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Sample records for rpa mediates recombination

  1. RPA antagonizes microhomology-mediated repair of DNA double-strand breaks.

    Science.gov (United States)

    Deng, Sarah K; Gibb, Bryan; de Almeida, Mariana Justino; Greene, Eric C; Symington, Lorraine S

    2014-04-01

    Microhomology-mediated end joining (MMEJ) is a Ku- and ligase IV-independent mechanism for the repair of DNA double-strand breaks that contributes to chromosome rearrangements. Here we used a chromosomal end-joining assay to determine the genetic requirements for MMEJ in Saccharomyces cerevisiae. We found that end resection influences the ability to expose microhomologies; however, it is not rate limiting for MMEJ in wild-type cells. The frequency of MMEJ increased by up to 350-fold in rfa1 hypomorphic mutants, suggesting that replication protein A (RPA) bound to the single-stranded DNA (ssDNA) overhangs formed by resection prevents spontaneous annealing between microhomologies. In vitro, the mutant RPA complexes were unable to fully extend ssDNA and were compromised in their ability to prevent spontaneous annealing. We propose that the helix-destabilizing activity of RPA channels ssDNA intermediates from mutagenic MMEJ to error-free homologous recombination, thus preserving genome integrity. PMID:24608368

  2. RPA Antagonizes Microhomology-Mediated Repair of DNA Double-Strand Breaks

    OpenAIRE

    Deng, Sarah K.; Gibb, Bryan; Almeida, Mariana Justino; Greene, Eric C.; Symington, Lorraine S.

    2014-01-01

    Microhomology-mediated end joining (MMEJ) is a Ku and Ligase IV independent mechanism for repair of DNA double-strand breaks, which contributes to chromosome rearrangements. Here we used a chromosomal end-joining assay to determine the genetic requirements for MMEJ in Saccharomyces cerevisiae. We found that end resection influences the ability to expose microhomologies; however, it is not rate limiting for MMEJ in wild-type cells. The frequency of MMEJ increased by up to 350-fold in rfa1 hypo...

  3. Stn1?Ten1 is an Rpa2?Rpa3-like complex at telomeres

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Jia; Yu, Eun Young; Yang, Yuting; Confer, Laura A.; Sun, Steven H.; Wan, Ke; Lue, Neal F.; Lei, Ming; (Weill); (Michigan-Med)

    2010-09-02

    In budding yeast, Cdc13, Stn1, and Ten1 form a heterotrimeric complex (CST) that is essential for telomere protection and maintenance. Previous bioinformatics analysis revealed a putative oligonucleotide/oligosaccharide-binding (OB) fold at the N terminus of Stn1 (Stn1N) that shows limited sequence similarity to the OB fold of Rpa2, a subunit of the eukaryotic ssDNA-binding protein complex replication protein A (RPA). Here we present functional and structural analyses of Stn1 and Ten1 from multiple budding and fission yeast. The crystal structure of the Candida tropicalis Stn1N complexed with Ten1 demonstrates an Rpa2N-Rpa3-like complex. In both structures, the OB folds of the two components pack against each other through interactions between two C-terminal helices. The structure of the C-terminal domain of Saccharomyces cerevisiae Stn1 (Stn1C) was found to comprise two related winged helix-turn-helix (WH) motifs, one of which is most similar to the WH motif at the C terminus of Rpa2, again supporting the notion that Stn1 resembles Rpa2. The crystal structure of the fission yeast Schizosaccharomyces pombe Stn1N-Ten1 complex exhibits a virtually identical architecture as the C. tropicalis Stn1N-Ten1. Functional analyses of the Candida albicans Stn1 and Ten1 proteins revealed critical roles for these proteins in suppressing aberrant telomerase and recombination activities at telomeres. Mutations that disrupt the Stn1-Ten1 interaction induce telomere uncapping and abolish the telomere localization of Ten1. Collectively, our structural and functional studies illustrate that, instead of being confined to budding yeast telomeres, the CST complex may represent an evolutionarily conserved RPA-like telomeric complex at the 3' overhangs that works in parallel with or instead of the well-characterized POT1-TPP1/TEBP{alpha}-{beta} complex.

  4. RecTE(Psy)-mediated recombineering in Pseudomonas syringae.

    Science.gov (United States)

    Swingle, Bryan

    2014-01-01

    A recently developed Pseudomonas syringae recombineering system simplifies the procedure for installing specific mutations at a chosen genomic locus. The procedure involves transforming P. syringae cells expressing recombineering functions with a PCR product that contains desired changes flanked by sequences homologous to a target location. Cells transformed with the substrate undergo homologous recombination between the genomic DNA and the recombineering substrate. The recombinants are found by selection for traits carried by the recombineering substrate, usually antibiotic resistance. PMID:24557893

  5. RNA-processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA.

    Science.gov (United States)

    Manfrini, Nicola; Trovesi, Camilla; Wery, Maxime; Martina, Marina; Cesena, Daniele; Descrimes, Marc; Morillon, Antonin; d'Adda di Fagagna, Fabrizio; Longhese, Maria Pia

    2015-02-01

    Eukaryotic cells respond to DNA double-strand breaks (DSBs) by activating a checkpoint that depends on the protein kinases Tel1/ATM and Mec1/ATR. Mec1/ATR is activated by RPA-coated single-stranded DNA (ssDNA), which arises upon nucleolytic degradation (resection) of the DSB. Emerging evidences indicate that RNA-processing factors play critical, yet poorly understood, roles in genomic stability. Here, we provide evidence that the Saccharomyces cerevisiae RNA decay factors Xrn1, Rrp6 and Trf4 regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. The lack of Xrn1 inhibits ssDNA generation at the DSB by preventing the loading of the MRX complex. By contrast, DSB resection is not affected in the absence of Rrp6 or Trf4, but their lack impairs the recruitment of RPA, and therefore of Mec1, to the DSB. Rrp6 and Trf4 inactivation affects neither Rad51/Rad52 association nor DSB repair by homologous recombination (HR), suggesting that full Mec1 activation requires higher amount of RPA-coated ssDNA than HR-mediated repair. Noteworthy, deep transcriptome analyses do not identify common misregulated gene expression that could explain the observed phenotypes. Our results provide a novel link between RNA processing and genome stability. PMID:25527408

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

    DEFF Research Database (Denmark)

    Toledo Lazaro, Luis Ignacio; Altmeyer, Matthias

    2013-01-01

    ATR, activated by replication stress, protects replication forks locally and suppresses origin firing globally. Here, we show that these functions of ATR are mechanistically coupled. Although initially stable, stalled forks in ATR-deficient cells undergo nucleus-wide breakage after unscheduled origin firing generates an excess of single-stranded DNA that exhausts the nuclear pool of RPA. Partial reduction of RPA accelerated fork breakage, and forced elevation of RPA was sufficient to delay such "replication catastrophe" even in the absence of ATR activity. Conversely, unscheduled origin firing induced breakage of stalled forks even in cells with active ATR. Thus, ATR-mediated suppression of dormant origins shields active forks against irreversible breakage via preventing exhaustion of nuclear RPA. This study elucidates how replicating genomes avoid destabilizing DNA damage. Because cancer cells commonly feature intrinsically high replication stress, this study also provides a molecular rationale for their hypersensitivity to ATR inhibitors.

  7. Transfection-mediated generation of functionally competent Tula hantavirus with recombinant S RNA segment

    OpenAIRE

    Plyusnin, Alexander; Kukkonen, Sami K.J.; Plyusnina, Angelina; Vapalahti, Olli; Vaheri, Antti

    2002-01-01

    Since the discovery of RNA recombination in polioviruses, there has been a general belief that this mechanism operates only in positive-sense RNA viruses. Recently, studying wild-type Tula hantavirus, we observed a mosaic-like structure of the S RNA segment that was consistent with generation by recombination between viruses from two genetic lineages. Here we show transfection-mediated rescue of Tula virus carrying recombinant S RNA segment. Independent attempts yielded S RNA molecules of sim...

  8. RNA Structures Facilitate Recombination-Mediated Gene Swapping in HIV-1 ?

    Science.gov (United States)

    Simon-Loriere, Etienne; Martin, Darren P.; Weeks, Kevin M.; Negroni, Matteo

    2010-01-01

    Many viruses, including retroviruses, undergo frequent recombination, a process which can increase their rate of adaptive evolution. In the case of HIV, recombination has been responsible for the generation of numerous intersubtype recombinant variants with epidemiological importance in the AIDS pandemic. Although it is known that fragments of genetic material do not combine randomly during the generation of recombinant viruses, the mechanisms that lead to preferential recombination at specific sites are not fully understood. Here we reanalyze recent independent data defining (i) the structure of a complete HIV-1 RNA genome and (ii) favorable sites for recombination. We show that in the absence of selection acting on recombinant genomes, regions harboring RNA structures in the NL4-3 model strain are strongly predictive of recombination breakpoints in the HIV-1 env genes of primary isolates. In addition, we found that breakpoints within recombinant HIV-1 genomes sampled from human populations, which have been acted upon extensively by natural selection, also colocalize with RNA structures. Critically, junctions between genes are enriched in structured RNA elements and are also preferred sites for generating functional recombinant forms. These data suggest that RNA structure-mediated recombination allows the virus to exchange intact genes rather than arbitrary subgene fragments, which is likely to increase the overall viability and replication success of the recombinant HIV progeny. PMID:20881047

  9. Phosphorylated RPA recruits PALB2 to stalled DNA replication forks to facilitate fork recovery.

    Science.gov (United States)

    Murphy, Anar K; Fitzgerald, Michael; Ro, Teresa; Kim, Jee Hyun; Rabinowitsch, Ariana I; Chowdhury, Dipanjan; Schildkraut, Carl L; Borowiec, James A

    2014-08-18

    Phosphorylation of replication protein A (RPA) by Cdk2 and the checkpoint kinase ATR (ATM and Rad3 related) during replication fork stalling stabilizes the replisome, but how these modifications safeguard the fork is not understood. To address this question, we used single-molecule fiber analysis in cells expressing a phosphorylation-defective RPA2 subunit or lacking phosphatase activity toward RPA2. Deregulation of RPA phosphorylation reduced synthesis at forks both during replication stress and recovery from stress. The ability of phosphorylated RPA to stimulate fork recovery is mediated through the PALB2 tumor suppressor protein. RPA phosphorylation increased localization of PALB2 and BRCA2 to RPA-bound nuclear foci in cells experiencing replication stress. Phosphorylated RPA also stimulated recruitment of PALB2 to single-strand deoxyribonucleic acid (DNA) in a cell-free system. Expression of mutant RPA2 or loss of PALB2 expression led to significant DNA damage after replication stress, a defect accentuated by poly-ADP (adenosine diphosphate) ribose polymerase inhibitors. These data demonstrate that phosphorylated RPA recruits repair factors to stalled forks, thereby enhancing fork integrity during replication stress. PMID:25113031

  10. Recombination-mediated genetic engineering of large genomic DNA transgenes.

    Science.gov (United States)

    Ejsmont, Radoslaw Kamil; Ahlfeld, Peter; Pozniakovsky, Andrei; Stewart, A Francis; Tomancak, Pavel; Sarov, Mihail

    2011-01-01

    Faithful gene activity reporters are a useful tool for evo-devo studies enabling selective introduction of specific loci between species and assaying the activity of large gene regulatory sequences. The use of large genomic constructs such as BACs and fosmids provides an efficient platform for exploration of gene function under endogenous regulatory control. Despite their large size they can be easily engineered using in vivo homologous recombination in Escherichia coli (recombineering). We have previously demonstrated that the efficiency and fidelity of recombineering are sufficient to allow high-throughput transgene engineering in liquid culture, and have successfully applied this approach in several model systems. Here, we present a detailed protocol for recombineering of BAC/fosmid transgenes for expression of fluorescent or affinity tagged proteins in Drosophila under endogenous in vivo regulatory control. The tag coding sequence is seamlessly recombineered into the genomic region contained in the BAC/fosmid clone, which is then integrated into the fly genome using ?C31 recombination. This protocol can be easily adapted to other recombineering projects. PMID:22065454

  11. Transfection-mediated generation of functionally competent Tula hantavirus with recombinant S RNA segment.

    Science.gov (United States)

    Plyusnin, Alexander; Kukkonen, Sami K J; Plyusnina, Angelina; Vapalahti, Olli; Vaheri, Antti

    2002-03-15

    Since the discovery of RNA recombination in polioviruses, there has been a general belief that this mechanism operates only in positive-sense RNA viruses. Recently, studying wild-type Tula hantavirus, we observed a mosaic-like structure of the S RNA segment that was consistent with generation by recombination between viruses from two genetic lineages. Here we show transfection-mediated rescue of Tula virus carrying recombinant S RNA segment. Independent attempts yielded S RNA molecules of similar structure; the majority of them carried a break point located close to one of the break points suggested for natural recombinants. Recombinant virus purified from the original variant was able to grow to the same titers in cell culture and showed the same characteristic immunofluorescence pattern when stained for the nucleocapsid protein. While competent, the recombinant virus appeared to be slightly less competitive than the wild type. Sequence analysis of the S cDNA clones obtained from the purified recombinant virus confirmed that all S RNA molecules were of recombinant origin. This provides the first example of a negative-sense RNA virus constructed using homologous recombination. PMID:11889055

  12. Double-check probing of DNA bending and unwinding by XPA–RPA: an architectural function in DNA repair

    OpenAIRE

    Missura, M.; Buterin, T.; Hindges, R.; Hu?bscher, U.; Kaspa?rkova?, J.; Brabec, V.; Naegeli, H.

    2001-01-01

    The multiprotein factor composed of XPA and replication protein A (RPA) is an essential subunit of the mammalian nucleotide excision repair system. Although XPA-RPA has been implicated in damage recognition, its activity in the DNA repair pathway remains controversial. By replacing DNA adducts with mispaired bases or non-hybridizing analogues, we found that the weak preference of XPA and RPA for damaged substrates is entirely mediated by indirect readout of DNA helix conformations. Further sc...

  13. Multiple host-cell recombination pathways act in Agrobacterium-mediated transformation of plant cells.

    Science.gov (United States)

    Mestiri, Imen; Norre, Frédéric; Gallego, Maria E; White, Charles I

    2014-02-01

    Using floral-dip, tumorigenesis and root callus transformation assays of both germline and somatic cells, we present here results implicating the four major non-homologous and homologous recombination pathways in Agrobacterium-mediated transformation of Arabidopsis thaliana. All four single mutant lines showed similar mild reductions in transformability, but knocking out three of four pathways severely compromised Agrobacterium-mediated transformation. Although integration of T-DNA into the plant genome is severely compromised in the absence of known DNA double-strand break repair pathways, it does still occur, suggesting the existence of other pathways involved in T-DNA integration. Our results highlight the functional redundancy of the four major plant recombination pathways in transformation, and provide an explanation for the lack of strong effects observed in previous studies on the roles of plant recombination functions in transformation. PMID:24299074

  14. A recurrent translocation is mediated by homologous recombination between HERV-H elements

    Directory of Open Access Journals (Sweden)

    Hermetz Karen E

    2012-01-01

    Full Text Available Abstract Background Chromosome rearrangements are caused by many mutational mechanisms; of these, recurrent rearrangements can be particularly informative for teasing apart DNA sequence-specific factors. Some recurrent translocations are mediated by homologous recombination between large blocks of segmental duplications on different chromosomes. Here we describe a recurrent unbalanced translocation casued by recombination between shorter homologous regions on chromosomes 4 and 18 in two unrelated children with intellectual disability. Results Array CGH resolved the breakpoints of the 6.97-Megabase (Mb loss of 18q and the 7.30-Mb gain of 4q. Sequencing across the translocation breakpoints revealed that both translocations occurred between 92%-identical human endogenous retrovirus (HERV elements in the same orientation on chromosomes 4 and 18. In addition, we find sequence variation in the chromosome 4 HERV that makes one allele more like the chromosome 18 HERV. Conclusions Homologous recombination between HERVs on the same chromosome is known to cause chromosome deletions, but this is the first report of interchromosomal HERV-HERV recombination leading to a translocation. It is possible that normal sequence variation in substrates of non-allelic homologous recombination (NAHR affects the alignment of recombining segments and influences the propensity to chromosome rearrangement.

  15. Overexpressed of RAD51 suppresses recombination defects: a possible mechanism to reverse genomic instability

    Energy Technology Data Exchange (ETDEWEB)

    Schild, David; Wiese, Claudia

    2009-10-15

    RAD51, a key protein in the homologous recombinational DNA repair (HRR) pathway, is the major strand-transferase required for mitotic recombination. An important early step in HRR is the formation of single-stranded DNA (ss-DNA) coated by RPA (a ss-DNA binding protein). Displacement of RPA by RAD51 is highly regulated and facilitated by a number of different proteins known as the 'recombination mediators'. To assist these recombination mediators, a second group of proteins also is required and we are defining these proteins here as 'recombination co-mediators'. Defects in either recombination mediators or comediators, including BRCA1 and BRCA2, lead to impaired HRR that can genetically be complemented for (i.e. suppressed) by overexpression of RAD51. Defects in HRR have long been known to contribute to genomic instability leading to tumor development. Since genomic instability also slows cell growth, precancerous cells presumably require genomic restabilization to gain a growth advantage. RAD51 is overexpressed in many tumors, and therefore, we hypothesize that the complementing ability of elevated levels of RAD51 in tumors with initial HRR defects limits genomic instability during carcinogenic progression. Of particular interest, this model may also help explain the high frequency of TP53 mutations in human cancers, since wild-type p53 represses RAD51.

  16. Multiple regulation of Rad51-mediated homologous recombination by fission yeast Fbh1.

    Science.gov (United States)

    Tsutsui, Yasuhiro; Kurokawa, Yumiko; Ito, Kentaro; Siddique, Md Shahjahan P; Kawano, Yumiko; Yamao, Fumiaki; Iwasaki, Hiroshi

    2014-08-01

    Fbh1, an F-box helicase related to bacterial UvrD, has been proposed to modulate homologous recombination in fission yeast. We provide several lines of evidence for such modulation. Fbh1, but not the related helicases Srs2 and Rqh1, suppressed the formation of crossover recombinants from single HO-induced DNA double-strand breaks. Purified Fbh1 in complex with Skp1 (Fbh1-Skp1 complex) inhibited Rad51-driven DNA strand exchange by disrupting Rad51 nucleoprotein filaments in an ATP-dependent manner; this disruption was alleviated by the Swi5-Sfr1 complex, an auxiliary activator of Rad51. In addition, the reconstituted SCFFbh1 complex, composed of purified Fbh1-Skp1 and Pcu1-Rbx1, displayed ubiquitin-ligase E3 activity toward Rad51. Furthermore, Fbh1 reduced the protein level of Rad51 in stationary phase in an F-box-dependent, but not in a helicase domain-independent manner. These results suggest that Fbh1 negatively regulates Rad51-mediated homologous recombination via its two putative, unrelated activities, namely DNA unwinding/translocation and ubiquitin ligation. In addition to its anti-recombinase activity, we tentatively suggest that Fbh1 might also have a pro-recombination role in vivo, because the Fbh1-Skp1 complex stimulated Rad51-mediated strand exchange in vitro after strand exchange had been initiated. PMID:25165823

  17. Partial Depletion of Histone H4 Increases Homologous Recombination-Mediated Genetic Instability

    OpenAIRE

    Prado, Fe?lix; Aguilera, Andre?s

    2005-01-01

    DNA replication can be a source of genetic instability. Given the tight connection between DNA replication and nucleosome assembly, we analyzed the effect of a partial depletion of histone H4 on genetic instability mediated by homologous recombination. A Saccharomyces cerevisiae strain was constructed in which the expression of histone H4 was driven by the regulated tet promoter. In agreement with defective nucleosome assembly, partial depletion of histone H4 led to subtle changes in plasmid ...

  18. Homologous-recombination-deficient tumours are dependent on Pol?-mediated repair.

    Science.gov (United States)

    Ceccaldi, Raphael; Liu, Jessica C; Amunugama, Ravindra; Hajdu, Ildiko; Primack, Benjamin; Petalcorin, Mark I R; O'Connor, Kevin W; Konstantinopoulos, Panagiotis A; Elledge, Stephen J; Boulton, Simon J; Yusufzai, Timur; D'Andrea, Alan D

    2015-02-12

    Large-scale genomic studies have shown that half of epithelial ovarian cancers (EOCs) have alterations in genes regulating homologous recombination (HR) repair. Loss of HR accounts for the genomic instability of EOCs and for their cellular hyper-dependence on alternative poly-ADP ribose polymerase (PARP)-mediated DNA repair mechanisms. Previous studies have implicated the DNA polymerase ? (Pol? also known as POLQ, encoded by POLQ) in a pathway required for the repair of DNA double-strand breaks, referred to as the error-prone microhomology-mediated end-joining (MMEJ) pathway. Whether Pol? interacts with canonical DNA repair pathways to prevent genomic instability remains unknown. Here we report an inverse correlation between HR activity and Pol? expression in EOCs. Knockdown of Pol? in HR-proficient cells upregulates HR activity and RAD51 nucleofilament assembly, while knockdown of Pol? in HR-deficient EOCs enhances cell death. Consistent with these results, genetic inactivation of an HR gene (Fancd2) and Polq in mice results in embryonic lethality. Moreover, Pol? contains RAD51 binding motifs and it blocks RAD51-mediated recombination. Our results reveal a synthetic lethal relationship between the HR pathway and Pol?-mediated repair in EOCs, and identify Pol? as a novel druggable target for cancer therapy. PMID:25642963

  19. Homeologous plastid DNA transformation in tobacco is mediated by multiple recombination events.

    Science.gov (United States)

    Kavanagh, T A; Thanh, N D; Lao, N T; McGrath, N; Peter, S O; Horváth, E M; Dix, P J; Medgyesy, P

    1999-07-01

    Efficient plastid transformation has been achieved in Nicotiana tabacum using cloned plastid DNA of Solanum nigrum carrying mutations conferring spectinomycin and streptomycin resistance. The use of the incompletely homologous (homeologous) Solanum plastid DNA as donor resulted in a Nicotiana plastid transformation frequency comparable with that of other experiments where completely homologous plastid DNA was introduced. Physical mapping and nucleotide sequence analysis of the targeted plastid DNA region in the transformants demonstrated efficient site-specific integration of the 7.8-kb Solanum plastid DNA and the exclusion of the vector DNA. The integration of the cloned Solanum plastid DNA into the Nicotiana plastid genome involved multiple recombination events as revealed by the presence of discontinuous tracts of Solanum-specific sequences that were interspersed between Nicotiana-specific markers. Marked position effects resulted in very frequent cointegration of the nonselected peripheral donor markers located adjacent to the vector DNA. Data presented here on the efficiency and features of homeologous plastid DNA recombination are consistent with the existence of an active RecA-mediated, but a diminished mismatch, recombination/repair system in higher-plant plastids. PMID:10388829

  20. Radiosensitization effect of recombinant adenoviral-mediated PUMA gene on pancreatic carcinoma cells

    International Nuclear Information System (INIS)

    Objective: To study the effect of PUMA gene mediated by recombinant adenovirus vector combined with radiation on the pancreatic carcinoma. Methods: The PANC-1 cells were infected with Ad- PUMA (MOI=10, 50 and 100, respectively) for 48 h. The expression of PUMA mRNA and protein was detected by RT-PCR and Western blot, respectively. PANC-1 cells were divided into 4 groups: control group, transfection group, irradiation group and combined treatment group. The cell growth inhibition rate and apoptotic rate of PANC-1 cells were assessed by MTT assay and flow cytometry. Human pancreatic carcinomas were transplanted subcutaneously in nude mice, which were randomized into 4 groups: control group, transfection group, irradiation group and combined treatment group. Tumor growth rate and apoptotic index at different time points were recorded in 35 days. Results: The expression of PUMA mRNA and protein was increased with the increase of MOI of Ad-PUMA, which was does-dependant (MOI=10, mRNA=0.46± 0.02, protein=0.75± 0.09; MOI=50, mRNA=1.12±0.09, protein=1.01±0.18; MOI=100, mRNA=1.50±0.08, protein= 1.80±0.15; P3, (39.5±9.23)mm3, (33.6±10.3)mm3 and (52.0±11.43)mm3, respectively, P<0.05]. And the apoptotic index was increased in the same manner (AI=0.43±0.05, 0.29±0.10, 0.24±0.05 and 0.00±0.00, respectively, P<0.05). Conclusions: Recombinant adenoviral-mediated PUMA gene combined with irradiation could increase the cell-killing effect on pancreatic carcinoma. It is better than that of either one kind of therapy. (authors)

  1. Matrix metalloproteinase?mediation of tumor targeting human recombinant tumor necrosis factor?? fusion protein.

    Science.gov (United States)

    Ren, Hui; Shao, Xin; Zeng, Liang; Wang, Fa; Huang, Di-Nan; Hou, Gan

    2015-08-01

    The aim of the present study was to use genetic engineering in order to establish an efficient tumor necrosis factor (TNF)?? fusion protein with low toxicity, which may be used to target tumors. Four types of matrix metalloproteinase (MMP)?mediated tumor targeting human recombinant TNF?? (rhTNF??) fusion protein vectors were constructed. These were subsequently introduced into Escherichia coli. rhTNF?? fusion protein with a glutathione S?transferase (GST)?tag was purified using GST resin affinity chromatography, and GST?tags were digested using factor Xa. The cytotoxic effects of the fusion protein on L929 cells were determined using MTT assays. At a concentration of 1 pM, the GST?tagged fusion protein exerted no cytotoxic effects on the cells, compared with the negative control cells (P=0.975>0.05). However, at a concentration of 1000 pM, the deblocking fusion protein exerted greater cytotoxic effects on L929 cells, compared with positive control cells (P<0.05). Treatment with the fusion protein also induced cell apoptosis in the nasopharyngeal cancer cell line, CNE?2Z, which secretes high levels of MMP?1. In conclusion, the results of the present study suggested that MMP?mediated rhTNF?? fusion protein induces CNE?2Z cells apoptosis. rhTNF?? exhibits high efficacy and tumor cell targeting capability, with low toxicity effects on healthy cells. PMID:25891416

  2. Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Risager, Peter Christian

    2013-01-01

    Background Infectious cDNA clones are a prerequisite for directed genetic manipulation of RNA viruses. Here, a strategy to facilitate manipulation and rescue of classical swine fever viruses (CSFVs) from full-length cDNAs present within bacterial artificial chromosomes (BACs) is described. This strategy allows manipulation of viral cDNA by targeted recombination-mediated mutagenesis within bacteria. Results A new CSFV-BAC (pBeloR26) derived from the Riems vaccine strain has been constructed and subsequently modified in the E2 coding sequence, using the targeted recombination strategy to enable rescue of chimeric pestiviruses (vR26_E2gif and vR26_TAV) with potential as new marker vaccine candidates. Sequencing of the BACs revealed a high genetic stability during passages within bacteria. The complete genome sequences of rescued viruses, after extensive passages in mammalian cells showed that modifications in the E2 protein coding sequence were stably maintained. A single amino acid substitution (D3431G) in the RNA dependent RNA polymerase was observed in the rescued viruses vR26_E2gif and vR26, which was reversion to the parental Riems sequence. Conclusions These results show that targeted recombination-mediated mutagenesis provides a powerful tool for expediting the construction of novel RNA genomes and should be applicable to the manipulation of other RNA viruses.

  3. RPA correlation effects in radiative pion capture

    International Nuclear Information System (INIS)

    A sum rule approach to radiative pion capture is given in terms of the energy-weighted and inverse-energy weighted sum rules. They are evaluated with RPA accuracy for Skyrme-like interactions. The static polarizabilities of the dipole, quadrupole and octupole isovector modes turn out to be the relevant quantities to determine the total branching ratios and mean photon energies. (orig.)

  4. Recombinant AAV-PR39-mediated hypoxia-inducible factor 1? gene expression attenuates myocardial infarction.

    Science.gov (United States)

    Sun, Lijun; Hao, Yuewen; Nie, Xiaowei; Xu, Jian; Li, Zhenwu; Zhang, Wei; Liu, Ying; Zhang, Xuexin

    2014-01-01

    PR39 is an angiogenic masterswitch protein, belonging to the second generation of angiogenic growth factors. However, the role of recombinant adeno-associated virus (AAV) carrying the PR39 fusion gene (AAV-PR39) in acute myocardial infarction remains unclear. Therefore, in this study, we investigated the role of AAV-PR39 in an experimental animal model of acute myocardial infarction. The PR39 gene was fused with the transmembrane peptide, TAT, 6xHis?tag and NT4 signal sequences. AAV-PR39 was then obtained by calcium phosphate co-precipitation. A total of 18 healthy Chinese mini pigs were randomly divided into an experimental groups (the AAV-PR39-treated group) and a control group [phosphated-buffered saline (PBS)-treated group]. Following the induction of myocardial infarction, enhanced 3.0T MR imaging was performed to observe the changes in myocardial signal intensity at 0 h, 1, 2 and 3 weeks. The expression of hypoxia-inducible factor?1? (HIF-1?) in the myocardial tissues was determined by SABC immunohistochemistry. In addition, in vitro experiments using CRL-1730 endothelial cells transfected with AAV vector containing NT4-TAT-His-PR39 revealed that the AAV-PR39-treated group had a significantly higher expression of HIF-1? compared with the control group. Moreover, PR39 regulated the HIF-1?-induced expression of angiogenic growth factors. Under hypoxic conditions, the anti-apoptotic effects in the AAV-PR39 group were more pronounced than those observed in the control (PBS-treated) group. In vivo, the enforced expression of recombinant PR39 elevated the level of HIF-1? under hypoxic conditions and decreased the size of the infarcted areas by upregulating the expression of HIF-1? in the areas surrounding the infarct area. Taken together, our data demonstrate that the recombinant AAV-PR39-mediated HIF-1? expression attenuates myocardial infarction, indicating that AAV-PR39 may serve as a novel therapeutic agent for the treatment of myocardial infarction. PMID:24253102

  5. SITE-SPECIFIC RECOMBINATION FOR PLANT GENETIC ENGINEERING: STRATEGY FOR AGRO-MEDIATED GENE STACKING

    Science.gov (United States)

    The precise rearrangement of DNA in planta can be achieved through site-specific recombination. For the past decade and a half, laboratory experiments have shown that site-specific recombination can delete genomic DNA, regulate gene expression, recombine chromosomes, and target new DNA into designat...

  6. Impairment of replication fork progression mediates RNA polII transcription-associated recombination

    OpenAIRE

    Prado, Fe?lix; Aguilera, Andre?s

    2005-01-01

    Homologous recombination safeguards genome integrity, but it can also cause genome instability of important consequences for cell proliferation and organism development. Transcription induces recombination, as shown in prokaryotes and eukaryotes for both spontaneous and developmentally regulated events such as those responsible for immunoglobulin class switching. Deciphering the molecular basis of transcription-associated recombination (TAR) is important in understanding genome instability. U...

  7. Roles of DNA helicases in the mediation and regulation of homologous recombination.

    Science.gov (United States)

    Daley, James M; Niu, Hengyao; Sung, Patrick

    2013-01-01

    Homologous recombination (HR) is an evolutionarily conserved process that eliminates DNA double-strand breaks from chromosomes, repairs injured DNA replication forks, and helps orchestrate meiotic chromosome segregation. Recent studies have shown that DNA helicases play multifaceted roles in HR mediation and regulation. In particular, the S. cerevisiae Sgs1 helicase and its human ortholog BLM helicase are involved in not only the resection of the primary lesion to generate single-stranded DNA to prompt the assembly of the HR machinery, but they also function in somatic cells to suppress the formation of chromosome arm crossovers during HR. On the other hand, the S. cerevisiae Mph1 and Srs2 helicases, and their respective functional equivalents in other eukaryotes, suppress spurious HR events and favor the formation of noncrossovers via distinct mechanisms. Thus, the functional integrity of the HR process and HR outcomes are dependent upon these helicase enzymes. Since mutations in some of these helicases lead to cancer predisposition in humans and mice, studies on them have clear relevance to human health and disease. PMID:23161012

  8. Localization and nucleotide sequences of genes mediating site-specific recombination of the SLP1 element in Streptomyces lividans.

    OpenAIRE

    Brasch, M. A.; Pettis, G. S.; Lee, S. C.; Cohen, S. N.

    1993-01-01

    SLP1 is a 17.2-kbp genetic element indigenous to the Streptomyces coelicolor chromosome. During conjugation, SLP1 can undergo excision and subsequent site-specific integration into the chromosomes of recipient cells. We report here the localization, nucleotide sequences, and initial characterization of the genes mediating these recombination events. A region of SLP1 adjacent to the previously identified site of integration, attP, was found to be sufficient to promote site-specific integration...

  9. Inhalation of Nebulized Perfluorochemical Enhances Recombinant Adenovirus and Adeno-Associated Virus-Mediated Gene Expression in Lung Epithelium

    OpenAIRE

    Beckett, Travis; Bonneau, Laura; Howard, Alan; Blanchard, James; Borda, Juan; Weiner, Daniel J.; Wang, Lili; Gao, Guang Ping; Kolls, Jay K.; Bohm, Rudolf; Liggitt, Denny; Weiss, Daniel J.

    2012-01-01

    Use of perfluorochemical liquids during intratracheal vector administration enhances recombinant adenovirus and adeno-associated virus (AAV)-mediated lung epithelial gene expression. We hypothesized that inhalation of nebulized perfluorochemical vapor would also enhance epithelial gene expression after subsequent intratracheal vector administration. Freely breathing adult C57BL/6 mice were exposed for selected times to nebulized perflubron or sterile saline in a sealed Plexiglas chamber. Reco...

  10. Generation of Cell Lines to Complement Adenovirus Vectors using Recombination-Mediated Cassette Exchange

    Directory of Open Access Journals (Sweden)

    Farley Daniel C

    2010-12-01

    Full Text Available Abstract Background Adenovirus serotype 5 (Ad5 has many favourable characteristics for development as a gene therapy vector. However, the utility of current Ad5 vectors is limited by transient transgene expression, toxicity and immunogenicity. The most promising form of vector is the high capacity type, which is deleted for all viral genes. However, these vectors can only be produced to relatively low titres and with the aid of helper virus. Therefore a continuing challenge is the generation of more effective Ad5 vectors that can still be grown to high titres. Our approach is to generate complementing cell lines to support the growth of Ad5 vectors with novel late gene deficiencies. Results We have used LoxP/Cre recombination mediated cassette exchange (RMCE to generate cell lines expressing Ad5 proteins encoded by the L4 region of the genome, the products of which play a pivotal role in the expression of Ad5 structural proteins. A panel of LoxP parent 293 cell lines was generated, each containing a GFP expression cassette under the control of a tetracycline-regulated promoter inserted at a random genome location; the cassette also contained a LoxP site between the promoter and GFP sequence. Clones displayed a variety of patterns of regulation, stability and level of GFP expression. Clone A1 was identified as a suitable parent for creation of inducible cell lines because of the tight inducibility and stability of its GFP expression. Using LoxP-targeted, Cre recombinase-mediated insertion of an L4 cassette to displace GFP from the regulated promoter in this parent clone, cell line A1-L4 was generated. This cell line expressed L4 100K, 22K and 33K proteins at levels sufficient to complement L4-33K mutant and L4-deleted viruses. Conclusions RMCE provides a method for rapid generation of Ad5 complementing cell lines from a pre-selected parental cell line, chosen for its desirable transgene expression characteristics. Parent cell lines can be selected for high or low gene expression, and for tight regulation, allowing viral protein expression to mirror that found during infection. Cell lines derived from a single parent will allow the growth of different vectors to be assessed without the complication of varying complementing protein expression.

  11. Efficient soluble expression of active recombinant human cyclin A2 mediated by E. coli molecular chaperones.

    Science.gov (United States)

    Grigoroudis, Asterios I; McInnes, Campbell; Premnath, Padmavathy Nandha; Kontopidis, George

    2015-09-01

    Bacterial expression of human proteins continues to present a critical challenge in protein crystallography and drug design. While human cyclin A constructs have been extensively characterized in complex with cyclin dependent kinase 2 (CDK2), efforts to express the monomeric human cyclin A2 in Escherichia coli in a stable form, without the kinase subunit, have been laden with technical difficulties, including solubility, yield and purity. Here, optimized conditions are described with the aim of generating for first time, sufficient quantities of human recombinant cyclin A2 in a soluble and active form for crystallization and ligand characterization purposes. The studies involve implementation of a His-tagged heterologous expression system under conditions of auto-induction and mediated by molecular chaperone-expressing plasmids. A high yield of human cyclin A2 was obtained in natively folded and soluble form, through co-expression with groups of molecular chaperones from E. coli in various combinations. A one-step affinity chromatography method was utilized to purify the fusion protein products to homogeneity, and the biological activity confirmed through ligand-binding affinity to inhibitory peptides, representing alternatives for the key determinants of the CDK2 substrate recruitment site on the cyclin regulatory subunit. As a whole, obtaining the active cyclin A without the CDK partner (referred to as monomeric in this work) in a straightforward and facile manner will obviate protein - production issues with the CDK2/cyclin A complex and enable drug discovery efforts for non-ATP competitive CDK inhibition through the cyclin groove. PMID:25956535

  12. Homologous recombination mediates cellular resistance and fraction size sensitivity to radiation therapy

    International Nuclear Information System (INIS)

    Purpose: Cellular sensitivity to radiotherapy total dose and fraction size is strongly influenced by DNA double strand break (DSB) repair. Here, we investigate response to radiotherapy fraction size using CHO cell lines deficient in specific DNA repair pathways in response to radiation induced DNA double strand breaks (DSB). Experimental design: We irradiated CHO cell lines, AA8 (WT), irs1SF (XRCC3-), V3-3 (DNA-PKcs-) and EM9 (XRCC1-) with 16 Gy in 1 Gy daily fractions over 3 weeks or 16 Gy in 4 Gy daily fractions over 4 days, and studied clonogenic survival, DNA DSB repair kinetics (RAD51 and 53BP1 foci staining) and cell cycle profiles (flow cytometry). Results: In response to fractionated radiotherapy, wild-type and DNA repair defective cells accumulated in late S/G2 phase. In cells proficient in homologous recombination (HR), accumulation in S/G2 resulted in reduced sensitivity to fraction size and increased cellular resistance (clonogenic survival). Sensitivity to fraction size was also lost in NHEJ-defective V3-3 cells, which likely rely on functional HR. By contrast, HR-defective irs1SF cells, with functional NHEJ, remained equally sensitive to fractionation throughout the 3-week treatment. Conclusions: The high fidelity of HR, which is independent of induced DNA damage level, is postulated to explain the low fractionation sensitivity and cellular resistance of cells in S/G2 phase. In conclusion, our results suggest that HR mediates resistance to fractionated radiotherapy, an observation that may help future efforts to improve radiotherapy outcome

  13. Quantization in the high-spin RPA

    International Nuclear Information System (INIS)

    The problem of how to quantize the angular momentum of the self-consistent cranking model at high spin when small oscillations (RPA) about the steady rotation are included is reexamined, in view of a recent criticism by Reinhardt of an earlier treatment. This criticism is shown to be unfounded. On the other hand, it is shown that Reinhardt's quantization procedure leads to some serious problems, and the result that the vibrational frequencies differ in the rotating and lab frames is called into question. (orig.)

  14. Recombination involving transposable elements: role of target molecule replication in Tn1 delta Ap-mediated replicon fusion.

    OpenAIRE

    Muster, C J; Shapiro, J A; MacHattie, L A

    1983-01-01

    Donor DNA molecules carrying Tn1 or Tn3 deletion mutants do not need to replicate in order to participate in replicon fusion recombination events during which the Tn1/Tn3 element is duplicated. We have assayed Tn1 delta Ap-mediated replicon fusion events involving plasmid R388 and the bacteriophage lambda-derived plasmid p lambda CM, and we find that the role of the recipient molecule is distinct. When p lambda CM carries Tn1 delta Ap, replicon fusion occurs in more than 1% of all cells assay...

  15. Generation of Nkx2.2:lacZ mice using Recombination-Mediated Cassette Exchange Technology

    OpenAIRE

    Arnes, Luis; Leclerc, Kevin; Friel, Jessica M.; Hipkens, Susan B.; Magnuson, Mark A.; Sussel, Lori

    2012-01-01

    Nkx2.2 encodes a homeodomain transcription factor required for the correct specification and/or differentiation of cells in the pancreas, intestine and CNS. To follow the fate of cells deleted for Nkx2.2 within these tissues, we generated Nkx2.2:lacZ knockin mice using a recombination-mediated cassette exchange (RMCE) approach. Expression analysis of lacZ and/or ?-galactosidase in Nkx2.2lacZ/+ heterozygote embryos and adults demonstrates that lacZ faithfully recapitulates endogenous Nkx2.2 e...

  16. Agrobacterium tumefaciens-Mediated Transformation for Investigation of Somatic Recombination in the Fungal Pathogen Armillaria mellea?

    OpenAIRE

    Baumgartner, Kendra; Fujiyoshi, Phillip; Foster, Gary D.; Bailey, Andy M.

    2010-01-01

    Armillaria root disease is one of the most damaging timber and fruit tree diseases in the world. Despite its economic importance, many basic questions about the biology of the causal fungi, Armillaria spp., are unanswered. For example, Armillaria undergoes matings between diploid and haploid mycelia, which can result in a recombinant diploid without meiosis. Evidence of such somatic recombination in natural populations suggests that this reproductive mode may affect the pathogen's ecology. In...

  17. Extrachromosomal homologous recombination and gene targeting in plant cells after Agrobacterium mediated transformation.

    OpenAIRE

    Offringa, R.; Groot, M. J.; Haagsman, H. J.; Does, M. P.; Den Elzen, P. J.; Hooykaas, P. J.

    1990-01-01

    We determined whether T-DNA molecules introduced into plant cells using Agrobacterium are suitable substrates for homologous recombination. For the detection of such recombination events different mutant versions of a NPTII construct were used. In a first set of experiments protoplasts of Nicotiana tabacum SR1 were cocultivated with two Agrobacterium tumefaciens strains. Each strain contained a different T-DNA, one carrying a 5' deleted NPTII gene and the other a NPTII gene with a 3' deletion...

  18. A set of vectors for introduction of antibiotic resistance genes by in vitro Cre-mediated recombination

    Directory of Open Access Journals (Sweden)

    Vassetzky Yegor S

    2008-12-01

    Full Text Available Abstract Background Introduction of new antibiotic resistance genes in the plasmids of interest is a frequent task in molecular cloning practice. Classical approaches involving digestion with restriction endonucleases and ligation are time-consuming. Findings We have created a set of insertion vectors (pINS carrying genes that provide resistance to various antibiotics (puromycin, blasticidin and G418 and containing a loxP site. Each vector (pINS-Puro, pINS-Blast or pINS-Neo contains either a chloramphenicol or a kanamycin resistance gene and is unable to replicate in most E. coli strains as it contains a conditional R6K? replication origin. Introduction of the antibiotic resistance genes into the vector of interest is achieved by Cre-mediated recombination between the replication-incompetent pINS and a replication-competent target vector. The recombination mix is then transformed into E. coli and selected by the resistance marker (kanamycin or chloramphenicol present in pINS, which allows to recover the recombinant plasmids with 100% efficiency. Conclusion Here we propose a simple strategy that allows to introduce various antibiotic-resistance genes into any plasmid containing a replication origin, an ampicillin resistance gene and a loxP site.

  19. The RPA at high spin and conservation laws

    International Nuclear Information System (INIS)

    RPA corrections to the self-consistent cranking model are studied for the self-contained system, with special emphasis on conservation of angular momentum and particle number. Some problems associated with the cranking interaction are solved, and a prescription is given for writing down wave functions and calculating transition amplitudes within the accuracy of the RPA. (Auth.)

  20. Role of Cyclic AMP-Dependent Kinase Response Element-Binding Protein in Recombinant Adeno-Associated Virus-Mediated Transduction of Heart Muscle Cells

    OpenAIRE

    Dean, Jarrod; Plante, Jeremy; Huggins, Gordon S.; Snyder, Richard O.; Aikawa, Ryuichi

    2009-01-01

    Recombinant adeno-associated virus (rAAV) vectors represent a promising approach to gene delivery for clinical use. Published data indicate that rAAV vector genomes persist in vivo as episomal chromatin in the skeletal muscle of nonhuman primates. In this study, we assessed the interconnection between the transcription factor cyclic AMP response element-binding protein (CREB) and recombinant AAV serotype 2 vector genomes after transduction in vitro and in vivo. rAAV-mediated myocyte transduct...

  1. RPA correction to the optical potential

    International Nuclear Information System (INIS)

    In studies of nucleon elastic scattering, a correction to the microscopic optical potential built from Melbourne g-matrix was found to be necessary at low nucleon incident energy. Indeed, at energies lower than 60 MeV, the absorption generated from Melbourne g-matrix is too weak within 25%. Coupling to collective excited states of the target nucleus are not included in the g-matrix and could explain the missing absorption. We propose to calculate this correction to the optical potential using the Gogny D1S effective nucleon-nucleon interaction in the coupling to excited states of the target. We use the Random Phase Approximation (RPA) description of the excited states of the target with the same interaction. (authors)

  2. RPA correction to the optical potential

    Directory of Open Access Journals (Sweden)

    Bauge E.

    2010-03-01

    Full Text Available In studies of nucleon elastic scattering, a correction to the microscopic optical potential built from Melbourne g-matrix was found to be necessary at low nucleon incident energy [1,2]. Indeed, at energies lower than 60 MeV, the absorption generated from Melbourne g-matrix is too weak within 25%. Coupling to collective excited states of the target nucleus are not included in the g-matrix and could explain the missing absorption. We propose to calculate this correction to the optical potential using the Gogny D1S effective nucleon-nucleon interaction in the coupling to excited states of the target. We use the Random Phase Approximation (RPA description of the excited states of the target with the same interaction.

  3. Extended RPA study of nuclear collective phenomena

    International Nuclear Information System (INIS)

    A fully microscopic study of nuclear collective phenomena is presented within the framework of an extended RPA which includes 1p-1h and 2p-2h excitations in a consistent way. This theory allows us to obtain a very realistic description of various excitation spectra. As a result, a strong evidence of correlation effects beyond mean-field theory emerges. The effective interaction used is a G-matrix derived from the meson-exchange potential. The extended theory introduces also additional correlations which screen the long-large part of the effective interaction. This effect significantly enhances the stability of the ground state against density fluctuations. In this connection a possible importance of relativistic effects is also discussed. 99 refs., 19 figs., 5 tabs. (author)

  4. Microhomology-Mediated End Joining in Fission Yeast Is Repressed by Pku70 and Relies on Genes Involved in Homologous Recombination

    OpenAIRE

    Decottignies, Anabelle

    2007-01-01

    Two DNA repair pathways are known to mediate DNA double-strand-break (DSB) repair: homologous recombination (HR) and nonhomologous end joining (NHEJ). In addition, a nonconservative backup pathway showing extensive nucleotide loss and relying on microhomologies at repair junctions was identified in NHEJ-deficient cells from a variety of organisms and found to be involved in chromosomal translocations. Here, an extrachromosomal assay was used to characterize this microhomology-mediated end-joi...

  5. V(D)J Recombinase-Mediated Processing of Coding Junctions at Cryptic Recombination Signal Sequences in Peripheral T Cells during Human Development1

    OpenAIRE

    Murray, Janet M.; O’neill, J. Patrick; Messier, Terri; Rivers, Jami; Walker, Vernon E.; Mcgonagle, Brien; Trombley, Lucy; Cowell, Lindsay G.; Kelsoe, Garnett; Mcblane, Fraser; Finette, Barry A.

    2006-01-01

    V(D)J recombinase mediates rearrangements at immune loci and cryptic recombination signal sequences (cRSS), resulting in a variety of genomic rearrangements in normal lymphocytes and leukemic cells from children and adults. The frequency at which these rearrangements occur and their potential pathologic consequences are developmentally dependent. To gain insight into V(D)J recombinase-mediated events during human development, we investigated 265 coding junctions associated with cRSS sites at ...

  6. Resolution of Dicentric Chromosomes by Ty-Mediated Recombination in Yeast

    OpenAIRE

    Surosky, Richard T.; Tye, Bik-Kwoon

    1985-01-01

    We have integrated a plasmid containing a yeast centromere, CEN5, into the HIS4 region of chromosome III by transformation. Of the three transformant colonies examined, none contained a dicentric chromosome, but all contained a rearranged chromosome III. In one transformant, rearrangement occurred by homologous recombination between two Ty elements; one on the left arm and the other on the right arm of chromosome III. This event produced a ring chromosome (ring chromosome III) of about 60 kb...

  7. MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering

    OpenAIRE

    Bonde, Mads T.; Klausen, Michael S.; Anderson, Mads V.; Wallin, Annika I.N.; Wang, Harris H.; Sommer, Morten O.A.

    2014-01-01

    Recombineering and multiplex automated genome engineering (MAGE) offer the possibility to rapidly modify multiple genomic or plasmid sites at high efficiencies. This enables efficient creation of genetic variants including both single mutants with specifically targeted modifications as well as combinatorial cell libraries. Manual design of oligonucleotides for these approaches can be tedious, time-consuming, and may not be practical for larger projects targeting many genomic sites. At present...

  8. Characterization of Alu and recombination-associated motifs mediating a large homozygous SPG7 gene rearrangement causing hereditary spastic paraplegia.

    Science.gov (United States)

    López, Eva; Casasnovas, Carlos; Giménez, Javier; Matilla-Dueñas, Antoni; Sánchez, Ivelisse; Volpini, Víctor

    2015-04-01

    Spastic paraplegia type 7 (SPG7) is one of the most common forms of autosomal recessive hereditary spastic paraplegia (AR-HSP). Although over 77 different mutations have been identified in SPG7 patients, only 9 gross deletions have been reported with only a few of them being fully characterized. Here, we present a detailed description of a large homozygous intragenic SPG7 gene rearrangement involving a 5144-base pair (bp) genomic loss (c. 1450-446_1779?+?746 delinsAAAGTGCT) encompassing exons 11 to 13, identified in a Spanish AR-HSP family. Analysis of the deletion junction sequences revealed that the 5' breakpoint of this SPG7 gene deletion was located within highly homologous Alu sequences where the 3' breakpoint appears to be flanked by the core crossover hotspot instigator (chi)-like sequence (GCTGG). Furthermore, an 8-bp (AAAGTTGCT) conserved sequence at the breakpoint junction was identified, suggesting that the most likely mechanism for the occurrence of this rearrangement is by Alu microhomology and chi-like recombination-associated motif-mediated multiple exon deletion. Our results are consistent with non-allelic homologous recombination and non-homologous end joining in deletion mutagenesis for the generation of rearrangements. This study provides more evidence associating repeated elements as a genetic mechanism underlying neurodegenerative disorders, highlighting their importance in human diseases. PMID:25398481

  9. P-glycoprotein-mediated resistance to chemotherapy in cancer cells: using recombinant cytosolic domains to establish structure-function relationships

    Directory of Open Access Journals (Sweden)

    Di Pietro A.

    1999-01-01

    Full Text Available Resistance to chemotherapy in cancer cells is mainly mediated by overexpression of P-glycoprotein (Pgp, a plasma membrane ATP-binding cassette (ABC transporter which extrudes cytotoxic drugs at the expense of ATP hydrolysis. Pgp consists of two homologous halves each containing a transmembrane domain and a cytosolic nucleotide-binding domain (NBD which contains two consensus Walker motifs, A and B, involved in ATP binding and hydrolysis. The protein also contains an S signature characteristic of ABC transporters. The molecular mechanism of Pgp-mediated drug transport is not known. Since the transporter has an extraordinarily broad substrate specificity, its cellular function has been described as a "hydrophobic vacuum cleaner". The limited knowledge about the mechanism of Pgp, partly due to the lack of a high-resolution structure, is well reflected in the failure to efficiently inhibit its activity in cancer cells and thus to reverse multidrug resistance (MDR. In contrast to the difficulties encountered when studying the full-length Pgp, the recombinant NBDs can be obtained in large amounts as soluble proteins. The biochemical and biophysical characterization of recombinant NBDs is shown here to provide a suitable alternative route to establish structure-function relationships. NBDs were shown to bind ATP and analogues as well as potent modulators of MDR, such as hydrophobic steroids, at a region close to the ATP site. Interestingly, flavonoids also bind to NBDs with high affinity. Their binding site partly overlaps both the ATP-binding site and the steroid-interacting region. Therefore flavonoids constitute a new promising class of bifunctional modulators of Pgp.

  10. P-glycoprotein-mediated resistance to chemotherapy in cancer cells: using recombinant cytosolic domains to establish structure-function relationships

    Scientific Electronic Library Online (English)

    A., Di Pietro; G., Dayan; G., Conseil; E., Steinfels; T., Krell; D., Trompier; H., Baubichon-Cortay; J.-M., Jault.

    1999-08-01

    Full Text Available Resistance to chemotherapy in cancer cells is mainly mediated by overexpression of P-glycoprotein (Pgp), a plasma membrane ATP-binding cassette (ABC) transporter which extrudes cytotoxic drugs at the expense of ATP hydrolysis. Pgp consists of two homologous halves each containing a transmembrane dom [...] ain and a cytosolic nucleotide-binding domain (NBD) which contains two consensus Walker motifs, A and B, involved in ATP binding and hydrolysis. The protein also contains an S signature characteristic of ABC transporters. The molecular mechanism of Pgp-mediated drug transport is not known. Since the transporter has an extraordinarily broad substrate specificity, its cellular function has been described as a "hydrophobic vacuum cleaner". The limited knowledge about the mechanism of Pgp, partly due to the lack of a high-resolution structure, is well reflected in the failure to efficiently inhibit its activity in cancer cells and thus to reverse multidrug resistance (MDR). In contrast to the difficulties encountered when studying the full-length Pgp, the recombinant NBDs can be obtained in large amounts as soluble proteins. The biochemical and biophysical characterization of recombinant NBDs is shown here to provide a suitable alternative route to establish structure-function relationships. NBDs were shown to bind ATP and analogues as well as potent modulators of MDR, such as hydrophobic steroids, at a region close to the ATP site. Interestingly, flavonoids also bind to NBDs with high affinity. Their binding site partly overlaps both the ATP-binding site and the steroid-interacting region. Therefore flavonoids constitute a new promising class of bifunctional modulators of Pgp.

  11. Long-term Cre-mediated Retrograde Tagging of Neurons Using a Novel Recombinant Pseudorabies Virus

    Directory of Open Access Journals (Sweden)

    Hassana Oyibo

    2014-09-01

    Full Text Available Brain regions contain diverse populations of neurons that project to different long-range targets. The study of these subpopulations in circuit function and behavior requires a toolkit to characterize and manipulate their activity in vivo. We have developed a novel set of reagents based on Pseudorabies Virus (PRV for efficient and long-term genetic tagging of neurons based on their projection targets. By deleting IE180, the master transcriptional regulator in the PRV genome, we have produced a mutant virus capable of infection and transgene expression in neurons but unable to replicate in or spread from those neurons. IE180-null mutants showed no cytotoxicity, and infected neurons exhibited normal physiological function more than 45 days after infection, indicating the utility of these engineered viruses for chronic experiments. To enable rapid and convenient construction of novel IE180-null recombinants, we engineered a bacterial artificial chromosome (BAC shuttle-vector system for moving new constructs into the PRV IE180-null genome. Using this system we generated an IE180-null recombinant virus expressing the site-specific recombinase Cre. This Cre-expressing virus (PRV-hSyn-Cre efficiently and robustly infects neurons in vivo and activates transgene expression from Cre-dependent vectors in local and retrograde projecting populations of neurons in the mouse. We also generated an assortment of recombinant viruses expressing fluorescent proteins (mCherry, EGFP, ECFP. These viruses exhibit long-term labeling of neurons in vitro but transient labeling in vivo. Together these novel IE180-null PRV reagents expand the toolkit for targeted gene expression in the brain, facilitating functional dissection of neuronal circuits in vivo.

  12. Long-term Cre-mediated retrograde tagging of neurons using a novel recombinant pseudorabies virus.

    Science.gov (United States)

    Oyibo, Hassana K; Znamenskiy, Petr; Oviedo, Hysell V; Enquist, Lynn W; Zador, Anthony M

    2014-01-01

    Brain regions contain diverse populations of neurons that project to different long-range targets. The study of these subpopulations in circuit function and behavior requires a toolkit to characterize and manipulate their activity in vivo. We have developed a novel set of reagents based on Pseudorabies Virus (PRV) for efficient and long-term genetic tagging of neurons based on their projection targets. By deleting IE180, the master transcriptional regulator in the PRV genome, we have produced a mutant virus capable of infection and transgene expression in neurons but unable to replicate in or spread from those neurons. IE180-null mutants showed no cytotoxicity, and infected neurons exhibited normal physiological function more than 45 days after infection, indicating the utility of these engineered viruses for chronic experiments. To enable rapid and convenient construction of novel IE180-null recombinants, we engineered a bacterial artificial chromosome (BAC) shuttle-vector system for moving new constructs into the PRV IE180-null genome. Using this system we generated an IE180-null recombinant virus expressing the site-specific recombinase Cre. This Cre-expressing virus (PRV-hSyn-Cre) efficiently and robustly infects neurons in vivo and activates transgene expression from Cre-dependent vectors in local and retrograde projecting populations of neurons in the mouse. We also generated an assortment of recombinant viruses expressing fluorescent proteins (mCherry, EGFP, ECFP). These viruses exhibit long-term labeling of neurons in vitro but transient labeling in vivo. Together these novel IE180-null PRV reagents expand the toolkit for targeted gene expression in the brain, facilitating functional dissection of neuronal circuits in vivo. PMID:25232307

  13. Porcine hepatocyte isolation and reversible immortalization mediated by retroviral transfer and site-specific recombination

    OpenAIRE

    Fan-ying Meng, Zhi-shui Chen

    2010-01-01

    AIM: To develop a hepatocyte cell line, we immortalized primary porcine hepatocytes with a retroviral vector SSR#69 containing the Simian Virus 40 T antigen (SV40Tag).METHODS: We first established a method of porcine hepatocyte isolation with a modified four-step retrograde perfusion technique. Then the porcine hepatocytes were immortalized with retroviral vector SSR#69 expressing SV40T and hygromycin-resistance genes flanked by paired loxP recombination targets. SV40T cDNA in the expanded ce...

  14. Nuclear response using realistic interactions and extended RPA theories

    International Nuclear Information System (INIS)

    Realistic interactions, renormalized within the Unitary Correlation Operator Method, were employed recently in Second RPA (SRPA) calculations of nuclear response. Results are presented and the main lessons learned are discussed. In particular, our results, which represent a great improvement over our earlier RPA calculations, as well as physical arguments, suggest the prospect of describing nuclear collective excitations realistically and consistently using extended RPA (ERPA) theories, like SRPA, and renormalized interactions with good convergence properties. Up to now, only two-body Hamiltonians have been considered and most of the results have been obtained using a softened Argonne V18 potential. Appropriate three-body terms can be included to improve the Hamiltonian. Prospects with chiral interactions will also be discussed. Further issues to be addressed are related to the ERPA method itself: The standard SRPA based on the quasi-boson approximation may not be the best RPA extension, as it suffers from intrinsic inconsistencies and instabilities.

  15. Rapid recombinant protein production from piggyBac transposon-mediated stable CHO cell pools.

    Science.gov (United States)

    Balasubramanian, Sowmya; Matasci, Mattia; Kadlecova, Zuzana; Baldi, Lucia; Hacker, David L; Wurm, Florian M

    2015-04-20

    Heterogeneous populations of stably transfected cells (cell pools) can serve for the rapid production of moderate amounts of recombinant proteins. Here, we propose the use of the piggyBac (PB) transposon system to improve the productivity and long-term stability of cell pools derived from Chinese hamster ovary (CHO) cells. PB is a naturally occurring genetic element that has been engineered to facilitate the integration of a transgene into the genome of the host cell. In this report PB-derived cell pools were generated after 10 days of selection with puromycin. The resulting cell pools had volumetric productivities that were 3-4 times higher than those achieved with cell pools generated by conventional plasmid transfection even though the number of integrated transgene copies per cell was similar in the two populations. In 14-day batch cultures, protein levels up to 600 and 800 mg/L were obtained for an Fc-fusion protein and a monoclonal antibody, respectively, at volumetric scales up to 1L. In general, the volumetric protein yield from cell pools remained constant for up to 3 months in the absence of selection. In conclusion, transfection of CHO cells with the PB transposon system is a simple, efficient, and reproducible approach to the generation of cell pools for the rapid production of recombinant proteins. PMID:25758242

  16. Srs2 promotes Mus81-Mms4-mediated resolution of recombination intermediates.

    Science.gov (United States)

    Chavdarova, Melita; Marini, Victoria; Sisakova, Alexandra; Sedlackova, Hana; Vigasova, Dana; Brill, Steven J; Lisby, Michael; Krejci, Lumir

    2015-04-20

    A variety of DNA lesions, secondary DNA structures or topological stress within the DNA template may lead to stalling of the replication fork. Recovery of such forks is essential for the maintenance of genomic stability. The structure-specific endonuclease Mus81-Mms4 has been implicated in processing DNA intermediates that arise from collapsed forks and homologous recombination. According to previous genetic studies, the Srs2 helicase may play a role in the repair of double-strand breaks and ssDNA gaps together with Mus81-Mms4. In this study, we show that the Srs2 and Mus81-Mms4 proteins physically interact in vitro and in vivo and we map the interaction domains within the Srs2 and Mus81 proteins. Further, we show that Srs2 plays a dual role in the stimulation of the Mus81-Mms4 nuclease activity on a variety of DNA substrates. First, Srs2 directly stimulates Mus81-Mms4 nuclease activity independent of its helicase activity. Second, Srs2 removes Rad51 from DNA to allow access of Mus81-Mms4 to cleave DNA. Concomitantly, Mus81-Mms4 inhibits the helicase activity of Srs2. Taken together, our data point to a coordinated role of Mus81-Mms4 and Srs2 in processing of recombination as well as replication intermediates. PMID:25765656

  17. Srs2 promotes Mus81–Mms4-mediated resolution of recombination intermediates

    Science.gov (United States)

    Chavdarova, Melita; Marini, Victoria; Sisakova, Alexandra; Sedlackova, Hana; Vigasova, Dana; Brill, Steven J.; Lisby, Michael; Krejci, Lumir

    2015-01-01

    A variety of DNA lesions, secondary DNA structures or topological stress within the DNA template may lead to stalling of the replication fork. Recovery of such forks is essential for the maintenance of genomic stability. The structure-specific endonuclease Mus81–Mms4 has been implicated in processing DNA intermediates that arise from collapsed forks and homologous recombination. According to previous genetic studies, the Srs2 helicase may play a role in the repair of double-strand breaks and ssDNA gaps together with Mus81–Mms4. In this study, we show that the Srs2 and Mus81–Mms4 proteins physically interact in vitro and in vivo and we map the interaction domains within the Srs2 and Mus81 proteins. Further, we show that Srs2 plays a dual role in the stimulation of the Mus81–Mms4 nuclease activity on a variety of DNA substrates. First, Srs2 directly stimulates Mus81–Mms4 nuclease activity independent of its helicase activity. Second, Srs2 removes Rad51 from DNA to allow access of Mus81–Mms4 to cleave DNA. Concomitantly, Mus81–Mms4 inhibits the helicase activity of Srs2. Taken together, our data point to a coordinated role of Mus81–Mms4 and Srs2 in processing of recombination as well as replication intermediates. PMID:25765656

  18. MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering

    DEFF Research Database (Denmark)

    Bonde, Mads; Klausen, Michael S.

