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Sample records for alternative replication factor

  1. Suppression of gross chromosomal rearrangements by a new alternative replication factor C complex

    International Nuclear Information System (INIS)

    Banerjee, Soma; Sikdar, Nilabja; Myung, Kyungjae

    2007-01-01

    Defects in DNA replication fidelity lead to genomic instability. Gross chromosomal rearrangement (GCR), a type of genomic instability, is highly enhanced by various initial mutations affecting DNA replication. Frequent observations of GCRs in many cancers strongly argue the importance of maintaining high fidelity of DNA replication to suppress carcinogenesis. Recent genome wide screens in Saccharomyces cerevisiae identified a new GCR suppressor gene, ELG1, enhanced level of genome instability gene 1. Its physical interaction with proliferating cell nuclear antigen (PCNA) and complex formation with Rfc2-5p proteins suggest that Elg1 functions to load/unload PCNA onto DNA during a certain DNA metabolism. High level of DNA damage accumulation and enhanced phenotypes with mutations in genes involved in cell cycle checkpoints, homologous recombination (HR), or chromatin assembly in the elg1 strain suggest that Elg1p-Rfc2-5p functions in a fundamental DNA metabolism to suppress genomic instability

  2. Elg1 forms an alternative RFC complex important for DNA replication and genome integrity

    NARCIS (Netherlands)

    Bellaoui, Mohammed; Chang, Michael; Ou, Jiongwen; Xu, Hong; Boone, Charles; Brown, Grant W

    2003-01-01

    Genome-wide synthetic genetic interaction screens with mutants in the mus81 and mms4 replication fork-processing genes identified a novel replication factor C (RFC) homolog, Elg1, which forms an alternative RFC complex with Rfc2-5. This complex is distinct from the DNA replication RFC, the DNA

  3. Host factors involved in chikungunya virus replication

    NARCIS (Netherlands)

    Scholte, Florine Elisabeth Maria

    2015-01-01

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

  4. Factors influencing microinjection molding replication quality

    Science.gov (United States)

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

    2018-01-01

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

  5. Factor Copula Models for Replicated Spatial Data

    KAUST Repository

    Krupskii, Pavel

    2016-12-19

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

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

    Directory of Open Access Journals (Sweden)

    Angeletti Peter C

    2010-06-01

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

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Moss Bernard

    2005-03-01

    and requiring all five known viral replication proteins. Therefore, small plasmids may be used as surrogates for the large poxvirus genome to study trans-acting factors and mechanism of viral DNA replication.

  9. Risk Factors as Major Determinants of Resilience: A Replication Study.

    Science.gov (United States)

    Eshel, Yohanan; Kimhi, Shaul; Lahad, Mooli; Leykin, Dmitry; Goroshit, Marina

    2018-03-16

    The present study was conducted in the context of current concerns about replication in psychological research. It claims that risk factors should be regarded as an integral part of the definition of individual resilience, which should be defined in terms of the balance between individual strength or protective factors, and individual vulnerability or risk factors (IND-SVR). Five independent samples, including 3457 Israeli participants, were employed to determine the effects of resilience promoting and resilience suppressing variables on the IND-SVR index of resilience, and on its two components: recovery from adversity, and distress symptoms. Five path analyses were employed for determining the role of distress symptoms as a measure of psychological resilience, as compared to other indices of this resilience. Results indicated the major role of risk factors (distress symptoms) as an integral component of resilience. This role was generally replicated in the five investigated samples. Risk factors are legitimate, valid, and useful parts of the definition of psychological resilience. Resilience research has shifted away from studying individual risk factors to investigating the process through which individuals overcome the hardships they experience. The present data seem to suggest that this shift should be reexamined.

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

    NARCIS (Netherlands)

    Booiman, T.

    2015-01-01

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

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

    DEFF Research Database (Denmark)

    Clausing, Emanuel; Mayer, Andreas; Chanarat, Sittinan

    2010-01-01

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

  12. MITA/STING and Its Alternative Splicing Isoform MRP Restrict Hepatitis B Virus Replication.

    Science.gov (United States)

    Liu, Shuhui; Zhao, Kaitao; Su, Xi; Lu, Lu; Zhao, He; Zhang, Xianwen; Wang, Yun; Wu, Chunchen; Chen, Jizheng; Zhou, Yuan; Hu, Xue; Wang, Yanyi; Lu, Mengji; Chen, Xinwen; Pei, Rongjuan

    2017-01-01

    An efficient clearance of hepatitis B virus (HBV) requires the coordinated work of both the innate and adaptive immune responses. MITA/STING, an adapter protein of the innate immune signaling pathways, plays a key role in regulating innate and adaptive immune responses to DNA virus infection. Previously, we identified an alternatively spliced isoform of MITA/STING, called MITA-related protein (MRP), and found that MRP could specifically block MITA-mediated interferon (IFN) induction while retaining the ability to activate NF-κB. Here, we asked whether MITA/STING and MRP were able to control the HBV replication. Both MITA/STING and MRP significantly inhibited HBV replication in vitro. MITA overexpression stimulated IRF3-IFN pathway; while MRP overexpression activated NF-κB pathway, suggesting these two isoforms may inhibit HBV replication through different ways. Using a hydrodynamic injection (HI) mouse model, we found that HBV replication was reduced following MITA/STING and MRP expression vectors in mice and was enhanced by the knockout of MITA/STING (MITA/STING-/-). The HBV specific humoral and CD8+ T cell responses were impaired in MITA/STING deficient mice, suggesting the participation of MITA/STING in the initiation of host adaptive immune responses. In summary, our data suggest that MITA/STING and MRP contribute to HBV control via modulation of the innate and adaptive responses.

  13. Supplementary Material for: Factor Copula Models for Replicated Spatial Data

    KAUST Repository

    Krupskii, Pavel

    2016-01-01

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

  14. Improved solubility of replication factor C (RFC) Walker A mutants.

    Science.gov (United States)

    Marzahn, Melissa R; Bloom, Linda B

    2012-06-01

    Protein insolubility often poses a significant problem during purification protocols and in enzyme assays, especially for eukaryotic proteins expressed in a recombinant bacterial system. The limited solubility of replication factor C (RFC), the clamp loader complex from Saccharomyces cerevisiae, has been previously documented. We found that mutant forms of RFC harboring a single point mutation in the Walker A motif were even less soluble than the wild-type complex. The addition of maltose at 0.75 M to the storage and assay buffers greatly increases protein solubility and prevents the complex from falling apart. Our analysis of the clamp loading reaction is dependent on fluorescence-based assays, which are environmentally sensitive. Using wt RFC as a control, we show that the addition of maltose to the reaction buffers does not affect fluorophore responses in the assays or the enzyme activity, indicating that maltose can be used as a buffer additive for further downstream analysis of these mutants. Copyright © 2012 Elsevier Inc. All rights reserved.

  15. Host DNA damage response factors localize to merkel cell polyomavirus DNA replication sites to support efficient viral DNA replication.

    Science.gov (United States)

    Tsang, Sabrina H; Wang, Xin; Li, Jing; Buck, Christopher B; You, Jianxin

    2014-03-01

    Accumulating evidence indicates a role for Merkel cell polyomavirus (MCPyV) in the development of Merkel cell carcinoma (MCC), making MCPyV the first polyomavirus to be clearly associated with human cancer. With the high prevalence of MCPyV infection and the increasing amount of MCC diagnosis, there is a need to better understand the virus and its oncogenic potential. In this study, we examined the relationship between the host DNA damage response (DDR) and MCPyV replication. We found that components of the ATM- and ATR-mediated DDR pathways accumulate in MCPyV large T antigen (LT)-positive nuclear foci in cells infected with native MCPyV virions. To further study MCPyV replication, we employed our previously established system, in which recombinant MCPyV episomal DNA is autonomously replicated in cultured cells. Similar to native MCPyV infection, where both MCPyV origin and LT are present, the host DDR machinery colocalized with LT in distinct nuclear foci. Immunofluorescence in situ hybridization and bromodeoxyuridine (BrdU) incorporation analysis showed that these DDR proteins and MCPyV LT in fact colocalized at the actively replicating MCPyV replication complexes, which were absent when a replication-defective LT mutant or an MCPyV-origin mutant was introduced in place of wild-type LT or wild-type viral origin. Inhibition of DDR kinases using chemical inhibitors and ATR/ATM small interfering RNA (siRNA) knockdown reduced MCPyV DNA replication without significantly affecting LT expression or the host cell cycle. This study demonstrates that these host DDR factors are important for MCPyV DNA replication, providing new insight into the host machinery involved in the MCPyV life cycle. MCPyV is the first polyomavirus to be clearly associated with human cancer. However, the MCPyV life cycle and its oncogenic mechanism remain poorly understood. In this report, we show that, in cells infected with native MCPyV virions, components of the ATM- and ATR-mediated DDR

  16. Mechanical Link between Cohesion Establishment and DNA Replication: Ctf7p/Eco1p, a Cohesion Establishment Factor, Associates with Three Different Replication Factor C Complexes

    OpenAIRE

    Kenna, Margaret A.; Skibbens, Robert V.

    2003-01-01

    CTF7/ECO1 is an essential yeast gene required for the establishment of sister chromatid cohesion. The findings that CTF7/ECO1, POL30 (PCNA), and CHL12/CTF18 (a replication factor C [RFC] homolog) genetically interact provided the first evidence that the processes of cohesion establishment and DNA replication are intimately coupled—a link now confirmed by other studies. To date, however, it is unknown how Ctf7p/Eco1p function is coupled to DNA replication or whether Ctf7p/Eco1p physically asso...

  17. Class I ADP-ribosylation factors are involved in enterovirus 71 replication.

    Science.gov (United States)

    Wang, Jianmin; Du, Jiang; Jin, Qi

    2014-01-01

    Enterovirus 71 is one of the major causative agents of hand, foot, and mouth disease in infants and children. Replication of enterovirus 71 depends on host cellular factors. The viral replication complex is formed in novel, cytoplasmic, vesicular compartments. It has not been elucidated which cellular pathways are hijacked by the virus to create these vesicles. Here, we investigated whether proteins associated with the cellular secretory pathway were involved in enterovirus 71 replication. We used a loss-of-function assay, based on small interfering RNA. We showed that enterovirus 71 RNA replication was dependent on the activity of Class I ADP-ribosylation factors. Simultaneous depletion of ADP-ribosylation factors 1 and 3, but not three others, inhibited viral replication in cells. We also demonstrated with various techniques that the brefeldin-A-sensitive guanidine nucleotide exchange factor, GBF1, was critically important for enterovirus 71 replication. Our results suggested that enterovirus 71 replication depended on GBF1-mediated activation of Class I ADP-ribosylation factors. These results revealed a connection between enterovirus 71 replication and the cellular secretory pathway; this pathway may represent a novel target for antiviral therapies.

  18. Class I ADP-ribosylation factors are involved in enterovirus 71 replication.

    Directory of Open Access Journals (Sweden)

    Jianmin Wang

    Full Text Available Enterovirus 71 is one of the major causative agents of hand, foot, and mouth disease in infants and children. Replication of enterovirus 71 depends on host cellular factors. The viral replication complex is formed in novel, cytoplasmic, vesicular compartments. It has not been elucidated which cellular pathways are hijacked by the virus to create these vesicles. Here, we investigated whether proteins associated with the cellular secretory pathway were involved in enterovirus 71 replication. We used a loss-of-function assay, based on small interfering RNA. We showed that enterovirus 71 RNA replication was dependent on the activity of Class I ADP-ribosylation factors. Simultaneous depletion of ADP-ribosylation factors 1 and 3, but not three others, inhibited viral replication in cells. We also demonstrated with various techniques that the brefeldin-A-sensitive guanidine nucleotide exchange factor, GBF1, was critically important for enterovirus 71 replication. Our results suggested that enterovirus 71 replication depended on GBF1-mediated activation of Class I ADP-ribosylation factors. These results revealed a connection between enterovirus 71 replication and the cellular secretory pathway; this pathway may represent a novel target for antiviral therapies.

  19. Chromatin-remodelling factors and the maintenance of transcriptional states through DNA replication.

    Science.gov (United States)

    Aligianni, Sofia; Varga-Weisz, Patrick

    2006-01-01

    At the replication fork, nucleosomes, transcription factors and RNA polymerases are stripped off the DNA, the DNA double strands are unzipped and DNA methylation marks may be erased. Therefore DNA replication is both a 'curse' and 'bliss' for the epigenome, as it disrupts its stability by causing chromatin perturbations, yet it offers an opportunity to initiate changes in chromatin architecture and gene expression patterns, especially during development. Thus the DNA replication site is a critical point for regulation. It has become apparent that there is a close functional relationship between those factors that regulate transcriptional competence and the DNA replication programme. In this review we discuss novel insights into how chromatin-remodelling factors at replication sites are involved in both the maintenance and regulation of transcriptional states.

  20. Chromosomal Replication Complexity: A Novel DNA Metrics and Genome Instability Factor.

    Directory of Open Access Journals (Sweden)

    Andrei Kuzminov

    2016-10-01

    Full Text Available As the ratio of the copy number of the most replicated to the unreplicated regions in the same chromosome, the definition of chromosomal replication complexity (CRC appears to leave little room for variation, being either two during S-phase or one otherwise. However, bacteria dividing faster than they replicate their chromosome spike CRC to four and even eight. A recent experimental inquiry about the limits of CRC in Escherichia coli revealed two major reasons to avoid elevating it further: (i increased chromosomal fragmentation and (ii complications with subsequent double-strand break repair. Remarkably, examples of stable elevated CRC in eukaryotic chromosomes are well known under various terms like "differential replication," "underreplication," "DNA puffs," "onion-skin replication," or "re-replication" and highlight the phenomenon of static replication fork (sRF. To accurately describe the resulting "amplification by overinitiation," I propose a new term: "replification" (subchromosomal overreplication. In both prokaryotes and eukaryotes, replification, via sRF processing, causes double-strand DNA breaks and, with their repair elevating chromosomal rearrangements, represents a novel genome instability factor. I suggest how static replication bubbles could be stabilized and speculate that some tandem duplications represent such persistent static bubbles. Moreover, I propose how static replication bubbles could be transformed into tandem duplications, double minutes, or inverted triplications. Possible experimental tests of these models are discussed.

  1. The host factor RAD51 is involved in mungbean yellow mosaic India virus (MYMIV) DNA replication.

    Science.gov (United States)

    Suyal, Geetika; Mukherjee, Sunil K; Choudhury, Nirupam R

    2013-09-01

    Geminiviruses replicate their single-stranded genomes with the help of only a few viral factors and various host cellular proteins primarily by rolling-circle replication (RCR) and/or recombination-dependent replication. AtRAD51 has been identified, using the phage display technique, as a host factor that potentially interacts with the Rep protein of mungbean yellow mosaic India virus (MYMIV), a member of the genus Begomovirus. In this study, we demonstrate the interaction between MYMIV Rep and a host factor, AtRAD51, using yeast two-hybrid and β-galactosidase assays, and this interaction was confirmed using a co-immunoprecipitation assay. The AtRAD51 protein complemented the rad51∆ mutation of Saccharomyces cerevisiae in an ex vivo yeast-based geminivirus DNA replication restoration assay. The semiquantitative RT-PCR and northern hybridization data revealed a higher level of expression of the Rad51 transcript in MYMIV-infected mungbean than in uninfected, healthy plants. Our findings provide evidence for a possible cross-talk between RAD51 and MYMIV Rep, which essentially controls viral DNA replication in plants, presumably in conjunction with other host factors. The present study demonstrates for the first time the involvement of a eukaryotic RAD51 protein in MYMIV replication, and this is expected to shed light on the machinery involved in begomovirus DNA replication.

  2. Insights into the functional characteristics of geminivirus rolling-circle replication initiator protein and its interaction with host factors affecting viral DNA replication.

    Science.gov (United States)

    Rizvi, Irum; Choudhury, Nirupam Roy; Tuteja, Narendra

    2015-02-01

    Geminiviruses are DNA viruses that infect several economically important crops, resulting in a reduction in their overall yield. These plant viruses have circular, single-stranded DNA genomes that replicate mainly by a rolling-circle mechanism. Geminivirus infection results in crosstalk between viral and cellular factors to complete the viral life cycle or counteract the infection as part of defense mechanisms of host plants. The geminiviral replication initiator protein Rep is the only essential viral factor required for replication. It is multifunctional and is known to interact with a number of host factors to modulate the cellular environment or to function as a part of the replication machinery. This review provides a holistic view of the research related to the viral Rep protein and various host factors involved in geminiviral DNA replication. Studies on the promiscuous nature of geminiviral satellite DNAs are also reviewed.

  3. Transforming growth factor-β1 suppresses hepatitis B virus replication by the reduction of hepatocyte nuclear factor-4α expression.

    Directory of Open Access Journals (Sweden)

    Ming-Hsiang Hong

    Full Text Available Several studies have demonstrated that cytokine-mediated noncytopathic suppression of hepatitis B virus (HBV replication may provide an alternative therapeutic strategy for the treatment of chronic hepatitis B infection. In our previous study, we showed that transforming growth factor-beta1 (TGF-β1 could effectively suppress HBV replication at physiological concentrations. Here, we provide more evidence that TGF-β1 specifically diminishes HBV core promoter activity, which subsequently results in a reduction in the level of viral pregenomic RNA (pgRNA, core protein (HBc, nucleocapsid, and consequently suppresses HBV replication. The hepatocyte nuclear factor 4alpha (HNF-4α binding element(s within the HBV core promoter region was characterized to be responsive for the inhibitory effect of TGF-β1 on HBV regulation. Furthermore, we found that TGF-β1 treatment significantly repressed HNF-4α expression at both mRNA and protein levels. We demonstrated that RNAi-mediated depletion of HNF-4α was sufficient to reduce HBc synthesis as TGF-β1 did. Prevention of HNF-4α degradation by treating with proteasome inhibitor MG132 also prevented the inhibitory effect of TGF-β1. Finally, we confirmed that HBV replication could be rescued by ectopic expression of HNF-4α in TGF-β1-treated cells. Our data clarify the mechanism by which TGF-β1 suppresses HBV replication, primarily through modulating the expression of HNF-4α gene.

  4. Only three personality factors are fully replicable across languages: Reply to Ashton and Lee

    Czech Academy of Sciences Publication Activity Database

    De Raad, B.; Barelds, D.P.H.; Mlacić, B.; Church, A.T.; Katigbak, M. S.; Ostendorf, F.; Hřebíčková, Martina; Di Bias, L.; Szirmak, S.

    2010-01-01

    Roč. 44, č. 4 (2010), s. 442-445 ISSN 0092-6566 R&D Projects: GA ČR GAP407/10/2394 Institutional research plan: CEZ:AV0Z70250504 Keywords : lexical approach * factor replicability * cross-cultural * three factor s Subject RIV: AN - Psychology Impact factor : 1.756, year: 2010

  5. Only three personality factors are fully replicable across languages: Reply to Ashton and Lee

    Czech Academy of Sciences Publication Activity Database

    De Raad, B.; Barelds, D.P.H.; Mlacić, B.; Church, A.T.; Katigbak, M. S.; Ostendorf, F.; Hřebíčková, Martina; Di Bias, L.; Szirmak, S.

    2010-01-01

    Roč. 44, č. 4 (2010), s. 442-445 ISSN 0092-6566 R&D Projects: GA ČR GAP407/10/2394 Institutional research plan: CEZ:AV0Z70250504 Keywords : lexical approach * factor replicability * cross - cultural * three factors Subject RIV: AN - Psychology Impact factor: 1.756, year: 2010

  6. miR-370 suppresses HBV gene expression and replication by targeting nuclear factor IA.

    Science.gov (United States)

    Fan, Hongxia; Lv, Ping; Lv, Jing; Zhao, Xiaopei; Liu, Min; Zhang, Guangling; Tang, Hua

    2017-05-01

    Hepatitis B virus (HBV) infection is a major health problem worldwide. The roles of microRNAs in the regulation of HBV expression are being increasingly recognized. In this study, we found that overexpression of miR-370 suppressed HBV gene expression and replication in Huh7 cells, whereas antisense knockdown of endogenous miR-370 enhanced HBV gene expression and replication in Huh7 cells and HepG2.2.15 cells. Further, we identified the transcription factor nuclear factor IA (NFIA) as a new host target of miR-370. Overexpression and knockdown studies showed that NFIA stimulated HBV gene expression and replication. Importantly, overexpression of NFIA counteracted the effect of miR-370 on HBV gene expression and replication. Further mechanistic studies showed that miR-370 suppressed HBV replication and gene expression by repressing HBV Enhancer I activity, and one of the NFIA binding site in the Enhancer I element was responsible for the repressive effect of miR-370 on HBV Enhancer I activity. Altogether, our results demonstrated that miR-370 suppressed HBV gene expression and replication through repressing NFIA expression, which stimulates HBV replication via direct regulation on HBV Enhancer I activities. Our findings may provide a new antiviral strategy for HBV infection. J. Med. Virol. 89:834-844, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. Replication-Coupled Recruitment of Viral and Cellular Factors to Herpes Simplex Virus Type 1 Replication Forks for the Maintenance and Expression of Viral Genomes

    Science.gov (United States)

    Dembowski, Jill A.

    2017-01-01

    Herpes simplex virus type 1 (HSV-1) infects over half the human population. Much of the infectious cycle occurs in the nucleus of cells where the virus has evolved mechanisms to manipulate host processes for the production of virus. The genome of HSV-1 is coordinately expressed, maintained, and replicated such that progeny virions are produced within 4–6 hours post infection. In this study, we selectively purify HSV-1 replication forks and associated proteins from virus-infected cells and identify select viral and cellular replication, repair, and transcription factors that associate with viral replication forks. Pulse chase analyses and imaging studies reveal temporal and spatial dynamics between viral replication forks and associated proteins and demonstrate that several DNA repair complexes and key transcription factors are recruited to or near replication forks. Consistent with these observations we show that the initiation of viral DNA replication is sufficient to license late gene transcription. These data provide insight into mechanisms that couple HSV-1 DNA replication with transcription and repair for the coordinated expression and maintenance of the viral genome. PMID:28095497

  8. Selective recruitment of nuclear factors to productively replicating herpes simplex virus genomes.

    Directory of Open Access Journals (Sweden)

    Jill A Dembowski

    2015-05-01

    Full Text Available Much of the HSV-1 life cycle is carried out in the cell nucleus, including the expression, replication, repair, and packaging of viral genomes. Viral proteins, as well as cellular factors, play essential roles in these processes. Isolation of proteins on nascent DNA (iPOND was developed to label and purify cellular replication forks. We adapted aspects of this method to label viral genomes to both image, and purify replicating HSV-1 genomes for the identification of associated proteins. Many viral and cellular factors were enriched on viral genomes, including factors that mediate DNA replication, repair, chromatin remodeling, transcription, and RNA processing. As infection proceeded, packaging and structural components were enriched to a greater extent. Among the more abundant proteins that copurified with genomes were the viral transcription factor ICP4 and the replication protein ICP8. Furthermore, all seven viral replication proteins were enriched on viral genomes, along with cellular PCNA and topoisomerases, while other cellular replication proteins were not detected. The chromatin-remodeling complexes present on viral genomes included the INO80, SWI/SNF, NURD, and FACT complexes, which may prevent chromatinization of the genome. Consistent with this conclusion, histones were not readily recovered with purified viral genomes, and imaging studies revealed an underrepresentation of histones on viral genomes. RNA polymerase II, the mediator complex, TFIID, TFIIH, and several other transcriptional activators and repressors were also affinity purified with viral DNA. The presence of INO80, NURD, SWI/SNF, mediator, TFIID, and TFIIH components is consistent with previous studies in which these complexes copurified with ICP4. Therefore, ICP4 is likely involved in the recruitment of these key cellular chromatin remodeling and transcription factors to viral genomes. Taken together, iPOND is a valuable method for the study of viral genome dynamics

  9. The structure of psychopathology in adolescence : Replication of a general psychopathology factor in the TRAILS study

    NARCIS (Netherlands)

    Laceulle, O.M.; Vollebergh, W.A.M.; Ormel, J.

    2015-01-01

    This study aimed to replicate a study by Caspi and colleagues, which proposed that the structure of psychopathology is characterized by a general psychopathology factor, in addition to smaller internalizing and externalizing factors. Our study expanded the approach of the original by using

  10. An Adenovirus DNA Replication Factor, but Not Incoming Genome Complexes, Targets PML Nuclear Bodies.

    Science.gov (United States)

    Komatsu, Tetsuro; Nagata, Kyosuke; Wodrich, Harald

    2016-02-01

    Promyelocytic leukemia protein nuclear bodies (PML-NBs) are subnuclear domains implicated in cellular antiviral responses. Despite the antiviral activity, several nuclear replicating DNA viruses use the domains as deposition sites for the incoming viral genomes and/or as sites for viral DNA replication, suggesting that PML-NBs are functionally relevant during early viral infection to establish productive replication. Although PML-NBs and their components have also been implicated in the adenoviral life cycle, it remains unclear whether incoming adenoviral genome complexes target PML-NBs. Here we show using immunofluorescence and live-cell imaging analyses that incoming adenovirus genome complexes neither localize at nor recruit components of PML-NBs during early phases of infection. We further show that the viral DNA binding protein (DBP), an early expressed viral gene and essential DNA replication factor, independently targets PML-NBs. We show that DBP oligomerization is required to selectively recruit the PML-NB components Sp100 and USP7. Depletion experiments suggest that the absence of one PML-NB component might not affect the recruitment of other components toward DBP oligomers. Thus, our findings suggest a model in which an adenoviral DNA replication factor, but not incoming viral genome complexes, targets and modulates PML-NBs to support a conducive state for viral DNA replication and argue against a generalized concept that PML-NBs target incoming viral genomes. The immediate fate upon nuclear delivery of genomes of incoming DNA viruses is largely unclear. Early reports suggested that incoming genomes of herpesviruses are targeted and repressed by PML-NBs immediately upon nuclear import. Genome localization and/or viral DNA replication has also been observed at PML-NBs for other DNA viruses. Thus, it was suggested that PML-NBs may immediately sense and target nuclear viral genomes and hence serve as sites for deposition of incoming viral genomes and

  11. The BRCT domain from the large subunit of human Replication Factor C

    NARCIS (Netherlands)

    Kobayashi, Masakazu

    2006-01-01

    The work described in this thesis deals with characterization of DNA binding by the BRCT domain of the large subunit of RFC. Replication Factor C (RFC) is a five protein complex involved in initiating and regulating new DNA synthesis. The first half of the thesis describes region of the RFC and

  12. 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 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...... 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....

  13. Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology

    Directory of Open Access Journals (Sweden)

    Das Atze T

    2006-01-01

    Full Text Available Abstract Background In experimental biology, including retrovirology and molecular biology, replicate measurement sessions very often show similar proportional differences between experimental conditions, but different absolute values, even though the measurements were presumably carried out under identical circumstances. Although statistical programs enable the analysis of condition effects despite this replication error, this approach is hardly ever used for this purpose. On the contrary, most researchers deal with such between-session variation by normalisation or standardisation of the data. In normalisation all values in a session are divided by the observed value of the 'control' condition, whereas in standardisation, the sessions' means and standard deviations are used to correct the data. Normalisation, however, adds variation because the control value is not without error, while standardisation is biased if the data set is incomplete. Results In most cases, between-session variation is multiplicative and can, therefore, be removed by division of the data in each session with a session-specific correction factor. Assuming one level of multiplicative between-session error, unbiased session factors can be calculated from all available data through the generation of a between-session ratio matrix. Alternatively, these factors can be estimated with a maximum likelihood approach. The effectiveness of this correction method, dubbed "factor correction", is demonstrated with examples from the field of molecular biology and retrovirology. Especially when not all conditions are included in every measurement session, factor correction results in smaller residual error than normalisation and standardisation and therefore allows the detection of smaller treatment differences. Factor correction was implemented into an easy-to-use computer program that is available on request at: biolab-services@amc.uva.nl?subject=factor. Conclusion Factor correction

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

    Directory of Open Access Journals (Sweden)

    Philippa M Beard

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

  15. Chl12 (Ctf18) Forms a Novel Replication Factor C-Related Complex and Functions Redundantly with Rad24 in the DNA Replication Checkpoint Pathway

    OpenAIRE

    Naiki, Takahiro; Kondo, Tae; Nakada, Daisuke; Matsumoto, Kunihiro; Sugimoto, Katsunori

    2001-01-01

    RAD24 has been identified as a gene essential for the DNA damage checkpoint in budding yeast. Rad24 is structurally related to subunits of the replication factor C (RFC) complex, and forms an RFC-related complex with Rfc2, Rfc3, Rfc4, and Rfc5. The rad24Δ mutation enhances the defect of rfc5-1 in the DNA replication block checkpoint, implicating RAD24 in this checkpoint. CHL12 (also called CTF18) encodes a protein that is structurally related to the Rad24 and RFC proteins. We show here that a...

  16. Alternative Measures of Total Factor Productivity Growth

    NARCIS (Netherlands)

    Ten Raa, T.; Shestalova, V.

    2006-01-01

    The four main approaches to the measurement of total factor productivity (TFP)-growth and its decomposition are (i) Solow's residual analysis, (ii) the Index Number Approach, (iii) Input-Output Analysis (IO), and (iv) Data Envelopment Analysis (DEA).The corresponding measures of TFP growth are based

  17. The number and kind of invariant personality (Q) factors: a partial replication of Eysenck and Eysenck.

    Science.gov (United States)

    Vagg, P R; Hammond, S B

    1976-06-01

    A study by Eysenck & Eysenck (1969) investigated the invariance across sex of factors derived from the Eysenck, Cattell and Guilford personality inventories. They found only neuroticism and extraversion invariant. The present study was designed as a partial replication of their study, but employed simpler, common-sense methods that gave the more moderate sized factors a chance to demonstrate the extent of their invariance across sex. Four invariant factors were found: the first two, neuroticism and sociability, were large and demonstrated almost complete invariance across sex; the third and fourth factors were moderate-sized and showed less, but substantial invariance across sex. They were called 'sensitivity v. practicality' and 'group-centred morality v. self-centred independence'.

  18. Chromatin determinants of the inner-centromere rely on replication factors with functions that impart cohesion

    Science.gov (United States)

    Abe, Takuya; Kawasumi, Ryotaro; Arakawa, Hiroshi; Hori, Tetsuya; Shirahige, Katsuhiko; Losada, Ana; Fukagawa, Tatsuo; Branzei, Dana

    2016-01-01

    Replication fork-associated factors promote genome integrity and protect against cancer. Mutations in the DDX11 helicase and the ESCO2 acetyltransferase also cause related developmental disorders classified as cohesinopathies. Here we generated vertebrate model cell lines of these disorders and cohesinopathies-related genes. We found that vertebrate DDX11 and Tim-Tipin are individually needed to compensate for ESCO2 loss in chromosome segregation, with DDX11 also playing complementary roles with ESCO2 in centromeric cohesion. Our study reveals that overt centromeric cohesion loss does not necessarily precede chromosome missegregation, while both these problems correlate with, and possibly originate from, inner-centromere defects involving reduced phosphorylation of histone H3T3 (pH3T3) in the region. Interestingly, the mitotic pH3T3 mark was defective in all analyzed replication-related mutants with functions in cohesion. The results pinpoint mitotic pH3T3 as a postreplicative chromatin mark that is sensitive to replication stress and conducts with different kinetics to robust centromeric cohesion and correct chromosome segregation. PMID:27636994

  19. Intermolecular RNA Recombination Occurs at Different Frequencies in Alternate Forms of Brome Mosaic Virus RNA Replication Compartments

    Directory of Open Access Journals (Sweden)

    Hernan Garcia-Ruiz

    2018-03-01

    Full Text Available Positive-strand RNA viruses replicate their genomes in membrane-bound replication compartments. Brome mosaic virus (BMV replicates in vesicular invaginations of the endoplasmic reticulum membrane. BMV has served as a productive model system to study processes like virus-host interactions, RNA replication and recombination. Here we present multiple lines of evidence showing that the structure of the viral RNA replication compartments plays a fundamental role and that recruitment of parental RNAs to a common replication compartment is a limiting step in intermolecular RNA recombination. We show that a previously defined requirement for an RNA recruitment element on both parental RNAs is not to function as a preferred crossover site, but in order for individual RNAs to be recruited into the replication compartments. Moreover, modulating the form of the replication compartments from spherular vesicles (spherules to more expansive membrane layers increased intermolecular RNA recombination frequency by 200- to 1000-fold. We propose that intermolecular RNA recombination requires parental RNAs to be recruited into replication compartments as monomers, and that recruitment of multiple RNAs into a contiguous space is much more common for layers than for spherules. These results could explain differences in recombination frequencies between viruses that replicate in association with smaller spherules versus larger double-membrane vesicles and convoluted membranes.

  20. The RFC2 gene encoding a subunit of replication factor C of Saccharomyces cerevisiae.

    OpenAIRE

    Noskov, V; Maki, S; Kawasaki, Y; Leem, S H; Ono, B; Araki, H; Pavlov, Y; Sugino, A

    1994-01-01

    Replication Factor C (RF-C) of Saccharomyces cerevisiae is a complex that consists of several different polypeptides ranging from 120- to 37 kDa (Yoder and Burgers, 1991; Fien and Stillman, 1992), similar to human RF-C. We have isolated a gene, RFC2, that appears to be a component of the yeast RF-C. The RFC2 gene is located on chromosome X of S. cerevisiae and is essential for cell growth. Disruption of the RFC2 gene led to a dumbbell-shaped terminal morphology, common to mutants having a def...

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

    Science.gov (United States)

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

    2009-01-01

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

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

    Science.gov (United States)

    Schultz, Kimberly L W; Friesen, Paul D

    2009-11-01

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

  3. Transcription factor genes essential for cell proliferation and replicative lifespan in budding yeast

    Energy Technology Data Exchange (ETDEWEB)

    Kamei, Yuka; Tai, Akiko; Dakeyama, Shota; Yamamoto, Kaori; Inoue, Yamato; Kishimoto, Yoshifumi; Ohara, Hiroya; Mukai, Yukio, E-mail: y_mukai@nagahama-i-bio.ac.jp

    2015-07-31

    Many of the lifespan-related genes have been identified in eukaryotes ranging from the yeast to human. However, there is limited information available on the longevity genes that are essential for cell proliferation. Here, we investigated whether the essential genes encoding DNA-binding transcription factors modulated the replicative lifespan of Saccharomyces cerevisiae. Heterozygous diploid knockout strains for FHL1, RAP1, REB1, and MCM1 genes showed significantly short lifespan. {sup 1}H-nuclear magnetic resonance analysis indicated a characteristic metabolic profile in the Δfhl1/FHL1 mutant. These results strongly suggest that FHL1 regulates the transcription of lifespan related metabolic genes. Thus, heterozygous knockout strains could be the potential materials for discovering further novel lifespan genes. - Highlights: • Involvement of yeast TF genes essential for cell growth in lifespan was evaluated. • The essential TF genes, FHL1, RAP1, REB1, and MCM1, regulate replicative lifespan. • Heterozygous deletion of FHL1 changes cellular metabolism related to lifespan.

  4. Expression of Factor X in BHK-21 Cells Promotes Low Pathogenic Influenza Viruses Replication

    Directory of Open Access Journals (Sweden)

    Shahla Shahsavandi

    2015-01-01

    Full Text Available A cDNA clone for factor 10 (FX isolated from chicken embryo inserted into the mammalian cell expression vector pCDNA3.1 was transfected into the baby hamster kidney (BHK-21 cell line. The generated BHK-21 cells with inducible expression of FX were used to investigate the efficacy of the serine transmembrane protease to proteolytic activation of influenza virus hemagglutinin (HA with monobasic cleavage site. Data showed that the BHK-21/FX stably expressed FX after ten serial passages. The cells could proteolytically cleave the HA of low pathogenic avian influenza virus at multiplicity of infection 0.01. Growth kinetics of the virus on BHK-21/FX, BHK-21, and MDCK cells were evaluated by titrations of virus particles in each culture supernatant. Efficient multicycle viral replication was markedly detected in the cell at subsequent passages. Virus titration demonstrated that BHK-21/FX cell supported high-titer growth of the virus in which the viral titer is comparable to the virus grown in BHK-21 or MDCK cells with TPCK-trypsin. The results indicate potential application for the BHK-21/FX in influenza virus replication procedure and related studies.

  5. Proliferating cell nuclear antigen (PCNA): a key factor in DNA replication and cell cycle regulation.

    Science.gov (United States)

    Strzalka, Wojciech; Ziemienowicz, Alicja

    2011-05-01

    PCNA (proliferating cell nuclear antigen) has been found in the nuclei of yeast, plant and animal cells that undergo cell division, suggesting a function in cell cycle regulation and/or DNA replication. It subsequently became clear that PCNA also played a role in other processes involving the cell genome. This review discusses eukaryotic PCNA, with an emphasis on plant PCNA, in terms of the protein structure and its biochemical properties as well as gene structure, organization, expression and function. PCNA exerts a tripartite function by operating as (1) a sliding clamp during DNA synthesis, (2) a polymerase switch factor and (3) a recruitment factor. Most of its functions are mediated by its interactions with various proteins involved in DNA synthesis, repair and recombination as well as in regulation of the cell cycle and chromatid cohesion. Moreover, post-translational modifications of PCNA play a key role in regulation of its functions. Finally, a phylogenetic comparison of PCNA genes suggests that the multi-functionality observed in most species is a product of evolution. Most plant PCNAs exhibit features similar to those found for PCNAs of other eukaryotes. Similarities include: (1) a trimeric ring structure of the PCNA sliding clamp, (2) the involvement of PCNA in DNA replication and repair, (3) the ability to stimulate the activity of DNA polymerase δ and (4) the ability to interact with p21, a regulator of the cell cycle. However, many plant genomes seem to contain the second, probably functional, copy of the PCNA gene, in contrast to PCNA pseudogenes that are found in mammalian genomes.

  6. Functional characterization of replication and stability factors of an incompatibility group P-1 plasmid from Xylella fastidiosa.

    Science.gov (United States)

    Lee, Min Woo; Rogers, Elizabeth E; Stenger, Drake C

    2010-12-01

    Xylella fastidiosa strain riv11 harbors a 25-kbp plasmid (pXF-RIV11) belonging to the IncP-1 incompatibility group. Replication and stability factors of pXF-RIV11 were identified and used to construct plasmids able to replicate in X. fastidiosa and Escherichia coli. Replication in X. fastidiosa required a 1.4-kbp region from pXF-RIV11 containing a replication initiation gene (trfA) and the adjacent origin of DNA replication (oriV). Constructs containing trfA and oriV from pVEIS01, a related IncP-1 plasmid of the earthworm symbiont Verminephrobacter eiseniae, also were competent for replication in X. fastidiosa. Constructs derived from pXF-RIV11 but not pVEIS01 replicated in Agrobacterium tumefaciens, Xanthomonas campestris, and Pseudomonas syringae. Although plasmids bearing replication elements from pXF-RIV11 or pVEIS01 could be maintained in X. fastidiosa under antibiotic selection, removal of selection resulted in plasmid extinction after 3 weekly passages. Addition of a toxin-antitoxin addiction system (pemI/pemK) from pXF-RIV11 improved plasmid stability such that >80 to 90% of X. fastidiosa cells retained plasmid after 5 weekly passages in the absence of antibiotic selection. Expression of PemK in E. coli was toxic for cell growth, but toxicity was nullified by coexpression of PemI antitoxin. Deletion of N-terminal sequences of PemK containing the conserved motif RGD abolished toxicity. In vitro assays revealed a direct interaction of PemI with PemK, suggesting that antitoxin activity of PemI is mediated by toxin sequestration. IncP-1 plasmid replication and stability factors were added to an E. coli cloning vector to constitute a stable 6.0-kbp shuttle vector (pXF20-PEMIK) suitable for use in X. fastidiosa.

  7. The DNA replication factor RFC1 is required for interference-sensitive meiotic crossovers in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Yingxiang Wang

    Full Text Available During meiotic recombination, induced double-strand breaks (DSBs are processed into crossovers (COs and non-COs (NCO; the former are required for proper chromosome segregation and fertility. DNA synthesis is essential in current models of meiotic recombination pathways and includes only leading strand DNA synthesis, but few genes crucial for DNA synthesis have been tested genetically for their functions in meiosis. Furthermore, lagging strand synthesis has been assumed to be unnecessary. Here we show that the Arabidopsis thaliana DNA replication factor C1 (RFC1 important for lagging strand synthesis is necessary for fertility, meiotic bivalent formation, and homolog segregation. Loss of meiotic RFC1 function caused abnormal meiotic chromosome association and other cytological defects; genetic analyses with other meiotic mutations indicate that RFC1 acts in the MSH4-dependent interference-sensitive pathway for CO formation. In a rfc1 mutant, residual pollen viability is MUS81-dependent and COs exhibit essentially no interference, indicating that these COs form via the MUS81-dependent interference-insensitive pathway. We hypothesize that lagging strand DNA synthesis is important for the formation of double Holliday junctions, but not alternative recombination intermediates. That RFC1 is found in divergent eukaryotes suggests a previously unrecognized and highly conserved role for DNA synthesis in discriminating between recombination pathways.

  8. Replication and recombination factors contributing to recombination-dependent bypass of DNA lesions by template switch.

    Directory of Open Access Journals (Sweden)

    Fabio Vanoli

    2010-11-01

    Full Text Available Damage tolerance mechanisms mediating damage-bypass and gap-filling are crucial for genome integrity. A major damage tolerance pathway involves recombination and is referred to as template switch. Template switch intermediates were visualized by 2D gel electrophoresis in the proximity of replication forks as X-shaped structures involving sister chromatid junctions. The homologous recombination factor Rad51 is required for the formation/stabilization of these intermediates, but its mode of action remains to be investigated. By using a combination of genetic and physical approaches, we show that the homologous recombination factors Rad55 and Rad57, but not Rad59, are required for the formation of template switch intermediates. The replication-proficient but recombination-defective rfa1-t11 mutant is normal in triggering a checkpoint response following DNA damage but is impaired in X-structure formation. The Exo1 nuclease also has stimulatory roles in this process. The checkpoint kinase, Rad53, is required for X-molecule formation and phosphorylates Rad55 robustly in response to DNA damage. Although Rad55 phosphorylation is thought to activate recombinational repair under conditions of genotoxic stress, we find that Rad55 phosphomutants do not affect the efficiency of X-molecule formation. We also examined the DNA polymerase implicated in the DNA synthesis step of template switch. Deficiencies in translesion synthesis polymerases do not affect X-molecule formation, whereas DNA polymerase δ, required also for bulk DNA synthesis, plays an important role. Our data indicate that a subset of homologous recombination factors, together with DNA polymerase δ, promote the formation of template switch intermediates that are then preferentially dissolved by the action of the Sgs1 helicase in association with the Top3 topoisomerase rather than resolved by Holliday Junction nucleases. Our results allow us to propose the choreography through which different

  9. Human factors in design modifications: panel alternative stop in Almaraz

    International Nuclear Information System (INIS)

    Roman, Y.; Bote, J.

    2015-01-01

    Human Factors Engineering has acquired a crucial role in the development of any design modification (DM), where every aspect relative to any interaction with the human user has to be taken into account at any stage thereof. Considering this, during the last years, Almaraz Nuclear Powe Plants has developed a program of Human Factors Engineering in order to reach the internationally recognized standards or systematic collected on NUREG 0711 Human Factors Engineering Program Review Model (NRC). One of the most important projects of this program at Almaraz Nuclear Power Plant has been the implementation of the Alternative Stop Panel and their corresponding Transfer Panels. (Author)

  10. DNA replication factor C1 mediates genomic stability and transcriptional gene silencing in Arabidopsis

    KAUST Repository

    Liu, Qian

    2010-07-01

    Genetic screening identified a suppressor of ros1-1, a mutant of REPRESSOR OF SILENCING1 (ROS1; encoding a DNA demethylation protein). The suppressor is a mutation in the gene encoding the largest subunit of replication factor C (RFC1). This mutation of RFC1 reactivates the unlinked 35S-NPTII transgene, which is silenced in ros1 and also increases expression of the pericentromeric Athila retrotransposons named transcriptional silent information in a DNA methylationindependent manner. rfc1 is more sensitive than the wild type to the DNA-damaging agent methylmethane sulphonate and to the DNA inter- and intra- cross-linking agent cisplatin. The rfc1 mutant constitutively expresses the G2/M-specific cyclin CycB1;1 and other DNA repair-related genes. Treatment with DNA-damaging agents mimics the rfc1 mutation in releasing the silenced 35S-NPTII, suggesting that spontaneously induced genomic instability caused by the rfc1 mutation might partially contribute to the released transcriptional gene silencing (TGS). The frequency of somatic homologous recombination is significantly increased in the rfc1 mutant. Interestingly, ros1 mutants show increased telomere length, but rfc1 mutants show decreased telomere length and reduced expression of telomerase. Our results suggest that RFC1 helps mediate genomic stability and TGS in Arabidopsis thaliana. © 2010 American Society of Plant Biologists.

  11. Targeting the centriolar replication factor STIL synergizes with DNA damaging agents for treatment of ovarian cancer

    Science.gov (United States)

    Rabinowicz, Noa; Mangala, Lingegowda S.; Brown, Kevin R.; Checa-Rodriguez, Cintia; Castiel, Asher; Moskovich, Oren; Zarfati, Giulia; Trakhtenbrot, Luba; Levy-Barda, Adva; Jiang, Dahai; Rodriguez-Aguayo, Cristian; Pradeep, Sunila; van Praag, Yael; Lopez-Berestein, Gabriel; David, Ahuvit; Novikov, Ilya; Huertas, Pablo; Rottapel, Robert; Sood, Anil K.; Izraeli, Shai

    2017-01-01

    Advanced ovarian cancer is an incurable disease. Thus, novel therapies are required. We wished to identify new therapeutic targets for ovarian cancer. ShRNA screen performed in 42 ovarian cancer cell lines identified the centriolar replication factor STIL as an essential gene for ovarian cancer cells. This was verified in-vivo in orthotopic human ovarian cancer mouse models. STIL depletion by administration of siRNA in neutral liposomes resulted in robust anti-tumor effect that was further enhanced in combination with cisplatin. Consistent with this finding, STIL depletion enhanced the extent of DNA double strand breaks caused by DNA damaging agents. This was associated with centrosomal depletion, ongoing genomic instability and enhanced formation of micronuclei. Interestingly, the ongoing DNA damage was not associated with reduced DNA repair. Indeed, we observed that depletion of STIL enhanced canonical homologous recombination repair and increased BRCA1 and RAD51 foci in response to DNA double strand breaks. Thus, inhibition of STIL significantly enhances the efficacy of DNA damaging chemotherapeutic drugs in treatment of ovarian cancer. PMID:28423708

  12. Only Three Factors of Personality Description Are Fully Replicable Across Languages: A Comparison of 14 Trait Taxonomies

    Czech Academy of Sciences Publication Activity Database

    De Raad, B.; Barelds, D.P.H.; Levert, E.; Ostendorf, F.; Mlačić, B.; Di Blas, L.; Hřebíčková, Martina; Szirmák, Z.; Szarota, P.; Perugini, M.; Church, A.T.; Katigbak, M. S.

    2010-01-01

    Roč. 98, č. 1 (2010), s. 160-173 ISSN 0022-3514 R&D Projects: GA ČR GA406/07/1561 Institutional research plan: CEZ:AV0Z70250504 Keywords : trait taxonomy * lexical approach to personality * cross-cultural replicability Subject RIV: AN - Psychology Impact factor : 5.205, year: 2010

  13. Only Three Factors of Personality Description Are Fully Replicable Across Languages: A Comparison of 14 Trait Taxonomies

    Czech Academy of Sciences Publication Activity Database

    De Raad, B.; Barelds, D.P.H.; Levert, E.; Ostendorf, F.; Mlačić, B.; Di Blas, L.; Hřebíčková, Martina; Szirmák, Z.; Szarota, P.; Perugini, M.; Church, A.T.; Katigbak, M. S.

    2010-01-01

    Roč. 98, č. 1 (2010), s. 160-173 ISSN 0022-3514 R&D Projects: GA ČR GA406/07/1561 Institutional research plan: CEZ:AV0Z70250504 Keywords : trait taxonomy * lexical approach to personality * cross - cultural replicability Subject RIV: AN - Psychology Impact factor: 5.205, year: 2010

  14. Molecular cloning and expression of the Saccharomyces cerevisiae RFC3 gene, an essential component of replication factor C.

    OpenAIRE

    Li, X; Burgers, P M

    1994-01-01

    Yeast replication factor C (RF-C) is a multi-polypeptide complex required for processive DNA replication by DNA polymerases delta and epsilon. The gene encoding the 40-kDa subunit of the Saccharomyces cerevisiae RF-C (RFC3) has been cloned. The RFC3 gene is required for yeast cell growth and has been mapped to the left arm of chromosome XIV. The deduced amino acid sequence of the RFC3 gene shows a high homology to the 36-, 37-, and 40-kDa subunits of human RF-C (also called activator 1), with...

  15. Replication of a Modified Factor Structure for the Eating Disorder Examination-Questionnaire: Extension to Clinical Eating Disorder and Non-clinical Samples in Portugal.

    Science.gov (United States)

    Machado, Paulo P P; Grilo, Carlos M; Crosby, Ross D

    2018-01-01

    Psychometric investigations of the Eating Disorder Examination-Questionnaire (EDE-Q) have generally not supported the original scale structure. The present study tested an alternative brief factor structure in two large Portuguese samples: (1) a non-clinical sample of N = 4117 female students and (2) a treatment-seeking sample of N = 609 patients diagnosed with eating disorders. Confirmatory factor analysis revealed a poor fit for the original EDE-Q structure in both the non-clinical and the clinical samples but revealed a good fit for the alternative 7-item 3-factor structure (dietary restraint, shape/weight overvaluation and body dissatisfaction). Factor loadings were invariant across samples and across the different specific eating disorder diagnoses in the clinical sample. These confirmatory factor analysis findings, which replicate findings from studies with diverse predominately overweight/obese samples, supported a modified 7-item, 3-factor structure for the EDE-Q. The reliable findings across different non-clinical and clinical eating disorder groups provide confidence regarding the potential utility of this brief version. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association.

  16. A Functional Role of Fibroblast Growth Factor Receptor 1 (FGFR1 in the Suppression of Influenza A Virus Replication.

    Directory of Open Access Journals (Sweden)

    Xin Liu

    Full Text Available Influenza A virus causes annual epidemics and occasional pandemics in humans. Here, we investigated four members of the fibroblast growth factor receptor (FGFR family; FGFR1 to 4, and examined their expression patterns in human lung epithelial cells A549 with influenza A virus infection. We identified a functional role of FGFR1 in influenza A/Puerto Rico/8/1934 (PR8 and A/Anhui/01/2005 (H5N1 virus replication. Our results showed that FGFR1 silencing by siRNA interference promoted influenza A/PR8 and H5N1 virus replication in A549 cells, while lentivirus-mediated exogenous FGFR1 expression significantly suppressed influenza A virus replication; however, FGFR4 did not have the same effects. Moreover, FGFR1 phosphorylation levels were downregulated in A549 cells by influenza A virus infection, while the repression of FGFR1 kinase using PD173074, a potent and selective FGFR1 inhibitor, could enhance virus replication. Furthermore, we found that FGFR1 inhibits influenza virus internalization, but not binding, during viral entry. These results suggested that FGFR1 specifically antagonizes influenza A virus replication, probably by blocking viral entry.

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

    OpenAIRE

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

    2009-01-01

    Apoptosis is an important antivirus defense. To define the poorly understood pathways by which invertebrates respond to viruses by inducing apoptosis, we have identified replication events that trigger apoptosis in baculovirus-infected cells. We used RNA silencing to ablate factors required for multiplication of Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV). Transfection with double-stranded RNA (dsRNA) complementary to the AcMNPV late expression factors (lefs) that are des...

  18. Insulin-like growth factor I has independent effects on bone matrix formation and cell replication

    International Nuclear Information System (INIS)

    Hock, J.M.; Centrella, M.; Canalis, E.

    1988-01-01

    The effects of insulin-like growth factor-I (IGF-I) and insulin on bone matrix synthesis and bone cell replication were studied in cultured 21-day-old fetal rat calvariae. Histomorphometry techniques were developed to measure the incorporation of [2,3- 3 H]proline and [methyl- 3 H]thymidine into bone matrix and bone cell nuclei, respectively, using autoradiographs of sagittal sections of calvariae cultured with IGF-I, insulin, or vehicle for up to 96 h. To confirm an effect on bone formation, IGF-I was also studied for its effects on [ 3 H]proline incorporation into collagenase-digestible protein (CDP) and noncollagen protein and on [ 3 H]thymidine incorporation into acid-precipitable material (DNA). IGF-I at 10(-9)-10(-7) M significantly increased the rate of bone matrix apposition and CDP after 24 h by 45-50% and increased cell labeling by 8-fold in the osteoprogenitor cell zone, by 4-fold in the osteoblast cell zone, and by 2-fold in the periosteal fibroblast zone. Insulin at 10(-9)-10(-6) M also increased matrix apposition rate and CDP by 40-50%, but increased cell labeling by 2-fold only at a concentration of 10(-7) M or higher and then only in the osteoprogenitor cell zone. When hydroxyurea was added to IGF-I-treated bones, the effects of IGF-I on DNA synthesis were abolished, but the increase in bone matrix apposition induced by IGF-I was only partly diminished. In conclusion, IGF-I stimulates matrix synthesis in calvariae, an effect that is partly, although not completely, dependent on its stimulatory effect on DNA synthesis

  19. A positive-strand RNA virus uses alternative protein-protein interactions within a viral protease/cofactor complex to switch between RNA replication and virion morphogenesis

    Science.gov (United States)

    Rey, Félix A.

    2017-01-01

    The viruses of the family Flaviviridae possess a positive-strand RNA genome and express a single polyprotein which is processed into functional proteins. Initially, the nonstructural (NS) proteins, which are not part of the virions, form complexes capable of genome replication. Later on, the NS proteins also play a critical role in virion formation. The molecular basis to understand how the same proteins form different complexes required in both processes is so far unknown. For pestiviruses, uncleaved NS2-3 is essential for virion morphogenesis while NS3 is required for RNA replication but is not functional in viral assembly. Recently, we identified two gain of function mutations, located in the C-terminal region of NS2 and in the serine protease domain of NS3 (NS3 residue 132), which allow NS2 and NS3 to substitute for uncleaved NS2-3 in particle assembly. We report here the crystal structure of pestivirus NS3-4A showing that the NS3 residue 132 maps to a surface patch interacting with the C-terminal region of NS4A (NS4A-kink region) suggesting a critical role of this contact in virion morphogenesis. We show that destabilization of this interaction, either by alanine exchanges at this NS3/4A-kink interface, led to a gain of function of the NS3/4A complex in particle formation. In contrast, RNA replication and thus replicase assembly requires a stable association between NS3 and the NS4A-kink region. Thus, we propose that two variants of NS3/4A complexes exist in pestivirus infected cells each representing a basic building block required for either RNA replication or virion morphogenesis. This could be further corroborated by trans-complementation studies with a replication-defective NS3/4A double mutant that was still functional in viral assembly. Our observations illustrate the presence of alternative overlapping surfaces providing different contacts between the same proteins, allowing the switch from RNA replication to virion formation. PMID:28151973

  20. A positive-strand RNA virus uses alternative protein-protein interactions within a viral protease/cofactor complex to switch between RNA replication and virion morphogenesis.

