (2012), s. 1-7. ISSN 1742-4690 EU Projects: European Commission(XE) 37693 - HIV PI RESISTANCE Grant ostatní: Dutch AIDS Fund(XE) 2006028; (NWO) VIDI(XE) 91796349 Institutional research plan: CEZ:AV0Z40550506 Keywords : HIV -1 * protease * Gag * resistance * cleavage Subject RIV: CE - Biochemistry Impact factor: 5.657, year: 2012

  7. Is the pollination efficiency of long-lived orchid flowers affected by age?

    OpenAIRE

    Rúbia Santos Fonseca; Flávia Aparecida dos Santos; Milene Faria Vieira

    2015-01-01

    The long-lived flowers of orchids increase the chances of pollination and thus the reproductive success of the species. However, a question arises: does the efficiency of pollination, expressed by fruit set, vary with the flower age? The objective of this study was to verify whether the flower age of Corymborkis flava(Sw.) Kuntze affects pollination efficiency. The following hypotheses were tested: 1) the fruit set of older flowers is lower than that of younger ones; 2) morphological observat...

  8. Study of Core Competency Elements and Factors Affecting Performance Efficiency of Government Teachers in Northeastern Thailand

    Science.gov (United States)

    Chansirisira, Pacharawit

    2012-01-01

    The research aimed to investigate the core competency elements and the factors affecting the performance efficiency of the civil service teachers in the northeastern region, Thailand. The research procedure consisted of two steps. In the first step, the data were collected using a questionnaire with the reliability (Cronbach's Alpha) of 0.90. The…

  9. 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

  10. Database replication

    OpenAIRE

    Popov, P. T.; Stankovic, V.

    2014-01-01

    A fault-tolerant node for synchronous heterogeneous database replication and a method for performing a synchronous heterogenous database replication at such a node are provided. A processor executes a computer program to generate a series of database transactions to be carried out at the fault-tolerant node. The fault-tolerant node comprises at least two relational database management systems, each of which are different relational database management system products, each implementing snapsh...

  11. CD40 ligand is pivotal to efficient control of virus replication in mice infected with lymphocytic choriomeningitis virus

    DEFF Research Database (Denmark)

    Thomsen, Allan Randrup; Nansen, A; Christensen, Jan Pravsgaard;

    1998-01-01

    internal organs approximately 6 mo after virus inoculation. Since the impairment of immune function seems to be more pronounced in CD40L-deficient mice than in mice lacking either CD4+ cells or B cells, these results indicate that CD40L is pivotal to sustain efficient antiviral immune surveillance...

  12. Growing Through Innovation Replicability

    DEFF Research Database (Denmark)

    Hsuan, Juliana; Lévesque, Moren

    2012-01-01

    We propose a formal model of firm growth through replication that considers the extent of the investment to adapt routines as replication unfolds and the portion of this investment that goes toward innovation in the routines. The use of these two investment constructs brings about four types of...... growth policies. We use a utility function that considers proxies for both growth and failure potential to uncover the role played in selecting these policies by the economic environment of the targeted market for expansion. Our analysis further reveals the importance of the innovation......-relative-to-imitation investment efficiency in adapting the routines to be replicated while selecting a growth policy. The refinement of a replication theory through our analysis of growth policies result in two testable hypotheses....

  13. Highly Efficient Modification of Bacterial Artificial Chromosomes (BACs) Using Novel Shuttle Vectors Containing the R6Kγ Origin of Replication

    OpenAIRE

    Gong, Shiaoching; Yang, Xiangdong William; Li, Chenjian; Heintz, Nathaniel

    2002-01-01

    Bacterial artificial chromosome (BAC) mediated transgenesis has proven to be a highly reliable way to obtain accurate transgene expression for in vivo studies of gene expression and function. A rate-limiting step in use of this technology to characterize large numbers of genes has been the process with which BACs can be modified by homologous recombination in Escherichia coli. We report here a highly efficient method for modifying BACs by using a novel set of shuttle vectors that contain the ...

  14. Hamster-Adapted Sin Nombre Virus Causes Disseminated Infection and Efficiently Replicates in Pulmonary Endothelial Cells without Signs of Disease

    OpenAIRE

    Safronetz, David; Prescott, Joseph; Haddock, Elaine; Scott, Dana P.; Feldmann, Heinz; Ebihara, Hideki

    2013-01-01

    To date, a laboratory animal model for the study of Sin Nombre virus (SNV) infection or associated disease has not been described. Unlike infection with Andes virus, which causes lethal hantavirus pulmonary syndrome (HPS)-like disease in hamsters, SNV infection is short-lived, with no viremia and little dissemination. Here we investigated the effect of passaging SNV in hamsters. We found that a host-adapted SNV achieves prolonged and disseminated infection in hamsters, including efficient rep...

  15. Crinivirus replication and host interactions

    Directory of Open Access Journals (Sweden)

    ZsofiaAKiss

    2013-05-01

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

  16. Factors affecting SFHR gene correction efficiency with single-stranded DNA fragment

    International Nuclear Information System (INIS)

    A 606-nt single-stranded (ss) DNA fragment, prepared by restriction enzyme digestion of ss phagemid DNA, improves the gene correction efficiency by 12-fold as compared with a PCR fragment, which is the conventional type of fragment used in the small fragment homologous replacement method [H. Tsuchiya, H. Harashima, H. Kamiya, Increased SFHR gene correction efficiency with sense single-stranded DNA, J. Gene Med. 7 (2005) 486-493]. To reveal the characteristic features of this gene correction with the ss DNA fragment, the effects on the gene correction in CHO-K1 cells of the chain length, 5'-phosphate, adenine methylation, and transcription were studied. Moreover, the possibility that the ss DNA fragment is integrated into the target DNA was examined with a radioactively labeled ss DNA fragment. The presence of methylated adenine, but not the 5'-phosphate, enhanced the gene correction efficiency, and the optimal length of the ss DNA fragment (∼600 nt) was determined. Transcription of the target gene did not affect the gene correction efficiency. In addition, the target DNA recovered from the transfected CHO-K1 cells was radioactive. The results obtained in this study indicate that length and adenine methylation were important factors affecting the gene correction efficiency, and that the ss DNA fragment was integrated into the double-stranded target DNA

  17. An improved protocol for efficient engraftment in NOD/LTSZ-SCIDIL-2Rγnull mice allows HIV replication and development of anti-HIV immune responses.

    Directory of Open Access Journals (Sweden)

    Maneesh Singh

    Full Text Available Cord blood hematopoietic progenitor cells (CB-HPCs transplanted immunodeficient NOD/LtsZ-scidIL2Rγ(null (NSG and NOD/SCID/IL2Rγ(null (NOG mice need efficient human cell engraftment for long-term HIV-1 replication studies. Total body irradiation (TBI is a classical myeloablation regimen used to improve engraftment levels of human cells in these humanized mice. Some recent reports suggest the use of busulfan as a myeloablation regimen to transplant HPCs in neonatal and adult NSG mice. In the present study, we further ameliorated the busulfan myeloablation regimen with fresh CB-CD34+cell transplantation in 3-4 week old NSG mice. In this CB-CD34+transplanted NSG mice engraftment efficiency of human CD45+cell is over 90% in peripheral blood. Optimal engraftment promoted early and increased CD3+T cell levels, with better lymphoid tissue development and prolonged human cell chimerism over 300 days. These humanized NSG mice have shown long-lasting viremia after HIV-1JRCSF and HIV-1Bal inoculation through intravenous and rectal routes. We also saw a gradual decline of the CD4+T cell count, widespread immune activation, up-regulation of inflammation marker and microbial translocation after HIV-1 infection. Humanized NSG mice reconstituted according to our new protocol produced, moderate cellular and humoral immune responses to HIV-1 postinfection. We believe that NSG mice reconstituted according to our easy to use protocol will provide a better in vivo model for HIV-1 replication and anti-HIV-1 therapy trials.

  18. DNA ligase I selectively affects DNA synthesis by DNA polymerases delta and epsilon suggesting differential functions in DNA replication and repair.

    OpenAIRE

    Mossi, R; Ferrari, E.; Hübscher, U

    1998-01-01

    The joining of single-stranded breaks in double-stranded DNA is an essential step in many important processes such as DNA replication, DNA repair, and genetic recombination. Several data implicate a role for DNA ligase I in DNA replication, probably coordinated by the action of other enzymes and proteins. Since both DNA polymerases delta and epsilon show multiple functions in different DNA transactions, we investigated the effect of DNA ligase I on various DNA synthesis events catalyzed by th...

  19. Detection efficiency for loophole-free Bell tests with entangled states affected by colored noise

    OpenAIRE

    Canas G.; Barra J.F.; Gomez E.S.; Lima G; Sciarrino F.; Cabello A.

    2013-01-01

    Loophole-free Bell tests for quantum nonlocality and long-distance secure communication require photodetection efficiencies beyond a threshold eta_{crit} that depends on the Bell inequality and the noise affecting the entangled state received by the distant parties. Most calculations of eta_{crit} assume that the noise is random and can be modeled as white noise. However, most sources suffer from colored noise. Indeed, since entangled states are usually created as a superposition of two possi...

  20. Millennial δ18O oscillations from a replicated Holocene speleothem record from Iberian Peninsula and hemispherical teleconecctions affecting the water cycle

    Science.gov (United States)

    Domínguez-Villar, David; Wang, Xianfeng; Krklec, Kristina; Cheng, Hai; Edwards, R. Lawrence

    2016-04-01

    We present a speleothem δ18O record from Kaite Cave in northern Iberian Peninsula covering the last 9.7 ka BP. The record is constructed from four different stalagmites that replicate each other. The age model is based on 63 U-Th dates and over 4500 laminae providing a robust time frame for the record. The δ18O record has characteristic millennial oscillations through the Holocene with periodicity around 2 ka during the Late Holocene and around 1 ka during the Early Holocene. Causes of the millennial δ18O variability are not dominated by the amount of rainfall or atmospheric temperature and other controls of the water cycle are more relevant. The aquifer at this site filters any seasonal bias and speleothems records the inter-annual δ18O variability in precipitation. On the other hand, moisture source analysis at this site shows that significant amount of precipitation is from recycled moisture (continental origin). A variable proportion of this parameter is capable to impact significantly past values of δ18O in precipitation. Thus, we interpret the millennial oscillations of the δ18O record as changes in the hydrological cycle resulting from variable percentages of the recycled precipitation over the Iberian Peninsula. We found that variable amount of recycled precipitation in Iberian Peninsula is related to the location of the Iceland Low pressure cell, although does not correlate with NAO index. Correlation of Kaite δ18O record during the Holocene with other representative records suggests that millennial oscillations are caused by variability of the Gulf Stream/North Atlantic Current that affects atmospheric pressure fields in the North Atlantic. Further correlation of Kaite δ18O record along the world supports that the recorded millennial oscillations of the water cycle are related to persistent variability on the tropical North Atlantic. Only during periods of major sea-ice variability in high-latitudes of the North Atlantic, the later region replaces

  1. Has the 2008 financial crisis affected stock market efficiency? The case of Eurozone

    Science.gov (United States)

    Anagnostidis, P.; Varsakelis, C.; Emmanouilides, C. J.

    2016-04-01

    In this paper, the impact of the 2008 financial crisis on the weak-form efficiency of twelve Eurozone stock markets is investigated empirically. Efficiency is tested via the Generalized Hurst Exponent method, while dynamic Hurst exponents are estimated by means of the rolling window technique. To account for biases associated with the finite sample size and the leptokurtosis of the financial data, the statistical significance of the Hurst exponent estimates is assessed through a series of Monte-Carlo simulations drawn from the class of α-stable distributions. According to our results, the 2008 crisis has adversely affected stock price efficiency in most of the Eurozone capital markets, leading to the emergence of significant mean-reverting patterns in stock price movements.

  2. Replicating vaccines

    Science.gov (United States)

    Early work on fish immunology and disease resistance demonstrated fish (like animals and humans) that survived infection were typically resistant to re-infection with the same pathogen. The concepts of resistance upon reinfection lead to the research and development of replicating (live) vaccines in...

  3. The ratio of unsaturated fatty acids in biosurfactants affects the efficiency of gene transfection.

    Science.gov (United States)

    Inoh, Yoshikazu; Furuno, Tadahide; Hirashima, Naohide; Kitamoto, Dai; Nakanishi, Mamoru

    2010-10-15

    An unsaturated hydrocarbon chain in phospholipid was reported to affect a phase transition and a fusogenic activity after mixing membranes, and consequently to achieve a high DNA transfection efficiency. We previously showed that a biosurfactant mannosylerythritol lipid-A (MEL-A) enhances the gene transfection efficiency of cationic liposomes. Here, we have studied the effects of unsaturated fatty acid ratio of MEL-A on the physicochemical properties and gene delivery into cells of cationic liposomes using MEL-A with three different unsaturated fatty acid ratios (9.1%, 21.5%, and 46.3%). The gene transfer efficiency of cationic liposomes containing MEL-A (21.5%) was much higher than that of those containing MEL-A (9.1%) and MEL-A (46.3%). MEL-A (21.5%)-containing cationic liposomes induced highly efficient membrane fusion after addition of anionic liposomes and led to subsequent DNA release. Imaging analysis revealed that MEL-A (21.5%)-containing liposomes fused with the plasma membrane and delivered DNA into the nucleus of NIH-3T3 cells, MEL-A (46.3%)-containing liposomes fused with the plasma membrane did not deliver DNA into the nucleus, and MEL-A (9.1%)-containing liposomes neither fused with the plasma membrane nor delivered DNA into the nucleus. Thus, it is understandable that the unsaturated fatty acid ratio of MEL-A strongly influences the gene transfection efficiency of cationic liposomes. PMID:20674726

  4. Human immunodeficiency virus integrase inhibitors efficiently suppress feline immunodeficiency virus replication in vitro and provide a rationale to redesign antiretroviral treatment for feline AIDS

    Directory of Open Access Journals (Sweden)

    Ciervo Alessandra

    2007-10-01

    Full Text Available Abstract Background Treatment of feline immunodeficiency virus (FIV infection has been hampered by the absence of a specific combination antiretroviral treatment (ART. Integrase strand transfer inhibitors (INSTIs are emerging as a promising new drug class for HIV-1 treatment, and we evaluated the possibility of inhibiting FIV replication using INSTIs. Methods Phylogenetic analysis of lentiviral integrase (IN sequences was carried out using the PAUP* software. A theoretical three-dimensional structure of the FIV IN catalytic core domain (CCD was obtained by homology modeling based on a crystal structure of HIV-1 IN CCD. The interaction of the transferred strand of viral DNA with the catalytic cavity of FIV IN was deduced from a crystal structure of a structurally similar transposase complexed with transposable DNA. Molecular docking simulations were conducted using a genetic algorithm (GOLD. Antiviral activity was tested in feline lymphoblastoid MBM cells acutely infected with the FIV Petaluma strain. Circular and total proviral DNA was quantified by real-time PCR. Results The calculated INSTI-binding sites were found to be nearly identical in FIV and HIV-1 IN CCDs. The close similarity of primate and feline lentivirus IN CCDs was also supported by phylogenetic analysis. In line with these bioinformatic analyses, FIV replication was efficiently inhibited in acutely infected cell cultures by three investigational INSTIs, designed for HIV-1 and belonging to different classes. Of note, the naphthyridine carboxamide INSTI, L-870,810 displayed an EC50 in the low nanomolar range. Inhibition of FIV integration in situ was shown by real-time PCR experiments that revealed accumulation of circular forms of FIV DNA within cells treated with L-870,810. Conclusion We report a drug class (other than nucleosidic reverse transcriptase inhibitors that is capable of inhibiting FIV replication in vitro. The present study helped establish L-870,810, a compound

  5. Sequence characteristics required for cooperative binding and efficient in vivo titration of the replication initiator protein DnaA in E. coli

    DEFF Research Database (Denmark)

    Hansen, Flemming G.; Christensen, Bjarke Bak; Atlung, Tove

    2007-01-01

    was eliminated by insertion of half a helical turn between any of the DnaA boxes. Titration strongly depends on the presence and orientation of the promoter distal R6 DnaA box located 104 bp upstream of the R5 box as well as neighbouring sequences downstream of R6. Titration depends on the integrity of a 43 bp......Plasmids carrying the mioC promoter region, which contains two DnaA boxes, R5 and R6 with one misfit to the consensus TT(A)/(T)TNCACA, are as efficient in in vivo titration of the DnaA protein as plasmids carrying a replication-inactivated oriC region with its eight DnaA boxes. Three additional Dna...... was located less than 20 bp upstream of the -35 sequence. Thus, the architectural requirements for titration and for repression of transcription are different. A new set of rules for identifying efficiently titrating DnaA box regions was formulated and used to analyse sequences for which good titration data...

  6. Factors Affecting the Capture Efficiency of a Fume Extraction Torch for Gas Metal Arc Welding.

    Science.gov (United States)

    Bonthoux, Francis

    2016-07-01

    Welding fumes are classified as Group 2B 'possibly carcinogenic' and this prompts to the implementation of local exhaust ventilation (LEV). The fume extraction torch with LEV integrated into the tool is the most attractive solution but its capture efficiency is often disappointing in practice. This study assesses the main parameters affecting fume capture efficiency namely the extraction flow rate, the positioning of the suction openings on the torch, the angle of inclination of the torch to the workpiece during welding, the metal transfer modes, and the welding deposition rate. The theoretical velocity induced by suction, estimated from the extraction flow rate and the position of the suction openings, is the main parameter affecting effectiveness of the device. This is the design parameter and its value should never be Welding with high deposition rates (>1.1g s(-1)) and spray transfer leads to low capture efficiency if induced velocities are <0.5 m s(-1) The results of the study can be used in the design of integrated on-torch extraction systems and provide information for fixing system objectives. PMID:27074798

  7. Factors that affect the reproductive efficiency of the recipient within a bovine embryo transfer program

    Directory of Open Access Journals (Sweden)

    Arturo Duica A.

    2007-12-01

    Full Text Available The embryo transfer is a biotechnological technique that allows increasing the descendant of animals with high genetic value. The positive results, represented in pregnancy after the application of this technique, are affected by some factors that are inherent to the donor, the embryo, the technique, and the recipients which receive a strange embryo in the uterus allowing pregnancy. This review describes some factors affecting the reproductive efficiency of the recipients of bovine embryos within a program of embryo transfer. Its important to evaluate the parameters in this kind of recipients, as race, age, physiological status, health status, weight, reproductive tract integrity and management, and also too monitoring the ovarian structures while the estrus synchronization, and within previous and posterior stages in embryo transfer procedure. Therefore an optimum follicular development will be determinant to corpus luteum formation which generates enough serum progesterone concentrations to offer a right uterine environment allowing the optimum embryo development. Controlling the factors that affect the efficiency of the embryo transfer, it will obtain an increasing of positive results represented in pregnancies and births of individuals come from animals with high genetic value.

  8. Conserved retinoblastoma protein-binding motif in human cytomegalovirus UL97 kinase minimally impacts viral replication but affects susceptibility to maribavir

    Directory of Open Access Journals (Sweden)

    Chou Sunwen

    2009-01-01

    Full Text Available Abstract The UL97 kinase has been shown to phosphorylate and inactivate the retinoblastoma protein (Rb and has three consensus Rb-binding motifs that might contribute to this activity. Recombinant viruses containing mutations in the Rb-binding motifs generally replicated well in human foreskin fibroblasts with only a slight delay in replication kinetics. Their susceptibility to the specific UL97 kinase inhibitor, maribavir, was also examined. Mutation of the amino terminal motif, which is involved in the inactivation of Rb, also renders the virus hypersensitive to the drug and suggests that the motif may play a role in its mechanism of action.

  9. Decision factors affecting transmission and distribution efficiency improvements by Northwest electric utilities

    Energy Technology Data Exchange (ETDEWEB)

    Hendrickson, P.L.; Darwin, R.F.

    1986-01-01

    The principal objective of this report was to assess and document the attitude of Northwest electric utilities toward possible BPA conservation acquisition programs that may provide incentive(s) to reduce losses on T and D lines. Secondary objectives were to examine existing incentives for making such improvements, to categorize prior T and D efficiency improvements, and to examine factors affecting the decision-making process for system improvements. Much of the information presented in the report is derived from a survey administered during personal interviews at 29 Northwest electric utilities between November 1984 and January 1985.

  10. Autologous peripheral blood stem cell harvest: Collection efficiency and factors affecting it

    Directory of Open Access Journals (Sweden)

    Aseem K Tiwari

    2016-01-01

    Full Text Available Background: Harvest of hematopoietic progenitor cells via leukapheresis is being used increasingly for transplants in India. Adequate yield of cells per kilogram body weight of recipient is required for successful engraftment. Collection efficiency (CE is an objective quality parameter used to assess the quality of leukapheresis program. In this study, we calculated the CE of the ComTec cell separator (Fresenius Kabi, Germany using two different formulae (CE1 and CE2 and analyzed various patient and procedural factors, which may affect it. Materials and Methods: One hundred and one consecutive procedures in 77 autologous donors carried out over 3 years period were retrospectively reviewed. Various characteristics like gender, age, weight, disease status, hematocrit, preprocedure total leukocyte count, preprocedure CD34 positive (CD34+ cells count, preprocedure absolute CD34+ cell count and processed apheresis volume effect on CE were compared. CE for each procedure was calculated using two different formulae, and results were compared using statistical correlation and regression analysis. Results: The mean CE1 and CE2 was 41.2 and 49.1, respectively. CE2 appeared to be more accurate indicator of overall CE as it considered the impact of continued mobilization of stem cells during apheresis procedure, itself. Of all the factors affecting CE, preprocedure absolute CD34+ was the only independent factor affecting CE. Conclusion: The only factor affecting CE was preprocedure absolute CD34+ cells. Though the mean CE2 was higher than CE1, it was not statistically significant.

  11. An Evaluation of the Critical Factors Affecting the Efficiency of Some Sorting Techniques

    Directory of Open Access Journals (Sweden)

    Olabiyisi S.O.

    2013-02-01

    Full Text Available Sorting allows information or data to be put into a meaningful order. As efficiency is a major concern of computing, data are sorted in order to gain the efficiency in retrieving or searching tasks. The factors affecting the efficiency of shell, Heap, Bubble, Quick and Merge sorting techniques in terms of running time, memory usage and the number of exchanges were investigated. Experiment was conducted for the decision variables generated from algorithms implemented in Java programming and factor analysis by principal components of the obtained experimental data was carried out in order to estimate the contribution of each factor to the success of the sorting algorithms. Further statistical analysis was carried out to generate eigenvalue of the extracted factor and hence, a system of linear equations which was used to estimate the assessment of each factor of the sorting techniques was proposed. The study revealed that the main factor affecting these sorting techniques was time taken to sort. It contributed 97.842%, 97.693%, 89.351%, 98.336% and 90.480% for Bubble sort, Heap sort, Merge sort, Quick sort and Shell sort respectively. The number of swap came second contributing 1.587% for Bubble sort, 2.305% for Heap sort, 10.63% for Merge sort, 1.643% for Quick sort and 9.514% for Shell sort. The memory used was the least of the factors contributing negligible percentage for the five sorting techniques. It contributed 0.571% for Bubble sort, 0.002% for Heap sort, 0.011% for Merge sort, 0.021% for Quick sort and 0.006% for Shell sort.

  12. Mutations in the M-Gene Segment Can Substantially Increase Replication Efficiency of NS1 Deletion Influenza A Virus in MDCK Cells

    NARCIS (Netherlands)

    Wielink, van R.; Harmsen, M.M.; Martens, D.E.; Peeters, B.P.H.; Wijffels, R.H.; Moormann, R.J.M.

    2012-01-01

    Influenza viruses unable to express NS1 protein (delNS1) replicate poorly and induce high amounts of interferon (IFN). They are therefore considered as candidate viruses for live-attenuated influenza vaccines. Their attenuated replication is generally assumed to result from the inability to counter

  13. Na~+/K~+-ATPase β1 subunit interacts with M2 proteins of influenza A and B viruses and affects the virus replication

    Institute of Scientific and Technical Information of China (English)

    GAO; George; Fu

    2010-01-01

    Interplay between the host and influenza virus has a pivotal role for the outcome of infection.The matrix proteins M2/BM2 from influenza (A and B) viruses are small type III integral membrane proteins with a single transmembrane domain,a short amino-terminal ectodomain and a long carboxy-terminal cytoplasmic domain.They function as proton channels,mainly forming a membrane-spanning pore through the transmembrane domain tetramer,and are essential for virus assembly and release of the viral genetic materials in the endosomal fusion process.However,little is known about the host factors which interact with M2/BM2 proteins and the functions of the long cytoplasmic domain are currently unknown.Starting with yeast two-hybrid screening and applying a series of experiments we identified that the β1 subunit of the host Na+/K+-ATPase β1 subunit (ATP1B1) interacts with the cytoplasmic domain of both the M2 and BM2 proteins.A stable ATP1B1 knockdown MDCK cell line was established and we showed that the ATP1B1 knockdown suppressed influenza virus A/WSN/33 replication,implying that the interaction is crucial for influenza virus replication in the host cell.We propose that influenza virus M2/BM2 cytoplasmic domain has an important role in the virus-host interplay and facilitates virus replication.

  14. Is the pollination efficiency of long-lived orchid flowers affected by age?

    Directory of Open Access Journals (Sweden)

    Rúbia Santos Fonseca

    2015-08-01

    Full Text Available The long-lived flowers of orchids increase the chances of pollination and thus the reproductive success of the species. However, a question arises: does the efficiency of pollination, expressed by fruit set, vary with the flower age? The objective of this study was to verify whether the flower age of Corymborkis flava(Sw. Kuntze affects pollination efficiency. The following hypotheses were tested: 1 the fruit set of older flowers is lower than that of younger ones; 2 morphological observations (perianth and stigmatic area, stigma receptivity test by using a solution of hydrogen peroxide and hand-pollination tests are equally effective in defining the period of stigmatic receptivity. Flowers were found to be receptive from the first to the fourth day of anthesis. Fruit set of older flowers (third and fourth day was lower than that of younger flowers. Morphological observations, the stigma receptivity test and hand-pollinations were equally effective in defining the period of stigmatic receptivity. However, to evaluate the maximum degree of stigma receptivity of orchid species with long-lived flowers, we recommend hand-pollinations, beyond the period of receptivity.

  15. Radiation use-efficiency of field beans as affected by soil phosphorus management

    International Nuclear Information System (INIS)

    A simple approach to modeling dry matter production is based on the assumption that radiation‐use efficiency (RUE), which is the amount of dry weight produced per unit of intercepted photosynthetically active radiation (IPAR), is relatively constant for crops adequately supplied with water and nutrients. Recent evidences, however, indicate that RUE is not constant but is strongly affected by environment. Soil stresses also appear to affect RUE but few responses have been documented. Growth analysis data from a field experiment were used to compute RUE of field beans grown at differential phosphorus (P) regimes. The main objective of this study was to assess the effects of soil P management on RUE. Applied P rates significantly increased RUE with values ranging from 0.86 g M/J at 0 kg P/ha to 1.09 g M/J at 200 kg P/ha. The relationship between total dry matter and cumulative EPAR was linear at low P regimes but resembled a curvilinear relationship at high P regimes. The RUE of beans under high soil P regimes was not constant but decreased over time. (author)

  16. Ocean Acidification Affects the Phyto-Zoo Plankton Trophic Transfer Efficiency

    Science.gov (United States)

    Cripps, Gemma; Flynn, Kevin J.; Lindeque, Penelope K.

    2016-01-01

    The critical role played by copepods in ocean ecology and biogeochemistry warrants an understanding of how these animals may respond to ocean acidification (OA). Whilst an appreciation of the potential direct effects of OA, due to elevated pCO2, on copepods is improving, little is known about the indirect impacts acting via bottom-up (food quality) effects. We assessed, for the first time, the chronic effects of direct and/or indirect exposures to elevated pCO2 on the behaviour, vital rates, chemical and biochemical stoichiometry of the calanoid copepod Acartia tonsa. Bottom-up effects of elevated pCO2 caused species-specific biochemical changes to the phytoplanktonic feed, which adversely affected copepod population structure and decreased recruitment by 30%. The direct impact of elevated pCO2 caused gender-specific respiratory responses in A.tonsa adults, stimulating an enhanced respiration rate in males (> 2-fold), and a suppressed respiratory response in females when coupled with indirect elevated pCO2 exposures. Under the combined indirect+direct exposure, carbon trophic transfer efficiency from phytoplankton-to-zooplankton declined to < 50% of control populations, with a commensurate decrease in recruitment. For the first time an explicit role was demonstrated for biochemical stoichiometry in shaping copepod trophic dynamics. The altered biochemical composition of the CO2-exposed prey affected the biochemical stoichiometry of the copepods, which could have ramifications for production of higher tropic levels, notably fisheries. Our work indicates that the control of phytoplankton and the support of higher trophic levels involving copepods have clear potential to be adversely affected under future OA scenarios. PMID:27082737

  17. Rotavirus variant replicates efficiently although encoding an aberrant NSP3 that fails to induce nuclear localization of poly(A)-binding protein.

    Science.gov (United States)

    Arnold, Michelle M; Brownback, Catie Small; Taraporewala, Zenobia F; Patton, John T

    2012-07-01

    The rotavirus (RV) non-structural protein NSP3 forms a dimer that has binding domains for the translation initiation factor eIF4G and for a conserved 3'-terminal sequence of viral mRNAs. Through these activities, NSP3 has been proposed to promote viral mRNA translation by directing circularization of viral polysomes. In addition, by disrupting interactions between eIF4G and the poly(A)-binding protein (PABP), NSP3 has been suggested to inhibit translation of host polyadenylated mRNAs and to stimulate relocalization of PABP from the cytoplasm to the nucleus. Herein, we report the isolation and characterization of SA11-4Fg7re, an SA11-4F RV derivative that contains a large sequence duplication initiating within the genome segment (gene 7) encoding NSP3. Our analysis showed that mutant NSP3 (NSP3m) encoded by SA11-4Fg7re is almost twice the size of the wild-type protein and retains the capacity to dimerize. However, in comparison to wild-type NSP3, NSP3m has a decreased capacity to interact with eIF4G and to suppress the translation of polyadenylated mRNAs. In addition, NSP3m fails to induce the nuclear accumulation of PABP in infected cells. Despite the defective activities of NSP3m, the levels of viral protein and progeny virus produced in SA11-4Fg7re- and SA11-4F-infected cells were indistinguishable. Collectively, these data are consistent with a role for NSP3 in suppressing host protein synthesis through antagonism of PABP activity, but also suggest that NSP3 functions may have little or no impact on the efficiency of virus replication in widely used RV-permissive cell lines. PMID:22442114

  18. Does Risk Management Affect On Bank Efficiency? An Analysis of Sri Lankan Banking Sector

    OpenAIRE

    J.M. Ruwani Fernando; P.D.Nimal

    2014-01-01

    Increasing competition in the finance sector in Sri Lank has created a huge competition among the banking sector. The high level of competition improved the bank efficiency and efficiency creates risk to the banks. Therefore, risk management is a vital in achieving efficiency. Therefore, this study addresses the question on “whether the Sri Lankan banks are efficient and how risk management improves the banks’ efficiency?. The main objective of the study was to identify the efficiency of the ...

  19. Factors Affecting Pheromone Production by the Pepper Weevil, Anthonomus eugenii Cano (Coleoptera: Curculionidae and Collection Efficiency

    Directory of Open Access Journals (Sweden)

    Fred J. Eller

    2014-11-01

    Full Text Available Several factors affecting pheromone production by male pepper weevils, Anthonomus eugenii Cano (Coleoptera: Curculionidae as well as collection efficiency were investigated. Factors studied included: porous polymer adsorbents (Tenax versus Super Q, male age, time of day, male density, and male diet. Super Q was found to be a superior adsorbent for the male-produced alcohols and geranic acid as well as the plant-produced E-β-ocimene. Pheromone production increased with male age up to about age 15 days old and then tapered off. Male pepper weevils produced the highest amount of pheromone between noon and 2 pm (i.e., 4 to 6 h after “lights on” and were producing ca. 800 ng/h during this period. Thereafter, pheromone production decreased and was extremely low during the scotophase (i.e., ca. 12 ng/h. Male pepper weevil density had a significant effect on both release rate and pheromone composition. Pheromone production on a per male basis was highest for individual males and the percentage of geranic acid in the blend was lowest for individual males. Male pepper weevils produced only extremely low amounts of pheromone when feeding on artificial diet; however, they produced very high amounts when on fresh peppers. Together, this information will be useful in designing better attractant lures for pepper weevils.

  20. Role of HIV-1 subtype C envelope V3 to V5 regions in viral entry, coreceptor utilization and replication efficiency in primary T-lymphocytes and monocyte-derived macrophages

    Directory of Open Access Journals (Sweden)

    Gopalan Sarla

    2007-11-01

    Full Text Available Abstract Background Several subtypes of HIV-1 circulate in infected people worldwide, including subtype B in the United States and subtype C in Africa and India. To understand the biological properties of HIV-1 subtype C, including cellular tropism, virus entry, replication efficiency and cytopathic effects, we reciprocally inserted our previously characterized envelope V3–V5 regions derived from 9 subtype C infected patients from India into a subtype B molecular clone, pNL4-3. Equal amounts of the chimeric viruses were used to infect T-lymphocyte cell lines (A3.01 and MT-2, coreceptor cell lines (U373-MAGI-CCR5/CXCR4, primary blood T-lymphocytes (PBL and monocyte-derived macrophages (MDM. Results We found that subtype C envelope V3–V5 region chimeras failed to replicate in T-lymphocyte cell lines but replicated in PBL and MDM. In addition, these chimeras were able to infect U373MAGI-CD4+-CCR5+ but not U373MAGI-CD4+-CXCR4+ cell line, suggesting CCR5 coreceptor utilization and R5 phenotypes. These subtype C chimeras were unable to induce syncytia in MT-2 cells, indicative of non-syncytium inducing (NSI phenotypes. More importantly, the subtype C envelope chimeras replicated at higher levels in PBL and MDM compared with subtype B chimeras and isolates. Furthermore, the higher levels subtype C chimeras replication in PBL and MDM correlated with increased virus entry in U373MAGI-CD4+-CCR5+. Conclusion Taken together, these results suggest that the envelope V3 to V5 regions of subtype C contributed to higher levels of HIV-1 replication compared with subtype B chimeras, which may contribute to higher viral loads and faster disease progression in subtype C infected individuals than other subtypes as well as rapid HIV-1 subtype C spread in India.

  1. Factors Affecting the Efficiency of Embryonic Cell Nuclear Transfer in Rabbits

    Institute of Scientific and Technical Information of China (English)

    CUI Kui-qing; LIU Qing-you; XIE Ying; WEI Jing-wei; SHI De-shun

    2005-01-01

    Factors affecting the efficiency of nuclear transfer (NT) in rabbits were examined in the present study. When 100 V mm-1of pulse strength and 15 μs of pulse duration were employed, 3 and 4 electronic pulses resulted in significantly more cytoplasts fused with donor cells compared with 2 electronic pulses (P<0.05), but no significant difference was found in the cleavage rate of reconstructed embryos among the three groups (P> 0.05). When the duration and number of electronic pulse were fixed at 15 μs and 3 times, increase of pulse intensity from 100 V mm-1 to 150 V mm-1 and 200 V mm-1 resulted in a significantly decrease in the cleavage rate of reconstructed embryos (P < 0.05), although the fusion rate did not significantly differ among the three groups (P > 0.05). Significantly more reconstructed embryos cleaved and developed to blastocysts when they were derived from donor embryos at the 8-16-cell stage, in comparison with the reconstructed embryos derived from donor embryos at the compact morula stage (P < 0.05), although the fusion rate was similar (P > 0.05). Activation of cytoplasts prior to fusion increased the cleavage rate (P < 0.05) and blastocyst development (P < 0.05) of reconstructed embryos, but decreased the fusion rate (P < 0.05) compared with cytoplasts activated post fusion. More reconstructed embryos developed to blastocysts when they were cultured in TCM + 3% OCS at the first 48 h and then cultured in TCM199+ 10% FCS, in comparison with the reconstructed embryos cultured in either TCM199+ 10% FCS or TCM199+ 3% OCS (P < 0.05). When 22 NT embryos were transferred into the oviducts of one recipient rabbit, one recipient rabbit delivered a female rabbit at 34 days of gestation. In conclusion, either electrofusion parameter or developmental stage of donor embryos have a significant effect on the efficiency of NT, NT embryos require different concentration of serum at their different development stages.

  2. The intracellular domain of Dumbfounded affects myoblast fusion efficiency and interacts with Rolling pebbles and Loner.

    Directory of Open Access Journals (Sweden)

    Sarada Bulchand

    Full Text Available Drosophila body wall muscles are multinucleated syncytia formed by successive fusions between a founder myoblast and several fusion competent myoblasts. Initial fusion gives rise to a bi/trinucleate precursor followed by more fusion cycles forming a mature muscle. This process requires the functions of various molecules including the transmembrane myoblast attractants Dumbfounded (Duf and its paralogue Roughest (Rst, a scaffold protein Rolling pebbles (Rols and a guanine nucleotide exchange factor Loner. Fusion completely fails in a duf, rst mutant, and is blocked at the bi/trinucleate stage in rols and loner single mutants. We analysed the transmembrane and intracellular domains of Duf, by mutating conserved putative signaling sites and serially deleting the intracellular domain. These were tested for their ability to translocate and interact with Rols and Loner and to rescue the fusion defect in duf, rst mutant embryos. Studying combinations of double mutants, further tested the function of Rols, Loner and other fusion molecules. Here we show that serial truncations of the Duf intracellular domain successively compromise its function to translocate and interact with Rols and Loner in addition to affecting myoblast fusion efficiency in embryos. Putative phosphorylation sites function additively while the extreme C terminus including a PDZ binding domain is dispensable for its function. We also show that fusion is completely blocked in a rols, loner double mutant and is compromised in other double mutants. These results suggest an additive function of the intracellular domain of Duf and an early function of Rols and Loner which is independent of Duf.

  3. Caregiving and Developmental Factors Differentiating Young At-Risk Urban Children Showing Resilient Versus Stress-Affected Outcomes: A Replication and Extension.

    Science.gov (United States)

    Wyman, Peter A.; And Others

    1999-01-01

    Tested hypotheses from an organizational-developmental model for childhood resilience among 7- to 9-year olds. Found that caregiving factors and early development differentiated children with resilient and stress-affected adaptations. Variables reflecting emotionally responsive, competent parenting were direct, proximal predictors of resilience…

  4. 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......-sex interaction relevant to Long alleles (more than 37 repeats). The different findings in Denmark and Italy suggest that gene/longevity associations are population-specific, and heavily affected by the population-specific genetic and environmental history....

  5. Replication in Economics

    OpenAIRE

    Hamermesh, Daniel S.

    2007-01-01

    This examination of the role and potential for replication in economics points out the paucity of both pure replication -- checking on others' published papers using their data -- and scientific replication -- using data representing different populations in one's own work or in a Comment. Several controversies in empirical economics illustrate how and how not to behave when replicating others' work. The incentives for replication facing editors, authors and potential replicators are examined...

  6. Efficient replication and expression of murine leukemia virus with major deletions in the enhancer region of U3

    DEFF Research Database (Denmark)

    Pedersen, K.; Lovmand, S.; Bonefeld-Jørgensen, Eva Cecilie; Pedersen, F.S.; Jørgensen, P.

    1992-01-01

    The effect of deletions within the enhancer region in the U3 part of the LTR derived from the murine retrovirus Akv was studied. The deletions were stably transmitted through normal virus replication as shown by sequence analysis of cloned polymerase chain reaction product of the cDNA copy of the...... viral RNA. Genetic tagging of the retrovirus with lacO facilitated the analysis. Among the individual mutated LTRs an over 100-fold difference in a transient expression assay was previously detected. This difference was not revealed in studies of viral replication in cell culture, where the expression...... level of virus with the deleted LTRs all reached the level of virus with the intact LTR. We propose that stimulatory cis-acting sequences either adjacent to the site of proviral integration or in the coding regions of the provirus may compensate for deletions in the LTR....

  7. Efficient Replication of Adeno-Associated Virus Type 2 Vectors: a cis-Acting Element outside of the Terminal Repeats and a Minimal Size

    OpenAIRE

    Tullis, Gregory E.; Shenk, Thomas

    2000-01-01

    Recombinant adeno-associated virus type 2 (AAV2) can be produced in adenovirus-infected cells by cotransfecting a plasmid containing the recombinant AAV2 genome, which is generally comprised of the viral terminal repeats flanking a transgene, together with a second plasmid expressing the AAV2 rep and cap genes. However, recombinant viruses generally replicate inefficiently, often producing 100-fold fewer virus particles per cell than can be obtained after transfection with a plasmid containin...

  8. Intracytoplasmic stable expression of IgG1 antibody targeting NS3 helicase inhibits replication of highly efficient hepatitis C Virus 2a clone

    OpenAIRE

    Clementi Massimo; Burioni Roberto; Liu Gerald; Prabhu Ramesh; Gunduz Feyza; Poat Bret; Hazari Sidhartha; Chandra Partha K; Garry Robert F; Dash Srikanta

    2010-01-01

    Abstract Background Hepatitis C virus (HCV) infection is a major public health problem with more than 170 million cases of chronic infections worldwide. There is no protective vaccine currently available for HCV, therefore the development of novel strategy to prevent chronic infection is important. We reported earlier that a recombinant human antibody clone blocks viral NS3 helicase activity and inhibits replication of HCV 1b virus. This study was performed further to explore the mechanism of...

  9. Regeneration in Jatropha curcas: Factors affecting the efficiency of in vitro regeneration

    KAUST Repository

    Sharma, Sweta K.

    2011-07-01

    Factors influencing in vitro regeneration through direct shoot bud induction from hypocotyl explants of Jatropha curcas were studied in the present investigation. Regeneration in J. curcas was found to be genotype dependent and out of four toxic and one non-toxic genotype studied, non-toxic was least responsive. The best results irrespective of genotype were obtained on the medium containing 0.5mgL-1 TDZ (Thidiazuron) and in vitro hypocotyl explants were observed to have higher regeneration efficiency as compared to ex vitro explant in both toxic and non-toxic genotypes. Adventitious shoot buds could be induced from the distal end of explants in all the genotypes. The number of shoot buds formed and not the number of explants responding to TDZ treatment were significantly affected by the position of the explant on the seedling axis. Explants from younger seedlings (≤15 days) were still juvenile and formed callus easily, whereas the regeneration response declined with increase in age of seedlings after 30 days. Transient reduction of Ca2+ concentrations to 0.22gL-1 in the germination medium increased the number of responding explants.Induced shoot buds, upon transfer to MS medium containing 2mgL-1 Kn (Kinetin) and 1mgL-1 BAP (6-benzylamino purine) elongated. These elongated shoots were further proliferated on MS medium supplemented with 1.5mgL-1 IAA (indole-3-acetic acid) and 0.5mgL-1 BAP and 3.01-3.91cm elongation was achieved after 6 weeks. No genotype specific variance in shoot elongation was observed among the toxic genotypes except the CSMCRI-JC2, which showed reduced response. And for proliferation among the toxic genotypes, CSMCRI-JC4 showed highest number of shoots formed. Among the rest, no significant differences were observed. The elongated shoot could be rooted by pulse treatment on half-strength MS medium supplemented with 2% sucrose, 3mgL-1 IBA (indole-3-butyric acid), 1mgL-1 IAA, 1mgL-1 NAA (α-naphthalene acetic acid) and subsequent transfer on 0

  10. Depletion of Cellular Pre-Replication Complex Factors Results in Increased Human Cytomegalovirus DNA Replication

    OpenAIRE

    Tamara Evans Braun; Emma Poole; John Sinclair

    2012-01-01

    Although HCMV encodes many genes required for the replication of its DNA genome, no HCMV-encoded orthologue of the origin binding protein, which has been identified in other herpesviruses, has been identified. This has led to speculation that HCMV may use other viral proteins or possibly cellular factors for the initiation of DNA synthesis. It is also unclear whether cellular replication factors are required for efficient replication of viral DNA during or after viral replication origin recog...

  11. Comparison of Soybean Transformation Efficiency and Plant Factors Affecting Transformation during the Agrobacterium Infection Process

    Directory of Open Access Journals (Sweden)

    Yuying Jia

    2015-08-01

    Full Text Available The susceptibility of soybean genotype to Agrobacterium infection is a key factor for the high level of genetic transformation efficiency. The objective of this study is to evaluate the plant factors related to transformation in cotyledonary nodes during the Agrobacterium infection process. This study selected three genotypes (Williams 82, Shennong 9 and Bert with high transformation efficiency, which presented better susceptibility to Agrobacterium infection, and three low transformation efficiency genotypes (General, Liaodou 16 and Kottman, which showed a relatively weak susceptibility. Gibberellin (GA levels and soybean GA20ox2 and CYP707A2 transcripts of high-efficiency genotypes increased and were higher than those of low-efficiency genotypes; however, the opposite performance was shown in abscisic acid (ABA. Higher zeatin riboside (ZR content and DNA quantity, and relatively higher expression of soybean IPT5, CYCD3 and CYCA3 were obtained in high-efficiency genotypes. High-efficiency genotypes had low methyl jasmonate (MeJA content, polyphenol oxidase (PPO and peroxidase (POD activity, and relatively lower expression of soybean OPR3, PPO1 and PRX71. GA and ZR were positive plant factors for Agrobacterium-mediated soybean transformation by facilitating germination and growth, and increasing the number of cells in DNA synthesis cycle, respectively; MeJA, PPO, POD and ABA were negative plant factors by inducing defence reactions and repressing germination and growth, respectively.

