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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. Mediator function of the human Rad51B-Rad51C complex in Rad51/RPA-catalyzed DNA strand exchange.

    Science.gov (United States)

    Sigurdsson, S; Van Komen, S; Bussen, W; Schild, D; Albala, J S; Sung, P

    2001-12-15

    Five Rad51-like proteins, referred to as Rad51 paralogs, have been described in vertebrates. We show that two of them, Rad51B and Rad51C, are associated in a stable complex. Rad51B-Rad51C complex has ssDNA binding and ssDNA-stimulated ATPase activities. We also examined the functional interaction of Rad51B-Rad51C with Rad51 and RPA. Even though RPA enhances Rad51-catalyzed DNA joint formation via removal of secondary structure in the ssDNA substrate, it can also compete with Rad51 for binding to the substrate, leading to suppressed reaction efficiency. The competition by RPA for substrate binding can be partially alleviated by Rad51B-Rad51C. This recombination mediator function of Rad51B-Rad51C is likely required for the assembly of the Rad51-ssDNA nucleoprotein filament in vivo. PMID:11751636

  3. 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...

  4. Opposing Roles for Two Molecular Forms of Replication Protein A in Rad51-Rad54-Mediated DNA Recombination in Plasmodium falciparum

    Science.gov (United States)

    Gopalakrishnan, Anusha M.; Kumar, Nirbhay

    2013-01-01

    ABSTRACT The bacterial RecA protein and its eukaryotic homologue Rad51 play a central role in the homologous DNA strand exchange reaction during recombination and DNA repair. Previously, our lab has shown that PfRad51, the Plasmodium falciparum homologue of Rad51, exhibited ATPase activity and promoted DNA strand exchange in vitro. In this study, we evaluated the catalytic functions of PfRad51 in the presence of putative interacting partners, especially P. falciparum homologues of Rad54 and replication protein A. PfRad54 accelerated PfRad51-mediated pairing between single-stranded DNA (ssDNA) and its homologous linear double-stranded DNA (dsDNA) in the presence of 0.5 mM CaCl2. We also present evidence that recombinant PfRPA1L protein serves the function of the bacterial homologue single-stranded binding protein (SSB) in initiating homologous pairing and strand exchange activity. More importantly, the function of PfRPA1L was negatively regulated in a dose-dependent manner by PfRPA1S, another RPA homologue in P. falciparum. Finally, we present in vivo evidence through comet assays for methyl methane sulfonate-induced DNA damage in malaria parasites and accompanying upregulation of PfRad51, PfRad54, PfRPA1L, and PfRPA1S at the level of transcript and protein needed to repair DNA damage. This study provides new insights into the role of putative Rad51-interacting proteins involved in homologous recombination and emphasizes the physiological role of DNA damage repair during the growth of parasites. PMID:23631919

  5. Human DNA Helicase B Functions in Cellular Homologous Recombination and Stimulates Rad51-Mediated 5?-3? Heteroduplex Extension In Vitro

    Science.gov (United States)

    Liu, Hanjian; Yan, Peijun; Fanning, Ellen

    2015-01-01

    Homologous recombination is involved in the repair of DNA damage and collapsed replication fork, and is critical for the maintenance of genomic stability. Its process involves a network of proteins with different enzymatic activities. Human DNA helicase B (HDHB) is a robust 5?-3? DNA helicase which accumulates on chromatin in cells exposed to DNA damage. HDHB facilitates cellular recovery from replication stress, but its role in DNA damage response remains unclear. Here we report that HDHB silencing results in reduced sister chromatid exchange, impaired homologous recombination repair, and delayed RPA late-stage foci formation induced by ionizing radiation. Ectopically expressed HDHB colocalizes with Rad51, Rad52, RPA, and ssDNA. In vitro, HDHB stimulates Rad51-mediated heteroduplex extension in 5?-3? direction. A helicase-defective mutant HDHB failed to promote this reaction. Our studies implicate HDHB promotes homologous recombination in vivo and stimulates 5?-3? heteroduplex extension during Rad51-mediated strand exchange in vitro. PMID:25617833

  6. Human DNA helicase B functions in cellular homologous recombination and stimulates Rad51-mediated 5'-3' heteroduplex extension in vitro.

    Science.gov (United States)

    Liu, Hanjian; Yan, Peijun; Fanning, Ellen

    2015-01-01

    Homologous recombination is involved in the repair of DNA damage and collapsed replication fork, and is critical for the maintenance of genomic stability. Its process involves a network of proteins with different enzymatic activities. Human DNA helicase B (HDHB) is a robust 5'-3' DNA helicase which accumulates on chromatin in cells exposed to DNA damage. HDHB facilitates cellular recovery from replication stress, but its role in DNA damage response remains unclear. Here we report that HDHB silencing results in reduced sister chromatid exchange, impaired homologous recombination repair, and delayed RPA late-stage foci formation induced by ionizing radiation. Ectopically expressed HDHB colocalizes with Rad51, Rad52, RPA, and ssDNA. In vitro, HDHB stimulates Rad51-mediated heteroduplex extension in 5'-3' direction. A helicase-defective mutant HDHB failed to promote this reaction. Our studies implicate HDHB promotes homologous recombination in vivo and stimulates 5'-3' heteroduplex extension during Rad51-mediated strand exchange in vitro. PMID:25617833

  7. Mediator function of the human Rad51B–Rad51C complex in Rad51/RPA-catalyzed DNA strand exchange

    OpenAIRE

    Sigurdsson, Stefan; Komen, Stephen; Bussen, Wendy; Schild, David; Albala, Joanna S.; Sung, Patrick

    2001-01-01

    Five Rad51-like proteins, referred to as Rad51 paralogs, have been described in vertebrates. We show that two of them, Rad51B and Rad51C, are associated in a stable complex. Rad51B–Rad51C complex has ssDNA binding and ssDNA-stimulated ATPase activities. We also examined the functional interaction of Rad51B–Rad51C with Rad51 and RPA. Even though RPA enhances Rad51-catalyzed DNA joint formation via removal of secondary structure in the ssDNA substrate, it can also compete with Rad51 for bin...

  8. 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.

  9. 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

  10. RPA and POT1: friends or foes at telomeres?

    Science.gov (United States)

    Flynn, Rachel Litman; Chang, Sandy; Zou, Lee

    2012-02-15

    Telomere maintenance in cycling cells relies on both DNA replication and capping by the protein complex shelterin. Two single-stranded DNA (ssDNA)-binding proteins, replication protein A (RPA) and protection of telomere 1 (POT1) play critical roles in DNA replication and telomere capping, respectively. While RPA binds to ssDNA in a non-sequence-specific manner, POT1 specifically recognizes singlestranded TTAGGG telomeric repeats. Loss of POT1 leads to aberrant accumulation of RPA at telomeres and activation of the ataxia telangiectasia and Rad3-related kinase (ATR)-mediated checkpoint response, suggesting that POT1 antagonizes RPA binding to telomeric ssDNA. The requirement for both POT1 and RPA in telomere maintenance and the antagonism between the two proteins raises the important question of how they function in concert on telomeric ssDNA. Two interesting models were proposed by recent studies to explain the regulation of POT1 and RPA at telomeres. Here, we discuss how these models help unravel the coordination, and also the antagonism, between POT1 and RPA during the cell cycle. PMID:22373525

  11. Cross-talk and regulatory interactions between the essential response regulator RpaB and cyanobacterial circadian clock output.

    Science.gov (United States)

    Espinosa, Javier; Boyd, Joseph S; Cantos, Raquel; Salinas, Paloma; Golden, Susan S; Contreras, Asuncion

    2015-02-17

    The response regulator RpaB (regulator of phycobilisome associated B), part of an essential two-component system conserved in cyanobacteria that responds to multiple environmental signals, has recently been implicated in the control of cell dimensions and of circadian rhythms of gene expression in the model cyanobacterium Synechococcus elongatus PCC 7942. However, little is known of the molecular mechanisms that underlie RpaB functions. In this study we show that the regulation of phenotypes by RpaB is intimately connected with the activity of RpaA (regulator of phycobilisome associated A), the master regulator of circadian transcription patterns. RpaB affects RpaA activity both through control of gene expression, a function requiring an intact effector domain, and via altering RpaA phosphorylation, a function mediated through the N-terminal receiver domain of RpaB. Thus, both phosphorylation cross-talk and coregulation of target genes play a role in the genetic interactions between the RpaA and RpaB pathways. In addition, RpaB?P levels appear critical for survival under light:dark cycles, conditions in which RpaB phosphorylation is environmentally driven independent of the circadian clock. We propose that the complex regulatory interactions between the essential and environmentally sensitive NblS-RpaB system and the SasA-RpaA clock output system integrate relevant extra- and intracellular signals to the circadian clock. PMID:25653337

  12. GENERATION OF RECOMBINANT BACULOVIRUS VIA LIPOSOME MEDIATED TRANSFECTION

    Science.gov (United States)

    Baculovirus expression vectors have become a popular method of producing recombinant proteins. Production of recombinant virus requires the transfection of both the native viral DNA and a transfer plasmid into insect cells where recombination takes place. While several methods of...

  13. 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

  14. From sum rules to RPA: 1. nuclei

    International Nuclear Information System (INIS)

    We take up the flexible formulation of RPA in subspaces of coordinate-like and momentum-like 1 ph operators which was developed in the preceeding paper. We draw the connection to many of the known collective approximations to RPA by proper choice of the subspace of operators. We finally apply the newly developed scheme to comparative studies of a hierachy of approaches for the RPA spectra of doubly magic nuclei described with Skyrme forces. (orig.)

  15. Crossover recombination mediated by HIM-18/SLX4-associated nucleases

    OpenAIRE

    Saito, Takamune T.; Colaia?covo, Monica P.

    2014-01-01

    Meiosis is a specialized cell division program that results in the formation of haploid gametes (i.e., sperm and eggs) from diploid parental cells, and is essential for all sexually reproducing organisms. Crossover formation, the reciprocal exchange of genetic information during recombination, is critical for accurate meiotic chromosome segregation. Misregulation of crossover formation leads to genomic instability and aneuploidy (cells with the incorrect number of chromosomes), resulting in t...

  16. Cre-mediated recombination in the skin melanocyte lineage.

    Science.gov (United States)

    Delmas, Véronique; Martinozzi, Silvia; Bourgeois, Yveline; Holzenberger, Martin; Larue, Lionel

    2003-06-01

    Organ-specific expression of a Cre recombinase allows the analysis of gene function in a particular tissue or cell type. Using a 6.1 kb promoter from the mouse tyrosinase gene, we generated and characterized two lines of transgenic mice that express Cre recombinase in melanoblasts. Utilizing a Cre-responsive reporter mouse strain, genetic recombination was detected in the melanoblasts of the skin from embryonic day 11.5. In addition, Cre-expression was detected in the skin and eyes of mice. Cre transgene activity was occasionally detected in the brain and peripheral nerves but not in other tissues. When Tyr::Cre mice were crossed with mice carrying a homozygous loxP conditional mutation for the insulin-like growth factor receptor gene (Igf1r), Cre-melanoblast-specific recombination pattern was confirmed and no abnormal phenotype was observed. In conclusion, Tyr::Cre transgenic mice provide a valuable tool to follow the cell lineage and to examine gene function in melanocyte development and transformation. PMID:12820167

  17. PCR-mediated recombination of the amplification products of the Hibiscus tiliaceus cytosolic glyceraldehyde-3-phosphate dehydrogenase gene.

    Science.gov (United States)

    Wu, Linghui; Tang, Tian; Zhou, Renchao; Shi, Suhua

    2007-03-31

    PCR-mediated recombination describes the process of in vitro chimera formation from related template sequences present in a single PCR amplification. The high levels of genetic redundancy in eukaryotic genomes should make recombination artifacts occur readily. However, few evolutionary biologists adequately consider this phenomenon when studying gene lineages. The cytosolic glyceraldehyde-3-phosphate dehydrogenase gene (GapC), which encodes a NADP-dependent nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase in the cytosol, is a classical low-copy nuclear gene marker and is commonly used in molecular evolutionary studies. Here, we report on the occurrence of PCR-mediated recombination in the GapC gene family of Hibiscus tiliaceus. The study suggests that recombinant areas appear to be correlated with DNA template secondary structures. Our observations highlight that recombination artifacts should be considered when studying specific and allelic phylogenies. The authors suggest that nested PCR be used to suppress PCR-mediated recombination. PMID:17394766

  18. 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.

  19. 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.

  20. Recombiner

    International Nuclear Information System (INIS)

    Purpose: To shorten the pre-heating time for a recombiner and obtain a uniform temperature distribution for the charged catalyst layer in a BWR type reactor. Constitution: A pre-heating heater is disposed to the outer periphery of a vessel for a recombiner packed with catalysts for recombining hydrogen and oxygen in gases flowing through a radioactive gaseous wastes processing system. Heat pipes for transmitting the heat applied to said container to the catalyst are disposed vertically and horizontally within the container. Different length of the heat pipes are combined. In this way, pre-heating time for the recombiner before the operation start and before the system switching can be shortened and the uniform pre-heating for the inside of the recombiner is also made possible. Further, heater control in the pre-heating can be carried out effectively and with ease. (Moriyama, K.)

  1. Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation

    OpenAIRE

    Gu, Gucci Jijuan; Friedman, Mikaela; Jost, Christian; Johnsson, Kai; Kamali-moghaddam, Masood; Plueckthun, Andreas; Landegren, Ulf; Soderberg, Ola

    2013-01-01

    While antibodies currently play a dominant role as affinity reagents in biological research and for diagnostics, a broad range of recombinant proteins are emerging as promising alternative affinity reagents in detection assays and quantification. DNA-mediated affinity-based assays, such as immuno-PCR and proximity ligation assays (PLA), use oligonucleotides attached to affinity reagents as reporter molecules. Conjugation of oligonucleotides to affinity reagents generally employs chemistries t...

  2. Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation

    Directory of Open Access Journals (Sweden)

    Mann Jennifer K

    2007-05-01

    Full Text Available Abstract Background The genetic code imposes a dilemma for cells. The DNA must be long enough to encode for the complexity of an organism, yet thin and flexible enough to fit within the cell. The combination of these properties greatly favors DNA collisions, which can knot and drive recombination of the DNA. Despite the well-accepted propensity of cellular DNA to collide and react with itself, it has not been established what the physiological consequences are. Results Here we analyze the effects of recombined and knotted plasmids in E. coli using the Hin site-specific recombination system. We show that Hin-mediated DNA knotting and recombination (i promote replicon loss by blocking DNA replication; (ii block gene transcription; and (iii cause genetic rearrangements at a rate three to four orders of magnitude higher than the rate for an unknotted, unrecombined plasmid. Conclusion These results show that DNA reactivity leading to recombined and knotted DNA is potentially toxic and may help drive genetic evolution.

  3. Genome-wide analyses of LINE–LINE-mediated nonallelic homologous recombination

    Science.gov (United States)

    Startek, Micha?; Szafranski, Przemyslaw; Gambin, Tomasz; Campbell, Ian M.; Hixson, Patricia; Shaw, Chad A.; Stankiewicz, Pawe?; Gambin, Anna

    2015-01-01

    Nonallelic homologous recombination (NAHR), occurring between low-copy repeats (LCRs) >10 kb in size and sharing >97% DNA sequence identity, is responsible for the majority of recurrent genomic rearrangements in the human genome. Recent studies have shown that transposable elements (TEs) can also mediate recurrent deletions and translocations, indicating the features of substrates that mediate NAHR may be significantly less stringent than previously believed. Using >4 kb length and >95% sequence identity criteria, we analyzed of the genome-wide distribution of long interspersed element (LINE) retrotransposon and their potential to mediate NAHR. We identified 17 005 directly oriented LINE pairs located genome at risk of LINE–LINE-mediated instability. Cross-referencing these regions with CNVs in the Baylor College of Medicine clinical chromosomal microarray database of 36 285 patients, we identified 516 CNVs potentially mediated by LINEs. Using long-range PCR of five different genomic regions in a total of 44 patients, we confirmed that the CNV breakpoints in each patient map within the LINE elements. To additionally assess the scale of LINE–LINE/NAHR phenomenon in the human genome, we tested DNA samples from six healthy individuals on a custom aCGH microarray targeting LINE elements predicted to mediate CNVs and identified 25 LINE–LINE rearrangements. Our data indicate that LINE–LINE-mediated NAHR is widespread and under-recognized, and is an important mechanism of structural rearrangement contributing to human genomic variability. PMID:25613453

  4. Efficient homologous recombination-mediated genome engineering in zebrafish using TALE nucleases.

    Science.gov (United States)

    Shin, Jimann; Chen, Jiakun; Solnica-Krezel, Lilianna

    2014-10-01

    Custom-designed nucleases afford a powerful reverse genetic tool for direct gene disruption and genome modification in vivo. Among various applications of the nucleases, homologous recombination (HR)-mediated genome editing is particularly useful for inserting heterologous DNA fragments, such as GFP, into a specific genomic locus in a sequence-specific fashion. However, precise HR-mediated genome editing is still technically challenging in zebrafish. Here, we establish a GFP reporter system for measuring the frequency of HR events in live zebrafish embryos. By co-injecting a TALE nuclease and GFP reporter targeting constructs with homology arms of different size, we defined the length of homology arms that increases the recombination efficiency. In addition, we found that the configuration of the targeting construct can be a crucial parameter in determining the efficiency of HR-mediated genome engineering. Implementing these modifications improved the efficiency of zebrafish knock-in generation, with over 10% of the injected F0 animals transmitting gene-targeting events through their germline. We generated two HR-mediated insertion alleles of sox2 and gfap loci that express either superfolder GFP (sfGFP) or tandem dimeric Tomato (tdTomato) in a spatiotemporal pattern that mirrors the endogenous loci. This efficient strategy provides new opportunities not only to monitor expression of endogenous genes and proteins and follow specific cell types in vivo, but it also paves the way for other sophisticated genetic manipulations of the zebrafish genome. PMID:25249466

  5. 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

  6. Cell depletion due to diphtheria toxin fragment A after Cre-mediated recombination.

    Science.gov (United States)

    Brockschnieder, Damian; Lappe-Siefke, Corinna; Goebbels, Sandra; Boesl, Michael R; Nave, Klaus-Armin; Riethmacher, Dieter

    2004-09-01

    Abnormal cell loss is the common cause of a large number of developmental and degenerative diseases. To model such diseases in transgenic animals, we have developed a line of mice that allows the efficient depletion of virtually any cell type in vivo following somatic Cre-mediated gene recombination. By introducing the diphtheria toxin fragment A (DT-A) gene as a conditional expression construct (floxed lacZ-DT-A) into the ubiquitously expressed ROSA26 locus, we produced a line of mice that would permit cell-specific activation of the toxin gene. Following Cre-mediated recombination under the control of cell-type-specific promoters, lacZ gene expression was efficiently replaced by de novo transcription of the Cre-recombined DT-A gene. We provide proof of this principle, initially for cells of the central nervous system (pyramidal neurons and oligodendrocytes), the immune system (B cells), and liver tissue (hepatocytes), that the conditional expression of DT-A is functional in vivo, resulting in the generation of novel degenerative disease models. PMID:15314171

  7. Recombineering

    Science.gov (United States)

    Marinelli, Laura J.; Hatfull, Graham F.; Piuri, Mariana

    2012-01-01

    Recombineering, a recently developed technique for efficient genetic manipulation of bacteria, is facilitated by phage-derived recombination proteins and has the advantage of using DNA substrates with short regions of homology. This system was first developed in E. coli but has since been adapted for use in other bacteria. It is now widely used in a number of different systems for a variety of purposes, and the construction of chromosomal gene knockouts, deletions, insertions, point mutations, as well as in vivo cloning, mutagenesis of bacterial artificial chromosomes and phasmids, and the construction of genomic libraries has been reported. However, these methods also can be effectively applied to the genetic modification of bacteriophage genomes, in both their prophage and lytically growing states. The ever-growing collection of fully sequenced bacteriophages raises more questions than they answer, including the unknown functions of vast numbers of genes with no known homologs and of unknown function. Recombineering of phage genomes is central to addressing these questions, enabling the simple construction of mutants, determination of gene essentiality, and elucidation of gene function. In turn, advances in our understanding of phage genomics should present similar recombineering tools for dissecting a multitude of other genetically naďve bacterial systems. PMID:22666652

  8. Efficient induction of productive Cre-mediated recombination in retinal pigment epithelium

    Science.gov (United States)

    Fu, Shuhua; Zhu, Meili; Wang, Changyun

    2014-01-01

    Purpose To dissect gene functions in the retinal pigment epithelium (RPE), we previously generated a tetracycline-inducible RPE-specific Cre mouse line. Although this Cre mouse line was useful for several conditional gene targeting studies that were conducted by different laboratories, its potential has not been fully exploited, presumably due to a lack of knowledge or procedure for inducing Cre expression appropriately in this mouse line. The goal of the current study is to establish a procedure that will improve the reproducibility of Cre-mediated recombination in this mouse line. Methods Analysis of Cre expression and function was performed in double transgenic mice derived from inducible RPE-specific Cre and Cre-activatable ROSA26 lacZ reporter mice. A tetracycline derivative, doxycycline, was supplied to mice intravitreally to induce Cre expression. Cre expression and function were examined with reverse transcription–PCR, immunoblotting, immunostaining, and in situ enzymatic assay for ?-galactosidase. Retinal integrity was examined with electroretinography and morphometry. Results Intravitreal Dox injection elevated Cre expression significantly and resulted in productive Cre-mediated recombination in approximately 60% of the RPE cells in this mouse line with no apparent change in retinal integrity. Conclusions Our results suggest that productive Cre-mediated recombination in this mouse line can be induced efficiently with intravitreal Dox delivery, with no apparent Dox or Cre toxicity. Therefore, our inducible RPE-specific Cre mice are suitable for Cre/lox-based gene activation and inactivation in adult RPE, which is critical to the effectiveness and suitability of this Cre mouse line in long-term studies requiring conditional gene targeting. PMID:24744608

  9. Hed1 regulates Rad51-mediated recombination via a novel mechanism

    OpenAIRE

    Busygina, Valeria; Sehorn, Michael G.; Shi, Idina Y.; Tsubouchi, Hideo; Roeder, G. Shirleen; Sung, Patrick

    2008-01-01

    Two RecA orthologs, Rad51 and Dmc1, mediate homologous recombination in meiotic cells. During budding yeast meiosis, Hed1 coordinates the actions of Rad51 and Dmc1 by down-regulating Rad51 activity. It is thought that Hed1-dependent attenuation of Rad51 facilitates formation of crossovers that are necessary for the correct segregation of chromosomes at the first meiotic division. We purified Hed1 in order to elucidate its mechanism of action. Hed1 binds Rad51 with high affinity and specificit...

  10. Kinetics of Recombinant Adeno-Associated Virus-Mediated Gene Transfer

    OpenAIRE

    Malik, Ajay K.; Monahan, Paul E.; Allen, David L.; Chen, Bing-guan; Samulski, R. Jude; Kurachi, Kotoku

    2000-01-01

    Recombinant adeno-associated virus (rAAV) vectors have been shown to be useful for efficient gene delivery to a variety of dividing and nondividing cells. Mechanisms responsible for the long-term, persistent expression of the rAAV transgene are not well understood. In this study we investigated the kinetics of rAAV-mediated human factor IX (hFIX) gene transfer into human primary myoblasts and myotubes. Transduction of both myoblasts and myotubes occured with a similar and high efficiency. Aft...

  11. Cell Depletion Due to Diphtheria Toxin Fragment A after Cre-Mediated Recombination

    OpenAIRE

    Brockschnieder, Damian; Lappe-siefke, Corinna; Goebbels, Sandra; Boesl, Michael R.; Nave, Klaus-armin; Riethmacher, Dieter

    2004-01-01

    Abnormal cell loss is the common cause of a large number of developmental and degenerative diseases. To model such diseases in transgenic animals, we have developed a line of mice that allows the efficient depletion of virtually any cell type in vivo following somatic Cre-mediated gene recombination. By introducing the diphtheria toxin fragment A (DT-A) gene as a conditional expression construct (floxed lacZ-DT-A) into the ubiquitously expressed ROSA26 locus, we produced a line of mice that w...

  12. RPA correction to the optical potential

    International Nuclear Information System (INIS)

    This work is dedicated to a microscopic derivation of the optical potential involved in nucleon elastic scattering studies, in the case of doubly closed-shell target nuclei and generally to nuclei well described by the random phase approximation (RPA). We use the so-called 'nuclear structure approach' developed by Vinh Mau and Bouyssy. First, we present results for a calculation using the Gogny force consistently to generate both the real Hartree-Fock term and the complex RPA term of the microscopic optical potential (MOP). Then we present the results obtained adding the RPA potential to the one obtained from g-matrix calculations (Melbourne and Santiago). The MOP is non-local complex and energy dependent. The integro-differential Schroedinger equation corresponding to the scattering problem is solved without any localization procedure. Illustrations are given for proton and neutron scattering from 40Ca and 208Pb. (author)

  13. HARP preferentially co-purifies with RPA bound to DNA-PK and blocks RPA phosphorylation.

    Science.gov (United States)

    Quan, Jinhua; Yusufzai, Timur

    2014-05-01

    The HepA-related protein (HARP/SMARCAL1) is an ATP-dependent annealing helicase that is capable of rewinding DNA structures that are stably unwound due to binding of the single-stranded DNA (ssDNA)-binding protein Replication Protein A (RPA). HARP has been implicated in maintaining genome integrity through its role in DNA replication and repair, two processes that generate RPA-coated ssDNA. In addition, mutations in HARP cause a rare disease known as Schimke immuno-osseous dysplasia. In this study, we purified HARP containing complexes with the goal of identifying the predominant factors that stably associate with HARP. We found that HARP preferentially interacts with RPA molecules that are bound to the DNA-dependent protein kinase (DNA-PK). We also found that RPA is phosphorylated by DNA-PK in vitro, while the RPA-HARP complexes are not. Our results suggest that, in addition to its annealing helicase activity, which eliminates the natural binding substrate for RPA, HARP blocks the phosphorylation of RPA by DNA-PK. PMID:24565939

  14. Integral representation of the RPA correlation energy

    CERN Document Server

    Dönau, F; Nazmitdinov, R G

    1999-01-01

    Using the spectral function F'(z)/F(z) the RPA correlation energy and other properties of a finite system can be written as a contour integral in a compact way. This yields a transparent expression and reduces drastically the numerical efforts for obtaining reliable values. The method applied to pairing vibrations in rotating nuclei as an illustrative example.

  15. Extended GIPQ description of the RPA excitations

    International Nuclear Information System (INIS)

    The work presents an application of the GIPQ quantization method, extended to include the wave function quantization. By explicit calculation on a particular proton-neutron system it is shown that the extended quantization gives the same excitation operator and energy as the RPA. (authors)

  16. A pink mouse reports the switch from red to green fluorescence upon Cre-mediated recombination

    Directory of Open Access Journals (Sweden)

    Hartwich Heiner

    2012-06-01

    Full Text Available Abstract Background Targeted genetic modification in the mouse becomes increasingly important in biomedical and basic science. This goal is most often achieved by use of the Cre/loxP system and numerous Cre-driver mouse lines are currently generated. Their initial characterization requires reporter mouse lines to study the in vivo spatiotemporal activity of Cre. Findings Here, we report a dual fluorescence reporter mouse line, which switches expression from the red fluorescent protein mCherry to eGFP after Cre-mediated recombination. Both fluorescent proteins are expressed from the ubiquitously active and strong CAGGS promoter. Among the founders, we noticed a pink mouse line, expressing high levels of the red fluorescent protein mCherry throughout the entire body. Presence of mCherry in the living animal as well as in almost all organs was clearly visible without optical equipment. Upon Cre-activity, mCherry expression was switched to eGFP, demonstrating functionality of this reporter mouse line. Conclusions The pink mouse presented here is an attractive novel reporter line for fluorescence-based monitoring of Cre-activity. The high expression of mCherry, which is visible to the naked eye, facilitates breeding and crossing, as no genotyping is required to identify mice carrying the reporter allele. The presence of two fluorescent proteins allows in vivo monitoring of recombined and non-recombined cells. Finally, the pink mouse is an eye-catching animal model to demonstrate the power of transgenic techniques in teaching courses.

  17. PCR-mediated recombination in development of microsatellite markers: mechanism and implications

    Scientific Electronic Library Online (English)

    Paula A., Roratto; Darine, Buchmann; Sandro, Santos; Marlise L., Bartholomei-Santos.

    Full Text Available Protocols for microsatellite-enrichment libraries have been widely applied to several species in order to supply the most informative molecular markers for population and inbreeding studies. One drawback of these protocols is the ratio of designed primer pairs that fail to amplify the expected fragm [...] ent, even after exhaustive optimization attempts. A possible cause of unsuccessful microsatellite primers may be that such loci are artifacts resulting from chimeric PCR products, instead of real genomic sequences. The microsatellite-enriched library constructed for Aegla longirostri (Crustacea, Decapoda, Anomura) showed that 29% of sequenced clones were chimeric products because these sequences shared one of the flanking regions around the same repeat motif but not the other. PCR-mediated recombination is a well-known event described for several procedures in which related sequences are used as a template. We have associated this phenomenon with microsatellite marker development. This study explained the high ratio of recombinant sequences generated in the A. longirostri microsatellite-enriched library. We discuss the mechanism and implications of PCR chimeric-product formation during microsatellite isolation.

  18. Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation.

    Science.gov (United States)

    Gu, Gucci Jijuan; Friedman, Mikaela; Jost, Christian; Johnsson, Kai; Kamali-Moghaddam, Masood; Plückthun, Andreas; Landegren, Ulf; Söderberg, Ola

    2013-01-25

    While antibodies currently play a dominant role as affinity reagents in biological research and for diagnostics, a broad range of recombinant proteins are emerging as promising alternative affinity reagents in detection assays and quantification. DNA-mediated affinity-based assays, such as immuno-PCR and proximity ligation assays (PLA), use oligonucleotides attached to affinity reagents as reporter molecules. Conjugation of oligonucleotides to affinity reagents generally employs chemistries that target primary amines or cysteines. Because of the random nature of these processes neither the number of oligonucleotides conjugated per molecule nor their sites of attachment can be accurately controlled for affinity reagents with several available amines and cysteines. Here, we present a straightforward and convenient approach to functionalize recombinant affinity reagents for PLA by expressing the reagents as fusion partners with SNAP protein tags. This allowed us to conjugate oligonucleotides in a site-specific fashion, yielding precisely one oligonucleotide per affinity reagent. We demonstrate this method using designed ankyrin repeat proteins (DARPins) recognizing the tumor antigen HER2 and we apply the conjugates in different assay formats. We also show that SNAP or CLIP tags, expressed as fusion partners of transfected genes, allow oligonucleotide conjugations to be performed in fixed cells, with no need for specific affinity reagents. The approach is used to demonstrate induced interactions between the fusion proteins FKBP and FRB by allowing the in situ conjugated oligonucleotides to direct the production of templates for localized rolling circle amplification reactions. PMID:22664266

  19. Inducible and Reversible Lentiviral and Recombination Mediated Cassette Exchange (RMCE) Systems for Controlling Gene Expression.

    Science.gov (United States)

    Bersten, David C; Sullivan, Adrienne E; Li, Dian; Bhakti, Veronica; Bent, Stephen J; Whitelaw, Murray L

    2015-01-01

    Manipulation of gene expression to invoke loss of function (LoF) or gain of function (GoF) phenotypes is important for interrogating complex biological questions both in vitro and in vivo. Doxycycline (Dox)-inducible gene expression systems are commonly used although success is often limited by high background and insufficient sensitivity to Dox. Here we develop broadly applicable platforms for reliable, tightly controlled and reversible Dox-inducible systems for lentiviral mediated generation of cell lines or FLP Recombination-Mediated Cassette Exchange (RMCE) into the Collagen 1a1 (Col1a1) locus (FLP-In Col1a1) in mouse embryonic stem cells. We significantly improve the flexibility, usefulness and robustness of the Dox-inducible system by using Tetracycline (Tet) activator (Tet-On) variants which are more sensitive to Dox, have no background activity and are expressed from single Gateway-compatible constructs. We demonstrate the usefulness of these platforms in ectopic gene expression or gene knockdown in multiple cell lines, primary neurons and in FLP-In Col1a1 mouse embryonic stem cells. We also improve the flexibility of RMCE Dox-inducible systems by generating constructs that allow for tissue or cell type-specific Dox-inducible expression and generate a shRNA selection algorithm that can effectively predict potent shRNA sequences able to knockdown gene expression from single integrant constructs. These platforms provide flexible, reliable and broadly applicable inducible expression systems for studying gene function. PMID:25768837

  20. Inducible and Reversible Lentiviral and Recombination Mediated Cassette Exchange (RMCE) Systems for Controlling Gene Expression

    Science.gov (United States)

    Bersten, David C.; Sullivan, Adrienne E.; Li, Dian; Bhakti, Veronica; Bent, Stephen J.; Whitelaw, Murray L.

    2015-01-01

    Manipulation of gene expression to invoke loss of function (LoF) or gain of function (GoF) phenotypes is important for interrogating complex biological questions both in vitro and in vivo. Doxycycline (Dox)-inducible gene expression systems are commonly used although success is often limited by high background and insufficient sensitivity to Dox. Here we develop broadly applicable platforms for reliable, tightly controlled and reversible Dox-inducible systems for lentiviral mediated generation of cell lines or FLP Recombination-Mediated Cassette Exchange (RMCE) into the Collagen 1a1 (Col1a1) locus (FLP-In Col1a1) in mouse embryonic stem cells. We significantly improve the flexibility, usefulness and robustness of the Dox-inducible system by using Tetracycline (Tet) activator (Tet-On) variants which are more sensitive to Dox, have no background activity and are expressed from single Gateway-compatible constructs. We demonstrate the usefulness of these platforms in ectopic gene expression or gene knockdown in multiple cell lines, primary neurons and in FLP-In Col1a1 mouse embryonic stem cells. We also improve the flexibility of RMCE Dox-inducible systems by generating constructs that allow for tissue or cell type-specific Dox-inducible expression and generate a shRNA selection algorithm that can effectively predict potent shRNA sequences able to knockdown gene expression from single integrant constructs. These platforms provide flexible, reliable and broadly applicable inducible expression systems for studying gene function. PMID:25768837

  1. 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.

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

    Science.gov (United States)

    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. PMID:24262008

  3. Voltage-dependent inhibition of recombinant NMDA receptor-mediated currents by 5-hydroxytryptamine.

    Science.gov (United States)

    Kloda, Anna; Adams, David J

    2005-02-01

    The effect of 5-HT and related indolealkylamines on heteromeric recombinant NMDA receptors expressed in Xenopus oocytes was investigated using the two-electrode voltage-clamp recording technique. In the absence of external Mg(2+) ions, 5-HT inhibited NMDA receptor-mediated currents in a concentration-dependent manner. The inhibitory effect of 5-HT was independent of the NR1a and NR2 subunit combination. The inhibition of glutamate-evoked currents by 5-HT was use- and voltage-dependent. The voltage sensitivity of inhibition for NR1a+NR2 subunit combinations by 5-HT was similar, exhibiting an e-fold change per approximately 20 mV, indicating that 5-HT binds to a site deep within the membrane electric field. The inhibition of the open NMDA receptor by external Mg(2+) and 5-HT was not additive, suggesting competition between Mg(2+) and 5-HT for a binding site in the NMDA receptor channel. The concentration-dependence curves for 5-HT and 5-methoxytryptamine (5-MeOT) inhibition of NMDA receptor-mediated currents are shifted to the right in the presence of external Mg(2+). The related indolealkylamines inhibited glutamate-evoked currents with the following order of inhibitory potency: 5-MeOT=5-methyltryptamine>tryptamine>7-methyltryptamine>5-HT>tryptophan=melatonin. Taken together, these data suggest that 5-HT and related compounds can attenuate glutamate-mediated excitatory synaptic responses and may provide a basis for drug treatment of excitoxic neurodegeneration. PMID:15655527

  4. Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes.

    Science.gov (United States)

    Yamane, Arito; Resch, Wolfgang; Kuo, Nan; Kuchen, Stefan; Li, Zhiyu; Sun, Hong-wei; Robbiani, Davide F; McBride, Kevin; Nussenzweig, Michel C; Casellas, Rafael

    2011-01-01

    The cytidine deaminase AID hypermutates immunoglobulin genes but can also target oncogenes, leading to tumorigenesis. The extent of AID's promiscuity and its predilection for immunoglobulin genes are unknown. We report here that AID interacted broadly with promoter-proximal sequences associated with stalled polymerases and chromatin-activating marks. In contrast, genomic occupancy of replication protein A (RPA), an AID cofactor, was restricted to immunoglobulin genes. The recruitment of RPA to the immunoglobulin loci was facilitated by phosphorylation of AID at Ser38 and Thr140. We propose that stalled polymerases recruit AID, thereby resulting in low frequencies of hypermutation across the B cell genome. Efficient hypermutation and switch recombination required AID phosphorylation and correlated with recruitment of RPA. Our findings provide a rationale for the oncogenic role of AID in B cell malignancy. PMID:21113164

  5. RPA and POT1: Friends or foes at telomeres?

    OpenAIRE

    Flynn, Rachel Litman; Chang, Sandy; Zou, Lee

    2012-01-01

    Telomere maintenance in cycling cells relies on both DNA replication and capping by the protein complex shelterin. Two single-stranded DNA (ssDNA)-binding proteins, replication protein A (RPA) and protection of telomere 1 (POT1) play critical roles in DNA replication and telomere capping, respectively. While RPA binds to ssDNA in a non-sequence-specific manner, POT1 specifically recognizes singlestranded TTAGGG telomeric repeats. Loss of POT1 leads to aberrant accumulation of RPA at telomeres...

  6. FLP-mediated recombination of FRT sites in the maize genome.

    OpenAIRE

    Lyznik, L. A.; Rao, K. V.; Hodges, T. K.

    1996-01-01

    Molecular evidence is provided for genomic recombinations in maize cells induced by the yeast FLP/FRT site-specific recombination system. The FLP protein recombined FRT sites previously integrated into the maize genome leading to excision of a selectable marker, the neo gene. NPTII activity was not observed after the successful recombination process; instead, the gusA gene was activated by the removal of the blocking DNA fragment. Genomic sequencing in the region of the FRT site (following th...

  7. Self-consistent RPA calculations with Skyrme-type interactions: The skyrme_rpa program

    Science.gov (United States)

    Colň, Gianluca; Cao, Ligang; Van Giai, Nguyen; Capelli, Luigi

    2013-01-01

    Random Phase Approximation (RPA) calculations are nowadays an indispensable tool in nuclear physics studies. We present here a complete version implemented with Skyrme-type interactions, with the spherical symmetry assumption, that can be used in cases where the effects of pairing correlations and of deformation can be ignored. The full self-consistency between the Hartree-Fock mean field and the RPA excitations is enforced, and it is numerically controlled by comparison with energy-weighted sum rules. The main limitations are that charge-exchange excitations and transitions involving spin operators are not included in this version. Program summaryProgram title: skyrme_rpa (v 1.00) Catalogue identifier: AENF_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AENF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5531 No. of bytes in distributed program, including test data, etc.: 39435 Distribution format: tar.gz Programming language: FORTRAN-90/95; easily downgradable to FORTRAN-77. Computer: PC with Intel Celeron, Intel Pentium, AMD Athlon and Intel Core Duo processors. Operating system: Linux, Windows. RAM: From 4 MBytes to 150 MBytes, depending on the size of the nucleus and of the model space for RPA. Word size: The code is written with a prevalent use of double precision or REAL(8) variables; this assures 15 significant digits. Classification: 17.24. Nature of problem: Systematic observations of excitation properties in finite nuclear systems can lead to improved knowledge of the nuclear matter equation of state as well as a better understanding of the effective interaction in the medium. This is the case of the nuclear giant resonances and low-lying collective excitations, which can be described as small amplitude collective motions in the framework of the Random Phase Approximation (RPA). This work provides a tool where one starts from an assumed form of nuclear effective interaction (the Skyrme forces) and builds the self-consistent Hartree-Fock mean field of a given nucleus, and then the RPA multipole excitations of that nucleus. Solution method: The Hartree-Fock (HF) equations are solved in a radial mesh, using a Numerov algorithm. The solutions are iterated until self-consistency is achieved (in practice, when the energy eigenvalues are stable within a desired accuracy). In the obtained mean field, unoccupied states necessary for the RPA calculations are found. For all single-particle states, box boundary conditions are assumed. To solve the RPA problem for a given value of total angular momentum and parity J? a coupled basis is constructed and the RPA matrix is diagonalized (protons and neutrons are treated explicitly, and no approximation related to the use of isospin formalism is introduced). The transition amplitudes and transition strengths associated to given external operators are calculated. The HF densities and RPA transition densities are also evaluated. Restrictions: The main restrictions are related to the assumed spherical symmetry and absence of pairing correlations. Running time: The typical running time depends strongly on the nucleus, on the multipolarity, on the choice of the model space and of course on the computer. It can vary from a few minutes to several hours.

  8. Macrophage-Mediated Optic Neuritis Induced by Retrograde Axonal Transport of Spike Gene Recombinant Mouse Hepatitis Virus

    OpenAIRE

    Shindler, Kenneth S.; Chatterjee, Dhriti; Biswas, Kaushiki; Goyal, Ashish; Dutt, Mahasweta; Nassrallah, Mayssa; Khan, Reas S.; Sarma, Jayasri Das

    2011-01-01

    Following intracranial inoculation, neurovirulent mouse hepatitis virus (MHV) strains induce acute inflammation, demyelination and axonal loss in the CNS. Prior studies using recombinant MHV strains that differ only in the spike gene, which encodes a glycoprotein involved in virus-host cell attachment, demonstrated that spike mediates anterograde axonal transport of virus to the spinal cord. A demyelinating MHV strain induces optic neuritis, but whether this is due to retrograde axonal transp...

  9. Linker-Mediated Recombinational Subcloning of Large DNA Fragments Using Yeast

    OpenAIRE

    Raymond, Christopher K.; Sims, Elizabeth H.; Olson, Maynard V.

    2002-01-01

    The homologous recombination pathway in yeast is an ideal tool for the sequence-specific assembly of plasmids. Complementary 80-nucleotide oligonucleotides that overlap a vector and a target fragment were found to serve as efficient recombination linkers for fragment subcloning. Using electroporation, single-stranded 80-mers were adequate for routine plasmid construction. A cycloheximide-based counterselection was introduced to increase the specificity of cloning by homologous recombination r...

  10. Recombinant antibody mediated delivery of organelle-specific DNA pH sensors along endocytic pathways

    Science.gov (United States)

    Modi, Souvik; Halder, Saheli; Nizak, Clément; Krishnan, Yamuna

    2013-12-01

    DNA has been used to build nanomachines with potential in cellulo and in vivo applications. However their different in cellulo applications are limited by the lack of generalizable strategies to deliver them to precise intracellular locations. Here we describe a new molecular design of DNA pH sensors with response times that are nearly 20 fold faster. Further, by changing the sequence of the pH sensitive domain of the DNA sensor, we have been able to tune their pH sensitive regimes and create a family of DNA sensors spanning ranges from pH 4 to 7.6. To enable a generalizable targeting methodology, this new sensor design also incorporates a `handle' domain. We have identified, using a phage display screen, a set of three recombinant antibodies (scFv) that bind sequence specifically to the handle domain. Sequence analysis of these antibodies revealed several conserved residues that mediate specific interactions with the cognate DNA duplex. We also found that all three scFvs clustered into different branches indicating that their specificity arises from mutations in key residues. When one of these scFvs is fused to a membrane protein (furin) that traffics via the cell surface, the scFv-furin chimera binds the `handle' and ferries a family of DNA pH sensors along the furin endocytic pathway. Post endocytosis, all DNA nanodevices retain their functionality in cellulo and provide spatiotemporal pH maps of retrogradely trafficking furin inside living cells. This new molecular technology of DNA-scFv-protein chimeras can be used to site-specifically complex DNA nanostructures for bioanalytical applications.DNA has been used to build nanomachines with potential in cellulo and in vivo applications. However their different in cellulo applications are limited by the lack of generalizable strategies to deliver them to precise intracellular locations. Here we describe a new molecular design of DNA pH sensors with response times that are nearly 20 fold faster. Further, by changing the sequence of the pH sensitive domain of the DNA sensor, we have been able to tune their pH sensitive regimes and create a family of DNA sensors spanning ranges from pH 4 to 7.6. To enable a generalizable targeting methodology, this new sensor design also incorporates a `handle' domain. We have identified, using a phage display screen, a set of three recombinant antibodies (scFv) that bind sequence specifically to the handle domain. Sequence analysis of these antibodies revealed several conserved residues that mediate specific interactions with the cognate DNA duplex. We also found that all three scFvs clustered into different branches indicating that their specificity arises from mutations in key residues. When one of these scFvs is fused to a membrane protein (furin) that traffics via the cell surface, the scFv-furin chimera binds the `handle' and ferries a family of DNA pH sensors along the furin endocytic pathway. Post endocytosis, all DNA nanodevices retain their functionality in cellulo and provide spatiotemporal pH maps of retrogradely trafficking furin inside living cells. This new molecular technology of DNA-scFv-protein chimeras can be used to site-specifically complex DNA nanostructures for bioanalytical applications. Electronic supplementary information (ESI) available: Detailed description of all oligonucleotide sequences used in this study; list of figures that support claims from the main text. Mainly these show sensor sequences, phage display results, scFv purification and binding data, cell images clamped at different pH and co-localization studies with endocytic tracers. See DOI: 10.1039/c3nr03769j

  11. 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.

