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Sample records for affect nonhomologous end-joining

  1. Nonhomologous DNA End Joining in Cell-Free Extracts

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    Sheetal Sharma

    2010-01-01

    Full Text Available Among various DNA damages, double-strand breaks (DSBs are considered as most deleterious, as they may lead to chromosomal rearrangements and cancer when unrepaired. Nonhomologous DNA end joining (NHEJ is one of the major DSB repair pathways in higher organisms. A large number of studies on NHEJ are based on in vitro systems using cell-free extracts. In this paper, we summarize the studies on NHEJ performed by various groups in different cell-free repair systems.

  2. The spatial organization of non-homologous end joining: From bridging to end joining

    OpenAIRE

    Ochi, Takashi; Wu, Qian; Blundell, Tom L

    2014-01-01

    Non-homologous end joining (NHEJ) repairs DNA double-strand breaks generated by DNA damage and also those occurring in V(D)J recombination in immunoglobulin and T cell receptor production in the immune system. In NHEJ DNA-PKcs assembles with Ku heterodimer on the DNA ends at double-strand breaks, in order to bring the broken ends together and to assemble other proteins, including DNA ligase IV (LigIV), required for DNA repair. Here we focus on structural aspects of the interactions of LigIV w...

  3. The endless tale of non-homologous end-joining

    Institute of Scientific and Technical Information of China (English)

    Eric Weterings; David J Chen

    2008-01-01

    DNA double-strand breaks (DSBs) are introduced in cells by ionizing radiation and reactive oxygen species. In addi-tion, they are commonly generated during V(D)J recombination, an essential aspect of the developing immune system. Failure to effectively repair these DSBs can result in chromosome breakage, cell death, onset of cancer, and defects in the immune system of higher vertebrates. Fortunately, all mammalian cells possess two enzymatic pathways that mediate the repair of DSBs: homologous recombination and non-homologous end-joining (NHEJ). The NHEJ process utilizes enzymes that capture both ends of the broken DNA molecule, bring them together in a synaptic DNA-protein complex, and finally repair the DNA break. In this review, all the known enzymes that play a role in the NHEJ process are discussed and a working model for the co-operation of these enzymes during DSB repair is presented.

  4. Analysis of Gene Targeting & Nonhomologous End-joining. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Haber, J. E.

    2002-11-30

    Overall, we identified a number of new proteins that participate in nonhomologous end-joining and also in telomere addition to the ends of broken chromosomes. We showed that NHEJ is severely reduced in cells expressing both yeast mating-type genes and then went on to identify the NEJ1 gene that was under this control. We showed the epistasis relations among a set of mutations that impair telomere addition and we showed that there are in fact two pathways to repair broken chromosomes in the absence of telomerase. We characterized the DNA damage checkpoint pathway in response to a single broken chromosome and characterized especially the adaptation of cells arrested by an unrepaired DSB. We demonstrated that the DNA damage response is nuclear-limited. We showed adaptation defects for Tid1and Srs2 proteins and showed that Srs2 was also recovery-defective, even when DNA was repaired.

  5. Non-homologous end joining: advances and frontiers.

    Science.gov (United States)

    Yang, Kai; Guo, Rong; Xu, Dongyi

    2016-07-01

    DNA double-strand breaks (DSBs) are the most serious form of DNA damage. In human cells, non-homologous end joining (NHEJ) is the major pathway for the repair of DSBs. Different types of DSBs result in different subsets of NHEJ repair strategies. These variations in NHEJ repair strategies depend on numerous elements, such as the flexible recruitment of NHEJ-related proteins, the complexity of the DSB ends, and the spatial- and temporal-ordered formation of the multi-protein complex. On the one hand, current studies of DNA DSBs repair focus on the repair pathway choices between homologous recombination and classic or alternative NHEJ. On the other hand, increasing researches have also deepened the significance and dug into the cross-links between the NHEJ pathway and the area of genome organization and aging. Although remarkable progress has been made in elucidating the underlying principles during the past decades, the detailed mechanism of action in response to different types of DSBs remains largely unknown and needs further evaluation in the future study. PMID:27217473

  6. Processing of DNA for nonhomologous end-joining by cell-free extract

    OpenAIRE

    Budman, Joe; Chu, Gilbert

    2005-01-01

    In mammalian cells, nonhomologous end-joining (NHEJ) repairs DNA double-strand breaks created by ionizing radiation and V(D)J recombination. We have developed a cell-free system capable of processing and joining noncompatible DNA ends. The system had key features of NHEJ in vivo, including dependence on Ku, DNA-PKcs, and XRCC4/Ligase4. The NHEJ reaction had striking properties. Processing of noncompatible ends involved polymerase and nuclease activities that often stabilized the alignment of ...

  7. Ancient and Recent Adaptive Evolution of Primate Non-Homologous End Joining Genes

    OpenAIRE

    Ann Demogines; Alysia M East; Ji-Hoon Lee; Grossman, Sharon R.; Sabeti, Pardis C.; Paull, Tanya T.; Sawyer, Sara L.

    2010-01-01

    In human cells, DNA double-strand breaks are repaired primarily by the non-homologous end joining (NHEJ) pathway. Given their critical nature, we expected NHEJ proteins to be evolutionarily conserved, with relatively little sequence change over time. Here, we report that while critical domains of these proteins are conserved as expected, the sequence of NHEJ proteins has also been shaped by recurrent positive selection, leading to rapid sequence evolution in other protein domains. In order to...

  8. DNA Ligases I and III Cooperate in Alternative Non-Homologous End-Joining in Vertebrates

    OpenAIRE

    Katja Paul; Minli Wang; Emil Mladenov; Alena Bencsik-Theilen; Theresa Bednar; Wenqi Wu; Hiroshi Arakawa; George Iliakis

    2013-01-01

    Biochemical and genetic studies suggest that vertebrates remove double-strand breaks (DSBs) from their genomes predominantly by two non-homologous end joining (NHEJ) pathways. While canonical NHEJ depends on the well characterized activities of DNA-dependent protein kinase (DNA-PK) and LIG4/XRCC4/XLF complexes, the activities and the mechanisms of the alternative, backup NHEJ are less well characterized. Notably, the contribution of LIG1 to alternative NHEJ remains conjectural and although bi...

  9. DNA ligase III promotes alternative nonhomologous end-joining during chromosomal translocation formation.

    OpenAIRE

    Deniz Simsek; Erika Brunet; Sunnie Yan-Wai Wong; Sachin Katyal; Yankun Gao; McKinnon, Peter J.; Jacqueline Lou; Lei Zhang; James Li; Rebar, Edward J; Gregory, Philip D.; Michael C. Holmes; Maria Jasin

    2011-01-01

    International audience Nonhomologous end-joining (NHEJ) is the primary DNA repair pathway thought to underlie chromosomal translocations and other genomic rearrangements in somatic cells. The canonical NHEJ pathway, including DNA ligase IV (Lig4), suppresses genomic instability and chromosomal translocations, leading to the notion that a poorly defined, alternative NHEJ (alt-NHEJ) pathway generates these rearrangements. Here, we investigate the DNA ligase requirement of chromosomal translo...

  10. The role of RecQ helicases in non-homologous end-joining

    DEFF Research Database (Denmark)

    Keijzers, Guido; Maynard, Scott; Shamanna, Raghavendra A;

    2014-01-01

    Abstract DNA double-strand breaks are highly toxic DNA lesions that cause genomic instability, if not efficiently repaired. RecQ helicases are a family of highly conserved proteins that maintain genomic stability through their important roles in several DNA repair pathways, including DNA double......-strand break repair. Double-strand breaks can be repaired by homologous recombination (HR) using sister chromatids as templates to facilitate precise DNA repair, or by an HR-independent mechanism known as non-homologous end-joining (NHEJ) (error-prone). NHEJ is a non-templated DNA repair process, in which DNA...... termini are directly ligated. Canonical NHEJ requires DNA-PKcs and Ku70/80, while alternative NHEJ pathways are DNA-PKcs and Ku70/80 independent. This review discusses the role of RecQ helicases in NHEJ, alternative (or back-up) NHEJ (B-NHEJ) and microhomology-mediated end-joining (MMEJ) in V...

  11. Cooperative Assembly of a Protein-DNA Filament for Nonhomologous End Joining*

    OpenAIRE

    Tsai, Chun J.; Chu, Gilbert

    2013-01-01

    Nonhomologous end joining repairs DNA double-strand breaks created by ionizing radiation and V(D)J recombination. Ku, XRCC4/Ligase IV (XL), and XLF have a remarkable mismatched end (MEnd) ligase activity, particularly for ends with mismatched 3′ overhangs, but the mechanism has remained obscure. Here, we showed XL required Ku to bind DNA, whereas XLF required both Ku and XL to bind DNA. We detected cooperative assembly of one or two Ku molecules and up to five molecules each of XL and XLF int...

  12. Lif1 SUMOylation and its role in non-homologous end-joining

    OpenAIRE

    Vigasova, Dana; Sarangi, Prabha; Kolesar, Peter; Vlasáková, Danuša; Slezakova, Zuzana; Altmannova, Veronika; Nikulenkov, Fedor; Anrather, Dorothea; Gith, Rainer; Zhao, Xiaolan; Chovanec, Miroslav; Krejci, Lumir

    2013-01-01

    Non-homologous end-joining (NHEJ) repairs DNA double-strand breaks by tethering and ligating the two DNA ends. The mechanisms regulating NHEJ efficiency and interplay between its components are not fully understood. Here, we identify and characterize the SUMOylation of budding yeast Lif1 protein, which is required for the ligation step in NHEJ. We show that Lif1 SUMOylation occurs throughout the cell cycle and requires the Siz SUMO ligases. Single-strand DNA, but not double-strand DNA or the ...

  13. Retinoblastoma family proteins: New players in DNA repair by non-homologous end-joining.

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    Huang, Paul H; Cook, Rebecca; Zoumpoulidou, Georgia; Luczynski, Maciej T; Mittnacht, Sibylle

    2016-03-01

    Loss of retinoblastoma protein (RB1) function is a major driver in cancer development. We have recently reported that, in addition to its well-documented functions in cell cycle and fate control, RB1 and its paralogs have a novel role in regulating DNA repair by non-homologous end joining (NHEJ). Here we summarize our findings and present mechanistic hypotheses on how RB1 may support the DNA repair process and the therapeutic implications for patients who harbor RB1-negative cancers. PMID:27308588

  14. A noncatalytic function of the ligation complex during nonhomologous end joining.

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    Cottarel, Jessica; Frit, Philippe; Bombarde, Oriane; Salles, Bernard; Négrel, Aurélie; Bernard, Stéphanie; Jeggo, Penny A; Lieber, Michael R; Modesti, Mauro; Calsou, Patrick

    2013-01-21

    Nonhomologous end joining is the primary deoxyribonucleic acid (DNA) double-strand break repair pathway in multicellular eukaryotes. To initiate repair, Ku binds DNA ends and recruits the DNA-dependent protein kinase (DNA-PK) catalytic subunit (DNA-PKcs) forming the holoenzyme. Early end synapsis is associated with kinase autophosphorylation. The XRCC4 (X4)-DNA Ligase IV (LIG4) complex (X4LIG4) executes the final ligation promoted by Cernunnos (Cer)-X4-like factor (XLF). In this paper, using a cell-free system that recapitulates end synapsis and DNA-PKcs autophosphorylation, we found a defect in both activities in human cell extracts lacking LIG4. LIG4 also stimulated the DNA-PKcs autophosphorylation in a reconstitution assay with purified components. We additionally uncovered a kinase autophosphorylation defect in LIG4-defective cells that was corrected by ectopic expression of catalytically dead LIG4. Finally, our data support a contribution of Cer-XLF to this unexpected early role of the ligation complex in end joining. We propose that productive end joining occurs by early formation of a supramolecular entity containing both DNA-PK and X4LIG4-Cer-XLF complexes on DNA ends. PMID:23337116

  15. Coincident In Vitro Analysis of DNA-PK-Dependent and -Independent Nonhomologous End Joining

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    Cynthia L. Hendrickson

    2010-01-01

    Full Text Available In mammalian cells, DNA double-strand breaks (DSBs are primarily repaired by nonhomologous end joining (NHEJ. The current model suggests that the Ku 70/80 heterodimer binds to DSB ends and recruits DNA-PKcs to form the active DNA-dependent protein kinase, DNA-PK. Subsequently, XRCC4, DNA ligase IV, XLF and most likely, other unidentified components participate in the final DSB ligation step. Therefore, DNA-PK plays a key role in NHEJ due to its structural and regulatory functions that mediate DSB end joining. However, recent studies show that additional DNA-PK-independent NHEJ pathways also exist. Unfortunately, the presence of DNA-PKcs appears to inhibit DNA-PK-independent NHEJ, and in vitro analysis of DNA-PK-independent NHEJ in the presence of the DNA-PKcs protein remains problematic. We have developed an in vitro assay that is preferentially active for DNA-PK-independent DSB repair based solely on its reaction conditions, facilitating coincident differential biochemical analysis of the two pathways. The results indicate the biochemically distinct nature of the end-joining mechanisms represented by the DNA-PK-dependent and -independent NHEJ assays as well as functional differences between the two pathways.

  16. Positive selection on the nonhomologous end-joining factor Cernunnos-XLF in the human lineage

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    Jurka Jerzy

    2006-06-01

    Full Text Available Abstract Background Cernunnos-XLF is a nonhomologous end-joining factor that is mutated in patients with a rare immunodeficiency with microcephaly. Several other microcephaly-associated genes such as ASPM and microcephalin experienced recent adaptive evolution apparently linked to brain size expansion in humans. In this study we investigated whether Cernunnos-XLF experienced similar positive selection during human evolution. Results We obtained or reconstructed full-length coding sequences of chimpanzee, rhesus macaque, canine, and bovine Cernunnos-XLF orthologs from sequence databases and sequence trace archives. Comparison of coding sequences revealed an excess of nonsynonymous substitutions consistent with positive selection on Cernunnos-XLF in the human lineage. The hotspots of adaptive evolution are concentrated around a specific structural domain, whose analogue in the structurally similar XRCC4 protein is involved in binding of another nonhomologous end-joining factor, DNA ligase IV. Conclusion Cernunnos-XLF is a microcephaly-associated locus newly identified to be under adaptive evolution in humans, and possibly played a role in human brain expansion. We speculate that Cernunnos-XLF may have contributed to the increased number of brain cells in humans by efficient double strand break repair, which helps to prevent frequent apoptosis of neuronal progenitors and aids mitotic cell cycle progression. Reviewers This article was reviewed by Chris Ponting and Richard Emes (nominated by Chris Ponting, Kateryna Makova, Gáspár Jékely and Eugene V. Koonin.

  17. Garcinol, a Histone Acetyltransferase Inhibitor, Radiosensitizes Cancer Cells by Inhibiting Non-Homologous End Joining

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    Oike, Takahiro [Division of Multistep Carcinogenesis, National Cancer Center Research Institute, Chuo-ku, Tokyo (Japan); Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo (Japan); Department of Radiation Oncology, Gunma University Graduate School of Medicine, Maebashi, Gunma (Japan); Ogiwara, Hideaki [Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo (Japan); Torikai, Kohta [Gunma University Heavy Ion Medical Center, Maebashi, Gunma (Japan); Nakano, Takashi [Department of Radiation Oncology, Gunma University Graduate School of Medicine, Maebashi, Gunma (Japan); Yokota, Jun [Division of Multistep Carcinogenesis, National Cancer Center Research Institute, Chuo-ku, Tokyo (Japan); Kohno, Takashi, E-mail: tkkohno@ncc.go.jp [Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo (Japan)

    2012-11-01

    Purpose: Non-homologous end joining (NHEJ), a major pathway used to repair DNA double-strand breaks (DSBs) generated by ionizing radiation (IR), requires chromatin remodeling at DSB sites through the acetylation of histones by histone acetyltransferases (HATs). However, the effect of compounds with HAT inhibitory activities on the DNA damage response (DDR), including the NHEJ and cell cycle checkpoint, as well as on the radiosensitivity of cancer cells, remains largely unclear. Here, we investigated whether garcinol, a HAT inhibitor found in the rinds of Garcinia indica fruit (called mangosteens), has effects on DDR, and whether it can be used for radiosensitization. Methods and Materials: The following assays were used to examine the effect of garcinol on the inhibition of DSB repair, including the following: a conventional neutral comet assay; a cell-based assay recently developed by us, in which NHEJ repair of DSBs on chromosomal DNA was evaluated; the micrococcal nuclease sensitivity assay; and immunoblotting for autophosphorylation of DNA-dependent protein kinase catalytic subunit (DNA-PKcs). We assessed the effect of garcinol on the cell cycle checkpoint after IR treatment by analyzing the phosphorylation levels of checkpoint kinases CHK1 and CHK2 and histone H3, and by cell cycle profile analysis using flow cytometry. The radiosensitizing effect of garcinol was assessed by a clonogenic survival assay, whereas its effects on apoptosis and senescence were examined by annexin V and senescence-associated {beta}-galactosidase (SA-{beta}-Gal) staining, respectively. Results: We found that garcinol inhibits DSB repair, including NHEJ, without affecting cell cycle checkpoint. Garcinol radiosensitized A549 lung and HeLa cervical carcinoma cells with dose enhancement ratios (at 10% surviving fraction) of 1.6 and 1.5, respectively. Cellular senescence induced by IR was enhanced by garcinol. Conclusion: These results suggest that garcinol is a radiosensitizer that

  18. DNA ligase III promotes alternative nonhomologous end-joining during chromosomal translocation formation.

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    Deniz Simsek

    2011-06-01

    Full Text Available Nonhomologous end-joining (NHEJ is the primary DNA repair pathway thought to underlie chromosomal translocations and other genomic rearrangements in somatic cells. The canonical NHEJ pathway, including DNA ligase IV (Lig4, suppresses genomic instability and chromosomal translocations, leading to the notion that a poorly defined, alternative NHEJ (alt-NHEJ pathway generates these rearrangements. Here, we investigate the DNA ligase requirement of chromosomal translocation formation in mouse cells. Mammals have two other DNA ligases, Lig1 and Lig3, in addition to Lig4. As deletion of Lig3 results in cellular lethality due to its requirement in mitochondria, we used recently developed cell lines deficient in nuclear Lig3 but rescued for mitochondrial DNA ligase activity. Further, zinc finger endonucleases were used to generate DNA breaks at endogenous loci to induce translocations. Unlike with Lig4 deficiency, which causes an increase in translocation frequency, translocations are reduced in frequency in the absence of Lig3. Residual translocations in Lig3-deficient cells do not show a bias toward use of pre-existing microhomology at the breakpoint junctions, unlike either wild-type or Lig4-deficient cells, consistent with the notion that alt-NHEJ is impaired with Lig3 loss. By contrast, Lig1 depletion in otherwise wild-type cells does not reduce translocations or affect microhomology use. However, translocations are further reduced in Lig3-deficient cells upon Lig1 knockdown, suggesting the existence of two alt-NHEJ pathways, one that is biased toward microhomology use and requires Lig3 and a back-up pathway which does not depend on microhomology and utilizes Lig1.

  19. Garcinol, a Histone Acetyltransferase Inhibitor, Radiosensitizes Cancer Cells by Inhibiting Non-Homologous End Joining

    International Nuclear Information System (INIS)

    Purpose: Non-homologous end joining (NHEJ), a major pathway used to repair DNA double-strand breaks (DSBs) generated by ionizing radiation (IR), requires chromatin remodeling at DSB sites through the acetylation of histones by histone acetyltransferases (HATs). However, the effect of compounds with HAT inhibitory activities on the DNA damage response (DDR), including the NHEJ and cell cycle checkpoint, as well as on the radiosensitivity of cancer cells, remains largely unclear. Here, we investigated whether garcinol, a HAT inhibitor found in the rinds of Garcinia indica fruit (called mangosteens), has effects on DDR, and whether it can be used for radiosensitization. Methods and Materials: The following assays were used to examine the effect of garcinol on the inhibition of DSB repair, including the following: a conventional neutral comet assay; a cell-based assay recently developed by us, in which NHEJ repair of DSBs on chromosomal DNA was evaluated; the micrococcal nuclease sensitivity assay; and immunoblotting for autophosphorylation of DNA-dependent protein kinase catalytic subunit (DNA-PKcs). We assessed the effect of garcinol on the cell cycle checkpoint after IR treatment by analyzing the phosphorylation levels of checkpoint kinases CHK1 and CHK2 and histone H3, and by cell cycle profile analysis using flow cytometry. The radiosensitizing effect of garcinol was assessed by a clonogenic survival assay, whereas its effects on apoptosis and senescence were examined by annexin V and senescence-associated β-galactosidase (SA-β-Gal) staining, respectively. Results: We found that garcinol inhibits DSB repair, including NHEJ, without affecting cell cycle checkpoint. Garcinol radiosensitized A549 lung and HeLa cervical carcinoma cells with dose enhancement ratios (at 10% surviving fraction) of 1.6 and 1.5, respectively. Cellular senescence induced by IR was enhanced by garcinol. Conclusion: These results suggest that garcinol is a radiosensitizer that inhibits NHEJ

  20. Transient stability of DNA ends allows nonhomologous end joining to precede homologous recombination.

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    Frank-Vaillant, Marie; Marcand, Stéphane

    2002-11-01

    The stability of DNA ends generated by the HO endonuclease in yeast is surprisingly high with a half-life of more than an hour. This transient stability is unaffected by mutations that abolish nonhomologous end joining (NHEJ). The unprocessed ends interact with Yku70p and Yku80p, two proteins required for NHEJ, but not significantly with Rad52p, a protein involved in homologous recombination (HR). Repair of a double-strand break by NHEJ is unaffected by the possibility of HR, although the use of HR is increased in NHEJ-defective cells. Partial in vitro 5' strand processing suppresses NHEJ but not HR. These results show that NHEJ precedes HR temporally, and that the availability of substrate dictates the particular pathway used. We propose that transient stability of DNA ends is a foundation for the permanent stability of telomeres. PMID:12453425

  1. ATRX loss promotes tumor growth and impairs nonhomologous end joining DNA repair in glioma.

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    Koschmann, Carl; Calinescu, Anda-Alexandra; Nunez, Felipe J; Mackay, Alan; Fazal-Salom, Janet; Thomas, Daniel; Mendez, Flor; Kamran, Neha; Dzaman, Marta; Mulpuri, Lakshman; Krasinkiewicz, Johnathon; Doherty, Robert; Lemons, Rosemary; Brosnan-Cashman, Jacqueline A; Li, Youping; Roh, Soyeon; Zhao, Lili; Appelman, Henry; Ferguson, David; Gorbunova, Vera; Meeker, Alan; Jones, Chris; Lowenstein, Pedro R; Castro, Maria G

    2016-03-01

    Recent work in human glioblastoma (GBM) has documented recurrent mutations in the histone chaperone protein ATRX. We developed an animal model of ATRX-deficient GBM and showed that loss of ATRX reduces median survival and increases genetic instability. Further, analysis of genome-wide data for human gliomas showed that ATRX mutation is associated with increased mutation rate at the single-nucleotide variant (SNV) level. In mouse tumors, ATRX deficiency impairs nonhomologous end joining and increases sensitivity to DNA-damaging agents that induce double-stranded DNA breaks. We propose that ATRX loss results in a genetically unstable tumor, which is more aggressive when left untreated but is more responsive to double-stranded DNA-damaging agents, resulting in improved overall survival. PMID:26936505

  2. Making ends meet: repairing breaks in bacterial DNA by non-homologous end-joining.

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    Richard Bowater

    2006-02-01

    Full Text Available DNA double-strand breaks (DSBs are one of the most dangerous forms of DNA lesion that can result in genomic instability and cell death. Therefore cells have developed elaborate DSB-repair pathways to maintain the integrity of genomic DNA. There are two major pathways for the repair of DSBs in eukaryotes: homologous recombination and non-homologous end-joining (NHEJ. Until very recently, the NHEJ pathway had been thought to be restricted to the eukarya. However, an evolutionarily related NHEJ apparatus has now been identified and characterized in the prokarya. Here we review the recent discoveries concerning bacterial NHEJ and discuss the possible origins of this repair system. We also examine the insights gained from the recent cellular and biochemical studies of this DSB-repair process and discuss the possible cellular roles of an NHEJ pathway in the life-cycle of prokaryotes and phages.

  3. Detection and Repair of Ionizing Radiation-Induced DNA Double Strand Breaks: New Developments in Nonhomologous End Joining

    International Nuclear Information System (INIS)

    DNA damage can occur as a result of endogenous metabolic reactions and replication stress or from exogenous sources such as radiation therapy and chemotherapy. DNA double strand breaks are the most cytotoxic form of DNA damage, and defects in their repair can result in genome instability, a hallmark of cancer. The major pathway for the repair of ionizing radiation-induced DSBs in human cells is nonhomologous end joining. Here we review recent advances on the mechanism of nonhomologous end joining, as well as new findings on its component proteins and regulation

  4. Efficient gene replacements in Toxoplasma gondii strains deficient for nonhomologous end joining.

    Science.gov (United States)

    Fox, Barbara A; Ristuccia, Jessica G; Gigley, Jason P; Bzik, David J

    2009-04-01

    A high frequency of nonhomologous recombination has hampered gene targeting approaches in the model apicomplexan parasite Toxoplasma gondii. To address whether the nonhomologous end-joining (NHEJ) DNA repair pathway could be disrupted in this obligate intracellular parasite, putative KU proteins were identified and a predicted KU80 gene was deleted. The efficiency of gene targeting via double-crossover homologous recombination at several genetic loci was found to be greater than 97% of the total transformants in KU80 knockouts. Gene replacement efficiency was markedly increased (300- to 400-fold) in KU80 knockouts compared to wild-type strains. Target DNA flanks of only approximately 500 bp were found to be sufficient for efficient gene replacements in KU80 knockouts. KU80 knockouts stably retained a normal growth rate in vitro and the high virulence phenotype of type I strains but exhibited an increased sensitivity to double-strand DNA breaks induced by treatment with phleomycin or gamma-irradiation. Collectively, these results revealed that a significant KU-dependent NHEJ DNA repair pathway is present in Toxoplasma gondii. Integration essentially occurs only at the homologous targeted sites in the KU80 knockout background, making this genetic background an efficient host for gene targeting to speed postgenome functional analysis and genetic dissection of parasite biology. PMID:19218423

  5. Direct Involvement of Retinoblastoma Family Proteins in DNA Repair by Non-homologous End-Joining

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    Rebecca Cook

    2015-03-01

    Full Text Available Deficiencies in DNA double-strand break (DSB repair lead to genetic instability, a recognized cause of cancer initiation and evolution. We report that the retinoblastoma tumor suppressor protein (RB1 is required for DNA DSB repair by canonical non-homologous end-joining (cNHEJ. Support of cNHEJ involves a mechanism independent of RB1’s cell-cycle function and depends on its amino terminal domain with which it binds to NHEJ components XRCC5 and XRCC6. Cells with engineered loss of RB family function as well as cancer-derived cells with mutational RB1 loss show substantially reduced levels of cNHEJ. RB1 variants disabled for the interaction with XRCC5 and XRCC6, including a cancer-associated variant, are unable to support cNHEJ despite being able to confer cell-cycle control. Our data identify RB1 loss as a candidate driver of structural genomic instability and a causative factor for cancer somatic heterogeneity and evolution.

  6. Structural Basis of DNA Ligase IV-Artemis Interaction in Nonhomologous End-Joining

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    Pablo De Ioannes

    2012-12-01

    Full Text Available DNA ligase IV (LigIV and Artemis are central components of the nonhomologous end-joining (NHEJ machinery that is required for V(DJ recombination and the maintenance of genomic integrity in mammalian cells. We report here crystal structures of the LigIV DNA binding domain (DBD in both its apo form and in complex with a peptide derived from the Artemis C-terminal region. We show that LigIV interacts with Artemis through an extended hydrophobic surface. In particular, we find that the helix α2 in LigIV-DBD is longer than in other mammalian ligases and presents residues that specifically interact with the Artemis peptide, which adopts a partially helical conformation on binding. Mutations of key residues on the LigIV-DBD hydrophobic surface abolish the interaction. Together, our results provide structural insights into the specificity of the LigIV-Artemis interaction and how the enzymatic activities of the two proteins may be coordinated during NHEJ.

  7. DNA ligases I and III cooperate in alternative non-homologous end-joining in vertebrates.

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    Katja Paul

    Full Text Available Biochemical and genetic studies suggest that vertebrates remove double-strand breaks (DSBs from their genomes predominantly by two non-homologous end joining (NHEJ pathways. While canonical NHEJ depends on the well characterized activities of DNA-dependent protein kinase (DNA-PK and LIG4/XRCC4/XLF complexes, the activities and the mechanisms of the alternative, backup NHEJ are less well characterized. Notably, the contribution of LIG1 to alternative NHEJ remains conjectural and although biochemical, cytogenetic and genetic experiments implicate LIG3, this contribution has not been formally demonstrated. Here, we take advantage of the powerful genetics of the DT40 chicken B-cell system to delineate the roles of LIG1 and LIG3 in alternative NHEJ. Our results expand the functions of LIG1 to alternative NHEJ and demonstrate a remarkable ability for LIG3 to backup DSB repair by NHEJ in addition to its essential function in the mitochondria. Together with results on DNA replication, these observations uncover a remarkable and previously unappreciated functional flexibility and interchangeability between LIG1 and LIG3.

  8. Ancient and recent adaptive evolution of primate non-homologous end joining genes.

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    Ann Demogines

    2010-10-01

    Full Text Available In human cells, DNA double-strand breaks are repaired primarily by the non-homologous end joining (NHEJ pathway. Given their critical nature, we expected NHEJ proteins to be evolutionarily conserved, with relatively little sequence change over time. Here, we report that while critical domains of these proteins are conserved as expected, the sequence of NHEJ proteins has also been shaped by recurrent positive selection, leading to rapid sequence evolution in other protein domains. In order to characterize the molecular evolution of the human NHEJ pathway, we generated large simian primate sequence datasets for NHEJ genes. Codon-based models of gene evolution yielded statistical support for the recurrent positive selection of five NHEJ genes during primate evolution: XRCC4, NBS1, Artemis, POLλ, and CtIP. Analysis of human polymorphism data using the composite of multiple signals (CMS test revealed that XRCC4 has also been subjected to positive selection in modern humans. Crystal structures are available for XRCC4, Nbs1, and Polλ; and residues under positive selection fall exclusively on the surfaces of these proteins. Despite the positive selection of such residues, biochemical experiments with variants of one positively selected site in Nbs1 confirm that functions necessary for DNA repair and checkpoint signaling have been conserved. However, many viruses interact with the proteins of the NHEJ pathway as part of their infectious lifecycle. We propose that an ongoing evolutionary arms race between viruses and NHEJ genes may be driving the surprisingly rapid evolution of these critical genes.

  9. Chemical Inhibitors of Non-Homologous End Joining Increase Targeted Construct Integration in Cryptococcus neoformans.

    Science.gov (United States)

    Arras, Samantha D M; Fraser, James A

    2016-01-01

    The development of a biolistic transformation protocol for Cryptococcus neoformans over 25 years ago ushered in a new era of molecular characterization of virulence in this previously intractable fungal pathogen. However, due to the low rate of homologous recombination in this species, the process of creating targeted gene deletions using biolistic transformation remains inefficient. To overcome the corresponding difficulty achieving molecular genetic modifications, members of the Cryptococcus community have investigated the use of specific genetic backgrounds or construct design strategies aimed at reducing ectopic construct integration via non-homologous end joining (NHEJ). One such approach involves deletion of components of the NHEJ-associated Ku heterodimer. While this strategy increases homologous recombination to nearly 100%, it also restricts strain generation to a ku80Δ genetic background and requires subsequent complex mating procedures to reestablish wild-type DNA repair. In this study, we have investigated the ability of known inhibitors of mammalian NHEJ to transiently phenocopy the C. neoformans Ku deletion strains. Testing of eight candidate inhibitors revealed a range of efficacies in C. neoformans, with the most promising compound (W7) routinely increasing the rate of gene deletion to over 50%. We have successfully employed multiple inhibitors to reproducibly enhance the deletion rate at multiple loci, demonstrating a new, easily applied methodology to expedite acquisition of precise genetic alterations in C. neoformans. Based on this success, we anticipate that the use of these inhibitors will not only become widespread in the Cryptococcus community, but may also find use in other fungal species as well. PMID:27643854

  10. Chemical Inhibitors of Non-Homologous End Joining Increase Targeted Construct Integration in Cryptococcus neoformans.

    Science.gov (United States)

    Arras, Samantha D M; Fraser, James A

    2016-01-01

    The development of a biolistic transformation protocol for Cryptococcus neoformans over 25 years ago ushered in a new era of molecular characterization of virulence in this previously intractable fungal pathogen. However, due to the low rate of homologous recombination in this species, the process of creating targeted gene deletions using biolistic transformation remains inefficient. To overcome the corresponding difficulty achieving molecular genetic modifications, members of the Cryptococcus community have investigated the use of specific genetic backgrounds or construct design strategies aimed at reducing ectopic construct integration via non-homologous end joining (NHEJ). One such approach involves deletion of components of the NHEJ-associated Ku heterodimer. While this strategy increases homologous recombination to nearly 100%, it also restricts strain generation to a ku80Δ genetic background and requires subsequent complex mating procedures to reestablish wild-type DNA repair. In this study, we have investigated the ability of known inhibitors of mammalian NHEJ to transiently phenocopy the C. neoformans Ku deletion strains. Testing of eight candidate inhibitors revealed a range of efficacies in C. neoformans, with the most promising compound (W7) routinely increasing the rate of gene deletion to over 50%. We have successfully employed multiple inhibitors to reproducibly enhance the deletion rate at multiple loci, demonstrating a new, easily applied methodology to expedite acquisition of precise genetic alterations in C. neoformans. Based on this success, we anticipate that the use of these inhibitors will not only become widespread in the Cryptococcus community, but may also find use in other fungal species as well.

  11. Proofreading activity of DNA polymerase Pol2 mediates 3'-end processing during nonhomologous end joining in yeast.

    Directory of Open Access Journals (Sweden)

    Shun-Fu Tseng

    2008-04-01

    Full Text Available Genotoxic agents that cause double-strand breaks (DSBs often generate damage at the break termini. Processing enzymes, including nucleases and polymerases, must remove damaged bases and/or add new bases before completion of repair. Artemis is a nuclease involved in mammalian nonhomologous end joining (NHEJ, but in Saccharomyces cerevisiae the nucleases and polymerases involved in NHEJ pathways are poorly understood. Only Pol4 has been shown to fill the gap that may form by imprecise pairing of overhanging 3' DNA ends. We previously developed a chromosomal DSB assay in yeast to study factors involved in NHEJ. Here, we use this system to examine DNA polymerases required for NHEJ in yeast. We demonstrate that Pol2 is another major DNA polymerase involved in imprecise end joining. Pol1 modulates both imprecise end joining and more complex chromosomal rearrangements, and Pol3 is primarily involved in NHEJ-mediated chromosomal rearrangements. While Pol4 is the major polymerase to fill the gap that may form by imprecise pairing of overhanging 3' DNA ends, Pol2 is important for the recession of 3' flaps that can form during imprecise pairing. Indeed, a mutation in the 3'-5' exonuclease domain of Pol2 dramatically reduces the frequency of end joins formed with initial 3' flaps. Thus, Pol2 performs a key 3' end-processing step in NHEJ.

  12. Role of the non-homologous DNA end joining pathway in the early steps of retroviral infection

    OpenAIRE

    Li, Ling; Olvera, Jennifer M.; Yoder, Kristine E.; Mitchell, Richard S.; Scott L Butler; Lieber, Michael; Martin, Sandra L.; Bushman, Frederic D.

    2001-01-01

    Early after infection, the retroviral RNA genome is reverse transcribed to generate a linear cDNA copy, then that copy is integrated into a chromosome of the host cell. We report that unintegrated viral cDNA is a substrate for the host cell non-homologous DNA end joining (NHEJ) pathway, which normally repairs cellular double-strand breaks by end ligation. NHEJ activity was found to be required for an end-ligation reaction that circularizes a portion of the unintegrated viral cDNA in infected ...

  13. The function of classical and alternative non-homologous end-joining pathways in the fusion of dysfunctional telomeres

    OpenAIRE

    Rai, Rekha; Zheng, Hong; He, Hua; Luo, Ying; Multani, Asha; Carpenter, Phillip B.; Chang, Sandy

    2010-01-01

    Repair of DNA double-stranded breaks (DSBs) is crucial for the maintenance of genome stability. DSBs are repaired by either error prone non-homologous end-joining (NHEJ) or error-free homologous recombination. NHEJ precedes either by a classic, Lig4-dependent process (C-NHEJ) or an alternative, Lig4-independent one (A-NHEJ). Dysfunctional telomeres arising either through natural attrition due to telomerase deficiency or by removal of telomere-binding proteins are recognized as DSBs. In this r...

  14. Nonhomologous end joining of complex DNA double-strand breaks with proximal thymine glycol and interplay with base excision repair.

    Science.gov (United States)

    Almohaini, Mohammed; Chalasani, Sri Lakshmi; Bafail, Duaa; Akopiants, Konstantin; Zhou, Tong; Yannone, Steven M; Ramsden, Dale A; Hartman, Matthew C T; Povirk, Lawrence F

    2016-05-01

    DNA double-strand breaks induced by ionizing radiation are often accompanied by ancillary oxidative base damage that may prevent or delay their repair. In order to better define the features that make some DSBs repair-resistant, XLF-dependent nonhomologous end joining of blunt-ended DSB substrates having the oxidatively modified nonplanar base thymine glycol at the first (Tg1), second (Tg2), third (Tg3) or fifth (Tg5) positions from one 3' terminus, was examined in human whole-cell extracts. Tg at the third position had little effect on end-joining even when present on both ends of the break. However, Tg as the terminal or penultimate base was a major barrier to end joining (>10-fold reduction in ligated products) and an absolute barrier when present at both ends. Dideoxy trapping of base excision repair intermediates indicated that Tg was excised from Tg1, Tg2 and Tg3 largely if not exclusively after DSB ligation. However, Tg was rapidly excised from the Tg5 substrate, resulting in a reduced level of DSB ligation, as well as slow concomitant resection of the opposite strand. Ligase reactions containing only purified Ku, XRCC4, ligase IV and XLF showed that ligation of Tg3 and Tg5 was efficient and only partially XLF-dependent, whereas ligation of Tg1 and Tg2 was inefficient and only detectable in the presence of XLF. Overall, the results suggest that promoting ligation of DSBs with proximal base damage may be an important function of XLF, but that Tg can still be a major impediment to repair, being relatively resistant to both trimming and ligation. Moreover, it appears that base excision repair of Tg can sometimes interfere with repair of DSBs that would otherwise be readily rejoined. PMID:27049455

  15. Characteristic studies of non-homologous end joining in human cells irradiated with high LET radiation

    Science.gov (United States)

    Okayasu, R.; Okada, M.; Okabe, A.; Takakura, K.

    We studied the repair process of G0/G1 phase normal (HFL III) and non homologous end joining (NHEJ) deficient human fibroblasts (180 BR) exposed to X-rays and high LET carbon ions (70 keV/μ m) using a modified fusion-based premature chromosome condensation (PCC) technique. We have succeeded in increasing the sensitivity of the PCC method by adding a potent DNA double strand break repair inhibitor, wortmannin, during the incubation period of this assay. With x-ray exposure (2 Gy or less), the rejoining of G1 chromosome breaks in 180BR cells are significantly slower and less efficient than that in normal cells. On the other hand, the difference in rejoining kinetics between 180BR and normal cells with high LET carbon exposure is much smaller than that with x-ray exposure. These results seem to reflect the radiation cell survival responses using the same cell lines. We also studied the auto-phosphorylation status of DNA dependent protein kinase catalytic subunit (DNA-PKcs) protein in cells exposed to high and low LET radiation. Our immuno-staining results using an antibody to detect an auto-phosphorylation site of DNA-PKcs further reveal the difficulty in NHEJ for cells exposed to high LET radiation. The peak time for the auto-phosphorylation in x-irradiated normal human cells is one hour post-irradiation, but the peak in the same cells irradiated with high LET carbon beams shifted to two hours post-irradiation, reflecting much slower NHEJ processing associated with the high LET radiation. These data help understand the mechanism underlying the biological effect induced by heavy ion particles in the space environment.

  16. Knock-in reporter mice demonstrate that DNA repair by non-homologous end joining declines with age.

    Directory of Open Access Journals (Sweden)

    Amita Vaidya

    2014-07-01

    Full Text Available Accumulation of genome rearrangements is a characteristic of aged tissues. Since genome rearrangements result from faulty repair of DNA double strand breaks (DSBs, we hypothesized that DNA DSB repair becomes less efficient with age. The Non-Homologous End Joining (NHEJ pathway repairs a majority of DSBs in vertebrates. To examine age-associated changes in NHEJ, we have generated an R26NHEJ mouse model in which a GFP-based NHEJ reporter cassette is knocked-in to the ROSA26 locus. In this model, NHEJ repair of DSBs generated by the site-specific endonuclease, I-SceI, reconstitutes a functional GFP gene. In this system NHEJ efficiency can be compared across tissues of the same mouse and in mice of different age. Using R26NHEJ mice, we found that NHEJ efficiency was higher in the skin, lung, and kidney fibroblasts, and lower in the heart fibroblasts and brain astrocytes. Furthermore, we observed that NHEJ efficiency declined with age. In the 24-month old animals compared to the 5-month old animals, NHEJ efficiency declined 1.8 to 3.8-fold, depending on the tissue, with the strongest decline observed in the skin fibroblasts. The sequence analysis of 300 independent NHEJ repair events showed that, regardless of age, mice utilize microhomology sequences at a significantly higher frequency than expected by chance. Furthermore, the frequency of microhomology-mediated end joining (MMEJ events increased in the heart and lung fibroblasts of old mice, suggesting that NHEJ becomes more mutagenic with age. In summary, our study provides a versatile mouse model for the analysis of NHEJ in a wide range of tissues and demonstrates that DNA repair by NHEJ declines with age in mice, which could provide a mechanism for age-related genomic instability and increased cancer incidence with age.

  17. A DNA-PKcs mutation in a radiosensitive T-B- SCID patient inhibits Artemis activation and nonhomologous end-joining

    NARCIS (Netherlands)

    M. van der Burg (Mirjam); H. IJspeert (Hanna); N.S. Verkaik (Nicole); T. Turul (Tuba); W.W. Wiegant (Wouter); K. Morotomi-Yano (Keiko); P.O. Mari (Pierre-Olivier); I. Tezcan (Ilhan); D.J. Chen (David); M.Z. Zdzienicka (Malgorzata); J.J.M. van Dongen (Jacques); D.C. van Gent (Dik)

    2009-01-01

    textabstractRadiosensitive T-B- severe combined immunodeficiency (RS-SCID) is caused by defects in the nonhomologous end-joining (NHEJ) DNA repair pathway, which results in failure of functional V(D)J recombination. Here we have identified the first human RS-SCID patient to our knowledge with a DNA-

  18. Change of gene structure and function by non-homologous end-joining, homologous recombination, and transposition of DNA.

    Directory of Open Access Journals (Sweden)

    Wolfgang Goettel

    2009-06-01

    Full Text Available An important objective in genome research is to relate genome structure to gene function. Sequence comparisons among orthologous and paralogous genes and their allelic variants can reveal sequences of functional significance. Here, we describe a 379-kb region on chromosome 1 of maize that enables us to reconstruct chromosome breakage, transposition, non-homologous end-joining, and homologous recombination events. Such a high-density composition of various mechanisms in a small chromosomal interval exemplifies the evolution of gene regulation and allelic diversity in general. It also illustrates the evolutionary pace of changes in plants, where many of the above mechanisms are of somatic origin. In contrast to animals, somatic alterations can easily be transmitted through meiosis because the germline in plants is contiguous to somatic tissue, permitting the recovery of such chromosomal rearrangements. The analyzed region contains the P1-wr allele, a variant of the genetically well-defined p1 gene, which encodes a Myb-like transcriptional activator in maize. The P1-wr allele consists of eleven nearly perfect P1-wr 12-kb repeats that are arranged in a tandem head-to-tail array. Although a technical challenge to sequence such a structure by shotgun sequencing, we overcame this problem by subcloning each repeat and ordering them based on nucleotide variations. These polymorphisms were also critical for recombination and expression analysis in presence and absence of the trans-acting epigenetic factor Ufo1. Interestingly, chimeras of the p1 and p2 genes, p2/p1 and p1/p2, are framing the P1-wr cluster. Reconstruction of sequence amplification steps at the p locus showed the evolution from a single Myb-homolog to the multi-gene P1-wr cluster. It also demonstrates how non-homologous end-joining can create novel gene fusions. Comparisons to orthologous regions in sorghum and rice also indicate a greater instability of the maize genome, probably due to

  19. Homologous recombination and non-homologous end-joining repair pathways in bovine embryos with different developmental competence

    International Nuclear Information System (INIS)

    This study investigated the expression of genes controlling homologous recombination (HR), and non-homologous end-joining (NHEJ) DNA-repair pathways in bovine embryos of different developmental potential. It also evaluated whether bovine embryos can respond to DNA double-strand breaks (DSBs) induced with ultraviolet irradiation by regulating expression of genes involved in HR and NHEJ repair pathways. Embryos with high, intermediate or low developmental competence were selected based on the cleavage time after in vitro insemination and were removed from in vitro culture before (36 h), during (72 h) and after (96 h) the expected period of embryonic genome activation. All studied genes were expressed before, during and after the genome activation period regardless the developmental competence of the embryos. Higher mRNA expression of 53BP1 and RAD52 was found before genome activation in embryos with low developmental competence. Expression of 53BP1, RAD51 and KU70 was downregulated at 72 h and upregulated at 168 h post-insemination in response to DSBs induced by ultraviolet irradiation. In conclusion, important genes controlling HR and NHEJ DNA-repair pathways are expressed in bovine embryos, however genes participating in these pathways are only regulated after the period of embryo genome activation in response to ultraviolet-induced DSBs.

  20. Exploitation of sulfonylurea resistance marker and non-homologous end joining mutants for functional analysis in Zymoseptoria tritici.

    Science.gov (United States)

    Sidhu, Y S; Cairns, T C; Chaudhari, Y K; Usher, J; Talbot, N J; Studholme, D J; Csukai, M; Haynes, K

    2015-06-01

    The lack of techniques for rapid assembly of gene deletion vectors, paucity of selectable marker genes available for genetic manipulation and low frequency of homologous recombination are major constraints in construction of gene deletion mutants in Zymoseptoria tritici. To address these issues, we have constructed ternary vectors for Agrobacterium tumefaciens mediated transformation of Z. tritici, which enable the single step assembly of multiple fragments via yeast recombinational cloning. The sulfonylurea resistance gene, which is a mutated allele of the Magnaporthe oryzae ILV2 gene, was established as a new dominant selectable marker for Z. tritici. To increase the frequency of homologous recombination, we have constructed Z. tritici strains deficient in the non-homologous end joining pathway of DNA double stranded break repair by inactivating the KU70 and KU80 genes. Targeted gene deletion frequency increased to more than 85% in both Z. tritici ku70 and ku80 null strains, compared to ⩽10% seen in the wild type parental strain IPO323. The in vitro growth and in planta pathogenicity of the Z. tritici ku70 and ku80 null strains were comparable to strain IPO323. Together these molecular tools add significantly to the platform available for genomic analysis through targeted gene deletion or promoter replacements and will facilitate large-scale functional characterization projects in Z. tritici. PMID:26092796

  1. Agrobacterium may delay plant nonhomologous end-joining DNA repair via XRCC4 to favor T-DNA integration.

    Science.gov (United States)

    Vaghchhipawala, Zarir E; Vasudevan, Balaji; Lee, Seonghee; Morsy, Mustafa R; Mysore, Kirankumar S

    2012-10-01

    Agrobacterium tumefaciens is a soilborne pathogen that causes crown gall disease in many dicotyledonous plants by transfer of a portion of its tumor-inducing plasmid (T-DNA) into the plant genome. Several plant factors that play a role in Agrobacterium attachment to plant cells and transport of T-DNA to the nucleus have been identified, but the T-DNA integration step during transformation is poorly understood and has been proposed to occur via nonhomologous end-joining (NHEJ)-mediated double-strand DNA break (DSB) repair. Here, we report a negative role of X-ray cross complementation group4 (XRCC4), one of the key proteins required for NHEJ, in Agrobacterium T-DNA integration. Downregulation of XRCC4 in Arabidopsis and Nicotiana benthamiana increased stable transformation due to increased T-DNA integration. Overexpression of XRCC4 in Arabidopsis decreased stable transformation due to decreased T-DNA integration. Interestingly, XRCC4 directly interacted with Agrobacterium protein VirE2 in a yeast two-hybrid system and in planta. VirE2-expressing Arabidopsis plants were more susceptible to the DNA damaging chemical bleomycin and showed increased stable transformation. We hypothesize that VirE2 titrates or excludes active XRCC4 protein available for DSB repair, thus delaying the closure of DSBs in the chromosome, providing greater opportunity for T-DNA to integrate. PMID:23064322

  2. Efficient gene targeting in a Candida guilliermondii non-homologous end-joining pathway-deficient strain.

    Science.gov (United States)

    Foureau, Emilien; Courdavault, Vincent; Rojas, Luisa Fernanda; Dutilleul, Christelle; Simkin, Andrew J; Crèche, Joël; Atehortùa, Lucia; Giglioli-Guivarc'h, Nathalie; Clastre, Marc; Papon, Nicolas

    2013-07-01

    The yeast, Candida guilliermondii, has been widely studied due to its biotechnological interest as well as its biological control potential. It integrates foreign DNA predominantly via ectopic events, likely through the well-known non-homologous end-joining (NHEJ) pathway involving the Ku70p/Ku80p heterodimer, Lig4p, Nej1p and Lif1p. This phenomenon remains highly deleterious for targeted gene knock-out strategies that require the homologous recombination process. Here, we have constructed a ku70 mutant strain derived from the ATCC 6260 reference strain of C. guilliermondii. Following a series of disruption attempts of various genes (FCY1, ADE2 and TRP5), using several previously described dominant selectable markers (URA5, SAT-1 and HPH#), we demonstrated that the efficiencies of homologous gene targeting in such a NHEJ-deficient strain was very high compared to the wild type strain. The C. guilliermondii ku70 deficient mutant thus represents a powerful recipient strain to knock-out genes efficiently in this yeast. PMID:23463324

  3. Non-Homologous End Joining Plays a Key Role in Transgene Concatemer Formation in Transgenic Zebrafish Embryos

    Directory of Open Access Journals (Sweden)

    Jun Dai, Xiaojuan Cui, Zuoyan Zhu, Wei Hu

    2010-01-01

    Full Text Available This study focused on concatemer formation and integration pattern of transgenes in zebrafish embryos. A reporter plasmid based on enhanced green fluorescent protein (eGFP driven by Cytomegalovirus (CMV promoter, pCMV-pax6in-eGFP, was constructed to reflect transgene behavior in the host environment. After removal of the insertion fragment by double digestion with various combinations of restriction enzymes, linearized pCMV-pax6in-eGFP vectors were generated with different combinations of 5′-protruding, 3′-protruding, and blunt ends that were microinjected into zebrafish embryos. Repair of double-strand breaks (DSBs was monitored by GFP expression following religation of the reporter gene. One-hundred-and-ninety-seven DNA fragments were amplified from GFP-positive embryos and sequenced to analyze the repair characteristics of different DSB end combinations. DSBs involving blunt and asymmetric protruding ends were repaired efficiently by direct ligation of blunt ends, ligation after blunting and fill-in, or removed by cutting. Repair of DSBs with symmetric 3′-3′ protrusions was less efficient and utilized template-directed repair. The results suggest that non-homologous end joining (NHEJ was the principal mechanism of exogenous gene concatemer formation and integration of transgenes into the genome of transgenic zebrafish.

  4. Homologous recombination and non-homologous end-joining repair pathways in bovine embryos with different developmental competence

    Energy Technology Data Exchange (ETDEWEB)

    Henrique Barreta, Marcos [Universidade Federal de Santa Catarina, Campus Universitario de Curitibanos, Curitibanos, SC (Brazil); Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil); Garziera Gasperin, Bernardo; Braga Rissi, Vitor; Cesaro, Matheus Pedrotti de [Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil); Ferreira, Rogerio [Centro de Educacao Superior do Oeste-Universidade do Estado de Santa Catarina, Chapeco, SC (Brazil); Oliveira, Joao Francisco de; Goncalves, Paulo Bayard Dias [Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil); Bordignon, Vilceu, E-mail: vilceu.bordignon@mcgill.ca [Department of Animal Science, McGill University, Ste-Anne-De-Bellevue, QC (Canada)

    2012-10-01

    This study investigated the expression of genes controlling homologous recombination (HR), and non-homologous end-joining (NHEJ) DNA-repair pathways in bovine embryos of different developmental potential. It also evaluated whether bovine embryos can respond to DNA double-strand breaks (DSBs) induced with ultraviolet irradiation by regulating expression of genes involved in HR and NHEJ repair pathways. Embryos with high, intermediate or low developmental competence were selected based on the cleavage time after in vitro insemination and were removed from in vitro culture before (36 h), during (72 h) and after (96 h) the expected period of embryonic genome activation. All studied genes were expressed before, during and after the genome activation period regardless the developmental competence of the embryos. Higher mRNA expression of 53BP1 and RAD52 was found before genome activation in embryos with low developmental competence. Expression of 53BP1, RAD51 and KU70 was downregulated at 72 h and upregulated at 168 h post-insemination in response to DSBs induced by ultraviolet irradiation. In conclusion, important genes controlling HR and NHEJ DNA-repair pathways are expressed in bovine embryos, however genes participating in these pathways are only regulated after the period of embryo genome activation in response to ultraviolet-induced DSBs.

  5. The DNA Ligase IV Syndrome R278H Mutation Impairs B Lymphopoiesis via Error-Prone Nonhomologous End-Joining.

    Science.gov (United States)

    Park, Jihye; Welner, Robert S; Chan, Mei-Yee; Troppito, Logan; Staber, Philipp B; Tenen, Daniel G; Yan, Catherine T

    2016-01-01

    Hypomorphic mutations in the nonhomologous end-joining (NHEJ) DNA repair protein DNA ligase IV (LIG4) lead to immunodeficiency with varying severity. In this study, using a murine knock-in model, we investigated the mechanisms underlying abnormalities in class switch recombination (CSR) associated with the human homozygous Lig4 R278H mutation. Previously, we found that despite the near absence of Lig4 end-ligation activity and severely reduced mature B cell numbers, Lig4(R278H/R278H) (Lig4(R/R)) mice exhibit only a partial CSR block, producing near normal IgG1 and IgE but substantially reduced IgG3, IgG2b, and IgA serum levels. In this study, to address the cause of these abnormalities, we assayed CSR in Lig4(R/R) B cells generated via preassembled IgH and IgK V region exons (HL). This revealed that Lig4(R278H) protein levels while intact exhibited a higher turnover rate during activation of switching to IgG3 and IgG2b, as well as delays in CSR kinetics associated with defective proliferation during activation of switching to IgG1 and IgE. Activated Lig4(R/R)HL B cells consistently accumulated high frequencies of activation-induced cytidine deaminase-dependent IgH locus chromosomal breaks and translocations and were more prone to apoptosis, effects that appeared to be p53-independent, as p53 deficiency did not markedly influence these events. Importantly, NHEJ instead of alternative end-joining (A-EJ) was revealed as the predominant mechanism catalyzing robust CSR. Defective CSR was linked to failed NHEJ and residual A-EJ access to unrepaired double-strand breaks. These data firmly demonstrate that Lig4(R278H) activity renders NHEJ to be more error-prone, and they predict increased error-prone NHEJ activity and A-EJ suppression as the cause of the defective B lymphopoiesis in Lig4 patients. PMID:26608917

  6. Genetic probing of homologous recombination and non-homologous end joining during meiotic prophase in irradiated mouse spermatocytes

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, Emad A. [Department of Endocrinology and Metabolism, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Department of Zoology, Faculty of Science, Assiut University, 71516 Assiut (Egypt); Philippens, Marielle E.P.; Kal, Henk B. [Department of Radiotherapy, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht (Netherlands); Rooij, Dirk G. de, E-mail: d.g.derooij@uu.nl [Department of Endocrinology and Metabolism, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam (Netherlands); Boer, Peter de [Department of Obstetrics and Gynaecology, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen (Netherlands)

    2010-06-01

    This study was designed to obtain a better insight into the relative contribution of homologous recombination (HR) and non-homologous end joining (NHEJ) to the repair of radiation-induced DNA double-strand breaks (DSBs) at first meiotic prophase. Early and late pachytene and early diplotene spermatocytes that had completed crossing over were sampled. We studied the kinetics of {gamma}-H2AX chromatin foci removal after irradiation of mice deficient for HR and mice deficient for NHEJ. Analyzing {gamma}-H2AX signals in unirradiated RAD54/RAD54B deficient spermatocytes indicated incomplete meiotic recombination repair due to the pronounced increase of {gamma}-H2AX foci in late prophase primary spermatocytes. In these mice, 8 h after irradiation, early pachytene spermatocytes showed a reduction of the numbers of {gamma}-H2AX foci by 52% compared to 82% in the wild type, the difference being significant. However, after crossing over (in late pachytene and early diplotene), no effect of RAD54/RAD54B deficiency on the reduction of irradiation-induced foci was observed. In NHEJ deficient SCID mice, repair kinetics in early spermatocytes were similar to those in wild type mice. However, 1 h after irradiation in late pachytene and early diplotene spermatocytes 1.7 times more foci were found than in wild type mice. This difference might be related to the absence of a DNA-PKcs dependent fast repair component in SCID mice. As subsequent repair is normal, HR likely is taking over. Taken together, the results obtained in RAD54/RAD54B deficient mice and in SCID mice indicate that DSB repair in early pachytene spermatocytes is mainly carried out through HR. In late spermatocytes (late pachytenes and early diplotenes) NHEJ is active. However, probably there is an interplay between these repair pathways and when in late spermatocytes the NHEJ pathway is compromised HR may take over.