  12. Screening and replication using the same data set: testing strategies for family-based studies in which all probands are affected.

    Directory of Open Access Journals (Sweden)

    Amy Murphy

    Full Text Available For genome-wide association studies in family-based designs, we propose a powerful two-stage testing strategy that can be applied in situations in which parent-offspring trio data are available and all offspring are affected with the trait or disease under study. In the first step of the testing strategy, we construct estimators of genetic effect size in the completely ascertained sample of affected offspring and their parents that are statistically independent of the family-based association/transmission disequilibrium tests (FBATs/TDTs that are calculated in the second step of the testing strategy. For each marker, the genetic effect is estimated (without requiring an estimate of the SNP allele frequency and the conditional power of the corresponding FBAT/TDT is computed. Based on the power estimates, a weighted Bonferroni procedure assigns an individually adjusted significance level to each SNP. In the second stage, the SNPs are tested with the FBAT/TDT statistic at the individually adjusted significance levels. Using simulation studies for scenarios with up to 1,000,000 SNPs, varying allele frequencies and genetic effect sizes, the power of the strategy is compared with standard methodology (e.g., FBATs/TDTs with Bonferroni correction. In all considered situations, the proposed testing strategy demonstrates substantial power increases over the standard approach, even when the true genetic model is unknown and must be selected based on the conditional power estimates. The practical relevance of our methodology is illustrated by an application to a genome-wide association study for childhood asthma, in which we detect two markers meeting genome-wide significance that would not have been detected using standard methodology.

  13. Factors Affecting the Technical Efficiency Level of Inshore Fisheries in Kuala Terengganu, Malaysia

    Directory of Open Access Journals (Sweden)

    Ismail Latiff

    2012-03-01

    Full Text Available The objective of this study is to determine factors affectingthe technical efficiency of the inshore fisheries in KualaTerengganu. Data for the study was collected from a surveyconducted between June and August 2007 where 100 fishermenin 14 villages were chosen by stratified sampling. Data envelopmentanalysis (DEA and Tobit analysis were employed to determinethe technical efficiency level and factors influencing technicalefficiency among the fishermen. Results of the study show that,most fishing units exhibit a low degree of technical efficiency.This implies that either fishing inputs were used inefficiently orinsufficient inputs were used in fishing activities. The meantechnical efficiency for the sample was estimated to be 55% forthe peak season and 40% for the non peak season. About 37%and 62% of the fishermen had less than 40% level of technicalefficiency in peak season and non peak season respectively.Management variables (planning, staffing and controlling anddemographic variables (size of horsepower, size of family andformal education exert positive effects on technical efficiencyof inshore fisheries in Kuala Terengganu. These findings suggestthat there is much room for improvement in efficiency among alarge segment of the inshore fishermen. With appropriate trainingand using more advanced technologies, fishermen’ level oftechnical efficiency can be raised.

  14. New Source Review and coal plant efficiency gains: How new and forthcoming air regulations affect outcomes

    International Nuclear Information System (INIS)

    Forthcoming carbon dioxide (CO2) regulations for existing power plants in the United States have heightened interest in thermal efficiency gains for coal-fired power plants. Plant modifications to improve thermal efficiency can trigger New Source Review (NSR), a Clean Air Act requirement to adopt of state-of-the-art pollution controls. This article explores whether existing coal plants would likely face additional pollution control requirements if they undertake modifications that trigger NSR. Despite emissions controls that are or will be installed under the Mercury and Air Toxics Standards (MATS) and Clean Air Interstate Rule (CAIR) or its replacement, 80% of coal units (76% of capacity) that are expected to remain in operation are not projected to meet the minimum NSR requirements for at least one pollutant: nitrogen oxides or sulfur dioxide. This is an important consideration for the U.S. Environmental Protection Agency and state policymakers as they determine the extent to which CO2 regulation will rely on unit-by-unit thermal efficiency gains versus potential flexible compliance strategies such as averaging, trading, energy efficiency, and renewable energy. NSR would likely delay and add cost to thermal efficiency projects at a majority of coal units, including projects undertaken to comply with forthcoming CO2 regulation. - Highlights: • We explore the status of the U.S. coal-fired fleet relative to New Source Review (NSR) requirements. • Modifications to improve thermal efficiency can trigger NSR. • Thermal efficiency gains may also be an important strategy for forthcoming CO2 regulation. • 80% Of non-retiring coal-fired units are projected not to meet minimum NSR requirements. • NSR is an important consideration for the design of CO2 regulations for existing plants

  15. Do transcriptional enhancers also augment DNA replication?

    OpenAIRE

    O'Connor, D T; Subramani, S

    1988-01-01

    Enhancers are DNA elements that augment transcription in cis, independent of distance and orientation. Evidence such as hormone dependent neoplastic cell growth and the stimulation of viral replication by sequences present in enhancers suggests that enhancers may also directly affect DNA replication. We tested this hypothesis in recombinant plasmids by asking whether sequences that stimulated DNA replication shared the properties of transcriptional enhancers. The homologous simian virus 40 (S...

  16. Replication licensing and the DNA damage checkpoint

    OpenAIRE

    Cook, Jeanette Gowen

    2009-01-01

    Accurate and timely duplication of chromosomal DNA requires that replication be coordinated with processes that ensure genome integrity. Significant advances in determining how the earliest steps in DNA replication are affected by DNA damage have highlighted some of the mechanisms to establish that coordination. Recent insights have expanded the relationship between the ATM and ATR-dependent checkpoint pathways and the proteins that bind and function at replication origins. These findings sug...

  17. How does crisis affect efficiency? An empirical study of East Asian markets

    Directory of Open Access Journals (Sweden)

    Syed Aun R. Rizvi

    2016-03-01

    Full Text Available Much research has been undertaken in the Efficient Market Hypothesis (EMH over the preceding two decades. With Asian countries emerging as a global powerhouse in terms of regional economics, the interest in their stock markets has picked up recently. Asian markets traditionally comprised of many emerging markets are generally assumed to be more volatile and speculative in nature. Based on this crux, we focus specifically on the response of these markets efficiency to major crisis. In recent years, the Asian markets have experienced a phenomenal boom in attracting foreign capital inflow, with Singapore evolving into a global financial hub in terms of banking and financial services. Scepticism and cautious nature raises the question of whether these stock markets are efficient enough for further investment and development. Our study is unique in nature, as we focus on the efficiency of these market in response to crisis periods, comparing it with their pre-crisis period, both in shorter term of 1 year as well as longer term of 5 years post and pre crisis period. Taking Malaysia, Indonesia, Singapore and South Korea owing to their economic and financial development, we use MF-DFA to derive efficiency measure for comparative analysis with its own past. The findings put forth a notion of generally a deteriorating and negative impact of the Asian financial crisis, while the sub-prime crisis impact varies based on the economic structure of the economies. The findings concur with the mainstream literature and similar studies for other countries and region.

  18. Fertilizer residence time affects nitrogen uptake efficiency and growth of sweet corn

    NARCIS (Netherlands)

    Zotarelli, L.; Scholberg, J.M.S.; Dukes, M.D.; Munoz-Carpena, R.

    2008-01-01

    Understanding plant N uptake dynamics is critical for increasing fertilizer N uptake efficiency (FUE) and minimize the risk of N leaching. The objective of this research was to determine the effect of residence time of N fertilizer on N uptake and FUE of sweet corn. Plants were grown in 25 L columns

  19. Cropping history affects nodulation and symbiotic efficiency of distinct hairy vetch genotypes with resident soil rhizobia

    Science.gov (United States)

    Presence of compatible rhizobia strains is essential for nodulation and BNF of hairy vetch (Vicia villosa, HV). We evaluated how past HV cultivation affects nodulation and nitrogen fixation across host genotypes. Five groups of HV genotypes were inoculated with soil dilutions from six paired fields,...

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    were generated that provided the foundation for an efficient recall response and protection upon subsequent viral challenge. Furthermore, the transgene specific response could be efficiently boosted by homologous re-immunization. Taken together, these studies indicate that adenoviral vectors can be...

  1. How decentralization affects efficiency and effectiveness of public expenditures: review of execution of delegated powers

    OpenAIRE

    E. Dobrolyubova

    2013-01-01

    This article reflects some results of the work undertaken by the expert working group on optimization of public expenditures in the area of governance which contributed to the overall efforts on evaluating efficiency of the federal budget expenditures and forming recommendations on the optimization of such expenditures in 2013. This evaluation was conducted jointly by the Russian Academy for National Economy and Public Administration (RANEPA) and National Research University - Higher School o...

  2. Phosphorus uptake efficiency of sorghum and rice genotypes as affected by phosphate sources of varying solubility

    International Nuclear Information System (INIS)

    Greenhouse experiments were carried out to assess the phosphate uptake efficiency (EPa) by the aerial plant parts and associated plant parameters in sorghum (Sorghum bicolor L. Moench) and rice (Oryza sativa) genotypes with differential tolerance to aluminum. The following plant parameters were determined: acid phosphomonoesterase activity (APA), arbuscular mycorrhiza colonized root length (%CRL), soil-pH and rhizosphere-pH and P uptake efficiency. Two Ultisols of low pH and low phosphate availability from the savanna of Venezuela were employed. In a greenhouse experiment five sorghum cultivars, i.e. Chaguaramas III (Ch III), Chaguaramas VII (Ch VII), Dekalb-59 (D-59), Criollo-26 and Ismael were studied. In another experiment four acid tolerant rice cultivars of Oryza sativa (CT-81-1, Fonaiap 2000, Fedearroz y CT-102-1) and one cultivar of Oryza glaberrima susceptible to Al toxicity were compared. P fertilization treatments were: control (0P), Riecito rock phosphate (RRP) and triple superphosphate (TSP). Significant sorghum genotypic differences were found in the parameters evaluated enabling them to grow on the acid soils. Their response was differential depending on the P source and the interaction between source and genotype. The use of the Al-tolerant cultivars Ch III, Ch VII is a potential means to obtain high dry matter production for cattle feeding when pasture supply is low. The cultivars Ch VII, Ch III and Ismael showed higher P-uptake efficiency index (EPa) when fertilized with the local Riecito rock phosphate, thus this PR can be considered to increase soil P status and improve agricultural production in the acid soils of the savannah of Venezuela. Cultivars with higher P uptake efficiency, in particular Ch III and Ch VII (tolerant to Al toxicity) expressed mechanisms such as high % of CRL by arbuscular mycorrhiza and increases in rhizospheric pH whereas cultivars with lower P uptake efficiency such as D-59 (susceptible to Al toxicity) expressed higher

  3. Archaeal DNA replication.

    Science.gov (United States)

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed. PMID:25421597

  4. Magnetic nanowires and hyperthermia: How geometry and material affect heat production efficiency

    KAUST Repository

    Contreras, M. F.

    2015-05-01

    Magnetic hyperthermia, which refers to the production of heat by magnetic nanostructures under an alternating magnetic field (AMF), has been previously investigated with superparamagnetic nanobeads as a cancer therapy method. Magnetic nanowires (NWs) used in hyperthermia can be very promising, as it has been shown that they have a larger magnetic moment per unit of volume compared to the nanobeads. Moreover, Fe NWs proved to have a higher heating efficiency compared to Fe nanobeads, when exposed to an AMF at the same concentration [1].

  5. FACTORS AFFECTING THE EFFICIENCY OF ARTIFICIAL INSEMINATION IN CATTLE AND BUFFALO IN PUNJAB, PAKISTAN

    OpenAIRE

    M. Anzar*, U. Farooq**, M.A. Mirza*, M. Shahab** and N. Ahmad*

    2003-01-01

    The main objective of this study was to identify the factors that affect the success of artificial insemination (A.I) services under field conditions. The data from a total of 459 inseminations were analyzed. The effects of farm, animal, semen/bull and A.I. technician on conception rate were studied. Milk progesterone concentration was used as an indicator of conception. Milk samples were collected from animals at day 0, 11 and 22 post-insemination and analysed for progesterone (P4) concentr...

  6. Agrobacterium-mediated transformation of sorghum: factors that affect transformation efficiency

    Directory of Open Access Journals (Sweden)

    Carlos Henrique S. Carvalho

    2004-01-01

    Full Text Available The results presented in this work support the hypothesis that Agrobacterium-mediated transformation of sorghum is feasible, analogous to what has been demonstrated for other cereals such as rice, maize, barley and wheat. The four factors that we found most influenced transformation were: the sensitivity of immature sorghum embryos to Agrobacterium infection, the growth conditions of the donor plant, type of explant and co-cultivation medium. A major problem during the development of our protocol was a necrotic response which developed in explants after co-cultivation. Immature sorghum embryos proved to be very sensitive to Agrobacterium infection and we found that the level of embryo death after co-cultivation was the limiting step in improving transformation efficiency. The addition of coconut water to the co-cultivation medium, the use of vigorous and actively growing immature embryos and the removal of excess bacteria significantly improved the survival rate of sorghum embryos and was critical for successful transformation. Hygromycin phosphotransferase (hpt proved to be a good selectable marker for sorghum. We also found that b-glucuronidase (GUS activity was low in most of the transgenic plant tissues tested, although it was very high in immature inflorescences. Although promising, the overall transformation efficiency of the protocol is still low and further optimization will require particular attention to be given to the number of Agrobacterium in the inoculum and the selection of sorghum genotypes and explants less sensitive to Agrobacterium infection.

  7. Organic matter and pH affect the analysis efficiency of (31)P-NMR.

    Science.gov (United States)

    Zhang, Wenqiang; Jin, Xin; Rong, Nan; Li, Jie; Shan, Baoqing

    2016-05-01

    Solution (31)P nuclear magnetic resonance spectroscopy ((31)P-NMR) is a useful method to analyze organic phosphorus (Po), but a general procedure for the analysis method is lacking. The authors used solution (31)P-NMR, which was found to be an effective method for analysis of Po in Haihe River sediment, to analyze the Po in the surface sediment in Eastern China at the regional scale, and found that the NaOH-ethylenediaminetetraacetic acid (EDTA) extraction rate was affected by environmental factors. At the regional scale, the extraction rate showed a positive relationship with loss on ignition, when the extraction rate was lower than 60%. The extraction rate had no relationship with the loss on ignition when the extraction rate was higher than 60%. The extraction rate showed a negative relationship with pH, which means that the extraction rate was higher in acidic sediment and lower in alkaline sediment. The ratio of TC/TN (the ratio of total carbon to total nitrogen) was considered to represent the origin of organic matter in the sediment. The extraction rate was high when the TC/TN ratio was lower than 20, meanwhile the extraction rate decreased as the TC/TN ratio increased. The results show that the origin of organic matter in sediment significantly affects the NaOH-EDTA extraction rate. This study will give theoretical support for building an effective and general solution (31)P-NMR analysis method. PMID:27155430

  8. Factors affecting the efficiency of foal production in a commercial oocyte transfer program.

    Science.gov (United States)

    Riera, Fernando L; Roldán, Jaime E; Gomez, José; Hinrichs, Katrin

    2016-04-01

    Transfer of donor oocytes to the oviducts of inseminated recipient mares (oocyte transfer, OT) presents a valuable method for production of foals from otherwise infertile mares. Little information is available, however, on factors affecting success of OT in a clinical setting. We report the findings over three breeding seasons in a commercial OT program developed at an equine embryo transfer center in Argentina. Overall, 25 mares were enrolled, and 197 follicle aspiration procedures were performed. The average mare age was 23 years. Follicle aspiration was performed with a needle placed through the flank; the oocyte recovery rate per follicle aspirated was 149 of 227 (66%). Induction of donor ovulation with deslorelin + hCG resulted in a significantly higher oocyte recovery rate than did induction with deslorelin alone (75% vs. 58%). There was no significant effect of mare age (17-20, 21-24, or 25-27 years) on oocyte recovery rate. Twelve oocytes were degenerating or lost during handling; transfer of the remaining 137 oocytes resulted in 42 pregnancies (31%) at 14 days. Of these, 32 (23% per transfer) went on to produce a foal or ongoing pregnancy. Transfer of oocytes recovered with a compact cumulus, without donor follicle induction, or less than 20 hours after induction was associated with a significantly reduced pregnancy rate (1/16, 6%), as was use of noncycling, hormone-treated recipients (2/22, 9%). To evaluate management factors affecting pregnancy rate, noncycling, hormone-treated recipients were disregarded, and only procedures using mature (expanded cumulus) oocytes recovered and transferred on the standard schedule (n = 99) were included. Mare age did not significantly affect rates of pregnancy or pregnancy loss. Similar pregnancy rates were obtained using recipients inseminated from 1 to 27 hours before transfer. Counterintuitively, insemination of recipients immediately (1-2 hours) after aspiration of the recipient follicle was associated with

  9. Microvesicle formulations used in topical drugs and cosmetics affect product efficiency, performance and allergenicity

    DEFF Research Database (Denmark)

    Madsen, Jakob Torp; Ejner Andersen, Klaus

    2010-01-01

    Attempts to improve the formulations of topical products are continuing processes (ie, to increase cosmetic performance, enhance effects, and protect ingredients from degradation). The development of micro- and nanovesicular systems has led to the marketing of topical drugs and cosmetics that use...... these technologies. Several articles have reported improved clinical efficacy by the encapsulation of pharmaceuticals in vesicular systems, and the numbers of publications and patents are rising. Some vesicular systems may deliver the drug deeper in the skin as compared to conventional vehicles, or even make...... transdermal delivery more efficient for a number of drugs. Vesicular systems may also allow a more precise drug delivery to the site of action (ie, the hair follicles) and thereby minimize the applied drug concentration, reducing potential side effects. On the other hand, this may increase the risk of other...

  10. DNA is a co-factor for its own replication in Xenopus egg extracts

    NARCIS (Netherlands)

    Lebofsky, Ronald; van Oijen, Antoine M.; Walter, Johannes C.

    2011-01-01

    Soluble Xenopus egg extracts efficiently replicate added plasmids using a physiological mechanism, and thus represent a powerful system to understand vertebrate DNA replication. Surprisingly, DNA replication in this system is highly sensitive to plasmid concentration, being undetectable below simila

  11. The chromosomal protein HMGBI inhibits DNA replication in vitro. The role of post-synthetic acetylation

    International Nuclear Information System (INIS)

    The effect of HMGB1 protein on the replication of closed circular plasmid DNA in cell free extract have been studied using parental form of the protein, post-synthetically acetylated HMGB1 and HMGB1 lacking its acidic C-terminal tail. We have shown that HMGB1 protein inhibits DNA replication and that this effect is eliminated upon either acetylation of the protein or removal of the acidic C-terminal domain. An explanation of these findings suggests interactions of HMGB1 with a protein(s) of the replication complex resulting in reduction of its functional efficiency. Acetylation of HMGB1 affects these interactions in a way that restores the initial replication capacity of the system. The eventual protein-protein interactions are supposed to proceed via the C-terminal domain of HMGB1. (authors)

  12. Affordability and other factors affecting the purchase of energy-efficient manufactured homes

    Energy Technology Data Exchange (ETDEWEB)

    Hattrup, M.P.; Lee, A.D.; Sandahl, L.J. [Pacific Northwest Lab., Richland, WA (United States); Onisko, S.A. [USDOE Bonneville Power Administration, Portland, OR (United States)

    1993-06-01

    The Pacific Northwest Laboratory (PNL) and the Bonneville Power Administration (Bonneville) conducted this study to evaluate the manufactured home owner`s purchase decision process and to provide Bonneville with a better understanding of how consumers view a manufactured home`s affordability and energy efficiency. This study addresses manufactured homes built under the US Department of Housing and Urban Development (HUD) standards; these homes are sometimes referred to as HUD-code homes or mobile homes. Manufactured home owners in Idaho, Montana, Oregon, and Washington were included in this analysis. This report adds to the information presented in Sandahl et al. (1992), which discussed the practices of lenders, appraisers, and dealers -- all of whom play a key role in the manufactured home market due to the impact their practices have on the overall affordability of manufactured homes. This report focuses exclusively on the most important, and probably least understood, player -- the home buyer. The primary data were collected via a mail survey sent to 1,550 manufactured home owners in Idaho, Montana, Oregon, and Washington in late 1992. A 71% response rate was achieved; 1,106 usable responses were received. This study focuses on the Pacific Northwest but presents information that may be relevant to other parts of the country.

  13. Transfer from long to short photoperiods affects production efficiency of day-neutral rice

    Science.gov (United States)

    Goldman, K. R.; Mitchell, C. A.

    1999-01-01

    The day-neutral, semidwarf rice (Oryza sativa L.) cultivar Ai-Nan-Tsao was grown in a greenhouse under summer conditions using high-pressure sodium lamps to extend the natural photoperiod. After allowing 2 weeks for germination, stand establishment, and thinning to a consistent planting density of 212 plants/m2, stands were maintained under continuous lighting for 35 or 49 days before shifting to 8- or 12-h photoperiods until harvest 76 days after planting. Non-shifted control treatments consisting of 8-, 12-, or 24-h photoperiods also were maintained throughout production. Tiller number increased as duration of exposure to continuous light increased before shifting to shorter photoperiods. However, shoot harvest index and yield efficiency rate were lower for all plants receiving continuous light than for those under the 8- or 12-h photoperiods. Stands receiving 12-h photoperiods throughout production had the highest grain yield per plant and equaled the 8-h-photoperiod control plants for the lowest tiller number per plant. As long as stands were exposed to continuous light, tiller formation continued. Shifting to shorter photoperiods late in the cropping cycle resulted in newly formed tillers that were either sterile or unable to mature grain before harvest. Late-forming tillers also suppressed yield of grain in early-forming tillers, presumably by competing for photosynthate or for remobilized assimilate during senescence. Stands receiving 12-h photoperiods throughout production not only produced the highest grain yield at harvest but had the highest shoot harvest index, which is important for resource-recovery strategies in advanced life-support systems proposed for space.

  14. Residential energy efficiency retrofits: How program design affects participation and outcomes

    International Nuclear Information System (INIS)

    Better methods of characterizing and addressing heterogeneity in preferences and decision making are needed to stimulate reductions in household greenhouse gas emissions. Four residential energy efficiency programs were delivered consecutively in the Region of Waterloo, Canada, between 1999 and 2011, and each offered a unique combination of information, financial reward structure, and price. A natural quasi-experimental intervention design was employed to assess differences in outcomes across these program structures. Participation at the initial (evaluation by an energy advisor) and follow-up (verification of retrofit) stages, and the material characteristics (e.g., energy performance) were measured and compared between the groups of houses included in each program at each stage. The programs appealed to people with different types of material concerns; each phase of the program was associated with houses with a different mix of material characteristics and depths of recommended and achieved changes. While a performance-based reward attracted fewer houses at each stage than a larger list-based reward, older houses with poorer energy performance were included at each stage. The findings support experimentation with program designs to target sub-populations of housing stock; future program designs should experiment more carefully and with larger performance-based rewards and test parallels with potential carbon market structures. - Highlights: • Multi-program data over 12 years detailing residential energy retrofits. • Natural experimental intervention research design for program evaluation. • Number and attributes of participating households differed by program design. • Financial rewards attracted more participants to the verification stage. • Performance-based incentives have the largest potential for energy savings

  15. SUMO and KSHV Replication

    International Nuclear Information System (INIS)

    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

  16. 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.

  17. The evolution of replicators.

    Science.gov (United States)

    Szathmáry, E

    2000-11-29

    Replicators of interest in chemistry, biology and culture are briefly surveyed from a conceptual point of view. Systems with limited heredity have only a limited evolutionary potential because the number of available types is too low. Chemical cycles, such as the formose reaction, are holistic replicators since replication is not based on the successive addition of modules. Replicator networks consisting of catalytic molecules (such as reflexively autocatalytic sets of proteins, or reproducing lipid vesicles) are hypothetical ensemble replicators, and their functioning rests on attractors of their dynamics. Ensemble replicators suffer from the paradox of specificity: while their abstract feasibility seems to require a high number of molecular types, the harmful effect of side reactions calls for a small system size. No satisfactory solution to this problem is known. Phenotypic replicators do not pass on their genotypes, only some aspects of the phenotype are transmitted. Phenotypic replicators with limited heredity include genetic membranes, prions and simple memetic systems. Memes in human culture are unlimited hereditary, phenotypic replicators, based on language. The typical path of evolution goes from limited to unlimited heredity, and from attractor-based to modular (digital) replicators. PMID:11127914

  18. Job replication on multiserver systems

    OpenAIRE

    Kim, Yusik; Righter, Rhonda; Wolff, Ronald

    2009-01-01

    Parallel processing is a way to use resources efficiently by processing several jobs simultaneously on different servers. In a well-controlled environment where the status of the servers and the jobs are well known, everything is nearly deterministic and replicating jobs on different servers is obviously a waste of resources. However, in a poorly controlled environment where the servers are unreliable and/or their capacity is highly variable, it is desirable to design a system tha...

  19. Does environmental regulation affect energy efficiency in China's thermal power generation? Empirical evidence from a slacks-based DEA model

    International Nuclear Information System (INIS)

    Data envelopment analysis (DEA) has gained much popularity in performance measurement of power industry. This paper presents a slack-based measure approach to investigating the relationship between fossil fuel consumption and the environmental regulation of China's thermal power generation. We first calculate the total-factor energy efficiency without considering environmental constraints. An environmental performance indicator is proposed through decomposing the total-factor energy efficiency. The proposed approach is then employed to examine whether environmental regulation affects the energy efficiency of China's thermal power generation. We find that the environmental efficiency plays a significant role in affecting energy performance of China's thermal generation sector. Decreasing the discharge of major pollutants can improve both energy performance and environmental efficiency. Besides, we also have three main findings: (1) The energy efficiency and environmental efficiency were relatively low. (2) The energy and environmental efficiency scores show great variations among provinces. (3) Both energy efficiency and environmental efficiency are of obvious geographical characteristics. According to our findings, we suggest some policy implications. - Highlights: • We assess the energy efficiency and the environmental efficiency of China's thermal power generation simultaneously. • The energy efficiency and the environmental efficiency were relatively low during 2007–2009. • The energy efficiency and environmental efficiency show obvious geographic characters. • The environmental performance of a DMU plays a decisive role in the energy performance

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

    Science.gov (United States)

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

    2012-01-01

    The replication of the genome is a spatio-temporally highly organized process. Yet, its flexibility throughout development suggests that this process is not genetically regulated. However, the mechanisms and chromatin modifications controlling replication timing are still unclear. We made use of the prominent structure and defined heterochromatic landscape of pericentric regions as an example of late replicating constitutive heterochromatin. We manipulated the major chromatin markers of these regions, namely histone acetylation, DNA and histone methylation, as well as chromatin condensation and determined the effects of these altered chromatin states on replication timing. Here, we show that manipulation of DNA and histone methylation as well as acetylation levels caused large-scale heterochromatin decondensation. Histone demethylation and the concomitant decondensation, however, did not affect replication timing. In contrast, immuno-FISH and time-lapse analyses showed that lowering DNA methylation, as well as increasing histone acetylation, advanced the onset of heterochromatin replication. While dnmt1(-)(/)(-) cells showed increased histone acetylation at chromocenters, histone hyperacetylation did not induce DNA demethylation. Hence, we propose that histone hypoacetylation is required to maintain normal heterochromatin duplication dynamics. We speculate that a high histone acetylation level might increase the firing efficiency of origins and, concomitantly, advances the replication timing of distinct genomic regions. PMID:21908399

  1. Identification and quantification of principal–agent problems affecting energy efficiency investments and use decisions in the trucking industry

    International Nuclear Information System (INIS)

    Energy related Principal–Agent (PA) problems cause inefficient combinations of investment, operating costs, and usage behavior. The complex market structure of the trucking industry contributes to split incentives because entities responsible for investments in energy efficiency do not always pay fuel costs and drivers are often not rewarded for fuel-efficient operation. Some contractual relationships exist in the trucking industry that hinder responses to fuel price signals. Up to 91% of total trucking fuel consumption in the U.S. is affected by “usage” PA problems, where the driver does not pay fuel costs and lacks incentive for fuel saving operation. Approximately 23% of trailers are exposed to an “efficiency problem” when owners of rented trailers do not pay fuel costs and therefore have little incentive to invest in efficiency upgrades such as improved trailer aerodynamics and reduced tire rolling resistance. This study shows that PA problems have the potential to significantly increase fuel consumption through avoided investments, insufficient maintenance, and fuel-wasting practices. Further research into the causes and effects of PA problems can shape policies to promote better alignment of costs and benefits, leading to reduced fuel use and carbon emissions. - Highlights: ► We identify and quantify principal agent market failures in the trucking industry. ► Up to 91% of truck fuel consumption is exposed to a usage principal–agent market failure. ► Twenty-three percent of trailers are exposed to an efficiency principal–agent market failure. ► These market failures at least partially insulate key decision makers from fuel price signals.

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

    Directory of Open Access Journals (Sweden)

    Maria Abildgaard Steffensen

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

  3. Factors that affect the quality and efficiency of artificial insemination in oestrus synchronization programmes in dairy cattle

    International Nuclear Information System (INIS)

    Experiments were performed during a three-year period in order to identify the factors affecting quality and efficiency of artificial insemination (AI) when it is used in cattle subjected to oestrus induction and synchronization (OIS) programmes. The study took place in the Western part of the country and 3 herds with a total of 6357 animals were used. The first study was a survey to evaluate the factors affecting the efficiency of AI in OIS. The second study examined the effects of body condition score (BCS) and three different regimes of OIS on the results of AI. Progesterone levels were measured in blood and milk using radioimmunoassay to determine the incidence of acyclic animals in the herds. Data were recorded and analysed using the artificial insemination database application (AIDA) and further statistical analyses were done using Systat. The results found in the survey showed a low conception rate (18%) and a great variability in the period from calving to conception (154 ± 98.11 days). The latter parameter was significantly different between herds (P<0.001). A high percentage of animals selected for OIS programmes (37%) showed a poor BCS (<2.5 on a scale of 1-5). Motility of semen used for AI was low (<30%) in 47% of the samples evaluated. The results from progesterone measurements demonstrated that the reasons for poor fertility were low accuracy in oestrus detection, poor response to treatment for OIS, non-fertilization, embryo mortality and functional disturbances present after treatment. Under our field conditions during the dry season, acyclicity (anoestrus) is a frequent problem in primiparous cows and in those with poor BCS. The BCS in heifers and the quality of different treatments had a significant effect on the conception rate. These results confirm that the use of progesterone measurement together with data management using AIDA is a very appropriate way to evaluate and improve the quality and efficiency of AI in OIS programmes. (author)

  4. Feeding guild of non-host community members affects host-foraging efficiency of a parasitic wasp.

    Science.gov (United States)

    De Rijk, Marjolein; Yang, Daowei; Engel, Bas; Dicke, Marcel; Poelman, Erik H

    2016-06-01

    Interactions between predator and prey, or parasitoid and host, are shaped by trait- and density-mediated processes involving other community members. Parasitoids that lay their eggs in herbivorous insects locate their hosts through infochemicals such as herbivore-induced plant volatiles (HIPVs) and host-produced kairomones. Hosts are frequently accompanied by non-host herbivores that are unsuitable for the parasitoid. These non-hosts may interfere with host location primarily through trait-mediated processes, by their own infochemicals, and their induction of the emission of plant volatiles. Although it is known that single non-hosts can interfere with parasitoid host location, it is still unknown whether the observed effects are due to species specific characteristics or to the feeding habits of the non-host herbivores. Here we addressed whether the feeding guild of non-host herbivores differentially affects foraging of the parasitoid Cotesia glomerata for its common host, caterpillars of Pieris brassicae feeding on Brassica oleracea plants. We used different phloem-feeding and leaf-chewing non-hosts to study their effects on host location by the parasitoid when searching for host-infested plants based on HIPVs and when searching for hosts on the plant using infochemicals. To evaluate the ultimate effect of these two phases in host location, we studied parasitism efficiency of parasitoids in small plant communities under field-tent conditions. We show that leaf-chewing non-hosts primarily affected host location through trait-mediated effects via plant volatiles, whereas phloem-feeding non-hosts exerted trait-mediated effects by affecting foraging efficiency of the parasitoid on the plant. These trait-mediated effects resulted in associational susceptibility of hosts in environments with phloem feeders and associational resistance in environments with non-host leaf chewers. PMID:27459770

  5. DNA Replication Origins

    OpenAIRE

    Leonard, Alan C.; Méchali, Marcel

    2013-01-01

    The onset of genomic DNA synthesis requires precise interactions of specialized initiator proteins with DNA at sites where the replication machinery can be loaded. These sites, defined as replication origins, are found at a few unique locations in all of the prokaryotic chromosomes examined so far. However, replication origins are dispersed among tens of thousands of loci in metazoan chromosomes, thereby raising questions regarding the role of specific nucleotide sequences and chromatin envir...

  6. MOLECULAR REPLICATOR DYNAMICS

    OpenAIRE

    BÄRBEL M. R. STADLER; Stadler, Peter F

    2003-01-01

    Template-dependent replication at the molecular level is the basis of reproduction in nature. A detailed understanding of the peculiarities of the chemical reaction kinetics associated with replication processes is therefore an indispensible prerequisite for any understanding of evolution at the molecular level. Networks of interacting self-replicating species can give rise to a wealth of different dynamical phenomena, from competitive exclusion to permanent coexistence, from global stability...

  7. RNA interference-mediated inhibition of Hepatitis B Virus replication

    Institute of Scientific and Technical Information of China (English)

    TANG Ni; ZHANG Bingqiang; YAN Ge; PU Dan; GAO Xiaolin; Tong-Chuan He; HUANG Ailong

    2004-01-01

    Persistent and recurrent infection of hepatitis B virus (HBV) represents one of the most common and severe viral infections of humans, and has caused a formidable health problem in the affected countries. Currently used antiviral drugs have a very limited success on controlling HBV replication and infection. RNA interference (RNAi), a process by which double-stranded RNA (dsRNA) directs sequence-specific degradation of target mRNA in mammalian and plant cells, has recently been used to knockdown gene expression in various species. In this study, we sought to determine whether RNAi-mediated silencing of HBV viral gene expression could lead to the effective inhibition of HBV replication. We first developed RNAi vectors that expressed small interfering RNA (siRNA) and targeted the HBV core or surface gene sequence. Our results demonstrated that these specific siRNAs efficiently reduced the levels of corresponding viral RNAs and proteins, and thus suppressed viral replication. Treatment with siRNA gave the greatest reduction in the levels of HBsAg (92%) and in HBeAg (85%) respectively in the cultured cell medium. Our findings further demonstrated that the RNAi-mediated antiviral effect was sequence-specific and dose-dependent. Therefore, our findings strongly suggest that RNAi-mediated silencing of HBV viral genes could effectively inhibit the replication of HBV, hence RNAi-based strategy should be further explored as a more efficacious antiviral therapy of HBV infection.

  8. Self-replicating systems.

    Science.gov (United States)

    Clixby, Gregory; Twyman, Lance

    2016-05-01

    Over the past 25 years, there has been a surge of development in research towards self-replication and self-replicating systems. The interest in these systems relates to one of the most fundamental questions posed in all fields of science - How did life on earth begin? Investigating how the self-replication process evolved may hold the key to understanding the emergence and evolution of living systems and, ultimately, gain a clear insight into the origin of life on earth. This introductory review aims to highlight the fundamental prerequisites of self-replication along with the important research that has been conducted over the past few decades. PMID:27086507

  9. The South Pacific epidemic strain of Zika virus replicates efficiently in human epithelial A549 cells leading to IFN-β production and apoptosis induction.

    Science.gov (United States)

    Frumence, Etienne; Roche, Marjolaine; Krejbich-Trotot, Pascale; El-Kalamouni, Chaker; Nativel, Brice; Rondeau, Philippe; Missé, Dorothée; Gadea, Gilles; Viranaicken, Wildriss; Desprès, Philippe

    2016-06-01

    Zika virus (ZIKV) is an emerging flavivirus since the first epidemics in South Pacific in 2007. The recent finding that ZIKV is now circulating in Western Hemisphere and can be associated to severe human diseases, warrants the need for its study. Here we evaluate the susceptibility of human lung epithelial A549 cells to South Pacific epidemic strain of ZIKV isolated in 2013. We showed that ZIKV growth in A549 cells is greatly efficient. ZIKV infection resulted in the secretion of IFN-β followed by the expression of pro-inflammatory cytokines such as IL-1β, and transcriptional activity of IFIT genes. At the maximum of virus progeny production, ZIKV triggers mitochondrial apoptosis through activation of caspases-3 and -9. Whereas at early infection times, the rapid release of IFN-β which exerts an antiviral effect against ZIKV might delay apoptosis in infected cells. PMID:27060565

  10. 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.

  11. Completion of DNA replication in Escherichia coli

    Science.gov (United States)

    Wendel, Brian M.; Courcelle, Charmain T.; Courcelle, Justin

    2014-01-01

    The mechanism by which cells recognize and complete replicated regions at their precise doubling point must be remarkably efficient, occurring thousands of times per cell division along the chromosomes of humans. However, this process remains poorly understood. Here we show that, in Escherichia coli, the completion of replication involves an enzymatic system that effectively counts pairs and limits cellular replication to its doubling point by allowing converging replication forks to transiently continue through the doubling point before the excess, over-replicated regions are incised, resected, and joined. Completion requires RecBCD and involves several proteins associated with repairing double-strand breaks including, ExoI, SbcDC, and RecG. However, unlike double-strand break repair, completion occurs independently of homologous recombination and RecA. In some bacterial viruses, the completion mechanism is specifically targeted for inactivation to allow over-replication to occur during lytic replication. The results suggest that a primary cause of genomic instabilities in many double-strand-break-repair mutants arises from an impaired ability to complete replication, independent from DNA damage. PMID:25368150

  12. Task-partitioning in insect societies: Non-random direct material transfers affect both colony efficiency and information flow.

    Science.gov (United States)

    Grüter, Christoph; Schürch, Roger; Farina, Walter M

    2013-06-21

    Task-partitioning is an important organisational principle in insect colonies and is thought to increase colony efficiency. In task-partitioning, tasks such as the collection of resources are divided into subtasks in which the material is passed from one worker to another. Previous models have assumed that worker-worker interactions are random, but experimental evidence suggests that receivers can have preferences to handle familiar materials. We used an agent-based simulation model to explore how non-random interactions during task-partitioning with direct transfer affect colony work efficiency. Because task-partitioning also allows receivers and donors to acquire foraging related information we analysed the effect of non-random interactions on informative interaction patterns. When receivers non-randomly rejected donors offering certain materials, donors overall experienced increased time delays, hive stay durations and a decreased number of transfer partners. However, the number of transfers was slightly increased, which can improve the acquisition and quality of information for donors. When receivers were non-randomly attracted to donors offering certain materials, donors experienced reduced transfer delays, hive stay durations and an increased number of simultaneous receivers. The number of transfers is slightly decreased. The effects of the two mechanisms "non-random rejection" and "non-random attraction" are biggest if the number of foragers and receivers is balanced. In summary, our results show that colony ergonomics are improved if receivers do not reject donors and if mechanisms exist that help receivers detect potential donors, such as learning the odour of the transferred food. Finally, our simulations suggest that non-random interactions can potentially affect the foraging patterns of colonies in changing environments. PMID:23454081

  13. FACTORS AFFECTING THE EFFICIENCY OF BUSINESS WITH INNOVATIVE TOOLS OF INTERCOMPANY AND STRATEGIC PLANNING AT INDUSTRIAL COMPANIES

    Directory of Open Access Journals (Sweden)

    Shchepakin M. B.

    2015-03-01

    Full Text Available Innovative tools of intercompany and strategic planning are designed to form interconnected tasks structural units of industrial enterprises and complexes in the sought after amount based on the cost of production of interdependent. Intercompany planning has no tools based on chain planning with cyclic calculations. Allocation of factors affecting business performance is a mandatory procedure in the development of innovative tools and intercompany strategic planning in industrial plants and complexes. Factors determining the efficiency of intercompany and strategic planning at industrial enterprises and complexes require detailed classification. The article examines the factors that determine the effectiveness of intercompany and strategic planning. The classification of factors, that are offered, which can form a conceptual framework of business development strategy for a long period of time, based on the use of interrelated production plans for the following criteria: conceptual, stabilization and functional. The developed classification of factors, which determines the efficiency of intercompany and strategic planning, allows us to: generate the concept of strategic business development; establish the optimum parameters of the structure and volume of internal and external supply, to determine the required size of lending and investment; achieve stabilization of interests of the economy and the level of investment attractiveness of the business, etc. Based on it, becomes possible to develop a methodology and logical approach to the formation of innovative tools intercompany and strategic planning at industrial enterprises (complexes

  14. Prioritization of the Factors Affecting Bank Efficiency Using Combined Data Envelopment Analysis and Analytical Hierarchy Process Methods

    Directory of Open Access Journals (Sweden)

    Mehdi Fallah Jelodar

    2016-01-01

    Full Text Available Bank branches have a vital role in the economy of all countries. They collect assets from various sources and put them in the hand of those sectors that need liquidity. Due to the limited financial and human resources and capitals and also because of the unlimited and new customers’ needs and strong competition between banks and financial and credit institutions, the purpose of this study is to provide an answer to the question of which of the factors affecting performance, creating value, and increasing shareholder dividends are superior to others and consequently managers should pay more attention to them. Therefore, in this study, the factors affecting performance (efficiency in the areas of management, personnel, finance, and customers were segmented and obtained results were ranked using both methods of Data Envelopment Analysis and hierarchical analysis. In both of these methods, the leadership style in the area of management; the recruitment and resource allocation in the area of financing; the employees’ satisfaction, dignity, and self-actualization in the area of employees; and meeting the new needs of customers got more weights.

  15. Plant water use efficiency over geological time--evolution of leaf stomata configurations affecting plant gas exchange.

    Directory of Open Access Journals (Sweden)

    Shmuel Assouline

    Full Text Available Plant gas exchange is a key process shaping global hydrological and carbon cycles and is often characterized by plant water use efficiency (WUE - the ratio of CO2 gain to water vapor loss. Plant fossil record suggests that plant adaptation to changing atmospheric CO2 involved correlated evolution of stomata density (d and size (s, and related maximal aperture, amax . We interpreted the fossil record of s and d correlated evolution during the Phanerozoic to quantify impacts on gas conductance affecting plant transpiration, E, and CO2 uptake, A, independently, and consequently, on plant WUE. A shift in stomata configuration from large s-low d to small s-high d in response to decreasing atmospheric CO2 resulted in large changes in plant gas exchange characteristics. The relationships between gas conductance, gws , A and E and maximal relative transpiring leaf area, (amax ⋅d, exhibited hysteretic-like behavior. The new WUE trend derived from independent estimates of A and E differs from established WUE-CO2 trends for atmospheric CO2 concentrations exceeding 1,200 ppm. In contrast with a nearly-linear decrease in WUE with decreasing CO2 obtained by standard methods, the newly estimated WUE trend exhibits remarkably stable values for an extended geologic period during which atmospheric CO2 dropped from 3,500 to 1,200 ppm. Pending additional tests, the findings may affect projected impacts of increased atmospheric CO2 on components of the global hydrological cycle.

  16. Access Factors Affecting Supply Chain Efficiency of Medical Supplies in public Health Centres in kenya: A Case Study of Public Health Centres in Elgeyo Marakwet Count

    OpenAIRE

    Mark Kemboi Kanda; Mike Amuhaya Iravo

    2015-01-01

    The purpose of this study was to determine factors affecting efficiency of supply chain of pharmaceutical products (drugs) to Public Health facilities in 47 Counties of Kenya. The study precisely sought to establish whether: procurement processes, ICT infrastructure, distribution channels and competency of medical staff in supply chain, are factors affecting efficiency of supply chain of pharmaceutical products to Health Centres in Kenya. A population size of 120 employees was targeted in 15 ...