  12. Quark recombination in inclusive spectra

    International Nuclear Information System (INIS)

    The reaction A1A2 ? (?/sup +-//K+)X has been analyzed using the quark recombination model where a secondary meson is mediated by combining spectator constituent quarks of the baryons belonging to the incident nucleus with the anti-quarks from the sea, the even taking place at a specific value of the Bjorken variable chi g approx. = 1/3. The inclusive cross-section R(E/d3sigma/dp3) is scaled in terms R(PA2??-x) and/or R(PP? ?-x), the scaling turns out to be a function of the probability functions that one or two constituent quarks will be wounded and also of the geometrical factors, depending on the location of the interaction. The model is moderately successful for low momenta secondary mesons. For high momentum component, the triple Regge mechanism with the ? and nucleon trajectory is invoked, where the elementary cross-sections are convoluted with the momentum distribution of the nucleons, bearing in mind the Pauli principle. The internal fermi motion is important. Finally, a generalized recombination model, depending on the probability distribution functions of up and down quarks is also developed to analyze the inclusive spectra

  13. 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)

  14. 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.

  15. PCR-mediated recombination in amplification products derived from polyploid cotton.

    Science.gov (United States)

    Cronn, R.; Cedroni, M.; Haselkorn, T.; Grover, C.; Wendel, J. F.

    2002-02-01

    PCR recombination describes a process of in vitro chimera formation from non-identical templates. The key requirement of this process is the inclusion of two partially homologous templates in one reaction, a condition met when amplifying any locus from polyploid organisms and members of multigene families from diploid organisms. Because polyploids possess two or more divergent genomes ("homoeologues") in a common nucleus, intergenic chimeras can form during the PCR amplification of any gene. Here we report a high frequency of PCR-induced recombination for four low-copy genes from allotetraploid cotton ( Gossypium hirsutum). Amplification products from these genes ( Myb3, Myb5, G1262 and CesA1) range in length from 860 to 4,050 bp. Intergenomic recombinants were formed frequently, accounting for 23 of the 74 (31.1%) amplicons evaluated, with the frequency of recombination in individual reactions ranging from 0% to approximately 89%. Inspection of the putative recombination zones failed to reveal sequence-specific attributes that promote recombination. The high levels of observed in vitro recombination indicate that the tacit assumption of exclusive amplification of target templates may often be violated, particularly from polyploid genomes. This conclusion has profound implications for population and evolutionary genetic studies, where unrecognized artifactually recombinant molecules may bias results or alter interpretations. PMID:12582722

  16. Imaginary eigenvalue solution in RPA and phase transition

    International Nuclear Information System (INIS)

    The phase transition (PT) of a many-particle system with a close-shell configuration, the stability of the Hartree-Fock (HF) solution and the random phase approximation (RPA) are studied by means of a generalized three-level solvable model. The question whether the occurrence of an imaginary eigenvalue solution in RPA (OISA) may be considered as a signature of PT is explored in some detail. It is found that there is no close relation between OISA and PT. Generally, OISA shows that RPA becomes poor

  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. Various applications of TALEN- and CRISPR/Cas9-mediated homologous recombination to modify the Drosophila genome.

    Science.gov (United States)

    Yu, Zhongsheng; Chen, Hanqing; Liu, Jiyong; Zhang, Hongtao; Yan, Yan; Zhu, Nannan; Guo, Yawen; Yang, Bo; Chang, Yan; Dai, Fei; Liang, Xuehong; Chen, Yixu; Shen, Yan; Deng, Wu-Min; Chen, Jianming; Zhang, Bo; Li, Changqing; Jiao, Renjie

    2014-01-01

    Modifying the genomes of many organisms is becoming as easy as manipulating DNA in test tubes, which is made possible by two recently developed techniques based on either the customizable DNA binding protein, TALEN, or the CRISPR/Cas9 system. Here, we describe a series of efficient applications derived from these two technologies, in combination with various homologous donor DNA plasmids, to manipulate the Drosophila genome: (1) to precisely generate genomic deletions; (2) to make genomic replacement of a DNA fragment at single nucleotide resolution; and (3) to generate precise insertions to tag target proteins for tracing their endogenous expressions. For more convenient genomic manipulations, we established an easy-to-screen platform by knocking in a white marker through homologous recombination. Further, we provided a strategy to remove the unwanted duplications generated during the "ends-in" recombination process. Our results also indicate that TALEN and CRISPR/Cas9 had comparable efficiency in mediating genomic modifications through HDR (homology-directed repair); either TALEN or the CRISPR/Cas9 system could efficiently mediate in vivo replacement of DNA fragments of up to 5 kb in Drosophila, providing an ideal genetic tool for functional annotations of the Drosophila genome. PMID:24659249

  19. The Interaction of cos with Chi Is Separable from DNA Packaging in recA- recBC-Mediated Recombination of Bacteriophage Lambda

    OpenAIRE

    Kobayashi, Ichizo; Stahl, Mary M.; Leach, David; Stahl, Franklin W.

    1983-01-01

    Chi (5'-GCTGGTGG) is a recombinator in RecA- RecBC-mediated recombination in Escherichia coli. In bacteriophage ? vegetative recombination, Chi is fully active only when it is correctly oriented with respect to cos, the site that defines the ends of the packaged chromosome. Here we demonstrate that packaging from cos is not necessary for this cos-Chi interaction. Our evidence suggests that correctly oriented cos is an activator of Chi. cos, as an activator, is (1) dominant over cos-, (2) ac...

  20. Dipole-mediated rectification of intramolecular photoinduced charge separation and charge recombination.

    Science.gov (United States)

    Bao, Duoduo; Upadhyayula, Srigokul; Larsen, Jillian M; Xia, Bing; Georgieva, Boriana; Nuńez, Vicente; Espinoza, Eli M; Hartman, Joshua D; Wurch, Michelle; Chang, Andy; Lin, Chung-Kuang; Larkin, Jason; Vasquez, Krystal; Beran, Gregory J O; Vullev, Valentine I

    2014-09-17

    Controlling charge transfer at a molecular scale is critical for efficient light harvesting, energy conversion, and nanoelectronics. Dipole-polarization electrets, the electrostatic analogue of magnets, provide a means for "steering" electron transduction via the local electric fields generated by their permanent electric dipoles. Here, we describe the first demonstration of the utility of anthranilamides, moieties with ordered dipoles, for controlling intramolecular charge transfer. Donor-acceptor dyads, each containing a single anthranilamide moiety, distinctly rectify both the forward photoinduced electron transfer and the subsequent charge recombination. Changes in the observed charge-transfer kinetics as a function of media polarity were consistent with the anticipated effects of the anthranilamide molecular dipoles on the rectification. The regioselectivity of electron transfer and the molecular dynamics of the dyads further modulated the observed kinetics, particularly for charge recombination. These findings reveal the underlying complexity of dipole-induced effects on electron transfer and demonstrate unexplored paradigms for molecular rectifiers. PMID:25162490

  1. BLM and RMI1 Alleviate RPA Inhibition of TopoIIIa Decatenase Activity

    DEFF Research Database (Denmark)

    Yang, Jay; Bachrati, Csanad Z

    2012-01-01

    RPA is a single-stranded DNA binding protein that physically associates with the BLM complex. RPA stimulates BLM helicase activity as well as the double Holliday junction dissolution activity of the BLM-topoisomerase IIIa complex. We investigated the effect of RPA on the ssDNA decatenase activity of topoisomerase IIIa. We found that RPA and other ssDNA binding proteins inhibit decatenation by topoisomerase IIIa. Complex formation between BLM, TopoIIIa, and RMI1 ablates inhibition of decatenation by ssDNA binding proteins. Together, these data indicate that inhibition by RPA does not involve species-specific interactions between RPA and BLM-TopoIIIa-RMI1, which contrasts with RPA modulation of double Holliday junction dissolution. We propose that topoisomerase IIIa and RPA compete to bind to single-stranded regions of catenanes. Interactions with BLM and RMI1 enhance toposiomerase IIIa activity, promoting decatenation in the presence of RPA.

  2. Generation of TALEN-Mediated GRdim Knock-In Rats by Homologous Recombination

    OpenAIRE

    Ponce Leo?n, Vero?nica; Me?rillat, Anne-marie; Tesson, Laurent; Anego?n, Ignacio; Hummler, Edith

    2014-01-01

    Transcription Activator-Like Effector Nucleases (TALEN) are potential tools for precise genome engineering of laboratory animals. We report the first targeted genomic integration in the rat using TALENs (Transcription Activator-Like Effector Nucleases) by homology-derived recombination (HDR). We assembled TALENs and designed a linear donor insert targeting a pA476T mutation in the rat Glucocorticoid Receptor (Nr3c1) namely GRdim, that prevents receptor homodimerization in the mouse. TALEN mRN...

  3. Recombinant gamma interferon causes neutrophil migration mediated by the release of a macrophage neutrophil chemotactic factor.

    OpenAIRE

    Ribeiro, R. A.; Cunha, F. Q.; Ferreira, S. H.

    1990-01-01

    A dose-dependent neutrophil migration was observed following the injection of purified (Hu IFN-gamma) or recombinant (rIFN-gamma) human gamma interferon into rat peritoneal cavities. This finding contrasts with their inability to cause chemotaxis in vitro in the Boyden chamber. Neutrophil migration into peritoneal cavities and subcutaneous air pouches induced by both preparations of interferon was abolished by pretreatment of the animals with dexamethasone. IFN-gamma-induced neutrophil migrat...

  4. 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...

  5. Recombinant Wolbachia heat shock protein 60 (HSP60) mediated immune responses in patients with lymphatic filariasis.

    Science.gov (United States)

    Shiny, Chandanapurath; Krushna, Nagampalli S A; Babu, Subash; Elango, S; Manokaran, Guruswamy; Narayanan, Rangarajan Badri

    2011-12-01

    Wolbachia, an endosymbiont present in filarial nematodes, have been implicated in a variety of roles, including the worm development and survival. Elucidation of the role of Wolbachia in filarial nematode biology and pathogenesis has become the focus of many studies and its contribution to parasite survival or immune response is still unclear. Recombinant Wolbachia HSP60 decreases T cell activation and lymphoproliferation in filarial infected people compared to endemic controls as observed by the assessment of T cell activation markers and cytokine responses in the peripheral blood mononuclear cells. Reduced T cell activation may be linked to T regulatory cell activity since it is associated with increased expression of CTLA4 and CD25 on CD4(+) T cells in filarial infected group upon stimulation with recombinant Wolbachia HSP60. In addition, elevated interleukin-10 and TGF-? cytokines corroborate the reduced CD4(+) T cell activation and interferon-? observed upon recombinant Wolbachia HSP60 stimulation in filarial patients. Hence, these findings indicate that Wolbachia HSP60 may also contribute to the immune modulation seen in filarial patients. PMID:21827871

  6. 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...

  7. 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-Dueńas, Antoni; Sánchez, Ivelisse; Volpini, Víctor

    2014-11-16

    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

  8. 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.

  9. 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 SciELO Brazil | Language: English Abstract in english 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.

  10. 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.

  11. Agrobacterium-mediated transformation for the investigation of somatic recombination in the fungal pathogen Armillaria

    Science.gov (United States)

    The honey fungus Armillaria mellea is a destructive soil-borne pathogen that affects over 300 plant species, and is of increasing interest due to its ability to decompose lignin. Here we report the transformation of this fungus. A range of techniques was evaluated, and Agrobacterium-mediated trans...

  12. 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.

  13. Generation of TALEN-mediated GRdim knock-in rats by homologous recombination.

    Science.gov (United States)

    Ponce de León, Verónica; Mérillat, Anne-Marie; Tesson, Laurent; Anegón, Ignacio; Hummler, Edith

    2014-01-01

    Transcription Activator-Like Effector Nucleases (TALEN) are potential tools for precise genome engineering of laboratory animals. We report the first targeted genomic integration in the rat using TALENs (Transcription Activator-Like Effector Nucleases) by homology-derived recombination (HDR). We assembled TALENs and designed a linear donor insert targeting a pA476T mutation in the rat Glucocorticoid Receptor (Nr3c1) namely GR(dim), that prevents receptor homodimerization in the mouse. TALEN mRNA and linear double-stranded donor were microinjected into rat one-cell embryos. Overall, we observed targeted genomic modifications in 17% of the offspring, indicating high TALEN cutting efficiency in rat zygotes. PMID:24523878

  14. 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

  15. Quantification of Cre-mediated recombination by a novel strategy reveals a stable extra-chromosomal deletion-circle in mice

    Directory of Open Access Journals (Sweden)

    Breuning Martijn H

    2008-02-01

    Full Text Available Abstract Background Inducible conditional knockout animals are widely used to get insight in the function of genes and the pathogenesis of human diseases. These models frequently rely on Cre-mediated recombination of sequences flanked by Lox-P sites. To understand the consequences of gene disruption, it is essential to know the efficiency of the recombination process. Results Here, we describe a modification of the multiplex ligation-dependent probe amplification (MLPA, called extension-MLPA (eMLPA, which enables quantification of relatively small differences in DNA that are a consequence of Cre-mediated recombination. eMLPA, here applied on an inducible Pkd1 conditional deletion mouse model, simultaneously measures both the reduction of the floxed allele and the increase of the deletion allele in a single reaction thereby minimizing any type of experimental variation. Interestingly, with this method we were also able to observe the presence of the excised DNA fragment. This extra-chromosomal deletion-circle was detectable up to 5 months after activation of Cre. Conclusion eMLPA is a novel strategy which easily can be applied to measure the Cre-mediated recombination efficiency in each experimental case with high accuracy. In addition the fate of the deletion-circle can be followed simultaneously.

  16. 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.

  17. 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.

  18. Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution.

    Science.gov (United States)

    Babcock, Melanie; Pavlicek, Adam; Spiteri, Elizabeth; Kashork, Catherine D; Ioshikhes, Ilya; Shaffer, Lisa G; Jurka, Jerzy; Morrow, Bernice E

    2003-12-01

    Low-copy repeats, or segmental duplications, are highly dynamic regions in the genome. The low-copy repeats on chromosome 22q11.2 (LCR22) are a complex mosaic of genes and pseudogenes formed by duplication processes; they mediate chromosome rearrangements associated with velo-cardio-facial syndrome/DiGeorge syndrome, der(22) syndrome, and cat-eye syndrome. The ability to trace the substrates and products of recombination events provides a unique opportunity to identify the mechanisms responsible for shaping LCR22s. We examined the genomic sequence of known LCR22 genes and their duplicated derivatives. We found Alu (SINE) elements at the breakpoints in the substrates and at the junctions in the truncated products of recombination for USP18, GGT, and GGTLA, consistent with Alu-mediated unequal crossing-over events. In addition, we were able to trace a likely interchromosomal Alu-mediated fusion between IGSF3 on 1p13.1 and GGT on 22q11.2. Breakpoints occurred inside Alu elements as well as in the 5' or 3' ends of them. A possible stimulus for the 5' or 3' terminal rearrangements may be the high sequence similarities between different Alu elements, combined with a potential recombinogenic role of retrotransposon target-site duplications flanking the Alu element, containing potentially kinkable DNA sites. Such sites may represent focal points for recombination. Thus, genome shuffling by Alu-mediated rearrangements has contributed to genome architecture during primate evolution. PMID:14656960

  19. Shuffling of Genes Within Low-Copy Repeats on 22q11 (LCR22) by Alu-Mediated Recombination Events During Evolution

    OpenAIRE

    Babcock, Melanie; Pavlicek, Adam; Spiteri, Elizabeth; Kashork, Catherine D.; Ioshikhes, Ilya; Shaffer, Lisa G.; Jurka, Jerzy; Morrow, Bernice E.

    2003-01-01

    Low-copy repeats, or segmental duplications, are highly dynamic regions in the genome. The low-copy repeats on chromosome 22q11.2 (LCR22) are a complex mosaic of genes and pseudogenes formed by duplication processes; they mediate chromosome rearrangements associated with velo-cardio-facial syndrome/DiGeorge syndrome, der(22) syndrome, and cat-eye syndrome. The ability to trace the substrates and products of recombination events provides a unique opportunity to identify the mechanisms responsi...

  20. TCreERT2, a Transgenic Mouse Line for Temporal Control of Cre-Mediated Recombination in Lineages Emerging from the Primitive Streak or Tail Bud

    OpenAIRE

    Anderson, Matthew J.; Naiche, L. A.; Wilson, Catherine P.; Elder, Cindy; Swing, Deborah A.; Lewandoski, Mark

    2013-01-01

    The study of axis extension and somitogenesis has been greatly advanced through the use of genetic tools such as the TCre mouse line. In this line, Cre is controlled by a fragment of the T (Brachyury) promoter that is active in progenitor cells that reside within the primitive streak and tail bud and which give rise to lineages emerging from these tissues as the embryonic axis extends. However, because TCre-mediated recombination occurs early in development, gene inactivation can result in an...

  1. Variational RPA for the Mie resonance in jellium

    CERN Document Server

    Bertsch, George F; 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.

  2. Evidence of Meiotic Crossover Control in Saccharomyces cerevisiae Through Mec1-Mediated Phosphorylation of Replication Protein A

    OpenAIRE

    Bartrand, Amy J.; Iyasu, Dagmawi; Marinco, Suzanne M.; Brush, George S.

    2006-01-01

    Replication protein A (RPA) is the major single-stranded DNA-binding protein in eukaryotes, essential for DNA replication, repair, and recombination. During mitosis and meiosis in budding yeast, RPA becomes phosphorylated in reactions that require the Mec1 protein kinase, a central checkpoint regulator and homolog of human ATR. Through mass spectrometry and site-directed mutagenesis, we have now identified a single serine residue in the middle subunit of the RPA heterotrimer that is targeted ...

  3. Estrogen Receptor ?-Mediated Nuclear Interaction Between IRS-1 and Rad51 Inhibits Homologous Recombination Directed DNA Repair in Medulloblastoma

    Science.gov (United States)

    URBANSKA, KATARZYNA; PANNIZZO, PAOLA; LASSAK, ADAM; GUALCO, ELISA; SURMACZ, EVA; CROUL, SIDNEY; VALLE, LUIS DEL; KHALILI, KAMEL; REISS, KRZYSZTOF

    2009-01-01

    In medulloblastomas, which are highly malignant cerebellar tumors of the childhood genotoxic treatments such as cisplatin or ?-irradiation are frequently associated with DNA damage, which often associates with unfaithful DNA repair, selection of new adaptations and possibly tumor recurrences. Therefore, better understanding of molecular mechanisms which control DNA repair fidelity upon DNA damage is a critical task. Here we demonstrate for the first time that estrogen receptor beta (ER?) can contribute to the development of genomic instability in medulloblastomas. Specifically, ER? was found highly expressed and active in mouse and human medulloblastoma cell lines. Nuclear ER? was also present in human medulloblastoma clinical samples. Expression of ER? coincided with nuclear translocation of insulin receptor substrate 1 (IRS-1), which was previously reported to interfere with the faithful component of DNA repair when translocated to the nucleus. We demonstrated that ER? and IRS-1 bind each other, and the interaction involves C-terminal domain of IRS-1 (aa 931–1233). Following cisplatin-induced DNA damage, nuclear IRS-1 localized at the sites of damaged DNA, and interacted with Rad51—an enzymatic component of homologous recombination directed DNA repair (HRR). In medulloblastoma cells, engineered to express HRR-DNA reporter plasmid, ER antagonist, ICI 182,780, or IRS mutant (931–1233) significantly increased DNA repair fidelity. These data strongly suggest that both molecular and pharmacological interventions are capable of preventing ER?-mediated IRS-1 nuclear translocation, which in turn improves DNA repair fidelity and possibly counteracts accumulation of malignant mutations in actively growing medulloblastomas. PMID:19117011

  4. Variational RPA for the dipole surface plasmon in metal clusters

    International Nuclear Information System (INIS)

    The deviation of the ionic background potential in simple metal clusters from the harmonic shape leads to a red shift of the surface plasmon from the Mie frequency, that is considerably larger than the spill-out correction. In order to estimate this effect, 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 has the same order of magnitude

  5. Mitotic crisis: The unmasking of a novel role for RPA

    OpenAIRE

    Anantha, Rachel William; Borowiec, James A.

    2009-01-01

    Mitotic DNA damage is a constant threat to genomic integrity, yet understanding of the cellular responses to this stress remain incomplete. Recent work by Anantha et al. (PNAS 2008; 105:12903–8) has found surprising evidence that RPA, the primary eukaryotic single-stranded DNA-binding protein, can stimulate the ability of cells to exit mitosis into a 2N G1 phase. Along with providing additional discussion of this study, we review evidence suggesting that DNA replication and repair factors c...

  6. Mitotic crisis: the unmasking of a novel role for RPA.

    Science.gov (United States)

    Anantha, Rachel William; Borowiec, James A

    2009-02-01

    Mitotic DNA damage is a constant threat to genomic integrity, yet understanding of the cellular responses to this stress remain incomplete. Recent work by Anantha et al. (2008; PNAS 105:12903-8) has found surprising evidence that RPA, the primary eukaryotic single-stranded DNA-binding protein, can stimulate the ability of cells to exit mitosis into a 2N G(1) phase. Along with providing additional discussion of this study, we review evidence suggesting that DNA replication and repair factors can modulate mitotic transit by acting through Polo-like kinase-1 (Plk1) and the centrosome. 'A crisis unmasks everyone.'-Mason Cooley, U.S. aphorist. PMID:19176996

  7. 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

  8. 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.

  9. Sequential and synergistic modification of human RPA stimulates chromosomal DNA repair.

    Science.gov (United States)

    Anantha, Rachel W; Vassin, Vitaly M; Borowiec, James A

    2007-12-01

    The activity of human replication protein A (RPA) in DNA replication and repair is regulated by phosphorylation of the middle RPA2 subunit. It has previously been shown that up to nine different N-terminal residues are modified in vivo and in response to genotoxic stress. Using a novel antibody against phospho-Ser(29), a moiety formed by cyclin-Cdk, we observed that RPA2 was phosphorylated during mitosis in nonstressed cells. Robust phosphorylation of Ser(29) was also seen in interphase cells following treatment with the DNA-damaging agent camptothecin, a rare example of stress stimulating the modification of a repair factor by cyclin-Cdk. RPA2 phosphorylation is regulated both in cis and trans. Cis-phosphorylation follows a preferred pathway. (That is, the initial modification of Ser(33) by ATR stimulates subsequent phosphorylation of Cdk sites Ser(23) and Ser(29)). These events then facilitate modification of Thr(21) and extreme N-terminal sites Ser(4) and Ser(8), probably by DNA-PK. Our data also indicate that the phosphorylation of one RPA molecule can influence the phosphorylation of other RPA molecules in trans. Cells in which endogenous RPA2 was "replaced" with a double S23A/S29A-RPA2 mutant were seen to have an abnormal cell cycle distribution both in normal and in stressed cells. Such cells also showed aberrant DNA damage-dependent RPA foci and had persistent staining of gammaH2AX following DNA damage. Our data indicate that RPA phosphorylation facilitates chromosomal DNA repair. We postulate that the RPA phosphorylation pattern provides a means to regulate the DNA repair pathway utilized. PMID:17928296

  10. RPA calculation of Gamow-Teller and M1 states includind ?-hole excitation

    International Nuclear Information System (INIS)

    The self-consistent RPA model with Skyrme type interactions is extended to include ?-hole excitations. Energies and transition strengths of Gamow-Teller and MI states are studied systematically. We find that the combined effects of RPA correlations and ?-hole excitation decrease the transition strengths by about 35%. (orig.)

  11. RPA phosphorylation facilitates mitotic exit in response to mitotic DNA damage.

    Science.gov (United States)

    Anantha, Rachel William; Sokolova, Elena; Borowiec, James A

    2008-09-01

    Human replication protein A (RPA) becomes phosphorylated on the RPA2 subunit by cyclin B-Cdc2 during mitosis, although the functional role of this modification is unclear. We find that this modification stimulates RPA2 to become hyperphosphorylated in response to mitotic DNA damage caused by bleomycin treatment. Cells in which endogenous RPA2 was replaced by a mutant subunit lacking both Cdc2 sites had a significant defect in mitotic release into a 2N G(1) phase after exposure to bleomycin. An increased percentage of these mutant cells also was positive initially for cyclin B expression and BubR1 chromatin staining, indicative of an extended spindle assembly checkpoint. The mutant cells that experienced mitotic DNA damage also underwent apoptosis at higher levels than cells expressing the WT subunit. Even so, we did not find the mutation had any dramatic effects on the level of DNA repair in mitosis. Cells lacking ATM (a checkpoint factor and RPA2 kinase) also were severely defective in mitotic exit and were unable to support RPA hyperphosphorylation after mitotic DNA damage. Although checkpoint 1 effector kinase (Chk1) had a more complex role, inhibition of Chk1 activity with UCN-01 also reduced mitotic exit. Chk1 activation and mitotic RPA hyperphosphorylation were found to be independent events. Our results demonstrate that mitotic RPA hyperphosphorylation facilitates release of cells from a damaged mitosis into a 2N G(1) phase, thereby increasing cell viability. PMID:18723675

  12. The resolution and regeneration of a cointegrate plasmid reveals a model for plasmid evolution mediated by conjugation and oriT site-specific recombination.

    Science.gov (United States)

    Wang, Pengxia; Zhang, Chunyi; Zhu, Yiguang; Deng, Yun; Guo, Suxia; Peng, Donghai; Ruan, Lifang; Sun, Ming

    2013-12-01

    Cointegrate plasmids are useful models for the study of plasmid evolution if their evolutionary processes can be replicated under laboratory conditions. pBMB0228, a 17?706?bp native plasmid originally isolated from Bacillus thuringiensis strain YBT-1518, carries two nematicidal crystal protein genes, cry6Aa and cry55Aa. In this study, we show that pBMB0228 is in fact a cointegrate of two plasmids and contains two functional replication regions and two functional mobilization regions. Upon introduction into B.?thuringiensis strain BMB171, pBMB0228 spontaneously resolves into two constituent plasmids via recombination at its oriT1 and oriT2 sites. The resolution does not require conjugation but can be promoted by conjugation. We further confirm that the resolution is mediated by oriT site-specific recombination requiring Mob02281 or Mob02282. Additionally, the two constituent plasmids of pBMB0228 are mobilizable, and can fuse back via oriT site-specific integration after entering into the same cell by conjugation. Our study confirms that native plasmid can reversibly interconvert between a cointegrate structure and its constituent plasmids. This study provides insight into the evolution of cointegrate plasmids, linking plasmid evolution with conjugation and the oriT site-specific recombination function of relaxase. PMID:23826996

  13. Microscopic nuclear-dissipation mechanism as damping of collective motion in the second RPA

    International Nuclear Information System (INIS)

    A microscopic model for the damping of the one-phonon RPA collective state, absolute value c > = Q/sub c/ 0 > /sub S//sub R/, has been previously described. This one-phonon RPA collective state is defined within a restricted subspace, S/sub R/, of the discrete 1p-1h structure. Its damping is described within an extended subspace, S = S/sub R/ + S/sub A/, by the time evolution of a wave packet according to the RPA and the Second RPA approximations of the complete Schroedinger equation when initialized with the one-phonon state. The one-phonon state, however, is unable to describe time-varying oscillations of the mean field. Such oscillations require wave packets formed by linear superposition of the RPA many-phonon eigenstates. Coherent time-varying oscillations of the mean field (multi-phonon initial states) are discussed

  14. Fowlpox virus recombinants expressing HPV-16 E6 and E7 oncogenes for the therapy of cervical carcinoma elicit humoral and cell-mediated responses in rabbits

    Directory of Open Access Journals (Sweden)

    Pacchioni Sole

    2010-04-01

    Full Text Available Abstract Background Around half million new cases of cervical cancer arise each year, making the development of an effective therapeutic vaccine against HPV a high priority. As the E6 and E7 oncoproteins are expressed in all HPV-16 tumour cells, vaccines expressing these proteins might clear an already established tumour and support the treatment of HPV-related precancerous lesions. Methods Three different immunisation regimens were tested in a pre-clinical trial in rabbits to evaluate the humoral and cell-mediated responses of a putative HPV-16 vaccine. Fowlpoxvirus (FP recombinants separately expressing the HPV-16 E6 (FPE6 and E7 (FPE7 transgenes were used for priming, followed by E7 protein boosting. Results All of the protocols were effective in eliciting a high antibody response. This was also confirmed by interleukin-4 production, which increased after simultaneous priming with both FPE6 and FPE7 and after E7 protein boost. A cell-mediated immune response was also detected in most of the animals. Conclusion These results establish a preliminary profile for the therapy with the combined use of avipox recombinants, which may represent safer immunogens than vaccinia-based vectors in immuno-compromised individuals, as they express the transgenes in most mammalian cells in the absence of a productive replication.

  15. Solving the RPA eigenvalue equation in real-space

    CERN Document Server

    Muta, A; Hashimoto, Y; Yabana, K

    2002-01-01

    We present a computational method to solve the RPA eigenvalue equation employing a uniform grid representation in three-dimensional Cartesian coordinates. The conjugate gradient method is used for this purpose as an interactive method for a generalized eigenvalue problem. No construction of unoccupied orbitals is required in the procedure. We expect this method to be useful for systems lacking spatial symmetry to calculate accurate eigenvalues and transition matrix elements of a few low-lying excitations. Some applications are presented to demonstrate the feasibility of the method, considering the simplified mean-field model as an example of a nuclear physics system and the electronic excitations in molecules with time-dependent density functional theory as an example of an electronic system. (author)

  16. Solving the RPA eigenvalue equation in real-space

    International Nuclear Information System (INIS)

    We present a computational method to solve the RPA eigenvalue equation employing a uniform grid representation in three-dimensional Cartesian coordinates. The conjugate gradient method is used for this purpose as an interactive method for a generalized eigenvalue problem. No construction of unoccupied orbitals is required in the procedure. We expect this method to be useful for systems lacking spatial symmetry to calculate accurate eigenvalues and transition matrix elements of a few low-lying excitations. Some applications are presented to demonstrate the feasibility of the method, considering the simplified mean-field model as an example of a nuclear physics system and the electronic excitations in molecules with time-dependent density functional theory as an example of an electronic system. (author)

  17. Roles of Bacillus subtilis DprA and SsbA in RecA-mediated genetic recombination.

    Science.gov (United States)

    Yadav, Tribhuwan; Carrasco, Begońa; Serrano, Ester; Alonso, Juan C

    2014-10-01

    Bacillus subtilis competence-induced RecA, SsbA, SsbB, and DprA are required to internalize and to recombine single-stranded (ss) DNA with homologous resident duplex. RecA, in the ATP · Mg(2+)-bound form (RecA · ATP), can nucleate and form filament onto ssDNA but is inactive to catalyze DNA recombination. We report that SsbA or SsbB bound to ssDNA blocks the RecA filament formation and fails to activate recombination. DprA facilitates RecA filamentation; however, the filaments cannot engage in DNA recombination. When ssDNA was preincubated with SsbA, but not SsbB, DprA was able to activate DNA strand exchange dependent on RecA · ATP. This work demonstrates that RecA · ATP, in concert with SsbA and DprA, catalyzes DNA strand exchange, and SsbB is an accessory factor in the reaction. In contrast, RecA · dATP efficiently catalyzes strand exchange even in the absence of single-stranded binding proteins or DprA, and addition of the accessory factors marginally improved it. We proposed that the RecA-bound nucleotide (ATP and to a lesser extent dATP) might dictate the requirement for accessory factors. PMID:25138221

  18. Human RPA phosphorylation by ATR stimulates DNA synthesis and prevents ssDNA accumulation during DNA-replication stress.

    Science.gov (United States)

    Vassin, Vitaly M; Anantha, Rachel William; Sokolova, Elena; Kanner, Shlomo; Borowiec, James A

    2009-11-15

    ATR is an essential kinase activated in response to DNA-replication stress, with a known target being the RPA2 subunit of human replication protein A (RPA). We find that S33-RPA2 phosphorylation by ATR occurs primarily in the late-S and G2 phases, probably at sites of residual stalled DNA-replication forks, with S33-P-RPA2 contained within nuclear repair centers. Although cells in which endogenous RPA2 was ;replaced' with an RPA2 protein with mutations T21A and S33A (T21A/S33A-RPA) had normal levels of DNA replication under non-stress conditions, the mutant cells were severely deficient in the amount of DNA synthesis occurring during replication stress. These cells also had abnormally high levels of chromatin-bound RPA, indicative of increased amounts of single-stranded DNA (ssDNA) and showed defective recovery from stress. Cells replaced with the mutant RPA2 also generated G1 cells with a broader DNA distribution and high levels of apoptosis following stress, compared with cells expressing wild-type RPA2. Surprisingly, cells expressing the wild-type RPA2 subunit had increased levels of stress-dependent DNA breaks. Our data demonstrate that RPA phosphorylation at the T21 and S33 sites facilitates adaptation of a DNA-replication fork to replication stress. PMID:19843584

  19. Recombination mediates production of an extrachromosomal circular DNA containing a transposon-like human element, THE-1.

    OpenAIRE

    Misra, R.; Matera, A. G.; Schmid, C. W.; Rush, M. G.

    1989-01-01

    An abundant class of HeLa extrachromosomal circular DNA containing the transposon-like element, THE-1, is shown to arise via site specific recombination. The chromosomal locus from which these circles are derived, however, is single-copy. Northern blot analysis detects homology to two polyadenylated RNAs in HeLa cells. The possible presence of an origin of replication and its role in generating these small polydisperse circles is discussed.

  20. Stable transgene expression in rod photoreceptors after recombinant adeno-associated virus-mediated gene transfer to monkey retina

    OpenAIRE

    Bennett, Jean; Maguire, Albert M.; Cideciyan, Artur V.; Schnell, Michael; Glover, Ernest; Anand, Vibha; Aleman, Tomas S.; Chirmule, Narendra; Gupta, Abha R.; Huang, Yijun; Gao, Guang-ping; Nyberg, William C.; Tazelaar, John; Hughes, Joseph; Wilson, James M.

    1999-01-01

    Recombinant adeno-associated virus (rAAV) is a promising vector for therapy of retinal degenerative diseases. We evaluated the efficiency, cellular specificity, and safety of retinal cell transduction in nonhuman primates after subretinal delivery of an rAAV carrying a cDNA encoding green fluorescent protein (EGFP), rAAV.CMV.EGFP. The treatment results in efficient and stable EGFP expression lasting >1 year. Transgene expression in the neural retina is limited exclusively to rod photoreceptor...

  1. Recombinant Mouse PAP Has pH-Dependent Ectonucleotidase Activity and Acts through A1-Adenosine Receptors to Mediate Antinociception

    OpenAIRE

    Sowa, Nathaniel A.; Vadakkan, Kunjumon I.; Zylka, Mark J.

    2009-01-01

    Prostatic acid phosphatase (PAP) is expressed in nociceptive neurons and functions as an ectonucleotidase. When injected intraspinally, the secretory isoforms of human and bovine PAP protein have potent and long-lasting antinociceptive effects that are dependent on A1-adenosine receptor (A1R) activation. In this study, we purified the secretory isoform of mouse (m)PAP using the baculovirus expression system to determine if recombinant mPAP also had antinociceptive properties. We found that mP...

  2. A Vector System for ABC Transporter-Mediated Secretion and Purification of Recombinant Proteins in Pseudomonas Species.

    Science.gov (United States)

    Ryu, Jaewook; Lee, Ukjin; Park, Jiye; Yoo, Do-Hyun; Ahn, Jung Hoon

    2015-03-01

    Pseudomonas fluorescens is an efficient platform for recombinant protein production. P. fluorescens has an ABC transporter secreting endogenous thermostable lipase (TliA) and protease, which can be exploited to transport recombinant proteins across the cell membrane. In this study, the expression vector pDART was constructed by inserting tliDEF, genes encoding the ABC transporter, along with the construct of the lipase ABC transporter recognition domain (LARD), into pDSK519, a widely used shuttle vector. When the gene for the target protein was inserted into the vector, the C-terminally fused LARD allowed it to be secreted through the ABC transporter into the extracellular medium. After secretion of the fused target protein, the LARD containing a hydrophobic C terminus enabled its purification through hydrophobic interaction chromatography (HIC) using a methyl-Sepharose column. Alkaline phosphatase (AP) and green fluorescent protein (GFP) were used to validate the expression, export, and purification of target proteins by the pDART system. Both proteins were secreted into the extracellular medium in P. fluorescens. In particular, AP was secreted in several Pseudomonas species with its enzymatic activity in extracellular media. Furthermore, purification of the target protein using HIC yielded some degree of AP and GFP purification, where AP was purified to almost a single product. The pDART system will provide greater convenience for the secretory production and purification of recombinant proteins in Gram-negative bacteria, such as Pseudomonas species. PMID:25548043

  3. Radiation protection authorized persons (RPA) in Germany; Der Strahlenschutzbevollmaechtigte in Deutschland

    Energy Technology Data Exchange (ETDEWEB)

    Sahre, P.; Beutmann, A.; Lorenz, J. [Verein fuer Kernverfahrenstechnik und Analytik Rossendorf e.V., Dresden (Germany); Leder, F. [Saechsisches Staatsministerium fuer Umwelt und Landwirtschaft, Dresden (Germany); Philipp, T. [Saechsisches Landesamt fuer Umwelt, Landwirtschaft und Geologie, Dresden (Germany)

    2013-07-01

    The radiation protection authorized person (RPA) is playing an important role in the fields of organization, realization and checking the radiation protection in Germany, first of all in big institutions like research centers, facilities and medical centers. The paper deals with the legal status of the RPA especially the clear dividing line between his tasks and the tasks of the radiation protection supervisor and the radiation protection commissioner. The paper shows that the embodiment of the RPA in the radiation protection law has advantages also in coordinating the tasks of radiation protection officer and radiation protection expert recommended by the European Union. (orig.)

  4. Novel ROSA26 Cre-reporter Knock-in C57BL/6N Mice Exhibiting Green Emission before and Red Emission after Cre-mediated Recombination

    Science.gov (United States)

    Hasegawa, Yoshikazu; Daitoku, Yoko; Sekiguchi, Keito; Tanimoto, Yoko; Mizuno-Iijima, Saori; Mizuno, Seiya; Kajiwara, Noriko; Ema, Masatsugu; Miwa, Yoshihiro; Mekada, Kazuyuki; Yoshiki, Atsushi; Takahashi, Satoru; Sugiyama, Fumihiro; Yagami, Ken-ichi

    2013-01-01

    The Cre/loxP system is a strategy for controlling temporal and/or spatial gene expression through genome alteration in mice. As successful Cre/loxP genome alteration depends on Cre-driver mice, Cre-reporter mice are essential for validation of Cre gene expression in vivo. In most Cre-reporter mouse strains, although the presence of reporter product indicates the expression of Cre recombinase, it has remained unclear whether a lack of reporter signal indicates either no Cre recombinase expression or insufficient reporter gene promoter activity. We produced a novel ROSA26 knock-in Cre-reporter C57BL/6N strain exhibiting green emission before and red after Cre-mediated recombination, designated as strain R26GRR. Ubiquitous green fluorescence and no red fluorescence were observed in R26GRR mice. To investigate the activation of tdsRed, EGFP-excised R26GRR, R26RR, mice were produced through the crossing of C57BL/6N mice with R26GRR/Ayu1-Cre F1 mice. R26RR mice showed extraordinarily strong red fluorescence in almost all tissues examined, suggesting ubiquitous activation of the second reporter in all tissues after Cre/loxP recombination. Moreover, endothelial cell lineage and pancreatic islet-specific expression of red fluorescence were detected in R26GRR/Tie2-Cre F1 mice and R26GRR /Ins1-Cre F1 mice, respectively. These results indicated that R26GRR mice are a useful novel Cre-reporter mouse strain. In addition, R26GRR mice with a pure C57BL/6N background represent a valuable source of green-to-red photoconvertible cells following Cre/loxP recombination for application in transplantation studies. The R26GRR mouse strain will be available from RIKEN BioResource Center (http://www.brc.riken.jp/lab/animal/en/). PMID:24172193

  5. 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.

  6. 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

  7. 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

  8. Induction of Protective CD4+ T Cell-Mediated Immunity by a Leishmania Peptide Delivered in Recombinant Influenza Viruses

    OpenAIRE

    Kedzierska, Katherine; Curtis, Joan M.; Valkenburg, Sophie A.; Hatton, Lauren A.; Kiu, Hiu; Doherty, Peter C.; Kedzierski, Lukasz

    2012-01-01

    The available evidence suggests that protective immunity to Leishmania is achieved by priming the CD4+ Th1 response. Therefore, we utilised a reverse genetics strategy to generate influenza A viruses to deliver an immunogenic Leishmania peptide. The single, immunodominant Leishmania-specific LACK158–173 CD4+ peptide was engineered into the neuraminidase stalk of H1N1 and H3N2 influenza A viruses. These recombinant viruses were used to vaccinate susceptible BALB/c mice to determine whether t...

  9. Passive immunity to yersiniae mediated by anti-recombinant V antigen and protein A-V antigen fusion peptide.

    OpenAIRE

    Motin, V. L.; Nakajima, R.; Smirnov, G. B.; Brubaker, R. R.

    1994-01-01

    LcrV (V antigen), a known unstable 37.3-kDa monomeric peptide encoded on the ca. 70-kb Lcr plasmid of Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica, has been implicated as a regulator of the low-calcium response, virulence factor, and protective antigen. In this study, lcrV of Y. pestis was cloned into protease-deficient Escherichia coli BL21. The resulting recombinant V antigen underwent marked degradation from the C-terminal end during purification, yielding majo...

  10. Evaluation of the effect of RFCA in patients with WPW syndrome using RPA

    International Nuclear Information System (INIS)

    Whether radionuclide phase analysis (RPA) could evaluate the effect of radiofrequency current ablation (RFCA) in patients with Wolff-Parkinson-White (WPW) syndrome was evaluated. 18 patients with WPW syndrome were studied using RPA pre- and post-RFCA. RPA identified the sites of pre-excitation in all patients before RFCA. Compared with the pre-RFCA study, the sites of pre-excitation disappeared in 12 cases, disappeared gradually in 4 cases and unchanged in 2 cases. 50 RFCA was successful in the former two patterns, but failed in the last pattern. RPA can evaluate the changes of pre-excitation sites in patients with WPW syndrome before and after RFCA. It was a noninvasive and reliable method for assessing and monitoring the effect of RFCA in patients with WPW syndrome

  11. Recombinant Listeria monocytogenes as a Live Vaccine Vehicle for the Induction of Protective Anti-Viral Cell-Mediated Immunity

    Science.gov (United States)

    Shen, Hao; Slifka, Mark K.; Matloubian, Mehrdad; Jensen, Eric R.; Ahmed, Rafi; Miller, Jeff F.

    1995-04-01

    Listeria monocytogenes (LM) is a Gram-positive bacterium that is able to enter host cells, escape from the endocytic vesicle, multiply within the cytoplasm, and spread directly from cell to cell without encountering the extracellular milieu. The ability of LM to gain access to the host cell cytosol allows proteins secreted by the bacterium to efficiently enter the pathway for major histocompatibility complex class I antigen processing and presentation. We have established a genetic system for expression and secretion of foreign antigens by recombinant strains, based on stable site-specific integration of expression cassettes into the LM genome. The ability of LM recombinants to induce protective immunity against a heterologous pathogen was demonstrated with lymphocytic choriomeningitis virus (LCMV). LM strains expressing the entire LCMV nucleoprotein or an H-2L^d-restricted nucleoprotein epitope (aa 118-126) were constructed. Immunization of mice with LM vaccine strains conferred protection against challenge with virulent strains of LCMV that otherwise establish chronic infection in naive adult mice. In vivo depletion of CD8^+ T cells from vaccinated mice abrogated their ability to clear viral infection, showing that protective anti-viral immunity was due to CD8^+ T cells.

  12. Validation of the RTOG recursive partitioning analysis (RPA) classification for brain metastases

    International Nuclear Information System (INIS)

    Purpose: The Radiation Therapy Oncology Group (RTOG) previously developed three prognostic classes for brain metastases using recursive partitioning analysis (RPA) of a large database. These classes were based on Karnofsky performance status (KPS), primary tumor status, presence of extracranial system metastases, and age. An analysis of RTOG 91-04, a randomized study comparing two dose-fractionation schemes with a comparison to the established RTOG database, was considered important to validate the RPA classes. Methods and Materials: A total of 445 patients were randomized on RTOG 91-04, a Phase III study of accelerated hyperfractionation versus accelerated fractionation. No difference was observed between the two treatment arms with respect to survival. Four hundred thirty-two patients were included in this analysis. The majority of the patients were under age 65, had KPS 70-80, primary tumor controlled, and brain-only metastases. The initial RPA had three classes, but only patients in RPA Classes I and II were eligible for RTOG 91-04. Results: For RPA Class I, the median survival time was 6.2 months and 7.1 months for 91-04 and the database, respectively. The 1-year survival was 29% for 91-04 versus 32% for the database. There was no significant difference in the two survival distributions (p = 0.72). For RPA Class II, the median survival time was 3.8 months for 91-04 versus 4.2 months for the database. The 1-year survival was 12% and 16% for 91-04 and the database,as 12% and 16% for 91-04 and the database, respectively (p = 0.22). Conclusion: This analysis indicates that the RPA classes are valid and reliable for historical comparisons. Both the RTOG and other clinical trial organizers should currently utilize this RPA classification as a stratification factor for clinical trials

  13. RPA and PCNA suppress formation of large deletion errors by yeast DNA polymerase ?

    OpenAIRE

    Fortune, John M.; Stith, Carrie M.; Kissling, Grace E.; Burgers, Peter M. J.; Kunkel, Thomas A.