  7. Combining carbon ion irradiation and non-homologous end-joining repair inhibitor NU7026 efficiently kills cancer cells

    International Nuclear Information System (INIS)

    Our previous data demonstrated that targeting non-homologous end-joining repair (NHEJR) yields a higher radiosensitivity than targeting homologous recombination repair (HRR) to heavy ions using DNA repair gene knockouts (KO) in mouse embryonic fibroblast (MEF). In this study, we determined if combining the use of an NHEJR inhibitor with carbon (C) ion irradiation was more efficient in killing human cancer cells compared with only targeting a HRR inhibitor. The TP53-null human non-small cell lung cancer cell line H1299 was used for testing the radiosensitizing effect of NHEJR-related DNA-dependent protein kinase (DNA-PK) inhibitor NU7026, HRR-related Rad51 inhibitor B02, or both to C ion irradiation using colony forming assays. The mechanism underlying the inhibitor radiosensitization was determined by flow cytometry after H2AX phosphorylation staining. HRR-related Rad54-KO, NHEJR-related Lig4-KO, and wild-type TP53-KO MEF were also included to confirm the suppressing effect specificity of these inhibitors. NU7026 showed significant sensitizing effect to C ion irradiation in a concentration-dependent manner. In contrast, B02 showed a slight sensitizing effect to C ion irradiation. The addition of NU7026 significantly increased H2AX phosphorylation after C ion and x-ray irradiations in H1299 cells, but not B02. NU7026 had no effect on radiosensitivity to Lig4-KO MEF and B02 had no effect on radiosensitivity to Rad54-KO MEF in both irradiations. These results suggest that inhibitors targeting the NHEJR pathway could significantly enhance radiosensitivity of human cancer cells to C ion irradiation, rather than targeting the HRR pathway. The online version of this article (doi:10.1186/s13014-015-0536-z) contains supplementary material, which is available to authorized users

  8. Effects of chemopreventive natural products on non-homologous end-joining DNA double-strand break repair.

    Science.gov (United States)

    Charles, Catherine; Nachtergael, Amandine; Ouedraogo, Moustapha; Belayew, Alexandra; Duez, Pierre

    2014-07-01

    Double-strand breaks (DSBs) may result from endogenous (e.g., reactive oxygen species, variable (diversity) joining, meiotic exchanges, collapsed replication forks, nucleases) or exogenous (e.g., ionizing radiation, chemotherapeutic agents, radiomimetic compounds) events. DSBs disrupt the integrity of DNA and failed or improper DSBs repair may lead to genomic instability and, eventually, mutations, cancer, or cell death. Non-homologous end-joining (NHEJ) is the major pathway used by higher eukaryotic cells to repair these lesions. Given the complexity of NHEJ and the number of proteins and cofactors involved, secondary metabolites from medicinal or food plants might interfere with the process, activating or inhibiting repair. Twelve natural products, arbutin, curcumin, indole-3-carbinol, and nine flavonoids (apigenin, baicalein, chalcone, epicatechin, genistein, myricetin, naringenin, quercetin, sakuranetin) were chosen for their postulated roles in cancer chemoprevention and/or treatment. The effects of these compounds on NHEJ were investigated with an in vitro protocol based on plasmid substrates. Plasmids were linearized by a restriction enzyme, generating cohesive ends, or by a combination of enzymes, generating incompatible ends; plasmids were then incubated with a nuclear extract prepared from normal human small-intestinal cells (FHS 74 Int), either treated with these natural products or untreated (controls). The NHEJ repair complex from nuclear extracts ligates linearized plasmids, resulting in plasmid oligomers that can be separated and quantified by on-chip microelectrophoresis. Some compounds (chalcone, epicatechin, myricetin, sakuranetin and arbutin) clearly activated NHEJ, whereas others (apigenin, baicalein and curcumin) significantly reduced the repair rate of both types of plasmid substrates. Although this in vitro protocol is only partly representative of the in vivo situation, the natural products appear to interfere with NHEJ repair and warrant

  9. Effects of camptothecin on double-strand break repair by non-homologous end-joining in DNA mismatch repair-deficient human colorectal cancer cell lines

    OpenAIRE

    Jacob, Sandrine; Miquel, Catherine; Sarasin, Alain; Praz, Françoise

    2005-01-01

    Loss of a functional mismatch repair (MMR) system in colorectal cancer (CRC) cells is associated with microsatellite instability and increased sensitivity to topoisomerase inhibitors. In this study, we have investigated whether a defect in double-strand break (DSB) repair by non-homologous end-joining (NHEJ) could explain why MMR-deficient CRC cells are hypersensitive to camptothecin (CPT), a topoisomerase I inhibitor. To evaluate the efficiency and the fidelity of DSB repair, we have transie...

  10. RECQ HELICASE RECQL4 PARTICIPATES IN NON-HOMOLOGOUS END JOINING AND INTERACTS WITH THE KU COMPLEX

    DEFF Research Database (Denmark)

    Shamanna, Raghavendra A; Singh, Dharmendra Kumar; Lu, Huiming;

    2014-01-01

    on the activity of DNA-PK, extracts from RECQL4 knockdown cells display reduced end-joining activity on DNA substrates with cohesive and non-cohesive ends. Depletion of RECQL4 also reduced the end joining activity on a GFP reporter plasmid in vivo. Knockdown of RECQL4 increased the sensitivity of cells to γ...

  11. Either non-homologous ends joining or homologous recombination is required to repair double-strand breaks in the genome of macrophage-internalized Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Anna Brzostek

    Full Text Available The intracellular pathogen Mycobacterium tuberculosis (Mtb is constantly exposed to a multitude of hostile conditions and is confronted by a variety of potentially DNA-damaging assaults in vivo, primarily from host-generated antimicrobial toxic radicals. Exposure to reactive nitrogen species and/or reactive oxygen species causes different types of DNA damage, including oxidation, depurination, methylation and deamination, that can result in single- or double-strand breaks (DSBs. These breaks affect the integrity of the whole genome and, when left unrepaired, can lead to cell death. Here, we investigated the role of the DSB repair pathways, homologous recombination (HR and non-homologous ends joining (NHEJ, in the survival of Mtb inside macrophages. To this end, we constructed Mtb strains defective for HR (ΔrecA, NHEJ [Δ(ku,ligD], or both DSB repair systems [Δ(ku,ligD,recA]. Experiments using these strains revealed that either HR or NHEJ is sufficient for the survival and propagation of tubercle bacilli inside macrophages. Inhibition of nitric oxide or superoxide anion production with L-NIL or apocynin, respectively, enabled the Δ(ku,ligD,recA mutant strain lacking both systems to survive intracellularly. Complementation of the Δ(ku,ligD,recA mutant with an intact recA or ku-ligD rescued the ability of Mtb to propagate inside macrophages.

  12. A mechanism for DNA-PK activation requiring unique contributions from each strand of a DNA terminus and implications for microhomology-mediated nonhomologous DNA end joining

    OpenAIRE

    Pawelczak, Katherine S; Turchi, John J.

    2008-01-01

    DNA-dependent protein kinase (DNA-PK) is an essential component of the nonhomologous end joining pathway (NHEJ), responsible for the repair of DNA double-strand breaks. Ku binds a DSB and recruits the catalytic subunit, DNA-PKcs, where it is activated once the kinase is bound to the DSB. The precise mechanism by which DNA activates DNA-PK remains unknown. We have investigated the effect of DNA structure on DNA-PK activation and results demonstrate that in Ku-dependent DNA-PKcs reactions, DNA-...

  13. Role of DNA Repair by Nonhomologous-End Joining in Bacillus subtilis Spore Resistance to Extreme Dryness, Mono- and Polychromatic UV, and Ionizing Radiation▿

    OpenAIRE

    Moeller, Ralf; Stackebrandt, Erko; Reitz, Günther; Berger, Thomas; Rettberg, Petra; Doherty, Aidan J; Horneck, Gerda; Nicholson, Wayne L.

    2007-01-01

    The role of DNA repair by nonhomologous-end joining (NHEJ) in spore resistance to UV, ionizing radiation, and ultrahigh vacuum was studied in wild-type and DNA repair mutants (recA, splB, ykoU, ykoV, and ykoU ykoV mutants) of Bacillus subtilis. NHEJ-defective spores with mutations in ykoU, ykoV, and ykoU ykoV were significantly more sensitive to UV, ionizing radiation, and ultrahigh vacuum than wild-type spores, indicating that NHEJ provides an important pathway during spore germination for r...

  14. The Ku70/80 ring in Non-Homologous End-Joining: easy to slip on, hard to remove

    DEFF Research Database (Denmark)

    Kragelund, Birthe Brandt; Weterings, Eric; Hartmann-Petersen, Rasmus;

    2016-01-01

    /80 heterodimer is a key-player in the NHEJ pathway and binds to DNA termini with high affinity, where it helps to protect DNA ends from degradation and to recruit other NHEJ factors required for repair. The mechanism of Ku70/80 detachment from the DNA helix after completion of DNA repair is incompletely......Non-homologous end-joining (NHEJ) is an essential DNA double strand break repair pathway during all cell cycle stages. Deficiency in NHEJ factors can lead to accumulation of unrepaired DNA breaks or faulty DNA repair, which may ultimately result in cell death, senescence or carcinogenesis. The Ku70...

  15. Agrobacterium tumefaciens T-DNA Integration and Gene Targeting in Arabidopsis thaliana Non-Homologous End-Joining Mutants

    Directory of Open Access Journals (Sweden)

    Qi Jia

    2012-01-01

    Full Text Available In order to study the role of AtKu70 and AtKu80 in Agrobacterium-mediated transformation and gene targeting, plant lines with a T-DNA insertion in AtKu80 or AtKu70 genes were functionally characterized. Such plant lines lacked both subunits, indicating that heterodimer formation between AtKu70 and AtKu80 is needed for the stability of the proteins. Homozygous mutants were phenotypically indistinguishable from wild-type plants and were fertile. However, they were hypersensitive to the genotoxic agent bleomycin, resulting in more DSBs as quantified in comet assays. They had lower end-joining efficiency, suggesting that NHEJ is a critical pathway for DSB repair in plants. Both Atku mutants and a previously isolated Atmre11 mutant were impaired in Agrobacterium T-DNA integration via floral dip transformation, indicating that AtKu70, AtKu80, and AtMre11 play an important role in T-DNA integration in Arabidopsis. The frequency of gene targeting was not significantly increased in the Atku80 and Atku70 mutants, but it was increased at least 10-fold in the Atmre11 mutant compared with the wild type.

  16. Cadmium delays non-homologous end joining (NHEJ) repair via inhibition of DNA-PKcs phosphorylation and downregulation of XRCC4 and Ligase IV

    Energy Technology Data Exchange (ETDEWEB)

    Li, Weiwei; Gu, Xueyan; Zhang, Xiaoning; Kong, Jinxin [Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000 (China); Ding, Nan [Gansu Key laboratory of Space Radiobiology, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Qi, Yongmei; Zhang, Yingmei [Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000 (China); Wang, Jufang [Gansu Key laboratory of Space Radiobiology, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Huang, Dejun, E-mail: huangdj@lzu.edu.cn [Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000 (China)

    2015-09-15

    Highlights: • Cadmium (Cd) exposure delayed the repair of DNA damage induced by X-ray. • Cd exposure altered the phosphorylation of DNA-PKcs on Thr-2609 and Ser-2056 sites. • Cd impaired the formation of XRCC4 and Ligase IV foci, and down-regulated their protein expression. • Zinc mitigated the effects of Cd on DDR by regulating pDNA-PKcs (Thr-2609), XRCC4 and Ligase IV. - Abstract: Although studies have shown that cadmium (Cd) interfered with DNA damage repair (DDR), whether Cd could affect non-homologous end joining (NHEJ) repair remains elusive. To further understand the effect of Cd on DDR, we used X-ray irradiation of Hela cells as an in vitro model system, along with γH2AX and 53BP1 as markers for DNA damage. Results showed that X-ray significantly increased γH2AX and 53BP1 foci in Hela cells (p < 0.01), all of which are characteristic of accrued DNA damage. The number of foci declined rapidly over time (1–8 h postirradiation), indicating an initiation of NHEJ process. However, the disappearance of γH2AX and 53BP1 foci was remarkably slowed by Cd pretreatment (p < 0.01), suggesting that Cd reduced the efficiency of NHEJ. To further elucidate the mechanisms of Cd toxicity, several markers of NHEJ pathway including Ku70, DNA-PKcs, XRCC4 and Ligase IV were examined. Our data showed that Cd altered the phosphorylation of DNA-PKcs, and reduced the expression of both XRCC4 and Ligase IV in irradiated cells. These observations are indicative of the impairment of NHEJ-dependent DNA repair pathways. In addition, zinc (Zn) mitigated the effects of Cd on NHEJ, suggesting that the Cd-induced NHEJ alteration may partly result from the displacement of Zn or from an interference with the normal function of Zn-containing proteins by Cd. Our findings provide a new insight into the toxicity of Cd on NHEJ repair and its underlying mechanisms in human cells.

  17. Cadmium delays non-homologous end joining (NHEJ) repair via inhibition of DNA-PKcs phosphorylation and downregulation of XRCC4 and Ligase IV

    International Nuclear Information System (INIS)

    Highlights: • Cadmium (Cd) exposure delayed the repair of DNA damage induced by X-ray. • Cd exposure altered the phosphorylation of DNA-PKcs on Thr-2609 and Ser-2056 sites. • Cd impaired the formation of XRCC4 and Ligase IV foci, and down-regulated their protein expression. • Zinc mitigated the effects of Cd on DDR by regulating pDNA-PKcs (Thr-2609), XRCC4 and Ligase IV. - Abstract: Although studies have shown that cadmium (Cd) interfered with DNA damage repair (DDR), whether Cd could affect non-homologous end joining (NHEJ) repair remains elusive. To further understand the effect of Cd on DDR, we used X-ray irradiation of Hela cells as an in vitro model system, along with γH2AX and 53BP1 as markers for DNA damage. Results showed that X-ray significantly increased γH2AX and 53BP1 foci in Hela cells (p < 0.01), all of which are characteristic of accrued DNA damage. The number of foci declined rapidly over time (1–8 h postirradiation), indicating an initiation of NHEJ process. However, the disappearance of γH2AX and 53BP1 foci was remarkably slowed by Cd pretreatment (p < 0.01), suggesting that Cd reduced the efficiency of NHEJ. To further elucidate the mechanisms of Cd toxicity, several markers of NHEJ pathway including Ku70, DNA-PKcs, XRCC4 and Ligase IV were examined. Our data showed that Cd altered the phosphorylation of DNA-PKcs, and reduced the expression of both XRCC4 and Ligase IV in irradiated cells. These observations are indicative of the impairment of NHEJ-dependent DNA repair pathways. In addition, zinc (Zn) mitigated the effects of Cd on NHEJ, suggesting that the Cd-induced NHEJ alteration may partly result from the displacement of Zn or from an interference with the normal function of Zn-containing proteins by Cd. Our findings provide a new insight into the toxicity of Cd on NHEJ repair and its underlying mechanisms in human cells

  18. Human induced pluripotent cells resemble embryonic stem cells demonstrating enhanced levels of DNA repair and efficacy of nonhomologous end-joining

    Energy Technology Data Exchange (ETDEWEB)

    Fan Jinshui; Robert, Carine [Department of Radiation Oncology, University of Maryland School of Medicine, 655 West Baltimore Street, BRB 7-023A, Baltimore, MD 21201 (United States); Jang, Yoon-Young; Liu Hua; Sharkis, Saul; Baylin, Stephen Bruce [Johns Hopkins University School of Medicine, Department of Oncology, Baltimore, MD 21231-1000 (United States); Rassool, Feyruz Virgilia, E-mail: frassool@som.umaryland.edu [Department of Radiation Oncology, University of Maryland School of Medicine, 655 West Baltimore Street, BRB 7-023A, Baltimore, MD 21201 (United States)

    2011-08-01

    Highlights: {yields} iPSC and hESC demonstrate a similar cell cycle profile, with increased S phase cells and decreased G0/G1. {yields} iPSC and hESC increased ROS and decreased DSBs, compared with differentiated parental cells. {yields} iPSC and hESC demonstrate elevated DSB repair activity, including nonhomologous end-joining, compared with differentiated parental cells. {yields} iPSC however show a partial apoptotic response to DNA damage, compared to hESC. {yields} DNA damage responses may constitute important markers for the efficacy of iPSC reprogramming. - Abstract: To maintain the integrity of the organism, embryonic stem cells (ESC) need to maintain their genomic integrity in response to DNA damage. DNA double strand breaks (DSBs) are one of the most lethal forms of DNA damage and can have disastrous consequences if not repaired correctly, leading to cell death, genomic instability and cancer. How human ESC (hESC) maintain genomic integrity in response to agents that cause DSBs is relatively unclear. Adult somatic cells can be induced to 'dedifferentiate' into induced pluripotent stem cells (iPSC) and reprogram into cells of all three germ layers. Whether iPSC have reprogrammed the DNA damage response is a critical question in regenerative medicine. Here, we show that hESC demonstrate high levels of endogenous reactive oxygen species (ROS) which can contribute to DNA damage and may arise from high levels of metabolic activity. To potentially counter genomic instability caused by DNA damage, we find that hESC employ two strategies: First, these cells have enhanced levels of DNA repair proteins, including those involved in repair of DSBs, and they demonstrate elevated nonhomologous end-joining (NHEJ) activity and repair efficacy, one of the main pathways for repairing DSBs. Second, they are hypersensitive to DNA damaging agents, as evidenced by a high level of apoptosis upon irradiation. Importantly, iPSC, unlike the parent cells they are derived

  19. Mutation of the BRCA1 SQ-cluster results in aberrant mitosis, reduced homologous recombination, and a compensatory increase in non-homologous end joining.

    Science.gov (United States)

    Beckta, Jason M; Dever, Seth M; Gnawali, Nisha; Khalil, Ashraf; Sule, Amrita; Golding, Sarah E; Rosenberg, Elizabeth; Narayanan, Aarthi; Kehn-Hall, Kylene; Xu, Bo; Povirk, Lawrence F; Valerie, Kristoffer

    2015-09-29

    Mutations in the breast cancer susceptibility 1 (BRCA1) gene are catalysts for breast and ovarian cancers. Most mutations are associated with the BRCA1 N- and C-terminal domains linked to DNA double-strand break (DSB) repair. However, little is known about the role of the intervening serine-glutamine (SQ) - cluster in the DNA damage response beyond its importance in regulating cell cycle checkpoints. We show that serine-to-alanine alterations at critical residues within the SQ-cluster known to be phosphorylated by ATM and ATR result in reduced homologous recombination repair (HRR) and aberrant mitosis. While a S1387A BRCA1 mutant - previously shown to abrogate S-phase arrest in response to radiation - resulted in only a modest decrease in HRR, S1387A together with an additional alteration, S1423A (BRCA12P), reduced HRR to vector control levels and similar to a quadruple mutant also including S1457A and S1524A (BRCA14P). These effects appeared to be independent of PALB2. Furthermore, we found that BRCA14P promoted a prolonged and struggling HRR late in the cell cycle and shifted DSB repair from HRR to non-homologous end joining which, in the face of irreparable chromosomal damage, resulted in mitotic catastrophe. Altogether, SQ-cluster phosphorylation is critical for allowing adequate time for completing normal HRR prior to mitosis and preventing cells from entering G1 prematurely resulting in gross chromosomal aberrations.

  20. Agrobacterium May Delay Plant Nonhomologous End-Joining DNA Repair via XRCC4 to Favor T-DNA Integration[W

    Science.gov (United States)

    Vaghchhipawala, Zarir E.; Vasudevan, Balaji; Lee, Seonghee; Morsy, Mustafa R.; Mysore, Kirankumar S.

    2012-01-01

    Agrobacterium tumefaciens is a soilborne pathogen that causes crown gall disease in many dicotyledonous plants by transfer of a portion of its tumor-inducing plasmid (T-DNA) into the plant genome. Several plant factors that play a role in Agrobacterium attachment to plant cells and transport of T-DNA to the nucleus have been identified, but the T-DNA integration step during transformation is poorly understood and has been proposed to occur via nonhomologous end-joining (NHEJ)–mediated double-strand DNA break (DSB) repair. Here, we report a negative role of X-RAY CROSS COMPLEMENTATION GROUP4 (XRCC4), one of the key proteins required for NHEJ, in Agrobacterium T-DNA integration. Downregulation of XRCC4 in Arabidopsis and Nicotiana benthamiana increased stable transformation due to increased T-DNA integration. Overexpression of XRCC4 in Arabidopsis decreased stable transformation due to decreased T-DNA integration. Interestingly, XRCC4 directly interacted with Agrobacterium protein VirE2 in a yeast two-hybrid system and in planta. VirE2-expressing Arabidopsis plants were more susceptible to the DNA damaging chemical bleomycin and showed increased stable transformation. We hypothesize that VirE2 titrates or excludes active XRCC4 protein available for DSB repair, thus delaying the closure of DSBs in the chromosome, providing greater opportunity for T-DNA to integrate. PMID:23064322

  1. Cell nonhomologous end joining capacity controls SAF-A phosphorylation by DNA-PK in response to DNA double-strand breaks inducers.

    Science.gov (United States)

    Britton, Sébastien; Froment, Carine; Frit, Philippe; Monsarrat, Bernard; Salles, Bernard; Calsou, Patrick

    2009-11-15

    Aiming to identify novel phosphorylation sites in response to DNA double-strand breaks (DSB) inducers, we have isolated a phosphorylation site on KU70. Unexpectedly, a rabbit antiserum raised against this site cross-reacted with a 120 kDa protein in cells treated by DNA DSB inducers. We identified this protein as SAF-A/hnRNP U, an abundant and essential nuclear protein containing regions binding DNA or RNA. The phosphorylation site was mapped at S59 position in a sequence context favoring a "S-hydrophobic" consensus model for DNA-PK phosphorylation site in vivo. This site was exclusively phosphorylated by DNA-PK in response to DNA DSB inducers. In addition, the extent and duration of this phosphorylation was in inverse correlation with the capacity of the cells to repair DSB by Nonhomologous End Joining. These results bring a new link between the hnRNP family and the DNA damage response. Addtionaly, the mapped phospho-site on SAF-A might serve as a potential bio-marker for DNA-PK activity in academic studies and clinical analyses of DNA-PK activators or inhibitors. PMID:19844162

  2. Non-homologous end joining dependency of {gamma}-irradiation-induced adaptive frameshift mutation formation in cell cycle-arrested yeast cells

    Energy Technology Data Exchange (ETDEWEB)

    Heidenreich, Erich [Institute of Cancer Research, Division of Molecular Genetics, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna (Austria)]. E-mail: erich.heidenreich@meduniwien.ac.at; Eisler, Herfried [Institute of Cancer Research, Division of Molecular Genetics, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna (Austria)

    2004-11-22

    There is a strong selective pressure favoring adaptive mutations which relieve proliferation-limiting adverse living conditions. Due to their importance for evolution and pathogenesis, we are interested in the mechanisms responsible for the formation of such adaptive, gain-of-fitness mutations in stationary-phase cells. During previous studies on the occurrence of spontaneous reversions of an auxotrophy-causing frameshift allele in the yeast Saccharomyces cerevisiae, we noticed that about 50% of the adaptive reversions depended on a functional non-homologous end joining (NHEJ) pathway of DNA double-strand break (DSB) repair. Here, we show that the occasional NHEJ component Pol4, which is the yeast ortholog of mammalian DNA polymerase lambda, is not required for adaptive mutagenesis. An artificially imposed excess of DSBs by {gamma}-irradiation resulted in a dramatic increase in the incidence of adaptive, cell cycle arrest-releasing frameshift reversions. By the use of DNA ligase IV-deficient strains we detected that the majority of the {gamma}-induced adaptive mutations were also dependent on a functional NHEJ pathway. This suggests that the same mutagenic NHEJ mechanism acts on spontaneously arising as well as on ionizing radiation-induced DSBs. Inaccuracy of the NHEJ repair pathway may extensively contribute to the incidence of frameshift mutations in resting (non-dividing) eukaryotic cells, and thus act as a driving force in tumor development.

  3. Non-homologous end joining pathway is the major route of protection against 4β-hydroxywithanolide E-induced DNA damage in MCF-7 cells.

    Science.gov (United States)

    You, B-J; Wu, Y-C; Lee, C-L; Lee, H-Z

    2014-03-01

    4β-Hydroxywithanolide E is a bioactive withanolide extracted from Physalis peruviana. 4β-Hydroxywithanolide E caused reactive oxygen species production and cell apoptosis in human breast cancer MCF-7 cells. We further found that 4β-hydroxywithanolide E induced DNA damage and regulated the DNA damage signaling in MCF-7 cells. The DNA damage sensors and repair proteins act promptly to remove DNA lesions by 4β-hydroxywithanolide E. The ataxia-telangiectasia mutated protein (ATM)-dependent DNA damage signaling pathway is involved in 4β-hydroxywithanolide E-induced apoptosis of MCF-7 cells. Non-homologous end joining pathway, but not homologous recombination, is the major route of protection of MCF-7 cells against 4β-hydroxywithanolide E-induced DNA damage. 4β-Hydroxywithanolide E had no significant impact on the base excision repair pathway. In this study, we examined the 4β-hydroxywithanolide E-induced DNA damage as a research tool in project investigating the DNA repair signaling in breast cancer cells. We also suggest that 4β-hydroxywithanolide E assert its anti-tumor activity in carcinogenic progression and develop into a dietary chemopreventive agent. PMID:24373828

  4. The fate of linear DNA in Saccharomyces cerevisiae and Candida glabrata: the role of homologous and non-homologous end joining.

    Directory of Open Access Journals (Sweden)

    Mary W Corrigan

    Full Text Available In vivo assembly of plasmids has become an increasingly used process, as high throughput studies in molecular biology seek to examine gene function. In this study, we investigated the plasmid construction technique called gap repair cloning (GRC in two closely related species of yeast - Saccharomyces cerevisiae and Candida glabrata. GRC utilizes homologous recombination (HR activity to join a linear vector and a linear piece of DNA that contains base pair homology. We demonstrate that a minimum of 20 bp of homology on each side of the linear DNA is required for GRC to occur with at least 10% efficiency. Between the two species, we determine that S. cerevisiae is slightly more efficient at performing GRC. GRC is less efficient in rad52 deletion mutants, which are defective in HR in both species. In dnl4 deletion mutants, which perform less non-homologous end joining (NHEJ, the frequency of GRC increases in C. glabrata, whereas GRC frequency only minimally increases in S. cerevisiae, suggesting that NHEJ is more prevalent in C. glabrata. Our studies allow for a model of the fate of linear DNA when transformed into yeast cells. This model is not the same for both species. Most significantly, during GRC, C. glabrata performs NHEJ activity at a detectable rate (>5%, while S. cerevisiae does not. Our model suggests that S. cerevisiae is more efficient at HR because NHEJ is less prevalent than in C. glabrata. This work demonstrates the determinants for GRC and that while C. glabrata has a lower efficiency of GRC, this species still provides a viable option for GRC.

  5. TDP2-dependent non-homologous end-joining protects against topoisomerase II-induced DNA breaks and genome instability in cells and in vivo.

    Directory of Open Access Journals (Sweden)

    Fernando Gómez-Herreros

    Full Text Available Anticancer topoisomerase "poisons" exploit the break-and-rejoining mechanism of topoisomerase II (TOP2 to generate TOP2-linked DNA double-strand breaks (DSBs. This characteristic underlies the clinical efficacy of TOP2 poisons, but is also implicated in chromosomal translocations and genome instability associated with secondary, treatment-related, haematological malignancy. Despite this relevance for cancer therapy, the mechanistic aspects governing repair of TOP2-induced DSBs and the physiological consequences that absent or aberrant repair can have are still poorly understood. To address these deficits, we employed cells and mice lacking tyrosyl DNA phosphodiesterase 2 (TDP2, an enzyme that hydrolyses 5'-phosphotyrosyl bonds at TOP2-associated DSBs, and studied their response to TOP2 poisons. Our results demonstrate that TDP2 functions in non-homologous end-joining (NHEJ and liberates DSB termini that are competent for ligation. Moreover, we show that the absence of TDP2 in cells impairs not only the capacity to repair TOP2-induced DSBs but also the accuracy of the process, thus compromising genome integrity. Most importantly, we find this TDP2-dependent NHEJ mechanism to be physiologically relevant, as Tdp2-deleted mice are sensitive to TOP2-induced damage, displaying marked lymphoid toxicity, severe intestinal damage, and increased genome instability in the bone marrow. Collectively, our data reveal TDP2-mediated error-free NHEJ as an efficient and accurate mechanism to repair TOP2-induced DSBs. Given the widespread use of TOP2 poisons in cancer chemotherapy, this raises the possibility of TDP2 being an important etiological factor in the response of tumours to this type of agent and in the development of treatment-related malignancy.

  6. Nucleosome resection at a double-strand break during Non-Homologous Ends Joining in mammalian cells - implications from repressive chromatin organization and the role of ARTEMIS

    Directory of Open Access Journals (Sweden)

    De Benedetti Arrigo

    2011-01-01

    Full Text Available Abstract Background The S. cerevisiae mating type switch model of double-strand break (DSB repair, utilizing the HO endonuclease, is one of the best studied systems for both Homologous Recombination Repair (HRR and direct ends-joining repair (Non-Homologous Ends Joining - NHEJ. We have recently transposed that system to a mammalian cell culture model taking advantage of an adenovirus expressing HO and an integrated genomic target. This made it possible to compare directly the mechanism of repair between yeast and mammalian cells for the same type of induced DSB. Studies of DSB repair have emphasized commonality of features, proteins and machineries between organisms, and differences when conservation is not found. Two proteins that stand out that differ between yeast and mammalian cells are DNA-PK, a protein kinase that is activated by the presence of DSBs, and Artemis, a nuclease whose activity is modulated by DNA-PK and ATM. In this report we describe how these two proteins may be involved in a specific pattern of ends-processing at the DSB, particularly in the context of heterochromatin. Findings We previously published that the repair of the HO-induced DSB was generally accurate and occurred by simple rejoining of the cohesive 3'-overhangs generated by HO. During continuous passage of those cells in the absence of puromycin selection, the locus appears to have become more heterochromatic and silenced by displaying several features. 1 The site had become less accessible to cleavage by the HO endonuclease; 2 the expression of the puro mRNA, which confers resistance to puromycin, had become reduced; 3 occupancy of nucleosomes at the site (ChIP for histone H3 was increased, an indicator for more condensed chromatin. After reselection of these cells by addition of puromycin, many of these features were reversed. However, even the reselected cells were not identical in the pattern of cleavage and repair as the cells when originally created

  7. Non-homologous end joining is the responsible pathway for the repair of fludarabine-induced DNA double strand breaks in mammalian cells

    International Nuclear Information System (INIS)

    Fludarabine (FLU), an analogue of adenosine, interferes with DNA synthesis and inhibits the chain elongation leading to replication arrest and DNA double strand break (DSB) formation. Mammalian cells use two main pathways of DSB repair to maintain genomic stability: homologous recombination (HR) and non-homologous end joining (NHEJ). The aim of the present work was to evaluate the repair pathways employed in the restoration of DSB formed following replication arrest induced by FLU in mammalian cells. Replication inhibition was induced in human lymphocytes and fibroblasts by FLU. DSB occurred in a dose-dependent manner on early/middle S-phase cells, as detected by γH2AX foci formation. To test whether conservative HR participates in FLU-induced DSB repair, we measured the kinetics of Rad51 nuclear foci formation in human fibroblasts. There was no significant induction of Rad51 foci after FLU treatment. To further confirm these results, we analyzed the frequency of sister chromatid exchanges (SCE) in both human cells. We did not find increased frequencies of SCE after FLU treatment. To assess the participation of NHEJ pathway in the repair of FLU-induced damage, we used two chemical inhibitors of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs), vanillin and wortmannin. Human fibroblasts pretreated with DNA-PKcs inhibitors showed increased levels of chromosome breakages and became more sensitive to cell death. An active role of NHEJ pathway was also suggested from the analysis of Chinese hamster cell lines. XR-C1 (DNA-PKcs-deficient) and XR-V15B (Ku80-deficient) cells showed hypersensitivity to FLU as evidenced by the increased frequency of chromosome aberrations, decreased mitotic index and impaired survival rates. In contrast, CL-V4B (Rad51C-deficient) and V-C8 (Brca2-deficient) cell lines displayed a FLU-resistant phenotype. Together, our results suggest a major role for NHEJ repair in the preservation of genome integrity against FLU-induced DSB

  8. Non-homologous end joining is the responsible pathway for the repair of fludarabine-induced DNA double strand breaks in mammalian cells

    Energy Technology Data Exchange (ETDEWEB)

    Campos-Nebel, Marcelo de [Departamento de Genetica, Instituto de Investigaciones Hematologicas Mariano R. Castex, Academia Nacional de Medicina, Buenos Aires (Argentina)], E-mail: mnebel@hematologia.anm.edu.ar; Larripa, Irene; Gonzalez-Cid, Marcela [Departamento de Genetica, Instituto de Investigaciones Hematologicas Mariano R. Castex, Academia Nacional de Medicina, Buenos Aires (Argentina)

    2008-11-10

    Fludarabine (FLU), an analogue of adenosine, interferes with DNA synthesis and inhibits the chain elongation leading to replication arrest and DNA double strand break (DSB) formation. Mammalian cells use two main pathways of DSB repair to maintain genomic stability: homologous recombination (HR) and non-homologous end joining (NHEJ). The aim of the present work was to evaluate the repair pathways employed in the restoration of DSB formed following replication arrest induced by FLU in mammalian cells. Replication inhibition was induced in human lymphocytes and fibroblasts by FLU. DSB occurred in a dose-dependent manner on early/middle S-phase cells, as detected by {gamma}H2AX foci formation. To test whether conservative HR participates in FLU-induced DSB repair, we measured the kinetics of Rad51 nuclear foci formation in human fibroblasts. There was no significant induction of Rad51 foci after FLU treatment. To further confirm these results, we analyzed the frequency of sister chromatid exchanges (SCE) in both human cells. We did not find increased frequencies of SCE after FLU treatment. To assess the participation of NHEJ pathway in the repair of FLU-induced damage, we used two chemical inhibitors of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs), vanillin and wortmannin. Human fibroblasts pretreated with DNA-PKcs inhibitors showed increased levels of chromosome breakages and became more sensitive to cell death. An active role of NHEJ pathway was also suggested from the analysis of Chinese hamster cell lines. XR-C1 (DNA-PKcs-deficient) and XR-V15B (Ku80-deficient) cells showed hypersensitivity to FLU as evidenced by the increased frequency of chromosome aberrations, decreased mitotic index and impaired survival rates. In contrast, CL-V4B (Rad51C-deficient) and V-C8 (Brca2-deficient) cell lines displayed a FLU-resistant phenotype. Together, our results suggest a major role for NHEJ repair in the preservation of genome integrity against FLU

  9. Flexibility in the order of action and in the enzymology of the nuclease, polymerases, and ligase of vertebrate nonhomologous DNA end joining: relevance to cancer, aging,and the immune system

    Institute of Scientific and Technical Information of China (English)

    Michael R Lieber; Haihui Lu; Jiafeng Gu; Klaus Schwarz

    2008-01-01

    Nonhomologous DNA end joining (NHEJ) is the primary pathway for repair of double-strand DNA breaks in hu-man cells and in multicellular eukaryotes. The causes of double-strand breaks often fragment the DNA at the site of damage, resulting in the loss of information there. NHEJ does not restore the lost information and may resect ad-ditional nucleotides during the repair process. The ability to repair a wide range of overhang and damage configura-tions reflects the flexibility of the nuclease, polymerases, and ligase of NHEJ. The flexibility of the individual com-ponents also explains the large number of ways in which NHEJ can repair any given pair of DNA ends. The loss of information locally at sites of NHEJ repair may contribute to cancer and aging, but the action by NHEJ ensures that entire segments of chromosomes are not lost.

  10. A Role for BLM in Double-Strand Break Repair Pathway Choice: Prevention of CtIP/Mre11-Mediated Alternative Nonhomologous End-Joining

    Directory of Open Access Journals (Sweden)

    Anastazja Grabarz

    2013-10-01

    Full Text Available The choice of the appropriate double-strand break (DSB repair pathway is essential for the maintenance of genomic stability. Here, we show that the Bloom syndrome gene product, BLM, counteracts CtIP/MRE11-dependent long-range deletions (>200 bp generated by alternative end-joining (A-EJ. BLM represses A-EJ in an epistatic manner with 53BP1 and RIF1 and is required for ionizing-radiation-induced 53BP1 focus assembly. Conversely, in the absence of 53BP1 or RIF1, BLM promotes formation of A-EJ long deletions, consistent with a role for BLM in DSB end resection. These data highlight a dual role for BLM that influences the DSB repair pathway choice: (1 protection against CtIP/MRE11 long-range deletions associated with A-EJ and (2 promotion of DNA resection. These antagonist roles can be regulated, according to cell-cycle stage, by interacting partners such as 53BP1 and TopIII, to avoid unscheduled resection that might jeopardize genome integrity.

  11. Use of a non-homologous end-joining-deficient strain (delta-ku70) of the biocontrol fungus Trichoderma virens to investigate the function of the laccase gene lcc1 in sclerotia degradation.

    Science.gov (United States)

    Catalano, Valentina; Vergara, Mariarosaria; Hauzenberger, Jasmin R; Seiboth, Bernhard; Sarrocco, Sabrina; Vannacci, Giovanni; Kubicek, Christian P; Seidl-Seiboth, Verena

    2011-02-01

    The aim of this study was to apply a generated Δtku70 strain with increased homologous recombination efficiency from the mycoparasitic fungus Trichoderma virens for studying the involvement of laccases in the degradation of sclerotia of plant pathogenic fungi. Inactivation of the non-homologous end-joining pathway has become a successful tool in filamentous fungi to overcome poor targeting efficiencies for genetic engineering. Here, we applied this principle to the biocontrol fungus T. virens, strain I10, by deleting its tku70 gene. This strain was subsequently used to delete the laccase gene lcc1, which we found to be expressed after interaction of T. virens with sclerotia of the plant pathogenic fungi Botrytis cinerea and Sclerotinia sclerotiorum. Lcc1 was strongly upregulated at early colonization of B. cinerea sclerotia and steadily induced during colonization of S. sclerotiorum sclerotia. The Δtku70Δlcc1 mutant was altered in its ability to degrade the sclerotia of B. cinerea and S. sclerotiorum. Interestingly, while the decaying ability for B. cinerea sclerotia was significantly decreased, that to degrade S. sclerotiorum sclerotia was even enhanced, suggesting the operation of different mechanisms in the mycoparasitism of these two types of sclerotia by the laccase LCC1. PMID:20872221

  12. Human transcriptional coactivator PC4 stimulates DNA end joining and activates DSB repair activity.

    Science.gov (United States)

    Batta, Kiran; Yokokawa, Masatoshi; Takeyasu, Kunio; Kundu, Tapas K

    2009-01-23

    Human transcriptional coactivator PC4 is a highly abundant nuclear protein that is involved in diverse cellular processes ranging from transcription to chromatin organization. Earlier, we have shown that PC4, a positive activator of p53, overexpresses upon genotoxic insult in a p53-dependent manner. In the present study, we show that PC4 stimulates ligase-mediated DNA end joining irrespective of the source of DNA ligase. Pull-down assays reveal that PC4 helps in the association of DNA ends through its C-terminal domain. In vitro nonhomologous end-joining assays with cell-free extracts show that PC4 enhances the joining of noncomplementary DNA ends. Interestingly, we found that PC4 activates double-strand break (DSB) repair activity through stimulation of DSB rejoining in vivo. Together, these findings demonstrate PC4 as an activator of nonhomologous end joining and DSB repair activity.

  13. Risky business: Microhomology-mediated end joining.

    Science.gov (United States)

    Sinha, Supriya; Villarreal, Diana; Shim, Eun Yong; Lee, Sang Eun

    2016-06-01

    Prevalence of microhomology (MH) at the breakpoint junctions in somatic and germ-line chromosomal rearrangements and in the programmed immune receptor rearrangements from cells deficient in classical end joining reveals an enigmatic process called MH-mediated end joining (MMEJ). MMEJ repairs DNA double strand breaks (DSBs) by annealing flanking MH and deleting genetic information at the repair junctions from yeast to humans. Being genetically distinct from canonical DNA DSB pathways, MMEJ is involved with the fusions of eroded/uncapped telomeres as well as with the assembly of chromosome fragments in chromothripsis. In this review article, we will discuss an up-to-date model representing the MMEJ process and the mechanism by which cells regulate MMEJ to limit repair-associated mutagenesis. We will also describe the possible therapeutic gains resulting from the inhibition of MMEJ in recombination deficient cancers. Lastly, we will embark on two contentious issues associated with MMEJ such as the significance of MH at the repair junction to be the hallmark of MMEJ and the relationship of MMEJ to other mechanistically related DSB repair pathways. PMID:26790771

  14. An essential role for CtIP in chromosomal translocation formation through an alternative end-joining pathway

    OpenAIRE

    Zhang, Yu; Jasin, Maria

    2010-01-01

    Chromosomal translocations arise from the misjoining of DNA breaks, but the identity of the DNA repair factors and activities involved in their formation has been elusive. Here we show that depletion of CtIP, a DNA end-resection factor, results in a substantial decrease in chromosomal translocation frequency in mouse cells. Moreover, microhomology usage, a signature of the alternative nonhomologous end-joining pathway (alt-NHEJ), is significantly lower in translocation breakpoint junctions re...

  15. Alternative end-joining pathway(s): bricolage at DNA breaks.

    Science.gov (United States)

    Frit, Philippe; Barboule, Nadia; Yuan, Ying; Gomez, Dennis; Calsou, Patrick

    2014-05-01

    To cope with DNA double strand break (DSB) genotoxicity, cells have evolved two main repair pathways: homologous recombination which uses homologous DNA sequences as repair templates, and non-homologous Ku-dependent end-joining involving direct sealing of DSB ends by DNA ligase IV (Lig4). During the last two decades a third player most commonly named alternative end-joining (A-EJ) has emerged, which is defined as any Ku- or Lig4-independent end-joining process. A-EJ increasingly appears as a highly error-prone bricolage on DSBs and despite expanding exploration, it still escapes full characterization. In the present review, we discuss the mechanism and regulation of A-EJ as well as its biological relevance under physiological and pathological situations, with a particular emphasis on chromosomal instability and cancer. Whether or not it is a genuine DSB repair pathway, A-EJ is emerging as an important cellular process and understanding A-EJ will certainly be a major challenge for the coming years. PMID:24613763

  16. CtIP promotes microhomology-mediated alternative end joining during class-switch recombination.

    Science.gov (United States)

    Lee-Theilen, Mieun; Matthews, Allysia J; Kelly, Dierdre; Zheng, Simin; Chaudhuri, Jayanta

    2011-01-01

    Immunoglobulin heavy chain (Igh locus) class-switch recombination (CSR) requires targeted introduction of DNA double strand breaks (DSBs) into repetitive 'switch'-region DNA elements in the Igh locus and subsequent ligation between distal DSBs. Both canonical nonhomologous end joining (C-NHEJ) that seals DNA ends with little or no homology and a poorly defined alternative end joining (A-NHEJ, also known as alt-NHEJ) process that requires microhomology ends for ligation have been implicated in CSR. Here, we show that the DNA end-processing factor CtIP is required for microhomology-directed A-NHEJ during CSR. Additionally, we demonstrate that microhomology joins that are enriched upon depletion of the C-NHEJ component Ku70 require CtIP. Finally, we show that CtIP binds to switch-region DNA in a fashion dependent on activation-induced cytidine deaminase. Our results establish CtIP as a bona fide component of microhomology-dependent A-NHEJ and unmask a hitherto unrecognized physiological role of microhomology-mediated end joining in a C-NHEJ-proficient environment.

  17. Essential Roles for Polymerase θ-Mediated End Joining in the Repair of Chromosome Breaks.

    Science.gov (United States)

    Wyatt, David W; Feng, Wanjuan; Conlin, Michael P; Yousefzadeh, Matthew J; Roberts, Steven A; Mieczkowski, Piotr; Wood, Richard D; Gupta, Gaorav P; Ramsden, Dale A

    2016-08-18

    DNA polymerase theta (Pol θ)-mediated end joining (TMEJ) has been implicated in the repair of chromosome breaks, but its cellular mechanism and role relative to canonical repair pathways are poorly understood. We show that it accounts for most repairs associated with microhomologies and is made efficient by coupling a microhomology search to removal of non-homologous tails and microhomology-primed synthesis across broken ends. In contrast to non-homologous end joining (NHEJ), TMEJ efficiently repairs end structures expected after aborted homology-directed repair (5' to 3' resected ends) or replication fork collapse. It typically does not compete with canonical repair pathways but, in NHEJ-deficient cells, is engaged more frequently and protects against translocation. Cell viability is also severely impaired upon combined deficiency in Pol θ and a factor that antagonizes end resection (Ku or 53BP1). TMEJ thus helps to sustain cell viability and genome stability by rescuing chromosome break repair when resection is misregulated or NHEJ is compromised. PMID:27453047

  18. Defective nonhomologous end joining blocks B-cell development in FLT3/ITD mice

    OpenAIRE

    Li, Li; Zhang, Li; Fan, Jinshui; Greenberg, Kathleen; Desiderio, Stephen; Rassool, Feyruz V.; Small, Donald

    2011-01-01

    We have generated an FLT3/ITD knock-in mouse model in which mice with an FLT3/ITD mutation develop myeloproliferative disease (MPD) and a block in early B-lymphocyte development. To elucidate the role of FLT3/ITD signaling in B-cell development, we studied VDJ recombination in the pro-B cells of FLT3/ITD mice and discovered an increased frequency of DNA double strand breaks (DSBs) introduced by the VDJ recombinase. Early pro-B cells from FLT3/ITD mice were found to have a lower efficiency and...

  19. DNA-Dependent Protein Kinase in Non-Homologous End-Joining: Guarding Strategic Positions

    OpenAIRE

    Weterings, Eric

    2005-01-01

    markdownabstract__Abstract__ Careful maintenance of genetic information throughout generations is of vital importance to all living creatures. A battery of both endogenous and exogenous factors continuously threatens genetic integrity by altering the DNA chemistry. As a consequence, DNA damage types are as diverse as their causes. DNA doublestrand breaks (DSBs) are among the most deleterious lesions, since they introduce chromosomal breakage or translocation and are able to trigger carcinogen...

  20. Ligase I and ligase III mediate the DNA double-strand break ligation in alternative end-joining.

    Science.gov (United States)

    Lu, Guangqing; Duan, Jinzhi; Shu, Sheng; Wang, Xuxiang; Gao, Linlin; Guo, Jing; Zhang, Yu

    2016-02-01

    In eukaryotes, DNA double-strand breaks (DSBs), one of the most harmful types of DNA damage, are repaired by homologous repair (HR) and nonhomologous end-joining (NHEJ). Surprisingly, in cells deficient for core classic NHEJ factors such as DNA ligase IV (Lig4), substantial end-joining activities have been observed in various situations, suggesting the existence of alternative end-joining (A-EJ) activities. Several putative A-EJ factors have been proposed, although results are mostly controversial. By using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, we generated mouse CH12F3 cell lines in which, in addition to Lig4, either Lig1 or nuclear Lig3, representing the cells containing a single DNA ligase (Lig3 or Lig1, respectively) in their nucleus, was completely ablated. Surprisingly, we found that both Lig1- and Lig3-containing complexes could efficiently catalyze A-EJ for class switching recombination (CSR) in the IgH locus and chromosomal deletions between DSBs generated by CRISPR/Cas9 in cis-chromosomes. However, only deletion of nuclear Lig3, but not Lig1, could significantly reduce the interchromosomal translocations in Lig4(-/-) cells, suggesting the unique role of Lig3 in catalyzing chromosome translocation. Additional sequence analysis of chromosome translocation junction microhomology revealed the specificity of different ligase-containing complexes. The data suggested the existence of multiple DNA ligase-containing complexes in A-EJ. PMID:26787905

  1. Redundant function of DNA ligase 1 and 3 in alternative end-joining during immunoglobulin class switch recombination.

    Science.gov (United States)

    Masani, Shahnaz; Han, Li; Meek, Katheryn; Yu, Kefei

    2016-02-01

    Nonhomologous end-joining (NHEJ) is the major DNA double-strand break (DSB) repair pathway in mammals and resolves the DSBs generated during both V(D)J recombination in developing lymphocytes and class switch recombination (CSR) in antigen-stimulated B cells. In contrast to the absolute requirement for NHEJ to resolve DSBs associated with V(D)J recombination, DSBs associated with CSR can be resolved in NHEJ-deficient cells (albeit at a reduced level) by a poorly defined alternative end-joining (A-EJ) pathway. Deletion of DNA ligase IV (Lig4), a core component of the NHEJ pathway, reduces CSR efficiency in a mouse B-cell line capable of robust cytokine-stimulated CSR in cell culture. Here, we report that CSR levels are not further reduced by deletion of either of the two remaining DNA ligases (Lig1 and nuclear Lig3) in Lig4(-/-) cells. We conclude that in the absence of Lig4, Lig1, and Lig3 function in a redundant manner in resolving switch region DSBs during CSR. PMID:26787901

  2. Efficient Gene Replacements in Toxoplasma gondii Strains Deficient for Nonhomologous End Joining▿ †

    OpenAIRE

    Fox, Barbara A.; Ristuccia, Jessica G.; Gigley, Jason P.; Bzik, David J.

    2009-01-01

    A high frequency of nonhomologous recombination has hampered gene targeting approaches in the model apicomplexan parasite Toxoplasma gondii. To address whether the nonhomologous end-joining (NHEJ) DNA repair pathway could be disrupted in this obligate intracellular parasite, putative KU proteins were identified and a predicted KU80 gene was deleted. The efficiency of gene targeting via double-crossover homologous recombination at several genetic loci was found to be greater than 97% of the to...

  3. Adeno-Associated Virus Site-Specific Integration Is Mediated by Proteins of the Nonhomologous End-Joining Pathway▿

    OpenAIRE

    Daya, Shyam; Cortez, Nenita; Berns, Kenneth I.

    2009-01-01

    Adeno-associated virus type 2 (AAV 2) is the only eukaryotic virus capable of site-specific integration; the target site is at chromosome 19q13.4, a site termed AAVS1. The biology of AAV latency has been extensively studied in cell culture, yet the precise mechanism and the required cellular factors are not known. In this study, we assessed the relative frequencies of stable site-specific integration by characterization of cell clones containing integrated AAV vectors. By this assay, two prot...

  4. Ectopic expression of RNF168 and 53BP1 increases mutagenic but not physiological non-homologous end joining

    DEFF Research Database (Denmark)

    Zong, Dali; Callén, Elsa; Pegoraro, Gianluca;

    2015-01-01

    BP1 and BRCA1 regulate the balance between NHEJ and HR. 53BP1 promotes CSR in part by mediating synapsis of distal DNA ends, and in addition, inhibits 5' end resection. BRCA1 antagonizes 53BP1 dependent DNA end-blocking activity during S phase, which would otherwise promote mutagenic NHEJ and genome...

  5. Transient disruption of non-homologous end-joining facilitates targeted genome manipulations in the filamentous fungus Aspergillus nidulans

    DEFF Research Database (Denmark)

    Nielsen, Jakob Blæsbjerg; Nielsen, Michael Lynge; Mortensen, Uffe Hasbro

    2008-01-01

    ) activity is abolished and gene targeting can be performed with success rates identical to those obtained with permanent nkuA knock-out strains. When gene targeting is complete, the functional nkuA allele can be re-established via a simple selection step, thereby eliminating the risk that defective NHEJ...... be restored by sexual crossing. (c) 2007 Elsevier Inc. All rights reserved....

  6. 53BP1 regulates DNA resection and the choice between classical and alternative end joining during class switch recombination.

    Science.gov (United States)

    Bothmer, Anne; Robbiani, Davide F; Feldhahn, Niklas; Gazumyan, Anna; Nussenzweig, Andre; Nussenzweig, Michel C

    2010-04-12

    Class switch recombination (CSR) diversifies antibodies by joining highly repetitive DNA elements, which are separated by 60-200 kbp. CSR is initiated by activation-induced cytidine deaminase, an enzyme that produces multiple DNA double-strand breaks (DSBs) in switch regions. Switch regions are joined by a mechanism that requires an intact DNA damage response and classical or alternative nonhomologous end joining (A-NHEJ). Among the DNA damage response factors, 53BP1 has the most profound effect on CSR. We explore the role of 53BP1 in intrachromosomal DNA repair using I-SceI to introduce paired DSBs in the IgH locus. We find that the absence of 53BP1 results in an ataxia telangiectasia mutated-dependent increase in DNA end resection and that resected DNA is preferentially repaired by microhomology-mediated A-NHEJ. We propose that 53BP1 favors long-range CSR in part by protecting DNA ends against resection, which prevents A-NHEJ-dependent short-range rejoining of intra-switch region DSBs.

  7. Genomic Scars Generated by Polymerase Theta Reveal the Versatile Mechanism of Alternative End-Joining

    Science.gov (United States)

    van Schendel, Robin; van Heteren, Jane; Welten, Richard; Tijsterman, Marcel

    2016-01-01

    For more than half a century, genotoxic agents have been used to induce mutations in the genome of model organisms to establish genotype-phenotype relationships. While inaccurate replication across damaged bases can explain the formation of single nucleotide variants, it remained unknown how DNA damage induces more severe genomic alterations. Here, we demonstrate for two of the most widely used mutagens, i.e. ethyl methanesulfonate (EMS) and photo-activated trimethylpsoralen (UV/TMP), that deletion mutagenesis is the result of polymerase Theta (POLQ)-mediated end joining (TMEJ) of double strand breaks (DSBs). This discovery allowed us to survey many thousands of available C. elegans deletion alleles to address the biology of this alternative end-joining repair mechanism. Analysis of ~7,000 deletion breakpoints and their cognate junctions reveals a distinct order of events. We found that nascent strands blocked at sites of DNA damage can engage in one or more cycles of primer extension using a more downstream located break end as a template. Resolution is accomplished when 3’ overhangs have matching ends. Our study provides a step-wise and versatile model for the in vivo mechanism of POLQ action, which explains the molecular nature of mutagen-induced deletion alleles. PMID:27755535

  8. Increasing the efficiency of homologous recombination vector-mediated end joining repair by inhibition of Lig4 gene using siRNA in sheep embryo fibroblasts.

    Science.gov (United States)

    Wei, Wang; Yushuang, Wang; Lanlan, Huang; Zijian, Jian; Xinhua, Wang; Shouren, Liu; Wenhui, Pi

    2016-09-01

    In animal cells, inhibition of non-homologous end joining (NHEJ) pathway improves the efficiency of homologous recombination (HR)-mediated double-strand brakes (DSBs) repair. To improve the efficiency of HR in sheep embryo fibroblasts, the NHEJ key molecule DNA ligase 4 (Lig4) was suppressed by siRNA interference. Four pairs of siRNA targeting Lig4 were designed and chemically synthesized. These siRNA were electro-transferred into sheep embryo fibroblasts respectively. Compared with the control groups, two pairs of siRNA were identified to effectively inhibit the expression of sheep Lig4 gene by qRT-PCR and Western blotting. The plasmid rejoining assay was adopted for examining the efficiency of HR-mediated DSB repair. I-SceⅠ endonuclease linearized vector and siRNA were co-transfected into sheep embryo fibroblasts. Flow cytometry analysis of cells after transfection for 72 h showed that suppression of Lig4 using siRNAs increased the rejoining efficiency of HR vector by 3-4 times compared with the control groups. Therefore, enhanced HR vector rejoining frequency by instant inhabition of Lig4 gene provides theoretical basis for improving gene targeting efficiency of sheep embryo fibroblasts. PMID:27644744

  9. A Role for BLM in Double-Strand Break Repair Pathway Choice: Prevention of CtIP/Mre11-Mediated Alternative Nonhomologous End-Joining

    DEFF Research Database (Denmark)

    Grabarz, Anastazja; Guirouilh-Barbat, Josée; Barascu, Aurelia;

    2013-01-01

    represses A-EJ in an epistatic manner with 53BP1 and RIF1 and is required for ionizing-radiation-induced 53BP1 focus assembly. Conversely, in the absence of 53BP1 or RIF1, BLM promotes formation of A-EJ long deletions, consistent with a role for BLM in DSB end resection. These data highlight a dual role...

  10. Constitutional Chromothripsis Rearrangements Involve Clustered Double-Stranded DNA Breaks and Nonhomologous Repair Mechanisms

    Directory of Open Access Journals (Sweden)

    Wigard P. Kloosterman

    2012-06-01

    Full Text Available Chromothripsis represents a novel phenomenon in the structural variation landscape of cancer genomes. Here, we analyze the genomes of ten patients with congenital disease who were preselected to carry complex chromosomal rearrangements with more than two breakpoints. The rearrangements displayed unanticipated complexity resembling chromothripsis. We find that eight of them contain hallmarks of multiple clustered double-stranded DNA breaks (DSBs on one or more chromosomes. In addition, nucleotide resolution analysis of 98 breakpoint junctions indicates that break repair involves nonhomologous or microhomology-mediated end joining. We observed that these eight rearrangements are balanced or contain sporadic deletions ranging in size between a few hundred base pairs and several megabases. The two remaining complex rearrangements did not display signs of DSBs and contain duplications, indicative of rearrangement processes involving template switching. Our work provides detailed insight into the characteristics of chromothripsis and supports a role for clustered DSBs driving some constitutional chromothripsis rearrangements.