  17. Mutations of amino acids in the DNA-recognition domain of Epstein-Barr virus ZEBRA protein alter its sub-nuclear localization and affect formation of replication compartments

    International Nuclear Information System (INIS)

    ZEBRA, a transcription factor and DNA replication protein encoded by the Epstein-Barr virus (EBV) BZLF1 gene, plays indispensable roles in the EBV lytic cycle. We recently described the phenotypes of 46 single amino acid substitutions introduced into the DNA-recognition region of ZEBRA [Heston, L., El-Guindy, A., Countryman, J., Dela Cruz, C., Delecluse, H.J., and Miller, G. 2006]. The 27 DNA-binding-proficient mutants exhibited distinct defects in their ability to activate expression of the kinetic classes of viral genes. Four phenotypic variants could be discerned: wild-type, defective at activating Rta, defective at activating early genes, and defective at activating late genes. Here we analyze the distribution of ZEBRA within the nucleus and the localization of EA-D (the viral DNA polymerase processivity factor), an indicator of the development of replication compartments, in representatives of each phenotypic group. Plasmids encoding wild-type (WT) and mutant ZEBRA were transfected into 293 cells containing EBV-bacmids. WT ZEBRA protein was diffusely and smoothly distributed throughout the nucleus, sparing nucleoli, and partially recruited to globular replication compartments. EA-D induced by WT ZEBRA was present diffusely in some cells and concentrated in globular replication compartments in other cells. The distribution of ZEBRA and EA-D proteins was identical to WT following transfection of K188R, a mutant with a conservative change. The distribution of S186A mutant ZEBRA protein, defective for activation of Rta and EA-D, was identical to WT, except that the mutant ZEBRA was never found in globular compartments. Co-expression of Rta with S186A mutant rescued diffuse EA-D but not globular replication compartments. The most striking observation was that several mutant ZEBRA proteins defective in activating EA-D (R179A, K181A and A185V) and defective in activating lytic viral DNA replication and late genes (Y180E and K188A) were localized to numerous punctate

  18. Transcription regulatory elements are punctuation marks for DNA replication.

    Science.gov (United States)

    Mirkin, Ekaterina V; Castro Roa, Daniel; Nudler, Evgeny; Mirkin, Sergei M

    2006-05-01

    Collisions between DNA replication and transcription significantly affect genome organization, regulation, and stability. Previous studies have described collisions between replication forks and elongating RNA polymerases. Although replication collisions with the transcription-initiation or -termination complexes are potentially even more important because most genes are not actively transcribed during DNA replication, their existence and mechanisms remained unproven. To address this matter, we have designed a bacterial promoter that binds RNA polymerase and maintains it in the initiating mode by precluding the transition into the elongation mode. By using electrophoretic analysis of replication intermediates, we have found that this steadfast transcription-initiation complex inhibits replication fork progression in an orientation-dependent manner during head-on collisions. Transcription terminators also appeared to attenuate DNA replication, but in the opposite, codirectional orientation. Thus, transcription regulatory signals may serve as "punctuation marks" for DNA replication in vivo. PMID:16670199

  19. Persistent HIV-1 replication during antiretroviral therapy

    Science.gov (United States)

    Martinez-Picado, Javier; Deeks, Steven G.

    2016-01-01

    Purpose of review The present review will highlight some of the recent findings regarding the capacity of HIV-1 to replicate during antiretroviral therapy (ART). Recent findings Although ART is highly effective at inhibiting HIV replication, it is not curative. Several mechanisms contribute to HIV persistence during ART, including HIV latency, immune dysfunction, and perhaps persistent low-level spread of the virus to uninfected cells (replication). The success in curing HIV will depend on efficiently targeting these three aspects. The degree to which HIV replicates during ART remains controversial. Most studies have failed to find any evidence of HIV evolution in blood, even with samples collected over many years, although a recent very intensive study of three individuals suggested that the virus population does shift, at least during the first few months of therapy. Stronger but still not definitive evidence for replication comes from a series of studies in which standard regimens were intensified with an integration inhibitor, resulting in changes in episomal DNA (blood) and cell-associated RNA (tissue). Limited drug penetration within tissues and the presence of immune sanctuaries have been argued as potential mechanisms allowing HIV to spread during ART. Mathematical models suggest that HIV replication and evolution is possible even without the selection of fully drug-resistant variants. As persistent HIV replication could have clinical consequences and might limit the efficacy of curative interventions, determining if HIV replicates during ART and why, should remain a key focus of the HIV research community. Summary Residual viral replication likely persists in lymphoid tissues, at least in a subset of individuals. Abnormal levels of immune activation might contribute to sustain virus replication. PMID:27078619

  20. 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

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

    OpenAIRE

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

    2009-01-01

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

  2. p53 represses human papillomavirus type 16 DNA replication via the viral E2 protein

    Directory of Open Access Journals (Sweden)

    Morgan Iain M

    2008-01-01

    Full Text Available Abstract Background Human papillomavirus (HPV DNA replication can be inhibited by the cellular tumour suppressor protein p53. However, the mechanism through which p53 inhibits viral replication and the role that this might play in the HPV life cycle are not known. The papillomavirus E2 protein is required for efficient HPV DNA replication and also regulates viral gene expression. E2 represses transcription of the HPV E6 and E7 oncogenes and can thereby modulate indirectly host cell proliferation and survival. In addition, the E2 protein from HPV 16 has been shown to bind p53 and to be capable of inducing apoptosis independently of E6 and E7. Results Here we use a panel of E2 mutants to confirm that mutations which block the induction of apoptosis via this E6/E7-independent pathway, have little or no effect on the induction of apoptosis by the E6/E7-dependent pathway. Although these mutations in E2 do not affect the ability of the protein to mediate HPV DNA replication, they do abrogate the repressive effects of p53 on the transcriptional activity of E2 and prevent the inhibition of E2-dependent HPV DNA replication by p53. Conclusion These data suggest that p53 down-regulates HPV 16 DNA replication via the E2 protein.

  3. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

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

  4. Atmospheric CO2 level affects plants' carbon use efficiency: insights from a 13C labeling experiment on sunflower stands

    Science.gov (United States)

    Gong, Xiaoying; Schäufele, Rudi; Schnyder, Hans

    2015-04-01

    The increase of atmospheric CO2 concentration has been shown to stimulate plant photosynthesis and (to a lesser extent) growth, thereby acting as a possible sink for the additional atmospheric CO2. However, this effect is dependent on the efficiency with which plants convert atmospheric carbon into biomass carbon, since a considerable proportion of assimilated carbon is returned to the atmosphere via plant respiration. As a core parameter for carbon cycling, carbon use efficiency of plants (CUE, the ratio of net primary production to gross primary production) quantifies the proportion of assimilated carbon that is incorporated into plant biomass. CUE has rarely been assessed based on measurements of complete carbon balance, due to methodological difficulties in measuring respiration rate of plants in light. Moreover, foliar respiration is known to be inhibited in light, thus foliar respiration rate is generally lower in light than in dark. However, this phenomenon, termed as inhibition of respiration in light (IRL), has rarely been assessed at the stand-scale and been incorporated into the calculation of CUE. Therefore, how CUE responses to atmospheric CO2 levels is still not clear. We studied CUE of sunflower stands grown at sub-ambient CO2 level (200 μmol mol-1) and elevated CO2 level (1000 μmol mol-1) using mesocosm-scale gas exchange facilities which enabled continuous measurements of 13CO2/12CO2 exchange. Appling steady-state 13C labeling, fluxes of respiration and photosynthesis in light were separated, and tracer kinetic in respiration was analyzed. This study provides the first data on CUE at a mesocosm-level including respiration in light in different CO2 environments. We found that CUE of sunflower was lower at an elevated CO2 level than at a sub-ambient CO2 level; and the ignorance of IRL lead to erroneous estimations of CUE. Variation in CUE at atmospheric CO2 levels was attributed to several mechanisms. In this study, CO2 enrichment i) affected the

  5. Human, donkey and cow milk differently affects energy efficiency and inflammatory state by modulating mitochondrial function and gut microbiota.

    Science.gov (United States)

    Trinchese, Giovanna; Cavaliere, Gina; Canani, Roberto Berni; Matamoros, Sebastien; Bergamo, Paolo; De Filippo, Chiara; Aceto, Serena; Gaita, Marcello; Cerino, Pellegrino; Negri, Rossella; Greco, Luigi; Cani, Patrice D; Mollica, Maria Pina

    2015-11-01

    Different nutritional components are able, by modulating mitochondrial function and gut microbiota composition, to influence body composition, metabolic homeostasis and inflammatory state. In this study, we aimed to evaluate the effects produced by the supplementation of different milks on energy balance, inflammatory state, oxidative stress and antioxidant/detoxifying enzyme activities and to investigate the role of the mitochondrial efficiency and the gut microbiota in the regulation of metabolic functions in an animal model. We compared the intake of human milk, gold standard for infant nutrition, with equicaloric supplementation of donkey milk, the best substitute for newborns due to its nutritional properties, and cow milk, the primary marketed product. The results showed a hypolipidemic effect produced by donkey and human milk intake in parallel with enhanced mitochondrial activity/proton leakage. Reduced mitochondrial energy efficiency and proinflammatory signals (tumor necrosis factor α, interleukin-1 and lipopolysaccharide levels) were associated with a significant increase of antioxidants (total thiols) and detoxifying enzyme activities (glutathione-S-transferase, NADH quinone oxidoreductase) in donkey- and human milk-treated animals. The beneficial effects were attributable, at least in part, to the activation of the nuclear factor erythroid-2-related factor-2 pathway. Moreover, the metabolic benefits induced by human and donkey milk may be related to the modulation of gut microbiota. In fact, milk treatments uniquely affected the proportions of bacterial phyla and genera, and we hypothesized that the increased concentration of fecal butyrate in human and donkey milk-treated rats was related to the improved lipid and glucose metabolism and detoxifying activities. PMID:26118693

  6. Dynamic replication of Web contents

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The phenomenal growth of the World Wide Web has brought huge increase in the traffic to the popular web sites.Long delays and denial of service experienced by the end-users,especially during the peak hours,continues to be the common problem while accessing popular sites.Replicating some of the objects at multiple sites in a distributed web-server environment is one of the possible solutions to improve the response time/Iatency. The decision of what and where to replicate requires solving a constraint optimization problem,which is NP-complete in general.In this paper, we consider the problem of placing copies of objects in a distributed web server system to minimize the cost of serving read and write requests when the web servers have Iimited storage capacity.We formulate the problem as a 0-1 optimization problem and present a polynomial time greedy algorithm with backtracking to dynamically replicate objects at the appropriate sites to minimize a cost function.To reduce the solution search space,we present necessary condi tions for a site to have a replica of an object jn order to minimize the cost function We present simulation resuIts for a variety of problems to illustrate the accuracy and efficiency of the proposed algorithms and compare them with those of some well-known algorithms.The simulation resuIts demonstrate the superiority of the proposed algorithms.

  7. The affect of erbium hydride on the conversion efficience to accelerated protons from ultra-shsort pulse laser irradiated foils

    Energy Technology Data Exchange (ETDEWEB)

    Offermann, Dustin Theodore [The Ohio State Univ., Columbus, OH (United States)

    2008-01-01

    This thesis work explores, experimentally, the potential gains in the conversion efficiency from ultra-intense laser light to proton beams using erbium hydride coatings. For years, it has been known that contaminants at the rear surface of an ultra-intense laser irradiated thin foil will be accelerated to multi-MeV. Inertial Confinement Fusion fast ignition using proton beams as the igniter source requires of about 1016 protons with an average energy of about 3MeV. This is far more than the 1012 protons available in the contaminant layer. Target designs must include some form of a hydrogen rich coating that can be made thick enough to support the beam requirements of fast ignition. Work with computer simulations of thin foils suggest the atomic mass of the non-hydrogen atoms in the surface layer has a strong affect on the conversion efficiency to protons. For example, the 167amu erbium atoms will take less energy away from the proton beam than a coating using carbon with a mass of 12amu. A pure hydrogen coating would be ideal, but technologically is not feasible at this time. In the experiments performed for my thesis, ErH3 coatings on 5 μm gold foils are compared with typical contaminants which are approximately equivalent to CH1.7. It will be shown that there was a factor of 1.25 ± 0.19 improvement in the conversion efficiency for protons above 3MeV using erbium hydride using the Callisto laser. Callisto is a 10J per pulse, 800nm wavelength laser with a pulse duration of 200fs and can be focused to a peak intensity of about 5 x 1019W/cm2. The total number of protons from either target type was on the order of 1010. Furthermore, the same experiment was performed on the Titan laser, which has a 500fs pulse duration, 150J of energy and can be focused to about 3 x 1020 W/cm2. In this experiment 1012 protons were seen from both erbium hydride and

  8. 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.

  9. Surface microstructure replication in injection molding

    DEFF Research Database (Denmark)

    Theilade, Uffe Arlø; Hansen, Hans Nørgaard

    2006-01-01

    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 molding has proven to be a feasible and efficient way to manufacture such components. In injection molding, the mold surface...... the ability to replicate surface microstructures under normal injection-molding conditions, i.e., with commodity materials within typical process windows. It was found that within typical process windows the replication quality depends significantly on several process parameters, and especially the...... 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...

  10. 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.

  11. Hepatitis B virus replication

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Hepadnaviruses, including human hepatitis B virus (HBV), replicate through reverse transcription of an RNA intermediate, the pregenomic RNA (pgRNA). Despite this kinship to retroviruses, there are fundamental differences beyond the fact that hepadnavirions contain DNA instead of RNA. Most peculiar is the initiation of reverse transcription: it occurs by protein-priming, is strictly committed to using an RNA hairpin on the pgRNA,ε, as template, and depends on cellular chaperones;moreover, proper replication can apparently occur only in the specialized environment of intact nucleocapsids.This complexity has hampered an in-depth mechanistic understanding. The recent successful reconstitution in the test tube of active replication initiation complexes from purified components, for duck HBV (DHBV),now allows for the analysis of the biochemistry of hepadnaviral replication at the molecular level. Here we review the current state of knowledge at all steps of the hepadnaviral genome replication cycle, with emphasis on new insights that turned up by the use of such cellfree systems. At this time, they can, unfortunately,not be complemented by three-dimensional structural information on the involved components. However, at least for the s RNA element such information is emerging,raising expectations that combining biophysics with biochemistry and genetics will soon provide a powerful integrated approach for solving the many outstanding questions. The ultimate, though most challenging goal,will be to visualize the hepadnaviral reverse transcriptase in the act of synthesizing DNA, which will also have strong implications for drug development.

  12. Psychology, replication & beyond.

    Science.gov (United States)

    Laws, Keith R

    2016-01-01

    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. PMID:27251381

  13. Conditionally replicating HIV and SIV variants.

    Science.gov (United States)

    Das, Atze T; Berkhout, Ben

    2016-05-01

    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 by the doxycycline (dox)-inducible Tet-On gene expression mechanism. These HIV-rtTA and SIV-rtTA variants are fully replication-competent, but replication is critically dependent on dox administration. We here describe how the dox-dependent virus variants may improve the safety of live-attenuated virus vaccines and how they can be used to study the immune responses that correlate with vaccine-induced protection. Furthermore, we review how these variants were initially designed and subsequently optimized by spontaneous viral evolution. These efforts yielded efficiently replicating and tightly dox-controlled HIV-rtTA and SIV-rtTA variants that replicate in a variety of cell and tissue culture systems, and in human immune system (HIS) mice and macaques, respectively. These viruses can be used as a tool in HIV and SIV biology studies and in vaccine research. We review how HIV-rtTA and SIV-rtTA were used to study the role of the viral TAR and Tat elements in virus replication. PMID:25982510

  14. A four-phase data replication algorithm for data grid

    OpenAIRE

    Alireza Saleh; Reza Javidan; Mohammad Taghi FatehiKhajeh

    2015-01-01

    Nowadays, scientific applications generate a huge amount of data in terabytes or petabytes. Data grids currently proposed solutions to large scale data management problems including efficient file transfer and replication. Data is typically replicated in a Data Grid to improve the job response time and data availability. A reasonable number and right locations for replicas has become a challenge in the Data Grid. In this paper, a four-phase dynamic data replication algorithm based on Temporal...

  15. Polyomavirus origin for DNA replication comprises multiple genetic elements.

    OpenAIRE

    Muller, W J; Mueller, C R; Mes, A M; Hassell, J A

    1983-01-01

    To define the minimal cis-acting sequences required for polyomavirus DNA replication (ori), we constructed a number of polyomavirus-plasmid recombinants and measured their replicative capacity after transfection of a permissive mouse cell line capable of providing polyomavirus large T antigen in trans (MOP cells). Recombinant plasmids containing a 251-base-pair fragment of noncoding viral DNA replicate efficiently in MOP cells. Mutational analyses of these viral sequences revealed that they c...

  16. Dietary energy sources affect the partition of body lipids and the hierarchy of energy metabolic pathways in growing pigs differing in feed efficiency

    OpenAIRE

    Gondret, Florence; Louveau, Isabelle; Mourot, Jacques; Duclos, Michel; Lagarrigue, Sandrine; Gilbert, Hélène; Van Milgen, Jacob

    2014-01-01

    The use and partition of feed energy are key elements in productive efficiency of pigs. This study aimed to determine whether dietary energy sources affect the partition of body lipids and tissue biochemical pathways of energy use between pigs differing in feed efficiency. Forty-eight barrows (pure Large White) from two divergent lines selected for residual feed intake (RFI), a measure of feed efficiency, were compared. From 74 d to 132 ± 0.5 d of age, pigs (n = 12 by line and by diet) were o...

  17. Optimal Allocation of Replicates for Measurement Evaluation Studies

    Institute of Scientific and Technical Information of China (English)

    Stanislav O.Zakharkin; Kyoungmi Kim; Alfred A.Bartolucci; Grier P.Page; David B.Allison

    2006-01-01

    Optimal experimental design is important for the efficient use of modern highthroughput technologies such as microarrays and proteomics. Multiple factors including the reliability of measurement system, which itself must be estimated from prior experimental work, could influence design decisions. In this study, we describe how the optimal number of replicate measures (technical replicates) for each biological sample (biological replicate) can be determined. Different allocations of biological and technical replicates were evaluated by minimizing the variance of the ratio of technical variance (measurement error) to the total variance (sum of sampling error and measurement error). We demonstrate that if the number of biological replicates and the number of technical replicates per biological sample are variable, while the total number of available measures is fixed, then the optimal allocation of replicates for measurement evaluation experiments requires two technical replicates for each biological replicate. Therefore, it is recommended to use two technical replicates for each biological replicate if the goal is to evaluate the reproducibility of measurements.

  18. In vitro replication capacity of HIV-2 variants from long-term aviremic individuals

    OpenAIRE

    Blaak, Hetty; Ende, Marchina; Boers, Patrick; Schuitemaker, H; Osterhaus, Albert

    2006-01-01

    textabstractTo establish whether efficient suppression of virus replication in HIV-2-infected individuals is associated with low replicative capacity of HIV-2, replication kinetics of HIV-2 variants from long-term aviremic individuals was analyzed and compared with that of the relatively slow-replicating HIV-1 variants from asymptomatics and long-term nonprogressors (AS/LTNP). On average, HIV-2 from aviremic individuals had lower replication rates than HIV-1 variants from AS/LTNP in cells of ...

  19. Rif1 Regulates Initiation Timing of Late Replication Origins throughout the S. cerevisiae Genome

    OpenAIRE

    Peace, Jared M.; Ter-Zakarian, Anna; Aparicio, Oscar M.

    2014-01-01

    Chromosomal DNA replication involves the coordinated activity of hundreds to thousands of replication origins. Individual replication origins are subject to epigenetic regulation of their activity during S-phase, resulting in differential efficiencies and timings of replication initiation during S-phase. This regulation is thought to involve chromatin structure and organization into timing domains with differential ability to recruit limiting replication factors. Rif1 has recently been identi...

  20. Factors affecting efficiency of four-eye sleeper poly-culture in Nghia Hung district, Nam Dinh province, Vietnam : a DEA approach to technical efficiency

    OpenAIRE

    Van Nguyen, Quang

    2010-01-01

    This research estimated the technical, scale efficiency and its determinants of four-eye sleeper (Bostrichthys sinensis Lacépède, 1801) poly-culture in Nghia Hung district, Nam Dinh province, Vietnam. A nonparametric DEA approach were applied to evaluate technical and scale efficiency of farm level using input orientation DEA model. The study was based on the cross sectional primary data collected from 70 four-eye sleeper poly-culture households in Nghia Hung district, Nam Dinh, in 2009. The ...

  1. Commentary on "Finance, Management, and Costs of Public and Private Schools in Indonesia" and "Do Local Contributions Affect the Efficiency of Public Primary Schools?"

    Science.gov (United States)

    Berger, Mark C.

    1996-01-01

    Studies on Indonesia and the Philippines in this special issue examine how local financial control affects costs of providing primary schooling. In both countries, schools with greater financial decentralization operated more efficiently. These results have important implications for U.S. schools, where decentralization reforms in Kentucky and…

  2. 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...

  3. 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.

  4. Deletions within the 3' Non-Translated Region of Alfalfa mosaic virus RNA4 Do Not Affect Replication but Significantly Reduce Long-Distance Movement of Chimeric Tobacco mosaic virus

    Directory of Open Access Journals (Sweden)

    Vidadi Yusibov

    2013-07-01

    Full Text Available Alfalfa mosaic virus (AlMV RNAs 1 and 2 with deletions in their 3' non‑translated regions (NTRs have been previously shown to be encapsidated into virions by coat protein (CP expressed from RNA3, indicating that the 3' NTRs of RNAs 1 and 2 are not required for virion assembly. Here, we constructed various mutants by deleting sequences within the 3' NTR of AlMV subgenomic (sg RNA4 (same as of RNA3 and examined the effect of these deletions on replication and translation of chimeric Tobacco mosaic virus (TMV expressing AlMV sgRNA4 from the TMV CP sg promoter (Av/A4 in tobacco protoplasts and Nicotiana benthamiana plants. While the Av/A4 mutants were as competent as the wild-type Av/A4 in RNA replication in protoplasts, their encapsidation, long-distance movement and virus accumulation varied significantly in N. benthamiana. These data suggest that the 3' NTR of AlMV sgRNA4 contains potential elements necessary for virus encapsidation.

  5. Deletions within the 3' non-translated region of Alfalfa mosaic virus RNA4 do not affect replication but significantly reduce long-distance movement of chimeric Tobacco mosaic virus.

    Science.gov (United States)

    Roy, Gourgopal; Fedorkin, Oleg; Fujiki, Masaaki; Skarjinskaia, Marina; Knapp, Elisabeth; Rabindran, Shailaja; Yusibov, Vidadi

    2013-07-01

    Alfalfa mosaic virus (AlMV) RNAs 1 and 2 with deletions in their 3' non‑translated regions (NTRs) have been previously shown to be encapsidated into virions by coat protein (CP) expressed from RNA3, indicating that the 3' NTRs of RNAs 1 and 2 are not required for virion assembly. Here, we constructed various mutants by deleting sequences within the 3' NTR of AlMV subgenomic (sg) RNA4 (same as of RNA3) and examined the effect of these deletions on replication and translation of chimeric Tobacco mosaic virus (TMV) expressing AlMV sgRNA4 from the TMV CP sg promoter (Av/A4) in tobacco protoplasts and Nicotiana benthamiana plants. While the Av/A4 mutants were as competent as the wild-type Av/A4 in RNA replication in protoplasts, their encapsidation, long-distance movement and virus accumulation varied significantly in N. benthamiana. These data suggest that the 3' NTR of AlMV sgRNA4 contains potential elements necessary for virus encapsidation. PMID:23867804

  6. Hepatitis D Virus Replication.

    Science.gov (United States)

    Taylor, John M

    2015-11-01

    This work reviews specific related aspects of hepatitis delta virus (HDV) reproduction, including virion structure, the RNA genome, the mode of genome replication, the delta antigens, and the assembly of HDV using the envelope proteins of its helper virus, hepatitis B virus (HBV). These topics are considered with perspectives ranging from a history of discovery through to still-unsolved problems. HDV evolution, virus entry, and associated pathogenic potential and treatment of infections are considered in other articles in this collection. PMID:26525452

  7. 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...

  8. An optimal replication strategy for data grid systems

    Institute of Scientific and Technical Information of China (English)

    JIANG Jianjin; YANG Guangwen

    2007-01-01

    Data access latency is an important metric of system performance in data grid.By means of efficient replication strategy,the amount of data transferred in a wide area network will decrease,and the average access latency of data will decrease ultimately.The motivation of our research is to solve the optimized replica distribution problem in a data grid;that is,the system should utilize many replicas for every data with storage constraints to minimize the average access latency of data.This paper proposes a model of replication strategy in federated data grid and gives the optimized solution.The analysis results and simulation results show that the optimized replication strategy proposed in this paper is superior to LRU caching strategy,uniform replication strategy,proportional replication strategy and square root replication strategy in terms of wide area network bandwidth requirement and in the average access latency of data.

  9. 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…

  10. Quantum efficiency affected by localized carrier distribution near the V-defect in GaN based quantum well

    International Nuclear Information System (INIS)

    It is known that due to the formation of in-plane local energy barrier, V-defects can screen the carriers which non-radiatively recombine in threading dislocations (TDs) and hence, enhance the internal quantum efficiency in GaN based light-emitting diodes. By a theoretical modeling capable of describing the inhomogeneous carrier distribution near the V-defect in GaN based quantum wells, we show that the efficient suppression of non-radiative (NR) recombination via TD requires the local energy barrier height of V-defect larger than ∼80 meV. The NR process in TD combined with V-defect influences the quantum efficiency mainly in the low injection current density regime suitably described by the linear dependence of carrier density. We provide a simple phenomenological expression for the NR recombination rate based on the model result

  11. International Expansion through Flexible Replication

    DEFF Research Database (Denmark)

    Jonsson, Anna; Foss, Nicolai Juul

    2011-01-01

    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, etc.) are replicated in a uniform manner across stores, and change only very slowly (if at all) in response to learning (“flexible replication”). We conclude by discussing the factors that influence the approach to replication adopted by an international replicator....

  12. Do soil organic carbon levels affect potential yields and nitrogen use efficiency? An analysis of winter wheat and spring barley field trials

    DEFF Research Database (Denmark)

    Oelofse, Myles; Markussen, Bo; Knudsen, Leif;

    2015-01-01

    Soil organic carbon (SOC) is broadly recognised as an important parameter affecting soil quality, and can therefore contribute to improving a number of soil properties that influence crop yield. Previous research generally indicates that soil organic carbon has positive effects on crop yields, but...... in many studies it is difficult to separate the effect of nutrients from the effect of SOC in itself. The aim of this study was to analyze whether the SOC content, in itself, has a significant effect on potential yields of commonly grown cereals across a wider range of soil types in Denmark. The...... yield, the yield with no fertiliser N application and the N use efficiency would be positively affected by SOC level. A statistical model was developed to explore relationships between SOC and potential yield, yields at zero N application and N use efficiency (NUE). The model included a variety of...

  13. 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.

  14. Analysis of Factors Affecting The Management of Overall Energy Efficiency of Tractor-Implement by Real-Time Performance Monitoring

    OpenAIRE

    Kazemi, N; M Almassi; Bahrami, H.; M.J Shaykhdavoodi; M Mesgarbashi

    2016-01-01

    Overall energy efficiency (OEE) is an important indicator of energy consumption in tillage operations. Tillage energy was studied objectivity to accurately measure the OEE of MF399-4WD tractor. The tractor was equipped with different types of sensors to measure and calibrate the required data including: fuel consumption, actual forward speed, wheel speed and slippage, engine speed, draft and drawbar power. The data were recorded with frequency of 1000 Hz and transmitted by employing a suitabl...

  15. Does the Size and Composition of the Board of Directors of Shinkin Banks Affect their Risk Taking and Efficiency?

    OpenAIRE

    Tsutomu Chano; Yoshiro Tsutsui

    2014-01-01

    This paper investigates the effect of the size and composition of the board of directors of Shinkin Banks on their efficiency and risk taking. Because employees are important stakeholders in Japanese firms, we define the relative size of the board of directors as the number of directors per employee. We also consider the composition of the board; specifically, we employ a dummy variable representing whether the board includes directors who were not employees of that Shinkin Bank, and also the...

  16. Prioritization of the Factors Affecting Bank Efficiency Using Combined Data Envelopment Analysis and Analytical Hierarchy Process Methods

    OpenAIRE

    Mehdi Fallah Jelodar

    2016-01-01

    Bank branches have a vital role in the economy of all countries. They collect assets from various sources and put them in the hand of those sectors that need liquidity. Due to the limited financial and human resources and capitals and also because of the unlimited and new customers’ needs and strong competition between banks and financial and credit institutions, the purpose of this study is to provide an answer to the question of which of the factors affecting performance, creating value, an...

  17. Do Water Rights Affect Technical Efficiency and Social Disparities of Crop Production in the Mediterranean? The Spanish Ebro Basin Evidence

    Directory of Open Access Journals (Sweden)

    Sonia Quiroga

    2014-11-01

    Full Text Available The coming agenda for the European Common Agricultural Policy includes more incentives for the environmental compliance of farmer’s activities. This will be particularly important in the case of water risk management in Mediterranean countries. Among the new challenges is the need to evaluate some of the instruments necessary to comply with the Water Framework Directive requirements that emphasize the management of water demand to achieve the environmental targets. Here we analyze the implications of changing water rights as a policy response to these challenges. We analyze two important aspects of the decision: (i the effects on the crop productivity and efficiency and (ii the effects on the rural income distribution. We provide the empirical estimations for the marginal effects on the two considered aspects. First, we calculate a stochastic frontier production function for five representative crops using historical data to estimate technical efficiency. Second, we use a decomposition of the Gini coefficient to estimate the impact of irrigation rights changes on yield disparity. In our estimates, we consider both bio-physical and socio-economic aspects to conclude that there are long term implications on both efficiency and social disparities. We find disparities in the adaptation strategies depending on the crop and the region analyzed.

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

    Directory of Open Access Journals (Sweden)

    Simon Gemble

    2015-07-01

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

  19. 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.

  20. A study of the volatilization-excitation phenomena affecting to the efficiency of spectrochemical buffers applied to uranium ore analysis

    International Nuclear Information System (INIS)

    A direct-current arc emission spectroscopy method allowing the determination of Alm Ca, Fe, Mg, Mn, Na, P, Si and Ti in uranium ores and geological materials has been developed by studying the efficiency of Ag2O, BaCO3, Bi2O3, CuF2, CuO, Ga2O3, GeO2, graphite, K2CO3, Li2B4O7, Li2CO3, Ni, PbS, Sb2O4, SrCO3, Tl2O3 and ZnO as spectrochemical buffers. Volatilization-excitation mechanisms of Li2CO3: graphite, GeO2: graphite and SrCO3: graphite buffer mixtures have been specially considered. Procedures to investigate phenomena taking place in the electrode, anodic load and arc plasma have been selected. Intensity-time curves; voltage variation between electrodes; vapour diffussion through the electrode walls; load depletion; reaction products formation and temperature, electron pressure and ionization degree in the arc plasma have been studied. Measurements of plasma parameters are performed by introducing thermometric and manometric species in both the anode and the cathode electrodes. The effects of different alkalin matrices on transportation phenomena are also considered. Emission efficiency of some analytical lines has been investigated by the application of a mathematical model enclosing fundamental parameters of the arc plasma. Efficiency of scattered primary X-rays of various wavelengths has been studied as a correction of matrix effects in the uranium determination. Results illustrate that the incoherently-scattered MoKβsub(1,3) radiation is the optimum reference line. (author)

  1. A New Replicator: A theoretical framework for analysing replication

    OpenAIRE

    Szathmáry Eörs; Zachar István

    2010-01-01

    Abstract Background Replicators are the crucial entities in evolution. The notion of a replicator, however, is far less exact than the weight of its importance. Without identifying and classifying multiplying entities exactly, their dynamics cannot be determined appropriately. Therefore, it is importance to decide the nature and characteristics of any multiplying entity, in a detailed and formal way. Results Replication is basically an autocatalytic process which enables us to rest on the not...

  2. Human cytomegalovirus induces JC virus DNA replication in human fibroblasts.

    Science.gov (United States)

    Heilbronn, R; Albrecht, I; Stephan, S; Bürkle, A; zur Hausen, H

    1993-01-01

    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. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:8248262

  3. Analysis of Factors Affecting The Management of Overall Energy Efficiency of Tractor-Implement by Real-Time Performance Monitoring

    Directory of Open Access Journals (Sweden)

    N Kazemi

    2016-04-01

    Full Text Available Overall energy efficiency (OEE is an important indicator of energy consumption in tillage operations. Tillage energy was studied objectivity to accurately measure the OEE of MF399-4WD tractor. The tractor was equipped with different types of sensors to measure and calibrate the required data including: fuel consumption, actual forward speed, wheel speed and slippage, engine speed, draft and drawbar power. The data were recorded with frequency of 1000 Hz and transmitted by employing a suitable wireless technology in the range of up to1.5 km to the user's personal computer and is stored in Excel format. The hardware and the software program, which was written in C# language, simultaneously monitor the changes in functional parameters and the monitoring can be done even from far away and via the Internet. The split factorial experiment with three factors including ballast, selected gear ratio and two wheel drive configurations (two and four wheel drive was employed to perform analysis of variance (ANOVA, POST ANOVA AND PATH ANALYSIS. The results show that the performance of remote monitoring devices installation was very accurate and high-quality. Furthermore, statistical analysis showed that three parameters including slippage, fuel consumption and tractor Power Equivalent (PEQ were the most effective parameters on overall energy efficiency of tractors – tillage. The variance analysis showed that the effect of gear ratio and drive configuration on the OEE were also significant at the one percent level. However, ballasting had no significant effect on the OEE.

  4. Replicated Spectrographs in Astronomy

    CERN Document Server

    Hill, Gary J

    2014-01-01

    As telescope apertures increase, the challenge of scaling spectrographic astronomical instruments becomes acute. The next generation of extremely large telescopes (ELTs) strain the availability of glass blanks for optics and engineering to provide sufficient mechanical stability. While breaking the relationship between telescope diameter and instrument pupil size by adaptive optics is a clear path for small fields of view, survey instruments exploiting multiplex advantages will be pressed to find cost-effective solutions. In this review we argue that exploiting the full potential of ELTs will require the barrier of the cost and engineering difficulty of monolithic instruments to be broken by the use of large-scale replication of spectrographs. The first steps in this direction have already been taken with the soon to be commissioned MUSE and VIRUS instruments for the Very Large Telescope and the Hobby-Eberly Telescope, respectively. MUSE employs 24 spectrograph channels, while VIRUS has 150 channels. We compa...

  5. File and object replication in data grids

    CERN Document Server

    Stockinger, H E; Allcock, B; Foster, I; Holtman, K; Tierney, B L

    2001-01-01

    Data replication is a key issue in a data grid and can be managed in different ways and at different levels of granularity: for example, at the file level or the object level. In the high-energy physics community, data grids are being developed to support the distributed analysis of experimental data. We have produced a prototype data replication tool, the Grid Data Management Pilot (GDMP) that is in production use in one physics experiment, with middleware provided by the Globus toolkit used for authentication, data movement and other purposes. We present a new, enhanced GDMP architecture and prototype implementation that uses Globus data-grid tools for efficient file replication. We also explain how this architecture can address object replication issues in an object-oriented database management system. File transfer over wide-area networks requires specific performance tuning in order to gain optimal data transfer rates. We present performance results obtained with GridFTP, an enhanced version of FTP, and ...

  6. Hepatitis Delta Virus RNA Replication

    Directory of Open Access Journals (Sweden)

    Chung-Hsin Tseng

    2009-11-01

    Full Text Available Hepatitis delta virus (HDV is a distant relative of plant viroids in the animal world. Similar to plant viroids, HDV replicates its circular RNA genome using a double rolling-circle mechanism. Nevertheless, the production of hepatitis delta antigen (HDAg, which is indispensible for HDV replication, is a unique feature distinct from plant viroids, which do not encode any protein. Here the HDV RNA replication cycle is reviewed, with emphasis on the function of HDAg in modulating RNA replication and the nature of the enzyme involved.

  7. The Evolutionarily Conserved Protein PHOTOSYNTHESIS AFFECTED MUTANT71 Is Required for Efficient Manganese Uptake at the Thylakoid Membrane in Arabidopsis.

    Science.gov (United States)

    Schneider, Anja; Steinberger, Iris; Herdean, Andrei; Gandini, Chiara; Eisenhut, Marion; Kurz, Samantha; Morper, Anna; Hoecker, Natalie; Rühle, Thilo; Labs, Mathias; Flügge, Ulf-Ingo; Geimer, Stefan; Schmidt, Sidsel Birkelund; Husted, Søren; Weber, Andreas P M; Spetea, Cornelia; Leister, Dario

    2016-04-01

    In plants, algae, and cyanobacteria, photosystem II (PSII) catalyzes the light-driven oxidation of water. The oxygen-evolving complex of PSII is a Mn4CaO5 cluster embedded in a well-defined protein environment in the thylakoid membrane. However, transport of manganese and calcium into the thylakoid lumen remains poorly understood. Here, we show that Arabidopsis thaliana PHOTOSYNTHESIS AFFECTED MUTANT71 (PAM71) is an integral thylakoid membrane protein involved in Mn(2+) and Ca(2+) homeostasis in chloroplasts. This protein is required for normal operation of the oxygen-evolving complex (as evidenced by oxygen evolution rates) and for manganese incorporation. Manganese binding to PSII was severely reduced in pam71 thylakoids, particularly in PSII supercomplexes. In cation partitioning assays with intact chloroplasts, Mn(2+) and Ca(2+) ions were differently sequestered in pam71, with Ca(2+) enriched in pam71 thylakoids relative to the wild type. The changes in Ca(2+) homeostasis were accompanied by an increased contribution of the transmembrane electrical potential to the proton motive force across the thylakoid membrane. PSII activity in pam71 plants and the corresponding Chlamydomonas reinhardtii mutant cgld1 was restored by supplementation with Mn(2+), but not Ca(2+) Furthermore, PAM71 suppressed the Mn(2+)-sensitive phenotype of the yeast mutant Δpmr1 Therefore, PAM71 presumably functions in Mn(2+) uptake into thylakoids to ensure optimal PSII performance. PMID:27020959

  8. Factors affecting adherence to the treatment regimen of tuberculosis patients: Assessing the efficiency of health belief model constructs

    Directory of Open Access Journals (Sweden)

    Mahmood Karimy

    2014-07-01

    Full Text Available Background: Low adherence to the treatment regimen in tuberculosis patients has been recognized as a major threat for tuberculosis (TB control program. Thus, the present study was conducted to assess the factors affecting adherence to the treatment regimen of TB patients via Health Belief Model (HBM. Methods: In this cross-sectional study,110 tuberculosis patients attending anti-TB center in Zabol were selected and included in the study using census method. Data were collected using Health Belief Model (HBM questionnaire and reviewing the patients' medical files. The collected data were analyzed by SPSS software using t-test, ANOVA and multiple regression analysis with 95 % confidence level. Results: The mean age of the participants was 55.7±18.6 years. 89% of the patients had pulmonary tuberculosis and 11% had extra-pulmonary tuberculosis. The multiple regression analysis showed knowledge, self-efficacy, perceived benefits and perceived threat were significant predictors of adherence to the treatment regimen. The HBM constructs accounted for 29% of the variance observed in adherence to the treatment regimen. Conclusion: The findings of the study highlight the need to increase awareness and change the patients’ beliefs about the risks of low adherence to the treatment regimen in patients.

  9. DNA Replication Dynamics of the GGGGCC Repeat of the C9orf72 Gene*

    OpenAIRE

    Thys, Ryan Griffin; Wang, Yuh-Hwa

    2015-01-01

    Background: The (GGGGCC)n hexanucleotide repeat expansion of C9orf72 is the most common genetic cause of ALS-FTD. Results: C9orf72 repeat expansion increases instability and decreases replication efficiency by disrupting replication fork progression. Conclusion: C9orf72 repeat length and replication direction contribute to repeat instability in human cells. Significance: DNA replication-induced instability at the C9orf72 GGGGCC repeat can lead to further expansion and more severe disease.

  10. Dynamics of pre-replication complex proteins during the cell division cycle.

    OpenAIRE

    Prasanth, Supriya G.; Méndez, Juan; Prasanth, Kannanganattu V.; Stillman, Bruce

    2004-01-01

    Replication of the human genome every time a cell divides is a highly coordinated process that ensures accurate and efficient inheritance of the genetic information. The molecular mechanism that guarantees that many origins of replication fire only once per cell-cycle has been the area of intense research. The origin recognition complex (ORC) marks the position of replication origins in the genome and serves as the landing pad for the assembly of a multiprotein, pre-replicative complex (pre-R...

  11. 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. PMID:26132923

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

    Directory of Open Access Journals (Sweden)

    Tormi Reinson

    Full Text Available 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.

  13. Row Ratios of Intercropping Maize and Soybean Can Affect Agronomic Efficiency of the System and Subsequent Wheat.

    Science.gov (United States)

    Zhang, Yitao; Liu, Jian; Zhang, Jizong; Liu, Hongbin; Liu, Shen; Zhai, Limei; Wang, Hongyuan; Lei, Qiuliang; Ren, Tianzhi; Yin, Changbin

    2015-01-01

    Intercropping is regarded as an important agricultural practice to improve crop production and environmental quality in the regions with intensive agricultural production, e.g., northern China. To optimize agronomic advantage of maize (Zea mays L.) and soybean (Glycine max L.) intercropping system compared to monoculture of maize, two sequential experiments were conducted. Experiment 1 was to screening the optimal cropping system in summer that had the highest yields and economic benefits, and Experiment 2 was to identify the optimum row ratio of the intercrops selected from Experiment 1. Results of Experiment 1 showed that maize intercropping with soybean (maize || soybean) was the optimal cropping system in summer. Compared to conventional monoculture of maize, maize || soybean had significant advantage in yield, economy, land utilization ratio and reducing soil nitrate nitrogen (N) accumulation, as well as better residual effect on the subsequent wheat (Triticum aestivum L.) crop. Experiment 2 showed that intercropping systems reduced use of N fertilizer per unit land area and increased relative biomass of intercropped maize, due to promoted photosynthetic efficiency of border rows and N utilization during symbiotic period. Intercropping advantage began to emerge at tasseling stage after N topdressing for maize. Among all treatments with different row ratios, alternating four maize rows with six soybean rows (4M:6S) had the largest land equivalent ratio (1.30), total N accumulation in crops (258 kg ha(-1)), and economic benefit (3,408 USD ha(-1)). Compared to maize monoculture, 4M:6S had significantly lower nitrate-N accumulation in soil both after harvest of maize and after harvest of the subsequent wheat, but it did not decrease yield of wheat. The most important advantage of 4M:6S was to increase biomass of intercropped maize and soybean, which further led to the increase of total N accumulation by crops as well as economic benefit. In conclusion, alternating

  14. Row Ratios of Intercropping Maize and Soybean Can Affect Agronomic Efficiency of the System and Subsequent Wheat.

    Directory of Open Access Journals (Sweden)

    Yitao Zhang

    Full Text Available Intercropping is regarded as an important agricultural practice to improve crop production and environmental quality in the regions with intensive agricultural production, e.g., northern China. To optimize agronomic advantage of maize (Zea mays L. and soybean (Glycine max L. intercropping system compared to monoculture of maize, two sequential experiments were conducted. Experiment 1 was to screening the optimal cropping system in summer that had the highest yields and economic benefits, and Experiment 2 was to identify the optimum row ratio of the intercrops selected from Experiment 1. Results of Experiment 1 showed that maize intercropping with soybean (maize || soybean was the optimal cropping system in summer. Compared to conventional monoculture of maize, maize || soybean had significant advantage in yield, economy, land utilization ratio and reducing soil nitrate nitrogen (N accumulation, as well as better residual effect on the subsequent wheat (Triticum aestivum L. crop. Experiment 2 showed that intercropping systems reduced use of N fertilizer per unit land area and increased relative biomass of intercropped maize, due to promoted photosynthetic efficiency of border rows and N utilization during symbiotic period. Intercropping advantage began to emerge at tasseling stage after N topdressing for maize. Among all treatments with different row ratios, alternating four maize rows with six soybean rows (4M:6S had the largest land equivalent ratio (1.30, total N accumulation in crops (258 kg ha(-1, and economic benefit (3,408 USD ha(-1. Compared to maize monoculture, 4M:6S had significantly lower nitrate-N accumulation in soil both after harvest of maize and after harvest of the subsequent wheat, but it did not decrease yield of wheat. The most important advantage of 4M:6S was to increase biomass of intercropped maize and soybean, which further led to the increase of total N accumulation by crops as well as economic benefit. In conclusion

  15. Replication of bacteriophage lambda DNA

    International Nuclear Information System (INIS)

    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

  16. Charter School Replication. Policy Guide

    Science.gov (United States)

    Rhim, Lauren Morando

    2009-01-01

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

  17. The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo.

    Science.gov (United States)

    Boubakri, Hasna; de Septenville, Anne Langlois; Viguera, Enrique; Michel, Bénédicte

    2010-01-01

    How living cells deal with head-on collisions of the replication and transcription complexes has been debated for a long time. Even in the widely studied model bacteria Escherichia coli, the enzymes that take care of such collisions are still unknown. We report here that in vivo, the DinG, Rep and UvrD helicases are essential for efficient replication across highly transcribed regions. We show that when rRNA operons (rrn) are inverted to face replication, the viability of the dinG mutant is affected and over-expression of RNase H rescues the growth defect, showing that DinG acts in vivo to remove R-loops. In addition, DinG, Rep and UvrD exert a common function, which requires the presence of two of these three helicases. After replication blockage by an inverted rrn, Rep in conjunction with DinG or UvrD removes RNA polymerase, a task that is fulfilled in its absence by the SOS-induced DinG and UvrD helicases. Finally, Rep and UvrD also act at inverted sequences other than rrn, and promote replication through highly transcribed regions in wild-type E. coli. PMID:19851282

  18. DATABASE REPLICATION IN HETEROGENOUS PLATFORM

    Directory of Open Access Journals (Sweden)

    Hendro Nindito

    2014-01-01

    Full Text Available 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 MySQL running on Linux as the destination. The method applied in this research is prototyping in which the processes of development and testing can be done interactively and repeatedly. The key result of this research is that the replication technology applied, which is called Oracle GoldenGate, can successfully manage to do its task in replicating data in real-time and heterogeneous platforms.