    2006-01-01

    In fulfilling its biosynthetic roles in nuclear replication and in several types of repair, DNA polymerase ? (pol ?) is assisted by replication protein A (RPA), the single-stranded DNA-binding protein complex, and by the processivity clamp proliferating cell nuclear antigen (PCNA). Here we report the effects of these accessory proteins on the fidelity of DNA synthesis in vitro by yeast pol ?. We show that when RPA and PCNA are included in reactions containing pol ?, rates for single base ...

  14. 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

  15. A new take on v(d)j recombination: transcription driven nuclear and chromatin reorganization in rag-mediated cleavage.

    Science.gov (United States)

    Chaumeil, Julie; Skok, Jane A

    2013-01-01

    It is nearly 30?years since the Alt lab first put forward the accessibility model, which proposes that cleavage of the various antigen receptor loci is controlled by lineage and stage specific factors that regulate RAG access. Numerous labs have since demonstrated that locus opening is regulated at multiple levels that include sterile transcription, changes in chromatin packaging, and alterations in locus conformation. Here we focus on the interplay between transcription and RAG binding in facilitating targeted cleavage. We discuss the results of recent studies that implicate transcription in regulating nuclear organization and altering the composition of resident nucleosomes to promote regional access to the recombinase machinery. Additionally we include new data that provide insight into the role of the RAG proteins in defining nuclear organization in recombining T cells. PMID:24367365

  16. Evaluation in mice of the capillary leak syndrome (CLS) mediated by the systemic administration of recombinant interleukin-2 (IL-2)

    International Nuclear Information System (INIS)

    Since a CLS with interstitial pulmonary edema has been the major toxicity of IL-2 administration in humans, the authors studied this CLS in mice by quantitating the IL-2 mediated, tissue extravasation (Ex) of intravenously injected 125I-bovine serum albumin (BSA). Mice received saline (HBSS) or 200,000 U of IL-2 intraperitoneally thrice daily from day 0-6 before tissues were counted. A permeability index (PI) was calculated by dividing the mean counts per minute (CPM) from tissues of treated mice by those from controls. In a representative experiment, increased BSA Ex was noted in the lungs of mice treated with IL-2 when compared with HBSS (6187 +/- 141 and 638 +/- 64 CPM +/- SEM, respectively; p2 < .001; PI = 9.7). Other tissues with increased BSA Ex included the liver, spleen, kidneys and mesenteric lymph nodes (PI = 6.7, 10.0, 6.3, 6.0, respectively). BSA Ex, which did not occur with the excipient control, was dependent upon the dose and the duration of IL-2. Serial lung weights showed dramatic increases in water weight induced by IL-2. Treatment of mice with radiation (500R), cyclophosphamide, or cortisone acetate significantly reduced IL-2 mediated BSA Ex. Thus, IL-2 induced a generalized CLS which is mediated directly or indirectly by cellular mechanisms

  17. 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

  18. 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

  19. Cre-mediated recombination can induce apoptosis in vivo by activating the p53 DNA damage-induced pathway

    OpenAIRE

    Zhu, Jianjian; Nguyen, Minh-thanh; Nakamura, Eiichiro; Yang, Junming; Mackem, Susan

    2012-01-01

    Cre-mediated apoptosis has been observed in many contexts in mice expressing Cre-recombinase, and can confound the analysis of genetically engineered conditional mutant or transgenic alleles. Several mechanisms have been proposed to explain this phenomenon. We find that the degree of apoptosis induced correlates roughly with the copy number of loxP sites present in the genome and that some level of increased apoptosis accompanies the presence of even only a few loxP sites, as occurs in condit...

  20. 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 (P<0.05). Notably, goats inoculated with rAd-F-H developed significantly higher VNA titers (P<0.05) and stronger cell-mediated immune responses than did goats inoculated with rAd-F or rAd-H alone. The results suggest that the three rAds might be attractive candidate differentiating infected from vaccinated animals (DIVA) vaccines for preventing PPRV infection. Notably, the rAd-F-H expressing F-H fusion protein is likely the most potent candidate of the rAds. PMID:23707075

  1. The lactoferrin receptor may mediate the reduction of eosinophils in the duodenum of pigs consuming milk containing recombinant human lactoferrin.

    Science.gov (United States)

    Cooper, Caitlin; Nonnecke, Eric; Lönnerdal, Bo; Murray, James

    2014-10-01

    Lactoferrin is part of the immune system and multiple tissues including the gastrointestinal (GI) tract, liver, and lung contain receptors for lactoferrin. Lactoferrin has many functions, including antimicrobial, immunomodulatory, and iron binding. Additionally, lactoferrin inhibits the migration of eosinophils, which are constitutively present in the GI tract, and increase during inflammation. Lactoferrin suppresses eosinophil infiltration into the lungs and eosinophil migration in -vitro. Healthy pigs have a large population of eosinophils in their small intestine and like humans, pigs have small intestinal lactoferrin receptors (LFR); thus, pigs were chosen to investigate the effects of consumption of milk containing recombinant human lactoferrin (rhLF-milk) on small intestinal eosinophils and expression of eosinophilic cytokines. In addition, LFR localization was analyzed in duodenum and circulating eosinophils to determine if the LFR could play a role in lactoferrin's ability to inhibit eosinophil migration. In the duodenum there were significantly fewer eosinophils/unit area in pigs fed rhLF-milk compared to pigs fed control milk (p = 0.025); this was not seen in the ileum (p = 0.669). In the duodenum, no differences were observed in expression of the LFR, or any eosinophil migratory cytokines, and the amount of LFR protein was not different (p = 0.386). Immunohistochemistry (IHC) showed that within the duodenum the LFR localized on the brush border of villi, crypts, and within the lamina propria. Circulating eosinophils also contained LFRs, which may be a mechanism allowing lactoferrin to directly inhibit eosinophil migration. PMID:25085595

  2. Phosphorylation and cellular function of the human Rpa2 N-terminus in the budding yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Ghospurkar, Padmaja L; Wilson, Timothy M; Liu, Shengqin; Herauf, Anna; Steffes, Jenna; Mueller, Erica N; Oakley, Gregory G; Haring, Stuart J

    2015-02-01

    Maintenance of genome integrity is critical for proper cell growth. This occurs through accurate DNA replication and repair of DNA lesions. A key factor involved in both DNA replication and the DNA damage response is the heterotrimeric single-stranded DNA (ssDNA) binding complex Replication Protein A (RPA). Although the RPA complex appears to be structurally conserved throughout eukaryotes, the primary amino acid sequence of each subunit can vary considerably. Examination of sequence differences along with the functional interchangeability of orthologous RPA subunits or regions could provide insight into important regions and their functions. This might also allow for study in simpler systems. We determined that substitution of yeast Replication Factor A (RFA) with human RPA does not support yeast cell viability. Exchange of a single yeast RFA subunit with the corresponding human RPA subunit does not function due to lack of inter-species subunit interactions. Substitution of yeast Rfa2 with domains/regions of human Rpa2 important for Rpa2 function (i.e., the N-terminus and the loop 3-4 region) supports viability in yeast cells, and hybrid proteins containing human Rpa2 N-terminal phospho-mutations result in similar DNA damage phenotypes to analogous yeast Rfa2 N-terminal phospho-mutants. Finally, the human Rpa2 N-terminus (NT) fused to yeast Rfa2 is phosphorylated in a manner similar to human Rpa2 in human cells, indicating that conserved kinases recognize the human domain in yeast. The implication is that budding yeast represents a potential model system for studying not only human Rpa2 N-terminal phosphorylation, but also phosphorylation of Rpa2 N-termini from other eukaryotic organisms. PMID:25499885

  3. Tensor hypercontracted ppRPA: Reducing the cost of the particle-particle random phase approximation from O(r 6) to O(r 4)

    Science.gov (United States)

    Shenvi, Neil; van Aggelen, Helen; Yang, Yang; Yang, Weitao

    2014-07-01

    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(r6), the THC-ppRPA algorithm scales asymptotically as only O(r4), 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.

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

    International Nuclear Information System (INIS)

    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(r6), the THC-ppRPA algorithm scales asymptotically as only O(r4), 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

  5. Recombinant arginine deiminase reduces inducible nitric oxide synthase iNOS-mediated neurotoxicity in a coculture of neurons and microglia.

    Science.gov (United States)

    Yu, Hao-Hsin; Wu, Fe-Lin Lin; Lin, Shan-Erh; Shen, Li-Jiuan

    2008-10-01

    Modulation of nitric oxide (NO) production is considered a promising approach to therapy of diseases involving excessive inducible nitric oxide synthase (iNOS) expression, such as certain neuronal diseases. Recombinant arginine deiminase (rADI, EC3.5.3.6) catalyzes the conversion of L-arginine (L-arg), the sole substrate of NOS for NO production, to L-citrulline (L-cit) and ammonia. To understand the effect of the depletion of L-arg by rADI on NO concentration and neuroprotection, a direct coculture of neuron SHSY5Y cells and microglia BV2 cells treated with lipopolysaccharide (LPS) and interferon-gamma (IFN-gamma) was used as a model of iNOS induction. The results showed that rADI preserved cell viability (4-fold higher compared with the cells treated with LPS/IFN-gamma only) by the MTT assay, corresponding with the results of neuronal viability by neuron-specific immunostaining assay. NO production (mean +/- SD) decreased from 67.0 +/- 1.3 to 19.5 +/- 5.5 microM after a 2-day treatment of rADI by the Griess assay; meanwhile, induction of iNOS protein expression by rADI was observed. In addition, rADI substantially preserved the neuronal function of dopamine uptake in the coculture. The replenishment of L-arg in the coculture eliminated the neuroprotective and NO-suppressive effects of rADI in the coculture, indicating that L-arg played a crucial role in the effects of rADI. These results highlight the important role of L-arg in the neuron-microglia coculture in excessive induction of iNOS. Regulation of L-arg by ADI demonstrated that rADI has a potentially therapeutic role in iNOS-related neuronal diseases. PMID:18627024

  6. Nuclear collective excitations using correlated realistic interactions: the role of explicit RPA correlations

    CERN Document Server

    Papakonstantinou, P; Roth, R

    2006-01-01

    We examine to which extent correlated realistic nucleon-nucleon interactions, derived within the Unitary Correlation Operator Method (UCOM), can describe nuclear collective motion in the framework of first-order random-phase approximation (RPA). To this end we employ the correlated Argonne V18 interaction in calculations within the so-called "Extended" RPA (ERPA) and investigate the response of closed-shell nuclei. The ERPA is a renormalized RPA version which considers explicitly the depletion of the Fermi sea due to long-range correlations and thus allows us to examine how these affect the excitation spectra. It is found that the effect on the properties of giant resonances is rather small. Compared to the standard RPA, where excitations are built on top of the uncorrelated Hartree-Fock (HF) ground state, their centroid energies decrease by up to 1 MeV, approximately, in the isovector channel. The isoscalar response is less affected in general. Thus, the disagreement between our previous UCOM-based RPA calcu...

  7. 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

    2011-05-01

    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. Thesein 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

  8. Benchmarking van der Waals functionals with noncontact RPA calculations on graphene-Ag(111)

    Science.gov (United States)

    Lon?ari?, Ivor; Despoja, Vito

    2014-08-01

    We have benchmarked long range behavior of seven different van der Waals functionals comparing them with our ACF-RPA correlation calculations for graphene on a Ag(111) system. Correlation given by the second version of van der Waals density functional vdW-DF2 agrees remarkably well with our random phase approximation (RPA) calculation in the long range region. In the intermediate and shorter range regions combining vdW-DF2 correlation with proper exchange functional becomes important. We compared the results of the van der Waals functionals in this region to the previous RPA calculations and to some extent to experimental observations, and calculated that the combined vdW-DF2(C09x) or rev-vdW-DF2 functionals show satisfactory behavior.

  9. Assays of dioxins and dioxin-like compounds in actually contaminated soils using transgenic tobacco plants carrying a recombinant mouse aryl hydrocarbon receptor-mediated ?-glucuronidase reporter gene expression system

    OpenAIRE

    Inui, Hideyuki; Gion, Keiko; Utani, Yasushi; Wakai, Taketo; Kodama, Susumu; Eun, Heesoo; Kim, Yun-seok; Ohkawa, Hideo

    2012-01-01

    The transgenic tobacco plant XD4V-26 carrying the recombinant mouse aryl hydrocarbon receptor XD4V-mediated ?-glucuronidase (GUS) reporter gene expression system was used for assay of dioxins and dioxin-like compounds consisting of polychlorodibenzo-p-dioxins, polychlorinated dibenzofurans, and coplanar polychlorinated biphenyls (Co-PCBs) in actually contaminated soils. The transgenic tobacco plant XD4V-26 showed a significant dose-dependent induced GUS activity when cultured on MS medium co...

  10. 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...

  11. 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.

  12. 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

  13. Estrogen receptor beta-mediated nuclear interaction between IRS-1 and Rad51 inhibits homologous recombination directed DNA repair in medulloblastoma.

    Science.gov (United States)

    Urbanska, Katarzyna; Pannizzo, Paola; Lassak, Adam; Gualco, Elisa; Surmacz, Eva; Croul, Sidney; Del Valle, Luis; Khalili, Kamel; Reiss, Krzysztof

    2009-05-01

    In medulloblastomas, which are highly malignant cerebellar tumors of the childhood genotoxic treatments such as cisplatin or gamma-irradiation are frequently associated with DNA damage, which often associates with unfaithful DNA repair, selection of new adaptations and possibly tumor recurrences. Therefore, better understanding of molecular mechanisms which control DNA repair fidelity upon DNA damage is a critical task. Here we demonstrate for the first time that estrogen receptor beta (ERbeta) can contribute to the development of genomic instability in medulloblastomas. Specifically, ERbeta was found highly expressed and active in mouse and human medulloblastoma cell lines. Nuclear ERbeta was also present in human medulloblastoma clinical samples. Expression of ERbeta coincided with nuclear translocation of insulin receptor substrate 1 (IRS-1), which was previously reported to interfere with the faithful component of DNA repair when translocated to the nucleus. We demonstrated that ERbeta and IRS-1 bind each other, and the interaction involves C-terminal domain of IRS-1 (aa 931-1233). Following cisplatin-induced DNA damage, nuclear IRS-1 localized at the sites of damaged DNA, and interacted with Rad51--an enzymatic component of homologous recombination directed DNA repair (HRR). In medulloblastoma cells, engineered to express HRR-DNA reporter plasmid, ER antagonist, ICI 182,780, or IRS mutant (931-1233) significantly increased DNA repair fidelity. These data strongly suggest that both molecular and pharmacological interventions are capable of preventing ERbeta-mediated IRS-1 nuclear translocation, which in turn improves DNA repair fidelity and possibly counteracts accumulation of malignant mutations in actively growing medulloblastomas. PMID:19117011

  14. 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

  15. The human recombinant c-kit receptor ligand, rhSCF, induces mediator release from human cutaneous mast cells and enhances IgE-dependent mediator release from both skin mast cells and peripheral blood basophils.

    Science.gov (United States)

    Columbo, M; Horowitz, E M; Botana, L M; MacGlashan, D W; Bochner, B S; Gillis, S; Zsebo, K M; Galli, S J; Lichtenstein, L M

    1992-07-15

    The gene product of the steel locus of the mouse represents a growth factor for murine mast cells and a ligand for the c-kit proto-oncogene receptor, a member of the tyrosine kinase receptor class of oncogenes (for review, see O. N. Witte. 1990. Cell 63:5). We have studied the effect of the human recombinant c-kit receptor ligand stem cell factor (rhSCF) on the release of inflammatory mediators from human skin mast cells and peripheral blood basophils and compared its activity to that of rhIL-3, rhSCF (1 ng/ml to 1 microgram/ml) activated the release of histamine and PGD2 from mast cells isolated from human skin. Analysis by digital video microscopy indicated that purified human skin mast cells (84 +/- 5% pure) responded to rhSCF (0.1 to 1 microgram/ml) challenge with a rapid, sustained rise in intracellular Ca2+ levels that was accompanied by secretion of histamine. A brief preincubation (10 min) of mast cells with rhSCF (0.1 pg/ml to 1 ng/ml) significantly enhanced (100 +/- 35%) the release of histamine induced by anti-IgE (3 micrograms/ml), but was much less effective on IgE-mediated release of PGD2. In contrast, a short term incubation with rhSCF did not potentiate the secretion of histamine activated by substance P (5 microM). A 24-h incubation of mast cells with rhSCF did not affect the release of mediators induced by anti-IgE (3 micrograms/ml), probably due to receptor desensitization, rhSCF (1 ng/ml to 3 micrograms/ml) neither caused release of histamine or leukotriene C4 (LTC4) release from leukocytes of 14 donors, nor induced a rise in intracellular Ca2+ levels in purified (greater than 70%) basophils. Brief preincubation (10 min) of leukocytes with rhSCF (1 ng/ml to 3 micrograms/ml) caused an enhancement (69 +/- 11%) of anti-IgE-induced release of histamine that was significant at concentrations as low as 3 ng/ml (p less than 0.05), whereas it appeared less effective in potentiating IgE-mediated LTC4 release. In contrast, a prolonged incubation (24 h) with rhSCF (0.1 pg/ml to 100 ng/ml) did not enhance the release of histamine or LTC4 induced by anti-IgE (0.1 microgram/ml), whereas rhIL-3 (3 ng/ml) significantly potentiated the release of both mediators.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:1378071

  16. Particle-particle and hole-hole RPA correlations at finite temperature and the temperature dependence of the level density parameter

    International Nuclear Information System (INIS)

    The pp-hh RPA equations obtained by summing the infinite series of ladder, upwards and backwards going diagrams in the temperature two particle Green's functions are derived at finite temperature. The contribution to the thermodynamic grand potential due to pp-hh RPA correlations is calculated simultaneously to that of ph RPA correlations. A schematic model is constructed which shows that, as for ph RPA states, the energies of pp and hh RPA states have no temperature dependence at not too high temperature. Within the same model, the temperature dependence of the level density parameter is discussed

  17. PhaG-mediated synthesis of Poly(3-hydroxyalkanoates) consisting of medium-chain-length constituents from nonrelated carbon sources in recombinant Pseudomonas fragi.

    Science.gov (United States)

    Fiedler, S; Steinbüchel, A; Rehm, B H

    2000-05-01

    Recently, a new metabolic link between fatty acid de novo biosynthesis and biosynthesis of poly(3-hydroxy-alkanoate) consisting of medium-chain-length constituents (C(6) to C(14)) (PHA(MCL)), catalyzed by the 3-hydroxydecanoyl-[acyl-carrier-protein]:CoA transacylase (PhaG), has been identified in Pseudomonas putida (B. H. A. Rehm, N. Krüger, and A. Steinbüchel, J. Biol. Chem. 273:24044-24051, 1998). To establish this PHA-biosynthetic pathway in a non-PHA-accumulating bacterium, we functionally coexpressed phaC1 (encoding PHA synthase 1) from Pseudomonas aeruginosa and phaG (encoding the transacylase) from P. putida in Pseudomonas fragi. The recombinant strains of P. fragi were cultivated on gluconate as the sole carbon source, and PHA accumulation to about 14% of the total cellular dry weight was achieved. The respective polyester was isolated, and GPC analysis revealed a weight average molar mass of about 130,000 g mol(-1) and a polydispersity of 2.2. The PHA was composed mainly (60 mol%) of 3-hydroxydecanoate. These data strongly suggested that functional expression of phaC1 and phaG established a new pathway for PHA(MCL) biosynthesis from nonrelated carbon sources in P. fragi. When fatty acids were used as the carbon source, no PHA accumulation was observed in PHA synthase-expressing P. fragi, whereas application of the beta-oxidation inhibitor acrylic acid mediated PHA(MCL) accumulation. The substrate for the PHA synthase PhaC1 is therefore presumably directly provided through the enzymatic activity of the transacylase PhaG by the conversion of (R)-3-hydroxydecanoyl-ACP to (R)-3-hydroxydecanoyl-CoA when the organism is cultivated on gluconate. Here we demonstrate for the first time the establishment of PHA(MCL) synthesis from nonrelated carbon sources in a non-PHA-accumulating bacterium, employing fatty acid de novo biosynthesis and the enzymes PhaG (a transacylase) and PhaC1 (a PHA synthase). PMID:10788390

  18. Recombinant adeno-associated virus 2-mediated transfer of the human superoxide-dismutase gene does not confer radioresistance on HeLa cervical carcinoma cells

    International Nuclear Information System (INIS)

    Background and purpose: The success rate of any therapeutic approach depends on the therapeutic window, which can be increased by either raising the resistance of the normal tissue without protecting the tumor cells or by sensitizing the tumor cells but not the normal cells. Two promising candidate genes for normal tissue protection against radiation-induced damage may be the copper-zinc (CuZnSOD) and manganese superoxide-dismutase genes (MnSOD). The recombinant adeno-associated virus 2 (rAAV-2) offers attractive advantages over other vector systems: low immunogenicity, ability to infect dividing and non-dividing tissues and a low chance of insertional mutagenesis, due to extra-chromosomal localization. We report the production of novel rAAV-2-SOD vectors and the investigation of their modulating effects on HeLa-RC cells after irradiation. Material and methods: rAAV-2 vectors were cloned containing the human CuZnSOD or MnSOD as transgene and vector stocks were produced. In the initial experiments human cervix carcinoma (HeLa-RC) cells were chosen for their susceptibility to rAAV-2. On day 0, cells were seeded and transduced with the rAAV-2-SOD vectors. On day 3, cells were harvested, irradiated (0.5-8 Gy) and reseeded in different assays (FACS, SOD, MTT and colony assays). Results: Although >70% of all cells expressed SOD and significant amounts of functional SOD protein were detected, no radioprotective effect of SOD was observed after transduction of HeLa-RC cells. rved after transduction of HeLa-RC cells. Conclusions: Novel rAAV-2-SOD vectors that could be produced at high titer, were able to efficiently infect cells and express the SOD genes. The absence of a radioprotective effect in HeLa-RC cancer cells indicates an additional safety feature and suggests that rAAV-mediated MnSOD overexpression might contribute to increasing the therapeutic index when applied for normal tissue protection

  19. Function of Rad51 paralogs in eukaryotic homologous recombinational repair

    International Nuclear Information System (INIS)

    Full text: Homologous recombinational repair (HRR) is an important mechanism for maintaining genetic integrity and cancer prevention by accurately repair of DNA double strand breaks induced by environmental insults or occurred in DNA replication. A critical step in HRR is the polymerization of Rad51 on single stranded DNA to form nuclear protein filaments, the later conduct DNA strand paring and exchange between homologous strands. A number of proteins, including replication protein A (RPA), Rad52 and Rad51 paralogs, are suggested to modulate or facilitate the process of Rad51 filament formation. Five Rad51 paralogs, namely XRCC2, XRCC3, Rad51B, Rad51C and Rad51D have been identified in eucaryotic cells. These proteins show distant protein sequence identity to Rad51, to yeast Rad51 paralogs (Rad55 and Rad57) and to each other. Hamster or chicken mutants of Rad51 paralogs exhibit hypersensitivity to a variety of DNA damaging agents, especially cross-linking agents, and are defective in assembly of Rad51 onto HRR site after DNA damage. Recent data from our and other labs showed that Rad51 paralogs constitute two distinct complexes in cell extracts, one contains XRCC2, Rad51B, Rad51C and Rad51D, and the other contains Rad51C and XRCC3. Rad51C is involved in both complexes. Our results also showed that XRCC3-Rad51C complex interacts with Rad51 in vivo. Furthermore, overexpression of Rad52 can partially suppress the hypersensitivity of XRCC2 mutant irs1 to ionizing radiatiy of XRCC2 mutant irs1 to ionizing radiation and corrected the defects in Rad51 focus formation. These results suggest that XRCC2 and other Rad51 paralogs play a mediator function to Rad51 in the early stage of HRR

  20. Quantum interference terms in nonmesonic weak decay of $\\Lambda$-hypernuclei within a RPA formalism

    CERN Document Server

    Bauer, E

    2007-01-01

    Single and double coincidence nucleon spectra in the $\\Lambda$-hypernuclei weak decay are evaluated and discussed using a microscopic formalism. Nuclear matter is employed together with the local density approximation which allows us to analyze the $^{12}_{\\Lambda}C$ hypernucleus non-mesonic weak decay. Final state interactions (FSI) are included via the first order (in the nuclear residual interaction) terms to the RPA, where the strong residual interaction is modelled by a Bonn potential. At this level of approximation, these FSI are pure quantum interference terms between the primary decay $(\\Lambda N \\to NN)$ and $(\\Lambda N \\to NN \\to NN)$, where the strong interaction is responsible for the last piece in the second reaction. Also the Pauli exchange contributions are explicitly evaluated. We show that the inclusion of Pauli exchange terms is important. A comparison with data is made. We conclude that the limitations in phase space in the RPA makes this approximation inadequate to reproduce the nucleon sp...

  1. Proton-neutron quasiparticle RPA with separable Gamow-Teller forces

    International Nuclear Information System (INIS)

    A comprehensive representation is presented of a generalized form of the proton-neutron quasiparticle RPA model, originally introduced by Halbleib and Sorensen almost thirty years ago. The model uses separable Gamow-Teller forces, including, in addition to the particle-hole force of the former model, the particle-particle force, which is of decisive importance for ?+ decay and ?? decay. The above model has further been extended to the treatment of odd-odd nuclei. An extension is also made to transitions from nuclear excited states. This is essential for calculations of nuclear weak transition rates in the high-temperature interior of massive stars. Complementing the discussion of Halbleib and Sorensen on the particle-hole force, the structure of the RPA dispersion relation is discussed with emphasis on effects of the particle-particle force. (orig.)

  2. Nuclear vorticity in isoscalar E1 modes: Skyrme-RPA analysis

    OpenAIRE

    Reinhard, P. -g; Nesterenko, V. O.; Repko, A.; Kvasil, J.

    2013-01-01

    Two basic concepts of nuclear vorticity, hydrodynamical (HD) and Rawenthall-Wambach (RW), are critically inspected. As a test case, we consider the interplay of irrotational and vortical motion in isoscalar electric dipole E1(T=0) modes in $^{208}$Pb, namely the toroidal and compression modes. The modes are described in a self-consistent random-phase-approximation (RPA) with the Skyrme force SLy6. They are examined in terms of strength functions, transition densities, curren...

  3. The Bogolubov Representation of the Polaron Model and Its Completely Integrable RPA-Approximation

    International Nuclear Information System (INIS)

    The polaron model in ionic crystal is studied in the N. Bogolubov representation using a special RPA-approximation. A new exactly solvable approximated polaron model is derived and described in detail. Its free energy at finite temperature is calculated analytically. The polaron free energy in the constant magnetic field at finite temperature is also discussed. Based on the structure of the N. Bogolubov unitary transformed polaron Hamiltonian a very important new result is stated: the full polaron model is exactly solvable. (author)

  4. The nuclear scissors mode within two approaches (Wigner function moments versus RPA)

    OpenAIRE

    Balbutsev, E. B.; Schuck, P.

    2005-01-01

    Two complementary methods to describe the collective motion, RPA and Wigner function moments 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 here is the subject of our special attention. The exact relation between the variables o...

  5. 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

  6. Self-Consistent Quasi-Particle RPA for the Description of Superfluid Fermi Systems

    CERN Document Server

    Rabhi, A; Chanfray, G; Schuck, P

    2002-01-01

    Self-Consistent Quasi-Particle RPA (SCQRPA) is for the first time applied to a more level pairing case. Various filling situations and values for the coupling constant are considered. Very encouraging results in comparison with the exact solution of the model are obtained. The nature of the low lying mode in SCQRPA is identified. The strong reduction of the number fluctuation in SCQRPA vs BCS is pointed out. The transition from superfluidity to the normal fluid case is carefully investigated.

  7. Angular-momentum projection for Hartree-Fock and RPA with realistic interactions

    International Nuclear Information System (INIS)

    Hartree-Fock (HF) with a Hamiltonian constructed from similarity transformed realistic NN potentials plus 3N contact interactions provides a good starting point for the description of closed shell nuclei. In conjunction with Many-Body-Perturbation-Theory, experimental ground-state energies and radii are well reproduced. To describe collective excitations, the Random-Phase-Approximation (RPA) is the method of choice. Beyond closed shells, e.g. in the sd-shell region, ground-states might exhibit intrinsic deformation, resulting in HF states where angular-momentum ceases to be a good quantum number. Lab-frame observables, like ground-state energies or rotational bands can be recovered from the intrinsic states via angular-momentum projection. We study axially deformed even-even sd-shell nuclei, namely 20Ne, 28Si and 32S. Starting from a HF ground state obtained by exact angular-momentum projection, we use the RPA to study collective excitations. The transition strengths obtained from the RPA are projected to good angular momentum in an exact formalism, without resorting to popular approximations. We investigate the effect of deformed intrinsic states on giant resonances.

  8. Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes

    OpenAIRE

    Yamane, Arito; Resch, Wolfgang; Kuo, Nan; Kuchen, Stefan; Li, Zhiyu; Sun, Hong-wei; Robbiani, Davide F.; Mcbride, Kevin; Nussenzweig, Michel C.; Casellas, Rafael

    2010-01-01

    The cytidine deaminase AID hypermutates immunoglobulin genes but can also target oncogenes, leading to tumorigenesis. The extent of AID’s promiscuity and its predilection for immunoglobulin genes are unknown. We report here that AID interacted broadly with promoter-proximal sequences associated with stalled polymerases and chromatin-activating marks. In contrast, genomic occupancy of replication protein A (RPA), an AID cofactor, was restricted to immunoglobulin genes. The recruitment of RPA...

  9. Longitudinal and transverse form factors of /sup 12/C(e,e') in continuum RPA-SK3 theory

    International Nuclear Information System (INIS)

    The separated structure functions for the reaction /sup 12/C(e,e') in the momentum transfer region 200 MeV/c?q?550 MeV/c are analysed in the frame of a continuum self-consistent RPA theory with a SK3 nucleon-nucleon force. The role of the RPA correlations is pointed out in the comparison with the HF predictions

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

    OpenAIRE

    Hellgren, Maria; Caruso, Fabio; 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 signific...

  11. 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.

  12. Secretion of recombinant archeal lipase mediated by SVP2 signal peptide in Escherichia coli and its optimization by response surface methodology.

    Science.gov (United States)

    Pournejati, Roya; Karbalaei-Heidari, Hamid Reza; Budisa, Nediljko

    2014-09-01

    Towards the targeting of recombinant Thermoanaerobacter thermohydrosulfuricus lipase (TtL) for secretion into the culture medium of Escherichia coli, we have investigated a combination of the archeal lipase gene with a Salinovibrio metalloprotease (SVP2) signal peptide sequence. The SVP2 signal peptide has shown all necessary features of a leader sequence for high level secretion of a recombinant target protein in E. coli. Two sets of primers were designed for amplification of the corresponding gene fragments by PCR. Firstly, the PCR product of the TtL gene with designed restriction sites of SacI and HindIII was cloned into pQE-80L plasmid, named as pQE80L-TtL. Afterwards, the amplified fragment of SVP2 signal peptide with EcoRI and SacI restriction sites was also cloned into pQE80L-TtL and the final construct pQE-STL was obtained. A study on the extracellular expression of recombinant STL revealed that most of the enzyme activity was located in the periplasmic space. Glycine and Triton X-100 were investigated to determine whether the leakage of recombinant STL from the outer membrane was promoted, and it was revealed that glycine has a positive effect. Statistical media optimization design was then applied to optimize the effect of seven factors including glycine, Triton X-100, IPTG, yeast extract concentration, incubation time, induction time, and temperature on the extracellular expression of STL. The optimum conditions for the secretion of the lipase was obtained by incubating recombinant E. coli BL21 cells in the medium supplemented by 1.27% glycine and 24h of incubation in the presence of 0.2mM IPTG concentration. PMID:24907409

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

    Science.gov (United States)

    Wildmann, Norman; Bange, Jens

    2014-05-01

    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 battery- and payload. The standard meteorological payload consists of temperature sensors, a humidity sensor, a flow probe, an inertial measurement unit and a GNSS. 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. Since 2010 the system has been tested and improved intensively. In September 2012 first comparative tests could successfully be performed at the Lindenberg observatory of Germany's National Meteorological Service (DWD). In 2013, several campaigns were done with the system, including fundamental boundary layer research, wind energy meteorology and assistive measurements to aerosol investigations. The results of a series of morning transition experiments in summer 2013 will be presented to demonstrate the capabilities of the measurement system. On several convective days between May and September, vertical soundings were done to record the evolution of the ABL in the early morning, from about one hour after sunrise, until noon. In between the soundings, flight legs of up to 1 km length were performed to measure turbulent statistics and fluxes at a constant altitude. With the help of surface flux measurements of a sonic anemometer, methods of similarity theory could be applied to the RPA flux measurements to compare them to literature. The results show prospects and limitations of boundary layer research with a single RPA at the present state of the art.

  14. The fission yeast RPA51 is a functional homolog of the budding yeast A49 subunit of RNA polymerase I and required for maximizing transcription of ribosomal DNA.

    Science.gov (United States)

    Nakagawa, Kaori; Hisatake, Koji; Imazawa, Yukiko; Ishiguro, Akira; Matsumoto, Masahito; Pape, Louise; Ishihama, Akira; Nogi, Yasuhisa

    2003-06-01

    Saccharomyces cerevisiae A49 and mouse PAF53 are subunits specific to RNA polymerase I (Pol I) in eukaryotes. It has been known that Pol I without A49 or PAF53 maintains non-specific transcription activities but a molecular role(s) of A49 (and PAF53) remains totally unknown. We studied the fission yeast gene encoding a protein of 415 amino acids exhibiting 30% and 19% identities to A49 and PAF53, respectively. We designate the corresponding protein RPA51 and gene encoding it rpa51+ since the gene encodes a Pol I subunit and an apparent molecular mass of the protein is 51 kDa. rpa51+ is required for cell growth at lower but not at higher temperatures and is able to complement S. cerevisiae rpa49Delta mutation, indicating that RPA51 is a functionally-conserved subunit of Pol I between the budding yeast and the fission yeast. Deletion analysis of rpa51+ shows that only two-thirds of the C-terminal region are required for the function. Transcripts analysis in vivo and in vitro shows that RPA51 plays a general role for maximizing transcription of rDNA whereas it is dispensable for non-specific transcription. We also found that RPA51 associates significantly with Pol I in the stationary phase, suggesting that Pol I inactivation in the stationary phase of yeast does not result from the RPA51 dissociation. PMID:12893961

  15. A Remotely Piloted Aircraft (RPA) as a Measurement Tool for Wind-Energy Research

    Science.gov (United States)

    Wildmann, Norman; Bange, Jens

    2014-05-01

    In wind energy meteorology, RPA have the clear advantage compared to manned aircraft that they allow to fly very close to the ground and even in between individual wind turbines in a wind farm. Compared to meteorological towers and lidar systems, the advantage is the flexibility of the system, which makes it possible to measure at the desired site on short notice and not only in main wind direction. At the Center of Applied Geoscience at the University of Tübingen, the research RPA MASC (Multi-purpose Airborne Sensor Carrier) was developed. RPA of type MASC have a wingspan of about 3 m and a maximum take-off weight of 7.5 kg, including payload. The standard meteorological payload includes instruments for temperature, humidity, barometric pressure and wind measurement. It is possible to resolve turbulence fluctuations of wind and temperature up to 20 Hz. The autopilot ROCS (Research Onboard Computer System), which is developed at the Institute of Flight Mechanics and Control, University of Stuttgart, makes it possible to automatically follow predefined waypoints at constant altitude and airspeed. At a cruising speed of 24 m/s and a battery life of approx. one hour, a range of 80 km is feasible. The project 'Lidar Complex', funded by the German Federal Ministry for the Environment, Nature Conservation and Nuclear Safety, is part of the research network 'WindForS', based in Southern Germany. The goal of the project is to establish lidar technology for wind energy plant site evaluation in complex terrain. Additional goals are the comparison of different measurement techniques and the validation of wind-field models in not IEC 61400 conform terrain. It is planned to design a turbulent wind-field generator, fed by real measurement data, which can be used to analyse WEC behaviour. Two test sites were defined for the 'Lidar Complex' project, one in IEC-conform terrain about 15 km from the Baltic Sea, the other in the Swabian Alb, only 2 km downstream of a 100 m steep escarpment. At both sites, flight measurements were performed in 2013 with the RPA MASC. The data that was collected allows to investigate the influence of thermal stability of the atmosphere at the test site and turbulence intensity around individual wind energy converters (WECs). Several measurement flights were done to investigate the wake structure downstream a running WEC. Preliminary results will be presented as well as an outlook for future research with the instrument.

  16. The Bogolubov representation of the polaron model and its completely integrable RPA-approximation

    Directory of Open Access Journals (Sweden)

    N.N.Bogolubov (jr.

    2010-01-01

    Full Text Available The polaron model in ionic crystal is studied in the Bogolubov representation using a special RPA-approximation. A new exactly solvable approximated polaron model is derived and described in detail. Its free energy at finite temperature is calculated analytically. The polaron free energy in the constant magnetic field at finite temperature is also discussed. Based on the structure of the Bogolubov unitary transformed polaron Hamiltonian there is stated a very important new result: the full polaron model is exactly solvable.

  17. Superallowed Fermi transitions in RPA with a relativistic point-coupling energy functional

    CERN Document Server

    Li, Z X; Chen, H; 10.1007/s11433-011-4320-2

    2011-01-01

    The self-consistent random phase approximation (RPA) approach with the residual interaction derived from a relativistic point-coupling energy functional is applied to evaluate the isospin symmetry-breaking corrections {\\delta}c for the 0+\\to0+ superallowed Fermi transitions. With these {\\delta}c values, together with the available experimental ft values and the improved radiative corrections, the unitarity of the Cabibbo-Kobayashi-Maskawa (CKM) matrix is examined. Even with the consideration of uncertainty, the sum of squared top-row elements has been shown to deviate from the unitarity condition by 0.1% for all the employed relativistic energy functionals.

  18. Superallowed Fermi transitions in RPA with a relativistic point-coupling energy functional

    Science.gov (United States)

    Li, Zhaoxi; Yao, Jiangming; Chen, Hong

    2011-06-01

    The self-consistent random phase approximation (RPA) approach with the residual interaction derived from a relativistic point-coupling energy functional is applied to evaluate the isospin symmetry-breaking corrections ? c for the 0+ ? 0+ superallowed Fermi transitions. With these ? c values, together with the available experimental f t values and the improved radiative corrections, the unitarity of the Cabibbo-Kobayashi-Maskawa (CKM) matrix is examined. Even with the consideration of uncertainty, the sum of squared top-row elements has been shown to deviate from the unitarity condition by 0.1% for all the employed relativistic energy functionals.

  19. A full-self-consistent RPA description of the 2??? decay

    International Nuclear Information System (INIS)

    The RPA treatment of a many body Hamiltonian describing the state of even-even nuclei involved in a 2??? decay is revisited. One shows that renormalizing the Gamow-Teller transition operator by accounting for the ground state correlations requires a similar renormalization for the 1+ dipole density operators which results in activating new boson degrees of freedom. Possible consequences on the Ikeda sum rule and the Gamow-Teller transition amplitude are suggested. A numerical application for a two levels model is presented. (author)

  20. 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

  1. 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.

  2. 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.

  3. Photoreactions of 12C, 16O and 40Ca in self-consistent RPA theory. Pt. 1

    International Nuclear Information System (INIS)

    The photoreactions of 12C, 16O and 40Ca from particle threshold up to 80 MeV are analysed in the frame of a self-consistent RPA theory with Skyrme interactions. The excitation of the E1 and E2 giant resonances is shown in the energy continuum by referring to photoabsorption (?,p) and (?,n) decay channels. The calculations are performed with a Skyrme III force for its better founded momentum dependence. Correlations between the nuclear dynamics and the properties of the interaction in the spin-spin channel, momentum and density dependence are pointed out. In this connection, an estimate is made of the MEC contribution included in RPA calculations by using Siegert's theorem in the electric transition operator. The E2 decay in (?,p) and (?,n) channels predicted by the RPA is compared with experimental observations of (?,?'), (?,?), (?,n) and (p,?) reactions. (orig.)

  4. 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

  5. Validation of the RTOG recursive partitioning analysis (RPA) classification for small-cell lung cancer-only brain metastases

    International Nuclear Information System (INIS)

    Purpose: Radiation Therapy Oncology Group (RTOG) developed a prognostic classification based on a recursive partitioning analysis (RPA) of patient pretreatment characteristics from three completed brain metastases randomized trials. Clinical trials for patients with brain metastases generally exclude small-cell lung cancer (SCLC) cases. We hypothesize that the RPA classes are valid in the setting of SCLC brain metastases. Methods and Materials: A retrospective review of 154 SCLC patients with brain metastases treated between April 1983 and May 2005 was performed. RPA criteria used for class assignment were Karnofsky performance status (KPS), primary tumor status (PT), presence of extracranial metastases (ED), and age. Results: Median survival was 4.9 months, with 4 patients (2.6%) alive at analysis. Median follow-up was 4.7 months (range, 0.3-40.3 months). Median age was 65 (range, 42-85 years). Median KPS was 70 (range, 40-100). Number of patients with controlled PT and no ED was 20 (13%) and with ED, 27 (18%); without controlled PT and ED, 34 (22%) and with ED, 73 (47%). RPA class distribution was: Class I: 8 (5%); Class II: 96 (62%); Class III: 51 (33%). Median survivals (in months) by RPA class were: Class I: 8.6; Class II: 4.2; Class III: 2.3 (p = 0.0023). Conclusions: Survivals for SCLC-only brain metastases replicate the results from the RTOG RPA classification. These classes are therefore valid for brain metastases from SCLC, support the inclusion of SCLC patim SCLC, support the inclusion of SCLC patients in future brain metastases trials, and may also serve as a basis for historical comparisons

  6. Prognostic factors in brain metastases: should patients be selected for aggressive treatment according to recursive partitioning analysis (RPA) classes?

    International Nuclear Information System (INIS)

    Purpose: To determine whether or not Radiation Therapy Oncology Group (RTOG) recursive partitioning analysis (RPA) derived prognostic classes for patients with brain metastases are generally applicable and can be recommended as rational strategy for patient selection for future clinical trials. Inclusion of time to non-CNS death as additional endpoint besides death from any cause might result in further valuable information, as survival limitation due to uncontrolled extracranial disease can be explored. Methods: We performed a retrospective analysis of prognostic factors for survival and time to non-CNS death in 528 patients treated at a single institution with radiotherapy or surgery plus radiotherapy for brain metastases. For this purpose, patients were divided into groups with Karnofsky performance status (KPS) 0.05 for RPA class II versus III). However, it was 8.5 months in RPA class II patients with controlled primary tumor, which was found to be the only prognostic factor for time to non-CNS death in patients with KPS ?70%. In patients with KPS <70%, no statistically significant prognostic factors were identified for this endpoint. Conclusions: Despite some differences, this analysis essentially confirmed the value of RPA-derived prognostic classes, as published by the RTOG, when survival was chosen as endpoint. RPA class I patients seem to be most likely to profit from aggressive treatment strategies and should be included in appropriate clinical trials. However, their number appears to be very limited. Considering time to non-CNS death, our results suggest that certain patients in RPA class II also might benefit from increased local control of brain metastases

  7. Intron-mediated recombination may cause a deletion in an alpha 1 type I collagen chain in a lethal form of osteogenesis imperfecta.

    OpenAIRE

    Barsh, G. S.; Roush, C. L.; Bonadio, J.; Byers, P. H.; Gelinas, R. E.

    1985-01-01

    To understand the nature of the mutation in type I collagen genes in cells from an infant with the perinatal lethal form of osteogenesis imperfecta (type II), we cloned and sequenced almost 2 kilobases of a normal alpha 1(I) collagen gene and the corresponding region of a mutant alpha 1(I) gene from cell strain CRL 1262. The mutant gene had undergone recombination between two non-homologous introns, which resulted in the loss of three exons coding for 84 amino acids in the triple-helical doma...

  8. Recombinant adeno-associated virus (rAAV)-mediated expression of a human gamma-globin gene in human progenitor-derived erythroid cells.

    OpenAIRE

    Miller, J. L.; Donahue, R. E.; Sellers, S. E.; Samulski, R. J.; Young, N. S.; Nienhuis, A. W.