  11. Efficient Gene Replacements in Toxoplasma gondii Strains Deficient for Nonhomologous End Joining▿ †

    Science.gov (United States)

    Fox, Barbara A.; Ristuccia, Jessica G.; Gigley, Jason P.; Bzik, David J.

    2009-01-01

    A high frequency of nonhomologous recombination has hampered gene targeting approaches in the model apicomplexan parasite Toxoplasma gondii. To address whether the nonhomologous end-joining (NHEJ) DNA repair pathway could be disrupted in this obligate intracellular parasite, putative KU proteins were identified and a predicted KU80 gene was deleted. The efficiency of gene targeting via double-crossover homologous recombination at several genetic loci was found to be greater than 97% of the total transformants in KU80 knockouts. Gene replacement efficiency was markedly increased (300- to 400-fold) in KU80 knockouts compared to wild-type strains. Target DNA flanks of only ∼500 bp were found to be sufficient for efficient gene replacements in KU80 knockouts. KU80 knockouts stably retained a normal growth rate in vitro and the high virulence phenotype of type I strains but exhibited an increased sensitivity to double-strand DNA breaks induced by treatment with phleomycin or γ-irradiation. Collectively, these results revealed that a significant KU-dependent NHEJ DNA repair pathway is present in Toxoplasma gondii. Integration essentially occurs only at the homologous targeted sites in the KU80 knockout background, making this genetic background an efficient host for gene targeting to speed postgenome functional analysis and genetic dissection of parasite biology. PMID:19218423

  12. Multifactorial Resistance of Bacillus subtilis Spores to High-Energy Proton Radiation: Role of Spore Structural Components and the Homologous Recombination and Non-Homologous End Joining DNA Repair Pathways

    OpenAIRE

    Moeller, Ralf; Reitz, Günther; Li, Zuofeng; Klein, Stuart; Nicholson, Wayne L.

    2012-01-01

    The space environment contains high-energy charged particles (e.g., protons, neutrons, electrons, α-particles, heavy ions) emitted by the Sun and galactic sources or trapped in the radiation belts. Protons constitute the majority (87%) of high-energy charged particles. Spores of Bacillus species are one of the model systems used for astro- and radiobiological studies. In this study, spores of different Bacillus subtilis strains were used to study the effects of high energetic proton irradiati...

  13. DNA双链断裂NHEJ修复及其与肿瘤的研究%Non-homologous end joining pathway of DSB repair and cancer

    Institute of Scientific and Technical Information of China (English)

    张耀伟

    2010-01-01

    非同源末端连接是哺乳动物最主要的DNA双链断裂(DSB)连接方式.肿瘤细胞非同源末端连接能力的提高与其放化疗抵抗有关,抑制肿瘤细胞非同源末端连接能力,可能增加其对放化疗的敏感性.因此,参与非同源末端连接的修复因子可能成为肿瘤分子靶向治疗及放化疗增敏的新治疗点.%Non-homologous end joining (NHEJ) is the major pathway for repairing DNA doublestrand break (DSB) in mammalian species. The capacity of NHEJ increases in tumor cell,which plays a role in radiation/chemotherapy-resistant agent Inhibiting DSB rejoining may play a crucial role in the enhancement of cellular radiation/chemotherapy-sensitizing. Thus, the protein molecule enrolled in NHEJ may be new potential targets for radiation/chemotherapy -sensitizing.

  14. DNA polymerases δ and λ cooperate in repairing double-strand breaks by microhomology-mediated end-joining in Saccharomyces cerevisiae.

    Science.gov (United States)

    Meyer, Damon; Fu, Becky Xu Hua; Heyer, Wolf-Dietrich

    2015-12-15

    Maintenance of genome stability is carried out by a suite of DNA repair pathways that ensure the repair of damaged DNA and faithful replication of the genome. Of particular importance are the repair pathways, which respond to DNA double-strand breaks (DSBs), and how the efficiency of repair is influenced by sequence homology. In this study, we developed a genetic assay in diploid Saccharomyces cerevisiae cells to analyze DSBs requiring microhomologies for repair, known as microhomology-mediated end-joining (MMEJ). MMEJ repair efficiency increased concomitant with microhomology length and decreased upon introduction of mismatches. The central proteins in homologous recombination (HR), Rad52 and Rad51, suppressed MMEJ in this system, suggesting a competition between HR and MMEJ for the repair of a DSB. Importantly, we found that DNA polymerase delta (Pol δ) is critical for MMEJ, independent of microhomology length and base-pairing continuity. MMEJ recombinants showed evidence that Pol δ proofreading function is active during MMEJ-mediated DSB repair. Furthermore, mutations in Pol δ and DNA polymerase 4 (Pol λ), the DNA polymerase previously implicated in MMEJ, cause a synergistic decrease in MMEJ repair. Pol λ showed faster kinetics associating with MMEJ substrates following DSB induction than Pol δ. The association of Pol δ depended on RAD1, which encodes the flap endonuclease needed to cleave MMEJ intermediates before DNA synthesis. Moreover, Pol δ recruitment was diminished in cells lacking Pol λ. These data suggest cooperative involvement of both polymerases in MMEJ. PMID:26607450

  15. DNA double strand break repair in mammalian cells: role of MRE11 and BLM proteins at the initiation of Non Homologous End Joining (NHEJ)

    International Nuclear Information System (INIS)

    DNA double strand breaks (DSBs) are highly cytotoxic lesions, which can lead to genetic rearrangements. Two pathways are responsible for repairing these lesions: homologous recombination (HR) and non homologous end joining (NHEJ). In our laboratory, an intrachromosomal substrate has been established in order to measure the efficiency and the fidelity of NHEJ in living cells (Guirouilh-Barbat 2004). This approach led us to identify a KU-independent alternative pathway, which uses micro homologies in the proximity of the junction to accomplish repair - the alternative NHEJ (Guirouilh-Barbat 2004, Guirouilh-Barbat et Rass 2007). The goal of my thesis consisted in identifying and characterising major actors of this pathway. In the absence of KU, alternative NHEJ would be initiated by ssDNA resection of damaged ends. We showed that the nuclease activity of MRE11 is necessary for this mechanism. MRE11 overexpression leads to a two fold stimulation of NHEJ efficiency, while the extinction of MRE11 by siRNA results in a two fold decrease. Our results demonstrate that the proteins RAD50 and CtIP act in the same pathway as MRE11. Moreover, in cells deficient for XRCC4, MIRIN - an inhibitor of the MRN complex - leads to a decrease in repair efficiency, implicating MRE11 in alternative NHEJ. We also showed that MRE11 can act in an ATM-dependent and independent manner (Rass et Grabarz Nat Struct Mol Biol 2009). The initiation of break resection needs to be pursued by a more extensive degradation of DNA, which is accomplished in yeast by the proteins Exo1 and Sgs1/Dna2. In human cells, in vitro studies have recently proposed a similar model of a two-step break resection. We chose to elucidate the role of one of the human homologs of Sgs1 - the RecQ helicase BLM - in the resection process. Our experiments show, that he absence of BLM decreases the efficiency of end joining by NHEJ, accompanied by an increase in error-prone events, especially long-range deletions (≥200 nt). This

  16. Silencing of end-joining repair for efficient site-specific gene insertion after TALEN/CRISPR mutagenesis in Aedes aegypti.

    Science.gov (United States)

    Basu, Sanjay; Aryan, Azadeh; Overcash, Justin M; Samuel, Glady Hazitha; Anderson, Michelle A E; Dahlem, Timothy J; Myles, Kevin M; Adelman, Zach N

    2015-03-31

    Conventional control strategies for mosquito-borne pathogens such as malaria and dengue are now being complemented by the development of transgenic mosquito strains reprogrammed to generate beneficial phenotypes such as conditional sterility or pathogen resistance. The widespread success of site-specific nucleases such as transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 in model organisms also suggests that reprogrammable gene drive systems based on these nucleases may be capable of spreading such beneficial phenotypes in wild mosquito populations. Using the mosquito Aedes aegypti, we determined that mutations in the FokI domain used in TALENs to generate obligate heterodimeric complexes substantially and significantly reduce gene editing rates. We found that CRISPR/Cas9-based editing in the mosquito Ae. aegypti is also highly variable, with the majority of guide RNAs unable to generate detectable editing. By first evaluating candidate guide RNAs using a transient embryo assay, we were able to rapidly identify highly effective guide RNAs; focusing germ line-based experiments only on this cohort resulted in consistently high editing rates of 24-90%. Microinjection of double-stranded RNAs targeting ku70 or lig4, both essential components of the end-joining response, increased recombination-based repair in early embryos as determined by plasmid-based reporters. RNAi-based suppression of Ku70 concurrent with embryonic microinjection of site-specific nucleases yielded consistent gene insertion frequencies of 2-3%, similar to traditional transposon- or ΦC31-based integration methods but without the requirement for an initial docking step. These studies should greatly accelerate investigations into mosquito biology, streamline development of transgenic strains for field releases, and simplify the evaluation of novel Cas9-based gene drive systems.

  17. Deletion of exon 8 from the EXT1 gene causes multiple osteochondromas (MO) in a family with three affected members.

    Science.gov (United States)

    Zhuang, Lei; Gerber, Simon D; Kuchen, Stefan; Villiger, Peter M; Trueb, Beat

    2016-01-01

    Multiple osteochondromas (also called hereditary multiple exostoses) is an autosomal dominant disorder characterized by multiple cartilaginous tumors, which are caused by mutations in the genes for exostosin-1 (EXT1) and exostosin-2 (EXT2). The goal of this study was to elucidate the genetic alterations in a family with three affected members. Isolation of RNA from the patients' blood followed by reverse transcription and PCR amplification of selected fragments showed that the three patients lack a specific region of 90 bp from their EXT1 mRNA. This region corresponds to the sequence of exon 8 from the EXT1 gene. No splice site mutation was found around exon 8. However, long-range PCR amplification of the region from intron 7 to intron 8 indicated that the three patients contain a deletion of 4318 bp, which includes exon 8 and part of the flanking introns. There is evidence that the deletion was caused by non-homologous end joining because the breakpoints are not located within a repetitive element, but contain multiple copies of the deletion hotspot sequence TGRRKM. Exon 8 encodes part of the active site of the EXT1 enzyme, including the DXD signature of all UDP-sugar glycosyltransferases. It is conceivable that the mutant protein exerts a dominant negative effect on the activity of the EXT glycosyltransferase since it might interact with normal copies of the enzyme to form an inactive hetero-oligomeric complex. We suggest that sequencing of RNA might be superior to exome sequencing to detect short deletions of a single exon.

  18. Interaction between non-homologous portuguese isolates of Albugo candida and Brassica oleracea

    OpenAIRE

    Jorge, Lurdes; Dias, João Silva

    2000-01-01

    The interaction of five non-homologous portuguese isolates of A. candida (four isolated from B. rapa – Ac506, Ac508, Ac509 and Ac510, and one from Raphanus sativus) in forty B. oleracea accessions from different geographic origins was evaluated at the cotyledonar stage. Some accessions presented susceptibility to the non-homologous isolates of B. rapa, mainly head cabbage ‘Large Blood Red’ and savoy cabbage ‘Brusselse Winter’. These accessions exhibited mean levels of infection higher than 20...

  19. An RNA secondary structure bias for non-homologous reverse transcriptase-mediated deletions in vivo

    DEFF Research Database (Denmark)

    Duch, Mogens; Carrasco, Maria L; Jespersen, Thomas;

    2004-01-01

    result from template switching during first-strand cDNA synthesis and that the choice of acceptor sites for non-homologous recombination are guided by non-paired regions. Our results may have implications for recombination events taking place within structured regions of retroviral RNA genomes......, especially in the absence of longer stretches of sequence similarity....

  20. Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution

    Directory of Open Access Journals (Sweden)

    Wolf Yuri I

    2010-04-01

    Full Text Available Abstract Background Evolutionarily unrelated proteins that catalyze the same biochemical reactions are often referred to as analogous - as opposed to homologous - enzymes. The existence of numerous alternative, non-homologous enzyme isoforms presents an interesting evolutionary problem; it also complicates genome-based reconstruction of the metabolic pathways in a variety of organisms. In 1998, a systematic search for analogous enzymes resulted in the identification of 105 Enzyme Commission (EC numbers that included two or more proteins without detectable sequence similarity to each other, including 34 EC nodes where proteins were known (or predicted to have distinct structural folds, indicating independent evolutionary origins. In the past 12 years, many putative non-homologous isofunctional enzymes were identified in newly sequenced genomes. In addition, efforts in structural genomics resulted in a vastly improved structural coverage of proteomes, providing for definitive assessment of (nonhomologous relationships between proteins. Results We report the results of a comprehensive search for non-homologous isofunctional enzymes (NISE that yielded 185 EC nodes with two or more experimentally characterized - or predicted - structurally unrelated proteins. Of these NISE sets, only 74 were from the original 1998 list. Structural assignments of the NISE show over-representation of proteins with the TIM barrel fold and the nucleotide-binding Rossmann fold. From the functional perspective, the set of NISE is enriched in hydrolases, particularly carbohydrate hydrolases, and in enzymes involved in defense against oxidative stress. Conclusions These results indicate that at least some of the non-homologous isofunctional enzymes were recruited relatively recently from enzyme families that are active against related substrates and are sufficiently flexible to accommodate changes in substrate specificity. Reviewers This article was reviewed by Andrei

  1. Suppression of DNA-dependent protein kinase sensitize cells to radiation without affecting DSB repair

    Energy Technology Data Exchange (ETDEWEB)

    Gustafsson, Ann-Sofie, E-mail: ann-sofie.gustafsson@bms.uu.se; Abramenkovs, Andris; Stenerlöw, Bo

    2014-11-15

    Highlights: • We reduced the level of DNA-PKcs with siRNA and examined cells after γ-irradiation. • Low DNA-PKcs levels lead to radiosensitivity but did not affect repair of DSB. • Low DNA-PKcs levels may block progression of mitosis. • DNA-PKcs role in mitotic progression is independent of its role in DSB repair. • We suggest different mechanisms by which loss of DNA-PKcs function sensitize cells. - Abstract: Efficient and correct repair of DNA double-strand break (DSB) is critical for cell survival. Defects in the DNA repair may lead to cell death, genomic instability and development of cancer. The catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) is an essential component of the non-homologous end joining (NHEJ) which is the major DSB repair pathway in mammalian cells. In the present study, by using siRNA against DNA-PKcs in four human cell lines, we examined how low levels of DNA-PKcs affected cellular response to ionizing radiation. Decrease of DNA-PKcs levels by 80–95%, induced by siRNA treatment, lead to extreme radiosensitivity, similar to that seen in cells completely lacking DNA-PKcs and low levels of DNA-PKcs promoted cell accumulation in G2/M phase after irradiation and blocked progression of mitosis. Surprisingly, low levels of DNA-PKcs did not affect the repair capacity and the removal of 53BP1 or γ-H2AX foci and rejoining of DSB appeared normal. This was in strong contrast to cells completely lacking DNA-PKcs and cells treated with the DNA-PKcs inhibitor NU7441, in which DSB repair were severely compromised. This suggests that there are different mechanisms by which loss of DNA-PKcs functions can sensitize cells to ionizing radiation. Further, foci of phosphorylated DNA-PKcs (T2609 and S2056) co-localized with DSB and this was independent of the amount of DNA-PKcs but foci of DNA-PKcs was only seen in siRNA-treated cells. Our study emphasizes on the critical role of DNA-PKcs for maintaining survival after radiation exposure

  2. Homologous and non-homologous recombination differentially affect DNA damage repair in mice.

    NARCIS (Netherlands)

    J. Essers (Jeroen); H. van Steeg (Harry); J. de Wit (Jan); M. Vermeij (Marcel); J.H.J. Hoeijmakers (Jan); R. Kanaar (Roland); S.M.A. Swagemakers (Sigrid)

    2000-01-01

    textabstractIonizing radiation and interstrand DNA crosslinking compounds provide important treatments against cancer due to their extreme genotoxicity for proliferating cells. Both the efficacies of such treatments and the mutagenic potential of these agents are modulated by the a

  3. Affectivity

    OpenAIRE

    Stenner, Paul; Greco, Monica

    2013-01-01

    The concept of affectivity has assumed central importance in much recent scholarship, and many in the social sciences and humanities now talk of an ‘affective turn’. The concept of affectivity at play in this ‘turn’ remains, however, somewhat vague and slippery. Starting with Silvan Tomkins’ influential theory of affect, this paper will explore the relevance of the general assumptions (or ‘utmost abstractions’) that inform thinking about affectivity. The technological and instrumentalist char...

  4. Productive homologous and non-homologous recombination of hepatitis C virus in cell culture

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Galli, Andrea; Li, Yi-Ping;

    2013-01-01

    . In addition, recombination is an important regulatory mechanism of cytopathogenicity for the related pestiviruses. Here we describe recombination of HCV RNA in cell culture leading to production of infectious virus. Initially, hepatoma cells were co-transfected with a replicating JFH1ΔE1E2 genome (genotype 2a...... incompetent genomes were co-transfected. Reverse genetic studies verified the viability of representative recombinants. After serial passage, subsequent recombination events reducing or eliminating the duplicated region were observed for some but not all recombinants. Furthermore, we found that inter......-genotypic recombination could occur, but at a lower frequency than intra-genotypic recombination. Productive recombination of attenuated HCV genomes depended on expression of all HCV proteins and tolerated duplicated sequence. In general, no strong site specificity was observed. Non-homologous recombination was observed...

  5. Productive homologous and non-homologous recombination of hepatitis C virus in cell culture.

    Directory of Open Access Journals (Sweden)

    Troels K H Scheel

    2013-03-01

    Full Text Available Genetic recombination is an important mechanism for increasing diversity of RNA viruses, and constitutes a viral escape mechanism to host immune responses and to treatment with antiviral compounds. Although rare, epidemiologically important hepatitis C virus (HCV recombinants have been reported. In addition, recombination is an important regulatory mechanism of cytopathogenicity for the related pestiviruses. Here we describe recombination of HCV RNA in cell culture leading to production of infectious virus. Initially, hepatoma cells were co-transfected with a replicating JFH1ΔE1E2 genome (genotype 2a lacking functional envelope genes and strain J6 (2a, which has functional envelope genes but does not replicate in culture. After an initial decrease in the number of HCV positive cells, infection spread after 13-36 days. Sequencing of recovered viruses revealed non-homologous recombinants with J6 sequence from the 5' end to the NS2-NS3 region followed by JFH1 sequence from Core to the 3' end. These recombinants carried duplicated sequence of up to 2400 nucleotides. HCV replication was not required for recombination, as recombinants were observed in most experiments even when two replication incompetent genomes were co-transfected. Reverse genetic studies verified the viability of representative recombinants. After serial passage, subsequent recombination events reducing or eliminating the duplicated region were observed for some but not all recombinants. Furthermore, we found that inter-genotypic recombination could occur, but at a lower frequency than intra-genotypic recombination. Productive recombination of attenuated HCV genomes depended on expression of all HCV proteins and tolerated duplicated sequence. In general, no strong site specificity was observed. Non-homologous recombination was observed in most cases, while few homologous events were identified. A better understanding of HCV recombination could help identification of natural

  6. Differential radiosensitivity phenotypes of DNA-PKcs mutations affecting NHEJ and HRR systems following irradiation with gamma-rays or very low fluences of alpha particles.

    Directory of Open Access Journals (Sweden)

    Yu-Fen Lin

    Full Text Available We have examined cell-cycle dependence of chromosomal aberration induction and cell killing after high or low dose-rate γ irradiation in cells bearing DNA-PKcs mutations in the S2056 cluster, the T2609 cluster, or the kinase domain. We also compared sister chromatid exchanges (SCE production by very low fluences of α-particles in DNA-PKcs mutant cells, and in homologous recombination repair (HRR mutant cells including Rad51C, Rad51D, and Fancg/xrcc9. Generally, chromosomal aberrations and cell killing by γ-rays were similarly affected by mutations in DNA-PKcs, and these mutant cells were more sensitive in G1 than in S/G2 phase. In G1-irradiated DNA-PKcs mutant cells, both chromosome- and chromatid-type breaks and exchanges were in excess than wild-type cells. For cells irradiated in late S/G2 phase, mutant cells showed very high yields of chromatid breaks compared to wild-type cells. Few exchanges were seen in DNA-PKcs-null, Ku80-null, or DNA-PKcs kinase dead mutants, but exchanges in excess were detected in the S2506 or T2609 cluster mutants. SCE induction by very low doses of α-particles is resulted from bystander effects in cells not traversed by α-particles. SCE seen in wild-type cells was completely abolished in Rad51C- or Rad51D-deficient cells, but near normal in Fancg/xrcc9 cells. In marked contrast, very high levels of SCEs were observed in DNA-PKcs-null, DNA-PKcs kinase-dead and Ku80-null mutants. SCE induction was also abolished in T2609 cluster mutant cells, but was only slightly reduced in the S2056 cluster mutant cells. Since both non-homologous end-joining (NHEJ and HRR systems utilize initial DNA lesions as a substrate, these results suggest the possibility of a competitive interference phenomenon operating between NHEJ and at least the Rad51C/D components of HRR; the level of interaction between damaged DNA and a particular DNA-PK component may determine the level of interaction of such DNA with a relevant HRR component.

  7. Genomic rearrangements at the FRA2H common fragile site frequently involve non-homologous recombination events across LTR and L1(LINE) repeats.

    Science.gov (United States)

    Brueckner, Lena M; Sagulenko, Evgeny; Hess, Elisa M; Zheglo, Diana; Blumrich, Anne; Schwab, Manfred; Savelyeva, Larissa

    2012-08-01

    Common fragile sites (cFSs) are non-random chromosomal regions that are prone to breakage under conditions of replication stress. DNA damage and chromosomal alterations at cFSs appear to be critical events in the development of various human diseases, especially carcinogenesis. Despite the growing interest in understanding the nature of cFS instability, only a few cFSs have been molecularly characterised. In this study, we fine-mapped the location of FRA2H using six-colour fluorescence in situ hybridisation and showed that it is one of the most active cFSs in the human genome. FRA2H encompasses approximately 530 kb of a gene-poor region containing a novel large intergenic non-coding RNA gene (AC097500.2). Using custom-designed array comparative genomic hybridisation, we detected gross and submicroscopic chromosomal rearrangements involving FRA2H in a panel of 54 neuroblastoma, colon and breast cancer cell lines. The genomic alterations frequently involved different classes of long terminal repeats and long interspersed nuclear elements. An analysis of breakpoint junction sequence motifs predominantly revealed signatures of microhomology-mediated non-homologous recombination events. Our data provide insight into the molecular structure of cFSs and sequence motifs affected by their activation in cancer. Identifying cFS sequences will accelerate the search for DNA biomarkers and targets for individualised therapies.

  8. DNA Ligase IV and Artemis Act Cooperatively to Suppress Homologous Recombination in Human Cells: Implications for DNA Double-Strand Break Repair

    OpenAIRE

    Aya Kurosawa; Shinta Saito; Sairei So; Mitsumasa Hashimoto; Kuniyoshi Iwabuchi; Haruka Watabe; Noritaka Adachi

    2013-01-01

    Nonhomologous end-joining (NHEJ) and homologous recombination (HR) are two major pathways for repairing DNA double-strand breaks (DSBs); however, their respective roles in human somatic cells remain to be elucidated. Here we show using a series of human gene-knockout cell lines that NHEJ repairs nearly all of the topoisomerase II- and low-dose radiation-induced DNA damage, while it negatively affects survival of cells harbouring replication-associated DSBs. Intriguingly, we find that loss of ...

  9. Ultraviolet sensitivity of the addition, deletion and replacement of long nonhomologous DNA segments by genetic transformation of Haemophilus influenzae

    Energy Technology Data Exchange (ETDEWEB)

    Walter, R.B.; Stuy, J.H. (Florida State Univ., Tallahassee (USA). Dept. of Biological Science)

    1982-03-01

    The construction and some properties of Haemophilus influenzae Rd strains with long and different R plasmid-derived DNA segments (nonhomologous inserts) at the same site in the HP1 prophage have previously been described. These inserts can be added to a recipient's genome by genetic transformation, they can be deleted from the recipient genome, or they can be replaced by another insert. It is reported that the UV inactivation of all three phenomena followed single hit kinetics. Deletion was roughly 10 times more resistant; its UV-sensitivity equalled that of a high-efficiency point mutation. There was an inverse correlation between UV-sensitivity and additive transformation efficiency of the various inserts; sensitivity may thus be a measure of insert size. This correlation was not seen for deletion. All three phenomena were more sensitive when they were measured on excision repair-deficient uvr/sup -/ recipients. The dose-reduction factor for addition was about 1.5 while it was about 2.6 for deletion.

  10. The EGFR mutation status affects the relative biological effectiveness of carbon-ion beams in non-small cell lung carcinoma cells.

    Science.gov (United States)

    Amornwichet, Napapat; Oike, Takahiro; Shibata, Atsushi; Nirodi, Chaitanya S; Ogiwara, Hideaki; Makino, Haruhiko; Kimura, Yuka; Hirota, Yuka; Isono, Mayu; Yoshida, Yukari; Ohno, Tatsuya; Kohno, Takashi; Nakano, Takashi

    2015-06-11

    Carbon-ion radiotherapy (CIRT) holds promise to treat inoperable locally-advanced non-small cell lung carcinoma (NSCLC), a disease poorly controlled by standard chemoradiotherapy using X-rays. Since CIRT is an extremely limited medical resource, selection of NSCLC patients likely to benefit from it is important; however, biological predictors of response to CIRT are ill-defined. The present study investigated the association between the mutational status of EGFR and KRAS, driver genes frequently mutated in NSCLC, and the relative biological effectiveness (RBE) of carbon-ion beams over X-rays. The assessment of 15 NSCLC lines of different EGFR/KRAS mutational status and that of isogenic NSCLC lines expressing wild-type or mutant EGFR revealed that EGFR-mutant NSCLC cells, but not KRAS-mutant cells, show low RBE. This was attributable to (i) the high X-ray sensitivity of EGFR-mutant cells, since EGFR mutation is associated with a defect in non-homologous end joining, a major pathway for DNA double-strand break (DSB) repair, and (ii) the strong cell-killing effect of carbon-ion beams due to poor repair of carbon-ion beam-induced DSBs regardless of EGFR mutation status. These data highlight the potential of EGFR mutation status as a predictor of response to CIRT, i.e., CIRT may show a high therapeutic index in EGFR mutation-negative NSCLC.

  11. Telomeric trans-silencing in Drosophila melanogaster: tissue specificity, development and functional interactions between non-homologous telomeres.

    Directory of Open Access Journals (Sweden)

    Thibaut Josse

    Full Text Available BACKGROUND: The study of P element repression in Drosophila melanogaster led to the discovery of the telomeric Trans-Silencing Effect (TSE, a homology-dependent repression mechanism by which a P-transgene inserted in subtelomeric heterochromatin (Telomeric Associated Sequences, "TAS" has the capacity to repress in trans, in the female germline, a homologous P-lacZ transgene located in euchromatin. TSE can show variegation in ovaries, displays a maternal effect as well as an epigenetic transmission through meiosis and involves heterochromatin and RNA silencing pathways. PRINCIPAL FINDINGS: Here, we analyze phenotypic and genetic properties of TSE. We report that TSE does not occur in the soma at the adult stage, but appears restricted to the female germline. It is detectable during development at the third instar larvae where it presents the same tissue specificity and maternal effect as in adults. Transgenes located in TAS at the telomeres of the main chromosomes can be silencers which in each case show the maternal effect. Silencers located at non-homologous telomeres functionally interact since they stimulate each other via the maternally-transmitted component. All germinally-expressed euchromatic transgenes tested, located on all major chromosomes, were found to be repressed by a telomeric silencer: thus we detected no TSE escaper. The presence of the euchromatic target transgene is not necessary to establish the maternal inheritance of TSE, responsible for its epigenetic behavior. A single telomeric silencer locus can simultaneously repress two P-lacZ targets located on different chromosomal arms. CONCLUSIONS AND SIGNIFICANCE: Therefore TSE appears to be a widespread phenomenon which can involve different telomeres and work across the genome. It can explain the P cytotype establishment by telomeric P elements in natural Drosophila populations.

  12. Evolution of bacterial phosphoglycerate mutases: non-homologous isofunctional enzymes undergoing gene losses, gains and lateral transfers.

    Directory of Open Access Journals (Sweden)

    Jeremy M Foster

    Full Text Available BACKGROUND: The glycolytic phosphoglycerate mutases exist as non-homologous isofunctional enzymes (NISE having independent evolutionary origins and no similarity in primary sequence, 3D structure, or catalytic mechanism. Cofactor-dependent PGM (dPGM requires 2,3-bisphosphoglycerate for activity; cofactor-independent PGM (iPGM does not. The PGM profile of any given bacterium is unpredictable and some organisms such as Escherichia coli encode both forms. METHODS/PRINCIPAL FINDINGS: To examine the distribution of PGM NISE throughout the Bacteria, and gain insight into the evolutionary processes that shape their phyletic profiles, we searched bacterial genome sequences for the presence of dPGM and iPGM. Both forms exhibited patchy distributions throughout the bacterial domain. Species within the same genus, or even strains of the same species, frequently differ in their PGM repertoire. The distribution is further complicated by the common occurrence of dPGM paralogs, while iPGM paralogs are rare. Larger genomes are more likely to accommodate PGM paralogs or both NISE forms. Lateral gene transfers have shaped the PGM profiles with intradomain and interdomain transfers apparent. Archaeal-type iPGM was identified in many bacteria, often as the sole PGM. To address the function of PGM NISE in an organism encoding both forms, we analyzed recombinant enzymes from E. coli. Both NISE were active mutases, but the specific activity of dPGM greatly exceeded that of iPGM, which showed highest activity in the presence of manganese. We created PGM null mutants in E. coli and discovered the ΔdPGM mutant grew slowly due to a delay in exiting stationary phase. Overexpression of dPGM or iPGM overcame this defect. CONCLUSIONS/SIGNIFICANCE: Our biochemical and genetic analyses in E. coli firmly establish dPGM and iPGM as NISE. Metabolic redundancy is indicated since only larger genomes encode both forms. Non-orthologous gene displacement can fully account for the non

  13. Type II Toxoplasma gondii KU80 Knockout Strains Enable Functional Analysis of Genes Required for Cyst Development and Latent Infection ▿ †

    OpenAIRE

    Fox, Barbara A.; Falla, Alejandra; Rommereim, Leah M.; Tomita, Tadakimi; Gigley, Jason P.; Mercier, Corinne; Cesbron-Delauw, Marie-France; Louis M Weiss; Bzik, David J.

    2011-01-01

    Type II Toxoplasma gondii KU80 knockouts (Δku80) deficient in nonhomologous end joining were developed to delete the dominant pathway mediating random integration of targeting episomes. Gene targeting frequency in the type II Δku80 Δhxgprt strain measured at the orotate (OPRT) and the uracil (UPRT) phosphoribosyltransferase loci was highly efficient. To assess the potential of the type II Δku80 Δhxgprt strain to examine gene function affecting cyst biology and latent stages of infection, we t...

  14. Human longevity and variation in DNA damage response and repair

    DEFF Research Database (Denmark)

    Debrabant, Birgit; Soerensen, Mette; Flachsbart, Friederike;

    2014-01-01

    others. Data were applied on 592 SNPs from 77 genes involved in nine sub-processes: DNA-damage response, base excision repair (BER), nucleotide excision repair, mismatch repair, non-homologous end-joining, homologous recombinational repair (HRR), RecQ helicase activities (RECQ), telomere functioning...... and mitochondrial DNA processes. The study population was 1089 long-lived and 736 middle-aged Danes. A self-contained set-based test of all SNPs displayed association with longevity (P-value=9.9 × 10-5), supporting that the overall pathway could affect longevity. Investigation of the nine sub-processes using...

  15. Mutations that affect meiosis in male mice influence the dynamics of the mid-preleptotene and bouquet stages

    International Nuclear Information System (INIS)

    Meiosis pairs and segregates homologous chromosomes and thereby forms haploid germ cells to compensate the genome doubling at fertilization. Homologue pairing in many eukaryotic species depends on formation of DNA double strand breaks (DSBs) during early prophase I when telomeres begin to cluster at the nuclear periphery (bouquet stage). By fluorescence in situ hybridization criteria, we observe that mid-preleptotene and bouquet stage frequencies are altered in male mice deficient for proteins required for recombination, ubiquitin conjugation and telomere length control. The generally low frequencies of mid-preleptotene spermatocytes were significantly increased in male mice lacking recombination proteins SPO11, MEI1, MLH1, KU80, ubiquitin conjugating enzyme HR6B, and in mice with only one copy of the telomere length regulator Terf1. The bouquet stage was significantly enriched in Atm -/-, Spo11 -/-, Mei1 m1Jcs/m1Jcs, Mlh1 -/-, Terf1 +/- and Hr6b -/- spermatogenesis, but not in mice lacking recombination proteins DMC1 and HOP2, the non-homologous end-joining DNA repair factor KU80 and the ATM downstream effector GADD45a. Mice defective in spermiogenesis (Tnp1 -/-, Gmcl1 -/-, Asm -/-) showed wild-type mid-preleptotene and bouquet frequencies. A low frequency of bouquet spermatocytes in Spo11 -/- Atm -/- spermatogenesis suggests that DSBs contribute to the Atm -/--correlated bouquet stage exit defect. Insignificant changes of bouquet frequencies in mice with defects in early stages of DSB repair (Dmc1 -/-, Hop2 -/-) suggest that there is an ATM-specific influence on bouquet stage duration. Altogether, it appears that several pathways influence telomere dynamics in mammalian meiosis

  16. Important DNA repair proteins in DNA double-strand break repair pathways

    International Nuclear Information System (INIS)

    DNA double-strand break repair pathway is one of DNA damage repair pathways. DNA repair genes can repair DNA damage, maintain the integrity of the genetic information and inhibit the formation of tumors. There are two mechanisms-non-homologous end joining and homologous recombination to repair DNA double-strand break. In this review, an overview of important repair proteins of non--homologous end joining and homologous recombination pathways was introduced. (authors)

  17. Microhomology-mediated end joining is the principal mediator of double-strand break repair during mitochondrial DNA lesions

    OpenAIRE

    Tadi, Satish Kumar; Sebastian, Robin; Dahal, Sumedha; Babu, Ravi K.; Choudhary, Bibha; Raghavan, Sathees C.

    2016-01-01

    Mitochondrial DNA (mtDNA) deletions are associated with various mitochondrial disorders. The deletions identified in humans are flanked by short, directly repeated mitochondrial DNA sequences; however, the mechanism of such DNA rearrangements has yet to be elucidated. In contrast to nuclear DNA (nDNA), mtDNA is more exposed to oxidative damage, which may result in double-strand breaks (DSBs). Although DSB repair in nDNA is well studied, repair mechanisms in mitochondria are not characterized....

  18. Sibling rivalry: competition between Pol X family members in V(D)J recombination and general double strand break repair.

    Science.gov (United States)

    Nick McElhinny, Stephanie A; Ramsden, Dale A

    2004-08-01

    The nonhomologous end-joining pathway is a major means for repairing double-strand breaks (DSBs) in all mitotic cell types. This repair pathway is also the only efficient means for resolving DSB intermediates in V(D)J recombination, a lymphocyte-specific genome rearrangement required for assembly of antigen receptors. A role for polymerases in end-joining has been well established. They are a major factor in determining the character of repair junctions but, in contrast to 'core' end-joining factors, typically appear to have a subtle impact on the efficiency of end-joining. Recent work implicates several members of the Pol X family in end-joining and suggests surprising complexity in the control of how these different polymerases are employed in this pathway. PMID:15242403

  19. DNA apoptosis and stability in B-cell chronic lymphoid leukaemia: implication of the DNA double-strand breaks repair system by non homologous recombination

    International Nuclear Information System (INIS)

    After an introduction presenting the diagnosis and treatment of chronic lymphoid leukaemia, its molecular and genetic characteristics, and its cellular origin and clonal evolution, this research thesis describes the apoptosis (definition and characteristics, cancer and chemotherapy, apoptotic ways induced by gamma irradiation), the genotoxic stresses, the different repair mechanisms for different damages, and the DNA repair processes. It reports how human chronic lymphocytic leukaemia B cells can escape DNA damage-induced apoptosis through the non-homologous end-joining DNA repair pathway, and presents non-homologous end-joining DNA repair as a potent mutagenic process in human chronic lymphocytic leukaemia B cells

  20. Affective Urbanism

    DEFF Research Database (Denmark)

    Samson, Kristine

    . Under these circumstances affective aesthetics operate strategically within the urban field of interests, capital flows and desires of the social. This ‘affective urbanism’ (Anderson & Holden 2008) is linked to a society influenced by new kinds of information flows, where culture is mediated and enacted...... and cultural festivals, both practices indicate that design is implemented as means of creating affective spaces in the city. Both cases show how immaterial production of affects and emotions in the city can be seen in relation to economic potential and urban development. Finally, I will discuss whether urban......Urban design and architecture are increasingly used as material and affective strategies for setting the scene, for manipulation and the production of urban life: The orchestration of atmospheres, the framing and staging of urban actions, the programming for contemplation, involvement, play...

  1. Affective Maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    . In particular, mapping environmental damage, endangered species, and human made disasters has become one of the focal point of affective knowledge production. These ‘more-than-humangeographies’ practices include notions of species, space and territory, and movement towards a new political ecology. This type...... of environmental knowledge production. It uses InfoAmazonia, the databased platform on Amazon rainforests, as an example of affective geo-visualization within information mapping that enhances embodiment in the experience of the information. Amazonia is defined as a digitally created affective (map)space within...

  2. Conjugated linoleic acid inhibiting DNA repair damaged by x-ray

    International Nuclear Information System (INIS)

    Non-homologous end-joining is the most effective repair of DNA double strand break. Epidermal growth factor receptor activates DSB repairs. Integration of EGFR inhibitors with radiation or chemotherapy were used in lung cancer treatment. Radiosensitivity effect of conjugated linoleic acid on tumor cells and reduced metastasis are reported

  3. Functional analysis of naturally occurring DCLRE1C mutations and correlation with the clinical phenotype of ARTEMIS deficiency

    NARCIS (Netherlands)

    K. Felgentreff (Kerstin); Y.N. Lee (Yu Nee); F. Frugoni (Francesco); L. Du (Likun); M. van der Burg (Mirjam); S. Giliani; I. Tezcan (Ilhan); I. Reisli (Ismail); E. Mejstříková (Ester); J.P. de Villartay; B.P. Sleckman (Barry P.); J. Manis (John); L.D. Notarangelo (Luigi Daniele)

    2015-01-01

    textabstractBackground The endonuclease ARTEMIS, which is encoded by the DCLRE1C gene, is a component of the nonhomologous end-joining pathway and participates in hairpin opening during the V(D)J recombination process and repair of a subset of DNA double-strand breaks. Patients with ARTEMIS deficien

  4. A new type of radiosensitive T-B-NK+ severe combined immunodeficiency caused by a LIG4 mutation

    NARCIS (Netherlands)

    M. van der Burg (Mirjam); M.Z. Zdzienicka (Malgorzata); D.C. van Gent (Dik); J.J.M. van Dongen (Jacques); L.R. van Veelen (Lieneke); N.S. Verkaik (Nicole); W.W. Wiegant (Wouter); N.G. Hartwig (Nico); B.H. Barendregt (Barbara); L.J.L. Brugmans (Linda); A. Raams (Anja); N.G.J. Jaspers (Nicolaas)

    2006-01-01

    textabstractV(D)J recombination of Ig and TCR loci is a stepwise process during which site-specific DNA double-strand breaks (DSBs) are made by RAG1/RAG2, followed by DSB repair by nonhomologous end joining. Defects in V(D)J recombination result in SCID characterized by absence of

  5. Clinical Spectrum of LIG4 Deficiency Is Broadened with Severe Dysmaturity, Primordial Dwarfism, and Neurological Abnormalities

    NARCIS (Netherlands)

    H. IJspeert (Hanna); A. Warris (Adilia); M. van der Flier (Michiel); I. Reisli (Ismail); S. Keles (Sevgi); S. Chishimba (Sandra); J.J.M. van Dongen (Jacques); D.C. van Gent (Dik); M. van der Burg (Mirjam)

    2013-01-01

    textabstractDNA double-strand break repair via non-homologous end joining (NHEJ) is involved in recombination of immunoglobulin and T-cell receptor genes. Mutations in NHEJ components result in syndromes that are characterized by microcephaly and immunodeficiency. We present a patient with lymphopen

  6. Role of DNA-PK subunits in radiosensitization by hyperthermia

    NARCIS (Netherlands)

    Woudstra, EC; Konings, AWT; Jeggo, PA; Kampinga, HH

    1999-01-01

    Thermal radiosensitization is thought to result from inhibition of repair of radiation-induced DNA damage, DNA double-strand breaks in particular. Since the DNA-dependent protein kinase (DNA-PK) complex plays a major role in the nonhomologous end-joining of DSBs, it has been suggested that inactivat

  7. Differential regulation of the cellular response to DNA double-strand breaks in G1

    DEFF Research Database (Denmark)

    Barlow, Jacqueline H; Lisby, Michael; Rothstein, Rodney

    2008-01-01

    Double-strand breaks (DSBs) are potentially lethal DNA lesions that can be repaired by either homologous recombination (HR) or nonhomologous end-joining (NHEJ). We show that DSBs induced by ionizing radiation (IR) are efficiently processed for HR and bound by Rfa1 during G1, while endonuclease...

  8. Analysis of DNA double-strand break repair pathways in mice

    International Nuclear Information System (INIS)

    During the last years significant new insights have been gained into the mechanism and biological relevance of DNA double-strand break (DSB) repair in relation to genome stability. DSBs are a highly toxic DNA lesion, because they can lead to chromosome fragmentation, loss and translocations, eventually resulting in cancer. DSBs can be induced by cellular processes such as V(D)J recombination or DNA replication. They can also be introduced by exogenous agents DNA damaging agents such as ionizing radiation or mitomycin C. During evolution several pathways have evolved for the repair of these DSBs. The most important DSB repair mechanisms in mammalian cells are nonhomologous end-joining and homologous recombination. By using an undamaged repair template, homologous recombination ensures accurate DSB repair, whereas the untemplated nonhomologous end-joining pathway does not. Although both pathways are active in mammals, the relative contribution of the two repair pathways to genome stability differs in the different cell types. Given the potential differences in repair fidelity, it is of interest to determine the relative contribution of homologous recombination and nonhomologous end-joining to DSB repair. In this review, we focus on the biological relevance of DSB repair in mammalian cells and the potential overlap between nonhomologous end-joining and homologous recombination in different tissues

  9. The Ku80 carboxy terminus stimulates joining and artemis-mediated processing of DNA ends

    DEFF Research Database (Denmark)

    Weterings, Eric; Verkaik, Nicole S; Keijzers, Guido;

    2008-01-01

    Repair of DNA double-strand breaks (DSBs) is predominantly mediated by nonhomologous end joining (NHEJ) in mammalian cells. NHEJ requires binding of the Ku70-Ku80 heterodimer (Ku70/80) to the DNA ends and subsequent recruitment of the DNA-dependent protein kinase catalytic subunit (DNA-PK(CS)) an...

  10. A robust network of double-strand break repair pathways governs genome integrity during C. elegans development.

    NARCIS (Netherlands)

    Pontier, D.B.; Tijsterman, M.

    2009-01-01

    To preserve genomic integrity, various mechanisms have evolved to repair DNA double-strand breaks (DSBs). Depending on cell type or cell cycle phase, DSBs can be repaired error-free, by homologous recombination, or with concomitant loss of sequence information, via nonhomologous end-joining (NHEJ) o

  11. Pathway choice in DNA double strand break repair: Observations of a balancing act

    NARCIS (Netherlands)

    I. Brandsma (Inger); D.C. van Gent (Dik)

    2012-01-01

    textabstractProper repair of DNA double strand breaks (DSBs) is vital for the preservation of genomic integrity. There are two main pathways that repair DSBs, Homologous recombination (HR) and Non-homologous end-joining (NHEJ). HR is restricted to the S and G2 phases of the cell cycle due to the req

  12. Double-strand break repair and G4 DNA stability in Caenorhabditis elegans

    NARCIS (Netherlands)

    Pontier, D.B.

    2010-01-01

    DNA double-strand breaks (DSBs) can be repaired by three canonical repair pathways. Homologous recombination (HR) uses the sister chromatid or homologous chromosome as a template to repair the DSB in an error-free manner. In non-homologous end-joining (NHEJ), the broken ends are ligated with little

  13. Catastrophic chromosomal restructuring during genome elimination in plants.

    Science.gov (United States)

    Tan, Ek Han; Henry, Isabelle M; Ravi, Maruthachalam; Bradnam, Keith R; Mandakova, Terezie; Marimuthu, Mohan Pa; Korf, Ian; Lysak, Martin A; Comai, Luca; Chan, Simon Wl

    2015-01-01

    Genome instability is associated with mitotic errors and cancer. This phenomenon can lead to deleterious rearrangements, but also genetic novelty, and many questions regarding its genesis, fate and evolutionary role remain unanswered. Here, we describe extreme chromosomal restructuring during genome elimination, a process resulting from hybridization of Arabidopsis plants expressing different centromere histones H3. Shattered chromosomes are formed from the genome of the haploid inducer, consistent with genomic catastrophes affecting a single, laggard chromosome compartmentalized within a micronucleus. Analysis of breakpoint junctions implicates breaks followed by repair through non-homologous end joining (NHEJ) or stalled fork repair. Furthermore, mutation of required NHEJ factor DNA Ligase 4 results in enhanced haploid recovery. Lastly, heritability and stability of a rearranged chromosome suggest a potential for enduring genomic novelty. These findings provide a tractable, natural system towards investigating the causes and mechanisms of complex genomic rearrangements similar to those associated with several human disorders. PMID:25977984

  14. The RSC and INO80 chromatin-remodeling complexes in DNA double-strand break repair.

    Science.gov (United States)

    Chambers, Anna L; Downs, Jessica A

    2012-01-01

    In eukaryotes, DNA is packaged into chromatin and is therefore relatively inaccessible to DNA repair enzymes. In order to perform efficient DNA repair, ATP-dependent chromatin-remodeling enzymes are required to alter the chromatin structure near the site of damage to facilitate processing and allow access to repair enzymes. Two of the best-studied remodeling complexes involved in repair are RSC (Remodels the Structure of Chromatin) and INO80 from Saccharomyces cerevisiae, which are both conserved in higher eukaryotes. RSC is very rapidly recruited to breaks and mobilizes nucleosomes to promote phosphorylation of H2A S129 and resection. INO80 enrichment at a break occurs later and is dependent on phospho-S129 H2A. INO80 activity at the break site also facilitates resection. Consequently, both homologous recombination and nonhomologous end-joining are defective in rsc mutants, while subsets of these repair pathways are affected in ino80 mutants.

  15. Affect Regulation

    DEFF Research Database (Denmark)

    Pedersen, Signe Holm; Poulsen, Stig Bernt; Lunn, Susanne

    2014-01-01

    Gergely and colleagues’ state that their Social Biofeedback Theory of Parental Affect Mirroring” can be seen as a kind of operationalization of the classical psychoanalytic concepts of holding, containing and mirroring. This article examines to what extent the social biofeedback theory of parenta...

  16. Affective Networks

    Directory of Open Access Journals (Sweden)

    Jodi Dean

    2010-02-01

    Full Text Available This article sets out the idea of affective networks as a constitutive feature of communicative capitalism. It explores the circulation of intensities in contemporary information and communication networks, arguing that this circulation should be theorized in terms of the psychoanalytic notion of the drive. The article includes critical engagements with theorists such as Guy Debord, Jacques Lacan, Tiziana Terranova, and Slavoj Zizek.

  17. DNA-PKcs Is Involved in Ig Class Switch Recombination in Human B Cells.

    Science.gov (United States)

    Björkman, Andrea; Du, Likun; Felgentreff, Kerstin; Rosner, Cornelia; Pankaj Kamdar, Radhika; Kokaraki, Georgia; Matsumoto, Yoshihisa; Davies, E Graham; van der Burg, Mirjam; Notarangelo, Luigi D; Hammarström, Lennart; Pan-Hammarström, Qiang

    2015-12-15

    Nonhomologous end-joining (NHEJ) is one of the major DNA double-strand break repair pathways in mammalian cells and is required for both V(D)J recombination and class switch recombination (CSR), two Ig gene-diversification processes occurring during B cell development. DNA-dependent protein kinase, catalytic subunit (DNA-PKcs) is a component of the classical NHEJ machinery and has a critical function during V(D)J recombination. However, its role in CSR has been controversial. In this study, we examined the pattern of recombination junctions from in vivo-switched B cells from two DNA-PKcs-deficient patients. One of them harbored mutations that did not affect DNA-PKcs kinase activity but caused impaired Artemis activation; the second patient had mutations resulting in diminished DNA-PKcs protein expression and kinase activity. These results were compared with those from DNA-PKcs-deficient mouse B cells. A shift toward the microhomology-based alternative end-joining at the recombination junctions was observed in both human and mouse B cells, suggesting that the classical NHEJ pathway is impaired during CSR when DNA-PKcs is defective. Furthermore, cells from the second patient showed additional or more severe alterations in CSR and/or NHEJ, which may suggest that DNA-PKcs and/or its kinase activity have additional, Artemis-independent functions during these processes. PMID:26546606

  18. [Affective dependency].

    Science.gov (United States)

    Scantamburlo, G; Pitchot, W; Ansseau, M

    2013-01-01

    Affective dependency is characterized by emotional distress (insecure attachment) and dependency to another person with a low self-esteem and reassurance need. The paper proposes a reflection on the definition of emotional dependency and the confusion caused by various denominations. Overprotective and authoritarian parenting, cultural and socio-environmental factors may contribute to the development of dependent personality. Psychological epigenetic factors, such as early socio-emotional trauma could on neuronal circuits in prefronto-limbic regions that are essential for emotional behaviour.We also focus on the interrelations between dependent personality, domestic violence and addictions. The objective for the clinician is to propose a restoration of self-esteem and therapeutic strategies focused on autonomy. PMID:23888587

  19. [Affective dependency].

    Science.gov (United States)

    Scantamburlo, G; Pitchot, W; Ansseau, M

    2013-01-01

    Affective dependency is characterized by emotional distress (insecure attachment) and dependency to another person with a low self-esteem and reassurance need. The paper proposes a reflection on the definition of emotional dependency and the confusion caused by various denominations. Overprotective and authoritarian parenting, cultural and socio-environmental factors may contribute to the development of dependent personality. Psychological epigenetic factors, such as early socio-emotional trauma could on neuronal circuits in prefronto-limbic regions that are essential for emotional behaviour.We also focus on the interrelations between dependent personality, domestic violence and addictions. The objective for the clinician is to propose a restoration of self-esteem and therapeutic strategies focused on autonomy.

  20. How does real affect affect affect recognition in speech?

    NARCIS (Netherlands)

    Truong, Khiet Phuong

    2009-01-01

    The aim of the research described in this thesis was to develop speech-based affect recognition systems that can deal with spontaneous (‘real’) affect instead of acted affect. Several affect recognition experiments with spontaneous affective speech data were carried out to investigate what combinati

  1. Nonhomologous Mechanisms of Repair of Chromosomal Breaks

    Energy Technology Data Exchange (ETDEWEB)

    Haber, J. E.

    2001-12-19

    Discovered three new proteins involved in DNA damage assessment. Interestingly they are all proteins involved in recombination, but they have very different roles in that process and other proteins that might be expected to be equivalently involved are not. This is developing into a very significant area of research.

  2. Vanillins—a novel family of DNA-PK inhibitors

    OpenAIRE

    Durant, Stephen; Karran, Peter

    2003-01-01

    Non-homologous DNA end-joining (NHEJ) is a major pathway of double strand break (DSB) repair in human cells. Here we show that vanillin (3-methoxy-4-hydroxybenzaldehyde)—a naturally occurring food component and an acknowledged antimutagen, anticlastogen and anticarcinogen—is an inhibitor of NHEJ. Vanillin blocked DNA end-joining by human cell extracts by directly inhibiting the activity of DNA-PK, a crucial NHEJ component. Inhibition was selective and vanillin had no detectable effect on othe...

  3. Histone H1 functions as a stimulatory factor in backup pathways of NHEJ

    OpenAIRE

    Rosidi, Bustanur; Wang, Minli; Wu, Wenqi; Sharma, Aparna; Wang, Huichen; Iliakis, George

    2008-01-01

    DNA double-strand breaks (DSBs) induced in the genome of higher eukaryotes by ionizing radiation (IR) are predominantly removed by two pathways of non-homologous end-joining (NHEJ) termed D-NHEJ and B-NHEJ. While D-NHEJ depends on the activities of the DNA-dependent protein kinase (DNA-PK) and DNA ligase IV/XRCC4/XLF, B-NHEJ utilizes, at least partly, DNA ligase III/XRCC1 and PARP-1. Using in vitro end-joining assays and protein fractionation protocols similar to those previously applied for ...

  4. Silencing of end-joining repair for efficient site-specific gene insertion after TALEN/CRISPR mutagenesis in Aedes aegypti

    OpenAIRE

    Basu, Sanjay; Aryan, Azadeh; Overcash, Justin M.; Samuel, Glady Hazitha; Anderson, Michelle A.E.; Dahlem, Timothy J.; Myles, Kevin M.; Adelman, Zach N.

    2015-01-01

    Mosquitoes are vectors of both parasites and viruses responsible for high-impact diseases including malaria, dengue, and chikungunya. Novel interventions based on genetic modification of the mosquito genome are currently being developed and implemented. To comprehensively exploit such interventions, detailed knowledge of mosquito physiology, genetics, and genome engineering are required. We developed and validated a two-step process for performing high-efficiency site-specific insertion of ge...

  5. Functional intersection of ATM and DNA-dependent protein kinase catalytic subunit in coding end joining during V(D)J recombination

    DEFF Research Database (Denmark)

    Lee, Baeck-Seung; Gapud, Eric J; Zhang, Shichuan;

    2013-01-01

    V(D)J recombination is initiated by the RAG endonuclease, which introduces DNA double-strand breaks (DSBs) at the border between two recombining gene segments, generating two hairpin-sealed coding ends and two blunt signal ends. ATM and DNA-dependent protein kinase catalytic subunit (DNA......-PKcs deficiency leads to a nearly complete block in coding join formation, as DNA-PKcs is required to activate Artemis, the endonuclease that opens hairpin-sealed coding ends. In contrast to loss of DNA-PKcs protein, here we show that inhibition of DNA-PKcs kinase activity has no effect on coding join formation......-PKcs) are serine-threonine kinases that orchestrate the cellular responses to DNA DSBs. During V(D)J recombination, ATM and DNA-PKcs have unique functions in the repair of coding DNA ends. ATM deficiency leads to instability of postcleavage complexes and the loss of coding ends from these complexes. DNA...

  6. Repair Pathway Choices and Consequences at the Double-Strand Break.

    Science.gov (United States)

    Ceccaldi, Raphael; Rondinelli, Beatrice; D'Andrea, Alan D

    2016-01-01

    DNA double-strand breaks (DSBs) are cytotoxic lesions that threaten genomic integrity. Failure to repair a DSB has deleterious consequences, including genomic instability and cell death. Indeed, misrepair of DSBs can lead to inappropriate end-joining events, which commonly underlie oncogenic transformation due to chromosomal translocations. Typically, cells employ two main mechanisms to repair DSBs: homologous recombination (HR) and classical nonhomologous end joining (C-NHEJ). In addition, alternative error-prone DSB repair pathways, namely alternative end joining (alt-EJ) and single-strand annealing (SSA), have been recently shown to operate in many different conditions and to contribute to genome rearrangements and oncogenic transformation. Here, we review the mechanisms regulating DSB repair pathway choice, together with the potential interconnections between HR and the annealing-dependent error-prone DSB repair pathways.

  7. Experiencing affective interactive art

    NARCIS (Netherlands)

    Bialoskorski, Leticia S.S.; Westerink, Joyce H.D.M.; Broek, van den Egon L.

    2010-01-01

    The progress in the field of affective computing enables the realization of affective art. This paper describes the affective interactive art system Mood Swings, which interprets and visualizes affect expressed by a person. Mood Swings is founded on the integration of a framework for affective move

  8. Genome Editing in Escherichia coli with Cas9 and synthetic CRISPRs

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Ze; Richardson, Sarah; Robinson, David; Deutsch, Samuel; Cheng, Jan-Fang

    2014-03-14

    Recently, the Cas9-CRISPR system has proven to be a useful tool for genome editing in eukaryotes, which repair the double stranded breaks made by Cas9 with non-homologous end joining or homologous recombination. Escherichia coli lacks non-homologous end joining and has a very low homologous recombination rate, effectively rendering targeted Cas9 activity lethal. We have developed a heat curable, serializable, plasmid based system for selectionless Cas9 editing in arbitrary E. coli strains that uses synthetic CRISPRs for targeting and -red to effect repairs of double stranded breaks. We have demonstrated insertions, substitutions, and multi-target deletions with our system, which we have tested in several strains.

  9. A model of oncogenic rearrangements: differences between chromosomal translocation mechanisms and simple double-strand break repair

    OpenAIRE

    Weinstock, David M.; Elliott, Beth; Jasin, Maria

    2006-01-01

    Recurrent reciprocal translocations are present in many hematologic and mesenchymal malignancies. Because significant sequence homology is absent from translocation breakpoint junctions, non-homologous end-joining (NHEJ) pathways of DNA repair are presumed to catalyze their formation. We developed translocation reporters for use in mammalian cells from which NHEJ events can be selected after precise chromosomal breakage. Translocations were efficiently recovered with these reporters using mou...

