Non-homologous end joining mediated DNA repair is impaired in the NUP98-HOXD13 mouse model for myelodysplastic syndrome.

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Puthiyaveetil, Abdul Gafoor; Reilly, Christopher M; Pardee, Timothy S; Caudell, David L

2013-01-01

Chromosomal translocations typically impair cell differentiation and often require secondary mutations for malignant transformation. However, the role of a primary translocation in the development of collaborating mutations is debatable. To delineate the role of leukemic translocation NUP98-HOXD13 (NHD13) in secondary mutagenesis, DNA break and repair mechanisms in stimulated mouse B lymphocytes expressing NHD13 were analyzed. Our results showed significantly reduced expression of non-homologous end joining (NHEJ)-mediated DNA repair genes, DNA Pkcs, DNA ligase4, and Xrcc4 leading to cell cycle arrest at G2/M phase. Our results showed that expression of NHD13 fusion gene resulted in impaired NHEJ-mediated DNA break repair. Copyright © 2012 Elsevier Ltd. All rights reserved.

BCR/ABL downregulates DNA-PK(CS)-dependent and upregulates backup non-homologous end joining in leukemic cells.

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Poplawski, Tomasz; Blasiak, Janusz

2010-06-01

Non-homologous end joining (NHEJ) and homologous recombination repair (HRR) are the main mechanisms involved in the processing of DNA double strand breaks (DSBs) in humans. We showed previously that the oncogenic tyrosine kinase BCR/ABL stimulated DSBs repair by HRR. To evaluate the role of BCR/ABL in DSBs repair by NHEJ we examined the ability of leukemic BCR/ABL-expressing cell line BV173 to repair DNA damage induced by two DNA topoisomerase II inhibitors: etoposide and sobuzoxane. DNA lesions induced by sobuzoxane are repaired by a NHEJ pathway which is dependent on the catalytic subunit of protein kinase dependent on DNA (DNA-PK(CS); D-NHEJ), whereas damage evoked by etoposide are repaired by two distinct NHEJ pathways, dependent on or independent of DNA-PK(CS) (backup NHEJ, B-NHEJ). Cells incubated with STI571, a highly specific inhibitor of BCR/ABL, displayed resistance to these agents associated with an accelerated kinetics of DSBs repair, as measured by the neutral comet assay and pulsed field gel electrophoresis. However, in a functional NHEJ assay, cells preincubated with STI571 repaired DSBs induced by a restriction enzyme with a lower efficacy than without the preincubation and addition of wortmannin, a specific inhibitor of DNA-PK(CS), did not change efficacy of the NHEJ reaction. We suggest that BCR/ABL switch on B-NHEJ which is more error-prone then D-NHEJ and in such manner contribute to the increase of the genomic instability of leukemic cells.

Biochemical Kinetics Model of DSB Repair and GammaH2AX FOCI by Non-homologous End Joining

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Cucinotta, Francis, A.; Pluth, Janice M.; Anderson, Jennifer A.; Harper, Jane V.; O'Neill, Peter

2007-01-01

We developed a biochemical kinetics approach to describe the repair of double strand breaks (DSB) produced by low LET radiation by modeling molecular events associated with the mechanisms of non-homologous end-joining (NHEJ). A system of coupled non-linear ordinary differential equations describes the induction of DSB and activation pathways for major NHEJ components including Ku(sub 70/80), DNA-PK(sub cs), and the Ligase IV-XRCC4 hetero-dimer. The autophosphorylation of DNA-PK(sub cs and subsequent induction of gamma-H2AX foci observed after ionizing radiation exposure were modeled. A two-step model of DNA-PK(sub cs) regulation of repair was developed with the initial step allowing access of other NHEJ components to breaks, and a second step limiting access to Ligase IV-XRCC4. Our model assumes that the transition from the first to second-step depends on DSB complexity, with a much slower-rate for complex DSB. The model faithfully reproduced several experimental data sets, including DSB rejoining as measured by pulsed-field electrophoresis (PFGE), quantification of the induction of gamma-H2AX foci, and live cell imaging of the induction of Ku(sub 70/80). Predictions are made for the behaviors of NHEJ components at low doses and dose-rates, where a steady-state is found at dose-rates of 0.1 Gy/hr or lower.

SV40 Utilizes ATM Kinase Activity to Prevent Non-homologous End Joining of Broken Viral DNA Replication Products

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Sowd, Gregory A.; Mody, Dviti; Eggold, Joshua; Cortez, David; Friedman, Katherine L.; Fanning, Ellen

2014-01-01

Simian virus 40 (SV40) and cellular DNA replication rely on host ATM and ATR DNA damage signaling kinases to facilitate DNA repair and elicit cell cycle arrest following DNA damage. During SV40 DNA replication, ATM kinase activity prevents concatemerization of the viral genome whereas ATR activity prevents accumulation of aberrant genomes resulting from breakage of a moving replication fork as it converges with a stalled fork. However, the repair pathways that ATM and ATR orchestrate to prevent these aberrant SV40 DNA replication products are unclear. Using two-dimensional gel electrophoresis and Southern blotting, we show that ATR kinase activity, but not DNA-PKcs kinase activity, facilitates some aspects of double strand break (DSB) repair when ATM is inhibited during SV40 infection. To clarify which repair factors associate with viral DNA replication centers, we examined the localization of DSB repair proteins in response to SV40 infection. Under normal conditions, viral replication centers exclusively associate with homology-directed repair (HDR) and do not colocalize with non-homologous end joining (NHEJ) factors. Following ATM inhibition, but not ATR inhibition, activated DNA-PKcs and KU70/80 accumulate at the viral replication centers while CtIP and BLM, proteins that initiate 5′ to 3′ end resection during HDR, become undetectable. Similar to what has been observed during cellular DSB repair in S phase, these data suggest that ATM kinase influences DSB repair pathway choice by preventing the recruitment of NHEJ factors to replicating viral DNA. These data may explain how ATM prevents concatemerization of the viral genome and promotes viral propagation. We suggest that inhibitors of DNA damage signaling and DNA repair could be used during infection to disrupt productive viral DNA replication. PMID:25474690

SV40 utilizes ATM kinase activity to prevent non-homologous end joining of broken viral DNA replication products.

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Gregory A Sowd

2014-12-01

Full Text Available Simian virus 40 (SV40 and cellular DNA replication rely on host ATM and ATR DNA damage signaling kinases to facilitate DNA repair and elicit cell cycle arrest following DNA damage. During SV40 DNA replication, ATM kinase activity prevents concatemerization of the viral genome whereas ATR activity prevents accumulation of aberrant genomes resulting from breakage of a moving replication fork as it converges with a stalled fork. However, the repair pathways that ATM and ATR orchestrate to prevent these aberrant SV40 DNA replication products are unclear. Using two-dimensional gel electrophoresis and Southern blotting, we show that ATR kinase activity, but not DNA-PK(cs kinase activity, facilitates some aspects of double strand break (DSB repair when ATM is inhibited during SV40 infection. To clarify which repair factors associate with viral DNA replication centers, we examined the localization of DSB repair proteins in response to SV40 infection. Under normal conditions, viral replication centers exclusively associate with homology-directed repair (HDR and do not colocalize with non-homologous end joining (NHEJ factors. Following ATM inhibition, but not ATR inhibition, activated DNA-PK(cs and KU70/80 accumulate at the viral replication centers while CtIP and BLM, proteins that initiate 5' to 3' end resection during HDR, become undetectable. Similar to what has been observed during cellular DSB repair in S phase, these data suggest that ATM kinase influences DSB repair pathway choice by preventing the recruitment of NHEJ factors to replicating viral DNA. These data may explain how ATM prevents concatemerization of the viral genome and promotes viral propagation. We suggest that inhibitors of DNA damage signaling and DNA repair could be used during infection to disrupt productive viral DNA replication.

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

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Campos-Nebel, Marcelo de; Larripa, Irene; Gonzalez-Cid, Marcela

2008-01-01

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

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

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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

Relative contribution of homologous recombination and non-homologous end-joining to DNA double-strand break repair after oxidative stress in Saccharomyces cerevisiae.

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Letavayová, Lucia; Marková, Eva; Hermanská, Katarína; Vlcková, Viera; Vlasáková, Danusa; Chovanec, Miroslav; Brozmanová, Jela

2006-05-10

Oxidative damage to DNA seems to be an important factor in developing many human diseases including cancer. It involves base and sugar damage, base-free sites, DNA-protein cross-links and DNA single-strand (SSB) and double-strand (DSB) breaks. Oxidative DSB can be formed in various ways such as their direct induction by the drug or their generation either through attempted and aborted repair of primary DNA lesions or through DNA replication-dependent conversion of SSB. In general, two main pathways are responsible for repairing DSB, homologous recombination (HR) and non-homologous end-joining (NHEJ), with both of them being potential candidates for the repair of oxidative DSB. We have examined relative contribution of HR and NHEJ to cellular response after oxidative stress in Saccharomyces cerevisiae. Therefore, cell survival, mutagenesis and DSB induction and repair in the rad52, yku70 and rad52 yku70 mutants after hydrogen peroxide (H(2)O(2)), menadione (MD) or bleomycin (BLM) exposure were compared to those obtained for the corresponding wild type. We show that MD exposure does not lead to observable DSB induction in yeast, suggesting that the toxic effects of this agent are mediated by other types of DNA damage. Although H(2)O(2) treatment generates some DSB, their yield is relatively low and hence DSB may only partially be responsible for toxicity of H(2)O(2), particularly at high doses of the agent. On the other hand, the basis of the BLM toxicity resides primarily in DSB induction. Both HR and NHEJ act on BLM-induced DSB, although their relative participation in the process is not equal. Based on our results we suggest that the complexity and/or the quality of the BLM-induced DSB might represent an obstacle for the NHEJ pathway.

Molecular mechanism of protein assembly on DNA double-strand breaks in the non-homologous end-joining pathway

International Nuclear Information System (INIS)

Yano, Ken-ichi; Morotomi-Yano, Keiko; Adachi, Noritaka; Akiyama, Hidenori

2009-01-01

Non-homologous end-joining (NHEJ) is the major repair pathway for DNA double-strand breaks (DSBs) in mammalian species. Upon DSB induction, a living cell quickly activates the NHEJ pathway comprising of multiple molecular events. However, it has been difficult to analyze the initial phase of DSB responses in living cells, primarily due to technical limitations. Recent advances in real-time imaging and site-directed DSB induction using laser microbeam allow us to monitor the spatiotemporal dynamics of NHEJ factors in the immediate-early phase after DSB induction. These new approaches, together with the use of cell lines deficient in each essential NHEJ factor, provide novel mechanistic insights into DSB recognition and protein assembly on DSBs in the NHEJ pathway. In this review, we provide an overview of recent progresses in the imaging analyses of the NHEJ core factors. These studies strongly suggest that the NHEJ core factors are pre-assembled into a large complex on DSBs prior to the progression of the biochemical reactions in the NHEJ pathway. Instead of the traditional step-by-step assembly model from the static view of NHEJ, a novel model for dynamic protein assembly in the NHEJ pathway is proposed. This new model provides important mechanistic insights into the protein assembly at DSBs and the regulation of DSB repair. (author)

CRISPR/Cas-mediated knock-in via non-homologous end-joining in the crustacean Daphnia magna.

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Kumagai, Hitoshi; Nakanishi, Takashi; Matsuura, Tomoaki; Kato, Yasuhiko; Watanabe, Hajime

2017-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas) is widely used for mediating the knock-in of foreign DNA into the genomes of various organisms. Here, we report a process of CRISPR/Cas-mediated knock-in via non-homologous end joining by the direct injection of Cas9/gRNA ribonucleoproteins (RNPs) in the crustacean Daphnia magna, which is a model organism for studies on toxicology, ecology, and evolution. First, we confirmed the cleavage activity of Cas9 RNPs comprising purified Cas9 proteins and gRNAs in D. magna. We used a gRNA that targets exon 10 of the eyeless gene. Cas9 proteins were incubated with the gRNAs and the resulting Cas9 RNPs were injected into D. magna eggs, which led to a typical phenotype of the eyeless mutant, i.e., eye deformity. The somatic and heritable mutagenesis efficiencies were up to 96% and 40%, respectively. Second, we tested the CRISPR/Cas-mediated knock-in of a plasmid by the injection of Cas9 RNPs. The donor DNA plasmid harboring the fluorescent reporter gene was designed to contain the gRNA recognition site. The co-injection of Cas9 RNPs together with the donor DNAs resulted in generation of one founder animal that produced fluorescent progenies. This transgenic Daphnia had donor DNA at the targeted genomic site, which suggested the concurrent cleavage of the injected plasmid DNA and genomic DNA. Owing to its simplicity and ease of experimental design, we suggest that the CRISPR/Cas-mediated knock-in method represents a promising tool for studying functional genomics in D. magna.

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

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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. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

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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.

Non-homologous end joining dependency of γ-irradiation-induced adaptive frameshift mutation formation in cell cycle-arrested yeast cells

International Nuclear Information System (INIS)

Heidenreich, Erich; Eisler, Herfried

2004-01-01

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 γ-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 γ-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

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

Unsolved mystery: the role of BRCA1 in DNA end-joining

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Saha, Janapriya; Davis, Anthony J.

2016-01-01

Heritable mutations in the tumor suppressor gene BRCA1 increase a woman's lifetime risk of developing breast and ovarian cancer. BRCA1's tumor suppressor function is directly linked to its myriad of functions in the cellular response to DNA double-strand breaks (DSBs). BRCA1 interacts with an extensive array of DNA damage responsive proteins and plays important roles in DSB repair, mediated by the homologous recombination pathway, and in the activation of cell cycle checkpoints. However, the role of BRCA1 in the other two DSB repair pathways, classical non-homologous end-joining (C-NHEJ) and alternative NHEJ (A-NHEJ), remains unclear. In this review, we will discuss the current literature on BRCA1's potential role(s) in modulating both C-NHEJ and A-NHEJ. We also present a model showing that BRCA1 contributes to genomic maintenance by promoting precise DNA repair across all cell cycle phases via the direct modulation of DNA end-joining

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

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Grabarz, Anastazja

2011-01-01

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

Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining

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Kukshal, Vandna; Kim, In-Kwon; Hura, Gregory L.; Tomkinson, Alan E.; Tainer, John A.; Ellenberger, Tom

2015-01-01

Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation. PMID:26130724

An efficient system for deletion of large DNA fragments in Escherichia coli via introduction of both Cas9 and the non-homologous end joining system from Mycobacterium smegmatis.

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Zheng, Xuan; Li, Shi-Yuan; Zhao, Guo-Ping; Wang, Jin

2017-04-15

Accompanied with the internal non-homologous end joining (NHEJ) system, Cas9 can be used to easily inactivate a gene or delete a fragment through introduction of DNA double-stranded breaks (DSBs) in eukaryotic cells. While in most prokaryotes (e.g. Escherichia coli), due to the lack of NHEJ, homologous recombination (HR) is required for repair of DSBs, which is less convenient. Here, a markerless system was developed for rapid gene inactivation or fragment deletion in E. coli via introduction of both Cas9 and a bacterial NHEJ system. Three bacterial NHEJ systems, i.e. Mycobacterium smegmatis (Msm), Mycobacterium tuberculosis (Mtb) and Bacillus subtilis (Bs), were tested in E. coli, and the MsmNHEJ system showed the best efficiency. With the employment of Cas9 and MsmNHEJ, we efficiently mutated lacZ gene, deleted glnALG operon and two large DNA fragments (67 kb and 123 kb) in E. coli, respectively. Moreover, the system was further designed to allow for continuous inactivation of genes or deletion of DNA fragments in E. coli. We envision this system can be extended to other bacteria, especially those with low HR efficiency. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification of auxotrophic mutants of the yeast Kluyveromyces marxianus by non-homologous end joining-mediated integrative transformation with genes from Saccharomyces cerevisiae.

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Yarimizu, Tohru; Nonklang, Sanom; Nakamura, Junpei; Tokuda, Shuya; Nakagawa, Takaaki; Lorreungsil, Sasithorn; Sutthikhumpha, Surasit; Pukahuta, Charida; Kitagawa, Takao; Nakamura, Mikiko; Cha-Aim, Kamonchai; Limtong, Savitree; Hoshida, Hisashi; Akada, Rinji

2013-12-01

The isolation and application of auxotrophic mutants for gene manipulations, such as genetic transformation, mating selection and tetrad analysis, form the basis of yeast genetics. For the development of these genetic methods in the thermotolerant fermentative yeast Kluyveromyces marxianus, we isolated a series of auxotrophic mutants with defects in amino acid or nucleic acid metabolism. To identify the mutated genes, linear DNA fragments of nutrient biosynthetic pathway genes were amplified from Saccharomyces cerevisiae chromosomal DNA and used to directly transform the K. marxianus auxotrophic mutants by random integration into chromosomes through non-homologous end joining (NHEJ). The appearance of transformant colonies indicated that the specific S. cerevisiae gene complemented the K. marxianus mutant. Using this interspecific complementation approach with linear PCR-amplified DNA, we identified auxotrophic mutations of ADE2, ADE5,7, ADE6, HIS2, HIS3, HIS4, HIS5, HIS6, HIS7, LYS1, LYS2, LYS4, LYS9, LEU1, LEU2, MET2, MET6, MET17, TRP3, TRP4 and TRP5 without the labour-intensive requirement of plasmid construction. Mating, sporulation and tetrad analysis techniques for K. marxianus were also established. With the identified auxotrophic mutant strains and S. cerevisiae genes as selective markers, NHEJ-mediated integrative transformation with PCR-amplified DNA is an attractive system for facilitating genetic analyses in the yeast K. marxianus. Copyright © 2013 John Wiley & Sons, Ltd.

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)

Deriano, L.

2005-01-01

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

Lipofection and nucleofection of substrate plasmid can generate widely different readings of DNA end-joining efficiency in different cell lines.

Science.gov (United States)

Magin, Simon; Saha, Janapriya; Wang, Minli; Mladenova, Veronika; Coym, Nadine; Iliakis, George

2013-02-01

In vivo plasmid end-joining assays are valuable tools for dissecting important qualitative and quantitative aspects of non-homologous end-joining (NHEJ)--a key mechanism for the repair of DNA double-strand breaks (DSBs) in higher eukaryotes. They enable the use of defined DNA ends as substrates for end-joining and the analysis by sequencing of the resulting junctions to identify the repair pathways engaged. Yet, plasmid assays have generated divergent results of end-joining capacity in the same DSB repair mutants when used under different conditions, which implies contributions from undefined and therefore uncontrolled parameters. To help standardize these assays, we searched for parameters underpinning these variations and identified transfection method as an important determinant. Here, we compare a lipid-based transfection method, lipofection, with an electroporation method, nucleofection, and find large, unanticipated and cell line-dependent differences in percent end-joining without recognizable trends. For example, in rodent cells, transfection using lipofection gives nearly WT end-joining in DNA-PKcs mutants and only mildly inhibited end-joining in Lig4 and Ku mutants. In contrast, transfection using nucleofection shows marked end-joining inhibition in all NHEJ mutants tested as compared to the WT. In human HCT116 cells, end-joining after nucleofection is strongly suppressed even in the WT and the differences to the mutants are small. After lipofection, in contrast, end-joining is high in WT cells and markedly suppressed in the mutants. We conclude that better understanding and control of the physicochemical/biological and analytical parameters underpinning these differences will be required to generate with plasmid assays results with quantitative power comparable to that of well-established methods of DSB analysis such as pulsed-field gel electrophoresis or γ-H2AX foci scoring. Until then, caution is needed in the interpretation of the results obtained

Sirt6 Promotes DNA End Joining in iPSCs Derived from Old Mice

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Wen Chen

2017-03-01

Full Text Available Induced pluripotent stem cells (iPSCs have great potential for treating age-related diseases, but the genome integrity of iPSCs is critically important. Here, we demonstrate that non-homologous end joining (NHEJ, rather than homologous recombination (HR, is less efficient in iPSCs from old mice than young mice. We further find that Sirt6 is downregulated in iPSCs from old mice. Sirt6 directly binds to Ku80 and facilitates the Ku80/DNA-PKcs interaction, thus promoting DNA-PKcs phosphorylation at residue S2056, leading to efficient NHEJ. Rescue experiments show that introducing a combination of Sirt6 and the Yamanaka factors during reprogramming significantly promotes DNA double-strand break (DSB repair by activating NHEJ in iPSCs derived from old mice. Thus, our study suggests a strategy to improve the quality of iPSCs derived from old donors by activating NHEJ and stabilizing the genome.

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.

Expression of Mycobacterium tuberculosis Ku and Ligase D in Escherichia coli results in RecA and RecB-independent DNA end-joining at regions of microhomology.

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Malyarchuk, Svitlana; Wright, Douglas; Castore, Reneau; Klepper, Emily; Weiss, Bernard; Doherty, Aidan J; Harrison, Lynn

2007-10-01

Unlike Escherichia coli, Mycobacterium tuberculosis (Mt) expresses a Ku-like protein and an ATP-dependent DNA ligase that can perform non-homologous end-joining (NHEJ). We have expressed the Mt-Ku and Mt-Ligase D in E. coli using an arabinose-inducible promoter and expression vectors that integrate into specific sites in the E. coli chromosome. E. coli strains have been generated that express the Mt-Ku and Mt-Ligase D on a genetic background that is wild-type for repair, or deficient in either the RecA or RecB protein. Transformation of these strains with linearized plasmid DNA containing a 2bp overhang has demonstrated that expression of both the Mt-Ku and Mt-Ligase D is required for DNA end-joining and that loss of RecA does not prevent this double-strand break repair. Analysis of the re-joined plasmid has shown that repair is predominantly inaccurate and results in the deletion of sequences. Loss of RecB did not prevent the formation of large deletions, but did increase the amount of end-joining. Sequencing the junctions has revealed that the majority of the ligations occurred at regions of microhomology (1-4bps), eliminating one copy of the homologous sequence at the junction. The Mt-Ku and Mt-Ligase D can therefore function in E. coli to re-circularize linear plasmid.

Highly precise and developmentally programmed genome assembly in Paramecium requires ligase IV-dependent end joining.

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Aurélie Kapusta

2011-04-01

Full Text Available During the sexual cycle of the ciliate Paramecium, assembly of the somatic genome includes the precise excision of tens of thousands of short, non-coding germline sequences (Internal Eliminated Sequences or IESs, each one flanked by two TA dinucleotides. It has been reported previously that these genome rearrangements are initiated by the introduction of developmentally programmed DNA double-strand breaks (DSBs, which depend on the domesticated transposase PiggyMac. These DSBs all exhibit a characteristic geometry, with 4-base 5' overhangs centered on the conserved TA, and may readily align and undergo ligation with minimal processing. However, the molecular steps and actors involved in the final and precise assembly of somatic genes have remained unknown. We demonstrate here that Ligase IV and Xrcc4p, core components of the non-homologous end-joining pathway (NHEJ, are required both for the repair of IES excision sites and for the circularization of excised IESs. The transcription of LIG4 and XRCC4 is induced early during the sexual cycle and a Lig4p-GFP fusion protein accumulates in the developing somatic nucleus by the time IES excision takes place. RNAi-mediated silencing of either gene results in the persistence of free broken DNA ends, apparently protected against extensive resection. At the nucleotide level, controlled removal of the 5'-terminal nucleotide occurs normally in LIG4-silenced cells, while nucleotide addition to the 3' ends of the breaks is blocked, together with the final joining step, indicative of a coupling between NHEJ polymerase and ligase activities. Taken together, our data indicate that IES excision is a "cut-and-close" mechanism, which involves the introduction of initiating double-strand cleavages at both ends of each IES, followed by DSB repair via highly precise end joining. This work broadens our current view on how the cellular NHEJ pathway has cooperated with domesticated transposases for the emergence of new

Highly precise and developmentally programmed genome assembly in Paramecium requires ligase IV-dependent end joining.

Science.gov (United States)

Kapusta, Aurélie; Matsuda, Atsushi; Marmignon, Antoine; Ku, Michael; Silve, Aude; Meyer, Eric; Forney, James D; Malinsky, Sophie; Bétermier, Mireille

2011-04-01

During the sexual cycle of the ciliate Paramecium, assembly of the somatic genome includes the precise excision of tens of thousands of short, non-coding germline sequences (Internal Eliminated Sequences or IESs), each one flanked by two TA dinucleotides. It has been reported previously that these genome rearrangements are initiated by the introduction of developmentally programmed DNA double-strand breaks (DSBs), which depend on the domesticated transposase PiggyMac. These DSBs all exhibit a characteristic geometry, with 4-base 5' overhangs centered on the conserved TA, and may readily align and undergo ligation with minimal processing. However, the molecular steps and actors involved in the final and precise assembly of somatic genes have remained unknown. We demonstrate here that Ligase IV and Xrcc4p, core components of the non-homologous end-joining pathway (NHEJ), are required both for the repair of IES excision sites and for the circularization of excised IESs. The transcription of LIG4 and XRCC4 is induced early during the sexual cycle and a Lig4p-GFP fusion protein accumulates in the developing somatic nucleus by the time IES excision takes place. RNAi-mediated silencing of either gene results in the persistence of free broken DNA ends, apparently protected against extensive resection. At the nucleotide level, controlled removal of the 5'-terminal nucleotide occurs normally in LIG4-silenced cells, while nucleotide addition to the 3' ends of the breaks is blocked, together with the final joining step, indicative of a coupling between NHEJ polymerase and ligase activities. Taken together, our data indicate that IES excision is a "cut-and-close" mechanism, which involves the introduction of initiating double-strand cleavages at both ends of each IES, followed by DSB repair via highly precise end joining. This work broadens our current view on how the cellular NHEJ pathway has cooperated with domesticated transposases for the emergence of new mechanisms

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

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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.

End-joining inhibition at telomeres requires the translocase and polySUMO-dependent ubiquitin ligase Uls1.

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Lescasse, Rachel; Pobiega, Sabrina; Callebaut, Isabelle; Marcand, Stéphane

2013-03-20

In eukaryotes, permanent inhibition of the non-homologous end joining (NHEJ) repair pathway at telomeres ensures that chromosome ends do not fuse. In budding yeast, binding of Rap1 to telomere repeats establishes NHEJ inhibition. Here, we show that the Uls1 protein is required for the maintenance of NHEJ inhibition at telomeres. Uls1 protein is a non-essential Swi2/Snf2-related translocase and a Small Ubiquitin-related Modifier (SUMO)-Targeted Ubiquitin Ligase (STUbL) with unknown targets. Loss of Uls1 results in telomere-telomere fusions. Uls1 requirement is alleviated by the absence of poly-SUMO chains and by rap1 alleles lacking SUMOylation sites. Furthermore, Uls1 limits the accumulation of Rap1 poly-SUMO conjugates. We propose that one of Uls1 functions is to clear non-functional poly-SUMOylated Rap1 molecules from telomeres to ensure the continuous efficiency of NHEJ inhibition. Since Uls1 is the only known STUbL with a translocase activity, it can be the general molecular sweeper for the clearance of poly-SUMOylated proteins on DNA in eukaryotes.

Role for Artemis nuclease in the repair of radiation-induced DNA double strand breaks by alternative end joining.

Science.gov (United States)

Moscariello, Mario; Wieloch, Radi; Kurosawa, Aya; Li, Fanghua; Adachi, Noritaka; Mladenov, Emil; Iliakis, George

2015-07-01

Exposure of cells to ionizing radiation or radiomimetic drugs generates DNA double-strand breaks that are processed either by homologous recombination repair (HRR), or by canonical, DNA-PKcs-dependent non-homologous end-joining (C-NHEJ). Chemical or genetic inactivation of factors involved in C-NHEJ or HRR, but also their local failure in repair proficient cells, promotes an alternative, error-prone end-joining pathway that serves as backup (A-EJ). There is evidence for the involvement of Artemis endonuclease, a protein deficient in a human radiosensitivity syndrome associated with severe immunodeficiency (RS-SCID), in the processing of subsets of DSBs by HRR or C-NHEJ. It is thought that within HRR or C-NHEJ Artemis processes DNA termini at complex DSBs. Whether Artemis has a role in A-EJ remains unknown. Here, we analyze using pulsed-field gel electrophoresis (PFGE) and specialized reporter assays, DSB repair in wild-type pre-B NALM-6 lymphocytes, as well as in their Artemis(-/-), DNA ligase 4(-/-) (LIG4(-/-)), and LIG4(-/-)/Artemis(-/-) double mutant counterparts, under conditions allowing evaluation of A-EJ. Our results substantiate the suggested roles of Artemis in C-NHEJ and HRR, but also demonstrate a role for the protein in A-EJ that is confirmed in Artemis deficient normal human fibroblasts. We conclude that Artemis is a nuclease participating in DSB repair by all major repair pathways. Copyright © 2015 Elsevier B.V. All rights reserved.

KIN17, XPC, DNA-PKCS and XRCC4 proteins in the cellular response to DNA damages. Relations between nucleotide excision repair and non-homologous end joining in a human syn-genic model

International Nuclear Information System (INIS)

Despras, Emmanuelle

2006-01-01

The response to genotoxic stress involves many cellular factors in a complex network of mechanisms that aim to preserve the genetic integrity of the organism. These mechanisms enclose the detection and repair of DNA lesions, the regulation of transcription and replication and, eventually, the setting of cell death. Among the nuclear proteins involved in this response, kin17 proteins are zinc-finger proteins conserved through evolution and activated by ultraviolet (UV) or ionizing radiations (IR). We showed that human kin17 protein (HSAkin17) is found in the cell under a soluble form and a form tightly anchored to nuclear structures. A fraction of HSAkin17 protein is directly associated with chromatin. HSAkin17 protein is recruited to nuclear structures 24 hours after treatment with various agents inducing DNA double-strand breaks (DSB) and/or replication forks blockage. Moreover, the reduction of total HSAkin17 protein level sensitizes RKO cells to IR. We also present evidence for the involvement of HSAkin17 protein in DNA replication. This hypothesis was further confirmed by the biochemical demonstration of its belonging to the replication complex. HSAkin17 protein could link DNA replication and DNA repair, a defect in the HSAkin17 pathway leading to an increased radiosensitivity. In a second part, we studied the interactions between two DNA repair mechanisms: nucleotide excision repair (NER) and non-homologous end joining (NHEJ). NER repairs a wide variety of lesions inducing a distortion of the DNA double helix including UV-induced pyrimidine dimers. NHEJ allows the repair of DSB by direct joining of DNA ends. We used a syn-genic model for DNA repair defects based on RNA interference developed in the laboratory. Epstein-Barr virus-derived vectors (pEBV) allow long-term expression of siRNA and specific extinction of the targeted gene. The reduction of the expression of genes involved in NER (XPA and XPC) or NHEJ (DNA-PKcs and XRCC4) leads to the expected

Recombination-assisted megaprimer (RAM) cloning

Science.gov (United States)

Mathieu, Jacques; Alvarez, Emilia; Alvarez, Pedro J.J.

2014-01-01

No molecular cloning technique is considered universally reliable, and many suffer from being too laborious, complex, or expensive. Restriction-free cloning is among the simplest, most rapid, and cost-effective methods, but does not always provide successful results. We modified this method to enhance its success rate through the use of exponential amplification coupled with homologous end-joining. This new method, recombination-assisted megaprimer (RAM) cloning, significantly extends the application of restriction-free cloning, and allows efficient vector construction with much less time and effort when restriction-free cloning fails to provide satisfactory results. The following modifications were made to the protocol:•Limited number of PCR cycles for both megaprimer synthesis and the cloning reaction to reduce error propagation.•Elimination of phosphorylation and ligation steps previously reported for cloning methods that used exponential amplification, through the inclusion of a reverse primer in the cloning reaction with a 20 base pair region of homology to the forward primer.•The inclusion of 1 M betaine to enhance both reaction specificity and yield. PMID:26150930

Environmentally friendly joining of tubes by their ends

DEFF Research Database (Denmark)

Silva, Carlos M.A.; Nielsen, Chris Valentin; Alves, Luis M.

2015-01-01

This paper proposes an environmentally friendly joining process for connecting tubes by their ends that has the potential to replace current solutions based on fastened, crimped, welded, brazed or adhesive bonded joints. The process is based on a new type of tubular lap joint produced by local...... of deformation and the process feasibility window, and destructive testing to establish the working limits of tubular lap joints under different type of loading conditions. Results demonstrate that the proposed joining process is a flexible and cost-effective technology for connecting tubes by their ends...

Double strand break rejoining by the Ku-dependent mechanism of non-homologous end-joining

International Nuclear Information System (INIS)

Jeggo, P.; Singleton, B.; Beamish, H.; Priestley, A.

1999-01-01

The DNA-dependent protein kinase functions in the repair of DNA double strand breaks (DSBs) and in V(D)J recombination. To gain insight into the function of DNA-PK in this process we have carried out a mutation analysis of Ku80 and DNA-PKcs. Mutations at multiple sites within the N-terminal two thirds of Ku80 result in loss of Ku70/80 interaction, loss of DNA end-binding activity and inability to complement Ku80 defective cell fines. In contrast, mutations in the carboxy terminal region of the protein do not impair DNA end-binding activity but decrease the ability of Ku to activate DNA-PK. To gain insight into important functional domains within DNA-PKcs, we have analysed defective mutants, including the mouse scid cell line, and the rodent mutants, ire-20 and V-3. Mutational changes in the carboxy terminal region have been identified in all cases. Our results strongly suggest that the C-terminus of DNA-PKcs is required for kinase activity. (author)

Influence of reduced glutathione on end-joining of DNA double-strand breaks: Cytogenetical and molecular approach

Energy Technology Data Exchange (ETDEWEB)

Ghoshal, Nitin [Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya-793022 (India); Sharma, Sheetal [Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012 (India); Banerjee, Atanu; Kurkalang, Sillarine [Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya-793022 (India); Raghavan, Sathees C. [Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012 (India); Chatterjee, Anupam, E-mail: chatterjeeanupam@hotmail.com [Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya-793022 (India)

2017-01-15

Highlights: • DNA lesions induced by Blem and radiation interact well and form higher frequency of exchange aberrations. • Cellular level of glutathione does influence such interaction of DNA lesions. • Oligomer-based cell-free assay system demonstrated better end-joining efficiency at higher level of endogenous GSH. - Abstract: Radiation induced DNA double-strand breaks (DSB) are the major initial lesions whose misrejoining may lead to exchange aberrations. However, the role of glutathione (GSH), a major cellular thiol, in regulating cell’s sensitivity to DNA damaging agents is not well understood. Influence of endogenous GSH on the efficiency of X-rays and bleomycin (Blem) induced DNA DSBs end-joining has been tested here cytogenetically, in human lymphocytes and Hct116 cells. In another approach, oligomeric DNA (75 bp) containing 5′-compatible and non-compatible overhangs mimicking the endogenous DSB were for rejoining in presence of cell-free extracts from cells having different endogenous GSH levels. Frequency of aberrations, particularly exchange aberrations, was significantly increased when Blem was combined with radiation. The exchange aberration frequency was further enhanced when combined treatment was given at 4 °C since DNA lesions are poorly repaired at 4 °C so that a higher number of DNA breaks persist and interact when shifted from 4 °C to 37 °C. The exchange aberrations increased further when the combined treatment was given to Glutathione-ester (GE) pre-treated cells, indicating more frequent rejoining of DNA lesions in presence of higher cellular GSH. This is further supported by the drastic reduction in frequency of exchange aberrations but significant increase in incidences of deletions when combined treatment was given to GSH-depleted cells. End-joining efficiency of DNA DSBs with compatible ends was better than for non-compatible ends. End-joining efficiency of testicular and MCF7 cell extracts was better than that of lungs and

Interplay between Ku and Replication Protein A in the Restriction of Exo1-mediated DNA Break End Resection*

Science.gov (United States)

Krasner, Danielle S.; Daley, James M.; Sung, Patrick; Niu, Hengyao

2015-01-01

DNA double-strand breaks can be eliminated via non-homologous end joining or homologous recombination. Non-homologous end joining is initiated by the association of Ku with DNA ends. In contrast, homologous recombination entails nucleolytic resection of the 5′-strands, forming 3′-ssDNA tails that become coated with replication protein A (RPA). Ku restricts end access by the resection nuclease Exo1. It is unclear how partial resection might affect Ku engagement and Exo1 restriction. Here, we addressed these questions in a reconstituted system with yeast proteins. With blunt-ended DNA, Ku protected against Exo1 in a manner that required its DNA end-binding activity. Despite binding poorly to ssDNA, Ku could nonetheless engage a 5′-recessed DNA end with a 40-nucleotide (nt) ssDNA overhang, where it localized to the ssDNA-dsDNA junction and efficiently blocked resection by Exo1. Interestingly, RPA could exclude Ku from a partially resected structure with a 22-nt ssDNA tail and thus restored processing by Exo1. However, at a 40-nt tail, Ku remained stably associated at the ssDNA-dsDNA junction, and RPA simultaneously engaged the ssDNA region. We discuss a model in which the dynamic equilibrium between Ku and RPA binding to a partially resected DNA end influences the timing and efficiency of the resection process. PMID:26067273

Environmental Stress Induces Trinucleotide Repeat Mutagenesis in Human Cells by Alt-Nonhomologous End Joining Repair.

Science.gov (United States)

Chatterjee, Nimrat; Lin, Yunfu; Yotnda, Patricia; Wilson, John H

2016-07-31

Multiple pathways modulate the dynamic mutability of trinucleotide repeats (TNRs), which are implicated in neurodegenerative disease and evolution. Recently, we reported that environmental stresses induce TNR mutagenesis via stress responses and rereplication, with more than 50% of mutants carrying deletions or insertions-molecular signatures of DNA double-strand break repair. We now show that knockdown of alt-nonhomologous end joining (alt-NHEJ) components-XRCC1, LIG3, and PARP1-suppresses stress-induced TNR mutagenesis, in contrast to the components of homologous recombination and NHEJ, which have no effect. Thus, alt-NHEJ, which contributes to genetic mutability in cancer cells, also plays a novel role in environmental stress-induced TNR mutagenesis. Published by Elsevier Ltd.

A sensitive short read homology search tool for paired-end read sequencing data.

Science.gov (United States)

Techa-Angkoon, Prapaporn; Sun, Yanni; Lei, Jikai

2017-10-16

Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the fast accumulation of transcriptomic data of non-model species and metagenomic data, profile homology search is widely adopted in integrated pipelines for functional analysis. While the state-of-the-art tool HMMER has achieved high sensitivity and accuracy in domain annotation, the sensitivity of HMMER on short reads declines rapidly. The low sensitivity on short read homology search can lead to inaccurate domain composition and abundance computation. Our experimental results showed that half of the reads were missed by HMMER for a RNA-Seq dataset. Thus, there is a need for better methods to improve the homology search performance for short reads. We introduce a profile homology search tool named Short-Pair that is designed for short paired-end reads. By using an approximate Bayesian approach employing distribution of fragment lengths and alignment scores, Short-Pair can retrieve the missing end and determine true domains. In particular, Short-Pair increases the accuracy in aligning short reads that are part of remote homologs. We applied Short-Pair to a RNA-Seq dataset and a metagenomic dataset and quantified its sensitivity and accuracy on homology search. The experimental results show that Short-Pair can achieve better overall performance than the state-of-the-art methodology of profile homology search. Short-Pair is best used for next-generation sequencing (NGS) data that lack reference genomes. It provides a complementary paired-end read homology search tool to HMMER. The source code is freely available at https://sourceforge.net/projects/short-pair/ .

Regulation of homologous recombination repair protein Rad51 by Ku70

International Nuclear Information System (INIS)

Du Liqing; Liu Qiang; Wang Yan; Xu Chang; Cao Jia; Fu Yue; Chen Fenghua; Fan Feiyue

2013-01-01

Objective: To explore the regulative effect of non-homologous end joining (NHEJ)protein Ku70 on homologous recombination repair protein Rad51, and to investigate the synergistic mechanism of homologous recombination repair in combination with NHEJ. Methods: Observed Rad51 protein expression after transfect Ku70 small interfering RNA or Ku70 plasmid DNA into tumor cells using Western blot. Results: Expression of Rad51 was obviously reduced after pretreated with Ku70 small interfering RNA. And with the increasing expression of Ku70 protein after transfection of Ku70 plasmid DNA PGCsi3.0-hKu70 into tumor cell lines, the Rad51 protein expression was increased. Conclusion: Ku70 protein has regulating effect on gene expression of Rad51, and it might participate in the collaboration between homologous recombination repair and NHEJ. (authors)

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

NARCIS (Netherlands)

E.P.W.C. Weterings (Eric); N.S. Verkaik (Nicole); H.T. Brüggenwirth (Hennie); D.C. van Gent (Dik); J.H.J. Hoeijmakers (Jan)

2003-01-01

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

Hyperactivation of PARP triggers nonhomologous end-joining in repair-deficient mouse fibroblasts.

Directory of Open Access Journals (Sweden)

Natalie R Gassman

Full Text Available Regulation of poly(ADP-ribose (PAR synthesis and turnover is critical to determining cell fate after genotoxic stress. Hyperactivation of PAR synthesis by poly(ADP-ribose polymerase-1 (PARP-1 occurs when cells deficient in DNA repair are exposed to genotoxic agents; however, the function of this hyperactivation has not been adequately explained. Here, we examine PAR synthesis in mouse fibroblasts deficient in the base excision repair enzyme DNA polymerase β (pol β. The extent and duration of PARP-1 activation was measured after exposure to either the DNA alkylating agent, methyl methanesulfonate (MMS, or to low energy laser-induced DNA damage. There was strong DNA damage-induced hyperactivation of PARP-1 in pol β nullcells, but not in wild-type cells. In the case of MMS treatment, PAR synthesis did not lead to cell death in the pol β null cells, but instead resulted in increased PARylation of the nonhomologous end-joining (NHEJ protein Ku70 and increased association of Ku70 with PARP-1. Inhibition of the NHEJ factor DNA-PK, under conditions of MMS-induced PARP-1 hyperactivation, enhanced necrotic cell death. These data suggest that PARP-1 hyperactivation is a protective mechanism triggering the classical-NHEJ DNA repair pathway when the primary alkylated base damage repair pathway is compromised.

Matrix-assisted peptide synthesis on nanoparticles.

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Khandadash, Raz; Machtey, Victoria; Weiss, Aryeh; Byk, Gerardo

2014-09-01

We report a new method for multistep peptide synthesis on polymeric nanoparticles of differing sizes. Polymeric nanoparticles were functionalized via their temporary embedment into a magnetic inorganic matrix that allows multistep peptide synthesis. The matrix is removed at the end of the process for obtaining nanoparticles functionalized with peptides. The matrix-assisted synthesis on nanoparticles was proved by generating various biologically relevant peptides. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

Identification and analysis of Ku70 and Ku80 homologs in the koji molds Aspergillus sojae and Aspergillus oryzae.

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Takahashi, Tadashi; Masuda, Tsutomu; Koyama, Yasuji

2006-01-01

Ku genes play a key role in the non-homologous end-joining pathway. We have identified Ku70 and Ku80 homologs in the koji molds Aspergillus sojae and Aspergillus oryzae, and have constructed the disruption mutants of Ku70, Ku80, and Ku70-80 to characterize the phenotypic change in these mutants. Neither Ku70- nor Ku80-disrupted strains show hypersensitivity to the DNA damaging agents methylmethane sulfonate (MMS) and phleomycin. Moreover, undesirable phenotypes, such as poor growth or repressed conidiospore formation, were not observed in the Ku-disrupted A. sojae and A. oryzae.

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

Murine leukemia viruses harboring an internal ribosome entry site (IRES)-directed translational cassette are able to replicate, but undergo loss of heterologous sequences upon continued passage. While complete loss of heterologous sequences is favored when these are flanked by a direct repeat......, deletion mutants with junction sites within the heterologous cassette may also be retrieved, in particular from vectors without flanking repeats. Such deletion mutants were here used to investigate determinants of reverse transcriptase-mediated non-homologous recombination. Based upon previous structural...... 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...

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

Directory of Open Access Journals (Sweden)

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.

Productive Homologous and Non-homologous Recombination of Hepatitis C Virus in Cell Culture

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Li, Yi-Ping; Mikkelsen, Lotte S.; Gottwein, Judith M.; Bukh, Jens

2013-01-01

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 recombinants

Nonhomologous DNA End Joining in Cell-Free Extracts

Directory of Open Access Journals (Sweden)

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.

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

-irradiation and resulted in accumulation of 53BP1 foci after irradiation, indicating defects in the processing of DSB. We find that RECQL4 interacts with the Ku70/Ku80 heterodimer, part of the DNA-dependent protein kinase (DNA-PK) complex, via its N-terminal domain. Further, RECQL4 stimulates higher order DNA binding...... of Ku70/Ku80 to a blunt end DNA substrate. Taken together, these results implicate that RECQL4 participates in the NHEJ pathway of DSB repair via a functional interaction with the Ku70/Ku80 complex. This is the first study to provide both in vitro and in vivo evidence for a role of a RecQ helicase...

Distinct DNA repair pathways involving RecA and nonhomologous end joining in Mycobacterium smegmatis.

OpenAIRE

Korycka-Machala, M; Brzostek, A; Rozalska, S; Rumijowska-Galewicz, A; Dziedzic, R; Bowater, R; Dziadek, J

2006-01-01

Mycobacterium smegmatis was used to study the relationship between DNA repair processes involving RecA and nonhomologous end joining (NHEJ). The effect of gene deletions in recA and/or in two genes involved in NHEJ (ku and ligD) was tested on the ability of bacteria to join breaks in plasmids transformed into them and in their response to chemicals that damage DNA. The results provide in vivo evidence that only NHEJ is required for the repair of noncompatible DNA ends. By contrast, the respon...

Development of a procedure for forming assisted thermal joining of tubes

Science.gov (United States)

Chen, Hui; Löbbe, Christian; Staupendahl, Daniel; Tekkaya, A. Erman

2018-05-01

With the demand of lightweight design in the automotive industry, not only the wall-thicknesses of tubular components of the chassis or spaceframe are continuously decreased. Also the thicknesses of exhaust system parts are reduced to save material and mass. However, thinner tubular parts bring about additional challenges in joining. Welding or brazing methods, which are utilized in joining tubes with specific requirements concerning leak tightness, are sensitive to the gap between the joining partners. Furthermore, a large joining area is required to ensure the durability of the joint. The introduction of a forming step in the assembled state prior to thermal joining can define and control the gap for subsequent brazing or welding. The mechanical pre-joint resulting from the previously described calibration step also results in easier handling of the tubes prior to thermal joining. In the presented investigation, a spinning process is utilized to produce force-fit joints of varying lengths and diameter reduction and form-fit joints with varying geometrical attributes. The spinning process facilitates a high formability and geometrical flexibility, while at the achievable precision is high and the process forces are low. The strength of the joints is used to evaluate the joint quality. Finally, a comparison between joints produced by forming with subsequent brazing and original tube is conducted, which presents the high performance of the developed procedure for forming assisted thermal joining.

FACS-Assisted CRISPR-Cas9 Genome Editing Facilitates Parkinson's Disease Modeling

Directory of Open Access Journals (Sweden)

Jonathan Arias-Fuenzalida

2017-11-01

Full Text Available Genome editing and human induced pluripotent stem cells hold great promise for the development of isogenic disease models and the correction of disease-associated mutations for isogenic tissue therapy. CRISPR-Cas9 has emerged as a versatile and simple tool for engineering human cells for such purposes. However, the current protocols to derive genome-edited lines require the screening of a great number of clones to obtain one free of random integration or on-locus non-homologous end joining (NHEJ-containing alleles. Here, we describe an efficient method to derive biallelic genome-edited populations by the use of fluorescent markers. We call this technique FACS-assisted CRISPR-Cas9 editing (FACE. FACE allows the derivation of correctly edited polyclones carrying a positive selection fluorescent module and the exclusion of non-edited, random integrations and on-target allele NHEJ-containing cells. We derived a set of isogenic lines containing Parkinson's-disease-associated mutations in α-synuclein and present their comparative phenotypes.

Distinct DNA repair pathways involving RecA and nonhomologous end joining in Mycobacterium smegmatis.

Science.gov (United States)

Korycka-Machala, Malgorzata; Brzostek, Anna; Rozalska, Sylwia; Rumijowska-Galewicz, Anna; Dziedzic, Renata; Bowater, Richard; Dziadek, Jaroslaw

2006-05-01

Mycobacterium smegmatis was used to study the relationship between DNA repair processes involving RecA and nonhomologous end joining (NHEJ). The effect of gene deletions in recA and/or in two genes involved in NHEJ (ku and ligD) was tested on the ability of bacteria to join breaks in plasmids transformed into them and in their response to chemicals that damage DNA. The results provide in vivo evidence that only NHEJ is required for the repair of noncompatible DNA ends. By contrast, the response of mycobacteria to mitomycin C preferentially involved a RecA-dependent pathway.

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

Science.gov (United States)

Weterings, Eric; Verkaik, Nicole S; Keijzers, Guido; Florea, Bogdan I; Wang, Shih-Ya; Ortega, Laura G; Uematsu, Naoya; Chen, David J; van Gent, Dik C

2009-03-01

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)) and the XRCC4/ligase IV complex. Activation of the DNA-PK(CS) serine/threonine kinase requires an interaction with Ku70/80 and is essential for NHEJ-mediated DSB repair. In contrast to previous models, we found that the carboxy terminus of Ku80 is not absolutely required for the recruitment and activation of DNA-PK(CS) at DSBs, although cells that harbored a carboxy-terminal deletion in the Ku80 gene were sensitive to ionizing radiation and showed reduced end-joining capacity. More detailed analysis of this repair defect showed that DNA-PK(CS) autophosphorylation at Thr2647 was diminished, while Ser2056 was phosphorylated to normal levels. This resulted in severely reduced levels of Artemis nuclease activity in vivo and in vitro. We therefore conclude that the Ku80 carboxy terminus is important to support DNA-PK(CS) autophosphorylation at specific sites, which facilitates DNA end processing by the Artemis endonuclease and the subsequent joining reaction.

DNA double-strand break response factors influence end-joining features of IgH class switch and general translocation junctions.

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Panchakshari, Rohit A; Zhang, Xuefei; Kumar, Vipul; Du, Zhou; Wei, Pei-Chi; Kao, Jennifer; Dong, Junchao; Alt, Frederick W

2018-01-23

Ig heavy chain (IgH) class switch recombination (CSR) in B lymphocytes switches IgH constant regions to change antibody functions. CSR is initiated by DNA double-strand breaks (DSBs) within a donor IgH switch (S) region and a downstream acceptor S region. CSR is completed by fusing donor and acceptor S region DSB ends by classical nonhomologous end-joining (C-NHEJ) and, in its absence, by alternative end-joining that is more biased to use longer junctional microhomologies (MHs). Deficiency for DSB response (DSBR) factors, including ataxia telangiectasia-mutated (ATM) and 53BP1, variably impair CSR end-joining, with 53BP1 deficiency having the greatest impact. However, studies of potential impact of DSBR factor deficiencies on MH-mediated CSR end-joining have been technically limited. We now use a robust DSB joining assay to elucidate impacts of deficiencies for DSBR factors on CSR and chromosomal translocation junctions in primary mouse B cells and CH12F3 B-lymphoma cells. Compared with wild-type, CSR and c-myc to S region translocation junctions in the absence of 53BP1, and, to a lesser extent, other DSBR factors, have increased MH utilization; indeed, 53BP1-deficient MH profiles resemble those associated with C-NHEJ deficiency. However, translocation junctions between c-myc DSB and general DSBs genome-wide are not MH-biased in ATM-deficient versus wild-type CH12F3 cells and are less biased in 53BP1- and C-NHEJ-deficient cells than CSR junctions or c-myc to S region translocation junctions. We discuss potential roles of DSBR factors in suppressing increased MH-mediated DSB end-joining and features of S regions that may render their DSBs prone to MH-biased end-joining in the absence of DSBR factors.

Requirement for XLF/Cernunnos in alignment-based gap filling by DNA polymerases lambda and mu for nonhomologous end joining in human whole-cell extracts.

Science.gov (United States)

Akopiants, Konstantin; Zhou, Rui-Zhe; Mohapatra, Susovan; Valerie, Kristoffer; Lees-Miller, Susan P; Lee, Kyung-Jong; Chen, David J; Revy, Patrick; de Villartay, Jean-Pierre; Povirk, Lawrence F

2009-07-01

XLF/Cernunnos is a core protein of the nonhomologous end-joining pathway of DNA double-strand break repair. To better define the role of Cernunnos in end joining, whole-cell extracts were prepared from Cernunnos-deficient human cells. These extracts effected little joining of DNA ends with cohesive 5' or 3' overhangs, and no joining at all of partially complementary 3' overhangs that required gap filling prior to ligation. Assays in which gap-filled but unligated intermediates were trapped using dideoxynucleotides revealed that there was no gap filling on aligned DSB ends in the Cernunnos-deficient extracts. Recombinant Cernunnos protein restored gap filling and end joining of partially complementary overhangs, and stimulated joining of cohesive ends more than twentyfold. XLF-dependent gap filling was nearly eliminated by immunodepletion of DNA polymerase lambda, but was restored by addition of either polymerase lambda or polymerase mu. Thus, Cernunnos is essential for gap filling by either polymerase during nonhomologous end joining, suggesting that it plays a major role in aligning the two DNA ends in the repair complex.

AAV-Mediated Gene Targeting Is Significantly Enhanced by Transient Inhibition of Nonhomologous End Joining or the Proteasome In Vivo

Science.gov (United States)

Paulk, Nicole K.; Loza, Laura Marquez; Finegold, Milton J.

2012-01-01

Abstract Recombinant adeno-associated virus (rAAV) vectors have clear potential for use in gene targeting but low correction efficiencies remain the primary drawback. One approach to enhancing efficiency is a block of undesired repair pathways like nonhomologous end joining (NHEJ) to promote the use of homologous recombination. The natural product vanillin acts as a potent inhibitor of NHEJ by inhibiting DNA-dependent protein kinase (DNA-PK). Using a homology containing rAAV vector, we previously demonstrated in vivo gene repair frequencies of up to 0.1% in a model of liver disease hereditary tyrosinemia type I. To increase targeting frequencies, we administered vanillin in combination with rAAV. Gene targeting frequencies increased up to 10-fold over AAV alone, approaching 1%. Fah−/−Ku70−/− double knockout mice also had increased gene repair frequencies, genetically confirming the beneficial effects of blocking NHEJ. A second strategy, transient proteasomal inhibition, also increased gene-targeting frequencies but was not additive to NHEJ inhibition. This study establishes the benefit of transient NHEJ inhibition with vanillin, or proteasome blockage with bortezomib, for increasing hepatic gene targeting with rAAV. Functional metabolic correction of a clinically relevant disease model was demonstrated and provided evidence for the feasibility of gene targeting as a therapeutic strategy. PMID:22486314

Contribution of canonical nonhomologous end joining to chromosomal rearrangements is enhanced by ATM kinase deficiency.

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Bhargava, Ragini; Carson, Caree R; Lee, Gabriella; Stark, Jeremy M

2017-01-24

A likely mechanism of chromosomal rearrangement formation involves joining the ends from two different chromosomal double-strand breaks (DSBs). These events could potentially be mediated by either of two end-joining (EJ) repair pathways [canonical nonhomologous end joining (C-NHEJ) or alternative end joining (ALT-EJ)], which cause distinct rearrangement junction patterns. The relative role of these EJ pathways during rearrangement formation has remained controversial. Along these lines, we have tested whether the DNA damage response mediated by the Ataxia Telangiectasia Mutated (ATM) kinase may affect the relative influence of C-NHEJ vs. ALT-EJ on rearrangement formation. We developed a reporter in mouse cells for a 0.4-Mbp deletion rearrangement that is formed by EJ between two DSBs induced by the Cas9 endonuclease. We found that disruption of the ATM kinase causes an increase in the frequency of the rearrangement as well as a shift toward rearrangement junctions that show hallmarks of C-NHEJ. Furthermore, ATM suppresses rearrangement formation in an experimental condition, in which C-NHEJ is the predominant EJ repair event (i.e., expression of the 3' exonuclease Trex2). Finally, several C-NHEJ factors are required for the increase in rearrangement frequency caused by inhibition of the ATM kinase. We also examined ATM effectors and found that H2AX shows a similar influence as ATM, whereas the influence of ATM on this rearrangement seems independent of 53BP1. We suggest that the contribution of the C-NHEJ pathway to the formation of a 0.4-Mbp deletion rearrangement is enhanced in ATM-deficient cells.

Requirement for XLF/Cernunnos in alignment-based gap filling by DNA polymerases ? and ? for nonhomologous end joining in human whole-cell extracts

OpenAIRE

Akopiants, Konstantin; Zhou, Rui-Zhe; Mohapatra, Susovan; Valerie, Kristoffer; Lees-Miller, Susan P.; Lee, Kyung-Jong; Chen, David J.; Revy, Patrick; de Villartay, Jean-Pierre; Povirk, Lawrence F.

2009-01-01

XLF/Cernunnos is a core protein of the nonhomologous end-joining pathway of DNA double-strand break repair. To better define the role of Cernunnos in end joining, whole-cell extracts were prepared from Cernunnos-deficient human cells. These extracts effected little joining of DNA ends with cohesive 5? or 3? overhangs, and no joining at all of partially complementary 3? overhangs that required gap filling prior to ligation. Assays in which gap-filled but unligated intermediates were trapped us...

Using Negotiated Joining to Construct and Fill Open-ended Roles in Elite Culinary Groups.

Science.gov (United States)

Tan, Vaughn

2015-03-01

This qualitative study examines membership processes in groups operating in an uncertain environment that prevents them from fully predefining new members' roles. I describe how nine elite high-end, cutting-edge culinary groups in the U.S. and Europe, ranging from innovative restaurants to culinary R&D groups, use negotiated joining-a previously undocumented process-to systematically construct and fill these emergent, open-ended roles. I show that negotiated joining is a consistently patterned, iterative process that begins with a role that both aspirant and target group explicitly understand to be provisional. This provisional role is then jointly modified and constructed by the aspirant and target group through repeated iterations of proposition, validation through trial and evaluation, and selective integration of validated role components. The initially provisional role stabilizes and the aspirant achieves membership if enough role components are validated; otherwise the negotiated joining process is abandoned. Negotiated joining allows the aspirant and target group to learn if a mutually desirable role is likely and, if so, to construct such a role. In addition, the provisional roles in negotiated joining can support absorptive capacity by allowing novel role components to enter target groups through aspirants' efforts to construct stable roles for themselves, while the internal adjustment involved in integrating newly validated role components can have the unintended side effect of supporting adaptation by providing opportunities for the groups to use these novel role components to modify their role structure and goals to suit a changing and uncertain environment. Negotiated joining thus reveals role ambiguity's hitherto unexamined beneficial consequences and provides a foundation for a contingency theory of new-member acquisition.