    1994-01-01

    Effective gene therapy for the severe hemoglobin (Hb) disorders, sickle-cell anemia and thalassemia, will require an efficient method to transfer, integrate, and express a globin gene in primary erythroid cells. To evaluate recombinant adeno-associated virus (rAAV) for this purpose, we constructed a rAAV vector encoding a human gamma-globin gene (pJM24/vHS432A gamma). Its 4725-nucleotide genome consists of two 180-bp AAV inverted terminal repeats flanking the core elements of hypersensitive s...

  9. Recombining WMAP: Beyond standard recombination

    CERN Document Server

    Bean, R; Silk, J; Bean, Rachel; Melchiorri, Alessandro; Silk, Joe

    2003-01-01

    We place new constraints on sources of ionizing and resonance radiation at the epoch of the recombination process using the recent CMB temperature and polarization spectra coming from 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 like the spectral index and its running. Physically motivated models, like those based on primordial black hole 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.

  10. Mycobacterial recombineering.

    Science.gov (United States)

    Murphy, Kenan C; Papavinasasundaram, Kadamba; Sassetti, Christopher M

    2015-01-01

    The precise knockout or modification of Mycobacterium tuberculosis genes has been critical for the identification of functions important for the growth and pathogenicity of this important bacterium. Schemes have been previously described, using both non-replicating vectors and transducing particles, for the introduction of gene knockout substrates into M. tuberculosis, where the endogenous recombination systems of the host (both homologous and illegitimate) compete for transfer of the modified allele to the chromosome. Recombineering technologies, first introduced in laboratory and pathogenic strains of Escherichia coli over the last 16 years, have been developed for use in M. tuberculosis. Described in this chapter is the use of the mycobacterial Che9c phage RecET recombination system, which has been used to make gene knockouts, reporter fusions, promoter replacements, and single base pair modifications within the M. tuberculosis and M. smegmatis chromosomes at very high frequency. Higher success rates, in a shorter period of time, are routinely observed when recombineering is compared to previously described M. tuberculosis gene knockout protocols. PMID:25779316

  11. Circulating Anti-Wild-Type Adeno-Associated Virus Type 2 (AAV2) Antibodies Inhibit Recombinant AAV2 (rAAV2)-Mediated, but Not rAAV5-Mediated, Gene Transfer in the Brain

    OpenAIRE

    Peden, Carmen S.; Burger, Corinna; Muzyczka, Nicholas; Mandel, Ronald J.

    2004-01-01

    Epidemiological studies report that 80% of the population maintains antibodies (Ab) to wild-type (wt) adeno-associated virus type 2 (AAV2), with 30% expressing neutralizing Ab (NAb). The blood-brain barrier (BBB) provides limited immune privilege to brain parenchyma, and the immune response to recombinant AAV (rAAV) administration in the brain of a naive animal is minimal. However, central nervous system transduction in preimmunized animals remains unstudied. Vector administration may disrupt...

  12. 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.

  13. Implication of RPA32 phosphorylation in S-phase checkpoint signalling at replication forks stalled with aphidicolin in Xenopus egg extracts.

    Science.gov (United States)

    Recolin, Bénédicte; Maiorano, Domenico

    2012-11-01

    Activation of the replication checkpoint relies upon uncoupling of DNA polymerases and helicase activities at replication forks, which in multicellular organism results in production of long stretches of single-stranded DNA bound by the trimeric, single stranded DNA binding protein, the RPA complex. Binding of RPA to this substrate promotes synthesis of replication intermediates that contributes to checkpoint activation by allowing binding of the 9-1-1 checkpoint clamp. The RPA32kDa subunit is also phosphorylated during this process but its role in checkpoint signalling is unclear. Here we have investigated the requirement for RPA32 phosphorylation in checkpoint activation in Xenopus egg extracts. We show that phospho-deficient mutants of RPA32 stimulate checkpoint signalling at replication forks arrested with aphidicolin at both the initiation and the elongation step of DNA replication, without affecting DNA synthesis. In contrast, we show that phospho-mimetic RPA32 mutants do not stimulate checkpoint activation at unwound forks. These results indicate that the hypophosphorylated, replication fork-associated form of RPA32 functions in S-phase-dependent checkpoint signalling at unwound forks in Xenopus egg extracts while RPA32 phosphorylation may be implicated in other pathways such as repair or restart of arrested replication forks. PMID:23047005

  14. Expression, purification and characterization of yeast protein disulfide isomerase produced by a recombinant baculovirus-mediated silkworm, Bombyx mori, pupae expression system.

    Science.gov (United States)

    Wang, Liyun; Shimizu, Yuri; Mizunaga, Takemitsu; Matsumoto, Shogo; Otsuka, Yuzuru

    2008-04-01

    Protein disulfide isomerase (PDI) is a multifunctional polypeptide presents in the endoplasmic reticulum of the cell. Silkworm (Bombyx mori) pupae were used as hosts to produce recombinant PDI (rPDI). The concentration-dependent chaperone activity of rPDI was evidenced by the inhibition of the aggregation of rhodanese. Approximately 297 microg rPDI was purified from a single silkworm pupa. Results of rPDI treated with endoglycosidase H and N-glycanase, PNGase F, indicate that non-N-glycosylated rPDI (occupying 90%) and N-glycosylated rPDI are expressed in the silkworm expression system. The difference in glycosylation between silkworm pupae and yeast is discussed. PMID:17985081

  15. Rapamycin inhibition of baculovirus recombinant (BVr) ribosomal protein S6 kinase (S6K1) is mediated by an event other than phosphorylation

    OpenAIRE

    Beigh Mushtaq A; Showkat Mehvish; ul Hussain Mahboob; Latoo Shafat A; Majeed Sheikh T; Andrabi Khurshid I

    2012-01-01

    Abstract Background Ribosomal protein S6 kinase 1(S6K1) is an evolutionary conserved kinase that is activated in response to growth factors and viral stimuli to influence cellular growth and proliferation. This downstream effector of target of rapamycin (TOR) signaling cascade is known to be directly activated by TOR- kinase mediated hydrophobic motif (HM) phosphorylation at Threonine 412 (T412). Selective loss of this phosphorylation by inactivation of TOR kinase or activation/recruitment of...

  16. 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...

  17. Protective Effect of Recombinant Adeno-Associated Virus 2/8-Mediated Gene Therapy from the Maternal Hyperphenylalaninemia in Offsprings of a Mouse Model of Phenylketonuria

    OpenAIRE

    Jung, Sung-chul; Park, Joo-won; Oh, Hyun-jeong; Choi, Jin-ok; Seo, Kyung-in; Park, Eun-sook; Park, Hae-young

    2008-01-01

    Phenylketonuria (PKU) is an autosomal recessively inherited metabolic disorder caused by a deficiency of phenylalanine hydroxylase (PAH). The accumulation of phenylalanine leads to severe mental and psychomotor retardation, and the fetus of an uncontrolled pregnant female patient presents with maternal PKU syndrome. We have reported previously on the cognitive outcome of biochemical and phenotypic reversal of PKU in a mouse model, Pahenu2, by the AAV serotype 2-mediated gene delivery of a hum...

  18. 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...

  19. Effect of isospin mixing on superallowed Fermi beta decay in self-consistent relativistic RPA approaches

    CERN Document Server

    Liang, Haozhao; Meng, Jie

    2009-01-01

    Self-consistent Random Phase Approximation (RPA) approaches in the relativistic framework are applied to calculate the isospin symmetry-breaking corrections $\\delta_c$ for the $0^+\\to0^+$ superallowed transitions. It is found that the corrections $\\delta_c$ are sensitive to the proper treatments of the Coulomb mean field, but not so much to specific effective interactions. With these corrections $\\delta_c$, the nucleus-independent $\\mathcal{F}t$ values are obtained in combination the experimental $ft$ values in the most recent survey and the improved radiative corrections. It is found that the constancy of the $\\mathcal{F}t$ values is satisfied for all effective interactions employed. Furthermore, the element $V_{ud}$ and unitarity of the Cabibbo-Kobayashi-Maskawa matrix are discussed.

  20. Mammalian Ino80 Mediates Double-Strand Break Repair through Its Role in DNA End Strand Resection ?

    Science.gov (United States)

    Gospodinov, Anastas; Vaissiere, Thomas; Krastev, Dragomir B.; Legube, Gaëlle; Anachkova, Boyka; Herceg, Zdenko

    2011-01-01

    Chromatin modifications/remodeling are important mechanisms by which cells regulate various functions through providing accessibility to chromatin DNA. Recent studies implicated INO80, a conserved chromatin-remodeling complex, in the process of DNA repair. However, the precise underlying mechanism by which this complex mediates repair in mammalian cells remains enigmatic. Here, we studied the effect of silencing of the Ino80 subunit of the complex on double-strand break repair in mammalian cells. Comet assay and homologous recombination repair reporter system analyses indicated that Ino80 is required for efficient double-strand break repair. Ino80 association with chromatin surrounding double-strand breaks suggested the direct involvement of INO80 in the repair process. Ino80 depletion impaired focal recruitment of 53BP1 but did not impede Rad51 focus formation, suggesting that Ino80 is required for the early steps of repair. Further analysis by using bromodeoxyuridine (BrdU)-labeled single-stranded DNA and replication protein A (RPA) immunofluorescent staining showed that INO80 mediates 5?-3? resection of double-strand break ends. PMID:21947284

  1. Mammalian Ino80 mediates double-strand break repair through its role in DNA end strand resection.

    Science.gov (United States)

    Gospodinov, Anastas; Vaissiere, Thomas; Krastev, Dragomir B; Legube, Gaëlle; Anachkova, Boyka; Herceg, Zdenko

    2011-12-01

    Chromatin modifications/remodeling are important mechanisms by which cells regulate various functions through providing accessibility to chromatin DNA. Recent studies implicated INO80, a conserved chromatin-remodeling complex, in the process of DNA repair. However, the precise underlying mechanism by which this complex mediates repair in mammalian cells remains enigmatic. Here, we studied the effect of silencing of the Ino80 subunit of the complex on double-strand break repair in mammalian cells. Comet assay and homologous recombination repair reporter system analyses indicated that Ino80 is required for efficient double-strand break repair. Ino80 association with chromatin surrounding double-strand breaks suggested the direct involvement of INO80 in the repair process. Ino80 depletion impaired focal recruitment of 53BP1 but did not impede Rad51 focus formation, suggesting that Ino80 is required for the early steps of repair. Further analysis by using bromodeoxyuridine (BrdU)-labeled single-stranded DNA and replication protein A (RPA) immunofluorescent staining showed that INO80 mediates 5'-3' resection of double-strand break ends. PMID:21947284

  2. Direct conversion of human fibroblasts into dopaminergic neural progenitor-like cells using TAT-mediated protein transduction of recombinant factors.

    Science.gov (United States)

    Mirakhori, Fahimeh; Zeynali, Bahman; Rassouli, Hassan; Salekdeh, Ghasem Hosseini; Baharvand, Hossein

    2015-04-17

    Recent progress in the generation of induced neural progenitor cells (iNPCs) holds tremendous potential for regenerative medicine. However, a major limitation is the lack of a reliable source for cell replacement therapy in neurological diseases such as Parkinson's disease (PD). Here, we show that the combination of small molecules (SM) and TAT-mediated protein transduction of SOX2 and LMX1a in a 3D sphere culture directly convert human fibroblasts to induced dopaminergic neural progenitor-like cells (iDPCs). The generated iDPCs expressed various NPC markers (SOX2, PAX6, NESTIN, OLIG2) and midbrain progenitor markers (EN1, LMX1a, FOXA2, WNT1) as detected by immunostaining and real-time PCR. Following differentiation, the majority of cells expressed neuronal dopaminergic markers as indicated by co-expression of TH with NURR1, and/or PITX3. We found that SOX2 and LMX1a TAT-mediated protein transduction in the combination of SM could directly convert human fibroblasts to self-renewal iDPCs. In conclusion, to our best knowledge, this is the first report of generation of safe DPCs and may suggest an alternative strategy for cell therapy for the treatment of neurodegenerative disorders. PMID:25767075

  3. 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).

  4. Pig gene knockout by rAAV-mediated homologous recombination: comparison of BRCA1 gene knockout efficiency in Yucatan and Göttingen fibroblasts with slightly different target sequences

    DEFF Research Database (Denmark)

    Luo, Yonglun; Bolund, Lars

    2012-01-01

    In this study, we compared the gene targeting efficiencies of two rAAV-BRCA1 KO targeting constructs in Yucatan and Göttingen minipig fibroblasts. The homology arms of the constructs consisted exclusively of exonic sequences amplified by PCR from Yucatan genomic DNA. The sequences were identical to those of the reference porcine genome of a Duroc sow (Ensembl Susscrofa 9) and the BRCA1 gene of the Landrace breed (NCBI acc. no. AB271921). Surprisingly, we found that the very efficient gene targeting observed for Yucatan fibroblasts (35% targeting efficiency) was completely absent using either of the two constructs in Göttingen fibroblasts. Sequencing of the relevant BRCA1 exon 11 region (~2 kb) in the Göttingen minipig revealed three single nucleotide differences in the sequence targeted by the left homology arm of the construct (0.3% of the bases) and three or seven in the two right homology regions (0.3 or 0.7% of the bases, respectively). Construction of a novel rAAV-BRCA1 targeting vector based on the Göttingen genomic DNA sequence re-established gene targeting although the efficiency was somewhat lower than that observed for Yucatan fibroblasts. These BRCA1 KO Göttingen fibroblast clones have been used as nuclear donor cells for somatic cell nuclear transfer to generate a Göttingen BRCA1 KO pig model as previously done with the Yucatan breed. The present study illustrates that even a few mismatches present in the homology arms of an efficient rAAV-targeting construct can completely abolish gene targeting by homologous recombination emphasizing the importance of using isogenic DNA even for creating targeting constructs consisting of exon sequences only.

  5. 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)

  6. 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).

  7. Operation of an efficient site-specific recombination system of Zygosaccharomyces rouxii in tobacco cells.

    OpenAIRE

    Onouchi, H.; Yokoi, K.; Machida, C.; Matsuzaki, H.; Oshima, Y.; Matsuoka, K.; Nakamura, K.; Machida, Y.

    1991-01-01

    Recombinase encoded by the R gene of pSR1 of Zygosaccharomyces rouxii mediates reciprocal recombination between two specific recombination sites (RSs) to induce excision or inversion of the DNA segment that is flanked by the RSs. We report here that site-specific recombination mediated by this system takes place effeciently in tobacco cells. To monitor the recombination events in tobacco cells, we have constructed two types of cryptic beta-glucuronidase reporter gene in such a way that recomb...

  8. 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.

  9. Restriction-Stimulated Homologous Recombination of Plasmids by the Rece Pathway of Escherichia Coli

    OpenAIRE

    Nussbaum, A.; Shalit, M.; Cohen, A.

    1992-01-01

    To test the double-strand break (DSB) repair model in recombination by the RecE pathway of Escherichia coli, we constructed chimeric phages that allow restriction-mediated release of linear plasmid substrates of the bioluminescence recombination assay in infected EcoRI(+) cells. Kinetics of DSB repair and expression of recombination products were followed by Southern hybridization and by the bioluminescence recombination assay, respectively. Plasmid recombinants were analyzed with restriction...

  10. 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

  11. 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...

  12. Generation of Modified Pestiviruses by Targeted Recombination

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Friis, Martin Barfred

    Infectious cDNA clones are a prerequisite for directed genetic manipulation of pestivirus RNA genomes. We have developed a novel strategy to facilitate manipulation and rescue of modified pestiviruses from infectious cDNA clones based on bacterial artificial chromosomes (BACs). The strategy involves targeted modification of viral cDNA genomes, cloned within BACs, by Red/ET recombination-mediated mutagenesis in E.coli DH10B cells. Using recombination-mediated mutagenesis for the targeted design, the work can be expedited and focused in principal on any sequence within the viral genome and hence is not limited to the use of internal restriction sites. Rescue of modified pestiviruses can be obtained by electroporation of cell cultures with full-length RNA transcripts in vitro transcribed from the recombined BAC clones. We have used this approach to generate a series of new pestivirus BACs modified within different genomic regions and infectious pestiviruses have been rescued from several of these new constructs,demonstrating that recombination-mediated mutagenesis of pestivirus BACs provides a useful tool for expediting the construction of recombinant pestiviruses.

  13. Recursive partitioning analysis (RPA) of prognostic factors in three radiation therapy oncology group (RTOG) brain metastases trials

    International Nuclear Information System (INIS)

    Purpose/Objective: Promising results from new approaches such as radiosurgery or stereotactic radiosurgery 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 RTOG brain metastases studies was considered necessary to fully evaluate the benefit of these new interventions. Materials and Methods: 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 pre-treatment characteristics and three treatment-related variables were analyzed. Results: Many factors such as total dose (? 52 Gy vs < 52 Gy), prior surgery (yes vs no), site of origin (breast vs lung vs others), and tumor response (complete or partial response vs stable or progressive disease) were identified as prognostic factors on univariate analysis but did not retain statistical significance with RPA. According to the RPA tree, the best survival (median 7.1 months) was observed in patients less than 65 years of age with a 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) wThe 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 stages: Stage I- patients with KPS ? 70, less than 65 yrs of age with controlled primary and no extracranial metastases; Stage III- KPS < 70; Stage II- all others. Using these stages, new treatment techniques can be tested on homogeneous patient groups

  14. Recursive partitioning analysis (RPA) class does not predict survival in patients with four or more brain metastases

    International Nuclear Information System (INIS)

    Background: We evaluated prognostic factors for survival in patients with four or more brain metastases in order to determine whether intense local treatment might be justified for some of them. If up to three brain metastases are present, surgical resection or radiosurgery are currently being considered in case of favorable prognostic factors. Patients and Methods: Retrospective intention-to-treat analysis of 113 patients who underwent whole-brain radiotherapy without surgical resection or radiosurgery at a single institution. Standard treatment was given with ten fractions of 3 Gy. Higher total doses were administered in 13% of patients. Recursive partitioning analysis (RPA) prognostic classes have been described by the radiation therapy oncology group (RTOG) in 1997 (class I: Karnofsky performance status [KPS] ? 70%, age ? 65 years, no extracranial metastases, controlled primary tumor; class III: KPS 50 years, p = 0.05). St0 years vs > 50 years, p = 0.05). Strong trends were found for KPS, extracranial metastases, control of the primary tumor, and breast primary tumor. Number of brain metastases, RPA class, and treatment-related factors such as total dose or remission of brain metastases had no appreciable influence on survival (Figure 1). Multivariate analysis failed to identify any significant prognostic factor. Conclusions: Patients with four or more brain metastases seem to represent a group with unfavorable prognosis where remission of brain metastases or administration of more than 30 Gy were not associated with increased survival. The number of patients in RPA class I was too small to draw final conclusions. However, there was absolutely no survival difference between patients in class II (median survival 3.6 months) and III (median 4.2 months). (orig.)

  15. Cre-mediated recombination in pituitary somatotropes

    OpenAIRE

    Nasonkin, Igor O.; Potok, Mary Anne; Camper, Sally A.

    2009-01-01

    We report a transgenic line with highly penetrant cre recombinase activity in the somatotrope cells of the anterior pituitary gland. Expression of the cre transgene is under the control of the locus control region of the human growth hormone gene cluster and the rat growth hormone promoter. Cre recombinase activity was assessed with two different lacZ reporter genes that require excision of a floxed stop sequence for expression: a chick ?-actin promoter with the CMV enhancer transgene and a ...

  16. PRODUCTION OF RECOMBINANT PROTEINS IN INSECT CELLS

    Directory of Open Access Journals (Sweden)

    Christian Kollewe

    2013-01-01

    Full Text Available Among the wide range of methods and expression hosts available for the heterologous production of recombinant proteins, insect cells are ideal for the production of complex proteins requiring extensive post-translational modification. This review article provides an overview of the available insect-cell expression systems and their properties, focusing on the widely-used Baculovirus Expression Vector System (BEVS. We discuss the different strategies used to generate recombinant baculovirus vectors and show how advanced techniques for virus titer determination can accelerate the production of recombinant proteins. The stable transfection of insect cells is an alternative to BEVS which has recently been augmented with recombinase-mediated cassette exchange for site-specific gene integration. We consider the advantages and limitations of these techniques for the production of recombinant proteins in insect cells and compare them to other expression platforms.

  17. Recursive partitioning analysis (RPA) class does not predict survival in patients with four or more brain metastases

    Energy Technology Data Exchange (ETDEWEB)

    Nieder, C.; Andratschke, N.; Grosu, A.L.; Molls, M. [Dept. of Radiotherapy and Radiologic Oncology, Klinikum rechts der Isar, Technical Univ. of Munich (Germany)

    2003-01-01

    Background: We evaluated prognostic factors for survival in patients with four or more brain metastases in order to determine whether intense local treatment might be justified for some of them. If up to three brain metastases are present, surgical resection or radiosurgery are currently being considered in case of favorable prognostic factors. Patients and Methods: Retrospective intention-to-treat analysis of 113 patients who underwent whole-brain radiotherapy without surgical resection or radiosurgery at a single institution. Standard treatment was given with ten fractions of 3 Gy. Higher total doses were administered in 13% of patients. Recursive partitioning analysis (RPA) prognostic classes have been described by the radiation therapy oncology group (RTOG) in 1997 (class I: Karnofsky performance status [KPS] {>=} 70%, age {<=} 65 years, no extracranial metastases, controlled primary tumor; class III: KPS < 70%; class II: others). Results: Median number of brain metastases was six (four to 50). Most patients (69%) had extracranial metastases as well. Criteria of RPA Class I (II) were met in 4% (41%), whereas 56% had KPS < 70% and thus were grouped into class III (Tables 1 and 2). Complete or partial remission of brain metastases was found in 46% of patients who underwent computed tomography. Median survival was 4 months, 1-year survival rate 15%. Only age was a borderline significant prognostic factor in univariate analysis ({<=} 50 years vs > 50 years, p = 0.05). Strong trends were found for KPS, extracranial metastases, control of the primary tumor, and breast primary tumor. Number of brain metastases, RPA class, and treatment-related factors such as total dose or remission of brain metastases had no appreciable influence on survival (Figure 1). Multivariate analysis failed to identify any significant prognostic factor. Conclusions: Patients with four or more brain metastases seem to represent a group with unfavorable prognosis where remission of brain metastases or administration of more than 30 Gy were not associated with increased survival. The number of patients in RPA class I was too small to draw final conclusions. However, there was absolutely no survival difference between patients in class II (median survival 3.6 months) and III (median 4.2 months). (orig.)

  18. The Structure of the yFACT Pob3-M Domain, Its Interaction with the DNA Replication Factor RPA, and a Potential Role in Nucleosome Deposition

    Energy Technology Data Exchange (ETDEWEB)

    VanDemark,A.; Blanksma, M.; Ferris, E.; Heroux, A.; Hill, C.; Formosa, T.

    2006-01-01

    We report the crystal structure of the middle domain of the Pob3 subunit (Pob3-M) of S. cerevisiae FACT (yFACT, facilitates chromatin transcription), which unexpectedly adopts an unusual double pleckstrin homology (PH) architecture. A mutation within a conserved surface cluster in this domain causes a defect in DNA replication that is suppressed by mutation of replication protein A (RPA). The nucleosome reorganizer yFACT therefore interacts in a physiologically important way with the central single-strand DNA (ssDNA) binding factor RPA to promote a step in DNA replication. Purified yFACT and RPA display a weak direct physical interaction, although the genetic suppression is not explained by simple changes in affinity between the purified proteins. Further genetic analysis suggests that coordinated function by yFACT and RPA is important during nucleosome deposition. These results support the model that the FACT family has an essential role in constructing nucleosomes during DNA replication, and suggest that RPA contributes to this process.

  19. Identifying Recombination Hot Spots in the HIV-1 Genome

    Science.gov (United States)

    Smyth, Redmond P.; Schlub, Timothy E.; Grimm, Andrew J.; Waugh, Caryll; Ellenberg, Paula; Chopra, Abha; Mallal, Simon; Cromer, Deborah

    2014-01-01

    ABSTRACT HIV-1 infection is characterized by the rapid generation of genetic diversity that facilitates viral escape from immune selection and antiretroviral therapy. Despite recombination's crucial role in viral diversity and evolution, little is known about the genomic factors that influence recombination between highly similar genomes. In this study, we use a minimally modified full-length HIV-1 genome and high-throughput sequence analysis to study recombination in gag and pol in T cells. We find that recombination is favored at a number of recombination hot spots, where recombination occurs six times more frequently than at corresponding cold spots. Interestingly, these hot spots occur near important features of the HIV-1 genome but do not occur at sites immediately around protease inhibitor or reverse transcriptase inhibitor drug resistance mutations. We show that the recombination hot and cold spots are consistent across five blood donors and are independent of coreceptor-mediated entry. Finally, we check common experimental confounders and find that these are not driving the location of recombination hot spots. This is the first study to identify the location of recombination hot spots between two similar viral genomes with great statistical power and under conditions that closely reflect natural recombination events among HIV-1 quasispecies. IMPORTANCE The ability of HIV-1 to evade the immune system and antiretroviral therapy depends on genetic diversity within the viral quasispecies. Retroviral recombination is an important mechanism that helps to generate and maintain this genetic diversity, but little is known about how recombination rates vary within the HIV-1 genome. We measured recombination rates in gag and pol and identified recombination hot and cold spots, demonstrating that recombination is not random but depends on the underlying gene sequence. The strength and location of these recombination hot and cold spots can be used to improve models of viral dynamics and evolution, which will be useful for the design of robust antiretroviral therapies. PMID:24371048

  20. Nuclear dissipation as damping of collective motion in the time-dependent RPA and extensions of it

    International Nuclear Information System (INIS)

    We have formulated a nonperturbative, microscopic dissipative process in the limit of an infinite mean free path which does not require any statistical assumptions. It attributes the damping of the collective motion to real transitions from the collective state to degenerate, more complicated nucelar states. The dissipation is described through wave packets which solve an approximate Schroedinger equation within extended subspaces, larger than the original subspace of the undamped motion. When the simple RPA is used, this process associates the dissipation with the escape width for direct particle emission. When the Second RPA is used, it associates the dissipation with the spreading width for transitions to the 2p-2h components of the nuclear compound states. The energy loss rate for sharp n-phonon initial states is proportional to the total collective energy. The classical dissipation, however, is obtained for coherent, multiphonon, initial packets which describe the damping of the mean field oscillations, and allow a theoretical connection with the Vibrating Potential Model, and thereby with models of one-body dissipation. The present model contrasts with linear response theories. Canonical coordinates for the collective degree of freedom are explicitly introduced. This allows the construction of a nonlinear frictional Hamiltonian which provides a connection with quantal friction. The dissipation process developed here is properly reversible rather than irreversible, in the sense that it is described by an approximate Schroedinger equation which honors time reversibility, rather than by a coarse grained master equation which violates it. Thus, the present theory contrasts with transport theories

  1. 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...

  2. The SIOD disorder protein SMARCAL1 is an RPA-interacting protein involved in replication fork restart

    Science.gov (United States)

    Ciccia, Alberto; Bredemeyer, Andrea L.; Sowa, Mathew E.; Terret, Marie-Emilie; Jallepalli, Prasad V.; Harper, J. Wade; Elledge, Stephen J.

    2009-01-01

    The integrity of genomic DNA is continuously challenged by the presence of DNA base lesions or DNA strand breaks. Here we report the identification of a new DNA damage response protein, SMARCAL1 (SWI/SNF-related, matrix associated, actin-dependent regulator of chromatin, subfamily a-like 1), which is a member of the SNF2 family and is mutated in Schimke immunoosseous dysplasia (SIOD). We demonstrate that SMARCAL1 directly interacts with Replication protein A (RPA) and is recruited to sites of DNA damage in an RPA-dependent manner. SMARCAL1-depleted cells display sensitivity to DNA-damaging agents that induce replication fork collapse, and exhibit slower fork recovery and delayed entry into mitosis following S-phase arrest. Furthermore, SIOD patient fibroblasts reconstituted with SMARCAL1 exhibit faster cell cycle progression after S-phase arrest. Thus, the symptoms of SIOD may be caused, at least in part, by defects in the cellular response to DNA replication stress. PMID:19793862

  3. Range-separated approach to the RPA correlation applied to van der Waals bond and to diffusion of defects

    Science.gov (United States)

    Bruneval, Fabien

    2013-03-01

    The Random Phase Approximation (RPA) is a promising approximation to the exchange-correlation energy of Density Functional Theory (DFT), since it contains the van der Waals (vdW) interaction and yields a potential with the correct band gap. However, its calculation is computationally very demanding. We apply a range separation concept [1] to RPA and demonstrate how it drastically speeds up the calculations without loss of accuracy. The scheme is succesfully applied to a layered system subjected to weak vdW attraction and to address the controversy of the self-diffusion in silicon [2]. We calculate the formation and migration energies of self-interstitials and vacancies taking into account atomic relaxations. The obtained activation energies deviate significantly from the earlier calculations that were affected by the band gap problem and challenge some of the experimental interpretations [3]: the diffusion of vacancies and interstitials have almost the same activation energy.[4pt] [1] J. Toulouse, F. Colonna, and A. Savin, Phys. Rev. A 70, 062505 (2004).[0pt] [2] F. Bruneval, Phys. Rev. Lett. 108, 256403 (2012).[0pt] [3] H. Bracht, E. E. Haller, and R. Clark-Phelps, Phys. Rev. Lett. 81, 393 (1998).

  4. 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.

  5. Efficient gene activation in mammalian cells by using recombinant adenovirus expressing site-specific Cre recombinase.

    OpenAIRE

    Kanegae, Y.; Lee, G.; Sato, Y.; Tanaka, M.; Nakai, M.; Sakaki, T.; Sugano, S.; Saito, I.

    1995-01-01

    A recombinant adenovirus (Ad) expressing Cre recombinase derived from bacteriophage P1 was constructed. To assay the Cre activity in mammalian cells, another recombinant Ad bearing an on/off-switching reporter unit, where a LacZ-expression unit can be activated by the Cre-mediated excisional deletion of an interposed stuffer DNA, was also constructed. Co-infection experiments together with the Cre-expressing and the reporter recombinant Ads showed that the Cre-mediated switching of gene expre...

  6. Telomere Recombination Preferentially Occurs at Short Telomeres in Telomerase-Null Type II Survivors

    OpenAIRE

    Fu, Xiao-hong; Duan, Yi-min; Liu, Yu-ting; Cai, Chen; Meng, Fei-long; Zhou, Jin-qiu

    2014-01-01

    In telomerase negative yeast cells, Rad52-dependent recombination is activated to maintain telomeres. This recombination-mediated telomere elongation usually involves two independent pathways, type I and type II, and leads to generation of type I and type II survivors. It remains elusive whether the recombination-mediated telomere elongation prefers to take place on shorter or longer telomeres. In this study, we exploited the de novo telomere addition system to examine the telomere recombinat...

  7. Multiprotein complex between the GPI-anchored CyRPA with PfRH5 and PfRipr is crucial for Plasmodium falciparum erythrocyte invasion.

    Science.gov (United States)

    Reddy, K Sony; Amlabu, Emmanuel; Pandey, Alok K; Mitra, Pallabi; Chauhan, Virander S; Gaur, Deepak

    2015-01-27

    Erythrocyte invasion by Plasmodium falciparum merozoites is a highly intricate process in which Plasmodium falciparum reticulocyte binding-like homologous protein 5 (PfRH5) is an indispensable parasite ligand that binds with its erythrocyte receptor, Basigin. PfRH5 is a leading blood-stage vaccine candidate because it exhibits limited polymorphisms and elicits potent strain-transcending parasite neutralizing antibodies. However, the mechanism by which it is anchored to the merozoite surface remains unknown because both PfRH5 and the PfRH5-interacting protein (PfRipr) lack transmembrane domains and GPI anchors. Here we have identified a conserved GPI-linked parasite protein, Cysteine-rich protective antigen (CyRPA) as an interacting partner of PfRH5-PfRipr that tethers the PfRH5/PfRipr/CyRPA multiprotein complex on the merozoite surface. CyRPA was demonstrated to be GPI-linked, localized in the micronemes, and essential for erythrocyte invasion. Specific antibodies against the three proteins successfully detected the intact complex in the parasite and coimmunoprecipitated the three interacting partners. Importantly, full-length CyRPA antibodies displayed potent strain-transcending invasion inhibition, as observed for PfRH5. CyRPA does not bind with erythrocytes, suggesting that its parasite neutralizing antibodies likely block its critical interaction with PfRH5-PfRipr, leading to a blockade of erythrocyte invasion. Further, CyRPA and PfRH5 antibody combinations produced synergistic invasion inhibition, suggesting that simultaneous blockade of the PfRH5-Basigin and PfRH5/PfRipr/CyRPA interactions produced an enhanced inhibitory effect. Our discovery of the critical interactions between PfRH5, PfRipr, and the GPI-anchored CyRPA clearly defines the components of the essential PfRH5 adhesion complex for P. falciparum erythrocyte invasion and offers it as a previously unidentified potent target for antimalarial strategies that could abrogate formation of the crucial multiprotein complex. PMID:25583518

  8. 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...

  9. 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

  10. Preparation and topology of the Mediator middle module

    OpenAIRE

    Koschubs, Tobias; Lorenzen, Kristina; Baumli, Sonja; Sandstro?m, Saana; Heck, Albert J. R.; Cramer, Patrick

    2010-01-01

    Mediator is the central coactivor complex required for regulated transcription by RNA polymerase (Pol) II. Mediator consists of 25 subunits arranged in the head, middle, tail and kinase modules. Structural and functional studies of Mediator are limited by the availability of protocols for the preparation of recombinant modules. Here, we describe protocols for obtaining pure endogenous and recombinant complete Mediator middle module from Saccharomyces cerevisiae that consists of seven subunits...

  11. 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 storage and release of liquid reagents, reconstitution of lyophilized reagents, aliquoting the sample into monitoring systems. PMID:20300675

  12. 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.

  13. {sup 10-11}Li and {sup 13-14}Be studied by projectile fragmentation and pp-RPA

    Energy Technology Data Exchange (ETDEWEB)

    Blanchon, G; Bonaccorso, A [Istituto Nazionale di Fisica Nucleare, Sez. di Pisa, Largo Pontecorvo 3, 56127 Pisa (Italy); Brink, D M [Department of Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Mau, N Vinh, E-mail: bonac@df.unipi.i [Institut de Physique Nucleaire, IN2P3-CNRS, F-91406, Orsay Cedex (France)

    2010-01-01

    The level ordering in the unbound nuclei {sup 10}Li and {sup 13}Be is established on a firm basis using a time dependent projectile fragmentation model, comparing to experimental data and using structure inputs obtained from a semi-phenomenological core-vibration coupling model of two-neutron halo nuclei. The information on the shell ordering corresponds to the understanding of the neutron-core interaction. This is a building block of any three body model of borromean nuclei. As a consistency test we show that the energy spectra of some Beryllium isotopes obtained by using pp-RPA predict the same shell ordering as extracted from the reaction model vs. data analysis and that the well known structure of {sup 11}Li is reproduced.

  14. Recombination and peak jumping

    OpenAIRE

    Crona, Kristina

    2014-01-01

    We find an advantage of recombination for a category of complex fitness landscapes. Recent studies of empirical fitness landscapes reveal complex gene interactions and multiple peaks, and recombination can be a powerful mechanism for escaping suboptimal peaks. However classical work on recombination largely ignores the effect of complex gene interactions. The advantage we find has no correspondence for 2-locus systems or for smooth landscapes. The effect is sometimes extreme...

  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. 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...

  17. Genetic recombination in Micromonospora.

    Science.gov (United States)

    Beretta, M; Betti, M; Polsinelli, M

    1971-08-01

    Biochemical mutants were obtained from Micromonospora chalcea, M. purpurea, and M. echinospora by using ultraviolet radiation or nitrosoguanidine. Crosses carried out between complementary nutritional mutants of the same species showed positive genetic interaction. Data are reported which indicate that the interaction between the crossed strains is due to genetic recombination. No evidence for interspecific genetic recombination was found. PMID:5113596

  18. Oxygen-hydrogen recombiner

    International Nuclear Information System (INIS)

    Purpose: To improve the oxygen-hydrogen removing performance, as well as enable to maintain the high performance in a range of increasing the processing gas flow rate within a recombiner with the reduced pressure and reduced amount of charged catalyst. Constitution: A plate-like metal catalyst comprising alumina added as a binder to the surface of a sponge-like metal support made of nickel-chromium alloy and particles of platinum type novel metal such as platinum or palladium having a catalytic activity supported on alumina is contained in a cartridge and filled within an oxygen-hydrogen recombiner. The recombiner is adapted so that the exhaust gas flow rate therein is within a range from 1 nm/sec to 4 nm/sec. It is possible with such a constitution to improve the recombining performance, reduce the pressure loss, decrease the size of the recombiner and facilitate the maintenance and check thereof. (Kawakami, Y.)

  19. Chi-Stimulated Recombination between Phage ? and the Plasmid ?dv

    OpenAIRE

    Stahl, Franklin W.; Stahl, Mary M.; Young, Lisa; Kobayashi, Ichizo

    1982-01-01

    Chi promotes Rec-mediated recombination between phage ? DNA and the homologous plasmid ?dv. In the absence of Chi, some of the interactions splice ?dv into ?, whereas others patch information from ?dv into ?. When Chi is in the phage DNA, splices and patches are increased in frequency by the same factor. This result strengthens the analogy between Chi and recombination-promoting elements in fungi. It also rules out one model for the previously reported orientation dependence of Chi phen...

  20. Recombinant adeno-associated virus-mediated high-efficiency, transient expression of the murine cationic amino acid transporter (ecotropic retroviral receptor) permits stable transduction of human HeLa cells by ecotropic retroviral vectors.

    OpenAIRE

    Bertran, J.; Miller, J. L.; Yang, Y.; Fenimore-justman, A.; Rueda, F.; Vanin, E. F.; Nienhuis, A. W.

    1996-01-01

    Adeno-associated virus has a broad host range, is nonpathogenic, and integrates into a preferred location on chromosome 19, features that have fostered development of recombinant adeno-associated viruses (rAAV) as gene transfer vectors for therapeutic applications. We have used an rAAV to transfer and express the murine cationic amino acid transporter which functions as the ecotropic retroviral receptor, thereby rendering human cells conditionally susceptible to infection by an ecotropic retr...

  1. A PHF8 Homolog in C. elegans Promotes DNA Repair via Homologous Recombination.

    Science.gov (United States)

    Lee, Changrim; Hong, Seokbong; Lee, Min Hye; Koo, Hyeon-Sook

    2015-01-01

    PHF8 is a JmjC domain-containing histone demethylase, defects in which are associated with X-linked mental retardation. In this study, we examined the roles of two PHF8 homologs, JMJD-1.1 and JMJD-1.2, in the model organism C. elegans in response to DNA damage. A deletion mutation in either of the genes led to hypersensitivity to interstrand DNA crosslinks (ICLs), while only mutation of jmjd-1.1 resulted in hypersensitivity to double-strand DNA breaks (DSBs). In response to ICLs, JMJD-1.1 did not affect the focus formation of FCD-2, a homolog of FANCD2, a key protein in the Fanconi anemia pathway. However, the dynamic behavior of RPA-1 and RAD-51 was affected by the mutation: the accumulations of both proteins at ICLs appeared normal, but their subsequent disappearance was retarded, suggesting that later steps of homologous recombination were defective. Similar changes in the dynamic behavior of RPA-1 and RAD-51 were seen in response to DSBs, supporting a role of JMJD-1.1 in homologous recombination. Such a role was also supported by our finding that the hypersensitivity of jmjd-1.1 worms to ICLs was rescued by knockdown of lig-4, a homolog of Ligase 4 active in nonhomologous end-joining. The hypersensitivity of jmjd-1.1 worms to ICLs was increased by rad-54 knockdown, suggesting that JMJD-1.1 acts in parallel with RAD-54 in modulating chromatin structure. Indeed, the level of histone H3 Lys9 tri-methylation, a marker of heterochromatin, was higher in jmjd-1.1 cells than in wild-type cells. We conclude that the histone demethylase JMJD-1.1 influences homologous recombination either by relaxing heterochromatin structure or by indirectly regulating the expression of multiple genes affecting DNA repair. PMID:25853498

  2. Dissociative recombination in aeronomy

    Science.gov (United States)

    Fox, J. L.

    1989-01-01

    The importance of dissociative recombination in planetary aeronomy is summarized, and two examples are discussed. The first is the role of dissociative recombination of N2(+) in the escape of nitrogen from Mars. A previous model is updated to reflect new experimental data on the electronic states of N produced in this process. Second, the intensity of the atomic oxygen green line on the nightside of Venus is modeled. Use is made of theoretical rate coefficients for production of O (1S) in dissociative recombination from different vibrational levels of O2(+).

  3. Non-parallel recombination limits Cre-LoxP-based reporters as precise indicators of conditional genetic manipulation

    OpenAIRE

    Liu, Jing; Willet, Spencer G.; Bankaitis, Eric D.; Xu, Yanwen; Wright, Chris; Gu, Guoqiang

    2013-01-01

    Cre/LoxP-mediated recombination allows for conditional gene activation or inactivation. When combined with an independent lineage-tracing reporter allele, this technique traces the lineage of presumptive genetically modified Cre-expressing cells. Several studies have suggested that floxed alleles have differential sensitivities to Cre-mediated recombination, which raises concerns regarding utilization of common Cre-reporters to monitor recombination of other floxed loci of interest. Here, we ...

  4. Cytotoxic T cells specific for a single peptide on the M2 protein of respiratory syncytial virus are the sole mediators of resistance induced by immunization with M2 encoded by a recombinant vaccinia virus.

    OpenAIRE

    Kulkarni, A. B.; Collins, P. L.; Bacik, I.; Yewdell, J. W.; Bennink, J. R.; Crowe, J. E.; Murphy, B. R.

    1995-01-01

    We have studied the immunobiology of respiratory syncytial virus (RSV), a major cause of respiratory tract morbidity in children. As part of these studies, it was previously found that immunization of BALB/c (H-2d) mice with a recombinant vaccinia virus (rVV) which encoded the M2 protein of RSV provided complete protection against infection with RSV. This protection was transient and associated with M2-specific CD8+ T-cell (TCD8+) responses. In this study, we used two approaches to demonstrat...

  5. Proteolytic cleavage of recombinant two-chain factor VIII during cell culture production is mediated by protease(s) from lysed cells. The use of pulse labelling directly in production medium

    OpenAIRE

    Hansen, Karen; Kjalke, Marianne; Rasmussen, Poul Baad; Kongerslev, Leif; Ezban, Mirella

    1997-01-01

    During the production by mammalian cells of recombinant factor VIII from which the B domain was deleted (rFVIII), proteolytic cleavages in the C-terminal part of the heavy chain were observed (Kjalke et al., 1995). By radioactive pulse labelling it was investigated whether the cleavages took place inside the cells during protein synthesis or after release in the medium. The rFVIII-producing CHO (Chinese hamster ovary) cells were cultured in the presence of 35S-methionine and then the cell lys...

  6. Oxygen-hydrogen recombiner

    International Nuclear Information System (INIS)

    Purpose: To reduce unreacted hydrogen flowing through a space between a catalyst and a recombiner to thereby reduce the hydrogen density at the exit of the recombiner. Constitution: A catalyst support plate is disposed on a recombiner, on which is placed catalysts comprising noble metals such as platinum and palladium supported on plate-like sponge metals. 10 or more buffle plates each with about 1 mm gap to the wall surface of the recombiner are inserted in perpendicular to the flowing direction in the catalysts. The catalysts are closely contacted with the buffle plates by their own weight and the pressure resulted from the gas stream, by which the gas tending to flow through the gap are changed in the flowing direction and flow in the catalyst layer to perform recombining reaction. While on the other hand, since the gap is retained to about 1 mm and 10 or more buffle plates are disposed, the amount of the unreacted hydrogen can be decreased. In this way, hydrogen density at the exit of the recombiner can be reduced and packing and exchange of the catalysts can be facilitated. (Yoshihara, H.)

  7. The theory and computational implementation of quadratically convergent Hartree-Fock orbital optimization methods and their relationship to the time-dependent Hartree-Fock and RPA methods

    International Nuclear Information System (INIS)

    The theory of quadratically convergent Hartree-Fock or self-consistent field (QC-SCF) orbital optimization is presented using the language of second quantization. Two methods that are appropriate for the computational implementation of QC-SCF are described: the Newton-Raphson method and an approximate super configuration interaction (CI) approach, both of which can be implemented such that no four-index transformation is necessary. The Newton-Raphson formulation of QC-SCF is shown to be equivalent to solving the frequency-independent coupled perturbation Hartree-Fock equations, and consequently a close relationship exists between QC-SCF and the more general time-dependent coupled perturbation Hartree-Fock (TDCPHF) theory and the related theories of random phase approximation (RPA) and time-dependent Hartree-Fock. Matrix element expressions that are needed for RPA naturally arise in QC-SCF too, and a list of these for open-shell ground state wavefunctions is also given. Computational techniques that are believed to be useful for the solution of the TDCPHF and RPA problems are also briefly discussed

  8. Calculation of the RPA response function of nuclei to quasi-elastic electron scattering with a density-dependent NN interaction

    International Nuclear Information System (INIS)

    So far, the non-relativistic longitudinal and transverse functions in electron quasi-elastic scattering on the nuclei failed in reproducing satisfactorily the existent experimental data. The calculations including relativistic RPA correlations utilize until now the relativistic Hartree approximation to describe the nuclear matter. But, this provides an incompressibility module two times higher than its experimental value what is an important drawback for the calculation of realistic relativistic RPA correlations. Hence, we have determined the RPA response functions of nuclei by utilising a description of the relativistic nuclear matter leading to an incompressibility module in agreement with the empirical value. To do that we have utilized an interaction in the relativistic Hartree approximation in which we have determined the coupling constants ?-N and ?-N as a function of the density in order to reproduce the saturation curve obtained by a Dirac-Brueckner calculation. The results which we have obtained show that the longitudinal response function and the Coulomb sum generally overestimated when one utilizes the pure relativistic Hartree approximation, are here in good agreement with the experimental data for several nuclei

  9. Recovery of Arrested Replication Forks by Homologous Recombination Is Error-Prone

    OpenAIRE

    Iraqui, Ismail; Chekkal, Yasmina; Jmari, Nada; Pietrobon, Violena; Fre?on, Karine; Costes, Audrey; Lambert, Sarah A. E.