    Directory of Open Access Journals (Sweden)

    Danilo Dubrau

    2017-02-01

    Full Text Available The viruses of the family Flaviviridae possess a positive-strand RNA genome and express a single polyprotein which is processed into functional proteins. Initially, the nonstructural (NS proteins, which are not part of the virions, form complexes capable of genome replication. Later on, the NS proteins also play a critical role in virion formation. The molecular basis to understand how the same proteins form different complexes required in both processes is so far unknown. For pestiviruses, uncleaved NS2-3 is essential for virion morphogenesis while NS3 is required for RNA replication but is not functional in viral assembly. Recently, we identified two gain of function mutations, located in the C-terminal region of NS2 and in the serine protease domain of NS3 (NS3 residue 132, which allow NS2 and NS3 to substitute for uncleaved NS2-3 in particle assembly. We report here the crystal structure of pestivirus NS3-4A showing that the NS3 residue 132 maps to a surface patch interacting with the C-terminal region of NS4A (NS4A-kink region suggesting a critical role of this contact in virion morphogenesis. We show that destabilization of this interaction, either by alanine exchanges at this NS3/4A-kink interface, led to a gain of function of the NS3/4A complex in particle formation. In contrast, RNA replication and thus replicase assembly requires a stable association between NS3 and the NS4A-kink region. Thus, we propose that two variants of NS3/4A complexes exist in pestivirus infected cells each representing a basic building block required for either RNA replication or virion morphogenesis. This could be further corroborated by trans-complementation studies with a replication-defective NS3/4A double mutant that was still functional in viral assembly. Our observations illustrate the presence of alternative overlapping surfaces providing different contacts between the same proteins, allowing the switch from RNA replication to virion formation.

  1. A DEAD box protein facilitates HIV-1 replication as a cellular co-factor of Rev

    International Nuclear Information System (INIS)

    HIV-1 Rev escorts unspliced viral mRNAs out of the nucleus of infected cells, which allows formation of infectious HIV-1 virions. We have identified a putative DEAD box (Asp-Glu-Ala-Asp) RNA helicase, DDX1, as a cellular co-factor of Rev, through yeast and mammalian two-hybrid systems using the N-terminal motif of Rev as 'bait'. DDX1 is not a functional homolog of HIV-1 Rev, but down-regulation of DDX1 resulted in an alternative splicing pattern of Rev-responsive element (RRE)-containing mRNA, and attenuation of Gag p24 antigen production from HLfb rev(-) cells rescued by exogenous Rev. Co-transfection of a DDX1 expression vector with HIV-1 significantly increased viral production. DDX1 binding to Rev, as well as to the RRE, strongly suggest that DDX1 affects Rev function through the Rev-RRE axis. Moreover, down-regulation of DDX1 altered the steady state subcellular distribution of Rev, from nuclear/nucleolar to cytoplasmic dominance. These findings indicate that DDX1 is a critical cellular co-factor for Rev function, which maintains the proper subcellular distribution of this lentiviral regulatory protein. Therefore, alterations in DDX1-Rev interactions could induce HIV-1 persistence and targeting DDX1 may lead to rationally designed and novel anti-HIV-1 strategies and therapeutics

  2. Identification of Poxvirus Genome Uncoating and DNA Replication Factors with Mutually Redundant Roles.

    Science.gov (United States)

    Liu, Baoming; Panda, Debasis; Mendez-Rios, Jorge D; Ganesan, Sundar; Wyatt, Linda S; Moss, Bernard

    2018-04-01

    Genome uncoating is essential for replication of most viruses. For poxviruses, the process is divided into two stages: removal of the envelope, allowing early gene expression, and breaching of the core wall, allowing DNA release, replication, and late gene expression. Subsequent studies showed that the host proteasome and the viral D5 protein, which has an essential role in DNA replication, are required for vaccinia virus (VACV) genome uncoating. In a search for additional VACV uncoating proteins, we noted a report that described a defect in DNA replication and late expression when the gene encoding a 68-kDa ankyrin repeat/F-box protein (68k-ank), associated with the cellular SCF (Skp1, cullin1, F-box-containing complex) ubiquitin ligase complex, was deleted from the attenuated modified vaccinia virus Ankara (MVA). Here we showed that the 68k-ank deletion mutant exhibited diminished genome uncoating, formation of DNA prereplication sites, and degradation of viral cores as well as an additional, independent defect in DNA synthesis. Deletion of the 68k-ank homolog of VACV strain WR, however, was without effect, suggesting the existence of compensating genes. By inserting VACV genes into an MVA 68k-ank deletion mutant, we discovered that M2, a member of the poxvirus immune evasion (PIE) domain superfamily and a regulator of NF-κB, and C5, a member of the BTB/Kelch superfamily associated with cullin-3-based ligase complexes, independently rescued the 68k-ank deletion phenotype. Thus, poxvirus uncoating and DNA replication are intertwined processes involving at least three viral proteins with mutually redundant functions in addition to D5. IMPORTANCE Poxviruses comprise a family of large DNA viruses that infect vertebrates and invertebrates and cause diseases of medical and zoological importance. Poxviruses, unlike most other DNA viruses, replicate in the cytoplasm, and their large genomes usually encode 200 or more proteins with diverse functions. About 90 genes may

  3. A conserved helicase processivity factor is needed for conjugation and replication of an integrative and conjugative element.

    Directory of Open Access Journals (Sweden)

    Jacob Thomas

    Full Text Available Integrative and conjugative elements (ICEs are agents of horizontal gene transfer and have major roles in evolution and acquisition of new traits, including antibiotic resistances. ICEs are found integrated in a host chromosome and can excise and transfer to recipient bacteria via conjugation. Conjugation involves nicking of the ICE origin of transfer (oriT by the ICE-encoded relaxase and transfer of the nicked single strand of ICE DNA. For ICEBs1 of Bacillus subtilis, nicking of oriT by the ICEBs1 relaxase NicK also initiates rolling circle replication. This autonomous replication of ICEBs1 is critical for stability of the excised element in growing cells. We found a conserved and previously uncharacterized ICE gene that is required for conjugation and replication of ICEBs1. Our results indicate that this gene, helP (formerly ydcP, encodes a helicase processivity factor that enables the host-encoded helicase PcrA to unwind the double-stranded ICEBs1 DNA. HelP was required for both conjugation and replication of ICEBs1, and HelP and NicK were the only ICEBs1 proteins needed for replication from ICEBs1 oriT. Using chromatin immunoprecipitation, we measured association of HelP, NicK, PcrA, and the host-encoded single-strand DNA binding protein Ssb with ICEBs1. We found that NicK was required for association of HelP and PcrA with ICEBs1 DNA. HelP was required for association of PcrA and Ssb with ICEBs1 regions distal, but not proximal, to oriT, indicating that PcrA needs HelP to progress beyond nicked oriT and unwind ICEBs1. In vitro, HelP directly stimulated the helicase activity of the PcrA homologue UvrD. Our findings demonstrate that HelP is a helicase processivity factor needed for efficient unwinding of ICEBs1 for conjugation and replication. Homologues of HelP and PcrA-type helicases are encoded on many known and putative ICEs. We propose that these factors are essential for ICE conjugation, replication, and genetic stability.

  4. A conserved helicase processivity factor is needed for conjugation and replication of an integrative and conjugative element.

    Science.gov (United States)

    Thomas, Jacob; Lee, Catherine A; Grossman, Alan D

    2013-01-01

    Integrative and conjugative elements (ICEs) are agents of horizontal gene transfer and have major roles in evolution and acquisition of new traits, including antibiotic resistances. ICEs are found integrated in a host chromosome and can excise and transfer to recipient bacteria via conjugation. Conjugation involves nicking of the ICE origin of transfer (oriT) by the ICE-encoded relaxase and transfer of the nicked single strand of ICE DNA. For ICEBs1 of Bacillus subtilis, nicking of oriT by the ICEBs1 relaxase NicK also initiates rolling circle replication. This autonomous replication of ICEBs1 is critical for stability of the excised element in growing cells. We found a conserved and previously uncharacterized ICE gene that is required for conjugation and replication of ICEBs1. Our results indicate that this gene, helP (formerly ydcP), encodes a helicase processivity factor that enables the host-encoded helicase PcrA to unwind the double-stranded ICEBs1 DNA. HelP was required for both conjugation and replication of ICEBs1, and HelP and NicK were the only ICEBs1 proteins needed for replication from ICEBs1 oriT. Using chromatin immunoprecipitation, we measured association of HelP, NicK, PcrA, and the host-encoded single-strand DNA binding protein Ssb with ICEBs1. We found that NicK was required for association of HelP and PcrA with ICEBs1 DNA. HelP was required for association of PcrA and Ssb with ICEBs1 regions distal, but not proximal, to oriT, indicating that PcrA needs HelP to progress beyond nicked oriT and unwind ICEBs1. In vitro, HelP directly stimulated the helicase activity of the PcrA homologue UvrD. Our findings demonstrate that HelP is a helicase processivity factor needed for efficient unwinding of ICEBs1 for conjugation and replication. Homologues of HelP and PcrA-type helicases are encoded on many known and putative ICEs. We propose that these factors are essential for ICE conjugation, replication, and genetic stability.

  5. The Mode of Replication Is a Major Factor in Segregational Plasmid Instability in Lactococcus lactis

    NARCIS (Netherlands)

    Kiewiet, Rense; Kok, Jan; Seegers, Jos F.M.L.; Venema, Gerard; Bron, Sierd

    1993-01-01

    The effects of the rolling-circle and theta modes of replication on the maintenance of recombinant plasmids in Lactococcus lactis were studied. Heterologous Escherichia coli or bacteriophage λ DNA fragments of various sizes were inserted into vectors based on either the rolling-circle-type plasmid

  6. Replication and heritability of prostate cancer risk variants: impact of population-specific factors.

    Science.gov (United States)

    Virlogeux, Victor; Graff, Rebecca E; Hoffmann, Thomas J; Witte, John S

    2015-06-01

    Prostate cancer incidence and mortality rates vary across populations, with African American men exhibiting the highest rates. To date, genome-wide association studies have identified 104 SNPs independently associated with prostate cancer in men of European ancestry. We investigated whether the ability to replicate findings for these 104 SNPs in African American, Asian, and Latino populations depends on variation in risk allele frequencies (RAF), strength of associations, and/or patterns of linkage disequilibrium (LD) at the associated loci. We extracted estimates of effect from the literature, and determined RAF and LD information across the populations from the 1000 Genomes Project. Risk variants were largely replicated across populations. Relative to Europeans, 83% had smaller effect sizes among African Americans and 73% demonstrated smaller effect sizes among Latinos. Among Asians, however, 56% showed larger effect sizes than among Europeans. The largest difference in RAFs was observed between European and African ancestry populations, but this difference did not impact our ability to replicate. The extent of LD within 250 kb of risk loci in Asian ancestry populations was suggestively lower for variants that did not replicate (P = 0.013). Despite substantial overlap in prostate cancer risk SNPs across populations, the variation in prostate cancer incidence among different populations may still in part reflect unique underlying genetic architectures. Studying different ancestral populations is crucial for deciphering the genetic basis of prostate cancer. ©2015 American Association for Cancer Research.

  7. Candidiasis: predisposing factors, prevention, diagnosis and alternative treatment.

    Science.gov (United States)

    Martins, Natália; Ferreira, Isabel C F R; Barros, Lillian; Silva, Sónia; Henriques, Mariana

    2014-06-01

    Candidiasis is the most common opportunistic yeast infection. Candida species and other microorganisms are involved in this complicated fungal infection, but Candida albicans continues to be the most prevalent. In the past two decades, it has been observed an abnormal overgrowth in the gastrointestinal, urinary and respiratory tracts, not only in immunocompromised patients, but also related to nosocomial infections and even in healthy individuals. There is a widely variety of causal factors that contribute to yeast infection which means that candidiasis is a good example of a multifactorial syndrome. Due to rapid increase in the incidence in these infections, this is the subject of numerous studies. Recently, the focus of attention is the treatment and, above all, the prevention of those complications. The diagnosis of candidiasis could become quite complicated. Prevention is the most effective "treatment," much more than eradication of the yeast with antifungal agents. There are several aspects to consider in the daily routine that can provide a strength protection. However, a therapeutic approach is necessary when the infection is established, and therefore, other alternatives should be explored. This review provides an overview on predisposition factors, prevention and diagnosis of candidiasis, highlighting alternative approaches for candidiasis treatment.

  8. The eukaryotic elongation factor 1A is critical for genome replication of the paramyxovirus respiratory syncytial virus.

    Directory of Open Access Journals (Sweden)

    Ting Wei

    Full Text Available The eukaryotic translation factor eEF1A assists replication of many RNA viruses by various mechanisms. Here we show that down-regulation of eEF1A restricts the expression of viral genomic RNA and the release of infectious virus, demonstrating a biological requirement for eEF1A in the respiratory syncytial virus (RSV life cycle. The key proteins in the replicase/transcriptase complex of RSV; the nucleocapsid (N protein, phosphoprotein (P and matrix (M protein, all associate with eEF1A in RSV infected cells, although N is the strongest binding partner. Using individually expressed proteins, N, but not P or M bound to eEF1A. This study demonstrates a novel interaction between eEF1A and the RSV replication complex, through binding to N protein, to facilitate genomic RNA synthesis and virus production.

  9. The eukaryotic elongation factor 1A is critical for genome replication of the paramyxovirus respiratory syncytial virus.

    Science.gov (United States)

    Wei, Ting; Li, Dongsheng; Marcial, Daneth; Khan, Moshin; Lin, Min-Hsuan; Snape, Natale; Ghildyal, Reena; Harrich, David; Spann, Kirsten

    2014-01-01

    The eukaryotic translation factor eEF1A assists replication of many RNA viruses by various mechanisms. Here we show that down-regulation of eEF1A restricts the expression of viral genomic RNA and the release of infectious virus, demonstrating a biological requirement for eEF1A in the respiratory syncytial virus (RSV) life cycle. The key proteins in the replicase/transcriptase complex of RSV; the nucleocapsid (N) protein, phosphoprotein (P) and matrix (M) protein, all associate with eEF1A in RSV infected cells, although N is the strongest binding partner. Using individually expressed proteins, N, but not P or M bound to eEF1A. This study demonstrates a novel interaction between eEF1A and the RSV replication complex, through binding to N protein, to facilitate genomic RNA synthesis and virus production.

  10. Cytokines Elevated in HIV Elite Controllers Reduce HIV ReplicationIn Vitroand Modulate HIV Restriction Factor Expression.

    Science.gov (United States)

    Jacobs, Evan S; Keating, Sheila M; Abdel-Mohsen, Mohamed; Gibb, Stuart L; Heitman, John W; Inglis, Heather C; Martin, Jeffrey N; Zhang, Jinbing; Kaidarova, Zhanna; Deng, Xutao; Wu, Shiquan; Anastos, Kathryn; Crystal, Howard; Villacres, Maria C; Young, Mary; Greenblatt, Ruth M; Landay, Alan L; Gange, Stephen J; Deeks, Steven G; Golub, Elizabeth T; Pillai, Satish K; Norris, Philip J

    2017-03-15

    A subset of HIV-infected individuals termed elite controllers (ECs) maintain CD4 + T cell counts and control viral replication in the absence of antiretroviral therapy (ART). Systemic cytokine responses may differentiate ECs from subjects with uncontrolled viral replication or from those who require ART to suppress viral replication. We measured 87 cytokines in four groups of women: 73 ECs, 42 with pharmacologically suppressed viremia (ART), 42 with uncontrolled viral replication (noncontrollers [NCs]), and 48 HIV-uninfected (NEG) subjects. Four cytokines were elevated in ECs but not NCs or ART subjects: CCL14, CCL21, CCL27, and XCL1. In addition, median stromal cell-derived factor-1 (SDF-1) levels were 43% higher in ECs than in NCs. The combination of the five cytokines suppressed R5 and X4 virus replication in resting CD4 + T cells, and individually SDF-1β, CCL14, and CCL27 suppressed R5 virus replication, while SDF-1β, CCL21, and CCL14 suppressed X4 virus replication. Functional studies revealed that the combination of the five cytokines upregulated CD69 and CCR5 and downregulated CXCR4 and CCR7 on CD4 + T cells. The CD69 and CXCR4 effects were driven by SDF-1, while CCL21 downregulated CCR7. The combination of the EC-associated cytokines induced expression of the anti-HIV host restriction factors IFITM1 and IFITM2 and suppressed expression of RNase L and SAMHD1. These results identify a set of cytokines that are elevated in ECs and define their effects on cellular activation, HIV coreceptor expression, and innate restriction factor expression. This cytokine pattern may be a signature characteristic of HIV-1 elite control, potentially important for HIV therapeutic and curative strategies. IMPORTANCE Approximately 1% of people infected with HIV control virus replication without taking antiviral medications. These subjects, termed elite controllers (ECs), are known to have stronger immune responses targeting HIV than the typical HIV-infected subject, but the

  11. Alternative Factor Models and Factorial Invariance of the GHQ-12: A Large Sample Analysis Using Confirmatory Factor Analysis

    Science.gov (United States)

    Shevlin, Mark; Adamson, Gary

    2005-01-01

    This study tested alternative factor models of the General Health Questionnaire-12 (GHQ-12), based on previous research findings, with a large sample using confirmatory factor analysis. An alternative models framework was used to test 6 factor analytic models. A 3-factor model was the best explanation of the sample data. The 3 factors were labeled…

  12. Replication Catastrophe

    DEFF Research Database (Denmark)

    Toledo, Luis; Neelsen, Kai John; Lukas, Jiri

    2017-01-01

    Proliferating cells rely on the so-called DNA replication checkpoint to ensure orderly completion of genome duplication, and its malfunction may lead to catastrophic genome disruption, including unscheduled firing of replication origins, stalling and collapse of replication forks, massive DNA...... increased DNA replication stress....

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

    Science.gov (United States)

    Leicher, Veronika; Mulder, Regina H.

    2016-01-01

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

  14. Personality profile of adult ADHD: the alternative five factor model.

    Science.gov (United States)

    Valero, Sergi; Ramos-Quiroga, Antoni; Gomà-i-Freixanet, Montserrat; Bosch, Rosa; Gómez-Barros, Nuria; Nogueira, Mariana; Palomar, Gloria; Corrales, Montse; Casas, Miquel

    2012-06-30

    Attention-deficit/hyperactivity disorder (ADHD) is one of the most frequently diagnosed disorders in childhood affecting around 3% to 5% of adults worldwide. Most of the studies have been carried out using the Five Factor Model (FFM). Given the value and importance of describing adult ADHD in terms of general personality structure for a better conceptualization of this disorder, this study contributes adding new data on an Alternative Five Factor Model (AFFM) of personality. The aim of the present study is twofold: To assess the personality profile of adults with ADHD under the AFFM perspective, and to test the discriminant validity of the Zuckerman-Kuhlman Personality Questionnaire (ZKPQ) in differentiating ADHD subjects vs. normal range controls. A sample of 217 adults (64% male) meeting ADHD diagnosis (DSM-IV) was paired by age and sex with 434 normal-range controls. Logistic regression analysis showed that high scores on Neuroticism-Anxiety, Impulsivity and General Activity, and low on Work Activity were the most powerful predictors of being endorsed with an ADHD diagnosis. Results may suggest refinements in the personality assessment of ADHD as it seems that the ZKPQ provides more specific subscales for the description and conceptualization of this disorder. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. Heroin use is associated with lower levels of restriction factors and type I interferon expression and facilitates HIV-1 replication.

    Science.gov (United States)

    Zhu, Jia-Wu; Liu, Feng-Liang; Mu, Dan; Deng, De-Yao; Zheng, Yong-Tang

    Heroin use is associated with increased incidence of infectious diseases such as HIV-1 infection, as a result of immunosuppression to a certain extent. Host restriction factors are recently identified cellular proteins with potent antiviral activities. Whether heroin use impacts on the in vivo expression of restriction factors that result in facilitating HIV-1 replication is poorly understood. Here we recruited 432 intravenous drug users (IDUs) and 164 non-IDUs at high-risk behaviors. Based on serological tests, significantly higher prevalence of HIV-1 infection was observed among IDUs compared with non-IDUs. We included those IDUs and non-IDUs without HIV-1 infection, and found IDUs had significantly lower levels of TRIM5α, TRIM22, APOBEC3G, and IFN-α, -β expression than did non-IDUs. We also directly examined plasma viral load in HIV-1 mono-infected IDUs and non-IDUs and found HIV-1 mono-infected IDUs had significantly higher plasma viral load than did non-IDUs. Moreover, intrinsically positive correlation between type I interferon and TRIM5α or TRIM22 was observed, however, which was dysregulated following heroin use. Collectively, heroin use benefits HIV-1 replication that may be partly due to suppression of host restriction factors and type I interferon expression. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  16. GRP78 Is an Important Host Factor for Japanese Encephalitis Virus Entry and Replication in Mammalian Cells.

    Science.gov (United States)

    Nain, Minu; Mukherjee, Sriparna; Karmakar, Sonali Porey; Paton, Adrienne W; Paton, James C; Abdin, M Z; Basu, Anirban; Kalia, Manjula; Vrati, Sudhanshu

    2017-03-15

    Japanese encephalitis virus (JEV), a mosquito-borne flavivirus, is the leading cause of viral encephalitis in Southeast Asia with potential to become a global pathogen. Here, we identify glucose-regulated protein 78 (GRP78) as an important host protein for virus entry and replication. Using the plasma membrane fractions from mouse neuronal (Neuro2a) cells, mass spectroscopy analysis identified GRP78 as a protein interacting with recombinant JEV envelope protein domain III. GRP78 was found to be expressed on the plasma membranes of Neuro2a cells, mouse primary neurons, and human epithelial Huh-7 cells. Antibodies against GRP78 significantly inhibited JEV entry in all three cell types, suggesting an important role of the protein in virus entry. Depletion of GRP78 by small interfering RNA (siRNA) significantly blocked JEV entry into Neuro2a cells, further supporting its role in virus uptake. Immunofluorescence studies showed extensive colocalization of GRP78 with JEV envelope protein in virus-infected cells. This interaction was also confirmed by immunoprecipitation studies. Additionally, GRP78 was shown to have an important role in JEV replication, as treatment of cells post-virus entry with subtilase cytotoxin that specifically cleaved GRP78 led to a substantial reduction in viral RNA replication and protein synthesis, resulting in significantly reduced extracellular virus titers. Our results indicate that GRP78, an endoplasmic reticulum chaperon of the HSP70 family, is a novel host factor involved at multiple steps of the JEV life cycle and could be a potential therapeutic target. IMPORTANCE Recent years have seen a rapid spread of mosquito-borne diseases caused by flaviviruses. The flavivirus family includes West Nile, dengue, Japanese encephalitis, and Zika viruses, which are major threats to public health with potential to become global pathogens. JEV is the major cause of viral encephalitis in several parts of Southeast Asia, affecting a predominantly pediatric

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

    Directory of Open Access Journals (Sweden)

    Vidya P Nair

    2016-04-01

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

  18. Dietary energy density and diet variety as risk factors for relapse in anorexia nervosa: a replication.

    Science.gov (United States)

    Schebendach, Janet; Mayer, Laurel E S; Devlin, Michael J; Attia, Evelyn; Walsh, B Timothy

    2012-01-01

    To replicate our previous findings of an association between energy density and diet variety in recently weight-restored patients with anorexia nervosa (AN) and clinical outcome in the year following treatment. Nineteen hospitalized, weight-restored women with AN completed a food record, from which a diet energy density score (DEDS) and a diet variety score (DVS) were calculated. After hospital discharge, patients were contacted regularly; at the end of one year, clinical outcome was determined using modified Morgan-Russell criteria. As in our previous study, outcome was dichotomized into "full, good, or fair" and "poor" groups. Data from 16 subjects were available. The DEDS was significantly lower (p < .05) in the poor outcome group (0.7 ± 1) compared with the "full, good, or fair" outcome group (0.9 ± 1). Although the DVS was also lower in the poor outcome group (13.9 ± 2) compared with the "full, good or fair" outcome group (15.7 ± 1.8), this difference was not statistically significant. In recently weight-restored patients with AN, a lower DEDS, but not DVS, is associated with poor clinical outcome after inpatient treatment. This finding may be important in the assessment of risk for relapse in patients with AN. Copyright © 2011 Wiley Periodicals, Inc.

  19. Validation-based insertional mutagenesis for identification of Nup214 as a host factor for EV71 replication in RD cells

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Bei; Zhang, XiaoYu; Zhao, Zhendong, E-mail: timjszzd@163.com

    2013-08-02

    Highlights: •We introduced a new mutagenesis strategy named VBIM to the viral research. •This method can identify either host factors or host restriction factors. •Using VBIM system, we identified Nup214 as a host factor for EV71 replication in RD cells. -- Abstract: Lentiviral validation-based insertional mutagenesis (VBIM) is a sophisticated, forward genetic approach that is used for the investigation of signal transduction in mammalian cells. Using VBIM, we conducted function-based genetic screening for host genes that affect enterovirus 71 (EV71) viral replication. This included host factors that are required for the life cycle of EV71 and host restriction factors that inhibit EV71 replication. Several cell clones, resistant to EV71, were produced using EV71 infection as a selection pressure and the nuclear pore protein 214 (Nup214) was identified as a host factor required for EV71 replication. In SD2-2, the corresponding VBIM lentivirus transformed clone, the expression of endogenous Nup214 was significantly down-regulated by the reverse inserted VBIM promoter. After Cre recombinase-mediated excision of the VBIM promoter, the expression of Nup214 recovered and the clone regained sensitivity to the EV71 infection. Furthermore, over-expression of Nup214 in the cells suggested that Nup214 was promoting EV71 replication. Results of this study indicate that a successful mutagenesis strategy has been established for screening host genes related to viral replication.

  20. Validation-based insertional mutagenesis for identification of Nup214 as a host factor for EV71 replication in RD cells

    International Nuclear Information System (INIS)

    Wang, Bei; Zhang, XiaoYu; Zhao, Zhendong

    2013-01-01

    Highlights: •We introduced a new mutagenesis strategy named VBIM to the viral research. •This method can identify either host factors or host restriction factors. •Using VBIM system, we identified Nup214 as a host factor for EV71 replication in RD cells. -- Abstract: Lentiviral validation-based insertional mutagenesis (VBIM) is a sophisticated, forward genetic approach that is used for the investigation of signal transduction in mammalian cells. Using VBIM, we conducted function-based genetic screening for host genes that affect enterovirus 71 (EV71) viral replication. This included host factors that are required for the life cycle of EV71 and host restriction factors that inhibit EV71 replication. Several cell clones, resistant to EV71, were produced using EV71 infection as a selection pressure and the nuclear pore protein 214 (Nup214) was identified as a host factor required for EV71 replication. In SD2-2, the corresponding VBIM lentivirus transformed clone, the expression of endogenous Nup214 was significantly down-regulated by the reverse inserted VBIM promoter. After Cre recombinase-mediated excision of the VBIM promoter, the expression of Nup214 recovered and the clone regained sensitivity to the EV71 infection. Furthermore, over-expression of Nup214 in the cells suggested that Nup214 was promoting EV71 replication. Results of this study indicate that a successful mutagenesis strategy has been established for screening host genes related to viral replication

  1. Factor Structure of the Profile of Mood States (POMS): Two Partial Replications.

    Science.gov (United States)

    Norcross, John C.; And Others

    1984-01-01

    Examined the factor structure of the Profile of Mood States (POMS) in samples of psychiatric outpatients (N=165) and adult smokers (N=298). Results indicated that the POMS appears to be an internally consistent, multidimensional instrument with a relatively stable factor structure. (LLL)

  2. A Novel, Broad-Spectrum Inhibitor of Enterovirus Replication That Targets Host Cell Factor Phosphatidylinositol 4-Kinase IIIβ

    Science.gov (United States)

    van der Schaar, Hilde M.; Leyssen, Pieter; Thibaut, Hendrik J.; de Palma, Armando; van der Linden, Lonneke; Lanke, Kjerstin H. W.; Lacroix, Céline; Verbeken, Erik; Conrath, Katja; MacLeod, Angus M.; Mitchell, Dale R.; Palmer, Nicholas J.; van de Poël, Hervé; Andrews, Martin

    2013-01-01

    Despite their high clinical and socioeconomic impacts, there is currently no approved antiviral therapy for the prophylaxis or treatment of enterovirus infections. Here we report on a novel inhibitor of enterovirus replication, compound 1, 2-fluoro-4-(2-methyl-8-(3-(methylsulfonyl)benzylamino)imidazo[1,2-a]pyrazin-3-yl)phenol. This compound exhibited a broad spectrum of antiviral activity, as it inhibited all tested species of enteroviruses and rhinoviruses, with 50% effective concentrations ranging between 4 and 71 nM. After a lengthy resistance selection process, coxsackievirus mutants resistant to compound 1 were isolated that carried substitutions in their 3A protein. Remarkably, the same substitutions were recently shown to provide resistance to inhibitors of phosphatidylinositol 4-kinase IIIβ (PI4KIIIβ), a lipid kinase that is essential for enterovirus replication, suggesting that compound 1 may also target this host factor. Accordingly, compound 1 directly inhibited PI4KIIIβ in an in vitro kinase activity assay. Furthermore, the compound strongly reduced the PI 4-phosphate levels of the Golgi complex in cells. Rescue of coxsackievirus replication in the presence of compound 1 by a mutant PI4KIIIβ carrying a substitution in its ATP-binding pocket revealed that the compound directly binds the kinase at this site. Finally, we determined that an analogue of compound 1, 3-(3-fluoro-4-methoxyphenyl)-2-methyl-N-(pyridin-4-ylmethyl)imidazo[1,2-a]pyrazin-8-amine, is well tolerated in mice and has a dose-dependent protective activity in a coxsackievirus serotype B4-induced pancreatitis model. PMID:23896472

  3. Tumor necrosis factor α promotes replication and pathogenicity of rat cytomegalovirus

    NARCIS (Netherlands)

    Horzinek, M.C.; Haagmans, B.L.; Stals, F.S.; Meide, P.H. van der; Bruggeman, C.A.; Schijns, Virgil E.C.J.

    1994-01-01

    We investigated the role of tumor necrosis factor alpha (TNF-α) in the pathogenesis of rat cytomegalovirus (RCMV) infection. TNF-α levels found in the sera of radiation-immunosuppressed rats in the course of infection (> 350 pg/ml) correlated with the development of RCMV disease. Administration of

  4. Linchpin DNA-binding residues serve as go/no-go controls in the replication factor C-catalyzed clamp-loading mechanism.

    Science.gov (United States)

    Liu, Juan; Zhou, Yayan; Hingorani, Manju M

    2017-09-22

    DNA polymerases depend on circular sliding clamps for processive replication. Clamps must be loaded onto primer-template DNA (ptDNA) by clamp loaders that open and close clamps around ptDNA in an ATP-fueled reaction. All clamp loaders share a core structure in which five subunits form a spiral chamber that binds the clamp at its base in a twisted open form and encloses ptDNA within, while binding and hydrolyzing ATP to topologically link the clamp and ptDNA. To understand how clamp loaders perform this complex task, here we focused on conserved arginines that might play a central coordinating role in the mechanism because they can alternately contact ptDNA or Walker B glutamate in the ATPase site and lie close to the clamp loader-clamp-binding interface. We mutated Arg-84, Arg-88, and Arg-101 in the ATPase-active B, C, and D subunits of Saccharomyces cerevisiae replication factor C (RFC) clamp loader, respectively, and assessed the impact on multiple transient events in the reaction: proliferating cell nuclear antigen (PCNA) clamp binding/opening/closure/release, ptDNA binding/release, and ATP hydrolysis/product release. The results show that these arginines relay critical information between the PCNA-binding, DNA-binding, and ATPase sites at all steps of the reaction, particularly at a checkpoint before RFC commits to ATP hydrolysis. Moreover, their actions are subunit-specific with RFC-C Arg-88 serving as an accelerator that enables rapid ATP hydrolysis upon contact with ptDNA and RFC-D Arg-101 serving as a brake that confers specificity for ptDNA as the correct substrate for loading PCNA. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Insulin-like growth factor binding protein-6 delays replicative senescence of human fibroblasts

    DEFF Research Database (Denmark)

    Micutkova, Lucia; Diener, Thomas; Li, Chen

    2011-01-01

    extracellular proteins with significantly different abundance in conditioned media from young and senescent fibroblasts. Among these was insulin-like growth factor binding protein-6 (IGFBP-6), which was chosen for further analysis. When IGFBP-6 gene expression was downregulated, cell proliferation was inhibited...... and apoptotic cell death was increased. Furthermore, downregulation of IGFBP-6 led to premature entry into cellular senescence. Since IGFBP-6 overexpression increased cellular lifespan, the data suggest that IGFBP-6, in contrast to other IGF binding proteins, is a negative regulator of cellular senescence...

  6. Auxiliary splice factor U2AF26 and transcription factor Gfi1 cooperate directly in regulating CD45 alternative splicing.

    NARCIS (Netherlands)

    Heyd, F.; Dam, G.B. ten; Moroy, T.

    2006-01-01

    By alternative splicing, different isoforms of the transmembrane tyrosine phosphatase CD45 are generated that either enhance or limit T cell receptor signaling. We report here that CD45 alternative splicing is regulated by cooperative action of the splice factor U2AF26 and the transcription factor

  7. The interactomes of influenza virus NS1 and NS2 proteins identify new host factors and provide insights for ADAR1 playing a supportive role in virus replication.

    Science.gov (United States)

    de Chassey, Benoît; Aublin-Gex, Anne; Ruggieri, Alessia; Meyniel-Schicklin, Laurène; Pradezynski, Fabrine; Davoust, Nathalie; Chantier, Thibault; Tafforeau, Lionel; Mangeot, Philippe-Emmanuel; Ciancia, Claire; Perrin-Cocon, Laure; Bartenschlager, Ralf; André, Patrice; Lotteau, Vincent

    2013-01-01

    Influenza A NS1 and NS2 proteins are encoded by the RNA segment 8 of the viral genome. NS1 is a multifunctional protein and a virulence factor while NS2 is involved in nuclear export of viral ribonucleoprotein complexes. A yeast two-hybrid screening strategy was used to identify host factors supporting NS1 and NS2 functions. More than 560 interactions between 79 cellular proteins and NS1 and NS2 proteins from 9 different influenza virus strains have been identified. These interacting proteins are potentially involved in each step of the infectious process and their contribution to viral replication was tested by RNA interference. Validation of the relevance of these host cell proteins for the viral replication cycle revealed that 7 of the 79 NS1 and/or NS2-interacting proteins positively or negatively controlled virus replication. One of the main factors targeted by NS1 of all virus strains was double-stranded RNA binding domain protein family. In particular, adenosine deaminase acting on RNA 1 (ADAR1) appeared as a pro-viral host factor whose expression is necessary for optimal viral protein synthesis and replication. Surprisingly, ADAR1 also appeared as a pro-viral host factor for dengue virus replication and directly interacted with the viral NS3 protein. ADAR1 editing activity was enhanced by both viruses through dengue virus NS3 and influenza virus NS1 proteins, suggesting a similar virus-host co-evolution.

  8. The interactomes of influenza virus NS1 and NS2 proteins identify new host factors and provide insights for ADAR1 playing a supportive role in virus replication.

    Directory of Open Access Journals (Sweden)

    Benoît de Chassey

    Full Text Available Influenza A NS1 and NS2 proteins are encoded by the RNA segment 8 of the viral genome. NS1 is a multifunctional protein and a virulence factor while NS2 is involved in nuclear export of viral ribonucleoprotein complexes. A yeast two-hybrid screening strategy was used to identify host factors supporting NS1 and NS2 functions. More than 560 interactions between 79 cellular proteins and NS1 and NS2 proteins from 9 different influenza virus strains have been identified. These interacting proteins are potentially involved in each step of the infectious process and their contribution to viral replication was tested by RNA interference. Validation of the relevance of these host cell proteins for the viral replication cycle revealed that 7 of the 79 NS1 and/or NS2-interacting proteins positively or negatively controlled virus replication. One of the main factors targeted by NS1 of all virus strains was double-stranded RNA binding domain protein family. In particular, adenosine deaminase acting on RNA 1 (ADAR1 appeared as a pro-viral host factor whose expression is necessary for optimal viral protein synthesis and replication. Surprisingly, ADAR1 also appeared as a pro-viral host factor for dengue virus replication and directly interacted with the viral NS3 protein. ADAR1 editing activity was enhanced by both viruses through dengue virus NS3 and influenza virus NS1 proteins, suggesting a similar virus-host co-evolution.

  9. Yeast screens for host factors in positive-strand RNA virus replication based on a library of temperature-sensitive mutants.

    Science.gov (United States)

    Nawaz-ul-Rehman, Muhammad Shah; Reddisiva Prasanth, K; Baker, Jannine; Nagy, Peter D

    2013-02-01

    RNA viruses exploit host cells by altering cellular pathways, recruiting host factors, remodeling intracellular membranes and escaping host antiviral responses. Model hosts, such as Saccharomyces cerevisiae (yeast), are valuable to identify host factors involved in viral RNA replication. The many advantages of using yeast include the availability of various yeast mutant libraries, such as (i) single gene-deletion library; (ii) the essential gene library (yTHC); and (iii) the yeast ORF over-expression library. Here, we have used a novel temperature-sensitive (ts) mutant library of essential yeast genes to identify 118 host proteins affecting replication of Tomato bushy stunt virus, in yeast model host. Testing 787 ts mutants led to the identification of host factors, of which 72 proteins facilitated TBSV replication in yeast and 46 proteins were inhibitory. Altogether, ~85% of the identified proteins are novel host factors affecting tombusvirus replication. The ts mutant library screen also led to the identification of 17 essential genes, which have been documented before, thus confirming the importance of these genomic screens. Overall, we show the power of ts mutant library in identification of host factors for RNA virus replication. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. Targeting DNA Replication Stress for Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    2016-08-01

    Full Text Available The human cellular genome is under constant stress from extrinsic and intrinsic factors, which can lead to DNA damage and defective replication. In normal cells, DNA damage response (DDR mediated by various checkpoints will either activate the DNA repair system or induce cellular apoptosis/senescence, therefore maintaining overall genomic integrity. Cancer cells, however, due to constitutive growth signaling and defective DDR, may exhibit “replication stress” —a phenomenon unique to cancer cells that is described as the perturbation of error-free DNA replication and slow-down of DNA synthesis. Although replication stress has been proven to induce genomic instability and tumorigenesis, recent studies have counterintuitively shown that enhancing replicative stress through further loosening of the remaining checkpoints in cancer cells to induce their catastrophic failure of proliferation may provide an alternative therapeutic approach. In this review, we discuss the rationale to enhance replicative stress in cancer cells, past approaches using traditional radiation and chemotherapy, and emerging approaches targeting the signaling cascades induced by DNA damage. We also summarize current clinical trials exploring these strategies and propose future research directions including the use of combination therapies, and the identification of potential new targets and biomarkers to track and predict treatment responses to targeting DNA replication stress.

  11. QTL replication and targeted association highlight the nerve growth factor gene for nonverbal communication deficits in autism spectrum disorders.

    Science.gov (United States)

    Lu, A T-H; Yoon, J; Geschwind, D H; Cantor, R M

    2013-02-01

    Autism Spectrum Disorder (ASD) has a heterogeneous etiology that is genetically complex. It is defined by deficits in communication and social skills and the presence of restricted and repetitive behaviors. Genetic analyses of heritable quantitative traits that correlate with ASD may reduce heterogeneity. With this in mind, deficits in nonverbal communication (NVC) were quantified based on items from the Autism Diagnostic Interview Revised. Our previous analysis of 228 families from the Autism Genetics Research Exchange (AGRE) repository reported 5 potential quantitative trait loci (QTL). Here we report an NVC QTL replication study in an independent sample of 213 AGRE families. One QTL was replicated (Panalysis of 476 haplotype blocks with 708 AGRE families using the Family Based Association Test (FBAT). Blocks in two QTL genes were associated with NVC with a P-value of 0.001. Three associated haplotype blocks were intronic to the Nerve Growth Factor (NGF) gene (P=0.001, 0.001, 0.002), and one was intronic to KCND3 (P=0.001). Individual haplotypes within the associated blocks drove the associations (0.003, 0.0004 and 0.0002) for NGF and 0.0001 for KCND3. Using the same methods, these genes were tested for association with NVC in an independent sample of 1517 families from an Autism Genome Project (AGP). NVC was associated with a haplotype in an adjacent NGF block (P=0.0005) and one 46 kb away from the associated block in KCND3 (0.008). These analyses illustrate the value of QTL and targeted association studies for genetically complex disorders such as ASD. NGF is a promising risk gene for NVC deficits.

  12. SARS-coronavirus replication/transcription complexes are membrane-protected and need a host factor for activity in vitro.

    Directory of Open Access Journals (Sweden)

    Martijn J van Hemert

    2008-05-01

    Full Text Available SARS-coronavirus (SARS-CoV replication and transcription are mediated by a replication/transcription complex (RTC of which virus-encoded, non-structural proteins (nsps are the primary constituents. The 16 SARS-CoV nsps are produced by autoprocessing of two large precursor polyproteins. The RTC is believed to be associated with characteristic virus-induced double-membrane structures in the cytoplasm of SARS-CoV-infected cells. To investigate the link between these structures and viral RNA synthesis, and to dissect RTC organization and function, we isolated active RTCs from infected cells and used them to develop the first robust assay for their in vitro activity. The synthesis of genomic RNA and all eight subgenomic mRNAs was faithfully reproduced by the RTC in this in vitro system. Mainly positive-strand RNAs were synthesized and protein synthesis was not required for RTC activity in vitro. All RTC activity, enzymatic and putative membrane-spanning nsps, and viral RNA cosedimented with heavy membrane structures. Furthermore, the pelleted RTC required the addition of a cytoplasmic host factor for reconstitution of its in vitro activity. Newly synthesized subgenomic RNA appeared to be released, while genomic RNA remained predominantly associated with the RTC-containing fraction. RTC activity was destroyed by detergent treatment, suggesting an important role for membranes. The RTC appeared to be protected by membranes, as newly synthesized viral RNA and several replicase/transcriptase subunits were protease- and nuclease-resistant and became susceptible to degradation only upon addition of a non-ionic detergent. Our data establish a vital functional dependence of SARS-CoV RNA synthesis on virus-induced membrane structures.

  13. DNA Virus Replication Compartments

    Science.gov (United States)

    Schmid, Melanie; Speiseder, Thomas; Dobner, Thomas

    2014-01-01

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

  14. FACTORINGALTERNATIVE OF SHORT-TERM FINANCING FOR COMPANIES

    Directory of Open Access Journals (Sweden)

    Nicoleta Barbuta-Misu

    2013-12-01

    Full Text Available In developed countries, had been created formidable conditions for encouraging the factoring business, because using this instrument of investment and financing have grown the economic and financial stability of the company and generated a more efficient management of accounts receivable by the policy of claims recovering. Also, the factoring may be considered both a commercial and financial activity. The essential role of the factoring companies is given by taking the place of company in activities that are not referring exclusively to the commercial field. Given the importance of this financing operation, in this paper are presented different ways of defining, their importance, advantages and disadvantages for the company, the return for the factoring of accounts receivables and the real cost of factoring.

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

    Science.gov (United States)

    Kafer, Etta; Chae, Suhn-Kee

    2008-09-01

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

  16. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

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

  17. A Salmonella small non-coding RNA facilitates bacterial invasion and intracellular replication by modulating the expression of virulence factors.

    Directory of Open Access Journals (Sweden)

    Hao Gong

    2011-09-01

    Full Text Available Small non-coding RNAs (sRNAs that act as regulators of gene expression have been identified in all kingdoms of life, including microRNA (miRNA and small interfering RNA (siRNA in eukaryotic cells. Numerous sRNAs identified in Salmonella are encoded by genes located at Salmonella pathogenicity islands (SPIs that are commonly found in pathogenic strains. Whether these sRNAs are important for Salmonella pathogenesis and virulence in animals has not been reported. In this study, we provide the first direct evidence that a pathogenicity island-encoded sRNA, IsrM, is important for Salmonella invasion of epithelial cells, intracellular replication inside macrophages, and virulence and colonization in mice. IsrM RNA is expressed in vitro under conditions resembling those during infection in the gastrointestinal tract. Furthermore, IsrM is found to be differentially expressed in vivo, with higher expression in the ileum than in the spleen. IsrM targets the mRNAs coding for SopA, a SPI-1 effector, and HilE, a global regulator of the expression of SPI-1 proteins, which are major virulence factors essential for bacterial invasion. Mutations in IsrM result in disregulation of expression of HilE and SopA, as well as other SPI-1 genes whose expression is regulated by HilE. Salmonella with deletion of isrM is defective in bacteria invasion of epithelial cells and intracellular replication/survival in macrophages. Moreover, Salmonella with mutations in isrM is attenuated in killing animals and defective in growth in the ileum and spleen in mice. Our study has shown that IsrM sRNA functions as a pathogenicity island-encoded sRNA directly involved in Salmonella pathogenesis in animals. Our results also suggest that sRNAs may represent a distinct class of virulence factors that are important for bacterial infection in vivo.

  18. Effects of physical, chemical or biological factors on DNA replication in mammalian cells. Part 2. Recovery of DNA complex, nucleoid and DNA replication after gamma irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Synzynys, B.I.; Kiseleva, V.I.; Trofimova, S.F.

    1984-11-01

    Murine LL cell line was employed in studies on the effects of gamma irradiation (6 Gy, 8 Gy/min from Co-60 source) on the kinetics and repair of DNA superstructure and recovery of DNA synthesis. Comparison of the kinetic data for the postradiation repair of the DNA-membrane complex, nucleoid, and recovery of DNA synthesis demonstrated that functional recovery of the former two factors preceded DNA synthesis by at least 2 h. In view of this lag, it appears that additional factors are involved in radiation damage that must be repaired before DNA synthesis commences. 10 references, 3 figures.

  19. Male infertility: lifestyle factors and holistic, complementary, and alternative therapies

    Directory of Open Access Journals (Sweden)

    David F Yao

    2016-01-01

    Full Text Available While we may be comfortable with an allopathic approach to male infertility, we are also responsible for knowledge about lifestyle modifications and holistic, complementary, and alternative therapies that are used by many of our patients. This paper provides an evidence-based review separating fact from fiction for several of these therapies. There is sufficient literature to support weight reduction by diet and exercise, smoking cessation, and alcohol moderation. Supplements that have demonstrated positive effects on male fertility on small randomized controlled trial (RCT include aescin, coenzyme Q 10 , glutathione, Korean red ginseng, L-carnitine, nigella sativa, omega-3, selenium, a combination of zinc and folate, and the Menevit antioxidant. There is no support for the use of Vitamin C, Vitamin E, or saffron. The data for Chinese herbal medications, acupuncture, mind-body practice, scrotal cooling, and faith-based healing are sparse or inconclusive.

  20. Database Replication

    Directory of Open Access Journals (Sweden)

    Marius Cristian MAZILU

    2010-12-01

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

  1. Factors Associated With the Control of Viral Replication and Virologic Breakthrough in a Recently Infected HIV-1 Controller.

    Science.gov (United States)

    Walker-Sperling, Victoria E; Pohlmeyer, Christopher W; Veenhuis, Rebecca T; May, Megan; Luna, Krystle A; Kirkpatrick, Allison R; Laeyendecker, Oliver; Cox, Andrea L; Carrington, Mary; Bailey, Justin R; Arduino, Roberto C; Blankson, Joel N

    2017-02-01

    HIV-1 controllers are patients who control HIV-1 viral replication without antiretroviral therapy. Control is achieved very early in the course of infection, but the mechanisms through which viral replication is restricted are not fully understood. We describe a patient who presented with acute HIV-1 infection and was found to have an HIV-1 RNA level of controlled in acute HIV-1 infection in some patients without protective HLA alleles and that NK cell responses may contribute to this early control of viral replication. © 2016.

  2. 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…

  3. Coxsackievirus mutants that can bypass host factor PI4KIIIbeta and the need for high levels of PI4P lipids for replication

    NARCIS (Netherlands)

    van der Schaar, H.M.; van der Linden, L.; Lanke, K.H.W.; Strating, J.R.P.M.; Purstinger, G.; Vries, E. De; de Haan, C.A.; Neyts, J.; Kuppeveld, F.J.M. van

    2012-01-01

    RNA viruses can rapidly mutate and acquire resistance to drugs that directly target viral enzymes, which poses serious problems in a clinical context. Therefore, there is a growing interest in the development of antiviral drugs that target host factors critical for viral replication, since they are

  4. A novel, broad-spectrum inhibitor of enterovirus replication that targets host cell factor phosphatidylinositol 4-kinase IIIβ

    NARCIS (Netherlands)

    van der Schaar, H.M.; Leyssen, Pieter; Thibaut, H.J.; de Palma, Armando; van der Linden, Lonneke; Lanke, Kjerstin H.W.; Lacroix, Céline; Verbeken, Erik; Conrath, Katja; Macleod, Angus M; Mitchell, Dale R; Palmer, Nicholas J; van de Poël, Hervé; Andrews, Martin; Neyts, Johan; van Kuppeveld, F.J.M.

    2013-01-01

    Despite their high clinical and socioeconomic impacts, there is currently no approved antiviral therapy for the prophylaxis or treatment of enterovirus infections. Here we report on a novel inhibitor of enterovirus replication, compound 1,

  5. Stable interaction between the human proliferating cell nuclear antigen loader complex Ctf18-replication factor C (RFC) and DNA polymerase {epsilon} is mediated by the cohesion-specific subunits, Ctf18, Dcc1, and Ctf8.

    Science.gov (United States)

    Murakami, Takeshi; Takano, Ryuji; Takeo, Satoshi; Taniguchi, Rina; Ogawa, Kaori; Ohashi, Eiji; Tsurimoto, Toshiki

    2010-11-05

    One of the proliferating cell nuclear antigen loader complexes, Ctf18-replication factor C (RFC), is involved in sister chromatid cohesion. To examine its relationship with factors involved in DNA replication, we performed a proteomics analysis of Ctf18-interacting proteins. We found that Ctf18 interacts with a replicative DNA polymerase, DNA polymerase ε (pol ε). Co-immunoprecipitation with recombinant Ctf18-RFC and pol ε demonstrated that their binding is direct and mediated by two distinct interactions, one weak and one stable. Three subunits that are specifically required for cohesion in yeast, Ctf18, Dcc1, and Ctf8, formed a trimeric complex (18-1-8) and together enabled stable binding with pol ε. The C-terminal 23-amino acid stretch of Ctf18 was necessary for the trimeric association of 18-1-8 and was required for the stable interaction. The weak interaction was observed with alternative loader complexes including Ctf18-RFC(5), which lacks Dcc1 and Ctf8, suggesting that the common loader structures, including the RFC small subunits (RFC2-5), are responsible for the weak interaction. The two interaction modes, mediated through distinguishable structures of Ctf18-RFC, both occurred through the N-terminal half of pol ε, which includes the catalytic domain. The addition of Ctf18-RFC or Ctf18-RFC(5) to the DNA synthesis reaction caused partial inhibition and stimulation, respectively. Thus, Ctf18-RFC has multiple interactions with pol ε that promote polymorphic modulation of DNA synthesis. We propose that their interaction alters the DNA synthesis mode to enable the replication fork to cooperate with the establishment of cohesion.

  6. Coagulation factor XI vaccination: an alternative strategy to prevent thrombosis.

    Science.gov (United States)

    Zhong, C; Zhang, L; Chen, L; Deng, L; Li, R

    2017-01-01

    Essentials Coagulation Factor (F) XI is a safe target for the development of antithrombotics. We designed an antigen comprising the human FXI catalytic domain and diphtheria toxin T domain. Antigen immunization reduced plasma FXI activity by 54% and prevented thrombosis in mice. FXI vaccination can serve as an effective strategy for thrombosis prevention. Background Coagulation factor XI serves as a signal amplifier in the intrinsic coagulation pathway. Blockade of FXI by mAbs or small-molecule inhibitors inhibits thrombosis without causing severe bleeding, which is an inherent risk of currently available antithrombotic agents. Objectives To design an FXI vaccine and assess its efficacy in inhibiting FXI activity and preventing thrombosis. Methods An FXI antigen was generated by fusing the catalytic domain of human FXI to the C-terminus of the transmembrane domain of diphtheria toxin. The anti-FXI antibody response, plasma FXI activity and antithrombotic efficacy in mice immunized with the FXI antigen were examined. Results The antigen elicited a significant antibody response against mouse FXI, and reduced the plasma FXI activity by 54.0% in mice. FXI vaccination markedly reduced the levels of coagulation and inflammation in a mouse model of inferior vena cava stenosis. Significant protective effects were also observed in mouse models of venous thrombosis and pulmonary embolism. Conclusions Our data demonstrate that FXI vaccination can serve as an effective strategy for thrombosis prevention. © 2016 The Authors. Journal of Thrombosis and Haemostasis published by Wiley Periodicals, Inc. on behalf of International Society on Thrombosis and Haemostasis.

  7. Factors Associated With the Control of Viral Replication and Virologic Breakthrough in a Recently Infected HIV-1 Controller

    Directory of Open Access Journals (Sweden)

    Victoria E. Walker-Sperling

    2017-02-01

    Full Text Available HIV-1 controllers are patients who control HIV-1 viral replication without antiretroviral therapy. Control is achieved very early in the course of infection, but the mechanisms through which viral replication is restricted are not fully understood. We describe a patient who presented with acute HIV-1 infection and was found to have an HIV-1 RNA level of <100 copies/mL. She did not have any known protective HLA alleles, but significant immune activation of CD8+ T cells and natural killer (NK cells was present, and both cell types inhibited viral replication. Virus cultured from this patient replicated as well in vitro as virus isolated from her partner, a patient with AIDS who was the source of transmission. Virologic breakthrough occurred 9 months after her initial presentation and was associated with an increase in CD4+ T cell activation levels and a significant decrease in NK cell inhibitory capacity. Remarkably, CD8+ T cell inhibitory capacity was preserved and there were no new escape mutations in targeted Gag epitopes. These findings suggest that fully replication-competent virus can be controlled in acute HIV-1 infection in some patients without protective HLA alleles and that NK cell responses may contribute to this early control of viral replication.

  8. Confirmatory Factor Analysis Alternative: Free, Accessible CBID Software.

    Science.gov (United States)

    Bott, Marjorie; Karanevich, Alex G; Garrard, Lili; Price, Larry R; Mudaranthakam, Dinesh Pal; Gajewski, Byron

    2018-02-01

    New software that performs Classical and Bayesian Instrument Development (CBID) is reported that seamlessly integrates expert (content validity) and participant data (construct validity) to produce entire reliability estimates with smaller sample requirements. The free CBID software can be accessed through a website and used by clinical investigators in new instrument development. Demonstrations are presented of the three approaches using the CBID software: (a) traditional confirmatory factor analysis (CFA), (b) Bayesian CFA using flat uninformative prior, and (c) Bayesian CFA using content expert data (informative prior). Outcomes of usability testing demonstrate the need to make the user-friendly, free CBID software available to interdisciplinary researchers. CBID has the potential to be a new and expeditious method for instrument development, adding to our current measurement toolbox. This allows for the development of new instruments for measuring determinants of health in smaller diverse populations or populations of rare diseases.

  9. Coxsackievirus mutants that can bypass host factor PI4KIIIβ and the need for high levels of PI4P lipids for replication.