    2014-01-01

    Recombineering and multiplex automated genome engineering (MAGE) offer the possibility to rapidly modify multiple genomic or plasmid sites at high efficiencies. This enables efficient creation of genetic variants including both single mutants with specifically targeted modifications as well as combinatorial cell libraries. Manual design of oligonucleotides for these approaches can be tedious, time-consuming, and may not be practical for larger projects targeting many genomic sites. At present, the change from a desired phenotype (e.g. altered expression of a specific protein) to a designed MAGE oligo, which confers the corresponding genetic change, is performed manually. To address these challenges, we have developed the MAGE Oligo Design Tool (MODEST). This web-based tool allows designing of MAGE oligos for (i) tuning translation rates by modifying the ribosomal binding site, (ii) generating translational gene knockouts and (iii) introducing other coding or non-coding mutations, including amino acid substitutions, insertions, deletions and point mutations. The tool automatically designs oligos based on desired genotypic or phenotypic changes defined by the user, which can be used for high efficiency recombineering and MAGE. MODEST is available for free and is open to all users at http://modest.biosustain.dtu.dk.

  19. MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering.

    Science.gov (United States)

    Bonde, Mads T; Klausen, Michael S; Anderson, Mads V; Wallin, Annika I N; Wang, Harris H; Sommer, Morten O A

    2014-07-01

    Recombineering and multiplex automated genome engineering (MAGE) offer the possibility to rapidly modify multiple genomic or plasmid sites at high efficiencies. This enables efficient creation of genetic variants including both single mutants with specifically targeted modifications as well as combinatorial cell libraries. Manual design of oligonucleotides for these approaches can be tedious, time-consuming, and may not be practical for larger projects targeting many genomic sites. At present, the change from a desired phenotype (e.g. altered expression of a specific protein) to a designed MAGE oligo, which confers the corresponding genetic change, is performed manually. To address these challenges, we have developed the MAGE Oligo Design Tool (MODEST). This web-based tool allows designing of MAGE oligos for (i) tuning translation rates by modifying the ribosomal binding site, (ii) generating translational gene knockouts and (iii) introducing other coding or non-coding mutations, including amino acid substitutions, insertions, deletions and point mutations. The tool automatically designs oligos based on desired genotypic or phenotypic changes defined by the user, which can be used for high efficiency recombineering and MAGE. MODEST is available for free and is open to all users at http://modest.biosustain.dtu.dk. PMID:24838561

  20. Photoinduced molecular dissociation and photoinduced recombination mediated by superfluid helium nanodroplets.

    Science.gov (United States)

    Kautsch, Andreas; Koch, Markus; Ernst, Wolfgang E

    2015-04-29

    We have investigated photoinduced chemical reaction dynamics of cold, isolated Cr2 molecules in helium nanodroplets (HeN), exploiting the quantum state specific spatial separation of solvated and surface locations on the droplet. The molecules are excited to achieve dissociation to a ground state (a(7)S3) and a metastable state (a(5)S2) atom. State specific spatial separation, in combination with efficient translational cooling to avoid ejection, causes the ground state atom to be solvated inside the droplet while the metastable atom migrates to the surface. A barrier between the two reactants formed by the HeN prevents recombination. We apply a resonance-enhanced multiphoton ionization scheme including the transition of the surface atom as well as a two-laser scheme including the transition of the solvated atom in order to verify the locations and separation of the dissociation products. Furthermore, ionization of the a(5)S2 surface atom triggers solvation followed by geminate recombination with the a(7)S3 atom, which is verified by the detection of Cr2(+) molecular ions. For small Cr clusters, our results indicate that they may be composed of chromium dimers that exhibit the same dissociation behavior. PMID:25894482

  1. Homologous recombination-mediated gene targeting in the liverwort Marchantia polymorpha L.

    OpenAIRE

    Kimitsune Ishizaki; Yasuyo Johzuka-Hisatomi; Sakiko Ishida; Shigeru Iida; Takayuki Kohchi

    2013-01-01

    The liverwort Marchantia polymorpha is an emerging model organism on account of its ideal characteristics for molecular genetics in addition to occupying a crucial position in the evolution of land plants. Here we describe a method for gene targeting by applying a positive/negative selection system for reduction of non-homologous random integration to an efficient Agrobacterium-mediated transformation system using M. polymorpha sporelings. The targeting efficiency was evaluated by knocking ou...

  2. Direct interferon-?-mediated protection caused by a recombinant coxsackievirus B3

    International Nuclear Information System (INIS)

    Coxsackievirus B3 (CVB3) is one of the most important causes of viral myocarditis. Cytokines are involved in the control of CVB3 replication and pathogenesis. Local expression of specific cytokines by recombinant CVB3 confers prevention of virus-caused myocarditis. Expression of IFN-? by CVB3(IFN-?) protected BALB/c and C57BL/6 mice when the lethal infection with the highly pathogenic CVB3H3 variant was given directly after or prior to CVB3(IFN-?) inoculation by decreasing the viral load and spread as well as tissue destruction. This direct effect was not restricted to the homologous virus. In vitro, cocultivation of CVB3(IFN-?)-infected cells induced a reduction of CVB3H3 replication and virus-induced cytopathogenicity

  3. The role of IGF-binding proteins in mediating the effects of recombinant human IGF-I on insulin requirements in type 1 diabetes mellitus.

    OpenAIRE

    Crowne, EC; Samra, JS; Cheetham, T.; Acerini, CL; WATTS, A; Holly, JM; Dunger, DB

    2001-01-01

    To determine the role of IGF-binding proteins in mediating the direct effects of recombinant human IGF-I on insulin requirements in type 1(insulin-dependent) diabetes mellitus, overnight changes in IGF-I, IGF-II, and IGF-binding protein-1, -2, and -3, collected under euglycemic conditions, were compared in nine subjects after double blind, randomized, sc administration of recombinant human IGF-I (40 microg/kg) or placebo at 1800 h. On both nights a somatostatin analog infusion (300 ng/kg x h)...

  4. Suppression of mutagenesis by Rad51D-mediated homologous recombination

    Energy Technology Data Exchange (ETDEWEB)

    Hinz, J M; Tebbs, R S; Wilson, P F; Nham, P B; Salazar, E P; Nagasawa, H; Urbin, S S; Thompson, L H

    2005-11-15

    Homologous recombinational repair (HRR) restores chromatid breaks arising during DNA replication and prevents chromosomal rearrangements that can occur from the misrepair of such breaks. In vertebrates, five Rad51 paralogs are identified that contribute in a nonessential but critical manner to HRR efficiency. We constructed and characterized a Rad51D knockout cell line in widely studied CHO cells. The rad51d mutant (51D1) displays sensitivity to a wide spectrum of induced DNA damage, indicating the broad relevance of HRR to genotoxicity. Untreated 51D1 cells exhibit {approx}5-fold elevated chromosomal breaks, a 12-fold increased rate of hprt mutation, and 4- to 10-fold increased rates of gene amplification at the dhfr and CAD loci, respectively. These results explicitly show the quantitative importance of HHR in preventing these types genetic alterations, which are associated with carcinogenesis. Thus, HRR copes in an error-free manner with spontaneous DNA damage encountered during DNA replication, and Rad51D is essential for this fidelity.

  5. Imaging of human sodium-iodide symporter gene expression mediated by recombinant adenovirus in skeletal muscle of living rats

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Hyun Suk; Park, Seong-Wook [Department of Internal Medicine (Cardiology), Asan Medical Center, University of Ulsan College of Medicine, 388-1 Pungnap-dong, Songpa-gu, 138-736, Seoul (Korea); Lee, Heuiran; Kim, Sung Jin [Department of Microbiology, University of Ulsan College of Medicine, Seoul (Korea); Lee, Won Woo [Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam (Korea); Department of Nuclear Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul (Korea); Yang, You-Jung; Moon, Dae Hyuk [Department of Nuclear Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul (Korea)

    2004-09-01

    We evaluated the feasibility of non-invasive imaging of recombinant adenovirus-mediated human sodium-iodide symporter (hNIS) gene expression by {sup 99m}TcO{sub 4}{sup -} scintigraphy in skeletal muscle of rats. Replication-defective recombinant adenovirus encoding hNIS gene [Rad-CMV-hNIS 5 x 10{sup 7}, 2 x 10{sup 8} or 1 x 10{sup 9} plaque forming units (pfu)] or {beta}-galactosidase gene (Rad-CMV-LacZ 1 x 10{sup 9} pfu) was injected into the right biceps femoris muscle of rats (n=5-6 for each group). Three days after gene transfer, scintigraphy was performed using a gamma camera 30 min after injection of {sup 99m}TcO{sub 4}{sup -} (1.85 MBq). An additional two rats injected with 1 x 10{sup 9} pfu of Rad-CMV-hNIS underwent {sup 99m}TcO{sub 4}{sup -} scintigraphy with sodium perchlorate. After the imaging studies, rats were sacrificed for assessment of the biodistribution of {sup 99m}TcO{sub 4}{sup -} and measurement of hNIS mRNA expression. In all the rats injected with 1 x 10{sup 9} pfu of Rad-CMV-hNIS, hNIS expression was successfully imaged by {sup 99m}TcO{sub 4}{sup -} scintigraphy, while rats injected with Rad-CMV-LacZ or lower doses of Rad-CMV-hNIS failed to show uptake. The biodistribution studies indicated that a significantly different amount of {sup 99m}TcO{sub 4}{sup -} was retained in the liver (p<0.001) and the right muscle (p<0.05), with the highest uptake in rats injected with 1 x 10{sup 9} pfu of Rad-CMV-hNIS. The muscular hNIS mRNA level quantified by real-time reverse transcription-polymerase chain reaction was significantly higher in rats injected with 1 x 10{sup 9} pfu of Rad-CMV-hNIS (p<0.05), with a positive correlation with the imaging counts (r=0.810, p<0.05) and the biodistribution (r=0.847, p<0.001). Hot spots in rats injected with 1 x 10{sup 9} pfu of Rad-CMV-hNIS were specifically inhibited by sodium perchlorate. This study illustrated that {sup 99m}TcO{sub 4}{sup -} scintigraphy can monitor Rad-CMV-hNIS-mediated gene expression in skeletal muscle of rats, non-invasively and quantitatively. (orig.)

  6. Imaging of human sodium-iodide symporter gene expression mediated by recombinant adenovirus in skeletal muscle of living rats

    International Nuclear Information System (INIS)

    We evaluated the feasibility of non-invasive imaging of recombinant adenovirus-mediated human sodium-iodide symporter (hNIS) gene expression by 99mTcO4- scintigraphy in skeletal muscle of rats. Replication-defective recombinant adenovirus encoding hNIS gene [Rad-CMV-hNIS 5 x 107, 2 x 108 or 1 x 109 plaque forming units (pfu)] or ?-galactosidase gene (Rad-CMV-LacZ 1 x 109 pfu) was injected into the right biceps femoris muscle of rats (n=5-6 for each group). Three days after gene transfer, scintigraphy was performed using a gamma camera 30 min after injection of 99mTcO4- (1.85 MBq). An additional two rats injected with 1 x 109 pfu of Rad-CMV-hNIS underwent 99mTcO4- scintigraphy with sodium perchlorate. After the imaging studies, rats were sacrificed for assessment of the biodistribution of 99mTcO4- and measurement of hNIS mRNA expression. In all the rats injected with 1 x 109 pfu of Rad-CMV-hNIS, hNIS expression was successfully imaged by 99mTcO4- scintigraphy, while rats injected with Rad-CMV-LacZ or lower doses of Rad-CMV-hNIS failed to show uptake. The biodistribution studies indicated that a significantly different amount of 99mTcO4- was retained in the liver (p9 pfu of Rad-CMV-hNIS. The muscular hNIS mRNA level quantified by real-time reverse transcription-polymerase chain reaction was significantly higher in rats injected with 1 x 109 pfu of Rad-CMV-hNIS (p9 pfu of Rad-CMV-hNIS were specifically inhibited by sodium perchlorate. This study illustrated that 99mTcO4- scintigraphy can monitor Rad-CMV-hNIS-mediated gene expression in skeletal muscle of rats, non-invasively and quantitatively. (orig.)

  7. Crystallization and Preliminary X-ray Analysis of Bacteriophasge T4 UvsY Recombination Mediator Protein

    International Nuclear Information System (INIS)

    Bacteriophage T4 UvsY protein is considered to be the prototype of recombination mediator proteins, a class of proteins which assist in the loading of recombinases onto DNA. Wild-type and Se-substituted UvsY protein have been expressed and purified and crystallized by hanging-drop vapor diffusion. The crystals diffract to 2.4 (angstrom) using in-house facilities and to 2.2 (angstrom) at NSLS, Brookhaven National Laboratory. The crystals belong to space group P422, P4222, P4212 or P42212, the ambiguity arising from pseudo-centering, with unit-cell parameters a = b = 76.93, c = 269.8 (angstrom). Previous biophysical characterization of UvsY indicates that it exists primarily as a hexamer in solution. Along with the absence of a crystallographic threefold, this suggests that the asymmetric unit of these crystals is likely to contain either three monomers, giving a solvent content of 71%, or six monomers, giving a solvent content of 41%

  8. A method for the solution of the RPA eigenvalue

    International Nuclear Information System (INIS)

    The RPA eigenvalue problem requires the diagonalization of a 2nx2n matrix. In practical calculations, n (the number of particle-hole basis states) can be a few hundred and the diagonalization of such a large non-symmetric matrix may take quite a long time. In this report we firstly discuss sufficient conditions for real and non-zero RPA eigenvalues. The presence of zero or imaginary eigenvalues is related to the relative importance of the groundstate correlations to the total interaction energy. We then rewrite the RPA eigenvalue problem for the cases where these conditions are fulfilled in a form which only requires the diagonalization of two symmetric nxn matrices. The extend to which this method can be applied when zero eigenvalues occur, is also discussed

  9. RPA-like calculations within limited particle-hole spaces

    International Nuclear Information System (INIS)

    Working in a boson formalism, we define a new class of phonon operators for RPA-like calculations. These operators remind the standard RPA ones, namely they have 'upward' and 'backward' amplitudes and an overall one-particle one-hole nature. However, their structure is more complex. As a basic feature, the vacuum of these phonon operators is characterized by only a limited (and variable at will) set of particle-hole excitations. In addition, multiphonon states constructed by repeated actions of these phonon operators on the vacuum state have a particle-hole structure never exceeding in complexity that of the vacuum itself. We discuss advantages and disadvantages deriving from the use of this new class of phonon operators and show an application of the formalism within the Lipkin model. Diagonalizations in multiphonon spaces built in terms of new and standard RPA phonon operators exhibit a faster convergence toward the exact results in the former case

  10. Recombinase Polymerase Amplification (RPA) of CaMV-35S Promoter and nos Terminator for Rapid Detection of Genetically Modified Crops

    OpenAIRE

    Chao Xu; Liang Li; Wujun Jin; Yusong Wan

    2014-01-01

    Recombinase polymerase amplification (RPA) is a novel isothermal DNA amplification and detection technology that enables the amplification of DNA within 30 min at a constant temperature of 37–42 °C by simulating in vivo DNA recombination. In this study, based on the regulatory sequence of the cauliflower mosaic virus 35S (CaMV-35S) promoter and the Agrobacterium tumefaciens nopaline synthase gene (nos) terminator, which are widely incorporated in genetically modified (GM) crops, we designe...

  11. Regulation of Rad51 recombinase presynaptic filament assembly via interactions with the Rad52 mediator and the Srs2 anti-recombinase.

    Science.gov (United States)

    Seong, Changhyun; Colavito, Sierra; Kwon, Youngho; Sung, Patrick; Krejci, Lumir

    2009-09-01

    Homologous recombination represents an important means for the error-free elimination of DNA double-strand breaks and other deleterious DNA lesions from chromosomes. The Rad51 recombinase, a member of the RAD52 group of recombination proteins, catalyzes the homologous recombination reaction in the context of a helical protein polymer assembled on single-stranded DNA (ssDNA) that is derived from the nucleolytic processing of a primary lesion. The assembly of the Rad51-ssDNA nucleoprotein filament, often referred to as the presynaptic filament, is prone to interference by the single-strand DNA-binding factor replication protein A (RPA). The Saccharomyces cerevisiae Rad52 protein facilitates presynaptic filament assembly by helping to mediate the displacement of RPA from ssDNA. On the other hand, disruption of the presynaptic filament by the Srs2 helicase leads to a net exchange of Rad51 for RPA. To understand the significance of protein-protein interactions in the control of Rad52- or Srs2-mediated presynaptic filament assembly or disassembly, we have examined two rad51 mutants, rad51 Y388H and rad51 G393D, that are simultaneously ablated for Rad52 and Srs2 interactions and one, rad51 A320V, that is differentially inactivated for Rad52 binding for their biochemical properties and also for functional interactions with Rad52 or Srs2. We show that these mutant rad51 proteins are impervious to the mediator activity of Rad52 or the disruptive function of Srs2 in concordance with their protein interaction defects. Our results thus provide insights into the functional significance of the Rad51-Rad52 and Rad51-Srs2 complexes in the control of presynaptic filament assembly and disassembly. Moreover, our biochemical studies have helped identify A320V as a separation-of-function mutation in Rad51 with regards to a differential ablation of Rad52 interaction. PMID:19605344

  12. Cell cycle-specific UNG2 phosphorylations regulate protein turnover, activity and association with RPA

    DEFF Research Database (Denmark)

    Hagen, Lars; Kavli, Bodil

    2008-01-01

    Human UNG2 is a multifunctional glycosylase that removes uracil near replication forks and in non-replicating DNA, and is important for affinity maturation of antibodies in B cells. How these diverse functions are regulated remains obscure. Here, we report three new phosphoforms of the non-catalytic domain that confer distinct functional properties to UNG2. These are apparently generated by cyclin-dependent kinases through stepwise phosphorylation of S23, T60 and S64 in the cell cycle. Phosphorylation of S23 in late G1/early S confers increased association with replication protein A (RPA) and replicating chromatin and markedly increases the catalytic turnover of UNG2. Conversely, progressive phosphorylation of T60 and S64 throughout S phase mediates reduced binding to RPA and flag UNG2 for breakdown in G2 by forming a cyclin E/c-myc-like phosphodegron. The enhanced catalytic turnover of UNG2 p-S23 likely optimises the protein to excise uracil along with rapidly moving replication forks. Our findings may aid further studies of how UNG2 initiates mutagenic rather than repair processing of activation-induced deaminase-generated uracil at Ig loci in B cells.

  13. Recombinase polymerase amplification (RPA) of CaMV-35S promoter and nos terminator for rapid detection of genetically modified crops.

    Science.gov (United States)

    Xu, Chao; Li, Liang; Jin, Wujun; Wan, Yusong

    2014-01-01

    Recombinase polymerase amplification (RPA) is a novel isothermal DNA amplification and detection technology that enables the amplification of DNA within 30 min at a constant temperature of 37-42 °C by simulating in vivo DNA recombination. In this study, based on the regulatory sequence of the cauliflower mosaic virus 35S (CaMV-35S) promoter and the Agrobacterium tumefaciens nopaline synthase gene (nos) terminator, which are widely incorporated in genetically modified (GM) crops, we designed two sets of RPA primers and established a real-time RPA detection method for GM crop screening and detection. This method could reliably detect as few as 100 copies of the target molecule in a sample within 15-25 min. Furthermore, the real-time RPA detection method was successfully used to amplify and detect DNA from samples of four major GM crops (maize, rice, cotton, and soybean). With this novel amplification method, the test time was significantly shortened and the reaction process was simplified; thus, this method represents an effective approach to the rapid detection of GM crops. PMID:25310647

  14. Recombinase Polymerase Amplification (RPA of CaMV-35S Promoter and nos Terminator for Rapid Detection of Genetically Modified Crops

    Directory of Open Access Journals (Sweden)

    Chao Xu

    2014-10-01

    Full Text Available Recombinase polymerase amplification (RPA is a novel isothermal DNA amplification and detection technology that enables the amplification of DNA within 30 min at a constant temperature of 37–42 °C by simulating in vivo DNA recombination. In this study, based on the regulatory sequence of the cauliflower mosaic virus 35S (CaMV-35S promoter and the Agrobacterium tumefaciens nopaline synthase gene (nos terminator, which are widely incorporated in genetically modified (GM crops, we designed two sets of RPA primers and established a real-time RPA detection method for GM crop screening and detection. This method could reliably detect as few as 100 copies of the target molecule in a sample within 15–25 min. Furthermore, the real-time RPA detection method was successfully used to amplify and detect DNA from samples of four major GM crops (maize, rice, cotton, and soybean. With this novel amplification method, the test time was significantly shortened and the reaction process was simplified; thus, this method represents an effective approach to the rapid detection of GM crops.

  15. Genome engineering and direct cloning of antibiotic gene clusters via phage ?BT1 integrase-mediated site-specific recombination in Streptomyces

    Science.gov (United States)

    Du, Deyao; Wang, Lu; Tian, Yuqing; Liu, Hao; Tan, Huarong; Niu, Guoqing

    2015-01-01

    Several strategies have been used to clone large DNA fragments directly from bacterial genome. Most of these approaches are based on different site-specific recombination systems consisting of a specialized recombinase and its target sites. In this study, a novel strategy based on phage ?BT1 integrase-mediated site-specific recombination was developed, and used for simultaneous Streptomyces genome engineering and cloning of antibiotic gene clusters. This method has been proved successful for the cloning of actinorhodin gene cluster from Streptomyces coelicolor M145, napsamycin gene cluster and daptomycin gene cluster from Streptomyces roseosporus NRRL 15998 at a frequency higher than 80%. Furthermore, the system could be used to increase the titer of antibiotics as we demonstrated with actinorhodin and daptomycin, and it will be broadly applicable in many Streptomyces. PMID:25737113

  16. Genome engineering and direct cloning of antibiotic gene clusters via phage ?BT1 integrase-mediated site-specific recombination in Streptomyces.

    Science.gov (United States)

    Du, Deyao; Wang, Lu; Tian, Yuqing; Liu, Hao; Tan, Huarong; Niu, Guoqing

    2015-01-01

    Several strategies have been used to clone large DNA fragments directly from bacterial genome. Most of these approaches are based on different site-specific recombination systems consisting of a specialized recombinase and its target sites. In this study, a novel strategy based on phage ?BT1 integrase-mediated site-specific recombination was developed, and used for simultaneous Streptomyces genome engineering and cloning of antibiotic gene clusters. This method has been proved successful for the cloning of actinorhodin gene cluster from Streptomyces coelicolor M145, napsamycin gene cluster and daptomycin gene cluster from Streptomyces roseosporus NRRL 15998 at a frequency higher than 80%. Furthermore, the system could be used to increase the titer of antibiotics as we demonstrated with actinorhodin and daptomycin, and it will be broadly applicable in many Streptomyces. PMID:25737113

  17. Smc5–Smc6 mediate DNA double-strand-break repair by promoting sister-chromatid recombination

    Science.gov (United States)

    De Piccoli, Giacomo; Cortes-Ledesma, Felipe; Ira, Gregory; Torres-Rosell, Jordi; Uhle, Stefan; Farmer, Sarah; Hwang, Ji-Young; Machin, Felix; Ceschia, Audrey; McAleenan, Alexandra; Cordon-Preciado, Violeta; Clemente-Blanco, Andrés; Vilella-Mitjana, Felip; Ullal, Pranav; Jarmuz, Adam; Leitao, Beatriz; Bressan, Debra; Dotiwala, Farokh; Papusha, Alma; Zhao, Xiaolan; Myung, Kyungjae; Haber, James E.; Aguilera, Andrés; Aragón, Luis

    2015-01-01

    DNA double-strand breaks (DSB) can arise during DNA replication, or after exposure to DNA-damaging agents, and their correct repair is fundamental for cell survival and genomic stability. Here, we show that the Smc5–Smc6 complex is recruited to DSBs de novo to support their repair by homologous recombination between sister chromatids. In addition, we demonstrate that Smc5–Smc6 is necessary to suppress gross chromosomal rearrangements. Our findings show that the Smc5–Smc6 complex is essential for genome stability as it promotes repair of DSBs by error-free sister-chromatid recombination (SCR), thereby suppressing inappropriate non-sister recombination events. PMID:16892052

  18. The role of IGF-binding proteins in mediating the effects of recombinant human IGF-I on insulin requirements in type 1 diabetes mellitus.

    Science.gov (United States)

    Crowne, E C; Samra, J S; Cheetham, T; Acerini, C L; Watts, A; Holly, J M; Dunger, D B

    2001-08-01

    To determine the role of IGF-binding proteins in mediating the direct effects of recombinant human IGF-I on insulin requirements in type 1(insulin-dependent) diabetes mellitus, overnight changes in IGF-I, IGF-II, and IGF-binding protein-1, -2, and -3, collected under euglycemic conditions, were compared in nine subjects after double blind, randomized, sc administration of recombinant human IGF-I (40 microg/kg) or placebo at 1800 h. On both nights a somatostatin analog infusion (300 ng/kg x h) suppressed endogenous GH production, and three timed discrete GH pulses (total, 0.029 IU/kg x night) ensured identical GH levels. After recombinant human IGF-I administration, IGF-I levels and the IGF-I/IGF-binding protein-3 ratio increased [mean +/- SEM:IGF-I, 401 +/- 22 ng/ml; placebo, 256 +/- 20 ng/ml (P = 0.0002); IGF-I, 0.108 +/- 0.006; placebo, 0.074 +/- 0.004 (P = 0.0003), respectively], and insulin requirements decreased (IGF-I, 0.12 +/- 0.03; placebo, 0.23 +/- 0.03 U/kg x min; P = 0.008). The normal within-individual inverse relationships between insulin and IGF-binding protein-1 levels were observed (lag time 2 h: r = -0.34; P < 0.01). Yet despite reduced free insulin levels (8.5 +/- 1.5; placebo, 12.2 +/- 1.2 mU/liter; P = 0.03), IGF-binding protein-1 levels were reduced after recombinant human IGF-I administration (53.7 +/- 6.8; placebo, 82.2 +/- 11.8 ng/ml; P = 0.008). The largest reductions in free insulin levels after recombinant human IGF-I and thus putative improvement in insulin sensitivity occurred in subjects with the smallest increase in the plasma IGF-I/IGF-binding protein-3 ratio (r = 0.7; P = 0.03). Taken together, these data are consistent with the hypothesis that transcapillary movement of IGF-I (perhaps mediated by IGF-binding protein-1), out of the circulation facilitates altered insulin sensitivity. These data have important implications for risk-benefit assessment of recombinant human IGF-I therapy in type 1 diabetes mellitus. PMID:11502796

  19. Srs2 and RecQ homologs cooperate in mei-3-mediated homologous recombination repair of Neurospora crassa

    OpenAIRE

    Suzuki, Keiichiro; Kato, Akihiro; Sakuraba, Yoshiyuki; Inoue, Hirokazu

    2005-01-01

    Homologous recombination and post-replication repair facilitate restart of stalled or collapsed replication forks. The SRS2 gene of Saccharomyces cerevisiae encodes a 3?–5? DNA helicase that functions both in homologous recombination repair and in post-replication repair. This study identifies and characterizes the SRS2 homolog in Neurospora crassa, which we call mus-50. A knockout mutant of N.crassa, mus-50, is sensitive to several DNA-damaging agents and genetic analyses indicate that...

  20. Variational RPA for the Mie resonance in jellium

    OpenAIRE

    Bertsch, G. F.; Guet, C.; Hagino, . K.

    2003-01-01

    The surface plasmon in simple metal clusters is red-shifted from the Mie frequency, the energy shift being significantly larger than the usual spill-out correction. Here we develop a variational approach to the RPA collective excitations. Using a simple trial form, we obtain analytic expressions for the energy shift beyond the spill-out contribution. We find that the additional red shift is proportional to the spill-out correction and can have the same order of magnitude.

  1. Giant resonances using realistic interactions and second RPA

    International Nuclear Information System (INIS)

    The Unitary Correlation Operator Method (UCOM) considers explicitly the short-range correlations induced in nuclei by the nucleon-nucleon (NN) interaction and provides a way to derive a universal, phase-shift equivalent effective NN potential starting from a realistic one. The correlated potential can then be used within standard many-body methods and tractable Hilbert spaces. Recent applications have shown that first-order RPA with a two-body UCOM potential can not, in general, reproduce quantitatively the properties of Giant Resonances (GRs), due to missing higher-order configurations and long-range correlations as well as neglected three-body terms in the Hamiltonian. In this work we employ a UCOM interaction in Second RPA (SRPA) calculations of GRs. We find that the inclusion of second-order configurations - which effectively dress the underlying single-particle states with self-energy insertions - produces sizable corrections. These appear essential for a realistic description of GRs when using the UCOM. We argue that effects of higher than second order should be negligible. Therefore, UCOM-SRPA emerges as a promising tool for consistent calculations of GRs in closed-shell nuclei. This is an interesting development, since SRPA can accommodate more physics than RPA (e.g., fragmentation). Remaining discrepancies due to missing three-body terms and self-consistency issues of the model are discussed

  2. Random-Matrix Approach to RPA equations. I

    CERN Document Server

    Barillier-Pertuisel, X; Weidenmüller, H A

    2008-01-01

    We study the RPA equations in their most general form by taking the matrix elements appearing in the RPA equations as random. This yields either a unitarily or an orthogonally invariant random-matrix model which is not of the Cartan type. The average spectrum of the model is studied with the help of a generalized Pastur equation. Two independent parameters govern the behaviour of the system: The strength $\\alpha^2$ of the coupling between positive- and negative-energy states and the distance between the origin and the centers of the two semicircles that describe the average spectrum for $\\alpha^2 = 0$, the latter measured in units of the equal radii of the two semicircles. With increasing $\\alpha^2$, positive- and negative-energy states become mixed and ever more of the spectral strength of the positive-energy states is transferred to those at negative energy, and vice versa. The two semicircles are deformed and pulled toward each other. As they begin to overlap, the RPA equations yield non--real eigenvalues:...

  3. DNA recombination during PCR.

    OpenAIRE

    Meyerhans, A.; Vartanian, J P; Wain-Hobson, S.

    1990-01-01

    PCR co-amplification of two distinct HIV1 tat gene sequences lead to the formation of recombinant DNA molecules. The frequency of such recombinants, up to 5.4% of all amplified molecules, could be decreased 2.7 fold by a 6 fold increase in Taq DNA polymerase elongation time. Crossover sites mapped essentially to three discrete regions suggesting specific Taq DNA polymerase pause or termination sites. PCR mediated recombination may be a problem when studying heterogeneous genetic material such...

  4. p16INK4a impairs homologous recombination-mediated DNA repair in human papillomavirus-positive head and neck tumors.

    Science.gov (United States)

    Dok, Rüveyda; Kalev, Peter; Van Limbergen, Evert Jan; Asbagh, Layka Abbasi; Vázquez, Iria; Hauben, Esther; Sablina, Anna; Nuyts, Sandra

    2014-03-15

    The p16INK4a protein is a principal cyclin-dependent kinase inhibitor that decelerates the cell cycle. Abnormally high levels of p16INK4a are commonly observed in human papillomavirus (HPV)-positive head and neck squamous cell carcinomas (HNSCC). We and others found that p16INK4a overexpression is associated with improved therapy response and survival of patients with HNSCC treated with radiotherapy. However, the functional role of p16INK4a in HNSCC remains unexplored. Our results implicate p16INK4a in regulation of homologous recombination-mediated DNA damage response independently from its role in control of the cell cycle. We found that expression of p16INK4a dramatically affects radiation sensitivity of HNSCC cells. p16INK4a overexpression impairs the recruitment of RAD51 to the site of DNA damage in HPV-positive cells by downregulating of cyclin D1 protein expression. Consistent with the in vitro findings, immunostaining of HNSCC patient samples revealed that high levels p16INK4a expression significantly correlated with decreased cyclin D1 expression. In summary, these findings reveal an unexpected function of p16INK4a in homologous recombination-mediated DNA repair response and imply p16INK4a status as an independent marker to predict response of patients with HNSCC to radiotherapy. PMID:24473065

  5. CYP3A5-mediated metabolism of midazolam in recombinant systems is highly sensitive to NADPH-cytochrome P450 reductase activity.

    Science.gov (United States)

    Christensen, Hege; Hestad, Anette L; Molden, Espen; Mathiesen, Liv

    2011-01-01

    Data from in vitro drug metabolism studies with recombinant enzyme systems are frequently used to predict human drug metabolism in vivo. However, for the CYP3A probe substrate midazolam (MDZ), considerable variability in enzyme kinetic parameters has been observed in different in vitro studies. The aim of this study was to explore the effect of varying activities of the electron donor NADPH-cytochrome P450 reductase (CPR) on CYP3A5-mediated metabolism of MDZ. Microsomes with similar levels of CYP3A5 but 12-fold difference in CPR activity showed a 30-fold difference in intrinsic clearance for the formation of 1'-OH-MDZ. Significantly higher K(m) and lower V(max) for the formation of 1'-OH-MDZ were found in microsomes with low CPR activity compared with microsomes with higher CPR activity (P?=?0.024 and 0.001). In the microsomes with lowest CPR activity, the formation of 1'-OH-MDZ displayed Michaelis-Menten kinetics, whereas substrate inhibition was observed in the two preparations with higher CPR activity. The present study shows that the CPR activity in different recombinant enzyme preparations is crucial for in vitro CYP3A5-mediated clearance of MDZ. This suggests that the CPR activity of enzyme preparations could be an important factor for the ability of in vitro data to predict human drug metabolism in vivo. PMID:20954901

  6. Transfer of the symbiotic plasmid of Rhizobium etli CFN42 requires cointegration with p42a, which may be mediated by site-specific recombination.

    Science.gov (United States)

    Brom, Susana; Girard, Lourdes; Tun-Garrido, Cristina; García-de los Santos, Alejandro; Bustos, Patricia; González, Víctor; Romero, David

    2004-11-01

    Plasmid p42a from Rhizobium etli CFN42 is self-transmissible and indispensable for conjugative transfer of the symbiotic plasmid (pSym). Most pSym transconjugants also inherit p42a. pSym transconjugants that lack p42a always contain recombinant pSyms, which we designated RpSyms*. RpSyms* do not contain some pSym segments and instead have p42a sequences, including the replication and transfer regions. These novel recombinant plasmids are compatible with wild-type pSym, incompatible with p42a, and self-transmissible. The symbiotic features of derivatives simultaneously containing a wild-type pSym and an RpSym* were analyzed. Structural analysis of 10 RpSyms* showed that 7 shared one of the two pSym-p42a junctions. Sequencing of this common junction revealed a 53-bp region that was 90% identical in pSym and p42a, including a 5-bp central region flanked by 9- to 11-bp inverted repeats reminiscent of bacterial and phage attachment sites. A gene encoding an integrase-like protein (intA) was localized downstream of the attachment site on p42a. Mutation or the absence of intA abolished pSym transfer from a recA mutant donor. Complementation with the wild-type intA gene restored transfer of pSym. We propose that pSym-p42a cointegration is required for pSym transfer; cointegration may be achieved either through homologous recombination among large reiterated sequences or through IntA-mediated site-specific recombination between the attachment sites. Cointegrates formed through the site-specific system but resolved through RecA-dependent recombination or vice versa generate RpSyms*. A site-specific recombination system for plasmid cointegration is a novel feature of these large plasmids and implies that there is unique regulation which affects the distribution of pSym in nature due to the role of the cointegrate in conjugative transfer. PMID:15516565

  7. Suppression of human alpha-globin gene expression mediated by the recombinant adeno-associated virus 2-based antisense vectors

    OpenAIRE

    1994-01-01

    We sought to investigate the usefulness of the adeno-associated virus 2 (AAV)-based vectors to suppress the excess production of the human alpha-globin gene product towards developing a treatment modality for beta-thalassemia since accumulation of free alpha-globin reduces the lifespan of red blood cells in these patients. We constructed recombinant AAV virions containing the human alpha-globin gene sequences in antisense orientation driven by the herpesvirus thymidine kinase (TK) promoter, t...

  8. Effects of recombinant adenovirus mediated retinoblastoma gene 94 combined with ?-ray on growth of esophageal carcinoma cells

    International Nuclear Information System (INIS)

    Objective: To study the combined effect of exogenous recombinant adenovirus-medicated retinoblastoma gene 94 (Ad-Rb94) combined with ?-ray on the growth of esophageal carcinoma cells. Methods: Cell culture were randomly divided into 5 groups: control group, recombinant adenovirus vector containing ?-galactosidase gene (Ad-LacZ) group, Ad-Rb94 group, ?-ray radiation group and Ad-Rb94 combined with ?-ray radiation group. EC109 cells were transfected by Ad-Rb94 and exposed to 4 Gy 137Cs ?-ray irradiation 6 hours after transfection. The inhibition rate of EC109 cells were detected by MTT assay. Results: EC109 cells transfected with Ad-Rb94 group, ?-ray radiation group and Ad-Rb94 combined with ?-ray radiation group were all inhibited. The inhibition rate of Ad-Rb94 combined with ?ray radiation group reached (40.30%±4.2%), significantly higher than Ad-Rb94 group (18.3±0.4%) and ?-ray radiation group (27.40%±2.9%) (?2=7.91, ?2=5.82, P2=5.12, P<0.05). Conclusion: The recombinant Ad-Rb94 gene transfection combined with ?-ray shows the synergism for the inhibition of the growth of EC109 cells. (authors)

  9. Srs2 and RecQ homologs cooperate in mei-3-mediated homologous recombination repair of Neurospora crassa.

    Science.gov (United States)

    Suzuki, Keiichiro; Kato, Akihiro; Sakuraba, Yoshiyuki; Inoue, Hirokazu

    2005-01-01

    Homologous recombination and post-replication repair facilitate restart of stalled or collapsed replication forks. The SRS2 gene of Saccharomyces cerevisiae encodes a 3'-5' DNA helicase that functions both in homologous recombination repair and in post-replication repair. This study identifies and characterizes the SRS2 homolog in Neurospora crassa, which we call mus-50. A knockout mutant of N.crassa, mus-50, is sensitive to several DNA-damaging agents and genetic analyses indicate that it is epistatic with mei-3 (RAD51 homolog), mus-11 (RAD52 homolog), mus-48 (RAD55 homolog) and mus-49 (RAD57 homolog), suggesting a role for mus-50 in homologous recombination repair. However, epistasis evidence has presented that MUS50 does not participate in post-replication repair in N.crassa. Also, the N.crassa mus-25 (RAD54 homolog) mus-50 double mutant is viable, which is in contrast to the lethal phenotype of the equivalent rad54 srs2 mutant in S.cerevisiae. Tetrad analysis revealed that mus-50 in combination with mutations in two RecQ homologs, qde-3 and recQ2, is lethal, and this lethality is suppressed by mutation in mei-3, mus-11 or mus-25. Evidence is also presented for the two independent pathways for recovery from camptothecin-induced replication fork arrest: one pathway is dependent on QDE3 and MUS50 and the other pathway is dependent on MUS25 and RECQ2. PMID:15800214

  10. Optimized effective potential method and application to static RPA correlation

    Science.gov (United States)

    Fukazawa, Taro; Akai, Hisazumi

    2015-03-01

    The optimized effective potential (OEP) method is a promising technique for calculating the ground state properties of a system within the density functional theory. However, it is not widely used as its computational cost is rather high and, also, some ambiguity remains in the theoretical framework. In order to overcome these problems, we first introduced a method that accelerates the OEP scheme in a static RPA-level correlation functional. Second, the Krieger–Li–Iafrate (KLI) approximation is exploited to solve the OEP equation. Although seemingly too crude, this approximation did not reduce the accuracy of the description of the magnetic transition metals (Fe, Co, and Ni) examined here, the magnetic properties of which are rather sensitive to correlation effects. Finally, we reformulated the OEP method to render it applicable to the direct RPA correlation functional and other, more precise, functionals. Emphasis is placed on the following three points of the discussion: (i) level-crossing at the Fermi surface is taken into account; (ii) eigenvalue variations in a Kohn–Sham functional are correctly treated; and (iii) the resultant OEP equation is different from those reported to date.

  11. Characterization of transferrin receptor-mediated endocytosis and cellular iron delivery of recombinant human serum transferrin from rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Zhang Deshui

    2012-11-01

    Full Text Available Abstract Background Transferrin (TF plays a critical physiological role in cellular iron delivery via the transferrin receptor (TFR-mediated endocytosis pathway in nearly all eukaryotic organisms. Human serum TF (hTF is extensively used as an iron-delivery vehicle in various mammalian cell cultures for production of therapeutic proteins, and is also being explored for use as a drug carrier to treat a number of diseases by employing its unique TFR-mediated endocytosis pathway. With the increasing concerns over the risk of transmission of infectious pathogenic agents of human plasma-derived TF, recombinant hTF is preferred to use for these applications. Here, we carry out comparative studies of the TFR binding, TFR-mediated endocytosis and cellular iron delivery of recombinant hTF from rice (rhTF, and evaluate its suitability for biopharmaceutical applications. Result Through a TFR competition binding affinity assay with HeLa human cervic carcinoma cells (CCL-2 and Caco-2 human colon carcinoma cells (HTB-37, we show that rhTF competes similarly as hTF to bind TFR, and both the TFR binding capacity and dissociation constant of rhTF are comparable to that of hTF. The endocytosis assay confirms that rhTF behaves similarly as hTF in the slow accumulation in enterocyte-like Caco-2 cells and the rapid recycling pathway in HeLa cells. The pulse-chase assay of rhTF in Caco-2 and HeLa cells further illustrates that rice-derived rhTF possesses the similar endocytosis and intracellular processing compared to hTF. The cell culture assays show that rhTF is functionally similar to hTF in the delivery of iron to two diverse mammalian cell lines, HL-60 human promyelocytic leukemia cells (CCL-240 and murine hybridoma cells derived from a Sp2/0-Ag14 myeloma fusion partner (HB-72, for supporting their proliferation, differentiation, and physiological function of antibody production. Conclusion The functional similarity between rice derived rhTF and native hTF in their cellular iron delivery, TFR binding, and TFR-mediated endocytosis and intracellular processing support that rice-derived rhTF can be used as a safe and animal-free alternative to serum hTF for bioprocessing and biopharmaceutical applications.

  12. Microhomology-mediated End Joining and Homologous Recombination share the initial end resection step to repair DNA double-strand breaks in mammalian cells.

    Science.gov (United States)

    Truong, Lan N; Li, Yongjiang; Shi, Linda Z; Hwang, Patty Yi-Hwa; He, Jing; Wang, Hailong; Razavian, Niema; Berns, Michael W; Wu, Xiaohua

    2013-05-01

    Microhomology-mediated end joining (MMEJ) is a major pathway for Ku-independent alternative nonhomologous end joining, which contributes to chromosomal translocations and telomere fusions, but the underlying mechanism of MMEJ in mammalian cells is not well understood. In this study, we demonstrated that, distinct from Ku-dependent classical nonhomologous end joining, MMEJ--even with very limited end resection--requires cyclin-dependent kinase activities and increases significantly when cells enter S phase. We also showed that MMEJ shares the initial end resection step with homologous recombination (HR) by requiring meiotic recombination 11 homolog A (Mre11) nuclease activity, which is needed for subsequent recruitment of Bloom syndrome protein (BLM) and exonuclease 1 (Exo1) to DNA double-strand breaks (DSBs) to promote extended end resection and HR. MMEJ does not require S139-phosphorylated histone H2AX (?-H2AX), suggesting that initial end resection likely occurs at DSB ends. Using a MMEJ and HR competition repair substrate, we demonstrated that MMEJ with short end resection is used in mammalian cells at the level of 10-20% of HR when both HR and nonhomologous end joining are available. Furthermore, MMEJ is used to repair DSBs generated at collapsed replication forks. These studies suggest that MMEJ not only is a backup repair pathway in mammalian cells, but also has important physiological roles in repairing DSBs to maintain cell viability, especially under genomic stress. PMID:23610439

  13. Seamless stitching of biosynthetic gene cluster containing type I polyketide synthases using Red/ET mediated recombination for construction of stably co-existing plasmids.

    Science.gov (United States)

    Su, Chun; Zhao, Xin-Qing; Wang, Hai-Na; Qiu, Rong-Guo; Tang, Li

    2015-01-10

    Type I polyketides are natural products with diverse functions that are important for medical and agricultural applications. Manipulation of large biosynthetic gene clusters containing type I polyketide synthases (PKS) for heterologous expression is difficult due to the existence of conservative sequences of PKS in multiple modules. Red/ET mediated recombination has permitted rapid manipulation of large fragments; however, it requires insertion of antibiotic selection marker in the cassette, raising the problem of interference of expression by leaving "scar" sequence. Here, we report a method for precise seamless stitching of large polyketide biosynthetic gene cluster using a 48.4kb fragment containing type I PKS involved in fostriecin biosynthesis as an example. rpsL counter-selection was used to assist seamless stitching of large fragments, where we have overcome both the size limitations and the restriction on endonuclease sites during the Red/ET recombination. The compatibility and stability of the co-existing vectors (p184 and pMT) which respectively accommodate 16kb and 32.4kb inserted fragments were demonstrated. The procedure described here is efficient for manipulation of large DNA fragments for heterologous expression. PMID:25311549

  14. Cultured mast cells from asthmatic patients and controls respond with similar sensitivity to recombinant Der P2 induced, IgE-mediated activation

    DEFF Research Database (Denmark)

    Krohn, Inge Jacoba Maria Kortekaas; Sverrild, Asger

    2013-01-01

    The function of cultured mast cells may depend on genetic or environmental influence on the stem cell donor. This study investigates whether asthma or atopy in the donor influenced the growth and sensitivity of mast cells cultured from asthma patients and healthy controls under identical conditions. Mast cells were cultured from peripheral blood from twelve patients with an objectively confirmed asthma diagnosis and eight healthy subjects. During the last 2 weeks of culture, mast cells were incubated with IL-4 and 80 kU/L recombinant human IgE containing two clones (7%+7%) specific for mite allergen Der p2. The sensitivity of IgE-mediated activation of mast cells was investigated as Fc?RI-mediated up-regulation of CD63. Ten subjects were atopic, defined as a positive skin prick test (>3 mm) to at least one of ten common allergens. After activation with recombinant Der p2, the maximum CD63 Median Fluorescence Intensity was 20 456 ± 1640 (SE) for asthma patients and 22 275 ± 1971 (SE) for controls (ns). The fraction of CD63 positive cells was 54.4% in asthma patients and 48.4% in controls (ns). The allergen concentration inducing 50% of the maximal CD63 response was similar in asthma patients (-0.4795 log ng/mL ± 0.092 (SE)) and controls (-0.6351 log ng/mL ± 0.083, ns) and in atopic and non-atopic subjects. When cultured, sensitised and activated under identical conditions, mast cells from allergic asthmatics and healthy controls respond similar. Activation of cultured mast cells appears to depend on culture conditions (IL-4, IgE) rather than on donor status as atopy and asthma. This article is protected by copyright. All rights reserved.

  15. Cultured mast cells from patients with asthma and controls respond with similar sensitivity to recombinant Der p2-induced, IgE-mediated activation

    DEFF Research Database (Denmark)

    Krohn, I K; Sverrild, A

    2013-01-01

    The function of cultured mast cells may depend on genetic or environmental influence on the stem cell donor. This study investigates whether asthma or atopy in the donor influenced the growth and sensitivity of mast cells cultured from patients with asthma and healthy controls under identical conditions. Mast cells were cultured from peripheral blood from twelve patients with an objectively confirmed asthma diagnosis and eight healthy subjects. During the last 2 weeks of culture, mast cells were incubated with IL-4 and 80 kU/l recombinant human IgE containing two clones (7% + 7%) specific for mite allergen Der p2. The sensitivity of IgE-mediated activation of mast cells was investigated as Fc?RI-mediated upregulation of CD63. Ten subjects were atopic, defined as a positive skin prick test (>3 mm) to at least one of ten common allergens. After activation with recombinant Der p2, the maximum CD63 median fluorescence intensity was 20 456 ± 1640 (SE) for patients with asthma and 22,275 ± 1971 (SE) for controls (ns). The fraction of CD63 positive cells was 54.4% in patients with asthma and 48.4% in controls (ns). The allergen concentration inducing 50% of the maximal CD63 response was similar in patients with asthma [-0.4795 log ng/ml ± 0.092 (SE)] and controls (-0.6351 log ng/ml ± 0.083, ns) and in atopic and non-atopic subjects. When cultured, sensitized and activated under identical conditions, mast cells from allergic asthmatics and healthy controls respond similar. Activation of cultured mast cells appears to depend on culture conditions (IL-4, IgE) rather than on donor status as atopy and asthma.

  16. Quantal Brownian Motion from RPA dynamics: The master and Fokker-Planck equations

    International Nuclear Information System (INIS)

    From the purely quantal RPA description of the damped harmonic oscillator and of the corresponding Brownian Motion within the full space (phonon subspace plus reservoir), a master equation (as well as a Fokker-Planck equation) for the reduced density matrix (for the reduced Wigner function, respectively) within the phonon subspace is extracted. The RPA master equation agrees with the master equation derived by the time-dependent perturbative approaches which utilize Tamm-Dancoff Hilbert spaces and invoke the rotating wave approximation. Since the RPA yields a full, as well as a contracted description, it can account for both the kinetic and the unperturbed oscillator momenta. The RPA description of the quantal Brownian Motion contrasts with the descriptions provided by the time perturbative approaches whether they invoke or not the rotating wave approximation. The RPA description also contrasts with the phenomenological phase space quantization. (orig.)

  17. Microhomology-mediated end joining in fission yeast is repressed by pku70 and relies on genes involved in homologous recombination.

    Science.gov (United States)

    Decottignies, Anabelle

    2007-07-01

    Two DNA repair pathways are known to mediate DNA double-strand-break (DSB) repair: homologous recombination (HR) and nonhomologous end joining (NHEJ). In addition, a nonconservative backup pathway showing extensive nucleotide loss and relying on microhomologies at repair junctions was identified in NHEJ-deficient cells from a variety of organisms and found to be involved in chromosomal translocations. Here, an extrachromosomal assay was used to characterize this microhomology-mediated end-joining (MMEJ) mechanism in fission yeast. MMEJ was found to require at least five homologous nucleotides and its efficiency was decreased by the presence of nonhomologous nucleotides either within the overlapping sequences or at DSB ends. Exo1 exonuclease and Rad22, a Rad52 homolog, were required for repair, suggesting that MMEJ is related to the single-strand-annealing (SSA) pathway of HR. In addition, MMEJ-dependent repair of DSBs with discontinuous microhomologies was strictly dependent on Pol4, a PolX DNA polymerase. Although not strictly required, Msh2 and Pms1 mismatch repair proteins affected the pattern of MMEJ repair. Strikingly, Pku70 inhibited MMEJ and increased the minimal homology length required for efficient MMEJ. Overall, this study strongly suggests that MMEJ does not define a distinct DSB repair mechanism but reflects "micro-SSA." PMID:17483423

  18. Atmospheric-pressure plasma jet induces DNA double-strand breaks that require a Rad51-mediated homologous recombination for repair in Saccharomyces cerevisiae.

    Science.gov (United States)

    Lee, Yoonna; Kim, Kangil; Kang, Kyu-Tae; Lee, Jong-Soo; Yang, Sang Sik; Chung, Woo-Hyun

    2014-10-15

    Non-thermal plasma generated under atmospheric pressure produces a mixture of chemically reactive molecules and has been developed for a number of biomedical applications. Recently, plasma jet has been proposed as novel cancer therapies based on the observation that free radicals generated by plasma jet induce mitochondria-mediated apoptotic cell death. We show here that air plasma jet induces DNA double-strand breaks (DSBs) in yeast chromosomes leading to genomic instability and loss of viability, which are alleviated by Rad51, the yeast homolog of Escherichiacoli RecA recombinase, through DNA damage repair by a homologous recombination (HR) process. Hypersensitivity of rad51 mutant to air plasma was not restored by antioxidant treatment unlike sod1 mutant that was highly sensitive to reactive oxygen species (ROS) challenge, suggesting that plasma jet induces DSB-mediated cell death independent of ROS generation. These results may provide a new insight into the mechanism of air plasma jet-induced cell death. PMID:25086216

  19. Thermal nuclear pairing within the self-consistent quasiparticle RPA

    CERN Document Server

    Dang, N Dinh

    2010-01-01

    The self-consistent quasiparticle RPA (SCQRPA) is constructed to study the effects of fluctuations on pairing properties in nuclei at finite temperature and z-projection M of angular momentum. Particle-number projection (PNP) is taken into account within the Lipkin-Nogami method. Several issues such as the smoothing of superfluid-normal phase transition, thermally assisted pairing in hot rotating nuclei, extraction of the nuclear pairing gap using an improved odd-even mass difference are discussed. A novel approach of embedding the PNP SCQRPA eigenvalues in the canonical and microcanonical ensembles is proposed and applied to describe the recent empirical thermodynamic quantities for iron, molybdenum, dysprosium, and ytterbium isotopes.

  20. Correlation between frequency of non-allelic homologous recombination and homology properties: evidence from homology-mediated CNV mutations in the human genome.

    Science.gov (United States)

    Peng, Zhen; Zhou, Weichen; Fu, Wenqing; Du, Renqian; Jin, Li; Zhang, Feng

    2015-03-01

    Non-allelic homologous recombination (NAHR) is one of the key mechanisms of DNA rearrangement. NAHR occurring between direct homologous repeats can generate genomic copy number variation (CNV) and make significant contributions to both genome evolution and human diseases such as cancer. Intriguingly, previous observations on the rare CNVs at certain genomic disorder loci suggested that NAHR frequency could be dependent on homology properties. However, such a correlation remains unclear at the other NAHR-mediated CNV loci, especially the common CNVs in human populations. Different from the rare CNVs associated with genomic disorders, it is challenging to identify de novo NAHR events at common CNV loci. Therefore, our previously proposed statistic M was employed in estimating relative mutation rate for the NAHR-mediated CNVs in human populations. By utilizing generalized regression neural network and principal component analysis in studying 4330 CNVs ascertained in 3 HapMap populations, we identified the CNVs mediated by NAHR between paired segmental duplications (SDs) and further revealed the correlations between SD properties and NAHR probability. SD length and inter-SD distance were shown to make major contributions to the occurrence of NAHR, whereas chromosomal position and sequence similarity of paired SDs are also involved in NAHR. An integrated effect of SD properties on NAHR frequency was revealed for the common CNVs in human populations. These observations can be well explained by ectopic synapsis in NAHR together with our proposed model of chromosomal compression/extension/looping (CCEL) for homology mis-pairing. Our findings showed the important roles of SDs in NAHR and human genomic evolution. PMID:25324539

  1. Inhibition of tumor growth in xenograft nude mice model by recombinant adenovirus-mediated human endostatin gene therapy

    International Nuclear Information System (INIS)

    Objective: To investigate the expression efficiency of adenovirus-mediated human endostatin gene (Ad/hEndo) in vitro and in vivo, and to observe its inhibition of tumor growth in xenografted nude mice model. Methods: The expression efficiency of endostatin gene was examined during the infection of Ad/hEndo in nasopharyngeal carcinoma (NPC) CNE-2 cell and human umbilical vein endothelial cells (ECV304) by Western blot and ELISA. The effect on inhibition of growth of NPC CNE-2 xenografted tumors in Balb/c nude mice was observed after administration with Ad/hEndo. The serum endostatin levels were measured by ELISA, and intratumoral microvessel density (MVD) was analyzed. Results: Western blot and ELISA analysis demonstrated high level of endostatin expression in CNE2 and ECV304 cells infected with Ad/ hEndo. The highest concentration of endostatin in supernatant reached 588.34 ng/ml after 72 h of Ad/hEndo infection at a MOI of 20. Ad/hEndo significantly inhibited growth of xenografted CNE-2 (nasopharyngeal carcinoma) tumors with inhibition rate of 46.43% (Ad/ hEndo group versus Ad/LacZ group, t=2.226, P<0.05) and 49.70% (Ad/ hEndo group versus DMEM group, t=2.254, P<0.05), respectively. In the study group, serum levels of endostatin in treated group were much higher than that of control groups for 3- and 7- day term. The intratumoral MVD also decreased significantly in the treated tumors (9.95±2.20 versus 18.54±1.80, t=7.158, P< 0.05). Conclusion: Adenovirus-mediated h0.05). Conclusion: Adenovirus-mediated human endostatin gene had obtained high level of expression in vitro and in vivo, and significantly inhibited the angiogenesis and growth of CNE-2 xenografted tumors in nude mice

  2. A subject with a novel type I bare lymphocyte syndrome has tapasin deficiency due to deletion of 4 exons by Alu-mediated recombination.

    Science.gov (United States)

    Yabe, Toshio; Kawamura, Sumiyo; Sato, Masako; Kashiwase, Koichi; Tanaka, Hidenori; Ishikawa, Yoshihide; Asao, Yoji; Oyama, Junko; Tsuruta, Kazuma; Tokunaga, Katsushi; Tadokoro, Kenji; Juji, Takeo

    2002-08-15

    HLA class I expression depends on the formation of a peptide-loading complex composed of class I heavy chain; beta(2)-microglobulin; the transporter associated with antigen processing (TAP); and tapasin, which links TAP to the heavy chain. Defects in TAP result in a class I deficiency called the type I bare lymphocyte syndrome (BLS). In the present study, we examined a subject with a novel type I BLS who does not exhibit apparent TAP abnormalities but who has a tapasin defect. The subject's TAPASIN gene has a 7.4-kilobase deletion between introns 3 and 7; an Alu repeat-mediated unequal homologous recombination may be the cause of the deletion. No tapasin polypeptide was detected in the subject's cells. The cell surface class I expression level in tapasin-deficient cells was markedly reduced but the reduction was not as profound as in TAP-deficient cells. These results suggest that tapasin deficiency is another cause of type I BLS. PMID:12149238

  3. An open-shell RPA by means of seniority and reduced isospin projections

    International Nuclear Information System (INIS)

    A real-particle RPA formalism for open-shell nuclei is presented which can be applied to both isoscalar vibration and isospin-splitting isovector vibration. In order to keep boson approximation meaningful even under the existence of partially-occupied orbits, one-body operator for description of normal mode is modified by means of projection operators which project onto wave functions with stretched seniority, defined in the isospin formalism, and with specific reduced isospin. Validity of boson approximation ensures bermiticity of RPA equations of motion and clarifies association with quasi-particle RPA. Nuclear excitation arising from the rearrangement of nucleons in the same partially-occupied orbit can be taken into account, while it is impossible in the RPA by Rowe who adopted one-body operators themselves for description of normal mode. (author)

  4. An in vivo assay for conjugation-mediated recombination yields novel results for Streptomyces plasmid pIJ101.

    Science.gov (United States)

    Ducote, Matthew J; Pettis, Gregg S

    2006-05-01

    Efficient transmission of circular plasmids in Streptomyces spp. proceeds by an uncharacterized mechanism that requires a cis-acting locus of transfer (clt) and often only a single plasmid-encoded protein. For circular plasmids from other bacteria, site- and strand-specific nicking takes place at the cis-acting oriT locus via the plasmid-encoded relaxase protein prior to single-strand transfer. Using an assay originally designed to demonstrate that conjugative transfer of plasmids containing tandem oriT loci results in the formation of a single composite oriT locus, we show here that an analogous construct involving the pIJ101 clt locus apparently does not undergo such a conjugation-mediated event during plasmid transfer. Our results, which imply that streptomycete plasmids are transferred by a functionally distinct mechanism compared to oriT-containing plasmids, are complementary to other recent evidences that support a novel double-stranded model for streptomycete circular plasmid transfer. PMID:16388851

  5. Giant resonances in exotic spherical nuclei within the RPA approach with the Gogny force

    OpenAIRE

    Péru, S.; Berger, J. F.; Bortignon, P. F.

    2005-01-01

    Theoretical results for giant resonances in the three doubly magic exotic nuclei $^{78}$Ni, $^{100}$Sn and $^{132}$Sn are obtained from Hartree-Fock (HF) plus Random Phase Approximation (RPA) calculations using the D1S parametrization of the Gogny two-body effective interaction. Special attention is paid to full consistency between the HF field and the RPA particle-hole residual interaction. The results for the exotic nuclei, on average, appear similar to those of stable one...

  6. Gap junction-mediated bystander effect in primary cultures of human malignant gliomas with recombinant expression of the HSVtk gene.

    Science.gov (United States)

    Asklund, Thomas; Appelskog, Ioulia B; Ammerpohl, Ole; Langmoen, Iver A; Dilber, M Sirac; Aints, Alar; Ekström, Tomas J; Almqvist, Per M

    2003-04-01

    The ability of herpes simplex virus type 1 thymidine kinase (HSV-tk)-expressing cells incubated with ganciclovir (GCV) to induce cytotoxicity in neighboring HSV-tk-negative (bystander) cells has been well documented. Although it has been suggested that this bystander cell killing occurs via the transfer of phosphorylated GCV, the mechanism(s) of this bystander effect and the importance of gap junctions for the effect of prodrug/suicide gene therapy in primary human glioblastoma cells remains elusive. Surgical biopsies of malignant gliomas were used to establish explant primary cultures. Proliferating tumor cells were characterized immunohistochemically and found to express glial tumor markers including nestin, vimentin, glial fibrillary acidic protein (GFAP), S-100, and gap junction protein connexin 43 (Cx43). Western blot analysis revealed the presence of phosphorylated isoforms of Cx43 and Calcein/DiI fluorescent dye transfer showed evidence of efficient gap junction communication (GJC). In order to study the effect(s) of prodrug/suicide gene therapy in these cultures, human glioblastoma cell cultures were transfected with the HSVtk gene for transient or stable expression. Ganciclovir treatment of these cultures led to >90% of cells dead within 1 week. Eradication of cells could be inhibited by the addition of alpha-glycyrrhetinic acid (AGA), a GJC inhibitor. In parallel experiments, AGA decreased the immunodetection of phosphorylated Cx43 as analyzed by Western blot and inhibited fluorescent dye transfer. In conclusion, these observations are consistent with GJC as the mediator of the bystander effect in primary cultures of human glioblastoma cells by the transfer of phosphorylated GCV from HSVtk gene transfected cells to untransfected ones. PMID:12651152

  7. Recombinant Programming

    OpenAIRE

    Pawlak, Renaud; Cuesta, Carlos; Younessi, Houman

    2004-01-01

    This research report presents a promising new approach to computation called Recombinant Programming. The novelty of our approach is that it separates the program into two layers of computation: the recombination and the interpretation layer. The recombination layer takes sequences as inputs and allows the programmer to recombine these sequences through the definition of cohesive code units called extensions. The output of such recombination is a mesh that can be used by the interpretation la...

  8. Low-energy effective interactions beyond cRPA by the functional renormalization group

    Science.gov (United States)

    Kinza, Michael; Honerkamp, Carsten

    2015-03-01

    In the derivation of low-energy effective models for solids targeting the bands near the Fermi level, the constrained random phase approximation (cRPA) has become an appreciated tool to compute the effective interactions. Here we present applications of a constrained functional renormalization group (cfRG) scheme to two simple multi-band systems and compare the resulting effective interactions to the cRPA. The employed wick-ordered fRG scheme generalizes the cRPA approach by including all interaction channels in an unbiased way. First we consider a multiband model for graphene, where we integrate out the ?-bands to get an effective theory for ?-bands. It turns out that terms beyond cRPA are strongly suppressed by xy -plane reflection-symmetry of the bands and that in our model, the cRPA stays qualitatively correct even if one breaks this symmetry slightly. The second example is a model for a Cu-O-chain, where we consider an effective theory for the Cu 3d-orbital. Here the fRG data points to relevant corrections compared to the cRPA results.