    2012-01-01

    Homologous recombination is a universal mechanism that allows repair of DNA and provides support for DNA replication. Homologous recombination is therefore a major pathway that suppresses non-homology-mediated genome instability. Here, we report that recovery of impeded replication forks by homologous recombination is error-prone. Using a fork-arrest-based assay in fission yeast, we demonstrate that a single collapsed fork can cause mutations and large-scale genomic changes, including deletio...

  10. CRE-LOX SITE-SPECIFIC RECOMBINATION BETWEEN ARABIDOPSIS AND TOBACCO CHROMOSOMES

    Science.gov (United States)

    To create hybrid chromosomes, we tested the Cre-lox system to mediate recombination between Arabidopsis thaliana and Nicotiana Tabacum chromosomes. Protoplasts of the two plants were fused to allow site-specific recombination to join a promoter from tobacco to a hygromycin resistance coding-region f...

  11. 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.

  12. 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

  13. 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.

  14. Recombinant bispecific antibodies for cellular cancer immunotherapy.

    Science.gov (United States)

    Müller, Dafne; Kontermann, Roland E

    2007-08-01

    Bispecific antibodies recognizing two different antigens present on different cells have been developed for cellular cancer therapy in which cytotoxic effector cells are recruited to tumor cells. Initial studies with bispecific antibodies have not reached satisfactory clinical endpoints, mainly due to low efficacy, Fc-mediated side effects and immunogenicity. This has resulted in a declining interest in bispecific antibodies for cancer therapy. However, growing knowledge in effector cell biology and the implementation of antibody engineering technologies has led to a revival and the development of novel or improved strategies. Various recombinant bispecific antibodies have demonstrated efficacy in vitro andin vivo, with the first recombinant antibody molecule currently in clinical trials for the treatment of B-cell malignancies. PMID:17694444

  15. Recombinant Protein Production by In Vivo Polymer Inclusion Display ?

    OpenAIRE

    Grage, Katrin; Peters, Verena; Rehm, Bernd H. A.

    2011-01-01

    A novel approach to produce purified recombinant proteins was established. The target protein is produced as polyhydroxyalkanoate (PHA) synthase fusion protein, which mediates intracellular formation of PHA inclusions displaying the target protein. After isolation of the PHA inclusions, the pure target protein was released by simple enterokinase digestion.

  16. Minutes and group memories from all NERBC/USGS-RPA power plant siting task force meetings through October, 1980. Appendix

    International Nuclear Information System (INIS)

    The New England River Basins Commission/United States Geological Survey-Resource Planning Analysis Office (NERBC/USGS-RPA) Power Plant Siting Task Force has formerly met seven times between July 1979 and August 1980. At the first meeting on July 13, 1979, the members agreed that there were many problems with the current process of selecting sites for power plants in New England, and that they would work by consensus to find solutions for these problems. At the second meeting on October 19, 1979, NERBC staff presented information on the site selection and approval processes in New England. The Task Force began a preliminary discussion of problems in these processes, and agreed that the initial scope of work of the Task Force would focus on issues in site selection. At the third meeting on January 18, 1980, the Task Force began initial discussions in three areas: imperfections in the site selection process, stakeholders in the site selection process, and principles to guide solutions to the problems in site selection. On March 7, 1980, at the fourth meeting, the Task Force continued discussions on imperfections, stakeholders, and principles. At the fifth meeting on May 2, 1980, the Task Force reached a wide range of agreements on the difficulties encountered in the site selection process and on the principles guiding problem solving in site selection. At the sixth meeting on May 29, 1980, the Task Force focused on solutions to the problems identified at earlier meetingshe problems identified at earlier meetings. Groups of Task Force members constructed eight different scenarios describing alternative power plant siting processes. In July 1980, the Task Force met for the seventh time and refined the eight scenarios, paring them down to five. An attempt was made to develop two scenarios using the common elements from the five. One of these two graphic models was based on government involvement in the site selection process, and the other was based on stakeholder involvement in the process

  17. Recombinational DNA repair and human disease

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Larry H.; Schild, David

    2002-11-30

    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 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.

  18. Adiabatic cooling and recombination heating in expanding recombination plasma

    International Nuclear Information System (INIS)

    Objective region of gain in Ne/Te plane for 3d5/2-2p3/2 transitions in H-like ion in recombination C plasma is given. The characteristics of plasma at the juncture of ionization and recombination are obtained. Adiabatic cooling Wp and recombination heating Ws are studied and their approximate expressions are given

  19. 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...

  20. 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.

  1. Introduction to dissociative recombination

    Science.gov (United States)

    Guberman, Steven L.; Mitchell, J. Brian A.

    1989-01-01

    Dissociative recombination (DR) of molecular ions with electrons has important consequences in many areas of physical science. Ab-initio calculations coupled with resonant scattering theory and multichannel quantum defect studies have produced detailed results illuminating the role of ion vibrational excitation, the quantum yields of the DR products, and the role of Rydberg states. The theoretical and experimental results are discussed.

  2. Constructing minimal ancestral recombination graphs.

    OpenAIRE

    Song, Ys; Hein, J.

    2005-01-01

    By viewing the ancestral recombination graph as defining a sequence of trees, we show how possible evolutionary histories consistent with given data can be constructed using the minimum number of recombination events. In contrast to previously known methods, which yield only estimated lower bounds, our method of detecting recombination always gives the minimum number of recombination events if the right kind of rooted trees are used in our algorithm. A new lower bound can be defined if rooted...

  3. Vaccination with recombinant 4 × M2e.HSP70c fusion protein as a universal vaccine candidate enhances both humoral and cell-mediated immune responses and decreases viral shedding against experimental challenge of H9N2 influenza in chickens.

    Science.gov (United States)

    Dabaghian, Mehran; Latify, Ali Mohammad; Tebianian, Majid; Nili, Hassan; Ranjbar, Ali Reza Tevangar; Mirjalili, Ali; Mohammadi, Mashallah; Banihashemi, Reza; Ebrahimi, Seyyed Mahmoud

    2014-11-01

    As cellular immunity is essential for virus clearance, it is commonly accepted that no adequate cellular immunity is achieved by all available inactivated HA-based influenza vaccines. Thus, an improved influenza vaccine to induce both humoral and cell-mediated immune responses is urgently required to control LPAI H9N2 outbreaks in poultry farms. M2e-based vaccines have been suggested and developed as a new generation of universal vaccine candidate against influenza A infection. Our previous study have shown that a prime-boost administration of recombinant 4×M2e.HSP70c (r4M2e/H70c) fusion protein compared to conventional HA-based influenza vaccines provided full protection against lethal dose of influenza A viruses in mice. In the present study, the immunogenicity and protective efficacy of (r4M2e/H70c) was examined in chickens. The data reported herein show that protection against H9N2 viral challenge was significantly increased in chickens by injection of r4M2e/H70c compared with injection of conventional HA-based influenza vaccine adjuvanted with MF59 or recombinant 4×M2e (r4M2e) without HSP70c. Oropharyngeal and cloacal shedding of the virus was detected in all of the r4M2e/H70c vaccinated birds at 2 days after challenge, but the titer was low and decreased rapidly to reach undetectable levels at 7 days after challenge. Moreover, comparison of protective efficacy against LPAI H9N2 in birds intramuscularly immunized with r4M2e/H70c likely represented the ability of the M2e-based vaccine in providing cross-protection against heterosubtypic H9N2 challenge and also allowed the host immune system to induce HA-homosubtype neutralizing antibody against H9N2 challenge. This protective immunity might be attributed to enhanced cell-mediated immunity, which is interpreted as increased lymphocytes proliferation, increased levels of Th1-type (IFN-?) and Th2-type (IL-4) cytokines production and increased CD4(+) to CD8(+) ratios, resulting from the injection of four tandem repeats of the ectodomain of the conserved influenza matrix protein M2 (4×M2e) genetically fused to C-terminus of Mycobacterium tuberculosis HSP70 (mHSP70c). PMID:25293397

  4. 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...

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

    International Nuclear Information System (INIS)

    The efficient implementation of electronic structure methods is essential for first principles modeling of molecules and solids. We present here a particularly efficient common framework for methods beyond semilocal density-functional theory (DFT), including Hartree-Fock (HF), hybrid density functionals, random-phase approximation (RPA), second-order Mřller-Plesset perturbation theory (MP2) and the GW method. This computational framework allows us to use compact and accurate numeric atom-centered orbitals (NAOs), popular in many implementations of semilocal DFT, as basis functions. The essence of our framework is to employ the ‘resolution of identity (RI)’ technique to facilitate the treatment of both the two-electron Coulomb repulsion integrals (required in all these approaches) and the linear density-response function (required for RPA and GW). This is possible because these quantities can be expressed in terms of the products of single-particle basis functions, which can in turn be expanded in a set of auxiliary basis functions (ABFs). The construction of ABFs lies at the heart of the RI technique, and we propose here a simple prescription for constructing ABFs 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 accuracy of our RI implementation for Gaussian and NAO basis functions, as well as the convergence behavior of our NAO basis sets fence behavior of our NAO basis sets for the above-mentioned methods. Benchmark results are presented for the ionization energies of 50 selected atoms and molecules from the G2 ion test set obtained with the GW and MP2 self-energy methods, and the G2-I atomization energies as well as the S22 molecular interaction energies obtained with the RPA method. (paper)

  6. 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 żmms1 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 żmms1 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.

  7. Oxygen-hydrogen recombiner

    International Nuclear Information System (INIS)

    Purpose: To reduce the amount of a catalyst and improve the hydrogen removing performance of a catalyst type oxygen-hydrogen recombiner in a radioactive gaseous wastes processing facility of BWR type nuclear power plants. Constitution: The catalyst (of palladium or platinum group) has a low activity at a low temperature. In view of the above, hydrogen gases injected from the outside for improving the catalyst activity even under a low temperature state such as reactor start-up and shut-down. When the hydrogen gas concentration increases, chemical combination between oxygen and hydrogen in the recombiner is increased, by which the amount of heat generation is increased to rise the temperature of the catalyst. In this way, the catalyst activity can be improved. Corresponding to the injection of the hydrogen gas, oxygen is also injected so as to attain 1 : 2 ratio. (Ikeda, J.)

  8. 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)

  9. Intrachromosomal recombination in plants.

    OpenAIRE

    Peterhans, A.; Schlu?pmann, H.; Basse, C.; Paszkowski, J.

    1990-01-01

    Molecular evidence for intrachromosomal recombination between closely linked DNA repeats within the plant genome is presented. The non-overlapping complementary deletion derivatives of the selectable neomycin phosphotransferase gene (nptII), when intact conferring kanamycin resistance, were inserted into the genome of Nicotiana tabacum. The functional marker gene was restored with frequencies between 10(-4) and 10(-6) per proliferating cell clone. Prolonged tissue culture prior to kanamycin s...

  10. 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

  11. Recombinant protective antigen anthrax vaccine improves survival when administered as a postexposure prophylaxis countermeasure with antibiotic in the New Zealand white rabbit model of inhalation anthrax.

    Science.gov (United States)

    Leffel, Elizabeth K; Bourdage, James S; Williamson, E Diane; Duchars, Matthew; Fuerst, Thomas R; Fusco, Peter C

    2012-08-01

    Inhalation anthrax is a potentially lethal form of disease resulting from exposure to aerosolized Bacillus anthracis spores. Over the last decade, incidents spanning from the deliberate mailing of B. anthracis spores to incidental exposures in users of illegal drugs have highlighted the importance of developing new medical countermeasures to protect people who have been exposed to "anthrax spores" and are at risk of developing disease. The New Zealand White rabbit (NZWR) is a well-characterized model that has a pathogenesis and clinical presentation similar to those seen in humans. This article reports how the NZWR model was adapted to evaluate postexposure prophylaxis using a recombinant protective antigen (rPA) vaccine in combination with an oral antibiotic, levofloxacin. NZWRs were exposed to multiples of the 50% lethal dose (LD(50)) of B. anthracis spores and then vaccinated immediately (day 0) and again on day 7 postexposure. Levofloxacin was administered daily beginning at 6 to 12 h postexposure for 7 treatments. Rabbits were evaluated for clinical signs of disease, fever, bacteremia, immune response, and survival. A robust immune response (IgG anti-rPA and toxin-neutralizing antibodies) was observed in all vaccinated groups on days 10 to 12. Levofloxacin plus either 30 or 100 ?g rPA vaccine resulted in a 100% survival rate (18 of 18 per group), and a vaccine dose as low as 10 ?g rPA resulted in an 89% survival rate (16 of 18) when used in combination with levofloxacin. In NZWRs that received antibiotic alone, the survival rate was 56% (10 of 18). There was no adverse effect on the development of a specific IgG response to rPA in unchallenged NZWRs that received the combination treatment of vaccine plus antibiotic. This study demonstrated that an accelerated two-dose regimen of rPA vaccine coadministered on days 0 and 7 with 7 days of levofloxacin therapy results in a significantly greater survival rate than with antibiotic treatment alone. Combination of vaccine administration and antibiotic treatment may be an effective strategy for treating a population exposed to aerosolized B. anthracis spores. PMID:22695155

  12. 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

  13. Harnessing recombination to speed adaptive evolution in Escherichia coli.

    Science.gov (United States)

    Winkler, James; Kao, Katy C

    2012-09-01

    Evolutionary engineering typically involves asexual propagation of a strain to improve a desired phenotype. However, asexual populations suffer from extensive clonal interference, a phenomenon where distinct lineages of beneficial clones compete and are often lost from the population given sufficient time. Improved adaptive mutants can likely be generated by genetic exchange between lineages, thereby reducing clonal interference. We present a system that allows continuous in situ recombination by using an Esherichia coli F-based conjugation system lacking surface exclusion. Evolution experiments revealed that Hfr-mediated recombination significantly speeds adaptation in certain circumstances. These results show that our system is stable, effective, and suitable for use in evolutionary engineering applications. PMID:22842472

  14. Intercultural Mediation

    Directory of Open Access Journals (Sweden)

    Dragos Marian Radulescu

    2012-11-01

    Full Text Available 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 politics conflicts. This article attempts to provide a new perspective about the intercultural mediation.

  15. Extremely radiation-resistant mutants of a halophilic archaeon with increased single-stranded DNA-binding protein (RPA) gene expression.

    Science.gov (United States)

    DeVeaux, Linda C; Müller, Jochen A; Smith, Jonathon; Petrisko, Jill; Wells, Douglas P; DasSarma, Shiladitya

    2007-10-01

    Extremely halophilic archaea are highly resistant to multiple stressors, including radiation, desiccation and salinity. To study the basis of stress resistance and determine the maximum tolerance to ionizing radiation, we exposed cultures of the model halophile Halobacterium sp. NRC-1 to four cycles of irradiation with high doses of 18-20 MeV electrons. Two independently obtained mutants displayed an LD(50) > 11 kGy, which is higher than the LD(50) of the extremely radiation-resistant bacterium Deinococcus radiodurans. Whole-genome transcriptome analysis comparing the mutants to the parental wild-type strain revealed up-regulation of an operon containing two single-stranded DNA-binding protein (RPA) genes, VNG2160 (rfa3) and VNG2162, and a third gene of unknown function, VNG2163. The putative transcription start site for the rfa3 operon was mapped approximately 40 bp upstream of the ATG start codon, and a classical TATA-box motif was found centered about 25 bp further upstream. We propose that RPA facilitates DNA repair machinery and/or protects repair intermediates to maximize the ionizing radiation resistance of this archaeon. PMID:17903038

  16. 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 ...

  17. 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

  18. 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.

  19. 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.

  20. 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...

  1. Genetically engineered poxviruses for recombinant gene expression, vaccination, and safety.

    OpenAIRE

    Moss, B.

    1996-01-01

    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...

  2. Similarity of Recombinant Human Perlecan Domain 1 by Alternative Expression Systems Bioactive Heterogenous Recombinant Human Perlecan D1

    Directory of Open Access Journals (Sweden)

    Ellis April L

    2010-09-01

    Full Text Available Abstract Background Heparan sulfate glycosaminoglycans are diverse components of certain proteoglycans and are known to interact with growth factors as a co-receptor necessary to induce signalling and growth factor activity. In this report we characterize heterogeneously glycosylated recombinant human perlecan domain 1 (HSPG2 abbreviated as rhPln.D1 synthesized in either HEK 293 cells or HUVECs by transient gene delivery using either adenoviral or expression plasmid technology. Results By SDS-PAGE analysis following anion exchange chromatography, the recombinant proteoglycans appeared to possess glycosaminoglycan chains ranging, in total, from 6 kDa to >90 kDa per recombinant. Immunoblot analysis of enzyme-digested high Mr rhPln.D1 demonstrated that the rhPln.D1 was synthesized as either a chondroitin sulfate or heparan sulfate proteoglycan, in an approximately 2:1 ratio, with negligible hybrids. Secondary structure analysis suggested helices and sheets in both recombinant species. rhPln.D1 demonstrated binding to rhFGF-2 with an apparent kD of 2 ± 0.2 nM with almost complete susceptibility to digestion by heparinase III in ligand blot analysis but not to chondroitinase digestion. Additionally, we demonstrate HS-mediated binding of both rhPln.D1 species to several other GFs. Finally, we corroborate the augmentation of FGF-mediated cell activation by rhPln.D1 and demonstrate mitogenic signalling through the FGFR1c receptor. Conclusions With importance especially to the emerging field of DNA-based therapeutics, we have shown here that proteoglycan synthesis, in different cell lines where GAG profiles typically differ, can be directed by recombinant technology to produce populations of bioactive recombinants with highly similar GAG profiles.

  3. Repressor titration: a novel system for selection and stable maintenance of recombinant plasmids.

    OpenAIRE

    Williams, S. G.; Cranenburgh, R. M.; Weiss, A. M.; Wrighton, C. J.; Sherratt, D. J.; Hanak, J. A.

    1998-01-01

    The propagation of recombinant plasmids in bacterial hosts, particularly in Escherichia coli, is essential for the amplification and manipulation of cloned DNA and the production of recombinant proteins. The isolation of bacterial transformants and subsequent stable plasmid maintenance have traditionally been accomplished using plasmid-borne selectable marker genes. Here we describe a novel system that employs plasmid-mediated repressor titration to activate a chromosomal selectable marker, r...

  4. Rad9 Is Required for B Cell Proliferation and Immunoglobulin Class Switch Recombination*

    OpenAIRE

    An, Lili; Wang, Yulan; Liu, Yuheng; Yang, Xiao; Liu, Chunchun; Hu, Zhishang; He, Wei; Song, Wenxia; Hang, Haiying

    2010-01-01

    B cell maturation and B cell-mediated antibody response require programmed DNA modifications such as the V(D)J recombination, the immunoglobulin (Ig) class switch recombination, and the somatic hypermutation to generate functional Igs. Many protein factors involved in DNA damage repair have been shown to be critical for the maturation and activation of B cells. Rad9 plays an important role in both DNA repair and cell cycle checkpoint control. However, its role in Ig generation has not been re...

  5. Telomeric transcripts stimulate telomere recombination to suppress senescence in cells lacking telomerase

    OpenAIRE

    Yu, Tai-yuan; Kao, Yu-wen; Lin, Jing-jer

    2014-01-01

    Telomerase expression is essential for the long-term proliferation of most cancer cells. In cancer cells lacking telomerase, an alternative lengthening of telomeres (ALT) pathway is activated to maintain telomere length through telomere recombination. Using yeast as a model system, we found that the noncoding telomeric repeat-containing RNA (TERRA) plays a major role in recombination-mediated maintenance of telomere in telomerase-deficient cells. Increased levels of telomere-associated TERRA ...

  6. Cell-Specific Inducible Gene Recombination in Postnatal Inner Ear Supporting Cells and Glia

    OpenAIRE

    Go?mez-casati, Mari?a Eugenia; Murtie, Joshua; Taylor, Bethany; Corfas, Gabriel

    2009-01-01

    Recent studies indicate that supporting cells play important roles in inner ear development, function, and regeneration after injury, but the molecular mechanisms underlying these processes remain poorly understood. Inducible cell-specific gene recombination in supporting cells could be a powerful tool to study the roles of specific molecules in these cells. Here we tested the feasibility, effectiveness, and cell specificity of inducible Cre-mediated gene recombination in the postnatal inner ...

  7. Mutations affecting RNA polymerase I-stimulated exchange and rDNA recombination in yeast

    International Nuclear Information System (INIS)

    HOT1 is a cis-acting recombination-stimulatory sequence isolated from the rDNA repeat unit of yeast. The ability of HOT1 to stimulate mitotic exchange appears to depend on its ability to promote high levels of RNA polymerase I transcription. A qualitative colony color sectoring assay was developed to screen for trans-acting mutations that alter the activity of HOT1. Both hypo-recombination and hyper-recombination mutants were isolated. Genetic analysis of seven HOT1 recombination mutants (hrm) that decrease HOT1 activity shows that they behave as recessive nuclear mutations and belong to five linkage groups. Three of these mutations, hrm1, hrm2, and hrm3, also decrease rDNA exchange but do not alter recombination in the absence of HOT1. Another mutation, hrm4, decreases HOT1-stimulated recombination but does not affect rDNA recombination or exchange in the absence of HOT1. Two new alleles of RAD52 were also isolated using this screen. With regard to HOT1 activity, rad52 is epistatic to all four hrm mutations indicating that the products of the HRM genes and of RAD52 mediate steps in the same recombination pathway. Finding mutations that decrease both the activity of HOT1 and exchange in the rDNA supports the hypothesis that HOT1 plays a role in rDNA recombination

  8. Purification of recombinant laccase from Trametes versicolor in Pichia methanolica and its use for the decolorization of anthraquinone dye.

    Science.gov (United States)

    Guo, Mei; Lu, Fuping; Liu, Minyao; Li, Tuoping; Pu, Jun; Wang, Na; Liang, Peng; Zhang, Chenyun

    2008-12-01

    A recombinant laccase from Trametes versicolor in Pichia methanolica was produced constitutively in a defined medium. The recombinant laccase was purified using ultrafiltration, anion-exchange chromatography, and gel filtration. The molecular weight of the purified laccase was estimated as 64 kDa by SDS-PAGE. The purified recombinant laccase decolorized more than 90% of Remazol Brilliant Blue R (RBBR) initially at 80 mg l(-1) after 16 h at 45 degrees C and pH 5 when 25 U laccase ml(-1) was used. The purified recombinant laccase could efficiently decolorize RBBR without additional redox mediators. PMID:18688574

  9. Hypoxia-induced hypothermia mediated by GABA in the rostral parapyramidal area of the medulla oblongata.

    Science.gov (United States)

    Osaka, T

    2014-05-16

    Hypoxia evokes a regulated decrease in the body core temperature (Tc) in a variety of animals. The neuronal mechanisms of this response include, at least in part, glutamatergic activation in the lateral preoptic area (LPO) of the hypothalamus. As the sympathetic premotor neurons in the medulla oblongata constitute a cardinal relay station in the descending neuronal pathway from the hypothalamus for thermoregulation, their inhibition can also be critically involved in the mechanisms of the hypoxia-induced hypothermia. Here, I examined the hypothesis that hypoxia-induced hypothermia is mediated by glutamate-responsive neurons in the LPO that activate GABAergic transmission in the rostral raphe pallidus (rRPa) and neighboring parapyramidal region (PPy) of the medulla oblongata in urethane-chloralose-anesthetized, neuromuscularly blocked, artificially ventilated rats. Unilateral microinjection of GABA (15nmol) into the rRPa and PPy regions elicited a prompt increase in tail skin temperature (Ts) and decreases in Tc, oxygen consumption rate (VO2), and heart rate. Next, when the GABAA receptor blocker bicuculline methiodide (bicuculline methiodide (BMI), 10pmol) alone was microinjected into the rRPa, it elicited unexpected contradictory responses: simultaneous increases in Ts, VO2 and heart rate and a decrease in Tc. Then, when BMI was microinjected bilaterally into the PPy, no direct effect on Ts was seen; and thermogenic and tachycardic responses were slight. However, pretreatment of the PPy with BMI, but not vehicle saline, greatly attenuated the hypothermic responses evoked by hypoxic (10%O2-90%N2, 5min) ventilation or bilateral microinjections of glutamate (5nmol, each side) into the LPO. The results suggest that hypoxia-induced hypothermia was mediated, at least in part, by the activation of GABAA receptors in the PPy. PMID:24607346

  10. Brca2-Pds5 complexes mobilize persistent meiotic recombination sites to the nuclear envelope.

    Science.gov (United States)

    Kusch, Thomas

    2015-02-15

    Homologous recombination is required for reciprocal exchange between homologous chromosome arms during meiosis. Only select meiotic recombination events become chromosomal crossovers; the majority of recombination outcomes are noncrossovers. Growing evidence suggests that crossovers are repaired after noncrossovers. Here, I report that persisting recombination sites are mobilized to the nuclear envelope of Drosophila pro-oocytes during mid-pachytene. Their number correlates with the average crossover rate per meiosis. Proteomic and interaction studies reveal that the recombination mediator Brca2 associates with lamin and the cohesion factor Pds5 to secure persistent recombination sites at the nuclear envelope. In Rad51(-/-) females, all persistent DNA breaks are directed to the nuclear envelope. By contrast, a reduction of Pds5 or Brca2 levels abolishes the movement and has a negative impact on crossover rates. The data suggest that persistent meiotic DNA double-strand breaks might correspond to crossovers, which are mobilized to the nuclear envelope for their repair. The identification of Brca2-Pds5 complexes as key mediators of this process provides a first mechanistic explanation for the contribution of lamins and cohesins to meiotic recombination. PMID:25588834

  11. Recombining WMAP: constraints on ionizing and resonance radiation at recombination

    OpenAIRE

    Bean, Rachel; Melchiorri, Alessandro; Silk, Joe

    2003-01-01

    We place new constraints on sources of ionizing and resonance radiation at the epoch of the recombination process using the recent CMB temperature and polarization spectra coming from 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...

  12. TPR-Mediated self-association of plant SGT1.

    OpenAIRE

    Nyarko, A.; Mosbahi, K.; Rowe, Aj; Leech, A.; Boter, M.; Shirasu, K.; Kleanthous, C.

    2007-01-01

    The tetratricopeptide repeat (TPR) domain mediates inter-protein associations in a number of systems. The domain is also thought to mediate oligomerization of some proteins, but this has remained controversial, with conflicting data appearing in the literature. By way of investigating such TPR-mediated self-associations we used a variety of biophysical techniques to characterize purified recombinant Sgt1, a TPR-containing protein found in all eukaryotes that is involved in a broad range of bi...

  13. 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)

  14. 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...

  15. Two-center dielectronic recombination

    CERN Document Server

    Müller, C; López-Urrutia, J R Crespo; Harman, Z

    2010-01-01

    In the presence of a neighboring atom, electron-ion recombination can proceed resonantly via excitation of an electron in the atom, with subsequent relaxation through radiative decay. It is shown that this two-center dielectronic process can largely dominate over single-center radiative recombination at internuclear distances as large as several nanometers. The relevance of the predicted process is demonstrated by using examples of water-dissolved alkali cations and warm dense matter.

  16. Biochemistry of eukaryotic homologous recombination

    OpenAIRE

    Heyer, Wolf-dietrich

    2007-01-01

    The biochemistry of eukaryotic homologous recombination caught fire with the discovery that Rad51 is the eukaryotic homolog of the bacterial RecA and T4 UvsX proteins; and this field is still hot. The core reaction of homologous recombination, homology search and DNA strand invasion, along with the proteins catalyzing it, are conserved throughout evolution in principle. However, the increased complexity of eukaryotic genomes and the diversity of eukaryotic cell biology pose additional challen...

  17. Intermolecular homologous recombination in plants.

    OpenAIRE

    Baur, M.; Potrykus, I.; Paszkowski, J.

    1990-01-01

    To study DNA topological requirements for homologous recombination in plants, we have constructed pairs of plasmids that contain nonoverlapping deletions in the neomycin phosphotransferase gene [APH(3')II], which, when intact, confers kanamycin resistance to plant cells. Protoplasts isolated from Nicotiana tabacum were cotransformed with complementary pairs of plasmids containing these truncated gene constructs. Homologous recombination or gene conversion within the homologous sequences (6 to...

  18. Do mitochondria recombine in humans?

    OpenAIRE

    Eyre-walker, A.

    2000-01-01

    Until very recently, mitochondria were thought to be clonally inherited through the maternal line in most higher animals. However, three papers published in 2000 claimed population-genetic evidence of recombination in human mitochondrial DNA. Here I review the current state of the debate. I review the evidence for the two main pathways by which recombination might occur: through paternal leakage and via a mitochondrial DNA sequence in the nuclear genome. There is no strong evidence for either...

  19. 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.

  20. Ethanol production by recombinant hosts

    Science.gov (United States)

    Ingram, Lonnie O. (Gainesville, FL); Beall, David S. (Gainesville, FL); Burchhardt, Gerhard F. H. (Gainesville, FL); Guimaraes, Walter V. (Vicosa, BR); Ohta, Kazuyoshi (Miyazaki, JP); Wood, Brent E. (Gainesville, FL); Shanmugam, Keelnatham T. (Gainesville, FL)

    1995-01-01

    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.

  1. The Slx5-Slx8 complex affects sumoylation of DNA repair proteins and negatively regulates recombination.

    DEFF Research Database (Denmark)

    Burgess, Rebecca C; Rahman, Sadia

    2007-01-01

    Recombination is important for repairing DNA lesions, yet it can also lead to genomic rearrangements. This process must be regulated, and recently, sumoylation-mediated mechanisms were found to inhibit Rad51-dependent recombination. Here, we report that the absence of the Slx5-Slx8 complex, a newly identified player in the SUMO (small ubiquitin-like modifier) pathway, led to increased Rad51-dependent and Rad51-independent recombination. The increases were most striking during S phase, suggesting an accumulation of DNA lesions during replication. Consistent with this view, Slx8 protein localized to replication centers. In addition, like SUMO E2 mutants, slx8Delta mutants exhibited clonal lethality, which was due to the overamplification of 2 microm, an extrachromosomal plasmid. Interestingly, in both SUMO E2 and slx8Delta mutants, clonal lethality was rescued by deleting genes required for Rad51-independent recombination but not those involved in Rad51-dependent events. These results suggest that sumoylation negatively regulates Rad51-independent recombination, and indeed, the Slx5-Slx8 complex affected the sumoylation of several enzymes involved in early steps of Rad51-independent recombination. We propose that, during replication, the Slx5-Slx8 complex helps prevent DNA lesions that are acted upon by recombination. In addition, the complex inhibits Rad51-independent recombination via modulating the sumoylation of DNA repair proteins. Udgivelsesdato: 2007-Sep

  2. Cellular Immune Responses in Asymptomatic Human Immunodeficiency Virus Type 1 (HIV-1) Infection and Effects of Vaccination with Recombinant Envelope Glycoprotein of HIV-1

    OpenAIRE

    Gorse, Geoffrey J.; Simionescu, Ramona E.; Patel, Gira B.

    2006-01-01

    Effects of human immunodeficiency virus type 1 (HIV-1) recombinant envelope glycoprotein vaccines on cell-mediated immune (CMI) responses were assessed in HIV-1-infected patients. Asymptomatic, antiretroviral-treatment-naďve, HIV-1-infected patients with CD4+ T-cell counts greater than 400/?l received multiple intramuscular injections of HIV-1 IIIB recombinant envelope glycoprotein (rgp160) vaccine or HIV-1 MN recombinant envelope glycoprotein (rgp120) vaccine (eight patients, referred to a...

  3. 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

  4. 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

  5. Subcloning plus insertion (SPI)--a novel recombineering method for the rapid construction of gene targeting vectors.

    Science.gov (United States)

    Reddy, Thimma R; Kelsall, Emma J; Fevat, Léna M S; Munson, Sarah E; Cowley, Shaun M

    2015-01-01

    Gene targeting refers to the precise modification of a genetic locus using homologous recombination. The generation of novel cell lines and transgenic mouse models using this method necessitates the construction of a 'targeting' vector, which contains homologous DNA sequences to the target gene, and has for many years been a limiting step in the process. Vector construction can be performed in vivo in Escherichia coli cells using homologous recombination mediated by phage recombinases using a technique termed recombineering. Recombineering is the preferred technique to subclone the long homology sequences (>4 kb) and various targeting elements including selection markers that are required to mediate efficient allelic exchange between a targeting vector and its cognate genomic locus. Typical recombineering protocols follow an iterative scheme of step-wise integration of the targeting elements and require intermediate purification and transformation steps. Here, we present a novel recombineering methodology of vector assembly using a multiplex approach. Plasmid gap repair is performed by the simultaneous capture of genomic sequence from mouse Bacterial Artificial Chromosome libraries and the insertion of dual bacterial and mammalian selection markers. This subcloning plus insertion method is highly efficient and yields a majority of correct recombinants. We present data for the construction of different types of conditional gene knockout, or knock-in, vectors and BAC reporter vectors that have been constructed using this method. SPI vector construction greatly extends the repertoire of the recombineering toolbox and provides a simple, rapid and cost-effective method of constructing these highly complex vectors. PMID:25590226

  6. An inverse-modelling approach for frequency response correction of capacitive humidity sensors in ABL research with small remotely piloted aircraft (RPA)

    Science.gov (United States)

    Wildmann, N.; Kaufmann, F.; Bange, J.

    2014-09-01

    The measurement of water vapour concentration in the atmosphere is an ongoing challenge in environmental research. Satisfactory solutions exist for ground-based meteorological stations and measurements of mean values. However, carrying out advanced research of thermodynamic processes aloft as well, above the surface layer and especially in the atmospheric boundary layer (ABL), requires the resolution of small-scale turbulence. Sophisticated optical instruments are used in airborne meteorology with manned aircraft to achieve the necessary fast-response measurements of the order of 10 Hz (e.g. LiCor 7500). Since these instruments are too large and heavy for the application on small remotely piloted aircraft (RPA), a method is presented in this study that enhances small capacitive humidity sensors to be able to resolve turbulent eddies of the order of 10 m. The sensor examined here is a polymer-based sensor of the type P14-Rapid, by the Swiss company Innovative Sensor Technologies (IST) AG, with a surface area of less than 10 mm2 and a negligible weight. A physical and dynamical model of this sensor is described and then inverted in order to restore original water vapour fluctuations from sensor measurements. Examples of flight measurements show how the method can be used to correct vertical profiles and resolve turbulence spectra up to about 3 Hz. At an airspeed of 25 m s-1 this corresponds to a spatial resolution of less than 10 m.

  7. Recombination diversifies chloroplast trnF pseudogenes in Arabidopsis lyrata.

    Science.gov (United States)

    Ansell, S W; Schneider, H; Pedersen, N; Grundmann, M; Russell, S J; Vogel, J C

    2007-11-01

    Extensive intraspecific variation in the chloroplast trnL(UAA)-trnF(GAA) spacer of model plant Arabidopsis lyrata is caused by multiple copies of a tandemly repeated trnF pseudogene undergoing parallel independent changes in copy number. Linkage disequilibrium and secondary structure analyses indicate that the diversification of pseudogene copies is driven by complex processes of structurally mediated illegitimate recombination. Disperse repeats sharing similar secondary structures interact, facilitating reciprocal exchange of structural motifs between copies via intramolecular and intermolecular recombinations, forming chimeric sequences and iterative expansion and contraction in pseudogene copy numbers. Widely held assumptions that chloroplast sequence evolution is simple and structural changes are informative are violated. Our findings have important implications for the use of this highly variable region in Brassicaceae studies. The reticulate evolution and nonindependent nucleotide substitution render the pseudogene inappropriate for standard phylogenetic reconstruction, but over short evolutionary timescales they may be useful for assessing gene flow, hybridization and introgression. PMID:17956401

  8. Current Drive in Recombining Plasma

    Energy Technology Data Exchange (ETDEWEB)

    P.F. Schmit and N.J. Fisch

    2012-05-15

    The Langevin equations describing the average collisional dynamics of suprathermal particles in nonstationary plasma remarkably admit an exact analytical solution in the case of recombining plasma. The current density produced by arbitrary particle fluxes is derived including the effect of charge recombination. Since recombination has the effect of lowering the charge density of the plasma, thus reducing the charged particle collisional frequencies, the evolution of the current density can be modified substantially compared to plasma with fixed charge density. The current drive efficiency is derived and optimized for discrete and continuous pulses of current, leading to the discovery of a nonzero "residual" current density that persists indefinitely under certain conditions, a feature not present in stationary plasmas.

  9. 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...

  10. The Dissociative Recombination of OH(+)

    Science.gov (United States)

    Guberman, Steven L.

    1995-01-01

    Theoretical quantum chemical calculations of the cross sections and rates for the dissociative recombination of the upsilon = 0 level of the ground state of OH(+) show that recombination occurs primarily along the 2 (2)Pi diabatic route. The products are 0((1)D) and a hot H atom with 6.1 eV kinetic energy. The coupling to the resonances is very small and the indirect recombination mechanism plays only a minor role. The recommended value for the rate coefficient is (6.3 +/- 0.7) x 10(exp -9)x (T(e)/1300)(exp -0.48) cu.cm/s for 10 less than T(e) less than 1000 K.

  11. Axion mediation

    Science.gov (United States)

    Baryakhtar, Masha; Hardy, Edward; March-Russell, John

    2013-07-01

    We explore the possibility that supersymmetry breaking is mediated to the Standard Model sector through the interactions of a generalized axion multiplet that gains a F-term expectation value. Using an effective field theory framework we enumerate the most general possible set of axion couplings and compute the Standard Model sector soft-supersymmetry-breaking terms. Unusual, non-minimal spectra, such as those of both natural and split supersymmetry are easily implemented. We discuss example models and low-energy spectra, as well as implications of the particularly minimal case of mediation via the QCD axion multiplet. We argue that if the Peccei-Quinn solution to the strong-CP problem is realized in string theory then such axion-mediation is generic, while in a field theory model it is a natural possibility in both DFSZ- and KSVZ-like regimes. Axion mediation can parametrically dominate gravity-mediation and is also cosmologically beneficial as the constraints arising from axino and gravitino overproduction are reduced. Finally, in the string context, axion mediation provides a motivated mechanism where the UV completion naturally ameliorates the supersymmetric flavor problem.

  12. Dissociative recombination of protonated methanol

    OpenAIRE

    Geppert, Wolf; Hamberg, Mathias; Thomas, Richard D.; O?sterdahl, Fabian; Hellberg, Fredrik; Zhaunerchyk, Vitali; Ehlerding, Anneli; Millar, Tom; Roberts, Helen; Semaniak, Jacek; Af Ugglas, Magnus; Ka?llberg, Anders; Simonsson, Ansgar; Kaminska, Magdalena; Larsson, Mats

    2006-01-01

    The branching ratios of the different reaction pathways and the overall rate coefficients of the dissociative recombination reactions of CH3OH2+ and CD3OD2+ have been measured at the CRYRING storage ring located in Stockholm, Sweden. Analysis of the data yielded the result that formation of methanol or deuterated methanol accounted for only 3 and 6% of the total rate in CH3OH2+ and CD3OD2+, respectively. Dissociative recombination of both isotopomeres mainly involves fragmentation of the C–...

  13. 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.

  14. Recombination in the evolution of human bocavirus.

    Science.gov (United States)

    Tyumentsev, Alexander I; Tikunova, Nina V; Tikunov, Artem Yu; Babkin, Igor V

    2014-12-01

    Whole genome sequencing of Novosibirsk human bocavirus (HBoV) isolates has detected an isolate that emerged via recombination between HBoV3 and HBoV4 genotypes. The recombination site is located between regions with abnormally low and abnormally high GC contents in the genome. This site is a bocavirus recombination hotspot and coincides with one of two parvovirus recombination hotspots. The Novosibirsk recombinant isolate, which is similar to a previously studied isolate from Thailand, utilizes the strategy of borrowing ORF3, which encodes structural proteins, of a rare genotype HBoV4. The role of recombination in HBoV evolution is discussed. PMID:25193564

  15. Decolorization of Alizarin Red and other synthetic dyes by a recombinant laccase from Pichia pastoris.

    Science.gov (United States)

    Zheng, Miaomiao; Chi, Yujie; Yi, Hongwei; Shao, Shuli

    2014-01-01

    A cDNA encoding for a laccase was isolated from the white-rot fungus Lenzites gibbosa by RT-PCR and expressed in the Pichia pastoris. The laccase native signal peptide efficiently directed the secretion of the recombinant laccase in an active form. Factors influencing laccase expression, such as pH, cultivation temperature, copper concentration and methanol concentration, were optimized. The recombinant enzyme was purified to electrophoretic homogeneity, and was estimated to have a MW of ~61.5 kDa. The purified enzyme behaved similarly to the native laccase produced by L. gibbosa and efficiently decolorized Alizarin Red, Neutral Red, Congo Red and Crystal Violet, without the addition of redox mediators. The decolorization capacity of this recombinant enzyme suggests that it could be a useful biocatalyst for the treatment of dye-containing effluents. This study is the first report on the synthetic dye decolorization by a recombinant L. gibbosa laccase. PMID:24078122

  16. Dissecting the Requirement for Subgenomic Promoter Sequences by RNA Recombination of Brome Mosaic Virus In Vivo: Evidence for Functional Separation of Transcription and Recombination

    OpenAIRE

    Wierzchoslawski, Rafal; Dzianott, Aleksandra; Bujarski, Jozef

    2004-01-01

    Previously, we and others mapped an increased homologous recombination activity within the subgenomic promoter (sgp) region in brome mosaic virus (BMV) RNA3 (A. Bruyere et al., J. Virol. 74:4214-4219, 2000; R. Wierzchoslawski et al., J. Virol. 77:6769-6776, 2003). In order to correlate sgp-mediated recombination and transcription, in the present work we used BMV RNA3 constructs that carried altered sgp repeats. We observed that the removal or extension of the poly(U) tract reduced or increase...

  17. Natural and recombinant fungal laccases for paper pulp bleaching.

    Science.gov (United States)

    Sigoillot, C; Record, E; Belle, V; Robert, J L; Levasseur, A; Punt, P J; van den Hondel, C A M J J; Fournel, A; Sigoillot, J C; Asther, M

    2004-04-01

    Three laccases, a natural form and two recombinant forms obtained from two different expression hosts, were characterized and compared for paper pulp bleaching. Laccase from Pycnoporus cinnabarinus, a well known lignolytic fungus, was selected as a reference for this study. The corresponding recombinant laccases were produced in Aspergillus oryzae and A. niger hosts using the lacI gene from P. cinnabarinus to develop a production process without using the expensive laccase inducers required by the native source. In flasks, production of recombinant enzymes by Aspergilli strains gave yields close to 80 mg l(-1). Each protein was purified to homogeneity and characterized, demonstrating that the three hosts produced proteins with similar physico-chemical properties, including electron paramagnetic resonance spectra and N-terminal sequences. However, the recombinant laccases have higher Michaelian (Km) constants, suggesting a decrease in substrate/enzyme affinity in comparison with the natural enzyme. Moreover, the natural laccase exhibited a higher redox potential (around 810 mV), compared with A. niger (760 mV) and A. oryzae (735 mV). Treatment of wheat straw Kraft pulp using laccases expressed in P. cinnabarinus or A. niger with 1-hydroxybenzotriazole as redox mediator achieved a delignification close to 75%, whereas the recombinant laccase from A. oryzae was not able to delignify pulp. These results were confirmed by thioacidolysis. Kinetic and redox potential data and pulp bleaching results were consistent, suggesting that the three enzymes are different and each fungal strain introduces differences during protein processing (folding and/or glycosylation). PMID:14600793

  18. Recombination in the human Pseudoautosomal region PAR1.

    Science.gov (United States)

    Hinch, Anjali G; Altemose, Nicolas; Noor, Nudrat; Donnelly, Peter; Myers, Simon R

    2014-07-01

    The pseudoautosomal region (PAR) is a short region of homology between the mammalian X and Y chromosomes, which has undergone rapid evolution. A crossover in the PAR is essential for the proper disjunction of X and Y chromosomes in male meiosis, and PAR deletion results in male sterility. This leads the human PAR with the obligatory crossover, PAR1, to having an exceptionally high male crossover rate, which is 17-fold higher than the genome-wide average. However, the mechanism by which this obligatory crossover occurs remains unknown, as does the fine-scale positioning of crossovers across this region. Recent research in mice has suggested that crossovers in PAR may be mediated independently of the protein PRDM9, which localises virtually all crossovers in the autosomes. To investigate recombination in this region, we construct the most fine-scale genetic map containing directly observed crossovers to date using African-American pedigrees. We leverage recombination rates inferred from the breakdown of linkage disequilibrium in human populations and investigate the signatures of DNA evolution due to recombination. Further, we identify direct PRDM9 binding sites using ChIP-seq in human cells. Using these independent lines of evidence, we show that, in contrast with mouse, PRDM9 does localise peaks of recombination in the human PAR1. We find that recombination is a far more rapid and intense driver of sequence evolution in PAR1 than it is on the autosomes. We also show that PAR1 hotspot activities differ significantly among human populations. Finally, we find evidence that PAR1 hotspot positions have changed between human and chimpanzee, with no evidence of sharing among the hottest hotspots. We anticipate that the genetic maps built and validated in this work will aid research on this vital and fascinating region of the genome. PMID:25033397

  19. Characterization of Recombinant Per a 10 from Periplaneta americana

    OpenAIRE

    Govindaraj, Dhanapal; Gaur, Shailendra Nath; Arora, Naveen

    2013-01-01

    Cockroach allergen is a major risk factor for IgE-mediated allergic response and asthma in sensitized individuals. Serine proteases have been identified from various sources and characterized as major allergens. The present study was aimed to express and characterize recombinant allergen Per a 10 (rPer a 10) from Periplaneta americana. rPer a 10 was expressed in Escherichia coli and purified in soluble form, yielding 0.75 mg/liter of culture. Homology of the Per a 10 protein sequence exhibite...

