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Sample records for class switch recombination

  1. Immunoglobulin class-switch recombination deficiencies.

    PubMed

    Durandy, Anne; Kracker, Sven

    2012-07-30

    Immunoglobulin class-switch recombination deficiencies (Ig-CSR-Ds) are rare primary immunodeficiencies characterized by defective switched isotype (IgG/IgA/IgE) production. Depending on the molecular defect in question, the Ig-CSR-D may be combined with an impairment in somatic hypermutation (SHM). Some of the mechanisms underlying Ig-CSR and SHM have been described by studying natural mutants in humans. This approach has revealed that T cell-B cell interaction (resulting in CD40-mediated signaling), intrinsic B-cell mechanisms (activation-induced cytidine deaminase-induced DNA damage), and complex DNA repair machineries (including uracil-N-glycosylase and mismatch repair pathways) are all involved in class-switch recombination and SHM. However, several of the mechanisms required for full antibody maturation have yet to be defined. Elucidation of the molecular defects underlying the diverse set of Ig-CSR-Ds is essential for understanding Ig diversification and has prompted better definition of the clinical spectrum of diseases and the development of increasingly accurate diagnostic and therapeutic approaches.

  2. Epigenetic Codes Programing Class Switch Recombination.

    PubMed

    Vaidyanathan, Bharat; Chaudhuri, Jayanta

    2015-01-01

    Class switch recombination imparts B cells with a fitness-associated adaptive -advantage during a humoral immune response by using a precision-tailored DNA excision and ligation process to swap the default constant region gene of the antibody with a new one that has unique effector functions. This secondary diversification of the antibody repertoire is a hallmark of the adaptability of B cells when confronted with environmental and pathogenic challenges. Given that the nucleotide sequence of genes during class switching remains unchanged (genetic constraints), it is logical and necessary therefore, to integrate the adaptability of B cells to an epigenetic state, which is dynamic and can be heritably modulated before, after, or even during an antibody-dependent immune response. Epigenetic regulation encompasses heritable changes that affect function (phenotype) without altering the sequence information embedded in a gene, and include histone, DNA and RNA modifications. Here, we review current literature on how B cells use an epigenetic code language as a means to ensure antibody plasticity in light of pathogenic insults.

  3. Epigenetic Codes Programing Class Switch Recombination

    PubMed Central

    Vaidyanathan, Bharat; Chaudhuri, Jayanta

    2015-01-01

    Class switch recombination imparts B cells with a fitness-associated adaptive ­advantage during a humoral immune response by using a precision-tailored DNA excision and ligation process to swap the default constant region gene of the antibody with a new one that has unique effector functions. This secondary diversification of the antibody repertoire is a hallmark of the adaptability of B cells when confronted with environmental and pathogenic challenges. Given that the nucleotide sequence of genes during class switching remains unchanged (genetic constraints), it is logical and necessary therefore, to integrate the adaptability of B cells to an epigenetic state, which is dynamic and can be heritably modulated before, after, or even during an antibody-dependent immune response. Epigenetic regulation encompasses heritable changes that affect function (phenotype) without altering the sequence information embedded in a gene, and include histone, DNA and RNA modifications. Here, we review current literature on how B cells use an epigenetic code language as a means to ensure antibody plasticity in light of pathogenic insults. PMID:26441954

  4. Interallelic class switch recombination contributes significantly to class switching in mouse B cells.

    PubMed

    Reynaud, Stéphane; Delpy, Laurent; Fleury, Laurence; Dougier, Hei-Lanne; Sirac, Christophe; Cogné, Michel

    2005-05-15

    Except for the expression of IgM and IgD, DNA recombination is constantly needed for the expression of other Ig classes and subclasses. The predominant path of class switch recombination (CSR) is intrachromosomal, and the looping-out and deletion model has been abundantly documented. However, switch regions also occasionally constitute convenient substrates for interchromosomal recombination, since it is noticeably the case in a number of chromosomal translocations causing oncogene deregulation in the course of lymphoma and myeloma. Although asymmetric accessibility of Ig alleles should theoretically limit its occurrence, interallelic CSR was shown to occur at low levels during IgA switching in rabbit, where the definition of allotypes within both V and C regions helped identify interchromosomally derived Ig. Thus, we wished to evaluate precisely interallelic CSR frequency in mouse B cells, by using a system in which only one allele (of b allotype) could express a functional VDJ region, whereas only interallelic CSR could restore expression of an excluded (a allotype) allele. In our study, we show that interchromosomal recombination of V(H) and Cgamma or Calpha occurs in vivo in B cells at a frequency that makes a significant contribution to physiological class switching: trans-association of V(H) and C(H) genes accounted for 7% of all alpha mRNA, and this frequency was about twice higher for the gamma3 transcripts, despite the much shorter distance between the J(H) region and the Cgamma3 gene, thus confirming that this phenomenon corresponded to site-specific switching and not to random recombination between long homologous loci.

  5. Ig heavy chain class switch recombination: mechanism and regulation

    PubMed Central

    Stavnezer, Janet; Schrader, Carol E.

    2014-01-01

    Ig heavy chain class switching occurs rapidly after activation of mature naïve B cells, resulting in a switch from expressing IgM and IgD to expression of IgG, IgE, or IgA; this switch improves the ability of antibodies to remove the pathogen that induces the humoral immune response. Class switching occurs by a deletional recombination between two different switch (S) regions, each of which is associated with a heavy chain constant (CH) region gene. Class switch recombination (CSR) is instigated by activation-induced cytidine deaminase (AID), which converts cytosines in S regions to uracils. The uracils are subsequently removed by two DNA repair pathways, resulting in mutations, single-strand DNA breaks, and the double-strand breaks required for CSR. We discuss several aspects of CSR, including how CSR is induced, CSR in B-cell progenitors, the roles for transcription and chromosomal looping in CSR, and the roles of certain DNA repair enzymes in CSR. PMID:25411432

  6. Parp3 Negatively Regulates Immunoglobulin Class Switch Recombination

    PubMed Central

    Robert, Isabelle; Gaudot, Léa; Rogier, Mélanie; Heyer, Vincent; Noll, Aurélia; Dantzer, Françoise; Reina-San-Martin, Bernardo

    2015-01-01

    To generate highly specific and adapted immune responses, B cells diversify their antibody repertoire through mechanisms involving the generation of programmed DNA damage. Somatic hypermutation (SHM) and class switch recombination (CSR) are initiated by the recruitment of activation-induced cytidine deaminase (AID) to immunoglobulin loci and by the subsequent generation of DNA lesions, which are differentially processed to mutations during SHM or to double-stranded DNA break intermediates during CSR. The latter activate the DNA damage response and mobilize multiple DNA repair factors, including Parp1 and Parp2, to promote DNA repair and long-range recombination. We examined the contribution of Parp3 in CSR and SHM. We find that deficiency in Parp3 results in enhanced CSR, while SHM remains unaffected. Mechanistically, this is due to increased occupancy of AID at the donor (Sμ) switch region. We also find evidence of increased levels of DNA damage at switch region junctions and a bias towards alternative end joining in the absence of Parp3. We propose that Parp3 plays a CSR-specific role by controlling AID levels at switch regions during CSR. PMID:26000965

  7. Reduced immunoglobulin class switch recombination in the absence of Artemis.

    PubMed

    Rivera-Munoz, Paola; Soulas-Sprauel, Pauline; Le Guyader, Gwenaël; Abramowski, Vincent; Bruneau, Sylvia; Fischer, Alain; Pâques, Frédéric; de Villartay, Jean-Pierre

    2009-10-22

    Nonhomologous end-joining DNA repair factors, including Artemis, are all required for the repair of DNA double-strand breaks, which occur during the assembly of the variable antigen recognition domain of B-cell receptors and T-cell receptors through the V(D)J recombination. Mature B cells further shape their immunoglobulin repertoire on antigen recognition notably through the class switch recombination (CSR) process. To analyze the role of Artemis during CSR, we developed a mature B-cell-specific Artemis conditional knockout mouse to bypass the absence of B cells caused by its early deficit. Although CSR is not overwhelmingly affected in these mice, class switching to certain isotypes is clearly reduced both in vitro on B-cell activation and in vivo after keyhole limpet hemocyanin immunization. The reduced CSR in Artemis-deficient B cells is accompanied by the increase in DNA microhomology usage at CSR junctions, the imprint of an alternative DNA end-joining pathway. Likewise, significant increase in DNA microhomology usage is the signature of CSR junctions obtained from human RS-SCID patients harboring hypomorphic Artemis mutations. Altogether, this indicates that Artemis participates in the repair of a subset of DNA breaks generated during CSR.

  8. Molecular Mechanisms of IgE Class Switch Recombination.

    PubMed

    Tong, Pei; Wesemann, Duane R

    2015-01-01

    Immunoglobulin (Ig) E is the most tightly regulated of all Ig heavy chain (IgH) isotypes and plays a key role in atopic disease. The gene encoding for IgH in mature B cells consists of a variable region exon-assembled from component gene segments via V(D)J recombination during early B cell development-upstream of a set of IgH constant region CH exons. Upon activation by antigen in peripheral lymphoid organs, B cells can undergo IgH class switch recombination (CSR), a process in which the initially expressed IgH μ constant region exons (Cμ) are deleted and replaced by one of several sets of downstream CH exons (e.g., Cγ, Cε, and Cα). Activation of the IL-4 receptor on B cells, together with other signals, can lead to the replacement of Cμ with Cε resulting in CSR to IgE through a series of molecular events involving irreversible remodeling of the IgH locus. Here, we discuss the molecular mechanisms of CSR and the unique features surrounding the generation of IgE-producing B cells.

  9. BRCT-domain protein BRIT1 influences class switch recombination.

    PubMed

    Yen, Wei-Feng; Chaudhry, Ashutosh; Vaidyanathan, Bharat; Yewdell, William T; Pucella, Joseph N; Sharma, Rahul; Liang, Yulong; Li, Kaiyi; Rudensky, Alexander Y; Chaudhuri, Jayanta

    2017-07-19

    DNA double-strand breaks (DSBs) serve as obligatory intermediates for Ig heavy chain (Igh) class switch recombination (CSR). The mechanisms by which DSBs are resolved to promote long-range DNA end-joining while suppressing genomic instability inherently associated with DSBs are yet to be fully elucidated. Here, we use a targeted short-hairpin RNA screen in a B-cell lymphoma line to identify the BRCT-domain protein BRIT1 as an effector of CSR. We show that conditional genetic deletion of BRIT1 in mice leads to a marked increase in unrepaired Igh breaks and a significant reduction in CSR in ex vivo activated splenic B cells. We find that the C-terminal tandem BRCT domains of BRIT1 facilitate its interaction with phosphorylated H2AX and that BRIT1 is recruited to the Igh locus in an activation-induced cytidine deaminase (AID) and H2AX-dependent fashion. Finally, we demonstrate that depletion of another BRCT-domain protein, MDC1, in BRIT1-deleted B cells increases the severity of CSR defect over what is observed upon loss of either protein alone. Our results identify BRIT1 as a factor in CSR and demonstrate that multiple BRCT-domain proteins contribute to optimal resolution of AID-induced DSBs.

  10. The role of G-density in switch region repeats for immunoglobulin class switch recombination.

    PubMed

    Zhang, Zheng Z; Pannunzio, Nicholas R; Hsieh, Chih-Lin; Yu, Kefei; Lieber, Michael R

    2014-12-01

    The boundaries of R-loops are well-documented at immunoglobulin heavy chain loci in mammalian B cells. Within primary B cells or B cell lines, the upstream boundaries of R-loops typically begin early in the repetitive portion of the switch regions. Most R-loops terminate within the switch repetitive zone, but the remainder can extend a few hundred base pairs further, where G-density on the non-template DNA strand gradually drops to the genome average. Whether the G-density determines how far the R-loops extend is an important question. We previously studied the role of G-clusters in initiating R-loop formation, but we did not examine the role of G-density in permitting the elongation of the R-loop, after it had initiated. Here, we vary the G-density of different portions of the switch region in a murine B cell line. We find that both class switch recombination (CSR) and R-loop formation decrease significantly when the overall G-density is reduced from 46% to 29%. Short 50 bp insertions with low G-density within switch regions do not appear to affect either CSR or R-loop elongation, whereas a longer (150 bp) insertion impairs both. These results demonstrate that G-density is an important determinant of the length over which mammalian genomic R-loops extend.

  11. Switch junction sequences in PMS2-deficient mice reveal a microhomology-mediated mechanism of Ig class switch recombination

    PubMed Central

    Ehrenstein, Michael R.; Rada, Cristina; Jones, Anne-Marie; Milstein, César; Neuberger, Michael S.

    2001-01-01

    Isotype switching involves a region-specific, nonhomologous recombinational deletion that has been suggested to occur by nonhomologous joining of broken DNA ends. Here, we find increased donor/acceptor homology at switch junctions from PMS2-deficient mice and propose that class switching can occur by microhomology-mediated end-joining. Interestingly, although isotype switching and somatic hypermutation show many parallels, we confirm that PMS2 deficiency has no major effect on the pattern of nucleotide substitutions generated during somatic hypermutation. This finding is in contrast to MSH2 deficiency. With MSH2, the altered pattern of switch recombination and hypermutation suggests parallels in the mechanics of the two processes, whereas the fact that PMS2 deficiency affects only switch recombination may reflect differences in the pathways of break resolution. PMID:11717399

  12. Regulating infidelity: RNA-mediated recruitment of AID to DNA during class switch recombination

    PubMed Central

    DiMenna, Lauren; Chaudhuri, Jayanta

    2016-01-01

    The mechanism by which the DNA deaminase AID is specifically recruited to repetitive switch region DNA during class switch recombination is still poorly understood. Work over the past decade has revealed a strong link between transcription and RNA polymerase-associated factors in AID recruitment, yet none of these processes satisfactorily explain how AID specificity is effected. Here we review a recent finding wherein AID is guided to switch regions not by a protein factor but by an RNA moiety, and especially one associated with a non-coding RNA that has been long thought of as being inert. This work explains the long-standing requirement of splicing of non-coding transcripts during class switching, and has implications in both B-cell-mediated immunity as well as the underlying pathological syndromes associated with the recombination reaction. PMID:26799454

  13. Regulating infidelity: RNA-mediated recruitment of AID to DNA during class switch recombination.

    PubMed

    DiMenna, Lauren J; Chaudhuri, Jayanta

    2016-03-01

    The mechanism by which the DNA deaminase activation-induced cytidine deaminase (AID) is specifically recruited to repetitive switch region DNA during class switch recombination is still poorly understood. Work over the past decade has revealed a strong link between transcription and RNA polymerase-associated factors in AID recruitment, yet none of these processes satisfactorily explain how AID specificity is affected. Here, we review a recent finding wherein AID is guided to switch regions not by a protein factor but by an RNA moiety, and especially one associated with a noncoding RNA that has been long thought of as being inert. This work explains the long-standing requirement of splicing of noncoding transcripts during class switching, and has implications in both B cell-mediated immunity as well as the underlying pathological syndromes associated with the recombination reaction.

  14. Enhancement of antibody class switch recombination by the cumulative activity of four separate elements1

    PubMed Central

    Dunnick, Wesley A.; Shi, Jian; Zerbato, Jennifer M.; Fontaine, Clinton A.; Collins, John T.

    2011-01-01

    Class switch recombination of antibody isotype is mediated by a recombinational DNA deletion event, and must be robustly upregulated during antigen-driven differentiation of B cells. The enhancer region 3′ of the Cα gene is important for the upregulation of switch recombination. Using a transgene of the entire heavy chain constant region locus, we now demonstrate that it is the four 3′ enhancer elements themselves (a total of 4.7 kb) that are responsible for the upregulation, rather than the 24 kb of DNA in between them. Neither allelic exclusion nor transgenic μ expression is reduced by deletion of the four 3′ enhancers. We also test deletions of two or three of the 3′ enhancers, and show that deletion of more 3′ enhancers results in a progressive reduction in both switch recombination and germline transcription of all heavy chain genes. Nevertheless, we find evidence for special roles for some 3′ enhancers--different heavy chain genes are affected by different 3′ enhancer deletions. Thus, we find that the dramatic induction of class switch recombination during antigen-driven differentiation is the result of an interaction among four separated regulatory elements. PMID:21949022

  15. DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner.

    PubMed

    Wiedemann, Eva-Maria; Peycheva, Mihaela; Pavri, Rushad

    2016-12-13

    Class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) locus generates antibody isotypes. CSR depends on double-strand breaks (DSBs) induced by activation-induced cytidine deaminase (AID). Although DSB formation and repair machineries are active in G1 phase, efficient CSR is dependent on cell proliferation and S phase entry; however, the underlying mechanisms are obscure. Here, we show that efficient CSR requires the replicative helicase, the Mcm complex. Mcm proteins are enriched at IgH switch regions during CSR, leading to assembly of facultative replication origins that require Mcm helicase function for productive CSR. Assembly of CSR-associated origins is facilitated by R loops and promotes the physical proximity (synapsis) of recombining switch regions, which is reduced by R loop inhibition or Mcm complex depletion. Thus, R loops contribute to replication origin specification that promotes DSB resolution in CSR. This suggests a mechanism for the dependence of CSR on S phase and cell division.

  16. Effect of CpG dinucleotides within IgH switch region repeats on immunoglobulin class switch recombination.

    PubMed

    Zhang, Zheng Z; Hsieh, Chih-Lin; Okitsu, Cindy Yen; Han, Li; Yu, Kefei; Lieber, Michael R

    2015-08-01

    Immunoglobulin (Ig) heavy chains undergo class switch recombination (CSR) to change the heavy chain isotype from IgM to IgG, A or E. The switch regions are several kilobases long, repetitive, and G-rich on the nontemplate strand. They are also relatively depleted of CpG (also called CG) sites for unknown reasons. Here we use synthetic switch regions at the IgH switch alpha (Sα) locus to test the effect of CpG sites and to try to understand why the IgH switch sequences evolved to be relatively depleted of CpG. We find that even just two CpG sites within an 80 bp synthetic switch repeat iterated 15 times (total switch region length of 1200 bp containing 30 CpG sites) are sufficient to dramatically reduce both Ig CSR and transcription through the switch region from the upstream Iα sterile transcript promoter, which is the promoter that directs transcripts through the Sα region. De novo DNA methylation occurs at the four CpG sites in and around the Iα promoter when each 80 bp Iα switch repeat contains the two CpG sites. Thus, a relatively low density of CpG sites within the switch repeats can induce upstream CpG methylation at the IgH alpha locus, and cause a substantial decrease in transcription from the sterile transcript promoter. This effect is likely the reason that switch regions evolved to contain very few CpG sites. We discuss these findings as they relate to DNA methylation and to Ig CSR.

  17. Aberrant recombination and repair during immunoglobulin class switching in BRCA1-deficient human B cells.

    PubMed

    Björkman, Andrea; Qvist, Per; Du, Likun; Bartish, Margarita; Zaravinos, Apostolos; Georgiou, Konstantinos; Børglum, Anders D; Gatti, Richard A; Törngren, Therese; Pan-Hammarström, Qiang

    2015-02-17

    Breast cancer type 1 susceptibility protein (BRCA1) has a multitude of functions that contribute to genome integrity and tumor suppression. Its participation in the repair of DNA double-strand breaks (DSBs) during homologous recombination (HR) is well recognized, whereas its involvement in the second major DSB repair pathway, nonhomologous end-joining (NHEJ), remains controversial. Here we have studied the role of BRCA1 in the repair of DSBs in switch (S) regions during immunoglobulin class switch recombination, a physiological, deletion/recombination process that relies on the classical NHEJ machinery. A shift to the use of microhomology-based, alternative end-joining (A-EJ) and increased frequencies of intra-S region deletions as well as insertions of inverted S sequences were observed at the recombination junctions amplified from BRCA1-deficient human B cells. Furthermore, increased use of long microhomologies was found at recombination junctions derived from E3 ubiquitin-protein ligase RNF168-deficient, Fanconi anemia group J protein (FACJ, BRIP1)-deficient, or DNA endonuclease RBBP8 (CtIP)-compromised cells, whereas an increased frequency of S-region inversions was observed in breast cancer type 2 susceptibility protein (BRCA2)-deficient cells. Thus, BRCA1, together with its interaction partners, seems to play an important role in repairing DSBs generated during class switch recombination by promoting the classical NHEJ pathway. This may not only provide a general mechanism underlying BRCA1's function in maintaining genome stability and tumor suppression but may also point to a previously unrecognized role of BRCA1 in B-cell lymphomagenesis.

  18. Class switch recombination signals induce lymphocyte-derived Spo11 expression and Spo11 antisense oligonucleotide inhibits class switching.

    PubMed

    Tokuyama, H; Tokuyama, Y

    2001-08-01

    Recently, we showed that mouse Spo11 is induced in normal mu(+) B cells by class switch recombination (CSR) stimuli, by RT-PCR using primers based on the reported cDNA sequence of testis-derived Spo11 (test-Spo11) cDNA. In the present study, we first determined the cDNA sequence of lymphocyte-derived Spo11 (lym-Spo11). The 5' upstream portion had an as yet unreported sequence but the remaining part from exons 2 to 12 and the subsequent 3'UTR was completely identical to that of test-Spo11. RT-PCR analysis indicated that lymphocytes express lym-Spo11 but not test-Spo11. Second, we showed that lym-Spo11 is strongly induced (above eightfold) in the IgA CSR system of LPS-stimulated mu(+)B cells in the presence of all-trans retinoic acid and IL-4. Finally, we examined whether lym-Spo11 antisense S-oligonucleotide (AS) can inhibit CSR reactions in three in vitro CSR systems, IgA,IgG1, and IgE. Lym-Spo11 AS or the sense oligonucleotide was added to the cultures at the start, and total RNA was extracted after 4 days. IgA, IgG1, and IgE mRNAs (J(H)C(H)) and mature germline C(H) transcripts (I(H)C(H)) were quantitatively assayed by RT-PCR. AS inhibited J(H)C(H) expression dose-dependently. In all three systems, the maximum inhibition by 20 microM AS was in the range of 60 to 90%. Interestingly, I(H)C(H) was also inhibited by AS to a similar extent as J(H)C(H). These results suggested that lym-Spo11 plays an important role in the initiation step of CSR.

  19. A DNA break– and phosphorylation-dependent positive feedback loop promotes immunoglobulin class-switch recombination

    PubMed Central

    Vuong, Bao Q; Ucher, Anna J; Donghia, Nina M; Gu, Xiwen; Nicolas, Laura; Nowak, Urszula; Rahman, Numa; Strout, Matthew P; Mills, Kevin D; Stavnezer, Janet; Chaudhuri, Jayanta

    2014-01-01

    The ability of activation-induced cytidine deaminase (AID) to efficiently mediate class-switch recombination (CSR) is dependent on its phosphorylation at Ser38; however, the trigger that induces AID phosphorylation and the mechanism by which phosphorylated AID drives CSR have not been elucidated. Here we found that phosphorylation of AID at Ser38 was induced by DNA breaks. Conversely, in the absence of AID phosphorylation, DNA breaks were not efficiently generated at switch (S) regions in the immunoglobulin heavy-chain locus (Igh), consistent with a failure of AID to interact with the endonuclease APE1. Additionally, deficiency in the DNA-damage sensor ATM impaired the phosphorylation of AID at Ser38 and the interaction of AID with APE1. Our results identify a positive feedback loop for the amplification of DNA breaks at S regions through the phosphorylation- and ATM-dependent interaction of AID with APE1. PMID:24097111

  20. YY1 Controls Immunoglobulin Class Switch Recombination and Nuclear Activation-Induced Deaminase Levels

    PubMed Central

    Zaprazna, Kristina

    2012-01-01

    Activation-induced deaminase (AID) is an enzyme required for class switch recombination (CSR) and somatic hypermutation (SHM), processes that ensure antibody maturation and expression of different immunoglobulin isotypes. AID function is tightly regulated by tissue- and stage-specific expression, nuclear localization, and protein stability. Transcription factor YY1 is crucial for early B cell development, but its function at late B cell stages is unknown. Here, we show that YY1 conditional knockout in activated splenic B cells interferes with CSR. Knockout of YY1 did not affect B cell proliferation, transcription of the AID and IgM genes, or levels of various switch region germ line transcripts. However, we show that YY1 physically interacts with AID and controls the accumulation of nuclear AID, at least in part, by increasing nuclear AID stability. We show for the first time that YY1 plays a novel role in CSR and controls nuclear AID protein levels. PMID:22290437

  1. Separate domains of AID are required for somatic hypermutation and class-switch recombination.

    PubMed

    Shinkura, Reiko; Ito, Satomi; Begum, Nasim A; Nagaoka, Hitoshi; Muramatsu, Masamichi; Kinoshita, Kazuo; Sakakibara, Yoshimasa; Hijikata, Hiroko; Honjo, Tasuku

    2004-07-01

    Activation-induced cytidine deaminase (AID) is essential for class-switch recombination (CSR) and somatic hypermutation (SHM). Mutants with changes in the C-terminal region of AID retain SHM but lose CSR activity. Here we describe five mutants with alterations in the N-terminal region of AID that caused selective deficiency in SHM but retained CSR, suggesting that the CSR and SHM activities of AID may dissociate via interaction of CSR- or SHM-specific cofactors with different domains of AID. Unlike cells expressing C-terminal AID mutants, B cells expressing N-terminal AID mutants had mutations in the switch micro region, indicating that such mutations are generated by reactions involved in CSR but not SHM. Thus, we propose that separate domains of AID interact with specific cofactors to regulate these two distinct genetic events in a target-specific way.

  2. Immunoglobulin Class Switch Recombination Is Impaired in Atm-deficient Mice

    PubMed Central

    Lumsden, Joanne M.; McCarty, Thomas; Petiniot, Lisa K.; Shen, Rhuna; Barlow, Carrolee; Wynn, Thomas A.; Morse, Herbert C.; Gearhart, Patricia J.; Wynshaw-Boris, Anthony; Max, Edward E.; Hodes, Richard J.

    2004-01-01

    Immunoglobulin class switch recombination (Ig CSR) involves DNA double strand breaks (DSBs) at recombining switch regions and repair of these breaks by nonhomologous end-joining. Because the protein kinase ataxia telengiectasia (AT) mutated (ATM) plays a critical role in DSB repair and AT patients show abnormalities of Ig isotype expression, we assessed the role of ATM in CSR by examining ATM-deficient mice. In response to T cell–dependent antigen (Ag), Atm−/− mice secreted substantially less Ag-specific IgA, IgG1, IgG2b, and IgG3, and less total IgE than Atm+/+ controls. To determine whether Atm−/− B cells have an intrinsic defect in their ability to undergo CSR, we analyzed in vitro responses of purified B cells. Atm−/− cells secreted substantially less IgA, IgG1, IgG2a, IgG3, and IgE than wild-type (WT) controls in response to stimulation with lipopolysaccharide, CD40 ligand, or anti-IgD plus appropriate cytokines. Molecular analysis of in vitro responses indicated that WT and Atm−/− B cells produced equivalent amounts of germline IgG1 and IgE transcripts, whereas Atm−/− B cells produced markedly reduced productive IgG1 and IgE transcripts. The reduction in isotype switching by Atm−/− B cells occurs at the level of genomic DNA recombination as measured by digestion–circularization PCR. Analysis of sequences at CSR sites indicated that there is greater microhomology at the μ–γ1 switch junctions in ATM B cells than in wild-type B cells, suggesting that ATM function affects the need or preference for sequence homology in the CSR process. These findings suggest a role of ATM in DNA DSB recognition and/or repair during CSR. PMID:15504820

  3. Switch Transcripts in Immunoglobulin Class Switching

    NASA Astrophysics Data System (ADS)

    Lorenz, Matthias; Jung, Steffen; Radbruch, Andreas

    1995-03-01

    B cells can exchange gene segments for the constant region of the immunoglobulin heavy chain, altering the class and effector function of the antibodies that they produce. Class switching is directed to distinct classes by cytokines, which induce transcription of the targeted DNA sequences. These transcripts are processed, resulting in spliced "switch" transcripts. Switch recombination can be directed to immunoglobulin G1 (IgG1) by the heterologous human metallothionein II_A promoter in mutant mice. Induction of the structurally conserved, spliced switch transcripts is sufficient to target switch recombination to IgG1, whereas transcription alone is not.

  4. The repetitive portion of the Xenopus IgH Mu switch region mediates orientation-dependent class switch recombination.

    PubMed

    Zhang, Zheng Z; Pannunzio, Nicholas R; Lu, Zhengfei; Hsu, Ellen; Yu, Kefei; Lieber, Michael R

    2015-10-01

    Vertebrates developed immunoglobulin heavy chain (IgH) class switch recombination (CSR) to express different IgH constant regions. Most double-strand breaks for Ig CSR occur within the repetitive portion of the switch regions located upstream of each set of constant domain exons for the Igγ, Igα or Igϵ heavy chain. Unlike mammalian switch regions, Xenopus switch regions do not have a high G-density on the non-template DNA strand. In previous studies, when Xenopus Sμ DNA was moved to the genome of mice, it is able to support substantial CSR when it is used to replace the murine Sγ1 region. Here, we tested both the 2kb repetitive portion and the 4.6 kb full-length portions of the Xenopus Sμ in both their natural (forward) orientation relative to the constant domain exons, as well as the opposite (reverse) orientation. Consistent with previous work, we find that the 4.6 kb full-length Sμ mediates similar levels of CSR in both the forward and reverse orientations. Whereas, the forward orientation of the 2kb portion can restore the majority of the CSR level of the 4.6 kb full-length Sμ, the reverse orientation poorly supports R-looping and no CSR. The forward orientation of the 2kb repetitive portion has more GG dinucleotides on the non-template strand than the reverse orientation. The correlation of R-loop formation with CSR efficiency, as demonstrated in the 2kb repetitive fragment of the Xenopus switch region, confirms a role played by R-looping in CSR that appears to be conserved through evolution.

  5. Non-homologous end joining in class switch recombination: the beginning of the end

    PubMed Central

    Kotnis, Ashwin; Du, Likun; Liu, Chonghai; Popov, Sergey W.; Pan-Hammarström, Qiang

    2008-01-01

    Immunoglobulin class switch recombination (CSR) is initiated by a B-cell-specific factor, activation-induced deaminase, probably through deamination of deoxycytidine residues within the switch (S) regions. The initial lesions in the S regions are subsequently processed, resulting in the production of DNA double-strand breaks (DSBs). These breaks will then be recognized, edited and repaired, finally leading to the recombination of the two S regions. Two major repair pathways have been implicated in CSR, the predominant non-homologous end joining (NHEJ) and the alternative end-joining (A-EJ) pathways. The former requires not only components of the ‘classical’ NHEJ machinery, i.e. Ku70/Ku80, DNA-dependent protein kinase catalytic subunit, DNA ligase IV and XRCC4, but also a number of DNA-damage sensors or adaptors, such as ataxia–telangiectasia mutated, γH2AX, 53BP1, MDC1, the Mre11–Rad50–NBS1 complex and the ataxia telangiectasia and Rad3-related protein (ATR). The latter pathway is not well characterized yet and probably requires microhomologies. In this review, we will focus on the current knowledge of the predominant NHEJ pathway in CSR and will also give a perspective on the A-EJ pathway. PMID:19008195

  6. Iron Inhibits Activation-induced Cytidine Deaminase Enzymatic Activity and Modulates Immunoglobulin Class Switch DNA Recombination*

    PubMed Central

    Li, Guideng; Pone, Egest J.; Tran, Daniel C.; Patel, Pina J.; Dao, Lisa; Xu, Zhenming; Casali, Paolo

    2012-01-01

    Immunoglobulin (Ig) class switch DNA recombination (CSR) and somatic hypermutation (SHM) are critical for the maturation of the antibody response. Activation-induced cytidine deaminase (AID) initiates CSR and SHM by deaminating deoxycytidines (dCs) in switch (S) and V(D)J region DNA, respectively, to generate deoxyuracils (dUs). Processing of dUs by uracil DNA glycosylase (UNG) yields abasic sites, which are excised by apurinic/apyrimidinic endonucleases, eventually generating double strand DNA breaks, the obligatory intermediates of CSR. Here, we found that the bivalent iron ion (Fe2+, ferrous) suppressed CSR, leading to decreased number of switched B cells, decreased postrecombination Iμ-CH transcripts, and reduced titers of secreted class-switched IgG1, IgG3, and IgA antibodies, without alterations in critical CSR factors, such as AID, 14-3-3γ, or PTIP, or in general germline IH-S-CH transcription. Fe2+ did not affect B cell proliferation or plasmacytoid differentiation. Rather, it inhibited AID-mediated dC deamination in a dose-dependent fashion. The inhibition of intrinsic AID enzymatic activity by Fe2+ was specific, as shown by lack of inhibition of AID-mediated dC deamination by other bivalent metal ions, such as Zn2+, Mn2+, Mg2+, or Ni2+, and the inability of Fe2+ to inhibit UNG-mediated dU excision. Overall, our findings have outlined a novel role of iron in modulating a B cell differentiation process that is critical to the generation of effective antibody responses to microbial pathogens and tumoral cells. They also suggest a possible role of iron in dampening AID-dependent autoimmunity and neoplastic transformation. PMID:22556412

  7. Evaluation of the adverse effect of low concentration of cadmium on interleukin-4 induced class switch recombination in Burkett's lymphoma Raji cell line.

    PubMed

    Poltoratsky, Vladimir

    2014-01-01

    Affinity maturation of B lymphocytes, a process that includes somatic hypermutation and class switch recombination, initiates global DNA rearrangements. The interruption of this process has an adverse effect on human health and results in immunodeficiency and autoimmune disease. Class switch recombination is a fundamental factor of the human adaptive immunity. Evaluation of the class switch recombination efficiency is an important component of laboratory diagnostic of immunotoxic components. Here, we describe a method for testing the efficiency of the class switch recombination. Cultivation of Raji Burkett's lymphoma cell line with anti-CD40 antibodies and recombinant interleukin-4 (IL-4) triggers a cascade of signal transduction network events that lead to switching the immunoglobulin isotopes from IgM to IgE. This chapter describes the methodology of class switch recombination assay for assessment of the effect of the environmental pollutants in toxicological laboratory diagnostics.

  8. CCCTC-Binding Factor Locks Premature IgH Germline Transcription and Restrains Class Switch Recombination

    PubMed Central

    Marina-Zárate, Ester; Pérez-García, Arantxa; Ramiro, Almudena R.

    2017-01-01

    In response to antigenic stimulation B cells undergo class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) to replace the primary IgM/IgD isotypes by IgG, IgE, or IgA. CSR is initiated by activation-induced cytidine deaminase (AID) through the deamination of cytosine residues at the switch (S) regions of IgH. B cell stimulation promotes germline transcription (GLT) of specific S regions, a necessary event prior to CSR because it facilitates AID access to S regions. Here, we show that CCCTC-binding factor (CTCF)-deficient mice are severely impaired in the generation of germinal center B cells and plasma cells after immunization in vivo, most likely due to impaired cell survival. Importantly, we find that CTCF-deficient B cells have an increased rate of CSR under various stimulation conditions in vitro. This effect is not secondary to altered cell proliferation or AID expression in CTCF-deficient cells. Instead, we find that CTCF-deficient B cells harbor an increased mutation frequency at switch regions, probably reflecting an increased accessibility of AID to IgH in the absence of CTCF. Moreover, CTCF deficiency triggers premature GLT of S regions in naïve B cells. Our results indicate that CTCF restricts CSR by enforcing GLT silencing and limiting AID access to IgH. PMID:28928744

  9. Histone chaperone Spt6 is required for class switch recombination but not somatic hypermutation

    PubMed Central

    Okazaki, Il-mi; Okawa, Katsuya; Kobayashi, Maki; Yoshikawa, Kiyotsugu; Kawamoto, Shimpei; Nagaoka, Hitoshi; Shinkura, Reiko; Kitawaki, Yoko; Taniguchi, Hisaaki; Natsume, Tohru; Iemura, Shun-Ichiro; Honjo, Tasuku

    2011-01-01

    Activation-induced cytidine deaminase (AID) is shown to be essential and sufficient to induce two genetic alterations in the Ig loci: class switch recombination (CSR) and somatic hypermutation (SHM). However, it is still unknown how a single-molecule AID differentially regulates CSR and SHM. Here we identified Spt6 as an AID-interacting protein by yeast two-hybrid screening and immunoprecipitation followed by mass spectrometry. Knockdown of Spt6 resulted in severe reduction of CSR in both the endogenous Ig locus in B cells and an artificial substrate in fibroblast cells. Conversely, knockdown of Spt6 did not reduce but slightly enhanced SHM in an artificial substrate in B cells, indicating that Spt6 is required for AID to induce CSR but not SHM. These results suggest that Spt6 is involved in differential regulation of CSR and SHM by AID. PMID:21518874

  10. AIDing Chromatin and Transcription-Coupled Orchestration of Immunoglobulin Class-Switch Recombination

    PubMed Central

    Vaidyanathan, Bharat; Yen, Wei-Feng; Pucella, Joseph N.; Chaudhuri, Jayanta

    2014-01-01

    Secondary diversification of the antibody repertoire upon antigenic challenge, in the form of immunoglobulin heavy chain (IgH) class-switch recombination (CSR) endows mature, naïve B cells in peripheral lymphoid organs with a limitless ability to mount an optimal humoral immune response, thus expediting pathogen elimination. CSR replaces the default constant (CH) region exons (Cμ) of IgH with any of the downstream CH exons (Cγ, Cε, or Cα), thereby altering effector functions of the antibody molecule. This process depends on, and is orchestrated by, activation-induced deaminase (AID), a DNA cytidine deaminase that acts on single-stranded DNA exposed during transcription of switch (S) region sequences at the IgH locus. DNA lesions thus generated are processed by components of several general DNA repair pathways to drive CSR. Given that AID can instigate DNA lesions and genomic instability, stringent checks are imposed that constrain and restrict its mutagenic potential. In this review, we will discuss how AID expression and substrate specificity and activity is rigorously enforced at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and how the DNA-damage response is choreographed with precision to permit targeted activity while limiting bystander catastrophe. PMID:24734031

  11. Endonuclease G plays a role in immunoglobulin class switch DNA recombination by introducing double-strand breaks in switch regions.

    PubMed

    Zan, Hong; Zhang, Jinsong; Al-Qahtani, Ahmed; Pone, Egest J; White, Clayton A; Lee, Derrik; Yel, Leman; Mai, Thach; Casali, Paolo

    2011-01-01

    Immunoglobulin (Ig) class switch DNA recombination (CSR) is the crucial mechanism diversifying the biological effector functions of antibodies. Generation of double-strand DNA breaks (DSBs), particularly staggered DSBs, in switch (S) regions of the upstream and downstream CH genes involved in the specific recombination process is an absolute requirement for CSR. Staggered DSBs would be generated through deamination of dCs on opposite DNA strands by activation-induced cytidine deaminase (AID), subsequent dU deglycosylation by uracil DNA glycosylase (Ung) and abasic site nicking by apurinic/apyrimidic endonuclease. However, consistent with the findings that significant amounts of DSBs can be detected in the IgH locus in the absence of AID or Ung, we have shown in human and mouse B cells that AID generates staggered DSBs not only by cleaving intact double-strand DNA, but also by processing blunt DSB ends generated in an AID-independent fashion. How these AID-independent DSBs are generated is still unclear. It is possible that S region DNA may undergo AID-independent cleavage by structure-specific nucleases, such as endonuclease G (EndoG). EndoG is an abundant nuclease in eukaryotic cells. It cleaves single and double-strand DNA, primarily at dG/dC residues, the preferential sites of DSBs in S region DNA. We show here that EndoG can localize to the nucleus of B cells undergoing CSR and binds to S region DNA, as shown by specific chromatin immunoprecipitation assays. Using knockout EndoG(-/-) mice and EndoG(-/-) B cells, we found that EndoG deficiency resulted in a two-fold reduction in CSR in vivo and in vitro, as demonstrated by reduced cell surface IgG1, IgG2a, IgG3 and IgA, reduced secreted IgG1, reduced circle Iγ1-Cμ, Iγ3-Cμ, Iɛ-Cμ, Iα-Cμ transcripts, post-recombination Iμ-Cγ1, Iμ-Cγ3, Iμ-Cɛ and Iμ-Cα transcripts. In addition to reduced CSR, EndoG(-/-) mice showed a significantly altered spectrum of mutations in IgH J(H)-iEμ DNA. Impaired CSR in

  12. Endonuclease G plays a role in immunoglobulin class switch DNA recombination by introducing double-strand breaks in switch regions

    PubMed Central

    Zan, Hong; Zhang, Jinsong; Al-Qahtani, Ahmed; Pone, Egest J.; White, Clayton A.; Lee, Derrik; Yel, Leman; Mai, Thach; Casali, Paolo

    2012-01-01

    Immunoglobulin (Ig) class switch DNA recombination (CSR) is the crucial mechanism diversifying the biological effector functions of antibodies. Generation of double-strand DNA breaks (DSBs), particularly staggered DSBs, in switch (S) regions of the upstream and downstream CH genes involved in the specific recombination process is an absolute requirement for CSR. Staggered DSBs would be generated through deamination of dCs on opposite DNA strands by activation-induced cytidine deaminase (AID), subsequent dU deglycosylation by uracil DNA glycosylase (Ung) and abasic site nicking by apurinic/apyrimidic endonuclease. However, consistent with the findings that significant amounts of DSBs can be detected in the IgH locus in the absence of AID or Ung, we have shown in human and mouse B cells that AID generates staggered DSBs not only by cleaving intact double-strand DNA, but also by processing blunt DSB ends generated in an AID-independent fashion. How these AID-independent DSBs are generated is still unclear. It is possible that S region DNA may undergo AID-independent cleavage by structure-specific nucleases, such as endonuclease G (EndoG). EndoG is an abundant nuclease in eukaryotic cells. It cleaves single- and double-strand DNA, primarily at dG/dC residues, the preferential sites of DSBs in S region DNA. We show here that EndoG can localize to the nucleus of B cells undergoing CSR and binds to S region DNA, as shown by specific chromatin immunoprecipitation assays. Using knockout EndoG−/− mice and EndoG−/− B cells, we found that EndoG deficiency resulted in defective CSR in vivo and in vitro, as demonstrated by reduced cell surface IgG1, IgG2a, IgG3 and IgA, reduced secreted IgG1, reduced circle Iγ1-Cμ, Iγ3-Cμ, Iε-Cμ, Iα-Cμ transcripts, post-recombination Iμ-Cγ1, Iμ-Cγ3, Iμ-Cε and Iμ-Cα transcripts. In addition to reduced CSR, EndoG−/− mice showed a significantly altered spectrum of mutations in IgH JH-iEμ DNA. Impaired CSR in Endo

  13. Individual substitution mutations in the AID C terminus that ablate IgH class switch recombination.

    PubMed

    Kadungure, Tatenda; Ucher, Anna J; Linehan, Erin K; Schrader, Carol E; Stavnezer, Janet

    2015-01-01

    Activation-induced cytidine deaminase (AID) is essential for class switch recombination (CSR) and somatic hypermutation (SHM) of Ig genes. The C terminus of AID is required for CSR but not for SHM, but the reason for this is not entirely clear. By retroviral transduction of mutant AID proteins into aid-/- mouse splenic B cells, we show that 4 amino acids within the C terminus of mouse AID, when individually mutated to specific amino acids (R190K, A192K, L196S, F198S), reduce CSR about as much or more than deletion of the entire C terminal 10 amino acids. Similar to ΔAID, the substitutions reduce binding of UNG to Ig Sμ regions and some reduce binding of Msh2, both of which are important for introducing S region DNA breaks. Junctions between the IgH donor switch (S)μ and acceptor Sα regions from cells expressing ΔAID or the L196S mutant show increased microhomology compared to junctions in cells expressing wild-type AID, consistent with problems during CSR and the use of alternative end-joining, rather than non-homologous end-joining (NHEJ). Unlike deletion of the AID C terminus, 3 of the substitution mutants reduce DNA double-strand breaks (DSBs) detected within the Sμ region in splenic B cells undergoing CSR. Cells expressing these 3 substitution mutants also have greatly reduced mutations within unrearranged Sμ regions, and they decrease with time after activation. These results might be explained by increased error-free repair, but as the C terminus has been shown to be important for recruitment of NHEJ proteins, this appears unlikely. We hypothesize that Sμ DNA breaks in cells expressing these C terminus substitution mutants are poorly repaired, resulting in destruction of Sμ segments that are deaminated by these mutants. This could explain why these mutants cannot undergo CSR.

  14. Pathophysiology of B-cell intrinsic immunoglobulin class switch recombination deficiencies.

    PubMed

    Durandy, Anne; Taubenheim, Nadine; Peron, Sophie; Fischer, Alain

    2007-01-01

    B-cell intrinsic immunoglobulin class switch recombination (Ig-CSR) deficiencies, previously termed hyper-IgM syndromes, are genetically determined conditions characterized by normal or elevated serum IgM levels and an absence or very low levels of IgG, IgA, and IgE. As a function of the molecular mechanism, the defective CSR is variably associated to a defect in the generation of somatic hypermutations (SHMs) in the Ig variable region. The study of Ig-CSR deficiencies contributed to a better delineation of the mechanisms underlying CSR and SHM, the major events of antigen-triggered antibody maturation. Four Ig-CSR deficiency phenotypes have been so far reported: the description of the activation-induced cytidine deaminase (AID) deficiency (Ig-CSR deficiency 1), caused by recessive mutations of AICDA gene, characterized by a defect in CSR and SHM, clearly established the role of AID in the induction of the Ig gene rearrangements underlying CSR and SHM. A CSR-specific function of AID has, however, been detected by the observation of a selective CSR defect caused by mutations affecting the C-terminus of AID. Ig-CSR deficiency 2 is the consequence of uracil-N-glycosylase (UNG) deficiency. Because UNG, a molecule of the base excision repair machinery, removes uracils from DNA and AID deaminates cytosines into uracils, that observation indicates that the AID-UNG pathway directly targets DNA of switch regions from the Ig heavy-chain locus to induce the CSR process. Ig-CSR deficiencies 3 and 4 are characterized by a selective CSR defect resulting from blocks at distinct steps of CSR. A further understanding of the CSR machinery is expected from their molecular definition.

  15. Class-Switch Recombination in the Absence of the IgH 3' Regulatory Region.

    PubMed

    Kim, Ahrom; Han, Li; Santiago, Gabriel E; Verdun, Ramiro E; Yu, Kefei

    2016-10-01

    The ∼28-kb 3' regulatory region (3'RR), which is located at the most distal 3' region of the Ig H chain locus, has multiple regulatory functions that control IgH expression, class-switch recombination (CSR), and somatic hypermutation. In this article, we report that deletion of the entire 3'RR in a mouse B cell line that is capable of robust cytokine-dependent CSR to IgA results in reduced, but not abolished, CSR. These data suggest that 3'RR is not absolutely required for CSR and, thus, is not essential for targeting activation-induced cytidine deaminase to S regions, as was suggested. Moreover, replacing 3'RR with a DNA fragment including only its four DNase I hypersensitive sites (lacking the large spacer regions) restores CSR to a level equivalent to or even higher than in wild-type cells, suggesting that the four hypersensitive sites contain most of the CSR-promoting functions of 3'RR. Stimulated cells express abundant germline transcripts, with the presence or absence of 3'RR, providing evidence that 3'RR has a role in promoting CSR that is unique from enhancing S region transcription.

  16. Class switch recombination process in ataxia telangiectasia patients with elevated serum levels of IgM.

    PubMed

    Mohammadinejad, Payam; Abolhassani, Hassan; Aghamohammadi, Asghar; Pourhamdi, Shabnam; Ghosh, Sujal; Sadeghi, Bamdad; Nasiri Kalmarzi, Rasoul; Durandy, Anne; Borkhardt, Arndt

    2015-01-01

    Ataxia telangiectasia (AT) is a rare primary immunodeficiency disorder with various clinical manifestations. Increased serum levels of IgM and recurrent infections, mainly sinopulmonary infections, can be the presenting feature in a number of AT patients and may be initially misdiagnosed as hyper-IgM (HIgM) syndrome. This study was designed to investigate class switch recombination (CSR) as a critical mechanism in B lymphocytes' maturation to produce different isotypes of antibody in response to antigen stimulation in AT cases with HIgM presentation. Quantitative IgE production after stimulation by IL-4 and CD40L was considered as an indicator for CSR function. We also compared their results with sex and age matched AT patients without HIgM presentation. We report four AT patients with recurrent infections during infancy and high serum levels of IgM. Laboratory evaluations revealed defective CSR while none of the three AT patients without HIgM presentation had a defect in the CSR process. The characterized defect in AT is a mutation in the ataxia telangiectasia mutated (ATM) gene. This gene may result in CSR defects due to impaired DNA break repair. A special association between AT and HIgM may indicate a new subgroup of AT patients according to their clinical phenotype and CSR condition.

  17. Scaffold functions of 14-3-3 adaptors in B cell immunoglobulin class switch DNA recombination.

    PubMed

    Lam, Tonika; Thomas, Lisa M; White, Clayton A; Li, Guideng; Pone, Egest J; Xu, Zhenming; Casali, Paolo

    2013-01-01

    Class switch DNA recombination (CSR) of the immunoglobulin heavy chain (IgH) locus crucially diversifies antibody biological effector functions. CSR involves the induction of activation-induced cytidine deaminase (AID) expression and AID targeting to switch (S) regions by 14-3-3 adaptors. 14-3-3 adaptors specifically bind to 5'-AGCT-3' repeats, which make up for the core of all IgH locus S regions. They selectively target the upstream and downstream S regions that are set to undergo S-S DNA recombination. We hypothesized that 14-3-3 adaptors function as scaffolds to stabilize CSR enzymatic elements on S regions. Here we demonstrate that all seven 14-3-3β, 14-3-3ε, 14-3-3γ, 14-3-3η, 14-3-3σ, 14-3-3τ and 14-3-3ζ adaptors directly interacted with AID, PKA-Cα (catalytic subunit) and PKA-RIα (regulatory inhibitory subunit) and uracil DNA glycosylase (Ung). 14-3-3 adaptors, however, did not interact with AID C-terminal truncation mutant AIDΔ(180-198) or AIDF193A and AIDL196A point-mutants (which have been shown not to bind to S region DNA and fail to mediate CSR). 14-3-3 adaptors colocalized with AID and replication protein A (RPA) in B cells undergoing CSR. 14-3-3 and AID binding to S region DNA was disrupted by viral protein R (Vpr), an accessory protein of human immunodeficiency virus type-1 (HIV-1), which inhibited CSR without altering AID expression or germline IH-CH transcription. Accordingly, we demonstrated that 14-3-3 directly interact with Vpr, which in turn, also interact with AID, PKA-Cα and Ung. Altogether, our findings suggest that 14-3-3 adaptors play important scaffold functions and nucleate the assembly of multiple CSR factors on S regions. They also show that such assembly can be disrupted by a viral protein, thereby allowing us to hypothesize that small molecule compounds that specifically block 14-3-3 interactions with AID, PKA and/or Ung can be used to inhibit unwanted CSR.

  18. Role of PTIP in class switch recombination and long-range chromatin interactions at the immunoglobulin heavy chain locus.

    PubMed

    Schwab, Kristopher R; Patel, Sanjeevkumar R; Dressler, Gregory R

    2011-04-01

    How distal transcriptional enhancer sequences interact with proximal promoters is poorly understood within the context of chromatin. In this report, we have used the immunoglobulin heavy chain locus to address the role of the PTIP protein in transcription regulation and class switch recombination in B cells, a process that depends on regulated transcription and DNA recombination via Pax5 and distal 3' enhancer sequences. We first show that PTIP is recruited to a Pax5 binding site to promote histone H3 lysine 4 (H3K4) methylation. Using a CD19-Cre driver strain, we deleted PTIP in mature B cells. Loss of PTIP inhibited class switch recombination by suppressing transcription and histone H3K4 methylation at the germ line transcript promoters. In the absence of PTIP, Pax5 binding to the promoter regions is reduced and long-range chromatin interactions between the distal enhancer at the 3' regulatory region and the germ line transcript promoters are not detected. We propose a model whereby PTIP stabilizes the Pax5 DNA interactions that promote chromatin looping and regulate transcriptional responses needed for class switch recombination.

  19. Impaired class switch recombination (CSR) in Waldenstrom macroglobulinemia (WM) despite apparently normal CSR machinery.

    PubMed

    Kriangkum, Jitra; Taylor, Brian J; Strachan, Erin; Mant, Michael J; Reiman, Tony; Belch, Andrew R; Pilarski, Linda M

    2006-04-01

    Analysis of clonotypic isotype class switching (CSR) in Waldenström macroglobulinemia (WM) and IgM monoclonal gammopathy of undetermined significance (MGUS) reveals a normal initial phase of B-cell activation as determined by constitutive and inducible expression of activation-induced cytidine deaminase (AID). Switch mu (Smu) analysis shows that large deletions are not common in WM or IgM MGUS. In CD40L/IL-4-stimulated WM cultures from 2 patients, we observed clonotypic IgG exhibiting intraclonal homogeneity associated with multiple hybrid Smu/Sgamma junctions. This suggests CSR had occurred within WM cells. Nevertheless, the estimated IgG/IgM-cell frequency was relatively low (1/1600 cells). Thus, for the majority of WM B cells, CSR does not occur even when stimulated in vitro, suggesting that the WM cell is constitutively unable to or being prevented from carrying out CSR. In contrast to WM, the majority of IgM MGUS clones exhibit intraclonal heterogeneity of IgH VDJ. Furthermore, most IgM MGUS accumulate more mutations in the upstream Smu region than do WM, making them unlikely WM progenitors. These observations suggest that switch sequence analysis may identify the subset of patients with IgM MGUS who are at risk of progression to WM.

  20. H3 trimethyl K9 and H3 acetyl K9 chromatin modifications are associated with class switch recombination.

    PubMed

    Kuang, Fei Li; Luo, Zhonghui; Scharff, Matthew D

    2009-03-31

    Class switch recombination (CSR) involves a DNA rearrangement in the Ig heavy chain (IgH) gene that allows the same variable (V) region to be expressed with any one of the downstream constant region (C) genes to encode antibodies with many different effector functions. One hypothesis for how CSR is targeted to different C region genes is that histone modifications increase accessibility and/or recruit activation-induced cytosine deaminase (AID) and its associated processes to particular donor and recipient switch regions. In this work, we identified H3 acetyl K9 and H3 trimethyl K9 as histone modifications that correlate with the recombining pair of donor and recipient switch regions. The appearance of H3 trimethyl K9 is surprising because usually it is thought to mark silent genes and heterochromatin. Nevertheless, the time course of appearance of these histone modifications, the regions in IgH they associate with, and their appearance independent of AID damage suggest that both modifications play a role in targeting CSR.

  1. An inherited immunoglobulin class-switch recombination deficiency associated with a defect in the INO80 chromatin remodeling complex

    PubMed Central

    Kracker, Sven; Di Virgilio, Michela; Schwartzentruber, Jeremy; Cuenin, Cyrille; Forveille, Monique; Deau, Marie-Céline; McBride, Kevin M.; Majewski, Jacek; Gazumyan, Anna; Seneviratne, Suranjith; Grimbacher, Bodo; Kutukculer, Necil; Herceg, Zdenko; Cavazzana, Marina; Jabado, Nada; Nussenzweig, Michel C.; Fischer, Alain; Durandy, Anne

    2015-01-01

    Background Immunoglobulin class-switch recombination defects (CSR-D) are rare primary immunodeficiencies characterized by impaired production of switched immunoglobulin isotypes and normal or elevated IgM levels. They are caused by impaired T:B cooperation or intrinsic B cell defects. However, many immunoglobulin CSR-Ds are still undefined at the molecular level. Objective This study's objective was to delineate new causes of immunoglobulin CSR-Ds and thus gain further insights into the process of immunoglobulin class-switch recombination (CSR). Methods Exome sequencing in 2 immunoglobulin CSR-D patients identified variations in the INO80 gene. Functional experiments were performed to assess the function of INO80 on immunoglobulin CSR. Results We identified recessive, nonsynonymous coding variations in the INO80 gene in 2 patients affected by defective immunoglobulin CSR. Expression of wild-type INO80 in patients' fibroblastic cells corrected their hypersensitivity to high doses of γ-irradiation. In murine CH12-F3 cells, the INO80 complex accumulates at Sα and Eμ regions of the IgH locus, and downregulation of INO80 as well as its partners Reptin and Pontin impaired CSR. In addition, Reptin and Pontin were shown to interact with activation-induced cytidine deaminase. Finally, an abnormal separation of sister chromatids was observed upon INO80 downregulation in CH12-F3 cells, pinpointing its role in cohesin activity. Conclusion INO80 deficiency appears to be associated with defective immunoglobulin CSR. We propose that the INO80 complex modulates cohesin function that may be required during immunoglobulin switch region synapsis. PMID:25312759

  2. An inherited immunoglobulin class-switch recombination deficiency associated with a defect in the INO80 chromatin remodeling complex.

    PubMed

    Kracker, Sven; Di Virgilio, Michela; Schwartzentruber, Jeremy; Cuenin, Cyrille; Forveille, Monique; Deau, Marie-Céline; McBride, Kevin M; Majewski, Jacek; Gazumyan, Anna; Seneviratne, Suranjith; Grimbacher, Bodo; Kutukculer, Necil; Herceg, Zdenko; Cavazzana, Marina; Jabado, Nada; Nussenzweig, Michel C; Fischer, Alain; Durandy, Anne

    2015-04-01

    Immunoglobulin class-switch recombination defects (CSR-D) are rare primary immunodeficiencies characterized by impaired production of switched immunoglobulin isotypes and normal or elevated IgM levels. They are caused by impaired T:B cooperation or intrinsic B cell defects. However, many immunoglobulin CSR-Ds are still undefined at the molecular level. This study's objective was to delineate new causes of immunoglobulin CSR-Ds and thus gain further insights into the process of immunoglobulin class-switch recombination (CSR). Exome sequencing in 2 immunoglobulin CSR-D patients identified variations in the INO80 gene. Functional experiments were performed to assess the function of INO80 on immunoglobulin CSR. We identified recessive, nonsynonymous coding variations in the INO80 gene in 2 patients affected by defective immunoglobulin CSR. Expression of wild-type INO80 in patients' fibroblastic cells corrected their hypersensitivity to high doses of γ-irradiation. In murine CH12-F3 cells, the INO80 complex accumulates at Sα and Eμ regions of the IgH locus, and downregulation of INO80 as well as its partners Reptin and Pontin impaired CSR. In addition, Reptin and Pontin were shown to interact with activation-induced cytidine deaminase. Finally, an abnormal separation of sister chromatids was observed upon INO80 downregulation in CH12-F3 cells, pinpointing its role in cohesin activity. INO80 deficiency appears to be associated with defective immunoglobulin CSR. We propose that the INO80 complex modulates cohesin function that may be required during immunoglobulin switch region synapsis. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

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

    PubMed

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

    2016-02-02

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

  4. 53BP1 regulates DNA resection and the choice between classical and alternative end joining during class switch recombination.

    PubMed

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

    2010-04-12

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

  5. Local increase in IgE and class switch recombination to IgE in nasal polyps in chronic rhinosinusitis.

    PubMed

    Baba, S; Kondo, K; Toma-Hirano, M; Kanaya, K; Suzukawa, K; Ushio, M; Suzukawa, M; Ohta, K; Yamasoba, T

    2014-01-01

    Chronic rhinosinusitis with nasal polyps is generally characterized by local Th2 inflammation and is categorized into two subtypes in Japan: eosinophilic chronic rhinosinusitis (similar to chronic rhinosinusitis with nasal polyps in western countries) and non-eosinophilic chronic rhinosinusitis (characterized by Th1-dominant inflammation). To investigate local IgE production and class switch recombination to IgE in these two subtypes of chronic rhinosinusitis with nasal polyps. The identity of IgE-positive cells was determined using double-immunofluorescent staining for IgE and cell-type-specific molecular markers. To investigate the local class switch recombination to IgE and IgE synthesis in the mucosa, we performed real-time polymerase chain reaction to examine the mRNA expression of Th2 cytokines and class-switch-related molecules, including IL-4, IL-5, IL-13, ε germline gene transcripts, IgE mature transcript, IgG mature transcript, RAG1, RAG2 and activation-induced cytidine deaminase in eosinophilic polyps, non-eosinophilic polyps and controls. The concentrations of total IgE and number of IgE-positive cells were significantly higher in the eosinophilic polyps compared with control and non-eosinophilic polyps. IgE-positive cells were predominantly mast cells in eosinophilic polyps and significantly correlated with the number of FcεR1-positive cells in the subepithelial layer. IL-5 and IL-13 mRNA and ε germline gene transcripts expression levels were significantly higher in eosinophilic polyps compared with control and non-eosinophilic polyps. In contrast, the number of plasma cells and the expression of IgG mature transcripts were increased in non-eosinophilic polyps compared with eosinophilic polyps. RAG2 mRNA was significantly increased in both eosinophilic and non-eosinophilic polyps compared with control mucosa. The current study suggests local class switching to IgE, production of IgE and IgE localization to the surface of mast cells in eosinophilic

  6. The role of germline promoters and I exons in cytokine-induced gene-specific class switch recombination.

    PubMed

    Dunnick, Wesley A; Shi, Jian; Holden, Victoria; Fontaine, Clinton; Collins, John T

    2011-01-01

    Germline transcription precedes class switch recombination (CSR). The promoter regions and I exons of these germline transcripts include binding sites for activation- and cytokine-induced transcription factors, and the promoter regions/I exons are essential for CSR. Therefore, it is a strong hypothesis that the promoter/I exons regions are responsible for much of cytokine-regulated, gene-specific CSR. We tested this hypothesis by swapping the germline promoter and I exons for the murine γ1 and γ2a H chain genes in a transgene of the entire H chain C-region locus. We found that the promoter/I exon for γ1 germline transcripts can direct robust IL-4-induced recombination to the γ2a gene. In contrast, the promoter/I exon for the γ2a germline transcripts works poorly in the context of the γ1 H chain gene, resulting in expression of γ1 H chains that is <1% the wild-type level. Nevertheless, the small amount of recombination to the chimeric γ1 gene is induced by IFN-γ. These results suggest that cytokine regulation of CSR, but not the magnitude of CSR, is regulated by the promoter/I exons.

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

    PubMed

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

    2014-10-01

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

  8. Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination

    PubMed Central

    Thomas-Claudepierre, Anne-Sophie; Robert, Isabelle; Rocha, Pedro P.; Raviram, Ramya; Schiavo, Ebe; Heyer, Vincent; Bonneau, Richard; Luo, Vincent M.; Reddy, Janardan K.; Borggrefe, Tilman; Skok, Jane A.

    2016-01-01

    Immunoglobulin (Ig) class switch recombination (CSR) is initiated by the transcription-coupled recruitment of activation-induced cytidine deaminase (AID) to Ig switch regions (S regions). During CSR, the IgH locus undergoes dynamic three-dimensional structural changes in which promoters, enhancers, and S regions are brought to close proximity. Nevertheless, little is known about the underlying mechanisms. In this study, we show that Med1 and Med12, two subunits of the mediator complex implicated in transcription initiation and long-range enhancer/promoter loop formation, are dynamically recruited to the IgH locus enhancers and the acceptor regions during CSR and that their knockdown in CH12 cells results in impaired CSR. Furthermore, we show that conditional inactivation of Med1 in B cells results in defective CSR and reduced acceptor S region transcription. Finally, we show that in B cells undergoing CSR, the dynamic long-range contacts between the IgH enhancers and the acceptor regions correlate with Med1 and Med12 binding and that they happen at a reduced frequency in Med1-deficient B cells. Our results implicate the mediator complex in the mechanism of CSR and are consistent with a model in which mediator facilitates the long-range contacts between S regions and the IgH locus enhancers during CSR and their transcriptional activation. PMID:26903242

  9. Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination.

    PubMed

    Thomas-Claudepierre, Anne-Sophie; Robert, Isabelle; Rocha, Pedro P; Raviram, Ramya; Schiavo, Ebe; Heyer, Vincent; Bonneau, Richard; Luo, Vincent M; Reddy, Janardan K; Borggrefe, Tilman; Skok, Jane A; Reina-San-Martin, Bernardo

    2016-03-07

    Immunoglobulin (Ig) class switch recombination (CSR) is initiated by the transcription-coupled recruitment of activation-induced cytidine deaminase (AID) to Ig switch regions (S regions). During CSR, the IgH locus undergoes dynamic three-dimensional structural changes in which promoters, enhancers, and S regions are brought to close proximity. Nevertheless, little is known about the underlying mechanisms. In this study, we show that Med1 and Med12, two subunits of the mediator complex implicated in transcription initiation and long-range enhancer/promoter loop formation, are dynamically recruited to the IgH locus enhancers and the acceptor regions during CSR and that their knockdown in CH12 cells results in impaired CSR. Furthermore, we show that conditional inactivation of Med1 in B cells results in defective CSR and reduced acceptor S region transcription. Finally, we show that in B cells undergoing CSR, the dynamic long-range contacts between the IgH enhancers and the acceptor regions correlate with Med1 and Med12 binding and that they happen at a reduced frequency in Med1-deficient B cells. Our results implicate the mediator complex in the mechanism of CSR and are consistent with a model in which mediator facilitates the long-range contacts between S regions and the IgH locus enhancers during CSR and their transcriptional activation.

  10. The transcription factor BATF controls the global regulators of class-switch recombination in both B cells and T cells.

    PubMed

    Ise, Wataru; Kohyama, Masako; Schraml, Barbara U; Zhang, Tingting; Schwer, Bjoern; Basu, Uttiya; Alt, Frederick W; Tang, Jun; Oltz, Eugene M; Murphy, Theresa L; Murphy, Kenneth M

    2011-06-01

    The transcription factor BATF controls the differentiation of interleukin 17 (IL-17)-producing helper T cells (T(H)17 cells) by regulating expression of the transcription factor RORγt itself and RORγt target genes such as Il17. Here we report the mechanism by which BATF controls in vivo class-switch recombination (CSR). In T cells, BATF directly controlled expression of the transcription factors Bcl-6 and c-Maf, both of which are needed for development of follicular helper T cells (T(FH) cells). Restoring T(FH) cell activity to Batf(-/-) T cells in vivo required coexpression of Bcl-6 and c-Maf. In B cells, BATF directly controlled the expression of both activation-induced cytidine deaminase (AID) and of germline transcripts of the intervening heavy-chain region and constant heavy-chain region (I(H)-C(H)). Thus, BATF functions at multiple hierarchical levels in two cell types to globally regulate switched antibody responses in vivo.

  11. A regulatory role for the cohesin loader NIPBL in nonhomologous end joining during immunoglobulin class switch recombination.