  10. Induction of Chromosomal Translocations in Mouse and Human Cells Using Site-Specific Endonucleases

    OpenAIRE

    Weinstock, David M.; Brunet, Erika; Jasin, Maria

    2008-01-01

    Reciprocal chromosomal translocations are early and essential events in the malignant transformation of several tumor types, yet the precise mechanisms that mediate translocation formation are poorly understood. We review here the development of approaches to induce and recover translocations between two targeted DNA double-strand breaks (DSBs) in mammalian chromosomes. Using mouse cells, we find that nonhomologous end-joining readily mediates translocation formation between two DSBs generate...

  11. 53BP1 mediates productive and mutagenic DNA repair through distinct phosphoprotein interactions

    DEFF Research Database (Denmark)

    Callen, E.; Wong, N.; Chen, H.-T.;

    2013-01-01

    The DNA damage response (DDR) protein 53BP1 protects DNA ends from excessive resection in G1, and thereby favors repair by nonhomologous end-joining (NHEJ) as opposed to homologous recombination (HR). During S phase, BRCA1 antagonizes 53BP1 to promote HR. The pro-NHEJ and antirecombinase functions...... productive CSR and suppresses mutagenic DNA repair through distinct phosphodependent interactions with RIF1 and PTIP. © 2013 Elsevier Inc....

  12. Rad54 and DNA Ligase IV cooperate to maintain mammalian chromatid stability

    OpenAIRE

    Mills, Kevin D.; Ferguson, David O.; Essers, Jeroen; Eckersdorff, Mark; Kanaar, Roland; Alt, Frederick W.

    2004-01-01

    Nonhomologous end joining (NHEJ) and homologous recombination (HR) represent the two major pathways of DNA double-strand break (DSB) repair in eukaryotic cells. NHEJ repairs DSBs by ligation of cognate broken ends irrespective of homologous flanking sequences, whereas HR repairs DSBs using an undamaged homologous template. Although both NHEJ and HR have been clearly implicated in the maintenance of genome stability, how these apparently independent and mechanistically distinct pathways are co...

  13. Cernunnos/XLF promotes the ligation of mismatched and noncohesive DNA ends

    OpenAIRE

    Tsai, Chun J.; Kim, Sunny A.; Chu, Gilbert

    2007-01-01

    Nonhomologous end-joining (NHEJ) repairs DNA double-strand breaks created by ionizing radiation or V(D)J recombination of the immunoglobulin genes. The breaks often leave mismatched or nonligatable ends, and NHEJ must repair the breaks with high efficiency and minimal nucleotide loss. Here, the NHEJ proteins Ku, DNA-dependent protein kinase catalytic subunit, XRCC4/Ligase IV, and Cernunnos/XRCC4-like factor joined mismatched and noncohesive DNA ends in the absence of processing factors. Depen...

  14. Molecular basis for DNA strand displacement by NHEJ repair polymerases

    OpenAIRE

    Bartlett, Edward J.; Brissett, Nigel C.; Plocinski, Przemyslaw; Carlberg, Tom; Doherty, Aidan J.

    2015-01-01

    The non-homologous end-joining (NHEJ) pathway repairs DNA double-strand breaks (DSBs) in all domains of life. Archaea and bacteria utilize a conserved set of multifunctional proteins in a pathway termed Archaeo-Prokaryotic (AP) NHEJ that facilitates DSB repair. Archaeal NHEJ polymerases (Pol) are capable of strand displacement synthesis, whilst filling DNA gaps or partially annealed DNA ends, which can give rise to unligatable intermediates. However, an associated NHEJ phosphoesterase (PE) re...

  15. Engineering new balancer chromosomes in C. elegans via CRISPR/Cas9

    Science.gov (United States)

    Iwata, Satoru; Yoshina, Sawako; Suehiro, Yuji; Hori, Sayaka; Mitani, Shohei

    2016-01-01

    Balancer chromosomes are convenient tools used to maintain lethal mutations in heterozygotes. We established a method for engineering new balancers in C. elegans by using the CRISPR/Cas9 system in a non-homologous end-joining mutant. Our studies will make it easier for researchers to maintain lethal mutations and should provide a path for the development of a system that generates rearrangements at specific sites of interest to model and analyse the mechanisms of action of genes. PMID:27650892

  16. Poly(ADP-ribose) polymerase inhibitor ABT-888 potentiates the cytotoxic activity of temozolomide in leukemia cells: influence of mismatch repair status and O6-methylguanine-DNA methyltransferase activity

    OpenAIRE

    Horton, Terzah M.; Jenkins, Gaye; Pati, Debananda; Zhang, Linna; Dolan, M. Eileen; Ribes-Zamora, Albert; Bertuch, Alison A.; Blaney, Susan M.; Delaney, Shannon L.; Hegde, Madhuri; Berg, Stacey L.

    2009-01-01

    The poly(ADP-ribose) polymerase (PARP) inhibitor ABT-888 potentiates the antitumor activity of temozolomide (TMZ). TMZ resistance results from increased O6-methylguanine-DNA methyltransferase (MGMT) activity and from mismatch repair (MMR) system mutations. We evaluated the relative importance of MGMT activity, MMR deficiency, nonhomologous end joining (NHEJ), and PARP activity in ABT-888 potentiation of TMZ. MMR-proficient and MMR-deficient leukemia cells with varying MGMT activity, as well a...

  17. Rad54 and Mus81 cooperation promotes DNA damage repair and restrains chromosome missegregation

    DEFF Research Database (Denmark)

    Ghamrasni, S El; Cardoso, R; Li, L;

    2016-01-01

    -damaging agents, defects on both the homologous recombination and non-homologous DNA end joining repair pathways and reduced fertility. We also observed that while Mus81 deficiency diminished the cleavage of common fragile sites, very strikingly, Rad54 loss impaired this cleavage to even a greater extent...... the importance of the cooperation between Rad54 and Mus81 for mediating DNA DSB repair and restraining chromosome missegregation....

  18. ATRX mutations and glioblastoma: Impaired DNA damage repair, alternative lengthening of telomeres, and genetic instability.

    Science.gov (United States)

    Koschmann, Carl; Lowenstein, Pedro R; Castro, Maria G

    2016-05-01

    Alpha thalassemia/mental retardation syndrome X-linked (ATRX) is mutated in nearly a third of pediatric glioblastoma (GBM) patients. We developed an animal model of ATRX-deficient GBM. Using this model combined with analysis of multiple human glioma genome-wide datasets, we determined that ATRX mutation leads to genetic instability, impaired non-homologous end joining, and alternate lengthening of telomeres (ALT). PMID:27314101

  19. Ku is required for telomeric C-rich strand maintenance but not for end-to-end chromosome fusions in Arabidopsis

    OpenAIRE

    Riha, Karel; Dorothy E Shippen

    2003-01-01

    Telomere dysfunction arising from mutations in telomerase or in telomere capping proteins leads to end-to-end chromosome fusions. Paradoxically, the Ku70/80 heterodimer, essential for nonhomologous end-joining double-strand break repair, is also found at telomeres, and in mammals it is required to prevent telomere fusion. Previously, we showed that inactivation of Ku70 in Arabidopsis results in telomere lengthening. Here, we have demonstrated that this telomere elongation is telomerase depend...

  20. Enrichment of G2/M cell cycle phase in human pluripotent stem cells enhances HDR-mediated gene repair with customizable endonucleases

    OpenAIRE

    Diane Yang; Scavuzzo, Marissa A.; Jolanta Chmielowiec; Robert Sharp; Aleksandar Bajic; Malgorzata Borowiak

    2016-01-01

    Efficient gene editing is essential to fully utilize human pluripotent stem cells (hPSCs) in regenerative medicine. Custom endonuclease-based gene targeting involves two mechanisms of DNA repair: homology directed repair (HDR) and non-homologous end joining (NHEJ). HDR is the preferred mechanism for common applications such knock-in, knock-out or precise mutagenesis, but remains inefficient in hPSCs. Here, we demonstrate that synchronizing synchronizing hPSCs in G2/M with ABT phase increases ...

  1. Repairing DNA damage by XRCC6/KU70 reverses TLR4-deficiency-worsened HCC development via restoring senescence and autophagic flux

    OpenAIRE

    Wang, Ziyan; Lin, Heng; Hua, Fang; Hu, Zhuo-Wei

    2013-01-01

    Hepatocellular carcinoma (HCC) is among the most lethal and prevalent cancers in the human population. The initiation and progression of HCC is closely associated with chronic liver inflammation. Recent research indicates that nonhomologous end joining (NHEJ), one of the DNA repair mechanisms, autophagy and senescence are all involved in the pathogenesis of HCC induced by carcinogens or oxidative stress. DNA repair proteins including XRCC6/KU70 and XRCC5/KU80 are the critical NHEJ factors tha...

  2. Single-stranded DNA oligomers stimulate error-prone alternative repair of DNA double-strand breaks through hijacking Ku protein.

    Science.gov (United States)

    Yuan, Ying; Britton, Sébastien; Delteil, Christine; Coates, Julia; Jackson, Stephen P; Barboule, Nadia; Frit, Philippe; Calsou, Patrick

    2015-12-01

    In humans, DNA double-strand breaks (DSBs) are repaired by two mutually-exclusive mechanisms, homologous recombination or end-joining. Among end-joining mechanisms, the main process is classical non-homologous end-joining (C-NHEJ) which relies on Ku binding to DNA ends and DNA Ligase IV (Lig4)-mediated ligation. Mostly under Ku- or Lig4-defective conditions, an alternative end-joining process (A-EJ) can operate and exhibits a trend toward microhomology usage at the break junction. Homologous recombination relies on an initial MRN-dependent nucleolytic degradation of one strand at DNA ends. This process, named DNA resection generates 3' single-stranded tails necessary for homologous pairing with the sister chromatid. While it is believed from the current literature that the balance between joining and recombination processes at DSBs ends is mainly dependent on the initiation of resection, it has also been shown that MRN activity can generate short single-stranded DNA oligonucleotides (ssO) that may also be implicated in repair regulation. Here, we evaluate the effect of ssO on end-joining at DSB sites both in vitro and in cells. We report that under both conditions, ssO inhibit C-NHEJ through binding to Ku and favor repair by the Lig4-independent microhomology-mediated A-EJ process. PMID:26350212

  3. Histone H1 functions as a stimulatory factor in backup pathways of NHEJ

    Science.gov (United States)

    Rosidi, Bustanur; Wang, Minli; Wu, Wenqi; Sharma, Aparna; Wang, Huichen; Iliakis, George

    2008-01-01

    DNA double-strand breaks (DSBs) induced in the genome of higher eukaryotes by ionizing radiation (IR) are predominantly removed by two pathways of non-homologous end-joining (NHEJ) termed D-NHEJ and B-NHEJ. While D-NHEJ depends on the activities of the DNA-dependent protein kinase (DNA-PK) and DNA ligase IV/XRCC4/XLF, B-NHEJ utilizes, at least partly, DNA ligase III/XRCC1 and PARP-1. Using in vitro end-joining assays and protein fractionation protocols similar to those previously applied for the characterization of DNA ligase III as an end-joining factor, we identify here histone H1 as an additional putative NHEJ factor. H1 strongly enhances DNA-end joining and shifts the product spectrum from circles to multimers. While H1 enhances the DNA-end-joining activities of both DNA Ligase IV and DNA Ligase III, the effect on ligase III is significantly stronger. Histone H1 also enhances the activity of PARP-1. Since histone H1 has been shown to counteract D-NHEJ, these observations and the known functions of the protein identify it as a putative alignment factor operating preferentially within B-NHEJ. PMID:18250087

  4. Mediatised affective activism

    DEFF Research Database (Denmark)

    Reestorff, Camilla Møhring

    2014-01-01

    bodies by addressing affective registers. The mediatised ‘affective environment’ (Massumi, 2009) cues bodies and generates spreadability, yet it also produces disconnections. These disconnections might redistribute the ‘economy of recognizability’ (Butler and Athanasiou, 2013); however, the Femen...

  5. Affectivity in the Liminal

    DEFF Research Database (Denmark)

    Thomassen, Bjørn

    In this paper I propose a return to the work of Arnold van Gennep, in order to briefly discuss how the terms of liminality and affectivity were always already connected. By linking the concept of liminality that van Gennep made famous to affectivity, we are actually not proposing new...... at the threshold. The paper contains three sections: a) liminality and affectivity in van Gennep’s life; b) liminality and affectivity as a theme in his work; c) liminality and affectivity as developed in the early reception of his work....

  6. Affectivity and race

    DEFF Research Database (Denmark)

    of the Nordic countries, Affectivity and Race draws on a variety of sources, including television programmes, news media, fictional literature, interviews, ethnographic observations, teaching curricula and policy documents, to explore the ways in which ideas about affectivity and emotion afford new insights...... into the experience of racial difference and the unfolding of political discourses on race in various social spheres. Organised around the themes of the politicisation of race through affect, the way that race produces affect and the affective experience of race, this interdisciplinary collection sheds light...... on the role of feelings in the formation of subjectivities, how race and whiteness are affectively circulated in public life and the ways in which emotions contribute to regimes of inclusion and exclusion. As such it will appeal to scholars across the social sciences, with interests in sociology, anthropology...

  7. The affect structure revisited

    OpenAIRE

    Elefant-Yanni, Véronique Rica; Victoria-Feser, Maria-Pia

    2005-01-01

    In affective psychology, there is a persistent controversy about the number, the nature and the definition of the affect structure dimensions. Responding to the methodological criticisms addressed to the preceding studies, we conciliated the principal theories regarding the affect structure with the same experimental setting. In particular, using the semantic items all around the circumplex we found three bipolar independent dimensions and using only the PANAS semantic items, we found two uni...

  8. TPhP exposure disturbs carbohydrate metabolism, lipid metabolism, and the DNA damage repair system in zebrafish liver

    Science.gov (United States)

    Du, Zhongkun; Zhang, Yan; Wang, Guowei; Peng, Jianbiao; Wang, Zunyao; Gao, Shixiang

    2016-02-01

    Triphenyl phosphate is a high production volume organophosphate flame retardant that has been detected in multiple environmental media at increasing concentrations. The environmental and health risks of triphenyl phosphate have drawn attention because of the multiplex toxicity of this chemical compound. However, few studies have paid close attention to the impacts of triphenyl phosphate on liver metabolism. We investigated hepatic histopathological, metabolomic and transcriptomic responses of zebrafish after exposure to 0.050 mg/L and 0.300 mg/L triphenyl phosphate for 7 days. Metabolomic analysis revealed significant changes in the contents of glucose, UDP-glucose, lactate, succinate, fumarate, choline, acetylcarnitine, and several fatty acids. Transcriptomic analysis revealed that related pathways, such as the glycosphingolipid biosynthesis, PPAR signaling pathway and fatty acid elongation, were significantly affected. These results suggest that triphenyl phosphate exposure markedly disturbs hepatic carbohydrate and lipid metabolism in zebrafish. Moreover, DNA replication, the cell cycle, and non-homologous end-joining and base excision repair were strongly affected, thus indicating that triphenyl phosphate hinders the DNA damage repair system in zebrafish liver cells. The present study provides a systematic analysis of the triphenyl phosphate-induced toxic effects in zebrafish liver and demonstrates that low concentrations of triphenyl phosphate affect normal metabolism and cell cycle.

  9. The role of DNA damage and repair in decitabine-mediated apoptosis in multiple myeloma.

    Science.gov (United States)

    Maes, Ken; De Smedt, Eva; Lemaire, Miguel; De Raeve, Hendrik; Menu, Eline; Van Valckenborgh, Els; McClue, Steve; Vanderkerken, Karin; De Bruyne, Elke

    2014-05-30

    DNA methyltransferase inhibitors (DNMTi) and histone deacetylase inhibitors (HDACi) are under investigation for the treatment of cancer, including the plasma cell malignancy multiple myeloma (MM). Evidence exists that DNA damage and repair contribute to the cytotoxicity mediated by the DNMTi decitabine. Here, we investigated the DNA damage response (DDR) induced by decitabine in MM using 4 human MM cell lines and the murine 5T33MM model. In addition, we explored how the HDACi JNJ-26481585 affects this DDR. Decitabine induced DNA damage (gamma-H2AX foci formation), followed by a G0/G1- or G2/M-phase arrest and caspase-mediated apoptosis. JNJ-26481585 enhanced the anti-MM effect of decitabine both in vitro and in vivo. As JNJ-26481585 did not enhance decitabine-mediated gamma-H2AX foci formation, we investigated the DNA repair response towards decitabine and/or JNJ-26481585. Decitabine augmented RAD51 foci formation (marker for homologous recombination (HR)) and/or 53BP1 foci formation (marker for non-homologous end joining (NHEJ)). Interestingly, JNJ-26481585 negatively affected basal or decitabine-induced RAD51 foci formation. Finally, B02 (RAD51 inhibitor) enhanced decitabine-mediated apoptosis. Together, we report that decitabine-induced DNA damage stimulates HR and/or NHEJ. JNJ-26481585 negatively affects RAD51 foci formation, thereby providing an additional explanation for the combinatory effect between decitabine and JNJ-26481585.

  10. Affected in the nightclub

    DEFF Research Database (Denmark)

    Demant, Jakob Johan

    2013-01-01

    simultaneously with the affects of love, joy, sympathy and so on. Alcohol, illicit drugs, bouncers, music and other human or non-human actants are part of the place. It is within this heterogeneous assemblage that affects become embodied. The data consists of 273 cases from a large Copenhagen nightclub where...

  11. Colors Can Affect Us!

    Institute of Scientific and Technical Information of China (English)

    张俊斌

    2006-01-01

    Different colors affect us differently.The following will show us how they work. Experiment proves that math problems worked on yellow paper have fewer mistakes than problems written on other colors of paper.

  12. Affective responses to dance.

    Science.gov (United States)

    Christensen, Julia F; Pollick, Frank E; Lambrechts, Anna; Gomila, Antoni

    2016-07-01

    The objective of the present work was the characterization of mechanisms by which affective experiences are elicited in observers when watching dance movements. A total of 203 dance stimuli from a normed stimuli library were used in a series of independent experiments. The following measures were obtained: (i) subjective measures of 97 dance-naïve participants' affective responses (Likert scale ratings, interviews); and (ii) objective measures of the physical parameters of the stimuli (motion energy, luminance), and of the movements represented in the stimuli (roundedness, impressiveness). Results showed that (i) participants' ratings of felt and perceived affect differed, (ii) felt and perceived valence but not arousal ratings correlated with physical parameters of the stimuli (motion energy and luminance), (iii) roundedness in posture shape was related to the experience of more positive emotion than edgy shapes (1 of 3 assessed rounded shapes showed a clear effect on positiveness ratings while a second reached trend level significance), (iv) more impressive movements resulted in more positive affective responses, (v) dance triggered affective experiences through the imagery and autobiographical memories it elicited in some people, and (vi) the physical parameters of the video stimuli correlated only weakly and negatively with the aesthetics ratings of beauty, liking and interest. The novelty of the present approach was twofold; (i) the assessment of multiple affect-inducing mechanisms, and (ii) the use of one single normed stimulus set. The results from this approach lend support to both previous and present findings. Results are discussed with regards to current literature in the field of empirical aesthetics and affective neuroscience. PMID:27235953

  13. Affects and assemblages

    DEFF Research Database (Denmark)

    Samson, Kristine

    and cultural geopgraphy. On this backdrop the paper states that affects and assemblages could serve as key notions for the reassembling the aesthetics of urban space. Thus, the paper suggest a less formal understanding of urban space and aesthetics, proposing an understanding of aesthetics......Affects and assemblages are Deleuzian Guattarian notions related to aesthetics and spatial territories. In recent urban geography and urban studies these notions are increasingly gaining more impact (Amin & Thrift 2002, Pile 2008, Farías & Bender 2010, Andersen & Harrison 2010, Thrift 2008). What...... happens to aesthetics and how does it change the existing social and geographical understanding of urban space? The paper sets out to reintroduce aesthetical aspects of affects and assemblages in relation to urban space and urban planning. It presupposes urban space as a continuous state of becoming where...

  14. The Affective Turn

    Directory of Open Access Journals (Sweden)

    Alí Lara

    2013-11-01

    Full Text Available In the last decade studies on affect and emotions have become relevant in the social sciences. This is not just a fad guideline, but instead a simultaneous reader of public life changes and subjective experience, from which it is also being transformed the knowledge production. Such a trend has been known as ‘The Affective Turn’ within the Anglophone Academy. Here we will translate it as ‘El Giro Afectivo’. This turn, so far, has not dabbled in the social science literature that is written in Spanish. This paper draws on a singular panorama of discussions about contemporary social studies of affect and emotion, and it’s vertebrate by some of its expressions in the contemporary academy.

  15. Affective Tourism Ethnography

    NARCIS (Netherlands)

    Buda, Dorina; Tucker, Hazel

    2015-01-01

    In this paper we aim to advance the concept of affective tourism ethnography. We take ethnography to refer to a research strategy rather than simply a methodological tool. This is because ethnography entails methods (individual interviews, focus groups, participant observation amongst others) and co

  16. Personalized affective music player

    NARCIS (Netherlands)

    Janssen, Joris H.; Broek, van den Egon L.; Westerink, Joyce H.D.M.; Cohn, J.; Nijholt, Anton; Pantic, M.

    2009-01-01

    We introduce and test an affective music player (AMP) that selects music for mood enhancement. Through a concise overview of content, construct, and ecological validity, we elaborate five considerations that form the foundation of the AMP. Based on these considerations, computational models are deve

  17. Affective Factors: Anxiety

    Science.gov (United States)

    Tasnimi, Mahshad

    2009-01-01

    Affective factors seem to play a crucial role in success or failure in second language acquisition. Negative attitudes can reduce learners' motivation and harm language learning, while positive attitudes can do the reverse. Discovering students' attitudes about language will help both teacher and student in teaching learning process. Anxiety is…

  18. Material and Affective Movements

    DEFF Research Database (Denmark)

    Rasmussen, Lisa Rosén

    2014-01-01

    . The chapter traces the former pupil’s memories of physical and affective movements within the larger context of school and discovers surprisingly diverse modes of knowing, relating, and attending to things, teachers and classmates among and between the three generations. It thus taps into the rich realms...

  19. Neurotransmitters affecting time perception

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    BACKGROUND:It has been demonstrated that dopamine and acetylcholine are the main neurotransmitters that affect time perception,which is also affected by other neurotransmitters.OBJECTIVE:To summarize how the neurotransmitter affect the time perception,and put forward the perspectives for further study on time perception.RETRIEVE STRATEGY:An online search for related literatures published in English was conducted in Elsevier SDOL(ScienceDirect Online)database from May 1990 to March 2007 using key words of "timing neurotransmitter".Totally 69 literatures were collected,and they were primarily checked.Inclusive criteria:Reviews and experimental studies;correlative studies of timing neurotransmitter.Exclusive criteria:Repeated studies.LITERATURE EVALUATION:The literatures were mainly sourced from Cognitive Brain Research and Neuroscience,and they were analyzed according to the inclusive criteria.Nineteen of them were involved,and all were experimental studies and reviews.DATA SYNTHESIS:The studies on time perception are developed mainly concentrating on dopamine and acetylcholine.Dopamine D2 receptors mainly affect the speed of internal clock.Dopamine receptors play an important role in both timing excitation and inhibition,which suggests the bi-directional regulation of dopamine.Injection of dopamine agonist can affect the attention to timing information.Injection of BW813U(antagonist of acetylcholine) can induce memory disorder,which indicates the effect of acetylcholine on timing memory,and further study shows that it is the effect of acetylcholine in precentral medial area.In a word,the study on the neurotransmitters affecting time perception is still at the primary stage.CONCLUSION:Dopamine and acetylcholine are the neurotransmitters known to be related to time perception.Dopamine in the basal ganglia is related to internal-clock in the range of seconds and minutes;Acetylcholine in prefrontal cortex is related to the mechanisms of temporal memory and attention

  20. DNA ligase IV and artemis act cooperatively to suppress homologous recombination in human cells: implications for DNA double-strand break repair.

    Directory of Open Access Journals (Sweden)

    Aya Kurosawa

    Full Text Available Nonhomologous end-joining (NHEJ and homologous recombination (HR are two major pathways for repairing DNA double-strand breaks (DSBs; however, their respective roles in human somatic cells remain to be elucidated. Here we show using a series of human gene-knockout cell lines that NHEJ repairs nearly all of the topoisomerase II- and low-dose radiation-induced DNA damage, while it negatively affects survival of cells harbouring replication-associated DSBs. Intriguingly, we find that loss of DNA ligase IV, a critical NHEJ ligase, and Artemis, an NHEJ factor with endonuclease activity, independently contribute to increased resistance to replication-associated DSBs. We also show that loss of Artemis alleviates hypersensitivity of DNA ligase IV-null cells to low-dose radiation- and topoisomerase II-induced DSBs. Finally, we demonstrate that Artemis-null human cells display increased gene-targeting efficiencies, particularly in the absence of DNA ligase IV. Collectively, these data suggest that DNA ligase IV and Artemis act cooperatively to promote NHEJ, thereby suppressing HR. Our results point to the possibility that HR can only operate on accidental DSBs when NHEJ is missing or abortive, and Artemis may be involved in pathway switching from incomplete NHEJ to HR.

  1. In Vitro Expansion of Bone Marrow Derived Mesenchymal Stem Cells Alters DNA Double Strand Break Repair of Etoposide Induced DNA Damage

    Directory of Open Access Journals (Sweden)

    Ian Hare

    2016-01-01

    Full Text Available Mesenchymal stem cells (MSCs are of interest for use in diverse cellular therapies. Ex vivo expansion of MSCs intended for transplantation must result in generation of cells that maintain fidelity of critical functions. Previous investigations have identified genetic and phenotypic alterations of MSCs with in vitro passage, but little is known regarding how culturing influences the ability of MSCs to repair double strand DNA breaks (DSBs, the most severe of DNA lesions. To investigate the response to DSB stress with passage in vitro, primary human MSCs were exposed to etoposide (VP16 at various passages with subsequent evaluation of cellular damage responses and DNA repair. Passage number did not affect susceptibility to VP16 or the incidence and repair kinetics of DSBs. Nonhomologous end joining (NHEJ transcripts showed little alteration with VP16 exposure or passage; however, homologous recombination (HR transcripts were reduced following VP16 exposure with this decrease amplified as MSCs were passaged in vitro. Functional evaluations of NHEJ and HR showed that MSCs were unable to activate NHEJ repair following VP16 stress in cells after successive passage. These results indicate that ex vivo expansion of MSCs alters their ability to perform DSB repair, a necessary function for cells intended for transplantation.

  2. CDK1 phosphorylates WRN at collapsed replication forks

    Science.gov (United States)

    Palermo, Valentina; Rinalducci, Sara; Sanchez, Massimo; Grillini, Francesca; Sommers, Joshua A.; Brosh, Robert M.; Zolla, Lello; Franchitto, Annapaola; Pichierri, Pietro

    2016-01-01

    Regulation of end-processing is critical for accurate repair and to switch between homologous recombination (HR) and non-homologous end joining (NHEJ). End resection is a two-stage process but very little is known about regulation of the long-range resection, especially in humans. WRN participates in one of the two alternative long-range resection pathways mediated by DNA2 or EXO1. Here we demonstrate that phosphorylation of WRN by CDK1 is essential to perform DNA2-dependent end resection at replication-related DSBs, promoting HR, replication recovery and chromosome stability. Mechanistically, S1133 phosphorylation of WRN is dispensable for relocalization in foci but is involved in the interaction with the MRE11 complex. Loss of WRN phosphorylation negatively affects MRE11 foci formation and acts in a dominant negative manner to prevent long-range resection altogether, thereby licensing NHEJ at collapsed forks. Collectively, we unveil a CDK1-dependent regulation of the WRN-DNA2-mediated resection and identify an undescribed function of WRN as a DSB repair pathway switch. PMID:27634057

  3. Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber.

    Science.gov (United States)

    Zhang, Zhonghua; Mao, Linyong; Chen, Huiming; Bu, Fengjiao; Li, Guangcun; Sun, Jinjing; Li, Shuai; Sun, Honghe; Jiao, Chen; Blakely, Rachel; Pan, Junsong; Cai, Run; Luo, Ruibang; Van de Peer, Yves; Jacobsen, Evert; Fei, Zhangjun; Huang, Sanwen

    2015-06-01

    Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber. PMID:26002866

  4. DNA-PK Deficiency in Alzheimer’s Disease

    Science.gov (United States)

    Kanungo, Jyotshna

    2016-01-01

    Alzheimer’s disease (AD) is characterized by neuronal death with an accumulaton of intra-cellular neurofibrillary tangles (NFT) and extracellular amyloid plaques. Reduced DNA repair ability has been reported in AD brains. In neurons, the predominant mechanism to repair double-strand DNA breaks (DSB) is non-homologous end joining (NHEJ) that requires DNA-dependent protein kinase (DNA-PK) activity. DNA-PK is a holoenzyme comprising the p460 kD DNA-PK catalytic subunit (DNA-PKcs) and its activator Ku, a heterodimer of p86 (Ku80) and p70 (Ku70) subunits. Upon binding to double-stranded DNA ends, Ku recruits DNA-PKcs to process NHEJ. In AD brains, reduced NHEJ activity as well as DNA-PKcs and Ku protein levels have been shown. Normal aging brains also show a reduction in both DNA-PKcs and Ku levels questioning a direct link between NHEJ ability and AD, and suggesting additional players/events in AD pathogenesis. Deficiency of Ku80, a somatostatin receptor, can disrupt somatostatin signaling thus inducing amyloid beta (Aβ) generation, which in turn can potentiate DNA-PKcs degradation and consequently loss of NHEJ activity, an additional step negatively affecting DSB repair. Trigger of these two different pathways culminating in genome instability may differentiate the outcomes between AD and normal aging. PMID:27376156

  5. The Catalytic Subunit of DNA-Dependent Protein Kinase Coordinates with Polo-Like Kinase 1 to Facilitate Mitotic Entry

    Directory of Open Access Journals (Sweden)

    Kyung-Jong Lee

    2015-04-01

    Full Text Available DNA-dependent protein kinase catalytic subunit (DNA-PKcs is the key regulator of the non-homologous end joining pathway of DNA double-strand break repair. We have previously reported that DNA-PKcs is required for maintaining chromosomal stability and mitosis progression. Our further investigations reveal that deficiency in DNA-PKcs activity caused a delay in mitotic entry due to dysregulation of cyclin-dependent kinase 1 (Cdk1, the key driving force for cell cycle progression through G2/M transition. Timely activation of Cdk1 requires polo-like kinase 1 (Plk1, which affects modulators of Cdk1. We found that DNA-PKcs physically interacts with Plk1 and could facilitate Plk1 activation both in vitro and in vivo. Further, DNA-PKcs–deficient cells are highly sensitive to Plk1 inhibitor BI2536, suggesting that the coordination between DNA-PKcs and Plk1 is not only crucial to ensure normal cell cycle progression through G2/M phases but also required for cellular resistance to mitotic stress. On the basis of the current study, it is predictable that combined inhibition of DNA-PKcs and Plk1 can be employed in cancer therapy strategy for synthetic lethality.

  6. The Catalytic Subunit of DNA-Dependent Protein Kinase Coordinates with Polo-Like Kinase 1 to Facilitate Mitotic Entry.

    Science.gov (United States)

    Lee, Kyung-Jong; Shang, Zeng-Fu; Lin, Yu-Fen; Sun, Jingxin; Morotomi-Yano, Keiko; Saha, Debabrata; Chen, Benjamin P C

    2015-04-01

    DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is the key regulator of the non-homologous end joining pathway of DNA double-strand break repair. We have previously reported that DNA-PKcs is required for maintaining chromosomal stability and mitosis progression. Our further investigations reveal that deficiency in DNA-PKcs activity caused a delay in mitotic entry due to dysregulation of cyclin-dependent kinase 1 (Cdk1), the key driving force for cell cycle progression through G2/M transition. Timely activation of Cdk1 requires polo-like kinase 1 (Plk1), which affects modulators of Cdk1. We found that DNA-PKcs physically interacts with Plk1 and could facilitate Plk1 activation both in vitro and in vivo. Further, DNA-PKcs-deficient cells are highly sensitive to Plk1 inhibitor BI2536, suggesting that the coordination between DNA-PKcs and Plk1 is not only crucial to ensure normal cell cycle progression through G2/M phases but also required for cellular resistance to mitotic stress. On the basis of the current study, it is predictable that combined inhibition of DNA-PKcs and Plk1 can be employed in cancer therapy strategy for synthetic lethality.

  7. CDK2 Is Required for the DNA Damage Response During Porcine Early Embryonic Development.

    Science.gov (United States)

    Wang, HaiYang; Kim, Nam-Hyung

    2016-08-01

    Cyclin-dependent kinase (CDK) 2 inhibition plays a central role in DNA damage-induced cell cycle arrest and DNA repair. However, whether CDK2 also influences early porcine embryo development is unknown. In this study, we examined whether CDK2 is involved in the regulation of oocyte meiosis and early embryonic development of porcine embryos. We found that disrupting CDK2 activity with RNAi or an inhibitor did not affect meiotic resumption or meiosis II arrest. However, CDK2 inhibitor-treated embryos showed delayed cleavage and ceased development before the blastocyst stage. Disrupting CDK2 activity is able to induce sustained DNA damage, as demonstrated by the formation of distinct gammaH2AX foci in nuclei of Day-3 and Day-5 embryos. Inhibiting CDK2 triggers a DNA damage checkpoint by activation of the ataxia telangiectasia mutated (ATM)-P53-P21 pathway. However, the mRNA expression of genes involved in nonhomologous end joining or homologous recombination pathways for double-strand break repair were reduced after administering CDK2 inhibitor to 5-day-old embryos. Furthermore, CDK2 inhibition caused apoptosis in Day-7 blastocysts. Thus, our results indicate that an ATM-P53-P21 DNA damage checkpoint is intact in the absence of CDK2; however, CDK2 is important for proper repair of the damaged DNA by either directly or indirectly influencing DNA repair-related gene expression. PMID:27307074

  8. G9a inhibition potentiates the anti-tumour activity of DNA double-strand break inducing agents by impairing DNA repair independent of p53 status.

    Science.gov (United States)

    Agarwal, Pallavi; Jackson, Stephen P

    2016-10-01

    Cancer cells often exhibit altered epigenetic signatures that can misregulate genes involved in processes such as transcription, proliferation, apoptosis and DNA repair. As regulation of chromatin structure is crucial for DNA repair processes, and both DNA repair and epigenetic controls are deregulated in many cancers, we speculated that simultaneously targeting both might provide new opportunities for cancer therapy. Here, we describe a focused screen that profiled small-molecule inhibitors targeting epigenetic regulators in combination with DNA double-strand break (DSB) inducing agents. We identify UNC0638, a catalytic inhibitor of histone lysine N-methyl-transferase G9a, as hypersensitising tumour cells to low doses of DSB-inducing agents without affecting the growth of the non-tumorigenic cells tested. Similar effects are also observed with another, structurally distinct, G9a inhibitor A-366. We also show that small-molecule inhibition of G9a or siRNA-mediated G9a depletion induces tumour cell death under low DNA damage conditions by impairing DSB repair in a p53 independent manner. Furthermore, we establish that G9a promotes DNA non-homologous end-joining in response to DSB-inducing genotoxic stress. This study thus highlights the potential for using G9a inhibitors as anti-cancer therapeutic agents in combination with DSB-inducing chemotherapeutic drugs such as etoposide. PMID:27431310

  9. Depletion of tyrosyl DNA phosphodiesterase 2 activity enhances etoposide-mediated double-strand break formation and cell killing.

    Science.gov (United States)

    Kont, Yasemin Saygideger; Dutta, Arijit; Mallisetty, Apurva; Mathew, Jeena; Minas, Tsion; Kraus, Christina; Dhopeshwarkar, Priyanka; Kallakury, Bhaskar; Mitra, Sankar; Üren, Aykut; Adhikari, Sanjay

    2016-07-01

    DNA topoisomerase 2 (Top2) poisons, including common anticancer drugs etoposide and doxorubicin kill cancer cells by stabilizing covalent Top2-tyrosyl-DNA 5'-phosphodiester adducts and DNA double-strand breaks (DSBs). Proteolytic degradation of the covalently attached Top2 leaves a 5'-tyrosylated blocked termini which is removed by tyrosyl DNA phosphodiesterase 2 (TDP2), prior to DSB repair through non-homologous end joining (NHEJ). Thus, TDP2 confers resistance of tumor cells to Top2-poisons by repairing such covalent DNA-protein adducts, and its pharmacological inhibition could enhance the efficacy of Top2-poisons. We discovered NSC111041, a selective inhibitor of TDP2, by optimizing a high throughput screening (HTS) assay for TDP2's 5'-tyrosyl phosphodiesterase activity and subsequent validation studies. We found that NSC111041 inhibits TDP2's binding to DNA without getting intercalated into DNA and enhanced etoposide's cytotoxicity synergistically in TDP2-expressing cells but not in TDP2 depleted cells. Furthermore, NSC111041 enhanced formation of etoposide-induced γ-H2AX foci presumably by affecting DSB repair. Immuno-histochemical analysis showed higher TDP2 expression in a sub-set of different type of tumor tissues. These findings underscore the feasibility of clinical use of suitable TDP2 inhibitors in adjuvant therapy with Top2-poisons for a sub-set of cancer patients with high TDP2 expression. PMID:27235629

  10. Synergistic effect of heat shock protein 90 inhibitor, 17-allylamino-17-demethoxygeldanamycin and X-rays, but not carbon-ion beams, on lethality in human oral squamous cell carcinoma cells

    International Nuclear Information System (INIS)

    The purpose of this study is to clarify the effect of a heat shock protein 90 inhibitor, 17-allylamino-17-demethoxygeldanamycin (17-AAG), in combination with X-rays or carbon-ion beams on cell killing in human oral squamous cell carcinoma LMF4 cells. Cell survival was measured by colony formation assay. Cell-cycle distribution was analyzed by flow cytometry. Expression of DNA repair-related proteins was investigated by western blotting. The results showed 17-AAG to have synergistic effects on cell lethality with X-rays, but not with carbon-ion beams. The 17-AAG decreased G2/M arrest induced by X-rays, but not by carbon-ion beams. Both X-ray and carbon-ion irradiation up-regulated expression of non-homologous end-joining-associated proteins, Ku70 and Ku80, but 17-AAG inhibited only X-ray-induced up-regulation of these proteins. These results show that 17-AAG with X-rays releases G2/M phase arrest; cells carrying misrepaired DNA damage then move on to the G1 phase. We demonstrate, for the first time, that the radiosensitization effect of 17-AAG is not seen with carbon-ion beams because 17-AAG does not affect these changes. (author)

  11. Pathway choice in DNA double strand break repair: observations of a balancing act

    Directory of Open Access Journals (Sweden)

    Brandsma Inger

    2012-11-01

    Full Text Available Abstract Proper repair of DNA double strand breaks (DSBs is vital for the preservation of genomic integrity. There are two main pathways that repair DSBs, Homologous recombination (HR and Non-homologous end-joining (NHEJ. HR is restricted to the S and G2 phases of the cell cycle due to the requirement for the sister chromatid as a template, while NHEJ is active throughout the cell cycle and does not rely on a template. The balance between both pathways is essential for genome stability and numerous assays have been developed to measure the efficiency of the two pathways. Several proteins are known to affect the balance between HR and NHEJ and the complexity of the break also plays a role. In this review we describe several repair assays to determine the efficiencies of both pathways. We discuss how disturbance of the balance between HR and NHEJ can lead to disease, but also how it can be exploited for cancer treatment.

  12. Molecular targets in cellular response to ionizing radiation and implications in space radiation protection

    Energy Technology Data Exchange (ETDEWEB)

    Belli, M.; Tabocchini, M.A. [Istituto Superiore di Sanita, Rome (Italy). Physics Lab.; Sapora, O. [Istituto Superiore di Sanita, Rome (Italy). Comparative Toxicology Lab.

    2002-12-01

    DNA repair systems and cell cycle checkpoints closely co-operate in the attempt of maintaining the genomic integrity of cells damaged by ionizing radiation. DNA double-strand breaks (DSB) are considered as the most biologically important radiation-induced damage. Their spatial distribution and association with other types of damage depend on radiation quality. It is believed these features affect damage reparability, thus explaining the higher efficiency for cellular effects of densely ionizing radiation with respect to {gamma}-rays. DSB repair systems identified in mammalian cells are homologous recombination (HR), single-strand annealing (SSA) and non-homologous end-joining (NHEJ). Some enzymes may participate in more than one of these repair systems. DNA damage also triggers biochemical signals activating checkpoints responsible for delay in cell cycle progression that allows more time for repair. Those at G1/S and S phases prevent replication of damaged DNA and those at G2/M phase prevent segregation of changed chromosomes. Individuals with lack or alterations of genes involved in DNA DSB repair and cell cycle checkpoints exhibit syndromes characterized by genome instability and predisposition to cancer. Information reviewed in this paper on the basic mechanisms of cellular response to ionizing radiation indicates their importance for a number of issues relevant to protection of astronauts from space radiation. (author)

  13. The Affective Turn

    DEFF Research Database (Denmark)

    Carnera, Alexander

    2012-01-01

    This paper confronts biopolitics with modern labour addressing questions of ‘governmentality’, ‘self-management’ and ‘social innovation’. It argues that the new modes of production within immaterial labour involve a new complex relation between on the one hand the ‘Art of Governance’ (Governmenta...... organizing good affective encounters based on limitations enhance and facilitate the performative dimension of self-management. Finally, the paper addresses the problem of critique confronting self-relation with Spinoza's ethics as an ethical difference of powe...... of biopolitics that surpasses that of governmentality. The affective self-relation is used as a research tool to analyse the creation of social and economic values in our new modes of productions, for instance, within free labour of the cultural industry. The movie The Five Obstructions is used to show how...

  14. Factors Affecting Wound Healing

    OpenAIRE

    Guo, S; DiPietro, L. A.

    2010-01-01

    Wound healing, as a normal biological process in the human body, is achieved through four precisely and highly programmed phases: hemostasis, inflammation, proliferation, and remodeling. For a wound to heal successfully, all four phases must occur in the proper sequence and time frame. Many factors can interfere with one or more phases of this process, thus causing improper or impaired wound healing. This article reviews the recent literature on the most significant factors that affect cutane...

  15. Cytoplasm Affects Embryonic Development

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ Recent studies by CAS researchers furnish strong evidence that a fertilized egg's nucleus isn't the sole site of control for an embryo's development. A research team headed by Prof. Zhu Zuoyan from the CAS Institute of Hydrobiology in Wuhan discovered that cytoplasm affects the number of vertebrae in cloned offspring created when nuclei from one fish genus were transplanted to enucleated eggs of another.

  16. Affective Image Colorization

    Institute of Scientific and Technical Information of China (English)

    Xiao-Hui Wang; Jia Jia; Han-Yu Liao; Lian-Hong Cai

    2012-01-01

    Colorization of gray-scale images has attracted many attentions for a long time.An important role of image color is the conveyer of emotions (through color themes).The colorization with an undesired color theme is less useful,even it is semantically correct.However this has been rarely considered.Automatic colorization respecting both the semantics and the emotions is undoubtedly a challenge.In this paper,we propose a complete system for affective image colorization.We only need the user to assist object segmentation along with text labels and an affective word.First,the text labels along with other object characters are jointly used to filter the internet images to give each object a set of semantically correct reference images.Second,we select a set of color themes according to the affective word based on art theories.With these themes,a generic algorithm is used to select the best reference for each object,balancing various requirements.Finally,we propose a hybrid texture synthesis approach for colorization.To the best of our knowledge,it is the first system which is able to efficiently colorize a gray-scale image semantically by an emotionally controllable fashion.Our experiments show the effectiveness of our system,especially the benefit compared with the previous Markov random field (MRF) based method.

  17. Visual affect recognition

    CERN Document Server

    Stathopoulou, I-O

    2010-01-01

    It is generally known that human faces, as well as body motions and gestures, provide a wealth of information about a person, such as age, race, sex and emotional state. This monograph primarily studies the perception of facial expression of emotion, and secondarily of motion and gestures, with the purpose of developing a fully automated visual affect recognition system for use in modes of human/computer interaction. The book begins with a survey of the literature on emotion perception, followed by a description of empirical studies conducted with human participants and the construction of a '

  18. The Affective Turn

    OpenAIRE

    Alí Lara; Giazú Enciso

    2013-01-01

    En la última década los estudios del afecto y las emociones han cobrado relevancia en las ciencias sociales. Esto no es simplemente una directriz de moda, es un indicador simultáneo de las modificaciones en la vida pública y de la experiencia subjetiva; a partir del cual se está transformando la producción de conocimiento. Tal tendencia ha sido conocida en la academia sajona como The Affective Turn, aquí traducido como “El giro afectivo” y que hasta el momento no ha incursionado como tal en l...

  19. Multisensory Perception of Affect

    Directory of Open Access Journals (Sweden)

    Beatrice de Gelder

    2011-10-01

    Full Text Available Multisensory integration must stand out among the fields of research that have witnessed a most impressive explosion of interest this last decade. One of these new areas of multisensory research concerns emotion. Since our first exploration of this phenomenon (de Gelder et al., 1999 a number of studies have appeared and they have used a wide variety of behavioral, neuropsychological and neuroscientifc methods. The goal of this presentation is threefold. First, we review the research on audiovisual perception of emotional signals from the face and the voice followed by a report or more recent studies on integrating emotional information provided by the voice and whole body expressions. We will also include some recent work on multisensory music perception. In the next section we discuss some methodological and theoretical issues. Finally, we will discuss findings about abnormal affective audiovisual integration in schizophrenia and in autism.

  20. Anticipated affect and behavioral choice

    NARCIS (Netherlands)

    R. Richard; J. van der Pligt; N.K. de Vries

    1996-01-01

    Most research on the impact of affect on attitudes and behavior emphasizes the effect of past and present affective reactions. In this article we focus on anticipated, postbehavioral, affective reactions. The influence of anticipated affective reactions on a number of behaviors was investigated in t

  1. Anticipated affect and behavioral choice.

    NARCIS (Netherlands)

    R. Richard; J. van der Pligt; N.K. de Vries

    1996-01-01

    Most research on the impact of affect on attitudes and behavior emphasizes the effect of past and present affective reactions. In this article we focus on anticipated, postbehavioral, affective reactions. The influence of anticipated affective reactions on a number of behaviors was investigated in t

  2. Anticipated affect and behavioral choice.

    OpenAIRE

    Richard, R.; Pligt, van der, J.; Vries, de, N.

    1996-01-01

    Most research on the impact of affect on attitudes and behavior emphasizes the effect of past and present affective reactions. In this article we focus on anticipated, postbehavioral, affective reactions. The influence of anticipated affective reactions on a number of behaviors was investigated in the context of Ajzen's theory of planned behavior (Ajzen, 1985, 1991). Results showed that anticipated affective reactions predicted behavioral intentions independent from general attitudes (evaluat...

  3. Nonhomologous Chromosome Pairing in Aegilops-Secale Hybrids.

    Science.gov (United States)

    Su, Yarui; Zhang, Dale; Li, Yuge; Li, Suoping

    2015-01-01

    Intergeneric hybrids and amphidiploid hybrids from crosses of Aegilopstauschii and Secale cereale were produced using young embryo rescue. The hybrids showed complete sets of both parental chromosomes. The dihaploid plants showed an average meiotic pairing configuration of 10.84 I + 1.57 II + 0.01 III. Genomic in situ staining revealed 3 types of bivalent associations, i.e. D-D, R-R and D-R at frequencies of 8.6, 8.2 and 83.3%, respectively. Trivalents consisted of D-R-D or R-D-R associations. These results suggested that both intra- and intergenomic chromosome homology were contributed to chromosome pairing. Derived amphidiploids with 2n = 28 paired at metaphase I of meiosis as 4.51 I + 11.70 II + 0.03 III. Chromosome pairing of amphidiploids appeared more or less regular, i.e. bivalent-like with some trivalent configurations. PMID:26950342

  4. A deficiency in DNA repair and DNA-PKcs expression in the radiosensitive BALB/c mouse

    Science.gov (United States)

    Okayasu, R.; Suetomi, K.; Yu, Y.; Silver, A.; Bedford, J. S.; Cox, R.; Ullrich, R. L.

    2000-01-01

    We have studied the efficiency of DNA double strand break (DSB) rejoining in primary cells from mouse strains that show large differences in in vivo radiosensitivity and tumor susceptibility. Cells from radiosensitive, cancer-prone BALB/c mice showed inefficient end joining of gamma ray-induced DSBs as compared with cells from all of the other commonly used strains and F1 hybrids of C57BL/6 and BALB/c mice. The BALB/c repair phenotype was accompanied by a significantly reduced expression level of DNA-PKcs protein as well as a lowered DNA-PK activity level as compared with the other strains. In conjunction with published reports, these data suggest that natural genetic variation in nonhomologous end joining processes may have a significant impact on the in vivo radiation response of mice.

  5. Opinion: uracil DNA glycosylase (UNG) plays distinct and non-canonical roles in somatic hypermutation and class switch recombination.

    Science.gov (United States)

    Yousif, Ashraf S; Stanlie, Andre; Begum, Nasim A; Honjo, Tasuku

    2014-10-01

    Activation-induced cytidine deaminase (AID) is essential to class switch recombination (CSR) and somatic hypermutation (SHM). Uracil DNA glycosylase (UNG), a member of the base excision repair complex, is required for CSR. The role of UNG in CSR and SHM is extremely controversial. AID deficiency in mice abolishes both CSR and SHM, while UNG-deficient mice have drastically reduced CSR but augmented SHM raising a possibility of differential functions of UNG in CSR and SHM. Interestingly, UNG has been associated with a CSR-specific repair adapter protein Brd4, which interacts with acetyl histone 4, γH2AX and 53BP1 to promote non-homologous end joining during CSR. A non-canonical scaffold function of UNG, but not the catalytic activity, can be attributed to the recruitment of essential repair proteins associated with the error-free repair during SHM, and the end joining during CSR. PMID:24994819

  6. Security affects us all!

    CERN Multimedia

    SMB Department

    2016-01-01

    In the hope of minimising the number of thefts of the Organization’s property, which can lead to months of work going to waste on certain projects, you are reminded of the importance that CERN attaches to the rules concerning the protection of equipment for which we are responsible. If you see any unusual behaviour or if you are the victim of a theft, don’t hesitate to report it by submitting a ticket through the CERN Portal or calling the CSA. Security affects us all!   CERN is attractive in more ways than one, and it remains as attractive as ever to thieves. With the nice weather and with the holiday season in full swing, the number of thefts recorded at CERN is on the rise. Items stolen include money, computers, electronic equipment, cable drums and copper antennae.   There are a few basic precautions that you should take to protect both your own and the Organization’s property: lock your door, don’t leave valuable items in your office, st...

  7. Affective World Literature

    DEFF Research Database (Denmark)

    Vilslev, Annette Thorsen

    The PhD dissertation compares the literary theory and novels of modern Japanese writer Natsume Sōseki. It reads Sōseki’s Theory of Literature (2009, Bungakuron, 1907) as an inherently comparative and interdisciplinary approach to theorizing feelings in world literature. More broadly, the disserta......The PhD dissertation compares the literary theory and novels of modern Japanese writer Natsume Sōseki. It reads Sōseki’s Theory of Literature (2009, Bungakuron, 1907) as an inherently comparative and interdisciplinary approach to theorizing feelings in world literature. More broadly......, the dissertation investigates the critical negotiation of the novel as a travelling genre in Japan in the beginning of the 20th century, and, more specifically, Sōseki’s work in relation to world literature and affect theory. Sōseki’s work is highly influential in Japan and East Asia, and his novels widely...... circulated beyond Japan. Using Sōseki’s theory as an example, and by comparing it to other theories, the dissertation argues that comparative literature needs to include not only more non-Western literature but also more non-Western literary theories in the ongoing debate of world literature. Close...

  8. Identifying Occupationally Specific Affective Behaviors.

    Science.gov (United States)

    Pucel, David J.

    1993-01-01

    Data from two groups of cosmetology instructors (n=15) and two groups of machinist instructors (n=17) validated the Occupational Affective Behavior Analysis instrument as capable of identifying affective behaviors viewed as important to success in a given occupation. (SK)

  9. Affective monitoring: A generic mechanism for affect elicitation

    Directory of Open Access Journals (Sweden)

    Hans ePhaf

    2012-03-01

    Full Text Available In this paper we sketch a new framework for affect elicitation, which is based on previous evolutionary and connectionist modeling and experimental work from our group. Affective monitoring is considered a local match-mismatch process within a module of the neural network. Negative affect is raised instantly by mismatches, incongruency, disfluency, novelty, incoherence, and dissonance, whereas positive affect follows from matches, congruency, fluency, familiarity, coherence, and resonance, at least when an initial mismatch can be solved quickly. Affective monitoring is considered an evolutionary-early conflict and change detection process operating at the same level as, for instance, attentional selection. It runs in parallel and imparts affective flavour to emotional behavior systems, which involve evolutionary-prepared stimuli and action tendencies related to for instance defensive, exploratory, attachment, or appetitive behavior. Positive affect is represented in the networks by high-frequency oscillations, presumably in the gamma band. Negative affect corresponds to more incoherent lower-frequency oscillations, presumably in the theta band. For affect to become conscious, large-scale synchronization of the oscillations over the network and the construction of emotional experiences are required. These constructions involve perceptions of bodily states and action tendencies, but also appraisals as well as efforts to regulate the emotion. Importantly, affective monitoring accompanies every kind of information processing, but conscious emotions, which result from the later integration of affect in a cognitive context, are much rarer events.

  10. Individual Difference Variables, Affective Differentiation, and the Structures of Affect

    Science.gov (United States)

    Terracciano, Antonio; McCrae, Robert R.; Hagemann, Dirk; Costa, Paul T.

    2008-01-01

    Methodological arguments are usually invoked to explain variations in the structure of affect. Using self-rated affect from Italian samples (N = 600), we show that individual difference variables related to affective differentiation can moderate the observed structure. Indices of circumplexity (Browne, 1992) and congruence coefficients to the hypothesized target were used to quantify the observed structures. Results did not support the circumplex model as a universal structure. A circular structure with axes of activation and valence was approximated only among more affectively differentiated groups: students and respondents with high scores on Openness to Feelings and measures of negative emotionality. A different structure, with unipolar Positive Affect and Negative Affect factors, was observed among adults and respondents with low Openness to Feelings and negative emotionality. The observed structure of affect will depend in part on the nature of the sample studied. PMID:12932207

  11. Individual difference variables, affective differentiation, and the structures of affect.

    Science.gov (United States)

    Terracciano, Antonio; McCrae, Robert R; Hagemann, Dirk; Costa, Paul T

    2003-10-01

    Methodological arguments are usually invoked to explain variations in the structure of affect. Using self-rated affect from Italian samples (N=600), we show that individual difference variables related to affective differentiation can moderate the observed structure. Indices of circumplexity and congruence coefficients to the hypothesized target were used to quantify the observed structures. Results did not support the circumplex model as a universal structure. A circular structure with axes of activation and valence was approximated only among more affectively differentiated groups: students and respondents with high scores on Openness to Feelings and measures of negative emotionality. A different structure, with unipolar Positive Affect and Negative Affect factors, was observed among adults and respondents with low Openness to Feelings and negative emotionality. The observed structure of affect will depend in part on the nature of the sample studied. PMID:12932207

  12. Affective Productions of Mathematical Experience

    Science.gov (United States)

    Walshaw, Margaret; Brown, Tony

    2012-01-01

    In underscoring the affective elements of mathematics experience, we work with contemporary readings of the work of Spinoza on the politics of affect, to understand what is included in the cognitive repertoire of the Subject. We draw on those resources to tell a pedagogical tale about the relation between cognition and affect in settings of…

  13. Application of Affect to CALL

    Institute of Scientific and Technical Information of China (English)

    李露

    2006-01-01

    This essay mainly attempts to discuss some affective factors in CALL, with focus on affective influence on English (foreign language) learning and thus concludes that in the process of CALL related affect should be activated and made good use of to better foreign language teaching and learning.

  14. Encountering science education's capacity to affect and be affected

    Science.gov (United States)

    Alsop, Steve

    2016-09-01

    What might science education learn from the recent affective turn in the humanities and social sciences? Framed as a response to Michalinos Zembylas's article, this essay draws from selected theorizing in affect theory, science education and science and technology studies, in pursuit of diverse and productive ways to talk of affect within science education. These discussions are framed by desires to transcend traditional epistemic boundaries and practices. The article concludes offering some associated ambiguities and tensions involved.

  15. Encountering science education's capacity to affect and be affected

    Science.gov (United States)

    Alsop, Steve

    2015-12-01

    What might science education learn from the recent affective turn in the humanities and social sciences? Framed as a response to Michalinos Zembylas's article, this essay draws from selected theorizing in affect theory, science education and science and technology studies, in pursuit of diverse and productive ways to talk of affect within science education. These discussions are framed by desires to transcend traditional epistemic boundaries and practices. The article concludes offering some associated ambiguities and tensions involved.