  9. Perfluorochemical (PFC liquid enhances recombinant adenovirus vector-mediated viral interleukin-10 (AdvIL-10 expression in rodent lung

    Directory of Open Access Journals (Sweden)

    Zimmerman Jerry J

    2007-05-01

    Full Text Available Abstract Adenovirus and cationic liposome mediated transfer of Interleukin-10 (IL-10, a potent anti-inflammatory cytokine, has been shown to decrease pro-inflammatory cytokine levels and overall lung inflammation in models of lung transplantation and injury. Limitations to current approaches of IL-10 gene therapy include poor vector delivery methods and pro-inflammatory properties of human IL-10 under certain conditions. We hypothesize that using perfluorochemical (PFC liquid to deliver the highly homologous viral IL-10 (vIL-10, which is predominantly anti-inflammatory with minimal pro-inflammatory activities, can potentially be a more effective strategy to combat inflammatory lung diseases. In this study, we compare the use of PFC liquid versus aerosolized method to deliver adenovirus encoding the vIL-10 gene (AdvIL-10 in C57Bl6 mice. Detectable vIL-10 levels were measured from bronchoalveolar lavage fluid and lung homogenates at one, four, ten and thirty days after AdvIL-10. Furthermore, we determined if use of PFC liquid could allow for the use of a lower dose of AdvIL-10 by comparing the levels of detectable vIL-10 at different doses of AdvIL-10 delivered +/- PFC liquid. Results showed that PFC liquid enhanced detectable vIL-10 by up to ten fold and that PFC liquid allowed the use of ten-fold less vector. PFC liquid increased detectable vIL-10 in lung homogenates at all time points; however, the increase in detectable vIL-10 in BAL fluid peaked at four days and was no longer evident by thirty days after intratracheal instillation. In summary, this is the first report utilizing PFC liquid to enhance the delivery of a potentially therapeutic molecule, vIL-10. We believe this strategy can be used to perform future studies on the use of the predominantly anti-inflammatory vIL-10 to treat inflammatory lung diseases.

  10. Two levels of interference in mouse meiotic recombination.

    Science.gov (United States)

    de Boer, Esther; Stam, Piet; Dietrich, Axel J J; Pastink, Albert; Heyting, Christa

    2006-06-20

    During meiosis, homologous chromosomes (homologs) undergo recombinational interactions, which can yield crossovers (COs) or noncrossovers. COs exhibit interference; they are more evenly spaced along the chromosomes than would be expected if they were placed randomly. The protein complexes involved in recombination can be visualized as immunofluorescent foci. We have analyzed the distribution of such foci along meiotic prophase chromosomes of the mouse to find out when interference is imposed and whether interference manifests itself at a constant level during meiosis. We observed strong interference among MLH1 foci, which mark CO positions in pachytene. Additionally, we detected substantial interference well before this point, in late zygotene, among MSH4 foci, and similarly, among replication protein A (RPA) foci. MSH4 foci and RPA foci both mark interhomolog recombinational interactions, most of which do not yield COs in the mouse. Furthermore, this zygotene interference did not depend on SYCP1, which is a transverse filament protein of mouse synaptonemal complexes. Interference is thus not specific to COs but may occur in other situations in which the spatial distribution of events has to be controlled. Differences between the distributions of MSH4/RPA foci and MLH1 foci along synaptonemal complexes might suggest that CO interference occurs in two successive steps. PMID:16766662

  11. Antitumor effect and mechanism of action of a tumor-targeting recombinant human tumor necrosis factor-? fusion protein mediated by urokinase.

    Science.gov (United States)

    Dai, You-Chao; Yang, Si-Min; Wang, Xin; Zhou, Yong-Jun; Hou, Gan; Huang, Di-Nan

    2015-06-01

    The aim of this study was to investigate the effect of the tumor?targeting recombinant human tumor necrosis factor (rhTNF)?? fusion protein mediated by urokinase on Sl80 tumor?bearing mice, as well as to explore its mechanisms of action. Furthermore, the study aimed to observe the effect of the protein on liver and kidney function. rhTNF?? fusion protein prokaryotic expression vectors were constructed using genetic engineering techniques, and were introduced into Escherichia coli. Expression of the fusion protein was induced, and it was then separated and purified in order to determine its cytotoxic activity on L929 cells. Kunming mice were randomly divided into four groups after being inoculated with S180 tumor cells. The groups were then injected with saline (control group, group S), or saline with 0.1 µg/ml fusion protein (low dose group, group L), 0.2 µg/ml fusion protein (middle dose group, group M) or 0.3 µg/ml (high dose group, group H). The mice were sacrificed after 12 days and liver [mg/kg; (liver weight/body weight) x 1,000] and kidney [mg/kg; (kidney weight/body weight) x 1,000] indices, tumor weight, the percentage reduction in mean tumor size, and the levels of alanine transaminase (ALT), albumin (ALB), creatinine (Cr) and blood urea nitrogen (BUN) in each group of mice were determined. In addition, the levels of urokinase?type plasminogen activator (uPA), the expression of bcl?2, bax and vascular endothelial growth factor (VEGF), and the percentage of apoptotic cells were measured with an enzyme?linked immunosorbent assay, streptavidin?biotin complex of immunohistochemistry and terminal deoxynucleotidyl transferase?mediated dUTP nick end labeling, respectively. The fusion protein significantly inhibited the growth of S180 tumor cells in vivo in a dose?dependent manner. With an increase in the dose of fusion protein, ALT, uPA, bcl?2 and VEGF levels decreased, and ALB levels increased. However, liver and kidney indices and bax expression were not significantly altered. Cr and BUN levels did not change significantly in the low and middle dose groups, but did increase in the high dose group. Compared with the control group, the percentage of apoptotic cells in the high?dose group was significantly higher. In conclusion, the fusion protein significantly inhibited S180 tumor growth in a mouse model, possibly by reducing the levels of uPA, bcl?2 and VEGF. There was a mildly toxic effect on the kidneys with the high dose, but a protective effect in the liver. PMID:25672264

  12. Recombinant AAV-mediated HSVtk gene transfer with direct intratumoral injections and Tet-On regulation for implanted human breast cancer

    Directory of Open Access Journals (Sweden)

    Sai-Qun LUO

    2006-03-01

    Full Text Available Abstract Background HSVtk/ganciclovir (GCV gene therapy has been extensively studied in tumors and relies largely on the gene expression of HSVtk. Most studies, however, have failed to demonstrate any significant benefit of a controlled gene expression strategy in cancer treatment. The Tet-On system is commonly used to regulate gene expression following Dox induction. We have evaluated the antitumor effect of HSVtk/ganciclovir gene therapy under Tet-On regulation by means of adeno-associated virus-2 (AAV-2-mediated HSVtk gene transfer with direct intratumoral injections in mice bearing breast cancer tumors. Methods Recombinant adeno-associated virus-2 (rAAV was constructed and transduced into MCF-7 cell line. GCV treatment to the rAAV infected MCF-7 cells was performed by MTT assay under the doxycycline (Dox induction or without Dox induction at a vp (viral particle number of ?104 /cell. The virus was administered intratumorally to nude mice that had also received GCV intraperitoneally. The antitumor effects were evaluated by measuring tumor regression and histological analysis. Results We have demonstrated that GCV treatment to the infected MCF-7 cells under the Dox induction was of more inhibited effects than those without Dox induction at ?104 vp/cell. In ex vivo experiments, tumor growth of BALB/C nude mice breast cancer was retarded after rAAV-2/HSVtk/Tet-On was injected into the tumors under the Dox induction. Infiltrating cells were also observed in tumors after Dox induction followed by GCV treatment and cells were profoundly damaged. The expression of HSVtk gene in MCF-7 cells and BALB/C nude mice tumors was up-regulated by Tet-On under Dox induction with reverse transcription-PCR (RT-PCR analysis. Conclusion The antitumor effect of rAAV-mediated HSVtk/GCV gene therapy under the Dox induction with direct intratumoral injections may be a useful treatment for breast cancer and other solid tumors.

  13. Mutations in the BRCT binding site of BRCA1 result in hyper-recombination

    Science.gov (United States)

    Dever, Seth M.; Golding, Sarah E.; Rosenberg, Elizabeth; Adams, Bret R.; Idowu, Michael O.; Quillin, John M.; Valerie, Nicholas; Xu, Bo; Povirk, Lawrence F.; Valerie, Kristoffer

    2011-01-01

    We introduced a K1702M mutation in the BRCA1 BRCT domain known to prevent the binding of proteins harboring pS-X-X-F motifs such as Abraxas-RAP80, BRIP1, and CtIP. Surprisingly, rather than impairing homologous recombination repair (HRR), expression of K1702M resulted in hyper-recombination coinciding with an accumulation of cells in S-G2 and no effect on nonhomologous end-joining. These cells also showed increased RAD51 and RPA nuclear staining. More pronounced effects were seen with a naturally occurring BRCT mutant (M1775R) that also produced elevated levels of ssDNA, in part co-localizing with RPA, in line with excessive DNA resection. M1775R induced unusual, thread-like promyelocytic leukemia (PML) nuclear bodies and clustered RPA foci rather than the typical juxtaposed RPA-PML foci seen with wild-type BRCA1. Interestingly, K1702M hyper-recombination diminished with a second mutation in the BRCA1 RING domain (I26A) known to reduce BRCA1 ubiquitin-ligase activity. These in vitro findings correlated with elevated nuclear RAD51 and RPA staining of breast cancer tissue from a patient with the M1775R mutation. Altogether, the disruption of BRCA1 (BRCT)-pS-X-X-F protein binding results in ubiquitination-dependent hyper-recombination via excessive DNA resection and the appearance of atypical PML-NBs. Thus, certain BRCA1 mutations that cause hyper-recombination instead of reduced DSB repair might lead to breast cancer. PMID:21666281

  14. RAD52 inactivation is synthetically lethal with deficiencies in BRCA1 and PALB2 in addition to BRCA2 through RAD51-mediated homologous recombination.

    Science.gov (United States)

    Lok, B H; Carley, A C; Tchang, B; Powell, S N

    2013-07-25

    Synthetic lethality is an approach to study selective cell killing based on genotype. Previous work in our laboratory has shown that loss of RAD52 is synthetically lethal with BRCA2 deficiency, while exhibiting no impact on cell growth and viability in BRCA2-proficient cells. We now show that this same synthetically lethal relationship is evident in cells with deficiencies in BRCA1 or PALB2, which implicates BRCA1, PALB2 and BRCA2 in an epistatic relationship with one another. When RAD52 was depleted in BRCA1- or PALB2-deficient cells, a severe reduction in plating efficiency was observed, with many abortive attempts at cell division apparent in the double-depleted background. In contrast, when RAD52 was depleted in a BRCA1- or PALB2-wildtype background, a negligible decrease in colony survival was observed. The frequency of ionizing radiation-induced RAD51 foci formation and double-strand break-induced homologous recombination (HR) was decreased by 3- and 10-fold, respectively, when RAD52 was knocked down in BRCA1- or PALB2-depleted cells, with minimal effect in BRCA1- or PALB2-proficient cells. RAD52 function was independent of BRCA1 status, as evidenced by the lack of any defect in RAD52 foci formation in BRCA1-depleted cells. Collectively, these findings suggest that RAD52 is an alternative repair pathway of RAD51-mediated HR, and a target for therapy in cells deficient in the BRCA1-PALB2-BRCA2 repair pathway. PMID:22964643

  15. Human recombinant interleukin-1 beta- and tumor necrosis factor alpha-mediated suppression of heparin-like compounds on cultured porcine aortic endothelial cells

    International Nuclear Information System (INIS)

    Cytokines are known to tip the balance of the coagulant-anticoagulant molecules on the endothelial cell surface toward intravascular coagulation. Their effects on endothelial cell surface-associated heparin-like compounds have not been examined yet. Incorporation of [35S]sulfate into heparan sulfate on cultured porcine aortic endothelial cells was suppressed by human recombinant interleukin-1 beta (rIL-1 beta) or tumor necrosis factor alpha (rTNF alpha) in a dose- and time-dependent manner with little effect on cell number, protein content, and [3H]leucine incorporation of cells. Maximal inhibition was achieved by incubation of cells with 100 ng/ml of rIL-1 beta or 5 ng/ml of rTNF alpha for 12-24 hours, resulting in a reduction of the synthesis of heparan sulfate on the cell surface by approximately 50%. The dose dependency was consistent with that seen in the stimulation of endothelial cell procoagulant activity by each cytokine. The suppression of heparan sulfate synthesis was sustained for at least 48 hours after pretreatment of cells with cytokines and was unchanged after the addition of indomethacin or polymyxin B. The rate of degradation of prelabeled 35S-heparan sulfate on the cell surface was not altered by cytokine treatments. Neither the size, the net negative charge, nor the proportion of the molecule with high affinity for antithrombin III of endothelial cell heparan sulfate was changed by cytokines. Furthermore, specific binding of 125I-labeled antithrombpecific binding of 125I-labeled antithrombin III to the endothelial cell surface was reduced to 40-60% of control by cytokines. In parallel with reduction in binding, antithrombin III cofactor activity was partially diminished in cytokine-treated endothelial cells. Thus, cytokine-mediated suppression of heparin-like substance on endothelial cells appears to be another cytokine-inducible endothelial effects affecting coagulation

  16. High-affinity DNA-binding domains of replication protein A (RPA) direct SMARCAL1-dependent replication fork remodeling.

    Science.gov (United States)

    Bhat, Kamakoti P; Bétous, Rémy; Cortez, David

    2015-02-13

    SMARCAL1 catalyzes replication fork remodeling to maintain genome stability. It is recruited to replication forks via an interaction with replication protein A (RPA), the major ssDNA-binding protein in eukaryotic cells. In addition to directing its localization, RPA also activates SMARCAL1 on some fork substrates but inhibits it on others, thereby conferring substrate specificity to SMARCAL1 fork-remodeling reactions. We investigated the mechanism by which RPA regulates SMARCAL1. Our results indicate that although an interaction between SMARCAL1 and RPA is essential for SMARCAL1 activation, the location of the interacting surface on RPA is not. Counterintuitively, high-affinity DNA binding of RPA DNA-binding domain (DBD) A and DBD-B near the fork junction makes it easier for SMARCAL1 to remodel the fork, which requires removing RPA. We also found that RPA DBD-C and DBD-D are not required for SMARCAL1 regulation. Thus, the orientation of the high-affinity RPA DBDs at forks dictates SMARCAL1 substrate specificity. PMID:25552480

  17. Ab initio self-consistent total-energy calculations within the EXX/RPA formalism

    Science.gov (United States)

    Nguyen, Ngoc Linh; Colonna, Nicola; de Gironcoli, Stefano

    2014-07-01

    Calculations of exact-exchange (EXX) and random phase approximation (RPA)-correlation energies within the formally exact adiabatic connection fluctuation-dissipation theorem formalism have recently been carried out for a number of isolated and condensed systems. Unfortunately, most of the applications have been done in a non-self-consistent procedure, and for several systems it has been found that RPA correlation energies may significantly depend on the choice of input single-particle wave functions. In this work, we develop an efficient approach to compute the EXX/RPA total energy self-consistently. We derive an expression for the RPA self-consistent potential based on the density functional perturbation theory and dielectric matrix approaches and implemented it within the plane-wave pseudopotential framework. The efficiency of this approach is greatly improved by exploiting an iterative procedure to compute the inverted Kohn-Sham density-density response function. We apply our implementation to study the binding energy curves and the structural properties of rare gasses such as Ar and Kr and alkaline-earth Be dimers. In addition, the EXX and RPA-correlation potentials of these systems at different dissociation distances are analyzed.

  18. High efficiency recombineering in lactic acid bacteria

    OpenAIRE

    van Pijkeren, Jan-Peter; BRITTON, ROBERT A.

    2012-01-01

    The ability to efficiently generate targeted point mutations in the chromosome without the need for antibiotics, or other means of selection, is a powerful strategy for genome engineering. Although oligonucleotide-mediated recombineering (ssDNA recombineering) has been utilized in Escherichia coli for over a decade, the successful adaptation of ssDNA recombineering to Gram-positive bacteria has not been reported. Here we describe the development and application of ssDNA recombineering in lact...

  19. A high-efficiency recombineering system with PCR-based ssDNA in Bacillus subtilis mediated by the native phage recombinase GP35.

    Science.gov (United States)

    Sun, Zhaopeng; Deng, Aihua; Hu, Ting; Wu, Jie; Sun, Qinyun; Bai, Hua; Zhang, Guoqiang; Wen, Tingyi

    2015-06-01

    Bacillus subtilis and its closely related species are important strains for industry, agriculture, and medicine. However, it is difficult to perform genetic manipulations using the endogenous recombination machinery. In many bacteria, phage recombineering systems have been employed to improve recombineering frequencies. To date, an efficient phage recombineering system for B. subtilis has not been reported. Here, we, for the first time, identified that GP35 from the native phage SPP1 exhibited a high recombination activity in B. subtilis. On this basis, we developed a high-efficiency GP35-meditated recombineering system. Taking single-stranded DNA (ssDNA) as a recombineering substrate, ten recombinases from diverse sources were investigated in B. subtilis W168. GP35 showed the highest recombineering frequency (1.71?±?0.15?×?10(-1)). Besides targeting the purine nucleoside phosphorylase gene (deoD), we also demonstrated the utility of GP35 and Beta from Escherichia coli lambda phage by deleting the alpha-amylase gene (amyE) and uracil phosphoribosyltransferase gene (upp). In all three genetic loci, GP35 exhibited a higher frequency than Beta. Moreover, a phylogenetic tree comparing the kinship of different recombinase hosts with B. subtilis was constructed, and the relationship between the recombineering frequency and the kinship of the host was further analyzed. The results suggested that closer kinship to B. subtilis resulted in higher frequency in B. subtilis. In conclusion, the recombinase from native phage or prophage can significantly promote the genetic recombineering frequency in its host, providing an effective genetic tool for constructing genetically engineered strains and investigating bacterial physiology. PMID:25750031

  20. The time course and chromosomal localization of recombination-related proteins at meiosis in the mouse are compatible with models that can resolve the early DNA-DNA interactions without reciprocal recombination.

    Science.gov (United States)

    Moens, Peter B; Kolas, Nadine K; Tarsounas, Madalena; Marcon, Edyta; Cohen, Paula E; Spyropoulos, Barbara

    2002-04-15

    During mouse meiosis, the early prophase RAD51/DMC1 recombination protein sites, which are associated with the chromosome cores and which serve as markers for ongoing DNA-DNA interactions, are in ten-fold excess of the eventual reciprocal recombinant events. Most, if not all, of these early interactions are eliminated as prophase progresses. The manner in which these sites are eliminated is the focus of this investigation. We report that these sites acquire replication protein A, RPA and the Escherichia coli MUTS homologue, MSH4p, and somewhat later the Bloom helicase, BLM, while simultaneously losing the RAD51/DMC1 component. Eventually the RPA component is also lost and BLM sites remain. At that time, the MUTL homologue, MLH1p, which is essential for reciprocal recombination in the mouse, appears in numbers and locations that correspond to the distribution of reciprocal recombination events. However, the MLH1 foci do not appear to coincide with the remaining BLM sites. The MLH1p is specifically localized to electron-microscope-defined recombination nodules. We consider the possibility that the homology-search RAD51/DMC1 complexes are involved in homologous chromosome synapsis but that most of these early DNA-DNA interactions are later resolved by the anti-recombination RPA/MSH4/BLM-topoisomerase complex, thereby preventing the formation of superfluous reciprocal recombinant events. PMID:11950880

  1. G-quadruplex formation in telomeres enhances POT1/TPP1 protection against RPA binding

    OpenAIRE

    Ray, Sujay; Bandaria, Jigar N.; Qureshi, Mohammad H.; Yildiz, Ahmet; Balci, Hamza

    2014-01-01

    This paper uses a single-molecule imaging approach based on energy transfer to study how telomeric DNA is protected against the DNA damage-signaling protein replication protein A (RPA). Telomeres terminate with a single-stranded overhang, which is protected by protection of telomere (POT1) and POT1-interacting protein 1 (TPP1) against RPA. Telomeric overhangs have a guanine-rich sequence, forming a four-stranded G-quadruplex structure. Using model telomeric DNA, we studied the competition bet...

  2. PARP-mediated Repair, Homologous Recombination, and Back-up Non-Homologous End Joining-Like Repair of Single-Strand Nicks

    OpenAIRE

    Metzger, Michael J.; Stoddard, Barry L.; Monnat, Raymond J.

    2013-01-01

    Double-strand breaks (DSBs) in chromosomal DNA can induce both homologous recombination (HR) and non-homologous recombination (NHEJ). Recently we showed that single-strand nicks induce HR with a significant reduction in toxicity and mutagenic effects associated with NHEJ. To further investigate the differences and similarities of DSB- and nick-induced repair, we used an integrated reporter system in human cells to measure HR and NHEJ produced by the homing endonuclease I-AniI and a designed ?...

  3. The time course and chromosomal localization of recombination-related proteins at meiosis in the mouse are compatible with models that can resolve the early DNA-DNA interactions without reciprocal recombination.

    OpenAIRE

    Moens, Pb; Kolas, Nk; Tarsounas, M.; Marcon, E.; Cohen, Pe; Spyropoulos, B.

    2002-01-01

    During mouse meiosis, the early prophase RAD51/DMC1 recombination protein sites, which are associated with the chromosome cores and which serve as markers for ongoing DNA-DNA interactions, are in ten-fold excess of the eventual reciprocal recombinant events. Most, if not all, of these early interactions are eliminated as prophase progresses. The manner in which these sites are eliminated is the focus of this investigation. We report that these sites acquire replication protein A, RPA and the ...

  4. Lyapunov stability and Poisson structure of the thermal TDHF and RPA equations

    International Nuclear Information System (INIS)

    The thermal TDHF equation is analyzed in the Liouville representation of quantum mechanics, where the matrix elements of the single-particle (s.p.) density ? behave as classical dynamical variables. By introducing the Lie-Poisson bracket associated with the unitary group of the s.p. Hilbert space, we show that TDHF has a hamiltonian, but non-canonical, classical form. Within this Poisson structure, either the s.p. energy or the s.p. grand potential ?(?) act as a Hamilton function. The Lyapunov stability of both the TDHF and RPA equations around a HF state then follows, since the HF approximation for thermal equilibrium is determined by minimizing ?(?). The RPA matrix in the Liouville space is expressed as the product of the Poisson tensor with the HF stability matrix, interpreted as a metric tensor generated by the entropy. This factorization displays the roles of the energy and entropy terms arising from ?(?) in the RPA dynamics, and it helps to construct the RPA modes. Several extensions are considered

  5. Recombination instability

    DEFF Research Database (Denmark)

    D'Angelo, N.

    1967-01-01

    A recombination instability is considered which may arise in a plasma if the temperature dependence of the volume recombination coefficient, alpha, is sufficiently strong. Two cases are analyzed: (a) a steady-state plasma produced in a neutral gas by X-rays or high energy electrons; and (b) an afterglow plasma.

  6. Ago2 facilitates Rad51 recruitment and DNA double-strand break repair by homologous recombination

    DEFF Research Database (Denmark)

    Gao, Min; Wei, Wei

    2014-01-01

    DNA double-strand breaks (DSBs) are highly cytotoxic lesions and pose a major threat to genome stability if not properly repaired. We and others have previously shown that a class of DSB-induced small RNAs (diRNAs) is produced from sequences around DSB sites. DiRNAs are associated with Argonaute (Ago) proteins and play an important role in DSB repair, though the mechanism through which they act remains unclear. Here, we report that the role of diRNAs in DSB repair is restricted to repair by homologous recombination (HR) and that it specifically relies on the effector protein Ago2 in mammalian cells. Interestingly, we show that Ago2 forms a complex with Rad51 and that the interaction is enhanced in cells treated with ionizing radiation. We demonstrate that Rad51 accumulation at DSB sites and HR repair depend on catalytic activity and small RNA-binding capability of Ago2. In contrast, DSB resection as well as RPA and Mre11 loading is unaffected by Ago2 or Dicer depletion, suggesting that Ago2 very likely functions directly in mediating Rad51 accumulation at DSBs. Taken together, our findings suggest that guided by diRNAs, Ago2 can promote Rad51 recruitment and/or retention at DSBs to facilitate repair by HR.

  7. Towards a unified description of ground and excited state properties: GW vs RPA and beyond

    Science.gov (United States)

    Rinke, Patrick

    2015-03-01

    In the quest for finding an ``optimal'' first principles electronic structure method, that combines accuracy and tractability with transferability across different chemical environments and dimensionalities (e.g. molecules, wires/tubes, surfaces, solids), the treatment of exchange and correlation in terms of ``exact-exchange plus correlation in the random-phase approximation (EX+cRPA)'' offers a promising avenue. Likewise one can express the same level of theory in the Green's function context through the GW approximation, which has the additional advantage that quasiparticle spectra as measured by direct and inverse photoemission become accessible. In this talk I will contrast both approaches and present the latest results from our continuous assessment. We find that self-consistent (sc) GW provides excellent charge densities, which is particularly important for charge transfer systems. Spectral properties for closed shell molecules are generally in good agreement with photoemission spectra, although a judicial choice of the starting point in perturbative G0W0 calculations can outperform scGW. Other ground state properties do not improve over EX+cRPA calculations. EX+cRPA, on the other hand, provides a good description of the ground state even for challenging cases like chemical reaction barrier heights and the f-electron metal cerium. The notorious underbinding of EX+cRPA can be corrected by going beyond RPA to renormalised second order perturbation theory (rPT2) that gives the overall most balanced performance. I will also discuss the associated rPT2 self-energy that goes beyond GW .

  8. Transformation of tobacco cpDNA with fusion E7GGG/GUS gene and homologous recombination mediated elimination of the marker gene.

    Czech Academy of Sciences Publication Activity Database

    B?íza, Jind?ich; Vlasák, Josef; Ryba, Š.; Ludvíková, V.; Niedermeierová, Hana

    Ro?. 27, ?. 2 ( 2013 ), s. 3644-3648. ISSN 1310-2818 R&D Projects: GA AV ?R IAA500960903 Institutional support: RVO:60077344 Keywords : E7GGG oncogene * chloroplast transformation * marker-free plant * homologous recombination Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.379, year: 2013

  9. Enhancement of Recombinant Adeno-Associated Virus Type 2-Mediated Transgene Expression in a Lung Epithelial Cell Line by Inhibition of the Epidermal Growth Factor Receptor

    OpenAIRE

    Andrew D Smith; Collaco, Roy F.; Trempe, James P.

    2003-01-01

    Recombinant adeno-associated viruses (rAAVs) have attracted considerable interest as gene delivery systems because they show long-term expression in vivo and transduce numerous cell types. Limitations to successful gene transduction from rAAVs have prompted investigations of a variety of treatments to enhance transgene expression from rAAV vectors. Tyrphostin-1, an epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor, dramatically enhances rAAV transgene expression. Elegant studi...

  10. Recombination-Mediated Changes in Coreceptor Usage Confer an Augmented Pathogenic Phenotype in a Nonhuman Primate Model of HIV-1-Induced AIDS?†

    Science.gov (United States)

    Nishimura, Yoshiaki; Shingai, Masashi; Lee, Wendy R.; Sadjadpour, Reza; Donau, Olivia K.; Willey, Ronald; Brenchley, Jason M.; Iyengar, Ranjini; Buckler-White, Alicia; Igarashi, Tatsuhiko; Martin, Malcolm A.

    2011-01-01

    Evolution of the env gene in transmitted R5-tropic human immunodeficiency virus type 1 (HIV-1) strains is the most widely accepted mechanism driving coreceptor switching. In some infected individuals, however, a shift in coreceptor utilization can occur as a result of the reemergence of a cotransmitted, but rapidly controlled, X4 virus. The latter possibility was studied by dually infecting rhesus macaques with X4 and R5 chimeric simian simian/human immunodeficiency viruses (SHIVs) and monitoring the replication status of each virus using specific primer pairs. In one of the infected monkeys, both SHIVs were potently suppressed by week 12 postinoculation, but a burst of viremia at week 51 was accompanied by an unrelenting loss of total CD4+ T cells and the development of clinical disease. PCR analyses of plasma viral RNA indicated an env gene segment containing the V3 region from the inoculated X4 SHIV had been transferred into the genetic background of the input R5 SHIV by intergenomic recombination, creating an X4 virus with novel replicative, serological, and pathogenic properties. These results indicate that the effects of retrovirus recombination in vivo can be functionally profound and may even occur when one of the recombination participants is undetectable in the circulation as cell-free virus. PMID:21813599

  11. Rescue of a Chlamydomonas inner-arm-dynein-deficient mutant by electroporation-mediated delivery of recombinant p28 light chain.

    Science.gov (United States)

    Hayashi, Masahito; Yanagisawa, Haru-Aki; Hirono, Masafumi; Kamiya, Ritsu

    2002-12-01

    We have recently shown that rabbit actin can be introduced by electroporation into the Chlamydomonas ida5 mutant lacking conventional actin and rescue its mutant phenotype [Hayashi et al., 2001: Cell Motil. Cytoskeleton 49:146-153]. In this study, we explored the possibility of using electroporation for functional assay of a recombinant protein. The p28 light chain of inner-arm dyneins was expressed in Escherichia coli, purified to homogeneity, and introduced by electroporation into a non-motile mutant ida4oda6 that lacks it. Because this protein was insoluble in the low ionic strength solution used in the previous study, electroporation was performed at physiological ionic strength in the presence of Ca(2+). Most cells shed their flagella after electroporation. Reflagellation took place within 3 h and up to 30% of the cells became motile, indicating that the introduced p28 retained its functional activity. Fluorescently-labeled p28 was equally effective; in this case fluorescence was observed along the flagella. The presence of Ca(2+) and deflagellation appeared to be important for efficient protein delivery, because a triple mutant with the fa1 mutation deficient in the flagellar shedding mechanism recovered motility only very poorly. Similar results were obtained with other combinations of recombinant proteins and mutants. This study thus demonstrates the feasibility of using electroporation for activity assays of recombinant proteins. PMID:12378537

  12. DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Willson Richard C

    2010-12-01

    Full Text Available Abstract Background Manufacturing large quantities of recombinant RNAs by overexpression in a bacterial host is hampered by their instability in intracellular environment. To overcome this problem, an RNA of interest can be fused into a stable bacterial RNA for the resulting chimeric construct to accumulate in the cytoplasm to a sufficiently high level. Being supplemented with cost-effective procedures for isolation of the chimera from cells and recovery of the recombinant RNA from stabilizing scaffold, this strategy might become a viable alternative to the existing methods of chemical or enzymatic RNA synthesis. Results Sequence encoding a 71-nucleotide recombinant RNA was inserted into a plasmid-borne deletion mutant of the Vibrio proteolyticus 5S rRNA gene in place of helix III - loop C segment of the original 5S rRNA. After transformation into Escherichia coli, the chimeric RNA (3×pen aRNA was expressed constitutively from E. coli rrnB P1 and P2 promoters. The RNA chimera accumulated to levels that exceeded those of the host's 5S rRNA. A novel method relying on liquid-solid partitioning of cellular constituents was developed for isolation of total RNA from bacterial cells. This protocol avoids toxic chemicals, and is therefore more suitable for large scale RNA purification than traditional methods. A pair of biotinylated 8-17 DNAzymes was used to bring about the quantitative excision of the 71-nt recombinant RNA from the chimera. The recombinant RNA was isolated by sequence-specific capture on beads with immobilized complementary deoxyoligonucleotide, while DNAzymes were recovered by biotin affinity chromatography for reuse. Conclusions The feasibility of a fermentation-based approach for manufacturing large quantities of small RNAs in vivo using a "5S rRNA scaffold" strategy is demonstrated. The approach provides a route towards an economical method for the large-scale production of small RNAs including shRNAs, siRNAs and aptamers for use in clinical and biomedical research.

  13. RPA spin-isospin nuclear response in the deep inelastic region

    International Nuclear Information System (INIS)

    The spin-isospin volume responses of a finite nucleus are evaluated in the RPA frame, utilizing a harmonic oscillator basis. Particular emphasis is given to the mixing between the longitudinal and transverse couplings, which arise at the nuclear surface. We show that it reduces somewhat the contrast between the two spin responses. We compare the calculated transverse response with the experimental one extracted from deep inelastic electron scattering

  14. Quasi-elastic scattering, RPA, 2p2h and neutrino--energy reconstruction

    CERN Document Server

    Nieves, J; Sanchez, F; Vacas, M J Vicente

    2013-01-01

    We discuss some nuclear effects, RPA correlations and 2p2h (multinucleon) mechanisms, on charged-current neutrino-nucleus reactions that do not produce a pion in the final state. We study a wide range of neutrino energies, from few hundreds of MeV up to 10 GeV. We also examine the influence of 2p2h mechanisms on the neutrino energy reconstruction.

  15. Self-consistent HF-RPA description of electron and photon nuclear reactions with Skyrme forces

    International Nuclear Information System (INIS)

    A mean-field nuclear dynamics is investigated in the analysis of nuclear electromagnetic processes at low and intermediate (q, ?) transfers. The theoretical framework is a self-consistent HF-RPA theory with Skyrme forces formulated in the one-nucleon energy continuum. We review the results obtained in the Skyrme HF-RPA model by focusing on some specific aspects of the theoretical frame and discussing their incidence in the prediction of data. Main points of interest are: (i) the quasiparticle formulation of the Skyrme HF-RPA nuclear dynamics with the identification of a quasi-particle effective mass, (ii) the gauge-invariance of the Skyrme Hamiltonian which produces nuclear electromagnetic currents satisfying the continuity equation, (iii) the excitation and decay properties of the one-nucleon energy continuum. The problems dealt with in the discussion of experimental data are the following: the quasi-deuteron effect in (?, p) and (?, n) reactions of closed shell nuclei at energies E??300 MeV, Giant Multipole Resonances versus momentum transfer in inclusive (e, e' x) responses, the reaction mechanism in polarized ( vector e, e' x) angular distributions at q?200 MeV/c, the evaluation of the missing strength in inclusive (e, e') longitudinal responses at high momentum transfer, final state interactions and missing momentum distributions in coincidence (e, e' p) reactions in the quasi-elastic region. (orig.)

  16. Self-consistent HF-RPA description of electron and photon nuclear reactions with Skyrme forces

    Science.gov (United States)

    Maria Saruis, Anna

    1993-12-01

    A mean-field nuclear dynamics is investigated in the analysis of nuclear electromagnetic processes at low and intermediate ( q, w) transfers. The theoretical framework is a self-consistent HF-RPA theory with Skyrme forces formulated in the one-nucleon energy continuum. We review the results obtained in the Skyrme HF-RPA model by focusing on some specific aspects of the theoretical frame and discussing their incidence in the prediction of data. Main points of interest are: (i) the quasiparticle formulation of the Skyrme HF-RPA nuclear dynamics with the identification of a quasi-particle effective mass, (ii) the gauge-invariance of the Skyrme Hamiltonian which produces nuclear electromagnetic currents satisfying the continuity equation, (iii) the excitation and decay properties of the one-nucleon energy continuum. The problems dealt with in the discussion of experimental data are the following: the quasi-deuteron effect in (?, p) and (?, n) reactions of closed shell nuclei at energies E? ? 300 MeV, Giant Multipole Resonances versus momentum transfer in inclusive ( e, e?x) responses, the reaction mechanism in polarized ( overlinee, e?x) angular distributions at q ? 200 {MeV}/{c}, the evaluation of the missing strength in inclusive ( e, e?) longitudinal responses at high momentum transfer, final state interactions and missing momentum distributions in coincidence ( e, e?p) reactions in the quasi-elastic region.

  17. 5' untranslated sequences modulate rapid mRNA degradation mediated by 3' AU-rich element in v-/c-fos recombinants.

    OpenAIRE

    Roy, N.; Laflamme, G.; Raymond, V.

    1992-01-01

    One major determinant of rapid mRNA decay is the presence of AU-rich sequences located in 3' untranslated regions (UTR). To assess for the contribution of upstream sequences on the activity of the 3' AU-rich destabilizing element, we have determined the decay-rates of v-/c-fos hybrid transcripts by quantitative RNA protection analysis. In a transient expression assay, v-/c-fos recombinants generated two mRNA populations via alternative splicing and removal of an optional intron entirely locat...

  18. Three distinct envelope domains, variably present in subgroup B feline leukemia virus recombinants, mediate Pit1 and Pit2 receptor recognition.

    OpenAIRE

    Boomer, S.; Eiden, M.; Burns, C. C.; Overbaugh, J.

    1997-01-01

    Subgroup B feline leukemia viruses (FeLV-Bs) evolve from subgroup A FeLV (FeLV-A) by recombining with portions of endogenous FeLV envelope sequences in the cat genome. The replication properties of FeLV-B are distinct from those of FeLV-A; FeLV-B infects many nonfeline cell lines and recognizes the human Pit1 (HuPit1) receptor, whereas FeLV-A infects primarily feline cells, using a distinct but as yet undefined receptor. Here, we demonstrate that some FeLV-Bs can also use human Pit2 (HuPit2) ...

  19. Independent combinatorial effect of antisense oligonucleotides and RNAi-mediated specific inhibition of the recombinant Rat P2X3 receptor

    OpenAIRE

    Hemmings-mieszczak, Maja; Dorn, Gabriele; Natt, Franc?ois J.; Hall, Jonathan; Wishart, William L.

    2003-01-01

    Synthetic 21-bp-long short interfering RNAs (siRNA) can stimulate sequence-specific mRNA degradation in mammalian cell cultures, a process referred to as RNA interference (RNAi). In the present study, the potential of RNAi was compared to the traditional antisense approach, acting mainly via RnaseH, for targeting the recombinant rat pain-related cation-channel P2X3 expressed in CHO-K1 and a rat brain tumour-derived cell line, 33B. Downregulation of the P2X3 receptor was evaluated at the mRNA,...

  20. Baculovirus-mediated gene transfer and recombinant protein expression do not interfere with insulin dependent phosphorylation of PKB/Akt in human SHSY-5Y and C3A cells

    Directory of Open Access Journals (Sweden)

    Selander Martin

    2007-02-01

    Full Text Available Abstract Background Recombinant adenovirus vectors and transfection agents comprising cationic lipids are widely used as gene delivery vehicles for functional expression in cultured cells. Consequently, these tools are utilized to investigate the effects of functional over-expression of proteins on insulin mediated events. However, we have previously reported that cationic lipid reagents cause a state of insulin unresponsiveness in cell cultures. In addition, we have found that cultured cells often do not respond to insulin stimulation following adenovirus treatment. Infection with adenovirus compromises vital functions of the host cell leading to the activation of protein kinases central to insulin signalling, such as protein kinase B/Akt. Therefore, we investigated the effect of adenovirus infection on insulin unresponsiveness by means of Akt activation in cultured cells. Moreover, we investigated the use of baculovirus as a heterologous viral gene delivery vehicle to circumvent these phenomena. Since the finding that baculovirus can efficiently transduce mammalian cells, the applications of this viral system in gene delivery has greatly expanded and one advantage is the virtual absence of cytotoxicity in mammalian cells. Results We show that infection of human neuroblastoma SHSY-5Y and liver C3A cells with recombinant adenovirus results in the activation of Akt in a dose dependent manner. In addition, this activation makes treated cells unresponsive to insulin stimulation as determined by an apparent lack of differential phosphorylation of Akt on serine-473. Our data further indicate that the use of recombinant baculovirus does not increase the phosphorylation of Akt in SHSY-5Y and C3A cells. Moreover, following infection with baculovirus, SHSY-5Y and C3A cells respond to insulin by means of phosphorylation of Akt on serine-473 in the same manner as uninfected cells. Conclusion Widely-used adenovirus vectors for gene delivery cause a state of insulin unresponsiveness in human SHSY-5Y and C3A cells in culture due to the activation of central protein kinases of the insulin signalling pathway. This phenomenon can be avoided when studying insulin signalling by using recombinant baculovirus as a heterologous viral expression system. In addition, our data may contribute to an understanding of the molecular mechanisms underlying baculovirus infection of human cells.

  1. SETD2-Dependent Histone H3K36 Trimethylation Is Required for Homologous Recombination Repair and Genome Stability

    Directory of Open Access Journals (Sweden)

    Sophia X. Pfister

    2014-06-01

    Full Text Available Modulating chromatin through histone methylation orchestrates numerous cellular processes. SETD2-dependent trimethylation of histone H3K36 is associated with active transcription. Here, we define a role for H3K36 trimethylation in homologous recombination (HR repair in human cells. We find that depleting SETD2 generates a mutation signature resembling RAD51 depletion at I-SceI-induced DNA double-strand break (DSB sites, with significantly increased deletions arising through microhomology-mediated end-joining. We establish a presynaptic role for SETD2 methyltransferase in HR, where it facilitates the recruitment of C-terminal binding protein interacting protein (CtIP and promotes DSB resection, allowing Replication Protein A (RPA and RAD51 binding to DNA damage sites. Furthermore, reducing H3K36me3 levels by overexpressing KDM4A/JMJD2A, an oncogene and H3K36me3/2 demethylase, or an H3.3K36M transgene also reduces HR repair events. We propose that error-free HR repair within H3K36me3-decorated transcriptionally active genomic regions promotes cell homeostasis. Moreover, these findings provide insights as to why oncogenic mutations cluster within the H3K36me3 axis.

  2. Recombinant adenovirus expressing F and H fusion proteins of peste des petits ruminants virus induces both humoral and cell-mediated immune responses in goats.

    Science.gov (United States)

    Wang, Yong; Liu, Guangqing; Chen, Zongyan; Li, Chuanfeng; Shi, Lijun; Li, Wenchao; Huang, Huaxin; Tao, Chunai; Cheng, Chaofei; Xu, Binrui; Li, Gang

    2013-07-15

    Peste des petits ruminants (PPR) is an acute and contagious disease of some small ruminants caused by peste des petits ruminants virus (PPRV). Fusion (F) protein and hemagglutinin (H) protein are two glycoproteins of PPRV that might induce a protective immune response. In this study, three replication-defective recombinant adenoviruses were constructed and the immunogenicity was evaluated in goats (the natural host). The recombinant adenoviruses (rAds) expressing F, H, and F-H fusion protein were named rAd-F, rAd-H, and rAd-F-H, respectively. In vitro, the proteins expressed in AAV-293 cells infected with different rAds were identified by Western blotting and immunofluorescence. The results showed that the proteins could be expressed in vitro. Three groups of goats (6 goats per group) were inoculated subcutaneously twice at 3-week intervals with the rAds. As negative controls, two additional groups were inoculated with wild-type adenovirus (wtAd) or PBS. In vivo, goats immunized with the rAds developed PPRV-specific virus neutralizing antibody (VNA) by 3 weeks after primary immunization. Moreover, the seroconversions were maintained for approximately 21 weeks after primary immunization. Stronger lymphocyte proliferation responses were induced in goats immunized with the three rAds than in the negative controls (PPPRV infection. Notably, the rAd-F-H expressing F-H fusion protein is likely the most potent candidate of the rAds. PMID:23707075

  3. Efficient generation of recombinant adenoviral vectors by Cre-lox recombination in vitro.

    OpenAIRE

    Aoki, K.; Barker, C.; Danthinne, X.; Imperiale, M. J.; Nabel, G. J.

    1999-01-01

    BACKGROUND: Although recombinant adenovirus vectors are attractive for use in gene expression studies and therapeutic applications, the construction of these vectors remains relatively time-consuming. We report here a strategy that simplifies the production of adenoviruses using the Cre-loxP system. MATERIALS AND METHODS: Full-length recombinant adenovirus DNA was generated in vitro by Cre-mediated recombination between loxP sites in a linearized shuttle plasmid containing a transgene and ade...

  4. Mph1p promotes gross chromosomal rearrangement through partial inhibition of homologous recombination.

    Science.gov (United States)

    Banerjee, Soma; Smith, Stephanie; Oum, Ji-Hyun; Liaw, Hung-Jiun; Hwang, Ji-Young; Sikdar, Nilabja; Motegi, Akira; Lee, Sang Eun; Myung, Kyungjae

    2008-06-30

    Gross chromosomal rearrangement (GCR) is a type of genomic instability associated with many cancers. In yeast, multiple pathways cooperate to suppress GCR. In a screen for genes that promote GCR, we identified MPH1, which encodes a 3'-5' DNA helicase. Overexpression of Mph1p in yeast results in decreased efficiency of homologous recombination (HR) as well as delayed Rad51p recruitment to double-strand breaks (DSBs), which suggests that Mph1p promotes GCR by partially suppressing HR. A function for Mph1p in suppression of HR is further supported by the observation that deletion of both mph1 and srs2 synergistically sensitize cells to methyl methanesulfonate-induced DNA damage. The GCR-promoting activity of Mph1p appears to depend on its interaction with replication protein A (RPA). Consistent with this observation, excess Mph1p stabilizes RPA at DSBs. Furthermore, spontaneous RPA foci at DSBs are destabilized by the mph1Delta mutation. Therefore, Mph1p promotes GCR formation by partially suppressing HR, likely through its interaction with RPA. PMID:18591428

  5. Mutations in the BRCT binding site of BRCA1 result in hyper-recombination

    OpenAIRE

    Dever, Seth M.; Golding, Sarah E.; Rosenberg, Elizabeth; Adams, Bret R.; Idowu, Michael O.; Quillin, John M.; Valerie, Nicholas; Xu, Bo; Povirk, Lawrence F.; Valerie, Kristoffer

    2011-01-01

    We introduced a K1702M mutation in the BRCA1 BRCT domain known to prevent the binding of proteins harboring pS-X-X-F motifs such as Abraxas-RAP80, BRIP1, and CtIP. Surprisingly, rather than impairing homologous recombination repair (HRR), expression of K1702M resulted in hyper-recombination coinciding with an accumulation of cells in S-G2 and no effect on nonhomologous end-joining. These cells also showed increased RAD51 and RPA nuclear staining. More pronounced effects were seen with a natur...

  6. DNA RECOMBINATION IN EUCARYOTIC CELLS BY THE BACTERIOPHAGE PHIC31 RECOMBINATION SYSTEM",

    Science.gov (United States)

    This invention provides methods for obtaining specific and stable integration of nucleic acids into eukaryotic cells. The invention makes use of site-specific recombination systems that use prokaryotic recombinase polypeptides, such as the ph:C31 integrase, that can mediate recombination between th...

  7. Microhomology-mediated End Joining and Homologous Recombination share the initial end resection step to repair DNA double-strand breaks in mammalian cells

    OpenAIRE

    Truong, Lan N.; Li, Yongjiang; Shi, Linda Z.; Hwang, Patty Yi-hwa; He, Jing; Wang, Hailong; Razavian, Niema; Berns, Michael W.; Wu, Xiaohua

    2013-01-01

    Microhomology-mediated end joining (MMEJ) is a major pathway for Ku-independent alternative nonhomologous end joining, which contributes to chromosomal translocations and telomere fusions, but the underlying mechanism of MMEJ in mammalian cells is not well understood. In this study, we demonstrated that, distinct from Ku-dependent classical nonhomologous end joining, MMEJ—even with very limited end resection—requires cyclin-dependent kinase activities and increases significantly when cell...

  8. Segmental genomic replacement by Cre-mediated recombination: genotoxic stress activation of the p53 promoter in single-copy transformants.

    OpenAIRE

    Bethke, B.; Sauer, B.

    1997-01-01

    Genotoxic stress results in transcriptional activation of the p53 promoter. To gain more detailed information on genotoxic induction of the p53 promoter at a uniform genomic locus, we have developed an efficient strategy for replacing a defined genomic segment in mouse NIH 3T3 cells with exogenous transfected DNA using a 'double lox' targeting strategy mediated by Cre DNA recombinase. The strategy utilizes a pair of heterospecific lox sites engineered both into the genome and onto the targeti...

  9. Tensor hypercontracted ppRPA: Reducing the cost of the particle-particle random phase approximation from O(r?{sup 6}) to O(r?{sup 4})

    Energy Technology Data Exchange (ETDEWEB)

    Shenvi, Neil; Yang, Yang; Yang, Weitao [Department of Chemistry, Duke University, Durham, NC 27708 (United States); Aggelen, Helen van [Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States)

    2014-07-14

    In recent years, interest in the random-phase approximation (RPA) has grown rapidly. At the same time, tensor hypercontraction has emerged as an intriguing method to reduce the computational cost of electronic structure algorithms. In this paper, we combine the particle-particle random phase approximation with tensor hypercontraction to produce the tensor-hypercontracted particle-particle RPA (THC-ppRPA) algorithm. Unlike previous implementations of ppRPA which scale as O(r{sup 6}), the THC-ppRPA algorithm scales asymptotically as only O(r{sup 4}), albeit with a much larger prefactor than the traditional algorithm. We apply THC-ppRPA to several model systems and show that it yields the same results as traditional ppRPA to within mH accuracy. Our method opens the door to the development of post-Kohn Sham functionals based on ppRPA without the excessive asymptotic cost of traditional ppRPA implementations.

  10. The nuclear scissors mode by two approaches (Wigner function moments versus RPA)

    International Nuclear Information System (INIS)

    Two complementary methods to describe the collective motion, RPA and Wigner Function Moments (WFM) method, are compared on an example of a simple model - harmonic oscillator with quadrupole-quadrupole residual interaction. It is shown that they give identical formulae for eigenfrequencies and transition probabilities of all collective excitations of the model including the scissors mode, which is a subject of our especial attention. The normalization factor of the 'synthetic' scissors state and its overlap with physical states are calculated analytically. The orthogonality of the spurious state to all physical states is proved rigorously

  11. An effective interaction derived from HJ potential for use in TDA and RPA calculations

    International Nuclear Information System (INIS)

    An effective interaction is derived by fitting the matrix elements of a sum of Yukawa terms to the G-matrix elements of a sum of Yukawa terms to the G-matrix elements derived from the Hamada-Johnston potential. Central, spin-orbit and tensor components are taken into account. Numerical results are given and compared with those obtained from the Paris and Reid potentials. As an application, the excitation spectra in 16O are investigated in the framework of the TDA and RPA. (author). 12 refs, 3 tabs

  12. PARP-mediated repair, homologous recombination, and back-up non-homologous end joining-like repair of single-strand nicks.

    Science.gov (United States)

    Metzger, Michael J; Stoddard, Barry L; Monnat, Raymond J

    2013-07-01

    Double-strand breaks (DSBs) in chromosomal DNA can induce both homologous recombination (HR) and non-homologous end-joining (NHEJ). Recently we showed that single-strand nicks induce HR with a significant reduction in toxicity and mutagenic effects associated with NHEJ. To further investigate the differences and similarities of DSB- and nick-induced repair, we used an integrated reporter system in human cells to measure HR and NHEJ produced by the homing endonuclease I-AniI and a designed 'nickase' variant that nicks the same target site, focusing on the PARP and HR repair pathways. PARP inhibitors, which block single-strand break repair, increased the rate of nick-induced HR up to 1.7-fold but did not affect DSB-induced HR or mutNHEJ. Additionally, expression of the PALB2 WD40 domain in trans acted as a dominant-negative inhibitor of both DSB- and nick-induced HR, sensitized cells to PARP inhibition, and revealed an alternative mutagenic repair pathway for nicks. Thus, while both DSB- and nick-induced HR use a common pathway, their substrates are differentially processed by cellular factors. These results also suggest that the synthetic lethality of PARP and BRCA may be due to repair of nicks through an error prone, NHEJ-like mechanism that is active when both PARP and HR pathways are blocked. PMID:23684799

  13. Mycobacterium tuberculosis antigen 85B and ESAT-6 expressed as a recombinant fusion protein in Mycobacterium smegmatis elicits cell-mediated immune response in a murine vaccination model.

    Science.gov (United States)

    Tsolaki, Anthony G; Nagy, Judit; Leiva, Sergio; Kishore, Uday; Rosenkrands, Ida; Robertson, Brian D

    2013-07-01

    In this study, we investigated the potential molecular and immunological differences of a recombinant fusion protein (Hybrid-1), comprising of the immunodominant antigens Ag85B and ESAT-6 from Mycobacterium tuberculosis, derived from two different expression systems, namely Mycobacterium smegmatis and Escherichia coli. The fusion protein was successfully expressed and purified from both bacterial hosts and analyzed for any host-dependent post-translational modifications that might affect the immunogenicity of the protein. We investigated the immunogenicity of Hybrid-1 expressed in the two host species in a murine vaccination model, together with a reference standard Hybrid-1 (expressed in E. coli) from the Statens Serum Institut. No evidence of any post-translation modification was found in the M. smegmatis-derived Hybrid-1 fusion protein, nor were there any significant differences in the T-cell responses obtained to the three antigens analyzed. In conclusion, the Hybrid-1 fusion protein was successfully expressed in a homologous expression system using M. smegmatis and this system is worth considering as a primary source for vaccination trials, as it provided protein of excellent yield, stability and free from lipopolysaccharide. PMID:23333882

  14. Cell-Mediated and Humoral Immune Responses after Immunization of Calves with a Recombinant Multiantigenic Mycobacterium avium subsp. paratuberculosis Subunit Vaccine at Different Ages

    DEFF Research Database (Denmark)

    Thakur, Aneesh; Aagaard, Claus

    2013-01-01

    Neonates and juvenile ruminants are very susceptible to paratuberculosis infection. This is likely due to a high degree of exposure from their dams and an immature immune system. To test the influence of age on vaccine-induced responses, a cocktail of recombinant Mycobacterium avium subsp. paratuberculosis proteins (MAP0217, MAP1508, MAP3701c, MAP3783, and MAP1609c/Ag85B) was formulated in a cationic liposome adjuvant (CAF01) and used to vaccinate animals of different ages. Male jersey calves were divided into three groups that were vaccinated at 2, 8, or 16 weeks of age and boosted twice at weeks 4 and 12 relative to the first vaccination. Vaccine-induced immune responses, the gamma interferon (IFN-?) cytokine secretion and antibody responses, were followed for 20 weeks. In general, the specific responses were significantly elevated in all three vaccination groups after the first booster vaccination with no or only a minor effect from the second booster. However, significant differences were observed in the immunogenicity levels of the different proteins, and it appears that the older age group produced a more consistent IFN-? response. In contrast, the humoral immune response is seemingly independent of vaccination age as we found no difference in the IgG1 responses when we compared the three vaccination groups. Combined, our results suggest that an appropriate age of vaccination should be considered in vaccination protocols and that there is a possible interference of vaccine-induced immune responses with weaning (week 8).

  15. Common AZFc structure may possess the optimal spermatogenesis efficiency relative to the rearranged structures mediated by non-allele homologous recombination

    Science.gov (United States)

    Yang, Bo; Ma, Yong-yi; Liu, Yun-qiang; Li, Lei; Yang, Dong; Tu, Wen-ling; Shen, Ying; Dong, Qiang; Yang, Yuan

    2015-01-01

    The azoopsermia factor c (AZFc) region of human Y-chromosome is an essential genomic segment for spermatogenesis with frequent non-allele homologous recombination (NAHR). Recent case-control studies on the association of the NAHR-based AZFc structural mutations with spermatogenic failure produced inconsistent results. To more precisely evaluate their spermatogenesis effects, we investigated the correlation between the subdivided AZFc mutations and sperm production in 3,439 Han Chinese males. Our results showed that both partial AZFc deletion-only and primary duplication mutation presented a significant risk for decreased sperm production. Restoration of the reduced dosage of the AZFc content to the normal level had a milder effect, whereas an overdose of the AZFc content arising from multiple duplications of a partial AZFc-deleted structure produced a more serious consequence compared to the partial deletion-only mutation. Additionally, the AZFc-mutated structures with excessive NAHR-substrate showed a notably negative effect on spermatogenesis. These results suggest that the recurrent NAHR-based AZFc mutations may be associated with decreased spermatogenesis efficiency in present population. More significantly, our finding implies that the overdose of AZFc NAHR-substrate may produce an additional risk for the massive AZFbc deletions during the multi-stage division process of germ cells and thus impair the global spermatogenesis efficiency in the carriers. PMID:26000765

  16. SANS [small-angle neutron scattering] evaluation of the RPA [random phase approximation] theory for binary homopolymer mixtures

    International Nuclear Information System (INIS)

    A well characterized binary mixture of normal (protonated) and perdeuterated monodisperse 1,2 polybutenes has been studied by small-angle neutron scattering (SANS). For scattering wavevectors q greater than the inverse radius-of-gyration R/sub g/-1, the SANS intensity is quantitatively predicted by the random phase approximation (RPA) theory of deGennes over all measured values of the segment-segment interaction parameter Chi. In the region (Chi s-Chi)Chi s-1 > 0.5 the interaction parameter determined using the RPA theory for q > R/sub g/-1 is greater than that calculated from the zero-angle intensity based on an Ornstein-Zernike plot, where Chi s represents the limit of single phase stability. These findings indicate a correlation between the critical fluctuation length ? and R/sub g/ which is not accounted for by the RPA theory

  17. Electroexcitation of Low-Lying Particle-Hole RPA States of 16O with WBP Interaction

    International Nuclear Information System (INIS)

    The nuclear structure of 16O is studied in the framework of the particle-hole random phase approximation (ph RPA). The Hamiltonian is diagonalized within a model space with particle orbits {1d5/2,1d3/2, and 2s1/2} and the hole orbits {1p3/2 and 1p1/2} using Warburton and Brown interaction WBP. The ph RPA calculations are tested, by comparing the electron scattering form factors with the available experimental data. The results of electron scattering form factors and reduced transition strength for the states: 1?, T = 0 (7.116 MeV); 2?, T = 1 (12.968 MeV); 2?, T = 1 (20.412 MeV); and 3?, T = 0 (6.129 MeV) are interpreted in terms of the harmonic-oscillator (HO) wave functions of size parameter b. The occupation probabilities of the single particle and hole orbits are calculated. The spurious states are removed by adding the center of mass (CM) correction to the nuclear Hamiltonian. A comparison with the available experiments data is presented. (nuclear physics)

  18. Gimeracil, an inhibitor of dihydropyrimidine dehydrogenase, inhibits the early step in homologous recombination

    International Nuclear Information System (INIS)

    Gimeracil (5-chloro-2, 4-dihydroxypyridine) is an inhibitor of dihydropyrimidine dehydrogenase (DPYD), which degrades pyrimidine including 5-fluorouracil in the blood. Gimeracil was originally added to an oral fluoropyrimidine derivative S-1 to yield prolonged 5-fluorouracil concentrations in serum and tumor tissues. We have already reported that gimeracil had radiosensitizing effects by partially inhibiting homologous recombination (HR) in the repair of DNA double strand breaks. We investigated the mechanisms of gimeracil radiosensitization. Comet assay and radiation-induced focus formation of various kinds of proteins involved in HR was carried out. Small interfering RNA (siRNA) for DPYD were transfected to HeLa cells to investigate the target protein for radiosensitization with gimeracil. SCneo assay was carried out to examine whether DPYD depletion by siRNA inhibited HR repair of DNA double strand breaks. Tail moments in neutral comet assay increased in gimeracil-treated cells. Gimeracil restrained the formation of foci of Rad51 and replication protein A (RPA), whereas it increased the number of foci of Nbs1, Mre11, Rad50, and FancD2. When HeLa cells were transfected with the DPYD siRNA before irradiation, the cells became more radiosensitive. The degree of radiosensitization by transfection of DPYD siRNA was similar to that of gimeracil. Gimeracil did not sensitize DPYD-depleted cells. Depletion of DPYD by siRNA significantly reduced the frequency of neopositive ntly reduced the frequency of neopositive clones in SCneo assay. Gimeracil partially inhibits the early step in HR. It was found that DPYD is the target protein for radiosensitization by gimeracil. The inhibitors of DPYD, such as gimeracil, could enhance the efficacy of radiotherapy through partial suppression of HR-mediated DNA repair. (author)

  19. Synthesis, characterization and immunological properties of LPS-based conjugate vaccine composed of O-polysaccharide from pseudomonas aeruginosa IATS 10 bound to recombinant exoprotein A

    International Nuclear Information System (INIS)

    Pseudomonas aeruginosa is an improtant opportunistic pathogen that can cause infection in immunocompromised patient. Lipopolysaccharide (LPS), the major surface antigen of P. aeruginosa, is immunogenic and elieits protective antibodies in animals. The O-polysaccharids (O-PS) from international Antigenic typing Scheme (IATS) 10, the antigenic determinant of LPS, was coupled to recombinant exoprotein A (rPA) through adipic acid dihydrazide (ADH) mediated by carbodiimide condensation reaction. Mice were immunized with the conjugate emulsifield with monophosphoryl lipid A-trehalose dicorynomycolate (MPL-T) and freund's adjuvants. The conjiugate emulsified with MPL-T adjuvant elicited the highest level of IgG and IgM followed by freuns's adjuvant. IgG titers using both MPL-T and freund's adjuvants were recorded to be higher than IgM titers after the second post of the immunization. Immunization of mice with the prepared conjugates emulsified with MPL-T and freund's adjvaided provide high level of protection (100%) against ten times the LD50 of homologous strain of P. aeruginsoa. the elicited high IgG level and the in vivo protection test results provided good evidences for the possible protection of the conjugate aginst subsequent infection with the pathogen. These findings will enable us to use it as protective vaccine candidate (authors).

  20. Chromosome fusions following telomere loss are mediated by single-strand annealing.

    Science.gov (United States)

    Wang, Xiaorong; Baumann, Peter

    2008-08-22

    Progressive telomere shortening eventually results in chromosome fusions and genome instability as the cell's ability to distinguish chromosome ends from DNA double-strand breaks is compromised. In fission yeast, such events frequently produce stable survivors with all circular chromosomes. To shed light on the repair pathways that mediate chromosome end fusions and generate circular chromosomes, we have examined a diverse array of DNA repair factors. We show that telomere attrition-induced chromosome fusions are dependent on the fission yeast homologs of Rad52, the ERCC1/XPF endonuclease, the single-stranded DNA-binding protein RPA, and the Srs2 and Werner/Bloom helicases, but not Ku and ligase 4. Consistent with a recombinational mechanism of single-strand annealing, cloned junctions map to four of five homology regions in subtelomeric DNA. A comparison with telomere uncapping caused by the absence of the double-stranded telomere-binding protein Taz1 demonstrates that the circumstances and cause of telomere dysfunction profoundly affect which DNA repair pathway is engaged. PMID:18722173

  1. Spectra of nuclei in the lead region in the framework of the RPA with OBE-G-matrix interactions

    International Nuclear Information System (INIS)

    On the base of an existing Computer program for the calculation of particle-hole RPA matrix elements (especially) for finite-range interactions as well for the solution of the particle-hole RPA equations the corresponding matrix elements for two-particle respectively two-hole nuclei were calculated (and tested) and the corresponding RPA equations solved. For the calculation of the nuclear spectra meson-exchange G-matrix interactions were used instead of phenomenological approaches. The former constitute only a part of the effective NN interaction. A direct comparison with the experimental spectra is therefore just as little convenient as the calculation of transition probabilities or an evaluating comparison of TDA and RPA. The results let nevertheless recognize following: (1) The density dependence of the effective NN interaction. (2) For the states of two-particle respectively two-hole nuclei the (?+rho) exchange plays no such dominating role as for unnatural-parity states in double-magic nuclei. (3) An approximation of the missing part of the effective NN interaction by delta-function interactions is not sufficient. (orig.)