    Science.gov (United States)

    van der Schaar, Hilde M; van der Linden, Lonneke; Lanke, Kjerstin H W; Strating, Jeroen R P M; Pürstinger, Gerhard; de Vries, Erik; de Haan, Cornelis A M; Neyts, Johan; van Kuppeveld, Frank J M

    2012-11-01

    RNA viruses can rapidly mutate and acquire resistance to drugs that directly target viral enzymes, which poses serious problems in a clinical context. Therefore, there is a growing interest in the development of antiviral drugs that target host factors critical for viral replication, since they are unlikely to mutate in response to therapy. We recently demonstrated that phosphatidylinositol-4-kinase IIIβ (PI4KIIIβ) and its product phosphatidylinositol-4-phosphate (PI4P) are essential for replication of enteroviruses, a group of medically important RNA viruses including poliovirus (PV), coxsackievirus, rhinovirus, and enterovirus 71. Here, we show that enviroxime and GW5074 decreased PI4P levels at the Golgi complex by directly inhibiting PI4KIIIβ. Coxsackievirus mutants resistant to these inhibitors harbor single point mutations in the non-structural protein 3A. These 3A mutations did not confer compound-resistance by restoring the activity of PI4KIIIβ in the presence of the compounds. Instead, replication of the mutant viruses no longer depended on PI4KIIIβ, since their replication was insensitive to siRNA-mediated depletion of PI4KIIIβ. The mutant viruses also did not rely on other isoforms of PI4K. Consistently, no high level of PI4P could be detected at the replication sites induced by the mutant viruses in the presence of the compounds. Collectively, these findings indicate that through specific single point mutations in 3A, CVB3 can bypass an essential host factor and lipid for its propagation, which is a new example of RNA viruses acquiring resistance against antiviral compounds, even when they directly target host factors.

  10. HIV-1 Induced Nuclear Factor I-B (NF-IB Expression Negatively Regulates HIV-1 Replication through Interaction with the Long Terminal Repeat Region

    Directory of Open Access Journals (Sweden)

    Sai Vikram Vemula

    2015-02-01

    Full Text Available Background: Retroviruses rely on host factors for cell entry, replication, transcription, and other major steps during their life cycle. Human Immunodeficiency Virus-1 (HIV-1 is well known for utilizing a plethora of strategies to evade the host immune response, including the establishment of latent infection within a subpopulation of susceptible cells. HIV-1 also manipulates cellular factors in latently infected cells and persists for long periods of time, despite the presence of successful highly active antiretroviral therapy (HAART. Results: In this study we demonstrate that Nuclear Factor-IB (NF-IB is induced during HIV-1 infection and its expression negatively impacts viral replication. During HIV-1 infection in peripheral blood mononuclear cells (PBMCs, and the T cell line, Jurkat or during induction of virus replication in latently infected cells, ACH2 and J1.1, we observed a time-dependent alteration in NF-IB expression pattern that correlated with HIV-1 viral expression. Using the Chip assay, we observed an association of NF-IB with the long terminal repeat region of HIV-1 (LTR (-386 to -453 nt, and this association negatively correlated with HIV-1 transcription. Furthermore, knock-down of NF-IB levels in J1.1 cells resulted in an increase of HIV-1 levels. Knock-down of NF-IB levels in J-Lat-Tat-GFP (A1, (a Jurkat cell GFP reporter model for latent HIV-1 infection resulted in an increase in GFP levels, indicating a potential negative regulatory role of NF-IB in HIV-1 replication. Conclusion: Overall, our results suggest that NF-IB may play a role in intrinsic antiretroviral defenses against HIV-1. These observations may offer new insights into the correlation of the latently infected host cell types and HIV-1, and help to define new therapeutic approaches for triggering the switch from latency to active replication thereby eliminating HIV-1 latent infection.

  11. Engineered zinc-finger transcription factors inhibit the replication and transcription of HBV in vitro and in vivo.

    Science.gov (United States)

    Luo, Wei; Wang, Junxia; Xu, Dengfeng; Bai, Huili; Zhang, Yangli; Zhang, Yuhong; Li, Xiaosong

    2018-04-01

    In the present study, an artificial zinc-finger transcription factor eukaryotic expression vector specifically recognizing and binding to the hepatitis B virus (HBV) enhancer (Enh) was constructed, which inhibited the replication and expression of HBV DNA. The HBV EnhI‑specific pcDNA3.1‑artificial transcription factor (ATF) vector was successfully constructed, and then transformed or injected into HepG2.2.15 cells and HBV transgenic mice, respectively. The results demonstrated that the HBV EnhI (1,070‑1,234 bp)‑specific ATF significantly inhibited the replication and transcription of HBV DNA in vivo and in vitro. The HBV EnhI‑specific ATF may be a meritorious component of progressive combination therapies for eliminating HBV DNA in infected patients. A radical cure for chronic HBV infection may become feasible by using this bioengineering technology.

  12. Effects of MS-8209, an Amphotericin B Derivative, on Tumor Necrosis Factor Alpha Synthesis and Human Immunodeficiency Virus Replication in Macrophages

    OpenAIRE

    Clayette, Pascal; Martin, Marc; Beringue, Vincent; Dereuddre-Bosquet, Nathalie; Adjou, Karim T.; Seman, Michel; Dormont, Dominique

    2000-01-01

    Amphotericin B derivatives, such as MS-8209, have been evaluated as a therapeutic approach to human immunodeficiency virus (HIV) infection. We show that MS-8209, like amphotericin B, increases tumor necrosis factor alpha (TNF-α) mRNA expression and TNF-α production and consequently HIV replication in human macrophages. These effects confirm the pharmacological risk associated with the administration of amphotericin B or its derivatives to HIV-infected patients.

  13. Effects of MS-8209, an amphotericin B derivative, on tumor necrosis factor alpha synthesis and human immunodeficiency virus replication in macrophages.

    Science.gov (United States)

    Clayette, P; Martin, M; Beringue, V; Dereuddre-Bosquet, N; Adjou, K T; Seman, M; Dormont, D

    2000-02-01

    Amphotericin B derivatives, such as MS-8209, have been evaluated as a therapeutic approach to human immunodeficiency virus (HIV) infection. We show that MS-8209, like amphotericin B, increases tumor necrosis factor alpha (TNF-alpha) mRNA expression and TNF-alpha production and consequently HIV replication in human macrophages. These effects confirm the pharmacological risk associated with the administration of amphotericin B or its derivatives to HIV-infected patients.

  14. Complementary and Alternative Medicines: Usage and Its Determinant Factors Among Outpatients in Southeast of Iran.

    Science.gov (United States)

    Ghaedi, Fateme; Dehghan, Mahlagha; Salari, Masoumeh; Sheikhrabori, Akbar

    2015-12-13

    Prevalence of complementary and alternative medicines is increasing specially in patients with chronic diseases. Therefore, based on the high prevalence of chronic disorders, the present study aimed to determine complementary and alternative medicine usage frequency and its determinant factors. This was a cross-sectional study. Five hundred clients participated in the study by using convenience sampling. A 2-part questionnaire (including demographic form and researcher-created questionnaire) was used for studying the prevalence of using complementary and alternative medicine methods, and users' satisfaction. Findings showed that 75.4% of people used at least one complementary and alternative medicine method. Most of users consumed medicinal plants (69.4%). The most common reason of using a complementary and alternative medicine method was common cold (32.9%). The highest satisfaction belonged to massage (2.94 ± 0.74). The usage of complementary and alternative medicine was 3.22 times higher in people with academic educations when compared with illiterate people. Concerning the high usage of complementary and alternative medicine, it is necessary to train specialists in this field in order to offer such treatments in a safe manner. Also, outcomes of application of complementary and alternative medicine methods should be studied. © The Author(s) 2015.

  15. Method for exploiting bias in factor analysis using constrained alternating least squares algorithms

    Science.gov (United States)

    Keenan, Michael R.

    2008-12-30

    Bias plays an important role in factor analysis and is often implicitly made use of, for example, to constrain solutions to factors that conform to physical reality. However, when components are collinear, a large range of solutions may exist that satisfy the basic constraints and fit the data equally well. In such cases, the introduction of mathematical bias through the application of constraints may select solutions that are less than optimal. The biased alternating least squares algorithm of the present invention can offset mathematical bias introduced by constraints in the standard alternating least squares analysis to achieve factor solutions that are most consistent with physical reality. In addition, these methods can be used to explicitly exploit bias to provide alternative views and provide additional insights into spectral data sets.

  16. Investigation into the use of complementary and alternative medicine and affecting factors in Turkish asthmatic patients.

    Science.gov (United States)

    Tokem, Yasemin; Aytemur, Zeynep Ayfer; Yildirim, Yasemin; Fadiloglu, Cicek

    2012-03-01

    The purpose of this study was to examine the frequency of complementary and alternative medicine usage in asthmatic patients living in the west of Turkey, the most frequently used complementary and alternative medicine methods and socio-demographic factors affecting this and factors related to the disease. While the rate of complementary and alternative medicine usage in asthmatic patients and the reasons for using it vary, practices specific to different countries and regions are of interest. Differing cultural and social factors even in geographically similar regions can affect the type of complementary and alternative medicine used. Two hundred asthmatic patients registered in the asthma outpatient clinic of a large hospital in Turkey and who had undergone pulmonary function tests within the previous six months were included in this study, which was planned according to a descriptive design. The patients filled out a questionnaire on their demographic characteristics and complementary and alternative medicine usage. The proportion of patients who reported using one or more of the complementary and alternative medicine methods was 63·0%. Of these patients, 61·9% were using plants and herbal treatments, 53·2% were doing exercises and 36·5% said that they prayed. The objectives of their use of complementary and alternative medicine were to reduce asthma-related complaints (58%) and to feel better (37·8%). The proportion of people experiencing adverse effects was 3·3% (n = 4). Factors motivating asthmatic patients to use complementary and alternative medicine were the existence of comorbid diseases and a long period since diagnosis (p complementary and alternative medicine and the severity of the disease, pulmonary function test parameters, the number of asthma attacks or hospitalisations because of asthma within the last year (p > 0·05). Understanding by nurses of the causes and patterns of the use of complementary and alternative medicine in asthmatic

  17. Transforming growth factor-beta promotes rhinovirus replication in bronchial epithelial cells by suppressing the innate immune response.

    Directory of Open Access Journals (Sweden)

    Nicole Bedke

    Full Text Available Rhinovirus (RV infection is a major cause of asthma exacerbations which may be due to a deficient innate immune response in the bronchial epithelium. We hypothesized that the pleiotropic cytokine, TGF-β, influences interferon (IFN production by primary bronchial epithelial cells (PBECs following RV infection. Exogenous TGF-β(2 increased RV replication and decreased IFN protein secretion in response to RV or double-stranded RNA (dsRNA. Conversely, neutralizing TGF-β antibodies decreased RV replication and increased IFN expression in response to RV or dsRNA. Endogenous TGF-β(2 levels were higher in conditioned media of PBECs from asthmatic donors and the suppressive effect of anti-TGF-β on RV replication was significantly greater in these cells. Basal SMAD-2 activation was reduced when asthmatic PBECs were treated with anti-TGF-β and this was accompanied by suppression of SOCS-1 and SOCS-3 expression. Our results suggest that endogenous TGF-β contributes to a suppressed IFN response to RV infection possibly via SOCS-1 and SOCS-3.

  18. miR-200c targets nuclear factor IA to suppress HBV replication and gene expression via repressing HBV Enhancer I activity.

    Science.gov (United States)

    Tian, Hui; He, Zhenkun

    2018-03-01

    Hepatitis B virus (HBV) chronic infection is a health problem in the worldwide, with a underlying higher risk of liver cirrhosis and hepaticocellular carcinoma. A number of studies indicate that microRNAs (miRNAs) play vital roles in HBV replication. This study was designed to explore the potential molecular mechanism of miR-200c in HBV replication. The expression of miR-200c, nuclear factor IA (NFIA) mRNA, HBV DNA, and HBV RNA (pregenomic RNA (pgRNA), and total RNA) were measured by qRCR. The levels of HBsAg and HBeAg were detected by ELISA. NFIA expression at protein level was measured by western blot. The direct interaction between miR-200c and NFIA were identified by Targetscan software and Dual-Luciferase reporter analysis. Enhance I activity were detected by Dual-Luciferase reporter assay. miR-200c expression was prominently reduced in pHBV1.3-tranfected Huh7 and in stable HBV-producing cell line (HepG2.2.15). The enforced expression of miR-200c significantly suppressed HBV replication, as demonstrated by the reduced levels of HBV protein (HBsAg and HBeAg) and, DNA and RNA (pgRNA and total RNA) levels. NFIA was proved to be a target of miR-200c and NFIA overexpression notably stimulated HBV replication. In addition, the inhibitory effect of miR-200c on HBV Enhance I activity was abolished following restoration of NFIA. miR-200c repressed HBV replication by directly targeting NFIA, which might provide a novel therapeutic target for HBV infection. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  19. Complementary and alternative medicine in inflammatory bowel disease patients: frequency and risk factors.

    Science.gov (United States)

    Fernández, Alberto; Barreiro-de Acosta, Manuel; Vallejo, Nicolau; Iglesias, Marta; Carmona, Amalia; González-Portela, Carlos; Lorenzo, Aurelio; Domínguez-Muñoz, J Enrique

    2012-11-01

    The use of complementary and alternative medicine in inflammatory bowel disease patients is progressively increased. To evaluate the use of complementary and alternative medicine in inflammatory bowel disease patients and to know potential risk factors for their use. The subjective response of these therapies and the impact on treatment adherence were also evaluated. Prospective, descriptive and transversal study. Inflammatory bowel disease patients were classified according to demographic and clinical characteristics. A questionnaire about the use of complementary and alternative medicine was collected. 705 patients were included. 126 patients (23%) had used complementary and alternative medicine. The most commonly used was herbal remedies (n=61), homoeopathy (n=36), acupuncture (n=31), kefir (n=31) and aloe vera (n=25). Factors associated with its use were extraintestinal manifestations (OR 1.69, CI 95% 1.11-2.57) and long-term evolution of the disease (OR 2.08, CI 95% 1.44-2.99). Most patients (74%) had the subjective feeling that use of complementary and alternative medicine had not improved their condition, 11 had adverse events related to its use and 11% of patients discontinued their conventional drugs. Use of complementary and alternative medicine in inflammatory bowel disease patients is frequent, especially in those with extraintestinal manifestations and long-term evolution. The use of these therapies was not perceived as a benefit for patients. Copyright © 2012 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

  20. Complementary and alternative medicine usage and its determinant factors among Iranian infertile couples.

    Science.gov (United States)

    Dehghan, Mahlagha; Mokhtarabadi, Sima; Heidari, Fatemeh Ghaedi

    2018-04-04

    Background The aim of this study was to determine the status of utilizing some complementary and alternative medicine techniques in infertile couples. Methods This was a cross-sectional study conducted on 250 infertile couples referred to a hospital in Kerman using convenience sampling. A researcher-made questionnaire was used to study the prevalence and user satisfaction of complementary and alternative medicines. Results Results indicated that 49.6% of the infertile couples used at least one of the complementary and alternative medicines during the past year. Most individuals used spiritual techniques (71.8% used praying and 70.2% used Nazr) and medicinal plants (54.8%). Safety is the most important factor affecting the satisfaction of infertile couples with complementary treatments (couples think that such treatments are safe (54.8%)). Discussion Concerning high prevalence of complementary and alternative treatments in infertile couples, incorporating such treatments into the healthcare education and promoting the awareness of infertile individuals seem crucial.

  1. Phosphorylation of the PCNA binding domain of the large subunit of replication factor C by Ca2+/calmodulin-dependent protein kinase II inhibits DNA synthesis

    DEFF Research Database (Denmark)

    Maga, G; Mossi, R; Fischer, R

    1997-01-01

    Replication factor C (RF-C) is a heteropentameric protein essential for DNA replication and DNA repair. It is a molecular matchmaker required for loading of the proliferating cell nuclear antigen (PCNA) sliding clamp onto double-strand DNA and for PCNA-dependent DNA synthesis by DNA polymerases...... delta and epsilon. The DNA and PCNA binding domains of the large 140 kDa subunit of human RF-C have been recently cloned [Fotedar, R., Mossi, R., Fitzgerald, P., Rousselle, T., Maga, G., Brickner, H., Messier, H., Khastilba. S., Hübscher, U., & Fotedar, A. (1996) EMBO J. 15, 4423-4433]. Here we show...... that the PCNA binding domain is phosphorylated by the Ca2+/calmodulin-dependent protein kinase II (CaMKII), an enzyme required for cell cycle progression in eukaryotic cells. The DNA binding domain, on the other hand, is not phosphorylated. Phosphorylation by CaMKII reduces the binding of PCNA to RF-C...

  2. The Confirmatory Factor Analysis of the Original Brief Intellectual Disability Scale and Alternative Models.

    Science.gov (United States)

    Mammen, Priya Mary; Asokan, Minju K; Russell, Sushila; Tsheringla, Sherab; Shankar, SatyaRaj; C Nair, Muttathu K; Sudhakar Russell, Paul Swamidhas

    2018-01-01

    Brief Intellectual Disability Scale (BIDS) is a measure validated for identification of children with intellectual disabilities (IDs) in countries with low disability resources. Following the publication of the exploratory factor analysis of BIDS, the authors have documented the confirmatory factor analysis (CFA) of BIDS in this study. A prospective cross-sectional study was conducted to document the CFA of the BIDS. Primary caregivers ( N = 124) of children with ID were recruited and rated the BIDS. We used alternative fit indices for the evaluation of comparative fit index (CFI) and root mean square error of approximation (RMSEA) to evaluate the model fit. The 2-index fit strategy was used to select the best factor model. The model fit index for the original 3-factor model and alternative 2-factor and 1-factor models with 9 items of the BIDS was under identified along with another 3-factor, 7-item model. Another 1-factor, 7-item model was identified but did not satisfy the 2-index fit strategy. A short version of the scale with a 2-factor and 7-item model of BIDS presented the best fit indices of CFI = 0.952 and RMSEA = 0.069. Although the original factor structure of BIDS was not confirmed in this study, another alternative a priori model for the construct validity of BIDS was confirmed. Therefore, the BIDS factor structure has been revised, refined, and trimmed to the final 2-factor, 7-item shorter version. Further documentation of the diagnostic accuracy, validity, and reliability of this shorter version of BDI is recommended.

  3. Robust Replication Control Is Generated by Temporal Gaps between Licensing and Firing Phases and Depends on Degradation of Firing Factor Sld2

    Directory of Open Access Journals (Sweden)

    Karl-Uwe Reusswig

    2016-10-01

    Full Text Available Temporal separation of DNA replication initiation into licensing and firing phases ensures the precise duplication of the genome during each cell cycle. Cyclin-dependent kinase (CDK is known to generate this separation by activating firing factors and at the same time inhibiting licensing factors but may not be sufficient to ensure robust separation at transitions between both phases. Here, we show that a temporal gap separates the inactivation of firing factors from the re-activation of licensing factors during mitosis in budding yeast. We find that gap size critically depends on phosphorylation-dependent degradation of the firing factor Sld2 mediated by CDK, DDK, Mck1, and Cdc5 kinases and the ubiquitin-ligases Dma1/2. Stable mutants of Sld2 minimize the gap and cause increased genome instability in an origin-dependent manner when combined with deregulation of other replication regulators or checkpoint mechanisms. Robust separation of licensing and firing phases therefore appears indispensable to safeguard genome stability.

  4. Replication of human syncytium-forming virus in human cells: effect of certain biological factors and selective chemicals.

    Science.gov (United States)

    Loh, P C; Ang, K S

    1981-01-01

    The growth characteristics of the human syncytium-forming virus (HSFV) were examined in several human cell lines of normal and malignant origins and composing of either fibroblastic or epithelial-like cells. Virus production occurred only in the fibroblastic diploid cell lines: HEF (human embryonic cells, Flow #5,000) and HFDL #645 (human fetal diploid lung), but not in the epithelial-like heteroploid cell lines: RA (a continuous line of human amnion), #999 (human bone marrow), and KB (carcinoma of the nasopharynx). While the single-cycle growth pattern of the virus in HEF and HFDL #645 cell lines were essentially similar, the virus yield per cell was greater in the HFDL #645 cells. Furthermore, the physiological state of the cell had a marked effect on virus production. Subconfluent actively growing HFDL #645 cells produced higher yields of virus than density-inhibited confluent HFDL #645 cell cultures. The replication of HSFV was inhibited by actinomycin D at concentrations that did not interfere with poliovirus replication (0.001 to 0.01 microgram/ml). Pretreatment and posttreatments of infected cell cultures with either the polycation polybrene (hexadimethrine bromide) or the synthetic glucocorticosteroid dexamethasone did not enhance HSFV production.

  5. Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle.

    Science.gov (United States)

    Gurudatta, B V; Yang, Jingping; Van Bortle, Kevin; Donlin-Asp, Paul G; Corces, Victor G

    2013-05-15

    DREF was first characterized for its role in the regulation of transcription of genes encoding proteins involved in DNA replication and found to interact with sequences similar to the DNA recognition motif of the BEAF-32 insulator protein. Insulators are DNA-protein complexes that mediate intra- and inter-chromosome interactions. Several DNA-binding insulator proteins have been described in Drosophila, including BEAF-32, dCTCF and Su(Hw). Here we find that DREF and BEAF-32 co-localize at the same genomic sites, but their enrichment shows an inverse correlation. Furthermore, DREF co-localizes in the genome with other insulator proteins, suggesting that the function of this protein may require components of Drosophila insulators. This is supported by the finding that mutations in insulator proteins modulate DREF-induced cell proliferation. DREF persists bound to chromatin during mitosis at a subset of sites where it also co-localizes with dCTCF, BEAF-32 and CP190. These sites are highly enriched for sites where Orc2 and Mcm2 are present during interphase and at the borders of topological domains of chromosomes defined by Hi-C. The results suggest that DREF and insulator proteins may help maintain chromosome organization during the cell cycle and mark a subset of genomic sites for the assembly of pre-replication complexes and gene bookmarking during the M/G1 transition.

  6. Peplau's Theory of Interpersonal Relations: An Alternate Factor Structure for Patient Experience Data?

    Science.gov (United States)

    Hagerty, Thomas A; Samuels, William; Norcini-Pala, Andrea; Gigliotti, Eileen

    2017-04-01

    A confirmatory factor analysis of data from the responses of 12,436 patients to 16 items on the Consumer Assessment of Healthcare Providers and Systems-Hospital survey was used to test a latent factor structure based on Peplau's middle-range theory of interpersonal relations. A two-factor model based on Peplau's theory fit these data well, whereas a three-factor model also based on Peplau's theory fit them excellently and provided a suitable alternate factor structure for the data. Though neither the two- nor three-factor model fit as well as the original factor structure, these results support using Peplau's theory to demonstrate nursing's extensive contribution to the experiences of hospitalized patients.

  7. Functions of replication factor C and proliferating-cell nuclear antigen: Functional similarity of DNA polymerase accessory proteins from human cells and bacteriophage T4

    International Nuclear Information System (INIS)

    Tsurimoto, Toshiki; Stillman, B.

    1990-01-01

    The proliferating-cell nuclear antigen (PCNA) and the replication factors A and C (RF-A and RF-C) are cellular proteins essential for complete elongation of DNA during synthesis from the simian virus 40 origin of DNA replication in vitro. All three cooperate to stimulate processive DNA synthesis by DNA polymerase δ on a primed single-stranded M13 template DNA and as such can be categorized as DNA polymerase accessory proteins. Biochemical analyses with highly purified RF-C and PCNA have demonstrated functions that are completely analogous to the functions of bacteriophage T4 DNA polymerase accessory proteins. A primer-template-specific DNA binding activity and a DNA-dependent ATPase activity copurified with the multisubunit protein RF-C and are similar to the functions of the phage T4 gene 44/62 protein complex. Furthermore, PCNA stimulated the RF-C ATPase activity and is, therefore, analogous to the phage T4 gene 45 protein, which stimulates the ATPase function of the gene 44/62 protein complex. Indeed, some primary sequence similarities between human PCNA and the phage T4 gene 45 protein could be detected. These results demonstrate a striking conservation of the DNA replication apparatus in human cells and bacteriophage T4

  8. Testing alternative factor models of PTSD and the robustness of the dysphoria factor.

    Science.gov (United States)

    Elklit, Ask; Armour, Cherie; Shevlin, Mark

    2010-01-01

    This study first aimed to examine the structure of self-reported posttraumatic stress disorder (PTSD) symptoms using three different samples. The second aim of the paper was to test the robustness of the factor analytic model when depression scores were controlled for. Based on previous factor analytic findings and the DSM-IV formulation, six confirmatory factor models were specified and estimated that reflected different symptom clusters. The best fitting model was subsequently re-fitted to the data after including a depression variable. The analyses were based on responses from 973 participants across three samples. Sample 1 consisted of 633 parents who were members of 'The National Association of Infant Death' and who had lost a child. Sample 2 consisted of 227 victims of rape, who completed a questionnaire within 4 weeks of the rape. Each respondent had been in contact with the Centre for Rape Victims (CRV) at the Aarhus University Hospital, Denmark. Sample 3 consisted of 113 refugees resident in Denmark. All participants had been referred to a treatment centre which focused on rehabilitating refugees through treatment for psychosocial integration problems (RRCF: Rehabliterings og Revliderings Centre for Flygtninge). In total 500 participants received a diagnosis of PTSD/sub-clinical PTSD (Sample 1, N=214; 2, N=176; 3, N=110). A correlated four-factor model with re-experiencing, avoidance, dysphoria, and arousal factors provided the best fit to the sample data. The average attenuation in the factor loadings was highest for the dysphoria factor (M=-.26, SD=.11) compared to the re-experiencing (M=-.14, SD=.18), avoidance (M=-.10, SD=.21), and arousal (M=-.09, SD=.13) factors. With regards to the best fitting factor model these results concur with previous research findings using different trauma populations but do not reflect the current DSM-IV symptom groupings. The attenuation of dysphoria factor loadings suggests that dysphoria is a non-specific component of

  9. Barrier to auto integration factor becomes dephosphorylated during HSV-1 Infection and Can Act as a host defense by impairing viral DNA replication and gene expression.

    Science.gov (United States)

    Jamin, Augusta; Thunuguntla, Prasanth; Wicklund, April; Jones, Clinton; Wiebe, Matthew S

    2014-01-01

    BAF (Barrier to Autointegration Factor) is a highly conserved DNA binding protein that senses poxviral DNA in the cytoplasm and tightly binds to the viral genome to interfere with DNA replication and transcription. To counteract BAF, a poxviral-encoded protein kinase phosphorylates BAF, which renders BAF unable to bind DNA and allows efficient viral replication to occur. Herein, we examined how BAF phosphorylation is affected by herpes simplex virus type 1 (HSV-1) infection and tested the ability of BAF to interfere with HSV-1 productive infection. Interestingly, we found that BAF phosphorylation decreases markedly following HSV-1 infection. To determine whether dephosphorylated BAF impacts HSV-1 productive infection, we employed cell lines stably expressing a constitutively unphosphorylated form of BAF (BAF-MAAAQ) and cells overexpressing wild type (wt) BAF for comparison. Although HSV-1 production in cells overexpressing wtBAF was similar to that in cells expressing no additional BAF, viral growth was reduced approximately 80% in the presence of BAF-MAAAQ. Experiments were also performed to determine the mechanism of the antiviral activity of BAF with the following results. BAF-MAAAQ was localized to the nucleus, whereas wtBAF was dispersed throughout cells prior to infection. Following infection, wtBAF becomes dephosphorylated and relocalized to the nucleus. Additionally, BAF was associated with the HSV-1 genome during infection, with BAF-MAAAQ associated to a greater extent than wtBAF. Importantly, unphosphorylated BAF inhibited both viral DNA replication and gene expression. For example, expression of two regulatory proteins, ICP0 and VP16, were substantially reduced in cells expressing BAF-MAAAQ. However, other viral genes were not dramatically affected suggesting that expression of certain viral genes can be differentially regulated by unphosphorylated BAF. Collectively, these results suggest that BAF can act in a phosphorylation-regulated manner to impair

  10. Alternative pathways of thromboplastin-dependent activation of human factor X in plasma

    International Nuclear Information System (INIS)

    Marlar, R.A.; Griffin, J.H.

    1981-01-01

    To determine the interrelationships of the major coagulation pathways, the activation of 3H-labeled factor X in normal and various deficient human plasmas was evaluated when clotting was triggered by dilute rabbit or human thromboplastin. Various dilutions of thromboplastin and calcium were added to plasma samples containing 3H-factor X, and the time course of factor X activation was determined. At a 1/250 dilution of rabbit brain thromboplastin, the rate of factor X activation in plasmas deficient in factor VIII or factor IX was 10% of the activation rate of normal plasma or of factor XI deficient plasma. Reconstitution of the deficient plasmas with factors VIII or IX, respectively, reconstituted normal factor X activation. Similar results were obtained when various dilutions of human thromboplastin replaced the rabbit thromboplastin. From these plasma experiments, it is inferred that the dilute thromboplastin-dependent activation of factor X requires factors VII, IX, and VIII. An alternative extrinsic pathway that involves factors IX and VIII may be the physiologic extrinsic pathway and hence help to explain the consistent clinical observations of bleeding diatheses in patients deficient in factors IX or VIII

  11. CENTRIOLE REPLICATION

    Science.gov (United States)

    Mizukami, Ikuko; Gall, Joseph

    1966-01-01

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

  12. Analysis of automotive rolling lobe air spring under alternative factors with finite element model

    International Nuclear Information System (INIS)

    Wong, Pak Kin; Xie, Zhengchao; Zhao, Jing; Xu, Tao; He, Feng

    2014-01-01

    Air springs are widely used in automotive suspensions for their superior performance in terms of low friction motion, adjustable load carrying capacity and user-friendly ride height control. However, it has posed great difficulties in constructing an accurate model as well as the analysis of the influence of alternative factors, such as cord angle, cord diameter and initial pressure. In this paper, a numerical model of the rolling lobe air spring (RLAS) is built by using finite element method and compared with an existing analytical model. An experiment with respect to the vertical stiffness of the RLAS is carried out to validate the accuracy of the proposed model. Evaluation result reveals that the existing analytical model cannot represent the performance of the RLAS very well, whereas the accuracy of the numerical model is very good. With the verified numerical model, the impacts of many alternative factors on the characteristics of the RLAS are analyzed. Numerical results show that the newly proposed model is reliable to determine the vertical characteristic and physical dimensions of the RLAS under the alternative factors.

  13. Evolution of Replication Machines

    Science.gov (United States)

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

    2016-01-01

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

  14. Human Mitochondrial DNA Replication

    Science.gov (United States)

    Holt, Ian J.; Reyes, Aurelio

    2012-01-01

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

  15. Alternative complement pathway and factor B activities in rats with altered blood levels of thyroid hormone

    International Nuclear Information System (INIS)

    Bitencourt, C.S.; Duarte, C.G.; Azzolini, A.E.C.S.; Assis-Pandochi, A.I.

    2012-01-01

    Evaluating the activity of the complement system under conditions of altered thyroid hormone levels might help elucidate the role of complement in triggering autoimmune processes. Here, we investigated alternative pathway (AP) activity in male Wistar rats (180 ± 10 g) after altering their thyroid hormone levels by treatment with triiodothyronine (T3), propylthiouracil (PTU) or thyroidectomy. T3 and thyroxine (T4) levels were determined by chemiluminescence assays. Hemolytic assays were performed to evaluate the lytic activity of the AP. Factor B activity was evaluated using factor B-deficient serum. An anti-human factor B antibody was used to measure factor B levels in serum by radial immunodiffusion. T3 measurements in thyroidectomized animals or animals treated with PTU demonstrated a significant reduction in hormone levels compared to control. The results showed a reduction in AP lytic activity in rats treated with increasing amounts of T3 (1, 10, or 50 µg). Factor B activity was also decreased in the sera of hyperthyroid rats treated with 1 to 50 µg T3. Additionally, treating rats with 25 µg T3 significantly increased factor B levels in their sera (P < 0.01). In contrast, increased factor B concentration and activity (32%) were observed in hypothyroid rats. We conclude that alterations in thyroid hormone levels affect the activity of the AP and factor B, which may in turn affect the roles of AP and factor B in antibody production

  16. [Factors determining the selection of treatment options of complementary and alternative medicine].

    Science.gov (United States)

    Zörgő, Szilvia; Purebl, György; Zana, Ágnes

    2016-04-10

    Complementary and alternative medicine have undoubtedly been gaining ground on the healthcare market, thus the vital question arises why patients choose these treatments, oftentimes at the cost of discontinuing the Western medical therapy. The aim of the authors was to investigate and scrutinize factors leading to the utilization of various alternative medical services. The basis of this qualitative research was medical anthropological fieldwork conducted at a clinic of Traditional Chinese Medicine including participant observation (355 hours), unstructured interviews with patients (n = 93) and in-depth interviews (n = 14). Patients of alternative medical systems often do not receive a diagnosis, explanation or cure for their illness from Western medicine, or they do not agree with what they are offered. In other instances, patients choose alternative medicine because it exhibits a philosophical congruence with their already existing explanatory model, that is, previous concepts of world, man or illness. A particular therapy is always part of a cultural system and it is embedded in a specific psycho-social context, hence choice of therapy must be interpreted in accordance with this perspective.

  17. Replication and extension of a hierarchical model of social anxiety and depression: fear of positive evaluation as a key unique factor in social anxiety.

    Science.gov (United States)

    Weeks, Justin W

    2015-01-01

    Wang, Hsu, Chiu, and Liang (2012, Journal of Anxiety Disorders, 26, 215-224) recently proposed a hierarchical model of social interaction anxiety and depression to account for both the commonalities and distinctions between these conditions. In the present paper, this model was extended to more broadly encompass the symptoms of social anxiety disorder, and replicated in a large unselected, undergraduate sample (n = 585). Structural equation modeling (SEM) and hierarchical regression analyses were employed. Negative affect and positive affect were conceptualized as general factors shared by social anxiety and depression; fear of negative evaluation (FNE) and disqualification of positive social outcomes were operationalized as specific factors, and fear of positive evaluation (FPE) was operationalized as a factor unique to social anxiety. This extended hierarchical model explicates structural relationships among these factors, in which the higher-level, general factors (i.e., high negative affect and low positive affect) represent vulnerability markers of both social anxiety and depression, and the lower-level factors (i.e., FNE, disqualification of positive social outcomes, and FPE) are the dimensions of specific cognitive features. Results from SEM and hierarchical regression analyses converged in support of the extended model. FPE is further supported as a key symptom that differentiates social anxiety from depression.

  18. Alternative management structures for municipal waste collection services: The influence of economic and political factors

    International Nuclear Information System (INIS)

    Plata-Díaz, Ana María; Zafra-Gómez, José Luis; Pérez-López, Gemma; López-Hernández, Antonio Manuel

    2014-01-01

    Highlights: • We analyzed the factors that influence on the restructuring of MSW services. • We evaluated five different alternatives for public and private service. • Our analysis covers a broad time horizon, 2002–2010. • We used a conditional fixed-effects logistic regression as the evaluation method. • Municipalities tend to contract out the MSW service in the presence of high costs and fiscal stress. - Abstract: Identifying and characterising the factors that determine why a local authority opts for a particular way of managing its waste collection service is an important issue, warranting research interest in the field of municipal solid waste (MSW) management. This paper presents empirical evidence spanning a broad time horizon (2002–2010) showing that economic and political factors impact in different ways on the provision of waste management services. We examine five alternatives in this area, including public and private service delivery formulas and, within each field, individual and joint options. Our findings highlight the importance of the service cost and that of the various indicators of fiscal stress as determinant factors of management decisions regarding the provision of MSW management services

  19. HIV-1 infection induces changes in expression of cellular splicing factors that regulate alternative viral splicing and virus production in macrophages

    Directory of Open Access Journals (Sweden)

    Purcell Damian FJ

    2008-02-01

    Full Text Available Abstract Background Macrophages are important targets and long-lived reservoirs of HIV-1, which are not cleared of infection by currently available treatments. In the primary monocyte-derived macrophage model of infection, replication is initially productive followed by a decline in virion output over ensuing weeks, coincident with a decrease in the levels of the essential viral transactivator protein Tat. We investigated two possible mechanisms in macrophages for regulation of viral replication, which appears to be primarily regulated at the level of tat mRNA: 1 differential mRNA stability, used by cells and some viruses for the rapid regulation of gene expression and 2 control of HIV-1 alternative splicing, which is essential for optimal viral replication. Results Following termination of transcription at increasing times after infection in macrophages, we found that tat mRNA did indeed decay more rapidly than rev or nef mRNA, but with similar kinetics throughout infection. In addition, tat mRNA decayed at least as rapidly in peripheral blood lymphocytes. Expression of cellular splicing factors in uninfected and infected macrophage cultures from the same donor showed an inverse pattern over time between enhancing factors (members of the SR family of RNA binding proteins and inhibitory factors (members of the hnRNP family. While levels of the SR protein SC35 were greatly up-regulated in the first week or two after infection, hnRNPs of the A/B and H groups were down-regulated. Around the peak of virus production in each culture, SC35 expression declined to levels in uninfected cells or lower, while the hnRNPs increased to control levels or above. We also found evidence for increased cytoplasmic expression of SC35 following long-term infection. Conclusion While no evidence of differential regulation of tat mRNA decay was found in macrophages following HIV-1 infection, changes in the balance of cellular splicing factors which regulate alternative

  20. The gene for replication factor C subunit 2 (RFC2) is within the 7q11.23 Williams syndrome deletion

    Energy Technology Data Exchange (ETDEWEB)

    Peoples, R.; Perez-Jurado, L.; Francke, U.; Yu-Ker Wang [Stanford Univ. Medical Center, CA (United States); Kaplan, P. [Children`s Hospital of Philadelphia, PA (United States)

    1996-06-01

    Williams syndrome (WS) is a developmental disorder with multiple system manifestations, including supraval var aortic stenosis (SVAS), peripheral pulmonic stenosis, connective tissue abnormalities, short stature, characteristic personality profile and cognitive deficits, and variable hypercalcemia in infancy. It is caused by heterozygosity for a chromosomal deletion of part of band 7q11.23 including the elastin locus (ELN). Since disruption of the ELN gene causes autosomal dominant SVAS, it is assumed that ELN haploinsufficiency is responsible for the cardiovascular features of WS. The deletion that extends from the ELN locus in both directions is {ge}200 kb in size, although estimates of {ge}2 Mb are suggested by high-resolution chromosome banding and physical mapping studies. We have searched for additional dosage-sensitive genes within the deletion that may be responsible for the noncardiovascular features. We report here that the gene for replication factor C subunit 2 (RFC2) maps within the WS deletion region and was found to be deleted in all of 18 WS patients studied. The protein product of RFC2 is part of a multimeric complex involved in DNA elongation during replication. 14 refs., 3 figs.

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  2. Replication Factor C Is a More Effective Proliferating Cell Nuclear Antigen (PCNA) Opener than the Checkpoint Clamp Loader, Rad24-RFC*

    Science.gov (United States)

    Thompson, Jennifer A.; Marzahn, Melissa R.; O'Donnell, Mike; Bloom, Linda B.

    2012-01-01

    Clamp loaders from all domains of life load clamps onto DNA. The clamp tethers DNA polymerases to DNA to increase the processivity of synthesis as well as the efficiency of replication. Here, we investigated proliferating cell nuclear antigen (PCNA) binding and opening by the Saccharomyces cerevisiae clamp loader, replication factor C (RFC), and the DNA damage checkpoint clamp loader, Rad24-RFC, using two separate fluorescence intensity-based assays. Analysis of PCNA opening by RFC revealed a two-step reaction in which RFC binds PCNA before opening PCNA rather than capturing clamps that have transiently and spontaneously opened in solution. The affinity of RFC for PCNA is about an order of magnitude lower in the absence of ATP than in its presence. The affinity of Rad24-RFC for PCNA in the presence of ATP is about an order magnitude weaker than that of RFC for PCNA, similar to the RFC-PCNA interaction in the absence of ATP. Importantly, fewer open clamp loader-clamp complexes are formed when PCNA is bound by Rad24-RFC than when bound by RFC. PMID:22115746

  3. Replication factor C is a more effective proliferating cell nuclear antigen (PCNA) opener than the checkpoint clamp loader, Rad24-RFC.

    Science.gov (United States)

    Thompson, Jennifer A; Marzahn, Melissa R; O'Donnell, Mike; Bloom, Linda B

    2012-01-13

    Clamp loaders from all domains of life load clamps onto DNA. The clamp tethers DNA polymerases to DNA to increase the processivity of synthesis as well as the efficiency of replication. Here, we investigated proliferating cell nuclear antigen (PCNA) binding and opening by the Saccharomyces cerevisiae clamp loader, replication factor C (RFC), and the DNA damage checkpoint clamp loader, Rad24-RFC, using two separate fluorescence intensity-based assays. Analysis of PCNA opening by RFC revealed a two-step reaction in which RFC binds PCNA before opening PCNA rather than capturing clamps that have transiently and spontaneously opened in solution. The affinity of RFC for PCNA is about an order of magnitude lower in the absence of ATP than in its presence. The affinity of Rad24-RFC for PCNA in the presence of ATP is about an order magnitude weaker than that of RFC for PCNA, similar to the RFC-PCNA interaction in the absence of ATP. Importantly, fewer open clamp loader-clamp complexes are formed when PCNA is bound by Rad24-RFC than when bound by RFC.

  4. A mutation in the DNA polymerase accessory factor of herpes simplex virus 1 restores viral DNA replication in the presence of raltegravir.

    Science.gov (United States)

    Zhou, Bin; Yang, Kui; Wills, Elizabeth; Tang, Liang; Baines, Joel D

    2014-10-01

    Previous reports showed that raltegravir, a recently approved antiviral compound that targets HIV integrase, can inhibit the nuclease function of human cytomegalovirus (HCMV terminase) in vitro. In this study, subtoxic levels of raltegravir were shown to inhibit the replication of four different herpesviruses, herpes simplex virus 1 (HSV-1), HSV-2, HCMV, and mouse cytomegalovirus, by 30- to 700-fold, depending on the dose and the virus tested. Southern blotting and quantitative PCR revealed that raltegravir inhibits DNA replication of HSV-1 rather than cleavage of viral DNA. A raltegravir-resistant HSV-1 mutant was generated by repeated passage in the presence of 200 μM raltegravir. The genomic sequence of the resistant virus, designated clone 7, contained mutations in 16 open reading frames. Of these, the mutations F198S in unique long region 15 (UL15; encoding the large terminase subunit), A374V in UL32 (required for DNA cleavage and packaging), V296I in UL42 (encoding the DNA polymerase accessory factor), and A224S in UL54 (encoding ICP27, an important transcriptional regulator) were introduced independently into the wild-type HSV-1(F) genome, and the recombinant viruses were tested for raltegravir resistance. Viruses bearing both the UL15 and UL32 mutations inserted within the genome of the UL42 mutant were also tested. While the UL15, UL32, and UL54 mutant viruses were fully susceptible to raltegravir, any virus bearing the UL42 mutation was as resistant to raltegravir as clone 7. Overall, these results suggest that raltegravir may be a valuable therapeutic agent against herpesviruses and the antiviral activity targets the DNA polymerase accessory factor rather than the nuclease activity of the terminase. This paper shows that raltegravir, the antiretrovirus drug targeting integrase, is effective against various herpesviruses. Drug resistance mapped to the herpesvirus DNA polymerase accessory factor, which was an unexpected finding. Copyright © 2014

  5. Inhibition of human immunodeficiency virus type 1 replication with artificial transcription factors targeting the highly conserved primer-binding site

    NARCIS (Netherlands)

    Eberhardy, Scott R.; Goncalves, Joao; Coelho, Sofia; Segal, David J.; Berkhout, Ben; Barbas, Carlos F.

    2006-01-01

    The human immunodeficiency virus type 1 (HIV-1) primer-binding site (PBS) is a highly conserved region in the HIV genome and represents an attractive target for the development of new anti-HIV therapies. In this study, we designed four artificial zinc finger transcription factors to bind at or

  6. Replication factor c recruits dna polymerase δ to sites of nucleotide excision repair but is not required for PCNA recruitment

    NARCIS (Netherlands)

    R.M. Overmeer (René); A.M. Gourdin (Audrey); G. Giglia-Mari (Giuseppina); H.J.M. Kool (Hanneke); A.B. Houtsmuller (Adriaan); T. Siegal (Tali); M.I. Fousteri (Maria); L.H.F. Mullenders (Leon); W. Vermeulen (Wim)

    2010-01-01

    textabstractNucleotide excision repair (NER) operates through coordinated assembly of repair factors into pre- and postincisioncomplexes. The postincision step of NER includes gap-filling DNA synthesis and ligation. However, the exact composition of this NER-associated DNA synthesis complex in vivo

  7. The DNA replication licensing factor miniature chromosome maintenance 7 is essential for RNA splicing of epidermal growth factor receptor, c-Met, and platelet-derived growth factor receptor.

    Science.gov (United States)

    Chen, Zhang-Hui; Yu, Yan P; Michalopoulos, George; Nelson, Joel; Luo, Jian-Hua

    2015-01-16

    Miniature chromosome maintenance 7 (MCM7) is an essential component of DNA replication licensing complex. Recent studies indicate that MCM7 is amplified and overexpressed in a variety of human malignancies. In this report, we show that MCM7 binds SF3B3. The binding motif is located in the N terminus (amino acids 221-248) of MCM7. Knockdown of MCM7 or SF3B3 significantly increased unspliced RNA of epidermal growth factor receptor, platelet-derived growth factor receptor, and c-Met. A dramatic drop of reporter gene expression of the oxytocin exon 1-intron-exon 2-EGFP construct was also identified in SF3B3 and MCM7 knockdown PC3 and DU145 cells. The MCM7 or SF3B3 depleted cell extract failed to splice reporter RNA in in vitro RNA splicing analyses. Knockdown of SF3B3 and MCM7 leads to an increase of cell death of both PC3 and DU145 cells. Such cell death induction is partially rescued by expressing spliced c-Met. To our knowledge, this is the first report suggesting that MCM7 is a critical RNA splicing factor, thus giving significant new insight into the oncogenic activity of this protein. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Recombination-dependent concatemeric viral DNA replication.

    Science.gov (United States)

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

    2011-09-01

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

  9. Circadian typology and the Alternative Five-Factor Model of personality.

    Science.gov (United States)

    Tonetti, Lorenzo; Pascalis, Vilfredo De; Fabbri, Marco; Martoni, Monica; Russo, Paolo Maria; Natale, Vincenzo

    2016-10-01

    Two studies were carried out to explore the relationship between circadian typology and the Alternative Five-Factor Model of personality. In the first study, 379 participants (232 females) were administered the reduced version of the Morningness-Eveningness Questionnaire and the Zuckerman-Kuhlman Personality Questionnaire. Evening types reported higher impulsive sensation-seeking scores than morning and intermediate types, whereas morning types scored higher than evening types on activity factor. In the second study, the association between morningness and activity personality factor was verified through the objective-actigraphic monitoring of the rest-activity cycle. Actigraphy allowed us to operationalise both circadian typology, through the computing of midpoint of sleep (early values, expressed in hours and minutes, correspond to an advanced phase of the sleep/wake cycle), and activity factor by the means of motor activity recording. Fifty-one individuals (30 females) wore an actigraph on the nondominant wrist continuously for 1 week. A negative correlation was observed between midpoint of sleep and mean diurnal motor activity, demonstrating that an early phase of the sleep/wake cycle (i.e. morningness preference) was related to higher diurnal motor activity. Assessed both subjectively and objectively, the results of both studies highlight a significant relationship between morningness and activity personality factor. © 2015 International Union of Psychological Science.

  10. Bayesian Factor Analysis as a Variable-Selection Problem: Alternative Priors and Consequences.

    Science.gov (United States)

    Lu, Zhao-Hua; Chow, Sy-Miin; Loken, Eric

    2016-01-01

    Factor analysis is a popular statistical technique for multivariate data analysis. Developments in the structural equation modeling framework have enabled the use of hybrid confirmatory/exploratory approaches in which factor-loading structures can be explored relatively flexibly within a confirmatory factor analysis (CFA) framework. Recently, Muthén & Asparouhov proposed a Bayesian structural equation modeling (BSEM) approach to explore the presence of cross loadings in CFA models. We show that the issue of determining factor-loading patterns may be formulated as a Bayesian variable selection problem in which Muthén and Asparouhov's approach can be regarded as a BSEM approach with ridge regression prior (BSEM-RP). We propose another Bayesian approach, denoted herein as the Bayesian structural equation modeling with spike-and-slab prior (BSEM-SSP), which serves as a one-stage alternative to the BSEM-RP. We review the theoretical advantages and disadvantages of both approaches and compare their empirical performance relative to two modification indices-based approaches and exploratory factor analysis with target rotation. A teacher stress scale data set is used to demonstrate our approach.

  11. Factors Influencing And Alternative Policies Offered Of Social Conflicts Indigenous Peoples Rights

    Directory of Open Access Journals (Sweden)

    Saiful Deni

    2017-06-01

    Full Text Available This paper is a review of the social conflicts of indigenous peoples especially in North Maluku. The purpose of this review is to find out some factors causing indigenous peoples social conflicts in North Maluku and to produce alternative solutions as a policy to develop indigenous peoples livelihoods. The review resulted in several factors causing social conflicts of indigenous peoples such as the unclear boundary between the two parties the customary violations by the forest businessmen the injustice of the law enforcement officers in solving the problems the destruction of the indigenous people and the forest community narrow forest the lack positive contribution of forest management so far to indigenous peoples and forest communities companies do not involve indigenous peoples andor forest communities in forest exploitation destruction of customary buildings as places of worship deforestation timber exploitation while timber by indigenous peoples is sacred wood or abstinence to be felled. Alternative solutions are required by local government such as policy on legal recognition of indigenous peoples indigenous peoples empowerment implementation of indigenous peoples aspirations indigenous peoples economic development based on local wisdom and dispute resolution of indigenous peoples through special courts of a holistic nature.

  12. The role of IREB2 and transforming growth factor beta-1 genetic variants in COPD: a replication case-control study

    LENUS (Irish Health Repository)

    Chappell, Sally L

    2011-02-14

    Abstract Background Genetic factors are known to contribute to COPD susceptibility and these factors are not fully understood. Conflicting results have been reported for many genetic studies of candidate genes based on their role in the disease. Genome-wide association studies in combination with expression profiling have identified a number of new candidates including IREB2. A meta-analysis has implicated transforming growth factor beta-1 (TGFbeta1) as a contributor to disease susceptibility. Methods We have examined previously reported associations in both genes in a collection of 1017 white COPD patients and 912 non-diseased smoking controls. Genotype information was obtained for seven SNPs in the IREB2 gene, and for four SNPs in the TGFbeta1 gene. Allele and genotype frequencies were compared between COPD cases and controls, and odds ratios were calculated. The analysis was adjusted for age, sex, smoking and centre, including interactions of age, sex and smoking with centre. Results Our data replicate the association of IREB2 SNPs in association with COPD for SNP rs2568494, rs2656069 and rs12593229 with respective adjusted p-values of 0.0018, 0.0039 and 0.0053. No significant associations were identified for TGFbeta1. Conclusions These studies have therefore confirmed that the IREB2 locus is a contributor to COPD susceptibility and suggests a new pathway in COPD pathogenesis invoking iron homeostasis.

  13. Binge eating disorder versus overeating: a failure to replicate and common factors in severely obese treatment seeking women.

    Science.gov (United States)

    Antoniou, M; Tasca, G A; Wood, J; Bissada, H

    2003-06-01

    The disordered eating symptoms, general psychopathology and dieting history among obese women diagnosed with Binge Eating Disorder (BED) and obese women who overeat (OE) are examined. One hundred and thirty women (n=83 with BED and n=47 who overeat) seeking treatment for an eating disorder were diagnosed using the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) criteria and the Eating Disorders Examination (EDE). They also completed a battery of psychometric tests. Despite adequate statistical power to detect differences, MANOVAs revealed very few significant differences between the groups. Loss of control of eating does not adequately differentiate these two groups within an eating disorders treatment-seeking context. It is likely that only the most acutely distressed from each group is seeking treatment, so that differences found in a community sample would not be found. Using a principal components analysis, factors within each group that may underlie the common psychopathology of both groups (i.e. disordered eating symptoms, general psychopathology and dieting history) were found.

  14. The Construct Validity of Scores on the Ways of Coping Questionnaire: Confirmatory Analysis of Alternative Factor Structures.

    Science.gov (United States)

    Edwards, Jeffrey R.; O'Neill, Regina M.

    1998-01-01

    Confirmatory factor analysis was used to evaluate alternative factor structures, based on previous exploratory factor analyses and coping dimensions derived from the theory of R. Lazarus, for the Ways of Coping Questionnaire (S. Folkman and R. Lazarus, 1988). Results from responses of 654 college graduates provide little support for the factor…

  15. Replication factor C from the hyperthermophilic archaeon Pyrococcus abyssi does not need ATP hydrolysis for clamp-loading and contains a functionally conserved RFC PCNA-binding domain.

    Science.gov (United States)

    Henneke, Ghislaine; Gueguen, Yannick; Flament, Didier; Azam, Philippe; Querellou, Joël; Dietrich, Jacques; Hübscher, Ulrich; Raffin, Jean-Paul

    2002-11-08

    The molecular organization of the replication complex in archaea is similar to that in eukaryotes. Only two proteins homologous to subunits of eukaryotic replication factor C (RFC) have been detected in Pyrococcus abyssi (Pab). The genes encoding these two proteins are arranged in tandem. We cloned these two genes and co-expressed the corresponding recombinant proteins in Escherichia coli. Two inteins present in the gene encoding the small subunit (PabRFC-small) were removed during cloning. The recombinant protein complex was purified by anion-exchange and hydroxyapatite chromatography. Also, the PabRFC-small subunit could be purified, while the large subunit (PabRFC-large) alone was completely insoluble. The highly purified PabRFC complex possessed an ATPase activity, which was not enhanced by DNA. The Pab proliferating cell nuclear antigen (PCNA) activated the PabRFC complex in a DNA-dependent manner, but the PabRFC-small ATPase activity was neither DNA-dependent nor PCNA-dependent. The PabRFC complex was able to stimulate PabPCNA-dependent DNA synthesis by the Pabfamily D heterodimeric DNA polymerase. Finally, (i) the PabRFC-large fraction cross-reacted with anti-human-RFC PCNA-binding domain antibody, corroborating the conservation of the protein sequence, (ii) the human PCNA stimulated the PabRFC complex ATPase activity in a DNA-dependent way and (iii) the PabRFC complex could load human PCNA onto primed single-stranded circular DNA, suggesting that the PCNA-binding domain of RFC has been functionally conserved during evolution. In addition, ATP hydrolysis was not required either for DNA polymerase stimulation or PCNA-loading in vitro.

  16. Human factors evaluation of teletherapy: Identification of problems and alternative approaches. Volume 1

    Energy Technology Data Exchange (ETDEWEB)

    Henriksen, K.; Kaye, R.D.; Jones, R. [Hughes Training, Inc., Falls Church, VA (United States); Morisseau, D.S.; Serig, D.I. [Nuclear Regulatory Commission, Washington, DC (United States). Div. of Systems Technology

    1995-07-01

    A series of human factors evaluations was undertaken to better understand the contributing factors to human error in the teletherapy environment. Teletherapy is a multi-disciplinary methodology for treating cancerous tissue through selective exposure to an external beam of ionizing radiation. The principal sources of radiation are a radioactive isotope, typically cobalt60 (Co-60), or a linear accelerator device capable of producing very high energy x-ray and electron beams. A team of human factors specialists, assisted by a panel of radiation oncologists, medical physicists, and radiation technologists, conducted site visits to radiation oncology departments at community hospitals, university centers, and free-standing clinics. A function and task analysis was initially performed to guide subsequent evaluations in the areas of user-system interfaces, procedures, training and qualifications, and organizational policies and practices. The final phase of the project focused on identification of the most significant human factors problems with respect to safe and effective operation of the teletherapy system and an identification and assessment of alternative approaches for resolving the problems. This report presents the findings of this final phase.