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...

Loss of Ubr2, an E3 ubiquitin ligase, leads to chromosome fragility and impaired homologous recombinational repair

International Nuclear Information System (INIS)

Ouyang, Yan; Kwon, Yong Tae; An, Jee Young; Eller, Danny; Tsai, S.-C.; Diaz-Perez, Silvia; Troke, Joshua J.; Teitell, Michael A.; Marahrens, York

2006-01-01

The N-end rule pathway of protein degradation targets proteins with destabilizing N-terminal residues. Ubr2 is one of the E3 ubiquitin ligases of the mouse N-end rule pathway. We have previously shown that Ubr2 -/- male mice are infertile, owing to the arrest of spermatocytes between the leptotene/zygotene and pachytene of meiosis I, the failure of chromosome pairing, and subsequent apoptosis. Here, we report that mouse fibroblast cells derived from Ubr2 -/- embryos display genome instability. The frequency of chromosomal bridges and micronuclei were much higher in Ubr2 -/- fibroblasts than in +/+ controls. Metaphase chromosome spreads from Ubr2 -/- cells revealed a high incidence of spontaneous chromosomal gaps, indicating chromosomal fragility. These fragile sites were generally replicated late in S phase. Ubr2 -/- cells were hypersensitive to mitomycin C, a DNA cross-linking agent, but displayed normal sensitivity to gamma-irradiation. A reporter assay showed that Ubr2 -/- cells are significantly impaired in the homologous recombination repair of a double strand break. In contrast, Ubr2 -/- cells appeared normal in an assay for non-homologous end joining. Our results therefore unveil the role of the ubiquitin ligase Ubr2 in maintaining genome integrity and in homologous recombination repair

Loss of Ubr2, an E3 ubiquitin ligase, leads to chromosome fragility and impaired homologous recombinational repair

Energy Technology Data Exchange (ETDEWEB)

Ouyang, Yan [Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States); Kwon, Yong Tae [Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 (United States); An, Jee Young [Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 (United States); Eller, Danny [Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States); Tsai, S.-C. [Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States); Diaz-Perez, Silvia [Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States); Troke, Joshua J. [Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States); Teitell, Michael A. [Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States); Marahrens, York [Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States)]. E-mail: ymarahrens@mednet.ucla.edu

2006-04-11

The N-end rule pathway of protein degradation targets proteins with destabilizing N-terminal residues. Ubr2 is one of the E3 ubiquitin ligases of the mouse N-end rule pathway. We have previously shown that Ubr2{sup -/-} male mice are infertile, owing to the arrest of spermatocytes between the leptotene/zygotene and pachytene of meiosis I, the failure of chromosome pairing, and subsequent apoptosis. Here, we report that mouse fibroblast cells derived from Ubr2{sup -/-} embryos display genome instability. The frequency of chromosomal bridges and micronuclei were much higher in Ubr2{sup -/-} fibroblasts than in +/+ controls. Metaphase chromosome spreads from Ubr2{sup -/-} cells revealed a high incidence of spontaneous chromosomal gaps, indicating chromosomal fragility. These fragile sites were generally replicated late in S phase. Ubr2{sup -/-} cells were hypersensitive to mitomycin C, a DNA cross-linking agent, but displayed normal sensitivity to gamma-irradiation. A reporter assay showed that Ubr2{sup -/-} cells are significantly impaired in the homologous recombination repair of a double strand break. In contrast, Ubr2{sup -/-} cells appeared normal in an assay for non-homologous end joining. Our results therefore unveil the role of the ubiquitin ligase Ubr2 in maintaining genome integrity and in homologous recombination repair.

Joining of Ni-TiC FGM and Ni-Al Intermetallics by Centrifugal Combustion Synthesis

International Nuclear Information System (INIS)

Ohmi, Tatsuya; Matsuura, Kiyotaka; Iguchi, Manabu; Mizuma, Kiminori

2008-01-01

A centrifugal combustion synthesis (CCS) process has been investigated to join a Ni-Al intermetallic compound and a Ni-TiC cermet. The cermet, a tubular graphite mold, and a green compact of reactants consisting of Al, Ni and NiO were set in a centrifugal caster. When the combustion synthesis reaction was induced in the centrifugal force field, a synthesized molten Ni-Al alloy flowed into the graphite mold and joined to the cermet. The soundness of the joint interface depended on the volume percentage of TiC phase in the cermet. A lot of defects were formed near the interface between the Ni-TiC cermet and the cast Ni-Al alloy when the volume percentage of TiC was 50% or higher. For this kind of cermet system, using a functionally graded cermet such as Ni-10 vol.%TiC/Ni-25 vol.%TiC/Ni-50 vol.%TiC overcame this difficulty. The four-point bending strength of the joined specimen consisting of the three-layered FGM cermet and cast Ni-29 mol%Al alloy was 1010 MPa which is close to the result for a Ni-29 mol%Al alloy specimen

Surface plasmon resonance assisted rapid laser joining of glass

Energy Technology Data Exchange (ETDEWEB)

Zolotovskaya, Svetlana A.; Tang, Guang; Abdolvand, Amin, E-mail: a.abdolvand@dundee.ac.uk [School of Engineering, Physics and Mathematics, University of Dundee, Dundee DD1 4HN (United Kingdom); Wang, Zengbo [School of Electronic Engineering, Bangor University, Bangor LL57 1UT (United Kingdom)

2014-08-25

Rapid and strong joining of clear glass to glass containing randomly distributed embedded spherical silver nanoparticles upon nanosecond pulsed laser irradiation (∼40 ns and repetition rate of 100 kHz) at 532 nm is demonstrated. The embedded silver nanoparticles were ∼30–40 nm in diameter, contained in a thin surface layer of ∼10 μm. A joint strength of 12.5 MPa was achieved for a laser fluence of only ∼0.13 J/cm{sup 2} and scanning speed of 10 mm/s. The bonding mechanism is discussed in terms of absorption of the laser energy by nanoparticles and the transfer of the accumulated localised heat to the surrounding glass leading to the local melting and formation of a strong bond. The presented technique is scalable and overcomes a number of serious challenges for a widespread adoption of laser-assisted rapid joining of glass substrates, enabling applications in the manufacture of microelectronic devices, sensors, micro-fluidic, and medical devices.

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......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)) and the XRCC4/ligase IV complex. Activation of the DNA-PK(CS) serine/threonine kinase requires an interaction with Ku70/80 and is essential for NHEJ-mediated DSB repair. In contrast to previous models, we found that the carboxy terminus of Ku80 is not absolutely required for the recruitment and activation...... was phosphorylated to normal levels. This resulted in severely reduced levels of Artemis nuclease activity in vivo and in vitro. We therefore conclude that the Ku80 carboxy terminus is important to support DNA-PK(CS) autophosphorylation at specific sites, which facilitates DNA end processing by the Artemis...

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

International Nuclear Information System (INIS)

Wang, Chen; Lees-Miller, Susan P.

2013-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Wang, Chen [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada); Lees-Miller, Susan P., E-mail: leesmill@ucalgary.ca [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada)

2013-07-01

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.

Mycobacterial nonhomologous end joining mediates mutagenic repair of chromosomal double-strand DNA breaks.

Science.gov (United States)

Stephanou, Nicolas C; Gao, Feng; Bongiorno, Paola; Ehrt, Sabine; Schnappinger, Dirk; Shuman, Stewart; Glickman, Michael S

2007-07-01

Bacterial nonhomologous end joining (NHEJ) is a recently described DNA repair pathway best characterized in mycobacteria. Bacterial NHEJ proteins LigD and Ku have been analyzed biochemically, and their roles in linear plasmid repair in vivo have been verified genetically; yet the contributions of NHEJ to repair of chromosomal DNA damage are unknown. Here we use an extensive set of NHEJ- and homologous recombination (HR)-deficient Mycobacterium smegmatis strains to probe the importance of HR and NHEJ in repairing diverse types of chromosomal DNA damage. An M. smegmatis Delta recA Delta ku double mutant has no apparent growth defect in vitro. Loss of the NHEJ components Ku and LigD had no effect on sensitivity to UV radiation, methyl methanesulfonate, or quinolone antibiotics. NHEJ deficiency had no effect on sensitivity to ionizing radiation in logarithmic- or early-stationary-phase cells but was required for ionizing radiation resistance in late stationary phase in 7H9 but not LB medium. In addition, NHEJ components were required for repair of I-SceI mediated chromosomal double-strand breaks (DSBs), and in the absence of HR, the NHEJ pathway rapidly mutates the chromosomal break site. The molecular outcomes of NHEJ-mediated chromosomal DSB repair involve predominantly single-nucleotide insertions at the break site, similar to previous findings using plasmid substrates. These findings demonstrate that prokaryotic NHEJ is specifically required for DSB repair in late stationary phase and can mediate mutagenic repair of homing endonuclease-generated chromosomal DSBs.

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.

Quantitative phase analysis and microstructure characterization of magnetite nanocrystals obtained by microwave assisted non-hydrolytic sol–gel synthesis

Energy Technology Data Exchange (ETDEWEB)

Sciancalepore, Corrado, E-mail: corrado.sciancalepore@unimore.it [Department of Engineering “Enzo Ferrari”, University of Modena and Reggio Emilia, Via Pietro Vivarelli 10, 41100 Modena (Italy); Bondioli, Federica [Department of Industrial Engineering, University of Parma, Parco Area delle Scienze, 181/A, 43124 Parma (Italy); INSTM Consortium, Via G. Giusti 9, 51121 Firenze (Italy); Manfredini, Tiziano [Department of Engineering “Enzo Ferrari”, University of Modena and Reggio Emilia, Via Pietro Vivarelli 10, 41100 Modena (Italy); INSTM Consortium, Via G. Giusti 9, 51121 Firenze (Italy); Gualtieri, Alessandro [Department of Chemical and Geological Science, University of Modena and Reggio Emilia, Via S. Eufemia 19, 41121 Modena Italy (Italy)

2015-02-15

An innovative preparation procedure, based on microwave assisted non-hydrolytic sol–gel synthesis, to obtain spherical magnetite nanoparticles was reported together with a detailed quantitative phase analysis and microstructure characterization of the synthetic products. The nanoparticle growth was analyzed as a function of the synthesis time and was described in terms of crystallization degree employing the Rietveld method on the magnetic nanostructured system for the determination of the amorphous content using hematite as internal standard. Product crystallinity increases as the microwave thermal treatment is increased and reaches very high percentages for synthesis times longer than 1 h. Microstructural evolution of nanocrystals was followed by the integral breadth methods to obtain information on the crystallite size-strain distribution. The results of diffraction line profile analysis were compared with nanoparticle grain distribution estimated by dimensional analysis of the transmission electron microscopy (TEM) images. A variation both in the average grain size and in the distribution of the coherently diffraction domains is evidenced, allowing to suppose a relationship between the two quantities. The traditional integral breadth methods have proven to be valid for a rapid assessment of the diffraction line broadening effects in the above-mentioned nanostructured systems and the basic assumption for the correct use of these methods are discussed as well. - Highlights: • Fe{sub 3}O{sub 4} nanocrystals were obtained by MW-assisted non-hydrolytic sol–gel synthesis. • Quantitative phase analysis revealed that crystallinity up to 95% was reached. • The strategy of Rietveld refinements was discussed in details. • Dimensional analysis showed nanoparticles ranging from 4 to 8 nm. • Results of integral breadth methods were compared with microscopic analysis.

Quantitative phase analysis and microstructure characterization of magnetite nanocrystals obtained by microwave assisted non-hydrolytic sol–gel synthesis

International Nuclear Information System (INIS)

Sciancalepore, Corrado; Bondioli, Federica; Manfredini, Tiziano; Gualtieri, Alessandro

2015-01-01

An innovative preparation procedure, based on microwave assisted non-hydrolytic sol–gel synthesis, to obtain spherical magnetite nanoparticles was reported together with a detailed quantitative phase analysis and microstructure characterization of the synthetic products. The nanoparticle growth was analyzed as a function of the synthesis time and was described in terms of crystallization degree employing the Rietveld method on the magnetic nanostructured system for the determination of the amorphous content using hematite as internal standard. Product crystallinity increases as the microwave thermal treatment is increased and reaches very high percentages for synthesis times longer than 1 h. Microstructural evolution of nanocrystals was followed by the integral breadth methods to obtain information on the crystallite size-strain distribution. The results of diffraction line profile analysis were compared with nanoparticle grain distribution estimated by dimensional analysis of the transmission electron microscopy (TEM) images. A variation both in the average grain size and in the distribution of the coherently diffraction domains is evidenced, allowing to suppose a relationship between the two quantities. The traditional integral breadth methods have proven to be valid for a rapid assessment of the diffraction line broadening effects in the above-mentioned nanostructured systems and the basic assumption for the correct use of these methods are discussed as well. - Highlights: • Fe 3 O 4 nanocrystals were obtained by MW-assisted non-hydrolytic sol–gel synthesis. • Quantitative phase analysis revealed that crystallinity up to 95% was reached. • The strategy of Rietveld refinements was discussed in details. • Dimensional analysis showed nanoparticles ranging from 4 to 8 nm. • Results of integral breadth methods were compared with microscopic analysis

Gimeracil sensitizes cells to radiation via inhibition of homologous recombination

International Nuclear Information System (INIS)

Takagi, Masaru; Sakata, Koh-ichi; Someya, Masanori; Tauchi, Hiroshi; Iijima, Kenta; Matsumoto, Yoshihisa; Torigoe, Toshihiko; Takahashi, Akari; Hareyama, Masato; Fukushima, Masakazu

2010-01-01

Background and purpose: 5-Chloro-2,4-dihydroxypyridine (Gimeracil) is a component of an oral fluoropyrimidine derivative S-1. Gimeracil is originally added to S-1 to yield prolonged 5-FU concentrations in tumor tissues by inhibiting dihydropyrimidine dehydrogenase, which degrades 5-FU. We found that Gimeracil by itself had the radiosensitizing effect. Methods and materials: We used various cell lines deficient in non-homologous end-joining (NHEJ) or homologous recombination (HR) as well as DLD-1 and HeLa in clonogenic assay. γ-H2AX focus formation and SCneo assay was performed to examine the effects of Gimeracil on DNA double strand break (DSB) repair mechanisms. Results: Results of γ-H2AX focus assay indicated that Gimeracil inhibited DNA DSB repair. It did not sensitize cells deficient in HR but sensitized those deficient in NHEJ. In SCneo assay, Gimeracil reduced the frequency of neo-positive clones. Additionally, it sensitized the cells in S-phase more than in G0/G1. Conclusions: Gimeracil inhibits HR. Because HR plays key roles in the repair of DSBH caused by radiotherapy, Gimeracil may enhance the efficacy of radiotherapy through the suppression of HR-mediated DNA repair pathways.

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

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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.

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

Science.gov (United States)

Weterings, Eric; Verkaik, Nicole S; Brüggenwirth, Hennie T; Hoeijmakers, Jan H J; van Gent, Dik C

2003-12-15

DNA 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 of DNA-PK prevents ligation of the two synapsed termini, but allows ligation to another DNA molecule. This alteration of the ligation route is independent of the type of ligase that we used, indicating that the intrinsic architecture of the DNA-PK complex itself is not able to support ligation of the synapsed DNA termini. We present a working model in which DNA-PK creates a stable molecular bridge between two DNA ends that is remodeled after DNA-PK autophosphorylation in such a way that the extreme termini become accessible without disrupting synapsis. We infer that joining of synapsed DNA termini would require an additional protein factor.

p53 regulates the repair of DNA double-strand breaks by both homologous and non-homologous recombination

International Nuclear Information System (INIS)

Willers, H.; Powell, S.N.; Dahm-Daphi, J.

2003-01-01

Full text: p53 is known to suppress spontaneous homologous recombination (HR), while its role in non-homologous recombination (NHR) remains to be clarified. Here, we sought to determine the influence of p53 on the repair of chromosomal double-strand breaks (DSBs) by HR or NHR using specially designed recombination substrates that integrate into the genome. Isogenic mouse fibroblast pairs with or without expression of exogenous p53 protein were utilized. A reporter plasmid carrying a mutated XGPRT gene was chromosomally integrated and DSBs were generated within the plasmid by the I-SceI endonuclease. Subsequent homology-mediated repair from an episomal donor resulted in XGPRT reconstitution and cellular resistance to a selection antibiotic. Analogously, the repair of chromosomal I-SceI breaks by NHR using another novel reporter plasmid restored XGPRT translation. For p53-null cells, the mean frequency of I-SceI break repair via HR was 5.5 x 10 -4 . The p53-Val135 mutant, which previously has been shown to suppress spontaneous HR by 14-fold employing the same cell system and reporter gene, only caused a 2- to 3-fold suppression of break-induced HR. In contrast, a dramatic effect of p53 on repair via NHR was found. Preliminary sequence analysis indicated that there was at least a 1000-fold reduction of illegitimate repair events resulting in loss of sequence at the break sites. The observed effects were mediated by p53 mutants defective in regulation of the cell-cycle and apoptosis. The main findings were: (1) p53 virtually blocked illegitimate rejoining of chromosomal ends. (2) The suppression of homologous DSB repair was less pronounced than the inhibition of spontaneous HR. We hypothesize that p53 allows to a certain extent error-free homology-dependent repair to proceed, while blocking error-prone NHR. The data support and extent a previous model, in which p53 maintains genomic stability by regulating recombination independently of its transactivation function

FANCD2 Maintains Fork Stability in BRCA1/2-Deficient Tumors and Promotes Alternative End-Joining DNA Repair

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Zeina Kais

2016-06-01

Full Text Available BRCA1/2 proteins function in homologous recombination (HR-mediated DNA repair and cooperate with Fanconi anemia (FA proteins to maintain genomic integrity through replication fork stabilization. Loss of BRCA1/2 proteins results in DNA repair deficiency and replicative stress, leading to genomic instability and enhanced sensitivity to DNA-damaging agents. Recent studies have shown that BRCA1/2-deficient tumors upregulate Polθ-mediated alternative end-joining (alt-EJ repair as a survival mechanism. Whether other mechanisms maintain genomic integrity upon loss of BRCA1/2 proteins is currently unknown. Here we show that BRCA1/2-deficient tumors also upregulate FANCD2 activity. FANCD2 is required for fork protection and fork restart in BRCA1/2-deficient tumors. Moreover, FANCD2 promotes Polθ recruitment at sites of damage and alt-EJ repair. Finally, loss of FANCD2 in BRCA1/2-deficient tumors enhances cell death. These results reveal a synthetic lethal relationship between FANCD2 and BRCA1/2, and they identify FANCD2 as a central player orchestrating DNA repair pathway choice at the replication fork.

[Regulation of acetylcholine synthesis in presynaptic endings of cholinergic neurons of the central nervous system].

Science.gov (United States)

Tuchek, S; Dolezhal, V; Richny, Ia

1984-01-01

Data on the acetylcholine (ACh) synthesis in nerve cells with special attention to its control are summarized in the paper. At rest or during moderate synaptic activity, the concentration of ACh in the compartment of its synthesis probably corresponds to the equilibrium between the substrates and products in the reaction catalysed by choline acetyltransferase. The release of ACh is followed by a transfer of ACh from the compartment of its synthesis to the compartment of release, and, automatically, by the synthesis of new ACh until a new equilibrium is reached in the compartment of synthesis. In addition, synaptic activity and the release of ACh support the synthesis of new ACh in the following ways: choline carriers are disinhibited by lowering the concentration of ACh in the nerve endings, and the transport of choline from the extracellular fluid to the cell interior according to its electro-chemical gradient is thus facilitated; the concentration of choline in the extracellular fluid is increased in the vicinity of the nerve endings as a consequence of the hydrolysis of the released ACh; postactivation hyperpolarization of the nerve endings brings about an increase of the choline transport and concentration in the nerve endings; presumably, the stimulation of muscarinic receptors brings about a further increase in the choline concentration in the vicinity of the nerve endings by the phosphatidylcholine hydrolysis intensification in postsynaptic cells; the decrease in the concentration of acetyl-CoA (as a consequence of the resynthesis of ACh) increases the activity of pyruvate dehydrogenase and the production of acetyl-CoA; conceivably, the increase in the concentration of Ca2+ ions in the nerve endings assists direct passage of acetyl-CoA from the mitochondria to the cytosol of the nerve endings, where the synthesis of ACh occurs.(ABSTRACT TRUNCATED AT 250 WORDS)

Computer-Assisted, Self-Interviewing (CASI) Compared to Face-to-Face Interviewing (FTFI) with Open-Ended, Non-Sensitive Questions

OpenAIRE

John Fairweather PhD; Tiffany Rinne PhD; Gary Steel PhD

2012-01-01

This article reports results from research on cultural models, and assesses the effects of computers on data quality by comparing open-ended questions asked in two formats—face-to-face interviewing (FTFI) and computer-assisted, self-interviewing (CASI). We expected that for our non-sensitive topic, FTFI would generate fuller and richer accounts because the interviewer could facilitate the interview process. Although the interviewer indeed facilitated these interviews, which resulted in more w...

Recovery of arrested replication forks by homologous recombination is error-prone.

Directory of Open Access Journals (Sweden)

Ismail Iraqui

Full Text Available Homologous recombination is a universal mechanism that allows repair of DNA and provides support for DNA replication. Homologous recombination is therefore a major pathway that suppresses non-homology-mediated genome instability. Here, we report that recovery of impeded replication forks by homologous recombination is error-prone. Using a fork-arrest-based assay in fission yeast, we demonstrate that a single collapsed fork can cause mutations and large-scale genomic changes, including deletions and translocations. Fork-arrest-induced gross chromosomal rearrangements are mediated by inappropriate ectopic recombination events at the site of collapsed forks. Inverted repeats near the site of fork collapse stimulate large-scale genomic changes up to 1,500 times over spontaneous events. We also show that the high accuracy of DNA replication during S-phase is impaired by impediments to fork progression, since fork-arrest-induced mutation is due to erroneous DNA synthesis during recovery of replication forks. The mutations caused are small insertions/duplications between short tandem repeats (micro-homology indicative of replication slippage. Our data establish that collapsed forks, but not stalled forks, recovered by homologous recombination are prone to replication slippage. The inaccuracy of DNA synthesis does not rely on PCNA ubiquitination or trans-lesion-synthesis DNA polymerases, and it is not counteracted by mismatch repair. We propose that deletions/insertions, mediated by micro-homology, leading to copy number variations during replication stress may arise by progression of error-prone replication forks restarted by homologous recombination.

Activities of wildtype and mutant p53 in suppression of homologous recombination as measured by a retroviral vector system

International Nuclear Information System (INIS)

Lu Xiongbin; Lozano, Guillermina; Donehower, Lawrence A.

2003-01-01

DNA repair of double strand breaks, interstrand DNA cross-links, and other types of DNA damage utilizes the processes of homologous recombination and non-homologous end joining to repair the damage. Aberrant homologous recombination is likely to be responsible for a significant fraction of chromosomal deletions, duplications, and translocations that are observed in cancer cells. To facilitate measurement of homologous recombination frequencies in normal cells, mutant cells, and cancer cells, we have developed a high titer retroviral vector containing tandem repeats of mutant versions of a GFP-Zeocin resistance fusion gene and an intact neomycin resistance marker. Recombination between the tandem repeats regenerates a functional GFP-Zeo R marker that can be easily scored. This retroviral vector was used to assess homologous recombination frequencies in human cancer cells and rodent fibroblasts with differing dosages of wild type or mutant p53. Absence of wild type p53 stimulated spontaneous and ionizing radiation-induced homologous recombination, confirming previous studies. Moreover, p53 +/- mouse fibroblasts show elevated levels of homologous recombination compared to their p53 +/+ counterparts following retroviral vector infection, indicating that p53 is haploinsufficient for suppression of homologous recombination. Transfection of vector-containing p53 null Saos-2 cells with various human cancer-associated p53 mutants revealed that these altered p53 proteins retain some recombination suppression function despite being totally inactive for transcriptional transactivation. The retroviral vector utilized in these studies may be useful in performing recombination assays on a wide array of cell types, including those not readily transfected by normal vectors

Altered kinetics of nonhomologous end joining and class switch recombination in ligase IV-deficient B cells.

Science.gov (United States)

Han, Li; Yu, Kefei

2008-11-24

Immunoglobulin heavy chain class switch recombination (CSR) is believed to occur through the generation and repair of DNA double-strand breaks (DSBs) in the long and repetitive switch regions. Although implied, the role of the major vertebrate DSB repair pathway, nonhomologous end joining (NHEJ), in CSR has been controversial. By somatic gene targeting of DNA ligase IV (Lig4; a key component of NHEJ) in a B cell line (CH12F3) capable of highly efficient CSR in vitro, we found that NHEJ is required for efficient CSR. Disruption of the Lig4 gene in CH12F3 cells severely inhibits the initial rate of CSR and causes a late cell proliferation defect under cytokine stimulation. However, unlike V(D)J recombination, which absolutely requires NHEJ, CSR accumulates to a substantial level in Lig4-null cells. The data revealed a fast-acting NHEJ and a slow-acting alterative end joining of switch region breaks during CSR.

Fumarase is involved in DNA double-strand break resection through a functional interaction with Sae2

DEFF Research Database (Denmark)

Leshets, Michael; Ramamurthy, Dharanidharan; Lisby, Michael

2018-01-01

One of the most severe forms of DNA damage is the double-strand break (DSB). Failure to properly repair the damage can cause mutation, gross chromosomal rearrangements and lead to the development of cancer. In eukaryotes, homologous recombination (HR) and non-homologous end joining (NHEJ) are the......One of the most severe forms of DNA damage is the double-strand break (DSB). Failure to properly repair the damage can cause mutation, gross chromosomal rearrangements and lead to the development of cancer. In eukaryotes, homologous recombination (HR) and non-homologous end joining (NHEJ......) are the main DSB repair pathways. Fumarase is a mitochondrial enzyme which functions in the tricarboxylic acid cycle. Intriguingly, the enzyme can be readily detected in the cytosolic compartment of all organisms examined, and we have shown that cytosolic fumarase participates in the DNA damage response...

Possible role of repetitious DNA in recombinatory joining during chromosome rearrangement in Drosophila melanogaster

International Nuclear Information System (INIS)

Lee, C.S.

1975-01-01

It is postulated that certain repetitious DNA components play a role in the recombination processes during chromosome rearrangements. When the distribution of silver grain densities after the in situ hybridization of repetitious DNA and the distribution of chromosome breaks due to x-irradiation are compared, a strong correlation is found for the euchromatic portion of the D. melanogaster salivary X chromosome. These observations justify the postulate above that certain repetitious DNA provides homologous regions in the DNA of broken chromosome ends necessary for proper recombinatory joining. (U.S.)

Differentiation of Human Induced Pluripotent or Embryonic Stem Cells Decreases the DNA Damage Repair by Homologous Recombination

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Kalpana Mujoo

2017-11-01

Full Text Available The nitric oxide (NO-cyclic GMP pathway contributes to human stem cell differentiation, but NO free radical production can also damage DNA, necessitating a robust DNA damage response (DDR to ensure cell survival. How the DDR is affected by differentiation is unclear. Differentiation of stem cells, either inducible pluripotent or embryonic derived, increased residual DNA damage as determined by γ-H2AX and 53BP1 foci, with increased S-phase-specific chromosomal aberration after exposure to DNA-damaging agents, suggesting reduced homologous recombination (HR repair as supported by the observation of decreased HR-related repair factor foci formation (RAD51 and BRCA1. Differentiated cells also had relatively increased fork stalling and R-loop formation after DNA replication stress. Treatment with NO donor (NOC-18, which causes stem cell differentiation has no effect on double-strand break (DSB repair by non-homologous end-joining but reduced DSB repair by HR. Present studies suggest that DNA repair by HR is impaired in differentiated cells.

Microwave-assisted synthesis and properties of a series of poly(2-alkyl-2-oxazoline)s

NARCIS (Netherlands)

Hoogenboom, R.; Fijten, M.W.M.; Thijs, H.M.L.; Lankvelt, van B.M.; Schubert, U.S.

2005-01-01

Microwave-assisted organic synthesis is a quickly expanding field of research. The fast non-contact (super)heating of the reaction mixtures has already resulted in many examples of increased reaction rates and improved yields. However, the number of investigations focusing on microwave-assisted

Alternative end-joining catalyzes robust IgH locus deletions and translocations in the combined absence of ligase 4 and Ku70.

Science.gov (United States)

Boboila, Cristian; Jankovic, Mila; Yan, Catherine T; Wang, Jing H; Wesemann, Duane R; Zhang, Tingting; Fazeli, Alex; Feldman, Lauren; Nussenzweig, Andre; Nussenzweig, Michel; Alt, Frederick W

2010-02-16

Class switch recombination (CSR) in B lymphocytes is initiated by introduction of multiple DNA double-strand breaks (DSBs) into switch (S) regions that flank immunoglobulin heavy chain (IgH) constant region exons. CSR is completed by joining a DSB in the donor S mu to a DSB in a downstream acceptor S region (e.g., S gamma1) by end-joining. In normal cells, many CSR junctions are mediated by classical nonhomologous end-joining (C-NHEJ), which employs the Ku70/80 complex for DSB recognition and XRCC4/DNA ligase 4 for ligation. Alternative end-joining (A-EJ) mediates CSR, at reduced levels, in the absence of C-NHEJ, even in combined absence of Ku70 and ligase 4, demonstrating an A-EJ pathway totally distinct from C-NHEJ. Multiple DSBs are introduced into S mu during CSR, with some being rejoined or joined to each other to generate internal switch deletions (ISDs). In addition, S-region DSBs can be joined to other chromosomes to generate translocations, the level of which is increased by absence of a single C-NHEJ component (e.g., XRCC4). We asked whether ISD and S-region translocations occur in the complete absence of C-NHEJ (e.g., in Ku70/ligase 4 double-deficient B cells). We found, unexpectedly, that B-cell activation for CSR generates substantial ISD in both S mu and S gamma1 and that ISD in both is greatly increased by the absence of C-NHEJ. IgH chromosomal translocations to the c-myc oncogene also are augmented in the combined absence of Ku70 and ligase 4. We discuss the implications of these findings for A-EJ in normal and abnormal DSB repair.

Analysis of the role of homology arms in gene-targeting vectors in human cells.

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Ayako Ishii

Full Text Available Random integration of targeting vectors into the genome is the primary obstacle in human somatic cell gene targeting. Non-homologous end-joining (NHEJ, a major pathway for repairing DNA double-strand breaks, is thought to be responsible for most random integration events; however, absence of DNA ligase IV (LIG4, the critical NHEJ ligase, does not significantly reduce random integration frequency of targeting vector in human cells, indicating robust integration events occurring via a LIG4-independent mechanism. To gain insights into the mechanism and robustness of LIG4-independent random integration, we employed various types of targeting vectors to examine their integration frequencies in LIG4-proficient and deficient human cell lines. We find that the integration frequency of targeting vector correlates well with the length of homology arms and with the amount of repetitive DNA sequences, especially SINEs, present in the arms. This correlation was prominent in LIG4-deficient cells, but was also seen in LIG4-proficient cells, thus providing evidence that LIG4-independent random integration occurs frequently even when NHEJ is functionally normal. Our results collectively suggest that random integration frequency of conventional targeting vectors is substantially influenced by homology arms, which typically harbor repetitive DNA sequences that serve to facilitate LIG4-independent random integration in human cells, regardless of the presence or absence of functional NHEJ.

Knock-in of large reporter genes in human cells via CRISPR/Cas9-induced homology-dependent and independent DNA repair.

Science.gov (United States)

He, Xiangjun; Tan, Chunlai; Wang, Feng; Wang, Yaofeng; Zhou, Rui; Cui, Dexuan; You, Wenxing; Zhao, Hui; Ren, Jianwei; Feng, Bo

2016-05-19

CRISPR/Cas9-induced site-specific DNA double-strand breaks (DSBs) can be repaired by homology-directed repair (HDR) or non-homologous end joining (NHEJ) pathways. Extensive efforts have been made to knock-in exogenous DNA to a selected genomic locus in human cells; which, however, has focused on HDR-based strategies and was proven inefficient. Here, we report that NHEJ pathway mediates efficient rejoining of genome and plasmids following CRISPR/Cas9-induced DNA DSBs, and promotes high-efficiency DNA integration in various human cell types. With this homology-independent knock-in strategy, integration of a 4.6 kb promoterless ires-eGFP fragment into the GAPDH locus yielded up to 20% GFP+ cells in somatic LO2 cells, and 1.70% GFP+ cells in human embryonic stem cells (ESCs). Quantitative comparison further demonstrated that the NHEJ-based knock-in is more efficient than HDR-mediated gene targeting in all human cell types examined. These data support that CRISPR/Cas9-induced NHEJ provides a valuable new path for efficient genome editing in human ESCs and somatic cells. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Ionizing radiation sensitivity of DNA polymerase lambda-deficient cells.

NARCIS (Netherlands)

Vermeulen, C.; Bertocci, B.; Begg, A.C.; Vens, C.

2007-01-01

Ionizing radiation induces a diverse spectrum of DNA lesions, including strand breaks and oxidized bases. In mammalian cells, ionizing radiation-induced lesions are targets of non-homologous end joining, homologous recombination, and base excision repair. In vitro assays show a potential involvement

Atomic Structure and Nonhomologous End-Joining Function of the Polymerase Component of Bacterial DNA Ligase D

Energy Technology Data Exchange (ETDEWEB)

Zhu,H.; Nandakumar, J.; Aniukwu, J.; Wang, L.; Glickman, M.; Lima, C.; Shuman, S.

2006-01-01

DNA ligase D (LigD) is a large polyfunctional protein that participates in a recently discovered pathway of nonhomologous end-joining in bacteria. LigD consists of an ATP-dependent ligase domain fused to a polymerase domain (Pol) and a phosphoesterase module. The Pol activity is remarkable for its dependence on manganese, its ability to perform templated and nontemplated primer extension reactions, and its preference for adding ribonucleotides to blunt DNA ends. Here we report the 1.5- Angstroms crystal structure of the Pol domain of Pseudomonas LigD and its complexes with manganese and ATP-dATP substrates, which reveal a minimized polymerase with a two-metal mechanism and a fold similar to that of archaeal DNA primase. Mutational analysis highlights the functionally relevant atomic contacts in the active site. Although distinct nucleoside conformations and contacts for ATP versus dATP are observed in the cocrystals, the functional analysis suggests that the ATP-binding mode is the productive conformation for dNMP and rNMP incorporation. We find that a mutation of Mycobacterium LigD that uniquely ablates the polymerase activity results in increased fidelity of blunt-end double-strand break repair in vivo by virtue of eliminating nucleotide insertions at the recombination junctions. Thus, LigD Pol is a direct catalyst of mutagenic nonhomologous end-joining in vivo. Our studies underscore a previously uncharacterized role for the primase-like polymerase family in DNA repair.

TDP2 suppresses chromosomal translocations induced by DNA topoisomerase II during gene transcription.

Science.gov (United States)

Gómez-Herreros, Fernando; Zagnoli-Vieira, Guido; Ntai, Ioanna; Martínez-Macías, María Isabel; Anderson, Rhona M; Herrero-Ruíz, Andrés; Caldecott, Keith W

2017-08-10

DNA double-strand breaks (DSBs) induced by abortive topoisomerase II (TOP2) activity are a potential source of genome instability and chromosome translocation. TOP2-induced DNA double-strand breaks are rejoined in part by tyrosyl-DNA phosphodiesterase 2 (TDP2)-dependent non-homologous end-joining (NHEJ), but whether this process suppresses or promotes TOP2-induced translocations is unclear. Here, we show that TDP2 rejoins DSBs induced during transcription-dependent TOP2 activity in breast cancer cells and at the translocation 'hotspot', MLL. Moreover, we find that TDP2 suppresses chromosome rearrangements induced by TOP2 and reduces TOP2-induced chromosome translocations that arise during gene transcription. Interestingly, however, we implicate TDP2-dependent NHEJ in the formation of a rare subclass of translocations associated previously with therapy-related leukemia and characterized by junction sequences with 4-bp of perfect homology. Collectively, these data highlight the threat posed by TOP2-induced DSBs during transcription and demonstrate the importance of TDP2-dependent non-homologous end-joining in protecting both gene transcription and genome stability.DNA double-strand breaks (DSBs) induced by topoisomerase II (TOP2) are rejoined by TDP2-dependent non-homologous end-joining (NHEJ) but whether this promotes or suppresses translocations is not clear. Here the authors show that TDP2 suppresses chromosome translocations from DSBs introduced during gene transcription.

Comparative analysis of the end-joining activity of several DNA ligases.

Directory of Open Access Journals (Sweden)

Robert J Bauer

Full Text Available DNA ligases catalyze the repair of phosphate backbone breaks in DNA, acting with highest activity on breaks in one strand of duplex DNA. Some DNA ligases have also been observed to ligate two DNA fragments with short complementary overhangs or blunt-ended termini. In this study, several wild-type DNA ligases (phage T3, T4, and T7 DNA ligases, Paramecium bursaria chlorella virus 1 (PBCV1 DNA ligase, human DNA ligase 3, and Escherichia coli DNA ligase were tested for their ability to ligate DNA fragments with several difficult to ligate end structures (blunt-ended termini, 3'- and 5'- single base overhangs, and 5'-two base overhangs. This analysis revealed that T4 DNA ligase, the most common enzyme utilized for in vitro ligation, had its greatest activity on blunt- and 2-base overhangs, and poorest on 5'-single base overhangs. Other ligases had different substrate specificity: T3 DNA ligase ligated only blunt ends well; PBCV1 DNA ligase joined 3'-single base overhangs and 2-base overhangs effectively with little blunt or 5'- single base overhang activity; and human ligase 3 had highest activity on blunt ends and 5'-single base overhangs. There is no correlation of activity among ligases on blunt DNA ends with their activity on single base overhangs. In addition, DNA binding domains (Sso7d, hLig3 zinc finger, and T4 DNA ligase N-terminal domain were fused to PBCV1 DNA ligase to explore whether modified binding to DNA would lead to greater activity on these difficult to ligate substrates. These engineered ligases showed both an increased binding affinity for DNA and increased activity, but did not alter the relative substrate preferences of PBCV1 DNA ligase, indicating active site structure plays a role in determining substrate preference.

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

Science.gov (United States)

Omelchenko, Marina V; Galperin, Michael Y; Wolf, Yuri I; Koonin, Eugene V

2010-04-30

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 (non)homologous relationships between proteins. 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. 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.

Pharmacodynamic Assay Panel for Monitoring Phospho-Signaling Networks | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

The DNA damage response (DDR) is a highly regulated signal transduction network that orchestrates the temporal and spatial organization of protein complexes required to repair (or tolerate) DNA damage (e.g., nucleotide excision repair, base excision repair, homologous recombination, non-homologous end joining, post-replication repair).

Inactivation of Pol θ and C-NHEJ eliminates off-target integration of exogenous DNA.

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Zelensky, Alex N; Schimmel, Joost; Kool, Hanneke; Kanaar, Roland; Tijsterman, Marcel

2017-07-07

Off-target or random integration of exogenous DNA hampers precise genomic engineering and presents a safety risk in clinical gene therapy strategies. Genetic definition of random integration has been lacking for decades. Here, we show that the A-family DNA polymerase θ (Pol θ) promotes random integration, while canonical non-homologous DNA end joining plays a secondary role; cells double deficient for polymerase θ and canonical non-homologous DNA end joining are devoid of any integration events, demonstrating that these two mechanisms define random integration. In contrast, homologous recombination is not reduced in these cells and gene targeting is improved to 100% efficiency. Such complete reversal of integration outcome, from predominately random integration to exclusively gene targeting, provides a rational way forward to improve the efficacy and safety of DNA delivery and gene correction approaches.Random off-target integration events can impair precise gene targeting and poses a safety risk for gene therapy. Here the authors show that repression of polymerase θ and classical non-homologous recombination eliminates random integration.

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

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

2016-02-02

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.

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.

MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems.

Science.gov (United States)

Sakuma, Tetsushi; Nakade, Shota; Sakane, Yuto; Suzuki, Ken-Ichi T; Yamamoto, Takashi

2016-01-01

Programmable nucleases enable engineering of the genome by utilizing endogenous DNA double-strand break (DSB) repair pathways. Although homologous recombination (HR)-mediated gene knock-in is well established, it cannot necessarily be applied in every cell type and organism because of variable HR frequencies. We recently reported an alternative method of gene knock-in, named the PITCh (Precise Integration into Target Chromosome) system, assisted by microhomology-mediated end-joining (MMEJ). MMEJ harnesses independent machinery from HR, and it requires an extremely short homologous sequence (5-25 bp) for DSB repair, resulting in precise gene knock-in with a more easily constructed donor vector. Here we describe a streamlined protocol for PITCh knock-in, including the design and construction of the PITCh vectors, and their delivery to either human cell lines by transfection or to frog embryos by microinjection. The construction of the PITCh vectors requires only a few days, and the entire process takes ∼ 1.5 months to establish knocked-in cells or ∼ 1 week from injection to early genotyping in frog embryos.

Coal and biomass-based chemicals via carbonylation, hydroformylation and homologation reactions

Energy Technology Data Exchange (ETDEWEB)

Sunavala, P.D.; Raghunath, B.

The paper emphasizes the importance of carbonylation, hydroformylation and homologation reactions in the manufacture of organic chemicals (such as acetic acid, acetic anhydride, cellulose acetate, vinyl acetate monomer, aliphatic amines, isocyanates, methanol, ethanol, n-butanol, ethylene glycol, acrylic acid, etc.) from coal and biomass feedstocks. Topics covered are: synthesis of acetic acid; manufacture of acetic anhydride; synthesis of vinyl acetate monomer by carbonylation; synthesis of aliphatic amines by hydroformylation; synthesis of organic diisocyanates; ethanol synthesis by homologation of methanol; synthesis of ethylene glycol via hydroformylation of formaldehyde; synthesis of n- butanol and n-butyraldehyde by propylene formylation; synthesis of acrylic acid; homologation reaction of carboxylic acid esters with ruthenium catalysts; and synthesis of phenyl isocyanate from nitrobenzene by reductive carbonylation. 26 refs.

Computer-Assisted, Self-Interviewing (CASI Compared to Face-to-Face Interviewing (FTFI with Open-Ended, Non-Sensitive Questions

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John Fairweather PhD

2012-07-01

Full Text Available This article reports results from research on cultural models, and assesses the effects of computers on data quality by comparing open-ended questions asked in two formats—face-to-face interviewing (FTFI and computer-assisted, self-interviewing (CASI. We expected that for our non-sensitive topic, FTFI would generate fuller and richer accounts because the interviewer could facilitate the interview process. Although the interviewer indeed facilitated these interviews, which resulted in more words in less time, the number of underlying themes found within the texts for each interview mode was the same, thus resulting in the same models of national culture and innovation being built for each mode. Our results, although based on an imperfect research design, suggest that CASI can be beneficial when using open-ended questions because CASI is easy to administer, capable of reaching more efficiently a large sample, and able to avoid the need to transcribe the recorded responses.

RNF4 is required for DNA double-strand break repair in vivo

DEFF Research Database (Denmark)

Vyas, R; Kumar, R; Clermont, F

2013-01-01

for both homologous recombination (HR) and non-homologous end joining repair. To establish a link between Rnf4 and the DNA damage response (DDR) in vivo, we generated an Rnf4 allelic series in mice. We show that Rnf4-deficiency causes persistent ionizing radiation-induced DNA damage and signaling...

Cross-sectional research into counselling for non-physician assisted suicide: who asks for it and what happens?

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Hagens, Martijn; Pasman, H Roeline W; Onwuteaka-Philipsen, Bregje D

2014-10-02

In the Netherlands, people with a wish to die can request physician assistance in dying. However, almost two thirds of the explicit requests do not result in physician assistance in dying. Some people with a wish to end life seek counselling outside the medical context to end their own life. The aim of this cross-sectional research was to obtain information about clients receiving counselling for non-physician assisted suicide, and the characteristics and outcome of the counselling itself. All counsellors working with foundation De Einder (an organisation that offers professional counselling for people with a wish to end life) (N=12) filled in registration forms about all clients they counselled in 2011 and/or 2012. Only client registration data forms with at least one face-to-face contact with the counsellor were selected for analysis (n=595). More than half of the clients were over 65 years old. More than one third of the clients had no wish to end life and 16% had an urgent wish to end life. Almost two thirds of the clients had not requested physician assistance in dying. Half of the clients had others involved in the counselling. More than half of the clients received explicit practical information concerning non-physician assisted suicide, while 13% of all clients actually ended their own life through non-physician assisted suicide. Clients without a (severe) disease were older than clients with a severe disease. They also had more problems of old age and existential suffering and more often wanted to be prepared for self-determination. The clients without a (severe) disease more often had no wish to end life and requested physician assistance in dying less often than clients with a severe disease. While some of the clients receiving counselling for non-physician assisted suicide seem to be looking for a peaceful death to escape from current suffering, others have no wish to end life and seem to be looking for reassurance in anticipation of prospective

Joining of advanced materials

CERN Document Server

Messler, Robert W

1993-01-01

Provides an unusually complete and readable compilation of the primary and secondary options for joining conventional materials in non-conventional ways. Provides unique coverage of adhesive bonding using both organic and inorganic adhesives, cements and mortars. Focuses on materials issues without ignoring issues related to joint design, production processing, quality assurance, process economics, and joining performance in service.Joining of advanced materials is a unique treatment of joining of both conventional and advanced metals andalloys, intermetallics, ceramics, glasses, polymers, a

SAMHD1 Promotes DNA End Resection to Facilitate DNA Repair by Homologous Recombination

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Waaqo Daddacha

2017-08-01

Full Text Available DNA double-strand break (DSB repair by homologous recombination (HR is initiated by CtIP/MRN-mediated DNA end resection to maintain genome integrity. SAMHD1 is a dNTP triphosphohydrolase, which restricts HIV-1 infection, and mutations are associated with Aicardi-Goutières syndrome and cancer. We show that SAMHD1 has a dNTPase-independent function in promoting DNA end resection to facilitate DSB repair by HR. SAMHD1 deficiency or Vpx-mediated degradation causes hypersensitivity to DSB-inducing agents, and SAMHD1 is recruited to DSBs. SAMHD1 complexes with CtIP via a conserved C-terminal domain and recruits CtIP to DSBs to facilitate end resection and HR. Significantly, a cancer-associated mutant with impaired CtIP interaction, but not dNTPase-inactive SAMHD1, fails to rescue the end resection impairment of SAMHD1 depletion. Our findings define a dNTPase-independent function for SAMHD1 in HR-mediated DSB repair by facilitating CtIP accrual to promote DNA end resection, providing insight into how SAMHD1 promotes genome integrity.

Plasma-assisted synthesis of MoS2

Science.gov (United States)

Campbell, Philip M.; Perini, Christopher J.; Chiu, Johannes; Gupta, Atul; Ray, Hunter S.; Chen, Hang; Wenzel, Kevin; Snyder, Eric; Wagner, Brent K.; Ready, Jud; Vogel, Eric M.

2018-03-01

There has been significant interest in transition metal dichalcogenides (TMDs), including MoS2, in recent years due to their potential application in novel electronic and optical devices. While synthesis methods have been developed for large-area films of MoS2, many of these techniques require synthesis temperatures of 800 °C or higher. As a result of the thermal budget, direct synthesis requiring high temperatures is incompatible with many integrated circuit processes as well as flexible substrates. This work explores several methods of plasma-assisted synthesis of MoS2 as a way to lower the synthesis temperature. The first approach used is conversion of a naturally oxidized molybdenum thin film to MoS2 using H2S plasma. Conversion is demonstrated at temperatures as low as 400 °C, and the conversion is enabled by hydrogen radicals which reduce the oxidized molybdenum films. The second method is a vapor phase reaction incorporating thermally evaporated MoO3 exposed to a direct H2S plasma, similar to chemical vapor deposition (CVD) synthesis of MoS2. Synthesis at 400 °C results in formation of super-stoichiometric MoS2 in a beam-interrupted growth process. A final growth method relies on a cyclical process in which a small amount of Mo is sputtered onto the substrate and is subsequently sulfurized in a H2S plasma. Similar results could be realized using an atomic layer deposition (ALD) process to deposit the Mo film. Compared to high temperature synthesis methods, the lower temperature samples are lower quality, potentially due to poor crystallinity or higher defect density in the films. Temperature-dependent conductivity measurements are consistent with hopping conduction in the plasma-assisted synthetic MoS2, suggesting a high degree of disorder in the low-temperature films. Optimization of the plasma-assisted synthesis process for slower growth rate and better stoichiometry is expected to lead to high quality films at low growth temperature.

Microwave-Assisted Synthesis of Phenothiazine and Quinoline Derivatives

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Găină, Luiza; Cristea, Castelia; Moldovan, Claudia; Porumb, Dan; Surducan, Emanoil; Deleanu, Călin; Mahamoud, Abdalah; Barbe, Jacques; Silberg, Ioan A.

2007-01-01

Application of a dynamic microwave power system in the chemical synthesis of some phenothiazine and quinoline derivatives is described. Heterocyclic ring formation, aromatic nucleophilic substitution and heterocyclic aldehydes/ketones condensation reactions were performed on solid support, or under solvent free reaction conditions. The microwave-assisted Duff formylation of phenothiazine was achieved. Comparison of microwave-assisted synthesis with the conventional synthetic methods demonstrates advantages related to shorter reaction times and in some cases better reaction yields.

Microwave-Assisted Synthesis of Phenothiazine and Qinoline Derivatives

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Ioan A. Silberg

2007-02-01

Full Text Available Application of a dynamic microwave power system in the chemical synthesis ofsome phenothiazine and quinoline derivatives is described. Heterocyclic ring formation,aromatic nucleophilic substitution and heterocyclic aldehydes/ketones condensationreactions were performed on solid support, or under solvent free reaction conditions. Themicrowave-assisted Duff formylation of phenothiazine was achieved. Comparison ofmicrowave-assisted synthesis with the conventional synthetic methods demonstratesadvantages related to shorter reaction times and in some cases better reaction yields.

Cancer and non-cancer risk at low doses of radiation: biological basis of radiation-environment interplay

International Nuclear Information System (INIS)

Sasaki, Masao S.

2013-01-01

Cancer and non-cancer risk at low doses of ionizing radiation remains poorly defined due to ambiguity at low doses caused by limitations in statistical power and information available on interplay with environment. To deal with these problems, a novel non-parametric statistics was developed based on artificial neural networks theorem and applied to cancer and non-cancer risk in A-bomb survivors. The analysis revealed several unique features at low doses that could not be accounted for by nominal radiation dose alone. They include (1) threshold that varies with organ, gender and age, including cardiovascular diseases, (2) prevalence of infectious diseases, and (3) suppression of pathogenesis of HTLV1. The threshold is unique as it is manifested as negative excess relative risk, a reduction of spontaneous rate at low doses. The response is consistent with currently emerging laboratory data on DNA double-strand break (DSB) repair pathway choice and its sustainability as epigenetic memory in accordance with histone code theory. In response to DSB, of radiation or DNA replication arrest origin, distinct and competitively operating repair pathways are instigated. Activation by low doses of restitution-directed canonical non-homologous end-joining (C-NHEJ) suppresses both error-prone alternative end-joining (Alt-NHEJ) and homologous recombination (HR). The latter two present major pathways to mutagenesis at stalled replication folk associated with endogenous and exogenous genotoxin such as tobacco smoke metabolites and AID-associated somatic hypermutation and class switch recombination in Ig gene. Suppression of these error-prone pathways by low doses of low LET radiation is consistent with the reduction of cancer occurrence by environmental genotoxin, immunodiversity and stable integration of retrovirus DNA, providing a significant modulator of dose linearity at low doses. Whole picture may bring about a new landscape of cancer and non-cancer molecular epidemiology which

XRCC1 suppresses somatic hypermutation and promotes alternative nonhomologous end joining in Igh genes.

Science.gov (United States)

Saribasak, Huseyin; Maul, Robert W; Cao, Zheng; McClure, Rhonda L; Yang, William; McNeill, Daniel R; Wilson, David M; Gearhart, Patricia J

2011-10-24

Activation-induced deaminase (AID) deaminates cytosine to uracil in immunoglobulin genes. Uracils in DNA can be recognized by uracil DNA glycosylase and abasic endonuclease to produce single-strand breaks. The breaks are repaired either faithfully by DNA base excision repair (BER) or mutagenically to produce somatic hypermutation (SHM) and class switch recombination (CSR). To unravel the interplay between repair and mutagenesis, we decreased the level of x-ray cross-complementing 1 (XRCC1), a scaffold protein involved in BER. Mice heterozygous for XRCC1 showed a significant increase in the frequencies of SHM in Igh variable regions in Peyer's patch cells, and of double-strand breaks in the switch regions during CSR. Although the frequency of CSR was normal in Xrcc1(+/-) splenic B cells, the length of microhomology at the switch junctions decreased, suggesting that XRCC1 also participates in alternative nonhomologous end joining. Furthermore, Xrcc1(+/-) B cells had reduced Igh/c-myc translocations during CSR, supporting a role for XRCC1 in microhomology-mediated joining. Our results imply that AID-induced single-strand breaks in Igh variable and switch regions become substrates simultaneously for BER and mutagenesis pathways.

Mycobacterium smegmatis Ku binds DNA without free ends.

Science.gov (United States)

Kushwaha, Ambuj K; Grove, Anne

2013-12-01

Ku is central to the non-homologous end-joining pathway of double-strand-break repair in all three major domains of life, with eukaryotic homologues being associated with more diversified roles compared with prokaryotic and archaeal homologues. Ku has a conserved central 'ring-shaped' core domain. While prokaryotic homologues lack the N- and C-terminal domains that impart functional diversity to eukaryotic Ku, analyses of Ku from certain prokaryotes such as Pseudomonas aeruginosa and Mycobacterium smegmatis have revealed the presence of distinct C-terminal extensions that modulate DNA-binding properties. We report in the present paper that the lysine-rich C-terminal extension of M. smegmatis Ku contacts the core protein domain as evidenced by an increase in DNA-binding affinity and a decrease in thermal stability and intrinsic tryptophan fluorescence upon its deletion. Ku deleted for this C-terminus requires free DNA ends for binding, but translocates to internal DNA sites. In contrast, full-length Ku can directly bind DNA without free ends, suggesting that this property is conferred by its C-terminus. Such binding to internal DNA sites may facilitate recruitment to sites of DNA damage. The results of the present study also suggest that extensions beyond the shared core domain may have independently evolved to expand Ku function.

End-to-End Adversarial Retinal Image Synthesis.

Science.gov (United States)

Costa, Pedro; Galdran, Adrian; Meyer, Maria Ines; Niemeijer, Meindert; Abramoff, Michael; Mendonca, Ana Maria; Campilho, Aurelio

2018-03-01

In medical image analysis applications, the availability of the large amounts of annotated data is becoming increasingly critical. However, annotated medical data is often scarce and costly to obtain. In this paper, we address the problem of synthesizing retinal color images by applying recent techniques based on adversarial learning. In this setting, a generative model is trained to maximize a loss function provided by a second model attempting to classify its output into real or synthetic. In particular, we propose to implement an adversarial autoencoder for the task of retinal vessel network synthesis. We use the generated vessel trees as an intermediate stage for the generation of color retinal images, which is accomplished with a generative adversarial network. Both models require the optimization of almost everywhere differentiable loss functions, which allows us to train them jointly. The resulting model offers an end-to-end retinal image synthesis system capable of generating as many retinal images as the user requires, with their corresponding vessel networks, by sampling from a simple probability distribution that we impose to the associated latent space. We show that the learned latent space contains a well-defined semantic structure, implying that we can perform calculations in the space of retinal images, e.g., smoothly interpolating new data points between two retinal images. Visual and quantitative results demonstrate that the synthesized images are substantially different from those in the training set, while being also anatomically consistent and displaying a reasonable visual quality.

Radio-sensitization of WRN helicase deficient cancer cells by targeting homologous recombination pathway

International Nuclear Information System (INIS)

Gupta, Pooja; Saha, Bhaskar; Patro, Birija Sankar; Chattopadhyay, Subrata

2016-01-01

Ionizing radiation (IR) induced DNA double-strand breaks (DSBs) are primarily repaired by non-homologous end joining (NHEJ). However, it is well established that a subset DSBs which are accumulated in IR-induced G2 phase are dependent on homologous recombination (HR). DNA repair deficient tumor cells have been shown to accumulate high levels of DNA damage. Consequently, these cells become hyperdependent on DNA damage response pathways, including the CHK1-kinase-mediated HR-repair. These observations suggest that DNA repair deficient tumors should exhibit increased radio-sensitivity under HR inhibition. Genetic defects leading to functional loss of werner (WRN) protein is associated with genomic instability and increased cancer incidence. WRN function is known to be abrogated in several human cancer cells due to hypermethylation of CpGisland-promoter and transcriptional silencing of WRN gene. In the current investigation, using isogenic pairs of cell lines differing only in the WRN function, we showed that WRN-deficient cell lines were hyper-radiosensitive to CHK1 pharmacologic inhibition. Here, we found that unrepaired DSB was drastically increased in WRN-deficient cells vis-à-vis WRN-proficient cells in response to IR and CHK1 inhibitor (CHK1i). Our results revealed a marginal role of NHEJ pathway accountable for the radio-sensitivity of WRN-deficient cells. Interestingly, silencing CTIP, a HR protein required for RAD51 loading, significantly abrogated the CHK1i-mediated radiosensitivity in WRN-deficient cells. Silencing of WRN or CTIP individually led to no significant difference in the extent of DNA end resection, as required during HR pathway. Imperatively, our results revealed that WRN and CTIP together play a complementary role in executing DNA end resection during HR-mediated repair of IR induced DSBs. Altogether, our data indicated that inhibition of IR-induced HR pathway at RAD51 loading, but not at DSB end resection, make the WRN-deficient cancer cells

Ultrasound-assisted sol-gel synthesis of ZrO2.

Science.gov (United States)

Guel, Marlene Lariza Andrade; Jiménez, Lourdes Díaz; Hernández, Dora Alicia Cortés

2017-03-01

Synthesis of tetragonal ZrO 2 by both conventional sol-gel and ultrasound-assisted sol-gel methods and using a non-ionic surfactant Tween-20, was performed. A porous microstructure composed of nanometric particles was observed. Tetragonal ZrO 2 was obtained using a low heat treatment temperature of powders, 500°C by both methods. A higher crystallinity and a shorter reaction time were observed when ultrasound was used in the sol-gel method due to the cavitation phenomenon. Copyright © 2016 Elsevier B.V. All rights reserved.