  19. LHCb experience with LFC replication

    CERN Document Server

    Carbone, Angelo; Dafonte Perez, Eva; D'Apice, Antimo; dell'Agnello, Luca; Duellmann, Dirk; Girone, Maria; Lo Re, Giuseppe; Martelli, Barbara; Peco, Gianluca; Ricci, Pier Paolo; Sapunenko, Vladimir; Vagnoni, Vincenzo; Vitlacil, Dejan

    2007-01-01

    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. 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 Informations (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements.

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

    OpenAIRE

    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 consi...

  1. Performance analysis of static locking in replicated distributed database systems

    Science.gov (United States)

    Kuang, Yinghong; Mukkamala, Ravi

    1991-01-01

    Data replications and transaction deadlocks can severely affect the performance of distributed database systems. Many current evaluation techniques ignore these aspects, because it is difficult to evaluate through analysis and time consuming to evaluate through simulation. Here, a technique is discussed that combines simulation and analysis to closely illustrate the impact of deadlock and evaluate performance of replicated distributed databases with both shared and exclusive locks.

  2. Factors affecting study efficiency and item non-response in health surveys in developing countries: the Jamaica national healthy lifestyle survey

    Directory of Open Access Journals (Sweden)

    Bennett Franklyn

    2007-02-01

    Full Text Available Abstract Background Health surveys provide important information on the burden and secular trends of risk factors and disease. Several factors including survey and item non-response can affect data quality. There are few reports on efficiency, validity and the impact of item non-response, from developing countries. This report examines factors associated with item non-response and study efficiency in a national health survey in a developing Caribbean island. Methods A national sample of participants aged 15–74 years was selected in a multi-stage sampling design accounting for 4 health regions and 14 parishes using enumeration districts as primary sampling units. Means and proportions of the variables of interest were compared between various categories. Non-response was defined as failure to provide an analyzable response. Linear and logistic regression models accounting for sample design and post-stratification weighting were used to identify independent correlates of recruitment efficiency and item non-response. Results We recruited 2012 15–74 year-olds (66.2% females at a response rate of 87.6% with significant variation between regions (80.9% to 97.6%; p Conclusion Informative health surveys are possible in developing countries. While survey response rates may be satisfactory, item non-response was high in respect of income and sexual practice. In contrast to developed countries, non-response to questions on income is higher and has different correlates. These findings can inform future surveys.

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

    Directory of Open Access Journals (Sweden)

    Samuel E Saunders

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

  4. Regulation of Replication Recovery and Genome Integrity

    DEFF Research Database (Denmark)

    Colding, Camilla Skettrup

    Preserving genome integrity is essential for cell survival. To this end, mechanisms that supervise DNA replication and respond to replication perturbations have evolved. One such mechanism is the replication checkpoint, which responds to DNA replication stress and acts to ensure replication pausing...

  5. Dietary energy sources affect the partition of body lipids and the hierarchy of energy metabolic pathways in growing pigs differing in feed efficiency.

    Science.gov (United States)

    Gondret, F; Louveau, I; Mourot, J; Duclos, M J; Lagarrigue, S; Gilbert, H; van Milgen, J

    2014-11-01

    The use and partition of feed energy are key elements in productive efficiency of pigs. This study aimed to determine whether dietary energy sources affect the partition of body lipids and tissue biochemical pathways of energy use between pigs differing in feed efficiency. Forty-eight barrows (pure Large White) from two divergent lines selected for residual feed intake (RFI), a measure of feed efficiency, were compared. From 74 d to 132 ± 0.5 d of age, pigs (n = 12 by line and by diet) were offered diets with equal protein and ME contents. A low fat, low fiber diet (LF) based on cereals and a high fat, high fiber diet (HF) where vegetal oils and wheat straw were used to partially substitute cereals, were compared. Irrespective of diet, gain to feed was 10% better (P percentage of PUFA, especially the EFA C18:2 and C18:3, was greater (P < 0.001) in backfat of HF-fed pigs. In both lines, these changes were associated with a marked decrease (P < 0.001) in the activities of two lipogenic enzymes, the fatty acid synthase (FASN) and the malic enzyme, in backfat. For the high RFI line, the hepatic lipid content was greater (P < 0.05) in pigs fed the HF diet than in pigs fed the LF diet, despite a reduced FASN activity (-32%; P < 0.001). In both lines, the HF diet also led to lower glycogen content (-70%) and lower glucokinase activity (-15%; P < 0.05) in the liver. These results show that dietary energy sources modified the partition of energy between liver, adipose tissue, and muscle in a way that was partly dependent of the genetics for feed efficiency, and changed the activity levels of biochemical pathways involved in lipid and glucose storage in tissues. PMID:25253805

  6. Replications of software engineering experiments

    OpenAIRE

    Carver, Jeffrey C.; Juristo Juzgado, Natalia; Baldassarre, María Teresa; Vegas Hernández, Sira

    2014-01-01

    There are many open issues that must be addressed before the replication process can be successfully formalized in empirical software engineering research. We define replication as the deliberate repetition of the same empirical study for the purpose of determining whether the results of the first experiment can be reproduced. This definition would appear at first glance to be good. However, it needs several clarifications that have not yet been forthcoming in software engineer...

  7. Where does DNA replication start in archaea?

    OpenAIRE

    Vas, Amit; Leatherwood, Janet

    2000-01-01

    Genome-wide measures of DNA strand composition have been used to find archaeal DNA replication origins. Archaea seem to replicate using a single origin (as do eubacteria) even though archaeal replication factors are more like those of eukaryotes.

  8. Break-Induced Replication and Genome Stability

    Directory of Open Access Journals (Sweden)

    Anna Malkova

    2012-10-01

    Full Text Available Genetic instabilities, including mutations and chromosomal rearrangements, lead to cancer and other diseases in humans and play an important role in evolution. A frequent cause of genetic instabilities is double-strand DNA breaks (DSBs, which may arise from a wide range of exogeneous and endogeneous cellular factors. Although the repair of DSBs is required, some repair pathways are dangerous because they may destabilize the genome. One such pathway, break-induced replication (BIR, is the mechanism for repairing DSBs that possesses only one repairable end. This situation commonly arises as a result of eroded telomeres or collapsed replication forks. Although BIR plays a positive role in repairing DSBs, it can alternatively be a dangerous source of several types of genetic instabilities, including loss of heterozygosity, telomere maintenance in the absence of telomerase, and non-reciprocal translocations. Also, mutation rates in BIR are about 1000 times higher as compared to normal DNA replication. In addition, micro-homology-mediated BIR (MMBIR, which is a mechanism related to BIR, can generate copy-number variations (CNVs as well as various complex chromosomal rearrangements. Overall, activation of BIR may contribute to genomic destabilization resulting in substantial biological consequences including those affecting human health.

  9. The hepatitis delta virus: Replication and pathogenesis.

    Science.gov (United States)

    Sureau, Camille; Negro, Francesco

    2016-04-01

    Hepatitis delta virus (HDV) is a defective virus and a satellite of the hepatitis B virus (HBV). Its RNA genome is unique among animal viruses, but it shares common features with some plant viroids, including a replication mechanism that uses a host RNA polymerase. In infected cells, HDV genome replication and formation of a nucleocapsid-like ribonucleoprotein (RNP) are independent of HBV. But the RNP cannot exit, and therefore propagate, in the absence of HBV, as the latter supplies the propagation mechanism, from coating the HDV RNP with the HBV envelope proteins for cell egress to delivery of the HDV virions to the human hepatocyte target. HDV is therefore an obligate satellite of HBV; it infects humans either concomitantly with HBV or after HBV infection. HDV affects an estimated 15 to 20million individuals worldwide, and the clinical significance of HDV infection is more severe forms of viral hepatitis - acute or chronic -, and a higher risk of developing cirrhosis and hepatocellular carcinoma in comparison to HBV monoinfection. This review covers molecular aspects of HDV replication cycle, including its interaction with the helper HBV and the pathogenesis of infection in humans. PMID:27084031

  10. Directed evolution of polymerase function by compartmentalized self-replication.

    Science.gov (United States)

    Ghadessy, F J; Ong, J L; Holliger, P

    2001-04-10

    We describe compartmentalized self-replication (CSR), a strategy for the directed evolution of enzymes, especially polymerases. CSR is based on a simple feedback loop consisting of a polymerase that replicates only its own encoding gene. Compartmentalization serves to isolate individual self-replication reactions from each other. In such a system, adaptive gains directly (and proportionally) translate into genetic amplification of the encoding gene. CSR has applications in the evolution of polymerases with novel and useful properties. By using three cycles of CSR, we obtained variants of Taq DNA polymerase with 11-fold higher thermostability than the wild-type enzyme or with a >130-fold increased resistance to the potent inhibitor heparin. Insertion of an extra stage into the CSR cycle before the polymerase reaction allows its application to enzymes other than polymerases. We show that nucleoside diphosphate kinase and Taq polymerase can form such a cooperative CSR cycle based on reciprocal catalysis, whereby nucleoside diphosphate kinase produces the substrates required for the replication of its own gene. We also find that in CSR the polymerase genes themselves evolve toward more efficient replication. Thus, polymerase genes and their encoded polypeptides cooperate to maximize postselection copy number. CSR should prove useful for the directed evolution of enzymes, particularly DNA or RNA polymerases, as well as for the design and study of in vitro self-replicating systems mimicking prebiotic evolution and viral replication. PMID:11274352

  11. Providing Reliability in Replicated Middleware Applications

    Directory of Open Access Journals (Sweden)

    R. Saravanan

    2009-01-01

    Full Text Available Problem statement: Data inconsistency is raised in actively replicated environment due to non-determinism in the applications that defeats the purpose of replication as a fault-tolerance strategy. Approach: We proposed an efficient framework RTC which ensured determinism among the replicas in fault tolerance middleware applications. This method exploits the technique of statically analyzing the application source code of client and identifies the variables and system calls which lead to non-deterministic state in the replicas. The source code consists of non-deterministic variables and system calls which are identified and set the flag field. The client request consist of flag field and the service request, which is sent to all the servers through time stamp based replication protocol (TSP that facilitate the multiple clients and the request is sent to the servers. The distributed coordination method was initiated if necessary; otherwise send any one response of the servers to the client by duplicate removal. Distributed coordination which involves, the selection of a primary replica based on the time stamp value. It is responsible for taking all non-deterministic decisions. The state of the primary replica was updated to all other replica connected asynchronously to maintain consistency. Results: We evaluated our technique by increasing the contamination percentage of non-determinism and increasing number of replicas. Conclusion: The method suggested by us reduces the communication and synchronization overhead which was proved through implementation. We evaluate our technique for the active replication of servers using micro benchmarks that contain various sources of non-determinism. Multi-threading, system call, shared I/O and random ( .

  12. Efficiency of zinc and phosphate fertilizers in maize as affected by direct placement of zinc, phosphorus, nitrogen and copper with seed

    International Nuclear Information System (INIS)

    An investigation was carried out under greenhouse condition on the alluvial soil of Delhi to study the efficiency of Zn and P fertilizers in maize as affected by direct placement of Zn, P, N and Cu with seed. Results indicated that placement of N,P, Zn and Cu directly with seed significantly increased the dry matter yield of plants as compared with control. The utilization of applied P was found to increase significantly at higher levels of N whereas at higher levels of P application the efficiency of fertilizer P utilization by maize was found to be low although in both the cases P derived from fertilizer showed significant increase with increasing levels of N and P. The utilization of fertilizer Zn by plants decreased with increasing levels of Zn applied. Total uptake of Zn by plants showed significant increase due to high levels of N application although Zn derived from fertilizer was found to decrease with increasing levels of N application. The copper content of plants increased due to Cu application. All the P and Zn applied were tagged with 32P and 65Zn respectively. (author)

  13. Highly efficient EIAV-mediated in utero gene transfer and expression in the major muscle groups affected by Duchenne muscular dystrophy.

    Science.gov (United States)

    Gregory, L G; Waddington, S N; Holder, M V; Mitrophanous, K A; Buckley, S M K; Mosley, K L; Bigger, B W; Ellard, F M; Walmsley, L E; Lawrence, L; Al-Allaf, F; Kingsman, S; Coutelle, C; Themis, M

    2004-07-01

    Gene therapy for Duchenne muscular dystrophy has so far not been successful because of the difficulty in achieving efficient and permanent gene transfer to the large number of affected muscles and the development of immune reactions against vector and transgenic protein. In addition, the prenatal onset of disease complicates postnatal gene therapy. We have therefore proposed a fetal approach to overcome these barriers. We have applied beta-galactosidase expressing equine infectious anaemia virus (EIAV) lentiviruses pseudotyped with VSV-G by single or combined injection via different routes to the MF1 mouse fetus on day 15 of gestation and describe substantial gene delivery to the musculature. Highly efficient gene transfer to skeletal muscles, including the diaphragm and intercostal muscles, as well as to cardiac myocytes was observed and gene expression persisted for at least 15 months after administration of this integrating vector. These findings support the concept of in utero gene delivery for therapeutic and long-term prevention/correction of muscular dystrophies and pave the way for a future application in the clinic. PMID:15141156

  14. A Transactional Asynchronous Replication Scheme for Mobile Database Systems

    Institute of Scientific and Technical Information of China (English)

    丁治明; 孟小峰; 王珊

    2002-01-01

    In mobile database systems, mobility of users has a significant impact on data replication. As a result, the various replica control protocols that exist today in traditional distributed and multidatabase environments are no longer suitable. To solve this problem, a new mobile database replication scheme, the Transaction-Level Result-Set Propagation (TLRSP)model, is put forward in this paper. The conflict detection and resolution strategy based on TLRSP is discussed in detail, and the implementation algorithm is proposed. In order to compare the performance of the TLRSP model with that of other mobile replication schemes, we have developed a detailed simulation model. Experimental results show that the TLRSP model provides an efficient support for replicated mobile database systems by reducing reprocessing overhead and maintaining database consistency.

  15. The importance of alfalfa mosaic virus coat protein dimers in the initiation of replication.

    Science.gov (United States)

    Choi, Jiwon; Kim, Bong-Suk; Zhao, Xiaoxia; Loesch-Fries, Sue

    2003-01-01

    Deletion and substitution mutations affecting the oligomerization of alfalfa mosaic virus (AMV) coat protein (CP) were studied in protoplasts to determine their effect on genome activation, an early step in AMV replication. The CP mutants that formed dimers, CPDeltaC9 and CPC-A(R)F, were highly active in initiating replication with 63-84% of wild-type (wt) CP activity. However, all mutants that did not form dimers, CPDeltaC18, CPDeltaC19, CPC-WFP, and CPC-W, were much less active with 19-33% of wt CP activity. The accumulation and solubility of mutant CPs expressed from a virus-based vector in Nicotiana benthamiana were similar to that of wt CP. Analysis of CP-RNA interactions indicated that CP dimers and CP monomers interacted very differently with AMV RNA 3' ends. These results suggest that CP dimers are more efficient for replication than CP monomers because of differences in RNA binding rather than differences in expression and accumulation of the mutant CPs in infected cells. PMID:12504539

  16. Mimiviruses: Replication, Purification, and Quantification.

    Science.gov (United States)

    Abrahão, Jônatas Santos; Oliveira, Graziele Pereira; Ferreira da Silva, Lorena Christine; Dos Santos Silva, Ludmila Karen; Kroon, Erna Geessien; La Scola, Bernard

    2016-01-01

    The aim of this protocol is to describe the replication, purification, and titration of mimiviruses. These viruses belong to the Mimiviridae family, the first member of which was isolated in 1992 from a cooling tower water sample collected during an outbreak of pneumonia in a hospital in Bradford, England. In recent years, several new mimiviruses have been isolated from different environmental conditions. These giant viruses are easily replicated in amoeba of the Acanthamoeba genus, its natural host. Mimiviruses present peculiar features that make them unique viruses, such as the particle and genome size and the genome's complexity. The discovery of these viruses rekindled discussions about their origin and evolution, and the genetic and structural complexity opened up a new field of study. Here, we describe some methods utilized for mimiviruses replication, purification, and titration. © 2016 by John Wiley & Sons, Inc. PMID:27153385

  17. Investigation of the impact of organic solvent type and solution pH on the extraction efficiency of naphthenic acids from oil sands process-affected water.

    Science.gov (United States)

    Huang, Rongfu; McPhedran, Kerry N; Sun, Nian; Chelme-Ayala, Pamela; Gamal El-Din, Mohamed

    2016-03-01

    Naphthenic acids (NAs) from oil sand process-affected water (OSPW) were liquid-liquid extracted using six organic solvents (n-pentane, n-hexane, cyclohexane, dichloromethane, ethyl ether, and ethyl acetate) at three pHs (2.0, 8.5, and 12.0). The NAs exist in ionic (ions) and non-ionic (molecules) forms in the water phase depending on their dissociation constants and the solution pH. Results showed the extractability of NA molecules depends on the solvent polarity and the extractability of NA ions on the water solubility in solvent. The organic solvent type and solution pH were found to not only impact the extracted amounts of each NA species, but also the NAs distribution in terms of molecule carbon number and hydrogen deficiency. Overall, it is concluded that ethyl ether can be used as an alternative to dichloromethane (DCM) given their similar extraction efficiencies and extracted NA profiles. This is important since DCM is known to have metabolic toxicity and transitioning to the safer ethyl ether would eliminate laboratory DCM exposures and risk to human health. Despite the higher extraction efficiency of NAs at pH 2.0, extraction at pH 12.0 could be useful for targeted extraction of low-concentration nonpolar organic compounds in OSPW. This knowledge may assist in the determination of the specific NAs species that are known to have chronic, sub-chronic and acute toxicity to various organisms, and the potential targeting of treatment to these NAs species. PMID:26741553

  18. Optimal Placement of Origins for DNA Replication

    OpenAIRE

    Karschau, Jens; Blow, J. Julian; de Moura, Alessandro P. S.

    2012-01-01

    DNA replication is an essential process in biology and its timing must be robust so that cells can divide properly. Random fluctuations in the formation of replication starting points, called origins, and the subsequent activation of proteins lead to variations in the replication time. We analyse these stochastic properties of DNA and derive the positions of origins corresponding to the minimum replication time. We show that under some conditions the minimization of replication time leads to ...

  19. Cellular factors required for papillomavirus DNA replication.

    OpenAIRE

    Melendy, T; Sedman, J; Stenlund, A

    1995-01-01

    In vitro replication of papillomavirus DNA has been carried out with a combination of purified proteins and partially purified extracts made from human cells. DNA synthesis requires the viral E1 protein and the papillomavirus origin of replication. The E2 protein stimulates DNA synthesis in a binding site-independent manner. Papillomavirus DNA replication is also dependent on the cellular factors replication protein A, replication factor C, and proliferating-cell nuclear antigen as well as a ...

  20. Glioma-associated endothelial cells show evidence of replicative senescence

    International Nuclear Information System (INIS)

    The innately programmed process of replicative senescence has been studied extensively with respect to cancer, but primarily from the perspective of tumor cells overcoming this stringent innate barrier and acquiring the capacity for unlimited proliferation. In this study, we focus on the potential role of replicative senescence affecting the non-transformed endothelial cells of the blood vessels within the tumor microenvironment. Based on the well-documented aberrant structural and functional features of blood vessels within solid tumors, we hypothesized that tumor-derived factors may lead to premature replicative senescence in tumor-associated brain endothelial cells (TuBEC). We show here that glioma tissue, but not normal brain tissue, contains cells that express the signature of replicative senescence, senescence-associated β-galactosidase (SA-β-gal), on CD31-positive endothelial cells. Primary cultures of human TuBEC stain for SA-β-gal and exhibit characteristics of replicative senescence, including increased levels of the cell cycle inhibitors p21 and p27, increased resistance to cytotoxic drugs, increased growth factor production, and inability to proliferate. These data provide the first demonstration that tumor-derived brain endothelial cells may have reached an end-stage of differentiation known as replicative senescence and underscore the need for anti-angiogenic therapies to target this unique tumor-associated endothelial cell population

  1. p53 represses human papillomavirus type 16 DNA replication via the viral E2 protein

    OpenAIRE

    Morgan Iain M; Taylor Ewan R; Kowalczyk Anna M; Brown Craig; Gaston Kevin

    2008-01-01

    Abstract Background Human papillomavirus (HPV) DNA replication can be inhibited by the cellular tumour suppressor protein p53. However, the mechanism through which p53 inhibits viral replication and the role that this might play in the HPV life cycle are not known. The papillomavirus E2 protein is required for efficient HPV DNA replication and also regulates viral gene expression. E2 represses transcription of the HPV E6 and E7 oncogenes and can thereby modulate indirectly host cell prolifera...

  2. Replication invariance on NTU games

    OpenAIRE

    Emilio Calvo; Iñaki Garci´a; Zarzuelo, José M.

    2001-01-01

    Two concepts of replication (conflictual and non-conflictual) are extended from the class of pure bargaining games to the class of NTU games. The behavior of the Harsanyi, Shapley NTU, Egalitarian and Maschler-Owen solutions of the replica games is compared with that of the Nash and Egalitarian solutions in pure bargaining games.

  3. The replication-transcription conflict

    OpenAIRE

    Soultanas, Panos

    2011-01-01

    In response to environmental and nutritional stimuli, a whole array of proteins remodel genome architecture, activate or transcribe genes, suppress genes, repair lesions and base-modifications, faithfully replicate and safely separate the parental and daughter genomes during cell division. Negotiating and resolving conflicts of genome trafficking is essential for genome stability.

  4. Assembling semiconductor nanocomposites using DNA replication technologies.

    Energy Technology Data Exchange (ETDEWEB)

    Heimer, Brandon W.; Crown, Kevin K.; Bachand, George David

    2005-11-01

    Deoxyribonucleic acid (DNA) molecules represent Nature's genetic database, encoding the information necessary for all cellular processes. From a materials engineering perspective, DNA represents a nanoscale scaffold with highly refined structure, stability across a wide range of environmental conditions, and the ability to interact with a range of biomolecules. The ability to mass-manufacture functionalized DNA strands with Angstrom-level resolution through DNA replication technology, however, has not been explored. The long-term goal of the work presented in this report is focused on exploiting DNA and in vitro DNA replication processes to mass-manufacture nanocomposite materials. The specific objectives of this project were to: (1) develop methods for replicating DNA strands that incorporate nucleotides with ''chemical handles'', and (2) demonstrate attachment of nanocrystal quantum dots (nQDs) to functionalized DNA strands. Polymerase chain reaction (PCR) and primer extension methodologies were used to successfully synthesize amine-, thiol-, and biotin-functionalized DNA molecules. Significant variability in the efficiency of modified nucleotide incorporation was observed, and attributed to the intrinsic properties of the modified nucleotides. Noncovalent attachment of streptavidin-coated nQDs to biotin-modified DNA synthesized using the primer extension method was observed by epifluorescence microscopy. Data regarding covalent attachment of nQDs to amine- and thiol-functionalized DNA was generally inconclusive; alternative characterization tools are necessary to fully evaluate these attachment methods. Full realization of this technology may facilitate new approaches to manufacturing materials at the nanoscale. In addition, composite nQD-DNA materials may serve as novel recognition elements in sensor devices, or be used as diagnostic tools for forensic analyses. This report summarizes the results obtained over the course of this 1-year

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

    Science.gov (United States)

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

    2016-08-01

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

  6. Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program.

    Science.gov (United States)

    Foti, Rossana; Gnan, Stefano; Cornacchia, Daniela; Dileep, Vishnu; Bulut-Karslioglu, Aydan; Diehl, Sarah; Buness, Andreas; Klein, Felix A; Huber, Wolfgang; Johnstone, Ewan; Loos, Remco; Bertone, Paul; Gilbert, David M; Manke, Thomas; Jenuwein, Thomas; Buonomo, Sara C B

    2016-01-21

    DNA replication is temporally and spatially organized in all eukaryotes, yet the molecular control and biological function of the replication-timing program are unclear. Rif1 is required for normal genome-wide regulation of replication timing, but its molecular function is poorly understood. Here we show that in mouse embryonic stem cells, Rif1 coats late-replicating domains and, with Lamin B1, identifies most of the late-replicating genome. Rif1 is an essential determinant of replication timing of non-Lamin B1-bound late domains. We further demonstrate that Rif1 defines and restricts the interactions between replication-timing domains during the G1 phase, thereby revealing a function of Rif1 as organizer of nuclear architecture. Rif1 loss affects both number and replication-timing specificity of the interactions between replication-timing domains. In addition, during the S phase, Rif1 ensures that replication of interacting domains is temporally coordinated. In summary, our study identifies Rif1 as the molecular link between nuclear architecture and replication-timing establishment in mammals. PMID:26725008

  7. Uptake and Replication of Salmonella enterica in Acanthamoeba rhysodes

    OpenAIRE

    Tezcan-Merdol, Dilek; Ljungström, Marianne; Winiecka-Krusnell, Jadwiga; Linder, Ewert; Engstrand, Lars; Rhen, Mikael

    2004-01-01

    The ability of salmonellae to become internalized and to survive and replicate in amoebae was evaluated by using three separate serovars of Salmonella enterica and five different isolates of axenic Acanthamoeba spp. In gentamicin protection assays, Salmonella enterica serovar Dublin was internalized more efficiently than Salmonella enterica serovar Enteritidis or Salmonella enterica serovar Typhimurium in all of the amoeba isolates tested. The bacteria appeared to be most efficiently internal...

  8. Flavin-dependent thymidylate synthase X limits chromosomal DNA replication

    OpenAIRE

    Escartin, Frédéric; Skouloubris, Stéphane; Liebl, Ursula; Myllykallio, Hannu

    2008-01-01

    We have investigated the hitherto unexplored possibility that differences in the catalytic efficiencies of thymidylate synthases ThyX and ThyA, enzymes that produce the essential DNA precursor dTMP, have influenced prokaryotic genome evolution. We demonstrate that DNA replication speed in bacteria and archaea that contain the low-activity ThyX enzyme is up to 10-fold decreased compared with species that contain the catalytically more efficient ThyA. Our statistical studies of >400 genomes ind...

  9. 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

    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

  10. Versatile Trans-Replication Systems for Chikungunya Virus Allow Functional Analysis and Tagging of Every Replicase Protein.

    Science.gov (United States)

    Utt, Age; Quirin, Tania; Saul, Sirle; Hellström, Kirsi; Ahola, Tero; Merits, Andres

    2016-01-01

    Chikungunya virus (CHIKV; genus Alphavirus, family Togaviridae) has recently caused several major outbreaks affecting millions of people. There are no licensed vaccines or antivirals, and the knowledge of the molecular biology of CHIKV, crucial for development of efficient antiviral strategies, remains fragmentary. CHIKV has a 12 kb positive-strand RNA genome, which is translated to yield a nonstructural (ns) or replicase polyprotein. CHIKV structural proteins are expressed from a subgenomic RNA synthesized in infected cells. Here we have developed CHIKV trans-replication systems, where replicase expression and RNA replication are uncoupled. Bacteriophage T7 RNA polymerase or cellular RNA polymerase II were used for production of mRNAs for CHIKV ns polyprotein and template RNAs, which are recognized by CHIKV replicase and encode for reporter proteins. CHIKV replicase efficiently amplified such RNA templates and synthesized large amounts of subgenomic RNA in several cell lines. This system was used to create tagged versions of ns proteins including nsP1 fused with enhanced green fluorescent protein and nsP4 with an immunological tag. Analysis of these constructs and a matching set of replicon vectors revealed that the replicases containing tagged ns proteins were functional and maintained their subcellular localizations. When cells were co-transfected with constructs expressing template RNA and wild type or tagged versions of CHIKV replicases, formation of characteristic replicase complexes (spherules) was observed. Analysis of mutations associated with noncytotoxic phenotype in CHIKV replicons showed that a low level of RNA replication is not a pre-requisite for reduced cytotoxicity. The CHIKV trans-replicase does not suffer from genetic instability and represents an efficient, sensitive and reliable tool for studies of different aspects of CHIKV RNA replication process. PMID:26963103

  11. Polycomb proteins control proliferation and transformation independently of cell cycle checkpoints by regulating DNA replication

    DEFF Research Database (Denmark)

    Piunti, Andrea; Rossi, Alessandra; Cerutti, Aurora;

    2014-01-01

    PRCs regulate cellular proliferation and transformation independently of the Ink4a/Arf-pRb-p53 pathway. We provide evidence that PRCs localize at replication forks, and that loss of their function directly affects the progression and symmetry of DNA replication forks. Thus, we have identified a novel...

  12. Cotton responses to simulated insect damage: radiation-use efficiency, canopy architecture and leaf nitrogen content as affected by loss of reproductive organs

    International Nuclear Information System (INIS)

    Key cotton pests feed preferentially on reproductive organs which are normally shed after injury. Loss of reproductive organs in cotton may decrease the rate of leaf nitrogen depletion associated with fruit growth and increase nitrogen uptake and reduction by extending the period of root and leaf growth compared with undamaged plants. Higher levels of leaf nitrogen resulting from more assimilation and less depletion could increase the photosynthetic capacity of damaged crops in relation to undamaged controls. To test this hypothesis, radiation-use efficiency (RUE = g dry matter per MJ of photosynthetically active radiation intercepted by the canopy) of crops in which flowerbuds and young fruits were manually removed was compared with that of undamaged controls. Removal of fruiting structures did not affect RUE when cotton was grown at low nitrogen supply and high plant density. In contrast, under high nitrogen supply and low plant density, fruit removal increased seasonal RUE by 20–27% compared to controls. Whole canopy measurements, however, failed to detect the expected variations in foliar nitrogen due to damage. Differences in RUE between damaged and undamaged canopies were in part associated with changes in plant and canopy structure (viz. internode number and length, canopy height, branch angle) that modified light distribution within the canopy. These structural responses and their influence on canopy light penetration and photosynthesis are synthetised in coefficients of light extinction (k) that were 10 to 30% smaller in damaged crops than in controls and in a positive correlation between RUE−1 and k for crops grown under favourable conditions (i.e. high nitrogen, low density). Changes in plant structure and their effects on canopy architecture and RUE should be considered in the analysis of cotton growth after damage by insects that induce abscission of reproductive organs. (author)

  13. Retroviral restriction factors TRIM5α: therapeutic strategy to inhibit HIV-1 replication.

    Science.gov (United States)

    Zhang, Jing; Ge, Weiying; Zhan, Peng; De Clercq, Erik; Liu, Xinyong

    2011-01-01

    Tripartite motif protein 5-alpha (TRIM5α) is a cytoplasmic protein that efficiently recognizes the incoming capsid (CA) protein of retroviruses and potently inhibits virus infection in a species-specific manner. Through directly recognizing and interacting with HIV CA, TRIM5α is capable of disrupting the ordered process of viral uncoating, eventually interfering with HIV-1 reverse transcription and virus replication. TRIM5α protein contains four domains: RING domain, B-box 2 domain, coiled-coil domain, and B30.2 domain (SPRY) domain. All of the domains are necessary for efficient retrovirus restriction and the B30.2 domain has been shown to be the determinant of the specificity of restriction. Species-specific innate resistance against viral infections offers novel avenues for antiviral therapeutics. Various mutants of TRIM5α have been described which differently affect the HIV-1 reverse transcription process. This makes the establishment of new and improved models for HIV replication and AIDS pathogenesis by monitoring endogenous TRIM5α an attractive approach. TRIM5α-mediated restriction is modulated by the host protein Cyclophilin A (Cyp A) which could effectively interact with the CA of HIV-1. Here we will review the structure and roles of TRIM5α protein, the interaction between Cyp A and TRIM5α, as well as gene therapy strategies associated with TRIM5α to inhibit HIV-1 infection. PMID:21568899

  14. Use of a standardized protocol to identify factors affecting the efficiency of artificial insemination services for cattle through progesterone measurement in fourteen countries

    International Nuclear Information System (INIS)

    -cyclic cows; within this group 10.4% of cows were anoestrous or anovulatory, 2.2% were non-pregnant but bearing an active corpus luteum, and 4.7% were already pregnant. The highest incidence of problems was observed in farms of Cuba, Costa Rica, Indonesia and Venezuela. Progesterone data also showed that 27.4% of inseminated cows did not conceive but subsequent heats were unobserved, resulting in their non-pregnancy status being identified only at manual pregnancy diagnosis, usually 80-120 days after service. A further 10.1% of inseminated cows most probably conceived but lost their embryos between 16 and 50-60 days after service. These results show that nearly half of the inseminations were associated with factors of management deficiency or human error in the farms or in the AI service, thus adversely affecting the reproductive performance of the herds and leading to low efficiency of AI services. (author)

  15. The Cellular TAR RNA Binding Protein, TRBP, Promotes HIV-1 Replication Primarily by Inhibiting the Activation of Double-Stranded RNA-Dependent Kinase PKR▿

    OpenAIRE

    Sanghvi, Viraj R.; Steel, Laura F

    2011-01-01

    The TAR RNA binding protein, TRBP, is a cellular double-stranded RNA (dsRNA) binding protein that can promote the replication of HIV-1 through interactions with the viral TAR element as well as with cellular proteins that affect the efficiency of translation of viral transcripts. The structured TAR element, present on all viral transcripts, can impede efficient translation either by sterically blocking access of translation initiation factors to the 5′-cap or by activating the dsRNA-dependent...

  16. Hyperthermia stimulates HIV-1 replication.

    OpenAIRE

    Ferdinand Roesch; Oussama Meziane; Anna Kula; Sébastien Nisole; Françoise Porrot; Ian Anderson; Fabrizio Mammano; Ariberto Fassati; Alessandro Marcello; Monsef Benkirane; Olivier Schwartz

    2012-01-01

    International audience 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 inve...

  17. Biomarkers of replicative senescence revisited

    DEFF Research Database (Denmark)

    Nehlin, Jan

    2016-01-01

    of telomere length and associated damage, and the accompanying changes that take place elicit signals that have an impact on a number of molecules and downstream events. Precise measurements of replicative senescence biomarkers in biological samples from individuals could be clinically associated...... with their chronological age and present health status, help define their current rate of aging and contribute to establish personalized therapy plans to reduce, counteract or even avoid the appearance of aging biomarkers....

  18. Regulating telomere length from the inside out: the replication fork model

    Science.gov (United States)

    2016-01-01

    Telomere length is regulated around an equilibrium set point. Telomeres shorten during replication and are lengthened by telomerase. Disruption of the length equilibrium leads to disease; thus, it is important to understand the mechanisms that regulate length at the molecular level. The prevailing protein-counting model for regulating telomerase access to elongate the telomere does not explain accumulating evidence of a role of DNA replication in telomere length regulation. Here I present an alternative model: the replication fork model that can explain how passage of a replication fork and regulation of origin firing affect telomere length. PMID:27401551

  19. 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...... 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...... 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...

  20. Effective ANT based Routing Algorithm for Data Replication in MANETs

    Directory of Open Access Journals (Sweden)

    N.J. Nithya Nandhini

    2013-12-01

    Full Text Available In mobile ad hoc network, the nodes often move and keep on change its topology. Data packets can be forwarded from one node to another on demand. To increase the data accessibility data are replicated at nodes and made as sharable to other nodes. Assuming that all mobile host cooperative to share their memory and allow forwarding the data packets. But in reality, all nodes do not share the resources for the benefits of others. These nodes may act selfishly to share memory and to forward the data packets. This paper focuses on selfishness of mobile nodes in replica allocation and routing protocol based on Ant colony algorithm to improve the efficiency. The Ant colony algorithm is used to reduce the overhead in the mobile network, so that it is more efficient to access the data than with other routing protocols. This result shows the efficiency of ant based routing algorithm in the replication allocation.

  1. 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....

  2. 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. PMID:26940865

  3. The cellular TAR RNA binding protein, TRBP, promotes HIV-1 replication primarily by inhibiting the activation of double-stranded RNA-dependent kinase PKR.

    Science.gov (United States)

    Sanghvi, Viraj R; Steel, Laura F

    2011-12-01

    The TAR RNA binding protein, TRBP, is a cellular double-stranded RNA (dsRNA) binding protein that can promote the replication of HIV-1 through interactions with the viral TAR element as well as with cellular proteins that affect the efficiency of translation of viral transcripts. The structured TAR element, present on all viral transcripts, can impede efficient translation either by sterically blocking access of translation initiation factors to the 5'-cap or by activating the dsRNA-dependent kinase, PKR. Several mechanisms by which TRBP can facilitate translation of viral transcripts have been proposed, including the binding and unwinding of TAR and the suppression of PKR activation. Further, TRBP has been identified as a cofactor of Dicer in the processing of microRNAs (miRNAs), and sequestration of TRBP by TAR in infected cells has been proposed as a viral countermeasure to potential host cell RNA interference-based antiviral activities. Here, we have addressed the relative importance of these various roles for TRBP in HIV-1 replication. Using Jurkat T cells, primary human CD4(+) T cells, and additional cultured cell lines, we show that depletion of TRBP has no effect on viral replication when PKR activation is otherwise blocked. Moreover, the presence of TAR-containing mRNAs does not affect the efficacy of cellular miRNA silencing pathways. These results establish that TRBP, when expressed at physiological levels, promotes HIV-1 replication mainly by suppressing the PKR-mediated antiviral response, while its contribution to HIV-1 replication through PKR-independent pathways is minimal. PMID:21937648

  4. In search of the holy replicator

    OpenAIRE

    Gilbert, David M.

    2004-01-01

    After 40 years of searching for the eukaryotic replicator sequence, it is time to abandon the concept of ‘the’ replicator as a single genetic entity. Here I propose a ‘relaxed replicon model’ in which a positive initiator–replicator interaction is facilitated by a combination of several complex features of chromatin. An important question for the future is whether the positions of replication origins are simply a passive result of local chromatin structure or are actively localized to coordin...

  5. Possible applications for replicating HIV 1 vectors

    OpenAIRE

    Das, Atze T.; Jeeninga, Rienk E.; Berkhout, Ben

    2010-01-01

    Since its discovery some 25 years ago, much has been learned about HIV type 1 and the molecular details of its replication cycle. This insight has been used to develop lentiviral vector systems that have advantages over conventional retroviral vector systems. For safety reasons, the lentiviral vector systems are replication incompetent and the risk of generating a replication competent virus has been minimized. Nevertheless, there may be certain applications for replication competent HIV base...

  6. A comparison of three replication strategies in complex multicellular organisms: Asexual replication, sexual replication with identical gametes, and sexual replication with distinct sperm and egg gametes

    OpenAIRE

    Tannenbaum, Emmanuel

    2007-01-01

    This paper studies the mutation-selection balance in three simplified replication models. The first model considers a population of organisms replicating via the production of asexual spores. The second model considers a sexually replicating population that produces identical gametes. The third model considers a sexually replicating population that produces distinct sperm and egg gametes. All models assume diploid organisms whose genomes consist of two chromosomes, each of which is taken to b...

  7. Asexual and sexual replication in sporulating organisms

    OpenAIRE

    Lee, Bohyun; Tannenbaum, Emmanuel

    2006-01-01

    This paper develops models describing asexual and sexual replication in sporulating organisms. Replication via sporulation is the replication strategy for all multicellular life, and may even be observed in unicellular life (such as with budding yeast). We consider diploid populations replicating via one of two possible sporulation mechanisms: (1) Asexual sporulation, whereby adult organisms produce single-celled diploid spores that grow into adults themselves. (2) Sexual sporulation, whereby...

  8. Mutator phenotypes due to DNA replication infidelity

    OpenAIRE

    Arana, Mercedes E.; Kunkel, Thomas A.

    2010-01-01

    This article considers the fidelity of DNA replication performed by eukaryotic DNA polymerases involved in replicating the nuclear genome. DNA replication fidelity can vary widely depending on the DNA polymerase, the composition of the error, the flanking sequence, the presence of DNA damage and the ability to correct errors. As a consequence, defects in processes that determine DNA replication fidelity can confer strong mutator phenotypes whose specificity can help determine the molecular na...

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

    International Nuclear Information System (INIS)

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

  10. A four-phase data replication algorithm for data grid

    Directory of Open Access Journals (Sweden)

    Alireza Saleh

    2015-04-01

    Full Text Available Nowadays, scientific applications generate a huge amount of data in terabytes or petabytes. Data grids currently proposed solutions to large scale data management problems including efficient file transfer and replication. Data is typically replicated in a Data Grid to improve the job response time and data availability. A reasonable number and right locations for replicas has become a challenge in the Data Grid. In this paper, a four-phase dynamic data replication algorithm based on Temporal and Geographical locality is proposed. It includes: 1 evaluating and identifying the popular data and triggering a replication operation when the popularity data passes a dynamic threshold; 2 analyzing and modeling the relationship between system availability and the number of replicas, and calculating a suitable number of new replicas; 3 evaluating and identifying the popular data in each site, and placing replicas among them; 4 removing files with least cost of average access time when encountering insufficient space for replication. The algorithm was tested using a grid simulator, OptorSim developed by European Data Grid Projects. The simulation results show that the proposed algorithm has better performance in comparison with other algorithms in terms of job execution time, effective network usage and percentage of storage filled.

  11. 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...

  12. DNA Replication Reaches the Breaking Point

    OpenAIRE

    Petrini, John H.J.

    2009-01-01

    DNA strand breaks that result in stalled or damaged replication forks can be detrimental to the DNA replication process. In this issue, Doksani et al. (2009) examine the impact of a single double-stranded DNA break on replication in the budding yeast, Saccharomyces cerevisiae.

  13. Chromosomal context and replication properties of ARS plasmids in Schizosaccharomyces pombe

    Indian Academy of Sciences (India)

    Aditya S Pratihar; Vishnu P Tripathi; Mukesh P Yadav; Dharani D Dubey

    2015-12-01

    Short, specific DNA sequences called as Autonomously Replicating Sequence (ARS) elements function as plasmid as well as chromosomal replication origins in yeasts. As compared to ARSs, different chromosomal origins vary greatly in their efficiency and timing of replication probably due to their wider chromosomal context. The two Schizosaccharomyces pombe ARS elements, ars727 and ars2OO4, represent two extremities in their chromosomal origin activity - ars727 is inactive and late replicating, while ars2OO4 is a highly active, early-firing origin. To determine the effect of chromosomal context on the activity of these ARS elements, we have cloned them with their extended chromosomal context as well as in the context of each other in both orientations and analysed their replication efficiency by ARS and plasmid stability assays. We found that these ARS elements retain their origin activity in their extended/altered context. However, deletion of a 133-bp region of the previously reported ars727-associated late replication enforcing element (LRE) caused advancement in replication timing of the resulting plasmid. These results confirm the role of LRE in directing plasmid replication timing and suggest that the plasmid origin efficiency of ars2OO4 or ars727 remains unaltered by the extended chromosomal context.

  14. Lipid Membranes in Poxvirus Replication

    Directory of Open Access Journals (Sweden)

    Jason P. Laliberte

    2010-04-01

    Full Text Available Poxviruses replicate in the cytoplasm, where they acquire multiple lipoprotein membranes. Although a proposal that the initial membrane arises de novo has not been substantiated, there is no accepted explanation for its formation from cellular membranes. A subsequent membrane-wrapping step involving modified trans-Golgi or endosomal cisternae results in a particle with three membranes. These wrapped virions traverse the cytoplasm on microtubules; the outermost membrane is lost during exocytosis, the middle one is lost just prior to cell entry, and the remaining membrane fuses with the cell to allow the virus core to enter the cytoplasm and initiate a new infection.

  15. Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription.

    OpenAIRE

    Kogoma, T

    1997-01-01

    Chromosome replication in Escherichia coli is normally initiated at oriC, the origin of chromosome replication. E. coli cells possess at least three additional initiation systems for chromosome replication that are normally repressed but can be activated under certain specific conditions. These are termed the stable DNA replication systems. Inducible stable DNA replication (iSDR), which is activated by SOS induction, is proposed to be initiated from a D-loop, an early intermediate in homologo...