    PubMed

    Enervald, Elin; Du, Likun; Visnes, Torkild; Björkman, Andrea; Lindgren, Emma; Wincent, Josephine; Borck, Guntram; Colleaux, Laurence; Cormier-Daire, Valerie; van Gent, Dik C; Pie, Juan; Puisac, Beatriz; de Miranda, Noel Fcc; Kracker, Sven; Hammarström, Lennart; de Villartay, Jean-Pierre; Durandy, Anne; Schoumans, Jacqueline; Ström, Lena; Pan-Hammarström, Qiang

    2013-11-18

    DNA double strand breaks (DSBs) are mainly repaired via homologous recombination (HR) or nonhomologous end joining (NHEJ). These breaks pose severe threats to genome integrity but can also be necessary intermediates of normal cellular processes such as immunoglobulin class switch recombination (CSR). During CSR, DSBs are produced in the G1 phase of the cell cycle and are repaired by the classical NHEJ machinery. By studying B lymphocytes derived from patients with Cornelia de Lange Syndrome, we observed a strong correlation between heterozygous loss-of-function mutations in the gene encoding the cohesin loading protein NIPBL and a shift toward the use of an alternative, microhomology-based end joining during CSR. Furthermore, the early recruitment of 53BP1 to DSBs was reduced in the NIPBL-deficient patient cells. Association of NIPBL deficiency and impaired NHEJ was also observed in a plasmid-based end-joining assay and a yeast model system. Our results suggest that NIPBL plays an important and evolutionarily conserved role in NHEJ, in addition to its canonical function in sister chromatid cohesion and its recently suggested function in HR.

  12. APE1 is dispensable for S-region cleavage but required for its repair in class switch recombination.

    PubMed

    Xu, Jianliang; Husain, Afzal; Hu, Wenjun; Honjo, Tasuku; Kobayashi, Maki

    2014-12-02

    Activation-induced cytidine deaminase (AID) is essential for antibody diversification, namely somatic hypermutation (SHM) and class switch recombination (CSR). The deficiency of apurinic/apyrimidinic endonuclease 1 (Ape1) in CH12F3-2A B cells reduces CSR to ∼20% of wild-type cells, whereas the effect of APE1 loss on SHM has not been examined. Here we show that, although APE1's endonuclease activity is important for CSR, it is dispensable for SHM as well as IgH/c-myc translocation. Importantly, APE1 deficiency did not show any defect in AID-induced S-region break formation, but blocked both the recruitment of repair protein Ku80 to the S region and the synapse formation between Sμ and Sα. Knockdown of end-processing factors such as meiotic recombination 11 homolog (MRE11) and carboxy-terminal binding protein (CtBP)-interacting protein (CtIP) further reduced the remaining CSR in Ape1-null CH12F3-2A cells. Together, our results show that APE1 is dispensable for SHM and AID-induced DNA breaks and may function as a DNA end-processing enzyme to facilitate the joining of broken ends during CSR.

  13. APE1 is dispensable for S-region cleavage but required for its repair in class switch recombination

    PubMed Central

    Xu, Jianliang; Husain, Afzal; Hu, Wenjun; Honjo, Tasuku; Kobayashi, Maki

    2014-01-01

    Activation-induced cytidine deaminase (AID) is essential for antibody diversification, namely somatic hypermutation (SHM) and class switch recombination (CSR). The deficiency of apurinic/apyrimidinic endonuclease 1 (Ape1) in CH12F3-2A B cells reduces CSR to ∼20% of wild-type cells, whereas the effect of APE1 loss on SHM has not been examined. Here we show that, although APE1’s endonuclease activity is important for CSR, it is dispensable for SHM as well as IgH/c-myc translocation. Importantly, APE1 deficiency did not show any defect in AID-induced S-region break formation, but blocked both the recruitment of repair protein Ku80 to the S region and the synapse formation between Sμ and Sα. Knockdown of end-processing factors such as meiotic recombination 11 homolog (MRE11) and carboxy-terminal binding protein (CtBP)-interacting protein (CtIP) further reduced the remaining CSR in Ape1-null CH12F3-2A cells. Together, our results show that APE1 is dispensable for SHM and AID-induced DNA breaks and may function as a DNA end-processing enzyme to facilitate the joining of broken ends during CSR. PMID:25404348

  14. Regulation of Immunoglobulin Class-Switch Recombination: Choreography of Noncoding Transcription, Targeted DNA Deamination, and Long-Range DNA Repair

    PubMed Central

    Matthews, Allysia J.; Zheng, Simin; DiMenna, Lauren J.; Chaudhuri, Jayanta

    2014-01-01

    Upon encountering antigens, mature IgM-positive B lymphocytes undergo class-switch recombination (CSR) wherein exons encoding the default Cμ constant coding gene segment of the immunoglobulin (Ig) heavy-chain (Igh) locus are excised and replaced with a new constant gene segment (referred to as “Ch genes”, e.g., Cγ, Cε, or Cα). The B cell thereby changes from expressing IgM to one producing IgG, IgE, or IgA, with each antibody isotype having a different effector function during an immune reaction. CSR is a DNA deletional-recombination reaction that proceeds through the generation of DNA double-strand breaks (DSBs) in repetitive switch (S) sequences preceding each Ch gene and is completed by end-joining between donor Sμ and acceptor S regions. CSR is a multistep reaction requiring transcription through S regions, the DNA cytidine deaminase AID, and the participation of several general DNA repair pathways including base excision repair, mismatch repair, and classical nonhomologous end-joining. In this review, we discuss our current understanding of how transcription through S regions generates substrates for AID-mediated deamination and how AID participates not only in the initiation of CSR but also in the conversion of deaminated residues into DSBs. Additionally, we review the multiple processes that regulate AID expression and facilitate its recruitment specifically to the Ig loci, and how deregulation of AID specificity leads to oncogenic translocations. Finally, we summarize recent data on the potential role of AID in the maintenance of the pluripotent stem cell state during epigenetic reprogramming. PMID:24507154

  15. Regulation of immunoglobulin class-switch recombination: choreography of noncoding transcription, targeted DNA deamination, and long-range DNA repair.

    PubMed

    Matthews, Allysia J; Zheng, Simin; DiMenna, Lauren J; Chaudhuri, Jayanta

    2014-01-01

    Upon encountering antigens, mature IgM-positive B lymphocytes undergo class-switch recombination (CSR) wherein exons encoding the default Cμ constant coding gene segment of the immunoglobulin (Ig) heavy-chain (Igh) locus are excised and replaced with a new constant gene segment (referred to as "Ch genes", e.g., Cγ, Cɛ, or Cα). The B cell thereby changes from expressing IgM to one producing IgG, IgE, or IgA, with each antibody isotype having a different effector function during an immune reaction. CSR is a DNA deletional-recombination reaction that proceeds through the generation of DNA double-strand breaks (DSBs) in repetitive switch (S) sequences preceding each Ch gene and is completed by end-joining between donor Sμ and acceptor S regions. CSR is a multistep reaction requiring transcription through S regions, the DNA cytidine deaminase AID, and the participation of several general DNA repair pathways including base excision repair, mismatch repair, and classical nonhomologous end-joining. In this review, we discuss our current understanding of how transcription through S regions generates substrates for AID-mediated deamination and how AID participates not only in the initiation of CSR but also in the conversion of deaminated residues into DSBs. Additionally, we review the multiple processes that regulate AID expression and facilitate its recruitment specifically to the Ig loci, and how deregulation of AID specificity leads to oncogenic translocations. Finally, we summarize recent data on the potential role of AID in the maintenance of the pluripotent stem cell state during epigenetic reprogramming.

  16. Analysis of DNA polymerase ν function in meiotic recombination, immunoglobulin class-switching, and DNA damage tolerance

    PubMed Central

    Takata, Kei-ichi; Yousefzadeh, Matthew J.; Zelazowski, Maciej J.; Bhetawal, Sarita; Lowery, Megan G.; Sandoval, Maria; Takata, Yoko; Lu, Yue; Lin, Kevin; Shen, Jianjun; Kusewitt, Donna F.; McBride, Kevin M.; Cole, Francesca

    2017-01-01

    DNA polymerase ν (pol ν), encoded by the POLN gene, is an A-family DNA polymerase in vertebrates and some other animal lineages. Here we report an in-depth analysis of pol ν–defective mice and human cells. POLN is very weakly expressed in most tissues, with the highest relative expression in testis. We constructed multiple mouse models for Poln disruption and detected no anatomic abnormalities, alterations in lifespan, or changed causes of mortality. Mice with inactive Poln are fertile and have normal testis morphology. However, pol ν–disrupted mice have a modestly reduced crossover frequency at a meiotic recombination hot spot harboring insertion/deletion polymorphisms. These polymorphisms are suggested to generate a looped-out primer and a hairpin structure during recombination, substrates on which pol ν can operate. Pol ν-defective mice had no alteration in DNA end-joining during immunoglobulin class-switching, in contrast to animals defective in the related DNA polymerase θ (pol θ). We examined the response to DNA crosslinking agents, as purified pol ν has some ability to bypass major groove peptide adducts and residues of DNA crosslink repair. Inactivation of Poln in mouse embryonic fibroblasts did not alter cellular sensitivity to mitomycin C, cisplatin, or aldehydes. Depletion of POLN from human cells with shRNA or siRNA did not change cellular sensitivity to mitomycin C or alter the frequency of mitomycin C-induced radial chromosomes. Our results suggest a function of pol ν in meiotic homologous recombination in processing specific substrates. The restricted and more recent evolutionary appearance of pol ν (in comparison to pol θ) supports such a specialized role. PMID:28570559

  17. Alternative end-joining catalyzes class switch recombination in the absence of both Ku70 and DNA ligase 4

    PubMed Central

    Boboila, Cristian; Yan, Catherine; Wesemann, Duane R.; Jankovic, Mila; Wang, Jing H.; Manis, John; Nussenzweig, Andre; Nussenzweig, Michel

    2010-01-01

    The classical nonhomologous end-joining (C-NHEJ) DNA double-strand break (DSB) repair pathway employs the Ku70/80 complex (Ku) for DSB recognition and the XRCC4/DNA ligase 4 (Lig4) complex for ligation. During IgH class switch recombination (CSR) in B lymphocytes, switch (S) region DSBs are joined by C-NHEJ to form junctions either with short microhomologies (MHs; “MH-mediated” joins) or no homologies (“direct” joins). In the absence of XRCC4 or Lig4, substantial CSR occurs via “alternative” end-joining (A-EJ) that generates largely MH-mediated joins. Because upstream C-NHEJ components remain in XRCC4- or Lig4-deficient B cells, residual CSR might be catalyzed by C-NHEJ using a different ligase. To address this, we have assayed for CSR in B cells deficient for Ku70, Ku80, or both Ku70 and Lig4. Ku70- or Ku80-deficient B cells have reduced, but still substantial, CSR. Strikingly, B cells deficient for both Ku plus Lig4 undergo CSR similarly to Ku-deficient B cells, firmly demonstrating that an A-EJ pathway distinct from C-NHEJ can catalyze CSR end-joining. Ku-deficient or Ku- plus Lig4-deficient B cells are also biased toward MH-mediated CSR joins; but, in contrast to XRCC4- or Lig4-deficient B cells, generate substantial numbers of direct CSR joins. Our findings suggest that more than one form of A-EJ can function in CSR. PMID:20142431

  18. Biased distribution of recombination sites within S regions upon immunoglobulin class switch recombination induced by transforming growth factor beta and lipopolysaccharide

    PubMed Central

    1992-01-01

    We have characterized extrachromosomal circular DNAs from adult mouse spleen cells that were induced to switch to immunoglobulin A (IgA) with bacterial lipopolysaccharide (LPS) and transforming growth factor beta (TGF-beta), and identified breakpoints of S mu/S gamma 3, S mu/S gamma 2, S mu/S alpha, S gamma 3/S alpha, and S gamma 2/S alpha recombinants. The S mu recombination donor sites clustered in the 3' half of the S mu region, while the S alpha recombination acceptor sites clustered in the 5' half of the S alpha region. In addition, donor and acceptor sites of S gamma regions also clustered in the 3' and 5' parts, respectively. These site preferences are in sharp contrast to the dispersed distribution of S mu/S gamma 1 breakpoints within both S mu and S gamma 1 regions upon IgG1 switch induced by LPS and interleukin 4. Our results support the hypotheses that TGF-beta increases the frequency of switch recombination events to IgA and that the switch recombination to IgA often proceeds by successive recombination of S mu/S gamma and S gamma/S alpha. PMID:1588279

  19. Identification of a stimulus-dependent DNase I hypersensitive site between the Ialpha and Calpha exons during immunoglobulin heavy chain class switch recombination.

    PubMed

    Ono, S J; Zhou, G; Tai, A K; Inaba, M; Kinoshita, K; Honjo, T

    2000-02-11

    The complete humoral response to foreign antigen depends upon two distinct recombination events within the heavy chain locus of immunoglobulin. The first recombination event takes place in what will become the antigen combining site of the antibody molecule, encoded by V, D and J segments. The second recombination event involves the looping-out of large spans of DNA which separate the various clusters of heavy chain exons which define the different immunoglobulin isotypes, or classes. While a great deal has been learned about the nature of the VDJ recombinase, very little is known about the nature of the class-switch recombinase. Using a cell system where class-switch recombination occurs primarily to the IgA locus, we have looked for stimulus-dependent changes in the chromatin structure of the IgA locus which might result from interactions between components of the recombinase and cis-elements within the region. We present evidence that strongly suggests that the class-switch recombinase interacts between the Ialpha and Calpha exons of IgA, just upstream of the highly reiterated DR1 and DR2 elements. However, although multiple potential SMAD-4 sites are located precisely within the DNase I hypersensitive site and 160 bp upstream of that site, we failed to detect any evidence of DNA/protein interactions near the hypersensitive site. Moreover, recombinant SMAD-3/4 proteins fail to interact with these sites with appreciable affinity in vitro. These data suggest that some other structural alteration at this site (e.g. RNA/DNA hybrid) may mediate the nuclease sensitivity.

  20. Rad52 competes with Ku70/Ku86 for binding to S-region DSB ends to modulate antibody class-switch DNA recombination.

    PubMed

    Zan, Hong; Tat, Connie; Qiu, Zhifang; Taylor, Julia R; Guerrero, Justin A; Shen, Tian; Casali, Paolo

    2017-02-08

    Antibody class-switch DNA recombination (CSR) is initiated by AID-introduced DSBs in the switch (S) regions targeted for recombination, as effected by Ku70/Ku86-mediated NHEJ. Ku-deficient B cells, however, undergo (reduced) CSR through an alternative(A)-NHEJ pathway, which introduces microhomologies in S-S junctions. As microhomology-mediated end-joining requires annealing of single-strand DNA ends, we addressed the contribution of single-strand annealing factors HR Rad52 and translesion DNA polymerase θ to CSR. Compared with their Rad52(+/+) counterparts, which display normal CSR, Rad52(-/-) B cells show increased CSR, fewer intra-Sμ region recombinations, no/minimal microhomologies in S-S junctions, decreased c-Myc/IgH translocations and increased Ku70/Ku86 recruitment to S-region DSB ends. Rad52 competes with Ku70/Ku86 for binding to S-region DSB ends. It also facilitates a Ku-independent DSB repair, which favours intra-S region recombination and mediates, particularly in Ku absence, inter-S-S recombination, as emphasized by the significantly greater CSR reduction in Rad52(-/-) versus Rad52(+/+) B cells on Ku86 knockdown.

  1. Rad52 competes with Ku70/Ku86 for binding to S-region DSB ends to modulate antibody class-switch DNA recombination

    PubMed Central

    Zan, Hong; Tat, Connie; Qiu, Zhifang; Taylor, Julia R.; Guerrero, Justin A.; Shen, Tian; Casali, Paolo

    2017-01-01

    Antibody class-switch DNA recombination (CSR) is initiated by AID-introduced DSBs in the switch (S) regions targeted for recombination, as effected by Ku70/Ku86-mediated NHEJ. Ku-deficient B cells, however, undergo (reduced) CSR through an alternative(A)-NHEJ pathway, which introduces microhomologies in S–S junctions. As microhomology-mediated end-joining requires annealing of single-strand DNA ends, we addressed the contribution of single-strand annealing factors HR Rad52 and translesion DNA polymerase θ to CSR. Compared with their Rad52+/+ counterparts, which display normal CSR, Rad52−/− B cells show increased CSR, fewer intra-Sμ region recombinations, no/minimal microhomologies in S–S junctions, decreased c-Myc/IgH translocations and increased Ku70/Ku86 recruitment to S-region DSB ends. Rad52 competes with Ku70/Ku86 for binding to S-region DSB ends. It also facilitates a Ku-independent DSB repair, which favours intra-S region recombination and mediates, particularly in Ku absence, inter-S–S recombination, as emphasized by the significantly greater CSR reduction in Rad52−/− versus Rad52+/+ B cells on Ku86 knockdown. PMID:28176781

  2. Noninfectious complications in patients with pediatric-onset common variable immunodeficiency correlated with defects in somatic hypermutation but not in class-switch recombination.

    PubMed

    Almejún, María Belén; Campos, Bárbara Carolina; Patiño, Virginia; Galicchio, Miguel; Zelazko, Marta; Oleastro, Matías; Oppezzo, Pablo; Danielian, Silvia

    2017-03-01

    Common variable immunodeficiency (CVID) is a heterogeneous syndrome characterized by impaired immunoglobulin production and usually presents with a normal quantity of peripheral B cells. Most attempts aiming to classify these patients have mainly been focused on T- or B-cell phenotypes and their ability to produce protective antibodies, but it is still a major challenge to find a suitable classification that includes the clinical and immunologic heterogeneity of these patients. In this study we evaluated the late stages of B-cell differentiation in a heterogeneous population of patients with pediatric-onset CVID to clinically correlate and assess their ability to perform somatic hypermutation (SHM), class-switch recombination (CSR), or both. We performed a previously reported assay, the restriction enzyme hotspot mutation assay (IgκREHMA), to evaluate in vivo SHM status. We amplified switch regions from genomic DNA to investigate the quality of the double-strand break repairs in the class-switch recombination process in vivo. We also tested the ability to generate immunoglobulin germline and circle transcripts and to upregulate the activation-induced cytidine deaminase gene through in vitro T-dependent and T-independent stimuli. Our results showed that patients could be classified into 2 groups according to their degree of SHM alteration. This stratification showed a significant association between patients of group A, severe alteration, and the presence of noninfectious complications. Additionally, 60% of patients presented with increased microhomology use at switched regions. In vitro activation revealed that patients with CVID behaved heterogeneously in terms of responsiveness to T-dependent stimuli. The correlation between noninfectious complications and SHM could be an important tool for physicians to further characterize patients with CVID. This categorization would help to improve elucidation of the complex mechanisms involved in B

  3. Non-canonical uracil processing in DNA gives rise to double-strand breaks and deletions: relevance to class switch recombination

    PubMed Central

    Bregenhorn, Stephanie; Kallenberger, Lia; Artola-Borán, Mariela; Peña-Diaz, Javier; Jiricny, Josef

    2016-01-01

    During class switch recombination (CSR), antigen-stimulated B-cells rearrange their immunoglobulin constant heavy chain (CH) loci to generate antibodies with different effector functions. CSR is initiated by activation-induced deaminase (AID), which converts cytosines in switch (S) regions, repetitive sequences flanking the CH loci, to uracils. Although U/G mispairs arising in this way are generally efficiently repaired to C/Gs by uracil DNA glycosylase (UNG)-initiated base excision repair (BER), uracil processing in S-regions of activated B-cells occasionally gives rise to double strand breaks (DSBs), which trigger CSR. Surprisingly, genetic experiments revealed that CSR is dependent not only on AID and UNG, but also on mismatch repair (MMR). To elucidate the role of MMR in CSR, we studied the processing of uracil-containing DNA substrates in extracts of MMR-proficient and –deficient human cells, as well as in a system reconstituted from recombinant BER and MMR proteins. Here, we show that the interplay of these repair systems gives rise to DSBs in vitro and to genomic deletions and mutations in vivo, particularly in an S-region sequence. Our findings further suggest that MMR affects pathway choice in DSB repair. Given its amenability to manipulation, our system represents a powerful tool for the molecular dissection of CSR. PMID:26743004

  4. Mismatch repair proteins MSH2, MLH1, and EXO1 are important for class-switch recombination events occurring in B cells that lack nonhomologous end joining.

    PubMed

    Eccleston, Jennifer; Yan, Catherine; Yuan, Karen; Alt, Frederick W; Selsing, Erik

    2011-02-15

    In the absence of core nonhomologous end-joining (NHEJ) factors, Ab gene class-switch recombination (CSR) uses an alternative end-joining (A-EJ) pathway to recombine switch (S) region DNA breaks. Previous reports showing decreased S-junction microhomologies in MSH2-deficient mice and an exonuclease 1 (EXO1) role in yeast microhomology-mediated end joining suggest that mismatch repair (MMR) proteins might influence A-EJ-mediated CSR. We have directly investigated whether MMR proteins collectively or differentially influence the A-EJ mechanism of CSR by analyzing CSR in mice deficient in both XRCC4 and individual MMR proteins. We find CSR is reduced and that Igh locus chromosome breaks are reduced in the MMR/XRCC4 double-deficient B cells compared with B cells deficient in XRCC4 alone, suggesting MMR proteins function upstream of double-strand break formation to influence CSR efficiency in these cells. Our results show that MLH1, EXO1, and MSH2 are all important for efficient A-EJ-mediated CSR, and we propose that MMR proteins convert DNA nicks and point mutations into dsDNA breaks for both C-NHEJ and A-EJ pathways of CSR. We also find Mlh1-XRCC4(-) B cells have an increased frequency of direct S junctions, suggesting that MLH1 proteins may have additional functions that influence A-EJ-mediated CSR.

  5. Microbiota regulate the ability of lung dendritic cells to induce IgA class-switch recombination and generate protective gastrointestinal immune responses

    PubMed Central

    Ruane, Darren; Chorny, Alejo; Lee, Haekyung; Faith, Jeremiah; Pandey, Gaurav; Shan, Meimei; Simchoni, Noa; Rahman, Adeeb; Garg, Aakash; Weinstein, Erica G.; Oropallo, Michael; Gaylord, Michelle; Ungaro, Ryan; Cunningham-Rundles, Charlotte; Alexandropoulos, Konstantina; Mucida, Daniel; Merad, Miriam; Cerutti, Andrea

    2016-01-01

    Protective immunoglobulin A (IgA) responses to oral antigens are usually orchestrated by gut dendritic cells (DCs). Here, we show that lung CD103+ and CD24+CD11b+ DCs induced IgA class-switch recombination (CSR) by activating B cells through T cell–dependent or –independent pathways. Compared with lung DCs (LDC), lung CD64+ macrophages had decreased expression of B cell activation genes and induced significantly less IgA production. Microbial stimuli, acting through Toll-like receptors, induced transforming growth factor-β (TGF-β) production by LDCs and exerted a profound influence on LDC-mediated IgA CSR. After intranasal immunization with inactive cholera toxin (CT), LDCs stimulated retinoic acid–dependent up-regulation of α4β7 and CCR9 gut-homing receptors on local IgA-expressing B cells. Migration of these B cells to the gut resulted in IgA-mediated protection against an oral challenge with active CT. However, in germ-free mice, the levels of LDC-induced, CT–specific IgA in the gut are significantly reduced. Herein, we demonstrate an unexpected role of the microbiota in modulating the protective efficacy of intranasal vaccination through their effect on the IgA class-switching function of LDCs. PMID:26712806

  6. Murine germinal center B cells require functional Fms-like tyrosine kinase 3 signaling for IgG1 class-switch recombination.

    PubMed

    Svensson, Mattias N D; Andersson, Karin M E; Wasén, Caroline; Erlandsson, Malin C; Nurkkala-Karlsson, Merja; Jonsson, Ing-Marie; Brisslert, Mikael; Bemark, Mats; Bokarewa, Maria I

    2015-12-01

    Switched antibody classes are important for efficient immune responses. Aberrant antibody production to otherwise harmless antigens may result in autoimmunity. The protein kinase fms-like tyrosine kinase 3 receptor (Flt3) has an important role during early B-cell development, but the role of Flt3 in peripheral B cells has not been assessed before. Herein we describe a previously unappreciated role for Flt3 in IgG1 class-switch recombination (CSR) and production. We show that Flt3 is reexpressed on B-cell lymphoma 6(+) germinal center B cells in vivo and following LPS activation of peripheral B cells in vitro. Absence of Flt3 signaling in Flt3 ligand-deficient mice results in impaired IgG1 CSR and accumulation of IgM-secreting plasma cells. On activated B cells, Flt3 is coexpressed and functions in synergy with the common-gamma chain receptor family. B cells from Flt3 ligand-deficient mice have impaired IL-4R signaling, with reduced phosphorylation of signal transducer and activator of transcription (Stat) 6, and demonstrate a failure to initiate CSR to IgG1 with low expression of γ1 germ-line transcripts, resulting in impaired IgG1 production. Thus, functional synergy between Flt3 and IL-4R signaling is critical for Stat-mediated regulation of sterile γ1 germ-line transcripts and CSR to IgG1.

  7. Microbiota regulate the ability of lung dendritic cells to induce IgA class-switch recombination and generate protective gastrointestinal immune responses.

    PubMed

    Ruane, Darren; Chorny, Alejo; Lee, Haekyung; Faith, Jeremiah; Pandey, Gaurav; Shan, Meimei; Simchoni, Noa; Rahman, Adeeb; Garg, Aakash; Weinstein, Erica G; Oropallo, Michael; Gaylord, Michelle; Ungaro, Ryan; Cunningham-Rundles, Charlotte; Alexandropoulos, Konstantina; Mucida, Daniel; Merad, Miriam; Cerutti, Andrea; Mehandru, Saurabh

    2016-01-11

    Protective immunoglobulin A (IgA) responses to oral antigens are usually orchestrated by gut dendritic cells (DCs). Here, we show that lung CD103(+) and CD24(+)CD11b(+) DCs induced IgA class-switch recombination (CSR) by activating B cells through T cell-dependent or -independent pathways. Compared with lung DCs (LDC), lung CD64(+) macrophages had decreased expression of B cell activation genes and induced significantly less IgA production. Microbial stimuli, acting through Toll-like receptors, induced transforming growth factor-β (TGF-β) production by LDCs and exerted a profound influence on LDC-mediated IgA CSR. After intranasal immunization with inactive cholera toxin (CT), LDCs stimulated retinoic acid-dependent up-regulation of α4β7 and CCR9 gut-homing receptors on local IgA-expressing B cells. Migration of these B cells to the gut resulted in IgA-mediated protection against an oral challenge with active CT. However, in germ-free mice, the levels of LDC-induced, CT-specific IgA in the gut are significantly reduced. Herein, we demonstrate an unexpected role of the microbiota in modulating the protective efficacy of intranasal vaccination through their effect on the IgA class-switching function of LDCs. © 2016 Ruane et al.

  8. Evolution of IgM, IgE and IgG(1-4 )antibody responses in early childhood monitored with recombinant allergen components: implications for class switch mechanisms.

    PubMed

    Niederberger, Verena; Niggemann, Bodo; Kraft, Dietrich; Spitzauer, Susanne; Valenta, Rudolf

    2002-02-01

    The formation of IgE antibodies against environmental allergens represents the hallmark of type I allergy. Data from in vitro cultured cells and experimental animal models provide controversial evidence for isotype switching from IgM to IgE production via sequential as well as non-sequential (i.e. direct) class switch. We analyzed the evolution of IgE responses in 11 children developing birch pollen and/or grass pollen allergy during the first 7 years of life using purified recombinant allergen molecules (major birch pollen allergen, Bet v 1; major timothy grass pollen allergens, Phl p 1, Phl p 2, Phl p 5). Demographic, clinical and serological data indicated a postnatal sensitization to pollen allergens. A parallel development of IgG(1-4) and IgE responses to recombinant allergen molecules compatible with a strictly sequential class switch to IgE was observed only in one child. The only partly synchronized and dissociated development of allergen-specific antibody responses found in all other cases can be best explained by a partly sequential class switch involving few switch stations or, more likely, by direct class switching. Kinetics and courses of allergen-specific antibody responses (IgM, IgG(1-4), IgE) during the first years of life suggest that, once established, allergen-specific IgE responses are driven by antigen contact rather than by cytokines controlling class switch to IgE.

  9. Recurrent disruption of the Imu splice donor site in t(14;18) positive lymphomas: a potential molecular basis for aberrant downstream class switch recombination.

    PubMed

    Ruminy, Philippe; Jardin, Fabrice; Penther, Dominique; Picquenot, Jean-Michel; Parmentier, Françoise; Buchonnet, Gérard; Bertrand, Philippe; Tilly, Hervé; Bastard, Christian

    2007-08-01

    t(14;18) positive lymphomas are mature germinal center B-cell neoplasms. In agreement with this cellular origin, most have somatically mutated immunoglobulin variable genes and the IGH@ locus has almost always been reorganized by class switch recombination (CSR). However, contrasting with normal B-cells, a majority of cases still express an IgM while the constant genes are normally rearranged only on the non-productive allele. Concurrently, aberrant intra-allelic junctions involving downstream switch regions, with a lack of engagement of the switch mu (Smu), often accumulate on the functional alleles, suggesting some recurrent CSR perturbation during the onset of the disease. To clarify these surprising observations, we addressed the accessibility of the Smu to the CSR machinery in a large series of patients by characterizing the mutations that are expected to accumulate at this place upon CSR activation. Our data indicate that the Smu is mutated in a large majority of cases, often on both alleles, indicating that these cells usually reach a differentiation stage where CSR is activated and where this region remains accessible. Interestingly, we also identified a significant cluster of mutations at the splicing donor site of the first exon of the Smu germline transcripts, on the functional allele. This location suggests a possible relation with CSR perturbations in lymphoma and the clustering points to a probable mechanism of selection. In conclusion, our data suggest that an acquired mutation at the splicing donor site of the Smu transcripts may participate in the selection of lymphoma cells and play a significant role during the onset of the disease.

  10. Elucidation of the enigmatic IgD class-switch recombination via germline deletion of the IgH 3′ regulatory region

    PubMed Central

    Rouaud, Pauline; Saintamand, Alexis; Saad, Faten; Carrion, Claire; Lecardeur, Sandrine; Cogné, Michel

    2014-01-01

    Classical class-switch recombination (cCSR) substitutes the Cμ gene with Cγ, Cε, or Cα, thereby generating IgG, IgE, or IgA classes, respectively. This activation-induced deaminase (AID)–driven process is controlled by the IgH 3′ regulatory region (3′RR). Regulation of rare IgD CSR events has been enigmatic. We show that μδCSR occurs in mouse mesenteric lymph node (MLN) B cells and is AID-dependent. AID attacks differ from those in cCSR because they are not accompanied by extensive somatic hypermutation (SHM) of targeted regions and because repaired junctions exhibit features of the alternative end-joining (A-EJ) pathway. In contrast to cCSR and SHM, μδCSR is 3′RR-independent, as its absence affects neither breakpoint locations in Sμ- and Sδ-like (σδ) nor mutation patterns at Sμ-σδ junctions. Although mutations occur in the immediate proximity of the μδ junctions, SHM is absent distal to the junctions within both Sμ and rearranged VDJ regions. In conclusion, μδCSR is active in MLNs, occurs independently of 3′RR-driven assembly, and is even dramatically increased in 3′RR-deficient mice, further showing that its regulation differs from cCSR. PMID:24752300

  11. Hotspots for Vitamin-Steroid-Thyroid Hormone Response Elements Within Switch Regions of Immunoglobulin Heavy Chain Loci Predict a Direct Influence of Vitamins and Hormones on B Cell Class Switch Recombination.

    PubMed

    Hurwitz, Julia L; Penkert, Rhiannon R; Xu, Beisi; Fan, Yiping; Partridge, Janet F; Maul, Robert W; Gearhart, Patricia J

    2016-03-01

    Vitamin A deficiencies are common throughout the world and have a significant negative influence on immune protection against viral infections. Mouse models demonstrate that the production of IgA, a first line of defense against viruses at mucosal sites, is inhibited in the context of vitamin A deficiency. In vitro, the addition of vitamin A to activated B cells can enhance IgA expression, but downregulate IgE. Previous reports have demonstrated that vitamin A modifies cytokine patterns, and in so doing may influence antibody isotype expression by an indirect mechanism. However, we have now discovered hundreds of potential response elements among Sμ, Sɛ, and Sα switch sites within immunoglobulin heavy chain loci. These hotspots appear in both mouse and human loci and include targets for vitamin receptors and related proteins (e.g., estrogen receptors) in the nuclear receptor superfamily. Full response elements with direct repeats are relatively infrequent or absent in Sγ regions although half-sites are present. Based on these results, we pose a hypothesis that nuclear receptors have a direct effect on the immunoglobulin heavy chain class switch recombination event. We propose that vitamin A may alter S site accessibility to activation-induced deaminase and nonhomologous end-joining machinery, thereby influencing the isotype switch, antibody production, and protection against viral infections at mucosal sites.

  12. A Role for the MutL Mismatch Repair Mlh3 Protein in Immunoglobulin Class Switch DNA Recombination and Somatic Hypermutation1

    PubMed Central

    Wu, Xiaoping; Tsai, Connie Y.; Patam, Marienida B.; Zan, Hong; Chen, Jessica P.; Lipkin, Steve M.; Casali, Paolo

    2015-01-01

    Class switch DNA recombination (CSR) and somatic hypermutation (SHM) are central to the maturation of the Ab response. Both processes involve DNA mismatch repair (MMR). MMR proteins are recruited to dU:dG mispairs generated by activation-induced cytidine deaminase-mediated deamination of dC residues, thereby promoting S-S region synapses and introduction of mismatches (mutations). The MutL homolog Mlh3 is the last complement of the mammalian set of MMR proteins. It is highly conserved in evolution and is essential to meiosis and microsatellite stability. We used the recently generated knockout mlh3−/− mice to address the role of Mlh3 in CSR and SHM. We found that Mlh3 deficiency alters both CSR and SHM. mlh3−/− B cells switched in vitro to IgG and IgA but displayed preferential targeting of the RGYW/WRCY (R = A or G, Y = C or T, W = A or T) motif by Sγ1 and Sγ3 breakpoints and introduced more insertions and fewer donor/acceptor microhomologies in Sμ-Sγ1 and Sμ-Sγ3 DNA junctions, as compared with mlh3+/+ B cells. mlh3−/− mice showed only a slight decrease in the frequency of mutations in the intronic DNA downstream of the rearranged JH4 gene. However, the residual mutations were altered in spectrum. They comprised a decreased proportion of mutations at dA/dT and showed preferential RGYW/WRCY targeting by mutations at dC/dG. Thus, the MMR Mlh3 protein plays a role in both CSR and SHM. PMID:16622010

  13. T cell-independent IgA class switch recombination is restricted to the GALT and occurs prior to manifest germinal center formation.

    PubMed

    Bergqvist, Peter; Stensson, Anneli; Lycke, Nils Y; Bemark, Mats

    2010-04-01

    Recently, we reported that CD40(-/-) mice, exhibiting exclusively T cell-independent IgA class switch recombination (CSR), demonstrated near normal levels of IgA plasma cells in the gut lamina propria (LP), despite the complete lack of germinal centers (GCs). In this study, we have extended our analysis focusing on how to reconcile these findings using flow cytometry and molecular markers for IgA CSR. In agreement with our previous results with small intestinal LP, the colon LP was found to host IgA CSR only when lymphoid follicles were present. Thus, no IgA CSR was observed in the nonorganized colon LP. By contrast, the Peyer's patch (PP) was the dominant IgA CSR site in both CD40(-/-) and wild type (WT) mice, and they both hosted similar levels of mRNA expression for B cell activating factor of the TNF family, a proliferation inducing ligand, and inducible NO synthase, potential switch-factors for IgA. Unexpectedly, we found that PP B cells undergoing IgA CSR were GL7-intermediate. These cells had not undergone somatic hypermutations (SHMs), whereas GL7-high cells in WT PP, which exhibited GCs, were heavily mutated. Moreover, IgA plasma cells in the LP of CD40(-/-) mice demonstrated few mutations in their Ig V regions, whereas WT LP B cells from different sites showed extensive SHMs, which were also clonally related. Therefore, IgA CSR can occur in PP at a stage preceding manifest GC (GL7-intermediate), whereas SHM require GC formations (GL7-high). These findings reconcile that IgA CSR can occur in PP in the absence of GC with the fact that CD40(-/-) mice host near normal levels of IgA plasma cells in the LP.

  14. Alternative end-joining and classical nonhomologous end-joining pathways repair different types of double-strand breaks during class-switch recombination.

    PubMed

    Cortizas, Elena M; Zahn, Astrid; Hajjar, Maurice E; Patenaude, Anne-Marie; Di Noia, Javier M; Verdun, Ramiro E

    2013-12-01

    Classical nonhomologous end-joining (C-NHEJ) and alternative end-joining (A-EJ) are the main DNA double-strand break (DSB) repair pathways when a sister chromatid is not available. However, it is not clear how one pathway is chosen over the other to process a given DSB. To address this question, we studied in mouse splenic B cells and CH12F3 cells how C-NHEJ and A-EJ repair DSBs initiated by the activation-induced deaminase during IgH (Igh) class-switch recombination (CSR). We show in this study that lowering the deamination density at the Igh locus increases DSB resolution by microhomology-mediated repair while decreasing C-NHEJ activity. This process occurs without affecting 53BP1 and γH2AX levels during CSR. Mechanistically, lowering deamination density increases exonuclease I recruitment and single-stranded DNA at the Igh locus and promotes C-terminal binding protein interacting protein and MSH2-dependent DSB repair during CSR. Indeed, reducing activation-induced deaminase levels increases CSR efficiency in C-NHEJ-defective cells, suggesting enhanced use of an A-EJ pathway. Our results establish a mechanism by which C-NHEJ and this C-terminal binding protein interacting protein/MSH2-dependent pathway that relies on microhomology can act concurrently but independently to repair different types of DSBs and reveal that the density of DNA lesions influences the choice of DSB repair pathway during CSR.

  15. Toll-like Receptors and B-cell Receptors Synergize to Induce Immunoglobulin Class Switch DNA Recombination: Relevance to Microbial Antibody Responses

    PubMed Central

    Pone, Egest J.; Zan, Hong; Zhang, Jinsong; Al-Qahtani, Ahmed; Xu, Zhenming; Casali, Paolo

    2011-01-01

    Differentiation of naïve B cells, including immunoglobulin (Ig) class switch DNA recombination (CSR), is critical for the immune response and depends on the extensive integration of signals from the B cell receptor (BCR), tumor necrosis factor (TNF) receptor family members, Toll-like receptors (TLRs) and cytokine receptors. TLRs and BCR synergize to induce CSR in T cell-dependent and T cell-independent antibody responses to microbial pathogens. BCR triggering together with simultaneous endosomal TLR engagement leads to enhanced B cell differentiation and antibody responses. The requirement of both BCR and TLR engagement would ensure appropriate antigen-specific activation in an infection. Co-stimulation of TLRs and BCR likely plays a significant role in anti-microbial antibody responses to contain pathogen loads until the T cell-dependent antibody responses peak. Furthermore, the temporal sequence of different signals is also critical for optimal B cell responses, as exemplified by the activation of B cells by initial TLR engagement, leading to the upregulation of co-stimulatory CD80 and MHC-II receptors, which, in turn, result in more efficient interactions with T cells, thereby enhancing the germinal center (GC) reaction and antibody affinity maturation. Overall, BCR and TLR stimulation and the integration with signals from the pathogen or immune cells and their products, determine the ensuing B cell antibody response. PMID:20370617

  16. Naturally occurring mutation affecting the MyD88-binding site of TNFRSF13B impairs triggering of class switch recombination

    PubMed Central

    Almejun, Maria B.; Cols, Montserrat; Zelazko, Marta; Oleastro, Matias; Cerutti, Andrea; Oppezzo, Pablo; Cunningham-Rundles, Charlotte; Danielian, Silvia

    2013-01-01

    Mutations in the transmembrane activator and calcium-modulating cyclophilin ligand interactor (TACI) were previously found to be associated with hypogammaglobulinemia in humans. It has been shown that proliferation inducing ligand (APRIL) elicits class switch recombination (CSR) by inducing recruitment of MyD88 to a TACI highly conserved cytoplasmic domain (THC). We have identified a patient with hypogammaglobulinemia carrying a missense mutation (S231R) predicted to affect the THC. Aiming to evaluate the relevance of this novel mutation of TACI in CSR induction, we tested the ability of TACI, TLR9, or/and CD40 ligands to trigger CSR in naive B cells and B-cell lines carrying S231R. IgG secretion was impaired when triggered by TACI or/and TLR9 ligands on S231R-naive B cells. Likewise, these stimuli induced less expression of activation-induced cytidine deaminase, I(γ)1-C(μ), and I(γ)1-C(μ), while induction by optimal CD40 stimulation was indistinguishable from controls. These cells also showed an impaired cooperation between TACI and TLR9 pathways, as well as a lack of APRIL-mediated enhancement of CD40 activation in suboptimal conditions. Finally, after APRIL ligation, S231R-mutated TACI failed to colocalize with MyD88. Collectively, these results highlight the requirement of an intact MyD88-binding site in TACI to trigger CSR. PMID:23225259

  17. Class E/F switching power amplifiers

    NASA Technical Reports Server (NTRS)

    Hajimiri, Seyed-Ali (Inventor); Aoki, Ichiro (Inventor); Rutledge, David B. (Inventor); Kee, Scott David (Inventor)

    2004-01-01

    The present invention discloses a new family of switching amplifier classes called class E/F amplifiers. These amplifiers are generally characterized by their use of the zero-voltage-switching (ZVS) phase correction technique to eliminate of the loss normally associated with the inherent capacitance of the switching device as utilized in class-E amplifiers, together with a load network for improved voltage and current wave-shaping by presenting class-F.sup.-1 impedances at selected overtones and class-E impedances at the remaining overtones. The present invention discloses a several topologies and specific circuit implementations for achieving such performance.

  18. Mouse homolog of Saccharomyces cerevisiae spo11 is induced in normal mu(+)B-cells by stimuli that cause germline C(H) transcription and subsequent class switch recombination.

    PubMed

    Tokuyama, H; Tokuyama, Y

    2000-05-25

    The first step of Ig heavy chain class switch recombination (CSR) is considered to be DNA double strand break (DSB) formation in the two switch (S) regions (S(mu) and downstream S(H)), although the underlying mechanism is unknown. Recently, it has been demonstrated that at least Spo11, a homolog of the novel type II topoisomerase (topo VI) that catalyzes DSB formation, is involved in the initiation of meiotic recombination of Saccaromyces cerevisiae. In the present study, we examined whether the mouse homolog of Spo11 is induced in normal mouse mu(+)B-cells by stimuli that cause an early step of CSR, germline C(H) transcription, and subsequent CSR. Two CSR systems were used: IgA CSR induced by all-trans retinoic acid, IL-5, and LPS, and IgG1 CSR induced by IL-4 and LPS. Germline transcript and mouse Spo11 expression were analyzed by RT-PCR. In both systems, first germline transcripts were clearly detected on day 2 and then Spo11 was detected on day 3, increasing thereafter with time. The time course of changes in Spo11 expression coincided with that of CSR. Spo11 seems to be induced by CSR-inducing stimuli, regardless of the direction of CSR. These results suggested that mouse Spo11 might participate in the initiation step of CSR.

  19. B cell TLR1/2, TLR4, TLR7 and TLR9 interact in induction of class switch DNA recombination: modulation by BCR and CD40, and relevance to T-independent antibody responses.

    PubMed

    Pone, Egest J; Lou, Zheng; Lam, Tonika; Greenberg, Milton L; Wang, Rui; Xu, Zhenming; Casali, Paolo

    2015-02-01

    Ig class switch DNA recombination (CSR) in B cells is crucial to the maturation of antibody responses. It requires IgH germline IH-CH transcription and expression of AID, both of which are induced by engagement of CD40 or dual engagement of a Toll-like receptor (TLR) and B cell receptor (BCR). Here, we have addressed cross-regulation between two different TLRs or between a TLR and CD40 in CSR induction by using a B cell stimulation system involving lipopolysaccharides (LPS). LPS-mediated long-term primary class-switched antibody responses and memory-like antibody responses in vivo and induced generation of class-switched B cells and plasma cells in vitro. Consistent with the requirement for dual TLR and BCR engagement in CSR induction, LPS, which engages TLR4 through its lipid A moiety, triggered cytosolic Ca2+ flux in B cells through its BCR-engaging polysaccharidic moiety. In the presence of BCR crosslinking, LPS synergized with a TLR1/2 ligand (Pam3CSK4) in CSR induction, but much less efficiently with a TLR7 (R-848) or TLR9 (CpG) ligand. In the absence of BCR crosslinking, R-848 and CpG, which per se induced marginal CSR, virtually abrogated CSR to IgG1, IgG2a, IgG2b, IgG3 and/or IgA, as induced by LPS or CD154 (CD40 ligand) plus IL-4, IFN-γ or TGF-β, and reduced secretion of class-switched Igs, without affecting B cell proliferation or IgM expression. The CSR inhibition by TLR9 was associated with the reduction in AID expression and/or IgH germline IH-S-CH transcription, and required co-stimulation of B cells by CpG with LPS or CD154. Unexpectedly, B cells also failed to undergo CSR or plasma cell differentiation when co-stimulated by LPS and CD154. Overall, by addressing the interaction of TLR1/2, TLR4, TLR7 and TLR9 in the induction of CSR and modulation of TLR-dependent CSR by BCR and CD40, our study suggests the complexity of how different stimuli cross-regulate an important B cell differentiation process and an important role of TLRs in inducing

  20. B cell TLR1/2, TLR4, TLR7 and TLR9 interact in induction of class switch DNA recombination: modulation by BCR and CD40, and relevance to T-independent antibody responses

    PubMed Central

    Pone, Egest J.; Lou, Zheng; Lam, Tonika; Greenberg, Milton L.; Wang, Rui; Xu, Zhenming; Casali, Paolo

    2015-01-01

    Ig class switch DNA recombination (CSR) in B cells is crucial to the maturation of antibody responses. It requires IgH germline IH-CH transcription and expression of AID, both of which are induced by engagement of CD40 or dual engagement of a Toll-like receptor (TLR) and B cell receptor (BCR). Here, we have addressed cross-regulation between two different TLRs or between a TLR and CD40 in CSR induction by using a B cell stimulation system involving lipopolysaccharides (LPS). LPS mediated long-term primary class-switched antibody responses and memory-like antibody responses in vivo and induced generation of class-switched B cells and plasma cells in vitro. Consistent with the requirement for dual TLR and BCR engagement in CSR induction, LPS, which engages TLR4 through its lipid A moiety, triggered cytosolic Ca2+ flux in B cells through its BCR-engaging polysaccharidic moiety. In the presence of BCR crosslinking, LPS synergized with a TLR1/2 ligand (Pam3CSK4) in CSR induction, but much less efficiently with a TLR7 (R-848) or TLR9 (CpG) ligand. In the absence of BCR crosslinking, R-848 and CpG, which per se induced marginal CSR, virtually abrogated CSR to IgG1, IgG2a, IgG2b, IgG3 and/or IgA, as induced by LPS or CD154 (CD40 ligand) plus IL-4, IFN-γ or TGF-β, and reduced secretion of class-switched Igs, without affecting B cell proliferation or IgM expression. The CSR inhibition by TLR9 was associated with the reduction in AID expression and/or IgH germline IH-S-CH transcription, and required co-stimulation of B cells by CpG with LPS or CD154. Unexpectedly, B cells also failed to undergo CSR or plasma cell differentiation when co-stimulated by LPS and CD154. Overall, by addressing the interaction of TLR1/2, TLR4, TLR7 and TLR9 in the induction of CSR and modulation of TLR-dependent CSR by BCR and CD40, our study suggests the complexity of how different stimuli cross-regulate an important B cell differentiation process and an important role of TLRs in inducing

  1. Homologous Elements hs3a and hs3b in the 3′ Regulatory Region of the Murine Immunoglobulin Heavy Chain (Igh) Locus Are Both Dispensable for Class-switch Recombination*

    PubMed Central

    Yan, Yi; Pieretti, Joyce; Ju, Zhongliang; Wei, Shiniu; Christin, John R.; Bah, Fatmata; Birshtein, Barbara K.; Eckhardt, Laurel A.

    2011-01-01

    Immunoglobulin heavy chain (IgH) genes are formed, tested, and modified to yield diverse, specific, and high affinity antibody responses to antigen. The processes involved must be regulated, however, to avoid unintended damage to chromosomes. The 3′ regulatory region of the Igh locus plays a major role in regulating class-switch recombination (CSR), the process by which antibody effector functions are modified during an immune response. Loss of all known enhancer-like elements in this region dramatically impairs CSR, but individual element deletions have no effect on this process. In the present study, we explored the hypothesis that an underlying functional redundancy in the homologous elements hs3a and hs3b was masking the importance of either element to CSR. Several transgenic mouse lines were generated, each carrying a bacterial artificial chromosome transgene that mimicked Igh locus structure but in which hs3a was missing and hs3b was flanked by loxP sites. Matings to Cyclization Recombination Enzyme-expressing mice established “pairs” of lines that differed only in the presence or absence of hs3b. Remarkably, CSR remained robust in the absence of both hs3a and hs3b, suggesting that the remaining two elements of the 3′ regulatory region, hs1.2 and hs4, although individually dispensable for CSR, are, together, sufficient to support CSR. PMID:21673112

  2. Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching

    PubMed Central

    Horns, Felix; Vollmers, Christopher; Croote, Derek; Mackey, Sally F; Swan, Gary E; Dekker, Cornelia L; Davis, Mark M; Quake, Stephen R

    2016-01-01

    Antibody class switching is a feature of the adaptive immune system which enables diversification of the effector properties of antibodies. Even though class switching is essential for mounting a protective response to pathogens, the in vivo patterns and lineage characteristics of antibody class switching have remained uncharacterized in living humans. Here we comprehensively measured the landscape of antibody class switching in human adult twins using antibody repertoire sequencing. The map identifies how antibodies of every class are created and delineates a two-tiered hierarchy of class switch pathways. Using somatic hypermutations as a molecular clock, we discovered that closely related B cells often switch to the same class, but lose coherence as somatic mutations accumulate. Such correlations between closely related cells exist when purified B cells class switch in vitro, suggesting that class switch recombination is directed toward specific isotypes by a cell-autonomous imprinted state. DOI: http://dx.doi.org/10.7554/eLife.16578.001 PMID:27481325

  3. Transcription-dependent R-loop formation at mammalian class switch sequences

    PubMed Central

    Tracy, Robert B.; Lieber, Michael R.

    2000-01-01

    Immunoglobulin class switching is mediated by recombination between switch sequences located immediately upstream of the immunoglobulin constant heavy chain genes. Targeting of recombination to particular switch sequences is associated temporally with transcription through these regions. We recently have provided evidence for inducible and stable RNA–DNA hybrid formation at switch sequences in the mouse genome that are mechanistically important for class switching in vivo. Here, we define in vitro the precise configuration of the DNA and RNA strands within this hybrid structure at the Sμ, Sγ3 and Sγ2b mouse switch sequences. We find that the G–rich (non-template) DNA strand of each switch sequence is hypersensitive to probes throughout much of its length, while the C–rich (template) DNA strand is essentially resistant. These results demonstrate formation of an R–loop, whereby the G–rich RNA strand forms a stable heteroduplex with its C–rich DNA strand counterpart, and the G–rich DNA strand exists primarily in a single-stranded state. We propose that the organized structure of the R–loop is essential for targeting the class switch recombination machinery to these sequences. PMID:10698946

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

    PubMed

    Vanoli, Fabio; Fumasoni, Marco; Szakal, Barnabas; Maloisel, Laurent; Branzei, Dana

    2010-11-11

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

  5. Adaptive control under arbitrary switching for a class of switched nonlinear systems with nonlinear parameterisation

    NASA Astrophysics Data System (ADS)

    Wang, C. Y.; Jiao, X. H.

    2015-10-01

    This paper is devoted to discuss arbitrarily switching control problem for a class of nonlinearly parameterised nonlinear switched systems. Compared with the existing results, improvements are that a systematic procedure is given for an explicit construction of a common smooth adaptive controller independent of the switching signals. Meanwhile, the developed design method can be extended to the adaptive arbitrarily switching stabilisation problem for a class of cascade switched nonlinear systems. The theoretical analysis is presented for the Lyapunov stability of the resulting closed-loop switched system and the convergence of the original switched system states at the equilibrium under arbitrary switching. Moreover, the effectiveness and feasibility of the developed method are demonstrated by both a numerical example and a chemical system.

  6. Downstream class switching leads to IgE antibody production by B lymphocytes lacking IgM switch regions

    PubMed Central

    Zhang, Tingting; Franklin, Andrew; Boboila, Cristian; McQuay, Amy; Gallagher, Michael P.; Manis, John P.; Khamlichi, Ahmed Amine; Alt, Frederick W.

    2010-01-01

    Ig heavy chain (IgH) class-switch recombination (CSR) replaces the IgH Cμ constant region exons with one of several sets of downstream IgH constant region exons (e.g., Cγ, Cε, or Cα), which affects switching from IgM to another IgH class (e.g., IgG, IgE, or IgA). Activation-induced cytidine deaminase (AID) initiates CSR by promoting DNA double-strand breaks (DSBs) within switch (S) regions flanking the donor Cμ (Sμ) and a downstream acceptor CH (e.g., Sγ, Sε, Sα) that are then joined to complete CSR. DSBs generated in Sμ frequently are joined within Sμ to form internal switch region deletions (ISD). AID-induced ISD and mutations have been considered rare in downstream S regions, suggesting that AID targeting to these S regions requires its prior recruitment to Sμ. We have now assayed for CSR and ISD in B cells lacking Sμ (Sμ−/− B cells). In Sμ−/− B cells activated for CSR to IgG1 and IgE, CSR to IgG1 was greatly reduced; but, surprisingly, CSR to IgE occurred at nearly normal levels. Moreover, normal B cells had substantial Sγ1 ISD and increased mutations in and near Sγ1, and levels of both were greatly increased in Sμ−/− B cells. Finally, Sμ−/− B cells underwent downstream CSR between Sγ1 and Sε on alleles that lacked Sμ CSR to these sequences. Our findings show that AID targets downstream S regions independently of CSR with Sμ and implicate an alternative pathway for IgE class switching that involves generation and joining of DSBs within two different downstream S regions before Sμ joining. PMID:20133637

  7. Switching fuzzy controller design based on switching Lyapunov function for a class of nonlinear systems.

    PubMed

    Ohtake, Hiroshi; Tanaka, Kazuo; Wang, Hua O

    2006-02-01

    This paper presents a switching fuzzy controller design for a class of nonlinear systems. A switching fuzzy model is employed to represent the dynamics of a nonlinear system. In our previous papers, we proposed the switching fuzzy model and a switching Lyapunov function and derived stability conditions for open-loop systems. In this paper, we design a switching fuzzy controller. We firstly show that switching fuzzy controller design conditions based on the switching Lyapunov function are given in terms of bilinear matrix inequalities, which is difficult to design the controller numerically. Then, we propose a new controller design approach utilizing an augmented system. By introducing the augmented system which consists of the switching fuzzy model and a stable linear system, the controller design conditions based on the switching Lyapunov function are given in terms of linear matrix inequalities (LMIs). Therefore, we can effectively design the switching fuzzy controller via LMI-based approach. A design example illustrates the utility of this approach. Moreover, we show that the approach proposed in this paper is available in the research area of piecewise linear control.

  8. Sequences of human immunoglobulin switch regions: implications for recombination and transcription.

    PubMed Central

    Mills, F C; Brooker, J S; Camerini-Otero, R D

    1990-01-01

    We have sequenced the entire human S mu and S gamma 4 immunoglobulin heavy chain class switch regions, and have also completed the sequence of human S epsilon. S mu is composed predominantly of GAGCT and GGGCT pentameric repeats, with these units also being found in S epsilon at a much lower density. S mu-S gamma 4 matches are infrequent, but S gamma 4 contains a cluster of repeated sequences similar to units in mouse gamma switch sites and unrelated to the S mu repeats, suggesting that S mu-S gamma homology is not important in mu-gamma switching. We examined our epsilon and gamma 4 sequences for features that could regulate production of 'sterile' transcripts preceding switch recombination. There is an Evolutionarily Conserved Sequence (ECS) upstream from the human and mouse S epsilon regions that overlaps and extends 5' to the start sites for human and mouse epsilon sterile transcripts. Similarly, an ECS upstream from S gamma 4 is homologous to a mouse sequence that overlaps and extends 5' to the start sites for mouse gamma 2b sterile transcripts. The epsilon and gamma 4 conserved segments contain potential Interferon Stimulable Response Elements (ISRE's) that are identical between human epsilon and gamma 4. PMID:2124350

  9. Technical network equipment qualification : cubicle-class switches.

    SciTech Connect

    Kellogg, Brian Richard; Brenkosh, Joseph Peter

    2003-12-01

    As part of the Testing Evaluation and Qualification Project, which was contracted by Organization 9336, this paper compares three cubicle-class switches from various vendors to assess how well they would perform in the unclassified networks at Sandia National Laboratories. The switches tested were the SMC TigerSwitch 6709L2, the Cisco Catalyst 2950G-12, and the Extreme Summit 5i. Each switch was evaluated by testing performance, functionality, interoperability, security, and total cost of ownership. The results of this report show the SMC TigerSwitch as being the best choice for cubicle use because of its high performance and very low cost. The Cisco Catalyst is also rated highly for cubicle use and in some cases may be preferred over the SMC TigerSwitch. The Extreme Summit 5i is not recommended for cubicle use due to its size and extremely loud fans but is a full featured, high performance switch that would work very well for access layer switching.

  10. Regulation and targeting of recombination in extrachromosomal substrates carrying immunoglobulin switch region sequences.

    PubMed Central

    Leung, H; Maizels, N

    1994-01-01

    We have used extrachromosomal substrates carrying immunoglobulin heavy-chain S mu and S gamma 3 switch region sequences to study activation and targeting of recombination by a transcriptional enhancer element. Substrates are transiently introduced into activated primary murine B cells, in which recombination involving S-region sequences deletes a conditionally lethal marker, and recombination is measured by transformation of Escherichia coli in the second step of the assay. Previously we found that as many as 25% of replicated substrates recombined during 40-h transfection of lipopolysaccharide (LPS)-stimulated primary cells and that efficient recombination was dependent on the presence of S-region sequences as well as a transcriptional activator region in the constructs (H. Leung and N. Maizels, Proc. Natl. Acad. Sci. USA 89:4154-4158, 1992). Here we show that recombination of the switch substrates is threefold more efficient in LPS-cultured primary B cells than in the T-cell line EL4; the activities responsible for switch substrate recombination thus appear to be more abundant or more active in cells which can carry out chromosomal switch recombination. We test the role of the transcriptional activator region and show that the immunoglobulin heavy-chain intron enhancer (E mu) alone stimulates recombination as well as E mu combined with a heavy-chain promoter and that mutations that diminish enhancer-dependent transcription 500-fold diminish recombinational activation less than 2-fold. These observations suggest that the enhancer stimulates recombination by a mechanism that does not depend on transcript production or that is insensitive to the level of transcript production over a very broad range. Furthermore, we find that E mu stimulates recombination when located either upstream or downstream of S mu but that the position of the recombinational activator does affect the targeting of recombination junctions, suggesting that the relatively imprecise targeting of

  11. Deletional switch recombination occurs in interleukin-4-induced isotype switching to IgE expression by human B cells.

    PubMed Central

    Shapira, S K; Jabara, H H; Thienes, C P; Ahern, D J; Vercelli, D; Gould, H J; Geha, R S

    1991-01-01

    There is controversy as to whether deletional rearrangement occurs between the IgM and IgE switch regions (S mu and S epsilon, respectively) during switching to the IgE isotype. We have addressed the issue by stimulating normal human B cells, sorted for lack of expression of surface IgE, to produce IgE by infection with Epstein-Barr virus (EBV) in the presence of interleukin 4 (IL-4). Genomic DNA was amplified for S mu/S epsilon switch junction fragments by utilizing the nested-primer polymerase chain reaction. Switch junction fragments were amplified from B cells infected with EBV in the presence of IL-4 but not from B cells infected with EBV alone. The DNA sequence of these "switch fragments" revealed direct joining of S mu to S epsilon in each case. The recombination sites within S mu were clustered within 900 base pairs at the 5' end of the switch region, suggesting that there are "hot spots" for recombination within S mu. The S epsilon recombination sites were scattered throughout the S epsilon region. These findings indicate that IL-4-induced isotype switching to IgE production in human B cells is accompanied by DNA rearrangements with joining of S mu to S epsilon. Images PMID:1881893

  12. Lysine residue at position 22 of the AID protein regulates its class switch activity.

    PubMed

    Geisberger, Roland; Huemer, Michael; Gassner, Franz J; Zaborsky, Nadja; Egle, Alexander; Greil, Richard

    2012-01-01

    Activation induced deaminase (AID) mediates class switch recombination and somatic hypermutation of immunoglobulin (Ig) genes in germinal centre B cells. In order to regulate its specific activity and as a means to keep off-target mutations low, several mechanisms have evolved, including binding to specific cofactors, phosphorylation and destabilization of nuclear AID protein. Although ubiquitination at lysine residues of AID is recognized as an essential step in initiating degradation of nuclear AID, any functional relevance of lysine modifications has remained elusive. Here, we report functional implications of lysine modifications of the human AID protein by generating a panel of lysine to arginine mutants of AID and assessment of their catalytic class switch activity. We found that only mutation of Lys22 to Arg resulted in a significant reduction of class switching to IgG1 in transfected primary mouse B cells. This decrease in activity was neither reflected in reduced hypermutation of Ig genes in AID-mutant transfected DT40 B cell lines nor recapitulated in bacterial deamination assays, pointing to involvement of post-translational modification of Lys22 for AID activity in B cells. Our results imply that lysine modification may represent a novel level of AID regulation and that Lys22 is important for effective AID activity.

  13. Immature B cells preferentially switch to IgE with increased direct Sμ to Sε recombination.

    PubMed

    Wesemann, Duane R; Magee, Jennifer M; Boboila, Cristian; Calado, Dinis Pedro; Gallagher, Michael P; Portuguese, Andrew J; Manis, John P; Zhou, Xiaolong; Recher, Mike; Rajewsky, Klaus; Notarangelo, Luigi D; Alt, Frederick W

    2011-12-19

    Immunoglobulin heavy chain (IgH) class-switch recombination (CSR) replaces initially expressed Cμ (IgM) constant regions (C(H)) exons with downstream C(H) exons. Stimulation of B cells with anti-CD40 plus interleukin-4 induces CSR from Cμ to Cγ1 (IgG1) and Cε (IgE), the latter of which contributes to the pathogenesis of atopic diseases. Although Cε CSR can occur directly from Cμ, most mature peripheral B cells undergo CSR to Cε indirectly, namely from Cμ to Cγ1, and subsequently to Cε. Physiological mechanisms that influence CSR to Cγ1 versus Cε are incompletely understood. In this study, we report a role for B cell developmental maturity in IgE CSR. Based in part on a novel flow cytometric IgE CSR assay, we show that immature B cells preferentially switch to IgE versus IgG1 through a mechanism involving increased direct CSR from Cμ to Cε. Our findings suggest that IgE dysregulation in certain immunodeficiencies may be related to impaired B cell maturation.

  14. Immature B cells preferentially switch to IgE with increased direct Sμ to Sε recombination

    PubMed Central

    Wesemann, Duane R.; Magee, Jennifer M.; Boboila, Cristian; Calado, Dinis Pedro; Gallagher, Michael P.; Portuguese, Andrew J.; Manis, John P.; Zhou, Xiaolong; Recher, Mike; Rajewsky, Klaus; Notarangelo, Luigi D.

    2011-01-01

    Immunoglobulin heavy chain (IgH) class-switch recombination (CSR) replaces initially expressed Cμ (IgM) constant regions (CH) exons with downstream CH exons. Stimulation of B cells with anti-CD40 plus interleukin-4 induces CSR from Cμ to Cγ1 (IgG1) and Cε (IgE), the latter of which contributes to the pathogenesis of atopic diseases. Although Cε CSR can occur directly from Cμ, most mature peripheral B cells undergo CSR to Cε indirectly, namely from Cμ to Cγ1, and subsequently to Cε. Physiological mechanisms that influence CSR to Cγ1 versus Cε are incompletely understood. In this study, we report a role for B cell developmental maturity in IgE CSR. Based in part on a novel flow cytometric IgE CSR assay, we show that immature B cells preferentially switch to IgE versus IgG1 through a mechanism involving increased direct CSR from Cμ to Cε. Our findings suggest that IgE dysregulation in certain immunodeficiencies may be related to impaired B cell maturation. PMID:22143888

  15. Kin17 facilitates multiple double-strand break repair pathways that govern B cell class switching

    PubMed Central

    Le, Michael X.; Haddad, Dania; Ling, Alexanda K.; Li, Conglei; So, Clare C.; Chopra, Amit; Hu, Rui; Angulo, Jaime F.; Moffat, Jason; Martin, Alberto

    2016-01-01

    Class switch recombination (CSR) in B cells requires the timely repair of DNA double-stranded breaks (DSBs) that result from lesions produced by activation-induced cytidine deaminase (AID). Through a genome-wide RNAi screen, we identified Kin17 as a gene potentially involved in the maintenance of CSR in murine B cells. In this study, we confirm a critical role for Kin17 in CSR independent of AID activity. Furthermore, we make evident that DSBs generated by AID or ionizing radiation require Kin17 for efficient repair and resolution. Our report shows that reduced Kin17 results in an elevated deletion frequency following AID mutational activity in the switch region. In addition, deficiency in Kin17 affects the functionality of multiple DSB repair pathways, namely homologous recombination, non-homologous end-joining, and alternative end-joining. This report demonstrates the importance of Kin17 as a critical factor that acts prior to the repair phase of DSB repair and is of bona fide importance for CSR. PMID:27853268

  16. Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory

    PubMed Central

    Ham, Timothy S.; Lee, Sung K.; Keasling, Jay D.; Arkin, Adam P.

    2008-01-01

    Background Inversion recombination elements present unique opportunities for computing and information encoding in biological systems. They provide distinct binary states that are encoded into the DNA sequence itself, allowing us to overcome limitations posed by other biological memory or logic gate systems. Further, it is in theory possible to create complex sequential logics by careful positioning of recombinase recognition sites in the sequence. Methodology/Principal Findings In this work, we describe the design and synthesis of an inversion switch using the fim and hin inversion recombination systems to create a heritable sequential memory switch. We have integrated the two inversion systems in an overlapping manner, creating a switch that can have multiple states. The switch is capable of transitioning from state to state in a manner analogous to a finite state machine, while encoding the state information into DNA. This switch does not require protein expression to maintain its state, and “remembers” its state even upon cell death. We were able to demonstrate transition into three out of the five possible states showing the feasibility of such a switch. Conclusions/Significance We demonstrate that a heritable memory system that encodes its state into DNA is possible, and that inversion recombination system could be a starting point for more complex memory circuits. Although the circuit did not fully behave as expected, we showed that a multi-state, temporal memory is achievable. PMID:18665232

  17. Mice deficient for the type II topoisomerase-like DNA transesterase Spo11 show normal immunoglobulin somatic hypermutation and class switching.