  17. Human factors evaluation of teletherapy: Identification of problems and alternative approaches. Volume 1

    International Nuclear Information System (INIS)

    Henriksen, K.; Kaye, R.D.; Jones, R.; Morisseau, D.S.; Serig, D.I.

    1995-07-01

    A series of human factors evaluations was undertaken to better understand the contributing factors to human error in the teletherapy environment. Teletherapy is a multi-disciplinary methodology for treating cancerous tissue through selective exposure to an external beam of ionizing radiation. The principal sources of radiation are a radioactive isotope, typically cobalt60 (Co-60), or a linear accelerator device capable of producing very high energy x-ray and electron beams. A team of human factors specialists, assisted by a panel of radiation oncologists, medical physicists, and radiation technologists, conducted site visits to radiation oncology departments at community hospitals, university centers, and free-standing clinics. A function and task analysis was initially performed to guide subsequent evaluations in the areas of user-system interfaces, procedures, training and qualifications, and organizational policies and practices. The final phase of the project focused on identification of the most significant human factors problems with respect to safe and effective operation of the teletherapy system and an identification and assessment of alternative approaches for resolving the problems. This report presents the findings of this final phase

  18. Proteome-wide overexpression of host proteins for identification of factors affecting tombusvirus RNA replication: an inhibitory role of protein kinase C.

    Science.gov (United States)

    Shah Nawaz-ul-Rehman, Muhammad; Martinez-Ochoa, Natalia; Pascal, Helene; Sasvari, Zsuzsanna; Herbst, Christin; Xu, Kai; Baker, Jannine; Sharma, Monika; Herbst, Alan; Nagy, Peter D

    2012-09-01

    To identify host genes affecting replication of Tomato bushy stunt virus (TBSV), a small model positive-stranded RNA virus, we overexpressed 5,500 yeast proteins individually in Saccharomyces cerevisiae, which supports TBSV replication. In total, we identified 141 host proteins, and overexpression of 40 of those increased and the remainder decreased the accumulation of a TBSV replicon RNA. Interestingly, 36 yeast proteins were identified previously by various screens, greatly strengthening the relevance of these host proteins in TBSV replication. To validate the results from the screen, we studied the effect of protein kinase C1 (Pkc1), a conserved host kinase involved in many cellular processes, which inhibited TBSV replication when overexpressed. Using a temperature-sensitive mutant of Pkc1p revealed a high level of TBSV replication at a semipermissive temperature, further supporting the idea that Pkc1p is an inhibitor of TBSV RNA replication. A direct inhibitory effect of Pkc1p was shown in a cell-free yeast extract-based TBSV replication assay, in which Pkc1p likely phosphorylates viral replication proteins, decreasing their abilities to bind to the viral RNA. We also show that cercosporamide, a specific inhibitor of Pkc-like kinases, leads to increased TBSV replication in yeast, in plant single cells, and in whole plants, suggesting that Pkc-related pathways are potent inhibitors of TBSV in several hosts.

  19. Exploring factors in the decision to choose sterilization vs alternatives in rural El Salvador.

    Science.gov (United States)

    Cremer, Miriam L; Holland, Erica; Monterroza, Maritza; Duran, Sonia; Singh, Rameet; Terbell, Heather; Edelman, Alison

    2008-01-01

    To explore the factors that influence rural Salvadoran women to undergo tubal sterilization versus opting for alternative methods of family planning. A moderator fluent in English and Spanish conducted eleven 90-minute focus groups consisting of 5-10 women each. Eligible women in the municipality of San Pedro Perulapan, El Salvador, were identified and recruited by local health workers. Participant demographics and information about family planning decisions were collected through detailed notes and tape-recorded sessions. The tapes were transcribed verbatim, and all data were analyzed using grounded theory procedures to identify common themes. Eighty women aged 24-45 years who had previously been sterilized participated in the study. Three major themes influenced a woman's decision to undergo sterilization instead of opting for alternative forms of family planning: (1) availability: tubal sterilization is readily available, (2) fears about side effects of other methods: these women associated negative side effects with other forms of family planning, (3) effectiveness: the women in these focus groups thought sterilization was more effective than other forms of family planning. This study shows that there is a lack of information, and misinformation, about other effective methods of contraception, especially the intrauterine device and oral contraceptives. Reproductive health education projects, especially those providing services in locations similar to rural El Salvador, should focus on providing accurate information about all forms of contraception, including tubal sterilization.

  20. Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages.

    Science.gov (United States)

    Palii, Carmen G; Perez-Iratxeta, Carolina; Yao, Zizhen; Cao, Yi; Dai, Fengtao; Davison, Jerry; Atkins, Harold; Allan, David; Dilworth, F Jeffrey; Gentleman, Robert; Tapscott, Stephen J; Brand, Marjorie

    2011-02-02

    TAL1/SCL is a master regulator of haematopoiesis whose expression promotes opposite outcomes depending on the cell type: differentiation in the erythroid lineage or oncogenesis in the T-cell lineage. Here, we used a combination of ChIP sequencing and gene expression profiling to compare the function of TAL1 in normal erythroid and leukaemic T cells. Analysis of the genome-wide binding properties of TAL1 in these two haematopoietic lineages revealed new insight into the mechanism by which transcription factors select their binding sites in alternate lineages. Our study shows limited overlap in the TAL1-binding profile between the two cell types with an unexpected preference for ETS and RUNX motifs adjacent to E-boxes in the T-cell lineage. Furthermore, we show that TAL1 interacts with RUNX1 and ETS1, and that these transcription factors are critically required for TAL1 binding to genes that modulate T-cell differentiation. Thus, our findings highlight a critical role of the cellular environment in modulating transcription factor binding, and provide insight into the mechanism by which TAL1 inhibits differentiation leading to oncogenesis in the T-cell lineage.

  1. Regulation ofEscherichia coliPathogenesis by Alternative Sigma Factor N.

    Science.gov (United States)

    Riordan, James T; Mitra, Avishek

    2017-06-01

    σ N (also σ 54 ) is an alternative sigma factor subunit of the RNA polymerase complex that regulates the expression of genes from many different ontological groups. It is broadly conserved in the Eubacteria with major roles in nitrogen metabolism, membrane biogenesis, and motility. σ N is encoded as the first gene of a five-gene operon including rpoN (σ N ), ptsN , hpf , rapZ , and npr that has been genetically retained among species of Escherichia , Shigella , and Salmonella . In an increasing number of bacteria, σ N has been implicated in the control of genes essential to pathogenic behavior, including those involved in adherence, secretion, immune subversion, biofilm formation, toxin production, and resistance to both antimicrobials and biological stressors. For most pathogens how this is achieved is unknown. In enterohemorrhagic Escherichia coli (EHEC) O157, Salmonella enterica , and Borrelia burgdorferi , regulation of virulence by σ N requires another alternative sigma factor, σ S , yet the model by which σ N -σ S virulence regulation is predicted to occur is varied in each of these pathogens. In this review, the importance of σ N to bacterial pathogenesis is introduced, and common features of σ N -dependent virulence regulation discussed. Emphasis is placed on the molecular mechanisms underlying σ N virulence regulation in E. coli O157. This includes a review of the structure and function of regulatory pathways connecting σ N to virulence expression, predicted input signals for pathway stimulation, and the role for cognate σ N activators in initiation of gene systems determining pathogenic behavior.

  2. The Interaction of Language-Specific and Universal Factors During the Acquisition of Morphophonemic Alternations With Exceptions.

    Science.gov (United States)

    Baer-Henney, Dinah; Kügler, Frank; van de Vijver, Ruben

    2015-09-01

    Using the artificial language paradigm, we studied the acquisition of morphophonemic alternations with exceptions by 160 German adult learners. We tested the acquisition of two types of alternations in two regularity conditions while additionally varying length of training. In the first alternation, a vowel harmony, backness of the stem vowel determines backness of the suffix. This process is grounded in substance (phonetic motivation), and this universal phonetic factor bolsters learning a generalization. In the second alternation, tenseness of the stem vowel determines backness of the suffix vowel. This process is not based in substance, but it reflects a phonotactic property of German and our participants benefit from this language-specific factor. We found that learners use both cues, while substantive bias surfaces mainly in the most unstable situation. We show that language-specific and universal factors interact in learning. Copyright © 2014 Cognitive Science Society, Inc.

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

    Science.gov (United States)

    Komatsu, Tetsuro; Nagata, Kyosuke

    2012-06-01

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

  4. Functional characterization of Bombyx mori nucleopolyhedrovirus late gene transcription and genome replication factors in the non-permissive insect cell line SF-21

    International Nuclear Information System (INIS)

    Berretta, Marcelo F.; Deshpande, Mandar; Crouch, Erin A.; Passarelli, A. Lorena

    2006-01-01

    We compared the abilities of late gene transcription and DNA replication machineries of the baculoviruses Autographa californica nucleopolyhedrovirus (AcMNPV) and Bombyx mori NPV (BmNPV) in SF-21 cells, an insect-derived cell line permissive for AcMNPV infection. It has been well established that 19 AcMNPV late expression factors (lefs) stimulate substantial levels of late gene promoter activity in SF-21 cells. Thus, we constructed a set of clones containing the BmNPV homologs of the AcMNPV lefs under control of the constitutive Drosophila heat shock 70 protein promoter and tested their ability to activate an AcMNPV late promoter-reporter gene cassette in SF-21 cells. We tested the potential of individual or predicted functional groups of BmNPV lefs to successfully replace the corresponding AcMNPV gene(s) in transient late gene expression assays. We found that most, but not all, BmNPV lefs were able to either fully or partially substitute for the corresponding AcMNPV homolog in the context of the remaining AcMNPV lefs with the exception of BmNPV p143, ie-2, and p35. BmNPV p143 was unable to support late gene expression or be imported into the nucleus of cells in the presence of the AcMNPV or the BmNPV LEF-3, a P143 nuclear shuttling factor. Our results suggest that host-specific factors may affect the function of homologous proteins

  5. Contextual and psychological factors shaping evaluations and acceptability of energy alternatives : Integrated review and research agenda

    NARCIS (Netherlands)

    Perlaviciute, Goda; Steg, Linda

    Sustainable energy transitions will be hampered without sufficient public support. Hence, it is important to understand what drives public acceptability of (sustainable) energy alternatives. Evaluations of specific costs, including risks, and benefits of different energy alternatives have been

  6. Factors affecting the use of complementary and alternative medicine among Japanese university students.

    Science.gov (United States)

    Ujiie, Yasuhiro; Okada, Hiroki

    2015-03-01

    Patients suffering from intractable diseases and individuals seeking relief from mild symptoms resort to treatments outside the modern medical paradigm, such as complementary and alternative medicine (CAM). In order to improve doctor-patient communication about CAM, it is essential to evaluate CAM usage among social groups likely to choose it in the future. Therefore, we aimed to evaluate how university students - individuals highly subject to future CAM usage - perceive CAM and the factors affecting their choice of CAM use. We conducted a questionnaire survey with 1,096 Japanese university students not studying medical subjects. The term CAM was known to 11% of the subjects. Modalities they most associated with CAM were art therapy (353 subjects), hot spring therapy (349), and aromatherapy (345). They had experience taking vitamins, trace elements, other supplements (498), and nutritional drinks (483). Several subjects wanted to experience shiatsu massage (373) and hot spring therapy (303). Multiple regression analysis of the modalities that the subjects wanted to experience revealed a 42% multiple coefficient of determination for prioritizing modalities that the subject associated with CAM, showing a large contribution of this deciding factor. Although most subjects were not familiar with the term CAM, many of them had decided to ingest substances in the CAM category on the basis of self-judgment and without adequate knowledge. Because such behavior can be detrimental to health, medical professionals should be aware of CAM usage among their patients and seek effective communication with them in order to enable safe CAM practice.

  7. The Journal Impact Factor: Moving Toward an Alternative and Combined Scientometric Approach.

    Science.gov (United States)

    Gasparyan, Armen Yuri; Nurmashev, Bekaidar; Yessirkepov, Marlen; Udovik, Elena E; Baryshnikov, Aleksandr A; Kitas, George D

    2017-02-01

    The Journal Impact Factor (JIF) is a single citation metric, which is widely employed for ranking journals and choosing target journals, but is also misused as the proxy of the quality of individual articles and academic achievements of authors. This article analyzes Scopus-based publication activity on the JIF and overviews some of the numerous misuses of the JIF, global initiatives to overcome the 'obsession' with impact factors, and emerging strategies to revise the concept of the scholarly impact. The growing number of articles on the JIF, most of which are in English, reflects interest of experts in journal editing and scientometrics toward its uses, misuses, and options to overcome related problems. Solely displaying values of the JIFs on the journal websites is criticized by experts as these average metrics do not reflect skewness of citation distribution of individual articles. Emerging strategies suggest to complement the JIFs with citation plots and alternative metrics, reflecting uses of individual articles in terms of downloads and distribution of related information through social media and networking platforms. It is also proposed to revise the original formula of the JIF calculation and embrace the concept of the impact and importance of individual articles. The latter is largely dependent on ethical soundness of the journal instructions, proper editing and structuring of articles, efforts to promote related information through social media, and endorsements of professional societies.

  8. Chronic fatigue syndrome and personality: a case-control study using the Alternative Five Factor Model.

    Science.gov (United States)

    Sáez-Francàs, Naia; Valero, Sergi; Calvo, Natalia; Gomà-I-Freixanet, Montserrat; Alegre, José; de Sevilla, Tomás Fernández; Casas, Miquel

    2014-05-30

    Neuroticism is the personality dimension most frequently associated with chronic fatigue syndrome (CFS). Most studies have also shown that CFS patients are less extraverted than non-CFS patients, but results have been inconsistent, possibly because the facets of the extraversion dimension have not been separately analyzed. This study has the following aims: to assess the personality profile of adults with CFS using the Alternative Five-Factor Model (AFFM), which considers Activity and Sociability as two separate factors of Extraversion, and to test the discriminant validity of a measure of the AFFM, the Zuckerman-Kuhlman Personality Questionnaire, in differentiating CFS subjects from normal-range matched controls. The CFS sample consisted of 132 consecutive patients referred for persistent fatigue or pain to the Department of Medicine of a university hospital. These were compared with 132 matched normal population controls. Significantly lower levels of Activity and significantly higher levels of Neuroticism-Anxiety best discriminated CFS patients from controls. The results are consistent with existing data on the relationship between Neuroticism and CFS, and clarify the relationship between Extraversion and CFS by providing new data on the relationship of Activity to CFS. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  9. Improving the Factor Structure of Psychological Scales: The Expanded Format as an Alternative to the Likert Scale Format

    Science.gov (United States)

    Zhang, Xijuan; Savalei, Victoria

    2016-01-01

    Many psychological scales written in the Likert format include reverse worded (RW) items in order to control acquiescence bias. However, studies have shown that RW items often contaminate the factor structure of the scale by creating one or more method factors. The present study examines an alternative scale format, called the Expanded format,…

  10. DNA replication and cancer

    DEFF Research Database (Denmark)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2017-11-03

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

  12. Abiotic Stresses Cause Differential Regulation of Alternative Splice Forms of GATA Transcription Factor in Rice

    Directory of Open Access Journals (Sweden)

    Priyanka Gupta

    2017-11-01

    Full Text Available The GATA gene family is one of the most conserved families of transcription factors, playing a significant role in different aspects of cellular processes, in organisms ranging from fungi to angiosperms. GATA transcription factors are DNA-binding proteins, having a class IV zinc-finger motif CX2CX17−20CX2C followed by a highly basic region and are known to bind a consensus sequence WGATAR. In plants, GATAs are known to be involved in light-dependent gene regulation and nitrate assimilation. However, a comprehensive analysis of these GATA gene members has not yet been highlighted in rice when subjected to environmental stresses. In this study, we present an overview of the GATA gene family in rice (OsGATA in terms of, their chromosomal distribution, domain architecture, and phylogeny. Our study has revealed the presence of 28 genes, encoding 35 putative GATA transcription factors belonging to seven subfamilies in the rice genome. Transcript abundance analysis in contrasting genotypes of rice—IR64 (salt sensitive and Pokkali (salt tolerant, for individual GATA members indicated their differential expression in response to various abiotic stresses such as salinity, drought, and exogenous ABA. One of the members of subfamily VII—OsGATA23a, emerged as a multi-stress responsive transcription factor giving elevated expression levels in response to salinity and drought. ABA also induces expression of OsGATA23a by 35 and 55-folds in IR64 and Pokkali respectively. However, OsGATA23b, an alternative splice variant of OsGATA23 did not respond to above-mentioned stresses. Developmental regulation of the OsGATA genes based on a publicly available microarray database showed distinct expression patterns for most of the GATA members throughout different stages of rice development. Altogether, our results suggest inherent roles of diverse OsGATA factors in abiotic stress signaling and also throw some light on the tight regulation of the spliced variants of

  13. Health, Islam and Alternative Capitalism. Three possible Key Factors in Developing Somaliland

    Directory of Open Access Journals (Sweden)

    Daria Zizzola

    2012-02-01

    Full Text Available The main aim of this paper is to investigate the socio, political and economic dynamics that have occurred in Somaliland in the last decades. Even though this country is still unrecognized by the international community, Somaliland’s economy has undertaken an enduring growth, above all in the private entrepreneurial sector. The author argues that religion has had an important role in the Somali cultural and social identification. According to this assumption, the article analyzes the Islamic factor by showing how it has led to the creation of many alternative connections supported by mutual trust and religious solidarity among involved communities. These connections are somehow fulfilling the absence of political legitimacy while progressively substituting conventional routes of intra-national negotiation, like diplomacy. To confirm this tendency, specific arguments are drawn from Somaliland’s health sector. The health care system is considered a preferential index to evaluate the level of national development. Above all, the private non-profit sector gives some evidence of the Somali capacity of running competitive private businesses while multiplying simultaneously their resources and suppliers with a consequent increase in autonomy and efficiency. This successful compromise bears the fruits of Somali engagement and can be identified by their inexhaustible adaptability to adverse conditions and their ability to avoid, not deny, the rational rules imposed by external actors and their ostensible, insurmountable interests.

  14. Circadian typology, age, and the alternative five-factor personality model in an adult women sample.

    Science.gov (United States)

    Muro, Anna; Gomà-i-Freixanet, Montserrat; Adan, Ana; Cladellas, Ramon

    2011-10-01

    Research on personality and circadian typology indicates evening-type women are more impulsive and novelty seeking, neither types are more anxious, and morning types tend to be more active, conscientious, and persistent. The purpose of this study is to examine the differences between circadian typologies in the light of the Zuckerman's Alternative Five-Factor Model (AFFM) of personality, which has a strong biological basis, in an adult sample of 412 women 18 to 55 yrs of age. The authors found morning-type women had significant higher scores than evening-type and neither-type women on Activity, and its subscales General Activity and Work Activity. In contrast, evening-type women scored significantly higher than morning-type women on Aggression-Hostility, Impulsive Sensation Seeking, and its subscale Sensation Seeking. In all groups, results were independent of age. These findings are in accordance with those previously obtained in female student samples and add new data on the AFFM. The need of using personality models that are biologically based in the study of circadian rhythms is discussed.

  15. IBD5 is a general risk factor for inflammatory bowel disease: replication of association with Crohn disease and identification of a novel association with ulcerative colitis.

    Science.gov (United States)

    Giallourakis, Cosmas; Stoll, Monika; Miller, Katie; Hampe, Jochen; Lander, Eric S; Daly, Mark J; Schreiber, Stefan; Rioux, John D

    2003-07-01

    Inflammatory bowel disease (IBD) refers to complex chronic relapsing autoimmune disorders of the gastrointestinal tract that have been traditionally classified into Crohn disease (CD) and ulcerative colitis (UC). We have previously reported that genetic variation within a 250-kb haplotype (IBD5) in the 5q31 cytokine gene cluster confers susceptibility to CD in a Canadian population. In the current study, we first replicated this association by examining 368 German trios with CD and demonstrating, by transmission/disequilibrium testing (TDT), that the same haplotype is associated with CD (chi2=5.97; P=.007). Our original association study focused on the role of IBD5 in CD; we next explored the potential contribution of this locus to UC susceptibility in 187 German trios. Given the TDT results in the present cohort with UC, IBD5 may also act as a susceptibility locus for UC (chi2=8.10; P=.002). We then examined locus-locus interactions between IBD5 and CARD15, a locus reported elsewhere to confer risk exclusively to CD. Our current results indicate that the two loci act independently to confer risk to CD but that these two loci may behave in an epistatic fashion to promote the development of UC. Moreover, IBD5 was not associated with particular clinical manifestations upon phenotypic stratification in the current cohort with CD. Taken together, our results suggest that IBD5 may act as a general risk factor for IBD, with loci such as CARD15 modifying the clinical characteristics of disease.

  16. Factors Influencing the Integration of Alternative Farm Enterprises into the Agro-Food System

    Science.gov (United States)

    Barlas, Y.; Damianos, D.; Dimara, E.; Kasimis, C.; Skuras, D.

    2001-01-01

    Financial stress and general crisis in European agriculture recently have generated a widespread interest in alternative paths of farm business development and structural adjustment. One of the options suggested by policy makers and adopted by farmers was the development of alternative farm enterprises (AFEs), in which farmers recombine resources…

  17. Regulation of beta cell replication

    DEFF Research Database (Denmark)

    Lee, Ying C; Nielsen, Jens Høiriis

    2008-01-01

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

  18. Defects of mitochondrial DNA replication.

    Science.gov (United States)

    Copeland, William C

    2014-09-01

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

  19. An Improved Phase-Locked-Loop Control with Alternative Damping Factors for VSC Connected to Weak AC System

    Directory of Open Access Journals (Sweden)

    Bin Yuan

    2016-01-01

    Full Text Available The gains of phase-locked-loop (PLL have significant impacts on the power transfer limits for the voltage source converter (VSC connected to weak AC system. Therefore, in this paper, an improved PLL control, respectively, with alternative damping factors for rectifier and inverter is proposed. First, it is proved that the impedance angle of AC system has a great impact on the small-signal stability of the VSC system. With the same variation tendency of Thévenin equivalent resistance, the limits of power transmission are changing in opposite trends for rectifier and inverter. Second, the improved PLL with alternative damping factors is proposed based on the participation factor analysis. Third, the optimal damping factors of the improved PLL control for rectifier and inverter are calculated. Simulations and calculations validated the following three conclusions: (1 in rectifying operation, the equivalent system resistance has a negative impact on the stability of the system and this is not the case for inverting operation; (2 adding the alternative damping factors to PLL control shows similar results compared with changing the impedance angle of AC system; (3 the proposed optimal damping factors of PLL can effectively extend the power transfer limits under both rectifier and inverter modes.

  20. Uncertain Context Factors in ERP Project Estimation are an Asset: Insights from a Semi-Replication Case Study in a Financial Services Firm

    NARCIS (Netherlands)

    Daneva, Maia

    This paper reports on the findings of a case study in a company in the financial services sector in which we replicated the use of a previously published approach to systematically balance the contextual uncertainties in the estimation of Enterprise Resource Planning (ERP) projects. The approach is

  1. Differential Requirement of Human Cytomegalovirus UL112-113 Protein Isoforms for Viral Replication.

    Science.gov (United States)

    Schommartz, Tim; Tang, Jiajia; Brost, Rebekka; Brune, Wolfram

    2017-09-01

    The UL112-113 gene is one of the few alternatively spliced genes of human cytomegalovirus (HCMV). It codes for four phosphoproteins, p34, p43, p50, and p84, all of which are expressed with early kinetics and accumulate at sites of viral DNA replication within the host cell nucleus. Although these proteins are known to play important, possibly essential, roles in the viral replication cycle, little is known about the contribution of individual UL112-113 protein products. Here we used splice site mutagenesis, intron deletion and substitution, and nonsense mutagenesis to prevent the individual expression of each UL112-113 protein isoform and to investigate the importance of each isoform for viral replication. We show that HCMV mutants lacking p34 or p50 expression replicated to high titers in human fibroblasts and endothelial cells, indicating that these proteins are nonessential for viral replication, while mutant viruses carrying a stop mutation within the p84 coding sequence were severely growth impaired. Viral replication could not be detected upon the inactivation of p43 expression, indicating that this UL112-113 protein is essential for viral replication. We also analyzed the ability of UL112-113 proteins to recruit other viral proteins to intranuclear prereplication compartments. While UL112-113 expression was sufficient to recruit the UL44-encoded viral DNA polymerase processivity factor, it was not sufficient for the recruitment of the viral UL84 and UL117 proteins. Remarkably, both the p43 and p84 isoforms were required for the efficient recruitment of pUL44, which is consistent with their critical role in the viral life cycle. IMPORTANCE Human cytomegalovirus requires gene products from 11 genetic loci for the lytic replication of its genome. One of these loci, UL112-113, encodes four proteins with common N termini by alternative splicing. In this study, we inactivated the expression of each of the four UL112-113 proteins individually and determined their

  2. 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.

  3. Prevalence and factors associated with the use of alternative (folk) medicine practitioners in 8 countries of the former Soviet Union.

    Science.gov (United States)

    Stickley, Andrew; Koyanagi, Ai; Richardson, Erica; Roberts, Bayard; Balabanova, Dina; McKee, Martin

    2013-04-11

    Research suggests that since the collapse of the Soviet Union there has been a sharp growth in the use of complementary and alternative medicine (CAM) in some former Soviet countries. However, as yet, comparatively little is known about the use of CAM in the countries throughout this region. Against this background, the aim of the current study was to determine the prevalence of using alternative (folk) medicine practitioners in eight countries of the former Soviet Union (fSU) and to examine factors associated with their use. Data were obtained from the Living Conditions, Lifestyles and Health (LLH) survey undertaken in eight former Soviet countries (Armenia, Belarus, Georgia, Kazakhstan, Kyrgyzstan, Moldova, Russia and Ukraine) in 2001. In this nationally representative cross-sectional survey, 18428 respondents were asked about how they treated 10 symptoms, with options including the use of alternative (folk) medicine practitioners. Multivariate logistic regression analysis was used to determine the factors associated with the treatment of differing symptoms by such practitioners in these countries. The prevalence of using an alternative (folk) medicine practitioner for symptom treatment varied widely between countries, ranging from 3.5% in Armenia to 25.0% in Kyrgyzstan. For nearly every symptom, respondents living in rural locations were more likely to use an alternative (folk) medicine practitioner than urban residents. Greater wealth was also associated with using these practitioners, while distrust of doctors played a role in the treatment of some symptoms. The widespread use of alternative (folk) medicine practitioners in some fSU countries and the growth of this form of health care provision in the post-Soviet period in conditions of variable licensing and regulation, highlights the urgent need for more research on this phenomenon and its potential effects on population health in the countries in this region.

  4. Structural and Functional Insights into the DNA Replication Factor Cdc45 Reveal an Evolutionary Relationship to the DHH Family of Phosphoesterases*

    Science.gov (United States)

    Krastanova, Ivet; Sannino, Vincenzo; Amenitsch, Heinz; Gileadi, Opher; Pisani, Francesca M.; Onesti, Silvia

    2012-01-01

    Cdc45 is an essential protein conserved in all eukaryotes and is involved both in the initiation of DNA replication and the progression of the replication fork. With GINS, Cdc45 is an essential cofactor of the Mcm2–7 replicative helicase complex. Despite its importance, no detailed information is available on either the structure or the biochemistry of the protein. Intriguingly, whereas homologues of both GINS and Mcm proteins have been described in Archaea, no counterpart for Cdc45 is known. Herein we report a bioinformatic analysis that shows a weak but significant relationship among eukaryotic Cdc45 proteins and a large family of phosphoesterases that has been described as the DHH family, including inorganic pyrophosphatases and RecJ ssDNA exonucleases. These enzymes catalyze the hydrolysis of phosphodiester bonds via a mechanism involving two Mn2+ ions. Only a subset of the amino acids that coordinates Mn2+ is conserved in Cdc45. We report biochemical and structural data on the recombinant human Cdc45 protein, consistent with the proposed DHH family affiliation. Like the RecJ exonucleases, the human Cdc45 protein is able to bind single-stranded, but not double-stranded DNA. Small angle x-ray scattering data are consistent with a model compatible with the crystallographic structure of the RecJ/DHH family members. PMID:22147708

  5. Predicting Language Outcomes for Children Learning Augmentative and Alternative Communication: Child and Environmental Factors

    Science.gov (United States)

    Brady, Nancy C.; Thiemann-Bourque, Kathy; Fleming, Kandace; Matthews, Kris

    2013-01-01

    Purpose: To investigate a model of language development for nonverbal preschool-age children learning to communicate with augmentative or alternative communication. Method: Ninety-three preschool children with intellectual disabilities were assessed at Time 1, and 82 of these children were assessed 1 year later, at Time 2. The outcome variable was…

  6. Alternative Break Programs and the Factors that Contribute to Changes in Students' Lives

    Science.gov (United States)

    Niehaus, Elizabeth Kathleen

    2012-01-01

    The purpose of this study was to explore the extent to and ways in which student participants in Alternative Break (AB) programs report that their AB experience influenced their intentions or plans to volunteer, engage in advocacy, or study or travel abroad, or their major or career plans. Additional analysis explored the specific program…

  7. Sociocognitive Factors and Perceived Consequences Associated with Alternative Forms of Alcohol Use

    Science.gov (United States)

    Braitman, Abby L.; Linden-Carmichael, Ashley N.; Stamates, Amy L.; Lau-Barraco, Cathy

    2017-01-01

    Objective: Popular media have highly publicized alternative forms of alcohol use (e.g., eyeballing, inhaling alcohol vapor) among college students as a growing concern, possibly associated with severe health risks. Formative research indicates rarity of use. Participants and Methods: College students (Study 1: n = 411; Study 2: n = 687) completed…

  8. Enhanced understanding of energy ratepayers: Factors influencing perceptions of government energy efficiency subsidies and utility alternative energy use

    International Nuclear Information System (INIS)

    Craig, Christopher A.; Allen, Myria W.

    2014-01-01

    This study explores factors related to energy consumers' perceptions of government subsidies for utility provided energy efficiency (EE) programs and for utility providers' use of more clean/alternative energy sources. Demographic factors, attitudes, planned purchases, and perceptions of utility provider motives in relation to governmental and utility provider EE initiatives (i.e. providing discounts and coupons for CFL bulbs), plus the influence of gain- and loss-framed messages are investigated. Over 2000 respondents completed a 16 item phone survey. Hierarchical regression explained 38% of the variance in reactions regarding government subsidies of the cost of utility provided EE programs and 43% of the variance in perceptions involving whether utility companies should use of more clean or alternative forms of energy. Gender and party differences emerged. Loss-framed messages were more important when the issue was government subsidies. Both gain- and loss-framed messages were important when clean/alternative energy was the issue. - Highlights: • Over 2000 ratepayers were surveyed on their attitudes, planned behaviors and perceptions towards energy efficiency programs. • Almost 40% of how ratepayers feel about government subsidies and utility use of clean/alternative energy was explained. • Loss-framed messages were more effective when the dependent variable was ratepayer perception of government subsidies

  9. Adenovirus DNA Replication

    Science.gov (United States)

    Hoeben, Rob C.; Uil, Taco G.

    2013-01-01

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

  10. Testing the Level of Alternative Institutions as a Slowdown Factor of Economic Development: the Case of Montenegro

    Directory of Open Access Journals (Sweden)

    Mimo Draškovic

    2017-05-01

    Full Text Available The purpose of the article is to test public's perception of the opportunistic behavior and alternative institutions existence and the degree of their influences on reproduction of the economic crisis. For that purpose, besides the theoretical considerations, the paper comprises quantitative analysis of affecting the inability of economic development, and reproduction of crisis, by the following factors: (a non-market enrichment and log-rolling structures, (b parties’ monopolies and lobbyism, and (c systemic corruption. Multiple regression linear approach is applied on a sample of 300 selected respondents in five towns in Montenegro: Podgorica, Niksic, Cetinje, Herceg Novi, and Kotor. On the basis of the conducted statistical examines: standard error of the regression estimate, correlation coefficient, and coefficient of determination are calculated on the basis of previously determined regression coefficients and forecast values of the linear function of free variables (factors: a, b, and c. The regression plots for each of the considered cases, which verify the starting hypothesis, are shown along with the discussion and conclusions. Our results indicate the need to reduce and eliminate effects of the above factors in the society and economy, since they represent concrete manifestations of alternative institutions’ negative impacts. The main conclusion of the research is that the authorities in Montenegro should identify all of the channels through which alternative institutions do affect the reduction of social and economic choices. In this sense, it is proposed overcoming the monistic neoliberal policies, along with affirmation of institutional pluralism.

  11. A potent complement factor C3 specific nanobody inhibiting multiple functions in the alternative pathway of human and murine complement.

    Science.gov (United States)

    Jensen, Rasmus K; Pihl, Rasmus; Gadeberg, Trine A F; Jensen, Jan K; Andersen, Kasper R; Thiel, Steffen; Laursen, Nick S; Andersen, Gregers Rom

    2018-03-01

    The complement system is a complex, carefully regulated proteolytic cascade for which suppression of aberrant activation is of increasing clinical relevance and inhibition of the complement alternative pathway is a subject of intense research. Here, we describe the nanobody hC3Nb1 that binds to multiple functional states of C3 with sub-nanomolar affinity. The nanobody causes a complete shutdown of alternative pathway activity in human and murine serum when present in concentrations comparable to C3, and hC3Nb1 is shown to prevent both proconvertase assembly as well as binding of the C3 substrate to C3 convertases. Our crystal structure of the C3b-hC3Nb1 complex and functional experiments demonstrate that proconvertase formation is blocked by steric hindrance between the nanobody and an Asn-linked glycan on complement factor B. In addition, hC3Nb1 is shown to prevent factor H binding to C3b rationalizing its inhibition of factor I activity. Our results identify hC3Nb1 as a versatile, inexpensive, and powerful inhibitor of the alternative pathway in both human and murine in vitro model systems of complement activation. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Factors Affecting the Development of Rural Tourism as Alternative Tourism and Its Impact

    OpenAIRE

    ÇEKEN, Hüseyin; DALGIN, Taner; ÇAKIR, Neşe

    2012-01-01

    New tourism trends in the world are developing in the direction of history, health, trekking, cultural and rural tourism depending on the demand. The importance of rural tourism is increasing day by day both in developed and developing countries as being alternative to or complimentary to existing tourism types. There is a great effort in the world to reinforce economies of rural areas by using touristic supply sources for rural tourism purposes. The achievements in the rural tourism applicat...

  13. DETERMINING FACTORS AND INDICATORS FOR ALTERNATIVE MODEL OF NATIONAL SOYBEAN PRODUCTION ENHANCEMENT

    Directory of Open Access Journals (Sweden)

    NELLY B.

    2017-02-01

    Full Text Available This research surveys, interviews and Questionnaire were conducted by relevant agencies. Data was analyzed by calculating the cumulative frequency distribution and the average value (Mean to 5 Likert scale, Validation, reliability, Pattern Model and Hypothesis were analyzed by SPSS 17 software for Windows. Validity model and the Measurement Model were examined by using Smart software PLS. The results show that the mean was 3.98 for Product Cost Appropriate and Stable Factor, 4.39 for High Productivity Factor, 4.36 for Enough Capital Factor, 3.73 for Character Farmers Factor, 4.28 for Information Access Factor, and 4.44 for High Production Factor. The data were valid and reliable. The relationship between the factors and indicators show strong correlation with an average of 0.96 with model pattern Quadratic and Cubic. Test Goodness of Fit model was fit. Hypothesis test results with five independent variables and one dependent variables were significant, excepted Character Farmers Factor and Information Access Factor were not significant to High Production Factor. Model was able to explain the phenomenon of high production by 91.7%, while the rest (8.3% was explained by other variables not included in the model under studied. Enhancement production of national soybean would be affected dominantly by sufficient capital (97%.

  14. Rescue from replication stress during mitosis.

    Science.gov (United States)

    Fragkos, Michalis; Naim, Valeria

    2017-04-03

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

  15. Stress-Stimulated Mitogen-Activated Protein Kinases Control the Stability and Activity of the Cdt1 DNA Replication Licensing Factor

    Science.gov (United States)

    Chandrasekaran, Srikripa; Tan, Ting Xu; Hall, Jonathan R.; Cook, Jeanette Gowen

    2011-01-01

    DNA replication is tightly coordinated both with cell cycle cues and with responses to extracellular signals to maintain genome stability. We discovered that human Cdt1, an essential origin licensing protein whose activity must be restricted to G1 phase, is a substrate of the stress-activated mitogen-activated protein (MAP) kinases p38 and c-Jun N-terminal kinase (JNK). These MAP kinases phosphorylate Cdt1 both during unperturbed G2 phase and during an acute stress response. Phosphorylation renders Cdt1 resistant to ubiquitin-mediated degradation during S phase and after DNA damage by blocking Cdt1 binding to the Cul4 adaptor, Cdt2. Mutations that block normal cell cycle-regulated MAP kinase-mediated phosphorylation interfere with rapid Cdt1 reaccumulation at the end of S phase. Phosphomimetic mutations recapitulate the stabilizing effects of Cdt1 phosphorylation but also reduce the ability of Cdt1 to support origin licensing. Two other CRL4Cdt2 targets, the cyclin-dependent kinase (CDK) inhibitor p21 and the methyltransferase PR-Set7/Set8, are similarly stabilized by MAP kinase activity. These findings support a model in which MAP kinase activity in G2 promotes reaccumulation of a low-activity Cdt1 isoform after replication is complete. PMID:21930785

  16. What factors are influencing preferences toward conventional versus complementary and alternative medical clinic advertisements?

    Science.gov (United States)

    Shin, Hye-Won; Chang, Dong-Seon; Lee, Hyangsook; Kang, O-Seok; Lee, Hyejung; Park, Hi-Joon; Chae, Younbyoung

    2011-10-01

    The present study aimed to determine whether health service advertisements are perceived differently depending on advertising conventional or complementary and alternative medicine clinics. A total of 42 adults (male=21, female=21) recruited through advertisements in Seoul, South Korea participated in this study. A standardized health service advertisement was designed with three controlled visual components such as (1) medical treatment information, (2) medical practitioner, and (3) medical facilities and it was shown to subjects while their eye movements were tracked and they were asked to rate their preferences for the different advertisements and their separate components. A multiple regression analysis was performed to see the correlation of the preferences for each of the three visual components with the overall preference rating of each health service advertisement. Preferences for the advertisement depended mostly on the preference for the medical treatment information, whereas advertisements for complementary and alternative medical clinics depended also on the preference for the medical practitioner. These results imply that the same health service advertisement will be perceived differently depending on whether it advertises Western or Oriental medical clinics.

  17. Resveratrol, by modulating RNA processing factor levels, can influence the alternative splicing of pre-mRNAs.

    Directory of Open Access Journals (Sweden)

    M Andrea Markus

    Full Text Available Alternative pre-mRNA splicing defects can contribute to, or result from, various diseases, including cancer. Aberrant mRNAs, splicing factors and other RNA processing factors have therefore become targets for new therapeutic interventions. Here we report that the natural polyphenol resveratrol can modulate alternative splicing in a target-specific manner. We transfected minigenes of several alternatively spliceable primary mRNAs into HEK293 cells in the presence or absence of 1, 5, 20 and 50 µM resveratrol and measured exon levels by semi-quantitative PCR after separation by agarose gel electrophoresis. We found that 20 µg/ml and 50 µg/ml of resveratrol affected exon inclusion of SRp20 and SMN2 pre-mRNAs, but not CD44v5 or tau pre-mRNAs. By Western blotting and immunofluorescence we showed that this effect may be due to the ability of resveratrol to change the protein level but not the localization of several RNA processing factors. The processing factors that increased significantly were ASF/SF2, hnRNPA1 and HuR, but resveratrol did not change the levels of RBM4, PTBP1 and U2AF35. By means of siRNA-mediated knockdown we depleted cells of SIRT1, regarded as a major target of resveratrol, and showed that the effect on splicing was not dependent on SIRT1. Our results suggest that resveratrol might be an attractive small molecule to treat diseases in which aberrant splicing has been implicated, and justify more extensive research on the effects of resveratrol on the splicing machinery.

  18. Two Different Replication Factor C Proteins, Ctf18 and RFC1, Separately Control PCNA-CRL4Cdt2-Mediated Cdt1 Proteolysis during S Phase and following UV Irradiation

    Science.gov (United States)

    Shiomi, Yasushi; Hayashi, Akiyo; Ishii, Takashi; Shinmyozu, Kaori; Nakayama, Jun-ichi; Sugasawa, Kaoru

    2012-01-01

    Recent work identified the E3 ubiquitin ligase CRL4Cdt2 as mediating the timely degradation of Cdt1 during DNA replication and following DNA damage. In both cases, proliferating cell nuclear antigen (PCNA) loaded on chromatin mediates the CRL4Cdt2-dependent proteolysis of Cdt1. Here, we demonstrate that while replication factor C subunit 1 (RFC1)-RFC is required for Cdt1 degradation after UV irradiation during the nucleotide excision repair process, another RFC complex, Ctf18-RFC, which is known to be involved in the establishment of cohesion, has a key role in Cdt1 degradation in S phase. Cdt1 segments having only the degron, a specific sequence element in target protein for ubiquitination, for CRL4Cdt2 were stabilized during S phase in Ctf18-depleted cells. Additionally, endogenous Cdt1 was stabilized when both Skp2 and Ctf18 were depleted. Since a substantial amount of PCNA was detected on chromatin in Ctf18-depleted cells, Ctf18 is required in addition to loaded PCNA for Cdt1 degradation in S phase. Our data suggest that Ctf18 is involved in recruiting CRL4Cdt2 to PCNA foci during S phase. Ctf18-mediated Cdt1 proteolysis occurs independent of cohesion establishment, and depletion of Ctf18 potentiates rereplication. Our findings indicate that individual RFC complexes differentially control CRL4Cdt2-dependent proteolysis of Cdt1 during DNA replication and repair. PMID:22493068

  19. An alternative approach for ζ-factor measurement using pure element nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Zanaga, Daniele; Altantzis, Thomas; Sanctorum, Jonathan [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Freitag, Bert [FEI Company, Building AAE, Achtseweg Noord 5, Eindhoven (Netherlands); Bals, Sara, E-mail: sara.bals@uantwerpen.be [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium)

    2016-05-15

    It is very challenging to measure the chemical composition of hetero nanostructures in a reliable and quantitative manner. Here, we propose a novel and straightforward approach that can be used to quantify energy dispersive X-ray spectra acquired in a transmission electron microscope. Our method is based on a combination of electron tomography and the so-called ζ-factor technique. We will demonstrate the reliability of our approach as well as its applicability by investigating Au-Ag and Au-Pt hetero nanostructures. Given its simplicity, we expect that the method could become a new standard in the field of chemical characterization using electron microscopy. - Highlights: • A new method to determine ζ-factors for EDXS quantification is proposed. • Pure element nanoparticles are used as standards in the determination of ζ-factors. • Electron tomography is used to measure volumes in determining the ζ-factors.

  20. Animal Mitochondrial DNA Replication

    Science.gov (United States)

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

    2016-01-01

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

  1. An alternative factorization of the quantum harmonic oscillator and two-parameter family of self-adjoint operators

    Energy Technology Data Exchange (ETDEWEB)

    Arcos-Olalla, Rafael, E-mail: olalla@fisica.ugto.mx [Departamento de Física, DCI Campus León, Universidad de Guanajuato, Apdo. Postal E143, 37150 León, Gto. (Mexico); Reyes, Marco A., E-mail: marco@fisica.ugto.mx [Departamento de Física, DCI Campus León, Universidad de Guanajuato, Apdo. Postal E143, 37150 León, Gto. (Mexico); Rosu, Haret C., E-mail: hcr@ipicyt.edu.mx [IPICYT, Instituto Potosino de Investigacion Cientifica y Tecnologica, Apdo. Postal 3-74 Tangamanga, 78231 San Luis Potosí, S.L.P. (Mexico)

    2012-10-01

    We introduce an alternative factorization of the Hamiltonian of the quantum harmonic oscillator which leads to a two-parameter self-adjoint operator from which the standard harmonic oscillator, the one-parameter oscillators introduced by Mielnik, and the Hermite operator are obtained in certain limits of the parameters. In addition, a single Bernoulli-type parameter factorization, which is different from the one introduced by M.A. Reyes, H.C. Rosu, and M.R. Gutiérrez [Phys. Lett. A 375 (2011) 2145], is briefly discussed in the final part of this work. -- Highlights: ► Factorizations with operators which are not mutually adjoint are presented. ► New two-parameter and one-parameter self-adjoint oscillator operators are introduced. ► Their eigenfunctions are two- and one-parameter deformed Hermite functions.

  2. Gas as a growth factor for the emerging economies: Natural gas resources Worldwide. Gas: alternative fuels

    International Nuclear Information System (INIS)

    Lecarpentier, Armelle

    2015-01-01

    All the qualities of gas - available, affordable, efficient, acceptable and reliable - make this energy a cornerstone both for the development of emerging countries and for new economic activities. Another advantage is that gas is available everywhere in a gaseous and/or liquid form, according to the particular infrastructure (gas pipeline, gas tankers). Moreover, gas can be consumed in different sectors - residential, commercial or industrial - and for different uses - electricity generation or clean fuel for transportation. A first part of this paper presents the natural gas resources Worldwide (Cedigaz data) while a second part reviews the development around the world of the use of gas - liquefied petroleum gas (LPG) and natural gas - as alternative fuels

  3. Evolution of transcriptional networks in yeast: alternative teams of transcriptional factors for different species

    Directory of Open Access Journals (Sweden)

    Adriana Muñoz

    2016-11-01

    Full Text Available Abstract Background The diversity in eukaryotic life reflects a diversity in regulatory pathways. Nocedal and Johnson argue that the rewiring of gene regulatory networks is a major force for the diversity of life, that changes in regulation can create new species. Results We have created a method (based on our new “ping-pong algorithm for detecting more complicated rewirings, where several transcription factors can substitute for one or more transcription factors in the regulation of a family of co-regulated genes. An example is illustrative. A rewiring has been reported by Hogues et al. that RAP1 in Saccharomyces cerevisiae substitutes for TBF1/CBF1 in Candida albicans for ribosomal RP genes. There one transcription factor substitutes for another on some collection of genes. Such a substitution is referred to as a “rewiring”. We agree with this finding of rewiring as far as it goes but the situation is more complicated. Many transcription factors can regulate a gene and our algorithm finds that in this example a “team” (or collection of three transcription factors including RAP1 substitutes for TBF1 for 19 genes. The switch occurs for a branch of the phylogenetic tree containing 10 species (including Saccharomyces cerevisiae, while the remaining 13 species (Candida albicans are regulated by TBF1. Conclusions To gain insight into more general evolutionary mechanisms, we have created a mathematical algorithm that finds such general switching events and we prove that it converges. Of course any such computational discovery should be validated in the biological tests. For each branch of the phylogenetic tree and each gene module, our algorithm finds a sub-group of co-regulated genes and a team of transcription factors that substitutes for another team of transcription factors. In most cases the signal will be small but in some cases we find a strong signal of switching. We report our findings for 23 Ascomycota fungi species.

  4. Psychology, replication & beyond.

    Science.gov (United States)

    Laws, Keith R

    2016-06-01

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

  5. Registered Replication Report

    DEFF Research Database (Denmark)

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

    2017-01-01

    In an anonymous 4-person economic game, participants contributed more money to a common project (i.e., cooperated) when required to decide quickly than when forced to delay their decision (Rand, Greene & Nowak, 2012), a pattern consistent with the social heuristics hypothesis proposed by Rand...... and colleagues. The results of studies using time pressure have been mixed, with some replication attempts observing similar patterns (e.g., Rand et al., 2014) and others observing null effects (e.g., Tinghög et al., 2013; Verkoeijen & Bouwmeester, 2014). This Registered Replication Report (RRR) assessed...... the size and variability of the effect of time pressure on cooperative decisions by combining 21 separate, preregistered replications of the critical conditions from Study 7 of the original article (Rand et al., 2012). The primary planned analysis used data from all participants who were randomly assigned...

  6. Space station crew safety alternatives study. Volume 3: Safety impact of human factors

    Science.gov (United States)

    Rockoff, L. A.; Raasch, R. F.; Peercy, R. L., Jr.

    1985-01-01

    The first 15 years of accumulated space station concepts for Initial Operational Capability (IOC) during the early 1990's was considered. Twenty-five threats to the space station are identified and selected threats addressed as impacting safety criteria, escape and rescue, and human factors safety concerns. Of the 25 threats identified, eight are discussed including strategy options for threat control: fire, biological or toxic contamination, injury/illness, explosion, loss of pressurization, radiation, meteoroid penetration and debris. Of particular interest here is volume three (of five volumes) pertaining to the safety impact of human factors.

  7. Replication, refinement & reachability

    DEFF Research Database (Denmark)

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

    2018-01-01

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

  8. An Improved Phase-Locked-Loop Control with Alternative Damping Factors for VSC Connected to Weak AC System

    OpenAIRE

    Yuan, Bin; Xu, Jianzhong; Zhao, Chengyong; Yuan, Yijia

    2016-01-01

    The gains of phase-locked-loop (PLL) have significant impacts on the power transfer limits for the voltage source converter (VSC) connected to weak AC system. Therefore, in this paper, an improved PLL control, respectively, with alternative damping factors for rectifier and inverter is proposed. First, it is proved that the impedance angle of AC system has a great impact on the small-signal stability of the VSC system. With the same variation tendency of Thévenin equivalent resistance, the li...

  9. Alternate Solution to Generalized Bernoulli Equations via an Integrating Factor: An Exact Differential Equation Approach

    Science.gov (United States)

    Tisdell, C. C.

    2017-01-01

    Solution methods to exact differential equations via integrating factors have a rich history dating back to Euler (1740) and the ideas enjoy applications to thermodynamics and electromagnetism. Recently, Azevedo and Valentino presented an analysis of the generalized Bernoulli equation, constructing a general solution by linearizing the problem…

  10. Loneliness and solitude in adolescence: A confirmatory factor analysis of alternative models

    DEFF Research Database (Denmark)

    Goossens, Luc; Lasgaard, Mathias; Luyckx, Koen

    2009-01-01

    The present study tested a four-factor model of adolescent loneliness and solitude that comprises peer-related loneliness, family loneliness, negative attitude toward solitude, and positive attitude toward solitude. Nine different instruments for a total of 14 scales and derivative subscales were...

  11. Mutations in Complement Factor H Impair Alternative Pathway Regulation on Mouse Glomerular Endothelial Cells in Vitro

    NARCIS (Netherlands)

    Loeven, M.A.; Rops, A.; Lehtinen, M.J.; Kuppevelt, T.H. van; Daha, M.R.; Smith, R.J.; Bakker, M.A.H.; Berden, J.H.; Rabelink, T.J.; Jokiranta, T.S.; Vlag, J. van der

    2016-01-01

    Complement factor H (FH) inhibits complement activation and interacts with glomerular endothelium via its complement control protein domains 19 and 20, which also recognize heparan sulfate (HS). Abnormalities in FH are associated with the renal diseases atypical hemolytic uremic syndrome and dense

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

    Science.gov (United States)

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

    2018-03-01

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

  13. Fast Alternating LS Algorithms for High Order CANDECOMP/PARAFAC Tensor Factorizations

    Czech Academy of Sciences Publication Activity Database

    Phan, A. H.; Tichavský, Petr; Cichocki, A.

    2013-01-01

    Roč. 61, č. 19 (2013), s. 4834-4846 ISSN 1053-587X R&D Projects: GA ČR GA102/09/1278 Institutional support: RVO:67985556 Keywords : Canonical polyadic decomposition * tensor decomposition Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 3.198, year: 2013 http://library.utia.cas.cz/separaty/2013/SI/tichavsky-0396774.pdf

  14. An alternative approach for addressing the failure probability-safety factor method with sensitivity analysis

    International Nuclear Information System (INIS)

    Castillo, Enrique; Conejo, Antonio J.; Minguez, Roberto; Castillo, Carmen

    2003-01-01

    The paper introduces a method for solving the failure probability-safety factor problem for designing engineering works proposed by Castillo et al. that optimizes an objective function subject to the standard geometric and code constraints, and two more sets of constraints that simultaneously guarantee given safety factors and failure probability bounds associated with a given set of failure modes. The method uses the dual variables and is especially convenient to perform a sensitivity analysis, because sensitivities of the objective function and the reliability indices can be obtained with respect to all data values. To this end, the optimization problems are transformed into other equivalent ones, in which the data parameters are converted into artificial variables, and locked to their actual values. In this way, some variables of the associated dual problems become the desired sensitivities. In addition, using the proposed methodology, calibration of codes based on partial safety factors can be done. The method is illustrated by its application to the design of a simple rubble mound breakwater and a bridge crane

  15. 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...

  16. Factors contributing to the use of complementary and alternative medicine in rural older women with chronic pain in South Korea.

    Science.gov (United States)

    Yoon, Saunjoo L; Kim, Jeong-Hee

    2013-11-01

    The aim of this study was to assess the prevalence of complementary and alternative medicines (CAM) use for managing pain and to investigate the factors predictive of current CAM use among rural older women in South Korea. Access to medical care among older adults in rural areas is poorer than in urban areas. A cross-sectional descriptive study with a stratified sample of 139 women aged over 65 with chronic pain residing in rural areas of Jeju Island, South Korea. A self-reported questionnaire was used to collect data. Most subjects reported using at least one type of CAM for relieving pain within the past 12 months. Almost half of them reported currently using CAM. Herbs were the most commonly used CAM. Only 'severity of pain' was presently associated with an increased use of CAM. It is imperative to take socio-geographic-cultural factors into consideration when planning health promotion programs and caring for clients. © 2013.

  17. The crucial role of the micro caregiving environment: Factors associated with attachment styles in alternative care in Chile.

    Science.gov (United States)

    Garcia Quiroga, Manuela; Hamilton-Giachritsis, Catherine

    2017-08-01

    The distribution of attachment styles has been shown to differ between groups of children living with their parents and children placed in alternative care (AC), defined as residential or foster. However, this is the first study in Latin America to explore possible factors affecting the quality of attachment in children living in both residential and foster care. Two groups of children (N=57) were compared: one group living in Residential Homes (RC) and the other in Foster Care (FC) in Chile. Children's, caregivers' and structural factors (e.g., child: caregiver ratios) and their links with attachment styles were investigated. The micro caregiving environment (i.e., the specific individual child caregiver relationship), especially the caregivers' engagement, sensitivity, disciplinary control and affection, as well as some structural factors (i.e., child: caregiver ratios), were linked to attachment security in children. Specifically, better emotional caregiving and lower child-caregiver ratios were associated with higher rates of secure attachment. The association between quality of care (as measured by the HOME inventory) and attachment styles seems to be influenced by caregiver relationships (as measured by CCSERSS). Caregiver relationship factors (i.e., affection, engagement and sensitivity) directly impact the quality of the attachment children establish with them while living in AC. However, the relationships that caregivers establish with children under their care can be facilitated by good quality structural factors, particularly child-caregiver ratios. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Expression analysis of an evolutionarily conserved alternative splicing factor, Sfrs10, in age-related macular degeneration.