  16. Interaction of DNA-dependent protein kinase with DNA and with Ku: biochemical and atomic-force microscopy studies.

    OpenAIRE

    Yaneva, M.; Kowalewski, T; Lieber, M R

    1997-01-01

    DNA-dependent protein kinase (DNA-PK or the scid factor) and Ku are critical for DNA end-joining in V(D)J recombination and in general non-homologous double-strand break repair. One model for the function of DNA-PK is that it forms a complex with Ku70/86, and this complex then binds to DNA ends, with Ku serving as the DNA-binding subunit. We find that DNA-PK can itself bind to linear DNA fragments ranging in size from 18 to 841 bp double-stranded (ds) DNA, as indicated by: (i) mobility shifts...

  17. REV7/MAD2L2: the multitasking maestro emerges as a barrier to recombination

    OpenAIRE

    Julian E Sale

    2015-01-01

    REV7/MAD2L2 plays important roles in translesion DNA synthesis and mitotic control. Two new papers extend its gamut by revealing its unexpected participation in pathway choice during DNA double-strand break repair. By inhibiting 5′ DNA end resection downstream of 53BP1 and RIF1, REV7/MAD2L2 promotes non-homologous end joining at the expense of homologous recombination. Importantly, loss of REV7/MAD2L2 renders PARP inhibitors ineffective in BRCA1-deficient tumours, suggesting another possible ...

  18. Autophosphorylation of the DNA-dependent protein kinase catalytic subunit is required for rejoining of DNA double-strand breaks

    OpenAIRE

    Chan, Doug W.; Chen, Benjamin Ping-Chi; Prithivirajsingh, Sheela; Kurimasa, Akihiro; Story, Michael D.; Qin, Jun; Chen, David J.

    2002-01-01

    Nonhomologous end-joining (NHEJ) is the predominant pathway that repairs DNA double-strand breaks (DSBs) in mammalian cells. The DNA-dependent protein kinase (DNA-PK), consisting of Ku and DNA-PK catalytic subunit (DNA-PKcs), is activated by DNA in vitro and is required for NHEJ. We report that DNA-PKcs is autophosphorylated at Thr2609 in vivo in a Ku-dependent manner in response to ionizing radiation. Phosphorylated DNA-PKcs colocalizes with both γ-H2AX and 53BP1 after DNA damage. Mutation o...

  19. ATM and Artemis promote homologous recombination of radiation-induced DNA double-strand breaks in G2

    OpenAIRE

    Beucher, Andrea; Birraux, Julie; Tchouandong, Leopoldine; Barton, Olivia; Shibata, Atsushi; Conrad, Sandro; Goodarzi, Aaron A.; KREMPLER, ANDREA; Jeggo, Penny; Lo¨brich, Markus

    2009-01-01

    Homologous recombination (HR) and non-homologous end joining (NHEJ) represent distinct pathways for repairing DNA double-strand breaks (DSBs). Previous work implicated Artemis and ATM in an NHEJ-dependent process, which repairs a defined subset of radiation-induced DSBs in G1-phase. Here, we show that in G2, as in G1, NHEJ represents the major DSB-repair pathway whereas HR is only essential for repair of ∼15% of X- or γ-ray-induced DSBs. In addition to requiring the known HR proteins, Brca2, ...

  20. Synapsis of DNA ends by DNA-dependent protein kinase

    OpenAIRE

    DeFazio, Lisa G.; Stansel, Rachel M.; Griffith, Jack D.; Chu, Gilbert

    2002-01-01

    The catalytic subunit of DNA-dependent protein kinase (DNA-PKCS) is required for a non-homologous end-joining pathway that repairs DNA double-strand breaks produced by ionizing radiation or V(D)J recombination; however, its role in this pathway has remained obscure. Using a neutravidin pull-down assay, we found that DNA-PKCS mediates formation of a synaptic complex containing two DNA molecules. Furthermore, kinase activity was cooperative with respect to DNA concentration, suggesting that act...

  1. Ku Regulates Signaling to DNA Damage Response Pathways through the Ku70 von Willebrand A Domain

    OpenAIRE

    Fell, Victoria L.; Schild-Poulter, Caroline

    2012-01-01

    The Ku heterodimer (Ku70/Ku80) is a main component of the nonhomologous end-joining (NHEJ) pathway that repairs DNA double-strand breaks (DSBs). Ku binds the broken DNA end and recruits other proteins to facilitate the processing and ligation of the broken end. While Ku interacts with many proteins involved in DNA damage/repair-related functions, few interactions have been mapped to the N-terminal von Willebrand A (vWA) domain, a predicted protein interaction domain. The mutagenesis of Ku70 v...

  2. Ku80-Deleted Cells are Defective at Base Excision Repair

    OpenAIRE

    Li, Han; Marple, Teresa; Hasty, Paul

    2013-01-01

    Ku80 forms a heterodimer with Ku70, called Ku, that repairs DNA double-strand breaks (DSBs) via the nonhomologous end joining (NHEJ) pathway. As a consequence of deleting NHEJ, Ku80-mutant cells are hypersensitive to agents that cause DNA DSBs like ionizing radiation. Here we show that Ku80 deletion also decreased resistance to ROS and alkylating agents that typically cause base lesions and single-strand breaks (SSBs). This is unusual since base excision repair (BER), not NHEJ, typically repa...

  3. Homologous recombination repairs secondary replication induced DNA double-strand breaks after ionizing radiation

    OpenAIRE

    Groth, Petra; Orta, Manuel Luís; Elvers, Ingegerd; Majumder, Muntasir Mamun; Lagerqvist, Anne; Helleday, Thomas

    2012-01-01

    Ionizing radiation (IR) produces direct two-ended DNA double-strand breaks (DSBs) primarily repaired by non-homologous end joining (NHEJ). It is, however, well established that homologous recombination (HR) is induced and required for repair of a subset of DSBs formed following IR. Here, we find that HR induced by IR is drastically reduced when post-DNA damage replication is inhibited in mammalian cells. Both IR-induced RAD51 foci and HR events in the hprt gene are reduced in the presence of ...

  4. Cryoelectron Microscopy Structure of the DNA-dependent Protein Kinase Catalytic Subunit (DNA-PKcs) at Subnanometer Resolution Reveals α-Helices and Insight into DNA Binding

    OpenAIRE

    Williams, Dewight R.; Lee, Kyung-Jong; Shi, Jian; Chen, David J.; Stewart, Phoebe L

    2008-01-01

    The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) regulates the non-homologous end joining pathway for repair of double-stranded DNA breaks. Here we present a 7Å resolution structure of DNA-PKcs determined by cryoEM single particle reconstruction. This structure is composed of density rods throughout the molecule indicative of α-helices and reveals new structural features not observed in lower resolution EM structures. Docking of homology models into the DNA-PKcs structure demonst...

  5. CRISPR-Cas9-guided Genome Engineering in C. elegans

    Science.gov (United States)

    Kim, Hyun-Min; Colaiácovo, Monica P.

    2016-01-01

    The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system is successfully being used for efficient and targeted genome editing in various organisms including the nematode C. elegans. Recent studies developed various CRISPR-Cas9 approaches to enhance genome engineering via two major DNA double-strand break repair pathways: non-homologous end joining and homologous recombination. Here we describe a protocol for Cas9-mediated C. elegans genome editing together with single guide RNA (sgRNA) and repair template cloning and injection methods required for delivering Cas9, sgRNAs and repair template DNA into the C. elegans germline. PMID:27366893

  6. Live cell imaging reveals at novel view of DNA

    International Nuclear Information System (INIS)

    Non-homologous end-joining (NHEJ) is the major repair pathway for DNA double-strand breaks (DSBs) that are the most severe form of DNA damages. Recently, live cell imaging techniques coupled with laser micro-irradiation were used to analyze the spatio-temporal behavior of the NHEJ core factors upon DSB induction in living cells. Based on the live cell imaging studies, we proposed a novel two-phase model for DSB sensing and protein assembly in the NHEJ pathway. This new model provides a novel view of the dynamic protein behavior on DSBs and broad implications for the molecular mechanism of NHEJ. (author)

  7. Current Progress in Therapeutic Gene Editing for Monogenic Diseases.

    Science.gov (United States)

    Prakash, Versha; Moore, Marc; Yáñez-Muñoz, Rafael J

    2016-03-01

    Programmable nucleases allow defined alterations in the genome with ease-of-use, efficiency, and specificity. Their availability has led to accurate and widespread genome engineering, with multiple applications in basic research, biotechnology, and therapy. With regard to human gene therapy, nuclease-based gene editing has facilitated development of a broad range of therapeutic strategies based on both nonhomologous end joining and homology-dependent repair. This review discusses current progress in nuclease-based therapeutic applications for a subset of inherited monogenic diseases including cystic fibrosis, Duchenne muscular dystrophy, diseases of the bone marrow, and hemophilia and highlights associated challenges and future prospects. PMID:26765770

  8. Functional redundancy between DNA ligases I and III in DNA replication in vertebrate cells

    OpenAIRE

    Arakawa, Hiroshi; Bednar, Theresa; Wang, Minli; Paul, Katja; Mladenov, Emil; Bencsik-Theilen, Alena A.; Iliakis, George

    2011-01-01

    In eukaryotes, the three families of ATP-dependent DNA ligases are associated with specific functions in DNA metabolism. DNA ligase I (LigI) catalyzes Okazaki-fragment ligation at the replication fork and nucleotide excision repair (NER). DNA ligase IV (LigIV) mediates repair of DNA double strand breaks (DSB) via the canonical non-homologous end-joining (NHEJ) pathway. The evolutionary younger DNA ligase III (LigIII) is restricted to higher eukaryotes and has been associated with base excisio...

  9. 53BP1 fosters fidelity of homology-directed DNA repair

    DEFF Research Database (Denmark)

    Ochs, Fena; Somyajit, Kumar; Altmeyer, Matthias;

    2016-01-01

    Repair of DNA double-strand breaks (DSBs) in mammals is coordinated by the ubiquitin-dependent accumulation of 53BP1 at DSB-flanking chromatin. Owing to its ability to limit DNA-end processing, 53BP1 is thought to promote nonhomologous end-joining (NHEJ) and to suppress homology-directed repair...... (HDR). Here, we show that silencing 53BP1 or exhausting its capacity to bind damaged chromatin changes limited DSB resection to hyper-resection and results in a switch from error-free gene conversion by RAD51 to mutagenic single-strand annealing by RAD52. Thus, rather than suppressing HDR, 53BP1...

  10. The response of the brain tissue to DNA double strand breaks

    International Nuclear Information System (INIS)

    Double-strand breaks (DSB) are the most deleterious form of DNA damage after ionizing radiation, the response of the brain tissue to DNA damage is related to the developmental dynamics of this system. Homology recombination is particularly important for proliferating cells, while non-homologous end joining is critical for differentiating cells. Defects in the related factors to DNA damage pathway underpin many human genopathy with neuropathology. Reviewed the signal conduction system involved in the DNA DSB response and human neuropathology genopathy related to DNA DSB factors deficiencies in the brain cells. (authors)

  11. Improved Gene Targeting through Cell Cycle Synchronization.

    Directory of Open Access Journals (Sweden)

    Vasiliki Tsakraklides

    Full Text Available Gene targeting is a challenge in organisms where non-homologous end-joining is the predominant form of recombination. We show that cell division cycle synchronization can be applied to significantly increase the rate of homologous recombination during transformation. Using hydroxyurea-mediated cell cycle arrest, we obtained improved gene targeting rates in Yarrowia lipolytica, Arxula adeninivorans, Saccharomyces cerevisiae, Kluyveromyces lactis and Pichia pastoris demonstrating the broad applicability of the method. Hydroxyurea treatment enriches for S-phase cells that are active in homologous recombination and enables previously unattainable genomic modifications.

  12. The role of DNA dependent protein kinase in synapsis of DNA ends

    OpenAIRE

    Weterings, Eric; Verkaik, Nicole; Brüggenwirth, Hennie; Gent, Dik; Hoeijmakers, Jan

    2010-01-01

    textabstractDNA dependent protein kinase (DNA-PK) plays a central role in the non-homologous end-joining pathway of DNA double strand break repair. Its catalytic subunit (DNA-PK(CS)) functions as a serine/threonine protein kinase. We show that DNA-PK forms a stable complex at DNA termini that blocks the action of exonucleases and ligases. The DNA termini become accessible after autophosphorylation of DNA-PK(CS), which we demonstrate to require synapsis of DNA ends. Interestingly, the presence...

  13. Displacement of DNA-PKcs from DNA ends by the Werner syndrome protein

    OpenAIRE

    Li, Baomin; Comai, Lucio

    2002-01-01

    The DNA-dependent protein kinase (DNA-PK) complex, which is composed of a DNA-dependent kinase subunit (DNA-PKcs) and the Ku70/80 heterodimer, is involved in DNA double-strand break repair by non-homologous end joining (NHEJ). Ku70/80 interacts with the Werner syndrome protein (WRN) and stimulates WRN exonuclease activity. To investigate a possible function of WRN in NHEJ, we have examined the relationship between DNA-PKcs, Ku and WRN. First, we showed that WRN forms a complex with DNA-PKcs a...

  14. Recognition of DNA Termini by the C-Terminal Region of the Ku80 and the DNA-Dependent Protein Kinase Catalytic Subunit

    OpenAIRE

    Woods, Derek S.; Catherine R Sears; Turchi, John J.

    2015-01-01

    DNA double strand breaks (DSBs) can be generated by endogenous cellular processes or exogenous agents in mammalian cells. These breaks are highly variable with respect to DNA sequence and structure and all are recognized in some context by the DNA-dependent protein kinase (DNA-PK). DNA-PK is a critical component necessary for the recognition and repair of DSBs via non-homologous end joining (NHEJ). Previously studies have shown that DNA-PK responds differentially to variations in DSB structur...

  15. Dynamic changes in subcellular localization of cattle XLF during cell cycle, and focus formation of cattle XLF at DNA damage sites immediately after irradiation

    OpenAIRE

    Koike, Manabu; Yutoku, Yasutomo; KOIKE, Aki

    2015-01-01

    Clinically, many chemotherapeutics and ionizing radiation (IR) have been applied for the treatment of various types of human and animal malignancies. These treatments kill tumor cells by causing DNA double-strand breaks (DSBs). Core factors of classical nonhomologous DNA-end joining (C-NHEJ) play a vital role in DSB repair. Thus, it is indispensable to clarify the mechanisms of C-NHEJ in order to develop next-generation chemotherapeutics for cancer. The XRCC4-like factor (XLF; also called Cer...

  16. DNA double strand break repair pathway choice following ionizing radiation

    International Nuclear Information System (INIS)

    A DNA double strand break (DSB) is one of the critical DNA lesions leading to cell death if unrepaired. DSB is repaired by two distinct repair pathways, i.e. non-homologous end-joining (NHEJ) or homologous recombination (HR). NHEJ contributes to DSB repair throughout the cell cycle, while HR is active during S/G2 phase following DNA replication. We aim to elucidate the molecular mechanisms underlying DSB repair pathway choice at two ended DSBs in G2 phase following ionizing radiation (IR). Here, we discuss recent work that provides new insights into DSB repair pathways choice including our study. (author)

  17. XLS (c9orf142) is a new component of mammalian DNA double-stranded break repair

    OpenAIRE

    Craxton, A; J. Somers; Munnur, D; Jukes-Jones, R; Cain, K.; Malewicz, M

    2015-01-01

    Repair of double-stranded DNA breaks (DSBs) in mammalian cells primarily occurs by the non-homologous end-joining (NHEJ) pathway, which requires seven core proteins (Ku70/Ku86, DNA-PKcs (DNA-dependent protein kinase catalytic subunit), Artemis, XRCC4-like factor (XLF), XRCC4 and DNA ligase IV). Here we show using combined affinity purification and mass spectrometry that DNA-PKcs co-purifies with all known core NHEJ factors. Furthermore, we have identified a novel evolutionary conserved protei...

  18. Whether Contexts Affecting TESOL Teachers

    Institute of Scientific and Technical Information of China (English)

    马炳军; 杨晓丽

    2013-01-01

    This article aims to verify whether contextual theories affect TESOL teachers in Chinese local classrooms via observing three different English teachers’classroom behaviors by using qualitative method. The findings indicate that three major aspects usually affect English teachers:(1) The teacher’s education context affects their TESOL classroom contexts;(2) The institution’s requirements affect the teacher’s classroom contexts; (3) The spirit of quality-oriented education from the New National Stan-dards for English influences the classroom contexts, which have proved the context theories.

  19. Human Technology and Human Affects

    DEFF Research Database (Denmark)

    Fausing, Bent

    2009-01-01

    Human Technology and Human Affects  This year Samsung introduced a mobile phone with "Soul". It was made with a human touch and included itself a magical touch. Which function does technology and affects get in everyday aesthetics like this, its images and interactions included this presentation....... The paper will investigate how technology, humanity, affects, and synaesthesia are presented and combined with examples from everyday aesthetics, e.g. early computer tv-commercial, net-commercial for mobile phones. Technology and affects point, is the conclusion, towards a forgotten pre-human and not he...

  20. Affective modulation of recognition bias

    NARCIS (Netherlands)

    R.H. Phaf; M. Rotteveel

    2005-01-01

    A correspondence of processing on the familiarity-novelty and positive-negative dimensions, particularly in the earliest processing stages, is proposed. Familiarity manipulations should, therefore, not only influence affective evaluations (e.g., the mere exposure effect), but affective manipulations

  1. Affect intensity and cardiac arousal.

    Science.gov (United States)

    Blascovich, J; Brennan, K; Tomaka, J; Kelsey, R M; Hughes, P; Coad, M L; Adlin, R

    1992-07-01

    Relationships between affect intensity and basal, evoked, and perceived cardiac arousal were investigated in 3 experiments. Affect intensity was assessed using Larsen and Diener's (1987) Affect Intensity Measure (AIM). Cardiac arousal was evoked with exercise in the 1st study and with mental arithmetic in the 2nd and 3rd. Perceived cardiac arousal was measured under optimal conditions using a standard heartbeat discrimination procedure. Women as a group scored higher on the AIM. Affect intensity was unrelated to basal or evoked cardiac arousal and was negatively related to perceived cardiac arousal in all 3 studies. Data suggest that affect intensity, although unrelated to actual physiological arousal, is negatively related to the accuracy with which individuals perceive their own arousal. Results are discussed within the context of an expanded arousal-regulation model (Blascovich, 1990). PMID:1494983

  2. Affective Computing and Intelligent Interaction

    CERN Document Server

    2012-01-01

    2012 International Conference on Affective Computing and Intelligent Interaction (ICACII 2012) was the most comprehensive conference focused on the various aspects of advances in Affective Computing and Intelligent Interaction. The conference provided a rare opportunity to bring together worldwide academic researchers and practitioners for exchanging the latest developments and applications in this field such as Intelligent Computing, Affective Computing, Machine Learning, Business Intelligence and HCI.   This volume is a collection of 119 papers selected from 410 submissions from universities and industries all over the world, based on their quality and relevancy to the conference. All of the papers have been peer-reviewed by selected experts.  

  3. The affective turn in ethnomusicology

    Directory of Open Access Journals (Sweden)

    Hofman Ana

    2015-01-01

    Full Text Available The affective turn, which has already questioned dominant paradigms in many disciplinary fields including cultural studies, philosophy, political theory, anthropology, psychology and neuroscience, has started to attract more attention in the field of ethnomusicology, becoming a particularly vibrant stream of thought. Drawing on the voices that call for the historicisation of and critical deliberation on the field of affect studies, the article strives to show how theories of affect might expand dominant paradigms in ethnomusicology and also points to their limitations.

  4. A PHF8 homolog in C. elegans promotes DNA repair via homologous recombination.

    Directory of Open Access Journals (Sweden)

    Changrim Lee

    Full Text Available PHF8 is a JmjC domain-containing histone demethylase, defects in which are associated with X-linked mental retardation. In this study, we examined the roles of two PHF8 homologs, JMJD-1.1 and JMJD-1.2, in the model organism C. elegans in response to DNA damage. A deletion mutation in either of the genes led to hypersensitivity to interstrand DNA crosslinks (ICLs, while only mutation of jmjd-1.1 resulted in hypersensitivity to double-strand DNA breaks (DSBs. In response to ICLs, JMJD-1.1 did not affect the focus formation of FCD-2, a homolog of FANCD2, a key protein in the Fanconi anemia pathway. However, the dynamic behavior of RPA-1 and RAD-51 was affected by the mutation: the accumulations of both proteins at ICLs appeared normal, but their subsequent disappearance was retarded, suggesting that later steps of homologous recombination were defective. Similar changes in the dynamic behavior of RPA-1 and RAD-51 were seen in response to DSBs, supporting a role of JMJD-1.1 in homologous recombination. Such a role was also supported by our finding that the hypersensitivity of jmjd-1.1 worms to ICLs was rescued by knockdown of lig-4, a homolog of Ligase 4 active in nonhomologous end-joining. The hypersensitivity of jmjd-1.1 worms to ICLs was increased by rad-54 knockdown, suggesting that JMJD-1.1 acts in parallel with RAD-54 in modulating chromatin structure. Indeed, the level of histone H3 Lys9 tri-methylation, a marker of heterochromatin, was higher in jmjd-1.1 cells than in wild-type cells. We conclude that the histone demethylase JMJD-1.1 influences homologous recombination either by relaxing heterochromatin structure or by indirectly regulating the expression of multiple genes affecting DNA repair.

  5. Stress factors in affective diseases.

    Science.gov (United States)

    Bidzińska, E J

    1984-02-01

    An investigation carried out on 97 patients with affective disorders and on 100 healthy control subjects, revealed that acute and chronic stress factors occurred more in the group of patients with affective disorders than among healthy control over a similar time period. The frequency of stressful life situations was the same before the first affective episode in patients with unipolar and bipolar illness. The possible participation of such factors in triggering the first phase of illness is discussed. Similar factors appeared in both types of affective disorders. Significantly more frequent among patients than in the control group were: marital and family conflicts, health problems, emotional and ambitional failures, lack of success and work overload.

  6. Categorization in the Affective Domain

    DEFF Research Database (Denmark)

    Sauciuc, Gabriela-Alina

    2011-01-01

    Data collected in Romance and Scandinavian languages (N=474) in a superordinate category name production task indicate that a multiple-strategy approach would be more suitable for accounting of categorization in the affective domain instead of a prototype approach as suggested by previous studies....... This paper will highlight performance aspects which appear to be consistent with such an interpretation, as well as an important layman- expert knowledge asymmetry in affective categorization....

  7. Staging of unipolar affective illness

    Directory of Open Access Journals (Sweden)

    Ewa Ferensztajn

    2014-12-01

    Full Text Available In this article, a concept of staging of unipolar affective illness (recurrent depression is presented. In respective subchapters, three most important aspects of this issue have been discussed: 1 staging of unipolar affective illness; 2 staging of treatment-resistant depression; and 3 conversion of unipolar into bipolar affective illness. The evidence for so called neuroprogression of the illness, accumulated in recent years, has allowed for a classification of staging based on a concept of allostasis and allostatic load. In the course of illness, changes in neuroendocrine system (mainly hypothalamic pituitary-adrenal (HPA axis, immunological system, mechanisms of oxidative stress, neurotransmitters, neurotrophic factors as well as structural and functional changes of the brain occur. In their paper of 2007, Fava and Tossani elaborated a concept of staging of unipolar affective illness presenting a continuum model of five consecutive stages with specific clinical features. In the present paper, a concept of treatment-resistant depression and staging of treatment resistance is presented in the context of several models. An important determinant of treatment-resistant depression is so called subthreshold bipolarity which is connected with worse efficacy of antidepressant drugs. In the course of illness, there is a possibility of changing diagnosis from recurrent depression into bipolar affective illness. The studies on this issue show that frequency of such diagnostic conversion is 1,5% of depressed patients per year.

  8. Family Intimacy and Affection: A Sociology of Positive Affect.

    Science.gov (United States)

    Martinson, Floyd M.

    This paper deals with aspects of positive family affect in intimate family relationships such as: (1) the nuclear family of orientation, including the child-parent subgroup and the sibling subgroup; (2) the nuclear family of procreation, including the marital subgroup and parent-child subgroup; and (3) the dating relationship. Interpersonal…

  9. Behavioral Management: An Affective Approach. (Affective Education Trainers Manual).

    Science.gov (United States)

    Heilman, John; Cole, Bob

    This manual provides a framework for training teachers who want to become more skilled in affective education. It is divided into three parts: teacher self-awareness, teacher-student interaction, and teacher-directed group activities. It is designed for use in a two-day workshop. Guidelines for discussions on expectations, responsibility,…

  10. Trends affecting hospitals' human resources.

    Science.gov (United States)

    Neudeck, M M

    1985-01-01

    Hospital workers at every level--from administrators to housekeepers--will be affected by the interaction of changes already underway in the healthcare industry. Societal forces that will affect the hospital workforce include demographic change, the rise of the participatory ethic and decentralization, a growing philosophy of job entitlement, and new pressures for unionization. At the same time, the industry is faced with changing manpower requirements, cost containment, and the oversupply of physicians. This article identifies some of the likely effects of these changes on hospital human resources and suggests ways that administrators can prepare for them.

  11. On Factors Affecting Listening Comprehension

    Institute of Scientific and Technical Information of China (English)

    苗琴

    2014-01-01

    In English teaching and learning, listening ability is an important part of communicative competence, is a very practical integrated skill. It has been a difficult skill in second language acquisition for many students. Many Chinese students are skilled in reading, but often they tend to neglect the listening. However, owing to the higher requirements of many English tests and the great importance in communication, students begin to pay attention to develop their English listening skills. But there are many factors affecting listening, the paper mainly focuses on linguistic factors and non-linguistic factors that affect listening, to provide a theoretical basis to help exploring ways of improving listening and comprehension skills.

  12. Affect, Emotion and Similar Concepts

    Directory of Open Access Journals (Sweden)

    J.L. Pio Abreu

    2013-12-01

    Full Text Available The author begins by commenting on the difficulty of the semantic delimitation between concepts of affect, emotion, sentiment, feeling, mood, and passion. This difficulty becomes greater when the terms are translated into different languages. He then foccuses on the concept of emotion, which has benefited from recent research, and its distinction from mood, a concept which is at the base of the psychopathology of bipolar disorders. Much more complex is the Portuguese concept of affect (different from the English concept, which has an interpersonal dimension and can be developed from recent discoveries of “mirror neurons” and “theory of mind”.

  13. Industrial applications of affective engineering

    CERN Document Server

    Shiizuka, Hisao; Lee, Kun-Pyo; Otani, Tsuyoshi; Lim, Chee-Peng

    2014-01-01

    This book examines the industrial applications of affective engineering. The contributors cover new analytical methods such as fluctuation, fuzzy logic, fractals, and complex systems. These chapters also include interdisciplinary research that traverses a wide range of fields, including information engineering, human engineering, cognitive science, psychology, and design studies. The text is split into two parts: theory and applications. This work is a collection of the best papers from ISAE2013 (International Symposium of Affective Engineering) held at Kitakyushu, Japan and Japan Kansei Engineering Meeting on March 6-8, 2013.

  14. Affective Computing and Sentiment Analysis

    CERN Document Server

    Ahmad, Khurshid

    2011-01-01

    This volume maps the watershed areas between two 'holy grails' of computer science: the identification and interpretation of affect -- including sentiment and mood. The expression of sentiment and mood involves the use of metaphors, especially in emotive situations. Affect computing is rooted in hermeneutics, philosophy, political science and sociology, and is now a key area of research in computer science. The 24/7 news sites and blogs facilitate the expression and shaping of opinion locally and globally. Sentiment analysis, based on text and data mining, is being used in the looking at news

  15. Come, see and experience affective interactive art

    NARCIS (Netherlands)

    Bialoskorski, Leticia S.S.; Westerink, Joyce H.D.M.; Broek, van den Egon L.; Nijholt, Anton; Reidsma, Dennis; Hondorp, Hendri

    2009-01-01

    The progress in the field of affective computing enables the realization of affective consumer products, affective games, and affective art. This paper describes the affective interactive art system Mood Swings, which interprets and visualizes affect expressed by a person. Mood Swings is founded on

  16. Mood Swings: An Affective Interactive Art System

    NARCIS (Netherlands)

    Bialoskorski, Leticia S.S.; Westerink, Joyce H.D.M.; Broek, van den Egon L.; Nijholt, Anton; Reidsma, Dennis; Hondorp, Hendri

    2009-01-01

    The progress in the field of affective computing enables the realization of affective consumer products, affective games, and affective art. This paper describes the affective interactive art system Mood Swings, which interprets and visualizes affect expressed by a person. Mood Swings is founded on

  17. Come, See and Experience Affective Interactive Art

    NARCIS (Netherlands)

    Bialoskorski, Leticia S.S.; Westerink, Joyce H.D.M.; Broek, van den Egon L.; Nijholt, A.; Reidsma, D.; Hondorp, G.H.W.

    2009-01-01

    The progress in the field of affective computing enables the realization of affective consumer products, affective games, and affective art. This paper describes the affective interactive art system Mood Swings, which interprets and visualizes affect expressed by a person. Mood Swings is founded on

  18. Xeroderma pigmentosum, complementation group D expression in H1299 lung cancer cells following benzo[a]pyrene exposure as well as in head and neck cancer patients.

    Science.gov (United States)

    Lin, Chang-Shen; Chiou, Wen-Yen; Lee, Ka-Wo; Chen, Tzu-Fen; Lin, Yuan-Jen; Huang, Jau-Ling

    2016-01-01

    DNA repair genes play critical roles in response to carcinogen-induced and anticancer therapy-induced DNA damage. Benzo[a]pyrene (BaP), the most carcinogenic polycyclic aromatic hydrocarbon (PAH), is classified as a group 1 carcinogen by International Agency for Research on Cancer. The aims of this study were to (1) evaluate the effects of BaP on DNA repair activity and expression of DNA repair genes in vitro and (2) examine the role of xeroderma pigmentosum, complementation group D (XPD) mRNA expression in human head and neck cancers. Host cell reactivation assay showed that BaP inhibited nucleotide excision repair in H1299 lung cancer cells. DNA repair through the non-homologous end-joining pathway was not affected by BaP. Real-time quantitative reverse-transcription polymerase chain reaction (RT-PCR) and Western blot demonstrated that XPD was downregulated by BaP treatment. BaP exposure did not apparently affect expression of another 11 DNA repair genes. BaP treatment increased the DNA damage marker γ-H2AX and ultraviolet (UV) sensitivity, supporting an impairment of DNA repair in BaP-treated cells. XPD expression was also examined by quantitative RT-PCR in 68 head and neck cancers, and a lower XPD mRNA level was found in smokers' cancer specimens. Importantly, reduced XPD expression was correlated with patient 5-year overall survival rate (35 vs. 56%) and was an independent prognostic factor (hazard ratio: 2.27). Data demonstrated that XPD downregulation was correlated with BaP exposure and human head and neck cancer survival. PMID:26731659

  19. Double-strand break repair and colorectal cancer: gene variants within 3′ UTRs and microRNAs binding as modulators of cancer risk and clinical outcome

    Science.gov (United States)

    Naccarati, Alessio; Rosa, Fabio; Vymetalkova, Veronika; Barone, Elisa; Jiraskova, Katerina; Di Gaetano, Cornelia; Novotny, Jan; Levy, Miroslav; Vodickova, Ludmila; Gemignani, Federica; Buchler, Tomas; Landi, Stefano

    2016-01-01

    Genetic variations in 3′ untranslated regions of target genes may affect microRNA binding, resulting in differential protein expression. microRNAs regulate DNA repair, and single-nucleotide polymorphisms in miRNA binding sites (miRSNPs) may account for interindividual differences in the DNA repair capacity. Our hypothesis is that miRSNPs in relevant DNA repair genes may ultimately affect cancer susceptibility and impact prognosis. In the present study, we analysed the association of polymorphisms in predicted microRNA target sites of double-strand breaks (DSBs) repair genes with colorectal cancer (CRC) risk and clinical outcome. Twenty-one miRSNPs in non-homologous end-joining and homologous recombination pathways were assessed in 1111 cases and 1469 controls. The variant CC genotype of rs2155209 in MRE11A was strongly associated with decreased cancer risk when compared with the other genotypes (OR 0.54, 95% CI 0.38–0.76, p = 0.0004). A reduced expression of the reporter gene was observed for the C allele of this polymorphism by in vitro assay, suggesting a more efficient interaction with potentially binding miRNAs. In colon cancer patients, the rs2155209 CC genotype was associated with shorter survival while the TT genotype of RAD52 rs11226 with longer survival when both compared with their respective more frequent genotypes (HR 1.63, 95% CI 1.06-2.51, p = 0.03 HR 0.60, 95% CI 0.41–0.89, p = 0.01, respectively). miRSNPs in DSB repair genes involved in the maintenance of genomic stability may have a role on CRC susceptibility and clinical outcome. PMID:26735576

  20. On the Primacy of Affect.

    Science.gov (United States)

    Zajonc, R. B.

    1984-01-01

    Reasserts view that there can be emotional or affective arousal without prior cognitive appraisal. Criticizes Lazarus's rejection of this view on the grounds that it presents no empirical evidence, is based on an arbitrary definition of emotion, and obliterates all distinctions between cognition, sensation, and perception. (CMG)

  1. A warm touch of affect?

    NARCIS (Netherlands)

    Willemse, Christian J.A.M.

    2015-01-01

    One of the research areas within affective Computer Mediated Communication currently under investigation is that of mediated social touch. A social touch is a complex composition of different physical parameters that can be simulated by haptic technologies. In this article we argue why we think it m

  2. Do recruitment ties affect wages?

    DEFF Research Database (Denmark)

    Larsen, Anna Folke; Rand, John; Torm, Nina Elisabeth

    This paper examines the extent to which recruitment ties affect individual wage outcomes in small and medium scale manufacturing firms. Based on a unique matched employer-employee dataset from Vietnam we find that there is a significant positive wage premium associated with obtaining a job through...

  3. Urban Interaction and Affective Experience

    DEFF Research Database (Denmark)

    Fritsch, Jonas; Brynskov, Martin

    2008-01-01

    in favor of three points in that direction: First we argue that interaction – and the definition of interaction – is central to unfold the potential of digital urban media, from big, shared screens and media facades to small pri-vate, networked mobile and embedded platforms. Then we argue that an affective...

  4. Clinical Judgment and Affective Disorders.

    Science.gov (United States)

    Strohmer, Douglas C.; And Others

    1984-01-01

    Addressed the limitations of previous work on counselor clinical judgment in a study involving 20 counselors who were asked to make a series of judgments. Results suggested the judgment processes of experienced counselors making diagnoses of affective disorders differs depending on the type of judgment. (JAC)

  5. Aesthetics, Affect, and Educational Politics

    Science.gov (United States)

    Means, Alex

    2011-01-01

    This essay explores aesthetics, affect, and educational politics through the thought of Gilles Deleuze and Jacques Ranciere. It contextualizes and contrasts the theoretical valences of their ethical and democratic projects through their shared critique of Kant. It then puts Ranciere's notion of dissensus to work by exploring it in relation to a…

  6. Unconscious Affective Responses to Food

    Science.gov (United States)

    Sato, Wataru; Sawada, Reiko; Kubota, Yasutaka; Toichi, Motomi; Fushiki, Tohru

    2016-01-01

    Affective or hedonic responses to food are crucial for humans, both advantageously (e.g., enhancing survival) and disadvantageously (e.g., promoting overeating and lifestyle-related disease). Although previous psychological studies have reported evidence of unconscious cognitive and behavioral processing related to food, it remains unknown whether affective reactions to food can be triggered unconsciously and its relationship with daily eating behaviors. We investigated these issues by using the subliminal affective priming paradigm. Photographs of food or corresponding mosaic images were presented in the peripheral visual field for 33 ms. Target photos of faces with emotionally neutral expressions were then presented, and participants rated their preferences for the faces. Eating behaviors were also assessed using questionnaires. The food images, relative to the mosaics, increased participants’ preference for subsequent target faces. Furthermore, the difference in the preference induced by food versus mosaic images was positively correlated with the tendency to engage in external eating. These results suggest that unconscious affective reactions are elicited by the sight of food and that these responses contribute to daily eating behaviors related to overeating. PMID:27501443

  7. Affective Development in University Education

    Science.gov (United States)

    Grootenboer, Peter

    2010-01-01

    There seems to be an increasing requirement for university courses and programs to develop students' affective qualities (beliefs, values, dispositions and attitudes). This study explored the ways academics determined what the desirable qualities were for their particular disciplines and the pedagogical strategies and approaches they used to…

  8. Double-strand break repair-adox: Restoration of suppressed double-strand break repair during mitosis induces genomic instability.

    Science.gov (United States)

    Terasawa, Masahiro; Shinohara, Akira; Shinohara, Miki

    2014-12-01

    Double-strand breaks (DSBs) are one of the severest types of DNA damage. Unrepaired DSBs easily induce cell death and chromosome aberrations. To maintain genomic stability, cells have checkpoint and DSB repair systems to respond to DNA damage throughout most of the cell cycle. The failure of this process often results in apoptosis or genomic instability, such as aneuploidy, deletion, or translocation. Therefore, DSB repair is essential for maintenance of genomic stability. During mitosis, however, cells seem to suppress the DNA damage response and proceed to the next G1 phase, even if there are unrepaired DSBs. The biological significance of this suppression is not known. In this review, we summarize recent studies of mitotic DSB repair and discuss the mechanisms of suppression of DSB repair during mitosis. DSB repair, which maintains genomic integrity in other phases of the cell cycle, is rather toxic to cells during mitosis, often resulting in chromosome missegregation and aberration. Cells have multiple safeguards to prevent genomic instability during mitosis: inhibition of 53BP1 or BRCA1 localization to DSB sites, which is important to promote non-homologous end joining or homologous recombination, respectively, and also modulation of the non-homologous end joining core complex to inhibit DSB repair. We discuss how DSBs during mitosis are toxic and the multiple safeguard systems that suppress genomic instability.

  9. Distinct roles of Ape1 protein, an enzyme involved in DNA repair, in high or low linear energy transfer ionizing radiation-induced cell killing.

    Science.gov (United States)

    Wang, Hongyan; Wang, Xiang; Chen, Guangnan; Zhang, Xiangming; Tang, Xiaobing; Park, Dongkyoo; Cucinotta, Francis A; Yu, David S; Deng, Xingming; Dynan, William S; Doetsch, Paul W; Wang, Ya

    2014-10-31

    High linear energy transfer (LET) radiation from space heavy charged particles or a heavier ion radiotherapy machine kills more cells than low LET radiation, mainly because high LET radiation-induced DNA damage is more difficult to repair. Relative biological effectiveness (RBE) is the ratio of the effects generated by high LET radiation to low LET radiation. Previously, our group and others demonstrated that the cell-killing RBE is involved in the interference of high LET radiation with non-homologous end joining but not homologous recombination repair. This effect is attributable, in part, to the small DNA fragments (≤40 bp) directly produced by high LET radiation, the size of which prevents Ku protein from efficiently binding to the two ends of one fragment at the same time, thereby reducing non-homologous end joining efficiency. Here we demonstrate that Ape1, an enzyme required for processing apurinic/apyrimidinic (known as abasic) sites, is also involved in the generation of small DNA fragments during the repair of high LET radiation-induced base damage, which contributes to the higher RBE of high LET radiation-induced cell killing. This discovery opens a new direction to develop approaches for either protecting astronauts from exposure to space radiation or benefiting cancer patients by sensitizing tumor cells to high LET radiotherapy. PMID:25210033

  10. DNA-dependent protein kinase inhibits AID-induced antibody gene conversion.

    Directory of Open Access Journals (Sweden)

    Adam J L Cook

    2007-04-01

    Full Text Available Affinity maturation and class switching of antibodies requires activation-induced cytidine deaminase (AID-dependent hypermutation of Ig V(DJ rearrangements and Ig S regions, respectively, in activated B cells. AID deaminates deoxycytidine bases in Ig genes, converting them into deoxyuridines. In V(DJ regions, subsequent excision of the deaminated bases by uracil-DNA glycosylase, or by mismatch repair, leads to further point mutation or gene conversion, depending on the species. In Ig S regions, nicking at the abasic sites produced by AID and uracil-DNA glycosylases results in staggered double-strand breaks, whose repair by nonhomologous end joining mediates Ig class switching. We have tested whether nonhomologous end joining also plays a role in V(DJ hypermutation using chicken DT40 cells deficient for Ku70 or the DNA-dependent protein kinase catalytic subunit (DNA-PKcs. Inactivation of the Ku70 or DNA-PKcs genes in DT40 cells elevated the rate of AID-induced gene conversion as much as 5-fold. Furthermore, DNA-PKcs-deficiency appeared to reduce point mutation. The data provide strong evidence that double-strand DNA ends capable of recruiting the DNA-dependent protein kinase complex are important intermediates in Ig V gene conversion.

  11. Zinc finger nucleases and their application%锌指核酶技术的原理及应用

    Institute of Scientific and Technical Information of China (English)

    邓珊珊; 王颖芝; 马端

    2010-01-01

    锌指核酶(zinc finger nucleases,ZFNs)是将锌指蛋白的DNA识别域和非特异性核酸内切酶FokⅠ人工连接而构成的一种核酶.1对ZFNs能在DNA上产生双链断裂(double-strand breaks,DSB),诱导细胞发生同源重组(homology recombination,HR)或非同源末端连接(nonhomologous end joining,NHEJ).最近锌指核酶技术在基因功能的研究中受到重视.作者就ZFNs的作用原理、关键技术及其应用领域进行介绍.%Zinc finger nuclease (ZFN), which is a chimeric fusion structure between a Cys2-His2 zinc-finger protein (ZFP) and the cleavage domain of Fok Ⅰ endonuclease,can be used to introduce targeted double-stranded breaks (DSBs). ZFN-mediated cleavage leads to mutations when double-stranded breaks are repaired by homologous recombination (HR) or nonhomologous end joining (NHEJ). In recent years, ZFNs are widely used in the fields of genetic research. In this review, the methodology and technical advantages of ZFNs were briefly discussed.

  12. Food aroma affects bite size

    Directory of Open Access Journals (Sweden)

    de Wijk René A

    2012-03-01

    Full Text Available Abstract Background To evaluate the effect of food aroma on bite size, a semisolid vanilla custard dessert was delivered repeatedly into the mouth of test subjects using a pump while various concentrations of cream aroma were presented retronasally to the nose. Termination of the pump, which determined bite size, was controlled by the subject via a push button. Over 30 trials with 10 subjects, the custard was presented randomly either without an aroma, or with aromas presented below or near the detection threshold. Results Results for ten subjects (four females and six males, aged between 26 and 50 years, indicated that aroma intensity affected the size of the corresponding bite as well as that of subsequent bites. Higher aroma intensities resulted in significantly smaller sizes. Conclusions These results suggest that bite size control during eating is a highly dynamic process affected by the sensations experienced during the current and previous bites.

  13. Salience-Affected Neural Networks

    CERN Document Server

    Remmelzwaal, Leendert A; Ellis, George F R

    2010-01-01

    We present a simple neural network model which combines a locally-connected feedforward structure, as is traditionally used to model inter-neuron connectivity, with a layer of undifferentiated connections which model the diffuse projections from the human limbic system to the cortex. This new layer makes it possible to model global effects such as salience, at the same time as the local network processes task-specific or local information. This simple combination network displays interactions between salience and regular processing which correspond to known effects in the developing brain, such as enhanced learning as a result of heightened affect. The cortex biases neuronal responses to affect both learning and memory, through the use of diffuse projections from the limbic system to the cortex. Standard ANNs do not model this non-local flow of information represented by the ascending systems, which are a significant feature of the structure of the brain, and although they do allow associational learning with...

  14. Psychological factors affecting equine performance

    Directory of Open Access Journals (Sweden)

    McBride Sebastian D

    2012-09-01

    Full Text Available Abstract For optimal individual performance within any equestrian discipline horses must be in peak physical condition and have the correct psychological state. This review discusses the psychological factors that affect the performance of the horse and, in turn, identifies areas within the competition horse industry where current behavioral research and established behavioral modification techniques could be applied to further enhance the performance of animals. In particular, the role of affective processes underpinning temperament, mood and emotional reaction in determining discipline-specific performance is discussed. A comparison is then made between the training and the competition environment and the review completes with a discussion on how behavioral modification techniques and general husbandry can be used advantageously from a performance perspective.

  15. Global Media, Biopolitics and Affect

    DEFF Research Database (Denmark)

    Knudsen, Britta Timm; Stage, Carsten

    Global Media, Biopolitics and Affect shows how mediations of bodily vulnerability have become a strong political force in contemporary societies. In discussions and struggles concerning war involvement, healthcare issues, charity, democracy movements, contested national pasts, and climate change......, performances of bodily vulnerability is increasingly used by citizens to raise awareness, create sympathy, encourage political action, and to circulate information in global media networks. The book thus argues that bodily vulnerability can serve as a catalyst for affectively charging and disseminating...... particular political events or issues by means of media. To investigate how, when and why that happens, and to evaluate the long-term social impacts of mediating bodily vulnerability, the book offers a theoretical framework for understanding the role of bodily vulnerability in contemporary digital media...

  16. Factors affecting forage stand establishment

    OpenAIRE

    Sulc R.M.

    1998-01-01

    Significant advances have been made in our knowledge of forage seed physiology, technology, and stand establishment practices; however, stand establishment continues to be one of the most common production problems affecting forage crops in the USA. There is a need for research on stand establishment of forage crops under abiotic and biotic stress. Although the forage seed industry produces and markets seed of high quality, new methods of assessing seed vigor are needed and their use should b...

  17. Pseudobulbar affect: prevalence and management

    OpenAIRE

    Ahmed A; Simmons Z

    2013-01-01

    Aiesha Ahmed, Zachary SimmonsDepartment of Neurology, Penn State Hershey Medical Center, Hershey, PA, USAAbstract: Pseudobulbar affect (PBA) may occur in association with a variety of neurological diseases, and so may be encountered in the setting of amyotrophic lateral sclerosis, extrapyramidal and cerebellar disorders, multiple sclerosis, traumatic brain injury, Alzheimer's disease, stroke, and brain tumors. The psychological consequences and the impact on social interactions may be...

  18. Trade Finance Affects Trade Dynamics

    OpenAIRE

    ARESPA CASTELLÓ, Marta; Gruber, Diego

    2016-01-01

    Existent literature is by no means conclusive on the effects of trade finance on trade and the economy. We propose a suitable framework to explore the linkages between international trade and finance based on an international real business cycle model where firms require external finance to import and can be financially constrained. We find that credit shocks do affect the dynamic properties of the economy and they have the potential to cause significant deviations in trade and economic perfo...

  19. The Affections of My Life

    Institute of Scientific and Technical Information of China (English)

    Zhang; Yan; Shi; Xiao; jing

    2013-01-01

    <正>When I look back over the 90 years of my life, through all the tumultuous events, highs and lows, joys and sorrows, I see that one bright, shining emotion has always warmed my heart: affection. The pillar supporting me throughout has been family love: the care of my parents, the love of my wife and children, and the close feelings between myself and my

  20. Environmental issues affecting CCT development

    Energy Technology Data Exchange (ETDEWEB)

    Reidy, M. [U.S. House of Representatives, Washington, DC (United States)

    1997-12-31

    While no final legislative schedule has been set for the new Congress, two issues with strong environmental ramifications which are likely to affect the coal industry seem to top the list of closely watched debates in Washington -- the Environmental Protection Agency`s proposed new ozone and particulate matter standards and utility restructuring. The paper discusses the background of the proposed standards, public comment, the Congressional review of regulations, other legislative options, and utility restructuring.

  1. Internal factors affecting brand performance

    OpenAIRE

    Harris, Fiona J.

    2002-01-01

    In terms of effective branding, several recent trends have indicated the need for greater attention within the organisation than has traditionally been the case. With increased emphasis on corporate branding, the team responsible for managing a brand is becoming larger and more diverse and all staff, as the corporate brand's representatives, affect consumers' perceptions of the corporate brand. Furthermore, the shift in emphasis in the literature from the externally perceived brand image to t...

  2. Towards Learning Affective Body Gesture

    OpenAIRE

    Kleinsmith, Andrea; Bianchi-Berthouze, Nadia

    2003-01-01

    Robots are assuming an increasingly important role in our society. They now become pets and help support children healing. In other words, they are now trying to entertain an active and affective communication with human agents. However, up to now, such systems have primarily relied on the human agents' ability to empathize with the system. Changes in the behavior of the system could therefore reult in changes of mood or behavior in the human partner. This paper describes experiments we carri...

  3. Emotional processing affects movement speed.

    Science.gov (United States)

    Hälbig, Thomas D; Borod, Joan C; Frisina, Pasquale G; Tse, Winona; Voustianiouk, Andrei; Olanow, C Warren; Gracies, Jean-Michel

    2011-09-01

    Emotions can affect various aspects of human behavior. The impact of emotions on behavior is traditionally thought to occur at central, cognitive and motor preparation stages. Using EMG to measure the effects of emotion on movement, we found that emotional stimuli differing in valence and arousal elicited highly specific effects on peripheral movement time. This result has conceptual implications for the emotion-motion link and potentially practical implications for neurorehabilitation and professional environments where fast motor reactions are critical.

  4. Effect of Wortmannin on the repair profiles of DNA double-strand breaks in the whole genome and in interstitial telomeric sequences of Chinese hamster cells

    International Nuclear Information System (INIS)

    The DNA breakage detection-fluorescence in situ hybridization (DBD-FISH) procedure was applied to analyze the effect of Wortmannin (WM) in the rejoining kinetics of ionizing radiation-induced DNA double-strand breaks (DSBs) in the whole genome and in the long interstitial telomeric repeat sequence (ITRS) blocks from Chinese hamster cell lines. The results indicate that the ITRS blocks from wild-type Chinese hamster cell lines, CHO9 and V79B, exhibit a slower initial rejoining rate of ionizing radiation-induced DSBs than the genome overall. Neither Rad51C nor the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) activities, involved in homologous recombination (HR) and in non-homologous end-joining (NHEJ) pathways of DSB repair respectively, influenced the rejoining kinetics within ITRS in contrast to DNA sequences in the whole genome. Nevertheless, DSB removal rate within ITRS was decreased in the absence of Ku86 activity, though at a lower affectation level than in the whole genome, thus homogenizing both rejoining kinetics rates. WM treatment slowed down the DSB rejoining kinetics rate in ITRS, this effect being more pronounced in the whole genome, resulting in a similar pattern to that of the Ku86 deficient cells. In fact, no WM effect was detected in the Ku86 deficient Chinese hamster cells, so probably WM does not add further impairment in DSB rejoining than that resulted as a consequence of absence of Ku activity. The same slowing effect was also observed after treatment of Rad51C and DNA-PKcs defective hamster cells by WM, suggesting that: (1) there is no potentiation of the HR when the NHEJ is impaired by WM, either in the whole genome or in the ITRS, and (2) that this impairment may probably involve more targets than DNA-PKcs. These results suggest that there is an intragenomic heterogeneity in DSB repair, as well as in the effect of WM on this process

  5. Artemisinin–Second Career as Anticancer Drug?

    Directory of Open Access Journals (Sweden)

    Thomas Efferth

    2015-10-01

    Full Text Available Artemisinin represents a showcase example not only for the activity of medicinal herbs deriving from traditional chinese medicine, but for phytotherapy in general. Its isolation from Sweet Wormwood (qinhao, Artemisia annua L. represents the starting point for an unprecedent success story in the treatment of malaria worldwide. Beyond the therapeutic value against Plasmodium parasites, it turned out in recent years that the bioactivity of artemisinin is not restricted to malaria. We and others found that this sesquiterpenoid also exerts profound anticancer activity in vitro and in vivo. Artemisinin-type drugs exert multi-factorial cellular and molecular actions in cancer cells. Ferrous iron reacts with artemisinin, which leads to the formation of reactive oxygen species and ultimately to a plethora anticancer effects of artemisinins, e.g. expression of antioxidant response genes, cell cycle arrest (G1 as well as G2 phase arrests, DNA damage that is repaird by base excision repair, homogous recombination and non-homologous end-joining, as well as different modes of cell death (intrinsic and extrinsic apoptosis, autophagy, necrosis, necroptosis, oncosis, and ferroptosis. Furthermore, artemisinins inhibit neoangiogenesis in tumors. The signaling of major transcription factors (NF-κB, MYC/MAX, AP-1, CREBP, mTOR etc. and signaling pathways are affected by artemisinins (e.g. Wnt/β-catenin pathway, AMPK pathway, metastatic pathways, nitric oxide signaling, and others. Several case reports on the compassionate use of artemisinins as well as clinical Phase I/II pilot studies indicate the clinical activity of artemisinins in veterinary and human cancer patients. Larger scale of Phase II and III clinical studies are required now to further develop artemisinin-type compounds as novel anticancer drugs.

  6. Increased DNA double-strand break was associated with downregulation of repair and upregulation of apoptotic factors in rat hippocampus after alcohol exposure.

    Science.gov (United States)

    Suman, Shubhankar; Kumar, Santosh; N'Gouemo, Prosper; Datta, Kamal

    2016-08-01

    Binge drinking is known to cause damage in critical areas of the brain, including the hippocampus, which is important for relational memory and is reported to be sensitive to alcohol toxicity. However, the roles of DNA double-strand break (DSB) and its repair pathways, homologous recombination (HR), and non-homologous end joining (NHEJ) in alcohol-induced hippocampal injury remain to be elucidated. The purpose of this first study was to assess alcohol-induced DNA DSB and the mechanism by which alcohol affects DSB repair pathways in rat hippocampus. Male Sprague-Dawley rats (8-10 weeks old) were put on a 4-day binge ethanol treatment regimen. Control animals were maintained under similar conditions but were given the vehicle without ethanol. All animals were humanely euthanized 24 h after the last dose of ethanol administration and the hippocampi were dissected for immunoblot and immunohistochemistry analysis. Ethanol exposure caused increased 4-hydroxynonenal (4-HNE) staining as well as elevated γH2AX and 53BP1 foci in hippocampal cells. Immunoblot analysis showed decreased Mre11, Rad51, Rad50, and Ku86 as well as increased Bax and p21 in samples from ethanol-treated rats. Additionally, we also observed increased activated caspase3 staining in hippocampal cells 24 h after ethanol withdrawal. Taken together, our data demonstrated that ethanol concurrently induced DNA DSB, downregulated DSB repair pathway proteins, and increased apoptotic factors in hippocampal cells. We believe these findings will provide the impetus for further research on DNA DSB and its repair pathways in relation to alcohol toxicity in brain. PMID:27565756

  7. Type II Toxoplasma gondii KU80 knockout strains enable functional analysis of genes required for cyst development and latent infection.

    Science.gov (United States)

    Fox, Barbara A; Falla, Alejandra; Rommereim, Leah M; Tomita, Tadakimi; Gigley, Jason P; Mercier, Corinne; Cesbron-Delauw, Marie-France; Weiss, Louis M; Bzik, David J

    2011-09-01

    Type II Toxoplasma gondii KU80 knockouts (Δku80) deficient in nonhomologous end joining were developed to delete the dominant pathway mediating random integration of targeting episomes. Gene targeting frequency in the type II Δku80 Δhxgprt strain measured at the orotate (OPRT) and the uracil (UPRT) phosphoribosyltransferase loci was highly efficient. To assess the potential of the type II Δku80 Δhxgprt strain to examine gene function affecting cyst biology and latent stages of infection, we targeted the deletion of four parasite antigen genes (GRA4, GRA6, ROP7, and tgd057) that encode characterized CD8(+) T cell epitopes that elicit corresponding antigen-specific CD8(+) T cell populations associated with control of infection. Cyst development in these type II mutant strains was not found to be strictly dependent on antigen-specific CD8(+) T cell host responses. In contrast, a significant biological role was revealed for the dense granule proteins GRA4 and GRA6 in cyst development since brain tissue cyst burdens were drastically reduced specifically in mutant strains with GRA4 and/or GRA6 deleted. Complementation of the Δgra4 and Δgra6 mutant strains using a functional allele of the deleted GRA coding region placed under the control of the endogenous UPRT locus was found to significantly restore brain cyst burdens. These results reveal that GRA proteins play a functional role in establishing cyst burdens and latent infection. Collectively, our results suggest that a type II Δku80 Δhxgprt genetic background enables a higher-throughput functional analysis of the parasite genome to reveal fundamental aspects of parasite biology controlling virulence, pathogenesis, and transmission. PMID:21531875

  8. Type II Toxoplasma gondii KU80 Knockout Strains Enable Functional Analysis of Genes Required for Cyst Development and Latent Infection ▿ †

    Science.gov (United States)

    Fox, Barbara A.; Falla, Alejandra; Rommereim, Leah M.; Tomita, Tadakimi; Gigley, Jason P.; Mercier, Corinne; Cesbron-Delauw, Marie-France; Weiss, Louis M.; Bzik, David J.

    2011-01-01

    Type II Toxoplasma gondii KU80 knockouts (Δku80) deficient in nonhomologous end joining were developed to delete the dominant pathway mediating random integration of targeting episomes. Gene targeting frequency in the type II Δku80 Δhxgprt strain measured at the orotate (OPRT) and the uracil (UPRT) phosphoribosyltransferase loci was highly efficient. To assess the potential of the type II Δku80 Δhxgprt strain to examine gene function affecting cyst biology and latent stages of infection, we targeted the deletion of four parasite antigen genes (GRA4, GRA6, ROP7, and tgd057) that encode characterized CD8+ T cell epitopes that elicit corresponding antigen-specific CD8+ T cell populations associated with control of infection. Cyst development in these type II mutant strains was not found to be strictly dependent on antigen-specific CD8+ T cell host responses. In contrast, a significant biological role was revealed for the dense granule proteins GRA4 and GRA6 in cyst development since brain tissue cyst burdens were drastically reduced specifically in mutant strains with GRA4 and/or GRA6 deleted. Complementation of the Δgra4 and Δgra6 mutant strains using a functional allele of the deleted GRA coding region placed under the control of the endogenous UPRT locus was found to significantly restore brain cyst burdens. These results reveal that GRA proteins play a functional role in establishing cyst burdens and latent infection. Collectively, our results suggest that a type II Δku80 Δhxgprt genetic background enables a higher-throughput functional analysis of the parasite genome to reveal fundamental aspects of parasite biology controlling virulence, pathogenesis, and transmission. PMID:21531875

  9. Nontoxic concentration of DNA-PK inhibitor NU7441 radio-sensitizes lung tumor cells with little effect on double strand break repair.