  16. Initiation of bacteriophage lambda DNA replication in vitro with purified lambda replication proteins.

    OpenAIRE

    Wold, M S; Mallory, J B; Roberts, J D; LeBowitz, J H; McMacken, R

    1982-01-01

    We have developed a soluble enzyme system that replicates exogenously added plasmid DNA (lambda dv) bearing the replication origin of the bacteriophage lambda chromosome. The system contains pure phage lambda O and P replication proteins and a partially purified mixture of Escherichia coli replication proteins [the enzyme system of Fuller, R.S., Kaguni, J.M. & Kornberg, A. (1981) Proc. Natl. Acad. Sci. USA 78, 7370-7374). The features of lambda dv replication in this system closely resemble t...

  17. Slower uncoating is associated with impaired replicative capability of simian-tropic HIV-1.

    Science.gov (United States)

    Kono, Ken; Takeda, Eri; Tsutsui, Hiromi; Kuroishi, Ayumu; Hulme, Amy E; Hope, Thomas J; Nakayama, Emi E; Shioda, Tatsuo

    2013-01-01

    Human immunodeficiency virus type 1 (HIV-1) productively infects only humans and chimpanzees, but not Old World monkeys, such as rhesus and cynomolgus (CM) monkeys. To establish a monkey model of HIV-1/AIDS, several HIV-1 derivatives have been constructed. We previously generated a simian-tropic HIV-1 that replicates efficiently in CM cells. This virus encodes a capsid protein (CA) with SIVmac239-derived loops between α-helices 4 and 5 (L4/5) and between α-helices 6 and 7 (L6/7), along with the entire vif from SIVmac239 (NL-4/5S6/7SvifS). These SIVmac239-derived sequences were expected to protect the virus from HIV-1 restriction factors in monkey cells. However, the replicative capability of NL-4/5S6/7SvifS in human cells was severely impaired. By long-term cultivation of human CEM-SS cells infected with NL-4/5S6/7SvifS, we succeeded in partially rescuing the impaired replicative capability of the virus in human cells. This adapted virus encoded a G-to-E substitution at the 116(th) position of the CA (NL-4/5SG116E6/7SvifS). In the work described here, we explored the mechanism by which the replicative capability of NL-4/5S6/7SvifS was impaired in human cells. Quantitative analysis (by real-time PCR) of viral DNA synthesis from infected cells revealed that NL-4/5S6/7SvifS had a major defect in nuclear entry. Mutations in CA are known to affect viral core stability and result in deleterious effects in HIV-1 infection; therefore, we measured the kinetics of uncoating of these viruses. The uncoating of NL-4/5S6/7SvifS was significantly slower than that of wild type HIV-1 (WT), whereas the uncoating of NL-4/5SG116E6/7SvifS was similar to that of WT. Our results suggested that the lower replicative capability of NL-4/5S6/7SvifS in human cells was, at least in part, due to the slower uncoating of this virus. PMID:23967315

  18. Mycobacteria Exploit Host Hyaluronan for Efficient Extracellular Replication

    OpenAIRE

    Yukio Hirayama; Mamiko Yoshimura; Yuriko Ozeki; Isamu Sugawara; Tadashi Udagawa; Satoru Mizuno; Naoki Itano; Koji Kimata; Aki Tamaru; Hisashi Ogura; Kazuo Kobayashi; Sohkichi Matsumoto

    2009-01-01

    In spite of the importance of hyaluronan in host protection against infectious organisms in the alveolar spaces, its role in mycobacterial infection is unknown. In a previous study, we found that mycobacteria interact with hyaluronan on lung epithelial cells. Here, we have analyzed the role of hyaluronan after mycobacterial infection was established and found that pathogenic mycobacteria can grow by utilizing hyaluronan as a carbon source. Both mouse and human possess 3 kinds of hyaluronan sy...

  19. Interaction between muscle temperature and contraction velocity affects mechanical efficiency during moderate-intensity cycling exercise in young and older women

    OpenAIRE

    Bell, Martin P.; Ferguson, Richard A

    2009-01-01

    The effect of elevated muscle temperature on mechanical efficiency was investigated during exercise at different pedal frequencies in young and older women. Eight young (24 ± 3 yr) and eight older (70 ± 4 yr) women performed 6-min periods of cycling at 75% ventilatory threshold at pedal frequencies of 45, 60, 75, and 90 rpm under control and passively elevated local muscle temperature conditions. Mechanical efficiency was calculated from the ratio of energy turnover (pulmonary O2 uptake) and ...

  20. Inference by replication in densely connected systems

    International Nuclear Information System (INIS)

    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

  1. Replication of Holograms with Corn Syrup by Rubbing

    Directory of Open Access Journals (Sweden)

    Arturo Olivares-Pérez

    2012-08-01

    Full Text Available Corn syrup films are used to replicate holograms in order to fabricate micro-structural patterns without the toxins commonly found in photosensitive salts and dyes. We use amplitude and relief masks with lithographic techniques and rubbing techniques in order to transfer holographic information to corn syrup material. Holographic diffraction patterns from holographic gratings and computer Fourier holograms fabricated with corn syrup are shown. We measured the diffraction efficiency parameter in order to characterize the film. The versatility of this material for storage information is promising. Holographic gratings achieved a diffraction efficiency of around 8.4% with an amplitude mask and 36% for a relief mask technique. Preliminary results using corn syrup as an emulsion for replicating holograms are also shown in this work.

  2. On the Specificity of Interaction between the Saccharomyces cerevisiae Clamp Loader Replication Factor C and Primed DNA Templates during DNA Replication*

    OpenAIRE

    Hingorani, Manju M.; Coman, Maria Magdalena

    2002-01-01

    Replication factor C (RFC) catalyzes assembly of circular proliferating cell nuclear antigen clamps around primed DNA, enabling processive synthesis by DNA polymerase during DNA replication and repair. In order to perform this function efficiently, RFC must rapidly recognize primed DNA as the substrate for clamp assembly, particularly during lagging strand synthesis. Earlier reports as well as quantitative DNA binding experiments from this study indicate, however, that RFC interacts with prim...

  3. Understanding how replication processes can maintain systems away from equilibrium using Algorithmic Information Theory.

    Science.gov (United States)

    Devine, Sean D

    2016-02-01

    Replication can be envisaged as a computational process that is able to generate and maintain order far-from-equilibrium. Replication processes, can self-regulate, as the drive to replicate can counter degradation processes that impact on a system. The capability of replicated structures to access high quality energy and eject disorder allows Landauer's principle, in conjunction with Algorithmic Information Theory, to quantify the entropy requirements to maintain a system far-from-equilibrium. Using Landauer's principle, where destabilising processes, operating under the second law of thermodynamics, change the information content or the algorithmic entropy of a system by ΔH bits, replication processes can access order, eject disorder, and counter the change without outside interventions. Both diversity in replicated structures, and the coupling of different replicated systems, increase the ability of the system (or systems) to self-regulate in a changing environment as adaptation processes select those structures that use resources more efficiently. At the level of the structure, as selection processes minimise the information loss, the irreversibility is minimised. While each structure that emerges can be said to be more entropically efficient, as such replicating structures proliferate, the dissipation of the system as a whole is higher than would be the case for inert or simpler structures. While a detailed application to most real systems would be difficult, the approach may well be useful in understanding incremental changes to real systems and provide broad descriptions of system behaviour. PMID:26723233

  4. Self-replication of DNA rings

    Science.gov (United States)

    Kim, Junghoon; Lee, Junwye; Hamada, Shogo; Murata, Satoshi; Ha Park, Sung

    2015-06-01

    Biology provides numerous examples of self-replicating machines, but artificially engineering such complex systems remains a formidable challenge. In particular, although simple artificial self-replicating systems including wooden blocks, magnetic systems, modular robots and synthetic molecular systems have been devised, such kinematic self-replicators are rare compared with examples of theoretical cellular self-replication. One of the principal reasons for this is the amount of complexity that arises when you try to incorporate self-replication into a physical medium. In this regard, DNA is a prime candidate material for constructing self-replicating systems due to its ability to self-assemble through molecular recognition. Here, we show that DNA T-motifs, which self-assemble into ring structures, can be designed to self-replicate through toehold-mediated strand displacement reactions. The inherent design of these rings allows the population dynamics of the systems to be controlled. We also analyse the replication scheme within a universal framework of self-replication and derive a quantitative metric of the self-replicability of the rings.

  5. Contributions to data replication in large-scale distributed systems

    OpenAIRE

    Monnet, Sébastien

    2015-01-01

    Data replication is a key mechanism for building a reliable and efficient data management system. Indeed, by keeping several replicas for each piece of data, it is possible to improve durability. Furthermore, well-placed copies reduce data accesstime. However, having multiple copies for a single piece of data creates consistency problems when the data is updated. Over the last years, I made contributions related to these three aspects: data durability, data access performance and data consist...

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

    Directory of Open Access Journals (Sweden)

    Gaëlle Demarre

    2010-05-01

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

  7. Lysis of dysplastic but not normal oral keratinocytes and tissue-engineered epithelia with conditionally replicating adenoviruses.

    Science.gov (United States)

    Gaballah, Kamis; Hills, Allison; Curiel, David; Hallden, Gunnel; Harrison, Paul; Partridge, Max

    2007-08-01

    There is no effective medical treatment for oral precancer, and surgery to remove these lesions is imprecise because abnormal mucosa extends beyond the visible lesion. Development of vectors for tumor-selective viral replication has been a significant advance, and viral lysis is well suited to destruction of oral precancerous mucosa. To facilitate evaluation of new treatments, we engineered dysplastic oral epithelium using keratinocytes isolated from dysplastic lesions. We show that these model systems recapitulate the key characteristics of the clinical lesions closely, and that topical delivery of the conditionally replicating adenovirus (CRAd) dl922-947 can lyse tissue-engineered epithelia that show mild, moderate, or severe dysplasia, but normal oral epithelia are very resistant to this treatment. The lytic effect is determined by various factors, including the grade and proliferation index of the dysplastic epithelia. The presence of suprabasal cycling cells, expression of the coxsackie adenovirus receptor (CAR), the transcription cofactor p300, and other aberrations that affect the regulation of the cell cycle or apoptosis and promote viral replication may also be important. The ability of dl922-947 to destroy engineered oral dysplasia was significantly greater than that observed using wild-type adenovirus, d/1520, or viruses modified to bypass cell entry dependent on the presence of CAR. Evidence of infection in clinical dysplastic lesions was also shown ex vivo using tissue explants. We conclude that dl922-947 may provide an efficient molecular cytotoxic to dissolve oral dysplastic lesions. PMID:17671197

  8. Wide area data replication in an ITER-relevant data environment

    International Nuclear Information System (INIS)

    The next generation of tokamak experiments will require a new way of approaching data sharing issues among fusion organizations. In the fusion community, many researchers at different worldwide sites will analyse data produced by International Thermonuclear Experimental Reactor (ITER), wherever it will be built. In this context, an efficient availability of the data in the sites where the computational resources are located becomes a major architectural issue for the deployment of ITER computational infrastructure. The approach described in this paper goes beyond the usual site-centric model mainly devoted to granting access exclusively to experimental data stored at the device sites. To this aim, we propose a new data replication architecture relying on a wide area network, based on a Master/Slave model and on synchronization techniques producing mirrored data sites. In this architecture, data replication will affect large databases (TB) as well as large UNIX-like file systems, using open source-based software components, namely MySQL, as database management system, and RSYNC and BBFTP for data transfer. A test-bed has been set up to evaluate the performance of the software components underlying the proposed architecture. The test-bed hardware layout deploys a cluster of four Dual-Xeon Supermicro each with a raid array of 1 TB. High performance network line (1 Gbit over 400 km) provides the infrastructure to test the components on a wide area network. The results obtained will be thoroughly discussed

  9. A replicating plasmid-based vector for GFP expression in Mycoplasma hyopneumoniae.

    Science.gov (United States)

    Ishag, H Z A; Liu, M J; Yang, R S; Xiong, Q Y; Feng, Z X; Shao, G Q

    2016-01-01

    Mycoplasma hyopneumoniae (M. hyopneumoniae) causes porcine enzootic pneumonia (PEP) that significantly affects the pig industry worldwide. Despite the availability of the whole genome sequence, studies on the pathogenesis of this organism have been limited due to the lack of a genetic manipulation system. Therefore, the aim of the current study was to generate a general GFP reporter vector based on a replicating plasmid. Here, we describe the feasibility of GFP reporter expression in M. hyopneumoniae (strain 168L) controlled by the p97 gene promoter of this mycoplasma. An expression plasmid (pMD18-TOgfp) containing the p97 gene promoter, and origin of replication (oriC) of M. hyopneumoniae, tetracycline resistant marker (tetM), and GFP was constructed and used to transform competent M. hyopneumoniae cells. We observed green fluorescence in M. hyopneumoniae transformants under fluorescence microscopy, which indicates that there was expression of the GFP reporter that was driven by the p97 gene promoter. Additionally, an electroporation method for M. hyopneumoniae with an efficiency of approximately 1 x 10(-6) transformants/μg plasmid DNA was optimized and is described herein. In conclusion, our data demonstrate the susceptibility of M. hyopneumoniae to genetic manipulation whereby foreign genes are expressed. This work may encourage the development of genetic tools to manipulate the genome of M. hyopneumoniae for functional genomic analyses. PMID:27173288

  10. Evaluating contextual factors affecting the technical efficiency of freshwater pond culture systems in Peninsular Malaysia: A two-stage DEA approach

    Directory of Open Access Journals (Sweden)

    Abdullahi Iliyasu

    2016-05-01

    Full Text Available The demand for animal protein, especially fish, is growing fast, perhaps due to the rapid expansion of populations, increases in income and changes in eating habits and life styles. Capture fisheries, which supply over 70% of the fish for human consumption in Malaysia, are over-exploited or depleted. Their yields have become stagnant over the last few decades and in some cases have even declined. Nevertheless, aquaculture has the potential to meet these challenges if practised well. This study therefore aims to estimate the technical efficiency of pond culture systems using data envelopment analysis (DEA. In addition, it investigates the determinants of technical efficiency by employing an ordinary least squares (OLS regression model. The estimated technical efficiency of pond culture was found to be 0.86, which means that the fish farmers in our sample could reach full technical efficiency through reducing their input usage by 14% with the current level of technology to produce the same output levels. The results of the OLS regression indicate that farmers’ age, experience, extension training and water management have positive and statistically significant impacts on technical efficiency. Information on water management practices could be passed on by extension agents to inefficient farms to assist them in catching up with the farms demonstrating best practice.

  11. Rif1 regulates initiation timing of late replication origins throughout the S. cerevisiae genome.

    Directory of Open Access Journals (Sweden)

    Jared M Peace

    Full Text Available Chromosomal DNA replication involves the coordinated activity of hundreds to thousands of replication origins. Individual replication origins are subject to epigenetic regulation of their activity during S-phase, resulting in differential efficiencies and timings of replication initiation during S-phase. This regulation is thought to involve chromatin structure and organization into timing domains with differential ability to recruit limiting replication factors. Rif1 has recently been identified as a genome-wide regulator of replication timing in fission yeast and in mammalian cells. However, previous studies in budding yeast have suggested that Rif1's role in controlling replication timing may be limited to subtelomeric domains and derives from its established role in telomere length regulation. We have analyzed replication timing by analyzing BrdU incorporation genome-wide, and report that Rif1 regulates the timing of late/dormant replication origins throughout the S. cerevisiae genome. Analysis of pfa4Δ cells, which are defective in palmitoylation and membrane association of Rif1, suggests that replication timing regulation by Rif1 is independent of its role in localizing telomeres to the nuclear periphery. Intra-S checkpoint signaling is intact in rif1Δ cells, and checkpoint-defective mec1Δ cells do not comparably deregulate replication timing, together indicating that Rif1 regulates replication timing through a mechanism independent of this checkpoint. Our results indicate that the Rif1 mechanism regulates origin timing irrespective of proximity to a chromosome end, and suggest instead that telomere sequences merely provide abundant binding sites for proteins that recruit Rif1. Still, the abundance of Rif1 binding in telomeric domains may facilitate Rif1-mediated repression of non-telomeric origins that are more distal from centromeres.

  12. DNA Replication via Entanglement Swapping

    CERN Document Server

    Pusuluk, Onur

    2010-01-01

    Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Molecular biology assumes that function is explained by structure, the complementary geometries of molecules and weak intermolecular hydrogen bonds. However, both this assumption and its converse are possible if organic molecules and quantum circuits/protocols are considered as hardware and software of living systems that are co-optimized during evolution. In this paper, we try to model DNA replication as a multiparticle entanglement swapping with a reliable qubit representation of nucleotides. In the model, molecular recognition of a nucleotide triggers an intrabase entanglement corresponding to a superposition state of different tautomer forms. Then, base pairing occurs by swapping intrabase entanglements with interbase entanglements.

  13. Therapeutic targeting of replicative immortality.

    Science.gov (United States)

    Yaswen, Paul; MacKenzie, Karen L; Keith, W Nicol; Hentosh, Patricia; Rodier, Francis; Zhu, Jiyue; Firestone, Gary L; Matheu, Ander; Carnero, Amancio; Bilsland, Alan; Sundin, Tabetha; Honoki, Kanya; Fujii, Hiromasa; Georgakilas, Alexandros G; Amedei, Amedeo; Amin, Amr; Helferich, Bill; Boosani, Chandra S; Guha, Gunjan; Ciriolo, Maria Rosa; Chen, Sophie; Mohammed, Sulma I; Azmi, Asfar S; Bhakta, Dipita; Halicka, Dorota; Niccolai, Elena; Aquilano, Katia; Ashraf, S Salman; Nowsheen, Somaira; Yang, Xujuan

    2015-12-01

    One of the hallmarks of malignant cell populations is the ability to undergo continuous proliferation. This property allows clonal lineages to acquire sequential aberrations that can fuel increasingly autonomous growth, invasiveness, and therapeutic resistance. Innate cellular mechanisms have evolved to regulate replicative potential as a hedge against malignant progression. When activated in the absence of normal terminal differentiation cues, these mechanisms can result in a state of persistent cytostasis. This state, termed "senescence," can be triggered by intrinsic cellular processes such as telomere dysfunction and oncogene expression, and by exogenous factors such as DNA damaging agents or oxidative environments. Despite differences in upstream signaling, senescence often involves convergent interdependent activation of tumor suppressors p53 and p16/pRB, but can be induced, albeit with reduced sensitivity, when these suppressors are compromised. Doses of conventional genotoxic drugs required to achieve cancer cell senescence are often much lower than doses required to achieve outright cell death. Additional therapies, such as those targeting cyclin dependent kinases or components of the PI3K signaling pathway, may induce senescence specifically in cancer cells by circumventing defects in tumor suppressor pathways or exploiting cancer cells' heightened requirements for telomerase. Such treatments sufficient to induce cancer cell senescence could provide increased patient survival with fewer and less severe side effects than conventional cytotoxic regimens. This positive aspect is countered by important caveats regarding senescence reversibility, genomic instability, and paracrine effects that may increase heterogeneity and adaptive resistance of surviving cancer cells. Nevertheless, agents that effectively disrupt replicative immortality will likely be valuable components of new combinatorial approaches to cancer therapy. PMID:25869441

  14. FDI会影响地方政府效率吗?①%Will FDI Affect the Efficiency of Local Government?

    Institute of Scientific and Technical Information of China (English)

    祁毓; 郭均均

    2012-01-01

    This paper takes the government efficiency as the very important characteristic of FDI social comprehensive effect, and investigates influence of FDI on local government efficiency by Empirical analysis, based on the measure and calculation of each provincial government efficiency and their decomposition value between 1996 and 2008. The result proves that, FDI has notable negative effect on local government efficiency, FDI has positive correlation with local government technological improvement, FDI has negative correlation with scale efficiency, and partially this negative correlation is notable. Besides, FDI's influence on local government efficiency has intimate connection with the degree of local fiscal decentralization, local educational level, the condition of transfer payment, and the capital stock.%本文以政府效率作为FDI社会综合效应的重要表征,在测算1996~2008年各省份地方政府效率及其分解值的基础上,实证考察了FDI对地方政府效率的影响。实证结果表明,FDI对地方政府效率产生了显著的负面效应,其中,FDI与地方政府的技术进步呈正相关但不显著,而与规模效率呈负相关且部分显著;此外,FDI对地方政府效率的影响与财政分权程度、教育水平、转移支付状况以及资本存量有着密切的联系。在此基础上,提出了如何改善招商引资策略和提高FDI消化能力来提高地方政府效率的基本思路。

  15. Replicating organizational knowledge: principles or templates?

    OpenAIRE

    Baden-Fuller, Charles; Winter, Sidney G.

    2005-01-01

    We discuss how firms can replicate practices and knowledge embedded in practices by following principles, with no direct reference to an extant working example (template). Definitions are provided for the key concepts of templates, principles, and background knowledge. We address the challenges of providing operational measures for successful replication, and for comparing the efficacy of principles and templates. By using two longitudinal case studies of replication across the units of two m...

  16. Federated SPARQL Queries Processing with Replicated Fragments

    OpenAIRE

    Montoya, Gabriela; Skaf-Molli, Hala; Molli, Pascal; Vidal, Maria-Esther

    2015-01-01

    Federated query engines allow to consume linked data from SPARQL endpoints. Replicating data fragments from different sources allows to reorganize data to better fit federated query processing of data consumers. However, existing federated query engines poorly support replication. In this paper, we propose a replication-aware federated query engine that extends state-of-art federated query engine ANAPSID and FedX with Fedra, a source selection strategy that approximates the source selection p...

  17. Persistent HIV-1 replication during antiretroviral therapy

    OpenAIRE

    Martinez-Picado, Javier; Deeks, Steven G

    2016-01-01

    Purpose of review The present review will highlight some of the recent findings regarding the capacity of HIV-1 to replicate during antiretroviral therapy (ART). Recent findings Although ART is highly effective at inhibiting HIV replication, it is not curative. Several mechanisms contribute to HIV persistence during ART, including HIV latency, immune dysfunction, and perhaps persistent low-level spread of the virus to uninfected cells (replication). The success in curing HIV will depend on ef...

  18. Controlled rereplication at DNA replication origins

    OpenAIRE

    Gómez, María

    2008-01-01

    No-more-than-once per cell cycle initiation of DNA replication is a golden rule to maintain genome stability and guarantee cell survival. In our recent work we discovered that small genome fragments of about 200 bp are repeatedly synthesised at human DNA replication origins at the time of origin firing during S phase in normal cells. Rereplicated DNA fragments coincide physical and temporarily with replication origin activity, implying that their generation is intimately associated with the i...

  19. Early weaning and postweaning nutritional management affect feedlot performance of angus x simmental heifers and the relationship of 12th rib fat and marbling score to feed efficiency.

    Science.gov (United States)

    Wertz, E; Berge, L L; Walker, P M; Faulkner, D B; McKeith, F K; Rodriguez-Zas, S

    2001-07-01

    Early-weaned Angus x Simmental heifers were used to evaluate the effects of postweaning nutritional management on feedlot performance, carcass merit, and the relationship of intramuscular and subcutaneous fat deposition to the feed efficiency among heifers fed for a high-quality market. Sixteen heifers were weaned at 73+/-5.5 d of age and grazed on endophyte-infected tall fescue for 18 mo before entering the feedlot (early-weaned-P). Eighty heifers from the following year's calf crop were weaned at 71+/-5.5 d of age and allowed either ad libitum access to a 25% concentrate diet (early-weaned-25C) or limit-fed a 90% concentrate diet (early-weaned-90C) to achieve a similar ADG. Following a 119-d growing period, 16 early-weaned-90C and 16 early-weaned-25C calves were paired based on BW and growth rate and individually fed during the finishing period along with the early-weaned-P heifers. Ultrasound measurements of s.c. and i.m. fat were recorded at approximately 60-d intervals throughout the finishing period. Feed efficiency was regressed against s.c. and i.m. fat, and i.m. fat was regressed on s.c. fat. Despite a similar ADG, early-weaned-90C calves gained more efficiently (P carcasses with less s.c. fat cover while gaining more efficiently than heifers finished as yearlings. PMID:11465351

  20. Handling Fragmented Database Replication through Binary Vote Assignment Grid Quorum

    Directory of Open Access Journals (Sweden)

    Ainul A.C. Fauzi

    2011-01-01

    Full Text Available Problem statement: Organizations critically needed to supply recent data to users who may be geographically remote, while at the same time handle a volume request of distributed data around multiple sites. The storage, availability and consistency are important issues to be addressed in order to allow distributed users efficiently and safely access data from many different sites. Approach: Data replication is a way to deal with this problem since it provides user with fast, local access to shared data and protects availability of applications because alternate data access options exist. Handling fragmented database replication becomes challenging issue to administrator since the distributed database was scattered into split replica partitions or fragments. Results: This study presented a new mechanism on how to handle the fragmented database replication through the Binary Vote Assignment on Grid Quorum (BVAGQ. We address how to build reliable system by using the proposed BVAGQ for distributed database fragmentation. Conclusion: The result shows that managing fragmented database replication and transaction through proposed BVAGQ is able to preserve the data consistency.

  1. 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.

  2. Cells and prions: a license to replicate.

    Science.gov (United States)

    Nuvolone, Mario; Aguzzi, Adriano; Heikenwalder, Mathias

    2009-08-20

    Prion diseases are neurodegenerative, infectious disorders characterized by the aggregation of a misfolded isoform of the cellular prion protein (PrP(C)). The infectious agent - termed prion - is mainly composed of misfolded PrP(Sc). In addition to the central nervous system prions can colonize secondary lymphoid organs and inflammatory foci. Follicular dendritic cells are important extraneural sites of prion replication. However, recent data point to a broader range of cell types that can replicate prions. Here, we review the state of the art in regards to peripheral prion replication, neuroinvasion and the determinants of prion replication competence. PMID:19527722

  3. Comparison of three replication strategies in complex multicellular organisms: Asexual replication, sexual replication with identical gametes, and sexual replication with distinct sperm and egg gametes

    Science.gov (United States)

    Tannenbaum, Emmanuel

    2008-01-01

    This paper studies the mutation-selection balance in three simplified replication models. The first model considers a population of organisms replicating via the production of asexual spores. The second model considers a sexually replicating population that produces identical gametes. The third model considers a sexually replicating population that produces distinct sperm and egg gametes. All models assume diploid organisms whose genomes consist of two chromosomes, each of which is taken to be functional if equal to some master sequence, and defective otherwise. In the asexual population, the asexual diploid spores develop directly into adult organisms. In the sexual populations, the haploid gametes enter a haploid pool, where they may fuse with other haploids. The resulting immature diploid organisms then proceed to develop into mature organisms. Based on an analysis of all three models, we find that, as organism size increases, a sexually replicating population can only outcompete an asexually replicating population if the adult organisms produce distinct sperm and egg gametes. A sexual replication strategy that is based on the production of large numbers of sperm cells to fertilize a small number of eggs is found to be necessary in order to maintain a sufficiently low cost for sex for the strategy to be selected for over a purely asexual strategy. We discuss the usefulness of this model in understanding the evolution and maintenance of sexual replication as the preferred replication strategy in complex, multicellular organisms.

  4. 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.......Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural...

  5. Cross-catalytic peptide nucleic acid (PNA) replication based on templated ligation

    DEFF Research Database (Denmark)

    Singhal, Abhishek; Nielsen, Peter E

    2014-01-01

    We report the first PNA self-replicating system based on template directed cross-catalytic ligation, a process analogous to biological replication. Using two template PNAs and four pentameric precursor PNAs, all four possible carbodiimide assisted amide ligation products were detected and...... identified by HPLC and MALDI-TOF analysis. We conclude that the two template complementary reaction products are generated via cross-catalysis, while the other two self-complementary (and in principle auto-catalytic) products are formed via intra-complex coupling between the two sets of complementary PNA...... precursors. Cross-catalytic product formation followed product inhibited kinetics, but approximately two replication rounds were observed. Analogous but less efficient replication was found for a similar tetrameric system. These results demonstrate that simpler nucleobase replication systems than natural...

  6. Acute MUS81 depletion leads to replication fork slowing and a constitutive DNA damage response

    DEFF Research Database (Denmark)

    Xing, Meichun; Wang, Xiaohui; Palmai-Pallag, Timea;

    2015-01-01

    The MUS81 protein belongs to a conserved family of DNA structure-specific nucleases that play important roles in DNA replication and repair. Inactivation of the Mus81 gene in mice has no major deleterious consequences for embryonic development, although cancer susceptibility has been reported. We...... have investigated the role of MUS81 in human cells by acutely depleting the protein using shRNAs. We found that MUS81 depletion from human fibroblasts leads to accumulation of ssDNA and a constitutive DNA damage response that ultimately activates cellular senescence. Moreover, we show that MUS81 is...... required for efficient replication fork progression during an unperturbed S-phase, and for recovery of productive replication following replication stalling. These results demonstrate essential roles for the MUS81 nuclease in maintenance of replication fork integrity....

  7. How does the connectivity of open-framework conglomerates within multi-scale hierarchical fluvial architecture affect oil sweep efficiency in waterflooding?

    CERN Document Server

    Gershenzon, Naum I; Ritzi, Robert W; Dominic, David F; Keefer, Don; Shaffer, Eric; Storsved, Brynne

    2015-01-01

    We studied the effects on oil sweep efficiency of the proportion, hierarchical organization, and connectivity of high-permeability open-framework conglomerate (OFC) cross-sets within the multi-scale stratal architecture found in fluvial deposits. Utilizing numerical simulations and the RVA/Paraview open-source visualization package, we analyzed oil production rate, water breakthrough time, and spatial and temporal distribution of residual oil saturation. The effective permeability of the reservoir exhibits large-scale anisotropy created by the organization of OFC cross-sets within unit bars, and the organization of unit bars within compound bars. As a result oil sweep efficiency critically depends on the direction of the pressure gradient. When pressure gradient is oriented normal to paleoflow direction, the total oil production and the water breakthrough time are larger, and remaining oil saturation is smaller. This result is found regardless of the proportion or connectivity of the OFC cross-sets, within th...

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

    Science.gov (United States)

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

    1994-07-01

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

  9. Factors Affecting the Efficiency of Excited-States Interactions of Complexes between Some Visible Light-Emitting Lanthanide Ions and Cyclophanes Containing Spirobiindanol Phosphonates

    Directory of Open Access Journals (Sweden)

    M. S. Attia

    2007-01-01

    Full Text Available The efficiency of excited-states interactions between lanthanide ions Tb3+ and Eu3+ and some new cyclophanes (I, II, and III has been studied in different media. High luminescence quantum yield values for terbium and europium complexes in DMSO and PMMA were obtained. The photophysical properties of the green and red emissive Tb3+ and Eu3+ complexes have been elucidated, respectively.

  10. Effect of parameter choice in root water uptake models – the arrangement of root hydraulic properties within the root architecture affects dynamics and efficiency of root water uptake

    OpenAIRE

    Bechmann, M.; Schneider, C; Carminati, A.; Vetterlein, D.; Attinger, S.; Hildebrandt, A

    2014-01-01

    Detailed three-dimensional models of root water uptake have become increasingly popular for investigating the process of root water uptake. However, they suffer from a lack of information on important parameters, particularly on the spatial distribution of root axial and radial conductivities, which vary greatly along a root system. In this paper we explore how the arrangement of those root hydraulic properties and branching within the root system affects modelled uptake dynamics, xylem water...

  11. How much do incentives affect car purchase? Agent-based microsimulation of consumer choice of new cars. Part 2. Forecasting effects of feebates based on energy-efficiency

    International Nuclear Information System (INIS)

    In this paper, we simulate the car market in order to forecast the effects of feebate systems based on an energy-labeling scheme using categories A to G. Very fuel-efficient (A) cars receive a cash incentive, highly inefficient (G) cars pay additional fees. Consumers have different price elasticities and behavioral options to react to feebates. They can switch to a smaller sized car, but as energy-efficiency varies widely within size segments, they can also stick to the preferred size class and choose a more efficient (smaller) engine. In addition, previously owned cars influence the next car to be chosen. We use an agent-based microsimulation approach particularly suited to predict environmental and market effects of feebates. Heteorogeneous agents choose from a choice set drawn from a detailed fleet of new cars. Incentives of EUR2000 for A-labeled cars induce an additional rated CO2 emission decrease of new car registrations between 3.4% and 4.3%, with CO2 abatement costs between EUR6 and EUR13 per ton, and otherwise little undesired market disturbance. The risk of rebound effects is estimated to be low. After adopting the frequencies of consumer segments to a given country, the model presented is applicable to all European car markets. (author)

  12. 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.

  13. Suppression of feline coronavirus replication in vitro by cyclosporin A

    Directory of Open Access Journals (Sweden)

    Tanaka Yoshikazu

    2012-04-01

    Full Text Available Abstract The feline infectious peritonitis virus (FIPV is a member of the feline coronavirus family that causes FIP, which is incurable and fatal in cats. Cyclosporin A (CsA, an immunosuppressive agent that targets the nuclear factor pathway of activated T-cells (NF-AT to bind cellular cyclophilins (CyP, dose-dependently inhibited FIPV replication in vitro. FK506 (an immunosuppressor of the pathway that binds cellular FK506-binding protein (FKBP but not CyP did not affect FIPV replication. Neither cell growth nor viability changed in the presence of either CsA or FK506, and these factors did not affect the NF-AT pathway in fcwf-4 cells. Therefore, CsA does not seem to exert inhibitory effects via the NF-AT pathway. In conclusion, CsA inhibited FIPV replication in vitro and further studies are needed to verify the practical value of CsA as an anti-FIPV treatment in vivo.

  14. 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…

  15. Plasmid deoxyribonucleic acid replication in Streptomyces griseus.

    OpenAIRE

    Xue, Y.; Zhuang, Z.; Zhu, Y.; Xu, Y.; Dong, K.

    1981-01-01

    A series of electron micrographs showing the presence of different molecular forms representing various replication stages of plasmid deoxyribonucleic acid from Streptomyces griseus was obtained. Based upon an analysis of these electron micrographs, a tentative model for plasmid deoxyribonucleic acid replication in S. griseus is proposed.

  16. 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…

  17. The avian-origin H3N2 canine influenza virus that recently emerged in the United States has limited replication in swine.

    Science.gov (United States)

    Abente, Eugenio J; Anderson, Tavis K; Rajao, Daniela S; Swenson, Sabrina; Gauger, Phillip C; Vincent, Amy L

    2016-09-01

    Equine-origin H3N8 has circulated in dogs in the United States since 1999. A genetically and antigenically distinct avian-origin H3N2 canine influenza was detected in March of 2015 in Chicago, Illinois. Subsequent outbreaks were reported with over 1000 dogs in the Midwest affected followed by 23 additional states with detections within 5 months. The potential for canine-to-swine transmission was unknown. Experimental infection in pigs showed this virus does not replicate efficiently in swine. PMID:27110913

  18. The important role of surface ligand on CdSe/CdS core/shell nanocrystals in affecting the efficiency of H2 photogeneration from water

    Science.gov (United States)

    Wang, Ping; Zhang, Jie; He, Haili; Xu, Xiaolong; Jin, Yongdong

    2015-03-01

    The use of colloidal semiconductor nanocrystals (NCs), especially those with a core/shell structure, for photocatalytic hydrogen (H2) production from water is currently one of the hottest research fields. Although the ligand on the semiconductor NC surface is crucial to the optical and optoelectronic properties of the NC, the study of the ligand effect on the photocatalytic activity of H2 generation is rarely reported. Herein, we employ nearly monodispersed CdSe/CdS core/shell NCs as a model photocatalytic system, and three kinds of ligands with different numbers of functional thiol groups (i.e., poly(acrylic acid), 3-mercaptopropionic acid and 2,3-dimercaptosuccinic acid) are selected as the ligands to investigate the effect of ligand on the efficiency of H2 photogeneration. The results show that the H2 photogeneration efficiency is highly dependent on the surface ligand of the NCs, and it increases with the increase of the number of the functional thiol groups in the ligand, and correspondingly, the photoluminescence intensity and average fluorescence lifetime, which are measured by steady state and time-resolved fluorescence measurements, are decreased. The surface trap-related charge separation efficiency, which is mediated by surface coating with different ligands, is supposed to cause the distinct ligand-dependent performance in the H2 evolution.The use of colloidal semiconductor nanocrystals (NCs), especially those with a core/shell structure, for photocatalytic hydrogen (H2) production from water is currently one of the hottest research fields. Although the ligand on the semiconductor NC surface is crucial to the optical and optoelectronic properties of the NC, the study of the ligand effect on the photocatalytic activity of H2 generation is rarely reported. Herein, we employ nearly monodispersed CdSe/CdS core/shell NCs as a model photocatalytic system, and three kinds of ligands with different numbers of functional thiol groups (i.e., poly(acrylic acid), 3

  19. Different effect of proteasome inhibition on vesicular stomatitis virus and poliovirus replication.

    Directory of Open Access Journals (Sweden)

    Nickolay Neznanov

    Full Text Available Proteasome activity is an important part of viral replication. In this study, we examined the effect of proteasome inhibitors on the replication of vesicular stomatitis virus (VSV and poliovirus. We found that the proteasome inhibitors significantly suppressed VSV protein synthesis, virus accumulation, and protected infected cells from toxic effect of VSV replication. In contrast, poliovirus replication was delayed, but not diminished in the presence of the proteasome inhibitors MG132 and Bortezomib. We also found that inhibition of proteasomes stimulated stress-related processes, such as accumulation of chaperone hsp70, phosphorylation of eIF2alpha, and overall inhibition of translation. VSV replication was sensitive to this stress with significant decline in replication process. Poliovirus growth was less sensitive with only delay in replication. Inhibition of proteasome activity suppressed cellular and VSV protein synthesis, but did not reduce poliovirus protein synthesis. Protein kinase GCN2 supported the ability of proteasome inhibitors to attenuate general translation and to suppress VSV replication. We propose that different mechanisms of translational initiation by VSV and poliovirus determine their sensitivity to stress induced by the inhibition of proteasomes. To our knowledge, this is the first study that connects the effect of stress induced by proteasome inhibition with the efficiency of viral infection.

  20. Levels of the E2 interacting protein TopBP1 modulate papillomavirus maintenance stage replication

    Energy Technology Data Exchange (ETDEWEB)

    Kanginakudru, Sriramana, E-mail: skangina@iu.edu [Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN (United States); DeSmet, Marsha, E-mail: mdesmet@iupui.edu [Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN (United States); Thomas, Yanique, E-mail: ysthomas@umail.iu.edu [Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN (United States); Morgan, Iain M., E-mail: immorgan@vcu.edu [VCU Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia (United States); Androphy, Elliot J., E-mail: eandro@iu.edu [Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN (United States); Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN (United States)

    2015-04-15

    The evolutionarily conserved DNA topoisomerase II beta-binding protein 1 (TopBP1) functions in DNA replication, DNA damage response, and cell survival. We analyzed the role of TopBP1 in human and bovine papillomavirus genome replication. Consistent with prior reports, TopBP1 co-localized in discrete nuclear foci and was in complex with papillomavirus E2 protein. Similar to E2, TopBP1 is recruited to the region of the viral origin of replication during G1/S and early S phase. TopBP1 knockdown increased, while over-expression decreased transient virus replication, without affecting cell cycle. Similarly, using cell lines harboring HPV-16 or HPV-31 genome, TopBP1 knockdown increased while over-expression reduced viral copy number relative to genomic DNA. We propose a model in which TopBP1 serves dual roles in viral replication: it is essential for initiation of replication yet it restricts viral copy number. - Highlights: • Protein interaction study confirmed In-situ interaction between TopBP1 and E2. • TopBP1 present at papillomavirus ori in G1/S and early S phase of cell cycle. • TopBP1 knockdown increased, over-expression reduced virus replication. • TopBP1 protein level change did not influence cell survival or cell cycle. • TopBP1 displaced from papillomavirus ori after initiation of replication.

  1. Levels of the E2 interacting protein TopBP1 modulate papillomavirus maintenance stage replication

    International Nuclear Information System (INIS)

    The evolutionarily conserved DNA topoisomerase II beta-binding protein 1 (TopBP1) functions in DNA replication, DNA damage response, and cell survival. We analyzed the role of TopBP1 in human and bovine papillomavirus genome replication. Consistent with prior reports, TopBP1 co-localized in discrete nuclear foci and was in complex with papillomavirus E2 protein. Similar to E2, TopBP1 is recruited to the region of the viral origin of replication during G1/S and early S phase. TopBP1 knockdown increased, while over-expression decreased transient virus replication, without affecting cell cycle. Similarly, using cell lines harboring HPV-16 or HPV-31 genome, TopBP1 knockdown increased while over-expression reduced viral copy number relative to genomic DNA. We propose a model in which TopBP1 serves dual roles in viral replication: it is essential for initiation of replication yet it restricts viral copy number. - Highlights: • Protein interaction study confirmed In-situ interaction between TopBP1 and E2. • TopBP1 present at papillomavirus ori in G1/S and early S phase of cell cycle. • TopBP1 knockdown increased, over-expression reduced virus replication. • TopBP1 protein level change did not influence cell survival or cell cycle. • TopBP1 displaced from papillomavirus ori after initiation of replication

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    DEFF Research Database (Denmark)

    Feng, Yunpeng; Vlassis, Arsenios; Roques, Céline;

    2016-01-01

    During DNA replication, thousands of replication origins are activated across the genome. Chromatin architecture contributes to origin specification and usage, yet it remains unclear which chromatin features impact on DNA replication. Here, we perform a RNAi screen for chromatin regulators......45 recruitment, but not MCM2-7 loading, is impaired in BRPF3-depleted cells, identifying a BRPF3-dependent function of HBO1 in origin activation that is complementary to its role in licencing. We thus propose that BRPF3-HBO1 acetylation of histone H3K14 around TSS facilitates efficient activation of...

  4. Complete in vitro replication of SV40 DNA and chromatin in saponin-treated permeable cells.

    OpenAIRE

    Hosogi,Nobuo; Hanakawa,Shiro; Watanabe,Sekiko; Oda,Takuzo

    1981-01-01

    A permeable cell system has been developed by treatment with saponin for studying in vitro replication of DNA and chromatin. DNA replication of simian virus 40 nucleoprotein complexes (SV40 chromatin) in saponin-treated permeable cells was found to be more efficient than that in digitonin-treated permeable cells. Autoradiography of the agarose-gel revealed that [alpha-32P]dCTP was incorporated into SV40 DNA I, II and replicating intermediates. The time course of the incorporation indicated co...

  5. p53 Protein Is a Suppressor of Papillomavirus DNA Amplificational Replication

    OpenAIRE

    Lepik, Dina; Ilves, Ivar; Kristjuhan, Arnold; Maimets, Toivo; Ustav, Mart

    1998-01-01

    p53 protein was able to block human and bovine papillomavirus DNA amplificational replication while not interfering with Epstein-Barr virus oriP once-per-cell cycle replication. Oligomerization, intact DNA-binding, replication protein A-binding, and proline-rich domains of the p53 protein were essential for efficient inhibition, while the N-terminal transcriptional activation and C-terminal regulatory domains were dispensable for the suppressor activity of the p53 protein. The inhibition of r...

  6. UvrD controls the access of recombination proteins to blocked replication forks

    OpenAIRE

    Lestini, Roxane; Michel, Bénédicte

    2007-01-01

    Blocked replication forks often need to be processed by recombination proteins prior to replication restart. In Escherichia coli, the UvrD repair helicase was recently shown to act at inactivated replication forks, where it counteracts a deleterious action of RecA. Using two mutants affected for different subunits of the polymerase III holoenzyme (Pol IIIh), we show here that the anti-RecA action of UvrD at blocked forks reflects two different activities of this enzyme. A defective UvrD mutan...

  7. Histone H3 lysine 56 acetylation and the response to DNA replication fork damage

    DEFF Research Database (Denmark)

    Wurtele, Hugo; Kaiser, Gitte Schalck; Bacal, Julien;

    2012-01-01

    In Saccharomyces cerevisiae, histone H3 lysine 56 acetylation (H3K56ac) occurs in newly synthesized histones that are deposited throughout the genome during DNA replication. Defects in H3K56ac sensitize cells to genotoxic agents, suggesting that this modification plays an important role in the DNA...... but are only mildly affected by hydroxyurea. We demonstrate that, after exposure to MMS, H3K56ac-deficient cells cannot complete DNA replication and eventually segregate chromosomes with intranuclear foci containing the recombination protein Rad52. In addition, we provide evidence that these...... lesions by recombination and/or from defects in the completion of DNA replication....

  8. Caspase-1 promotes Epstein-Barr virus replication by targeting the large tegument protein deneddylase to the nucleus of productively infected cells.