Synthesis of variable size molecules using poly-homologation of boron compounds

International Nuclear Information System (INIS)

Goddard, J.P.

2002-01-01

During this work, we developed a method of original synthesis allowing to lead mixtures of molecules of variable size with an aim of discovering new chelating molecules of cesium. This method utilizes a reaction of poly-homologation of borated compounds with the nucleophilic ones comprising a grouping leaving in alpha of the negative charge. We tested various families from nucleophilic like anions of sulfones, sulfonium ylides, anions of hydrazones, tri-methylsilyldiazomethane and arsonium ylides. The first three families did not allow us to carry out reactions of poly-homologation. The tri-methylsilyldiazomethane possesses not either the capacity to carry out reactions successive insertions but this property was exploited to propose a chemical conversion of olefinic hydrocarbon into alkyl-methanol corresponding. The arsonium ylides made it possible to carry out reactions of poly-homologation with boronates and boranes. The alkyl-arsonium ylides were used to form polymers of controlled size having a ramification on each carbon atom of the principal chain. This type of polymer is not accessible by the current methods of polymerization. The allyl-arsonium ylides have a particular reactivity since the allyl boranes formed during the insertion reactions undergo a sigma-tropic [1,3] rearrangement before reacting again with a ylide. It is thus possible to lead with polymers of big size to which the structure is close to that of the natural rubber. By this method it is possible to lead with linear or cyclic polymers. This method is currently under development at the laboratory to form chelating structures of cesium. (author) [fr

Aqueous Microwave-Assisted Solid-Phase Synthesis Using Boc-Amino Acid Nanoparticles

Directory of Open Access Journals (Sweden)

Yoshinobu Fukumori

2013-07-01

Full Text Available We have previously developed water-based microwave (MW-assisted peptide synthesis using Fmoc-amino acid nanopaticles. It is an organic solvent-free, environmentally friendly method for peptide synthesis. Here we describe water-based MW-assisted solid-phase synthesis using Boc-amino acid nanoparticles. The microwave irradiation allowed rapid solid-phase reaction of nanoparticle reactants on the resin in water. We also demonstrated the syntheses of Leu-enkephalin, Tyr-Gly-Gly-Phe-Leu-OH, and difficult sequence model peptide, Val-Ala-Val-Ala-Gly-OH, using our water-based MW-assisted protocol with Boc-amino acid nanoparticles.

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......) 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...

Deciphering the Role of Alternative Non-Homologous End Joining (Alt-NHEJ) DNA Repair in Breast Cancer

Science.gov (United States)

2017-12-01

consecutive TTAGGG repeats. To detect rare reads containing fusion junctions, we exploited the novel sequence arrangement created by the ligation of the 39G...journal.pgen.1001005 (2010). 14 van Kregten, M. et al. T-DNA integration in plants results from polymerase-theta-mediated DNA repair. Nat Plants 2

Targeted Gene Knock Out Using Nuclease-Assisted Vector Integration: Hemi- and Homozygous Deletion of JAG1.

Science.gov (United States)

Gapinske, Michael; Tague, Nathan; Winter, Jackson; Underhill, Gregory H; Perez-Pinera, Pablo

2018-01-01

Gene editing technologies are revolutionizing fields such as biomedicine and biotechnology by providing a simple means to manipulate the genetic makeup of essentially any organism. Gene editing tools function by introducing double-stranded breaks at targeted sites within the genome, which the host cells repair preferentially by Non-Homologous End Joining. While the technologies to introduce double-stranded breaks have been extensively optimized, this progress has not been matched by the development of methods to integrate heterologous DNA at the target sites or techniques to detect and isolate cells that harbor the desired modification. We present here a technique for rapid introduction of vectors at target sites in the genome that enables efficient isolation of successfully edited cells.

GlidArc-assisted production of synthesis gas from various carbonaceous feedstocks

International Nuclear Information System (INIS)

Czernichowski, A.; Czernichowski, P.; Czernichowski, M.

2003-01-01

Pure Hydrogen or its mixture with Carbon Monoxide (called Synthesis Gas) will be massively extracted from various fossil or renewable feedstocks. Such matters contain contaminants (principally Sulphur) that make conventional catalytic reforming technologies very difficult to run without a prior deep cleaning of the feeds in order to avoid the reformer's catalyst poisoning. We propose a non-catalytic process in which almost any carbonaceous feed is converted into the Synthesis Gas in a presence of high-voltage discharges (called GlidArc) that assist the exothermic Partial Oxidation POX). The unique oxidant is air. This contribution presents some of our tests with natural gas, cyclohexane, heptane, toluene, various gasolines, and various diesel oils (including logistic ones). In two separate contributions to this Conference we present our more expanded studies on the GlidArc-assisted POX reforming of commercial propane and rapeseed oil (canola). Our reactors (1- or 2-Liter scale) work at atmospheric pressure and need less than 0.5 kW electric power (rather about 0.1 kW) to produce up to 9 m 3 (n)/h of Nitrogen-diluted SynGas containing up to 27% of H 2 and up to 23% of CO. Such assisting power represents roughly less than 5% (rather around 2%) with respect to the Lower Heating Value of produced Synthesis Gas (up to 11 kW). Recycling such relatively small portion of the power is an acceptable compromise. All tested feeds are totally reformed. No soot is observed at a sufficient O/C ratio. (author)

Tungsten foil laminate for structural divertor applications - Joining of tungsten foils

Science.gov (United States)

Reiser, Jens; Rieth, Michael; Möslang, Anton; Dafferner, Bernhard; Hoffmann, Jan; Mrotzek, Tobias; Hoffmann, Andreas; Armstrong, D. E. J.; Yi, Xiaoou

2013-05-01

This paper is the fourth in our series on tungsten laminates. The aim of this paper is to discuss laminate synthesis, meaning the joining of tungsten foils. It is obvious that the properties of the tungsten laminate strongly depend on the combination of (i) interlayer and (ii) joining technology, as this combination defines (i) the condition of the tungsten foil after joining (as-received or recrystallised) as well as (ii) the characteristics of the interface between the tungsten foil and the interlayer (wettability or diffusion leading to a solid solution or the formation of intermetallics). From the example of tungsten laminates joined by brazing with (i) an eutectic silver copper brazing filler, (ii) copper, (iii) titanium, and (iv) zirconium, the microstructure will be discussed, with special focus on the interface. Based on our assumptions of the mechanism of the extraordinary ductility of tungsten foil we present three syntheses strategies and make recommendations for the synthesis of high temperature tungsten laminates.

Resistance of hypoxic cells to ionizing radiation is influenced by homologous recombination status

International Nuclear Information System (INIS)

Sprong, Debbie; Janssen, Hilde L.; Vens, Conchita; Begg, Adrian C.

2006-01-01

Purpose: To determine the role of DNA repair in hypoxic radioresistance. Methods and Materials: Chinese hamster cell lines with mutations in homologous recombination (XRCC2, XRCC3, BRAC2, RAD51C) or nonhomologous end-joining (DNA-PKcs) genes were irradiated under normoxic (20% oxygen) and hypoxic (<0.1% oxygen) conditions, and the oxygen enhancement ratio (OER) was calculated. In addition, Fanconi anemia fibroblasts (complementation groups C and G) were compared with fibroblasts from nonsyndrome patients. RAD51 foci were studied using immunofluorescence. Results: All hamster cell lines deficient in homologous recombination showed a decrease in OER (1.5-2.0 vs. 2.6-3.0 for wild-types). In contrast, the OER for the DNA-PKcs-deficient line was comparable to wild-type controls. The two Fanconi anemia cell strains also showed a significant reduction in OER. The OER for RAD51 foci formation at late times after irradiation was considerably lower than that for survival in wild-type cells. Conclusion: Homologous recombination plays an important role in determining hypoxic cell radiosensitivity. Lower OERs have also been reported in cells deficient in XPF and ERCC1, which, similar to homologous recombination genes, are known to play a role in cross-link repair. Because Fanconi anemia cells are also sensitive to cross-linking agents, this strengthens the notion that the capacity to repair cross-links determines hypoxic radiosensitivity

Microwave-Assisted Eco-Friendly Synthesis of Organics and Nanomaterials

Science.gov (United States)

This presentation summarizes our recent activity in MW-assisted synthesis, which involves benign alternatives, such as the use of supported reagents, and greener reaction medium in aqueous or solvent-free conditions.1 The greener synthesis of heterocyclic compounds, coupling reac...

A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related

Directory of Open Access Journals (Sweden)

Vasieva Olga

2011-01-01

Full Text Available Abstract Background The ageing of the worldwide population means there is a growing need for research on the biology of ageing. DNA damage is likely a key contributor to the ageing process and elucidating the role of different DNA repair systems in ageing is of great interest. In this paper we propose a data mining approach, based on classification methods (decision trees and Naive Bayes, for analysing data about human DNA repair genes. The goal is to build classification models that allow us to discriminate between ageing-related and non-ageing-related DNA repair genes, in order to better understand their different properties. Results The main patterns discovered by the classification methods are as follows: (a the number of protein-protein interactions was a predictor of DNA repair proteins being ageing-related; (b the use of predictor attributes based on protein-protein interactions considerably increased predictive accuracy of attributes based on Gene Ontology (GO annotations; (c GO terms related to "response to stimulus" seem reasonably good predictors of ageing-relatedness for DNA repair genes; (d interaction with the XRCC5 (Ku80 protein is a strong predictor of ageing-relatedness for DNA repair genes; and (e DNA repair genes with a high expression in T lymphocytes are more likely to be ageing-related. Conclusions The above patterns are broadly integrated in an analysis discussing relations between Ku, the non-homologous end joining DNA repair pathway, ageing and lymphocyte development. These patterns and their analysis support non-homologous end joining double strand break repair as central to the ageing-relatedness of DNA repair genes. Our work also showcases the use of protein interaction partners to improve accuracy in data mining methods and our approach could be applied to other ageing-related pathways.

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 with improved proof-reading enhances homology-directed repair.

Science.gov (United States)

Kato-Inui, Tomoko; Takahashi, Gou; Hsu, Szuyin; Miyaoka, Yuichiro

2018-05-18

Genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) predominantly induces non-homologous end joining (NHEJ), which generates random insertions or deletions, whereas homology-directed repair (HDR), which generates precise recombination products, is useful for wider applications. However, the factors that determine the ratio of HDR to NHEJ products after CRISPR/Cas9 editing remain unclear, and methods by which the proportion of HDR products can be increased have not yet been fully established. We systematically analyzed the HDR and NHEJ products after genome editing using various modified guide RNAs (gRNAs) and Cas9 variants with an enhanced conformational checkpoint to improve the fidelity at endogenous gene loci in HEK293T cells and HeLa cells. We found that these modified gRNAs and Cas9 variants were able to enhance HDR in both single-nucleotide substitutions and a multi-kb DNA fragment insertion. Our results suggest that the original CRISPR/Cas9 system from the bacterial immune system is not necessarily the best option for the induction of HDR in genome editing and indicate that the modulation of the kinetics of conformational checkpoints of Cas9 can optimize the HDR/NHEJ ratio.

Competition between replicative and translesion polymerases during homologous recombination repair in Drosophila.

Directory of Open Access Journals (Sweden)

Daniel P Kane

Full Text Available In metazoans, the mechanism by which DNA is synthesized during homologous recombination repair of double-strand breaks is poorly understood. Specifically, the identities of the polymerase(s that carry out repair synthesis and how they are recruited to repair sites are unclear. Here, we have investigated the roles of several different polymerases during homologous recombination repair in Drosophila melanogaster. Using a gap repair assay, we found that homologous recombination is impaired in Drosophila lacking DNA polymerase zeta and, to a lesser extent, polymerase eta. In addition, the Pol32 protein, part of the polymerase delta complex, is needed for repair requiring extensive synthesis. Loss of Rev1, which interacts with multiple translesion polymerases, results in increased synthesis during gap repair. Together, our findings support a model in which translesion polymerases and the polymerase delta complex compete during homologous recombination repair. In addition, they establish Rev1 as a crucial factor that regulates the extent of repair synthesis.

Tungsten foil laminate for structural divertor applications – Joining of tungsten foils

Energy Technology Data Exchange (ETDEWEB)

Reiser, Jens, E-mail: jens.reiser@kit.edu [Karlsruhe Institute of Technology (KIT), Institute for Applied Materials (IAM-AWP) (Germany); Rieth, Michael; Möslang, Anton; Dafferner, Bernhard; Hoffmann, Jan [Karlsruhe Institute of Technology (KIT), Institute for Applied Materials (IAM-AWP) (Germany); Mrotzek, Tobias; Hoffmann, Andreas [PLANSEE SE, Reutte (Austria); Armstrong, D.E.J.; Yi, Xiaoou [University of Oxford, Department of Materials (United Kingdom)

2013-05-15

This paper is the fourth in our series on tungsten laminates. The aim of this paper is to discuss laminate synthesis, meaning the joining of tungsten foils. It is obvious that the properties of the tungsten laminate strongly depend on the combination of (i) interlayer and (ii) joining technology, as this combination defines (i) the condition of the tungsten foil after joining (as-received or recrystallised) as well as (ii) the characteristics of the interface between the tungsten foil and the interlayer (wettability or diffusion leading to a solid solution or the formation of intermetallics). From the example of tungsten laminates joined by brazing with (i) an eutectic silver copper brazing filler, (ii) copper, (iii) titanium, and (iv) zirconium, the microstructure will be discussed, with special focus on the interface. Based on our assumptions of the mechanism of the extraordinary ductility of tungsten foil we present three syntheses strategies and make recommendations for the synthesis of high temperature tungsten laminates.

Microwave-Assisted Synthesis of "N"-Phenylsuccinimide

Science.gov (United States)

Shell, Thomas A.; Shell, Jennifer R.; Poole, Kathleen A.; Guetzloff, Thomas F.

2011-01-01

A microwave-assisted synthesis of "N"-phenylsuccinimide has been developed for the second-semester organic teaching laboratory. Utilizing this procedure, "N"-phenylsuccinimide can be synthesized in moderate yields (40-60%) by heating a mixture of aniline and succinic anhydride in a domestic microwave oven for four minutes. This technique reduces…

Mouse embryonic stem cells, but not somatic cells, predominantly use homologous recombination to repair double-strand DNA breaks.

Science.gov (United States)

Tichy, Elisia D; Pillai, Resmi; Deng, Li; Liang, Li; Tischfield, Jay; Schwemberger, Sandy J; Babcock, George F; Stambrook, Peter J

2010-11-01

Embryonic stem (ES) cells give rise to all cell types of an organism. Since mutations at this embryonic stage would affect all cells and be detrimental to the overall health of an organism, robust mechanisms must exist to ensure that genomic integrity is maintained. To test this proposition, we compared the capacity of murine ES cells to repair DNA double-strand breaks with that of differentiated cells. Of the 2 major pathways that repair double-strand breaks, error-prone nonhomologous end joining (NHEJ) predominated in mouse embryonic fibroblasts, whereas the high fidelity homologous recombinational repair (HRR) predominated in ES cells. Microhomology-mediated end joining, an emerging repair pathway, persisted at low levels in all cell types examined. The levels of proteins involved in HRR and microhomology-mediated end joining were highly elevated in ES cells compared with mouse embryonic fibroblasts, whereas those for NHEJ were quite variable, with DNA Ligase IV expression low in ES cells. The half-life of DNA Ligase IV protein was also low in ES cells. Attempts to increase the abundance of DNA Ligase IV protein by overexpression or inhibition of its degradation, and thereby elevate NHEJ in ES cells, were unsuccessful. When ES cells were induced to differentiate, however, the level of DNA Ligase IV protein increased, as did the capacity to repair by NHEJ. The data suggest that preferential use of HRR rather than NHEJ may lend ES cells an additional layer of genomic protection and that the limited levels of DNA Ligase IV may account for the low level of NHEJ activity.

Microwave-Assisted Green Synthesis of Silver Nanostructures

Science.gov (United States)

This account summarizes a microwave (MW)-assisted synthetic approach for producing silver nanostructures. The rapid and in-core MW heating has received considerable attention as a promising new method for the one-pot synthesis of metallic nanostructures in solutions. Conceptually...

Homologous Recombination Defective Arabidopsis Mutants Exhibit Enhanced Sensitivity to Abscisic Acid.

Directory of Open Access Journals (Sweden)

Sujit Roy

Full Text Available Abscisic acid (ABA acts as an important plant hormone in regulating various aspects of plant growth and developmental processes particularly under abiotic stress conditions. An increased ABA level in plant cells inhibits DNA replication and cell division, causing plant growth retardation. In this study, we have investigated the effects of ABA on the growth responses of some major loss-of-function mutants of DNA double-stand break (DSB repair genes in Arabidopsis during seed germination and early stages of seedling growth for understanding the role of ABA in the induction of genome instability in plants. A comparative analysis of ABA sensitivity of wild-type Arabidopsis and the knockout mutant lines related to DSB sensors, including atatm, atatr, the non-homologous end joining (NHEJ pathway genes, and mutants related to homologous recombination (HR pathway genes showed relatively enhanced sensitivity of atatr and HR-related mutants to ABA treatment. The expression levels of HR-related genes were increased in wild-type Arabidopsis (Col-0 during seed germination and early stages of seedling growth. Immunoblotting experiments detected phosphorylation of histone H2AX in wild-type (Col-0 and DSB repair gene mutants after ABA treatment, indicating the activation of DNA damage response due to ABA treatment. Analyses of DSB repair kinetics using comet assay under neutral condition have revealed comparatively slower DSB repair activity in HR mutants. Overall, our results have provided comprehensive information on the possible effect of ABA on DNA repair machinery in plants and also indicated potential functional involvement of HR pathway in repairing ABA induced DNA damage in Arabidopsis.

Arabidopsis DNA polymerase lambda mutant is mildly sensitive to DNA double strand breaks but defective in integration of a transgene

Czech Academy of Sciences Publication Activity Database

Furukawa, T.; Angelis, Karel; Britt, A.B.

2015-01-01

Roč. 6, MAY 27 (2015) ISSN 1664-462X R&D Projects: GA ČR GA13-06595S Institutional support: RVO:61389030 Keywords : DNA polymerase * DNA repair * Non homologous end joining Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.495, year: 2015

Quantum chemistry-assisted synthesis route development

International Nuclear Information System (INIS)

Hori, Kenji; Sumimoto, Michinori; Murafuji, Toshihiro

2015-01-01

We have been investigating “quantum chemistry-assisted synthesis route development” using in silico screenings and applied the method to several targets. Another example was conducted to develop synthesis routes for a urea derivative, namely 1-(4-(trifluoromethyl)-2-oxo-2H-chromen-7-yl)urea. While five synthesis routes were examined, only three routes passed the second in silico screening. Among them, the reaction of 7-amino-4-(trifluoromethyl)-2H-chromen-2-one and O-methyl carbamate with BF 3 as an additive was ranked as the first choice for synthetic work. We were able to experimentally obtain the target compound even though its yield was as low as 21 %. The theoretical result was thus consistent with that observed. The summary of transition state data base (TSDB) is also provided. TSDB is the key to reducing time of in silico screenings

Distinct roles of FANCO/RAD51C in DNA damage signaling and repair: implications for fanconi anemia and breast cancer susceptibility

International Nuclear Information System (INIS)

Nagaraju, G.; Somyajit, K.; Subramanya, S.

2012-01-01

Unrepaired or misrepaired chromosomal double-strand breaks (DSBs) can cause gross chromosomal rearrangements which eventually can lead to tumorigenesis through inactivation of tumor suppressor genes or activation of oncogenes. There are two major mechanisms of DSB repair: non-homologous end joining (NHEJ) and homologous recombination (HR). DSBs that are generated during S and G2 phase of the cell are preferentially repaired by sister chromatid recombination (SCR), an HR pathway that utilizes neighboring sister chromatid as a template. Since the copied information is accurate, SCR is potentially an error-free pathway. HR also plays a critical role in the repair of daughter strand gaps (DSGs) that arise as a result of replication fork stalling and facilitates replication fork recovery. Furthermore, in collaboration with nucleotide excision repair and translesion synthesis, HR is involved in the repair of DNA interstrand cross-links (ICLs). Thus, HR is important for the maintenance of genome integrity and its dysfunction can lead to various genetic disorders and cancer

Microwave-assisted transformations and synthesis of polymer nanocomposites and nanomaterials

Science.gov (United States)

The use of emerging MW-assisted chemistry techniques in conjunction with greener reaction media is dramatically reducing chemical waste and reaction times in several organic transformations and material synthesis. This account summarizes our own experience in developing MW-assist...

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

influences subsequent analyses of the manipulated strain. Our system will facilitate construction of large numbers of defined mutations in A. nidulans. Moreover, as the system can likely be adapted to other filamentous fungi, we expect it will be particularly beneficial in species where NHEJ cannot...... be restored by sexual crossing. (c) 2007 Elsevier Inc. All rights reserved....

The homology groups of moduli spaces on non-classical Klein surfaces

International Nuclear Information System (INIS)

Zaw, Myint

2001-08-01

We describe the moduli space M-vector±(g,c) of non-classical directed Klein surfaces of genus g=h-c-1 with c≥0 distinguished points as a configuration space B ± (h,c) of classes h-slit pairs in C. Based on this model, we prove that M-vector ± (g,c) is non-orientable for any g and c and we compute the homology groups of the moduli spaces M-vector ± (g,c) for g≤2. (author)

Microwave-assisted green synthesis and antimicrobial activity of ...

African Journals Online (AJOL)

Microwave-assisted green synthesis and antimicrobial activity of silver nanoparticles derived from a ... Journal Home > Vol 16, No 12 (2017) > ... has been prepared by a simple, eco-friendly, cost-effective, rapid green chemistry methodology.

Microwave-assisted silica-promoted solvent-free synthesis of ...

Indian Academy of Sciences (India)

method using microwave irradiation with an excellent yield. The newly ... Table 1. Silica promoted microwave-assisted solvent-free synthesis of quinazolinone ... Time (min). Yield (%)a ..... thanks SC/ST cell of Bangalore University for research.

Computer-assisted spectral design and synthesis

Science.gov (United States)

Vadakkumpadan, Fijoy; Wang, Qiqi; Sun, Yinlong

2005-01-01

In this paper, we propose a computer-assisted approach for spectral design and synthesis. This approach starts with some initial spectrum, modifies it interactively, evaluates the change, and decides the optimal spectrum. Given a requested change as function of wavelength, we model the change function using a Gaussian function. When there is the metameric constraint, from the Gaussian function of request change, we propose a method to generate the change function such that the result spectrum has the same color as the initial spectrum. We have tested the proposed method with different initial spectra and change functions, and implemented an interactive graphics environment for spectral design and synthesis. The proposed approach and graphics implementation for spectral design and synthesis can be helpful for a number of applications such as lighting of building interiors, textile coloration, and pigment development of automobile paints, and spectral computer graphics.

Enantiopure vs. Racemic Naphthalimide End-Capped Helicenic Non-Fullerene Electron Acceptors: Impact on Organic Photovoltaics Performance

OpenAIRE

Josse , Pierre; Favereau , Ludovic; Shen , Chengshuo; Dabos-Seignon , Sylvie; Blanchard , Philippe; Cabanetos , Clement; Crassous , Jeanne

2017-01-01

International audience; Impact of the enantiopurity on organic photovoltaics (OPV) performance was investigated through the synthesis of racemic and enantiomerically pure naphthalimide end-capped helicenes and their application as non-fullerene molecular electron acceptors in OPV devices. A very strong increase of the device performance was observed by simply switching from the racemic to the enantiopure forms of these π-helical non-fullerene acceptors with power conversion efficiencies jumpi...

Microwave-assisted 'greener' synthesis of organics and nanomaterials

Science.gov (United States)

Microwave selective heating techniques in conjunction with greener reaction media are dramatically reducing chemical waste and reaction times in several organic transformations and material synthesis. This presentation summarizes author’s own experience in developing MW-assisted ...

Rapid and convenient semi-automated microwave-assisted solid-phase synthesis of arylopeptoids

DEFF Research Database (Denmark)

Rasmussen, Jakob Ewald; Boccia, Marcello Massimo; Nielsen, John

2014-01-01

A facile and expedient route to the synthesis of arylopeptoid oligomers (N-alkylated aminomethyl benz-amides) using semi-automated microwave-assisted solid-phase synthesis is presented. The synthesis was optimized for the incorporation of side chains derived from sterically hindered or unreactive...

Evolution of saxitoxin synthesis in cyanobacteria and dinoflagellates.

Science.gov (United States)

Hackett, Jeremiah D; Wisecaver, Jennifer H; Brosnahan, Michael L; Kulis, David M; Anderson, Donald M; Bhattacharya, Debashish; Plumley, F Gerald; Erdner, Deana L

2013-01-01

Dinoflagellates produce a variety of toxic secondary metabolites that have a significant impact on marine ecosystems and fisheries. Saxitoxin (STX), the cause of paralytic shellfish poisoning, is produced by three marine dinoflagellate genera and is also made by some freshwater cyanobacteria. Genes involved in STX synthesis have been identified in cyanobacteria but are yet to be reported in the massive genomes of dinoflagellates. We have assembled comprehensive transcriptome data sets for several STX-producing dinoflagellates and a related non-toxic species and have identified 265 putative homologs of 13 cyanobacterial STX synthesis genes, including all of the genes directly involved in toxin synthesis. Putative homologs of four proteins group closely in phylogenies with cyanobacteria and are likely the functional homologs of sxtA, sxtG, and sxtB in dinoflagellates. However, the phylogenies do not support the transfer of these genes directly between toxic cyanobacteria and dinoflagellates. SxtA is split into two proteins in the dinoflagellates corresponding to the N-terminal portion containing the methyltransferase and acyl carrier protein domains and a C-terminal portion with the aminotransferase domain. Homologs of sxtB and N-terminal sxtA are present in non-toxic strains, suggesting their functions may not be limited to saxitoxin production. Only homologs of the C-terminus of sxtA and sxtG were found exclusively in toxic strains. A more thorough survey of STX+ dinoflagellates will be needed to determine if these two genes may be specific to SXT production in dinoflagellates. The A. tamarense transcriptome does not contain homologs for the remaining STX genes. Nevertheless, we identified candidate genes with similar predicted biochemical activities that account for the missing functions. These results suggest that the STX synthesis pathway was likely assembled independently in the distantly related cyanobacteria and dinoflagellates, although using some

Chronic exposure to sublethal doses of radiation mimetic ZeocinTM selects for clones deficient in homologous recombination

International Nuclear Information System (INIS)

Delacote, Fabien; Deriano, Ludovic; Lambert, Sarah; Bertrand, Pascale; Saintigny, Yannick; Lopez, Bernard S.

2007-01-01

DNA double-strand breaks (DSBs) are highly toxic lesions leading to genome variability/instability. The balance between homologous recombination (HR) and non-homologous end-joining (NHEJ), two alternative DSB repair systems, is essential to ensure genome maintenance in mammalian cells. Here, we transfected CHO hamster cells with the pcDNA TM 3.1/Zeo plasmid, and selected transfectants with Zeocin TM , a bleomycin analog which produces DSBs. Despite the presence of a Zeocin TM resistance gene in pcDNA TM 3.1/Zeo, Zeocin TM induced 8-10 γ-H2AX foci per cell. This shows that the Zeocin TM resistance gene failed to fully detoxify cells treated with Zeocin TM , and that during selection cells were submitted to a chronic sublethal DSB stress. Selected clones show decreases in both spontaneous and induced intrachromosomal HR. In contrast, in an in vitro assay, these clones show an increase in NHEJ products specific to the KU86 pathway. We selected cells, in the absence of pcDNA TM 3.1/Zeo, with low and sublethal doses of Zeocin TM , producing a mean 8-10 γ-H2AX foci per cell. Newly selected clones exhibited similar phenotypes: HR decrease accompanied by an increase in KU86-dependent NHEJ efficiency. Thus chronic exposure to sublethal numbers of DSBs selects cells whose HR versus NHEJ balance is altered. This may well have implications for radio- and chemotherapy, and for management of environmental hazards

Automated Controller Synthesis for non-Deterministic Piecewise-Affine Hybrid Systems

DEFF Research Database (Denmark)

Grunnet, Jacob Deleuran

formations. This thesis uses a hybrid systems model of a satellite formation with possible actuator faults as a motivating example for developing an automated control synthesis method for non-deterministic piecewise-affine hybrid systems (PAHS). The method does not only open an avenue for further research...... in fault tolerant satellite formation control, but can be used to synthesise controllers for a wide range of systems where external events can alter the system dynamics. The synthesis method relies on abstracting the hybrid system into a discrete game, finding a winning strategy for the game meeting...... game and linear optimisation solvers for controller refinement. To illustrate the efficacy of the method a reoccurring satellite formation example including actuator faults has been used. The end result is the application of PAHSCTRL on the example showing synthesis and simulation of a fault tolerant...

Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold

DEFF Research Database (Denmark)

Molina, Rafael; Marcaida, María José; Redondo, Pilar

2015-01-01

strand break could be an approach to reduce the toxicity associated with non-homologous end joining by promoting the use of homologous recombination to repair the cleavage of a single DNA break. Taking advantage of the sequential DNA cleavage mechanism of I-DmoI LAGLIDADG homing endonuclease, we have......Homing endonucleases are useful tools for genome modification because of their capability to recognize and cleave specifically large DNA targets. These endonucleases generate a DNA double strand break that can be repaired by the DNA damage response machinery. The break can be repaired by homologous...

Author Details

African Journals Online (AJOL)

Sanie-Jahromi, Fatemeh. Vol 18, No 4 (2017) - Articles Extremely low frequency electromagnetic field in combination with β-Lapachone up-regulates the genes of non-homologous end joining. Abstract PDF. ISSN: 1110-8630. AJOL African Journals Online. HOW TO USE AJOL... for Researchers · for Librarians · for Authors ...

Microwave-assisted one-pot synthesis of benzothiazole and ...

Indian Academy of Sciences (India)

Microwave-assisted synthesis of benzothiazole and benzoxazole libraries via PIFA promoted cyclocondensation of 2-aminothiophenols/2-aminophenols with aldehydes under one-pot condition in good to excellent yields was achieved. Twenty compounds have been investigated for their analgesic activity and showed ...

Microwave-assisted one-step synthesis of acetate-capped NaYF4

DEFF Research Database (Denmark)

Reddy, Kumbam Lingeshwar; Prabhakar, Neeraj; Arppe, Riikka

2017-01-01

Acetate-capped hydrophilic cubic phase NaYF4:Yb/Er upconversion nanophosphors were effectively synthesized in a single step employing a facile microwave-assisted synthesis route by applying relatively low temperatures in a short span of time compared to the conventional synthetic methods. The nan......Acetate-capped hydrophilic cubic phase NaYF4:Yb/Er upconversion nanophosphors were effectively synthesized in a single step employing a facile microwave-assisted synthesis route by applying relatively low temperatures in a short span of time compared to the conventional synthetic methods...

Investigation of Thermoelectric Parameters of Bi2Te3: TEGs Assembled using Pressure-Assisted Silver Powder Sintering-Based Joining Technology

Science.gov (United States)

Stranz, Andrej; Waag, Andreas; Peiner, Erwin

2015-06-01

Operation of thermoelectric generator (TEG) modules based on bismuth telluride alloys at temperatures higher than 250°C is mostly limited by the melting point of the assembly solder. Although the thermoelectric parameters of bismuth telluride materials degrade for temperatures >130°C, the power output of the module can be enhanced with an increase in the temperature difference. For this, a temperature-stable joining technique, especially for the hot side of the modules, is required. Fabrication and process parameters of TEG modules consisting of bismuth telluride legs, alumina ceramics and copper interconnects using a joining technique based on pressure-assisted silver powder sintering are described. Measurements of the thermal force, electrical resistance, and output power are presented that were performed for hot side module temperatures up to 350°C and temperature differences higher than 300°C. Temperature cycling and results measured during extended high-temperature operation are addressed.

GlidArc-assisted production of synthesis gas from LPG (Propane)

International Nuclear Information System (INIS)

Czernichowski, A.; Czernichowski, P.; Czernichowski, M.

2003-01-01

Small and medium size reformers that run on widely available Liquefied Petroleum Gas (LPG, containing mostly the propane) can provide Synthesis Gas (or Hydrogen extracted from it) to some Fuel Cell powered cars, boats, homes, farms etc. reducing therefore costs of the pure Hydrogen distribution. We contribute to such idea realization through our simply, plasma-assisted reformer avoiding a need of poison resistant catalysts or prior LPG desulfurizer. In fact, any level of sulphur in LPG is accepted for our non-catalytic reformer based on high-voltage discharges (called GlidArc). The discharges catalytically assist the exothermic partial oxidation process. Electric power assistance is less than 2% of the Lower Heating Value (LHV) of produced SynGas. Recycling such a small portion of the energy is therefore an acceptable compromise. The unique oxidant source is air. This contribution presents our expanded tests with commercial LPG in a 1-L reactor working at atmospheric pressure. At a 0.1 kW electric power assistance we produce a Nitrogen-diluted SynGas containing up to 45% of H 2 +CO at the output flow rate corresponding up to 2.7 m 3 (n)/h of pure H 2 +CO mixture that is equivalent to LHV output power of 8.6 kW. The LPG is totally reformed at more than 70% energetic efficiency and at the total absence of soot. (author)

The PCNA-associated protein PARI negatively regulates homologous recombination via the inhibition of DNA repair synthesis

DEFF Research Database (Denmark)

Burkovics, Peter; Dome, Lili; Juhasz, Szilvia

2016-01-01

to inhibit homologous recombination (HR) events. Here, we describe a biochemical mechanism in which PARI functions as an HR regulator after replication fork stalling and during double-strand break repair. In our reconstituted biochemical system, we show that PARI inhibits DNA repair synthesis during...... recombination events in a PCNA interaction-dependent way but independently of its UvrD-like helicase domain. In accordance, we demonstrate that PARI inhibits HR in vivo, and its knockdown suppresses the UV sensitivity of RAD18-depleted cells. Our data reveal a novel human regulatory mechanism that limits...

Microwave assisted one-pot synthesis of benzothiazole and ...

Indian Academy of Sciences (India)

Dr.P.T.P

1. Microwave assisted one-pot synthesis of benzothiazole and benzoxazole libraries as analgesic agents. C PRAVEEN a. , A NANDAKUMAR a. , P DHEENKUMAR b. , D MURALIDHARAN a and P T. PERUMAL a,. * a. Organic Chemistry Division, Central Leather Research Institute, Adyar, Chennai 600020,. Tamilnadu ...

Joining elements of silicon carbide

International Nuclear Information System (INIS)

Olson, B.A.

1979-01-01

A method of joining together at least two silicon carbide elements (e.g.in forming a heat exchanger) is described, comprising subjecting to sufficiently non-oxidizing atmosphere and sufficiently high temperature, material placed in space between the elements. The material consists of silicon carbide particles, carbon and/or a precursor of carbon, and silicon, such that it forms a joint joining together at least two silicon carbide elements. At least one of the elements may contain silicon. (author)

Analysis of DNA double-strand break repair pathways in mice

International Nuclear Information System (INIS)

Brugmans, Linda; Kanaar, Roland; Essers, Jeroen

2007-01-01

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

Barbiturate End-Capped Non-Fullerene Acceptors for Organic Solar Cells: Tuning Acceptor Energetics to Suppress Geminate Recombination Losses

KAUST Repository

Tan, Ching-Hong

2018-01-10

We report the synthesis of two barbiturate end-capped non-fullerene acceptors and demonstrate their efficient function in high voltage output organic solar cells. The acceptor with the lower LUMO level is shown to exhibit suppressed geminate recombination losses, resulting in enhanced photocurrent generation and higher overall device efficiency.

Barbiturate End-Capped Non-Fullerene Acceptors for Organic Solar Cells: Tuning Acceptor Energetics to Suppress Geminate Recombination Losses

KAUST Repository

Tan, Ching-Hong; Gorman, Jeffrey; Wadsworth, Andrew; Holliday, Sarah; Subramaniyan, Selvam; Jenekhe, Samson A.; Baran, Derya; McCulloch, Iain; Durrant, James

2018-01-01

We report the synthesis of two barbiturate end-capped non-fullerene acceptors and demonstrate their efficient function in high voltage output organic solar cells. The acceptor with the lower LUMO level is shown to exhibit suppressed geminate recombination losses, resulting in enhanced photocurrent generation and higher overall device efficiency.

Performance of electro-plated and joined components for divertor application

International Nuclear Information System (INIS)

Krauss, Wolfgang; Lorenz, Julia; Konys, Jürgen

2013-01-01

Highlights: • Active interlayers of Ni and Pd were electroplated on W to assist joining. • Demonstrator types of W-steel and W–W joints were successfully fabricated. • Diffusion processes increase operation temperature above brazing temperature. • Ni electro-plating is less sensitive to variation of deposition parameters than Pd. • Shear tests showed values in resistance comparable to those of commercial fillers. -- Abstract: A general challenge in divertor development, independently of design type and cooling medium water or helium, is the reliable and adapted joining of components. Depending on the design variants, the characteristics of the joints will be focused on functional or structural behavior to guarantee e.g. good thermal conductivity and sufficient mechanical strength. All variants will have in common that tungsten is the plasma facing material. Thus, material combinations to be joined will range from Cu base over steel to tungsten. Especially tungsten shows lacks in adapted joining due to its metallurgical behavior ranging from immiscibility over bad wetting up to brittle intermetallic phase formation. Joining assisted by electro-chemical deposition of functional and filler layers showed that encouraging progress was achieved in wetting applying nickel interlayers. Nickel proved to be a good reference material but alternative elements (e.g. Pd, Fe) may be more attractive in fusion to manufacture suitable joints. Replacing of Ni as activator element by Pd for W/W or W/steel joints was achieved and joining with Cu-filler was successfully performed. Manufactured joints were characterized applying metallurgical testing and SEM/EDX analyses demonstrating the applicability of Pd activator. First shear tests showed that the joints exhibit mechanical stability sufficient for technical application

On the Moral Acceptability of Physician-Assisted Dying for Non-Autonomous Psychiatric Patients.

Science.gov (United States)

Varelius, Jukka

2016-05-01

Several authors have recently suggested that the suffering caused by mental illness could provide moral grounds for physician-assisted dying. Yet they typically require that psychiatric-assisted dying could come to question in the cases of autonomous, or rational, psychiatric patients only. Given that also non-autonomous psychiatric patients can sometimes suffer unbearably, this limitation appears questionable. In this article, I maintain that restricting psychiatric-assisted dying to autonomous, or rational, psychiatric patients would not be compatible with endorsing certain end-of-life practices commonly accepted in current medical ethics and law, practices often referred to as 'passive euthanasia'. © 2015 John Wiley & Sons Ltd.

Microwave-Assisted Synthesis – Catalytic Applications in Aqueous Media

Science.gov (United States)

The development of sustainable methods directed towards the synthesis of molecules is due to the heightened awareness and recognition of alternative eco-friendly and economical protocols that have minimum impact on environment. Among others, microwave (MW)-assisted methodology ha...

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...... in genotyping procedures and investigated SNPs, potentially inducing differences in the coverage of gene regions. Specifically, five genes were not covered at all in the German data. Therefore, investigations in additional study populations are needed before final conclusion can be drawn....

The ethylene glycol template assisted hydrothermal synthesis of Co3O4 nanowires; structural characterization and their application as glucose non-enzymatic sensor

International Nuclear Information System (INIS)

Khun, K.; Ibupoto, Z.H.; Liu, X.; Beni, V.; Willander, M.

2015-01-01

Highlights: • Ethylene glycol assisted Co 3 O 4 nanowires were synthesized by hydrothermal method. • The grown Co 3 O 4 nanowires were used for sensitive non-enzymatic glucose sensor. • The proposed glucose sensor shows a wide linear range with fast response. • The Co 3 O 4 modified electrode is a highly specific enzyme-less glucose sensor. - Abstract: In the work reported herein the ethylene glycol template assisted hydrothermal synthesis, onto Au substrate, of thin and highly dense cobalt oxide (Co 3 O 4 ) nanowires and their characterization and their application for non-enzymatic glucose sensing are reported. The structure and composition of Co 3 O 4 nanowires have been fully characterized using scanning electron microscopy, X-ray diffraction, high resolution transmission electron microscopy and X-ray photoelectron spectroscopy. The synthesized Co 3 O 4 nanowires resulted to have high purity and showed diameter of approximately 10 nm. The prepared Co 3 O 4 nanowires coated gold electrodes were applied to the non-enzymatic detection of glucose. The developed sensor showed high sensitivity (4.58 × 10 1 μA mM −1 cm −2 ), a wide linear range of concentration (1.00 × 10 −4 –1.2 × 10 1 mM) and a detection limit of 2.65 × 10 −5 mM. The developed glucose sensor has also shown to be very stable and selective over interferents such as uric acid and ascorbic acid. Furthermore, the proposed fabrication process was shown to be highly reproducible response (over nine electrodes)

CRISPR/Cas9 – Mediated Precise Targeted Integration In Vivo Using a Double Cut Donor with Short Homology Arms

Directory of Open Access Journals (Sweden)

Xuan Yao

2017-06-01

Full Text Available Precisely targeted genome editing is highly desired for clinical applications. However, the widely used homology-directed repair (HDR-based genome editing strategies remain inefficient for certain in vivo applications. We here demonstrate a microhomology-mediated end-joining (MMEJ-based strategy for precisely targeted gene integration in transfected neurons and hepatocytes in vivo with efficiencies up to 20%, much higher (up to 10 fold than HDR-based strategy in adult mouse tissues. As a proof of concept of its therapeutic potential, we demonstrate the efficacy of MMEJ-based strategy in correction of Fah mutation and rescue of Fah−/− liver failure mice, offering an efficient approach for precisely targeted gene therapies.

Chrysler Upset Protrusion Joining Techniques for Joining Dissimilar Metals

Energy Technology Data Exchange (ETDEWEB)

Logan, Stephen [FCA US LLC, Auburn Hills, MI (United States)

2017-09-28

The project goal was to develop and demonstrate a robust, cost effective, and versatile joining technique, known as Upset Protrusion Joining (UPJ), for joining challenging dissimilar metal com-binations, especially those where one of the metals is a die cast magnesium (Mg) component. Since two of the key obstacles preventing more widespread use of light metals (especially in high volume automotive applications) are 1) a lack of robust joining techniques and 2) susceptibility to galvanic corrosion, and since the majority of the joint combinations evaluated in this project include die cast Mg (the lightest structural metal) as one of the two materials being joined, and since die casting is the most common and cost effective process for producing Mg components, then successful project completion provides a key enabler to high volume application of lightweight materials, thus potentially leading to reduced costs, and encouraging implementation of lightweight multi-material vehicles for significant reductions in energy consumption and reduced greenhouse gas emissions. Eco-nomic benefits to end-use consumers are achieved primarily via the reduction in fuel consumption. Unlike currently available commercial processes, the UPJ process relies on a very robust mechanical joint rather than intermetallic bonding, so the more cathodic material can be coated prior to joining, thus creating a robust isolation against galvanic attack on the more anodic material. Additionally, since the UPJ protrusion is going through a hole that can be pre-drilled or pre-punched prior to coating, the UPJ process is less likely to damage the coating when the joint is being made. Further-more, since there is no additional cathodic material (such as a steel fastener) used to create the joint, there is no joining induced galvanic activity beyond that of the two parent materials. In accordance with its originally proposed plan, this project has successfully developed process variants of UPJ to enable

Increased sensitivity to ionizing radiation by targeting the homologous recombination pathway in glioma initiating cells.

Science.gov (United States)

Lim, Yi Chieh; Roberts, Tara L; Day, Bryan W; Stringer, Brett W; Kozlov, Sergei; Fazry, Shazrul; Bruce, Zara C; Ensbey, Kathleen S; Walker, David G; Boyd, Andrew W; Lavin, Martin F

2014-12-01

Glioblastoma is deemed the most malignant form of brain tumour, particularly due to its resistance to conventional treatments. A small surviving group of aberrant stem cells termed glioma initiation cells (GICs) that escape surgical debulking are suggested to be the cause of this resistance. Relatively quiescent in nature, GICs are capable of driving tumour recurrence and undergo lineage differentiation. Most importantly, these GICs are resistant to radiotherapy, suggesting that radioresistance contribute to their survival. In a previous study, we demonstrated that GICs had a restricted double strand break (DSB) repair pathway involving predominantly homologous recombination (HR) associated with a lack of functional G1/S checkpoint arrest. This unusual behaviour led to less efficient non-homologous end joining (NHEJ) repair and overall slower DNA DSB repair kinetics. To determine whether specific targeting of the HR pathway with small molecule inhibitors could increase GIC radiosensitivity, we used the Ataxia-telangiectasia mutated inhibitor (ATMi) to ablate HR and the DNA-dependent protein kinase inhibitor (DNA-PKi) to inhibit NHEJ. Pre-treatment with ATMi prior to ionizing radiation (IR) exposure prevented HR-mediated DNA DSB repair as measured by Rad51 foci accumulation. Increased cell death in vitro and improved in vivo animal survival could be observed with combined ATMi and IR treatment. Conversely, DNA-PKi treatment had minimal impact on GICs ability to resolve DNA DSB after IR with only partial reduction in cell survival, confirming the major role of HR. These results provide a mechanistic insight into the predominant form of DNA DSB repair in GICs, which when targeted may be a potential translational approach to increase patient survival. Copyright © 2014. Published by Elsevier B.V.

Mutagenic effects of carbon ions near the range end in plants

Energy Technology Data Exchange (ETDEWEB)

Hase, Yoshihiro, E-mail: hase.yoshihiro@jaea.go.jp [Ion Beam Mutagenesis Research Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 1233 Watanuki, Takasaki, Gunma 370-1292 (Japan); Yoshihara, Ryouhei; Nozawa, Shigeki; Narumi, Issay [Ion Beam Mutagenesis Research Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 1233 Watanuki, Takasaki, Gunma 370-1292 (Japan)

2012-03-01

To gain insight into the mutagenic effects of accelerated heavy ions in plants, the mutagenic effects of carbon ions near the range end (mean linear energy transfer (LET): 425 keV/{mu}m) were compared with the effects of carbon ions penetrating the seeds (mean LET: 113 keV/{mu}m). Mutational analysis by plasmid rescue of Escherichia coli rpsL from irradiated Arabidopsis plants showed a 2.7-fold increase in mutant frequency for 113 keV/{mu}m carbon ions, whereas no enhancement of mutant frequency was observed for carbon ions near the range end. This suggested that carbon ions near the range end induced mutations that were not recovered by plasmid rescue. An Arabidopsis DNA ligase IV mutant, deficient in non-homologous end-joining repair, showed hyper-sensitivity to both types of carbon-ion irradiation. The difference in radiation sensitivity between the wild type and the repair-deficient mutant was greatly diminished for carbon ions near the range end, suggesting that these ions induce irreparable DNA damage. Mutational analysis of the Arabidopsis GL1 locus showed that while the frequency of generation of glabrous mutant sectors was not different between the two types of carbon-ion irradiation, large deletions (>{approx}30 kb) were six times more frequently induced by carbon ions near the range end. When 352 keV/{mu}m neon ions were used, these showed a 6.4 times increase in the frequency of induced large deletions compared with the 113 keV/{mu}m carbon ions. We suggest that the proportion of large deletions increases with LET in plants, as has been reported for mammalian cells. The nature of mutations induced in plants by carbon ions near the range end is discussed in relation to mutation detection by plasmid rescue and transmissibility to progeny.

AUGMENTING 3D CITY MODEL COMPONENTS BY GEODATA JOINS TO FACILITATE AD-HOC GEOMETRIC-TOPOLOGICALLY SOUND INTEGRATION

Directory of Open Access Journals (Sweden)

R. Kaden

2012-07-01

Full Text Available Virtual 3D city models are integrated complex compositions of spatial data of different themes, origin, quality, scale, and dimensions. Within this paper, we address the problem of spatial compatibility of geodata aiming to provide support for ad-hoc integration of virtual 3D city models including geodata of different sources and themes like buildings, terrain, and city furniture. In contrast to related work which is dealing with the integration of redundant geodata structured according to different data models and ontologies, we focus on the integration of complex 3D models of the same representation (here: CityGML but regarding to the geometric-topological consistent matching of non-homologous objects, e.g. a building is connected to a road, and their geometric homogenisation. Therefore, we present an approach including a data model for a Geodata Join and the general concept of an integration procedure using the join information. The Geodata Join aims to bridge the lack of information between fragmented geodata by describing the relationship between adjacent objects from different datasets. The join information includes the geometrical representation of those parts of an object, which have a specific/known topological or geometrical relationship to another object. This part is referred to as a Connector and is either described by points, lines, or surfaces of the existing object geometry or by additional join geometry. In addition, the join information includes the specification of the connected object in the other dataset and the description of the topological and geometrical relationship between both objects, which is used to aid the matching process. Furthermore, the Geodata Join contains object-related information like accuracy values and restrictions of movement and deformation which are used to optimize the integration process. Based on these parameters, a functional model including a matching algorithm, transformation methods, and

Transition piece for joining together tubular pieces

International Nuclear Information System (INIS)

Holko, K.H.

1981-01-01

A transition piece for joining together tubular pieces formed respectively from a low alloy or carbon steel and a high temperature alloy containing at least 16% chromium includes a plurality of tubular parts welded together and formed from materials of selected composition with a maximum chromium content difference of 5% between adjacent parts when the chromium content of each part is below 10% and a maximum chromium difference of 7% between adjacent parts when the chromium content of either part is above 10%. The transition parts are also graded as to such characteristics as thermal expansion coefficient. The transition parts at opposite ends of the transition joint have chromium percentages similar to the tubular pieces to which they are to be joined. The parts may be joined by fusion and/or friction welding and parts may be formed by fusion weld deposition. (author)

Scarless Cas9 Assisted Recombineering (no-SCAR) in Escherichia coli, an Easy-to-Use System for Genome Editing.

Science.gov (United States)

Reisch, Christopher R; Prather, Kristala L J

2017-01-05

The discovery and development of genome editing systems that leverage the site-specific DNA endonuclease system CRISPR/Cas9 has fundamentally changed the ease and speed of genome editing in many organisms. In eukaryotes, the CRISPR/Cas9 system utilizes a "guide" RNA to enable the Cas9 nuclease to make a double-strand break at a particular genome locus, which is repaired by non-homologous end joining (NHEJ) repair enzymes, often generating random mutations in the process. A specific alteration of the target genome can also be generated by supplying a DNA template in vivo with a desired mutation, which is incorporated by homology-directed repair. However, E. coli lacks robust systems for double-strand break repair. Thus, in contrast to eukaryotes, targeting E. coli chromosomal DNA with Cas9 causes cell death. However, Cas9-mediated killing of bacteria can be exploited to select against cells with a specified genotype within a mixed population. In combination with the well described λ-Red system for recombination in E. coli, we created a highly efficient system for marker-free and scarless genome editing. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Metabolism of whole body protein in pregnant and non-pregnant gilts using 15N-glycine single-dose end-product method

International Nuclear Information System (INIS)

Wu De; Liu Huifang; Zhou Anguo; Wang Kangning; Yang Feng

2007-01-01

The metabolism of whole-body protein for pregnant and non-pregnant gilts was investigated using single-dose of 15 N-glycine end-product method. The results showed that there were no differences (P>0.05) in protein dynamic metabolism, amino acids utilization rate between pregnant and non-pregnant gilts at breeding. However, N flux, protein turnover rate, protein synthesis rate and breakdown rate of pregnant gilts were lower (P<0.05) than those of non-pregnant gilts at 30days after breeding, but the protein aggradiation's rate increased by 25% (P<0.05). During late gestation, N flux, protein turnover rate, protein synthesis rate and breakdown rate of pregnant sows were significantly increased (P<0.01), and protein aggradation's rate increased by 71.1%, compared with that of non-pregnant gilts. (authors)

Break-induced ATR and Ddb1-Cul4(Cdt)² ubiquitin ligase-dependent nucleotide synthesis promotes homologous recombination repair in fission yeast

DEFF Research Database (Denmark)

Moss, Jennifer; Tinline-Purvis, Helen; Walker, Carol A

2010-01-01

Nucleotide synthesis is a universal response to DNA damage, but how this response facilitates DNA repair and cell survival is unclear. Here we establish a role for DNA damage-induced nucleotide synthesis in homologous recombination (HR) repair in fission yeast. Using a genetic screen, we found...... the Ddb1-Cul4(Cdt)² ubiquitin ligase complex and ribonucleotide reductase (RNR) to be required for HR repair of a DNA double-strand break (DSB). The Ddb1-Cul4(Cdt)² ubiquitin ligase complex is required for degradation of Spd1, an inhibitor of RNR in fission yeast. Accordingly, deleting spd1(+) suppressed...

Individual capacity for DNA repair and maintenance of genomic integrity: a fertile ground for studies in the field of assisted reproduction

Directory of Open Access Journals (Sweden)

Radoslava Vazharova

2016-05-01

Full Text Available Many factors may affect the chances for successful pregnancy, especially at a later age. Fertility evaluations including genetic analysis are recommended to couples that have not achieved pregnancy within 6–12 months of unprotected intercourse. This review discusses some of the common polymorphisms in genes coding for proteins functioning in DNA damage identification and repair and maintenance of genomic integrity that may affect the chances of success in natural conception as well as in assisted reproduction (AR. Common polymorphisms in genes coding for proteins functioning in DNA damage identification and repair and maintenance of genomic integrity may affect the chances of success in assisted reproduction as well as in natural conception. The effects of carriership of different alleles of key genes of DNA repair may have differential effects in men and women and at different ages, suggesting complex interactions with the mechanisms controlling cell and tissue aging and programmed cell death. Future studies in the field are needed in order to elucidate the genotype–phenotype relationships and to translate the knowledge about individual repair capacity and maintenance of genomic integrity to potential clinical applications. Abbreviations: aCGH: microarray-based comparative genomic hybridization; AR: assisted reproduction; ATM: ataxia-telangiectasia mutated; ATP: adenosine triphosphate; BER: base excision repair; BFE: basic fertility evaluation; DMSO: dimethyl sulfoxide; FSH: follicle-stimulating hormone; GNRHR: gonadotropin-releasing hormone receptor; HMG: high-mobility group; ICSI: intracytoplasmic sperm injection; IUI: intrauterine insemination; IVF: in vitro fertilization; LH: luteinizing hormone; LIF: leukaemia inhibitory factor; MTR: methionine synthase; MTRR: methionine synthase reductase; NGS: next-generation sequencing; NER: nucleotide excision repair; NHEJ: non-homologous end joining; PAH: polycyclic aromatic hydrocarbons; PCOS

The Microwave-Assisted Green Synthesis of TiC Powders.

Science.gov (United States)

Wang, Hui; Zhu, Wencheng; Liu, Yanchun; Zeng, Lingke; Sun, Luyi

2016-11-08

Titanium carbide (TiC) is an important engineering material and has found widespread applications. Currently, TiC is typically synthesized through carbothermal reduction, requiring a high temperature (ca. 1700-2300 °C) and long reaction time (ca. 10-20 h), which is not eco-friendly. During a conventional reaction path, anatase TiO₂ (A-TiO₂) was first converted to rutile TiO₂ (R-TiO₂), which was subsequently reduced to TiC. Herein, we explored the synthesis of TiC powders with the assistance of microwave heating. In particular, we achieved the conversion of A-TiO₂, which was more reactive than R-TiO₂ for the carbothermal reduction, to TiC, which was directly due to quick microwave heating. As such, the carbothermal reduction started at a much lower temperature of ca. 1200 °C and finished within 30 min when reacting at 1400 °C, leading to significant energy saving. This study shows that microwave-assisted synthesis can be an effective and green process for preparing TiC powders, which is promising for future large-scale production. The influence of the reaction temperature, the reaction duration, and the carbon content on the synthesis of TiC powders was investigated.

Synthesis of benzamides by microwave assisted ring opening of less reactive dimethylaminobenzylidene oxazolone

Directory of Open Access Journals (Sweden)

Saurabh C. Khadse

2017-02-01

Full Text Available This paper presents the synthesis of some benzamide compounds (B1–B10 by microwave-assisted ring opening of 4-(4-dimethylaminobenzylidene-2-phenyl-5-oxazolone (AZ4. By conventional synthesis involving heating, it was found difficult to obtain ring-opened products, probably due to poor tendency of the carbonyl carbon (C5 of AZ4 to undergo nucleophilic attack by mono/or disubstituted anilines. Microwave assisted reactions were easy to perform, have reduced the reaction time and produced good yields.

Scarless Cas9 Assisted Recombineering (no‐SCAR) in Escherichia coli, an Easy‐to‐Use System for Genome Editing

OpenAIRE

Reisch, Christopher R; Jones, Kristala L.

2018-01-01

The discovery and development of genome editing systems that leverage the site‐specific DNA endonuclease system CRISPR/Cas9 has fundamentally changed the ease and speed of genome editing in many organisms. In eukaryotes, the CRISPR/Cas9 system utilizes a “guide” RNA to enable the Cas9 nuclease to make a double‐strand break at a particular genome locus, which is repaired by non‐homologous end joining (NHEJ) repair enzymes, often generating random mutations in the process. A specific alteration...

RNF138 joins the HR team

DEFF Research Database (Denmark)

Bekker-Jensen, Simon; Mailand, Niels

2015-01-01

Two studies show that the E3 ubiquitin ligase RNF138 is recruited to DNA double-strand break sites, where it ubiquitylates key repair factors to promote DNA-end resection and homologous recombination. These findings add insights into the multilayered regulatory mechanisms underlying DNA double-st...

Synthetic lethality between murine DNA repair factors XLF and DNA-PKcs is rescued by inactivation of Ku70

DEFF Research Database (Denmark)

Xing, Mengtan; Bjørås, Magnar; Daniel, Jeremy A

2017-01-01

DNA double-strand breaks (DSBs) are recognized and repaired by the Classical Non-Homologous End-Joining (C-NHEJ) and Homologous Recombination pathways. C-NHEJ includes the core Ku70 and Ku80 (or Ku86) heterodimer that binds DSBs and thus promotes recruitment of accessory downstream NHEJ factors XLF......, PAXX, DNA-PKcs, Artemis and other core subunits, XRCC4 and DNA Ligase 4 (Lig4). In the absence of core C-NHEJ factors, DNA repair can be performed by Alternative End-Joining, which likely depends on DNA Ligase 1 and DNA Ligase 3. Genetic inactivation of C-NHEJ factors, such as Ku70, Ku80, XLF, PAXX...... with severe apoptosis in the central nervous system. Here, we demonstrate that inactivation of the Ku70 gene rescues the synthetic lethality between XLF and DNA-PKcs, resulting in triple knockout mice that are indistinguishable from Ku70-deficient littermates by size or levels of genomic instability. Moreover...