    Directory of Open Access Journals (Sweden)

    Devi Krishna Priya Karunakaran

    Full Text Available Age-related macular degeneration (AMD is the most common cause of blindness in the elderly population. Hypoxic stress created in the micro-environment of the photoreceptors is thought to be the underlying cause that results in the pathophysiology of AMD. However, association of AMD with alternative splicing mediated gene regulation is not well explored. Alternative Splicing is one of the primary mechanisms in humans by which fewer protein coding genes are able to generate a vast proteome. Here, we investigated the expression of a known stress response gene and an alternative splicing factor called Serine-Arginine rich splicing factor 10 (Sfrs10. Sfrs10 is a member of the serine-arginine (SR rich protein family and is 100% identical at the amino acid level in most mammals. Immunoblot analysis on retinal extracts from mouse, rat, and chicken showed a single immunoreactive band. Further, immunohistochemistry on adult mouse, rat and chicken retinae showed pan-retinal expression. However, SFRS10 was not detected in normal human retina but was observed as distinct nuclear speckles in AMD retinae. This is in agreement with previous reports that show Sfrs10 to be a stress response gene, which is upregulated under hypoxia. The difference in the expression of Sfrs10 between humans and lower mammals and the upregulation of SFRS10 in AMD is further reflected in the divergence of the promoter sequence between these species. Finally, SFRS10+ speckles were independent of the SC35+ SR protein speckles or the HSF1+ stress granules. In all, our data suggests that SFRS10 is upregulated and forms distinct stress-induced speckles and might be involved in AS of stress response genes in AMD.

  19. A potent complement factor C3 specific nanobody inhibiting multiple functions in the alternative pathway of human and murine complement

    DEFF Research Database (Denmark)

    Jensen, Rasmus K; Pihl, Rasmus; Gadeberg, Trine A F

    2018-01-01

    The complement system is a complex, carefully regulated proteolytic cascade for which suppression of aberrant activation is of increasing clinical relevance and inhibition of the complement alternative pathway is a subject of intense research. Here, we describe the nanobody hC3Nb1 that binds...... to multiple functional states of C3 with sub-nanomolar affinity. The nanobody causes a complete shutdown of alternative pathway activity in human and murine serum when present in concentrations comparable to C3, and hC3Nb1 is shown to prevent both proconvertase assembly as well as binding of the C3 substrate...... to C3 convertases. Our crystal structure of the C3b-hC3Nb1 complex and functional experiments demonstrate that proconvertase formation is blocked by steric hindrance between the nanobody and an Asn-linked glycan on complement factor B. In addition, hC3Nb1 is shown to prevent factor H binding to C3b...

  20. The replication of expansive production knowledge

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  1. Janez Rugelj's alternative therapeutic community after the five-factor model of personality

    Directory of Open Access Journals (Sweden)

    Judita Bagon

    2000-12-01

    Full Text Available The Alternative Therapeutic Community (ATC of Dr. J. Rugelj is a specific social community consisting of people in distress (always consisting of about 120 people, who have all been handicapped in their lives in one way or another. The group is also specific because of their way towards recovery, i.e., intensively reactivating the mecanisms of healthy life to surmount their psychical and social deficiency. The results of measuring the structure of personality according to BFQ – the "Big Five" model of personality – show that the ATC as a whole achieves lower scores than the normal population on all dimensions and subdimensions. The difference is statistically significant regarding the dimension of Emotional stability as well as the subdimension Emotional control. The ATC is not a uniform group, so the results differ according to the diagnosis. The members with the diagnosis of 'a neurotic' or 'a psychotic' achieve below-average results, while the accompanying members achieve similar results as the control group (selected from the non-members of the ATC. The results of the members diagnosed as 'an alcoholic' are somewhat surprising – they do not differ considerably on any dimension or subdimension from the results achieved by the control group – not even on the Emotional stability scale. As regards the total period of staying in the program, the results of subdimensions remain mostly unchanged. However, during the time spent in the program the results on the subdimensions change: the group which has been in the program for 1 to 2 years generally scores higher than the group of beginners (the difference is statistically significant only for the dimension Emotional control, but the results of the group participating in the program for longer time (more than three years are lower again, until they stabilize in the central position (T=50. The results on theHonesty scale (which may also show positive or negative self-image show no

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

    Science.gov (United States)

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

    2013-04-01

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

  3. 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.

  4. Gene-specific factors determine mitotic expression and bookmarking via alternate regulatory elements.

    Science.gov (United States)

    Arampatzi, Panagiota; Gialitakis, Manolis; Makatounakis, Takis; Papamatheakis, Joseph

    2013-02-01

    Transcriptional silencing during mitosis is caused by inactivation of critical transcriptional regulators and/or chromatin condensation. Inheritance of gene expression patterns through cell division involves various bookmarking mechanisms. In this report, we have examined the mitotic and post-mitotic expression of the DRA major histocompatibility class II (MHCII) gene in different cell types. During mitosis the constitutively MHCII-expressing B lymphoblastoid cells showed sustained occupancy of the proximal promoter by the cognate enhanceosome and general transcription factors. In contrast, although mitotic epithelial cells were depleted of these proteins irrespectively of their MHCII transcriptional activity, a distal enhancer selectively recruited the PP2A phosphatase via NFY and maintained chromatin accessibility. Based on our data, we propose a novel chromatin anti-condensation role for this element in mitotic bookmarking and timing of post-mitotic transcriptional reactivation.

  5. Sound absorption coefficient in situ: an alternative for estimating soil loss factors.

    Science.gov (United States)

    Freire, Rosane; Meletti de Abreu, Marco Henrique; Okada, Rafael Yuri; Soares, Paulo Fernando; GranhenTavares, Célia Regina

    2015-01-01

    The relationship between the sound absorption coefficient and factors of the Universal Soil Loss Equation (USLE) was determined in a section of the Maringá Stream basin, Paraná State, by using erosion plots. In the field, four erosion plots were built on a reduced scale, with dimensions of 2.0×12.5m. With respect to plot coverage, one was kept with bare soil and the others contained forage grass (Brachiaria), corn and wheat crops, respectively. Planting was performed without any type of conservation practice in an area with a 9% slope. A sedimentation tank was placed at the end of each plot to collect the material transported. For the acoustic system, pink noise was used in the measurement of the proposed monitoring, for collecting information on incident and reflected sound pressure levels. In general, obtained values of soil loss confirmed that 94.3% of material exported to the basin water came from the bare soil plot, 2.8% from the corn plot, 1.8% from the wheat plot, and 1.1% from the forage grass plot. With respect to the acoustic monitoring, results indicated that at 16kHz erosion plot coverage type had a significant influence on the sound absorption coefficient. High correlation coefficients were found in estimations of the A and C factors of the USLE, confirming that the acoustic technique is feasible for the determination of soil loss directly in the field. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    Ramachandran, Srinivas; Ahmad, Kami; Henikoff, Steven

    2017-04-01

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

  7. An alternative approach for evaluating the phenotypic virulence factors of pathogenic Escherichia coli

    Directory of Open Access Journals (Sweden)

    Kamelia M. Osman

    2018-02-01

    Full Text Available Escherichia coli is a recognized zoonotic food-borne pathogen; however, the use of polymerase chain reaction (PCR in the underdeveloped countries to differentiate pathogenic from non-pathogenic E. coli is a problematic issue. Our grail was to assess the phenotypic virulence markers motility, hemolysin, congo red agar, embryo lethality assay and serum resistance for pathogenic E. coli (PEC correlated to PCR tests which is currently used world-wide to evaluate the PEC. The 448 strains of Escherichia coli that were isolated from different sources, were characterized for phenotypic virulence factors such as motility, hemolysin, Congo red binding, Embryo Lethality assay (ELA and serum resistance, as well as antibiotic susceptibility using disc diffusion method to 23 antibiotics. Results exhibited 100% motility and Congo red binding, 97.1% for hemolysin production and 90.2% in the ELA. As a result, we were able to hypothetically conclude that the aforementioned virulence markers are plain, straightforward, economical, rapid, more dynamic, uncomplicated methodology, duplicatable and cost next to nothing when compared to the molecular PCR. Their implementation in a diagnostic microbiology laboratory for vetting is a rewarding task in the underdeveloped countries. It augments endeavors to minimize the use of PCR in our investigations especially during epidemiological and outbreak investigations of PEC.

  8. Heritability of dimensions of Eysenck's pen model and the alternative five-factor model of personality

    Directory of Open Access Journals (Sweden)

    Smederevac Snežana

    2006-01-01

    Full Text Available The main aim of this study is to estimate the heritability of AFFM and PEN dimensions, including 67 pairs of twins (34 monozygotic and 33 dizygotic of both genders, aged 18 - 44. The heritability has been estimated by the biometric method, two full (ACE and ADE and three reduced (AE, DE and CE models tested for each personality trait. Taking into consideration the AFFM dimensions, additive genetic factors and a non-shared environment contribute the most significantly to the phenotypic variation of activity, sociability and the impulsive sensation seeking; anxiety and aggressiveness are best accounted for by the dominant genetic effects. In the PEN domain, fit indicators suggest that ACE and the reduced AE models provide the best explanation for the phenotypic manifestations of neuroticism, while ACE and CE models account for the variation of L scale. Although the fit indicators calculated for extraversion and psychotic behavior are somewhat problematic, the parameter estimates show that extraversion is best accounted for by the additive genetic variance, shared environmental effects, and the non-shared environment, whereas psychotic behavior is the most adequately explained by both shared and non-shared environmental effects.

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

    Directory of Open Access Journals (Sweden)

    Andy W. K. Yeung

    2017-09-01

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

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

    Science.gov (United States)

    Yeung, Andy W. K.

    2017-01-01

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

  11. Capturing the DSM-5 Alternative Personality Disorder Model Traits in the Five-Factor Model's Nomological Net.

    Science.gov (United States)

    Suzuki, Takakuni; Griffin, Sarah A; Samuel, Douglas B

    2017-04-01

    Several studies have shown structural and statistical similarities between the Diagnostic and Statistical Manual of Mental Disorders (5th ed.; DSM-5) alternative personality disorder model and the Five-Factor Model (FFM). However, no study to date has evaluated the nomological network similarities between the two models. The relations of the Revised NEO Personality Inventory (NEO PI-R) and the Personality Inventory for DSM-5 (PID-5) with relevant criterion variables were examined in a sample of 336 undergraduate students (M age  = 19.4; 59.8% female). The resulting profiles for each instrument were statistically compared for similarity. Four of the five domains of the two models have highly similar nomological networks, with the exception being FFM Openness to Experience and PID-5 Psychoticism. Further probing of that pair suggested that the NEO PI-R domain scores obscured meaningful similarity between PID-5 Psychoticism and specific aspects and lower-order facets of Openness. The results support the notion that the DSM-5 alternative personality disorder model trait domains represent variants of the FFM domains. Similarities of Openness and Psychoticism domains were supported when the lower-order aspects and facets of Openness domain were considered. The findings support the view that the DSM-5 trait model represents an instantiation of the FFM. © 2015 Wiley Periodicals, Inc.

  12. The effect of regular walking and alternate day fasting on health-related factors in overweight and obese females

    Directory of Open Access Journals (Sweden)

    Roya Seighali

    2017-03-01

    Full Text Available Introduction: Obesity is a complex health problem. The aim of this study was to determine the effects of regular walking with alternate day fasting (ADF on health-related factors of overweight and obese females.‎  Methods: 30 healthy inactive, overweight and obese women were divided randomly into three equal groups.  The groups were: control group (BMI: 30.72±4.40 kg/m2; the experimental group I: ADF along with regular walking with 50% to 65% maximal heart rate (BMI: 28.69 ±2.81 kg/m2 and the experimental group II: ADF (BMI: 30.56 ±3.66 kg/m2. Participants were under the diet for six weeks. The diet ADF means that, they had days of fasting and free day (with regular walking, alternately. Two days before and two days after the end of the study, the participants’ fasting blood sugar were measured after 12 hours. Resting heart rate, blood pressure and body composition were assessed in the same day. The collected data were analyzed using paired t-test and ANOVA test. Results: Body mass index in both experimental groups had significant decrease‎ (P

  13. The Use of Twitter by the Trauma and Orthopaedic Surgery Journals: Twitter Activity, Impact Factor, and Alternative Metrics.

    Science.gov (United States)

    Hughes, Hannah; Hughes, Andrew; Murphy, Colin

    2017-12-10

    Aim Social media (SoMe) platforms have become leading methods of communication and dissemination of scientific information in the medical community. They allow for immediate discussion and widespread engagement around important topics. It has been hypothesized that the activity on Twitter positively correlates with highly cited articles. The purpose of this study was to analyze the prevalence and activity of Trauma and Orthopaedic Surgery journals on Twitter, with the hypothesis that the impact factor is positively associated with the Twitter usage. Methods The top 50 Trauma and Orthopaedic Surgery journals, ranked by 2016 Impact Factor were analyzed. The Twitter profiles of each journal or affiliated society were identified. Other SoMe platforms used were also recorded. The Twitonomy software (Digonomy Pty Ltd, New South Wales, Australia) was used to analyze the Twitter profiles over a one-year period. The Twitter Klout scores were recorded for each journal to approximate the SoMe influence. The Altmetric scores (the total number of mentions via alternative metrics) were also recorded. The statistical analysis was carried out to identify correlations between journal Impact Factors, SoMe activity, Twitter Klout scores and Altmetric scores.  Results Twenty-two journals (44%) were dedicated to the Twitter profiles. Fourteen journals (28%) were associated with societies that had profiles and 14 journals (28%) had no Twitter presence. The mean Impact Factor overall was 2.16 +/- 0.14 (range, 1.07-5.16). The journals with dedicated Twitter profiles had higher Impact Factors than those without (mean 2.41 vs. 1.61; P=0.005). A greater number of Twitter followers were associated with higher Impact Factors (R2 0.317, P=0.03). The journals with higher Twitter Klout scores had higher Impact Factors (R2 0.357, P=0.016). The Altmetric score was positively associated with an Impact Factor (R2 0.310, P=0.015). The journals with higher numbers of retweets (virtual citations in

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

    Science.gov (United States)

    Branzei, Dana; Szakal, Barnabas

    2017-08-01

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

  15. Personality profile of binge drinking in university students is modulated by sex. A study using the Alternative Five Factor Model.

    Science.gov (United States)

    Adan, Ana; Navarro, José Francisco; Forero, Diego A

    2016-08-01

    The prevalence of binge drinking (BD), found especially among young people, is increasing worldwide and has become an important social and health concern. We studied, for the first time, the personality profile, using the Alternative Five Factor Model, among university students with BD and healthy controls, taking into account the possible influence of sex. 70 participants with BD (30 men) and 70 healthy controls (30 men) were included, selected to control for characteristics that are known to be related to BD (physical and mental disorders, consumption of other drugs, circadian rhythms), completed the Zuckerman-Kuhlman Personality Questionnaire (ZKPQ). The scores on Neuroticism-Anxiety and Impulsive Sensation-Seeking were higher in the BD group compared to the controls (pAnxiety are due to higher scores in the women's group (p=0.014), while those in Impulsive Sensation-Seeking are due to higher scores in the men's group (p=0.009), both in the Impulsivity and in the Sensation-Seeking subscales (p<0.045). Sex could be a factor that modulates the endophenotype of drug dependence (impulsive and anxious personality) and the prevention and/or treatment programs for BD should include not only the management of the personality risk factors but also different tailored approaches according to sex. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  16. Identifying sub-categories of social fears using an alternative factor analytic structure of the Social Phobia and Anxiety Inventory.

    Science.gov (United States)

    Panayiotou, Georgia; Michaelides, Michalis P; Theodorou, Marios; Neophytou, Klavdia

    2017-05-01

    This study evaluates an alternative factor structure of the Social Phobia and Anxiety Inventory (Turner et al., 1989), a widely used measure of social anxiety. Existing models ignore variance due to the different social contexts where social fears are expressed. Taking a different approach to scoring than previous studies, this investigation proposes a new model, which, in addition to 4-5 symptom dimensions, is able to capture the situations (strangers, authority figures, members of the opposite sex and people in general) that are of concern to the examinee. To test this model, all 96 items of the Social Phobia scale, rather than the average of the sub-items of its 23 questions were subjected to confirmatory factor analysis. The model shows good fit and is superior to models ignoring the "situation" factors, which show good predictive validity in respect to real life demographics. Utilization of all single questions of the SPAI can capture a wider range of social fears related to social anxiety than using the average of the items, which has implications for the understanding and clinical assessment of social anxiety. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

  17. Situational and psychosocial factors mediating coordinated joint attention with augmentative and alternative communication systems with beginning communicators without disabilities.

    Science.gov (United States)

    Benigno, Joann P; Bennett, Jamie L; McCarthy, John W; Smith, Julia L

    2011-06-01

    This study examined how infants' age, joint attention (JA) skills, caregiver ratings of language and temperament, and caregiver JA style related to JA in a structured literacy task with an augmentative and alternative communication (AAC) system. Sixteen infants (mean = 10.6 months) without disabilities participated in two storybook reading interactions with an experimenter in two conditions where the AAC system was either aligned or divided from the experimenter's eye gaze. Individual differences in JA skills, caregiver JA style, and temperament were associated with coordinated JA across both conditions. The findings suggest it is important to examine both extrinsic and intrinsic factors, which may not only reduce attention demands but also mediate the success of JA interactions with AAC systems.

  18. Down-Regulation of the Alternative Sigma Factor SigJ Confers a Photoprotective Phenotype to Anabaena PCC 7120.

    Science.gov (United States)

    Srivastava, Amit; Brilisauer, Klaus; Rai, Ashutosh K; Ballal, Anand; Forchhammer, Karl; Tripathi, Anil K

    2017-02-01

    Alternative sigma factors belonging to Group 3 are thought to play an important role in the adaptation of cyanobacteria to environmental challenges by altering expression of genes needed for coping with such stresses. In this study, the role of an alternative sigma factor, SigJ, was analyzed in the filamentous nitrogen-fixing cyanobacterium, Anabaena sp. PCC 7120 by knocking down the expression of the sigJ gene (alr0277) employing an antisense RNA-mediated approach. In the absence of any stress, the knock-down (KD0277) or the wild-type strain both grew similarly. Upon exposure to high-intensity light, KD0277 showed substantially reduced bleaching of its pigments, higher photosynthetic activity and consequently better survival than the wild type. KD0277 also showed an enhanced accumulation of two carotenoids, which were identified as myxoxanthophyll and keto-myxoxanthophyll. Further, KD0277 was more tolerant to ammonium-triggered photodamage than the wild type. Moreover, PSII was better protected against photodamage in KD0277 than in the wild type. Down-regulation of sigJ in Anabaena PCC 7120, however, reduced its ability to cope with desiccation. This study demonstrates that down-regulation of the sigJ gene in Anabaena PCC 7120 differentially affects its ability to tolerate two environmentally relevant stresses, i.e. high-intensity light and desiccation. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

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

    Science.gov (United States)

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

    2013-02-01

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

  20. High-Resolution Mapping and Dynamics of the Transcriptome, Transcription Factors, and Transcription Co-Factor Networks in Classically and Alternatively Activated Macrophages

    Directory of Open Access Journals (Sweden)

    Amitabh Das

    2018-01-01

    Full Text Available Macrophages are the prime innate immune cells of the inflammatory response, and the combination of multiple signaling inputs derived from the recognition of host factors [e.g., interferon-g (IFN-γ] and invading pathogen products (e.g., toll-like receptors (TLRs agonists are required to maintain essential macrophage function. The profound effects on biological outcomes of inflammation associated with IFN-γ pretreatment (“priming” and TLR4 ligand bacterial lipopolysaccharide (LPS-induced macrophage activation (M1 or classical activation have long been recognized, but the underlying mechanisms are not well defined. Therefore, we analyzed gene expression profiles of macrophages and identified genes, transcription factors (TFs, and transcription co-factors (TcoFs that are uniquely or highly expressed in IFN-γ-mediated TLR4 ligand LPS-inducible versus only TLR4 ligand LPS-inducible primary macrophages. This macrophage gene expression has not been observed in macrophage cell lines. We also showed that interleukin (IL-4 and IL-13 (M2 or alternative activation elicited the induction of a distinct subset of genes related to M2 macrophage polarization. Importantly, this macrophage gene expression was also associated with promoter conservation. In particular, our approach revealed novel roles for the TFs and TcoFs in response to inflammation. We believe that the systematic approach presented herein is an important framework to better understand the transcriptional machinery of different macrophage subtypes.

  1. Carotenoid Biosynthetic Pathways Are Regulated by a Network of Multiple Cascades of Alternative Sigma Factors in Azospirillum brasilense Sp7.

    Science.gov (United States)

    Rai, Ashutosh Kumar; Dubey, Ashutosh Prakash; Kumar, Santosh; Dutta, Debashis; Mishra, Mukti Nath; Singh, Bhupendra Narain; Tripathi, Anil Kumar

    2016-11-01

    Carotenoids constitute an important component of the defense system against photooxidative stress in bacteria. In Azospirillum brasilense Sp7, a nonphotosynthetic rhizobacterium, carotenoid synthesis is controlled by a pair of extracytoplasmic function sigma factors (RpoEs) and their cognate zinc-binding anti-sigma factors (ChrRs). Its genome harbors two copies of the gene encoding geranylgeranyl pyrophosphate synthase (CrtE), the first critical step in the carotenoid biosynthetic pathway in bacteria. Inactivation of each of two crtE paralogs found in A. brasilense caused reduction in carotenoid content, suggesting their involvement in carotenoid synthesis. However, the effect of crtE1 deletion was more pronounced than that of crtE2 deletion. Out of the five paralogs of rpoH in A. brasilense, overexpression of rpoH1 and rpoH2 enhanced carotenoid synthesis. Promoters of crtE2 and rpoH2 were found to be dependent on RpoH2 and RpoE1, respectively. Using a two-plasmid system in Escherichia coli, we have shown that the crtE2 gene of A. brasilense Sp7 is regulated by two cascades of sigma factors: one consisting of RpoE1and RpoH2 and the other consisting of RpoE2 and RpoH1. In addition, expression of crtE1 was upregulated indirectly by RpoE1 and RpoE2. This study shows, for the first time in any carotenoid-producing bacterium, that the regulation of carotenoid biosynthetic pathway involves a network of multiple cascades of alternative sigma factors. Carotenoids play a very important role in coping with photooxidative stress in prokaryotes and eukaryotes. Although extracytoplasmic function (ECF) sigma factors are known to directly regulate the expression of carotenoid biosynthetic genes in bacteria, regulation of carotenoid biosynthesis by one or multiple cascades of sigma factors had not been reported. This study provides the first evidence of the involvement of multiple cascades of sigma factors in the regulation of carotenoid synthesis in any bacterium by showing the

  2. A Nonnegative Latent Factor Model for Large-Scale Sparse Matrices in Recommender Systems via Alternating Direction Method.

    Science.gov (United States)

    Luo, Xin; Zhou, MengChu; Li, Shuai; You, Zhuhong; Xia, Yunni; Zhu, Qingsheng

    2016-03-01

    Nonnegative matrix factorization (NMF)-based models possess fine representativeness of a target matrix, which is critically important in collaborative filtering (CF)-based recommender systems. However, current NMF-based CF recommenders suffer from the problem of high computational and storage complexity, as well as slow convergence rate, which prevents them from industrial usage in context of big data. To address these issues, this paper proposes an alternating direction method (ADM)-based nonnegative latent factor (ANLF) model. The main idea is to implement the ADM-based optimization with regard to each single feature, to obtain high convergence rate as well as low complexity. Both computational and storage costs of ANLF are linear with the size of given data in the target matrix, which ensures high efficiency when dealing with extremely sparse matrices usually seen in CF problems. As demonstrated by the experiments on large, real data sets, ANLF also ensures fast convergence and high prediction accuracy, as well as the maintenance of nonnegativity constraints. Moreover, it is simple and easy to implement for real applications of learning systems.

  3. Factors Affecting Recruitment and Attrition in Randomised Controlled Trials of Complementary and Alternative Medicine for Pregnancy-Related Issues.

    Science.gov (United States)

    Close, Ciara; Sinclair, Marlene; McCullough, Julie E M; Liddle, Sarah Dianne; Hughes, Ciara M

    2016-01-01

    Background . Randomised controlled trials (RCTs) investigating Complementary and Alternative Medicine (CAM) for pregnancy-related issues have encountered issues with recruitment and attrition. Little is known about the cause of these issues. Methods . Data was gathered from an antenatal CAM randomised controlled trial. During foetal anomaly appointments, women meeting inclusion criteria were invited to participate in the trial. Numbers of women invited and eligible were recorded. Reasons for noninterest were noted and analysed. Focus groups exploring trial experience of participants were also conducted. Findings . Of the 428 women invited to participate, 376 were eligible and just under a quarter participated. Reasons for nonparticipation included concerns about CAM and lack of interest in participation in research. Other factors negatively affecting recruitment included recruitment timing, competition for participants, limited support from staff, and inadequate trial promotion. Factors encouraging recruitment included being interested in research and seeking pain relief. Reasons for dropping out were time constraints, travel issues, work commitments, and pregnancy issues. Several women in the sham and usual care group dropped out due to dissatisfaction with treatment allocation. Conclusion . CAM researchers must explore problems encountered with recruitment and attrition so that evidence-based implementation strategies to address the issues can be developed.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  5. Impairment of mature B-cell maintenance upon combined deletion of the alternative NF-?B transcription factors RELB and NF-?B2 in B cells$

    OpenAIRE

    De Silva, Nilushi S.; Silva, Kathryn; Anderson, Michael M.; Bhagat, Govind; Klein, Ulf

    2016-01-01

    B-cell activating factor (BAFF) is critical for the survival and maturation of mature B-cells. BAFF, via the BAFF receptor (BAFFR), activates multiple signaling pathways in B-cells, including the alternative nuclear factor-?B (NF-?B) pathway. The transcription factors RELB and NF-?B2 (p100/p52) are the downstream mediators of the alternative pathway; however, the B-cell-intrinsic functions of these NF-?B subunits have not been studied in vivo using conditional alleles, either individually or ...

  6. 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

  7. DNA replication origins in archaea

    Directory of Open Access Journals (Sweden)

    Zhenfang eWu

    2014-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Alexandra M. Gehring

    2017-10-01

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

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

    Science.gov (United States)

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

    2017-01-05

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

  10. 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.

  11. Deber (de + infinitive: a case of free variation in Spanish? Conditional factors in a phenomenon of syntactical alternation

    Directory of Open Access Journals (Sweden)

    José Luis Blas Arroyo

    2011-06-01

    Full Text Available The present study analyzes the results of variationist research on the alternation between deber and deber de + infinitive; it is based on samples of oral speech contained in the Macrocorpus sociolingüistico de Castellón y sus comarcas [Sociolinguistic macro-corpus of Castellón and surrounding districts]. The study confirms the findings of other research projects by revealing that an advanced stage has been reached in the replacement of the variant deber de by the periphrasis without a preposition (deber in the Spanish-speaking world, although data from speech communities in the Castellón region show the persistence of the former usage in certain linguistic contexts. Such uses do not reflect the prescriptions of academic norms by revealing a functional opposition between the epistemic and deontic modalities, but they do show the importance of other factors relating to modalization. These include, on the one hand, emphasis and the degree of spontaneity of interactions; and on the other, attenuation and orational modality. These sets of factors condition the use of periphrasis with a preposition in opposing ways. Whereas the first set – especially emphasis – are associated with the presence of such a variant, the second act as a serious stimulus against it. Of the other factors selected by multivariate analysis it is possible to distinguish between a number of groups, in accordance with the differences observed. Among those which show the greatest number of such differences, some are revealed in an apparently anarchical fashion (the number of syllables in the verbal complex or in the opposite manner to what might have been expected (the phono-syntactical context. Others show a high level of interaction or dependence with diverse factors, and cannot therefore be demonstrated to have explicative relevance in themselves (grammatical person, degree of animacy. Other factors display more consistent differences which cannot, however, be

  12. 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.

  13. The alternative five-factor model of personality, nicotine dependence and relapse after treatment for smoking cessation.

    Science.gov (United States)

    Nieva, Gemma; Valero, Sergi; Bruguera, Eugeni; Andión, Óscar; Trasovares, M Victoria; Gual, Antoni; Casas, Miquel

    2011-10-01

    Personality is one of several factors that have been related to the initiation, maintenance and cessation of smoking. This paper aims to analyze the relationship between the alternative five-factor model of personality (AFFM), nicotine dependence (ND), nicotine use (NU) and cessation after twelve months of a cognitive-behavioral therapy combined with medication. In this prospective study, a sample of 103 smokers who were taking part in a workplace smoking cessation intervention, answered the Zuckerman-Kuhlman Personality Questionnaire. ND and NU were measured with the Fagerström Test for the Nicotine Dependence (FTND) and the number of cigarettes smoked per day (CPD), respectively. Tobacco cessation was self-reported at twelve months follow-up and biologically confirmed. Results varied according to gender. In men, low scores on Sociability predicted high ND and large number of CPD. In addition, low scores on Sensation Seeking and high scores on Impulsivity predicted also a high smoking rate at baseline. No personality traits were found to explain ND in women, but high Impulsivity-Sensation Seeking and General Activity predicted high CPD. Predictors of cessation also differed by gender. Apart from FTND level, high levels on Impulsivity predicted relapse in males. In women, high levels on Sociability predicted relapse. This model correctly classified two thirds of abstainers and relapsers for men and three fourths for women at 12months. Furthermore an interaction between personality and gender was observed. The AFFM appears to have a substantial power for predicting cessation. Personality assessment when beginning treatment for smoking cessation could allow incorporating strategies to improve outcomes. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. Analysis of factors that affect the potential of star fruit (Averhoa Bilimbi) and cactus (Gymnocalycium Hossei) extracts as alternative battery

    Science.gov (United States)

    Rahmawati, Sitti; Agnesstacia

    2014-03-01

    This research analyzes the factors that affect the work of the battery from the star fruit extract and the cactus extract. The value voltage and current generated are measure the work of the battery. Voltage measurement based on the electrode distance function, and electrode surface area. Voltage as a surface area electrode function and electrode distance function determined the current density and the voltage generated. From the experimental results obtained that the battery voltage is large enough, it is about 1.8 V for the extract of star fruit, and 1.7 V for the extract of cactus, which means that the juice extract from star fruit and the juice extract of cactus can become an alternative as battery replacement. The measurements with different electrode surface area on the star fruit and cactus extract which has the depth of the electrode 0.5 cm to 4 cm causes a decrease in the electric current generated from 12.5 mA to 1.0 mA, but obtained the same voltage.

  15. An alternative to the search for single polymorphisms: toward molecular personality scales for the five-factor model.

    Science.gov (United States)

    McCrae, Robert R; Scally, Matthew; Terracciano, Antonio; Abecasis, Gonçalo R; Costa, Paul T

    2010-12-01

    There is growing evidence that personality traits are affected by many genes, all of which have very small effects. As an alternative to the largely unsuccessful search for individual polymorphisms associated with personality traits, the authors identified large sets of potentially related single nucleotide polymorphisms (SNPs) and summed them to form molecular personality scales (MPSs) with from 4 to 2,497 SNPs. Scales were derived from two thirds of a large (N = 3,972) sample of individuals from Sardinia who completed the Revised NEO Personality Inventory (P. T. Costa, Jr., & R. R. McCrae, 1992) and were assessed in a genomewide association scan. When MPSs were correlated with the phenotype in the remaining one third of the sample, very small but significant associations were found for 4 of the 5e personality factors when the longest scales were examined. These data suggest that MPSs for Neuroticism, Openness to Experience, Agreeableness, and Conscientiousness (but not Extraversion) contain genetic information that can be refined in future studies, and the procedures described here should be applicable to other quantitative traits. PsycINFO Database Record (c) 2010 APA, all rights reserved.

  16. Lymph node size as a simple prognostic factor in node negative colon cancer and an alternative thesis to stage migration.

    Science.gov (United States)

    Märkl, Bruno; Schaller, Tina; Kokot, Yuriy; Endhardt, Katharina; Kretsinger, Hallie; Hirschbühl, Klaus; Aumann, Georg; Schenkirsch, Gerhard

    2016-10-01

    Stage migration is an accepted explanation for the association between lymph node (LN) yield and outcome in colon cancer. To investigate whether the alternative thesis of immune response is more likely, we performed a retrospective study. We enrolled 239 cases of node negative cancers, which were categorized according to the number of LNs with diameters larger than 5 mm (LN5) into the groups LN5-very low (0 to 1 LN5), LN5-low (2 to 5 LN5), and LN5-high (≥6 LN5). Significant differences were found in pT3/4 cancers with median survival times of 40, 57, and 71 months (P = .022) in the LN5-very low, LN5-low, and LN5-high groups, respectively. Multivariable analysis revealed that LN5 number and infiltration type were independent prognostic factors. LN size is prognostic in node negative colon cancer. The correct explanation for outcome differences associated with LN harvest is probably the activation status of LNs. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Religious factors of social modernization/alternative modernization of orthodoxy in the context of M.Weber’s theory

    Directory of Open Access Journals (Sweden)

    Y. Y. Medviedieva

    2016-09-01

    Full Text Available The article deals with the definition of religious factors modernization / alternative modernization Orthodoxy in the context of the theory of Max Weber, as well as defining features of the relationship between the state and the Orthodox Church in the context of the relations of domination Weber types of rationality and social action. The author in the context of the use of the conceptual apparatus of the theory of Max Weber concluded that the result of clashes and compromises between the religious ethic of ascetic and mystical mood of monasticism with the apparatus of state violence became associated with the position of religion in relation to the «world» practice of social escapism. Christianity, according to the researcher, provides the legitimacy of traditional authority, which uses a charismatic, as the Orthodox Church confirms its divine origin, even in the absence of policy charismatic qualities, due to which there is a profanation of charisma. Therefore, all politicians, from the time of the Byzantine Empire in the communist and today’s post-communist politicians, not only did not go to the elimination of the Church as a political force and as the ideology of the center, and converted the church into one of the feudal corporations and obedient ally in the implementation of political security functions in relation to society and increase the prestige of the regime and the state as a whole.

  18. Alternative Sigma Factor HrpL of Pectobacterium carotovorum 35 is Important for the Development of Soft-rot Symptoms

    Directory of Open Access Journals (Sweden)

    Hyo-Song Nam

    2011-08-01

    Full Text Available A bacterial artificial chromosome library of Pectobacterium carotovorum 35 was constructed to characterize the genome and to sequence its hrp region. The hrp cluster of P. carotovorum 35 consisted of 26 open reading frames in five operons. A promoter-based green fluorescent protein technology was used to identify the genes regulated by the alternative sigma factor, HrpL, in P. carotovorum 35. The majority of the selected clones contained the hrpJ operon promoter sequence, which harbors a hrp box, but no putative hrp boxes were detected within the promoter sequences of two other hrpL-regulated genes encoding for pectate lyase and large repetitive protein. Although the promoters of five other hrp operons also contained hrp boxes, their expression was not HrpL-dependent in the promoter-based selection in E. coli. However, transcriptional analysis showed that expression from all operons harboring hrp boxes, except for the hrpN operon, was reduced significantly in the hrpL mutant. The severity of soft-rot symptoms when the hrpL mutant was applied to the surface of tobacco leaves, mimicking natural infection, was greatly attenuated. These results indicate that the hrpL gene of P. carotovorum 35 may be involved in the development of soft-rot symptoms.

  19. DATABASE REPLICATION IN HETEROGENOUS PLATFORM

    OpenAIRE

    Hendro Nindito; Evaristus Didik Madyatmadja; Albert Verasius Dian Sano

    2014-01-01

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

  20. Reasons, perceived efficacy, and factors associated with complementary and alternative medicine use among Malaysian patients with HIV/AIDS.

    Science.gov (United States)

    Hasan, Syed Shahzad; See, Choon Keong; Choong, Christopher Lee Kwok; Ahmed, Syed Imran; Ahmadi, Keivan; Anwar, Mudassir

    2010-11-01

    The primary objective of this study was to evaluate the pattern of use, reasons for use, and perceived effect of complementary and alternative medicine (CAM), accompanied by identification and comparison of the factors that are potentially associated with CAM use. This cross-sectional study was carried out in 325 randomly sampled patients with human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS), at HIV/AIDS referral clinics in the Hospital Sungai Buloh, Malaysia. Simple random sampling was used, where randomization was done using patients' medical record numbers. Semistructured face-to-face interviews were conducted using 38 questions pertaining to type, pattern, perceived efficacy, adverse effects, and influential factors associated with CAM use. In addition, CD4 count and viral load readings were recorded. Of 325 randomly sampled patients with HIV/AIDS, 254 of them were using some forms of CAM, resulting in a utilization rate of 78.2%. Vitamins and supplements (52.6%), herbal products (33.8%), and massage (16.6%) were the top three most frequently used CAM modalities. Sociodemographic factors including education level (p = 0.021, r(s) = 0.148), monthly income (p = 0.001, r(s) = 0.260), and family history of CAM use (p = 0.001, r(s) = 0.231) were significantly associated and positively correlated with CAM use. However, the majority of these patients (68%) did not disclose CAM use to health care professionals. About half of those who rated their health as good or very good perceived it as a result of CAM use. This study confirmed the range of 30%-100% CAM use among individuals infected with HIV/AIDS. Although, on the one hand some types of CAM reduced viral load and enhanced the immune system, on the other hand some forms of CAM produced a detrimental effect on the virological suppression, opening this platform to more research and investigation in order to optimize the use of CAM among patients with HIV/AIDS.

  1. Negative Regulation of Interferon-β Production by Alternative Splicing of Tumor Necrosis Factor Receptor-Associated Factor 3 in Ducks

    Directory of Open Access Journals (Sweden)

    Xiaoqin Wei

    2018-03-01

    Full Text Available Tumor necrosis factor receptor-associated factor 3 (TRAF3, an intracellular signal transducer, is identified as an important component of Toll-like receptors and RIG-I-like receptors induced type I interferon (IFN signaling pathways. Previous studies have clarified TRAF3 function in mammals, but little is known about the role of TRAF3 in ducks. Here, we cloned and characterized the full-length duck TRAF3 (duTRAF3 gene and an alternatively spliced isoform of duTRAF3 (duTRAF3-S lacking the fragment encoding amino acids 217–319, from duck embryo fibroblasts (DEFs. We found that duTRAF3 and duTRAF3-S played different roles in regulating IFN-β production in DEFs. duTRAF3 through its TRAF domain interacted with duMAVS or duTRIF, leading to the production of IFN-β. However, duTRAF3-S, containing the TRAF domain, was unable to bind duMAVS or duTRIF due to the intramolecular binding between the N- and C-terminal of duTRAF3-S that blocked the function of its TRAF domain. Further analysis identified that duTRAF3-S competed with duTRAF3 itself for binding to duTRAF3, perturbing duTRAF3 self-association, which impaired the assembly of duTRAF3-duMAVS/duTRIF complex, ultimately resulted in a reduced production of IFN-β. These findings suggest that duTRAF3 is an important regulator of duck innate immune signaling and reveal a novel mechanism for the negative regulation of IFN-β production via changing the formation of the homo-oligomerization of wild molecules, implying a novel regulatory role of truncated proteins.

  2. Analysis of replication profiles reveals key role of RFC-Ctf18 in yeast replication stress response.

    Science.gov (United States)

    Crabbé, Laure; Thomas, Aubin; Pantesco, Véronique; De Vos, John; Pasero, Philippe; Lengronne, Armelle

    2010-11-01

    Maintenance of genome integrity relies on surveillance mechanisms that detect and signal arrested replication forks. Although evidence from budding yeast indicates that the DNA replication checkpoint (DRC) is primarily activated by single-stranded DNA (ssDNA), studies in higher eukaryotes have implicated primer ends in this process. To identify factors that signal primed ssDNA in Saccharomyces cerevisiae, we have screened a collection of checkpoint mutants for their ability to activate the DRC, using the repression of late origins as readout for checkpoint activity. This quantitative analysis reveals that neither RFC(Rad24) and the 9-1-1 clamp nor the alternative clamp loader RFC(Elg1) is required to signal paused forks. In contrast, we found that RFC(Ctf18) is essential for the Mrc1-dependent activation of Rad53 and for the maintenance of paused forks. These data identify RFC(Ctf18) as a key DRC mediator, potentially bridging Mrc1 and primed ssDNA to signal paused forks.

  3. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

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

  4. An Exploratory Study of the Factors That Influence Enrolling in Alternative Educational Options: Adult Perceptions and Implications for Policy and Practice

    Science.gov (United States)

    Kocsis-McNerney, Violet

    2013-01-01

    This research obtained information using focus groups as qualitative method to determine the factors that influenced alternative education decisions. The purpose of this study was to help bridge theory, research, and educational practices and examine policy reform efforts. Through the lenses of returning adult education students, this research…

  5. Replication of bacteriophage lambda DNA

    International Nuclear Information System (INIS)

    Tsurimoto, T.; Matsubara, K.

    1983-01-01

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

  6. LHCb experience with LFC replication

    CERN Document Server

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

    2008-01-01

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

  7. 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.

  8. Novel forms of Paired-like homeodomain transcription factor 2 (PITX2): Generation by alternative translation initiation and mRNA splicing

    OpenAIRE

    Bernard Daniel J; Hjalt Tord A; Lamba Pankaj

    2008-01-01

    Abstract Background Members of the Paired-like homeodomain transcription factor (PITX) gene family, particularly PITX1 and PITX2, play important roles in normal development and in differentiated cell functions. Three major isoforms of PITX2 were previously reported to be produced through both alternative mRNA splicing (PITX2A and PITX2B) and alternative promoter usage (PITX2C). The proteins derived from these mRNAs contain identical homeodomain and carboxyl termini. Differences in the amino-t...

  9. Fidelity of a human cell DNA replication complex

    International Nuclear Information System (INIS)

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

    1988-01-01

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

  10. Fidelity of a human cell DNA replication complex

    Energy Technology Data Exchange (ETDEWEB)

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

    1988-10-01

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

  11. A Bayesian bird's eye view of ‘Replications of important results in social psychology’

    Science.gov (United States)

    Schönbrodt, Felix D.; Yao, Yuling; Gelman, Andrew; Wagenmakers, Eric-Jan

    2017-01-01

    We applied three Bayesian methods to reanalyse the preregistered contributions to the Social Psychology special issue ‘Replications of Important Results in Social Psychology’ (Nosek & Lakens. 2014 Registered reports: a method to increase the credibility of published results. Soc. Psychol. 45, 137–141. (doi:10.1027/1864-9335/a000192)). First, individual-experiment Bayesian parameter estimation revealed that for directed effect size measures, only three out of 44 central 95% credible intervals did not overlap with zero and fell in the expected direction. For undirected effect size measures, only four out of 59 credible intervals contained values greater than 0.10 (10% of variance explained) and only 19 intervals contained values larger than 0.05. Second, a Bayesian random-effects meta-analysis for all 38 t-tests showed that only one out of the 38 hierarchically estimated credible intervals did not overlap with zero and fell in the expected direction. Third, a Bayes factor hypothesis test was used to quantify the evidence for the null hypothesis against a default one-sided alternative. Only seven out of 60 Bayes factors indicated non-anecdotal support in favour of the alternative hypothesis (BF10>3), whereas 51 Bayes factors indicated at least some support for the null hypothesis. We hope that future analyses of replication success will embrace a more inclusive statistical approach by adopting a wider range of complementary techniques. PMID:28280547

  12. Chromatin replication and histone dynamics

    DEFF Research Database (Denmark)

    Alabert, Constance; Jasencakova, Zuzana; Groth, Anja

    2017-01-01

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

  13. A randomized study of raisins versus alternative snacks on glycemic control and other cardiovascular risk factors in patients with type 2 diabetes mellitus.

    Science.gov (United States)

    Bays, Harold; Weiter, Kathy; Anderson, James

    2015-02-01

    Just as the type and duration of physical activity can have variable effects on the glucose levels and other cardiometabolic parameters among patients with type 2 diabetes mellitus (T2DM), so can the types of foods have variable effects as well. This 12-week randomized study of 51 study participants evaluated the impact of routine consumption of dark raisins versus alternative processed snacks on glucose levels and other cardiovascular risk factors among patients with type T2DM. In this study, compared to alternative processed snacks, those who consumed raisins had a significant 23% reduction in postprandial glucose levels (P = 0.024). Also compared to snacks, those who consumed raisins had a 19% reduction in fasting glucose and 0.12% reduction in hemoglobin A1c, although these latter findings did not achieve statistical significance. Regarding blood pressure, compared to alternative processed snacks, those who consumed raisins had a significant 8.7 mmHg reduction in systolic blood pressure (P = 0.035) (7.5% [P = 0.031]) but did not experience a significant reduction in diastolic blood pressure. Compared to alternative processed snacks, those who consumed raisins did not have a significant improvement in body weight, body mass index, waist circumference, fasting insulin, homeostatic model assessment of insulin resistance, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol (HDL), triglyceride, or non-HDL cholesterol levels. Overall, these data support raisins as a healthy alternative compare to processed snacks in patients with T2DM.

  14. Co-Construction as a Facilitative Factor in Supporting the Personal Narratives of Children Who Use Augmentative and Alternative Communication

    Science.gov (United States)

    Solomon-Rice, Patti; Soto, Gloria

    2011-01-01

    Adult co-construction with children who use augmentative and alternative communication (AAC) has been found to facilitate child communicative competence in general, but few studies have examined adult co-construction during the telling of personal narratives. This study explored the use of adult co-constructive strategies during personal…

  15. BEGA Starter/Alternator - Vector Control Implementation and Performance for Wide Speed Range at Unity Power Factor Operation

    DEFF Research Database (Denmark)

    Blaabjerg, Frede; Boldea, Ion; Coroban-Schramel, Vasile

    2008-01-01

    Biaxial Excitation Generator for Automobile (BEGA) is proposed as a solution for integrated starter/alternator systems used in hybrid electric vehicles (HEVs). This paper demonstrates through experiments and simulations that BEGA has a very large constant power speed range (CPSR), theoretically...

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

    Directory of Open Access Journals (Sweden)

    Bazilė Ravoitytė

    2017-01-01

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

  17. Synchronous replication of remote storage

    OpenAIRE

    Mirzoev, Dr. Timur

    2014-01-01

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

  18. Psycho-socioeconomic factors affecting complementary and alternative medicine use among selected rural communities in Malaysia: a cross-sectional study.

    Science.gov (United States)

    Ganasegeran, Kurubaran; Rajendran, Anantha Kumar; Al-Dubai, Sami Abdo Radman

    2014-01-01

    The use of complementary and alternative medicine (CAM) as a source of cure has gained much spectrum worldwide, despite skeptics and advocates of evidence-based practice conceptualized such therapies as human nostrum. This study aimed to explore the factors affecting CAM use among rural communities in Malaysia. A cross-sectional study was carried out on 288 occupants across four rural villages within the District of Selama, Perak, Malaysia. A survey that consisted of socio-economic characteristics, history of CAM use and the validated Holistic Complementary and Alternative Medicine Questionnaire (HCAMQ) were used. The prevalence of self-reported CAM use over the past one year was 53.1%. Multiple logistic regression analyses yielded three significant predictors of CAM use: monthly household income of less than MYR 2500, higher education level, and positive attitude towards CAM. Psycho-socioeconomic factors were significantly associated with CAM use among rural communities in Malaysia.

  19. Transcription factor EBF1 is essential for the maintenance of B cell identity and prevention of alternative fates in committed cells.

    Science.gov (United States)

    Nechanitzky, Robert; Akbas, Duygu; Scherer, Stefanie; Györy, Ildiko; Hoyler, Thomas; Ramamoorthy, Senthilkumar; Diefenbach, Andreas; Grosschedl, Rudolf

    2013-08-01

    The transcription factors EBF1 and Pax5 have been linked to activation of the B cell lineage program and irreversible loss of alternative lineage potential (commitment), respectively. Here we conditionally deleted Ebf1 in committed pro-B cells after transfer into alymphoid mice. We found that those cells converted into innate lymphoid cells (ILCs) and T cells with variable-diversity-joining (VDJ) rearrangements of loci encoding both B cell and T cell antigen receptors. As intermediates in lineage conversion, Ebf1-deficient CD19(+) cells expressing Pax5 and transcriptional regulators of the ILC and T cell fates were detectable. In particular, genes encoding the transcription factors Id2 and TCF-1 were bound and repressed by EBF1. Thus, both EBF1 and Pax5 are required for B lineage commitment by repressing distinct and common determinants of alternative cell fates.

  20. Planktonic replication is essential for biofilm formation by Legionella pneumophila in a complex medium under static and dynamic flow conditions

    DEFF Research Database (Denmark)

    Mampel, J.; Spirig, T.; Weber, S.S.

    2006-01-01

    Legionella pneumophila persists for a long time in aquatic habitats, where the bacteria associate with biofilms and replicate within protozoan predators. While L. pneumophila serves as a paradigm for intracellular growth within protozoa, it is less clear whether the bacteria form or replicate......A mutant lacking the alternative sigma factor sigma(28) was reduced, which demonstrated that bacterial factors are required. Accumulation of biomass coincided with an increase in the optical density at 600 nm and ceased when the bacteria reached the stationary growth phase. L. pneumophila neither grew nor......, and no sizeable patches of clonally growing bacteria were observed. Our findings indicate that biofilm formation by L. pneumophila in a rich medium is due to growth of planktonic bacteria rather than to growth of sessile bacteria. In agreement with this conclusion, GFP-labeled L. pneumophila initially adhered...

  1. Alternative security

    International Nuclear Information System (INIS)

    Weston, B.H.

    1990-01-01

    This book contains the following chapters: The Military and Alternative Security: New Missions for Stable Conventional Security; Technology and Alternative Security: A Cherished Myth Expires; Law and Alternative Security: Toward a Just World Peace; Politics and Alternative Security: Toward a More Democratic, Therefore More Peaceful, World; Economics and Alternative Security: Toward a Peacekeeping International Economy; Psychology and Alternative Security: Needs, Perceptions, and Misperceptions; Religion and Alternative Security: A Prophetic Vision; and Toward Post-Nuclear Global Security: An Overview

  2. Accounting for PDMS shrinkage when replicating structures

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  3. Murine leukemia virus (MLV replication monitored with fluorescent proteins

    Directory of Open Access Journals (Sweden)

    Bittner Alexandra

    2004-12-01

    Full Text Available Abstract Background Cancer gene therapy will benefit from vectors that are able to replicate in tumor tissue and cause a bystander effect. Replication-competent murine leukemia virus (MLV has been described to have potential as cancer therapeutics, however, MLV infection does not cause a cytopathic effect in the infected cell and viral replication can only be studied by immunostaining or measurement of reverse transcriptase activity. Results We inserted the coding sequences for green fluorescent protein (GFP into the proline-rich region (PRR of the ecotropic envelope protein (Env and were able to fluorescently label MLV. This allowed us to directly monitor viral replication and attachment to target cells by flow cytometry. We used this method to study viral replication of recombinant MLVs and split viral genomes, which were generated by replacement of the MLV env gene with the red fluorescent protein (RFP and separately cloning GFP-Env into a retroviral vector. Co-transfection of both plasmids into target cells resulted in the generation of semi-replicative vectors, and the two color labeling allowed to determine the distribution of the individual genomes in the target cells and was indicative for the occurrence of recombination events. Conclusions Fluorescently labeled MLVs are excellent tools for the study of factors that influence viral replication and can be used to optimize MLV-based replication-competent viruses or vectors for gene therapy.

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

    Science.gov (United States)

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

    2018-01-01

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

  5. Alternative Sigma Factors SigF, SigE, and SigG Are Essential for Sporulation in Clostridium botulinum ATCC 3502

    OpenAIRE

    Kirk, David G.; Zhang, Zhen; Korkeala, Hannu; Lindström, Miia

    2014-01-01

    Clostridium botulinum produces heat-resistant endospores that may germinate and outgrow into neurotoxic cultures in foods. Sporulation is regulated by the transcription factor Spo0A and the alternative sigma factors SigF, SigE, SigG, and SigK in most spore formers studied to date. We constructed mutants of sigF, sigE, and sigG in C. botulinum ATCC 3502 and used quantitative reverse transcriptase PCR and electron microscopy to assess their expression of the sporulation pathway on transcription...

  6. Activation-induced tumor necrosis factor receptor-associated factor 3 (Traf3) alternative splicing controls the noncanonical nuclear factor κB pathway and chemokine expression in human T cells.

    Science.gov (United States)

    Michel, Monika; Wilhelmi, Ilka; Schultz, Astrid-Solveig; Preussner, Marco; Heyd, Florian

    2014-05-09

    The noncanonical nuclear factor κB (ncNFκB) pathway regulates the expression of chemokines required for secondary lymphoid organ formation and thus plays a pivotal role in adaptive immunity. Whereas ncNFκB signaling has been well described in stromal cells and B cells, its role and regulation in T cells remain largely unexplored. ncNFκB activity critically depends on the upstream NFκB-inducing kinase (NIK). NIK expression is negatively regulated by the full-length isoform of TNF receptor-associated factor 3 (Traf3) as formation of a NIK-Traf3-Traf2 complex targets NIK for degradation. Here we show that T cell-specific and activation-dependent alternative splicing generates a Traf3 isoform lacking exon 8 (Traf3DE8) that, in contrast to the full-length protein, activates ncNFκB signaling. Traf3DE8 disrupts the NIK-Traf3-Traf2 complex and allows accumulation of NIK to initiate ncNFκB signaling in activated T cells. ncNFκB activity results in expression of several chemokines, among them B cell chemoattractant (CxCL13), both in a model T cell line and in primary human CD4(+) T cells. Because CxCL13 plays an important role in B cell migration and activation, our data suggest an involvement and provide a mechanistic basis for Traf3 alternative splicing and ncNFκB activation in contributing to T cell-dependent adaptive immunity.

  7. The causes of replication stress and their consequences on genome stability and cell fate.

    Science.gov (United States)

    Magdalou, Indiana; Lopez, Bernard S; Pasero, Philippe; Lambert, Sarah A E

    2014-06-01

    Alterations of the dynamics of DNA replication cause genome instability. These alterations known as "replication stress" have emerged as a major source of genomic instability in pre-neoplasic lesions, contributing to cancer development. The concept of replication stress covers a wide variety of events that distort the temporal and spatial DNA replication program. These events have endogenous or exogenous origins and impact globally or locally on the dynamics of DNA replication. They may arise within a short window of time (acute stress) or during each S phase (chronic stress). Here, we review the known situations in which the dynamics of DNA replication is distorted. We have united them in four main categories: (i) inadequate firing of replication origins (deficiency or excess), (ii) obstacles to fork progression, (iii) conflicts between replication and transcription and (iv) DNA replication under inappropriate metabolic conditions (unbalanced DNA replication). Because the DNA replication program is a process tightly regulated by many factors, replication stress often appears as a cascade of events. A local stress may prevent the completion of DNA replication at a single locus and subsequently compromise chromosome segregation in mitosis and therefore have a global effect on genome integrity. Finally, we discuss how replication stress drives genome instability and to what extent it is relevant to cancer biology. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Alternate stresses and temperature variation as factors of influence of ultrasonic vibration on mechanical and functional properties of shape memory alloys.