  2. Pleiotropic effects of immobilized versus soluble recombinant HIV-1 Tat protein on CD3-mediated activation, induction of apoptosis, and HIV-1 long terminal repeat transactivation in purified CD4+ T lymphocytes.

    Science.gov (United States)

    Zauli, G; Gibellini, D; Celeghini, C; Mischiati, C; Bassini, A; La Placa, M; Capitani, S

    1996-09-01

    CD3 mAb and HIV-1 Tat protein co-immobilized on plastic were able to induce a strong proliferation of resting human CD4 T cells, cultured in a serum-free chemically defined medium. Blocking studies performed with heparin or peptides containing the RGD sequence demonstrated that the heparin-binding basic domain of Tat plays a predominant role in CD4+ T cell activation. Moreover, the enhanced proliferative response of CD4+ T cells to immobilized Tat appeared to be mediated by alpha 5, beta 1, and alpha v subunits of surface integrin receptors. In contrast, soluble Tat showed a dose-dependent inhibitory activity on the proliferative response of resting CD4+ T cells stimulated by CD3 mAb co-immobilized with Tat or fibronectin, but not with CD28 mAb. In transient transfection assays performed with an HIV-1 long terminal repeat (LTR)-chloramphenicol acetyltransferase (CAT) plasmid CD3 mAb co-immobilized with Tat or fibronectin or CD28 mAb significantly stimulated CAT activity over the background. On the other hand, while immobilized Tat alone had no effects on LTR transactivation, soluble Tat was able to transactivate LTR-CAT in a dose-dependent manner. When CD4+ T cells activated by CD3 mAb co-immobilized with Tat were recovered, cultured for 7 days with 25 U/ml recombinant IL-2, and given an additional activation signal by recross-linking CD3 mAb, a marked increase of apoptosis was observed with respect to cells not subjected to CD3 mAb recross-linking. While co-immobilized Tat plus CD3 mAb did not show any significant effect on activation-induced cell death, high concentrations of soluble Tat synergized with immobilized CD3 mAb in the induction of apoptosis. PMID:8757349

  3. High efficiency recombineering in lactic acid bacteria.

    Science.gov (United States)

    van Pijkeren, Jan-Peter; Britton, Robert A

    2012-05-01

    The ability to efficiently generate targeted point mutations in the chromosome without the need for antibiotics, or other means of selection, is a powerful strategy for genome engineering. Although oligonucleotide-mediated recombineering (ssDNA recombineering) has been utilized in Escherichia coli for over a decade, the successful adaptation of ssDNA recombineering to gram-positive bacteria has not been reported. Here we describe the development and application of ssDNA recombineering in lactic acid bacteria. Mutations were incorporated in the chromosome of Lactobacillus reuteri and Lactococcus lactis without selection at frequencies ranging between 0.4% and 19%. Whole genome sequence analysis showed that ssDNA recombineering is specific and not hypermutagenic. To highlight the utility of ssDNA recombineering we reduced the intrinsic vancomymycin resistance of L. reuteri >100-fold. By creating a single amino acid change in the D-Ala-D-Ala ligase enzyme we reduced the minimum inhibitory concentration for vancomycin from >256 to 1.5?µg/ml, well below the clinically relevant minimum inhibitory concentration. Recombineering thus allows high efficiency mutagenesis in lactobacilli and lactococci, and may be used to further enhance beneficial properties and safety of strains used in medicine and industry. We expect that this work will serve as a blueprint for the adaptation of ssDNA recombineering to other gram-positive bacteria. PMID:22328729

  4. Unwinding of synthetic replication and recombination substrates by Srs2.

    Science.gov (United States)

    Marini, Victoria; Krejci, Lumir

    2012-10-01

    The budding yeast Srs2 protein possesses 3' to 5' DNA helicase activity and channels untimely recombination to post-replication repair by removing Rad51 from ssDNA. However, it also promotes recombination via a synthesis-dependent strand-annealing pathway (SDSA). Furthermore, at the replication fork, Srs2 is required for fork progression and prevents the instability of trinucleotide repeats. To better understand the multiple roles of the Srs2 helicase during these processes, we analysed the ability of Srs2 to bind and unwind various DNA substrates that mimic structures present during DNA replication and recombination. While leading or lagging strands were efficiently unwound, the presence of ssDNA binding protein RPA presented an obstacle for Srs2 translocation. We also tested the preferred directionality of unwinding of various substrates and studied the effect of Rad51 and Mre11 proteins on Srs2 helicase activity. These biochemical results help us understand the possible role of Srs2 in the processing of stalled or blocked replication forks as a part of post-replication repair as well as homologous recombination (HR). PMID:22921573

  5. Recombinant Technology and Probiotics

    Directory of Open Access Journals (Sweden)

    Icy D’Silva

    2011-09-01

    Full Text Available Recombinant technology has led the way to monumental advances in the development of useful molecules, including the development of safe probiotics. The development of novel approaches using recombinant technology and probiotics that allow accurate targeting of therapeutics to the mucosa is an interesting area of research. The creation and use of recombinant probiotics expressing recombinantovalbumin, recombinant ovalbumin mutants and yet-to-be-designed recombinant hypo/non-allergenic molecules offer the opportunity to further investigate their effects for food, nutrition, environment andhealth. This review highlights advances in native probiotics and recombinant probiotics expressing native and recombinant molecules for food, nutrition, environment and health.

  6. Recombinant Technology and Probiotics

    OpenAIRE

    Icy D’Silva

    2011-01-01

    Recombinant technology has led the way to monumental advances in the development of useful molecules, including the development of safe probiotics. The development of novel approaches using recombinant technology and probiotics that allow accurate targeting of therapeutics to the mucosa is an interesting area of research. The creation and use of recombinant probiotics expressing recombinantovalbumin, recombinant ovalbumin mutants and yet-to-be-designed recombinant hypo/non-allergenic molecule...

  7. The effects of the plasmon-LO phonon interaction on the critical densities of RPA approach in a quasi-one-dimensional system

    Scientific Electronic Library Online (English)

    P. C. M., Machado; F. A. P., Osório; A. N., Borges.

    2006-06-01

    Full Text Available In this work we have studied the electron LO phonon interaction on the pair-correlation function g(x) and its dependence on the electronic density for a GaAs-AlGaAs rectangular quantum wire within the random-phase approximation (RPA). We assumed two different values of the wire width. As negative no [...] n-physical results are found for lower electronic densities and small interparticle separations in the RPA approach, we have delimited the regions where the RPA approach cannot be used for the calculation of the Q1D electron gas collective excitation.

  8. Recombinations in staphylococcal cassette chromosome mec elements compromise the molecular detection of methicillin resistance in Staphylococcus aureus

    KAUST Repository

    Hill-Cawthorne, Grant A.

    2014-06-27

    Clinical laboratories are increasingly using molecular tests for methicillin-resistant Staphylococcus aureus (MRSA) screening. However, primers have to be targeted to a variable chromosomal region, the staphylococcal cassette chromosome mec (SCCmec). We initially screened 726 MRSA isolates from a single UK hospital trust by recombinase polymerase amplification (RPA), a novel, isothermal alternative to PCR. Undetected isolates were further characterised using multilocus sequence, spa typing and whole genome sequencing. 96% of our tested phenotypically MRSA isolates contained one of the six orfX-SCCmec junctions our RPA test and commercially available molecular tests target. However 30 isolates could not be detected. Sequencing of 24 of these isolates demonstrated recombinations within the SCCmec element with novel insertions that interfered with the RPA, preventing identification as MRSA. This result suggests that clinical laboratories cannot rely solely upon molecular assays to reliably detect all methicillin-resistance. The presence of significant recombinations in the SCCmec element, where the majority of assays target their primers, suggests that there will continue to be isolates that escape identification. We caution that dependence on amplification-based molecular assays will continue to result in failure to diagnose a small proportion (?4%) of MRSA isolates, unless the true level of SCCmec natural diversity is determined by whole genome sequencing of a large collection of MRSA isolates. © 2014 Hill-Cawthorne et al.

  9. Mean-Field and RPA Approaches to Stable and Unstable Nuclei with Semi-Realistic Interactions

    International Nuclear Information System (INIS)

    We have developed semi-realistic NN interactions [1, 2] by modifying the M3Y interaction [3] that was derived from the G-matrix. The modification has been made so that the saturation and the spin-orbit splittings could be reproduced. The new interactions contain finite-range LS and tensor channels, as well as Yukawa-form central channels having reasonable spin and spin-isospin properties. In order to handle such interactions in practical calculations, we have also developed new numerical methods [4-6], in which the Gaussian expansion method [7] is applied. It is noted that these methods have the following advantages: (i) we can efficiently describe the energy-dependent asymptotics of single-particle wave functions at large r, as is typified in arguments on the deformed neutron halo in 40Mg [6], (ii) we can handle various effective interactions, including those having non-locality, and (iii) a single-set of bases is applicable to wide mass range of nuclei and therefore is suitable to systematic calculations. Thereby we can implement Hartree-Fock, Hartree-Fock-Bogolyubov and RPA calculations for stable and unstable nuclei with the semi-realistic interactions. It will be shown first that the new interactions have desired characters for the nuclear matter and for the single- and double-closed nuclei. We shall particularly focus on roles of specific channels of the effective interaction, by studying (a) 'shell evolution' and role of the spin-isospin and the tensor channels [8] in stable and unstable nuclei, and (b) the magnetic response in a fully self-consistent RPA calculation with the tensor force [9]. All these properties seem to be simultaneously and naturally reproduced by the semi-realistic interactions. Thus the semi-realistic interactions are promising in describing various aspects of nuclear structure from stable to drip-line nuclei, in a self-consistent and unified manner. Since they have microscopic origin with minimal modification, we can expect high predictability for unstable nuclei by applying these interactions. Prediction will be given for the neutron drip line for some isotopes and on excited states of several unstable nuclei.(author)

  10. Single-stranded heteroduplex intermediates in ? Red homologous recombination

    Directory of Open Access Journals (Sweden)

    Zhang Youming

    2010-07-01

    Full Text Available Abstract Background The Red proteins of lambda phage mediate probably the simplest and most efficient homologous recombination reactions yet described. However the mechanism of dsDNA recombination remains undefined. Results Here we show that the Red proteins can act via full length single stranded intermediates to establish single stranded heteroduplexes at the replication fork. We created asymmetrically digestible dsDNA substrates by exploiting the fact that Red? exonuclease activity requires a 5' phosphorylated end, or is blocked by phosphothioates. Using these substrates, we found that the most efficient configuration for dsDNA recombination occurred when the strand that can prime Okazaki-like synthesis contained both homology regions on the same ssDNA molecule. Furthermore, we show that Red recombination requires replication of the target molecule. Conclusions Hence we propose a new model for dsDNA recombination, termed 'beta' recombination, based on the formation of ssDNA heteroduplexes at the replication fork. Implications of the model were tested using (i an in situ assay for recombination, which showed that recombination generated mixed wild type and recombinant colonies; and (ii the predicted asymmetries of the homology arms, which showed that recombination is more sensitive to non-homologies attached to 5' than 3' ends. Whereas beta recombination can generate deletions in target BACs of at least 50 kb at about the same efficiency as small deletions, the converse event of insertion is very sensitive to increasing size. Insertions up to 3 kb are most efficiently achieved using beta recombination, however at greater sizes, an alternative Red-mediated mechanism(s appears to be equally efficient. These findings define a new intermediate in homologous recombination, which also has practical implications for recombineering with the Red proteins.

  11. TFD extension of a self-consistent RPA to finite temperatures

    International Nuclear Information System (INIS)

    The self-consistent RPA (SCRPA) developed by Schuck and coauthors is extended to finite temperatures. The corresponding equations are derived by using the formalism of thermofield dynamics. The intrinsic energy of a system is calculated as the expectation value of the Hamiltonian with respect to a T-dependent thermal vacuum state for a thermal-phonon operator. A nonvanishing number of thermal quasiparticles in the vacuum state are assumed. By virtue of the assumption, the thermal Hartree-Fock (HF) equations appear to be coupled to the equations of motion for phonon variables. The thermal occupation numbers are also calculated in a consistent way with the energies of the HF quasiparticles. The approximation is applied to the two-level Lipkin model. Advantages of the thermal SCRPA (TSCRPA) are most obvious at temperatures near the phase-transition point. In the TSCRPA, the phase transition occurs at lower T than in other approximations. Moreover, within the TSCRPA, a statistical behavior of the Lipkin model is described with an appropriate accuracy at any T even if the HF transformation parameter is kept fixed at a value corresponding to the 'spherical' phase of the HF field

  12. Electronic structure of linear polyacenes in the SCF-RPA method

    Science.gov (United States)

    Baldo, Marcello; Grassi, Antonio; Pucci, Renato; Tomasello, Pasquale

    1982-09-01

    The excited states of the ?-electron system of linear polyacenes are studied with the self-consistent field-random phase approximation (SCF-RPA) scheme. The semiempirical Pariser-Parr-Pople (PPP) model is used. The parametrization is derived by fitting the benzene and it is held fixed throughout the polyacene series. Substantial improvement with respect to Tamm-Dancoff results [J. Chem. Phys. 24, 250 (1956)] for the singlet oscillator strengths is obtained. It is pointed out that the ratio between the experimental oscillator strength of the strong 1B3u transition and the total f-sum rule strength shows a drastic drop for naphthacene and pentacene. It is argued that this behavior is associated with a deep modification of the ?-electron correlation structure of these two molecules with respect to the smaller ones. The calculated energies are compared with experimental and Tamm-Dancoff values. The assignments of Meyer et al. [J. Chem. Phys. 56, 801 (1972)] for the triplet excited states of naphthalene and anthracene are confirmed. Theoretical implications of the results are discussed and possible developments and improvement of the theory are indicated.

  13. Characteristics and concepts of dynamic hub proteins in DNA processing machinery from studies of RPA.

    Science.gov (United States)

    Sugitani, Norie; Chazin, Walter J

    2015-03-01

    DNA replication, damage response and repair require the coordinated action of multi-domain proteins operating within dynamic multi-protein machines that act upon the DNA substrate. These modular proteins contain flexible linkers of various lengths, which enable changes in the spatial distribution of the globular domains (architecture) that harbor their essential biochemical functions. This mobile architecture is uniquely suited to follow the evolving substrate landscape present over the course of the specific process performed by the multi-protein machinery. A fundamental advance in understanding of protein machinery is the realization of the pervasive role of dynamics. Not only is the machine undergoing dynamic transformations, but the proteins themselves are flexible and constantly adapting to the progression through the steps of the overall process. Within this dynamic context the activity of the constituent proteins must be coordinated, a role typically played by hub proteins. A number of important characteristics of modular proteins and concepts about the operation of dynamic machinery have been discerned. These provide the underlying basis for the action of the machinery that reads DNA, and responds to and repairs DNA damage. Here, we introduce a number of key characteristics and concepts, including the modularity of the proteins, linkage of weak binding sites, direct competition between sites, and allostery, using the well recognized hub protein replication protein A (RPA). PMID:25542993

  14. Centrifugal step emulsification applied for absolute quantification of nucleic acids by digital droplet RPA.

    Science.gov (United States)

    Schuler, Friedrich; Schwemmer, Frank; Trotter, Martin; Wadle, Simon; Zengerle, Roland; von Stetten, Felix; Paust, Nils

    2015-07-01

    Aqueous microdroplets provide miniaturized reaction compartments for numerous chemical, biochemical or pharmaceutical applications. We introduce centrifugal step emulsification for the fast and easy production of monodisperse droplets. Homogenous droplets with pre-selectable diameters in a range from 120 ?m to 170 ?m were generated with coefficients of variation of 2-4% and zero run-in time or dead volume. The droplet diameter depends on the nozzle geometry (depth, width, and step size) and interfacial tensions only. Droplet size is demonstrated to be independent of the dispersed phase flow rate between 0.01 and 1 ?l s(-1), proving the robustness of the centrifugal approach. Centrifugal step emulsification can easily be combined with existing centrifugal microfluidic unit operations, is compatible to scalable manufacturing technologies such as thermoforming or injection moulding and enables fast emulsification (>500 droplets per second and nozzle) with minimal handling effort (2-3 pipetting steps). The centrifugal microfluidic droplet generation was used to perform the first digital droplet recombinase polymerase amplification (ddRPA). It was used for absolute quantification of Listeria monocytogenes DNA concentration standards with a total analysis time below 30 min. Compared to digital droplet polymerase chain reaction (ddPCR), with processing times of about 2 hours, the overall processing time of digital analysis was reduced by more than a factor of 4. PMID:25947077

  15. Detection of a Rickettsia Closely Related to Rickettsia aeschlimannii, “Rickettsia heilongjiangensis,” Rickettsia sp. Strain RpA4, and Ehrlichia muris in Ticks Collected in Russia and Kazakhstan

    OpenAIRE

    Shpynov, Stanislav; Fournier, Pierre-edouard; Rudakov, Nikolay; Tankibaev, Marat; Tarasevich, Irina; Raoult, Didier

    2004-01-01

    Using PCR, we screened 411 ticks from four genera collected in Russia and Kazakhstan for the presence of rickettsiae and ehrlichiae. In Russia, we detected “Rickettsia heilongjiangensis,” Rickettsia sp. strain RpA4, and Ehrlichia muris. In Kazakhstan, we detected Rickettsia sp. strain RpA4 and a rickettsia closely related to Rickettsia aeschlimannii. These agents should be considered in a differential diagnosis of tick-borne infections in these areas.

  16. Improving baculovirus recombination

    OpenAIRE

    Zhao, Yuguang; Chapman, David A. G.; Jones, Ian M.

    2003-01-01

    Recombinant baculoviruses have established themselves as a favoured technology for the high-level expression of recombinant proteins. The construction of recombinant viruses, however, is a time consuming step that restricts consideration of the technology for high throughput developments. Here we use a targeted gene knockout technology to inactivate an essential viral gene that lies adjacent to the locus used for recombination. Viral DNA prepared from the knockout fails to initiate an infecti...

  17. Therapeutic Recombinant Monoclonal Antibodies

    Science.gov (United States)

    Bakhtiar, Ray

    2012-01-01

    During the last two decades, the rapid growth of biotechnology-derived techniques has led to a myriad of therapeutic recombinant monoclonal antibodies with significant clinical benefits. Recombinant monoclonal antibodies can be obtained from a number of natural sources such as animal cell cultures using recombinant DNA engineering. In contrast to…

  18. Applications of the Remotely Piloted Aircraft (RPA) 'MASC' in Atmospheric Boundary Layer Research

    Science.gov (United States)

    Wildmann, Norman; Platis, Andreas; Tupman, David-James; Bange, Jens

    2015-04-01

    The remotely piloted aircraft (RPA) MASC (Multipurpose Airborne Sensor Carrier) was developed at the University of Tübingen in cooperation with the University of Stuttgart, University of Applied Sciences Ostwestfalen-Lippe and 'ROKE-Modelle'. Its purpose is the investigation of thermodynamic processes in the atmospheric boundary layer (ABL), including observations of temperature, humidity and wind profiles, as well as the measurement of turbulent heat, moisture and momentum fluxes. The aircraft is electrically powered, has a maximum wingspan of 3.40~m and a total weight of 5-8~kg, depending on the battery- and payload. The standard meteorological payload consists of two temperature sensors, a humidity sensor, a flow probe, an inertial measurement unit and a GNSS. The sensors were optimized for the resolution of small-scale turbulence down to length scales in the sub-meter range. In normal operation, the aircraft is automatically controlled by the ROCS (Research Onboard Computer System) autopilot to be able to fly predefined paths at constant altitude and airspeed. Only take-off and landing are carried out by a human RC pilot. Since 2012, the system is operational and has since then been deployed in more than ten measurement campaigns, with more than 100 measurement flights. The fields of research that were tackled in these campaigns include sensor validation, fundamental boundary-layer research and wind-energy research. In 2014, for the first time, two MASC have been operated at the same time within a distance of a few kilometres, in order to investigate the wind field over an escarpment in the Swabian Alb. Furthermore, MASC was first deployed off-shore in October 2014, starting from the German island Heligoland in the North Sea, for the purpose of characterization of the marine boundary layer for offshore wind parks. Detailed descriptions of the experimental setup and first preliminary results will be presented.

  19. Theory of dissociative recombination

    International Nuclear Information System (INIS)

    An analytic expression is derived for the cross section for the dissociative recombination of an electron with a molecular ion. A Morse potential is adopted as the internuclear potential for both the electronic ground state of the molecular ion and the resonance state of the molecule. The recombination coefficient is found by taking the average of the dissociative-recombination cross section over a Maxwellian distribution. This yields the temperature dependence of the recombination coefficient alpha approx.T/sup -1/2/. The temperature dependence of the coefficient for the dissociative recombination e+NO+ is calculated as an example. The results agree well with experiment

  20. Extended recombinant bacterial ghost system.

    Science.gov (United States)

    Lubitz, W; Witte, A; Eko, F O; Kamal, M; Jechlinger, W; Brand, E; Marchart, J; Haidinger, W; Huter, V; Felnerova, D; Stralis-Alves, N; Lechleitner, S; Melzer, H; Szostak, M P; Resch, S; Mader, H; Kuen, B; Mayr, B; Mayrhofer, P; Geretschläger, R; Haslberger, A; Hensel, A

    1999-08-20

    Controlled expression of cloned PhiX174 gene E in Gram-negative bacteria results in lysis of the bacteria by formation of an E-specific transmembrane tunnel structure built through the cell envelope complex. Bacterial ghosts from a variety of bacteria are used as non-living candidate vaccines. In the recombinant ghost system, foreign proteins are attached on the inside of the inner membrane as fusions with specific anchor sequences. Ghosts have a sealed periplasmic space and the export of proteins into this space vastly extends the capacity of ghosts or recombinant ghosts to function as carriers of foreign antigens. In addition, S-layer proteins forming shell-like self assembly structures can be expressed in candidate vaccine strains prior to E-mediated lysis. Such recombinant S-layer proteins carrying foreign epitopes further extend the possibilities of ghosts as carriers of foreign epitopes. As ghosts have inherent adjuvant properties, they can be used as adjuvants in combination with subunit vaccines. Subunits or other ligands can also be coupled to matrixes like dextran which are used to fill the internal lumen of ghosts. Oral, aerogenic or parenteral immunization of experimental animals with recombinant ghosts induced specific humoral and cellular immune responses against bacterial and target components including protective mucosal immunity. The most relevant advantage of recombinant bacterial ghosts as immunogens is that no inactivation procedures that denature relevant immunogenic determinants are employed in this production. This fact explains the superior quality of ghosts when compared to other inactivated vaccines. The endotoxic component of the outer membrane does not limit the use of ghosts as vaccine candidates but triggers the release of several potent immunoregulatory cytokines. As carriers, there is no limitation in the size of foreign antigens that can be inserted in the membrane and the capacity of all spaces including the membranes, peri-plasma and internal lumen of the ghosts can be fully utilized. This extended recombinant ghost system represents a new strategy for adjuvant free combination vaccines. PMID:10486935

  1. Fundamental study of recombination and recombineering in Escherichia coli

    OpenAIRE

    Sun, Xiaohang; Huang, Yang

    2008-01-01

    Recombination and recombineering systems have been used in Escherichia coli to recombinant DNA sequences. With endonuclease and DNA lipase the bacterial plasmid and target DNA fragment can bind together and recombinant for a new DNA sequences. Red Proteins have been used in recombineering system to perform the function as the enzymes in recombination system, and faster and easier than the other way of recombinant new DNA sequences in E.coli. In this report we get to know the pr...

  2. A dynamic model for replication protein A (RPA) function in DNA processing pathways

    OpenAIRE

    Fanning, Ellen; Klimovich, Vitaly; Nager, Andrew R.

    2006-01-01

    Processing of DNA in replication, repair and recombination pathways in cells of all organisms requires the participation of at least one major single-stranded DNA (ssDNA)-binding protein. This protein protects ssDNA from nucleolytic damage, prevents hairpin formation and blocks DNA reannealing until the processing pathway is successfully completed. Many ssDNA-binding proteins interact physically and functionally with a variety of other DNA processing proteins. These interactions are thought t...

  3. Recombination and Genetic Diversity

    Scientific Electronic Library Online (English)

    T. C., Coutinho; T.T.da, Silva; G.L., Toledo.

    2012-12-01

    Full Text Available In this paper we present a spatial stochastic model for genetic recombination, that answers if diversity is preserved in an infinite population of recombinat-ing individuals distributed spatially. We show that, for finite times, recombination may maintain all the various potential different types, b [...] ut when time grows infinitely, the diversity of individuals extinguishes off. So under the model premisses, recombination and spatial localization alone are not enough to explain diversity in a population. Further we discuss an application of the model to a controversy regarding the diversity of "Major Histocompatibility Complex" (MHC).

  4. Generation and Characterization of Recombinantly Polysialylated Antibody

    OpenAIRE

    Chen, Chen

    2011-01-01

    With high affinity and specificity, antibodies are now proven biotherapuetics for a wide range of diseases, such as cancer and immunological conditions. However, antibody Fc-domain mediated cross reactivity with associated side effects has hindered the development of antibody therapy in a number of applications. The development of engineered recombinant antibody fragments to address the problems seen with whole monoclonal antibodies (mAbs). Their smaller size enables rapid anti...

  5. DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1

    Science.gov (United States)

    Ira, Grzegorz; Pellicioli, Achille; Balijja, Alitukiriza; Wang, Xuan; Fiorani, Simona; Carotenuto, Walter; Liberi, Giordano; Bressan, Debra; Wan, Lihong; Hollingsworth, Nancy M.; Haber, James E.; Foiani, Marco

    2015-01-01

    A single double-strand break (DSB) induced by HO endonuclease triggers both repair by homologous recombination and activation of the Mec1-dependent DNA damage checkpoint in budding yeast1–6. Here we report that DNA damage checkpoint activation by a DSB requires the cyclin-dependent kinase CDK1 (Cdc28) in budding yeast. CDK1 is also required for DSB-induced homologous recombination at any cell cycle stage. Inhibition of homologous recombination by using an analogue-sensitive CDK1 protein7,8 results in a compensatory increase in non-homologous end joining. CDK1 is required for efficient 5? to 3? resection of DSB ends and for the recruitment of both the single-stranded DNA-binding complex, RPA, and the Rad51 recombination protein. In contrast, Mre11 protein, part of the MRX complex, accumulates at unresected DSB ends. CDK1 is not required when the DNA damage checkpoint is initiated by lesions that are processed by nucleotide excision repair. Maintenance of the DSB-induced checkpoint requires continuing CDK1 activity that ensures continuing end resection. CDK1 is also important for a later step in homologous recombination, after strand invasion and before the initiation of new DNA synthesis. PMID:15496928

  6. Two fast temperature sensors for probing of the atmospheric boundary layer using small remotely piloted aircraft (RPA

    Directory of Open Access Journals (Sweden)

    N. Wildmann

    2013-08-01

    Full Text Available Two types of temperature sensors are designed and tested: a thermocouple and a fine wire resistance thermometer. The intention of this study is to figure out which kind of measurement principle is in general more suited for atmospheric boundary layer meteorology with small remotely piloted aircraft (RPA. The sensors are calibrated in a NIST traceable climate chamber and validated in flight against tower measurements, radiosondes and remote sensing. The sensors have a measurement range of at least ?10–50 °C, an absolute RMS error of less than ±0.2 K which is stable over the lifetime of the sensors, and a resolution of about 0.01 K. Both devices are tested for typical errors like radiation error and adiabatic heating, as well as for their dynamic response. Spectral resolutions of up to approximately 10 Hz can be obtained with both sensors, which makes them suitable for turbulence measurement. Their low cost of less than 100 EUR in pure hardware is a major advantage for research with small RPA.

  7. Static correlation and electron localization in molecular dimers from the self-consistent RPA and GW approximation

    CERN Document Server

    Hellgren, Maria; Rohr, Daniel R; Ren, Xinguo; Rubio, Angel; Scheffler, Matthias; Rinke, Patrick

    2014-01-01

    We investigate static correlation and delocalization errors in the self-consistent GW and random-phase approximation (RPA) by studying molecular dissociation of the H_2 and LiH molecules. Although both approximations are diagrammatically identical, the non-locality and frequency dependence of the GW self-energy crucially influence the different energy contributions to the total energy as compared to the use of a static local potential in the RPA. The latter leads to significantly larger correlation energies which allows for a better description of static correlation at intermediate bond distances. The substantial error found in GW is further analyzed by comparing spin-restricted and spin-unrestricted calculations. At large but finite nuclear separation their difference gives an estimate of the so-called fractional spin error normally determined only in the dissociation limit. Furthermore, a calculation of the dipole moment of the LiH molecule at dissociation reveals a large delocalization error in GW making t...

  8. Single-stranded heteroduplex intermediates in ? Red homologous recombination

    OpenAIRE

    Zhang Youming; Friedrich Anne; Fu Jun; Erler Axel; Maresca Marcello; Stewart A Francis

    2010-01-01

    Abstract Background The Red proteins of lambda phage mediate probably the simplest and most efficient homologous recombination reactions yet described. However the mechanism of dsDNA recombination remains undefined. Results Here we show that the Red proteins can act via full length single stranded intermediates to establish single stranded heteroduplexes at the replication fork. We created asymmetrically digestible dsDNA substrates by exploiting the fact that Red? exonuclease activity requir...

  9. Low frequency recombination lines

    International Nuclear Information System (INIS)

    Low frequency recombination lines are those transitions with frequencies significantly less than 1 GHz. The authors discuss observations of extended low brightness HII regions, conventional HII regions, line enhancement caused by background continum sources and low frequency carbon recombination lines. (Auth.)

  10. Distinct Classes of Proteasome-Modulating Agents Cooperatively Augment Recombinant Adeno-Associated Virus Type 2 and Type 5-Mediated Transduction from the Apical Surfaces of Human Airway Epithelia

    OpenAIRE

    YAN, ZIYING; ZAK, ROMAN; Zhang, Yulong; Ding, Wei; Godwin, Simon; Munson, Keith; Peluso, Richard; Engelhardt, John F.

    2004-01-01

    Tripeptidyl aldehyde proteasome inhibitors have been shown to effectively increase viral capsid ubiquitination and transduction of recombinant adeno-associated virus type 2 (rAAV-2) and rAAV-5 serotypes. In the present study we have characterized a second class of proteasome-modulating agents (anthracycline derivatives) for their ability to induce rAAV transduction. The anthracycline derivatives doxorubicin and aclarubicin were chosen for analysis because they have been shown to interact with...

  11. Bocavirus Infection Induces a DNA Damage Response That Facilitates Viral DNA Replication and Mediates Cell Death?

    OpenAIRE

    Luo, Yong; Chen, Aaron Yun; Qiu, Jianming

    2010-01-01

    Minute virus of canines (MVC) is an autonomous parvovirus that replicates efficiently without helper viruses in Walter Reed/3873D (WRD) canine cells. We previously showed that MVC infection induces mitochondrion-mediated apoptosis and G2/M-phase arrest in infected WRD cells. However, the mechanism responsible for these effects has not been established. Here, we report that MVC infection triggers a DNA damage response in infected cells, as evident from phosphorylation of H2AX and RPA32. We dis...

  12. The use of recombinant DNA plasmids for the determination of DNA-repair and recombination in cultured mammalian cells.

    OpenAIRE

    Cox, R.; Masson, W. K.; Debenham, P. G.; Webb, M. B.

    1984-01-01

    Using the recombinant plasmid pSV2gpt and DNA transfer techniques, cell mediated DNA ligation and recombination of plasmid DNA have been demonstrated in four human cell lines. Data suggesting the involvement of a possible defect in the cellular equilibrium between ligation and exonuclease digestion of double strand DNA scissions in an ataxia-telangiectasia (A-T) cell line is discussed. The same A-T line was grossly proficient in DNA recombination but it will be necessary to distinguish betwee...

  13. Enabling simulation at the fifth rung of DFT: Large scale RPA calculations with excellent time to solution

    Science.gov (United States)

    Del Ben, Mauro; Schütt, Ole; Wentz, Tim; Messmer, Peter; Hutter, Jürg; VandeVondele, Joost

    2015-02-01

    The Random Phase Approximation (RPA), which represents the fifth rung of accuracy in Density Functional Theory (DFT), is made practical for large systems. Energies of condensed phase systems containing thousands of explicitly correlated electrons and 1500 atoms can now be computed in minutes and less than 1 h, respectively. GPU acceleration is employed for dense and sparse linear algebra, while communication is minimized by a judicious data layout. The performance of the algorithms, implemented in the widely used CP2K simulation package, has been investigated on hybrid Cray XC30 and XK7 architectures, up to 16,384 nodes. Our results emphasize the importance of good network performance, in addition to the availability of GPUs and generous on node memory. A new level of predictivity has thus become available for routine application in Monte Carlo and molecular dynamics simulations.

  14. Experimental investigation of hole boring and light sail regimes of RPA by varying laser and target parameters

    International Nuclear Information System (INIS)

    Temporal evolution of plasma jets from micrometre-scale thick foils following the interaction of intense (3 × 1020 W cm?2) laser pulses is studied systematically by time resolved optical interferometry. The fluid velocity in the plasma jets is determined by comparing the data with 2D hydrodynamic simulation, which agrees with the expected hole-boring (HB) velocity due to the laser radiation pressure. The homogeneity of the plasma density across the jets has been found to be improved substantially when irradiating the laser at circular polarization compared to linear polarization. While overdense plasma jets were formed efficiently for micrometre thick targets, decreasing the target areal density and/or increasing the irradiance on the target have provided indication of transition from the ‘HB’ to the ‘light sail (LS)’ regime of RPA, characterized by the appearance of narrow-band spectral features at several MeV/nucleon in proton and carbon spectra. (paper)

  15. Recursive partitioning analysis (RPA) of prognostic factors in three Radiation Therapy Oncology Group (RTOG) brain metastases trials

    International Nuclear Information System (INIS)

    Purpose: Promising results from new approaches such as radiosurgery or stereotactic surgery of brain metastases have recently been reported. Are these results due to the therapy alone or can the results be attributed in part to patient selection? An analysis of tumor/patient characteristics and treatment variables in previous Radiation Therapy Oncology Group (RTOG) brain metastases studies was considered necessary to fully evaluate the benefit of these new interventions. Methods and Materials: The database included 1200 patients from three consecutive RTOG trials conducted between 1979 and 1993, which tested several different dose fractionation schemes and radiation sensitizers. Using recursive partitioning analysis (RPA), a statistical methodology which creates a regression tree according to prognostic significance, eighteen pretreatment characteristics and three treatment-related variables were analyzed. Results: According to the RPA tree the best survival (median: 7.1 months) was observed in patients < 65 years of age with a Karnofsky Performance Status (KPS) of at least 70, and a controlled primary tumor with the brain the only site of metastases. The worst survival (median: 2.3 months) was seen in patients with a KPS less than 70. All other patients had relatively minor differences in observed survival, with a median of 4.2 months. Conclusions: Based on this analysis, we suggest the following three classes: Class 1: patients with KPS ? 70, < 65 years of age witnts with KPS ? 70, < 65 years of age with controlled primary and no extracranial metastases; Class 3: KPS < 70; Class 2- all others. Using these classes or stages, new treatment techniques can be tested on homogeneous patient groups

  16. Shu1 Promotes Homolog Bias of Meiotic Recombination in Saccharomyces cerevisiae

    OpenAIRE

    Hong, Soogil; Kim, Keun Pil

    2013-01-01

    Homologous recombination occurs closely between homologous chromatids with highly ordered recombinosomes through RecA homologs and mediators. The present study demonstrates this relationship during the period of “partner choice” in yeast meiotic recombination. We have examined the formation of recombination intermediates in the absence or presence of Shu1, a member of the PCSS complex, which also includes Psy3, Csm2, and Shu2. DNA physical analysis indicates that Shu1 is essential for pro...

  17. Expression of Recombinant Antibodies

    OpenAIRE

    Frenzel, Andre?; Hust, Michael; Schirrmann, Thomas

    2013-01-01

    Recombinant antibodies are highly specific detection probes in research, diagnostics, and have emerged over the last two decades as the fastest growing class of therapeutic proteins. Antibody generation has been dramatically accelerated by in vitro selection systems, particularly phage display. An increasing variety of recombinant production systems have been developed, ranging from Gram-negative and positive bacteria, yeasts and filamentous fungi, insect cell lines, mammalian cells to transg...

  18. Effect of insertions, deletions, and double-strand breaks on homologous recombination in mouse L cells.

    OpenAIRE

    Brenner, D. A.; Smigocki, A. C.; Camerini-otero, R. D.

    1985-01-01

    We have used DNA-mediated gene transfer to study homologous recombination in cultured mammalian cells. A family of plasmids with insertion and deletion mutations in the coding region of the herpes simplex type 1 thymidine kinase (tk) gene served as substrates for DNA-mediated gene transfer into mouse Ltk- cells by the calcium phosphate technique. Intermolecular recombination events were scored by the number of colonies in hypoxanthine-aminopterin-thymidine selective medium. We used supercoile...

  19. Recombination Phenotypes of Escherichia coli greA Mutants

    Directory of Open Access Journals (Sweden)

    Poteete Anthony R

    2011-03-01

    Full Text Available Abstract Background The elongation factor GreA binds to RNA polymerase and modulates transcriptional pausing. Some recent research suggests that the primary role of GreA may not be to regulate gene expression, but rather, to promote the progression of replication forks which collide with RNA polymerase, and which might otherwise collapse. Replication fork collapse is known to generate dsDNA breaks, which can be recombinogenic. It follows that GreA malfunction could have consequences affecting homologous recombination. Results Escherichia coli mutants bearing substitutions of the active site acidic residues of the transcription elongation factor GreA, D41N and E44K, were isolated as suppressors of growth inhibition by a toxic variant of the bacteriophage lambda Red-beta recombination protein. These mutants, as well as a D41A greA mutant and a greA deletion, were tested for proficiency in recombination events. The mutations were found to increase the efficiency of RecA-RecBCD-mediated and RecA-Red-mediated recombination, which are replication-independent, and to decrease the efficiency of replication-dependent Red-mediated recombination. Conclusion These observations provide new evidence for a role of GreA in resolving conflicts between replication and transcription.

  20. Cre-/IoxP-Mediated Recombination between the SIL and SCL Genes Leads to a Block in T-Cell Development at the CD4-CD8- to CD4+CD8+ Transition

    Directory of Open Access Journals (Sweden)

    Yue Cheng

    2007-04-01

    Full Text Available In the most common form of stem cell leukemia (SCL gene rearrangement, an interstitial deletion of 82 kb brings SCL under the control of regulatory elements that normally govern expression of the ubiquitously expressed SCL interrupting locus (SIL gene, which is located directly upstream of SCL. To investigate the effect of this fusion in a mouse model, a bacterial artificial chromosome (BAC clone containing both human SIL and SCL genes was isolated, and IoxP sites were inserted into intron 1 of both the SIL and SCL genes, corresponding to the sites at which recombination occurs in human T-cell acute lymphocytic leukemia patients. This BAC clone was used to generate transgenic SILIoxloxSCL mice. These transgenic mice were subsequently bred to Lck-Cre mice that express the Cre recombinase specifically in the thymus. The BAC transgene was recombined between the two IoxP sites in over 50% of the thymocytes from SILIoxloxSCL/Cre double-transgenic mice, bringing the SCL gene under the direct control of SIL regulatory elements. Aberrant SCL gene expression in the thymus was verified by reverse transcription- polymerase chain reaction. Using FACS analysis, we found that mice carrying both SILIoxloxSCL and Cre transgenes have increased CD4-/CD8- thymocytes compared with transgenenegative mice. In the spleen, these transgenic mice show a marked reduction in the number of mature CD4+ or CD8+ cells. These results demonstrate that conditional activation of SCL under control of SIL regulatory elements can impair normal T-cell development.

  1. Regulation of Meiotic Recombination

    Energy Technology Data Exchange (ETDEWEB)

    Gregory p. Copenhaver

    2011-11-09

    Meiotic recombination results in the heritable rearrangement of DNA, primarily through reciprocal exchange between homologous chromosome or gene conversion. In plants these events are critical for ensuring proper chromosome segregation, facilitating DNA repair and providing a basis for genetic diversity. Understanding this fundamental biological mechanism will directly facilitate trait mapping, conventional plant breeding, and development of genetic engineering techniques that will help support the responsible production and conversion of renewable resources for fuels, chemicals, and the conservation of energy (1-3). Substantial progress has been made in understanding the basal recombination machinery, much of which is conserved in organisms as diverse as yeast, plants and mammals (4, 5). Significantly less is known about the factors that regulate how often and where that basal machinery acts on higher eukaryotic chromosomes. One important mechanism for regulating the frequency and distribution of meiotic recombination is crossover interference - or the ability of one recombination event to influence nearby events. The MUS81 gene is thought to play an important role in regulating the influence of interference on crossing over. The immediate goals of this project are to use reverse genetics to identify mutants in two putative MUS81 homologs in the model plant Arabidopsis thaliana, characterize those mutants and initiate a novel forward genetic screen for additional regulators of meiotic recombination. The long-term goal of the project is to understand how meiotic recombination is regulated in higher eukaryotes with an emphasis on the molecular basis of crossover interference. The ability to monitor recombination in all four meiotic products (tetrad analysis) has been a powerful tool in the arsenal of yeast geneticists. Previously, the qrt mutant of Arabidopsis, which causes the four pollen products of male meiosis to remain attached, was developed as a facile system for assaying recombination using tetrad analysis in a higher eukaryotic system (6). This system enabled the measurement of the frequency and distribution of recombination events at a genome wide level in wild type Arabidopsis (7), construction of genetic linkage maps which include positions for each centromere (8), and modeling of the strength and pattern of interference (9). This proposal extends the use of tetrad analysis in Arabidopsis by using it as the basis for assessing the phenotypes of mutants in genes important for recombination and the regulation of crossover interference and performing a novel genetic screen. In addition to broadening our knowledge of a classic genetic problem - the regulation of recombination by crossover interference - this proposal also provides broader impact by: generating pedagogical tools for use in hands-on classroom experience with genetics, building interdisciplinary collegial partnerships, and creating a platform for participation by junior scientists from underrepresented groups. There are three specific aims: (1) Isolate mutants in Arabidopsis MUS81 homologs using T-DNA and TILLING (2) Characterize recombination levels and interference in mus81 mutants (3) Execute a novel genetic screen, based on tetrad analysis, for genes that regulate meiotic recombination

  2. Mediation Analysis

    OpenAIRE

    Mackinnon, David P.; Fairchild, Amanda J.; Fritz, Matthew S.

    2007-01-01

    Mediating variables are prominent in psychological theory and research. A mediating variable transmits the effect of an independent variable on a dependent variable. Differences between mediating variables and confounders, moderators, and covariates are outlined. Statistical methods to assess mediation and modern comprehensive approaches are described. Future directions for mediation analysis are discussed.

  3. Three body recombination of ultracold dipoles to weakly bound dimers

    CERN Document Server

    Ticknor, Chris

    2010-01-01

    We use universality in two-body dipolar physics to study three-body recombination. We present results for the universal structure of weakly bound two-dipole states that depend only on the s-wave scattering length ($a$). We study threshold three-body recombination rates into weakly-bound dimer states as a function of the scattering length. A Fermi Golden rule analysis is used to estimate rates for different events mediated by the dipole-dipole interaction and a phenomenological contact interaction. The three-body recombination rate in the limit where $a\\gg D$ contains terms which scale as $a^{4}$, $a^{2}D^{2}$ and $D^{4}$, where $D$ is the dipolar length. When $a \\ll D$, the three-boby recombination rate scales as $D^4$.

  4. Recombinational DNA repair and human disease

    International Nuclear Information System (INIS)

    We review the genes and proteins related to the homologous recombinational repair (HRR) pathway that are implicated in cancer through either genetic disorders that predispose to cancer through chromosome instability or the occurrence of somatic mutations that contribute to carcinogenesis. Ataxia telangiectasia (AT), Nijmegen breakage syndrome (NBS), and an ataxia-like disorder (ATLD), are chromosome instability disorders that are defective in the ataxia telangiectasia mutated (ATM), NBS, and Mre11 genes, respectively. These genes are critical in maintaining cellular resistance to ionizing radiation (IR), which kills largely by the production of double-strand breaks (DSBs). Bloom syndrome involves a defect in the BLM helicase, which seems to play a role in restarting DNA replication forks that are blocked at lesions, thereby promoting chromosome stability. The Werner syndrome gene (WRN) helicase, another member of the RecQ family like BLM, has very recently been found to help mediate homologous recombination. Fanconi anemia (FA) is a genetically complex chromosomal instability disorder involving seven or more genes, one of which is BRCA2. FA may be at least partially caused by the aberrant production of reactive oxidative species. The breast cancer-associated BRCA1 and BRCA2 proteins are strongly implicated in HRR; BRCA2 associates with Rad51 and appears to regulate its activity. We discuss in detail the phenotypes of the various mutant cell lines and the signaling patus mutant cell lines and the signaling pathways mediated by the ATM kinase. ATM's phosphorylation targets can be grouped into oxidative stress-mediated transcriptional changes, cell cycle checkpoints, and recombinational repair. We present the DNA damage response pathways by using the DSB as the prototype lesion, whose incorrect repair can initiate and augment karyotypic abnormalities

  5. Intercultural Mediation

    OpenAIRE

    Dragos Marian Radulescu; Denisa Mitrut

    2012-01-01

    The Intercultural Mediator facilitates exchanges between people of different socio-cultural backgrounds and acts as a bridge between immigrants and national and local associations, health organizations, services and offices in order to foster integration of every single individual. As the use mediation increases, mediators are more likely to be involved in cross-cultural mediation, but only the best mediators have the opportunity to mediate cross border business disputes or international poli...

  6. Recombineering Pseudomonas syringae

    Science.gov (United States)

    Here we report the identification of functions that promote genomic recombination of linear DNA introduced into Pseudomonas cells by electroporation. The genes encoding these functions were identified in Pseudomonas syringae pv. syringae B728a based on similarity to the lambda Red Exo/Beta and RecE...

  7. Recombineering linear BACs.

    Science.gov (United States)

    Chen, Qingwen; Narayanan, Kumaran

    2015-01-01

    Recombineering is a powerful genetic engineering technique based on homologous recombination that can be used to accurately modify DNA independent of its sequence or size. One novel application of recombineering is the assembly of linear BACs in E. coli that can replicate autonomously as linear plasmids. A circular BAC is inserted with a short telomeric sequence from phage N15, which is subsequently cut and rejoined by the phage protelomerase enzyme to generate a linear BAC with terminal hairpin telomeres. Telomere-capped linear BACs are protected against exonuclease attack both in vitro and in vivo in E. coli cells and can replicate stably. Here we describe step-by-step protocols to linearize any BAC clone by recombineering, including inserting and screening for presence of the N15 telomeric sequence, linearizing BACs in vivo in E. coli, extracting linear BACs, and verifying the presence of hairpin telomere structures. Linear BACs may be useful for functional expression of genomic loci in cells, maintenance of linear viral genomes in their natural conformation, and for constructing innovative artificial chromosome structures for applications in mammalian and plant cells. PMID:25239740

  8. Recombinant hormones in osteoporosis

    DEFF Research Database (Denmark)

    Rejnmark, Lars; Rejnmark, Lars

    2013-01-01

    For the last 10 years, bone anabolic therapy with the recombinant human parathyroid hormone (rhPTH) analogue, teriparatide (rhPTH[1 - 34]), or full-length rhPTH(1 - 84) has been an option in the treatment of osteoporosis. Both drugs are given as a daily subcutaneous injection. In the USA, only teriparatide is marketed.

  9. Microfluidic lab-on-a-foil for nucleic acid analysis based on isothermal recombinase polymerase amplification (RPA).

    Science.gov (United States)

    Lutz, Sascha; Weber, Patrick; Focke, Max; Faltin, Bernd; Hoffmann, Jochen; Müller, Claas; Mark, Daniel; Roth, Günter; Munday, Peter; Armes, Niall; Piepenburg, Olaf; Zengerle, Roland; von Stetten, Felix

    2010-04-01

    For the first time we demonstrate a self-sufficient lab-on-a-foil system for the fully automated analysis of nucleic acids which is based on the recently available isothermal recombinase polymerase amplification (RPA). The system consists of a novel, foil-based centrifugal microfluidic cartridge including prestored liquid and dry reagents, and a commercially available centrifugal analyzer for incubation at 37 degrees C and real-time fluorescence detection. The system was characterized with an assay for the detection of the antibiotic resistance gene mecA of Staphylococcus aureus. The limit of detection was <10 copies and time-to-result was <20 min. Microfluidic unit operations comprise storage and release of liquid reagents, reconstitution of lyophilized reagents, aliquoting the sample into < or = 30 independent reaction cavities, and mixing of reagents with the DNA samples. The foil-based cartridge was produced by blow-molding and sealed with a self-adhesive tape. The demonstrated system excels existing PCR based lab-on-a-chip platforms in terms of energy efficiency and time-to-result. Applications are suggested in the field of mobile point-of-care analysis, B-detection, or in combination with continuous monitoring systems. PMID:20300675

  10. Resonant scattering and recombination of pseudodegenerate WIMPs

    International Nuclear Information System (INIS)

    We consider the direct and indirect detection signatures of weakly interacting massive particles (WIMPs) ?0 in kinematic regimes with a heavier, but nearly degenerate, charged state ?±. For small splittings of O(10) MeV, the scattering of WIMPs off nuclei may be dominated by inelastic recombination processes mediated by the formation of (?-N) bound states, leading to a distinct signature for direct detection. These cross sections are bound primarily by limits on the abundance of heavy isotopes, and may be considerably larger than the elastic scattering cross section in more conventional models. If the mass splitting is too large for recombination to occur, there may still be a significant resonant enhancement of loop-induced electromagnetic form factors of the WIMP, which can enhance the elastic scattering cross section. We also discuss how this regime affects the annihilation cross section and indirect detection signatures, and note the possibility of a significant mono-energetic ? signal, mediated by resonant processes near the (?+?-) bound-state threshold.

  11. Schizosaccharomyces pombe Mms1 channels repair of perturbed replication into Rhp51 independent homologous recombination

    DEFF Research Database (Denmark)

    Vejrup-Hansen, Rasmus; Mizuno, Ken'Ichi

    2011-01-01

    In both Schizosaccharomyces pombe and Saccharomyces cerevisiae, Mms22 and Mms1 form a complex with important functions in the response to DNA damage, loss of which leads to perturbations during replication. Furthermore, in S. cerevisiae, Mms1 has been suggested to function in concert with a Cullin-like protein, Rtt101/Cul8, a potential paralog of Cullin 4. We performed epistasis analysis between ¿mms1 and mutants of pathways with known functions in genome integrity, and measured the recruitment of homologous recombination proteins to blocked replication forks and recombination frequencies. We show that, in S. pombe, the functions of Mms1 and the conserved components of the Cullin 4 ubiquitin ligase, Pcu4 and Ddb1, do not significantly overlap. Furthermore, unlike in S. cerevisiae, the function of the H3K56 acetylase Rtt109 is not essential for Mms1 function. We provide evidence that Mms1 function is particularly important when a single strand break is converted into a double strand break during replication. Genetic data connect Mms1 to a Mus81 and Rad22(Rad52) dependent, but Rhp51 independent, branch of homologous recombination. This is supported by results demonstrating that Mms1 is recruited to a site-specific replication fork barrier and that, in a ¿mms1 strain, Rad22(Rad52) and RPA recruitment to blocked forks are reduced, whereas Rhp51 recruitment is unaffected. In addition, Mms1 appears to specifically promote chromosomal rearrangements in a recombination assay. These observations suggest that Mms1 acts to channel repair of perturbed replication into a particular sub-pathway of homologous recombination.

  12. Function and regulation of the Mediator complex.

    Science.gov (United States)

    Conaway, Ronald C; Conaway, Joan Weliky

    2011-04-01

    Over the past few years, advances in biochemical and genetic studies of the structure and function of the Mediator complex have shed new light on its subunit architecture and its mechanism of action in transcription by RNA polymerase II (pol II). The development of improved methods for reconstitution of recombinant Mediator subassemblies is enabling more in-depth analyses of basic features of the mechanisms by which Mediator interacts with and controls the activity of pol II and the general initiation factors. The discovery and characterization of multiple, functionally distinct forms of Mediator characterized by the presence or absence of the Cdk8 kinase module have led to new insights into how Mediator functions in both Pol II transcription activation and repression. Finally, progress in studies of the mechanisms by which the transcriptional activation domains (ADs) of DNA binding transcription factors target Mediator have brought to light unexpected complexities in the way Mediator participates in signal transduction. PMID:21330129

  13. Cell biology of mitotic recombination.

    Science.gov (United States)

    Lisby, Michael; Rothstein, Rodney

    2015-03-01

    Homologous recombination provides high-fidelity DNA repair throughout all domains of life. Live cell fluorescence microscopy offers the opportunity to image individual recombination events in real time providing insight into the in vivo biochemistry of the involved proteins and DNA molecules as well as the cellular organization of the process of homologous recombination. Herein we review the cell biological aspects of mitotic homologous recombination with a focus on Saccharomyces cerevisiae and mammalian cells, but will also draw on findings from other experimental systems. Key topics of this review include the stoichiometry and dynamics of recombination complexes in vivo, the choreography of assembly and disassembly of recombination proteins at sites of DNA damage, the mobilization of damaged DNA during homology search, and the functional compartmentalization of the nucleus with respect to capacity of homologous recombination. PMID:25731763

  14. Cell biology of mitotic recombination

    DEFF Research Database (Denmark)

    Lisby, Michael; Rothstein, Rodney

    2015-01-01

    Homologous recombination provides high-fidelity DNA repair throughout all domains of life. Live cell fluorescence microscopy offers the opportunity to image individual recombination events in real time providing insight into the in vivo biochemistry of the involved proteins and DNA molecules as well as the cellular organization of the process of homologous recombination. Herein we review the cell biological aspects of mitotic homologous recombination with a focus on Saccharomyces cerevisiae and mammalian cells, but will also draw on findings from other experimental systems. Key topics of this review include the stoichiometry and dynamics of recombination complexes in vivo, the choreography of assembly and disassembly of recombination proteins at sites of DNA damage, the mobilization of damaged DNA during homology search, and the functional compartmentalization of the nucleus with respect to capacity of homologous recombination.

  15. Generation and Characterization of Human Monoclonal Antibodies Targeting Anthrax Protective Antigen following Vaccination with a Recombinant Protective Antigen Vaccine.

    Science.gov (United States)

    Chi, Xiangyang; Li, Jianmin; Liu, Weicen; Wang, Xiaolin; Yin, Kexin; Liu, Ju; Zai, Xiaodong; Li, Liangliang; Song, Xiaohong; Zhang, Jun; Zhang, Xiaopeng; Yin, Ying; Fu, Ling; Xu, Junjie; Yu, Changming; Chen, Wei

    2015-05-01

    The anthrax protective antigen (PA) is the central component of the three-part anthrax toxin, and it is the primary immunogenic component in the approved AVA anthrax vaccine and the "next-generation" recombinant PA (rPA) anthrax vaccines. Animal models have indicated that PA-specific antibodies (AB) are sufficient to protect against infection with Bacillus anthracis. In this study, we investigated the PA domain specificity, affinity, mechanisms of neutralization, and synergistic effects of PA-specific antibodies from a single donor following vaccination with the rPA vaccine. Antibody-secreting cells were isolated 7 days after the donor received a boost vaccination, and 34 fully human monoclonal antibodies (hMAb) were identified. Clones 8H6, 4A3, and 22F1 were able to neutralize lethal toxin (LeTx) both in vitro and in vivo. Clone 8H6 neutralized LeTx by preventing furin cleavage of PA in a dose-dependent manner. Clone 4A3 enhanced degradation of nicked PA, thereby interfering with PA oligomerization. The mechanism of 22F1 is still unclear. A fourth clone, 2A6, that was protective only in vitro was found to be neutralizing in vivo in combination with a toxin-enhancing antibody, 8A7, which binds to domain 3 of PA and PA oligomers. These results provide novel insights into the antibody response elicited by the rPA vaccine and may be useful for PA-based vaccine and immunotherapeutic cocktail design. PMID:25787135

  16. A Differential Recombination Chamber

    International Nuclear Information System (INIS)

    Tbe recombination chambers previously described by the authors, i.e. ionization chambers providing conditions for columnar recombination of ions, are principally used to determine the quality factor (QF) of mixed penetrating radiation. A measure of the QF is the efficiency of ion collection in the chamber at a given voltage of the electric field. The present paper describes a modification to the recombination chamber making it suitable for direct measurement of the dose-equivalent (DE). For this purpose, the measuring electrode or system of electrodes divides the operating volume of the chamber into two parts with a fixed ratio between the mass of gas contained between the measuring electrode and the input electrodes on either side. The voltage of the electric field or the gas pressure differ on either side of the measuring electrode, and are so selected that the efficiency of ion collection in one of the parts, as a result of the columnar recombination occurring in the gas, changes linearly with QF. The other part operates in conditions close to saturation. The directions of the electric field in relation to the measuring electrode are opposite in the two parts of the chamber. Thus, the measuring current is the difference in the charges collected per unit of time from the operating volumes of the chamber. In view of the differences in ion collection efficiency, this differential current is proportional to QF. The proportionality of the current to absorbed dose-rate iity of the current to absorbed dose-rate is also obvious. As a result, the current measured is proportional to the product of dose-rate and QF, i.e. to the DE rate. The differential recombination chamber can be used for continuous recording of the degree of radiation hazard from mixed penetrating radiation of any composition and spectrum which changes quantitatively and qualitatively with time. A further advantage of the differential chamber over the normal recombination chamber is the reduced need for stability of the electrometer. Thus it can be used with a conventional small electrometer as a portable instrument for dosimetric control. The authors have constructed one of the first models of such a differential recombination chamber. It can be used both for dosimetric control measurements and for laboratory investigations. The chamber contains 25 flat electrodes made of a tissue-equivalent material. The distance between the electrodes is fixed by spacers. Appropriate connection of the external leads of the electrodes permits the instrument to be used both as a differential chamber and as a double differential-saturated chamber, mainly for determining the QF of radiation. From the data obtained in investigations of ion recombination characteristics in gases, we can choose optimum values for the distances between the electrodes, the pressure and the composition of the gas mixture, depending on the use to which the chamber is to be put. (author)

  17. AECL passive autocatalytic recombiners

    International Nuclear Information System (INIS)

    Atomic Energy of Canada Limited's (AECL) Passive Autocatalytic Recombiner (PAR) is a passive device used for hydrogen mitigation under post-accident conditions in nuclear reactor containment. The PAR employs a proprietary AECL catalyst which promotes the exothermal reaction between hydrogen and oxygen to form water vapour. The heat of reaction combined with the PAR geometry establishes a convective flow through the recombiner, where ambient hydrogen-rich gas enters the PAR inlet and hot, humid, hydrogen-depleted gas exits the outlet. AECL's PAR has been extensively qualified for CANDU and light water reactors (LWRs), and has been supplied to France, Finland, Ukraine, South Korea and is currently being deployed in Canadian nuclear power plants. (author)

  18. Exploding foil recombination laser

    International Nuclear Information System (INIS)

    In addition to experiments using the collisional-excitation approach to a soft x-ray laser, the authors tested a recombination-pumped laser scheme. Intense (I/sub L/ approx. 2 x 1014 W/cm2) 0.53-?m light of 100- to 200-ps duration from the Novette laser was used to fully ionize a magnesium exploding-foil target. After the peak of the laser pulse, the plasma cooled rapidly due to expansion, electron conduction, and radiation. In the regime of high electron density (approx. 1020 cm-3) and low electron temperature (approx. 100 eV), three-body recombination preferentially populates the upper levels of the hydrogen-like magnesium ion. The population of the lower levels is depleted by fast radiative decay. This process can result in a population inversion on the n = 4 to 3, 130-A transition

  19. Relativistic dielectronic recombination theory

    International Nuclear Information System (INIS)

    Dielectronic recombination (DR) is an inverse Auger process in which a free electron is captured by a recombining ion to form a doubly excited autoionizing state. The subsequent decay of the autoionizing state to a stabilized bound state by emitting photons completes the recombination process. DR is an important recombination process for high temperature plasmas. It can affect the ionization balance and level kinetics of the hot plasmas. In addition, the dielectronic satellite lines observed in the emission spectra are frequently used as plasmas diagnostic tools. In the past decade, intense theoretical and experimental studies on the DR process have been carried out. Most of the earlier theoretical calculations on the DR rate coefficients were done either by using a term average approximation or in LS coupling without including the effects of relativity and configuration interaction. The early experimental investigations were concentrated on few times ionized low-Z ions. Recently, the development of electron beam ion trap (EBIT), electron beam ion source (EBIS) and heavy ion storage ring has become possible to produce very highly-charged heavy ions (e.g. U82+ and Xe53+)and to study the interaction between electrons and these ions. For highly-charged heavy ions, one excepts that the nonrelativistic method would be inadequate and a relativistic treatment is necessary. To meet this challenge we have developed a relativistic package based on the multiconfiguration Dirac-Fock method and have carried out systematic relativistic calculations of DR cross sections and rate coefficients and resonant transfer and excitation cross sections in ion-atom collisions. In this paper, we will briefly discuss the relativistic calculations of atomic structure and transition rates and will focus for attention on the effects of relativity and intermediate coupling on the DR cross sections and rate coefficients

  20. Demystified… recombinant antibodies

    OpenAIRE

    Smith, K. A.; Nelson, P N; Warren, P.; Astley, S J; Murray, P G; Greenman, J.

    2004-01-01

    Recombinant antibodies are important tools for biomedical research and are increasingly being used as clinical diagnostic/therapeutic reagents. In this article, a background to humanised antibodies is given, together with details of the generation of antibody fragments—for example, single chain Fv fragments. Phage antibody fragments are fast becoming popular and can be generated by simple established methods of affinity enrichment from libraries derived from immune cells. Phage display method...

  1. Recombination in nuclear collisions

    OpenAIRE

    Rudolph C. Hwa

    2010-01-01

    Recombination is a hadronization process that converts partons to hadrons at late time, but the description has no quantitative significance without some meaningful input on the parton distributions at earlier time. Thus observations of particle spectra and correlations have definitive implications on the partonic processes at all transverse momenta. After presenting a general review of the subject at the Workshop, I selected two topics in nuclear collisions for more detaile...

  2. Nonradiative recombination in semiconductors

    CERN Document Server

    Abakumov, VN; Yassievich, IN

    1991-01-01

    In recent years, great progress has been made in the understandingof recombination processes controlling the number of excessfree carriers in semiconductors under nonequilibrium conditions. As a result, it is now possible to give a comprehensivetheoretical description of these processes. The authors haveselected a number of experimental results which elucidate theunderlying physical problems and enable a test of theoreticalmodels. The following topics are dealt with: phenomenological theory ofrecombination, theoretical models of shallow and deep localizedstates, cascade model of carrier captu

  3. Dielectronic recombination theory

    Science.gov (United States)

    Lagattuta, K. J.