Microwave-assisted Synthesis of an Important Intermediate of Benazepril

OpenAIRE

Mistry, B; Medhane, Dipti; Mohanraj, Krishnapriya; Ghone, Sanjeevani A.

2010-01-01

Rapid and efficient methods for the synthesis of an important intermediate of benazepril ethyl 3-phthalimido-2,3,4,5-tetrahydro-1H-[1]benzazepin-2-one-1-acetate under the influence of microwave irradiation are described. A comparative study of conventional and microwave assisted method is briefly discussed.

Some homological properties of skew PBW extensions arising in non-commutative algebraic geometry

Directory of Open Access Journals (Sweden)

Lezama Oswaldo

2017-06-01

Full Text Available In this short paper we study for the skew PBW (Poincar-Birkhoff-Witt extensions some homological properties arising in non-commutative algebraic geometry, namely, Auslander-Gorenstein regularity, Cohen-Macaulayness and strongly noetherianity. Skew PBW extensions include a considerable number of non-commutative rings of polynomial type such that classical PBW extensions, quantum polynomial rings, multiplicative analogue of the Weyl algebra, some Sklyanin algebras, operator algebras, diffusion algebras, quadratic algebras in 3 variables, among many others. Parametrization of the point modules of some examples is also presented.

Summary of Dissimilar Metal Joining Trials Conducted by Edison Welding Institute

Energy Technology Data Exchange (ETDEWEB)

MJ Lambert

2005-11-18

Under the direction of the NASA-Glenn Research Center, the Edison Welding Institute (EWI) in Columbus, OH performed a series of non-fusion joining experiments to determine the feasibility of joining refractory metals or refractory metal alloys to Ni-based superalloys. Results, as reported by EWI, can be found in the project report for EWI Project 48819GTH (Attachment A, at the end of this document), dated October 10, 2005. The three joining methods used in this investigation were inertia welding, magnetic pulse welding, and electro-spark deposition joining. Five materials were used in these experiments: Mo-47Re, T-111, Hastelloy X, Mar M-247 (coarse-grained, 0.5 mm to several millimeter average grain size), and Mar M-247 (fine-grained, approximately 50 {micro}m average grain size). Several iterative trials of each material combination with each joining method were performed to determine the best practice joining method. Mo-47Re was found to be joined easily to Hastelloy X via inertia welding, but inertia welding of the Mo-alloy to both Mar M-247 alloys resulted in inconsistent joint strength and large reaction layers between the two metals. T-111 was found to join well to Hastelloy X and coarse-grained Mar M-247 via inertia welding, but joining to fine-grained Mar M-247 resulted in low joint strength. Magnetic pulse welding (MPW) was only successful in joining T-111 tubing to Hastelloy X bar stock. The joint integrity and reaction layer between the metals were found to be acceptable. This single joining trial, however, caused damage to the electromagnetic concentrators used in this process. Subsequent design efforts to eliminate the problem resulted in a loss of power imparted to the accelerating work piece, and results could not be reproduced. Welding trials of Mar M-247 to T-111 resulted in catastrophic failure of the bar stock, even at lower power. Electro-spark deposition joining of Mo-47Re, in which the deposited material was Hastelloy X, did not have a

Summary of Dissimilar Metal Joining Trials Conducted by Edison Welding Institute

International Nuclear Information System (INIS)

MJ Lambert

2005-01-01

Under the direction of the NASA-Glenn Research Center, the Edison Welding Institute (EWI) in Columbus, OH performed a series of non-fusion joining experiments to determine the feasibility of joining refractory metals or refractory metal alloys to Ni-based superalloys. Results, as reported by EWI, can be found in the project report for EWI Project 48819GTH (Attachment A, at the end of this document), dated October 10, 2005. The three joining methods used in this investigation were inertia welding, magnetic pulse welding, and electro-spark deposition joining. Five materials were used in these experiments: Mo-47Re, T-111, Hastelloy X, Mar M-247 (coarse-grained, 0.5 mm to several millimeter average grain size), and Mar M-247 (fine-grained, approximately 50 (micro)m average grain size). Several iterative trials of each material combination with each joining method were performed to determine the best practice joining method. Mo-47Re was found to be joined easily to Hastelloy X via inertia welding, but inertia welding of the Mo-alloy to both Mar M-247 alloys resulted in inconsistent joint strength and large reaction layers between the two metals. T-111 was found to join well to Hastelloy X and coarse-grained Mar M-247 via inertia welding, but joining to fine-grained Mar M-247 resulted in low joint strength. Magnetic pulse welding (MPW) was only successful in joining T-111 tubing to Hastelloy X bar stock. The joint integrity and reaction layer between the metals were found to be acceptable. This single joining trial, however, caused damage to the electromagnetic concentrators used in this process. Subsequent design efforts to eliminate the problem resulted in a loss of power imparted to the accelerating work piece, and results could not be reproduced. Welding trials of Mar M-247 to T-111 resulted in catastrophic failure of the bar stock, even at lower power. Electro-spark deposition joining of Mo-47Re, in which the deposited material was Hastelloy X, did not have a

Microwave-assisted Synthesis of an Important Intermediate of Benazepril

Science.gov (United States)

Mistry, B; Medhane, Dipti; Mohanraj, Krishnapriya; Ghone, Sanjeevani A.

2010-01-01

Rapid and efficient methods for the synthesis of an important intermediate of benazepril ethyl 3-phthalimido-2,3,4,5-tetrahydro-1H-[1]benzazepin-2-one-1-acetate under the influence of microwave irradiation are described. A comparative study of conventional and microwave assisted method is briefly discussed. PMID:21188052

Non-binary Entanglement-assisted Stabilizer Quantum Codes

OpenAIRE

Riguang, Leng; Zhi, Ma

2011-01-01

In this paper, we show how to construct non-binary entanglement-assisted stabilizer quantum codes by using pre-shared entanglement between the sender and receiver. We also give an algorithm to determine the circuit for non-binary entanglement-assisted stabilizer quantum codes and some illustrated examples. The codes we constructed do not require the dual-containing constraint, and many non-binary classical codes, like non-binary LDPC codes, which do not satisfy the condition, can be used to c...

Synthesis and phase behavior of end-functionalized associating polymers

Science.gov (United States)

Wrue, Michelle H.

We have explored polymer blend phase behavior in the presence of multiple hydrogen bonding end-groups. This work details the synthesis of functionalized polymers and their subsequent use in miscibility studies. The synthesis of end-functionalized hydrogen bonding polymers and the investigation of their physical properties and miscibility is presented. Mono-functional and telechelic ureidopyrimidinone (UPy) functionalized polymers were prepared by two main routes: post-polymerization functionalization (of commercially available or synthesized polymers); and polymerization of monomers using a functionalized initiator. UPy-functionalized polymers were prepared with a variety of polymer backbones including poly(ethylene oxide)s; poly(butadiene)s, poly(dimethyl siloxanxe)s; poly(styrene)s and poly(methyl methacrylate)s. The most successful route to polymers with UPy end-groups was atom transfer radical polymerization (ATRP) using a UPy-functionalized initiator, followed by atom transfer radical coupling (ATRC). The incorporation of ureidopyrimidinone end-groups was shown to affect the physical properties of the polymer backbone. Parent polymers that were liquids became viscous liquids or waxy solids upon UPy-functionalization of chain end. UPy-functionalization of a hydroxyl-terminated polybutadiene (HO-PB-OH) resulted in a waxy solid while the HO-PB-OH precursor was a viscous liquid. The thermal properties of functionalized polymers also differed from those of the unfunctionalized parent polymers. Hot-stage optical microscopy revealed that UPy-functionalized PEO displayed a depressed melting point relative to the analogous unfunctionalized precursor. Differential scanning calorimetry was also used to investigate the synthesized UPy-polymers. UPy-functionalized polystyrenes and poly(methyl methacrylate)s showed an increased T g compared to the equivalent homopolymer standards. This increased Tg was determined to be dependent upon the fraction of UPy groups present and

Transcriptional transitions in Nicotiana benthamiana leaves upon induction of oil synthesis by WRINKLED1 homologs from diverse species and tissues.

Science.gov (United States)

Grimberg, Åsa; Carlsson, Anders S; Marttila, Salla; Bhalerao, Rishikesh; Hofvander, Per

2015-08-08

Carbon accumulation and remobilization are essential mechanisms in plants to ensure energy transfer between plant tissues with different functions or metabolic needs and to support new generations. Knowledge about the regulation of carbon allocation into oil (triacylglycerol) in plant storage tissue can be of great economic and environmental importance for developing new high-yielding oil crops. Here, the effect on global gene expression as well as on physiological changes in leaves transiently expressing five homologs of the transcription factor WRINKLED1 (WRI1) originating from diverse species and tissues; Arabidopsis thaliana and potato (Solanum tuberosum) seed embryo, poplar (Populus trichocarpa) stem cambium, oat (Avena sativa) grain endosperm, and nutsedge (Cyperus esculentus) tuber parenchyma, were studied by agroinfiltration in Nicotiana benthamiana. All WRI1 homologs induced oil accumulation when expressed in leaf tissue. Transcriptome sequencing revealed that all homologs induced the same general patterns with a drastic shift in gene expression profiles of leaves from that of a typical source tissue to a source-limited sink-like tissue: Transcripts encoding enzymes for plastid uptake and metabolism of phosphoenolpyruvate, fatty acid and oil biosynthesis were up-regulated, as were also transcripts encoding starch degradation. Transcripts encoding enzymes in photosynthesis and starch synthesis were instead down-regulated. Moreover, transcripts representing fatty acid degradation were up-regulated indicating that fatty acids might be degraded to feed the increased need to channel carbons into fatty acid synthesis creating a futile cycle. RT-qPCR analysis of leaves expressing Arabidopsis WRI1 showed the temporal trends of transcripts selected as 'markers' for key metabolic pathways one to five days after agroinfiltration. Chlorophyll fluorescence measurements of leaves expressing Arabidopsis WRI1 showed a significant decrease in photosynthesis, even though

Recent developments on ultrasound-assisted organic synthesis in aqueous medium

Directory of Open Access Journals (Sweden)

Banerjee Bubun

2017-01-01

Full Text Available In the recent past, a number of methods were reported on the application of ultrasound in organic reactions for the synthesis of diverse organic scaffolds. On the other hand, as far as green chemistry is concerned, water is the safest of all solvents. Thus, a “strong collaboration” between ultrasonic irradiation and aqueous medium holds the key to the development of an environmentally sustainable protocol. The present review summarizes the latest developments in ultrasound-assisted and water-mediated organic synthesis reported to date.

[End-of-life care and end-of-life medical decisions: the ITAELD study].

Science.gov (United States)

Miccinesi, Guido; Puliti, Donella; Paci, Eugenio

2011-01-01

To describe the attitudes towards end of life care and the practice of end-of-life medical decisions with possible life-shortening effect among Italian physicians. Cross sectional study (last death among the assisted patients in the last 12 months was considered). In the year 2007, 5,710 GPs and 8,950 hospital physicians were invited all over Italy to participate in the ITAELDstudy through anonymous mail questionnaire. Proportion of agreement with statements on end-of-life care issues. Proportion of deaths with an end-of-life medical decision. The response rate was 19.2%. The 65% of respondents agreed with the duty to respect any non-treatment request of the competent patient, the 55% agreed with the same duty in case of advanced directives, the 39% in case of proxy's request. The 53% of respondents agreed with the ethical acceptability of active euthanasia in selected cases. Among 1,850 deaths the 57.7% did not receive any end-of-life medical decision. For a further 21.0% no decision was possible, being sudden and unexpected deaths. In the remaining 21.3% at least one end-of-life medical decision was reported: 0.8% was classified as physician assisted death, 20.5% as non-treatment decision. Among all deceased the 19.6% were reported to have been deeply sedated. Being favourable to the use of opioids in terminal patients was associated to non-treatment decisions with possible but non-intentional life shortening effect; agreeing with the duty to fully respect any actual non-treatment request of the competent patient was associated to end-of life medical decisions with intentional life-shortening effect (adjusted OR>10 in both cases). The life stance and ethical beliefs of physicians determine their behaviour at the end of life wherever specific statements of law are lacking. Therefore education and debate are needed on these issues.

Joining of Aluminium Alloy and Steel by Laser Assisted Reactive Wetting

Science.gov (United States)

Liedl, Gerhard; Vázquez, Rodrigo Gómez; Murzin, Serguei P.

2018-03-01

Compounds of dissimilar materials, like aluminium and steel offer an interesting opportunity for the automotive industry to reduce the weight of a car body. Thermal joining of aluminium and steel leads to the formation of brittle intermetallic compounds, which negatively affects the properties of the welded joint. Amongst others, growth of such intermetallic compounds depends on maximum temperature and on the time at certain temperatures. Laser welding with its narrow well seam and its fast heating and cooling cycles provides an excellent opportunity to obtain an ultrathin diffusion zone. Joining of sheet metal DC01 with aluminium alloy AW6016 has been chosen for research. The performed experimental studies showed that by a variation of the beam power and scanning speed it is possible to obtain an ultrathin diffusion zone with narrow intermetallic interlayers. With the aim of supporting further investigation of laser welding of the respective and other dissimilar pairings a multi-physical simulation model has been developed.

What information do parents need when facing end-of-life decisions for their child? A meta-synthesis of parental feedback.

Science.gov (United States)

Xafis, Vicki; Wilkinson, Dominic; Sullivan, Jane

2015-04-30

The information needs of parents facing end-of-life decisions for their child are complex due to the wide-ranging dimensions within which such significant events unfold. While parents acknowledge that healthcare professionals are their main source of information, they also turn to a variety of additional sources of written information in an attempt to source facts, discover solutions, and find hope. Much has been written about the needs of parents faced with end-of-life decisions for their child but little is known about the written information needs such parents have. Research in the adult intensive care context has shown that written resources impact positively on the understanding of medical facts, including diagnoses and prognoses, communication between families and healthcare professionals, and the emotional wellbeing of families after their relative's death. A meta-synthesis of predominantly empirical research pertaining to features which assist or impede parental end-of-life decisions was undertaken to provide insight and guidance in our development of written resources (short print and online comprehensive version) for parents. The most prominently cited needs in the literature related to numerous aspects of information provision; the quantity, quality, delivery, and timing of information and its provision impacted not only on parents' ability to make end-of-life decisions but also on their emotional wellbeing. The meta-synthesis supports the value of written materials, as these provide guidance for both parents and healthcare professionals in pertinent content areas. Further research is required to determine the impact that written resources have on parental end-of-life decision-making and on parents' wellbeing during and after their experience and time in the hospital environment.

How Can an Emergency Department Assist Patients and Caregivers at the End of Life?

Science.gov (United States)

... And Caregivers At The End Of Life? How Can An Emergency Department Assist Patients And Caregivers At ... your family. Five ways that the Emergency Department can help 1. Assist in the recognition and understanding ...

DEXTROSE-TEMPLATED MICROWAVE-ASSISTED COMBUSTION SYNTHESIS OF SPONGY METAL OXIDES

Science.gov (United States)

Microwave-assisted combustion synthesis of porous nanocrystalline titania and carbon coated titania is reported using dextrose as template and the product was compared with the one obtained using conventional heating furnace. Out of three compositions viz., 1:1, 1:3, and 1:5 (met...

Precision Joining Center

Science.gov (United States)

Powell, J. W.; Westphal, D. A.

1991-08-01

A workshop to obtain input from industry on the establishment of the Precision Joining Center (PJC) was held on July 10-12, 1991. The PJC is a center for training Joining Technologists in advanced joining techniques and concepts in order to promote the competitiveness of U.S. industry. The center will be established as part of the DOE Defense Programs Technology Commercialization Initiative, and operated by EG&G Rocky Flats in cooperation with the American Welding Society and the Colorado School of Mines Center for Welding and Joining Research. The overall objectives of the workshop were to validate the need for a Joining Technologists to fill the gap between the welding operator and the welding engineer, and to assure that the PJC will train individuals to satisfy that need. The consensus of the workshop participants was that the Joining Technologist is a necessary position in industry, and is currently used, with some variation, by many companies. It was agreed that the PJC core curriculum, as presented, would produce a Joining Technologist of value to industries that use precision joining techniques. The advantage of the PJC would be to train the Joining Technologist much more quickly and more completely. The proposed emphasis of the PJC curriculum on equipment intensive and hands-on training was judged to be essential.

Development of joining techniques for fabrication of fuel rod simulators

International Nuclear Information System (INIS)

Moorhead, A.J.; McCulloch, R.W.; Reed, R.W.; Woodhouse, J.J.

1980-10-01

Much of the safety-related thermal-hydraulic tests on nuclear reactors are conducted not in the reactor itself, but in mockup segments of a core that uses resistance-heated fuel rod simulators (FRS) in place of the radioactive fuel rods. Laser welding and furnace brazing techniques are described for joining subassemblies for FRS that have survived up to 1000 h steady-state operation at 700 to 1100 0 C cladding temperatures and over 5000 thermal transients, ranging from 10 to 100 0 C/s. A pulsed-laser welding procedure that includes use of small-diameter filler wire is used to join one end of a resistance heating element of Pt-8 W, Fe-22 Cr-5.5 Al-0.5 Co, or 80 Ni-20 Cr (wt %) to a tubular conductor of an appropriate intermediate material. The other end of the heating element is laser welded to an end plug, which in turn is welded to a central conductor rod

Synthesis of yttrium oxide nanoparticles via a facile microplasma-assisted process

NARCIS (Netherlands)

Lin, Liangliang; Starostin, Sergey A.; Li, Sirui; Khan, Saif A.; Hessel, Volker

2018-01-01

Plasma electrochemistry is an emerging technique for nanomaterial synthesis. The present study reports the preparation of yttrium oxide nanoparticles via a simple, environmentally benign, microplasma-assisted process operated in pin-to-liquid configuration under ambient atmospheric conditions using

Electrochemically Active Biofilms Assisted Nanomaterial Synthesis for Environmental Applications

KAUST Repository

Ahmed, Elaf

2017-12-01

Nanomaterials have a great potential for environmental applications due to their high surface areas and high reactivity. This dissertation investigated the use of electrochemically active biofilms (EABs) as a synthesis approach for the fabrication and environmental applications of different nanomaterials. Bacteria in EABs generate electrons upon consuming electron donor and have the ability to transport these electrons to solid or insoluble substrates through extracellular electron transport (EET) mechanism. The extracellularly transported electrons, once utilized, can lead to nanoparticle synthesis. In this dissertation, noble metal (i.e., Au, Pd, and Pt) ultra-small nanoparticles (USNPs) were first synthesized with the assistance by the EABs. The assynthesized USNPs had a size range between 2 and 7 nm and exhibited excellent catalytic performance in dye decomposition. Also in this research, a two-dimensional (2D) cobalt nanosheet was successfully synthesized in the presence of EABs. A simple biogenic route led to the transformation of cobalt acetate to produce a green, toxic free homogeneous 2D cobalt nanosheet structure. Further, TiO2 nanotubes were successfully combined with the noble metal USNPs to enhance their photocatalytic activity. In this work, for the first time, the noble metal USNPs were directly reduced and decorated on the internal surfaces of the TiO2 nanotubes structure assisted by the EABs. The USNPs modified TiO2 nanotubes generated significantly improved photoelectrocatatlyic performances. This dissertation shines lights on the use of EABs in ultra-small nanoparticle synthesis.

Synthesis of some labelled non-proteinogenic amino acids

International Nuclear Information System (INIS)

Adrianens, P.; Vanderhaeghe, H.

1987-01-01

The literature on the synthesis of labeled non-proteinogenic amino acids contains approximately 300 papers, whereas syntheses of labeled proteinogenic amino acids are dealt with in some 800-1000 publications. However, most of the methods described in this paper for the synthesis of non-proteinogenic amino acids are also used for the preparation of the essential amino acids addition, the first category also contains β, γ...amino acids, seleno amino acids, N-methyl and α-methyl amino acids and sometimes have atoms or groups which are not present in the protein building blocks. Furthermore the latter group is more easily available so that methods for synthesis of non-proteinogenic amino acids are more needed

Gelatine-assisted synthesis of magnetite nanoparticles for magnetic hyperthermia

Energy Technology Data Exchange (ETDEWEB)

Alves, André F.; Mendo, Sofia G. [Universidade de Lisboa, Centro de Química e Bioquímica, Faculdade de Ciências (Portugal); Ferreira, Liliana P. [Universidade de Lisboa, Biosystems and Integrative Sciences Institute, Faculdade de Ciências (Portugal); Mendonça, Maria Helena [Universidade de Lisboa, Centro de Química e Bioquímica, Faculdade de Ciências (Portugal); Ferreira, Paula [University of Aveiro, Department of Materials and Ceramic Engineering, CICECO - Aveiro Institute of Materials (Portugal); Godinho, Margarida; Cruz, Maria Margarida [Universidade de Lisboa, Biosystems and Integrative Sciences Institute, Faculdade de Ciências (Portugal); Carvalho, Maria Deus, E-mail: mdcarvalho@ciencias.ulisboa.pt [Universidade de Lisboa, Centro de Química e Bioquímica, Faculdade de Ciências (Portugal)

2016-01-15

Magnetite nanoparticles were synthesized by the co-precipitation method exploring the use of gelatine and agar as additives. For comparison, magnetite nanoparticles were also prepared by standard co-precipitation, by co-precipitation with the addition of a surfactant (sodium dodecyl sulphate) and by the thermal decomposition method. The structure and morphology of the synthesized nanoparticles were investigated by powder X-ray diffraction and transmission electron microscopy. Their magnetic properties were studied by SQUID magnetometry and {sup 57}Fe Mössbauer spectroscopy. The nanoparticles potential for applications in magnetic hyperthermia was evaluated through heating efficiency under alternating magnetic field. The results show that all synthesis methods produce Fe{sub 3−x}O{sub 4} nanoparticles with similar sizes. The nanoparticles synthesized in the gelatine medium display the narrowest particle size distribution, the lowest oxidation degree, one of the highest saturation magnetization values and the best hyperthermia efficiency, proving that this gelatine-assisted synthesis is an efficient, environmental friendly, and low-cost method to produce magnetite nanoparticles. Graphical Abstract: A new gelatine-assisted method is an efficient and low-cost way to synthesize magnetite nanoparticles with enhanced magnetic hyperthermia.

Evolutionary synthesis of optimum light ends recovery unit with exergy analysis application

International Nuclear Information System (INIS)

Khalili-Garakani, Amirhossein; Ivakpour, Javad; Kasiri, Norollah

2016-01-01

Highlights: • Presenting an evolutionary synthesis algorithm. • Reducing configuration nominees based on exergy loss diagram of distillation columns. • Reduction of search space without decreasing the comprehensiveness and precision of the synthesis algorithm. • Rigorous simulation and optimization of sequences. - Abstract: Exergy analysis proved to be important in understanding of regions with poor energy efficiency and improve the design of distillation processes. In this study a new method based on exergy analysis is developed for the synthesis of a light ends recovery unit. The algorithm is some kinds of evolutionary one which employ total exergy loss diagrams of distillation columns for limiting the search space and reducing configuration nominees. The new method presented here for the light end separation unit, applies exergy loss diagrams as a powerful tool in locating the weak spot in the distillation columns of the Brugma sequence (as a first guess) and change the structure of the sequence step by step to achieve the best sequence. The results show that the new method could reduce the amount of calculations between 16% and 55% of the cases considered in this case study. The reduction of the search space takes place without decreasing the comprehensiveness and precision of the synthesis algorithm. Besides the amount of reduction in total annual cost and exergy loss of the optimum sequence is considerable.

Non-governmental organizations assisting victims of crime in Belgrade: Survey results

Directory of Open Access Journals (Sweden)

Milivojević Sanja K.

2003-01-01

Full Text Available This paper presents the results of survey regarding non-governmental organizations assisting victims of crime in Belgrade. The survey was completed at the end of 2002 for purposes of establishing a Victim Support Service in Serbia. In introduction authors give a short review of victim support services development in the World and the region, explaining the need for such service in Serbia, the subject and the aim of the article as well as the purpose of the survey. Second part of the paper contains the sample, methodology and the aim of the interview with NGO representatives. In the third section authors present the analysis of the survey data. Finally, in conclusion authors summarize the data and observed problems, suggestions for possible solution and directions of future development of services and organizations assisting victims of crime in Serbia.

Liver Receptor Homolog-1 Is Critical for Adequate Up-regulation of Cyp7a1 Gene Transcription and Bile Salt Synthesis During Bile Salt Sequestration

NARCIS (Netherlands)

Out, Carolien; Hageman, Jurre; Bloks, Vincent W.; Gerrits, Han; Gelpke, Maarten D. Sollewijn; Bos, Trijnie; Havinga, Rick; Smit, Martin J.; Kuipers, Folkert; Groen, Albert K.

Liver receptor homolog-1 (LRH-1) is a nuclear receptor that controls a variety of metabolic pathways. In cultured cells, LRH-1 induces the expression of CYP7A1 and CYP8B1, key enzymes in bile salt synthesis. However, hepatic Cyp7a1 mRNA levels were not reduced upon hepatocyte-specific Lrh-1 deletion

Non linear structures seismic analysis by modal synthesis

International Nuclear Information System (INIS)

Aita, S.; Brochard, D.; Guilbaud, D.; Gibert, R.J.

1987-01-01

The structures submitted to a seismic excitation, may present a great amplitude response which induces a non linear behaviour. These non linearities have an important influence on the response of the structure. Even in this case (local shocks) the modal synthesis method remains attractive. In this paper we will present the way of taking into account, a local non linearity (shock between structures) in the seismic response of structures, by using the modal synthesis method [fr

In vivo laser assisted end-to-end anastomosis with ICG-infused chitosan patches

Science.gov (United States)

Rossi, Francesca; Matteini, Paolo; Esposito, Giuseppe; Scerrati, Alba; Albanese, Alessio; Puca, Alfredo; Maira, Giulio; Rossi, Giacomo; Pini, Roberto

2011-07-01

Laser assisted vascular repair is a new optimized technique based on the use of ICG-infused chitosan patch to close a vessel wound, with or even without few supporting single stitches. We present an in vivo experimental study on an innovative end-to-end laser assisted vascular anastomotic (LAVA) technique, performed with the application of ICGinfused chitosan patches. The photostability and the mechanical properties of ICG-infused chitosan films were preliminary measured. The in vivo study was performed in 10 New Zealand rabbits. After anesthesia, a 3-cm segment of the right common carotid artery was exposed, thus clamped proximally and distally. The artery was then interrupted by means of a full thickness cut. Three single microsutures were used to approximate the two vessel edges. The ICG-infused chitosan patch was rolled all over the anastomotic site and welded by the use of a diode laser emitting at 810 nm and equipped with a 300 μm diameter optical fiber. Welding was obtained by delivering single laser spots to induce local patch/tissue adhesion. The result was an immediate closure of the anastomosis, with no bleeding at clamps release. Thus animals underwent different follow-up periods, in order to evaluate the welded vessels over time. At follow-up examinations, all the anastomoses were patent and no bleeding signs were documented. Samples of welded vessels underwent histological examinations. Results showed that this technique offer several advantages over conventional suturing methods: simplification of the surgical procedure, shortening of the operative time, better re-endothelization and optimal vascular healing process.

Isolation and expression of human cytokine synthesis inhibitory factor cDNA clones: Homology to Epstein-Barr virus open reading frame BCRFI

Energy Technology Data Exchange (ETDEWEB)

Vieira, P.; De Waal-Malefyt, R.; Dang, M.N.; Johnson, K.E.; Kastelein, R.; Fiorentino, D.F.; DeVries, J.E.; Roncarolo, M.G.; Mosmann, T.R.; Moore, K.W. (DNAX Research Inst. of Molecular and Cellular Biology, Palo Alto, CA (United States))

1991-02-15

The authors demonstrated the existence of human cytokine synthesis inhibitory factor (DSIF) (interleukin 10 (IL-10)). cDNA clones encoding human IL-10 (hIL-10) were isolated from a tetanus toxin-specific human T-cell clone. Like mouse IL-10, hIL-10 exhibits strong DNA and amino acid sequence homology to an open reading frame in the Epstein-Barr virus, BDRFL. hIL-10 and the BCRFI product inhibit cytokine synthesis by activated human peripheral blood mononuclear cells and by a mouse Th1 clone. Both hIL-10 and mouse IL-10 sustain the viability of a mouse mast cell line in culture, but BCRFI lacks comparable activity in this way, suggesting that BCRFI may have conserved only a subset of hIL-10 activities.

Isolation and expression of human cytokine synthesis inhibitory factor cDNA clones: Homology to Epstein-Barr virus open reading frame BCRFI

International Nuclear Information System (INIS)

Vieira, P.; De Waal-Malefyt, R.; Dang, M.N.; Johnson, K.E.; Kastelein, R.; Fiorentino, D.F.; DeVries, J.E.; Roncarolo, M.G.; Mosmann, T.R.; Moore, K.W.

1991-01-01

The authors demonstrated the existence of human cytokine synthesis inhibitory factor (DSIF) [interleukin 10 (IL-10)]. cDNA clones encoding human IL-10 (hIL-10) were isolated from a tetanus toxin-specific human T-cell clone. Like mouse IL-10, hIL-10 exhibits strong DNA and amino acid sequence homology to an open reading frame in the Epstein-Barr virus, BDRFL. hIL-10 and the BCRFI product inhibit cytokine synthesis by activated human peripheral blood mononuclear cells and by a mouse Th1 clone. Both hIL-10 and mouse IL-10 sustain the viability of a mouse mast cell line in culture, but BCRFI lacks comparable activity in this way, suggesting that BCRFI may have conserved only a subset of hIL-10 activities

DNA-binding determinants promoting NHEJ by human Polμ.

Science.gov (United States)

Martin, Maria Jose; Juarez, Raquel; Blanco, Luis

2012-12-01

Non-homologous end-joining (NHEJ), the preferred pathway to repair double-strand breaks (DSBs) in higher eukaryotes, relies on a collection of molecular tools to process the broken ends, including specific DNA polymerases. Among them, Polµ is unique as it can catalyze DNA synthesis upon connection of two non-complementary ends. Here, we demonstrate that this capacity is intrinsic to Polµ, not conferred by other NHEJ factors. To understand the molecular determinants of its specific function in NHEJ, the interaction of human Polµ with DNA has been directly visualized by electromobility shift assay and footprinting assays. Stable interaction with a DNA gap requires the presence of a recessive 5'-P, thus orienting the catalytic domain for primer and nucleotide binding. Accordingly, recognition of the 5'-P is crucial to align the two DNA substrates of the NHEJ reaction. Site-directed mutagenesis demonstrates the relevance of three specific residues (Lys(249), Arg(253) and Arg(416)) in stabilizing the primer strand during end synapsis, allowing a range of microhomology-induced distortions beneficial for NHEJ. Moreover, our results suggest that the Polµ BRCT domain, thought to be exclusively involved in interaction with NHEJ core factors, has a direct role in binding the DNA region neighbor to the 5'-P, thus boosting Polµ-mediated NHEJ reactions.

Synthesis of non-siliceous mesoporous oxides.

Science.gov (United States)

Gu, Dong; Schüth, Ferdi

2014-01-07

Mesoporous non-siliceous oxides have attracted great interest due to their unique properties and potential applications. Since the discovery of mesoporous silicates in 1990s, organic-inorganic assembly processes by using surfactants or block copolymers as soft templates have been considered as a feasible path for creating mesopores in metal oxides. However, the harsh sol-gel conditions and low thermal stabilities have limited the expansion of this method to various metal oxide species. Nanocasting, using ordered mesoporous silica or carbon as a hard template, has provided possibilities for preparing novel mesoporous materials with new structures, compositions and high thermal stabilities. This review concerns the synthesis, composition, and parameter control of mesoporous non-siliceous oxides. Four synthesis routes, i.e. soft-templating (surfactants or block copolymers as templates), hard-templating (mesoporous silicas or carbons as sacrificial templates), colloidal crystal templating (3-D ordered colloidal particles as a template), and super lattice routes, are summarized in this review. Mesoporous metal oxides with different compositions have different properties. Non-siliceous mesoporous oxides are comprehensively described, including a discussion of constituting elements, synthesis, and structures. General aspects concerning pore size control, atomic scale crystallinity, and phase control are also reviewed.

Bio-assisted synthesis and characterization of nanostructured bismuth (III) sulphide using Clostridium acetobutylicum

International Nuclear Information System (INIS)

Kamaraj, Sathish Kumar; Venkatachalam, Ganesh; Arumugam, Palaniappan; Berchmans, Sheela

2014-01-01

Nanostructured bismuth (III) sulphide is synthesized at room temperature using a hydrogen sulphide producing microorganism namely Clostridium acetobutylicum. On contrary to chemical routes involving both the high and room temperature methods, the present experimental procedure involves a bio-assisted approach. This method is free from the usage of toxic and hazardous chemicals making it an environment friendly route. The synthesized bismuth sulphide is characterized using transmission electron microscope (TEM), powder X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and cyclic voltammetry (CV). From our experiments we find that bismuth sulphide produced using this bio-assisted approach exhibits a hexagonal shaped plate-like structures and is stabilized by the extracellular proteins present in the culture medium. - Graphical abstract: A green chemistry approach towards the synthesis of bismuth (III) sulphide nanostructures at room temperature using a hydrogen sulphide producing microorganism namely, Clostridium acetobutylicum is demonstrated. - Highlights: • Environmentally benign (greener) route towards synthesis of Bi 2 S 3 nanostructures. • Bio-assisted synthesis of Bi 2 S 3 at room temperature using Clostridium acetobutylicum. • Extracellular proteins in H 2 S producing microorganism as stabilizer for Bi 2 S 3 NPs. • Hexagonal platelets of Bi 2 S 3 possessing an orthorhombic crystalline structure

Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination

Energy Technology Data Exchange (ETDEWEB)

Hoang, Margaret L.; Tan, Frederick J.; Lai, David C.; Celniker, Sue E.; Hoskins, Roger A.; Dunham, Maitreya J.; Zheng, Yixian; Koshland, Douglas

2010-08-27

Genome rearrangements often result from non-allelic homologous recombination (NAHR) between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs) induce NAHR-dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR) occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR-dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer.

Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination.

Directory of Open Access Journals (Sweden)

Margaret L Hoang

2010-12-01

Full Text Available Genome rearrangements often result from non-allelic homologous recombination (NAHR between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs induce NAHR-dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR-dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer.

Microwave-assisted synthesis and antioxidant properties of hydrazinyl thiazolyl coumarin derivatives

Directory of Open Access Journals (Sweden)

Osman Hasnah

2012-04-01

Full Text Available Abstract Background Coumarin derivatives exhibit a wide range of biological properties including promising antioxidant activity. Furthermore, microwave-assisted organic synthesis has delivered rapid routes to N- and O-containing heterocycles, including coumarins and thiazoles. Combining these features, the use of microwave-assisted processes will provide rapid access to a targeted coumarin library bearing a hydrazino pharmacophore for evaluation of antioxidant properties Results Microwave irradiation promoted 3 of the 4 steps in a rapid, convergent synthesis of a small library of hydrazinyl thiazolyl coumarin derivatives, all of which exhibited significant antioxidant activity comparable to that of the natural antioxidant quercetin, as established by DPPH and ABTS radical assays Conclusions Microwave dielectric heating provides a rapid and expedient route to a series of hydrazinyl thiazolyl coumarins to investigate their radical scavenging properties. Given their favourable properties, in comparison with known antioxidants, these coumarin derivatives are promising leads for further development and optimization.

Microwave Assisted Organic Synthesis of Heterocycles in Aqueous Media: Recent Advances in Medicinal Chemistry.

Science.gov (United States)

Frecentese, Francesco; Saccone, Irene; Caliendo, Giuseppe; Corvino, Angela; Fiorino, Ferdinando; Magli, Elisa; Perissutti, Elisa; Severino, Beatrice; Santagada, Vincenzo

2016-01-01

Green chemistry is a discipline of great interest in medicinal chemistry. It involves all fields of chemistry and it is based on the principle to conduct chemical reactions protecting the environment at the same time, through the use of chemical procedures able to avoid pollution. In this context, water as solvent is a good choice because it is abundant, nontoxic, non-caustic, and non-combustible. Even if microwave assisted organic reactions in conventional solvents have quickly progressed, in the recent years medicinal chemists have focused their attention to processes deemed not dangerous for the environment, using nanotechnology and greener solvents as water. Several reports of reaction optimizations and selectivities, demonstrating the capability of microwave to allow the obtaining of increased yields have been recently published using water as solvent. In this review, we selected the available knowledge related to microwave assisted organic synthesis in aqueous medium, furnishing examples of the newest strategies to obtain useful scaffolds and novel derivatives for medicinal chemistry purposes. The intention of this review is to demonstrate the exclusive ability of MAOS in water as solvent or as co-solvent. For this purpose we report here the most representative applications of MAOS using water as solvent, focusing on medicinal chemistry processes leading to interesting nitrogen containing heterocycles with potential pharmaceutical applications.

DNA ligase C1 mediates the LigD-independent nonhomologous end-joining pathway of Mycobacterium smegmatis.

Science.gov (United States)

Bhattarai, Hitesh; Gupta, Richa; Glickman, Michael S

2014-10-01

Nonhomologous end joining (NHEJ) is a recently described bacterial DNA double-strand break (DSB) repair pathway that has been best characterized for mycobacteria. NHEJ can religate transformed linear plasmids, repair ionizing radiation (IR)-induced DSBs in nonreplicating cells, and seal I-SceI-induced chromosomal DSBs. The core components of the mycobacterial NHEJ machinery are the DNA end binding protein Ku and the polyfunctional DNA ligase LigD. LigD has three autonomous enzymatic modules: ATP-dependent DNA ligase (LIG), DNA/RNA polymerase (POL), and 3' phosphoesterase (PE). Although genetic ablation of ku or ligD abolishes NHEJ and sensitizes nonreplicating cells to ionizing radiation, selective ablation of the ligase activity of LigD in vivo only mildly impairs NHEJ of linearized plasmids, indicating that an additional DNA ligase can support NHEJ. Additionally, the in vivo role of the POL and PE domains in NHEJ is unclear. Here we define a LigD ligase-independent NHEJ pathway in Mycobacterium smegmatis that requires the ATP-dependent DNA ligase LigC1 and the POL domain of LigD. Mycobacterium tuberculosis LigC can also support this backup NHEJ pathway. We also demonstrate that, although dispensable for efficient plasmid NHEJ, the activities of the POL and PE domains are required for repair of IR-induced DSBs in nonreplicating cells. These findings define the genetic requirements for a LigD-independent NHEJ pathway in mycobacteria and demonstrate that all enzymatic functions of the LigD protein participate in NHEJ in vivo. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

On (co)homology of Frobenius Poisson algebras

OpenAIRE

Zhu, Can; Van Oystaeyen, Fred; ZHANG, Yinhuo

2014-01-01

In this paper, we study Poisson (co)homology of a Frobenius Poisson algebra. More precisely, we show that there exists a duality between Poisson homology and Poisson cohomology of Frobenius Poisson algebras, similar to that between Hochschild homology and Hochschild cohomology of Frobenius algebras. Then we use the non-degenerate bilinear form on a unimodular Frobenius Poisson algebra to construct a Batalin-Vilkovisky structure on the Poisson cohomology ring making it into a Batalin-Vilkovisk...

Development of Joining Technologies for the ITER Blanket First Wall

Energy Technology Data Exchange (ETDEWEB)

Choi, Byoung Kwon; Jung, Yang Il; Park, Dong Jun; Kim, Hyun Gil; Park, Sang Yoon; Park, Jeong Yong; Jeong, Yong Hwan; Lee, Dong Won; Kim, Suk Kwon [KAERI, Daejeon (Korea, Republic of)

2011-01-15

The design of the ITER blanket first wall includes the Beryllium amour tiles joined to CuCrZr heat sink with stainless steel cooling tubes. For the ITER application, the Be/CuCrZr/SS joint was proposed as a first wall material. The joining of Be/CuCrZr as well as CuCrZr/SS was generally carried out by using a hot isostatic pressing (CuC) in many countries. The joining strength for Be/CuCrZr is relatively lower than that for CuCrZr/SS, since we usually forms surface oxides (BeO) and brittle a metallics with Cu. Therefore, the joining technology for the Be/CuCrZr joint has been investigated. Be is apt to adsorb oxygen in an air atmosphere, so we should be etched to eliminate the surface pre-oxide using a chemical solution and Ar ions in a vacuum chamber. Then we is coated with a first was to prevent further oxidation. The kinds of a first we are chosen to be able to enhance the joining strength as inhibiting excessive be diffusion. The performance of the Be/CuCrZr/SS joint used for the ITER first wall is primarily dependent on the joining strength of the Be/CuCrZr interface. The Cr/Cu and Ti/Cr/Cu interlayers enabled the successful joining of be tile to CuCrZr plate. Moreover, ion-beam assisted deposition (IBAD) increased joining strength of the Be/CuCrZr joint mock-ups. IBAD induced the increased packing of depositing atoms, which resulted in denser and more adhesive interlayers. The interlayers formed by IBAD process revealed about 40% improved resistance to the scratch test. It is suggested that the improved adhesion of coating interlayers enabled tight joining of Be and CuCrZr blocks. As compared to without IBAD coating, the shear strength as well as the 4-point bend strength were increased more than 20% depending on interlayer types and coating conditions

Development of Joining Technologies for the ITER Blanket First Wall

International Nuclear Information System (INIS)

Choi, Byoung Kwon; Jung, Yang Il; Park, Dong Jun; Kim, Hyun Gil; Park, Sang Yoon; Park, Jeong Yong; Jeong, Yong Hwan; Lee, Dong Won; Kim, Suk Kwon

2011-01-01

The design of the ITER blanket first wall includes the Beryllium amour tiles joined to CuCrZr heat sink with stainless steel cooling tubes. For the ITER application, the Be/CuCrZr/SS joint was proposed as a first wall material. The joining of Be/CuCrZr as well as CuCrZr/SS was generally carried out by using a hot isostatic pressing (CuC) in many countries. The joining strength for Be/CuCrZr is relatively lower than that for CuCrZr/SS, since we usually forms surface oxides (BeO) and brittle a metallics with Cu. Therefore, the joining technology for the Be/CuCrZr joint has been investigated. Be is apt to adsorb oxygen in an air atmosphere, so we should be etched to eliminate the surface pre-oxide using a chemical solution and Ar ions in a vacuum chamber. Then we is coated with a first was to prevent further oxidation. The kinds of a first we are chosen to be able to enhance the joining strength as inhibiting excessive be diffusion. The performance of the Be/CuCrZr/SS joint used for the ITER first wall is primarily dependent on the joining strength of the Be/CuCrZr interface. The Cr/Cu and Ti/Cr/Cu interlayers enabled the successful joining of be tile to CuCrZr plate. Moreover, ion-beam assisted deposition (IBAD) increased joining strength of the Be/CuCrZr joint mock-ups. IBAD induced the increased packing of depositing atoms, which resulted in denser and more adhesive interlayers. The interlayers formed by IBAD process revealed about 40% improved resistance to the scratch test. It is suggested that the improved adhesion of coating interlayers enabled tight joining of Be and CuCrZr blocks. As compared to without IBAD coating, the shear strength as well as the 4-point bend strength were increased more than 20% depending on interlayer types and coating conditions

Rapid synthesis of single-phase bismuth ferrite by microwave-assisted hydrothermal method

Energy Technology Data Exchange (ETDEWEB)

Cao, Wenqian [College of Materials Science and Engineering, China Jiliang University, 258 Xueyuan Street, Xiasha Higher Education District, Hangzhou 310018, Zhejiang Province (China); Chen, Zhi, E-mail: zchen0@gmail.com [College of Materials Science and Engineering, China Jiliang University, 258 Xueyuan Street, Xiasha Higher Education District, Hangzhou 310018, Zhejiang Province (China); Gao, Tong; Zhou, Dantong; Leng, Xiaonan; Niu, Feng [College of Materials Science and Engineering, China Jiliang University, 258 Xueyuan Street, Xiasha Higher Education District, Hangzhou 310018, Zhejiang Province (China); Zhu, Yuxiang [College of Materials Science and Engineering, China Jiliang University, 258 Xueyuan Street, Xiasha Higher Education District, Hangzhou 310018, Zhejiang Province (China); Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin (China); Qin, Laishun, E-mail: qinlaishun@yeah.net [College of Materials Science and Engineering, China Jiliang University, 258 Xueyuan Street, Xiasha Higher Education District, Hangzhou 310018, Zhejiang Province (China); Wang, Jiangying; Huang, Yuexiang [College of Materials Science and Engineering, China Jiliang University, 258 Xueyuan Street, Xiasha Higher Education District, Hangzhou 310018, Zhejiang Province (China)

2016-06-01

This paper describes on the fast synthesis of bismuth ferrite by the simple microwave-assisted hydrothermal method. The phase transformation and the preferred growth facets during the synthetic process have been investigated by X-ray diffraction. Bismuth ferrite can be quickly prepared by microwave hydrothermal method by simply controlling the reaction time, which is further confirmed by Fourier Transform infrared spectroscopy and magnetic measurement. - Graphical abstract: Single-phase BiFeO{sub 3} could be realized at a shortest reaction time of 65 min. The reaction time has strong influences on the phase transformation and the preferred growth facets. - Highlights: • Rapid synthesis (65 min) of BiFeO{sub 3} by microwave-assisted hydrothermal method. • Reaction time has influence on the purity and preferred growth facets. • FTIR and magnetic measurement further confirm the pure phase.

Rapid synthesis of single-phase bismuth ferrite by microwave-assisted hydrothermal method

International Nuclear Information System (INIS)

Cao, Wenqian; Chen, Zhi; Gao, Tong; Zhou, Dantong; Leng, Xiaonan; Niu, Feng; Zhu, Yuxiang; Qin, Laishun; Wang, Jiangying; Huang, Yuexiang

2016-01-01

This paper describes on the fast synthesis of bismuth ferrite by the simple microwave-assisted hydrothermal method. The phase transformation and the preferred growth facets during the synthetic process have been investigated by X-ray diffraction. Bismuth ferrite can be quickly prepared by microwave hydrothermal method by simply controlling the reaction time, which is further confirmed by Fourier Transform infrared spectroscopy and magnetic measurement. - Graphical abstract: Single-phase BiFeO_3 could be realized at a shortest reaction time of 65 min. The reaction time has strong influences on the phase transformation and the preferred growth facets. - Highlights: • Rapid synthesis (65 min) of BiFeO_3 by microwave-assisted hydrothermal method. • Reaction time has influence on the purity and preferred growth facets. • FTIR and magnetic measurement further confirm the pure phase.

Human Assisted Robotic Vehicle Studies - A conceptual end-to-end mission architecture

Science.gov (United States)

Lehner, B. A. E.; Mazzotta, D. G.; Teeney, L.; Spina, F.; Filosa, A.; Pou, A. Canals; Schlechten, J.; Campbell, S.; Soriano, P. López

2017-11-01

With current space exploration roadmaps indicating the Moon as a proving ground on the way to human exploration of Mars, it is clear that human-robotic partnerships will play a key role for successful future human space missions. This paper details a conceptual end-to-end architecture for an exploration mission in cis-lunar space with a focus on human-robot interactions, called Human Assisted Robotic Vehicle Studies (HARVeSt). HARVeSt will build on knowledge of plant growth in space gained from experiments on-board the ISS and test the first growth of plants on the Moon. A planned deep space habitat will be utilised as the base of operations for human-robotic elements of the mission. The mission will serve as a technology demonstrator not only for autonomous tele-operations in cis-lunar space but also for key enabling technologies for future human surface missions. The successful approach of the ISS will be built on in this mission with international cooperation. Mission assets such as a modular rover will allow for an extendable mission and to scout and prepare the area for the start of an international Moon Village.

Homology of genes for exopolysaccharide synthesis in Rhizobium leguminosarum and effect of cloned exo genes on nodule formation

International Nuclear Information System (INIS)

Skorupska, A.; Derylo, M.

1993-01-01

A 5.4 kb BamHI fragment of Rhizobium leguminosarum (R.l.) bv. trifolii TA1 was found to carry genes involved in exopolysaccharide synthesis (exo genes). This fragment was strongly hybridized to the total DNA from DNA from R.l. bv. viciae and bv. phaseoli digested with EcoRI. No homology was found with total DNA of R. melilotic and Rhizobium sp. NGR 234. The exo genes R.l. bv. trifolii TA1 conjugally introduced into R.l. bv. viciae 1302 considerably affected the symbiosis: the nodules induced on vetch were abortive and did not fix nitrogen. On the other hand, Phaseolus beans infected with R.l. bv. trifolii exo genes formed the nitrogen-fixing nodules. It can be conduced that additional copies of exo genes introduced into wild type R.l. strains can disturb the synthesis of acidic exopolysaccharides and affect symbiosis of the plants forming indeterminate nodules, but do not affect symbiosis of the plants forming the determinate nodules. (author). 29 refs, 2 figs, 2 tabs

The ethylene glycol template assisted hydrothermal synthesis of Co{sub 3}O{sub 4} nanowires; structural characterization and their application as glucose non-enzymatic sensor

Energy Technology Data Exchange (ETDEWEB)

Khun, K., E-mail: kimleang.khun@liu.se [Department of Science and Technology, Linköping University, SE-60174 Norrköping (Sweden); Ibupoto, Z.H. [Dr M.A. Kazi Institute of Chemistry, University of Sindh Jamshoro, Sindh Jamshoro (Pakistan); Liu, X. [Department of Physics, Chemistry and Biology, Linköping University, 58183 Linköping (Sweden); Beni, V. [Biosensors and Biolelectronics Centre, Department of Physics, Chemistry and Biology, Linköping University, 58183 Linköping (Sweden); Willander, M. [Department of Science and Technology, Linköping University, SE-60174 Norrköping (Sweden)

2015-04-15

Highlights: • Ethylene glycol assisted Co{sub 3}O{sub 4} nanowires were synthesized by hydrothermal method. • The grown Co{sub 3}O{sub 4} nanowires were used for sensitive non-enzymatic glucose sensor. • The proposed glucose sensor shows a wide linear range with fast response. • The Co{sub 3}O{sub 4} modified electrode is a highly specific enzyme-less glucose sensor. - Abstract: In the work reported herein the ethylene glycol template assisted hydrothermal synthesis, onto Au substrate, of thin and highly dense cobalt oxide (Co{sub 3}O{sub 4}) nanowires and their characterization and their application for non-enzymatic glucose sensing are reported. The structure and composition of Co{sub 3}O{sub 4} nanowires have been fully characterized using scanning electron microscopy, X-ray diffraction, high resolution transmission electron microscopy and X-ray photoelectron spectroscopy. The synthesized Co{sub 3}O{sub 4} nanowires resulted to have high purity and showed diameter of approximately 10 nm. The prepared Co{sub 3}O{sub 4} nanowires coated gold electrodes were applied to the non-enzymatic detection of glucose. The developed sensor showed high sensitivity (4.58 × 10{sup 1} μA mM{sup −1} cm{sup −2}), a wide linear range of concentration (1.00 × 10{sup −4}–1.2 × 10{sup 1} mM) and a detection limit of 2.65 × 10{sup −5} mM. The developed glucose sensor has also shown to be very stable and selective over interferents such as uric acid and ascorbic acid. Furthermore, the proposed fabrication process was shown to be highly reproducible response (over nine electrodes)

Laser beam joining of non-oxidic ceramics for ultra high temperature resistant joints

International Nuclear Information System (INIS)

Lippmann, W.; Knorr, J.; Wolf, R.; Reinecke, A.M.; Rasper, R.

2004-01-01

The excellent technical properties of silicon carbide (SiC) and silicon nitride (Si 3 N 4 ) ceramics, such as resistance to extreme temperatures, oxidation, mechanical wear, aggressive chemical substances and radioactive radiation and also its high thermal conductivity and good temperature-shock resistance, make these ceramics ideally suited for use in the field of nuclear technology. However, their practical use has been limited so far because of the unavailability of effective joining techniques for these ceramics, especially for high temperature applications. A new joining technology (CERALINK registered ) has been developed in a network project which allowed high temperature resistant and vacuum-tight joining of SiC or Si 3 N 4 ceramics. A power laser is used as heat source, which makes it possible to join ceramic components in free atmosphere in combination with a pure oxidic braze filler. As no furnace is necessary, there are no limitations on the component dimensions by the furnace-geometry. During the joining process, the heated area can be limited to the seam area so that this technology can also be used to encapsulate materials with a low melting point. The seam has a high mechanical strength, it is resistant to a wide range of chemicals and radiation and it is also vacuum-tight. The temperature resistance can be varied by variation of the braze filler composition - usually between 1,400 C and >1,600 C. Beside the optimum filler it is also important to select the suitable laser wavelength. The paper will demonstrate the influence of different wave lengths, i. e. various laser types, on the seam quality. Examples are chosen to illustrate the strengths and limitations of the new technology

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. © 2014 The Authors. Cancer Science published by Wiley Publishing Asia Pty Ltd on behalf of Japanese Cancer Association.

A local homology theory for linearly compact modules

International Nuclear Information System (INIS)

Nguyen Tu Cuong; Tran Tuan Nam

2004-11-01

We introduce a local homology theory for linearly modules which is in some sense dual to the local cohomology theory of A. Grothendieck. Some basic properties of local homology modules are shown such as: the vanishing and non-vanishing, the noetherianness of local homology modules. By using duality, we extend some well-known results in theory of local cohomology of A. Grothendieck. (author)

Fast and scalable inequality joins

KAUST Repository

Khayyat, Zuhair

2016-09-07

Inequality joins, which is to join relations with inequality conditions, are used in various applications. Optimizing joins has been the subject of intensive research ranging from efficient join algorithms such as sort-merge join, to the use of efficient indices such as (Formula presented.)-tree, (Formula presented.)-tree and Bitmap. However, inequality joins have received little attention and queries containing such joins are notably very slow. In this paper, we introduce fast inequality join algorithms based on sorted arrays and space-efficient bit-arrays. We further introduce a simple method to estimate the selectivity of inequality joins which is then used to optimize multiple predicate queries and multi-way joins. Moreover, we study an incremental inequality join algorithm to handle scenarios where data keeps changing. We have implemented a centralized version of these algorithms on top of PostgreSQL, a distributed version on top of Spark SQL, and an existing data cleaning system, Nadeef. By comparing our algorithms against well-known optimization techniques for inequality joins, we show our solution is more scalable and several orders of magnitude faster. © 2016 Springer-Verlag Berlin Heidelberg

C-terminal low-complexity sequence repeats of Mycobacterium smegmatis Ku modulate DNA binding.

Science.gov (United States)

Kushwaha, Ambuj K; Grove, Anne

2013-01-24

Ku protein is an integral component of the NHEJ (non-homologous end-joining) pathway of DSB (double-strand break) repair. Both eukaryotic and prokaryotic Ku homologues have been characterized and shown to bind DNA ends. A unique feature of Mycobacterium smegmatis Ku is its basic C-terminal tail that contains several lysine-rich low-complexity PAKKA repeats that are absent from homologues encoded by obligate parasitic mycobacteria. Such PAKKA repeats are also characteristic of mycobacterial Hlp (histone-like protein) for which they have been shown to confer the ability to appose DNA ends. Unexpectedly, removal of the lysine-rich extension enhances DNA-binding affinity, but an interaction between DNA and the PAKKA repeats is indicated by the observation that only full-length Ku forms multiple complexes with a short stem-loop-containing DNA previously designed to accommodate only one Ku dimer. The C-terminal extension promotes DNA end-joining by T4 DNA ligase, suggesting that the PAKKA repeats also contribute to efficient end-joining. We suggest that low-complexity lysine-rich sequences have evolved repeatedly to modulate the function of unrelated DNA-binding proteins.

The Ku80 Carboxy Terminus Stimulates Joining and Artemis-Mediated Processing of DNA Ends▿

Science.gov (United States)

Weterings, Eric; Verkaik, Nicole S.; Keijzers, Guido; Florea, Bogdan I.; Wang, Shih-Ya; Ortega, Laura G.; Uematsu, Naoya; Chen, David J.; van Gent, Dik C.

2009-01-01

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-PKCS) and the XRCC4/ligase IV complex. Activation of the DNA-PKCS serine/threonine kinase requires an interaction with Ku70/80 and is essential for NHEJ-mediated DSB repair. In contrast to previous models, we found that the carboxy terminus of Ku80 is not absolutely required for the recruitment and activation of DNA-PKCS at DSBs, although cells that harbored a carboxy-terminal deletion in the Ku80 gene were sensitive to ionizing radiation and showed reduced end-joining capacity. More detailed analysis of this repair defect showed that DNA-PKCS autophosphorylation at Thr2647 was diminished, while Ser2056 was phosphorylated to normal levels. This resulted in severely reduced levels of Artemis nuclease activity in vivo and in vitro. We therefore conclude that the Ku80 carboxy terminus is important to support DNA-PKCS autophosphorylation at specific sites, which facilitates DNA end processing by the Artemis endonuclease and the subsequent joining reaction. PMID:19103741

Comparative analysis of the practice of China and Russia joining the WTO

Directory of Open Access Journals (Sweden)

Anastasia Sergeyevna Loginova

2015-09-01

Full Text Available Objective to examine the positive and negative experience of China39s joining the World Trade Organization WTO that joined it on terms similar to the Russian ones for the best understanding of the advantages and disadvantages of joining and building the appropriate policy. Methods the objective of the work has been achieved through the application of both general and specific scientific methods. In particular the analysis and synthesis allowed to study the social and economic context of the state in the framework of joining the WTO the consequences of such membership and to identify the key areas for improvement of this step for Russia. Statistical techniques were used in the process of gathering information about the key economic indicators. The fundamental method was comparativelegal which made it possible to draw parallels in joining the WTO by various states. Results basing on the measures taken by China both before and after joining the WTO as well as evaluation of their implication the conclusion was made about its successful experience. The actions before joining were very effective. In particular they are applicable to the fields of agriculture automotive industry investment policy etc. The measures of nonaddress subsidizing maintaining the socioeconomic stability in the country the export orientation of the economy along with functioning of special economic zones with joint ventures are in the authors39 opinion constructive actions for Russiarsquos adaptation to the WTO. Scientific novelty for the first time the thesis is put forward about the similarity of the Russia and China conditions when joining the WTO. The analysis is made of the complex measures preceding and following the joining. The necessity is grounded of reflecting the China39s positive and negative experiences in the Russian policy. Practical significance the main provisions and conclusions can be used in the research activity in addressing the issues of Russiarsquos

RTEL1: an essential helicase for telomere maintenance and the regulation of homologous recombination.