    Science.gov (United States)

    Belyaev, Sergey; Volkov, Alexander; Resnina, Natalia

    2014-01-01

    It is known that the main factors in a variation in the shape memory alloy properties under insonation are heating of the material and alternate stresses action. In the present work the experimental study of the mechanical behaviour and functional properties of shape memory alloy under the action of alternate stresses and varying temperature was carried out. The data obtained had demonstrated that an increase in temperature of the sample resulted in a decrease or increase in deformation stress depending on the structural state of the TiNi sample. It was shown that in the case of the alloy in the martensitic state, a decrease in stress was observed, and on the other hand, in the austenitic state an increase in stress took place. It was found that action of alternate stresses led to appearance of strain jumps on the strain-temperature curves during cooling and heating the sample through the temperature range of martensitic transformation under the constant stress. The value of the strain jumps depended on the amplitude of alternate stresses and the completeness of martensitic transformation. It was shown that the heat action of ultrasonic vibration to the mechanical behaviour of shape memory alloys was due to the non-monotonic dependence of yield stress on the temperature. The force action of ultrasonic vibration to the functional properties was caused by formation of additional oriented martensite. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. Using the Descriptive Bootstrap to Evaluate Result Replicability (Because Statistical Significance Doesn't)

    Science.gov (United States)

    Spinella, Sarah

    2011-01-01

    As result replicability is essential to science and difficult to achieve through external replicability, the present paper notes the insufficiency of null hypothesis statistical significance testing (NHSST) and explains the bootstrap as a plausible alternative, with a heuristic example to illustrate the bootstrap method. The bootstrap relies on…

  10. SMARCAL1 Resolves Replication Stress at ALT Telomeres.

    Science.gov (United States)

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

    2016-02-09

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

  11. Biomarkers of replicative senescence revisited

    DEFF Research Database (Denmark)

    Nehlin, Jan

    2016-01-01

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

  12. Comparing alternative factor models of PTSD symptoms across earthquake victims and violent riot witnesses in China: evidence for a five-factor model proposed by Elhai et al. (2011).

    Science.gov (United States)

    Wang, Li; Zhang, Jianxin; Shi, Zhanbiao; Zhou, Mingjie; Li, Zhongquan; Zhang, Kan; Liu, Zhengkui; Elhai, Jon D

    2011-08-01

    The present study investigated the factor structure of posttraumatic stress disorder (PTSD) symptoms measured by the PTSD Checklist (PCL) in two large samples exposed to different traumatic events (an earthquake and a violent riot) from China. Despite the samples' difference in type of trauma, demographics, symptom severity, and elapsed time since trauma exposure, the results of a series of confirmatory factor analyses indicate that a five-factor intercorrelated model (intrusion, avoidance, numbing, dysphoric arousal, and anxious arousal) fit the data significantly better than the other alternative models including: the three-factor DSM-IV model, the four-factor numbing model (King et al., 1998), and the four-factor dysphoria model (Simms et al., 2002) in both samples. Implications and limitations regarding the results are discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. Alternative additives; Alternative additiver

    Energy Technology Data Exchange (ETDEWEB)

    2007-08-15

    In this project a number of industrial and agricultural waste products have been characterised and evaluated in terms of alkali-getter performance. The intended use is for biomass-fired power stations aiming at reducing corrosion or slagging related problems. The following products have been obtained, characterised and evaluated: 1) Brewery draff 2) Danish de-gassed manure 3) Paper sludge 4) Moulding sand 5) Spent bleaching earth 6) Anorthosite 7) Sand 8) Clay-sludge. Most of the above alternative additive candidates are deemed unsuitable due to insufficient chemical effect and/or expensive requirements for pre-treatment (such as drying and transportation). 3 products were selected for full-scale testing: de-gassed manure, spent bleaching earth and clay slugde. The full scale tests were undertaken at the biomass-fired power stations in Koege, Slagelse and Ensted. Spent bleaching earth (SBE) and clay sludge were the only tested additive candidates that had a proven ability to react with KCl, to thereby reduce Cl-concentrations in deposits, and reduce the deposit flux to superheater tubes. Their performance was shown to nearly as good as commercial additives. De-gassed manure, however, did not evaluate positively due to inhibiting effects of Ca in the manure. Furthermore, de-gassed manure has a high concentration of heavy metals, which imposes a financial burden with regard to proper disposal of the ash by-products. Clay-sludge is a wet clay slurring, and drying and transportation of this product entails substantial costs. Spent bleaching does not require much pre-treatment and is therefore the most promising alternative additive. On the other hand, bleaching earth contains residual plant oil which means that a range of legislation relating to waste combustion comes into play. Not least a waste combustion fee of 330 DKK/tonne. For all alternative (and commercial) additives disposal costs of the increase ash by-products represents a significant cost. This is

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

    Science.gov (United States)

    Jones, Martin H.; McMichael, Stephanie N.

    2015-01-01

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

  15. International Expansion through Flexible Replication

    DEFF Research Database (Denmark)

    Jonsson, Anna; Foss, Nicolai Juul

    2011-01-01

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

  16. The role of dimerization in prion replication.

    Science.gov (United States)

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

    2002-04-01

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

  17. Impairment of Mature B Cell Maintenance upon Combined Deletion of the Alternative NF-κB Transcription Factors RELB and NF-κB2 in B Cells.

    Science.gov (United States)

    De Silva, Nilushi S; Silva, Kathryn; Anderson, Michael M; Bhagat, Govind; Klein, Ulf

    2016-03-15

    BAFF is critical for the survival and maturation of mature B cells. BAFF, via BAFFR, activates multiple signaling pathways in B cells, including the alternative NF-κB pathway. The transcription factors RELB and NF-κB2 (p100/p52) are the downstream mediators of the alternative pathway; however, the B cell-intrinsic functions of these NF-κB subunits have not been studied in vivo using conditional alleles, either individually or in combination. We in this study report that B cell-specific deletion of relb led to only a slight decrease in the fraction of mature splenic B cells, whereas deletion of nfkb2 caused a marked reduction. This phenotype was further exacerbated upon combined deletion of relb and nfkb2 and most dramatically affected the maintenance of marginal zone B cells. BAFF stimulation, in contrast to CD40 activation, was unable to rescue relb/nfkb2-deleted B cells in vitro. RNA-sequencing analysis of BAFF-stimulated nfkb2-deleted versus normal B cells suggests that the alternative NF-κB pathway, in addition to its critical role in BAFF-mediated cell survival, may control the expression of genes involved in the positioning of B cells within the lymphoid microenvironment and in the establishment of T cell-B cell interactions. Thus, by ablating the downstream transcription factors of the alternative NF-κB pathway specifically in B cells, we identify in this study a critical role for the combined activity of the RELB and NF-κB2 subunits in B cell homeostasis that cannot be compensated for by the canonical NF-κB pathway under physiological conditions. Copyright © 2016 by The American Association of Immunologists, Inc.

  18. Physically Embedded Minimal Self-Replicating Systems

    DEFF Research Database (Denmark)

    Fellermann, Harold

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

  19. Home Alone: Elimination of All but One Alternative Sigma Factor in Listeria monocytogenes Allows Prediction of New Roles for σB

    Directory of Open Access Journals (Sweden)

    Yichang Liu

    2017-10-01

    Full Text Available Among Listeria monocytogenes' four alternative σ factors, σB controls the largest regulon. As σB-dependent transcription of some genes may be masked by overlaps among regulons, and as some σB-dependent genes are expressed only under very specific conditions, we hypothesized that the σB regulon is not yet fully defined. To further extend our understanding of the σB regulon, we used RNA-seq to identify σB-dependent genes in an L. monocytogenes strain that expresses σB following rhamnose induction, and in which genes encoding the other alternative sigma factors have been deleted. Analysis of RNA-seq data with multiple bioinformatics approaches, including a sliding window method that detects differentially transcribed 5′ untranslated regions (UTRs, identified 105 σB-dependent transcription units (TUs comprising 201 genes preceded by σB-dependent promoters. Of these 105 TUs, 7 TUs comprising 15 genes had not been identified previously as σB-dependent. An additional 23 genes not reported previously as σB-dependent were identified in 9 previously recognized σB-dependent TUs. Overall, 38 of these 201 genes had not been identified previously as members of the L. monocytogenes σB regulon. These newly identified σB-dependent genes encode proteins annotated as being involved in transcriptional regulation, oxidative and osmotic stress response, and in metabolism of energy, carbon and nucleotides. In total, 18 putative σB-dependent promoters were newly identified. Interestingly, a number of genes previously identified as σB-dependent did not show significant evidence for σB-dependent transcription in our experiments. Based on promoter analyses, a number of these genes showed evidence for co-regulation by σB and other transcriptional factors, suggesting that some σB-dependent genes require additional transcriptional regulators along with σB for transcription. Over-expression of a single alternative sigma factor in the absence of all

  20. Specificity and function of Archaeal DNA replication initiator proteins

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  1. Hyperthermia stimulates HIV-1 replication.

    Directory of Open Access Journals (Sweden)

    Ferdinand Roesch

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

  2. Chameleon Chasing II: A Replication.

    Science.gov (United States)

    Newsom, Doug A.; And Others

    1993-01-01

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

  3. Manual of Cupule Replication Technology

    Directory of Open Access Journals (Sweden)

    Giriraj Kumar

    2015-09-01

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

  4. Regulation of Nod factor biosynthesis by alternative NodD proteins at distinct stages of symbiosis provides additional compatibility scrutiny

    DEFF Research Database (Denmark)

    Kelly, Simon; Sullivan, John T; Kawaharada, Yasuyuki

    2018-01-01

    The Lotus japonicus symbiont Mesorhizobium loti R7A encodes two copies of nodD and here we identify striking differences in Nod factor biosynthesis gene induction by NodD1 and NodD2 both in vitro and in planta. We demonstrate that induction of Nod factor biosynthesis genes is preferentially...... of nodD that provides the host plant with another level of compatibility scrutiny at the stage of infection thread development. This article is protected by copyright. All rights reserved....

  5. Chemokine ligand 2 and paraoxonase-1 in non-alcoholic fatty liver disease: The search for alternative causative factors.

    Science.gov (United States)

    Camps, Jordi; Joven, Jorge

    2015-03-14

    The incidence and prevalence of non-alcoholic fatty liver disease (NAFLD) is constantly increasing. Despite this is apparently associated with the growing increase in obesity, insulin resistance and obesity-related metabolic disturbances their presence is not a necessary or sufficient condition to explain the accumulation of fat in the liver. Conversely, NAFLD is a predictor of other metabolic risks. NAFLD is currently the most frequent chronic liver disease but should not be considered benign or anecdotic because a considerable proportion of patients with NAFLD progress to cirrhosis and end-stage liver disease. Consequently, the search for alternative molecular mechanisms with therapeutic implications in NAFLD and associated disorders deserves a careful consideration. Mitochondria are possible targets as these organelles generate energy from nutrient oxidation. Some findings, generated in patients with extreme obesity and in murine models, support the notion that NAFLD could be a mitochondrial disease. This is plausible because mitochondrial dysfunction affects the accumulation of lipids in hepatocytes and promotes lipid peroxidation, the production of reactive oxygen species, the release of cytokines causing inflammation and cell death. Here we discuss basic research and mechanistic studies targeting the role of chemokine ligand 2 in liver inflammation and that of the paraoxonases in the oxidative stress. Their combination and association with mitochondrial dysfunction may uncover mechanisms underlying the progression of NAFLD and may help to identify novel therapeutic targets.

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

    Science.gov (United States)

    Falaschi, Arturo; Abdurashidova, Gulnara; Biamonti, Giuseppe

    2010-02-01

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

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

    Science.gov (United States)

    McElreath, Richard; Smaldino, Paul E

    2015-01-01

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

  8. Simian virus Large T antigen interacts with the N-terminal domain of the 70 kD subunit of Replication Protein A in the same mode as multiple DNA damage response factors.

    Directory of Open Access Journals (Sweden)

    Boting Ning

    Full Text Available Simian virus 40 (SV40 serves as an important model organism for studying eukaryotic DNA replication. Its helicase, Large T-antigen (Tag, is a multi-functional protein that interacts with multiple host proteins, including the ubiquitous ssDNA binding protein Replication Protein A (RPA. Tag recruits RPA, actively loads it onto the unwound DNA, and together they promote priming of the template. Although interactions of Tag with RPA have been mapped, no interaction between Tag and the N-terminal protein interaction domain of the RPA 70kDa subunit (RPA70N has been reported. Here we provide evidence of direct physical interaction of Tag with RPA70N and map the binding sites using a series of pull-down and mutational experiments. In addition, a monoclonal anti-Tag antibody, the epitope of which overlaps with the binding site, blocks the binding of Tag to RPA70N. We use NMR chemical shift perturbation analysis to show that Tag uses the same basic cleft in RPA70N as multiple of DNA damage response proteins. Mutations in the binding sites of both RPA70N and Tag demonstrate that specific charge reversal substitutions in either binding partner strongly diminish the interaction. These results expand the known repertoire of contacts between Tag and RPA, which mediate the many critical roles of Tag in viral replication.

  9. A novel role for RAD54: this host protein modulates geminiviral DNA replication.

    Science.gov (United States)

    Kaliappan, Kosalai; Choudhury, Nirupam Roy; Suyal, Geetika; Mukherjee, Sunil Kumar

    2012-03-01

    Geminiviruses primarily encode only few factors, such as replication initiator protein (Rep), and need various host cellular machineries for rolling-circle replication (RCR) and/or recombination-dependent replication (RDR). We have identified a host factor, RAD54, in a screen for Rep-interacting partners and observed its role in DNA replication of the geminivirus mungbean yellow mosaic India virus (MYMIV). We identified the interacting domains ScRAD54 and MYMIV-Rep and observed that ScRAD54 enhanced MYMIV-Rep nicking, ATPase, and helicase activities. An in vitro replication assay demonstrated that the geminiviral DNA replication reaction depends on the viral Rep protein, viral origin of replication sequences, and host cell-cycle proteins. Rad54-deficient yeast nuclear extract did not support in vitro viral DNA replication, while exogenous addition of the purified ScRAD54 protein enhanced replication. The role of RAD54 in in planta replication was confirmed by the transient replication assay; i.e., agroinoculation studies. RAD54 is a well-known recombination/repair protein that uses its DNA-dependent ATPase activity in conjunction with several other host factors. However, this study demonstrates for the first time that the eukaryotic rolling-circle replicon depends on the RAD54 protein.

  10. GEMC1 is a TopBP1-interacting protein required for chromosomal DNA replication.

    Science.gov (United States)

    Balestrini, Alessia; Cosentino, Claudia; Errico, Alessia; Garner, Elizabeth; Costanzo, Vincenzo

    2010-05-01

    Many of the factors required for chromosomal DNA replication have been identified in unicellular eukaryotes. However, DNA replication is poorly understood in multicellular organisms. Here, we report the identification of GEMC1 (geminin coiled-coil containing protein 1), a novel vertebrate protein required for chromosomal DNA replication. GEMC1 is highly conserved in vertebrates and is preferentially expressed in proliferating cells. Using Xenopus laevis egg extract we show that Xenopus GEMC1 (xGEMC1) binds to the checkpoint and replication factor TopBP1, which promotes binding of xGEMC1 to chromatin during pre-replication complex (pre-RC) formation. We demonstrate that xGEMC1 interacts directly with replication factors such as Cdc45 and the kinase Cdk2-CyclinE, through which it is heavily phosphorylated. Phosphorylated xGEMC1 stimulates initiation of DNA replication, whereas depletion of xGEMC1 prevents the onset of DNA replication owing to the impairment of Cdc45 loading onto chromatin. Similarly, inhibition of GEMC1 expression with morpholino and siRNA oligos prevents DNA replication in embryonic and somatic vertebrate cells. These data suggest that GEMC1 promotes initiation of chromosomal DNA replication in multicellular organisms by mediating TopBP1- and Cdk2-dependent recruitment of Cdc45 onto replication origins.

  11. GEMC1 is a TopBP1 interacting protein required for chromosomal DNA replication

    Science.gov (United States)

    Balestrini, Alessia; Cosentino, Claudia; Errico, Alessia; Garner, Elizabeth; Costanzo, Vincenzo

    2010-01-01

    Many factors required for chromosomal DNA replication have been identified in unicellular eukaryotes. However, DNA replication in complex multicellular organisms is poorly understood. Here, we report the identification of GEMC1, a novel vertebrate protein required for chromosomal DNA replication. GEMC1 is highly conserved in vertebrates and is preferentially expressed in proliferating cells. Using Xenopus egg extract we show that Xenopus GEMC1 (xGEMC1) binds to checkpoint and replication factor TopBP1, which promotes xGEMC1 binding to chromatin during pre-replication complex (pre-RC) formation. We demonstrate that xGEMC1 directly interacts with replication factors such as Cdc45 and Cdk2-CyclinE by which it is heavily phosphorylated. Phosphorylated xGEMC1 stimulates initiation of DNA replication whereas depletion of xGEMC1 prevents DNA replication onset due to impairment of Cdc45 loading onto chromatin. Likewise, inhibition of GEMC1 expression by morpholino and siRNA oligos prevents DNA replication in embryonic and somatic vertebrate cells. These data suggest that GEMC1 promotes initiation of chromosomal DNA replication in higher eukaryotes by mediating TopBP1 and Cdk2 dependent recruitment of Cdc45 onto replication origins. PMID:20383140

  12. Novel forms of Paired-like homeodomain transcription factor 2 (PITX2: Generation by alternative translation initiation and mRNA splicing

    Directory of Open Access Journals (Sweden)

    Bernard Daniel J

    2008-03-01

    Full Text Available Abstract Background Members of the Paired-like homeodomain transcription factor (PITX gene family, particularly PITX1 and PITX2, play important roles in normal development and in differentiated cell functions. Three major isoforms of PITX2 were previously reported to be produced through both alternative mRNA splicing (PITX2A and PITX2B and alternative promoter usage (PITX2C. The proteins derived from these mRNAs contain identical homeodomain and carboxyl termini. Differences in the amino-termini of the proteins may confer functional differences in some contexts. Results Here, we report the identification of two novel PITX2 isoforms. First, we demonstrate that the Pitx2c mRNA generates two protein products, PITX2Cα and PITX2Cβ, via alternative translation initiation. Second, we identified a novel mRNA splice variant, Pitx2b2, which uses the same 5' splice donor in intron 2 as Pitx2b (hereafter referred to as Pitx2b1, but employs an alternative 3' splice acceptor, leading to an in-frame deletion of 39 base pairs relative to Pitx2b1. Pitx2b2 mRNA is expressed in both murine and human pituitary. The data show that in a murine gonadotrope cell line and adult murine pituitary what was previously thought to be PITX2B1 is actually PITX2Cβ, or perhaps PITX2B2. PITX2B1 is expressed at lower levels than previously thought. PITX2Cβ and PITX2B2 activate gonadotrope-specific gene promoter-reporters similarly to known PITX2 isoforms. Conclusion We have identified and characterized two novel isoforms of PITX2, generated by alternative translation initiation (PITX2Cβ and alternative mRNA splicing (PITX2B2. These proteins show similar DNA binding and trans-activation functions as other PITX2 isoforms in vitro, though their conservation across species suggests that they may play distinct, as yet unidentified, roles in vivo.

  13. DSM-5 alternative personality disorder model traits as maladaptive extreme variants of the five-factor model: An item-response theory analysis.

    Science.gov (United States)

    Suzuki, Takakuni; Samuel, Douglas B; Pahlen, Shandell; Krueger, Robert F

    2015-05-01

    Over the past two decades, evidence has suggested that personality disorders (PDs) can be conceptualized as extreme, maladaptive variants of general personality dimensions, rather than discrete categorical entities. Recognizing this literature, the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) alternative PD model in Section III defines PDs partially through 25 maladaptive traits that fall within 5 domains. Empirical evidence based on the self-report measure of these traits, the Personality Inventory for DSM-5 (PID-5), suggests that these five higher-order domains share a structure and correlate in meaningful ways with the five-factor model (FFM) of general personality. In the current study, item response theory was used to compare the DSM-5 alternative PD model traits to those from a normative FFM inventory (the International Personality Item Pool-NEO [IPIP-NEO]) in terms of their measurement precision along the latent dimensions. Within a combined sample of 3,517 participants, results strongly supported the conclusion that the DSM-5 alternative PD model traits and IPIP-NEO traits are complimentary measures of 4 of the 5 FFM domains (with perhaps the exception of openness to experience vs. psychoticism). Importantly, the two measures yield largely overlapping information curves on these four domains. Differences that did emerge suggested that the PID-5 scales generally have higher thresholds and provide more information at the upper levels, whereas the IPIP-NEO generally had an advantage at the lower levels. These results support the general conceptualization that 4 domains of the DSM-5 alternative PD model traits are maladaptive, extreme versions of the FFM. (PsycINFO Database Record (c) 2015 APA, all rights reserved).

  14. Transcriptional and physiological changes during Mycobacterium tuberculosis reactivation from non-replicating persistence

    Directory of Open Access Journals (Sweden)

    Peicheng Du

    2016-08-01

    Full Text Available Mycobacterium tuberculosis can persist for years in the hostile environment of the host in a non-replicating or slowly replicating state. While active disease predominantly results from reactivation of a latent infection, the molecular mechanisms of M. tuberculosis reactivation are still poorly understood. We characterized the physiology and global transcriptomic profiles of M. tuberculosis during reactivation from hypoxia-induced non-replicating persistence. We found that M. tuberculosis reactivation upon reaeration was associated with a lag phase, in which the recovery of cellular physiological and metabolic functions preceded the resumption of cell replication. Enrichment analysis of the transcriptomic dynamics revealed changes to many metabolic pathways and transcription regulons/subnetworks that orchestrated the metabolic and physiological transformation in preparation for cell division. In particular, we found that M. tuberculosis reaeration lag phase is associated with down-regulation of persistence-associated regulons/subnetworks, including DosR, MprA, SigH, SigE and ClgR, as well as metabolic pathways including those involved in the uptake of lipids and their catabolism. More importantly, we identified a number of up-regulated transcription regulons and metabolic pathways, including those involved in metal transport and remobilization, second messenger-mediated responses, DNA repair and recombination, and synthesis of major cell wall components. We also found that inactivation of the major alternative sigma factors SigE or SigH disrupted exit from persistence, underscoring the importance of the global transcriptional reprogramming during M. tuberculosis reactivation. Our observations suggest that M. tuberculosis lag phase is associated with a global gene expression reprogramming that defines the initiation of a reactivation process.

  15. Telomere elongation chooses TERRA ALTernatives.

    Science.gov (United States)

    Arora, Rajika; Azzalin, Claus M

    2015-01-01

    Alternative Lengthening of Telomeres (ALT) mechanisms allow telomerase-negative immortal cells to buffer replicative telomere shortening. ALT is naturally active in a number of human cancers and might be selected upon telomerase inactivation. ALT is thought to operate through homologous recombination (HR) occurring between telomeric repeats from independent chromosome ends. Indeed, suppression of a number of HR factors impairs ALT cell proliferation. Yet, how HR is initiated at ALT telomeres remains elusive. Mounting evidence suggests that the long noncoding telomeric RNA TERRA renders ALT telomeres recombinogenic by forming RNA:DNA hybrids with the telomeric C-rich strand. TERRA and telomeric hybrids act in concert with a number of other factors, including the RNA endoribonuclease RNaseH1 and the single stranded DNA binding protein RPA. The functional interaction network built upon these different players seems indispensable for ALT telomere maintenance, and digging into the molecular details of this previously unappreciated network might open the way to novel avenues for cancer treatments.

  16. Replicator dynamics in value chains

    DEFF Research Database (Denmark)

    Cantner, Uwe; Savin, Ivan; Vannuccini, Simone

    2016-01-01

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

  17. Replication Clamps and Clamp Loaders

    Science.gov (United States)

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

    2013-01-01

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

  18. Utilizing interview and self-report assessment of the Five-Factor Model to examine convergence with the alternative model for personality disorders.

    Science.gov (United States)

    Helle, Ashley C; Trull, Timothy J; Widiger, Thomas A; Mullins-Sweatt, Stephanie N

    2017-07-01

    An alternative model for personality disorders is included in Section III (Emerging Models and Measures) of Diagnostic and Statistical Manual of Mental Disorders, (5th ed.; DSM-5). The DSM-5 dimensional trait model is an extension of the Five-Factor Model (FFM; American Psychiatric Association, 2013). The Personality Inventory for DSM-5 (PID-5) assesses the 5 domains and 25 traits in the alternative model. The current study expands on recent research to examine the relationship of the PID-5 with an interview measure of the FFM. The Structured Interview for the Five Factor Model of Personality (SIFFM) assesses the 5 bipolar domains and 30 facets of the FFM. Research has indicated that the SIFFM captures maladaptive aspects of personality (as well as adaptive). The SIFFM, NEO PI-R, and PID-5 were administered to participants to examine their respective convergent and discriminant validity. Results provide evidence for the convergence of the 2 models using self-report and interview measures of the FFM. Clinical implications and future directions are discussed, particularly a call for the development of a structured interview for the assessment of the DSM-5 dimensional trait model. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    Mitali Das

    2014-01-01

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

  1. Alternative Fuels

    Science.gov (United States)

    Alternative fuels include gaseous fuels such as hydrogen, natural gas, and propane; alcohols such as ethanol, methanol, and butanol; vegetable and waste-derived oils; and electricity. Overview of alternative fuels is here.

  2. Linear, Non-Linear and Alternative Algorithms in the Correlation of IEQ Factors with Global Comfort: A Case Study

    Directory of Open Access Journals (Sweden)

    Francesco Fassio

    2014-11-01

    Full Text Available Indoor environmental quality (IEQ factors usually considered in engineering studies, i.e., thermal, acoustical, visual comfort and indoor air quality are individually associated with the occupant satisfaction level on the basis of well-established relationships. On the other hand, the full understanding of how single IEQ factors contribute and interact to determine the overall occupant satisfaction (global comfort is currently an open field of research. The lack of a shared approach in treating the subject depends on many aspects: absence of established protocols for the collection of subjective and objective measurements, the amount of variables to consider and in general the complexity of the technical issues involved. This case study is aimed to perform a comparison between some of the models available, studying the results of a survey conducted with objective and subjective method on a classroom within University of Roma TRE premises. Different models are fitted on the same measured values, allowing comparison between different weighting schemes between IEQ categories obtained with different methods. The critical issues, like differences in the weighting scheme obtained with different IEQ models and the variability of the weighting scheme with respect to the time of exposure of the users in the building, identified during this small scale comfort assessment study, provide the basis for a survey activity on a larger scale, basis for the development of an improved IEQ assessment method.

  3. Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants

    Czech Academy of Sciences Publication Activity Database

    Růčková, Eva; Friml, J.; Procházková Schrumpfová, Petra; Fajkus, Jiří

    2008-01-01

    Roč. 66, č. 6 (2008), s. 637-646 ISSN 0167-4412 R&D Projects: GA MŠk(CZ) LC06004; GA ČR(CZ) GA521/05/0055; GA AV ČR(CZ) IAA600040505 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : alternative telomere lengthening * plant * replicative telomere shortening Subject RIV: BO - Biophysics Impact factor: 3.541, year: 2008

  4. Exploiting replicative stress to treat cancer

    DEFF Research Database (Denmark)

    Dobbelstein, Matthias; Sørensen, Claus Storgaard

    2015-01-01

    DNA replication in cancer cells is accompanied by stalling and collapse of the replication fork and signalling in response to DNA damage and/or premature mitosis; these processes are collectively known as 'replicative stress'. Progress is being made to increase our understanding of the mechanisms...... that govern replicative stress, thus providing ample opportunities to enhance replicative stress for therapeutic purposes. Rather than trying to halt cell cycle progression, cancer therapeutics could aim to increase replicative stress by further loosening the checkpoints that remain available to cancer cells...

  5. Blinded with Science or Informed by Charts? A Replication Study

    OpenAIRE

    Dragicevic , Pierre; Jansen , Yvonne

    2018-01-01

    International audience; We provide a reappraisal of Tal and Wansink's study "Blinded with Science" , where seemingly trivial charts were shown to increase belief in drug efficacy, presumably because charts are associated with science. Through a series of four replications conducted on two crowdsourcing platforms, we investigate an alternative explanation, namely, that the charts allowed participants to better assess the drug's efficacy. Considered together, our experiments suggest that the ch...

  6. Five-Factor Model personality disorder prototypes: a review of their development, validity, and comparison to alternative approaches.

    Science.gov (United States)

    Miller, Joshua D

    2012-12-01

    In this article, the development of Five-Factor Model (FFM) personality disorder (PD) prototypes for the assessment of DSM-IV PDs are reviewed, as well as subsequent procedures for scoring individuals' FFM data with regard to these PD prototypes, including similarity scores and simple additive counts that are based on a quantitative prototype matching methodology. Both techniques, which result in very strongly correlated scores, demonstrate convergent and discriminant validity, and provide clinically useful information with regard to various forms of functioning. The techniques described here for use with FFM data are quite different from the prototype matching methods used elsewhere. © 2012 The Author. Journal of Personality © 2012, Wiley Periodicals, Inc.

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

    OpenAIRE

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

    2013-01-01

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

  8. Evaluating WAIS-IV structure through a different psychometric lens: structural causal model discovery as an alternative to confirmatory factor analysis.

    Science.gov (United States)

    van Dijk, Marjolein J A M; Claassen, Tom; Suwartono, Christiany; van der Veld, William M; van der Heijden, Paul T; Hendriks, Marc P H

    Since the publication of the WAIS-IV in the U.S. in 2008, efforts have been made to explore the structural validity by applying factor analysis to various samples. This study aims to achieve a more fine-grained understanding of the structure of the Dutch language version of the WAIS-IV (WAIS-IV-NL) by applying an alternative analysis based on causal modeling in addition to confirmatory factor analysis (CFA). The Bayesian Constraint-based Causal Discovery (BCCD) algorithm learns underlying network structures directly from data and assesses more complex structures than is possible with factor analysis. WAIS-IV-NL profiles of two clinical samples of 202 patients (i.e. patients with temporal lobe epilepsy and a mixed psychiatric outpatient group) were analyzed and contrasted with a matched control group (N = 202) selected from the Dutch standardization sample of the WAIS-IV-NL to investigate internal structure by means of CFA and BCCD. With CFA, the four-factor structure as proposed by Wechsler demonstrates acceptable fit in all three subsamples. However, BCCD revealed three consistent clusters (verbal comprehension, visual processing, and processing speed) in all three subsamples. The combination of Arithmetic and Digit Span as a coherent working memory factor could not be verified, and Matrix Reasoning appeared to be isolated. With BCCD, some discrepancies from the proposed four-factor structure are exemplified. Furthermore, these results fit CHC theory of intelligence more clearly. Consistent clustering patterns indicate these results are robust. The structural causal discovery approach may be helpful in better interpreting existing tests, the development of new tests, and aid in diagnostic instruments.

  9. 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....

  10. Evaluating replicability of laboratory experiments in economics.

    Science.gov (United States)

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

    2016-03-25

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

  11. Variance Swap Replication: Discrete or Continuous?

    Directory of Open Access Journals (Sweden)

    Fabien Le Floc’h

    2018-02-01

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

  12. Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation

    Science.gov (United States)

    Li, Wencheng; You, Bei; Hoque, Mainul; Zheng, Dinghai; Luo, Wenting; Ji, Zhe; Park, Ji Yeon; Gunderson, Samuel I.; Kalsotra, Auinash; Manley, James L.; Tian, Bin

    2015-01-01

    Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3’ untranslated regions (3’UTRs) and/or coding sequences. How core cleavage/polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3’UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1 and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI-25/68 or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly inhibiting C/P events in introns near the 5’ end of gene and U2 suppressing those in introns with features for efficient splicing. Furthermore, PABPN1 inhibits expression of transcripts with pAs near the transcription start site (TSS), a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results support an APA code where an APA event in a given cellular context is regulated by a number of parameters, including relative location to the TSS, splicing context, distance between competing pAs, surrounding cis elements and concentrations of core C/P factors. PMID:25906188

  13. Systematic profiling of poly(A+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation.

    Directory of Open Access Journals (Sweden)

    Wencheng Li

    2015-04-01

    Full Text Available Alternative cleavage and polyadenylation (APA results in mRNA isoforms containing different 3' untranslated regions (3'UTRs and/or coding sequences. How core cleavage/polyadenylation (C/P factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3'UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A sites (pAs, CFI-25/68, PABPN1 and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI-25/68 or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly inhibiting C/P events in introns near the 5' end of gene and U2 suppressing those in introns with features for efficient splicing. Furthermore, PABPN1 inhibits expression of transcripts with pAs near the transcription start site (TSS, a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results support an APA code where an APA event in a given cellular context is regulated by a number of parameters, including relative location to the TSS, splicing context, distance between competing pAs, surrounding cis elements and concentrations of core C/P factors.

  14. [Reproductive behavior of the green birdmouth wrasse Gomphosus caeruleus on a Reunion Island reef: Mode of reproduction, environmental factors and reproductive strategy alternation].

    Science.gov (United States)

    Desvignes, Thomas; Bourjon, Philippe; Chanet, Bruno

    2018-01-01

    The green birdmouth wrasse Gomphosus caeruleus is present all year round on the coral reefs of Reunion Island (Indian Ocean). A group of individuals was followed on one of these reefs with the objective of studying the reproduction mode of the species, the influence of environmental factors, and social behaviors on the control of reproduction. Our observations revealed that G. caeruleus is, like many Labridae, a protogynous hermaphrodite species, probably diandric, that the reproduction of G. caeruleus is, like in other reef fish species, influenced by the lunar cycle with a peak of reproductive activity during waxing gibbous phase, and that G. caeruleus displays social behavior leading to alternating haremic mating system on a single territory and lek-like mating systems without aggressions between males. These observations enhanced our knowledge of the reproduction of Labridae and reef species. Copyright © 2017 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

  15. Assembly and activation of alternative complement components on endothelial cell-anchored ultra-large von Willebrand factor links complement and hemostasis-thrombosis.

    Directory of Open Access Journals (Sweden)

    Nancy A Turner

    Full Text Available Vascular endothelial cells (ECs express and release protein components of the complement pathways, as well as secreting and anchoring ultra-large von Willebrand factor (ULVWF multimers in long string-like structures that initiate platelet adhesion during hemostasis and thrombosis. The alternative complement pathway (AP is an important non-antibody-requiring host defense system. Thrombotic microangiopathies can be associated with defective regulation of the AP (atypical hemolytic-uremic syndrome or with inadequate cleavage by ADAMTS-13 of ULVWF multimeric strings secreted by/anchored to ECs (thrombotic thrombocytopenic purpura. Our goal was to determine if EC-anchored ULVWF strings caused the assembly and activation of AP components, thereby linking two essential defense mechanisms.We quantified gene expression of these complement components in cultured human umbilical vein endothelial cells (HUVECs by real-time PCR: C3 and C5; complement factor (CF B, CFD, CFP, CFH and CFI of the AP; and C4 of the classical and lectin (but not alternative complement pathways. We used fluorescent microscopy, monospecific antibodies against complement components, fluorescent secondary antibodies, and the analysis of >150 images to quantify the attachment of HUVEC-released complement proteins to ULVWF strings secreted by, and anchored to, the HUVECs (under conditions of ADAMTS-13 inhibition. We found that HUVEC-released C4 did not attach to ULVWF strings, ruling out activation of the classical and lectin pathways by the strings. In contrast, C3, FB, FD, FP and C5, FH and FI attached to ULVWF strings in quantitative patterns consistent with assembly of the AP components into active complexes. This was verified when non-functional FB blocked the formation of AP C3 convertase complexes (C3bBb on ULVWF strings.AP components are assembled and activated on EC-secreted/anchored ULVWF multimeric strings. Our findings provide one possible molecular mechanism for clinical

  16. Quantitative Proteomic Analysis of Replicative and Nonreplicative Forms Reveals Important Insights into Chromatin Biology of Trypanosoma cruzi*

    Science.gov (United States)

    Leandro de Jesus, Teresa Cristina; Calderano, Simone Guedes; Vitorino, Francisca Nathalia de Luna; Llanos, Ricardo Pariona; Lopes, Mariana de Camargo; de Araújo, Christiane Bezerra; Thiemann, Otavio Henrique; Reis, Marcelo da Silva; Elias, Maria Carolina

    2017-01-01

    Chromatin associated proteins are key regulators of many important processes in the cell. Trypanosoma cruzi, a protozoa flagellate that causes Chagas disease, alternates between replicative and nonreplicative forms accompanied by a shift on global transcription levels and by changes in its chromatin architecture. Here, we investigated the T. cruzi chromatin proteome using three different protocols and compared it between replicative (epimastigote) and nonreplicative (trypomastigote) forms by high-resolution mass spectrometry. More than 2000 proteins were identified and quantified both in chromatin and nonchromatin extracts. Besides histones and other known nuclear proteins, trypanosomes chromatin also contains metabolic (mainly from carbohydrate pathway), cytoskeleton and many other proteins with unknown functions. Strikingly, the two parasite forms differ greatly regarding their chromatin-associated factors composition and amount. Although the nucleosome content is the same for both life forms (as seen by MNase digestion), the remaining proteins were much less detected in nonreplicative forms, suggesting that they have a naked chromatin. Proteins associated to DNA proliferation, such as PCNA, RPA, and DNA topoisomerases were exclusively found in the chromatin of replicative stages. On the other hand, the nonreplicative stages have an enrichment of a histone H2B variant. Furthermore, almost 20% of replicative stages chromatin-associated proteins are expressed in nonreplicative forms, but located at nonchromatin space. We identified different classes of proteins including phosphatases and a Ran-binding protein, that may shuttle between chromatin and nonchromatin space during differentiation. Seven proteins, including those with unknown functions, were selected for further validation. We confirmed their location in chromatin and their differential expression, using Western blotting assays and chromatin immunoprecipitation (ChIP). Our results indicate that the

  17. The hunt for origins of DNA replication in multicellular eukaryotes

    DEFF Research Database (Denmark)

    Urban, J. M.; Foulk, M. S.; Casella, Cinzia

    2015-01-01

    Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope...

  18. The absence of a DNA replication checkpoint in porcine zygotes

    Czech Academy of Sciences Publication Activity Database

    Vacková, I.; Křen, Radomír; Loi, P.; Krylov, V.; Fulka Jr., J.

    2006-01-01

    Roč. 14, 1 (2006), s. 33-37 ISSN 0967-1994 Institutional research plan: CEZ:AV0Z50450515 Keywords : checkpoint * DNA replication * fertilization Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.782, year: 2006

  19. Repair replication in replicating and nonreplicating DNA after irradiation with uv light

    Energy Technology Data Exchange (ETDEWEB)

    Slor, H.; Cleaver, J.E.

    1978-06-01

    Ultraviolet light induces more pyrimidine dimers and more repair replication in DNA that replicates within 2 to 3 h of irradiation than in DNA that does not replicate during this period. This difference may be due to special conformational changes in DNA and chromatin that might be associated with semiconservative DNA replication.

  20. DNA replication machinery is required for development in Drosophila.

    Science.gov (United States)

    Kohzaki, Hidetsugu; Asano, Maki; Murakami, Yota

    2018-01-01

     In Drosophila , some factors involved in chromosome replication seem to be involved in gene amplification and endoreplication, which are actively utilized in particular tissue development, but direct evidence has not been shown. Therefore, we examined the effect of depletion of replication factors on these processes. First, we confirmed RNAi knockdown can be used for the depletion of replication factors by comparing the phenotypes of RNAi knockdown and deletion or point mutants of the components of DNA licensing factor, MCM2, MCM4 and Cdt1. Next, we found that tissue-specific RNAi knockdown of replication factors caused tissue-specific defects, probably due to defects in DNA replication. In particular, we found that depletion inhibited gene amplification of the chorion gene in follicle cells and endoreplication in salivary glands, showing that chromosomal DNA replication factors are required for these processes. Finally, using RNAi, we screened the genes for chromosomal DNA replication that affected tissue development. Interestingly, wing specific knockdown of Mcm10 induced wing formation defects. These results suggest that some components of chromosomal replication machinery are directly involved in tissue development.

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

    Czech Academy of Sciences Publication Activity Database

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

    2005-01-01

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

  2. Long-term radiographic evaluation of risk factors related to implant treatment: suggestion for alternative statistical analysis of marginal bone loss.

    Science.gov (United States)

    Hasegawa, Masakazu; Hotta, Yasunori; Hoshino, Takahiro; Ito, Koji; Komatsu, Shinichi; Saito, Takashi

    2016-10-01

    Secular change in marginal bone loss (MBL), which is the index adopted for implant success criteria, has often been used to evaluate risk factors. However, the need to revise these criteria has recently been indicated due to rapid developments in implant treatment. The purpose of this study was to evaluate risk factors by analyzing MBL with an alternative statistical method. The analyses were performed on the outcomes of 366 patients with 1,902 implants during an average follow-up period of 84.8 months (with a maximum follow-up of 258 months). Instead of evaluating annual MBL, time was calculated as one of the explanatory variables because the correlation between MBL and time was small (correlation coefficient of 0.09010). Analysis of covariance (ANCOVA) was used for exploratory assessment of each factor, and multiple regression analysis was then utilized to identify risk factors. The multiple regression analysis was performed twice, once among all implants and another in which one implant per patient was randomly selected. As a result of multiple regression analysis, smoking habits showed a significant effect on MBL. Age, sex, diabetes mellitus, implant positions, guided bone regeneration, and sinus floor elevation did not affect MBL. IMZ ® implants were associated with significantly higher MBL than were ANKYLOS ® and SPI ® implants. There was no significant difference between Straumann ® and other implants. Our results showed that another statistical process, which eliminated the effect of time rather than comparing annual MBL, could be applied to evaluate MBL because the correlation between MBL and time was small. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Personality and consultations with complementary and alternative medicine practitioners: a five-factor model investigation of the degree of use and motives.

    Science.gov (United States)

    Sirois, Fuschia M; Purc-Stephenson, Rebecca J

    2008-11-01

    As interest in and use of complementary and alternative medicine (CAM) providers continues to grow, it is important to understand which characteristics incline people to experiment with and become frequent consumers of CAM practitioners. The purpose of this study was to examine how personality, as assessed by the five-factor model, was related to the breadth, frequency, and types of provider-based CAM use. Relationships between the personality factors (Openness, Conscientiousness, Extraversion, Agreeableness, and Neuroticism) and motives for consulting CAM providers were also explored. A convenience sample of 184 current CAM clients recruited through the offices of 12 conventional medicine and 17 CAM practitioners completed a survey package including measures of health status, CAM use, personality, and motivations for using CAM. Only Openness and Agreeableness were consistently linked to different dimensions of CAM use, with each associated with consultations with CAM practitioners, and homeopaths and naturopaths in particular. After controlling for sociodemographic and health status variables in the stepwise multiple regressions, Openness was associated with the variety of CAM providers tried, whereas Agreeableness was linked to both the breadth and frequency of CAM consultations. Holistic and proactive health motivations were associated with both personality factors, and Agreeableness was also associated with motives reflecting a desire for shared decision-making. Findings indicate that individuals who are open and agreeable, as described by the five-factor model of personality, consult CAM practitioners to a greater extent. The motives involved suggest a congruency between CAM and their own perspectives regarding health and patient-provider interactions, which may have implications for understanding treatment adherence and outcomes.

  4. MicroRNA-126-mediated control of cell fate in B-cell myeloid progenitors as a potential alternative to transcriptional factors.

    Science.gov (United States)

    Okuyama, Kazuki; Ikawa, Tomokatsu; Gentner, Bernhard; Hozumi, Katsuto; Harnprasopwat, Ratanakanit; Lu, Jun; Yamashita, Riu; Ha, Daon; Toyoshima, Takae; Chanda, Bidisha; Kawamata, Toyotaka; Yokoyama, Kazuaki; Wang, Shusheng; Ando, Kiyoshi; Lodish, Harvey F; Tojo, Arinobu; Kawamoto, Hiroshi; Kotani, Ai

    2013-08-13

    Lineage specification is thought to be largely regulated at the level of transcription, where lineage-specific transcription factors drive specific cell fates. MicroRNAs (miR), vital to many cell functions, act posttranscriptionally to decrease the expression of target mRNAs. MLL-AF4 acute lymphocytic leukemia exhibits both myeloid and B-cell surface markers, suggesting that the transformed cells are B-cell myeloid progenitor cells. Through gain- and loss-of-function experiments, we demonstrated that microRNA 126 (miR-126) drives B-cell myeloid biphenotypic leukemia differentiation toward B cells without changing expression of E2A immunoglobulin enhancer-binding factor E12/E47 (E2A), early B-cell factor 1 (EBF1), or paired box protein 5, which are critical transcription factors in B-lymphopoiesis. Similar induction of B-cell differentiation by miR-126 was observed in normal hematopoietic cells in vitro and in vivo in uncommitted murine c-Kit(+)Sca1(+)Lineage(-) cells, with insulin regulatory subunit-1 acting as a target of miR-126. Importantly, in EBF1-deficient hematopoietic progenitor cells, which fail to differentiate into B cells, miR-126 significantly up-regulated B220, and induced the expression of B-cell genes, including recombination activating genes-1/2 and CD79a/b. These data suggest that miR-126 can at least partly rescue B-cell development independently of EBF1. These experiments show that miR-126 regulates myeloid vs. B-cell fate through an alternative machinery, establishing the critical role of miRNAs in the lineage specification of multipotent mammalian cells.

  5. Alternative Oxidase Transcription Factors AOD2 and AOD5 ofNeurospora crassaControl the Expression of Genes Involved in Energy Production and Metabolism.

    Science.gov (United States)

    Qi, Zhigang; Smith, Kristina M; Bredeweg, Erin L; Bosnjak, Natasa; Freitag, Michael; Nargang, Frank E

    2017-02-09

    In Neurospora crassa , blocking the function of the standard mitochondrial electron transport chain results in the induction of an alternative oxidase (AOX). AOX transfers electrons directly from ubiquinol to molecular oxygen. AOX serves as a model of retrograde regulation since it is encoded by a nuclear gene that is regulated in response to signals from mitochondria. The N. crassa transcription factors AOD2 and AOD5 are necessary for the expression of the AOX gene. To gain insight into the mechanism by which these factors function, and to determine if they have roles in the expression of additional genes in N. crassa , we constructed strains expressing only tagged versions of the proteins. Cell fractionation experiments showed that both proteins are localized to the nucleus under both AOX inducing and noninducing conditions. Furthermore, chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) analysis revealed that the proteins are bound to the promoter region of the AOX gene under both conditions. ChIP-seq also showed that the transcription factors bind to the upstream regions of a number of genes that are involved in energy production and metabolism. Dependence on AOD2 and AOD5 for the expression of several of these genes was verified by quantitative PCR. The majority of ChIP-seq peaks observed were enriched for both AOD2 and AOD5. However, we also observed occasional sites where one factor appeared to bind preferentially. The most striking of these was a conserved sequence that bound large amounts of AOD2 but little AOD5. This sequence was found within a 310 bp repeat unit that occurs at several locations in the genome. Copyright © 2017 Qi et al.

  6. The Interstellar Ethics of Self-Replicating Probes

    Science.gov (United States)

    Cooper, K.

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

  7. The effects of modified alternate-day fasting diet on weight loss and CAD risk factors in overweight and obese women

    Directory of Open Access Journals (Sweden)

    Eshghinia Samira

    2013-01-01

    Full Text Available Abstract Background Obesity is a worldwide health problem with increasing prevalence. Decrease in energy intake has been shown to lower the risk of coronary artery disease in obese subjects. The common form of dietary restriction is daily calorie restriction (CR. Another form is alternate-day fasting (ADF. This study examined the ability of modified ADF to facilitate weight loss and lower cardiovascular risk factors in overweight and obese women. Methods 15 adult subjects completed an 8 weeks trial (2 weeks observed and 6 weeks ADF. All women consumed very low calorie diet on the fast day and usually diet in every other day. Body weight (BW, fat mass and blood pressure (BP were measured. Fasting blood samples were collected at the first and 57th day of trial for biochemical analysis. Results During the course of the trial, BW of the subjects decreased (p Conclusion These finding suggest that short time ADF is a viable dietary option to help obese individuals lose weight and decrease some CAD risk factors. More and longer-term studies in human subjects are needed to support this important result.

  8. Genetic selection of peptide aptamers that interact and inhibit both Small protein B and alternative ribosome-rescue factor A of Aeromonas veronii C4

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2016-08-01

    Full Text Available Aeromonas veronii is a pathogenic gram-negative bacterium, which infects a variety of animals and results in mass mortality. The stalled-ribosome rescues are reported to ensure viability and virulence under stress conditions, of which primarily include trans-translation and alternative ribosome-rescue factor A (ArfA in A. veronii. For identification of specific peptides that interact and inhibit the stalled-ribosome rescues, peptide aptamer library (pTRG-SN-peptides was constructed using pTRG as vector and Staphylococcus aureus nuclease (SN as scaffold protein, in which 16 random amino acids were introduced to form an exposed surface loop. In the meantime both Small Protein B (SmpB which acts as one of the key components in trans-translation, and alternative ribosome-rescue factor A (ArfA were inserted to pBT to constitute pBT-SmpB and pBT-ArfA, respectively. The peptide aptamer PA-2 was selected from pTRG-SN-peptides by bacterial two-hybrid system (B2H employing pBT-SmpB or pBT-ArfA as baits. The conserved sites G133K134 and D138K139R140 of C-terminal SmpB were identified by interacting with N-terminal SN, and concurrently the residue K62 of ArfA was recognized by interacting with the surface loop of the specific peptide aptamer PA-2. The expression plasmids pN-SN or pN-PA-2, which combined the duplication origin of pRE112 with the neokanamycin promoter expressing SN or PA-2, were created and transformed into A. veronii C4, separately. The engineered A. veronii C4 which endowing SN or PA-2 expression impaired growth capabilities under stress conditions including temperatures, sucrose, glucose, potassium chloride (KCl and antibiotics, and the stress-related genes rpoS and nhaP were down-regulated significantly by Quantitative Real-time PCR (qRT-PCR when treating in 2.0% KCl. Thus,the engineered A. veronii C4 conferring PA-2 expression might be potentially attenuated vaccine, and also the peptide aptamer PA-2 could develop as anti

  9. Adressing Replication and Model Uncertainty

    DEFF Research Database (Denmark)

    Ebersberger, Bernd; Galia, Fabrice; Laursen, Keld

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

  10. Uracil DNA glycosylase BKRF3 contributes to Epstein-Barr virus DNA replication through physical interactions with proteins in viral DNA replication complex.

    Science.gov (United States)

    Su, Mei-Tzu; Liu, I-Hua; Wu, Chia-Wei; Chang, Shu-Ming; Tsai, Ching-Hwa; Yang, Pei-Wen; Chuang, Yu-Chia; Lee, Chung-Pei; Chen, Mei-Ru

    2014-08-01

    Epstein-Barr virus (EBV) BKRF3 shares sequence homology with members of the uracil-N-glycosylase (UNG) protein family and has DNA glycosylase activity. Here, we explored how BKRF3 participates in the DNA replication complex and contributes to viral DNA replication. Exogenously expressed Flag-BKRF3 was distributed mostly in the cytoplasm, whereas BKRF3 was translocated into the nucleus and colocalized with the EBV DNA polymerase BALF5 in the replication compartment during EBV lytic replication. The expression level of BKRF3 increased gradually during viral replication, coupled with a decrease of cellular UNG2, suggesting BKRF3 enzyme activity compensates for UNG2 and ensures the fidelity of viral DNA replication. In immunoprecipitation-Western blotting, BKRF3 was coimmuno-precipitated with BALF5, the polymerase processivity factor BMRF1, and the immediate-early transactivator Rta. Coexpression of BMRF1 appeared to facilitate the nuclear targeting of BKRF3 in immunofluorescence staining. Residues 164 to 255 of BKRF3 were required for interaction with Rta and BALF5, whereas residues 81 to 166 of BKRF3 were critical for BMRF1 interaction in glutathione S-transferase (GST) pulldown experiments. Viral DNA replication was defective in cells harboring BKRF3 knockout EBV bacmids. In complementation assays, the catalytic mutant BKRF3(Q90L,D91N) restored viral DNA replication, whereas the leucine loop mutant BKRF3(H213L) only partially rescued viral DNA replication, coupled with a reduced ability to interact with the viral DNA polymerase and Rta. Our data suggest that BKRF3 plays a critical role in viral DNA synthesis predominantly through its interactions with viral proteins in the DNA replication compartment, while its enzymatic activity may be supplementary for uracil DNA glycosylase (UDG) function during virus replication. Catalytic activities of both cellular UDG UNG2 and viral UDGs contribute to herpesviral DNA replication. To ensure that the enzyme activity executes at

  11. Human Cytomegalovirus Can Procure Deoxyribonucleotides for Viral DNA Replication in the Absence of Retinoblastoma Protein Phosphorylation.

    Science.gov (United States)

    Kuny, Chad V; Kalejta, Robert F

    2016-10-01

    Viral DNA replication requires deoxyribonucleotide triphosphates (dNTPs). These molecules, which are found at low levels in noncycling cells, are generated either by salvage pathways or through de novo synthesis. Nucleotide synthesis utilizes the activity of a series of nucleotide-biosynthetic enzymes (NBEs) whose expression is repressed in noncycling cells by complexes between the E2F transcription factors and the retinoblastoma (Rb) tumor suppressor. Rb-E2F complexes are dissociated and NBE expression is activated during cell cycle transit by cyclin-dependent kinase (Cdk)-mediated Rb phosphorylation. The DNA virus human cytomegalovirus (HCMV) encodes a viral Cdk (v-Cdk) (the UL97 protein) that phosphorylates Rb, induces the expression of cellular NBEs, and is required for efficient viral DNA synthesis. A long-held hypothesis proposed that viral proteins with Rb-inactivating activities functionally similar to those of UL97 facilitated viral DNA replication in part by inducing the de novo production of dNTPs. However, we found that dNTPs were limiting even in cells infected with wild-type HCMV in which UL97 is expressed and Rb is phosphorylated. Furthermore, we revealed that both de novo and salvage pathway enzymes contribute to viral DNA replication during HCMV infection and that Rb phosphorylation by cellular Cdks does not correct the viral DNA replication defect observed in cells infected with a UL97-deficient virus. We conclude that HCMV can obtain dNTPs in the absence of Rb phosphorylation and that UL97 can contribute to the efficiency of DNA replication in an Rb phosphorylation-independent manner. Transforming viral oncoproteins, such as adenovirus E1A and papillomavirus E7, inactivate Rb. The standard hypothesis for how Rb inactivation facilitates infection with these viruses is that it is through an increase in the enzymes required for DNA synthesis, which include nucleotide-biosynthetic enzymes. However, HCMV UL97, which functionally mimics these viral

  12. Genome-wide identification of hypoxia-inducible factor-1 and -2 binding sites in hypoxic human macrophages alternatively activated by IL-10.

    Science.gov (United States)

    Tausendschön, Michaela; Rehli, Michael; Dehne, Nathalie; Schmidl, Christian; Döring, Claudia; Hansmann, Martin-Leo; Brüne, Bernhard

    2015-01-01

    Macrophages (MΦ) often accumulate in hypoxic areas, where they significantly influence disease progression. Anti-inflammatory cytokines, such as IL-10, generate alternatively activated macrophages that support tumor growth. To understand how alternative activation affects the transcriptional profile of hypoxic macrophages, we globally mapped binding sites of hypoxia-inducible factor (HIF)-1α and HIF-2α in primary human monocyte-derived macrophages prestimulated with IL-10. 713 HIF-1 and 795 HIF-2 binding sites were identified under hypoxia. Pretreatment with IL-10 altered the binding pattern, with 120 new HIF-1 and 188 new HIF-2 binding sites emerging. HIF-1 binding was most prominent in promoters, while HIF-2 binding was more abundant in enhancer regions. Comparison of ChIP-seq data obtained in other cells revealed a highly cell type specific binding of HIF. In MΦ HIF binding occurred preferentially in already active enhancers or promoters. To assess the roles of HIF on gene expression, primary human macrophages were treated with siRNA against HIF-1α or HIF-2α, followed by genome-wide gene expression analysis. Comparing mRNA expression to the HIF binding profile revealed a significant enrichment of hypoxia-inducible genes previously identified by ChIP-seq. Analysis of gene expression under hypoxia alone and hypoxia/IL-10 showed the enhanced induction of a set of genes including PLOD2 and SLC2A3, while another group including KDM3A and ADM remained unaffected or was reduced by IL-10. Taken together IL-10 influences the DNA binding pattern of HIF and the level of gene induction. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Fox-2 Splicing Factor Binds to a Conserved Intron Motif to PromoteInclusion of Protein 4.1R Alternative Exon 16

    Energy Technology Data Exchange (ETDEWEB)

    Ponthier, Julie L.; Schluepen, Christina; Chen, Weiguo; Lersch,Robert A.; Gee, Sherry L.; Hou, Victor C.; Lo, Annie J.; Short, Sarah A.; Chasis, Joel A.; Winkelmann, John C.; Conboy, John G.