    A theory now in wide use for the calculation of dielectronic recombination cross sections (sigma(sup DR)) and rate coefficients (alpha(sup DR)) was one introduced originally by Feshbach for nuclear physics applications and then later adapted for atomic scattering problems by Hahn. In the following, we briefly review this theory in a very general form, which allows one to account for the effects of overlapping and interacting resonances, as well as continuum-continuum coupling. An extension of our notation will then also allow for the inclusion of the effects of direct radiative recombination, along with a treatment of the interference between radiative and dielectronic recombination. Other approaches to the calculation of sigma(sup DR) have been described by Fano and by Seaton. We will not consider those theories here. Calculations of alpha(sup DR) have progressed considerably over the last 25 years, since the early work of Burgess. Advances in the reliability of theoretical predictions have also been promoted recently by a variety of direct laboratory measurements of sigma(sup DR). While the measurements of sigma(sup DR) for delta n not = 0 excitations have tended to agree very well with calculations; the case of delta n = 0 has been problematic. However, by invoking a mechanism originally proposed by Jacobs, which takes into account the effect of stray electric fields on high Rydberg states (HRS) participating in the DR process, new calculations have improved the agreement between theory and experiment for these cases. Nevertheless, certain discrepancies still remain.

  4. Dielectronic recombination theory

    International Nuclear Information System (INIS)

    A theory now in wide use for the calculation of dielectronic recombination cross sections (?DR) and rate coefficients (?DR) was one introduced originally by Feshbach for nuclear physics applications, and then later adapted for atomic scattering problems by Hahn. In the following, we briefly review this theory in a very general form, which allows one to account for the effects of overlapping and interacting resonances, as well as continuum-continuum coupling. An extension of our notation will then also allow for the inclusion of the effects of direct radiative recombination, along with a treatment of the interference between radiative and dielectronic recombination. Other approaches to the calculation of ?DR have been described by Fano and by Seaton. We will not consider those theories here. Calculations of ?DR have progressed considerably over the last 25 years, since the early work of Burgess. Advances in the reliability of theoretical predictions have also been promoted recently b a variety of direct laboratory measurements of ?DR. While the measurements of ?DR for ?n ? 0 excitations have tended to agree very well with calculations, the case of ?n = 0 has been much problematic. However, by invoking a mechanism originally proposed by Jacobs, which takes into account the effect of stray electric fields on high Rydberg states (HRS) participating in the DR process, new calculations have improved the agreement between theory and experiment for these cases. Nevertheless, certain discrepancies still remain

  5. Architecture of recombination intermediates visualized by in-gel FRET of ? integrase–Holliday junction–arm DNA complexes

    OpenAIRE

    Radman-Livaja, Marta; Biswas, Tapan; Mierke, Dale; Landy, Arthur

    2005-01-01

    ? Integrase (Int) mediates recombination between attachment sites on phage and Escherichia coli DNA. Int is assisted by accessory protein-induced DNA loops in bridging pairs of distinct “arm-type” and “core-type” DNA sites to form synapsed recombination complexes that subsequently recombine by means of a Holliday junction (HJ) intermediate. An in-gel FRET assay was developed and used to measure 15 distances between six points in two Int–HJ complexes containing arm-DNA oligonucleoti...

  6. Homologous Recombination via Synthesis-Dependent Strand Annealing in Yeast Requires the Irc20 and Srs2 DNA Helicases

    OpenAIRE

    Miura, Tohru; Yamana, Yoshimasa; Usui, Takehiko; Ogawa, Hiroaki I.; Yamamoto, Masa-toshi; Kusano, Kohji

    2012-01-01

    Synthesis-dependent strand-annealing (SDSA)-mediated homologous recombination replaces the sequence around a DNA double-strand break (DSB) with a copy of a homologous DNA template, while maintaining the original configuration of the flanking regions. In somatic cells at the 4n stage, Holliday-junction-mediated homologous recombination and nonhomologous end joining (NHEJ) cause crossovers (CO) between homologous chromosomes and deletions, respectively, resulting in loss of heterozygosity (LOH)...

  7. Detecting variable (V, diversity (D and joining (J gene segment recombination using a two-colour fluorescence system

    Directory of Open Access Journals (Sweden)

    Scott Gina B

    2010-03-01

    Full Text Available Abstract Background Diversity of immunoglobulins and the T cell antigen receptors is achieved via the recombination activating gene (RAG-mediated rearrangement of variable (V, diversity (D and joining (J gene segments, and this underpins the efficient recognition of a seemingly limitless array of antigens. Analysis of V(DJ recombination activity is typically performed using extrachromosomal recombination substrates that are recovered from transfected cells and selected using bacterial transformation. We have developed a two-colour fluorescence-based system that simplifies detection of both deletion and inversion joining events mediated by RAG proteins. Results This system employs two fluorescent reporter genes that differentially mark unrearranged substrates and those that have undergone RAG-mediated deletion or inversion events. The recombination products bear the hallmarks of true V(DJ recombination and activity can be detected using fluorescence microscopy or flow cytometry. Recombination events can be detected without the need for cytotoxic selection of recombination products and the system allows analysis of recombination activity using substrates integrated into the genome. Conclusions This system will be useful in the analysis and exploitation of the V(DJ recombination machinery and suggests that similar approaches could be used to replace expression of one gene with another during lymphocyte development.

  8. Mediators of homologous DNA pairing.

    Science.gov (United States)

    Zelensky, Alex; Kanaar, Roland; Wyman, Claire

    2014-12-01

    Homologous DNA pairing and strand exchange are at the core of homologous recombination. These reactions are promoted by a DNA-strand-exchange protein assembled into a nucleoprotein filament comprising the DNA-pairing protein, ATP, and single-stranded DNA. The catalytic activity of this molecular machine depends on control of its dynamic instability by accessory factors. Here we discuss proteins known as recombination mediators that facilitate formation and functional activation of the DNA-strand-exchange protein filament. Although the basics of homologous pairing and DNA-strand exchange are highly conserved in evolution, differences in mediator function are required to cope with differences in how single-stranded DNA is packaged by the single-stranded DNA-binding protein in different species, and the biochemical details of how the different DNA-strand-exchange proteins nucleate and extend into a nucleoprotein filament. The set of (potential) mediator proteins has apparently expanded greatly in evolution, raising interesting questions about the need for additional control and coordination of homologous recombination in more complex organisms. PMID:25301930

  9. Pre-Exposure to Ionizing Radiation Stimulates DNA Double Strand Break End Resection, Promoting the Use of Homologous Recombination Repair

    Science.gov (United States)

    Oike, Takahiro; Okayasu, Ryuichi; Murakami, Takeshi; Nakano, Takashi; Shibata, Atsushi

    2015-01-01

    The choice of DNA double strand break (DSB) repair pathway is determined at the stage of DSB end resection. Resection was proposed to control the balance between the two major DSB repair pathways, homologous recombination (HR) and non-homologous end joining (NHEJ). Here, we examined the regulation of DSB repair pathway choice at two-ended DSBs following ionizing radiation (IR) in G2 phase of the cell cycle. We found that cells pre-exposed to low-dose IR preferred to undergo HR following challenge IR in G2, whereas NHEJ repair kinetics in G1 were not affected by pre-IR treatment. Consistent with the increase in HR usage, the challenge IR induced Replication protein A (RPA) foci formation and RPA phosphorylation, a marker of resection, were enhanced by pre-IR. However, neither major DNA damage signals nor the status of core NHEJ proteins, which influence the choice of repair pathway, was significantly altered in pre-IR treated cells. Moreover, the increase in usage of HR due to pre-IR exposure was prevented by treatment with ATM inhibitor during the incubation period between pre-IR and challenge IR. Taken together, the results of our study suggest that the ATM-dependent damage response after pre-IR changes the cellular environment, possibly by regulating gene expression or post-transcriptional modifications in a manner that promotes resection. PMID:25826455

  10. Recombinant Collagenlike Proteins

    Science.gov (United States)

    Fertala, Andzej

    2007-01-01

    A group of collagenlike recombinant proteins containing high densities of biologically active sites has been invented. The method used to express these proteins is similar to a method of expressing recombinant procollagens and collagens described in U. S. Patent 5,593,859, "Synthesis of human procollagens and collagens in recombinant DNA systems." Customized collagenous proteins are needed for biomedical applications. In particular, fibrillar collagens are attractive for production of matrices needed for tissue engineering and drug delivery. Prior to this invention, there was no way of producing customized collagenous proteins for these and other applications. Heretofore, collagenous proteins have been produced by use of such biological systems as yeasts, bacteria, and transgenic animals and plants. These products are normal collagens that can also be extracted from such sources as tendons, bones, and hides. These products cannot be made to consist only of biologically active, specific amino acid sequences that may be needed for specific applications. Prior to this invention, it had been established that fibrillar collagens consist of domains that are responsible for such processes as interaction with cells, binding of growth factors, and interaction with a number of structural proteins present in the extracellular matrix. A normal collagen consists of a sequence of domains that can be represented by a corresponding sequence of labels, e.g., D1D2D3D4. A collagenlike protein of the present invention contains regions of collagen II that contain multiples of a single domain (e.g., D1D1D1D1 or D4D4D4D4) chosen for its specific biological activity. By virtue of the multiplicity of the chosen domain, the density of sites having that specific biological activity is greater than it is in a normal collagen. A collagenlike protein according to this invention can thus be made to have properties that are necessary for tissue engineering.

  11. Primordial magnetogenesis before recombination

    CERN Document Server

    Fabre, Ophélia

    2015-01-01

    The origin of large magnetic fields in the Universe remains currently unknown. We investigate here a mechanism before recombination based on known physics. The source of the vorticity is due to the changes in the photon distribution function caused by the fluctuations in the background photons. We show that the magnetic field generated in the MHD limit, due to the Coulomb scattering, is of the order $10^{-49}$ G. We explicitly show that the magnetic fields generated from this process are sustainable and are not erased by resistive diffusion. We compare the results with current observations and discuss the implications.

  12. Resonant scattering and recombination of pseudo-degenerate WIMPs

    OpenAIRE

    Pospelov, Maxim; Ritz, Adam

    2008-01-01

    We consider the direct and indirect detection signatures of WIMPs \\chi^0 in kinematic regimes with a heavier, but nearly degenerate, charged state \\chi^{+-}. For small splittings of O(10) MeV, the scattering of WIMPs off nuclei may be dominated by inelastic recombination processes mediated by the formation of (\\chi^- N) bound states, leading to a distinct signature for direct detection. These cross-sections are bound primarily by limits on the abundance of heavy isotopes, an...

  13. Somatic and Germinal Recombination of a Direct Repeat in Arabidopsis

    OpenAIRE

    Assaad, F. F.; Signer, E. R.

    1992-01-01

    Homologous recombination between a pair of directly repeated transgenes was studied in Arabidopsis. The test construct included two different internal, non-overlapping deletion alleles of npt (neomycin phosphotransferase) flanking an active HPT (hygromycin phosphotransferase) gene. This construct was introduced into Arabidopsis by agrobacterium-mediated transformation with selection for resistance to hygromycin, and two independent single-insert lines were analyzed. Selection for active NPT b...

  14. Mediator Complex Regulates Alternative mRNA Processing via the Med23 Subunit

    OpenAIRE

    Huang, Yan; Li, Wencheng; Yao, Xiao; Lin, Qi-jiang; Yin, Jing-wen; Liang, Yan; Heiner, Monika; Tian, Bin; HUI, JINGYI; Wang, Gang

    2012-01-01

    Mediator complex is an integrative hub for transcriptional regulation. Here we show that Mediator regulates alternative mRNA processing via its Med23 subunit. Combining tandem affinity purification and mass spectrometry, we identified a number of mRNA processing factors that bind to a soluble recombinant Mediator subunit MED23 but not to several other Mediator components. One of these factors, hnRNP L, specifically interacts with MED23 in vitro and in vivo. Consistently, Mediator partially co...

  15. Human XPC-hHR23B interacts with XPA-RPA in the recognition of triplex-directed psoralen DNA interstrand crosslinks

    OpenAIRE

    Thoma, Brian S.; Wakasugi, Mitsuo; Christensen, Jesper; Reddy, Madhava C; Karen M. Vasquez

    2005-01-01

    DNA interstrand crosslinks (ICLs) represent a severe form of damage that blocks DNA metabolic processes and can lead to cell death or carcinogenesis. The repair of DNA ICLs in mammals is not well characterized. We have reported previously that a key protein complex of nucleotide excision repair (NER), XPA-RPA, recognizes DNA ICLs. We now report the use of triplex technology to direct a site-specific psoralen ICL to a target DNA substrate to determine whether the human global genome NER damage...

  16. Unraveling recombination rate evolution using ancestral recombination maps

    DEFF Research Database (Denmark)

    Munch, Kasper; Schierup, Mikkel H

    2014-01-01

    Recombination maps of ancestral species can be constructed from comparative analyses of genomes from closely related species, exemplified by a recently published map of the human-chimpanzee ancestor. Such maps resolve differences in recombination rate between species into changes along individual branches in the speciation tree, and allow identification of associated changes in the genomic sequences. We describe how coalescent hidden Markov models are able to call individual recombination events in ancestral species through inference of incomplete lineage sorting along a genomic alignment. In the great apes, speciation events are sufficiently close in time that a map can be inferred for the ancestral species at each internal branch - allowing evolution of recombination rate to be tracked over evolutionary time scales from speciation event to speciation event. We see this approach as a way of characterizing the evolution of recombination rate and the genomic properties that influence it.

  17. Effect of the topoisomerase-II inhibitor etoposide on meiotic recombination in male mice.

    Science.gov (United States)

    Russell, L B; Hunsicker, P R; Hack, A M; Ashley, T

    2000-01-24

    Unlike other chemicals that have been tested in mammalian germ cells, the type-II topoisomerase inhibitor etoposide exhibits significant mutagenicity in primary spermatocytes. Because this is the cell stage during which meiotic recombination normally occurs, and because topoisomerases play a role in recombination, we studied the effect of etoposide on crossing-over in male mice. Exposure to those meiotic prophase stages (probably early to mid-pachytene) during which specific-locus deletion mutations can be induced resulted in decreased crossing-over in the p-Tyr(c) interval of mouse chromosome 7. Accompanying cytological studies with fluorescent antibodies indicated that while there was no detectable effect on the number of recombination nodules (MLH1 foci), there were marked changes in the stage of appearance and localization of RAD51 and RPA proteins. These temporal and spatial protein patterns suggest the formation of multiple lesions in the DNA after MLH1 has already disappeared from spermatocytes. Since etoposide blocks religation of the cut made by type II topoisomerases, repair of DNA damage may result in rejoining of the original DNA strands, undoing the reciprocal exchange that had already occurred and resulting in reduced crossing-over despite a normal frequency of MLH1 foci. Crossing-over could conceivably be affected differentially in different chromosomal regions. If, however, the predominant action of etoposide is to decrease homologous meiotic recombination, the chemical could be expected to increase nondisjunction, an event associated with human genetic risk. Three periods in spermatogenesis respond to etoposide in different ways. Exposure of (a) late differentiating spermatogonia (and, possibly, preleptotene spermatocytes) results in cell death; (b) early- to mid-pachytene induces specific-locus deletions and crossover reduction; and, (c) late pachytene-through-diakinesis leads to genetically unbalanced conceptuses as a result of clastogenic damage. PMID:10648907

  18. MRG15 Is a Novel PALB2-interacting Factor Involved in Homologous Recombination*

    OpenAIRE

    Sy, Shirley M. -h; Huen, Michael S. Y.; Chen, Junjie

    2009-01-01

    PALB2 is an integral component of the BRCA complex important for recombinational DNA repair. However, exactly how this activity is regulated in vivo remains unexplored. Here we provide evidefice to show that MRG15 is a novel PALB2-associated protein that ensures regulated recombination events. We found that the direct interaction between MRG15 and PALB2 is mediated by an evolutionarily conserved region on PALB2. Intriguingly, although damage-induced RAD51 foci formation and mitomycin C sensit...

  19. Role of Blm and collaborating factors in recombination and survival following replication stress in Ustilago maydis

    OpenAIRE

    Mao, Ninghui; Kojic, Milorad; Holloman, William K.

    2009-01-01

    Inactivation of the structural gene for the RecQ family member, BLM in human, Sgs1 in budding yeast, or Rqh1 in fission yeast leads to inappropriate recombination, chromosome abnormalities, and disturbed replication fork progression. Studies with yeasts have demonstrated that auxiliary gene functions can contribute in overlapping ways with Sgs1 or Rqh1 to circumvent or overcome lesions in DNA caused by certain genotoxic agents. In the combined absence of these functions, recombination-mediate...

  20. Lambda red mediated gap repair utilizes a novel replicative intermediate in Escherichia coli.

    Science.gov (United States)

    Reddy, Thimma R; Fevat, Léna M S; Munson, Sarah E; Stewart, A Francis; Cowley, Shaun M

    2015-01-01

    The lambda phage Red recombination system can mediate efficient homologous recombination in Escherichia coli, which is the basis of the DNA engineering technique termed recombineering. Red mediated insertion of DNA requires DNA replication, involves a single-stranded DNA intermediate and is more efficient on the lagging strand of the replication fork. Lagging strand recombination has also been postulated to explain the Red mediated repair of gapped plasmids by an Okazaki fragment gap filling model. Here, we demonstrate that gap repair involves a different strand independent mechanism. Gap repair assays examining the strand asymmetry of recombination did not show a lagging strand bias. Directly testing an ssDNA plasmid showed lagging strand recombination is possible but dsDNA plasmids did not employ this mechanism. Insertional recombination combined with gap repair also did not demonstrate preferential lagging strand bias, supporting a different gap repair mechanism. The predominant recombination route involved concerted insertion and subcloning though other routes also operated at lower frequencies. Simultaneous insertion of DNA resulted in modification of both strands and was unaffected by mutations to DNA polymerase I, responsible for Okazaki fragment maturation. The lower efficiency of an alternate Red mediated ends-in recombination pathway and the apparent lack of a Holliday junction intermediate suggested that gap repair does not involve a different Red recombination pathway. Our results may be explained by a novel replicative intermediate in gap repair that does not involve a replication fork. We exploited these observations by developing a new recombineering application based on concerted insertion and gap repair, termed SPI (subcloning plus insertion). SPI selected against empty vector background and selected for correct gap repair recombinants. We used SPI to simultaneously insert up to four different gene cassettes in a single recombineering reaction. Consequently, our findings have important implications for the understanding of E. coli replication and Red recombination. PMID:25803509

  1. Efficient point mutagenesis in mycobacteria using single-stranded DNA recombineering: characterization of antimycobacterial drug targets.

    Science.gov (United States)

    van Kessel, Julia C; Hatfull, Graham F

    2008-03-01

    Construction of genetically isogenic strains of mycobacteria is complicated by poor recombination rates and the lack of generalized transducing phages for Mycobacterium tuberculosis. We report here a powerful method for introducing single point mutations into mycobacterial genomes using oligonucleotide-derived single-stranded DNA recombineering and mycobacteriophage-encoded proteins. Phage Che9c gp61-mediated recombination is sufficiently efficient that single base changes can be introduced without requirement for direct selection, with isogenic mutant strains identified simply by PCR. Efficient recombination requires only short (50 nucleotide) oligonucleotides, but there is an unusually strong strand bias and an oligonucleotide targeting lagging strand DNA synthesis can recombine more than 10,000-fold efficiently than its complementary oligonucleotide. This ssDNA recombineering provides a simple assay for comparing the activities of related phage recombinases, and we find that both Escherichia coli RecET and phage lambda Red recombination proteins function inefficiently in mycobacteria, illustrating the utility of developing recombineering in new bacterial systems using host-specific bacteriophage recombinases. ssDNA mycobacterial recombineering provides a simple approach to characterizing antimycobacterial drug targets, and we have constructed and characterized single point mutations that confer resistance to isoniazid, rifampicin, ofloxacin and streptomycin. PMID:18221264

  2. CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri.

    Science.gov (United States)

    Oh, Jee-Hwan; van Pijkeren, Jan-Peter

    2014-01-01

    Clustered regularly interspaced palindromic repeats (CRISPRs) and the CRISPR-associated (Cas) nuclease protect bacteria and archeae from foreign DNA by site-specific cleavage of incoming DNA. Type-II CRISPR-Cas systems, such as the Streptococcus pyogenes CRISPR-Cas9 system, can be adapted such that Cas9 can be guided to a user-defined site in the chromosome to introduce double-stranded breaks. Here we have developed and optimized CRISPR-Cas9 function in the lactic acid bacterium Lactobacillus reuteri ATCC PTA 6475. We established proof-of-concept showing that CRISPR-Cas9 selection combined with single-stranded DNA (ssDNA) recombineering is a realistic approach to identify at high efficiencies edited cells in a lactic acid bacterium. We show for three independent targets that subtle changes in the bacterial genome can be recovered at efficiencies ranging from 90 to 100%. By combining CRISPR-Cas9 and recombineering, we successfully applied codon saturation mutagenesis in the L. reuteri chromosome. Also, CRISPR-Cas9 selection is critical to identify low-efficiency events such as oligonucleotide-mediated chromosome deletions. This also means that CRISPR-Cas9 selection will allow identification of recombinant cells in bacteria with low recombineering efficiencies, eliminating the need for ssDNA recombineering optimization procedures. We envision that CRISPR-Cas genome editing has the potential to change the landscape of genome editing in lactic acid bacteria, and other Gram-positive bacteria. PMID:25074379

  3. CRISPR–Cas9-assisted recombineering in Lactobacillus reuteri

    Science.gov (United States)

    Oh, Jee-Hwan; van Pijkeren, Jan-Peter

    2014-01-01

    Clustered regularly interspaced palindromic repeats (CRISPRs) and the CRISPR-associated (Cas) nuclease protect bacteria and archeae from foreign DNA by site-specific cleavage of incoming DNA. Type-II CRISPR–Cas systems, such as the Streptococcus pyogenes CRISPR–Cas9 system, can be adapted such that Cas9 can be guided to a user-defined site in the chromosome to introduce double-stranded breaks. Here we have developed and optimized CRISPR–Cas9 function in the lactic acid bacterium Lactobacillus reuteri ATCC PTA 6475. We established proof-of-concept showing that CRISPR–Cas9 selection combined with single-stranded DNA (ssDNA) recombineering is a realistic approach to identify at high efficiencies edited cells in a lactic acid bacterium. We show for three independent targets that subtle changes in the bacterial genome can be recovered at efficiencies ranging from 90 to 100%. By combining CRISPR–Cas9 and recombineering, we successfully applied codon saturation mutagenesis in the L. reuteri chromosome. Also, CRISPR–Cas9 selection is critical to identify low-efficiency events such as oligonucleotide-mediated chromosome deletions. This also means that CRISPR–Cas9 selection will allow identification of recombinant cells in bacteria with low recombineering efficiencies, eliminating the need for ssDNA recombineering optimization procedures. We envision that CRISPR–Cas genome editing has the potential to change the landscape of genome editing in lactic acid bacteria, and other Gram-positive bacteria. PMID:25074379

  4. Hadron Correlations and Parton Recombination

    OpenAIRE

    Fries, Rainer J.

    2007-01-01

    Parton recombination has been found to be an extremely useful model to understand hadron production at the Relativistic Heavy Ion Collider. It is particularly important to explore its connections with hard processes. This article reviews some of the aspects of the quark recombination model and places particular emphasis on hadron correlations.

  5. Substrate and target sequence length influence RecTE(Psy) recombineering efficiency in Pseudomonas syringae.

    Science.gov (United States)

    Bao, Zhongmeng; Cartinhour, Sam; Swingle, Bryan

    2012-01-01

    We are developing a new recombineering system to assist experimental manipulation of the Pseudomonas syringae genome. P. syringae is a globally dispersed plant pathogen and an important model species used to study the molecular biology of bacteria-plant interactions. We previously identified orthologs of the lambda Red bet/exo and Rac recET genes in P. syringae and confirmed that they function in recombineering using ssDNA and dsDNA substrates. Here we investigate the properties of dsDNA substrates more closely to determine how they influence recombineering efficiency. We find that the length of flanking homologies and length of the sequences being inserted or deleted have a large effect on RecTE(Psy) mediated recombination efficiency. These results provide information about the design elements that should be considered when using recombineering. PMID:23226333

  6. Double strand interaction is the predominant pathway for intermolecular recombination of adeno-associated viral genomes

    International Nuclear Information System (INIS)

    Intermolecular recombination is the foundation for dual vector mediated larger gene transfer by recombinant adeno-associated virus (rAAV). To identify precursors for intermolecular recombination, we sequentially infected skeletal muscle with AAV LacZ trans-splicing viruses. At 1 month postinfection, nearly all inputting single-strand (ss) AAV genomes were cleared out in muscle. If ss-ss interaction is absolutely required for intermolecular recombination, LacZ expression from sequential infection will be negligible to that from coinfection. Interestingly, expression from sequential infection reached ?50% of that from coinfection at the 1-month time-point in BL6 mice. In immune deficient SCID mice, expression from sequential infection was comparable to that from coinfection at the 4- and 13-month time points. Our results suggest that ds interaction represents the predominant pathway for AAV intermolecular recombination

  7. Substrate and Target Sequence Length Influence RecTEPsy Recombineering Efficiency in Pseudomonas syringae

    Science.gov (United States)

    Bao, Zhongmeng; Cartinhour, Sam; Swingle, Bryan

    2012-01-01

    We are developing a new recombineering system to assist experimental manipulation of the Pseudomonas syringae genome. P. syringae is a globally dispersed plant pathogen and an important model species used to study the molecular biology of bacteria-plant interactions. We previously identified orthologs of the lambda Red bet/exo and Rac recET genes in P. syringae and confirmed that they function in recombineering using ssDNA and dsDNA substrates. Here we investigate the properties of dsDNA substrates more closely to determine how they influence recombineering efficiency. We find that the length of flanking homologies and length of the sequences being inserted or deleted have a large effect on RecTEPsy mediated recombination efficiency. These results provide information about the design elements that should be considered when using recombineering. PMID:23226333

  8. Mouse Sycp1 functions in synaptonemal complex assembly, meiotic recombination, and XY body formation.

    Science.gov (United States)

    de Vries, Femke A T; de Boer, Esther; van den Bosch, Mike; Baarends, Willy M; Ooms, Marja; Yuan, Li; Liu, Jian-Guo; van Zeeland, Albert A; Heyting, Christa; Pastink, Albert

    2005-06-01

    In meiotic prophase, synaptonemal complexes (SCs) closely appose homologous chromosomes (homologs) along their length. SCs are assembled from two axial elements (AEs), one along each homolog, which are connected by numerous transverse filaments (TFs). We disrupted the mouse gene encoding TF protein Sycp1 to analyze the role of TFs in meiotic chromosome behavior and recombination. Sycp1(-/-) mice are infertile, but otherwise healthy. Sycp1(-/-) spermatocytes form normal AEs, which align homologously, but do not synapse. Most Sycp1(-/-) spermatocytes arrest in pachynema, whereas a small proportion reaches diplonema, or, exceptionally, metaphase I. In leptotene Sycp1(-/-) spermatocytes, gammaH2AX (indicative of DNA damage, including double-strand breaks) appears normal. In pachynema, Sycp1(-/-) spermatocytes display a number of discrete gammaH2AX domains along each chromosome, whereas gammaH2AX disappears from autosomes in wild-type spermatocytes. RAD51/DMC1, RPA, and MSH4 foci (which mark early and intermediate steps in pairing/recombination) appear in similar numbers as in wild type, but do not all disappear, and MLH1 and MLH3 foci (which mark late steps in crossing over) are not formed. Crossovers were rare in metaphase I of Sycp1(-/-) mice. We propose that SYCP1 has a coordinating role, and ensures formation of crossovers. Unexpectedly, Sycp1(-/-) spermatocytes did not form XY bodies. PMID:15937223

  9. Adenovirus-mediated gene transfer of cGMP-dependent protein kinase increases the sensitivity of cultured vascular smooth muscle cells to the antiproliferative and pro-apoptotic effects of nitric oxide/cGMP.

    Science.gov (United States)

    Chiche, J D; Schlutsmeyer, S M; Bloch, D B; de la Monte, S M; Roberts, J D; Filippov, G; Janssens, S P; Rosenzweig, A; Bloch, K D

    1998-12-18

    Studies in vitro have underestimated the importance of cGMP-dependent protein kinase (PKG) in the modulation of vascular smooth muscle cell (SMC) proliferation and apoptosis in vivo. This is attributable, in part, to a rapid decline in PKG levels as vascular SMC are passaged in culture. We used a recombinant adenovirus encoding PKG (Ad.PKG) to augment kinase activity in cultured rat pulmonary artery SMC (RPaSMC). Incubation of Ad. PKG-infected RPaSMC (multiplicity of infection = 200) with 8-Br-cGMP decreased serum-stimulated DNA synthesis by 85% and cell proliferation at day 5 by 74%. The effect of 8-Br-cGMP on DNA synthesis in Ad.PKG-infected RPaSMC was blocked by KT5823 (PKG inhibitor), but not by KT5720 (cAMP-dependent protein kinase inhibitor). A nitric oxide (NO) donor compound, S-nitrosoglutathione, at concentrations as low as 100 nM, inhibited DNA synthesis in Ad. PKG-infected RPaSMC, but not in uninfected cells or in cells infected with a control adenovirus. In addition, 8-Br-cGMP and S-nitrosoglutathione induced apoptosis in serum-deprived RPaSMC infected with Ad.PKG, but not in uninfected cells or in cells infected with a control adenovirus. These results demonstrate that modulation of PKG levels in vascular SMC can alter the sensitivity of these cells to NO and cGMP. Moreover, these observations suggest an important role for PKG in the regulation of vascular SMC proliferation and apoptosis by NO and cGMP. PMID:9852090

  10. [The role of functional status and recursive partition analysis (RPA) classes for the choice of fractionation regimen in patients with high-grade gliomas].

    Science.gov (United States)

    Izma?lov, T R; Pan'shin, G A; Datsenko, P V

    2012-01-01

    The treatment results of 396 patients with morphologically verified grade 3-4 malignant brain tumors receiving conventional irradiation regimen and irradiation by medium-sized fractions were analyzed to form institutional guidelines.The standard mode of fractionation with a single dose of 2 Gy and total focal dose (TFD) of 60 Gy is appropriate for patients with initial Karnofsky status of 60-100% and Recursive Partition Analysis (RPA) class I-III. TFD increase to 60-62 Gy in grade 4 gliomas and 54-56 Gy in grade 3 gliomas grants a significant improve in overall survival. An increase of a single irradiation fraction to 3 Gy may be used for patients with initially low functional status (Karnofsky 30-50%) and RPA classes IV-VI. In these cases it is advisable to use the TFD of 45 Gy or more (TFD of equivalent regimen with a dose greater than 54 Gy). The mentioned fractionation regimens could be recommended for the use in clinical practice to improve the results of high-grade gliomas treatment. PMID:22888653

  11. Resolution-of-identity approach to Hartree-Fock, hybrid density functionals, RPA, MP2, and \\textit{GW} with numeric atom-centered orbital basis functions

    CERN Document Server

    Ren, Xinguo; Blum, Volker; Wieferink, Jürgen; Tkatchenko, Alexandre; Sanfilippo, Andrea; Reuter, Karsten; Scheffler, Matthias

    2012-01-01

    We present a computational framework that allows for all-electron Hartree-Fock (HF), hybrid density functionals, random-phase approximation (RPA), second-order M{\\o}ller-Plesset perturbation theory (MP2), and $GW$ calculations based on efficient and accurate numeric atomic-centered orbital (NAO) basis sets. The common feature in these approaches is that their key quantities are expressible in terms of products of single-particle basis functions, which can in turn be expanded in a set of auxiliary basis functions. This is a technique known as the "resolution of identity (RI)" which facilitates an efficient treatment of both the two-electron Coulomb repulsion integrals (required in all these approaches) as well as the linear response function (required for RPA and $GW$). We propose a simple prescription for constructing the auxiliary basis which can be applied regardless of whether the underlying radial functions have a specific analytical shape (e.g., Gaussian) or are numerically tabulated. We demonstrate the ...

  12. In vivo effects of anti-inflammatory agents on arachidonic acid (AA) metabolites in the pleural fluid of rats injured in a reverse passive Arthus (RPA) reaction

    International Nuclear Information System (INIS)

    Leukotriene (LT)C4-D4, prostaglandin (PG)E2, thromboxane B2 (TXB), and 6-ketoprostaglandin F1? (6-KP) were measured by radioimmunoassay in pleural fluid of rats immunologically injured in an RPA paradigm. Rats given intravenous BSA were injected intrapleurally 20 min. later with anti-BSA. Phenidone (30 mg/kg), indomethacin (0.3-100 mg/kg), dazoxiben (100 mg/kg), AA-861 (2,3,5 trimethyl-6(12 hydroxy-5,10-dodecadinyl)-1,4-benzoquinone; 100 mg/kg) or vehicle was given intragastrically 1 hr prior to injury. Pleural fluid samples were collected 1 hr after injury. Statistically significant (P 4-D4 after phenidone and AA-861 treatment, in PGE2 and 6-KP after phenidone and indomethacin treatment and in TXB after dazoxiben and indomethacin treatment. Dazoxiben significantly (p < 0.05) increased 6-KP. These data suggest that anti-inflammatory agents given in this in vivo RPA paradigm inhibited AA metabolism in a predictable manner. Also, drug administration was associated with changes in metabolite concentrations at additional pathway sites. Consequently, this paradigm may be a useful model in evaluating shifts in AA metabolism brought about by inflammatory responses and treatments

  13. Randomized Phase II Trial of High-Dose Melatonin and Radiation Therapy for RPA Class 2 Patients With Brain Metastases (RTOG 0119)

    International Nuclear Information System (INIS)

    Purpose: To determine if high-dose melatonin for Radiation Therapy Oncology Group (RTOG) recursive partitioning analysis (RPA) Class 2 patients with brain metastases improved survival over historical controls, and to determine if the time of day melatonin was given affected its toxicity or efficacy. RTOG 0119 was a phase II randomized trial for this group of patients. Methods and Materials: RTOG RPA Class 2 patients with brain metastases were randomized to 20 mg of melatonin, given either in the morning (8-9 AM) or in the evening (8-9 PM). All patients received radiation therapy (30 Gy in 10 fractions) in the afternoon. Melatonin was continued until neurologic deterioration or death. The primary endpoint was overall survival time. Neurologic deterioration, as reflected by the Mini-Mental Status Examination, was also measured. Results: Neither of the randomized groups had survival distributions that differed significantly from the historic controls of patients treated with whole-brain radiotherapy. The median survivals of the morning and evening melatonin treatments were 3.4 and 2.8 months, while the RTOG historical control survival was 4.1 months. Conclusions: High-dose melatonin did not show any beneficial effect in this group of patients

  14. Delayed recombination and standard rulers

    International Nuclear Information System (INIS)

    Measurements of baryonic acoustic oscillations (BAOs) in galaxy surveys have been recognized as a powerful tool for constraining dark energy. However, this method relies on the knowledge of the size of the acoustic horizon at recombination derived from cosmic microwave background (CMB) anisotropy measurements. This estimate is typically derived assuming a standard recombination scheme; additional radiation sources can delay recombination altering the cosmic ionization history and the cosmological inferences drawn from CMB and BAO data. In this paper we quantify the effect of delayed recombination on the determination of dark energy parameters from future BAO surveys such as the Baryon Oscillation Spectroscopic Survey and the Wide-Field Multi-Object Spectrograph. We find the impact to be small but still not negligible. In particular, if recombination is nonstandard (to a level still allowed by CMB data), but this is ignored, future surveys may incorrectly suggest the presence of a redshift-dependent dark energy component. On the other hand, in the case of delayed recombination, adding to the analysis one extra parameter describing deviations from standard recombination does not significantly degrade the error bars on dark energy parameters and yields unbiased estimates. This is due to the CMB-BAO complementarity.

  15. Intermediates in serine recombinase-mediated site-specific recombination.

    Science.gov (United States)

    Marshall Stark, W; Boocock, Martin R; Olorunniji, Femi J; Rowland, Sally-J

    2011-04-01

    Site-specific recombinases are enzymes that promote precise rearrangements of DNA sequences. They do this by cutting and rejoining the DNA strands at specific positions within a pair of target sites recognized and bound by the recombinase. One group of these enzymes, the serine recombinases, initiates strand exchange by making double-strand breaks in the DNA of the two sites, in an intermediate built around a catalytic tetramer of recombinase subunits. However, these catalytic steps are only the culmination of a complex pathway that begins when recombinase subunits recognize and bind to their target sites as dimers. To form the tetramer-containing reaction intermediate, two dimer-bound sites are brought together by protein dimer-dimer interactions. During or after this initial synapsis step, the recombinase subunit and tetramer conformations change dramatically by repositioning of component subdomains, bringing about a transformation of the enzyme from an inactive to an active configuration. In natural serine recombinase systems, these steps are subject to elaborate regulatory mechanisms in order to ensure that cleavage and rejoining of DNA strands only happen when and where they should, but we and others have identified recombinase mutants that have lost dependence on this regulation, thus facilitating the study of the basic steps leading to catalysis. We describe how our studies on activated mutants of two serine recombinases, Tn3 resolvase and Sin, are providing us with insights into the structural changes that occur before catalysis of strand exchange, and how these steps in the reaction pathway are regulated. PMID:21428950

  16. Recombineering: genetic engineering in bacteria using homologous recombination.

    Science.gov (United States)

    Thomason, Lynn C; Sawitzke, James A; Li, Xintian; Costantino, Nina; Court, Donald L

    2014-01-01

    The bacterial chromosome and bacterial plasmids can be engineered in vivo by homologous recombination using PCR products and synthetic oligonucleotides as substrates. This is possible because bacteriophage-encoded recombination proteins efficiently recombine sequences with homologies as short as 35 to 50 bases. Recombineering allows DNA sequences to be inserted or deleted without regard to location of restriction sites. This unit first describes preparation of electrocompetent cells expressing the recombineering functions and their transformation with dsDNA or ssDNA. It then presents support protocols that describe several two-step selection/counter-selection methods of making genetic alterations without leaving any unwanted changes in the targeted DNA, and a method for retrieving onto a plasmid a genetic marker (cloning by retrieval) from the Escherichia coli chromosome or a co-electroporated DNA fragment. Additional protocols describe methods to screen for unselected mutations, removal of the defective prophage from recombineering strains, and other useful techniques. Curr. Protoc. Mol. Biol. 106:1.16.1-1.16.39. © 2014 by John Wiley & Sons, Inc. PMID:24733238

  17. Controlled release from recombinant polymers.

    Science.gov (United States)

    Price, Robert; Poursaid, Azadeh; Ghandehari, Hamidreza

    2014-09-28

    Recombinant polymers provide a high degree of molecular definition for correlating structure with function in controlled release. The wide array of amino acids available as building blocks for these materials lend many advantages including biorecognition, biodegradability, potential biocompatibility, and control over mechanical properties among other attributes. Genetic engineering and DNA manipulation techniques enable the optimization of structure for precise control over spatial and temporal release. Unlike the majority of chemical synthetic strategies used, recombinant DNA technology has allowed for the production of monodisperse polymers with specifically defined sequences. Several classes of recombinant polymers have been used for controlled drug delivery. These include, but are not limited to, elastin-like, silk-like, and silk-elastinlike proteins, as well as emerging cationic polymers for gene delivery. In this article, progress and prospects of recombinant polymers used in controlled release will be reviewed. PMID:24956486

  18. Hydrogen recombiner development at AECL

    International Nuclear Information System (INIS)

    Catalytic recombiners have been developed at AECL for the purpose of hydrogen removal in post-accident nuclear containment buildings. The recombiners are based on a particular catalyst designed by AECL which has extraordinary resistance to fouling from water and water vapour and a large thermodynamic range of operation. The catalysts were developed, originally, for the purpose of heavy water manufacturing by way of a catalytic exchange process. Application of these catalyst materials in recombiners for containment applications began in the late 1980's. The first application was a passive recombiner, qualified for use in control of radiolytic hydrogen in the headspace of a pool-type experimental reactor of AECL design in 1988. The passive, or natural convection recombiner concept has continued development to commercial stage for application in power reactor containments. This paper reviews the AECL recombiner development, describes the current model and shows results from tests of full-scale recombiners in the Large Scale Vented Combustion Test Facility at AECL-WL. The AECL recombiner is designed for compactness and ease of engineering into containment. The design is a simple, open-ended rectangular enclosure with catalyst elements arranged inside to promote optimum convective flow driven by heat of recombination at the catalyst surface. Self start, as evidenced by catalyst heating and initiation of flow, is achieved in less than 1% hydrogen, with available oxygen, at room temperature and 100% relative humidity. This low temperature start-up in condensing atmospheres is viewed as the most challenging condition for wet-proofing effectiveness. Cold start-up is a vital performance requirement in containments, such as CANDU, where engineered air-cooling systems are operating and where long-term hydrogen control is required, after containment atmospheres have cooled. Once started, the removal capacity scales linearly with the inlet cross-section area and the partial pressure of hydrogen. The recombiner also reacts carbon monoxide, in the presence of hydrogen, at approximately the same rate as the hydrogen. The catalyst materials and wet-proofing are unaffected by radiation or high temperatures. Large scale tests confirm self-start behavior and demonstrate strong mixing, irrespective of recombiner placement. (author)

  19. fpr, a deficient Xer recombination site from a Salmonella plasmid, fails to confer stability by dimer resolution: comparative studies with the pJHCMW1 mwr site.

    Science.gov (United States)

    Tran, Tung; Sherratt, David J; Tolmasky, Marcelo E

    2010-02-01

    Salmonella plasmid pFPTB1 includes a Tn3-like transposon and a Xer recombination site, fpr, which mediates site-specific recombination at efficiencies lower than those required for stabilizing a plasmid by dimer resolution. Mutagenesis and comparative studies with mwr, a site closely related to fpr, indicate that there is an interdependence of the sequences in the XerC binding region and the central region in Xer site-specific recombination sites. PMID:19966005

  20. Progenitors of Recombining Supernova Remnants

    OpenAIRE

    Moriya, Takashi J.

    2012-01-01

    Usual supernova remnants have either ionizing plasma or plasma in collisional ionization equilibrium, i.e., the ionization temperature is lower than or equal to the electron temperature. However, the existence of recombining supernova remnants, i.e., supernova remnants with the ionization temperature higher than the electron temperature, is recently confirmed. One suggested way to have recombining plasma in a supernova remnant is to have a dense circumstellar medium at the t...

  1. Inhomogeneous recombinations during cosmic reionization

    OpenAIRE

    Sobacchi, Emanuele; Mesinger, Andrei

    2014-01-01

    By depleting the ionizing photon budget available to expand cosmic HII regions, recombining systems (or Lyman limit systems) can have a large impact during (and following) cosmic reionization. Unfortunately, directly resolving such structures in large-scale reionization simulations is computationally impractical. Instead, here we implement a sub-grid prescription for tracking inhomogeneous recombinations in the intergalactic medium. Building on previous work parameterizing p...

  2. Dielectronic recombination on heliumlike argon

    International Nuclear Information System (INIS)

    We have used the electron-energy dependence of yields of heliumlike and lithiumlike argon ions from the Kansas State University electron-beam ions source (EBIS) to measure the ratio of the cross section for ? n=1 dielectronic recombination of heliumlike argon to that for electron ionization of lithiumlike argon. By normalizing to the latter cross section we obtain absolute dielectronic recombination cross sections and find good agreement with theoretical calculations for the lower-energy resonances

  3. Eukaryotes arose after genetic recombination

    Directory of Open Access Journals (Sweden)

    Stupar Milanko R.

    2006-01-01

    Full Text Available Division of ancestral prokaryotic pragenome into two circular double-stranded DNA molecules by genetic recombination, is a base for future separate evolution of nuclear and mitochondrial gene compartment. This suggests monophyletic origin of both, mitochondrion and nucleus. Presumed organism which genome undergoes genetic recombination has to be searched among an aerobic, oxygen nonproducing, archaeon with no rigid cell wall, but a plasma membrane. Plastid evolves from an aerobic, oxygen producing protoeukaryote, after mitoplastid genome duplication and subsequent functional segregation.

  4. Recombinant snake venom prothrombin activators

    OpenAIRE

    Lövgren, Ann

    2012-01-01

    Three prothrombin activators; ecarin, which was originally isolated from the venom of the saw-scaled viper Echis carinatus, trocarin from the rough-scaled snake Tropidechis carinatus, and oscutarin from the Taipan snake Oxyuranus scutellatus, were expressed in mammalian cells with the purpose to obtain recombinant prothrombin activators that could be used to convert prothrombin to thrombin. We have previously reported that recombinant ecarin can efficiently generate thrombin without the need ...

  5. Tunnel recombinations in yttrium orthophosphate

    International Nuclear Information System (INIS)

    The tunnel luminescence induced by recombination of radiative centres is investigated in synthetic crystals of YPO4. Its spectrum, kinetics, effects of accumulation and connection with thermostimulated processes are studied in the temperature range from 80 to 220 K. It is shown that tunnel recombinations occur only in the genetically associated electron-hole centres. The paramagnetic centres (Zr3+, O-, SiO43-, Eu2+, ASO44-) are interpreted; their thermal stability and connection with the luminescence are investigated

  6. Ethanol production by recombinant hosts

    Science.gov (United States)

    Fowler, David E. (Gainesville, FL); Horton, Philip G. (Gainesville, FL); Ben-Bassat, Arie (Gainesville, FL)

    1996-01-01

    Novel plasmids comprising genes which code for the alcohol dehydrogenase and pyruvate decarboxylase are described. Also described are recombinant hosts which have been transformed with genes coding for alcohol dehydrogenase and pyruvate. By virtue of their transformation with these genes, the recombinant hosts are capable of producing significant amounts of ethanol as a fermentation product. Also disclosed are methods for increasing the growth of recombinant hosts and methods for reducing the accumulation of undesirable metabolic products in the growth medium of these hosts. Also disclosed are recombinant host capable of producing significant amounts of ethanol as a fermentation product of oligosaccharides and plasmids comprising genes encoding polysaccharases, in addition to the genes described above which code for the alcohol dehydrogenase and pyruvate decarboxylase. Further, methods are described for producing ethanol from oligomeric feedstock using the recombinant hosts described above. Also provided is a method for enhancing the production of functional proteins in a recombinant host comprising overexpressing an adhB gene in the host. Further provided are process designs for fermenting oligosaccharide-containing biomass to ethanol.

  7. Delayed recombination and cosmic parameters

    International Nuclear Information System (INIS)

    Current cosmological constraints from cosmic microwave background anisotropies are typically derived assuming a standard recombination scheme, however additional resonance and ionizing radiation sources can delay recombination, altering the cosmic ionization history and the cosmological inferences drawn from the cosmic microwave background data. We show that for recent observations of the cosmic microwave background anisotropy, from the Wilkinson microwave anisotropy probe satellite mission (WMAP) 5-year survey and from the arcminute cosmology bolometer array receiver experiment, additional resonance radiation is nearly degenerate with variations in the spectral index, ns, and has a marked effect on uncertainties in constraints on the Hubble constant, age of the universe, curvature and the upper bound on the neutrino mass. When a modified recombination scheme is considered, the redshift of recombination is constrained to z*=1078±11, with uncertainties in the measurement weaker by 1 order of magnitude than those obtained under the assumption of standard recombination while constraints on the shift parameter are shifted by 1? to R=1.734±0.028. From the WMAP5 data we obtain the following constraints on the resonance and ionization sources parameters: ??i<0.058 at 95% c.l.. Although delayed recombination limits the precision of parameter estimation from the WMAP satellite, we demonstrate that this should not be demonstrate that this should not be the case for future, smaller angular scales measurements, such as those by the Planck satellite mission.

  8. Interchromatid and Interhomolog Recombination in Arabidopsis thaliana

    Science.gov (United States)

    Molinier, Jean; Ries, Gerhard; Bonhoeffer, Sebastian; Hohn, Barbara

    2004-01-01

    Intermolecular recombination events were monitored in Arabidopsis thaliana lines using specially designed recombination traps consisting of tandem disrupted ?-glucuronidase or luciferase reporter genes in direct repeat orientation. Recombination frequencies (RFs) varied between the different lines, indicating possible position effects influencing intermolecular recombination processes. The RFs between sister chromatids and between homologous chromosomes were measured in plants either hemizygous or homozygous for a transgene locus. The RFs in homozygous plants exceeded those of hemizygous plants by a factor of >2, implying that in somatic plant cells both sister chromatid recombination and recombination between homologous chromosomes exist for recombinational DNA repair. In addition, different DNA-damaging agents stimulated recombination in homozygous and hemizygous plants to different extents in a manner dependent on the type of DNA damage and on the genomic region. The genetic and molecular analysis of recombination events showed that most of the somatic recombination events result from gene conversion, although a pop-out event has also been characterized. PMID:14729918

  9. Epoetin: human recombinant erythropoietin.

    Science.gov (United States)

    Flaharty, K K; Grimm, A M; Vlasses, P H

    1989-11-01

    The chemistry, pharmacology, pharmacokinetics, clinical uses and efficacy, adverse effects, drug interactions, dosage and administration, and formulary considerations of epoetin are described. Erythropoietin, a glycoprotein hormone primarily synthesized in the kidney, is the chief regulator of red blood cell production. Erythropoietin concentrations increase in response to a hypoxic state, resulting in increased red blood cell formation, accelerated hemoglobin production, and premature movement of reticulocytes into the circulation. The human gene responsible for the production of erythropoietin recently was cloned, and the recombinant product--epoetin--has been made available through mass production. The apparent volume of distribution of i.v. epoetin approximates the assumed plasma volume both in healthy volunteers and in patients with chronic renal failure. Little is known about the metabolism and route of elimination of epoetin and erythropoietin. Epoetin recently was approved by the FDA for treatment of anemia associated with chronic renal failure. Clinical trials in patients receiving hemodialysis or peritoneal dialysis and in predialysis patients with renal dysfunction demonstrate epoetin's efficacy. Other potential indications include augmentation of blood production in patients enrolled in autologous blood donation programs and treatment of anemias associated with rheumatoid arthritis, sickle cell disease, acquired immunodeficiency syndrome, cancer, and premature birth. The most frequent adverse effect associated with epoetin therapy is the worsening or development of hypertension. Other adverse effects include thrombocytosis, hyperkalemia, rise in serum urea concentration, iron deficiency, and flu-like symptoms. No drug interactions with epoetin have been reported in humans. The recommended starting epoetin dosage in patients with chronic renal failure is 50-100 IU/kg three times weekly. Epoetin is available only as an injection for i.v. or s.c. administration. Epoetin provides a new therapeutic approach to the treatment of anemia associated with chronic renal failure in hemodialysis, peritoneal dialysis, and predialysis patients. Benefits of epoetin therapy include reduced need for blood transfusions, the amelioration of anemic symptoms, and an improved quality of life. PMID:2680241

  10. Recombinant glycosylasparaginase and in vitro correction of aspartylglycosaminuria.

    Science.gov (United States)

    Mononen, I; Heisterkamp, N; Dunder, U; Romppanen, E L; Noronkoski, T; Kuronen, I; Groffen, J

    1995-03-01

    Aspartylglycosaminuria (AGU) is the most common disorder of glycoprotein degradation. AGU patients are deficient in glycosylasparaginase (GA), which results in accumulation of aspartylglucosamine in body fluids and tissues. Human glycosylasparaginase was stably overexpressed in NIH-3T3 mouse fibroblasts, in which the unusual posttranslational processing and maturation of the enzyme occurred in a high degree. The recombinant enzyme was isolated as two isoforms, which were both phosphorylated, and actively transported into AGU fibroblasts and lymphoblasts through mannose-6-phosphate receptor-mediated endocytosis. The rate of uptake into fibroblasts was half-maximal when the concentration of GA in the medium was 5 x 10(-8) M. Immunofluorescence microscopy suggested compartmentalization of the recombinant enzyme in the lysosomes. Supplementation of culture medium with either isoform cleared AGU lymphoblasts of stored aspartylglucosamine when glycosylasparaginase activity in the cells reached 3-4% of that in normal lymphoblasts. A relatively small amount of recombinant GA in the culture medium was sufficient to reverse pathology in the target cells, indicating high corrective quality of the enzyme preparations. The combined evidence indicates that enzyme replacement therapy with the present recombinant glycosylasparaginase might reverse pathology at least in somatic cells of AGU patients. PMID:7896015

  11. Magnetic susceptibility of a CuO2 plane in the La2CuO4 system: I. RPA treatment of the Dzyaloshinskii-Moriya Interactions

    CERN Document Server

    Tabunshchyk, K V

    2005-01-01

    Motivated by recent experiments on undoped La2CuO4, which found pronounced temperature-dependent anisotropies in the low-field magnetic susceptibility, we have investigated a two-dimensional square lattice of S=1/2 spins that interact via Heisenberg exchange plus the symmetric and anti-symmetric Dzyaloshinskii-Moriya anisotropies. We describe the transition to a state with long-ranged order, and find the spin-wave excitations, with a mean-field theory, linear spin-wave analysis, and using Tyablikov's RPA decoupling scheme. We find the different components of the susceptibility within all of these approximations, both below and above the N'eel temperature, and obtain evidence of strong quantum fluctuations and spin-wave interactions in a broad temperature region near the transition.

  12. Investigations for designing catalytic recombiners

    International Nuclear Information System (INIS)

    In case of a severe accident in pressurised water reactors (PWR) a high amount of hydrogen up to about 20,000 m3 might be generated and released into the containments. The mixture consisting of hydrogen and oxygen may either burn or detonate, if ignited. In case of detonation the generated shock wave may endanger the components of the plant or the plant itself. Consequently, effective removal of hydrogen is required. The fact that hydrogen and oxygen react exo-thermally on catalytically acting surfaces already at low temperatures generating steam and heat is made use of in catalytic recombiners. They consist of substrates coated with catalyst (mainly platinum or palladium) which are arranged inside a casing. Being passively acting measures, recombiners do not need any additional energy supply. Experimental investigations on catalytic hydrogen recombination are conducted at FZJ (Forschungszentrum Juelich) using three test facilities. The results yield insight in the development potential of contemporary recombiner systems as well as of innovative systems. Detailed investigations on a recombiner section show strong temperature gradients over the surface of a catalytically coated sample. Dependent on the flow velocity, ignition temperature may be reached at the leading edge already at an inlet hydrogen concentration of about 5 vol.-%. The thermal strain of the substrate leads to considerable detachment of catalyst particles probably causing unintended ignition of the flammable mixture. Temperature peaks can be prevented effectively by leaving the first part of the plate uncoated. In order to avoid overheating of the catalyst elements of a recombiner even at high hydrogen concentrations a modular system of porous substrates is proposed. The metallic substrates are coated with platinum at low catalyst densities thus limiting the activity of the single specimen. A modular arrangement of these elements provides high recombination rates over a large hydrogen concentration range without igniting the mixture

  13. Upstream and downstream processing of recombinant IgA.

    Science.gov (United States)

    Reinhart, David; Kunert, Renate

    2015-02-01

    Immunoglobulin A (IgA) is the most abundant antibody class in the human body and has a unique role in mediating immunity. The ever-increasing knowledge about the potential of IgAs has renewed interest in this antibody class for therapeutic use against a variety of infectious and malignant diseases, and as a preventive agent for mucosal pathogens. Despite the considerable therapeutic potential of IgA the exploration thereof has often been hampered due to difficulties in producing and purifying desired quantities. Large amounts of pure IgA will be required for in vivo studies. This work reviews current achievements and bottlenecks in upstream and downstream processing of recombinant IgA from a biotechnological point of view. We also highlight recent accomplishments with diverse expression systems and presents different affinity techniques for the capture of recombinant IgA to compare their purification potential. PMID:25257601

  14. Genetically Engineered Poxviruses for Recombinant Gene Expression, Vaccination, and Safety

    Science.gov (United States)

    Moss, Bernard

    1996-10-01

    Vaccinia virus, no longer required for immunization against smallpox, now serves as a unique vector for expressing genes within the cytoplasm of mammalian cells. As a research tool, recombinant vaccinia viruses are used to synthesize and analyze the structure--function relationships of proteins, determine the targets of humoral and cell-mediated immunity, and investigate the types of immune response needed for protection against specific infectious diseases and cancer. The vaccine potential of recombinant vaccinia virus has been realized in the form of an effective oral wild-life rabies vaccine, although no product for humans has been licensed. A genetically altered vaccinia virus that is unable to replicate in mammalian cells and produces diminished cytopathic effects retains the capacity for high-level gene expression and immunogenicity while promising exceptional safety for laboratory workers and potential vaccine recipients.

  15. Recombining WMAP: Constraints on ionizing and resonance radiation at recombination

    International Nuclear Information System (INIS)

    We place new constraints on sources of ionizing and resonance radiation at the epoch of the recombination process using the recent cosmic microwave background temperature and polarization spectra coming from the Wilkinson Microwave Anisotropy Probe (WMAP). We find that non-standard recombination scenarios are still consistent with the current data. In light of this we study the impact that such models can have on the determination of several cosmological parameters. In particular, the constraints on curvature and baryon density appear to be weakly affected by a modified recombination scheme. However, it may affect the current WMAP constraints on inflationary parameters such as the spectral index ns and its running. Physically motivated models, such as those based on primordial black holes or super heavy dark matter decay, are able to provide a good fit to the current data. Future observations in both temperature and polarization will be needed to more stringently test these models

  16. PROGENITORS OF RECOMBINING SUPERNOVA REMNANTS

    Energy Technology Data Exchange (ETDEWEB)

    Moriya, Takashi J., E-mail: takashi.moriya@ipmu.jp [Kavli Institute for the Physics and Mathematics of the Universe, Todai Institutes for Advanced Study, University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8583 (Japan)

    2012-05-01

    Usual supernova remnants have either ionizing plasma or plasma in collisional ionization equilibrium, i.e., the ionization temperature is lower than or equal to the electron temperature. However, the existence of recombining supernova remnants, i.e., supernova remnants with ionization temperature higher than the electron temperature, has been recently confirmed. One suggested way to have recombining plasma in a supernova remnant is to have a dense circumstellar medium at the time of the supernova explosion. If the circumstellar medium is dense enough, collisional ionization equilibrium can be established in the early stage of the evolution of the supernova remnant and subsequent adiabatic cooling, which occurs after the shock wave gets out of the dense circumstellar medium, makes the electron temperature lower than the ionization temperature. We study the circumstellar medium around several supernova progenitors and show which supernova progenitors can have a circumstellar medium dense enough to establish collisional ionization equilibrium soon after the explosion. We find that the circumstellar medium around red supergiants (especially massive ones) and the circumstellar medium dense enough to make Type IIn supernovae can establish collisional ionization equilibrium soon after the explosion and can evolve to become recombining supernova remnants. Wolf-Rayet stars and white dwarfs have the possibility to be recombining supernova remnants but the fraction is expected to be very small. As the occurrence rate of the explosions of red supergiants is much higher than that of Type IIn supernovae, the major progenitors of recombining supernova remnants are likely to be red supergiants.

  17. DNA-pairing and annealing processes in homologous recombination and homology-directed repair.

    Science.gov (United States)

    Morrical, Scott W

    2015-02-01

    The formation of heteroduplex DNA is a central step in the exchange of DNA sequences via homologous recombination, and in the accurate repair of broken chromosomes via homology-directed repair pathways. In cells, heteroduplex DNA largely arises through the activities of recombination proteins that promote DNA-pairing and annealing reactions. Classes of proteins involved in pairing and annealing include RecA-family DNA-pairing proteins, single-stranded DNA (ssDNA)-binding proteins, recombination mediator proteins, annealing proteins, and nucleases. This review explores the properties of these pairing and annealing proteins, and highlights their roles in complex recombination processes including the double Holliday junction (DhJ) formation, synthesis-dependent strand annealing, and single-strand annealing pathways--DNA transactions that are critical both for genome stability in individual organisms and for the evolution of species. PMID:25646379

  18. Workshop on Radio Recombination Lines

    CERN Document Server

    1980-01-01

    Since their first detection 15 years ago, radio recombination lines from several elements have been observed in a wide variety of objects including HII regions, planetary nebulae, molecular clouds, the diffuse interstellar medium, and recently, other galaxies. The observations span almost the entire range from 0.1 to 100 GHz, and employ both single­ djsh and aperture synthesis techniques. The theory of radio recombination lines has also advanced strongly, to the point where it is perhaps one of the best-understood in astro­ physics. In a parallel development, it has become possible over the last decade to study these same highly-excited atoms in the laboratory; this work provides further confirmation of the theoretical framework. However there has been continuing controversy over the astrophysical interpre­ tation of radio recombination line observations, especially regarding the role of stimulated emission. A workshop was held in Ottawa on 24-25 August, 1979, bringing together many of the active scientist...

  19. Inhomogeneous recombinations during cosmic reionization

    CERN Document Server

    Sobacchi, Emanuele

    2014-01-01

    By depleting the ionizing photon budget available to expand cosmic HII regions, recombining systems (or Lyman limit systems) can have a large impact during (and following) cosmic reionization. Unfortunately, directly resolving such structures in large-scale reionization simulations is computationally impractical. Instead, here we implement a sub-grid prescription for tracking inhomogeneous recombinations in the intergalactic medium. Building on previous work parameterizing photo-heating feedback on star-formation, we present large-scale, semi-numeric reionization simulations which self-consistently track the local (sub-grid) evolution of both sources and sinks of ionizing photons. Our simple, single-parameter model naturally results in both an extended reionization and a modest, slowly-evolving emissivity, consistent with observations. Recombinations are instrumental in slowing the growth of large HII regions, and damping the rapid rise of the ionizing background in the late stages of (and following) reioniza...

  20. Containment protection with hydrogen recombiners

    International Nuclear Information System (INIS)

    Core meltdown and concrete - melt interactions cause free hydrogen to be produced. Devices protecting against concrete - melt interactions can largely help to avoid hydrogen releases outside the containment. In the hydrogen -steam - air system, the hydrogen concentration should not exceed the limits of deflagration; on no account must it reach the detonation level. Minimum steam fractions can be maintained by means of hydrogen recombiners. The devices should be designed so that the limits of hydrogen concentration can be observed. In the process of catalytic recombination, hydrogen is oxidized at an early stage without producing any flames and before reaching the level of ignitability. (orig.)

  1. Selenium incorporation using recombinant techniques

    International Nuclear Information System (INIS)

    An overview of techniques for recombinant incorporation of selenium and subsequent purification and crystallization of the resulting labelled protein. Using selenomethionine to phase macromolecular structures is common practice in structure determination, along with the use of selenocysteine. Selenium is consequently the most commonly used heavy atom for MAD. In addition to the well established recombinant techniques for the incorporation of selenium in prokaryal expression systems, there have been recent advances in selenium labelling in eukaryal expression, which will be discussed. Tips and things to consider for the purification and crystallization of seleno-labelled proteins are also included

  2. Homologous recombination in Sulfolobus acidocaldarius: genetic assays and functional properties.

    Science.gov (United States)

    Grogan, Dennis W

    2009-02-01

    HR (homologous recombination) is expected to play important roles in the molecular biology and genetics of archaea, but, so far, few functional properties of archaeal HR have been measured in vivo. In the extreme thermoacidophile Sulfolobus acidocaldarius, a conjugational mechanism of DNA transfer enables quantitative analysis of HR between chromosomal markers. Early studies of this system indicated that HR occurred frequently between closely spaced mutations within the pyrE gene, and this result was later supported by various analyses involving defined point mutations and deletions. These properties of intragenic HR suggested a non-reciprocal mechanism in which donor sequences become incorporated into the recipient genome as short segments. Because fragmentation of donor DNA during cell-to-cell transfer could not be excluded from contributing to this result, subsequent analyses have focused on electroporation of selectable donor DNA directly into recipient strains. For example, S. acidocaldarius was found to incorporate synthetic ssDNA (single-stranded DNA) of more than approximately 20 nt readily into its genome. With respect to various molecular properties of the ssDNA substrates, the process resembled bacteriophage lambdaRed-mediated 'recombineering' in Escherichia coli. Another approach used electroporation of a multiply marked pyrE gene to measure donor sequence tracts transferred to the recipient genome in individual recombination events. Initial results indicate multiple discontinuous tracts in the majority of recombinants, representing a relatively broad distribution of tract lengths. This pattern suggests that properties of the HR process could, in principle, account for many of the apparent peculiarities of intragenic recombination initiated by S. acidocaldarius conjugation. PMID:19143608

  3. Mutations, duplication, and deletion of recombined switch regions suggest a role for DNA replication in the immunoglobulin heavy-chain switch.