    Directory of Open Access Journals (Sweden)

    Stefano Gastaldello

    Full Text Available The large tegument proteins of herpesviruses contain N-terminal cysteine proteases with potent ubiquitin and NEDD8-specific deconjugase activities, but the function of the enzymes during virus replication remains largely unknown. Using as model BPLF1, the homologue encoded by Epstein-Barr virus (EBV, we found that induction of the productive virus cycle does not affect the total level of ubiquitin-conjugation but is accompanied by a BPLF1-dependent decrease of NEDD8-adducts and accumulation of free NEDD8. Expression of BPLF1 promotes cullin degradation and the stabilization of cullin-RING ligases (CRLs substrates in the nucleus, while cytoplasmic CRLs and their substrates are not affected. The inactivation of nuclear CRLs is reversed by the N-terminus of CAND1, which inhibits the binding of BPLF1 to cullins and prevents efficient viral DNA replication. Targeting of the deneddylase activity to the nucleus is dependent on processing of the catalytic N-terminus by caspase-1. Inhibition of caspase-1 severely impairs viral DNA synthesis and the release of infectious virus, pointing a previously unrecognized role of the cellular response to danger signals triggered by EBV reactivation in promoting virus replication.

  9. Effect of specific amino acid substitutions in the putative fusion peptide of structural glycoprotein E2 on Classical Swine Fever Virus replication

    International Nuclear Information System (INIS)

    E2, along with Erns and E1, is an envelope glycoprotein of Classical Swine Fever Virus (CSFV). E2 is involved in several virus functions: cell attachment, host range susceptibility and virulence in natural hosts. Here we evaluate the role of a specific E2 region, 818CPIGWTGVIEC828, containing a putative fusion peptide (FP) sequence. Reverse genetics utilizing a full-length infectious clone of the highly virulent CSFV strain Brescia (BICv) was used to evaluate how individual amino acid substitutions within this region of E2 may affect replication of BICv. A synthetic peptide representing the complete E2 FP amino acid sequence adopted a β-type extended conformation in membrane mimetics, penetrated into model membranes, and perturbed lipid bilayer integrity in vitro. Similar peptides harboring amino acid substitutions adopted comparable conformations but exhibited different membrane activities. Therefore, a preliminary characterization of the putative FP 818CPIGWTGVIEC828 indicates a membrane fusion activity and a critical role in virus replication. - Highlights: • A putative fusion peptide (FP) region in CSFV E2 protein was shown to be critical for virus growth. • Synthetic FPs were shown to efficiently penetrate into lipid membranes using an in vitro model. • Individual residues in the FP affecting virus replication were identified by reverse genetics. • The same FP residues are also responsible for mediating membrane fusion

  10. Effect of specific amino acid substitutions in the putative fusion peptide of structural glycoprotein E2 on Classical Swine Fever Virus replication

    Energy Technology Data Exchange (ETDEWEB)

    Fernández-Sainz, I.J. [Plum Island Animal Disease Center, ARS, USDA (United States); Largo, E. [Biophysics Unit (CSIC-UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao (Spain); Gladue, D.P.; Fletcher, P. [Plum Island Animal Disease Center, ARS, USDA (United States); O’Donnell, V. [Plum Island Animal Disease Center, ARS, USDA (United States); Plum Island Animal Disease Center, DHS, Greenport, NY 11944 (United States); Holinka, L.G. [Plum Island Animal Disease Center, ARS, USDA (United States); Carey, L.B. [Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), E-08003 Barcelona (Spain); Lu, X. [Plum Island Animal Disease Center, DHS, Greenport, NY 11944 (United States); Nieva, J.L. [Biophysics Unit (CSIC-UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao (Spain); Borca, M.V., E-mail: manuel.borca@ars.usda.gov [Plum Island Animal Disease Center, ARS, USDA (United States)

    2014-05-15

    E2, along with E{sup rns} and E1, is an envelope glycoprotein of Classical Swine Fever Virus (CSFV). E2 is involved in several virus functions: cell attachment, host range susceptibility and virulence in natural hosts. Here we evaluate the role of a specific E2 region, {sup 818}CPIGWTGVIEC{sup 828}, containing a putative fusion peptide (FP) sequence. Reverse genetics utilizing a full-length infectious clone of the highly virulent CSFV strain Brescia (BICv) was used to evaluate how individual amino acid substitutions within this region of E2 may affect replication of BICv. A synthetic peptide representing the complete E2 FP amino acid sequence adopted a β-type extended conformation in membrane mimetics, penetrated into model membranes, and perturbed lipid bilayer integrity in vitro. Similar peptides harboring amino acid substitutions adopted comparable conformations but exhibited different membrane activities. Therefore, a preliminary characterization of the putative FP {sup 818}CPIGWTGVIEC{sup 828} indicates a membrane fusion activity and a critical role in virus replication. - Highlights: • A putative fusion peptide (FP) region in CSFV E2 protein was shown to be critical for virus growth. • Synthetic FPs were shown to efficiently penetrate into lipid membranes using an in vitro model. • Individual residues in the FP affecting virus replication were identified by reverse genetics. • The same FP residues are also responsible for mediating membrane fusion.

  11. A Necessary Condition for Coexistence of Autocatalytic Replicators in a Prebiotic Environment

    OpenAIRE

    Grover, Martha A; Hernandez, Andres F.

    2013-01-01

    A necessary, but not sufficient, mathematical condition for the coexistence of short replicating species is presented here. The mathematical condition is obtained for a prebiotic environment, simulated as a fed-batch reactor, which combines monomer recycling, variable reaction order and a fixed monomer inlet flow with two replicator types and two monomer types. An extensive exploration of the parameter space in the model validates the robustness and efficiency of the mathematical condition, w...

  12. Interaction between human immunodeficiency virus and Toxoplasma gondii replication in dually infected monocytoid cells.

    OpenAIRE

    Welker, Y; Molina, J. M.; Poirot, C.; Ferchal, F; Decazes, J M; Lagrange, P.; Derouin, F.

    1993-01-01

    THP-1 monocytoid cells, either not infected or chronically infected with human immunodeficiency virus type 1 (HIV-1), were challenged with Toxoplasma gondii. Parasitic growth, as assessed by trophozoite counting and measurement of supernatant p30 membrane antigen, was similar in HIV-infected and noninfected THP-1 cells. Also, T. gondii did not affect HIV replication. These experiments therefore failed to demonstrate any interaction between HIV-1 and T. gondii replication in concurrently infec...

  13. Cyclophilin Inhibitors Block Arterivirus Replication by Interfering with Viral RNA Synthesis

    OpenAIRE

    de Wilde, A. H.; Li, Y; van der Meer, Y.; Vuagniaux, G; Lysek, R.; Fang, Y; Snijder, E J; van Hemert, M. J.

    2013-01-01

    Virus replication strongly depends on cellular factors, in particular, on host proteins. Here we report that the replication of the arteriviruses equine arteritis virus (EAV) and porcine reproductive and respiratory syndrome virus (PRRSV) is strongly affected by low-micromolar concentrations of cyclosporine A (CsA), an inhibitor of members of the cyclophilin (Cyp) family. In infected cells, the expression of a green fluorescent protein (GFP) reporter gene inserted into the PRRSV genome was in...

  14. Entrepreneurial Efficiency

    OpenAIRE

    Katsuya Takii

    2004-01-01

    This paper examines a particular aspect of entrepreneurship, namely firms' ability to respond appropriately to unexpected changes in the environment (i.e., their adaptability). An increase in firms' adaptability improves allocative efficiency in a competitive economy, but can reduce it when opportunities are distorted. It is shown that adaptability can aggravate distortions in the presence of political risk. Because efficiency affects the total factor productivity (TFP) of an economy, the mod...

  15. Inferring Where and When Replication Initiates from Genome-Wide Replication Timing Data

    Science.gov (United States)

    Baker, A.; Audit, B.; Yang, S. C.-H.; Bechhoefer, J.; Arneodo, A.

    2012-06-01

    Based on an analogy between DNA replication and one dimensional nucleation-and-growth processes, various attempts to infer the local initiation rate I(x,t) of DNA replication origins from replication timing data have been developed in the framework of phase transition kinetics theories. These works have all used curve-fit strategies to estimate I(x,t) from genome-wide replication timing data. Here, we show how to invert analytically the Kolmogorov-Johnson-Mehl-Avrami model and extract I(x,t) directly. Tests on both simulated and experimental budding-yeast data confirm the location and firing-time distribution of replication origins.

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

    Directory of Open Access Journals (Sweden)

    Richard A. Klein

    2014-04-01

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

  17. The antiestrogen endoxifen protects rat liver mitochondria from permeability transition pore opening and oxidative stress at concentrations that do not affect the phosphorylation efficiency

    International Nuclear Information System (INIS)

    Endoxifen (EDX) is a key active metabolite of tamoxifen (TAM) with higher affinity and specificity to estrogen receptors that also inhibits aromatase activity. It is safe and well tolerated by healthy humans, but its use requires toxicological characterization. In this study, the effects of EDX on mitochondria, the primary targets for xenobiotic-induced toxicity, were monitored to clarify its potential side effects. EDX up to 30 nmol/mg protein did not affect the mitochondrial oxidative phosphorylation. At 50 nmol EDX/mg protein, EDX decreased the ADP phosphorylation rate and a partial collapse of mitochondrial membrane potential (Δψ), that parallels a state 4 stimulation, was observed. As the stimulation of state 4 was not inhibited by oligomycin and 50 nmol EDX/mg protein caused a slight decrease in the light scattering of mitochondria, these data suggest that EDX promotes membrane permeabilization to protons, whereas TAM at the same concentration induced mitochondrial membrane disruption. Moreover, EDX at 10 nmol/mg protein prevented and reversed the Ca2+-induced depolarization of ΔΨ and the release of mitochondrial Ca2+, similarly to cyclosporine A, indicating that EDX did not affect Ca2+ uptake, but directly interfered with the proteins of the mitochondrial permeability transition (MPT) megacomplex, inhibiting MPT induction. At this concentration, EDX exhibited antioxidant activity that may account for the protective effect against MPT pore opening. In conclusion, EDX within the range of concentrations reached in tissues did not significantly damage the bioenergetic functions of mitochondria, contrarily to the prodrug TAM, and prevented the MPT pore opening and the oxidative stress in mitochondria, supporting that EDX may be a less toxic drug for women with breast carcinoma. - Highlights: ► Mitochondria are important targets of Endoxifen. ► Endoxifen prevents mitochondrial permeability transition. ► Endoxifen prevents oxidative stress in mitochondria

  18. The antiestrogen endoxifen protects rat liver mitochondria from permeability transition pore opening and oxidative stress at concentrations that do not affect the phosphorylation efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Ribeiro, Mariana P.C.; Silva, Filomena S.G.; Santos, Armanda E. [Center for Neuroscience and Cell Biology, University of Coimbra, 3000-354 Coimbra (Portugal); Laboratory of Biochemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra (Portugal); Santos, Maria S. [Center for Neuroscience and Cell Biology, University of Coimbra, 3000-354 Coimbra (Portugal); Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3004-517 Coimbra (Portugal); Custódio, José B.A., E-mail: custodio@ci.uc.pt [Center for Neuroscience and Cell Biology, University of Coimbra, 3000-354 Coimbra (Portugal); Laboratory of Biochemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra (Portugal)

    2013-02-15

    Endoxifen (EDX) is a key active metabolite of tamoxifen (TAM) with higher affinity and specificity to estrogen receptors that also inhibits aromatase activity. It is safe and well tolerated by healthy humans, but its use requires toxicological characterization. In this study, the effects of EDX on mitochondria, the primary targets for xenobiotic-induced toxicity, were monitored to clarify its potential side effects. EDX up to 30 nmol/mg protein did not affect the mitochondrial oxidative phosphorylation. At 50 nmol EDX/mg protein, EDX decreased the ADP phosphorylation rate and a partial collapse of mitochondrial membrane potential (Δψ), that parallels a state 4 stimulation, was observed. As the stimulation of state 4 was not inhibited by oligomycin and 50 nmol EDX/mg protein caused a slight decrease in the light scattering of mitochondria, these data suggest that EDX promotes membrane permeabilization to protons, whereas TAM at the same concentration induced mitochondrial membrane disruption. Moreover, EDX at 10 nmol/mg protein prevented and reversed the Ca{sup 2+}-induced depolarization of ΔΨ and the release of mitochondrial Ca{sup 2+}, similarly to cyclosporine A, indicating that EDX did not affect Ca{sup 2+} uptake, but directly interfered with the proteins of the mitochondrial permeability transition (MPT) megacomplex, inhibiting MPT induction. At this concentration, EDX exhibited antioxidant activity that may account for the protective effect against MPT pore opening. In conclusion, EDX within the range of concentrations reached in tissues did not significantly damage the bioenergetic functions of mitochondria, contrarily to the prodrug TAM, and prevented the MPT pore opening and the oxidative stress in mitochondria, supporting that EDX may be a less toxic drug for women with breast carcinoma. - Highlights: ► Mitochondria are important targets of Endoxifen. ► Endoxifen prevents mitochondrial permeability transition. ► Endoxifen prevents oxidative

  19. 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.

  20. Phosphoproteomic Analysis of KSHV-Infected Cells Reveals Roles of ORF45-Activated RSK during Lytic Replication.

    Directory of Open Access Journals (Sweden)

    Denis Avey

    2015-07-01

    Full Text Available Kaposi's Sarcoma-Associated Herpesvirus (KSHV is an oncogenic virus which has adapted unique mechanisms to modulate the cellular microenvironment of its human host. The pathogenesis of KSHV is intimately linked to its manipulation of cellular signaling pathways, including the extracellular signal-regulated kinase (ERK mitogen-activated protein kinase (MAPK pathway. We have previously shown that KSHV ORF45 contributes to the sustained activation of both ERK and p90 ribosomal S6 kinase (RSK, a major functional mediator of ERK/MAPK signaling during KSHV lytic replication. ORF45-activated RSK is required for optimal KSHV lytic gene expression and progeny virion production, though the underlying mechanisms downstream of this activation are still unclear. We hypothesized that the activation of RSK by ORF45 causes differential phosphorylation of cellular and viral substrates, affecting biological processes essential for efficient KSHV lytic replication. Accordingly, we observed widespread and significant differences in protein phosphorylation upon induction of lytic replication. Mass-spectrometry-based phosphoproteomic screening identified putative substrates of ORF45-activated RSK in KSHV-infected cells. Bioinformatic analyses revealed that nuclear proteins, including several transcriptional regulators, were overrepresented among these candidates. We validated the ORF45/RSK-dependent phosphorylation of several putative substrates by employing KSHV BAC mutagenesis, kinase inhibitor treatments, and/or CRISPR-mediated knockout of RSK in KSHV-infected cells. Furthermore, we assessed the consequences of knocking out these substrates on ORF45/RSK-dependent regulation of gene expression and KSHV progeny virion production. Finally, we show data to support that ORF45 regulates the translational efficiency of a subset of viral/cellular genes with complex secondary structure in their 5' UTR. Altogether, these data shed light on the mechanisms by which KSHV ORF45

  1. Study on the micro-replication of shark skin

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Direct replication of creatural scarfskins to form biomimetic surfaces with relatively vivid morphology is a new attempt of the bio-replicated forming technology at animal body. Taking shark skins as the replication templates, and the micro-embossing and micro-molding as the material forming methods, the micro-replicating technology of the outward morphology on shark skins was demonstrated. The preliminary analysis on replication precision indicates that the bio-replicated forming technology can replicate the outward morphology of the shark scales with good precision, which validates the application of the bio-replicated forming technology in the direct morphology replication of the firm creatural scarfskins.

  2. 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

  3. Changing Dermatopathology Protocols for Processing Small Skin Biopsies: Decreases in Slide Quantity Does Not Affect Patient Care and Allows for Optimal Efficiency.

    Science.gov (United States)

    Mudaliar, Kumaran; Speiser, Jodi; Hutchens, Kelli A

    2016-06-01

    In dermatopathology, no standard protocol exists for processing small biopsy specimens. In our original protocol, 2 routine initial slides per biopsy were prepared. For 1003 biopsies, we noted how often the second slide helped in diagnosis or eliminated the need for additional deeper sections. After obtaining these data, we switched to processing only 1 initial slide (new protocol) and again evaluated 1003 biopsies. During the original protocol, the second slide never helped to make a diagnosis that was not apparent on the first slide. When deeper sections were ordered (10.4% of cases), they helped in the diagnosis 34.6% of the time. In the new protocol, deeper sections were ordered in 15.9% of cases and helped in the diagnosis 32.7% of the time when ordered. Comparing rates of deeper sections ordered showed no significant difference for benign, inflammatory/reactive, and premalignant/malignant groups (P > 0.1). However, there was a significant increase in deeper sections ordered for melanocytic lesions from 16.9% to 32.3% (P Switching protocols, the estimated annual cost savings is $2890. The majority of cases at our institution are properly diagnosed using only 1 slide. From our study findings, we conclude that 1 slide preparation for small biopsies is the best practice for our institution and one that does not affect diagnostic accuracy, reduces costs, and helps in effective time management. PMID:27101126

  4. The intracellular dynamics of hepatitis B virus (HBV) replication with reproduced virion "re-cycling".

    Science.gov (United States)

    Nakabayashi, Jun

    2016-05-01

    Hepatitis B virus (HBV) is a causative agent of hepatitis. Clinical outcome of hepatitis type B depends on the viral titer observed in the peripheral blood of the patient. In the chronic hepatitis patient, production of HBV virion remains low level. On the other hand, the viral load prominently increases in fulminant hepatitis patient as compared with that in the chronic hepatitis patient. We previously proposed a mathematical model describing the intracellular dynamics of HBV replication. Our model clarified that there are two distinguishable replication patterns of HBV named "arrested" and "explosive" replication. In the arrested replication, the amount of virion newly reproduced from an infected cell remains low level, while the amount of virion extremely increases in the explosive replication. Viral load is drastically changed by slight alteration of expression ratio of 3.5kb RNA to 2.4kb mRNA of HBV. Though our model provided the switching mechanism determining the replication pattern of HBV, HBV dynamics is determined by not only the expression pattern of viral genes. In this study, "recycling" of HBV virion in the replication cycle is investigated as a new factor affecting the intracellular dynamics of HBV replication. A part of newly produced virion of HBV is reused as a core particle that is a resource of HBV replication. This recycling of HBV virion lowers the threshold for the explosive replication when waiting time for the next cycle of the replication is large. It is seemingly contradicting that prominent production of HBV is caused by large recycling rate and small release rate of HBV virion from infected cell to extracellular space. But the recycling of HBV virion can contribute to the positive feedback cycle of HBV replication for the explosive replication to accumulate the core particle as a resource of HBV replication in an infected cell. Accumulation of core particle in the infected cell can be risk factor for the exacerbation of hepatitis rather

  5. Removal of harmful cyanobacterial blooms in Taihu Lake using local soils III. Factors affecting the removal efficiency and an in situ field experiment using chitosan-modified local soils

    International Nuclear Information System (INIS)

    Effects of ionic strength, pH, organic content, cell concentration, and growth phase on the removal of MA cells using chitosan-modified sepiolite were studied in the laboratory. The MA removal efficiency increased with the increase of salinity for normal clay flocculation. In contrast, for chitosan-modified clays/soils, MA removal efficiency increased with the decrease of salinity. The removal efficiency of chitosan-modified sepiolite was not significantly affected by pH (6-9), but dropped dramatically beyond pH 10. Humic acid had a small negative effect on the removal of MA cells. Cells were removed more effectively by clays around the early senescence growth phase than other growth stages. The removal efficiency increased as the cell concentration increased. In a field enclosure of Taihu Lake, a loading of 0.025 g/L chitosan-modified local soils removed 99% algal cells and no increase of chlorophyll-a was observed during the following one month's monitoring process. - A loading of 0.025 g/L chitosan-modified local soils removed 99% algal cells in 16 h in a field enclosure of Taihu Lake

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

    Science.gov (United States)

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

    2016-07-01

    A recent study of the replicability of key psychological findings is a major contribution toward understanding the human side of the scientific process. Despite the careful and nuanced analysis reported, the simple narrative disseminated by the mass, social, and scientific media was that in only 36% of the studies were the original results replicated. In the current study, however, we showed that 77% of the replication effect sizes reported were within a 95% prediction interval calculated using the original effect size. Our analysis suggests two critical issues in understanding replication of psychological studies. First, researchers' intuitive expectations for what a replication should show do not always match with statistical estimates of replication. Second, when the results of original studies are very imprecise, they create wide prediction intervals-and a broad range of replication effects that are consistent with the original estimates. This may lead to effects that replicate successfully, in that replication results are consistent with statistical expectations, but do not provide much information about the size (or existence) of the true effect. In this light, the results of the Reproducibility Project: Psychology can be viewed as statistically consistent with what one might expect when performing a large-scale replication experiment. PMID:27474140

  7. Improvements Relating to Database Replication Protocols

    OpenAIRE

    Stankovic, V.; Popov, P. T.

    2013-01-01

    The present invention concerns improvements relating to database replication. More specifically, aspects of the present invention relate to a fault-tolerant node and a method for avoiding non-deterministic behaviour in the management of synchronous database systems.

  8. 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...

  9. The Anisotropy of Replicated Aluminum Foams

    OpenAIRE

    Furman, Eugeny L.; Arcady B. Finkelstein; Maxim L. Cherny

    2014-01-01

    The replication casting process gives the open-cell aluminum foams that can be used in many industrial applications as well as in filtering technology. The essential requirement for filters is the uniformity of filtering degree which is defined by the minimal pore size. However the structure of replication castings is often inhomogeneous and the minimal pore radius is decreasing in the direction of melt infiltration. The objective of this investigation is to study the dynamics of melt impregn...

  10. Early steps of retrovirus replicative cycle

    OpenAIRE

    Saïb Ali; Nisole Sébastien

    2004-01-01

    Abstract During the last two decades, the profusion of HIV research due to the urge to identify new therapeutic targets has led to a wealth of information on the retroviral replication cycle. However, while the late stages of the retrovirus life cycle, consisting of virus replication and egress, have been partly unraveled, the early steps remain largely enigmatic. These early steps consist of a long and perilous journey from the cell surface to the nucleus where the proviral DNA integrates in...

  11. Database Replication Using Generalized Snapshot Isolation

    OpenAIRE

    Elnikety, Sameh; Pedone, Fernando; Zwaenepoel, Willy

    2005-01-01

    Generalized snapshot isolation extends snapshot isolation as used in Oracle and other databases in a manner suitable for replicated databases. While (conventional) snapshot isolation requires that transactions observe the “latest” snapshot of the database, generalized snapshot isolation allows the use of “older” snapshots, facilitating a replicated implementation. We show that many of the desirable properties of snapshot isolation remain. In particular, read-only transactions never block or a...

  12. Autogenesis: the evolution of replicative systems.

    Science.gov (United States)

    Csányi, V; Kampis, G

    1985-05-21

    Questions concerning the nature and origin of living systems and the hierarchy of their evolutionary processes are considered, and several problems which arise in connection with formerly developed theories--the autopoiesis of Maturana & Varela, the POL theory of Haukioja and the earlier developed evolutionary theory of Csányi--are discussed. The organization of living systems, the use of informational terms and the question how reproduction can enter into their characterization, problems of autonomy and identity are included in the list. It is suggested that replication--a copying process achieved by a special network of interrelatedness of components and component-producing processes that produces the same network as that which produced them--characterizes the living organization. The information "used" in this copying process, whether it is stored by special means or distributed in the whole system, is called replicative information. A theoretical model is introduced for the spontaneous emergence of replicative organization, called autogenesis. Autogenesis commences in a system by an organized "small" subsystem, referred to as AutoGenetic System Precursor (AGSP), which conveys replicative information to the system. During autogenesis, replicative information increases in system and compartment(s) form. A compartment is the co-replicating totality of components. The end state of autogenesis is an invariantly self-replicating organization which is unable to undergo further intrinsic organizational changes. It is suggested that replicative unities--such as living organisms--evolve via autogenesis. Levels of evolution emerge as a consequence of the relative autonomy of the autogenetic unities. On the next level they can be considered as components endowed with functions and a new autogenetic process can commence. Thus evolution proceeds towards its end state through the parallel autogenesis of the various levels. In terms of applications, ontogenesis is dealt with

  13. Registered Replication Report: Hart & Albarracín (2011).

    Science.gov (United States)

    2016-01-01

    Language can be viewed as a complex set of cues that shape people's mental representations of situations. For example, people think of behavior described using imperfective aspect (i.e., what a person was doing) as a dynamic, unfolding sequence of actions, whereas the same behavior described using perfective aspect (i.e., what a person did) is perceived as a completed whole. A recent study found that aspect can also influence how we think about a person's intentions (Hart & Albarracín, 2011). Participants judged actions described in imperfective as being more intentional (d between 0.67 and 0.77) and they imagined these actions in more detail (d = 0.73). The fact that this finding has implications for legal decision making, coupled with the absence of other direct replication attempts, motivated this registered replication report (RRR). Multiple laboratories carried out 12 direct replication studies, including one MTurk study. A meta-analysis of these studies provides a precise estimate of the size of this effect free from publication bias. This RRR did not find that grammatical aspect affects intentionality (d between 0 and -0.24) or imagery (d = -0.08). We discuss possible explanations for the discrepancy between these results and those of the original study. PMID:26817732

  14. Correlative light and electron microscopy enables viral replication studies at the ultrastructural level.

    Science.gov (United States)

    Hellström, Kirsi; Vihinen, Helena; Kallio, Katri; Jokitalo, Eija; Ahola, Tero

    2015-11-15

    Electron microscopy (EM) is a powerful tool to study structural changes within cells caused e.g. by ectopic protein expression, gene silencing or virus infection. Correlative light and electron microscopy (CLEM) has proven to be useful in cases when it is problematic to identify a particular cell among a majority of unaffected cells at the EM level. In this technique the cells of interest are first identified by fluorescence microscopy and then further processed for EM. CLEM has become crucial when studying positive-strand RNA virus replication, as it takes place in nanoscale replication sites on specific cellular membranes. Here we have employed CLEM for Semliki Forest virus (SFV) replication studies both by transfecting viral replication components to cells or by infecting different cell types. For the transfection-based system, we developed an RNA template that can be detected in the cells even in the absence of replication and thus allows exploration of lethal mutations in viral proteins. In infected mammalian and mosquito cells, we were able to find replication-positive cells by using a fluorescently labeled viral protein even in the cases of low infection efficiency. The fluorescent region within these cells was shown to correspond to an area rich in modified membranes. These results show that CLEM is a valuable technique for studying virus replication and membrane modifications at the ultrastructural level. PMID:25916619

  15. Diversification of DnaA dependency for DNA replication in cyanobacterial evolution.

    Science.gov (United States)

    Ohbayashi, Ryudo; Watanabe, Satoru; Ehira, Shigeki; Kanesaki, Yu; Chibazakura, Taku; Yoshikawa, Hirofumi

    2016-05-01

    Regulating DNA replication is essential for all living cells. The DNA replication initiation factor DnaA is highly conserved in prokaryotes and is required for accurate initiation of chromosomal replication at oriC. DnaA-independent free-living bacteria have not been identified. The dnaA gene is absent in plastids and some symbiotic bacteria, although it is not known when or how DnaA-independent mechanisms were acquired. Here, we show that the degree of dependency of DNA replication on DnaA varies among cyanobacterial species. Deletion of the dnaA gene in Synechococcus elongatus PCC 7942 shifted DNA replication from oriC to a different site as a result of the integration of an episomal plasmid. Moreover, viability during the stationary phase was higher in dnaA disruptants than in wild-type cells. Deletion of dnaA did not affect DNA replication or cell growth in Synechocystis sp. PCC 6803 or Anabaena sp. PCC 7120, indicating that functional dependency on DnaA was already lost in some nonsymbiotic cyanobacterial lineages during diversification. Therefore, we proposed that cyanobacteria acquired DnaA-independent replication mechanisms before symbiosis and such an ancestral cyanobacterium was the sole primary endosymbiont to form a plastid precursor. PMID:26517699

  16. The Research of Allocative Efficiency of Airlines and Its Affecting Factors in China%中国航空公司配置效率及其影响因素研究

    Institute of Scientific and Technical Information of China (English)

    杨秀云; 朱贻宁; 毛舒怡

    2015-01-01

    使用随机前沿分析(SFA )测度了2001-2012年6家上市航空公司的配置效率,并对影响航空公司配置效率的因素进行分析。研究结果表明:中国航空公司配置效率处于中等水平,中小型航空公司优于大型航空公司;航空公司的公司治理、日常运营水平以及基地建设均影响配置效率,其中总资产、飞行班次和其正相关,国有控股比例、飞行小时以及基地数量则呈负相关。外部因素中,积极的国家行业政策和人民币汇率升值会对航空公司配置效率有正影响。因此,航空公司应加强业内合作,代码共享,基地保障共享,减少重复航线,降低飞行总时间,控制基地数量,进而提升其配置效率水平和优化成本结构,最终获得较高的利润。%T he allocative efficiency of the six listed airline companies is measured by the stochastic frontier analysis (SFA ) from 2001 to 2012 ,the affective factors of the allocative efficiency are analyzed as well .The results are following :the allocative efficiency of the airlines is in a medium level ,which the medium or small scale airlines showbetter allocative efficiency than the big .Furthermore ,the allocative efficiency is affected by corporate governance ,operation and base amount of the airlines ,which the total assets ,flights , positive industry police and appreciation of exchange rate shows a positive correlation , however ,the state own stock ratio ,flights time and base amount make a negative one .Therefore ,the allocative efficiency ,cost structure and profit could be changed better for the airlines by cooperating , sharing code and base ,reducing the duplication of routes ,flight hours and base amount .

  17. HIV-1 Replication and the Cellular Eukaryotic Translation Apparatus

    Directory of Open Access Journals (Sweden)

    Santiago Guerrero

    2015-01-01

    Full Text Available Eukaryotic translation is a complex process composed of three main steps: initiation, elongation, and termination. During infections by RNA- and DNA-viruses, the eukaryotic translation machinery is used to assure optimal viral protein synthesis. Human immunodeficiency virus type I (HIV-1 uses several non-canonical pathways to translate its own proteins, such as leaky scanning, frameshifting, shunt, and cap-independent mechanisms. Moreover, HIV-1 modulates the host translation machinery by targeting key translation factors and overcomes different cellular obstacles that affect protein translation. In this review, we describe how HIV-1 proteins target several components of the eukaryotic translation machinery, which consequently improves viral translation and replication.

  18. HIV-1 replication and the cellular eukaryotic translation apparatus.

    Science.gov (United States)

    Guerrero, Santiago; Batisse, Julien; Libre, Camille; Bernacchi, Serena; Marquet, Roland; Paillart, Jean-Christophe

    2015-01-01

    Eukaryotic translation is a complex process composed of three main steps: initiation, elongation, and termination. During infections by RNA- and DNA-viruses, the eukaryotic translation machinery is used to assure optimal viral protein synthesis. Human immunodeficiency virus type I (HIV-1) uses several non-canonical pathways to translate its own proteins, such as leaky scanning, frameshifting, shunt, and cap-independent mechanisms. Moreover, HIV-1 modulates the host translation machinery by targeting key translation factors and overcomes different cellular obstacles that affect protein translation. In this review, we describe how HIV-1 proteins target several components of the eukaryotic translation machinery, which consequently improves viral translation and replication. PMID:25606970

  19. Roles for Dam methylation in bacterial chromosome replication

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Koch, Birgit; Skovgaard, Ole;

    these by whole genome sequencing. In one case the suppression was due to deletion of two Ts upstream of the ybfF gene. This led to increased SeqA production and presumably prolonged hemimethylation. The increased SeqA level affected replication initiation in two ways not described previously. First...... about one third of the cell cycle. During sequestration at least three mechanisms operate to lower the activity of the initiator protein, DnaA. First, the dnaA promoter, which also contains an excess of GATC sequences, is sequestered for the same period of time as oriC to prevent de novo DnaA synthesis...

  20. Genome instability induced by structured DNA and replication fork restart

    OpenAIRE

    Schalbetter, Stephanie

    2012-01-01

    DNA replication is a central mechanism to all forms of life. Errors occurring during DNA replication can result in mutagenesis and genome rearrangements, which can cause various diseases. In this work I have investigated the stability of direct tandem repeats (TRs) in the context of replication and replication-associated repair mechanisms. During DNA replication the replication fork encounters many obstacles, such as DNA-protein barriers, secondary DNA structures and DNA lesions. How and if r...

  1. HSF1 overexpression enhances oncolytic effect of replicative adenovirus

    Directory of Open Access Journals (Sweden)

    Deng Youwen

    2010-05-01

    Full Text Available Abstract Background E1B55kD deleted oncolytic adenovirus was designed to achieve cancer-specific cytotoxicity, but showed limitations in clinical study. To find a method to increase its efficacy, we investigated the correlation between oncolytic effect of such oncolytic adenovirus Adel55 and intracellular heat shock transcription factor 1 (HSF1 activity. Methods In the present study, human breast cancer cell line Bcap37 was stably transfected with constitutively active HSF1 (cHSF1 or HSF1 specific siRNA (HSF1i to establish increased or decreased HSF1 expression levels. Cytotoxicity of Adel55 was analyzed in these cell lines in vitro and in vivo. Furthermore, Adel55 incorporated with cHSF1 (Adel55-cHSF1 was used to treat various tumor xenografts. Results Adel55 could achieve more efficient oncolysis in cHSF1 transfected Bcap37 cells, both in vitro and in vivo. However, inhibition of HSF1 expression by HSF1i could rescue Bcap37 cell line from oncolysis by Adel55. A time course study of viral replication established a correlation between higher replication of Adel55 and cytolysis or tumor growth inhibition. Then, we constructed Adel55-cHSF1 for tumor gene therapy and demonstrated that it is more potent than Adel55 itself in oncolysis and replication in both Bcap37 and SW620 xenografts. Conclusions cHSF1 enhances the Adel55 cell-killing potential through increasing the viral replication and is a potential therapeutic implication to augment the potential of E1B55kD deleted oncolytic adenovirus by increasing its burst.

  2. Synthetic lethality of cohesins with PARPs and replication fork mediators.

    Directory of Open Access Journals (Sweden)

    Jessica L McLellan

    Full Text Available Synthetic lethality has been proposed as a way to leverage the genetic differences found in tumor cells to affect their selective killing. Cohesins, which tether sister chromatids together until anaphase onset, are mutated in a variety of tumor types. The elucidation of synthetic lethal interactions with cohesin mutants therefore identifies potential therapeutic targets. We used a cross-species approach to identify robust negative genetic interactions with cohesin mutants. Utilizing essential and non-essential mutant synthetic genetic arrays in Saccharomyces cerevisiae, we screened genome-wide for genetic interactions with hypomorphic mutations in cohesin genes. A somatic cell proliferation assay in Caenorhabditis elegans demonstrated that the majority of interactions were conserved. Analysis of the interactions found that cohesin mutants require the function of genes that mediate replication fork progression. Conservation of these interactions between replication fork mediators and cohesin in both yeast and C. elegans prompted us to test whether other replication fork mediators not found in the yeast were required for viability in cohesin mutants. PARP1 has roles in the DNA damage response but also in the restart of stalled replication forks. We found that a hypomorphic allele of the C. elegans SMC1 orthologue, him-1(e879, genetically interacted with mutations in the orthologues of PAR metabolism genes resulting in a reduced brood size and somatic cell defects. We then demonstrated that this interaction is conserved in human cells by showing that PARP inhibitors reduce the viability of cultured human cells depleted for cohesin components. This work demonstrates that large-scale genetic interaction screening in yeast can identify clinically relevant genetic interactions and suggests that PARP inhibitors, which are currently undergoing clinical trials as a treatment of homologous recombination-deficient cancers, may be effective in treating

  3. Replication protein A: directing traffic at the intersection of replication and repair

    OpenAIRE

    Oakley, Greg G.; Patrick, Steve M.

    2010-01-01

    Since the initial discovery of replication protein A (RPA) as a DNA replication factor, much progress has been made on elucidating critical roles for RPA in other DNA metabolic pathways. RPA has been shown to be required for DNA replication, DNA repair, DNA recombination, and the DNA damage response pathway with roles in checkpoint activation. This review summarizes the current understanding of RPA structure, phosphorylation and protein-protein interactions in mediating these DNA metabolic pr...

  4. Anti-HCV RNA Aptamers Targeting the Genomic cis-Acting Replication Element

    Directory of Open Access Journals (Sweden)

    Alfredo Berzal-Herranz

    2011-12-01

    Full Text Available Hepatitis C virus (HCV replication is dependent on the existence of several highly conserved functional genomic RNA domains. The cis-acting replication element (CRE, located within the 3' end of the NS5B coding region of the HCV genome, has been shown essential for efficient viral replication. Its sequence and structural features determine its involvement in functional interactions with viral RNA-dependent RNA polymerase and distant RNA domains of the viral genome. This work reports the use of an in vitro selection strategy to select aptamer RNA molecules against the complete HCV-CRE. After six selection cycles, five potential target sites were identified within this domain. Inhibition assays using a sample of representative aptamers showed that the selected RNAs significantly inhibit the replication (>80% of a subgenomic HCV replicon in Huh-7 cell cultures. These results highlight the potential of aptamer RNA molecules as therapeutic antiviral agents.

  5. A Necessary Condition for Coexistence of Autocatalytic Replicators in a Prebiotic Environment

    Directory of Open Access Journals (Sweden)

    Martha A. Grover

    2013-07-01

    Full Text Available A necessary, but not sufficient, mathematical condition for the coexistence of short replicating species is presented here. The mathematical condition is obtained for a prebiotic environment, simulated as a fed-batch reactor, which combines monomer recycling, variable reaction order and a fixed monomer inlet flow with two replicator types and two monomer types. An extensive exploration of the parameter space in the model validates the robustness and efficiency of the mathematical condition, with nearly 1.7% of parameter sets meeting the condition and half of those exhibiting sustained coexistence. The results show that it is possible to generate a condition of coexistence, where two replicators sustain a linear growth simultaneously for a wide variety of chemistries, under an appropriate environment. The presence of multiple monomer types is critical to sustaining the coexistence of multiple replicator types.

  6. Identification of replication factor C from Saccharomyces cerevisiae: a component of the leading-strand DNA replication complex.

    OpenAIRE

    Fien, K; Stillman, B

    1992-01-01

    A number of proteins have been isolated from human cells on the basis of their ability to support DNA replication in vitro of the simian virus 40 (SV40) origin of DNA replication. One such protein, replication factor C (RFC), functions with the proliferating cell nuclear antigen (PCNA), replication protein A (RPA), and DNA polymerase delta to synthesize the leading strand at a replication fork. To determine whether these proteins perform similar roles during replication of DNA from origins in...

  7. Sleeping Beauty transposon-based system for rapid generation of HBV-replicating stable cell lines.

    Science.gov (United States)

    Wu, Yong; Zhang, Tian-Ying; Fang, Lin-Lin; Chen, Zi-Xuan; Song, Liu-Wei; Cao, Jia-Li; Yang, Lin; Yuan, Quan; Xia, Ning-Shao

    2016-08-01

    The stable HBV-replicating cell lines, which carry replication-competent HBV genome stably integrated into the genome of host cell, are widely used to evaluate the effects of antiviral agents. However, current methods to generate HBV-replicating cell lines, which are mostly dependent on random integration of foreign DNA via plasmid transfection, are less-efficient and time-consuming. To address this issue, we constructed an all-in-one Sleeping Beauty transposon system (denoted pTSMP-HBV vector) for robust generation of stable cell lines carrying replication-competent HBV genome of different genotype. This vector contains a Sleeping Beauty transposon containing HBV 1.3-copy genome with an expression cassette of the SV40 promoter driving red fluorescent protein (mCherry) and self-cleaving P2A peptide linked puromycin resistance gene (PuroR). In addition, a PGK promoter-driven SB100X hyperactive transposase cassette is placed in the outside of the transposon in the same plasmid.The HBV-replicating stable cells could be obtained from pTSMP-HBV transfected HepG2 cells by red fluorescence-activated cell sorting and puromycin resistant cell selection within 4-week. Using this system, we successfully constructed four cell lines carrying replication-competent HBV genome of genotypes A-D. The replication and viral protein expression profiles of these cells were systematically characterized. In conclusion, our study provides a high-efficiency strategy to generate HBV-replicating stable cell lines, which may facilitate HBV-related virological study. PMID:27091097

  8. Phosphorus Use Efficiency by Brazilian Upland Rice Genotypes Evaluated by the 32P Dilution Technique

    International Nuclear Information System (INIS)

    The objectives of this work were to identify the most efficient upland rice genotypes in phosphorus (P) utilization, and to verify if P from the seed affects the classification of upland rice genotypes on P uptake efficiency. The experiment was conducted in a greenhouse of the Center for Nuclear Energy in Agriculture (CENA/USP), Piracicaba, Sao Paulo, Brazil, using the 32P isotope technique, and plants were grown in pots with samples of dystrophic Typic Haplustox (Oxisol). The experimental design was completely randomized with four replications. The treatments consisted of 47 upland rice genotypes and two standard plant species, efficient or inefficient in P uptake. The results were assessed through correlation and cluster analysis (multivariate). The Carisma upland rice genotype was the most efficient in P uptake, and Caripuna was the most efficient on P utilization. The P derived from seed does not influence the identification of upland rice genotypes in P uptake efficiency. (author)

  9. Assessment of the Role of the Central DNA Flap in Human Immunodeficiency Virus Type 1 Replication by Using a Single-Cycle Replication System

    OpenAIRE

    Ao, Zhujun; Yao, Xiaojian; Éric A Cohen

    2004-01-01

    In this study, reverse transcriptase (RT)- and integrase (IN)-defective human immunodeficiency virus type 1 (HIV-1) was transcomplemented with Vpr-RT-IN fusion proteins to delineate pol sequences important for HIV-1 replication. Our results reveal that a 194-bp sequence encompassing the 3′end of the IN gene and containing the central DNA flap is necessary and sufficient for efficient HIV-1 single-cycle replication in dividing and nondividing cells. Furthermore, we show that the central DNA fl...

  10. Replication-Competent Foamy Virus Vaccine Vectors as Novel Epitope Scaffolds for Immunotherapy.

    Directory of Open Access Journals (Sweden)

    Janet Lei

    Full Text Available The use of whole viruses as antigen scaffolds is a recent development in vaccination that improves immunogenicity without the need for additional adjuvants. Previous studies highlighted the potential of foamy viruses (FVs in prophylactic vaccination and gene therapy. Replication-competent FVs can trigger immune signaling and integrate into the host genome, resulting in persistent antigen expression and a robust immune response. Here, we explored feline foamy virus (FFV proteins as scaffolds for therapeutic B and T cell epitope delivery in vitro. Infection- and cancer-related B and T cell epitopes were grafted into FFV Gag, Env, or Bet by residue replacement, either at sites of high local sequence homology between the epitope and the host protein or in regions known to tolerate sequence alterations. Modified proviruses were evaluated in vitro for protein steady state levels, particle release, and virus titer in permissive cells. Modification of Gag and Env was mostly detrimental to their function. As anticipated, modification of Bet had no impact on virion release and affected virus titers of only some recombinants. Further evaluation of Bet as an epitope carrier was performed using T cell epitopes from the model antigen chicken ovalbumin (OVA, human tyrosinase-related protein 2 (TRP-2, and oncoprotein E7 of human papillomavirus type 16 (HPV16E7. Transfection of murine cells with constructs encoding Bet-epitope chimeric proteins led to efficient MHC-I-restricted epitope presentation as confirmed by interferon-gamma enzyme-linked immunospot assays using epitope-specific cytotoxic T lymphocyte (CTL lines. FFV infection-mediated transduction of cells with epitope-carrying Bet also induced T-cell responses, albeit with reduced efficacy, in a process independent from the presence of free peptides. We show that primate FV Bet is also a promising T cell epitope carrier for clinical translation. The data demonstrate the utility of replication

  11. 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.

  12. 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.

  13. Self-replication with magnetic dipolar colloids

    Science.gov (United States)

    Dempster, Joshua M.; Zhang, Rui; Olvera de la Cruz, Monica

    2015-10-01

    Colloidal self-replication represents an exciting research frontier in soft matter physics. Currently, all reported self-replication schemes involve coating colloidal particles with stimuli-responsive molecules to allow switchable interactions. In this paper, we introduce a scheme using ferromagnetic dipolar colloids and preprogrammed external magnetic fields to create an autonomous self-replication system. Interparticle dipole-dipole forces and periodically varying weak-strong magnetic fields cooperate to drive colloid monomers from the solute onto templates, bind them into replicas, and dissolve template complexes. We present three general design principles for autonomous linear replicators, derived from a focused study of a minimalist sphere-dimer magnetic system in which single binding sites allow formation of dimeric templates. We show via statistical models and computer simulations that our system exhibits nonlinear growth of templates and produces nearly exponential growth (low error rate) upon adding an optimized competing electrostatic potential. We devise experimental strategies for constructing the required magnetic colloids based on documented laboratory techniques. We also present qualitative ideas about building more complex self-replicating structures utilizing magnetic colloids.