    2006-03-01

    Activation of protein 4.1R exon 16 (E16) inclusion during erythropoiesis represents a physiologically important splicing switch that increases 4.1R affinity for spectrin and actin. Previous studies showed that negative regulation of E16 splicing is mediated by the binding of hnRNP A/B proteins to silencer elements in the exon and that downregulation of hnRNP A/B proteins in erythroblasts leads to activation of E16 inclusion. This paper demonstrates that positive regulation of E16 splicing can be mediated by Fox-2 or Fox-1, two closely related splicing factors that possess identical RNA recognition motifs. SELEX experiments with human Fox-1 revealed highly selective binding to the hexamer UGCAUG. Both Fox-1 and Fox-2 were able to bind the conserved UGCAUG elements in the proximal intron downstream of E16, and both could activate E16 splicing in HeLa cell co-transfection assays in a UGCAUG-dependent manner. Conversely, knockdown of Fox-2 expression, achieved with two different siRNA sequences resulted in decreased E16 splicing. Moreover, immunoblot experiments demonstrate mouse erythroblasts express Fox-2, but not Fox-1. These findings suggest that Fox-2 is a physiological activator of E16 splicing in differentiating erythroid cells in vivo. Recent experiments show that UGCAUG is present in the proximal intron sequence of many tissue-specific alternative exons, and we propose that the Fox family of splicing enhancers plays an important role in alternative splicing switches during differentiation in metazoan organisms.

  14. Overcoming natural replication barriers: differential helicase requirements.

    Science.gov (United States)

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

    2012-02-01

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

  15. How alternative are alternative fuels?

    OpenAIRE

    Soffritti, Tiziana; Danielis, Romeo

    1998-01-01

    Could alternative fuel vehicles contribute to a substantial reduction of air pollution? Is there a market for alternative fuel vehicles? Could a market be created via a pollution tax? The article answers these questions on the basis of the available estimates.

  16. Viral and Cellular Determinants of Hepatitis C Virus RNA Replication in Cell Culture

    Science.gov (United States)

    Lohmann, Volker; Hoffmann, Sandra; Herian, Ulrike; Penin, Francois; Bartenschlager, Ralf

    2003-01-01

    Studies on the replication of hepatitis C virus (HCV) have been facilitated by the development of selectable subgenomic replicons replicating in the human hepatoma cell line Huh-7 at a surprisingly high level. Analysis of the replicon population in selected cells revealed the occurrence of cell culture-adaptive mutations that enhance RNA replication substantially. To gain a better understanding of HCV cell culture adaptation, we characterized conserved mutations identified by sequence analysis of 26 independent replicon cell clones for their effect on RNA replication. Mutations enhancing replication were found in nearly every nonstructural (NS) protein, and they could be subdivided into at least two groups by their effect on replication efficiency and cooperativity: (i) mutations in NS3 with a low impact on replication but that enhanced replication cooperatively when combined with highly adaptive mutations and (ii) mutations in NS4B, -5A, and -5B, causing a strong increase in replication but being incompatible with each other. In addition to adaptive mutations, we found that the host cell plays an equally important role for efficient RNA replication. We tested several passages of the same Huh-7 cell line and found up to 100-fold differences in their ability to support replicon amplification. These differences were not due to variations in internal ribosome entry site-dependent translation or RNA degradation. In a search for cellular factor(s) that might be responsible for the different levels of permissiveness of Huh-7 cells, we found that replication efficiency decreased with increasing amounts of transfected replicon RNA, indicating that viral RNA or proteins are cytopathic or that host cell factors in Huh-7 cells limit RNA amplification. In summary, these data show that the efficiency of HCV replication in cell culture is determined both by adaptation of the viral sequence and by the host cell itself. PMID:12584326

  17. Bromodomain Protein Brd4 Plays a Key Role in Merkel Cell Polyomavirus DNA Replication

    Science.gov (United States)

    Wang, Xin; Li, Jing; Schowalter, Rachel M.; Jiao, Jing; Buck, Christopher B.; You, Jianxin

    2012-01-01

    Merkel cell polyomavirus (MCV or MCPyV) is the first human polyomavirus to be definitively linked to cancer. The mechanisms of MCV-induced oncogenesis and much of MCV biology are largely unexplored. In this study, we demonstrate that bromodomain protein 4 (Brd4) interacts with MCV large T antigen (LT) and plays a critical role in viral DNA replication. Brd4 knockdown inhibits MCV replication, which can be rescued by recombinant Brd4. Brd4 colocalizes with the MCV LT/replication origin complex in the nucleus and recruits replication factor C (RFC) to the viral replication sites. A dominant negative inhibitor of the Brd4-MCV LT interaction can dissociate Brd4 and RFC from the viral replication complex and abrogate MCV replication. Furthermore, obstructing the physiologic interaction between Brd4 and host chromatin with the chemical compound JQ1(+) leads to enhanced MCV DNA replication, demonstrating that the role of Brd4 in MCV replication is distinct from its role in chromatin-associated transcriptional regulation. Our findings demonstrate mechanistic details of the MCV replication machinery; providing novel insight to elucidate the life cycle of this newly discovered oncogenic DNA virus. PMID:23144621

  18. SMC1-mediated intra-S-phase arrest facilitates bocavirus DNA replication.

    Science.gov (United States)

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

    2013-04-01

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

  19. Bromodomain protein Brd4 plays a key role in Merkel cell polyomavirus DNA replication.

    Directory of Open Access Journals (Sweden)

    Xin Wang

    Full Text Available Merkel cell polyomavirus (MCV or MCPyV is the first human polyomavirus to be definitively linked to cancer. The mechanisms of MCV-induced oncogenesis and much of MCV biology are largely unexplored. In this study, we demonstrate that bromodomain protein 4 (Brd4 interacts with MCV large T antigen (LT and plays a critical role in viral DNA replication. Brd4 knockdown inhibits MCV replication, which can be rescued by recombinant Brd4. Brd4 colocalizes with the MCV LT/replication origin complex in the nucleus and recruits replication factor C (RFC to the viral replication sites. A dominant negative inhibitor of the Brd4-MCV LT interaction can dissociate Brd4 and RFC from the viral replication complex and abrogate MCV replication. Furthermore, obstructing the physiologic interaction between Brd4 and host chromatin with the chemical compound JQ1(+ leads to enhanced MCV DNA replication, demonstrating that the role of Brd4 in MCV replication is distinct from its role in chromatin-associated transcriptional regulation. Our findings demonstrate mechanistic details of the MCV replication machinery; providing novel insight to elucidate the life cycle of this newly discovered oncogenic DNA virus.

  20. Analysis of JC virus DNA replication using a quantitative and high-throughput assay

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States); Gagnon, David [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Gjoerup, Ole [Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111 (United States); Archambault, Jacques [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Bullock, Peter A., E-mail: Peter.Bullock@tufts.edu [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States)

    2014-11-15

    Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication.

  1. 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....

  2. BPIFB6 Regulates Secretory Pathway Trafficking and Enterovirus Replication

    Science.gov (United States)

    Morosky, Stefanie; Lennemann, Nicholas J.

    2016-01-01

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

  3. Human geminin promotes pre-RC formation and DNA replication by stabilizing CDT1 in mitosis

    DEFF Research Database (Denmark)

    Ballabeni, Andrea; Melixetian, Marina; Zamponi, Raffaella

    2004-01-01

    Geminin is an unstable inhibitor of DNA replication that negatively regulates the licensing factor CDT1 and inhibits pre-replicative complex (pre-RC) formation in Xenopus egg extracts. Here we describe a novel function of Geminin. We demonstrate that human Geminin protects CDT1 from proteasome...

  4. Enzymatic recognition of DNA replication origins

    International Nuclear Information System (INIS)

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

    1983-01-01

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

  5. The use of transformed Escherichia coli for experimental angiogenesis induced by regulated in situ production of vascular endothelial growth factor--an alternative gene therapy.

    Science.gov (United States)

    Celec, Peter; Gardlík, Roman; Pálffy, Roland; Hodosy, Július; Stuchlík, Stanislav; Drahovská, Hana; Stuchlíková, Martina; Minárik, Gabriel; Lukács, Ján; Jurkovicová, Ingrid; Hulín, Ivan; Turna, Ján; Jakubovský, Ján; Kopáni, Martin; Danisovic, Lubos; Jandzík, Dávid; Kúdela, Matús; Yonemitsu, Yoshikazu

    2005-01-01

    Defects in angiogenesis (blood vessel formation) are responsible for two most important causes of death in developed countries (ischemic heart disease and cancer). Vascular endothelial growth factor (VEGF) plays a pivotal role in physiological and pathological regulation of angiogenesis. In the last years several studies have indicated the possibilities of VEGF in the therapy of ischemic heart disease. However, especially VEGF gene therapy (naked DNA, plasmids and adenovirus mediated) is associated with adverse side effects regarding the expression regulation. To prepare bacterial strains producing VEGF using plasmids containing the VEGF cDNA for the use in experimental angiogenesis. Escherichia coli strain BL21(DE3) was transformed with Bluescript vector containing the inserts with cDNA sequences coding VEGF-A isoforms (VEGF121, VEGF164, VEGF189). Selection of recombinants was achieved by cultivating E. coli cells on ampicillin-added medium. The expression of target genes in the T7 expression system was induced by isopropyl-beta-D-thiogalactoside (IPTG). Polyacrylamide gel electrophoresis of the cell lysates showed the presence of polypeptides of molecular weight corresponding with known values of VEGF isoforms. Blood vessel formation induced by bacterial VEGF production was proved in vivo in mice seven days after intraperitoneal injection of transformed bacteria by light microscopy. CONCLUSION AND HYPOTHESIS: In summary, E. coli strain expressing VEGF was prepared and its biological effect confirmed. Bacteria, which produce angiogenic factors, provide a new modality for experimental angiogenesis and may be also suitable for clinical use. The in situ production of therapeutic proteins using optimalized prokaryotic expression systems can represent a useful tool for treatment based on molecular biomedicine. The main advantage of the described approach lies in the enhanced regulation control--bacterial expression can be regulated positively (induction by exogenous

  6. Alternative sigma factors SigF, SigE, and SigG are essential for sporulation in Clostridium botulinum ATCC 3502.

    Science.gov (United States)

    Kirk, David G; Zhang, Zhen; Korkeala, Hannu; Lindström, Miia

    2014-08-01

    Clostridium botulinum produces heat-resistant endospores that may germinate and outgrow into neurotoxic cultures in foods. Sporulation is regulated by the transcription factor Spo0A and the alternative sigma factors SigF, SigE, SigG, and SigK in most spore formers studied to date. We constructed mutants of sigF, sigE, and sigG in C. botulinum ATCC 3502 and used quantitative reverse transcriptase PCR and electron microscopy to assess their expression of the sporulation pathway on transcriptional and morphological levels. In all three mutants the expression of spo0A was disrupted. The sigF and sigE mutants failed to induce sigG and sigK beyond exponential-phase levels and halted sporulation during asymmetric cell division. In the sigG mutant, peak transcription of sigE was delayed and sigK levels remained lower than that in the parent strain. The sigG mutant forespore was engulfed by the mother cell and possessed a spore coat but no peptidoglycan cortex. The findings suggest that SigF and SigE of C. botulinum ATCC 3502 are essential for early sporulation and late-stage induction of sigK, whereas SigG is essential for spore cortex formation but not for coat formation, as opposed to previous observations in B. subtilis sigG mutants. Our findings add to a growing body of evidence that regulation of sporulation in C. botulinum ATCC 3502, and among the clostridia, differs from the B. subtilis model. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  7. Investigation of oxidation and tautomerization of a recently synthesized Schiff base in micellar media using multivariate curve resolution alternative least squares and rank annihilation factor analysis methods.

    Science.gov (United States)

    Afkhami, Abbas; Khajavi, Farzad; Khanmohammadi, Hamid

    2009-08-11

    The oxidation of the recently synthesized Schiff base 3,6-bis((2-aminoethyl-5-Br-salicyliden)thio)pyridazine (PABST) with hydrogen peroxide was investigated using spectrophotometric studies. The reaction rate order and observed rate constant of the oxidation reaction was obtained in the mixture of N,N-dimethylformamide (DMF):water (30:70, v/v) at pH 10 using multivariate cure resolution alternative least squares (MCR-ALS) method and rank annihilation factor analysis (RAFA). The effective parameters on the oxidation rate constant such as percents of DMF, the effect of transition metals like Cu(2+), Zn(2+), Mn(2+) and Hg(2+) and the presence of surfactants were investigated. The keto-enol equilibria in DMF:water (30:70, v/v) solution at pH 7.6 was also investigated in the presence of surfactants. At concentrations above critical micelle concentration (cmc) of cationic surfactant cetyltrimethylammonium bromide (CTAB), the keto form was the predominant species, while at concentrations above cmc of anionic surfactant sodium dodecyl sulfate (SDS), the enol form was the predominant species. The kinetic reaction order and the rate constant of tautomerization in micellar medium were obtained using MCR-ALS and RAFA. The results obtained by both the methods were in a good agreement with each other. Also the effect of different volume percents of DMF on the rate constant of tautomerization was investigated. The neutral surfactant (Triton X-100) had no effect on tautomerization equilibrium.

  8. Essential Role of Rta in Lytic DNA Replication of Epstein-Barr Virus

    Science.gov (United States)

    Ghiassi-Nejad, Maryam; Golden, Sean; Delecluse, Henri-Jacques; Miller, George

    2013-01-01

    Two transcription factors, ZEBRA and Rta, switch Epstein-Barr virus (EBV) from the latent to the lytic state. While ZEBRA also plays an obligatory role as an activator of replication, it is not known whether Rta is directly required for replication. Rta is dispensable for amplification of an oriLyt-containing plasmid in a transient-replication assay. Here, we assessed the requirement for Rta in activation of viral DNA synthesis from the endogenous viral genome, a function that has not been established. Initially, we searched for a ZEBRA mutant that supports viral replication but not transcription. We found that Z(S186A), a mutant of ZEBRA unable to activate transcription of Rta or viral genes encoding replication proteins, is competent to bind to oriLyt and to function as an origin recognition protein. Ectopic expression of the six components of the EBV lytic replication machinery failed to rescue replication by Z(S186A). However, addition of Rta to Z(S186A) and the mixture of replication factors activated viral replication and late gene expression. Deletion mutagenesis of Rta indicated that the C-terminal 10 amino acids (aa) were essential for the function of Rta in replication. In vivo DNA binding studies revealed that Rta interacted with the enhancer region of oriLyt. In addition, expression of Rta and Z(S186A) together, but not individually, activated synthesis of the BHLF1 transcript, a lytic transcript required for the process of viral DNA replication. Our findings demonstrate that Rta plays an indispensable role in the process of lytic DNA replication. PMID:23077295

  9. Human Genome Replication Proceeds through Four Chromatin States

    Science.gov (United States)

    Julienne, Hanna; Zoufir, Azedine; Audit, Benjamin; Arneodo, Alain

    2013-01-01

    Advances in genomic studies have led to significant progress in understanding the epigenetically controlled interplay between chromatin structure and nuclear functions. Epigenetic modifications were shown to play a key role in transcription regulation and genome activity during development and differentiation or in response to the environment. Paradoxically, the molecular mechanisms that regulate the initiation and the maintenance of the spatio-temporal replication program in higher eukaryotes, and in particular their links to epigenetic modifications, still remain elusive. By integrative analysis of the genome-wide distributions of thirteen epigenetic marks in the human cell line K562, at the 100 kb resolution of corresponding mean replication timing (MRT) data, we identify four major groups of chromatin marks with shared features. These states have different MRT, namely from early to late replicating, replication proceeds though a transcriptionally active euchromatin state (C1), a repressive type of chromatin (C2) associated with polycomb complexes, a silent state (C3) not enriched in any available marks, and a gene poor HP1-associated heterochromatin state (C4). When mapping these chromatin states inside the megabase-sized U-domains (U-shaped MRT profile) covering about 50% of the human genome, we reveal that the associated replication fork polarity gradient corresponds to a directional path across the four chromatin states, from C1 at U-domains borders followed by C2, C3 and C4 at centers. Analysis of the other genome half is consistent with early and late replication loci occurring in separate compartments, the former correspond to gene-rich, high-GC domains of intermingled chromatin states C1 and C2, whereas the latter correspond to gene-poor, low-GC domains of alternating chromatin states C3 and C4 or long C4 domains. This new segmentation sheds a new light on the epigenetic regulation of the spatio-temporal replication program in human and provides a

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

    Directory of Open Access Journals (Sweden)

    Norbert S Hill

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

  11. Break-induced telomere synthesis underlies alternative telomere maintenance.

    Science.gov (United States)

    Dilley, Robert L; Verma, Priyanka; Cho, Nam Woo; Winters, Harrison D; Wondisford, Anne R; Greenberg, Roger A

    2016-11-03

    Homology-directed DNA repair is essential for genome maintenance through templated DNA synthesis. Alternative lengthening of telomeres (ALT) necessitates homology-directed DNA repair to maintain telomeres in about 10-15% of human cancers. How DNA damage induces assembly and execution of a DNA replication complex (break-induced replisome) at telomeres or elsewhere in the mammalian genome is poorly understood. Here we define break-induced telomere synthesis and demonstrate that it utilizes a specialized replisome, which underlies ALT telomere maintenance. DNA double-strand breaks enact nascent telomere synthesis by long-tract unidirectional replication. Proliferating cell nuclear antigen (PCNA) loading by replication factor C (RFC) acts as the initial sensor of telomere damage to establish predominance of DNA polymerase δ (Pol δ) through its POLD3 subunit. Break-induced telomere synthesis requires the RFC-PCNA-Pol δ axis, but is independent of other canonical replisome components, ATM and ATR, or the homologous recombination protein Rad51. Thus, the inception of telomere damage recognition by the break-induced replisome orchestrates homology-directed telomere maintenance.

  12. Functional diversity of human basic helix-loop-helix transcription factor TCF4 isoforms generated by alternative 5' exon usage and splicing.

    Directory of Open Access Journals (Sweden)

    Mari Sepp

    Full Text Available BACKGROUND: Transcription factor 4 (TCF4 alias ITF2, E2-2, ME2 or SEF2 is a ubiquitous class A basic helix-loop-helix protein that binds to E-box DNA sequences (CANNTG. While involved in the development and functioning of many different cell types, recent studies point to important roles for TCF4 in the nervous system. Specifically, human TCF4 gene is implicated in susceptibility to schizophrenia and TCF4 haploinsufficiency is the cause of the Pitt-Hopkins mental retardation syndrome. However, the structure, expression and coding potential of the human TCF4 gene have not been described in detail. PRINCIPAL FINDINGS: In the present study we used human tissue samples to characterize human TCF4 gene structure and TCF4 expression at mRNA and protein level. We report that although widely expressed, human TCF4 mRNA expression is particularly high in the brain. We demonstrate that usage of numerous 5' exons of the human TCF4 gene potentially yields in TCF4 protein isoforms with 18 different N-termini. In addition, the diversity of isoforms is increased by alternative splicing of several internal exons. For functional characterization of TCF4 isoforms, we overexpressed individual isoforms in cultured human cells. Our analysis revealed that subcellular distribution of TCF4 isoforms is differentially regulated: Some isoforms contain a bipartite nuclear localization signal and are exclusively nuclear, whereas distribution of other isoforms relies on heterodimerization partners. Furthermore, the ability of different TCF4 isoforms to regulate E-box controlled reporter gene transcription is varied depending on whether one or both of the two TCF4 transcription activation domains are present in the protein. Both TCF4 activation domains are able to activate transcription independently, but act synergistically in combination. CONCLUSIONS: Altogether, in this study we have described the inter-tissue variability of TCF4 expression in human and provided evidence

  13. Architecture of Burkholderia cepacia complex σ70 gene family: evidence of alternative primary and clade-specific factors, and genomic instability

    Directory of Open Access Journals (Sweden)

    Menard Aymeric

    2007-09-01

    Full Text Available Abstract Background The Burkholderia cepacia complex (Bcc groups bacterial species with beneficial properties that can improve crop yields or remediate polluted sites but can also lead to dramatic human clinical outcomes among cystic fibrosis (CF or immuno-compromised individuals. Genome-wide regulatory processes of gene expression could explain parts of this bacterial duality. Transcriptional σ70 factors are components of these processes. They allow the reversible binding of the DNA-dependent RNA polymerase to form the holoenzyme that will lead to mRNA synthesis from a DNA promoter region. Bcc genome-wide analyses were performed to investigate the major evolutionary trends taking place in the σ70 family of these bacteria. Results Twenty σ70 paralogous genes were detected in the Burkholderia cenocepacia strain J2315 (Bcen-J2315 genome, of which 14 were of the ECF (extracytoplasmic function group. Non-ECF paralogs were related to primary (rpoD, alternative primary, stationary phase (rpoS, flagellin biosynthesis (fliA, and heat shock (rpoH factors. The number of σ70 genetic determinants among this genome was of 2,86 per Mb. This number is lower than the one of Pseudomonas aeruginosa, a species found in similar habitats including CF lungs. These two bacterial groups showed strikingly different σ70 family architectures, with only three ECF paralogs in common (fecI-like, pvdS and algU. Bcen-J2315 σ70 paralogs showed clade-specific distributions. Some paralogs appeared limited to the ET12 epidemic clone (ecfA2, particular Bcc species (sigI, the Burkholderia genus (ecfJ, ecfF, and sigJ, certain proteobacterial groups (ecfA1, ecfC, ecfD, ecfE, ecfG, ecfL, ecfM and rpoS, or were broadly distributed in the eubacteria (ecfI, ecfK, ecfH, ecfB, and rpoD-, rpoH-, fliA-like genes. Genomic instability of this gene family was driven by chromosomal inversion (ecfA2, recent duplication events (ecfA and RpoD, localized (ecfG and large scale deletions (sig

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

    Science.gov (United States)

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

    2013-01-01

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

  15. Using Replication Projects in Teaching Research Methods

    Science.gov (United States)

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

    2014-01-01

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

  16. 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…

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

    OpenAIRE

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

    2014-01-01

    This dataset is from the Many Labs Replication Project in which 13 effects were replicated across 36 samples and over 6,000 participants. Data from the replications are included, along with demographic variables about the participants and contextual information about the environment in which the replication was conducted. Data were collected in-lab and online through a standardized procedure administered via an online link. The dataset is stored on the Open Science Framework website. These da...

  18. Ultrastructure of the replication sites of positive-strand RNA viruses

    Energy Technology Data Exchange (ETDEWEB)

    Harak, Christian; Lohmann, Volker, E-mail: volker_lohmann@med.uni-heidelberg.de

    2015-05-15

    Positive strand RNA viruses replicate in the cytoplasm of infected cells and induce intracellular membranous compartments harboring the sites of viral RNA synthesis. These replication factories are supposed to concentrate the components of the replicase and to shield replication intermediates from the host cell innate immune defense. Virus induced membrane alterations are often generated in coordination with host factors and can be grouped into different morphotypes. Recent advances in conventional and electron microscopy have contributed greatly to our understanding of their biogenesis, but still many questions remain how viral proteins capture membranes and subvert host factors for their need. In this review, we will discuss different representatives of positive strand RNA viruses and their ways of hijacking cellular membranes to establish replication complexes. We will further focus on host cell factors that are critically involved in formation of these membranes and how they contribute to viral replication. - Highlights: • Positive strand RNA viruses induce massive membrane alterations. • Despite the great diversity, replication complexes share many similarities. • Host factors play a pivotal role in replication complex biogenesis. • Use of the same host factors by several viruses hints to similar functions.

  19. Proteomics Reveals Global Regulation of Protein SUMOylation by ATM and ATR Kinases during Replication Stress

    Directory of Open Access Journals (Sweden)

    Stephanie Munk

    2017-10-01

    Full Text Available The mechanisms that protect eukaryotic DNA during the cumbersome task of replication depend on the precise coordination of several post-translational modification (PTM-based signaling networks. Phosphorylation is a well-known regulator of the replication stress response, and recently an essential role for SUMOs (small ubiquitin-like modifiers has also been established. Here, we investigate the global interplay between phosphorylation and SUMOylation in response to replication stress. Using SUMO and phosphoproteomic technologies, we identify thousands of regulated modification sites. We find co-regulation of central DNA damage and replication stress responders, of which the ATR-activating factor TOPBP1 is the most highly regulated. Using pharmacological inhibition of the DNA damage response kinases ATR and ATM, we find that these factors regulate global protein SUMOylation in the protein networks that protect DNA upon replication stress and fork breakage, pointing to integration between phosphorylation and SUMOylation in the cellular systems that protect DNA integrity.

  20. Proteomics Reveals Global Regulation of Protein SUMOylation by ATM and ATR Kinases during Replication Stress

    DEFF Research Database (Denmark)

    Munk, Stephanie; Sigurðsson, Jón Otti; Xiao, Zhenyu

    2017-01-01

    The mechanisms that protect eukaryotic DNA during the cumbersome task of replication depend on the precise coordination of several post-translational modification (PTM)-based signaling networks. Phosphorylation is a well-known regulator of the replication stress response, and recently an essential......-regulation of central DNA damage and replication stress responders, of which the ATR-activating factor TOPBP1 is the most highly regulated. Using pharmacological inhibition of the DNA damage response kinases ATR and ATM, we find that these factors regulate global protein SUMOylation in the protein networks that protect...... DNA upon replication stress and fork breakage, pointing to integration between phosphorylation and SUMOylation in the cellular systems that protect DNA integrity. Munk et al. use mass spectrometry-based proteomics to analyze the interplay between SUMOylation and phosphorylation in replication stress...

  1. Suppression of Poxvirus Replication by Resveratrol

    Directory of Open Access Journals (Sweden)

    Shuai Cao

    2017-11-01

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

  2. Characteristics of the poliovirus replication complex.

    Science.gov (United States)

    Bienz, K; Egger, D; Pfister, T

    1994-01-01

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

  3. 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…

  4. Alternative Therapies

    Science.gov (United States)

    ... the widespread and erroneous belief that they are natural and do no harm, and because their use offers the opportunity for more control over treatment options and procedures. Alternative therapies can reduce stress, pain, and/or fatigue. Some therapies are covered ...

  5. Growing Alternatives

    DEFF Research Database (Denmark)

    Bagger-Petersen, Mai Corlin

    2014-01-01

    From 2014, Anhui Province will pilot a reform of the residential land market in China, thus integrating rural Anhui in the national housing market. In contrast, artist and activist Ou Ning has proposed the Bishan time money currency, intending to establish an alternative economic circuit in Bishan...

  6. Magnetostrictive Alternator

    Science.gov (United States)

    Dyson, Rodger; Bruder, Geoffrey

    2013-01-01

    This innovation replaces the linear alternator presently used in Stirling engines with a continuous-gradient, impedance-matched, oscillating magnetostrictive transducer that eliminates all moving parts via compression, maintains high efficiency, costs less to manufacture, reduces mass, and eliminates the need for a bearing system. The key components of this new technology are the use of stacked magnetostrictive materials, such as Terfenol-D, under a biased magnetic and stress-induced compression, continuous-gradient impedance-matching material, coils, force-focusing metallic structure, and supports. The acoustic energy from the engine travels through an impedancematching layer that is physically connected to the magnetostrictive mass. Compression bolts keep the structure under compressive strain, allowing for the micron-scale compression of the magnetostrictive material and eliminating the need for bearings. The relatively large millimeter displacement of the pressure side of the impedance-matching material is reduced to micron motion, and undergoes stress amplification at the magnetostrictive interface. The alternating compression and expansion of the magnetostrictive material creates an alternating magnetic field that then induces an electric current in a coil that is wound around the stack. This produces electrical power from the acoustic pressure wave and, if the resonant frequency is tuned to match the engine, can replace the linear alternator that is commonly used.

  7. Combined Roles of Human IgG Subclass, Alternative Complement Pathway Activation, and Epitope Density in the Bactericidal Activity of Antibodies to Meningococcal Factor H Binding Protein

    Science.gov (United States)

    Giuntini, Serena; Reason, Donald C.

    2012-01-01

    Meningococcal vaccines containing factor H binding protein (fHbp) are in clinical development. fHbp binds human fH, which enables the meningococcus to resist complement-mediated bacteriolysis. Previously, we found that chimeric human IgG1 mouse anti-fHbp monoclonal antibodies (MAbs) had human complement-mediated bactericidal activity only if the MAb inhibited fH binding. Since IgG subclasses differ in their ability to activate complement, we investigated the role of human IgG subclasses on antibody functional activity. We constructed chimeric MAbs in which three different murine fHbp-specific binding domains were each paired with human IgG1, IgG2, or IgG3. Against a wild-type group B isolate, all three IgG3 MAbs, irrespective of their ability to inhibit fH binding, had bactericidal activity that was >5-fold higher than the respective IgG1 MAbs, while the IgG2 MAbs had the least activity. Against a mutant with increased fHbp expression, the anti-fHbp MAbs elicited greater C4b deposition (classical pathway) and greater bactericidal activity than against the wild-type strain, and the IgG1 MAbs had similar or greater activity than the respective IgG3 MAbs. The bactericidal activity against both wild-type and mutant strains also was dependent, in part, on activation of the alternative complement pathway. Thus, at lower epitope density in the wild-type strain, the IgG3 anti-fHbp MAbs had the greatest bactericidal activity. At a higher epitope density in the mutant, the IgG1 MAbs had similar or greater bactericidal activity than the IgG3 MAbs, and the activity was less dependent on the inhibition of fH binding than at a lower epitope density. PMID:22064712

  8. Examining the Relations Among the DSM-5 Alternative Model of Personality, the Five-Factor Model, and Externalizing and Internalizing Behavior.

    Science.gov (United States)

    Sleep, Chelsea E; Hyatt, Courtland S; Lamkin, Joanna; Maples-Keller, Jessica L; Miller, Joshua D

    2017-01-26

    Given long-standing criticisms of the DSM's reliance on categorical models of psychopathology, including the poor reliability and validity of personality-disorder diagnoses, the American Psychiatric Association (APA) published an alternative model (AM) of personality disorders in Section III of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5; APA, 2013), which, in part, comprises 5 pathological trait domains based on the 5-factor model (FFM). However, the empirical profiles and discriminant validity of the AM traits remain in question. We recruited a sample of undergraduates (N = 340) for the current study to compare the relations found between a measure of the DSM-5 AM traits (i.e., the Personality Inventory for DSM-5; PID-5; Krueger, Derringer, Markon, Watson, & Skodol, 2012) and a measure of the FFM (i.e., the International Personality Item Pool; IPIP; Goldberg, 1999) in relation to externalizing and internalizing symptoms. In general, the domains from the 2 measures were significantly related and demonstrated similar patterns of relations with these criteria, such that Antagonism/low Agreeableness and Disinhibition/low Conscientiousness were related to externalizing behaviors, whereas Negative Affectivity/Neuroticism was most significantly related to internalizing symptoms. However, the PID-5 demonstrated large interrelations among its domains and poorer discriminant validity than the IPIP. These results provide additional support that the conception of the trait model included in the DSM-5 AM is an extension of the FFM, but highlight some of the issues that arise due to the PID-5's more limited discriminant validity. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  9. Host ESCRT proteins are required for bromovirus RNA replication compartment assembly and function.

    Directory of Open Access Journals (Sweden)

    Arturo Diaz

    2015-03-01

    Full Text Available Positive-strand RNA viruses genome replication invariably is associated with vesicles or other rearranged cellular membranes. Brome mosaic virus (BMV RNA replication occurs on perinuclear endoplasmic reticulum (ER membranes in ~70 nm vesicular invaginations (spherules. BMV RNA replication vesicles show multiple parallels with membrane-enveloped, budding retrovirus virions, whose envelopment and release depend on the host ESCRT (endosomal sorting complexes required for transport membrane-remodeling machinery. We now find that deleting components of the ESCRT pathway results in at least two distinct BMV phenotypes. One group of genes regulate RNA replication and the frequency of viral replication complex formation, but had no effect on spherule size, while a second group of genes regulate RNA replication in a way or ways independent of spherule formation. In particular, deleting SNF7 inhibits BMV RNA replication > 25-fold and abolishes detectable BMV spherule formation, even though the BMV RNA replication proteins accumulate and localize normally on perinuclear ER membranes. Moreover, BMV ESCRT recruitment and spherule assembly depend on different sets of protein-protein interactions from those used by multivesicular body vesicles, HIV-1 virion budding, or tomato bushy stunt virus (TBSV spherule formation. These and other data demonstrate that BMV requires cellular ESCRT components for proper formation and function of its vesicular RNA replication compartments. The results highlight growing but diverse interactions of ESCRT factors with many viruses and viral processes, and potential value of the ESCRT pathway as a target for broad-spectrum antiviral resistance.

  10. Replication Vesicles are Load- and Choke-Points in the Hepatitis C Virus Lifecycle

    Science.gov (United States)

    Clausznitzer, Diana; Schulze, Manuel; Hüber, Christian M.; Lenz, Simon M.; Schlöder, Johannes P.; Trippler, Martin; Bartenschlager, Ralf; Lohmann, Volker; Kaderali, Lars

    2013-01-01

    Hepatitis C virus (HCV) infection develops into chronicity in 80% of all patients, characterized by persistent low-level replication. To understand how the virus establishes its tightly controlled intracellular RNA replication cycle, we developed the first detailed mathematical model of the initial dynamic phase of the intracellular HCV RNA replication. We therefore quantitatively measured viral RNA and protein translation upon synchronous delivery of viral genomes to host cells, and thoroughly validated the model using additional, independent experiments. Model analysis was used to predict the efficacy of different classes of inhibitors and identified sensitive substeps of replication that could be targeted by current and future therapeutics. A protective replication compartment proved to be essential for sustained RNA replication, balancing translation versus replication and thus effectively limiting RNA amplification. The model predicts that host factors involved in the formation of this compartment determine cellular permissiveness to HCV replication. In gene expression profiling, we identified several key processes potentially determining cellular HCV replication efficiency. PMID:23990783

  11. Replication vesicles are load- and choke-points in the hepatitis C virus lifecycle.

    Directory of Open Access Journals (Sweden)

    Marco Binder

    Full Text Available Hepatitis C virus (HCV infection develops into chronicity in 80% of all patients, characterized by persistent low-level replication. To understand how the virus establishes its tightly controlled intracellular RNA replication cycle, we developed the first detailed mathematical model of the initial dynamic phase of the intracellular HCV RNA replication. We therefore quantitatively measured viral RNA and protein translation upon synchronous delivery of viral genomes to host cells, and thoroughly validated the model using additional, independent experiments. Model analysis was used to predict the efficacy of different classes of inhibitors and identified sensitive substeps of replication that could be targeted by current and future therapeutics. A protective replication compartment proved to be essential for sustained RNA replication, balancing translation versus replication and thus effectively limiting RNA amplification. The model predicts that host factors involved in the formation of this compartment determine cellular permissiveness to HCV replication. In gene expression profiling, we identified several key processes potentially determining cellular HCV replication efficiency.

  12. A quantitative and high-throughput assay of human papillomavirus DNA replication.

    Science.gov (United States)

    Gagnon, David; Fradet-Turcotte, Amélie; Archambault, Jacques

    2015-01-01

    Replication of the human papillomavirus (HPV) double-stranded DNA genome is accomplished by the two viral proteins E1 and E2 in concert with host DNA replication factors. HPV DNA replication is an established model of eukaryotic DNA replication and a potential target for antiviral therapy. Assays to measure the transient replication of HPV DNA in transfected cells have been developed, which rely on a plasmid carrying the viral origin of DNA replication (ori) together with expression vectors for E1 and E2. Replication of the ori-plasmid is typically measured by Southern blotting or PCR analysis of newly replicated DNA (i.e., DpnI digested DNA) several days post-transfection. Although extremely valuable, these assays have been difficult to perform in a high-throughput and quantitative manner. Here, we describe a modified version of the transient DNA replication assay that circumvents these limitations by incorporating a firefly luciferase expression cassette in cis of the ori. Replication of this ori-plasmid by E1 and E2 results in increased levels of firefly luciferase activity that can be accurately quantified and normalized to those of Renilla luciferase expressed from a control plasmid, thus obviating the need for DNA extraction, digestion, and analysis. We provide a detailed protocol for performing the HPV type 31 DNA replication assay in a 96-well plate format suitable for small-molecule screening and EC50 determinations. The quantitative and high-throughput nature of the assay should greatly facilitate the study of HPV DNA replication and the identification of inhibitors thereof.

  13. 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.

  14. DNA Replication Arrest and DNA Damage Responses Induced by Alkylating Minor Groove Binders

    National Research Council Canada - National Science Library

    Kuo, Shue-Ru

    2001-01-01

    .... Both DNA-PK and the unknown factor are functioned as trans-acting inhibitors. RPA is the major eukaryotic single-stranded DNA binding protein required for DNA replication, repair and recombination...

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

    Directory of Open Access Journals (Sweden)

    Nicholas Chia

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

  16. Specificity and Function of Archaeal DNA Replication Initiator Proteins

    Directory of Open Access Journals (Sweden)

    Rachel Y. Samson

    2013-02-01

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

  17. Phosphorylated STAT5 directly facilitates parvovirus B19 DNA replication in human erythroid progenitors through interaction with the MCM complex.

    Science.gov (United States)

    Ganaie, Safder S; Zou, Wei; Xu, Peng; Deng, Xuefeng; Kleiboeker, Steve; Qiu, Jianming

    2017-05-01

    Productive infection of human parvovirus B19 (B19V) exhibits high tropism for burst forming unit erythroid (BFU-E) and colony forming unit erythroid (CFU-E) progenitor cells in human bone marrow and fetal liver. This exclusive restriction of the virus replication to human erythroid progenitor cells is partly due to the intracellular factors that are essential for viral DNA replication, including erythropoietin signaling. Efficient B19V replication also requires hypoxic conditions, which upregulate the signal transducer and activator of transcription 5 (STAT5) pathway, and phosphorylated STAT5 is essential for virus replication. In this study, our results revealed direct involvement of STAT5 in B19V DNA replication. Consensus STAT5-binding elements were identified adjacent to the NS1-binding element within the minimal origins of viral DNA replication in the B19V genome. Phosphorylated STAT5 specifically interacted with viral DNA replication origins both in vivo and in vitro, and was actively recruited within the viral DNA replication centers. Notably, STAT5 interacted with minichromosome maintenance (MCM) complex, suggesting that STAT5 directly facilitates viral DNA replication by recruiting the helicase complex of the cellular DNA replication machinery to viral DNA replication centers. The FDA-approved drug pimozide dephosphorylates STAT5, and it inhibited B19V replication in ex vivo expanded human erythroid progenitors. Our results demonstrated that pimozide could be a promising antiviral drug for treatment of B19V-related diseases.

  18. Ultrastructural Characterization of Zika Virus Replication Factories

    Directory of Open Access Journals (Sweden)

    Mirko Cortese

    2017-02-01

    Full Text Available Summary: A global concern has emerged with the pandemic spread of Zika virus (ZIKV infections that can cause severe neurological symptoms in adults and newborns. ZIKV is a positive-strand RNA virus replicating in virus-induced membranous replication factories (RFs. Here we used various imaging techniques to investigate the ultrastructural details of ZIKV RFs and their relationship with host cell organelles. Analyses of human hepatic cells and neural progenitor cells infected with ZIKV revealed endoplasmic reticulum (ER membrane invaginations containing pore-like openings toward the cytosol, reminiscent to RFs in Dengue virus-infected cells. Both the MR766 African strain and the H/PF/2013 Asian strain, the latter linked to neurological diseases, induce RFs of similar architecture. Importantly, ZIKV infection causes a drastic reorganization of microtubules and intermediate filaments forming cage-like structures surrounding the viral RF. Consistently, ZIKV replication is suppressed by cytoskeleton-targeting drugs. Thus, ZIKV RFs are tightly linked to rearrangements of the host cell cytoskeleton. : Cortese et al. show that ZIKV infection in both human hepatoma and neuronal progenitor cells induces drastic structural modification of the cellular architecture. Microtubules and intermediate filaments surround the viral replication factory composed of vesicles corresponding to ER membrane invagination toward the ER lumen. Importantly, alteration of microtubule flexibility impairs ZIKV replication. Keywords: Zika virus, flavivirus, human neural progenitor cells, replication factories, replication organelles, microtubules, intermediate filaments, electron microscopy, electron tomography, live-cell imaging

  19. Alternative 23

    OpenAIRE

    Jackson, Mark

    2014-01-01

    Alternative 23 is a curated exhibition of works by Steve Aylett, David Blandy & Daniel Locke, Let Me Feel Your Finger First, Laura Oldfield Ford, Plastique Fantastique and Henrik Schrat, including the first screening of Let Me Feel Your Finger First’s Postcolonial Capers.\\ud \\ud In 1985 DC Comics in the US had taken the commercial decision to unify the complex and contradictory character story arcs from its various strips such as Superman, Batman and Green Lantern. The resultant crossover ser...

  20. Transcriptional control of DNA replication licensing by Myc

    Science.gov (United States)

    Valovka, Taras; Schönfeld, Manuela; Raffeiner, Philipp; Breuker, Kathrin; Dunzendorfer-Matt, Theresia; Hartl, Markus; Bister, Klaus

    2013-12-01

    The c-myc protooncogene encodes the Myc transcription factor, a global regulator of fundamental cellular processes. Deregulation of c-myc leads to tumorigenesis, and c-myc is an important driver in human cancer. Myc and its dimerization partner Max are bHLH-Zip DNA binding proteins involved in transcriptional regulation of target genes. Non-transcriptional functions have also been attributed to the Myc protein, notably direct interaction with the pre-replicative complex (pre-RC) controlling the initiation of DNA replication. A key component of the pre-RC is the Cdt1 protein, an essential factor in origin licensing. Here we present data suggesting that the CDT1 gene is a transcriptional target of the Myc-Max complex. Expression of the CDT1 gene in v-myc-transformed cells directly correlates with myc expression. Also, human tumor cells with elevated c-myc expression display increased CDT1 expression. Occupation of the CDT1 promoter by Myc-Max is demonstrated by chromatin immunoprecipitation, and transactivation by Myc-Max is shown in reporter assays. Ectopic expression of CDT1 leads to cell transformation. Our results provide a possible direct mechanistic link of Myc's canonical function as a transcription factor to DNA replication. Furthermore, we suggest that aberrant transcriptional activation of CDT1 by deregulated myc alleles contributes to the genomic instabilities observed in tumor cells.

  1. 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

  2. Replication and Analysis of Ebbinghaus' Forgetting Curve.

    Science.gov (United States)

    Murre, Jaap M J; Dros, Joeri

    2015-01-01

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

  3. Replication and Analysis of Ebbinghaus’ Forgetting Curve

    Science.gov (United States)

    Murre, Jaap M. J.; Dros, Joeri

    2015-01-01

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

  4. Replication and Analysis of Ebbinghaus' Forgetting Curve.

    Directory of Open Access Journals (Sweden)

    Jaap M J Murre

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

  5. Replication-Competent Controlled Herpes Simplex Virus.

    Science.gov (United States)

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

    2015-10-01

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

  6. High aspect ratio PDMS replication through proton beam fabricated Ni masters

    International Nuclear Information System (INIS)

    Kan, J.A. van; Wang, L.P.; Shao, P.G.; Bettiol, A.A.; Watt, F.

    2007-01-01

    In application areas where multiple samples are required (for example tissue engineering substrates), proton beam writing (PBW) is a suitable technique to fabricate high quality metal masters. These masters can then be used to replicate multiple copies in polymers, either through nanoimprinting or softlithography. Since poly(dimethyl siloxane) (PDMS) is a compatible material in tissue engineering we explore PDMS casting on Ni masters as an alternative way to replicate high aspect ratio micro structures. Ni masters with grooves spaced 2.5 μm apart, and 13 μm deep were successfully replicated in PDMS: These PDMS structures, which have aspect ratio of more than 5, are comparable to the best high aspect ratios reported in PDMS replication

  7. AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

    Directory of Open Access Journals (Sweden)

    Sara Ballouz

    2016-04-01

    Full Text Available In addition to detecting novel transcripts and higher dynamic range, a principal claim for RNA-sequencing has been greater replicability, typically measured in sample-sample correlations of gene expression levels. Through a re-analysis of ENCODE data, we show that replicability of transcript abundances will provide misleading estimates of the replicability of conditional variation in transcript abundances (i.e., most expression experiments. Heuristics which implicitly address this problem have emerged in quality control measures to obtain 'good' differential expression results. However, these methods involve strict filters such as discarding low expressing genes or using technical replicates to remove discordant transcripts, and are costly or simply ad hoc. As an alternative, we model gene-level replicability of differential activity using co-expressing genes. We find that sets of housekeeping interactions provide a sensitive means of estimating the replicability of expression changes, where the co-expressing pair can be regarded as pseudo-replicates of one another. We model the effects of noise that perturbs a gene's expression within its usual distribution of values and show that perturbing expression by only 5% within that range is readily detectable (AUROC~0.73. We have made our method available as a set of easily implemented R scripts.

  8. Electron microscopy of DNA replication in 3-D: Evidence for similar-sized replication foci throughout S-phase

    Czech Academy of Sciences Publication Activity Database

    Koberna, Karel; Ligasová, Anna; Malínský, Jan; Pliss, A.; Siegel, A. J.; Cvačková, Zuzana; Fidlerová, Helena; Mašata, Martin; Fialová, Markéta; Raška, Ivan; Berezney, R.

    2005-01-01

    Roč. 94, č. 1 (2005), s. 126-138 ISSN 0730-2312 R&D Projects: GA ČR GA304/01/0729; GA ČR GA304/03/1121; GA ČR GA304/02/0342; GA AV ČR IAA5039103 Institutional research plan: CEZ:AV0Z5039906 Keywords : mammalian DNA replication Subject RIV: EA - Cell Biology Impact factor: 3.591, year: 2005

  9. Effects of morphine on replication of herpes simplex virus type 1 and 2

    African Journals Online (AJOL)

    USER

    2009-05-17

    May 17, 2009 ... virus genome has a double strand DNA which codes over. 70 gene products. HSV infection is the most ... essential for viral replication, unlike viral DNA poly- merase. It seems that an alternative method of ... tral red was used and plaques were counted after 12 h. Determination of morphine cytotoxicity.

  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. Surface Microstructure Replication in Injection Moulding

    DEFF Research Database (Denmark)

    Hansen, Hans Nørgaard; Arlø, Uffe Rolf

    2005-01-01

    topography is transcribed onto the plastic part through complex mechanisms. This replication however, is not perfect, and the replication quality depends on the plastic material properties, the topography itself, and the process conditions. This paper describes and discusses an investigation of injection......In recent years polymer components with surface microstructures have been in rising demand for applications such as lab-on-a-chip and optical components. Injection moulding has proven to be a feasible and efficient way to manufacture such components. In injection moulding the mould surface...... moulding of surface microstructures. Emphasis is put on the ability to replicate surface microstructures under normal injection moulding conditions, notably with low cost materials at low mould temperatures. The replication of surface microstructures in injection moulding has been explored...

  12. Lipid Tales of Viral Replication and Transmission.

    Science.gov (United States)

    Altan-Bonnet, Nihal

    2017-03-01

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

  13. 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...

  14. Molecular Mechanisms of DNA Replication Checkpoint Activation

    Directory of Open Access Journals (Sweden)

    Bénédicte Recolin

    2014-03-01

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

  15. Muscle-specific splicing factors ASD-2 and SUP-12 cooperatively switch alternative pre-mRNA processing patterns of the ADF/cofilin gene in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Genta Ohno

    Full Text Available Pre-mRNAs are often processed in complex patterns in tissue-specific manners to produce a variety of protein isoforms from single genes. However, mechanisms orchestrating the processing of the entire transcript are not well understood. Muscle-specific alternative pre-mRNA processing of the unc-60 gene in Caenorhabditis elegans, encoding two tissue-specific isoforms of ADF/cofilin with distinct biochemical properties in regulating actin organization, provides an excellent in vivo model of complex and tissue-specific pre-mRNA processing; it consists of a single first exon and two separate series of downstream exons. Here we visualize the complex muscle-specific processing pattern of the unc-60 pre-mRNA with asymmetric fluorescence reporter minigenes. By disrupting juxtaposed CUAAC repeats and UGUGUG stretch in intron 1A, we demonstrate that these elements are required for retaining intron 1A, as well as for switching the processing patterns of the entire pre-mRNA from non-muscle-type to muscle-type. Mutations in genes encoding muscle-specific RNA-binding proteins ASD-2 and SUP-12 turned the colour of the unc-60 reporter worms. ASD-2 and SUP-12 proteins specifically and cooperatively bind to CUAAC repeats and UGUGUG stretch in intron 1A, respectively, to form a ternary complex in vitro. Immunohistochemical staining and RT-PCR analyses demonstrate that ASD-2 and SUP-12 are also required for switching the processing patterns of the endogenous unc-60 pre-mRNA from UNC-60A to UNC-60B in muscles. Furthermore, systematic analyses of partially spliced RNAs reveal the actual orders of intron removal for distinct mRNA isoforms. Taken together, our results demonstrate that muscle-specific splicing factors ASD-2 and SUP-12 cooperatively promote muscle-specific processing of the unc-60 gene, and provide insight into the mechanisms of complex pre-mRNA processing; combinatorial regulation of a single splice site by two tissue-specific splicing regulators

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

    Science.gov (United States)

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

    2015-09-01

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

  17. Replication and Analysis of Ebbinghaus? Forgetting Curve

    OpenAIRE

    Murre, Jaap M. J.; Dros, Joeri

    2015-01-01

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

  18. Evolution of Database Replication Technologies for WLCG

    OpenAIRE

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

    2015-01-01

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

  19. The Legal Road To Replicating Silicon Valley

    OpenAIRE

    John Armour; Douglas Cumming

    2004-01-01

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

  20. Alternative detente

    International Nuclear Information System (INIS)

    Soper, K.; Ryle, M.

    1988-01-01

    The influence of the Chernobyl accident on the disarmament and anti-nuclear movements is discussed. The accident directed attention towards the areas in common rather than the areas of disagreement. It also demonstrated the environmental impact of radioactivity, strengthening the ecological case of the anti-nuclear movement. The issues are discussed for the Western and Eastern bloc countries and the relationship between the two. Sections focus on the Eco-protest, Green politics and economics and on the politics of minority protest and the Green alternative. (U.K.)

  1. An alternative explanation of the change in T-dependence of the effective Debye-Waller factor at T{sub c} or T{sub B}

    Energy Technology Data Exchange (ETDEWEB)

    Ngai, K. L. [Dipartimento di Fisica, Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); CNR-IPCF, Largo Bruno Pontecorvo 3, I-56127 Pisa (Italy); Habasaki, J. [Tokyo Institute of Technology, Yokohama 226-8502 (Japan)

    2014-09-21

    The cusp-like temperature dependence of the Debye-Waller factor or non-ergodicity parameter f{sub Q}(T) at some temperature T{sub c} above T{sub g} found by experiments in several fragile glassformers has been considered as critical evidence for validity of the ideal Mode Coupling Theory (MCT). A comprehensive review of experimental data of f{sub Q}(T) and beyond brings out various problems of the MCT predictions. For example, the molten salt, 0.4Ca(NO{sub 3}){sub 2}-0.6KNO{sub 3} (CKN), was the first glassformer measured by neutron scattering to verify the cusp-like behavior of f{sub Q}(T) at T{sub c} predicted by ideal MCT. While the fits of the other scaling laws of MCT to viscosity, light scattering, and dielectric relaxation data all give T{sub c} in the range from 368 to 375 K, there is no evidence of cusp-like behavior of f{sub Q}(T) at T{sub c} from more accurate neutron scattering data obtained later on by Mezei and Russina [J. Phys.: Condens. Matter 11, A341 (1999)] at temperatures below 400 K. In several molecular glass-formers, experiments have found at temperatures below T{sub c} that [1−f{sub Q}(T)] is manifested as nearly constant loss (NCL) in the frequency dependent susceptibility. The NCL persists down to below T{sub g} and is not predicted by the ideal MCT. No clear evidence of the change of T-dependence of f{sub Q}(T) at any T{sub c} was found in intermediate and strong glassformers, although ideal MCT does not distinguish fragile and strong glassformers in predicting the critical behavior of f{sub Q}(T) a priori. Experiments found f{sub Q}(T) changes T-dependence not only at T{sub c} but also at the glass transition temperature T{sub g}. The changes of T-dependence of f{sub Q}(T) at T{sub c} and T{sub g} are accompanied by corresponding changes of dynamic variables and thermodynamic quantities at T{sub B} ≈ T{sub c} and at T{sub g}. The dynamic variables include the relaxation time τ{sub α}(T), the non-exponentiality parameter n(T), and

  2. Comparison of roll-to-roll replication approaches for microfluidic and optical functions in lab-on-a-chip diagnostic devices

    Science.gov (United States)

    Brecher, Christian; Baum, Christoph; Bastuck, Thomas

    2015-03-01

    Economically advantageous microfabrication technologies for lab-on-a-chip diagnostic devices substituting commonly used glass etching or injection molding processes are one of the key enablers for the emerging market of microfluidic devices. On-site detection in fields of life sciences, point of care diagnostics and environmental analysis requires compact, disposable and highly functionalized systems. Roll-to-roll production as a high volume process has become the emerging fabrication technology for integrated, complex high technology products within recent years (e.g. fuel cells). Differently functionalized polymer films enable researchers to create a new generation of lab-on-a-chip devices by combining electronic, microfluidic and optical functions in multilayer architecture. For replication of microfluidic and optical functions via roll-to-roll production process competitive approaches are available. One of them is to imprint fluidic channels and optical structures of micro- or nanometer scale from embossing rollers into ultraviolet (UV) curable lacquers on polymer substrates. Depending on dimension, shape and quantity of those structures there are alternative manufacturing technologies for the embossing roller. Ultra-precise diamond turning, electroforming or casting polymer materials are used either for direct structuring or manufacturing of roller sleeves. Mastering methods are selected for application considering replication quality required and structure complexity. Criteria for the replication quality are surface roughness and contour accuracy. Structure complexity is evaluated by shapes producible (e.g. linear, circular) and aspect ratio. Costs for the mastering process and structure lifetime are major cost factors. The alternative replication approaches are introduced and analyzed corresponding to the criteria presented. Advantages and drawbacks of each technology are discussed and exemplary applications are presented.

  3. Alternative crops

    International Nuclear Information System (INIS)

    Andreasen, L.M.; Boon, A.D.