  20. Recombination sites in plasmid drug resistance gene amplification.

    OpenAIRE

    Peterson, B. C.; Rownd, R. H.

    1985-01-01

    The resistance plasmid NR1 derivative pRR330 consists of a neomycin-kanamycin resistance gene (neo-kan) flanked by directly repeated sequences of both insertion element IS1 DNA (768 base pairs) and 840 base pairs of DNA which are a part of the chloramphenicol acetyltransferase (cam) gene. Most Escherichia coli cell populations that were cultured in high neomycin concentrations carried plasmids whose neo-kan gene amplification was mediated either by IS1 DNA or by cam DNA as homologous recombin...

  1. Radiative recombination of complex ions

    Science.gov (United States)

    Gould, R. J.

    1978-01-01

    The rates of radiative capture by atomic systems is computed for the first four ionization stages of the abundant elements C, N, O, Ne, Mg, Si, S, and Ar. A simple prescription is given for calculating the rates for systems in higher ionization stages. Results for capture to atomic helium are also given. In the general case, recent calculations of photoionization cross sections have been used to compute capture rates to levels of the ground-state configuration of the recombined species. Captures to other levels of the valence shell and to the higher shells are evaluated using hydrogenic formulae but with a correction factor which takes into account the nonhydrogenic nature of these states. This correction factor is due to the incomplete shielding by the inner electrons and represents essentially an effective charge for the recombining ion; it is determined semiempirically from an appropriate weighting of values derived from the observed level structure for each species. In some cases, for the capture to neutral atomic systems, its application increases the resulting computed recombination rate by a significant amount (about 50%). Computed recombination rates are tabulated for the four ionization stages at an electron temperature of 10,000 K and for the first stage at 100 K. A convenient procedure is outlined for evaluating the rates at other temperatures in the general neighborhood of these values.

  2. Recombination luminescence in rigid media

    International Nuclear Information System (INIS)

    When separated ion-pairs result from the ?-irradiation of pure or doped matrices or from solute photoionization, some of the photoejected electrons undergo spontaneous recombination, giving rise to the so-called isothermal luminescence (ITL). Cation-anion recombination takes place when molecular diffusion is possible; that is, it appears mostly in thermoluminescence (TL), upon warming irradiated samples. Electrons are photoextracted from matrix traps or from anions, and the neutralization luminescence is designated as stimulated luminescence (SL). ITL, TL, and SL all constitute very sensitive test for the presence of charged species. ITL decay kinetics throw some light on the recombination mechanism. In TL studies, the maxima of the glow curves correlate with phase transition temperatures (crystal ? crystal or glass ? crystal), providing insight into matrix molecular dynamics. From SL spectra, positive and negative charges can be discriminated, and various characteristics of the negative ions - electrons or anions - can be attained. The global SL irrespective of its spectrum composition, SL emission spectra, and SL excitation spectra or stimulation spectra are reviewed. The SL spectra, being specific of negative charged species, complement optical absorption spectroscopy when cations and anions have undistinguishable spectra. Even though radiative charge recombination constitutes the final step of ion-pair existence, it may serve to track back the successive stagrve to track back the successive stages of photoelectron life: electron ejection, matrix trapping or the attachments of electrons to molecules or radicals, and the release of trapped electrons. (Yamashita, S.)

  3. Improving recombinant protein purification yield

    Science.gov (United States)

    Production of adequate amounts of recombinant proteins is essential for antibody production, biochemical activity study, and structural determination during the post-genomic era. It’s technologically challenging and a limiting factor for tung oil research because analytical reagents such as high qua...

  4. Recombination Activator Function of the Novel RAD51- and RAD51B-binding Protein, Human EVL*S?

    OpenAIRE

    Takaku, Motoki; Machida, Shinichi; Hosoya, Noriko; Nakayama, Shugo; Takizawa, Yoshimasa; Sakane, Isao; Shibata, Takehiko; Miyagawa, Kiyoshi; Kurumizaka, Hitoshi

    2009-01-01

    The RAD51 protein is a central player in homologous recombinational repair. The RAD51B protein is one of five RAD51 paralogs that function in the homologous recombinational repair pathway in higher eukaryotes. In the present study, we found that the human EVL (Ena/Vasp-like) protein, which is suggested to be involved in actin-remodeling processes, unexpectedly binds to the RAD51 and RAD51B proteins and stimulates the RAD51-mediated homologous pairing and strand exchang...

  5. In utero recombinant adeno-associated virus gene transfer in mice, rats, and primates

    OpenAIRE

    Marrero Luis; Dunn Daisy; Larson Janet E; Garrett Deiadra J; Craig, Cohen J.

    2003-01-01

    Abstract Background Gene transfer into the amniotic fluid using recombinant adenovirus vectors was shown previously to result in high efficiency transfer of transgenes into the lungs and intestines. Adenovirus mediated in utero gene therapy, however, resulted in expression of the transgene for less than 30 days. Recombinant adenovirus associated viruses (rAAV) have the advantage of maintaining the viral genome in daughter cells thus providing for long-term expression of transgenes. Methods Re...

  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. The ?0 polarization and the recombination mechanism

    International Nuclear Information System (INIS)

    We use the recombination and the Thomas Precession Model to obtain a prediction for the ?0 polarization in the p+p??0+X reaction. We study the effect of the recombination function on the ?0 polarization

  8. The ?0 polarization and the recombination mechanism

    International Nuclear Information System (INIS)

    We use the recombination and the Thomas Precession Model to obtain a prediction for the ?0 polarization in the p+p ? ?0 + X reaction. We study the effect of the recombination function on the ?0 polarization. (author)

  9. 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)

  10. Cervical cancer isolate PT3, super-permissive for adeno-associated virus replication, over-expresses DNA polymerase ?, PCNA, RFC and RPA

    Directory of Open Access Journals (Sweden)

    Melchert Russell B

    2009-04-01

    Full Text Available Abstract Background Adeno-associated virus (AAV type 2 is an important virus due to its use as a safe and effective human gene therapy vector and its negative association with certain malignancies. AAV, a dependo-parvovirus, autonomously replicates in stratified squamous epithelium. Such tissue occurs in the nasopharynx and anogenitals, from which AAV has been clinically isolated. Related autonomous parvoviruses also demonstrate cell tropism and preferentially replicate in oncogenically transformed cells. Combining these two attributes of parvovirus tropism, squamous and malignant, we assayed if AAV might replicate in squamous cervical carcinoma cell isolates. Results Three primary isolates (PT1-3 and two established cervical cancer cell lines were compared to normal keratinocytes (NK for their ability to replicate AAV. One isolate, PT3, allowed for high levels of AAV DNA replication and virion production compared to others. In research by others, four cellular components are known required for in vitro AAV DNA replication: replication protein A (RPA, replication factor C (RFC, proliferating cell nuclear antigen (PCNA, and DNA polymerase delta (POLD1. Thus, we examined PT3 cells for expression of these components by DNA microarray and real-time quantitative PCR. All four components were over-expressed in PT3 over two representative low-permissive cell isolates (NK and PT1. However, this super-permissiveness did not result in PT3 cell death by AAV infection. Conclusion These data, for the first time, provide evidence that these four cellular components are likely important for AAV in vivo DNA replication as well as in vitro. These data also suggest that PT3 will be a useful reagent for investigating the AAV-permissive transcriptome and AAV anti-cancer effect.

  11. 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

  12. Phage display mediated immuno-PCR

    OpenAIRE

    Guo, Yong-chao; Zhou, Ya-feng; Zhang, Xian-en; Zhang, Zhi-ping; Qiao, Yan-mei; Bi, Li-jun; Wen, Ji-kai; Liang, Mi-fang; Zhang, Ji-bin

    2006-01-01

    Immuno-PCR (IPCR) is a powerful detection technology in immunological study and clinical diagnosis due to its ultrasensitivity. Here we introduce a new strategy termed phage display mediated immuno-PCR (PD-IPCR). Instead of utilization of monoclonal antibody (mAb) and chemically bond DNA that required in the conventional IPCR, a recombinant phage particle is applied as a ready reagent for IPCR experiment. The surface displayed single chain variable fragment (scFv) and phage DNA themselves can...

  13. 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...

  14. Osmoregulation of Dimer Resolution at the Plasmid pJHCMW1 mwr Locus by Escherichia coli XerCD Recombination

    OpenAIRE

    Pham, H.; Dery, Kj; Sherratt, Dj; Tolmasky, Me

    2002-01-01

    Xer-mediated dimer resolution at the mwr site of plasmid pJHCMW1 is osmoregulated in Escherichia coli. Whereas under low-salt conditions, the site-specific recombination reaction is efficient, under high-salt conditions, it proceeds inefficiently. Regulation of dimer resolution is independent of H-NS and is mediated by changes in osmolarity rather than ionic effects. The low level of recombination at high salt concentrations can be overcome by high levels of PepA or by mutating the ARG box to...

  15. Recombination properties of P1 dlac.

    OpenAIRE

    Porter, R. D.

    1982-01-01

    The P1 dlac prophage plasmid of Escherichia coli K-12 has been utilized as the recipient DNA substrate in experiments with lambda plac5 transduction and with Hfr and F' conjugation. The P1 dlac plasmid does not recombine with lambda plac5 at the elevated levels seen for the F42lac plasmid. Recombination between lambda plac5 and P1 dlac is essentially indistinguishable from recombination between lambda plac5 and a chromosomal lac gene in tems of both level of recombination and recombination pa...

  16. Recombinant protein production in bacterial hosts.

    Science.gov (United States)

    Overton, Tim W

    2014-05-01

    The production of recombinant proteins is crucial for both the development of new protein drugs and the structural determination of drug targets. As such, recombinant protein production has a major role in drug development. Bacterial hosts are commonly used for the production of recombinant proteins, accounting for approximately 30% of current biopharmaceuticals on the market. In this review, I introduce fundamental concepts in recombinant protein production in bacteria, from drug development to production scales. Recombinant protein production processes can often fail, but how can this failure be minimised to rapidly deliver maximum yields of high-quality protein and so accelerate drug discovery? PMID:24246684

  17. Homology-associated nonhomologous recombination in mammalian gene targeting.

    OpenAIRE

    Sakagami, K.; Tokinaga, Y.; Yoshikura, H.; Kobayashi, I.

    1994-01-01

    Nonhomologous (illegitimate) recombination of DNA underlies many changes in the genome. It involves no or little homology between recombining DNAs and has been considered unrelated with homologous recombination, which requires long homology. In mouse cells, however, we found recombination products whose sequences suggest that homologous interaction between DNAs caused nonhomologous recombination with another DNA. The intermediates of homologous recombination were apparently trapped at various...

  18. Accelerated homologous recombination and subsequent genome modification in Drosophila.

    Science.gov (United States)

    Baena-Lopez, Luis Alberto; Alexandre, Cyrille; Mitchell, Alice; Pasakarnis, Laurynas; Vincent, Jean-Paul

    2013-12-01

    Gene targeting by 'ends-out' homologous recombination enables the deletion of genomic sequences and concurrent introduction of exogenous DNA with base-pair precision without sequence constraint. In Drosophila, this powerful technique has remained laborious and hence seldom implemented. We describe a targeting vector and protocols that achieve this at high frequency and with very few false positives in Drosophila, either with a two-generation crossing scheme or by direct injection in embryos. The frequency of injection-mediated gene targeting can be further increased with CRISPR-induced double-strand breaks within the region to be deleted, thus making homologous recombination almost as easy as conventional transgenesis. Our targeting vector replaces genomic sequences with a multifunctional fragment comprising an easy-to-select genetic marker, a fluorescent reporter, as well as an attP site, which acts as a landing platform for reintegration vectors. These vectors allow the insertion of a variety of transcription reporters or cDNAs to express tagged or mutant isoforms at endogenous levels. In addition, they pave the way for difficult experiments such as tissue-specific allele switching and functional analysis in post-mitotic or polyploid cells. Therefore, our method retains the advantages of homologous recombination while capitalising on the mutagenic power of CRISPR. PMID:24154526

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

    Science.gov (United States)

    Iraqui, Ismail; Chekkal, Yasmina; Jmari, Nada; Pietrobon, Violena; Fréon, Karine; Costes, Audrey; Lambert, Sarah A E

    2012-01-01

    Homologous recombination is a universal mechanism that allows repair of DNA and provides support for DNA replication. Homologous recombination is therefore a major pathway that suppresses non-homology-mediated genome instability. Here, we report that recovery of impeded replication forks by homologous recombination is error-prone. Using a fork-arrest-based assay in fission yeast, we demonstrate that a single collapsed fork can cause mutations and large-scale genomic changes, including deletions and translocations. Fork-arrest-induced gross chromosomal rearrangements are mediated by inappropriate ectopic recombination events at the site of collapsed forks. Inverted repeats near the site of fork collapse stimulate large-scale genomic changes up to 1,500 times over spontaneous events. We also show that the high accuracy of DNA replication during S-phase is impaired by impediments to fork progression, since fork-arrest-induced mutation is due to erroneous DNA synthesis during recovery of replication forks. The mutations caused are small insertions/duplications between short tandem repeats (micro-homology) indicative of replication slippage. Our data establish that collapsed forks, but not stalled forks, recovered by homologous recombination are prone to replication slippage. The inaccuracy of DNA synthesis does not rely on PCNA ubiquitination or trans-lesion-synthesis DNA polymerases, and it is not counteracted by mismatch repair. We propose that deletions/insertions, mediated by micro-homology, leading to copy number variations during replication stress may arise by progression of error-prone replication forks restarted by homologous recombination. PMID:23093942

  20. Sexual recombination in Aspergillus tubingensis.

    Science.gov (United States)

    Olarte, Rodrigo A; Horn, Bruce W; Singh, Rakhi; Carbone, Ignazio

    2015-01-01

    Aspergillus tubingensis from section Nigri (black Aspergilli) is closely related to A. niger and is used extensively in the industrial production of enzymes and organic acids. We recently discovered sexual reproduction in A. tubingensis, and in this study we demonstrate that the progeny are products of meiosis. Progeny were obtained from six crosses involving five MAT1-1 strains and two MAT1-2 strains. We examined three loci, including mating type (MAT), RNA polymerase II (RPB2) and ?-tubulin (BT2), and found that 84% (58/69) of progeny were recombinants. Recombination associated with sexual reproduction in A. tubingensis provides a new option for the genetic improvement of industrial strains for enzyme and organic acid production. PMID:25572097

  1. Functional Interactions of Meiotic Recombination Factors Rdh54 and Dmc1

    OpenAIRE

    Chi, Peter; Kwon, Youngho; Moses, Dana N.; Seong, Changhyun; Sehorn, Michael G.; Singh, Akhilesh K.; Tsubouchi, Hideo; Greene, Eric C.; Klein, Hannah L.; Sung, Patrick

    2008-01-01

    Genetic studies in budding and fission yeasts have provided evidence that Rdh54, a Swi2/Snf2-like factor, synergizes with the Dmc1 recombinase to mediate inter-homologue recombination during meiosis. Rdh54 associates with Dmc1 in the yeast two-hybrid assay, but whether the Rdh54-Dmc1 interaction is direct and the manner in which these two recombination factors may functionally co-operate to accomplish their biological task have not yet been defined. Here, using purified Schizosaccharomyces po...

  2. Failure patterns by prognostic group as determined by recursive partitioning analysis (RPA) of 1547 on four radiation therapy oncology group studies in operable non-small cell lung cancer (NSCLC)

    International Nuclear Information System (INIS)

    Purpose: To identify groups of patients who might benefit from more aggressive systemic or local treatment based on failure patterns when unresectable NSCLC was treated by radiation therapy alone. Methods: 1547 patients from 4 RTOG trials treated by RT alone were analyzed for the patterns of first failure by PRA class which was defined by prognostic factors, e.g., stage, KPS, weight loss, pleural effusion, age. All patients were AJCC stage II, IIIA or IIIB with KPS of at least 50 and n previous radiotherapy or chemotherapy for their NSCLC. Progressions in the primary (within irradiated fields), thorax (outside irradiated area), brain and distant metastasis other than brain were compared (two-sided) for each failure category by RPA. Results: The RPA classes are four distinct subgroups that had significantly different median survivals of 12.6, 8.3, 6.2 and 3.3 months for classes I, II, III and IV respectively (all groups p=0.0002). Pair comparison showed that RPA I vs IV p<0.0001, I vs III p=0.006, II vs IV p<0.0001, and III vs IV p=0.06. Conclusions: These results suggest the burden of disease and physiologic compromise in class IV patients are sufficient to cause death before specific sites of failure can be discerned. Site specific treatment strategies (intensive local therapy, combination chemotherapy, prophylactic cranial irradiation) may lead to improved outcome in class I and II, but are unlikely to alter outcome in class III and IV III and IV

  3. Effects of nuclear mutations for recombination and repair functions and of caffeine on mitochondrial recombination

    International Nuclear Information System (INIS)

    Studies of both prokaryotic and eukaryotic organisms indicate that pathways governing repair of damage to nuclear DNA caused by x-ray or ultraviolet irradiation overlap with those controlling recombination. Fourteen nuclear mutants of Saccharomyces cerevisiae were tested in order to determine whether these mutant genes affected mitochondrial recombination. None of the mutations studied significantly affected mitochondrial recombination. The nuclear recombination and repair pathways studied do not overlap with the nuclear pathway which controls recombination of mitochondrial DNA. A second set of experiments was designed to test the effect of caffeine on both nuclear and mitochondrial recombination in Saccharomyces cerevisiae. (U.S.)

  4. 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.

  5. Acceleration of azo dye decolorization by using quinone reductase activity of azoreductase and quinone redox mediator.

    Science.gov (United States)

    Liu, Guangfei; Zhou, Jiti; Wang, Jing; Zhou, Mi; Lu, Hong; Jin, Ruofei

    2009-06-01

    This study demonstrated the effective application of intracellular azoreductase in mediated decolorization of azo dyes. Using the quinone reductase activity of overexpressed azoreductase AZR and quinone redox mediators, the decolorization performance of the recombinant strain Escherichia coli YB was significantly enhanced. In the presence of 0.2 mM lawsone, 75% acid red 27 (1 mM) was decolorized by E. coli YB in only 2 h, which was the highest bacterial decolorization rate ever reported. Compared to lawsone, menadione was a less effective redox mediator. Glucose was found to be the best carbon source for mediated decolorization by E. coli YB. The recombinant strain could complete four rounds of mediated decolorization repeatedly in 12 h. In addition, a 10-min pre-incubation of E. coli JM109 and activated sludge with 2-methylhydroquinone resulted in great improvement of mediated decolorization performance, which may be applied in practical treatment. PMID:19208470

  6. 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...

  7. Dissociative recombination in interstellar clouds

    Science.gov (United States)

    Black, John H.; Van Dishoeck, Ewine F.

    1989-01-01

    Molecular ions play a significant role in the chemistry and evolution of interstellar molecular clouds, even though these regions are overwhelmingly neutral. The dissociative recombination (DR) process governs the abundances of many of these ions and of related neutral species. The gas-phase ion-molecule chemistry of the simplest species is summarized, with emphasis on those problems which are most sensitive to uncertain rates or product branching ratios of DR processes. Examples of the kinds of information needed about DR processes are presented. The importance of the H3(+) ion and prospects for its direct observation are discussed.

  8. Recombination of three ultracold fermionic atoms

    OpenAIRE

    Suno, H.; Esry, B. D.; Greene, Chris H.

    2002-01-01

    Three-body recombination of identical, spin-polarized fermionic atoms in the ultracold limit is investigated. The mechanisms for recombination are described in terms of the ``scattering volume'' $V_p$ in the framework of the adiabatic hyperspherical representation. We have calculated numerically the recombination rate $K_3$ as a function of $V_p$ and have found that $K_3$ scales as $|V_p|^{8/3}$ for small $|V_p|$. A comparison with experimental data is also presented.

  9. Phase II Radiation Therapy Oncology Group trial of conventional radiation therapy followed by treatment with recombinant interferon-? for supratentorial glioblastoma: Results of RTOG 9710

    International Nuclear Information System (INIS)

    Purpose: The aim of this study was to determine whether recombinant human interferon ?-1a (rhIFN-?), when given after radiation therapy, improves survival in glioblastoma. Methods and Materials: After surgery, 109 patients with newly diagnosed supratentorial glioblastoma were enrolled and treated with radiation therapy (60 Gy). A total of 55 patients remained stable after radiation and were treated with rhIFN-? (6 MU/day i.m., 3 times/week). Outcomes were compared with Radiation Therapy Oncology Group glioma historical database. Results: RhIFN-? was well tolerated, with 1 Grade 4 toxicity and 8 other patients experiencing Grade 3 toxicity. Median survival time (MST) of the 55 rhIFN-?-treated patients was 13.4 months. MST for the 34 rhIFN-?-treated in RPA Classes III and IV was 16.9 vs. 12.4 months for historical controls (hazard ratio [HR] = 1.27, 95% confidence interval [CI] = 0.89-1.81). There was also a trend toward improved survival across all RPA Classes comparing the 55 rhIFN-? treated patients and 1,658 historical controls (HR = 1.24, 95% CI = 0.94-1.63). The high rate of early failures (54/109) after radiation and before initiation of rhIFN-? was likely caused by stricter interpretation of early radiographic changes in the current study. Matched-pair and intent-to-treat analyses performed to try to address this bias showed no difference in survival between study patients and controls. Conclusion: RhIFN-? given after conventional radiation therapy was nventional radiation therapy was well tolerated, with a trend toward survival benefit in patients who remained stable after radiation therapy. These data suggest that rhIFN-? warrants further evaluation in additional studies, possibly in combination with current temozolomide-based regimens

  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. Recombination of three ultracold fermionic atoms.

    Science.gov (United States)

    Suno, H; Esry, B D; Greene, Chris H

    2003-02-01

    Three-body recombination of identical, spin-polarized fermionic atoms in the ultracold limit is investigated using model interactions. The mechanisms for recombination are parametrized by the "scattering volume" V(p) and described in the framework of the adiabatic hyperspherical representation. We have calculated the recombination rate K3 as a function of V(p) and have found K3 proportional, variant |V(p)|(8/3) for small |V(p)|. Recombination near a two-body Feshbach resonance can thus be significant. PMID:12633352

  12. Experimental recombination rates for highly charged ions

    Energy Technology Data Exchange (ETDEWEB)

    Reinhold Schuch [Dept. of Atomic Physics, Stockholm Univ., Frescativ., Stockholm (Sweden)

    2000-01-01

    Recent studies of recombination between free electrons and highly charged ions using electron coolers of heavy-ion storage rings have produced accurate rate coefficients of interest for plasma modeling and diagnostics. Some surprises were discovered which can lead to revisions of recombination models. With bare ions one finds at low energy a strong and puzzling deviation from radiative recombination theory. Dielectronic recombination with C3+, N4+ show that jj coupling gives essential contributions to the cross section also for light ions. (author)

  13. Identifying the nature of charge recombination in organic solar cells from charge-transfer state electroluminescence

    Energy Technology Data Exchange (ETDEWEB)

    Wetzelaer, Gert-Jan A.H. [Molecular Electronics, Zernike Institute for Advanced Materials, University of Groningen (Netherlands); Dutch Polymer Institute, Eindhoven (Netherlands); Kuik, Martijn [Molecular Electronics, Zernike Institute for Advanced Materials, University of Groningen (Netherlands); Blom, Paul W.M. [Molecular Electronics, Zernike Institute for Advanced Materials, University of Groningen (Netherlands); TNO/Holst Centre, Eindhoven (Netherlands)

    2012-10-15

    Charge-transfer (CT) state electroluminescence is investigated in several polymer:fullerene bulk heterojunction solar cells. The ideality factor of the electroluminescence reveals that the CT emission in polymer:fullerene solar cells originates from free-carrier bimolecular recombination at the donor-acceptor interface, rather than a charge-trap-mediated process. The fingerprint of the presence of nonradiative trap-assisted recombination, a voltage-dependent CT electroluminescence quantum efficiency, is only observed for the P3HT:PCBM system, which is explained by a reduction of the competing bimolecular recombination rate. These results are in agreement with measurements of the illumination-intensity dependence of the open-circuit voltage. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  14. Dissociative recombination in planetary ionospheres

    Science.gov (United States)

    Fox, J. L.

    1993-01-01

    Ionization in planetary atmospheres can be produced by solar photoionization, photoelectron impact ionization, and, in auroral regions, by impact of precipitating particles. This ionization is lost mainly in dissociative recombination (DR) of molecular ions. Although atomic ions cannot undergo DR, they can be transformed locally through ion-molecule reactions into molecular ions, or they may be transported vertically or horizontally to regions of the atmosphere where such transformations are possible. Because DR reactions tend to be very exothermic, they can be an important source of kinetically or internally excited fragments. In interplanetary thermospheres, the neutral densities decrease exponentially with altitude. Below the homopause (or turbopause), the atmosphere is assumed to be throughly mixed by convection and/or turbulence. Above the homopause, diffusion is the major transport mechanism, and each species is distributed according to its mass, with the logarithmic derivative of the density with repect to altitude given approximately by -1/H, where H = kT/mg is the scale height. In this expression, T is the neutral temperature, g is the local acceleratiion of gravity, and m is the mass of the species. Thus lighter species become relatively more abundant, and heavier species less abundant, as the altitude increases. This variation of the neutral composition can lead to changes in the ion composition; furthermore, as the neutral densities decrease, dissociative recombination becomes more important relative to ion-neutral reactions as a loss mechanism for molecular ions.

  15. 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)

  16. Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution

    OpenAIRE

    Monjane Adérito L; van der Walt Eric; Varsani Arvind; Rybicki Edward P; Martin Darren P

    2011-01-01

    Abstract Background Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae), the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat p...

  17. 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

  18. Molecular mechanism of class switch recombination: linkage with somatic hypermutation.

    Science.gov (United States)

    Honjo, Tasuku; Kinoshita, Kazuo; Muramatsu, Masamichi

    2002-01-01

    Class switch recombination (CSR) and somatic hypermutation (SHM) have been considered to be mediated by different molecular mechanisms because both target DNAs and DNA modification products are quite distinct. However, involvement of activation-induced cytidine deaminase (AID) in both CSR and SHM has revealed that the two genetic alteration mechanisms are surprisingly similar. Accumulating data led us to propose the following scenario: AID is likely to be an RNA editing enzyme that modifies an unknown pre-mRNA to generate mRNA encoding a nicking endonuclease specific to the stem-loop structure. Transcription of the S and V regions, which contain palindromic sequences, leads to transient denaturation, forming the stem-loop structure that is cleaved by the AID-regulated endonuclease. Cleaved single-strand tails will be processed by error-prone DNA polymerase-mediated gap-filling or exonuclease-mediated resection. Mismatched bases will be corrected or fixed by mismatch repair enzymes. CSR ends are then ligated by the NHEJ system while SHM nicks are repaired by another ligation system. PMID:11861601

  19. Distance from cohesive end site cos determines the replication requirement for recombination in phage lambda.

    OpenAIRE

    Stahl, F. W.; Kobayashi, I.; Stahl, M. M.

    1982-01-01

    Previous work showed that crossing-over in the middle of the chromosome of phage lambda requires more DNA replication than does crossing-over near the termini. Relocation of cos, the sequence that determines the lambda termini, alters the requirements for replication in a given marked interval, demonstrating that distance from cos determines the amount of DNA replication that is required for genetic exchange. This result supports a break and copy mechanism for recombination mediated by the re...

  20. Episomal Persistence of Recombinant Adenoviral Vector Genomes during the Cell Cycle In Vivo

    OpenAIRE

    Ehrhardt, Anja; Xu, Hui; Kay, Mark A.

    2003-01-01

    Previously we showed that recombinant adenoviral helper-dependent (HD) vectors result in long-term transgene expression levels in vivo which slowly declined by 95% over a period of 1 year. In this study, we further establish that this was not predominantly immune mediated. To determine if cell turnover was responsible for the loss of transgene expression, we induced rapid hepatocyte cell cycling in mouse liver, by performing a surgical two-thirds partial hepatectomy. We observed a 55 and 65% ...

  1. Recombinant norovirus-specific scFv inhibit virus-like particle binding to cellular ligands

    OpenAIRE

    Hardy Michele E; Ettayebi Khalil

    2008-01-01

    Abstract Background Noroviruses cause epidemic outbreaks of gastrointestinal illness in all age-groups. The rapid onset and ease of person-to-person transmission suggest that inhibitors of the initial steps of virus binding to susceptible cells have value in limiting spread and outbreak persistence. We previously generated a monoclonal antibody (mAb) 54.6 that blocks binding of recombinant norovirus-like particles (VLP) to Caco-2 intestinal cells and inhibits VLP-mediated hemagglutination. In...

  2. 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

  3. 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.

  4. 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...

  5. Titania Photocatalysis beyond Recombination: A Critical Review

    Directory of Open Access Journals (Sweden)

    Bunsho Ohtani

    2013-11-01

    Full Text Available This short review paper shows the significance of recombination of a photoexcited electron and a hole in conduction and valence bands, respectively, of a titania photocatalyst, since recombination has not yet been fully understood and has not been evaluated adequately during the past several decades of research on heterogeneous photocatalysis.

  6. 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.

  7. 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.

  8. 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.)

  9. [Construction and application of a recombinant plasmid inducing cell death in hepatocytes after transfection].

    Science.gov (United States)

    Gao, Chunchen; Zhao, Junlong; Han, Jun; Li, Dongdong; Zhao, Gaoyang; Han, Hua; Qin, Hongyan

    2015-04-01

    Objective The mechanisms of mesenchymal stromal cells (MSCs)-mediated treatment of liver damage have been unclear. Two major mechanisms, which involve paracrine effects and/or direct trans-differentiation, have been proposed. To clarify which mechanism is more important, we planned to construct a recombinant plasmid expressing green fluorescent protein (GFP) driven by the cytomegalovirus (CMV) promoter and Pseudomonas aeruginosa exotoxin 40 (PE40) driven by the albumin (alb) promoter, which can induce cell death as soon as MSCs differentiate into hepatocytes. Methods To construct the recombinant eukaryotic expression vector pFlag-CMV-GFP-TM-albp-PE40, GFP, transmembrane domain of DLL1, alb promoter and PE40 were obtained by PCR and were inserted into pFlag-CMV-1. The expression of GFP was observed under a fluorescence microscope and the killing effect on hepatocytes was analyzed by flow cytometry. Results The recombinant plasmid inducing cell death in hepatocytes was successfully constructed, suggesting that the plasmid could be employed to study the mechanism of MSCs-mediated treatment on liver damage. Conclusion This study might provide a promising tool for revealing the mechanism of MSCs-mediated treatment on liver diseases. PMID:25854570

  10. Metabolism of postsynaptic recombination intermediates.

    Science.gov (United States)

    Adelman, Carrie A; Boulton, Simon J

    2010-09-10

    DNA double strand breaks and blocked or collapsed DNA replication forks are potentially genotoxic lesions that can result in deletions, aneuploidy or cell death. Homologous recombination (HR) is an essential process employed during repair of these forms of damage. HR allows for accurate restoration of the damaged DNA through use of a homologous template for repair. Although inroads have been made towards understanding the mechanisms of HR, ambiguity still surrounds aspects of the process. Until recently, relatively little was known concerning metabolism of postsynaptic RAD51 filaments or how synthesis dependent strand annealing intermediates are processed. This review discusses recent findings implicating RTEL1, HELQ and the Caenorhabditis elegans RAD51 paralog RFS-1 in post-strand exchange events during HR. PMID:20493853

  11. Quality control of homologous recombination.

    Science.gov (United States)

    Liu, Ting; Huang, Jun

    2014-10-01

    Exogenous and endogenous genotoxic agents, such as ionizing radiation and numerous chemical agents, cause DNA double-strand breaks (DSBs), which are highly toxic and lead to genomic instability or tumorigenesis if not repaired accurately and efficiently. Cells have over evolutionary time developed certain repair mechanisms in response to DSBs to maintain genomic integrity. Major DSB repair mechanisms include non-homologous end joining and homologous recombination (HR). Using sister homologues as templates, HR is a high-fidelity repair pathway that can rejoin DSBs without introducing mutations. However, HR execution without appropriate guarding may lead to more severe gross genome rearrangements. Here we review current knowledge regarding the factors and mechanisms required for accomplishment of accurate HR. PMID:24858417

  12. 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.

  13. 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...

  14. 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

  15. Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination.

    Science.gov (United States)

    Colloms, Sean D; Merrick, Christine A; Olorunniji, Femi J; Stark, W Marshall; Smith, Margaret C M; Osbourn, Anne; Keasling, Jay D; Rosser, Susan J

    2014-02-01

    Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by C31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. C31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition. PMID:24225316

  16. The Cre/loxP recombination system for production of infectious mouse polyomavirus.

    Science.gov (United States)

    Hron, Tomáš; Spanielová, Hana; Suchanová, Ji?ina; Forstová, Jitka

    2013-09-01

    Murine polyomavirus mutants are frequently produced for experimental as well as therapy purposes. Commonly used methods for preparation of mutant viral genomes from recombinant vectors are laborious and give variable yields and quality. We describe an efficient and reproducible Cre/loxP-mediated recombination system that generates polyomavirus genomes from recombinant plasmid in vivo. We designed and constructed two variants of recombinant vectors containing the wild-type polyomavirus genome flanked by loxP homologous sites. The loxP sites were introduced either into the intronic region of early genes or between the two poly(A) signal sites of convergent transcriptional units. After cotransfection of the recombinant plasmids with the Cre-expressing vector into mouse 3T6 cells, we obtained infectious virus from the genome variant containing loxP site in the intronic region, but we failed to isolate any infectious virus from the viral genome containing loxP site between poly(A) signals. We show that the Cre/loxP-based method of polyomavirus production is simple, expedient, and reproducible and works with satisfactory efficiency. PMID:23800406

  17. 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.

  18. Containment air circulation for optimal hydrogen recombination

    International Nuclear Information System (INIS)

    An accepted first-line defense for hydrogen mitigation is to design for the hydrogen to be rapidly mixed with the containment atmosphere and diluted to below flammability concentrations. Then, as hydrogen continues to be produced in the longer term, recombiners can be used to remove hydrogen: recombiners can be located in forced-air ducts or passive recombiners can be distributed within containment and the heat of recombination used to promote local air circulation. However, this principle does not eliminate the possibility of high hydrogen concentrations at locations removed from the recombiners. An improvement on this strategy is to arrange for a specific, buoyancy-driven, overall circulation of the containment atmosphere such that the recombiners can be located within the recirculation flow, immediately downstream of the hydrogen source. This would make the mixing process more predictable and solve the mass-transfer problem associated with distributed recombiners. Ideally, the recombiners would be located just above the hydrogen source so that the heat of recombination would assist the overall circulation. In this way, the hydrogen would be removed as close as possible to the source, thereby minimizing the amount of hydrogen immediately downstream of the source and reducing the hydrogen concentration to acceptable levels at other locations. Such a strategy requires the containment volume to be divided into an upflow path, past the hydrogen source and the recombiner, and a downflow path to complete the circuit. The flow could be generated actively using fans or passively using buoyancy forces arising from the difference in density of gases in the upfiow and downflow paths; the gases in the downflow path being cooled at an elevated heat sink. (author)

  19. 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

  20. Expression of human factor IX by microencapsulated recombinant fibroblasts.

    Science.gov (United States)

    Liu, H W; Ofosu, F A; Chang, P L

    1993-06-01

    Deficiency of clotting factor IX (FIX) causes hemophilia B in humans. We propose a novel approach to its treatment by engineering FIX-secreting cell lines suitable for implantation in different allogeneic hosts. To prevent graft rejection following implantation, the recombinant cells can be protected with biocompatible membranes that permit exit of FIX but not entry of cellular immune mediators. To explore the feasibility of this approach, we now report on the creation of mouse Ltk- fibroblast cell lines that can deliver FIX through such immune-protective membranes. Mouse fibroblasts (Ltk-) were transfected with the cDNA for human FIX and clones secreting high levels of FIX were isolated. About 70% of the secreted FIX was biologically active. Over 98% of the recovered biological activity was precipitable by barium citrate, indicating appropriate. gamma-carboxylation of the secreted FIX. The secreted FIX was similar in molecular weight and immunoreactivity to plasma-derived human FIX. Upon enclosure in microcapsules fabricated from the biocompatible polymers, alginate-polylysine-alginate, the cells survived the encapsulation procedure with about 70-90% viability, proliferated within the microcapsules to twice their original number within 2 weeks, and continued to secrete FIX into the culture medium at similar rates as the unencapsulated cells. The biological activity, degree of post-translational gamma-carboxylation, and immunoreactivity of the FIX recovered from the culture media of the encapsulated cells were identical to those of the FIX secreted by the unencapsulated cells. In conclusion, fibroblasts engineered to secrete recombinant human FIX can proliferate and continue to secrete biologically active FIX through the alginate microcapsules. This demonstrates the feasibility of using microencapsulated recombinant cells to deliver human FIX and the potential for allogeneic somatic gene therapy for hemophilia B. PMID:8338876

  1. Failure patterns by prognostic group determined by recursive partitioning analysis (RPA) of 1547 patients on four radiation therapy oncology group (RTOG) studies in inoperable nonsmall-cell lung cancer (NSCLC)

    International Nuclear Information System (INIS)

    Purpose: To identify groups of patients who might benefit from more aggressive systemic or local treatment, based on failure patterns when unresectable NSCLC was treated by radiation therapy (RT) alone. Methods: From 4 RTOG trials, 1547 patients treated by RT alone were analyzed for patterns of first failure by RPA class defined by prognostic factors, including KPS, weight loss, nodal stage, pleural effusion, age and radiation therapy dose. All patients had NSCLC AJCC Stage II, IIIA, or IIIB, KPS > 50, with no previous RT or chemotherapy. Progressions in the primary (within irradiated fields), thorax (outside irradiated area, but within thorax), brain and distant metastasis other than brain were compared (2-sided) for each failure category by RPA. Results: The RPA classes were 4 distinct subgroups that had significantly different median survivals of 12.6, 8.3, 6.3 and 3.3 months for Classes I, II, III and IV, respectively, (all groups, p = 0.0002). There were 583, 667, 249 and 48 patients in Classes I, II, III and IV, respectively. Primary failure was seen in 27%, 25%, 21% and 10% for Classes I, II, III, and IV, respectively (I vs. IV, p = 0.014; II vs. IV, p = 0.022). Distant metastasis, including brain metastasis, occurred at significantly higher rates among Classes I and II (58% and 54%) than in Classes III and IV (42% and 27%). A higher rate (58%) of death without an identifiable site of failure was found in Class IV than in Classes I, II and III (27%, 28% and 36%in Classes I, II and III (27%, 28% and 36%, respectively). Conclusions: The data suggest that physiologic compromise from the intrathoracic disease in Class IV patients is sufficient to cause death before specific sites of failure became evident. Clinical investigations using treatments directed at specific sites of failure could lead to improved outcome for Class I, II and, possibly, Class III patients. Inclusion of Class IV patients in clinical trials may obscure outcomes

  2. Inhibitor specificity of recombinant and endogenous caspase-9.

    Science.gov (United States)

    Ryan, Ciara A; Stennicke, Henning R; Nava, Victor E; Burch, Jennifer B; Hardwick, J Marie; Salvesen, Guy S

    2002-09-01

    Apoptosis triggered through the intrinsic pathway by radiation and anti-neoplastic drugs is initiated by the activation of caspase-9. To elucidate control mechanisms in this pathway we used a range of synthetic and natural reagents. The inhibitory potency of acetyl-Asp-Glu-Val-Asp-aldehyde ('Ac-DEVD-CHO'), benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone ('Z-VAD-FMK') and the endogenous caspase inhibitor X-chromosome-linked inhibitor of apoptosis protein ('XIAP') against recombinant caspase-9 were predictive of the efficacy of these compounds in a cell-free system. However, the viral proteins CrmA and p35, although potent inhibitors of recombinant caspase-9, had almost no ability to block caspase-9 in this system. These findings were also mirrored in cell expression studies. We hypothesize that the viral inhibitors CrmA and p35 are excluded from reacting productively with the natural form of active caspase-9 in vivo, making the potency of inhibitors highly context-dependent. This is supported by survival data from a mouse model of apoptosis driven by Sindbis virus expressing either p35 or a catalytic mutant of caspase-9. These results consolidate previous findings that CrmA is a potent inhibitor of caspase-9 in vitro, yet fails to block caspase-9-mediated cell death. PMID:12067274

  3. 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 1.2mM. 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 0.93µg/L and a broad dynamic range from 0.93 to 40.32?g/L for MC-LR, demonstrating the improved analytical performance. PMID:25459056

  4. Electron-ion recombination rates for merged-beams experiments

    Energy Technology Data Exchange (ETDEWEB)

    Pajek, M. [Pedagogical Univ., Kielce (Poland)

    1994-12-31

    Energy dependence of the electron-ion recombination rates are studied for different recombination processes (radiative recombination, three-body recombination, dissociative recombination) for Maxwellian relative velocity distribution of arbitrary asymmetry. The results are discussed in context of the electron-ion merged beams experiments in cooling ion storage rings. The question of indication of a possible contribution of the three-body recombination to the measured recombination rates versus relative energy is particularly addressed. Its influence on the electron beam temperature derived from the energy dependence of recombination rate is discussed.

  5. Recombinant IgE antibody engineering to target EGFR.

    Science.gov (United States)

    Spillner, Edzard; Plum, Melanie; Blank, Simon; Miehe, Michaela; Singer, Josef; Braren, Ingke

    2012-09-01

    Monoclonal antibodies have become a mainstay for the targeted treatment of cancer today. Some of the most successful targets of monoclonal antibodies are constituted by the epidermal growth factor receptor family spearheaded by the epidermal growth factor receptor (EGFR). Prompted by studies indicating that IgE compared to IgG may harness alternate effector functions to eradicate malignant cells, we addressed the establishment, engineering, and the potential tumoricidal effects of recombinant anti-EGFR IgE. Therefore, two different therapeutic EGFR-specific antibodies, 225 and 425, were chosen for re-cloning into different chimeric IgE and IgG formats and produced in human cells. Simultaneous antibody binding to the sEGFR demonstrated accessibility of both epitopes for recombinant IgE. Proliferation and cytotoxicity assays demonstrated signal blocking and effector mediating capability of IgE isotypes. Pronounced degranulation in the presence of sEGFR upon activation exclusively with two IgE antibodies verified the epitope proximity and provides evidence that tumor-targeting by anti-EGFR IgE is safe with regard to soluble target structures. Degranulation mediated by tumor cells expressing EGFR could be demonstrated for singular and combined IgE antibodies; however, use of two IgE specificities was not superior to use of one IgE alone. The data suggest that the surface distribution of EGFR is optimally suited to mount a robust effector cell trigger and corroborate the potential and specificity of the IgE/IgE receptor network to react to xenobiotic or pathogenic patterns for targeting malignancies. PMID:22674055

  6. Influence of exogenous phytohormones, methyl jasmonate and suppressors of jasmonate biosynthesis on Agrobacterium-mediated transient expression in Nicotiana excelsior

    OpenAIRE

    Kuchuk M. V.; Gerasymenko I. M.; Sindarovska Y. R.; Sheludko Y. V.

    2012-01-01

    Our aim was to investigate the influence of some exogenous agents on the recombinant protein accumulation in plants via Agrobacterium-mediated transient expression. Methods. Agrobacterium-mediated transient expression method, spectrophotometric methods for protein analysis, statistical calculations. Results. It was shown that the tested compounds in different concentrations (namely, auxins, cytokinin, methyl jasmonate and suppressors of jasmonate biosynthesis (phenidon and diethyldithiocarbam...