    PubMed

    Klein, Ulf; Esposito, Gloria; Baudat, Frédéric; Keeney, Scott; Jasin, Maria

    2002-02-01

    Somatic hypermutation in B cells undergoing T cell dependent immune responses generates high affinity antibodies that provide protective immunity. B cells also switch from the expression of immunoglobulin (Ig) M and IgD to that of other Ig classes through somatic DNA recombination. Recent work has implicated DNA strand breaks, possibly DNA double strand breaks (DSB), as the initiating lesions in both class switch recombination and hypermutation, although the etiology of these lesions is not understood. Spo11, a protein structurally related to archaeal type II topoisomerases, generates DSB that initiate meiotic recombination. This characteristic, together with its expression pattern, marks this enzyme as a potential candidate for the initiation of hypermutation, and perhaps also for Ig class switching. To investigate whether Spo11 is involved in these processes, we studied the T cell dependent immune response of Spo11-deficient (Spo11(-/-)) mice against the hapten nitrophenyl (NP). We found that V186.2-bearing IgG1 transcripts had normal levels and patterns of somatic hypermutation. Furthermore, Spo11(-/-) mice showed normal serum levels of all Ig isotypes. These results indicate that Spo11 is not required for Ig hypermutation or class switch recombination.

  18. Fission yeast switches mating type by a replication–recombination coupled process

    PubMed Central

    Arcangioli, Benoit; de Lahondès, Raynald

    2000-01-01

    Fission yeast exhibits a homothallic life cycle, in which the mating type of the cell mitotically alternates in a highly regulated fashion. Pedigree analysis of dividing cells has shown that only one of the two sister cells switches mating type. It was shown recently that a site- and strand-specific DNA modification at the mat1 locus precedes mating-type switching. By tracking the fate of mat1 DNA throughout the cell cycle with a PCR assay, we identified a novel DNA intermediate of mating-type switching in S-phase. The time and rate of appearance and disappearance of this DNA intermediate are consistent with a model in which mating-type switching occurs through a replication–recombination coupled pathway. Such a process provides experimental evidence in support of a copy choice recombination model in Schizosaccharomyces pombe mating-type switching and is reminiscent of the sister chromatid recombination used to complete replication in the presence of certain types of DNA damage. PMID:10716938

  19. Orientation-specific joining of AID-initiated DNA breaks promotes antibody class switching.

    PubMed

    Dong, Junchao; Panchakshari, Rohit A; Zhang, Tingting; Zhang, Yu; Hu, Jiazhi; Volpi, Sabrina A; Meyers, Robin M; Ho, Yu-Jui; Du, Zhou; Robbiani, Davide F; Meng, Feilong; Gostissa, Monica; Nussenzweig, Michel C; Manis, John P; Alt, Frederick W

    2015-09-03

    During B-cell development, RAG endonuclease cleaves immunoglobulin heavy chain (IgH) V, D, and J gene segments and orchestrates their fusion as deletional events that assemble a V(D)J exon in the same transcriptional orientation as adjacent Cμ constant region exons. In mice, six additional sets of constant region exons (CHs) lie 100-200 kilobases downstream in the same transcriptional orientation as V(D)J and Cμ exons. Long repetitive switch (S) regions precede Cμ and downstream CHs. In mature B cells, class switch recombination (CSR) generates different antibody classes by replacing Cμ with a downstream CH (ref. 2). Activation-induced cytidine deaminase (AID) initiates CSR by promoting deamination lesions within Sμ and a downstream acceptor S region; these lesions are converted into DNA double-strand breaks (DSBs) by general DNA repair factors. Productive CSR must occur in a deletional orientation by joining the upstream end of an Sμ DSB to the downstream end of an acceptor S-region DSB. However, the relative frequency of deletional to inversional CSR junctions has not been measured. Thus, whether orientation-specific joining is a programmed mechanistic feature of CSR as it is for V(D)J recombination and, if so, how this is achieved is unknown. To address this question, we adapt high-throughput genome-wide translocation sequencing into a highly sensitive DSB end-joining assay and apply it to endogenous AID-initiated S-region DSBs in mouse B cells. We show that CSR is programmed to occur in a productive deletional orientation and does so via an unprecedented mechanism that involves in cis Igh organizational features in combination with frequent S-region DSBs initiated by AID. We further implicate ATM-dependent DSB-response factors in enforcing this mechanism and provide an explanation of why CSR is so reliant on the 53BP1 DSB-response factor.

  20. Switch recombination breakpoints are strictly correlated with DNA recognition motifs for immunoglobulin S gamma 3 DNA-binding proteins

    PubMed Central

    1992-01-01

    The deletion looping out model of switch (S) recombination predicts that the intervening DNA between switch regions will be excised as a circle. Circular excision products of immunoglobulin switch recombination have been recently isolated from lipopolysaccharide (LPS)- stimulated spleen cells. The recombination breakpoints in these large circles were found to fall within switch regions. Since switch recombination is clearly focused on switch regions, we hypothesized that some DNA-binding protein factor might be involved in specifically recognizing and facilitating the alignment of switch regions before recombination. Two DNA-binding proteins that specifically interact with two discrete regions of the S gamma 3 tandem repeat have been identified in crude and partially purified nuclear extracts derived from LPS- and dextran sulfate (DxS)-activated splenic B cells. The first factor has been found indistinguishable from NF-kappa B by mobility shift assays, methylation interference, competition binding studies, and supershift analysis using an antiserum specific for the p50 component. The second appears to be composed of two closely traveling mobilities that do not separate upon partial purification. This second complex is unique and specific for S gamma 3 by methylation interference assays and competition-binding analysis. The sites at which recombination occurs in the S gamma 3 switch region have been analyzed and found to strictly correlate with the binding sites of the S gamma 3 switch binding proteins. PMID:1500850

  1. Aging murine B cells have decreased class switch induced by anti-CD40 or BAFF

    PubMed Central

    Frasca, Daniela; Riley, Richard L.; Blomberg, Bonnie B.

    2007-01-01

    We previously demonstrated that in vitro stimulated splenic B cells from senescent mice are deficient in production of multiple class switch isotypes, class switch recombination (CSR), induction of the E2A-encoded transcription factor E47, and activation-induced cytidine deaminase (AID) which is necessary for CSR and somatic hypermutation. Both anti-CD40 as well as BAFF have been shown to be able to induce CSR. We have investigated the ability of BAFF/IL-4, as compared to anti-CD40/IL-4, to induce CSR to γ1 in splenic B cells from young and old mice. We found that anti-CD40/IL-4 is a better CSR stimulus than BAFF/IL-4 in young B cells, as measured by RT-PCR of post-switch transcripts and flow cytometry. CSR is reduced in old B cells and this is independent of the stimulus. AID and γ1PSTs are significantly reduced in old B cells stimulated with anti-CD40/IL-4, but only slightly reduced with BAFF/IL-4. BAFF receptor mRNA expression (BAFF-R, TACI, BCMA) is not affected by aging. The age-related decrease in CSR induced by anti-CD40/IL-4 is primarily associated with a decrease in E47, whereas the less affected response to BAFF/IL-4 is associated with decreases in both E47 and NF-kB. Therefore, NF-kB is not involved in the decreased response of old B cells to anti-CD40/IL-4. These differences in B cell responses to CD40/IL-4 and BAFF/IL-4 may help to explain the maintenance of TI vs TD responses in senescent mice. PMID:17067770

  2. Bach2 represses plasma cell gene regulatory network in B cells to promote antibody class switch.

    PubMed

    Muto, Akihiko; Ochiai, Kyoko; Kimura, Yoshitaka; Itoh-Nakadai, Ari; Calame, Kathryn L; Ikebe, Dai; Tashiro, Satoshi; Igarashi, Kazuhiko

    2010-12-01

    Two transcription factors, Pax5 and Blimp-1, form a gene regulatory network (GRN) with a double-negative loop, which defines either B-cell (Pax5 high) or plasma cell (Blimp-1 high) status as a binary switch. However, it is unclear how this B-cell GRN registers class switch DNA recombination (CSR), an event that takes place before the terminal differentiation to plasma cells. In the absence of Bach2 encoding a transcription factor required for CSR, mouse splenic B cells more frequently and rapidly expressed Blimp-1 and differentiated to IgM plasma cells as compared with wild-type cells. Genetic loss of Blimp-1 in Bach2(-/-) B cells was sufficient to restore CSR. These data with mathematical modelling of the GRN indicate that Bach2 achieves a time delay in Blimp-1 induction, which inhibits plasma cell differentiation and promotes CSR (Delay-Driven Diversity model for CSR). Reduction in mature B-cell numbers in Bach2(-/-) mice was not rescued by Blimp-1 ablation, indicating that Bach2 regulates B-cell differentiation and function through Blimp-1-dependent and -independent GRNs.

  3. Global gene regulation during activation of immunoglobulin class switching in human B cells

    PubMed Central

    Zhang, Youming; Fear, David J.; Willis-Owen, Saffron A. G.; Cookson, William O.; Moffatt, Miriam F.

    2016-01-01

    Immunoglobulin class switch recombination (CSR) to IgE is a tightly regulated process central to atopic disease. To profile the B-cell transcriptional responses underlying the activation of the germinal centre activities leading to the generation of IgE, naïve human B-cells were stimulated with IL-4 and anti-CD40. Gene expression and alternative splicing were profiled over 12 days using the Affymetrix Human Exon 1.0 ST Array. A total of 1,399 genes, forming 13 temporal profiles were differentially expressed. CCL22 and CCL17 were dramatically induced but followed a temporal trajectory distinct from classical mediators of isotype switching. AICDA, NFIL3, IRF4, XBP1 and BATF3 shared a profile with several genes involved in innate immunity, but with no recognised role in CSR. A transcription factor BHLHE40 was identified at the core of this profile. B-cell activation was also accompanied by variation in exon retention affecting >200 genes including CCL17. The data indicate a circadian component and central roles for the Th2 chemokines CCL22 and CCL17 in the activation of CSR. PMID:27897229

  4. Orientation-Specific Joining of AID-initiated DNA Breaks Promotes Antibody Class Switching

    PubMed Central

    Zhang, Yu; Hu, Jiazhi; Volpi, Sabrina A.; Meyers, Robin M.; Ho, Yu-Jui; Du, Zhou; Robbiani, Davide F.; Meng, Feilong; Gostissa, Monica; Nussenzweig, Michel C.; Manis, John P.; Alt, Frederick W.

    2015-01-01

    During B cell development, RAG endonuclease cleaves immunoglobulin heavy chain (IgH) V, D, and J gene segments and orchestrates their fusion as deletional events that assemble a V(D)J exon in the same transcriptional orientation as adjacent Cμ constant region exons1,2. In mice, six additional sets of constant region exons (CHs) lie 100-200 kb downstream in the same transcriptional orientation as V(D)J and Cμ exons2. Long repetitive switch (S) regions precede Cμ and downstream CHs. In mature B cells, class switch recombination (CSR) generates different antibody classes by replacing Cμ with a downstream CH2. Activation-Induced Cytidine Deaminase (AID) initiates CSR by promoting deamination lesions within Sμ and a downstream acceptor S region2,3; these lesions are converted into DNA double-strand breaks (DSBs) by general DNA repair factors3. Productive CSR must occur in a deletional orientation by joining the upstream end of an Sμ DSB to the downstream end of an acceptor S region DSB (Fig. 1a). However, the relative frequency of deletional to inversional CSR junctions had not been measured. Thus, whether orientation-specific joining is a programmed mechanistic feature of CSR as it is for V(D)J recombination and, if so, how this is achieved was unknown. To address this question, we adapted high-throughput genome-wide translocation sequencing (HTGTS)4 into a highly sensitive DSB end-joining assay and applied it to endogenous AID-initiated S region DSBs. We find that CSR indeed is programmed to occur in a productive deletional orientation and does so via an unprecedented mechanism that involves in cis IgH organizational features in combination with frequent S region DSBs initiated by AID. We further implicate ATM-dependent DSB response (DSBR) factors in enforcing this mechanism and provide a solution to the enigma of why CSR is so reliant on the 53BP1 DSBR factor. PMID:26308889

  5. English-Thai Code-Switching of Teachers in ESP Classes

    ERIC Educational Resources Information Center

    Promnath, Korawan; Tayjasanant, Chamaipak

    2016-01-01

    The term code-switching (CS) that occurs in everyday situations, or naturalistic code-switching, has been a controversial strategy regarding whether it benefits or impedes language learning. The aim of this study was to investigate CS in conversations between teachers and students of ESP classes in order to explore the types and functions of CS…

  6. CD27− B-Cells Produce Class Switched and Somatically Hyper-Mutated Antibodies during Chronic HIV-1 Infection

    PubMed Central

    Cagigi, Alberto; Du, Likun; Dang, Linh Vu Phuong; Grutzmeier, Sven; Atlas, Ann; Chiodi, Francesca

    2009-01-01

    Class switch recombination and somatic hypermutation occur in mature B-cells in response to antigen stimulation. These processes are crucial for the generation of functional antibodies. During HIV-1 infection, loss of memory B-cells, together with an altered differentiation of naïve B-cells result in production of low quality antibodies, which may be due to impaired immunoglobulin affinity maturation. In the current study, we evaluated the effect of HIV-1 infection on class switch recombination and somatic hypermutation by studying the expression of activation-induced cytidine deaminase (AID) in peripheral B-cells from a cohort of chronically HIV-1 infected patients as compared to a group of healthy controls. In parallel, we also characterized the phenotype of B-cells and their ability to produce immunoglobulins in vitro. Cells from HIV-1 infected patients showed higher baseline levels of AID expression and increased IgA production measured ex-vivo and upon CD40 and TLR9 stimulation in vitro. Moreover, the percentage of CD27−IgA+ and CD27−IgG+ B-cells in blood was significantly increased in HIV-1 infected patients as compared to controls. Interestingly, our results showed a significantly increased number of somatic hypermutations in the VH genes in CD27− cells from patients. Taken together, these results show that during HIV-1 infection, CD27− B-cells can also produce class switched and somatically hypermutated antibodies. Our data add important information for the understanding of the mechanisms underlying the loss of specific antibody production observed during HIV-1 infection. PMID:19412542

  7. Extract of Nippostrongylus brasiliensis Stimulates Polyclonal Type-2 Immunoglobulin Response by Inducing De Novo Class Switch

    PubMed Central

    Ehigiator, Humphrey N.; Stadnyk, Andrew W.; Lee, Timothy D. G.

    2000-01-01

    Infection with the nematode parasite Nippostrongylus brasiliensis induces a pronounced type-2 T-cell response that is associated with marked polyclonal immunoglobulin E (IgE) and IgG1 production in mice. To examine the differential roles of the infection and products produced by nematodes, we investigated a soluble extract of N. brasiliensis for the ability to mediate this type-2 response. We found that the extract induced a marked increase in IgE and IgG1 levels, similar to that induced by the infection. The extract did not affect the level of IgG2a in serum, showing that the effect was specific to IgE and IgG1 (type-2-associated immunoglobulin) rather than inducing a nonspecific increase in all immunoglobulin isotypes. This response was also associated with increased interleukin-4 production in vitro. These results confirm that the extract, like infection, is a strong inducer of polyclonal type-2 responses and a reliable model for investigating the regulation of nematode-induced responses. The extract induced the production of IgG1 when added to in vitro cultures of lipopolysaccharide-stimulated B cells. This provides evidence for the induction of class switch. It did not induce upregulation of IgG1 in naive (unstimulated) B cells or expand B cells in in vitro cultures. Analysis of DNA from the spleens of mice treated with the extract by digestion-circularization PCR demonstrated a marked increase in the occurrence of γ1 switch region gene recombination in the cells in vivo. These results provide strong evidence that soluble worm products are able to mediate the marked polyclonal γ1/ɛ response and that infection is not required to mediate this response. Furthermore, these data provide evidence that the soluble nematode extract induces this effect by causing de novo class switch of B cells and not by an expansion of IgG1 B cells or an increase in antibody production by IgG1 plasma cells. PMID:10948105

  8. Global finite-time stabilisation of a class of switched nonlinear systems

    NASA Astrophysics Data System (ADS)

    Liang, Ying-Jiu; Ma, Ruicheng; Wang, Min; Fu, Jun

    2015-12-01

    This paper is concerned with the global finite-time stabilisation problem for a class of switched nonlinear systems under arbitrary switchings. All subsystems of the studied switched system under consideration are in lower triangular form. Based on the adding one power integrator technique, both a class of non-Lipschitz continuous state feedback controllers and a common Lyapunov function are simultaneously constructed such that the closed-loop switched system is global finite-time stable under arbitrary switchings. In the controller design process, a common coordinate transformation of all subsystems is exploited to avoid using individual coordinate transformations for subsystems. Finally, two examples are given to show the effectiveness of the proposed method.

  9. Resolution by unassisted Top3 points to template switch recombination intermediates during DNA replication.

    PubMed

    Glineburg, M Rebecca; Chavez, Alejandro; Agrawal, Vishesh; Brill, Steven J; Johnson, F Brad

    2013-11-15

    The evolutionarily conserved Sgs1/Top3/Rmi1 (STR) complex plays vital roles in DNA replication and repair. One crucial activity of the complex is dissolution of toxic X-shaped recombination intermediates that accumulate during replication of damaged DNA. However, despite several years of study the nature of these X-shaped molecules remains debated. Here we use genetic approaches and two-dimensional gel electrophoresis of genomic DNA to show that Top3, unassisted by Sgs1 and Rmi1, has modest capacities to provide resistance to MMS and to resolve recombination-dependent X-shaped molecules. The X-shaped molecules have structural properties consistent with hemicatenane-related template switch recombination intermediates (Rec-Xs) but not Holliday junction (HJ) intermediates. Consistent with these findings, we demonstrate that purified Top3 can resolve a synthetic Rec-X but not a synthetic double HJ in vitro. We also find that unassisted Top3 does not affect crossing over during double strand break repair, which is known to involve double HJ intermediates, confirming that unassisted Top3 activities are restricted to substrates that are distinct from HJs. These data help illuminate the nature of the X-shaped molecules that accumulate during replication of damaged DNA templates, and also clarify the roles played by Top3 and the STR complex as a whole during the resolution of replication-associated recombination intermediates.

  10. Investigation of a hybrid optical-electronic switch supporting different service classes

    NASA Astrophysics Data System (ADS)

    Samoud, Wiem; Ware, Cédric; Lourdiane, Mounia

    2014-09-01

    Optical fiber is considered the most competitive wired transmission support thanks to its low attenuation, wide optical bandwidth, long reach, and low cost. However, optics do not yet perform higher functionalities such as switching. In fact, all-optical switches face a contention issue, due to the lack of practical optical buffers. Thus, the switching function is still performed electronically, which requires energetically costly optical-to-electronic conversions. The energy consumption is a critical issue within the growing data traffic. Thus, a proposition of hybrid switch architecture supplementing optical switch with an electronic buffer. In this paper, we propose to investigate the performance of hybrid switch that supports different priority classes where the priority is defined in terms of Packet Loss Ratio (PLR). We show that the hybrid switch is a good trade off since it allows significant performance improvements towards a buffer-less all optical switch in terms of PLR and sustainable load, for relatively few electronic ports of the buffer, which would reduce energy consumption compared to an electronic switch.

  11. Output-feedback stabilisation for a class of switched nonlinear systems with unknown control coefficients

    NASA Astrophysics Data System (ADS)

    Long, Lijun; Zhao, Jun

    2013-03-01

    This article investigates the problem of global stabilisation for a class of switched nonlinear systems with unknown control coefficients by output feedback. Full state measurements are unavailable. We first show that via a coordinate transformation, the unknown control coefficients are lumped together and the original switched nonlinear system is transformed into a new switched nonlinear system for which control design becomes feasible. Second, for the new switched nonlinear system, based on backstepping, we design output-feedback controllers for subsystems and construct a common Lyapunov function, which rely on the designed state observer, to guarantee asymptotic stability of the closed-loop system under arbitrary switchings. Finally, as an application of the proposed design method, global stabilisation of a mass-spring-damper system is achieved by output feedback.

  12. Chromatin reader Brd4 functions in Ig class switching as a repair complex adaptor of nonhomologous end-joining.

    PubMed

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

    2014-07-03

    Class switch recombination (CSR) is a B cell-specific genomic alteration induced by activation-induced cytidine deaminase (AID)-dependent DNA break at the immunoglobulin heavy-chain locus, followed by repair. Although chromatin-associated factors in promoting AID-induced DNA break have been widely reported, the involvement of chromatin adaptors at the repair phase of CSR remains unknown. Here, we show that the acetylated histone reader Brd4 is critical for nonhomologous end-joining (NHEJ) repair of AID- and I-SceI-induced DNA breaks. Brd4 was recruited to the DNA break regions, and its depletion from the chromatin caused CSR impairment without affecting the DNA break generation. Inhibition of Brd4 suppressed the accumulation of 53BP1 and uracil DNA glycosylase at the switch regions, perturbed the switch junctional microhomology, and reduced Igh/c-myc translocation. We conclude that Brd4 serves as a chromatin platform required for the recruitment of repair components during CSR and general DNA damage. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Linkage relationships in the bovine MHC region. High recombination frequency between class II subregions.

    PubMed

    Andersson, L; Lundén, A; Sigurdardottir, S; Davies, C J; Rask, L

    1988-01-01

    Class II genes of the bovine major histocompatibility complex (MHC) have been investigated by Southern blot analysis using human DNA probes. Previous studies revealed the presence of bovine DO beta, DQ alpha, DQ beta, DR alpha, and DR beta genes, and restriction fragment length polymorphisms for each of these genes were documented. In the present study, the presence of three additional class II genes, designated DZ alpha, DY alpha, and DY beta, are reported. DZ alpha was assumed to correspond to the human DZ alpha gene while the other two were designated DY because their relationship to human class II genes could not be firmly established. The linkage relationships among bovine class II genes and two additional loci, TCP1B and C4, were investigated by family segregation analysis and analysis of linkage disequilibrium. The results clearly indicated that all these loci belong to the same linkage group. This linkage group is divided into two subregions separated by a fairly high recombination frequency. One region includes the C4, DQ alpha, DQ beta, DR alpha, and DR beta loci and the other one is composed of the DO beta, DY alpha, DY beta, and TCP1B loci. No recombinant was observed within any of these subregions and there was a strong or fairly strong linkage disequilibrium between loci within groups. In contrast, as many as five recombinants among three different families were detected in the interval between these subregions giving a recombination frequency estimate of 0.17 +/- 0.07. The fairly high recombination frequency observed between class II genes in cattle is strikingly different from the corresponding recombination estimates in man and mouse. The finding implies either a much larger molecular distance between some of the bovine class II genes or alternatively the presence of a recombinational "hot spot" in the bovine class II region.

  14. Two classes of ODE models with switch-like behavior

    PubMed Central

    Just, Winfried; Korb, Mason; Elbert, Ben; Young, Todd

    2013-01-01

    In cases where the same real-world system can be modeled both by an ODE system ⅅ and a Boolean system 𝔹, it is of interest to identify conditions under which the two systems will be consistent, that is, will make qualitatively equivalent predictions. In this note we introduce two broad classes of relatively simple models that provide a convenient framework for studying such questions. In contrast to the widely known class of Glass networks, the right-hand sides of our ODEs are Lipschitz-continuous. We prove that if 𝔹 has certain structures, consistency between ⅅ and 𝔹 is implied by sufficient separation of time scales in one class of our models. Namely, if the trajectories of 𝔹 are “one-stepping” then we prove a strong form of consistency and if 𝔹 has a certain monotonicity property then there is a weaker consistency between ⅅ and 𝔹. These results appear to point to more general structure properties that favor consistency between ODE and Boolean models. PMID:24244061

  15. CD11b regulates antibody class switching via induction of AID.

    PubMed

    Park, Seohyun; Sim, Hyunsub; Kim, Hye-In; Jeong, Daecheol; Wu, Guang; Cho, Soo Young; Lee, Young Seek; Kwon, Hyung-Joo; Lee, Keunwook

    2017-07-01

    The integrin CD11b, which is encoded by the integrin subunit alpha M (ITGAM), is primarily expressed on the surface of innate immune cells. Genetic variations in ITGAM are among the strongest risk factors for systemic lupus erythematosus, an autoimmune disease characterized by the presence of autoantibodies. However, the regulatory function of CD11b in the antibody responses remains unclear. Here, we report the induction of CD11b in activated B2 B cells and define its unexpected role in immunoglobulin heavy chain class switch recombination (CSR). LPS-activated B cells lacking CD11b yielded fewer IgG subtypes such as IgG1 and IgG2a in vitro, and immunization-dependent CSR and affinity maturation of antibodies were severely impaired in CD11b-deficient mice. Notably, we observed the reduced expression of activation-induced cytidine deaminase (AID), an enzyme that initiates CSR and somatic hypermutation, and ectopic expression of AID was sufficient to rescue the defective CSR of CD11b-deficient B cells. LPS-induced phosphorylation of NF-κB p65 and IκBα was attenuated in CD11b-deficient B cells, and hyperactivation of IκB kinase 2 restored the defective AID expression and CSR, which implied that CD11b regulates the NF-κB-dependent induction of AID. Overall, our experimental evidence emphasized the function of CD11b in antibody responses and the role of CD11b as a vital regulator of CSR. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Capsular Switching and Other Large-Scale Recombination Events in Invasive Sequence Type 1 Group B Streptococcus

    PubMed Central

    Neemuchwala, Alefiya; Teatero, Sarah; Athey, Taryn B.T.; McGeer, Allison

    2016-01-01

    We report several cases of recombination events leading to capsular switching among sequence type (ST) 1 group B Streptococcus strains. These strains otherwise shared a common genome backbone with serotype V ST1 strains. However, the genomes of ST1 serotype V strains and those of serotypes VI, VII, and VIII strains differed substantially. PMID:27767925

  17. Observer-based H∞ resilient control for a class of switched LPV systems and its application

    NASA Astrophysics Data System (ADS)

    Yang, Dong; Zhao, Jun

    2016-11-01

    This paper deals with the issue of observer-based H∞ resilient control for a class of switched linear parameter-varying (LPV) systems by utilising a multiple parameter-dependent Lyapunov functions method. First, attention is focused upon the design of a resilient observer, an observer-based resilient controller and a parameter and estimate state-dependent switching signal, which can stabilise and achieve the disturbance attenuation for the given systems. Then, a solvability condition of the H∞ resilient control problem is given in terms of matrix inequality for the switched LPV systems. This condition allows the H∞ resilient control problem for each individual subsystem to be unsolvable. The observer, controller, and switching signal are explicitly computed by solving linear matrix inequalities (LMIs). Finally, the effectiveness of the proposed control scheme is illustrated by its application to a turbofan engine, which can hardly be handled by the existing approaches.

  18. Decentralised adaptive control for a class of stochastic switched interconnected nonlinear systems

    NASA Astrophysics Data System (ADS)

    Hua, Changchun; Liu, Guopin; Bai, Zhenhua; Guan, Xinping

    2016-12-01

    In this paper, we focus on the problem of adaptive stabilisation for a class of interconnected uncertain switched stochastic nonlinear systems. Classical adaptive and backstepping technique are employed for control synthesis. Instead of estimating the switching parameters directly, we design the adaptive controller based on the estimations of bounds on switching time-varying parameters. A smooth function is introduced to deal with the difficulties caused by unknown interactions and tuning function approach is used to circumvent the overparameter problem. It is shown that under the action of the proposed controller all the signals of the overall closed-loop systems are globally uniformly bounded in probability under arbitrary switching. Simulation results are presented to illustrate the effectiveness of the proposed approach.

  19. Whole-class interactions and code-switching in secondary mathematics teaching in Mauritius

    NASA Astrophysics Data System (ADS)

    Salehmohamed, Asifa; Rowland, Tim

    2014-09-01

    This paper reports a study of whole-class interactions in mathematics classrooms in a girls' secondary school in Mauritius. It focuses on three teachers and their instructional language practices. Analysis of audio-recordings of lessons showed that code-switching was commonly practised by all the teachers in the study. The teachers' comments on their use of language within the classroom show that although they are aware of the languages they use, they are not always conscious of their code-switching. Different functions of the teachers' code-switching practices were identified, indicating it can be an important support for learning mathematics, despite some related tensions that teachers face in using code-switch in their teaching. The paper concludes with some implications for national policy and for teacher education.

  20. Adaptive fuzzy backstepping control for a class of switched nonlinear systems with actuator faults

    NASA Astrophysics Data System (ADS)

    Hou, Yingxue; Tong, Shaocheng; Li, Yongming

    2016-11-01

    This paper investigates the problem of fault-tolerant control (FTC) for a class of switched nonlinear systems. These systems are under arbitrary switchings and are subject to both lock-in-place and loss-of-effectiveness actuator faults. In the control design, fuzzy logic systems are used to identify the unknown switched nonlinear systems. Under the framework of the backstepping control design, FTC, fuzzy adaptive control and common Lyapunov function stability theory, an adaptive fuzzy control approach is developed. It is proved that the proposed control approach can guarantee that all the signals in the closed-loop switched system are semi-globally uniformly ultimately bounded (SGUUB) and the tracking error remains an adjustable neighbourhood of the origin. Two simulation examples are provided to illustrate the effectiveness of the proposed approach.

  1. Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE.

    PubMed

    Wu, Yee Ling; Stubbington, Michael J T; Daly, Maria; Teichmann, Sarah A; Rada, Cristina

    2017-01-01

    Noncoding transcripts originating upstream of the immunoglobulin constant region (I transcripts) are required to direct activation-induced deaminase to initiate class switching in B cells. Differential regulation of Iε and Iγ1 transcription in response to interleukin 4 (IL-4), hence class switching to IgE and IgG1, is not fully understood. In this study, we combine novel mouse reporters and single-cell RNA sequencing to reveal the heterogeneity in IL-4-induced I transcription. We identify an early population of cells expressing Iε but not Iγ1 and demonstrate that early Iε transcription leads to switching to IgE and occurs at lower activation levels than Iγ1. Our results reveal how probabilistic transcription with a lower activation threshold for Iε directs the early choice of IgE versus IgG1, a key physiological response against parasitic infestations and a mediator of allergy and asthma. © 2017 Wu et al.

  2. Characterization of the Class 3 Integron and the Site-Specific Recombination System It Determines

    PubMed Central

    Collis, Christina M.; Kim, Mi-Jurng; Partridge, Sally R.; Stokes, H. W.; Hall, Ruth M.

    2002-01-01

    Integrons capture gene cassettes by using a site-specific recombination mechanism. As only one class of integron and integron-determined site-specific recombination system has been studied in detail, the properties of a second class, the only known class 3 integron, were examined. The configuration of the three potentially definitive features of integrons, the intI3 gene, the adjacent attI3 recombination site, and the Pc promoter that directs transcription of the cassettes, was similar to that found in the corresponding region (5′ conserved segment) of class 1 integrons. The integron features are flanked by a copy of the terminal inverted repeat, IRi, from class 1 integrons on one side and a resolvase-encoding tniR gene on the other, suggesting that they are part of a transposable element related to Tn402 but with the integron module in the opposite orientation. The IntI3 integrase was active and able to recognize and recombine both known types of IntI-specific recombination sites, the attI3 site in the integron, and different cassette-associated 59-be (59-base element) sites. Both integration of circularized cassettes into the attI3 site and excision of integrated cassettes were also catalyzed by IntI3. The attI3 site was localized to a short region adjacent to the intI3 gene. Recombination between a 59-be and secondary sites was also catalyzed by IntI3, but at frequencies significantly lower than observed with IntI1, the class 1 integron integrase. PMID:12003943

  3. mTOR kinase inhibitors promote antibody class switching via mTORC2 inhibition.

    PubMed

    Limon, Jose J; So, Lomon; Jellbauer, Stefan; Chiu, Honyin; Corado, Juana; Sykes, Stephen M; Raffatellu, Manuela; Fruman, David A

    2014-11-25

    The mammalian target of rapamycin (mTOR) is a kinase that functions in two distinct complexes, mTORC1 and mTORC2. In peripheral B cells, complete deletion of mTOR suppresses germinal center B-cell responses, including class switching and somatic hypermutation. The allosteric mTORC1 inhibitor rapamycin blocks proliferation and differentiation, but lower doses can promote protective IgM responses. To elucidate the complexity of mTOR signaling in B cells further, we used ATP-competitive mTOR kinase inhibitors (TOR-KIs), which inhibit both mTORC1 and mTORC2. Although TOR-KIs are in clinical development for cancer, their effects on mature lymphocytes are largely unknown. We show that high concentrations of TOR-KIs suppress B-cell proliferation and differentiation, yet lower concentrations that preserve proliferation increase the fraction of B cells undergoing class switching in vitro. Transient treatment of mice with the TOR-KI compound AZD8055 increased titers of class-switched high-affinity antibodies to a hapten-protein conjugate. Mechanistic investigation identified opposing roles for mTORC1 and mTORC2 in B-cell differentiation and showed that TOR-KIs enhance class switching in a manner dependent on forkhead box, subgroup O (FoxO) transcription factors. These observations emphasize the distinct actions of TOR-KIs compared with rapamycin and suggest that TOR-KIs might be useful to enhance production of class-switched antibodies following vaccination.

  4. Evolution by selection, recombination, and gene duplication in MHC class I genes of two Rhacophoridae species

    PubMed Central

    2013-01-01

    Background Comparison of major histocompatibility complex (MHC) genes across vertebrate species can reveal molecular mechanisms underlying the evolution of adaptive immunity-related proteins. As the first terrestrial tetrapods, amphibians deserve special attention because of their exposure to probably increased spectrum of microorganisms compared with ancestral aquatic fishes. Knowledge regarding the evolutionary patterns and mechanisms associated with amphibian MHC genes remains limited. The goal of the present study was to isolate MHC class I genes from two Rhacophoridae species (Rhacophorus omeimontis and Polypedates megacephalus) and examine their evolution. Results We identified 27 MHC class I alleles spanning the region from exon 2 to 4 in 38 tree frogs. The available evidence suggests that these 27 sequences all belong to classical MHC class I (MHC Ia) genes. Although several anuran species only display one MHC class Ia locus, at least two or three loci were observed in P. megacephalus and R. omeimontis, indicating that the number of MHC class Ia loci varies among anuran species. Recombination events, which mainly involve the entire exons, played an important role in shaping the genetic diversity of the 27 MHC class Ia alleles. In addition, signals of positive selection were found in Rhacophoridae MHC class Ia genes. Amino acid sites strongly suggested by program to be under positive selection basically accorded with the putative antigen binding sites deduced from crystal structure of human HLA. Phylogenetic relationships among MHC class I alleles revealed the presence of trans-species polymorphisms. Conclusions In the two Rhacophoridae species (1) there are two or three MHC class Ia loci; (2) recombination mainly occurs between the entire exons of MHC class Ia genes; (3) balancing selection, gene duplication and recombination all contribute to the diversity of MHC class Ia genes. These findings broaden our knowledge on the evolution of amphibian MHC systems

  5. IgD class switching is initiated by microbiota and limited to mucosa-associated lymphoid tissue in mice.

    PubMed

    Choi, Jin Huk; Wang, Kuan-Wen; Zhang, Duanwu; Zhan, Xiaowei; Wang, Tao; Bu, Chun-Hui; Behrendt, Cassie L; Zeng, Ming; Wang, Ying; Misawa, Takuma; Li, Xiaohong; Tang, Miao; Zhan, Xiaoming; Scott, Lindsay; Hildebrand, Sara; Murray, Anne R; Moresco, Eva Marie Y; Hooper, Lora V; Beutler, Bruce

    2017-02-14

    Class-switch recombination (CSR) alters the Ig isotype to diversify antibody effector functions. IgD CSR is a rare event, and its regulation is poorly understood. We report that deficiency of 53BP1, a DNA damage-response protein, caused age-dependent overproduction of secreted IgD resulting from increased IgD CSR exclusively within B cells of mucosa-associated lymphoid tissues. IgD overproduction was dependent on activation-induced cytidine deaminase, hematopoietic MyD88 expression, and an intact microbiome, against which circulating IgD, but not IgM, was reactive. IgD CSR occurred via both alternative nonhomologous end-joining and homologous recombination pathways. Microbiota-dependent IgD CSR also was detected in nasal-associated lymphoid tissue of WT mice. These results identify a pathway, present in WT mice and hyperactivated in 53BP1-deficient mice, by which microbiota signal via Toll-like receptors to elicit IgD CSR.

  6. Looping out and deletion mechanism for the immunoglobulin heavy-chain class switch.

    PubMed Central

    Jäck, H M; McDowell, M; Steinberg, C M; Wabl, M

    1988-01-01

    In the mouse pre-B-cell line 18-81, cells can switch production in vitro from immunoglobulin mu chain to gamma 2b chain. The gene encoding the gamma 2b chain is created by a rearrangement of the mu gene. This rearrangement always takes place within a homolog. In cells with a gamma 2b gene, most of the time the gene segment encoding the constant region of the mu chain is deleted, but often the rearrangement leads to cells that produce no immunoglobulin, and all DNA sequences are retained. The latter result is due to an inversion. Inversions exclude the unequal sister chromatid exchange model of the heavy-chain class switch. Looping out is an intermediate step in the process of generating an inversion. Our findings demonstrate that the switch rearrangement occurs by looping out and deletion. Images PMID:2830623

  7. Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation

    PubMed Central

    Günal-Sadık, Gamze; Paszkowski-Rogacz, Maciej; Singaravelu, Kalaimathy; Beyer, Andreas; Buchholz, Frank; Jessberger, Rolf

    2014-01-01

    The immunoglobulin heavy chain locus (Igh) features higher-order chromosomal interactions to facilitate stage-specific assembly of the Ig molecule. Cohesin, a ring-like protein complex required for sister chromatid cohesion, shapes chromosome architecture and chromatin interactions important for transcriptional regulation and often acts together with CTCF. Cohesin is likely involved in B cell activation and Ig class switch recombination. Hence, binding profiles of cohesin in resting mature murine splenic B lymphocytes and at two stages after cell activation were elucidated by chromatin immunoprecipitation and deep sequencing. Comparative genomic analysis revealed cohesin extensively changes its binding to transcriptional control elements after 48 h of stimulation with LPS/IL-4. Cohesin was clearly underrepresented at switch regions regardless of their activation status, suggesting that switch regions need to be cohesin-poor. Specific binding changes of cohesin at B-cell specific gene loci Pax5 and Blimp-1 indicate new cohesin-dependent regulatory pathways. Together with conserved cohesin/CTCF sites at the Igh 3′RR, a prominent cohesin/CTCF binding site was revealed near the 3′ end of Cα where PolII localizes to 3′ enhancers. Our study shows that cohesin likely regulates B cell activation and maturation, including Ig class switching. PMID:25375358

  8. Bounds and invariant sets for a class of discrete-time switching systems with perturbations

    NASA Astrophysics Data System (ADS)

    Haimovich, H.; Seron, M. M.

    2014-02-01

    We present a novel method to compute componentwise ultimate bounds and invariant regions for a class of switching discrete-time linear systems with perturbation bounds that may depend nonlinearly on a delayed state. The method has the important advantage that it allows each component of the perturbation vector to have an independent bound and that the bounds and sets obtained are also given componentwise. This componentwise method does not employ a standard norm for bounding either the perturbation or state vectors, and thus may avoid conservativeness due to different perturbation or state vector components having substantially different bounds. We also establish the relationship between the class of switching linear systems to which the proposed method can be applied and those that admit a common quadratic Lyapunov function. We illustrate the application of our method via numerical examples, including the fault tolerance analysis of the feedback control of a winding machine.

  9. swi6, a gene required for mating-type switching, prohibits meiotic recombination in the mat2-mat3 "cold spot" of fission yeast.

    PubMed

    Klar, A J; Bonaduce, M J

    1991-12-01

    Mitotic interconversion of the mating-type locus (mat1) of the fission yeast Schizosaccharomyces pombe is initiated by a double-strand break at mat1. The mat2 and mat3 loci act as nonrandom donors of genetic information for mat1 switching such that switches occur primarily (or only) to the opposite mat1 allele. Location of the mat1 "hot spot" for transposition should be contrasted with the "cold spot" of meiotic recombination located within the adjoining mat2-mat3 interval. That is, meiotic interchromosomal recombination in mat2, mat3 and the intervening 15-kilobase region does not occur at all. swi2 and swi6 switching-deficient mutants possess the normal level of double-strand break at mat1, yet they fail to switch efficiently. By testing for meiotic recombination in the cold spot, we found the usual lack of recombination in a swi2 mutant but a significant level of recombination in a swi6 mutant. Therefore, the swi6 gene function is required to keep the donor loci inert for interchromosomal recombination. This finding, combined with the additional result that switching primarily occurs intrachromosomally, suggests that the donor loci are made accessible for switching by folding them onto mat1, thus causing the cold spot of recombination.

  10. Swi6, a Gene Required for Mating-Type Switching, Prohibits Meiotic Recombination in the Mat2-Mat3 ``cold Spot'' of Fission Yeast

    PubMed Central

    Klar, AJS.; Bonaduce, M. J.

    1991-01-01

    Mitotic interconversion of the mating-type locus (mat1) of the fission yeast Schizosaccharomyces pombe is initiated by a double-strand break at mat1. The mat2 and mat3 loci act as nonrandom donors of genetic information for mat1 switching such that switches occur primarily (or only) to the opposite mat1 allele. Location of the mat1 ``hot spot'' for transposition should be contrasted with the ``cold spot'' of meiotic recombination located within the adjoining mat2-mat3 interval. That is, meiotic interchromosomal recombination in mat2, mat3 and the intervening 15-kilobase region does not occur at all. swi2 and swi6 switching-deficient mutants possess the normal level of double-strand break at mat1, yet they fail to switch efficiently. By testing for meiotic recombination in the cold spot, we found the usual lack of recombination in a swi2 mutant but a significant level of recombination in a swi6 mutant. Therefore, the swi6 gene function is required to keep the donor loci inert for interchromosomal recombination. This finding, combined with the additional result that switching primarily occurs intrachromosomally, suggests that the donor loci are made accessible for switching by folding them onto mat1, thus causing the cold spot of recombination. PMID:1783290

  11. Light chain-deficient mice produce novel multimeric heavy-chain-only IgA by faulty class switching.

    PubMed

    Matheson, Louise S; Osborn, Michael J; Smith, Jennifer A; Corcos, Daniel; Hamon, Maureen; Chaouaf, Rima; Coadwell, John; Morgan, Geoff; Oxley, David; Brüggemann, Marianne

    2009-08-01

    Recently, we identified that diverse heavy chain (H-chain)-only IgG is spontaneously produced in light chain (L-chain)-deficient mice (L(-/-) with silenced kappa and lambda loci) despite a block in B cell development. In murine H-chain IgG, the first Cgamma exon, C(H)1, is removed after DNA rearrangement and secreted polypeptides are comparable with camelid-type H-chain IgG. Here we show that L(-/-) mice generate a novel class of H-chain Ig with covalently linked alpha chains, not identified in any other healthy mammal. Surprisingly, diverse H-chain-only IgA can be released from B cells at levels similar to conventional IgA and is found in serum and sometimes in milk and saliva. Surface IgA without L-chain is expressed in B220(+) spleen cells, which exhibited a novel B cell receptor, suggesting that associated conventional differentiation events occur. To facilitate the cellular transport and release of H-chain-only IgA, chaperoning via BiP association seems to be prevented as only alpha chains lacking C(H)1 are released from the cell. This appears to be accomplished by imprecise class-switch recombination (CSR) from Smu into the alpha constant region, which removes all or part of the Calpha1 exon at the genomic level.

  12. The switching gene swi6 affects recombination and gene expression in the mating-type region of Schizosaccharomyces pombe.

    PubMed

    Lorentz, A; Heim, L; Schmidt, H

    1992-06-01

    The products of 11 switching (swi) genes are required for efficient mating-type (MT) switching in homothallic (h90) strains of Schizosaccharomyces pombe. The MT region of h90 comprises three cassette genes: the expression site mat1:1 and two silent loci, mat2:2 and mat3:3. Besides reducing MT switching, the swi6 mutation leads to deletions in the MT region caused by intrachromosomal cross-overs between two paired cassettes. These deletions only arise if DNA double-strand breaks are present at mat1:1, which initiate MT switching. Furthermore, swi6 allows meiotic recombination in the K region, a region of 16 kb between mat2:2 and mat3:3; in wild-type strains no recombination occurs in K. swi6 also allows the simultaneous expression of two different cassettes in the same haploid cell. Thus swi6 may have an influence on the general chromatin structure in the MT region.

  13. Efficiency of Recombination Reactions Catalyzed by Class 1 Integron Integrase IntI1

    PubMed Central

    Collis, Christina M.; Recchia, Gavin D.; Kim, Mi-Jurng; Stokes, H. W.; Hall, Ruth M.

    2001-01-01

    The class 1 integron integrase, IntI1, recognizes two distinct types of recombination sites, attI sites, found in integrons, and members of the 59-be family, found in gene cassettes. The efficiencies of the integrative version of the three possible reactions, i.e., between two 59-be, between attI1 and a 59-be, or between two attI1 sites, were compared. Recombination events involving two attI1 sites were significantly less efficient than the reactions in which a 59-be participated, and the attI1 × 59-be reaction was generally preferred over the 59-be × 59-be reaction. Recombination of attI1 with secondary sites was less efficient than the 59-be × secondary site reaction. PMID:11274113

  14. Polymorphism, recombination, and linkage disequilibrium within the HLA class II region

    SciTech Connect

    Begovich, A.B.; McClure, G.R.; Suraj, V.C.; Helmuth, R.C.; Fildes, N.; Bugawan, T.L.; Erlich, H.A. ); Klitz, W. )

    1992-01-01

    Thirty-nine CEPH families, comprised of 502 individuals, have been typed for the HLA class II genes DRB1, DQA1, DQB1, and DPB1 using nonradioactive sequence-specific oligonucleotide probes to analyze polymerase chain reaction amplified DNA. This population, which consists of 266 independent chromosomes, contains 27 DRB1, 7 DQA1, 12 DQB1, and 17 DPB1 alleles. Analysis of the distribution of allele frequencies using the homozygosity statistic, which gives an indication of past selection pressures, suggests that balancing selection has acted on the DRB1, DQA1, and DQB1 loci. The distribution of DPB1 alleles, however, suggests a different evolutionary past. Family data permits the estimation of recombination rates and the unambiguous assignment of haplotypes. No recombinants were found between DRB1, DQA1, and DQB1; however, recombinants were detected between DQB1 and DPB1, resulting in an estimated recombination fraction of [ge]0.008 [+-] 0.004. Only 33 distinct DRB1-DQA1-DQB1 haplotypes were found in this population which illustrates the extreme nonrandom haplotypic association of alleles at these loci. A few of these haplotypes are unusual (previously unreported) for a Caucasian population and most likely result from past recombination events between the DR and DQ subregions. Examination of disequilibrium across the HLA region using these data and the available serologic HLA-A and HLA-B types of these samples shows that global disequilibrium between these loci declines with the recombination fraction, approaching statistic nonsignificance at the most distant interval, HLA-A and HLA-DP. DR-DQ haplotypes in linkage disequilibrium with DPB1 and B are noted and, finally, the evolutionary origin of certain class II haplotypes is addressed. 63 refs., 3 figs., 8 tabs.

  15. Disodium cromoglycate inhibits S mu-->S epsilon deletional switch recombination and IgE synthesis in human B cells

    PubMed Central

    1994-01-01

    IgE synthesis requires interleukin 4 (IL-4) and a T-B cell interaction that involves the B cell antigen CD40 and its ligand expressed on activated T cells. IL-4 induces epsilon germline transcription whereas ligation of CD40 results in deletional S mu-->S epsilon switch recombination, expression of mature epsilon transcripts, and IgE synthesis and secretion. We demonstrate that disodium cromoglycate (DSCG), a drug commonly used for the prophylactic treatment of allergic disease, inhibits T cell-driven IgE synthesis by human B cells at concentrations readily achievable in the course of inhaled therapy for asthma. Inhibition of IgE synthesis by DSCG was not the result of drug toxicity because DSCG did not affect the viability of T and B cells or their proliferation to mitogens. DSCG did not interfere with CD40 ligand expression by T cells but clearly targeted the B cells because it inhibited IgE synthesis induced by anti-CD40 and IL-4 in populations of highly purified B cells. DSCG had no effect on the induction of epsilon germline transcripts by IL-4 but strongly inhibited CD40 mediated S mu-->S epsilon deletional switch recombination in IL-4- treated B cells as assayed by nested primer PCR. The effect of DSCG was not specific for CD40-mediated induction of IgE isotype switching because DSCG inhibited IgE synthesis as well as S mu-->S epsilon deletional switch recombination induced by hydrocortisone and IL-4 in B cells. Moreover, the effect of DSCG was not specific for IgE isotype switching because DSCG inhibited the synthesis of IgG4 by B cells sorted for lack of surface expression of IgG4 and stimulated with anti- CD40 and IL-4. DSCG caused only minimal inhibition (< 15%) of spontaneous IgE synthesis by lymphocytes from patients with the hyper- IgE syndrome and did not affect pokeweed mitogen-induced IgG and IgA synthesis by lymphocytes suggesting that it has little effect on B cells that have already undergone isotype switching. These results indicate that DSCG

  16. Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region.

    PubMed

    Kauppi, Liisa; Sajantila, Antti; Jeffreys, Alec J

    2003-01-01

    Recombination, demographic history, drift and selection influence the extent of linkage disequilibrium (LD) in the human genome, but their relative contributions remain unclear. To investigate the effect of meiotic recombination versus population history on LD, three populations with different demographic histories (UK north Europeans, Saami and Zimbabweans) were genotyped for high-frequency single-nucleotide polymorphisms (SNPs) across a 75 kb DNA segment of the MHC class II region. This region spans three well-characterized recombination hotspots and a 60 kb long LD block. Despite a high level of underlying haplotype diversity and considerable divergence in haplotype composition between populations, all three populations showed very similar patterns of LD. Surprisingly, the entire 60 kb LD block was present even in Africans, although it was relatively difficult to detect owing to a systematic deficiency of high frequency SNPs. In contrast, DNA within recombination hotspots did not show this low nucleotide diversity in Africans. Thus, while population history has some influence on LD, our findings suggest that recombination hotspots play a major global role in shaping LD patterns as well as helping to maintain localized SNP diversity in this region of the MHC.

  17. Design of sliding mode control for a class of uncertain switched systems

    NASA Astrophysics Data System (ADS)

    Liu, Yonghui; Jia, Tinggang; Niu, Yugang; Zou, Yuanyuan

    2015-04-01

    This paper considers the problem of sliding mode control for a class of uncertain switched systems with parameter uncertainties and external disturbances. A key feature of the controlled system is that each subsystem is not required to share the same input channel, which was usually assumed in some existing works. By means of a weighted sum of the input matrix, a common sliding surface is designed in this work. It is shown that the reachability of the sliding surface can be ensured by the present sliding mode controller. Moreover, the sliding motion on the specified sliding surface is asymptotically stable under the proposed switching signal dependent on the state and time. Additionally, the above results are further extended to the case that the system states are unavailable. Both the sliding surface and sliding mode controller are designed by utilising state-observer. Finally, numerical simulation examples are given to illustrate the effectiveness of the present method.

  18. A class-based scheduling algorithm with high throughput for optical burst switching networks

    NASA Astrophysics Data System (ADS)

    Wu, Guiling; Chen, Jianping; Li, Xinwan; Wang, Hui

    2005-02-01

    Optical burst switching (OBS) is more efficient and feasible solution to build terabit IP-over-WDM optical network by employing relatively matured photonic and opto-electronic devices and combining the advantage of high bandwidth of optical transmission/switching and high flexibility of electronic control/processing. Channel scheduling algorithm is one of the key issues related to OBS networks. In this paper, a class-based scheduling algorithm is presented with emphasis on fairly utilizing the bandwidth among different services. A maximum reserved channel numbers and a maximum channel search times is introduced for each service based on its class of services, load and available bandwidth resource in the class-based scheduling algorithm. The performance of the scheduling algorithm is studied in detail by simulation. The results show that the scheduling algorithm can allocate the bandwidth more fairly among different services and the total burst loss ratio under high throughput can be lowered with acceptable expense on delay performance of services with lower delay requirement. Problems related with burst loss ratio and the delay requirement of different services can be well solved simultaneously.

  19. Increased levels of (class switched) memory B cells in peripheral blood of current smokers.

    PubMed

    Brandsma, Corry-Anke; Hylkema, Machteld N; Geerlings, Marie; van Geffen, Wouter H; Postma, Dirkje S; Timens, Wim; Kerstjens, Huib A M

    2009-11-12

    There is increasing evidence that a specific immune response contributes to the pathogenesis of COPD. B-cell follicles are present in lung tissue and increased anti-elastin titers have been found in plasma of COPD patients. Additionally, regulatory T cells (Tregs) have been implicated in its pathogenesis as they control immunological reactions. We hypothesize that the specific immune response in COPD is smoke induced, either by a direct effect of smoking or as a result of smoke-induced lung tissue destruction (i.e. formation of neo-epitopes or auto antigens). Furthermore, we propose that Tregs are involved in the suppression of this smoke-induced specific immune response.The presence of B cells, memory B cells and Tregs was assessed by flow cytometry in peripheral blood of 20 COPD patients and 29 healthy individuals and related to their current smoking status.COPD patients had lower (memory) B-cell percentages and higher Treg percentages in peripheral blood than healthy individuals, with a significant negative correlation between these cells. Interestingly, current smokers had higher percentages of (class-switched) memory B cells than ex-smokers and never smokers, irrespective of COPD.This increase in (class-switched) memory B cells in current smokers is intriguing and suggests that smoke-induced neo-antigens may be constantly induced in the lung. The negative correlation between B cells and Tregs in blood is in line with previously published observations that Tregs can suppress B cells. Future studies focusing on the presence of these (class switched) memory B cells in the lung, their antigen specificity and their interaction with Tregs are necessary to further elucidate the specific B-cell response in COPD.

  20. IgH class switching exploits a general property of two DNA breaks to be joined in cis over long chromosomal distances.

    PubMed

    Gostissa, Monica; Schwer, Bjoern; Chang, Amelia; Dong, Junchao; Meyers, Robin M; Marecki, Gregory T; Choi, Vivian W; Chiarle, Roberto; Zarrin, Ali A; Alt, Frederick W

    2014-02-18

    Antibody class switch recombination (CSR) in B lymphocytes joins two DNA double-strand breaks (DSBs) lying 100-200 kb apart within switch (S) regions in the immunoglobulin heavy-chain locus (IgH). CSR-activated B lymphocytes generate multiple S-region DSBs in the donor Sμ and in a downstream acceptor S region, with a DSB in Sμ being joined to a DSB in the acceptor S region at sufficient frequency to drive CSR in a large fraction of activated B cells. Such frequent joining of widely separated CSR DSBs could be promoted by IgH-specific or B-cell-specific processes or by general aspects of chromosome architecture and DSB repair. Previously, we found that B cells with two yeast I-SceI endonuclease targets in place of Sγ1 undergo I-SceI-dependent class switching from IgM to IgG1 at 5-10% of normal levels. Now, we report that B cells in which Sγ1 is replaced with a 28 I-SceI target array, designed to increase I-SceI DSB frequency, undergo I-SceI-dependent class switching at almost normal levels. High-throughput genome-wide translocation sequencing revealed that I-SceI-generated DSBs introduced in cis at Sμ and Sγ1 sites are joined together in T cells at levels similar to those of B cells. Such high joining levels also occurred between I-SceI-generated DSBs within c-myc and I-SceI- or CRISPR/Cas9-generated DSBs 100 kb downstream within Pvt1 in B cells or fibroblasts, respectively. We suggest that CSR exploits a general propensity of intrachromosomal DSBs separated by several hundred kilobases to be frequently joined together and discuss the relevance of this finding for recurrent interstitial deletions in cancer.

  1. Input-to-state stability analysis for a class of nonlinear switched descriptor systems

    NASA Astrophysics Data System (ADS)

    Gao, Zairui; Yang, Kun; Shen, Yanxia; Ji, Zhicheng

    2015-12-01

    This paper considers the problem of input-to-state stability for a class of nonlinear switched descriptor systems. According to the definition of input-to-state stability, sufficient conditions are derived to ensure that the system is input-to-state stable based on the dwell time approach and the Gronwall-Bellman inequality. Compared with existing methods, it is more convenient to design the controller for each subsystem, because it does not need to construct the input-to-state stable control Lyapunov function and design the specific structure of the control inputs. Finally, two numerical examples illustrate the feasibility and effectiveness of the proposed method.

  2. Immunoglobulin class switching appears to be regulated by B cell antigen receptor-specific T cell action

    PubMed Central

    Lange, Hans; Hecht, Oliver; Zemlin, Michael; Trad, Ahmad; Tanasa, Radu I.; Schroeder, Harry W.; Lemke, Hilmar

    2013-01-01

    Summary Antigen affinity is commonly viewed as the driving force behind the selection for dominant clonotypes that can occur during the T cell-dependent processes of class switch recombination (CSR) and immune maturation. To test this view, we analyzed the variable gene repertoires of natural monoclonal antibodies to the hapten 2-phenyloxazolone (phOx) as well as those generated after phOx protein carrier-induced thymus-dependent or Ficoll-induced thymus independent antigen stimulation. In contrast to expectations, the extent of IgM heterogeneity proved similar and many IgM from these three populations exhibited similar or even greater affinities than the classic Ox1 clonotype that dominates only after CSR among primary and memory IgG. The population of clones that were selected during CSR exhibited a reduced VH/VL repertoire that was enriched for variable domains with shorter and more uniform CDR-H3 lengths and almost completely stripped of variable domains encoded by the large VH1 family. Thus, contrary to the current paradigm, T-cell dependent clonal selection during CSR appeared to select for VH family and CDR-H3 loop content even when the affinity provided by alternative clones exhibited similar to increased affinity for antigen. PMID:22531925

  3. Insertional events as well as translocations may arise during aberrant immunoglobulin switch recombination in a patient with multiple myeloma.

    PubMed

    Pratt, G; Fenton, J A; Davies, F E; Rawstron, A C; Richards, S J; Collins, J E; Owen, R G; Jack, A S; Smith, G M; Morgan, G J

    2001-02-01

    The majority of patients with multiple myeloma have translocations involving the immunoglobulin heavy chain switch regions on chromosome 14q32 and a promiscuous range of partner chromosomes. We describe a patient with an insertion of 132 bp of chromosome 22q12 sequence into the 5' region flanking S(mu) on chromosome 14q32. The 132 bp region from chromosome 22q12 contains the whole of exon 3 from a novel gene of unknown function in man. The significance of such insertional events remains unclear. The description of insertional events occurring as a result of abnormal switch recombination suggests that, in myeloma, dysregulation of oncogenes may occur by a mechanism other than chromosomal translocation.

  4. Stability and stabilization studies for a class of switched nonlinear systems via vector norms approach.

    PubMed

    Sakly, Anis; Kermani, Marwen

    2015-07-01

    This paper is concerned with the problems of stability analysis and stabilization with a state feedback controller through pole placement for a class of both continuous and discrete-time switched nonlinear systems. These systems are modeled by differential or difference equations. Then, a transformation under the arrow form is employed. Note that, the main contribution in this work is twofold: firstly, based on the construction of an appropriated common Lyapunov function, as well the use of the vector norms notion, the recourse to the Kotelyanski lemma, the M-matrix proprieties, the aggregation techniques and the application of the Borne-Gentina criterion, new sufficient stability conditions under arbitrary switching for the autonomous system are deduced. Secondly, this result is extended for designing a state feedback controller by using pole assignment control, which guarantee that the corresponding closed-loop system is globally asymptotically stable under arbitrary switching. The main novelties features of these obtained results are the explicitness and the simplicity in their application. Moreover, they allow us to avoid the search of a common Lyapunov function which is a difficult matter. Finally, as validation to stabilize a shunt DC motor under variable mechanical loads is performed to demonstrate the effectiveness of the proposed results.

  5. Identifying Effective Enzyme Activity Targets for Recombinant Class I and Class II Collagenase for Successful Human Islet Isolation

    PubMed Central

    Balamurugan, Appakalai N.; Green, Michael L.; Breite, Andrew G.; Loganathan, Gopalakrishnan; Wilhelm, Joshua J.; Tweed, Benjamin; Vargova, Lenka; Lockridge, Amber; Kuriti, Manikya; Hughes, Michael G.; Williams, Stuart K.; Hering, Bernhard J.; Dwulet, Francis E.; McCarthy, Robert C.

    2016-01-01

    Background Isolation following a good manufacturing practice-compliant, human islet product requires development of a robust islet isolation procedure where effective limits of key reagents are known. The enzymes used for islet isolation are critical but little is known about the doses of class I and class II collagenase required for successful islet isolation. Methods We used a factorial approach to evaluate the effect of high and low target activities of recombinant class I (rC1) and class II (rC2) collagenase on human islet yield. Consequently, 4 different enzyme formulations with divergent C1:C2 collagenase mass ratios were assessed, each supplemented with the same dose of neutral protease. Both split pancreas and whole pancreas models were used to test enzyme targets (n = 20). Islet yield/g pancreas was compared with historical enzymes (n = 42). Results Varying the Wunsch (rC2) and collagen degradation activity (CDA, rC1) target dose, and consequently the C1:C2 mass ratio, had no significant effect on tissue digestion. Digestions using higher doses of Wunsch and CDA resulted in comparable islet yields to those obtained with 60% and 50% of those activities, respectively. Factorial analysis revealed no significant main effect of Wunsch activity or CDA for any parameter measured. Aggregate results from 4 different collagenase formulations gave 44% higher islet yield (>5000 islet equivalents/g) in the body/tail of the pancreas (n = 12) when compared with those from the same segment using a standard natural collagenase/protease mixture (n = 6). Additionally, islet yields greater than 5000 islet equivalents/g pancreas were also obtained in whole human pancreas. Conclusions A broader C1:C2 ratio can be used for human islet isolation than has been used in the past. Recombinant collagenase is an effective replacement for the natural enzyme and we have determined that high islet yield can be obtained even with low doses of rC1:rC2, which is beneficial for the survival

  6. Recombination events near the immunoglobulin Cmu gene join variable and constant region genes, switch heavy-chain expression, or inactivate the locus.

    PubMed

    Cory, S; Webb, E; Gough, J; Adams, J M

    1981-04-28

    Immunoglobulin heavy-chain expression is initiated by recombination between a variable region (VH) gene and one of several joining region (JH) genes located near the mu constant region (Cmu) gene, and the active VH gene can subsequently switch to another CH gene. That the general mechanism for CH switching involves recombination between sites within the JH-Cmu intervening sequence and the 5' flanking region of another CH gene is supported here by Southern blot hybridization analysis of eight IgG- and IgA-secreting plasmacytomas. An alternative model requiring successive VH linkage to similar JH clusters near each CH gene is shown to be very unlikely since the mouse genome appears to contain only one complement of the JH locus and no JH gene was detectable within large cloned sequences flanking germline C gamma 3 and C gamma 1 genes. Thus, VH-JH joining and CH switching are mediated by separate regions of "the joining-switch" or J-S element. In each plasmacytoma examined, the J-S element had undergone recombination within both the JH locus and the switch region and was shown to be linked to the functional CH gene in an IgG3, and IgG1, and three IgA secretors. Both JH joining and CH switching occurred by deletion of DNA. Switch recombination occurred at more than one site within the J-S element in different lines, even for recombination with the same CH gene. Significantly, although heavy-chain expression is restricted to one allele ("allelic exclusion"), all rearranged in each plasmacytoma. Some rearrangements were aberrant, involving, for example, deletion of all JH genes from the allele. Hence, an error-prone recombination machinery may account for allelic exclusion in many plasmacytomas.

  7. H∞ control of a class of 2-D continuous switched delayed systems via state-dependent switching

    NASA Astrophysics Data System (ADS)

    Ghous, Imran; Xiang, Zhengrong

    2016-01-01

    This paper addresses the problem of state feedback H∞ stabilisation of 2-D (two-dimensional) continuous switched state delayed systems represented by the Roesser model using the multiple Lyapunov functional approach. First, an asymptotical stability condition of 2-D continuous switched systems with state-dependent switching is derived. Second, a sufficient condition for H∞ performance of the underlying system is established. Third, a state feedback controller is proposed to ensure that the resulting closed-loop system has a prescribed H∞ performance level under a state-dependent switching signal. All the results are developed in terms of linear matrix inequalities. Finally, three examples are provided to demonstrate the validity and effectiveness of the proposed method.

  8. A Butter Aroma Recombinate Activates Human Class-I Odorant Receptors.

    PubMed

    Geithe, Christiane; Andersen, Gaby; Malki, Agne; Krautwurst, Dietmar

    2015-11-04

    With ∼400 olfactory G protein-coupled receptors (GPCR), humans sensitively perceive ∼230 key aroma compounds as best natural agonists of ∼10000 food volatiles. An understanding of odorant coding, thus, critically depends on the knowledge about interactions of key food aroma chemicals and their mixtures with their cognate receptors. Genetically designed test cell systems enable the screening, deorphaning, and characterization of single odorant receptors (OR). This study shows for the food aroma-specific and quantitative butter aroma recombinate, and its single components, specific in vitro class-I OR activity patterns, as well as the activation of selected OR in a concentration-dependent manner. Recently, chemosensory receptors, especially class-I OR, were demonstrated to be expressed on blood leukocytes, which may encounter foodborne aroma compounds postprandially. This study shows that butter aroma recombinate induced chemotaxis of isolated human neutrophils in a defined gradient, and in a concentration-dependent and pertussis toxin-sensitive manner, suggesting at least a GPCR-mediated activation of blood leukocytes by key food odorants.

  9. Human malignant T cells capable of inducing an immunoglobulin class switch

    PubMed Central

    1985-01-01

    Evidence is presented for the existence of a "switch" T cell derived from a patient with mycosis fungoides/Sezary's syndrome. The serum immunoglobulin profile in this patient revealed high IgG and IgA but no detectable IgM. Peripheral blood mononuclear cells from this patient secreted only IgG and IgA in the presence of pokeweed mitogen. T cells (Trac) co-cultured with normal allogeneic non-T cells and pokeweed mitogen resulted in only IgG and IgA PFC, with little or no IgM secretion. There was no evidence of active suppression of IgM. Rather, these T cells appeared to induce an Ig class switch from IgM to IgG and IgA, when co-cultured with mu+ tonsillar B cells. Further evidence was obtained using mononuclear cells derived from a patient with immunodeficiency and hyper-IgM, a syndrome characterized by a lack of IgG and IgA secretion. The addition of Trac cells to either peripheral blood mononuclear cells or non-T cells from a patient with hyper-IgM syndrome resulted in new secretion of IgG, with a concomitant decrease in IgM secretion, whereas control T cells were not effective in inducing secretion of any isotype other than IgM. Isolated Tac+ T cells from Trac appear to be responsible for this effect. PMID:2981951

  10. Potassium-lead-switched G-quadruplexes: a new class of DNA logic gates.

    PubMed

    Li, Tao; Wang, Erkang; Dong, Shaojun

    2009-10-28

    A cation-driven allosteric G-quadruplex DNAzyme (PW17) was utilized to devise a conceptually new class of DNA logic gate based on cation-tuned ligand binding and release. K(+) favors the binding of hemin to parallel-stranded PW17, thereby promoting the DNAzyme activity, whereas Pb(2+) induces PW17 to undergo a parallel-to-antiparallel conformation transition and thus drives hemin to release from the G-quadruplex, deactivating the DNAzyme. Such a K(+)-Pb(2+) switched G-quadruplex, in fact, functions as a two-input INHIBIT logic gate. With the introduction of another input EDTA, this G-quadruplex can be further utilized to construct a reversibly operated IMPLICATION gate.