    OpenAIRE

    Dunnick, W; Wilson, M; Stavnezer, J

    1989-01-01

    The heavy-chain switch from immunoglobulin M (IgM) expression to IgA expression is mediated by a recombination event between segments of DNA called switch regions. The switch regions lie two to six kilobases upstream of the mu and alpha constant region coding segments. Switch recombination to IgA expression results in a recombinant mu-alpha switch region upstream of the expressed alpha constant region gene. We have characterized the products of switch recombination by a lymphoma cell line, I....

  4. DNA damage during the G0/G1 phase triggers RNA-templated, Cockayne syndrome B-dependent homologous recombination.

    Science.gov (United States)

    Wei, Leizhen; Nakajima, Satoshi; Böhm, Stefanie; Bernstein, Kara A; Shen, Zhiyuan; Tsang, Michael; Levine, Arthur S; Lan, Li

    2015-07-01

    Damage repair mechanisms at transcriptionally active sites during the G0/G1 phase are largely unknown. To elucidate these mechanisms, we introduced genome site-specific oxidative DNA damage and determined the role of transcription in repair factor assembly. We find that KU and NBS1 are recruited to damage sites independent of transcription. However, assembly of RPA1, RAD51C, RAD51, and RAD52 at such sites is strictly governed by active transcription and requires both wild-type Cockayne syndrome protein B (CSB) function and the presence of RNA in the G0/G1 phase. We show that the ATPase activity of CSB is indispensable for loading and binding of the recombination factors. CSB counters radiation-induced DNA damage in both cells and zebrafish models. Taken together, our results have uncovered a novel, RNA-based recombination mechanism by which CSB protects genome stability from strand breaks at transcriptionally active sites and may provide insight into the clinical manifestations of Cockayne syndrome. PMID:26100862

  5. DNA annealing by Rad52 Protein is stimulated by specific interaction with the complex of replication protein A and single-stranded DNA

    OpenAIRE

    Sugiyama, Tomohiko; New, James H.; Kowalczykowski, Stephen C.

    1998-01-01

    Homologous recombination in Saccharomyces cerevisiae depends critically on RAD52 function. In vitro, Rad52 protein preferentially binds single-stranded DNA (ssDNA), mediates annealing of complementary ssDNA, and stimulates Rad51 protein-mediated DNA strand exchange. Replication protein A (RPA) is a ssDNA-binding protein that is also crucial to the recombination process. Herein we report that Rad52 protein effects the annealing of RPA–ssDNA complexes, complexes that are otherwise unable to ann...

  6. Genetics Home Reference: Recombinant 8 syndrome

    Science.gov (United States)

    ... this population have been found. What are the genetic changes related to recombinant 8 syndrome? Recombinant 8 ... Center . Where can I find general information about genetic conditions? The Handbook provides basic information about genetics ...

  7. Pulsed ion-ion recombination laser

    Science.gov (United States)

    Petrash, Gueorgii G.; Zemskov, K. I.

    2003-11-01

    A new mechanism of pulsed laser using ion-ion recombination is considered. Advantages of using ion-ion recombination in pulsed operation are considered and estimates of possible characteristics of the lasers are presented.

  8. Recombination in immunoglobulin gene loci

    OpenAIRE

    Komisarenko S. V.; Halytskiy V. A.

    2009-01-01

    Gene network of the lymphoid cell differentiation coordinates precisely the recombination process in immunoglobulin gene loci. In our opinion, cellular microRNAs can contribute to the allelic exclusion through microRNA-directed DNA methylation and participate in retargeting recombinases activity from the gene loci of heavy immunoglobulin chains to the gene loci of light chains

  9. Population inversion in recombining hydrogen plasma

    International Nuclear Information System (INIS)

    The collisional-radiative model is applied to a recombining hydrogen plasma in order to investigate the plasma condition in which the population inversion between the energy levels of hydrogen can be generated. The population inversion is expected in a plasma where the three body recombination has a large contribution to the recombining processes and the effective recombination rate is beyond a certain value for a given electron density and temperature. Calculated results are presented in figures and tables. (author)

  10. The Recombinational Anatomy of a Mouse Chromosome

    OpenAIRE

    Paigen, Kenneth; Szatkiewicz, Jin P.; Sawyer, Kathryn; Leahy, Nicole; Parvanov, Emil D.; Ng, Siemon H. S.; Graber, Joel H.; Broman, Karl W.; Petkov, Petko M.

    2008-01-01

    Among mammals, genetic recombination occurs at highly delimited sites known as recombination hotspots. They are typically 1–2 kb long and vary as much as a 1,000-fold or more in recombination activity. Although much is known about the molecular details of the recombination process itself, the factors determining the location and relative activity of hotspots are poorly understood. To further our understanding, we have collected and mapped the locations of 5,472 crossover events along mouse ...

  11. Pairing and recombination features during meiosis in Cebus paraguayanus (Primates: Platyrrhini

    Directory of Open Access Journals (Sweden)

    Garcia-Cruz Raquel

    2009-06-01

    Full Text Available Abstract Background Among neotropical Primates, the Cai monkey Cebus paraguayanus (CPA presents long, conserved chromosome syntenies with the human karyotype (HSA as well as numerous C+ blocks in different chromosome pairs. In this study, immunofluorescence (IF against two proteins of the Synaptonemal Complex (SC, namely REC8 and SYCP1, two recombination protein markers (RPA and MLH1, and one protein involved in the pachytene checkpoint machinery (BRCA1 was performed in CPA spermatocytes in order to analyze chromosome meiotic behavior in detail. Results Although in the vast majority of pachytene cells all autosomes were paired and synapsed, in a small number of nuclei the heterochromatic C-positive terminal region of bivalent 11 remained unpaired. The analysis of 75 CPA cells at pachytene revealed a mean of 43.22 MLH1 foci per nucleus and 1.07 MLH1 foci in each CPA bivalent 11, always positioned in the region homologous to HSA chromosome 21. Conclusion Our results suggest that C blocks undergo delayed pairing and synapsis, although they do not interfere with the general progress of pairing and synapsis.

  12. Bocavirus infection induces a DNA damage response that facilitates viral DNA replication and mediates cell death.

    Science.gov (United States)

    Luo, Yong; Chen, Aaron Yun; Qiu, Jianming

    2011-01-01

    Minute virus of canines (MVC) is an autonomous parvovirus that replicates efficiently without helper viruses in Walter Reed/3873D (WRD) canine cells. We previously showed that MVC infection induces mitochondrion-mediated apoptosis and G(2)/M-phase arrest in infected WRD cells. However, the mechanism responsible for these effects has not been established. Here, we report that MVC infection triggers a DNA damage response in infected cells, as evident from phosphorylation of H2AX and RPA32. We discovered that both ATM (ataxia telangiectasia-mutated kinase) and ATR (ATM- and Rad3-related kinase) were phosphorylated in MVC-infected WRD cells and confirmed that ATM activation was responsible for the phosphorylation of H2AX, whereas ATR activation was required for the phosphorylation of RPA32. Both pharmacological inhibition of ATM activation and knockdown of ATM in MVC-infected cells led to a significant reduction in cell death, a moderate correction of cell cycle arrest, and most importantly, a reduction in MVC DNA replication and progeny virus production. Parallel experiments with an ATR-targeted small interfering RNA (siRNA) had no effect. Moreover, we identified that this ATM-mediated cell death is p53 dependent. In addition, we localized the Mre11-Rad50-Nbs1 (MRN) complex, the major mediator as well as a substrate of the ATM-mediated DNA damage response pathway to MVC replication centers during infection, and show that Mre11 knockdown led to a reduction in MVC DNA replication. Our findings are the first to support the notion that an autonomous parvovirus is able to hijack the host DNA damage machinery for its own replication and for the induction of cell death. PMID:21047968

  13. Dielectronic recombination in laser generated plasmas

    International Nuclear Information System (INIS)

    Dielectronic recombination coefficients have been computed for hydrogenic ions from HeII to FeXVI over a range of conditions typical of laser generated plasma. The results are displayed in a set a graphs together with the corresponding collisional radiative recombination coefficients. A comparison of these results indicates plasma conditions where dielectronic recombination is a significant process. (author)

  14. The effect of a single recombination event

    DEFF Research Database (Denmark)

    Schierup, Mikkel Heide; Jensen, Thomas Mailund

    We investigate the variance in how visible a single recombination event is in a SNP data set as a function of the type of recombination event and its age. Data is simulated under the coalescent with recombination and inference is by the popular composite likelihood methods. The major determinant of the effect of a recombination event is the genealogical type of the event and whether SNP variation is present that can reveal the genealogical consequences of the recombination event. Recombination events that only change some branch lengths in the genealogy have a very small, but detectable, effect. The more lineages left when the recombination event occurs, the larger effect it has, implying that it is mainly young recombination events that we detect when estimating the rate. If the population is growing, though, more lineages are present back in time and relatively more ancient recombination events may leave a stronger effect on data. We also investigate the amount of recombination events expected to be shared by two populations as a function of their separation time and explicitly model the European and African population in at attempt to survey how large an effect recombination events shared by these two populations are expected to contribute compared to the effect of private recombination events

  15. ZFN-mediated gene targeting of the Arabidopsis protoporphyrinogen oxidase gene through Agrobacterium-mediated floral dip transformation

    OpenAIRE

    Pater, Sylvia; Pinas, Johan E.; Hooykaas, Paul J. J.; Zaal, Bert J.

    2012-01-01

    Previously, we showed that ZFN-mediated induction of double-strand breaks (DSBs) at the intended recombination site enhanced the frequency of gene targeting (GT) at an artificial target locus using Agrobacterium-mediated floral dip transformation. Here, we designed zinc finger nucleases (ZFNs) for induction of DSBs in the natural protoporphyrinogen oxidase (PPO) gene, which can be conveniently utilized for GT experiments. Wild-type Arabidopsis plants and plants expressing the ZFNs were transf...

  16. Characterization of recombinantly expressed matrilin VWA domains.

    Science.gov (United States)

    Becker, Ann-Kathrin A; Mikolajek, Halina; Werner, Jörn M; Paulsson, Mats; Wagener, Raimund

    2015-03-01

    VWA domains are the predominant independent folding units within matrilins and mediate protein-protein interactions. Mutations in the matrilin-3 VWA domain cause various skeletal diseases. The analysis of the pathological mechanisms is hampered by the lack of detailed structural information on matrilin VWA domains. Attempts to resolve their structures were hindered by low solubility and a tendency to aggregation. We therefore took a comprehensive approach to improve the recombinant expression of functional matrilin VWA domains to enable X-ray crystallography and nuclear magnetic resonance (NMR) studies. The focus was on expression in Escherichia coli, as this allows incorporation of isotope-labeled amino acids, and on finding conditions that enhance solubility. Indeed, circular dichroism (CD) and NMR measurements indicated a proper folding of the bacterially expressed domains and, interestingly, expression of zebrafish matrilin VWA domains and addition of N-ethylmaleimide yielded the most stable proteins. However, such proteins did still not crystallize and allowed only partial peak assignment in NMR. Moreover, bacterially expressed matrilin VWA domains differ in their solubility and functional properties from the same domains expressed in eukaryotic cells. Structural studies of matrilin VWA domains will depend on the use of eukaryotic expression systems. PMID:25462806

  17. Detection of Quantitative Trait Loci Influencing Recombination Using Recombinant Inbred Lines

    OpenAIRE

    Dole, Jefferey; Weber, David F.

    2007-01-01

    The genetic basis of variation in recombination in higher plants is polygenic and poorly understood, despite its theoretical and practical importance. Here a method of detecting quantitative trait loci (QTL) influencing recombination in recombinant inbred lines (RILs) is proposed that relies upon the fact that genotype data within RILs carry the signature of past recombination. Behavior of the segregational genetic variance in numbers of chromosomal crossovers (recombination) over generations...

  18. To the theory of dissociative recombination

    International Nuclear Information System (INIS)

    An analytical expression for cross section of dissociative recombination of electron and molecular ion has been obtained. The Morse potential has been choosen as an internuclear potential of both ground electron state of the molecular ion and resonance molecular state. To obtain the recombination coefficient, averaging of dissociative recombination cross section in the Maxwell distribution has been performed in consequence of which the recombination coefficient temperature dependence, ? approximately Tsup(-1/2), has been determined. The temperature dependence of the dissociative recombination which well agrees with experiment has been calculated for the e+NO+ process as an example

  19. Coherent and stochastic contributions of compound resonances in atomic processes: electron recombination, photoionization and scattering

    CERN Document Server

    Flambaum, V V; Gribakin, G F

    2014-01-01

    In open-shell atoms and ions, processes such as photoionization, combination (Raman) scattering, electron scattering and recombination, are often mediated by many-electron compound resonances. We show that their interference (neglected in independent-resonance approximation) leads to a coherent contribution, which determines the energy-averaged total cross sections of electron- and photon-induced reactions found from the optical theorem. On the other hand, the partial cross sections (e.g., electron recombination, combination photon scattering) are dominated by the stochastic contributions. Thus, the optical theorem provides a link between the stochastic and coherent contributions of the compound resonances.

  20. Dimerization of human recombinant resistin involves covalent and noncovalent interactions.

    Science.gov (United States)

    Raghu, Pullakhandam; Ghosh, Sudip; Soundarya, Kanukolanu; Haseeb, Abdul; Aruna, Battu; Ehtesham, Nasreen Z

    2004-01-16

    Resistin, an adipocyte secreted cysteine rich hormone has been implicated as molecular link between obesity and type 2 diabetes in a murine model. Although, at the protein level mouse and human resistin show remarkable similarities with respect to conserved cysteine residues, the physiological role of human resistin is not yet clear. In the present study we describe the purification and refolding of human recombinant resistin using two different refolding processes. Gel filtration analysis of protein refolded by both the methods revealed that human recombinant resistin, like mouse resistin, has a tendency to form dimers. Interestingly, dimerization of resistin appears to be mediated by both covalent (disulfide bond mediated) and non-covalent interactions as seen on reducing and non-reducing SDS-PAGE. Circular dichroism spectral analysis revealed that human resistin peptide backbone is a mixture of alpha-helical and beta-sheet conformation with significant amounts of unordered structure, similar to the mouse resistin. It is likely that the first cysteine (Cyst22) of human resistin, which is equivalent to mouse Cyst26, may be involved in stabilizing the dimers through covalent interaction. PMID:14697240

  1. Homologous Recombination in Negative Sense RNA Viruses

    Directory of Open Access Journals (Sweden)

    Michael Worobey

    2011-08-01

    Full Text Available Recombination is an important process that influences biological evolution at many different levels. More and more homologous recombination events have been reported among negative sense RNA viruses recently. While sporadic authentic examples indicate that homologous recombination does occur, recombination seems to be generally rare or even absent in most negative sense RNA viruses, and most of the homologous recombination events reported in the literature were likely generated artificially due to lab contamination or inappropriate bioinformatics methods. Homologous recombination in negative sense RNA viruses should be reported with caution in the future, and only after stringent quality control efforts. Moreover, co-infection experiments should be performed to confirm whether recombination can occur.

  2. Progenitors of Recombining Supernova Remnants

    CERN Document Server

    Moriya, Takashi J

    2012-01-01

    Usual supernova remnants have either ionizing plasma or plasma in collisional ionization equilibrium, i.e., the ionization temperature is lower than or equal to the electron temperature. However, the existence of recombining supernova remnants, i.e., supernova remnants with the ionization temperature higher than the electron temperature, is recently confirmed. One suggested way to have recombining plasma in a supernova remnant is to have a dense circumstellar medium at the time of the supernova explosion. If the circumstellar medium is dense enough, collisional ionization equilibrium can be established in the early stage of the evolution of the supernova remnant and subsequent adiabatic cooling which occurs after the shock wave gets out of the dense circumstellar medium makes the electron temperature lower than the ionization temperature. We study the circumstellar medium around several supernova progenitors and show which supernova progenitors can have a circumstellar medium which is dense enough to establis...

  3. Shu1 promotes homolog bias of meiotic recombination in Saccharomyces cerevisiae.

    Science.gov (United States)

    Hong, Soogil; Kim, Keun Pil

    2013-11-01

    Homologous recombination occurs closely between homologous chromatids with highly ordered recombinosomes through RecA homologs and mediators. The present study demonstrates this relationship during the period of "partner choice" in yeast meiotic recombination. We have examined the formation of recombination intermediates in the absence or presence of Shu1, a member of the PCSS complex, which also includes Psy3, Csm2, and Shu2. DNA physical analysis indicates that Shu1 is essential for promoting the establishment of homolog bias during meiotic homologous recombination, and the partner choice is switched by Mek1 kinase activity. Furthermore, Shu1 promotes both crossover (CO) and non-crossover (NCO) pathways of meiotic recombination. The inactivation of Mek1 kinase allows for meiotic recombination to progress efficiently, but is lost in homolog bias where most doublestrand breaks (DSBs) are repaired via stable intersister joint molecules. Moreover, the Srs2 helicase deletion cells in the budding yeast show slightly reduced COs and NCOs, and Shu1 promotes homolog bias independent of Srs2. Our findings reveal that Shu1 and Mek1 kinase activity have biochemically distinct roles in partner choice, which in turn enhances the understanding of the mechanism associated with the precondition for homolog bias. PMID:24213600

  4. Gated rotation mechanism of site-specific recombination by ?C31 integrase.

    Science.gov (United States)

    Olorunniji, Femi J; Buck, Dorothy E; Colloms, Sean D; McEwan, Andrew R; Smith, Margaret C M; Stark, W Marshall; Rosser, Susan J

    2012-11-27

    Integrases, such as that of the Streptomyces temperate bacteriophage ?C31, promote site-specific recombination between DNA sequences in the bacteriophage and bacterial genomes to integrate or excise the phage DNA. ?C31 integrase belongs to the serine recombinase family, a large group of structurally related enzymes with diverse biological functions. It has been proposed that serine integrases use a "subunit rotation" mechanism to exchange DNA strands after double-strand DNA cleavage at the two recombining att sites, and that many rounds of subunit rotation can occur before the strands are religated. We have analyzed the mechanism of ?C31 integrase-mediated recombination in a topologically constrained experimental system using hybrid "phes" recombination sites, each of which comprises a ?C31 att site positioned adjacent to a regulatory sequence recognized by Tn3 resolvase. The topologies of reaction products from circular substrates containing two phes sites support a right-handed subunit rotation mechanism for catalysis of both integrative and excisive recombination. Strand exchange usually terminates after a single round of 180° rotation. However, multiple processive "360° rotation" rounds of strand exchange can be observed, if the recombining sites have nonidentical base pairs at their centers. We propose that a regulatory "gating" mechanism normally blocks multiple rounds of strand exchange and triggers product release after a single round. PMID:23150546

  5. Inhibited Recombination of Charged Magnetoexcitons

    CERN Document Server

    Okamura, H; Sundaram, M; Gossard, A C

    1998-01-01

    Time-resolved photoluminescence measurements show that the decay time for charged excitons in a GaAs two-dimensional electron gas increases by an order of magnitude at high magnetic fields. Unlike neutral excitons, the charged exciton center-of-mass is spatially confined in a ``magnetically-adjustable quantum dot'' by the cyclotron orbit and the quantum well. The inhibited recombination is explained by a reduced phase coherence volume of the magnetically-confined charged excitons.

  6. Vortex Collisions Crossing or Recombination?

    CERN Document Server

    Bou-Diab, M; Blatter, G; Bou-Diab, Malek; Dodgson, Matthew J. W.; Blatter, Gianni

    2000-01-01

    We investigate the collision of two vortex lines moving with viscous dynamics and driven towards each other by an applied current. Using London theory in the approach phase we observe a non-trivial vortex conformation producing anti-parallel segments; their attractive interaction triggers a violent collision. The collision region is analyzed using the time-dependent Ginzburg-Landau equation. While we find vortices will always recombine through exchange of segments, a crossing channel appears naturally through a double collision process.

  7. Vortex Collisions: Crossing or Recombination?

    OpenAIRE

    Bou-diab, Malek; Dodgson, Matthew J. W.; Blatter, Gianni

    2000-01-01

    We investigate the collision of two vortex lines moving with viscous dynamics and driven towards each other by an applied current. Using London theory in the approach phase we observe a non-trivial vortex conformation producing anti-parallel segments; their attractive interaction triggers a violent collision. The collision region is analyzed using the time-dependent Ginzburg-Landau equation. While we find vortices will always recombine through exchange of segments, a crossin...

  8. Yeast Pch2 promotes domainal axis organization, timely recombination progression, and arrest of defective recombinosomes during meiosis

    OpenAIRE

    Bo?rner, G. Valentin; Barot, Aekam; Kleckner, Nancy

    2008-01-01

    We show that, during budding yeast meiosis, axis ensemble Hop1/Red1 and synaptonemal complex (SC) component Zip1 tend to occur in alternating strongly staining domains. The widely conserved AAA+-ATPase Pch2 mediates this pattern, likely by means of direct intervention along axes. Pch2 also coordinately promotes timely progression of cross-over (CO) and noncross-over (NCO) recombination. Oppositely, in a checkpoint-triggering aberrant situation (zip1?), Pch2 mediates robust arrest of stalled ...

  9. Recombinant platelet factor 4: a therapeutic, anti-neoplastic chimera?

    Science.gov (United States)

    Lippi, Giuseppe; Favaloro, Emmanuel J

    2010-07-01

    Angiogenesis plays a pivotal role in many serious and life-threatening disorders (e.g., cancer, atherosclerosis, diabetes, arthritis, psoriasis, nephropathy, and retinopathy) and is regulated by a delicate equilibrium between a variety of pro- and anti-angiogenic factors. Although recombinant platelet factor 4 (PF4) was originally developed and evaluated as a clinical alternative to protamine for heparin neutralization, the current scientific evidence supports a role for this protein and derivative peptides in inhibiting tumor growth and spread, by suppression of tumor-induced neovascularization in many different types of solid tumors. As a heparin-binding tetramer, recombinant PF4 interferes with several steps of endothelial cell proliferation, migration, and angiogenesis, regulates apoptotic death through activation of distinct signal transduction pathways, inhibits growth factor receptor binding, amplifies the inflammatory response of natural killer cells through regulation of cytokines production, and induces and maintains a nonspecific immune response to cancer cells. These biological evidences paved the way for the development and marketing of novel PF4-based angiostatic agents characterized by reduced toxicity and improved bioavailability, thus raising the possibility of an alternative approach for preventing and treating growth and metastasis of tumors. Some PF4-derived molecules such as carboxyl-terminal fragments of recombinant human PF4 and modified and chimeric peptides have already been developed that exhibit stronger anti-angiogenic properties than the parent molecule and may serve as leads for further therapeutic developments. Newer means of delivering of this anti-angiogenic agent are also being attempted, including PF4-bearing polymeric microspheres, vector-mediated PF4 transduction, transgene transfection into oncolytic viruses, and molecular targeting therapy against PF4 and rHuPF4 conjugates. These delivery systems aim to produce high concentrations of the therapeutic agent in a local area for a sustained period, thereby avoiding the typical problems encountered with long-term administration of recombinant proteins. PMID:20632253

  10. Experimental evidence of ternary recombinations

    International Nuclear Information System (INIS)

    Full text: About four decades ago D'Angelo [1] noticed that the measured rate coefficients for the radiative recombination (RR) for a fully stripped ions were orders of magnitude larger than that predicted by early theories. He noted that the discrepancy was, in fact, due to the dominance of another recombination process often called ternary recombination (TR) because in this phenomenon two electrons and one ion get involved. This picture becomes more complicated for projectiles, containing one or more electrons as dielectronic recombinations (DR) also start contributing. Thus, it has been impossible to decouple TR from RR and DR processes yet. It may be worth mentioning that experimental situations allow low lying bound levels through RR and DR processes while TR into high Rydberg states is conceivable at low electron energies. One observes a transition in a time resolved spectroscopy experiment whose upper level is produced by RR and DR. TR may lead to the same transition after a certain time as electron has to cascade down to the same low lying level from a Rydberg state. Thus one may see that RR and DR are prompt and TR is a delayed one. However, separation of these processes was not possible yet. One needs the right situation which may well resolve TR from RR and DR. Such situation was evident in a beam-foil experiment favoring nuclear reactions. Residue nuclei may undergo electron capture processes such as DR and TR. These nuclei being fully striped ions would nse nuclei being fully striped ions would not allow DR to take place. Impact of 170MeV Ni ions on carbon foil in beam-foil experiments led to formation of the residues 62,64Zn, 65Ga, 68Ge, and 68As. X-rays due to M1 transition from such residue H-like ions were observed in the time resolved x-ray spectroscopy. Prompt x-ray produced by RR and the delayed by TR are quite well distinguished in the decay curve. Such results reveals experimental evidence of ternary recombination for the first time. Experimental technique, novel analysis, and salient results will be highlighted

  11. Post-Replication Repair Suppresses Duplication-Mediated Genome Instability

    OpenAIRE

    Putnam, Christopher D.; Hayes, Tikvah K.; Kolodner, Richard D.

    2010-01-01

    RAD6 is known to suppress duplication-mediated gross chromosomal rearrangements (GCRs) but not single-copy sequence mediated GCRs. Here, we found that the RAD6- and RAD18-dependent post-replication repair (PRR) and the RAD5-, MMS2-, UBC13-dependent error-free PRR branch acted in concert with the replication stress checkpoint to suppress duplication-mediated GCRs formed by homologous recombination (HR). The Rad5 helicase activity, but not its RING finger, was required to prevent duplication-me...

  12. PRACTICAL ASPECTS OF MEDIATION

    OpenAIRE

    IULIA FLOCA

    2011-01-01

    Today the Romanian state gives some advantages to those who use mediation. If the Romanian state would take further steps, mediation would work as in the countries with old tradition. The article refers to success and failure got in the two years of practice. The mediation can be seen in two aspects: The first aspect regarding the mediation itself can lead to a mediation agreement. The mediation agreement gives both winnings to the conflict parts and professional satisfactions to the mediator...

  13. Construction of recombinant industrial Saccharomyces cerevisiae strain with bglS gene insertion into PEP4 locus by homologous recombination.

    Science.gov (United States)

    Zhang, Qiang; Chen, Qi-He; Fu, Ming-Liang; Wang, Jin-Ling; Zhang, Hong-Bo; He, Guo-Qing

    2008-07-01

    The bglS gene encoding endo-l,3-1,4-beta-glucanase from Bacillus subtilis was cloned and sequenced in this study. The bglS expression cassette, including PGK1 promoter, bglS gene fused to the signal sequence of the yeast mating pheromone alpha-factor (MFalpha1(S)), and ADH1 terminator with G418-resistance as the selected marker, was constructed. Then one of the PEP4 allele of Saccharomyces cerevisiae WZ65 strain was replaced by bglS expression cassette using chromosomal integration of polymerase chain reaction (PCR)-mediated homologous recombination, and the bglS gene was expressed simultaneously. The recombinant strain S. cerevisiae (SC-betaG) was preliminarily screened by the clearing hydrolysis zone formed after the barley beta-glucan was hydrolyzed in the plate and no proteinase A (PrA) activity was measured in fermenting liquor. The results of PCR analysis of genome DNA showed that one of the PEP4 allele had been replaced and bglS gene had been inserted into the locus of PEP4 gene in recombinant strains. Different endo-l,3-1,4-beta-glucanase assay methods showed that the recombinant strain SC-betaG had high endo-l,3-1,4-beta-glucanase expression level with the maximum of 69.3 U/(h.ml) after 60 h of incubation. Meanwhile, the Congo Red method was suitable for the determination of endo-l,3-1,4-beta-glucanase activity during the actual brewing process. The current research implies that the constructed yeast strain could be utilized to improve the industrial brewing property of beer. PMID:18600782

  14. Recombinant Goat VEGF164 Increases Hair Growth by Painting Process on the Skin of Shaved Mouse.

    Science.gov (United States)

    Bao, Wenlei; Yin, Jianxin; Liang, Yan; Guo, Zhixin; Wang, Yanfeng; Liu, Dongjun; Wang, Xiao; Wang, Zhigang

    2014-09-01

    To detect goat vascular endothelial growth factor (VEGF)-mediated regrowth of hair, full-length VEGF164 cDNA was cloned from Inner Mongolia cashmere goat (Capra hircus) into the pET-his prokaryotic expression vector, and the recombinant plasmid was transferred into E. coli BL21 cells. The expression of recombinant 6×his-gVEGF164 protein was induced by 0.5 mM isopropyl thio-?-D-galactoside at 32°C. Recombinant goat VEGF164 (rgVEGF164) was purified and identi ed by western blot using monoclonal anti-his and anti-VEGF antibodies. The rgVEGF164 was smeared onto the dorsal area of a shaved mouse, and we noted that hair regrowth in this area was faster than in the control group. Thus, rgVEGF164 increases hair growth in mice. PMID:25178380

  15. Reflectometric interference spectroscopy-based immunosensing using immobilized antibody via His-tagged recombinant protein A.

    Science.gov (United States)

    Choi, Hyung Woo; Sakata, Yasuhiko; Ooya, Tooru; Takeuchi, Toshifumi

    2015-02-01

    The proposed approach demonstrated in this study provides an immunosensing system based on reflectometric interference spectroscopy (RIfS) in combination with an antibody immobilization method using histidine-tagged recombinant protein A. Carboxymethyldextran (CMD) was immobilized on a 3-aminopropyltriethoxysilane-treated a silicon nitride-coated silicon wafer, followed by chelating histidine-tagged recombinant protein A with copper (II) ions. The CMD-layer was found to be advantageous in terms of not only immobilization of histidine-tagged recombinant protein A-mediated an antibody against myoglobin (anti-Myo) but also prevention of non-specific binding of myoglobin. Myoglobin was repeatedly detected, and the apparent detection limit was 0.1 ?g mL(-1). The proposed RIfS-based protein sensing system, in conjunction with the easy preparation of silicon-based inexpensive immunosensing chips, is expected to be applicable for label-free optical detection for other proteins in various fields. PMID:25060725

  16. Effects of Recombination on Complex Regulatory Circuits

    Science.gov (United States)

    Martin, Olivier C.; Wagner, Andreas

    2009-01-01

    Mutation and recombination are the two main forces generating genetic variation. Most of this variation may be deleterious. Because recombination can reorganize entire genes and genetic circuits, it may have much greater consequences than point mutations. We here explore the effects of recombination on models of transcriptional regulation circuits that play important roles in embryonic development. We show that recombination has weaker deleterious effects on the expression phenotypes of these circuits than mutations. In addition, if a population of such circuits evolves under the influence of mutation and recombination, we find that three key properties emerge: (1) deleterious effects of mutations are reduced dramatically; (2) the diversity of genotypes in the population is greatly increased, a feature that may be important for phenotypic innovation; and (3) cis-regulatory complexes appear. These are combinations of regulatory interactions that influence the expression of one gene and that mitigate deleterious recombination effects. PMID:19652184

  17. Detecting the cosmological recombination signal from space

    CERN Document Server

    Desjacques, Vincent; Silk, Joseph; de Bernardis, Francesco; Doré, Olivier

    2015-01-01

    Spectral distortions of the CMB have recently experienced an increased interest. One of the inevitable distortion signals of our cosmological concordance model is created by the cosmological recombination process, just a little before photons last scatter at redshift $z\\simeq 1100$. These cosmological recombination lines, emitted by the hydrogen and helium plasma, should still be observable as tiny deviation from the CMB blackbody spectrum in the cm--dm spectral bands. In this paper, we present a forecast for the detectability of the recombination signal with future satellite experiments. We argue that serious consideration for future CMB experiments in space should be given to probing spectral distortions and, in particular, the recombination line signals. The cosmological recombination radiation not only allows determination of standard cosmological parameters, but also provides a direct observational confirmation for one of the key ingredients of our cosmological model: the cosmological recombination histo...

  18. Heterogeneity in recombinant protein production

    DEFF Research Database (Denmark)

    Schalén, Martin; Johanson, Ted

    2012-01-01

    A crucial step in biotechnology is the scale-up process. Normally, lab scale verification and optimization of production processes and strains are performed in small reactors with perfect mixing and hence the cells experience a homogenous environment. The gradients that occur in industrial scale bioreactors are often not taken into consideration in these experiments. Gradients occur due to insufficient mixing in the reactor, and affect the process in a variety of ways. When cells travel through the reactor and encounter different substrate concentrations, oxygen availability, pH, temperature, etc. the cell physiology is affected. Cells are stressed, and this may severely affect growth, by-product accumulation, biomass yield and recombinant product yield. The stress caused by exposure to divergent microenvironments, genetic differences of individual cells, differing cell cycle stage and cell age, all contribute to make a population in a fermenter heterogeneous, resulting in cell-to-cell variation in physiological parameters of the microbial culture. Our study aims at investigating how population heterogeneity and recombinant protein production is affected by environmental gradients in bioreactors. For this purpose, a Saccharomyces cerevisiae strain, that functions as a protein production reporter, has been developed. A heterologous protein has been tagged with a fluorescent protein providing a way to measure the amount of heterologous protein produced by the cells on single cell level. Gradients are simulated in small bioreactors and the population heterogeneity can be visualised by analysing single cells with flow cytometry. This can give new insights to cell physiology and recombinant protein production at the industrial scale.

  19. Putative antirecombinase Srs2 DNA helicase promotes noncrossover homologous recombination avoiding loss of heterozygosity.

    Science.gov (United States)

    Miura, Tohru; Shibata, Takehiko; Kusano, Kohji

    2013-10-01

    DNA damage alone or DNA replication fork arrest at damaged sites may induce DNA double-strand breaks and initiate homologous recombination. This event can result in a crossover with a homologous chromosome, causing loss of heterozygosity along the chromosome. It is known that Srs2 acts as an antirecombinase at the replication fork: it is recruited by the SUMO (a small ubiquitin-related modifier)-conjugated DNA-polymerase sliding clamp (PCNA) and interferes with Rad51/Rad52-mediated homologous recombination. Here, we report that Srs2 promotes another type of homologous recombination that produces noncrossover products only, in collaboration with PCNA and Rad51. Srs2 proteins lacking the Rad51-binding domain, PCNA-SUMO-binding motifs, or ATP hydrolysis-dependent DNA helicase activity reduce this noncrossover recombination. However, the removal of either the Rad51-binding domain or the PCNA-binding motif strongly increases crossovers. Srs2 gene mutations are epistatic to mutations in the PCNA modification-related genes encoding PCNA, Siz1 (a SUMO ligase) and Rad6 (a ubiquitin-conjugating protein). Knocking out RAD51 blocked this recombination but enhanced nonhomologous end-joining. We hypothesize that, during DNA double-strand break repair, Srs2 mediates collaboration between the Rad51 nucleofilament and PCNA-SUMO and directs the heteroduplex intermediate to DNA synthesis in a moving bubble. This Rad51/Rad52/Srs2/PCNA-mediated noncrossover pathway avoids both interchromosomal crossover and imprecise end-joining, two potential paths leading to loss of heterozygosity, and contributes to genome maintenance and human health. PMID:24043837

  20. Unveiling novel RecO distant orthologues involved in homologous recombination.

    Science.gov (United States)

    Marsin, Stéphanie; Mathieu, Aurélie; Kortulewski, Thierry; Guérois, Raphaël; Radicella, J Pablo

    2008-01-01

    The generation of a RecA filament on single-stranded DNA is a critical step in homologous recombination. Two main pathways leading to the formation of the nucleofilament have been identified in bacteria, based on the protein complexes mediating RecA loading: RecBCD (AddAB) and RecFOR. Many bacterial species seem to lack some of the components involved in these complexes. The current annotation of the Helicobacter pylori genome suggests that this highly diverse bacterial pathogen has a reduced set of recombination mediator proteins. While it is now clear that homologous recombination plays a critical role in generating H. pylori diversity by allowing genomic DNA rearrangements and integration through transformation of exogenous DNA into the chromosome, no complete mediator complex is deduced from the sequence of its genome. Here we show by bioinformatics analysis the presence of a RecO remote orthologue that allowed the identification of a new set of RecO proteins present in all bacterial species where a RecR but not RecO was previously identified. HpRecO shares less than 15% identity with previously characterized homologues. Genetic dissection of recombination pathways shows that this novel RecO and the remote RecB homologue present in H. pylori are functional in repair and in RecA-dependent intrachromosomal recombination, defining two initiation pathways with little overlap. We found, however, that neither RecOR nor RecB contributes to transformation, suggesting the presence of a third, specialized, RecA-dependent pathway responsible for the integration of transforming DNA into the chromosome of this naturally competent bacteria. These results provide insight into the mechanisms that this successful pathogen uses to generate genetic diversity and adapt to changing environments and new hosts. PMID:18670631

  1. Calculation of Gamow-Teller #betta#-strength functions in the Rubidium region in the RPA approximation with Nilsson model wave functions

    International Nuclear Information System (INIS)

    We calculate allowed Gamow-Teller and, in a few cases, Fermi #betta#strength functions in a model that is applicable to studies of nuclei throughout the periodic system. For our first study we have selected a sequence of rubidium isotopes, namely 8937Rb - 9937Rb. We develop a model that use calculated Nilsson model wave functions, spherical or deformed, as the case may be, as the starting point for determining the wave functions of the mother and daughter nuclei in the #betta# decay. Pairing is treated in the BCS approximation. To account for the retardation of low-energy GT-decay rates we add, as is customarily done, a simple residual interaction specific to GT decay, namely V sub (GT)=:#betta#-1 x #betta#1:, to the Hamiltonian. This residual interaction is treated in the RPA approximation. The strength of the interaction is adjusted to get agreement between the calculated and experimental energy of the giant Gamow-Teller resonance for 208Pb and 144Sm. Since the present model is based on calculated wave functions and single-particle levels, studies of nuclei far from stability, where little experimental information is available, are more straightforward relative to calculations where experimental levels are used. The model can treat deformed nuclei employing wave functions calculated to desired accuracy, within the framework of the model, for the deformed single-particle well. The calcualtions show that use of single-particle parameters appropriate to the region studied and taking deformation into account is important. We find good agreement between calculated and experimental spectra over the region studied, provided an appropriate choice of single-particle parameters and deformation is made. (Authors)

  2. Recombinant DNA technology in apple.

    Science.gov (United States)

    Gessler, Cesare; Patocchi, Andrea

    2007-01-01

    This review summarizes the achievements of almost 20 years of recombinant DNA technology applied to apple, grouping the research results into the sections: developing the technology, insect resistance, fungal disease resistance, self-incompatibility, herbicide resistance, fire blight resistance, fruit ripening, allergens, rooting ability, and acceptance and risk assessment. The diseases fire blight, caused by Erwinia amylovora, and scab, caused by Venturia inaequalis, were and still are the prime targets. Shelf life improvement and rooting ability of rootstocks are also relevant research areas. The tools to create genetically modified apples of added value to producers, consumers, and the environment are now available. PMID:17522823

  3. PhiC31 integrase induces efficient site-specific recombination in the Capra hircus genome.

    Science.gov (United States)

    Ma, Haiyan; Ma, Qingwen; Lu, Yao; Wang, Juan; Hu, Wei; Gong, Zhijuan; Cai, Linlin; Huang, Ying; Huang, Shu-Zhen; Zeng, Fanyi

    2014-08-01

    Streptomyces phage ?C31 integrase induces efficient site-specific recombination capable of integrating exogenous genes at pseudo attP sites in human, mouse, rat, rabbit, sheep, Drosophila, and bovine genomes. However, the ?C31-mediated recombination between attB and the corresponding pseudo attP sites has not been investigated in Capra hircus. Here, we identified eight pseudo attP sites located in the intron or intergenic regions of the C. hircus genome, and demonstrated different levels of foreign gene expression after ?C31 integrase-mediated integration. These pseudo attP sites share similar sequences with each other and with pseudo attP sites in other mammalian genomes, and these are associated with a neighboring consensus motif found in other genomes. The application of the ?C31 integrase system in C. hircus provides a new option for genetic engineering of this economically important goat species. PMID:24754538

  4. Mediated homogenization

    International Nuclear Information System (INIS)

    Homogenization protocols model the quantum mechanical evolution of a system to a fixed state independently from its initial configuration by repeatedly coupling it with a collection of identical ancillas. Here we analyze these protocols within the formalism of ''relaxing'' channels providing an easy-to-check sufficient condition for homogenization. In this context we describe mediated homogenization schemes where a network of connected qudits relaxes to a fixed state by only partially interacting with a bath. We also study configurations which allow us to introduce entanglement among the elements of the network. Finally we analyze the effect of having competitive configurations with two different baths and we prove the convergence to dynamical equilibrium for Heisenberg chains

  5. Roles of histone acetylation and chromatin remodeling factor in a meiotic recombination hotspot

    OpenAIRE

    Yamada, Takatomi; Mizuno, Ken-ichi; Hirota, Kouji; Kon, Ning; Wahls, Wayne P.; Hartsuiker, Edgar; Murofushi, Hiromu; Shibata, Takehiko; Ohta, Kunihiro

    2004-01-01

    Histone acetyltransferases (HATs) and ATP-dependent chromatin remodeling factors (ADCRs) are involved in selective gene regulation via modulation of local chromatin configuration. Activation of the recombination hotspot ade6-M26 of Schizosaccharomyces pombe is mediated by a cAMP responsive element (CRE)-like sequence, M26, and a heterodimeric ATF/CREB transcription factor, Atf1·Pcr1. Chromatin remodeling occurs meiotically around M26. We examined the roles of HATs and ADCRs in chromatin remo...

  6. Expression of recombinant plasmids in mammalian cells is enhanced by sodium butyrate.

    OpenAIRE

    Gorman, C. M.; Howard, B. H.; Reeves, R.

    1983-01-01

    We have studied the effects of sodium butyrate on DNA-mediated gene transfer in an effort to investigate interrelationships between chromatin structure and expression of recombinant plasmids. Our results demonstrate that butyrate affects the early stages of gene activity following DNA uptake at least two levels. First, the number of cells able to express foreign DNA increases from 10% to up to 40%. Second, there is an increase in enhancer-dependent transcription, approximately 30 fold in HeLa...

  7. Erlotinib attenuates homologous recombinational repair of chromosomal breaks in human breast cancer cells

    OpenAIRE

    Li, Liping; Wang, Hong; Yang, Eddy S; Arteaga, Carlos L.; Xia, Fen

    2008-01-01

    The epidermal growth factor receptor family (EGFR) has been implicated in a number of cancers, including breast, and its members have become the target of novel cancer therapies. In this report, we show a novel link between erlotinib, a potent EGFR inhibitor, DNA damage, and homology-directed recombinational repair (HDR) in human breast cancer cells. Erlotinib suppresses HDR. This is not secondary to erlotinib-mediated changes in cell cycle and is associated with increased ?-H2AX foci, which...

  8. Expression, Purification, and Analysis of Recombinant Drosophila Dicer-1 and Dicer-2 Enzymes

    OpenAIRE

    Ye, Xuecheng; Liu, Qinghua

    2008-01-01

    RNA interference (RNAi) is a form of posttranscriptional gene silencing mediated by microRNA (miRNA) and small interfering RNA (siRNA). In Drosophila melanogaster, the RNase III enzymes Dicer-1 and Dicer-2 generate miRNA and siRNA, respectively. We describe the methods for the expression, purification, and analysis of recombinant Dicer-1 and Dicer-2 enzymes. Our studies demonstrate that Dicer-1 and Dicer-2 display different substrate specificities and ATP requirements.

  9. Regulation of human lung fibroblast glycosaminoglycan production by recombinant interferons, tumor necrosis factor, and lymphotoxin.

    OpenAIRE

    Elias, J. A.; Krol, R C; Freundlich, B.; Sampson, P M

    1988-01-01

    Mononuclear cells may be important regulators of fibroblast glycosaminoglycan (GAG) biosynthesis. However, the soluble factors mediating these effects, the importance of intercytokine interactions in this regulation and the mechanisms of these alterations remain poorly understood. We analyzed the effect of recombinant (r) tumor necrosis factor (TNF), lymphotoxin (LT), and gamma, alpha, and beta 1 interferons (INF-gamma, -alpha and -beta 1), alone and in combination, on GAG production by norma...

  10. Expression, purification, and characterization of recombinant human transferrin from rice (Oryza sativa L.)

    OpenAIRE

    Zhang, Deshui; Nandi, Somen; Bryan, Paula; Pettit, Steve; Nguyen, Diane; Santos, Mary Ann; Huang, Ning

    2010-01-01

    Transferrin is an essential ingredient used in cell culture media due to its crucial role in regulating cellular iron uptake, transport, and utilization. It is also a promising drug carrier used to increase a drug’s therapeutic index via the unique transferrin receptor-mediated endocytosis pathway. Due to the high risk of contamination with blood-borne pathogens from the use of human- or animal plasma-derived transferrin, recombinant transferrin is preferred for use as a replacement for nat...

  11. Nonreciprocal homologous recombination between Agrobacterium transferred DNA and a plant chromosomal locus.

    OpenAIRE

    Offringa, R.; Franke-van Dijk, M. E.; Groot, M. J.; Den Elzen, P. J.; Hooykaas, P. J.

    1993-01-01

    Previously, we demonstrated the occurrence of gene targeting in tobacco cells after Agrobacterium-mediated transformation. In these experiments a defective kanamycin resistance (Kmr) gene residing at a chromosomal location was restored via homologous recombination with an incoming transferred DNA (T-DNA) repair construct (pSDM101) containing a different defective Kmr gene. In this article we describe gene targeting experiments with the same target line, but using an improved repair construct,...

  12. Recombinant protein production in yeasts.

    Science.gov (United States)

    Mattanovich, Diethard; Branduardi, Paola; Dato, Laura; Gasser, Brigitte; Sauer, Michael; Porro, Danilo

    2012-01-01

    Recombinant protein production is a multibillion-dollar market. The development of a new product begins with the choice of a production host. While one single perfect host for every protein does not exist, several expression systems ranging from bacterial hosts to mammalian cells have been established. Among them, yeast cell factories combine the advantages of being single cells, such as fast growth and easy genetic manipulation, as well as eukaryotic features including a secretory pathway leading to correct protein processing and post-translational modifications. In this respect, especially the engineering of yeast glycosylation to produce glycoproteins of human-like glycan structures is of great interest. Additionally, different attempts of cellular engineering as well as the design of different production processes that are leading to improved productivities are presented. With the advent of cheaper next-generation sequencing techniques, systems biotechnology approaches focusing on genome scale analyses will advance and accelerate yeast cell factories and thus recombinant protein production processes in the near future. In this review we summarize advantages and limitations of the main and most promising yeast hosts, including Saccharomyces cerevisiae, Pichia pastoris, and Hansenula polymorpha as those presently used in large scale production of heterologous proteins. PMID:22160907

  13. Charge recombination in undoped cuprates

    Science.gov (United States)

    Lenar?i?, Zala; Prelovšek, Peter

    2014-12-01

    We theoretically analyze the process of charge recombination in the planar Mott-Hubbard insulators with the aim to explain the short picosecond-range lifetimes of photoexcited carriers, experimentally studied via pump-probe experiments on the undoped cuprates. The recombination mechanism consists of two essential ingredients: the formation of a metastable s -type bound holon-doublon pair, i.e., the Mott exciton, and the decay of such an excitonic state via the multimagnon emission. In spite of the large gap that requires many bosons to be emitted, the latter process is fast due to a large exchange scale and strong charge-spin coupling in planar systems. As the starting microscopic model we consider the single-band Hubbard model and then a more realistic three-band model for cuprates, both leading to the same minimal one. The decay rate of the exciton is evaluated numerically via the Fermi golden rule, having consistency also with the direct time-evolution calculation. The decay rate reveals exponential dependence on the ratio of the Mott-Hubbard gap and the exchange coupling, the result qualitatively reproduced also within a toy exciton-boson model.

  14. Recombination chambers for BNCT dosimetry

    International Nuclear Information System (INIS)

    Parallel plate recombination ionization chambers are known as the detectors which can be used for determination of gamma and high-LET dose components and for characterization of radiation quality of mixed radiation fields. Specially designed chambers can operate correctly even at dose rates of therapeutic beams. In this work the investigations were extended to a set of cylindrical chambers including a TE chamber and three graphite chambers filled with different gases - CO2, N2 and 10BF3, in order to determine the thermal neutrons, 14N capture, gamma, and fast neutron dose components. The separation of the dose components is based on differences of the shape of the saturation curve, in dependence on LET spectrum of the investigated radiation. The measurements using all the chambers and a parallel plate recombination chamber were performed in a reactor beam of NRI Rez (Czech Republic). The gamma component was determined with accuracy of about 5%, while the variations of its value could be monitored with accuracy of about 0.5%. Relative changes of the beam components could be detected with accuracy of about 5% using the parallel plate chamber. The use of the chambers filled with different gases considerably improved the resolution of the method. (author)

  15. Micro dynamics in mediation

    OpenAIRE

    Boserup, Hans

    2014-01-01

    The author has identified a number of styles in mediation, which lead to different processes and different outcomes. Through discourse and conversation analysis he examines the micro dynamics in three of these, the postmodern styles: systemic, transformative and narrative mediation. The differences between the three mediation ideologies and practice is illustrated through role play scripts enacted in each style. Mediator and providers of mediation and trainers in mediation are encouraged to a...

  16. Molecular requirements for radiation-activated recombination

    International Nuclear Information System (INIS)

    Purpose/Objective: The major stumbling block to successful gene therapy today is poor gene transfer. We hypothesized that ionizing radiation might activate cellular recombination, and so improve stable gene transfer. We further hypothesized that known DNA-damage-repair proteins might also be important in radiation-activated recombination. Materials and Methods: The effect of irradiation on stable gene transfer efficiency was determined in human (A549 and 39F) and rodent (NIH/3T3) cell lines. Continuous low dose rate and multiple radiation fractions were also tested. Nuclear extracts were made and the effect of irradiation on inter-plasmid recombination/ligation determined. Multiple DNA damage-repair deficient cell lines were tested for radiation-activated recombination. Results: A significant radiation dose-dependent improvement in stable plasmid transfection (by as much as 1300 fold) is demonstrated in neoplastic and primary cells. An improvement in transient plasmid transfection is also seen, with as much as 85% of cells transiently expressing b-galactosidase (20-50 fold improvement). Stable transfection is only improved for linearized or nicked plasmids. Cells have improved gene transfer for at least 96 hours after irradiation. Both fractionated and continuous low dose rate irradiation are effective at improving stable gene transfer in mammalian cells, thus making relatively high radiation dose delivery clinically feasible. Inter-plasmid recombination is radiation Inter-plasmid recombination is radiation dose dependent in nuclear extract assays, and the type of overhang (3', 5' or blunt end) significantly affects recombination efficiency and the type of product. The most common end-joining activity involves filling-in of the overhang followed by blunt end ligation. Adenovirus is a linear, double stranded DNA virus. We demonstrate that adenoviral infection efficiency is increased by irradiation. The duration of transgene expression is lengthened because the virus integrates with high efficiency (?10% of treated cells) into cellular DNA. The mechanism of radiation enhanced stable gene transfer requires effector proteins to accomplish the recombination. The Ku proteins, which are required for V(D)J recombination, account for at least 90% of radiation induced recombination. There is also an absolute requirement for the Ataxia Telangiectasia gene (ATM) for any radiation induced recombination to occur, although the transfection efficiency in unirradiated cells is unaffected by ATM. Removal of p53 by transfection of E6 (Human Papilloma Virus) significantly inhibits radiation activated recombination, and this is confirmed in nuclear extract recombination assays. Conclusions: Ionizing radiation activates a recombination pathway which may be useful in gene therapy. The molecular mechanism of radiation activated recombination requires a number of DNA-damage-repair proteins

  17. Efficient transfer of base changes from a vector to the rice genome by homologous recombination: involvement of heteroduplex formation and mismatch correction

    OpenAIRE

    Johzuka-hisatomi, Yasuyo; Terada, Rie; Iida, Shigeru

    2008-01-01

    Gene targeting refers to the alteration of a specific DNA sequence in an endogenous gene at its original locus in the genome by homologous recombination. Through a gene-targeting procedure with positive–negative selection, we previously reported the generation of fertile transgenic rice plants with a positive marker inserted into the Adh2 gene by using an Agrobacterium-mediated transformation vector containing the positive marker flanked by two 6-kb homologous segments for recombination. We...

  18. Construction and characterization of recombinant Japanese encephalitis virus carrying brainspecific miRNA target sequences

    Directory of Open Access Journals (Sweden)

    Wen-yuan CAO

    2014-08-01

    Full Text Available Objective?To construct the recombinant Japanese encephalitis virus ( JEV carrying brain-specific miRNA targeting sequences. Methods?The target sequences of brain-specific miR-124 and miR-125 were introduced into the infectious cDNA clone of JEV to generate recombinant plasmids based on reverse genetics technology. The recombinant plasmids were linearized with Xho ? and served as templates of transcription with SP6 RNA polymerase to generate infectious viral RNA. The RNA transcripts were then transfected into BHK-21 cells, and the supernatant was obtained after incubated at 37?, 5% CO2 for 3 days. The cytopathic changes of BHK-21 cells inoculated with the supernatant were observed after one passage. The rescued viruses carrying miRNA target sequences were validated by RT-PCR, standard plaque forming test on BHK-21 cells and growth curves analysis. Results?Two recombinant viruses carrying miR-124 or miR-125 target sequence were rescued, respectively. The insertion of miRNA target sequences was confirmed by DNA sequencing. The rescued viruses yielded similar plaque morphology and replication efficiency compared with wild type JEV. Conclusion?The recombinant JEV containing brain-specific miRNA target sequences can be obtained by reverse genetics technique, which could be used in further studies of miRNA-mediated tissue-specific attenuation mechanism of JEV. DOI: 10.11855/j.issn.0577-7402.2014.06.01

  19. Chaperone-based procedure to increase yields of soluble recombinant proteins produced in E. coli

    Directory of Open Access Journals (Sweden)

    Mogk Axel

    2007-06-01

    Full Text Available Abstract Background The overproduction of recombinant proteins in host cells often leads to their misfolding and aggregation. Previous attempts to increase the solubility of recombinant proteins by co-overproduction of individual chaperones were only partially successful. We now assessed the effects of combined overproduction of the functionally cooperating chaperone network of the E. coli cytosol on the solubility of recombinant proteins. Results A two-step procedure was found to show the strongest enhancement of solubility. In a first step, the four chaperone systems GroEL/GroES, DnaK/DnaJ/GrpE, ClpB and the small HSPs IbpA/IbpB, were coordinately co-overproduced with recombinant proteins to optimize de novo folding. In a second step, protein biosynthesis was inhibited to permit chaperone mediated refolding of misfolded and aggregated proteins in vivo. This novel strategy increased the solubility of 70% of 64 different heterologous proteins tested up to 42-fold. Conclusion The engineered E. coli strains and the two-step procedure presented here led to a remarkable increase in the solubility of a various recombinant proteins and should be applicable to a wide range of target proteins produced in biotechnology.

  20. Recombinant I?B?-loaded curcumin nanoparticles for improved cancer therapeutics

    Science.gov (United States)

    Banerjee, Subhamoy; Sahoo, Amaresh Kumar; Chattopadhyay, Arun; Sankar Ghosh, Siddhartha

    2014-08-01

    The field of recombinant protein therapeutics has been evolving rapidly, making significant impact on clinical applications for several diseases, including cancer. However, the functional aspects of proteins rely exclusively on their structural integrity, in which nanoparticle mediated delivery offers unique advantages over free proteins. In the present work, a novel strategy has been developed where the nanoparticles (NPs) used for the delivery of the recombinant protein could contribute to enhancing the therapeutic efficacy of the recombinant protein. The transcription factor, NF?B, involved in cell growth and its inhibitor, I?B?, regulates its proliferation. Another similar naturally available molecule, which inhibits the function of NF?B, is curcumin. Hence, we have developed a ‘green synthesis’ method for preparing water-soluble curcumin nanoparticles to stabilize recombinant I?B? protein. The NPs were characterized by UV-vis and fluorescence spectroscopy, transmission electron microscopy (TEM) and dynamic light scattering before administration into human cervical carcinoma (HeLa) and glioblastoma (U87MG) cells. Experimental results demonstrated that this combined module had enhanced therapeutic efficacy, causing apoptotic cell death, which was confirmed by cytotoxicity assay and flowcytometry analyses. The expression of apoptotic genes studied by semi-quantitative reverse transcription PCR delineated the molecular pathways involved in cell death. Thus, our study revealed that the functional delivery of recombinant I?B?-loaded curcumin NPs has promise as a natural-product-based protein therapeutics against cancer cells.

  1. Phenomenological Implications of Deflected Mirage Mediation: Comparison with Mirage Mediation

    OpenAIRE

    Altunkaynak, Baris; Everett, Lisa L.; Kim, Ian-woo; Nelson, Brent D.; Rao, Yongyan

    2010-01-01

    We compare the collider phenomenology of mirage mediation and deflected mirage mediation, which are two recently proposed "mixed" supersymmetry breaking scenarios motivated from string compactifications. The scenarios differ in that deflected mirage mediation includes contributions from gauge mediation in addition to the contributions from gravity mediation and anomaly mediation also present in mirage mediation. The threshold effects from gauge mediation can drastically alte...

  2. Telomeric recombination induced by dysfunctional telomeres

    OpenAIRE

    Brault, Marie Eve; Autexier, Chantal

    2011-01-01

    Telomeric recombination has been observed in telomerase-negative alternative lengthening of telomeres in human cancer cells and following telomerase inhibition or gene deletion. This study shows that telomeric recombination mechanisms can also be activated by dysfunctional telomeres without telomerase inhibition in telomerase-positive cells.

  3. Recombinant organisms for production of industrial products

    OpenAIRE

    Adrio, Jose-luis; Demain, Arnold L.

    2009-01-01

    A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding...

  4. Cell Biology of Homologous Recombination in Yeast

    OpenAIRE

    Eckert-boulet, Nadine; Rothstein, Rodney; Lisby, Michael

    2011-01-01

    Homologous recombination is an important pathway for error-free repair of DNA lesions, such as single-and double-strand breaks, and for rescue of collapsed replication forks. Here, we describe protocols for live cell imaging of single-lesion recombination events in the yeast Saccharomyces cerevisiae using fluorescence microscopy.

  5. Cell biology of homologous recombination in yeast

    DEFF Research Database (Denmark)

    Eckert-Boulet, Nadine Valerie; Rothstein, Rodney

    2011-01-01

    Homologous recombination is an important pathway for error-free repair of DNA lesions, such as single- and double-strand breaks, and for rescue of collapsed replication forks. Here, we describe protocols for live cell imaging of single-lesion recombination events in the yeast Saccharomyces cerevisiae using fluorescence microscopy.

  6. Electron-ion recombination at low energy

    International Nuclear Information System (INIS)

    The work is based on results obtained with a merged-beams experiment. A beam of electronics with a well characterized density and energy distribution was merged with a fast, monoenergetic ion beam. Results have been obtained for radiative recombination and dielectronic recombination at low relative energies (0 to ?70eV). The obtained energy resolution was improved by about a factor of 30. High vacuum technology was used to suppress interactions with electrons from the environments. The velocity distribution of the electron beam was determined. State-selective dielectronic-recombination measurements were performable. Recombination processes were studied. The theoretical background for radiative recombination and Kramers' theory are reviewed. The quantum mechanical result and its relation to the semiclassical theory is discussed. Radiative recombination was also measured with several different non-bare ions, and the applicability of the semiclassical theory to non-bare ions was investigated. The use of an effective charge is discussed. For dielectronic recombination, the standard theoretical approach in the isolated resonance and independent-processes approximation is debated. The applicability of this method was tested. The theory was able to reproduce most of the experimental data except when the recombination process was sensitive to couplings between different electronic configurations. The influence of external perturbing electrostatic fields is discussed. (AB) (31 refs.)

  7. Dielectronic recombination of the helium ion

    International Nuclear Information System (INIS)

    Dielectronic recombination of the helium ion under conditions of intersecting beams is observed for the first time. Two peaks are observed in the energy dependence of the cross section of the process. The dielectronic recombination cross section is comparable to the cross section for excitation of the resonant level of the helium ion

  8. Polynomial identities for ternary intermolecular recombination

    OpenAIRE

    Bremner, Murray R.

    2010-01-01

    The operation of binary intermolecular recombination, originating in the theory of DNA computing, permits a natural generalization to n-ary operations which perform simultaneous recombination of n molecules. In the case n = 3, we use computer algebra to determine the polynomial identities of degree

  9. RNAi and heterochromatin repress centromeric meiotic recombination

    DEFF Research Database (Denmark)

    Ellermeier, Chad; Higuchi, Emily C

    2010-01-01

    During meiosis, the formation of viable haploid gametes from diploid precursors requires that each homologous chromosome pair be properly segregated to produce an exact haploid set of chromosomes. Genetic recombination, which provides a physical connection between homologous chromosomes, is essential in most species for proper homologue segregation. Nevertheless, recombination is repressed specifically in and around the centromeres of chromosomes, apparently because rare centromeric (or pericentromeric) recombination events, when they do occur, can disrupt proper segregation and lead to genetic disabilities, including birth defects. The basis by which centromeric meiotic recombination is repressed has been largely unknown. We report here that, in fission yeast, RNAi functions and Clr4-Rik1 (histone H3 lysine 9 methyltransferase) are required for repression of centromeric recombination. Surprisingly, one mutant derepressed for recombination in the heterochromatic mating-type region during meiosis and several mutants derepressed for centromeric gene expression during mitotic growth are not derepressed for centromeric recombination during meiosis. These results reveal a complex relation between types of repression by heterochromatin. Our results also reveal a previously undemonstrated role for RNAi and heterochromatin in the repression of meiotic centromeric recombination and, potentially, in the prevention of birth defects by maintenance of proper chromosome segregation during meiosis.

  10. Modifiers of (CAG)(n) instability in Machado-Joseph disease (MJD/SCA3) transmissions: an association study with DNA replication, repair and recombination genes.