Science.gov (United States)

Uringa, Evert-Jan; Youds, Jillian L; Lisaingo, Kathleen; Lansdorp, Peter M; Boulton, Simon J

2011-03-01

Telomere maintenance and DNA repair are crucial processes that protect the genome against instability. RTEL1, an essential iron-sulfur cluster-containing helicase, is a dominant factor that controls telomere length in mice and is required for telomere integrity. In addition, RTEL1 promotes synthesis-dependent strand annealing to direct DNA double-strand breaks into non-crossover outcomes during mitotic repair and in meiosis. Here, we review the role of RTEL1 in telomere maintenance and homologous recombination and discuss models linking RTEL1's enzymatic activity to its function in telomere maintenance and DNA repair.

An Adaptive Genetic Algorithm with Dynamic Population Size for Optimizing Join Queries

OpenAIRE

Vellev, Stoyan

2008-01-01

The problem of finding the optimal join ordering executing a query to a relational database management system is a combinatorial optimization problem, which makes deterministic exhaustive solution search unacceptable for queries with a great number of joined relations. In this work an adaptive genetic algorithm with dynamic population size is proposed for optimizing large join queries. The performance of the algorithm is compared with that of several classical non-determinis...

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

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...

Homologation Reaction of Ketones with Diazo Compounds.

Science.gov (United States)

Candeias, Nuno R; Paterna, Roberta; Gois, Pedro M P

2016-03-09

This review covers the addition of diazo compounds to ketones to afford homologated ketones, either in the presence or in the absence of promoters or catalysts. Reactions with diazoalkanes, aryldiazomethanes, trimethylsilyldiazomethane, α-diazo esters, and disubstituted diazo compounds are covered, commenting on the complex regiochemistry of the reaction and the nature of the catalysts and promoters. The recent reports on the enantioselective version of ketone homologation reactions are gathered in one section, followed by reports on the use of cyclic ketones ring expansion in total synthesis. Although the first reports of this reaction appeared in the literature almost one century ago, the recent achievements, in particular, for the asymmetric version, forecast the development of new breakthroughs in the synthetically valuable field of diazo chemistry.

Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.

Science.gov (United States)

Jamsen, Joonas A; Beard, William A; Pedersen, Lars C; Shock, David D; Moon, Andrea F; Krahn, Juno M; Bebenek, Katarzyna; Kunkel, Thomas A; Wilson, Samuel H

2017-08-15

DNA polymerase (pol) μ is a DNA-dependent polymerase that incorporates nucleotides during gap-filling synthesis in the non-homologous end-joining pathway of double-strand break repair. Here we report time-lapse X-ray crystallography snapshots of catalytic events during gap-filling DNA synthesis by pol μ. Unique catalytic intermediates and active site conformational changes that underlie catalysis are uncovered, and a transient third (product) metal ion is observed in the product state. The product manganese coordinates phosphate oxygens of the inserted nucleotide and PP i . The product metal is not observed during DNA synthesis in the presence of magnesium. Kinetic analyses indicate that manganese increases the rate constant for deoxynucleoside 5'-triphosphate insertion compared to magnesium. The likely product stabilization role of the manganese product metal in pol μ is discussed. These observations provide insight on structural attributes of this X-family double-strand break repair polymerase that impact its biological function in genome maintenance.DNA polymerase (pol) μ functions in DNA double-strand break repair. Here the authors use time-lapse X-ray crystallography to capture the states of pol µ during the conversion from pre-catalytic to product complex and observe a third transiently bound metal ion in the product state.

Synthesis of Mesoporous Nanocrystalline Zirconia by Surfactant-Assisted Hydrothermal Approach.

Science.gov (United States)

Nath, Soumav; Biswas, Ashik; Kour, Prachi P; Sarma, Loka S; Sur, Ujjal Kumar; Ankamwar, Balaprasad G

2018-08-01

In this paper, we have reported the chemical synthesis of thermally stable mesoporous nanocrystalline zirconia with high surface area using a surfactant-assisted hydrothermal approach. We have employed different type of surfactants such as CTAB, SDS and Triton X-100 in our synthesis. The synthesized nanocrystalline zirconia multistructures exhibit various morphologies such as rod, mortar-pestle with different particle sizes. We have characterized the zirconia multistructures by X-ray diffraction study, Field emission scanning electron microscopy, Attenuated total refection infrared spectroscopy, UV-Vis spectroscopy and photoluminescence spectroscopy. The thermal stability of as synthesized zirconia multistructures was studied by thermo gravimetric analysis, which shows the high thermal stability of nanocrystalline zirconia around 900 °C temperature.

Joining of parts via magnetic heating of metal aluminum powders

Science.gov (United States)

Baker, Ian

2013-05-21

A method of joining at least two parts includes steps of dispersing a joining material comprising a multi-phase magnetic metal-aluminum powder at an interface between the at least two parts to be joined and applying an alternating magnetic field (AMF). The AMF has a magnetic field strength and frequency suitable for inducing magnetic hysteresis losses in the metal-aluminum powder and is applied for a period that raises temperature of the metal-aluminum powder to an exothermic transformation temperature. At the exothermic transformation temperature, the metal-aluminum powder melts and resolidifies as a metal aluminide solid having a non-magnetic configuration.

Neurally adjusted ventilatory assist decreases ventilator-induced lung injury and non-pulmonary organ dysfunction in rabbits with acute lung injury

NARCIS (Netherlands)

Brander, Lukas; Sinderby, Christer; Lecomte, François; Leong-Poi, Howard; Bell, David; Beck, Jennifer; Tsoporis, James N.; Vaschetto, Rosanna; Schultz, Marcus J.; Parker, Thomas G.; Villar, Jesús; Zhang, Haibo; Slutsky, Arthur S.

2009-01-01

OBJECTIVE: To determine if neurally adjusted ventilatory assist (NAVA) that delivers pressure in proportion to diaphragm electrical activity is as protective to acutely injured lungs (ALI) and non-pulmonary organs as volume controlled (VC), low tidal volume (Vt), high positive end-expiratory

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.

Science.gov (United States)

Zhang, Chengxin; Zheng, Wei; Freddolino, Peter L; Zhang, Yang

2018-03-10

Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO, to deduce Gene Ontology attributes of proteins by combining sequence homology-based annotation with low-resolution structure prediction and comparison, and partner's homology-based protein-protein network mapping. The pipeline was tested on a large-scale set of 1000 non-redundant proteins from the CAFA3 experiment. Under the stringent benchmark conditions where templates with >30% sequence identity to the query are excluded, MetaGO achieves average F-measures of 0.487, 0.408, and 0.598, for Molecular Function, Biological Process, and Cellular Component, respectively, which are significantly higher than those achieved by other state-of-the-art function annotations methods. Detailed data analysis shows that the major advantage of the MetaGO lies in the new functional homolog detections from partner's homology-based network mapping and structure-based local and global structure alignments, the confidence scores of which can be optimally combined through logistic regression. These data demonstrate the power of using a hybrid model incorporating protein structure and interaction networks to deduce new functional insights beyond traditional sequence homology-based referrals, especially for proteins that lack homologous function templates. The MetaGO pipeline is available at http://zhanglab.ccmb.med.umich.edu/MetaGO/. Copyright © 2018. Published by Elsevier Ltd.

Dead Ends and Detours En Route to Total Syntheses of the 1990s A list of abbreviations can be found at the end of the article.

Science.gov (United States)

Sierra; de La Torre MC

2000-05-01

From the very beginning organic chemistry and total synthesis have been intimately joined. In fact, one of the first things that freshmen in organic chemistry learn is how to join two molecules together to obtain a more complex one. Of course they still have a long way to go to become fully mature synthetic chemists, but they must have the primary instinct to build molecules, as synthesis is the essence of organic chemistry. With the different points of view that actually coexist in the chemical community about the maturity of the science (art, or both) of organic synthesis, it is clear that nowadays we know how to make almost all of the most complex molecules ever isolated. The primary question is how easy is it to accomplish? For the readers of papers describing the total synthesis of either simple or complex molecules, it appears that the routes followed are, most of the time, smooth and free of troubles. The synthetic scheme written on paper is, apparently, done in the laboratory with few, if any, modifications and these, essentially, seem to be based on finding the optimal experimental conditions to effect the desired reaction. Failures in the planned synthetic scheme to achieve the goal, detours imposed by unexpected reactivity, or the absence of reactivity are almost never discussed, since they may diminish the value of the work reported. This review attempts to look at total synthesis from a different side; it will focus on troubles found during the synthetic work that cause detours from the original synthetic plan, or on the dead ends that eventually may force redesign. From there, the evolution from the original route to the final successful one that achieves the synthetic target will be presented. The syntheses discussed in this paper have been selected because they contain explicit information about the failures of the original synthetic plan, together with the evolution of the final route to the target molecule. Therefore, they contain a lot of useful

Ultrasound assisted two-stage biodiesel synthesis from non-edible Schleichera triguga oil using heterogeneous catalyst: Kinetics and thermodynamic analysis.

Science.gov (United States)

Sarve, Antaram N; Varma, Mahesh N; Sonawane, Shriram S

2016-03-01

Present work deals with the ultrasound-assisted biodiesel production from low cost, substantial acid value kusum (Schleichera triguga) oil using a two-step method of esterification in presence of acid (H2SO4) catalyst followed by transesterification using a basic heterogeneous barium hydroxide (Ba(OH)2) catalyst. The initial acid value of kusum oil was reduced from 21.65 to 0.84 mg of KOH/g of oil, by acid catalyzed esterification with 4:1 methanol to oil molar ratio, catalyst concentration 1% (v/v), ultrasonic irradiation time 20 min at 40 °C. Then, Ba(OH)2 concentration of 3% (w/w), methanol to oil molar ratio of 9:1, ultrasonic irradiation time of 80 min, and temperature of 50 °C was found to be the optimum conditions for transesterification step and triglyceride conversion of 96.8% (wt) was achieved. This paper also examined the kinetics as well as the evaluation of thermodynamic parameters for both esterification and transesterification reactions. The lower value of activation energy and higher values of kinetic constants indicated a fast rate of reaction, which could be attributed to the physical effect of emulsification, in which the microturbulence generated due to radial motion of bubbles, creates an intimate mixing of the immiscible reactants causing the increase in the interfacial area, giving faster reaction kinetics. The positive values of Gibbs-free energy (ΔG), enthalpy (ΔH) and negative value of entropy (ΔS) revealed that both the esterification and transesterification were non-spontaneous, endothermic and endergonic reactions. Therefore, the present work has not only established the escalation obtained due to ultrasonication but also exemplified the two-step approach for synthesis of biodiesel from non-edible kusum oil based on the use of heterogeneous catalyst for the transesterification step. Copyright © 2015 Elsevier B.V. All rights reserved.

Top-Down-Assisted Bottom-Up Method for Homologous Protein Sequencing: Hemoglobin from 33 Bird Species

Science.gov (United States)

Song, Yang; Laskay, Ünige A.; Vilcins, Inger-Marie E.; Barbour, Alan G.; Wysocki, Vicki H.

2015-11-01

Ticks are vectors for disease transmission because they are indiscriminant in their feeding on multiple vertebrate hosts, transmitting pathogens between their hosts. Identifying the hosts on which ticks have fed is important for disease prevention and intervention. We have previously shown that hemoglobin (Hb) remnants from a host on which a tick fed can be used to reveal the host's identity. For the present research, blood was collected from 33 bird species that are common in the U.S. as hosts for ticks but that have unknown Hb sequences. A top-down-assisted bottom-up mass spectrometry approach with a customized searching database, based on variability in known bird hemoglobin sequences, has been devised to facilitate fast and complete sequencing of hemoglobin from birds with unknown sequences. These hemoglobin sequences will be added to a hemoglobin database and used for tick host identification. The general approach has the potential to sequence any set of homologous proteins completely in a rapid manner.

Chromosome aberration model combining radiation tracks, chromatin structure, DSB repair and chromatin mobility

International Nuclear Information System (INIS)

Friedland, W.; Kundrat, P.

2015-01-01

The module that simulates the kinetics and yields of radiation-induced chromosome aberrations within the biophysical code PARTRAC is described. Radiation track structures simulated by Monte Carlo methods are overlapped with multi-scale models of DNA and chromatin to assess the resulting DNA damage. Spatial mobility of individual DNA ends from double-strand breaks is modelled simultaneously with their processing by the non-homologous end-joining enzymes. To score diverse types of chromosome aberrations, the joined ends are classified regarding their original chromosomal location, orientation and the involvement of centromeres. A comparison with experimental data on dicentrics induced by gamma and alpha particles shows that their relative dose dependence is predicted correctly, although the absolute yields are overestimated. The critical model assumptions on chromatin mobility and on the initial damage recognition and chromatin remodelling steps and their future refinements to solve this issue are discussed. (authors)

The microorganisms in chronically infected end-stage and non-end-stage cystic fibrosis patients

DEFF Research Database (Denmark)

Rudkjøbing, Vibeke B; Thomsen, Trine R; Alhede, Morten

2011-01-01

Patients suffering from cystic fibrosis (CF) develop chronic lung infections because of highly viscous mucus, where bacteria can form biofilms. In this study, we investigated the microorganisms present in the lungs of end-stage and non-end-stage patients using standard culturing techniques and mo...

Current topics in DNA double-strand break repair

International Nuclear Information System (INIS)

Kobayashi, Junya; Takata, Minoru; Iwabuchi, Kuniyoshi; Miyagawa, Kiyoshi; Sonoda, Eiichiro; Suzuki, Keiji; Tauchi, Hiroshi

2008-01-01

DNA double strand break (DSB) is one of the most critical types of damage which is induced by ionizing radiation. In this review, we summarize current progress in investigations on the function of DSB repair-related proteins. We focused on recent findings in the analysis of the function of proteins such as 53BP1, histone H2AX, Mus81-Eme1, Fanc complex, and UBC13, which are found to be related to homologous recombination repair or to non-homologous end joining. In addition to the function of these proteins in DSB repair, the biological function of nuclear foci formation following DSB induction is discussed. (author)

Field-assisted synthesis of SERS-active silver nanoparticles using conducting polymers

Science.gov (United States)

Xu, Ping; Jeon, Sea-Ho; Mack, Nathan H.; Doorn, Stephen K.; Williams, Darrick J.; Han, Xijiang; Wang, Hsing-Lin

2010-08-01

A gradient of novel silver nanostructures with widely varying sizes and morphologies is fabricated on a single conducting polyaniline-graphite (P-G) membrane with the assistance of an external electric field. It is believed that the formation of such a silver gradient is a synergetic consequence of the generation of a silver ion concentration gradient along with an electrokinetic flow of silver ions in the field-assisted model, which greatly influences the nucleation and growth mechanism of Ag particles on the P-G membrane. The produced silver dendrites, flowers and microspheres, with sharp edges, intersections and bifurcations, all present strong surface enhanced Raman spectroscopy (SERS) responses toward an organic target molecule, mercaptobenzoic acid (MBA). This facile field-assisted synthesis of Ag nanoparticles via chemical reduction presents an alternative approach to nanomaterial fabrication, which can yield a wide range of unique structures with enhanced optical properties that were previously inaccessible by other synthetic routes.A gradient of novel silver nanostructures with widely varying sizes and morphologies is fabricated on a single conducting polyaniline-graphite (P-G) membrane with the assistance of an external electric field. It is believed that the formation of such a silver gradient is a synergetic consequence of the generation of a silver ion concentration gradient along with an electrokinetic flow of silver ions in the field-assisted model, which greatly influences the nucleation and growth mechanism of Ag particles on the P-G membrane. The produced silver dendrites, flowers and microspheres, with sharp edges, intersections and bifurcations, all present strong surface enhanced Raman spectroscopy (SERS) responses toward an organic target molecule, mercaptobenzoic acid (MBA). This facile field-assisted synthesis of Ag nanoparticles via chemical reduction presents an alternative approach to nanomaterial fabrication, which can yield a wide range

Microwave assisted synthesis of CdS nanoparticles and their size evolution

International Nuclear Information System (INIS)

Lopez, I. A.; Vazquez, A.; Gomez, I.

2013-01-01

The study of the size evolution of CdS nanoparticles in aqueous dispersion is presented in this paper. The sodium citrate was employed as stabilizer of CdS nanoparticles synthesized by microwave assisted synthesis. Analysis of this study was carried out by UV-Vis spectrophotometry, by comparison of the band gap energy using theoretical and empirical models. Results obtained show that the synthesis conditions produce CdS nanoparticles with diameters below of 6 nm, which remains stabilized by at least 14 days. These characteristics were confirmed by transmission electron microscopy. The X-ray diffraction pattern confirms cubic phase of the CdS nanoparticles. (Author)

Microwave assisted synthesis of CdS nanoparticles and their size evolution

Energy Technology Data Exchange (ETDEWEB)

Lopez, I. A.; Vazquez, A.; Gomez, I., E-mail: idaliagomezmx@yahoo.com.mx [Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Quimicas, Laboratorio de Materiales I, Av. Universidad, Cd. Universitaria, 66451 San Nicolas de los Garza, Nuevo Leon (Mexico)

2013-05-01

The study of the size evolution of CdS nanoparticles in aqueous dispersion is presented in this paper. The sodium citrate was employed as stabilizer of CdS nanoparticles synthesized by microwave assisted synthesis. Analysis of this study was carried out by UV-Vis spectrophotometry, by comparison of the band gap energy using theoretical and empirical models. Results obtained show that the synthesis conditions produce CdS nanoparticles with diameters below of 6 nm, which remains stabilized by at least 14 days. These characteristics were confirmed by transmission electron microscopy. The X-ray diffraction pattern confirms cubic phase of the CdS nanoparticles. (Author)

Microwave-Assisted Synthesis of Alumina Nanoparticles Using Some Plants Extracts

Directory of Open Access Journals (Sweden)

Meisam Hasanpoor

2017-01-01

Full Text Available In present study we used five green plants for microwave assisted synthesis of Alumina nanoparticles from Aluminum nitrate. Structural characterization was studied using x-ray diffraction that showed semi- crystalline and possibly, amorphous structure. Fourier infrared spectroscopy was used to determine Al-O bond and functional groups responsible for synthesis of nanoparticles. FTIR confirmed existence of Al-O band and bio-functional groups, originated from plant extract. Morphology and size of nanoparticles were investigated using scanning electron microscopy, transmission electron microscopy and atomic force microscopy techniques. It was observed that nanoparticles have near-spherical shape. Average size of clusters of nanoparticles varied with different routes from of 60 nm to 300 nm. AFM images showed that Individual nanoparticles were less than 10 nm.

Joining by plastic deformation

DEFF Research Database (Denmark)

Mori, Ken-ichiro; Bay, Niels; Fratini, Livan

2013-01-01

As the scale and complexity of products such as aircraft and cars increase, demand for new functional processes to join mechanical parts grows. The use of plastic deformation for joining parts potentially offers improved accuracy, reliability and environmental safety as well as creating opportuni......As the scale and complexity of products such as aircraft and cars increase, demand for new functional processes to join mechanical parts grows. The use of plastic deformation for joining parts potentially offers improved accuracy, reliability and environmental safety as well as creating...

Ceramic joining

Energy Technology Data Exchange (ETDEWEB)

Loehman, R.E. [Sandia National Lab., Albuquerque, NM (United States)

1996-04-01

This paper describes the relation between reactions at ceramic-metal interfaces and the development of strong interfacial bonds in ceramic joining. Studies on a number of systems are described, including silicon nitrides, aluminium nitrides, mullite, and aluminium oxides. Joints can be weakened by stresses such as thermal expansion mismatch. Ceramic joining is used in a variety of applications such as solid oxide fuel cells.

Organic synthesis

Energy Technology Data Exchange (ETDEWEB)

Thomas, S.E.

1991-01-01

This paper reports on reactions of organoboranes. Organoboron routes to unsaturated hydrocarbons. Boronic ester homologation. Properties of organosilicon compounds. Alkene synthesis (Peterson olefination). Allylsilanes and acylsilanes.

End-of-Life Education and Discussions With Assisted Living Certified Nursing Assistants.

Science.gov (United States)

Mohlman, Wendy L; Dassel, Kara; Supiano, Katherine P; Caserta, Michael

2018-06-01

In previous work, the current researchers examined attitudes and experiences of certified nursing assistants (CNAs) providing end-of-life (EOL) care in an assisted living facility (ALF). Results showed that 70% of participating CNAs felt unprepared to provide EOL care, largely due to not having received prior EOL care education within their schools or workplaces. Therefore, the goal of the current study was to implement and evaluate EOL and postmortem education to ALF CNAs. A focus group of 14 CNAs within an ALF was provided EOL education pertaining to the physiological and psychological changes observed in patients nearing EOL and postmortem care. Immediately following training, CNAs participated in a 30-minute focus group in which they discussed their experiences and educational needs regarding EOL care. Responses were recorded, transcribed, and analyzed for common themes using descriptive qualitative inquiry. All participants reported that CNA programs need to place greater emphasis on teaching EOL care, and 80% desired continuing education on EOL care through their employers. There is a need for CNAs to receive EOL care education to understand the psychological and physical signs and symptoms associated with the dying process to provide best practices in postmortem care. [Journal of Gerontological Nursing, 44(6), 41-48.]. Copyright 2018, SLACK Incorporated.

End-point impedance measurements across dominant and nondominant hands and robotic assistance with directional damping.

Science.gov (United States)

Erden, Mustafa Suphi; Billard, Aude

2015-06-01

The goal of this paper is to perform end-point impedance measurements across dominant and nondominant hands while doing airbrush painting and to use the results for developing a robotic assistance scheme. We study airbrush painting because it resembles in many ways manual welding, a standard industrial task. The experiments are performed with the 7 degrees of freedom KUKA lightweight robot arm. The robot is controlled in admittance using a force sensor attached at the end-point, so as to act as a free-mass and be passively guided by the human. For impedance measurements, a set of nine subjects perform 12 repetitions of airbrush painting, drawing a straight-line on a cartoon horizontally placed on a table, while passively moving the airbrush mounted on the robot's end-point. We measure hand impedance during the painting task by generating sudden and brief external forces with the robot. The results show that on average the dominant hand displays larger impedance than the nondominant in the directions perpendicular to the painting line. We find the most significant difference in the damping values in these directions. Based on this observation, we develop a "directional damping" scheme for robotic assistance and conduct a pilot study with 12 subjects to contrast airbrush painting with and without robotic assistance. Results show significant improvement in precision with both dominant and nondominant hands when using robotic assistance.

Induction of human immunodeficiency virus (HIV-1 envelope specific cell-mediated immunity by a non-homologous synthetic peptide.

Directory of Open Access Journals (Sweden)

Ammar Achour

2007-11-01

Full Text Available Cell mediated immunity, including efficient CTL response, is required to prevent HIV-1 from cell-to-cell transmission. In previous investigations, we have shown that B1 peptide derived by Fourier transformation of HIV-1 primary structures and sharing no sequence homology with the parent proteins was able to generate antiserum which recognizes envelope and Tat proteins. Here we have investigated cellular immune response towards a novel non-homologous peptide, referred to as cA1 peptide.The 20 amino acid sequence of cA1 peptide was predicted using the notion of peptide hydropathic properties; the peptide is encoded by the complementary anti-sense DNA strand to the sense strand of previously described non-homologous A1 peptide. In this report we demonstrate that the cA1 peptide can be a target for major histocompatibility complex (MHC class I-restricted cytotoxic T lymphocytes in HIV-1-infected or envelope-immunized individuals. The cA1 peptide is recognized in association with different MHC class I allotypes and could prime in vitro CTLs, derived from gp160-immunized individuals capable to recognize virus variants.For the first time a theoretically designed immunogen involved in broad-based cell-immune memory activation is described. Our findings may thus contribute to the advance in vaccine research by describing a novel strategy to develop a synthetic AIDS vaccine.

Use of the 2-chlorotrityl chloride resin for microwave-assisted solid phase peptide synthesis.

Science.gov (United States)

Ieronymaki, Matthaia; Androutsou, Maria Eleni; Pantelia, Anna; Friligou, Irene; Crisp, Molly; High, Kirsty; Penkman, Kirsty; Gatos, Dimitrios; Tselios, Theodore

2015-09-01

A fast and efficient microwave (MW)-assisted solid-phase peptide synthesis protocol using the 2-chlorotrityl chloride resin and the Fmoc/tBu methodology, has been developed. The established protocol combines the advantages of MW irradiation and the acid labile 2-chlorotrityl chloride resin. The effect of temperature during the MW irradiation, the degree of resin substitution during the coupling of the first amino acids and the rate of racemization for each amino acid were evaluated. The suggested solid phase methodology is applicable for orthogonal peptide synthesis and for the synthesis of cyclic peptides. © 2015 Wiley Periodicals, Inc.

Highly efficient isocyanate-free microwave-assisted synthesis of [6]-oligourea

KAUST Repository

Qaroush, Abdussalam K.

2013-01-01

A new eco-friendly, isocyanate-free, energy-saving method for the production of [6]-oligourea, utilizing a green carbonylating agent, viz. propylene carbonate, is reported. It comprises an organocatalyzed, microwave-assisted, solvent-free synthesis. Two modes of microwave-assisted synthesis, viz. dynamic and fixed energy modes, were applied. Upon optimization, the dynamic mode gave 79% yields of [6]-oligourea. On the other hand, almost quantitative yields were obtained using the fixed mode, within 20 min, at 10 W and with the same catalyst loading. Combination of both organocatalysis and microwave energy input appears to be a key issue for the efficiency of the reaction, with the fixed energy mode being best suited. It should be noted that all data reported are reproducible (due to the homogeneous microwave technology used by CEM Discover S-Class of microwave reactors). To the best of our knowledge, this is the best eco-friendly synthetic approach for the preparation of the title oligomers. It paves the way for using more of the biorenewable and sustainable chemicals as a feedstock for the production of polyureas. The oligomer produced was analyzed by EA, ATR-FTIR, XRD, 1H and 13CNMR. Furthermore, thermal properties of the resulting [6]-oligourea were analyzed using TGA and DSC. © The Royal Society of Chemistry 2013.

Comparison of Conventional and Microwave-assisted Synthesis of Benzimidazole Derivative from Citronellal in Kaffir lime oil (Citrus hystrix DC.)

Science.gov (United States)

Warsito, W.; Noorhamdani, A. S.; Suratmo; Dwi Sapri, R.; Alkaroma, D.; Azhar, A. Z.

2018-04-01

Simple method has been used for the synthesis of benzimidazole derivative from citronellal in kaffir lime oil under microwave irradiation. These compounds were synthesized also by conventional heating for comparison. In addtion, microwave-assited synthesis was also compared between using to dichloromethane and methanol solvents with variation of reaction time for 30 to 70 minutes and 4 to 12 h for conventional heating. The 2-citronellyl benzimidazole compound synthesized were characterised by FT-IR, GC-MS, 1H and 13C NMR spectroscopy. Comparison between conventional and microwave-assisted synthesis was done by comparing between correlation of reaction time and percentage yield. The time optimum of microwave-assisted and conventional synthesis using dichloromethane solvent respectively at 60 minutes (yield 19.23%) and 8 hours (yield 11.54%). In addition, microwave-assited synthesis increasing 157.81 times compared by conventional heating. While using methanol solvent tends to increase linearly however the percentage of yield only 0.77 times of synthesis using dichloromethane solvent.

A novel missense RAG-1 mutation results in T−B−NK+ SCID in Athabascan-speaking Dine Indians from the Canadian Northwest Territories

OpenAIRE

Xiao, Zheng; Yannone, Steven M; Dunn, Elizabeth; Cowan, Morton J

2008-01-01

DNA double-strand repair factors in the non-homologous end joining (NHEJ) pathway resolve DNA double-strand breaks introduced by the recombination-activating gene (RAG) proteins during V(D)J recombination of T and B lymphocyte receptor genes. Defective NHEJ and subsequent failure of V(D)J recombination leads to severe combined immunodeficiency disease (SCID). We originally linked T−B−NK+ SCID in Athabascan-speaking Native Americans in the Southwestern US and Northwest Territories of Canada to...

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

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

International Nuclear Information System (INIS)

Fan Jinshui; Robert, Carine; Jang, Yoon-Young; Liu Hua; Sharkis, Saul; Baylin, Stephen Bruce; Rassool, Feyruz Virgilia

2011-01-01

Highlights: → iPSC and hESC demonstrate a similar cell cycle profile, with increased S phase cells and decreased G0/G1. → iPSC and hESC increased ROS and decreased DSBs, compared with differentiated parental cells. → iPSC and hESC demonstrate elevated DSB repair activity, including nonhomologous end-joining, compared with differentiated parental cells. → iPSC however show a partial apoptotic response to DNA damage, compared to hESC. → 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 from, mimic hESC in their ROS levels

Chromosome End Repair and Genome Stability in Plasmodium falciparum

Directory of Open Access Journals (Sweden)

Susannah F. Calhoun

2017-08-01

Full Text Available The human malaria parasite Plasmodium falciparum replicates within circulating red blood cells, where it is subjected to conditions that frequently cause DNA damage. The repair of DNA double-stranded breaks (DSBs is thought to rely almost exclusively on homologous recombination (HR, due to a lack of efficient nonhomologous end joining. However, given that the parasite is haploid during this stage of its life cycle, the mechanisms involved in maintaining genome stability are poorly understood. Of particular interest are the subtelomeric regions of the chromosomes, which contain the majority of the multicopy variant antigen-encoding genes responsible for virulence and disease severity. Here, we show that parasites utilize a competitive balance between de novo telomere addition, also called “telomere healing,” and HR to stabilize chromosome ends. Products of both repair pathways were observed in response to DSBs that occurred spontaneously during routine in vitro culture or resulted from experimentally induced DSBs, demonstrating that both pathways are active in repairing DSBs within subtelomeric regions and that the pathway utilized was determined by the DNA sequences immediately surrounding the break. In combination, these two repair pathways enable parasites to efficiently maintain chromosome stability while also contributing to the generation of genetic diversity.

Join Operations in Temporal Databases

DEFF Research Database (Denmark)

Gao, D.; Jensen, Christian Søndergaard; Snodgrass, R.T.

2005-01-01

Joins are arguably the most important relational operators. Poor implementations are tantamount to computing the Cartesian product of the input relations. In a temporal database, the problem is more acute for two reasons. First, conventional techniques are designed for the evaluation of joins...... with equality predicates rather than the inequality predicates prevalent in valid-time queries. Second, the presence of temporally varying data dramatically increases the size of a database. These factors indicate that specialized techniques are needed to efficiently evaluate temporal joins. We address...... this need for efficient join evaluation in temporal databases. Our purpose is twofold. We first survey all previously proposed temporal join operators. While many temporal join operators have been defined in previous work, this work has been done largely in isolation from competing proposals, with little...

High yield polyol synthesis of round- and sharp-end silver nanowires with high aspect ratio

Energy Technology Data Exchange (ETDEWEB)

Nekahi, A.; Marashi, S.P.H., E-mail: pmarashi@aut.ac.ir; Fatmesari, D. Haghshenas

2016-12-01

Long silver nanowires (average length of 28 μm, average aspect ratio of 130) with uniform diameter along their length were produced by polyol synthesis of AgNO{sub 3} in ethylene glycol in the presence of PVP as preferential growth agent. Nanowires were produced with no addition of chloride salts such as NaCl or CuCl{sub 2} (or other additives such as Na{sub 2}S) which are usually used for lowering reduction rate of Ag ions by additional etchant of O{sub 2}/Cl{sup −}. Lower reduction rate was obtained by increasing the injection time of PVP and AgNO{sub 3} solutions, which was the significant factor in the formation of nanowires. Therefore, there was enough time for reduced Ag atoms to be deposited preferentially in the direction of PVP chains, resulting in high yield (the fraction of nanowires in the products) of nanowires (more than 95%) with high aspect ratio. The produced nanowires had both round- and sharp-ends with pentagonal cross section. Higher energy level of Ag atoms in borders of MTPs, which increases the dissolution rate of precipitated atoms, in addition to partial melting of MTPs at high synthesis temperatures, leads to the curving of the surfaces of exposed (111) crystalline planes in some MTPs and the formation of round-end silver nanowires. - Highlights: • Long silver nanowires with high aspect ratio of 130 were produced. • More than 95% nanowires were produced in products. • The produced nanowires had round- and sharp-ends with pentagonal cross section. • Additives were needed neither for high yield synthesis nor for round-end nanowires. • Melting and etching of MTPs in high energy borders resulted to round-end nanowires.

Role of Double-Strand Break End-Tethering during Gene Conversion in Saccharomyces cerevisiae.

Directory of Open Access Journals (Sweden)

Suvi Jain

2016-04-01

Full Text Available Correct repair of DNA double-strand breaks (DSBs is critical for maintaining genome stability. Whereas gene conversion (GC-mediated repair is mostly error-free, repair by break-induced replication (BIR is associated with non-reciprocal translocations and loss of heterozygosity. We have previously shown that a Recombination Execution Checkpoint (REC mediates this competition by preventing the BIR pathway from acting on DSBs that can be repaired by GC. Here, we asked if the REC can also determine whether the ends that are engaged in a GC-compatible configuration belong to the same break, since repair involving ends from different breaks will produce potentially deleterious translocations. We report that the kinetics of repair are markedly delayed when the two DSB ends that participate in GC belong to different DSBs (termed Trans compared to the case when both DSB ends come from the same break (Cis. However, repair in Trans still occurs by GC rather than BIR, and the overall efficiency of repair is comparable. Hence, the REC is not sensitive to the "origin" of the DSB ends. When the homologous ends for GC are in Trans, the delay in repair appears to reflect their tethering to sequences on the other side of the DSB that themselves recombine with other genomic locations with which they share sequence homology. These data support previous observations that the two ends of a DSB are usually tethered to each other and that this tethering facilitates both ends encountering the same donor sequence. We also found that the presence of homeologous/repetitive sequences in the vicinity of a DSB can distract the DSB end from finding its bona fide homologous donor, and that inhibition of GC by such homeologous sequences is markedly increased upon deleting Sgs1 but not Msh6.

Detecting false positive sequence homology: a machine learning approach.

Science.gov (United States)

Fujimoto, M Stanley; Suvorov, Anton; Jensen, Nicholas O; Clement, Mark J; Bybee, Seth M

2016-02-24

Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging from building phylogenies to predicting functional gene annotations. There are many existing heuristic tools, most commonly based on bidirectional BLAST searches that are used to identify homologous genes and combine them into two fundamentally distinct classes: orthologs and paralogs. Due to only using heuristic filtering based on significance score cutoffs and having no cluster post-processing tools available, these methods can often produce multiple clusters constituting unrelated (non-homologous) sequences. Therefore sequencing data extracted from incomplete genome/transcriptome assemblies originated from low coverage sequencing or produced by de novo processes without a reference genome are susceptible to high false positive rates of homology detection. In this paper we develop biologically informative features that can be extracted from multiple sequence alignments of putative homologous genes (orthologs and paralogs) and further utilized in context of guided experimentation to verify false positive outcomes. We demonstrate that our machine learning method trained on both known homology clusters obtained from OrthoDB and randomly generated sequence alignments (non-homologs), successfully determines apparent false positives inferred by heuristic algorithms especially among proteomes recovered from low-coverage RNA-seq data. Almost ~42 % and ~25 % of predicted putative homologies by InParanoid and HaMStR respectively were classified as false positives on experimental data set. Our process increases the quality of output from other clustering algorithms by providing a novel post-processing method that is both fast and efficient at removing low quality clusters of putative homologous genes recovered by heuristic-based approaches.

End of Life Care

Science.gov (United States)

... Related Topics Choosing Wisely Join our e-newsletter! Aging & Health A to Z End of Life Care ... be used. Ice chips, popsicles, moist swabs, or artificial saliva can help prevent the mouth from becoming ...

Sonochemical-assisted magnesium borate synthesis from different boron sources

Directory of Open Access Journals (Sweden)

Yildirim Meral

2017-03-01

Full Text Available In this study, sonochemical-assisted magnesium borate synthesis is studied from different boron sources. Various reaction parameters are successfully applied by a simple and green method. X-ray diffraction (XRD, Fourier transform infrared (FT-IR and Raman spectroscopies are used to characterize the synthesized magnesium borates on the other hand surface morphologies are investigated by using scanning electron microscope (SEM. The XRD analyses showed that the products were admontite [MgO(B2O33 · 7(H2O] with JCPDS (Joint Committee on Powder Diffraction Standards no. of 01-076-0540 and mcallisterite [Mg2(B6O7(OH62 · 9(H2O] with JCPDS no. of 01-070-1902. The results that found in the spectroscopic studies were in a good agreement with characteristic magnesium borate bands in both regions of infra-red and visible. According to SEM results, obtained borates were in micro and sub-micro scales. By the use of ultrasonication, reaction yields were found between 84.2 and 97.9%. As a result, it is concluded that the sonochemical approach is a practicable synthesis method to get high efficiency and high crystallinity in the synthesis magnesium borate compounds.

De novo CNV formation in mouse embryonic stem cells occurs in the absence of Xrcc4-dependent nonhomologous end joining.

Directory of Open Access Journals (Sweden)

Martin F Arlt

2012-09-01

Full Text Available Spontaneous copy number variant (CNV mutations are an important factor in genomic structural variation, genomic disorders, and cancer. A major class of CNVs, termed nonrecurrent CNVs, is thought to arise by nonhomologous DNA repair mechanisms due to the presence of short microhomologies, blunt ends, or short insertions at junctions of normal and de novo pathogenic CNVs, features recapitulated in experimental systems in which CNVs are induced by exogenous replication stress. To test whether the canonical nonhomologous end joining (NHEJ pathway of double-strand break (DSB repair is involved in the formation of this class of CNVs, chromosome integrity was monitored in NHEJ-deficient Xrcc4(-/- mouse embryonic stem (ES cells following treatment with low doses of aphidicolin, a DNA replicative polymerase inhibitor. Mouse ES cells exhibited replication stress-induced CNV formation in the same manner as human fibroblasts, including the existence of syntenic hotspot regions, such as in the Auts2 and Wwox loci. The frequency and location of spontaneous and aphidicolin-induced CNV formation were not altered by loss of Xrcc4, as would be expected if canonical NHEJ were the predominant pathway of CNV formation. Moreover, de novo CNV junctions displayed a typical pattern of microhomology and blunt end use that did not change in the absence of Xrcc4. A number of complex CNVs were detected in both wild-type and Xrcc4(-/- cells, including an example of a catastrophic, chromothripsis event. These results establish that nonrecurrent CNVs can be, and frequently are, formed by mechanisms other than Xrcc4-dependent NHEJ.

Xrcc1-dependent and Ku-dependent DNA double-strand break repair kinetics in Arabidopsis plants.

Science.gov (United States)

Charbonnel, Cyril; Gallego, Maria E; White, Charles I

2010-10-01

Double-strand breakage (DSB) of DNA involves loss of information on the two strands of the DNA fibre and thus cannot be repaired by simple copying of the complementary strand which is possible with single-strand DNA damage. Homologous recombination (HR) can precisely repair DSB using another copy of the genome as template and non-homologous recombination (NHR) permits repair of DSB with little or no dependence on DNA sequence homology. In addition to the well-characterised Ku-dependent non-homologous end-joining (NHEJ) pathway, much recent attention has been focused on Ku-independent NHR. The complex interrelationships and regulation of NHR pathways remain poorly understood, even more so in the case of plants, and we present here an analysis of Ku-dependent and Ku-independent repair of DSB in Arabidopsis thaliana. We have characterised an Arabidopsis xrcc1 mutant and developed quantitative analysis of the kinetics of appearance and loss of γ-H2AX foci as a tool to measure DSB repair in dividing root tip cells of γ-irradiated plants in vivo. This approach has permitted determination of DSB repair kinetics in planta following a short pulse of γ-irradiation, establishing the existence of a Ku-independent, Xrcc1-dependent DSB repair pathway. Furthermore, our data show a role for Ku80 during the first minutes post-irradiation and that Xrcc1 also plays such a role, but only in the absence of Ku. The importance of Xrcc1 is, however, clearly visible at later times in the presence of Ku, showing that alternative end-joining plays an important role in DSB repair even in the presence of active NHEJ. © 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd.

Acyclic Diene Metathesis (ADMET Polymerization for Precise Synthesis of Defect-Free Conjugated Polymers with Well-Defined Chain Ends

Directory of Open Access Journals (Sweden)

Tahmina Haque

2015-03-01

Full Text Available This accounts introduces unique characteristics by adopting the acyclic diene metathesis (ADMET polymerization for synthesis of conjugated polymers, poly(arylene vinylenes, known as promising molecular electronics. The method is more suitable than the other methods in terms of atom efficiency affording defect-free, stereo-regular (exclusive trans polymers with well-defined chain ends; the resultant polymers possess better property than those prepared by the conventional methods. The chain ends (vinyl group in the resultant polymer prepared by ruthenium-carbene catalyst(s can be modified by treating with molybdenum-alkylidene complex (olefin metathesis followed by addition of various aldehyde (Wittig type cleavage, affording the end-functionalized polymers exclusively. An introduction of initiating fragment, the other conjugated segment, and one-pot synthesis of end-functionalized block copolymers, star shape polymers can be achieved by adopting this methodology.

The effect of temperature in flux-assisted synthesis of SnNb2O6

KAUST Repository

Noureldine, Dalal; Takanabe, Kazuhiro

2014-01-01

A flux-assisted method was used to synthesize SnNb2O6 as a visible-light-responsive metal oxide photocatalyst. The role of synthesis temperature was investigated in detail using different reaction temperatures (300, 500, 600, 800, 1000 °C

In-Network Processing of an Iceberg Join Query in Wireless Sensor Networks Based on 2-Way Fragment Semijoins

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Hyunchul Kang

2015-03-01

Full Text Available We investigate the in-network processing of an iceberg join query in wireless sensor networks (WSNs. An iceberg join is a special type of join where only those joined tuples whose cardinality exceeds a certain threshold (called iceberg threshold are qualified for the result. Processing such a join involves the value matching for the join predicate as well as the checking of the cardinality constraint for the iceberg threshold. In the previous scheme, the value matching is carried out as the main task for filtering non-joinable tuples while the iceberg threshold is treated as an additional constraint. We take an alternative approach, meeting the cardinality constraint first and matching values next. In this approach, with a logical fragmentation of the join operand relations on the aggregate counts of the joining attribute values, the optimal sequence of 2-way fragment semijoins is generated, where each fragment semijoin employs a Bloom filter as a synopsis of the joining attribute values. This sequence filters non-joinable tuples in an energy-efficient way in WSNs. Through implementation and a set of detailed experiments, we show that our alternative approach considerably outperforms the previous one.

In-Network Processing of an Iceberg Join Query in Wireless Sensor Networks Based on 2-Way Fragment Semijoins

Science.gov (United States)

Kang, Hyunchul

2015-01-01

We investigate the in-network processing of an iceberg join query in wireless sensor networks (WSNs). An iceberg join is a special type of join where only those joined tuples whose cardinality exceeds a certain threshold (called iceberg threshold) are qualified for the result. Processing such a join involves the value matching for the join predicate as well as the checking of the cardinality constraint for the iceberg threshold. In the previous scheme, the value matching is carried out as the main task for filtering non-joinable tuples while the iceberg threshold is treated as an additional constraint. We take an alternative approach, meeting the cardinality constraint first and matching values next. In this approach, with a logical fragmentation of the join operand relations on the aggregate counts of the joining attribute values, the optimal sequence of 2-way fragment semijoins is generated, where each fragment semijoin employs a Bloom filter as a synopsis of the joining attribute values. This sequence filters non-joinable tuples in an energy-efficient way in WSNs. Through implementation and a set of detailed experiments, we show that our alternative approach considerably outperforms the previous one. PMID:25774710

Blind-date Conversation Joining

Directory of Open Access Journals (Sweden)

Luca Cesari

2013-07-01

Full Text Available We focus on a form of joining conversations among multiple parties in service-oriented applications where a client may asynchronously join an existing conversation without need to know in advance any information about it. More specifically, we show how the correlation mechanism provided by orchestration languages enables a form of conversation joining that is completely transparent to clients and that we call 'blind-date joining'. We provide an implementation of this strategy by using the standard orchestration language WS-BPEL. We then present its formal semantics by resorting to COWS, a process calculus specifically designed for modelling service-oriented applications. We illustrate our approach by means of a simple, but realistic, case study from the online games domain.

Polymer-Assisted Hydrothermal Synthesis of Hierarchically Arranged Hydroxyapatite Nanoceramic

Directory of Open Access Journals (Sweden)

A. Joseph Nathanael

2013-01-01

Full Text Available Flower-like hydroxyapatite (HA nanostructures were synthesized by a polymer-assisted hydrothermal method. The thickness of the petals/plates decreased from 200 nm to 40 nm as the polymer concentration increased. The thickness also decreased as the hydrothermal treatment time increased from 6 to 12 hr. The HRTEM and SAED patterns suggest that the floral-like HA nanostructures are single crystalline in nature. Structural analysis based on XRD and Raman experiments implied that the produced nanostructure is a pure form of HA without any other impurities. The possible formation mechanism was discussed for the formation of flower-like HA nanostructures during polymer-assisted hydrothermal synthesis. Finally, in vitro cellular analysis revealed that the hierarchically arranged HA nanoceramic had improved cell viability relative to other structures. The cells were actively proliferated over these nanostructures due to lower cytotoxicity. Overall, the size and the crystallinity of the nanostructures played a role in improving the cell proliferation.

Biosynthesis of amidated joining peptide from pro-adrenocorticotropin-endorphin

Energy Technology Data Exchange (ETDEWEB)

Cullen, E.I.; Mains, R.E. (Johns Hopkins Univ. School of Medicine, Baltimore, MD (USA))

1987-09-01

Joining peptide is the major alpha-amidated product of pro-ACTH/endorphin (PAE) in AtT-20 corticotropic tumor cells. To study intracellular joining peptide synthesis, affinity purified antibodies directed against gamma-MSH, joining peptide, and ACTH were used to immunoprecipitate extracts from biosynthetically labeled AtT-20 cells. Immunoprecipitates were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and by tryptic peptide mapping on HPLC. In steady labeling experiments, radioactivity in amidated joining peptide (JP) increased roughly linearly with time, in the manner of a final product, whereas radioactivity associated with PAE (1-94)NH2 reached a constant value after 2-4 h, indicating that PAE(1-94)NH2 is an intermediate in the biosynthesis of JP. Radioactivity appeared in ACTH(1-39) well before JP, consistent with a cleavage order in which ACTH is cleaved from PAE(1-95) before JP sequences are cleaved from PAE(1-74). This conclusion was supported by tryptic peptide analyses of immunoprecipitates, which indicated that less than 5% of JP-related material is cleaved from PAE(1-74) before being cleaved from ACTH-related sequences. After a pulse label, radioactivity in PAE(1-94)NH2 reached a peak value after 1 h of chase and declined with a half-life of less than 1 h. Amidated JP increased to a constant level after 2 h of chase. Enough radiolabeled PAE(1-94)NH2 was detected to account for about half of the radioactivity found in amidated JP, indicating that about half of JP-related material is first cleaved from PAE(1-95) before being amidated. This result was corroborated using HPLC purification to determine both amidated and glycine-extended forms of JP.

Biosynthesis of amidated joining peptide from pro-adrenocorticotropin-endorphin

International Nuclear Information System (INIS)

Cullen, E.I.; Mains, R.E.

1987-01-01

Joining peptide is the major alpha-amidated product of pro-ACTH/endorphin (PAE) in AtT-20 corticotropic tumor cells. To study intracellular joining peptide synthesis, affinity purified antibodies directed against gamma-MSH, joining peptide, and ACTH were used to immunoprecipitate extracts from biosynthetically labeled AtT-20 cells. Immunoprecipitates were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and by tryptic peptide mapping on HPLC. In steady labeling experiments, radioactivity in amidated joining peptide (JP) increased roughly linearly with time, in the manner of a final product, whereas radioactivity associated with PAE (1-94)NH2 reached a constant value after 2-4 h, indicating that PAE(1-94)NH2 is an intermediate in the biosynthesis of JP. Radioactivity appeared in ACTH(1-39) well before JP, consistent with a cleavage order in which ACTH is cleaved from PAE(1-95) before JP sequences are cleaved from PAE(1-74). This conclusion was supported by tryptic peptide analyses of immunoprecipitates, which indicated that less than 5% of JP-related material is cleaved from PAE(1-74) before being cleaved from ACTH-related sequences. After a pulse label, radioactivity in PAE(1-94)NH2 reached a peak value after 1 h of chase and declined with a half-life of less than 1 h. Amidated JP increased to a constant level after 2 h of chase. Enough radiolabeled PAE(1-94)NH2 was detected to account for about half of the radioactivity found in amidated JP, indicating that about half of JP-related material is first cleaved from PAE(1-95) before being amidated. This result was corroborated using HPLC purification to determine both amidated and glycine-extended forms of JP

Lightning Fast and Space Efficient Inequality Joins

KAUST Repository

Khayyat, Zuhair

2015-09-01

Inequality joins, which join relational tables on inequality conditions, are used in various applications. While there have been a wide range of optimization methods for joins in database systems, from algorithms such as sort-merge join and band join, to various indices such as B+-tree,R*-tree and Bitmap, inequality joins have received little attention and queries containing such joins are usually very slow. In this paper, we introduce fast inequality join algorithms. We put columns to be joined in sorted arrays and we use permutation arrays to encode positions of tuples in one sorted array w.r.t. the other sorted array. In contrast to sort-merge join, we use space effcient bit-arrays that enable optimizations, such as Bloom filter indices, for fast computation of the join results. We have implemented a centralized version of these algorithms on top of PostgreSQL, and a distributed version on top of Spark SQL. We have compared against well known optimization techniques for inequality joins and show that our solution is more scalable and several orders of magnitude faster.

Lightning fast and space efficient inequality joins

KAUST Repository

Khayyat, Zuhair

2015-09-01

Inequality joins, which join relational tables on inequality conditions, are used in various applications. While there have been a wide range of optimization methods for joins in database systems, from algorithms such as sort-merge join and band join, to various indices such as B+-tree, R*-tree and Bitmap, inequality joins have received little attention and queries containing such joins are usually very slow. In this paper, we introduce fast inequality join algorithms. We put columns to be joined in sorted arrays and we use permutation arrays to encode positions of tuples in one sorted array w.r.t. the other sorted array. In contrast to sort-merge join, we use space efficient bit-arrays that enable optimizations, such as Bloom filter indices, for fast computation of the join results. We have implemented a centralized version of these algorithms on top of PostgreSQL, and a distributed version on top of Spark SQL. We have compared against well known optimization techniques for inequality joins and show that our solution is more scalable and several orders of magnitude faster.

Lightning fast and space efficient inequality joins

KAUST Repository

Khayyat, Zuhair; Lucia, William; Singh, Meghna; Ouzzani, Mourad; Papotti, Paolo; Quiané -Ruiz, Jorge-Arnulfo; Tang, Nan; Kalnis, Panos

2015-01-01

Inequality joins, which join relational tables on inequality conditions, are used in various applications. While there have been a wide range of optimization methods for joins in database systems, from algorithms such as sort-merge join and band join, to various indices such as B+-tree, R*-tree and Bitmap, inequality joins have received little attention and queries containing such joins are usually very slow. In this paper, we introduce fast inequality join algorithms. We put columns to be joined in sorted arrays and we use permutation arrays to encode positions of tuples in one sorted array w.r.t. the other sorted array. In contrast to sort-merge join, we use space efficient bit-arrays that enable optimizations, such as Bloom filter indices, for fast computation of the join results. We have implemented a centralized version of these algorithms on top of PostgreSQL, and a distributed version on top of Spark SQL. We have compared against well known optimization techniques for inequality joins and show that our solution is more scalable and several orders of magnitude faster.

Microwave-assisted synthesis of iron oxide nanoparticles in biocompatible organic environment

Science.gov (United States)

Aivazoglou, E.; Metaxa, E.; Hristoforou, E.

2018-04-01

The development of magnetite and maghemite particles in uniform nanometer size has triggered the interest of the research community due to their many interesting properties leading to a wide range of applications, such as catalysis, nanomedicine-nanobiology and other engineering applications. In this study, a simple, time-saving and low energy-consuming, microwave-assisted synthesis of iron oxide nanoparticles, is presented. The nanoparticles were prepared by microwave-assisted synthesis using polyethylene glycol (PEG) or PEG and β-cyclodextrin (β-CD)/water solutions of chloride salts of iron in the presence of ammonia solution. The prepared nano-powders were characterized using X-Ray Diffraction (XRD), Transition Electron Microscopy (TEM), Fourier-transform Infrared Spectroscopy (FTIR), Raman Spectroscopy, Vibrating Sample Magnetometer (VSM), X-Ray Photoelectron Spectroscopy (XPS) and Thermal analysis (TG/DSC). The produced nanoparticles are crystallized mostly in the magnetite and maghemite lattice exhibiting very similar shape and size, with indications of partial PEG coating. Heating time, microwave power and presence of PEG, are the key factors shaping the size properties of nanoparticles. The average size of particles ranges from 10.3 to 19.2 nm. The nanoparticles exhibit a faceted morphology, with zero contamination levels. The magnetic measurements indicate that the powders are soft magnetic materials with negligible coercivity and remanence, illustrating super-paramagnetic behavior.

Joining of HHF materials applying electroplating technology

Energy Technology Data Exchange (ETDEWEB)

Krauss, Wolfgang, E-mail: wolfgang.krauss@kit.edu; Lorenz, Julia; Konys, Jürgen

2014-10-15

Highlights: • Electroplating of fillers is industrially relevant for brazing in fusion. • Interlayers (Ni or Pd) improve adherence and reduce failure risks. • Tungsten and Eurofer joints successfully fabricated by electroplating. • Mechanical and non-destructive testing integrated into qualification. • Shear strength of W joints comparable with conventionally brazed steel. - Abstract: Tungsten will be used as armor material for blanket shielding and is designated as high heat flux material for divertors, beyond application of improved W composite alloys as structural material. Independent from design (water- or helium-cooled), a successful development is inherently correlated with joining of tungsten with functional components. Depending on the design variants, the fabricated joints have to guarantee specific functional or structural properties, e.g., good thermal conductivity or mechanical load transmission. Tungsten shows lacks in adapted joining due to its metallurgical behavior ranging from immiscibility over bad wetting to brittle intermetallic phase formation. Electroplating has shown to overcome such drawbacks and that homogeneous functional (e.g., Ni or Pd) and filler (e.g., Cu) layers can be deposited. In this paper the progress achieved in development of electroplating processes for joining W to W or steel to steel will be shown. The main focus will be the characterization of the processed joints applying metallurgical investigations including SEM/EDX analyses and non-destructive testing. The mechanical stability of the produced joints is demonstrated by presenting recent shear test data. The W–W joints failed due to cracking in W, whereas the steel–steel joints cracked in the brazing zone at about 200 N/mm{sup 2} load.

RPA accumulation during class switch recombination represents 5'-3' DNA-end resection during the S-G2/M phase of the cell cycle.

Science.gov (United States)

Yamane, Arito; Robbiani, Davide F; Resch, Wolfgang; Bothmer, Anne; Nakahashi, Hirotaka; Oliveira, Thiago; Rommel, Philipp C; Brown, Eric J; Nussenzweig, Andre; Nussenzweig, Michel C; Casellas, Rafael

2013-01-31

Activation-induced cytidine deaminase (AID) promotes chromosomal translocations by inducing DNA double-strand breaks (DSBs) at immunoglobulin (Ig) genes and oncogenes in the G1 phase. RPA is a single-stranded DNA (ssDNA)-binding protein that associates with resected DSBs in the S phase and facilitates the assembly of factors involved in homologous repair (HR), such as Rad51. Notably, RPA deposition also marks sites of AID-mediated damage, but its role in Ig gene recombination remains unclear. Here, we demonstrate that RPA associates asymmetrically with resected ssDNA in response to lesions created by AID, recombination-activating genes (RAG), or other nucleases. Small amounts of RPA are deposited at AID targets in G1 in an ATM-dependent manner. In contrast, recruitment in the S-G2/M phase is extensive, ATM independent, and associated with Rad51 accumulation. In the S-G2/M phase, RPA increases in nonhomologous-end-joining-deficient lymphocytes, where there is more extensive DNA-end resection. Thus, most RPA recruitment during class switch recombination represents salvage of unrepaired breaks by homology-based pathways during the S-G2/M phase of the cell cycle. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

The OGCleaner: filtering false-positive homology clusters.

Science.gov (United States)

Fujimoto, M Stanley; Suvorov, Anton; Jensen, Nicholas O; Clement, Mark J; Snell, Quinn; Bybee, Seth M

2017-01-01

Detecting homologous sequences in organisms is an essential step in protein structure and function prediction, gene annotation and phylogenetic tree construction. Heuristic methods are often employed for quality control of putative homology clusters. These heuristics, however, usually only apply to pairwise sequence comparison and do not examine clusters as a whole. We present the Orthology Group Cleaner (the OGCleaner), a tool designed for filtering putative orthology groups as homology or non-homology clusters by considering all sequences in a cluster. The OGCleaner relies on high-quality orthologous groups identified in OrthoDB to train machine learning algorithms that are able to distinguish between true-positive and false-positive homology groups. This package aims to improve the quality of phylogenetic tree construction especially in instances of lower-quality transcriptome assemblies. https://github.com/byucsl/ogcleaner CONTACT: sfujimoto@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Coherent synthesis with dedicated instrumentation for MW-assisted chemistry (T3)

International Nuclear Information System (INIS)

Keil, E.M.

2002-01-01

Full text: Microwave (MW) assisted organic chemistry is a still new and exciting field in organic synthesis. The streamlining power of this type of methodology is typically characterized by an increase in yield and a decrease in reaction times. Within quite a short time all major companies which need to synthesize new compounds efficiently and successfully has realized these advantages and have invested in this technology. The instruments presented here are specifically designed for organic synthesis. They incorporate single mode resonator (SRM) and dynamic field tuning designs. This latest developments in modern microwave technology is used due to the high demand for reproducible control and the wide variety of reaction types used in organic synthesis. In coherent synthesis, microwave assisted organic reactions can be performed under extreme temperature and pressure conditions. It is therefore essential to have sensitive control and advanced, adjustable energy-steering systems. The dynamic field tuning system is based upon proprietary technology involving improved software and hardware. The system is capable of detecting the absorbance characteristics of the reaction mixture and optimizes the coupling and quantity of energy delivered. It provides optimal efficiency and even temperature distribution in the reaction mixture regardless of involved materials, as e.g. a wide range of solvents or reagents. Built-in temperature and pressure sensors allow real time monitoring and control of each individual reaction. The work flow manager software is a platform from where to plan and perform experiments, monitor reactions and document all results. The chemical reactions are performed in uniquely designed process vials which allow even energy distribution throughout the entire reaction volume. The vials are manufactured from microwave-immune materials that are free from contaminants. The closure design is optimized for a complete seal allowing safe working pressures up to

Joining uranium to steel

International Nuclear Information System (INIS)

Perkins, M.A.