  11. H ∞ Cluster Synchronization for a Class of Neutral Complex Dynamical Networks with Markovian Switching

    PubMed Central

    2014-01-01

    H ∞ cluster synchronization problem for a class of neutral complex dynamical networks (NCDNs) with Markovian switching is investigated in this paper. Both the retarded and neutral delays are considered to be interval mode dependent and time varying. The concept of H ∞ cluster synchronization is proposed to quantify the attenuation level of synchronization error dynamics against the exogenous disturbance of the NCDNs. Based on a novel Lyapunov functional, by employing some integral inequalities and the nature of convex combination, mode delay-range-dependent H ∞ cluster synchronization criteria are derived in the form of linear matrix inequalities which depend not only on the disturbance attenuation but also on the initial values of the NCDNs. Finally, numerical examples are given to demonstrate the feasibility and effectiveness of the proposed theoretical results. PMID:24892088

  12. The dependence of Ig class-switching on the nuclear export sequence of AID likely reflects interaction with factors additional to Crm1 exportin.

    PubMed

    Ellyard, Julia I; Benk, Amelie S; Taylor, Benjamin; Rada, Cristina; Neuberger, Michael S

    2011-02-01

    Activation-induced deaminase (AID) is a B lymphocyte-specific DNA deaminase that triggers Ig class-switch recombination (CSR) and somatic hypermutation. It shuttles between cytoplasm and nucleus, containing a nuclear export sequence (NES) at its carboxyterminus. Intriguingly, the precise nature of this NES is critical to AID's function in CSR, though not in somatic hypermutation. Many alterations to the NES, while preserving its nuclear export function, destroy CSR ability. We have previously speculated that AID's ability to potentiate CSR may critically depend on the affinity of interaction between its NES and Crm1 exportin. Here, however, by comparing multiple AID NES mutants, we find that - beyond a requirement for threshold Crm1 binding - there is little correlation between CSR and Crm1 binding affinity. The results suggest that CSR, as well as the stabilisation of AID, depend on an interaction between the AID C-terminal decapeptide and factor(s) additional to Crm1.

  13. The dependence of Ig class-switching on the nuclear export sequence of AID likely reflects interaction with factors additional to Crm1 exportin

    PubMed Central

    Ellyard, Julia I; Benk, Amelie S; Taylor, Benjamin; Rada, Cristina; Neuberger, Michael S

    2011-01-01

    Activation-induced deaminase (AID) is a B lymphocyte-specific DNA deaminase that triggers Ig class-switch recombination (CSR) and somatic hypermutation. It shuttles between cytoplasm and nucleus, containing a nuclear export sequence (NES) at its carboxyterminus. Intriguingly, the precise nature of this NES is critical to AID's function in CSR, though not in somatic hypermutation. Many alterations to the NES, while preserving its nuclear export function, destroy CSR ability. We have previously speculated that AID's ability to potentiate CSR may critically depend on the affinity of interaction between its NES and Crm1 exportin. Here, however, by comparing multiple AID NES mutants, we find that – beyond a requirement for threshold Crm1 binding – there is little correlation between CSR and Crm1 binding affinity. The results suggest that CSR, as well as the stabilisation of AID, depend on an interaction between the AID C-terminal decapeptide and factor(s) additional to Crm1. PMID:21268017

  14. The stability of AID and its function in class-switching are critically sensitive to the identity of its nuclear-export sequence.

    PubMed

    Geisberger, Roland; Rada, Cristina; Neuberger, Michael S

    2009-04-21

    The carboxyterminal region of activation-induced deaminase (AID) is required for its function in Ig class switch recombination (CSR) and also contains a nuclear-export sequence (NES). Here, based on an extensive fine-structure mutation analysis of the AID NES, as well as from AID chimeras bearing heterologous NESs, we show that while a functional NES is indeed essential for CSR, it is not sufficient. The precise nature of the NES is critical both for AID stabilization and CSR function: minor changes in the NES can perturb stabilization and CSR without jeopardizing nuclear export. The results indicate that the AID NES fulfills a function beyond simply providing a signal for nuclear export and suggest the possibility that the quality of exportin-binding may be critical to the stabilization of AID and its activity in CSR.

  15. Oral-nasopharyngeal dendritic cells mediate T cell-independent IgA class switching on B-1 B cells.

    PubMed

    Kataoka, Kosuke; Fujihashi, Keiko; Terao, Yutaka; Gilbert, Rebekah S; Sekine, Shinichi; Kobayashi, Ryoki; Fukuyama, Yoshiko; Kawabata, Shigetada; Fujihashi, Kohtaro

    2011-01-01

    Native cholera toxin (nCT) as a nasal adjuvant was shown to elicit increased levels of T-independent S-IgA antibody (Ab) responses through IL-5- IL-5 receptor interactions between CD4+ T cells and IgA+ B-1 B cells in murine submandibular glands (SMGs) and nasal passages (NPs). Here, we further investigate whether oral-nasopharyngeal dendritic cells (DCs) play a central role in the induction of B-1 B cell IgA class switch recombination (CSR) for the enhancement of T cell-independent (TI) mucosal S-IgA Ab responses. High expression levels of activation-induced cytidine deaminase, Iα-Cμ circulation transcripts and Iμ-Cα transcripts were seen on B-1 B cells purified from SMGs and NPs of both TCRβ⁻/⁻ mice and wild-type mice given nasal trinitrophenyl (TNP)-LPS plus nCT, than in the same tissues of mice given nCT or TNP-LPS alone. Further, DCs from SMGs, NPs and NALT of mice given nasal TNP-LPS plus nCT expressed significantly higher levels of a proliferation-inducing ligand (APRIL) than those in mice given TNP-LPS or nCT alone, whereas the B-1 B cells in SMGs and NPs showed elevated levels of transmembrane activator and calcium modulator cyclophilin ligand interactor (TACI) expression. Interestingly, high frequencies of IgA+ B-1 B cells were induced when peritoneal IgA⁻ IgM+ B cells were stimulated with mucosal DCs from mice given nasal TNP-LPS plus nCT. Taken together, these findings show that nasal nCT plays a key role in the enhancement of mucosal DC-mediated TI IgA CSR by B-1 B cells through their interactions with APRIL and TACI.

  16. Immunogenicity of recombinant class 1 protein from Neisseria meningitidis refolded into phospholipid vesicles and detergent.

    PubMed

    Niebla, O; Alvarez, A; Martín, A; Rodríguez, A; Delgado, M; Falcón, V; Guillén, G

    2001-05-14

    The possibility of eliciting bactericidal antibodies against a recombinant class 1 protein (P1) from Neisseria meningitidis, joined to the first 45 amino acids of the neisserial LpdA protein (PM82), was examined. P1 was produced in Escherichia coli as intracellular inclusion bodies, from which it was purified and reconstituted by (a) inclusion into phospholipid vesicles and detergent and (b) refolding in 0.1% SDS. When Balb/c mice were immunised, high titres of subtype-specific bactericidal antibodies against P1 were obtained in both cases. These results suggest that in spite of being a denaturing agent, it is possible to use SDS to reconstitute the P1 protein in a conformation that exposes the immunodominat regions.

  17. A recombinationally repressed region between mat2 and mat3 loci shares homology to centromeric repeats and regulates directionality of mating-type switching in fission yeast.

    PubMed

    Grewal, S I; Klar, A J

    1997-08-01

    Cells of the fission yeast Schizosaccharomyces pombe switch mating type by replacing genetic information at the transcriptionally active mat1 locus with sequences copied from one of two closely linked silent loci, mat2-P or mat3-M. By a process referred to as directionality of switching, cells predominantly switch to the opposite mat1 allele; the mat1-P allele preferentially recombines with mat3, while mat1-M selects the mat2. In contrast to efficient recombination at mat1, recombination within the adjoining mat2-mat3 interval is undetectable. We defined the role of sequences between mat2 and mat3, designated the K-region, in directionality as well as recombinational suppression. Cloning and sequencing analysis revealed that a part of the K-region is homologous to repeat sequences present at centromeres, which also display transcriptional and recombinational suppression. Replacement of 7.5 kb of the K-region with the ura4+ gene affected directionality in a variegated manner. Analysis of the swi6-mod locus, which was previously shown to affect directionality, in K delta::ura4+ strains suggested the existence of at least two overlapping directionality mechanisms. Our work furthers the model that directionality is regulated by cell-type-specific organization of the heterochromatin-like structure in the mating-type region and provides evidence that the K-region contributes to silencing of the mat2-mat3 interval.

  18. A Recombinationally Repressed Region between Mat2 and Mat3 Loci Shares Homology to Centromeric Repeats and Regulates Directionality of Mating-Type Switching in Fission Yeast

    PubMed Central

    Grewal, SIS.; Klar, AJS.

    1997-01-01

    Cells of the fission yeast Schizosaccharomyces pombe switch mating type by replacing genetic information at the transcriptionally active mat1 locus with sequences copied from one of two closely linked silent loci, mat2-P or mat3-M. By a process referred to as directionality of switching, cells predominantly switch to the opposite mat1 allele; the mat1-P allele preferentially recombines with mat3, while mat1-M selects the mat2. In contrast to efficient recombination at mat1, recombination within the adjoining mat2-mat3 interval is undetectable. We defined the role of sequences between mat2 and mat3, designated the K-region, in directionality as well as recombinational suppression. Cloning and sequencing analysis revealed that a part of the K-region is homologous to repeat sequences present at centromeres, which also display transcriptional and recombinational suppression. Replacement of 7.5 kb of the K-region with the ura4(+) gene affected directionality in a variegated manner. Analysis of the swi6-mod locus, which was previously shown to affect directionality, in KΔ::ura4(+) strains suggested the existence of at least two overlapping directionality mechanisms. Our work furthers the model that directionality is regulated by cell-type-specific organization of the heterochromatin-like structure in the mating-type region and provides evidence that the K-region contributes to silencing of the mat2-mat3 interval. PMID:9258669

  19. Restoration of Retarded Influenza Virus-specific Immunoglobulin Class Switch in Aged Mice

    PubMed Central

    Zhang, Yongxin; Wang, Ying; Zhang, Monica; Liu, Lin; Mbawuike, Innocent N

    2016-01-01

    Objective The declined immune response to infection causes significant higher morbidity and mortality in aging in spite of the coexisted hyperimmunoglobulinemia (HIG). This study is to reveal the cellular basis of HIG and mechanism of weakened HA-specific IgG response in aged mice and to test cell therapy in the treatment of age-related IgG antibody production deficiency with immunocyte adoptive transfer. Methods BALB/c mice was immunized with Influenza A/Taiwan vaccine and challenged with the same strain of virus. ELISA was used to assess the levels of total immunoglobulins and antigen specific antibody response. The flow cytometry and ELISPOT were used to evaluate the frequencies of total immunoglobulin- and specific antibody-producing and secreting B lymphocytes. In vitro expanded mononuclear cells, CD4+ T lymphocytes and CD20+ B lymphocytes from old and young mice were adoptively transferred into influenza virus-challenged aged mice, and HA-specific IgG responses were observed. Results It is found that old mice exhibited higher levels of total serum IgG, IgM and IgA, higher frequencies of IgG+, IgM+ and IgA+ cells, and greater antigen-specific IgM and IgA responses to influenza infection, in comparison to young mice. However, influenza antigen- specific IgG and its subclass responses in old mice were significantly lower. Conclusion The retarded specific IgG response could be attributed to an insufficiency of immunoglobulin class switch in aging. Correlation analysis indicated that HIG and deficient specific IgG production in aged mice could be independent to each other in their pathogenesis. Correction of deficient specific IgG production by adoptive transfer of in vitro expanded and unexpanded CD4+ cells from immunized young mice suggests the CD4+ cell dysfunction contributes to the insufficiency of immunoglobulin class switch in aged mice. The transfusion of in vitro expanded lymphocytes could be a potential effective therapy for the age

  20. Molecular characterization of the Pb recombination hotspot in the mouse major histocompatibility complex class II region.

    PubMed

    Isobe, Taku; Yoshino, Masayasu; Mizuno, Ken-Ichi; Lindahl, Kirsten Fischer; Koide, Tsuyoshi; Gaudieri, Silvana; Gojobori, Takashi; Shiroishi, Toshihiko

    2002-08-01

    In the mouse major histocompatibility complex (MHC) class II region, meiotic recombination breakpoints are clustered in four specific sites known as hotspots. Here we reveal the primary structure of a hotspot near the Pb gene. A total of 12 crossover points were found to be confined to a 15-kb DNA segment of the Pb pseudogene. Moreover, the crossover points are concentrated in a 341-bp segment, which includes a part of exon 4 and intron 4 of the Pb gene. All four MHC hotspots appear to be located within genes or at the 3' end of genes, contrasting with characterized hotspots in budding yeast, which are mostly located at the 5'-promoter regions of genes. The Pb hotspot has several consensus motifs, an octamer transcription factor-binding sequence, the B-motif-like transcription factor-binding sequence, and tandem repeats of tetramer sequence-all of which are shared by the other three hotspots. Systematic analysis of the public database demonstrated that the full motif set occurs rarely in the nucleotide sequence of the entire MHC class II region. All results suggest that the motif set has an indispensable role in determining their site specificity.

  1. Iron Binding Properties of Recombinant Class A Protein Disulfide Isomerase from Arabidopsis thaliana.

    PubMed

    Remelli, William; Santabarbara, Stefano; Carbonera, Donatella; Bonomi, Francesco; Ceriotti, Aldo; Casazza, Anna Paola

    2017-04-07

    The protein disulfide isomerase (PDI) family comprises a wide set of enzymes mainly involved in thiol-disulfide exchange reactions in the endoplasmic reticulum. Class A PDIs (PDI-A) constitute the smallest members of the family, consisting of a single thioredoxin (TRX) module without any additional domains. To date, their catalytic activity and cellular function are still poorly understood. To gain insight into the role of higher-plant class A PDIs, the biochemical properties of rAtPDI-A, the recombinant form of Arabidopsis thaliana PDI-A, have been investigated. As expressed, rAtPDI-A has only little oxidoreductase activity, but it appears to be capable of binding an iron-sulfur (Fe-S) cluster, most likely a [2Fe-2S] center, at the interface between two protein monomers. A mutational survey of all cysteine residues of rAtPDI-A indicates that only the second and third cysteines of the CXXXCKHC stretch, containing the putative catalytic site CKHC, are primarily involved in cluster coordination. A key role is also played by the lysine residue. Its substitution with glycine, which restores the canonical PDI active site CGHC, does not influence the oxidoreductase activity of the protein, which remains marginal, but strongly affects the binding of the cluster. It is therefore proposed that the unexpected ability of rAtPDI-A to accommodate an Fe-S cluster is due to its very unique CKHC motif, which is conserved in all higher-plant class A PDIs, differentiating them from all other members of the PDI family.

  2. Inducible CTCF insulator delays the IgH 3' regulatory region-mediated activation of germline promoters and alters class switching.

    PubMed

    Braikia, Fatima-Zohra; Oudinet, Chloé; Haddad, Dania; Oruc, Zeliha; Orlando, Domenico; Dauba, Audrey; Le Bert, Marc; Khamlichi, Ahmed Amine

    2017-06-06

    Class switch recombination (CSR) plays an important role in adaptive immune response by enabling mature B cells to switch from IgM expression to the expression of downstream isotypes. CSR is preceded by inducible germline (GL) transcription of the constant genes and is controlled by the 3' regulatory region (3'RR) in a stimulus-dependent manner. Why the 3'RR-mediated up-regulation of GL transcription is delayed to the mature B-cell stage is presently unknown. Here we show that mice devoid of an inducible CTCF binding element, located in the α constant gene, display a marked isotype-specific increase of GL transcription in developing and resting splenic B cells and altered CSR in activated B cells. Moreover, insertion of a GL promoter downstream of the CTCF insulator led to premature activation of the ectopic promoter. This study provides functional evidence that the 3'RR has a developmentally controlled potential to constitutively activate GL promoters but that this activity is delayed, at least in part, by the CTCF insulator, which borders a transcriptionally active domain established by the 3'RR in developing B cells.

  3. Immunization with Outer Membrane Vesicles Displaying Designer Glycotopes Yields Class-Switched, Glycan-Specific Antibodies.

    PubMed

    Valentine, Jenny L; Chen, Linxiao; Perregaux, Emily C; Weyant, Kevin B; Rosenthal, Joseph A; Heiss, Christian; Azadi, Parastoo; Fisher, Adam C; Putnam, David; Moe, Gregory R; Merritt, Judith H; DeLisa, Matthew P

    2016-06-23

    The development of antibodies against specific glycan epitopes poses a significant challenge due to difficulties obtaining desired glycans at sufficient quantity and purity, and the fact that glycans are usually weakly immunogenic. To address this challenge, we leveraged the potent immunostimulatory activity of bacterial outer membrane vesicles (OMVs) to deliver designer glycan epitopes to the immune system. This approach involved heterologous expression of two clinically important glycans, namely polysialic acid (PSA) and Thomsen-Friedenreich antigen (T antigen) in hypervesiculating strains of non-pathogenic Escherichia coli. The resulting glycOMVs displayed structural mimics of PSA or T antigen on their surfaces, and induced high titers of glycan-specific IgG antibodies following immunization in mice. In the case of PSA glycOMVs, serum antibodies potently killed Neisseria meningitidis serogroup B (MenB), whose outer capsule is PSA, in a serum bactericidal assay. These findings demonstrate the potential of glycOMVs for inducing class-switched, humoral immune responses against glycan antigens. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Immunization with outer membrane vesicles displaying designer glycotopes yields class-switched, glycan-specific antibodies

    PubMed Central

    Valentine, Jenny L.; Chen, Linxiao; Perregaux, Emily C.; Weyant, Kevin B.; Rosenthal, Joseph A.; Heiss, Christian; Azadi, Parastoo; Fisher, Adam C.; Putnam, David; Moe, Gregory R.; Merritt, Judith H.; DeLisa, Matthew P.

    2016-01-01

    Summary The development of antibodies against specific glycan epitopes poses a significant challenge due to difficulties obtaining desired glycans at sufficient quantity and purity, and the fact that glycans are usually weakly immunogenic. To address this challenge, we leveraged the potent immunostimulatory activity of bacterial outer membrane vesicles (OMVs) to deliver designer glycan epitopes to the immune system. This approach involved heterologous expression of two clinically important glycans, namely polysialic acid (PSA) and Thomsen-Friedenreich antigen (T antigen) in hypervesiculating strains of non-pathogenic Escherichia coli. The resulting glycOMVs displayed structural mimics of PSA or T antigen on their surfaces, and induced high titers of glycan-specific IgG antibodies following immunization in mice. In the case of PSA glycOMVs, serum antibodies potently killed Neisseria meningitidis serogroup B (MenB), whose outer capsule is PSA, in a serum bactericidal assay. These findings demonstrate the potential of glycOMVs for inducing class-switched, humoral immune responses against glycan antigens. PMID:27341433

  5. A DFT study of a new class of gold nanocluster-photochrome multi-functional switches.

    PubMed

    Fihey, Arnaud; Maurel, François; Perrier, Aurélie

    2014-12-21

    With the help of a computational scheme combining molecular dynamics, DFT and TD-DFT methods, the conformational, electronic and optical properties of a new class of hybrid compounds where a photochromic molecule belonging to the dithienylethene family (DTE) is covalently linked to a Au25 nanocluster (gold nanocluster or GNC) are investigated. We compare two types of hybrid GNC-DTE systems where the aromatic linker between the metallic and the DTE moieties is either a phenyl or a thiophene ring. By examining the perturbation of the DTE electronic structure after grafting upon the GNC, we show that the hybrid system with a phenyl linker should preserve its photochromic activity. For the latter system, we have then studied the possible energy and electron transfer between the GNC and the DTE units. The energy transfer between the two moieties can be a priori discarded while a uni-directional electron transfer should take place from the GNC to the excited DTE. We show that this transfer can be controlled by switching the state of the molecule.

  6. Complex Breakpoints and Template Switching Associated with Non-canonical Termination of Homologous Recombination in Mammalian Cells

    PubMed Central

    Hartlerode, Andrea J.; Rajendran, Anbazhagan; Manis, John P.

    2016-01-01

    A proportion of homologous recombination (HR) events in mammalian cells resolve by “long tract” gene conversion, reflecting copying of several kilobases from the donor sister chromatid prior to termination. Cells lacking the major hereditary breast/ovarian cancer predisposition genes, BRCA1 or BRCA2, or certain other HR-defective cells, reveal a bias in favor of long tract gene conversion, suggesting that this aberrant HR outcome might be connected with genomic instability. If termination of gene conversion occurs in regions lacking homology with the second end of the break, the normal mechanism of HR termination by annealing (i.e., homologous pairing) is not available and termination must occur by as yet poorly defined non-canonical mechanisms. Here we use a previously described HR reporter to analyze mechanisms of non-canonical termination of long tract gene conversion in mammalian cells. We find that non-canonical HR termination can occur in the absence of the classical non-homologous end joining gene XRCC4. We observe obligatory use of microhomology (MH)-mediated end joining and/or nucleotide addition during rejoining with the second end of the break. Notably, non-canonical HR termination is associated with complex breakpoints. We identify roles for homology-mediated template switching and, potentially, MH-mediated template switching/microhomology-mediated break-induced replication, in the formation of complex breakpoints at sites of non-canonical HR termination. This work identifies non-canonical HR termination as a potential contributor to genomic instability and to the formation of complex breakpoints in cancer. PMID:27832076

  7. Analyses of a whole-genome inter-clade recombination map of hepatitis delta virus suggest a host polymerase-driven and viral RNA structure-promoted template-switching mechanism for viral RNA recombination.

    PubMed

    Chao, Mei; Wang, Tzu-Chi; Lin, Chia-Chi; Yung-Liang Wang, Robert; Lin, Wen-Bin; Lee, Shang-En; Cheng, Ying-Yu; Yeh, Chau-Ting; Iang, Shan-Bei

    2017-09-22

    The genome of hepatitis delta virus (HDV) is a 1.7-kb single-stranded circular RNA that folds into an unbranched rod-like structure and has ribozyme activity. HDV redirects host RNA polymerase(s) (RNAP) to perform viral RNA-directed RNA transcription. RNA recombination is known to contribute to the genetic heterogeneity of HDV, but its molecular mechanism is poorly understood. Here, we established a whole-genome HDV-1/HDV-4 recombination map using two cloned sequences coexisting in cultured cells. Our functional analyses of the resulting chimeric delta antigens (the only viral-encoded protein) and recombinant genomes provide insights into how recombination promotes the genotypic and phenotypic diversity of HDV. Our examination of crossover distribution and subsequent mutagenesis analyses demonstrated that ribozyme activity on HDV genome, which is required for viral replication, also contributes to the generation of an inter-clade junction. These data provide circumstantial evidence supporting our contention that HDV RNA recombination occurs via a replication-dependent mechanism. Furthermore, we identify an intrinsic asymmetric bulge on the HDV genome, which appears to promote recombination events in the vicinity. We therefore propose a mammalian RNAP-driven and viral-RNA-structure-promoted template-switching mechanism for HDV genetic recombination. The present findings improve our understanding of the capacities of the host RNAP beyond typical DNA-directed transcription.

  8. Analyses of a whole-genome inter-clade recombination map of hepatitis delta virus suggest a host polymerase-driven and viral RNA structure-promoted template-switching mechanism for viral RNA recombination

    PubMed Central

    Chao, Mei; Wang, Tzu-Chi; Lin, Chia-Chi; Yung-Liang Wang, Robert; Lin, Wen-Bin; Lee, Shang-En; Cheng, Ying-Yu; Yeh, Chau-Ting; Iang, Shan-Bei

    2017-01-01

    The genome of hepatitis delta virus (HDV) is a 1.7-kb single-stranded circular RNA that folds into an unbranched rod-like structure and has ribozyme activity. HDV redirects host RNA polymerase(s) (RNAP) to perform viral RNA-directed RNA transcription. RNA recombination is known to contribute to the genetic heterogeneity of HDV, but its molecular mechanism is poorly understood. Here, we established a whole-genome HDV-1/HDV-4 recombination map using two cloned sequences coexisting in cultured cells. Our functional analyses of the resulting chimeric delta antigens (the only viral-encoded protein) and recombinant genomes provide insights into how recombination promotes the genotypic and phenotypic diversity of HDV. Our examination of crossover distribution and subsequent mutagenesis analyses demonstrated that ribozyme activity on HDV genome, which is required for viral replication, also contributes to the generation of an inter-clade junction. These data provide circumstantial evidence supporting our contention that HDV RNA recombination occurs via a replication-dependent mechanism. Furthermore, we identify an intrinsic asymmetric bulge on the HDV genome, which appears to promote recombination events in the vicinity. We therefore propose a mammalian RNAP-driven and viral-RNA-structure-promoted template-switching mechanism for HDV genetic recombination. The present findings improve our understanding of the capacities of the host RNAP beyond typical DNA-directed transcription.

  9. Diversity of metalloproteinases in Bothrops neuwiedi snake venom transcripts: evidences for recombination between different classes of SVMPs

    PubMed Central

    2011-01-01

    Background Snake venom metalloproteinases (SVMPs) are widely distributed in snake venoms and are versatile toxins, targeting many important elements involved in hemostasis, such as basement membrane proteins, clotting proteins, platelets, endothelial and inflammatory cells. The functional diversity of SVMPs is in part due to the structural organization of different combinations of catalytic, disintegrin, disintegrin-like and cysteine-rich domains, which categorizes SVMPs in 3 classes of precursor molecules (PI, PII and PIII) further divided in 11 subclasses, 6 of them belonging to PII group. This heterogeneity is currently correlated to genetic accelerated evolution and post-translational modifications. Results Thirty-one SVMP cDNAs were full length cloned from a single specimen of Bothrops neuwiedi snake, sequenced and grouped in eleven distinct sequences and further analyzed by cladistic analysis. Class P-I and class P-III sequences presented the expected tree topology for fibrinolytic and hemorrhagic SVMPs, respectively. In opposition, three distinct segregations were observed for class P-II sequences. P-IIb showed the typical segregation of class P-II SVMPs. However, P-IIa grouped with class P-I cDNAs presenting a 100% identity in the 365 bp at their 5' ends, suggesting post-transcription events for interclass recombination. In addition, catalytic domain of P-IIx sequences segregated with non-hemorrhagic class P-III SVMPs while their disintegrin domain grouped with other class P-II disintegrin domains suggesting independent evolution of catalytic and disintegrin domains. Complementary regions within cDNA sequences were noted and may participate in recombination either at DNA or RNA levels. Proteins predicted by these cDNAs show the main features of the correspondent classes of SVMP, but P-IIb and P-IIx included two additional cysteines cysteines at the C-termini of the disintegrin domains in positions not yet described. Conclusions In B. neuwiedi venom gland

  10. Novel conditions on exponential stability of a class of delayed neural networks with state-dependent switching.

    PubMed

    Zhang, Guodong; Shen, Yi

    2015-11-01

    This paper is concerned with the global exponential stability on a class of delayed neural networks with state-dependent switching. Under the novel conditions, some sufficient criteria ensuring exponential stability of the proposed system are obtained. In particular, the obtained conditions complement and improve earlier publications on conventional neural networks with continuous or discontinuous right-hand side. Numerical simulations are also presented to illustrate the effectiveness of the obtained results.

  11. Classes in Translating and Interpreting Produce Differential Gains in Switching and Updating

    PubMed Central

    Dong, Yanping; Liu, Yuhua

    2016-01-01

    The present longitudinal study was intended to investigate whether the two bilingual experiences of written translation and consecutive interpreting (featured with similar language switching experience but different processing demands) would produce different cognitive control effects in young adults. Three groups of Chinese–English young adult bilinguals, who differed mainly in their half-year long bilingual experience: one for general L2 training, one for written translation and one for oral consecutive interpreting, were tested twice on the number Stroop, switching color-shape and N-back tasks. The results show that the interpreting experience produced significant cognitive advantages in switching (switch cost) and updating, while the translating experience produced marginally significant improvements in updating. The findings indicate that the experience of language switching under higher processing demands brings more domain-general advantages, suggesting that processing demand may be a decisive factor for the presence or absence of the hot-debated bilingual advantages. PMID:27625620

  12. MHC class II tetramers made from isolated recombinant α and β chains refolded with affinity-tagged peptides.

    PubMed

    Braendstrup, Peter; Justesen, Sune; Osterbye, Thomas; Nielsen, Lise Lotte Bruun; Mallone, Roberto; Vindeløv, Lars; Stryhn, Anette; Buus, Søren

    2013-01-01

    Targeting CD4+ T cells through their unique antigen-specific, MHC class II-restricted T cell receptor makes MHC class II tetramers an attractive strategy to identify, validate and manipulate these cells at the single cell level. Currently, generating class II tetramers is a specialized undertaking effectively limiting their use and emphasizing the need for improved methods of production. Using class II chains expressed individually in E. coli as versatile recombinant reagents, we have previously generated peptide-MHC class II monomers, but failed to generate functional class II tetramers. Adding a monomer purification principle based upon affinity-tagged peptides, we here provide a robust method to produce class II tetramers and demonstrate staining of antigen-specific CD4+ T cells. We also provide evidence that both MHC class II and T cell receptor molecules largely accept affinity-tagged peptides. As a general approach to class II tetramer generation, this method should support rational CD4+ T cell epitope discovery as well as enable specific monitoring and manipulation of CD4+ T cell responses.

  13. High-level recombinant protein production in CHO cells using an adenoviral vector and the cumate gene-switch.

    PubMed

    Gaillet, Bruno; Gilbert, Rénald; Amziani, Rachid; Guilbault, Claire; Gadoury, Christine; Caron, Antoine W; Mullick, Alaka; Garnier, Alain; Massie, Bernard

    2007-01-01

    To facilitate and accelerate the production of eukaryotic proteins with correct post-translational modifications, we have developed a protein production system based on the transduction of Chinese hamster ovary (CHO) cells using adenovirus vectors (AdVs). We have engineered a CHO cell line (CHO-cTA) that stably expresses the transactivator (cTA) of our newly developed cumate gene-switch transcription system. This cell line is adapted to suspension culture and can grow in serum-free and protein-free medium. To increase the transduction level of AdVs, we have also generated a cell line (CHO-cTA-CAR) that expresses additional amounts of the coxackievirus and adenovirus receptor (CAR) on its surface. Recombinant protein production was tested using an AdV carrying the secreted alkaline phosphatase (SEAP) under the control of the CR5 promoter, which is strongly and specifically activated by binding to cTA. The SEAP expression was linked to the expression of the green fluorescent protein (GFP) through an internal ribosome entry site (IRES) to facilitate titration of the AdV. We monitored SEAP expression on a daily basis for 9 days after transduction of CHO-cTA and CHO-cTA-CAR using different quantities of AdVs at 37 and 30 degrees C. Incubation at the latter temperature increased the production of SEAP at least 10-fold, and the presence of CAR increased the transduction level of the AdV. Maximum SEAP production (63 mg/L) was achieved at 6-7 days post-infection at 30 degrees C by transducing CHO-cTA-CAR with 500 infectious particles/cell. Because numerous AdVs can now be generated within a few weeks and large-scale production of AdVs is now a routine procedure, this system could be used to produce rapidly milligram quantities of a battery of recombinant proteins as well as for large-scale protein production.

  14. Laser triggering of water switches in terrawatt-class pulse power accelerators.

    SciTech Connect

    Woodworth, Joseph Ray; Johnson, David Lee (Titan Pulse Sciences, San Leandro, CA); Wilkins, Frank (Bechtel Nevada, Las Vegas, NV); Van De Valde, David (EG&G Technical Services, Albuquerque, NM); Sarkisov, Gennady Sergeevich; Zameroski, Nathan D.; Starbird, Robert L.

    2005-12-01

    Focused Beams from high-power lasers have been used to command trigger gas switches in pulse power accelerators for more than two decades. This Laboratory-Directed Research and Development project was aimed at determining whether high power lasers could also command trigger water switches on high-power accelerators. In initial work, we determined that focused light from three harmonics of a small pulsed Nd:YAG laser at 1064 nm, 532 nm, and 355 nm could be used to form breakdown arcs in water, with the lowest breakdown thresholds of 110 J/cm{sup 2} or 14 GW/cm{sup 2} at 532 nm in the green. In laboratory-scale laser triggering experiments with a 170-kV pulse-charged water switch with a 3-mm anode-cathode gap, we demonstrated that {approx}90 mJ of green laser energy could trigger the gap with a 1-{sigma} jitter of less than 2ns, a factor of 10 improvement over the jitter of the switch in its self breaking mode. In the laboratory-scale experiments we developed optical techniques utilizing polarization rotation of a probe laser beam to measure current in switch channels and electric field enhancements near streamer heads. In the final year of the project, we constructed a pulse-power facility to allow us to test laser triggering of water switches from 0.6- MV to 2.0 MV. Triggering experiments on this facility using an axicon lens for focusing the laser and a switch with a 740 kV self-break voltage produced consistent laser triggering with a {+-} 16-ns 1-{sigma} jitter, a significant improvement over the {+-} 24-ns jitter in the self-breaking mode.

  15. [Utility of predeposit autologous blood donation by switch back method combined with recombinant human erythropoietin in gynecological surgery].

    PubMed

    Itani, Y; Ito, K; Hori, K; Tamori, N; Adachi, S

    1996-03-01

    To apply recombinant human (rh)erythropoietin (EPO) to predeposit autologous blood donation (P.A.B.D.) in cancer patients clinically, (1) we tested the effects of rh-EPO on 2 ovarian cancer cell lines in vitro at first, then, (2) studied the effect of the rh-EPO for switch back (SB) method that is a variant of P.A.B.D. clinically. Rh-EPO (0.068-68U/ml) caused no significant and reproducible stimulation of clonal growth to SHIN-3 (derived from serous cyst adenocarcinoma) and MN-1 (derived from mucinous cyst adenocarcinoma). Twenty-five cases were studied. The change in the hemoglobin concentration (delta Hb) was -0.43 +/- 1.38g/dl (mean +/- SD) and the change in the total amount of hemoglobin (total delta Hb) which is calculated on the basis of whole blood volume was 111.5 +/- 53.2g/body in 16 cases with rh-EPO. The delta Hb and total delta Hb were -3.25 +/- 0.78g/dl and 30.1 +/- 41.7g/body in 9 cases without rh-EPO. The rh-EPO combined cases were significantly increased in both delta Hb and total delta Hb (p < 0.05, unpaired student t test). We therefore conclude that it would be very beneficial to use rh-EPO combined with the SB method in P.A.B.D. for high maximum surgical blood order schedule (MSBOS) cases such as gynecological malignancies.

  16. Global tracking for a class of uncertain nonlinear systems with unknown sign-switching control direction by output feedback

    NASA Astrophysics Data System (ADS)

    Roux Oliveira, Tiago; Jacoud Peixoto, Alessandro; Hsu, Liu

    2015-09-01

    This paper addresses the design of a sliding mode controller for a class of high-order uncertain nonlinear plants with unmatched state-dependent nonlinearities and unknown sign of the high frequency gain, i.e., the control direction is assumed unknown. Differently from most previous studies, the control direction is allowed to switch its sign. We show that it is possible to obtain global exact tracking using only output-feedback by coupling a relay periodic switching function with a norm state observer. One significant advantage of the new scheme is its robustness and improved transient response under arbitrary changes of the control direction which have been theoretically demonstrated for jump variations and successfully tested by simulations. The proposed controller is also evaluated with a DC motor control experiment.

  17. Delay-dependent finite-time boundedness of a class of Markovian switching neural networks with time-varying delays.

    PubMed

    Zhong, Qishui; Cheng, Jun; Zhao, Yuqing

    2015-07-01

    In this paper, a novel method is developed for delay-dependent finite-time boundedness of a class of Markovian switching neural networks with time-varying delays. New sufficient condition for stochastic boundness of Markovian jumping neural networks is presented and proved by an newly augmented stochastic Lyapunov-Krasovskii functional and novel activation function conditions, the state trajectory remains in a bounded region of the state space over a given finite-time interval. Finally, a numerical example is given to illustrate the efficiency and less conservative of the proposed method.

  18. The Ets-1 transcription factor is required for Stat1-mediated T-bet expression and IgG2a class switching in mouse B cells.

    PubMed

    Nguyen, Hai Vu; Mouly, Enguerran; Chemin, Karine; Luinaud, Romain; Despres, Raymonde; Fermand, Jean-Paul; Arnulf, Bertrand; Bories, Jean-Christophe

    2012-05-03

    In response to antigens and cytokines, mouse B cells undergo class-switch recombination (CSR) and differentiate into Ig-secreting cells. T-bet, a T-box transcription factor that is up-regulated in lymphocytes by IFN-γ or IL-27, was shown to regulate CSR to IgG2a after T cell-independent B-cell stimulations. However, the molecular mechanisms controlling this process remain unclear. In the present study, we show that inactivation of the Ets-1 transcription factor results in a severe decrease in IgG2a secretion in vivo and in vitro. No T-bet expression was observed in Ets-1-deficient (Ets-1(-/-)) B cells stimulated with IFN-γ and lipopolysaccharide, and forced expression of T-bet in these cells rescued IgG2a secretion. Furthermore, we identified a transcriptional enhancer in the T-bet locus with an activity in B cells that relies on ETS-binding sites. After IFN-γ stimulation of Ets-1(-/-) B cells, activated Stat1, which forms a complex with Ets-1 in wild-type cells, no longer binds to the T-bet enhancer or promotes histone modifications at this site. These results demonstrate that Ets-1 is critical for IgG2a CSR and acts as an essential cofactor for Stat1 in the regulation of T-bet expression in B cells.

  19. A PTIP-PA1 subcomplex promotes transcription for IgH class switching independently from the associated MLL3/MLL4 methyltransferase complex.

    PubMed

    Starnes, Linda M; Su, Dan; Pikkupeura, Laura M; Weinert, Brian T; Santos, Margarida A; Mund, Andreas; Soria, Rebeca; Cho, Young-Wook; Pozdnyakova, Irina; Kubec Højfeldt, Martina; Vala, Andrea; Yang, Wenjing; López-Méndez, Blanca; Lee, Ji-Eun; Peng, Weiqun; Yuan, Joan; Ge, Kai; Montoya, Guillermo; Nussenzweig, André; Choudhary, Chunaram; Daniel, Jeremy A

    2016-01-15

    Class switch recombination (CSR) diversifies antibodies for productive immune responses while maintaining stability of the B-cell genome. Transcription at the immunoglobulin heavy chain (Igh) locus targets CSR-associated DNA damage and is promoted by the BRCT domain-containing PTIP (Pax transactivation domain-interacting protein). Although PTIP is a unique component of the mixed-lineage leukemia 3 (MLL3)/MLL4 chromatin-modifying complex, the mechanisms for how PTIP promotes transcription remain unclear. Here we dissected the minimal structural requirements of PTIP and its different protein complexes using quantitative proteomics in primary lymphocytes. We found that PTIP functions in transcription and CSR separately from its association with the MLL3/MLL4 complex and from its localization to sites of DNA damage. We identified a tandem BRCT domain of PTIP that is sufficient for CSR and identified PA1 as its main functional protein partner. Collectively, we provide genetic and biochemical evidence that a PTIP-PA1 subcomplex functions independently from the MLL3/MLL4 complex to mediate transcription during CSR. These results further our understanding of how multifunctional chromatin-modifying complexes are organized by subcomplexes that harbor unique and distinct activities. © 2016 Starnes et al.; Published by Cold Spring Harbor Laboratory Press.

  20. A PTIP–PA1 subcomplex promotes transcription for IgH class switching independently from the associated MLL3/MLL4 methyltransferase complex

    PubMed Central

    Starnes, Linda M.; Su, Dan; Pikkupeura, Laura M.; Weinert, Brian T.; Santos, Margarida A.; Mund, Andreas; Soria, Rebeca; Cho, Young-Wook; Pozdnyakova, Irina; Kubec Højfeldt, Martina; Vala, Andrea; Yang, Wenjing; López-Méndez, Blanca; Lee, Ji-Eun; Peng, Weiqun; Yuan, Joan; Ge, Kai; Montoya, Guillermo; Nussenzweig, André; Choudhary, Chunaram; Daniel, Jeremy A.

    2016-01-01

    Class switch recombination (CSR) diversifies antibodies for productive immune responses while maintaining stability of the B-cell genome. Transcription at the immunoglobulin heavy chain (Igh) locus targets CSR-associated DNA damage and is promoted by the BRCT domain-containing PTIP (Pax transactivation domain-interacting protein). Although PTIP is a unique component of the mixed-lineage leukemia 3 (MLL3)/MLL4 chromatin-modifying complex, the mechanisms for how PTIP promotes transcription remain unclear. Here we dissected the minimal structural requirements of PTIP and its different protein complexes using quantitative proteomics in primary lymphocytes. We found that PTIP functions in transcription and CSR separately from its association with the MLL3/MLL4 complex and from its localization to sites of DNA damage. We identified a tandem BRCT domain of PTIP that is sufficient for CSR and identified PA1 as its main functional protein partner. Collectively, we provide genetic and biochemical evidence that a PTIP–PA1 subcomplex functions independently from the MLL3/MLL4 complex to mediate transcription during CSR. These results further our understanding of how multifunctional chromatin-modifying complexes are organized by subcomplexes that harbor unique and distinct activities. PMID:26744420

  1. Addressing the Problem of Switched Class Labels in Latent Variable Mixture Model Simulation Studies

    ERIC Educational Resources Information Center

    Tueller, Stephen J.; Drotar, Scott; Lubke, Gitta H.

    2011-01-01

    The discrimination between alternative models and the detection of latent classes in the context of latent variable mixture modeling depends on sample size, class separation, and other aspects that are related to power. Prior to a mixture analysis it is useful to investigate model performance in a simulation study that reflects the research…

  2. Addressing the Problem of Switched Class Labels in Latent Variable Mixture Model Simulation Studies

    ERIC Educational Resources Information Center

    Tueller, Stephen J.; Drotar, Scott; Lubke, Gitta H.

    2011-01-01

    The discrimination between alternative models and the detection of latent classes in the context of latent variable mixture modeling depends on sample size, class separation, and other aspects that are related to power. Prior to a mixture analysis it is useful to investigate model performance in a simulation study that reflects the research…

  3. Processing of recombinant Listeria monocytogenes proteins for MHC class I presentation follows a dedicated, high-efficiency pathway

    PubMed Central

    Wolf, Benjamin J.; Princiotta, Michael F.

    2013-01-01

    CD8+ T lymphocytes recognize short peptides of ~8–10 amino acids bound to MHC class I molecules (pMHC) on the surface of antigen presenting cells. These peptides can be generated from either endogenous proteins synthesized by the biosynthetic machinery of the presenting cell or from exogenously sourced proteins. Because much of the research characterizing the MHC class I processing pathway has focused on endogenously synthesized proteins, it is not known whether differences exist in the processing pathway followed by endogenously synthesized versus exogenously sourced proteins. To highlight potential differences in the processing of endogenous versus exogenous proteins, we developed a model system to measure the efficiency of pMHC generation from nearly identical recombinant proteins expressed from vaccinia virus and Listeria monocytogenes. In these experiments, we uncovered a striking difference in the way recombinant Listeria antigens are processed and presented when compared to endogenously synthesized viral proteins. Specifically, we find that pMHC production from secreted Listeria proteins occurs at the same rate, independent of the cellular half-life of the protein from which it is derived, whereas the rate of pMHC production from endogenously synthesized viral proteins is absolutely dependent on its protein half-life. Accordingly, our data demonstrate the existence of a distinct and highly efficient MHC class I presentation pathway used for the processing of at least some exogenously synthesized proteins. PMID:23396941

  4. B cell Rab7 mediates induction of activation-induced cytidine deaminase expression and class-switching in T-dependent and T-independent antibody responses.

    PubMed

    Pone, Egest J; Lam, Tonika; Lou, Zheng; Wang, Rui; Chen, Yuhui; Liu, Dongfang; Edinger, Aimee L; Xu, Zhenming; Casali, Paolo

    2015-04-01

    Class switch DNA recombination (CSR) is central to the maturation of the Ab response because it diversifies Ab effector functions. Like somatic hypermutation, CSR requires activation-induced cytidine deaminase (AID), whose expression is restricted to B cells, as induced by CD40 engagement or dual TLR-BCR engagement (primary CSR-inducing stimuli). By constructing conditional knockout Igh(+/C)γ(1-cre)Rab7(fl/fl) mice, we identified a B cell-intrinsic role for Rab7, a small GTPase involved in intracellular membrane functions, in mediating AID induction and CSR. Igh(+/C)γ(1-cre)Rab7(fl/fl) mice displayed normal B and T cell development and were deficient in Rab7 only in B cells undergoing Igh(C)γ(1-cre) Iγ1-Sγ1-Cγ1-cre transcription, as induced--like Igh germline Iγ1-Sγ1-Cγ1 and Iε-Sε-Cε transcription--by IL-4 in conjunction with a primary CSR-inducing stimulus. These mice could not mount T-independent or T-dependent class-switched IgG1 or IgE responses while maintaining normal IgM levels. Igh(+/C)γ(1-cre)Rab7(fl/fl) B cells showed, in vivo and in vitro, normal proliferation and survival, normal Blimp-1 expression and plasma cell differentiation, as well as intact activation of the noncanonical NF-κB, p38 kinase, and ERK1/2 kinase pathways. They, however, were defective in AID expression and CSR in vivo and in vitro, as induced by CD40 engagement or dual TLR1/2-, TLR4-, TLR7-, or TLR9-BCR engagement. In Igh(+/C)γ(1-cre)Rab7(fl/fl) B cells, CSR was rescued by enforced AID expression. These findings, together with our demonstration that Rab7-mediated canonical NF-κB activation, as critical to AID induction, outline a novel role of Rab7 in signaling pathways that lead to AID expression and CSR, likely by promoting assembly of signaling complexes along intracellular membranes.

  5. Improved stability of a class of switched neutral systems via Lyapunov-Krasovskii functionals and an average dwell-time scheme

    NASA Astrophysics Data System (ADS)

    Li, Tai-Fang; Dimirovski, Georgi M.; Liu, Yanyan; Zhao, Jun

    2013-06-01

    This article is concerned with the stability analysis for a class of switched neutral systems with mixed time-varying delays. The upper bound of derivative of the discrete time-varying delay is not restricted to one. A delay-dependent criterion of exponential stability under switching signals with an average dwell time is developed by employing free weighting matrices. The criterion is given in the form of linear matrix inequality. A state decay estimation for the switched system is explicitly given by considering the individual rate of decay of state for each subsystem. Two simulation examples are given to illustrate the effectiveness of the proposed method.

  6. Engineering of Conditional Class I Hdac Knockout Mice and Generation of a Time-Spatial Knockout by a Dual Recombination System.

    PubMed

    Bayer, Sieglinde; Wirth, Matthias

    2017-01-01

    The protein sequences of class I HDACs in mice and humans are 96-99 % identical. These highly conserved proteins have crucial roles in biological processes, such as proliferation and development, which is reflected in the lethality that occurs in conventional whole body knockout mice. Therefore, conditional knockouts are inevitable to investigate the functions of class I HDACs in mice. Here, we describe the generation of conditional class I Hdac knockout mice, using Hdac1 as an example. We explain a relatively quick procedure to generate the necessary target vectors by recombination-mediated genetic engineering and gateway techniques. Furthermore, we show how to culture, target, and screen for positively recombined ES cells. Additionally, we present a dual recombination system, which allows the deletion of class I Hdacs at any time by a tamoxifen inducible Cre.

  7. Synchronization of a Class of Switched Neural Networks with Time-Varying Delays via Nonlinear Feedback Control.

    PubMed

    Wang, Leimin; Shen, Yi; Zhang, Guodong

    2016-10-01

    This paper is concerned with the synchronization problem for a class of switched neural networks (SNNs) with time-varying delays. First, a new crucial lemma which includes and extends the classical exponential stability theorem is constructed. Then by using the lemma, new algebraic criteria of ψ -type synchronization (synchronization with general decay rate) for SNNs are established via the designed nonlinear feedback control. The ψ -type synchronization which is in a general framework is obtained by introducing a ψ -type function. It contains exponential synchronization, polynomial synchronization, and other synchronization as its special cases. The results of this paper are general, and they also complement and extend some previous results. Finally, numerical simulations are carried out to demonstrate the effectiveness of the obtained results.

  8. Hierarchical multiobjective routing model in Multiprotocol Label Switching networks with two service classes - a Pareto archive strategy

    NASA Astrophysics Data System (ADS)

    Girão-Silva, Rita; Craveirinha, José; Clímaco, João

    2012-05-01

    The article begins by reviewing a two-level hierarchical multicriteria routing model for Multiprotocol Label Switching networks with two service classes (QoS, i.e. with Quality of Service requirements, and Best Effort services) and alternative routing, as well as the foundations of a heuristic resolution approach, previously proposed by the authors. Afterwards a new variant of this heuristic approach, which includes a Pareto archive strategy, is described. In this archive, non-dominated solutions obtained throughout the heuristic are kept. At the end of the main procedure of the heuristic, these solutions are evaluated and a final solution for the routing problem is chosen using a reference point-based approach. The application of this procedure to two test networks will show, with analytic and discrete-event simulation models, that, in certain initial conditions, this approach provides improvements in the final results concerning the top-level objective functions, especially in more 'difficult' situations detected through sensitivity analysis.

  9. C-type lectin-like receptor LOX-1 promotes dendritic cell-mediated class-switched B cell responses.

    PubMed

    Joo, HyeMee; Li, Dapeng; Dullaers, Melissa; Kim, Tae-Whan; Duluc, Dorothee; Upchurch, Katherine; Xue, Yaming; Zurawski, Sandy; Le Grand, Roger; Liu, Yong-Jun; Kuroda, Marcelo; Zurawski, Gerard; Oh, SangKon

    2014-10-16

    Lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is a pattern-recognition receptor for a variety of endogenous and exogenous ligands. However, LOX-1 function in the host immune response is not fully understood. Here, we report that LOX-1 expressed on dendritic cells (DCs) and B cells promotes humoral responses. On B cells LOX-1 signaling upregulated CCR7, promoting cellular migration toward lymphoid tissues. LOX-1 signaling on DCs licensed the cells to promote B cell differentiation into class-switched plasmablasts and led to downregulation of chemokine receptor CXCR5 and upregulation of chemokine receptor CCR10 on plasmablasts, enabling their exit from germinal centers and migration toward local mucosa and skin. Finally, we found that targeting influenza hemagglutinin 1 (HA1) subunit to LOX-1 elicited HA1-specific protective antibody responses in rhesus macaques. Thus, LOX-1 expressed on B cells and DC cells has complementary functions to promote humoral immune responses.

  10. Analysis of strand transfer and template switching mechanisms of DNA gap repair by homologous recombination in Escherichia coli: predominance of strand transfer.

    PubMed

    Izhar, Lior; Goldsmith, Moshe; Dahan, Ronny; Geacintov, Nicholas; Lloyd, Robert G; Livneh, Zvi

    2008-09-12

    Daughter strand gaps formed upon interruption of replication at DNA lesions in Escherichia coli can be repaired by either translesion DNA synthesis or homologous recombination (HR) repair. Using a plasmid-based assay system that enables discrimination between strand transfer and template switching (information copying) modes of HR gap repair, we found that approximately 80% of strand gaps were repaired by physical strand transfer from the donor, whereas approximately 20% appear to be repaired by template switching. HR gap repair operated on both small and bulky lesions and largely depended on RecA and RecF but not on the RecBCD nuclease. In addition, we found that HR was mildly reduced in cells lacking the RuvABC and RecG proteins involved in resolution of Holliday junctions. These results, obtained for the first time under conditions that detect the two HR gap repair mechanisms, provide in vivo high-resolution molecular evidence for the predominance of the strand transfer mechanism in HR gap repair. A small but significant portion of HR gap repair appears to occur via a template switching mechanism.

  11. Viral double-stranded RNA triggers Ig class switching by activating upper respiratory mucosa B cells through an innate TLR3 pathway involving BAFF.

    PubMed

    Xu, Weifeng; Santini, Paul A; Matthews, Allysia J; Chiu, April; Plebani, Alessandro; He, Bing; Chen, Kang; Cerutti, Andrea

    2008-07-01

    Class switch DNA recombination (CSR) from IgM to IgG and IgA is crucial for antiviral immunity. Follicular B cells undergo CSR upon engagement of CD40 by CD40 ligand on CD4+ T cells. This T cell-dependent pathway requires 5-7 days, which is too much of a delay to block quickly replicating pathogens. To compensate for this limitation, extrafollicular B cells rapidly undergo CSR through a T cell-independent pathway that involves innate Ag receptors of the TLR family. We found that a subset of upper respiratory mucosa B cells expressed TLR3 and responded to viral dsRNA, a cognate TLR3 ligand. In the presence of dsRNA, mucosal B cells activated NF-kappaB, a transcription factor critical for CSR. Activation of NF-kappaB required TRIF (Toll/IL-1R domain-containing protein inducing IFN-beta), a canonical TLR3 adapter protein, and caused germline transcription of downstream CH genes as well as expression of AID (activation-induced cytidine deaminase), a DNA-editing enzyme essential for CSR. Subsequent IgG and IgA production was enhanced by BAFF (B cell-activating factor of the TNF family), an innate mediator released by TLR3-expressing mucosal dendritic cells. Indeed, these innate immune cells triggered IgG and IgA responses upon exposure to dsRNA. By showing active TLR3 signaling and ongoing CSR in upper respiratory mucosa B cells from patients with CD40 signaling defects, our findings indicate that viral dsRNA may initiate frontline IgG and IgA responses through an innate TLR3-dependent pathway involving BAFF.

  12. Viral Double-Stranded RNA Triggers Ig Class Switching by Activating Upper Respiratory Mucosa B Cells through an Innate TLR3 Pathway Involving BAFF1

    PubMed Central

    Xu, Weifeng; Santini, Paul A.; Matthews, Allysia J.; Chiu, April; Plebani, Alessandro; He, Bing; Chen, Kang; Cerutti, Andrea

    2011-01-01

    Class switch DNA recombination (CSR) from IgM to IgG and IgA is crucial for antiviral immunity. Follicular B cells undergo CSR upon engagement of CD40 by CD40 ligand on CD4+ T cells. This T cell-dependent pathway requires 5–7 days, which is too much of a delay to block quickly replicating pathogens. To compensate for this limitation, extrafollicular B cells rapidly undergo CSR through a T cell-independent pathway that involves innate Ag receptors of the TLR family. We found that a subset of upper respiratory mucosa B cells expressed TLR3 and responded to viral dsRNA, a cognate TLR3 ligand. In the presence of dsRNA, mucosal B cells activated NF-κB, a transcription factor critical for CSR. Activation of NF-κB required TRIF (Toll/IL-1R domain-containing protein inducing IFN-β), a canonical TLR3 adapter protein, and caused germline transcription of downstream CH genes as well as expression of AID (activation-induced cytidine deaminase), a DNA-editing enzyme essential for CSR. Subsequent IgG and IgA production was enhanced by BAFF (B cell-activating factor of the TNF family), an innate mediator released by TLR3-expressing mucosal dendritic cells. Indeed, these innate immune cells triggered IgG and IgA responses upon exposure to dsRNA. By showing active TLR3 signaling and ongoing CSR in upper respiratory mucosa B cells from patients with CD40 signaling defects, our findings indicate that viral dsRNA may initiate frontline IgG and IgA responses through an innate TLR3-dependent pathway involving BAFF. PMID:18566393

  13. Balancing selection and recombination as evolutionary forces caused population genetic variations in golden pheasant MHC class I genes.

    PubMed

    Zeng, Qian-Qian; He, Ke; Sun, Dan-Dan; Ma, Mei-Ying; Ge, Yun-Fa; Fang, Sheng-Guo; Wan, Qiu-Hong

    2016-02-18

    The major histocompatibility complex (MHC) genes are vital partners in the acquired immune processes of vertebrates. MHC diversity may be directly associated with population resistance to infectious pathogens. Here, we screened for polymorphisms in exons 2 and 3 of the IA1 and IA2 genes in 12 golden pheasant populations across the Chinese mainland to characterize their genetic variation levels, to understand the effects of historical positive selection and recombination in shaping class I diversity, and to investigate the genetic structure of wild golden pheasant populations. Among 339 individual pheasants, we identified 14 IA1 alleles in exon 2 (IA1-E2), 11 IA1-E3 alleles, 27 IA2-E2 alleles, and 28 IA2-E3 alleles. The non-synonymous substitution rate was significantly greater than the synonymous substitution rate at sequences in the IA2 gene encoding putative peptide-binding sites but not in the IA1 gene; we also found more positively selected sites in IA2 than in IA1. Frequent recombination events resulted in at least 9 recombinant IA2 alleles, in accordance with the intermingling pattern of the phylogenetic tree. Although some IA alleles are widely shared among studied populations, large variation occurs in the number of IA alleles across these populations. Allele frequency analysis across 2 IA loci showed low levels of genetic differentiation among populations on small geographic scales; however, significant genetic differentiation was observed between pheasants from the northern and southern regions of the Yangtze River. Both STRUCTURE analysis and F-statistic (F ST ) value comparison classified those populations into 2 major groups: the northern region of the Yangtze River (NYR) and the southern region of the Yangtze River (SYR). More extensive polymorphisms in IA2 than IA1 indicate that IA2 has undergone much stronger positive-selection pressure during evolution. Moreover, the recombination events detected between the genes and the intermingled phylogenetic

  14. Characterization and functional analysis of a recombinant tau class glutathione transferase GmGSTU2-2 from Glycine max.

    PubMed

    Skopelitou, Katholiki; Muleta, Abdi W; Papageorgiou, Anastassios C; Chronopoulou, Evangelia G; Pavli, Ourania; Flemetakis, Emmanouil; Skaracis, Georgios N; Labrou, Nikolaos E

    2017-01-01

    The plant tau class glutathione transferases (GSTs) perform diverse catalytic as well as non-catalytic roles in detoxification of xenobiotics, prevention of oxidative damage and endogenous metabolism. In the present work, the tau class isoenzyme GSTU2-2 from Glycine max (GmGSTU2-2) was characterized. Gene expression analysis of GmGSTU2 suggested a highly specific and selective induction pattern to osmotic stresses, indicating that gene expression is controlled by a specific mechanism. Purified, recombinant GmGSTU2-2 was shown to exhibit wide-range specificity towards xenobiotic compounds and ligand-binding properties, suggesting that the isoenzyme could provide catalytic flexibility in numerous metabolic conditions. Homology modeling and phylogenetic analysis suggested that the catalytic and ligand binding sites of GmGSTU2-2 are well conserved compared to other tau class GSTs. Structural analysis identified key amino acid residues in the hydrophobic binding site and provided insights into the substrate specificity of this enzyme. The results established that GmGSTU2-2 participates in a broad network of catalytic and regulatory functions involved in the plant stress response.

  15. Accumulation of class switched IgD-IgM- memory B cells in the cerebrospinal fluid during neuroinflammation.

    PubMed

    Cepok, Sabine; von Geldern, Gloria; Grummel, Verena; Hochgesand, Sonja; Celik, Handan; Hartung, Hanspeter; Hemmer, Bernhard

    2006-11-01

    Inflammatory diseases of the central nervous system (CNS) are characterized by cerebrospinal fluid (CSF) pleocytosis often involving the recruitment of B cells. Little is still known about B cells that are found in the CSF during neuroinflammation. To address the phenotype of these B cells, we studied the distribution of the major B cell subsets in peripheral blood (PB) and CSF of 25 patients with inflammatory diseases of the nervous system by flow cytometry. Six different B cell subsets were identified in PB and CSF according to the surface expression of IgM, IgD, CD27 and CD19. In all patients analysed, memory B cells outnumbered naïve B cells in the CSF, whereas naïve B cells were more prevalent in PB. The accumulation of memory B cells in the CSF was largely due to the recruitment of IgM-IgD- class switched memory B cells. The distribution of IgM+IgD+, IgM-IgD+, IgM+IgD- memory cells and immature cells did not differ significantly between CSF and PB. These findings demonstrate a selective recruitment of IgM-IgD- memory B cells to the CSF suggesting a specific role of these cells during neuroinflammation.

  16. [Serodiagnosis of chlamydiosis: "Chlamy-IgG-DS-Tr"-- the first domestic immunoenzyme recombinant test-system for determination of anti-Chlamydia trachomatis class G antibodies].

    PubMed

    Manzeniuk, I N; Vorob'eva, M S; Nikitiuk, N M; Fedosov, S A; Gorbunov, M A; Gnedoĭ, S N; Losev, V I; Krivenchuk, N A

    2000-01-01

    The first Native test-system for determination of class G antibodies to Chlamydia trachomatis with chlamydia recombinant antigen was elaborated Test-system efficacy was demonstrated in clinical trials. The sensibility, specific activity and suitability of the "Chlamy-IgG-DS-Tr" were the same as for import analogous.

  17. Transcriptional activation by LR1 at the Eµ enhancer and switch region sites

    PubMed Central

    Hanakahi, L. A.; Maizels, Nancy

    2000-01-01

    LR1 is a B cell-specific, sequence-specific duplex DNA binding activity which is induced in B cells carrying out class switch recombination. Here we identify several properties of LR1 which enable it to function in transcriptional regulation. We show that LR1 contributes to transcriptional activation by the Eµ immunoglobulin heavy chain intron enhancer by binding to a site within the enhancer core. We further show that LR1 bends DNA upon binding. In addition, we show that LR1 is itself a bona fide transcriptional activator, as multimerized LR1 sites produce an element which can enhance transcription from a minimal promoter. In order for class switch recombination to occur, an activating signal must be transmitted via the Eµ core, and both S regions targeted for recombination must be actively transcribed. The properties of LR1 that we have identified suggest distinct potential functions of LR1 duplex DNA binding activity in class switch recombination. First, LR1 may contribute to recombinational activation by the Eµ core. Second, there are multiple potential LR1 duplex binding sites in each of the G-rich switch regions, and LR1 bound at contiguous sites may enhance recombination by stimulating transcription of the S regions. PMID:10908319

  18. Adaptive Fuzzy Output-Feedback Stabilization Control for a Class of Switched Nonstrict-Feedback Nonlinear Systems.

    PubMed

    Li, Yongming; Tong, Shaocheng

    2017-04-01

    This paper proposes an fuzzy adaptive output-feedback stabilization control method for nonstrict feedback uncertain switched nonlinear systems. The controlled system contains unmeasured states and unknown nonlinearities. First, a switched state observer is constructed in order to estimate the unmeasured states. Second, a variable separation approach is introduced to solve the problem of nonstrict feedback. Third, fuzzy logic systems are utilized to identify the unknown uncertainties, and an adaptive fuzzy output feedback stabilization controller is set up by exploiting the backstepping design principle. At last, by applying the average dwell time method and Lyapunov stability theory, it is proven that all the signals in the closed-loop switched system are bounded, and the system output converges to a small neighborhood of the origin. Two examples are given to further show the effectiveness of the proposed switched control approach.

  19. Base pair switching by interconversion of sugar puckers in DNA extended by proteins of RecA-family: A model for homology search in homologous genetic recombination

    PubMed Central

    Nishinaka, Taro; Shinohara, Akira; Ito, Yutaka; Yokoyama, Shigeyuki; Shibata, Takehiko

    1998-01-01

    Escherichia coli RecA is a representative of proteins from the RecA family, which promote homologous pairing and strand exchange between double-stranded DNA and single-stranded DNA. These reactions are essential for homologous genetic recombination in various organisms. From NMR studies, we previously reported a novel deoxyribose-base stacking interaction between adjacent residues on the extended single-stranded DNA bound to RecA protein. In this study, we found that the same DNA structure was induced by the binding to Saccharomyces cerevisiae Rad51 protein, indicating that the unique DNA structure induced by the binding to RecA-homologs was conserved from prokaryotes to eukaryotes. On the basis of this structure, we have formulated the structure of duplex DNA within filaments formed by RecA protein and its homologs. Two types of molecular structures are presented. One is the duplex structure that has the N-type sugar pucker. Its helical pitch is ≈95 Å (18.6 bp/turn), corresponding to that of an active, or ATP-form of the RecA filament. The other is one that has the S-type sugar pucker. Its helical pitch is ≈64 Å (12.5 bp/turn), corresponding to that of an inactive, or ADP-form of the RecA filament. During this modeling, we found that the interconversion of sugar puckers between the N-type and the S-type rotates bases horizontally, while maintaining the deoxyribose-base stacking interaction. We propose that this base rotation enables base pair switching between double-stranded DNA and single-stranded DNA to take place, facilitating homologous pairing and strand exchange. A possible mechanism for strand exchange involving DNA rotation also is discussed. PMID:9736691

  20. Induction of apoptosis after switch-on of the hepatitis B virus X gene mediated by the Cre/loxP recombination system.

    PubMed

    Shintani, Y; Yotsuyanagi, H; Moriya, K; Fujie, H; Tsutsumi, T; Kanegae, Y; Kimura, S; Saito, I; Koike, K

    1999-12-01

    The HBx protein of hepatitis B virus is a multifunctional protein that is implicated in the pathogenesis of hepatocellular carcinoma by regulating gene transcription, causing cell proliferation and, as shown recently, inducing cell death. However, analysis of the effects of HBx in stable cultured cell clones has been hampered because only cell lines that adapted to the effects of HBx were selected during the establishment of cell clones. Here, we describe a system in which transcription of the X gene of hepatitis B virus is switched on by the use of the site-specific Cre recombinase. Two human liver cell lines, HLF and HepG2, were used, the former with a mutant p53 allele and the latter with wild-type p53. The stable cell clones isolated, which carried the X gene in a transcriptionally silent state, were infected with recombinant adenovirus carrying Cre recombinase. Ninety-six hours after adenovirus infection, cell clones that expressed HBx had undergone TUNEL-positive cell death with characteristics of apoptosis. Apoptosis was induced despite concomitant inactivation of the p53 protein as a result of its cytoplasmic translocation by HBx. In contrast, neither the X gene-carrying cells infected with wild-type adenovirus nor various control cells infected with Cre-expressing adenovirus exhibited apoptosis. These results indicate that the expression of HBx protein leads to liver cell apoptosis independently of the p53 pathway. The significance of HBx-induced apoptosis in natural infection is unclear, but it may contribute to the development of hepatitis and serve to spread progeny virus to neighbouring cells while evading the host immune responses.

  1. Spectrum Recombination.

    ERIC Educational Resources Information Center

    Greenslade, Thomas B., Jr.

    1984-01-01

    Describes several methods of executing lecture demonstrations involving the recombination of the spectrum. Groups the techniques into two general classes: bringing selected portions of the spectrum together using lenses or mirrors and blurring the colors by rapid movement or foreshortening. (JM)

  2. Spectrum Recombination.

    ERIC Educational Resources Information Center

    Greenslade, Thomas B., Jr.