    Science.gov (United States)

    Martins, Sandra; Pearson, Christopher E; Coutinho, Paula; Provost, Sylvie; Amorim, António; Dubé, Marie-Pierre; Sequeiros, Jorge; Rouleau, Guy A

    2014-10-01

    Twelve neurological disorders are caused by gene-specific CAG/CTG repeat expansions that are highly unstable upon transmission to offspring. This intergenerational repeat instability is clinically relevant since disease onset, progression and severity are associated with repeat size. Studies of model organisms revealed the involvement of some DNA replication and repair genes in the process of repeat instability, however, little is known about their role in patients. Here, we used an association study to search for genetic modifiers of (CAG)n instability in 137 parent-child transmissions in Machado-Joseph disease (MJD/SCA3). With the hypothesis that variants in genes involved in DNA replication, repair or recombination might alter the MJD CAG instability patterns, we screened 768 SNPs from 93 of these genes. We found a variant in ERCC6 (rs2228528) associated with an expansion bias of MJD alleles. When using a gene-gene interaction model, the allele combination G-A (rs4140804-rs2972388) of RPA3-CDK7 is also associated with MJD instability in a direction-dependent manner. Interestingly, the transcription-coupled repair factor ERCC6 (aka CSB), the single-strand binding protein RPA, and the CDK7 kinase part of the TFIIH transcription repair complex, have all been linked to transcription-coupled repair. This is the first study performed in patient samples to implicate specific modifiers of CAG instability in humans. In summary, we found variants in three transcription-coupled repair genes associated with the MJD mutation that points to distinct mechanisms of (CAG)n instability. PMID:25026993

  11. PRACTICAL ASPECTS OF MEDIATION

    Directory of Open Access Journals (Sweden)

    IULIA FLOCA

    2011-04-01

    Full Text Available Today the Romanian state gives some advantages to those who use mediation. If the Romanian state would take further steps, mediation would work as in the countries with old tradition. The article refers to success and failure got in the two years of practice. The mediation can be seen in two aspects: The first aspect regarding the mediation itself can lead to a mediation agreement. The mediation agreement gives both winnings to the conflict parts and professional satisfactions to the mediator. The second part concerns the mediation contract. It is very important for the mediator who wants to practice and to gain money. The mediation will work in Romania when the mediator passes from the pro-bono stage to winnings. The article refers to the conditions of the appearance of mediation in Romania, the purpose for which it was founded, the usefulness of mediations to relieve the number of court cases and increase the efficiency of the courts, as well as the results obtained from the adoption of the mediation laws until now. The practical aspects leading to the mode in which Romanians perceive mediation and wish to participate or not in the sessions of mediation Recommendations for promoting mediation in Romania

  12. Dissociative recombination of He2+

    International Nuclear Information System (INIS)

    We present calculated cross sections for dissociative recombination of the He2+ molecular ion in the 1 to 15 eV energy region, where the cross section is dominated by a series of resonances, the repulsive Rydberg states converging to the first excited state of the ion. The resonance parameters for this system were obtained from electron scattering calculations using the complex Kohn variational method. The dissociation dynamics were studied using a time-dependent wave packet calculation. The calculated cross section is reported and compared to available experiment. The effects of rotation and vibration on the total cross section is examined, as well as the effect of electronic couplings on the final state distribution

  13. Simplifying transgene locus structure through Cre-lox recombination.

    Science.gov (United States)

    Srivastava, Vibha; Ow, David W

    2015-01-01

    Transgene silencing is often associated with multicopy integrations, which occur frequently during plant transformation. Transgene expression can be restored in a number of multicopy loci by converting them to single copy. This chapter describes a plant transformation protocol based on use of the Cre-lox system, which allows conversion of a multicopy transgene locus into single copy. The strategy is based on designing a transformation vector with lox sites, developing transgenic lines, and introducing Cre activity to initiate Cre-lox recombination, which leads to the simplification of a multicopy locus to a single- or low-copy state. This method is compatible with both gene gun and Agrobacterium-mediated gene delivery and should be particularly useful for crops that are difficult to transform. PMID:25740358

  14. Recombinant activated factor VII: 30 years of research and innovation.

    Science.gov (United States)

    Hedner, Ulla

    2015-06-01

    Recombinant activated factor VII (rFVIIa) was initially developed to treat bleeding episodes in patients with congenital haemophilia and inhibitors. The story of its development began in the 1970s, when FVIIa was identified as one of the activated coagulation factors that has minimal potential for inducing thromboembolic side-effects. Extensive research over the last 30 years has greatly increased our knowledge of the characteristics of FVII, its activation, and the mechanisms by which rFVIIa restores haemostasis. In haemophilia, the haemostatic effect of rFVIIa is mediated via binding to thrombin-activated platelets at the site of injury, thereby enhancing thrombin generation also in the absence of factor (F) VIII or FIX. The mechanism of action of rFVIIa has also allowed its successful use in other clinical scenarios characterised by impaired thrombin generation, and its licensed uses have now been extended to acquired haemophilia, congenital FVII deficiency and Glanzmann's thrombasthenia. PMID:26073368

  15. Fundamental Studies of Recombinant Hydrogenases

    Energy Technology Data Exchange (ETDEWEB)

    Adams, Michael W

    2014-01-25

    This research addressed the long term goals of understanding the assembly and organization of hydrogenase enzymes, of reducing them in size and complexity, of determining structure/function relationships, including energy conservation via charge separation across membranes, and in screening for novel H2 catalysts. A key overall goal of the proposed research was to define and characterize minimal hydrogenases that are produced in high yields and are oxygen-resistant. Remarkably, in spite of decades of research carried out on hydrogenases, it is not possible to readily manipulate or design the enzyme using molecular biology approaches since a recombinant form produced in a suitable host is not available. Such resources are essential if we are to understand what constitutes a “minimal” hydrogenase and design such catalysts with certain properties, such as resistance to oxygen, extreme stability and specificity for a given electron donor. The model system for our studies is Pyrococcus furiosus, a hyperthermophile that grows optimally at 100°C, which contains three different nickel-iron [NiFe-] containing hydrogenases. Hydrogenases I and II are cytoplasmic while the other, MBH, is an integral membrane protein that functions to both evolve H2 and pump protons. Three important breakthroughs were made during the funding period with P. furiosus soluble hydrogenase I (SHI). First, we produced an active recombinant form of SHI in E. coli by the co-expression of sixteen genes using anaerobically-induced promoters. Second, we genetically-engineered P. furiosus to overexpress SHI by an order of magnitude compared to the wild type strain. Third, we generated the first ‘minimal’ form of SHI, one that contained two rather than four subunits. This dimeric form was stable and active, and directly interacted with a pyruvate-oxidizing enzyme with any intermediate electron carrier. The research resulted in five peer-reviewed publications.

  16. Sensitive biosensor based on recombinant PP1? for microcystin detection.

    Science.gov (United States)

    Catanante, Gaëlle; Espin, Laura; Marty, Jean-Louis

    2015-05-15

    A novel electrochemical microcystin-LR (MC-LR) biosensor based on the inhibition of recombinant protein phosphate type 1 (PP1?) is reported in this work. The use of innovative recombinant enzyme led to investigate new commercially available substrate, electrochemically active after their dephosphorylation by PP1?. Only two of selected substrates, 1-naphylphosphate and phosphoparacetamol, showed a good affinity toward PP1?. Kinetic parameters were performed by classical colorimetric assays and revealed that phosphoparacetamol is an excellent synthetic substrate with a Km value of 1.2 mM. The reported biosensor is constructed by entrapment of the enzyme in Polyvinyl Alcohol (azid unit) on Cobalt-Phtalocyanine (CoPC) modified screen printed electrode. Electrocatalytic mediator demonstrated a significant improvement in the electrochemical detection of dephosphorylated substrate. The standard inhibition curve has provided a limit of detection at 0.93 µg/L and a broad dynamic range from 0.93 to 40.32 ?g/L for MC-LR, demonstrating the improved analytical performance. PMID:25459056

  17. DNA sequence alignment by microhomology sampling during homologous recombination.

    Science.gov (United States)

    Qi, Zhi; Redding, Sy; Lee, Ja Yil; Gibb, Bryan; Kwon, YoungHo; Niu, Hengyao; Gaines, William A; Sung, Patrick; Greene, Eric C

    2015-02-26

    Homologous recombination (HR) mediates the exchange of genetic information between sister or homologous chromatids. During HR, members of the RecA/Rad51 family of recombinases must somehow search through vast quantities of DNA sequence to align and pair single-strand DNA (ssDNA) with a homologous double-strand DNA (dsDNA) template. Here, we use single-molecule imaging to visualize Rad51 as it aligns and pairs homologous DNA sequences in real time. We show that Rad51 uses a length-based recognition mechanism while interrogating dsDNA, enabling robust kinetic selection of 8-nucleotide (nt) tracts of microhomology, which kinetically confines the search to sites with a high probability of being a homologous target. Successful pairing with a ninth nucleotide coincides with an additional reduction in binding free energy, and subsequent strand exchange occurs in precise 3-nt steps, reflecting the base triplet organization of the presynaptic complex. These findings provide crucial new insights into the physical and evolutionary underpinnings of DNA recombination. PMID:25684365

  18. General Gaugino Mediation

    OpenAIRE

    Sudano, Matthew

    2010-01-01

    The spectrum of a class of gaugino mediation models with arbitrary hidden sector is considered. These models are defined by a diagonal breaking of the mediating gauge group, which places them outside the realm of General Gauge Mediation. While gauginos get masses as in ordinary gauge mediation, the scalar masses are screened.

  19. Recent Developments in Dissociative Recombination

    International Nuclear Information System (INIS)

    There have been a number of recent developments in dissociative recombination research as it relates to ITER, that should be highlighted. These concern primarily experimental and modelling issues and this document will not touch upon the topics of the other scientists involved in DR studies that are present at the meeting. The topic of branching ratios in general is a topic fundamental to DR especially how it influences the formation of radical and stable neutral molecules that again might play a role in particle formation. It should be remembered that the reactions of neutral radicals to form cyclic compounds are responsible for the formation of soot in combustion, though the role played by ions in flames is at best uncertain. In the near wall plasma environment, ion processes may well be more important since neutral species are rarer. Modelling studies by Pernot and collaborators at the Universite de Paris-Sud have shown that if one compares the yields of individual neutral species in ion-chemistry models (in this particular case, the ionosphere of Titan), and if one assumes that DR reactions of hydrocarbon ions primarily decay via the ejection of a hydrogen ion (which is assumed by most Titan ionospheric models) and if one compares these predictions with those coming from a model where actual measured branching ratios are used, differences of up to 5 orders of magnitude are found. This shows very clearly the need for branching ratio studies. In early merged beam sting ratio studies. In early merged beam studies of DR performed in Canada in the 1970's, it was noticed that cross sections for polyatomic species typically displayed a sharp fall-off above 0.1 eV. This has since been seen in many storage ring studies and clearly this has important consequences for ITER chemistry where plasma temperatures are likely to be well above ambient. In a recent analysis, Jungen and Pratt have explained this phenomenon on the basis that the recombination is dominated by the indirect process (initial capture into a vibrationally excited, neutral Rydberg state) in which the propensity rule (+?v=1) dominates the capture. When the electron energy exceeds that between the v'=0 and v'=1 levels of the ion, where the capture must now involve a ?v=2 transition, this will be much less effective and so the cross section drops precipitously. This assumes of course that the recombining ion is primarily in the ground v=0 level. H3+ continues to be an active subject of research and a very recent experiment at the TSR ring in Heidelberg has examined the influence of rotational excitation on the rate of the recombination. This is a very beautiful study but an important outcome is that even though a cryogenically cooled storage trap was used to produce the ions, the internal rotational temperature of the ions was never found to be below 150K. This suggests that ion cooling by storage in the ring leads eventually to an equilibrium value for the internal energy of the ions as they are de-excited/re-excited by passage through the electron cooler. As observed in earlier merged beam experiments in Canada, the extraction field in the ion source plays an important role in determining the excitation state of the ions as collisions outside the source can lead to re-heating. Indeed in the TSR experiments using a conventional Penning source and a normal extraction field, the ions were found to have a rotational temperature of several thousands of degrees. This clearly has important significance for earlier measurements taken in storage rings. Finally, the world will soon have a new storage ring facility for dissociative recombination research and this will be in Langzhou in China. This machine will have a higher magnetic rigidity that previous rings used for DR and so heavier ions and higher mass resolution experiments can be performed there. Experimental operation of this new ring is expected to commence in 2012/2013. (author)

  20. Inference about recombination from haplotype data: lower bounds and recombination hotspots.

    Science.gov (United States)

    Bafna, Vineet; Bansal, Vikas

    2006-03-01

    Recombination is an important evolutionary mechanism responsible for creating the patterns of haplotype variation observable in human populations. Recently, there has been extensive research on understanding the fine-scale variation in recombination across the human genome using DNA polymorphism data. Historical recombination events leave signature patterns in haplotype data. A nonparametric approach for estimating the number of historical recombination events is to compute the minimum number of recombination events in the history of a set of haplotypes. In this paper, we provide new and improved methods for computing lower bounds on the minimum number of recombination events. These methods are shown to detect a higher number of recombination events for a haplotype dataset from a region in the lipoprotein lipase gene than previous lower bounds. We apply our methods to two datasets for which recombination hotspots have been experimentally determined and demonstrate a high density of detectable recombination events in the regions annotated as recombination hotspots. The programs implementing the methods in this paper are available at www.cs.ucsd.edu/users/vibansal/RecBounds/. PMID:16597254

  1. Recombination Every Day: Abundant Recombination in a Virus during a Single Multi-Cellular Host Infection

    Directory of Open Access Journals (Sweden)

    Froissart Remy

    2005-01-01

    Full Text Available Viral recombination can dramatically impact evolution and epidemiology. In viruses, the recombination rate depends on the frequency of genetic exchange between different viral genomes within an infected host cell and on the frequency at which such co-infections occur. While the recombination rate has been recently evaluated in experimentally co-infected cell cultures for several viruses, direct quantification at the most biologically significant level, that of a host infection, is still lacking. This study fills this gap using the cauliflower mosaic virus as a model. We distributed four neutral markers along the viral genome, and co-inoculated host plants with marker-containing and wild-type viruses. The frequency of recombinant genomes was evaluated 21 d post-inoculation. On average, over 50% of viral genomes recovered after a single host infection were recombinants, clearly indicating that recombination is very frequent in this virus. Estimates of the recombination rate show that all regions of the genome are equally affected by this process. Assuming that ten viral replication cycles occurred during our experiment-based on data on the timing of coat protein detection-the per base and replication cycle recombination rate was on the order of 2 x 10-5 to 4 x 10-5. This first determination of a virus recombination rate during a single multi-cellular host infection indicates that recombination is very frequent in the everyday life of this virus.

  2. Role of attP in Integrase-Mediated Integration of the Shigella Resistance Locus Pathogenicity Island of Shigella flexneri

    OpenAIRE

    Turner, Sally A.; Luck, Shelley N.; Sakellaris, Harry; Rajakumar, Kumar; Adler, Ben

    2004-01-01

    The Shigella resistance locus (SRL) pathogenicity island (PAI) in Shigella spp. mediates resistance to streptomycin, ampicillin, chloramphenicol, and tetracycline. It can be excised from the chromosome via site-specific recombination mediated by the P4-related int gene. Here, we show that SRL PAI attP is capable of RecA-independent, site-specific, int-mediated integration into two bacterial tRNA attB sites.

  3. Dual regulation of Dmc1-driven DNA strand exchange by Swi5–Sfr1 activation and Rad22 inhibition

    OpenAIRE

    Murayama, Yasuto; Kurokawa, Yumiko; Tsutsui, Yasuhiro; Iwasaki, Hiroshi

    2013-01-01

    Meiotic recombination requires two key recombinases: the ubiquitously expressed Rad51 and the meiosis-specific Dmc1. Rad52 and its fission yeast ortholog, Rad22, are mediators that help load Rad51 onto ssDNA coated with replication protein A (RPA). Here, Iwasaki and colleagues reveal how the Swi5–Sfr1 complex functions as both a mediator (loading DMC1 onto ssDNA) and an activator (stimulating Dmc1-driven strand exchange). In contrast, Rad22 inhibits Dmc1 by competing for binding to RPA-coat...

  4. Polynomial identities for ternary intermolecular recombination

    CERN Document Server

    Bremner, Murray R

    2010-01-01

    The operation of binary intermolecular recombination, originating in the theory of DNA computing, permits a natural generalization to n-ary operations which perform simultaneous recombination of n molecules. In the case n = 3, we use computer algebra to determine the polynomial identities of degree <= 9 satisfied by this trilinear nonassociative operation. Our approach requires computing a basis for the nullspace of a large integer matrix, and for this we compare two methods: (i) the row canonical form, and (ii) the Hermite normal form with lattice basis reduction. In the conclusion, we formulate some conjectures for the general case of n-ary intermolecular recombination.

  5. Charges recombination in ? particle tracks in argon

    International Nuclear Information System (INIS)

    The creation and evolution of (neutral) excited states and ionized states in ? particle tracks in high pressure argon are studied. The main features of recently published experimental results on the recombination luminescence can be explained and a track model is proposed. Details are given on the track radius, on the electrons thermallization, and on collisions between electrons and triplet excited states. The most important result is that at high pressure and high electron and ion densities a collective electron-ion recombination is possible, that is more efficient that the well known dissociative recombination

  6. Dissociative Recombination without a Curve Crossing

    Science.gov (United States)

    Guberman, Steven L.

    1994-01-01

    Ab initio calculations show that a curve crossing is not always needed for a high dissociative- recombination cross section. For HeH(+), in which no neutral states cross the ion potential curve, dissociative recombination is driven by the nuclear kinetic-energy operator on adiabatic potential curves. The kinetic-energy derivative operator allows for capture into repulsive curves that are outside of the classical turning points for the nuclear motion. The dominant dissociative route is the C (2)Sigma(+) state leading to H(n = 2) atoms. An analogous mechanism is proposed for the dissociative recombination of H3(+).

  7. Recombinant vaccine for canine parvovirus in dogs.

    OpenAIRE

    Lo?pez Turiso, J. A.; Corte?s, E.; Marti?nez, C.; Ruiz Yba?n?ez, R.; Simarro, I.; Vela, C.; Casal, I.

    1992-01-01

    VP2 is the major component of canine parvovirus (CPV) capsids. The VP2-coding gene was engineered to be expressed by a recombinant baculovirus under the control of the polyhedrin promoter. A transfer vector that contains the lacZ gene under the control of the p10 promoter was used in order to facilitate the selection of recombinants. The expressed VP2 was found to be structurally and immunologically indistinguishable from authentic VP2. The recombinant VP2 shows also the capability to self-as...

  8. Random recombination and evolution of drug resistance.

    Science.gov (United States)

    Kleinman, Alan

    2015-05-20

    The effects of random recombination on the random mutation and natural selection phenomenon can be understood by considering the mathematical behavior of this phenomenon. This phenomenon operates in a mathematically predicable behavior, which when understood, explains the empirical observations of this phenomenon. The mathematical behavior of random recombination is derived using the principles given by probability theory. The derivation of the equations describing the random recombination phenomenon is done in the context of an empirical example. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25645658

  9. BAC-recombineering for studying plant gene regulation: developmental control and cellular localization of SnRK1 kinase subunits.

    Science.gov (United States)

    Bitrián, Marta; Roodbarkelari, Farshad; Horváth, Mihály; Koncz, Csaba

    2011-03-01

    Recombineering, permitting precise modification of genes within bacterial artificial chromosomes (BACs) through homologous recombination mediated by lambda phage-encoded Red proteins, is a widely used powerful tool in mouse, Caenorhabditis and Drosophila genetics. As Agrobacterium-mediated transfer of large DNA inserts from binary BACs and TACs into plants occurs at low frequency, recombineering is so far seldom exploited in the analysis of plant gene functions. We have constructed binary plant transformation vectors, which are suitable for gap-repair cloning of genes from BACs using recombineering methods previously developed for other organisms. Here we show that recombineering facilitates PCR-based generation of precise translational fusions between coding sequences of fluorescent reporter and plant proteins using galK-based exchange recombination. The modified target genes alone or as part of a larger gene cluster can be transferred by high-frequency gap-repair into plant transformation vectors, stably maintained in Agrobacterium and transformed without alteration into plants. Versatile application of plant BAC-recombineering is illustrated by the analysis of developmental regulation and cellular localization of interacting AKIN10 catalytic and SNF4 activating subunits of Arabidopsis Snf1-related (SnRK1) protein kinase using in vivo imaging. To validate full functionality and in vivo interaction of tagged SnRK1 subunits, it is demonstrated that immunoprecipitated SNF4-YFP is bound to a kinase that phosphorylates SnRK1 candidate substrates, and that the GFP- and YFP-tagged kinase subunits co-immunoprecipitate with endogenous wild type AKIN10 and SNF4. PMID:21235649

  10. Testing for recombinant human erythropoietin

    Science.gov (United States)

    Joris R Delanghe (Ghent University Hospital Clinical Chemistry)

    2008-08-10

    ERYTHROPOIETIN (Epo) may have effects on exercise capacity and physiological regulation beyond a simple increase in red cell mass and the associated improvement in oxygen transport (4). In the context of a larger study on this topic, Lundby and colleagues (11) also asked questions about the reliability of urine testing for recombinant human Epo (rHuEpo). They studied eight healthy male subjects during a 4-wk "loading" and 2-wk "boosting" phase of Epo use followed by a 2-wk maintenance phase. In the parent study they showed that the effects of Epo on exercise performance were confined to its impact on red cell mass and not to other physiological effects of the hormone. These results were consistent with ideas about the relationship between maximal oxygen uptake and red cell mass or total body hemoglobin that emerged in the 1950s. The findings are timely and have implications for public policy relating to the control of doping practices. In this short report a number of challenges related to urine testing for Epo are highlighted.

  11. Lack of MSH2 involvement differentiates V(D)J recombination from other non-homologous end joining events.

    Science.gov (United States)

    Larijani, Mani; Zaheen, Ahmad; Frieder, Darina; Wang, Yuxun; Wu, Gillian E; Edelmann, Winfried; Martin, Alberto

    2005-01-01

    V(D)J recombination and class switch recombination are the two DNA rearrangement events used to diversify the mouse and human antibody repertoires. While their double strand breaks (DSBs) are initiated by different mechanisms, both processes use non-homologous end joining (NHEJ) in the repair phase. DNA mismatch repair elements (MSH2/MSH6) have been implicated in the repair of class switch junctions as well as other DNA DSBs that proceed through NHEJ. MSH2 has also been implicated in the regulation of factors such as ATM and the MRN (Mre11, Rad50, Nbs1) complex, which are involved in V(D)J recombination. These findings led us to examine the role of MSH2 in V(D)J repair. Using MSH2-/- and MSH2+/+ mice and cell lines, we show here that all pathways involving MSH2 are dispensable for the generation of an intact pre-immune repertoire by V(D)J recombination. In contrast to switch junctions and other DSBs, the usage of terminal homology in V(D)J junctions is not influenced by MSH2. Thus, whether the repair complex for V(D)J recombination is of a canonical NHEJ type or a separate microhomology-mediated-end joining (MMEJ) type, it does not involve MSH2. This highlights a distinction between the repair of V(D)J recombination and other NHEJ reactions. PMID:16314305

  12. Lack of MSH2 involvement differentiates V(D)J recombination from other non-homologous end joining events

    Science.gov (United States)

    Larijani, Mani; Zaheen, Ahmad; Frieder, Darina; Wang, Yuxun; Wu, Gillian E.; Edelmann, Winfried; Martin, Alberto

    2005-01-01

    V(D)J recombination and class switch recombination are the two DNA rearrangement events used to diversify the mouse and human antibody repertoires. While their double strand breaks (DSBs) are initiated by different mechanisms, both processes use non-homologous end joining (NHEJ) in the repair phase. DNA mismatch repair elements (MSH2/MSH6) have been implicated in the repair of class switch junctions as well as other DNA DSBs that proceed through NHEJ. MSH2 has also been implicated in the regulation of factors such as ATM and the MRN (Mre11, Rad50, Nbs1) complex, which are involved in V(D)J recombination. These findings led us to examine the role of MSH2 in V(D)J repair. Using MSH2?/? and MSH2+/+ mice and cell lines, we show here that all pathways involving MSH2 are dispensable for the generation of an intact pre-immune repertoire by V(D)J recombination. In contrast to switch junctions and other DSBs, the usage of terminal homology in V(D)J junctions is not influenced by MSH2. Thus, whether the repair complex for V(D)J recombination is of a canonical NHEJ type or a separate microhomology-mediated-end joining (MMEJ) type, it does not involve MSH2. This highlights a distinction between the repair of V(D)J recombination and other NHEJ reactions. PMID:16314305

  13. Recombination Form and Epidemiology of HIV-1 Unique Recombinant Strains Identified in Yunnan, China

    OpenAIRE

    Li, Lin; Chen, LiLi; Yang, Shaomin; Li, Tianyi; Li, JianJian; Liu, Yongjian; Jia, Lei; Yang, Bihui; Bao, Zuoyi; Li, Hanping; Wang, Xiaolin; Zhuang, Daomin; Liu, Siyang; Li, Jingyun

    2012-01-01

    Several studies identified HIV-1 recombination in some distinct areas in Yunnan, China. However, no comprehensive studies had been fulfilled in the whole province up to now. To illustrate the epidemiology and recombination form of Unique Recombinant Forms (URFs) circulating in Yunnan, 788 HIV-1 positive individuals residing in 15 prefectures of Yunnan were randomly enrolled into the study. Full-length gag and pol genes were amplified and sequenced. Maximum likelihood tree was constructed for ...

  14. A pulsed ion-ion recombination laser

    Science.gov (United States)

    Petrash, G. G.; Zemskov, K. I.

    2003-01-01

    A new mechanism of pulsed laser oscillation based on ion-ion recombination is proposed. The advantages of utilizing this mechanism in a pulsed mode are considered, and the expected characteristics of the proposed lasers are estimated.

  15. Gene mapping with recombinant inbreds in maize

    International Nuclear Information System (INIS)

    Recombinant inbred lines of maize have been developed for the rapid mapping of molecular probes to chromosomal location. Two recombinant inbred families have been constructed from F2 populations of T232 x CM37 and CO159 x Tx303. A genetic map based largely on isozymes and restriction fragment length polymorphisms has been produced that covers virtually the entire maize genome. In order to map a new gene, an investigator has only to determine its allelic distribution among the recombinant inbred lines and then compare it by computer with the distributions of all previously mapped loci. The availability of the recombinant inbreds and the associated data base constitute an efficient means of mapping new molecular markers in maize

  16. Constraints from jet calculus on quark recombination

    International Nuclear Information System (INIS)

    Within the quantum-chromodynamic jet-calculus formalism, we deduce an equation describing recombination of quarks and antiquarks into mesons within a quark or gluon jet. This equation relates the recombination function R(x1,x2,x) used in current literature to the fragmentation function for producing that same meson out of the parton initiating the jet. We submit currently used recombination functions to our consistency test, taking as input mainly the u-quark fragmentation ''data'' into ?+ mesons. The qq-bar?? recombination functions popular in the literature are consistent with measured fragmentation functions, but they must be supplemented by other contributions to provide the full D?+/sub u/. We also discuss the Q2 dependence of the resulting fragmentation functions

  17. Sturmian theory of three-body recombination

    CERN Document Server

    Forrey, Robert C

    2013-01-01

    A Sturmian theory of three-body recombination is presented which provides a unified treatment of bound states, quasi-bound states, and continuum states. The Sturmian representation provides a numerical quadrature of the two-body continuum which may be used to generate a complete set of states within any desired three-body recombination pathway. Consequently, the dynamical calculation may be conveniently formulated using the simplest energy transfer mechanism, even for reactive systems which allow substantial rearrangement. For a three atom system which is not in thermal equilibrium, the steady-state recombination rate constants are shown to be weakly dependent on tunneling widths and pressure. Numerical results are presented for H2 recombination due to collisions with H and He using quantum mechanical coupled states and infinite order sudden approximations. These results may be used to remove some of the uncertainties that are currently limiting astrophysical simulations of primordial star formation.

  18. Microhomology-mediated deletion and gene conversion in African trypanosomes

    OpenAIRE

    Glover, Lucy; Jun, Junho; Horn, David

    2010-01-01

    Antigenic variation in African trypanosomes is induced by DNA double-strand breaks (DSBs). In these protozoan parasites, DSB repair (DSBR) is dominated by homologous recombination (HR) and microhomology-mediated end joining (MMEJ), while non-homologous end joining (NHEJ) has not been reported. To facilitate the analysis of chromosomal end-joining, we established a system whereby inter-allelic repair by HR is lethal due to loss of an essential gene. Analysis of intrachromosomal end joining in ...

  19. Production of recombinant allergens in plants

    OpenAIRE

    Schmidt, Georg; Gadermaier, Gabriele; Pertl, Heidi; Siegert, Marc; Oksman-caldentey, Kirsi-marja; Ritala, Anneli; Himly, Martin; Obermeyer, Gerhard; Ferreira, Fatima

    2008-01-01

    A large percentage of allergenic proteins are of plant origin. Hence, plant-based expression systems are considered ideal for the recombinant production of certain allergens. First attempts to establish production of plant-derived allergens in plants focused on transient expression in Nicotiana benthamiana infected with recombinant viral vectors. Accordingly, allergens from birch and mugwort pollen, as well as from apple have been expressed in plants. Production of house dust mite allergens h...

  20. Competition between ion recombination and scavenging

    International Nuclear Information System (INIS)

    Complete text of publication follows. In low permittivity solvents ion recombination is dominated by the effects of the relative drift of the ions caused by the Coulomb attraction. However, such systems are frequently investigated by scavenging methods. Since the work of Tachiya on electric field effects, drift has been known to affect the steady-state scavenging rate constant. However, during the recombination drift depends on the instantaneous distance between the ions, and is therefore inherently transient. This paper describes an investigation of this problem using simulation methods. It is found that, within the constraint of the diffusion approximation, there are conditions where the Smoluchowski time-dependent rate constant underestimates the degree to which scavenging intercepts geminate recombination. For this to be a substantial effect the initial distance between the ions must be relatively small (e.g. 4 nm) compared to the typical thermalisation distance of an electron (e.g. 8 nm). Simulations have been used to generate numerical time-dependent rate constants for scavenging. But these proved barely more successful than the Smoluchowski theory, in spite of having been calculated from the simulation results. Stratification of results by recombination time shows that there is a strong correlation between the recombination time and the scavenging time. It was hypothesised that this correlation arises through the strong transient drift as the ions approach one transient drift as the ions approach one another. This hypothesis was confirmed by the application of a novel simulation method in which the ion trajectories are simulated conditional on the recombination time. It was found that in every case the scavenging rate increases sharply just prior to recombination. This dependence of scavenging rate on recombination time is a fundamental breakdown of the assumptions underlying both the theory of diffusion kinetics and the IRT method. Nonetheless, a path decomposition method has been devised that allows IRT simulations to be corrected for this effect with good accuracy.

  1. SIR epidemics in monogamous populations with recombination

    OpenAIRE

    Zanette, Damián H

    2011-01-01

    We study the propagation of an SIR (susceptible--infectious--recovered) disease over an agent population which, at any instant, is fully divided into couples of agents. Couples are occasionally allowed to exchange their members. This process of couple recombination can compensate the instantaneous disconnection of the interaction pattern and thus allow for the propagation of the infection. We study the incidence of the disease as a function of its infectivity and of the recombination rate of ...

  2. Recombinant DNA production of spider silk proteins

    OpenAIRE

    Tokareva, Olena; Michalczechen-lacerda, Valqui?ria A.; Rech, Eli?bio L.; Kaplan, David L.

    2013-01-01

    Spider dragline silk is considered to be the toughest biopolymer on Earth due to an extraordinary combination of strength and elasticity. Moreover, silks are biocompatible and biodegradable protein-based materials. Recent advances in genetic engineering make it possible to produce recombinant silks in heterologous hosts, opening up opportunities for large-scale production of recombinant silks for various biomedical and material science applications. We review the current strategies to produce...

  3. Electron Recombination with Small Molecular Ions

    OpenAIRE

    Brinne Roos, Johanna

    2007-01-01

    In this thesis I have theoretically studied electron recombination processes with small molecular ions. In these kind of processes resonant states are involved. To calculate the potential energy for these states as a function of internuclear distance, structure calculations and scattering calculations have to be performed. So far I have been studying the ion-pair formation with in electron recombination with H3+. The cross section for this process has been calculated using different kind of m...

  4. Algae-based oral recombinant vaccines

    OpenAIRE

    ElizabethASpecht

    2014-01-01

    Recombinant subunit vaccines are some of the safest and most effective vaccines available, but their high cost and the requirement of advanced medical infrastructure for administration make them impractical for many developing world diseases. Plant-based vaccines have shifted that paradigm by paving the way for recombinant vaccine production at agricultural scale using an edible host. However, enthusiasm for “molecular pharming” in food crops has waned in the last decade due to difficulty...

  5. Mechanisms of nonhomologous recombination in mammalian cells.

    OpenAIRE

    Roth, D B; Porter, T N; Wilson, J. H.

    1985-01-01

    The primary mechanism of nonhomologous recombination in transfected DNA involves breakage followed by end joining. To probe the joining step in more detail, linear simian virus 40 genomes with mismatched ends were transfected into cultured monkey cells, and individual viable recombinants were analyzed. The transfected genomes carried mismatched ends as a result of cleavage with two restriction enzymes, the recognition sites of which are located in the intron of the gene encoding the T antigen...

  6. Pure red cell aplasia induced only by intravenous administration of recombinant human erythropoietin.

    Science.gov (United States)

    Shimizu, Hiroaki; Saitoh, Takayuki; Ota, Fumie; Jimbo, Takahiro; Tsukada, Yoshito; Murakami, Hirokazu; Nojima, Yoshihisa

    2011-01-01

    Antibody (Ab)-mediated pure red cell aplasia (PRCA) is a rare but important side effect in patients with chronic kidney disease who receive recombinant human erythropoietin (rhEPO). Ab-mediated PRCA was first reported in the 1990s, and the incidence subsequently increased and reached a peak in 2001. After improvements in rhEPO products and the administration route, the incidence was reduced by 90%, and now Ab-mediated PRCA only develops in a limited number of patients who receive rhEPO subcutaneously for a long period. We describe here the clinical course of one such rare patient with Ab-mediated PRCA. The patient was a 70-year-old man with chronic renal failure secondary to diabetic nephropathy. He had not received rhEPO therapy before the initiation of hemodialysis. He started hemodialysis and began to receive rhEPO therapy intravenously. Three months later, his hemoglobin level started declining and he became transfusion dependent. A diagnosis of Ab-mediated PRCA was made by bone marrow examination and detection of anti-EPO Abs. He was successfully treated with cyclosporine and became independent of blood transfusions. This case is a reminder that vigilance is required regarding the development of Ab-mediated PRCA upon rhEPO therapy, regardless of the administration route. PMID:21654161

  7. Electron thermalization in a recombining plasma

    International Nuclear Information System (INIS)

    Electron temperatures different from neutral and ion temperatures can persist for appreciable periods in a low-density plasma decaying by dissociative recombination. Such temperature differences can be initially due to the process generating the plasma. The energy dependence of the recombination cross section can also result in an elevation of the electron temperature during the recombination process. The time dependence of the electron temperature and recombination rate is calculated for a variety of experimental conditions. Corrections to the observed recombination rate for these effects are important only if the dimensionless parameter C = (16/3)(2m/sub e/kT/sub A//?)1/2 (n/sub A/ sigma/sub MT//m/sub A/ n/sub e/0 ?/sub R//sup A/) is less than unity. (T/sub A/, n/sub A/, and m/subA/ are the neutral particle temperature, number density, and mass, respectively; n/sube/0 and m/sube/ the electron initial number density and mass; sigma/sub MT/ the electron-neutral momentum-transfer cross section; and ?/subR//supA/ the electron-ion dissociative recombination rate constant at T/sub e/ = T/sub A/.) (U.S.)

  8. Recombination analysis based on the complete genome of bocavirus

    Directory of Open Access Journals (Sweden)

    Chen Shengxia

    2011-04-01

    Full Text Available Abstract Bocavirus include bovine parvovirus, minute virus of canine, porcine bocavirus, gorilla bocavirus, and Human bocaviruses 1-4 (HBoVs. Although recent reports showed that recombination happened in bocavirus, no systematical study investigated the recombination of bocavirus. The present study performed the phylogenetic and recombination analysis of bocavirus over the complete genomes available in GenBank. Results confirmed that recombination existed among bocavirus, including the likely inter-genotype recombination between HBoV1 and HBoV4, and intra-genotype recombination among HBoV2 variants. Moreover, it is the first report revealing the recombination that occurred between minute viruses of canine.

  9. Optimizing delignification and pitch removal by treating eucalypt pulp with Myceliophthora laccase and a phenolic mediator

    OpenAIRE

    Rico Campos, Alejandro; Babot, Esteban Daniel; Rencoret, Jorge; Río Andrade, José Carlos del; Martínez Ferrer, Ángel Tomás; Gutiérrez Suárez, Ana

    2012-01-01

    This work shows the ability of two natural phenols, namely syringaldehyde and methyl syringate, to act as mediators of recombinant Myceliophthora thermophila laccase (MtL) in eucalypt-pulp delignification. After alkaline peroxide extraction, the properties of the enzymatically-treated pulps improved with respect to the control. Likewise, removal of the main lipophilic extractives present in eucalypt pulp, such as free and conjugated sterols, was observed after the above laccase-mediator treat...

  10. Production and immunological analysis of IgE reactive recombinant egg white allergens expressed in Escherichia coli.

    Science.gov (United States)

    Dhanapala, Pathum; Doran, Tim; Tang, Mimi L K; Suphioglu, Cenk

    2015-05-01

    IgE-mediated allergy to chicken egg affects a large number of children and adults worldwide. The current management strategy for egg allergy is strict avoidance, however this is impractical due to the presence of eggs in a range of foods and pharmaceutical products including vaccines. Strict avoidance also poses nutritional disadvantages due to high nutritional value of eggs. Allergen specific immunotherapy is being pursued as a curative treatment, in which an allergic individual is gradually exposed to the allergen to induce tolerance. Use of recombinant proteins for immunotherapy has been beneficial due to the purity of the recombinant proteins compared to natural proteins. In this study, we produced IgE reactive recombinant egg white proteins that can be used for future immunotherapy. Using E. coli as an expression system, we successfully produced recombinant versions of Gal d 1, 2 and 3, that were IgE reactive when tested against a pool of egg allergic patients' sera. The IgE reactivity indicates that these recombinant proteins are capable of eliciting an immune response, thus being potential candidates for immunotherapy. We have, for the first time, attempted to produce recombinant versions of all 4 major egg white allergens in E. coli, and successfully produced 3, with only Gal d 4 showing loss of IgE reactivity in the recombinant version. The results suggest that egg allergy in Australian populations may mainly be due to IgE reactivity to Gal d 3 and 4, while Gal d 1 shows higher IgE reactivity. This is the first report of a collective and comparative immunological analysis of all 4 egg white allergens. The significance of this study is the potential use of the IgE reactive recombinant egg white proteins in immunotherapy to treat egg allergic patients. PMID:25656803

  11. Abnormal meiotic recombination with complex chromosomal rearrangement in an azoospermic man.

    Science.gov (United States)

    Wang, Liu; Iqbal, Furhan; Li, Guangyuan; Jiang, Xiaohua; Bukhari, Ihtisham; Jiang, Hanwei; Yang, Qingling; Zhong, Liangwen; Zhang, Yuanwei; Hua, Juan; Cooke, Howard J; Shi, Qinghua

    2015-06-01

    Spermatocyte spreading and immunostaining were applied to detect meiotic prophase I progression, homologous chromosome pairing, synapsis and recombination in an azoospermic reciprocal translocation 46, XY, t(5;7;9;13)(5q11;7p11;7p15;9q12;13p12) carrier. Histological examination of the haematoxylin and eosin stained testicular sections revealed reduced germ cells with no spermatids or sperm in the patient. TdT (terminal deoxynucleotidyl transferase)-mediated dUDP nick-end labelling assay showed apoptotic cells in testicular sections of translocation carrier. Immnunofluorescence analysis indicated the presence of an octavalent in all the pachytene spermatocytes analysed in the patient. Meiotic progression was disturbed, as an increase in zygotene (P < 0.001) and decrease in the pachytene spermatocytes (P < 0.001) were observed in the t(5;7;9;13) carrier compared with controls. It was further observed that 93% of octavalents were found partially asynapsed between homologous chromosomes. A significant decrease in the recombination frequency was observed on 5p, 5q, 7q, 9p and 13q in the translocation carrier compared with the reported controls. A significant reduction in XY recombination frequency was also found in the participants. Our results indicated that complex chromosomal rearrangements can impair synaptic integrity of translocated chromosomes, which may reduce chromosomal recombination on translocated as well as non-translocated chromosomes, a phenomenon commonly known as interchromosomal effect. PMID:25892501

  12. Attenuated Salmonella typhimurium SL3261 as a vaccine vector for recombinant antigen in rabbits.

    Science.gov (United States)

    Ashby, Deborah; Leduc, Isabelle; Lauzon, Wallace; Lee, B Craig; Singhal, Neera; Cameron, D William

    2005-04-01

    Oral live Salmonella vaccine vectors expressing recombinant guest antigens help stimulate systemic, mucosal, humoral, and cell-mediated immune responses against Salmonella and recombinant antigens. It may be possible to use them effectively against Haemophilus ducreyi, the bacterium that causes chancroid, a sexually transmitted genital ulcer disease. This study aimed to test the feasibility of using oral Salmonella vaccine vectors for the evaluation of chancroid vaccine candidates in the temperature-dependent rabbit model of H. ducreyi infection, an in vivo quantitative virulence assay of inducible immunity. We identified 10(8) to 10(9) CFU to be a safe and immunogenic oral dose range of S. typhimurium SL3261, by monitoring post-administration onset and course of illness and antibody titre by enzyme immunoassay (EIA). We successfully transduced plasmid pTETnir15 into the strain to produce recombinant S. typhimurium SL3261(pTETnir15), successfully expressed tetanus toxin fragment C (TetC) in it, and elicited serum anti-TetC titres of 1:6400 by EIA, 4 weeks after inoculation. The course of experimentally induced H. ducreyi skin lesions in rabbits treated with SL3261(pTETnir15) was similar to that in saline-treated controls. We describe a framework that successfully uses Salmonella as a vector for recombinant control antigen in the rabbit model of H. ducreyi infection, and is suitable for pre-clinical evaluation of Salmonella vector-based H. ducreyi vaccine antigen candidates. PMID:15914198

  13. Rad52 forms DMA repair and recombination centers during S phase

    DEFF Research Database (Denmark)

    Lisby, M.; Rothstein, R.

    2001-01-01

    Maintenance of genomic integrity and stable transmission of genetic information depend on a number of DNA repair processes. Failure to faithfully perform these processes can result in genetic alterations and subsequent development of cancer and other genetic diseases. In the eukaryote Saccharomyces cerevisiae, homologous recombination is the major pathway for repairing DNA double-strand breaks. The key role played by Rad52 in this pathway has been attributed to its ability to seek out and mediate annealing of homologous DNA strands. In this study, we find that S. cerevisiae Rad52 fused to green fluorescent protein (GFP) is fully functional in DNA repair and recombination. After induction of DNA double-strand breaks by gamma -irradiation, meiosis, or the HO endonuclease, Rad52-GFP relocalizes from a diffuse nuclear distribution to distinct foci. Interestingly, Rad52 foci are formed almost exclusively during the 5 phase of mitotic cells, consistent with coordination between recombinational repair and DNA replication. This notion is further strengthened by the dramatic increase in the frequency of Rad52 focus formation observed in a pol12-100 replication mutant and a mec1 DNA damage checkpoint mutant. Furthermore, our data indicate that each Rad52 focus represents a center of recombinational repair capable of processing multiple DNA lesions.

  14. Effect of Chloride Passivation on Recombination Dynamics in CdTe Colloidal Quantum Dots.

    Science.gov (United States)

    Espinobarro-Velazquez, Daniel; Leontiadou, Marina A; Page, Robert C; Califano, Marco; O'Brien, Paul; Binks, David J

    2015-04-27

    Colloidal quantum dots (CQDs) can be used in conjunction with organic charge-transporting layers to produce light-emitting diodes, solar cells and other devices. The efficacy of CQDs in these applications is reduced by the non-radiative recombination associated with surface traps. Here we investigate the effect on the recombination dynamics in CdTe CQDs of the passivation of these surface traps by chloride ions. Radiative recombination dominates in these passivated CQDs, with the radiative lifetime scaling linearly with CQD volume over ?r =20-55 ns. Before chloride passivation or after exposure to air, two non-radiative components are also observed in the recombination transients, with sample-dependent lifetimes typically of less than 1 ns and a few ns. The non-radiative dynamics can be explained by Auger-mediated trapping of holes and the lifetimes of this process calculated by an atomistic model are in agreement with experimental values if assuming surface oxidation of the CQDs. PMID:25630838

  15. General Gauge Mediation

    OpenAIRE

    Meade, Patrick; Seiberg, Nathan; Shih, David

    2008-01-01

    We give a general definition of gauge mediated supersymmetry breaking which encompasses all the known gauge mediation models. In particular, it includes both models with messengers as well as direct mediation models. A formalism for computing the soft terms in the generic model is presented. Such a formalism is necessary in strongly-coupled direct mediation models where perturbation theory cannot be used. It allows us to identify features of the entire class of gauge mediati...

  16. Bayesian Mediation Analysis

    OpenAIRE

    Yuan, Ying; Mackinnon, David P.

    2009-01-01

    This article proposes Bayesian analysis of mediation effects. Compared to conventional frequentist mediation analysis, the Bayesian approach has several advantages. First, it allows researchers to incorporate prior information into the mediation analysis, thus potentially improving the efficiency of estimates. Second, under the Bayesian mediation analysis, inference is straightforward and exact, which makes it appealing for studies with small samples. Third, the Bayesian approach is conceptua...

  17. Mediation as Signal

    OpenAIRE

    Holler, M. J.; Lindner, I.

    2004-01-01

    This paper analyzes mediation as a signal. Starting from a stylized case, a game theoretical model of one-sided incomplete information, taken from Cho and Kreps (1987), is applied to discuss strategic effects of mediation. It turns out that to reject mediation can be interpreted as a ”negative signal” while the interpretation of accepting or proposing mediation is ambiguous and does not necessarily change the prior beliefs of the uninformed party. This asymmetry suggests th...

  18. Mediation in cadastral audits

    OpenAIRE

    C?rc?ek, Jure

    2012-01-01

    This thesis presents methods of solving disputes with help of mediation in cases of cadastral audits, such as boundary assessments, reparcelations and boundary equalizations. Mediation is a process where clients try to resolve their dispute peacefully with help of a third person (mediator). The thesis also describes the case definition of the border and in non - judicial proceedings, as well as a detailed description of the law on mediation in civil matters, and the Law on alternative disp...

  19. Generalized Causal Mediation Analysis

    OpenAIRE

    Albert, Jeffrey M.; Nelson, Suchitra

    2011-01-01

    The goal of mediation analysis is to assess direct and indirect effects of a treatment or exposure on an outcome. More generally, we may be interested in the context of a causal model as characterized by a directed acyclic graph (DAG), where mediation via a specific path from exposure to outcome may involve an arbitrary number of links (or ‘stages’). Methods for estimating mediation (or pathway) effects are available for a continuous outcome and a continuous mediator related via a linear ...

  20. Hybrid Gauge Mediation

    OpenAIRE

    Mcgarrie, Moritz

    2011-01-01

    Inspired by four dimensional (de)constructions, we use the framework of "General gauge mediation in five dimensions" to interpolate between gaugino and ordinary gauge mediation. In particular we emphasise that an intermediate hybrid regime of mediation may be obtained in these higher dimensional models as has been obtained in the quiver gauge models.

  1. Bayesian Mediation Analysis

    Science.gov (United States)

    Yuan, Ying; MacKinnon, David P.

    2009-01-01

    In this article, we propose Bayesian analysis of mediation effects. Compared with conventional frequentist mediation analysis, the Bayesian approach has several advantages. First, it allows researchers to incorporate prior information into the mediation analysis, thus potentially improving the efficiency of estimates. Second, under the Bayesian…

  2. Role of teh Rad52 Amino-terminal DNA Binding Activity in DNA Strand Capture in Homologous Recombination

    DEFF Research Database (Denmark)

    Shi, Idina; Hallwyl, Swee Chuang Lim

    2009-01-01

    Saccharomyces cerevisiae Rad52 protein promotes homologous recombination by nucleating the Rad51 recombinase onto replication protein A-coated single-stranded DNA strands and also by directly annealing such strands. We show that the purified rad52-R70A mutant protein, with a compromised amino-terminal DNA binding domain, is capable of Rad51 delivery to DNA but is deficient in DNA annealing. Results from chromatin immunoprecipitation experiments find that rad52-R70A associates with DNA double-strand breaks and promotes recruitment of Rad51 as efficiently as wild-type Rad52. Analysis of gene conversion intermediates reveals that rad52-R70A cells can mediate DNA strand invasion but are unable to complete the recombination event. These results provide evidence that DNA binding by the evolutionarily conserved amino terminus of Rad52 is needed for the capture of the second DNA end during homologous recombination.

  3. Recombination Form and Epidemiology of HIV-1 Unique Recombinant Strains Identified in Yunnan, China

    Science.gov (United States)

    Li, Lin; Chen, Lili; Yang, Shaomin; Li, Tianyi; Li, Jianjian; Liu, Yongjian; Jia, Lei; Yang, Bihui; Bao, Zuoyi; Li, Hanping; Wang, Xiaolin; Zhuang, Daomin; Liu, Siyang; Li, Jingyun

    2012-01-01

    Several studies identified HIV-1 recombination in some distinct areas in Yunnan, China. However, no comprehensive studies had been fulfilled in the whole province up to now. To illustrate the epidemiology and recombination form of Unique Recombinant Forms (URFs) circulating in Yunnan, 788 HIV-1 positive individuals residing in 15 prefectures of Yunnan were randomly enrolled into the study. Full-length gag and pol genes were amplified and sequenced. Maximum likelihood tree was constructed for phylogenetic analysis. Recombinant breakpoints and genomic schematics were identified with online software jpHMM. 63 (10.2%) unique recombinant strains were identified from 617 strains with subtypes. The URFs distributed significantly differently among prefectures (Pearson chi-square test, P<0.05). IDUs contained more URFs than sexual transmitted population (Pearson chi-square test, P<0.05). Two main recombinant forms were identified by considering the presence of CRF01_AE segments in full length gag-pol genes, which were B?/C and B?/C/CRF01-AE recombinants. Three clusters were identified in the ML tree which contained more than three sequences and supported by high bootstrap values. One CRF was identified. Many of URFs contained identical breakpoints. The results will contribute to our understanding on HIV recombination and provide clues to the identification of potential CRFs in China. PMID:23056447

  4. Recombination of electrons with an anisotropic velocity distribution. Continuation of recombination continuum to series lines

    International Nuclear Information System (INIS)

    For ions in recombination with electrons with directional motion, the recombination continuum to a J = 0 state is ? polarized, and this polarization characteristic should continue across the ionization threshold down to the series lines. A Monte Carlo calculation has been performed for electron collisions on a classical atom in excited states. No evidence is found to support the above conclusion. (author)

  5. Coherent and stochastic contributions of compound resonances in atomic processes: Electron recombination, photoionization, and scattering

    Science.gov (United States)

    Flambaum, V. V.; Kozlov, M. G.; Gribakin, G. F.

    2015-05-01

    In open-shell atoms and ions, processes such as photoionization, combination (Raman) scattering, electron scattering, and recombination are often mediated by many-electron compound resonances. We show that their interference (neglected in the independent-resonance approximation) leads to a coherent contribution, which determines the energy-averaged total cross sections of electron- and photon-induced reactions obtained using the optical theorem. In contrast, the partial cross sections (e.g., electron recombination or photon Raman scattering) are dominated by the stochastic contributions. Thus, the optical theorem provides a link between the stochastic and coherent contributions of the compound resonances. Similar conclusions are valid for reactions via compound states in molecules and nuclei.

  6. Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains

    Directory of Open Access Journals (Sweden)

    Penn Charles W

    2009-12-01

    Full Text Available Abstract Background Homologous recombination mediated by the ?-Red genes is a common method for making chromosomal modifications in Escherichia coli. Several protocols have been developed that differ in the mechanisms by which DNA, carrying regions homologous to the chromosome, are delivered into the cell. A common technique is to electroporate linear DNA fragments into cells. Alternatively, DNA fragments are generated in vivo by digestion of a donor plasmid with a nuclease that does not cleave the host genome. In both cases the ?-Red gene products recombine homologous regions carried on the linear DNA fragments with the chromosome. We have successfully used both techniques to generate chromosomal mutations in E. coli K-12 strains. However, we have had limited success with these ?-Red based recombination techniques in pathogenic E. coli strains, which has led us to develop an enhanced protocol for recombineering in such strains. Results Our goal was to develop a high-throughput recombineering system, primarily for the coupling of genes to epitope tags, which could also be used for deletion of genes in both pathogenic and K-12 E. coli strains. To that end we have designed a series of donor plasmids for use with the ?-Red recombination system, which when cleaved in vivo by the I-SceI meganuclease generate a discrete linear DNA fragment, allowing for C-terminal tagging of chromosomal genes with a 6 × His, 3 × FLAG, 4 × ProteinA or GFP tag or for the deletion of chromosomal regions. We have enhanced existing protocols and technologies by inclusion of a cassette conferring kanamycin resistance and, crucially, by including the sacB gene on the donor plasmid, so that all but true recombinants are counter-selected on kanamycin and sucrose containing media, thus eliminating the need for extensive screening. This method has the added advantage of limiting the exposure of cells to the potential damaging effects of the ?-Red system, which can lead to unwanted secondary alterations to the chromosome. Conclusion We have developed a counter-selective recombineering technique for epitope tagging or for deleting genes in E. coli. We have demonstrated the versatility of the technique by modifying the chromosome of the enterohaemorrhagic O157:H7 (EHEC, uropathogenic CFT073 (UPEC, enteroaggregative O42 (EAEC and enterotoxigenic H10407 (ETEC E. coli strains as well as in K-12 laboratory strains.

  7. A recombinase-mediated system for elimination of antibiotic resistance gene markers from genetically engineered Bacillus thuringiensis strains.

    OpenAIRE

    Sanchis, V.; Agaisse, H.; Chaufaux, J.; Lereclus, D.

    1997-01-01

    A TnpI-mediated site-specific recombination system to construct genetically modified Bacillus thuringiensis strains was developed. Recombinant B. thuringiensis strains from which antibiotic resistance genes can be selectively eliminated were obtained in vivo with a new vector based on the specific resolution site of transposon Tn4430. For example, a cryIC gene, whose product is active against Spodoptera littoralis, was introduced into B. thuringiensis Kto harboring a cryIA(c) gene active agai...

  8. General gauge mediation

    International Nuclear Information System (INIS)

    We give a general definition of gauge mediated supersymmetry breaking which encompasses all the known gauge mediation models. In particular, it includes both models with messengers as well as direct mediation models. A formalism for computing the soft terms in the generic model is presented. Such a formalism is necessary in strongly-coupled direct mediation models where perturbation theory cannot be used. It allows us to identify features of the entire class of gauge mediation models and to distinguish them from specific signatures of various subclasses. (author)

  9. Graded recombination layers for multijunction photovoltaics.

    Science.gov (United States)

    Koleilat, Ghada I; Wang, Xihua; Sargent, Edward H

    2012-06-13

    Multijunction devices consist of a stack of semiconductor junctions having bandgaps tuned across a broad spectrum. In solar cells this concept is used to increase the efficiency of photovoltaic harvesting, while light emitters and detectors use it to achieve multicolor and spectrally tunable behavior. In series-connected current-matched multijunction devices, the recombination layers must allow the hole current from one cell to recombine, with high efficiency and low voltage loss, with the electron current from the next cell. We recently reported a tandem solar cell in which the recombination layer was implemented using a progression of n-type oxides whose doping densities and work functions serve to connect, with negligible resistive loss at solar current densities, the constituent cells. Here we present the generalized conditions for design of efficient graded recombination layer solar devices. We report the number of interlayers and the requirements on work function and doping of each interlayer, to bridge an work function difference as high as 1.6 eV. We also find solutions that minimize the doping required of the interlayers in order to minimize optical absorption due to free carriers in the graded recombination layer (GRL). We demonstrate a family of new GRL designs experimentally and highlight the benefits of the progression of dopings and work functions in the interlayers. PMID:22554234

  10. Recombination in Eukaryotic Single Stranded DNA Viruses

    Directory of Open Access Journals (Sweden)

    Philippe Roumagnac

    2011-09-01

    Full Text Available Although single stranded (ss DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.

  11. Polyploidization increases meiotic recombination frequency in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Rehmsmeier Marc

    2011-04-01

    Full Text Available Abstract Background Polyploidization is the multiplication of the whole chromosome complement and has occurred frequently in vascular plants. Maintenance of stable polyploid state over generations requires special mechanisms to control pairing and distribution of more than two homologous chromosomes during meiosis. Since a minimal number of crossover events is essential for correct chromosome segregation, we investigated whether polyploidy has an influence on the frequency of meiotic recombination. Results Using two genetically linked transgenes providing seed-specific fluorescence, we compared a high number of progeny from diploid and tetraploid Arabidopsis plants. We show that rates of meiotic recombination in reciprocal crosses of genetically identical diploid and autotetraploid Arabidopsis plants were significantly higher in tetraploids compared to diploids. Although male and female gametogenesis differ substantially in meiotic recombination frequency, both rates were equally increased in tetraploids. To investigate whether multivalent formation in autotetraploids was responsible for the increased recombination rates, we also performed corresponding experiments with allotetraploid plants showing strict bivalent pairing. We found similarly increased rates in auto- and allotetraploids, suggesting that the ploidy effect is independent of chromosome pairing configurations. Conclusions The evolutionary success of polyploid plants in nature and under domestication has been attributed to buffering of mutations and sub- and neo-functionalization of duplicated genes. Should the data described here be representative for polyploid plants, enhanced meiotic recombination, and the resulting rapid creation of genetic diversity, could have also contributed to their prevalence.

  12. Fanconi Anemia Protein FANCD2 Promotes Immunoglobulin Gene Conversion and DNA Repair through a Mechanism Related to Homologous Recombination

    OpenAIRE

    Yamamoto, Kazuhiko; Hirano, Seiki; Ishiai, Masamichi; Morishima, Kenichi; Kitao, Hiroyuki; Namikoshi, Keiko; Kimura, Masayo; Matsushita, Nobuko; Arakawa, Hiroshi; Buerstedde, Jean-marie; Komatsu, Kenshi; Thompson, Larry H.; Takata, Minoru

    2005-01-01

    Recent studies show overlap between Fanconi anemia (FA) proteins and those involved in DNA repair mediated by homologous recombination (HR). However, the mechanism by which FA proteins affect HR is unclear. FA proteins (FancA/C/E/F/G/L) form a multiprotein complex, which is responsible for DNA damage-induced FancD2 monoubiquitination, a key event for cellular resistance to DNA damage. Here, we show that FANCD2-disrupted DT40 chicken B-cell line is defective in HR-mediated DNA double-strand br...

  13. Comparison of recombination models in organic bulk heterojunction solar cells

    International Nuclear Information System (INIS)

    Recombination in bulk-heterojunction (BHJ) organic solar cells is the key loss mechanism, and it directly affects characteristic parameters such as power conversion efficiency, short-circuit current, open-circuit voltage, and fill factor. However, which recombination mechanism dominates the loss in organic materials is unclear at present. In this work, we simulate state-of-art BHJ solar cells using five recombination models, including direct recombination, Langevin recombination, charge transfer state recombination, trap-assisted recombination, and recombination via tail. All processes are strongly dependent on charge carrier mobility and exhibit a similar recombination distribution in active layer. For high mobilities, all models present a similar behavior along with the increased mobilities, whereas, there are slight differences in open-circuit voltage between trap/tail model and other ones at lower mobilities, resulting from the interaction between photo-carriers and dark-carriers

  14. Regulation of Homologous Recombination by SUMOylation : SUMO, DNA Repair and New Insights into Telomere Maintenance

    DEFF Research Database (Denmark)

    Pinela da Silva, Sonia Cristina

    2014-01-01

    Double-strand breaks (DSBs) are one of the most deleterious types of DNA lesions challenging genome integrity. The DNA damage response (DDR) promotes fast and effective detection and repair of the damaged DNA, leading to cell cycle arrest through checkpoint activation and the recruitment of repair factors such as the homologous recombination (HR) machinery. HR constitutes the main DSB repair pathway in Saccharomyces cerevisiae and despite being largely considered an error-free process and essential for genome stability, uncontrolled recombination can lead to loss of heterozygosity, translocations, deletions, and genome rearrangements that can lead to cell death or cancer in humans. The post-translational modification by SUMO (small ubiquitinlike modifier) has proven to be an important regulator of HR and genome integrity, but the molecular mechanisms responsible for these roles are still unclear. In this study I present new insights for the role of SUMOylation in regulating HR by dissecting the role of SUMO in the interaction between the central HR-mediator protein Rad52 and its paralogue Rad59 and the outcome of recombination. This data provides evidence for the importance of SUMO in promoting protein-protein interactions at the sites of repair, enabling effective Rad51-mediated recombination through the concerted action of the Rad52-Rad59 complex and the helicase Srs2. In addition, I also peer into the role of Rad52 SUMOylation in the context of persistent DSBs and telomere homeostasis. Furthermore, I characterize Mte1, a novel protein involved in DDR that associates with the helicase Mph1 and Rad52. Moreover, I find that Mte1 associates with dysfunctional single-stranded telomeric DNA, constituting a novel factor in telomere homeostasis, potentially associated with replication-stress relief.

  15. Removal of nonhomologous DNA ends in double-strand break recombination: The role of the yeast ultraviolet repair gene RAD1

    International Nuclear Information System (INIS)

    Double-strand breaks (DSBs) in Saccharomyces cerevisiae can be repaired by gene conversions or by deletions resulting from single-strand annealing between direct repeats of homologous sequences. Although rad1 mutants are resistant to x-rays and can complete DSB-mediated mating-type switching, they could not complete recombination when the ends of the break contained approximately 60 base pairs of nonhomology. Recombination was restored when the ends of the break were made homologous to donor sequences. Additionally, the absence of RAD1 led to the frequent appearance of a previously unobserved type of recombination product. These data suggest RAD1 is required to remove nonhomologous DNA from the 3' ends of recombining DNA, a process analogous to the excision of photodimers during repair of ultraviolet-damaged DNA

  16. A Novel Mouse Synaptonemal Complex Protein Is Essential for Loading of Central Element Proteins, Recombination, and Fertility

    OpenAIRE

    Schramm, Sabine; Fraune, Johanna; Naumann, Ronald; Hernandez-hernandez, Abrahan; Ho?o?g, Christer; Cooke, Howard J.; Alsheimer, Manfred; Benavente, Ricardo

    2011-01-01

    The synaptonemal complex (SC) is a proteinaceous, meiosis-specific structure that is highly conserved in evolution. During meiosis, the SC mediates synapsis of homologous chromosomes. It is essential for proper recombination and segregation of homologous chromosomes, and therefore for genome haploidization. Mutations in human SC genes can cause infertility. In order to gain a better understanding of the process of SC assembly in a model system that would be relevant for humans, we are investi...

  17. Recombinant Glycans on an S-Layer Self-Assembly Protein: A New Dimension for Nanopatterned Biomaterials

    OpenAIRE

    Steiner, Kerstin; Hanreich, Angelika; Kainz, Birgit; Hitchen, Paul G; Anne; Messner, Paul; Schäffer, Christina

    2008-01-01

    Crucial biological phenomena are mediated through carbohydrates that are displayed in a defined manner and interact with molecular scale precision. We lay the groundwork for the integration of recombinant carbohydrates into a “biomolecular construction kit” for the design of new biomaterials, by utilizing the self-assembly system of the crystalline cell surface (S)-layer protein SgsE of Geobacillus stearothermophilus NRS 2004/3a. SgsE is a naturally O-glycosylated protein, with intrinsic prop...