  7. Alu repeats increase local recombination rates

    Directory of Open Access Journals (Sweden)

    Hedges Dale J

    2009-11-01

    Full Text Available Abstract Background Recombination rates vary widely across the human genome, but little of that variation is correlated with known DNA sequence features. The genome contains more than one million Alu mobile element insertions, and these insertions have been implicated in non-homologous recombination, modulation of DNA methylation, and transcriptional regulation. If individual Alu insertions have even modest effects on local recombination rates, they could collectively have a significant impact on the pattern of linkage disequilibrium in the human genome and on the evolution of the Alu family itself. Results We carried out sequencing, SNP identification, and SNP genotyping around 19 AluY insertion loci in 347 individuals sampled from diverse populations, then used the SNP genotypes to estimate local recombination rates around the AluY loci. The loci and SNPs were chosen so as to minimize other factors (such as SNP ascertainment bias and SNP density that could influence recombination rate estimates. We detected a significant increase in recombination rate within ~2 kb of the AluY insertions in our African population sample. To test this observation against a larger set of AluY insertions, we applied our locus- and SNP-selection design and analyses to the HapMap Phase II data. In that data set, we observed a significantly increased recombination rate near AluY insertions in both the CEU and YRI populations. Conclusion We show that the presence of a fixed AluY insertion is significantly predictive of an elevated local recombination rate within 2 kb of the insertion, independent of other known predictors. The magnitude of this effect, approximately a 6% increase, is comparable to the effects of some recombinogenic DNA sequence motifs identified via their association with recombination hot spots.

  8. A MEDIATOR METHYLATION MYSTERY: JMJD1C DEMETHYLATES MDC1 TO REGULATE DNA DAMAGE REPAIR

    OpenAIRE

    Lu, Jian; Matunis, Michael J.

    2013-01-01

    Mediator of DNA-Damage Checkpoint 1 (MDC1) has a central role in repair of DNA double-strand breaks (DSBs) by both homologous recombination and nonhomologous end joining, and its function is regulated by post-translational phosphorylation, ubiquitylation, and SUMOylation. In this issue, a new study by Watanabe et al. reveals that methylation of MDC1 is also critical for its function in DSB repair and specifically affects repair through BRCA1-dependent homologous recombination.

  9. Recombination in narrow-gapped semiconductors

    International Nuclear Information System (INIS)

    In narrow-gapped semiconductors of the type Hgsub(1-x)Cdsub(x)Te as well as in lead chalcogenides and their mixed crystals with energy gaps of some tenths of eV, the band-band recombination processes dominate if the samples are sufficiently perfect in their crystal lattices. The relative importance of the radiative or Auger recombination depends on the width of the energy gap and the charge carrier concentration. In the extreme case of very narrow energy gaps plasmon and one-electron recombination occurs additionally

  10. Secretion of the antibacterial recombinant protein enbocin.

    Science.gov (United States)

    Goo, Tae Won; Yun, Eun Young; Kim, Sung Wan; Choi, Kwang Ho; Kang, Seok Woo; Kwon, Kisang; Choi, Joung-Soon; Kwon, O-Yu

    2008-01-01

    The insect baculovirus expression vector system (BEVS) is useful for the production of biologically active recombinant proteins. However, the overexpression of foreign proteins in this system often results in misfolded proteins and the formation of protein aggregates. To overcome this limitation, we have developed a versatile baculovirus expression and secretion system using the Bombyx mori protein disulfide isomerase (bPDI) as a fusion partner. bPDI gene fusion improved the secretion and antibacterial activity of recombinant enbocin proteins. Thus, bPDI gene fusion is a useful addition to the BEVS for the large-scale production of bioactive recombinant proteins. PMID:18533475

  11. Plasma shielding effects on ionic recombination

    International Nuclear Information System (INIS)

    Monte Carlo calculations of the ion-ion recombination rate coefficient for the Kr++F-+Ar reaction. The effect of other ions on the recombination rate is taken into account by use of the Debye screened potential rather than the Coulomb potential. This potential should be valid for ion densities between 1013 and 1015 cm-3. Results are presented for ion densities in this range and for neutral pressures of 0.5 to 8.0 atm. It is found that screening effects significantly decrease the ion-ion recombination rate

  12. 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

  13. 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(+).

  14. Halogen recombination: dissociation reactions. Current status

    International Nuclear Information System (INIS)

    Recombination and dissociation rate constants for halogens, obtained by a variety of experimental techniques, are assembled and compared. In general, more accurate and precise rate constants are obtained by more recent investigators, who learned from the experiences of their predecessors. Surprisingly, a large amount of data on recombination of halogen atoms, in the presence of even the simplest third bodies, is still not available. On the other hand, much of the available data can now be considered quite reliable. Trajectory calculations yield recombination rate constants in fair agreement with experiments. 6 figures, 70 references

  15. Low levels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders.

    Science.gov (United States)

    Frahry, Matthew Blake; Sun, Cheng; Chong, Rebecca A; Mueller, Rachel Lockridge

    2015-02-01

    Across the tree of life, species vary dramatically in nuclear genome size. Mutations that add or remove sequences from genomes-insertions or deletions, or indels-are the ultimate source of this variation. Differences in the tempo and mode of insertion and deletion across taxa have been proposed to contribute to evolutionary diversity in genome size. Among vertebrates, most of the largest genomes are found within the salamanders, an amphibian clade with genome sizes ranging from ~14 to ~120 Gb. Salamander genomes have been shown to experience slower rates of DNA loss through small (i.e., deletions than do other vertebrate genomes. However, no studies have addressed DNA loss from salamander genomes resulting from larger deletions. Here, we focus on one type of large deletion-ectopic-recombination-mediated removal of LTR retrotransposon sequences. In ectopic recombination, double-strand breaks are repaired using a "wrong" (i.e., ectopic, or non-allelic) template sequence-typically another locus of similar sequence. When breaks occur within the LTR portions of LTR retrotransposons, ectopic-recombination-mediated repair can produce deletions that remove the internal transposon sequence and the equivalent of one of the two LTR sequences. These deletions leave a signature in the genome-a solo LTR sequence. We compared levels of solo LTRs in the genomes of four salamander species with levels present in five vertebrates with smaller genomes. Our results demonstrate that salamanders have low levels of solo LTRs, suggesting that ectopic-recombination-mediated deletion of LTR retrotransposons occurs more slowly than in other vertebrates with smaller genomes. PMID:25608479

  16. 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.

  17. 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

  18. On the possibility of coherently stimulated recombination and cosmological structure generation: recombination instability.

    OpenAIRE

    Klemperer, W.; Luo, X.; Rosner, R.; Schramm, D. N.

    1995-01-01

    Possible instabilities during cosmological recombination may produce an epoch of nonlinear density growth and fractal-like structural patterns out to the horizon scale at that epoch (approximately 200 Mpc today). With this motivation, we examine the consequences of the change in effective radiative recombination reaction rate coefficients produced by intense stimulated emission. The proton-electron recombination is considered as a natural laser, leading to the formation of spatially nonunifor...

  19. Conjugational Recombination in Escherichia Coli: Genetic Analysis of Recombinant Formation in Hfr X F(-) Crosses

    OpenAIRE

    Lloyd, R. G.; Buckman, C.

    1995-01-01

    The formation of recombinants during conjugation between Hfr and F(-) strains of Escherichia coli was investigated using unselected markers to monitor integration of Hfr DNA into the circular recipient chromosome. In crosses selecting a marker located ~500 kb from the Hfr origin, 60-70% of the recombinants appeared to inherit the Hfr DNA in a single segment, with the proximal exchange located >300 kb from the selected marker. The proportion of recombinants showing multiple exchanges increased...

  20. 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

  1. Selection for Recombination in Structured Populations

    OpenAIRE

    Martin, Guillaume; Otto, Sarah P.; Lenormand, Thomas

    2006-01-01

    In finite populations, linkage disequilibria generated by the interaction of drift and directional selection (Hill-Robertson effect) can select for sex and recombination, even in the absence of epistasis. Previous models of this process predict very little advantage to recombination in large panmictic populations. In this article we demonstrate that substantial levels of linkage disequilibria can accumulate by drift in the presence of selection in populations of any size, provided that the po...

  2. Sister chromatid cohesion and recombination in meiosis

    OpenAIRE

    Heemst, D.; Heyting, C.

    2000-01-01

    Sister chromatids are associated from their formation until their disjunction. Cohesion between sister chromatids is provided by protein complexes, of which some components are conserved across the kingdoms and between the mitotic and meiotic cell cycles. Sister chromatid cohesion is intimately linked to other aspects of chromosome behaviour and metabolism, in particular chromosome condensation, recombination and segregation. Recombination, sister chromatid cohesion and the relation between t...

  3. Rapid host adaptation by extensive recombination

    OpenAIRE

    Walt, Eric; Rybicki, Edward P.; Varsani, Arvind; Polston, J. E.; Billharz, Rosalind; Donaldson, Lara; Monjane, Ade?rito L.; Martin, Darren P.

    2009-01-01

    Experimental investigations into virus recombination can provide valuable insights into the biochemical mechanisms and the evolutionary value of this fundamental biological process. Here, we describe an experimental scheme for studying recombination that should be applicable to any recombinogenic viruses amenable to the production of synthetic infectious genomes. Our approach is based on differences in fitness that generally exist between synthetic chimaeric genomes and the wild-type viruses ...

  4. Dielectronic recombination at low temperatures. III. Recombination coefficients for Mg, Al, Si

    International Nuclear Information System (INIS)

    Effective dielectronic recombination coefficients are calculated for the total recombination, as well as for selected lines and ground and metastable terms of ions of Mg, Al and Si. We restrict the calculation to those ions for which the recombining ion has n=3 valence electrons. Coupling schemes are discussed, and we conclude that in most cases pure LS coupling is not appropriate for the resonance states. The effective recombination coefficients are fitted to a convenient function of temperature in the range 103 K to 6 x 104 K

  5. Determination of recombination in Mycoplasma hominis

    DEFF Research Database (Denmark)

    Jacobsen, Iben SŘgaard; Boesen, Thomas

    2002-01-01

    Mycoplasma hominis has been previously described as a heterogeneous species, and in the present study intraspecies diversity of 20 M. hominis isolates from different individuals was analyzed using parts of the unlinked gyrase B (gyrB), elongation factor Tu (tuf), SRalpha homolog (ftsY), hitB-hitL, excinuclease ABC subunit A (uvrA) and glyceraldehyde-3-phosphate dehydrogenase (gap) genes. The level of variability of these M. hominis genes was low compared with the housekeeping genes from Helicobacter pylori and Neisseria meningitidis, but only few M. hominis isolates had identical sequences in all genes indicating the presence of recombination. In order to test for intergenic recombination, phylogenetic trees were reconstructed for each of the genes but no well-supported bifurcating phylogenetic trees could be obtained. The genes were tested for intragenic recombination using the correlation between linkage disequilibrium and distance between the segregating sites, by the homoplasy ratio (H ratio), and by compatibility matrices. The gap gene showed well-supported evidence for high levels of recombination, whereas recombination was less frequent and not significant within the other genes. The analysis revealed intergenic and intragenic recombination in M. hominis and this may explain the high intraspecies variability. The results obtained in the present study may be of importance for future population studies of Mycoplasma species.

  6. 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

  7. Electron - ion recombination processes - an overview

    International Nuclear Information System (INIS)

    Extensive theoretical and experimental studies have been carried out for the past 20 years on electron - ion recombination processes, as they are applied to the analysis of astrophysical and laboratory plasmas. We review the basic understanding gained through these efforts, with emphasis on some of the more recent progress made in recombination theory as the recombining system is affected by time-dependent electric fields and plasma particles at low temperature. Together with collisional ionization and excitation processes, recombination is important in determining ionization balance and excited-state population in non-equilibrium plasmas. The radiation emitted by plasmas is usually the principal medium with which to study the plasma condition, as it is produced mainly during the recombination and decay of excited states of ions inside the plasma. This is especially true when the plasma under study is not readily accessible by direct probes, as in astrophysical plasmas. Moreover, external probes may sometimes cause undesirable disturbances of the plasma. Electron-ion recombination proceeds in several different modes. The direct modes include three-body recombination (TBR) and one-step radiative recombination (RR), all to the ground- and singly-excited states of the target ions. By contrast, the indirect resonant mode is a two-step dielectronic recombination (DR), which proceeds first with the formation of doubly-excited states by radiationless excitation/capture. The by radiationless excitation/capture. The resonant states thus formed may relax by autoionization and/or radiative cascades. For more exotic modes of recombination, we consider off-shell dielectronic recombination (radiative DR = RDR), in which an electron capture is accompanied by simultaneous radiative emission and excitation of the target ion. Some discussion on attachment of electrons to neutral atoms, resulting in the formation of negative ions, is also given. When resonance states involve one or more electrons in high Rydberg states, presence of an external or intrinsic electric field in the vicinity of the target ions can seriously affect the ionic states involved and the resulting reaction rates. Such perturbative fields can be intrinsic, as in the case of the plasma ion field, or externally imposed. A proper theoretical treatment of this difficult problem is crucial in understanding the recombination process which takes place in a field contaminated environment. The simple off-shell dressing procedure of high Rydberg states by a time-dependent field is reviewed, and the possibility of an anomalously large enhancement in the rates, due to the momentum coherence effect (MCE), is discussed. The presently available data on recombination rates are summarized, and several important deficiencies and future directions for further research are pointed out. Based on the detailed calculations for a number of cases, several empirical rate formulae for RR and DR processes have been generated to summarize the data for ready applications. As the collection of atoms is cooled to very low temperatures, T 8 Ryd, and the bound electrons are ionized by laser irradiation to states of very precisely controlled energies, the prospect for accurate experimental measurements of very-low-energy recombination rates is considered, where the electron temperature can be very low. Therefore, it is of interest to reconsider theoretically some new phenomena which may occur at such cold environments, in which the electron de Broglie wavelength can be very large, and both the density and coherent effects, as well as possible field effects, must be properly taken into account. Finally, a broader understanding of the various recombination processes may be achieved by studying their relationships to other reactions initiated by electron, ion and photon impact. (author)

  8. [High level expression of recombinant chicken interferon-gamma in insect cells].

    Science.gov (United States)

    Kong, Gui-mei; Xu, Jin-jun; Qin, Ai-jian; Jin, Wen-jie; Liu, Yue-long

    2005-10-01

    The recombinant transfer vector pFastBacl-ChIFN-y was constructed by plasmid pcDNA-ChIFN-gamma digested with EcoR I and Not I enzymes and cloned into pFastbacl. Then the transfer vector was transformed into E. coli competent cells DH10Bac which contained the bacmid with amini-attTn7 target site and the helper plasmid. The recombinant bacmid-ChIFN-gamma was generated by transposing themini-Tn7 element located in pFastBacl-ChIFN-gamma to themini-attTn7 attachment site on the Bacmid. Subsequently the recombinant Bacmid-ChIFN-gamma was transfected into the Sf9 insect cells mediated by lipofectin to produce recombinant baculovirus and express recombinant ChIFN-gamma (rChIFN-gamma) products. The result showed that the rChIFN-gamma was successfully expressed in Sf9 cells infected with the recombinant virus by indirect immunofluorescence assay (IFA) at 5 days post-transfection. The biological activity of rChIFN-gamma was identified by its inhibition to Vesicular stomatitis virus-induced cytotoxicity of chicken embryonic fibroblasts (CEF) in vitro. The results showed that the most efficient expression of rChIFN-gamma could be obtained at 96h post-infection with multiplicity of infection (MOI) equal to 1. It is interesting that the viruses such as Avian influenza virus H5N1 or Marek's disease virus (GA strain) could not grow in CEF pre-treated with rChIFN-gamma. Cell pathogenic efficient (CPE) in the CEF infected with H5N1 and GA strain is apparently inhibited by the rChIFN-gamma. However only difference between the HA titres of the supernatant of the pre-treated cells is observed without any obvious inhibition effect in CEF infected with Newcastle disease virus (F48E8 strain). PMID:16342758

  9. Nap1 stimulates homologous recombination by RAD51 and RAD54 in higher-ordered chromatin containing histone H1.

    Science.gov (United States)

    Machida, Shinichi; Takaku, Motoki; Ikura, Masae; Sun, Jiying; Suzuki, Hidekazu; Kobayashi, Wataru; Kinomura, Aiko; Osakabe, Akihisa; Tachiwana, Hiroaki; Horikoshi, Yasunori; Fukuto, Atsuhiko; Matsuda, Ryo; Ura, Kiyoe; Tashiro, Satoshi; Ikura, Tsuyoshi; Kurumizaka, Hitoshi

    2014-01-01

    Homologous recombination plays essential roles in mitotic DNA double strand break (DSB) repair and meiotic genetic recombination. In eukaryotes, RAD51 promotes the central homologous-pairing step during homologous recombination, but is not sufficient to overcome the reaction barrier imposed by nucleosomes. RAD54, a member of the ATP-dependent nucleosome remodeling factor family, is required to promote the RAD51-mediated homologous pairing in nucleosomal DNA. In higher eukaryotes, most nucleosomes form higher-ordered chromatin containing the linker histone H1. However, the mechanism by which RAD51/RAD54-mediated homologous pairing occurs in higher-ordered chromatin has not been elucidated. In this study, we found that a histone chaperone, Nap1, accumulates on DSB sites in human cells, and DSB repair is substantially decreased in Nap1-knockdown cells. We determined that Nap1 binds to RAD54, enhances the RAD54-mediated nucleosome remodeling by evicting histone H1, and eventually stimulates the RAD51-mediated homologous pairing in higher-ordered chromatin containing histone H1. PMID:24798879

  10. Performance testing of passive autocatalytic recombiners (PARs)

    International Nuclear Information System (INIS)

    Passive autocatalytic recombiners (PARs) have been under consideration in the U.S. as a combustible gas control system in advanced light water reactor (ALWR) containments for design basis and severe accidents. PARs do not require a source of power. Instead they use palladium or platinum as a catalyst to recombine hydrogen and oxygen gases into water vapor upon contact with the catalyst. Energy from the recombination of hydrogen with oxygen is released at a relatively slow but continuous rate into the containment which prevents the pressure from becoming too high. The heat produced creates strong buoyancy effects which increases the influx of the surrounding gases to the recombiner. These natural convective flow currents promote mixing of combustible gases in the containment. PARs are self-starting and self-feeding under a very wide range of conditions. The recombination rate of the PAR system needs to be great enough to keep the concentration of hydrogen (or oxygen) below acceptable limits. There are several catalytic recombiner concepts under development worldwide. The USNRC is evaluating a specific design of a PAR which is in an advanced stage of engineering development and has been proposed for ALWR designs. Sandia National laboratories (SNL), under the sponsorship and the direction of the USNRC, is conducting an experimental program to evaluate the performance of PARs. The PAR will be tested at the SURTSEY facility at SNL. The test plan currently includes the following experiments: experiments will be conducted to define the startup characteristics of PARs (i.e., to define what is the lowest hydrogen concentration that the PAR starts recombining the hydrogen with oxygen); experiments will be used to define the hydrogen depletion rate of PARs as a function of hydrogen concentration; and experiments will be used to define the PAR performance in the presence of high concentrations of steam. (author)

  11. 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.

  12. Expression, purification and characterization of recombinant toxins consisting of truncated gastrin 17 and pseudomonas exotoxin.

    Science.gov (United States)

    Feng, Xiao-Li; Liu, Xi-Lin; Lu, Shi-Ying; Ren, Hong-Lin; Li, Yan-Song; Hu, Pan; Wang, Quan; Tong, Weihua; Yan, Dong-Ming; Zhou, Yu; Zhang, Song; Jin, Wen; Liu, Zeng-Shan

    2015-01-01

    Gastric cancer is a major cause of mortality and morbidity around world. However the effectiveness of the current approaches to the diagnosis and treatment of gastric cancer is limited. Recombinant targeted toxins may represent a novel direction of cancer therapy. In this study, we aimed to explore whether recombinant toxins fused with the truncated forms of G17 could target to kill cancer cells by recognizing CCK2R. Four recombinant Pseudomonas toxins PE38 fused with the forward or reverse truncated forms of G17 (G14 and G13) were successfully constructed, expressed, and purified. Their characteristics were further analyzed by SDS-PAGE, western blot and indirect immunofluorescence assay. The cytotoxicity assay demonstrated that only reversely fused recombinant toxins rG14PE38 and rG13PE38 exhibited certain toxicity on several cancer cell lines, and a competition assay indicated that the binding of the reverse gastrin-endotoxin to CCK2R (+) cells may be mediated by interaction between gastrin/gastrin-like and CCK2R. PMID:25353354

  13. H-Ras regulation of TRAIL death receptor mediated apoptosis

    OpenAIRE

    Chen, Jun-jie; Bozza, William P.; Di, Xu; Zhang, Yaqin; Hallett, William; Zhang, Baolin

    2014-01-01

    TNF-related apoptosis-inducing ligand (TRAIL) induces apoptosis through the death receptors (DRs) 4 and/or 5 expressed on the cell surface. Multiple clinical trials are underway to evaluate the antitumor activity of recombinant human TRAIL and agonistic antibodies to DR4 or DR5. However, their therapeutic potential is limited by the high frequency of cancer resistance. Here we provide evidence demonstrating the role of H-Ras in TRAIL receptor mediated apoptosis. By analyzing the genome wide m...

  14. 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 ...

  15. 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

  16. Recombinant collagen and gelatin for drug delivery.

    Science.gov (United States)

    Olsen, David; Yang, Chunlin; Bodo, Michael; Chang, Robert; Leigh, Scott; Baez, Julio; Carmichael, David; Perälä, Maritta; Hämäläinen, Eija-Riitta; Jarvinen, Marko; Polarek, James

    2003-11-28

    The tools of recombinant protein expression are now being used to provide recombinant sources of both collagen and gelatin. The primary focus of this review is to discuss alternatives to bovine collagen for biomedical applications. Several recombinant systems have been developed for production of human sequence collagens. Mammalian and insect cells were initially used, but were thought to be too costly for commercial production. Yeast have been engineered to express high levels of type I homotrimer and heterotrimer and type II and type III collagen. Co-expression of collagen genes and cDNAs encoding the subunits of prolyl hydroxylase has lead to the synthesis of completely hydroxylated, thermostable collagens. Human types I and III collagen homotrimers have been expressed in transgenic tobacco plants, while transgenic mice have been engineered to produce full-length type I procollagen homotrimer as well as a alpha2 (I) homotrimeric mini-collagen. Most recently, a transgenic silkworm system was used to produce a fusion protein containing a collagenous sequence. Each of these transgenic systems holds great promise for the cost-effective large-scale production of recombinant human collagens. As seen in other recombinant expression systems, transgenic silkworms, tobacco, and mice lack sufficient endogenous prolyl hydroxylase activity to produce fully hydroxylated collagen. In mice and tobacco, this was overcome by over-expression of prolyl hydroxylase, analogous to what has been done in yeast and insect cell culture. In addition to recombinant alternatives to bovine collagen, other sources such as fish and sponge collagen are discussed briefly. Recombinant gelatin has been expressed in Pichia pastoris and Hansenula polymorpha in both non-hydroxylated and hydroxylated forms. Pichia was shown to be a highly productive system for gelatin production. The recombinant gelatins produced in yeast are of defined molecular weight and physio-chemical properties and represent a new biomaterial not previously available from animal sources. Genetic engineering has made great progress in the areas of recombinant collagen and gelatin expression, and there are now several alternatives to bovine material that offer an enhanced safety profile, greater reproducibility and quality, and the ability of these materials to be tailored to enhance product performance. PMID:14623401

  17. 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.

  18. Theory of ion-ion recombination

    International Nuclear Information System (INIS)

    A new, basic theory of ion-ion recombination as a function of gas density N is developed from basic microscopic principles. An equation for the distribution in phase space of ion pairs is derived together with an expression for the resulting rate ? of recombination. Alpha is determined by the limiting step of the rate ?sub(rn) for ion reaction and of the rate ?sub(tr) for ion transport to the reaction zone. An analytical solution of the time-dependent Debye-Smoluchowski equation, is provided for transport-reaction under a general interaction V, for an instantaneous reaction (?sub(rn) >?sub(tr)) and for a finite rate (?sub(rn) approximately equal to ?sub(tr)) of reaction within a kinetic sink rendered compressible by variation of gas density. Expressions for the transient recombination rates ?(t) are then derived, and illustrated. A theory that investigates the variation of ? with ion density N+- is also developed. Here the ion-ion interaction V cannot be assumed to be pure coulomb but is solved self-consistently with the recombination. Recombination rates for various systems are illustrated as a function of N by a simplified method for the reaction rate. Finally, two theoretical procedures are proposed for the solution of the general phase-space ion distributions. (author)

  19. The prostaglandin E2 EP1 receptor mediates pain perception and regulates blood pressure

    OpenAIRE

    Stock, Jeffrey L.; Shinjo, Katsuhiro; Burkhardt, John; Roach, Marsha; Taniguchi, Kana; Ishikawa, Toshihisa; Kim, Hyung-suk; Flannery, Patrick J.; Coffman, Thomas M.; Mcneish, John D.; Audoly, Laurent P.

    2001-01-01

    The lipid mediator prostaglandin E2 (PGE2) has diverse biological activity in a variety of tissues. Four different receptor subtypes (EP1–4) mediate these wide-ranging effects. The EP-receptor subtypes differ in tissue distribution, ligand-binding affinity, and coupling to intracellular signaling pathways. To identify the physiological roles for one of these receptors, the EP1 receptor, we generated EP1-deficient (EP1–/–) mice using homologous recombination in embryonic stem cells deriv...

  20. Frequent recombination in telomeric DNA may extend the proliferative life of telomerase-negative cells.

    Science.gov (United States)

    Bailey, Susan M; Brenneman, Mark A; Goodwin, Edwin H

    2004-01-01

    For cells on the path to carcinogenesis, the key to unlimited growth potential lies in overcoming the steady loss of telomeric sequence commonly referred to as the 'end-replication problem' that occurs with each cell division. Most human tumors have reactivated telomerase, a specialized reverse transcriptase that directs RNA-templated addition of telomeric repeats on to chromosomal termini. However, approximately 10% of tumors maintain their telomeres through a recombination-based mechanism, termed alternative lengthening of telomeres or ALT. Here we demonstrate that telomeric DNA undergoes a high rate of a particular type of recombination visualized cytogenetically as sister chromatid exchange (SCE), and that this rate is dependent on genotype. A novel model of ALT is presented in which it is argued that telomeric exchanges, if they are unequal and occur at a sufficiently high frequency, will allow cells to proliferate indefinitely without polymerase-mediated extension of telomeric sequence. PMID:15258249

  1. Limiting efficiency calculation of silicon single-nanowire solar cells with considering Auger recombination

    Science.gov (United States)

    Zhai, Xiongfei; Wu, Shaolong; Shang, Aixue; Li, Xiaofeng

    2015-02-01

    Single-nanowire solar cells (SNSCs) have attracted considerable attention due to their unique light-harvesting capability mediated by the optical antenna effect and the high photoconversion efficiency due to the orthogonalization of the carrier collection to the photon incidence. We present a detailed prediction of the light-conversion efficiency of Si SNSCs based on finite-element simulation and thermodynamic balance analysis, with especially focusing on the comparison between SNSCs and film systems. Carrier losses due to radiative and Auger recombinations are introduced in the analysis of the limiting efficiency, which show that the Auger recombination plays a key role in accurately predicting the efficiency of Si SNSCs, otherwise, the device performance would be strongly overestimated. The study paves a more realistic way to evaluate the nanostructured solar cells based on indirect-band photoactive materials.

  2. Mediation and Conflict Management

    OpenAIRE

    Eisenkopf, Gerald

    2009-01-01

    Mediation is a popular process to manage conflicts, but there is little systematic insight into its mechanisms. This paper discusses the results from an experiment in which a mediator can induce two conflict parties to behave cooperatively. If the mediator recommends cooperative behavior and threatens to punish deviations, she achieves the efficient solution. Similar results even obtain if the mediator is biased towards one party or has no incentive to prevent the conflict. Communication betw...

  3. Shared mediated workspaces

    OpenAIRE

    Handberg, Leif; Gullstro?m, Charlie

    2012-01-01

    Shared mediated spaces provide viable alternatives for meetings and interactions. The development of collaborative mediated workspaces and shared negotiation spaces will have a fundamental impact on all human practices. Previous design-led research, has identified spatial design concepts, such as mediated gaze, and spatial montage, which, if unaddressed, may be said to impose friction, and thus impact negatively on the experience of mediated presence. The current paper discusses a set of conc...

  4. 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

  5. A New Calculation of the Recombination Epoch

    CERN Document Server

    Seager, S; Scott, D; Seager, Sara; Sasselov, Dimitar D.; Scott, Douglas

    1999-01-01

    We have developed an improved recombination calculation of H, HeI, and HeII in the early Universe which involves a line-by-line treatment of each atomic level. We find two major differences compared with previous calculations. Firstly, the ionization fraction x_e is approximately 10% smaller for redshifts <~800, due to non-equilibrium processes in the excited states of H. Secondly, HeI recombination is much slower than previously thought, and is delayed until just before H recombines. We describe the basic physics behind the new results and present a simple way to reproduce our calculation. This should enable fast computation of the ionization history (and quantities such as the power spectrum of CMB anisotropies which depend on it) for arbitrary cosmologies, without the need to consider the hundreds of atomic levels used in our complete model.

  6. Recombinant human erythropoietin in sports: a review

    Scientific Electronic Library Online (English)

    Rafael Maia de Almeida, Bento; Lúcia Menezes Pinto, Damasceno; Francisco Radler de, Aquino Neto.

    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 syst [...] em. 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.

  7. Recombinant human erythropoietin in sports: a review

    Directory of Open Access Journals (Sweden)

    Bento Rafael Maia de Almeida

    2003-01-01

    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.

  8. Together yes, but not coupled: new insights into the roles of RAD51 and DMC1 in plant meiotic recombination.

    Science.gov (United States)

    Pradillo, Mónica; López, Eva; Linacero, Rosario; Romero, Concepción; Cuńado, Nieves; Sánchez-Morán, Eugenio; Santos, Juan L

    2012-03-01

    The eukaryotic recombinases RAD51 and DMC1 are essential for DNA strand-exchange between homologous chromosomes during meiosis. RAD51 is also expressed during mitosis, and mediates homologous recombination (HR) between sister chromatids. It has been suggested that DMC1 might be involved in the switch from intersister chromatid recombination in somatic cells to interhomolog meiotic recombination. At meiosis, the Arabidopsis Atrad51 null mutant fails to synapse and has extensive chromosome fragmentation. The Atdmc1 null mutant is also asynaptic, but in this case chromosome fragmentation is absent. Thus in plants, AtDMC1 appears to be indispensable for interhomolog homologous recombination, whereas AtRAD51 seems to be more involved in intersister recombination. In this work, we have studied a new AtRAD51 knock-down mutant, Atrad51-2, which expresses only a small quantity of RAD51 protein. Atrad51-2 mutant plants are sterile and hypersensitive to DNA double-strand break induction, but their vegetative development is apparently normal. The meiotic phenotype of the mutant consists of partial synapsis, an elevated frequency of univalents, a low incidence of chromosome fragmentation and multivalent chromosome associations. Surprisingly, non-homologous chromosomes are involved in 51% of bivalents. The depletion of AtDMC1 in the Atrad51-2 background results in the loss of bivalents and in an increase of chromosome fragmentation. Our results suggest that a critical level of AtRAD51 is required to ensure the fidelity of HR during interchromosomal exchanges. Assuming the existence of asymmetrical DNA strand invasion during the initial steps of recombination, we have developed a working model in which the initial step of strand invasion is mediated by AtDMC1, with AtRAD51 required to check the fidelity of this process. PMID:22066484

  9. Pulsed metal-vapor recombination laser.

    Science.gov (United States)

    Thareja, R K; Khare, A

    1987-01-01

    A visible cadmium-ion recombination laser based on an electron-ion recombination pumping mechanism is reported. Laser oscillation is observed in the 4f (2)F(7/2)-5d(2)D(5/2) and 4f(2)F(5/2)-5d (2)D(3/2) transitions of Cd II over a range of discharge parameters in the presence of low-pressure helium gas in a sealed discharge tube. Laser oscillation in a sealed discharge tube using a simple capacitor discharge is reported for the first time to the authors' knowlege. PMID:19738782

  10. Dielectronic recombination of xenonlike tungsten ions

    OpenAIRE

    Schippers, S.; Bernhardt, D.; Mu?ller, A.; Krantz, C.; Grieser, M.; Repnow, R.; Wolf, A.; Lestinsky, M.; Hahn, M.; Novotny?, O.; Savin, D. W.

    2011-01-01

    Dielectronic recombination (DR) of xenonlike W20+ forming W19+ has been studied experimentally at a heavy-ion storage-ring. A merged-beams method has been employed for obtaining absolute rate coefficients for electron-ion recombination in the collision energy range 0-140 eV. The measured rate coefficient is dominated by strong DR resonances even at the lowest experimental energies. At plasma temperatures where the fractional abundance of W20+ is expected to peak in a fusion ...

  11. SIR epidemics in monogamous populations with recombination

    CERN Document Server

    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 couples, thus characterizing the interplay between the epidemic dynamics and the evolution of the population's interaction pattern.

  12. Recombinant microorganisms for increased production of organic acids

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. 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.

  14. Frequency and Spectrum of Genomic Integration of Recombinant Adeno-Associated Virus Serotype 8 Vector in Neonatal Mouse Liver?

    OpenAIRE

    Inagaki, Katsuya; Piao, Chuncheng; Kotchey, Nicole M.; Wu, Xiaolin; Nakai, Hiroyuki

    2008-01-01

    Neonatal injection of recombinant adeno-associated virus serotype 8 (rAAV8) vectors results in widespread transduction in multiple organs and therefore holds promise in neonatal gene therapy. On the other hand, insertional mutagenesis causing liver cancer has been implicated in rAAV-mediated neonatal gene transfer. Here, to better understand rAAV integration in neonatal livers, we investigated the frequency and spectrum of genomic integration of rAAV8 vectors in the liver following intraperit...

  15. Protective cellular responses elicited by vaccination with influenza nucleoprotein delivered by a live recombinant attenuated Salmonella vaccine

    OpenAIRE

    Ashraf, Shamaila; Kong, Wei; Wang, Shifeng; Yang, Jiseon; Curtiss, Roy

    2011-01-01

    Orally administered recombinant attenuated Salmonella vaccines (RASV) elicit humoral and mucosal immune responses against the immunizing antigen. The challenge in developing an effective vaccine against a virus or an intracellular bacterium delivered by RASVs is to introduce the protective antigen inside the host cell cytoplasm for presentation to MHC-I molecules for an efficient cell mediated immune response. To target the influenza nucleoprotein (NP) into the host cell cytosol, we construct...

  16. Preclinical Characterization of Recombinant Human Tissue Kallikrein-1 as a Novel Treatment for Type 2 Diabetes Mellitus

    OpenAIRE

    Kolodka, Tadeusz; Charles, Matthew L.; Raghavan, Arvind; Radichev, Ilian A.; Amatya, Christina; Ellefson, Jacob; Savinov, Alexei Y.; Nag, Abhijeet; Williams, Mark S.; Robbins, Mark S.

    2014-01-01

    Modulation of the kallikrein-kinin system (KKS) has been shown to have beneficial effects on glucose homeostasis and several other physiological responses relevant to the progression of type 2 diabetes mellitus (T2D). The importance of bradykinin and its receptors in mediating these responses is well documented, but the role of tissue kallikrein-1, the protease that generates bradykinin in situ, is much less understood. We developed and tested DM199, recombinant human tissue kallikrein-1 p...

  17. Injection of Recombinant Human Type VII Collagen Corrects the Disease Phenotype in a Murine Model of Dystrophic Epidermolysis Bullosa

    OpenAIRE

    Remington, Jennifer; Wang, Xinyi; Hou, Yingpin; Zhou, Hui; Burnett, Julie; Muirhead, Trevor; Uitto, Jouni; Keene, Douglas R.; Woodley, David T.; Chen, Mei

    2008-01-01

    Patients with recessive dystrophic epidermolysis bullosa (RDEB) have incurable skin fragility, blistering, and scarring due to mutations in the gene that encodes for type VII collagen (C7) that mediates dermal–epidermal adherence in human skin. We showed previously that intradermal injection of recombinant C7 into transplanted human DEB skin equivalents stably restored C7 expression at the basement membrane zone (BMZ) and reversed the RDEB disease features. In this study, we evaluated the f...

  18. An Efficient Procedure for Marker-Free Mutagenesis of S. coelicolor by Site-Specific Recombination for Secondary Metabolite Overproduction

    OpenAIRE

    Zhang, Bo; Zhang, Lin; Dai, Ruixue; Yu, Meiying; Zhao, Guoping; Ding, Xiaoming

    2013-01-01

    Streptomyces bacteria are known for producing important natural compounds by secondary metabolism, especially antibiotics with novel biological activities. Functional studies of antibiotic-biosynthesizing gene clusters are generally through homologous genomic recombination by gene-targeting vectors. Here, we present a rapid and efficient method for construction of gene-targeting vectors. This approach is based on Streptomyces phage ?BT1 integrase-mediated multisite in vitro site-specific rec...

  19. An ultrasensitive site-specific DNA recombination assay based on dual-color fluorescence cross-correlation spectroscopy

    OpenAIRE

    Jahnz, Michael; Schwille, Petra

    2005-01-01

    Site-specific exchange of genetic information is mediated by DNA recombinases, such as FLP or Cre, and has become a valuable tool in modern molecular biology. The so far low number of suitable recombinating enzymes has driven current research activities towards alteration of catalytic properties, such as thermostability or recognition sequences. However, identification and analysis of new mutants requires sensitive in vitro activity assays, which traditionally are based on gel electrophoresis...

  20. TransFLP — A Method to Genetically Modify Vibrio cholerae Based on Natural Transformation and FLP-recombination

    OpenAIRE

    Blokesch, Melanie

    2012-01-01

    Several methods are available to manipulate bacterial chromosomes1-3. Most of these protocols rely on the insertion of conditionally replicative plasmids (e.g. harboring pir-dependent or temperature-sensitive replicons1,2). These plasmids are integrated into bacterial chromosomes based on homology-mediated recombination. Such insertional mutants are often directly used in experimental settings. Alternatively, selection for plasmid excision followed by its loss can be performed, which for Gram...

  1. 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...

  2. 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.

  3. Reduced recombination patterns in Robertsonian hybrids between chromosomal races of the house mouse: chiasma analyses.

    Science.gov (United States)

    Dumas, D; Catalan, J; Britton-Davidian, J

    2015-01-01

    The recombination suppression models of chromosomal speciation posit that chromosomal rearrangements act as partial barriers to gene flow allowing these regions to accumulate genetic incompatibilities, thus contributing to the divergence of populations. Empirical and theoretical studies exploring the requirements of these models have mostly focused on the role of inversions. Here, the recombination landscape of heterozygosity for Robertsonian (Rb) fusions is investigated in the house mouse. Laboratory-bred F1 males and females between highly differentiated races from Tunisia (Rb: 2n=22, Standard, St: 2n=40) were produced in which all Rb fusions are present as trivalents in meiosis. Recombination patterns were determined by the analysis of chiasmata and compared with previous data on the Tunisian parental mice. A comparative analysis was performed on wild-caught male mice spanning the hybrid zone between two Italian races (2n=40, 2n=22). The results showed that the chiasma characteristics of both male and female Tunisian F1 and Italian hybrids clearly differed from those of Rb and St mice. Not only was the mean chiasma number (CN) intermediate between those of the parental mice in both geographic samples, but the distribution of chiasmata along the chromosomal arms of the F1 showed a distinct mosaic pattern. In short, the proximal region in the F1 exhibited a reduced CN similar to that observed in homozygous Rb, whereas distal regions more closely matched those in St mice. These results suggest that Rb rearrangements (homozygous or heterozygous) reduce recombination in the proximal regions of the chromosomes supporting their potential role in recombination-mediated speciation models. PMID:25074574

  4. Cytotoxicity Associated with Artemis Overexpression After Lentiviral Vector-Mediated Gene Transfer

    OpenAIRE

    Multhaup, Megan; Karlen, Andrea D.; Swanson, Debra L.; Wilber, Andrew; Somia, Nikunj V.; Cowan, Morton J.; Mcivor, R. Scott

    2010-01-01

    Artemis is one of the newest proteins identified in V(D)J recombination. Deficiency of functional Artemis can result in severe combined immunodeficiency (SCID). In this article by Multhaup and colleagues, the authors conduct preclinical in vitro studies examining the safety and efficacy of lentiviral-mediated delivery of Artemis in Artemis-deficient mammalian cells.

  5. TLR9 signaling in B cells determines class switch recombination to IgG2a.

    OpenAIRE

    Jegerlehner, A.; Maurer, P.; Bessa, J.; Hinton, Hj; Kopf, M.; Bachmann, Mf

    2007-01-01

    Although IgG2a is the most potent Ab isotype in the host response to viral and bacterial infections, the regulation of class switch recombination to IgG2a in vivo is not yet well understood. Recognition of pathogen-associated molecular patterns by dendritic cells expressing TLRs, like TLR7, recognizing ssRNA, or TLR9, recognizing DNA rich in nonmethylated CG motifs (CpG), favors induction of Th1 responses. It is generally assumed that these Th1 responses are responsible for the TLR-mediated i...

  6. 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 ...

  7. Production and delivery of recombinant subunit vaccines

    OpenAIRE

    Andersson, Christin

    2000-01-01

    Recombinant strategies are today dominating in thedevelopment of modern subunit vaccines. This thesis describesstrategies for the production and recovery of protein subunitimmunogens, and how genetic design of the expression vectorscan be used to adapt the immunogens for incorporation intoadjuvant systems. In addition, different strategies fordelivery of subunit vaccines by RNA or DNA immunization havebeen investigated. Attempts to create general production strategies forrecombinant protein i...

  8. Evidence for homologous recombination in Chikungunya Virus.

    Science.gov (United States)

    Casal, Pablo E; Chouhy, Diego; Bolatti, Elisa M; Perez, Germán R; Stella, Emma J; Giri, Adriana A

    2015-04-01

    Chikungunya Virus (CHIKV), a mosquito-transmitted alphavirus, causes acute fever and joint pain in humans. Recently, endemic CHIKV infection outbreaks have jeopardized public health in wider geographical regions. Here, we analyze the phylogenetic associations of CHIKV and explore the potential recombination events on 152 genomic isolates deposited in GenBank database. The CHIKV genotypes [West African, Asian, East/Central/South African (ECSA)], and a clear division of ECSA clade into three sub-groups (I-II-III), were defined by Bayesian analysis; similar results were obtained using E1 gene sequences. A nucleotide identity-based approach is provided to facilitate CHIKV classification within ECSA clade. Using seven methods to detect recombination, we found a statistically significant event (p-values range: 1.14×10(-7)-4.45×10(-24)) located within the nsP3 coding region. This finding was further confirmed by phylogenetic networks (PHI Test, p=0.004) and phylogenetic tree incongruence analysis. The recombinant strain, KJ679578/India/2011 (ECSA III), derives from viruses of ECSA III and ECSA I. Our study demonstrates that recombination is an additional mechanism of genetic diversity in CHIKV that might assist in the cross-species transmission process. PMID:25701772

  9. 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

  10. 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.