  14. Extremal dynamics in random replicator ecosystems

    International Nuclear Information System (INIS)

    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

  15. High Power Picosecond Laser Surface Micro-texturing of H13 Tool Steel and Pattern Replication onto ABS Plastics via Injection Moulding

    Science.gov (United States)

    Otanocha, Omonigho B.; Li, Lin; Zhong, Shan; Liu, Zhu

    2016-03-01

    H13 tool steels are often used as dies and moulds for injection moulding of plastic components. Certain injection moulded components require micro-patterns on their surfaces in order to modify the physical properties of the components or for better mould release to reduce mould contamination. With these applications it is necessary to study micro-patterning to moulds and to ensure effective pattern transfer and replication onto the plastic component during moulding. In this paper, we report an investigation into high average powered (100 W) picosecond laser interactions with H13 tool steel during surface micro-patterning (texturing) and the subsequent pattern replication on ABS plastic material through injection moulding. Design of experiments and statistical modelling were used to understand the influences of laser pulse repetition rate, laser fluence, scanning velocity, and number of scans on the depth of cut, kerf width and heat affected zones (HAZ) size. The characteristics of the surface patterns are analysed. The process parameter interactions and significance of process parameters on the processing quality and efficiency are characterised. An optimum operating window is recommended. The transferred geometry is compared with the patterns generated on the dies. A discussion is made to explain the characteristics of laser texturing and pattern replication on plastics.

  16. PTEN Controls the DNA Replication Process through MCM2 in Response to Replicative Stress

    Directory of Open Access Journals (Sweden)

    Jiawen Feng

    2015-11-01

    Full Text Available PTEN is a tumor suppressor frequently mutated in human cancers. PTEN inhibits the phosphatidylinositol 3-kinase (PI3K-AKT cascade, and nuclear PTEN guards the genome by multiple mechanisms. Here, we report that PTEN physically associates with the minichromosome maintenance complex component 2 (MCM2, which is essential for DNA replication. Specifically, PTEN dephosphorylates MCM2 at serine 41 (S41 and restricts replication fork progression under replicative stress. PTEN disruption results in unrestrained fork progression upon replication stalling, which is similar to the phenotype of cells expressing the phosphomimic MCM2 mutant S41D. Moreover, PTEN is necessary for prevention of chromosomal aberrations under replication stress. This study demonstrates that PTEN regulates DNA replication through MCM2 and loss of PTEN function leads to replication defects and genomic instability. We propose that PTEN plays a critical role in maintaining genetic stability through a replication-specific mechanism, and this is a crucial facet of PTEN tumor suppressor activity.

  17. 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.

  18. Rainbow Induced Subgraphs in Replication Graphs

    CERN Document Server

    Szykuła, Marek

    2012-01-01

    A graph $G$ is called a replication graph of a graph $H$ if $G$ is obtained from $H$ by replacing vertices of $H$ by arbitrary cliques of vertices and then replacing each edge in $H$ by all the edges between corresponding cligues. For a given graph $H$ the $\\rho_R(H)$ is the minimal number of vertices of a replication graph $G$ of $H$ such that every proper vertex coloring of $G$ contains a rainbow induced subgraph isomorphic to $H$ having exactly one vertex in each replication clique of $G$. We prove some bounds for $\\rho_R$ for some classes of graphs and compute some exact values. Also some experimental results obtained by a computer search are presented and conjectures based on them are formulated.

  19. Autonomic Data Replication in Cloud Environment

    Directory of Open Access Journals (Sweden)

    Dhananjaya Gupt,

    2013-04-01

    Full Text Available Cloud computing is an emerging practice that offers more flexibility in infrastructure and reduces cost than our traditional computing models. Cloud providers offer everything from access to raw storage capacity resources to complete application services. The services that are provided by the cloud can be accessed from anywhere and data flows from one place to another. Since data is moving via network, there are chances of data loss. So we need to keep multiple copies of data and thus data replication is one of the main issues in cloud computing. In this paper we have implemented automatic replication of data from local host to cloud environment. Data replication is implemented by using HADOOP which stores the data at various nodes. If one node goes down then data can be retrieved from other node seamlessly.

  20. Evolution of Database Replication Technologies for WLCG

    Science.gov (United States)

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

    2015-12-01

    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. Extremal dynamics in random replicator ecosystems

    Science.gov (United States)

    Kärenlampi, Petri P.

    2015-10-01

    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.

  2. Synchronization of DNA array replication kinetics

    Science.gov (United States)

    Manturov, Alexey O.; Grigoryev, Anton V.

    2016-04-01

    In the present work we discuss the features of the DNA replication kinetics at the case of multiplicity of simultaneously elongated DNA fragments. The interaction between replicated DNA fragments is carried out by free protons that appears at the every nucleotide attachment at the free end of elongated DNA fragment. So there is feedback between free protons concentration and DNA-polymerase activity that appears as elongation rate dependence. We develop the numerical model based on a cellular automaton, which can simulate the elongation stage (growth of DNA strands) for DNA elongation process with conditions pointed above and we study the possibility of the DNA polymerases movement synchronization. The results obtained numerically can be useful for DNA polymerase movement detection and visualization of the elongation process in the case of massive DNA replication, eg, under PCR condition or for DNA "sequencing by synthesis" sequencing devices evaluation.

  3. Transitions: The Evolution of Linguistic Replicators

    Science.gov (United States)

    Kirby, Simon

    Maynard Smith and Szathmáry (1995) propose a series of major transitions in the evolutionary history of life. Their work provides a rich framework for thinking about replication. They identified the importance of language in this light, but language is a new system of replication in more than one sense: it is both an enabler of cultural replicators with unlimited heredity, and also a new kind of evolutionary system itself. Iterated learning is the process of linguistic transmission, and it drives both language change and the transitions to qualitatively new kinds of linguistic system. By seeing language as an evolutionary system, the biggest payoff we get may be the ability to take biologists' insights into the evolution of life and apply them to the evolution of language.

  4. ADDING A NEW SITE IN AN EXISTING ORACLE MULTIMASTER REPLICATION WITHOUT QUIESCING THE REPLICATION

    Directory of Open Access Journals (Sweden)

    Hakik Paci

    2011-09-01

    Full Text Available This paper presents a new solution, which adds a new database server on an existing Oracle MultimasterData replication system with Online Instantiation method. During this time the system is down, because wecannot execute DML statements on replication objects but we can only make queries. The time for addingthe new database server depends on the number of objects, on the replication group and on the networkconditions. We propose to add a new layer between replication objects and the database sessions, whichcontain DML statements. The layer eliminates the system down time exploiting our developed packages.The packages will be active only during the addition of a new site process and will modify all DMLstatements and queries based on replication objects.

  5. Dust Affects Solar-Cell Efficiency

    Science.gov (United States)

    Molki, A.

    2010-01-01

    Over the past two decades governmental agencies have played an integral role in the advancement of renewable energy education by providing useful information for educators and students. The effect of such efforts has encouraged primary and secondary educational institutions to introduce the subject of renewable energy within their science…

  6. Does weather affect US bank loan efficiency?

    OpenAIRE

    Mamatzakis, E

    2013-01-01

    The impact of strong emotions or mood on decision making and risk taking is well recognized in behavioral economics and finance. Yet, and in spite of the immense interest, no study, so far, has provided any comprehensive evidence on the impact of weather conditions. This paper provides the theoretical framework to study the impact of weather through its influence on bank manager’s mood on bank inefficiency. In particular, we provide empirical evidence of the dynamic interactions between weath...

  7. Origin of replication of the DNA of a herpesvirus (pseudorabies).

    OpenAIRE

    Ben-Porat, T; Veach, R A

    1980-01-01

    During the first round of the replication of pseudorabies virus DNA, replicating DNA is mainly in the form of circles. The main origin of replication is located inthe region of the molecule bearing the inverted repeat. Replication proceeds unidirectionally from the origin.

  8. 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...

  9. The Role of Lipids in Retrovirus Replication

    Directory of Open Access Journals (Sweden)

    Abdul A. Waheed

    2010-05-01

    Full Text Available Retroviruses undergo several critical steps to complete a replication cycle. These include the complex processes of virus entry, assembly, and budding that often take place at the plasma membrane of the host cell. Both virus entry and release involve membrane fusion/fission reactions between the viral envelopes and host cell membranes. Accumulating evidence indicates important roles for lipids and lipid microdomains in virus entry and egress. In this review, we outline the current understanding of the role of lipids and membrane microdomains in retroviral replication.

  10. The replication of expansive production knowledge

    DEFF Research Database (Denmark)

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

    2012-01-01

    ; 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...... 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...

  11. Replication technology for photonic band gap applications

    Science.gov (United States)

    Grigaliunas, V.; Kopustinskas, V.; Meskinis, S.; Margelevicius, M.; Mikulskas, I.; Tomasiunas, R.

    2001-06-01

    Replication technology was applied for photonic structure fabrication in silicon substrate. It was revealed, that thin thermoplastic polymer layers on silicon substrates may be patterned by hot embossing technique for dry etching masking. Ni mold used for plain hot embossing into polymer layers was fabricated by Ni electrochemical deposition on the reference silicon surface structure, which was obtained by direct electron beam (EB) writing and SF 6/N 2 reactive ion etching (RIE) technique. It is shown that the shape of replicated photonic structures is determined by RIE parameters.

  12. Regulation of eukaryotic DNA replication and nuclear structure

    Institute of Scientific and Technical Information of China (English)

    WUJIARUI

    1999-01-01

    In eukaryote,nuclear structure is a key component for the functions of eukaryotic cells.More and more evidences show that the nuclear structure plays important role in regulating DNA replication.The nuclear structure provides a physical barrier for the replication licensing,participates in the decision where DNA replication initiates,and organizes replication proteins as replication factory for DNA replication.Through these works,new concepts on the regulation of DNA replication have emerged,which will be discussed in this minireview.

  13. Origin DNA Melting and Unwinding in DNA Replication

    OpenAIRE

    Gai, Dahai; Chang, Y Paul; Chen, Xiaojiang S.

    2010-01-01

    Genomic DNA replication is a necessary step in the life cycles of all organisms. To initiate DNA replication, the double-stranded DNA (dsDNA) at the origin of replication must be separated or melted; this melted region is propagated and a mature replication fork is formed. To accomplish origin recognition, initial DNA melting, and the eventual formation of a replication fork, coordinated activity of initiators, helicases, and other cellular factors are required. In this review, we focus on re...

  14. Spatial regulation and organization of DNA replication within the nucleus

    OpenAIRE

    Natsume, Toyoaki; Tanaka, Tomoyuki U.

    2009-01-01

    Duplication of chromosomal DNA is a temporally and spatially regulated process. The timing of DNA replication initiation at various origins is highly coordinated; some origins fire early and others late during S phase. Moreover, inside the nuclei, the bulk of DNA replication is physically organized in replication factories, consisting of DNA polymerases and other replication proteins. In this review article, we discuss how DNA replication is organized and regulated spatially within the nucleu...

  15. A moving DNA replication factory in Caulobacter crescentus

    OpenAIRE

    Jensen, Rasmus B.; Wang, Sherry C.; Shapiro, Lucy

    2001-01-01

    The in vivo intracellular location of components of the Caulobacter replication apparatus was visualized during the cell cycle. Replisome assembly occurs at the chromosomal origin located at the stalked cell pole, coincident with the initiation of DNA replication. The replisome gradually moves to midcell as DNA replication proceeds and disassembles upon completion of DNA replication. Although the newly replicated origin regions of the chromosome are rapidly moved to opposite cell poles by an ...

  16. Understanding replication of experiments in software engineering: a classification

    OpenAIRE

    Gómez Gómez, Omar Salvador; Juristo Juzgado, Natalia; Vegas Hernández, Sira

    2014-01-01

    Context: Replication plays an important role in experimental disciplines. There are still many uncertain- ties about how to proceed with replications of SE experiments. Should replicators reuse the baseline experiment materials? How much liaison should there be among the original and replicating experiment- ers, if any? What elements of the experimental configuration can be changed for the experiment to be considered a replication rather than a new experiment? Objective: To improve our unders...

  17. SEC14L2 enables pan-genotype HCV replication in cell culture.

    Science.gov (United States)

    Saeed, Mohsan; Andreo, Ursula; Chung, Hyo-Young; Espiritu, Christine; Branch, Andrea D; Silva, Jose M; Rice, Charles M

    2015-08-27

    Since its discovery in 1989, efforts to grow clinical isolates of the hepatitis C virus (HCV) in cell culture have met with limited success. Only the JFH-1 isolate has the capacity to replicate efficiently in cultured hepatoma cells without cell culture-adaptive mutations. We hypothesized that cultured cells lack one or more factors required for the replication of clinical isolates. To identify the missing factors, we transduced Huh-7.5 human hepatoma cells with a pooled lentivirus-based human complementary DNA (cDNA) library, transfected the cells with HCV subgenomic replicons lacking adaptive mutations, and selected for stable replicon colonies. This led to the identification of a single cDNA, SEC14L2, that enabled RNA replication of diverse HCV genotypes in several hepatoma cell lines. This effect was dose-dependent, and required the continuous presence of SEC14L2. Full-length HCV genomes also replicated and produced low levels of infectious virus. Remarkably, SEC14L2-expressing Huh-7.5 cells also supported HCV replication following inoculation with patient sera. Mechanistic studies suggest that SEC14L2 promotes HCV infection by enhancing vitamin E-mediated protection against lipid peroxidation. This provides a foundation for development of in vitro replication systems for all HCV isolates, creating a useful platform to dissect the mechanisms by which cell culture-adaptive mutations act. PMID:26266980

  18. Adenovirus E1A/E1B Transformed Amniotic Fluid Cells Support Human Cytomegalovirus Replication

    Directory of Open Access Journals (Sweden)

    Natascha Krömmelbein

    2016-02-01

    Full Text Available The human cytomegalovirus (HCMV replicates to high titers in primary human fibroblast cell cultures. A variety of primary human cells and some tumor-derived cell lines do also support permissive HCMV replication, yet at low levels. Cell lines established by transfection of the transforming functions of adenoviruses have been notoriously resistant to HCMV replication and progeny production. Here, we provide first-time evidence that a permanent cell line immortalized by adenovirus type 5 E1A and E1B (CAP is supporting the full HCMV replication cycle and is releasing infectious progeny. The CAP cell line had previously been established from amniotic fluid cells which were likely derived from membranes of the developing fetus. These cells can be grown under serum-free conditions. HCMV efficiently penetrated CAP cells, expressed its immediate-early proteins and dispersed restrictive PML-bodies. Viral DNA replication was initiated and viral progeny became detectable by electron microscopy in CAP cells. Furthermore, infectious virus was released from CAP cells, yet to lower levels compared to fibroblasts. Subviral dense bodies were also secreted from CAP cells. The results show that E1A/E1B expression in transformed cells is not generally repressive to HCMV replication and that CAP cells may be a good substrate for dense body based vaccine production.

  19. Identification and characterization of the role of c-terminal Src kinase in dengue virus replication.

    Science.gov (United States)

    Kumar, Rinki; Agrawal, Tanvi; Khan, Naseem Ahmed; Nakayama, Yuji; Medigeshi, Guruprasad R

    2016-01-01

    We screened a siRNA library targeting human tyrosine kinases in Huh-7 cells and identified c-terminal Src kinase (Csk) as one of the kinases involved in dengue virus replication. Knock-down of Csk expression by siRNAs or inhibition of Csk by an inhibitor reduced dengue virus RNA levels but did not affect viral entry. Csk partially colocalized with viral replication compartments. Dengue infection was drastically reduced in cells lacking the three ubiquitous src family kinases, Src, Fyn and Yes. Csk knock-down in these cells failed to block dengue virus replication suggesting that the effect of Csk is via regulation of Src family kinases. Csk was found to be hyper-phosphorylated during dengue infection and inhibition of protein kinase A led to a block in Csk phosphorylation and dengue virus replication. Overexpression studies suggest an important role for the kinase and SH3 domains in this process. Our results identified a novel role for Csk as a host tyrosine kinase involved in dengue virus replication and provide further insights into the role of host factors in dengue replication. PMID:27457684

  20. Levels of the E2 interacting protein TopBP1 modulate papillomavirus maintenance stage replication.

    Science.gov (United States)

    Kanginakudru, Sriramana; DeSmet, Marsha; Thomas, Yanique; Morgan, Iain M; Androphy, Elliot J

    2015-04-01

    The evolutionarily conserved DNA topoisomerase II beta-binding protein 1 (TopBP1) functions in DNA replication, DNA damage response, and cell survival. We analyzed the role of TopBP1 in human and bovine papillomavirus genome replication. Consistent with prior reports, TopBP1 co-localized in discrete nuclear foci and was in complex with papillomavirus E2 protein. Similar to E2, TopBP1 is recruited to the region of the viral origin of replication during G1/S and early S phase. TopBP1 knockdown increased, while over-expression decreased transient virus replication, without affecting cell cycle. Similarly, using cell lines harboring HPV-16 or HPV-31 genome, TopBP1 knockdown increased while over-expression reduced viral copy number relative to genomic DNA. We propose a model in which TopBP1 serves dual roles in viral replication: it is essential for initiation of replication yet it restricts viral copy number. PMID:25666521

  1. Replication and transcription on a collision course: eukaryotic regulation mechanisms and implications for DNA stability.

    Directory of Open Access Journals (Sweden)

    Alessandra eBrambati

    2015-04-01

    Full Text Available DNA replication and transcription are vital cellular processes during which the genetic information is copied into complementary DNA and RNA molecules. Highly complex machineries required for DNA and RNA synthesis compete for the same DNA template, therefore being on a collision course. Unscheduled replication-transcription clashes alter the gene transcription program and generate replication stress, reducing fork speed. Molecular pathways and mechanisms that minimize the conflict between replication and transcription have been extensively characterized in prokaryotic cells and recently identified also in eukaryotes. A pathological outcome of replication-transcription collisions is the formation of stable RNA:DNA hybrids in molecular structures called R-loops. Growing evidence suggests that R-loop accumulation promotes both genetic and epigenetic instability, thus severely affecting genome functionality. In the present review, we summarize the current knowledge related to replication and transcription conflicts in eukaryotes, their consequences on genome instability and the pathways involved in their resolution. These findings are relevant to clarify the molecular basis of cancer and neurodegenerative diseases.

  2. Bio-replicated forming of the biomimetic drag-reducing surfaces in large area based on shark skin

    Institute of Scientific and Technical Information of China (English)

    HAN Xin; ZHANG DeYuan; LI Xiang; LI YuanYue

    2008-01-01

    On the investigation of biomimetic drag-reducing surface, direct replication of the firm scarfskins on low-resistance creatures to form biomimetic drag-reducing surfaces with relatively vivid morphology relative to the living prototype is a new attempt of the bio-replicated forming technology. Taking shark skin as the bio-replication template, the hot embossing method was applied to the micro-replication of its outward morphology. Furthermore, the skins were jointed together to form the drag-reducing sur-face in large area. The results of the resistance measurements in a water tunnel according to the flat-plate sample pieces have shown that the biomimetic shark-skin coating fabricated by the bio-replicated forming method has significant drag reduction effect, and that the drag reduction effi-ciency reached 8.25% in the test conditions.

  3. Thioredoxin 80-Activated-Monocytes (TAMs) Inhibit the Replication of Intracellular Pathogens

    DEFF Research Database (Denmark)

    Cortes-Bratti, Ximena; Brasseres, Eugenie; Herrera-Rodriquez, Fabiola; Botero-Kleiven, Silvia; Coppotelli, Giuseppe; Andersen, Jens Bo; G. Masucci, Maria; Holmgren, Arne; Chaves-Olarte, Esteban; Frisan, Teresa; Avila-Carino, Javier

    2011-01-01

    a role of TAMs in the control of intracellular bacterial infections. As model pathogens we have chosen Listeria monocytogenes and Brucella abortus which replicate in the cytosol and the endoplasmic reticulum respectively. Our data indicate that TAMs efficiently inhibit intracellular growth of both L...

  4. The origin recognition complex links replication, sister chromatid cohesion and transcriptional silencing in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Suter, Bernhard; Tong, Amy; Chang, Michael; Yu, Lisa; Brown, Grant W; Boone, Charles; Rine, Jasper

    2004-01-01

    Mutations in genes encoding the origin recognition complex (ORC) of Saccharomyces cerevisiae affect initiation of DNA replication and transcriptional repression at the silent mating-type loci. To explore the function of ORC in more detail, a screen for genetic interactions was undertaken using large

  5. 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.

  6. Representation dimension of m-replicated algebras

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Let A be a finite-dimensional hereditary algebra over an algebraically closed field and A(m) be the m-replicated algebra of A.We prove that the representation dimension of A(m) is at most 3,and that the dominant dimension of A(m) is at least m.

  7. Two Replicable Suppressor Situations in Personality Research

    Science.gov (United States)

    Paulhus, Delroy L.; Robins, Richard W.; Trzesniewski, Kali H.; Tracy, Jessica L.

    2004-01-01

    Suppressor situations occur when the simultaneous inclusion of two predictors improves one or both validities. A common allegation is that suppressor effects rarely replicate and have little substantive import. We present substantive examples from two established research domains to counter this skepticism. In the first domain, we show how…

  8. Replication and Inhibitors of Enteroviruses and Parechoviruses.

    Science.gov (United States)

    van der Linden, Lonneke; Wolthers, Katja C; van Kuppeveld, Frank J M

    2015-08-01

    The Enterovirus (EV) and Parechovirus genera of the picornavirus family include many important human pathogens, including poliovirus, rhinovirus, EV-A71, EV-D68, and human parechoviruses (HPeV). They cause a wide variety of diseases, ranging from a simple common cold to life-threatening diseases such as encephalitis and myocarditis. At the moment, no antiviral therapy is available against these viruses and it is not feasible to develop vaccines against all EVs and HPeVs due to the great number of serotypes. Therefore, a lot of effort is being invested in the development of antiviral drugs. Both viral proteins and host proteins essential for virus replication can be used as targets for virus inhibitors. As such, a good understanding of the complex process of virus replication is pivotal in the design of antiviral strategies goes hand in hand with a good understanding of the complex process of virus replication. In this review, we will give an overview of the current state of knowledge of EV and HPeV replication and how this can be inhibited by small-molecule inhibitors. PMID:26266417

  9. Replication and Inhibitors of Enteroviruses and Parechoviruses

    Directory of Open Access Journals (Sweden)

    Lonneke van der Linden

    2015-08-01

    Full Text Available The Enterovirus (EV and Parechovirus genera of the picornavirus family include many important human pathogens, including poliovirus, rhinovirus, EV-A71, EV-D68, and human parechoviruses (HPeV. They cause a wide variety of diseases, ranging from a simple common cold to life-threatening diseases such as encephalitis and myocarditis. At the moment, no antiviral therapy is available against these viruses and it is not feasible to develop vaccines against all EVs and HPeVs due to the great number of serotypes. Therefore, a lot of effort is being invested in the development of antiviral drugs. Both viral proteins and host proteins essential for virus replication can be used as targets for virus inhibitors. As such, a good understanding of the complex process of virus replication is pivotal in the design of antiviral strategies goes hand in hand with a good understanding of the complex process of virus replication. In this review, we will give an overview of the current state of knowledge of EV and HPeV replication and how this can be inhibited by small-molecule inhibitors.

  10. Methylation: a regulator of HIV-1 replication?

    OpenAIRE

    Jeang Kuan-Teh; Yedavalli Venkat RK

    2007-01-01

    Abstract Recent characterizations of methyl transferases as regulators of cellular processes have spurred investigations into how methylation events might influence the HIV-1 life cycle. Emerging evidence suggests that protein-methylation can positively and negatively regulate HIV-1 replication. How DNA- and RNA- methylation might impact HIV-1 is also discussed.

  11. Impact of Chromatin on HIV Replication

    OpenAIRE

    Agosto, Luis M.; Matthew Gagne; Henderson, Andrew J.

    2015-01-01

    Chromatin influences Human Immunodeficiency Virus (HIV) integration and replication. This review highlights critical host factors that influence chromatin structure and organization and that also impact HIV integration, transcriptional regulation and latency. Furthermore, recent attempts to target chromatin associated factors to reduce the HIV proviral load are discussed.

  12. 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

  13. Distributed Databases Management Using Replication Method

    OpenAIRE

    Mircea Petrini

    2009-01-01

    Over the last several years, research into fully distributed database has slowly but surely found its way into commercial products. Today, many of the mainstream enterprise database products offer at least some level of transparent distributed database access. This paper studies the replication method as a component of the distributed databases management.

  14. Epigallocatechin gallate inhibits HBV DNA synthesis in a viral replication - inducible cell line

    Institute of Scientific and Technical Information of China (English)

    Wei He; Li-Xia Li; Qing-Jiao Liao; Chun-Lan Liu; Xu-Lin Chen

    2011-01-01

    AIM: To analyze the antiviral mechanism of Epigallocatechin gallate (EGCG) against hepatitis B virus (HBV) replication. METHODS: In this research, the HBV-replicating cell line HepG2.117 was used to investigate the antiviral mechanism of EGCG. Cytotoxicity of EGCG was analyzed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Hepatitis B virus e antigen (HBeAg) and hepatitis B virus surface antigen (HBsAg) in the supernatant were detected by enzyme-linked immunosorbent assay. Precore mRNA and pregenomic RNA (pgRNA) levels were determined by semi-quantitative reverse transcription polymerase chain reaction (PCR) assay. The effect of EGCG on HBV core promoter activity was measured by dual luciferase reporter assay. HBV covalently closed circular DNA and replicative intermediates of DNA were quantified by real-time PCR assay. RESULTS: When HepG2.117 cells were grown in the presence of EGCG, the expression of HBeAg was suppressed, however, the expression of HBsAg was not affected. HBV precore mRNA level was also downregulated by EGCG, while the transcription of precore mRNA was not impaired. The synthesis of both HBV covalently closed circular DNA and replicative intermediates of DNA were reduced by EGCG treatment to a similar extent, however, HBV pgRNA transcripted from chromosome-integrated HBV genome was not affected by EGCG treatment, indicating that EGCG targets only replicative intermediates of DNA synthesis. CONCLUSION: In HepG2.117 cells, EGCG inhibits HBV replication by impairing HBV replicative intermediates of DNA synthesis and such inhibition results in reduced production of HBV covalently closed circular DNA.

  15. 5-azacytidine and 5-azadeoxycytidine inhibit human immunodeficiency virus type 1 replication in vitro.

    Science.gov (United States)

    Bouchard, J; Walker, M C; Leclerc, J M; Lapointe, N; Beaulieu, R; Thibodeau, L

    1990-01-01

    Chemotherapeutic agents which affect the integration, stability, or inducibility of the human immunodeficiency virus (HIV) provirus would have considerable value in treating acquired immunodeficiency syndrome. Two nucleoside analogs of cytosine, 5-azacytidine and 5-azadeoxycytidine, which seem to have such value because of their capabilities to affect both the stability and the methylation patterns of the nucleic acids into which they are incorporated, were tested for their ability to inhibit the replication of HIV type 1 (HIV-1) in human CEM T cells in vitro. 5-Azadeoxycytidine (1 microM) completely inhibited HIV replication in CEM cells, by the criteria of reduced viral antigen expression and decreased supernatant reverse transcriptase activity, with little toxicity for the treated cells. 5-azacytidine (1 microM) also inhibited HIV replication, but less effectively. When added 2 or more h after CEM cells were infected with HIV-1, both 5-azacytosine derivatives were less effective than they were when added at the time of infection. Even 2 h of exposure to 5-azadeoxycytidine was sufficient for inhibition of HIV replication. Although long exposure to either analog at concentrations of 1 microM would result in pronounced cellular cytotoxicity, the the fact that short exposures to the same dose of drug inhibit HIV replication but are not toxic for the cells implies that cellular toxicity itself is not an important mechanism of the antiviral action of the analogs. PMID:1691617

  16. Molecular genetic analysis of a vaccinia virus gene with an essential role in DNA replication

    International Nuclear Information System (INIS)

    The poxvirus, vaccinia, is large DNA virus which replicates in the cytoplasma of the host cell. The virus is believed to encode most or all of the functions required for the temporally regulated transcription and replication of its 186 kilobase genome. Physical and genetic autonomy from the host make vaccinia a useful eukaryotic organism in which to study replication genes and proteins, using a combination of biochemical and genetic techniques. Essential viral functions for replication are identified by conditional lethal mutants that fail to synthesize DNA at the non-permissive temperatures. One such group contains the non-complementing alleles ts17, ts24, ts69 (WR strain). Studies were undertaken to define the phenotype of ts mutants, and to identify and characterize the affected gene and protein. Mutant infection was essentially normal at 32 degree C, but at 39 degree C the mutants did not incorporate 3H-thymidine into nascent viral DNA or synthesize late viral proteins. If mutant cultures were shifted to non-permissive conditions at the height of replication, DNA synthesis was halted rapidly, implying that the mutants are defective in DNA elongation. The gene affected in the WR mutants and in ts6389, a DNA-minus mutant of the IHD strain, was mapped by marker rescue and corresponds to open reading frame 5 (orfD5) of the viral HindIII D fragment

  17. Mrc1 is a replication fork component whose phosphorylation in response to DNA replication stress activates Rad53

    OpenAIRE

    Osborn, Alexander J.; Elledge, Stephen J.

    2003-01-01

    When DNA replication is stalled, a signal transduction pathway is activated that promotes the stability of stalled forks and resumption of DNA synthesis. In budding yeast, this pathway includes the kinases Mec1 and Rad53. Here we report that the Mediator protein Mrc1, which is required for normal DNA replication and for activation of Rad53, is present at replication forks. Mrc1 initially binds early-replicating sequences and moves along chromatin with the replication f...

  18. A reduction in ribonucleotide reductase activity slows down the chromosome replication fork but does not change its localization.

    Directory of Open Access Journals (Sweden)

    Ingvild Odsbu

    Full Text Available BACKGROUND: It has been proposed that the enzymes of nucleotide biosynthesis may be compartmentalized or concentrated in a structure affecting the organization of newly replicated DNA. Here we have investigated the effect of changes in ribonucleotide reductase (RNR activity on chromosome replication and organization of replication forks in Escherichia coli. METHODOLOGY/PRINCIPAL FINDINGS: Reduced concentrations of deoxyribonucleotides (dNTPs obtained by reducing the activity of wild type RNR by treatment with hydroxyurea or by mutation, resulted in a lengthening of the replication period. The replication fork speed was found to be gradually reduced proportionately to moderate reductions in nucleotide availability. Cells with highly extended C periods showed a "delay" in cell division i.e. had a higher cell mass. Visualization of SeqA structures by immunofluorescence indicated no change in organization of the new DNA upon moderate limitation of RNR activity. Severe nucleotide limitation led to replication fork stalling and reversal. Well defined SeqA structures were not found in situations of extensive replication fork repair. In cells with stalled forks obtained by UV irradiation, considerable DNA compaction was observed, possibly indicating a reorganization of the DNA into a "repair structure" during the initial phase of the SOS response. CONCLUSION/SIGNIFICANCE: The results indicate that the replication fork is slowed down in a controlled manner during moderate nucleotide depletion and that a change in the activity of RNR does not lead to a change in the organization of newly replicated DNA. Control of cell division but not control of initiation was affected by the changes in replication elongation.

  19. A conditionally replicating HIV-1 vector interferes with wild-type HIV-1 replication and spread.

    OpenAIRE

    Dropulić, B; Hĕrmánková, M; Pitha, P M

    1996-01-01

    Defective-interfering viruses are known to modulate virus pathogenicity. We describe conditionally replicating HIV-1 (crHIV) vectors that interfere with wild-type HIV-1 (wt-HIV) replication and spread. crHIV vectors are defective-interfering HIV genomes that do not encode viral proteins and replicate only in the presence of wt-HIV helper virus. In cells that contain both wt-HIV and crHIV genomes, the latter are shown to have a selective advantage for packaging into progeny virions because the...

  20. Denaturation of the simian virus 40 origin of replication mediated by human replication protein A.

    OpenAIRE

    Iftode, C.; Borowiec, J A

    1997-01-01

    The initiation of simian virus 40 (SV40) replication requires recognition of the viral origin of replication (ori) by SV40 T antigen, followed by denaturation of ori in a reaction dependent upon human replication protein A (hRPA). To understand how origin denaturation is achieved, we constructed a 48-bp SV40 "pseudo-origin" with a central 8-nucleotide (nt) bubble flanked by viral sequences, mimicking a DNA structure found within the SV40 T antigen-ori complex. hRPA bound the pseudo-origin wit...

  1. 中国能源效率影响因素研究——基于VEC模型的实证检验%On Influencing Factors Affecting China's Energy Efficiency:An Empirical Test Based on the VEC Model

    Institute of Scientific and Technical Information of China (English)

    杨冕; 杨福霞; 陈兴鹏

    2011-01-01

    Energy efficiency is called "the fifth category of energy" for its significant function in optimizing the energy-economic system. Using the method of the generalized impulse response function, which is based on the vector error-correction (VEC) model, this paper is aimed at examining influential factors affecting China' s energy efficiency and the dynamic interactions among them. First, by analyzing characteristics of the energy efficiency and development status of China' s energy-economic system, we proposed four indexes including relative energy price, the proportion of the secondary industry to GDP, advance in science and technology, and the proportion of coal to total energy consumption. All time series data corresponding to each indexe were obtained from China Statistics Yearbook or China Compendium of Statistics during the period 1949-2004 except the third index, for which we calculated the technological knowledge stock instead. Before running the model, the stationarity of each time series and the cointegration relationship among them were tested. All the time series data were found to be stationary after the first differencing, and the cointegration relationship were unique. Results of the generalized impulse response indicate that the rise of relative energy price has a significant promotion to the advance in energy efficiency in China, and the average response of energy efficiency to one S.D.innovations of relative energy price reaches 4.16% during the study period. Advance in science and technology also improves significantly the energy efficiency, and the average response of energy efficiency to one S.D. innovations of it was found to be 4.08%. On the contrary, alterations of other two variables impede the improvement of China' s energy efficiency. For example, the average response of energy efficiency to one S.D. innovations of the industrial structure and energy structure is-0.14% and-4.61%, respectively, during the study period. Meanwhile

  2. The p53 Protein Does Not Facilitate Adenovirus Type 5 Replication in Normal Human Cells

    OpenAIRE

    Chahal, Jasdave S.; Flint, S J

    2013-01-01

    Although several adenovirus type 5 (Ad5) proteins prevent deleterious consequences of activation of p53, it has been reported that viral replication proceeds more efficiently when human tumor cells produce wild-type compared to mutant p53. We have now exploited RNA interference and lentiviral vectors to achieve essentially complete knockdown of p53 in normal human cells: no effects on the kinetics or efficiency of viral gene expression or production of infectious particles were observed.

  3. The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.

    Directory of Open Access Journals (Sweden)

    Franck Picard

    2014-05-01

    Full Text Available The duplication of mammalian genomes is under the control of a spatiotemporal program that orchestrates the positioning and the timing of firing of replication origins. The molecular mechanisms coordinating the activation of about [Formula: see text] predicted origins remain poorly understood, partly due to the intrinsic rarity of replication bubbles, making it difficult to purify short nascent strands (SNS. The precise identification of origins based on the high-throughput sequencing of SNS constitutes a new methodological challenge. We propose a new statistical method with a controlled resolution, adapted to the detection of replication origins from SNS data. We detected an average of 80,000 replication origins in different cell lines. To evaluate the consistency between different protocols, we compared SNS detections with bubble trapping detections. This comparison demonstrated a good agreement between genome-wide methods, with 65% of SNS-detected origins validated by bubble trapping, and 44% of bubble trapping origins validated by SNS origins, when compared at the same resolution. We investigated the interplay between the spatial and the temporal programs of replication at fine scales. We show that most of the origins detected in regions replicated in early S phase are shared by all the cell lines investigated whereas cell-type-specific origins tend to be replicated in late S phase. We shed a new light on the key role of CpG islands, by showing that 80% of the origins associated with CGIs are constitutive. Our results further show that at least 76% of CGIs are origins of replication. The analysis of associations with chromatin marks at different timing of cell division revealed new potential epigenetic regulators driving the spatiotemporal activity of replication origins. We highlight the potential role of H4K20me1 and H3K27me3, the coupling of which is correlated with increased efficiency of replication origins, clearly identifying those

  4. A host small GTP-binding protein ARL8 plays crucial roles in tobamovirus RNA replication.

    Science.gov (United States)

    Nishikiori, Masaki; Mori, Masashi; Dohi, Koji; Okamura, Hideyasu; Katoh, Etsuko; Naito, Satoshi; Meshi, Tetsuo; Ishikawa, Masayuki

    2011-12-01

    Tomato mosaic virus (ToMV), like other eukaryotic positive-strand RNA viruses, replicates its genomic RNA in replication complexes formed on intracellular membranes. Previous studies showed that a host seven-pass transmembrane protein TOM1 is necessary for efficient ToMV multiplication. Here, we show that a small GTP-binding protein ARL8, along with TOM1, is co-purified with a FLAG epitope-tagged ToMV 180K replication protein from solubilized membranes of ToMV-infected tobacco (Nicotiana tabacum) cells. When solubilized membranes of ToMV-infected tobacco cells that expressed FLAG-tagged ARL8 were subjected to immunopurification with anti-FLAG antibody, ToMV 130K and 180K replication proteins and TOM1 were co-purified and the purified fraction showed RNA-dependent RNA polymerase activity that transcribed ToMV RNA. From uninfected cells, TOM1 co-purified with FLAG-tagged ARL8 less efficiently, suggesting that a complex containing ToMV replication proteins, TOM1, and ARL8 are formed on membranes in infected cells. In Arabidopsis thaliana, ARL8 consists of four family members. Simultaneous mutations in two specific ARL8 genes completely inhibited tobamovirus multiplication. In an in vitro ToMV RNA translation-replication system, the lack of either TOM1 or ARL8 proteins inhibited the production of replicative-form RNA, indicating that TOM1 and ARL8 are required for efficient negative-strand RNA synthesis. When ToMV 130K protein was co-expressed with TOM1 and ARL8 in yeast, RNA 5'-capping activity was detected in the membrane fraction. This activity was undetectable or very weak when the 130K protein was expressed alone or with either TOM1 or ARL8. Taken together, these results suggest that TOM1 and ARL8 are components of ToMV RNA replication complexes and play crucial roles in a process toward activation of the replication proteins' RNA synthesizing and capping functions. PMID:22174675

  5. Study on the micro-replication of shark skin

    Institute of Scientific and Technical Information of China (English)

    HAN Xin; ZHANG DeYuan

    2008-01-01

    Direct replication of creatural scarfskins to form biomimetic surfaces with relatively vivid morphology is a new attempt of the bio-replicated forming technology at animal body.Taking shark skins as the replication templates,and the micro-em-bossing and micro-molding as the material forming methods,the micro-replicating technology of the outward morphology on shark skins was demonstrated.The pre-liminary analysis on replication precision indicates that the bio-replicated forming technology can replicate the outward morphology of the shark scales with good precision,which validates the application of the bio-replicated forming technology in the direct morphology replication of the firm creatural scarfskins.

  6. Single molecule analysis of Trypanosoma brucei DNA replication dynamics.

    Science.gov (United States)

    Calderano, Simone Guedes; Drosopoulos, William C; Quaresma, Marina Mônaco; Marques, Catarina A; Kosiyatrakul, Settapong; McCulloch, Richard; Schildkraut, Carl L; Elias, Maria Carolina

    2015-03-11

    Eukaryotic genome duplication relies on origins of replication, distributed over multiple chromosomes, to initiate DNA replication. A recent genome-wide analysis of Trypanosoma brucei, the etiological agent of sleeping sickness, localized its replication origins to the boundaries of multigenic transcription units. To better understand genomic replication in this organism, we examined replication by single molecule analysis of replicated DNA. We determined the average speed of replication forks of procyclic and bloodstream form cells and we found that T. brucei DNA replication rate is similar to rates seen in other eukaryotes. We also analyzed the replication dynamics of a central region of chromosome 1 in procyclic forms. We present evidence for replication terminating within the central part of the chromosome and thus emanating from both sides, suggesting a previously unmapped origin toward the 5' extremity of chromosome 1. Also, termination is not at a fixed location in chromosome 1, but is rather variable. Importantly, we found a replication origin located near an ORC1/CDC6 binding site that is detected after replicative stress induced by hydroxyurea treatment, suggesting it may be a dormant origin activated in response to replicative stress. Collectively, our findings support the existence of more replication origins in T. brucei than previously appreciated. PMID:25690894

  7. The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo

    OpenAIRE

    Boubakri, Hasna; de Septenville, Anne Langlois; Viguera, Enrique; Michel, Bénédicte

    2009-01-01

    How living cells deal with head-on collisions of the replication and transcription complexes has been debated for a long time. Even in the widely studied model bacteria Escherichia coli, the enzymes that take care of such collisions are still unknown. We report here that in vivo, the DinG, Rep and UvrD helicases are essential for efficient replication across highly transcribed regions. We show that when rRNA operons (rrn) are inverted to face replication, the viability of the dinG mutant is a...

  8. Selective Serotonin Reuptake Inhibitor Fluoxetine Inhibits Replication of Human Enteroviruses B and D by Targeting Viral Protein 2C

    OpenAIRE

    Ulferts, R.; van der Linden, L.; Thibaut, H.J.; Lanke, K. H. W.; Leyssen, P.; Coutard, B.; De Palma, A.M.; Canard, B; Neyts, J.; Van Kuppeveld, F. J. M.

    2013-01-01

    Although the genus Enterovirus contains many important human pathogens, there is no licensed drug for either the treatment or the prophylaxis of enterovirus infections. We report that fluoxetine (Prozac)-a selective serotonin reuptake inhibitor-inhibits the replication of human enterovirus B (HEV-B) and HEV-D but does not affect the replication of HEV-A and HEV-C or human rhinovirus A or B. We show that fluoxetine interferes with viral RNA replication, and we identified viral protein 2C as th...

  9. ACH-806, an NS4A antagonist, inhibits hepatitis C virus replication by altering the composition of viral replication complexes.

    Science.gov (United States)

    Yang, Wengang; Sun, Yongnian; Hou, Xiaohong; Zhao, Yongsen; Fabrycki, Joanne; Chen, Dawei; Wang, Xiangzhu; Agarwal, Atul; Phadke, Avinash; Deshpande, Milind; Huang, Mingjun

    2013-07-01

    Treatment of hepatitis C patients with direct-acting antiviral drugs involves the combination of multiple small-molecule inhibitors of distinctive mechanisms of action. ACH-806 (or GS-9132) is a novel, small-molecule inhibitor specific for hepatitis C virus (HCV). It inhibits viral RNA replication in HCV replicon cells and was active in genotype 1 HCV-infected patients in a proof-of-concept clinical trial (1). Here, we describe a potential mechanism of action (MoA) wherein ACH-806 alters viral replication complex (RC) composition and function. We found that ACH-806 did not affect HCV polyprotein translation and processing, the early events of the formation of HCV RC. Instead, ACH-806 triggered the formation of a homodimeric form of NS4A with a size of 14 kDa (p14) both in replicon cells and in Huh-7 cells where NS4A was expressed alone. p14 production was negatively regulated by NS3, and its appearance in turn was associated with reductions in NS3 and, especially, NS4A content in RCs due to their accelerated degradation. A previously described resistance substitution near the N terminus of NS3, where NS3 interacts with NS4A, attenuated the reduction of NS3 and NS4A conferred by ACH-806 treatment. Taken together, we show that the compositional changes in viral RCs are associated with the antiviral activity of ACH-806. Small molecules, including ACH-806, with this novel MoA hold promise for further development and provide unique tools for clarifying the functions of NS4A in HCV replication. PMID:23629709

  10. Short hairpin-looped oligodeoxynucleotides reduce hepatitis C virus replication

    Directory of Open Access Journals (Sweden)

    Broecker Felix

    2012-07-01

    Full Text Available Abstract Background Persistent infection with hepatitis C virus (HCV is a leading cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Standard therapy consists of a combination of interferon-alpha and ribavirin, but many patients respond poorly, especially those infected with HCV genotypes 1 and 4. Furthermore, standard therapy is associated with severe side-effects. Thus, alternative therapeutic approaches against HCV are needed. Findings Here, we studied the effect of a new class of antiviral agents against HCV, short, partially double-stranded oligodeoxynucleotides (ODNs, on viral replication. We targeted the 5’ nontranslated region (5’ NTR of the HCV genome that has previously been shown as effective target for small interfering RNAs (siRNAs in vitro. One of the investigated ODNs, ODN 320, significantly and efficiently reduced replication of HCV replicons in a sequence-, time- and dose-dependent manner. ODN 320 targets a genomic region highly conserved among different HCV genotypes and might thus be able to inhibit a broad range of genotypes and subtypes. Conclusions ODNs provide an additional approach for inhibition of HCV, might be superior to siRNAs in terms of stability and cellular delivery, and suitable against HCV resistant to standard therapy. This study underlines the potential of partially double-stranded ODNs as antiviral agents.