    Science.gov (United States)

    Sunada, Shigeaki; Kanai, Hideki; Lee, Younghyun; Yasuda, Takeshi; Hirakawa, Hirokazu; Liu, Cuihua; Fujimori, Akira; Uesaka, Mitsuru; Okayasu, Ryuichi

    2016-09-01

    High-linear energy transfer (LET) heavy ions have been increasingly employed as a useful alternative to conventional photon radiotherapy. As recent studies suggested that high LET radiation mainly affects the nonhomologous end-joining (NHEJ) pathway of DNA double strand break (DSB) repair, we further investigated this concept by evaluating the combined effect of an NHEJ inhibitor (NU7441) at a non-toxic concentration and carbon ions. NU7441-treated non-small cell lung cancer (NSCLC) A549 and H1299 cells were irradiated with X-rays and carbon ions (290 MeV/n, 50 keV/μm). Cell survival was measured by clonogenic assay. DNA DSB repair, cell cycle distribution, DNA fragmentation and cellular senescence induction were studied using a flow cytometer. Senescence-associated protein p21 was detected by western blotting. In the present study, 0.3 μM of NU7441, nontoxic to both normal and tumor cells, caused a significant radio-sensitization in tumor cells exposed to X-rays and carbon ions. This concentration did not seem to cause inhibition of DNA DSB repair but induced a significant G2/M arrest, which was particularly emphasized in p53-null H1299 cells treated with NU7441 and carbon ions. In addition, the combined treatment induced more DNA fragmentation and a higher degree of senescence in H1299 cells than in A549 cells, indicating that DNA-PK inhibitor contributes to various modes of cell death in a p53-dependent manner. In summary, NSCLC cells irradiated with carbon ions were radio-sensitized by a low concentration of DNA-PK inhibitor NU7441 through a strong G2/M cell cycle arrest. Our findings may contribute to further effective radiotherapy using heavy ions. PMID:27341700

  10. Combining Heavy Ion Radiation and Artificial MicroRNAs to Target the Homologous Recombination Repair Gene Efficiently Kills Human Tumor Cells

    International Nuclear Information System (INIS)

    Purpose: Previously, we demonstrated that heavy ions kill more cells at the same dose than X-rays because DNA-clustered lesions produced by heavy ions affect nonhomologous end-joining (NHEJ) repair but not homologous recombination repair (HRR). We have also shown that our designed artificial microRNAs (amiRs) could efficiently target XRCC4 (an essential factor for NHEJ) or XRCC2 (an essential factor for HRR) and sensitize human tumor cells to X-rays. Based on these data, we were interested in testing the hypothesis that combining heavy ions and amiRs to target HRR but not NHEJ should more efficiently kill human tumor cells. Methods and Materials: Human tumor cell lines (U87MG, a brain tumor cell line, and A549, a lung cancer cell line) and their counterparts, overexpressed with amiR to target XRCC2, XRCC4 or both, were used in this study. Survival sensitivities were examined using a clonogenic assay after these cells were exposed to X-rays or heavy ions. In addition, these cell lines were subcutaneously injected into nude mice to form xenografts and the tumor size was compared after the tumor areas were exposed to X-rays or heavy ions. Results: Although targeting either XRCC4 (NHEJ factor) or XRCC2 (HRR factor) sensitized the human tumor cells to X-rays, in vitro and the xenograft animal model, targeting only XRCC2 but not XRCC4 sensitized the human tumor cells to heavy ions in vitro and in the xenograft animal model. Conclusions: Combining heavy ions with targeting the HRR pathway, but not the NHEJ pathway, could significantly improve the efficiency of tumor cell death.

  11. Linear Energy Transfer-Dependent Change in Rice Gene Expression Profile after Heavy-Ion Beam Irradiation

    Science.gov (United States)

    Ishii, Kotaro; Kazama, Yusuke; Morita, Ryouhei; Hirano, Tomonari; Ikeda, Tokihiro; Usuda, Sachiko; Hayashi, Yoriko; Ohbu, Sumie; Motoyama, Ritsuko; Nagamura, Yoshiaki; Abe, Tomoko

    2016-01-01

    A heavy-ion beam has been recognized as an effective mutagen for plant breeding and applied to the many kinds of crops including rice. In contrast with X-ray or γ-ray, the heavy-ion beam is characterized by a high linear energy transfer (LET). LET is an important factor affecting several aspects of the irradiation effect, e.g. cell survival and mutation frequency, making the heavy-ion beam an effective mutagen. To study the mechanisms behind LET-dependent effects, expression profiling was performed after heavy-ion beam irradiation of imbibed rice seeds. Array-based experiments at three time points (0.5, 1, 2 h after the irradiation) revealed that the number of up- or down-regulated genes was highest 2 h after irradiation. Array-based experiments with four different LETs at 2 h after irradiation identified LET-independent regulated genes that were up/down-regulated regardless of the value of LET; LET–dependent regulated genes, whose expression level increased with the rise of LET value, were also identified. Gene ontology (GO) analysis of LET-independent up-regulated genes showed that some GO terms were commonly enriched, both 2 hours and 3 weeks after irradiation. GO terms enriched in LET-dependent regulated genes implied that some factor regulates genes that have kinase activity or DNA-binding activity in cooperation with the ATM gene. Of the LET-dependent up-regulated genes, OsPARP3 and OsPCNA were identified, which are involved in DNA repair pathways. This indicates that the Ku-independent alternative non-homologous end-joining pathway may contribute to repairing complex DNA legions induced by high-LET irradiation. These findings may clarify various LET-dependent responses in rice. PMID:27462908

  12. Stripped-down DNA repair in a highly reduced parasite

    Directory of Open Access Journals (Sweden)

    Fast Naomi M

    2007-03-01

    Full Text Available Abstract Background Encephalitozoon cuniculi is a member of a distinctive group of single-celled parasitic eukaryotes called microsporidia, which are closely related to fungi. Some of these organisms, including E. cuniculi, also have uniquely small genomes that are within the prokaryotic range. Thus, E. cuniculi has undergone a massive genome reduction which has resulted in a loss of genes from diverse biological pathways, including those that act in DNA repair. DNA repair is essential to any living cell. A loss of these mechanisms invariably results in accumulation of mutations and/or cell death. Six major pathways of DNA repair in eukaryotes include: non-homologous end joining (NHEJ, homologous recombination repair (HRR, mismatch repair (MMR, nucleotide excision repair (NER, base excision repair (BER and methyltransferase repair. DNA polymerases are also critical players in DNA repair processes. Given the close relationship between microsporidia and fungi, the repair mechanisms present in E. cuniculi were compared to those of the yeast Saccharomyces cerevisiae to ascertain how the process of genome reduction has affected the DNA repair pathways. Results E. cuniculi lacks 16 (plus another 6 potential absences of the 56 DNA repair genes sought via BLASTP and PSI-BLAST searches. Six of 14 DNA polymerases or polymerase subunits are also absent in E. cuniculi. All of these genes are relatively well conserved within eukaryotes. The absence of genes is not distributed equally among the different repair pathways; some pathways lack only one protein, while there is a striking absence of many proteins that are components of both double strand break repair pathways. All specialized repair polymerases are also absent. Conclusion Given the large number of DNA repair genes that are absent from the double strand break repair pathways, E. cuniculi is a prime candidate for the study of double strand break repair with minimal machinery. Strikingly, all of the

  13. Combining Heavy Ion Radiation and Artificial MicroRNAs to Target the Homologous Recombination Repair Gene Efficiently Kills Human Tumor Cells

    Energy Technology Data Exchange (ETDEWEB)

    Zheng Zhiming [Department of Neurosurgery, Provincial Hospital Affiliated to Shandong University, Shandong University, Jinan (China); Department of Radiation Oncology, School of Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); Wang Ping; Wang Hongyan; Zhang Xiangming [Department of Radiation Oncology, School of Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); Wang Minli [Division of Life Sciences, Universities Space Research Association, Houston, Texas (United States); Cucinotta, Francis A. [National Aeronautics and Space Administration, Lyndon B. Johnson Space Center, Houston, Texas (United States); Wang Ya, E-mail: ywang94@emory.edu [Department of Radiation Oncology, School of Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia (United States)

    2013-02-01

    Purpose: Previously, we demonstrated that heavy ions kill more cells at the same dose than X-rays because DNA-clustered lesions produced by heavy ions affect nonhomologous end-joining (NHEJ) repair but not homologous recombination repair (HRR). We have also shown that our designed artificial microRNAs (amiRs) could efficiently target XRCC4 (an essential factor for NHEJ) or XRCC2 (an essential factor for HRR) and sensitize human tumor cells to X-rays. Based on these data, we were interested in testing the hypothesis that combining heavy ions and amiRs to target HRR but not NHEJ should more efficiently kill human tumor cells. Methods and Materials: Human tumor cell lines (U87MG, a brain tumor cell line, and A549, a lung cancer cell line) and their counterparts, overexpressed with amiR to target XRCC2, XRCC4 or both, were used in this study. Survival sensitivities were examined using a clonogenic assay after these cells were exposed to X-rays or heavy ions. In addition, these cell lines were subcutaneously injected into nude mice to form xenografts and the tumor size was compared after the tumor areas were exposed to X-rays or heavy ions. Results: Although targeting either XRCC4 (NHEJ factor) or XRCC2 (HRR factor) sensitized the human tumor cells to X-rays, in vitro and the xenograft animal model, targeting only XRCC2 but not XRCC4 sensitized the human tumor cells to heavy ions in vitro and in the xenograft animal model. Conclusions: Combining heavy ions with targeting the HRR pathway, but not the NHEJ pathway, could significantly improve the efficiency of tumor cell death.

  14. Efficient gene targeting in Penicillium chrysogenum using novel Agrobacterium-mediated transformation approaches.

    Science.gov (United States)

    de Boer, Paulo; Bronkhof, Jurian; Dukiќ, Karolina; Kerkman, Richard; Touw, Hesselien; van den Berg, Marco; Offringa, Remko

    2013-12-01

    The industrial production of β-lactam antibiotics by Penicillium chrysogenum has increased tremendously over the last decades, however, further optimization via classical strain and process improvement has reached its limits. The availability of the genome sequence provides new opportunities for directed strain improvement, but this requires the establishment of an efficient gene targeting (GT) system. Recently, mutations affecting the non-homologous end joining (NHEJ) pathway were shown to increase GT efficiencies following PEG-mediated DNA transfer in P. chrysogenum from 1% to 50%. Apart from direct DNA transfer many fungi can efficiently be transformed using the T-DNA transfer system of the soil bacterium Agrobacterium tumefaciens, however, for P. chrysogenum no robust system for Agrobacterium-mediated transformation was available. We obtained efficient AMT of P. chrysogenum spores with the nourseothricin acetyltransferase gene as selection marker, and using this system we investigated if AMT in a NHEJ mutant background could further enhance GT efficiencies. In general, AMT resulted in higher GT efficiencies than direct DNA transfer, although the final frequencies depended on the Agrobacterium strain and plasmid backbone used. Providing overlapping and complementing fragments on two different plasmid backbones via the same Agrobacterium host was shown to be most effective. This so-called split-marker or bi-partite method resulted in highly efficient GT (>97%) almost exclusively without additional ectopic T-DNA insertions. As this method provides for an efficient GT method independent of protoplasts, it can be applied to other fungi for which no protoplasts can be generated or for which protoplast transformation leads to varying results.

  15. Polycyclic aromatic hydrocarbons-induced ROS accumulation enhances mutagenic potential of T-antigen from human polyomavirus JC.

    Science.gov (United States)

    Wilk, Anna; Waligórski, Piotr; Lassak, Adam; Vashistha, Himanshu; Lirette, David; Tate, David; Zea, Arnold H; Koochekpour, Shahriar; Rodriguez, Paulo; Meggs, Leonard G; Estrada, John J; Ochoa, Augusto; Reiss, Krzysztof

    2013-11-01

    Polycyclic aromatic hydrocarbons (PAHs) are the products of incomplete combustion of organic materials, which are present in cigarette smoke, deep-fried food, and in natural crude oil. Since PAH-metabolites form DNA adducts and cause oxidative DNA damage, we asked if these environmental carcinogens could affect transforming potential of the human Polyomavirus JC oncoprotein, T-antigen (JCV T-antigen). We extracted DMSO soluble PAHs from Deepwater Horizon oil spill in the Gulf of Mexico (oil-PAHs), and detected several carcinogenic PAHs. The oil-PAHs were tested in exponentially growing cultures of normal mouse fibroblasts (R508), and in R508 stably expressing JCV T-antigen (R508/T). The oil-PAHs were cytotoxic only at relatively high doses (1:50-1:100 dilution), and at 1:500 dilution the growth and cell survival rates were practically unaffected. This non-toxic dose triggered however, a significant accumulation of reactive oxygen species (ROS), caused oxidative DNA damage and the formation of DNA double strand breaks (DSBs). Although oil-PAHs induced similar levels of DNA damage in R508 and R508/T cells, only T-antigen expressing cells demonstrated inhibition of high fidelity DNA repair by homologous recombination (HRR). In contrast, low-fidelity repair by non-homologous end joining (NHEJ) was unaffected. This potential mutagenic shift between DNA repair mechanisms was accompanied by a significant increase in clonal growth of R508/T cells chronically exposed to low doses of the oil-PAHs. Our results indicate for the first time carcinogenic synergy in which oil-PAHs trigger oxidative DNA damage and JCV T-antigen compromises DNA repair fidelity. PMID:23558788

  16. Psychological Factors Affecting Infertile Women

    Directory of Open Access Journals (Sweden)

    Sati Unal

    2010-10-01

    Full Text Available AIM: This study was performed to determine the psychological factors affecting infertile women presenting at the infertility outpatients department. METHOD: The sample of this cross-sectional study consisted of 344 women who presented at the IVF center of a special branch hospital or a university hospital, March 2008 through September 2008, as determined by the non-random sampling method. All participating women gave their informed consent. The data were collected using the Data Form that consisted of questions on socio-demographic features and the Infertility Distress Scale (IDS. In the results, percentages were provided along with the Kruskal-Wallis H, Mann-Whitney U and Spearman correlation tests. RESULTS: The mean IDS was 39.01±9.6. There was a statistically significant linear relationship between the mean IDS score and age (r=0.106, p=0.048, marriage duration (r=0.232, p<0.001 and duration of desire to have a child (r=0.217, p<0.001. Women who were primary school graduates (X²=13.03, p=0.004, did not work (p=0.007, had no social security benefits (p=0.021 or from low socioeconomic status (X²=24.85, p<0.001 had significantly higher mean IDS scores. CONCLUSION: The results of this study show women become more adversely affected by infertility as their age, duration of marriage, and duration of desire to have a child increase. Women who are primary school graduates, do not work, have no social security benefits or have lower income are affected more negatively. We believe that taking these features into account when evaluating and planning supportive approaches for women presenting at the infertility treatment center and determining the psychological state of the women using the IDS will increase treatment success. [TAF Prev Med Bull 2010; 9(5.000: 481-486

  17. affective variables of language learning

    Institute of Scientific and Technical Information of China (English)

    李文敬

    2011-01-01

    why people enjoy different degrees of success in second language learning,given similar opportunities.in the presence of overly negative emotions such as anxiety,fear,stress,anger or depression,our optimal learning potential maybe compromised.the affective domain refers to the emotional domain that has to do with the emotional behavior of human beings.it includes such factors as self-confidence,extroversion,anxiety,attitudes and motivation.three major factors are introduced here:self-confidence,anxiety and motivation.

  18. Mood Swings: An Affective Interactive Art System

    Science.gov (United States)

    Bialoskorski, Leticia S. S.; Westerink, Joyce H. D. M.; van den Broek, Egon L.

    The progress in the field of affective computing enables the realization of affective consumer products, affective games, and affective art. This paper describes the affective interactive art system Mood Swings, which interprets and visualizes affect expressed by a person. Mood Swings is founded on the integration of a framework for affective movements and a color model. This enables Mood Swings to recognize affective movement characteristics as expressed by a person and display a color that matches the expressed emotion. With that, a unique interactive system is introduced, which can be considered as art, a game, or a combination of both.

  19. Pseudobulbar affect: prevalence and management

    Directory of Open Access Journals (Sweden)

    Ahmed A

    2013-11-01

    Full Text Available Aiesha Ahmed, Zachary SimmonsDepartment of Neurology, Penn State Hershey Medical Center, Hershey, PA, USAAbstract: Pseudobulbar affect (PBA may occur in association with a variety of neurological diseases, and so may be encountered in the setting of amyotrophic lateral sclerosis, extrapyramidal and cerebellar disorders, multiple sclerosis, traumatic brain injury, Alzheimer's disease, stroke, and brain tumors. The psychological consequences and the impact on social interactions may be substantial. Although it is most commonly misidentified as a mood disorder, particularly depression or a bipolar disorder, there are characteristic features that can be recognized clinically or assessed by validated scales, resulting in accurate identification of PBA, and thus permitting proper management and treatment. Mechanistically, PBA is a disinhibition syndrome in which pathways involving serotonin and glutamate are disrupted. This knowledge has permitted effective treatment for many years with antidepressants, particularly tricyclic antidepressants and selective serotonin reuptake inhibitors. A recent therapeutic breakthrough occurred with the approval by the Food and Drug Administration of a dextromethorphan/quinidine combination as being safe and effective for treatment of PBA. Side effect profiles and contraindications differ for the various treatment options, and the clinician must be familiar with these when choosing the best therapy for an individual, particularly elderly patients and those with multiple comorbidities and concomitant medications.Keywords: pseudobulbar affect, emotional lability, depression, amyotrophic lateral sclerosis, multiple sclerosis

  20. Bipolar Affective Disorder and Migraine

    Directory of Open Access Journals (Sweden)

    Birk Engmann

    2012-01-01

    Full Text Available This paper consists of a case history and an overview of the relationship, aetiology, and treatment of comorbid bipolar disorder migraine patients. A MEDLINE literature search was used. Terms for the search were bipolar disorder bipolar depression, mania, migraine, mood stabilizer. Bipolar disorder and migraine cooccur at a relatively high rate. Bipolar II patients seem to have a higher risk of comorbid migraine than bipolar I patients have. The literature on the common roots of migraine and bipolar disorder, including both genetic and neuropathological approaches, is broadly discussed. Moreover, bipolar disorder and migraine are often combined with a variety of other affective disorders, and, furthermore, behavioural factors also play a role in the origin and course of the diseases. Approach to treatment options is also difficult. Several papers point out possible remedies, for example, valproate, topiramate, which acts on both diseases, but no first-choice treatments have been agreed upon yet.

  1. Rheumatoid arthritis affecting temporomandibular joint

    Directory of Open Access Journals (Sweden)

    Amandeep Sodhi

    2015-01-01

    Full Text Available Rheumatoid arthritis (RA is a chronic, systemic, autoimmune inflammatory disorder that is characterized by joint inflammation, erosive properties and symmetric multiple joint involvement. Temporomandibular joint (TMJ is very rare to be affected in the early phase of the disease, thus posing diagnostic challenges for the dentist. Conventional radiographs fail to show the early lesions due to its limitations. More recently cone-beam computed tomography (CBCT has been found to diagnose the early degenerative changes of TMJ and hence aid in the diagnosis of the lesions more accurately. Our case highlights the involvement of TMJ in RA and the role of advanced imaging (CBCT in diagnosing the bony changes in the early phase of the disease.

  2. Nutritional Factors Affecting Mental Health

    Science.gov (United States)

    Lim, So Young; Kim, Eun Jin; Kim, Arang; Lee, Hee Jae; Choi, Hyun Jin

    2016-01-01

    Dietary intake and nutritional status of individuals are important factors affecting mental health and the development of psychiatric disorders. Majority of scientific evidence relating to mental health focuses on depression, cognitive function, and dementia, and limited evidence is available about other psychiatric disorders including schizophrenia. As life span of human being is increasing, the more the prevalence of mental disorders is, the more attention rises. Lists of suggested nutritional components that may be beneficial for mental health are omega-3 fatty acids, phospholipids, cholesterol, niacin, folate, vitamin B6, and vitamin B12. Saturated fat and simple sugar are considered detrimental to cognitive function. Evidence on the effect of cholesterol is conflicting; however, in general, blood cholesterol levels are negatively associated with the risk of depression. Collectively, the aims of this review are to introduce known nutritional factors for mental health, and to discuss recent issues of the nutritional impact on cognitive function and healthy brain aging.

  3. Emotion Eliciting in Affective Design

    DEFF Research Database (Denmark)

    Lai, Yoke Chin

    2014-01-01

    outlines the concept of an integrated design method that is developed to aid novice designer through the conceptual design stage. Multi-modal stimulation is used in this design method to induce user’s emotion, a key element in the user’s mental model. Visio-haptic Augmented Reality technology is integrated...... with 3D digital prototype as emotion stimulus. To form a closed loop reflective model, the emotion response from the user is assessed with an emotion assessment tool. Emotion ontology is established to form the backbone of the emotion assessment tool.......A successful product needs the designer’s conceptual model congruent with the user’s mental model. The fundamental affective design principle also applies to assistive product design. Eliciting effectively the user’s mental model has been a big challenge for most novice designers. This paper...

  4. Affective dimensions of intergroup humiliation.

    Directory of Open Access Journals (Sweden)

    Bernhard Leidner

    Full Text Available Despite the wealth of theoretical claims about the emotion of humiliation and its effect on human relations, there has been a lack of empirical research investigating what it means to experience humiliation. We studied the affective characteristics of humiliation, comparing the emotional experience of intergroup humiliation to two other emotions humiliation is often confused with: anger and shame. The defining characteristics of humiliation were low levels of guilt and high levels of other-directed outrage (like anger and unlike shame, and high levels of powerlessness (like shame and unlike anger. Reasons for the similarities and differences of humiliation with anger and shame are discussed in terms of perceptions of undeserved treatment and injustice. Implications for understanding the behavioral consequences of humiliation and future work investigating the role of humiliation in social life are discussed.

  5. Nutritional Factors Affecting Mental Health.

    Science.gov (United States)

    Lim, So Young; Kim, Eun Jin; Kim, Arang; Lee, Hee Jae; Choi, Hyun Jin; Yang, Soo Jin

    2016-07-01

    Dietary intake and nutritional status of individuals are important factors affecting mental health and the development of psychiatric disorders. Majority of scientific evidence relating to mental health focuses on depression, cognitive function, and dementia, and limited evidence is available about other psychiatric disorders including schizophrenia. As life span of human being is increasing, the more the prevalence of mental disorders is, the more attention rises. Lists of suggested nutritional components that may be beneficial for mental health are omega-3 fatty acids, phospholipids, cholesterol, niacin, folate, vitamin B6, and vitamin B12. Saturated fat and simple sugar are considered detrimental to cognitive function. Evidence on the effect of cholesterol is conflicting; however, in general, blood cholesterol levels are negatively associated with the risk of depression. Collectively, the aims of this review are to introduce known nutritional factors for mental health, and to discuss recent issues of the nutritional impact on cognitive function and healthy brain aging. PMID:27482518

  6. Affective and Cognitive Aspects of Bilingualism.

    Science.gov (United States)

    Herrell, Ileana Collado; Herrell, James M.

    1980-01-01

    A study showing that lexically equivalent words in two languages have different affective meanings, that affective intensity of dominant language words is greater than for second language equivalents, and that the difference is greatest for words with high affective meaning demonstrates that affective meaning is an important component of…

  7. Ash in fire affected ecosystems

    Science.gov (United States)

    Pereira, Paulo; Jordan, Antonio; Cerda, Artemi; Martin, Deborah

    2015-04-01

    Ash in fire affected ecosystems Ash lefts an important footprint in the ecosystems and has a key role in the immediate period after the fire (Bodi et al., 2014; Pereira et al., 2015). It is an important source of nutrients for plant recover (Pereira et al., 2014a), protects soil from erosion and controls soil hydrological process as runoff, infiltration and water repellency (Cerda and Doerr, 2008; Bodi et al., 2012, Pereira et al., 2014b). Despite the recognition of ash impact and contribution to ecosystems recuperation, it is assumed that we still have little knowledge about the implications of ash in fire affected areas. Regarding this situation we wanted to improve our knowledge in this field and understand the state of the research about fire ash around world. The special issue about "The role of ash in fire affected ecosystems" currently in publication in CATENA born from the necessity of joint efforts, identify research gaps, and discuss future cooperation in this interdisciplinary field. This is the first special issue about fire ash in the international literature. In total it will be published 10 papers focused in different aspects of the impacts of ash in fire affected ecosystems from several parts of the world: • Fire reconstruction using charcoal particles (Burjachs and Espositio, in press) • Ash slurries impact on rheological properties of Runoff (Burns and Gabet, in press) • Methods to analyse ash conductivity and sorbtivity in the laboratory and in the field (Balfour et al., in press) • Termogravimetric and hydrological properties of ash (Dlapa et al. in press) • Effects of ash cover in water infiltration (Leon et al., in press) • Impact of ash in volcanic soils (Dorta Almenar et al., in press; Escuday et al., in press) • Ash PAH and Chemical extracts (Silva et al., in press) • Microbiology (Barreiro et al., in press; Lombao et al., in press) We believe that this special issue will contribute importantly to the better understanding of

  8. Twitter, Journalism and Affective Labour

    Directory of Open Access Journals (Sweden)

    Eugenia Siapera

    2015-03-01

    Full Text Available The rise of the network aspects of journalism in the context of social mediasuch as Twitter, and the increased importance accorded to community building and maintenance as well as to reciprocity, point to the need to take into account the affective part of journalistic labour. This refers to these aspects of journalistic work that are linked to the creation of networks and communities, to interactions with readers and the forming of bonds between journalists and their readers. An analysis of the affective labour of journalists on Twitter, we argue, is necessary in order to understand the potential and ambiguities of this part of their labour. Based on a set of in-depth interviews with Twitter journalists, this article found three main repertoires of affective labour: the organic relations repertoire, which points to the increasing importance of authenticity as a means of establishing credibility on Twitter; the temporal repertoire; and the repertoire of responsibility. The importance of the affective labour of journalism is found in its biopolitical productivity. The development of an organic relationship with followers, the emergence of stronger bonds between core groups that then become communities, the extension of care and help to the network, are all evidence of the importance of this biopolitical productivity and point to the construction of a new and potentially more radical sociopolitical role for journalism. However, this potential is ambiguous insofar as these elements contain unresolved tensions and ambiguities. These include the trade in selves and the associated commodification; the re-formulation of time, especially its diachronic dimension, as accumulation of social capital; the role of reciprocity and responsibility in reproducing inequalities; and care as care for only those deemed deserving. These ambiguities severely undermine and limit the potentials of affective labour, pointing to the need to develop a purposeful political

  9. How feeling betrayed affects cooperation.

    Directory of Open Access Journals (Sweden)

    Pouria Ramazi

    Full Text Available For a population of interacting self-interested agents, we study how the average cooperation level is affected by some individuals' feelings of being betrayed and guilt. We quantify these feelings as adjusted payoffs in asymmetric games, where for different emotions, the payoff matrix takes the structure of that of either a prisoner's dilemma or a snowdrift game. Then we analyze the evolution of cooperation in a well-mixed population of agents, each of whom is associated with such a payoff matrix. At each time-step, an agent is randomly chosen from the population to update her strategy based on the myopic best-response update rule. According to the simulations, decreasing the feeling of being betrayed in a portion of agents does not necessarily increase the level of cooperation in the population. However, this resistance of the population against low-betrayal-level agents is effective only up to some extend that is explicitly determined by the payoff matrices and the number of agents associated with these matrices. Two other models are also considered where the betrayal factor of an agent fluctuates as a function of the number of cooperators and defectors that she encounters. Unstable behaviors are observed for the level of cooperation in these cases; however, we show that one can tune the parameters in the function to make the whole population become cooperative or defective.

  10. How feeling betrayed affects cooperation.

    Science.gov (United States)

    Ramazi, Pouria; Hessel, Jop; Cao, Ming

    2015-01-01

    For a population of interacting self-interested agents, we study how the average cooperation level is affected by some individuals' feelings of being betrayed and guilt. We quantify these feelings as adjusted payoffs in asymmetric games, where for different emotions, the payoff matrix takes the structure of that of either a prisoner's dilemma or a snowdrift game. Then we analyze the evolution of cooperation in a well-mixed population of agents, each of whom is associated with such a payoff matrix. At each time-step, an agent is randomly chosen from the population to update her strategy based on the myopic best-response update rule. According to the simulations, decreasing the feeling of being betrayed in a portion of agents does not necessarily increase the level of cooperation in the population. However, this resistance of the population against low-betrayal-level agents is effective only up to some extend that is explicitly determined by the payoff matrices and the number of agents associated with these matrices. Two other models are also considered where the betrayal factor of an agent fluctuates as a function of the number of cooperators and defectors that she encounters. Unstable behaviors are observed for the level of cooperation in these cases; however, we show that one can tune the parameters in the function to make the whole population become cooperative or defective. PMID:25922933

  11. Affective Priming Caused by Lying

    Directory of Open Access Journals (Sweden)

    Megumi Sato

    2011-10-01

    Full Text Available Typically, arousal increases when telling a lie, as indicated in psychophysiological studies about lie detection. But the emotional valence induced by lying is unknown, though intuition indicates that it may be negative. Indeed, the Electrodermal Activity (EDA, used in such studies, only shows arousal changes during an emotional response. In this study, we examined the emotional valence induced by lying using two tasks. First, in the deceptive task, participants answered “no” to every question regarding the nature of displayed playing cards. Therefore, they told a lie about specific cards. During the task, their EDA was recorded. Secondly, in the figure estimation task, they assessed pictures by “like” or “dislike” after looking at playing cards visibly or subliminally as prime stimuli. We expected them to tend to estimate figures by “dislike” when cards relevant to deception were previously shown. This would mean that an affective priming effect due to telling a lie happened. Actually, this effect was found only when prime stimuli were displayed visibly. This result suggests that lying per se induces negative emotions even without motivation or punishment due to lying. Furthermore, we found that such effect was more blatant in participants whose EDA changes were salient while lying.

  12. Bilingualism affects audiovisual phoneme identification.

    Science.gov (United States)

    Burfin, Sabine; Pascalis, Olivier; Ruiz Tada, Elisa; Costa, Albert; Savariaux, Christophe; Kandel, Sonia

    2014-01-01

    We all go through a process of perceptual narrowing for phoneme identification. As we become experts in the languages we hear in our environment we lose the ability to identify phonemes that do not exist in our native phonological inventory. This research examined how linguistic experience-i.e., the exposure to a double phonological code during childhood-affects the visual processes involved in non-native phoneme identification in audiovisual speech perception. We conducted a phoneme identification experiment with bilingual and monolingual adult participants. It was an ABX task involving a Bengali dental-retroflex contrast that does not exist in any of the participants' languages. The phonemes were presented in audiovisual (AV) and audio-only (A) conditions. The results revealed that in the audio-only condition monolinguals and bilinguals had difficulties in discriminating the retroflex non-native phoneme. They were phonologically "deaf" and assimilated it to the dental phoneme that exists in their native languages. In the audiovisual presentation instead, both groups could overcome the phonological deafness for the retroflex non-native phoneme and identify both Bengali phonemes. However, monolinguals were more accurate and responded quicker than bilinguals. This suggests that bilinguals do not use the same processes as monolinguals to decode visual speech.

  13. [Harmful practices affecting women's health].

    Science.gov (United States)

    1990-07-01

    The harmful practices discussed in this article are based on case histories form the Central Maternity in Niamey, yet these practices universally affect women throughout Africa. Nutritional taboos are aimed at certain diseases such as measles, diarrhea, dysentery, malnutrition and anemia and consumption of foods rich in proteins and lipids are forbidden. Children are forbidden from eating eggs; pregnant women are forbidden from eating fruits and vegetables because of the fear of hemorrhaging from the sugar content in the fruit; camel meat is forbidden for fear of extending the pregnancy. Female circumcision, a dangerous practice, especially during childbirth, causes many medical problems that remain permanent. Adolescent pregnancy and marriages are practiced to avoid delinquency among children; yet such practices take place because of arranged marriages for a dowry to young men or to older rich men and these forced marriages to adolescents are the causes of increases in divorce, prostitution and desertion. These young marriages have serious consequences on the health status of the mother and the infant, often leading to maternal and infant death. The high level of fertility in Niger is a response to the social structure of the family. It is a patrilineal system that encourages women to have many children, especially sons. In Niger, pregnancy is surrounded by supernatural and mysterious forces, where a child is the intervention for ancestral spirits. In Islam a child is considered a "Gift of God". A woman is expected to work until the delivery of her baby otherwise she is jeered by her neighbors. During delivery women are not expected to cry or show any pain for fear of dishonoring her family irregardless of any medical compilations she faces. Women in Africa are exploited as free labor, deteriorate and age rapidly, are generally illiterate and are not protected under any laws. PMID:12342832

  14. A Multimodal Theory of Affect Diffusion.

    Science.gov (United States)

    Peters, Kim; Kashima, Yoshihisa

    2015-09-01

    There is broad consensus in the literature that affect diffuses through social networks (such that a person may "acquire" or "catch" an affective state from his or her social contacts). It is further assumed that affect diffusion primarily occurs as the result of people's tendencies to synchronize their affective actions (such as smiles and frowns). However, as we show, there is a lack of clarity in the literature about the substrate and scope of affect diffusion. One consequence of this is a difficulty in distinguishing between affect diffusion and several other affective influence phenomena that look similar but have very different consequences. There is also a growing body of evidence that action synchrony is unlikely to be the only, or indeed the most important, pathway for affect diffusion. This paper has 2 key aims: (a) to craft a formal definition of affect diffusion that does justice to the core of the phenomenon while distinguishing it from other phenomena with which it is frequently confounded and (b) to advance a theory of the mechanisms of affect diffusion. This theory, which we call the multimodal theory of affect diffusion, identifies 3 parallel multimodal mechanisms that may act as routes for affect diffusion. It also provides a basis for novel predictions about the conditions under which affect is most likely to diffuse. PMID:26011791

  15. Factors Affecting Aerosol Radiative Forcing

    Science.gov (United States)

    Wang, Jingxu; Lin, Jintai; Ni, Ruijing

    2016-04-01

    Rapid industrial and economic growth has meant a large amount of aerosols in the atmosphere with strong radiative forcing (RF) upon the climate system. Over parts of the globe, the negative forcing of aerosols has overcompensated for the positive forcing of greenhouse gases. Aerosol RF is determined by emissions and various chemical-transport-radiative processes in the atmosphere, a multi-factor problem whose individual contributors have not been well quantified. In this study, we analyze the major factors affecting RF of secondary inorganic aerosols (SIOAs, including sulfate, nitrate and ammonium), primary organic aerosol (POA), and black carbon (BC). We analyze the RF of aerosols produced by 11 major regions across the globe, including but not limited to East Asia, Southeast Asia, South Asia, North America, and Western Europe. Factors analyzed include population size, per capita gross domestic production (GDP), emission intensity (i.e., emissions per unit GDP), chemical efficiency (i.e., mass per unit emissions) and radiative efficiency (i.e., RF per unit mass). We find that among the 11 regions, East Asia produces the largest emissions and aerosol RF, due to relatively high emission intensity and a tremendous population size. South Asia produce the second largest RF of SIOA and BC and the highest RF of POA, in part due to its highest chemical efficiency among all regions. Although Southeast Asia also has large emissions, its aerosol RF is alleviated by its lowest chemical efficiency. The chemical efficiency and radiative efficiency of BC produced by the Middle East-North Africa are the highest across the regions, whereas its RF is lowered by a small per capita GDP. Both North America and Western Europe have low emission intensity, compensating for the effects on RF of large population sizes and per capita GDP. There has been a momentum to transfer industries to Southeast Asia and South Asia, and such transition is expected to continue in the coming years. The

  16. Antecedents and Consequences of Affective Commitment

    NARCIS (Netherlands)

    Bloemer, J.M.M.; Odekerken-Schröder, G.J.

    2003-01-01

    The primary objective of this study is to assess the impact of three psychological antecedents (position involvement, volitional choice and informational complexity) on affective commitment in a financial service setting. Furthermore, this study addresses the consequences of affective commitment on

  17. Dispositional affectivity and work outcomes of expatriates

    DEFF Research Database (Denmark)

    Selmer, Jan; Lauring, Jakob

    2013-01-01

    to examine the relationship between dispositional affectivity and their work outcomes. Results showed consistent positive associations between positive affectivity and all the studied work outcomes and the opposite relationships for negative affectivity. Implications and suggestions for future research......How the two components of dispositional affectivity, positive affectivity, representing the predisposition to respond positively to environmental stimuli, and negative affectivity, depicting the opposite reaction, influence work has been the focus of much research. Although dispositional...... affectivity appears to be a promising construct to explain and predict many attitudinal and behavioral outcomes in the workplace, few studies have empirically investigated dispositional affectivity and the work of expatriates. Hence, data from a net-based survey including 350 expatriates in Denmark were used...

  18. On English learning Disability and Affect

    Institute of Scientific and Technical Information of China (English)

    LIU Fang

    2007-01-01

    This paper introduces the definitions and causes of LD,pointing out that English LD is definitely concerned with the factor of affect by exploring the three theories like Affective Filter Hypothesis,Humanistic Approach to Education and Attribution Theory.

  19. Can the Weather Affect My Child's Asthma?

    Science.gov (United States)

    ... Baby's Growth Can the Weather Affect My Child's Asthma? KidsHealth > For Parents > Can the Weather Affect My ... empeorar el asma de mi hijo? Weather and Asthma The effect of weather on asthma symptoms isn' ...

  20. HIV Infection Seems to Affect Nervous System

    Science.gov (United States)

    ... fullstory_159344.html HIV Infection Seems to Affect Nervous System But symptoms tend to subside once antiretroviral drugs ... mild, it is clear that HIV affects the nervous system within days of infection," she said in a ...

  1. How Do Beta Blocker Drugs Affect Exercise?

    Science.gov (United States)

    ... Stroke More How do beta blocker drugs affect exercise? Updated:Aug 5,2015 Beta blockers are a ... about them: Do they affect your ability to exercise? The answer can vary a great deal, depending ...

  2. Affect and Metaphor Sensing in Virtual Drama

    OpenAIRE

    Li Zhang; John Barnden

    2010-01-01

    We report our developments on metaphor and affect sensing for several metaphorical language phenomena including affects as external entities metaphor, food metaphor, animal metaphor, size metaphor, and anger metaphor. The metaphor and affect sensing component has been embedded in a conversational intelligent agent interacting with human users under loose scenarios. Evaluation for the detection of several metaphorical language phenomena and affect is provided. Our paper contributes to the jour...

  3. Demographics, Affect, and Adolescents' Health Behaviors.

    Science.gov (United States)

    Terre, Lisa; And Others

    1992-01-01

    Examined relationship between affect, demographics, and health-related lifestyle among 139 public high school students. Data analyses revealed distinctive demographic and affective correlates of different health behaviors. No one variable uniformly predicted adolescents' health behaviors. Demographics and affect showed differential relationships…

  4. Empirical Testing of an Affective Learning Paradigm.

    Science.gov (United States)

    Asmus, Edward P., Jr.

    1980-01-01

    This investigation of a college music course examined the effectiveness of a cyclical affective learning paradigm based on the premise that student affect toward a course of instruction will dictate, in part, cognitive performance. Results suggest that teachers would be better advised to concentrate on cognitive instruction than on affect.…

  5. Circadian polymorphisms associated with affective disorders

    OpenAIRE

    Kripke, Daniel F; Nievergelt, Caroline M; Joo, EJ; Shekhtman, Tatyana; Kelsoe, John R.

    2009-01-01

    Background: Clinical symptoms of affective disorders, their response to light treatment, and sensitivity to other circadian interventions indicate that the circadian system has a role in mood disorders. Possibly the mechanisms involve circadian seasonal and photoperiodic mechanisms. Since genetic susceptibilities contribute a strong component to affective disorders, we explored whether circadian gene polymorphisms were associated with affective disorders in four complementary studies.Methods:...

  6. Affective Arousal as Information: How Affective Arousal Influences Judgments, Learning, and Memory

    OpenAIRE

    Storbeck, Justin; Clore, Gerald L.

    2008-01-01

    The affect-as-information framework posits that affect is embodied information about value and importance. The valence dimension of affect provides evaluative information about stimulus objects, which plays a role in judgment and decisionmaking. Affect can also provide evaluative information about one's own cognitions and response inclinations, information that guides thinking and reasoning. In particular, positive affect often promotes, and negative affect inhibits, accessible responses or d...

  7. Dynamic artificial neural networks with affective systems.

    Science.gov (United States)

    Schuman, Catherine D; Birdwell, J Douglas

    2013-01-01

    Artificial neural networks (ANNs) are processors that are trained to perform particular tasks. We couple a computational ANN with a simulated affective system in order to explore the interaction between the two. In particular, we design a simple affective system that adjusts the threshold values in the neurons of our ANN. The aim of this paper is to demonstrate that this simple affective system can control the firing rate of the ensemble of neurons in the ANN, as well as to explore the coupling between the affective system and the processes of long term potentiation (LTP) and long term depression (LTD), and the effect of the parameters of the affective system on its performance. We apply our networks with affective systems to a simple pole balancing example and briefly discuss the effect of affective systems on network performance.

  8. College English Listening Teaching Based on Affect

    Institute of Scientific and Technical Information of China (English)

    张冬梅

    2015-01-01

    With the continuous development of language teaching theories,the affective factors in language learning has got wide-spread attention.Research is carried out on the influence of learners'affective factors on the college English listening teaching,aiming to break the learning barricades caused by the affect.The theoretical background of affect and the current study situation abroad and domestically are introduced firstly,and together with the fact that learners'affect has widely been neglected in the teaching process.An interview and a questionnaire are used to test learners'affect in English listening class.In the end,how to solve the problems in college English listening teaching from the aspect of affect is discussed.

  9. Audio-visual affective expression recognition

    Science.gov (United States)

    Huang, Thomas S.; Zeng, Zhihong

    2007-11-01

    Automatic affective expression recognition has attracted more and more attention of researchers from different disciplines, which will significantly contribute to a new paradigm for human computer interaction (affect-sensitive interfaces, socially intelligent environments) and advance the research in the affect-related fields including psychology, psychiatry, and education. Multimodal information integration is a process that enables human to assess affective states robustly and flexibly. In order to understand the richness and subtleness of human emotion behavior, the computer should be able to integrate information from multiple sensors. We introduce in this paper our efforts toward machine understanding of audio-visual affective behavior, based on both deliberate and spontaneous displays. Some promising methods are presented to integrate information from both audio and visual modalities. Our experiments show the advantage of audio-visual fusion in affective expression recognition over audio-only or visual-only approaches.

  10. Nurse Educator’s Affective Teaching Strategies

    OpenAIRE

    Myra C. Britiller; Frances Margott C. Ramos; Darryl Marvin C. Reyes; Kimberlyn D. Salazar; Joyce Ann M. Sandoval; Lovelyn Q. Ramirez

    2014-01-01

    Teaching is highly charged with feeling, aroused by and directed towards not just people, but also values and ideals (Garritz, 2010). Emotions and feelings greatly affect the way the students learn and acquire knowledge. There must be a balance between the three domains of learning because once one domain is left behind, the other domains will be affected. The purpose of this study is to determine nurse educators’ affective teaching strategies. Specifically, it assessed the strate...

  11. IMPROVE AFFECTIVE LEARNING WITH EEG APPROACH

    OpenAIRE

    Xiaowei Li; Qinglin Zhao; Li Liu; Hong Peng; Yanbing Qi; Chengsheng Mao; Zheng Fang; Quanying Liu; Bin Hu

    2010-01-01

    With the development of computer science, cognitive science and psychology, a new paradigm, affective learning, has emerged into e-learning domain. Although scientists and researchers have achieved fruitful outcomes in exploring the ways of detecting and understanding learners affect, e.g. eyes motion, facial expression etc., it sounds still necessary to deepen the recognition of learners affect in learning procedure with innovative methodologies. Our research focused on using bio-signals bas...

  12. Factors Affecting University Library Website Design

    OpenAIRE

    Kim, Yongi-Mi; University of Oklahoma

    2011-01-01

    Existing studies have extensively explored factors that affect users’ intentions to use university library website resources (ULWR); yet little attention has been given to factors affecting university library website design. This paper investigates factors that affect university library website design and assesses the success of the university library website from both designers’ and users’ perspectives. The findings show that when planning a website, university web designers consider univers...

  13. Factors affecting bone strength other than osteoporosis.

    Science.gov (United States)

    Ratti, Chiara; Vulcano, Ettore; Canton, Gianluca; Marano, Marco; Murena, Luigi; Cherubino, Paolo

    2013-10-01

    Osteoporosis is the most common cause of bone fragility, especially in post-menopausal women. Bone strength may be compromised by several other medical conditions and medications, which must be ruled out in the clinical management of patients affected by fragility fractures. Indeed, 20-30% of women and up to 50% of men affected by bone fragility are diagnosed with other conditions affecting bone strength other than osteoporosis. These conditions include disorders of bone homeostasis, impaired bone remodeling, collagen disorders, and medications qualitatively and quantitatively affecting bone strength. Proper diagnosis allows correct treatment to prevent the occurrence of fragility fractures. PMID:24046057

  14. Genetic search feature selection for affective modeling

    DEFF Research Database (Denmark)

    Martínez, Héctor P.; Yannakakis, Georgios N.

    2010-01-01

    Automatic feature selection is a critical step towards the generation of successful computational models of affect. This paper presents a genetic search-based feature selection method which is developed as a global-search algorithm for improving the accuracy of the affective models built. The met......Automatic feature selection is a critical step towards the generation of successful computational models of affect. This paper presents a genetic search-based feature selection method which is developed as a global-search algorithm for improving the accuracy of the affective models built...

  15. The Dark Side of the Affective Profiles

    Directory of Open Access Journals (Sweden)

    Danilo Garcia

    2015-12-01

    Full Text Available The affective profiles model is based on the combination of individuals’ experience of high/low positive affect and high/low negative affect: self-fulfilling, high affective, low affective, and self-destructive. We used the profiles as the backdrop for the investigation of individual differences in malevolent character traits (i.e., the Dark Triad: psychopathy, Machiavellianism, and narcissism. A total of 1,000 participants (age: M = 31.50 SD = 10.27, 667 males and 333 females, recruited through Amazons’ Mechanical Turk (MTurk, responded to the Positive Affect Negative Affect Schedule and the Dark Triad Dirty Dozen. Individuals with a high affective profile reported higher degree of narcissism than those with any other profile, and together with individuals with a self-destructive profile, also higher degree of Machiavellianism and psychopathy than individuals with a low affective and self-fulfilling profile. Males scored higher in Machiavellianism and psychopathy. Together with earlier findings, our results show that while individuals in both the self-fulfilling and high affective profiles are extrovert and self-directed, only those in the high affective profile express an immature and malevolent character (i.e., high levels of all Dark Triad traits. Conversely, individuals in the self-fulfilling profile have earlier reported higher levels of cooperativeness and faith. More importantly, the unique association between high levels of positive emotions and narcissism and the unified association between negative emotions to both psychopathy and Machiavellianism imply a dyad rather than a triad of malevolent character traits.

  16. Chromosome analysis of arsenic affected cattle

    Directory of Open Access Journals (Sweden)

    S. Shekhar

    2014-10-01

    Full Text Available Aim: The aim was to study the chromosome analysis of arsenic affected cattle. Materials and Methods: 27 female cattle (21 arsenic affected and 6 normal were selected for cytogenetical study. The blood samples were collected, incubated, and cultured using appropriate media and specific methods. The samples were analyzed for chromosome number and morphology, relative length of the chromosome, arm ratio, and centromere index of X chromosome and chromosomal abnormalities in arsenic affected cattle to that of normal ones. Results: The diploid number of metaphase chromosomes in arsenic affected cattle as well as in normal cattle were all 2n=60, 58 being autosomes and 2 being sex chromosomes. From the centromeric position, karyotyping studies revealed that all the 29 pair of autosomes was found to be acrocentric or telocentric, and the sex chromosomes (XX were submetacentric in both normal and arsenic affected cattle. The relative length of all the autosome pairs and sex chrosomosome pair was found to be higher in normal than that of arsenic affected cattle. The mean arm ratio of X-chromosome was higher in normal than that of arsenic affected cattle, but it is reverse in case of centromere index value of X-chromosome. There was no significant difference of arm ratio and centromere index of X-chromosomes between arsenic affected and normal cattle. No chromosomal abnormalities were found in arsenic affected cattle. Conclusion: The chromosome analysis of arsenic affected cattle in West Bengal reported for the first time in this present study which may serve as a guideline for future studies in other species. These reference values will also help in comparison of cytological studies of arsenic affected cattle to that of various toxicants.

  17. Affective Scaffolds, Expressive Arts, and Cognition

    Science.gov (United States)

    Maiese, Michelle

    2016-01-01

    Some theorists have argued that elements of the surrounding world play a crucial role in sustaining and amplifying both cognition and emotion. Such insights raise an interesting question about the relationship between cognitive and affective scaffolding: in addition to enabling the realization of specific affective states, can an affective niche also enable the realization of certain cognitive capacities? In order to gain a better understanding of this relationship between affective niches and cognition, I will examine the use of expressive arts in the context of psychotherapy and peacebuilding. In these settings, environmental resources and interpersonal scaffolds not only evoke emotion and encourage the adoption of particular bodily affective styles, but also support the development of capacities for self-awareness and interpersonal understanding. These affective scaffolds play a crucial role in therapy and peacebuilding, in fact, insofar as they facilitate the development of self-knowledge, enhance capacities associated with social cognition, and build positive rapport and trust among participants. I will argue that this is because affectivity is linked to the way that subjects frame and attend to their surroundings. Insofar as the regulation and modification of emotion goes hand in hand with opening up new interpretive frames and establishing new habits of mind, the creation of an affective niche can contribute significantly to various modes of cognition. PMID:27014164

  18. How Does Climate Change Affect Biodiversity?

    DEFF Research Database (Denmark)

    Bastos Araujo, Miguel; Rahbek, Carsten

    2006-01-01

    The most recent and complex bioclimate models excel at describing species' current distributions. Yet, it is unclear which models will best predict how climate change will affect their future distributions.......The most recent and complex bioclimate models excel at describing species' current distributions. Yet, it is unclear which models will best predict how climate change will affect their future distributions....

  19. 1989 Summary of New Legislation Affecting Education.

    Science.gov (United States)

    New York State Education Dept., Albany. Office of the Counsel.

    This summary of major legislation enacted by the 1989 New York State Legislature affecting education and the professions is organized in eight sections: (1) laws affecting school districts generally; (2) state aid; (3) taxation and financial administration; (4) miscellaneous; (5) laws of local application; (6) higher education; (7) laws affecting…

  20. Summary of New Legislation Affecting Education, 1993.

    Science.gov (United States)

    New York State Education Dept., Albany.

    This document summarizes major legislation, enacted by the 1993 New York State Legislature, that affected education and its related professions. Eight sections offer brief descriptions of legislation enacted in the following areas: laws affecting school districts generally; cultural education; state aid; taxation and financial administration;…

  1. 40 CFR 1502.15 - Affected environment.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Affected environment. 1502.15 Section 1502.15 Protection of Environment COUNCIL ON ENVIRONMENTAL QUALITY ENVIRONMENTAL IMPACT STATEMENT § 1502.15 Affected environment. The environmental impact statement shall succinctly describe...

  2. Nonverbal synchrony and affect in dyadic interactions

    Directory of Open Access Journals (Sweden)

    Wolfgang eTschacher

    2014-11-01

    Full Text Available In an experiment on dyadic social interaction, we invited participants to verbal interactions in cooperative, competitive, and 'fun task' conditions. We focused on the link between interactants' affectivity and their nonverbal synchrony, and explored which further variables contributed to affectivity: interactants' personality traits, sex, and the prescribed interaction tasks. Nonverbal synchrony was quantified by the coordination of interactants' body movement, using an automated video-analysis algorithm (Motion Energy Analysis, MEA. Traits were assessed with standard questionnaires of personality, attachment, interactional style, psychopathology and interpersonal reactivity. We included 168 previously unacquainted individuals who were randomly allocated to same-sex dyads (84 females, 84 males, mean age 27.3 years. Dyads discussed four topics of general interest drawn from an urn of eight topics, and finally engaged in a fun interaction. Each interaction lasted five minutes. In between interactions, participants repeatedly assessed their affect. Using hierarchical linear modeling, we found moderate to strong effect sizes for synchrony to occur, especially in competitive and fun task conditions. Positive affect was associated positively with synchrony, negative affect was associated negatively. As for causal direction, data supported the interpretation that synchrony entailed affect rather than vice versa. The link between nonverbal synchrony and affect was strongest in female dyads. The findings extend previous reports of synchrony and mimicry associated with emotion in relationships and suggest a possible mechanism of the synchrony-affect correlation.

  3. 40 CFR 62.14102 - Affected facilities.

    Science.gov (United States)

    2010-07-01

    ... plastics/rubber recycling unit (as defined in 40 CFR 60.51b) are not subject to this subpart if the owner... Requirements for Large Municipal Waste Combustors Constructed on or Before September 20, 1994 § 62.14102 Affected facilities. (a) The affected facility to which this subpart applies is each municipal...

  4. Affective priming with auditory speech stimuli

    NARCIS (Netherlands)

    J. Degner

    2011-01-01

    Four experiments explored the applicability of auditory stimulus presentation in affective priming tasks. In Experiment 1, it was found that standard affective priming effects occur when prime and target words are presented simultaneously via headphones similar to a dichotic listening procedure. In

  5. How Does Social Trust Affect Economic Growth?

    DEFF Research Database (Denmark)

    Bjørnskov, Christian

    set is available. The results indicate that trust affects schooling and the rule of law directly. These variables in turn affect the investment rate (schooling) and provide a direct effect (rule of law) on the growth rate. The paper closes with a short discussion of the relevance of the findings....

  6. Affective multimodal mirror: sensing and eliciting laughter

    NARCIS (Netherlands)

    Melder, W.A.; Truong, K.P.; Uyl, M. den; Leeuwen, D.A. van; Neerincx, M.A.; Loos, L.R.; Stock Plum, B.

    2007-01-01

    In this paper, we present a multimodal affective mirror that senses and elicits laughter. Currently, the mirror contains a vocal and a facial affect-sensing module, a component that fuses the output of these two modules to achieve a user-state assessment, a user state transition model, and a compone

  7. Leader affective presence and innovation in teams.

    Science.gov (United States)

    Madrid, Hector P; Totterdell, Peter; Niven, Karen; Barros, Eduardo

    2016-05-01

    Affective presence is a novel personality construct that describes the tendency of individuals to make their interaction partners feel similarly positive or negative. We adopt this construct, together with the input-process-output model of teamwork, to understand how team leaders influence team interaction and innovation performance. In 2 multisource studies, based on 350 individuals working in 87 teams of 2 public organizations and 734 individuals working in 69 teams of a private organization, we tested and supported hypotheses that team leader positive affective presence was positively related to team information sharing, whereas team leader negative affective presence was negatively related to the same team process. In turn, team information sharing was positively related to team innovation, mediating the effects of leader affective presence on this team output. The results indicate the value of adopting an interpersonal individual differences approach to understanding how affect-related characteristics of leaders influence interaction processes and complex performance in teams. (PsycINFO Database Record

  8. Affective Arousal as Information: How Affective Arousal Influences Judgments, Learning, and Memory.

    Science.gov (United States)

    Storbeck, Justin; Clore, Gerald L

    2008-09-01

    The affect-as-information framework posits that affect is embodied information about value and importance. The valence dimension of affect provides evaluative information about stimulus objects, which plays a role in judgment and decisionmaking. Affect can also provide evaluative information about one's own cognitions and response inclinations, information that guides thinking and reasoning. In particular, positive affect often promotes, and negative affect inhibits, accessible responses or dominant modes of thinking. Affect thus moderates many of the textbook phenomena in cognitive psychology. In the current review, we suggest additionally that the arousal dimension of affect amplifies reactions, leading to intensified evaluations, increased reliance on particular styles of learning, and enhanced long-term memory for events. We conclude that whereas valenced affective cues serve as information about value, the arousal dimension provides information about urgency or importance. PMID:25067943

  9. Affective brain–computer music interfacing

    Science.gov (United States)

    Daly, Ian; Williams, Duncan; Kirke, Alexis; Weaver, James; Malik, Asad; Hwang, Faustina; Miranda, Eduardo; Nasuto, Slawomir J.

    2016-08-01

    Objective. We aim to develop and evaluate an affective brain–computer music interface (aBCMI) for modulating the affective states of its users. Approach. An aBCMI is constructed to detect a user's current affective state and attempt to modulate it in order to achieve specific objectives (for example, making the user calmer or happier) by playing music which is generated according to a specific affective target by an algorithmic music composition system and a case-based reasoning system. The system is trained and tested in a longitudinal study on a population of eight healthy participants, with each participant returning for multiple sessions. Main results. The final online aBCMI is able to detect its users current affective states with classification accuracies of up to 65% (3 class, p\\lt 0.01) and modulate its user's affective states significantly above chance level (p\\lt 0.05). Significance. Our system represents one of the first demonstrations of an online aBCMI that is able to accurately detect and respond to user's affective states. Possible applications include use in music therapy and entertainment.