1976-05-01

A method has been devised which will allow the joining of uranium to steel by fusion welding through the use of an intermediate material. Uranium-0.5 titanium was joined to AISI 304L stainless steel by using a vanadium insert. Also, a method is now available for selecting possible filler metals when two entirely dissimilar metals need to be joined. This method allows a quantitative ranking to be made of the possible filler metals and thus the most likely candidate can be selected

DNA-PK, ATM and ATR collaboratively regulate p53-RPA interaction to facilitate homologous recombination DNA repair.

Science.gov (United States)

Serrano, M A; Li, Z; Dangeti, M; Musich, P R; Patrick, S; Roginskaya, M; Cartwright, B; Zou, Y

2013-05-09

Homologous recombination (HR) and nonhomologous end joining (NHEJ) are two distinct DNA double-stranded break (DSB) repair pathways. Here, we report that DNA-dependent protein kinase (DNA-PK), the core component of NHEJ, partnering with DNA-damage checkpoint kinases ataxia telangiectasia mutated (ATM) and ATM- and Rad3-related (ATR), regulates HR repair of DSBs. The regulation was accomplished through modulation of the p53 and replication protein A (RPA) interaction. We show that upon DNA damage, p53 and RPA were freed from a p53-RPA complex by simultaneous phosphorylations of RPA at the N-terminus of RPA32 subunit by DNA-PK and of p53 at Ser37 and Ser46 in a Chk1/Chk2-independent manner by ATR and ATM, respectively. Neither the phosphorylation of RPA nor of p53 alone could dissociate p53 and RPA. Furthermore, disruption of the release significantly compromised HR repair of DSBs. Our results reveal a mechanism for the crosstalk between HR repair and NHEJ through the co-regulation of p53-RPA interaction by DNA-PK, ATM and ATR.

Authenticated join processing in outsourced databases

KAUST Repository

Yang, Yin

2009-01-01

Database outsourcing requires that a query server constructs a proof of result correctness, which can be verified by the client using the data owner\\'s signature. Previous authentication techniques deal with range queries on a single relation using an authenticated data structure (ADS). On the other hand, authenticated join processing is inherently more complex than ranges since only the base relations (but not their combination) are signed by the owner. In this paper, we present three novel join algorithms depending on the ADS availability: (i) Authenticated Indexed Sort Merge Join (AISM), which utilizes a single ADS on the join attribute, (ii) Authenticated Index Merge Join (AIM) that requires an ADS (on the join attribute) for both relations, and (iii) Authenticated Sort Merge Join (ASM), which does not rely on any ADS. We experimentally demonstrate that the proposed methods outperform two benchmark algorithms, often by several orders of magnitude, on all performance metrics, and effectively shift the workload to the outsourcing service. Finally, we extend our techniques to complex queries that combine multi-way joins with selections and projections. ©2009 ACM.

Authenticated join processing in outsourced databases

KAUST Repository

Yang, Yin; Papadias, Dimitris; Papadopoulos, Stavros; Kalnis, Panos

2009-01-01

Database outsourcing requires that a query server constructs a proof of result correctness, which can be verified by the client using the data owner's signature. Previous authentication techniques deal with range queries on a single relation using an authenticated data structure (ADS). On the other hand, authenticated join processing is inherently more complex than ranges since only the base relations (but not their combination) are signed by the owner. In this paper, we present three novel join algorithms depending on the ADS availability: (i) Authenticated Indexed Sort Merge Join (AISM), which utilizes a single ADS on the join attribute, (ii) Authenticated Index Merge Join (AIM) that requires an ADS (on the join attribute) for both relations, and (iii) Authenticated Sort Merge Join (ASM), which does not rely on any ADS. We experimentally demonstrate that the proposed methods outperform two benchmark algorithms, often by several orders of magnitude, on all performance metrics, and effectively shift the workload to the outsourcing service. Finally, we extend our techniques to complex queries that combine multi-way joins with selections and projections. ©2009 ACM.

Efficient and 'green' microwave-assisted synthesis of haloalkylphosphonates via the Michaelis-Arbuzov reaction

Czech Academy of Sciences Publication Activity Database

Jansa, Petr; Holý, Antonín; Dračínský, Martin; Baszczyňski, Ondřej; Česnek, Michal; Janeba, Zlatko

2011-01-01

Roč. 13, č. 4 (2011), s. 882-888 ISSN 1463-9262 R&D Projects: GA AV ČR KJB400550903; GA MŠk 1M0508 Institutional research plan: CEZ:AV0Z40550506 Keywords : microwave-assisted synthesis * haloalkylphosphonates * Michaelis-Arbuzov reaction Subject RIV: CC - Organic Chemistry Impact factor: 6.320, year: 2011

Assembly and dynamics of the bacteriophage T4 homologous recombination machinery

Directory of Open Access Journals (Sweden)

Morrical Scott W

2010-12-01

Full Text Available Abstract Homologous recombination (HR, a process involving the physical exchange of strands between homologous or nearly homologous DNA molecules, is critical for maintaining the genetic diversity and genome stability of species. Bacteriophage T4 is one of the classic systems for studies of homologous recombination. T4 uses HR for high-frequency genetic exchanges, for homology-directed DNA repair (HDR processes including DNA double-strand break repair, and for the initiation of DNA replication (RDR. T4 recombination proteins are expressed at high levels during T4 infection in E. coli, and share strong sequence, structural, and/or functional conservation with their counterparts in cellular organisms. Biochemical studies of T4 recombination have provided key insights on DNA strand exchange mechanisms, on the structure and function of recombination proteins, and on the coordination of recombination and DNA synthesis activities during RDR and HDR. Recent years have seen the development of detailed biochemical models for the assembly and dynamics of presynaptic filaments in the T4 recombination system, for the atomic structure of T4 UvsX recombinase, and for the roles of DNA helicases in T4 recombination. The goal of this chapter is to review these recent advances and their implications for HR and HDR mechanisms in all organisms.

Induction of homologous recombination in Saccharomyces cerevisiae.

Science.gov (United States)

Simon, J R; Moore, P D

1988-09-01

We have investigated the effects of UV irradiation of Saccharomyces cerevisiae in order to distinguish whether UV-induced recombination results from the induction of enzymes required for homologous recombination, or the production of substrate sites for recombination containing regions of DNA damage. We utilized split-dose experiments to investigate the induction of proteins required for survival, gene conversion, and mutation in a diploid strain of S. cerevisiae. We demonstrate that inducing doses of UV irradiation followed by a 6 h period of incubation render the cells resistant to challenge doses of UV irradiation. The effects of inducing and challenge doses of UV irradiation upon interchromosomal gene conversion and mutation are strictly additive. Using the yeast URA3 gene cloned in non-replicating single- and double-stranded plasmid vectors that integrate into chromosomal genes upon transformation, we show that UV irradiation of haploid yeast cells and homologous plasmid DNA sequences each stimulate homologous recombination approximately two-fold, and that these effects are additive. Non-specific DNA damage has little effect on the stimulation of homologous recombination, as shown by studies in which UV-irradiated heterologous DNA was included in transformation/recombination experiments. We further demonstrate that the effect of competing single- and double-stranded heterologous DNA sequences differs in UV-irradiated and unirradiated cells, suggesting an induction of recombinational machinery in UV-irradiated S. cerevisiae cells.

Prevalence of Germline Mutations in Genes Engaged in DNA Damage Repair by Homologous Recombination in Patients with Triple-Negative and Hereditary Non-Triple-Negative Breast Cancers.

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Pawel Domagala

Full Text Available This study sought to assess the prevalence of common germline mutations in several genes engaged in the repair of DNA double-strand break by homologous recombination in patients with triple-negative breast cancers and hereditary non-triple-negative breast cancers. Tumors deficient in this type of DNA damage repair are known to be especially sensitive to DNA cross-linking agents (e.g., platinum drugs and to poly(ADP-ribose polymerase (PARP inhibitors.Genetic testing was performed for 36 common germline mutations in genes engaged in the repair of DNA by homologous recombination, i.e., BRCA1, BRCA2, CHEK2, NBN, ATM, PALB2, BARD1, and RAD51D, in 202 consecutive patients with triple-negative breast cancers and hereditary non-triple-negative breast cancers.Thirty five (22.2% of 158 patients in the triple-negative group carried mutations in genes involved in DNA repair by homologous recombination, while 10 (22.7% of the 44 patients in the hereditary non-triple-negative group carried such mutations. Mutations in BRCA1 were most frequent in patients with triple-negative breast cancer (18.4%, and mutations in CHEK2 were most frequent in patients with hereditary non-triple-negative breast cancers (15.9%. In addition, in the triple-negative group, mutations in CHEK2, NBN, and ATM (3.8% combined were found, while mutations in BRCA1, NBN, and PALB2 (6.8% combined were identified in the hereditary non-triple-negative group.Identifying mutations in genes engaged in DNA damage repair by homologous recombination other than BRCA1/2 can substantially increase the proportion of patients with triple-negative breast cancer and hereditary non-triple-negative breast cancer who may be eligible for therapy using PARP inhibitors and platinum drugs.

The synthesis of [O-methyl-{sup 11}C]venlafaxine: a non-classical, fast-acting antidepressant

Energy Technology Data Exchange (ETDEWEB)

Gee, A.D.; Gjedde, A. [Aarhus Univ. Hospital, PET Center, Aarhus (Denmark); Smith, D.F. [Aarhus Univ. Psychiatric Hospital, Inst. for Biological Psychiatry, Risskov (Denmark)

1997-01-01

As part of our program to develop PET tracers for the 5-HT reuptake site, venlafaxine, a non-classical, fast-acting antidepressant, was selected as a candidate for labelling with {sup 11}C for in vivo evaluation. [O-methyl-{sup 11}C]venlafaxine was produced by the alkylation of O-desmethyl venlafaxine with [{sup 11}C]methyl iodide followed by HPLC purification and formulation. Radiochemically pure [O-methyl-{sup 11}C]venlafaxine was obtained in a 30 {+-} 5% decay corrected radiochemical yield and a specific activity > 50 GBq/{mu}mol(1.4 Ci/{mu}mol) at the end of synthesis. For a typical production starting with 46 GBq (1.3 Ci) [{sup 11}C]CO{sub 2}, 5.2 GBq (140 mCi) [O-methyl-{sup 11}C]venlafaxine was obtained as a sterile, formulated solution in a synthesis time of 30 min (counted from EOB). (Author).

Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway

Science.gov (United States)

Weeden, Clare E.; Chen, Yunshun; Ma, Stephen B.; Hu, Yifang; Ramm, Georg; Sutherland, Kate D.; Smyth, Gordon K.

2017-01-01

Lung squamous cell carcinoma (SqCC), the second most common subtype of lung cancer, is strongly associated with tobacco smoking and exhibits genomic instability. The cellular origins and molecular processes that contribute to SqCC formation are largely unexplored. Here we show that human basal stem cells (BSCs) isolated from heavy smokers proliferate extensively, whereas their alveolar progenitor cell counterparts have limited colony-forming capacity. We demonstrate that this difference arises in part because of the ability of BSCs to repair their DNA more efficiently than alveolar cells following ionizing radiation or chemical-induced DNA damage. Analysis of mice harbouring a mutation in the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a key enzyme in DNA damage repair by nonhomologous end joining (NHEJ), indicated that BSCs preferentially repair their DNA by this error-prone process. Interestingly, polyploidy, a phenomenon associated with genetically unstable cells, was only observed in the human BSC subset. Expression signature analysis indicated that BSCs are the likely cells of origin of human SqCC and that high levels of NHEJ genes in SqCC are correlated with increasing genomic instability. Hence, our results favour a model in which heavy smoking promotes proliferation of BSCs, and their predilection for error-prone NHEJ could lead to the high mutagenic burden that culminates in SqCC. Targeting DNA repair processes may therefore have a role in the prevention and therapy of SqCC. PMID:28125611

Microwave assisted synthesis of luminescent carbonaceous nanoparticles from silk fibroin for bioimaging.

Science.gov (United States)

Gao, Hongzhi; Teng, Choon Peng; Huang, Donghong; Xu, Wanqing; Zheng, Chaohui; Chen, Yisong; Liu, Minghuan; Yang, Da-Peng; Lin, Ming; Li, Zibiao; Ye, Enyi

2017-11-01

Bombyx mori silk as a natural protein based biopolymer with high nitrogen content, is abundant and sustainable because of its mass product all over the world per year. In this study, we developed a facile and fast microwave-assisted synthesis of luminescent carbonaceous nanoparticles using Bombyx mori silk fibroin and silk solution as the precursors. As a result, the obtained carbonaceous nanoparticles exhibit a photoluminescence quantum yield of ~20%, high stability, low cytotoxicity, high biocompatibility. Most importantly, we successfully demonstrated bioimaging using these luminescent carbonaceous nanoparticles with excitation dependent luminescence. In addition, the microwave-assisted hydrothermal method can be extended to convert other biomass into functional nanomaterials. Copyright © 2017 Elsevier B.V. All rights reserved.

The DNA-dependent protein kinase: a multifunctional protein kinase with roles in DNA double strand break repair and mitosis

OpenAIRE

Jette, Nicholas; Lees-Miller, Susan P.

2014-01-01

The DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase composed of a large catalytic subunit (DNA-PKcs) and the Ku70/80 heterodimer. Over the past two decades, significant progress has been made in elucidating the role of DNA-PK in non-homologous end joining (NHEJ), the major pathway for repair of ionizing radiation-induced DNA double strand breaks in human cells and recently, additional roles for DNA-PK have been reported. In this review, we will describe the biochemi...

Nrf2 facilitates repair of radiation induced DNA damage through homologous recombination repair pathway in a ROS independent manner in cancer cells

Energy Technology Data Exchange (ETDEWEB)

Jayakumar, Sundarraj; Pal, Debojyoti; Sandur, Santosh K., E-mail: sskumar@barc.gov.in

2015-09-15

Highlights: • Nrf2 inhibition in A549 cells led to attenuated DNA repair and radiosensitization. • Influence of Nrf2 on DNA repair is not linked to its antioxidant function. • Nrf2 influences DNA repair through homologous recombination (HR) repair pathway. • Many genes involved in HR pathway show ARE sequences in their upstream region. - Abstract: Nrf2 is a redox sensitive transcription factor that is involved in the co-ordinated transcription of genes involved in redox homeostasis. But the role of Nrf2 in DNA repair is not investigated in detail. We have employed A549 and MCF7 cells to study the role of Nrf2 on DNA repair by inhibiting Nrf2 using all-trans retinoic acid (ATRA) or by knock down approach prior to radiation exposure (4 Gy). DNA damage and repair analysis was studied by γH2AX foci formation and comet assay. Results suggested that the inhibition of Nrf2 in A549 or MCF7 cells led to significant slowdown in DNA repair as compared to respective radiation controls. The persistence of residual DNA damage even in the presence of free radical scavenger N-acetyl cysteine, suggested that the influence of Nrf2 on DNA repair was not linked to its antioxidant functions. Further, its influence on non-homologous end joining repair pathway was studied by inhibiting both Nrf2 and DNA-PK together. This led to synergistic reduction of survival fraction, indicating that Nrf2 may not be influencing the NHEJ pathway. To investigate the role of homologous recombination repair (HR) pathway, RAD51 foci formation was monitored. There was a significant reduction in the foci formation in cells treated with ATRA or shRNA against Nrf2 as compared to their respective radiation controls. Further, Nrf2 inhibition led to significant reduction in mRNA levels of RAD51. BLAST analysis was also performed on upstream regions of DNA repair genes to identify antioxidant response element and found that many repair genes that are involved in HR pathway may be regulated by Nrf2

Microwave-assisted hydrothermal synthesis of lead zirconate fine powders

Directory of Open Access Journals (Sweden)

Apinpus Rujiwatra

2011-01-01

Full Text Available A rapid synthesis of lead zirconate fine powders by microwave-assisted hydrothermal technique is reported. The influences of type of lead precursor, concentration of potassium hydroxide mineraliser, applied microwave power and irradiation time are described. The synthesised powders were characterised by powder X-ray diffraction, field emission scanning electron microscopy, energy-dispersive X-ray spectroscopic microanalysis and light scattering technique. The merits of the microwave application in reducing reaction time and improving particle mono-dispersion and size uniformity as well as the drawbacks, viz. low purity of the desired phase and increasing demand of mineraliser, are discussed in relation to conventional heating method.

Inhibitors of the proteasome suppress homologous DNA recombination in mammalian cells.

Science.gov (United States)

Murakawa, Yasuhiro; Sonoda, Eiichiro; Barber, Louise J; Zeng, Weihua; Yokomori, Kyoko; Kimura, Hiroshi; Niimi, Atsuko; Lehmann, Alan; Zhao, Guang Yu; Hochegger, Helfrid; Boulton, Simon J; Takeda, Shunichi

2007-09-15

Proteasome inhibitors are novel antitumor agents against multiple myeloma and other malignancies. Despite the increasing clinical application, the molecular basis of their antitumor effect has been poorly understood due to the involvement of the ubiquitin-proteasome pathway in multiple cellular metabolisms. Here, we show that treatment of cells with proteasome inhibitors has no significant effect on nonhomologous end joining but suppresses homologous recombination (HR), which plays a key role in DNA double-strand break (DSB) repair. In this study, we treat human cells with proteasome inhibitors and show that the inhibition of the proteasome reduces the efficiency of HR-dependent repair of an artificial HR substrate. We further show that inhibition of the proteasome interferes with the activation of Rad51, a key factor for HR, although it does not affect the activation of ATM, gammaH2AX, or Mre11. These data show that the proteasome-mediated destruction is required for the promotion of HR at an early step. We suggest that the defect in HR-mediated DNA repair caused by proteasome inhibitors contributes to antitumor effect, as HR plays an essential role in cellular proliferation. Moreover, because HR plays key roles in the repair of DSBs caused by chemotherapeutic agents such as cisplatin and by radiotherapy, proteasome inhibitors may enhance the efficacy of these treatments through the suppression of HR-mediated DNA repair pathways.

Turbo Charge CPU Utilization in Fork/Join Using the ManagedBlocker

CERN Multimedia

CERN. Geneva

2017-01-01

Fork/Join is a framework for parallelizing calculations using recursive decomposition, also called divide and conquer. These algorithms occasionally end up duplicating work, especially at the beginning of the run. We can reduce wasted CPU cycles by implementing a reserved caching scheme. Before a task starts its calculation, it tries to reserve an entry in the shared map. If it is successful, it immediately begins. If not, it blocks until the other thread has finished its calculation. Unfortunately this might result in a significant number of blocked threads, decreasing CPU utilization. In this talk we will demonstrate this issue and offer a solution in the form of the ManagedBlocker. Combined with the Fork/Join, it can keep parallelism at the desired level.

Homotopic Chain Maps Have Equal s-Homology and d-Homology

Directory of Open Access Journals (Sweden)

M. Z. Kazemi-Baneh

2016-01-01

Full Text Available The homotopy of chain maps on preabelian categories is investigated and the equality of standard homologies and d-homologies of homotopic chain maps is established. As a special case, if X and Y are the same homotopy type, then their nth d-homology R-modules are isomorphic, and if X is a contractible space, then its nth d-homology R-modules for n≠0 are trivial.

Microwave-assisted synthesis of iron oxide nanoparticles in biocompatible organic environment

Directory of Open Access Journals (Sweden)

E. Aivazoglou

2018-04-01

Full Text Available The development of magnetite and maghemite particles in uniform nanometer size has triggered the interest of the research community due to their many interesting properties leading to a wide range of applications, such as catalysis, nanomedicine-nanobiology and other engineering applications. In this study, a simple, time-saving and low energy-consuming, microwave-assisted synthesis of iron oxide nanoparticles, is presented. The nanoparticles were prepared by microwave-assisted synthesis using polyethylene glycol (PEG or PEG and β-cyclodextrin (β-CD/water solutions of chloride salts of iron in the presence of ammonia solution. The prepared nano-powders were characterized using X-Ray Diffraction (XRD, Transition Electron Microscopy (TEM, Fourier-transform Infrared Spectroscopy (FTIR, Raman Spectroscopy, Vibrating Sample Magnetometer (VSM, X-Ray Photoelectron Spectroscopy (XPS and Thermal analysis (TG/DSC. The produced nanoparticles are crystallized mostly in the magnetite and maghemite lattice exhibiting very similar shape and size, with indications of partial PEG coating. Heating time, microwave power and presence of PEG, are the key factors shaping the size properties of nanoparticles. The average size of particles ranges from 10.3 to 19.2 nm. The nanoparticles exhibit a faceted morphology, with zero contamination levels. The magnetic measurements indicate that the powders are soft magnetic materials with negligible coercivity and remanence, illustrating super-paramagnetic behavior.

Parallel trajectory similarity joins in spatial networks

KAUST Repository

Shang, Shuo

2018-04-04

The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider two cases of trajectory similarity joins (TS-Joins), including a threshold-based join (Tb-TS-Join) and a top-k TS-Join (k-TS-Join), where the objects are trajectories of vehicles moving in road networks. Given two sets of trajectories and a threshold θ, the Tb-TS-Join returns all pairs of trajectories from the two sets with similarity above θ. In contrast, the k-TS-Join does not take a threshold as a parameter, and it returns the top-k most similar trajectory pairs from the two sets. The TS-Joins target diverse applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide purposeful definitions of similarity. To enable efficient processing of the TS-Joins on large sets of trajectories, we develop search space pruning techniques and enable use of the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer search framework that lays the foundation for the algorithms for the Tb-TS-Join and the k-TS-Join that rely on different pruning techniques to achieve efficiency. For each trajectory, the algorithms first find similar trajectories. Then they merge the results to obtain the final result. The algorithms for the two joins exploit different upper and lower bounds on the spatiotemporal trajectory similarity and different heuristic scheduling strategies for search space pruning. Their per-trajectory searches are independent of each other and can be performed in parallel, and the mergings have constant cost. An empirical study with real data offers insight in the performance of the algorithms and demonstrates that they are capable of outperforming well-designed baseline algorithms by an order of magnitude.

Parallel trajectory similarity joins in spatial networks

KAUST Repository

Shang, Shuo; Chen, Lisi; Wei, Zhewei; Jensen, Christian S.; Zheng, Kai; Kalnis, Panos

2018-01-01

The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider two cases of trajectory similarity joins (TS-Joins), including a threshold-based join (Tb-TS-Join) and a top-k TS-Join (k-TS-Join), where the objects are trajectories of vehicles moving in road networks. Given two sets of trajectories and a threshold θ, the Tb-TS-Join returns all pairs of trajectories from the two sets with similarity above θ. In contrast, the k-TS-Join does not take a threshold as a parameter, and it returns the top-k most similar trajectory pairs from the two sets. The TS-Joins target diverse applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide purposeful definitions of similarity. To enable efficient processing of the TS-Joins on large sets of trajectories, we develop search space pruning techniques and enable use of the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer search framework that lays the foundation for the algorithms for the Tb-TS-Join and the k-TS-Join that rely on different pruning techniques to achieve efficiency. For each trajectory, the algorithms first find similar trajectories. Then they merge the results to obtain the final result. The algorithms for the two joins exploit different upper and lower bounds on the spatiotemporal trajectory similarity and different heuristic scheduling strategies for search space pruning. Their per-trajectory searches are independent of each other and can be performed in parallel, and the mergings have constant cost. An empirical study with real data offers insight in the performance of the algorithms and demonstrates that they are capable of outperforming well-designed baseline algorithms by an order of magnitude.

Towards mastering CRISPR-induced gene knock-in in plants: Survey of key features and focus on the model Physcomitrella patens.

Science.gov (United States)

Collonnier, Cécile; Guyon-Debast, Anouchka; Maclot, François; Mara, Kostlend; Charlot, Florence; Nogué, Fabien

2017-05-15

Beyond its predominant role in human and animal therapy, the CRISPR-Cas9 system has also become an essential tool for plant research and plant breeding. Agronomic applications rely on the mastery of gene inactivation and gene modification. However, if the knock-out of genes by non-homologous end-joining (NHEJ)-mediated repair of the targeted double-strand breaks (DSBs) induced by the CRISPR-Cas9 system is rather well mastered, the knock-in of genes by homology-driven repair or end-joining remains difficult to perform efficiently in higher plants. In this review, we describe the different approaches that can be tested to improve the efficiency of CRISPR-induced gene modification in plants, which include the use of optimal transformation and regeneration protocols, the design of appropriate guide RNAs and donor templates and the choice of nucleases and means of delivery. We also present what can be done to orient DNA repair pathways in the target cells, and we show how the moss Physcomitrella patens can be used as a model plant to better understand what DNA repair mechanisms are involved, and how this knowledge could eventually be used to define more performant strategies of CRISPR-induced gene knock-in. Copyright © 2017 Elsevier Inc. All rights reserved.

Additive-assisted synthesis of boride, carbide, and nitride micro/nanocrystals

International Nuclear Information System (INIS)

Chen, Bo; Yang, Lishan; Heng, Hua; Chen, Jingzhong; Zhang, Linfei; Xu, Liqiang; Qian, Yitai; Yang, Jian

2012-01-01

General and simple methods for the syntheses of borides, carbides and nitrides are highly desirable, since those materials have unique physical properties and promising applications. Here, a series of boride (TiB 2 , ZrB 2 , NbB 2 , CeB 6 , PrB 6 , SmB 6 , EuB 6 , LaB 6 ), carbide (SiC, TiC, NbC, WC) and nitride (TiN, BN, AlN, MgSiN 2 , VN) micro/nanocrystals were prepared from related oxides and amorphous boron/active carbon/NaN 3 with the assistance of metallic Na and elemental S. In-situ temperature monitoring showed that the reaction temperature could increase quickly to ∼850 °C, once the autoclave was heated to 100 °C. Such a rapid temperature increase was attributed to the intense exothermic reaction between Na and S, which assisted the formation of borides, carbides and nitrides. The as-obtained products were characterized by XRD, SEM, TEM, and HRTEM techniques. Results in this report will greatly benefit the future extension of this approach to other compounds. - Graphical abstract: An additive-assisted approach is successfully developed for the syntheses of borides, carbides and nitrides micro/nanocrystals with the assistance of the exothermic reaction between Na and S. Highlights: ► An additive-assisted synthesis strategy is developed for a number of borides, carbides and nitrides. ► The reaction mechanism is demonstrated by the case of SiC nanowires. ► The formation of SiC nanowires is initiated by the exothermic reaction of Na and S.

On the Expressiveness of Joining

Directory of Open Access Journals (Sweden)

Thomas Given-Wilson

2015-08-01

Full Text Available The expressiveness of communication primitives has been explored in a common framework based on the pi-calculus by considering four features: synchronism (asynchronous vs synchronous, arity (monadic vs polyadic data, communication medium (shared dataspaces vs channel-based, and pattern-matching (binding to a name vs testing name equality vs intensionality. Here another dimension coordination is considered that accounts for the number of processes required for an interaction to occur. Coordination generalises binary languages such as pi-calculus to joining languages that combine inputs such as the Join Calculus and general rendezvous calculus. By means of possibility/impossibility of encodings, this paper shows coordination is unrelated to the other features. That is, joining languages are more expressive than binary languages, and no combination of the other features can encode a joining language into a binary language. Further, joining is not able to encode any of the other features unless they could be encoded otherwise.

Microwave-assisted synthesis of α-aryl malonates: Key intermediates for the

Directory of Open Access Journals (Sweden)

Mohamed A. Ibrahim

2016-11-01

Full Text Available We disclose a new microwave-assisted protocol for the effective α-arylation of diethyl malonate. The coupling of aryl halides with diethyl malonate proceeds smoothly in short reaction time in the presence of a catalytic amount of Cu(OTf2, 2-picolinic acid and Cs2CO3 in toluene using microwave irradiation. The resulting α-aryl malonates are then used as key intermediates for synthesis of variety of heterocyclic compounds, including benzodiazepines, isoquinolines and pyrrolopyridine scaffolds.

Double strand break repair: two mechanisms in competition but tightly linked to cell cycle

International Nuclear Information System (INIS)

Delacote, F.

2002-11-01

DNA double strand breaks (DSB) are highly toxic damage although they can be induced to create genetic diversity. Two distinct pathways can repair DSB: Homologous Recombination (HR) and Non Homologous End Joining (NHEJ). If un- or mis-repaired, this damage can lead to cancer. Thus, it is essential to investigate how these two pathways are regulated for DSB repair. NHEJ inhibition leads to HR DSB repair stimulation. However, this channeling to HR is tightly linked to cell cycle since NHEJ and HR are active in G1/early S and late S/G2, respectively. Our results suggest that G1-unrepaired DSB go through S phase to be repaired by HR in G2. Those results allow a better understanding of DSB repair mechanisms regulation. (author)

Microwave-assisted rapid extracellular synthesis of stable bio-functionalized silver nanoparticles from guava ( Psidium guajava) leaf extract

Science.gov (United States)

Raghunandan, Deshpande; Mahesh, Bedre D.; Basavaraja, S.; Balaji, S. D.; Manjunath, S. Y.; Venkataraman, A.

2011-05-01

Our research interest centers on microwave-assisted rapid extracellular synthesis of bio-functionalized silver nanoparticles of 26 ± 5 nm from guava ( Psidium guajava) leaf extract with control over dimension and composition. The reaction occurs very rapidly as the formation of spherical nanoparticles almost completed within 90 s. The probable pathway of the biosynthesis is suggested. Appearance, crystalline nature, size and shape of nanoparticles are understood by UV-vis (UV-vis spectroscopy), FTIR (fourier transform infrared spectroscopy), XRD (X-ray diffraction), FESEM (field emission scanning electron microscopy) and TEM (transmission electron microscopy) techniques. Microwave-assisted route is selected for the synthesis of silver nanoparticles to carry out the reaction fast, suppress the enzymatic action and to keep the process environmentally clean and green.

Microwave-assisted rapid extracellular synthesis of stable bio-functionalized silver nanoparticles from guava (Psidium guajava) leaf extract

Energy Technology Data Exchange (ETDEWEB)

Raghunandan, Deshpande [H.K.E.S' s College of Pharmacy (India); Mahesh, Bedre D. [Gulbarga University, Materials Chemistry Laboratory, Department of Material Science (India); Basavaraja, S. [Jawaharlal Nehru Centre for Advanced Scientific Research, Veeco-India Nanotechnology Laboratory (India); Balaji, S. D. [Gulbarga University, Materials Chemistry Laboratory, Department of Material Science (India); Manjunath, S. Y. [Sri Krupa, Institute of Pharmaceutical Science (India); Venkataraman, A., E-mail: raman_chem@rediffmail.com [Gulbarga University, Materials Chemistry Laboratory, Department of Material Science (India)

2011-05-15

Our research interest centers on microwave-assisted rapid extracellular synthesis of bio-functionalized silver nanoparticles of 26 {+-} 5 nm from guava (Psidium guajava) leaf extract with control over dimension and composition. The reaction occurs very rapidly as the formation of spherical nanoparticles almost completed within 90 s. The probable pathway of the biosynthesis is suggested. Appearance, crystalline nature, size and shape of nanoparticles are understood by UV-vis (UV-vis spectroscopy), FTIR (fourier transform infrared spectroscopy), XRD (X-ray diffraction), FESEM (field emission scanning electron microscopy) and TEM (transmission electron microscopy) techniques. Microwave-assisted route is selected for the synthesis of silver nanoparticles to carry out the reaction fast, suppress the enzymatic action and to keep the process environmentally clean and green.

Microwave-assisted rapid extracellular synthesis of stable bio-functionalized silver nanoparticles from guava (Psidium guajava) leaf extract

International Nuclear Information System (INIS)

Raghunandan, Deshpande; Mahesh, Bedre D.; Basavaraja, S.; Balaji, S. D.; Manjunath, S. Y.; Venkataraman, A.

2011-01-01

Our research interest centers on microwave-assisted rapid extracellular synthesis of bio-functionalized silver nanoparticles of 26 ± 5 nm from guava (Psidium guajava) leaf extract with control over dimension and composition. The reaction occurs very rapidly as the formation of spherical nanoparticles almost completed within 90 s. The probable pathway of the biosynthesis is suggested. Appearance, crystalline nature, size and shape of nanoparticles are understood by UV–vis (UV–vis spectroscopy), FTIR (fourier transform infrared spectroscopy), XRD (X-ray diffraction), FESEM (field emission scanning electron microscopy) and TEM (transmission electron microscopy) techniques. Microwave-assisted route is selected for the synthesis of silver nanoparticles to carry out the reaction fast, suppress the enzymatic action and to keep the process environmentally clean and green.

ATM loss leads to synthetic lethality in BRCA1 BRCT mutant mice associated with exacerbated defects in homology-directed repair.

Science.gov (United States)

Chen, Chun-Chin; Kass, Elizabeth M; Yen, Wei-Feng; Ludwig, Thomas; Moynahan, Mary Ellen; Chaudhuri, Jayanta; Jasin, Maria

2017-07-18

BRCA1 is essential for homology-directed repair (HDR) of DNA double-strand breaks in part through antagonism of the nonhomologous end-joining factor 53BP1. The ATM kinase is involved in various aspects of DNA damage signaling and repair, but how ATM participates in HDR and genetically interacts with BRCA1 in this process is unclear. To investigate this question, we used the Brca1 S1598F mouse model carrying a mutation in the BRCA1 C-terminal domain of BRCA1. Whereas ATM loss leads to a mild HDR defect in adult somatic cells, we find that ATM inhibition leads to severely reduced HDR in Brca1 S1598F cells. Consistent with a critical role for ATM in HDR in this background, loss of ATM leads to synthetic lethality of Brca1 S1598F mice. Whereas both ATM and BRCA1 promote end resection, which can be regulated by 53BP1, 53bp1 deletion does not rescue the HDR defects of Atm mutant cells, in contrast to Brca1 mutant cells. These results demonstrate that ATM has a role in HDR independent of the BRCA1-53BP1 antagonism and that its HDR function can become critical in certain contexts.

Highly efficient generation of knock-in transgenic medaka by CRISPR/Cas9-mediated genome engineering.

Science.gov (United States)

Watakabe, Ikuko; Hashimoto, Hisashi; Kimura, Yukiko; Yokoi, Saori; Naruse, Kiyoshi; Higashijima, Shin-Ichi

2018-01-01

Medaka ( Oryzias latipes ) is a popular animal model used in vertebrate genetic analysis. Recently, an efficient (~ 30%) knock-in system via non-homologous end joining (NHEJ) was established in zebrafish using the CRISPR/Cas9 system. If the same technique were applicable in medaka, it would greatly expand the usefulness of this model organism. The question of the applicability of CRISPR/Cas9 in medaka, however, has yet to be addressed. We report the highly efficient generation of knock-in transgenic medaka via non-homologous end joining (NHEJ). Donor plasmid containing a heat-shock promoter and a reporter gene was co-injected with a short guide RNA (sgRNA) targeted for genome digestion, an sgRNA targeted for donor plasmid digestion, and Cas9 mRNA. Broad transgene expression in the expression domain of a target gene was observed in approximately 25% of injected embryos. By raising these animals, we established stable knock-in transgenic fish with several different constructs for five genetic loci, obtaining transgenic founders at efficiencies of > 50% for all five loci. Further, we show that the method is useful for obtaining mutant alleles. In the experiments where transgene integrations were targeted between the transcription start site and the initiation methionine, the resultant transgenic fish became mutant alleles. With its simplicity, design flexibility, and high efficiency, we propose that CRISPR/Cas9-mediated knock-in via NHEJ will become a standard method for the generation of transgenic and mutant medaka.

Common Influence Join

DEFF Research Database (Denmark)

Yiu, Man Lung; Mamoulis, Nikos; Karras, Panagiotis

2008-01-01

We identify and formalize a novel join operator for two spatial pointsets P and Q. The common influence join (CIJ) returns the pairs of points (p,q),p isin P,q isin Q, such that there exists a location in space, being closer to p than to any other point in P and at the same time closer to q than ......-demand, is very efficient in practice, incurring only slightly higher I/O cost than the theoretical lower bound cost for the problem....

Repair of DNA DSB in higher eukaryotes

International Nuclear Information System (INIS)

Wang, H.; Perrault, A.R.; Takeda, Y.; Iliakis, G.

2003-01-01

Cells of higher eukaryotes process within minutes double strand breaks (DSBs) in their genome using a NHEJ apparatus that engages DNA-PKcs, Ku, DNA ligase IV, XRCC4, and other as of yet unidentified factors. Although chemical inhibition, or mutation, in any of these factors delays processing, cells ultimately remove the majority of DNA DSBs using an alternative pathway operating with slower kinetics. This alternative pathway is active in mutants deficient in genes of the RAD52 epistasis group. We proposed, therefore, that it reflects an alternative form of NHEJ that operates as a backup (B-NHEJ) to the DNA-PK- dependent (D-NHEJ) pathway, rather than homology directed repair of DSBs. We studied the role of Ku and DNA-PKcs in the coordination of these pathways using as a model end joining of restriction endonuclease linearized plasmid DNA in whole cell extracts. Efficient error-free endjoining observed in such in-vitro reactions is strongly inhibited by anti-Ku antibodies. The inhibition requires DNA-PKcs, despite that fact that Ku efficiently binds DNA ends in the presence of antibodies, or in the absence of DNA-PKcs. Strong inhibition of DNA endjoining is also mediated by wortmannin, an inhibitor of DNA-PKcs, in the presence but not in the absence of Ku, and this inhibition can be rescued by pre-incubating the reaction with double stranded oligonucleotides. The results are compatible with a role of Ku in directing endjoining to a DNA-PK dependent pathway, mediated by efficient end binding and productive interactions with DNA-PKcs. On the other hand, efficient end joining is observed in extracts of cells lacking DNA-PKcs, as well as in Ku-depleted extracts sugggesting the operation of alternative pathways. Extracts depleted of Ku and DNA-PKcs rejoin blunt ends, as well as homologous ends with 3' or 5' protruding single strands with similar efficiency, but addition of Ku suppresses joining of blunt ends and homologous ends with 3' overhangs. We propose that the

Speeding Up Neighbour-Joining Tree Construction

DEFF Research Database (Denmark)

Brodal, Gerth Stølting; Fagerberg, Rolf; Mailund, Thomas

A widely used method for constructing phylogenetic trees is the neighbour-joining method of Saitou and Nei. We develope heuristics for speeding up the neighbour-joining method which generate the same phylogenetic trees as the original method. All heuristics are based on using a quad-tree to guide...... the search for the next pair of nodes to join, but di#er in the information stored in quad-tree nodes, the way the search is performed, and in the way the quad-tree is updated after a join. We empirically evaluate the performance of the heuristics on distance matrices obtained from the Pfam collection...... of alignments, and compare the running time with that of the QuickTree tool, a well-known and widely used implementation of the standard neighbour-joining method. The results show that the presented heuristics can give a significant speed-up over the standard neighbour-joining method, already for medium sized...

PCR artifact in testing for homologous recombination in genomic editing in zebrafish.

Directory of Open Access Journals (Sweden)

Minho Won

Full Text Available We report a PCR-induced artifact in testing for homologous recombination in zebrafish. We attempted to replace the lnx2a gene with a donor cassette, mediated by a TALEN induced double stranded cut. The donor construct was flanked with homology arms of about 1 kb at the 5' and 3' ends. Injected embryos (G0 were raised and outcrossed to wild type fish. A fraction of the progeny appeared to have undergone the desired homologous recombination, as tested by PCR using primer pairs extending from genomic DNA outside the homology region to a site within the donor cassette. However, Southern blots revealed that no recombination had taken place. We conclude that recombination happened during PCR in vitro between the donor integrated elsewhere in the genome and the lnx2a locus. We conclude that PCR alone may be insufficient to verify homologous recombination in genome editing experiments in zebrafish.

Khovanov homology for virtual knots with arbitrary coefficients

International Nuclear Information System (INIS)

Manturov, Vassily O

2007-01-01

The Khovanov homology theory over an arbitrary coefficient ring is extended to the case of virtual knots. We introduce a complex which is well-defined in the virtual case and is homotopy equivalent to the original Khovanov complex in the classical case. Unlike Khovanov's original construction, our definition of the complex does not use any additional prescription of signs to the edges of a cube. Moreover, our method enables us to construct a Khovanov homology theory for 'twisted virtual knots' in the sense of Bourgoin and Viro (including knots in three-dimensional projective space). We generalize a number of results of Khovanov homology theory (the Wehrli complex, minimality problems, Frobenius extensions) to virtual knots with non-orientable atoms

Non-physician-assisted suicide in The Netherlands: a cross-sectional survey among the general public.

Science.gov (United States)

Schoonman, Merel Kristi; van Thiel, Ghislaine José Madeleine Wilhelmien; van Delden, Johannes Jozef Marten

2014-12-01

In The Netherlands, approximately 45% of patients' requests for euthanasia are granted by a physician. After a rejected request, some patients approach non-physicians and ask them for assistance in suicide. Recently, a non-physician who assisted his mother's suicide was declared guilty without punishment. The aim of the current study was to investigate the opinion of the Dutch general public on non-physician-assisted suicide. A cross-sectional survey among the Dutch general public was performed. A total of 1113 respondents were included (response rate 80%). The survey covered two case descriptions in which a patient asks a non-physician for assisted suicide after a non-granted request for physician-assisted dying. In both cases, a son, friend or professional facilitates the suicide by either the provision of information or the purchase of lethal medication. Respondents were invited to give their opinion on these cases and in addition on 10 propositions on non-physician-assisted suicide. When a son provides information on how to acquire lethal medication in case of a patient with a terminal illness, this involvement is accepted by 62% of the respondents. The actual purchase of lethal medication receives less support (38%). If the patient suffers without a serious disease, both forms of assistance are less accepted (46% and 24%, respectively). In addition, only 21% support the legalisation of non-physician-assisted suicide. The Dutch public prefer involvement of a physician in assisted suicide (69%). The Dutch general public consider non-physician-assisted suicide in some specific cases a tolerable alternative for patients with a rejected request for physician-assisted dying if the assistance is limited to the provision of information. However, the majority do not support the legalisation of non-physician-assisted suicide. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Clinical and molecular studies in four patients with SRY-positive 46,XX testicular disorders of sex development: implications for variable sex development and genomic rearrangements.

Science.gov (United States)

Nakashima, Shinichi; Ohishi, Akira; Takada, Fumio; Kawamura, Hideki; Igarashi, Maki; Fukami, Maki; Ogata, Tsutomu

2014-10-01

We report four patients with SRY-positive 46,XX testicular disorders of sex development (46,XX-TDSD) (cases 1-4). Case 1 exhibited underdeveloped external genitalia with hypospadias, case 2 manifested micropenis and cases 3 and 4 showed normal external genitalia. The Xp;Yp translocations occurred between the X- and the Y-differential regions in case 1, between PRKX and inverted PRKY in case 2 and between the X-chromosomal short arm pseudoautosomal region and the Y-differential regions in cases 3 and 4. The distance of the Yp breakpoint from SRY was ~0.75 Mb in case 1, ~6.5 Mb in case 2, ~2.3 Mb in case 3 and ~72 kb in case 4. The Xp;Yp translocation occurred within an 87-bp homologous segment of PRKX and PRKY in case 2, and between non-homologous regions with addition of an 18-bp sequence of unknown origin in case 4. X-inactivation analysis revealed random inactivation in cases 1-4. The results argue against the notion that undermasculinization in 46,XX-TDSD is prone to occur when translocated Yp materials are small (<100 kb of the Y-differential region), and imply that the Xp;Yp translocations result from several mechanisms including non-allelic homologous recombination and non-homologous end joining.

Cavitation assisted synthesis of fatty acid methyl esters from sustainable feedstock in presence of heterogeneous catalyst using two step process.

Science.gov (United States)

Dubey, Sumit M; Gole, Vitthal L; Gogate, Parag R

2015-03-01

The present work reports the intensification aspects for the synthesis of fatty acid methyl esters (FAME) from a non-edible high acid value Nagchampa oil (31 mg of KOH/g of oil) using two stage acid esterification (catalyzed by H₂SO₄) followed by transesterification in the presence of heterogeneous catalyst (CaO). Intensification aspects of both stages have been investigated using sonochemical reactors and the obtained degree of intensification has been established by comparison with the conventional approach based on mechanical agitation. It has been observed that reaction temperature for esterification reduced from 65 to 40 °C for the ultrasonic approach whereas there was a significant reduction in the optimum reaction time for transesterification from 4h for the conventional approach to 2.5h for the ultrasound assisted approach. Also the reaction temperature reduced marginally from 65 to 60 °C and yield increased from 76% to 79% for the ultrasound assisted approach. Energy requirement and activation energy for both esterification and transesterification was lower for the ultrasound based approach as compared to the conventional approach. The present work has clearly established the intensification obtained due to the use of ultrasound and also illustrated the two step approach for the synthesis of FAME from high acid value feedstock based on the use of heterogeneous catalyst for the transesterification step. Copyright © 2014 Elsevier B.V. All rights reserved.

Efficient Joins with Compressed Bitmap Indexes

Energy Technology Data Exchange (ETDEWEB)

Computational Research Division; Madduri, Kamesh; Wu, Kesheng

2009-08-19

We present a new class of adaptive algorithms that use compressed bitmap indexes to speed up evaluation of the range join query in relational databases. We determine the best strategy to process a join query based on a fast sub-linear time computation of the join selectivity (the ratio of the number of tuples in the result to the total number of possible tuples). In addition, we use compressed bitmaps to represent the join output compactly: the space requirement for storing the tuples representing the join of two relations is asymptotically bounded by min(h; n . cb), where h is the number of tuple pairs in the result relation, n is the number of tuples in the smaller of the two relations, and cb is the cardinality of the larger column being joined. We present a theoretical analysis of our algorithms, as well as experimental results on large-scale synthetic and real data sets. Our implementations are efficient, and consistently outperform well-known approaches for a range of join selectivity factors. For instance, our count-only algorithm is up to three orders of magnitude faster than the sort-merge approach, and our best bitmap index-based algorithm is 1.2x-80x faster than the sort-merge algorithm, for various query instances. We achieve these speedups by exploiting several inherent performance advantages of compressed bitmap indexes for join processing: an implicit partitioning of the attributes, space-efficiency, and tolerance of high-cardinality relations.

Formation of base triplets by non-Watson-Crick bonds mediates homologous recognition in RecA recombination filaments.

OpenAIRE

Rao, B J; Radding, C M

1994-01-01

Whereas complementary strands of DNA recognize one another by forming Watson-Crick base pairs, the way in which RecA protein enables a single strand to recognize homology in duplex DNA has remained unknown. Recent experiments, however, have shown that a single plus strand in the RecA filament can recognize an identical plus strand via bonds that, by definition, are non-Watson-Crick. In experiments reported here, base substitutions had the same qualitative and quantitative effects on the pairi...

Homological stabilizer codes

Energy Technology Data Exchange (ETDEWEB)

Anderson, Jonas T., E-mail: jonastyleranderson@gmail.com

2013-03-15

In this paper we define homological stabilizer codes on qubits which encompass codes such as Kitaev's toric code and the topological color codes. These codes are defined solely by the graphs they reside on. This feature allows us to use properties of topological graph theory to determine the graphs which are suitable as homological stabilizer codes. We then show that all toric codes are equivalent to homological stabilizer codes on 4-valent graphs. We show that the topological color codes and toric codes correspond to two distinct classes of graphs. We define the notion of label set equivalencies and show that under a small set of constraints the only homological stabilizer codes without local logical operators are equivalent to Kitaev's toric code or to the topological color codes. - Highlights: Black-Right-Pointing-Pointer We show that Kitaev's toric codes are equivalent to homological stabilizer codes on 4-valent graphs. Black-Right-Pointing-Pointer We show that toric codes and color codes correspond to homological stabilizer codes on distinct graphs. Black-Right-Pointing-Pointer We find and classify all 2D homological stabilizer codes. Black-Right-Pointing-Pointer We find optimal codes among the homological stabilizer codes.

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...

Non-faith-based arguments against physician-assisted suicide and euthanasia.

Science.gov (United States)

Sulmasy, Daniel P; Travaline, John M; Mitchell, Louise A; Ely, E Wesley

2016-08-01

This article is a complement to "A Template for Non-Religious-Based Discussions Against Euthanasia" by Melissa Harintho, Nathaniel Bloodworth, and E. Wesley Ely which appeared in the February 2015 Linacre Quarterly . Herein we build upon Daniel Sulmasy's opening and closing arguments from the 2014 Intelligence Squared debate on legalizing assisted suicide, supplemented by other non-faith-based arguments and thoughts, providing four nontheistic arguments against physician-assisted suicide and euthanasia: (1) "it offends me"; (2) slippery slope; (3) "pain can be alleviated"; (4) physician integrity and patient trust. Lay Summary: Presented here are four non-religious, reasonable arguments against physician-assisted suicide and euthanasia: (1) "it offends me," suicide devalues human life; (2) slippery slope, the limits on euthanasia gradually erode; (3) "pain can be alleviated," palliative care and modern therapeutics more and more adequately manage pain; (4) physician integrity and patient trust, participating in suicide violates the integrity of the physician and undermines the trust patients place in physicians to heal and not to harm.

Evolutionary origin and divergence of GnIH and its homologous peptides.

Science.gov (United States)

Tsutsui, Kazuyoshi; Osugi, Tomohiro

2009-03-01

Probing undiscovered hypothalamic neuropeptides that play important roles in the regulation of pituitary function in vertebrates is essential for the progress of neuroendocrinology. In 2000, we discovered a novel hypothalamic dodecapeptide inhibiting gonadotropin release in quail and termed it gonadotropin-inhibitory hormone (GnIH). GnIH acts on the pituitary and gonadotropin-releasing hormone (GnRH) neurons in the hypothalamus via a novel G protein-coupled receptor for GnIH to inhibit gonadal development and maintenance by decreasing gonadotropin release and synthesis. Similar findings were observed in other avian species. Thus, GnIH is a key factor controlling avian reproduction. To give our findings a broader perspective, we also found GnIH homologous peptides in the hypothalamus of other vertebrates, such as mammals, reptiles, amphibians and teleosts. GnIH and its homologs share a common C-terminal LPXRFamide (X=L or Q) motif. A mammalian GnIH homolog also inhibited gonadotropin release in mammals like the GnIH action in birds. In contrast to higher vertebrates, hypophysiotropic activities of GnIH homologs were different in lower vertebrates. To clarify the evolutionary origin of GnIH and its homologs, we further sought to identify novel LPXRFamide peptides from the brain of sea lamprey and hagfish, two extant groups of the oldest lineage of vertebrates, Agnatha. In these agnathans, LPXRFamide peptide and its cDNA were identified only from the brain of hagfish. Based on these findings over the past decade, this paper summarizes the evolutionary origin and divergence of GnIH and its homologous peptides.

Microwave-Assisted Hydrothermal Synthesis of Cellulose/Hydroxyapatite Nanocomposites

Directory of Open Access Journals (Sweden)

Lian-Hua Fu

2016-09-01

Full Text Available In this paper, we report a facile, rapid, and green strategy for the synthesis of cellulose/hydroxyapatite (HA nanocomposites using an inorganic phosphorus source (sodium dihydrogen phosphate dihydrate (NaH2PO4·2H2O, or organic phosphorus sources (adenosine 5′-triphosphate disodium salt (ATP, creatine phosphate disodium salt tetrahydrate (CP, or D-fructose 1,6-bisphosphate trisodium salt octahydrate (FBP through the microwave-assisted hydrothermal method. The effects of the phosphorus sources, heating time, and heating temperature on the phase, size, and morphology of the products were systematically investigated. The experimental results revealed that the phosphate sources played a critical role on the phase, size, and morphology of the minerals in the nanocomposites. For example, the pure HA was obtained by using NaH2PO4·2H2O as phosphorus source, while all the ATP, CP, and FBP led to the byproduct, calcite. The HA nanostructures with various morphologies (including nanorods, pseudo-cubic, pseudo-spherical, and nano-spherical particles were obtained by varying the phosphorus sources or adjusting the reaction parameters. In addition, this strategy is surfactant-free, avoiding the post-treatment procedure and cost for the surfactant removal from the product. We believe that this work can be a guidance for the green synthesis of cellulose/HA nanocomposites in the future.

Welding and Joining of Titanium Aluminides

Science.gov (United States)

Cao, Jian; Qi, Junlei; Song, Xiaoguo; Feng, Jicai

2014-01-01

Welding and joining of titanium aluminides is the key to making them more attractive in industrial fields. The purpose of this review is to provide a comprehensive overview of recent progress in welding and joining of titanium aluminides, as well as to introduce current research and application. The possible methods available for titanium aluminides involve brazing, diffusion bonding, fusion welding, friction welding and reactive joining. Of the numerous methods, solid-state diffusion bonding and vacuum brazing have been most heavily investigated for producing reliable joints. The current state of understanding and development of every welding and joining method for titanium aluminides is addressed respectively. The focus is on the fundamental understanding of microstructure characteristics and processing–microstructure–property relationships in the welding and joining of titanium aluminides to themselves and to other materials. PMID:28788113

Glass-Metal Joining in Nuclear Environment: the State of the Art

International Nuclear Information System (INIS)

Jacobs, M.

2007-01-01

Full text of publication follows: In the ITER fusion machine and in material testing fission reactors, it is not possible to avoid the use of non-metallic materials like glass for example. There is therefore a need to apply metal to glass joints. This problem arose already at the beginning of the 19. century when the electric light bulb was invented. Nowadays this type of glass-metal joint is very successful and widely used in the electronic industry. In the case of ITER and material testing reactors, glass-metal joints are necessary for the fixation of the optical windows and optical fibres to a metal structure to perform diagnostics. These types of joints are still difficult to make and their behaviour is not fully understood. A joint between glass and metal for a nuclear or fusion application has indeed to resist high temperatures and high neutron fluences, while keeping a good mechanical strength and remaining leak tight. These characteristics are difficult to obtain under these severe conditions. This paper presents an overview of the different joining technologies that can be used to join glass to metal in a severe nuclear environment. The working mechanism of the technologies are explained, together with their respective advantages and drawbacks. Three different types of joining are discussed: fastening, liquid phase joining and solid phase joining. Fastening is a mechanical attachment technique, not achieving easily hermetic seals. Liquid and solid phase joining on the other hand form a real bond, what makes the joint much stronger. The most important technologies using liquid phase joining are adhesive bonding, fusion welding and brazing. In the case of the solid phase joining the choices are ultrasonic torsion welding, diffusion bonding and electrostatic bonding. If it is usually not possible to join the glass directly to the metal, an interlayer must be used. One speaks then of indirect joining. The paper will conclude with a discussion on the best

The synthesis of no-carrier-added DL-4-[18F]fluorodeprenyl via the nucleophilic aromatic substitution reaction

International Nuclear Information System (INIS)

Plenevaux, Alain; Guillaume, Marcel

1991-01-01

No-carrier-added DL-α-methyl-β-4-[ 18 F]fluorophenyl-N-methyl-N-propynylethylamine (DL-4-[ 18 F]fluorodeprenyl) was synthesized via a 3-step procedure. The overall yield was 11%, the synthesis time was 90 min and the specific activity >0.57 Ci/μmol (end of synthesis). This synthesis approach, the conversion of an aromatic aldehyde to a homologous methyl ketone, extends the flexibility of the nucleophilic aromatic substitution reaction by applying it to the synthesis of radiotracers which do not bear electron-withdrawing activating groups on the aromatic ring. The tissue distribution of DL-4-[ 18 F]fluorodeprenyl in mice at 1, 10 and 50 min was also measured and showed that metabolic defluorination was not significant. Clearance or radioactivity from brain after injection of DL-4-[ 18 F]fluorodeprenyl was more rapid than that previously observed for [ 11 C]L-deprenyl. (author)

Microwave-assisted clean synthesis of amides via aza-wittig reaction under solvent-free condition

Energy Technology Data Exchange (ETDEWEB)

Sathishkumar, Murugan; Nagarajan, Sangaraiah; Velan, Poovan Shanmuga; Dinesh, Murugan; Ponnuswamy, Alagusundaram [Department of Organic Chemistry, School of Chemistry, Madurai Kamaraj University, Tamilnadu (India)

2011-09-15

A solvent-free microwave-assisted coupling of phosphazenes with acyl chlorides or carboxylic anhydrides in presence of triethylphosphite has been accomplished resulting in a clean synthesis of amides in good yields. Unlike the prevailing time-consuming solution phase methodologies employing chlorinated solvents, benzene (carcinogenic), etc, the present protocol is an eco friendly, rapid and simple approach. (author)

Facile and efficient one-pot solvothermal and microwave-assisted synthesis of stable colloidal solutions of MFe2O4 spinel magnetic nanoparticles

International Nuclear Information System (INIS)

Solano, Eduardo; Perez-Mirabet, Leonardo; Martinez-Julian, Fernando; Guzmán, Roger; Arbiol, Jordi; Puig, Teresa; Obradors, Xavier; Yañez, Ramón; Pomar, Alberto; Ricart, Susagna; Ros, Josep

2012-01-01

Well-defined synthesis conditions of high quality MFe 2 O 4 (M = Mn, Fe, Co, Ni, Zn, and Cu) spinel ferrite magnetic nanoparticles, with diameters below 10 nm, have been described based on facile and efficient one-pot solvothermal or microwave-assisted heating procedures. Both methods are reproducible and scalable and allow forming concentrated stable colloidal solutions in polar solvents, but microwave-assisted heating allows reducing 15 times the required annealing time and leads to an enhanced monodispersity of the nanoparticles. Non-agglomerated nanoparticles dispersions have been achieved using a simple one-pot approach where a single compound, triethyleneglycol, behaves at the same time as solvent and capping ligand. A narrow nanoparticle size distribution and high quality crystallinity have been achieved through selected nucleation and growth conditions. High resolution transmission electron microscopy images and electron energy loss spectroscopy analysis confirm the expected structure and composition and show that similar crystal faceting has been formed in both synthetic approaches. The spinel nanoparticles behave as ferrimagnets with a high saturation magnetization and are superparamagnetic at room temperature. The influence of synthesis route on phase purity and unconventional magnetic properties is discussed in some particular cases such as CuFe 2 O 4 , CoFe 2 O 4 , and ZnFe 2 O 4 .

Homology analyses of the protein sequences of fatty acid synthases from chicken liver, rat mammary gland, and yeast

International Nuclear Information System (INIS)

Chang, Soo-Ik; Hammes, G.G.