  11. Cytolytic replication of echoviruses in colon cancer cell lines

    Directory of Open Access Journals (Sweden)

    Gullberg Maria

    2011-10-01

    Full Text Available Abstract Background Colorectal cancer is one of the most common cancers in the world, killing nearly 50% of patients afflicted. Though progress is being made within surgery and other complementary treatments, there is still need for new and more effective treatments. Oncolytic virotherapy, meaning that a cancer is cured by viral infection, is a promising field for finding new and improved treatments. We have investigated the oncolytic potential of several low-pathogenic echoviruses with rare clinical occurrence. Echoviruses are members of the enterovirus genus within the family Picornaviridae. Methods Six colon cancer cell lines (CaCo-2, HT29, LoVo, SW480, SW620 and T84 were infected by the human enterovirus B species echovirus 12, 15, 17, 26 and 29, and cytopathic effects as well as viral replication efficacy were investigated. Infectivity was also tested in spheroids grown from HT29 cells. Results Echovirus 12, 17, 26 and 29 replicated efficiently in almost all cell lines and were considered highly cytolytic. The infectivity of these four viruses was further evaluated in artificial tumors (spheroids, where it was found that echovirus 12, 17 and 26 easily infected the spheroids. Conclusions We have found that echovirus 12, 17 and 26 have potential as oncolytic agents against colon cancer, by comparing the cytolytic capacity of five low-pathogenic echoviruses in six colon cancer cell lines and in artificial tumors.

  12. Big Data Archives: Replication and synchronizing on a large scale

    Science.gov (United States)

    King, T. A.; Walker, R. J.

    2015-12-01

    Modern data archives provide unique challenges to replication and synchronization because of their large size. We collect more digital information today than any time before and the volume of data collected is continuously increasing. Some of these data are from unique observations, like those from planetary missions that should be preserved for use by future generations. In addition data from NASA missions are considered federal records and must be retained. While the data may be stored on resilient hardware (i.e. RAID systems) they also must be protected from local or regional disasters. Meeting this challenge requires creating multiple copies. This task is complicated by the fact that new data are constantly being added creating what are called "active archives". Having reliable, high performance tools for replicating and synchronizing active archives in a timely fashion is critical to preservation of the data. When archives were smaller using tools like bbcp, rsync and rcp worked fairly well. While these tools are affective they are not optimized for synchronizing big data archives and their poor performance at scale lead us to develop a new tool designed specifically for big data archives. It combines the best features of git, bbcp, rsync and rcp. We call this tool "Mimic" and we discuss the design of the tool, performance comparisons and its use at NASA's Planetary Plasma Interactions (PPI) Node of the Planetary Data System (PDS).

  13. DESIGN SAMPLING AND REPLICATION ASSIGNMENT UNDER FIXED COMPUTING BUDGET

    Institute of Scientific and Technical Information of China (English)

    Loo Hay LEE; Ek Peng CHEW

    2005-01-01

    For many real world problems, when the design space is huge and unstructured, and time consuming simulation is needed to estimate the performance measure, it is important to decide how many designs to sample and how long to run for each design alternative given that we have only a fixed amount of computing time. In this paper, we present a simulation study on how the distribution of the performance measures and distribution of the estimation errors/noises will affect the decision.From the analysis, it is observed that when the underlying distribution of the noise is bounded and if there is a high chance that we can get the smallest noise, then the decision will be to sample as many as possible, but if the noise is unbounded, then it will be important to reduce the noise level first by assigning more replications for each design. On the other hand, if the distribution of the performance measure indicates that we will have a high chance of getting good designs, the suggestion is also to reduce the noise level, otherwise, we need to sample more designs so as to increase the chances of getting good designs. For the special case when the distributions of both the performance measures and noise are normal, we are able to estimate the number of designs to sample, and the number of replications to run in order to obtain the best performance.

  14. Effect of deoxyribonucleic acid replication inhibitors on bacterial recombination

    International Nuclear Information System (INIS)

    Two inhibitors of replicative deoxyribonucleic acid (DNA) synthesis, nalidixic acid (NAL) and 6-(p-hydroxyphenylazo)-uracil (HPUra), showed different effects on genetic recombination and DNA repair in Bacillus subtilis. Previous work (Pedrini et al., 1972) showed that NAL does not interfere with the transformation process of B. subtilis. The results reported in this work demonstrated that the drug was also without effect on the transfection SPP1 or SPO-1 phage DNA (a process that requires a recombination event). The drug was also ineffective on the host cell reactivation of ultraviolet-irradiated SPP1 phage, as well as on transfection with ultraviolet-irradiated DNA of the same phage. HPUra instead markedly reduced the transformation process, as well as transfection, by SPO-1 DNA, but it did not affect the host cell reactivation of SPO-1 phage. In conclusion, whereas the NAL target seems to be specific for replicative DNA synthesis, the HPUra target (i.e., the DNA polymerase III of B. subtilis) seems to be involved also in recombination, but not in the excision repair process. The mutations conferring NAL and HPUra resistance used in this work were mapped by PBS-1 transduction

  15. cmp, a cis-acting plasmid locus that increases interaction between replication origin and initiator protein.

    OpenAIRE

    Gennaro, M L; Novick, R P

    1986-01-01

    pT181, a 4.4-kilobase multicopy plasmid of Staphylococcus aureus, encodes a trans-acting initiator protein, RepC, which was rate limiting for replication. Deletions in a 500-base-pair region of the plasmid external to the minimal replicon decreased the ability of the plasmid to compete with a coexisting incompatible plasmid. These deletions, which define a region called cmp (for competition), appeared to affect the interaction of RepC and the plasmid origin of replication. However, in the hom...

  16. Inhibition of viral replication by nitric oxide and its reversal by ferrous sulfate and tricarboxylic acid cycle metabolites

    OpenAIRE

    1995-01-01

    IFN-gamma-induced nitric oxide (NO) in the murine macrophage-derived cell line RAW 264.7 was previously shown to inhibit replication of the poxviruses ectromelia and vaccinia (VV) and HSV-1. In the current study we demonstrate that murine macrophages activated as a consequence of VV infection express inducible nitric oxide synthase. These activated macrophages were resistant to infection with VV and efficiently blocked the replication of VV and HSV-1 in infected bystander cells of epithelial ...

  17. Ring finger protein 39 genetic variants associate with HIV-1 plasma viral loads and its replication in cell culture

    OpenAIRE

    Lin, Ying-Ju; Chen, Chia-Yen; Jeang, Kuan-Teh; Liu, Xiang; Wang, Jen-Hsien; Hung, Chien-Hui; Tsang, Hsinyi; Lin, Ting-Hsu; Liao, Chiu-Chu; Huang, Shao-Mei; Lin, Cheng-Wen; Ho, Mao-Wang; Chien, Wen-Kuei; Chen, Jin-Hua; Ho, Tsung-Jung

    2014-01-01

    Background The human immunodeficiency virus (HIV-1) exploits host proteins to complete its life cycle. Genome-wide siRNA approaches suggested that host proteins affect HIV-1 replication. However, the results barely overlapped. RING finger protein 39 (RNF39) has been identified from genome-wide association studies. However, its function during HIV-1 replication remains unclear. Methods and results We investigated the relationship between common RNF39 genetic variants and HIV-1 viral loads. The...

  18. The thiazolobenzimidazole TBZE-029 inhibits enterovirus replication by targeting a short region immediately downstream from motif C in the nonstructural protein 2C.

    NARCIS (Netherlands)

    Palma, A.M. de; Heggermont, W.; Lanke, K.H.W.; Coutard, B.; Bergmann, M.; Monforte, A.M.; Canard, B.; Clercq, E. de; Chimirri, A.; Purstinger, G.; Rohayem, J.; Kuppeveld, F.J.M. van; Neyts, J.

    2008-01-01

    TBZE-029 {1-(2,6-difluorophenyl)-6-trifluoromethyl-1H,3H-thiazolo[3,4-a]benzimidazole} is a novel selective inhibitor of the replication of several enteroviruses. We show that TBZE-029 exerts its antiviral activity through inhibition of viral RNA replication, without affecting polyprotein processing

  19. Template Directed Replication Supports the Maintenance of the Metabolically Coupled Replicator System

    Science.gov (United States)

    Könnyű, Balázs; Czárán, Tamás

    2015-06-01

    The RNA World scenario of prebiotic chemical evolution is among the most plausible conceptual framework available today for modelling the origin of life. RNA offers genetic and catalytic (metabolic) functionality embodied in a single chemical entity, and a metabolically cooperating community of RNA molecules would constitute a viable infrabiological subsystem with a potential to evolve into proto-cellular life. Our Metabolically Coupled Replicator System (MCRS) model is a spatially explicit computer simulation implementation of the RNA-World scenario, in which replicable ribozymes cooperate in supplying each other with monomers for their own replication. MCRS has been repeatedly demonstrated to be viable and evolvable, with different versions of the model improved in depth (chemical detail of metabolism) or in extension (additional functions of RNA molecules). One of the dynamically relevant extensions of the MCRS approach to prebiotic RNA evolution is the explicit inclusion of template replication into its assumptions, which we have studied in the present version. We found that this modification has not changed the behaviour of the system in the qualitative sense, just the range of the parameter space which is optimal for the coexistence of metabolically cooperating replicators has shifted in terms of metabolite mobility. The system also remains resistant and tolerant to parasitic replicators.

  20. Accounting for PDMS shrinkage when replicating structures

    International Nuclear Information System (INIS)

    Polydimethylsiloxane (PDMS) is a widely used material for fabrication of microfluidic devices and for replication of micro- and nanotextured surfaces. Shrinkage of PDMS in the fabrication process can lead to leaking devices and poor alignment of layers. However, corrections to the mold master 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). (technical note)

  1. The Solution to Science's Replication Crisis

    CERN Document Server

    Knuteson, Bruce

    2016-01-01

    The solution to science's replication crisis is a new ecosystem in which scientists sell what they learn from their research. In each pairwise transaction, the information seller makes (loses) money if he turns out to be correct (incorrect). Responsibility for the determination of correctness is delegated, with appropriate incentives, to the information purchaser. Each transaction is brokered by a central exchange, which holds money from the anonymous information buyer and anonymous information seller in escrow, and which enforces a set of incentives facilitating the transfer of useful, bluntly honest information from the seller to the buyer. This new ecosystem, capitalist science, directly addresses socialist science's replication crisis by explicitly rewarding accuracy and penalizing inaccuracy.

  2. Entropy involved in fidelity of DNA replication

    CERN Document Server

    Arias-Gonzalez, J Ricardo

    2012-01-01

    Information has an entropic character which can be analyzed within the Statistical Theory in molecular systems. R. Landauer and C.H. Bennett showed that a logical copy can be carried out in the limit of no dissipation if the computation is performed sufficiently slowly. Structural and recent single-molecule assays have provided dynamic details of polymerase machinery with insight into information processing. We introduce a rigorous characterization of Shannon Information in biomolecular systems and apply it to DNA replication in the limit of no dissipation. Specifically, we devise an equilibrium pathway in DNA replication to determine the entropy generated in copying the information from a DNA template in the absence of friction. Both the initial state, the free nucleotides randomly distributed in certain concentrations, and the final state, a polymerized strand, are mesoscopic equilibrium states for the nucleotide distribution. We use empirical stacking free energies to calculate the probabilities of incorpo...

  3. Novel Approaches to Inhibiting HIV-1 Replication

    OpenAIRE

    Adamson, Catherine S.; Freed, Eric O.

    2009-01-01

    Considerable success has been achieved in the treatment of HIV-1 infection, and more than two-dozen antiretroviral drugs are available targeting several distinct steps in the viral replication cycle. However, resistance to these compounds emerges readily, even in the context of combination therapy. Drug toxicity, adverse drug-drug interactions, and accompanying poor patient adherence can also lead to treatment failure. These considerations make continued development of novel antiretroviral th...

  4. Asexual and sexual replication in sporulating organisms

    Science.gov (United States)

    Lee, Bohyun; Tannenbaum, Emmanuel

    2007-08-01

    Replication via sporulation is the replication strategy for all multicellular life, and may even be observed in unicellular life (such as with budding yeast). We consider diploid populations replicating via one of two possible sporulation mechanisms. (1) Asexual sporulation, whereby adult organisms produce single-celled diploid spores that grow into adults themselves. (2) Sexual sporulation, whereby adult organisms produce single-celled diploid spores that divide into haploid gametes. The haploid gametes enter a haploid “pool,” where they may recombine with other haploids to form a diploid spore that then grows into an adult. We consider a haploid fusion rate given by second-order reaction kinetics. We work with a simplified model where the diploid genome consists of only two chromosomes, each of which may be rendered defective with a single point mutation of the wild-type. We find that the asexual strategy is favored when the rate of spore production is high compared to the characteristic growth rate from a spore to a reproducing adult. Conversely, the sexual strategy is favored when the rate of spore production is low compared to the characteristic growth rate from a spore to a reproducing adult. As the characteristic growth time increases, or as the population density increases, the critical ratio of spore production rate to organism growth rate at which the asexual strategy overtakes the sexual one is pushed to higher values. Therefore, the results of this model suggest that, for complex multicellular organisms, sexual replication is favored at high population densities and low growth and sporulation rates.

  5. The Role of Lipids in Retrovirus Replication

    OpenAIRE

    Waheed, Abdul A.; Freed, Eric O.

    2010-01-01

    Retroviruses undergo several critical steps to complete a replication cycle. These include the complex processes of virus entry, assembly, and budding that often take place at the plasma membrane of the host cell. Both virus entry and release involve membrane fusion/fission reactions between the viral envelopes and host cell membranes. Accumulating evidence indicates important roles for lipids and lipid microdomains in virus entry and egress. In this review, we outline the current understandi...

  6. Studies on Prion Replication in Spleen

    OpenAIRE

    Raeber, Alex J.; Fabio Montrasio; Ivan Hegyi; Rico Frigg; Klein, Michael A.; Adriano Aguzzi; Charles Weissmann

    2001-01-01

    Some of the early events following scrapie infection take place in the lymphoreticular system (LRS) and result in significant replication of prions in lymphoid organs. The identity of the cells in the LRS that produce prions and their role in neuroinvasion are still unknown. We find that in the spleen of scrapie-infected mice, prions are associated with T and B cells and to a somewhat lesser degree with the stroma, which contains the follicular dendritic cells (FDC's); curiously, no infectivi...

  7. The Maximum Principle for Replicator Equations

    OpenAIRE

    K. Sigmund

    1984-01-01

    By introducing a non-Euclidean metric on the unit simplex, it is possible to identify an interesting class of gradient systems within the ubiquitous "replicator equations" of evolutionary biomathematics. In the case of homogeneous potentials, this leads to maximum principles governing the increase of the average fitness, both in population genetics and in chemical kinetics. This research was carried out as part of the Dynamics of Macrosystems Feasibility Study in the System and Decision ...

  8. The switch between EBV latency and replication.

    OpenAIRE

    Miller, G

    1989-01-01

    This paper reviews experiments done in the author's laboratory which led to the discovery of an Epstein-Barr virus (EBV) gene, BZLF1, whose product, ZEBRA, switches the virus from latency to the replicative phase of its life cycle. Recent experiments are summarized which explore the effects of EBV genome rearrangements and cell background on the expression of ZEBRA, and which investigate the viral targets of ZEBRA action.

  9. The Anisotropy of Replicated Aluminum Foams

    Directory of Open Access Journals (Sweden)

    Eugeny L. Furman

    2014-01-01

    Full Text Available The replication casting process gives the open-cell aluminum foams that can be used in many industrial applications as well as in filtering technology. The essential requirement for filters is the uniformity of filtering degree which is defined by the minimal pore size. However the structure of replication castings is often inhomogeneous and the minimal pore radius is decreasing in the direction of melt infiltration. The objective of this investigation is to study the dynamics of melt impregnation of the porous medium by vacuum suction to identify the possibility of reducing the anisotropy. Theoretical data illustrate the processes at the boundary between melt and gas medium. The experiments were carried out using the replication aluminum samples produced according to commercial technology. It was found that the permeability coefficient varies throughout the height of castings. A method for estimation of pressure on the line of melt movement was proposed. The resistance of NaCl layer and circular vents of the mold causes the inhomogeneity of castings. Finally the ways of minimizing the anisotropy were offered.

  10. Early steps of retrovirus replicative cycle

    Directory of Open Access Journals (Sweden)

    Saïb Ali

    2004-05-01

    Full Text Available Abstract During the last two decades, the profusion of HIV research due to the urge to identify new therapeutic targets has led to a wealth of information on the retroviral replication cycle. However, while the late stages of the retrovirus life cycle, consisting of virus replication and egress, have been partly unraveled, the early steps remain largely enigmatic. These early steps consist of a long and perilous journey from the cell surface to the nucleus where the proviral DNA integrates into the host genome. Retroviral particles must bind specifically to their target cells, cross the plasma membrane, reverse-transcribe their RNA genome, while uncoating the cores, find their way to the nuclear membrane and penetrate into the nucleus to finally dock and integrate into the cellular genome. Along this journey, retroviruses hijack the cellular machinery, while at the same time counteracting cellular defenses. Elucidating these mechanisms and identifying which cellular factors are exploited by the retroviruses and which hinder their life cycle, will certainly lead to the discovery of new ways to inhibit viral replication and to improve retroviral vectors for gene transfer. Finally, as proven by many examples in the past, progresses in retrovirology will undoubtedly also provide some priceless insights into cell biology.

  11. Protected Data Objects Replication in Data Grid

    Directory of Open Access Journals (Sweden)

    G. Aruna Kranthi

    2012-02-01

    Full Text Available Secret distribution and erasure convention - based approaches have been used in distributed storage systems to provide the confidentiality, integrity, and availability of critical information. To achieve performance goals in data accesses, these data fragmentation approaches can be combined with dynamic replication. In this paper, we consider data partitioning (both secret distribution and erasure convention and dynamic replication in data grids, in which security and data access performance are critical issues. More specifically, we investigate the problem of optimal allocation of sensitive data objects that aredivided by using secret distribution scheme or erasure convention scheme and/or replicated. The grid topology we consider consists of two layers. In the upper layer, multiple clusters form a network topology that can be represented by a general graph. The topology within each cluster is represented by a tree graph. We decompose the share replica allocation problem into two sub problems: the Optimal Inter cluster Resident Set Problem (OIRSP that determines which clusters share replicas and the Optimal Intra need cluster Share Allocation Problem (OISAP that determines the number of share replicas needed in a cluster and their placements. We develop two heuristic algorithms for the two sub problems.

  12. Diversification of self-replicating molecules

    Science.gov (United States)

    Sadownik, Jan W.; Mattia, Elio; Nowak, Piotr; Otto, Sijbren

    2016-03-01

    How new species emerge in nature is still incompletely understood and difficult to study directly. Self-replicating molecules provide a simple model that allows us to capture the fundamental processes that occur in species formation. We have been able to monitor in real time and at a molecular level the diversification of self-replicating molecules into two distinct sets that compete for two different building blocks (‘food’) and so capture an important aspect of the process by which species may arise. The results show that the second replicator set is a descendant of the first and that both sets are kinetic products that oppose the thermodynamic preference of the system. The sets occupy related but complementary food niches. As diversification into sets takes place on the timescale of weeks and can be investigated at the molecular level, this work opens up new opportunities for experimentally investigating the process through which species arise both in real time and with enhanced detail.

  13. Resíduos vegetais na superfície do solo afetam a acidez do solo e a eficiência do herbicida flumetsulam Soil surface residues affect soil acidity and flumetsulam herbicid efficiency

    Directory of Open Access Journals (Sweden)

    Antonio Sergio do Amaral

    2000-10-01

    Full Text Available Com o objetivo de avaliar o potencial de resíduos de duas espécies vegetais em alterar a acidez do solo e a atividade do herbicida flumetsulam, foi conduzido um experimento em casa de vegetação no Departamento de Solos da Universidade Federal do Rio Grande do Sul, em novembro de 1998. Amostras da camada superficial (0-20cm de um cambissolo húmico distrófico foram colocadas em vasos, com capacidade de 1,0kg, onde se aplicou na superfície: 0, 5 e 10t ha-1 de resíduos de aveia-preta e de ervilhaca comum, com e sem aplicação do herbicida. Utilizou-se aveia-branca como cultura reagente. O delineamento experimental foi o inteiramente casualizado com três repetições. O resíduo da ervilhaca aumentou o pH do solo e ambos os resíduos diminuíram o alumínio trocável na camada de 0-3cm de profundidade, sendo o efeito da ervilhaca mais pronunciado. O decréscimo do alumínio trocável foi relacionado a dois mecanismos: complexação pela matéria orgânica e aumento do pH. Os resíduos vegetais aplicados sobre a superfície do solo aumentaram a eficiência do herbicida flumetsulam, especialmente quando o herbicida foi aplicado sobre os resíduos da leguminosa, que teve maior efeito na elevação do pH do solo.An experiment was conducted in the greenhouse of the Soils Department of the Federal University of Rio Grande do Sul, in November of 1998, to evaluate the potential of two crop residues to modify the acidity of the soil and the activity of the flumetsulam herbicide. The experimental units consisted of pots containing an Haplumbrept soil from the surface layer (0-20cm in with it was applyed 0, 5 and 10t ha-1 of black oat and of common vicia residues, with and without the herbicide application in the soil surface, and arranged in a complete randomized design, with three replications. White oat was used as test culture. Vicia residues increase soil pH and both residues decreased exchangeable Al in the 0-3cm layer, with the effect of vicia

  14. Cytoskeletal Dynamics: Concepts in Measles Virus Replication and Immunomodulation

    Directory of Open Access Journals (Sweden)

    Sibylle Schneider-Schaulies

    2011-01-01

    Full Text Available In common with most viruses, measles virus (MV relies on the integrity of the cytoskeleton of its host cells both with regard to efficient replication in these cells, but also retention of their motility which favors viral dissemination. It is, however, the surface interaction of the viral glycoprotein (gp complex with receptors present on lymphocytes and dendritic cells (DCs, that signals effective initiation of host cell cytoskeletal dynamics. For DCs, these may act to regulate processes as diverse as viral uptake and sorting, but also the ability of these cells to successfully establish and maintain functional immune synapses (IS with T cells. In T cells, MV signaling causes actin cytoskeletal paralysis associated with a loss of polarization, adhesion and motility, which has been linked to activation of sphingomyelinases and subsequent accumulation of membrane ceramides. MV modulation of both DC and T cell cytoskeletal dynamics may be important for the understanding of MV immunosuppression at the cellular level.

  15. Functional redundancy between DNA ligases I and III in DNA replication in vertebrate cells

    Science.gov (United States)

    Arakawa, Hiroshi; Bednar, Theresa; Wang, Minli; Paul, Katja; Mladenov, Emil; Bencsik-Theilen, Alena A.; Iliakis, George

    2012-01-01

    In eukaryotes, the three families of ATP-dependent DNA ligases are associated with specific functions in DNA metabolism. DNA ligase I (LigI) catalyzes Okazaki-fragment ligation at the replication fork and nucleotide excision repair (NER). DNA ligase IV (LigIV) mediates repair of DNA double strand breaks (DSB) via the canonical non-homologous end-joining (NHEJ) pathway. The evolutionary younger DNA ligase III (LigIII) is restricted to higher eukaryotes and has been associated with base excision (BER) and single strand break repair (SSBR). Here, using conditional knockout strategies for LIG3 and concomitant inactivation of the LIG1 and LIG4 genes, we show that in DT40 cells LigIII efficiently supports semi-conservative DNA replication. Our observations demonstrate a high functional versatility for the evolutionary new LigIII in DNA replication and mitochondrial metabolism, and suggest the presence of an alternative pathway for Okazaki fragment ligation. PMID:22127868

  16. Sulfolobus Replication Factor C stimulates the activity of DNA Polymerase B1

    DEFF Research Database (Denmark)

    Xing, Xuanxuan; Zhang, Likui; Guo, Li;

    2014-01-01

    Replication factor C (RFC) is known to function in loading proliferating cell nuclear antigen (PCNA) onto primed DNA, allowing PCNA to tether DNA polymerase for highly processive DNA synthesis in eukaryotic and archaeal replication. In this report, we show that an RFC complex from the...... with the ability of RFC to facilitate DNA binding by PolB1 through protein-protein interaction. These results suggest that Sulfolobus RFC may play a role in recruiting DNA polymerase for efficient primer extension, in addition to clamp loading, during DNA replication....... hyperthermophilic archaea of the genus Sulfolobus physically interacts with DNA polymerase B1 (PolB1) and enhances both the polymerase and 3'-5' exonuclease activities of PolB1 in an ATP-independent manner. Stimulation of the PolB1 activity by RFC is independent of the ability of RFC to bind DNA but is consistent...

  17. Bio-Cryptography Based Secured Data Replication Management in Cloud Storage

    Directory of Open Access Journals (Sweden)

    Elango Pitchai

    2016-07-01

    Full Text Available Cloud computing is new way of economical and efficient storage. The single data mart storage system is a less secure because data remain under a single data mart. This can lead to data loss due to different causes like hacking, server failure etc. If an attacker chooses to attack a specific client, then he can aim at a fixed cloud provider, try to have access to the client’s information. This makes an easy job of the attackers, both inside and outside attackers get the benefit of using data mining to a great extent. Inside attackers refer to malicious employees at a cloud provider. Thus single data mart storage architecture is the biggest security threat concerning data mining on cloud, so in this paper present the secure replication approach that encrypt based on biocrypt and replicate the data in distributed data mart storage system. This approach involves the encryption, replication and storage of data

  18. Colloidal pattern replication through contact photolithography operated in a "Talbot-Fabry-Perot" regime

    CERN Document Server

    Emplit, Aline; Huynen, Isabelle; Vlad, Alexandru; Sarrazin, Michael

    2014-01-01

    We detail on a continuous colloidal pattern replication by using contact photolithography. Chrome on quartz masks are fabricated using colloidal nanosphere lithography and subsequently used as photolithography stamps. Hexagonal pattern arrangements with different dimensions (980, 620 and 480 nm, using colloidal particles with respective diameters) have been studied. When the mask and the imaged resist layer were in intimate contact, a high fidelity pattern replica was obtained after photolithography exposure and processing. In turn, the presence of an air-gap in between has been found to affect the projected image onto the photoresist layer, strongly dependent on the mask feature size and air-gap height. Pattern replication, inversion and hybridization was achieved for 980 nm-period mask; no hybridization for the 620 nm; and only pattern replication for the 480 nm. These results are interpreted in the framework of a "Talbot-Fabry-Perot" effect. Numerical simulations corroborate with the experimental findings ...

  19. 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.

  20. Ultrastructural organization of replicating chromatin in prematurely condensed chromosomes

    Directory of Open Access Journals (Sweden)

    Arifulin E. A.

    2015-08-01

    Full Text Available Aim. The ultrastructural aspect of replicating chromatin organization is a matter of dispute. Here, we have analyzed the ultrastructural organization of replication foci using prematurely condensed chromosomes (PCC. Methods. To investigate the ultrastructure of replicating chromatin, we have used correlative light and electron microscopy as well as immunogold staining. Results. Replication in PCC occurs in the gaps between condensed chromatin domains. Using correlative light and electron microscopy, we observed that the replication foci contain decondensed chromatin as well as 80 and 130 nm globules, those were also found in condensed non-replicating chromatin domains. Using immunogolding, we demonstrated that DNA replication in S-phase PCC occurs in loose chromatin on the periphery of dense chromatin domains. Conclusion. Replication in PCC occurred in the decondensed chromatin neighboring the condensed chromatin without formation of special structures.

  1. On the scattering of DNA replication completion times

    Science.gov (United States)

    Meilikhov, E. Z.; Farzetdinova, R. M.

    2015-07-01

    Stochasticity of Eukaryotes' DNA replication should not lead to large fluctuations of replication times, which could result in mitotic catastrophes. Fundamental problem that cells face is how to be ensured that entire genome is replicated on time. We develop analytic approach of calculating DNA replication times, that being simplified and approximate, leads, nevertheless, to results practically coincident with those that were obtained by some sophisticated methods. In the framework of that model we consider replication times' scattering and discuss the influence of repair stopping on kinetics of DNA replication. Our main explicit formulae for DNA replication time t r ∝ ( N is the total number of DNA base pairs) is of general character and explains basic features of DNA replication kinetics.

  2. Relief of preintegration inhibition and characterization of additional blocks for HIV replication in primary mouse T cells.

    Directory of Open Access Journals (Sweden)

    Jing-xin Zhang

    Full Text Available Development of a small animal model to study HIV replication and pathogenesis has been hampered by the failure of the virus to replicate in non-primate cells. Most studies aimed at achieving replication in murine cells have been limited to fibroblast cell lines, but generating an appropriate model requires overcoming blocks to viral replication in primary T cells. We have studied HIV-1 replication in CD4(+ T cells from human CD4/CCR5/Cyclin T1 transgenic mice. Expression of hCD4 and hCCR5 in mouse CD4(+ T cells enabled efficient entry of R5 strain HIV-1. In mouse T cells, HIV-1 underwent reverse transcription and nuclear import as efficiently as in human T cells. In contrast, chromosomal integration of HIV-1 proviral DNA was inefficient in activated mouse T cells. This process was greatly enhanced by providing a secondary T cell receptor (TCR signal after HIV-1 infection, especially between 12 to 24 h post infection. This effect was specific for primary mouse T cells. The pathways involved in HIV replication appear to be PKCtheta-, CARMA1-, and WASp-independent. Treatment with Cyclosporin A (CsA further relieved the pre-integration block. However, transcription of HIV-1 RNA was still reduced in mouse CD4(+ T cells despite expression of the hCyclin T1 transgene. Additional post-transcriptional defects were observed at the levels of Gag expression, Gag processing, Gag release and virus infectivity. Together, these post-integration defects resulted in a dramatically reduced yield of infectious virus (300-500 fold after a single cycle of HIV-1 replication. This study implies the existence of host factors, in addition to those already identified, that are critical for HIV-1 replication in mouse cells. This study also highlights the differences between primary T cells and cell lines regarding pre-integration steps in the HIV-1 replication cycle.

  3. Replication of Crohn's disease-associated AIEC within macrophages is dependent on TNF-α secretion.

    Science.gov (United States)

    Bringer, Marie-Agnès; Billard, Elisabeth; Glasser, Anne-Lise; Colombel, Jean-Frédéric; Darfeuille-Michaud, Arlette

    2012-03-01

    Adherent and invasive Escherichia coli (AIEC) associated with Crohn's disease are able to survive and to replicate extensively in active phagolysosomes within macrophages. AIEC-infected macrophages release large amounts of tumour necrosis factor-alpha (TNF-α) and do not undergo cell death. The aim of the present study was to determine what benefit AIEC bacteria could gain from inducing the release of large amounts of TNF-α by infected macrophages and to what extent the neutralization of TNF-α could affect AIEC intramacrophagic replication. Our results showed that the amount of TNF-α released by infected macrophages is correlated with the load of intramacrophagic AIEC bacteria and their intracellular replication. TNF-α secretion was not related to the number of bacteria entering host cells because when the number of bacteria internalized in macrophage was decreased by blocking lipid raft-dependent and clathrin-coated pits-dependent endocytosis, the amount of TNF-α secreted by infected macrophages was not modified. Interestingly, dose-dependent increases in the number of intracellular AIEC LF82 bacteria were observed when infected macrophages were stimulated with exogenous TNF-α, and neutralization of TNF-α secreted by AIEC-infected macrophages using anti-TNF-α antibodies induced a significant decrease in the number of intramacrophagic bacteria. These results indicate that AIEC bacteria use TNF-α as a Trojan horse to ensure their intracellular replication because replication of AIEC bacteria within macrophages induces the release of TNF-α, which in turn increases the intramacrophagic replication of AIEC. Neutralizing TNF-α secreted by infected macrophages may represent an effective strategy to control AIEC intracellular replication. PMID:22042084

  4. Cyclophilin inhibitors block arterivirus replication by interfering with viral RNA synthesis.

    Science.gov (United States)

    de Wilde, Adriaan H; Li, Yanhua; van der Meer, Yvonne; Vuagniaux, Grégoire; Lysek, Robert; Fang, Ying; Snijder, Eric J; van Hemert, Martijn J

    2013-02-01

    Virus replication strongly depends on cellular factors, in particular, on host proteins. Here we report that the replication of the arteriviruses equine arteritis virus (EAV) and porcine reproductive and respiratory syndrome virus (PRRSV) is strongly affected by low-micromolar concentrations of cyclosporine A (CsA), an inhibitor of members of the cyclophilin (Cyp) family. In infected cells, the expression of a green fluorescent protein (GFP) reporter gene inserted into the PRRSV genome was inhibited with a half-maximal inhibitory concentration (IC(50)) of 5.2 μM, whereas the GFP expression of an EAV-GFP reporter virus was inhibited with an IC(50) of 0.95 μM. Debio-064, a CsA analog that lacks its undesirable immunosuppressive properties, inhibited EAV replication with an IC(50) that was 3-fold lower than that of CsA, whereas PRRSV-GFP replication was inhibited with an IC(50) similar to that of CsA. The addition of 4 μM CsA after infection prevented viral RNA and protein synthesis in EAV-infected cells, and CsA treatment resulted in a 2.5- to 4-log-unit reduction of PRRSV or EAV infectious progeny. A complete block of EAV RNA synthesis was also observed in an in vitro assay using isolated viral replication structures. The small interfering RNA-mediated knockdown of Cyp family members revealed that EAV replication strongly depends on the expression of CypA but not CypB. Furthermore, upon fractionation of intracellular membranes in density gradients, CypA was found to cosediment with membranous EAV replication structures, which could be prevented by CsA treatment. This suggests that CypA is an essential component of the viral RNA-synthesizing machinery. PMID:23152531

  5. Affect Regulation

    DEFF Research Database (Denmark)

    Pedersen, Signe Holm; Poulsen, Stig Bernt; Lunn, Susanne

    2014-01-01

    Gergely and colleagues’ state that their Social Biofeedback Theory of Parental Affect Mirroring” can be seen as a kind of operationalization of the classical psychoanalytic concepts of holding, containing and mirroring. This article examines to what extent the social biofeedback theory of parenta...

  6. Microinjection of Francisella tularensis and Listeria monocytogenes reveals the importance of bacterial and host factors for successful replication.

    Science.gov (United States)

    Meyer, Lena; Bröms, Jeanette E; Liu, Xijia; Rottenberg, Martin E; Sjöstedt, Anders

    2015-08-01

    Certain intracellular bacteria use the host cell cytosol as the replicative niche. Although it has been hypothesized that the successful exploitation of this compartment requires a unique metabolic adaptation, supportive evidence is lacking. For Francisella tularensis, many genes of the Francisella pathogenicity island (FPI) are essential for intracellular growth, and therefore, FPI mutants are useful tools for understanding the prerequisites of intracytosolic replication. We compared the growth of bacteria taken up by phagocytic or nonphagocytic cells with that of bacteria microinjected directly into the host cytosol, using the live vaccine strain (LVS) of F. tularensis; five selected FPI mutants thereof, i.e., ΔiglA, ΔiglÇ ΔiglG, ΔiglI, and ΔpdpE strains; and Listeria monocytogenes. After uptake in bone marrow-derived macrophages (BMDM), ASC(-/-) BMDM, MyD88(-/-) BMDM, J774 cells, or HeLa cells, LVS, ΔpdpE and ΔiglG mutants, and L. monocytogenes replicated efficiently in all five cell types, whereas the ΔiglA and ΔiglC mutants showed no replication. After microinjection, all 7 strains showed effective replication in J774 macrophages, ASC(-/-) BMDM, and HeLa cells. In contrast to the rapid replication in other cell types, L. monocytogenes showed no replication in MyD88(-/-) BMDM and LVS showed no replication in either BMDM or MyD88(-/-) BMDM after microinjection. Our data suggest that the mechanisms of bacterial uptake as well as the permissiveness of the cytosolic compartment per se are important factors for the intracytosolic replication. Notably, none of the investigated FPI proteins was found to be essential for intracytosolic replication after microinjection. PMID:26034213

  7. Ultrastructural organization of replicating chromatin in prematurely condensed chromosomes

    OpenAIRE

    Arifulin E. A.

    2015-01-01

    Aim. The ultrastructural aspect of replicating chromatin organization is a matter of dispute. Here, we have analyzed the ultrastructural organization of replication foci using prematurely condensed chromosomes (PCC). Methods. To investigate the ultrastructure of replicating chromatin, we have used correlative light and electron microscopy as well as immunogold staining. Results. Replication in PCC occurs in the gaps between condensed chromatin domains. Using correlative light and electron mic...

  8. The Meaning of Failed Replications: A Review and Proposal

    OpenAIRE

    Clemens, Michael A.

    2015-01-01

    The welcome rise of replication tests in economics has not been accompanied by a single, clear definition of replication. A discrepant replication, in current usage of the term, can signal anything from an unremarkable disagreement over methods to scientific incompetence or misconduct. This paper proposes an unambiguous definition of replication, one that reflects currently common but unstandardized use. It contrasts this definition with decades of unsuccessful attempts to standardize termino...

  9. Inhibition of Human BK Polyomavirus Replication by Small Noncoding RNAs

    OpenAIRE

    Tikhanovich, I.; Liang, B.; Seoighe, C.; et al.

    2011-01-01

    Small noncoding RNAs regulate a variety of cellular processes, including genomic imprinting, chromatin remodeling, replication, transcription, and translation. Here, we report small replication-regulating RNAs (srRNAs) that specifically inhibit DNA replication of the human BK polyomavirus (BKV) in vitro and in vivo. srRNAs from FM3A murine mammary tumor cells were enriched by DNA replication assay-guided fractionation and hybridization to the BKV noncoding control region (NCCR) and synthesize...

  10. Inhibition of Human BK Polyomavirus Replication by Small Noncoding RNAs▿

    OpenAIRE

    Tikhanovich, Irina; Liang, Bo; Seoighe, Cathal; Folk, William R.; Nasheuer, Heinz Peter

    2011-01-01

    Small noncoding RNAs regulate a variety of cellular processes, including genomic imprinting, chromatin remodeling, replication, transcription, and translation. Here, we report small replication-regulating RNAs (srRNAs) that specifically inhibit DNA replication of the human BK polyomavirus (BKV) in vitro and in vivo. srRNAs from FM3A murine mammary tumor cells were enriched by DNA replication assay-guided fractionation and hybridization to the BKV noncoding control region (NCCR) and synthesize...

  11. Policy and procedures for the replication of custom plant designs

    International Nuclear Information System (INIS)

    The replication of custom plant designs is encouraged as another method to standardize nuclear power plants. Replication is defined for Regulatory purposes as the duplication of a plant preliminary design as it exists at the completion of the Regulatory staff's technical review at the construction permit stage of licensing. A listing is given of policies established for the licensing of replicate plants and procedures established for the submittal and processing of replicate plant applications

  12. Replication Methods in the Pricing and Hedging of Barrier Options

    OpenAIRE

    Tichý Tomáš

    2004-01-01

    This paper considers various options replication methods. Firstly, a specific type of barrier option, an up-and-out call, is considered. Other barrier options are briefly also described, and various types of barriers are considered. Secondly, a general definition of replication methods is provided. Two methods are thus examined in detail: The first one, based on ever-changing positions in replicating portfolio, is referred to as a dynamic replication method. The second one is denoted as a sta...

  13. Mathematical Framework for A Novel Database Replication Algorithm

    Directory of Open Access Journals (Sweden)

    Divakar Singh Yadav

    2013-10-01

    Full Text Available In this paper, the detailed overview of the database replication is presented. Thereafter, PDDRA (Pre-fetching based dynamic data replication algorithm algorithm as recently published is detailed. In this algorithm, further, modifications are suggested to minimize the delay in data replication. Finally a mathematical framework is presented to evaluate mean waiting time before a data can be replicated on the requested site.

  14. Enhanced inhibition of parvovirus B19 replication by cidofovir in extendedly exposed erythroid progenitor cells.

    Science.gov (United States)

    Bonvicini, Francesca; Bua, Gloria; Manaresi, Elisabetta; Gallinella, Giorgio

    2016-07-15

    Human parvovirus B19 (B19V) commonly induces self-limiting infections but can also cause severe clinical manifestations in patients with underlying haematological disorders or with immune system deficits. Currently, therapeutic options for B19V entirely rely on symptomatic and supportive treatments since a specific antiviral therapy is not yet available. Recently a first step in the research for active compounds inhibiting B19V replication has allowed identifying the acyclic nucleoside phosphonate cidofovir (CDV). Herein, the effect of CDV against B19V replication was characterized in human erythroid progenitor cells (EPCs) cultured and infected following different experimental approaches to replicate in vitro the infection of an expanding erythroid cell population in the bone marrow. B19V replication was selectively inhibited both in infected EPCs extendedly exposed to CDV 500μM (viral inhibition 82%) and in serially infected EPCs cultures with passage of the virus progeny, constantly under drug exposure (viral inhibition 99%). In addition, a potent inhibitory effect against B19V (viral inhibition 92%) was assessed in a short-term infection of EPCs treated with CDV 500μM 1day before viral infection. In the evaluated experimental conditions, the enhanced effect of CDV against B19V might be ascribed both to the increased intracellular drug concentration achieved by extended exposure, and to a progressive reduction in efficiency of the replicative process within treated EPCs population. PMID:27071853

  15. Homologous Recombination as a Replication Fork Escort: Fork-Protection and Recovery

    Directory of Open Access Journals (Sweden)

    Audrey Costes

    2012-12-01

    Full Text Available Homologous recombination is a universal mechanism that allows DNA repair and ensures the efficiency of DNA replication. The substrate initiating the process of homologous recombination is a single-stranded DNA that promotes a strand exchange reaction resulting in a genetic exchange that promotes genetic diversity and DNA repair. The molecular mechanisms by which homologous recombination repairs a double-strand break have been extensively studied and are now well characterized. However, the mechanisms by which homologous recombination contribute to DNA replication in eukaryotes remains poorly understood. Studies in bacteria have identified multiple roles for the machinery of homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving the homologous recombination machinery to support the robustness of DNA replication. In addition to its role in fork-recovery and in rebuilding a functional replication fork apparatus, homologous recombination may also act as a fork-protection mechanism. We discuss that some of the fork-escort functions of homologous recombination might be achieved by loading of the recombination machinery at inactivated forks without a need for a strand exchange step; as well as the consequence of such a model for the stability of eukaryotic genomes.

  16. Plasticity of DNA Replication Initiation in Epstein-Barr Virus Episomes

    Directory of Open Access Journals (Sweden)

    Norio Paolo

    2004-01-01

    Full Text Available In mammalian cells, the activity of the sites of initiation of DNA replication appears to be influenced epigenetically, but this regulation is not fully understood. Most studies of DNA replication have focused on the activity of individual initiation sites, making it difficult to evaluate the impact of changes in initiation activity on the replication of entire genomic loci. Here, we used single molecule analysis of replicated DNA (SMARD to study the latent duplication of Epstein-Barr virus (EBV episomes in human cell lines. We found that initiation sites are present throughout the EBV genome and that their utilization is not conserved in different EBV strains. In addition, SMARD shows that modifications in the utilization of multiple initiation sites occur across large genomic regions (tens of kilobases in size. These observations indicate that individual initiation sites play a limited role in determining the replication dynamics of the EBV genome. Long-range mechanisms and the genomic context appear to play much more important roles, affecting the frequency of utilization and the order of activation of multiple initiation sites. Finally, these results confirm that initiation sites are extremely redundant elements of the EBV genome. We propose that these conclusions also apply to mammalian chromosomes.

  17. Segment-specific terminal sequences of Bunyamwera bunyavirus regulate genome replication

    International Nuclear Information System (INIS)

    Bunyamwera virus (BUNV) is the prototype of both the Orthobunyavirus genus and the Bunyaviridae family of segmented negative sense RNA viruses. The tripartite BUNV genome consists of small (S), medium (M), and large (L) segments that are transcribed to give a single mRNA and replicated to generate an antigenome that is the template for synthesis of further genomic RNA strands. We modified an existing cDNA-derived RNA synthesis system to allow identification of BUNV RNA replication and transcription products by direct metabolic labeling. Direct RNA analysis allowed us to distinguish between template activities that affected either RNA replication or mRNA transcription, an ability that was not possible using previous reporter gene expression assays. We generated genome analogs containing the entire nontranslated terminal sequences of the S, M, and L BUNV segments surrounding a common sequence. Analysis of RNAs synthesized from these templates revealed that the relative abilities of BUNV segments to perform RNA replication was M > L > S. Exchange of segment-specific terminal nucleotides identified a 12-nt region located within both the 3' and 5' termini of the M segment that correlated with its high replication ability

  18. 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...

  19. 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...

  20. (+)RNA viruses rewire cellular pathways to build replication organelles

    NARCIS (Netherlands)

    Belov, G.A.; Kuppeveld, F.J.M. van

    2012-01-01

    Positive-strand RNA [(+)RNA] viruses show a significant degree of conservation of their mechanisms of replication. The universal requirement of (+)RNA viruses for cellular membranes for genome replication, and the formation of membranous replication organelles with similar architecture, suggest that