    1984-01-01

    Describes several methods of executing lecture demonstrations involving the recombination of the spectrum. Groups the techniques into two general classes: bringing selected portions of the spectrum together using lenses or mirrors and blurring the colors by rapid movement or foreshortening. (JM)

  3. The Arabidopsis MutS homolog AtMSH4 functions at an early step in recombination: evidence for two classes of recombination in Arabidopsis

    PubMed Central

    Higgins, James D.; Armstrong, Susan J.; Franklin, F. Christopher H.; Jones, Gareth H.

    2004-01-01

    MSH4, a meiosis-specific member of the MutS-homolog family of genes, is required for normal levels of recombination and fertility in budding yeast, mouse, and Caenorhabditis elegans. In this paper, we report the identification and characterization of the Arabidopsis homolog of MSH4 (AtMSH4). We demonstrate that AtMSH4 expression can only be detected in floral tissues, consistent with a role in reproduction. Immunofluorescence studies indicate that its expression is limited to early meiotic prophase I, preceding the synapsis of homologous chromosomes. A T-DNA insertional mutant (Atmsh4) exhibited normal vegetative growth but a severe reduction in fertility, consistent with a meiotic defect; this was confirmed by cytological analysis of meiosis. RNAi-induced down-regulation of the MSH4 gene resulted in a similar fertility and meiotic phenotype. We demonstrate that prophase I chromosome synapsis is delayed and may be incomplete in Atmsh4, and metaphase I chiasma frequency is greatly reduced to ∼15% of wild type, leading to univalence and nondisjunction. We show that these residual chiasmata are randomly distributed among cells and chromosomes. These features of chiasma frequency and distribution in Atmsh4 show close parallels to MSH4-independent crossovers in budding yeast that have been proposed to originate by a separate pathway. Furthermore, the characteristics of the MSH4-independent chiasmata in the Atmsh4 mutant closely parallel those of second-pathway crossovers that have been postulated from Arabidopsis crossover analysis and mathematical modeling. Taken together, this evidence strongly indicates that Arabidopsis possesses two crossover pathways. PMID:15489296

  4. The diabetogenic mouse MHC class II molecule I-A[superscript g7] is endowed with a switch that modulates TCR affinity

    SciTech Connect

    Yoshida, Kenji; Corper, Adam L.; Herro, Rana; Jabri, Bana; Wilson, Ian A.; Teyton, Luc

    2010-07-22

    Genetic susceptibility to autoimmunity is frequently associated with specific MHC alleles. Diabetogenic MHC class II molecules, such as human HLA-DQ8 and mouse I-A{sup g7}, typically have a small, uncharged amino acid residue at position 57 of their {beta} chain ({beta}57); this results in the absence of a salt bridge between {beta}57 and Arg{alpha}76, which is adjacent to the P9 pocket of the peptide-binding groove. However, the influence of Arg{alpha}76 on the selection of the TCR repertoire remains unknown, particularly when the MHC molecule binds a peptide with a neutral amino acid residue at position P9. Here, we have shown that diabetogenic MHC class II molecules bound to a peptide with a neutral P9 residue primarily selected and expanded cells expressing TCRs bearing a negatively charged residue in the first segment of their complementarity determining region 3{beta}. The crystal structure of one such TCR in complex with I-Ag7 bound to a peptide containing a neutral P9 residue revealed that a network of favorable long-range (greater than 4 {angstrom}) electrostatic interactions existed among Arg{alpha}76, the neutral P9 residue, and TCR, which supported the substantially increased TCR/peptide-MHC affinity. This network could be modulated or switched to a lower affinity interaction by the introduction of a negative charge at position P9 of the peptide. Our results support the existence of a switch at residue {beta}57 of the I-A{sup g7} and HLA-DQ8 class II molecules and potentially link normal thymic TCR selection with abnormal peripheral behavior.

  5. The diabetogenic mouse MHC class II molecule I-A[subscript g7] is endowed with a switch that modulates TCR affinity

    SciTech Connect

    Yoshida, Kenji; Corper, Adam L.; Herro, Rana; Jabri, Bana; Wilson, Ian A.; Teyton, Luc

    2011-11-16

    Genetic susceptibility to autoimmunity is frequently associated with specific MHC alleles. Diabetogenic MHC class II molecules, such as human HLA-DQ8 and mouse I-A{sub g7}, typically have a small, uncharged amino acid residue at position 57 of their {beta} chain ({beta}57); this results in the absence of a salt bridge between {beta}57 and Arg{alpha}76, which is adjacent to the P9 pocket of the peptide-binding groove. However, the influence of Arg{alpha}76 on the selection of the TCR repertoire remains unknown, particularly when the MHC molecule binds a peptide with a neutral amino acid residue at position P9. Here, we have shown that diabetogenic MHC class II molecules bound to a peptide with a neutral P9 residue primarily selected and expanded cells expressing TCRs bearing a negatively charged residue in the first segment of their complementarity determining region 3{beta}. The crystal structure of one such TCR in complex with I-A{sub g7} bound to a peptide containing a neutral P9 residue revealed that a network of favorable long-range (greater than 4 {angstrom}) electrostatic interactions existed among Arg{alpha}76, the neutral P9 residue, and TCR, which supported the substantially increased TCR/peptide-MHC affinity. This network could be modulated or switched to a lower affinity interaction by the introduction of a negative charge at position P9 of the peptide. Our results support the existence of a switch at residue {beta}57 of the I-Ag7 and HLA-DQ8 class II molecules and potentially link normal thymic TCR selection with abnormal peripheral behavior.

  6. Finite-time H∞ control for a class of discrete-time Markovian jump systems with partly unknown time-varying transition probabilities subject to average dwell time switching

    NASA Astrophysics Data System (ADS)

    Cheng, Jun; Zhu, Hong; Zhong, Shouming; Zhang, Yuping; Li, Yuanyuan

    2015-04-01

    An extension of a fixed transition probability (TP) Markovian switching model to combine time-varying TPs has offered another set of useful regime-switching models. This paper is concerned with the problem of finite-time H∞ control for a class of discrete-time Markovian jump systems with partly unknown time-varying TPs subject to average dwell time switching. The so-called time-varying TPs mean that the TPs are varying but invariant within an interval. The variation of the TPs considered here is subject to a class of slow switching signal. Based on selecting the appropriate Lyapunov-Krasovskii functional, sufficient conditions of finite-time boundedness of Markovian jump systems are derived and the system trajectory stays within a prescribed bound. Finally, an example is given to illustrate the efficiency of the proposed method.

  7. Comparative in Vitro Analysis of Proliferation, Ig Secretion, and Ig Class Switching by Murine Marginal Zone and Follicular B Cells

    DTIC Science & Technology

    1993-04-01

    FL). IgG2a, IgE, and IgA ) found in the culture supernatants. and sorted cells were immediately reanalyzed to confirm their stai oDetermination of...the Bnh ouL.EPA.Czae.nd.Snou190Ati isotspe switch of murine B cells.. J, Evp. Aed. 155:734. immunogilobulins induce death by apoptosis in WEHI -21S1 8...J. A. Boersma. and E. Claassen. 1992. Complement- Tcells in the development of an IgG and IgA antibody re- meiae folclrlclzto TidpnettPC- n sponse. J

  8. Purified recombinant hypothetical protein coded by open reading frame Rv1885c of Mycobacterium tuberculosis exhibits a monofunctional AroQ class of periplasmic chorismate mutase activity.

    PubMed

    Prakash, Prachee; Aruna, Bandi; Sardesai, Abhijit A; Hasnain, Seyed E

    2005-05-20

    Naturally occurring variants of the enzyme chorismate mutase are known to exist that exhibit diversity in enzyme structure, regulatory properties, and association with other proteins. Chorismate mutase was not annotated in the initial genome sequence of Mycobacterium tuberculosis (Mtb) because of low sequence similarity between known chorismate mutases. Recombinant protein coded by open reading frame Rv1885c of Mtb exhibited chorismate mutase activity in vitro. Biochemical and biophysical characterization of the recombinant protein suggests its resemblance to the AroQ class of chorismate mutases, prototype examples of which include the Escherichia coli and yeast chorismate mutases. We also demonstrate that unlike the corresponding proteins of E. coli, Mtb chorismate mutase does not have any associated prephenate dehydratase or dehydrogenase activity, indicating its monofunctional nature. The Rv1885c-encoded chorismate mutase showed allosteric regulation by pathway-specific as well as cross-pathway-specific ligands, as evident from proteolytic cleavage protection and enzyme assays. The predicted N-terminal signal sequence of Mtb chorismate mutase was capable of functioning as one in E. coli, suggesting that Mtb chorismate mutase belongs to the AroQ class of chorismate mutases. It was evident that Rv1885c may not be the only enzyme with chorismate mutase enzyme function within Mtb, based on our observation of the presence of chorismate mutase activity displayed by another hypothetical protein coded by open reading frame Rv0948c, a novel instance of the existence of two monofunctional chorismate mutases ever reported in any pathogenic bacterium.

  9. Adaptive neural network tracking control for a class of switched stochastic pure-feedback nonlinear systems with backlash-like hysteresis

    NASA Astrophysics Data System (ADS)

    Niu, Ben; Qin, Tian; Fan, Xiaodong

    2016-10-01

    In this paper, an adaptive neural network tracking control approach is proposed for a class of switched stochastic pure-feedback nonlinear systems with backlash-like hysteresis. In the design procedure, an affine variable is constructed, which avoids the use of the mean value theorem, and the additional first-order low-pass filter is employed to deal with the problem of explosion of complexity. Then, a common Lyapunov function and a state feedback controller are explicitly obtained for all subsystems. It is proved that the proposed controller that guarantees all signals in the closed-loop system are semi-globally uniformly ultimately bounded and the tracking error remains an adjustable neighbourhood of the origin. Finally, simulation results show the effectiveness of the presented control design approach.

  10. Natural selection coupled with intragenic recombination shapes diversity patterns in the major histocompatibility complex class II genes of the giant panda.

    PubMed

    Chen, Yi-Yan; Zhang, Ying-Ying; Zhang, He-Min; Ge, Yun-Fa; Wan, Qiu-Hong; Fang, Sheng-Guo

    2010-05-15

    Ample variations of the major histocompatibility complex (MHC) genes are essential for vertebrates to adapt to various environmental conditions. In this study, we investigated the genetic variations and evolutionary patterns of seven functional MHC class II genes (one DRA, two DRB, two DQA, and two DQB) of the giant panda. The results showed the presence of two monomorphic loci (DRA and DQB2) and five polymorphic loci with different numbers of alleles (seven at DRB1, six at DRB3, seven at DQA1, four at DQA2, six at DQB1). The presence of balancing selection in the giant panda was supported by the following pieces of evidence: (1) The observed heterozygosity was higher than expected. (2) Amino acid heterozygosity was significantly higher at antigen-binding sites (ABS) compared with non-ABS sequences. (3) The selection parameter omega (d(N)/d(S)) was significantly higher at ABS compared with non-ABS sequences. (4) Approximately 95.45% of the positively selected codons (P>0.95) were located at or adjacent to an ABS. Furthermore, this study showed that (1) The Qinling subspecies exhibited high omega values across each locus (all >1), supporting its extensive positive selection. (2) The Sichuan subspecies displayed small omega at DRB1 (omega<0.72) and DQA2 (omega<0.48), suggesting that these sites underwent strong purifying selection. (3) Intragenic recombination was detected in DRB1, DQA1, and DQB1. The molecular diversity in classic Aime-MHC class II genes implies that the giant panda had evolved relatively abundant variations in its adaptive immunity along the history of host-pathogen co-evolution. Collectively, these findings indicate that natural selection accompanied by recombination drives the contrasting diversity patterns of the MHC class II genes between the two studied subspecies of giant panda.

  11. Polymorphism, recombination and alternative unscrambling in the DNA polymerase alpha gene of the ciliate Stylonychia lemnae (Alveolata; class Spirotrichea).

    PubMed Central

    Ardell, David H; Lozupone, Catherine A; Landweber, Laura F

    2003-01-01

    DNA polymerase alpha is the most highly scrambled gene known in stichotrichous ciliates. In its hereditary micronuclear form, it is broken into >40 pieces on two loci at least 3 kb apart. Scrambled genes must be reassembled through developmental DNA rearrangements to yield functioning macronuclear genes, but the mechanism and accuracy of this process are unknown. We describe the first analysis of DNA polymorphism in the macronuclear version of any scrambled gene. Six functional haplotypes obtained from five Eurasian strains of Stylonychia lemnae were highly polymorphic compared to Drosophila genes. Another incompletely unscrambled haplotype was interrupted by frameshift and nonsense mutations but contained more silent mutations than expected by allelic inactivation. In our sample, nucleotide diversity and recombination signals were unexpectedly high within a region encompassing the boundary of the two micronuclear loci. From this and other evidence we infer that both members of a long repeat at the ends of the loci provide alternative substrates for unscrambling in this region. Incongruent genealogies and recombination patterns were also consistent with separation of the two loci by a large genetic distance. Our results suggest that ciliate developmental DNA rearrangements may be more probabilistic and error prone than previously appreciated and constitute a potential source of macronuclear variation. From this perspective we introduce the nonsense-suppression hypothesis for the evolution of ciliate altered genetic codes. We also introduce methods and software to calculate the likelihood of hemizygosity in ciliate haplotype samples and to correct for multiple comparisons in sliding-window analyses of Tajima's D. PMID:14704164

  12. A recombinant fusion protein displaying murine and human MHC class I- and II-specific epitopes protects against Leishmania amazonensis infection.

    PubMed

    Martins, Vívian T; Lage, Daniela P; Duarte, Mariana C; Carvalho, Ana Maria R S; Costa, Lourena E; Mendes, Tiago A O; Vale, Danniele L; Menezes-Souza, Daniel; Roatt, Bruno M; Tavares, Carlos A P; Soto, Manuel; Coelho, Eduardo A F

    2017-03-01

    Tegumentary leishmaniasis (TL) constitutes a major public health problem with significant morbidity worldwide. Synthetic peptide-based vaccines are attractive candidates to protect against leishmaniasis, since T cell-specific epitopes can be delivery to antigen-presenting cells, leading to the generation of a Th1 cell-mediated immunity. In this context, the present study aims to evaluate the immunogenicity and protective efficacy of a vaccine composed of major histocompatibility complex class I and II-restricted epitopes derived from four Leishmania infantum proteins to protect mice against Leishmania amazonensis infection. This recombinant fusion protein was administered in BALB/c mice alone or with saponin. As controls, animals received saline or saponin. In the results, the administration of the recombinant protein plus saponin induced a specific IFN-γ, IL-12 and GM-CSF production, as well as high IgG2a isotype antibody levels, which protected mice against a challenge using L. amazonensis promastigotes. Lower parasite burden was found in the infected footpads, liver, spleen and draining lymph node of vaccinated mice, when compared to those from the control groups. In addition, protection was associated with a lower IL-4 and IL-10 response, which was accompanied by the antileishmanial nitrite production by spleen cells of the animals. Interestingly, the recombinant protein administered alone induced a partial protection against challenge. In conclusion, this study shows a new vaccine candidate based on T cell-specific epitopes that was able to induce protection against L. amazonensis infection. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. The GPS motif is a molecular switch for bimodal activities of adhesion class G protein-coupled receptors.

    PubMed

    Prömel, Simone; Frickenhaus, Marie; Hughes, Samantha; Mestek, Lamia; Staunton, David; Woollard, Alison; Vakonakis, Ioannis; Schöneberg, Torsten; Schnabel, Ralf; Russ, Andreas P; Langenhan, Tobias

    2012-08-30

    Adhesion class G protein-coupled receptors (aGPCR) form the second largest group of seven-transmembrane-spanning (7TM) receptors whose molecular layout and function differ from canonical 7TM receptors. Despite their essential roles in immunity, tumorigenesis, and development, the mechanisms of aGPCR activation and signal transduction have remained obscure to date. Here, we use a transgenic assay to define the protein domains required in vivo for the activity of the prototypical aGPCR LAT-1/Latrophilin in Caenorhabditis elegans. We show that the GPCR proteolytic site (GPS) motif, the molecular hallmark feature of the entire aGPCR class, is essential for LAT-1 signaling serving in two different activity modes of the receptor. Surprisingly, neither mode requires cleavage but presence of the GPS, which relays interactions with at least two different partners. Our work thus uncovers the versatile nature of aGPCR activity in molecular detail and places the GPS motif in a central position for diverse protein-protein interactions.

  14. Immunization with Recombinant HLA Classes I and II, HIV-1 gp140, and SIV p27 Elicits Protection against Heterologous SHIV Infection in Rhesus Macaques▿†

    PubMed Central

    Mörner, Andreas; Jansson, Marianne; Bunnik, Evelien M.; Schøller, Jørgen; Vaughan, Robert; Wang, Yufei; Montefiori, David C.; Otting, Nel; Bontrop, Ronald; Bergmeier, Lesley A.; Singh, Mahavir; Wyatt, Richard T.; Schuitemaker, Hanneke; Biberfeld, Gunnel; Thorstensson, Rigmor; Lehner, Thomas

    2011-01-01

    Major histocompatibility complex (MHC) molecules expressed on the surface of human immunodeficiency virus (HIV) are potential targets for neutralizing antibodies. Since MHC molecules are polymorphic, nonself MHC can also be immunogenic. We have used combinations of novel recombinant HLA class I and II and HIV/simian immunodeficiency virus (SIV) antigens, all linked to dextran, to investigate whether they can elicit protective immunity against heterologous simian/human immunodeficiency virus (SHIV) challenge in rhesus macaques. Three groups of animals were immunized with HLA (group 1, n = 8), trimeric YU2 HIV type 1 (HIV-1) gp140 and SIV p27 (HIV/SIV antigens; group 2, n = 8), or HLA plus HIV/SIV antigens (group 3, n = 8), all with Hsp70 and TiterMax Gold adjuvant. Another group (group 4, n = 6) received the same vaccine as group 3 without TiterMax Gold. Two of eight macaques in group 3 were completely protected against intravenous challenge with 18 50% animal infective doses (AID50) of SHIV-SF162P4/C grown in human cells expressing HLA class I and II lineages represented in the vaccine, while the remaining six macaques showed decreased viral loads compared to those in unimmunized animals. Complement-dependent neutralizing activity in serum and high levels of anti-HLA antibodies were elicited in groups 1 and 3, and both were inversely correlated with the plasma viral load at 2 weeks postchallenge. Antibody-mediated protection was strongly supported by the fact that transfer of pooled serum from the two challenged but uninfected animals protected two naïve animals against repeated low-dose challenge with the same SHIV stock. This study demonstrates that immunization with recombinant HLA in combination with HIV-1 antigens might be developed into an alternative strategy for a future AIDS vaccine. PMID:21490092

  15. Evolutionary genetics and vector adaptation of recombinant viruses of the western equine encephalitis antigenic complex provides new insights into alphavirus diversity and host switching

    PubMed Central

    Allison, Andrew B.; Stallknecht, David E.; Holmes, Edward C.

    2014-01-01

    Western equine encephalitis virus (WEEV), Highlands J virus (HJV), and Fort Morgan virus (FMV) are the sole representatives of the WEE antigenic complex of the genus Alphavirus, family Togaviridae, that are endemic to North America. All three viruses have their ancestry in a recombination event involving eastern equine encephalitis virus (EEEV) and a Sindbis (SIN)-like virus that gave rise to a chimeric alphavirus that subsequently diversified into the present-day WEEV, HJV, and FMV. Here, we present a comparative analysis of the genetic, ecological, and evolutionary relationships among these recombinant-origin viruses, including the description of a nsP4 polymerase mutation in FMV that allows it to circumvent the host range barrier to Asian tiger mosquito cells, a vector species that is normally refractory to infection. Notably, we also provide evidence that the recombination event that gave rise to these three WEEV antigenic complex viruses may have occurred in North America. PMID:25463613

  16. Evolutionary genetics and vector adaptation of recombinant viruses of the western equine encephalitis antigenic complex provides new insights into alphavirus diversity and host switching.

    PubMed

    Allison, Andrew B; Stallknecht, David E; Holmes, Edward C

    2015-01-01

    Western equine encephalitis virus (WEEV), Highlands J virus (HJV), and Fort Morgan virus (FMV) are the sole representatives of the WEE antigenic complex of the genus Alphavirus, family Togaviridae, that are endemic to North America. All three viruses have their ancestry in a recombination event involving eastern equine encephalitis virus (EEEV) and a Sindbis (SIN)-like virus that gave rise to a chimeric alphavirus that subsequently diversified into the present-day WEEV, HJV, and FMV. Here, we present a comparative analysis of the genetic, ecological, and evolutionary relationships among these recombinant-origin viruses, including the description of a nsP4 polymerase mutation in FMV that allows it to circumvent the host range barrier to Asian tiger mosquito cells, a vector species that is normally refractory to infection. Notably, we also provide evidence that the recombination event that gave rise to these three WEEV antigenic complex viruses may have occurred in North America.

  17. GFP-based evaluation system of recombinant expression through the secretory pathway in insect cells and its application to the extracellular domains of class C GPCRs.

    PubMed

    Ashikawa, Yuji; Ihara, Makoto; Matsuura, Noriko; Fukunaga, Yuko; Kusakabe, Yuko; Yamashita, Atsuko

    2011-10-01

    Applications of the GFP-fusion technique have greatly facilitated evaluations of the amounts and qualities of sample proteins used for structural analyses. In this study, we applied the GFP-based sample evaluation to secreted protein expression by insect cells. We verified that a GFP variant, GFPuv, retains proper folding and monodispersity within all expression spaces in Sf9 cells, such as the cytosol, organelles, and even the extracellular space after secretion, and thus can serve as a proper folding reporter for recombinant proteins. We then applied the GFPuv-based system to the extracellular domains of class C G-protein coupled receptors (GPCRs) and examined their localization, folding, and oligomerization upon insect cell expression. The extracellular domain of metabotropic glutamate receptor 1 (mGluR1) exhibited good secreted expression by Sf9 cells, and the secreted proteins formed dimer with a monodisperse hydrodynamic state favorable for crystallization, consistent with the results from previous successful structural analyses. In contrast, the extracellular domains of sweet/umami taste receptors (T1R) almost completely remained in the cell. Notably, the T1R and mGluR1 subfractions that remained in the cellular space showed polydisperse hydrodynamic states with large aggregated fractions, without forming dimers. These results indicated that the proper folding and oligomerization of the extracellular domains of the class C GPCR are achieved through the secretory pathway.

  18. High levels of IgG class antibodies to recombinant HSP60 kDa of Yersinia enterocolitica in sera of patients with uveitis

    PubMed Central

    Cancino-Diaz, J C; Vargas-Rodríguez, L; Grinberg-Zylberbaum, N; Reyes-López, M A; Domínguez-López, M L; Pablo-Velazquez, A; Cancino-Diaz, M E

    2004-01-01

    Aims: To determine the levels of IgG class antibodies to recombinant heat shock protein 60 kDa of Yersinia enterocolitica (rHSP60Ye), Klebsiella pneumoniae (rHSP60Kp), Escherichia coli (rHSP60Ec), Shigella flexneri (rHSP60Sf), and Streptococcus pyogenes (rHSP60Sp) in the serum of patients with HLA-B27 associated acute anterior uveitis (HLA-B27 associated AAU), idiopathic acute anterior uveitis (idiopathic AAU), pars planitis, Vogt-Koyanagi-Harada (VKH), and healthy subjects. Methods: The genes that code for HSP60Ye, HSP60Kp, HSP60Ec, HSP60Sf, and HSP60Sp were cloned by PCR from genomic DNA. The rHSPs were purified by affinity using a Ni-NTA resin. The serum levels of IgG class antibodies to rHSP60s were determined by ELISA in patients with uveitis (n = 42) and in healthy subjects (n = 25). Results: The majority of patients with uveitis had higher levels of IgG class antibodies to rHSP60Ye compared with levels of healthy subjects (p = 0.01), although these differences were only observed in the HLA-B27 associated AAU (p = 0.005) and in pars planitis patients (p = 0.001). The levels of IgG antibodies to the rHSP60Kp, rHSP60Sf, rHSP60Ec, and rHSP60Sp were similar in patients with uveitis and in healthy subjects (p>0.05). Conclusion: The results suggest that HSP60Ye could be involved in the aetiology of HLA-B27 associated AAU and pars planitis. PMID:14736785

  19. Biochemical characterization of a recombinant plant class III chitinase from the pitcher of the carnivorous plant Nepenthes alata.

    PubMed

    Ishisaki, Kana; Arai, Sachiko; Hamada, Tatsuro; Honda, Yuji

    2012-11-01

    A class III chitinase belonging to the GH18 family from Nepenthes alata (NaCHIT3) was expressed in Escherichia coli. The enzyme exhibited hydrolytic activity toward colloidal chitin, ethylene glycol chitin, and (GlcNAc)(n) (n=5 and 6). The enzyme hydrolyzed the fourth glycosidic linkage from the non-reducing end of (GlcNAc)(6). The anomeric form of the products indicated it was a retaining enzyme. The colloidal chitin hydrolytic reaction displayed high activity between pH 3.9 and 6.9, but the pH optimum of the (GlcNAc)(6) hydrolytic reaction was 3.9 at 37 °C. The optimal temperature for activity was 65 °C in 50 mM sodium acetate buffer (pH 3.9). The pH optima of NaCHIT3 and NaCHIT1 might be related to their roles in chitin degradation in the pitcher fluid.

  20. New Switches for Utility-Scale Inverters: First In-Class Demonstration of a Completely New Type of SiC Bipolar Switch (15kV-20kV) for Utility-Scale Inverters

    SciTech Connect

    2011-12-31

    Solar ADEPT Project: The SiCLAB is developing a new power switch for utility-scale PV inverters that would improve the performance and significantly reduce the size, weight, and energy loss of PV systems. A power switch controls the electrical energy flowing through an inverter, which takes the electrical current from a PV solar panel and converts it into the type and amount of electricity that is compatible with the electric grid. SiCLAB is using silicon carbide (SiC) semiconductors in its new power switches, which are more efficient than the silicon semiconductors used to conduct electricity in most conventional power switches today. Switches with SiC semiconductors can operate at much higher temperatures, as well as higher voltage and power levels than silicon switches. SiC-based power switches are also smaller than those made with silicon alone, so they result in much smaller and lighter electrical devices. In addition to their use in utility-scale PV inverters, SiCLAB’s new power switches can also be used in wind turbines, railways, and other smart grid applications.

  1. Absence of SUN-domain protein Slp1 blocks karyogamy and switches meiotic recombination and synapsis from homologs to sister chromatids

    PubMed Central

    Vasnier, Christelle; de Muyt, Arnaud; Zhang, Liangran; Tessé, Sophie; Kleckner, Nancy E.; Zickler, Denise; Espagne, Eric

    2014-01-01

    Karyogamy, the process of nuclear fusion is required for two haploid gamete nuclei to form a zygote. Also, in haplobiontic organisms, karyogamy is required to produce the diploid nucleus/cell that then enters meiosis. We identify sun like protein 1 (Slp1), member of the mid–Sad1p, UNC-84–domain ubiquitous family, as essential for karyogamy in the filamentous fungus Sordaria macrospora, thus uncovering a new function for this protein family. Slp1 is required at the last step, nuclear fusion, not for earlier events including nuclear movements, recognition, and juxtaposition. Correspondingly, like other family members, Slp1 localizes to the endoplasmic reticulum and also to its extensions comprising the nuclear envelope. Remarkably, despite the absence of nuclear fusion in the slp1 null mutant, meiosis proceeds efficiently in the two haploid “twin” nuclei, by the same program and timing as in diploid nuclei with a single dramatic exception: the normal prophase program of recombination and synapsis between homologous chromosomes, including loading of recombination and synaptonemal complex proteins, occurs instead between sister chromatids. Moreover, the numbers of recombination-initiating double-strand breaks (DSBs) and ensuing recombinational interactions, including foci of the essential crossover factor Homo sapiens enhancer of invasion 10 (Hei10), occur at half the diploid level in each haploid nucleus, implying per-chromosome specification of DSB formation. Further, the distribution of Hei10 foci shows interference like in diploid meiosis. Centromere and spindle dynamics, however, still occur in the diploid mode during the two meiotic divisions. These observations imply that the prophase program senses absence of karyogamy and/or absence of a homolog partner and adjusts the interchromosomal interaction program accordingly. PMID:25210014

  2. Absence of SUN-domain protein Slp1 blocks karyogamy and switches meiotic recombination and synapsis from homologs to sister chromatids.

    PubMed

    Vasnier, Christelle; de Muyt, Arnaud; Zhang, Liangran; Tessé, Sophie; Kleckner, Nancy E; Zickler, Denise; Espagne, Eric

    2014-09-23

    Karyogamy, the process of nuclear fusion is required for two haploid gamete nuclei to form a zygote. Also, in haplobiontic organisms, karyogamy is required to produce the diploid nucleus/cell that then enters meiosis. We identify sun like protein 1 (Slp1), member of the mid-Sad1p, UNC-84-domain ubiquitous family, as essential for karyogamy in the filamentous fungus Sordaria macrospora, thus uncovering a new function for this protein family. Slp1 is required at the last step, nuclear fusion, not for earlier events including nuclear movements, recognition, and juxtaposition. Correspondingly, like other family members, Slp1 localizes to the endoplasmic reticulum and also to its extensions comprising the nuclear envelope. Remarkably, despite the absence of nuclear fusion in the slp1 null mutant, meiosis proceeds efficiently in the two haploid "twin" nuclei, by the same program and timing as in diploid nuclei with a single dramatic exception: the normal prophase program of recombination and synapsis between homologous chromosomes, including loading of recombination and synaptonemal complex proteins, occurs instead between sister chromatids. Moreover, the numbers of recombination-initiating double-strand breaks (DSBs) and ensuing recombinational interactions, including foci of the essential crossover factor Homo sapiens enhancer of invasion 10 (Hei10), occur at half the diploid level in each haploid nucleus, implying per-chromosome specification of DSB formation. Further, the distribution of Hei10 foci shows interference like in diploid meiosis. Centromere and spindle dynamics, however, still occur in the diploid mode during the two meiotic divisions. These observations imply that the prophase program senses absence of karyogamy and/or absence of a homolog partner and adjusts the interchromosomal interaction program accordingly.

  3. Early hepatic and peritoneal changes and immune response in goats vaccinated with a recombinant glutathione transferase sigma class and challenged with Fasciola hepatica.

    PubMed

    Zafra, R; Pérez-Écija, R A; Buffoni, L; Pacheco, I L; Martínez-Moreno, A; LaCourse, E J; Perally, S; Brophy, P M; Pérez, J

    2013-06-01

    Changes and local immune response were evaluated in the peritoneal cell populations, duodenal lamina propria and liver from goats immunized with recombinant glutathione transferase sigma class (rFhGST-S1) during early stages of infection with Fasciola hepatica. Group 1 (n=7) was unimmunized and uninfected; group 2 (n=10) was immunized with adjuvant Quil A and infected; group 3 (n=10) was immunised with rFhGST-S1 and infected. Three goats from each group were killed at 7-9 days post-infection (dpi) to evaluate early changes and immune response. The remaining goats were killed at 15 weeks post-infection (wpi). rFhGST-S1 vaccination induced variable response: three goats showed low fluke burden at 15 wpi and two goats showed low hepatic damage at early infection stages. This response was associated to a severe infiltrate of eosinophils in peritoneal fluid and hepatic necrotic foci, high iNOS expression in peritoneal cells and abundant infiltrate of eosinophils surrounding hepatic migrating flukes. T lymphocyte subsets were found in the vicinity of necrotic areas but they were absent in the vicinity of migrating larvae. No significant variation for T cell subsets, except for CD4 and γδ T lymphocytes, that were higher in the Quil A group compared to the rFhGST-S1 group. Expression of IL4 and IFN-γ in the hepatic inflammatory infiltrates was very occasional. Copyright © 2012 Elsevier Ltd. All rights reserved.

  4. Discovery and development of avotermin (recombinant human transforming growth factor beta 3): a new class of prophylactic therapeutic for the improvement of scarring.

    PubMed

    Occleston, Nick L; O'Kane, Sharon; Laverty, Hugh G; Cooper, Mark; Fairlamb, David; Mason, Tracey; Bush, Jim A; Ferguson, Mark W J

    2011-09-01

    Scarring in the skin following surgery or trauma may be associated with adverse aesthetic, functional, growth and psychological effects, such that both physicians and patients regard it as important to minimize the appearance of scars. The prophylactic improvement of cutaneous scar appearance represents a significant opportunity to improve the well-being of patients. Human recombinant transforming growth factor beta 3 (avotermin) is the first in a new class of therapeutic agents to address this medical need. Herein we describe scar-free healing in early embryonic development, including the identification of the cellular and molecular mechanisms underpinning the scarring process. This understanding has led to the discovery of novel therapeutics such as transforming growth factor beta 3, which can be administered to improve scar appearance in human subjects through pharmacological action. We discuss the pioneering development of transforming growth factor beta 3 in this new therapeutic area showing how it has been possible to translate preclinical concepts into clinical application, namely the improvement of scar appearance following surgery.

  5. Ubiquitination Events That Regulate Recombination of Immunoglobulin Loci Gene Segments

    PubMed Central

    Chao, Jaime; Rothschild, Gerson; Basu, Uttiya

    2014-01-01

    Programed DNA mutagenesis events in the immunoglobulin (Ig) loci of developing B cells utilize the common and conserved mechanism of protein ubiquitination for subsequent proteasomal degradation to generate the required antigen-receptor diversity. Recombinase proteins RAG1 and RAG2, necessary for V(D)J recombination, and activation-induced cytidine deaminase, an essential mutator protein for catalyzing class switch recombination and somatic hypermutation, are regulated by various ubiquitination events that affect protein stability and activity. Programed DNA breaks in the Ig loci can be identified by various components of DNA repair pathways, also regulated by protein ubiquitination. Errors in the ubiquitination pathways for any of the DNA double-strand break repair proteins can lead to inefficient recombination and repair events, resulting in a compromised adaptive immune system or development of cancer. PMID:24653725

  6. Plasmonic enhanced ultrafast switch.

    SciTech Connect

    Subramania,Ganapathi Subramanian; Reno, John Louis; Passmore, Brandon Scott; Harris, Tom.; Shaner, Eric Arthur; Barrick, Todd A.

    2009-09-01

    Ultrafast electronic switches fabricated from defective material have been used for several decades in order to produce picosecond electrical transients and TeraHertz radiation. Due to the ultrashort recombination time in the photoconductor materials used, these switches are inefficient and are ultimately limited by the amount of optical power that can be applied to the switch before self-destruction. The goal of this work is to create ultrafast (sub-picosecond response) photoconductive switches on GaAs that are enhanced through plasmonic coupling structures. Here, the plasmonic coupler primarily plays the role of being a radiation condenser which will cause carriers to be generated adjacent to metallic electrodes where they can more efficiently be collected.

  7. Mechanisms Promoting Translocations in Editing and Switching Peripheral B Cells

    PubMed Central

    Wang, Jing H.; Gostissa, Monica; Yan, Catherine T.; Goff, Peter; Hickernell, Thomas; Hansen, Erica; Difilippantonio, Simone; Wesemann, Duane R.; Zarrin, Ali A.; Rajewsky, Klaus; Nussenzweig, Andre; Alt, Frederick W.

    2010-01-01

    V(D)J recombination assembles immunoglobulin (Ig) heavy or light chain (IgH or IgL) variable region exons in developing bone marrow B cells, while class switch recombination (CSR) exchanges IgH constant region exons in peripheral B cells. Both processes employ DNA double strand breaks (DSBs) repaired by non-homologous end-joining (NHEJ). Errors in either V(D)J recombination or CSR can initiate chromosomal translocations, including oncogenic IgH/c-myc translocations of peripheral B cell lymphomas. Collaboration between these processes also has been proposed to initiate translocations. However, occurrence of V(D)J recombination in peripheral B cells is controversial. Here, we report that activated NHEJ-deficient splenic B cells accumulate V(D)J recombination-associated IgL chromosomal breaks, as well as CSR-associated IgH breaks, often in the same cell. Moreover, IgL breaks frequently are joined to IgH breaks to form translocations, a phenomenon associated with specific IgH/IgL co-localization. IgH and c-myc also co-localize in these cells; correspondingly, introduction of frequent c-myc DSBs robustly promotes IgH/c-myc translocations. Our studies reveal peripheral B cells that attempt secondary V(D)J recombination and elucidate a role for mechanistic factors in promoting recurrent translocations in tumors. PMID:19587764

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

    PubMed

    Prado, Félix; Aguilera, Andrés

    2005-03-23

    Homologous recombination safeguards genome integrity, but it can also cause genome instability of important consequences for cell proliferation and organism development. Transcription induces recombination, as shown in prokaryotes and eukaryotes for both spontaneous and developmentally regulated events such as those responsible for immunoglobulin class switching. Deciphering the molecular basis of transcription-associated recombination (TAR) is important in understanding genome instability. Using novel plasmid-borne recombination constructs in Saccharomyces cerevisiae, we show that RNA polymerase II (RNAPII) transcription induces recombination by impairing replication fork progression. RNAPII transcription concomitant to head-on oncoming replication causes a replication fork pause (RFP) that is linked to a significant increase in recombination. However, transcription that is codirectional with replication has little effect on replication fork progression and recombination. Transcription occurring in the absence of replication does not affect either recombination or replication fork progression. The Rrm3 helicase, which is required for replication fork progression through nucleoprotein complexes, facilitates replication through the transcription-dependent RFP site and reduces recombination. Therefore, our work provides evidence that one mechanism responsible for TAR is RNAP-mediated replication impairment.

  9. Exciter switch

    NASA Technical Reports Server (NTRS)

    Mcpeak, W. L.

    1975-01-01

    A new exciter switch assembly has been installed at the three DSN 64-m deep space stations. This assembly provides for switching Block III and Block IV exciters to either the high-power or 20-kW transmitters in either dual-carrier or single-carrier mode. In the dual-carrier mode, it provides for balancing the two drive signals from a single control panel located in the transmitter local control and remote control consoles. In addition to the improved switching capabilities, extensive monitoring of both the exciter switch assembly and Transmitter Subsystem is provided by the exciter switch monitor and display assemblies.

  10. Switch wear leveling

    DOEpatents

    Wu, Hunter; Sealy, Kylee; Gilchrist, Aaron

    2015-09-01

    An apparatus for switch wear leveling includes a switching module that controls switching for two or more pairs of switches in a switching power converter. The switching module controls switches based on a duty cycle control technique and closes and opens each switch in a switching sequence. The pairs of switches connect to a positive and negative terminal of a DC voltage source. For a first switching sequence a first switch of a pair of switches has a higher switching power loss than a second switch of the pair of switches. The apparatus includes a switch rotation module that changes the switching sequence of the two or more pairs of switches from the first switching sequence to a second switching sequence. The second switch of a pair of switches has a higher switching power loss than the first switch of the pair of switches during the second switching sequence.

  11. Enhancement of passively Q-switched performance at 1.34 μm with a class of Nd:GdxY(1-)xVO(4) crystals.

    PubMed

    Li, Xin; Li, Guiqiu; Zhao, Shengzhi; Xu, Chao; Li, Yufei; Liu, Hong; Zhang, Huaijin

    2010-10-11

    Passively Q-switched operation at 1.34 μm in which V:YAG was employed as saturable absorber has been demonstrated with a series of mixed Nd:GdxY(1-)xVO(4) crystals. The Q-switched laser pulse performance with these Nd-doped mixed vanadate crystals, especially Nd:Gd(0.63)Y(0.37)VO(4), was enhanced in respect to Nd:GdVO(4) under the identical conditions. The average output power of 171.3 mW with the shortest pulse width of 44.4 ns, largest single pulse energy of 21.7 μJ, and highest peak power of 489 W at the incident pump power of 5.04 W were obtained with Nd:Gd(0.63)Y(0.37)VO(4) crystal.

  12. Multiscroll attractors by switching systems.

    PubMed

    Campos-Cantón, E; Barajas-Ramírez, J G; Solís-Perales, G; Femat, R

    2010-03-01

    In this paper, we present a class of three-dimensional dynamical systems having multiscrolls which we call unstable dissipative systems (UDSs). The UDSs are dissipative in one of its components but unstable in the other two. This class of systems is constructed with a switching law to display various multiscroll strange attractors. The multiscroll strange attractors result from the combination of several unstable "one-spiral" trajectories by means of switching. Each of these trajectories lies around a saddle hyperbolic stationary point. Thus, we describe how a piecewise-linear switching system yields multiscroll attractors, symmetric or asymmetric, with chaotic behavior.

  13. Coaxial Switch

    DTIC Science & Technology

    2014-04-23

    08-2015 Publication Coaxial Switch David J. Bamford et al Naval Undersea Warfare Center Division, Newport 1176 Howell Street, Bldg 102T, Code 00L...Distribution A A coaxial switch having a housing and a shaft extending through and rotatably mounted to the housing. The shaft extends from opposite...conductor members are electrically connected together. When the coaxial switch is engaged, the conductor members are inserted into the connector body

  14. Norovirus recombination.

    PubMed

    Bull, Rowena A; Tanaka, Mark M; White, Peter A

    2007-12-01

    RNA recombination is a significant driving force in viral evolution. Increased awareness of recombination within the genus Norovirus of the family Calicivirus has led to a rise in the identification of norovirus (NoV) recombinants and they are now reported at high frequency. Currently, there is no classification system for recombinant NoVs and a widely accepted recombinant genotyping system is still needed. Consequently, there is duplication in reporting of novel recombinants. This has led to difficulties in defining the number and types of recombinants in circulation. In this study, 120 NoV nucleotide sequences were compiled from the current GenBank database and published literature. NoV recombinants and their recombination breakpoints were identified using three methods: phylogenetic analysis, SimPlot analysis and the maximum chi2 method. A total of 20 NoV recombinant types were identified in circulation worldwide. The recombination point is the ORF1/2 overlap in all isolates except one, which demonstrated a double recombination event within the polymerase region.

  15. Differences in Meiotic Recombination Rates in Childhood Acute Lymphoblastic Leukemia at an MHC Class II Hotspot Close to Disease Associated Haplotypes

    PubMed Central

    Thompson, Pamela; Urayama, Kevin; Zheng, Jie; Yang, Peng; Ford, Matt; Buffler, Patricia; Chokkalingam, Anand; Lightfoot, Tracy; Taylor, Malcolm

    2014-01-01

    Childhood Acute Lymphoblastic Leukemia (ALL) is a malignant lymphoid disease of which B-cell precursor- (BCP) and T-cell- (T) ALL are subtypes. The role of alleles encoded by major histocompatibility loci (MHC) have been examined in a number of previous studies and results indicating weak, multi-allele associations between the HLA-DPB1 locus and BCP-ALL suggested a role for immunosusceptibility and possibly infection. Two independent SNP association studies of ALL identified loci approximately 37 kb from one another and flanking a strong meiotic recombination hotspot (DNA3), adjacent to HLA-DOA and centromeric of HLA-DPB1. To determine the relationship between this observation and HLA-DPB1 associations, we constructed high density SNP haplotypes of the 316 kb region from HLA-DMB to COL11A2 in childhood ALL and controls using a UK GWAS data subset and the software PHASE. Of four haplotype blocks identified, predicted haplotypes in Block 1 (centromeric of DNA3) differed significantly between BCP-ALL and controls (P = 0.002) and in Block 4 (including HLA-DPB1) between T-ALL and controls (P = 0.049). Of specific common (>5%) haplotypes in Block 1, two were less frequent in BCP-ALL, and in Block 4 a single haplotype was more frequent in T-ALL, compared to controls. Unexpectedly, we also observed apparent differences in ancestral meiotic recombination rates at DNA3, with BCP-ALL showing increased and T-ALL decreased levels compared to controls. In silico analysis using LDsplit sotware indicated that recombination rates at DNA3 are influenced by flanking loci, including SNPs identified in childhood ALL association studies. The observed differences in rates of meiotic recombination at this hotspot, and potentially others, may be a characteristic of childhood leukemia and contribute to disease susceptibility, alternatively they may reflect interactions between ALL-associated haplotypes in this region. PMID:24959916

  16. DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

    PubMed Central

    Sander, Adam F.; Lavstsen, Thomas; Rask, Thomas S.; Lisby, Michael; Salanti, Ali; Fordyce, Sarah L.; Jespersen, Jakob S.; Carter, Richard; Deitsch, Kirk W.; Theander, Thor G.; Pedersen, Anders Gorm; Arnot, David E.

    2014-01-01

    Many bacterial, viral and parasitic pathogens undergo antigenic variation to counter host immune defense mechanisms. In Plasmodium falciparum, the most lethal of human malaria parasites, switching of var gene expression results in alternating expression of the adhesion proteins of the Plasmodium falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome-wide recombination hotspots in var genes, we show that during the parasite’s sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum-erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens. PMID:24253306

  17. Optical switches and switching methods

    DOEpatents

    Doty, Michael

    2008-03-04

    A device and method for collecting subject responses, particularly during magnetic imaging experiments and testing using a method such as functional MRI. The device comprises a non-metallic input device which is coupled via fiber optic cables to a computer or other data collection device. One or more optical switches transmit the subject's responses. The input device keeps the subject's fingers comfortably aligned with the switches by partially immobilizing the forearm, wrist, and/or hand of the subject. Also a robust nonmetallic switch, particularly for use with the input device and methods for optical switching.

  18. Polymorphisms in HLA Class I Genes Associated with both Favorable Prognosis of Human Immunodeficiency Virus (HIV) Type 1 Infection and Positive Cytotoxic T-Lymphocyte Responses to ALVAC-HIV Recombinant Canarypox Vaccines

    PubMed Central

    Kaslow, Richard A.; Rivers, Charles; Tang, Jianming; Bender, Thomas J.; Goepfert, Paul A.; El Habib, Raphaelle; Weinhold, Kent; Mulligan, Mark J.

    2001-01-01

    Carriers of certain human leukocyte antigen class I alleles show favorable prognosis of human immunodeficiency virus type 1 (HIV-1) infection, presumably due to effective CD8+ cytotoxic T-lymphocyte responses, but close relationships between class I variants mediating such responses to natural and to vaccine HIV-1 antigen have not been established. During 6 to 30 months of administration and follow-up in trials of ALVAC-HIV recombinant canarypox vaccines, cells from 42% of 291 HIV-1-negative vaccinated subjects typed at class I loci responded to an HIV-1 protein in a lytic bulk CD8+ cytotoxic T-lymphocyte assay. By 2 weeks after the second dose, higher proportions of vaccinees carrying one of two alleles consistently associated with slower progression of natural HIV-1 infection reacted at least once: B∗27 carriers reacted to Gag (64%; odds ratio [OR] = 10.3, P = 0.001) and Env (36%; OR = 4.6, P = 0.04), and B∗57 carriers reacted to Env (44%; OR = 6.6, P < 0.05). By 2 weeks after the third or fourth dose, B∗27 carriers had responded (two or more reactions) to Gag (33%; OR = 4.4, P < 0.05) and B∗57 carriers had responded to both Gag (39%; OR = 5.3, P = 0.013) and Env (39%; OR = 9.5, P = 0.002). Homozygosity at class I loci, although conferring an unfavorable prognosis following natural infection, showed no such disadvantage for vaccine response. Individual class I alleles have not previously demonstrated such clear and consistent relationship with both the clinical course of an infection and cellular immunity to a vaccine against the infectious agent. This proof of principle that class I an alleles modulate both processes has implications for development of HIV-1 and presumably other vaccines. PMID:11507213

  19. ION SWITCH

    DOEpatents

    Cook, B.

    1959-02-10

    An ion switch capable of transferring large magnitudes of power is described. An ion switch constructed in accordance with the invention includes a pair of spaced control electrodes disposed in a highly evacuated region for connection in a conventional circuit to control the passing of power therethrough. A controllable ionic conduction path is provided directiy between the control electrodes by a source unit to close the ion switch. Conventional power supply means are provided to trigger the source unit and control the magnitude, durations and pulse repetition rate of the aforementioned ionic conduction path.

  20. Arterial switch.

    PubMed

    Planche, C; Lacour-Gayet, F; Serraf, A

    1998-01-01

    A relatively large spectra of anatomic variations are found within the unifying features of discordant ventriculoarterial connections. Variants that lend themselves to anatomic repair by the arterial switch operation are discussed, these include transposition of the great arteries with intact ventricular septum (TGA IVS), TGA associated with a ventricular septal defect (TGA VSD), double-outlet right ventricle with subpulmonary VSD (DORV VSD), and TGA or DORV with VSD associated with coarctation. Double discordance with VSD, which is currently treated by double switch or Rastelli and atrial switch and which probably represents, in our department, the only remaining indication for atrial switch, is not discussed. Also, we exclude TGA associated with pulmonary stenosis, which is treated by Rastelli or REV operation.

  1. Magnetic switching

    NASA Astrophysics Data System (ADS)

    Kirbie, H. C.

    1989-04-01

    Magnetic switching is a pulse compression technique that uses a saturable inductor (reactor) to pass pulses of energy between two capacitors. A high degree of pulse compression can be achieved in a network when several of these simple, magnetically switched circuits are connected in series. Individual inductors are designed to saturate in cascade as a pulse moves along the network. The technique is particularly useful when a single-pulse network must be very reliable or when a multi-pulse network must operate at a high pulse repetition frequency (PRF). Today, magnetic switches trigger spark gaps, sharpen the risetimes of high energy pulses, power large lasers, and drive high PRF linear induction accelerators. This paper will describe the technique of magnetic pulse compression using simple networks and design equations. A brief review of modern magnetic materials and of their role in magnetic switch design will be presented.

  2. Acceleration switch

    DOEpatents

    Abbin, J.P. Jr.; Devaney, H.F.; Hake, L.W.

    1979-08-29

    The disclosure relates to an improved integrating acceleration switch of the type having a mass suspended within a fluid filled chamber, with the motion of the mass initially opposed by a spring and subsequently not so opposed.

  3. Acceleration switch

    DOEpatents

    Abbin, Jr., Joseph P.; Devaney, Howard F.; Hake, Lewis W.

    1982-08-17

    The disclosure relates to an improved integrating acceleration switch of the type having a mass suspended within a fluid filled chamber, with the motion of the mass initially opposed by a spring and subsequently not so opposed.

  4. Nucleosome Switches

    NASA Astrophysics Data System (ADS)

    Schwab, David J.; Bruinsma, Robijn F.; Rudnick, Joseph; Widom, Jonathan

    2008-06-01

    We present a statistical-mechanical model for the positioning of nucleosomes along genomic DNA molecules as a function of the strength of the binding potential and the chemical potential of the nucleosomes. We show that a significant section of the DNA is composed of two-level nucleosome switching regions where the nucleosome distribution undergoes a localized, first-order transition. The location of the nucleosome switches shows a strong correlation with the location of gene-regulation regions.

  5. Nucleosome switches.

    PubMed

    Schwab, David J; Bruinsma, Robijn F; Rudnick, Joseph; Widom, Jonathan

    2008-06-06

    We present a statistical-mechanical model for the positioning of nucleosomes along genomic DNA molecules as a function of the strength of the binding potential and the chemical potential of the nucleosomes. We show that a significant section of the DNA is composed of two-level nucleosome switching regions where the nucleosome distribution undergoes a localized, first-order transition. The location of the nucleosome switches shows a strong correlation with the location of gene-regulation regions.

  6. LARP1 functions as a molecular switch for mTORC1-mediated translation of an essential class of mRNAs

    PubMed Central

    Hong, Sungki; Freeberg, Mallory A; Han, Ting; Kamath, Avani; Yao, Yao; Fukuda, Tomoko; Suzuki, Tsukasa; Kim, John K; Inoki, Ken

    2017-01-01

    The RNA binding protein, LARP1, has been proposed to function downstream of mTORC1 to regulate the translation of 5’TOP mRNAs such as those encoding ribosome proteins (RP). However, the roles of LARP1 in the translation of 5’TOP mRNAs are controversial and its regulatory roles in mTORC1-mediated translation remain unclear. Here we show that LARP1 is a direct substrate of mTORC1 and Akt/S6K1. Deep sequencing of LARP1-bound mRNAs reveal that non-phosphorylated LARP1 interacts with both 5’ and 3’UTRs of RP mRNAs and inhibits their translation. Importantly, phosphorylation of LARP1 by mTORC1 and Akt/S6K1 dissociates it from 5’UTRs and relieves its inhibitory activity on RP mRNA translation. Concomitantly, phosphorylated LARP1 scaffolds mTORC1 on the 3’UTRs of translationally-competent RP mRNAs to facilitate mTORC1-dependent induction of translation initiation. Thus, in response to cellular mTOR activity, LARP1 serves as a phosphorylation-sensitive molecular switch for turning off or on RP mRNA translation and subsequent ribosome biogenesis. DOI: http://dx.doi.org/10.7554/eLife.25237.001 PMID:28650797

  7. Genetic Recombination

    ERIC Educational Resources Information Center

    Whitehouse, H. L. K.

    1973-01-01

    Discusses the mechanisms of genetic recombination with particular emphasis on the study of the fungus Sordaria brevicollis. The study of recombination is facilitated by the use of mutants of this fungus in which the color of the ascospores is affected. (JR)

  8. Genetic Recombination

    ERIC Educational Resources Information Center

    Whitehouse, H. L. K.

    1973-01-01

    Discusses the mechanisms of genetic recombination with particular emphasis on the study of the fungus Sordaria brevicollis. The study of recombination is facilitated by the use of mutants of this fungus in which the color of the ascospores is affected. (JR)

  9. Nondisjunction of chromosome 15: origin and recombination.

    PubMed Central

    Robinson, W P; Bernasconi, F; Mutirangura, A; Ledbetter, D H; Langlois, S; Malcolm, S; Morris, M A; Schinzel, A A

    1993-01-01

    Thirty-two cases of uniparental disomy (UPD), ascertained from Prader-Willi syndrome patients (N = 27) and Angelman syndrome patients (N = 5), are used to investigate the pattern of recombination associated with nondisjunction of chromosome 15. In addition, the meiotic stage of nondisjunction is inferred by using markers mapping near the centromere. Two basic approaches to the analysis of recombination are utilized. Standard methods of centromere mapping are employed to determine the level of recombination in specific pairwise intervals along the chromosome. This method shows a significant reduction in recombination for two of five intervals examined. Second, the observed frequency of each recombinant class (i.e., zero, one, two, three, or more observable crossovers) is compared with expected values. This is useful for testing whether the reduction in recombination can be attributed solely to a proportion of cases with no recombination at all (because of asynapsis), with the remaining groups showing normal recombination (or even excess recombination), or whether recombination is uniformly reduced. Analysis of maternal UPD(15) data shows a slight reduction in the multiple-recombinant classes, with a corresponding increase in both the zero- and one-recombinant classes over expected values. The majority, more than 82%, of the extra chromosomes in maternal UPD(15) cases are due to meiotic I nondisjunction events. In contrast, most paternal UPD(15) cases so far examined appear to have a postzygotic origin of the extra paternal chromosome. PMID:8352279

  10. Switched steerable multiple beam antenna system

    NASA Technical Reports Server (NTRS)

    Iwasaki, Richard S. (Inventor)

    1988-01-01

    A steerable multibeam five element cross-feed cluster antenna system is described. The feed power is divided into five branches. Each branch includes a switching network comprised of a plurality of time delay elements each individually controlled by a respective electromagnetic latching switch. Frequency independent individual two-dimensional beam steering at intermediate (IF) scanning frequencies is thereby provided wherein discrete incremental time delays are introduced by the switching networks into each branch and the signals recombined thereafter to form each beam. The electromagnetic latched switching reduces power consumption and permits higher power switching and reciprocal coincident tranmsit and receive operation. Frequency independence due to incremental time delay switching permits coincident reciprocal operation and steering for transmit-receive signal paths carrying different transmit-receive frequencies. Diagonal quarter wave plates in the waveguides alter polarization from the circular to orthogonal linear to provide transmitter-receiver isolation.

  11. The effect of the acidic tail on the DNA-binding properties of the HMG1,2 class of proteins: insights from tail switching and tail removal.

    PubMed

    Lee, K B; Thomas, J O

    2000-11-24

    The high-mobility group (HMG) proteins HMG1, HMG2 and HMG2a are relatively abundant vertebrate DNA-binding and bending proteins that bind with structure specificity, rather than sequence specificity, and appear to play an architectural role in the assembly of nucleoprotein complexes. They have two homologous "HMG-box" DNA-binding domains (which show about 80 % homology) connected by a short basic linker to an acidic carboxy-terminal tail that differs in length between HMG1 and 2. To gain insights into the role of the acidic tail, we examined the DNA-binding properties of HMG1, HMG2b and HMG2a from chicken erythrocytes (corresponding to HMG1, HMG2 and HMG2a in other vertebrates). HMG1, with the longest acidic tail, is less effective than HMG2a and 2b (at a given molar input ratio) in supercoiling relaxed, closed circular DNA, in inducing ligase-mediated circularisation of an 88 bp DNA fragment, and in binding to four-way DNA junctions in a gel-shift assay. Removal of the acidic tail increases the affinity of the HMG boxes for DNA and largely abolishes the differences between the three species. Switching the acidic tail of HMG1 for that of HMG2a or 2b gives hybrid proteins with essentially the same DNA-binding properties as HMG2a, 2b. The length (and possibly sequence) of the acidic tail thus appears to be the dominant factor in mediating the differences in properties between HMG1, 2a and 2b and finely tunes the rather similar DNA-binding properties of the tandem HMG boxes, presumably to fulfill different cellular roles. The tail is essential for structure-selective DNA-binding of the HMG boxes to DNA minicircles in the presence of equimolar linear DNA, and has little effect on the affinity for this already highly distorted DNA ligand, in contrast to binding to linear and four-way junction DNA. Copyright 2000 Academic Press.

  12. Optical switch

    DOEpatents

    Reedy, Robert P.

    1987-01-01

    An optical switching device (10) is provided whereby light from a first glass fiber (16) or a second glass fiber (14) may be selectively transmitted into a third glass fiber (18). Each glass fiber is provided with a focusing and collimating lens system (26, 28, 30). In one mode of operation, light from the first glass fiber (16) is reflected by a planar mirror (36) into the third glass fiber (18). In another mode of operation, light from the second glass fiber (14) passes directly into the third glass fiber (18). The planar mirror (36) is attached to a rotatable table (32) which is rotated to provide the optical switching.

  13. Optical switch

    DOEpatents

    Reedy, R.P.

    1987-11-10

    An optical switching device is provided whereby light from a first glass fiber or a second glass fiber may be selectively transmitted into a third glass fiber. Each glass fiber is provided with a focusing and collimating lens system. In one mode of operation, light from the first glass fiber is reflected by a planar mirror into the third glass fiber. In another mode of operation, light from the second glass fiber passes directly into the third glass fiber. The planar mirror is attached to a rotatable table which is rotated to provide the optical switching. 3 figs.

  14. Optical switch

    DOEpatents

    Reedy, R.P.

    1985-01-18

    An optical switching device is provided whereby light from a first glass fiber or a second glass fiber may be selectively transmitted into a third glass fiber. Each glass fiber is provided with a focusing and collimating lens system. In one mode of operation, light from the first glass fiber is reflected by a planar mirror into the third glass fiber. In another mode of operation, light from the second glass fiber passes directly into the third glass fiber. The planar mirror is attached to a rotatable table which is rotated to provide the optical switching.

  15. Multiple classes of transcription factors regulate the expression of VASCULAR-RELATED NAC-DOMAIN7, a master switch of xylem vessel differentiation.

    PubMed

    Endo, Hitoshi; Yamaguchi, Masatoshi; Tamura, Taizo; Nakano, Yoshimi; Nishikubo, Nobuyuki; Yoneda, Arata; Kato, Ko; Kubo, Minoru; Kajita, Shinya; Katayama, Yoshihiro; Ohtani, Misato; Demura, Taku

    2015-02-01

    The secondary cell walls of xylem cells, including vessel elements, provide mechanical strength and contribute to the conduction of water and minerals. VASCULAR-RELATED NAC-DOMAIN7 (VND7) is a NAC-domain transcription factor that regulates the expression of genes required for xylem vessel element formation. Transient expression assays using 68 transcription factors that are expressed during xylem vessel differentiation showed that 14 transcription factors, including VND1-VND7, are putative positive regulators of VND7 expression. Electrophoretic mobility shift assays revealed that all seven VND proteins bound to the VND7 promoter region at its SMBE/TERE motif, indicating that VND7 is a direct target of all of the VND transcription factors. Overexpression of VND1-VND5, GATA12 and ANAC075, newly identified transcription factors that function upstream of VND7, resulted in ectopic xylem vessel element formation. These data suggest that VND7 transcription is a regulatory target of multiple classes of transcription factors.

  16. Switching Transistor

    NASA Technical Reports Server (NTRS)

    1981-01-01

    Westinghouse Electric Corporation's D60T transistors are used primarily as switching devices for controlling high power in electrical circuits. It enables reduction in the number and size of circuit components and promotes more efficient use of energy. Wide range of application from a popcorn popper to a radio frequency generator for solar cell production.

  17. Switching subtype-selectivity: Fragment replacement strategy affords novel class of peroxisome proliferator-activated receptor α/δ (PPARα/δ) dual agonists.

    PubMed

    Shioi, Ryuta; Okazaki, Shogo; Noguchi-Yachide, Tomomi; Ishikawa, Minoru; Makishima, Makoto; Hashimoto, Yuichi; Yamaguchi, Takao

    2017-07-15

    Peroxisome proliferator-activated receptors (PPARs) are important drug targets for treatment of dyslipidemia, type 2 diabetes, cardiovascular disease, nonalcoholic fatty liver disease and nonalcoholic steatohepatitis, and great efforts have been made to develop novel PPAR ligands. However, most existing PPAR ligands contain a carboxylic acid (CA) or thiazolidinedione (TZD) structure (acidic head group) that is essential for activity. We recently discovered non-CA/TZD class PPARα/δ partial agonists, which contain an acetamide moiety and adjacent methyl group, linked to a 1,2,4-oxadiazole ring ("fragment a"). We hypothesized that the acetamide structure might interact with the CA/TZD-binding pocket. To test this idea, we firstly replaced fragment a in one of our compounds with the α-alkoxy-CA structure often found in PPAR agonists. Secondly, we replaced the α-alkoxy-CA head group of several reported PPAR agonists with our acetamide-based fragment a. The agonistic activities of the synthesized hybrid compounds toward PPARs (PPARα, PPARγ and PPARδ) were evaluated by means of cell-based reporter gene assays. All the hybrid molecules showed PPAR-agonistic activities, but replacement of the α-alkoxy-CA head group altered the maximum efficacy and the subtype-specificity. The acetamide-based hybrid molecules showed partial agonism toward PPARα and PPARδ, whereas the α-alkoxy-CA-based molecules were generally selective for PPARα and PPARγ, with relatively high activation efficacies. Thus, the fragment replacement strategy appears promising for the development of novel acetamide-based PPARα/δ dual agonists. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Nondisjunction of chromosome 15: Origin and recombination

    SciTech Connect

    Robinson, W.P.; Bernasconi, F.; Schinzel, A.A.; Mutirangura, A.; Ledbetter, D.H. ); Langlois, S. ); Morris, M.A.; Malcolm, S.

    1993-09-01

    Thirty-two cases of uniparental disomy (UPD), ascertained from Prader-Willi syndrome patients (N=27) and Angelman syndrome patients (N-5), are used to investigate the pattern of recombination associated with nondisjunction of chromosome 15. In addition, the meiotic stage of nondisjunction is inferred by using markers mapping near the centromere. Two basic approaches to the analysis of recombination in specific pairwise intervals along the chromosome. This method shows a significant reduction in recombination for two of five intervals examined. Second, the observed frequency of each recombinant class (i.e., zero, one, two, three, or more observable crossovers) is compared with expected values. This is useful for testing whether the reduction in recombination can be attributed solely to a proportion of cases with no recombination at all (because of asynapsis), with the remaining groups showing normal recombination (or even excess recombination), or whether recombination is uniformly reduced. Analysis of maternal UPD(15) data shows a slight reduction in the multiple-recombinant classes, with a corresponding increase in both the zero- and one-recombinant classes over expected values. The majority, more than 82%, of the extra chromosomes in maternal UPD(15) cases are due to meiotic I nondisjunction events. In contrast, more paternal UPD(15) cases so far examined appear to have a postzygotic origin of the extra paternal chromosome. 33 refs., 1 fig., 7 tabs.

  19. Future switching satellites

    NASA Technical Reports Server (NTRS)

    Campanella, S. Joseph; Pontano, Benjamin A.; Chalmers, Harvey

    1988-01-01

    Communications satellites of the future are likely to use much narrower beams in order to increase the uplink G/T and the downlink EIRP so that small earth terminals of the VSAT class can achieve full mesh connectivity. These satellites will need onboard switches to route traffic from originating upbeams to destination downbeams. This paper presents a new approach to accomplishing this rerouting using destination-directed packets that inherently carry the information needed to control the onboard switch connections and to adjust the traffic flow among the beams and the stations. The method also inherently provides channel multiplication and DAMA advantages which result in maximally efficient utilization of the space segment resource.

  20. Switched power workshop. [Switched power electron guns

    SciTech Connect

    Palmer, R.B.

    1988-01-01

    This paper discusses the design of a switched power electron gun. Particular topics discussed are: vacuum photodiode switch; laser switched solid state diodes; gun performance; charging supply; and laser requirements. (LSP)

  1. Learner Code-Switching versus English Only

    ERIC Educational Resources Information Center

    Sampson, Andrew

    2012-01-01

    This article describes a study into the functions of code-switching in EFL classes at a Colombian language school. It was undertaken to decide whether the official "English-only" policy in place in this and other classrooms is pedagogically justified. The results suggest that code-switching may not necessarily be connected to ability…

  2. B cell function in mice transgenic for mCTLA4-H gamma 1: lack of germinal centers correlated with poor affinity maturation and class switching despite normal priming of CD4+ T cells

    PubMed Central

    1994-01-01

    This report outlines the B cell phenotype of transgenic mice that overexpresses the mouse CTLA-4-human gamma 1 (mCTLA4-H gamma 1) protein. Despite the fact that these mice prime CD4+ T cells (Ronchese, F., B. Housemann, S. Hubele, and P. Lane. 1994. J. Exp. Med. 179:809), antibody responses to T-dependent antigens are severely impaired. In contrast, T-independent responses are normal which suggests mCTLA4-H gamma 1 does not act directly on B cells, but acts indirectly by impairing T cell help. The impaired antibody defect is associated with impaired class switching, with low total immunoglobulin (Ig)G and antigen-specific IgG responses, and an absence of germinal center formation in spleen and lymph nodes but not gut-associated tissues. The defective germinal center formation is associated with a reduction in the degree of somatic mutation in hybridomas made from transgenic mice in comparison with those made from normal mice. It seems likely that mCTLA4-H gamma 1 exerts its effect by blocking an interaction between T and B cells that induce T cell help for B cells. PMID:7509361

  3. The strength of an Ig switch region is determined by its ability to drive R loop formation and its number of WGCW sites.