1989-01-01

Homology analyses of the protein sequences of chicken liver and rat mammary gland fatty acid synthases were carried out. The amino acid sequences of the chicken and rat enzymes are 67% identical. If conservative substitutions are allowed, 78% of the amino acids are matched. A region of low homologies exists between the functional domains, in particular around amino acid residues 1059-1264 of the chicken enzyme. Homologies between the active sites of chicken and rat and of chicken and yeast enzymes have been analyzed by an alignment method. A high degree of homology exists between the active sites of the chicken and rat enzymes. However, the chicken and yeast enzymes show a lower degree of homology. The DADPH-binding dinucleotide folds of the β-ketoacyl reductase and the enoyl reductase sites were identified by comparison with a known consensus sequence for the DADP- and FAD-binding dinucleotide folds. The active sites of all of the enzymes are primarily in hydrophobic regions of the protein. This study suggests that the genes for the functional domains of fatty acid synthase were originally separated, and these genes were connected to each other by using different connecting nucleotide sequences in different species. An alternative explanation for the differences in rat and chicken is a common ancestry and mutations in the joining regions during evolution

Investigating homology between proteins using energetic profiles.

Science.gov (United States)

Wrabl, James O; Hilser, Vincent J

2010-03-26

Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding) and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved local stability, may

Investigating homology between proteins using energetic profiles.

Directory of Open Access Journals (Sweden)

James O Wrabl

2010-03-01

Full Text Available Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved

Welding and Joining of Titanium Aluminides

Directory of Open Access Journals (Sweden)

Jian Cao

2014-06-01

Full Text Available Welding and joining of titanium aluminides is the key to making them more attractive in industrial fields. The purpose of this review is to provide a comprehensive overview of recent progress in welding and joining of titanium aluminides, as well as to introduce current research and application. The possible methods available for titanium aluminides involve brazing, diffusion bonding, fusion welding, friction welding and reactive joining. Of the numerous methods, solid-state diffusion bonding and vacuum brazing have been most heavily investigated for producing reliable joints. The current state of understanding and development of every welding and joining method for titanium aluminides is addressed respectively. The focus is on the fundamental understanding of microstructure characteristics and processing–microstructure–property relationships in the welding and joining of titanium aluminides to themselves and to other materials.

Microwave-assisted synthesis and micellization behavior of soy-based copoly(2-oxazoline)s

OpenAIRE

Hoogenboom, Richard; Leenen, Mark A. M.; Huang, Haiying; Fustin, Charles-Andr?; Gohy, Jean-Fran?ois; Schubert, Ulrich S.

2006-01-01

Polymers based on renewable resources are promising candidates for replacing common organic polymers, and thus, for reducing oil consumption. In this contribution we report the microwave-assisted synthesis of block and statistical copolymers from 2-ethyl-2-oxazoline and 2-?soy alkyl?-2-oxazoline via a cationic ring-opening polymerization mechanism. The synthesized copolymers were characterized by gel permeation chromatography and 1H-NMR spectroscopy. The micellization of these amphiphilic cop...

Combined feedforward and model-assisted active disturbance rejection control for non-minimum phase system.

Science.gov (United States)

Sun, Li; Li, Donghai; Gao, Zhiqiang; Yang, Zhao; Zhao, Shen

2016-09-01

Control of the non-minimum phase (NMP) system is challenging, especially in the presence of modelling uncertainties and external disturbances. To this end, this paper presents a combined feedforward and model-assisted Active Disturbance Rejection Control (MADRC) strategy. Based on the nominal model, the feedforward controller is used to produce a tracking performance that has minimum settling time subject to a prescribed undershoot constraint. On the other hand, the unknown disturbances and uncertain dynamics beyond the nominal model are compensated by MADRC. Since the conventional Extended State Observer (ESO) is not suitable for the NMP system, a model-assisted ESO (MESO) is proposed based on the nominal observable canonical form. The convergence of MESO is proved in time domain. The stability, steady-state characteristics and robustness of the closed-loop system are analyzed in frequency domain. The proposed strategy has only one tuning parameter, i.e., the bandwidth of MESO, which can be readily determined with a prescribed robustness level. Some comparative examples are given to show the efficacy of the proposed method. This paper depicts a promising prospect of the model-assisted ADRC in dealing with complex systems. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

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

Non-Markovianity-assisted high-fidelity Deutsch-Jozsa algorithm in diamond

Science.gov (United States)

Dong, Yang; Zheng, Yu; Li, Shen; Li, Cong-Cong; Chen, Xiang-Dong; Guo, Guang-Can; Sun, Fang-Wen

2018-01-01

The memory effects in non-Markovian quantum dynamics can induce the revival of quantum coherence, which is believed to provide important physical resources for quantum information processing (QIP). However, no real quantum algorithms have been demonstrated with the help of such memory effects. Here, we experimentally implemented a non-Markovianity-assisted high-fidelity refined Deutsch-Jozsa algorithm (RDJA) with a solid spin in diamond. The memory effects can induce pronounced non-monotonic variations in the RDJA results, which were confirmed to follow a non-Markovian quantum process by measuring the non-Markovianity of the spin system. By applying the memory effects as physical resources with the assistance of dynamical decoupling, the probability of success of RDJA was elevated above 97% in the open quantum system. This study not only demonstrates that the non-Markovianity is an important physical resource but also presents a feasible way to employ this physical resource. It will stimulate the application of the memory effects in non-Markovian quantum dynamics to improve the performance of practical QIP.

Ring-constrained Join

DEFF Research Database (Denmark)

Yiu, Man Lung; Karras, Panagiotis; Mamoulis, Nikos

2008-01-01

. This new operation has important applications in decision support, e.g., placing recycling stations at fair locations between restaurants and residential complexes. Clearly, RCJ is defined based on a geometric constraint but not on distances between points. Thus, our operation is fundamentally different......We introduce a novel spatial join operator, the ring-constrained join (RCJ). Given two sets P and Q of spatial points, the result of RCJ consists of pairs (p, q) (where p ε P, q ε Q) satisfying an intuitive geometric constraint: the smallest circle enclosing p and q contains no other points in P, Q...

Performance Comparison of the Optimized Inverted Joined Wing Airplane Concept and Classical Configuration Airplanes

Directory of Open Access Journals (Sweden)

Sieradzki Adam

2016-09-01

Full Text Available The joined wing concept is an unconventional airplane configuration, known since the mid-twenties of the last century. It has several possible advantages, like reduction of the induced drag and weight due to the closed wing concept. The inverted joined wing variant is its rarely considered version, with the front wing being situated above the aft wing. The following paper presents a performance prediction of the recently optimized configuration of this airplane. Flight characteristics obtained numerically were compared with the performance of two classical configuration airplanes of similar category. Their computational fluid dynamics (CFD models were created basing on available documentation, photographs and some inverse engineering methods. The analysis included simulations performed for a scale of 3-meter wingspan inverted joined wing demonstrator and also for real-scale manned airplanes. Therefore, the results of CFD calculations allowed us to assess the competitiveness of the presented concept, as compared to the most technologically advanced airplanes designed and manufactured to date. At the end of the paper, the areas where the inverted joined wing is better than conventional airplane were predicted and new research possibilities were described.

Why not Commercial Assistance for Suicide? On the Question of Argumentative Coherence of Endorsing Assisted Suicide.

Science.gov (United States)

Kipke, Roland

2015-09-01

Most people who endorse physician-assisted suicide are against commercially assisted suicide - a suicide assisted by professional non-medical providers against payment. The article questions if this position - endorsement of physician-assisted suicide on the one hand and rejection of commercially assisted suicide on the other hand - is a coherent ethical position. To this end the article first discusses some obvious advantages of commercially assisted suicide and then scrutinizes six types of argument about whether they can justify the rejection of commercially assisted suicide while simultaneously endorsing physician-assisted suicide. The conclusion is that they cannot provide this justification and that the mentioned position is not coherent. People who endorse physician-assisted suicide have to endorse commercially assisted suicide as well, or they have to revise their endorsement of physician-assisted suicide. © 2014 John Wiley & Sons Ltd.

A RecET-assisted CRISPR-Cas9 genome editing in Corynebacterium glutamicum.

Science.gov (United States)

Wang, Bo; Hu, Qitiao; Zhang, Yu; Shi, Ruilin; Chai, Xin; Liu, Zhe; Shang, Xiuling; Zhang, Yun; Wen, Tingyi

2018-04-23

Extensive modification of genome is an efficient manner to regulate the metabolic network for producing target metabolites or non-native products using Corynebacterium glutamicum as a cell factory. Genome editing approaches by means of homologous recombination and counter-selection markers are laborious and time consuming due to multiple round manipulations and low editing efficiencies. The current two-plasmid-based CRISPR-Cas9 editing methods generate false positives due to the potential instability of Cas9 on the plasmid, and require a high transformation efficiency for co-occurrence of two plasmids transformation. Here, we developed a RecET-assisted CRISPR-Cas9 genome editing method using a chromosome-borne Cas9-RecET and a single plasmid harboring sgRNA and repair templates. The inducible expression of chromosomal RecET promoted the frequencies of homologous recombination, and increased the efficiency for gene deletion. Due to the high transformation efficiency of a single plasmid, this method enabled 10- and 20-kb region deletion, 2.5-, 5.7- and 7.5-kb expression cassette insertion and precise site-specific mutation, suggesting a versatility of this method. Deletion of argR and farR regulators as well as site-directed mutation of argB and pgi genes generated the mutant capable of accumulating L-arginine, indicating the stability of chromosome-borne Cas9 for iterative genome editing. Using this method, the model-predicted target genes were modified to redirect metabolic flux towards 1,2-propanediol biosynthetic pathway. The final engineered strain produced 6.75 ± 0.46 g/L of 1,2-propanediol that is the highest titer reported in C. glutamicum. Furthermore, this method is available for Corynebacterium pekinense 1.563, suggesting its universal applicability in other Corynebacterium species. The RecET-assisted CRISPR-Cas9 genome editing method will facilitate engineering of metabolic networks for the synthesis of interested bio-based products from renewable

N-terminal domains of human DNA polymerase lambda promote primer realignment during translesion DNA synthesis

Science.gov (United States)

Taggart, David J.; Dayeh, Daniel M.; Fredrickson, Saul W.; Suo, Zucai

2014-01-01

within the non-homologous end joining pathway. PMID:25108835

Using Start/End Timings of Spectral Transitions Between Phonemes in Concatenative Speech Synthesis

OpenAIRE

Toshio Hirai; Seiichi Tenpaku; Kiyohiro Shikano

2002-01-01

The definition of "phoneme boundary timing" in a speech corpus affects the quality of concatenative speech synthesis systems. For example, if the selected speech unit is not appropriately match to the speech unit of the required phoneme environment, the quality may be degraded. In this paper, a dynamic segment boundary defi- nition is proposed. In the definition, the concatenation point is chosen from the start or end timings of spectral transition depending on the phoneme environment at the ...

Living in the hands of God. English Sunni e-fatwas on (non-)voluntary euthanasia and assisted suicide.

Science.gov (United States)

Van den Branden, Stef; Broeckaert, Bert

2011-02-01

Ever since the start of the twentieth century, a growing interest and importance of studying fatwas can be noted, with a focus on Arabic printed fatwas (Wokoeck 2009). The scholarly study of end-of-life ethics in these fatwas is a very recent feature, taking a first start in the 1980s (Anees 1984; Rispler-Chaim 1993). Since the past two decades, we have witnessed the emergence of a multitude of English fatwas that can easily be consulted through the Internet ('e-fatwas'), providing Muslims worldwide with a form of Islamic normative guidance on a huge variety of topics. Although English online fatwas do provide guidance for Muslims and Muslim minorities worldwide on a myriad of topics including end-of-life issues, they have hardly been studied. This study analyses Islamic views on (non-)voluntary euthanasia and assisted suicide as expressed in English Sunni fatwas published on independent--i.e. not created by established organisations--Islamic websites. We use Tyan's definition of a fatwa to distinguish between fatwas and other types of texts offering Islamic guidance through the Internet. The study of e-fatwas is framed in the context of Bunt's typology of Cyber Islamic Environments (Bunt 2009) and in the framework of Roy's view on the virtual umma (Roy 2002). '(Non-)voluntary euthanasia and assisted suicide' are defined using Broeckaert's conceptual framework on treatment decisions at the end of life (Broeckaert 2008). We analysed 32 English Sunni e-fatwas. All of the e-fatwas discussed here firmly speak out against every form of active termination of life. They often bear the same structure, basing themselves solely on Quranic verses and prophetic traditions, leaving aside classical jurisprudential discussions on the subject. In this respect they share the characteristics central in Roy's typology of the fatwa in the virtual umma. On the level of content, they are in line with the international literature on Islamic end-of-life ethics. English Sunni e-fatwas make

Laser-assisted fabrication of materials

CERN Document Server

Manna, Indranil

2013-01-01

Laser assisted fabrication involves shaping of materials using laser as a source of heat. It can be achieved by removal of materials (laser assisted cutting, drilling, etc.), deformation (bending, extrusion), joining (welding, soldering) and addition of materials (surface cladding or direct laser cladding). This book on ´Laser assisted Fabrication’ is aimed at developing in-depth engineering concepts on various laser assisted macro and micro-fabrication techniques with the focus on application and a review of the engineering background of different micro/macro-fabrication techniques, thermal history of the treated zone and microstructural development and evolution of properties of the treated zone.

Microwave-assisted combustion synthesis of NiAl intermetallics in a single mode applicator: Modeling and optimisation

International Nuclear Information System (INIS)

Poli, G.; Sola, R.; Veronesi, P.

2006-01-01

The microwave-assisted combustion synthesis of NiAl intermetallics in a single mode applicator has been simulated numerically and performed with the aim of achieving the highest yields, energy efficiency and process reproducibility. The electromagnetic field modeling of the microwave system allowed to chose the proper experimental set-up and the materials more suitable for the application, minimising the reflected power and the risks of arcing. In all the experimental conditions tested, conversions of 3-5 g 1:1 atomic ratio Ni and Al powder compacts into NiAl ranged from 98.7% to 100%, requiring from 30 to 180 s with power from 500 to 1500 W. The optimisation procedure allowed to determine and quantify the effects of the main process variables on the ignition time, the NiAl yields and the specific energy consumption, leading to a fast, reproducible and cost-effective process of microwave-assisted combustion synthesis of NiAl intermetallics

DNA double-strand break repair: a tale of pathway choices

Institute of Scientific and Technical Information of China (English)

Jing Li; Xingzhi Xu

2016-01-01

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.

Crotacetin, a novel snake venom C-type lectin, is homolog of convulxin

Directory of Open Access Journals (Sweden)

G. Rádis-Baptista

2005-12-01

Full Text Available Snake venom (sv C-type lectins encompass a group of hemorrhagic toxins, which are able to interfere with hemostasis. They share significant similarity in their primary structures with C-type lectins of other animals, and also present a conserved carbohydrate recognition domain (CRD. A very well studied sv C-type lectin is the heterodimeric toxin, convulxin (CVX, from the venoms of South American rattlesnakes, Crotalus durissus terrificus and C. d. cascavella. It consists of two subunits, alfa (CVXalpha , 13.9 kDa and beta (CVXbeta , 12.6 kDa, joined by inter and intra-chain disulfide bounds, and is arranged in a tetrameric alpha4beta4 conformation. Convulxin is able to activate platelet and induce their aggregation by acting via p62/GPVI collagen receptor. Several cDNA precursors, homolog of CVX subunits, were cloned by PCR homology screening. As determined by computational analysis, one of them, named crotacetin beta subunit, was predicted as a polypeptide with a tridimensional conformation very similar to other subunits of convulxin-like snake toxins. Crotacetin was purified from C. durissus venoms by gel permeation and reverse phase high performance liquid chromatography. The heterodimeric crotacetin is expressed in the venoms of several C. durissus subspecies, but it is prevalent in the venom of C. durissus cascavella. As inferred from homology modeling, crotacetin induces platelet aggregation but noticeably exhibits antimicrobial activity against Gram-positive and Gram-negative bacteria.

A non-destructive genotyping system from a single seed for marker-assisted selection in watermelon.

Science.gov (United States)

Meru, G; McDowell, D; Waters, V; Seibel, A; Davis, J; McGregor, C

2013-03-11

Genomic tools for watermelon breeding are becoming increasingly available. A high throughput genotyping system would facilitate the use of DNA markers in marker-assisted selection. DNA extraction from leaf material requires prior seed germination and is often time-consuming and cost prohibitive. In an effort to develop a more efficient system, watermelon seeds of several genotypes and various seed sizes were sampled by removing ⅓ or ½ sections from the distal ends for DNA extraction, while germinating the remaining proximal parts of the seed. Removing ⅓ of the seed from the distal end had no effect on seed germination percentage or seedling vigor. Different DNA extraction protocols were tested to identify a method that could yield DNA of sufficient quality for amplification by polymerase chain reaction. A sodium dodecyl sulfate extraction protocol with 1% polyvinylpyrrolidone yielded DNA that could be amplified with microsatellite primers and was free of pericarp contamination. In this study, an efficient, non-destructive genotyping protocol for watermelon seed was developed.

Microwave assisted synthesis of hydroxyapatite nano strips

Energy Technology Data Exchange (ETDEWEB)

Ruban Kumar, A.; Kalainathan, S.; Saral, A.M. [School of Advanced Sciences, VIT University, Vellore 632014, Tamil Nadu (India)

2010-07-15

Synthesis of hydroxyapatite (HAP) nano strips was carried out by chemical precipitation method followed by microwave irradiation. The microwave assisted reactions proceed at fast rates. It is found that the presence of the complex reagent EDTA plays an important role in the morphological changes of nanostructure hydroxyapatite. EDTA acts as a hexadentate unit by wrapping itself around the Ca{sup 2+} metal ion with, four oxygen and two nitrogen atoms and forms several five member chelate rings. The relative specific surface energies associated with the facets of the crystal determines the shape of the crystal. Scanning electron microscopy revealed the presence of hydroxyapatite nano strips with the range 50-100 nm in EDTA influenced HAP powders. Fourier transform-infrared spectroscopy (FT-IR) result combined with the X-ray diffraction (XRD) indicates the presence of amorphous hydroxyapatite (HAP) in the as-prepared material. X-ray patterns collected on the powder after heat-treatment at 1100 C for 2 h in air exhibits single phase of HAP. (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Dual CRISPR-Cas9 Cleavage Mediated Gene Excision and Targeted Integration in Yarrowia lipolytica.

Science.gov (United States)

Gao, Difeng; Smith, Spencer; Spagnuolo, Michael; Rodriguez, Gabriel; Blenner, Mark

2018-05-29

CRISPR-Cas9 technology has been successfully applied in Yarrowia lipolytica for targeted genomic editing including gene disruption and integration; however, disruptions by existing methods typically result from small frameshift mutations caused by indels within the coding region, which usually resulted in unnatural protein. In this study, a dual cleavage strategy directed by paired sgRNAs is developed for gene knockout. This method allows fast and robust gene excision, demonstrated on six genes of interest. The targeted regions for excision vary in length from 0.3 kb up to 3.5 kb and contain both non-coding and coding regions. The majority of the gene excisions are repaired by perfect nonhomologous end-joining without indel. Based on this dual cleavage system, two targeted markerless integration methods are developed by providing repair templates. While both strategies are effective, homology mediated end joining (HMEJ) based method are twice as efficient as homology recombination (HR) based method. In both cases, dual cleavage leads to similar or improved gene integration efficiencies compared to gene excision without integration. This dual cleavage strategy will be useful for not only generating more predictable and robust gene knockout, but also for efficient targeted markerless integration, and simultaneous knockout and integration in Y. lipolytica. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microwave-assisted hydrothermal synthesis of CePO4 nanostructures: Correlation between the structural and optical properties

International Nuclear Information System (INIS)

Palma-Ramírez, D.; Domínguez-Crespo, M.A.; Torres-Huerta, A.M.; Dorantes-Rosales, H.; Ramírez-Meneses, E.; Rodríguez, E.

2015-01-01

Highlights: • An enhancement in the hydrothermal synthesis for obtaining of CePO 4 is presented. • Microwave energy can replace the energy by convection for obtaining CePO 4 . • CePO 4 demonstrates to be an option to increase the optical properties of polymers. • Adjusting the pH, the sintering process is not necessary to obtain the desire phase. • CePO 4 morphologies undergo evolution from nanorods to semispherical nanoparticles. - Abstract: In this work, the microwave-assisted hydrothermal method is proposed as an alternative to the synthesis of cerium phosphate (CePO 4 ) nanostructures to evaluate the influence of different synthesis parameters on both the structural and optical properties. In order to reach this goal, two different sets of experiments were designed, varying the reaction temperature (130 and 180 °C), synthesis time (15 and 30 min) and sintering temperature (400 and 600 °C), maintaining a constant pH = 3. Thereafter, two experimental conditions were selected to assess changes in the properties of CePO 4 nanopowders with pH (1, 5, 9 and 11). The crystal structure and morphology of the nanostructures were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM) and scanning electron microscopy (SEM), respectively. Diffuse reflectance properties of CePO 4 with different microstructures were studied. The results demonstrated that by using the microwave-assisted hydrothermal method, the shape, size and structural phase of CePO 4 can be modulated by using relatively low synthesis temperatures and short reaction times, and depending on pH, a sintering process is not needed to obtain either a desired phase or size. Under the selected experimental conditions, the materials underwent an evolution from nanorods to semispherical nanoparticles, accompanied by a phase transition from hexagonal to monoclinic

Template assisted synthesis and optical properties of gold nanoparticles.

Science.gov (United States)

Fodor, Petru; Lasalvia, Vincenzo

2009-03-01

A hybrid nanofabrication method (interference lithography + self assembly) was explored for the fabrication of arrays of gold nanoparticles. To ensure the uniformity of the nanoparticles, a template assisted synthesis was used in which the gold is electrodeposited in the pores of anodized aluminum membranes. The spacing between the pores and their ordering is controlled in the first fabrication step of the template in which laser lithography and metal deposition are used to produce aluminum films with controlled strain profiles. The diameter of the pores produced after anodizing the aluminum film in acidic solution determines the diameter of the gold particles, while their aspect ratio is controlled through the deposition time. Optical absorbance spectroscopy is used to evaluate the ability to tune the nanoparticles plasmon resonance spectra through control over their size and aspect ratio.

Chow groups of intersections of quadrics via homological projective duality and (Jacobians of) non-commutative motives

Science.gov (United States)

Bernardara, M.; Tabuada, G.

2016-06-01

Conjectures of Beilinson-Bloch type predict that the low-degree rational Chow groups of intersections of quadrics are one-dimensional. This conjecture was proved by Otwinowska in [20]. By making use of homological projective duality and the recent theory of (Jacobians of) non-commutative motives, we give an alternative proof of this conjecture in the case of a complete intersection of either two quadrics or three odd-dimensional quadrics. Moreover, we prove that in these cases the unique non-trivial algebraic Jacobian is the middle one. As an application, we make use of Vial's work [26], [27] to describe the rational Chow motives of these complete intersections and show that smooth fibrations into such complete intersections over bases S of small dimension satisfy Murre's conjecture (when \\dim (S)≤ 1), Grothendieck's standard conjecture of Lefschetz type (when \\dim (S)≤ 2), and Hodge's conjecture (when \\dim(S)≤ 3).

A procedure for calibration and validation of FE modelling of laser-assisted metal to polymer direct joining

Science.gov (United States)

Lambiase, F.; Genna, S.; Kant, R.

2018-01-01

The quality of the joints produced by means of Laser-Assisted Metal to Polymer direct joining (LAMP) is strongly influenced by the temperature field produced during the laser treatment. The main phenomena including the adhesion of the plastic to the metal sheet and the development of bubbles (on the plastic surface) depend on the temperature reached by the polymer at the interface. Such a temperature should be higher than the softening temperature, but lower than the degradation temperature of the polymer. However, the temperature distribution is difficult to be measured by experimental tests since the most polymers (which are transparent to the laser radiation) are often opaque to the infrared wavelength. Thus, infrared analysis involving pyrometers and infrared camera is not suitable for this purpose. On the other hand, thermocouples are difficult to be placed at the interface without influencing the temperature conditions. In this paper, an integrated approach involving both experimental measurements and a Finite Element (FE) model were used to perform such an analysis. LAMP of Polycarbonate and AISI304 stainless steel was performed by means of high power diode laser and the main process parameters i.e. laser power and scanning speed were varied. Comparing the experimental measurements and the FE model prediction of the thermal field, a good correspondence was achieved proving the suitability of the developed model and the proposed calibration procedure to be ready used for process design and optimization.

Trajectory similarity join in spatial networks

KAUST Repository

Shang, Shuo

2017-09-07

The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider the case of trajectory similarity join (TS-Join), where the objects are trajectories of vehicles moving in road networks. Thus, given two sets of trajectories and a threshold θ, the TS-Join returns all pairs of trajectories from the two sets with similarity above θ. This join targets applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide a purposeful definition of similarity. To enable efficient TS-Join processing on large sets of trajectories, we develop search space pruning techniques and take into account the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer algorithm. For each trajectory, the algorithm first finds similar trajectories. Then it merges the results to achieve a final result. The algorithm exploits an upper bound on the spatiotemporal similarity and a heuristic scheduling strategy for search space pruning. The algorithm\\'s per-trajectory searches are independent of each other and can be performed in parallel, and the merging has constant cost. An empirical study with real data offers insight in the performance of the algorithm and demonstrates that is capable of outperforming a well-designed baseline algorithm by an order of magnitude.

Recent Developments for Ultrasonic-Assisted Friction Stir Welding: Joining, Testing, Corrosion - an Overview

Science.gov (United States)

Thomä, M.; Wagner, G.; Straß, B.; Conrad, C.; Wolter, B.; Benfer, S.; Fürbeth, W.

2016-03-01

Due to the steadily increasing demand on innovative manufacturing processes, modern lightweight construction concepts become more and more important. Especially joints of dissimilar metals offer a variety of advantages due to their high potential for lightweight construction. The focus of the investigations was Al/Mg-joints. Friction Stir Welding (FSW) is an efficient process to realize high strength joints between these materials in ductile condition. Furthermore, for a simultaneous transmission of power ultrasound during the FSW-process (US-FSW) a positive effect on the achievable tensile strength of the Al/Mg-joints was proven. In the present work the industrial used die cast alloys EN AC-48000 (AlSi12CuNiMg) and AZ80 (MgAl8Zn) were joined by a machining center modified especially for Ultrasound Supported Friction Stir Welding. The appearing welding zone and the formation of intermetallic phases under the influence of power ultrasound were examined in particular. In order to identify optimal process parameters extensive preliminary process analyzes have been carried out. Following this, an ultrasound-induced more intensive stirring of the joining zone and as a result of this a considerably modified intermetallic zone was detected. At the same time an increase of the tensile strength of about 25% for US-FSW-joints and for fatigue an up to three times higher number of cycles to failure in comparison to a conventional welding process was observed. Moreover, detailed corrosion analyzes have shown that especially the welding zone was influenced by the corrosive attack. To expand and deepen the knowledge of the US-FSW-process further material combinations such as Ti/Steel and Al/Steel will be considered in future.

Recent Developments for Ultrasonic-Assisted Friction Stir Welding: Joining, Testing, Corrosion - an Overview

International Nuclear Information System (INIS)

Thomä, M; Wagner, G; Straß, B; Conrad, C; Wolter, B; Benfer, S; Fürbeth, W

2016-01-01

Due to the steadily increasing demand on innovative manufacturing processes, modern lightweight construction concepts become more and more important. Especially joints of dissimilar metals offer a variety of advantages due to their high potential for lightweight construction. The focus of the investigations was Al/Mg-joints. Friction Stir Welding (FSW) is an efficient process to realize high strength joints between these materials in ductile condition. Furthermore, for a simultaneous transmission of power ultrasound during the FSW-process (US-FSW) a positive effect on the achievable tensile strength of the Al/Mg-joints was proven. In the present work the industrial used die cast alloys EN AC-48000 (AlSi12CuNiMg) and AZ80 (MgAl8Zn) were joined by a machining center modified especially for Ultrasound Supported Friction Stir Welding. The appearing welding zone and the formation of intermetallic phases under the influence of power ultrasound were examined in particular. In order to identify optimal process parameters extensive preliminary process analyzes have been carried out. Following this, an ultrasound-induced more intensive stirring of the joining zone and as a result of this a considerably modified intermetallic zone was detected. At the same time an increase of the tensile strength of about 25% for US-FSW-joints and for fatigue an up to three times higher number of cycles to failure in comparison to a conventional welding process was observed. Moreover, detailed corrosion analyzes have shown that especially the welding zone was influenced by the corrosive attack. To expand and deepen the knowledge of the US-FSW-process further material combinations such as Ti/Steel and Al/Steel will be considered in future. (paper)

Recrafting the neighbor-joining method

Directory of Open Access Journals (Sweden)

Pedersen Christian NS

2006-01-01

Full Text Available Abstract Background The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Θ(n3 algorithm upon which all existing implementations are based. Results In this paper we present techniques for speeding up the canonical neighbor-joining method. Our algorithms construct the same phylogenetic trees as the canonical neighbor-joining method. The best-case running time of our algorithms are O(n2 but the worst-case remains O(n3. We empirically evaluate the performance of our algoritms on distance matrices obtained from the Pfam collection of alignments. The experiments indicate that the running time of our algorithms evolve as Θ(n2 on the examined instance collection. We also compare the running time with that of the QuickTree tool, a widely used efficient implementation of the canonical neighbor-joining method. Conclusion The experiments show that our algorithms also yield a significant speed-up, already for medium sized instances.

Impacts of care-giving and sources of support: a comparison of end-of-life and non-end-of-life caregivers in Canada.

Science.gov (United States)

Williams, Allison M; Wang, Li; Kitchen, Peter

2016-03-01

This is the second in a series of papers that deal with care-giving in Canada, as based on data available from the Canadian General Social Survey (2007). Building on the first paper, which reviewed the differences between short-term, long-term and end-of-life (EOL) caregivers, this paper uniquely examines the caregiver supports employed by EOL caregivers when compared to non-EOL caregivers (short-term and long-term caregivers combined). Both papers employ data from Statistics Canada's General Social Survey (GSS Cycle 21: 2007). The GSS includes three modules, where respondents were asked questions about the unpaid home care assistance that they had provided in the last 12 months to someone at EOL or with either a long-term health condition or a physical limitation. The objective of this research paper was to investigate the link between the impact of the care-giving experience and the caregiver supports received, while also examining the differences in these across EOL and non-EOL caregivers. By way of factor analysis and regression modelling, we examine differences between two types of caregivers: (i) EOL and (ii) non-EOL caregivers. The study revealed that with respect to socio-demographic characteristics, health outcomes and caregiver supports, EOL caregivers were consistently worse off. This suggests that although all non-EOL caregivers are experiencing negative impacts from their care-giving role, comparatively greater supports are needed for EOL caregivers. © 2015 The Authors. Health and Social Care in the Community Published by John Wiley & Sons Ltd.

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.

RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency.

Science.gov (United States)

Song, Jun; Yang, Dongshan; Xu, Jie; Zhu, Tianqing; Chen, Y Eugene; Zhang, Jifeng

2016-01-28

Zinc-finger nuclease, transcription activator-like effector nuclease and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) are becoming major tools for genome editing. Importantly, knock-in in several non-rodent species has been finally achieved thanks to these customizable nucleases; yet the rates remain to be further improved. We hypothesize that inhibiting non-homologous end joining (NHEJ) or enhancing homology-directed repair (HDR) will improve the nuclease-mediated knock-in efficiency. Here we show that the in vitro application of an HDR enhancer, RS-1, increases the knock-in efficiency by two- to five-fold at different loci, whereas NHEJ inhibitor SCR7 has minimal effects. We then apply RS-1 for animal production and have achieved multifold improvement on the knock-in rates as well. Our work presents tools to nuclease-mediated knock-in animal production, and sheds light on improving gene-targeting efficiencies on pluripotent stem cells.

RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency

Science.gov (United States)

Song, Jun; Yang, Dongshan; Xu, Jie; Zhu, Tianqing; Chen, Y. Eugene; Zhang, Jifeng

2016-01-01

Zinc-finger nuclease, transcription activator-like effector nuclease and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) are becoming major tools for genome editing. Importantly, knock-in in several non-rodent species has been finally achieved thanks to these customizable nucleases; yet the rates remain to be further improved. We hypothesize that inhibiting non-homologous end joining (NHEJ) or enhancing homology-directed repair (HDR) will improve the nuclease-mediated knock-in efficiency. Here we show that the in vitro application of an HDR enhancer, RS-1, increases the knock-in efficiency by two- to five-fold at different loci, whereas NHEJ inhibitor SCR7 has minimal effects. We then apply RS-1 for animal production and have achieved multifold improvement on the knock-in rates as well. Our work presents tools to nuclease-mediated knock-in animal production, and sheds light on improving gene-targeting efficiencies on pluripotent stem cells. PMID:26817820

Willmore energy for joining of carbon nanostructures

Science.gov (United States)

Sripaturad, P.; Alshammari, N. A.; Thamwattana, N.; McCoy, J. A.; Baowan, D.

2018-06-01

Numerous types of carbon nanostructure have been found experimentally, including nanotubes, fullerenes and nanocones. These structures have applications in various nanoscale devices and the joining of these structures may lead to further new configurations with more remarkable properties and applications. The join profile between different carbon nanostructures in a symmetric configuration may be modelled using the calculus of variations. In previous studies, carbon nanostructures were assumed to deform according to perfect elasticity, thus the elastic energy, depending only on the axial curvature, was used to determine the join profile consisting of a finite number of discrete bonds. However, one could argue that the relevant energy should also involve the rotational curvature, especially when its size is comparable to the axial curvature. In this paper, we use the Willmore energy, a natural generalisation of the elastic energy that depends on both the axial and rotational curvatures. Catenoids are absolute minimisers of this energy and pieces of these may be used to join various nanostructures. We focus on the cases of joining a fullerene to a nanotube and joining two fullerenes along a common axis. By comparing our results with the earlier work, we find that both energies give similar joining profiles. Further work on other configurations may reveal which energy provides a better model.

Ultrasonic-assisted synthesis of monodisperse single-crystalline silver nanoplates and gold nanorings.

Science.gov (United States)

Jiang, Li-Ping; Xu, Shu; Zhu, Jian-Min; Zhang, Jian-Rong; Zhu, Jun-Jie; Chen, Hong-Yuan

2004-09-20

A simple sonochemical route was developed for the crystal growth of uniform silver nanoplates and ringlike gold nanocrystals in a N,N-dimethylformamide solution. The platelike structures were generated from the selective growth on different crystal planes in the presence of poly(vinylpyrrolidone) and the ultrasonic-assisted Ostwald ripening processes. The silver nanoplates in solution served as the templates for the synthesis of ringlike gold crystals via a displacement reaction. Both the silver nanoplates and gold nanorings were highly oriented single crystals with (111) planes as the basal planes. Copyright 2004 American Chemical Society

Bluetongue virus non-structural protein 1 is a positive regulator of viral protein synthesis

Directory of Open Access Journals (Sweden)

Boyce Mark

2012-08-01

Full Text Available Abstract Background Bluetongue virus (BTV is a double-stranded RNA (dsRNA virus of the Reoviridae family, which encodes its genes in ten linear dsRNA segments. BTV mRNAs are synthesised by the viral RNA-dependent RNA polymerase (RdRp as exact plus sense copies of the genome segments. Infection of mammalian cells with BTV rapidly replaces cellular protein synthesis with viral protein synthesis, but the regulation of viral gene expression in the Orbivirus genus has not been investigated. Results Using an mRNA reporter system based on genome segment 10 of BTV fused with GFP we identify the protein characteristic of this genus, non-structural protein 1 (NS1 as sufficient to upregulate translation. The wider applicability of this phenomenon among the viral genes is demonstrated using the untranslated regions (UTRs of BTV genome segments flanking the quantifiable Renilla luciferase ORF in chimeric mRNAs. The UTRs of viral mRNAs are shown to be determinants of the amount of protein synthesised, with the pre-expression of NS1 increasing the quantity in each case. The increased expression induced by pre-expression of NS1 is confirmed in virus infected cells by generating a replicating virus which expresses the reporter fused with genome segment 10, using reverse genetics. Moreover, NS1-mediated upregulation of expression is restricted to mRNAs which lack the cellular 3′ poly(A sequence identifying the 3′ end as a necessary determinant in specifically increasing the translation of viral mRNA in the presence of cellular mRNA. Conclusions NS1 is identified as a positive regulator of viral protein synthesis. We propose a model of translational regulation where NS1 upregulates the synthesis of viral proteins, including itself, and creates a positive feedback loop of NS1 expression, which rapidly increases the expression of all the viral proteins. The efficient translation of viral reporter mRNAs among cellular mRNAs can account for the observed

Bluetongue virus non-structural protein 1 is a positive regulator of viral protein synthesis.

Science.gov (United States)

Boyce, Mark; Celma, Cristina C P; Roy, Polly

2012-08-29

Bluetongue virus (BTV) is a double-stranded RNA (dsRNA) virus of the Reoviridae family, which encodes its genes in ten linear dsRNA segments. BTV mRNAs are synthesised by the viral RNA-dependent RNA polymerase (RdRp) as exact plus sense copies of the genome segments. Infection of mammalian cells with BTV rapidly replaces cellular protein synthesis with viral protein synthesis, but the regulation of viral gene expression in the Orbivirus genus has not been investigated. Using an mRNA reporter system based on genome segment 10 of BTV fused with GFP we identify the protein characteristic of this genus, non-structural protein 1 (NS1) as sufficient to upregulate translation. The wider applicability of this phenomenon among the viral genes is demonstrated using the untranslated regions (UTRs) of BTV genome segments flanking the quantifiable Renilla luciferase ORF in chimeric mRNAs. The UTRs of viral mRNAs are shown to be determinants of the amount of protein synthesised, with the pre-expression of NS1 increasing the quantity in each case. The increased expression induced by pre-expression of NS1 is confirmed in virus infected cells by generating a replicating virus which expresses the reporter fused with genome segment 10, using reverse genetics. Moreover, NS1-mediated upregulation of expression is restricted to mRNAs which lack the cellular 3' poly(A) sequence identifying the 3' end as a necessary determinant in specifically increasing the translation of viral mRNA in the presence of cellular mRNA. NS1 is identified as a positive regulator of viral protein synthesis. We propose a model of translational regulation where NS1 upregulates the synthesis of viral proteins, including itself, and creates a positive feedback loop of NS1 expression, which rapidly increases the expression of all the viral proteins. The efficient translation of viral reporter mRNAs among cellular mRNAs can account for the observed replacement of cellular protein synthesis with viral protein

Ultrasound assisted combustion synthesis of TiC in Al-Ti-C system.

Science.gov (United States)

Liu, Zhiwei; Rakita, Milan; Xu, Wilson; Wang, Xiaoming; Han, Qingyou

2015-11-01

This research investigated the effects of high-intensity ultrasound on the combustion synthesis of TiC particles in Al-Ti-C system. The process involved that high-intensity ultrasound was applied on the surface of a compacted Al-Ti-C pellet directly through a Nb probe during the thermal explosion reaction. By comparing with the sample without ultrasonic treatment, it was found that the thermal explosion reaction for synthesizing TiC phase could take place thoroughly in the ultrasonically treated sample. During the process of synthesizing TiC phase, the dissolution of solid graphite particles into the Al-Ti melt, as well as the nucleation and growth of TiC particles could be promoted effectively due to the effects of ultrasound, leading to an enhancement of the formation of TiC particles. Ultrasound assisted combustion synthesis as a simple and effective approach was proposed for synthesizing materials in this research. Copyright © 2015 Elsevier B.V. All rights reserved.

Academic Labor Markets and Assistant Professors' Employment Outcomes

Science.gov (United States)

Hargens, Lowell L.

2012-01-01

Using data for 638 assistant professors who joined graduate sociology departments between 1975 and 1992, I examine the claim that when the labor market for new doctorates is weak, assistant professors experience less favorable employment outcomes than when that labor market is strong. Surprisingly, I find that those hired during the weak…

Tin-Assisted Synthesis of ɛ -Ga2O3 by Molecular Beam Epitaxy

Science.gov (United States)

Kracht, M.; Karg, A.; Schörmann, J.; Weinhold, M.; Zink, D.; Michel, F.; Rohnke, M.; Schowalter, M.; Gerken, B.; Rosenauer, A.; Klar, P. J.; Janek, J.; Eickhoff, M.

2017-11-01

The synthesis of ɛ -Ga2O3 and β -Ga2O3 by plasma-assisted molecular beam epitaxy on (001 )Al2O3 substrates is studied. The growth window of β -Ga2O3 in the Ga-rich regime, usually limited by the formation of volatile gallium suboxide, is expanded due to the presence of tin during the growth process, which stabilizes the formation of gallium oxides. X-ray diffraction, transmission electron microscopy, time-of-flight secondary-ion mass spectrometry, Raman spectroscopy, and atomic force microscopy are used to analyze the influence of tin on the layer formation. We demonstrate that it allows the synthesis of phase-pure ɛ -Ga2O3 . A growth model based on the oxidation of gallium suboxide by reduction of an intermediate sacrificial tin oxide is suggested.

Summary of Prior Work on Joining of Oxide Dispersion-Strengthened Alloys

Energy Technology Data Exchange (ETDEWEB)

Wright, Ian G [ORNL; Tatlock, Gordon J [ORNL; Badairy, H. [University of Liverpool; Chen, C-L. [University of Liverpool

2009-08-01

There is a range of joining techniques available for use with ODS alloys, but care should be exercised in matching the technique to the final duty requirements of the joint. The goal for joining ODS alloys is a joint with no local disruption of the distribution of the oxide dispersion, and no significant change in the size and orientation of the alloy microstructure. Not surprisingly, the fusion welding processes typically employed with wrought alloys produce the least satisfactory results with ODS alloys, but some versions, such as fusion spot welding, and the laser and electron-beam welding technologies, have demonstrated potential for producing sound joints. Welds made using solid-state spot welding reportedly have exhibited parent metal properties. Thus, it is possible to employ processes that result in significant disruption of the alloy microstructure, as long as the processing parameters are adjustment to minimize the extent of or influence of the changes in the alloy microstructure. Selection among these joining approaches largely depends on the particular application and component configuration, and an understanding of the relationships among processing, alloy microstructure, and final properties is key. Recent developments have resulted in friction welding evolving to be a prime method for joining ODS sheet products, and variants of brazing/diffusion bonding have shown excellent promise for use with tubes and pipes. The techniques that come closest to the goal defined above involve solid-state diffusion bonding and, in particular, it has been found that secondary recrystallization of joints made by pulsed plasma-assisted diffusion can produce the desired, continuous, large alloy grain structure through the joint. Such joints have exhibited creep rupture failure at >82% of the load needed to fail the monolithic parent alloy at 1000 C.

Study on Effect of Ultrasonic Vibration on Grinding Force and Surface Quality in Ultrasonic Assisted Micro End Grinding of Silica Glass

Directory of Open Access Journals (Sweden)

Zhang Jianhua

2014-01-01

Full Text Available Ultrasonic vibration assisted micro end grinding (UAMEG is a promising processing method for micro parts made of hard and brittle materials. First, the influence of ultrasonic assistance on the mechanism of this processing technology is theoretically analyzed. Then, in order to reveal the effects of ultrasonic vibration and grinding parameters on grinding forces and surface quality, contrast grinding tests of silica glass with and without ultrasonic assistance using micro radial electroplated diamond wheel are conducted. The grinding forces are measured using a three-component dynamometer. The surface characteristics are detected using the scanning electron microscope. The experiment results demonstrate that grinding forces are significantly reduced by introducing ultrasonic vibration into conventional micro end grinding (CMEG of silica glass; ultrasonic assistance causes inhibiting effect on variation percentages of tangential grinding force with grinding parameters; ductile machining is easier to be achieved and surface quality is obviously improved due to ultrasonic assistance in UAMEG. Therefore, larger grinding depth and feed rate adopted in UAMEG can lead to the improvement of removal rate and machining efficiency compared with CMEG.

Live cell imaging reveals at novel view of DNA

International Nuclear Information System (INIS)

Moritomi-Yano, Keiko; Yano, Ken-ichi

2010-01-01

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)

Efficient Oligo nucleotide mediated CRISPR-Cas9 Gene Editing in Aspergilli

DEFF Research Database (Denmark)

Nødvig, Christina Spuur; Hoof, Jakob Blæsbjerg; Kogle, Martin Engelhard

2018-01-01

CRISPR-Cas9 technologies are revolutionizing fungal gene editing. Here we show that survival of specific Cas9/sgRNA mediated DNA double strand breaks (DSBs) depends on the non-homologous end-joining, NHEJ, DNA repair pathway and we use this observation to develop a tool to assess protospacer....... niger, and in A. oryzae indicating that this type of repair may be wide spread in filamentous fungi. Importantly, we demonstrate that by using single-stranded oligo nucleotides for CRISPR-Cas9 mediated gene editing it is possible to introduce specific point mutations as well gene deletions...

MICROWAVE JOINING OF ALUMINA CERAMIC AND HYDROXYLAPATITE BIOCERAMIC

Institute of Scientific and Technical Information of China (English)

无

1999-01-01

Microwave joining is a rapid developmental new techniqu e in recent years.This paper introduces a new microwave joining equipment which was made by our lab,succeeds in alumina ceramic-hydroxylapatite bioceramic j o in in the equipment, and analyzes the join situation of join boundary by using s canni ng electron microscope(SEM),this paper analyzes the mechanism of microwave joini ng also.

Trends in the Microwave-Assisted Synthesis of Metal Oxide Nanoparticles Supported on Carbon Nano tubes and Their Applications

International Nuclear Information System (INIS)

Motshekga, S.C.; Pillai, S.K.; Ray, S.S.; Motshekga, S.C.; Ray, S.S.; Jalama, K.; Krause, Rui.W.M.

2012-01-01

The study of coating carbon nano tubes with metal/oxides nanoparticles is now becoming a promising and challenging area of research. To optimize the use of carbon nano tubes in various applications, it is necessary to attach functional groups or other nano structures to their surface. The combination of the distinctive properties of carbon nano tubes and metal/oxides is expected to be applied in field emission displays, nano electronic devices, novel catalysts, and polymer or ceramic reinforcement. The synthesis of these composites is still largely based on conventional techniques, such as wet impregnation followed by chemical reduction of the metal nanoparticle precursors. These techniques based on thermal heating can be time consuming and often lack control of particle size and morphology. Hence, there is interest in microwave technology recently, where using microwaves represents an alternative way of power input into chemical reactions through dielectric heating. This paper covers the synthesis and applications of carbon-nano tube-coated metal/oxides nanoparticles prepared by a microwave-assisted method. The reviewed studies show that the microwave-assisted synthesis of the composites allows processes to be completed within a shorter reaction time with uniform and well-dispersed nanoparticle formation.

Recent Trends in the Microwave-Assisted Synthesis of Metal Oxide Nanoparticles Supported on Carbon Nanotubes and Their Applications

Directory of Open Access Journals (Sweden)

Sarah C. Motshekga

2012-01-01

Full Text Available The study of coating carbon nanotubes with metal/oxides nanoparticles is now becoming a promising and challenging area of research. To optimize the use of carbon nanotubes in various applications, it is necessary to attach functional groups or other nanostructures to their surface. The combination of the distinctive properties of carbon nanotubes and metal/oxides is expected to be applied in field emission displays, nanoelectronic devices, novel catalysts, and polymer or ceramic reinforcement. The synthesis of these composites is still largely based on conventional techniques, such as wet impregnation followed by chemical reduction of the metal nanoparticle precursors. These techniques based on thermal heating can be time consuming and often lack control of particle size and morphology. Hence, there is interest in microwave technology recently, where using microwaves represents an alternative way of power input into chemical reactions through dielectric heating. This paper covers the synthesis and applications of carbon-nanotube-coated metal/oxides nanoparticles prepared by a microwave-assisted method. The reviewed studies show that the microwave-assisted synthesis of the composites allows processes to be completed within a shorter reaction time with uniform and well-dispersed nanoparticle formation.

Prospects of joining multi-material structures

Science.gov (United States)

Sankaranarayanan, R.; Hynes, N. Rajesh Jesudoss

2018-05-01

Spring up trends and necessities make the pipelines for the brand new Technologies. The same way, Multimaterial structures emerging as fruitful alternatives for the conventional structures in the manufacturing sector. Especially manufacturing of transport vehicles is placing a perfect platform for these new structures. Bonding or joining technology plays a crucial role in the field of manufacturing for sustainability. These latest structures are purely depending on such joining technologies so that multi-material structuring can be possible practically. The real challenge lies on joining dissimilar materials of different properties and nature. Escalation of thermoplastic usage in large structural components also faces similar ambiguity for joining multi-material structures. Adhesive bonding, mechanical fastening and are the answering technologies for multi-material structures. This current paper analysis the prospects of these bonding technologies to meet the challenges of tomorrow.

Synthesis and characterization of PMMA/clay nanocomposites prepared by in situ polymerization assisted by sonication

International Nuclear Information System (INIS)

Prado, Bruna R.; Bartoli, Julio R.; Ito, Edson N.

2015-01-01

In this work is presented the synthesis of nanocomposites of poly(methyl methacrylate), PMMA, with organically montmorillonite (OMMT) modified clays by in situ polymerization assisted by sonication. A statistically designed experiment was used, central composing design (CCD), to study the effect of synthesis variables on the dispersion of nanoparticles in PMMA matrix. The processing and formulation factors studied were: energy of sonication and Flory-Huggins interaction parameter between PMMA and organoclay. The structural (XRD) and morphological (TEM) characterizations of the PMMA/OMMT nanocomposites are compared with the literature. It was observed significant exfoliation of OMMT modified with hydroxyl groups in the nanocomposites of PMMA, mainly at the low ultrasonic energy level (90 and 105 kJ) studied. (author)

A homologous radioimmunoassay for canine prolactin: plasma levels huring the reproductive cycle

International Nuclear Information System (INIS)

Coster, R. De; Beerens, D.; Mey, J. De; Beckers, J.-F.

1983-01-01

A method is described for the purification of canine prolactin, involving preparative isoelectrofocusing. Canine prolactin has a molecular weight of 23 000 daltons, an isoelectric point of 5.7 and exhibits a high degree of homogeneity in polyacrylamide gels stained by means of a silver method. A specific, homologous radioimmunoassay is described using the Bolton-Hunter method for preparation of the labelled ligand, with a sensitivity of 0.1 ng/tube. Basal plasma prolactin levels of 2-4 ng/ml obtained through the oestrous cycle remained fairly constant but a rise of 9 ng/ml was found at the end of dioestrus in non-pregnant bitches. Level also rose 30 days after mating to reach a peak of about 50 ng/ml near parturition and during early lactation. (author)

Caffeine suppresses homologous recombination through interference with RAD51-mediated joint molecule formation

Science.gov (United States)

Zelensky, Alex N.; Sanchez, Humberto; Ristic, Dejan; Vidic, Iztok; van Rossum-Fikkert, Sari E.; Essers, Jeroen; Wyman, Claire; Kanaar, Roland

2013-01-01

Caffeine is a widely used inhibitor of the protein kinases that play a central role in the DNA damage response. We used chemical inhibitors and genetically deficient mouse embryonic stem cell lines to study the role of DNA damage response in stable integration of the transfected DNA and found that caffeine rapidly, efficiently and reversibly inhibited homologous integration of the transfected DNA as measured by several homologous recombination-mediated gene-targeting assays. Biochemical and structural biology experiments revealed that caffeine interfered with a pivotal step in homologous recombination, homologous joint molecule formation, through increasing interactions of the RAD51 nucleoprotein filament with non-homologous DNA. Our results suggest that recombination pathways dependent on extensive homology search are caffeine-sensitive and stress the importance of considering direct checkpoint-independent mechanisms in the interpretation of the effects of caffeine on DNA repair. PMID:23666627

Pure homology of algebraic varieties

OpenAIRE

Weber, Andrzej

2003-01-01

We show that for a complete complex algebraic variety the pure component of homology coincides with the image of intersection homology. Therefore pure homology is topologically invariant. To obtain slightly more general results we introduce "image homology" for noncomplete varieties.

Somatic association of telocentric chromosomes carrying homologous centromeres in common wheat.

Science.gov (United States)

Mello-Sampayo, T

1973-01-01

Measurements of distances between telocentric chromosomes, either homologous or representing the opposite arms of a metacentric chromosome (complementary telocentrics), were made at metaphase in root tip cells of common wheat carrying two homologous pairs of complementary telocentrics of chromosome 1 B or 6 B (double ditelosomic 1 B or 6 B). The aim was to elucidate the relative locations of the telocentric chromosomes within the cell. The data obtained strongly suggest that all four telocentrics of chromosome 1 B or 6 B are spacially and simultaneously co-associated. In plants carrying two complementary (6 B (S) and 6 B (L)) and a non-related (5 B (L)) telocentric, only the complementary chromosomes were found to be somatically associated. It is thought, therefore, that the somatic association of chromosomes may involve more than two chromosomes in the same association and, since complementary telocentrics are as much associated as homologous, that the homology between centromeres (probably the only homologous region that exists between complementary telocentrics) is a very important condition for somatic association of chromosomes. The spacial arrangement of chromosomes was studied at anaphase and prophase and the polar orientation of chromosomes at prophase was found to resemble anaphase orientation. This was taken as good evidence for the maintenance of the chromosome arrangement - the Rabl orientation - and of the peripheral location of the centromere and its association with the nuclear membrane. Within this general arrangement homologous telocentric chromosomes were frequently seen to have their centromeres associated or directed towards each other. The role of the centromere in somatic association as a spindle fibre attachment and chromosome binder is discussed. It is suggested that for non-homologous chromosomes to become associated in root tips, the only requirement needed should be the homology of centromeres such as exists between complementary

One-pot Microwave-Assisted Synthesis of 1H-Phenanthro[9,10- d][1,2,3]triazole

Directory of Open Access Journals (Sweden)

Mehrak Faraji

2008-09-01

Full Text Available In this study, a fast and good yield one-pot microwave-assisted synthesis (45 seconds of 1H-phenanthro[9,10-d][1,2,3]triazole by a 1,3-dipolar cycloaddition reaction of sodium azide and 9-bromophenanthrene in the presence of potassium tert-butoxide in DMSO as solvent is reported.

Protective effect of a non specific inflammation on bone marrow protein synthesis in irradiated mice

International Nuclear Information System (INIS)

Herodin, F.; Roques, P.; Court, L.

1988-01-01

Gamma radiations exert a decrease in mouse bone marrow total protein synthesis. A non-specific inflammatory process induced with polyacrylamide microbeads stimulates spleen and marrow protein synthesis and protects the medullar protein synthesis in irradiated mice [fr

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)

DNA Polymerases λ and β: The Double-Edged Swords of DNA Repair

Directory of Open Access Journals (Sweden)

Elisa Mentegari

2016-08-01

Full Text Available DNA is constantly exposed to both endogenous and exogenous damages. More than 10,000 DNA modifications are induced every day in each cell’s genome. Maintenance of the integrity of the genome is accomplished by several DNA repair systems. The core enzymes for these pathways are the DNA polymerases. Out of 17 DNA polymerases present in a mammalian cell, at least 13 are specifically devoted to DNA repair and are often acting in different pathways. DNA polymerases β and λ are involved in base excision repair of modified DNA bases and translesion synthesis past DNA lesions. Polymerase λ also participates in non-homologous end joining of DNA double-strand breaks. However, recent data have revealed that, depending on their relative levels, the cell cycle phase, the ratio between deoxy- and ribo-nucleotide pools and the interaction with particular auxiliary proteins, the repair reactions carried out by these enzymes can be an important source of genetic instability, owing to repair mistakes. This review summarizes the most recent results on the ambivalent properties of these enzymes in limiting or promoting genetic instability in mammalian cells, as well as their potential use as targets for anticancer chemotherapy.

DNA Polymerases λ and β: The Double-Edged Swords of DNA Repair.

Science.gov (United States)

Mentegari, Elisa; Kissova, Miroslava; Bavagnoli, Laura; Maga, Giovanni; Crespan, Emmanuele

2016-08-31

DNA is constantly exposed to both endogenous and exogenous damages. More than 10,000 DNA modifications are induced every day in each cell's genome. Maintenance of the integrity of the genome is accomplished by several DNA repair systems. The core enzymes for these pathways are the DNA polymerases. Out of 17 DNA polymerases present in a mammalian cell, at least 13 are specifically devoted to DNA repair and are often acting in different pathways. DNA polymerases β and λ are involved in base excision repair of modified DNA bases and translesion synthesis past DNA lesions. Polymerase λ also participates in non-homologous end joining of DNA double-strand breaks. However, recent data have revealed that, depending on their relative levels, the cell cycle phase, the ratio between deoxy- and ribo-nucleotide pools and the interaction with particular auxiliary proteins, the repair reactions carried out by these enzymes can be an important source of genetic instability, owing to repair mistakes. This review summarizes the most recent results on the ambivalent properties of these enzymes in limiting or promoting genetic instability in mammalian cells, as well as their potential use as targets for anticancer chemotherapy.

Efficient synthesis of sulfonamide derivatives on solid supports catalyzed using solvent-free and microwave-assisted methods

Energy Technology Data Exchange (ETDEWEB)

Camargo-Ordonez, Argelia; Moreno-Reyes, Christian; Olazaran-Santibanez, Fabian; Martinez-Hernandez, Sheila; Bocanegra-Garcia, Virgilio; Rivera, Gildardo [Universidad Autonoma de Tamaulipas, Reynosa (Mexico). Dep. de Farmacia y Quimica Medicinal

2011-07-01

In this work we report the synthesis of sulfonamide derivatives using a conventional procedure and with solid supports, such as silica gel, florisil, alumina, 4A molecular sieves, montmorillonite KSF, and montmorillonite K10 using solvent-free and microwave-assisted methods. Our results show that solid supports have a catalytic activity in the formation of sulfonamide derivatives. We found that florisil, montmorillonite KSF, and K10 could be used as inexpensive alternative catalysts that are easily separated from the reaction media. Additionally, solvent-free and microwave-assisted methods were more efficient in reducing reaction time and in increasing yield. (author)

Efficient synthesis of sulfonamide derivatives on solid supports catalyzed using solvent-free and microwave-assisted methods

International Nuclear Information System (INIS)

Camargo-Ordonez, Argelia; Moreno-Reyes, Christian; Olazaran-Santibanez, Fabian; Martinez-Hernandez, Sheila; Bocanegra-Garcia, Virgilio; Rivera, Gildardo

2011-01-01

In this work we report the synthesis of sulfonamide derivatives using a conventional procedure and with solid supports, such as silica gel, florisil, alumina, 4A molecular sieves, montmorillonite KSF, and montmorillonite K10 using solvent-free and microwave-assisted methods. Our results show that solid supports have a catalytic activity in the formation of sulfonamide derivatives. We found that florisil, montmorillonite KSF, and K10 could be used as inexpensive alternative catalysts that are easily separated from the reaction media. Additionally, solvent-free and microwave-assisted methods were more efficient in reducing reaction time and in increasing yield. (author)

Dynamic optimization of a dead-end filtration trajectory: non-ideal cake filtration

NARCIS (Netherlands)

Blankert, B.; Kattenbelt, C.; Betlem, Bernardus H.L.; Roffel, B.