  10. Affect and Public Support for Military Action

    Directory of Open Access Journals (Sweden)

    Dukhong Kim

    2014-12-01

    Full Text Available This study examines the effects of affect on public opinion on foreign policy. It extends the existing studies which show a significant role that affect, as measured by feelings toward a country, plays in shaping public opinion on military action. According to the existing theory, the mass public, which does not have high levels of political information and knowledge, can rely on affect to make reasonable decisions and opinions. This is possible because affect works as an information shortcut or heuristic that can help those individuals who lack cognitive capacity to engage in a systematic search for information and a decision-making process. The research finding confirms this theory. More importantly, this study extends the existing studies by elaborating the conditions under which affect works in accounting for individuals’ support for military intervention. The effect of affect is conditioned by the level of political knowledge, which shows that knowledgeable individuals are more adept at using affect as a heuristic tool.

  11. Embodied affectivity: On moving and being moved

    Directory of Open Access Journals (Sweden)

    Thomas eFuchs

    2014-06-01

    Full Text Available There is a growing body of research indicating that bodily sensation and behaviour strongly influences one’s emotional reaction towards certain situations or objects. On this background, a framework model of embodied affectivity is suggested: we regard emotions as resulting from the circular interaction between affective qualities or affordances in the environment and the subject’s bodily resonance, be it in the form of sensations, postures, expressive movements or movement tendencies. Motion and emotion are thus intrinsically connected: one is moved by movement (perception; impression; affection and moved to move (action; expression; e-motion. Through its resonance, the body functions as a medium of emotional perception: it colours or charges self-experience and the environment with affective valences while it remains itself in the background of one’s own awareness. This model is then applied to emotional social understanding or interaffectivity which is regarded as an intertwinement of two cycles of embodied affectivity, thus continuously modifying each partner’s affective affordances and bodily resonance. We conclude with considerations of how embodied affectivity is altered in psychopathology and can be addressed in psychotherapy of the embodied self.

  12. Affective Atmospheres in the House of Usher

    DEFF Research Database (Denmark)

    Brink, Dennis Meyhoff

    2016-01-01

    Emotional intensities do not only pertain to the ‘inner life’ of individuals; they are also to be found, as the saying goes, ‘in the air,’ i.e. as shared atmospheres that envelope, permeate, and affect us. Such affective atmospheres are omnipresent in Edgar Allan Poe’s short story “The Fall...... and atmospheres in literary and cultural studies are extraordinarily productive for an analysis of Poe’s short story: on the one hand they can help us understand the many descriptions of affective atmospheres in Poe’s story, and on the other hand Poe’s text can help us discuss existing theories and develop new...... concepts in order to contribute to the ongoing theorization of affects and atmospheres. Inspired by a number of close readings of Poe’s story, the essay thus proposes new concepts such as affective emission, affective ecosystem, and affective possession. Furthermore, it argues that Poe’s story reveals why...

  13. Affective brain-computer music interfacing

    Science.gov (United States)

    Daly, Ian; Williams, Duncan; Kirke, Alexis; Weaver, James; Malik, Asad; Hwang, Faustina; Miranda, Eduardo; Nasuto, Slawomir J.

    2016-08-01

    Objective. We aim to develop and evaluate an affective brain-computer music interface (aBCMI) for modulating the affective states of its users. Approach. An aBCMI is constructed to detect a user's current affective state and attempt to modulate it in order to achieve specific objectives (for example, making the user calmer or happier) by playing music which is generated according to a specific affective target by an algorithmic music composition system and a case-based reasoning system. The system is trained and tested in a longitudinal study on a population of eight healthy participants, with each participant returning for multiple sessions. Main results. The final online aBCMI is able to detect its users current affective states with classification accuracies of up to 65% (3 class, p\\lt 0.01) and modulate its user's affective states significantly above chance level (p\\lt 0.05). Significance. Our system represents one of the first demonstrations of an online aBCMI that is able to accurately detect and respond to user's affective states. Possible applications include use in music therapy and entertainment.

  14. Embodied affectivity: on moving and being moved.

    Science.gov (United States)

    Fuchs, Thomas; Koch, Sabine C

    2014-01-01

    There is a growing body of research indicating that bodily sensation and behavior strongly influences one's emotional reaction toward certain situations or objects. On this background, a framework model of embodied affectivity is suggested: we regard emotions as resulting from the circular interaction between affective qualities or affordances in the environment and the subject's bodily resonance, be it in the form of sensations, postures, expressive movements or movement tendencies. Motion and emotion are thus intrinsically connected: one is moved by movement (perception; impression; affection) and moved to move (action; expression; e-motion). Through its resonance, the body functions as a medium of emotional perception: it colors or charges self-experience and the environment with affective valences while it remains itself in the background of one's own awareness. This model is then applied to emotional social understanding or interaffectivity which is regarded as an intertwinement of two cycles of embodied affectivity, thus continuously modifying each partner's affective affordances and bodily resonance. We conclude with considerations of how embodied affectivity is altered in psychopathology and can be addressed in psychotherapy of the embodied self. PMID:24936191

  15. Implicit processing of visual emotions is affected by sound-induced affective states and individual affective traits.

    Directory of Open Access Journals (Sweden)

    Tiziana Quarto

    Full Text Available The ability to recognize emotions contained in facial expressions are affected by both affective traits and states and varies widely between individuals. While affective traits are stable in time, affective states can be regulated more rapidly by environmental stimuli, such as music, that indirectly modulate the brain state. Here, we tested whether a relaxing or irritating sound environment affects implicit processing of facial expressions. Moreover, we investigated whether and how individual traits of anxiety and emotional control interact with this process. 32 healthy subjects performed an implicit emotion processing task (presented to subjects as a gender discrimination task while the sound environment was defined either by a a therapeutic music sequence (MusiCure, b a noise sequence or c silence. Individual changes in mood were sampled before and after the task by a computerized questionnaire. Additionally, emotional control and trait anxiety were assessed in a separate session by paper and pencil questionnaires. Results showed a better mood after the MusiCure condition compared with the other experimental conditions and faster responses to happy faces during MusiCure compared with angry faces during Noise. Moreover, individuals with higher trait anxiety were faster in performing the implicit emotion processing task during MusiCure compared with Silence. These findings suggest that sound-induced affective states are associated with differential responses to angry and happy emotional faces at an implicit stage of processing, and that a relaxing sound environment facilitates the implicit emotional processing in anxious individuals.

  16. Affective Body Movements (for Robots) Across Cultures

    DEFF Research Database (Denmark)

    Rehm, Matthias

    2016-01-01

    Humans are very good in expressing and interpreting emotions from a variety of different sources like voice, facial expression, or body movements. In this article, we concentrate on body movements and show that those are not only a source of affective information but might also have a different i...... with a study on creating an affective knocking movement for a humanoid robot and give details about a co-creation experiment for collecting a cross-cultural database on affective body movements and about the probabilistic model derived from this data....

  17. Affectivity in the Young Sartre's Intersubjective Theory

    Directory of Open Access Journals (Sweden)

    Carlos de la Puente

    2006-12-01

    Full Text Available The intersubjective theory that Sartre proposed in Being and Nothingness contends that human encounters are necessarily reifying. The author proposes that one of the constitutive theoretical elements of this pessimistic view of human encounters is Sartre’s conception of affectivity as a degradation of consciousness. The author explores this vision of affection that Sartre initially developed in his essay Outline of a Theory of Emotions, and concludes that it was this mode of understanding affectivity that later decisively influenced his contention in Being and Nothingness that the essence of human relations is conflict.

  18. Introduction: Analysing Emotion and Theorising Affect

    Directory of Open Access Journals (Sweden)

    Peta Tait

    2016-08-01

    Full Text Available This discussion introduces ideas of emotion and affect for a volume of articles demonstrating the scope of approaches used in their study within the humanities and creative arts. The volume offers multiple perspectives on emotion and affect within 20th-century and 21st-century texts, arts and organisations and their histories. The discussion explains how emotion encompasses the emotions, emotional feeling, sensation and mood and how these can be analysed particularly in relation to literature, art and performance. It briefly summarises concepts of affect theory within recent approaches before introducing the articles.

  19. How positive affect modulates cognitive control: New insights into the specificity of positive affect effects

    OpenAIRE

    Fröber, Kerstin

    2013-01-01

    Converging evidence suggests that positive affect modulates cognitive control by increasing cognitive flexibility. The present thesis is aimed to shed further light on this relationship between positive affect and cognitive control by investigating possible influences of arousal (Part I), dissociating between proactive and reactive control (Part II), and testing an increased novelty bias under positive affect (Part III). Arousal differences between positive affective states were manipulate...

  20. Affective Videogames and Modes of Affective Gaming: Assist Me, Challenge Me, Emote Me

    OpenAIRE

    Gilleade, Kiel; Dix, Alan; Allanson, Jen

    2005-01-01

    In this paper we describe the fundamentals of affective gaming from a physiological point of view, covering some of the origins of the genre, how affective videogames operate and current conceptual and technological capabilities. We ground this overview of the ongoing research by taking an in-depth look at one of our own early biofeedback-based affective games. Based on our analysis of existing videogames and our own experience with affective videogames, we propose a new approach to game desi...

  1. Mechanically loaded myotubes affect osteoclast formation

    NARCIS (Netherlands)

    P. Juffer; R.T. Jaspers; J. Klein-Nulend; A.D. Bakker

    2014-01-01

    In response to mechanical loading skeletal muscle produces numerous growth factors and cytokines that enter the circulation. We hypothesized that myotubes produce soluble factors that affect osteoclast formation and aimed to identify which osteoclastogenesis-modulating factors are differentially pro

  2. 28 CFR 55.15 - Affected activities.

    Science.gov (United States)

    2010-07-01

    ... RIGHTS ACT REGARDING LANGUAGE MINORITY GROUPS Minority Language Materials and Assistance § 55.15 Affected... of applicable language minority groups to be effectively informed of and participate effectively...

  3. Environmental factors affecting autoimmune thyroid disease

    Energy Technology Data Exchange (ETDEWEB)

    Safran, M.; Paul, T.L.; Roti, E.; Braverman, L.E.

    1987-06-01

    A number of environmental factors affect the incidence and progression of autoimmune thyroid disease. Exposure to excess iodine, certain drugs, infectious agents and pollutants, and stress have all been implicated.

  4. Gasoline Composition Regulations Affecting LUST Sites

    Science.gov (United States)

    Passage of the Clean Air Act Amendments in 1990 imposed requirements on gasoline composition in the United States. Impacts to ground water are affected by the provisions that required oxygenated additives and limited benzene concentration. Reformulated and oxygenated gasoline w...

  5. Will Stress during Pregnancy Affect My Baby?

    Science.gov (United States)

    ... Research Information Clinical Trials Resources and Publications Will stress during pregnancy affect my baby? Skip sharing on ... health care provider during your prenatal visits. Posttraumatic Stress Disorder (PTSD) and Pregnancy PTSD is a more ...

  6. Heart Disease Affects Women of All Ages

    Science.gov (United States)

    Skip Navigation Bar Home Current Issue Past Issues Heart Disease Affects Women of All Ages Past Issues / Winter ... weeks of a heart attack. For Women with Heart Disease: About 6 million American women have coronary heart ...

  7. Smoking Affects You | Smokefree.gov

    Science.gov (United States)

    */ 18 Ways Smoking Affects Your Health Smoking harms nearly every organ of the body. Some of these harmful effects are immediate. Find out the health effects of smoking and what happens to your body when you quit.

  8. Designing Affective Atmospheres on the Move

    DEFF Research Database (Denmark)

    Wind, Simon; Lanng, Ditte Bendix

    travelling “unfolds affects as much as reasons” (Jensen, 2013, p.99). Practices, embodiment, technologies and materialities interconnect in non-quantifiable experiences of mobilities, which may fruitfully be unfolded by means of the concept of “atmosphere”. According to Böhme, atmosphere cannot be reduced...... of atmosphere in mobilities design. Following the pragmatist stance that theories are tools to understand and intervene in the world around us. To do so it draws, on the one hand, on “affective atmospheres” in relation to mobilities research, as articulated by Bissel (2010) and Anderson (2009), and...... an analytical tool for capturing atmospheres as well as an interventionist tool for orchestrating atmospheres in everyday urban spaces of mobilities. References Anderson, B. (2009) ´Affective Atmospheres´, in: Emotion, Space and Society, pp. 77–81 Bissel, D. (2010) ´Passenger mobilities: affective atmospheres...

  9. Cognitive and affective control in insomnia

    Directory of Open Access Journals (Sweden)

    Ralph Erich Schmidt

    2011-12-01

    Full Text Available Insomnia is a prevalent disabling chronic disorder. The aim of this paper is fourfold: (a to review evidence suggesting that dysfunctional forms of cognitive control, such as thought suppression, worry, rumination, and imagery control, are associated with sleep disturbance; (b to review a new budding field of scientific investigation―the role of dysfunctional affect control in sleep disturbance, such as problems with down-regulating negative and positive affective states; (c to review evidence that sleep disturbance can impair next-day affect control; and (d to outline, on the basis of the reviewed evidence, how the repetitive-thought literature and the affective science literature can be combined to further understanding of, and intervention for, insomnia.

  10. ENVIRONMENTAL FACTORS AFFECTING BREAST CANCER SUSCEPTIBILITY

    Science.gov (United States)

    Environmental Factors Affecting Breast Cancer SusceptibilitySuzanne. E. FentonUS EPA, ORD, MD-67 NHEERL, Reproductive Toxicology Division, Research Triangle Park, NC 27711.Breast cancer is still the most common malignancy afflicting women in the Western world. Alt...

  11. Organizational behavior: affect in the workplace.

    Science.gov (United States)

    Brief, Arthur P; Weiss, Howard M

    2002-01-01

    The study of affect in the workplace began and peaked in the 1930s, with the decades that followed up to the 1990s not being particularly fertile. Whereas job satisfaction generally continues to be loosely but not carefully thought of and measured as an affective state, critical work in the 1990s has raised serious questions about the affective status of job satisfaction in terms of its causes as well as its definition and measurement. Recent research has focused on the production of moods and emotions at work, with an emphasis, at least conceptually, on stressful events, leaders, work groups, physical settings, and rewards/punishment. Other recent research has addressed the consequences of workers' feelings, in particular, a variety of performance outcomes (e.g., helping behaviors and creativity). Even though recent interest in affect in the workplace has been intense, many theoretical and methodological opportunities and challenges remain.

  12. Nurse Educator’s Affective Teaching Strategies

    Directory of Open Access Journals (Sweden)

    Myra C. Britiller

    2014-02-01

    Full Text Available Teaching is highly charged with feeling, aroused by and directed towards not just people, but also values and ideals (Garritz, 2010. Emotions and feelings greatly affect the way the students learn and acquire knowledge. There must be a balance between the three domains of learning because once one domain is left behind, the other domains will be affected. The purpose of this study is to determine nurse educators’ affective teaching strategies. Specifically, it assessed the strategies of nurse educators on how to develop the affective domain of student nurses. In addition, the study assessed the values of student nurses in terms of God-centeredness, Leadership, Integrity, and Nationalism. Lastly, the researchers proposed innovative teaching methodologies to enhance the attitudes of nursing students. This study used descriptive research design. The respondents of the study were the nursing students and clinical instructors of Lyceum of the Philippines University – Batangas. 190 student nurses were chosen through stratified random sampling while 10 clinical instructors were chosen based on the number of times they handled the students both in lecture and clinical area. The instruments were selfmade and standardized questionnaire and interview guide to obtain the data needed for the study. The data gathered are compiled, organized and tabulated for statistical treatment. Weighted mean was utilized to compute the quantitative data whereas the interview was used to form the qualitative analysis. Role modelling is the most common strategy of nurse educators to enhance the affective domain of student nurses. Their actions consciously and unconsciously affecting the attitude of the students. Hence, confidence among the students needs most attention in developing affective domain as it produce change in other values presented in the study. The proposed teaching strategies aim to enhance the affective domain of nursing students in line with the

  13. Which Factors Affect Adolescent Food Preferences?

    OpenAIRE

    Seray Kabaran; Mercanlıgil, Seyit M.

    2013-01-01

    Hunger, extreme desire to eat a certain food, taste, price, and convenience are among the main There are various factors that affect food preferences. Hunger, extreme desire to eat a certain food, taste, price, and convenience are among the main factors affecting food preferences. Additionally, general nutritional habits, family, friends, commercials, and availability of the food are also important for food preferences. Also, past experiences with foods are related to preferring or rejecting ...

  14. Psychometric properties of the Affect Phobia Test.

    Science.gov (United States)

    Frankl, My; Philips, Björn; Berggraf, Lene; Ulvenes, Pål; Johansson, Robert; Wennberg, Peter

    2016-10-01

    The aim of this study was to make the first evaluation of the psychometric properties of the Affect Phobia Test, using the Swedish translation - a test developed to screen the ability to experience, express and regulate emotions. Data was collected from a clinical sample (N = 82) of patients with depression and/or anxiety participating in randomized controlled trial of Internet-based affect-focused treatment, and a university student sample (N = 197). The internal consistency for the total score was satisfactory (Clinical sample α = 0.88/Student sample α = 0.84) as well as for all the affective domains, except Anger/Assertion (α = 0.44/0.36), Sadness/Grief (α = 0.24/0.46) and Attachment/Closeness (α = 0.67/0.69). Test retest reliability was satisfactory (ICC > 0.77) for the total score and for all the affective domains except for Sadness/Grief (ICC = 0.04). The exploratory factor analysis resulted in a six-factor solution and did only moderately match the test's original affective domains. An empirical cut-off between the clinical and the university student sample were calculated and yielded a cut-off of 72 points. As expected, the Affect Phobia test showed negative significant correlations in the clinical group with measures on depression (rxy  = -0.229; p < 0.01) and anxiety (rxy  = -0.315; p < 0.05). The conclusion is that the psychometric properties are satisfactory for the total score of the Affect Phobia Test but not for some of the test's affective domains. Consequently the domains should not be used as subscales. The test can discriminate between individuals who seek help for psychological problems and those who do not. PMID:27461917

  15. Contributions of Philip Teitelbaum to affective neuroscience

    OpenAIRE

    Berridge, Kent C.

    2011-01-01

    As part of a festschrift issue for Philip Teitelbaum, I offer here the thesis that Teitelbaum deserves to be viewed as an important forefather to the contemporary field of affective neuroscience (which studies motivation, emotion and affect in the brain). Teitelbaum’s groundbreaking analyses of motivation deficits induced by lateral hypothalamic damage, of roles of food palatability in revealing residual function, and of recovery of ‘lost’ functions helped shape modern understanding of how mo...

  16. Cognitive and Affective Control in Insomnia

    OpenAIRE

    Ralph Erich Schmidt; Harvey, Allison G.; Martial eVan Der Linden

    2011-01-01

    Insomnia is a prevalent disabling chronic disorder. The aim of this paper is fourfold: (a) to review evidence suggesting that dysfunctional forms of cognitive control, such as thought suppression, worry, rumination, and imagery control, are associated with sleep disturbance; (b) to review a new budding field of scientific investigation – the role of dysfunctional affect control in sleep disturbance, such as problems with down-regulating negative and positive affective states; (c) to review ev...

  17. The Magic of (A)ffective Management

    OpenAIRE

    Weir, Ryan

    2014-01-01

    (A)ffective management is a people-first approach to managing employees. After all, employees and supervisors are people first. No matter how hard any individual may try, inevitably the stress and strain of life outside of work can and will bleed through into the work environment. The (A)ffective and effective manager understands this and incorporates this understanding into how he/she interacts with superiors and subordinates in the work environment on a daily basis. This article offers stra...

  18. The Affective Legacy of Silent Spring

    OpenAIRE

    Alex Lockwood

    2012-01-01

    In the fiftieth year since the publication of Silent Spring, the importance of Rachel Carson’s work can be measured in its affective influence on contemporary environmental writing across the humanities. The ground broken by Silent Spring in creating new forms of writing has placed affect at the very centre of contemporary narratives that call for pro-environmental beliefs and behaviours. A critical public-feelings framework is used to explore these issues and trace their passage from the pri...

  19. Factors Affecting Intensive Care Units Nursing Workload

    OpenAIRE

    Mohammadkarim BAHADORI; RAVANGARD, Ramin; Raadabadi, Mehdi; Mosavi, Seyed Masod; Gholami Fesharaki, Mohammad; Mehrabian, Fardin

    2014-01-01

    Background: The nursing workload has a close and strong association with the quality of services provided for the patients. Therefore, paying careful attention to the factors affecting nursing workload, especially those working in the intensive care units (ICUs), is very important. Objectives: This study aimed to determine the factors affecting nursing workload in the ICUs of the hospitals affiliated to Tehran University of Medical Sciences. Materials and Methods: This was a cross-sectional a...

  20. Learning Representations of Affect from Speech

    OpenAIRE

    Ghosh, Sayan; Laksana, Eugene; Morency, Louis-Philippe; Scherer, Stefan

    2015-01-01

    There has been a lot of prior work on representation learning for speech recognition applications, but not much emphasis has been given to an investigation of effective representations of affect from speech, where the paralinguistic elements of speech are separated out from the verbal content. In this paper, we explore denoising autoencoders for learning paralinguistic attributes i.e. categorical and dimensional affective traits from speech. We show that the representations learnt by the bott...

  1. Affective Decision Making in Insurance Markets

    OpenAIRE

    Anat Bracha

    2004-01-01

    This paper suggests incorporating affective considerations into decision making theory and insurance decision in particular. I describe a decision maker with two internal accounts - the rational account and the mental account. The rational account decides on insurance to maximize expected (perceived) utility, while the mental account chooses risk perceptions which then affect the perceived expected utility. The two accounts interact to reach a decision which is composed of both risk perceptio...

  2. Pedagogical affect, student interest, and learning performance

    OpenAIRE

    Abrantes, José Luís; Seabra, Cláudia; Lages, Luis Filipe

    2007-01-01

    Using a sample of more than 1000 students, this study reveals that students’ perceived learning depends directly on their interest, pedagogical affect, and their learning performance and indirectly on the student–instructor interaction, the instructor's responsiveness, course organization, the instructor's likeability/concern, and the student's learning performance. Likeability/concern indirectly affects student interest by influencing learning performance. The results yield recommendations f...

  3. Affect Intensity Estimation Using Multiple Modalities

    OpenAIRE

    Patwardhan, Amol; Knapp, Gerald

    2016-01-01

    One of the challenges in affect recognition is accurate estimation of the emotion intensity level. This research proposes development of an affect intensity estimation model based on a weighted sum of classification confidence levels, displacement of feature points and speed of feature point motion. The parameters of the model were calculated from data captured using multiple modalities such as face, body posture, hand movement and speech. A preliminary study was conducted to compare the accu...

  4. Affective content analysis of music video clip

    OpenAIRE

    Yazdani, Ashkan; Kappeler, Krista; Ebrahimi, Touradj

    2011-01-01

    Nowadays, the amount of multimedia contents is explosively increasing and it is often a challenging problem to find a con- tent that will be appealing or matches users’ current mood or affective state. In order to achieve this goal, an efficient indexing technique should be developed to annotate multi- media contents such that these annotations can be used in a retrieval process using an appropriate query. One approach to such indexing techniques is to determine the affect ( type and intensit...

  5. Overcoming Affective Barriers in College English Learning

    Institute of Scientific and Technical Information of China (English)

    任永东

    2014-01-01

    Nowadays, the development of economy as well as the progress of society requires better English competence of col-lege students. As a result, a large number of college students are obsessedby affective barriers in their English learning, especially when they have to cope with CET 4 or CET 6, which is more and more difficult. This paper focuses on how to help college stu-dents overcome their affective barriers more effectively to improve their English learning.

  6. Factors affecting reading recall(Part 1)

    OpenAIRE

    Hirano, Kinue

    2004-01-01

    Previous research has investigated whether many variables affect a reader's ability to understand and recall a text written in a first or second language. The present study reviewed some of the literature related to factors that affect reading recall: background knowledge, the syntactic complexity of the text, the language of recall, the importance of the structure of a passage, story schema, and sex differences and reading ability. Thus the factors considered in this paper should be taken in...

  7. Stability of Facial Affective Expressions in Schizophrenia

    Directory of Open Access Journals (Sweden)

    H. Fatouros-Bergman

    2012-01-01

    Full Text Available Thirty-two videorecorded interviews were conducted by two interviewers with eight patients diagnosed with schizophrenia. Each patient was interviewed four times: three weekly interviews by the first interviewer and one additional interview by the second interviewer. 64 selected sequences where the patients were speaking about psychotic experiences were scored for facial affective behaviour with Emotion Facial Action Coding System (EMFACS. In accordance with previous research, the results show that patients diagnosed with schizophrenia express negative facial affectivity. Facial affective behaviour seems not to be dependent on temporality, since within-subjects ANOVA revealed no substantial changes in the amount of affects displayed across the weekly interview occasions. Whereas previous findings found contempt to be the most frequent affect in patients, in the present material disgust was as common, but depended on the interviewer. The results suggest that facial affectivity in these patients is primarily dominated by the negative emotions of disgust and, to a lesser extent, contempt and implies that this seems to be a fairly stable feature.

  8. Affective neuroscience and psychophysiology: toward a synthesis.

    Science.gov (United States)

    Davidson, Richard J

    2003-09-01

    This article reviews the author's program of research on the neural substrates of emotion and affective style and their behavioral and peripheral biological correlates. Two core dimensions along which affect is organized are approach and withdrawal. Some of the key circuitry underlying approach and withdrawal components of emotion is reviewed with an emphasis on the role played by different sectors of the prefrontal cortex (PFC) and amygdala. Affective style refers to individual differences in valence-specific features of emotional reactivity and regulation. The different parameters of affective style can be objectively measured using specific laboratory probes. Relations between individual differences in prefrontal and amygdala function and specific components of affective style are illustrated. The final section of the article concludes with a brief discussion of plasticity in the central circuitry of emotion and the possibility that this circuitry can be shaped by training experiences that might potentially promote a more resilient, positive affective style. The implications of this body of work for a broader conception of psychophysiology and for training the next generation of psychophysiologists are considered in the conclusion. PMID:14696720

  9. Affective Biases in Humans and Animals.

    Science.gov (United States)

    Robinson, E S J; Roiser, J P

    2016-01-01

    Depression is one of the most common but poorly understood psychiatric conditions. Although drug treatments and psychological therapies are effective in some patients, many do not achieve full remission and some patients receive no apparent benefit. Developing new improved treatments requires a better understanding of the aetiology of symptoms and evaluation of novel therapeutic targets in pre-clinical studies. Recent developments in our understanding of the basic cognitive processes that may contribute to the development of depression and its treatment offer new opportunities for both clinical and pre-clinical research. This chapter discusses the clinical evidence supporting a cognitive neuropsychological model of depression and antidepressant efficacy, and how this information may be usefully translated to pre-clinical investigation. Studies using neuropsychological tests in depressed patients and at risk populations have revealed basic negative emotional biases and disrupted reward and punishment processing, which may also impact on non-affective cognition. These affective biases are sensitive to antidepressant treatments with early onset effects observed, suggesting an important role in recovery. This clinical work into affective biases has also facilitated back-translation to animals and the development of assays to study affective biases in rodents. These animal studies suggest that, similar to humans, rodents in putative negative affective states exhibit negative affective biases on decision-making and memory tasks. Antidepressant treatments also induce positive biases in these rodent tasks, supporting the translational validity of this approach. Although still in the early stages of development and validation, affective biases in depression have the potential to offer new insights into the clinical condition, as well as facilitating the development of more translational approaches for pre-clinical studies. PMID:27660073

  10. Dynamic musical communication of core affect.

    Science.gov (United States)

    Flaig, Nicole K; Large, Edward W

    2014-01-01

    Is there something special about the way music communicates feelings? Theorists since Meyer (1956) have attempted to explain how music could stimulate varied and subtle affective experiences by violating learned expectancies, or by mimicking other forms of social interaction. Our proposal is that music speaks to the brain in its own language; it need not imitate any other form of communication. We review recent theoretical and empirical literature, which suggests that all conscious processes consist of dynamic neural events, produced by spatially dispersed processes in the physical brain. Intentional thought and affective experience arise as dynamical aspects of neural events taking place in multiple brain areas simultaneously. At any given moment, this content comprises a unified "scene" that is integrated into a dynamic core through synchrony of neuronal oscillations. We propose that (1) neurodynamic synchrony with musical stimuli gives rise to musical qualia including tonal and temporal expectancies, and that (2) music-synchronous responses couple into core neurodynamics, enabling music to directly modulate core affect. Expressive music performance, for example, may recruit rhythm-synchronous neural responses to support affective communication. We suggest that the dynamic relationship between musical expression and the experience of affect presents a unique opportunity for the study of emotional experience. This may help elucidate the neural mechanisms underlying arousal and valence, and offer a new approach to exploring the complex dynamics of the how and why of emotional experience. PMID:24672492

  11. Leader affective presence and innovation in teams.

    Science.gov (United States)

    Madrid, Hector P; Totterdell, Peter; Niven, Karen; Barros, Eduardo

    2016-05-01

    Affective presence is a novel personality construct that describes the tendency of individuals to make their interaction partners feel similarly positive or negative. We adopt this construct, together with the input-process-output model of teamwork, to understand how team leaders influence team interaction and innovation performance. In 2 multisource studies, based on 350 individuals working in 87 teams of 2 public organizations and 734 individuals working in 69 teams of a private organization, we tested and supported hypotheses that team leader positive affective presence was positively related to team information sharing, whereas team leader negative affective presence was negatively related to the same team process. In turn, team information sharing was positively related to team innovation, mediating the effects of leader affective presence on this team output. The results indicate the value of adopting an interpersonal individual differences approach to understanding how affect-related characteristics of leaders influence interaction processes and complex performance in teams. (PsycINFO Database Record PMID:26783828

  12. Affective Coding: the Emotional Dimension of Agency

    Directory of Open Access Journals (Sweden)

    Antje eGentsch

    2014-08-01

    Full Text Available The sense of agency (the registration that I am the initiator and controller of my actions and relevant events is associated with several affective dimensions. This makes it surprising that the emotion factor has been largely neglected in the field of agency research. Current empirical investigations of the sense of agency mainly focus on sensorimotor signals (efference copy and cognitive cues (intentions, beliefs and on how they are integrated. Here we argue that this picture is not sufficient to explain agency experience, since agency and emotions constantly interact in our daily life by several ways. Reviewing first recent empirical evidence, we show that self-action perception is in fact modulated by the affective valence of outcomes already at the sensorimotor level. We hypothesize that the affective coding between agency and action outcomes plays an essential role in agency processing, i.e. the prospective, immediate or retrospective shaping of agency representations by affective components. This affective coding of agency be differentially altered in various neuropsychiatric diseases (e.g. schizophrenia vs. depression, thus helping to explain the dysfunctions and content of agency experiences in these diseases.

  13. Recent developments in affective recommender systems

    Science.gov (United States)

    Katarya, Rahul; Verma, Om Prakash

    2016-11-01

    Recommender systems (RSs) are playing a significant role since 1990s as they provide relevant, personalized information to the users over the internet. Lots of work have been done in information filtering, utilization, and application related to RS. However, an important area recently draws our attention which is affective recommender system. Affective recommender system (ARS) is latest trending area of research, as publication in this domain are few and recently published. ARS is associated with human behaviour, human factors, mood, senses, emotions, facial expressions, body gesture and physiological with human-computer interaction (HCI). Due to this assortment and various interests, more explanation is required, as it is in premature phase and growing as compared to other fields. So we have done literature review (LR) in the affective recommender systems by doing classification, incorporate reputed articles published from the year 2003 to February 2016. We include articles which highlight, analyse, and perform a study on affective recommender systems. This article categorizes, synthesizes, and discusses the research and development in ARS. We have classified and managed ARS papers according to different perspectives: research gaps, nature, algorithm or method adopted, datasets, the platform on executed, types of information and evaluation techniques applied. The researchers and professionals will positively support this survey article for understanding the current position, research in affective recommender systems and will guide future trends, opportunity and research focus in ARS.

  14. Dynamic Musical Communication of Core Affect

    Directory of Open Access Journals (Sweden)

    Nicole eFlaig

    2014-03-01

    Full Text Available Is there something special about the way music communicates feelings? Theorists since Meyer (1956 have attempted to explain how music could stimulate varied and subtle affective experiences by violating learned expectancies, or by mimicking other forms of social interaction. Our proposal is that music speaks to the brain in its own language; it need not imitate any other form of communication. We review recent theoretical and empirical literature, which suggests that all conscious processes consist of dynamic neural events, produced by spatially dispersed processes in the physical brain. Intentional thought and affective experience arise as dynamical aspects of neural events taking place in multiple brain areas simultaneously. At any given moment, this content comprises a unified scene that is integrated into a dynamic core through synchrony of neuronal oscillations. We propose that 1 neurodynamic synchrony with musical stimuli gives rise to musical qualia including tonal and temporal expectancies, and that 2 music-synchronous responses couple into core neurodynamics, enabling music to directly modulate core affect. Expressive music performance, for example, may recruit rhythm-synchronous neural responses to support affective communication. We suggest that the dynamic relationship between musical expression and the experience of affect presents a unique opportunity for the study of emotional experience. This may help elucidate the neural mechanisms underlying arousal and valence, and offer a new approach to exploring the complex dynamics of the how and why of emotional experience.

  15. Continuous Analysis of Affect from Voice and Face

    NARCIS (Netherlands)

    Gunes, Hatice; Nicolaou, Mihalis A.; Pantic, Maja; Salah, Albert Ali; Gevers, Theo

    2011-01-01

    Human affective behavior is multimodal, continuous and complex. Despite major advances within the affective computing research field, modeling, analyzing, interpreting and responding to human affective behavior still remains a challenge for automated systems as affect and emotions are complex constr

  16. Sequence Affects the Cyclization of DNA Minicircles.

    Science.gov (United States)

    Wang, Qian; Pettitt, B Montgomery

    2016-03-17

    Understanding how the sequence of a DNA molecule affects its dynamic properties is a central problem affecting biochemistry and biotechnology. The process of cyclizing short DNA, as a critical step in molecular cloning, lacks a comprehensive picture of the kinetic process containing sequence information. We have elucidated this process by using coarse-grained simulations, enhanced sampling methods, and recent theoretical advances. We are able to identify the types and positions of structural defects during the looping process at a base-pair level. Correlations along a DNA molecule dictate critical sequence positions that can affect the looping rate. Structural defects change the bending elasticity of the DNA molecule from a harmonic to subharmonic potential with respect to bending angles. We explore the subelastic chain as a possible model in loop formation kinetics. A sequence-dependent model is developed to qualitatively predict the relative loop formation time as a function of DNA sequence. PMID:26938490

  17. Do recreational activities affect coastal biodiversity?

    Science.gov (United States)

    Riera, Rodrigo; Menci, Cristiano; Sanabria-Fernández, José Antonio; Becerro, Mikel A.

    2016-09-01

    Human activities are largely affecting coastal communities worldwide. Recreational perturbations have been overlooked in comparison to other perturbations, yet they are potential threats to marine biodiversity. They affect coastal communities in different ways, underpinning consistent shifts in fish and invertebrates assemblages. Several sites were sampled subjected to varying effects by recreational fishermen (low and high pressure) and scuba divers (low and high) in an overpopulated Atlantic island. Non-consistent differences in ecological, trophic and functional diversity were found in coastal communities, considering both factors ("diving" and "fishing"). Multivariate analyses only showed significant differences in benthic invertebrates between intensively-dived and non-dived sites. The lack of clear trends may be explained by the depletion of coastal resources in the study area, an extensively-affected island by overfishing.

  18. Affective processing in bilingual speakers: disembodied cognition?

    Science.gov (United States)

    Pavlenko, Aneta

    2012-01-01

    A recent study by Keysar, Hayakawa, and An (2012) suggests that "thinking in a foreign language" may reduce decision biases because a foreign language provides a greater emotional distance than a native tongue. The possibility of such "disembodied" cognition is of great interest for theories of affect and cognition and for many other areas of psychological theory and practice, from clinical and forensic psychology to marketing, but first this claim needs to be properly evaluated. The purpose of this review is to examine the findings of clinical, introspective, cognitive, psychophysiological, and neuroimaging studies of affective processing in bilingual speakers in order to identify converging patterns of results, to evaluate the claim about "disembodied cognition," and to outline directions for future inquiry. The findings to date reveal two interrelated processing effects. First-language (L1) advantage refers to increased automaticity of affective processing in the L1 and heightened electrodermal reactivity to L1 emotion-laden words. Second-language (L2) advantage refers to decreased automaticity of affective processing in the L2, which reduces interference effects and lowers electrodermal reactivity to negative emotional stimuli. The differences in L1 and L2 affective processing suggest that in some bilingual speakers, in particular late bilinguals and foreign language users, respective languages may be differentially embodied, with the later learned language processed semantically but not affectively. This difference accounts for the reduction of framing biases in L2 processing in the study by Keysar et al. (2012). The follow-up discussion identifies the limits of the findings to date in terms of participant populations, levels of processing, and types of stimuli, puts forth alternative explanations of the documented effects, and articulates predictions to be tested in future research. PMID:23163422

  19. Affective privilege: Asymmetric interference by emotional distracters

    Directory of Open Access Journals (Sweden)

    Crystal eReeck

    2011-09-01

    Full Text Available Numerous theories posit that affectively salient stimuli are privileged in their capacity to capture attention and disrupt ongoing cognition. Two underlying assumptions in this theoretical position are that the potency of affective stimuli transcends task boundaries (i.e., emotional distracters do not have to belong to a current task-set to disrupt processing and that there is an asymmetry between emotional and cognitive processing (i.e., emotional distracters disrupt cognitive processing, but not vice versa. These assumptions have remained largely untested, as common experimental probes of emotion-cognition interaction rarely manipulate task-relevance and only examine one side of the presumed asymmetry of interference. To test these propositions directly, a face-word Stroop protocol was adapted to independently manipulate (a the congruency between target and distracter stimulus features, (b the affective salience of distracter features, and (c the task-relevance of emotional compared to non-emotional target features. A three-way interaction revealed interdependent effects of distracter relevance, congruence, and affective salience. Compared to task-irrelevant distracters, task-relevant congruent distracters facilitated performance and task-relevant incongruent distracters impaired performance, but the latter effect depended on the nature of the target feature and task. Specifically, task-irrelevant emotional distracters resulted in equivalent performance costs as task-relevant non-emotional distracters, whereas task-irrelevant non-emotional distracters did not produce performance costs comparable to those generated by task-relevant emotional distracters. These results document asymmetric cross-task interference effects for affectively salient stimuli, supporting the notion of affective prioritization in human information processing.

  20. Factors affecting tenure choice in Hong Kong

    OpenAIRE

    Liang, Jiancong; 梁健聰

    2014-01-01

    This study investigates the factors that affect the home-ownership propensity of households using a modified two-period equilibrium model. In particular, the study examines the impacts of some social, political and economic factors that in theory should affect housing tenure choice but have limited empirical evidence so far. To test the impacts of these factors, five sets of Hong Kong Census and By-Census cross sectional data over the period from 1991 to 2011 were used to estimate Binary Logi...

  1. How does concurrent sourcing affect performance?

    DEFF Research Database (Denmark)

    Mols, Niels Peter

    2010-01-01

    /methodology/approach – Based on transaction cost, agency, neoclassical economic, knowledge-based, and resource-based theory, it is proposed to show how concurrent sourcing affects performance. Findings – The paper argues that concurrent sourcing improves performance when firms face a combination of volume uncertainty......Abstract Purpose – “Concurrent sourcing” is a term used by Parmigiani to describe the phenomenon where a firm simultaneously buys and makes the same good or service. The purpose of this paper is to develop propositions that suggest how concurrent sourcing affects performance. Design...

  2. Theories of willpower affect sustained learning.

    Science.gov (United States)

    Miller, Eric M; Walton, Gregory M; Dweck, Carol S; Job, Veronika; Trzesniewski, Kali H; McClure, Samuel M

    2012-01-01

    Building cognitive abilities often requires sustained engagement with effortful tasks. We demonstrate that beliefs about willpower-whether willpower is viewed as a limited or non-limited resource-impact sustained learning on a strenuous mental task. As predicted, beliefs about willpower did not affect accuracy or improvement during the initial phases of learning; however, participants who were led to view willpower as non-limited showed greater sustained learning over the full duration of the task. These findings highlight the interactive nature of motivational and cognitive processes: motivational factors can substantially affect people's ability to recruit their cognitive resources to sustain learning over time. PMID:22745675

  3. Working night shifts affects surgeons' biological rhythm

    DEFF Research Database (Denmark)

    Amirian, Ilda; Andersen, Lærke T; Rosenberg, Jacob;

    2015-01-01

    Scale and Visual Analog Scale of fatigue, general well-being, and sleep quality. RESULTS: For both metabolite of melatonin and cortisol, a significant difference (P ...BACKGROUND: Chronic sleep deprivation combined with work during the night is known to affect performance and compromise residents' own safety. The aim of this study was to examine markers of circadian rhythm and the sleep-wake cycle in surgeons working night shifts. METHODS: Surgeons were monitored...... and on PC1. For all subjective measures, a marked deterioration was seen on PC1. CONCLUSION: Surgeons' circadian rhythm was affected by working night shifts....

  4. Prototyping teams of affective agents in robocode

    OpenAIRE

    Rebelo, António; Catalão, Fábio; Alves, João; Marreiros, Goreti; Cesar ANALIDE; Novais, Paulo; Neves, José

    2015-01-01

    The study of the impact of emotion and affect in decision making processes involved in a working team stands for a multi-disciplinary issue (e.g. with insights from disciplines such as Psychology, Neuroscience, Philosophy and Computer Science). On the one hand, and in order to create such an environment we look at a team of affective agents to play into a battlefield, which present different emotional profiles (e.g. personality and mood). An emotional system, based on the OCC (Ortony, Clore a...

  5. Affective Variables of Second Language Learning

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    <正>There are various factors influencing second language learning(L2 learning). Among then,affective variables directly or indirectly have an effect on the success of L2 learning. Based on the applied linguistics theories,the paper mainly discusses three major groups of affective variables—attitude,motivation,personality and how they influence L2 learning.It aims to make both language teachers and learners understand the importance of these variables so as to improve the efficiency of L2 learning and teaching.

  6. ON AFFECTIVE BARRIERS TO LANGUAGE LEARNING

    Institute of Scientific and Technical Information of China (English)

    XiangMaoying

    2004-01-01

    Affective factors play a significant role in languagelearning. This paper argues that positive emotions can facilitatethe language learning process and improve learners' languageperformance, while negative emotions will bring barriers tolanguage learning and reduce learners learning capacity. Withtwo true stories as an introduction and some relevant answersobtained from my questionnaire, this paper mainly discusses theinfluences of negative emotional factors on language learning.such as anxiety, low self-esteem, insecure classroomatmosphere, lack of rapport between teachers and students, etc.Some suggestions about how to overcome affective barriers areput forward.

  7. Does Political Ideology Affect Economic Growth?

    DEFF Research Database (Denmark)

    Bjørnskov, Christian

    2005-01-01

    This paper asks the question whether political ideology affects economic growth. Voters may demand inefficient levels of redistribution and government intervention, and they may care too little for aspects that really matter for the economy. Their norms and perceptions of society might, via...... their political ideology, affect economic performance. The paper presents evidence suggesting that rightwing societies have grown faster in the last decades than other democratic societies. Further analysis suggests that these societies develop better legal systems and less government intervention, which in turn...

  8. Mood swings: design and evaluation of affective interactive art

    NARCIS (Netherlands)

    Bialoskorski, Leticia S.S.; Westerink, Joyce H.D.M.; Broek, van den Egon L.

    2009-01-01

    The field of affective computing is concerned with developing emphatic products, such as affective consumer products, affective games, and affective art. This paper describes Mood Swings, an affective interactive art system, which interprets and visualizes affect expressed by a person. Mood Swings c

  9. DNA repair genes BRCA1 and DNA-PKcs have great potential in radiation therapy%DNA修复基因BRCA1和DNA-PKcs在放射治疗中有很大的潜能

    Institute of Scientific and Technical Information of China (English)

    Jiao Yang; Ximing Xu; Yanrong Hao

    2012-01-01

    Radiotherapy is a part of the front-line treatment regime for many cancers. The mechanisms of radiation-induced effects in cancers mainly involves double-strand breaks (DBS) which plays very important role in maintaining the stability of gene. As DNA repair gene breast cancer 1 (BRCA1) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) can act to maintain genetic stability though two distinct and complementary mechanisms for DNA DSB repair-homologous recombination (HR) and non-homologous end joining (NHEJ). Therefor, BRCA1 and DNA-PKcs are closely associated with radiation sensitivity, which means that they may be used as a useful tool to predict radio sensitivity in human tumour cells.

  10. Molecular basis for DNA strand displacement by NHEJ repair polymerases.

    Science.gov (United States)

    Bartlett, Edward J; Brissett, Nigel C; Plocinski, Przemyslaw; Carlberg, Tom; Doherty, Aidan J

    2016-03-18

    The non-homologous end-joining (NHEJ) pathway repairs DNA double-strand breaks (DSBs) in all domains of life. Archaea and bacteria utilize a conserved set of multifunctional proteins in a pathway termed Archaeo-Prokaryotic (AP) NHEJ that facilitates DSB repair. Archaeal NHEJ polymerases (Pol) are capable of strand displacement synthesis, whilst filling DNA gaps or partially annealed DNA ends, which can give rise to unligatable intermediates. However, an associated NHEJ phosphoesterase (PE) resects these products to ensure that efficient ligation occurs. Here, we describe the crystal structures of these archaeal (Methanocella paludicola) NHEJ nuclease and polymerase enzymes, demonstrating their strict structural conservation with their bacterial NHEJ counterparts. Structural analysis, in conjunction with biochemical studies, has uncovered the molecular basis for DNA strand displacement synthesis in AP-NHEJ, revealing the mechanisms that enable Pol and PE to displace annealed bases to facilitate their respective roles in DSB repair. PMID:26405198

  11. DNA ligase IV as a new molecular target for temozolomide

    Energy Technology Data Exchange (ETDEWEB)

    Kondo, Natsuko [Department of Biology, School of Medicine, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521 (Japan); Department of Neurosurgery, School of Medicine, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521 (Japan); Takahashi, Akihisa; Mori, Eiichiro; Ohnishi, Ken [Department of Biology, School of Medicine, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521 (Japan); McKinnon, Peter J. [Department of Genetics and Tumor Cell Biology, St. Jude Children' s Research Hospital, Memphis, TN 38105 (United States); Sakaki, Toshisuke; Nakase, Hiroyuki [Department of Neurosurgery, School of Medicine, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521 (Japan); Ohnishi, Takeo, E-mail: tohnishi@naramed-u.ac.jp [Department of Biology, School of Medicine, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521 (Japan)

    2009-10-02

    Temozolomide (TMZ) is a methylating agent used in chemotherapy against glioblastoma. This work was designed to clarify details in repair pathways acting to remove DNA double-strand breaks (DSBs) induced by TMZ. Cultured mouse embryonic fibroblasts were used which were deficient in DSB repair genes such as homologous recombination repair-related genes X-ray repair cross-complementing group 2 (XRCC2)and radiation sensitive mutant54 (Rad54), non-homologous end joining repair-related gene DNAligase IV (Lig4). Cell sensitivity to drug treatments was assessed using colony forming assays. The most effective molecular target which was correlated with TMZ cell sensitivity was Lig4. In addition, it was found that small interference RNAs (siRNA) for Lig4 efficiently enhanced cell lethality induced by TMZ in human glioblastoma A172 cells. These findings suggest that down regulation of Lig4 might provide a useful tool for cell sensitization during TMZ chemotherapy.

  12. TALEN-Mediated Mutagenesis and Genome Editing.

    Science.gov (United States)

    Ma, Alvin C H; Chen, Yi; Blackburn, Patrick R; Ekker, Stephen C

    2016-01-01

    Transcription activator-like effectors (TALEs) are important genomic tools with customizable DNA-binding motifs for locus-specific modifications. In particular, TALE nucleases or TALENs have been successfully used in the zebrafish model system to introduce targeted mutations via repair of double-stranded breaks (DSBs) either through nonhomologous end joining (NHEJ) or by homology-directed repair (HDR) and homology-independent repair in the presence of a donor template. Compared with other customizable nucleases, TALENs offer high binding specificity and fewer sequence constraints in targeting the genome, with comparable mutagenic activity. Here, we describe a detailed in silico design tool for zebrafish genome editing for TALENs and CRISPR/Cas9 custom restriction enzymes using Mojo Hand 2.0 software. PMID:27464798

  13. TALE nucleases and next generation GM crops.

    Science.gov (United States)

    Mahfouz, Magdy M; Li, Lixin

    2011-01-01

    Site-specific and adaptable DNA binding domains are essential modules to develop genome engineering technologies for crop improvement. Transcription activator-like effectors (TALEs) proteins are used to provide a highly specific and adaptable DNA binding modules. TALE chimeric nucleases (TALENs) were used to generate site-specific double strand breaks (DSBs) in vitro and in yeast, Caenorhabditis elegans, mammalian and plant cells. The genomic DSBs can be generated at predefined and user-selected loci and repaired by either the non-homologous end joining (NHEJ) or homology dependent repair (HDR). Thus, TALENs can be used to achieve site-specific gene addition, stacking, deletion or inactivation. TALE-based genome engineering tools should be powerful to develop new agricultural biotechnology approaches for crop improvement. Here, we discuss the recent research and the potential applications of TALENs to accelerate the generation of genomic variants through targeted mutagenesis and to produce a non-transgenic GM crops with the desired phenotype.

  14. [Research progress in the third-generation genomic editing technology - CRISPR/Cas9].

    Science.gov (United States)

    Zhou, Yalan; Zong, Yanan; Kong, Xiangdong

    2016-10-01

    CRISPR/Cas9 technology originated from type II CRISPR/Cas system, which is widely found in bacteria and equips them with acquired immunity against viruses and plasmids. CRISPR-associated protein Cas9 is a RNA-guided endonuclease, which can efficiently introduce double-strand breaks at specific sites and activate homologous recombination and/or non-homologous end joining mechanism for the repair of impaired DNA. Features such as easy-to-use, cost-effectiveness, multiple targeting ability have made it the third-generation genomic engineering tool following ZFNs and TALENs. Here the history of discovery and molecular mechanism of the CRISPR/Cas9 technology are reviewed. The rapid advance in its various applications, especially for the treatment of human genetic disorders, as well as some concomitant problems are discussed. PMID:27577230

  15. Mutations in XRCC4 cause primordial dwarfism without causing immunodeficiency.

    Science.gov (United States)

    Saito, Shinta; Kurosawa, Aya; Adachi, Noritaka

    2016-08-01

    In successive reports from 2014 to 2015, X-ray repair cross-complementing protein 4 (XRCC4) has been identified as a novel causative gene of primordial dwarfism. XRCC4 is indispensable for non-homologous end joining (NHEJ), the major pathway for repairing DNA double-strand breaks. As NHEJ is essential for V(D)J recombination during lymphocyte development, it is generally believed that abnormalities in XRCC4 cause severe combined immunodeficiency. Contrary to expectations, however, no overt immunodeficiency has been observed in patients with primordial dwarfism harboring XRCC4 mutations. Here, we describe the various XRCC4 mutations that lead to disease and discuss their impact on NHEJ and V(D)J recombination. PMID:27169690

  16. TALE nucleases and next generation GM crops.

    KAUST Repository

    Mahfouz, Magdy M.

    2011-04-01

    Site-specific and adaptable DNA binding domains are essential modules to develop genome engineering technologies for crop improvement. Transcription activator-like effectors (TALEs) proteins are used to provide a highly specific and adaptable DNA binding modules. TALE chimeric nucleases (TALENs) were used to generate site-specific double strand breaks (DSBs) in vitro and in yeast, Caenorhabditis elegans, mammalian and plant cells. The genomic DSBs can be generated at predefined and user-selected loci and repaired by either the non-homologous end joining (NHEJ) or homology dependent repair (HDR). Thus, TALENs can be used to achieve site-specific gene addition, stacking, deletion or inactivation. TALE-based genome engineering tools should be powerful to develop new agricultural biotechnology approaches for crop improvement. Here, we discuss the recent research and the potential applications of TALENs to accelerate the generation of genomic variants through targeted mutagenesis and to produce a non-transgenic GM crops with the desired phenotype.

  17. [Application of CRISPR-Cas9 genome editing for constructing animal models of human diseases].

    Science.gov (United States)

    Ou, Zhanhui; Sun, Xiaofang

    2016-08-01

    The CRISPR-Cas9 system is a new targeted nuclease for genome editing, which can directly introduce modifications at the targeted genomic locus. The system utilizes a short single guide RNA (sgRNA) to direct the endonuclease Cas9 in the genome. Upon targeting, Cas9 can generate DNA double-strand breaks (DSBs). As such DSBs are repaired by non-homologous end joining (NHEJ) or homology directed repair (HDR), therefore facilitates introduction of random or specific mutations, repair of endogenous mutations, or insertion of DNA elements. The system has been successfully used to generate gene targeted cell lines including those of human, animals and plants. This article reviews recent advances made in this rapidly evolving technique for the generation of animal models for human diseases.

  18. CRISPR-Cas9-Guided Genome Engineering in C. elegans.

    Science.gov (United States)

    Kim, Hyun-Min; Colaiácovo, Monica P

    2016-07-01

    The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system is successfully being used for efficient and targeted genome editing in various organisms, including the nematode C. elegans. Recent studies have developed various CRISPR-Cas9 approaches to enhance genome engineering via two major DNA double-strand break repair pathways: non-homologous end joining and homologous recombination. Here we describe a protocol for Cas9-mediated C. elegans genome editing together with single guide RNA (sgRNA) and repair template cloning, as well as injection methods required for delivering Cas9, sgRNAs, and repair template DNA into the C. elegans germline. © 2016 by John Wiley & Sons, Inc.

  19. Stem Cells: The Pursuit of Genomic Stability

    Directory of Open Access Journals (Sweden)

    Saranya P. Wyles

    2014-11-01

    Full Text Available Stem cells harbor significant potential for regenerative medicine as well as basic and clinical translational research. Prior to harnessing their reparative nature for degenerative diseases, concerns regarding their genetic integrity and mutation acquisition need to be addressed. Here we review pluripotent and multipotent stem cell response to DNA damage including differences in DNA repair kinetics, specific repair pathways (homologous recombination vs. non-homologous end joining, and apoptotic sensitivity. We also describe DNA damage and repair strategies during reprogramming and discuss potential genotoxic agents that can reduce the inherent risk for teratoma formation and mutation accumulation. Ensuring genomic stability in stem cell lines is required to achieve the quality control standards for safe clinical application.

  20. DNA End Resection:Facts and Mechanisms

    Institute of Scientific and Technical Information of China (English)

    Ting Liu; a Jun Huang; b

    2016-01-01

    DNA double-strand breaks (DSBs), which arise following exposure to a number of endogenous and exogenous agents, can be repaired by either the homologous recombination (HR) or non-homologous end-joining (NHEJ) pathways in eukaryotic cells. A vital step in HR repair is DNA end resection, which generates a long 30 single-stranded DNA (ssDNA) tail that can invade the homologous DNA strand. The generation of 30 ssDNA is not only essential for HR repair, but also promotes activation of the ataxia telangiectasia and Rad3-related protein (ATR). Multiple fac-tors, including the MRN/X complex, C-terminal-binding protein interacting protein (CtIP)/Sae2, exonuclease 1 (EXO1), Bloom syndrome protein (BLM)/Sgs1, DNA2 nuclease/helicase, and several chromatin remodelers, cooperate to complete the process of end resection. Here we review the basic machinery involved in DNA end resection in eukaryotic cells.

  1. In normal human fibroblasts variation in DSB repair capacity cannot be ascribed to radiation-induced changes in the localisation, expression or activity of major NHEJ proteins

    DEFF Research Database (Denmark)

    Kasten-Pisula, Ulla; Vronskaja, Svetlana; Overgaard, Jens;

    2008-01-01

    BACKGROUND AND PURPOSE: The aim of the present study was to test whether for normal human fibroblasts the variation in double-strand break (DSB) repair capacity results from radiation-induced differences in localisation, expression or activity of major non-homologous end-joining (NHEJ) proteins...... in the nucleus with no detectable amount in the cytoplasm. This distribution was not altered upon irradiation. In non-irradiated cells the level of these proteins varied with a CV ranging between 16% and 20%, but there was no correlation with the respective cellular DSB repair capacity. Irradiation (3.5 and 15Gy...... in the activity of the DNA-PK complex induced upon irradiation. CONCLUSIONS: For normal human fibroblasts, the level or activity of NHEJ proteins measured prior to or after irradiation cannot be used to predict the DSB repair capacity or cellular radiosensitivity. Udgivelsesdato: 2008-Mar...

  2. CRISPR-Cas9-Guided Genome Engineering in C. elegans.

    Science.gov (United States)

    Kim, Hyun-Min; Colaiácovo, Monica P

    2016-01-01

    The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system is successfully being used for efficient and targeted genome editing in various organisms, including the nematode C. elegans. Recent studies have developed various CRISPR-Cas9 approaches to enhance genome engineering via two major DNA double-strand break repair pathways: non-homologous end joining and homologous recombination. Here we describe a protocol for Cas9-mediated C. elegans genome editing together with single guide RNA (sgRNA) and repair template cloning, as well as injection methods required for delivering Cas9, sgRNAs, and repair template DNA into the C. elegans germline. © 2016 by John Wiley & Sons, Inc. PMID:27366893

  3. Tankyrases Promote Homologous Recombination and Check Point Activation in Response to DSBs.

    Directory of Open Access Journals (Sweden)

    Zita Nagy

    2016-02-01

    Full Text Available DNA lesions are sensed by a network of proteins that trigger the DNA damage response (DDR, a signaling cascade that acts to delay cell cycle progression and initiate DNA repair. The Mediator of DNA damage Checkpoint protein 1 (MDC1 is essential for spreading of the DDR signaling on chromatin surrounding Double Strand Breaks (DSBs by acting as a scaffold for PI3K kinases and for ubiquitin ligases. MDC1 also plays a role both in Non-Homologous End Joining (NHEJ and Homologous Recombination (HR repair pathways. Here we identify two novel binding partners of MDC1, the poly (ADP-ribose Polymerases (PARPs TNKS1 and 2. We find that TNKSs are recruited to DNA lesions by MDC1 and regulate DNA end resection and BRCA1A complex stabilization at lesions leading to efficient DSB repair by HR and proper checkpoint activation.