    PubMed

    Zhang, Zheng Z; Pannunzio, Nicholas R; Han, Li; Hsieh, Chih-Lin; Yu, Kefei; Lieber, Michael R

    2014-07-24

    R loops exist at the murine IgH switch regions and possibly other locations, but their functional importance is unclear. In biochemical systems, R loop initiation requires DNA sequence regions containing clusters of G nucleotides, but cellular studies have not been done. Here, we vary the G-clustering, total switch region length, and the number of target sites (WGCW sites for the activation-induced deaminase) at synthetic switch regions in a murine B cell line to determine the effect on class switch recombination (CSR). G-clusters increase CSR regardless of their immediate proximity to the WGCW sites. This increase is accompanied by an increase in R loop formation. CSR efficiency correlates better with the absolute number of WGCW sites in the switch region rather than the total switch region length or density of WGCW sites. Thus, the overall strength of the switch region depends on G-clusters, which initiate R loop formation, and on the number of WGCW sites.

  4. The Strength of an Ig Switch Region is Determined by its Ability to Drive R-loop Formation and its Number of WGCW Sites

    PubMed Central

    Zhang, Zheng Z.; Pannunzio, Nicholas R.; Han, Li; Hsieh, Chih-Lin; Yu, Kefei; Lieber, Michael R.

    2014-01-01

    SUMMARY R-loops exist at the murine IgH switch regions and possibly other locations, but their functional importance is unclear. In biochemical systems, R-loop initiation requires DNA sequence regions containing clusters of G nucleotides, but cellular studies have not been done. Here, we vary the G-clustering, total switch region length, and the number of target sites (WGCW sites for the activation-induced deaminase) at synthetic switch regions in a murine B cell line to determine the effect on class switch recombination (CSR). G-clusters increase CSR, regardless of their immediate proximity to the WGCW sites. This increase is accompanied by an increase in R-loop formation. CSR efficiency correlates better with the absolute number of WGCW sites in the switch region rather than the total switch region length or density of WGCW sites. Thus, the overall strength of the switch region depends on G-clusters, which initiate R-loop formation, and on the number of WGCW sites. PMID:25017067

  5. Recombinant allergens

    PubMed Central

    Jutel, Marek; Solarewicz-Madejek, Katarzyna; Smolinska, Sylwia

    2012-01-01

    Allergen specific immunotherapy (SIT) is the only known causative treatment of allergic diseases. Recombinant allergen-based vaccination strategies arose from a strong need to both to improve safety and enhance efficacy of SIT. In addition, new vaccines can be effective in allergies including food allergy or atopic dermatitis, which poorly respond to the current treatment with allergen extracts. A number of successful clinical studies with both wild-type and hypoallergenic derivatives of recombinant allergens vaccines have been reported for the last decade. They showed high efficacy and safety profile as well as very strong modulation of T and B cell responses to specific allergens. PMID:23095874

  6. Global asymptotic stabilisation for switched planar systems

    NASA Astrophysics Data System (ADS)

    Zhang, Junfeng; Han, Zhengzhi; Huang, Jun

    2015-04-01

    This paper studies the stabilisation problem of a class of switched planar systems. The present method is different from the existing one designing directly controllers for the underlying systems. The controllers are constructed through two steps. Firstly, by means of the backstepping approach, homogeneous controllers stabilising the nominal systems are obtained. Secondly, the controllers stabilising the planar subsystems are attained by modifying the obtained homogeneous controllers. The controllers depend on perturbations of the switched systems. Finally, by using the multiple Lyapunov functions approach, a sufficient condition of the stabilisation for switched planar systems is given. The conclusions are extended to multiple dimensional switched systems. An illustrative example verifies the validity of the design.

  7. Recombinant gonadotropins.

    PubMed

    Lathi, R B; Milki, A A

    2001-10-01

    Recombinant DNA technology makes it possible to produce large amounts of human gene products for pharmacologic applications, supplanting the need for human tissues. The genes for the alpha and beta subunits of follicle-stimulating hormone (FSH), luteinizing hormone (LH), and human chorionic gonadotropin (hCG) have been characterized and cloned. Recombinant FSH (rFSH) has been shown to be safe and effective in the treatment of fertility disorders. In comparison with the urinary gonadotropin products, human menopausal gonadotropins (HMG), and urinary follitropins (uFSH), rFSH is more potent and better tolerated by patients. Recombinant HCG appears to be as efficacious as urinary HCG with the benefit of improved local tolerance. Recombinant LH (rLH) is likely to be recommended as a supplement to rFSH for ovulation induction in hypogonadotropic women. It may also benefit in vitro fertilization patients undergoing controlled ovarian hyperstimulation with rFSH combined with pituitary suppression, with a gonadotropin-releasing hormone agonist or antagonist.

  8. A recombinant single-chain human class II MHC molecule (HLA-DR1) as a covalently linked heterotrimer of alpha chain, beta chain, and antigenic peptide, with immunogenicity in vitro and reduced affinity for bacterial superantigens.

    PubMed

    Zhu, X; Bavari, S; Ulrich, R; Sadegh-Nasseri, S; Ferrone, S; McHugh, L; Mage, M

    1997-08-01

    Major histocompatibility complex (MHC) class II molecules bind to numerous peptides and display these on the cell surface for T cell recognition. In a given immune response, receptors on T cells recognize antigenic peptides that are a minor population of MHC class II-bound peptides. To control which peptides are presented to T cells, it may be desirable to use recombinant MHC molecules with covalently bound antigenic peptides. To study T cell responses to such homogeneous peptide-MHC complexes, we engineered an HLA-DR1 cDNA coding for influenza hemagglutinin, influenza matrix, or HIV p24 gag peptides covalently attached via a peptide spacer to the N terminus of the DR1 beta chain. Co-transfection with DR alpha cDNA into mouse L cells resulted in surface expression of HLA-DR1 molecules that reacted with monoclonal antibodies (mAb) specific for correctly folded HLA-DR epitopes. This suggested that the spacer and peptide did not alter expression or folding of the molecule. We then engineered an additional peptide spacer between the C terminus of a truncated beta chain (without transmembrane or cytoplasmic domains) and the N terminus of full-length DR alpha chain. Transfection of this cDNA into mouse L cells resulted in surface expression of the entire covalently linked heterotrimer of peptide, beta chain, and alpha chain with the expected molecular mass of approximately 66 kDa. These single-chain HLA-DR1 molecules reacted with mAb specific for correctly folded HLA-DR epitopes, and identified one mAb with [MHC + peptide] specificity. Affinity-purified soluble secreted single-chain molecules with truncated alpha chain moved in electrophoresis as compact class II MHC dimers. Cell surface two-chain or single-chain HLA-DR1 molecules with a covalent HA peptide stimulated HLA-DR1-restricted HA-specific T cells. They were immunogenic in vitro for peripheral blood mononuclear cells. The two-chain and single-chain HLA-DR1 molecules with covalent HA peptide had reduced binding

  9. Accurately Measuring Recombination between Closely Related HIV-1 Genomes

    PubMed Central

    Grimm, Andrew J.; Mak, Johnson; Davenport, Miles P.

    2010-01-01

    Retroviral recombination is thought to play an important role in the generation of immune escape and multiple drug resistance by shuffling pre-existing mutations in the viral population. Current estimates of HIV-1 recombination rates are derived from measurements within reporter gene sequences or genetically divergent HIV sequences. These measurements do not mimic the recombination occurring in vivo, between closely related genomes. Additionally, the methods used to measure recombination make a variety of assumptions about the underlying process, and often fail to account adequately for issues such as co-infection of cells or the possibility of multiple template switches between recombination sites. We have developed a HIV-1 marker system by making a small number of codon modifications in gag which allow recombination to be measured over various lengths between closely related viral genomes. We have developed statistical tools to measure recombination rates that can compensate for the possibility of multiple template switches. Our results show that when multiple template switches are ignored the error is substantial, particularly when recombination rates are high, or the genomic distance is large. We demonstrate that this system is applicable to other studies to accurately measure the recombination rate and show that recombination does not occur randomly within the HIV genome. PMID:20442872

  10. Molecular switches and motors on surfaces.

    PubMed

    Pathem, Bala Krishna; Claridge, Shelley A; Zheng, Yue Bing; Weiss, Paul S

    2013-01-01

    Molecular switches and motors respond structurally, electronically, optically, and/or mechanically to external stimuli, testing and potentially enabling extreme miniaturization of optoelectronic devices, nanoelectromechanical systems, and medical devices. The assembly of motors and switches on surfaces makes it possible both to measure the properties of individual molecules as they relate to their environment and to couple function between assembled molecules. In this review, we discuss recent progress in assembling molecular switches and motors on surfaces, measuring static and dynamic structures, understanding switching mechanisms, and constructing functional molecular materials and devices. As demonstrative examples, we choose a representative molecule from three commonly studied classes including molecular switches, photochromic molecules, and mechanically interlocked molecules. We conclude by offering perspectives on the future of molecular switches and motors on surfaces.

  11. Wide Bandgap Extrinsic Photoconductive Switches

    NASA Astrophysics Data System (ADS)

    Sullivan, James Stephen

    Wide Bandgap Extrinsic Photoconductive Switches Semi-insulating Gallium Nitride, 4H and 6H Silicon Carbide are attractive materials for compact, high voltage, extrinsic, photoconductive switches due to their wide bandgap, high dark resistance, high critical electric field strength and high electron saturation velocity. These wide bandgap semiconductors are made semi-insulating by the addition of vanadium (4H and 6H-SiC) and iron (2H-GaN) impurities that form deep acceptors. These deep acceptors trap electrons donated from shallow donor impurities. The electrons can be optically excited from these deep acceptor levels into the conduction band to transition the wide bandgap semiconductor materials from a semi-insulating to a conducting state. Extrinsic photoconductive switches with opposing electrodes have been constructed using vanadium compensated 6H-SiC and iron compensated 2H-GaN. These extrinsic photoconductive switches were tested at high voltage and high power to determine if they could be successfully used as the closing switch in compact medical accelerators. The successful development of a vanadium compensated, 6H-SiC extrinsic photoconductive switch for use as a closing switch for compact accelerator applications was realized by improvements made to the vanadium, nitrogen and boron impurity densities. The changes made to the impurity densities were based on the physical intuition outlined and simple rate equation models. The final 6H-SiC impurity 'recipe' calls for vanadium, nitrogen and boron densities of 2.5 e17 cm-3, 1.25e17 cm-3 and ≤ 1e16 cm-3, respectively. This recipe was originally developed to maximize the quantum efficiency of the vanadium compensated 6H-SiC, while maintaining a thermally stable semi-insulating material. The rate equation models indicate that, besides increasing the quantum efficiency, the impurity recipe should be expected to also increase the carrier recombination time. Three generations of 6H-SiC materials were tested. The

  12. Controlled release from recombinant polymers.

    PubMed

    Price, Robert; Poursaid, Azadeh; Ghandehari, Hamidreza

    2014-09-28

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

  13. Controlled Release from Recombinant Polymers

    PubMed Central

    Price, Robert; Poursaid, Azadeh; Ghandehari, Hamidreza

    2014-01-01

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

  14. Arginine methylation regulates antibody responses through modulating cell division and isotype switching in B cells.

    PubMed

    Hata, Kikumi; Mizuguchi, Junichiro

    2013-03-01

    Protein arginine methylation plays crucial roles, including signal transduction, transcriptional control, cell proliferation and/or differentiation. B cells undergo clonal division, isotype switching and differentiate into antibody forming cells following stimulation with Toll-like receptor-ligand, lipopolysaccharide (LPS) and T cell-derived signals, including CD40-ligand (CD40-L) and interleukin 4 (IL-4). Whether protein arginine methylation affects B cell division and/or isotype switching to IgG1 in response to LPS, IL-4, and CD40-L was examined using the arginine methyl transferase inhibitor adenosine-2',3'-dialdehyde (AdOx). Addition of AdOx substantially reduced the number of division cycles of stimulated B cells, whereas cell viability remained intact. Upon stimulation with LPS/IL-4/CD40-L, the proportion of surface IgG1 positive cells in each division cycle was slightly diminished by AdOx. However, the degree of expression of γ1 germ line transcript and activation-induced cytidine deaminase (AID) in response to LPS/IL-4/CD40-L were unaffected by addition of AdOx, suggesting that AdOx influences class switch recombination independent of AID expression through transcriptional control. Taken together, arginine methylation appears to be involved in B cell isotype switching, as well as in clonal expansion of B cells in response to LPS/IL-4/CD40-L.

  15. Magnetic switching

    SciTech Connect

    Birx, D.; Cook, E.; Hawkins, S.; Poor, S.; Reginato, L.; Schmidt, J.; Smith, M.

    1983-06-01

    The paper discusses the development program in magnetic switching which was aimed at solving the rep-rate and reliability limitations of the ATA spark gaps. The end result has been a prototype physically very similar to the present Advanced Test Accelerator (ATA) pulse power unit but vastly superior in performance. This prototype, which is easily adaptable to the existing systems, has achieved a burst rep-rate of 20 kHz and an output voltage of 500 kV. A one-on-one substitution of the existing pulse power module would result in a 100 MeV accelerator. Furthermore, the high efficiency of the magnetic pulse compression stages has allowed CW operation of the prototype at one kilohertz opening up other applications for the pulse power. Performance and design details will be described.

  16. An evaluation of Access Tier local area network switches.

    SciTech Connect

    Eldridge, John M.; Olsberg, Ronald R.

    2004-06-01

    This reports tabulates the Test and Evaluation results of the Access Class Switch tests conducted by members of Department 9336. About 15 switches were reviewed for use in the enterprise network as access tier switches as defined in a three tier architecture. The Access Switch Tier has several functions including: aggregate customer desktop ports, preserve and apply QoS tags, provide switched LAN access, provide VLAN assignment, as well as others. The typical switch size is 48 or less user ports. The evaluation team reviewed network switch evaluation reports from the Tolly Group as well as other sources. We then used these reports as a starting point to identify particular switches for evaluation. In general we reviewed the products of dominant equipment manufacturers. Also, based on architectural design requirements, the majority of the switches tested were of relatively small monolithic unit variety.

  17. Plasma Switch Development.

    DTIC Science & Technology

    1984-06-08

    switch :9 (1) the low-pressure gas switch 17 (2) the surface flashover switch ,18 (3) the thyrtron,’ŕ (4) the high pressure...spark gap, (5) the magnetic switch .’ 9 20 and (6) the ECS. The ongoing research for both the low pressure gas and surface flashover closing- switches has... investigations into optimizing gas mixtures for opening switch applications 1 ’"’"’’’a𔃻 ; and a preliminary study of the discharge stabili-

  18. Class Schedules Need Class.

    ERIC Educational Resources Information Center

    Monfette, Ronald J.

    1986-01-01

    Argues that college publications, including class schedules, must be accurate, timely, and easy to read and follow. Describes Schoolcraft College's unified format approach to publications marketing. Offers suggestions on the design, format, and distribution of class schedules. (DMM)

  19. Finite-time synchronization of uncertain coupled switched neural networks under asynchronous switching.

    PubMed

    Wu, Yuanyuan; Cao, Jinde; Li, Qingbo; Alsaedi, Ahmed; Alsaadi, Fuad E

    2017-01-01

    This paper deals with the finite-time synchronization problem for a class of uncertain coupled switched neural networks under asynchronous switching. By constructing appropriate Lyapunov-like functionals and using the average dwell time technique, some sufficient criteria are derived to guarantee the finite-time synchronization of considered uncertain coupled switched neural networks. Meanwhile, the asynchronous switching feedback controller is designed to finite-time synchronize the concerned networks. Finally, two numerical examples are introduced to show the validity of the main results. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. CD40 Ligand and Appropriate Cytokines Induce Switching to IgG, IgA, and IgE and Coordinated Germinal Center and Plasmacytoid Phenotypic Differentiation in a Human Monoclonal IgM+IgD+ B Cell Line1

    PubMed Central

    Cerutti, Andrea; Zan, Hong; Schaffer, Andras; Bergsagel, Leif; Harindranath, Nagaradona; Max, Edward E.; Casali, Paolo

    2015-01-01

    B lymphocytes are induced to undergo Ig class switching and a complex phenotypic differentiation by the milieu of the germinal center. Partly as a result of the lack of a suitable in vitro B cell model, the relationship between these processes in the humans has never been formally established in vitro. We have identified a human monoclonal B cell line, CL-01, that expresses surface IgM and IgD and, upon induction with CD40 ligand, IL-4, and IL-10, switches to all seven downstream isotypes, showing typical DNA switch recombination preceded by germline transcription of targeted CH regions. In CL-01 cells, switch-inducing stimuli trigger concomitant changes in expression of surface IgD, CD23, CD38, and CD77 that parallel those reported in ex vivo isolated tonsillar centroblasts, centrocytes, and memory B cells. Eventually, in the presence of IL-6, CL-01 cells express CD56 and accumulate cytoplasmic IgG and IgA, both traits of plasmacytoid differentiation. Analysis of transcription and recombination of the Ig H locus in sorted CL-01 cells suggest that Ig class switching begins in centroblasts, it extends to all isotypes in centrocytes, and it is extinct in memory B cells. Thus, we have induced coordinated Ig class switching, progression through germinal center phenotypic stages, and differentiation to memory B cells and plasma cells at the level of a single B clonotype. Our data suggest that these processes are likely regulated by a common maturation program, the activation of which may require CD40 ligand, IL-4, IL-10, and IL-6 only. PMID:9498752

  1. Phenotypic switching in bacteria

    NASA Astrophysics Data System (ADS)

    Merrin, Jack

    genetic networks that would implement a more general theoretical model of phenotypic switching. We will use a new cloning strategy in order to systematically assemble a large number of genetic features, such as site-specific recombination components from the R64 plasmid, which invert several coexisting DNA segments. The inversion of these segments would lead to discrete phenotypic transitions inside a living cell. These artificial phenotypic switches can be controlled precisely in experiments and may serve as a benchmark for their natural counterparts.

  2. Latching relay switch assembly

    DOEpatents

    Duimstra, Frederick A.

    1991-01-01

    A latching relay switch assembly which includes a coil section and a switch or contact section. The coil section includes at least one permanent magnet and at least one electromagnet. The respective sections are, generally, arranged in separate locations or cavities in the assembly. The switch is latched by a permanent magnet assembly and selectively switched by an overriding electromagnetic assembly.

  3. Exponential stability and robust H∞ control of a class of discrete-time switched non-linear systems with time-varying delays via T-S fuzzy model

    NASA Astrophysics Data System (ADS)

    Mao, Yanbing; Zhang, Hongbin

    2014-05-01

    This paper deals with stability and robust H∞ control of discrete-time switched non-linear systems with time-varying delays. The T-S fuzzy models are utilised to represent each sub-non-linear system. Thus, with two level functions, namely, crisp switching functions and local fuzzy weighting functions, we introduce a discrete-time switched fuzzy systems, which inherently contain the features of the switched hybrid systems and T-S fuzzy systems. Piecewise fuzzy weighting-dependent Lyapunov-Krasovskii functionals (PFLKFs) and average dwell-time approach are utilised in this paper for the exponentially stability analysis and controller design, and with free fuzzy weighting matrix scheme, switching control laws are obtained such that H∞ performance is satisfied. The conditions of stability and the control laws are given in the form of linear matrix inequalities (LMIs) that are numerically feasible. The state decay estimate is explicitly given. A numerical example and the control of delayed single link robot arm with uncertain part are given to demonstrate the efficiency of the proposed method.

  4. Radiation hard vacuum switch

    DOEpatents

    Boettcher, Gordon E.

    1990-03-06

    A vacuum switch with an isolated trigger probe which is not directly connected to the switching electrodes. The vacuum switch within the plasmatron is triggered by plasma expansion initiated by the trigger probe which travels through an opening to reach the vacuum switch elements. The plasma arc created is directed by the opening to the space between the anode and cathode of the vacuum switch to cause conduction.

  5. Radiation hard vacuum switch

    DOEpatents

    Boettcher, Gordon E.

    1990-01-01

    A vacuum switch with an isolated trigger probe which is not directly connected to the switching electrodes. The vacuum switch within the plasmatron is triggered by plasma expansion initiated by the trigger probe which travels through an opening to reach the vacuum switch elements. The plasma arc created is directed by the opening to the space between the anode and cathode of the vacuum switch to cause conduction.

  6. Mechanisms and Factors that Influence High Frequency Retroviral Recombination

    PubMed Central

    Delviks-Frankenberry, Krista; Galli, Andrea; Nikolaitchik, Olga; Mens, Helene; Pathak, Vinay K.; Hu, Wei-Shau

    2011-01-01

    With constantly changing environmental selection pressures, retroviruses rely upon recombination to reassort polymorphisms in their genomes and increase genetic diversity, which improves the chances for the survival of their population. Recombination occurs during DNA synthesis, whereby reverse transcriptase undergoes template switching events between the two copackaged RNAs, resulting in a viral recombinant with portions of the genetic information from each parental RNA. This review summarizes our current understanding of the factors and mechanisms influencing retroviral recombination, fidelity of the recombination process, and evaluates the subsequent viral diversity and fitness of the progeny recombinant. Specifically, the high mutation rates and high recombination frequencies of HIV-1 will be analyzed for their roles in influencing HIV-1 global diversity, as well as HIV-1 diagnosis, drug treatment, and vaccine development. PMID:21994801

  7. Temporal switching jitter in photoconductive switches

    SciTech Connect

    GAUDET,JOHN A.; SKIPPER,MICHAEL C.; ABDALLA,MICHAEL D.; AHERN,SEAN M.; MAR,ALAN; LOUBRIEL,GUILLERMO M.; ZUTAVERN,FRED J.; O'MALLEY,MARTIN W.; HELGESON,WESLEY D.; ROMERO,SAMUEL P.

    2000-04-13

    This paper reports on a recent comparison made between the Air Force Research Laboratory (AFRL) gallium arsenide, optically-triggered switch test configuration and the Sandia National Laboratories (SNL) gallium arsenide, optically-triggered switch test configuration. The purpose of these measurements was to compare the temporal switch jitter times. It is found that the optical trigger laser characteristics are dominant in determining the PCSS jitter.

  8. Characteristics of current filamentation in high gain photoconductive semiconductor switching

    SciTech Connect

    Zutavern, F J; Loubriel, G M; O'Malley, M W; Helgeson, W D; McLaughlin, D L; Denison, G J

    1992-01-01

    Characteristics of current filamentation are reported for high gain photoconductive semiconductor switches (PCSS). Infrared photoluminescence is used to monitor carrier recombination radiation during fast initiation of high gain switching in large (1.5 cm gap) lateral GaAs PCSS. Spatial modulation of the optical trigger, a 200--300 ps pulse width laser, is examined. Effects on the location and number of current filaments, rise time, and delay to high gain switching, minimum trigger energy, and degradation of switch contacts are presented. Implications of these measurements for the theoretical understanding and practical development of these switches are discussed. Efforts to increase current density and reduce switch size and optical trigger energy requirements are described. Results from contact development and device lifetime testing are presented and the impact of these results on practical device applications is discussed.

  9. Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development[W][OPEN

    PubMed Central

    Palumbo, Maria Concetta; Zenoni, Sara; Fasoli, Marianna; Massonnet, Mélanie; Farina, Lorenzo; Castiglione, Filippo; Pezzotti, Mario; Paci, Paola

    2014-01-01

    We developed an approach that integrates different network-based methods to analyze the correlation network arising from large-scale gene expression data. By studying grapevine (Vitis vinifera) and tomato (Solanum lycopersicum) gene expression atlases and a grapevine berry transcriptomic data set during the transition from immature to mature growth, we identified a category named “fight-club hubs” characterized by a marked negative correlation with the expression profiles of neighboring genes in the network. A special subset named “switch genes” was identified, with the additional property of many significant negative correlations outside their own group in the network. Switch genes are involved in multiple processes and include transcription factors that may be considered master regulators of the previously reported transcriptome remodeling that marks the developmental shift from immature to mature growth. All switch genes, expressed at low levels in vegetative/green tissues, showed a significant increase in mature/woody organs, suggesting a potential regulatory role during the developmental transition. Finally, our analysis of tomato gene expression data sets showed that wild-type switch genes are downregulated in ripening-deficient mutants. The identification of known master regulators of tomato fruit maturation suggests our method is suitable for the detection of key regulators of organ development in different fleshy fruit crops. PMID:25490918

  10. Implications of recombination for HIV diversity.

    PubMed

    Ramirez, Bertha Cecilia; Simon-Loriere, Etienne; Galetto, Roman; Negroni, Matteo

    2008-06-01

    The human immunodeficiency virus (HIV) population is characterised by extensive genetic variability that results from high error and recombination rates of the reverse transcription process, and from the fast turnover of virions in HIV-infected individuals. Among the viral variants encountered at the global scale, recombinant forms are extremely abundant. Some of these recombinants (known as circulating recombinant forms) become fixed and undergo rapid expansion in the population. The reasons underlying their epidemiological success remain at present poorly understood and constitute a fascinating area for future research to improve our understanding of immune escape, pathogenicity and transmission. Recombinant viruses are generated during reverse transcription as a consequence of template switching between the two genetically different genomic RNAs present in a heterozygous virus. Recombination can thereby generate shortcuts in evolution by producing mosaic reverse transcription products of parental genomes. Therefore, in a single infectious cycle multiple mutations that are positively selected can be combined or, conversely, negatively selected mutations can be removed. Recombination is therefore involved in different aspects of HIV evolution, adaptation to its host, and escape from antiviral treatments.

  11. Latching micro optical switch

    DOEpatents

    Garcia, Ernest J; Polosky, Marc A

    2013-05-21

    An optical switch reliably maintains its on or off state even when subjected to environments where the switch is bumped or otherwise moved. In addition, the optical switch maintains its on or off state indefinitely without requiring external power. External power is used only to transition the switch from one state to the other. The optical switch is configured with a fixed optical fiber and a movable optical fiber. The movable optical fiber is guided by various actuators in conjunction with a latching mechanism that configure the switch in one position that corresponds to the on state and in another position that corresponds to the off state.

  12. Expression of recombinant antibodies.

    PubMed

    Frenzel, André; Hust, Michael; Schirrmann, Thomas

    2013-01-01

    Recombinant antibodies are highly specific detection probes in research, diagnostics, and have emerged over the last two decades as the fastest growing class of therapeutic proteins. Antibody generation has been dramatically accelerated by in vitro selection systems, particularly phage display. An increasing variety of recombinant production systems have been developed, ranging from Gram-negative and positive bacteria, yeasts and filamentous fungi, insect cell lines, mammalian cells to transgenic plants and animals. Currently, almost all therapeutic antibodies are still produced in mammalian cell lines in order to reduce the risk of immunogenicity due to altered, non-human glycosylation patterns. However, recent developments of glycosylation-engineered yeast, insect cell lines, and transgenic plants are promising to obtain antibodies with "human-like" post-translational modifications. Furthermore, smaller antibody fragments including bispecific antibodies without any glycosylation are successfully produced in bacteria and have advanced to clinical testing. The first therapeutic antibody products from a non-mammalian source can be expected in coming next years. In this review, we focus on current antibody production systems including their usability for different applications.

  13. Expression of Recombinant Antibodies

    PubMed Central

    Frenzel, André; Hust, Michael; Schirrmann, Thomas

    2013-01-01

    Recombinant antibodies are highly specific detection probes in research, diagnostics, and have emerged over the last two decades as the fastest growing class of therapeutic proteins. Antibody generation has been dramatically accelerated by in vitro selection systems, particularly phage display. An increasing variety of recombinant production systems have been developed, ranging from Gram-negative and positive bacteria, yeasts and filamentous fungi, insect cell lines, mammalian cells to transgenic plants and animals. Currently, almost all therapeutic antibodies are still produced in mammalian cell lines in order to reduce the risk of immunogenicity due to altered, non-human glycosylation patterns. However, recent developments of glycosylation-engineered yeast, insect cell lines, and transgenic plants are promising to obtain antibodies with “human-like” post-translational modifications. Furthermore, smaller antibody fragments including bispecific antibodies without any glycosylation are successfully produced in bacteria and have advanced to clinical testing. The first therapeutic antibody products from a non-mammalian source can be expected in coming next years. In this review, we focus on current antibody production systems including their usability for different applications. PMID:23908655

  14. Heat Switches for ADRs

    NASA Technical Reports Server (NTRS)

    DiPirro, M. J.; Shirron, P. J.

    2014-01-01

    Heat switches are key elements in the cyclic operation of Adiabatic Demagnetization Refrigerators (ADRs). Several of the types of heat switches that have been used for ADRs are described in this paper. Key elements in selection and design of these switches include not only ON/OFF switching ratio, but also method of actuation, size, weight, and structural soundness. Some of the trade-off are detailed in this paper.

  15. Heat switches for ADRs

    NASA Astrophysics Data System (ADS)

    DiPirro, M. J.; Shirron, P. J.

    2014-07-01

    Heat switches are key elements in the cyclic operation of Adiabatic Demagnetization Refrigerators (ADRs). Several of the types of heat switches that have been used for ADRs are described in this paper. Key elements in selection and design of these switches include not only ON/OFF switching ratio, but also method of actuation, size, weight, and structural soundness. Some of the trade-off are detailed in this paper.

  16. Remote switch actuator

    DOEpatents

    Haas, Edwin Gerard; Beauman, Ronald; Palo, Jr., Stefan

    2013-01-29

    The invention provides a device and method for actuating electrical switches remotely. The device is removably attached to the switch and is actuated through the transfer of a user's force. The user is able to remain physically removed from the switch site obviating need for protective equipment. The device and method allow rapid, safe actuation of high-voltage or high-current carrying electrical switches or circuit breakers.

  17. Apollo Ring Optical Switch

    SciTech Connect

    Maestas, J.H.

    1987-03-01

    An optical switch was designed, built, and installed at Sandia National Laboratories in Albuquerque, New Mexico, to facilitate the integration of two Apollo computer networks into a single network. This report presents an overview of the optical switch as well as its layout, switch testing procedure and test data, and installation.

  18. Triggered plasma opening switch

    DOEpatents

    Mendel, Clifford W.

    1988-01-01

    A triggerable opening switch for a very high voltage and current pulse includes a transmission line extending from a source to a load and having an intermediate switch section including a plasma for conducting electrons between transmission line conductors and a magnetic field for breaking the plasma conduction path and magnetically insulating the electrons when it is desired to open the switch.

  19. 47 CFR 32.6210 - Central office switching expenses.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 2 2010-10-01 2010-10-01 false Central office switching expenses. 32.6210 Section 32.6210 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES... Central office switching expenses. Class B telephone companies shall use this account for expenses of the...

  20. Detecting and Analyzing Genetic Recombination Using RDP4.

    PubMed

    Martin, Darren P; Murrell, Ben; Khoosal, Arjun; Muhire, Brejnev

    2017-01-01

    Recombination between nucleotide sequences is a major process influencing the evolution of most species on Earth. The evolutionary value of recombination has been widely debated and so too has its influence on evolutionary analysis methods that assume nucleotide sequences replicate without recombining. When nucleic acids recombine, the evolution of the daughter or recombinant molecule cannot be accurately described by a single phylogeny. This simple fact can seriously undermine the accuracy of any phylogenetics-based analytical approach which assumes that the evolutionary history of a set of recombining sequences can be adequately described by a single phylogenetic tree. There are presently a large number of available methods and associated computer programs for analyzing and characterizing recombination in various classes of nucleotide sequence datasets. Here we examine the use of some of these methods to derive and test recombination hypotheses using multiple sequence alignments.

  1. Robust stabilisation and L2 -gain analysis for switched systems with actuator saturation under asynchronous switching

    NASA Astrophysics Data System (ADS)

    Wang, Juan; Zhao, Jun

    2016-09-01

    Robust stabilisation and L2-gain analysis for a class of switched systems with actuator saturation are studied in this paper. The switching signal of the controllers lags behind that of the system modes, which leads to the asynchronous switching between the candidate controllers and the subsystems. By combining the piecewise Lyapunov function method with the convex hull technique, sufficient conditions in terms of LMIs for the solvability of the robust stabilisation and weighted L2-gain problems are presented respectively under the dwell time scheme. Finally, a numerical example is given to demonstrate the feasibility and effectiveness of the proposed results.

  2. Multilingual Switch in Peer Classroom Interaction

    ERIC Educational Resources Information Center

    Unamuno, Virginia

    2008-01-01

    Focusing on code-switching from conversation analysis and sociolinguistic perspectives, this paper examines interactions between 10-12-year-old language learners of immigrant origin and locally born students as they are engaging in verbal pair work. All are students attending language classes in state primary schools in Barcelona in which Catalan…

  3. Switching from Computer to Microcomputer Architecture Education

    ERIC Educational Resources Information Center

    Bolanakis, Dimosthenis E.; Kotsis, Konstantinos T.; Laopoulos, Theodore

    2010-01-01

    In the last decades, the technological and scientific evolution of the computing discipline has been widely affecting research in software engineering education, which nowadays advocates more enlightened and liberal ideas. This article reviews cross-disciplinary research on a computer architecture class in consideration of its switching to…

  4. Q-Switching in a Neodymium Laser

    ERIC Educational Resources Information Center

    Holgado, Warein; Sola, Inigo J.; Jarque, Enrique Conejero; Jarabo, Sebastian; Roso, Luis

    2012-01-01

    We present a laboratory experiment for advanced undergraduate or graduate laser-related classes to study the performance of a neodymium laser. In the experiment, the student has to build the neodymium laser using an open cavity. After that, the cavity losses are modulated with an optical chopper located inside, so the Q-switching regime is…

  5. Switching from Computer to Microcomputer Architecture Education

    ERIC Educational Resources Information Center

    Bolanakis, Dimosthenis E.; Kotsis, Konstantinos T.; Laopoulos, Theodore

    2010-01-01

    In the last decades, the technological and scientific evolution of the computing discipline has been widely affecting research in software engineering education, which nowadays advocates more enlightened and liberal ideas. This article reviews cross-disciplinary research on a computer architecture class in consideration of its switching to…

  6. Q-Switching in a Neodymium Laser

    ERIC Educational Resources Information Center

    Holgado, Warein; Sola, Inigo J.; Jarque, Enrique Conejero; Jarabo, Sebastian; Roso, Luis

    2012-01-01

    We present a laboratory experiment for advanced undergraduate or graduate laser-related classes to study the performance of a neodymium laser. In the experiment, the student has to build the neodymium laser using an open cavity. After that, the cavity losses are modulated with an optical chopper located inside, so the Q-switching regime is…

  7. REMOTE CONTROLLED SWITCHING DEVICE

    DOEpatents

    Hobbs, J.C.

    1959-02-01

    An electrical switching device which can be remotely controlled and in which one or more switches may be accurately operated at predetermined times or with predetermined intervening time intervals is described. The switching device consists essentially of a deck, a post projecting from the deck at right angles thereto, cam means mounted for rotation around said posts and a switch connected to said deck and actuated by said cam means. Means is provided for rotating the cam means at a constant speed and the switching apparatus is enclosed in a sealed container with external adjusting means and electrical connection elements.

  8. Analysis of a digital microstrip optical switch: a novel method.

    PubMed

    Al-Ruwaihi, K M; Hindy, M A

    1997-02-20

    A time domain analysis of an optically controlled digital microstrip switch for microwave integrated circuits on Si substrates is studied. A new model for high-frequency pulse propagation on a microstrip optical switch for different optical parameters is presented. A frequency-dependent macromodel for a microstrip line with a gap is implemented in Spice 3, taking into consideration high-frequency pulse dispersion, conductor and dielectric losses, metallization thickness, gap length, and different optical parameters such as optical energy, surface recombination velocities, and diffusion of generated carriers. In addition, the developed model has been used to optimize the switching frequency, gap length, level of optical power, and suitable substrate material parameters.

  9. On the Switching Control

    NASA Astrophysics Data System (ADS)

    Balas, Valentina E.; Balas, Marius M.

    2009-04-01

    The paper is discussing the measures able to reject the instability that may unexpectedly appear in particular conditions, in switching controllers applications. The switching controllers' effect is explained by the combined effects of the unsuitable choice of the switching moments (in the first or third quadrants of the phase trajectory of the switching error) and of the temporal aliasing that can distort the digital control systems when the sampling rate is close to the frequency of the oscillations that are produced by the commutation. The correct switching moments are located into the second and fourth quadrants of the phase trajectory of the switching error, but an active preparation of the commutation may be simply achieved by using a tracking controller, that is driving the output of open loop controller to follow the output of the close loop controller, permanently minimizing the switching error. Simulations issued from a dc driver speed controller and from an aircraft are provided.

  10. Optoelectronic techniques for broadband switching

    NASA Astrophysics Data System (ADS)

    Su, S. F.; Jou, L.; Lenart, J.

    1988-01-01

    Optoelectronic switching employs a hybrid optical/electronic principle to perform the switching function and is applicable for either analog broadband or high-bit rate digital switching. The major advantages of optoelectronic switching include high isolation, low crosstalk, small physical size, light weight, and low power consumption. These advantages make optoelectronic switching an excellent candidate for on-board satellite switching. This paper describes a number of optoelectronic switching architectures. System components required for implementing these switching architectures are discussed. Performance of these architectures are evaluated by calculating their crosstalk, isolation, insertion loss, matrix size, drive power, throughput, and switching speed. Technologies needed for monolithic optoelectronic switching are also identified.

  11. Ultrafast all-optical switching with photonic nanojets and semiconductor nanoparticles

    NASA Astrophysics Data System (ADS)

    Born, Brandon; Krupa, Jeffrey D. A.; Geoffroy-Gagnon, Simon; Holzman, Jonathan F.

    2016-03-01

    The potential of terabit-per-second fibre optics can be unlocked with emerging all-optical networks and processors employing all-optical switching. To be effective, all-optical switching must support operations with femtojoule switching energies and femtosecond switching times. With this in mind, this work studies geometrical and material characteristics for all-optical switching and develops a new all-optical switching architecture. A nanojet focal geometry is applied, in the form of dielectric spheres, to direct high-intensity photonic nanojets into peripheral semiconductors. Theoretical and experimental analyses demonstrate photonic nanojets, enabling femtojoule switching energies through localized photoinjection, and semiconductor nanoparticles, enabling femtosecond switching times through localized recombination.

  12. Antibody Isotype Switching in Vertebrates.

    PubMed

    Senger, Kate; Hackney, Jason; Payandeh, Jian; Zarrin, Ali A

    2015-01-01

    The humoral or antibody-mediated immune response in vertebrates has evolved to respond to diverse antigenic challenges in various anatomical locations. Diversification of the immunoglobulin heavy chain (IgH) constant region via isotype switching allows for remarkable plasticity in the immune response, including versatile tissue distribution, Fc receptor binding, and complement fixation. This enables antibody molecules to exert various biological functions while maintaining antigen-binding specificity. Different immunoglobulin (Ig) classes include IgM, IgD, IgG, IgE, and IgA, which exist as surface-bound and secreted forms. High-affinity autoantibodies are associated with various autoimmune diseases such as lupus and arthritis, while defects in components of isotype switching are associated with infections. A major route of infection used by a large number of pathogens is invasion of mucosal surfaces within the respiratory, digestive, or urinary tract. Most infections of this nature are initially limited by effector mechanisms such as secretory IgA antibodies. Mucosal surfaces have been proposed as a major site for the genesis of adaptive immune responses, not just in fighting infections but also in tolerating commensals and constant dietary antigens. We will discuss the evolution of isotype switching in various species and provide an overview of the function of various isotypes with a focus on IgA, which is universally important in gut homeostasis as well as pathogen clearance. Finally, we will discuss the utility of antibodies as therapeutic modalities.

  13. "Racializing" Class

    ERIC Educational Resources Information Center

    Hatt-Echeverria, Beth; Urrieta, Luis, Jr.

    2003-01-01

    In an effort to explore how racial and class oppressions intersect, the authors use their autobiographical narratives to depict cultural and experiential continuity and discontinuity in growing up white working class versus Chicano working class. They specifically focus on "racializing class" due to the ways class is often used as a copout by…

  14. Recombinant protein polymers in biomaterials.

    PubMed

    Kim, Wookhyun

    2013-01-01

    Naturally occurring protein-based materials have been found that function as critical components in biomechanical response, fibers and adhesives. A relatively small but growing number of recombinant protein-based materials that mimic the desired features of their natural sources, such as collagens, elastins and silks, are considered as an alternative to conventional synthetic polymers. Advances in genetic engineering have facilitated the synthesis of repetitive protein polymers with precise control of molecular weights which are designed by using synthetic genes encoding tandem repeats of oligopeptide originating from a modular domain of natural proteins. Many repeat sequences as protein polymer building blocks adopt a well-defined secondary structure and undergo self-assembly to result in physically cross-linked networks or with chemical cross-linking so that further form three-dimensional architectures similar to natural counterparts. In this review, recombinant protein polymers currently developed will be presented that have emerged as promising class of next generation biomaterials.

  15. Monolithic Microwave Switching Matrix

    NASA Technical Reports Server (NTRS)

    Fujikawa, Gene; Ch'en, Daniel R.; Petersen, Wendell C.

    1989-01-01

    Gallium arsenide integrated-circuit chip switches any of three microwave input signals to any of three output ports. Measuring 4.9 mm on side, chip contains nine field-effect transistor (FET) crosspoint switches. Housed in custom-designed package with standard connectors for easy integration into system. FET's on chip operated as passive switches and consume no static power and insignificant amounts of switching power. Chip module cascades with similar modules into large arrays handling as many as 100 inputs and 100 outputs. Applications include switching and routing vast amounts of data between computers at extremely high speed. On communications satellite, chip switches microwave signals to and from Earth stations and other satellites.

  16. Effective switching frequency multiplier inverter

    DOEpatents

    Su, Gui-Jia; Peng, Fang Z.

    2007-08-07

    A switching frequency multiplier inverter for low inductance machines that uses parallel connection of switches and each switch is independently controlled according to a pulse width modulation scheme. The effective switching frequency is multiplied by the number of switches connected in parallel while each individual switch operates within its limit of switching frequency. This technique can also be used for other power converters such as DC/DC, AC/DC converters.

  17. Double-Bounce Switching

    DTIC Science & Technology

    1983-06-01

    module. Adjustments provided to investigate double- bounce switching are noted. limitation is at a higher level and occurs in the conventionally...To be presented at the 4th IEEE PUlsed Power Conference, June 6-8, 1983, Albuquerque, NM. DOUBLE- BOUNCE SWITCHING* George B. Frazier and Steven R...Ashby Physics International Company 2700 Merced Street San Leandro, California 94577 Abstract Double- bounce switching is a technique for

  18. Avalanche Photoconductive Switching

    DTIC Science & Technology

    1989-06-01

    held off across the switch. In our case this corresponds to 70 kV/cm and is limited by surface flashover . The pulse length is determined by the...off across the gap of the switch, which in turn appears to be limited by surface flashover . There appears to be a threshold electric field of 20-60...and understand this mode of operation. Introduction Laser activated photoconductive switching in semiconductors is a promising technology for high

  19. Thermally actuated thermionic switch

    DOEpatents

    Barrus, Donald M.; Shires, Charles D.

    1988-01-01

    A thermally actuated thermionic switch which responds to an increase of temperature by changing from a high impedance to a low impedance at a predictable temperature set point. The switch has a bistable operation mode switching only on temperature increases. The thermionic material may be a metal which is liquid at the desired operation temperature and held in matrix in a graphite block reservoir, and which changes state (ionizes, for example) so as to be electrically conductive at a desired temperature.

  20. Thermally actuated thermionic switch

    DOEpatents

    Barrus, D.M.; Shires, C.D.

    1982-09-30

    A thermally actuated thermionic switch which responds to an increase of temperature by changing from a high impedance to a low impedance at a predictable temperature set point. The switch has a bistable operation mode switching only on temperature increases. The thermionic material may be a metal which is liquid at the desired operation temperature and held in matrix in a graphite block reservoir, and which changes state (ionizes, for example) so as to be electrically conductive at a desired temperature.

  1. Solid state switch

    DOEpatents

    Merritt, Bernard T.; Dreifuerst, Gary R.

    1994-01-01

    A solid state switch, with reverse conducting thyristors, is designed to operate at 20 kV hold-off voltage, 1500 A peak, 1.0 .mu.s pulsewidth, and 4500 pps, to replace thyratrons. The solid state switch is more reliable, more economical, and more easily repaired. The switch includes a stack of circuit card assemblies, a magnetic assist and a trigger chassis. Each circuit card assembly contains a reverse conducting thyristor, a resistor capacitor network, and triggering circuitry.

  2. AC magnetohydrodynamic microfluidic switch

    SciTech Connect

    Lemoff, A V; Lee, A P

    2000-03-02

    A microfluidic switch has been demonstrated using an AC Magnetohydrodynamic (MHD) pumping mechanism in which the Lorentz force is used to pump an electrolytic solution. By integrating two AC MHD pumps into different arms of a Y-shaped fluidic circuit, flow can be switched between the two arms. This type of switch can be used to produce complex fluidic routing, which may have multiple applications in {micro}TAS.

  3. Therapeutic Recombinant Monoclonal Antibodies

    ERIC Educational Resources Information Center

    Bakhtiar, Ray

    2012-01-01

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

  4. Therapeutic Recombinant Monoclonal Antibodies

    ERIC Educational Resources Information Center

    Bakhtiar, Ray

    2012-01-01

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

  5. Alarm toe switch

    DOEpatents

    Ganyard, Floyd P.

    1982-01-01

    An alarm toe switch inserted within a shoe for energizing an alarm circuit n a covert manner includes an insole mounting pad into which a miniature reed switch is fixedly molded. An elongated slot perpendicular to the reed switch is formed in the bottom surface of the mounting pad. A permanent cylindrical magnet positioned in the forward portion of the slot with a diameter greater than the pad thickness causes a bump above the pad. A foam rubber block is also positioned in the slot rearwardly of the magnet and holds the magnet in normal inoperative relation. A non-magnetic support plate covers the slot and holds the magnet and foam rubber in the slot. The plate minimizes bending and frictional forces to improve movement of the magnet for reliable switch activation. The bump occupies the knuckle space beneath the big toe. When the big toe is scrunched rearwardly the magnet is moved within the slot relative to the reed switch, thus magnetically activating the switch. When toe pressure is released the foam rubber block forces the magnet back into normal inoperative position to deactivate the reed switch. The reed switch is hermetically sealed with the magnet acting through the wall so the switch assembly S is capable of reliable operation even in wet and corrosive environments.

  6. Reusable fast opening switch

    DOEpatents

    Van Devender, J.P.; Emin, D.

    1983-12-21

    A reusable fast opening switch for transferring energy, in the form of a high power pulse, from an electromagnetic storage device such as an inductor into a load. The switch is efficient, compact, fast and reusable. The switch comprises a ferromagnetic semiconductor which undergoes a fast transition between conductive and metallic states at a critical temperature and which undergoes the transition without a phase change in its crystal structure. A semiconductor such as europium rich europhous oxide, which undergoes a conductor to insulator transition when it is joule heated from its conductor state, can be used to form the switch.

  7. Reusable fast opening switch

    DOEpatents

    Van Devender, John P.; Emin, David

    1986-01-01

    A reusable fast opening switch for transferring energy, in the form of a high power pulse, from an electromagnetic storage device such as an inductor into a load. The switch is efficient, compact, fast and reusable. The switch comprises a ferromagnetic semiconductor which undergoes a fast transition between conductive and insulating states at a critical temperature and which undergoes the transition without a phase change in its crystal structure. A semiconductor such as europium rich europhous oxide, which undergoes a conductor to insulator transition when it is joule heated from its conductor state, can be used to form the switch.

  8. Platform switching and bone platform switching.

    PubMed

    Carinci, Francesco; Brunelli, Giorgio; Danza, Matteo

    2009-01-01

    Bone platform switching involves an inward bone ring in the coronal part of the implant that is in continuity with the alveolar bone crest. Bone platform switching is obtained by using a dental fixture with a reverse conical neck. A retrospective study was performed to evaluate the effectiveness of conventional vs reverse conical neck implants. In the period between May 2004 and November 2007, 86 patients (55 females and 31 males; median age, 53 years) were operated and 234 implants were inserted: 40 and 194 were conventional vs reverse conical neck implants, respectively. Kaplan-Meier algorithm and Cox regression were used to detect those variables associated with the clinical outcome. No differences in survival and success rates were detected between conventional vs reverse conical neck implants alone or in combination with any of the studied variables. Although bone platform switching leads to several advantages, no statistical difference in alveolar crest resorption is detected in comparison with reverse conical neck implants. We suppose that the proximity of the implant abutment junction to the alveolar crestal bone gives no protection against the microflora contained in the micrograph. Additional studies on larger series and a combination of platform switching and bone platform switching could lead to improved clinical outcomes.

  9. Asymmetrical Switch Costs in Children

    ERIC Educational Resources Information Center

    Ellefson, Michelle R.; Shapiron, Laura R.; Chater, Nick

    2006-01-01

    Switching between tasks produces decreases in performance as compared to repeating the same task. Asymmetrical switch costs occur when switching between two tasks of unequal difficulty. This asymmetry occurs because the cost is greater when switching to the less difficult task than when switching to the more difficult task. Various theories about…

  10. TOPO3alpha influences antigenic variation by monitoring expression-site-associated VSG switching in Trypanosoma brucei.

    PubMed

    Kim, Hee-Sook; Cross, George A M

    2010-07-08

    Homologous recombination (HR) mediates one of the major mechanisms of trypanosome antigenic variation by placing a different variant surface glycoprotein (VSG) gene under the control of the active expression site (ES). It is believed that the majority of VSG switching events occur by duplicative gene conversion, but only a few DNA repair genes that are central to HR have been assigned a role in this process. Gene conversion events that are associated with crossover are rarely seen in VSG switching, similar to mitotic HR. In other organisms, TOPO3alpha (Top3 in yeasts), a type IA topoisomerase, is part of a complex that is involved in the suppression of crossovers. We therefore asked whether a related mechanism might suppress VSG recombination. Using a set of reliable recombination and switching assays that could score individual switching mechanisms, we discovered that TOPO3alpha function is conserved in Trypanosoma brucei and that TOPO3alpha plays a critical role in antigenic switching. Switching frequency increased 10-40-fold in the absence of TOPO3alpha and this hyper-switching phenotype required RAD51. Moreover, the preference of 70-bp repeats for VSG recombination was mitigated, while homology regions elsewhere in ES were highly favored, in the absence of TOPO3alpha. Our data suggest that TOPO3alpha may remove undesirable recombination intermediates constantly arising between active and silent ESs, thereby balancing ES integrity against VSG recombination.

  11. Expression, purification, and analysis of three recombinant ECD disintegrins (r-colombistatins) from P-III class snake venom metalloproteinases affecting platelet aggregation and SK-MEL-28 cell adhesion

    PubMed Central

    Suntravat, Montamas; Helmke, Thomas J.; Atphaisit, Chairat; Cuevas, Esteban; Lucena, Sara E.; Uzcátegui, Nestor L.; Sánchez, Elda E.; Rodriguez-Acosta, Alexis

    2016-01-01

    Crotalid venoms are rich sources of components that affect the hemostatic system. Snake venom metalloproteinases are zinc-dependent enzymes responsible for hemorrhage that also interfere with hemostasis. The disintegrin domain is a part of snake venom metalloproteinases, which involves the binding of integrin receptors. Integrins play an essential role in cancer survival and invasion, and they have been major targets for drug development and design. Both native and recombinant disintegrins have been widely investigated for their anti-cancer activities in biological systems as well as in vitro and in vivo systems. Here, three new cDNAs encoding ECD disintegrin-like domains of metalloproteinase precursor sequences obtained from a Venezuelan mapanare (Bothrops colombiensis) venom gland cDNA library have been cloned. Three different N- and C-terminal truncated ECD disintegrin-like domains of metalloproteinases named colombistatins 2, 3, and 4 were amplified by PCR, cloned into a pGEX-4T-1 vector, expressed in Escherichia coli BL21, and tested for inhibition of platelet aggregation and inhibition of adhesion of human skin melanoma (SK-Mel-28) cancer cell lines on collagen I. Purified recombinant colombistatins 2, 3, and 4 were able to inhibit ristocetin- and collagen-induced platelet aggregation. r-Colombistatins 2 showed the most potent inhibiting SK-Mel-28 cancer cells adhesion to collagen. These results suggest that colombistatins may have utility in the development of therapeutic tools in the treatment of melanoma cancers and also thrombotic diseases. PMID:27641750

  12. Design and characterization of the Pegasus I plasma flow switch

    SciTech Connect

    Wysocki, F.J.; Bartsch, R.R.; Bowers, R.L.; Cochrane, J.C.; Greene, A.E.; Ladish, J.S.; Lee, P.H.Y.; Parker, J.V.; Peterson, D.L.; Benage, J.F.; Gribble, R.F.; Shlachter, J.S.; Scudder, D.W. ); Roderick, N.F. ); Turchi, P.J. )

    1992-01-01

    A plasma flow switch (PFS) based on an experimental design utilized at the Air Force Weapons Laboratory (AFWL) has been fielded on the Pegasus I system. Currents of as much as 5.8 MA have been switched on a time scale (10--90%) of 200 ns into a static load. Tests with a foil load have resulted in a less than ideal current transfer because of interaction between the dynamic load and the plasma flow switch. Two-dimensional radiation magnetohydrodynamic (RMHD) calculations have been used to characterize the behavior of the PFS and to aid in the design. These calculations have also been used to investigate several classes of perturbations in the switch-plasma, the interaction of the switch-plasma with the coaxial electrodes, and their effect on switching efficiency. The Pegasus I PFS experiments reproduce the results obtained at AFWL throughout the switch initiation and switching phases. However, early in the foil implosion the switched current drops significantly. We believe this current drop results from a small amount of residual plasma left behind in the PFS region that impedes the magnetic-flux transport, thereby preventing efficient foil implosion. The experimental results suggest that the method of PFS initiation (viz. chordal wire arrays) may be an important factor in switch operation.

  13. Photoionization and Recombination

    NASA Technical Reports Server (NTRS)

    Nahar, Sultana N.

    2000-01-01

    Theoretically self-consistent calculations for photoionization and (e + ion) recombination are described. The same eigenfunction expansion for the ion is employed in coupled channel calculations for both processes, thus ensuring consistency between cross sections and rates. The theoretical treatment of (e + ion) recombination subsumes both the non-resonant recombination ("radiative recombination"), and the resonant recombination ("di-electronic recombination") processes in a unified scheme. In addition to the total, unified recombination rates, level-specific recombination rates and photoionization cross sections are obtained for a large number of atomic levels. Both relativistic Breit-Pauli, and non-relativistic LS coupling, calculations are carried out in the close coupling approximation using the R-matrix method. Although the calculations are computationally intensive, they yield nearly all photoionization and recombination parameters needed for astrophysical photoionization models with higher precision than hitherto possible, estimated at about 10-20% from comparison with experimentally available data (including experimentally derived DR rates). Results are electronically available for over 40 atoms and ions. Photoionization and recombination of He-, and Li-like C and Fe are described for X-ray modeling. The unified method yields total and complete (e+ion) recombination rate coefficients, that can not otherwise be obtained theoretically or experimentally.

  14. DEK is required for homologous recombination repair of DNA breaks.

    PubMed

    Smith, Eric A; Gole, Boris; Willis, Nicholas A; Soria, Rebeca; Starnes, Linda M; Krumpelbeck, Eric F; Jegga, Anil G; Ali, Abdullah M; Guo, Haihong; Meetei, Amom R; Andreassen, Paul R; Kappes, Ferdinand; Vinnedge, Lisa M Privette; Daniel, Jeremy A; Scully, Ralph; Wiesmüller, Lisa; Wells, Susanne I

    2017-03-20

    DEK is a highly conserved chromatin-bound protein whose upregulation across cancer types correlates with genotoxic therapy resistance. Loss of DEK induces genome instability and sensitizes cells to DNA double strand breaks (DSBs), suggesting defects in DNA repair. While these DEK-deficiency phenotypes were thought to arise from a moderate attenuation of non-homologous end joining (NHEJ) repair, the role of DEK in DNA repair remains incompletely understood. We present new evidence demonstrating the observed decrease in NHEJ is insufficient to impact immunoglobulin class switching in DEK knockout mice. Furthermore, DEK knockout cells were sensitive to apoptosis with NHEJ inhibition. Thus, we hypothesized DEK plays additional roles in homologous recombination (HR). Using episomal and integrated reporters, we demonstrate that HR repair of conventional DSBs is severely compromised in DEK-deficient cells. To define responsible mechanisms, we tested the role of DEK in the HR repair cascade. DEK-deficient cells were impaired for γH2AX phosphorylation and attenuated for RAD51 filament formation. Additionally, DEK formed a complex with RAD51, but not BRCA1, suggesting a potential role regarding RAD51 filament formation, stability, or function. These findings define DEK as an important and multifunctional mediator of HR, and establish a synthetic lethal relationship between DEK loss and NHEJ inhibition.

  15. DEK is required for homologous recombination repair of DNA breaks

    PubMed Central

    Smith, Eric A.; Gole, Boris; Willis, Nicholas A.; Soria, Rebeca; Starnes, Linda M.; Krumpelbeck, Eric F.; Jegga, Anil G.; Ali, Abdullah M.; Guo, Haihong; Meetei, Amom R.; Andreassen, Paul R.; Kappes, Ferdinand; Vinnedge, Lisa M. Privette; Daniel, Jeremy A.; Scully, Ralph; Wiesmüller, Lisa; Wells, Susanne I.

    2017-01-01

    DEK is a highly conserved chromatin-bound protein whose upregulation across cancer types correlates with genotoxic therapy resistance. Loss of DEK induces genome instability and sensitizes cells to DNA double strand breaks (DSBs), suggesting defects in DNA repair. While these DEK-deficiency phenotypes were thought to arise from a moderate attenuation of non-homologous end joining (NHEJ) repair, the role of DEK in DNA repair remains incompletely understood. We present new evidence demonstrating the observed decrease in NHEJ is insufficient to impact immunoglobulin class switching in DEK knockout mice. Furthermore, DEK knockout cells were sensitive to apoptosis with NHEJ inhibition. Thus, we hypothesized DEK plays additional roles in homologous recombination (HR). Using episomal and integrated reporters, we demonstrate that HR repair of conventional DSBs is severely compromised in DEK-deficient cells. To define responsible mechanisms, we tested the role of DEK in the HR repair cascade. DEK-deficient cells were impaired for γH2AX phosphorylation and attenuated for RAD51 filament formation. Additionally, DEK formed a complex with RAD51, but not BRCA1, suggesting a potential role regarding RAD51 filament formation, stability, or function. These findings define DEK as an important and multifunctional mediator of HR, and establish a synthetic lethal relationship between DEK loss and NHEJ inhibition. PMID:28317934

  16. Quantum cryptography without switching.

    PubMed

    Weedbrook, Christian; Lance, Andrew M; Bowen, Warwick P; Symul, Thomas; Ralph, Timothy C; Lam, Ping Koy

    2004-10-22

    We propose a new coherent state quantum key distribution protocol that eliminates the need to randomly switch between measurement bases. This protocol provides significantly higher secret key rates with increased bandwidths than previous schemes that only make single quadrature measurements. It also offers the further advantage of simplicity compared to all previous protocols which, to date, have relied on switching.

  17. Power-Switching Circuit

    NASA Technical Reports Server (NTRS)

    Praver, Gerald A.; Theisinger, Peter C.; Genofsky, John

    1987-01-01

    Functions of circuit breakers, meters, and switches combined. Circuit that includes power field-effect transistors (PFET's) provides on/off switching, soft starting, current monitoring, current tripping, and protection against overcurrent for 30-Vdc power supply at normal load currents up to 2 A. Has no moving parts.

  18. Reflective HTS switch

    DOEpatents

    Martens, J.S.; Hietala, V.M.; Hohenwarter, G.K.G.

    1994-09-27

    A HTS (High Temperature Superconductor) switch includes a HTS conductor for providing a superconducting path for an electrical signal and an serpentine wire actuator for controllably heating a portion of the conductor sufficiently to cause that portion to have normal, and not superconducting, resistivity. Mass of the portion is reduced to decrease switching time. 6 figs.

  19. Reflective HTS switch

    SciTech Connect

    Martens, Jon S.; Hietala, Vincent M.; Hohenwarter, Gert K. G.

    1994-01-01

    A HTS switch includes a HTS conductor for providing a superconducting path for an electrical signal and an serpentine wire actuator for controllably heating a portion of the conductor sufficiently to cause that portion to have normal, and not superconducting, resistivity. Mass of the portion is reduced to decrease switching time.

  20. Manually operated coded switch

    DOEpatents

    Barnette, Jon H.

    1978-01-01

    The disclosure relates to a manually operated recodable coded switch in which a code may be inserted, tried and used to actuate a lever controlling an external device. After attempting a code, the switch's code wheels must be returned to their zero positions before another try is made.

  1. A Novel Molecular Switch

    PubMed Central

    Daber, Robert; Lewis, Mitchell

    2009-01-01

    Transcriptional regulation is a fundamental process for regulating the flux of all metabolic pathways. For the last several decades, the lac operon has served as a valuable model for studying transcription. More recently, the switch that controls the operon has also been successfully adapted to function in mammalian cells. Here we describe how, using directed evolution, we have created a novel switch that recognizes an asymmetric operator sequence. The new switch has a repressor with altered headpiece domains for operator recognition, and a redesigned dimer interface to create a heterodimeric repressor. Quite unexpectedly, the heterodimeric switch functions better than the natural system. It can repress more tightly than the naturally occurring switch of the lac operon; it is less leaky and can be induced more efficiently. Ultimately these novel repressors could be evolved to recognize eukaryotic promoters and used to regulate gene expression in mammalian systems. PMID:19540845

  2. Erected mirror optical switch

    DOEpatents

    Allen, James J.

    2005-06-07

    A microelectromechanical (MEM) optical switching apparatus is disclosed that is based on an erectable mirror which is formed on a rotatable stage using surface micromachining. An electrostatic actuator is also formed on the substrate to rotate the stage and mirror with a high angular precision. The mirror can be erected manually after fabrication of the device and used to redirect an incident light beam at an arbitrary angel and to maintain this state in the absence of any applied electrical power. A 1.times.N optical switch can be formed using a single rotatable mirror. In some embodiments of the present invention, a plurality of rotatable mirrors can be configured so that the stages and mirrors rotate in unison when driven by a single micromotor thereby forming a 2.times.2 optical switch which can be used to switch a pair of incident light beams, or as a building block to form a higher-order optical switch.

  3. CLASS for Class.

    NASA Astrophysics Data System (ADS)

    Bluestein, Howard B.

    1993-09-01

    Faculty and students from the School of Meteorology at the University of Oklahoma and staff members from the Atmospheric Technology Division at the National Center for Atmospheric Research (NCAR) participated in a special course given during the last two weeks of May 1992. The purpose of the course was to give students the opportunity to use the NCAR mobile CLASS (Cross-Chain LORAN Atmospheric Sounding System) in the field and to interpret data they collected themselves in the context of material learned earlier in a lecture setting. Soundings were obtained in parts of Texas and Oklahoma in the environment of multicell storms, in supercells, in a gust front, and on the cold side of a cold front.

  4. Monitoring DNA recombination initiated by HO endonuclease.

    PubMed

    Sugawara, Neal; Haber, James E

    2012-01-01

    DNA double-strand breaks (DSBs) have proven to be very potent initiators of recombination in yeast and other organisms. A single, site-specific DSB initiates homologous DNA repair events such as gene conversion, break-induced replication, and single-strand annealing, as well as nonhomologous end joining, microhomology-mediated end joining, and new telomere addition. When repair is either delayed or prevented, a single DSB can trigger checkpoint-mediated cell cycle arrest. In budding yeast, expressing the HO endonuclease under the control of a galactose-inducible promoter has been instrumental in the study of these processes by providing us a way to synchronously induce a DSB at a unique site in vivo. We describe how the HO endonuclease has been used to study the recombination events in mating-type (MAT) switching. Southern blots provide an overview of the process by allowing one to examine the formation of the DSB, DNA degradation at the break, and formation of the product. Denaturing gels and slot blots as well as PCR have provided important tools to follow the progression of resection in wild-type and mutant cells. PCR has also been important in allowing us to follow the kinetics of certain recombination intermediates such as the initiation of repair DNA synthesis or the removal of nonhomologous Y sequences during MAT switching. Finally chromatin immunoprecipitation has been used to follow the recruitment of key proteins to the DSB and in subsequent steps in DSB repair.

  5. [Switching and combining strategies of antidepressant medications].

    PubMed

    Charpeaud, Thomas; Moliere, Fanny; Bubrovszky, Maxime; Haesebaert, Frédéric; Allaïli, Najib; Bation, Rémy; Nieto, Isabel; Richieri, Raphaëlle; Saba, Ghassen; Bellivier, Frank; Bennabi, Djamila; Holtzmann, Jérôme; Camus, Vincent; Courtet, Philippe; Courvoisier, Pierre; d'Amato, Thierry; Doumy, Olivier; Garnier, Marion; Bougerol, Thierry; Lançon, Christophe; Haffen, Emmanuel; Leboyer, Marion; Llorca, Pierre-Michel; Vaiva, Guillaume; El-Hage, Wissam; Aouizerate, Bruno

    2016-03-01

    Switching antidepressant medication may be helpful in depressed patients having no benefit from the initial antidepressant treatment. Before considering switching strategy, the initial antidepressant treatment should produce no therapeutic effect after at least 4 weeks of administration at adequate dosage. Choosing an antidepressant of pharmacologically distinct profile fails to consistently demonstrate a significant superiority in terms of effectiveness over the switching to another antidepressant within the same pharmacological class. Augmenting SSRI/SNRIs with mirtazapine/mianserin has become the most recommended strategy of antidepressant combinations. Augmenting SSRI with tricyclic drugs is now a less recommended strategy of antidepressant combinations given the increased risk for the occurrence of pharmacokinetic drug-drug interactions and adverse effects.

  6. Switching quantum dynamics for fast stabilization

    NASA Astrophysics Data System (ADS)

    Scaramuzza, Pierre; Ticozzi, Francesco

    2015-06-01

    Control strategies for dissipative preparation of target quantum states, both pure and mixed, and subspaces are obtained by switching between a set of available semigroup generators. We show that the class of problems of interest can be recast, from a control-theoretic perspective, into a switched-stabilization problem for linear dynamics. This is attained by a suitable affine transformation of the coherence-vector representation. In particular, we propose and compare stabilizing time-based and state-based switching rules for entangled state preparation, showing that the latter not only ensure faster convergence with respect to nonswitching methods, but can be designed so that they retain robustness with respect to initialization, as long as the target is a pure state or a subspace.

  7. Production systems for recombinant antibodies.

    PubMed

    Schirrmann, Thomas; Al-Halabi, Laila; Dübel, Stefan; Hust, Michael

    2008-05-01

    Recombinant antibodies are the fastest growing class of therapeutic proteins. Furthermore, antibodies are key detection reagents in research and diagnostics. The increasing demand for antibodies with regards to amount and quality resulted in the development of a variety of recombinant production systems employing gram-negative and gram-positive bacteria, yeast and filamentous fungi, insect cell lines as well as mammalian cell lines. More recently, antibodies were also successfully produced in transgenic plants and animals. Currently, the production of recombinant antibodies for therapy is performed in mammalian cell lines to reduce the risk of immunogenicity caused by non-human post-translational modifications, in particular glycosylation. However, novel strategies already allow human-like glycosylation patterns in yeast, insect cell lines and transgenic plants. Furthermore, therapeutic strategies not requiring glycosylation of the Fc portion have been conceived, most prominently using bispecific antibodies or scFv fusion proteins, which can be produced in bacteria. Here, we review all current antibody production systems considering their advantages and limitations with respect to intended applications.