  11. Dosimetry of mixed radiation using recombination chamber

    International Nuclear Information System (INIS)

    Advantages and shortcomings of mixed radiation dosimetry based on recombination detectors are presented. The methods considered here are particularly advantageous for radiation protection dosimetry in the vicinity of high-energy particle accelerators and in other radiation fields with a complex composition and a broad energy spectrum

  12. Recombinant Bovine Growth Hormone Criticism Grows.

    Science.gov (United States)

    Gaard, Greta

    1995-01-01

    Discusses concerns related to the use of recombinant bovine growth hormone in the United States and other countries. Analyses the issue from the perspectives of animal rights, human health, world hunger, concerns of small and organic farmers, costs to the taxpayer, and environmental questions. A sidebar discusses Canadian review of the hormone.…

  13. 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

  14. Recombinant MVA vaccines: dispelling the myths.

    Science.gov (United States)

    Cottingham, Matthew G; Carroll, Miles W

    2013-09-01

    Diseases such as HIV/AIDS, tuberculosis, malaria and cancer are prime targets for prophylactic or therapeutic vaccination, but have proven partially or wholly resistant to traditional approaches to vaccine design. New vaccines based on recombinant viral vectors expressing a foreign antigen are under intense development for these and other indications. One of the most advanced and most promising vectors is the attenuated, non-replicating poxvirus MVA (modified vaccinia virus Ankara), a safer derivative of the uniquely successful smallpox vaccine. Despite the ability of recombinant MVA to induce potent humoral and cellular immune responses against transgenic antigen in humans, especially when used as the latter element of a heterologous prime-boost regimen, doubts are occasionally expressed about the ultimate feasibility of this approach. In this review, five common misconceptions over recombinant MVA are discussed, and evidence is cited to show that recombinant MVA is at least sufficiently genetically stable, manufacturable, safe, and immunogenic (even in the face of prior anti-vector immunity) to warrant reasonable hope over the feasibility of large-scale deployment, should useful levels of protection against target pathogens, or therapeutic benefit for cancer, be demonstrated in efficacy trials. PMID:23523407

  15. Recombinant poxviruses as mucosal vaccine vectors.

    Science.gov (United States)

    Gherardi, M Magdalena; Esteban, Mariano

    2005-11-01

    The majority of infections initiate their departure from a mucosal surface, such as Human immunodeficiency virus (HIV), a sexually transmitted virus. Therefore, the induction of mucosal immunity is a high priority in the development of vaccines against mucosal pathogens. The selection of an appropriate antigen delivery system is necessary to induce an efficient mucosal immune response. Poxvirus vectors have been the most intensively studied live recombinant vector, and numerous studies have demonstrated their ability to induce mucosal immune responses against foreign expressed antigens. Previous studies have demonstrated that recombinants based on the attenuated modified vaccinia virus Ankara (MVA) vector were effective in inducing protective responses against different respiratory viruses, such as influenza and respiratory syncytial virus, following immunization via mucosal routes. Recent studies performed in the murine and macaque models have shown that recombinant MVA (rMVA) does not only stimulate HIV-specific immunity in the genital and rectal tracts following mucosal delivery, but can also control simian/human immunodeficiency viraemia and disease progression. In addition, a prime-boost vaccination approach against tuberculosis emphasized the importance of the intranasal rMVA antigen delivery to induce protective immunity against Mycobacterium tuberculosis. The aim of this review is to summarize the studies employing recombinant poxviruses, specifically rMVA as a mucosal delivery vector. The results demonstrate that rMVAs can activate specific immune responses at mucosal surfaces, and encourage further studies to characterize and improve the MVA mucosal immunogenicity of poxvirus vectors. PMID:16227213

  16. Windows in direct dissociative recombination cross sections

    Science.gov (United States)

    Guberman, Steven L.

    1986-01-01

    Model potential curves are used to show that large windows are present in direct dissociative-recombination cross sections from excited molecular-ion vibrational levels. The windows are due to the overlap of vibrational wave functions of the repulsive neutral states with the nodes of the ion vibrational wave function.

  17. 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.

  18. Short communication: A comparative analysis of recombinant chymosins.

    Science.gov (United States)

    Vallejo, J A; Ageitos, J M; Poza, M; Villa, T G

    2012-02-01

    The first step in cheesemaking is the milk clotting process, in which ?-caseinolytic enzymes contribute to micelle precipitation. The best enzyme for this purpose is chymosin because of its high degree of specificity toward ?-casein. Although recombinant bovine chymosin is the most frequently used chymosin in the industry, new sources of recombinant chymosin, such as goat, camel, or buffalo, are now available. The present work represents a comparative study of 4 different recombinant chymosins (goat and buffalo chymosins expressed in Pichia pastoris, and bovine and camel chymosin expressed in Aspergillus niger). Recombinant goat chymosin exhibited the best catalytic efficiency compared with the buffalo, bovine, or camel recombinant enzymes. Moreover, recombinant goat chymosin exhibited the best specific proteolytic activity, a wider pH range of action, and a lower glycosylation degree than the other 3 enzymes. In conclusion, we propose that recombinant goat chymosin represents a serious alternative to recombinant bovine chymosin for use in the cheesemaking industry. PMID:22281325

  19. The $\\Lambda_0$ Polarization and the Recombination Mechanism

    CERN Document Server

    Herrera-Corral, G; Montańo-Zetina, L M; Simăo, F R A; Montańo, Luis M.

    1997-01-01

    We use the recombination and the Thomas Precession Model to obtain a prediction for the $\\Lambda _0$ polarization in the $p+p \\to \\Lambda_0+X$ reaction. We study the effect of the recombination function on the

  20. 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.

  1. Some recent developments in the recombination model

    International Nuclear Information System (INIS)

    A critical review of the recombination model for hadron production at low P/sub T/ is first given, emphasizing not so much the successes as unanswered questions that the model faces. A systematic program to answer some of the basic questions is then developed. The theoretical framework is quantum chromodynamics. First, in what may appear as a digression, the possibility of formation of valence quark clusters (called valons) in a nucleon due to gluon bremsstrahlung and quark-pair creation is considered. Evidences are found not only for the valons in neutrino scattering data, but also indications for their momentum distribution in a nucleon. When similar considerations are applied to a meson, the meaning of the recombination function is discussed and its normalization as well as its shape are determined. Next, the problem of quark decay in a hard scattering process (e.g., pion production in e+e- annihilation) is considered. The joint distribution of partons in a quark jet is determined in QCD. The quark decay function for pions in the recombination model is then obtained with excellent fit to the data. Similar investigation is applied to the problem of photoproduction of pions in the fragmentation region; again good agreement with data is achieved. The results indicate the reliability of the recombination model when the two-parton distributions can be calculated in QCD. Finally, hadron initiated reactions are considered. A duality between quark recombination and valon fragmentation is suggested. The picture is consistent with dual Regge model. A possible way to determine the inclusive distribution in the context of QCD is suggested

  2. Genetic recombination of poliovirus in a cell-free?system

    OpenAIRE

    Duggal, Rohit; Cuconati, Andrea; Gromeier, Matthias; Wimmer, Eckard

    1997-01-01

    Genetic recombination of plus-strand RNA viruses is an important process for promoting genetic variation. By using genetically marked poliovirus RNAs, we have demonstrated that genetic recombination can occur in a cell-free system that generates infective virus from added poliovirus RNA. Recombinant polioviruses were isolated, and the region of crossing over was roughly mapped. Recombinants could be isolated even under conditions where the yield of viruses from one of the parental RNAs was de...

  3. A novel human enterovirus recombinant from a child with diarrhea.

    Science.gov (United States)

    Sun, Guangming; Yi, Maoli; Tian, Hua; Shao, Chen; Yang, Shixing; Han, Jun; Wang, Xiaochun; Wang, Yong; Shen, Quan; Wang, Hua; Shao, Shihe; Yang, Yan; Zhang, Wen

    2014-02-01

    Recombination is a well-known phenomenon for enteroviruses. In the present study, a novel recombinant HEV-B strain (ChZJ-1) was found in a 2-year-old child with diarrhea in Zhenjiang, China. The whole genome of ChZJ-1 was determined. Recombination and phylogenetic analysis revealed that ChZJ-1 might have been produced by recombination between coxsackievirus B5 and echovirus 18. PMID:23959204

  4. Hyper-Recombining Recipient Strains in Bacterial Conjugation

    OpenAIRE

    Feinstein, Sheldon I.; Low, K. Brooks

    1986-01-01

    Using a direct enrichment and screening procedure, mutants of Escherichia coli have been isolated in which recombination frequencies for several intragenic Hfr x F- crosses are significantly higher (twofold to sixfold) than in the parental strains. These hyper-recombination mutations comprised five new mutS- and one new mutL- allele. Together with other known mut - alleles, they were analyzed for effects on intragenic recombination using several types of crosses. Hyper-recombination was fou...

  5. Chi-dependent intramolecular recombination in Escherichia coli.

    OpenAIRE

    Friedman-ohana, R.; Karunker, I.; Cohen, A.

    1998-01-01

    Homologous recombination in Escherichia coli is enhanced by a cis-acting octamer sequence named Chi (5'-GCTGGTGG-3') that interacts with RecBCD. To gain insight into the mechanism of Chi-enhanced recombination, we recruited an experimental system that permits physical monitoring of intramolecular recombination by linear substrates released by in vivo restriction from infecting chimera phage. Recombination of the released substrates depended on recA, recBCD and cis-acting Chi octamers. Recombi...

  6. Recombination analysis of Soybean mosaic virus sequences reveals evidence of RNA recombination between distinct pathotypes

    OpenAIRE

    Gagarinova, Alla G.; Babu, Mohan; Stro?mvik, Martina V.; Wang, Aiming

    2008-01-01

    RNA recombination is one of the two major factors that create RNA genome variability. Assessing its incidence in plant RNA viruses helps understand the formation of new isolates and evaluate the effectiveness of crop protection strategies. To search for recombination in Soybean mosaic virus (SMV), the causal agent of a worldwide seed-borne, aphid-transmitted viral soybean disease, we obtained all full-length genome sequences of SMV as well as partial sequences encoding the N-terminal most (P1...

  7. Serial recombination during circulation of type 1 wild-vaccine recombinant polioviruses in China.

    Science.gov (United States)

    Liu, Hong-Mei; Zheng, Du-Ping; Zhang, Li-Bi; Oberste, M Steven; Kew, Olen M; Pallansch, Mark A

    2003-10-01

    Type 1 wild-vaccine recombinant polioviruses sharing a 367-nucleotide (nt) block of Sabin 1-derived sequence spanning the VP1 and 2A genes circulated widely in China from 1991 to 1993. We surveyed the sequence relationships among 34 wild-vaccine recombinants by comparing six genomic intervals: the conserved 5'-untranslated region (5'-UTR) (nt 186 to 639), the hypervariable portion of the 5'-UTR (nt 640 to 742), the VP4 and partial VP2 genes (nt 743 to 1176), the VP1 gene (nt 2480 to 3385), the 2A gene (nt 3386 to 3832), and the partial 3D gene (nt 6011 to 6544). The 5'-UTR, capsid (VP4-VP2 and VP1), and 2A sequence intervals had similar phylogenies. By contrast, the partial 3D sequences could be distributed into five divergent genetic classes. Most (25 of 34) of the wild-vaccine recombinant isolates showed no evidence of additional recombination beyond the initial wild-Sabin recombination event. Eight isolates from 1992 to 1993, however, appear to be derived from three independent additional recombination events, and one 1993 isolate was derived from two consecutive events. Complete genomic sequences of a representative isolate for each 3D sequence class demonstrated that these exchanges had occurred in the 2B, 2C, and 3D genes. The 3D gene sequences were not closely related to those of the Sabin strains or 53 diverse contemporary wild poliovirus isolates from China, but all were related to the 3D genes of species C enteroviruses. The appearance within approximately 2.5 years of five recombinant classes derived from a single ancestral infection illustrates the rapid emergence of new recombinants among circulating wild polioviruses. PMID:14512548

  8. Theory of spin-dependent recombination in semiconductors

    Science.gov (United States)

    Haberkorn, R.; Dietz, W.

    1980-08-01

    The pair model of spin-dependent recombination of carriers in semiconductors, as discussed by Kaplan, Solomon and Mott, is solved exactly in several limiting cases. The model accounts for the large influence of a saturating microwave field in ESR experiments on recombination in crystalline and amorphous silicon. Further, the effect of a static magnetic field on recombination is explored.

  9. Genetic Analysis of Meiotic Recombination in Schizosaccharomyces pombe

    OpenAIRE

    Smith, Gerald R.

    2009-01-01

    The fission yeast Schizosaccharomyces pombe is well-suited for studying meiotic recombination. Methods are described here for culturing S. pombe and for genetic assays of intragenic recombination (gene conversion), intergenic recombination (crossing-over), and spore viability. Both random spore and tetrad analyses are described.

  10. 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.

  11. Causal mediation analysis with multiple mediators.

    Science.gov (United States)

    Daniel, R M; De Stavola, B L; Cousens, S N; Vansteelandt, S

    2015-03-01

    In diverse fields of empirical research-including many in the biological sciences-attempts are made to decompose the effect of an exposure on an outcome into its effects via a number of different pathways. For example, we may wish to separate the effect of heavy alcohol consumption on systolic blood pressure (SBP) into effects via body mass index (BMI), via gamma-glutamyl transpeptidase (GGT), and via other pathways. Much progress has been made, mainly due to contributions from the field of causal inference, in understanding the precise nature of statistical estimands that capture such intuitive effects, the assumptions under which they can be identified, and statistical methods for doing so. These contributions have focused almost entirely on settings with a single mediator, or a set of mediators considered en bloc; in many applications, however, researchers attempt a much more ambitious decomposition into numerous path-specific effects through many mediators. In this article, we give counterfactual definitions of such path-specific estimands in settings with multiple mediators, when earlier mediators may affect later ones, showing that there are many ways in which decomposition can be done. We discuss the strong assumptions under which the effects are identified, suggesting a sensitivity analysis approach when a particular subset of the assumptions cannot be justified. These ideas are illustrated using data on alcohol consumption, SBP, BMI, and GGT from the Izhevsk Family Study. We aim to bridge the gap from "single mediator theory" to "multiple mediator practice," highlighting the ambitious nature of this endeavor and giving practical suggestions on how to proceed. PMID:25351114

  12. 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.

  13. Food components inhibiting recombinant human histidine decarboxylase activity.

    Science.gov (United States)

    Nitta, Yoko; Kikuzaki, Hiroe; Ueno, Hiroshi

    2007-01-24

    Histidine decarboxylase (HDC) catalyzes histamine formation from histidine. Histamine is a bioactive amine acting as a neurotransmitter as well as a chemical mediator. Phenolic food components have been tested for their ability to inhibit recombinant human HDC. Epicatechin gallate (ECG) was found to be a potent inhibitor as it inhibited HDC activity in a competitive manner with Ki = 10 muM against l-histidine. Epigallocatechin gallate (EGCG) showed time-dependent inhibition which disappeared under anaerobic conditions. It is probable that time-dependent inhibition could be due to the result of autoxidation of EGCG. The initial burst observed for EGCG suggests that EGCG itself is involved in HDC inhibition as observed for ECG. Our present results have shown that the tested food components can inhibit HDC activity. This inhibition likely affects histamine biosynthesis and possibly leads to controlling the biological action induced by histamine. Therefore, those food components exhibiting HDC inhibitory activity might be potentially useful in controlling histamine-induced biological actions. PMID:17227057

  14. 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.

  15. 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...

  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. The labelling of recombinant L-asparaginase with 125I

    International Nuclear Information System (INIS)

    Recombinant L-asparaginase is labelled with 125I by the method of Chloramine-T. After purification using Sephadex G-25, 125I-recombinant L-asparaginase is separated by RP-HPLC and determined by ?-counter. The radiochemical purity of 125I-recombinant L-asparaginase is more than 95%. 125I-recombinant L-asparaginase is analysed by double immunological diffusion and is demonstrated. The results show that the biological activity is the same as recombinant L-asparaginase

  18. Use of Helical Transport Channels for Bunch Recombination

    International Nuclear Information System (INIS)

    Cooling scenarios for a high-luminosity Muon Collider require bunch recombination for optimal luminosity. In this report we note that the tunable chronicity property of a helical transport channel (HTC) makes it a desirable component of a bunch recombiner. A large chronicity HTC is desirable for the bunch recombining transport, while more isochronous transport may be preferred for rf manipulations. Scenarios for bunch recombination are presented, with initial 1-D simulations, in order to set the stage for future 3-D simulation and optimization. HTC transports may enable a very compact bunch recombiner.

  19. Cre-mediated targeted gene activation in the middle silk glands of transgenic silkworms (Bombyx mori).

    Science.gov (United States)

    Duan, Jianping; Xu, Hanfu; Ma, Sanyuan; Guo, Huizhen; Wang, Feng; Zhao, Ping; Xia, Qingyou

    2013-06-01

    Cre-mediated recombination is widely used to manipulate defined genes spatiotemporally in vivo. The present study evaluated the Cre/loxP system in Bombyx mori by establishing two transgenic lines. One line contained a Cre recombinase gene controlled by a sericin-1 gene (Ser1) promoter. The other line contained a loxP-Stop-loxP-DsRed cassette driven by the same Ser1 promoter. The precise deletion of the Stop fragment was found to be triggered by Cre-mediated site-specific excision, and led to the expression of DsRed fluorescence protein in the middle silk glands of all double-transgenic hybrids. This result was also confirmed by phenotypical analysis. Hence, the current study demonstrated the feasibility of Cre-mediated site-specific recombination in B. mori, and opened a new window for further refining genetic tools in silkworms. PMID:23264031

  20. Characterization and downstream mannose phosphorylation of human recombinant ?-L-iduronidase produced in Arabidopsis complex glycan-deficient (cgl) seeds.

    Science.gov (United States)

    He, Xu; Pierce, Owen; Haselhorst, Thomas; von Itzstein, Mark; Kolarich, Daniel; Packer, Nicolle H; Gloster, Tracey M; Vocadlo, David J; Qian, Yi; Brooks, Doug; Kermode, Allison R

    2013-12-01

    Mucopolysaccharidosis (MPS) I is a lysosomal storage disease caused by a deficiency of ?-L-iduronidase (IDUA) (EC 3.2.1.76); enzyme replacement therapy is the conventional treatment for this genetic disease. Arabidopsis cgl mutants are characterized by a deficiency of the activity of N-acetylglucosaminyl transferase I (EC 2.4.1.101), the first enzyme in the pathway of hybrid and complex N-glycan biosynthesis. To develop a seed-based platform for the production of recombinant IDUA for potential treatment of MPS I, cgl mutant seeds were generated to express human IDUA at high yields and to avoid maturation of the N-linked glycans on the recombinant human enzyme. Enzyme kinetic data showed that cgl-IDUA has similar enzymatic properties to the commercial recombinant IDUA derived from cultured Chinese hamster ovary (CHO) cells (Aldurazyme™). The N-glycan profile showed that cgl-derived IDUA contained predominantly high-mannose-type N-glycans (94.5%), and the residual complex/hybrid N-glycan-containing enzyme was efficiently removed by an additional affinity chromatography step. Furthermore, purified cgl-IDUA was amenable to sequential in vitro processing by soluble recombinant forms of the two enzymes that mediate the addition of the mannose-6-phosphate (M6P) tag in mammalian cells-UDP-GlcNAc:lysosomal enzyme N-acetylglucosamine (GlcNAc)-1-phosphotransferase-and GlcNAc-1-phosphodiester ?-N-acetylglucosaminidase (the 'uncovering enzyme'). Arabidopsis seeds provide an alternative system for producing recombinant lysosomal enzymes for enzyme replacement therapy; the purified enzymes can be subjected to downstream processing to create the M6P, a recognition marker essential for efficient receptor-mediated uptake into lysosomes of human cells. PMID:23898885

  1. Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii

    Science.gov (United States)

    Snitkin, Evan S.; Zelazny, Adrian M.; Montero, Clemente I.; Stock, Frida; Mijares, Lilia; Murray, Patrick R.; Segre, Julie A.; Mullikin, Jim; Blakesley, Robert; Young, Alice; Chu, Grace; Ramsahoye, Colleen; Lovett, Sean; Han, Joel; Legaspi, Richelle; Sison, Christina; Gregory, Michael; Montemayor, Casandra; Gestole, Marie; Hargrove, April; Johnson, Taccara; Myrick, Jerlil; Riebow, Nancy; Schmidt, Brian; Novotny, Betsy; Gupta, Jyoti; Benjamin, Betty; Brooks, Shelise; Coleman, Holly; Ho, Shi-ling; Schandler, Karen; Smith, Lauren; Stantripop, Mal; Maduro, Quino; Bouffard, Gerry; Dekhtyar, Mila; Guan, Xiaobin; Masiello, Cathy; Maskeri, Baishali; McDowell, Jenny; Park, Morgan; Thomas, Pamela

    2011-01-01

    Acinetobacter baumannii is an emerging human pathogen and a significant cause of nosocomial infections among hospital patients worldwide. The enormous increase in multidrug resistance among hospital isolates and the recent emergence of pan-drug–resistant strains underscores the urgency to understand how A. baumannii evolves in hospital environments. To this end, we undertook a genomic study of a polyclonal outbreak of multidrug-resistant A. baumannii at the research-based National Institutes of Health Clinical Center. Comparing the complete genome sequences of the three dominant outbreak strain types enabled us to conclude that, despite all belonging to the same epidemic lineage, the three strains diverged before their arrival at the National Institutes of Health. The simultaneous presence of three divergent strains from this lineage supports its increasing prevalence in international hospitals and suggests an ongoing adaptation to the hospital environment. Further genomic comparisons uncovered that much of the diversification that occurred since the divergence of the three outbreak strains was mediated by homologous recombination across 20% of their genomes. Inspection of recombinant regions revealed that several regions were associated with either the loss or swapping out of genes encoding proteins that are exposed to the cell surface or that synthesize cell-surface molecules. Extending our analysis to a larger set of international clinical isolates revealed a previously unappreciated ability of A. baumannii to vary surface molecules through horizontal gene transfer, with subsequent intraspecies dissemination by homologous recombination. These findings have immediate implications in surveillance, prevention, and treatment of A. baumannii infections. PMID:21825119

  2. Cell line-specific control of recombinant monoclonal antibody production by CHO cells.

    Science.gov (United States)

    O'Callaghan, Peter M; McLeod, Jane; Pybus, Leon P; Lovelady, Clare S; Wilkinson, Stephen J; Racher, Andrew J; Porter, Alison; James, David C

    2010-08-15

    In this study we compare the cellular control of recombinant human IgG(4) monoclonal antibody (Mab) synthesis in different CHO cell lines. Based on comprehensive empirical analyses of mRNA and polypeptide synthetic intermediates we constructed cell line-specific mathematical models of recombinant Mab manufacture in seven GS-CHO cell lines varying in specific production rate (qMab) over 350-fold. This comparative analysis revealed that control of qMab involved both genetic construct and cell line-specific factors. With respect to the former, all cell lines exhibited excess production of light chain (LC) mRNA and polypeptide relative to heavy chain (HC) mediated by more rapid LC transcription and enhanced LC mRNA stability. Downstream of this, cell lines differed markedly in their relative rates of recombinant mRNA translation, Mab assembly and secretion although HC mRNA abundance and the rate of HC translation generally exerted most control over qMab--the latter being directly proportional to qMab. This study shows that (i) cell lines capable of high qMab exceed a threshold functional competency in all synthetic processes, (ii) the majority of cells in parental and transfected cell populations are functionally limited and (iii) cell engineering strategies to increase Mab production should be cell line specific. PMID:20589672

  3. 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

  4. In utero recombinant adeno-associated virus gene transfer in mice, rats, and primates

    Directory of Open Access Journals (Sweden)

    Marrero Luis

    2003-09-01

    Full Text Available Abstract Background Gene transfer into the amniotic fluid using recombinant adenovirus vectors was shown previously to result in high efficiency transfer of transgenes into the lungs and intestines. Adenovirus mediated in utero gene therapy, however, resulted in expression of the transgene for less than 30 days. Recombinant adenovirus associated viruses (rAAV have the advantage of maintaining the viral genome in daughter cells thus providing for long-term expression of transgenes. Methods Recombinant AAV2 carrying green fluorescent protein (GFP was introduced into the amniotic sac of fetal rodents and nonhuman primates. Transgene maintenance and expression was monitor. Results Gene transfer resulted in rapid uptake and long-term gene expression in mice, rats, and non-human primates. Expression and secretion of the reporter gene, GFP, was readily demonstrated within 72 hours post-therapy. In long-term studies in rats and nonhuman primates, maintenance of GFP DNA, protein expression, and reporter gene secretion was documented for over one year. Conclusions Because only multipotential stem cells are present at the time of therapy, these data demonstrated that in utero gene transfer with AAV2 into stem cells resulted in long-term systemic expression of active transgene roducts. Thus, in utero gene transfer via the amniotic fluid may be useful in treatment of gene disorders.

  5. Metabolism of palmatine by human hepatocytes and recombinant cytochromes P450.

    Science.gov (United States)

    Vrba, Jiri; Papouskova, Barbora; Pyszkova, Michaela; Zatloukalova, Martina; Lemr, Karel; Ulrichova, Jitka; Vacek, Jan

    2015-01-01

    In this study, we developed a new liquid chromatography-mass spectrometry (LC-MS) method for analysis of the protoberberine alkaloid palmatine and its metabolites with separation performed on a cyanopropyl-modified stationary phase. Palmatine (10 ?M) was metabolized using suspensions of human hepatocytes and human recombinant cytochrome P450 (CYP) enzymes. Our analyses using electrospray ionization-quadrupole time-of-flight mass spectrometry revealed that palmatine was relatively resistant to the metabolic activity of human hepatocytes and recombinant CYP enzymes. However, we found that the biotransformation of palmatine in human hepatocytes included O-demethylation or hydroxylation, and that the product of palmatine demethylation was conjugated by glucuronidation or sulfation. Moreover, we found that human recombinant CYP2D6 and, to a lesser extent, CYP1A2 can mediate O-demethylation of palmatine. These results provide fundamental insights into the biotransformation of palmatine in human in vitro models and, together with the LC-MS method, can be applied for further studies on the biotransformation of palmatine and other protoberberine alkaloids. PMID:25285405

  6. Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii.

    Science.gov (United States)

    Snitkin, Evan S; Zelazny, Adrian M; Montero, Clemente I; Stock, Frida; Mijares, Lilia; Murray, Patrick R; Segre, Julie A

    2011-08-16

    Acinetobacter baumannii is an emerging human pathogen and a significant cause of nosocomial infections among hospital patients worldwide. The enormous increase in multidrug resistance among hospital isolates and the recent emergence of pan-drug-resistant strains underscores the urgency to understand how A. baumannii evolves in hospital environments. To this end, we undertook a genomic study of a polyclonal outbreak of multidrug-resistant A. baumannii at the research-based National Institutes of Health Clinical Center. Comparing the complete genome sequences of the three dominant outbreak strain types enabled us to conclude that, despite all belonging to the same epidemic lineage, the three strains diverged before their arrival at the National Institutes of Health. The simultaneous presence of three divergent strains from this lineage supports its increasing prevalence in international hospitals and suggests an ongoing adaptation to the hospital environment. Further genomic comparisons uncovered that much of the diversification that occurred since the divergence of the three outbreak strains was mediated by homologous recombination across 20% of their genomes. Inspection of recombinant regions revealed that several regions were associated with either the loss or swapping out of genes encoding proteins that are exposed to the cell surface or that synthesize cell-surface molecules. Extending our analysis to a larger set of international clinical isolates revealed a previously unappreciated ability of A. baumannii to vary surface molecules through horizontal gene transfer, with subsequent intraspecies dissemination by homologous recombination. These findings have immediate implications in surveillance, prevention, and treatment of A. baumannii infections. PMID:21825119

  7. 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.

  8. 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.

  9. Low temperature delayed recombination and trap tunneling

    Science.gov (United States)

    Mihóková, E.; Schulman, L. S.

    2015-02-01

    Delayed recombination of charge carriers at an activator is a significant problem for fast scintillators and is usually associated with thermal effects. However, experimental results have shown that this phenomenon can occur even at the lowest temperatures. We here provide evidence in support of the idea that this is due to quantum tunneling between activator and nearby traps, and provide analytic estimates relating the energy levels and locations of those traps to the observed delayed recombination. Several calculations are devoted to showing that deviations from the simplest estimates in fact do not occur. Moreover, these estimates are consistent with lower dimensional numerical calculations for a physically significant range of trap distances. In two examples involving the activator Pr, the formulas developed are used to give the locations of traps based on likely values of trap energy depth.

  10. 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

  11. Production of recombinant proteins in Escherichia coli

    Scientific Electronic Library Online (English)

    Wolfgang, Schumann; Luis Carlos S., Ferreira.

    Full Text Available Attempts to obtain a recombinant protein using prokaryotic expression systems can go from a rewarding and rather fast procedure to a frustrating time-consuming experience. In most cases production of heterologous proteins in Escherichia coli K12 strains has remained an empirical exercise in which di [...] fferent systems are tested without a careful insight into the various factors affecting adequate expression of the encoded protein. The present review will deal with E. coli as protein factory and will cover some of the aspects related to transcriptional and translational expression signals, factors affecting protein stability and solubility and targeting of proteins to different cell compartments. Based on the knowledge accumulated over the last decade, we believe that the rate of success for those dedicated to expression of recombinant proteins based on the use E. coli strains can still be significantly improved.

  12. Recombinant protein production 6 (Vienna, February 2011).

    Science.gov (United States)

    Gasser, Brigitte; Mattanovich, Diethard; Sauer, Michael; Maurer, Michael

    2013-01-25

    The sixth edition of the Conference on Recombinant Protein Production saw a return of physiology-based cell and process engineering. While the application of omics technologies to cell engineering has been constantly on the rise during the past decade, the concept of systems biotechnology is now also applied on bioprocesses bringing new insights into process design and production strategies. The conference brought an extensive comparative view on host cell physiology, covering all areas of bacterial, yeast, fungal, insect, plant and mammalian protein production hosts. Global (genome scale) cellular analysis led to local cell engineering strategies covering also interspecies host optimization strategies, and bringing energy requirements during recombinant protein production back into focus. Additionally, the development of novel secretion systems was presented, giving one example of how to combine industry's needs with highly ambitious fundamental research. PMID:22032951

  13. CFD analysis of passive autocatalytic recombiner

    International Nuclear Information System (INIS)

    In water cooled 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 concentration limits and ignition 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 CFD model has been developed. An In-house 3D CFD model has been developed to study the mechanism of catalytic recombination and has been tested for two literatures quoted experiments. (author)

  14. Recombination energy in double white dwarf formation

    CERN Document Server

    Nandez, Jose L A; Lombardi, James C

    2015-01-01

    In this Letter we investigate the role of recombination energy during a common envelope event. We confirm that taking this energy into account helps to avoid the formation of the circumbinary envelope commonly found in previous studies. For the first time, we can model a complete common envelope event, with a clean compact double white dwarf binary system formed at the end. The resulting binary orbit is almost perfectly circular. In addition to considering recombination energy, we also show that between 1/4 and 1/2 of the released orbital energy is taken away by the ejected material. We apply this new method to the case of the double-white dwarf system WD 1101+364, and we find that the progenitor system at the start of the common envelope event consisted of a $\\sim1.5M_\\odot$ red giant star in a $\\sim 30$ day orbit with a white dwarf companion.

  15. Dissipative Stern-Gerlach recombination experiment

    International Nuclear Information System (INIS)

    The possibility of obtaining the initial pure state in a usual Stern-Gerlach experiment through the recombination of the two emerging beams is investigated. We have extended the previous work of Englert, Schwinger, and Scully [Found Phys. 18, 1045 (1988)] including the fluctuations of the magnetic field generated by a properly chosen magnet. As a result we obtained an attenuation factor to the possible revival of coherence when the beams are perfectly recombined. When the source of the magnetic field is a superconducting quantum interference device (SQUID) the attenuation factor can be controlled by external circuits and the spin decoherence directly measured. For the proposed SQUID with dimensions in the scale of microns the attenuation factor has been shown unimportant when compared with the interaction time of the spin with the magnet

  16. 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.

  17. 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.

  18. Antagonistic experimental coevolution with a parasite increases host recombination frequency

    Directory of Open Access Journals (Sweden)

    Kerstes Niels AG

    2012-02-01

    Full Text Available Abstract Background One of the big remaining challenges in evolutionary biology is to understand the evolution and maintenance of meiotic recombination. As recombination breaks down successful genotypes, it should be selected for only under very limited conditions. Yet, recombination is very common and phylogenetically widespread. The Red Queen Hypothesis is one of the most prominent hypotheses for the adaptive value of recombination and sexual reproduction. The Red Queen Hypothesis predicts an advantage of recombination for hosts that are coevolving with their parasites. We tested predictions of the hypothesis with experimental coevolution using the red flour beetle, Tribolium castaneum, and its microsporidian parasite, Nosema whitei. Results By measuring recombination directly in the individuals under selection, we found that recombination in the host population was increased after 11 generations of coevolution. Detailed insights into genotypic and phenotypic changes occurring during the coevolution experiment furthermore helped us to reconstruct the coevolutionary dynamics that were associated with this increase in recombination frequency. As coevolved lines maintained higher genetic diversity than control lines, and because there was no evidence for heterozygote advantage or for a plastic response of recombination to infection, the observed increase in recombination most likely represented an adaptive host response under Red Queen dynamics. Conclusions This study provides direct, experimental evidence for an increase in recombination frequency under host-parasite coevolution in an obligatory outcrossing species. Combined with earlier results, the Red Queen process is the most likely explanation for this observation.

  19. Recombination Pattern Reanalysis of Some HIV-1 Circulating Recombination Forms Suggest the Necessity and Difficulty of Revision

    Science.gov (United States)

    Jia, Lei; Li, Lin; Li, Hanping; Liu, Siyang; Wang, Xiaolin; Bao, Zuoyi; Li, Tianyi; Zhuang, Daomin; Liu, Yongjian; Li, Jingyun

    2014-01-01

    Background Recombination is one of the major mechanisms underlying the generation of HIV-1 variability. Currently 61 circulating recombinant forms of HIV-1 have been identified. With the development of recombination detection techniques and accumulation of HIV-1 reference stains, more accurate mosaic structures of circulating recombinant forms (CRFs), like CRF04 and CRF06, have undergone repeated analysis and upgrades. Such revisions may also be necessary for other CRFs. Unlike previous studies, whose results are based primarily on a single recombination detection program, the current study was based on multiple recombination analysis, which may have produced more impartial results. Methods Representative references of 3 categories of intersubtype recombinants were selected, including BC recombinants (CRF07 and CRF08), BG recombinants (CRF23 and CRF24), and BF recombinants (CRF38 and CRF44). They were reanalyzed in detail using both the jumping profile hidden Markov model and RDP3. Results The results indicate that revisions and upgrades are very necessary and the entire re-analysis suggested 2 types of revision: (i) length of inserted fragments; and (ii) number of inserted fragments. The reanalysis also indicated that determination of small regions of about 200 bases or fewer should be performed with more caution. Conclusion Results indicated that the involvement of multiple recombination detection programs is very necessary. Additionally, results suggested two major challenges, one involving the difficulty of accurately determining the locations of breakpoints and the second involving identification of small regions of about 200 bases or fewer with greater caution. Both indicate the complexity of HIV-1 recombination. The resolution would depend critically on development of a recombination analysis algorithm, accumulation of HIV-1 stains, and a higher sequencing quality. With the changes in recombination pattern, phylogenetic relationships of some CRFs may also change. All these results may be critical to understand the role of recombination in a complex and dynamic HIV evolution. PMID:25203725

  20. 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

  1. 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

  2. Recombinant Amphiphilic Protein Micelles for Drug Delivery

    OpenAIRE

    Kim, Wookhyun; Xiao, Jiantao; Chaikof, Elliot L.

    2011-01-01

    Amphiphilic block polypeptides can self-assemble into a range of nanostructures in solution, including micelles and vesicles. Our group has recently described the capacity of recombinant amphiphilic diblock copolypeptides to form highly stable micelles. In this report, we demonstrate the utility of protein nanoparticles to serve as a vehicle for controlled drug delivery. Drug-loaded micelles were produced by encapsulating dipyridamole as a model hydrophobic drug with anti-inflammatory activit...

  3. Recombinant spider silk with antimicrobial properties

    OpenAIRE

    Nileba?ck, Linnea

    2013-01-01

    Immobilizing antimicrobial substances onto biocompatible materials is an important approach for the design of novel, functionalized medical devices. By choosing antimicrobial substances from innate immune systems, the risk for development of resistance in pathogenic microbes is lower than if conventional antibiotics are used. Combining natural antimicrobial peptides and bactericidal enzymes with strong and elastic spider silk through recombinant protein technology would enable large-scale pro...

  4. 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.

  5. Relativistic effects in dielectronic recombination probabilities

    International Nuclear Information System (INIS)

    The method of the relativistic parametric potential was used to compute autoionization and radiative transition probabilities for Li-like Mg, Fe, Ni and Mo (Dielectronic Recombination on He-like). Computations were performed with different values of c, enabling analysis of the behaviour of relativistic corrections. It is shown that for atoms up to Fe, the dominant effect is the spin orbit interaction. The effects of the wave-functions being relativistic contribute only a few percent

  6. The stability of recombined milk fat globules.

    OpenAIRE

    Melsen, J. P.

    1987-01-01

    The stability of the fat globules in recombined milk products against creaming, flocculation, clustering, partial coalescence and real coalescence, with the emphasis on partial coalescence, was studied. (partial) Coalescence was characterized by determining changes in globule size distribution and fat content. Without crystals the emulsions were mostly stable at rest and during flow. If crystals were present, natural cream and emulsions of milk fat-in-whey were unstable in a flow, while emuls...

  7. Recombinant Salmonella vectors in vaccine development.

    Science.gov (United States)

    Curtiss, R; Kelly, S M; Tinge, S A; Tacket, C O; Levine, M M; Srinivasan, J; Koopman, M

    1994-01-01

    A diversity of means are available for the attenuation of Salmonella which can be used to immunize animals and humans orally to elicit mucosal, humoral and cellular immune responses. Avirulent Salmonellae can be genetically engineered to express foreign antigens and the recombinant avirulent Salmonellae are capable of stable, high-level expression of the foreign antigen in the orally immunized animal or human host. The resulting vaccines are safe, efficacious, and are easy and economical to use. PMID:7958478

  8. Dielectronic Recombination Rates In Astrophysical Plasmas

    CERN Document Server

    Bachari, F; Maero, G; Quarati, P; Bachari, Fatima; Ferro, Fabrizio; Maero, Giancarlo; Quarati, Piero

    2006-01-01

    In this work we introduce a new expression of the plasma Dielecronic Recombination (DR) rate as a function of the temperature, derived assuming a small deformation of the Maxwell-Boltzmann distribution and containing corrective factors, in addition to the usual exponential behaviour, caused by non-linear effects in slightly non ideal plasmas. We then compare the calculated DR rates with the experimental DR fits in the low temperature region.

  9. 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.

  10. 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...

  11. Charge Recombination and Thermoluminescence in Photosystem II

    OpenAIRE

    Rappaport, Fabrice; Cuni, Aude; Xiong, Ling; Sayre, Richard; Lavergne, Je?ro?me

    2005-01-01

    In the recombination process of Photosystem II \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}(S_{2}Q_{{\\mathrm{A}}}^{-}{\\rightarrow}S_{1}Q_{{\\mathrm{A}}})\\end{equation*}\\end{document} the limiting step is the electron transfer from the reduced primary acceptor pheophytin Ph? to the oxi...

  12. 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...

  13. 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.)

  14. Recombinant glucagon: a differential biological activity.

    Science.gov (United States)

    Basso, Angelina M M; Pelegrini, Patrícia B; Mulinari, Fernanda; Costa, Michelle C; Viana, Antonio B; Silva, Luciano P; Grossi-de-Sa, Maria Fatima

    2015-01-01

    In Brazil, there is a growing demand for specialised pharmaceuticals, and the high cost of their importation results in increasing costs, reaching US$ 1.34 billion in 2012 and US$ 1.61 billion in 2013. Worldwide expenses related to drugs could reach US$ 1.3 trillion in 2018, especially due to new treatments for hepatitis C and cancer. Specialised or high-cost pharmaceutical drugs used for the treatment of viral hepatitis, multiple sclerosis, HIV and diabetes are distributed free of charge by the Brazilian government. The glucagon peptide was included in this group of high-cost biopharmaceuticals in 2008. Although its main application is the treatment of hypoglycaemia in diabetic patients, it can also be used with patients in an alcoholic coma, for those patients with biliary tract pain, and as a bronchodilator. Therefore, in order to reduce biopharmaceutical production costs, the Brazilian government passed laws focusing on the development and increase of a National Pharmaceutical Industrial Centre, including the demand for the national production of glucagon. For that reason and given the importance and high cost of recombinant glucagon, the purpose of this study was to develop methods to improve production, purification and performance of the biological activity of recombinant glucagon. Glucagon was recombined into a plasmid vector containing a Glutathione S-transferase tag, and the peptide was expressed in a heterologous Escherichia coli system. After purification procedures and molecular analyses, the biological activity of this recombinant glucagon was examined using in vivo assays and showed a highly significant (p?biological activity. PMID:25852997

  15. Asthma and Therapeutics: Recombinant Therapies in Asthma

    OpenAIRE

    Cockcroft Donald W

    2005-01-01

    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 (Ig)E (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. E...

  16. Dissociative recombination of small molecular ions

    International Nuclear Information System (INIS)

    In this thesis an analysis is given of merged electron-ion beam experiment and work on dissociative recombination of molecular ions and electrons is described. Chapter II covers a brief introduction of the theory of dissociative recombination. In chapter III, a description is given of the merged electron-ion beam experiment and a method is described which allows the determination of the mean angle between the electron and ion trajectories in a merged electron-ion beam experiment. In chapter IV a paper on the three dominant atmospheric diatomic ions NO+, O2+ and N2+ is presented and in chapter V the dissociative recombination for N2H+ and N2D+ is discussed. In chapter VI two papers on the polyatomic ions of the carbon-containing molecular ions are presented, and in chapter VII a letter with some results of the work presented in more detail in the chapters IV, V and VI is presented. The magnitude and the energy dependence of the cross-section measured by the merged beam technique and by other techniques is compared and discussed. (Auth.)

  17. Dissociative recombination of molecular ions with electrons

    Science.gov (United States)

    Johnsen, Rainer

    1990-01-01

    An overview is presented for the present state of the art of laboratory measurements of the dissociative recombination of molecular ions with electrons. Most work has focussed on obtaining rates and their temperature dependence, as these are of primary interest for model calculations of ionospheres. A comparison of data obtained using the microwave afterglow method, the flowing afterglow technique, and the merged beam technique shows that generally the agreement is quite good, but there are some serious discrepancies, especially in the case of H(3+) recombination, that need to be resolved. Results of some earlier experimental work need to be reexamined in the light of more recent developments. Such cases are pointed out and a compilation of rate coefficients that have withstood scrutiny is presented. Recent advances in experimental methods, such as the use of laser-in-duced fluorescence, make it possible to identify some neutral products of dissociative recombination. What has been done so far and what results one might expect from future work are briefly reviewed.

  18. Creating porcine biomedical models through recombineering.

    Science.gov (United States)

    Rogatcheva, Margarita M; Rund, Laurie A; Swanson, Kelly S; Marron, Brandy M; Beever, Jonathan E; Counter, Christopher M; Schook, Lawrence B

    2004-01-01

    Recent advances in genomics provide genetic information from humans and other mammals (mouse, rat, dog and primates) traditionally used as models as well as new candidates (pigs and cattle). In addition, linked enabling technologies, such as transgenesis and animal cloning, provide innovative ways to design and perform experiments to dissect complex biological systems. Exploitation of genomic information overcomes the traditional need to choose naturally occurring models. Thus, investigators can utilize emerging genomic knowledge and tools to create relevant animal models. This approach is referred to as reverse genetics. In contrast to 'forward genetics', in which gene(s) responsible for a particular phenotype are identified by positional cloning (phenotype to genotype), the 'reverse genetics' approach determines the function of a gene and predicts the phenotype of a cell, tissue, or organism (genotype to phenotype). The convergence of classical and reverse genetics, along with genomics, provides a working definition of a 'genetic model' organism (3). The recent construction of phenotypic maps defining quantitative trait loci (QTL) in various domesticated species provides insights into how allelic variations contribute to phenotypic diversity. Targeted chromosomal regions are characterized by the construction of bacterial artificial chromosome (BAC) contigs to isolate and characterize genes contributing towards phenotypic variation. Recombineering provides a powerful methodology to harvest genetic information responsible for phenotype. Linking recombineering with gene-targeted homologous recombination, coupled with nuclear transfer (NT) technology can provide 'clones' of genetically modified animals. PMID:18629152

  19. Ly alpha escape during cosmological hydrogen recombination

    CERN Document Server

    Chluba, J

    2009-01-01

    We give a formulation of the radiative transfer equation for Lyman alpha photons which allows us to include the two-photon corrections for the 3s-1s and 3d-1s decay channels during cosmological hydrogen recombination. We use this equation to compute the corrections to the Sobolev escape probability for Lyman alpha photons during hydrogen recombination, which then allow us to calculate the changes in the free electron fraction and CMB temperature and polarization power spectra. We show that the effective escape probability changes by DP/P ~+ 11% at z~1400 in comparison with the one obtained using the Sobolev approximation. This speeds up of hydrogen recombination by DN_e/N_e ~- 1.6% at z~1190, implying |DC_l/C_l| ~1%-3% at l >~ 1500 with shifts in the positions of the maxima and minima in the CMB power spectra. These corrections will be important for the analysis of future CMB data. The total correction is the result of the superposition of three independent processes, related to (i) time-dependent aspects of ...

  20. Evolutionary Origin of Recombination during Meiosis

    Science.gov (United States)

    Carol Bernstein (University of Arizona; Cell Biology and Anatomy)

    2010-07-14

    Recent evidence indicates that meiosis arose very early in eukaryotic evolution, which suggests that essential features of meiosis were already present in the prokaryotic ancestors of eukaryotes. Furthermore, in extant organisms, proteins with central functions in meiosis are similar in sequence and function to key proteins in bacterial transformation. In particular, RecA recombinaseâ??which performs the central functions of DNA homology search and strand exchange in bacterial transformationâ??has orthologs in eukaryotes that carry out similar functions in meiotic recombination. Both transformation and meiosis (including meiotic recombination) in eukaryotic microorganisms are induced by stressful conditions, such as overcrowding, resource depletion, and DNA-damaging conditions, suggesting that these processes are adaptations for dealing with stress. If such environmental stresses were a persistent challenge to the survival of early microorganisms, then continuity of selection through the prokaryote to eukaryote transition probably would have followed a course in which bacterial transformation naturally gave rise to the recombination process that is central to eukaryote meiosis.