2007-01-01

A control strategy aimed at minimizing energy consumption is formulated for non-ideal dead-end cake filtration with an inside-out hollow fiber ultrafiltration membrane system. The non-ideal behavior was assumed to originate from cake compression, non-linear cake resistance and a variable pump

Activities of HIP joining of plasma-facing armors in the blanket first-wall in Korea

Energy Technology Data Exchange (ETDEWEB)

Jung, Yang-Il, E-mail: yijung@kaeri.re.kr [Korea Atomic Energy Research Institute, Daedeok-daero, Daejeon 34057 (Korea, Republic of); Park, Jeong-Yong; Choi, Byoung-Kwon; Lee, Jung-Suk; Kim, Hyun-Gil; Park, Dong-Jun; Park, Jung-Hwan; Kim, Suk-Kwon; Lee, Dong-Won [Korea Atomic Energy Research Institute, Daedeok-daero, Daejeon 34057 (Korea, Republic of); Cho, Seungyon [National Fusion Research Institute, Gwahak-ro, Yuseong, Daejeon 34133 (Korea, Republic of)

2016-11-01

Highlights: • HIP joints of Be/CuCrZr, Be/FMS, W/FMS were demonstrated. • The process conditions for HIP joining were developed. • For the joining of Be, coating interlayers as well as thick diffusion barrier was developed. • For the joining of W, double-staged HIP was applied for the joint integrity. • No significant defects nor a brittle failure were observed along the joint interface. - Abstract: Joining technology for dissimilar materials was developed for the fabrication of an ITER blanket first-wall, which consisted of Be, CuCrZr, and stainless steel (SS). The Be/CuCrZr/SS joint was fabricated using a hot isostatic pressing (HIP) method. Beryllium armor was joined to the CuCrZr/SS block at 580 °C under 100 MPa. The optimal interlayer coatings of Cr/Cu and Ti/Cr/Cu were developed using an ion-beam assisted physical vapor deposition. Beryllium is also a candidate armor material for the TBM first-wall. Successful joining of Be to ferritic-martensitic steel (FMS) was accomplished using an HIP method by introducing the thick diffusion barrier. A thick diffusion barrier of a Cu foil(10 μm) limited the excessive diffusion and prevented the formation of brittle phases at the Be/FMS interface. Be and FMS were bonded at 650–850 °C; however, a temperature of lower than 750 °C was recommended to avoid material degradation of FMS. In addition, the joining of W to FMS has been developed. Tungsten is another armor material applicable to more severe plasma conditions. The large difference in the thermal expansion between W and FMS was resolved by introducing the Ti interlayer and Mo separator. Moreover, the double-staged HIP (the first stage at 900 °C and 100 MPa and the second stage at 750 °C and 70 MPa) was applied to suppress the edge delamination of W/FMS joints during thermal history.

Conjoint Forming - Technologies for Simultaneous Forming and Joining

International Nuclear Information System (INIS)

Groche, P; Wohletz, S; Mann, A; Krech, M; Monnerjahn, V

2016-01-01

The market demand for new products optimized for e. g. lightweight applications or smart components leads to new challenges in production engineering. Hybrid structures represent one promising approach. They aim at higher product performance by using a suitable combination of different materials. The developments of hybrid structures stimulate the research on joining of dissimilar materials. Since they allow for joining dissimilar materials without external heating technologies based on joining by plastic deformation seem to be of special attractiveness. The paper at hand discusses the conjoint forming approach. This approach combines forming and joining in one process. Two or more workpieces are joined while at least one workpiece is plastically deformed. After presenting the fundamental joining mechanisms, the conjoint forming approach is discussed comprehensively. Examples of conjoint processes demonstrate the effectiveness and reveal the underlying phenomena. (paper)

Lectures on functor homology

CERN Document Server

Touzé, Antoine

2015-01-01

This book features a series of lectures that explores three different fields in which functor homology (short for homological algebra in functor categories) has recently played a significant role. For each of these applications, the functor viewpoint provides both essential insights and new methods for tackling difficult mathematical problems. In the lectures by Aurélien Djament, polynomial functors appear as coefficients in the homology of infinite families of classical groups, e.g. general linear groups or symplectic groups, and their stabilization. Djament’s theorem states that this stable homology can be computed using only the homology with trivial coefficients and the manageable functor homology. The series includes an intriguing development of Scorichenko’s unpublished results. The lectures by Wilberd van der Kallen lead to the solution of the general cohomological finite generation problem, extending Hilbert’s fourteenth problem and its solution to the context of cohomology. The focus here is o...

The pharmacotherapy implications of ventricular assist device in the patient with end-stage heart failure.

Science.gov (United States)

Von Ruden, Serena A S; Murray, Margaret A; Grice, Jennifer L; Proebstle, Amy K; Kopacek, Karen J

2012-04-01

Advances in mechanical circulatory support, such as the use of ventricular assist devices (VADs), have become a means for prolonging survival in end-stage heart failure (HF). VADs decrease the symptoms of HF and improve quality of life by replacing some of the work of a failing heart. They unload the ventricle to provide improved cardiac output and end-organ perfusion, resulting in improvement in cardiorenal syndromes and New York Heart Association functional class rating. VADs are currently used asa bridge to heart transplantation, a bridge to recovery of cardiac function, or as destination therapy. Complications of VAD include bleeding, infections, arrhythmias, multiple organ failure, right ventricular failure, and neurological dysfunction. Patients with VAD have unique pharmacotherapeutic requirements in terms of anticoagulation, appropriate antibiotic selection, and continuation of HF medications. Pharmacists in acute care and community settings are well prepared to care for the patient with VAD. These patients require thorough counseling and follow-up with regard to prevention and treatment of infections, appropriate levels of anticoagulation, and maintenance of fluid balance. A basic understanding of this unique therapy can assist pharmacists in attending to the needs of patients with VAD.

Support groups for HIV-positive people in South Africa: Who joins ...

African Journals Online (AJOL)

Non-members had tested due to illness, reported considerably more pain and were more likely to have no income. PLWHA experienced high mental, physical and social distress which must be addressed. Attention to gender differences is called for. While all members joined the support group to gain information and learn ...

Microwave-assisted hydrothermal synthesis of CePO{sub 4} nanostructures: Correlation between the structural and optical properties

Energy Technology Data Exchange (ETDEWEB)

Palma-Ramírez, D. [Instituto Politécnico Nacional, CICATA-Unidad Altamira, Km 14.5, Carretera Tampico-Puerto Industrial Altamira, C.P. 89600 Altamira, Tamps (Mexico); Domínguez-Crespo, M.A., E-mail: mdominguezc@ipn.mx [Instituto Politécnico Nacional, CICATA-Unidad Altamira, Km 14.5, Carretera Tampico-Puerto Industrial Altamira, C.P. 89600 Altamira, Tamps (Mexico); Torres-Huerta, A.M. [Instituto Politécnico Nacional, CICATA-Unidad Altamira, Km 14.5, Carretera Tampico-Puerto Industrial Altamira, C.P. 89600 Altamira, Tamps (Mexico); Dorantes-Rosales, H. [Instituto Politécnico Nacional, ESIQIE, Departamento de Metalurgia, C.P. 07300 México D.F. (Mexico); Ramírez-Meneses, E. [Universidad Iberoamericana, Departamento de Ingeniería y Ciencias Químicas, Prolongación Paseo de la Reforma 880, Lomas de Santa Fe, C.P. 01219 México D.F. (Mexico); Rodríguez, E. [Instituto Politécnico Nacional, CICATA-Unidad Altamira, Km 14.5, Carretera Tampico-Puerto Industrial Altamira, C.P. 89600 Altamira, Tamps (Mexico)

2015-09-15

Highlights: • An enhancement in the hydrothermal synthesis for obtaining of CePO{sub 4} is presented. • Microwave energy can replace the energy by convection for obtaining CePO{sub 4}. • CePO{sub 4} demonstrates to be an option to increase the optical properties of polymers. • Adjusting the pH, the sintering process is not necessary to obtain the desire phase. • CePO{sub 4} morphologies undergo evolution from nanorods to semispherical nanoparticles. - Abstract: In this work, the microwave-assisted hydrothermal method is proposed as an alternative to the synthesis of cerium phosphate (CePO{sub 4}) nanostructures to evaluate the influence of different synthesis parameters on both the structural and optical properties. In order to reach this goal, two different sets of experiments were designed, varying the reaction temperature (130 and 180 °C), synthesis time (15 and 30 min) and sintering temperature (400 and 600 °C), maintaining a constant pH = 3. Thereafter, two experimental conditions were selected to assess changes in the properties of CePO{sub 4} nanopowders with pH (1, 5, 9 and 11). The crystal structure and morphology of the nanostructures were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM) and scanning electron microscopy (SEM), respectively. Diffuse reflectance properties of CePO{sub 4} with different microstructures were studied. The results demonstrated that by using the microwave-assisted hydrothermal method, the shape, size and structural phase of CePO{sub 4} can be modulated by using relatively low synthesis temperatures and short reaction times, and depending on pH, a sintering process is not needed to obtain either a desired phase or size. Under the selected experimental conditions, the materials underwent an evolution from nanorods to semispherical nanoparticles, accompanied by a phase transition from hexagonal to monoclinic.

Microwave-Assisted Synthesis of a MK2 Inhibitor by Suzuki-Miyaura Coupling for Study in Werner Syndrome Cells

Directory of Open Access Journals (Sweden)

Mark C. Bagley

2015-06-01

Full Text Available Microwave-assisted Suzuki-Miyaura cross-coupling reactions have been employed towards the synthesis of three different MAPKAPK2 (MK2 inhibitors to study accelerated aging in Werner syndrome (WS cells, including the cross-coupling of a 2-chloroquinoline with a 3-pyridinylboronic acid, the coupling of an aryl bromide with an indolylboronic acid and the reaction of a 3-amino-4-bromopyrazole with 4-carbamoylphenylboronic acid. In all of these processes, the Suzuki-Miyaura reaction was fast and relatively efficient using a palladium catalyst under microwave irradiation. The process was incorporated into a rapid 3-step microwave-assisted method for the synthesis of a MK2 inhibitor involving 3-aminopyrazole formation, pyrazole C-4 bromination using N-bromosuccinimide (NBS, and Suzuki-Miyaura cross-coupling of the pyrazolyl bromide with 4-carbamoylphenylboronic acid to give the target 4-arylpyrazole in 35% overall yield, suitable for study in WS cells.

Biological defense mechanisms against DNA double-strand break and their possible medical applications

International Nuclear Information System (INIS)

Matsumoto, Yoshihisa

2011-01-01

Radiation is now widely used for clinical diagnosis and therapeutics. On the other hand, radiation influences various tissues represented by immunological and reproductive systems, and is also recognized as one of the cause of carcinogenesis. Such pleiotropic effects of radiation are mediated through generation of damages on DNA molecule, vitally important genetic macromolecule. Among various types of DNA damages, double-strand break (DSB) is considered most critical and, therefore, responsible for biological effects. DSB is repaired mainly through two pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). Understanding of these mechanisms has been greatly deepened in past 20 years and is now providing a promising approach toward cancer therapy. We have studied the mechanisms of NHEJ, focusing especially on the role of phosphorylation and the assembly of machinery therein, which will be introduced below. (author)

Repair of endogenous and ionizing radiation-induced DNA damages: mechanisms and biological functions

International Nuclear Information System (INIS)

Boiteux, S.

2002-01-01

The cellular DNA is continuously exposed to endogenous and exogenous stress. Oxidative stress due to cellular metabolism is the major cause of endogenous DNA damage. On the other hand, ionizing radiation (IR) is an important exogenous stress. Both induce similar DNA damages: damaged bases, abasic sites and strand breakage. Most of these lesions are lethal and/or mutagenic. The survival of the cell is managed by efficient and accurate DNA repair mechanisms that remove lesions before their replication or transcription. DNA repair pathways involved in the removal of IR-induced lesions are briefly described. Base excision repair (BER) is mostly involved in the removal of base damage, abasic sites and single strand breaks. In contrast, DNA double strand breaks are mostly repaired by non-homologous end joining (NHEJ) or homologous recombination (HR). How DNA repair pathways prevent cancer process is also discussed. (author)

Nuclear non-proliferation

International Nuclear Information System (INIS)

Anon.

1984-01-01

DOE's nuclear non-proliferation responsibilities are defined by the provisions of the Atomic Energy Act of 1954, as amended, and of the Nuclear Non-Proliferation Act of 1978 (NNPA). The Department's major responsibilities in this area are to: (1) provide technical assistance to the Department of State in negotiating agreements for civil cooperation in the peaceful uses of nuclear energy with other countries and international organizations; (2) join with other agencies to reach executive branch judgments with respect to the issuance of export licenses by the Nuclear Regulatory Commission; (3) be responsible for processing subsequent arrangements with other agencies as required by the Nuclear Non-Proliferation Act; (4) control the distribution of special nuclear materials, components, equipment, and nuclear technology exports; (5) participate in bilateral and multilateral cooperation with foreign governments and organizations to promote the peaceful uses of nuclear energy; and (6) act as a primary technical resource with respect to US participation in the International Atomic Energy Agency

Plasma-assisted synthesis of monodispersed and robust Ruthenium ultrafine nanocatalysts for organosilane oxidation and oxygen evolution reactions

NARCIS (Netherlands)

Gnanakumar, E.S.; Ng, W.; Filiz, B.C.; Rothenberg, G.; Wang, S.; Xu, H.; Pastor-Pérez, L.; Pastor-Blas, M.M.; Sepúlveda-Escribano, A.; Yan, N.; Shiju, N.R.

2017-01-01

We report a facile and general approach for preparing ultrafine ruthenium nanocatalysts by using a plasma-assisted synthesis at <100 °C. The resulting Ru nanoparticles are monodispersed (typical size 2 nm) and remain that way upon loading onto carbon and TiO2 supports. This gives robust catalysts

Synthesis of Calcite Nano Particles from Natural Limestone assisted with Ultrasonic Technique

Science.gov (United States)

Handayani, M.; Sulistiyono, E.; Firdiyono, F.; Fajariani, E. N.

2018-03-01

This article represents a precipitation method assisted with ultrasonic process to synthesize precipitated calcium carbonate nano particles from natural limestone. The synthesis of nanoparticles material of precipitated calcium carbonate from commercial calcium carbonate was done for comparison. The process was performed using ultrasonic waves at optimum condition, that is, at temperature of 80oC for 10 minutes with various amplitudes. Synthesized precipitated calcium carbonate nanoparticles were characterized using X-Ray Diffraction (XRD), Scanning Electron Microscope (SEM) and Particle Size Analyzer (PSA). The result of PSA measurements showed that precipitated calcium carbonate nano particles was obtained with the average size of 109 nm.

Microwave-Assisted Synthesis of Nanoporous Aluminum-Based Coordination Polymers as Catalysts for Selective Sulfoxidation Reaction

Directory of Open Access Journals (Sweden)

Madhan Vinu

2017-10-01

Full Text Available A series of aluminum-based coordination polymers or metal–organic frameworks (Al–MOFs, i.e., DUT-4, DUT-5, MIL-53, NH2-MIL-53, and MIL-100, have been facile prepared by microwave (MW-assisted reactions and used as catalysts for selective sulfoxidation reactions. The MW-assisted synthesis drastically reduced the reaction time from few days to hours. The prepared MOFs have smaller and uniform particle sizes and better yield compared to conventional hydrothermal method. Furthermore, the Al–MOFs have been successfully demonstrated as catalysts in oxidation reaction of methyl phenyl sulfide with H2O2 as oxidant, even under mild conditions, with more than 95% conversion.

On the formation of Mo{sub 2}C nanocrystals by a novel system through microwave assisted combustion synthesis

Energy Technology Data Exchange (ETDEWEB)

Hoseinpur, Arman, E-mail: arman_hoseinpur@metaleng.iust.ac.ir [School of Metallurgy and Materials Engineering, Iran University of Science and Technology (IUST), 16846-13114, Narmak, Tehran, Islamic Republic of Iran (Iran, Islamic Republic of); Jalaly, Maisam [Nanotechnology Department, School of New Technologies, Iran University of Science and Technology (IUST), 16846-13114, Narmak, Tehran, Islamic Republic of Iran (Iran, Islamic Republic of); Bafghi, Mohammad Sh. [School of Metallurgy and Materials Engineering, Iran University of Science and Technology (IUST), 16846-13114, Narmak, Tehran, Islamic Republic of Iran (Iran, Islamic Republic of); Khaki, Jalil Vahdati [Department of Materials Engineering, Ferdowsi University of Mashhad, 91775-1111, Islamic Republic of Iran (Iran, Islamic Republic of)

2015-10-15

This research is devoted to microwave assisted combustion synthesis of Mo{sub 2}C nanoparticles. The ternary system of MoO{sub 3}–Zn–C was used as a novel approach for the in-situ synthesis of Mo{sub 2}C in which the zincothermic reduction of MoO{sub 3} was responsible for the combustion to take place. Results showed that the formation of Mo{sub 2}C was assisted by the zincothermic reaction, although further microwave heating up to 6 min was necessary to complete the reaction. The effects of the microwave heating and mechanical activation on the reaction progress were investigated. X-ray powder diffraction was used to examine the synthesis progress. Final products (Mo{sub 2}C and ZnO) were successfully separated from each other and the synthesized carbide was characterized by transmission electron microscopy (TEM), showing the formation of Mo{sub 2}C hexagonal nanocrystals during combustion process. - Highlights: • Hexagonal β-Mo{sub 2}C nanocrystals were successfully synthesized. • MoO{sub 3}–Zn–C powder mixture was selected as the initial mixture for the in-situ synthesis of Mo{sub 2}C. • 30 min of mechanical activation was necessary for the carbide formation to be completed. • The zincothermic reduction of MoO{sub 3} by Zn was responsible for the combustion. • The final products included of Mo{sub 2}C and ZnO in which ZnO was removed by acid leaching.

Chromosome End Repair and Genome Stability in Plasmodium falciparum.

Science.gov (United States)

Calhoun, Susannah F; Reed, Jake; Alexander, Noah; Mason, Christopher E; Deitsch, Kirk W; Kirkman, Laura A

2017-08-08

The human malaria parasite Plasmodium falciparum replicates within circulating red blood cells, where it is subjected to conditions that frequently cause DNA damage. The repair of DNA double-stranded breaks (DSBs) is thought to rely almost exclusively on homologous recombination (HR), due to a lack of efficient nonhomologous end joining. However, given that the parasite is haploid during this stage of its life cycle, the mechanisms involved in maintaining genome stability are poorly understood. Of particular interest are the subtelomeric regions of the chromosomes, which contain the majority of the multicopy variant antigen-encoding genes responsible for virulence and disease severity. Here, we show that parasites utilize a competitive balance between de novo telomere addition, also called "telomere healing," and HR to stabilize chromosome ends. Products of both repair pathways were observed in response to DSBs that occurred spontaneously during routine in vitro culture or resulted from experimentally induced DSBs, demonstrating that both pathways are active in repairing DSBs within subtelomeric regions and that the pathway utilized was determined by the DNA sequences immediately surrounding the break. In combination, these two repair pathways enable parasites to efficiently maintain chromosome stability while also contributing to the generation of genetic diversity. IMPORTANCE Malaria is a major global health threat, causing approximately 430,000 deaths annually. This mosquito-transmitted disease is caused by Plasmodium parasites, with infection with the species Plasmodium falciparum being the most lethal. Mechanisms underlying DNA repair and maintenance of genome integrity in P. falciparum are not well understood and represent a gap in our understanding of how parasites survive the hostile environment of their vertebrate and insect hosts. Our work examines DNA repair in real time by using single-molecule real-time (SMRT) sequencing focused on the subtelomeric

Distancing sedation in end-of-life care from physician-assisted suicide and euthanasia

Science.gov (United States)

Soh, Tze Ling Gwendoline Beatrice; Krishna, Lalit Kumar Radha; Sim, Shin Wei; Yee, Alethea Chung Peng

2016-01-01

Lipuma equates continuous sedation until death (CSD) to physician-assisted suicide/euthanasia (PAS/E) based on the premise that iatrogenic unconsciousness negates social function and, thus, personhood, leaving a patient effectively ‘dead’. Others have extrapolated upon this position further, to suggest that any use of sedation and/or opioids at the end of life would be analogous to CSD and thus tantamount to PAS/E. These posits sit diametrically opposite to standard end-of-life care practices. This paper will refute Lipuma’s position and the posits borne from it. We first show that prevailing end-of-life care guidelines require proportional and monitored use of sedatives and/or opioids to attenuate fears that the use of such treatment could hasten death. These guidelines also classify CSD as a last resort treatment, employed only when symptoms prove intractable, and not amenable to all standard treatment options. Furthermore, CSD is applied only when deemed appropriate by a multidisciplinary palliative medicine team. We also show that empirical data based on local views of personhood will discount concerns that iatrogenic unconsciousness is tantamount to a loss of personhood and death. PMID:27211055

Distancing sedation in end-of-life care from physician-assisted suicide and euthanasia.

Science.gov (United States)

Soh, Tze Ling Gwendoline Beatrice; Krishna, Lalit Kumar Radha; Sim, Shin Wei; Yee, Alethea Chung Peng

2016-05-01

Lipuma equates continuous sedation until death (CSD) to physician-assisted suicide/euthanasia (PAS/E) based on the premise that iatrogenic unconsciousness negates social function and, thus, personhood, leaving a patient effectively 'dead'. Others have extrapolated upon this position further, to suggest that any use of sedation and/or opioids at the end of life would be analogous to CSD and thus tantamount to PAS/E. These posits sit diametrically opposite to standard end-of-life care practices. This paper will refute Lipuma's position and the posits borne from it. We first show that prevailing end-of-life care guidelines require proportional and monitored use of sedatives and/or opioids to attenuate fears that the use of such treatment could hasten death. These guidelines also classify CSD as a last resort treatment, employed only when symptoms prove intractable, and not amenable to all standard treatment options. Furthermore, CSD is applied only when deemed appropriate by a multidisciplinary palliative medicine team. We also show that empirical data based on local views of personhood will discount concerns that iatrogenic unconsciousness is tantamount to a loss of personhood and death. Copyright: © Singapore Medical Association.

Kluyveromyces marxianus as a host for heterologous protein synthesis.

Science.gov (United States)

Gombert, Andreas K; Madeira, José Valdo; Cerdán, María-Esperanza; González-Siso, María-Isabel

2016-07-01

The preferentially respiring and thermotolerant yeast Kluyveromyces marxianus is an emerging host for heterologous protein synthesis, surpassing the traditional preferentially fermenting yeast Saccharomyces cerevisiae in some important aspects: K . marxianus can grow at temperatures 10 °C higher than S. cerevisiae, which may result in decreased costs for cooling bioreactors and reduced contamination risk; has ability to metabolize a wider variety of sugars, such as lactose and xylose; is the fastest growing eukaryote described so far; and does not require special cultivation techniques (such as fed-batch) to avoid fermentative metabolism. All these advantages exist together with a high secretory capacity, performance of eukaryotic post-translational modifications, and with a generally regarded as safe (GRAS) status. In the last years, replication origins from several Kluyveromyces spp. have been used for the construction of episomal vectors, and also integrative strategies have been developed based on the tendency for non-homologous recombination displayed by K. marxianus. The recessive URA3 auxotrophic marker and the dominant Kan(R) are mostly used for selection of transformed cells, but other markers have been made available. Homologous and heterologous promoters and secretion signals have been characterized, with the K. marxianus INU1 expression and secretion system being of remarkable functionality. The efficient synthesis of roughly 50 heterologous proteins has been demonstrated, including one thermophilic enzyme. In this mini-review, we summarize the physiological characteristics of K. marxianus relevant for its use in the efficient synthesis of heterologous proteins, the efforts performed hitherto in the development of a molecular toolbox for this purpose, and some successful examples.

DNA-dependent protein kinase (DAN-PK), a key enzyme in the re-ligation of DNA double-strand breaks

International Nuclear Information System (INIS)

Hennequin, C.; Averbeck, D.

1999-01-01

Repair pathways of DNA are now defined and some important findings have been discovered in the last few years. DNA non-homologous end-joining (NEH) is a crucial process in the repair of radiation-induced double-strand breaks (DSBs). NHEj implies at least three steps: the DNA free-ends must get closer, preparation of the free-ends by exonucleases and then a transient hybridization in a region of DNA with weak homology. DNA-dependent protein kinase (DNA-PK) is the key enzyme in this process. DNA-PK is a nuclear serine/threonine kinase that comprises three components: a catalytic subunit (DNA-PK cs ) and two regulatory subunits, DNA-binding proteins, Ku80 and Ku70. The severe combined immuno-deficient (scid) mice are deficient in DNA-PK cs : this protein is involved both in DNA repair and in the V(D)J recombination of immunoglobulin and T-cell receptor genes. It is a protein-kinase of the P13-kinase family and which can phosphorylate Ku proteins, p53 and probably some other proteins still unknown. DNA-PK is an important actor of DSBs repair (induced by ionising radiations or by drugs like etoposide), but obviously it is not the only mechanism existing in the cell for this function. Some others, like homologous recombination, seem also to have a great importance for cell survival. (authors)

The chlamydial functional homolog of KsgA confers kasugamycin sensitivity to Chlamydia trachomatis and impacts bacterial fitness

Directory of Open Access Journals (Sweden)

Maurelli Anthony T

2009-12-01

Full Text Available Abstract Background rRNA adenine dimethyltransferases, represented by the Escherichia coli KsgA protein, are highly conserved phylogenetically and are generally not essential for growth. They are responsible for the post-transcriptional transfer of two methyl groups to two universally conserved adenosines located near the 3'end of the small subunit rRNA and participate in ribosome maturation. All sequenced genomes of Chlamydia reveal a ksgA homolog in each species, including C. trachomatis. Yet absence of a S-adenosyl-methionine synthetase in Chlamydia, the conserved enzyme involved in the synthesis of the methyl donor S-adenosyl-L-methionine, raises a doubt concerning the activity of the KsgA homolog in these organisms. Results Lack of the dimethylated adenosines following ksgA inactivation confers resistance to kasugamycin (KSM in E. coli. Expression of the C. trachomatis L2 KsgA ortholog restored KSM sensitivity to the E. coli ksgA mutant, suggesting that the chlamydial KsgA homolog has specific rRNA dimethylase activity. C. trachomatis growth was sensitive to KSM and we were able to isolate a KSM resistant mutant of C. trachomatis containing a frameshift mutation in ksgA, which led to the formation of a shorter protein with no activity. Growth of the C. trachomatis ksgA mutant was negatively affected in cell culture highlighting the importance of the methylase in the development of these obligate intracellular and as yet genetically intractable pathogens. Conclusion The presence of a functional rRNA dimethylase enzyme belonging to the KsgA family in Chlamydia presents an excellent chemotherapeutic target with real potential. It also confirms the existence of S-adenosyl-methionine - dependent methylation reactions in Chlamydia raising the question of how these organisms acquire this cofactor.

Thin layer joining by gas adsorption

Energy Technology Data Exchange (ETDEWEB)

Taga, Yasunori, E-mail: y-taga@isc.chubu.ac.jp; Fukumura, Toshio

2014-10-01

Highlights: • We report thin layer molecular joining between glass and COP by gas adsorption. Thickness of joining layer is 1–2 nm and joining process was carried out at low temperature at about 100 °C. • Adhesion strength measured by 180 degree peel test revealed to be 1–10 N/25 mm and the joined stack showed high durability for practical use. - Abstract: Attempt has been made to join borosilicate glass and cycloolefin (COP) polymer film by using gas adsorption method. After corona plasma treat, COP was exposed to (3-glycidoxypropyl) trimethoxysilane (GPS) and glass to (3-aminopropyl) triethoxysilane (APS) both in air atmosphere, resulting in co-adsorption of water vapor in the atmosphere and organosilane gases. Surface characterization of plasma treated and gas adsorbed surfaces was carried out by X-ray photoelectron spectroscopy (XPS) using Mg Kα X-ray source. Joining was carried out by a roll laminator after contact of both surfaces at room temperature, followed by annealing at 130 °C for 10 min. Adhesion strength was evaluated by 180 degree peel test based on ASTM D-903 and durability was examined under the conditions of 60 °C and 95% RH. It was found that after plasma treatment, complex functional groups such as C-H, C-O, C=O, O-C=O and CO{sub 3} were found on COP and O-H on glass. Thickness of GPS gas adsorption layer on COP was evaluated by the XPS to be at least 1.1 nm by taking inelastic mean free path of Si{sub 2p} photoelectron into consideration. Joining force was found to be more than 5 N/25 mm corresponding to almost equal to COP bulk tensile strength. In addition, durability of this adhesion strength remained unchanged over 2000 h even after exposure to the durability test conditions of 60 °C and 95% RH. The results can be explained in terms of formation of H-H hydrogen bonding and Si-O covalent bonding via silanols will be made at the interface as a result of lamination and annealing processes. In conclusion, ultrathin joining method

Spatio-temporal joins on symbolic indoor tracking data

DEFF Research Database (Denmark)

Lu, Hua; Yang, Bin; Jensen, Christian S.

2011-01-01

and studies probabilistic, spatio-temporal joins on historical indoor tracking data. Two meaningful types of join are defined. They return object pairs that satisfy spatial join predicates either at a time point or during a time interval. The predicates considered include “same X,” where X is a semantic...

Mechanism of Particle Formation in Silver/Epoxy Nanocomposites Obtained through a Visible-Light-Assisted in Situ Synthesis.

Science.gov (United States)

dell'Erba, Ignacio E; Martínez, Francisco D; Hoppe, Cristina E; Eliçabe, Guillermo E; Ceolín, Marcelo; Zucchi, Ileana A; Schroeder, Walter F

2017-10-03

A detailed understanding of the processes taking place during the in situ synthesis of metal/polymer nanocomposites is crucial to manipulate the shape and size of nanoparticles (NPs) with a high level of control. In this paper, we report an in-depth time-resolved analysis of the particle formation process in silver/epoxy nanocomposites obtained through a visible-light-assisted in situ synthesis. The selected epoxy monomer was based on diglycidyl ether of bisphenol A, which undergoes relatively slow cationic ring-opening polymerization. This feature allowed us to access a full description of the formation process of silver NPs before this was arrested by the curing of the epoxy matrix. In situ time-resolved small-angle X-ray scattering investigation was carried out to follow the evolution of the number and size of the silver NPs as a function of irradiation time, whereas rheological experiments combined with near-infrared and ultraviolet-visible spectroscopies were performed to interpret how changes in the rheological properties of the matrix affect the nucleation and growth of particles. The analysis of the obtained results allowed us to propose consistent mechanisms for the formation of metal/polymer nanocomposites obtained by light-assisted one-pot synthesis. Finally, the effect of a thermal postcuring treatment of the epoxy matrix on the particle size in the nanocomposite was investigated.

Physicochemical characterization of microwave assisted synthesis of silver nanoparticles using Aloe Vera (Aloe barbadensis)

Science.gov (United States)

Kuponiyi, Abiola John

Biosynthesis of silver nanoparticles (AgNP) using different biological extracts is gaining recognition for its numerous applications in different disciplines. Although different approaches (physical and chemical) have been used for the synthesis of AgNP, the green chemistry method is most preferable because of its high efficacy, cost effectiveness, and environmental benignity. Aloe Vera (AV) contains chemical compounds (anthraquinones) that are known to possess antibacterial, antivirus and anticancer properties and the extract is a good chemical reduction agent for AgNP. Hence, it was hypothesized that a microwave assisted synthesis will produce highly concentrated, homogeneous, stable and biologically active AgNP. Thus, the main objective of the study was to evaluate the effect of microwave assisted synthesis of AgNP, the effect of pulse laser treatment on size reduction of a microwave synthesized AgNP, and the physicochemical characterization of AgNP synthesized with Aloe Vera water and ethanol extract. The experiment was conducted in two phases. Phase 1 was first conducted to optimize the experimental variables, thus establishing the optimum variables to apply in the second phase. The experiment in Phase 1 was conducted using three-factor factorial experimental design comprised of the following factors: 1) Extraction Solvent, 2) Heating Methods, 3) pH; and their corresponding levels were water and ethanol, conventional and microwave, pH (7, 8, 10 and 12), respectively. All synthesis was conducted at constant temperature of 80°C. Phase II experimental treatments were Laser ablation (0, 5, and 10 min) and Storage time (Week 1, 2 & 3). The Phase I of the results showed that increased AgNP concentrations were significantly (p 0.05) impact the particle size distribution. Hence, the Zeta potential of the particles has values typically ranging between +100 mV to -100 mV, hence indicative of colloidal stability matrix. Furthermore, the Polydispersity indexes of Week 1

Boolean Operations, Joins, and the Extended Low Hierarchy

OpenAIRE

Hemaspaandra, Lane A.; Jiang, Zhigen; Rothe, Joerg; Watanabe, Osamu

1999-01-01

We prove that the join of two sets may actually fall into a lower level of the extended low hierarchy than either of the sets. In particular, there exist sets that are not in the second level of the extended low hierarchy, EL_2, yet their join is in EL_2. That is, in terms of extended lowness, the join operator can lower complexity. Since in a strong intuitive sense the join does not lower complexity, our result suggests that the extended low hierarchy is unnatural as a complexity measure. We...

Simulation methods supporting homologation of Electronic Stability Control in vehicle variants

Science.gov (United States)

Lutz, Albert; Schick, Bernhard; Holzmann, Henning; Kochem, Michael; Meyer-Tuve, Harald; Lange, Olav; Mao, Yiqin; Tosolin, Guido

2017-10-01

Vehicle simulation has a long tradition in the automotive industry as a powerful supplement to physical vehicle testing. In the field of Electronic Stability Control (ESC) system, the simulation process has been well established to support the ESC development and application by suppliers and Original Equipment Manufacturers (OEMs). The latest regulation of the United Nations Economic Commission for Europe UN/ECE-R 13 allows also for simulation-based homologation. This extends the usage of simulation from ESC development to homologation. This paper gives an overview of simulation methods, as well as processes and tools used for the homologation of ESC in vehicle variants. The paper first describes the generic homologation process according to the European Regulation (UN/ECE-R 13H, UN/ECE-R 13/11) and U.S. Federal Motor Vehicle Safety Standard (FMVSS 126). Subsequently the ESC system is explained as well as the generic application and release process at the supplier and OEM side. Coming up with the simulation methods, the ESC development and application process needs to be adapted for the virtual vehicles. The simulation environment, consisting of vehicle model, ESC model and simulation platform, is explained in detail with some exemplary use-cases. In the final section, examples of simulation-based ESC homologation in vehicle variants are shown for passenger cars, light trucks, heavy trucks and trailers. This paper is targeted to give a state-of-the-art account of the simulation methods supporting the homologation of ESC systems in vehicle variants. However, the described approach and the lessons learned can be used as reference in future for an extended usage of simulation-supported releases of the ESC system up to the development and release of driver assistance systems.

Mod two homology and cohomology

CERN Document Server

Hausmann, Jean-Claude

2014-01-01

Cohomology and homology modulo 2 helps the reader grasp more readily the basics of a major tool in algebraic topology. Compared to a more general approach to (co)homology this refreshing approach has many pedagogical advantages: It leads more quickly to the essentials of the subject, An absence of signs and orientation considerations simplifies the theory, Computations and advanced applications can be presented at an earlier stage, Simple geometrical interpretations of (co)chains. Mod 2 (co)homology was developed in the first quarter of the twentieth century as an alternative to integral homology, before both became particular cases of (co)homology with arbitrary coefficients. The first chapters of this book may serve as a basis for a graduate-level introductory course to (co)homology. Simplicial and singular mod 2 (co)homology are introduced, with their products and Steenrod squares, as well as equivariant cohomology. Classical applications include Brouwer's fixed point theorem, Poincaré duality, Borsuk-Ula...

From non-preemptive to preemptive scheduling using synchronization synthesis.

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Černý, Pavol; Clarke, Edmund M; Henzinger, Thomas A; Radhakrishna, Arjun; Ryzhyk, Leonid; Samanta, Roopsha; Tarrach, Thorsten

2017-01-01

We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We guarantee that our synthesis does not introduce deadlocks and that the synchronization inserted is optimal w.r.t. a given objective function. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and generation of a set of global constraints over synchronization placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronization placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronization solution. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient. The implicit specification helped us find one concurrency bug previously missed when model-checking using an explicit, user-provided specification. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronization placements are produced for our experiments, favoring a minimal number of synchronization operations or maximum concurrency, respectively.

On the homology and the cohomology of certain polycyclic groups

International Nuclear Information System (INIS)

Majumdar, S.

1987-10-01

The homology and the cohomology of infinite non-abelian split extensions of cyclic groups by cyclic groups have been computed through construction of nice free resolutions for these groups. (author). 16 refs

Non-spherical core collapse supernovae. III. Evolution towards homology and dependence on the numerical resolution

Science.gov (United States)

Gawryszczak, A.; Guzman, J.; Plewa, T.; Kifonidis, K.

2010-10-01

moderate latitudes to the polar regions of our grid within only 300 s after core bounce. This effect - if confirmed by 3D simulations - might actually be responsible for the global asymmetry of the nickel lines in SN 1987A. Yet, it also poses difficulties for the analysis of 2D SASI-dominated explosions in terms of the maximum nickel velocities, since discretization errors at the poles are considered non-negligible. Conclusions: The simulations demonstrate that significant radial and lateral motions in the post-shock region, produced by convective overturn and the SASI during the early explosion phase, contribute to the evolution for minutes and hours after shock revival. They lead to both later clump formation, and a significant prolate deformation of the ejecta which are observed even as late as one week after the explosion. This ejecta deformation may be considered final, since the expansion has long become homologous by that time. As pointed out in the recent analysis by Kjaer et al., such an ejecta morphology is in good agreement with the observational data of SN 1987A. Systematic future studies are needed to investigate how the SASI-induced late-time lateral expansion that we find in this work depends on the dominant mode of the SASI when the early explosion phase ends, and to which extent it is affected by the dimensionality of the simulations. The impact on and importance of the SASI for the distribution of iron group nuclei and the morphology of the young SNR argues for future three-dimensional explosion and post-explosion studies on singularity-free grids that cover the entire sphere. Given the results of our 2D resolution study, present three-dimensional simulations must be regarded as underresolved, and their conclusions must be verified by a proper numerical convergence analysis in three dimensions.

Recrafting the Neighbor-Joining Method

DEFF Research Database (Denmark)

Mailund; Brodal, Gerth Stølting; Fagerberg, Rolf

2006-01-01

Background: The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Θ(n3) algorithm upon which all existing implementations are based. Methods: In this paper we present techniques for speeding...... up the canonical neighbor-joining method. Our algorithms construct the same phylogenetic trees as the canonical neighbor-joining method. The best-case running time of our algorithms are O(n2) but the worst-case remains O(n3). We empirically evaluate the performance of our algoritms on distance...... matrices obtained from the Pfam collection of alignments. Results: The experiments indicate that the running time of our algorithms evolve as Θ(n2) on the examined instance collection. We also compare the running time with that of the QuickTree tool, a widely used efficient implementation of the canonical...

Trichloroacetimidates as Alkylating Reagents and Their Application in the Synthesis of Pyrroloindoline Natural Products and Synthesis of Small Molecule Inhibitors of Src Homology 2 Domain-Containing Inositol Phosphatase (SHIP)

Science.gov (United States)

Adhikari, Arijit A.

was applied towards the synthesis of natural products and their analogs. The pyrroloindoline ring system is found in many alkaloids and cyclic peptides which mainly differ in the substitution at the C3a position. To provide rapid access to these natural products a diversity-oriented strategy was established via displacement of C3a-trichloroacetimidate pyrroloindoline. Carbon, oxygen, sulfur and nitrogen nucleophiles were all shown to undergo substitution reactions with these trichloroacetimidates in the presence of a Lewis acid catalyst. In order to demonstrate the utility of this new method it was applied towards the synthesis of arundinine and a formal synthesis of psychotriasine. Current investigations involve the application of this method towards the synthesis of a complex pyrroloindoline natural product kapakahine C and the progress made therein has been discussed. The reactivity of trichloroacetimidates was also investigated for the selective C3-alkylation of 2,3-disubstituted indoles to provide indolenines. Indolenines serve as useful intermediates in the synthesis of many complex alkaloids. Different benzylic and allylic trichloroacetimidates were shown to provide 3,3'-disubstituted indolenines with high yields in the presence of catalytic amounts of Lewis acids. Various substituted indoles were evaluated under these reaction conditions. This methodology was also applied towards the synthesis of the core tetracyclic ring system found in communesin natural products. In addition to the above work, synthesis of small molecule inhibitors of Src Homology 2 Domain-Containing Inositol Phosphatase (SHIP) has also been described. Aberrations in the phosphoinositide 3-kinase (PI3K) cellular signaling pathway can lead to diseased cellular states like cancer. Herein we have reported stereoselective synthesis of two quinoline based small molecule SHIP inhibitors. The lead compounds and their analogs were tested for their activities against SHIP by Malachite green assay

Microwave assisted facile green synthesis of silver and gold nanocatalysts using the leaf extract of Aerva lanata

Science.gov (United States)

Joseph, Siby; Mathew, Beena

2015-02-01

Herein, we report a simple microwave assisted method for the green synthesis of silver and gold nanoparticles by the reduction of aqueous metal salt solutions using leaf extract of the medicinal plant Aerva lanata. UV-vis., FTIR, XRD, and HR-TEM studies were conducted to assure the formation of nanoparticles. XRD studies clearly confirmed the crystalline nature of the synthesized nanoparticles. From the HR-TEM images, the silver nanoparticles (AgNPs) were found to be more or less spherical and gold nanoparticles (AuNPs) were observed to be of different morphology with an average diameter of 18.62 nm for silver and 17.97 nm for gold nanoparticles. In order to evaluate the effect of microwave heating upon rate of formation, the synthesis was also conducted under ambient condition without the assistance of microwave radiation and the former method was found to be much faster than the later. The synthesized nanoparticles were used as nanocatalysts in the reduction of 4-nitrophenol to 4-aminophenol by NaBH4.

Optimized Solid Phase-Assisted Synthesis of Dendrons Applicable as Scaffolds for Radiolabeled Bioactive Multivalent Compounds Intended for Molecular Imaging

Directory of Open Access Journals (Sweden)

Gabriel Fischer

2014-05-01

Full Text Available Dendritic structures, being highly homogeneous and symmetric, represent ideal scaffolds for the multimerization of bioactive molecules and thus enable the synthesis of compounds of high valency which are e.g., applicable in radiolabeled form as multivalent radiotracers for in vivo imaging. As the commonly applied solution phase synthesis of dendritic scaffolds is cumbersome and time-consuming, a synthesis strategy was developed that allows for the efficient assembly of acid amide bond-based highly modular dendrons on solid support via standard Fmoc solid phase peptide synthesis protocols. The obtained dendritic structures comprised up to 16 maleimide functionalities and were derivatized on solid support with the chelating agent DOTA. The functionalized dendrons furthermore could be efficiently reacted with structurally variable model thiol-bearing bioactive molecules via click chemistry and finally radiolabeled with 68Ga. Thus, this solid phase-assisted dendron synthesis approach enables the fast and straightforward assembly of bioactive multivalent constructs for example applicable as radiotracers for in vivo imaging with Positron Emission Tomography (PET.

Stationary and non-stationary occurrences of miniature end plate potentials are well described as stationary and non-stationary Poisson processes in the mollusc Navanax inermis.

Science.gov (United States)

Cappell, M S; Spray, D C; Bennett, M V

1988-06-28

Protractor muscles in the gastropod mollusc Navanax inermis exhibit typical spontaneous miniature end plate potentials with mean amplitude 1.71 +/- 1.19 (standard deviation) mV. The evoked end plate potential is quantized, with a quantum equal to the miniature end plate potential amplitude. When their rate is stationary, occurrence of miniature end plate potentials is a random, Poisson process. When non-stationary, spontaneous miniature end plate potential occurrence is a non-stationary Poisson process, a Poisson process with the mean frequency changing with time. This extends the random Poisson model for miniature end plate potentials to the frequently observed non-stationary occurrence. Reported deviations from a Poisson process can sometimes be accounted for by the non-stationary Poisson process and more complex models, such as clustered release, are not always needed.

Homologous Recombination-Independent Large Gene Cassette Knock-in in CHO Cells Using TALEN and MMEJ-Directed Donor Plasmids

Directory of Open Access Journals (Sweden)

Tetsushi Sakuma

2015-10-01

Full Text Available Gene knock-in techniques have rapidly evolved in recent years, along with the development and maturation of genome editing technology using programmable nucleases. We recently reported a novel strategy for microhomology-mediated end-joining-dependent integration of donor DNA by using TALEN or CRISPR/Cas9 and optimized targeting vectors, named PITCh (Precise Integration into Target Chromosome vectors. Here we describe TALEN and PITCh vector-mediated integration of long gene cassettes, including a single-chain Fv-Fc (scFv-Fc gene, in Chinese hamster ovary (CHO cells, with comparison of targeting and cloning efficiency among several donor design and culture conditions. We achieved 9.6-kb whole plasmid integration and 7.6-kb backbone-free integration into a defined genomic locus in CHO cells. Furthermore, we confirmed the reasonable productivity of recombinant scFv-Fc protein of the knock-in cells. Using our protocol, the knock-in cell clones could be obtained by a single transfection and a single limiting dilution using a 96-well plate, without constructing targeting vectors containing long homology arms. Thus, the study described herein provides a highly practical strategy for gene knock-in of large DNA in CHO cells, which accelerates high-throughput generation of cell lines stably producing any desired biopharmaceuticals, including huge antibody proteins.

Homologous Recombination-Independent Large Gene Cassette Knock-in in CHO Cells Using TALEN and MMEJ-Directed Donor Plasmids.

Science.gov (United States)

Sakuma, Tetsushi; Takenaga, Mitsumasa; Kawabe, Yoshinori; Nakamura, Takahiro; Kamihira, Masamichi; Yamamoto, Takashi

2015-10-09

Gene knock-in techniques have rapidly evolved in recent years, along with the development and maturation of genome editing technology using programmable nucleases. We recently reported a novel strategy for microhomology-mediated end-joining-dependent integration of donor DNA by using TALEN or CRISPR/Cas9 and optimized targeting vectors, named PITCh (Precise Integration into Target Chromosome) vectors. Here we describe TALEN and PITCh vector-mediated integration of long gene cassettes, including a single-chain Fv-Fc (scFv-Fc) gene, in Chinese hamster ovary (CHO) cells, with comparison of targeting and cloning efficiency among several donor design and culture conditions. We achieved 9.6-kb whole plasmid integration and 7.6-kb backbone-free integration into a defined genomic locus in CHO cells. Furthermore, we confirmed the reasonable productivity of recombinant scFv-Fc protein of the knock-in cells. Using our protocol, the knock-in cell clones could be obtained by a single transfection and a single limiting dilution using a 96-well plate, without constructing targeting vectors containing long homology arms. Thus, the study described herein provides a highly practical strategy for gene knock-in of large DNA in CHO cells, which accelerates high-throughput generation of cell lines stably producing any desired biopharmaceuticals, including huge antibody proteins.

Joining Forces: The Chemical Biology-Medicinal Chemistry Continuum.

Science.gov (United States)

Plowright, Alleyn T; Ottmann, Christian; Arkin, Michelle; Auberson, Yves P; Timmerman, Henk; Waldmann, Herbert

2017-09-21

The scientific advances being made across all disciplines are creating ever-increasing opportunities to enhance our knowledge of biological systems and how they relate to human disease. One of the central driving forces in discovering new medicines is medicinal chemistry, where the design and synthesis of novel compounds has led to multiple drugs. Chemical biology, sitting at the interface of many disciplines, has now emerged as a major contributor to the understanding of biological systems and is becoming an integral part of drug discovery. Bringing chemistry and biology much closer and blurring the boundaries between disciplines is creating new opportunities to probe and understand biology; both disciplines play key roles and need to join forces and work together effectively to synergize their impact. The power of chemical biology will then reach its full potential and drive innovation, leading to the discovery of transformative medicines to treat patients. Advances in cancer biology and drug discovery highlight this potential. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microwave-assisted synthesis of poly(3-hexylthiophene) via direct oxidation with FeCl{sub 3}

Energy Technology Data Exchange (ETDEWEB)

Nicho, M.E., E-mail: menicho@uaem.mx [Centro de Investigacion en Ingenieria y Ciencias Aplicadas, Universidad Autonoma del Estado de Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, C.P. 62210 Cuernavaca, Morelos (Mexico); Garcia-Escobar, C.H.; Hernandez-Martinez, D. [Centro de Investigacion en Ingenieria y Ciencias Aplicadas, Universidad Autonoma del Estado de Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, C.P. 62210 Cuernavaca, Morelos (Mexico); Linzaga-Elizalde, I. [Centro de Investigaciones Quimicas (CIQ) de la UAEM (Mexico); Cadenas-Pliego, G. [Centro de Investigacion en Quimica Aplicada, Saltillo, Coahuila (Mexico)

2012-09-20

In this work, CoolMate microwave synthesis system was employed to synthesize soluble poly(3-hexylthiophene) by direct oxidation of 3-hexylthiophene monomer with FeCl{sub 3} as oxidant. P3HT was synthesized varying reaction time by 2 h, 1 h and 0.5 h. According to the results optimal microwave radiation time for synthesis was 1 h. On the other hand, P3HT was synthesized in two different solvents: chloroform (CHCl{sub 3}) and dichloromethane (CH{sub 2}Cl{sub 2}). The obtained yields depend on the solvent and the reaction time used in the synthesis, microwave-assisted synthesis leads to outstanding increase in yield (with dichloromethane solvent). Homogeneous thin films were prepared by spin-coating technique from toluene. Physicochemical characterization of P3HT polymers was carried out: changes in weight molecular distribution and polydispersity were obtained by HPLC (high-performance liquid chromatography); dyads and triads percent were analyzed by NMR (nuclear magnetic resonance). Surface topographical changes were obtained by atomic force microscopy (AFM). AFM images revealed that the surface morphology depends on synthesis method, reaction time and solvent used. Finally the samples were characterized by thermogravimetric analysis (TGA) and ultraviolet-visible analysis (UV-vis). Compared with the traditional method (without microwave), this method provided considerable decrease in the reaction time, both lower polydispersity and molecular weight, less volume of solvents for the synthesis, as well as more alternatives for solvent choice. The results confirmed the versatility of the procedure by microwave, which yields polymeric materials in 1 h and has no adverse effects on the polymers quality.

Suppressive effect on polyclonal B-cell activation of a synthetic peptide homologous to a transmembrane component of oncogenic retroviruses

Energy Technology Data Exchange (ETDEWEB)

Mitani, M.; Cianciolo, G.J.; Snyderman, R.; Yasuda, M.; Good, R.A.; Day, N.K.

1987-01-01

Purified feline leukemia virus, UV light-inactivated feline leukemia virus, and a synthetic peptide (CKS-17) homologous to a well-conserved region of the transmembrane components of several human and animal retroviruses were each studied for their effect on IgG production by feline peripheral blood lymphocytes. Using a reverse hemolytic plaque assay, both the viable virus and the UV-inactivated feline leukemia virus, but not the CKS-17, activated B lymphocytes to secrete IgG. When staphylococcal protein A, a polyclonal B-cell activator, was used to stimulate IgG synthesis by feline lymphocytes, the viable virus, the UV-inactivated virus, and the CKS-17 peptide each strongly suppressed IgG secretion without compromising viability of the lymphocytes. These finding suggest that the immunosuppressive influences of feline leukemia virus on immunoglobulin synthesis may reside in a conserved portion of the envelope glycoprotein that includes the region homologous to CKS-17.

Suppressive effect on polyclonal B-cell activation of a synthetic peptide homologous to a transmembrane component of oncogenic retroviruses

International Nuclear Information System (INIS)

Mitani, M.; Cianciolo, G.J.; Snyderman, R.; Yasuda, M.; Good, R.A.; Day, N.K.

1987-01-01

Purified feline leukemia virus, UV light-inactivated feline leukemia virus, and a synthetic peptide (CKS-17) homologous to a well-conserved region of the transmembrane components of several human and animal retroviruses were each studied for their effect on IgG production by feline peripheral blood lymphocytes. Using a reverse hemolytic plaque assay, both the viable virus and the UV-inactivated feline leukemia virus, but not the CKS-17, activated B lymphocytes to secrete IgG. When staphylococcal protein A, a polyclonal B-cell activator, was used to stimulate IgG synthesis by feline lymphocytes, the viable virus, the UV-inactivated virus, and the CKS-17 peptide each strongly suppressed IgG secretion without compromising viability of the lymphocytes. These finding suggest that the immunosuppressive influences of feline leukemia virus on immunoglobulin synthesis may reside in a conserved portion of the envelope glycoprotein that includes the region homologous to CKS-17

Solvent-assisted in situ synthesis of cysteamine-capped silver nanoparticles

Science.gov (United States)

Oliva, José M.; Ríos de la Rosa, Julio M.; Sayagués, María J.; Sánchez-Alcázar, José A.; Merkling, Patrick J.; Zaderenko, Ana P.

2018-03-01

Silver nanoparticles offer a huge potential for biomedical applications owing to their exceptional properties and small size. Specifically, cysteamine-capped silver nanoparticles could form the basis for new anticancer therapies combining the cytotoxic effect of the silver core with the inherent antitumor activity of cysteamine, which inhibit cancer cell proliferation and suppress invasion and metastasis. In addition, the capability of the cysteamine coating monolayer to couple a variety of active principles and targeting (bio)molecules of interest proves key to the tailoring of this platform in order to exploit the pathophysiology of specific tumor types. Nevertheless, the chain length and conformational flexibility of cysteamine, together with its ability to attach to the surface of silver nanoparticles via both the thiol and the amine group, have made the in situ synthesis of these particles an especially challenging task. Herein we report a solvent-assisted in situ synthesis method that solves this problem. The obtained nanoparticles have been fully characterized by UV-visible absorption spectroscopy, Fourier transform infrared spectroscopy, transmission electron microscopy, electron diffraction measurement, high resolution transmission electron microscopy, scanning transmission electron microscopy, energy dispersive x-ray spectroscopy nanoanalysis, and dynamic light scattering measurement. Our synthesis method achieves extremely high yield and surface coating ratio, and colloidal stability over a wide range of pH values including physiological pH. Additionally, we have demonstrated that cysteamine-capped nanoparticles obtained by this method can be conjugated to an antibody for active targeting of the epidermal growth factor receptor, which plays an important role in the pathogenesis and progression of a wide variety of tumors, and induce cell death in human squamous carcinoma cells. We believe this method can be readily extended to combinations of noble

Join or be excluded from biomedicine? JOINS and Post-colonial Korea.

Science.gov (United States)

Ma, Eunjeong

2015-04-01

This paper discusses re-emergence of Korean medicine(s) in the global context with a focus on a natural drug JOINS, a highly contentious drug regarding its legal status. By following through its life world, the paper contends that the drug is the embodiment of the postcolonial anxiety that crosses the intersections between the aspiring nation and globalizing strategies of the bio-pharmaceutical industry. JOINS is a natural drug prescribed to alleviate the symptoms of degenerative arthritis. SK Chemicals, Ltd., a giant domestic pharmaceutical company developed the drug by utilizing the knowledge of traditional pharmacopeia and put it on the market in 2001. In the domestic market, the drug is treated as a prescription drug, implying that Western medicine-trained doctors (as opposed to Korean medicine doctors) are entitled to prescribe drugs. It also indicates that the drug has undergone a series of lab tests such as toxicity, efficacy, and clinical trials in compliance with regulatory guidelines. However, the domestic standards are not rigorous enough to satisfy international standards, so that it is exported as a nutritional supplement abroad. The government, the pharmaceutical industry, and the Western medicine profession are happy with how the drug stands domestically and internationally. Rather, it is Korean doctors who try to disrupt the status quo and reclaim their rights to traditional knowledge, who have been alienated from the pharmaceuticalization of traditional knowledge. Thus, the JOINS tablet embodies the complex web of modern Korean society, professional interests, the pharmaceutical industry, and globalization.

Accuracy of non assisted glenohumeral joint injection in the office setting

Energy Technology Data Exchange (ETDEWEB)

Sidon, Eliezer, E-mail: eli.sidon@gmail.com [Department of Orthopedics, Rabin Medical Center, Beilinson Campus, Petach Tikva 49100 (Israel); Velkes, Steven, E-mail: velkes@yahoo.com [Department of Orthopedics, Rabin Medical Center, Beilinson Campus, Petach Tikva 49100 (Israel); Shemesh, Shai, E-mail: shai.shemesh@gmail.com [Department of Orthopedics, Rabin Medical Center, Beilinson Campus, Petach Tikva 49100 (Israel); Levy, Jakob, E-mail: Jlevy@clalit.org.il [Department of Imaging, Rabin Medical Center, Beilinson Campus, Petach Tikva 49100 (Israel); Glaser, Ernesto, E-mail: glaser.ernesto@gmail.com [Department of Imaging, Rabin Medical Center, Beilinson Campus, Petach Tikva 49100 (Israel); Kosashvili, Yona, E-mail: yonasofi@gmail.com [Department of Orthopedics, Rabin Medical Center, Beilinson Campus, Petach Tikva 49100 (Israel)

2013-12-01

Purpose: The diagnostic and therapeutic success of shoulder joint injection depends on its accuracy. Two recent studies reported high success (93–96%) for non-imaging-assisted anterior injection in anesthetized patients. This study examined the accuracy of anterior shoulder injection in awake patients under conditions similar to the office setting. Methods: The study group consisted of 166 consecutive patients with shoulder pain who underwent diagnostic magnetic resonance arthrography at a tertiary medical center in 2011–2012. As part of the examination, contrast material was injected into the glenohumeral joint via an anterior approach by a certified musculoskeletal radiologist without any image assistance. Success was defined as contrast material limited to the intra-articular joint on the scan, without scatter to the periauricular tissue. Results: A successful injection was verified by magnetic resonance arthography in 163 patients (98.2%). Conclusions: Non-assisted anterior shoulder injection is highly accurate (98.2%) in the hands of an experienced radiologist, even in awake patients.

Flexible composite via rapid titania coating by microwave-assisted ...