  8. Expression, purification, and analysis of three recombinant ECD disintegrins (r-colombistatins) from P-III class snake venom metalloproteinases affecting platelet aggregation and SK-MEL-28 cell adhesion.

    PubMed

    Suntravat, Montamas; Helmke, Thomas J; Atphaisit, Chairat; Cuevas, Esteban; Lucena, Sara E; Uzcátegui, Nestor L; Sánchez, Elda E; Rodriguez-Acosta, Alexis

    2016-11-01

    Crotalid venoms are rich sources of components that affect the hemostatic system. Snake venom metalloproteinases are zinc-dependent enzymes responsible for hemorrhage that also interfere with hemostasis. The disintegrin domain is a part of snake venom metalloproteinases, which involves the binding of integrin receptors. Integrins play an essential role in cancer survival and invasion, and they have been major targets for drug development and design. Both native and recombinant disintegrins have been widely investigated for their anti-cancer activities in biological systems as well as in vitro and in vivo systems. Here, three new cDNAs encoding ECD disintegrin-like domains of metalloproteinase precursor sequences obtained from a Venezuelan mapanare (Bothrops colombiensis) venom gland cDNA library have been cloned. Three different N- and C-terminal truncated ECD disintegrin-like domains of metalloproteinases named colombistatins 2, 3, and 4 were amplified by PCR, cloned into a pGEX-4T-1 vector, expressed in Escherichia coli BL21, and tested for inhibition of platelet aggregation and inhibition of adhesion of human skin melanoma (SK-Mel-28) cancer cell lines on collagen I. Purified recombinant colombistatins 2, 3, and 4 were able to inhibit ristocetin- and collagen-induced platelet aggregation. r-Colombistatins 2 showed the most potent inhibiting SK-Mel-28 cancer cells adhesion to collagen. These results suggest that colombistatins may have utility in the development of therapeutic tools in the treatment of melanoma cancers and also thrombotic diseases. Copyright © 2016. Published by Elsevier Ltd.

  9. Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

    PubMed Central

    Hanage, William P.; Harris, Simon R.; Bentley, Stephen; Fraser, Christophe

    2014-01-01

    The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that recombination has a major impact on the evolution of the pathogen, including acquisition of antibiotic resistance and serotype-switching. Nevertheless, the mechanism and the rates of recombination in an epidemiological context remain poorly understood. Here, we proposed several mathematical models to describe the rate and size of recombination in the evolutionary history of two very distinct pneumococcal lineages, PMEN1 and CC180. We found that, in both lineages, the process of homologous recombination was best described by a heterogeneous model of recombination with single, short, frequent replacements, which we call micro-recombinations, and rarer, multi-fragment, saltational replacements, which we call macro-recombinations. Macro-recombination was associated with major phenotypic changes, including serotype-switching events, and thus was a major driver of the diversification of the pathogen. We critically evaluate biological and epidemiological processes that could give rise to the micro-recombination and macro-recombination processes. PMID:24786281

  10. Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution.

    PubMed

    Mostowy, Rafal; Croucher, Nicholas J; Hanage, William P; Harris, Simon R; Bentley, Stephen; Fraser, Christophe

    2014-05-01

    The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that recombination has a major impact on the evolution of the pathogen, including acquisition of antibiotic resistance and serotype-switching. Nevertheless, the mechanism and the rates of recombination in an epidemiological context remain poorly understood. Here, we proposed several mathematical models to describe the rate and size of recombination in the evolutionary history of two very distinct pneumococcal lineages, PMEN1 and CC180. We found that, in both lineages, the process of homologous recombination was best described by a heterogeneous model of recombination with single, short, frequent replacements, which we call micro-recombinations, and rarer, multi-fragment, saltational replacements, which we call macro-recombinations. Macro-recombination was associated with major phenotypic changes, including serotype-switching events, and thus was a major driver of the diversification of the pathogen. We critically evaluate biological and epidemiological processes that could give rise to the micro-recombination and macro-recombination processes.

  11. Antisense transcripts from immunoglobulin heavy-chain locus V(D)J and switch regions

    PubMed Central

    Perlot, Thomas; Li, Gang; Alt, Frederick W.

    2008-01-01

    Activation-induced cytosine deaminase (AID) is essential for both somatic hypermutation (SHM) and class switch recombination (CSR), two processes involved in antibody diversification. Previously, various groups showed both in vitro and in vivo that AID initiates SHM and CSR by deaminating cytosines in DNA in a transcription-dependent manner. Although in vivo both DNA strands are equally targeted by AID, many in vitro and bacterial experiments found that AID almost exclusively targets the nontemplate strand of a transcribed substrate. Here, we report the detection of antisense transcripts in assembled Ig heavy chain (IgH) variable region exons and their immediate downstream region, as well as in switch regions, sequences that, respectively, are targets for SHM and CSR in vivo. In contrast, we did not detect antisense transcripts from the Cμ constant region exons, which lie between the IgH variable region exons and downstream S regions and which are not normally an AID target. Expression of the antisense variable region/flanking region and the S-region transcripts were found in all lymphocytes that transcribe these sequences in the sense direction. Steady-state levels of antisense transcripts appeared very low, and start sites potentially appeared heterogeneous. We discuss the potential implications of antisense IgH locus transcription for AID targeting or other processes. PMID:18292225

  12. Optical packet switching

    NASA Astrophysics Data System (ADS)

    Shekel, Eyal; Ruschin, Shlomo; Majer, Daniel; Levy, Jeff; Matmon, Guy; Koenigsberg, Lisa; Vecht, Jacob; Geron, Amir; Harlavan, Rotem; Shfaram, Harel; Arbel, Arnon; McDermott, Tom; Brewer, Tony

    2005-02-01

    We report here a scalable, multichassis, 6.3 terabit core router, which utilizes our proprietary optical switch. The router is commercially available and deployed in several customer sites. Our solution combines optical switching with electronic routing. An internal optical packet switching network interconnects the router"s electronic line cards, where routing and buffering functions take place electronically. The system architecture and performance will be described. The optical switch is based on Optical Phased Array (OPA) technology. It is a 64 x 64, fully non-blocking, optical crossbar switch, capable of switching in a fraction of a nanosecond. The basic principles of operation will be explained. Loss and crosstalk results will be presented, as well as the results of BER measurements of a 160 Gbps transmission through one channel. Basic principles of operation and measured results will be presented for the burst-mode-receivers, arbitration algorithm and synchronization. Finally, we will present some of our current research work on a next-generation optical switch. The technological issues we have solved in our internal optical packet network can have broad applicability to any global optical packet network.

  13. Optical Circuit Switched Protocol

    NASA Technical Reports Server (NTRS)

    Monacos, Steve P. (Inventor)

    2000-01-01

    The present invention is a system and method embodied in an optical circuit switched protocol for the transmission of data through a network. The optical circuit switched protocol is an all-optical circuit switched network and includes novel optical switching nodes for transmitting optical data packets within a network. Each optical switching node comprises a detector for receiving the header, header detection logic for translating the header into routing information and eliminating the header, and a controller for receiving the routing information and configuring an all optical path within the node. The all optical path located within the node is solely an optical path without having electronic storage of the data and without having optical delay of the data. Since electronic storage of the header is not necessary and the initial header is eliminated by the first detector of the first switching node. multiple identical headers are sent throughout the network so that subsequent switching nodes can receive and read the header for setting up an optical data path.

  14. Direct evaluation of a kinetic model for RecA-mediated DNA-strand exchange: the importance of nucleic acid dynamics and entropy during homologous genetic recombination.

    PubMed

    Xiao, Jie; Lee, Andrew M; Singleton, Scott F

    2006-08-01

    The Escherichia coli RecA protein is the prototype of a class of proteins that play central roles in genomic repair and recombination in all organisms. The unresolved mechanistic strategy by which RecA aligns a single strand of DNA with a duplex DNA and mediates a DNA strand switch is central to understanding homologous recombination. We explored the mechanism of RecA-mediated DNA-strand exchange using oligonucleotide substrates with the intrinsic fluorophore 6-methylisoxanthopterin. Pre-steady-state spectrofluorometric analysis elucidated the earliest transient intermediates formed during recombination and delineated the mechanistic strategy by which RecA facilitates this process. The structural features of the first detectable intermediate and the energetic characteristics of its formation were consistent with interactions between a few bases of the single-stranded DNA and the minor groove of a locally melted or stretched duplex DNA. Further analysis revealed RecA to be an unusual enzyme in that entropic rather than enthalpic contributions dominate its catalytic function, and no unambiguously active role for the protein was detected in the earliest molecular events of recombination. The data best support the conclusion that the mechanistic strategy of RecA likely relies on intrinsic DNA dynamics.

  15. Electromechanical magnetization switching

    SciTech Connect

    Chudnovsky, Eugene M.; Jaafar, Reem

    2015-03-14

    We show that the magnetization of a torsional oscillator that, in addition to the magnetic moment also possesses an electrical polarization, can be switched by the electric field that ignites mechanical oscillations at the frequency comparable to the frequency of the ferromagnetic resonance. The 180° switching arises from the spin-rotation coupling and is not prohibited by the different symmetry of the magnetic moment and the electric field as in the case of a stationary magnet. Analytical equations describing the system have been derived and investigated numerically. Phase diagrams showing the range of parameters required for the switching have been obtained.

  16. Sleep State Switching

    PubMed Central

    Saper, Clifford B.; Fuller, Patrick M.; Pedersen, Nigel P.; Lu, Jun; Scammell, Thomas E.

    2010-01-01

    We take for granted the ability to fall asleep or to snap out of sleep into wakefulness, but these changes in behavioral state require specific switching mechanisms in the brain that allow well-defined state transitions. In this review, we examine the basic circuitry underlying the regulation of sleep and wakefulness, and discuss a theoretical framework wherein the interactions between reciprocal neuronal circuits enable relatively rapid and complete state transitions. We also review how homeostatic, circadian, and allostatic drives help regulate sleep state switching, and discuss how breakdown of the switching mechanism may contribute to sleep disorders such as narcolepsy. PMID:21172606

  17. Photoconductive switch package

    DOEpatents

    Ca[rasp, George J

    2013-10-22

    A photoconductive switch is formed of a substrate that has a central portion of SiC or other photoconductive material and an outer portion of cvd-diamond or other suitable material surrounding the central portion. Conducting electrodes are formed on opposed sides of the substrate, with the electrodes extending beyond the central portion and the edges of the electrodes lying over the outer portion. Thus any high electric fields produced at the edges of the electrodes lie outside of and do not affect the central portion, which is the active switching element. Light is transmitted through the outer portion to the central portion to actuate the switch.

  18. SPARK GAP SWITCH

    DOEpatents

    Neal, R.B.

    1957-12-17

    An improved triggered spark gap switch is described, capable of precisely controllable firing time while switching very large amounts of power. The invention in general comprises three electrodes adjustably spaced and adapted to have a large potential impressed between the outer electrodes. The central electrode includes two separate elements electrically connected togetaer and spaced apart to define a pair of spark gaps between the end electrodes. Means are provided to cause the gas flow in the switch to pass towards the central electrode, through a passage in each separate element, and out an exit disposed between the two separate central electrode elements in order to withdraw ions from the spark gap.

  19. Photoconductive switch package

    DOEpatents

    Caporaso, George J.

    2015-10-27

    A photoconductive switch is formed of a substrate that has a central portion of SiC or other photoconductive material and an outer portion of cvd-diamond or other suitable material surrounding the central portion. Conducting electrodes are formed on opposed sides of the substrate, with the electrodes extending beyond the central portion and the edges of the electrodes lying over the outer portion. Thus any high electric fields produced at the edges of the electrodes lie outside of and do not affect the central portion, which is the active switching element. Light is transmitted through the outer portion to the central portion to actuate the switch.

  20. Solid state switch

    DOEpatents

    Merritt, B.T.; Dreifuerst, G.R.

    1994-07-19

    A solid state switch, with reverse conducting thyristors, is designed to operate at 20 kV hold-off voltage, 1,500 A peak, 1.0 [mu]s pulsewidth, and 4,500 pps, to replace thyratrons. The solid state switch is more reliable, more economical, and more easily repaired. The switch includes a stack of circuit card assemblies, a magnetic assist and a trigger chassis. Each circuit card assembly contains a reverse conducting thyristor, a resistor capacitor network, and triggering circuitry. 6 figs.

  1. Recombination of cluster ions

    NASA Technical Reports Server (NTRS)

    Johnsen, Rainer

    1993-01-01

    Some of our recent work on molecular band emissions from recombination of molecular dimer ions (N4(+) and CO(+) CO) is discussed. Much of the experimental work was done by Y. S. Cao; the results on N4(+) recombination have been published. A brief progress report is given on our ongoing measurements of neutral products of recombination using the flowing-afterglow Langmuir-probe technique in conjunction with laser-induced fluorescence.

  2. Cutting Classes

    ERIC Educational Resources Information Center

    Hacker, Andrew

    1976-01-01

    Provides critical reviews of three books, "The Political Economy of Social Class", "Ethnicity: Theory and Experience," and "Ethnicity in the United States," focusing on the political economy of social class and ethnicity. (Author/AM)

  3. Solar array switching unit

    NASA Technical Reports Server (NTRS)

    Craig, Jr., Calvin L. (Inventor)

    2000-01-01

    A solar array switching (SASU) unit (22) according to the present invention includes a control system (24), a solar cell array (26) and switch circuits (28). The SASU unit (22) is associated with a power card (30) for receiving an output from the array (26). The array (26) has a number (0.5Y) of rows (38) each of which includes a pair of cell strings (42) separated by one of the switch circuits (28). Each of the strings (42) includes a number (X) of cells in electrical series. The SASU (22) switches the array (26) between a short string configuration where the array (26) effectively includes Y strings of X length, and a long string configuration where the array (26) effectively includes 0.5Y strings of 2X length. The SASU (22) thereby facilitates the use of solar power for space missions where solar intensity, operating temperature or other factors vary significantly.

  4. An optical switch

    DOEpatents

    Christophorou, L.G.; Hunter, S.R.

    1987-04-30

    The invention is a gas mixture for a diffuse discharge switch having an electron attaching gas wherein electron attachment is brought about by indirect excitation of molecules to long live states by exposure to laser light. 3 figs.

  5. Switching and stopping antidepressants

    PubMed Central

    Keks, Nicholas; Hope, Judy; Keogh, Simone

    2016-01-01

    SUMMARY Switching from one antidepressant to another is frequently indicated due to an inadequate treatment response or unacceptable adverse effects. All antidepressant switches must be carried out cautiously and under close observation. Conservative switching strategies involve gradually tapering the first antidepressant followed by an adequate washout period before the new antidepressant is started. This can take a long time and include periods of no treatment with the risk of potentially life-threatening exacerbations of illness. Clinical expertise is needed for more rapid or cross-taper switching as drug toxicity, including serotonin syndrome, may result from inappropriate co-administration of antidepressants. Some antidepressants must not be combined. Antidepressants can cause withdrawal syndromes if discontinued abruptly after prolonged use. Relapse and exacerbation of depression can also occur. Gradual dose reduction over days to weeks reduces the risk and severity of complications. PMID:27346915

  6. Roles for APRIN (PDS5B) in homologous recombination and in ovarian cancer prediction

    PubMed Central

    Couturier, Anthony M.; Fleury, Hubert; Patenaude, Anne-Marie; Bentley, Victoria L.; Rodrigue, Amélie; Coulombe, Yan; Niraj, Joshi; Pauty, Joris; Berman, Jason N.; Dellaire, Graham; Di Noia, Javier M.; Mes-Masson, Anne-Marie; Masson, Jean-Yves

    2016-01-01

    APRIN (PDS5 cohesin associated factor B) interacts with both the cohesin complex and the BRCA2 tumor suppressor. How APRIN influences cohesion and DNA repair processes is not well understood. Here, we show that APRIN is recruited to DNA damage sites. We find that APRIN interacts directly with RAD51, PALB2 and BRCA2. APRIN stimulates RAD51-mediated DNA strand invasion. APRIN also binds DNA with an affinity for D-loop structures and single-strand (ss) DNA. APRIN is a new homologous recombination (HR) mediator as it counteracts the RPA inhibitory effect on RAD51 loading to ssDNA. We show that APRIN strongly improves the annealing of complementary-strand DNA and that it can stimulate this process in synergy with BRCA2. Unlike cohesin constituents, its depletion has no impact on class switch recombination, supporting a specific role for this protein in HR. Furthermore, we show that low APRIN expression levels correlate with a better survival in ovarian cancer patients and that APRIN depletion sensitizes cells to the PARP inhibitor Olaparib in xenografted zebrafish. Our findings establish APRIN as an important and specific actor of HR, with cohesin-independent functions. PMID:27924011

  7. Class Size.

    ERIC Educational Resources Information Center

    Underwood, Siobhan; Lumsden, Linda S.

    1994-01-01

    The items featured in this annotated bibliography touch on several aspects of the multifaceted class-size debate. Allen Odden reviews the literature and contends that class-size reduction should be used "sparingly and strategically." C. M. Achilles and colleagues examines two different class-size situations and find student test…

  8. Class Matters

    ERIC Educational Resources Information Center

    Valdata, Patricia

    2005-01-01

    Ever since George Washington opted for the title of president rather than king, Americans have been uncomfortable with the idea of class distinctions. This article presents an interview with Dr. Janet Galligani Casey regarding the idea of class distinctions. Galligani Casey, who grew up in a working-class neighborhood in Somerville, Massachusetts,…

  9. Sequence determinants of breakpoint location during HIV-1 intersubtype recombination.

    PubMed

    Baird, Heather A; Galetto, Román; Gao, Yong; Simon-Loriere, Etienne; Abreha, Measho; Archer, John; Fan, Jun; Robertson, David L; Arts, Eric J; Negroni, Matteo

    2006-01-01

    Retroviral recombination results from strand switching, during reverse transcription, between the two copies of genomic RNA present in the virus. We analysed recombination in part of the envelope gene, between HIV-1 subtype A and D strains. After a single infection cycle, breakpoints clustered in regions corresponding to the constant portions of Env. With some exceptions, a similar distribution was observed after multiple infection cycles, and among recombinant sequences in the HIV Sequence Database. We compared the experimental data with computer simulations made using a program that only allows recombination to occur whenever an identical base is present in the aligned parental RNAs. Experimental recombination was more frequent than expected on the basis of simulated recombination when, in a region spanning 40 nt from the 5' border of a breakpoint, no more than two discordant bases between the parental RNAs were present. When these requirements were not fulfilled, breakpoints were distributed randomly along the RNA, closer to the distribution predicted by computer simulation. A significant preference for recombination was also observed for regions containing homopolymeric stretches. These results define, for the first time, local sequence determinants for recombination between divergent HIV-1 isolates.

  10. Sequence determinants of breakpoint location during HIV-1 intersubtype recombination

    PubMed Central

    Baird, Heather A.; Galetto, Román; Gao, Yong; Simon-Loriere, Etienne; Abreha, Measho; Archer, John; Fan, Jun; Robertson, David L.; Arts, Eric J.; Negroni, Matteo

    2006-01-01

    Retroviral recombination results from strand switching, during reverse transcription, between the two copies of genomic RNA present in the virus. We analysed recombination in part of the envelope gene, between HIV-1 subtype A and D strains. After a single infection cycle, breakpoints clustered in regions corresponding to the constant portions of Env. With some exceptions, a similar distribution was observed after multiple infection cycles, and among recombinant sequences in the HIV Sequence Database. We compared the experimental data with computer simulations made using a program that only allows recombination to occur whenever an identical base is present in the aligned parental RNAs. Experimental recombination was more frequent than expected on the basis of simulated recombination when, in a region spanning 40 nt from the 5′ border of a breakpoint, no more than two discordant bases between the parental RNAs were present. When these requirements were not fulfilled, breakpoints were distributed randomly along the RNA, closer to the distribution predicted by computer simulation. A significant preference for recombination was also observed for regions containing homopolymeric stretches. These results define, for the first time, local sequence determinants for recombination between divergent HIV-1 isolates. PMID:17003055

  11. Optical fiber crossbar switch

    NASA Astrophysics Data System (ADS)

    Kilcoyne, Michael K.; Beccue, Stephen M.; Brar, Berinder; Robinson, G.; Pedrotti, Kenneth D.; Haber, William A.

    1990-07-01

    Advances in high performance computers and signal processing systems have led to parallel system architectures. The main limitation in achieving the performance expected of these parallel systems has been the realization of an efficient means to interconnect many processors into a effective parallel system. Electronic interconnections have proved cumbersome, costly and ineffective. The Optical Fiber Crossbar Switch (OFCS) is a compact low power, multi-gigahertz bandwidth multi-channel switch which can be used in large scale computer and telecommunication applications. The switch operates in the optical domain using GaAs semiconductor lasers to transmit wideband multiple channel optical data over fiber optic cables. Recently, a 32 X 32 crossbar switching system was completed and demonstrated. Error free performance was obtained at a data bandwidth of 410 MBPS, using a silicon switch IC. The switch can be completely reconfigured in less than 50 nanoseconds under computer control. The fully populated OFCS has the capability to handle 12.8 gigabits per second (GBPS) of data while switching this data over 32 channels without the loss of a single bit during switching. GaAs IC technology has now progressed to the point that 16 X 16 GaAs based crossbar switch Ics are available which have increased the data bandwidth capability to 2.4 GBPS. The present optical interfaces are integrated GaAs transmitter drivers, GaAs lasers, and integrated GaAs optical receivers with data bandwidths exceeding 2.4 GBPS. A system using all Ill-V switching and optoelectronic components is presently under development for both NASA and DoD programs. The overall system is designed to operate at 1.3 GBPS. It is expected that these systems will find wide application in high capacity computing systems based on parallel microprocessor architecture which require high data bandwidth communication between processors. The OFCS will also have application in commercial optical telecommunication systems

  12. Cygnus PFL Switch Jitter

    SciTech Connect

    C. Mitton, G. Corrow, M. Hansen, D. Henderson, et al.

    2007-07-21

    The Cygnus Dual Beam Radiographic Facility consists of two identical radiographic sources: Cygnus 1 and Cygnus 2. Each source has the following X-ray output: 1-mm diameter spot size, 4 rads at 1 m, 50-ns full-widthhalf-maximum. The diode pulse has the following electrical specifications: 2.25 MV, 60 kA, 60 ns. This Radiographic Facility is located in an underground tunnel test area at the Nevada Test Site (NTS). The sources were developed to produce high-resolution images on subcritical tests performed at NTS. Subcritical tests are single-shot, high-value events. For this application, it is desirable to maintain a high level of reproducibility in source output. The major components of the Cygnus machines are Marx generator, water-filled pulse forming line (PFL), water-filled coaxial transmission line, threecell inductive voltage adder, and rod-pinch diode. A primary source of fluctuation in Cygnus shot-to-shot performance may be jitter in breakdown of the main PFL switch, which is a “self-break” switch. The PFL switch breakdown time determines the peak PFL charging voltage, which ultimately affects the source X-ray spectrum and dose. Therefore, PFL switch jitter may contribute to shot-to-shot variation in these parameters, which are crucial to radiographic quality. In this paper we will present PFL switch jitter analysis for both Cygnus machines and present the correlation with dose. For this analysis, the PFL switch on each machine was maintained at a single gap setting, which has been used for the majority of shots at NTS. In addition the PFL switch performance for one larger switch gap setting will be examined.

  13. uv preilluminated gas switches

    SciTech Connect

    Bradley, L.P.; Orham, E.L.; Stowers, I.F.; Braucht, J.R.

    1980-06-03

    We have designed, built, and characterized uv preilluminated gas switches for a trigger circuit and a low inductance discharge circuit. These switches have been incorporated into a 54 x 76 x 150 cm pulser module to produce a 1 Ma output current rising at 5 x 10/sup 12/ amps/sec with 1 ns jitter. Twenty such modules will be used on the Nova Inertial Confinement Fusion Laser System for plasma retropulse shutters.

  14. High Power Switching Transistor

    NASA Technical Reports Server (NTRS)

    Hower, P. L.; Kao, Y. C.; Carnahan, D. C.

    1983-01-01

    Improved switching transistors handle 400-A peak currents and up to 1,200 V. Using large diameter silicon wafers with twice effective area as D60T, form basis for D7 family of power switching transistors. Package includes npn wafer, emitter preform, and base-contact insert. Applications are: 25to 50-kilowatt high-frequency dc/dc inverters, VSCF converters, and motor controllers for electrical vehicles.

  15. Cygnus Water Switch Jitter

    SciTech Connect

    Charles V. Mitton, George D. Corrow, Mark D. Hansen, David J. Henderson, et al.

    2008-03-01

    The Cygnus Dual Beam Radiographic Facility consists of two identical radiographic sources - Cygnus 1 and Cygnus 2. Each source has the following x-ray output: 1-mm diameter spot size, 4 rad at 1 m, 50-ns Full Width Half Max. The diode pulse has the following electrical specifications: 2.25 MV, 60 kA, 60 ns. This Radiographic Facility is located in an underground tunnel test area at the Nevada Test Site (NTS). The sources were developed to produce high-resolution images on subcritical tests which are performed at NTS. Subcritical tests are single-shot, high-value events. For this application, it is desirable to maintain a high level of reproducibility in source output. The major components of the Cygnus machines are: Marx generator, water-filled pulse–forming line (PFL), water-filled coaxial transmission line, three-cell inductive voltage adder, and rod-pinch diode. A primary source of fluctuation in Cygnus shot-to-shot performance is jitter in breakdown of the main PFL switch, which is a “self-break” switch. The PFL switch breakdown time determines the peak PFL charging voltage, which ultimately affects the diode pulse. Therefore, PFL switch jitter contributes to shot-to-shot variation in source endpoint energy and dose. In this paper we will present PFL switch jitter analysis for both Cygnus machines and give the correlation with diode performance. For this analysis the PFL switch on each machine was maintained at a single gap setting which has been used for the majority of shots at NTS. In addition to this analysis, PFL switch performance for different switch gap settings taken recently will be examined. Lastly, implications of source jitter for radiographic diagnosis of subcritical shots will be discussed.

  16. Finding a stabilising switching law for switching nonlinear models

    NASA Astrophysics Data System (ADS)

    Lendek, Zs.; Raica, P.; Lauber, J.; Guerra, T. M.

    2016-09-01

    This paper considers the stabilisation of switching nonlinear models by switching between the subsystems. We assume that arbitrary switching between two subsystems is possible once a subsystem has been active for a predefined number of samples. We use a Takagi-Sugeno representation of the models and a switching Lyapunov function is employed to develop sufficient stability conditions. If the conditions are satisfied, we construct a switching law that stabilises the system. The application of the conditions is illustrated in several examples.

  17. Toehold Switches: De-Novo-Designed Regulators of Gene Expression

    PubMed Central

    Green, Alexander A.; Silver, Pamela A.; Collins, James J.; Yin, Peng

    2014-01-01

    SUMMARY Efforts to construct synthetic networks in living cells have been hindered by the limited number of regulatory components that provide wide dynamic range and low crosstalk. Here, we report a new class of de-novo-designed prokaryotic riboregulators called toehold switches that activate gene expression in response to cognate RNAs with arbitrary sequences. Toehold switches provide a high level of orthogonality and can be forward-engineered to provide average dynamic range above 400. We show that switches can be integrated into the genome to regulate endogenous genes and use them as sensors that respond to endogenous RNAs. We exploit the orthogonality of toehold switches to regulate 12 genes independently and to construct a genetic circuit that evaluates 4-input AND logic. Toehold switches, with their wide dynamic range, orthogonality, and programmability, represent a versatile and powerful platform for regulation of translation, offering diverse applications in molecular biology, synthetic biology, and biotechnology. PMID:25417166

  18. Molecular switches activated by electromagnetic pulses: First-principles calculations

    SciTech Connect

    Felicissimo, Viviane Costa; Rocha Martins, Jonathan da; Boldt, Isabel Sager; Chacham, Helio

    2009-12-15

    In the present work, we investigate, through ab initio molecular dynamics simulations, the molecular switching action (a hydrogen tautomerization reaction) in porphyrazine and phthalocyanine induced by electromagnetic pulses. We find that femtosecond pulses attainable from laser sources can induce the switching mechanism in porphyrazine and phthalocyanine through several reaction pathways. We investigate the dependence of the switching mechanism on the parameters (duration, frequency, and polarization) of the electromagnetic pulse and on isotopic substitutions. We also find that the dynamics of inner hydrogen switching in phthalocyanine can be induced by weaker electromagnetic pulses than in porphyrazine. This indicates that molecules of this class with larger numbers of aromatic rings will be more efficient in displaying the pulse-induced switching.

  19. Simplified Design Equations for Class-E Neural Prosthesis Transmitters

    PubMed Central

    Troyk, Philip; Hu, Zhe

    2013-01-01

    Extreme miniaturization of implantable electronic devices is recognized as essential for the next generation of neural prostheses, owing to the need for minimizing the damage and disruption of the surrounding neural tissue. Transcutaneous power and data transmission via a magnetic link remains the most effective means of powering and controlling implanted neural prostheses. Reduction in the size of the coil, within the neural prosthesis, demands the generation of a high-intensity radio frequency magnetic field from the extracoporeal transmitter. The Class-E power amplifier circuit topology has been recognized as a highly effective means of producing large radio frequency currents within the transmitter coil. Unfortunately, design of a Class-E circuit is most often fraught by the need to solve a complex set of equations so as to implement both the zero-voltage-switching and zero-voltage-derivative-switching conditions that are required for efficient operation. This paper presents simple explicit design equations for designing the Class-E circuit topology. Numerical design examples are presented to illustrate the design procedure. PMID:23292784

  20. Simplified design equations for Class-E neural prosthesis transmitters.

    PubMed

    Troyk, Philip; Hu, Zhe

    2013-05-01

    Extreme miniaturization of implantable electronic devices is recognized as essential for the next generation of neural prostheses, owing to the need for minimizing the damage and disruption of the surrounding neural tissue. Transcutaneous power and data transmission via a magnetic link remains the most effective means of powering and controlling implanted neural prostheses. Reduction in the size of the coil, within the neural prosthesis, demands the generation of a high-intensity radio frequency magnetic field from the extracoporeal transmitter. The Class-E power amplifier circuit topology has been recognized as a highly effective means of producing large radio frequency currents within the transmitter coil. Unfortunately, design of a Class-E circuit is most often fraught by the need to solve a complex set of equations so as to implement both the zero-voltage-switching and zero-voltage-derivative-switching conditions that are required for efficient operation. This paper presents simple explicit design equations for designing the Class-E circuit topology. Numerical design examples are presented to illustrate the design procedure.

  1. Functional redundancy between the XLF and DNA-PKcs DNA repair factors in V(D)J recombination and nonhomologous DNA end joining.

    PubMed

    Oksenych, Valentyn; Kumar, Vipul; Liu, Xiangyu; Guo, Chunguang; Schwer, Bjoern; Zha, Shan; Alt, Frederick W

    2013-02-05

    Classical nonhomologous end joining (C-NHEJ) is a major mammalian DNA double-strand break (DSB) repair pathway that is required for assembly of antigen receptor variable region gene segments by V(D)J recombination. Recombination activating gene endonuclease initiates V(D)J recombination by generating DSBs between two V(D)J coding gene segments and flanking recombination signal sequences (RS), with the two coding ends and two RS ends joined by C-NHEJ to form coding joins and signal joins, respectively. During C-NHEJ, recombination activating gene factor generates two coding ends as covalently sealed hairpins and RS ends as blunt 5'-phosphorylated DSBs. Opening and processing of coding end hairpins before joining by C-NHEJ requires the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). However, C-NHEJ of RS ends, which do not require processing, occurs relatively normally in the absence of DNA-PKcs. The XRCC4-like factor (XLF) is a C-NHEJ component that is not required for C-NHEJ of chromosomal signal joins or coding joins because of functional redundancy with ataxia telangiectasia mutated kinase, a protein that also has some functional overlap with DNA-PKcs in this process. Here, we show that XLF has dramatic functional redundancy with DNA-PKcs in the V(D)J SJ joining process, which is nearly abrogated in their combined absence. Moreover, we show that XLF functionally overlaps with DNA-PKcs in normal mouse development, promotion of genomic stability in mouse fibroblasts, and in IgH class switch recombination in mature B cells. Our findings suggest that DNA-PKcs has fundamental roles in C-NHEJ processes beyond end processing that have been masked by functional overlaps with XLF.

  2. Micro-Ball-Lens Optical Switch Driven by SMA Actuator

    NASA Technical Reports Server (NTRS)

    Yang, Eui-Hyeok

    2003-01-01

    The figure is a simplified cross section of a microscopic optical switch that was partially developed at the time of reporting the information for this article. In a fully developed version, light would be coupled from an input optical fiber to one of two side-by-side output optical fibers. The optical connection between the input and the selected output fiber would be made via a microscopic ball lens. Switching of the optical connection from one output fiber to another would be effected by using a pair of thin-film shape-memory-alloy (SMA) actuators to toggle the lens between two resting switch positions. There are many optical switches some made of macroscopic parts by conventional fabrication techniques and some that are microfabricated and, hence, belong to the class of microelectromechanical systems (MEMS). Conventionally fabricated optical switches tend to be expensive. MEMS switches can be mass-produced at relatively low cost, but their attractiveness has been diminished by the fact that, heretofore, MEMS switches have usually been found to exhibit high insertion losses. The present switch is intended to serve as a prototype of low-loss MEMS switches. In addition, this is the first reported SMA-based optical switch. The optical fibers would be held in V grooves in a silicon frame. The lens would have a diameter of 1 m; it would be held by, and positioned between, the SMA actuators, which would be made of thin films of TiNi alloy. Although the SMA actuators are depicted here as having simple shapes for the sake of clarity of illustration, the real actuators would have complex, partly net-like shapes. With the exception of the lens and the optical fibers, the SMA actuators and other components of the switch would be made by microfabrication techniques. The components would be assembled into a sandwich structure to complete the fabrication of the switch. To effect switching, an electric current would be passed through one of the SMA actuators to heat it above

  3. The mismatch repair system reduces meiotic homeologous recombination and stimulates recombination-dependent chromosome loss.

    PubMed Central

    Chambers, S R; Hunter, N; Louis, E J; Borts, R H

    1996-01-01

    Efficient genetic recombination requires near-perfect homology between participating molecules. Sequence divergence reduces the frequency of recombination, a process that is dependent on the activity of the mismatch repair system. The effects of chromosomal divergence in diploids of Saccharomyces cerevisiae in which one copy of chromosome III is derived from a closely related species, Saccharomyces paradoxus, have been examined. Meiotic recombination between the diverged chromosomes is decreased by 25-fold. Spore viability is reduced with an observable increase in the number of tetrads with only two or three viable spores. Asci with only two viable spores are disomic for chromosome III, consistent with meiosis I nondisjunction of the homeologs. Asci with three viable spores are highly enriched for recombinants relative to tetrads with four viable spores. In 96% of the class with three viable spores, only one spore possesses a recombinant chromosome III, suggesting that the recombination process itself contributes to meiotic death. This phenomenon is dependent on the activities of the mismatch repair genes PMS1 and MSH2. A model of mismatch-stimulated chromosome loss is proposed to account for this observation. As expected, crossing over is increased in pms1 and msh2 mutants. Furthermore, genetic exchange in pms1 msh2 double mutants is affected to a greater extent than in either mutant alone, suggesting that the two proteins act independently to inhibit homeologous recombination. All mismatch repair-deficient strains exhibited reductions in the rate of chromosome III nondisjunction. PMID:8887641

  4. Recombination between bacteriophage lambda and plasmid pBR322 in Escherichia coli.

    PubMed Central

    Pogue-Geile, K L; Dassarma, S; King, S R; Jaskunas, S R

    1980-01-01

    Recombinant lambda phages were isolated that resulted from recombination between the lambda genome and plasmid pBR322 in Escherichia coli, even though these deoxyribonucleic acids (DNAs) did not share extensive regions of homology. The characterization of these recombinant DNAs by heteroduplex analysis and restriction endonucleases is described. All but one of the recombinants appeared to have resulted from reciprocal recombination between a site on lambda DNA and a site on the plasmid. In general, there were two classes of recombinants. One class appeared to have resulted from recombination at the phage attachment site that probably resulted from lambda integration into secondary attachment sites on the plasmid. Seven different secondary attachment sites on pBR322 were found. The other class resulted from plasmid integration at other sites that were widely scattered on the lambda genome. For this second class of recombinants, more than one site on the plasmid could recombine with lambda DNA. Thus, the recombination did not appear to be site specific with respect to lambda or the plasmid. Possible mechanisms for generating these recombinants are discussed. Images PMID:6247334

  5. Recombinant Baculovirus Isolation.

    PubMed

    King, Linda A; Hitchman, Richard; Possee, Robert D

    2016-01-01

    Although there are several different methods available of making recombinant baculovirus expression vectors (reviewed in Chapter 3 ), all require a stage in which insect cells are transfected with either the virus genome alone (Bac-to-Bac(®) or BaculoDirect™, Invitrogen) or virus genome and transfer vector. In the latter case, this allows the natural process of homologous recombination to transfer the foreign gene, under control of the polyhedrin or other baculovirus gene promoter, from the transfer vector to the virus genome to create the recombinant virus. Previously, many methods required a plaque-assay to separate parental and recombinant virus prior to amplification and use of the recombinant virus. Fortunately, this step is no longer required for most systems currently available. This chapter provides an overview of the historical development of increasingly more efficient systems for the isolation of recombinant baculoviruses (Chapter 3 provides a full account of the different systems and transfer vectors available). The practical details cover: transfection of insect cells with either virus DNA or virus DNA and plasmid transfer vector; a reliable plaque-assay method that can be used to separate recombinant virus from parental (nonrecombinant) virus where this is necessary; methods for the small-scale amplification of recombinant virus; and subsequent titration by plaque-assay or real-time polymerase chain reaction (PCR). Methods unique to the Bac-to-Bac(®) system are also covered and include the transformation of bacterial cells and isolation of bacmid DNA ready for transfection of insect cells.

  6. Response switching and self-efficacy in Peer Instruction classrooms

    NASA Astrophysics Data System (ADS)

    Miller, Kelly; Schell, Julie; Ho, Andrew; Lukoff, Brian; Mazur, Eric

    2015-06-01

    Peer Instruction, a well-known student-centered teaching method, engages students during class through structured, frequent questioning and is often facilitated by classroom response systems. The central feature of any Peer Instruction class is a conceptual question designed to help resolve student misconceptions about subject matter. We provide students two opportunities to answer each question—once after a round of individual reflection and then again after a discussion round with a peer. The second round provides students the choice to "switch" their original response to a different answer. The percentage of right answers typically increases after peer discussion: most students who answer incorrectly in the individual round switch to the correct answer after the peer discussion. However, for any given question there are also students who switch their initially right answer to a wrong answer and students who switch their initially wrong answer to a different wrong answer. In this study, we analyze response switching over one semester of an introductory electricity and magnetism course taught using Peer Instruction at Harvard University. Two key features emerge from our analysis: First, response switching correlates with academic self-efficacy. Students with low self-efficacy switch their responses more than students with high self-efficacy. Second, switching also correlates with the difficulty of the question; students switch to incorrect responses more often when the question is difficult. These findings indicate that instructors may need to provide greater support for difficult questions, such as supplying cues during lectures, increasing times for discussions, or ensuring effective pairing (such as having a student with one right answer in the pair). Additionally, the connection between response switching and self-efficacy motivates interventions to increase student self-efficacy at the beginning of the semester by helping students develop early mastery or

  7. Low inductance gas switching.

    SciTech Connect

    Chavez, Ray; Harjes, Henry Charles III; Wallace, Zachariah; Elizondo, Juan E.

    2007-10-01

    The laser trigger switch (LTS) is a key component in ZR-type pulsed power systems. In ZR, the pulse rise time through the LTS is > 200 ns and additional stages of pulse compression are required to achieve the desired <100 ns rise time. The inductance of the LTS ({approx}500nH) in large part determines the energy transfer time through the switch and there is much to be gained in improving system performance and reducing system costs by reducing this inductance. The current path through the cascade section of the ZR LTS is at a diameter of {approx} 6-inches which is certainly not optimal from an inductance point of view. The LTS connects components of much greater diameter (typically 4-5 feet). In this LDRD the viability of switch concepts in which the diameter of cascade section is greatly increased have been investigated. The key technical question to be answered was, will the desired multi-channel behavior be maintained in a cascade section of larger diameter. This LDRD proceeded in 2 distinct phases. The original plan for the LDRD was to develop a promising switch concept and then design, build, and test a moderate scale switch which would demonstrate the key features of the concept. In phase I, a switch concept which meet all electrical design criteria and had a calculated inductance of 150 nH was developed. A 1.5 MV test switch was designed and fabrication was initiated. The LDRD was then redirected due to budgetary concerns. The fabrication of the switch was halted and the focus of the LDRD was shifted to small scale experiments designed to answer the key technical question concerning multi-channel behavior. In phase II, the Multi-channel switch test bed (MCST) was designed and constructed. The purpose of MCST was to provide a versatile, fast turn around facility for the study the multi-channel electrical breakdown behavior of a ZR type cascade switch gap in a parameter space near that of a ZR LTS. Parameter scans on source impedance, gap tilt, gap spacing and

  8. Innovative switching technology

    NASA Astrophysics Data System (ADS)

    Rosen, A.; Stabile, P. J.; Gombar, A. M.; Janton, W. M.; Gilbert, D. B.; Herczfeld, P. R.; Bahasadri, A.

    1991-03-01

    We have developed an all-semiconductor high-power optical switch. Potential uses include both military applications, such as ultra-wide-band impulse radar and high-frequency antenna couplers, and commercial use, such as high-power switching for utility companies. Under this three-year program, we have demonstrated various switching applications from dc to GHz frequencies. The generic switches comprise a 2-D semiconductor laser diode array and Si or GaAs devices. In the Si area (linear switches - no gain) and dc-biased network, a single two-sided PIN device, activated by two 1 kW laser arrays, has yielded a holding voltage of 1.3 kV and conducted 192 A. Similar devices have later yielded a holding voltage of 3.3 kV, demonstrating the capability of switching more than 500 kW with a single two-sided PIN device. The same generic technology was also demonstrated in high-power high-frequency antenna coupler applications as well as in mm-wave (60 GHz) attenuators and phase shifters. PIN devices tested in a RF circuit between 2-30 MHz yielded an isolation value of between 28 and 49 dB in the off-state, and insertion losses as low as 0.1 dB when illuminated with 280 W (peak) optical power at 808 nm. In the area of GaAs, PIN, and bulk devices under this project, we were able to deliver devices for experiments in both opening and closing switches. We have demonstrated a compact, all-semiconductor switch system that has switched up to 8.5 MW into a 38 (omega) load. The system uses a 2-D laser diode array with a peak power of 850 W to rigger a 1.5 cm long GaAs photoconductor into a high-gain combination mode known as 'lock on'. The highest power switch was pulse-charged to 55 kV and delivered 470 A to a 38 (omega) load in 160 ns long pulse. In the area of 2-D laser arrays, a peak power density of 7 kW/cm(exp 2) was achieved.

  9. Printed Antennas Made Reconfigurable by Use of MEMS Switches

    NASA Technical Reports Server (NTRS)

    Simons, Rainee N.

    2005-01-01

    A class of reconfigurable microwave antennas now undergoing development comprise fairly conventional printed-circuit feed elements and radiating patches integrated with novel switches containing actuators of the microelectromechanical systems (MEMS) type. In comparison with solid-state electronic control devices incorporated into some prior printed microwave antennas, the MEMS-based switches in these antennas impose lower insertion losses and consume less power. Because the radio-frequency responses of the MEMS switches are more nearly linear, they introduce less signal distortion. In addition, construction and operation are simplified because only a single DC bias line is needed to control each MEMS actuator.

  10. A radiation hard vacuum switch

    DOEpatents

    Boettcher, G.E.

    1988-07-19

    A vacuum switch with an isolated trigger probe which is not directly connected to the switching electrodes. The vacuum switch within the plasmatron is triggered by plasma expansion initiated by the trigger probe which travels through an opening to reach the vacuum switch elements. The plasma arc created is directed by the opening to the space between the anode and cathode of the vacuum switch to cause conduction. 3 figs.

  11. Long Life MEM Switch Technology

    DTIC Science & Technology

    2006-05-23

    The first type of MEM switch developed was the miniature switched capacitor. This device is 150-300 times smaller than conventional MEM switches...down and the shunt capacitance to the ground is increased. The mechanical behavior of the MEM capacitor is designed using conventional mechanical...switched capacitors. It proves that by decreasing the size, miniature switched capacitors with Con/ Coff =2.8 for a single bridge and Con/ Coff =1.9 for a 3

  12. Development of a rapid in vitro protein refolding assay which discriminates between peptide-bound and peptide-free forms of recombinant porcine major histocompatibility class I complex (SLA-I).

    PubMed

    Oleksiewicz, M B; Kristensen, B; Ladekjaer-Mikkelsen, A-S; Nielsen, J

    2002-05-01

    The extracellular domains of swine leukocyte antigen class I (SLA-I, major histocompatibility complex protein class I) were cloned and sequenced for two haplotypes (H4 and H7) which do not share any alleles based on serological typing, and which are the most important in Danish farmed pigs. The extracellular domain of SLA-I was connected to porcine beta2 microglobulin by glycine-rich linkers. The engineered single-chain proteins, consisting of fused SLA-I and beta2 microglobulin, were overexpressed as inclusion bodies in Escherichia coli. Also, variants were made of the single-chain proteins, by linking them through glycine-rich linkers to peptides representing T-cell epitopes from classical swine fever virus (CSFV) and foot-and-mouth disease virus (FMDV). An in vitro refold assay was developed, using a monoclonal anti-SLA antibody (PT85A) to gauge refolding. The single best-defined, SLA-I restricted porcine CD8(+) T-cell epitope currently known is a 9-residue peptide from the polyprotein of CSFV (J. Gen. Virol. 76 (1995) 3039). Based on results with the CSFV epitope and two porcine haplotypes (H4 and H7), the in vitro refold assay appeared able to discriminate between peptide-free and peptide-occupied forms of SLA-I. It remains to be seen whether the rapid and technically very simple in vitro refold assay described here will prove generally applicable for the screening of virus-derived peptides for SLA-I binding.

  13. Integration of photonic nanojets and semiconductor nanoparticles for enhanced all-optical switching

    PubMed Central

    Born, Brandon; Krupa, Jeffrey D. A.; Geoffroy-Gagnon, Simon; Holzman, Jonathan F.

    2015-01-01

    All-optical switching is the foundation of emerging all-optical (terabit-per-second) networks and processors. All-optical switching has attracted considerable attention, but it must ultimately support operation with femtojoule switching energies and femtosecond switching times to be effective. Here we introduce an all-optical switch architecture in the form of a dielectric sphere that focuses a high-intensity photonic nanojet into a peripheral coating of semiconductor nanoparticles. Milli-scale spheres coated with Si and SiC nanoparticles yield switching energies of 200 and 100 fJ with switching times of 10 ps and 350 fs, respectively. Micro-scale spheres coated with Si and SiC nanoparticles yield switching energies of 1 pJ and 20 fJ with switching times of 2 ps and 270 fs, respectively. We show that femtojoule switching energies are enabled by localized photoinjection from the photonic nanojets and that femtosecond switching times are enabled by localized recombination within the semiconductor nanoparticles. PMID:26314911

  14. Integration of photonic nanojets and semiconductor nanoparticles for enhanced all-optical switching

    NASA Astrophysics Data System (ADS)

    Born, Brandon; Krupa, Jeffrey D. A.; Geoffroy-Gagnon, Simon; Holzman, Jonathan F.

    2015-08-01

    All-optical switching is the foundation of emerging all-optical (terabit-per-second) networks and processors. All-optical switching has attracted considerable attention, but it must ultimately support operation with femtojoule switching energies and femtosecond switching times to be effective. Here we introduce an all-optical switch architecture in the form of a dielectric sphere that focuses a high-intensity photonic nanojet into a peripheral coating of semiconductor nanoparticles. Milli-scale spheres coated with Si and SiC nanoparticles yield switching energies of 200 and 100 fJ with switching times of 10 ps and 350 fs, respectively. Micro-scale spheres coated with Si and SiC nanoparticles yield switching energies of 1 pJ and 20 fJ with switching times of 2 ps and 270 fs, respectively. We show that femtojoule switching energies are enabled by localized photoinjection from the photonic nanojets and that femtosecond switching times are enabled by localized recombination within the semiconductor nanoparticles.

  15. Integration of photonic nanojets and semiconductor nanoparticles for enhanced all-optical switching.

    PubMed

    Born, Brandon; Krupa, Jeffrey D A; Geoffroy-Gagnon, Simon; Holzman, Jonathan F

    2015-08-28

    All-optical switching is the foundation of emerging all-optical (terabit-per-second) networks and processors. All-optical switching has attracted considerable attention, but it must ultimately support operation with femtojoule switching energies and femtosecond switching times to be effective. Here we introduce an all-optical switch architecture in the form of a dielectric sphere that focuses a high-intensity photonic nanojet into a peripheral coating of semiconductor nanoparticles. Milli-scale spheres coated with Si and SiC nanoparticles yield switching energies of 200 and 100 fJ with switching times of 10 ps and 350 fs, respectively. Micro-scale spheres coated with Si and SiC nanoparticles yield switching energies of 1 pJ and 20 fJ with switching times of 2 ps and 270 fs, respectively. We show that femtojoule switching energies are enabled by localized photoinjection from the photonic nanojets and that femtosecond switching times are enabled by localized recombination within the semiconductor nanoparticles.

  16. Switching power pulse system

    DOEpatents

    Aaland, K.

    1983-08-09

    A switching system for delivering pulses of power from a source to a load using a storage capacitor charged through a rectifier, and maintained charged to a reference voltage level by a transistor switch and voltage comparator. A thyristor is triggered to discharge the storage capacitor through a saturable reactor and fractional turn saturable transformer having a secondary to primary turn ratio N of n:l/n = n[sup 2]. The saturable reactor functions as a soaker'' while the thyristor reaches saturation, and then switches to a low impedance state. The saturable transformer functions as a switching transformer with high impedance while a load coupling capacitor charges, and then switches to a low impedance state to dump the charge of the storage capacitor into the load through the coupling capacitor. The transformer is comprised of a multilayer core having two secondary windings tightly wound and connected in parallel to add their output voltage and reduce output inductance, and a number of single turn windings connected in parallel at nodes for the primary winding, each single turn winding linking a different one of the layers of the multilayer core. The load may be comprised of a resistive beampipe for a linear particle accelerator and capacitance of a pulse forming network. To hold off discharge of the capacitance until it is fully charged, a saturable core is provided around the resistive beampipe to isolate the beampipe from the capacitance until it is fully charged. 5 figs.

  17. Atomic Scale Plasmonic Switch.

    PubMed

    Emboras, Alexandros; Niegemann, Jens; Ma, Ping; Haffner, Christian; Pedersen, Andreas; Luisier, Mathieu; Hafner, Christian; Schimmel, Thomas; Leuthold, Juerg

    2016-01-13

    The atom sets an ultimate scaling limit to Moore's law in the electronics industry. While electronics research already explores atomic scales devices, photonics research still deals with devices at the micrometer scale. Here we demonstrate that photonic scaling, similar to electronics, is only limited by the atom. More precisely, we introduce an electrically controlled plasmonic switch operating at the atomic scale. The switch allows for fast and reproducible switching by means of the relocation of an individual or, at most, a few atoms in a plasmonic cavity. Depending on the location of the atom either of two distinct plasmonic cavity resonance states are supported. Experimental results show reversible digital optical switching with an extinction ratio of 9.2 dB and operation at room temperature up to MHz with femtojoule (fJ) power consumption for a single switch operation. This demonstration of an integrated quantum device allowing to control photons at the atomic level opens intriguing perspectives for a fully integrated and highly scalable chip platform, a platform where optics, electronics, and memory may be controlled at the single-atom level.

  18. Silicon carbide photoconductive switches

    NASA Astrophysics Data System (ADS)

    Saddow, Stephen E.

    1994-09-01

    The optoelectronic properties of p-type 6-H silicon carbide (6H-SiC) have been investigated in an experiment that used lateral and vertical photoconductive (PC) switches. Both photovoltaic and photoconductive effects are reported, which were observed on switches using both geometries and measured at several wavelengths near the 6H-SiC absorption edge. PC techniques were employed to measure the surface and bulk carrier lifetimes of 40 and 200 ns, respectively. The switches displayed a high-speed photovoltaic response to picosecond laser excitations in the UV and visible spectral regions. In particular, efficient subnanosecond optical absorption processes were observed in the visible region. The photovoltage was measured as a function of both laser wavelength (and hence absorption depth) and laser beam position within the switching gap. The switch response to picosecond laser pulses in the UV, violet, green, and red spectral regions was shown to have subnanosecond photovoltaic response times. Finally, since the optical absorption coefficient had not been well established for device-grade 6H-SiC, the optical absorption coefficient near the 6H-SiC bandgap energy (Eg) was also measured, and the bandgap was determined to be approximately 3.1 eV.

  19. Multiple switch actuator

    DOEpatents

    Beyer, Edward T.

    1976-01-06

    The present invention relates to switches and switch actuating devices to be operated for purposes of arming a bomb or other missile as it is dropped or released from an aircraft. The particular bomb or missile in which this invention is applied is one in which there is a plurality of circuits which are to be armed by the closing of switches upon dropping or releasing of the bomb. The operation of the switches to closed position is normally accomplished by means of a pull-out wire; that is, a wire which is withdrawn from the bomb or missile at the time of release of the bomb, one end of the wire being attached to the aircraft. The conditions to be met are that the arming switches must be positively and surely maintained in open position until the bomb is released and the arming action is effected. The action of the pull-out wire in achieving the arming action must be sure and positive with minimum danger of malfunctioning, jamming or binding.

  20. Thermionic gas switch

    DOEpatents

    Hatch, G.L.; Brummond, W.A.; Barrus, D.M.

    1984-04-05

    The present invention is directed to an improved temperature responsive thermionic gas switch utilizing a hollow cathode and a folded emitter surface area. The folded emitter surface area of the thermionic switch substantially increases the on/off ratio by changing the conduction surface area involved in the two modes thereof. The improved switch of this invention provides an on/off ratio of 450:1 compared to the 10:1 ratio of the prior known thermionic switch, while providing for adjusting the on current. In the improved switch of this invention the conduction area is made small in the off mode, while in the on mode the conduction area is made large. This is achieved by utilizing a folded hollow cathode configuration and utilizing a folded emitter surface area, and by making the dimensions of the folds small enough so that a space charge will develop in the convolutions of the folds and suppress unignited current, thus limiting the current carrying surface in the off mode.

  1. Adaptive Fuzzy Control Design for Stochastic Nonlinear Switched Systems With Arbitrary Switchings and Unmodeled Dynamics.

    PubMed

    Li, Yongming; Sui, Shuai; Tong, Shaocheng

    2017-02-01

    This paper deals with the problem of adaptive fuzzy output feedback control for a class of stochastic nonlinear switched systems. The controlled system in this paper possesses unmeasured states, completely unknown nonlinear system functions, unmodeled dynamics, and arbitrary switchings. A state observer which does not depend on the switching signal is constructed to tackle the unmeasured states. Fuzzy logic systems are employed to identify the completely unknown nonlinear system functions. Based on the common Lyapunov stability theory and stochastic small-gain theorem, a new robust adaptive fuzzy backstepping stabilization control strategy is developed. The stability of the closed-loop system on input-state-practically stable in probability is proved. The simulation results are given to verify the efficiency of the proposed fuzzy adaptive control scheme.

  2. The fox and the cabra: an ERP analysis of reading code switched nouns and verbs in bilingual short stories.

    PubMed

    Ng, Shukhan; Gonzalez, Christian; Wicha, Nicole Y Y

    2014-04-04

    Comprehending a language (or code) switch within a sentence context triggers 2 electrophysiological signatures: an early left anterior negativity post code switch onset - a LAN - followed by a Late Positive Component (LPC). Word class and word position modulate lexico-semantic processes in the monolingual brain, e.g., larger N400 amplitude for nouns than verbs and for earlier than later words in the sentence. Here we test whether the bilingual brain is affected by word class and word position when code switching, or if the cost of switching overrides these lexico-semantic and sentence context factors. Adult bilinguals read short stories in English containing 8 target words. Targets were nouns or verbs, occurred early or late in a story and were presented alternately in English (non-switch) or Spanish (switch) across different story versions. Overall, switched words elicited larger LAN and LPC amplitude than non-switched words. The N400 amplitude was larger for nouns than verbs, more focal for switches than non-switches, and for early than late nouns but not for early than late verbs. Moreover, an early LPC effect was observed only for switched nouns, but not verbs. Together, this indicates that referential elements (nouns) may be harder to process and integrate than relational elements (verbs) in discourse, and when switched, nouns incur higher integration cost. Word position did not modulate the code switching effects, implying that switching between languages may invoke discourse independent processes.

  3. Recombination and Replication

    PubMed Central

    Syeda, Aisha H.; Hawkins, Michelle; McGlynn, Peter

    2014-01-01

    The links between recombination and replication have been appreciated for decades and it is now generally accepted that these two fundamental aspects of DNA metabolism are inseparable: Homologous recombination is essential for completion of DNA replication and vice versa. This review focuses on the roles that recombination enzymes play in underpinning genome duplication, aiding replication fork movement in the face of the many replisome barriers that challenge genome stability. These links have many conserved features across all domains of life, reflecting the conserved nature of the substrate for these reactions, DNA. PMID:25341919

  4. Dissociative recombination in aeronomy

    NASA Technical Reports Server (NTRS)

    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(+).

  5. Microfabricated triggered vacuum switch

    DOEpatents

    Roesler, Alexander W.; Schare, Joshua M.; Bunch, Kyle

    2010-05-11

    A microfabricated vacuum switch is disclosed which includes a substrate upon which an anode, cathode and trigger electrode are located. A cover is sealed over the substrate under vacuum to complete the vacuum switch. In some embodiments of the present invention, a metal cover can be used in place of the trigger electrode on the substrate. Materials used for the vacuum switch are compatible with high vacuum, relatively high temperature processing. These materials include molybdenum, niobium, copper, tungsten, aluminum and alloys thereof for the anode and cathode. Carbon in the form of graphitic carbon, a diamond-like material, or carbon nanotubes can be used in the trigger electrode. Channels can be optionally formed in the substrate to mitigate against surface breakdown.

  6. Optical computer switching network

    NASA Technical Reports Server (NTRS)

    Clymer, B.; Collins, S. A., Jr.

    1985-01-01

    The design for an optical switching system for minicomputers that uses an optical spatial light modulator such as a Hughes liquid crystal light valve is presented. The switching system is designed to connect 80 minicomputers coupled to the switching system by optical fibers. The system has two major parts: the connection system that connects the data lines by which the computers communicate via a two-dimensional optical matrix array and the control system that controls which computers are connected. The basic system, the matrix-based connecting system, and some of the optical components to be used are described. Finally, the details of the control system are given and illustrated with a discussion of timing.

  7. Switching power supply

    DOEpatents

    Mihalka, A.M.

    1984-06-05

    The invention is a repratable capacitor charging, switching power supply. A ferrite transformer steps up a dc input. The transformer primary is in a full bridge configuration utilizing power MOSFETs as the bridge switches. The transformer secondary is fed into a high voltage, full wave rectifier whose output is connected directly to the energy storage capacitor. The transformer is designed to provide adequate leakage inductance to limit capacitor current. The MOSFETs are switched to the variable frequency from 20 to 50 kHz to charge a capacitor from 0.6 kV. The peak current in a transformer primary and secondary is controlled by increasing the pulse width as the capacitor charges. A digital ripple counter counts pulses and after a preselected desired number is reached an up-counter is clocked.

  8. SWITCH user's manual

    NASA Technical Reports Server (NTRS)

    1987-01-01

    The planning program, SWITCH, and its surrounding changed-goal-replanning program, Runaround, are described. The evolution of SWITCH and Runaround from an earlier planner, DEVISER, is recounted. SWITCH's plan representation, and its process of building a plan by backward chaining with strict chronological backtracking, are described. A guide for writing knowledge base files is provided, as are narrative guides for installing the program, running it, and interacting with it while it is running. Some utility functions are documented. For the sake of completeness, a narrative guide to the experimental discrepancy-replanning feature is provided. Appendices contain knowledge base files for a blocksworld domain, and a DRIBBLE file illustrating the output from, and user interaction with, the program in that domain.

  9. Optical Computer Switching Network

    NASA Astrophysics Data System (ADS)

    Clymer, B.; Collins, S. A., Jr.

    1985-02-01

    In this paper we present the design for an optical switching system for minicomputers that uses an optical spatial light modulator such as a Hughes liquid crystal light valve. The switching system is designed to connect 80 minicomputers coupled to the switching system by optical fibers. The system has two major parts: the connection system that connects the data lines by which the computers communicate via a two-dimensional optical matrix array and the control system that controls which computers are connected. We first present the basic system, then describe the matrix-based connecting system and review some of the optical components to be used. Finally, the details of the control system are given and illustrated with a discussion of timing.

  10. Optical computer switching network

    NASA Astrophysics Data System (ADS)

    Clymer, B.; Collins, S. A., Jr.

    1985-02-01

    The design for an optical switching system for minicomputers that uses an optical spatial light modulator such as a Hughes liquid crystal light valve is presented. The switching system is designed to connect 80 minicomputers coupled to the switching system by optical fibers. The system has two major parts: the connection system that connects the data lines by which the computers communicate via a two-dimensional optical matrix array and the control system that controls which computers are connected. The basic system, the matrix-based connecting system, and some of the optical components to be used are described. Finally, the details of the control system are given and illustrated with a discussion of timing.

  11. Optical computer switching network

    NASA Technical Reports Server (NTRS)

    Clymer, B.; Collins, S. A., Jr.

    1985-01-01

    The design for an optical switching system for minicomputers that uses an optical spatial light modulator such as a Hughes liquid crystal light valve is presented. The switching system is designed to connect 80 minicomputers coupled to the switching system by optical fibers. The system has two major parts: the connection system that connects the data lines by which the computers communicate via a two-dimensional optical matrix array and the control system that controls which computers are connected. The basic system, the matrix-based connecting system, and some of the optical components to be used are described. Finally, the details of the control system are given and illustrated with a discussion of timing.

  12. FAST ACTING CURRENT SWITCH

    DOEpatents

    Batzer, T.H.; Cummings, D.B.; Ryan, J.F.

    1962-05-22

    A high-current, fast-acting switch is designed for utilization as a crowbar switch in a high-current circuit such as used to generate the magnetic confinement field of a plasma-confining and heat device, e.g., Pyrotron. The device particularly comprises a cylindrical housing containing two stationary, cylindrical contacts between which a movable contact is bridged to close the switch. The movable contact is actuated by a differential-pressure, airdriven piston assembly also within the housing. To absorb the acceleration (and the shock imparted to the device by the rapidly driven, movable contact), an adjustable air buffer assembly is provided, integrally connected to the movable contact and piston assembly. Various safety locks and circuit-synchronizing means are also provided to permit proper cooperation of the invention and the high-current circuit in which it is installed. (AEC)

  13. Mating-type Gene Switching in Saccharomyces cerevisiae.

    PubMed

    Lee, Cheng-Sheng; Haber, James E

    2015-04-01

    The budding yeast Saccharomyces cerevisiae has two alternative mating types designated MATa and MATα. These are distinguished by about 700 bp of unique sequences, Ya or Yα, including divergent promoter sequences and part of the open reading frames of genes that regulate mating phenotype. Homothallic budding yeast, carrying an active HO endonuclease gene, HO, can switch mating type through a recombination process known as gene conversion, in which a site-specific double-strand break (DSB) created immediately adjacent to the Y region results in replacement of the Y sequences with a copy of the opposite mating type information, which is harbored in one of two heterochromatic donor loci, HMLα or HMRa. HO gene expression is tightly regulated to ensure that only half of the cells in a lineage switch to the opposite MAT allele, thus promoting conjugation and diploid formation. Study of the silencing of these loci has provided a great deal of information about the role of the Sir2 histone deacetylase and its associated Sir3 and Sir4 proteins in creating heterochromatic regions. MAT switching has been examined in great detail to learn about the steps in homologous recombination. MAT switching is remarkably directional, with MATa recombining preferentially with HMLα and MATα using HMRa. Donor preference is controlled by a cis-acting recombination enhancer located near HML. RE is turned off in MATα cells but in MATa binds multiple copies of the Fkh1 transcription factor whose forkhead-associated phosphothreonine binding domain localizes at the DSB, bringing HML into conjunction with MATa.

  14. SHOCKPROOF MAGNETIC REED SWITCH

    DOEpatents

    Medal, E.

    1962-03-13

    A shockproof magnetic reed switch is described which comprises essentially a plurality of pairs of reed contacts of magnetic, electrical conducting material which are arranged generally in circumferential spaced relationship. At least two of the pairs are disposed to operate at a predetermined angle with respect to each other, and the contacts are wired in the circuit, so that the continuity, or discontinuity, of the circuit is not affected by a shock imposed on the switch. The contacts are hermetically sealed within an outer tubular jacket. (AEC)

  15. Thermionic gas switch

    DOEpatents

    Hatch, George L.; Brummond, William A.; Barrus, Donald M.

    1986-01-01

    A temperature responsive thermionic gas switch having folded electron emitting surfaces. An ionizable gas is located between the emitter and an interior surface of a collector, coaxial with the emitter. In response to the temperature exceeding a predetermined level, sufficient electrons are derived from the emitter to cause the gas in the gap between the emitter and collector to become ionized, whereby a very large increase in current in the gap occurs. Due to the folded emitter surface area of the switch, increasing the "on/off" current ratio and adjusting the "on" current capacity is accomplished.

  16. Organometallic spintronics: dicobaltocene switch.

    PubMed

    Liu, Rui; Ke, San-Huang; Baranger, Harold U; Yang, Weitao

    2005-10-01

    A single-molecule spintronic switch and spin valve using two cobaltocene moieties is proposed. Spin-dependent transport through a lead-molecule-lead junction has been calculated using first-principles density functional and nonequilibrium Green function methods. We find that the antiparallel (singlet) configuration of the cobaltocene spins blocks electron transport near the Fermi energy, while the spin parallel (triplet) configuration enables much higher current. The energy difierence between the antiparallel and parallel states depends on the insulating spacer separating the two cobaltocenes, allowing switching through the application of a moderate magnetic field.