    1992-01-01

    Surplus cereal production in the EEC and decreasing product prices, mainly for cereals, has prompted considerable interest for new earnings in arable farming. The objective was to examine whether suggested new crops (fibre, oil, medicinal and alternative grains crops) could be considered as real alternatives. Whether a specific crop can compete economically with cereals and whether there is a market demand for the crop is analyzed. The described possibilities will result in ca. 50,000 hectares of new crops. It is expected that they would not immediately provide increased earnings, but in the long run expected price developments are more positive than for cereals. The area for new crops will not solve the current surplus cereal problem as the area used for new crops is only 3% of that used for cereals. Preconditions for many new crops is further research activities and development work as well as the establishment of processing units and organizational initiatives. Presumably, it is stated, there will then be a basis for a profitable production of new crops for some farmers. (AB) (47 refs.)

  4. 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.

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

    Science.gov (United States)

    Prakash, Aishwarya; Borgstahl, Gloria E O

    2012-01-01

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

  6. Separase prevents genomic instability by controlling replication fork speed

    Science.gov (United States)

    Cucco, Francesco; Palumbo, Elisa; Camerini, Serena; D’Alessio, Barbara; Quarantotti, Valentina; Casella, Maria Luisa; Rizzo, Ilaria Maria; Cukrov, Dubravka; Delia, Domenico; Russo, Antonella; Crescenzi, Marco

    2018-01-01

    Abstract Proper chromosome segregation is crucial for preserving genomic integrity, and errors in this process cause chromosome mis-segregation, which may contribute to cancer development. Sister chromatid separation is triggered by Separase, an evolutionary conserved protease that cleaves the cohesin complex, allowing the dissolution of sister chromatid cohesion. Here we provide evidence that Separase participates in genomic stability maintenance by controlling replication fork speed. We found that Separase interacted with the replication licensing factors MCM2–7, and genome-wide data showed that Separase co-localized with MCM complex and cohesin. Unexpectedly, the depletion of Separase increased the fork velocity about 1.5-fold and caused a strong acetylation of cohesin's SMC3 subunit and altered checkpoint response. Notably, Separase silencing triggered genomic instability in both HeLa and human primary fibroblast cells. Our results show a novel mechanism for fork progression mediated by Separase and thus the basis for genomic instability associated with tumorigenesis. PMID:29165708

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

    Science.gov (United States)

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

    2013-04-01

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

  8. Dynamics of Escherichia coli Chromosome Segregation during Multifork Replication

    DEFF Research Database (Denmark)

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

    2007-01-01

    Slowly growing Escherichia coli cells have a simple cell cycle, with replication and progressive segregation of the chromosome completed before cell division. In rapidly growing cells, initiation of replication occurs before the previous replication rounds are complete. At cell division...

  9. Energy alternatives

    International Nuclear Information System (INIS)

    1981-01-01

    English. A special committe of the Canadian House of Commons was established on 23 May 1980 to investigate the use of alternative energy sources such as 'gasohol', liquified coal, solar energy, methanol, wind and tidal power, biomass, and propane. In its final report, the committee envisions an energy system for Canada based on hydrogen and electricity, using solar and geothermal energy for low-grade heat. The committe was not able to say which method of generating electricty would dominate in the next century, although it recommends that fossil fuels should not be used. The fission process is not specifically discussed, but the outlook for fusion was investigated, and continued governmental support of fusion research is recommended. The report proposes some improvements in governmental energy organizations and programs

  10. Replication ofVibrio choleraeclassical CTX phage.

    Science.gov (United States)

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

    2017-02-28

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

  11. Genetically engineered fusion of MAP-1 and factor H domains 1-5 generates a potent dual upstream inhibitor of both the lectin and alternative complement pathways

    DEFF Research Database (Denmark)

    Nordmaj, Mie Anemone; Munthe-Fog, Lea; Hein, Estrid

    2015-01-01

    Inhibition of the complement cascade has emerged as an option for treatment of a range of diseases. Mannose-binding lectin/ficolin/collectin-associated protein (MAP-1) is a pattern recognition molecule (PRM)-associated inhibitor of the lectin pathway. The central regulator of the alternative path...

  12. Replication of HIV-1 in vivo and in vitro.

    Science.gov (United States)

    Orenstein, Jan Marc

    2007-01-01

    A complex relationship exists between HIV and its cellular targets. The lethal effect of HIV on circulating CD4(+) helper T lymphocytes parallels the degree of the infected individual's immunodeficiency and ultimately the transition to AIDS and death. However, as with other members of the Lentivirus family of retroviruses, the ubiquitous, mobile macrophage is also a prime target for HIV infection, and apparently, in most instances, is the initial infected cell, since most people are infected with a CCR5 chemokine-tropic virus. Unlike the lymphocyte, the macrophage is apparently a more stable viral host, capable of a long infected life as an HIV reservoir and a chronic source of infectious virus. Published in vitro studies have indicated that whereas lymphocytes replicate HIV solely on their plasma membrane, macrophages have been envisaged to predominantly replicate HIV within cytoplasmic vacuoles, and thus have been likened to a "Trojan horse," when it comes to the immune system. Recent studies have revealed an ingenious way by which the cultured monocyte-derived macrophage (MDM) replicates HIV and releases it into the medium. The key macrophage organelle appears to be what is alternatively referred to as the "late endosome" (LE) or the "multivesicular body" (MVB), which have a short and a long history, respectively. Proof of the association is that chemically, LE/MVB and their vesicles possess several pathopneumonic membrane markers (e.g., CD63) that are found on released HIV particles. The hypothesis is that HIV usurps this vesicle-forming mechanism and employs it for its own replication. Release of the intravacuolar virus from the cell is hypothesized to occur by a process referred to as exocytosis, resulting from the fusion of virus-laden LE/MVB with the plasma membrane of the macrophage. Interestingly, LE/MVB are also involved in the infection stage of MDM by HIV. Close review of the literature reveals that along with the Golgi, which contributes to the

  13. Stearoyl coenzyme A desaturase 1 is associated with hepatitis C virus replication complex and regulates viral replication

    DEFF Research Database (Denmark)

    Nguyen, LN; Lim, YS; Pham, Long

    2014-01-01

    The hepatitis C virus (HCV) life cycle is tightly regulated by lipid metabolism of host cells. In order to identify host factors involved in HCV propagation, we have recently screened a small interfering RNA (siRNA) library targeting host genes that control lipid metabolism and lipid droplet...... formation using cell culture-grown HCV (HCVcc)-infected cells. We selected and characterized the gene encoding stearoyl coenzyme A (CoA) desaturase 1 (SCD1). siRNA-mediated knockdown or pharmacological inhibition of SCD1 abrogated HCV replication in both subgenomic replicon and Jc1-infected cells, while...... exogenous supplementation of either oleate or palmitoleate, products of SCD1 activity, resurrected HCV replication in SCD1 knockdown cells. SCD1 was coimmunoprecipitated with HCV nonstructural proteins and colocalized with both double-stranded RNA (dsRNA) and HCV nonstructural proteins, indicating that SCD1...

  14. Optical tweezers reveal how proteins alter replication

    Science.gov (United States)

    Chaurasiya, Kathy

    Single molecule force spectroscopy is a powerful method that explores the DNA interaction properties of proteins involved in a wide range of fundamental biological processes such as DNA replication, transcription, and repair. We use optical tweezers to capture and stretch a single DNA molecule in the presence of proteins that bind DNA and alter its mechanical properties. We quantitatively characterize the DNA binding mechanisms of proteins in order to provide a detailed understanding of their function. In this work, we focus on proteins involved in replication of Escherichia coli (E. coli ), endogenous eukaryotic retrotransposons Ty3 and LINE-1, and human immunodeficiency virus (HIV). DNA polymerases replicate the entire genome of the cell, and bind both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) during DNA replication. The replicative DNA polymerase in the widely-studied model system E. coli is the DNA polymerase III subunit alpha (DNA pol III alpha). We use optical tweezers to determine that UmuD, a protein that regulates bacterial mutagenesis through its interactions with DNA polymerases, specifically disrupts alpha binding to ssDNA. This suggests that UmuD removes alpha from its ssDNA template to allow DNA repair proteins access to the damaged DNA, and to facilitate exchange of the replicative polymerase for an error-prone translesion synthesis (TLS) polymerase that inserts nucleotides opposite the lesions, so that bacterial DNA replication may proceed. This work demonstrates a biophysical mechanism by which E. coli cells tolerate DNA damage. Retroviruses and retrotransposons reproduce by copying their RNA genome into the nuclear DNA of their eukaryotic hosts. Retroelements encode proteins called nucleic acid chaperones, which rearrange nucleic acid secondary structure and are therefore required for successful replication. The chaperone activity of these proteins requires strong binding affinity for both single- and double-stranded nucleic

  15. Autophagy Negatively Regulates Transmissible Gastroenteritis Virus Replication.

    Science.gov (United States)

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

    2016-03-31

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

  16. Methadone enhances human influenza A virus replication.

    Science.gov (United States)

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

    2017-01-01

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

  17. 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.

  18. Replicating viruses for gynecologic cancer therapy.

    Science.gov (United States)

    Park, J W; Kim, M

    2016-01-01

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

  19. 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.

  20. RADX interacts with single-stranded DNA to promote replication fork stability

    DEFF Research Database (Denmark)

    Schubert, Lisa; Ho, Teresa; Hoffmann, Saskia

    2017-01-01

    has an essential genome maintenance role, protecting ssDNA regions from nucleolytic degradation and providing a recruitment platform for proteins involved in responses to replication stress and DNA damage. Here, we identify the uncharacterized protein RADX (CXorf57) as an ssDNA-binding factor in human...... cells. RADX binds ssDNA via an N-terminal OB fold cluster, which mediates its recruitment to sites of replication stress. Deregulation of RADX expression and ssDNA binding leads to enhanced replication fork stalling and degradation, and we provide evidence that a balanced interplay between RADX and RPA...

  1. Role of vif in replication of human immunodeficiency virus type 1 in CD4+ T lymphocytes.

    OpenAIRE

    Gabuzda, D H; Lawrence, K; Langhoff, E; Terwilliger, E; Dorfman, T; Haseltine, W A; Sodroski, J

    1992-01-01

    The viral infectivity factor gene vif of human immunodeficiency virus type 1 has been shown to affect the infectivity but not the production of virus particles. In this study, the effect of vif in the context of the HXB2 virus on virus replication in several CD4+ T-cell lines was investigated. vif was found to be required for replication in the CD4+ T-cell lines CEM and H9 as well as in peripheral blood T lymphocytes. vif was not required for replication in the SupT1, C8166, and Jurkat T-cell...

  2. Nrf2-dependent induction of innate host defense via heme oxygenase-1 inhibits Zika virus replication

    Science.gov (United States)

    Huang, Hanxia; Falgout, Barry; Takeda, Kazuyo; Yamada, Kenneth M.; Dhawan, Subhash

    2017-01-01

    We identified primary human monocyte-derived macrophages (MDM) as vulnerable target cells for Zika virus (ZIKV) infection. We demonstrate dramatic effects of hemin, the natural inducer of the heme catabolic enzyme heme oxygenase-1 (HO-1), in the reduction of ZIKV replication in vitro. Both LLC-MK2 monkey kidney cells and primary MDM exhibited hemin-induced HO-1 expression with major reductions of > 90% in ZIKV replication, with little toxicity to infected cells. Silencing expression of HO-1 or its upstream regulatory gene, nuclear factor erythroid-related factor 2 (Nrf2), attenuated hemin-induced suppression of ZIKV infection, suggesting an important role for induction of these intracellular mediators in retarding ZIKV replication. The inverse correlation between hemin-induced HO-1 levels and ZIKV replication provides a potentially useful therapeutic modality based on stimulation of an innate cellular response against Zika virus infection. PMID:28068513

  3. Impairment of mature B-cell maintenance upon combined deletion of the alternative NF-κB transcription factors RELB and NF-κB2 in B cells$

    Science.gov (United States)

    De Silva, Nilushi S.; Silva, Kathryn; Anderson, Michael M.; Bhagat, Govind; Klein, Ulf

    2016-01-01

    B-cell activating factor (BAFF) is critical for the survival and maturation of mature B-cells. BAFF, via the BAFF receptor (BAFFR), activates multiple signaling pathways in B-cells, including the alternative nuclear factor-κB (NF-κB) pathway. The transcription factors RELB and NF-κB2 (p100/p52) are the downstream mediators of the alternative pathway; however, the B-cell-intrinsic functions of these NF-κB subunits have not been studied in vivo using conditional alleles, either individually or in combination. We here report that B-cell-specific deletion of relb led to only a slight decrease in the fraction of mature splenic B cells, whereas deletion of nfkb2 caused a marked reduction. This phenotype was further exacerbated upon combined deletion of relb and nfkb2 and most dramatically affected the maintenance of marginal zone B-cells. BAFF-stimulation, in contrast to CD40-activation, was unable to rescue relb/nfkb2-deleted B-cells in vitro. RNA-sequencing analysis of BAFF-stimulated nfkb2-deleted vs. normal B-cells suggests that the alternative NF-κB pathway, in addition to its critical role in BAFF-mediated cell survival, may control the expression of genes involved in the positioning of B-cells within the lymphoid microenvironment and in the establishment of T-cell-B-cell interactions. Thus, by ablating the downstream transcription factors of the alternative NF-κB pathway specifically in B-cells, we here identify a critical role for the combined activity of the RELB and NF-κB2 subunits in B-cell homeostasis that cannot be compensated for by the canonical NF-κB pathway under physiological conditions. PMID:26851215

  4. PTEN Regulates DNA Replication Progression and Stalled Fork Recovery

    Science.gov (United States)

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

    2015-01-01

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

  5. Alternative fuelds in urban fleets

    International Nuclear Information System (INIS)

    Lindsay, T.

    1994-01-01

    In this presentation the author addresses four main objectives. They are to: discuss programs that are driving the introduction of alternative fuels into fleet operations in urban areas around the country; define alternative fuels; quantify the present use and future projections on alternative fuel vehicles (AVFs) in the Chicago metropolitan statistical area; and discuss benefits of increased use of alternative fuels in urban areas. Factors which touch on these points include: present domestic dependence on petroleum for autos, with usage exceeding production; the large populations in urban areas which do not meet Clean Air Standards; recent legislative initiatives which give guidance and aid in the adoption of such strategies

  6. Alternative fuelds in urban fleets

    Energy Technology Data Exchange (ETDEWEB)

    Lindsay, T.

    1994-12-31

    In this presentation the author addresses four main objectives. They are to: discuss programs that are driving the introduction of alternative fuels into fleet operations in urban areas around the country; define alternative fuels; quantify the present use and future projections on alternative fuel vehicles (AVFs) in the Chicago metropolitan statistical area; and discuss benefits of increased use of alternative fuels in urban areas. Factors which touch on these points include: present domestic dependence on petroleum for autos, with usage exceeding production; the large populations in urban areas which do not meet Clean Air Standards; recent legislative initiatives which give guidance and aid in the adoption of such strategies.

  7. DNA replication stress and cancer chemotherapy.

    Science.gov (United States)

    Kitao, Hiroyuki; Iimori, Makoto; Kataoka, Yuki; Wakasa, Takeshi; Tokunaga, Eriko; Saeki, Hiroshi; Oki, Eiji; Maehara, Yoshihiko

    2018-02-01

    DNA replication is one of the fundamental biological processes in which dysregulation can cause genome instability. This instability is one of the hallmarks of cancer and confers genetic diversity during tumorigenesis. Numerous experimental and clinical studies have indicated that most tumors have experienced and overcome the stresses caused by the perturbation of DNA replication, which is also referred to as DNA replication stress (DRS). When we consider therapeutic approaches for tumors, it is important to exploit the differences in DRS between tumor and normal cells. In this review, we introduce the current understanding of DRS in tumors and discuss the underlying mechanism of cancer therapy from the aspect of DRS. © 2017 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

  8. Towards scalable Byzantine fault-tolerant replication

    Science.gov (United States)

    Zbierski, Maciej

    2017-08-01

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

  9. The replication of expansive production knowledge

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  10. 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.

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

    Science.gov (United States)

    Smith, Owen K; Aladjem, Mirit I

    2014-10-09

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

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

    NARCIS (Netherlands)

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

    2016-01-01

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

  13. Alternative REST Splicing Underappreciated

    OpenAIRE

    Chen, Guo-Lin; Miller, Gregory

    2017-01-01

    As a major orchestrator of the cellular epigenome, the repressor element-1 silencing transcription factor (REST) can either repress or activate thousands of genes depending on cellular context, suggesting a highly context-dependent REST function tuned by environmental cues. While REST shows cell-type non-selective active transcription, an N-terminal REST4 isoform caused by alternative splicing - inclusion of an extra exon (N3c) which introduces a pre-mature stop codon - has been implicated in...

  14. Distinct functions of human RecQ helicases during DNA replication

    Czech Academy of Sciences Publication Activity Database

    Urban, Václav; Dobrovolná, Jana; Janščák, Pavel

    2017-01-01

    Roč. 225, červen (2017), s. 20-26 ISSN 0301-4622 R&D Projects: GA ČR(CZ) GA14-05743S; GA MŠk LH14037 Institutional support: RVO:68378050 Keywords : DNA replication * Replication stress * RecQ helicases * Genomic instability * Cancer Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 2.402, year: 2016

  15. Signal replication in a DNA nanostructure

    Science.gov (United States)

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

    2017-01-01

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

  16. Chromatin challenges during DNA replication and repair

    DEFF Research Database (Denmark)

    Groth, Anja; Rocha, Walter; Verreault, Alain

    2007-01-01

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

  17. Temporal organization of cellular self-replication

    Science.gov (United States)

    Alexandrov, Victor; Pugatch, Rami

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

  18. 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.

  19. FANCM, BRCA1, and BLM cooperatively resolve the replication stress at the ALT telomeres.

    Science.gov (United States)

    Pan, Xiaolei; Drosopoulos, William C; Sethi, Louisa; Madireddy, Advaitha; Schildkraut, Carl L; Zhang, Dong

    2017-07-18

    In the mammalian genome, certain genomic loci/regions pose greater challenges to the DNA replication machinery (i.e., the replisome) than others. Such known genomic loci/regions include centromeres, common fragile sites, subtelomeres, and telomeres. However, the detailed mechanism of how mammalian cells cope with the replication stress at these loci/regions is largely unknown. Here we show that depletion of FANCM, or of one of its obligatory binding partners, FAAP24, MHF1, and MHF2, induces replication stress primarily at the telomeres of cells that use the alternative lengthening of telomeres (ALT) pathway as their telomere maintenance mechanism. Using the telomere-specific single-molecule analysis of replicated DNA technique, we found that depletion of FANCM dramatically reduces the replication efficiency at ALT telomeres. We further show that FANCM, BRCA1, and BLM are actively recruited to the ALT telomeres that are experiencing replication stress and that the recruitment of BRCA1 and BLM to these damaged telomeres is interdependent and is regulated by both ATR and Chk1. Mechanistically, we demonstrated that, in FANCM-depleted ALT cells, BRCA1 and BLM help to resolve the telomeric replication stress by stimulating DNA end resection and homologous recombination (HR). Consistent with their roles in resolving the replication stress induced by FANCM deficiency, simultaneous depletion of BLM and FANCM, or of BRCA1 and FANCM, leads to increased micronuclei formation and synthetic lethality in ALT cells. We propose that these synthetic lethal interactions can be explored for targeting the ALT cancers.

  20. The Hepatitis B Virus (HBV) HBx Protein Activates AKT To Simultaneously Regulate HBV Replication and Hepatocyte Survival

    Science.gov (United States)

    Rawat, Siddhartha

    2014-01-01

    ABSTRACT Chronic infection with hepatitis B virus (HBV) is a risk factor for developing liver diseases such as hepatocellular carcinoma (HCC). HBx is a multifunctional protein encoded by the HBV genome; HBx stimulates HBV replication and is thought to play an important role in the development of HBV-associated HCC. HBx can activate the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway in some cell lines; however, whether HBx regulates PI3K/AKT signaling in normal hepatocytes has not been evaluated. In studies described here, we assessed HBx activation of PI3K/AKT signaling in an ex vivo model of cultured primary hepatocytes and determined how this HBx activity affects HBV replication. We report that HBx activates AKT in primary hepatocytes and that the activation of AKT decreases HBV replication and HBV mRNA and core protein levels. We show that the transcription factor hepatocyte nuclear factor 4α (HNF4α) is a target of HBx-regulated AKT, and we link HNF4α to HBx-regulated AKT modulation of HBV transcription and replication. Although we and others have shown that HBx stimulates and is likely required for HBV replication, we now report that HBx also activates signals that can diminish the overall level of HBV replication. While this may seem counterintuitive, we show that an important effect of HBx activation of AKT is inhibition of apoptosis. Consequently, our studies suggest that HBx balances HBV replication and cell survival by stimulating signaling pathways that enhance hepatocyte survival at the expense of higher levels of HBV replication. IMPORTANCE Chronic hepatitis B virus (HBV) infection is a common cause of the development of liver cancer. Regulation of cell signaling pathways by the HBV HBx protein is thought to influence the development of HBV-associated liver cancer. HBx stimulates, and may be essential for, HBV replication. We show that HBx activates AKT in hepatocytes to reduce HBV replication. While this seems contradictory to an

  1. 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.

  2. The alternative sigma factor SigB of Corynebacterium glutamicum modulates global gene expression during transition from exponential growth to stationary phase

    OpenAIRE

    Larisch, Christof; Nakunst, Diana; Hüser, Andrea T; Tauch, Andreas; Kalinowski, Jörn

    2007-01-01

    Abstract Background Corynebacterium glutamicum is a gram-positive soil bacterium widely used for the industrial production of amino acids. There is great interest in the examination of the molecular mechanism of transcription control. One of these control mechanisms are sigma factors. C. glutamicum ATCC 13032 has seven putative sigma factor-encoding genes, including sigA and sigB. The sigA gene encodes the essential primary sigma factor of C. glutamicum and is responsible for promoter recogni...

  3. RNA Binding Protein RBM38 Regulates Expression of the 11-kDa Protein of Parvovirus B19 which Facilitates Viral DNA Replication.

    Science.gov (United States)

    Ganaie, Safder S; Chen, Aaron Yun; Huang, Chun; Xu, Peng; Kleiboeker, Steve; Du, Aifang; Qiu, Jianming

    2018-02-07

    Human parvovirus B19 (B19V) expresses a single precursor mRNA (pre-mRNA), which undergoes alternative splicing and alternative polyadenylation to generate 12 viral mRNA transcripts that encode two structural proteins (VP1 and VP2) and three nonstructural proteins (NS1, 7.5-kDa, and 11-kDa). Splicing at the second 5' donor site (D2) of the B19V pre-mRNA is essential for the expression of VP2 and 11-kDa. We have previously identified that a cis -acting intronic splicing enhancer 2 (ISE2) that lies immediately after the D2 site facilitates recognition of the D2 donor for its efficient splicing. In this study, we report that ISE2 is critical for expression of the 11-kDa viral non-structural protein. We found that ISE2 harbors a consensus RNA-binding motif protein 38 (RBM38) binding sequence-5' -UGUGUG-3'. RBM38 is expressed during the middle stage of erythropoiesis. We first confirmed that the RBM38 binds specifically with the ISE2 element in vitro. Knockdown of RBM38 significantly decreases the level of the spliced mRNA at D2 that encodes 11-kDa protein and, thereafter, expression of the 11-kDa protein, but not the D2-spliced mRNA that encodes VP2. Importantly, we found that the 11-kDa protein enhances viral DNA replication and virion release. Accordingly, knockdown of RBM38 decreases virus replication via downregulating 11-kDa expression. Taken together, these results suggest that the 11-kDa protein facilitates B19V DNA replication, and that RBM38 is an essential host factor for B19V pre-mRNA splicing and for the expression of the 11-kDa protein. IMPORTANCE B19V is a human pathogen that can cause fifth disease, arthropathy, anemia in immune compromised patients and sickle cell disease patients, myocarditis, and hydrops fetalis in pregnant women. Human erythroid progenitor cells (EPCs) are most susceptible to B19V infection and fully support viral DNA replication. The exclusive tropism of B19V to erythroid lineage cells is not only dependent on the expression of viral

  4. Investigation of the HIV-1 matrix interactome during virus replication.

    Science.gov (United States)

    Li, Yan; Frederick, Kristin M; Haverland, Nicole A; Ciborowski, Pawel; Belshan, Michael

    2016-02-01

    Like all viruses, human immunodeficiency virus type 1 (HIV-1) requires host cellular factors for productive replication. Identification of these factors may lead to the development of novel cell-based inhibitors. A Strep-tag was inserted into the C-terminus of the matrix (MA) region of the HIV-1 gag gene. The resultant virus was replication competent and used to infect Jurkat T-cells. MA complexes were affinity purified with Strep-Tactin agarose. Protein quantification was performed using sequential window acquisition of all theoretical fragment ion spectra (SWATH) MS, data were log2 -transformed, and Student t-tests with Bonferroni correction used to determine statistical significance. Several candidate proteins were validated by immunoblot and investigated for their role in virus infection by siRNA knockdown assays. A total of 17 proteins were found to be statistically different between the infected versus uninfected and untagged control samples. X-ray repair cross-complementing protein 6 (Ku70), X-ray repair cross-complementing protein 5 (Ku80), and Y-box binding protein 1 (YB-1) were confirmed to interact with MA by immunoblot. Knockdown of two candidates, EZRIN and Y-box binding protein 1, enhanced HIV infection in vitro. The Strep-tag allowed for the capture of viral protein complexes in the context of virus replication. Several previously described factors were identified and at least two candidate proteins were found to play a role in HIV-1 infection. These data further increase our understanding of HIV host -cell interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Ori-somes, NP complexes descending from origin regions of animal chromosomal DNA replication. A micromorphological study

    Czech Academy of Sciences Publication Activity Database

    Korb, Jan; Štokrová, Jitka; Říman, Josef

    2001-01-01

    Roč. 19, č. 2 (2001), s. 343-350 ISSN 0739-1102 Institutional research plan: CEZ:AV0Z5052915 Keywords : origin regions of DNA replication * replicative structure s * electron microscopy Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.243, year: 2001

  6. DNA-protein interaction dynamics at the Lamin B2 replication origin.

    Science.gov (United States)

    Puzzi, Luca; Marchetti, Laura; Peverali, Fiorenzo A; Biamonti, Giuseppe; Giacca, Mauro

    2015-01-01

    To date, a complete understanding of the molecular events leading to DNA replication origin activation in mammalian cells still remains elusive. In this work, we report the results of a high resolution chromatin immunoprecipitation study to detect proteins interacting with the human Lamin B2 replication origin. In addition to the pre-RC component ORC4 and to the transcription factors USF and HOXC13, we found that 2 components of the AP-1 transcription factor, c-Fos and c-Jun, are also associated with the origin DNA during the late G1 phase of the cell cycle and that these factors interact with ORC4. Both DNA replication and AP-1 factor binding to the origin region were perturbed by cell treatment with merbarone, a topoisomerase II inhibitor, suggesting that DNA topology is essential for determining origin function.

  7. Sustainability of a Compartmentalized Host-Parasite Replicator System under Periodic Washout-Mixing Cycles

    Directory of Open Access Journals (Sweden)

    Taro Furubayashi

    2018-01-01

    Full Text Available The emergence and dominance of parasitic replicators are among the major hurdles for the proliferation of primitive replicators. Compartmentalization of replicators is proposed to relieve the parasite dominance; however, it remains unclear under what conditions simple compartmentalization uncoupled with internal reaction secures the long-term survival of a population of primitive replicators against incessant parasite emergence. Here, we investigate the sustainability of a compartmentalized host-parasite replicator (CHPR system undergoing periodic washout-mixing cycles, by constructing a mathematical model and performing extensive simulations. We describe sustainable landscapes of the CHPR system in the parameter space and elucidate the mechanism of phase transitions between sustainable and extinct regions. Our findings revealed that a large population size of compartments, a high mixing intensity, and a modest amount of nutrients are important factors for the robust survival of replicators. We also found two distinctive sustainable phases with different mixing intensities. These results suggest that a population of simple host–parasite replicators assumed before the origin of life can be sustained by a simple compartmentalization with periodic washout-mixing processes.

  8. Analysis of JC virus DNA replication using a quantitative and high-throughput assay.

    Science.gov (United States)

    Shin, Jong; Phelan, Paul J; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert; Gagnon, David; Gjoerup, Ole; Archambault, Jacques; Bullock, Peter A

    2014-11-01

    Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Partial Purification of a Megadalton DNA Replication Complex by Free Flow Electrophoresis.

    Science.gov (United States)

    Li, Caroline M; Miao, Yunan; Lingeman, Robert G; Hickey, Robert J; Malkas, Linda H

    2016-01-01

    We describe a gentle and rapid method to purify the intact multiprotein DNA replication complex using free flow electrophoresis (FFE). In particular, we applied FFE to purify the human cell DNA synthesome, which is a multiprotein complex that is fully competent to carry-out all phases of the DNA replication process in vitro using a plasmid containing the simian virus 40 (SV40) origin of DNA replication and the viral large tumor antigen (T-antigen) protein. The isolated native DNA synthesome can be of use in studying the mechanism by which mammalian DNA replication is carried-out and how anti-cancer drugs disrupt the DNA replication or repair process. Partially purified extracts from HeLa cells were fractionated in a native, liquid based separation by FFE. Dot blot analysis showed co-elution of many proteins identified as part of the DNA synthesome, including proliferating cell nuclear antigen (PCNA), DNA topoisomerase I (topo I), DNA polymerase δ (Pol δ), DNA polymerase ɛ (Pol ɛ), replication protein A (RPA) and replication factor C (RFC). Previously identified DNA synthesome proteins co-eluted with T-antigen dependent and SV40 origin-specific DNA polymerase activity at the same FFE fractions. Native gels show a multiprotein PCNA containing complex migrating with an apparent relative mobility in the megadalton range. When PCNA containing bands were excised from the native gel, mass spectrometric sequencing analysis identified 23 known DNA synthesome associated proteins or protein subunits.

  10. Partial Purification of a Megadalton DNA Replication Complex by Free Flow Electrophoresis.

    Directory of Open Access Journals (Sweden)

    Caroline M Li

    Full Text Available We describe a gentle and rapid method to purify the intact multiprotein DNA replication complex using free flow electrophoresis (FFE. In particular, we applied FFE to purify the human cell DNA synthesome, which is a multiprotein complex that is fully competent to carry-out all phases of the DNA replication process in vitro using a plasmid containing the simian virus 40 (SV40 origin of DNA replication and the viral large tumor antigen (T-antigen protein. The isolated native DNA synthesome can be of use in studying the mechanism by which mammalian DNA replication is carried-out and how anti-cancer drugs disrupt the DNA replication or repair process. Partially purified extracts from HeLa cells were fractionated in a native, liquid based separation by FFE. Dot blot analysis showed co-elution of many proteins identified as part of the DNA synthesome, including proliferating cell nuclear antigen (PCNA, DNA topoisomerase I (topo I, DNA polymerase δ (Pol δ, DNA polymerase ɛ (Pol ɛ, replication protein A (RPA and replication factor C (RFC. Previously identified DNA synthesome proteins co-eluted with T-antigen dependent and SV40 origin-specific DNA polymerase activity at the same FFE fractions. Native gels show a multiprotein PCNA containing complex migrating with an apparent relative mobility in the megadalton range. When PCNA containing bands were excised from the native gel, mass spectrometric sequencing analysis identified 23 known DNA synthesome associated proteins or protein subunits.

  11. 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.

  12. Potential biomarkers of DNA replication stress in cancer

    DEFF Research Database (Denmark)

    Ren, Liqun; Chen, Long; Wu, Wei

    2017-01-01

    oncogene-induced RS and CIN, with a particular emphasis on regions of the human genome that show enhanced sensitivity to the destabilizing effects of RS, such as common fragile sites. Because RS exists in a wide range of cancer types, we propose that the proteins involved counteracting this stress......Oncogene activation is an established driver of tumorigenesis. An apparently inevitable consequence of oncogene activation is the generation of DNA replication stress (RS), a feature common to most cancer cells. RS, in turn, is a causal factor in the development of chromosome instability (CIN...

  13. Replication and analysis of Ebbinghaus' forgetting curve

    NARCIS (Netherlands)

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

    2015-01-01

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

  14. Surface microstructure replication in injection molding

    DEFF Research Database (Denmark)

    Theilade, Uffe Arlø; Hansen, Hans Nørgaard

    2006-01-01

    molding of surface microstructures. The fundamental problem of surface microstructure replication has been studied. The research is based on specific microstructures as found in lab-on-a-chip products and on rough surfaces generated from EDM (electro discharge machining) mold cavities. Emphasis is put...

  15. Conditionally replicating HIV and SIV variants

    NARCIS (Netherlands)

    Das, Atze T.; Berkhout, Ben

    2016-01-01

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

  16. Inhibition of DNA replication by ultraviolet light

    Energy Technology Data Exchange (ETDEWEB)

    Edenberg, H.J.

    1976-08-01

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

  17. Treatment with PTEN-Long protein inhibits hepatitis C virus replication.

    Science.gov (United States)

    Wu, Qi; Li, Zhubing; Liu, Qiang

    2017-11-01

    Hepatitis C virus (HCV) infection is a confirmed risk factor for hepatocellular carcinoma (HCC). Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) possesses tumor suppression function that is frequently defective in HCC tumors. PTEN-Long, a translation isoform of PTEN, functions in a cell non-autonomous manner. In this study, we demonstrated that intracellular overexpression of PTEN-Long inhibits HCV replication. More importantly, we showed that treatment with extracellular PTEN-Long protein inhibits HCV replication in a dose-dependent manner. Furthermore, we showed that PTEN-Long interacts with HCV core protein and this interaction is required for HCV replication inhibition by PTEN-Long. In summary, we demonstrated, for the first time, that PTEN-Long protein, an isoform of the canonical PTEN and in the form of extracellular protein treatment, inhibits HCV replication. Our study offers an opportunity for developing additional anti-HCV agents. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Replicating a self-affirmation intervention to address gender differences: Successes and challenges

    Science.gov (United States)

    Kost-Smith, Lauren E.; Pollock, Steven J.; Finkelstein, Noah D.; Cohen, Geoffrey L.; Ito, Tiffany A.; Miyake, Akira

    2012-02-01

    We previously reported on the success of a psychological intervention implemented to reduce gender differences in achievement in an introductory college physics course. In this prior study, we found that the gender gap on exams and the FMCE among students who completed two 15-minute self-affirmation writing exercises was significantly reduced compared to the gender gap among students who completed neutral writing exercises. In a follow-up study we replicated the self-affirmation intervention in a later semester of the same course, with the same instructor. In this paper, we report the details and preliminary results of the replication study, where we find similar patterns along exams and course grades, but do not observe these patterns along the FMCE. We begin to investigate the critical features of replicating educational interventions, finding that replicating educational interventions is challenging, complex, and involves potentially subtle factors, some of which we explore and others that require further research.

  19. DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments.

    Science.gov (United States)

    Lanzén, Anders; Lekang, Katrine; Jonassen, Inge; Thompson, Eric M; Troedsson, Christofer

    2017-01-01

    Human impact on marine benthic communities has traditionally been assessed using visible morphological traits and has focused on the macrobenthos, whereas the ecologically important organisms of the meio- and microbenthos have received less attention. DNA metabarcoding offers an alternative to this approach and enables a larger fraction of the biodiversity in marine sediments to be monitored in a cost-efficient manner. Although this methodology remains poorly standardised and challenged by biases inherent to rRNA copy number variation, DNA extraction, PCR, and limitations related to taxonomic identification, it has been shown to be semi-quantitative and useful for comparing taxon abundances between samples. Here, we evaluate the effect of replicating genomic DNA extraction in order to counteract small scale spatial heterogeneity and improve diversity and community structure estimates in metabarcoding-based monitoring. For this purpose, we used ten technical replicates from three different marine sediment samples. The effect of sequence depth was also assessed, and in silico pooling of DNA extraction replicates carried out in order to maintain the number of reads constant. Our analyses demonstrated that both sequencing depth and DNA extraction replicates could improve diversity estimates as well as the ability to separate samples with different characteristics. We could not identify a "sufficient" replicate number or sequence depth, where further improvements had a less significant effect. Based on these results, we consider replication an attractive alternative to directly increasing the amount of sample used for DNA extraction and strongly recommend it for future metabarcoding studies and routine assessments of sediment biodiversity.

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

    Directory of Open Access Journals (Sweden)

    Michelle Hawkins

    2013-11-01

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

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

    Science.gov (United States)

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

    2016-10-21

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

  2. DNA replication and repair in Tilapia cells

    International Nuclear Information System (INIS)

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

    1984-01-01

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

  3. Alternatives to the journal impact factor: I3 and the top-10% (or top-25%?) of the most-highly cited papers

    NARCIS (Netherlands)

    Leydesdorff, L.

    2012-01-01

    Journal impact factors (IFs) can be considered historically as the first attempt to normalize citation distributions by using averages over 2 years. However, it has been recognized that citation distributions vary among fields of science and that one needs to normalize for this. Furthermore, the

  4. A Case Study of the Progressive Impact of School-Wide Positive Behavior Support on Five Selected Student Performance Factors in a Missouri K-12 Alternative Public School

    Science.gov (United States)

    Becker, Colleen Gilday

    2013-01-01

    The purpose of this case study was to examine the School-Wide Positive Behavior Support (SWPBS) impact on five selected student performance factors. A literature review revealed there have been many SWPBS research studies regarding traditional public schools. However, there have not been any published empirical SWPBS studies involving K-12…

  5. Replicable effects of primes on human behavior.

    Science.gov (United States)

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

    2016-10-01

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

  6. Ultrastructural Characterization of Zika Virus Replication Factories.

    Science.gov (United States)

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

    2017-02-28

    A global concern has emerged with the pandemic spread of Zika virus (ZIKV) infections that can cause severe neurological symptoms in adults and newborns. ZIKV is a positive-strand RNA virus replicating in virus-induced membranous replication factories (RFs). Here we used various imaging techniques to investigate the ultrastructural details of ZIKV RFs and their relationship with host cell organelles. Analyses of human hepatic cells and neural progenitor cells infected with ZIKV revealed endoplasmic reticulum (ER) membrane invaginations containing pore-like openings toward the cytosol, reminiscent to RFs in Dengue virus-infected cells. Both the MR766 African strain and the H/PF/2013 Asian strain, the latter linked to neurological diseases, induce RFs of similar architecture. Importantly, ZIKV infection causes a drastic reorganization of microtubules and intermediate filaments forming cage-like structures surrounding the viral RF. Consistently, ZIKV replication is suppressed by cytoskeleton-targeting drugs. Thus, ZIKV RFs are tightly linked to rearrangements of the host cell cytoskeleton. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  7. Molecular Biology of Rotavirus Entry and Replication

    Science.gov (United States)

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

    2009-01-01

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

  8. The molecular biology of Bluetongue virus replication.

    Science.gov (United States)

    Patel, Avnish; Roy, Polly

    2014-03-01

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

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

    OpenAIRE

    Mubarak, Fadhlul

    2015-01-01

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

  10. Preclinical evaluation of a replication-deficient intranasal DeltaNS1 H5N1 influenza vaccine.

    Directory of Open Access Journals (Sweden)

    Julia Romanova

    Full Text Available BACKGROUND: We developed a novel intranasal influenza vaccine approach that is based on the construction of replication-deficient vaccine viruses that lack the entire NS1 gene (DeltaNS1 virus. We previously showed that these viruses undergo abortive replication in the respiratory tract of animals. The local release of type I interferons and other cytokines and chemokines in the upper respiratory tract may have a "self-adjuvant effect", in turn increasing vaccine immunogenicity. As a result, DeltaNS1 viruses elicit strong B- and T- cell mediated immune responses. METHODOLOGY/PRINCIPAL FINDINGS: We applied this technology to the development of a pandemic H5N1 vaccine candidate. The vaccine virus was constructed by reverse genetics in Vero cells, as a 5:3 reassortant, encoding four proteins HA, NA, M1, and M2 of the A/Vietnam/1203/04 virus while the remaining genes were derived from IVR-116. The HA cleavage site was modified in a trypsin dependent manner, serving as the second attenuation factor in addition to the deleted NS1 gene. The vaccine candidate was able to grow in the Vero cells that were cultivated in a serum free medium to titers exceeding 8 log(10 TCID(50/ml. The vaccine virus was replication deficient in interferon competent cells and did not lead to viral shedding in the vaccinated animals. The studies performed in three animal models confirmed the safety and immunogenicity of the vaccine. Intranasal immunization protected ferrets and mice from being infected with influenza H5 viruses of different clades. In a primate model (Macaca mulatta, one dose of vaccine delivered intranasally was sufficient for the induction of antibodies against homologous A/Vietnam/1203/04 and heterologous A/Indonesia/5/05 H5N1 strains. CONCLUSION/SIGNIFICANCE: Our findings show that intranasal immunization with the replication deficient H5N1 DeltaNS1 vaccine candidate is sufficient to induce a protective immune response against H5N1 viruses. This approach

  11. Calcein represses human papillomavirus 16 E1-E2 mediated DNA replication via blocking their binding to the viral origin of replication.

    Science.gov (United States)

    Das, Dipon; Smith, Nathan W; Wang, Xu; Richardson, Stacie L; Hartman, Matthew C T; Morgan, Iain M

    2017-08-01

    Human papillomaviruses are causative agents in several human diseases ranging from genital warts to ano-genital and oropharyngeal cancers. Currently only symptoms of HPV induced disease are treated; there are no antivirals available that directly target the viral life cycle. Previously, we determined that the cellular protein TopBP1 interacts with the HPV16 replication/transcription factor E2. This E2-TopBP1 interaction is essential for optimal E1-E2 DNA replication and for the viral life cycle. The drug calcein disrupts the interaction of TopBP1 with itself and other host proteins to promote cell death. Here we demonstrate that calcein blocks HPV16 E1-E2 DNA replication via blocking the viral replication complex forming at the origin of replication. This occurs at non-toxic levels of calcein and demonstrates specificity as it does not block the ability of E2 to regulate transcription. We propose that calcein or derivatives could be developed as an anti-HPV therapeutic. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. PCNA-Dependent Cleavage and Degradation of SDE2 Regulates Response to Replication Stress.

    Directory of Open Access Journals (Sweden)

    Ukhyun Jo

    2016-12-01

    Full Text Available Maintaining genomic integrity during DNA replication is essential for cellular survival and for preventing tumorigenesis. Proliferating cell nuclear antigen (PCNA functions as a processivity factor for DNA replication, and posttranslational modification of PCNA plays a key role in coordinating DNA repair against replication-blocking lesions by providing a platform to recruit factors required for DNA repair and cell cycle control. Here, we identify human SDE2 as a new genome surveillance factor regulated by PCNA interaction. SDE2 contains an N-terminal ubiquitin-like (UBL fold, which is cleaved at a diglycine motif via a PCNA-interacting peptide (PIP box and deubiquitinating enzyme activity. The cleaved SDE2 is required for negatively regulating ultraviolet damage-inducible PCNA monoubiquitination and counteracting replication stress. The cleaved SDE2 products need to be degraded by the CRL4CDT2 ubiquitin E3 ligase in a cell cycle- and DNA damage-dependent manner, and failure to degrade SDE2 impairs S phase progression and cellular survival. Collectively, this study uncovers a new role for CRL4CDT2 in protecting genomic integrity against replication stress via regulated proteolysis of PCNA-associated SDE2 and provides insights into how an integrated UBL domain within linear polypeptide sequence controls protein stability and function.

  13. Anadromous char as an alternate food choice to marine animals: A synthesis of Hg concentrations, population features and other influencing factors

    Energy Technology Data Exchange (ETDEWEB)

    Evans, Marlene S., E-mail: marlene.evans@ec.gc.ca [Environment Canada, Water Science and Technology Directorate, 11 Innovation Blvd., Saskatoon SK S7N 3H5 (Canada); Muir, Derek C.G. [Environment Canada, Water Science and Technology Directorate, 867 Lakeshore Rd., Burlington, ON L7R 4A6 (Canada); Keating, Jonathan [Environment Canada, Water Science and Technology Directorate, 11 Innovation Blvd., Saskatoon SK S7N 3H5 (Canada); Wang, Xiaowa [Environment Canada, Water Science and Technology Directorate, 867 Lakeshore Rd., Burlington, ON L7R 4A6 (Canada)

    2015-03-15

    This study was conducted to confirm sporadic measurements made over the late 1970s to the early 1990s which determined that mercury (Hg) concentrations were low in anadromous char across Arctic and subarctic Canada including northern Québec and Labrador. Over 2004–2013, anadromous char populations across northern Canada were investigated at 20 sites for Hg concentrations and life history characteristics. Hg concentrations were extremely low in anadromous char muscle, typically < 0.05 μg/g (wet weight) and, at each location, generally increased with fish length, age and nitrogen isotope (δ{sup 15}N) ratio and decreased with condition factor and %lipid; correlations with carbon isotope (δ{sup 13}C) ratio were inconsistent. Location and year were significant variables influencing Hg concentrations over the study area; longitude and latitude also were significant influencing variables. Char length, weight, age, condition factor and lipid content explained additional variance. A tendency towards higher Hg concentrations with increasing latitude may be partially related to decreasing growth of char towards the north. However, Hg concentrations in char were positively correlated with growth rates suggesting that Hg concentrations in char also were higher in the more productive study areas, including to the west where mainland riverine inputs of terrestrial carbon, nutrients, and Hg were greater. The data base for assessing time trends in char was limited by the small number of years investigated at most locations, variable fish size across years, small sample size, etc. Where temporal trends were detected, they were of increase on the long term (1970s, 1980s or early 1990s to the present) but of decrease on the short term (early 2000s to present) with Nain (Labrador) showing the converse pattern. Higher Hg concentrations were also related to lower condition factor and cooler springs. Hg concentrations in anadromous char are compared with other terrestrial, aquatic

  14. Anadromous char as an alternate food choice to marine animals: A synthesis of Hg concentrations, population features and other influencing factors

    International Nuclear Information System (INIS)

    Evans, Marlene S.; Muir, Derek C.G.; Keating, Jonathan; Wang, Xiaowa

    2015-01-01

    This study was conducted to confirm sporadic measurements made over the late 1970s to the early 1990s which determined that mercury (Hg) concentrations were low in anadromous char across Arctic and subarctic Canada including northern Québec and Labrador. Over 2004–2013, anadromous char populations across northern Canada were investigated at 20 sites for Hg concentrations and life history characteristics. Hg concentrations were extremely low in anadromous char muscle, typically < 0.05 μg/g (wet weight) and, at each location, generally increased with fish length, age and nitrogen isotope (δ 15 N) ratio and decreased with condition factor and %lipid; correlations with carbon isotope (δ 13 C) ratio were inconsistent. Location and year were significant variables influencing Hg concentrations over the study area; longitude and latitude also were significant influencing variables. Char length, weight, age, condition factor and lipid content explained additional variance. A tendency towards higher Hg concentrations with increasing latitude may be partially related to decreasing growth of char towards the north. However, Hg concentrations in char were positively correlated with growth rates suggesting that Hg concentrations in char also were higher in the more productive study areas, including to the west where mainland riverine inputs of terrestrial carbon, nutrients, and Hg were greater. The data base for assessing time trends in char was limited by the small number of years investigated at most locations, variable fish size across years, small sample size, etc. Where temporal trends were detected, they were of increase on the long term (1970s, 1980s or early 1990s to the present) but of decrease on the short term (early 2000s to present) with Nain (Labrador) showing the converse pattern. Higher Hg concentrations were also related to lower condition factor and cooler springs. Hg concentrations in anadromous char are compared with other terrestrial, aquatic and

  15. Effects of interferon-α/β on HBV replication determined by viral load.

    Directory of Open Access Journals (Sweden)

    Yongjun Tian

    2011-07-01

    Full Text Available Interferons α and β (IFN-α/β are type I interferons produced by the host to control microbial infections. However, the use of IFN-α to treat hepatitis B virus (HBV patients generated sustained response to only a minority of patients. By using HBV transgenic mice as a model and by using hydrodynamic injection to introduce HBV DNA into the mouse liver, we studied the effect of IFN-α/β on HBV in vivo. Interestingly, our results indicated that IFN-α/β could have opposite effects on HBV: they suppressed HBV replication when viral load was high and enhanced HBV replication when viral load was low. IFN-α/β apparently suppressed HBV replication via transcriptional and post-transcriptional regulations. In contrast, IFN-α/β enhanced viral replication by inducing the transcription factor HNF3γ and activating STAT3, which together stimulated HBV gene expression and replication. Further studies revealed an important role of IFN-α/β in stimulating viral growth and prolonging viremia when viral load is low. This use of an innate immune response to enhance its replication and persistence may represent a novel strategy that HBV uses to enhance its growth and spread in the early stage of viral infection when the viral level is low.

  16. Effects of Interferon-α/β on HBV Replication Determined by Viral Load

    Science.gov (United States)

    Tian, Yongjun; Chen, Wen-ling; Ou, Jing-hsiung James

    2011-01-01

    Interferons α and β (IFN-α/β) are type I interferons produced by the host to control microbial infections. However, the use of IFN-α to treat hepatitis B virus (HBV) patients generated sustained response to only a minority of patients. By using HBV transgenic mice as a model and by using hydrodynamic injection to introduce HBV DNA into the mouse liver, we studied the effect of IFN-α/β on HBV in vivo. Interestingly, our results indicated that IFN-α/β could have opposite effects on HBV: they suppressed HBV replication when viral load was high and enhanced HBV replication when viral load was low. IFN-α/β apparently suppressed HBV replication via transcriptional and post-transcriptional regulations. In contrast, IFN-α/β enhanced viral replication by inducing the transcription factor HNF3γ and activating STAT3, which together stimulated HBV gene expression and replication. Further studies revealed an important role of IFN-α/β in stimulating viral growth and prolonging viremia when viral load is low. This use of an innate immune response to enhance its replication and persistence may represent a novel strategy that HBV uses to enhance its growth and spread in the early stage of viral infection when the viral level is low. PMID:21829354

  17. Endogenous MOV10 inhibits the retrotransposition of endogenous retroelements but not the replication of exogenous retroviruses

    Directory of Open Access Journals (Sweden)

    Arjan-Odedra Shetal

    2012-06-01

    Full Text Available Abstract Background The identification of cellular factors that regulate the replication of exogenous viruses and endogenous mobile elements provides fundamental understanding of host-pathogen relationships. MOV10 is a superfamily 1 putative RNA helicase that controls the replication of several RNA viruses and whose homologs are necessary for the repression of endogenous mobile elements. Here, we employ both ectopic expression and gene knockdown approaches to analyse the role of human MOV10 in the replication of a panel of exogenous retroviruses and endogenous retroelements. Results MOV10 overexpression substantially decreased the production of infectious retrovirus particles, as well the propagation of LTR and non-LTR endogenous retroelements. Most significantly, RNAi-mediated silencing of endogenous MOV10 enhanced the replication of both LTR and non-LTR endogenous retroelements, but not the production of infectious retrovirus particles demonstrating that natural levels of MOV10 suppress retrotransposition, but have no impact on infection by exogenous retroviruses. Furthermore, functional studies showed that MOV10 is not necessary for miRNA or siRNA-mediated mRNA silencing. Conclusions We have identified novel specificity for human MOV10 in the control of retroelement replication and hypothesise that MOV10 may be a component of a cellular pathway or process that selectively regulates the replication of endogenous retroelements in somatic cells.

  18. Endogenous MOV10 inhibits the retrotransposition of endogenous retroelements but not the replication of exogenous retroviruses

    Science.gov (United States)

    2012-01-01

    Background The identification of cellular factors that regulate the replication of exogenous viruses and endogenous mobile elements provides fundamental understanding of host-pathogen relationships. MOV10 is a superfamily 1 putative RNA helicase that controls the replication of several RNA viruses and whose homologs are necessary for the repression of endogenous mobile elements. Here, we employ both ectopic expression and gene knockdown approaches to analyse the role of human MOV10 in the replication of a panel of exogenous retroviruses and endogenous retroelements. Results MOV10 overexpression substantially decreased the production of infectious retrovirus particles, as well the propagation of LTR and non-LTR endogenous retroelements. Most significantly, RNAi-mediated silencing of endogenous MOV10 enhanced the replication of both LTR and non-LTR endogenous retroelements, but not the production of infectious retrovirus particles demonstrating that natural levels of MOV10 suppress retrotransposition, but have no impact on infection by exogenous retroviruses. Furthermore, functional studies showed that MOV10 is not necessary for miRNA or siRNA-mediated mRNA silencing. Conclusions We have identified novel specificity for human MOV10 in the control of retroelement replication and hypothesise that MOV10 may be a component of a cellular pathway or process that selectively regulates the replication of endogenous retroelements in somatic cells. PMID:22727223

  19. Mycobacterium tuberculosis Ser/Thr protein kinase B mediates an oxygen-dependent replication switch

    Energy Technology Data Exchange (ETDEWEB)

    Ortega, Corrie; Liao, Reiling; Anderson, Lindsey N.; Rustad, Tige; Ollodart, Anja R.; Wright, Aaron T.; Sherman, David R.; Grundner, Christoph

    2014-01-07

    In the majority of cases, Mycobacterium tuberculosis (Mtb) infections are clinically latent, characterized by little or no bacterial replication and drug tolerance. Low oxygen tension is a major host factor inducing bacteriostasis, but the molecular mechanisms driving oxygen-dependent replication are poorly understood. Mtb encodes eleven serine/threonine protein kinases, a family of signaling molecules known to regulate similar replicative adaptations in other bacteria. Here, we tested the role of serine/threonine phosphorylation in the Mtb response to altered oxygen status, using an in vitro model of latency (hypoxia) and reactivation (reaeration). Broad kinase inhibition compromised survival of Mtb in hypoxia. Activity-based protein profiling and genetic mutation identified PknB as the kinase critical for surviving hypoxia. Mtb replication was highly sensitive to changes in PknB levels in aerated culture, and even more so in hypoxia. A mutant overexpressing PknB specifically in hypoxia showed a 10-fold loss in viability in low oxygen conditions. In contrast, chemically reducing PknB activity during hypoxia specifically compromised resumption of growth during reaeration. These data support a model in which PknB activity is reduced to achieve bacteriostasis, and elevated when replication resumes. Together, these data show that phosphosignaling controls replicative transitions associated with latency and reactivation, that PknB is a major regulator of these transitions, and that PknB could provide a highly vulnerable therapeutic target at every step of the Mtb life cycle - active disease, latency, and reactivation.

  20. UGGT1 enhances enterovirus 71 pathogenicity by promoting viral RNA synthesis and viral replication.

    Directory of Open Access Journals (Sweden)

    Peng-Nien Huang

    2017-05-01

    Full Text Available Positive-strand RNA virus infections can induce the stress-related unfolded protein response (UPR in host cells. This study found that enterovirus A71 (EVA71 utilizes host UDP-glucose glycoprotein glucosyltransferase 1 (UGGT1, a key endoplasmic reticulum protein (ER involved in UPR, to enhance viral replication and virulence. EVA71 forms replication complexes (RCs on cellular membranes that contain a mix of host and viral proteins to facilitate viral replication, but the components and processes involved in the assembly and function of RCs are not fully understood. Using EVA71 as a model, this study found that host UGGT1 and viral 3D polymerase co-precipitate along with other factors on membranous replication complexes to enhance viral replication. Increased UGGT1 levels elevated viral growth rates, while viral pathogenicity was observed to be lower in heterozygous knockout mice (Uggt1 +/- mice. These findings provide important insight on the role of UPR and host UGGT1 in regulating RNA virus replication and pathogenicity.