  18. Non-gaussianities from perturbing recombination

    International Nuclear Information System (INIS)

    We approximately compute the bispectrum induced on the CMB temperature by fluctuations in the standard recombination epoch. Of all the second order sources that can induce non-Gaussianity during recombination, we concentrate on those proportional to the perturbation in the free electron density, which is about a factor of 5 larger than the other first order perturbations. This term induces some non-Gaussianity by delaying the time of recombination and by changing the photon diffusion scale. We find that the signal is not scale invariant, peaked on squeezed triangles with the smaller multipole around the scale of the first acoustic peak, and that its size corresponds to an effective fNL ? ?3.5, which could be marginally detected by Planck if both temperature and polarization are measured

  19. Recombinant human erythropoietin in sports: a review

    Directory of Open Access Journals (Sweden)

    Rafael Maia de Almeida Bento

    2003-06-01

    Full Text Available Erythropoietin is an endogenous hormone of glicoproteic nature secreted by the kidneys and is the main regulator of the erythropoiesis. An alteration in its production generates a disturbance in the plasmatic concentration giving rise to several types of pathologies related to the hematopoietic system. The recombinant forms of erythropoietin have indiscriminately been used by athletes, mainly in endurance sports, by increasing the erythrocytes concentration, generating a better delivery of oxygen to the muscle tissue. The administration of recombinant erythropoietin was prohibited by the International Olympic Committee and its use considered as doping. This review has the intention to describe the physical, biological and pharmacokinetic properties of the endogenous erythropoietin, as well as its recombinant form, describing also its use in sports and the process of searching methodologies for its detection in doping control.

  20. Recombinant microorganisms for increased production of organic acids

    Science.gov (United States)

    Yi, Jian; Kleff, Susanne; Guettler, Michael V

    2013-04-30

    Disclosed are recombinant microorganisms for producing organic acids. The recombinant microorganisms express a polypeptide that has the enzymatic activity of an enzyme that is utilized in the pentose phosphate cycle. The recombinant microorganism may include recombinant Actinobacillus succinogenes that has been transformed to express a Zwischenferment (Zwf) gene. The recombinant microorganisms may be useful in fermentation processes for producing organic acids such as succinic acid and lactic acid. Also disclosed are novel plasmids that are useful for transforming microorganisms to produce recombinant microorganisms that express enzymes such as Zwf.

  1. Recombinant microorganisms for increased production of organic acids

    Energy Technology Data Exchange (ETDEWEB)

    Yi, Jian (East Lansing, MI); Kleff, Susanne (East Lansing, MI); Guettler, Michael V. (Holt, MI)

    2012-02-21

    Disclosed are recombinant microorganisms for producing organic acids. The recombinant microorganisms express a polypeptide that has the enzymatic activity of an enzyme that is utilized in the pentose phosphate cycle. The recombinant microorganism may include recombinant Actinobacillus succinogenes that has been transformed to express a Zwischenferment (Zwf) gene. The recombinant microorganisms may be useful in fermentation processes for producing organic acids such as succinic acid and lactic acid. Also disclosed are novel plasmids that are useful for transforming microorganisms to produce recombinant microorganisms that express enzymes such as Zwf.

  2. Dissociative recombination of CF+: Experiment and theory

    International Nuclear Information System (INIS)

    We present results from our recent studies of the dissociative recombination of the CF+ cation. On one hand, dissociative recombination was measured with 3 MeV CF+ ions in the heavy-ion Test Storage Ring in Heidelberg, using the twin electron beam configuration with an electron cooler and a separated electron target for collision measurements. In this experiment, the low temperatures of the electron beam provided by a photocathode (temperature in co-moving frame below 1 meV) account for a fast kinetic cooling of the heavy-ion beam and a high resolution in the measured rate coefficients. Fragment imaging measurements show a complete switching of the dissociation route by only a small change of the collision energy and the disappearance of neutral Rydberg product states on crossing the DE threshold. On the other hand, extensive calculations of energy positions and autoionization widths for the doubly excited states of CF between the first and second ionization thresholds have been obtained from electron scattering calculations using the complex Kohn variational method, followed by calculations of the dissociative recombination process with the multichannel quantum defect theory. In preliminary computations, only the first dissociative state in each molecular symmetry, which lies closest in energy to the ion potential at its equilibrium internuclear separation, and thus is dominant for the low-energy dissociative recombination, was included. Althougative recombination, was included. Although only the direct mechanism of dissociative recombination reaction has been considered in this step, the size and the shape of the DR rate coefficient are already well reproduced.

  3. Dielectronic recombination measurements of multicharged ions

    International Nuclear Information System (INIS)

    Dielectronic recombination rates have been measured for several charge states of isoelectronic Li-like, Be-like, B-like, and Na-like ions. The amount of electron capture attending the passage of MeV/nucleon ion beams through a collinear, magnetically confined space-charge-limited electron beam as a function of relative energy has been observed. The experimental rates are consistent in magnitude and shape with rates determined from distorted-wave calculations of the dielectronic-recombination cross sections. 72 refs., 6 figs

  4. Dielectronic recombination measurements of multicharged ions

    Energy Technology Data Exchange (ETDEWEB)

    Dittner, P.F.

    1987-01-01

    Dielectronic recombination rates have been measured for several charge states of isoelectronic Li-like, Be-like, B-like, and Na-like ions. The amount of electron capture attending the passage of MeV/nucleon ion beams through a collinear, magnetically confined space-charge-limited electron beam as a function of relative energy has been observed. The experimental rates are consistent in magnitude and shape with rates determined from distorted-wave calculations of the dielectronic-recombination cross sections. 72 refs., 6 figs.

  5. Strategies of Loop Recombination in Ciliates

    CERN Document Server

    Brijder, R; Muskulus, M; Brijder, Robert; Hoogeboom, Hendrik Jan; Muskulus, Michael

    2006-01-01

    Gene assembly in ciliates is an extremely involved DNA transformation process, which transforms a nucleus, the micronucleus, to another functionally different nucleus, the macronucleus. In this paper we characterize which loop recombination operations (one of the three types of molecular operations that accomplish gene assembly) can possibly be applied in the transformation of a given gene from its micronuclear form to its macronuclear form. We also characterize in which order these loop recombination operations are applicable. This is done in the abstract and more general setting of so-called legal strings.

  6. Size effects on generation recombination noise

    CERN Document Server

    Gomila, G

    2002-01-01

    We carry out an analytical theory of generation-recombination noise for a two level resistor model which goes beyond those presently available by including the effects of both space charge fluctuations and diffusion current. Finite size effects are found responsible for the saturation of the low frequency current spectral density at high enough applied voltages. The saturation behaviour is controlled essentially by the correlations coming from the long range Coulomb interaction. It is suggested that the saturation of the current fluctuations for high voltage bias constitutes a general feature of generation-recombination noise.

  7. Theoretical models for recombination in expanding gas

    International Nuclear Information System (INIS)

    In laser isotope separation of atomic uranium, one is confronted with the theoretical problem of estimating the concentration of thermally ionized uranium atoms. To investigate this problem theoretical models for recombination in an expanding gas and in the absence of local thermal equilibrium have been constructed. The expansion of the gas is described by soluble models of the hydrodynamic equation, and the recombination by rate equations. General results for the freezing effect for the suitable ranges of the gas parameters are obtained. The impossibility of thermal equilibrium in expanding two-component systems is proven

  8. Characterization of Bacillus subtilis recombinational pathways.

    OpenAIRE

    Alonso, J.C.; Lüder, G; Tailor, R H

    1991-01-01

    Recombination in Bacillus subtilis requires the products of numerous rec loci. To dissect the various mechanisms which may be involved in genetic recombination, we constructed a series of isogenic strains containing more than one mutant rec allele. On the basis of their impairment in genetic exchange, the various loci (represented by specific rec alleles) were classified into different epistatic groups. Group alpha consists of rec genes represented by recB, recD, recF, recG, recL, and recR mu...

  9. Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts

    KAUST Repository

    Huang, Chao-Li

    2015-03-15

    Background: Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants. Results: Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting. Conclusion: Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification. © Huang et al.

  10. Mrc1 Is Required for Sister Chromatid Cohesion To Aid in Recombination Repair of Spontaneous Damage

    OpenAIRE

    Xu, Hong; Boone, Charles; Klein, Hannah L

    2004-01-01

    The SRS2 gene of Saccharomyces cerevisiae encoding a 3??5? DNA helicase is part of the postreplication repair pathway and functions to ensure proper repair of DNA damage arising during DNA replication through pathways that do not involve homologous recombination. Through a synthetic gene array analysis, genes that are essential when Srs2 is absent have been identified. Among these are MRC1, TOF1, and CSM3, which mediate the intra-S checkpoint response. srs2? mrc1? synthetic lethality ...

  11. A facile method for reversibly linking a recombinant protein to DNA.

    OpenAIRE

    Goodman, RP; Erben, CM; Malo, J; Ho, WM; Mckee, ML; Kapanidis, AN; Turberfield, AJ

    2009-01-01

    We present a facile method for linking recombinant proteins to DNA. It is based on the nickel-mediated interaction between a hexahistidine tag (His(6)-tag) and DNA functionalized with three nitrilotriacetic acid (NTA) groups. The resulting DNA-protein linkage is site-specific. It can be broken quickly and controllably by the addition of a chelating agent that binds nickel. We have used this new linker to bind proteins to a variety of DNA motifs commonly used in the fabrication of nanostructur...

  12. Jahn-teller interactions in the dissociative recombination of H3+.

    Science.gov (United States)

    Jungen, Ch; Pratt, S T

    2009-01-16

    A simple analytical approach is presented to describe the dissociative recombination (DR) of an electron with H3+ and its isotopomers. The principal assumption is that resonant capture mediated by the Jahn-Teller interaction dominates the cross section. The only input required comes from spectroscopic data on the 3pE;{'} Rydberg state of H3 and the nu_{2} vibrational frequencies of H3+ and its isotopomers. The approach provides an independent prediction of the low-energy DR cross sections and rates, and is in good agreement with the latest experimental and theoretical determinations. PMID:19257270

  13. [Immunogenicity of recombinant S. typhimurium ex. pressing a hybrid antigen of Plasmodium falciparum].

    Science.gov (United States)

    Huang, J; Wang, C; Ren, D; Li, Q; Zhong, X

    1996-06-01

    We have expressed a 74-peptide hybrid Plasmodium falciparum antigen as fusion protein in attenuated Salmonella typhimurium SL3261. Live organisms were orally immunized Rabbits with a dose of 2 x 10(9)cfu. Specific anti-serum were detected by ELISA after immunization. Obvious Delayed type hypersensitivity (DTH) could be induced by PfAg and GZ-C antigen. The recombinant vaccine had no evident side-effects to the hosts. Our studies indicate that attenuated Salmonella typhimurium SL3261 can express synthetic P. falciparum antigen with several epitopes and live organisms can activate special cell-mediated immunity and humoral immunity. PMID:9639818

  14. Discovery of a Predicted DNA Knot Substantiates a Model for Site-Specific Recombination

    Science.gov (United States)

    Wasserman, Steven A.; Dungan, Jan M.; Cozzarelli, Nicholas R.

    1985-07-01

    The mechanism of site-specific genetic recombination mediated by Tn3 resolvase has been investigated by a topological approach. Extrapolation of a detailed model of synapsis and strand exchange predicts the formation of an additional DNA product with a specific knotted structure. Two-dimensional gel electrophoresis of DNA reacted in vitro revealed a product, about 0.1 percent of the total, with the appropriate mobility. A technique for determining DNA topology by electron microscopy was improved such that less than a nanogram of DNA was required. The structure of the knot was as predicted, providing strong evidence for the model and showing the power of the topological method.

  15. Unveiling Novel RecO Distant Orthologues Involved in Homologous Recombination

    OpenAIRE

    Marsin, Stéphanie; Mathieu, Aurélie; Kortulewski, Thierry; Guérois, Raphaël; Radicella, J. Pablo

    2008-01-01

    The generation of a RecA filament on single-stranded DNA is a critical step in homologous recombination. Two main pathways leading to the formation of the nucleofilament have been identified in bacteria, based on the protein complexes mediating RecA loading: RecBCD (AddAB) and RecFOR. Many bacterial species seem to lack some of the components involved in these complexes. The current annotation of the Helicobacter pylori genome suggests that this highly diverse bacterial pathogen has a reduced...

  16. Mediation and Legal Assistance

    Directory of Open Access Journals (Sweden)

    Larisa Zaitseva

    2015-02-01

    Full Text Available The development of alternative dispute resolution procedures raises a number of new problems and questions for jurisprudence and legal practice. Many of these are closely related to the implementation of mediation procedures. Significant attention has been paid in the legal literature to the need for mediators’ legal education. Nowadays a professional lawyer usually performs the functions of a mediator. Nevertheless, in some countries the competence of mediators can be limited. In fact, such persons may be prohibited from providing any legal assistance to the parties. A direct prohibition of this kind exists in Russian legislation. To what degree is this prohibition realistic and reasonable? Different countries enjoy different approaches to the possibility of providing disputing parties with a mediator’s legal assistance in addressing issues requiring legal advice or in the drafting of legal documents. Different approaches to this issue have appeared for various reasons. The absence of consensus is caused by a contradiction between the principle of mediator neutrality in the conflict resolution process and the goals of dispute settlement in which a legally competent intermediary is involved. To ensure the effectiveness of the mediation process, legislators should seek out more flexible ways of regulating procedure. Mandatory regulation itself contradicts the spirit of ‘semi-formal’ alternative (extrajudicial methods for conflict resolution. As such, the presence of direct prohibitions or severe restrictions may not only become challenging in the performance of law but such peremptory norms can also make mediation unattractive and ineffective for some particular types of dispute, such as labor disputes. The principle of preserving a mediator’s neutrality is possible if exercised within the framework of a balanced approach to reasonable limits and discretionary rules for the provision of certain types of legal assistance to disputing parties.The present article aims to consider the possibilities and limitations on a mediator’s ability to provide particular types of legal assistance where the guarantee of non-discrimination between disputing parties’ interests is presupposed.

  17. Avoidance of Protein Fold Disruption in Natural Virus Recombinants

    Science.gov (United States)

    Lefeuvre, Pierre; Lett, Jean-Michel; Reynaud, Bernard; Martin, Darren P

    2007-01-01

    With the development of reliable recombination detection tools and an increasing number of available genome sequences, many studies have reported evidence of recombination in a wide range of virus genera. Recombination is apparently a major mechanism in virus evolution, allowing viruses to evolve more quickly by providing immediate direct access to many more areas of a sequence space than are accessible by mutation alone. Recombination has been widely described amongst the insect-transmitted plant viruses in the genus Begomovirus (family Geminiviridae), with potential recombination hot- and cold-spots also having been identified. Nevertheless, because very little is understood about either the biochemical predispositions of different genomic regions to recombine or what makes some recombinants more viable than others, the sources of the evolutionary and biochemical forces shaping distinctive recombination patterns observed in nature remain obscure. Here we present a detailed analysis of unique recombination events detectable in the DNA-A and DNA-A-like genome components of bipartite and monopartite begomoviruses. We demonstrate both that recombination breakpoint hot- and cold-spots are conserved between the two groups of viruses, and that patterns of sequence exchange amongst the genomes are obviously non-random. Using a computational technique designed to predict structural perturbations in chimaeric proteins, we demonstrate that observed recombination events tend to be less disruptive than sets of simulated ones. Purifying selection acting against natural recombinants expressing improperly folded chimaeric proteins is therefore a major determinant of natural recombination patterns in begomoviruses. PMID:18052529

  18. Microhomology-Mediated Mechanisms Underlie Non-Recurrent Disease-Causing Microdeletions of the FOXL2 Gene or Its Regulatory Domain

    OpenAIRE

    Verdin, Hannah; D Haene, Barbara; Beysen, Diane; Novikova, Yana; Menten, Bjo?rn; Sante, Tom; Lapunzina, Pablo; Nevado, Julian; Carvalho, Claudia M. B.; Lupski, James R.; Baere, Elfride

    2013-01-01

    Genomic disorders are often caused by recurrent copy number variations (CNVs), with nonallelic homologous recombination (NAHR) as the underlying mechanism. Recently, several microhomology-mediated repair mechanisms—such as microhomology-mediated end-joining (MMEJ), fork stalling and template switching (FoSTeS), microhomology-mediated break-induced replication (MMBIR), serial replication slippage (SRS), and break-induced SRS (BISRS)—were described in the etiology of non-recurrent CNVs in h...

  19. Oxidative refolding of rPA in l-ArgHCl and in ionic liquids: A correlation between hydrophobicity, salt effects, and refolding yield.

    Science.gov (United States)

    Tischer, Alexander; Lilie, Hauke; Auton, Matthew; Lange, Christian

    2014-11-01

    The ionic liquid 1-ethyl-3-methyl imidazolium chloride (EMIM Cl) and the amino acid l-arginine hydrochloride (l-ArgHCl) have been successfully used to improve the yield of oxidative refolding for various proteins. However, the molecular mechanisms behind the actions of such solvent additives-especially of ionic liquids-are still not well understood. To analyze these mechanisms, we have determined the transfer free energies from water into ionic liquid solutions of proteinogenic amino acids and of diketopiperazine as peptide bond analogue. For EMIM Cl and 1-ethyl-3-methyl imidazolium diethyl phosphate, which had a suppressive effect on protein refolding, as well as for l-ArgHCl favorable interactions with amino acid side chains, but no favorable interactions with the peptide backbone could be observed. A quantitative analysis of other ionic liquids together with their already published effects on protein refolding showed that only solvent additives within a certain range of hydrophobicity, chaotropicity and kosmotropicity were effective for the refolding of recombinant plasminogen activator. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 1129-1140, 2014. PMID:24931846

  20. The efficacy of recombinant versus urinary HCG in ART outcome

    OpenAIRE

    Eftekhar, Maryam; Khalili, Mohammad Ali; Rahmani, Elham

    2012-01-01

    Background: Human chorionic gonadotropin (HCG) has been used as a replacement for the mid-cycle luteinizing hormone (LH) surge for several years. The recent arrival of recombinant DNA technology has made recombinant HCG (rHCG) accessible.

  1. Prospects for Mirage Mediation

    OpenAIRE

    Pierce, Aaron; Thaler, Jesse

    2006-01-01

    Mirage mediation reduces the fine-tuning in the minimal supersymmetric standard model by dynamically arranging a cancellation between anomaly-mediated and modulus-mediated supersymmetry breaking. We explore the conditions under which a mirage "messenger scale" is generated near the weak scale and the little hierarchy problem is solved. We do this by explicitly including the dynamics of the SUSY-breaking sector needed to cancel the cosmological constant. The most plausible sc...

  2. General resonance mediation

    International Nuclear Information System (INIS)

    We extend the framework of general gauge mediation to cases where the mediating fields have a nontrivial spectral function, as might arise from strong dynamics. We demonstrate through examples that this setup describes a broad class of possible models of gauge mediated supersymmetry breaking. A main emphasis is to give general formulas for cross sections for ?(visible ? hidden) in these resonance models. We will also give formulas for soft masses, A-terms and demonstrate the framework with a holographic setup.

  3. Catalytic hydrogen recombination for nuclear containments

    International Nuclear Information System (INIS)

    Catalytic recombiners appear to be a credible option for hydrogen mitigation in nuclear containments. The passive operation, versatility and ease of back fitting are appealing for existing stations and new designs. Recently, a generation of wet-proofed catalyst materials have been developed at AECL which are highly specific to H2-O2, are active at ambient temperatures and are being evaluated for containment applications. Two types of catalytic recombiners were evaluated for hydrogen removal in containments based on the AECL catalyst. The first is a catalytic combustor for application in existing air streams such as provided by fans or ventilation systems. The second is an autocatalytic recombiner which uses the enthalpy of reaction to produce natural convective flow over the catalyst elements. Intermediate-scale results obtained in 6 m3 and 10 m3 spherical and cylindrical vessels are given to demonstrate self-starting limits, operating limits, removal capacity, scaling parameters, flow resistance, mixing behaviour in the vicinity of an operating recombiner and sensitivity to poisoning, fouling and radiation. (author). 13 refs., 10 figs

  4. Magnetic affinity separation of recombinant fusion proteins.

    Czech Academy of Sciences Publication Activity Database

    Šafa?ík, Ivo; Šafa?íková, Miroslava

    2010-01-01

    Ro?. 38, ?. 1 (2010), s. 1-7. ISSN 1303-5002 R&D Projects: GA MŠk(CZ) OC 157; GA MPO(CZ) 2A-1TP1/094 Institutional research plan: CEZ:AV0Z60870520 Keywords : recombinant fusion proteins * affinity tags * magnetic separation Subject RIV: CE - Biochemistry

  5. Mismatch repair during homologous and homeologous recombination.

    Science.gov (United States)

    Spies, Maria; Fishel, Richard

    2015-03-01

    Homologous recombination (HR) and mismatch repair (MMR) are inextricably linked. HR pairs homologous chromosomes before meiosis I and is ultimately responsible for generating genetic diversity during sexual reproduction. HR is initiated in meiosis by numerous programmed DNA double-strand breaks (DSBs; several hundred in mammals). A characteristic feature of HR is the exchange of DNA strands, which results in the formation of heteroduplex DNA. Mismatched nucleotides arise in heteroduplex DNA because the participating parental chromosomes contain nonidentical sequences. These mismatched nucleotides may be processed by MMR, resulting in nonreciprocal exchange of genetic information (gene conversion). MMR and HR also play prominent roles in mitotic cells during genome duplication; MMR rectifies polymerase misincorporation errors, whereas HR contributes to replication fork maintenance, as well as the repair of spontaneous DSBs and genotoxic lesions that affect both DNA strands. MMR suppresses HR when the heteroduplex DNA contains excessive mismatched nucleotides, termed homeologous recombination. The regulation of homeologous recombination by MMR ensures the accuracy of DSB repair and significantly contributes to species barriers during sexual reproduction. This review discusses the history, genetics, biochemistry, biophysics, and the current state of studies on the role of MMR in homologous and homeologous recombination from bacteria to humans. PMID:25731766

  6. Recombination times in germanium under high pressure

    International Nuclear Information System (INIS)

    The influence of pressure on a well defined recombination process was studied. The centres were introduced by ?irradiation and the lifetime determined by the decay time of photoconductivity. An optical pressure vessel is described which allows for a hydrostatic variation of 3000 bars. The diffusion constant and lifetime measurements are presented and analysed. (V.J.C.)

  7. Selected techniques in recombinant DNA technology

    International Nuclear Information System (INIS)

    Recombined DNA technology comprises a complex of techniques in the fields of nucleic acid biochemistry and molecular biology. This presentation gives an introduction, a brief description and example of the procedures of some of the basic techniques in the DNA cloning work currently used. 8 refs

  8. Theory of dielectronic recombination and plasma effects

    International Nuclear Information System (INIS)

    Current status of the various theoretical approaches to calculation of dielectronic recombination rates is summarized, with emphasis on the available data base and on the plasma effects of both the plasma ion (and external) fields and plasma electron collisional effects which seriously affect the rates and complicate compilation of data. (author)

  9. Asthma and Therapeutics: Recombinant Therapies in Asthma

    Directory of Open Access Journals (Sweden)

    Cockcroft Donald W

    2005-03-01

    Full Text Available Abstract Numerous recombinant therapies are being investigated for the treatment of asthma. This report reviews the current status of several of these novel agents. Anti-immunoglobulin (IgE (omalizumab, Xolair markedly inhibits all aspects of the allergen challenge in subjects who have reduction of free serum IgE to undetectable levels. Several clinical studies in atopic asthma have demonstrated benefit by improved symptoms and lung function and a reduction in corticosteroid requirements. Early use in atopic asthmatics may be even more effective. Several approaches target interleukin (IL-4. Soluble IL-4 receptor has been shown to effectively replace inhaled corticosteroid; further studies are under way. Recombinant anti-IL-5 and recombinant IL-12 inhibit blood and sputum eosinophils and allergen-induced eosinophilia without any effect on airway responsiveness, allergen-induced airway responses, or allergen-induced airway hyperresponsiveness. Efalizumab, a recombinant antibody that inhibits lymphocyte trafficking, is effective in psoriasis. A bronchoprovocation study showed a reduction in allergen-induced late asthmatic response and allergen-induced eosinophilia, which suggests that it should be effective in clinical asthma. These exciting novel therapies provide not only promise of new therapies for asthma but also valuable tools for investigation of asthma mechanisms.

  10. Dielectronic recombination cross section for Boron III

    International Nuclear Information System (INIS)

    The dielectronic recombination cross section has been estimated for the B2+ target and projectile electron energies in the range 0.1approx.0.5 Ry, corresponding to the 2s?2p (?n = 0) excitation accompanied by capture of the continuum electron into a high Rydberg state (nl ). Contributions from n-19 cm2

  11. On the radiative recombination of the electrons

    International Nuclear Information System (INIS)

    A process of the radiative recombination of the non-relativistic electron with a hydrogen-like ion is considered. A simple expression is derived for the total cross section of the process with the use of the analytic properties of the electron Green function in a Coulomb field. The dipole approximation is used

  12. Dielectronic recombination cross section for Cl7+

    International Nuclear Information System (INIS)

    The resonant dielectronic recombination cross section is estimated for a Cl7+ target interacting with incident electrons in the 10approx.20-rydberg range. Cross sections averaged over energy bins of size ?E = 0.1 Ry are approximately (1--3) x 10-19 cm2

  13. Atom and ion recombination in spurs

    International Nuclear Information System (INIS)

    The proportion of singlets generated during a recombination of atoms or ions in a radiolytic spur reaction is examined from the viewpoint of a combinational analysis. The results obtained differ from other, already conflicting, published work. The problem is formulated in a way that enables spin relaxation effects to be incorporated. (author)

  14. Algae-based oral recombinant vaccines

    Directory of Open Access Journals (Sweden)

    ElizabethASpecht

    2014-02-01

    Full Text Available Recombinant subunit vaccines are some of the safest and most effective vaccines available, but their high cost and the requirement of advanced medical infrastructure for administration make them impractical for many developing world diseases. Plant-based vaccines have shifted that paradigm by paving the way for recombinant vaccine production at agricultural scale using an edible host. However, enthusiasm for “molecular pharming” in food crops has waned in the last decade due to difficulty in developing transgenic crop plants and concerns of contaminating the food supply. Microalgae are poised to become the next candidate in recombinant subunit vaccine production, and they present several advantages over terrestrial crop plant-based platforms including scalable and contained growth, rapid transformation, easily obtained stable cell lines, and consistent transgene expression levels. Algae have been shown to accumulate and properly fold several vaccine antigens, and efforts are underway to create recombinant algal fusion proteins that can enhance antigenicity for effective orally-delivered vaccines. These approaches have the potential to revolutionize the way subunit vaccines are made and delivered – from costly parenteral administration of purified protein, to an inexpensive oral algae tablet with effective mucosal and system immune reactivity.

  15. Gas recombination assembly for electrochemical cells

    Science.gov (United States)

    Levy, Isaac (New Fairfield, CT); Charkey, Allen (Brookfield, CT)

    1989-01-01

    An assembly for recombining gases generated in electrochemical cells wherein a catalyst strip is enveloped within a hydrophobic, gas-porous film which, in turn, is encased between gas-porous, metallic layers. The sandwich construction of metallic layers and film is formed into a spiral with a tab for connection to the cell.

  16. Implementing general gauge mediation

    International Nuclear Information System (INIS)

    Recently there has been much progress in building models of gauge mediation, often with predictions different than those of minimal gauge mediation. Meade, Seiberg, and Shih have characterized the most general spectrum which can arise in gauge-mediated models. We discuss some of the challenges of building models of general gauge mediation, especially the problem of messenger parity and issues connected with R symmetry breaking and CP violation. We build a variety of viable, weakly coupled models which exhibit some or all of the possible low energy parameters.

  17. A general theoretical description of N-body recombination

    CERN Document Server

    Mehta, N P; D'Incao, J P; Von Stecher, J; Greene, Chris H

    2009-01-01

    We present a formula for the cross section and event rate constant describing recombination of N particles in terms of general S-matrix elements. Our result immediately yields the generalized Wigner threshold scaling for the recombination of N bosons. We find that four-boson recombination is resonantly enhanced by the presence of metastable states in the entrance channel. Hence, recombination into a trimer-atom channel could be an effective mechanism for the formation of Efimov trimers.

  18. A molecular recombination map of Antirrhinum majus

    Directory of Open Access Journals (Sweden)

    Hudson Andrew

    2010-12-01

    Full Text Available Abstract Background Genetic recombination maps provide important frameworks for comparative genomics, identifying gene functions, assembling genome sequences and for breeding. The molecular recombination map currently available for the model eudicot Antirrhinum majus is the result of a cross with Antirrhinum molle, limiting its usefulness within A. majus. Results We created a molecular linkage map of A. majus based on segregation of markers in the F2 population of two inbred lab strains of A. majus. The resulting map consisted of over 300 markers in eight linkage groups, which could be aligned with a classical recombination map and the A. majus karyotype. The distribution of recombination frequencies and distorted transmission of parental alleles differed from those of a previous inter-species hybrid. The differences varied in magnitude and direction between chromosomes, suggesting that they had multiple causes. The map, which covered an estimated of 95% of the genome with an average interval of 2 cM, was used to analyze the distribution of a newly discovered family of MITE transposons and tested for its utility in positioning seven mutations that affect aspects of plant size. Conclusions The current map has an estimated interval of 1.28 Mb between markers. It shows a lower level of transmission ratio distortion and a longer length than the previous inter-species map, making it potentially more useful. The molecular recombination map further indicates that the IDLE MITE transposons are distributed throughout the genome and are relatively stable. The map proved effective in mapping classical morphological mutations of A. majus.

  19. Regulation of homologous recombination at telomeres in budding yeast

    DEFF Research Database (Denmark)

    Eckert-Boulet, Nadine; Lisby, Michael

    2010-01-01

    Homologous recombination is suppressed at normal length telomere sequences. In contrast, telomere recombination is allowed when telomeres erode in the absence of telomerase activity or as a consequence of nucleolytic degradation or incomplete replication. Here, we review the mechanisms that contribute to regulating mitotic homologous recombination at telomeres and the role of these mechanisms in signalling short telomeres in the budding yeast Saccharomyces cerevisiae.

  20. Trans-Centromere Effects on Meiotic Recombination in the Zebrafish

    OpenAIRE

    Demarest, Bradley L.; Horsley, Wyatt H.; Locke, Erin E.; Boucher, Kenneth; Grunwald, David J.; Trede, Nikolaus S.

    2011-01-01

    We report that lack of crossover along one chromosome arm is associated with high-frequency occurrence of recombination close to the opposing arm's centromere during zebrafish meiotic recombination. Our data indicate that recombination behavior on the two arms of a chromosome is linked. These results inform mapping strategies for telomeric mutants.

  1. Gimeracil sensitizes cells to radiation via inhibition of homologous recombination

    International Nuclear Information System (INIS)

    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. ?-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 ?-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.

  2. Teaching Mediated Public Relations.

    Science.gov (United States)

    Kent, Michael L.

    2001-01-01

    Discusses approaches to teaching a mediated public relations course, emphasizing the World Wide Web. Outlines five course objectives, assignments and activities, evaluation, texts, and lecture topics. Argues that students mastering these course objectives will understand ethical issues relating to media use, using mediated technology in public…

  3. 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.

  4. Expression, Delivery and Function of Insecticidal Proteins Expressed by Recombinant Baculoviruses

    Science.gov (United States)

    Kroemer, Jeremy A.; Bonning, Bryony C.; Harrison, Robert L.

    2015-01-01

    Since the development of methods for inserting and expressing genes in baculoviruses, a line of research has focused on developing recombinant baculoviruses that express insecticidal peptides and proteins. These recombinant viruses have been engineered with the goal of improving their pesticidal potential by shortening the time required for infection to kill or incapacitate insect pests and reducing the quantity of crop damage as a consequence. A wide variety of neurotoxic peptides, proteins that regulate insect physiology, degradative enzymes, and other potentially insecticidal proteins have been evaluated for their capacity to reduce the survival time of baculovirus-infected lepidopteran host larvae. Researchers have investigated the factors involved in the efficient expression and delivery of baculovirus-encoded insecticidal peptides and proteins, with much effort dedicated to identifying ideal promoters for driving transcription and signal peptides that mediate secretion of the expressed target protein. Other factors, particularly translational efficiency of transcripts derived from recombinant insecticidal genes and post-translational folding and processing of insecticidal proteins, remain relatively unexplored. The discovery of RNA interference as a gene-specific regulation mechanism offers a new approach for improvement of baculovirus biopesticidal efficacy through genetic modification. PMID:25609310

  5. Expression, Delivery and Function of Insecticidal Proteins Expressed by Recombinant Baculoviruses

    Directory of Open Access Journals (Sweden)

    Jeremy A. Kroemer

    2015-01-01

    Full Text Available Since the development of methods for inserting and expressing genes in baculoviruses, a line of research has focused on developing recombinant baculoviruses that express insecticidal peptides and proteins. These recombinant viruses have been engineered with the goal of improving their pesticidal potential by shortening the time required for infection to kill or incapacitate insect pests and reducing the quantity of crop damage as a consequence. A wide variety of neurotoxic peptides, proteins that regulate insect physiology, degradative enzymes, and other potentially insecticidal proteins have been evaluated for their capacity to reduce the survival time of baculovirus-infected lepidopteran host larvae. Researchers have investigated the factors involved in the efficient expression and delivery of baculovirus-encoded insecticidal peptides and proteins, with much effort dedicated to identifying ideal promoters for driving transcription and signal peptides that mediate secretion of the expressed target protein. Other factors, particularly translational efficiency of transcripts derived from recombinant insecticidal genes and post-translational folding and processing of insecticidal proteins, remain relatively unexplored. The discovery of RNA interference as a gene-specific regulation mechanism offers a new approach for improvement of baculovirus biopesticidal efficacy through genetic modification.

  6. Mrc1 is required for sister chromatid cohesion to aid in recombination repair of spontaneous damage.

    Science.gov (United States)

    Xu, Hong; Boone, Charles; Klein, Hannah L

    2004-08-01

    The SRS2 gene of Saccharomyces cerevisiae encoding a 3'-->5' DNA helicase is part of the postreplication repair pathway and functions to ensure proper repair of DNA damage arising during DNA replication through pathways that do not involve homologous recombination. Through a synthetic gene array analysis, genes that are essential when Srs2 is absent have been identified. Among these are MRC1, TOF1, and CSM3, which mediate the intra-S checkpoint response. srs2 Delta mrc1 Delta synthetic lethality is due to inappropriate recombination, as the lethality can be suppressed by genetic elimination of homologous recombination. srs2 Delta mrc1 Delta synthetic lethality is dependent on the role of Mrc1 in DNA replication but independent of the role of Mrc1 in a DNA damage checkpoint response. mrc1 Delta, tof1 Delta and csm3 Delta mutants have sister chromatid cohesion defects, implicating sister chromatid cohesion established at the replication fork as an important factor in promoting repair of stalled replication forks through gap repair. PMID:15282308

  7. Oligonucleotide recombination enabled site-specific mutagenesis in bacteria.

    Science.gov (United States)

    Swingle, Bryan M

    2013-01-01

    Recombineering refers to a strategy for engineering DNA sequences using a specialized mode of homologous recombination. This technology can be used for rapidly constructing precise changes in bacterial genome sequences in vivo. Oligonucleotide recombination is one type of recombineering that uses ssDNA oligonucleotides to direct chromosomal mutations. Oligo recombination occurs without addition of any exogenous functions, making this approach potentially useful in many different bacteria. Here we describe the basic technique for constructing a site-specific genomic mutation in Pseudomonas syringae. PMID:23423893

  8. Isolation of a recombination-deficient mutant of Rhodopseudomonas capsulata

    Energy Technology Data Exchange (ETDEWEB)

    Genthner, F.J.; Wall, J.D.

    1984-12-01

    To facilitate genetic analysis in the purple photosynthetic bacterium Rhodopseudomonas capsulata, a recombination-deficient derivative was sought. A UV irradiation-sensitive mutant (FG106F) was isolated after mutagenesis, and two procedures were used to determine the recombinational capacity of the mutant. First, recombinants were not detected after transduction of this derivative by the phage-like vector gene transfer agent. Second, an R-prime plasmid containing appropriately marked genes for photosynthesis was introduced by conjugation, and again no recombinants were observed. Additional phenotypes displayed by the mutant that are characteristic of a defect in recombination were an increased sensitivity to DNA-damaging antibiotics and a tendency to filament.

  9. Radiative recombination of hot carriers in narrow-gap semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Pavlov, N. V.; Zegrya, G. G., E-mail: Zegrya@theory.ioffe.ru [Russian Academy of Sciences, Ioffe Physical Technical Institute (Russian Federation)

    2012-01-15

    The mechanism of the radiative recombination of hot carriers in narrow-gap semiconductors is analyzed using the example of indium antimonide. It is shown that the CHCC Auger recombination process may lead to pronounced carrier heating at high excitation levels. The distribution functions and concentrations of hot carriers are determined. The radiative recombination rate of hot carriers and the radiation gain coefficient are calculated in terms of the Kane model. It is demonstrated that the radiative recombination of hot carriers will make a substantial contribution to the total radiative recombination rate at high carrier concentrations.

  10. The cell pole: the site of cross talk between the DNA uptake and genetic recombination machinery.

    Science.gov (United States)

    Kidane, Dawit; Ayora, Silvia; Sweasy, Joann B; Graumann, Peter L; Alonso, Juan C

    2012-01-01

    Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as "guardians", protects ssDNA from degradation and limit the RecA recombinase loading. Then, the "mediators" overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by "modulators", catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or "resolver" cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the "rescuers" will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective. PMID:23046409

  11. Monitoring homologous recombination in rice (Oryza sativa L.)

    Energy Technology Data Exchange (ETDEWEB)

    Yang Zhuanying; Tang Li [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China); Li Meiru [South China Botanic Garden, Chinese Academy of Sciences, Guangzhou 510650 (China); Chen Lei; Xu Jie [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China); Wu Goujiang [South China Botanic Garden, Chinese Academy of Sciences, Guangzhou 510650 (China); Li Hongqing, E-mail: hqli@scnu.edu.cn [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China)

    2010-09-10

    Here we describe a system to assay homologous recombination during the complete life cycle of rice (Oryza sativa L.). Rice plants were transformed with two copies of non-functional GUS reporter overlap fragments as recombination substrate. Recombination was observed in all plant organs examined, from the seed stage until the flowering stage of somatic plant development. Embryogenic cells exhibited the highest recombination ability with an average of 3 x 10{sup -5} recombination events per genome, which is about 10-fold of that observed in root cells, and two orders of that observed in leaf cells. Histological analysis revealed that recombination events occurred in diverse cell types, but preferentially in cells with small size. Examples of this included embryogenic cells in callus, phloem cells in the leaf vein, and cells located in the root apical meristem. Steady state RNA analysis revealed that the expression levels of rice Rad51 homologs are positively correlated with increased recombination rates in embryogenic calli, roots and anthers. Finally, radiation treatment of plantlets from distinct recombination lines increased the recombination frequency to different extents. These results showed that homologous recombination frequency can be effectively measured in rice using a transgene reporter assay. This system will facilitate the study of DNA damage signaling and homologous recombination in rice, a model monocot.

  12. FASEB Summer Research Conference. Genetic Recombination and Chromosome Rearrangements

    Energy Technology Data Exchange (ETDEWEB)

    Jinks-Robertson, Sue

    2002-02-01

    The 2001 meeting entitled ''Genetic Recombination and Genome Rearrangements'' was held July 21-26 in Snowmass, Colorado. The goal of the meeting was to bring together scientists using diverse approaches to study all aspects of genetic recombination. This goal was achieved by integrating talks covering the genetics, biochemistry and structural biology of homologous recombination, site-specific recombination, and nonhomologous recombination. The format of the meeting consisted of a keynote address on the opening evening, two formal plenary sessions on each of the four full meeting days, a single afternoon workshop consisting of short talks chosen from among submitted abstracts, and afternoon poster sessions on each of the four full meeting days. The eight plenary session were entitled: (1) Recombination Mechanisms, (2) Prokaryotic Recombination, (3) Repair and Recombination, (4) Site-specific Recombination and Transposition, (5) Eukaryotic Recombination I, (6) Genome Rearrangements, (7) Meiosis, and (8) Eukaryotic Recombination II. Each session included a mix of genetic, biochemical and structural talks; talks were limited to 20 minutes, followed by 10 minutes of very lively, general discussion. Much of the data presented in the plenary sessions was unpublished, thus providing attendees with the most up-to-date knowledge of this rapidly-moving field.

  13. Monitoring homologous recombination in rice (Oryza sativa L.)

    International Nuclear Information System (INIS)

    Here we describe a system to assay homologous recombination during the complete life cycle of rice (Oryza sativa L.). Rice plants were transformed with two copies of non-functional GUS reporter overlap fragments as recombination substrate. Recombination was observed in all plant organs examined, from the seed stage until the flowering stage of somatic plant development. Embryogenic cells exhibited the highest recombination ability with an average of 3 x 10-5 recombination events per genome, which is about 10-fold of that observed in root cells, and two orders of that observed in leaf cells. Histological analysis revealed that recombination events occurred in diverse cell types, but preferentially in cells with small size. Examples of this included embryogenic cells in callus, phloem cells in the leaf vein, and cells located in the root apical meristem. Steady state RNA analysis revealed that the expression levels of rice Rad51 homologs are positively correlated with increased recombination rates in embryogenic calli, roots and anthers. Finally, radiation treatment of plantlets from distinct recombination lines increased the recombination frequency to different extents. These results showed that homologous recombination frequency can be effectively measured in rice using a transgene reporter assay. This system will facilitate the study of DNA damage signaling and homologous recombination in rice, a model monocot.

  14. Detection of quantitative trait Loci influencing recombination using recombinant inbred lines.

    Science.gov (United States)

    Dole, Jefferey; Weber, David F

    2007-12-01

    The genetic basis of variation in recombination in higher plants is polygenic and poorly understood, despite its theoretical and practical importance. Here a method of detecting quantitative trait loci (QTL) influencing recombination in recombinant inbred lines (RILs) is proposed that relies upon the fact that genotype data within RILs carry the signature of past recombination. Behavior of the segregational genetic variance in numbers of chromosomal crossovers (recombination) over generations is described for self-, full-sib-, and half-sib-generated RILs with no dominance in true crossovers. This genetic variance, which as a fraction of the total phenotypic variance contributes to the statistical power of the method, was asymptotically greatest with half sibbing, less with sibbing, and least with selfing. The statistical power to detect a recombination QTL declined with diminishing QTL effect, genome target size, and marker density. For reasonably tight marker linkage power was greater with less intense inbreeding for later generations and vice versa for early generations. Generational optima for segregation variance and statistical power were found, whose onset and narrowness varied with marker density and mating design, being more pronounced for looser marker linkage. Application of this method to a maize RIL population derived from inbred lines Mo17 and B73 and developed by selfing suggested two putative QTL (LOD > 2.4) affecting certain chromosomes, and using a canonical transformation another putative QTL was detected. However, permutation tests failed to support their presence (experimentwise alpha = 0.05). Other populations with more statistical power and chosen specifically for recombination QTL segregation would be more effective. PMID:17947433

  15. Molecular mechanisms of DNA recombination: testing mitotic and meiotic models

    International Nuclear Information System (INIS)

    A hyperhaploid n + 1 strain of Saccharomyces cerevisiae (LBL1) disomic for chromosome VII was employed to isolate hyper-rec and hypo-rec mutations affecting spontaneous mitotic gene conversion and intergenic recombination. The genotype of LBL1 permits simultaneous and independent identification of rec mutations that enhance or diminish gene conversion and those that enhance or diminish intergenic recombination. Five phenotypic groups of rec mutants were isolated following ultraviolet light mutagenesis. Rec mutations that simultaneously abolish or enhance both classes of recombinational events were detected. These results demonstrate that gene conversion and intergenic recombination are under joint genetic control in mitotic cells. Conversion-specific and intergenic recombination-specific rec mutants were also recovered. Their properties indicate that conversion and intergenic recombination are separable pheonomena dependent upon discrete REC genes. The rec mutants isolated in LBL1 provide a method to test molecular models of mitotic and meiotic recombination

  16. Mechanisms and Factors that Influence High Frequency Retroviral Recombination

    Directory of Open Access Journals (Sweden)

    Krista Delviks-Frankenberry

    2011-09-01

    Full Text Available With constantly changing environmental selection pressures, retroviruses rely upon recombination to reassort polymorphisms in their genomes and increase genetic diversity, which improves the chances for the survival of their population. Recombination occurs during DNA synthesis, whereby reverse transcriptase undergoes template switching events between the two copackaged RNAs, resulting in a viral recombinant with portions of the genetic information from each parental RNA. This review summarizes our current understanding of the factors and mechanisms influencing retroviral recombination, fidelity of the recombination process, and evaluates the subsequent viral diversity and fitness of the progeny recombinant. Specifically, the high mutation rates and high recombination frequencies of HIV-1 will be analyzed for their roles in influencing HIV-1 global diversity, as well as HIV-1 diagnosis, drug treatment, and vaccine development.

  17. Mechanisms and factors that influence high frequency retroviral recombination

    DEFF Research Database (Denmark)

    Delviks-Frankenberry, Krista; Galli, Andrea

    2011-01-01

    With constantly changing environmental selection pressures, retroviruses rely upon recombination to reassort polymorphisms in their genomes and increase genetic diversity, which improves the chances for the survival of their population. Recombination occurs during DNA synthesis, whereby reverse transcriptase undergoes template switching events between the two copackaged RNAs, resulting in a viral recombinant with portions of the genetic information from each parental RNA. This review summarizes our current understanding of the factors and mechanisms influencing retroviral recombination, fidelity of the recombination process, and evaluates the subsequent viral diversity and fitness of the progeny recombinant. Specifically, the high mutation rates and high recombination frequencies of HIV-1 will be analyzed for their roles in influencing HIV-1 global diversity, as well as HIV-1 diagnosis, drug treatment, and vaccine development.

  18. Induction of molecular and genetic recombination in eukaryotic cells

    International Nuclear Information System (INIS)

    The purpose of this review was to generally describe mitotic and meiotic recombination and to relate these processes to DNA repair. The results and mechanisms which have been described for genetic recombination in lower eukaryocytes are related to recent observations with mammalian cell systems in an attempt to bridge the gap between these categories of eukaryotes. The types of genetic recombinations which can be identified in lower eukaryotes, the effects of various mutagens and radiations, the similarities between spontaneous mitotic and meiotic recombination, the importance of recombination in DNA repair, and the role of various mechanisms in recombination are described. Molecular recombination is discussed. Gene conversion (informational transfer) is related to biochemical changes and is a very sensitive genetic tool for detecting DNA alterations

  19. Chemical inhibitor targeting the replication protein A-DNA interaction increases the efficacy of Pt-based chemotherapy in lung and ovarian cancer.

    Science.gov (United States)

    Mishra, Akaash K; Dormi, Silvana S; Turchi, Alaina M; Woods, Derek S; Turchi, John J

    2015-01-01

    Platinum-based chemotherapeutics exert their therapeutic efficacy via the formation of DNA adducts which interfere with DNA replication, transcription and cell division and ultimately induce cell death. Repair and tolerance of these Pt-DNA lesions by nucleotide excision repair (NER) and homologous recombination (HR) can substantially reduce the effectiveness of therapy. Inhibition of these repair pathways, therefore, holds the potential to sensitize cancer cells to Pt treatment and increase clinical efficacy. Replication Protein A (RPA) plays essential roles in both NER and HR, along with its role in DNA replication and DNA damage checkpoint activation. Each of these functions is, in part, mediated by RPA binding to single-stranded DNA (ssDNA). Here we report the synthesis and characterization of novel derivatives of RPA small molecule inhibitors and their activity in models of epithelial ovarian cancer (EOC) and non-small cell lung cancer (NSCLC). We have synthesized analogs of our previously reported RPA inhibitor TDRL-505 and determined the structure-activity relationships. These data led us to the identification of TDRL-551, which exhibited a greater than 2-fold increase in in vitro activity. TDRL-551 showed synergy with Pt in tissue culture models of EOC and in vivo efficacy, as a single agent and in combination with platinum, in a NSCLC xenograft model. These data demonstrate the utility of RPA inhibition in EOC and NSCLC and the potential in developing novel anticancer therapeutics that target RPA-DNA interactions. PMID:25449597

  20. Single--crossover recombination in discrete time

    CERN Document Server

    von Wangenheim, Ute; Baake, Michael

    2009-01-01

    Modelling the process of recombination leads to a large coupled nonlinear dynamical system. Here, we consider a particular case of recombination in {\\em discrete} time, allowing only for {\\em single crossovers}. While the analogous dynamics in {\\em continuous} time admits a closed solution, this no longer works for discrete time. A more general model (i.e. without the restriction to single crossovers) has been studied before and was solved algorithmically by means of Haldane linearisation. Using the special formalism introduced by Baake and Baake (2003), we obtain further insight into the single-crossover dynamics and the particular difficulties that arise in discrete time. We then transform the equations to a solvable system in a two-step procedure: linearisation followed by diagonalisation. Still, the coefficients of the second step must be determined in a recursive manner, but once this is done for a given system, they allow for an explicit solution valid for all times.

  1. Regulation of DNA pairing in homologous recombination.

    Science.gov (United States)

    Daley, James M; Gaines, William A; Kwon, YoungHo; Sung, Patrick

    2014-11-01

    Homologous recombination (HR) is a major mechanism for eliminating DNA double-strand breaks from chromosomes. In this process, the break termini are resected nucleolytically to form 3' ssDNA (single-strand DNA) overhangs. A recombinase (i.e., a protein that catalyzes homologous DNA pairing and strand exchange) assembles onto the ssDNA and promotes pairing with a homologous duplex. DNA synthesis then initiates from the 3' end of the invading strand, and the extended DNA joint is resolved via one of several pathways to restore the integrity of the injured chromosome. It is crucial that HR be carefully orchestrated because spurious events can create cytotoxic intermediates or cause genomic rearrangements and loss of gene heterozygosity, which can lead to cell death or contribute to the development of cancer. In this review, we will discuss how DNA motor proteins regulate HR via a dynamic balance of the recombination-promoting and -attenuating activities that they possess. PMID:25190078

  2. SIR epidemics in monogamous populations with recombination

    Directory of Open Access Journals (Sweden)

    Damián H. Zanette

    2011-03-01

    Full Text Available We study the propagation of an SIR (susceptible--infectious--recovered disease over an agent population which, at any instant, is fully divided into couples of agents. Couples are occasionally allowed to exchange their members. This process of couple recombination can compensate the instantaneous disconnection of the interaction pattern and thus allow for the propagation of the infection. We study the incidence of the disease as a function of its infectivity and of the recombination rate of couples, thus characterizing the interplay between the epidemic dynamics and the evolution of the population's interaction pattern.Received: 12 August 2010;Accepted: 18 February 2011; Edited by: G. C. Barker; Reviewed by: B. Blasius, ICBM, University of Oldenburg, Germany; DOI: 10.4279/PIP.030001Cite as: D. H. Zanette, Papers in Physics 3, 030001 (2011

  3. CFD Analysis of Passive Autocatalytic Recombiner

    International Nuclear Information System (INIS)

    In water-cooled nuclear power reactors, significant quantities of hydrogen could be produced following a postulated loss-of-coolant accident (LOCA) along with non availability of emergency core cooling system (ECCS). Passive autocatalytic recombiners (PAR) are implemented in the containment of water-cooled power reactors to mitigate the risk of hydrogen combustion. In the presence of hydrogen with available oxygen, a catalytic reaction occurs spontaneously at the catalyst surfaces below conventional ignition concentration limits and temperature and even in presence of steam. Heat of reaction produces natural convection flow through the enclosure and promotes mixing in the containment. For the assessment of the PAR performance in terms of maximum temperature of catalyst surface and outlet hydrogen concentration an in-house 3D CFD model has been developed. The code has been used to study the mechanism of catalytic recombination and has been tested for two literature-quoted experiments

  4. Scaling and fractal behaviour underlying meiotic recombination.

    Science.gov (United States)

    Waxman, D; Stoletzki, N

    2010-01-01

    In this paper we investigate some of the mathematical properties of meiotic recombination. Working within the framework of a genetic model with n loci, where alpha alleles are possible at each locus, we find that the proportion of all possible diploid parental genotypes that can produce a particular haploid gamete is exp[-n log(alpha(2)/[2alpha-1])]. We show that this proportion connects recombination with a fractal geometry of dimension log(2alpha-1)/log(alpha). The fractal dimension of a geometric object manifests itself when it is measured at increasingly smaller length scales. Decreasing the length scale of a geometric object is found to be directly analogous, in a genetics problem, to specifying a multilocus haplotype at a larger number of loci, and it is here that the fractal dimension reveals itself. PMID:19712721

  5. Rapid one-step recombinational cloning

    OpenAIRE

    Fu, Changlin; Wehr, Daniel R.; Edwards, Janice; Hauge, Brian

    2008-01-01

    As an increasing number of genes and open reading frames of unknown function are discovered, expression of the encoded proteins is critical toward establishing function. Accordingly, there is an increased need for highly efficient, high-fidelity methods for directional cloning. Among the available methods, site-specific recombination-based cloning techniques, which eliminate the use of restriction endonucleases and ligase, have been widely used for high-throughput (HTP) procedures. We have de...

  6. The landscape of recombination in African Americans.

    OpenAIRE

    Hinch, Ag; Tandon, A.; Patterson, N.; Song, Y.; Rohland, N.; Palmer, Cd; Chen, Gk; Wang, K.; Buxbaum, Sg; Akylbekova, El; Aldrich, Mc; Ambrosone, Cb; Amos, C.; Bandera, Ev; Berndt, Si

    2011-01-01

    Recombination, together with mutation, gives rise to genetic variation in populations. Here we leverage the recent mixture of people of African and European ancestry in the Americas to build a genetic map measuring the probability of crossing over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans. At intervals of more than three megabases it is nearly identical to a map built in Europeans. At finer scales it differs significantly, and ...

  7. Managing meiotic recombination in plant breeding

    OpenAIRE

    Wijnker, T.G.; Jong, J.H.S.G.M., de

    2008-01-01

    Crossover recombination is a crucial process in plant breeding because it allows plant breeders to create novel allele combnations on chromosomes that can be used for breeding superior F1 hybrids. Gaining control over this process, in terms of increasing crossover incidence, altering crossover positions on chromosomes or silencing crossover formation, is essential for plant breeders to effectively engineer the allelic composition of chromosomes. We review the various means of crossover contro...

  8. Construction of recombinant DNA by exonuclease recession.

    OpenAIRE

    Yang, Y. S.; Watson, W. J.; Tucker, P. W.; Capra, J. D.

    1993-01-01

    We describe a new exonuclease-based method for joining and/or constructing two or more DNA molecules. DNA fragments containing ends complementary to those of a vector or another independent molecules were generated by the polymerase chain reaction. The 3' ends of these molecules as well as the vector DNA were then recessed by exonuclease activity and annealed in an orientation-determined manner via their complementary single-stranded regions. This recombinant DNA can be transformed directly i...

  9. Dissociative recombination of BeH^+

    OpenAIRE

    Roos, J.B.; Larsson, M; Larson, AA.; Orel, A. E.

    2009-01-01

    The cross section for dissociative recombination of BeH^+ is calculated by solution of the time-dependent Schrodinger equation in the local complex potential approximation. The effects of couplings between resonant states and the Rydberg states converging to the ground state of the ion are studied. The relevant potentials, couplings and autoionization widths are extracted using ab initio electron scattering and structure calculations, followed by a diabatization procedure. T...

  10. Domain Recombination: A Workhorse for Evolutionary Innovation

    Science.gov (United States)

    Gordana Apic (UK; Cambridge Cell Networks REV)

    2010-09-14

    Although the combination of modular domains within proteins has been proposed as a determining feature of evolutionary innovation and flexibility, direct evidence for this mechanism of evolution has been sketchy. Two papers, one creating new domain combinations in the yeast mating pathway and another involving a comprehensive analysis of protein function and domain architecture across major organisms, have provided firm evidence that the recombining of domains can lead to evolutionary innovation. The results will guide future studies in synthetic and evolutionary biology.

  11. Cytological studies of recombination in rhesus males

    OpenAIRE

    Hassold, T.; Hansen, T.; Hunt, P.; Vandevoort, C.

    2009-01-01

    An immunofluorescence approach was used to directly examine meiotic recombination events in 483 pachytene spermatocytes from 11 male rhesus monkeys. Specifically, we examined the nuclear localization patterns of the DNA mismatch repair protein MLH1, known from analyses of other mammalian species to be a useful marker of meiotic cross-overs. Our results indicated that rhesus pachytene spermatocytes contain approximately 40 cross-overs per cell, corresponding to about one cross-over per chromos...

  12. Recombinant organisms capable of fermenting cellobiose

    Science.gov (United States)

    Ingram, Lonnie O. (Gainesville, FL); Lai, Xiaokuang (Gainesville, FL); Moniruzzaman, Mohammed (Gainesville, FL); York, Sean W. (Gainesville, FL)

    2000-01-01

    This invention relates to a recombinant microorganism which expresses pyruvate decarboxylase, alcohol dehydrogenase, Klebsiella phospho-.beta.-glucosidase and Klebsiella (phosphoenolpyruvate-dependent phosphotransferase system) cellobiose-utilizing Enzyme II, wherein said phospho-.beta.-glucosidase and said (phosphoenolpyruvate-dependent phosphotransferase) cellobiose-utilizing Enzyme II are heterologous to said microorganism and wherein said microorganism is capable of utilizing both hemicellulose and cellulose, including cellobiose, in the production of ethanol.

  13. Production of recombinant antibodies using bacteriophages

    OpenAIRE

    Shukra, A. M.; Sridevi, N. V.; Dev Chandran,; Kapil Maithal,

    2014-01-01

    Recombinant antibody fragments such as Fab, scFv, diabodies, triabodies, single domain antibodies and minibodies have recently emerged as potential alternatives to monoclonal antibodies, which can be engineered using phage display technology. These antibodies match the strengths of conventionally produced monoclonal antibodies and offer advantages for the development of immunodiagnostic kits and assays. These fragments not only retain the specificity of the whole monoclonal ...

  14. Recombinant CBM-fusion technology : applications overview

    OpenAIRE

    Oliveira, Carla Cristina Marques de; Carvalho, Vera; Domingues, Lucília; Gama, F. M.

    2015-01-01

    Carbohydrate-binding modules (CBMs) are small components of several enzymes, which present an independent fold and function, and specific carbohydrate-binding activity. Their major function is to bind the enzyme to the substrate enhancing its catalytic activity, especially in the case of insoluble substrates. The immense diversity of CBMs, together with their unique properties, has long raised their attention for many biotechnological applications. Recombinant DNA technology has been used for...

  15. Designing recombinant Pseudomonas strains to enhance biodesulfurization.

    OpenAIRE

    Gallardo, M.E.; Ferrández, A; De Lorenzo, V.; García, J.L.; Díaz, E.

    1997-01-01

    The dsz biodesulfurization cluster from Rhodococcus erythropolis IGTS8 has been engineered under the control of heterologous broad-host-range regulatory signals to alleviate the mechanism of sulfur repression, and it was stably inserted into the chromosomes of different Pseudomonas strains. The recombinant bacteria were able to desulfurize dibenzothiophene more efficiently than the native host. Furthermore, these new biocatalysts combine relevant industrial and environmental traits, such as p...

  16. A Holliday recombination intermediate is twofold symmetric.

    OpenAIRE

    Churchill, M E; Tullius, T. D.; Kallenbach, N. R.; Seeman, N. C.

    1988-01-01

    Four-arm Holliday structures are ephemeral intermediates in genetic recombination. We have used an oligodeoxynucleotide system to form immobile DNA junctions, which are stable analogs of Holliday structures. We have probed the equilibrium structure of a junction by means of hydroxyl radicals generated by the reaction of iron(II)EDTA with hydrogen peroxide. The hydroxyl radical cleavage pattern shows twofold symmetry throughout the molecule. Strong protection from hydroxyl radical attack is ev...

  17. Recombinant human erythropoietin in sports: a review

    OpenAIRE

    Rafael Maia de Almeida Bento; Lúcia Menezes Pinto Damasceno; Francisco Radler De Aquino Neto,

    2003-01-01

    Erythropoietin is an endogenous hormone of glicoproteic nature secreted by the kidneys and is the main regulator of the erythropoiesis. An alteration in its production generates a disturbance in the plasmatic concentration giving rise to several types of pathologies related to the hematopoietic system. The recombinant forms of erythropoietin have indiscriminately been used by athletes, mainly in endurance sports, by increasing the erythrocytes concentration, generating a better delivery of ox...

  18. Virus Strain Discrimination Using Recombinant Antibodies

    OpenAIRE

    Boonham, N.; Barker, I.

    2000-01-01

    Most routine testing for plant viruses is currently carried out using monoclonal and polyclonal antibodies. Traditional methods of antibody production however can be time consuming and require the use of expensive cell culture facilities. Recombinant antibody technology however is starting to make an impact in this area, enabling the selection of antibody fragments in a few weeks compared with the many months associated with traditional methods and requires only basic microbiological faciliti...

  19. Modelling of procecces in catalytic recombiners

    International Nuclear Information System (INIS)

    In order to achieve a high degree of safety in nuclear power plants and prevent possible accident scenarios, their consequences are calculated and analysed with numeric codes. One of the most important part of nuclear safety research of hazardous incidents are development and validation of these numeric models, which are implemented into accident codes. The severe hydrogen release during a core meltdown is one of the considered scenario of performed accident analyses. One of the most important measure for the elimination of the hydrogen is catalytic recombiners. Converting the hydrogen with the atmospheric oxygen to water vapor in an exothermic reaction will prevent possible detonation of the hydrogen/air atmosphere. Within the dissertation the recombiner simulation REKO-DIREKT was developed and validated by an extensive experimental database. The performance of recombiners with regard to the conversion of the hydrogen and the temperature development is modelled. The REKO-DIREKT program is unique and has made significant revolution in research of hydrogen safety. For the first time it has been possible to show the performance of the recombiner so great in detail by using REKO-DIREKT. In the future engineers of nuclear power plants will have opportunity to have precise forecasts about the process of the possible accidents with hydrogen release. Also with presence of water vapor or with oxygen depletion which are included in the model. The major discussion of the hydrogen ignition at hot catalyst steel plates can be evaluated in the future with REKO-DIREKT more reliably than the existing used models. (orig.)

  20. Generalized causal mediation analysis.

    Science.gov (United States)

    Albert, Jeffrey M; Nelson, Suchitra

    2011-09-01

    The goal of mediation analysis is to assess direct and indirect effects of a treatment or exposure on an outcome. More generally, we may be interested in the context of a causal model as characterized by a directed acyclic graph (DAG), where mediation via a specific path from exposure to outcome may involve an arbitrary number of links (or "stages"). Methods for estimating mediation (or pathway) effects are available for a continuous outcome and a continuous mediator related via a linear model, while for a categorical outcome or categorical mediator, methods are usually limited to two-stage mediation. We present a method applicable to multiple stages of mediation and mixed variable types using generalized linear models. We define pathway effects using a potential outcomes framework and present a general formula that provides the effect of exposure through any specified pathway. Some pathway effects are nonidentifiable and their estimation requires an assumption regarding the correlation between counterfactuals. We provide a sensitivity analysis to assess the impact of this assumption. Confidence intervals for pathway effect estimates are obtained via a bootstrap method. The method is applied to a cohort study of dental caries in very low birth weight adolescents. A simulation study demonstrates low bias of pathway effect estimators and close-to-nominal coverage rates of confidence intervals. We also find low sensitivity to the counterfactual correlation in most scenarios. PMID:21306353