  17. Intrachromosomal recombination between well-separated, homologous sequences in mammalian cells.

    PubMed

    Baker, M D; Read, L R; Ng, P; Beatty, B G

    1999-06-01

    In the present study, we investigated intrachromosomal homologous recombination in a murine hybridoma in which the recipient for recombination, the haploid, endogenous chromosomal immunoglobulin mu-gene bearing a mutation in the constant (Cmu) region, was separated from the integrated single copy wild-type donor Cmu region by approximately 1 Mb along the hybridoma chromosome. Homologous recombination between the donor and recipient Cmu region occurred with high frequency, correcting the mutant chromosomal mu-gene in the hybridoma. This enabled recombinant hybridomas to synthesize normal IgM and to be detected as plaque-forming cells (PFC). Characterization of the recombinants revealed that they could be placed into three distinct classes. The generation of the class I recombinants was consistent with a simple unequal sister chromatid exchange (USCE) between the donor and recipient Cmu region, as they contained the three Cmu-bearing fragments expected from this recombination, the original donor Cmu region along with both products of the single reciprocal crossover. However, a simple mechanism of homologous recombination was not sufficient in explaining the more complex Cmu region structures characterizing the class II and class III recombinants. To explain these recombinants, a model is proposed in which unequal pairing between the donor and recipient Cmu regions located on sister chromatids resulted in two crossover events. One crossover resulted in the deletion of sequences from one chromatid forming a DNA circle, which then integrated into the sister chromatid by a second reciprocal crossover.

  18. Switched-Observer-Based Adaptive Neural Control of MIMO Switched Nonlinear Systems With Unknown Control Gains.

    PubMed

    Long, Lijun; Zhao, Jun

    2017-07-01

    In this paper, the problem of adaptive neural output-feedback control is addressed for a class of multi-input multioutput (MIMO) switched uncertain nonlinear systems with unknown control gains. Neural networks (NNs) are used to approximate unknown nonlinear functions. In order to avoid the conservativeness caused by adoption of a common observer for all subsystems, an MIMO NN switched observer is designed to estimate unmeasurable states. A new switched observer-based adaptive neural control technique for the problem studied is then provided by exploiting the classical average dwell time (ADT) method and the backstepping method and the Nussbaum gain technique. It effectively handles the obstacle about the coexistence of multiple Nussbaum-type function terms, and improves the classical ADT method, since the exponential decline property of Lyapunov functions for individual subsystems is no longer satisfied. It is shown that the technique proposed is able to guarantee semiglobal uniformly ultimately boundedness of all the signals in the closed-loop system under a class of switching signals with ADT, and the tracking errors converge to a small neighborhood of the origin. The effectiveness of the approach proposed is illustrated by its application to a two inverted pendulum system.

  19. The Evolution of Phenotypic Switching in Subdivided Populations

    PubMed Central

    Carja, Oana; Liberman, Uri; Feldman, Marcus W.

    2014-01-01

    Stochastic switching is an example of phenotypic bet hedging, where offspring can express a phenotype different from that of their parents. Phenotypic switching is well documented in viruses, yeast, and bacteria and has been extensively studied when the selection pressures vary through time. However, there has been little work on the evolution of phenotypic switching under both spatially and temporally fluctuating selection pressures. Here we use a population genetic model to explore the interaction of temporal and spatial variation in determining the evolutionary dynamics of phenotypic switching. We find that the stable switching rate is mainly determined by the rate of environmental change and the migration rate. This stable rate is also a decreasing function of the recombination rate, although this is a weaker effect than those of either the period of environmental change or the migration rate. This study highlights the interplay of spatial and temporal environmental variability, offering new insights into how migration can influence the evolution of phenotypic switching rates, mutation rates, or other sources of phenotypic variation. PMID:24496012

  20. Surface recombination in semiconductors

    SciTech Connect

    Langer, J.M.; Walukiewicz, W.

    1995-07-01

    We propose two general criteria for a surface defect state to act as an efficient, nonradiative recombination center. The first is that the thermal ionization energy should not deviate from the mid-gap energy by more than the relaxation energy of the defect, In this case the activation energy for the recombination is given by the barrier for the capture of the first carrier, whereas the second carrier is captured athermally. The second citerion is related to the position of the average dangling bond energy relative to the band edges. If, as in the cases of InP or InAs, it is located close to a band edge, a low surface recombination velocity is expected. However a much faster recombination is predicated and experimentally observed in the materials with the average dangling bond energy located close to the mid-gap. The relevance of these criteria for the novel wide-gap optoelectronic materials is discussed.

  1. Main electrical switch banks, plant switch house, looking to the ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Main electrical switch banks, plant switch house, looking to the North - Bureau of Mines Metallurgical Research Laboratory, Original Building, Date Street north of U.S. Highway 93, Boulder City, Clark County, NV

  2. Hybrid solid state switch replaces motor- driven power switch

    NASA Technical Reports Server (NTRS)

    Booth, R. A.; Schloss, A. I.

    1967-01-01

    Hybrid solid state switch replaces existing motor-driven power switches used on spacecraft. It uses a transistor circuit to limit the open circuit voltage and allow small relay contacts to handle high transient currents at reasonable cycle life.

  3. 41. INTERIOR VIEW, GREEN SWITCH TOWER, COS COB, SHOWING SWITCH ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    41. INTERIOR VIEW, GREEN SWITCH TOWER, COS COB, SHOWING SWITCH LEVER ASSEMBLAGE AND DISPLAY BOARD - New York, New Haven & Hartford Railroad, Automatic Signalization System, Long Island Sound shoreline between Stamford & New Haven, Stamford, Fairfield County, CT

  4. 35. END VIEW, INTERIOR, SHOWING SWITCHING LEVERS, BERK SWITCH TOWER, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    35. END VIEW, INTERIOR, SHOWING SWITCHING LEVERS, BERK SWITCH TOWER, SOUTH NORWALK - New York, New Haven & Hartford Railroad, Automatic Signalization System, Long Island Sound shoreline between Stamford & New Haven, Stamford, Fairfield County, CT

  5. 36. INTERIOR VIEW, BERK SWITCH TOWER, SOUTH NORWALK, SHOWING SWITCHING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    36. INTERIOR VIEW, BERK SWITCH TOWER, SOUTH NORWALK, SHOWING SWITCHING LEVERS FROM OPERATOR'S POSITION - New York, New Haven & Hartford Railroad, Automatic Signalization System, Long Island Sound shoreline between Stamford & New Haven, Stamford, Fairfield County, CT

  6. 43. OBLIQUE VIEW, GREEN SWITCH TOWER, COS COB, SHOWING SWITCH ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    43. OBLIQUE VIEW, GREEN SWITCH TOWER, COS COB, SHOWING SWITCH LEVER ASSEMBLAGE AND DISPLAY BOARD - New York, New Haven & Hartford Railroad, Automatic Signalization System, Long Island Sound shoreline between Stamford & New Haven, Stamford, Fairfield County, CT

  7. Multiphoton Assisted Recombination

    NASA Astrophysics Data System (ADS)

    Shuman, E. S.; Jones, R. R.; Gallagher, T. F.

    2008-12-01

    We have observed multiphoton assisted recombination in the presence of a 38.8 GHz microwave field. Stimulated emission of up to ten microwave photons results in energy transfer from continuum electrons, enabling recombination. The maximum electron energy loss is far greater than the 2Up predicted by the standard “simpleman’s” model. The data are well reproduced by both an approximate analytic expression and numerical simulations in which the combined Coulomb and radiation fields are taken into account.

  8. Activated recombinant adenovirus proteinases

    DOEpatents

    Anderson, C.W.; Mangel, W.F.

    1999-08-10

    This application describes methods and expression constructs for producing activatable recombinant adenovirus proteinases. Purified activatable recombinant adenovirus proteinases and methods of purification are described. Activated adenovirus proteinases and methods for obtaining activated adenovirus proteinases are further included. Isolated peptide cofactors of adenovirus proteinase activity, methods of purifying and identifying peptide cofactors are also described. Antibodies immunoreactive with adenovirus proteinases, immunospecific antibodies, and methods for preparing them are also described. Other related methods and materials are also described. 29 figs.

  9. Activated recombinant adenovirus proteinases

    DOEpatents

    Anderson, Carl W.; Mangel, Walter F.

    1999-08-10

    This application describes methods and expression constructs for producing activatable recombinant adenovirus proteinases. Purified activatable recombinant adenovirus proteinases and methods of purification are described. Activated adenovirus proteinases and methods for obtaining activated adenovirus proteinases are further included. Isolated peptide cofactors of adenovirus proteinase activity, methods of purifying and identifying said peptide cofactors are also described. Antibodies immunoreactive with adenovirus proteinases, immunospecific antibodies, and methods for preparing them are also described. Other related methods and materials are also described.

  10. Recombination and chromosome segregation.

    PubMed Central

    Sherratt, David J; Søballe, Britta; Barre, François-Xavier; Filipe, Sergio; Lau, Ivy; Massey, Thomas; Yates, James

    2004-01-01

    The duplication of DNA and faithful segregation of newly replicated chromosomes at cell division is frequently dependent on recombinational processes. The rebuilding of broken or stalled replication forks is universally dependent on homologous recombination proteins. In bacteria with circular chromosomes, crossing over by homologous recombination can generate dimeric chromosomes, which cannot be segregated to daughter cells unless they are converted to monomers before cell division by the conserved Xer site-specific recombination system. Dimer resolution also requires FtsK, a division septum-located protein, which coordinates chromosome segregation with cell division, and uses the energy of ATP hydrolysis to activate the dimer resolution reaction. FtsK can also translocate DNA, facilitate synapsis of sister chromosomes and minimize entanglement and catenation of newly replicated sister chromosomes. The visualization of the replication/recombination-associated proteins, RecQ and RarA, and specific genes within living Escherichia coli cells, reveals further aspects of the processes that link replication with recombination, chromosome segregation and cell division, and provides new insight into how these may be coordinated. PMID:15065657

  11. Persistence to antihypertensive drug classes

    PubMed Central

    Qvarnström, Miriam; Kahan, Thomas; Kieler, Helle; Brandt, Lena; Hasselström, Jan; Boström, Kristina Bengtsson; Manhem, Karin; Hjerpe, Per; Wettermark, Björn

    2016-01-01

    Abstract The aim was to study persistence to, and switching between, antihypertensive drug classes and to determine factors associated with poor persistence. This was an observational cohort study. The Swedish Primary Care Cardiovascular Database includes data from medical records, socioeconomic data, filled prescriptions, and hospitalizations from national registries for 75,000 patients with hypertension. Patients included in the study were initiated on antihypertensive drug treatment in primary healthcare in 2006 to 2007. We defined class persistence as the proportion remaining on the initial drug class, including 30 days of gap. Patients with a filled prescription of another antihypertensive drug class after discontinuation of the initial drug, including 30 days of gap, were classified as switchers. Persistence to the various drug classes were compared with that for diuretics. We identified 4997 patients (mean age 60 ± 12 years in men and 63 ± 13 years in women). Out of these, 95 (2%) filled their first prescription for fixed combination therapy and 4902 (98%) for monotherapy, including angiotensin converting enzyme inhibitors (37%), angiotensin receptor blockers (4%), beta blockers (21%), calcium channel blockers (8%), and diuretics (28%). Persistence to the initial drug class was 57% after 1 year and 43% after 2 years. There were no differences in persistence between diuretics and any of the other antihypertensive drug classes, after adjustment for confounders. Discontinuation (all adjusted) was more common in men (P = 0.004), younger patients (P < 0.001), those with mild systolic blood pressure elevation (P < 0.001), and patients born outside the Nordic countries (P < 0.001). Among 1295 patients who switched drug class after their first prescription, only 21% had a blood pressure recorded before the switch occurred; and out them 69% still had high blood pressures. In conclusion, there appears to be no difference in drug class

  12. Multiple epigenetic events regulate mating-type switching of fission yeast.

    PubMed

    Klar, A J; Ivanova, A V; Dalgaard, J Z; Bonaduce, M J; Grewal, S I

    1998-01-01

    Two epigenetic events at mat1, one of which is DNA strand specific, are required to initiate recombination during mating-type switching. The third, a chromosomally borne imprinted event at the mat2/3 interval regulates silencing and directionality of switching, and prohibits interchromosomal recombination. We speculate that the unit of inheritance in the mat2/3 interval is both DNA plus its associated chromatin structure. Such a control is likely to be essential in maintaining particular states of gene expression during development.

  13. Photonic MEMS switch applications

    NASA Astrophysics Data System (ADS)

    Husain, Anis

    2001-07-01

    As carriers and service providers continue their quest for profitable network solutions, they have shifted their focus from raw bandwidth to rapid provisioning, delivery and management of revenue generating services. Inherently transparent to data rate the transmission wavelength and data format, MEMS add scalability, reliability, low power and compact size providing flexible solutions to the management and/or fiber channels in long haul, metro, and access networks. MEMS based photonic switches have gone from the lab to commercial availability and are now currently in carrier trials and volume production. 2D MEMS switches offer low up-front deployment costs while remaining scalable to large arrays. They allow for transparent, native protocol transmission. 2D switches enable rapid service turn-up and management for many existing and emerging revenue rich services such as storage connectivity, optical Ethernet, wavelength leasing and optical VPN. As the network services evolve, the larger 3D MEMS switches, which provide greater scalability and flexibility, will become economically viable to serve the ever-increasing needs.

  14. Kiowa Creek Switching Station

    SciTech Connect

    Not Available

    1990-03-01

    The Western Area Power Administration (Western) proposes to construct, operate, and maintain a new Kiowa Creek Switching Station near Orchard in Morgan County, Colorado. Kiowa Creek Switching Station would consist of a fenced area of approximately 300 by 300 feet and contain various electrical equipment typical for a switching station. As part of this new construction, approximately one mile of an existing 115-kilovolt (kV) transmission line will be removed and replaced with a double circuit overhead line. The project will also include a short (one-third mile) realignment of an existing line to permit connection with the new switching station. In accordance with the Council on Environmental Quality (CEQ) regulations for implementing the procedural provisions of the National Environmental Policy Act of 1969 (NEPA), 40 CFR Parts 1500--1508, the Department of Energy (DOE) has determined that an environmental impact statement (EIS) is not required for the proposed project. This determination is based on the information contained in this environmental assessment (EA) prepared by Western. The EA identifies and evaluates the environmental and socioeconomic effects of the proposed action, and concludes that the advance impacts on the human environment resulting from the proposed project would not be significant. 8 refs., 3 figs., 1 tab.

  15. Multipath star switch controller

    NASA Technical Reports Server (NTRS)

    Anderson, T. O.

    1980-01-01

    Device concept permits parallel computers to scan several commonnetwork-connected data stations at maximum rate. Sequencers leap-frog to bypass ports already being serviced by another computer. Two-path system for 16-port star switch controller is cost effective if added bandwidth or increased reliability is desired. Triple-path system would be cost effective for 32-port controller.

  16. Waveguide switch protector

    NASA Technical Reports Server (NTRS)

    Kolbly, R. B.

    1972-01-01

    Device for detecting excessive operation of electric motors used to drive waveguide switches is described. Purpose of device is to prevent burnout of electric motor in event of waveguide stoppage at some point other than extreme limits of travel. Operation of equipment, components used to sense motor performance, and schematic diagram are included.

  17. Gas injected vacuum switch

    DOEpatents

    Hardin, K. Dan

    1977-01-01

    The disclosure relates to a gas injected vacuum switch comprising a housing having an interior chamber, a conduit for evacuating the interior chamber, within the chamber an anode and a cathode spaced from the anode, and a detonator for injecting electrically conductive gas into the chamber between the anode and the cathode to provide a current path therebetween.

  18. Silicon Carbide Photoconductive Switches

    DTIC Science & Technology

    1994-09-01

    The optoelectronic properties of p-type 6-H silicon carbide (6H-SiC) have been investigated in an experiment that used lateral and vertical...and the bandgap was determined to be approximately 3.1 eV. 6H-SiC, Photoconductive, Photovoltaic, Absorption coefficient, Switch, Silicon carbide

  19. An integrated circuit switch

    NASA Technical Reports Server (NTRS)

    Bonin, E. L.

    1969-01-01

    Multi-chip integrated circuit switch consists of a GaAs photon-emitting diode in close proximity with S1 phototransistor. A high current gain is obtained when the transistor has a high forward common-emitter current gain.

  20. Molecular Rotors as Switches

    PubMed Central

    Xue, Mei; Wang, Kang L.

    2012-01-01

    The use of a functional molecular unit acting as a state variable provides an attractive alternative for the next generations of nanoscale electronics. It may help overcome the limits of conventional MOSFETd due to their potential scalability, low-cost, low variability, and highly integratable characteristics as well as the capability to exploit bottom-up self-assembly processes. This bottom-up construction and the operation of nanoscale machines/devices, in which the molecular motion can be controlled to perform functions, have been studied for their functionalities. Being triggered by external stimuli such as light, electricity or chemical reagents, these devices have shown various functions including those of diodes, rectifiers, memories, resonant tunnel junctions and single settable molecular switches that can be electronically configured for logic gates. Molecule-specific electronic switching has also been reported for several of these device structures, including nanopores containing oligo(phenylene ethynylene) monolayers, and planar junctions incorporating rotaxane and catenane monolayers for the construction and operation of complex molecular machines. A specific electrically driven surface mounted molecular rotor is described in detail in this review. The rotor is comprised of a monolayer of redox-active ligated copper compounds sandwiched between a gold electrode and a highly-doped P+ Si. This electrically driven sandwich-type monolayer molecular rotor device showed an on/off ratio of approximately 104, a read window of about 2.5 V, and a retention time of greater than 104 s. The rotation speed of this type of molecular rotor has been reported to be in the picosecond timescale, which provides a potential of high switching speed applications. Current-voltage spectroscopy (I-V) revealed a temperature-dependent negative differential resistance (NDR) associated with the device. The analysis of the device I–V characteristics suggests the source of the

  1. Exhaust Fan Temperature Switch

    SciTech Connect

    Ball, G.S.; /Fermilab

    1989-05-11

    The 13000 cfm 'emergency' vent fan must be protected from over cooling which would result in a mechanical failure. Over cooling could result from a catastrophic cryogen release from the cryostat(s) or Argon Storage Dewar. In order to protect the fan, a VPT has been calibrated for -31 C to open a switch which sends a signal to allow warm gas to enter the sump by means of a motor controlled louver installed at 'sidewalk level' in the ductwork between the assembly hall and the Argon Dewar Enclosure. The bulb of the VPT is enclosed in a thermal well and will be placed in the gas stream directly above the fan. The switching unit will be mounted nearby on the wall in order to isolate it from vibrational effects. Should the fan be activated due to a cryogen release, it should not experience any problems when operating above -40 C. The switch was set and checked in a saturated calcium chloride solution cooled to -31 C by running cold gaseous Nitrogen through a copper tube coiled in a dewar. Switching temperature was measured by a thermocouple tied to the VPT bulb. The thermocouple was checked in LN2, in an ice water bath, and against an ordinary thermometer (which was assumed to be accurate to plus or minus 0.3 C) at room temperature. The results are shown below in 'Table 1' By interpolation of the data, thermocouple error at -31.0 C was found to be 0.43 C on the warm side. Since this error was small, it was ignored. 'Table 2' shows the results of the tests. Ten readings were taken with the switch wired in the 'normally open' mode. This results in a signal at room temperature. The worst deviation was 2.5 C. Three readings were then taken from the 'normally closed' wiring arrangement (the way it will be wired for installation). The greatest deviation was 1.2 C. The next day, the switch was checked five times wired in the 'normally open' configuration. The greatest error was 1.1 C. A graph has been prepared showing the switching and resetting temperatures. The errors these

  2. A Network Flow Model for Load Balancing in Circuit-Switched Multicomputers

    DTIC Science & Technology

    1990-05-01

    Availability Codes Avail and/or D -ist Special Abstract In multicomputers that utilize circuit switching or wormhole rout- ing, communication overhead...the implementations can be divided into two broad classes: store-and-forward and circuit switching or wormhole routing. There are finer distinctions...heavily on the number of links (the graph theoretic distance) between source and destination. 5.2 Circuit Switching or Wormhole routing For our purposes

  3. Self-organized atomic switch networks

    NASA Astrophysics Data System (ADS)

    Stieg, Adam Z.; Avizienis, Audrius V.; Sillin, Henry O.; Martin-Olmos, Cristina; Lam, Miu-Ling; Aono, Masakazu; Gimzewski, James K.

    2014-01-01

    The spontaneous emergence of complex behavior in dynamical systems occurs through the collective interaction of nonlinear elements toward a highly correlated, non-equilibrium critical state. Criticality has been proposed as a model for understanding complexity in systems whose behavior can be approximated as a state lying somewhere between order and chaos. Here we present unique, purpose-built devices, known as atomic switch networks (ASN), specifically designed to generate the class of emergent properties which underlie critical dynamics in complex systems. The network is an open, dissipative system comprised of highly interconnected (˜109/cm2) atomic switch interfaces wired through the spontaneous electroless deposition of metallic silver fractal architectures. The functional topology of ASN architectures self-organizes to produce persistent critical dynamics without fine-tuning, indicating a capacity for memory and learning via persistent critical states toward potential utility in real-time, neuromorphic computation.

  4. "transistor-like" spin nano-switches: Physics and applications

    NASA Astrophysics Data System (ADS)

    Diep, Vinh Quang

    Progress in the last two decades has effectively integrated spintronics and nanomagnetics into a single field, creating a new class of spin-based devices that are now being widely used in magnetic memory devices. However, it is not clear if these advances could also be used to build logic devices. The objective of this thesis is three-fold: The first is to describe a general paradigm for combining Read and Write units used in memory devices into transistor like nano-switches having input-output isolation and gain. Such switches could be used to build logic circuits without the need of any external circuits or amplification. The second is to describe an experimentally benchmarked simulation model for designing a concrete implementation of a transistor-like switch based on: Giant Spin Hall Effect (Write), Magnetic Tunnel Junction (Read) and magnetic coupling for isolation. It turns out that the model can also be used to analyze/design stray fields in perpendicular magnetic tunnel junction (pMTJ), an important problem in scaled pMTJ devices. The third is to discuss the novel features and possible new class of circuits of spin nano-switches. We will first describe a spin switch nano-oscillator based on the standard principle of incorporating feedback into a device with gain. We then discuss how spin nano-switches can be used to implement different types of neural networks such as second generation, third generation and deep belief neural networks.

  5. Heat-transfer thermal switch

    NASA Technical Reports Server (NTRS)

    Friedell, M. V.; Anderson, A. J.

    1974-01-01

    Thermal switch maintains temperature of planetary lander, within definite range, by transferring heat. Switch produces relatively large stroke and force, uses minimum electrical power, is lightweight, is vapor pressure actuated, and withstands sterilization temperatures without damage.

  6. Automatic thermal switch. [spacecraft applications

    NASA Technical Reports Server (NTRS)

    Cunningham, J. W.; Wing, L. D. (Inventor)

    1983-01-01

    An automatic thermal switch to control heat flow includes two thermally conductive plates and a thermally conductive switch saddle pivotally mounted to the first plate. A flexible heat carrier is connected between the switch saddle and the second plate. A phase-change power unit, including a piston coupled to the switch saddle, is in thermal contact with the first thermally conductive plate. A biasing element biases the switch saddle in a predetermined position with respect to the first plate. When the phase-change power unit is actuated by an increase in heat transmitted through the first place, the piston extends and causes the switch saddle to pivot, thereby varying the thermal conduction between the two plates through the switch saddle and flexible heat carrier. The biasing element, switch saddle, and piston can be arranged to provide either a normally closed or normally opened thermally conductive path between the two plates.

  7. Switching power pulse system

    DOEpatents

    Aaland, Kristian

    1983-01-01

    A switching system for delivering pulses of power from a source (10) to a load (20) using a storage capacitor (C3) charged through a rectifier (D1, D2), and maintained charged to a reference voltage level by a transistor switch (Q1) and voltage comparator (12). A thyristor (22) is triggered to discharge the storage capacitor through a saturable reactor (18) and fractional turn saturable transformer (16) having a secondary to primary turn ratio N of n:l/n=n.sup.2. The saturable reactor (18) functions as a "soaker" while the thyristor reaches saturation, and then switches to a low impedance state. The saturable transformer functions as a switching transformer with high impedance while a load coupling capacitor (C4) charges, and then switches to a low impedance state to dump the charge of the storage capacitor (C3) into the load through the coupling capacitor (C4). The transformer is comprised of a multilayer core (26) having two secondary windings (28, 30) tightly wound and connected in parallel to add their output voltage and reduce output inductance, and a number of single turn windings connected in parallel at nodes (32, 34) for the primary winding, each single turn winding linking a different one of the layers of the multilayer core. The load may be comprised of a resistive beampipe (40) for a linear particle accelerator and capacitance of a pulse forming network (42). To hold off discharge of the capacitance until it is fully charged, a saturable core (44) is provided around the resistive beampipe (40) to isolate the beampipe from the capacitance (42) until it is fully charged.

  8. Recombination-dependent concatemeric viral DNA replication.

    PubMed

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

    2011-09-01

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

  9. Transparent electrode for optical switch

    DOEpatents

    Goldhar, J.; Henesian, M.A.

    1984-10-19

    The invention relates generally to optical switches and techniques for applying a voltage to an electro-optical crystal, and more particularly, to transparent electodes for an optical switch. System architectures for very large inertial confinement fusion (ICF) lasers require active optical elements with apertures on the order of one meter. Large aperture optical switches are needed for isolation of stages, switch-out from regenerative amplifier cavities and protection from target retroreflections.

  10. Radiation sensitive solid state switch

    NASA Technical Reports Server (NTRS)

    Hutto, R. J. (Inventor)

    1973-01-01

    A mechanically operable solid state switch suited for use in achieving a variable circuit-switching function is described. This switch is characterized by an annular array of photoresponsive switching devices, disposed in communication with an included source of radiation, and a plurality of interchangeable, mechanically operable interrupter disks. Each disk has a predetermined pattern of transparent and opaque portions. Operative displacement of each disk serves to make and break selected electrical circuits through the photo responsive devices of said array.

  11. Easily-wired toggle switch

    NASA Technical Reports Server (NTRS)

    Dean, W. T.; Stringer, E. J.

    1979-01-01

    Crimp-type connectors reduce assembly and disassembly time. With design, no switch preparation is necessary and socket contracts are crimped to wires inserted in module attached to back of toggle switch engaging pins inside module to make electrical connections. Wires are easily removed with standard detachment tool. Design can accommodate wires of any gage and as many terminals can be placed on switch as wire gage and switch dimensions will allow.

  12. The fox and the cabra: An ERP analysis of reading code switched nouns and verbs in bilingual short stories

    PubMed Central

    Ng, Shukhan; Gonzalez, Christian; Wicha, Nicole Y. Y.

    2014-01-01

    Comprehending a language (or code) switch within a sentence context triggers 2 electrophysiological signatures: an early left anterior negativity post code switch onset – a LAN – followed by a Late Positive Component (LPC). Word class and word position modulate lexico-semantic processes in the monolingual brain, e.g., larger N400 amplitude for nouns than verbs and for earlier than later words in the sentence. Here we test whether the bilingual brain is affected by word class and word position when code switching, or if the cost of switching overrides these lexico-semantic and sentence context factors. Adult bilinguals read short stories in English containing 8 target words. Targets were nouns or verbs, occurred early or late in a story and were presented alternately in English (non-switch) or Spanish (switch) across different story versions. Overall, switched words elicited larger LAN and LPC amplitude than nonswitched words. The N400 amplitude was larger for nouns than verbs, more focal for switches than non-switches, and for early than late nouns but not for early than late verbs. Moreover, an early LPC effect was observed only for switched nouns, but not verbs. Together, this indicates that referential elements (nouns) may be harder to process and integrate than relational elements (verbs) in discourse, and when switched, nouns incur higher integration cost. Word position did not modulate the code switching effects, implying that switching between languages may invoke discourse independent processes. PMID:24530431

  13. Observer-Based Output-Feedback Asynchronous Control for Switched Fuzzy Systems.

    PubMed

    Wang, Tiechao; Tong, Shaocheng

    2017-09-01

    This paper investigates an output-feedback control design problem for a class of switched continuous-time Takagi-Sugeno (T-S) fuzzy systems. The considered fuzzy systems consist of several switching modes and each switching mode is described by T-S fuzzy models. In addition, there exists the asynchronous switching between the system switching modes and the controller switching modes. By using parallel distributed compensation design method, the output-feedback control schemes are developed based on state observers for the measurable and immeasurable premise variables cases. The sufficient conditions of ensuring the switched control system stabilization are proposed based on the theory of Lyapunov stability and average-dwell time methods. The controller and observer gains are obtained via two-step method. An illustrated numerical example is provided to show the effectiveness of the proposed control approaches.

  14. Illuminated push-button switch

    NASA Technical Reports Server (NTRS)

    Iwagiri, T.

    1983-01-01

    An illuminated push-button switch is described. It is characterized by the fact that is consists of a switch group, an operator button opening and closing the switch group, and a light-emitting element which illuminates the face of the operator button.

  15. Illuminated push-button switch

    NASA Astrophysics Data System (ADS)

    Iwagiri, T.

    1983-05-01

    An illuminated push-button switch is described. It is characterized by the fact that is consists of a switch group, an operator button opening and closing the switch group, and a light-emitting element which illuminates the face of the operator button.

  16. Organic Materials For Optical Switching

    NASA Technical Reports Server (NTRS)

    Cardelino, Beatriz H.

    1993-01-01

    Equations predict properties of candidate materials. Report presents results of theoretical study of nonlinear optical properties of organic materials. Such materials used in optical switching devices for computers and telecommunications, replacing electronic switches. Optical switching potentially offers extremely high information throughout in compact hardware.

  17. Numerical analysis of electric field profiles in high-voltage GaAs photoconductive switches and comparison to experiment

    SciTech Connect

    Kingsley, L.E. . Pulse Power Center); Donaldson, W.R. . Lab. for Laser Energetics)

    1993-12-01

    The electric field in GaAs photoconductive switches has been observed with an ultrafast electro-optic imaging system to develop complex spatial and temporal structure immediately after illumination. High-field domains form at the switch cathode as the photogenerated carriers recombine for bias fields above [approximately]10 kV/cm. At these biases, the switch also remained conductive for a much longer time ([approximately]100 ns) than the material recombination time ([approximately]1 ns). A model which includes field-dependent mobility was developed to explain this data. Simulation of the electric field profile across the switch indicates that high-field domains which form at the switch cathode are the result of negative differential resistance.

  18. Estimation of the in vivo recombination rate for a plant RNA virus.

    PubMed

    Tromas, Nicolas; Zwart, Mark P; Poulain, Maïté; Elena, Santiago F

    2014-03-01

    Phylogenomic evidence suggested that recombination is an important evolutionary force for potyviruses, one of the larger families of plant RNA viruses. However, mixed-genotype potyvirus infections are marked by low levels of cellular coinfection, precluding template switching and recombination events between virus genotypes during genomic RNA replication. To reconcile these conflicting observations, we evaluated the in vivo recombination rate (rg) of Tobacco etch virus (TEV; genus Potyvirus, family Potyviridae) by coinfecting plants with pairs of genotypes marked with engineered restriction sites as neutral markers. The recombination rate was then estimated using two different approaches: (i) a classical approach that assumed recombination between marked genotypes can occur in the whole virus population, rendering an estimate of rg = 7.762 × 10(-8) recombination events per nucleotide site per generation, and (ii) an alternative method that assumed recombination between marked genotypes can occur only in coinfected cells, rendering a much higher estimate of rg = 3.427 × 10(-5) recombination events per nucleotide site per generation. This last estimate is similar to the TEV mutation rate, suggesting that recombination should be at least as important as point mutation in creating variability. Finally, we compared our mutation and recombination rate estimates to those reported for animal RNA viruses. Our analysis suggested that high recombination rates may be an unavoidable consequence of selection for fast replication at the cost of low fidelity.

  19. Somatic recombination, gene amplification and cancer.

    PubMed

    Ramel, C; Cederberg, H; Magnusson, J; Vogel, E; Natarajan, A T; Mullender, L H; Nivard, J M; Parry, J M; Leyson, A; Comendador, M A; Sierra, L M; Ferreiro, J A; Consuegra, S

    1996-06-12

    The principle objective of this research programme, to analyse chemical induction of somatic recombination and related endpoints, i.e., mobilization of transposing elements and gene amplification, has been approached by means of several assay systems. These have included Drosophila, Saccharomyces and mammalian cell cultures. 6.1. Screening assays for mitotic recombination. A large number of chemicals have been investigated in the three Drosophila assay systems employed--the multiple wing hair/flare wing spot system developed by Graf et al., 1984, the white-ivory system developed by Green et al., 1986 and the white/white+ eye spot assay developed by Vogel (Vogel and Nivard, 1993). Particularly the screening of 181 chemicals, covering a wide array of chemical classes, by the last mentioned assay has shown that measurement of somatic recombination in Drosophila constitutes a sensitive and efficient short-term test which shows a remarkably good correlation with the agent score of 83 short-term tests analysed by ICPEMC (Mendelsohn et al., 1992; Table 2) as well as the assay performance in international collaborative programmes measuring carcinogen/non-carcinogens (de Serres and Ashby, 1981; Ashby et al., 1985, 1988). Also the wing spot assay has gained wide international recognition as a similarly sensitive test. These two assay systems in Drosophila measure both intrachromosomal events and interchromosomal recombination. The white-ivory system on the other hand is based on the loss of a tandem duplication in the white locus, the mechanism of which is less known, but probably involves intrachromosomal recombination. The difference in the mechanism between this assay and the former two was indicated by the lack of response to methotrexate in the white-ivory assay, while this compound was strongly recombinogenic in both the wing spot and white/white+ assays. The use of different strains of Drosophila with the white/white+ assay demonstrated the importance of the

  20. Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives.

    PubMed

    Bujarski, Jozef J

    2013-01-01

    RNA recombination is one of the driving forces of genetic variability in (+)-strand RNA viruses. Various types of RNA-RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings) along with non-replicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (1) How various factors modulate the ability of viral replicase to switch templates, (2) What is the intracellular location of RNA-RNA template switchings, (3) Mechanisms and factors responsible for non-replicative RNA recombination, (4) Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (5) What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented.

  1. Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives

    PubMed Central

    Bujarski, Jozef J.

    2013-01-01

    RNA recombination is one of the driving forces of genetic variability in (+)-strand RNA viruses. Various types of RNA–RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings) along with non-replicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (1) How various factors modulate the ability of viral replicase to switch templates, (2) What is the intracellular location of RNA–RNA template switchings, (3) Mechanisms and factors responsible for non-replicative RNA recombination, (4) Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (5) What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented. PMID:23533000

  2. Initiation of meiotic recombination by double-strand DNA breaks in S. pombe.

    PubMed

    Klar, A J; Miglio, L M

    1986-08-29

    Mitotic gene conversion and reciprocal recombination have recently been shown to be efficiently initiated by double-strand DNA breaks (DSBs) in both Saccharomyces cerevisiae and Schizosaccharomyces pombe. We tested whether DSBs could also initiate meiotic recombination at the mat1 locus in S. pombe. The mat1 switching-mechanism-generated DSB found in mitotically growing cells can be repaired without mat1 switching, since strains deleted for both donor loci (mat2-P and mat3-M) have the break but do not produce inviable cells. A (mat1-P X mat1-M) cross produced a high frequency (20%) of 3:1 gene conversions of mat1 in meiotic tetrads. Gene conversion events were associated with the recombination of flanking markers. Strains lacking the DSB failed to convert. Thus, the DSB at mat1 promotes efficient meiotic recombination in fission yeast.

  3. CMOS analog switches for adaptive filters

    NASA Technical Reports Server (NTRS)

    Dixon, C. E.

    1980-01-01

    Adaptive active low-pass filters incorporate CMOS (Complimentary Metal-Oxide Semiconductor) analog switches (such as 4066 switch) that reduce variation in switch resistance when filter is switched to any selected transfer function.

  4. High gain GaAs photoconductive semiconductor switches: Switch longevity

    SciTech Connect

    Loubriel, G.M.; Zutavern, F.J.; Mar, A.

    1998-07-01

    Optically activated, high gain GaAs switches are being tested for many different pulsed power applications that require long lifetime (longevity). The switches have p and n contact metallization (with intentional or unintentional dopants) configured in such a way as to produce p-i-n or n-i-n switches. The longevity of the switches is determined by circuit parameters and by the ability of the contacts to resist erosion. This paper will describe how the switches performed in test-beds designed to measure switch longevity. The best longevity was achieved with switches made with diffused contacts, achieving over 50 million pulses at 10 A and over 2 million pulses at 80 A.

  5. Regulation of Meiotic Recombination

    SciTech Connect

    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

  6. Sonic crystal acoustic switch device.

    PubMed

    Alagoz, Serkan; Alagoz, Baris Baykant

    2013-06-01

    This study reports a wave-controlled sonic crystal switch device that exhibits a destructive interference-based wave to wave reverse switching effect. By applying control waves, this acoustic device, composed of a two-dimensional square lattice sonic crystal block, reduces acoustic wave transmission from input to output. The finite difference time domain simulation and experimental results confirm the wave-to-wave reverse switching effect at the peak frequencies of the second band. The proposed sonic crystal switch prototype provides a contrast rate of 86% at 11.3 kHz frequency. This wave-to-wave switching effect is useful for controlling wave propagation for smart structure applications.

  7. Plasma opening switch

    DOEpatents

    Savage, Mark E.; Mendel, Jr., Clifford W.

    2001-01-01

    A command triggered plasma opening switch assembly using an amplification stage. The assembly surrounds a coaxial transmission line and has a main plasma opening switch (POS) close to the load and a trigger POS upstream from the main POS. The trigger POS establishes two different current pathways through the assembly depended on whether it has received a trigger current pulse. The initial pathway has both POS's with plasma between their anodes and cathodes to form a short across the transmission line and isolating the load. The final current pathway is formed when the trigger POS receives a trigger current pulse which energizes its fast coil to push the conductive plasma out from between its anode and cathode, allowing the main transmission line current to pass to the fast coil of the main POS, thus pushing its plasma out the way so as to establish a direct current pathway to the load.

  8. Switched Matrix Accelerator

    SciTech Connect

    Whittum, David H

    2000-10-04

    We describe a new concept for a microwave circuit functioning as a charged-particle accelerator at mm-wavelengths, permitting an accelerating gradient higher than conventional passive circuits can withstand consistent with cyclic fatigue. The device provides acceleration for multiple bunches in parallel channels, and permits a short exposure time for the conducting surface of the accelerating cavities. Our analysis includes scalings based on a smooth transmission line model and a complementary treatment with a coupled-cavity simulation. We provide also an electromagnetic design for the accelerating structure, arriving at rough dimensions for a seven-cell accelerator matched to standard waveguide and suitable for bench tests at low power in air at 91.392. GHz. A critical element in the concept is a fast mm-wave switch suitable for operation at high-power, and we present the considerations for implementation in an H-plane tee. We discuss the use of diamond as the photoconductor switch medium.

  9. Optical fiber switch

    DOEpatents

    Early, James W.; Lester, Charles S.

    2002-01-01

    Optical fiber switches operated by electrical activation of at least one laser light modulator through which laser light is directed into at least one polarizer are used for the sequential transport of laser light from a single laser into a plurality of optical fibers. In one embodiment of the invention, laser light from a single excitation laser is sequentially transported to a plurality of optical fibers which in turn transport the laser light to separate individual remotely located laser fuel ignitors. The invention can be operated electro-optically with no need for any mechanical or moving parts, or, alternatively, can be operated electro-mechanically. The invention can be used to switch either pulsed or continuous wave laser light.

  10. Cryogenic switched MOSFET characterization

    NASA Technical Reports Server (NTRS)

    1981-01-01

    Both p channel and n channel enhancement mode MOSFETs can be readily switched on and off at temperatures as low as 2.8 K so that switch sampled readout of a VLWIR Ge:Ga focal plane is electronically possible. Noise levels as low as 100 rms electrons per sample (independent of sample rate) can be achieved using existing p channel MOSFETs, at overall rates up to 30,000 samples/second per multiplexed channel (e.g., 32 detectors at a rate of almost 1,000 frames/second). Run of the mill devices, including very low power dissipation n channel FETs would still permit noise levels of the order of 500 electrons/sample.

  11. The quantum cryptographic switch

    NASA Astrophysics Data System (ADS)

    Srinatha, N.; Omkar, S.; Srikanth, R.; Banerjee, Subhashish; Pathak, Anirban

    2014-01-01

    We illustrate the principle of a cryptographic switch for a quantum scenario, in which a third party (Charlie) can control to a continuously varying degree the amount of information the receiver (Bob) receives, after the sender (Alice) has sent her information through a quantum channel. Suppose Charlie transmits a Bell state to Alice and Bob. Alice uses dense coding to transmit two bits to Bob. Only if the 2-bit information corresponding to the choice of the Bell state is made available by Charlie to Bob can the latter recover Alice's information. By varying the amount of information Charlie gives, he can continuously alter the information recovered by Bob. The performance of the protocol as subjected to the squeezed generalized amplitude damping channel is considered. We also present a number of practical situations where a cryptographic switch would be of use.

  12. MULTIPLE SPARK GAP SWITCH

    DOEpatents

    Schofield, A.E.

    1958-07-22

    A multiple spark gap switch of unique construction is described which will permit controlled, simultaneous discharge of several capacitors into a load. The switch construction includes a disc electrode with a plurality of protuberances of generally convex shape on one surface. A firing electrode is insulatingly supponted In each of the electrode protuberances and extends substantially to the apex thereof. Individual electrodes are disposed on an insulating plate parallel with the disc electrode to form a number of spark gaps with the protuberances. These electrodes are each connected to a separate charged capacitor and when a voltage ls applied simultaneously between the trigger electrodes and the dlsc electrode, each spark gap fires to connect its capacitor to the disc electrode and a subsequent load.

  13. Many-Body Switches

    NASA Astrophysics Data System (ADS)

    MacDonald, Allan H.

    2014-03-01

    Most current electronic devices use gate voltages to switch individual electron transport channels or off. This architecture necessarily leads to operating voltages that are much larger than the temperature thermal energy, and places lower bounds on power consumption that are becoming. I will discuss strategies for achieving devices in which gates are used to collective many-electron states, in principle allowing charge transport to be switched by smaller voltage changes and both operating voltages and power consumption to reduced. I will specifically address devices based on the properties of itinerant electroninsulating magnetic systems, and devices based on bilayer exciton condensation. This work is based on work performed in collaboration with Sanjay Banerjee and Frank Register.

  14. RNA structures, genomic organization and selection of recombinant HIV.

    PubMed

    Simon-Loriere, Etienne; Rossolillo, Paola; Negroni, Matteo

    2011-01-01

    Recombination is an evolutionary mechanism intrinsic to the evolution of many RNA viruses. In retroviruses and notably in the case of HIV, recombination is so frequent that it can be considered as part of its mode of replication. This process not only plays a central role in shaping HIV genetic diversity worldwide, but has also been involved in immune escape and development of resistance to antiviral treatments. Recombination does not create new mutations in the existing genetic repertoire of the virus, but creates new combinations of pre-existing polymorphisms. The simultaneous insertion of multiple substitutions in a single replication cycle leaves little room for the progressive coevolution of regions of proteins, RNA or, more in general, genomes, to accommodate these drastic sequence changes. Therefore, recombination, while allowing the virus to rapidly explore larger sequence space than the slow accumulation of point mutations, also runs the risk of generating non functional viruses. Recombination is the consequence of a switch in the template used during reverse transcription and is promoted by the presence of structured regions in the genomic RNA template. In this review, we discuss new observations suggesting that the distribution of RNA structures along the HIV genome may enhance recombination rates in regions where the resultant progeny is less likely to be impaired, and could therefore maximize the evolutionary value of this source of genetic diversity.

  15. Automatic switching matrix

    DOEpatents

    Schlecht, Martin F.; Kassakian, John G.; Caloggero, Anthony J.; Rhodes, Bruce; Otten, David; Rasmussen, Neil

    1982-01-01

    An automatic switching matrix that includes an apertured matrix board containing a matrix of wires that can be interconnected at each aperture. Each aperture has associated therewith a conductive pin which, when fully inserted into the associated aperture, effects electrical connection between the wires within that particular aperture. Means is provided for automatically inserting the pins in a determined pattern and for removing all the pins to permit other interconnecting patterns.

  16. Composite Material Switches

    NASA Technical Reports Server (NTRS)

    Javadi, Hamid (Inventor)

    2001-01-01

    A device to protect electronic circuitry from high voltage transients is constructed from a relatively thin piece of conductive composite sandwiched between two conductors so that conduction is through the thickness of the composite piece. The device is based on the discovery that conduction through conductive composite materials in this configuration switches to a high resistance mode when exposed to voltages above a threshold voltage.

  17. CREE: Making the Switch

    SciTech Connect

    Grider, David; Palmer, John

    2014-03-06

    CREE, with the help of ARPA-E funding, has developed a Silicon Carbide (SIC) transistor which can be used to create solid state transformers capable of meeting the unique needs of the emerging smart grid. SIC transistors are different from common silicon computer chips in that they handle grid scale voltages with ease and their high frequency switching is well suited to the intermittent nature of renewable energy generation.

  18. CREE: Making the Switch

    ScienceCinema

    Grider, David; Palmer, John

    2016-07-12

    CREE, with the help of ARPA-E funding, has developed a Silicon Carbide (SIC) transistor which can be used to create solid state transformers capable of meeting the unique needs of the emerging smart grid. SIC transistors are different from common silicon computer chips in that they handle grid scale voltages with ease and their high frequency switching is well suited to the intermittent nature of renewable energy generation.

  19. Switching surface chemistry with supramolecular machines.

    PubMed

    Bunker, Bruce C; Huber, Dale L; Kushmerick, James G; Dunbar, Timothy; Kelly, Michael; Matzke, Carolyn; Cao, Jianguo; Jeppesen, Jan O; Perkins, Julie; Flood, Amar H; Stoddart, J Fraser

    2007-01-02

    Tethered supramolecular machines represent a new class of active self-assembled monolayers in which molecular configurations can be reversibly programmed using electrochemical stimuli. We are using these machines to address the chemistry of substrate surfaces for integrated microfluidic systems. Interactions between the tethered tetracationic cyclophane host cyclobis(paraquat-p-phenylene) and dissolved pi-electron-rich guest molecules, such as tetrathiafulvalene, have been reversibly switched by oxidative electrochemistry. The results demonstrate that surface-bound supramolecular machines can be programmed to adsorb or release appropriately designed solution species for manipulating surface chemistry.

  20. Organic optical bistable switch

    NASA Astrophysics Data System (ADS)

    Xue, Jiangeng; Forrest, Stephen R.

    2003-01-01

    We demonstrate an organic optical bistable switch by integrating an efficient organic photodetector on top of a transparent electrophosphorescent organic light-emitting diode (TOLED). The bistability is achieved with an external field-effect transistor providing positive feedback. In the "LOW" state, the TOLED is off and the current in the photodetector is solely its dark current. In the "HIGH" state, the TOLED emits light that is directly coupled into the integrated photodetector through the transparent cathode. The photocurrent then is fed back to the TOLED, maintaining it in the HIGH state. The green electrophosphorescent material, fac tris(2-phenylpyridine) iridium [Ir(ppy)3] doped into a 4,4'-N,N'-dicarbazole-biphenyl host was used as the luminescent material in the TOLED, while alternating thin layers of copper phthalocyanine and 3,4,9,10-perylenetetracarboxylic bis-benzimidazole were used as the active region of the organic photodetector. The circuit has a 3 dB bandwidth of 25 kHz, and can be switched between HIGH and LOW using pulses as narrow as 60 ns. The bistable switch can be both electrically and optically reset, making it a candidate for image-retaining displays (e.g., electronic paper) and other photonic logic applications. The integrated organic device also has broad use as a linear circuit element in applications such as automatic brightness control.

  1. Cygnus Diverter Switch Analysis

    SciTech Connect

    G. Corrow, M. Hansen, D. Henderson, C. Mitton et al.

    2008-02-01

    The Cygnus Dual Beam Radiographic Facility consists of two 2.25-MV, 60-kA, 50-ns x-ray sources fielded in an underground laboratory at the Nevada Test Site. The tests performed in this laboratory involve study of the dynamic properties of plutonium and are called subcritical experiments. From end-to-end, the Cygnus machines utilize the following components: Marx generator, water-filled pulse-forming line (PFL), waterfilled coaxial transmission line (WTL), 3-cell inductive voltage adder (IVA), and rod-pinch diode. The upstream WTL interface to the PFL is via a radial insulator with coaxial geometry. The downstream WTL terminates in a manifold where the center conductor splits into three lines which individually connect to each of the IVA cell inputs. There is an impedance mismatch at this juncture. It is a concern that a reflected pulse due to anomalous behavior in the IVA or diode might initiate breakdown upon arrival at the upstream PFL/WTL insulator. Therefore near the beginning of the WTL a radial diverter switch is installed to protect the insulator from over voltage and breakdown. The diverter has adjustable gap spacing, and an in-line aqueous-solution (sodium thiosulfate) resistor array for energy dissipation. There are capacitive voltage probes at both ends of the WTL and on the diverter switch. These voltage signals will be analyzed to determine diverter performance. Using this analysis the usefulness of the diverter switch will be evaluated.

  2. Ultrafast gas switching experiments

    NASA Astrophysics Data System (ADS)

    Frost, C. A.; Martin, T. H.; Patterson, P. E.; Rinehart, L. F.; Rohwein, G. J.; Roose, L. D.; Aurand, J. F.; Buttram, M. T.

    1993-06-01

    Recent experiments which studied the physics of ultrafast gas breakdown under the extreme overvoltages which occur when a high pressure gas switch is pulse charged to hundreds of kV in 1 ns or less are described. The highly overvolted peaking gaps produce powerful electromagnetic pulses with risetimes less than 100 ps which can be used for ultrawideband radar systems, particle accelerators, laser drivers, bioelectromagnetic studies, electromagnetic effects testing, and for basic studies of gas breakdown physics. Pulses with 50 to 100 ps risetimes to peak levels of 75 to 160 kV at pulse repetition frequencies (PRF) to 1 kHz were produced and accurately measured. A unique gas switch was developed to hold off hundreds of kV with parasitic inductance less than 1 nH. An advanced diagnostic system using Fourier compensation was developed to measure single-shot risetimes below 35 ps. The complete apparatus is described and waveforms are presented. The measured data are compared with a theoretical model which predicts key features including dependence on gas species and pressure. This technology was applied to practical systems driving ultrawideband radiating antennas and bounded wave simulators. A thyristor/pulse transformer based system using a highly overvolted cable switch was developed. This pulser driving a Sandia-designed TEM cell, provides an ultra wideband impulse with less than 200 ps risetime to the test object at a PRF greater than 1 kHz at grater tha n 100 kV/m E field.

  3. "Platform switching": serendipity.

    PubMed

    Kalavathy, N; Sridevi, J; Gehlot, Roshni; Kumar, Santosh

    2014-01-01

    Implant dentistry is the latest developing field in terms of clinical techniques, research, material science and oral rehabilitation. Extensive work is being done to improve the designing of implants in order to achieve better esthetics and function. The main drawback with respect to implant restoration is achieving good osseointegration along with satisfactory stress distribution, which in turn will improve the prognosis of implant prosthesis by reducing the crestal bone loss. Many concepts have been developed with reference to surface coating of implants, surgical techniques for implant placement, immediate and delayed loading, platform switching concept, etc. This article has made an attempt to review the concept of platform switching was in fact revealed accidentally due to the nonavailability of the abutment appropriate to the size of the implant placed. A few aspect of platform switching, an upcoming idea to reduce crestal bone loss have been covered. The various methods used for locating and preparing the data were done through textbooks, Google search and related articles.

  4. Ferroelectric switching of elastin

    PubMed Central

    Liu, Yuanming; Cai, Hong-Ling; Zelisko, Matthew; Wang, Yunjie; Sun, Jinglan; Yan, Fei; Ma, Feiyue; Wang, Peiqi; Chen, Qian Nataly; Zheng, Hairong; Meng, Xiangjian; Sharma, Pradeep; Zhang, Yanhang; Li, Jiangyu

    2014-01-01

    Ferroelectricity has long been speculated to have important biological functions, although its very existence in biology has never been firmly established. Here, we present compelling evidence that elastin, the key ECM protein found in connective tissues, is ferroelectric, and we elucidate the molecular mechanism of its switching. Nanoscale piezoresponse force microscopy and macroscopic pyroelectric measurements both show that elastin retains ferroelectricity at 473 K, with polarization on the order of 1 μC/cm2, whereas coarse-grained molecular dynamics simulations predict similar polarization with a Curie temperature of 580 K, which is higher than most synthetic molecular ferroelectrics. The polarization of elastin is found to be intrinsic in tropoelastin at the monomer level, analogous to the unit cell level polarization in classical perovskite ferroelectrics, and it switches via thermally activated cooperative rotation of dipoles. Our study sheds light onto a long-standing question on ferroelectric switching in biology and establishes ferroelectricity as an important biophysical property of proteins. This is a critical first step toward resolving its physiological significance and pathological implications. PMID:24958890

  5. Ultrafast gas switching experiments

    SciTech Connect

    Frost, C.A.; Martin, T.H.; Patterson, P.E.; Rinehart, L.F.; Rohwein, G.J.; Roose, L.D.; Aurand, J.F.; Buttram, M.T.

    1993-08-01

    We describe recent experiments which studied the physics of ultrafast gas breakdown under the extreme overvoltages which occur when a high pressure gas switch is pulse charged to hundreds of kV in 1 ns or less. The highly overvolted peaking gaps produce powerful electromagnetic pulses with risetimes < 100 ps which can be used for ultrawideband radar systems, particle accelerators, laser drivers, bioelectromagnetic studies, electromagnetic effects testing, and for basic studies of gas breakdown physics. We have produced and accurately measured pulses with 50 to 100 ps risetimes to peak levels of 75 to 160 kV at pulse repetition frequencies (PRF) to 1 kHz. A unique gas switch was developed to hold off hundreds of kV with parasitic inductance less than 1 nH. An advanced diagnostic system using Fourier compensation was developed to measure single-shot risetimes below 35 ps. The complete apparatus is described and waveforms are presented. The measured data are compared with a theoretical model which predicts key features including dependence on gas species and technology to practical systems antennas and bounded wave developed a thyristor/pulse transformer based system using a highly overvolted cable switch. This pulser driving a Sandia-designed TEM cell, provides an ultra wideband impulse with < 200 ps risetime to the test object at a PRF > Khz at > 100 kV/m E field.

  6. Ultrafast gas switching experiments

    SciTech Connect

    Frost, C.A.; Martin, T.H.; Patterson, P.E.; Rinehart, L.F.; Rohwein, G.J.; Roose, L.D.; Aurand, J.F.; Buttram, M.T.

    1996-11-01

    We describe recent experiments which studied the physics of ultrafast gas breakdown under the extreme overvoltages which occur when a high pressure gas switch is pulse charged to hundreds of kV in 1 ns or less. The highly overvolted peaking gaps produce powerful electromagnetic pulses with risetimes < 100 ps which can be used for ultrawideband radar systems, particle accelerators, laser drivers, bioelectromagnetic studies, electromagnetic effects testing, and for basic studies of gas breakdown physics. We have produced and accurately measured pulses with 50 to 100 ps risetimes to peak levels of 75 to 160 kV at pulse repetition frequencies (PRF) to I kHz. A unique gas switch was developed to hold off hundreds of kV with parasitic inductance less than I nH. An advanced diagnostic system using Fourier compensation was developed to measure single-shot risetimes below 35 ps. The complete apparatus is described and wave forms are presented. The measured data are compared with a theoretical model which predicts key features including dependence on gas species and pressure. We have applied this technology to practical systems driving ultrawideband radiating antennas and bounded wave simulators. For example, we have developed a thyristor/pulse transformer based system using a highly overvolted cable switch. This pulser driving a Sandia- designed TEM cell, provides an ultra wideband impulse with < 200 ps risetime to the test object at a PRF > 1 kHz at > 100 kV/m E field.

  7. Regulation and pharmacokinetics of inducible recombinant TRAIL expression.

    PubMed

    Dong, Aiwen; Hu, Jie; Zhao, Lili; Xu, Huiling; Liu, Xinyuan

    2007-12-01

    TRAIL is a potent antitumor agent, but its potential toxicity to normal human tissues limits its clinical applications in future. Therapy of human tumors might benefit from the use of vectors enabling tight control of TRAIL expression in vivo. To this aim, we constructed an adenoviral vector carrying the RU486-dependent gene switch system for the regulable expression of recombinant TRAIL. Only was apoptotic recombinant TRAIL expressed and cytotoxicity observed upon binding of RU 486 to the inducible promoter. Expression levels and kinetics of recombinant TRAIL expression could be achieved by modulating the concentration of the inducer. As a broad implication, our data provide an alternative approach to circumvent the potential toxicity of TRAIL in future human trials and this system may be utilized to treat human cancer using a long-term expression vector.

  8. Universality class in conformal inflation

    SciTech Connect

    Kallosh, Renata; Linde, Andrei E-mail: alinde@stanford.edu

    2013-07-01

    We develop a new class of chaotic inflation models with spontaneously broken conformal invariance. Observational consequences of a broad class of such models are stable with respect to strong deformations of the scalar potential. This universality is a critical phenomenon near the point of enhanced symmetry, SO(1,1), in case of conformal inflation. It appears because of the exponential stretching of the moduli space and the resulting exponential flattening of scalar potentials upon switching from the Jordan frame to the Einstein frame in this class of models. This result resembles stretching and flattening of inhomogeneities during inflationary expansion. It has a simple interpretation in terms of velocity versus rapidity near the Kähler cone in the moduli space, similar to the light cone of special theory of relativity. This effect makes inflation possible even in the models with very steep potentials. We describe conformal and superconformal versions of this cosmological attractor mechanism.

  9. Assessment of Recombination in the S-segment Genome of Crimean-Congo Hemorrhagic Fever Virus in Iran

    PubMed Central

    Chinikar, Sadegh; Shah-Hosseini, Nariman; Bouzari, Saeid; Shokrgozar, Mohammad Ali; Mostafavi, Ehsan; Jalali, Tahmineh; Khakifirouz, Sahar; Groschup, Martin H; Niedrig, Matthias

    2016-01-01

    Background: Crimean-Congo Hemorrhagic Fever Virus (CCHFV) belongs to genus Nairovirus and family Bunyaviridae. The main aim of this study was to investigate the extent of recombination in S-segment genome of CCHFV in Iran. Methods: Samples were isolated from Iranian patients and those available in GenBank, and analyzed by phylogenetic and bootscan methods. Results: Through comparison of the phylogenetic trees based on full length sequences and partial fragments in the S-segment genome of CCHFV, genetic switch was evident, due to recombination event. Moreover, evidence of multiple recombination events was detected in query isolates when bootscan analysis was used by SimPlot software. Conclusion: Switch of different genomic regions between different strains by recombination could contribute to CCHFV diversification and evolution. The occurrence of recombination in CCHFV has a critical impact on epidemiological investigations and vaccine design. PMID:27047968

  10. Recombinant renewable polyclonal antibodies.

    PubMed

    Ferrara, Fortunato; D'Angelo, Sara; Gaiotto, Tiziano; Naranjo, Leslie; Tian, Hongzhao; Gräslund, Susanne; Dobrovetsky, Elena; Hraber, Peter; Lund-Johansen, Fridtjof; Saragozza, Silvia; Sblattero, Daniele; Kiss, Csaba; Bradbury, Andrew R M

    2015-01-01

    Only a small fraction of the antibodies in a traditional polyclonal antibody mixture recognize the target of interest, frequently resulting in undesirable polyreactivity. Here, we show that high-quality recombinant polyclonals, in which hundreds of different antibodies are all directed toward a target of interest, can be easily generated in vitro by combining phage and yeast display. We show that, unlike traditional polyclonals, which are limited resources, recombinant polyclonal antibodies can be amplified over one hundred million-fold without losing representation or functionality. Our protocol was tested on 9 different targets to demonstrate how the strategy allows the selective amplification of antibodies directed toward desirable target specific epitopes, such as those found in one protein but not a closely related one, and the elimination of antibodies recognizing common epitopes, without significant loss of diversity. These recombinant renewable polyclonal antibodies are usable in different assays, and can be generated in high throughput. This approach could potentially be used to develop highly specific recombinant renewable antibodies against all human gene products.

  11. The dissociative recombination of ?

    NASA Astrophysics Data System (ADS)

    Laubé, S.; Lehfaoui, L.; Rowe, B. R.; Mitchell, J. B. A.

    1998-09-01

    The dissociative recombination rate coefficient for 0953-4075/31/18/016/img2 has been measured at 300 K using a flowing afterglow Langmuir probe-mass spectrometer apparatus. A value of 0953-4075/31/18/016/img3 has been found.

  12. Introduction to dissociative recombination

    NASA Technical Reports Server (NTRS)

    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.

  13. Recombinant renewable polyclonal antibodies

    PubMed Central

    Ferrara, Fortunato; D’Angelo, Sara; Gaiotto, Tiziano; Naranjo, Leslie; Tian, Hongzhao; Gräslund, Susanne; Dobrovetsky, Elena; Hraber, Peter; Lund-Johansen, Fridtjof; Saragozza, Silvia; Sblattero, Daniele; Kiss, Csaba; Bradbury, Andrew RM

    2015-01-01

    Only a small fraction of the antibodies in a traditional polyclonal antibody mixture recognize the target of interest, frequently resulting in undesirable polyreactivity. Here, we show that high-quality recombinant polyclonals, in which hundreds of different antibodies are all directed toward a target of interest, can be easily generated in vitro by combining phage and yeast display. We show that, unlike traditional polyclonals, which are limited resources, recombinant polyclonal antibodies can be amplified over one hundred million-fold without losing representation or functionality. Our protocol was tested on 9 different targets to demonstrate how the strategy allows the selective amplification of antibodies directed toward desirable target specific epitopes, such as those found in one protein but not a closely related one, and the elimination of antibodies recognizing common epitopes, without significant loss of diversity. These recombinant renewable polyclonal antibodies are usable in different assays, and can be generated in high throughput. This approach could potentially be used to develop highly specific recombinant renewable antibodies against all human gene products. PMID:25530082

  14. Recombinant DNA for Teachers.

    ERIC Educational Resources Information Center

    Duvall, James G., III

    1992-01-01

    A science teacher describes his experience at a workshop to learn to teach the Cold Spring Harbor DNA Science Laboratory Protocols. These protocols lead students through processes for taking E. coli cells and transforming them into a new antibiotic resistant strain. The workshop featured discussions of the role of DNA recombinant technology in…

  15. Recombineering linear BACs.

    PubMed

    Chen, Qingwen; Narayanan, Kumaran

    2015-01-01

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

  16. Recombinant DNA for Teachers.

    ERIC Educational Resources Information Center

    Duvall, James G., III

    1992-01-01

    A science teacher describes his experience at a workshop to learn to teach the Cold Spring Harbor DNA Science Laboratory Protocols. These protocols lead students through processes for taking E. coli cells and transforming them into a new antibiotic resistant strain. The workshop featured discussions of the role of DNA recombinant technology in…

  17. Photoconductive semiconductor switches: Laser Q-switch trigger and switch-trigger laser integration

    SciTech Connect

    Loubriel, G.M.; Mar, A.; Hamil, R.A.; Zutavern, F.J.; Helgeson, W.D.

    1997-12-01

    This report provides a summary of the Pulser In a Chip 9000-Discretionary LDRD. The program began in January of 1997 and concluded in September of 1997. The over-arching goal of this LDRD is to study whether laser diode triggered photoconductive semiconductor switches (PCSS) can be used to activate electro-optic devices such as Q-switches and Pockels cells and to study possible laser diode/switch integration. The PCSS switches we used were high gain GaAs switches because they can be triggered with small amounts of laser light. The specific goals of the LDRD were to demonstrate: (1) that small laser diode arrays that are potential candidates for laser-switch integration will indeed trigger the PCSS switch, and (2) that high gain GaAs switches can be used to trigger optical Q-switches in lasers such as the lasers to be used in the X-1 Advanced Radiation Source and the laser used for direct optical initiation (DOI) of explosives. The technology developed with this LDRD is now the prime candidate for triggering the Q switch in the multiple lasers in the laser trigger system of the X-1 Advanced Radiation Source and may be utilized in other accelerators. As part of the LDRD we developed a commercial supplier. To study laser/switch integration we tested triggering the high gain GaAs switches with: edge emitting laser diodes, vertical cavity surface emitting lasers (VCSELs), and transverse junction stripe (TJS) lasers. The first two types of lasers (edge emitting and VCSELs) did activate the PCSS but are harder to integrate with the PCSS for a compact package. The US lasers, while easier to integrate with the switch, did not trigger the PCSS at the US laser power levels we used. The PCSS was used to activate the Q-switch of the compact laser to be used in the X-1 Advanced Radiation Source.

  18. Fast optical switch having reduced light loss

    NASA Technical Reports Server (NTRS)

    Nelson, Bruce N. (Inventor); Cooper, Ronald F. (Inventor)

    1992-01-01

    An electrically controlled optical switch uses an electro-optic crystal of the type having at least one set of fast and slow optical axes. The crystal exhibits electric field induced birefringence such that a plane of polarization oriented along a first direction of a light beam passing through the crystal may be switched to a plane of polarization oriented along a second direction. A beam splitting polarizer means is disposed at one end of the crystal and directs a light beam passing through the crystal whose plane of polarization is oriented along the first direction differently from a light beam having a plane of polarization oriented along the second direction. The electro-optic crystal may be chosen from the crystal classes 43m, 42m, and 23. In a preferred embodiment, the electro-optic crystal is a bismuth germanium oxide crystal or a bismuth silicon oxide crystal. In another embodiment of the invention, polarization control optics are provided which transmit substantially all of the incident light to the electro-optic crystal, substantially reducing the insertion loss of the switch.

  19. Phenotypic switching in gene regulatory networks.

    PubMed

    Thomas, Philipp; Popović, Nikola; Grima, Ramon

    2014-05-13

    Noise in gene expression can lead to reversible phenotypic switching. Several experimental studies have shown that the abundance distributions of proteins in a population of isogenic cells may display multiple distinct maxima. Each of these maxima may be associated with a subpopulation of a particular phenotype, the quantification of which is important for understanding cellular decision-making. Here, we devise a methodology which allows us to quantify multimodal gene expression distributions and single-cell power spectra in gene regulatory networks. Extending the commonly used linear noise approximation, we rigorously show that, in the limit of slow promoter dynamics, these distributions can be systematically approximated as a mixture of Gaussian components in a wide class of networks. The resulting closed-form approximation provides a practical tool for studying complex nonlinear gene regulatory networks that have thus far been amenable only to stochastic simulation. We demonstrate the applicability of our approach in a number of genetic networks, uncovering previously unidentified dynamical characteristics associated with phenotypic switching. Specifically, we elucidate how the interplay of transcriptional and translational regulation can be exploited to control the multimodality of gene expression distributions in two-promoter networks. We demonstrate how phenotypic switching leads to birhythmical expression in a genetic oscillator, and to hysteresis in phenotypic induction, thus highlighting the ability of regulatory networks to retain memory.

  20. Class Size.

    ERIC Educational Resources Information Center

    Varner, Sherrell E.

    Two basic reasons for concern over classroom size are the desire to optimize learning conditions and the tremendous impact of class size on school finances. The first reason of concern is not as well defined as the second. Rather than looking for the optimum figure, as has been done in the past, the question should read "Best classroom size for…