  4. The DNA repair complex DNA-PK, a pharmacological target in cancer chemotherapy and radiotherapy; Le complexe de reparation de l'ADN DNA-PK, une cible pharmacologique en chimiotherapie et radiotherapie anticancereuse

    Energy Technology Data Exchange (ETDEWEB)

    Salles, B.; Calsou, P.; Frit, P.; Muller, C. [Institut de Pharmacologie et Biologie Structurale (IPBS), UMR CNRS 5089, 31 - Toulouse (France)

    2006-05-15

    A line of investigation in the search for sensitizing tumor cells to chemotherapy or radiotherapy relies on the selection of DNA repair inhibitors. In the area of DNA repair mechanisms, DNA-dependent protein kinase (DNA-PK) represents a key complex. Indeed DNA-PK is involved in the non-homologous end joining (NHEJ) process that corresponds to the major activity responsible for cell survival after ionizing radiation or chemotherapeutic treatment producing DNA double strand breaks. DNA-PK belongs to the PI3-K related kinase family and specific inhibitors have been recently selected and evaluated as radio- and chemo-sensitizers. These drugs, along with other ways to inhibit the DSBs repair process, are presented and discussed. (authors)

  5. Mutations in XRCC4 cause primordial dwarfism without causing immunodeficiency.

    Science.gov (United States)

    Saito, Shinta; Kurosawa, Aya; Adachi, Noritaka

    2016-08-01

    In successive reports from 2014 to 2015, X-ray repair cross-complementing protein 4 (XRCC4) has been identified as a novel causative gene of primordial dwarfism. XRCC4 is indispensable for non-homologous end joining (NHEJ), the major pathway for repairing DNA double-strand breaks. As NHEJ is essential for V(D)J recombination during lymphocyte development, it is generally believed that abnormalities in XRCC4 cause severe combined immunodeficiency. Contrary to expectations, however, no overt immunodeficiency has been observed in patients with primordial dwarfism harboring XRCC4 mutations. Here, we describe the various XRCC4 mutations that lead to disease and discuss their impact on NHEJ and V(D)J recombination.

  6. The DNA repair complex DNA-PK, a pharmacological target in cancer chemotherapy and radiotherapy

    International Nuclear Information System (INIS)

    A line of investigation in the search for sensitizing tumor cells to chemotherapy or radiotherapy relies on the selection of DNA repair inhibitors. In the area of DNA repair mechanisms, DNA-dependent protein kinase (DNA-PK) represents a key complex. Indeed DNA-PK is involved in the non-homologous end joining (NHEJ) process that corresponds to the major activity responsible for cell survival after ionizing radiation or chemotherapeutic treatment producing DNA double strand breaks. DNA-PK belongs to the PI3-K related kinase family and specific inhibitors have been recently selected and evaluated as radio- and chemo-sensitizers. These drugs, along with other ways to inhibit the DSBs repair process, are presented and discussed. (authors)

  7. Tankyrases Promote Homologous Recombination and Check Point Activation in Response to DSBs.

    Science.gov (United States)

    Nagy, Zita; Kalousi, Alkmini; Furst, Audrey; Koch, Marc; Fischer, Benoit; Soutoglou, Evi

    2016-02-01

    DNA lesions are sensed by a network of proteins that trigger the DNA damage response (DDR), a signaling cascade that acts to delay cell cycle progression and initiate DNA repair. The Mediator of DNA damage Checkpoint protein 1 (MDC1) is essential for spreading of the DDR signaling on chromatin surrounding Double Strand Breaks (DSBs) by acting as a scaffold for PI3K kinases and for ubiquitin ligases. MDC1 also plays a role both in Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR) repair pathways. Here we identify two novel binding partners of MDC1, the poly (ADP-ribose) Polymerases (PARPs) TNKS1 and 2. We find that TNKSs are recruited to DNA lesions by MDC1 and regulate DNA end resection and BRCA1A complex stabilization at lesions leading to efficient DSB repair by HR and proper checkpoint activation. PMID:26845027

  8. DNA double-strand break repair: a tale of pathway choices.

    Science.gov (United States)

    Li, Jing; Xu, Xingzhi

    2016-07-01

    Deoxyribonucleic acid double-strand breaks (DSBs) are cytotoxic lesions that must be repaired either through homologous recombination (HR) or non-homologous end-joining (NHEJ) pathways. DSB repair is critical for genome integrity, cellular homeostasis and also constitutes the biological foundation for radiotherapy and the majority of chemotherapy. The choice between HR and NHEJ is a complex yet not completely understood process that will entail more future efforts. Herein we review our current understandings about how the choice is made over an antagonizing balance between p53-binding protein 1 and breast cancer 1 in the context of cell cycle stages, downstream effects, and distinct chromosomal histone marks. These exciting areas of research will surely bring more mechanistic insights about DSB repair and be utilized in the clinical settings. PMID:27217474

  9. Phosphorylation: The Molecular Switch of Double-Strand Break Repair

    Directory of Open Access Journals (Sweden)

    K. C. Summers

    2011-01-01

    Full Text Available Repair of double-stranded breaks (DSBs is vital to maintaining genomic stability. In mammalian cells, DSBs are resolved in one of the following complex repair pathways: nonhomologous end-joining (NHEJ, homologous recombination (HR, or the inclusive DNA damage response (DDR. These repair pathways rely on factors that utilize reversible phosphorylation of proteins as molecular switches to regulate DNA repair. Many of these molecular switches overlap and play key roles in multiple pathways. For example, the NHEJ pathway and the DDR both utilize DNA-PK phosphorylation, whereas the HR pathway mediates repair with phosphorylation of RPA2, BRCA1, and BRCA2. Also, the DDR pathway utilizes the kinases ATM and ATR, as well as the phosphorylation of H2AX and MDC1. Together, these molecular switches regulate repair of DSBs by aiding in DSB recognition, pathway initiation, recruitment of repair factors, and the maintenance of repair mechanisms.

  10. Tankyrases Promote Homologous Recombination and Check Point Activation in Response to DSBs

    Science.gov (United States)

    Furst, Audrey; Koch, Marc; Fischer, Benoit; Soutoglou, Evi

    2016-01-01

    DNA lesions are sensed by a network of proteins that trigger the DNA damage response (DDR), a signaling cascade that acts to delay cell cycle progression and initiate DNA repair. The Mediator of DNA damage Checkpoint protein 1 (MDC1) is essential for spreading of the DDR signaling on chromatin surrounding Double Strand Breaks (DSBs) by acting as a scaffold for PI3K kinases and for ubiquitin ligases. MDC1 also plays a role both in Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR) repair pathways. Here we identify two novel binding partners of MDC1, the poly (ADP-ribose) Polymerases (PARPs) TNKS1 and 2. We find that TNKSs are recruited to DNA lesions by MDC1 and regulate DNA end resection and BRCA1A complex stabilization at lesions leading to efficient DSB repair by HR and proper checkpoint activation. PMID:26845027

  11. Controlling DNA-End Resection: An Emerging Task for Ubiquitin and SUMO.

    Science.gov (United States)

    Himmels, Sarah-Felicitas; Sartori, Alessandro A

    2016-01-01

    DNA double-strand breaks (DSBs) are one of the most detrimental lesions, as their incorrect or incomplete repair can lead to genomic instability, a hallmark of cancer. Cells have evolved two major competing DSB repair mechanisms: Homologous recombination (HR) and non-homologous end joining (NHEJ). HR is initiated by DNA-end resection, an evolutionarily conserved process that generates stretches of single-stranded DNA tails that are no longer substrates for religation by the NHEJ machinery. Ubiquitylation and sumoylation, the covalent attachment of ubiquitin and SUMO moieties to target proteins, play multifaceted roles in DNA damage signaling and have been shown to regulate HR and NHEJ, thus ensuring appropriate DSB repair. Here, we give a comprehensive overview about the current knowledge of how ubiquitylation and sumoylation control DSB repair by modulating the DNA-end resection machinery. PMID:27602047

  12. Fast and sensitive detection of indels induced by precise gene targeting

    DEFF Research Database (Denmark)

    Yang, Zhang; Steentoft, Catharina; Hauge, Camilla;

    2015-01-01

    The nuclease-based gene editing tools are rapidly transforming capabilities for altering the genome of cells and organisms with great precision and in high throughput studies. A major limitation in application of precise gene editing lies in lack of sensitive and fast methods to detect...... and characterize the induced DNA changes. Precise gene editing induces double-stranded DNA breaks that are repaired by error-prone non-homologous end joining leading to introduction of insertions and deletions (indels) at the target site. These indels are often small and difficult and laborious to detect...... by traditional methods. Here we present a method for fast, sensitive and simple indel detection that accurately defines indel sizes down to ±1 bp. The method coined IDAA for Indel Detection by Amplicon Analysis is based on tri-primer amplicon labelling and DNA capillary electrophoresis detection, and IDAA...

  13. Modulation of DNA double-strand break repair activity in cell-free extracts of gamma-irradiated mouse testicular cells

    International Nuclear Information System (INIS)

    DNA double-strand breaks (DSBs) are potentially mutagenic lesions demanding effective damage recognition and repair. Even a single DSB can be detrimental if left unrepaired or misrepaired, and if present in gamete, it can cause foetal wastage or malformations/congenital defects in the offspring. The threats posed by DSBs have triggered the evolution of two major pathways of DSB repair, homologous recombination-mediated repair (HRR) and non-homologous end-joining (NHEJ), conserved from bacteria to mammals. Though HRR is more predominant in bacteria and yeast, NHEJ is more efficient in mammalian somatic cells. Studies in our laboratory have shown that both the pathways are equally efficient in mammalian male germ cells

  14. APOBEC3B-Mediated Cytidine Deamination Is Required for Estrogen Receptor Action in Breast Cancer

    Directory of Open Access Journals (Sweden)

    Manikandan Periyasamy

    2015-10-01

    Full Text Available Estrogen receptor α (ERα is the key transcriptional driver in a large proportion of breast cancers. We report that APOBEC3B (A3B is required for regulation of gene expression by ER and acts by causing C-to-U deamination at ER binding regions. We show that these C-to-U changes lead to the generation of DNA strand breaks through activation of base excision repair (BER and to repair by non-homologous end-joining (NHEJ pathways. We provide evidence that transient cytidine deamination by A3B aids chromatin modification and remodelling at the regulatory regions of ER target genes that promotes their expression. A3B expression is associated with poor patient survival in ER+ breast cancer, reinforcing the physiological significance of A3B for ER action.

  15. Homology Directed Knockin of Point Mutations in the Zebrafish tardbp and fus Genes in ALS Using the CRISPR/Cas9 System.

    Directory of Open Access Journals (Sweden)

    Gary Alan Barclay Armstrong

    Full Text Available The methodology for site-directed editing of single nucleotides in the vertebrate genome is of considerable interest for research in biology and medicine. The clustered regularly interspaced short palindromic repeats (CRISPR/CRISPR-associated protein 9 type II (Cas9 system has emerged as a simple and inexpensive tool for editing genomic loci of interest in a variety of animal models. In zebrafish, error-prone non-homologous end joining (NHEJ has been used as a simple method to disrupt gene function. We sought to develop a method to easily create site-specific SNPs in the zebrafish genome. Here, we report simple methodologies for using CRISPR/Cas9-mediated homology directed repair using single-stranded oligodeoxynucleotide donor templates (ssODN for site-directed single nucleotide editing, for the first time in two disease-related genes, tardbp and fus.

  16. Recombinant protein production from stable mammalian cell lines and pools.

    Science.gov (United States)

    Hacker, David L; Balasubramanian, Sowmya

    2016-06-01

    We highlight recent developments for the production of recombinant proteins from suspension-adapted mammalian cell lines. We discuss the generation of stable cell lines using transposons and lentivirus vectors (non-targeted transgene integration) and site-specific recombinases (targeted transgene integration). Each of these methods results in the generation of cell lines with protein yields that are generally superior to those achievable through classical plasmid transfection that depends on the integration of the transfected DNA by non-homologous DNA end-joining. This is the main reason why these techniques can also be used for the generation of stable cell pools, heterogenous populations of recombinant cells generated by gene delivery and genetic selection without resorting to single cell cloning. This allows the time line from gene transfer to protein production to be reduced.

  17. Functional redundancy between DNA ligases I and III in DNA replication in vertebrate cells

    Science.gov (United States)

    Arakawa, Hiroshi; Bednar, Theresa; Wang, Minli; Paul, Katja; Mladenov, Emil; Bencsik-Theilen, Alena A.; Iliakis, George

    2012-01-01

    In eukaryotes, the three families of ATP-dependent DNA ligases are associated with specific functions in DNA metabolism. DNA ligase I (LigI) catalyzes Okazaki-fragment ligation at the replication fork and nucleotide excision repair (NER). DNA ligase IV (LigIV) mediates repair of DNA double strand breaks (DSB) via the canonical non-homologous end-joining (NHEJ) pathway. The evolutionary younger DNA ligase III (LigIII) is restricted to higher eukaryotes and has been associated with base excision (BER) and single strand break repair (SSBR). Here, using conditional knockout strategies for LIG3 and concomitant inactivation of the LIG1 and LIG4 genes, we show that in DT40 cells LigIII efficiently supports semi-conservative DNA replication. Our observations demonstrate a high functional versatility for the evolutionary new LigIII in DNA replication and mitochondrial metabolism, and suggest the presence of an alternative pathway for Okazaki fragment ligation. PMID:22127868

  18. [Application of CRISPR-Cas9 genome editing for constructing animal models of human diseases].

    Science.gov (United States)

    Ou, Zhanhui; Sun, Xiaofang

    2016-08-10

    The CRISPR-Cas9 system is a new targeted nuclease for genome editing, which can directly introduce modifications at the targeted genomic locus. The system utilizes a short single guide RNA (sgRNA) to direct the endonuclease Cas9 in the genome. Upon targeting, Cas9 can generate DNA double-strand breaks (DSBs). As such DSBs are repaired by non-homologous end joining (NHEJ) or homology directed repair (HDR), therefore facilitates introduction of random or specific mutations, repair of endogenous mutations, or insertion of DNA elements. The system has been successfully used to generate gene targeted cell lines including those of human, animals and plants. This article reviews recent advances made in this rapidly evolving technique for the generation of animal models for human diseases. PMID:27455021

  19. Role of affective attitudes and anticipated affective reactions in predicting health behaviors

    OpenAIRE

    Conner, M; McEachan, R.; Taylor, N; O'Hara, J.; Lawton, R

    2015-01-01

    Objective: Two measures of affect-affective attitude (AA) and anticipated affective reaction (AAR)- have frequently been used individually, but rarely simultaneously, in correlational studies predicting health behaviors. This research assessed their individual and combined impact in predicting intention and action for a range of health behaviors, controlling for theory of planned behavior (TPB) variables. Method: Self-reported intentions and performance of health behaviors were the main outco...

  20. Affective influences on ethical decision making: The roles of mood, incidental emotions, and affective forecasting

    OpenAIRE

    Noval, Laura Jimena

    2015-01-01

    The main goal of my dissertation is to expand studies on the influence of affect in behavioral business ethics by focusing on affective influences that remain underexplored - e.g., incidental and anticipated emotions - as well as the interaction of affect with cognition. This dissertation is thus divided in three papers, each providing an unique contribution to the aforementioned goals and to the literature in ethical decision making: PAPER 1) a conceptual paper that explores the role of mood...

  1. Mechanisms of DNA repair and radio-induced mutagenesis in higher eukaryotes; Mecanismes de reparation et mutagenese radio-induite chez les eucaryotes superieurs

    Energy Technology Data Exchange (ETDEWEB)

    Averbeck, D. [Centre Universitaire d' Orsay, Institut Curie, Section de Recherche, Lab. Raymond-Latarjet, UMR 2027 CNRS, 91 (France)

    2000-10-01

    Cells of higher eukaryotes possess several very efficient systems for the repair of radiation-induced lesions in DNA. Different strategies have been adopted at the cellular level to remove or even tolerate various types of lesions in order to assure survival and limit the mutagenic consequences. In mammalian cells, the main DNA repair systems comprise direct reversion of damage, excision of damage and exchange mechanisms with intact DNA. Among these, the direct ligation of single strand breaks (SSB) by a DNA ligase and the multi-enzymatic repair systems of mismatch repair, base and nucleotide excision repair as well as the repair of double strand breaks (DSB) by homologous recombination or non homologous end-joining are the most important systems. Most of these processes are error-free except the non homologous end-joining pathway used for the repair of DSB. Moreover, certain lesions can be tolerated by more or less accurately acting polymerases capable of performing trans-lesion DNA syntheses. The DNA repair systems are intimately integrated in the network of cellular regulation. Some of their components are DNA damage inducible. Radiation-induced mutagenesis is largely due to unrepaired DNA damage but also involves error-prone repair processes like the repair of DSB by non-homologous end-joining. Generally, mammalian cells are well prepared to repair radiation-induced lesions. However, some questions remain to be asked about mechanistic details and efficiencies of the systems for removing certain types of radiation-damage and about their order and timing of action. The answers to these questions would be important for radioprotection as well as radiotherapy. (author)

  2. c-Myc Suppression of DNA Double-strand Break Repair

    Directory of Open Access Journals (Sweden)

    Zhaozhong Li

    2012-12-01

    Full Text Available c-Myc is a transcriptional factor that functions as a central regulator of cell growth, proliferation, and apoptosis. Overexpression of c-Myc also enhances DNA double-strand breaks (DSBs, genetic instability, and tumorigenesis. However, the mechanism(s involved remains elusive. Here, we discovered that γ-ray ionizing radiation-induced DSBs promote c-Myc to form foci and to co-localize with γ-H2AX. Conditional expression of c-Myc in HO15.19 c-Myc null cells using the Tet-Off/Tet-On inducible system results in down-regulation of Ku DNA binding and suppressed activities of DNA-dependent protein kinase catalytic subunit (DNA-PKcs and DNA end-joining, leading to inhibition of DSB repair and enhanced chromosomal and chromatid breaks. Expression of c-Myc reduces both signal and coding joins with decreased fidelity during V(DJ recombination. Mechanistically, c-Myc directly interacts with Ku70 protein through its Myc box II (MBII domain. Removal of the MBII domain from c-Myc abrogates its inhibitory effects on Ku DNA binding, DNA-PKcs, and DNA end-joining activities, which results in loss of c-Myc's ability to block DSB repair and V(DJ recombination. Interestingly, c-Myc directly disrupts the Ku/DNA-PKcs complex in vitro and in vivo. Thus, c-Myc suppression of DSB repair and V(DJ recombination may occur through inhibition of the nonhomologous end-joining pathway, which provides insight into the mechanism of c-Myc in the development of tumors through promotion of genomic instability.

  3. View How Glaucoma May Affect Vision

    Science.gov (United States)

    ... inbox. Sign up View How Glaucoma May Affect Vision Normal Vision This is an example of normal vision. This is also an example of how someone ... gradual and often imperceptible failing of side (peripheral) vision. Intermediate Glaucoma As glaucoma progresses, the center of ...

  4. On the chronobiology of seasonal affective disorder

    NARCIS (Netherlands)

    Koorengevel, Kathelijne Mara

    2002-01-01

    Chronobiological hypotheses about the pathogenesis of affective disorders have a long history. According to the modern variants, abnormalities of either a sleep-wake cycle dependent process S, or a circadian pacemaker related process C, or an abnor-mal interaction between these two processes underli

  5. How gluten properties are affected by pentosans

    NARCIS (Netherlands)

    Wang, M.; Vliet, T. van; Hamer, R.J.

    2004-01-01

    During the wet separation of starch and gluten, both water extractable pentosans (WEP) and water unextractable solids (WUS) have a negative effect on gluten yield. Gluten properties are also affected: the gluten becomes less extensible. In comparison to the control, addition of WUS or WEP resulted i

  6. INTERNATIONAL DIFFERENCES IN FACTORS AFFECTING LABOUR MOBILITY.

    Science.gov (United States)

    SELLIER, F.; ZARKA, C.

    THE GEOGRAPHICAL, OCCUPATIONAL, AND INTERFIRM MOBILITY, AND THE FACTORS AFFECTING THESE MOVEMENTS FOR WORKERS IN FRANCE, ITALY, GERMANY, AND SWEDEN IN THE PERIOD SINCE THE SECOND WORLD WAR ARE STUDIED. DATA OBTAINED FROM INDUSTRIAL SURVEYS AND GENERAL CENSUSES WERE USED TO COMPARE THE FOUR COUNTRIES WITH EACH OTHER AND WITH THE UNITED STATES.…

  7. [Affective disorders: endocrine and metabolic comorbidities].

    Science.gov (United States)

    Cermolacce, M; Belzeaux, R; Adida, M; Azorin, J-M

    2014-12-01

    Links between affective and endocrine-metabolic disorders are numerous and complex. In this review, we explore most frequent endocrine-metabolic comorbidities. On the one hand, these comorbidities imply numerous iatrogenic effects from antipsychotics (metabolic side-effects) or from lithium (endocrine side-effects). On the other hand, these comorbidities are also associated with affective disorders independently from medication. We will successively examine metabolic syndrome, glycemic disturbances, obesity and thyroid disorders among patients with affective disorders. Endocrinemetabolic comorbidities can be individually encountered, but can also be associated. Therefore, they substantially impact morbidity and mortality by increasing cardiovascular risk factors. Two distinct approaches give an account of processes involved in these comorbidities: common environmental factors (iatrogenic effects, lifestyle), and/or shared physiological vulnerabilities. In conclusion, we provide a synthesis of important results and recommendations related to endocrine-metabolic comorbidities in affective disorders : heavy influence on morbidity and mortality, undertreatment of somatic diseases, importance of endocrine and metabolic side effects from main mood stabilizers, impact from sex and age on the prevalence of comorbidities, influence from previous depressive episodes in bipolar disorders, and relevance of systematic screening for subclinical (biological) disturbances. PMID:25550238

  8. Go Naked: Diapers Affect Infant Walking

    Science.gov (United States)

    Cole, Whitney G.; Lingeman, Jesse M.; Adolph, Karen E.

    2012-01-01

    In light of cross-cultural and experimental research highlighting effects of childrearing practices on infant motor skill, we asked whether wearing diapers, a seemingly innocuous childrearing practice, affects infant walking. Diapers introduce bulk between the legs, potentially exacerbating infants' poor balance and wide stance. We show that…

  9. Do moods affect programmers’ debug performance?

    NARCIS (Netherlands)

    Khan, I.A.; Brinkman, W.P.; Hierons, R.M.

    2010-01-01

    There is much research that shows people’s mood can affect their activities. This paper argues that this also applies to programmers, especially their debugging. Literature-based framework is presented linking programming with various cognitive activities as well as linking cognitive activities with

  10. Acknowledging the Affective in Higher Education

    Science.gov (United States)

    Beard, Colin; Clegg, Sue; Smith, Karen

    2007-01-01

    This article argues that we need richer conceptions of students as affective and embodied selves and a clearer theorisation of the role of emotion in educational encounters. These areas are currently under-researched and under-theorised in higher education. The first part of the article explores the literature on emotion. The second reports on a…

  11. Processing speaker affect during spoken sentence comprehension

    NARCIS (Netherlands)

    van Leeuwen, A.R.; Quené, H.; van Berkum, J.J.A.

    2013-01-01

    Anne van Leeuwen Utrecht institute of Linguistics OTS, Utrecht University Processing speaker affect during spoken sentence comprehension We often smile (and frown) while we talk. Speakers use facial expression, posture and prosody to provide additional cues that signal speaker stance. Speaker stance

  12. Infrasound from Wind Turbines Could Affect Humans

    Science.gov (United States)

    Salt, Alec N.; Kaltenbach, James A.

    2011-01-01

    Wind turbines generate low-frequency sounds that affect the ear. The ear is superficially similar to a microphone, converting mechanical sound waves into electrical signals, but does this by complex physiologic processes. Serious misconceptions about low-frequency sound and the ear have resulted from a failure to consider in detail how the ear…

  13. Affective Education for Visually Impaired Children.

    Science.gov (United States)

    Locke, Don C.; Gerler, Edwin R., Jr.

    1981-01-01

    Evaluated the effectiveness of the Human Development Program (HDP) and the Developing Understanding of Self and Others (DUSO) program used with visually impaired children. Although HDP and DUSO affected the behavior of visually impaired children, they did not have any effect on children's attitudes toward school. (RC)

  14. How luck and performance affect stealing

    DEFF Research Database (Denmark)

    Gravert, Christina Annette

    2013-01-01

    This paper investigates how the way of earning payoff affects the probability of stealing. The participants who earned their payoff according to performance were three times more likely to take the (undeserved) maximum payoff than participants with randomly allocated payoff. Conditional on steali...

  15. New Regulations Affect School Debt Financing.

    Science.gov (United States)

    Olson, Carol Duane

    1993-01-01

    Provides an overview of changes in Treasury Regulations as they affect school debt financing, including bond and note construction and acquisition issues, other types of equipment and property financing, as well as tax and revenue anticipation notes for working capital needs. (MLF)

  16. Trauma and suicidality in war affected communities

    NARCIS (Netherlands)

    J. Jankovic; S. Bremner; M. Bogic; D. Lecic-Tosevski; D. Ajdukovic; T. Franciskovic; G.M. Galeazzi; A. Kucukalic; N. Morina; M. Popovski; M. Schützwohl; S. Priebe

    2012-01-01

    Purpose: The aim was to assess whether experiences of war trauma remain directly associated with suicidality in war affected communities when other risk factors are considered. Materials and methods: In the main sample 3313 participants from former Yugoslavia who experienced war trauma were recruite

  17. Active Affective Learning for Accelerated Schools.

    Science.gov (United States)

    Richardson, Robert B.

    This paper provides the groundwork for Active Affective Learning and teaching adapted to the needs of the disadvantaged, at-risk students served by the Accelerated Schools Movement. One of the "golden rules" for the practice of Accelerated Learning, according to psychiatrist Georgi Lozanov, has been to maintain an "up-beat" classroom presentation…

  18. Attention to Affect in Language Learning

    Science.gov (United States)

    Arnold, Jane

    2011-01-01

    As language teachers, we have to pay attention to many things in our work so why add "attention to affect"? Perhaps the simplest, most direct answer is that whatever we focus most on in our particular context, be it general English, morphosyntax, phonetics, literature, English for academic writing or any other special area, attention to affect…

  19. AMPK Activation Affects Glutamate Metabolism in Astrocytes

    DEFF Research Database (Denmark)

    Voss, Caroline Marie; Pajęcka, Kamilla; Stridh, Malin H;

    2015-01-01

    skeleton into the TCA cycle was reduced. On the other hand, glutamate uptake into the astrocytes as well as its conversion to glutamine catalyzed by glutamine synthetase was not affected by AMPK activation. Interestingly, synthesis and release of citrate, which are hallmarks of astrocytic function, were...

  20. Environmental issues affecting clean coal technology deployment

    Energy Technology Data Exchange (ETDEWEB)

    Miller, M.J. [Electric Power Research Inst., Palo Alto, CA (United States)

    1997-12-31

    The author outlines what he considers to be the key environmental issues affecting Clean Coal Technology (CCT) deployment both in the US and internationally. Since the international issues are difficult to characterize given different environmental drivers in various countries and regions, the primary focus of his remarks is on US deployment. However, he makes some general remarks, particularly regarding the environmental issues in developing vs. developed countries and how these issues may affect CCT deployment. Further, how environment affects deployment depends on which particular type of clean coal technology one is addressing. It is not the author`s intention to mention many specific technologies other than to use them for the purposes of example. He generally categorizes CCTs into four groups since environment is likely to affect deployment for each category somewhat differently. These four categories are: Precombustion technologies such as coal cleaning; Combustion technologies such as low NOx burners; Postcombustion technologies such as FGD systems and postcombustion NOx control; and New generation technologies such as gasification and fluidized bed combustion.

  1. Affective Disorders (Depression and Mania) in Adolescents

    OpenAIRE

    Kutcher, Stanley P.

    1986-01-01

    Affective disorders in adolescents are common and can be clearly differentiated from the “growing up process”. Basic questions about etiology, pathophysiology, psychobiology and treatment of these disorders remain to be answered. Current knowledge suggests that close co-operation between primary care physicians and psychiatrists with specialized training in adolescent psychiatry is necessary for optimum identification and management of these disorders.

  2. Gamma flicker elicits positive affect without awareness

    NARCIS (Netherlands)

    B.T. Heerebout; A.E.Y Tap; M. Rotteveel; R.H. Phaf

    2013-01-01

    High-frequency oscillations emerged as a neural code for both positive affect and fluent attentional processing from evolutionary simulations with artificial neural networks. Visual 50 Hz flicker, which entrains neural oscillations in the gamma band, has been shown to foster attentional switching, b

  3. Affective Learning and the Classroom Debate

    Science.gov (United States)

    Jagger, Suzy

    2013-01-01

    A commonly used teaching method to promote student engagement is the classroom debate. This study evaluates how affective characteristics, as defined in Bloom's taxonomy, were stimulated during debates that took place on a professional ethics module for first year computing undergraduates. The debates led to lively interactive group…

  4. Environmental Factors Affecting Preschoolers' Motor Development

    Science.gov (United States)

    Venetsanou, Fotini; Kambas, Antonis

    2010-01-01

    The process of development occurs according to the pattern established by the genetic potential and also by the influence of environmental factors. The aim of the present study was to focus on the main environmental factors affecting motor development. The review of the literature revealed that family features, such as socioeconomic status,…

  5. Physical conditions affecting pyrethroid toxicity in arthropods.

    NARCIS (Netherlands)

    Jagers op Akkerhuis, G.A.J.M.

    1993-01-01

    The aim of this thesis was to obtain mechanistic information about how the toxicity of pesticides in the field is affected by physical factors, pesticide bioavailability and arthropod behaviour. The pyrethroid insecticide deltamethrin and linyphiid spiders were selected as pesticide-effect model. In

  6. Economic and Cultural Factors Affecting University Excellence

    Science.gov (United States)

    Jabnoun, Naceur

    2009-01-01

    Purpose: The ranking of top universities in the world has generated increased interest in the factors that enhance university performance. The purpose of this paper is to identify economic and cultural factors that affect the number of top ranking universities in each country. Design/methodology/approach: This paper first identifies the number of…

  7. Does Labor Diversity Affect Firm Performance?

    DEFF Research Database (Denmark)

    Pytlikova, Mariola; Pozzoli, Dario; Parrotta, Pierpaolo

    Using an employer-employee dataset, we analyze how diversity in cultural background, skills and demographic characteristics affects total factor productivity (TFP) of firms in Denmark. Implementing structural estimation of firms’ production function, we find evidence that labor diversity in skills...

  8. Ophthalmic implications of seasonal affective disorder

    International Nuclear Information System (INIS)

    A review of seasonal affective disorder (SAD) is presented with a discussion of its standard treatment of phototherapy. A number of ophthalmic implications related to SAD are proposed. These implications relate to both the condition and the phototherapy used in its treatment, especially the use of full spectrum light which contains ultraviolet and near ultraviolet radiation. 12 references

  9. Methods of Assessment for Affected Family Members

    Science.gov (United States)

    Orford, Jim; Templeton, Lorna; Velleman, Richard; Copello, Alex

    2010-01-01

    The article begins by making the point that a good assessment of the needs and circumstances of family members is important if previous neglect of affected family members is to be reversed. The methods we have used in research studies are then described. They include a lengthy semi-structured interview covering seven topic areas and standard…

  10. Affect and Learning : a computational analysis

    NARCIS (Netherlands)

    Broekens, Douwe Joost

    2007-01-01

    In this thesis we have studied the influence of emotion on learning. We have used computational modelling techniques to do so, more specifically, the reinforcement learning paradigm. Emotion is modelled as artificial affect, a measure that denotes the positiveness versus negativeness of a situation

  11. Affective loop experiences: designing for interactional embodiment.

    Science.gov (United States)

    Höök, Kristina

    2009-12-12

    Involving our corporeal bodies in interaction can create strong affective experiences. Systems that both can be influenced by and influence users corporeally exhibit a use quality we name an affective loop experience. In an affective loop experience, (i) emotions are seen as processes, constructed in the interaction, starting from everyday bodily, cognitive or social experiences; (ii) the system responds in ways that pull the user into the interaction, touching upon end users' physical experiences; and (iii) throughout the interaction the user is an active, meaning-making individual choosing how to express themselves-the interpretation responsibility does not lie with the system. We have built several systems that attempt to create affective loop experiences with more or less successful results. For example, eMoto lets users send text messages between mobile phones, but in addition to text, the messages also have colourful and animated shapes in the background chosen through emotion-gestures with a sensor-enabled stylus pen. Affective Diary is a digital diary with which users can scribble their notes, but it also allows for bodily memorabilia to be recorded from body sensors mapping to users' movement and arousal and placed along a timeline. Users can see patterns in their bodily reactions and relate them to various events going on in their lives. The experiences of building and deploying these systems gave us insights into design requirements for addressing affective loop experiences, such as how to design for turn-taking between user and system, how to create for 'open' surfaces in the design that can carry users' own meaning-making processes, how to combine modalities to create for a 'unity' of expression, and the importance of mirroring user experience in familiar ways that touch upon their everyday social and corporeal experiences. But a more important lesson gained from deploying the systems is how emotion processes are co-constructed and experienced

  12. DNA synthesis on discontinuous templates by human DNA polymerases: implications for non-homologous DNA recombination.

    OpenAIRE

    Islas, L; Fairley, C F; Morgan, W. F.

    1998-01-01

    DNA polymerases catalyze the synthesis of DNA using a continuous uninterrupted template strand. However, it has been shown that a 3'-->5' exonuclease-deficient form of the Klenow fragment of Escherichia coli DNA polymerase I as well as DNA polymerase of Thermus aquaticus can synthesize DNA across two unlinked DNA templates. In this study, we used an oligonucleotide-based assay to show that discontinuous DNA synthesis was present in HeLa cell extracts. DNA synthesis inhibitor studies as well a...

  13. The spectrum and frequency of self-inflicted and host gene mutations produced by the transposon Ac in maize.

    Science.gov (United States)

    Huang, Jun T; Dooner, Hugo K

    2012-10-01

    The autonomous transposon Activator (Ac) is a powerful mutagen. Ac-induced mutations range from small footprints of host sequences to large rearrangements of transposon or host sequences. These mutations arise by different repair mechanisms of the double-strand break produced by Ac excision: footprints by nonhomologous end joining and rearrangements by various mechanisms, including DNA replication repair. Footprints greatly outnumber other mutations, masking them because they usually share a nonfunctional phenotype. To determine the spectrum and frequencies of host and self-mutations generated by Ac, we used an allele harboring Ac in the 5' untranslated region bronze (bz). In this system, simple excisions produce purple revertants, whereas deletions of host or transposon sequences produce stable bronze (bz-s) mutants. Internal and terminal deletions of Ac predominated among the 72 bz-s derivatives. Most internal deletions (52 of 54) behaved as nonautonomous Dissociation (Ds) elements. All nine terminal deletions or fractured Ac (fAc) elements had rearrangements of adjacent host sequences. Most Ds and fAc deletion junctions displayed microhomologies and contained filler DNA from nearby sequences, suggesting an origin by DNA repair synthesis followed by microhomology-mediated end joining. All mutations occurred more frequently in pollen, where one in 200 grains carried new Ds or fAc elements.

  14. A genome-wide screening uncovers the role of CCAR2 as an antagonist of DNA end resection

    Science.gov (United States)

    López-Saavedra, Ana; Gómez-Cabello, Daniel; Domínguez-Sánchez, María Salud; Mejías-Navarro, Fernando; Fernández-Ávila, María Jesús; Dinant, Christoffel; Martínez-Macías, María Isabel; Bartek, Jiri; Huertas, Pablo

    2016-01-01

    There are two major and alternative pathways to repair DNA double-strand breaks: non-homologous end-joining and homologous recombination. Here we identify and characterize novel factors involved in choosing between these pathways; in this study we took advantage of the SeeSaw Reporter, in which the repair of double-strand breaks by homology-independent or -dependent mechanisms is distinguished by the accumulation of green or red fluorescence, respectively. Using a genome-wide human esiRNA (endoribonuclease-prepared siRNA) library, we isolate genes that control the recombination/end-joining ratio. Here we report that two distinct sets of genes are involved in the control of the balance between NHEJ and HR: those that are required to facilitate recombination and those that favour NHEJ. This last category includes CCAR2/DBC1, which we show inhibits recombination by limiting the initiation and the extent of DNA end resection, thereby acting as an antagonist of CtIP. PMID:27503537

  15. TRF2/RAP1 and DNA-PK mediate a double protection against joining at telomeric ends.

    Science.gov (United States)

    Bombarde, Oriane; Boby, Céline; Gomez, Dennis; Frit, Philippe; Giraud-Panis, Marie-Josèphe; Gilson, Eric; Salles, Bernard; Calsou, Patrick

    2010-05-01

    DNA-dependent protein kinase (DNA-PK) is a double-strand breaks repair complex, the subunits of which (KU and DNA-PKcs) are paradoxically present at mammalian telomeres. Telomere fusion has been reported in cells lacking these proteins, raising two questions: how is DNA-PK prevented from initiating classical ligase IV (LIG4)-dependent non-homologous end-joining (C-NHEJ) at telomeres and how is the backup end-joining (EJ) activity (B-NHEJ) that operates at telomeres under conditions of C-NHEJ deficiency controlled? To address these questions, we have investigated EJ using plasmid substrates bearing double-stranded telomeric tracks and human cell extracts with variable C-NHEJ or B-NHEJ activity. We found that (1) TRF2/RAP1 prevents C-NHEJ-mediated end fusion at the initial DNA-PK end binding and activation step and (2) DNA-PK counteracts a potent LIG4-independent EJ mechanism. Thus, telomeres are protected against EJ by a lock with two bolts. These results account for observations with mammalian models and underline the importance of alternative non-classical EJ pathways for telomere fusions in cells. PMID:20407424

  16. More forks on the road to replication stress recovery

    Institute of Scientific and Technical Information of China (English)

    Chris Allen; Amanda K. Ashley; Robert Hromas; Jac A. Nickoloff

    2011-01-01

    High-fidelity replication of DNA, and its accurate segregation to daughter cells, is critical for maintaining genome stability and suppressing cancer. DNA replication forks are stalled by many DNA lesions, activating checkpoint proteins that stabilize stalled forks.Stalled forks may eventually collapse, producing a broken DNA end. Fork restart is typically mediated by proteins initially identified by their rotes in homologous recombination repair of DNA double-strand breaks (DSBs). In recent years, several proteins involved in DSB repair by non-homologous end joining (NHEJ) have been implicated in the replication stress response, including DNA-PKcs, Ku,DNA Ligase IV-XRCC4, Artemis, XLF and Metnase. It is currently unclear whether NHEJ proteins are involved in the replication stress response through indirect (signaling) roles, and/or direct roles involving DNA end joining. Additional complexity in the replication stress response centers around RPA, which undergoes significant post-translational modification after stress, and RAD52, a conserved HR protein whose role in DSB repair may have shifted to another protein in higher eukaryotes, such as BRCA2, but retained its rote in fork restart. Most cancer therapeutic strategies create DNA reputation stress. Thus, it is imperative to gain a better understanding of replication stress response proteins and pathways to improve cancer therapy.

  17. Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells.

    Science.gov (United States)

    Schwer, Bjoern; Wei, Pei-Chi; Chang, Amelia N; Kao, Jennifer; Du, Zhou; Meyers, Robin M; Alt, Frederick W

    2016-02-23

    High-throughput, genome-wide translocation sequencing (HTGTS) studies of activated B cells have revealed that DNA double-strand breaks (DSBs) capable of translocating to defined bait DSBs are enriched around the transcription start sites (TSSs) of active genes. We used the HTGTS approach to investigate whether a similar phenomenon occurs in primary neural stem/progenitor cells (NSPCs). We report that breakpoint junctions indeed are enriched around TSSs that were determined to be active by global run-on sequencing analyses of NSPCs. Comparative analyses of transcription profiles in NSPCs and B cells revealed that the great majority of TSS-proximal junctions occurred in genes commonly expressed in both cell types, possibly because this common set has higher transcription levels on average than genes transcribed in only one or the other cell type. In the latter context, among all actively transcribed genes containing translocation junctions in NSPCs, those with junctions located within 2 kb of the TSS show a significantly higher transcription rate on average than genes with junctions in the gene body located at distances greater than 2 kb from the TSS. Finally, analysis of repair junction signatures of TSS-associated translocations in wild-type versus classical nonhomologous end-joining (C-NHEJ)-deficient NSPCs reveals that both C-NHEJ and alternative end-joining pathways can generate translocations by joining TSS-proximal DSBs to DSBs on other chromosomes. Our studies show that the generation of transcription-associated DSBs is conserved across divergent cell types.

  18. Bax-induced apoptosis shortens the life span of DNA repair defect Ku70-knockout mice by inducing emphysema.

    Science.gov (United States)

    Matsuyama, Shigemi; Palmer, James; Bates, Adam; Poventud-Fuentes, Izmarie; Wong, Kelvin; Ngo, Justine; Matsuyama, Mieko

    2016-06-01

    Cells with DNA damage undergo apoptosis or cellular senescence if the damage cannot be repaired. Recent studies highlight that cellular senescence plays a major role in aging. However, age-associated diseases, including emphysema and neurodegenerative disorders, are caused by apoptosis of lung alveolar epithelial cells and neurons, respectively. Therefore, enhanced apoptosis also promotes aging and shortens the life span depending on the cell type. Recently, we reported that ku70(-) (/) (-)bax(-) (/) (-) and ku70(-) (/) (-)bax(+/) (-) mice showed significantly extended life span in comparison with ku70(-) (/) (-)bax(+/+) mice. Ku70 is essential for non-homologous end joining pathway for DNA double strand break repair, and Bax plays an important role in apoptosis. Our study suggests that Bax-induced apoptosis has a significant impact on shortening the life span of ku70(-) (/) (-) mice, which are defective in one of DNA repair pathways. The lung alveolar space gradually enlarges during aging, both in mouse and human, and this age-dependent change results in the decrease of respiration capacity during aging that can lead to emphysema in more severe cases. We found that emphysema occurred in ku70(-) (/) (-) mice at the age of three-months old, and that Bax deficiency was able to suppress it. These results suggest that Bax-mediated apoptosis induces emphysema in ku70(-) (/) (-) mice. We also found that the number of cells, including bronchiolar epithelial cells and type 2 alveolar epithelial cells, shows a higher DNA double strand break damage response in ku70 KO mouse lung than in wild type. Recent studies suggest that non-homologous end joining activity decreases with increased age in mouse and rat model. Together, we hypothesize that the decline of Ku70-dependent DNA repair activity in lung alveolar epithelial cells is one of the causes of age-dependent decline of lung function resulting from excess Bax-mediated apoptosis of lung alveolar epithelial cells (and their

  19. Multi-modal affect induction for affective brain-computer interfaces

    NARCIS (Netherlands)

    Mühl, C.; Broek, E.L. van den; Brouwer, A.M.; Nijboer, F.; Wouwe, N.C. van; Heylen, D.

    2011-01-01

    Reliable applications of affective brain-computer interfaces (aBCI) in realistic, multi-modal environments require a detailed understanding of the processes involved in emotions. To explore the modalityspecific nature of affective responses, we studied neurophysiological responses (i.e., EEG) of 24

  20. Construction of Multi-Mode Affective Learning System: Taking Affective Design as an Example

    Science.gov (United States)

    Lin, Hao-Chiang Koong; Su, Sheng-Hsiung; Chao, Ching-Ju; Hsieh, Cheng-Yen; Tsai, Shang-Chin

    2016-01-01

    This study aims to design a non-simultaneous distance instruction system with affective computing, which integrates interactive agent technology with the curricular instruction of affective design. The research subjects were 78 students, and prototype assessment and final assessment were adopted to assess the interface and usability of the system.…

  1. Affective Match: Leader Emotional Displays, Follower Positive Affect, and Follower Performance

    NARCIS (Netherlands)

    F.J.A. Damen (Frederic); B. van Knippenberg (Barbara); D.L. van Knippenberg (Daan)

    2006-01-01

    textabstractLeader emotions may play an important role in leadership effectiveness. Extending this earlier research on leader emotional displays and leadership effectiveness, we propose that the “affective match” between follower positive affect (PA) and leaders’ emotional displays moderates the eff

  2. Affective Development in Advanced Old Age: Analyses of Terminal Change in Positive and Negative Affect

    Science.gov (United States)

    Schilling, Oliver K.; Wahl, Hans-Werner; Wiegering, Sarah

    2013-01-01

    Late-life development of affect may unfold terminal changes that are driven more by end-of-life processes and not so much by time since birth. This study aimed to explore time-to-death-related effects in measures of affect in a sample of the very old. We used longitudinal data (2 measurement occasions: 2002 and 2003) from 140 deceased…

  3. Leader Affect and Leadership Effectiveness: How leader affective displays influence follower outcomes

    NARCIS (Netherlands)

    V.A. Visser (Victoria)

    2013-01-01

    textabstractThe aim of this dissertation is to uncover the relationship between leader affective displays and leadership effectiveness. Five empirical studies were conducted to test the influence of several leader affective displays on different follower outcomes that indicate leadership effectivene

  4. Affective Game Design: Creating Better Game Experiences based on Players Affective Reaction Model

    OpenAIRE

    Rúben Pinto Aguiar

    2014-01-01

    In this thesis, we demonstrate a generalizable approach for building predictive models of players’ affective reactions across games and genres. Our aim is two-fold: 1) That game developers can use these models to more easily and accurately tune game parameters, allowing improved gaming experiences, and 2) That these models can be used as the basis for parameterisable and adaptive affective gaming.

  5. Human activities affecting trace gases and climate

    International Nuclear Information System (INIS)

    The Earth's climate has been in a constant state of change throughout geologic time due to natural perturbations in the global geobiosphere. However, various human activities have the potential to cause future global warming over a relatively short amount of time. These activities, which affect the Earth's climate by altering the concentrations of trace gases in the atmosphere, include energy consumption, particularly fossil-fuel consumption; industrial processes (production and use of chlorofluorocarbons, halons, and chlorocarbons, landfilling of wastes, and cement manufacture); changes in land use patterns, particularly deforestation and biomass burning; and agricultural practices (waste burning, fertilizer usage, rice production, and animal husbandry). Population growth is an important underlying factor affecting the level of growth in each activity. This paper describes how the human activities listed above contribute to atmospheric change, the current pattern of each activity, and how levels of each activity have changed since the early part of this century

  6. Detecting affective states in virtual rehabilitation

    Directory of Open Access Journals (Sweden)

    Jesús Rivas

    2015-10-01

    Full Text Available Virtual rehabilitation supports motor training following stroke by means of tailored virtual environments. To optimize therapy outcome, virtual rehabilitation systems automatically adapt to the different patients’ changing needs. Adaptation decisions should ideally be guided by both the observable performance and the hidden mind state of the user. We hypothesize that some affective aspects can be inferred from observable metrics. Here we present preliminary results of a classification exercise to decide on 4 states; tiredness, tension, pain and satisfaction. Descriptors of 3D hand movement and finger pressure were collected from 2 post-stroke participants while they practice on a virtual rehabilitation platform. Linear Support Vector Machine models were learnt to unfold a predictive relation between observation and the affective states considered. Initial results are promising (ROC Area under the curve (mean+/-std: 0.713 +/- 0.137. Confirmation of these opens the door to incorporate surrogates of mind state into the algorithm deciding on therapy adaptation.

  7. FACTORS AFFECTING PERSISTENCE IN STUDENTS' LEARNING

    Institute of Scientific and Technical Information of China (English)

    ShenPanyang

    2004-01-01

    It is one thing that currently in China English learning persists through a student's whole study life, but it is another how long his persistence, an important factor in any language learning, can last. The factors affecting a student's persistence in this regard practically merits our attention. This paper traces and observes twenty students chosen by random. The research conducted here included their study motivation, academic excellence, psychological aspects relating to language learning and established corresponding models showing how these factors affect a student's persistence in his English learning. Although a small sample number was taken,of different students in China.the twenty students were typical of different students in China. The students' backgrounds were varied including both educational and environmental. Some suggestions are given indicating three separate but inter-related ways in how to further develop a student's persistence.

  8. How do humans affect wildlife nematodes?

    Science.gov (United States)

    Weinstein, Sara B.; Lafferty, Kevin D.

    2015-01-01

    Human actions can affect wildlife and their nematode parasites. Species introductions and human-facilitated range expansions can create new host–parasite interactions. Novel hosts can introduce parasites and have the potential to both amplify and dilute nematode transmission. Furthermore, humans can alter existing nematode dynamics by changing host densities and the abiotic conditions that affect larval parasite survival. Human impacts on wildlife might impair parasites by reducing the abundance of their hosts; however, domestic animal production and complex life cycles can maintain transmission even when wildlife becomes rare. Although wildlife nematodes have many possible responses to human actions, understanding host and parasite natural history, and the mechanisms behind the changing disease dynamics might improve disease control in the few cases where nematode parasitism impacts wildlife.

  9. Action video game experience affects oculomotor performance.

    Science.gov (United States)

    West, Greg L; Al-Aidroos, Naseem; Pratt, Jay

    2013-01-01

    Action video games have been show to affect a variety of visual and cognitive processes. There is, however, little evidence of whether playing video games can also affect motor action. To investigate the potential link between experience playing action video games and changes in oculomotor action, we tested habitual action video game players (VGPs) and non-video game players (NVGPs) in a saccadic trajectory deviation task. We demonstrate that spatial curvature of a saccadic trajectory towards or away from distractor is profoundly different between VGPs and NVGPs. In addition, task performance accuracy improved over time only in VGPs. Results are discussed in the context of the competing interplay between stimulus-driven motor programming and top-down inhibition during oculomotor execution.

  10. ANALYSIS OF THE FACTORS AFFECTING THE AVERAGE

    Directory of Open Access Journals (Sweden)

    Carmen BOGHEAN

    2013-12-01

    Full Text Available Productivity in agriculture most relevantly and concisely expresses the economic efficiency of using the factors of production. Labour productivity is affected by a considerable number of variables (including the relationship system and interdependence between factors, which differ in each economic sector and influence it, giving rise to a series of technical, economic and organizational idiosyncrasies. The purpose of this paper is to analyse the underlying factors of the average work productivity in agriculture, forestry and fishing. The analysis will take into account the data concerning the economically active population and the gross added value in agriculture, forestry and fishing in Romania during 2008-2011. The distribution of the average work productivity per factors affecting it is conducted by means of the u-substitution method.

  11. Recall of Events Affects Perception of Happiness

    Institute of Scientific and Technical Information of China (English)

    Angelica Moe

    2014-01-01

    This study assessed the relationships between recall of positive and negative events, API (attention to positive) and ANI (attention to negative information), and perception of happiness, with the hypothesis that recall affects the perception of happiness and that ANI and API affect recall. One hundred and five women filled in the APNI scale to assess API and ANI and were asked to listen to and recall a story presenting both positive and negative events, and provide an assessment of the character perceived happiness. Finally, they were asked to choose an ending for the story. Results showed that recall is related to the perception of happiness more than API and ANI, and that relationships occur among recall, API, ANI, and perception of happiness. A positive ending for the story was preferred. Discussion focuses on the implications of individual differences in paying attention to and recall positive and negative information.

  12. Thyroid Functions and Bipolar Affective Disorder

    Directory of Open Access Journals (Sweden)

    Subho Chakrabarti

    2011-01-01

    Full Text Available Accumulating evidence suggests that hypothalamo-pituitary-thyroid (HPT axis dysfunction is relevant to the pathophysiology and clinical course of bipolar affective disorder. Hypothyroidism, either overt or more commonly subclinical, appears to the commonest abnormality found in bipolar disorder. The prevalence of thyroid dysfunction is also likely to be greater among patients with rapid cycling and other refractory forms of the disorder. Lithium-treatment has potent antithyroid effects and can induce hypothyroidism or exacerbate a preexisting hypothyroid state. Even minor perturbations of the HPT axis may affect the outcome of bipolar disorder, necessitating careful monitoring of thyroid functions of patients on treatment. Supplementation with high dose thyroxine can be considered in some patients with treatment-refractory bipolar disorder. Neurotransmitter, neuroimaging, and genetic studies have begun to provide clues, which could lead to an improved understanding of the thyroid-bipolar disorder connection, and more optimal ways of managing this potentially disabling condition.

  13. Factors Affecting the Productivity of Government Workers

    Directory of Open Access Journals (Sweden)

    Jerry P. Haenisch

    2012-01-01

    Full Text Available While there have been a variety of studies concerning government worker motivation and productivity, few, if any, studies have focused specifically on state government workers’ perceptions about what factors affect their productivity. With more than 5 million workers employed by state governments in the United States, any improvement in state workplace productivity could have significant financial and service impact for society. In this study, state government workers identified those factors perceived as most affecting their workplace productivity. Data were collected through a survey offered to state government workers in the state of Wyoming. Factor analysis was used to derive key productivity factors from survey responses. The results indicate that state government workers appreciate having freedom and autonomy, like their jobs and the sense of achievement, and welcome teamwork, but feel limited by poor supervision and management, poor communications, and insufficient budgets and staffing. To improve productivity, the workers would eliminate bureaucracy, supervise better, and improve communication.

  14. Interactive affective sharing versus non-interactive affective sharing in work groups : Comparative effects of group affect on work group performance and dynamics

    NARCIS (Netherlands)

    Klep, Annefloor; Wisse, Barbara; Van Der Flier, Henk

    2011-01-01

    This study explores whether the dynamic path to group affect, which is characterized by interactive affective sharing processes, yields different effects on task performance and group dynamics than the static path to group affect, which arises from non-interactive affective sharing. The results of o

  15. Factors Affecting Audit Committee Quality in Nigeria

    OpenAIRE

    Okaro Sunday Chukwunedu; Okafor Gloria Ogochukwu; Oraka Azubuike Onuora

    2014-01-01

    The purpose of this paper is to identify factors that affect audit committee quality in Nigeria. A hand administered questionnaire survey of 52 accounting professionals was undertaken. Descriptive statistics were used to determine the most common factors. Independent t-tests were used to determine whether there were any significant differences in the perceptions of the factors according to gender, job type and experience. The questionnaire findings, which include some factors peculiar to Nige...

  16. How a sustainable message affects brand attributes

    OpenAIRE

    Huertas García, Ruben; Consolación Segura, Carolina María; Mas Machuca, Marta

    2016-01-01

    © Emerald Group Publishing Limited. Purpose - The purpose of this paper is to understand how an advertising campaign incorporating an ecological message affects heuristic structure of consumer preferences for hedonic (design and aesthetics) and utilitarian benefits (functionality and performance) provided by the product advertised. Also, the second objective is to reach an understanding of how brand equity moderates these relationships. Design/methodology/approach - The paper proposes a two-s...

  17. Does Labour Diversity affect Firm Productivity?

    DEFF Research Database (Denmark)

    Parrotta, Pierpaolo; Pozzoli, Dario; Pytlikova, Mariola

    Using a matched employer-employee dataset, we analyze how workforce diversity in cultural background, education and demographic characteristics affects productivity of firms in Denmark. Implementing a structural estimation of the firms' production function (Ackerberg et al., 2006) we find...... that labor diversity in education significantly enhances a firm's value added. Conversely, diversity in ethnicity and demographics induces negative effects on firm productivity. Hence, the negative effects, coming from communication and integration costs connected to a more culturally and demographically...

  18. Institutional Factors Affecting Agricultural Land Markets

    OpenAIRE

    Ciaian, Pavel; Kancs, D'Artis; Swinnen, Johan F.M.; Van Herck, Kristine; Vranken, Liesbet

    2012-01-01

    This paper analyses the main institutional factors affecting the rental and sales markets for agricultural land. Particular attention is paid to the effects of the common agricultural policy on land markets, and more specifically the underlying mechanism through which agricultural subsidies are capitalised into land values and farmland rents. This paper also provides a broad overview of the empirical studies that estimate the impact of agricultural support policies on land rents and land pric...

  19. Do moods affect programmers’ debug performance?

    OpenAIRE

    Khan, I A; Brinkman, W.P.; Hierons, R. M.

    2010-01-01

    There is much research that shows people’s mood can affect their activities. This paper argues that this also applies to programmers, especially their debugging. Literature-based framework is presented linking programming with various cognitive activities as well as linking cognitive activities with moods. Further, the effect of mood on debugging was tested in two experiments. In the first experiment, programmers (n = 72) saw short movie clips selected for their ability to provoke specific mo...

  20. Positive affect regulation in anxiety disorders

    OpenAIRE

    Eisner, Lori R.; Johnson, Sheri L; Carver, Charles S.

    2009-01-01

    Although individual differences exist in how people respond to positive affect (PA), little research addresses PA regulation in people with anxiety disorders. The goal of this study was to provide information about responses to PA in people with symptoms of social phobia, generalized anxiety disorder, panic disorder, agoraphobia, and obsessive-compulsive disorder. The tendency to dampen PA and the ability to savor PA were examined in an undergraduate sample. Analyses examined the unique links...